From 4d7025f1f46a331d76a05d28d270109654d40a97 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Kirill=20M=C3=BCller?= Date: Fri, 21 Apr 2023 19:19:48 +0200 Subject: [PATCH 1/8] revdepcheck results for 6222e73a6 --- revdep/README.md | 102 +- revdep/cran.md | 242 ++- revdep/failures.md | 678 +++++++- revdep/problems.md | 3807 ++++++++++++++++++++++++++++++++++++++++---- 4 files changed, 4488 insertions(+), 341 deletions(-) diff --git a/revdep/README.md b/revdep/README.md index 4bd01ab14be..f040817e449 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,19 +1,91 @@ # Revdeps -## New problems (12) +## Failed to check (11) -|package |version |error |warning |note | -|:------------|:-------|:------|:-------|:----| -|[backbone](problems.md#backbone)|2.1.1 |__+1__ | | | -|[deepdep](problems.md#deepdep)|0.4.1 |__+1__ | | | -|[egor](problems.md#egor)|1.22.12 |__+1__ | | | -|[GREMLINS](problems.md#gremlins)|0.2.0 |__+1__ |__+1__ |1 | -|[incidentally](problems.md#incidentally)|1.0.1 | |__+1__ | | -|[mstknnclust](problems.md#mstknnclust)|0.3.1 | |__+1__ | | -|[nat](problems.md#nat)|1.8.19 |__+1__ |1 | | -|[netmeta](problems.md#netmeta)|2.7-0 |__+1__ | |1 | -|[NetOrigin](problems.md#netorigin)|1.1-4 |__+1__ | | | -|[poppr](problems.md#poppr)|2.9.3 |__+1__ |1 |1 | -|[sfnetworks](problems.md#sfnetworks)|0.6.1 |__+1__ | | | -|[signnet](problems.md#signnet)|1.0.0 |__+1__ | |1 | +|package |version |error |warning |note | +|:---------|:-------|:-----|:-------|:----| +|beadplexr |? | | | | +|NA |? | | | | +|DRviaSPCN |? | | | | +|genekitr |? | | | | +|immcp |? | | | | +|MACP |? | | | | +|numbat |? | | | | +|NA |? | | | | +|NA |? | | | | +|tidySEM |? | | | | +|vivid |? | | | | + +## New problems (68) + +|package |version |error |warning |note | +|:--------------|:--------|:------|:-------|:--------| +|[alakazam](problems.md#alakazam)|1.2.1 |__+1__ |1 | | +|[aniSNA](problems.md#anisna)|1.0 |__+1__ | | | +|[bc3net](problems.md#bc3net)|1.0.4 |__+1__ | | | +|[bio3d](problems.md#bio3d)|2.4-4 |__+1__ | |1 | +|[causaloptim](problems.md#causaloptim)|0.9.7 |__+1__ | | | +|[chemodiv](problems.md#chemodiv)|0.2.0 |__+1__ | | | +|[CINNA](problems.md#cinna)|1.2.0 |__+1__ |__+1__ |1 | +|[clustAnalytics](problems.md#clustanalytics)|0.5.2 |__+2__ |__+1__ |1 | +|[crosstalkr](problems.md#crosstalkr)|1.0.1 | |__+1__ | | +|[dnet](problems.md#dnet)|1.1.7 |__+1__ | | | +|[DrDimont](problems.md#drdimont)|0.1.4 |__+1__ |__+1__ | | +|[DTSEA](problems.md#dtsea)|0.0.3 |__+1__ |__+1__ | | +|[dynwrap](problems.md#dynwrap)|1.2.3 |__+1__ | | | +|[edgebundle](problems.md#edgebundle)|0.4.1 |__+1__ | |1 | +|[einet](problems.md#einet)|0.1.0 |__+1__ | | | +|[emba](problems.md#emba)|0.1.8 | |__+1__ |1 | +|[etree](problems.md#etree)|0.1.0 |__+1__ | | | +|[gemtc](problems.md#gemtc)|1.0-1 |__+1__ | | | +|[geonetwork](problems.md#geonetwork)|0.5.0 |__+1__ | | | +|[GISSB](problems.md#gissb)|1.1 |__+1__ | |1 | +|[grand](problems.md#grand)|0.9.0 |__+1__ |__+1__ | | +|[graph4lg](problems.md#graph4lg)|1.8.0 |__+1__ |__+1__ |1 __+1__ | +|[graphkernels](problems.md#graphkernels)|1.6.1 |__+1__ | |1 | +|[graphlayouts](problems.md#graphlayouts)|0.8.4 |__+2__ | |1 | +|[graphsim](problems.md#graphsim)|1.0.3 |__+1__ | | | +|[iGraphMatch](problems.md#igraphmatch)|2.0.1 |__+1__ |__+1__ | | +|[influenceR](problems.md#influencer)|0.1.0.1 |__+1__ | | | +|[intergraph](problems.md#intergraph)|2.0-2 |__+1__ | | | +|[invertiforms](problems.md#invertiforms)|0.1.1 |__+2__ | | | +|[ITNr](problems.md#itnr)|0.7.0 |__+1__ | | | +|[LEANR](problems.md#leanr)|1.4.9 |__+1__ | | | +|[leiden](problems.md#leiden)|0.4.3 |__+1__ |__+1__ |1 | +|[leidenAlg](problems.md#leidenalg)|1.0.5 |__+2__ | |1 | +|[leidenbase](problems.md#leidenbase)|0.1.18 |__+2__ |__+1__ |1 | +|[meconetcomp](problems.md#meconetcomp)|0.2.0 |__+1__ | | | +|[metanetwork](problems.md#metanetwork)|0.7.0 |__+2__ | | | +|[migraph](problems.md#migraph)|0.13.2 |__+2__ | | | +|[missSBM](problems.md#misssbm)|1.0.3 |__+2__ |__+1__ |1 | +|[molnet](problems.md#molnet)|0.1.0 |__+1__ |__+1__ | | +|[motifr](problems.md#motifr)|1.0.0 |__+1__ | | | +|[multinets](problems.md#multinets)|0.2.2 |__+2__ | | | +|[mwcsr](problems.md#mwcsr)|0.1.6 |__+2__ |__+1__ |1 | +|[nda](problems.md#nda)|0.1.6 |__+1__ | | | +|[netplot](problems.md#netplot)|0.1-1 |__+1__ |__+1__ | | +|[netrankr](problems.md#netrankr)|1.2.0 |__+2__ |__+1__ |1 | +|[netseg](problems.md#netseg)|1.0-1 |__+2__ |__+1__ | | +|[nett](problems.md#nett)|1.0.0 |__+1__ |__+1__ | | +|[poppr](problems.md#poppr)|2.9.4 |__+1__ |1 | | +|[psSubpathway](problems.md#pssubpathway)|0.1.1 |__+1__ |__+1__ | | +|[rmonad](problems.md#rmonad)|0.7.0 |__+1__ | | | +|[rsetse](problems.md#rsetse)|0.5.0 |__+1__ |__+1__ | | +|[rSpectral](problems.md#rspectral)|1.0.0.10 |__+2__ | |1 | +|[sbm](problems.md#sbm)|0.4.5 |__+1__ |__+1__ | | +|[sccore](problems.md#sccore)|1.0.3 |__+2__ | |1 | +|[ScorePlus](problems.md#scoreplus)|0.1 |__+1__ | |1 | +|[secrlinear](problems.md#secrlinear)|1.1.4 |__+1__ |1 | | +|[shazam](problems.md#shazam)|1.1.2 |__+1__ |1 | | +|[sigmajs](problems.md#sigmajs)|0.1.5 |__+1__ | |1 | +|[signnet](problems.md#signnet)|1.0.1 |__+2__ |__+1__ |1 | +|[SNscan](problems.md#snscan)|1.0 |__+1__ | | | +|[SOMbrero](problems.md#sombrero)|1.4-1 |__+1__ |__+1__ | | +|[spreadr](problems.md#spreadr)|0.2.0 | |__+1__ |1 | +|[SubpathwayLNCE](problems.md#subpathwaylnce)|1.0 |__+1__ | |1 | +|[SubtypeDrug](problems.md#subtypedrug)|0.1.5 |__+1__ |__+1__ | | +|[tgver](problems.md#tgver)|0.3.0 | |__+1__ | | +|[threejs](problems.md#threejs)|0.3.3 |__+2__ | |1 | +|[tosr](problems.md#tosr)|0.1.2 |__+1__ | | | +|[webSDM](problems.md#websdm)|1.1-3 |__+1__ | |1 | diff --git a/revdep/cran.md b/revdep/cran.md index 793c3275f52..c358ecf8f9e 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,49 +1,265 @@ ## revdepcheck results -We checked 12 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. +We checked 778 reverse dependencies (775 from CRAN + 3 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. - * We saw 12 new problems - * We failed to check 0 packages + * We saw 68 new problems + * We failed to check 8 packages Issues with CRAN packages are summarised below. ### New problems (This reports the first line of each new failure) -* backbone +* alakazam + checking examples ... ERROR + +* aniSNA + checking examples ... ERROR + +* bc3net + checking examples ... ERROR + +* bio3d + checking examples ... ERROR + +* causaloptim + checking tests ... ERROR + +* chemodiv + checking examples ... ERROR + +* CINNA + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* clustAnalytics + checking examples ... ERROR + checking tests ... ERROR + checking re-building of vignette outputs ... WARNING + +* crosstalkr + checking re-building of vignette outputs ... WARNING + +* dnet + checking examples ... ERROR + +* DrDimont + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* DTSEA + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* dynwrap + checking examples ... ERROR + +* edgebundle + checking examples ... ERROR + +* einet checking tests ... ERROR -* deepdep +* emba + checking re-building of vignette outputs ... WARNING + +* etree checking tests ... ERROR -* egor +* gemtc checking tests ... ERROR -* GREMLINS +* geonetwork + checking examples ... ERROR + +* GISSB + checking examples ... ERROR + +* grand checking examples ... ERROR checking re-building of vignette outputs ... WARNING -* incidentally +* graph4lg + checking examples ... ERROR checking re-building of vignette outputs ... WARNING + checking data for non-ASCII characters ... NOTE + +* graphkernels + checking examples ... ERROR + +* graphlayouts + checking examples ... ERROR + checking tests ... ERROR -* mstknnclust +* graphsim + checking examples ... ERROR + +* iGraphMatch + checking examples ... ERROR checking re-building of vignette outputs ... WARNING -* nat +* influenceR checking tests ... ERROR -* netmeta +* intergraph checking examples ... ERROR -* NetOrigin +* invertiforms checking examples ... ERROR + checking tests ... ERROR + +* ITNr + checking examples ... ERROR + +* LEANR + checking tests ... ERROR + +* leiden + checking tests ... ERROR + checking re-building of vignette outputs ... WARNING + +* leidenAlg + checking examples ... ERROR + checking tests ... ERROR + +* leidenbase + checking examples ... ERROR + checking tests ... ERROR + checking re-building of vignette outputs ... WARNING + +* meconetcomp + checking examples ... ERROR + +* metanetwork + checking examples ... ERROR + checking tests ... ERROR + +* migraph + checking examples ... ERROR + checking tests ... ERROR + +* missSBM + checking examples ... ERROR + checking tests ... ERROR + checking re-building of vignette outputs ... WARNING + +* molnet + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* motifr + checking examples ... ERROR + +* multinets + checking examples ... ERROR + checking tests ... ERROR + +* mwcsr + checking examples ... ERROR + checking tests ... ERROR + checking re-building of vignette outputs ... WARNING + +* nda + checking examples ... ERROR + +* netplot + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* netrankr + checking examples ... ERROR + checking tests ... ERROR + checking re-building of vignette outputs ... WARNING + +* netseg + checking examples ... ERROR + checking tests ... ERROR + checking re-building of vignette outputs ... WARNING + +* nett + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING * poppr checking tests ... ERROR -* sfnetworks +* psSubpathway + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* rmonad + checking examples ... ERROR + +* rsetse + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* rSpectral + checking examples ... ERROR + checking tests ... ERROR + +* sbm + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* sccore + checking examples ... ERROR + checking tests ... ERROR + +* ScorePlus + checking examples ... ERROR + +* secrlinear + checking examples ... ERROR + +* shazam + checking examples ... ERROR + +* sigmajs checking tests ... ERROR * signnet checking examples ... ERROR + checking tests ... ERROR + checking re-building of vignette outputs ... WARNING + +* SNscan + checking examples ... ERROR + +* SOMbrero + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* spreadr + checking re-building of vignette outputs ... WARNING + +* SubpathwayLNCE + checking running R code from vignettes ... ERROR + +* SubtypeDrug + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* tgver + checking re-building of vignette outputs ... WARNING + +* threejs + checking examples ... ERROR + checking tests ... ERROR + +* tosr + checking tests ... ERROR + +* webSDM + checking examples ... ERROR + +### Failed to check +* beadplexr (NA) +* DRviaSPCN (NA) +* genekitr (NA) +* immcp (NA) +* MACP (NA) +* numbat (NA) +* tidySEM (NA) +* vivid (NA) diff --git a/revdep/failures.md b/revdep/failures.md index 9a207363396..cf2b04aead8 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -1 +1,677 @@ -*Wow, no problems at all. :)* \ No newline at end of file +# beadplexr + +
+ +* Version: 0.4.1 +* GitHub: NA +* Source code: https://github.com/cran/beadplexr +* Date/Publication: 2022-03-05 13:50:02 UTC +* Number of recursive dependencies: 128 + +Run `revdepcheck::cloud_details(, "beadplexr")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/beadplexr/new/beadplexr.Rcheck’ +* using R version 4.1.1 (2021-08-10) +* using platform: x86_64-pc-linux-gnu (64-bit) +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘beadplexr/DESCRIPTION’ ... OK +* checking extension type ... Package +* this is package ‘beadplexr’ version ‘0.4.1’ +* package encoding: UTF-8 +* checking package namespace information ... OK +... + Running ‘testthat.R’ +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... NONE + ‘cba_macsplex_example.Rmd’ using ‘UTF-8’... OK + ‘legendplex_analysis.Rmd’ using ‘UTF-8’... OK + ‘preparing_flow_data.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 NOTE + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/beadplexr/old/beadplexr.Rcheck’ +* using R version 4.1.1 (2021-08-10) +* using platform: x86_64-pc-linux-gnu (64-bit) +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘beadplexr/DESCRIPTION’ ... OK +* checking extension type ... Package +* this is package ‘beadplexr’ version ‘0.4.1’ +* package encoding: UTF-8 +* checking package namespace information ... OK +... + Running ‘testthat.R’ +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... NONE + ‘cba_macsplex_example.Rmd’ using ‘UTF-8’... OK + ‘legendplex_analysis.Rmd’ using ‘UTF-8’... OK + ‘preparing_flow_data.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 NOTE + + + + + +``` +# NA + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/NA +* Number of recursive dependencies: 0 + +Run `revdepcheck::cloud_details(, "NA")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + +``` +# DRviaSPCN + +
+ +* Version: 0.1.2 +* GitHub: NA +* Source code: https://github.com/cran/DRviaSPCN +* Date/Publication: 2022-03-03 16:00:02 UTC +* Number of recursive dependencies: 170 + +Run `revdepcheck::cloud_details(, "DRviaSPCN")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/DRviaSPCN/new/DRviaSPCN.Rcheck’ +* using R version 4.1.1 (2021-08-10) +* using platform: x86_64-pc-linux-gnu (64-bit) +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘DRviaSPCN/DESCRIPTION’ ... OK +* checking extension type ... Package +* this is package ‘DRviaSPCN’ version ‘0.1.2’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘clusterProfiler’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/DRviaSPCN/old/DRviaSPCN.Rcheck’ +* using R version 4.1.1 (2021-08-10) +* using platform: x86_64-pc-linux-gnu (64-bit) +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘DRviaSPCN/DESCRIPTION’ ... OK +* checking extension type ... Package +* this is package ‘DRviaSPCN’ version ‘0.1.2’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘clusterProfiler’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# genekitr + +
+ +* Version: 1.1.9 +* GitHub: https://github.com/GangLiLab/genekitr +* Source code: https://github.com/cran/genekitr +* Date/Publication: 2023-04-15 07:50:02 UTC +* Number of recursive dependencies: 206 + +Run `revdepcheck::cloud_details(, "genekitr")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/genekitr/new/genekitr.Rcheck’ +* using R version 4.1.1 (2021-08-10) +* using platform: x86_64-pc-linux-gnu (64-bit) +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘genekitr/DESCRIPTION’ ... OK +* checking extension type ... Package +* this is package ‘genekitr’ version ‘1.1.9’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘clusterProfiler’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/genekitr/old/genekitr.Rcheck’ +* using R version 4.1.1 (2021-08-10) +* using platform: x86_64-pc-linux-gnu (64-bit) +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘genekitr/DESCRIPTION’ ... OK +* checking extension type ... Package +* this is package ‘genekitr’ version ‘1.1.9’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘clusterProfiler’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# immcp + +
+ +* Version: 1.0.3 +* GitHub: https://github.com/YuanlongHu/immcp +* Source code: https://github.com/cran/immcp +* Date/Publication: 2022-05-12 05:50:02 UTC +* Number of recursive dependencies: 195 + +Run `revdepcheck::cloud_details(, "immcp")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/immcp/new/immcp.Rcheck’ +* using R version 4.1.1 (2021-08-10) +* using platform: x86_64-pc-linux-gnu (64-bit) +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘immcp/DESCRIPTION’ ... OK +* this is package ‘immcp’ version ‘1.0.3’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘clusterProfiler’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/immcp/old/immcp.Rcheck’ +* using R version 4.1.1 (2021-08-10) +* using platform: x86_64-pc-linux-gnu (64-bit) +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘immcp/DESCRIPTION’ ... OK +* this is package ‘immcp’ version ‘1.0.3’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘clusterProfiler’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# MACP + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/mrbakhsh/MACP +* Source code: https://github.com/cran/MACP +* Date/Publication: 2023-02-28 17:32:30 UTC +* Number of recursive dependencies: 234 + +Run `revdepcheck::cloud_details(, "MACP")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/MACP/new/MACP.Rcheck’ +* using R version 4.1.1 (2021-08-10) +* using platform: x86_64-pc-linux-gnu (64-bit) +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘MACP/DESCRIPTION’ ... OK +* checking extension type ... Package +* this is package ‘MACP’ version ‘0.1.0’ +* package encoding: UTF-8 +* checking package namespace information ... OK +... +* checking installed files from ‘inst/doc’ ... OK +* checking files in ‘vignettes’ ... OK +* checking examples ... OK +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... NONE + ‘MACP_tutorial.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 3 NOTEs + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/MACP/old/MACP.Rcheck’ +* using R version 4.1.1 (2021-08-10) +* using platform: x86_64-pc-linux-gnu (64-bit) +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘MACP/DESCRIPTION’ ... OK +* checking extension type ... Package +* this is package ‘MACP’ version ‘0.1.0’ +* package encoding: UTF-8 +* checking package namespace information ... OK +... +* checking installed files from ‘inst/doc’ ... OK +* checking files in ‘vignettes’ ... OK +* checking examples ... OK +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... NONE + ‘MACP_tutorial.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 3 NOTEs + + + + + +``` +# numbat + +
+ +* Version: 1.3.0 +* GitHub: https://github.com/kharchenkolab/numbat +* Source code: https://github.com/cran/numbat +* Date/Publication: 2023-04-02 17:50:03 UTC +* Number of recursive dependencies: 132 + +Run `revdepcheck::cloud_details(, "numbat")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/numbat/new/numbat.Rcheck’ +* using R version 4.1.1 (2021-08-10) +* using platform: x86_64-pc-linux-gnu (64-bit) +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘numbat/DESCRIPTION’ ... OK +* this is package ‘numbat’ version ‘1.3.0’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'ggtree', 'scistreer' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/numbat/old/numbat.Rcheck’ +* using R version 4.1.1 (2021-08-10) +* using platform: x86_64-pc-linux-gnu (64-bit) +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘numbat/DESCRIPTION’ ... OK +* this is package ‘numbat’ version ‘1.3.0’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'ggtree', 'scistreer' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# NA + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/NA +* Number of recursive dependencies: 0 + +Run `revdepcheck::cloud_details(, "NA")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + +``` +# NA + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/NA +* Number of recursive dependencies: 0 + +Run `revdepcheck::cloud_details(, "NA")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + +``` +# tidySEM + +
+ +* Version: 0.2.3 +* GitHub: https://github.com/cjvanlissa/tidySEM +* Source code: https://github.com/cran/tidySEM +* Date/Publication: 2022-04-14 17:50:02 UTC +* Number of recursive dependencies: 173 + +Run `revdepcheck::cloud_details(, "tidySEM")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/tidySEM/new/tidySEM.Rcheck’ +* using R version 4.1.1 (2021-08-10) +* using platform: x86_64-pc-linux-gnu (64-bit) +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘tidySEM/DESCRIPTION’ ... OK +* checking extension type ... Package +* this is package ‘tidySEM’ version ‘0.2.3’ +* package encoding: UTF-8 +* checking package namespace information ... OK +... +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... NONE + ‘Generating_syntax.Rmd’ using ‘UTF-8’... OK + ‘Plotting_graphs.Rmd’ using ‘UTF-8’... OK + ‘Tabulating_results.Rmd’ using ‘UTF-8’... OK + ‘sem_graph.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 NOTE + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/tidySEM/old/tidySEM.Rcheck’ +* using R version 4.1.1 (2021-08-10) +* using platform: x86_64-pc-linux-gnu (64-bit) +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘tidySEM/DESCRIPTION’ ... OK +* checking extension type ... Package +* this is package ‘tidySEM’ version ‘0.2.3’ +* package encoding: UTF-8 +* checking package namespace information ... OK +... +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... NONE + ‘Generating_syntax.Rmd’ using ‘UTF-8’... OK + ‘Plotting_graphs.Rmd’ using ‘UTF-8’... OK + ‘Tabulating_results.Rmd’ using ‘UTF-8’... OK + ‘sem_graph.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 NOTE + + + + + +``` +# vivid + +
+ +* Version: 0.2.7 +* GitHub: NA +* Source code: https://github.com/cran/vivid +* Date/Publication: 2023-04-11 13:50:02 UTC +* Number of recursive dependencies: 209 + +Run `revdepcheck::cloud_details(, "vivid")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/vivid/new/vivid.Rcheck’ +* using R version 4.1.1 (2021-08-10) +* using platform: x86_64-pc-linux-gnu (64-bit) +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘vivid/DESCRIPTION’ ... OK +* this is package ‘vivid’ version ‘0.2.7’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... NOTE +... +* checking installed files from ‘inst/doc’ ... OK +* checking files in ‘vignettes’ ... OK +* checking examples ... OK +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... NONE + ‘vividVignette.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 NOTE + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/vivid/old/vivid.Rcheck’ +* using R version 4.1.1 (2021-08-10) +* using platform: x86_64-pc-linux-gnu (64-bit) +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘vivid/DESCRIPTION’ ... OK +* this is package ‘vivid’ version ‘0.2.7’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... NOTE +... +* checking installed files from ‘inst/doc’ ... OK +* checking files in ‘vignettes’ ... OK +* checking examples ... OK +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... NONE + ‘vividVignette.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 NOTE + + + + + +``` diff --git a/revdep/problems.md b/revdep/problems.md index 158821a8ccd..4251463aae3 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1,91 +1,3159 @@ -# backbone +# alakazam
-* Version: 2.1.1 -* GitHub: https://github.com/zpneal/backbone -* Source code: https://github.com/cran/backbone -* Date/Publication: 2022-10-18 17:35:06 UTC +* Version: 1.2.1 +* GitHub: NA +* Source code: https://github.com/cran/alakazam +* Date/Publication: 2022-09-20 22:10:02 UTC +* Number of recursive dependencies: 117 + +Run `revdepcheck::cloud_details(, "alakazam")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘alakazam-Ex.R’ failed + The error most likely occurred in: + + > ### Name: getMRCA + > ### Title: Retrieve the first non-root node of a lineage tree + > ### Aliases: getMRCA + > + > ### ** Examples + > + > # Define example graph + ... + > + > # Use unweighted path length and do not exclude any nodes + > getMRCA(graph, path="steps", root="Germline") + This graph was created by an old(er) igraph version. + Call upgrade_graph() on it to use with the current igraph version + For now we convert it on the fly... + Error in vcount(graph) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: getMRCA -> getPathLengths -> data.frame -> V -> vcount + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘AminoAcids-Vignette.Rmd’ using rmarkdown + A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TinyTeX with tinytex::reinstall_tinytex(repository = "illinois"). + + tlmgr: Local TeX Live (2022) is older than remote repository (2023). + Cross release updates are only supported with + update-tlmgr-latest(.sh/.exe) --update + See https://tug.org/texlive/upgrade.html for details. + Warning in system2("tlmgr", args, ...) : + running command ''tlmgr' search --file --global '/grffile.sty'' had status 1 + ... + REAL() can only be applied to a 'numeric', not a 'logical' + --- failed re-building ‘Topology-Vignette.Rmd’ + + SUMMARY: processing the following files failed: + ‘AminoAcids-Vignette.Rmd’ ‘Diversity-Vignette.Rmd’ + ‘Fastq-Vignette.Rmd’ ‘Files-Vignette.Rmd’ ‘GeneUsage-Vignette.Rmd’ + ‘Lineage-Vignette.Rmd’ ‘Topology-Vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# aniSNA + +
+ +* Version: 1.0 +* GitHub: NA +* Source code: https://github.com/cran/aniSNA +* Date/Publication: 2023-02-17 09:50:09 UTC +* Number of recursive dependencies: 58 + +Run `revdepcheck::cloud_details(, "aniSNA")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘aniSNA-Ex.R’ failed + The error most likely occurred in: + + > ### Name: elk_network_2010 + > ### Title: An igraph object depicting the network obtained from + > ### elk_interactions_2010 + > ### Aliases: elk_network_2010 + > ### Keywords: datasets + > + > ### ** Examples + > + > igraph::E(elk_network_2010) + This graph was created by an old(er) igraph version. + Call upgrade_graph() on it to use with the current igraph version + For now we convert it on the fly... + Error in ecount(graph) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: -> ecount + Execution halted + ``` + +# bc3net + +
+ +* Version: 1.0.4 +* GitHub: NA +* Source code: https://github.com/cran/bc3net +* Date/Publication: 2016-11-28 08:21:04 +* Number of recursive dependencies: 9 + +Run `revdepcheck::cloud_details(, "bc3net")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘bc3net-Ex.R’ failed + The error most likely occurred in: + + > ### Name: enrichment + > ### Title: Function that performs a functional enrichment analysis based on + > ### a one-sided Fisher's exact teset (hypergeometric test). + > ### Aliases: enrichment + > + > ### ** Examples + > + ... + > # as a reference list. + > + > data(exanet) + > data(exgensets) + > + > candidate=V(getgcc(exanet))$name + Error in clusters(net) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: V -> is_igraph -> %in% -> getgcc -> clusters + Execution halted + ``` + +# bio3d + +
+ +* Version: 2.4-4 +* GitHub: NA +* Source code: https://github.com/cran/bio3d +* Date/Publication: 2022-10-26 22:45:06 UTC +* Number of recursive dependencies: 77 + +Run `revdepcheck::cloud_details(, "bio3d")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘bio3d-Ex.R’ failed + The error most likely occurred in: + + > ### Name: print.cna + > ### Title: Summarize and Print Features of a cna Network Graph + > ### Aliases: print.cna summary.cna + > ### Keywords: utilities + > + > ### ** Examples + > + ... + + x<- summary(net) + + x$members[[2]] + + + + detach(hivp) + + + + } + Error in igraph::ecount(x$network) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: print -> print.cna -> paste -> + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 11.0Mb + sub-directories of 1Mb or more: + libs 7.3Mb + ``` + +# causaloptim + +
+ +* Version: 0.9.7 +* GitHub: https://github.com/sachsmc/causaloptim +* Source code: https://github.com/cran/causaloptim +* Date/Publication: 2023-03-24 12:00:15 UTC +* Number of recursive dependencies: 63 + +Run `revdepcheck::cloud_details(, "causaloptim")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Error in `vcount(graph)`: REAL() can only be applied to a 'numeric', not a 'logical' + Backtrace: + ▆ + 1. └─igraph::V(`*tmp*`) at test-known-bounds.R:57:4 + 2. └─igraph::vcount(graph) + ── Error ('test-known-bounds.R:144:5'): Mediator ─────────────────────────────── + Error in `vcount(graph)`: REAL() can only be applied to a 'numeric', not a 'logical' + Backtrace: + ▆ + 1. └─igraph::V(`*tmp*`) at test-known-bounds.R:144:4 + 2. └─igraph::vcount(graph) + + [ FAIL 4 | WARN 0 | SKIP 0 | PASS 7 ] + Error: Test failures + Execution halted + ``` + +# chemodiv + +
+ +* Version: 0.2.0 +* GitHub: https://github.com/hpetren/chemodiv +* Source code: https://github.com/cran/chemodiv +* Date/Publication: 2023-01-12 09:30:06 UTC +* Number of recursive dependencies: 168 + +Run `revdepcheck::cloud_details(, "chemodiv")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘chemodiv-Ex.R’ failed + The error most likely occurred in: + + > ### Name: molNetPlot + > ### Title: Plot molecular networks + > ### Aliases: molNetPlot + > + > ### ** Examples + > + > data(minimalSampData) + ... + > data(minimalNPCTable) + > data(minimalMolNet) + > groups <- c("A", "A", "B", "B") + > molNetPlot(minimalSampData, minimalMolNet) + It is recommended to include an npcTable for an improved + network visualization. + Error in vertex.attributes(graph) : + VECTOR_ELT() can only be applied to a 'list', not a 'environment' + Calls: molNetPlot ... node_tibble -> as_tibble -> vertex_attr -> vertex.attributes + Execution halted + ``` + +# CINNA + +
+ +* Version: 1.2.0 +* GitHub: NA +* Source code: https://github.com/cran/CINNA +* Date/Publication: 2022-04-07 15:12:31 UTC +* Number of recursive dependencies: 143 + +Run `revdepcheck::cloud_details(, "CINNA")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘CINNA-Ex.R’ failed + The error most likely occurred in: + + > ### Name: calculate_centralities + > ### Title: Centrality measure calculation + > ### Aliases: calculate_centralities + > + > ### ** Examples + > + > + > data("zachary") + > p <- proper_centralities(zachary) + Error in is_directed(x) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: proper_centralities -> is_directed + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘CINNA.Rmd’ using rmarkdown + Quitting from lines 67-71 (CINNA.Rmd) + Error: processing vignette 'CINNA.Rmd' failed with diagnostics: + REAL() can only be applied to a 'numeric', not a 'logical' + --- failed re-building ‘CINNA.Rmd’ + + SUMMARY: processing the following file failed: + ‘CINNA.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘circlize’ + All declared Imports should be used. + ``` + +# clustAnalytics + +
+ +* Version: 0.5.2 +* GitHub: NA +* Source code: https://github.com/cran/clustAnalytics +* Date/Publication: 2022-11-09 11:50:09 UTC +* Number of recursive dependencies: 71 + +Run `revdepcheck::cloud_details(, "clustAnalytics")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘clustAnalytics-Ex.R’ failed + The error most likely occurred in: + + > ### Name: FOMD + > ### Title: FOMD (Fraction Over Median Degree) + > ### Aliases: FOMD + > + > ### ** Examples + > + > data(karate, package="igraphdata") + > FOMD(karate, membership(cluster_louvain(karate))) + Error in matrix(.Call(R_igraph_get_edgelist, graph, TRUE), ncol = 2) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: FOMD ... igraph_to_edgelist -> cbind -> as_edgelist -> matrix + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ── Error ('test_scoring_functions.R:8:5'): test scoring functions ────────────── + Error in `edge.attributes(g)`: VECTOR_ELT() can only be applied to a 'list', not a 'environment' + Backtrace: + ▆ + 1. ├─testthat::expect_equal_to_reference(...) at test_scoring_functions.R:8:4 + 2. │ └─testthat::expect_known_value(..., update = update) + 3. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 4. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 5. └─clustAnalytics::scoring_functions(...) + 6. ├─"weight" %in% names(edge.attributes(g)) + 7. └─igraph::edge.attributes(g) + + [ FAIL 3 | WARN 0 | SKIP 0 | PASS 0 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘cluster_stability.Rmd’ using rmarkdown + Quitting from lines 24-29 (cluster_stability.Rmd) + Error: processing vignette 'cluster_stability.Rmd' failed with diagnostics: + VECTOR_ELT() can only be applied to a 'list', not a 'environment' + --- failed re-building ‘cluster_stability.Rmd’ + + --- re-building ‘graph_rewiring_functions.Rmd’ using rmarkdown + Quitting from lines 30-32 (graph_rewiring_functions.Rmd) + Error: processing vignette 'graph_rewiring_functions.Rmd' failed with diagnostics: + ... + VECTOR_ELT() can only be applied to a 'list', not a 'environment' + --- failed re-building ‘stability_significance_examples.Rmd’ + + SUMMARY: processing the following files failed: + ‘cluster_stability.Rmd’ ‘graph_rewiring_functions.Rmd’ + ‘other_functions.Rmd’ ‘scoring_functions.Rmd’ + ‘stability_significance_examples.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.6Mb + sub-directories of 1Mb or more: + libs 6.1Mb + ``` + +# crosstalkr + +
+ +* Version: 1.0.1 +* GitHub: NA +* Source code: https://github.com/cran/crosstalkr +* Date/Publication: 2023-01-31 09:00:07 UTC +* Number of recursive dependencies: 167 + +Run `revdepcheck::cloud_details(, "crosstalkr")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘crosstalkr_vignette.Rmd’ using rmarkdown + Quitting from lines 72-77 (crosstalkr_vignette.Rmd) + Error: processing vignette 'crosstalkr_vignette.Rmd' failed with diagnostics: + REAL() can only be applied to a 'numeric', not a 'logical' + --- failed re-building ‘crosstalkr_vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘crosstalkr_vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# dnet + +
+ +* Version: 1.1.7 +* GitHub: https://github.com/hfang-bristol/dnet +* Source code: https://github.com/cran/dnet +* Date/Publication: 2020-02-20 10:10:07 UTC +* Number of recursive dependencies: 51 + +Run `revdepcheck::cloud_details(, "dnet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘dnet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: dDAGancestor + > ### Title: Function to find common ancestors of two terms/nodes from a + > ### direct acyclic graph (DAG) + > ### Aliases: dDAGancestor + > + > ### ** Examples + > + ... + > + > # 2) randomly give two terms + > term1 <- sample(V(g)$name,1) + This graph was created by an old(er) igraph version. + Call upgrade_graph() on it to use with the current igraph version + For now we convert it on the fly... + Error in vcount(graph) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: sample -> V -> vcount + Execution halted + ``` + +# DrDimont + +
+ +* Version: 0.1.4 +* GitHub: NA +* Source code: https://github.com/cran/DrDimont +* Date/Publication: 2022-09-23 15:40:02 UTC +* Number of recursive dependencies: 127 + +Run `revdepcheck::cloud_details(, "DrDimont")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘DrDimont-Ex.R’ failed + The error most likely occurred in: + + > ### Name: compute_drug_response_scores + > ### Title: Calculate drug response score + > ### Aliases: compute_drug_response_scores + > + > ### ** Examples + > + > data(drug_target_edges_example) + ... + > example_drug_response_scores <- compute_drug_response_scores( + + differential_graph=differential_graph_example, + + drug_targets=drug_target_edges_example$targets, + + settings=example_settings) + [23-04-21 14:50:48] Computing drug response scores based on the mean of the differential scores ... + + Error in matrix(.Call(R_igraph_get_edgelist, graph, TRUE), ncol = 2) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: compute_drug_response_scores -> -> as_edgelist -> matrix + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘DrDimont_Vignette.Rmd’ using rmarkdown + Quitting from lines 400-409 (DrDimont_Vignette.Rmd) + Error: processing vignette 'DrDimont_Vignette.Rmd' failed with diagnostics: + VECTOR_ELT() can only be applied to a 'list', not a 'environment' + --- failed re-building ‘DrDimont_Vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘DrDimont_Vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# DTSEA + +
+ +* Version: 0.0.3 +* GitHub: NA +* Source code: https://github.com/cran/DTSEA +* Date/Publication: 2022-11-06 13:20:02 UTC +* Number of recursive dependencies: 72 + +Run `revdepcheck::cloud_details(, "DTSEA")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘DTSEA-Ex.R’ failed + The error most likely occurred in: + + > ### Name: calculate_p0 + > ### Title: Function to calculate the p0 vector used in Random Walk with + > ### Restart (RwR) + > ### Aliases: calculate_p0 + > + > ### ** Examples + > + ... + > + > # Compute the p0 vector + > p0 <- calculate_p0(nodes = example_ppi, disease = example_disease_list) + This graph was created by an old(er) igraph version. + Call upgrade_graph() on it to use with the current igraph version + For now we convert it on the fly... + Error in vcount(graph) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: calculate_p0 -> V -> vcount + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘DTSEA.Rmd’ using rmarkdown + Quitting from lines 54-67 (DTSEA.Rmd) + Error: processing vignette 'DTSEA.Rmd' failed with diagnostics: + REAL() can only be applied to a 'numeric', not a 'logical' + --- failed re-building ‘DTSEA.Rmd’ + + SUMMARY: processing the following file failed: + ‘DTSEA.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# dynwrap + +
+ +* Version: 1.2.3 +* GitHub: https://github.com/dynverse/dynwrap +* Source code: https://github.com/cran/dynwrap +* Date/Publication: 2023-03-01 17:10:02 UTC +* Number of recursive dependencies: 97 + +Run `revdepcheck::cloud_details(, "dynwrap")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘dynwrap-Ex.R’ failed + The error most likely occurred in: + + > ### Name: trajectory_type_dag + > ### Title: A DAG connecting different trajectory types + > ### Aliases: trajectory_type_dag + > ### Keywords: create_ti_method + > + > ### ** Examples + > + > trajectory_type_dag + This graph was created by an old(er) igraph version. + Call upgrade_graph() on it to use with the current igraph version + For now we convert it on the fly... + Error in is_directed(object) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: ... print.igraph -> .print.header -> paste0 -> is_directed + Execution halted + ``` + +# edgebundle + +
+ +* Version: 0.4.1 +* GitHub: https://github.com/schochastics/edgebundle +* Source code: https://github.com/cran/edgebundle +* Date/Publication: 2022-11-22 07:00:02 UTC +* Number of recursive dependencies: 55 + +Run `revdepcheck::cloud_details(, "edgebundle")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘edgebundle-Ex.R’ failed + The error most likely occurred in: + + > ### Name: metro_multicriteria + > ### Title: Metro Map Layout + > ### Aliases: metro_multicriteria + > + > ### ** Examples + > + > # the algorithm has problems with parallel edges + ... + decompose, spectrum + + The following object is masked from ‘package:base’: + + union + + > g <- simplify(metro_berlin) + Error in simplify(metro_berlin) : + REAL() can only be applied to a 'numeric', not a 'logical' + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 22 marked UTF-8 strings + ``` + +# einet + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/travisbyrum/einet +* Source code: https://github.com/cran/einet +* Date/Publication: 2020-04-23 17:20:03 UTC +* Number of recursive dependencies: 67 + +Run `revdepcheck::cloud_details(, "einet")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 1. ├─testthat::expect_lte(effective_information(karate) - 2.35, MAX_ERROR) at test_effective_information.R:76:2 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. ├─einet::effective_information(karate) + 5. ├─einet:::effective_information.igraph(karate) + 6. │ └─einet:::check_network(graph) + 7. │ └─graph %>% igraph::simplify(remove.loops = FALSE) %>% ... + 8. ├─igraph::as.directed(.) + 9. │ └─igraph::is_igraph(graph) + 10. │ └─"igraph" %in% class(graph) + 11. └─igraph::simplify(., remove.loops = FALSE) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 12 ] + Error: Test failures + Execution halted + ``` + +# emba + +
+ +* Version: 0.1.8 +* GitHub: https://github.com/bblodfon/emba +* Source code: https://github.com/cran/emba +* Date/Publication: 2021-01-07 04:00:02 UTC +* Number of recursive dependencies: 76 + +Run `revdepcheck::cloud_details(, "emba")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘emba.Rmd’ using rmarkdown + Quitting from lines 208-210 (emba.Rmd) + Error: processing vignette 'emba.Rmd' failed with diagnostics: + REAL() can only be applied to a 'numeric', not a 'logical' + --- failed re-building ‘emba.Rmd’ + + SUMMARY: processing the following file failed: + ‘emba.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# etree + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/ricgbl/etree +* Source code: https://github.com/cran/etree +* Date/Publication: 2022-07-16 08:30:02 UTC +* Number of recursive dependencies: 128 + +Run `revdepcheck::cloud_details(, "etree")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 3. │ └─testthat:::quasi_capture(...) + 4. │ ├─testthat (local) .capture(...) + 5. │ │ └─base::withCallingHandlers(...) + 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 7. └─etree::etree(resp_cls, covs_cls, split_type = "cluster") + 8. └─base::lapply(covariates, dist_comp) + 9. └─etree (local) FUN(X[[i]], ...) + 10. └─base::sapply(x, function(i) is.null(igraph::edge.attributes(i)$weight)) + 11. └─base::lapply(X = X, FUN = FUN, ...) + 12. └─etree (local) FUN(X[[i]], ...) + 13. └─igraph::edge.attributes(i) + + [ FAIL 25 | WARN 1 | SKIP 0 | PASS 46 ] + Error: Test failures + Execution halted + ``` + +# gemtc + +
+ +* Version: 1.0-1 +* GitHub: https://github.com/gertvv/gemtc +* Source code: https://github.com/cran/gemtc +* Date/Publication: 2021-05-14 23:20:02 UTC +* Number of recursive dependencies: 58 + +Run `revdepcheck::cloud_details(, "gemtc")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘test.R’ + Running the tests in ‘tests/test.R’ failed. + Last 13 lines of output: + 5. └─testthat:::compare.default(act$val, exp$val, ...) + 6. ├─base::all.equal(x, y, ...) + 7. └─base::all.equal.default(x, y, ...) + 8. └─base::all.equal.list(target, current, ...) + 9. ├─base::all.equal(...) + 10. └─base::all.equal.default(...) + 11. └─base::all.equal.list(target, current, ...) + 12. └─base::attr.all.equal(target, current, ...) + 13. ├─base::length(target) + 14. └─igraph:::length.igraph(target) + 15. └─igraph::vcount(x) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 376 ] + Error: Test failures + Execution halted + ``` + +# geonetwork + +
+ +* Version: 0.5.0 +* GitHub: NA +* Source code: https://github.com/cran/geonetwork +* Date/Publication: 2023-04-14 08:30:02 UTC +* Number of recursive dependencies: 156 + +Run `revdepcheck::cloud_details(, "geonetwork")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘geonetwork-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.geonetwork + > ### Title: Plot a geonetwork + > ### Aliases: plot.geonetwork + > + > ### ** Examples + > + > plot(eurodist, axes = TRUE, type = "n") + Error in vertex.attributes(graph) : + VECTOR_ELT() can only be applied to a 'list', not a 'environment' + Calls: plot ... plot.geonetwork -> -> vertex_attr -> vertex.attributes + Execution halted + ``` + +# GISSB + +
+ +* Version: 1.1 +* GitHub: NA +* Source code: https://github.com/cran/GISSB +* Date/Publication: 2023-01-10 18:33:14 UTC +* Number of recursive dependencies: 114 + +Run `revdepcheck::cloud_details(, "GISSB")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘GISSB-Ex.R’ failed + The error most likely occurred in: + + > ### Name: path_leaflet + > ### Title: Visualize the shortest path with Leaflet + > ### Aliases: path_leaflet + > + > ### ** Examples + > + > + ... + > shortest_path_igraph(from_node_ID = 25, + + to_node_ID = 33, + + unit = "minutes", + + path = TRUE, + + graph_object = graph_sampledata) %>% + + path_leaflet(graph_object = graph_sampledata) + Error in edge.attributes(graph) : + VECTOR_ELT() can only be applied to a 'list', not a 'environment' + Calls: %>% ... edge_tibble -> as_tibble -> edge_attr -> edge.attributes + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 866 marked UTF-8 strings + ``` + +# grand + +
+ +* Version: 0.9.0 +* GitHub: https://github.com/zpneal/grand +* Source code: https://github.com/cran/grand +* Date/Publication: 2023-02-10 10:30:02 UTC * Number of recursive dependencies: 36 -Run `revdepcheck::cloud_details(, "backbone")` for more info +Run `revdepcheck::cloud_details(, "grand")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘grand-Ex.R’ failed + The error most likely occurred in: + + > ### Name: grand + > ### Title: Apply Guidelines for Reporting About Network Data (GRAND) to an + > ### igraph object + > ### Aliases: grand + > + > ### ** Examples + > + > data(airport) #Load example data + > airport <- grand(airport) #Apply GRAND interactively + Error in igraph::is_simple(G) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: grand -> + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘grand.Rmd’ using rmarkdown + Quitting from lines 167-178 (grand.Rmd) + Error: processing vignette 'grand.Rmd' failed with diagnostics: + REAL() can only be applied to a 'numeric', not a 'logical' + --- failed re-building ‘grand.Rmd’ + + SUMMARY: processing the following file failed: + ‘grand.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# graph4lg + +
+ +* Version: 1.8.0 +* GitHub: NA +* Source code: https://github.com/cran/graph4lg +* Date/Publication: 2023-01-30 14:00:05 UTC +* Number of recursive dependencies: 119 + +Run `revdepcheck::cloud_details(, "graph4lg")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘graph4lg-Ex.R’ failed + The error most likely occurred in: + + > ### Name: add_nodes_attr + > ### Title: Add attributes to the nodes of a graph + > ### Aliases: add_nodes_attr + > + > ### ** Examples + > + > data("data_tuto") + ... + > graph <- data_tuto[[3]] + > df_nodes <- data.frame(Id = igraph::V(graph)$name, + + Area = runif(50, min = 10, max = 60)) + This graph was created by an old(er) igraph version. + Call upgrade_graph() on it to use with the current igraph version + For now we convert it on the fly... + Error in vcount(graph) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: data.frame -> -> vcount + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘genetic_graph_2.Rmd’ using rmarkdown + Quitting from lines 227-228 (genetic_graph_2.Rmd) + Error: processing vignette 'genetic_graph_2.Rmd' failed with diagnostics: + REAL() can only be applied to a 'numeric', not a 'logical' + --- failed re-building ‘genetic_graph_2.Rmd’ + + --- re-building ‘graph_comparisons_4.Rmd’ using rmarkdown + --- finished re-building ‘graph_comparisons_4.Rmd’ + ... + Quitting from lines 426-430 (landscape_graph_3.Rmd) + Error: processing vignette 'landscape_graph_3.Rmd' failed with diagnostics: + REAL() can only be applied to a 'numeric', not a 'logical' + --- failed re-building ‘landscape_graph_3.Rmd’ + + SUMMARY: processing the following files failed: + ‘genetic_graph_2.Rmd’ ‘landscape_graph_3.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Error loading dataset 'data_tuto': + Error in vcount(x) : + REAL() can only be applied to a 'numeric', not a 'logical' + + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘Rdpack’ + All declared Imports should be used. + ``` + +# graphkernels + +
+ +* Version: 1.6.1 +* GitHub: NA +* Source code: https://github.com/cran/graphkernels +* Date/Publication: 2021-12-20 09:00:02 UTC +* Number of recursive dependencies: 9 + +Run `revdepcheck::cloud_details(, "graphkernels")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘graphkernels-Ex.R’ failed + The error most likely occurred in: + + > ### Name: CalculateConnectedGraphletKernel + > ### Title: Connected graphlet kernel + > ### Aliases: CalculateConnectedGraphletKernel + > ### Keywords: graph kernel graphlet + > + > ### ** Examples + > + > data(mutag) + > K <- CalculateConnectedGraphletKernel(mutag, 4) + Error in is_directed(graph) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: CalculateConnectedGraphletKernel -> as_adj_list -> is_directed + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 15.6Mb + sub-directories of 1Mb or more: + libs 15.4Mb + ``` + +# graphlayouts + +
+ +* Version: 0.8.4 +* GitHub: https://github.com/schochastics/graphlayouts +* Source code: https://github.com/cran/graphlayouts +* Date/Publication: 2022-11-24 06:20:02 UTC +* Number of recursive dependencies: 93 + +Run `revdepcheck::cloud_details(, "graphlayouts")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘graphlayouts-Ex.R’ failed + The error most likely occurred in: + + > ### Name: layout_multilevel + > ### Title: multilevel layout + > ### Aliases: layout_multilevel layout_as_multilevel + > ### layout_igraph_multilevel + > + > ### ** Examples + > + ... + union + + > data("multilvl_ex") + > + > # compute a layout for the whole network + > xy <- layout_as_multilevel(multilvl_ex,type = "all", alpha = 25, beta = 45) + Error in igraph::vertex_attr_names(g) : + VECTOR_ELT() can only be applied to a 'list', not a 'environment' + Calls: layout_as_multilevel -> %in% -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-layout_multilevel.R:3:3'): layout_mulitlevel works ───────────── + Error in `igraph::vertex_attr_names(g)`: VECTOR_ELT() can only be applied to a 'list', not a 'environment' + Backtrace: + ▆ + 1. ├─testthat::expect_is(...) at test-layout_multilevel.R:3:2 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. └─graphlayouts::layout_as_multilevel(...) + 5. ├─"lvl" %in% igraph::vertex_attr_names(g) + 6. └─igraph::vertex_attr_names(g) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 71 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 9.1Mb + sub-directories of 1Mb or more: + help 2.4Mb + libs 6.5Mb + ``` + +# graphsim + +
+ +* Version: 1.0.3 +* GitHub: https://github.com/TomKellyGenetics/graphsim +* Source code: https://github.com/cran/graphsim +* Date/Publication: 2022-09-12 06:12:54 UTC +* Number of recursive dependencies: 121 + +Run `revdepcheck::cloud_details(, "graphsim")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘graphsim-Ex.R’ failed + The error most likely occurred in: + + > ### Name: generate_expression + > ### Title: Generate Simulated Expression + > ### Aliases: generate_expression generate_expression_mat + > ### Keywords: graph igraph mvtnorm network simulation + > + > ### ** Examples + > + ... + > # absolute = FALSE (geometric distance by default) + > # compute states directly from graph attributes for TGF-\eqn{\Beta} pathway + > TGFBeta_Smad_state <- E(TGFBeta_Smad_graph)$state + This graph was created by an old(er) igraph version. + Call upgrade_graph() on it to use with the current igraph version + For now we convert it on the fly... + Error in ecount(graph) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: E -> ecount + Execution halted + ``` + +# iGraphMatch + +
+ +* Version: 2.0.1 +* GitHub: https://github.com/dpmcsuss/iGraphMatch +* Source code: https://github.com/cran/iGraphMatch +* Date/Publication: 2022-09-13 18:30:02 UTC +* Number of recursive dependencies: 80 + +Run `revdepcheck::cloud_details(, "iGraphMatch")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘iGraphMatch-Ex.R’ failed + The error most likely occurred in: + + > ### Name: C.Elegans + > ### Title: Chemical synapses and electrical synapses networks of roundworm + > ### Aliases: C.Elegans + > ### Keywords: datasets + > + > ### ** Examples + > + > data(C.Elegans) + > g1 <- C.Elegans[[1]] + > g2 <- C.Elegans[[2]] + > plot(g1, g2) + Error in igraph::vcount(x) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: plot -> plot -> .local -> identity_match -> + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘iGraphMatch.Rmd’ using rmarkdown + Quitting from lines 951-987 (iGraphMatch.Rmd) + Error: processing vignette 'iGraphMatch.Rmd' failed with diagnostics: + REAL() can only be applied to a 'numeric', not a 'logical' + --- failed re-building ‘iGraphMatch.Rmd’ + + SUMMARY: processing the following file failed: + ‘iGraphMatch.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# influenceR + +
+ +* Version: 0.1.0.1 +* GitHub: https://github.com/rcc-uchicago/influenceR +* Source code: https://github.com/cran/influenceR +* Date/Publication: 2021-09-25 10:15:40 UTC +* Number of recursive dependencies: 35 + +Run `revdepcheck::cloud_details(, "influenceR")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 4. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 5. └─influenceR::betweenness(flo_graph) + 6. └─igraph::get.edgelist(g, names = F) + 7. └─base::matrix(.Call(R_igraph_get_edgelist, graph, TRUE), ncol = 2) + ── Error ('test_reference.R:72:3'): bridging matches reference function ──────── + Error in `vcount(graph)`: REAL() can only be applied to a 'numeric', not a 'logical' + Backtrace: + ▆ + 1. └─influenceR (local) bridge_test(flo_graph) at test_reference.R:72:2 + 2. └─igraph::V(g) at test_reference.R:26:2 + 3. └─igraph::vcount(graph) + + [ FAIL 5 | WARN 2 | SKIP 0 | PASS 0 ] + Error: Test failures + Execution halted + ``` + +# intergraph + +
+ +* Version: 2.0-2 +* GitHub: NA +* Source code: https://github.com/cran/intergraph +* Date/Publication: 2016-12-05 18:28:47 +* Number of recursive dependencies: 49 + +Run `revdepcheck::cloud_details(, "intergraph")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘intergraph-Ex.R’ failed + The error most likely occurred in: + + > ### Name: asDF + > ### Title: Convert network to data frame(s) + > ### Aliases: asDF asDF.igraph asDF.network + > + > ### ** Examples + > + > # using method for 'network' objects + ... + ..$ label : chr [1:15] "a" "b" "c" "d" ... + ..$ na : logi [1:15] FALSE FALSE FALSE FALSE FALSE FALSE ... + ..$ vertex.names : chr [1:15] "a" "b" "c" "d" ... + > + > # using method for 'igraph' objects + > d2 <- asDF(exIgraph) + Error in matrix(.Call(R_igraph_get_edgelist, graph, TRUE), ncol = 2) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: asDF ... asDF.igraph -> as.data.frame -> -> matrix + Execution halted + ``` + +# invertiforms + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/RoheLab/invertiforms +* Source code: https://github.com/cran/invertiforms +* Date/Publication: 2022-11-25 12:40:10 UTC +* Number of recursive dependencies: 50 + +Run `revdepcheck::cloud_details(, "invertiforms")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘invertiforms-Ex.R’ failed + The error most likely occurred in: + + > ### Name: DoubleCenter + > ### Title: Construct and use DoubleCenter transformations + > ### Aliases: DoubleCenter transform,DoubleCenter,sparseMatrix-method + > ### inverse_transform,DoubleCenter,sparseLRMatrix-method + > ### inverse_transform,DoubleCenter,vsp_fa-method + > + > ### ** Examples + ... + + > library(igraphdata) + > + > data("karate", package = "igraphdata") + > + > A <- get.adjacency(karate) + Error in vcount(graph) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: get.adjacency -> get.adjacency.sparse -> vcount + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ▆ + 1. └─igraph::get.adjacency(karate) at test-PerturbedLaplacian.R:6:0 + 2. └─igraph:::get.adjacency.sparse(...) + 3. └─igraph::vcount(graph) + ── Error ('test-RegularizedLaplacian.R:6:1'): (code run outside of `test_that()`) ── + Error in `vcount(graph)`: REAL() can only be applied to a 'numeric', not a 'logical' + Backtrace: + ▆ + 1. └─igraph::get.adjacency(karate) at test-RegularizedLaplacian.R:6:0 + 2. └─igraph:::get.adjacency.sparse(...) + 3. └─igraph::vcount(graph) + + [ FAIL 4 | WARN 0 | SKIP 0 | PASS 0 ] + Error: Test failures + Execution halted + ``` + +# ITNr + +
+ +* Version: 0.7.0 +* GitHub: NA +* Source code: https://github.com/cran/ITNr +* Date/Publication: 2023-03-31 14:10:11 UTC +* Number of recursive dependencies: 82 + +Run `revdepcheck::cloud_details(, "ITNr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ITNr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ITNproperties + > ### Title: ITN Properties + > ### Aliases: ITNproperties + > + > ### ** Examples + > + > ##Load the network + > data(ELEnet16) + > + > ##Calculate the network properties + > ITNPROP<-ITNproperties(ELEnet16,TRUE) + Error in matrix(.Call(R_igraph_get_edgelist, graph, TRUE), ncol = 2) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: ITNproperties -> cbind -> -> matrix + Execution halted + ``` + +# LEANR + +
+ +* Version: 1.4.9 +* GitHub: NA +* Source code: https://github.com/cran/LEANR +* Date/Publication: 2016-11-12 15:47:01 +* Number of recursive dependencies: 64 + +Run `revdepcheck::cloud_details(, "LEANR")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ── Error ('test_output.R:8:1'): (code run outside of `test_that()`) ──────────── + Error in `vcount(graph)`: REAL() can only be applied to a 'numeric', not a 'logical' + Backtrace: + ▆ + 1. └─LEANR::run.lean(...) at test_output.R:8:0 + 2. └─LEANR:::reduce.graph.fromdata(g, ranking, add.scored.genes, keep.nodes.without.scores) + 3. ├─base::intersect(V(g)$name, gene.list.char) + 4. │ ├─base::unique(y[match(as.vector(x), y, 0L)]) + 5. │ └─base::as.vector(x) + 6. └─igraph::V(g) + 7. └─igraph::vcount(graph) + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ] + Error: Test failures + Execution halted + ``` + +# leiden + +
+ +* Version: 0.4.3 +* GitHub: https://github.com/TomKellyGenetics/leiden +* Source code: https://github.com/cran/leiden +* Date/Publication: 2022-09-10 17:22:53 UTC +* Number of recursive dependencies: 147 + +Run `revdepcheck::cloud_details(, "leiden")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 16: test_code(NULL, exprs, env) + 17: source_file(path, child_env(env), wrap = wrap) + 18: FUN(X[[i]], ...) + 19: lapply(test_paths, test_one_file, env = env, wrap = wrap) + 20: doTryCatch(return(expr), name, parentenv, handler) + 21: tryCatchOne(expr, names, parentenv, handlers[[1L]]) + 22: tryCatchList(expr, classes, parentenv, handlers) + 23: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL}) + 24: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, wrap = wrap)) + 25: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package) + 26: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package, parallel = parallel) + 27: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed") + 28: test_check("leiden") + An irrecoverable exception occurred. R is aborting now ... + Segmentation fault (core dumped) + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘benchmarking.Rmd’ using knitr + Warning: The closing backticks on line 337 ("```") in benchmarking.Rmd do not match the opening backticks "````" on line 334. You are recommended to fix either the opening or closing delimiter of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). + Warning: The closing backticks on line 400 ("```") in benchmarking.Rmd do not match the opening backticks "````" on line 396. You are recommended to fix either the opening or closing delimiter of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). + Warning: The closing backticks on line 408 ("```") in benchmarking.Rmd do not match the opening backticks "````" on line 404. You are recommended to fix either the opening or closing delimiter of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). + --- finished re-building ‘benchmarking.Rmd’ + + --- re-building ‘run_bipartite.Rmd’ using knitr + + *** caught segfault *** + ... + zero-length arrow is of indeterminate angle and so skipped + Warning in doTryCatch(return(expr), name, parentenv, handler) : + zero-length arrow is of indeterminate angle and so skipped + --- finished re-building ‘run_multiplex.Rmd’ + + SUMMARY: processing the following file failed: + ‘run_bipartite.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.0Mb + sub-directories of 1Mb or more: + doc 5.9Mb + ``` + +# leidenAlg + +
+ +* Version: 1.0.5 +* GitHub: https://github.com/kharchenkolab/leidenAlg +* Source code: https://github.com/cran/leidenAlg +* Date/Publication: 2022-09-30 07:20:02 UTC +* Number of recursive dependencies: 68 + +Run `revdepcheck::cloud_details(, "leidenAlg")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘leidenAlg-Ex.R’ failed + The error most likely occurred in: + + > ### Name: as.dendrogram.fakeCommunities + > ### Title: Returns pre-calculated dendrogram + > ### Aliases: as.dendrogram.fakeCommunities + > + > ### ** Examples + > + > rLeidenComm = suppressWarnings(rleiden.community(exampleGraph, n.cores=1)) + Error in edge_attr_names(graph) : + VECTOR_ELT() can only be applied to a 'list', not a 'environment' + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 2. └─igraph::is_weighted(graph) + 3. ├─"weight" %in% edge_attr_names(graph) + 4. └─igraph::edge_attr_names(graph) + ── Error ('test_functions.R:25:2'): membership.fakeCommunities() functionality ── + Error in `edge_attr_names(graph)`: VECTOR_ELT() can only be applied to a 'list', not a 'environment' + Backtrace: + ▆ + 1. └─leidenAlg::leiden.community(exampleGraph) at test_functions.R:25:8 + 2. └─igraph::is_weighted(graph) + 3. ├─"weight" %in% edge_attr_names(graph) + 4. └─igraph::edge_attr_names(graph) + + [ FAIL 4 | WARN 0 | SKIP 0 | PASS 0 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# leidenbase + +
+ +* Version: 0.1.18 +* GitHub: https://github.com/cole-trapnell-lab/leidenbase +* Source code: https://github.com/cran/leidenbase +* Date/Publication: 2023-04-15 09:20:02 UTC +* Number of recursive dependencies: 54 + +Run `revdepcheck::cloud_details(, "leidenbase")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘leidenbase-Ex.R’ failed + The error most likely occurred in: + + > ### Name: leiden_find_partition + > ### Title: Leiden find partition community detection function + > ### Aliases: leiden_find_partition + > + > ### ** Examples + > + > library(igraph) + ... + + > fpath <- system.file( 'testdata', 'igraph_n1500_edgelist.txt.gz', package = 'leidenbase' ) + > zfp <- gzfile(fpath) + > igraph <- read_graph( file = zfp, format='edgelist', n=1500 ) + > res <- leiden_find_partition(igraph=igraph, + + partition_type='CPMVertexPartition', + + resolution_parameter=1e-5) + Error in leiden_find_partition(igraph = igraph, partition_type = "CPMVertexPartition", : + REAL() can only be applied to a 'numeric', not a 'NULL' + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Error in `leidenbase::leiden_find_partition(igraph, partition_type = "RBConfigurationVertexPartition", + node_sizes = nodsiz, seed = 123456, resolution_parameter = 0.5)`: REAL() can only be applied to a 'numeric', not a 'NULL' + Backtrace: + ▆ + 1. └─leidenbase::leiden_find_partition(...) at test-leidenbase.R:224:2 + ── Error ('test-leidenbase.R:245:3'): modularity and significance return values ── + Error in `leidenbase::leiden_find_partition(igraph, partition_type = "CPMVertexPartition", + seed = 123456, resolution_parameter = 0.1)`: REAL() can only be applied to a 'numeric', not a 'NULL' + Backtrace: + ▆ + 1. └─leidenbase::leiden_find_partition(...) at test-leidenbase.R:245:2 + + [ FAIL 11 | WARN 0 | SKIP 0 | PASS 6 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘leidenbase.Rmd’ using rmarkdown + Quitting from lines 87-92 (leidenbase.Rmd) + Error: processing vignette 'leidenbase.Rmd' failed with diagnostics: + REAL() can only be applied to a 'numeric', not a 'NULL' + --- failed re-building ‘leidenbase.Rmd’ + + SUMMARY: processing the following file failed: + ‘leidenbase.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 19.1Mb + sub-directories of 1Mb or more: + libs 18.8Mb + ``` + +# meconetcomp + +
+ +* Version: 0.2.0 +* GitHub: https://github.com/ChiLiubio/meconetcomp +* Source code: https://github.com/cran/meconetcomp +* Date/Publication: 2022-10-05 15:20:02 UTC +* Number of recursive dependencies: 147 + +Run `revdepcheck::cloud_details(, "meconetcomp")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘meconetcomp-Ex.R’ failed + The error most likely occurred in: + + > ### Name: cal_module + > ### Title: Assign modules to each network + > ### Aliases: cal_module + > + > ### ** Examples + > + > data(soil_amp_network) + > soil_amp_network <- cal_module(soil_amp_network) + Error in is_directed(network_list[[i]]$res_network) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: cal_module -> is_directed + Execution halted + ``` + +# metanetwork + +
+ +* Version: 0.7.0 +* GitHub: https://github.com/MarcOhlmann/metanetwork +* Source code: https://github.com/cran/metanetwork +* Date/Publication: 2022-12-05 14:10:02 UTC +* Number of recursive dependencies: 106 + +Run `revdepcheck::cloud_details(, "metanetwork")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘metanetwork-Ex.R’ failed + The error most likely occurred in: + + > ### Name: append_agg_nets + > ### Title: append aggregated networks + > ### Aliases: append_agg_nets append_agg_nets.metanetwork + > + > ### ** Examples + > + > library(metanetwork) + > data(meta_angola) + > meta_angola = append_agg_nets(meta_angola) + Error in graph_attr(x, name) : + VECTOR_ELT() can only be applied to a 'list', not a 'environment' + Calls: append_agg_nets ... sapply -> lapply -> FUN -> $ -> $.igraph -> graph_attr + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Error in `graph_attr(x, name)`: VECTOR_ELT() can only be applied to a 'list', not a 'environment' + Backtrace: + ▆ + 1. ├─testthat::expect_is(...) at test-vismetaNetwork.R:34:2 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. └─metanetwork::diff_plot(...) + 5. ├─c(g1$name, g2$name) %in% ... + 6. ├─g1$name + 7. └─igraph:::`$.igraph`(g1, "name") + 8. └─igraph::graph_attr(x, name) + + [ FAIL 16 | WARN 8 | SKIP 0 | PASS 32 ] + Error: Test failures + Execution halted + ``` + +# migraph + +
+ +* Version: 0.13.2 +* GitHub: https://github.com/snlab-ch/migraph +* Source code: https://github.com/cran/migraph +* Date/Publication: 2022-12-20 16:20:02 UTC +* Number of recursive dependencies: 138 + +Run `revdepcheck::cloud_details(, "migraph")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘migraph-Ex.R’ failed + The error most likely occurred in: + + > ### Name: add + > ### Title: Adding and copying attributes from one graph to another + > ### Aliases: add add_node_attribute add_tie_attribute copy_node_attributes + > ### join_ties + > + > ### ** Examples + > + > add_node_attribute(mpn_elite_mex, "wealth", 1:35) + Error in igraph::vcount(as_igraph(object)) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: add_node_attribute -> network_nodes -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 8. └─igraph::vertex_attr_names(graph) + ── Error ('test-viz_layout_partition.R:20:3'): concentric layout works ───────── + Error in `vertex_attr_names(graph)`: VECTOR_ELT() can only be applied to a 'list', not a 'environment' + Backtrace: + ▆ + 1. └─migraph::layout_tbl_graph_concentric(ison_southern_women) at test-viz_layout_partition.R:20:2 + 2. ├─migraph::is_twomode(object) + 3. └─migraph:::is_twomode.igraph(object) + 4. └─igraph::is.bipartite(object) + 5. ├─"type" %in% vertex_attr_names(graph) + 6. └─igraph::vertex_attr_names(graph) + + [ FAIL 74 | WARN 0 | SKIP 0 | PASS 99 ] + Error: Test failures + Execution halted + ``` + +# missSBM + +
+ +* Version: 1.0.3 +* GitHub: https://github.com/grossSBM/missSBM +* Source code: https://github.com/cran/missSBM +* Date/Publication: 2022-08-23 12:10:06 UTC +* Number of recursive dependencies: 113 + +Run `revdepcheck::cloud_details(, "missSBM")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘missSBM-Ex.R’ failed + The error most likely occurred in: + + > ### Name: frenchblog2007 + > ### Title: Political Blogosphere network prior to 2007 French presidential + > ### election + > ### Aliases: frenchblog2007 + > ### Keywords: datasets + > + > ### ** Examples + ... + > + > data(frenchblog2007) + > igraph::V(frenchblog2007)$party + This graph was created by an old(er) igraph version. + Call upgrade_graph() on it to use with the current igraph version + For now we convert it on the fly... + Error in vcount(graph) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: -> vcount + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 396 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-consistency-on-fully-observed-network.R:9:3'): SimpleSBM_fit_missSBM and missSBMfit are coherent ── + Error in `vcount(graph)`: REAL() can only be applied to a 'numeric', not a 'logical' + Backtrace: + ▆ + 1. ├─war$belligerent %>% igraph::as_adj() at test-consistency-on-fully-observed-network.R:9:2 + 2. └─igraph::as_adj(.) + 3. └─igraph:::get.adjacency.sparse(...) + 4. └─igraph::vcount(graph) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 396 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘case_study_war_networks.Rmd’ using rmarkdown + Quitting from lines 60-65 (case_study_war_networks.Rmd) + Error: processing vignette 'case_study_war_networks.Rmd' failed with diagnostics: + REAL() can only be applied to a 'numeric', not a 'logical' + --- failed re-building ‘case_study_war_networks.Rmd’ + + SUMMARY: processing the following file failed: + ‘case_study_war_networks.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 10.6Mb + sub-directories of 1Mb or more: + libs 8.6Mb + ``` + +# molnet + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/molnet +* Date/Publication: 2021-08-06 08:30:02 UTC +* Number of recursive dependencies: 123 + +Run `revdepcheck::cloud_details(, "molnet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘molnet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: determine_drug_targets + > ### Title: Determine drug target nodes in network + > ### Aliases: determine_drug_targets + > + > ### ** Examples + > + > data(drug_gene_interactions) + ... + + combined_graphs[["annotations"]], + + drug_target_interaction, + + settings) + This graph was created by an old(er) igraph version. + Call upgrade_graph() on it to use with the current igraph version + For now we convert it on the fly... + Error in vcount(graph) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: determine_drug_targets -> find_targets -> %in% -> -> vcount + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Molnet_Vignette.Rmd’ using rmarkdown + Quitting from lines 310-312 (Molnet_Vignette.Rmd) + Error: processing vignette 'Molnet_Vignette.Rmd' failed with diagnostics: + VECTOR_ELT() can only be applied to a 'list', not a 'environment' + --- failed re-building ‘Molnet_Vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘Molnet_Vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# motifr + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/marioangst/motifr +* Source code: https://github.com/cran/motifr +* Date/Publication: 2020-12-10 15:40:02 UTC +* Number of recursive dependencies: 121 + +Run `revdepcheck::cloud_details(, "motifr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘motifr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: directed_dummy_net + > ### Title: Two-level directed network dummy example + > ### Aliases: directed_dummy_net + > ### Keywords: datasets + > + > ### ** Examples + > + > plot_mnet(directed_dummy_net) + Error in vertex.attributes(graph) : + VECTOR_ELT() can only be applied to a 'list', not a 'environment' + Calls: plot_mnet ... node_tibble -> as_tibble -> vertex_attr -> vertex.attributes + Execution halted + ``` + +# multinets + +
+ +* Version: 0.2.2 +* GitHub: https://github.com/neylsoncrepalde/multinets +* Source code: https://github.com/cran/multinets +* Date/Publication: 2019-12-14 17:20:03 UTC +* Number of recursive dependencies: 72 + +Run `revdepcheck::cloud_details(, "multinets")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘multinets-Ex.R’ failed + The error most likely occurred in: + + > ### Name: extract_highlevel + > ### Title: Extract the high level of a multilevel network + > ### Aliases: extract_highlevel + > + > ### ** Examples + > + > organizations <- extract_highlevel(linked_sim) + Error in vertex_attr_names(graph) : + VECTOR_ELT() can only be applied to a 'list', not a 'environment' + Calls: extract_highlevel ... is_multilevel -> -> %in% -> vertex_attr_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 11. └─igraph::is_bipartite(x) + 12. ├─"type" %in% vertex_attr_names(graph) + 13. └─igraph::vertex_attr_names(graph) + ── Error ('test-mode_transformation.R:15:3'): mode transformation works without specifying 'which' ── + Error in `vertex_attr_names(graph)`: VECTOR_ELT() can only be applied to a 'list', not a 'environment' + Backtrace: + ▆ + 1. └─igraph::bipartite_projection(g.bip) at test-mode_transformation.R:15:2 + 2. └─igraph:::handle_vertex_type_arg(types, graph) + 3. ├─"type" %in% vertex_attr_names(graph) + 4. └─igraph::vertex_attr_names(graph) + + [ FAIL 4 | WARN 0 | SKIP 0 | PASS 10 ] + Error: Test failures + Execution halted + ``` + +# mwcsr + +
+ +* Version: 0.1.6 +* GitHub: https://github.com/ctlab/mwcsr +* Source code: https://github.com/cran/mwcsr +* Date/Publication: 2022-07-12 17:50:02 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "mwcsr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘mwcsr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: get_instance_type + > ### Title: Check the type and the validity of an MWCS instance + > ### Aliases: get_instance_type + > + > ### ** Examples + > + > data(mwcs_example) + > get_instance_type(mwcs_example) + Error in igraph::is_directed(g) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: get_instance_type -> check_graph -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ▆ + 1. └─mwcsr::solve_mwcsp(solver, sgmwcs_small_instance) at test_virgo.R:48:4 + 2. └─mwcsr:::check_graph(instance) + 3. └─igraph::is_directed(g) + ── Error ('test_virgo.R:80:5'): heuristic virgo_solver works on SGMWCS ───────── + Error in `graph_attr(x, name)`: VECTOR_ELT() can only be applied to a 'list', not a 'environment' + Backtrace: + ▆ + 1. ├─si$signals at test_virgo.R:80:4 + 2. └─igraph:::`$.igraph`(si, signals) at test_virgo.R:80:4 + 3. └─igraph::graph_attr(x, name) + + [ FAIL 9 | WARN 1 | SKIP 6 | PASS 30 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘tutorial.Rmd’ using rmarkdown + Quitting from lines 43-46 (tutorial.Rmd) + Error: processing vignette 'tutorial.Rmd' failed with diagnostics: + REAL() can only be applied to a 'numeric', not a 'logical' + --- failed re-building ‘tutorial.Rmd’ + + SUMMARY: processing the following file failed: + ‘tutorial.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 17.4Mb + sub-directories of 1Mb or more: + java 2.5Mb + libs 14.2Mb + ``` + +# nda + +
+ +* Version: 0.1.6 +* GitHub: https://github.com/kzst/nda +* Source code: https://github.com/cran/nda +* Date/Publication: 2022-10-14 13:10:02 UTC +* Number of recursive dependencies: 81 + +Run `revdepcheck::cloud_details(, "nda")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘nda-Ex.R’ failed + The error most likely occurred in: + + > ### Name: biplot.nda + > ### Title: Biplot function for Network-based Dimensionality Reduction and + > ### Analysis (NDA) + > ### Aliases: biplot.nda + > ### Keywords: plot + > + > ### ** Examples + ... + > + > # Biplot function without feature selection + > + > data("CrimesUSA1990.X") + > df<-CrimesUSA1990.X + > p<-ndr(df) + Error in find_partition(graph, igraph::E(graph)$weight, resolution, n.iterations) : + REAL() can only be applied to a 'numeric', not a 'NULL' + Calls: ndr -> -> find_partition + Execution halted + ``` + +# netplot + +
+ +* Version: 0.1-1 +* GitHub: https://github.com/USCCANA/netplot +* Source code: https://github.com/cran/netplot +* Date/Publication: 2021-06-16 07:10:02 UTC +* Number of recursive dependencies: 82 + +Run `revdepcheck::cloud_details(, "netplot")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘netplot-Ex.R’ failed + The error most likely occurred in: + + > ### Name: make_colors + > ### Title: Create a vector of colors for vertices and edges + > ### Aliases: make_colors make_edges_colors make_vertex_colors + > + > ### ** Examples + > + > + > data(UKfaculty, package="igraphdata") + > col <- make_vertex_colors(UKfaculty, "Group") + Error in igraph::vertex_attr(x, attr) : + VECTOR_ELT() can only be applied to a 'list', not a 'environment' + Calls: make_vertex_colors -> get_vertex_attr -> + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘base-and-grid.Rmd’ using rmarkdown + --- finished re-building ‘base-and-grid.Rmd’ + + --- re-building ‘examples.Rmd’ using rmarkdown + Quitting from lines 32-43 (examples.Rmd) + Error: processing vignette 'examples.Rmd' failed with diagnostics: + REAL() can only be applied to a 'numeric', not a 'logical' + --- failed re-building ‘examples.Rmd’ + + SUMMARY: processing the following file failed: + ‘examples.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# netrankr + +
+ +* Version: 1.2.0 +* GitHub: https://github.com/schochastics/netrankr +* Source code: https://github.com/cran/netrankr +* Date/Publication: 2022-09-26 21:00:02 UTC +* Number of recursive dependencies: 65 + +Run `revdepcheck::cloud_details(, "netrankr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘netrankr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: aggregate_positions + > ### Title: Quantification of (indirect) relations + > ### Aliases: aggregate_positions + > + > ### ** Examples + > + > library(igraph) + ... + > + > data("dbces11") + > # degree + > dbces11 %>% + + indirect_relations(type = "adjacency") %>% + + aggregate_positions(type = "sum") + Error in igraph::is_directed(g) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: %>% ... aggregate_positions -> indirect_relations -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test_dominance.R:11:3'): neighborhood-inclusion is correct ────────── + Error in `igraph::is_directed(g)`: REAL() can only be applied to a 'numeric', not a 'logical' + Backtrace: + ▆ + 1. ├─testthat::expect_equal(...) at test_dominance.R:11:2 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. └─netrankr::neighborhood_inclusion(dbces11, sparse = FALSE) + 5. └─igraph::is_directed(g) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 78 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘benchmarks.Rmd’ using rmarkdown + --- finished re-building ‘benchmarks.Rmd’ + + --- re-building ‘centrality_indices.Rmd’ using rmarkdown + --- finished re-building ‘centrality_indices.Rmd’ + + --- re-building ‘indirect_relations.Rmd’ using rmarkdown + Quitting from lines 61-79 (indirect_relations.Rmd) + Error: processing vignette 'indirect_relations.Rmd' failed with diagnostics: + ... + REAL() can only be applied to a 'numeric', not a 'logical' + --- failed re-building ‘use_case.Rmd’ + + SUMMARY: processing the following files failed: + ‘indirect_relations.Rmd’ ‘neighborhood_inclusion.Rmd’ + ‘partial_centrality.Rmd’ ‘positional_dominance.Rmd’ + ‘probabilistic_cent.Rmd’ ‘threshold_graph.Rmd’ ‘use_case.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 12.5Mb + sub-directories of 1Mb or more: + doc 1.6Mb + libs 10.6Mb + ``` + +# netseg + +
+ +* Version: 1.0-1 +* GitHub: https://github.com/mbojan/netseg +* Source code: https://github.com/cran/netseg +* Date/Publication: 2022-08-25 12:10:06 UTC +* Number of recursive dependencies: 61 + +Run `revdepcheck::cloud_details(, "netseg")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘netseg-Ex.R’ failed + The error most likely occurred in: + + > ### Name: EF3 + > ### Title: Example data from Figure III of Echenique and Fryer (2006) + > ### Aliases: EF3 + > ### Keywords: datasets + > + > ### ** Examples + > + ... + + vertex.color = igraph::V(EF3)$type+1, + + vertex.label.family = "", + + sub = "Source: Echenique & Fryer (2006)", + + main = "Neighborhood racial segregation\n in a fictional city" + + ) + + } + Error in vcount(graph) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: plot -> plot.igraph -> vcount + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 7. │ │ └─base::withVisible(code) + 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 9. ├─netseg::smi(as.directed(WhiteKinship), "gender") + 10. └─igraph::as.directed(WhiteKinship) + ── Error ('test-ssi.R:4:3'): values of ssi for EF3 data correspond to values from the paper ── + Error in `igraph::is.directed(g)`: REAL() can only be applied to a 'numeric', not a 'logical' + Backtrace: + ▆ + 1. └─netseg::ssi(EF3, "race") at test-ssi.R:4:2 + 2. ├─base::stopifnot(!igraph::is.directed(g), !igraph::any_multiple(g)) + 3. └─igraph::is.directed(g) + + [ FAIL 15 | WARN 0 | SKIP 0 | PASS 59 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘netseg.Rmd’ using rmarkdown + Quitting from lines 46-47 (netseg.Rmd) + Error: processing vignette 'netseg.Rmd' failed with diagnostics: + REAL() can only be applied to a 'numeric', not a 'logical' + --- failed re-building ‘netseg.Rmd’ + + SUMMARY: processing the following file failed: + ‘netseg.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# nett + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/aaamini/nett +* Source code: https://github.com/cran/nett +* Date/Publication: 2022-11-09 10:50:05 UTC +* Number of recursive dependencies: 97 + +Run `revdepcheck::cloud_details(, "nett")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘nett-Ex.R’ failed + The error most likely occurred in: + + > ### Name: fast_cpl + > ### Title: CPL algorithm for community detection (fast) + > ### Aliases: fast_cpl + > ### Keywords: comm_detect + > + > ### ** Examples + > + > head(fast_cpl(igraph::as_adj(polblogs), 2), 50) + Error in vcount(graph) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: head ... spec_repr -> -> get.adjacency.sparse -> vcount + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Community_Detection.Rmd’ using rmarkdown + --- finished re-building ‘Community_Detection.Rmd’ + + --- re-building ‘Visualization.Rmd’ using rmarkdown + Quitting from lines 99-105 (Visualization.Rmd) + Error: processing vignette 'Visualization.Rmd' failed with diagnostics: + REAL() can only be applied to a 'numeric', not a 'logical' + --- failed re-building ‘Visualization.Rmd’ + ... + --- finished re-building ‘explore-comm.Rmd’ + + --- re-building ‘hard_dcsbm_testing.Rmd’ using rmarkdown + --- finished re-building ‘hard_dcsbm_testing.Rmd’ + + SUMMARY: processing the following file failed: + ‘Visualization.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# poppr + +
+ +* Version: 2.9.4 +* GitHub: https://github.com/grunwaldlab/poppr +* Source code: https://github.com/cran/poppr +* Date/Publication: 2023-03-23 03:20:02 UTC +* Number of recursive dependencies: 98 + +Run `revdepcheck::cloud_details(, "poppr")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘test-all.R’ + Running the tests in ‘tests/test-all.R’ failed. + Last 13 lines of output: + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-msn.R:445:3'): Minimum spanning networks can subset populations ── + ucl(bmsn) not identical to ucl(pmsn). + Component 10: Component 3: 1 string mismatch + ── Failure ('test-msn.R:449:3'): Minimum spanning networks can subset populations ── + ucl(bmsn12) not identical to ucl(pmsn12). + Component 10: Component 3: 1 string mismatch + ── Failure ('test-msn.R:453:3'): Minimum spanning networks can subset populations ── + ucl(bmsn1) not identical to ucl(pmsn1). + Component 10: Component 3: 1 string mismatch + + [ FAIL 3 | WARN 0 | SKIP 181 | PASS 375 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘algo.Rnw’ using knitr + Error: processing vignette 'algo.Rnw' failed with diagnostics: + Running 'texi2dvi' on 'algo.tex' failed. + LaTeX errors: + ! LaTeX Error: File `colortbl.sty' not found. + + Type X to quit or to proceed, + or enter new name. (Default extension: sty) + ... + l.270 \long + \def\@secondoffive#1#2#3#4#5{#2}^^M + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘algo.Rnw’ + + SUMMARY: processing the following file failed: + ‘algo.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# psSubpathway + +
+ +* Version: 0.1.1 +* GitHub: NA +* Source code: https://github.com/cran/psSubpathway +* Date/Publication: 2019-10-02 12:40:02 UTC +* Number of recursive dependencies: 105 + +Run `revdepcheck::cloud_details(, "psSubpathway")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘psSubpathway-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plotSpwNetmap + > ### Title: Polt a subpathway network map + > ### Aliases: plotSpwNetmap + > + > ### ** Examples + > + > # load depend package. + ... + The following object is masked from ‘package:base’: + + union + + > # plot network graph of the subpathway 00982_2 + > plotSpwNetmap(spwid="00982_2",layout=layout_nicely) + Error in vcount(graph) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: plotSpwNetmap -> plot -> plot.igraph -> vcount + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘vignette.Rmd’ using rmarkdown + Quitting from lines 173-178 (vignette.Rmd) + Error: processing vignette 'vignette.Rmd' failed with diagnostics: + REAL() can only be applied to a 'numeric', not a 'logical' + --- failed re-building ‘vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# rmonad + +
+ +* Version: 0.7.0 +* GitHub: https://github.com/arendsee/rmonad +* Source code: https://github.com/cran/rmonad +* Date/Publication: 2020-02-14 07:00:02 UTC +* Number of recursive dependencies: 81 + +Run `revdepcheck::cloud_details(, "rmonad")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘rmonad-Ex.R’ failed + The error most likely occurred in: + + > ### Name: missues + > ### Title: Tabulates all errors, warnings and notes + > ### Aliases: missues + > + > ### ** Examples + > + > data(gff) + > m <- gff$good_result + > missues(m) + This graph was created by an old(er) igraph version. + Call upgrade_graph() on it to use with the current igraph version + For now we convert it on the fly... + Error in vcount(graph) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: missues ... .process_tag_and_index -> .get_ids -> -> vcount + Execution halted + ``` + +# rsetse + +
+ +* Version: 0.5.0 +* GitHub: https://github.com/JonnoB/rSETSe +* Source code: https://github.com/cran/rsetse +* Date/Publication: 2021-06-11 10:00:02 UTC +* Number of recursive dependencies: 81 + +Run `revdepcheck::cloud_details(, "rsetse")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘rsetse-Ex.R’ failed + The error most likely occurred in: + + > ### Name: calc_tension_strain_hd + > ### Title: Calculate line tension and strain from the topology and node + > ### embeddings for high dimensional feature networks + > ### Aliases: calc_tension_strain_hd + > + > ### ** Examples + > + ... + > g <- biconnected_network %>% + + prepare_edges(., k = 1000) %>% + + #prepare the continuous features as normal + + prepare_continuous_force(., node_names = "name", force_var = "force") %>% + + #prepare the categorical features as normal + + prepare_categorical_force(., node_names = "name", force_var = "group") + Error in igraph::as_data_frame(g, what = "both") : + VECTOR_ELT() can only be applied to a 'list', not a 'environment' + Calls: %>% ... prepare_continuous_force -> prepare_edges -> + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Categorical-and-continuous-features.Rmd’ using rmarkdown + Quitting from lines 31-35 (Categorical-and-continuous-features.Rmd) + Error: processing vignette 'Categorical-and-continuous-features.Rmd' failed with diagnostics: + VECTOR_ELT() can only be applied to a 'list', not a 'environment' + --- failed re-building ‘Categorical-and-continuous-features.Rmd’ + + --- re-building ‘separate-peels-quintet.Rmd’ using rmarkdown + --- finished re-building ‘separate-peels-quintet.Rmd’ + + SUMMARY: processing the following file failed: + ‘Categorical-and-continuous-features.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# rSpectral + +
+ +* Version: 1.0.0.10 +* GitHub: https://github.com/cmclean5/rSpectral +* Source code: https://github.com/cran/rSpectral +* Date/Publication: 2023-01-18 12:00:02 UTC +* Number of recursive dependencies: 44 + +Run `revdepcheck::cloud_details(, "rSpectral")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘rSpectral-Ex.R’ failed + The error most likely occurred in: + + > ### Name: spectral_igraph_communities + > ### Title: Spectral clustering for 'igraph' objects + > ### Aliases: spectral_igraph_communities + > + > ### ** Examples + > + > data(karate,package='igraphdata') + > c<-spectral_igraph_communities(karate) + Error in matrix(.Call(R_igraph_get_edgelist, graph, TRUE), ncol = 2) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: spectral_igraph_communities ... spectral_igraph_membership -> as.data.frame -> -> matrix + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 4. └─igraph::get.edgelist(g, names = TRUE) + 5. └─base::matrix(.Call(R_igraph_get_edgelist, graph, TRUE), ncol = 2) + ── Error ('test-igraph.R:24:3'): membership fix_neig=1 is correct ────────────── + Error in `matrix(.Call(R_igraph_get_edgelist, graph, TRUE), ncol = 2)`: REAL() can only be applied to a 'numeric', not a 'logical' + Backtrace: + ▆ + 1. └─rSpectral::spectral_igraph_communities(karate, fix_neig = 1) at test-igraph.R:24:2 + 2. └─rSpectral::spectral_igraph_membership(...) + 3. ├─base::as.data.frame(igraph::get.edgelist(g, names = TRUE)) + 4. └─igraph::get.edgelist(g, names = TRUE) + 5. └─base::matrix(.Call(R_igraph_get_edgelist, graph, TRUE), ncol = 2) + + [ FAIL 3 | WARN 0 | SKIP 0 | PASS 4 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.9Mb + sub-directories of 1Mb or more: + libs 5.2Mb + ``` + +# sbm + +
+ +* Version: 0.4.5 +* GitHub: https://github.com/GrossSBM/sbm +* Source code: https://github.com/cran/sbm +* Date/Publication: 2023-01-09 10:30:02 UTC +* Number of recursive dependencies: 108 + +Run `revdepcheck::cloud_details(, "sbm")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘sbm-Ex.R’ failed + The error most likely occurred in: + + > ### Name: war + > ### Title: War data set + > ### Aliases: war + > ### Keywords: datasets + > + > ### ** Examples + > + > data(war) + > class(war$belligerent) + [1] "igraph" + > igraph::gorder(war$alliance) + Error in igraph::gorder(war$alliance) : + REAL() can only be applied to a 'numeric', not a 'logical' + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Multipartite_EcologicalNetwork.Rmd’ using rmarkdown + --- finished re-building ‘Multipartite_EcologicalNetwork.Rmd’ + + --- re-building ‘MultiplexNetwork_principle.Rmd’ using rmarkdown + --- finished re-building ‘MultiplexNetwork_principle.Rmd’ + + --- re-building ‘Multiplex_allianceNwar_case_study.Rmd’ using rmarkdown + Quitting from lines 56-59 (Multiplex_allianceNwar_case_study.Rmd) + ... + --- failed re-building ‘Multiplex_allianceNwar_case_study.Rmd’ + + --- re-building ‘SBM_fungus_tree_network.Rmd’ using rmarkdown + --- finished re-building ‘SBM_fungus_tree_network.Rmd’ + + SUMMARY: processing the following file failed: + ‘Multiplex_allianceNwar_case_study.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# sccore + +
+ +* Version: 1.0.3 +* GitHub: https://github.com/kharchenkolab/sccore +* Source code: https://github.com/cran/sccore +* Date/Publication: 2023-03-13 00:00:02 UTC +* Number of recursive dependencies: 76 + +Run `revdepcheck::cloud_details(, "sccore")` for more info
## Newly broken +* checking examples ... ERROR + ``` + Running examples in ‘sccore-Ex.R’ failed + The error most likely occurred in: + + > ### Name: graphToAdjList + > ### Title: Convert igraph graph into an adjacency list + > ### Aliases: graphToAdjList + > + > ### ** Examples + > + > library(dplyr) + ... + + The following objects are masked from ‘package:base’: + + intersect, setdiff, setequal, union + + > edge.list.fact <- igraph::as_edgelist(conosGraph) %>% as_factor() + Error in matrix(.Call(R_igraph_get_edgelist, graph, TRUE), ncol = 2) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: %>% -> as_factor -> -> matrix + Execution halted + ``` + * checking tests ... ERROR ``` - Running ‘tinytest.R’ - Running the tests in ‘tests/tinytest.R’ failed. + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: - test_backbone.R............... 29 tests OK - test_backbone.R............... 30 tests OK - test_backbone.R............... 30 tests OK - test_backbone.R............... 30 tests OK - test_backbone.R............... 30 tests OK - test_backbone.R............... 31 tests OK - test_backbone.R............... 32 tests OK - test_backbone.R............... 33 tests OK - test_backbone.R............... 34 tests OK - test_backbone.R............... 35 tests OK - test_backbone.R............... 36 tests OK - test_backbone.R............... 36 tests OK Error in i_set_vertex_attr(x, attr(value, "name"), index = value, value = attr(value, : - Length of new attribute value must be 1 or 110, the number of target vertices, not 10 - Calls: ... FUN -> eval -> eval -> -> i_set_vertex_attr + 2. ├─sccore::as_factor(.) + 3. └─igraph::as_edgelist(conosGraph) + 4. └─base::matrix(.Call(R_igraph_get_edgelist, graph, TRUE), ncol = 2) + ── Error ('test_helpers.R:43:2'): graphToAdjList() functionality ─────────────── + Error in `matrix(.Call(R_igraph_get_edgelist, graph, TRUE), ncol = 2)`: REAL() can only be applied to a 'numeric', not a 'logical' + Backtrace: + ▆ + 1. ├─igraph::as_edgelist(conosGraph) %>% as_factor() at test_helpers.R:43:8 + 2. ├─sccore::as_factor(.) + 3. └─igraph::as_edgelist(conosGraph) + 4. └─base::matrix(.Call(R_igraph_get_edgelist, graph, TRUE), ncol = 2) + + [ FAIL 4 | WARN 0 | SKIP 0 | PASS 2 ] + Error: Test failures Execution halted ``` -# deepdep +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.9Mb + sub-directories of 1Mb or more: + libs 7.1Mb + ``` + +# ScorePlus + +
+ +* Version: 0.1 +* GitHub: NA +* Source code: https://github.com/cran/ScorePlus +* Date/Publication: 2019-06-14 08:40:03 UTC +* Number of recursive dependencies: 16 + +Run `revdepcheck::cloud_details(, "ScorePlus")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ScorePlus-Ex.R’ failed + The error most likely occurred in: + + > ### Name: SCORE + > ### Title: community detection method called SCORE Spectral Clustering On + > ### Ratios-of-Eigenvectors (SCORE) + > ### Aliases: SCORE + > + > ### ** Examples + > + ... + The following object is masked from ‘package:base’: + + union + + > data('karate') + > A = get.adjacency(karate) + Error in vcount(graph) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: get.adjacency -> get.adjacency.sparse -> vcount + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# secrlinear + +
+ +* Version: 1.1.4 +* GitHub: NA +* Source code: https://github.com/cran/secrlinear +* Date/Publication: 2021-05-04 04:50:05 UTC +* Number of recursive dependencies: 69 + +Run `revdepcheck::cloud_details(, "secrlinear")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘secrlinear-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Arvicola + > ### Title: Water Vole Capture Dataset + > ### Aliases: arvicola + > ### Keywords: datasets + > + > ### ** Examples + > + ... + > + > ## for speed, pre-compute distance matrix + > userd <- networkdistance (traps(arvicola), glymemask, glymemask) + This graph was created by an old(er) igraph version. + Call upgrade_graph() on it to use with the current igraph version + For now we convert it on the fly... + Error in vcount(graph) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: networkdistance -> cbind -> V -> vcount + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘secrlinear-vignette.Rmd’ using rmarkdown + A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TinyTeX with tinytex::reinstall_tinytex(repository = "illinois"). + + tlmgr: Local TeX Live (2022) is older than remote repository (2023). + Cross release updates are only supported with + update-tlmgr-latest(.sh/.exe) --update + See https://tug.org/texlive/upgrade.html for details. + Warning in system2("tlmgr", args, ...) : + ... + + Error: processing vignette 'secrlinear-vignette.Rmd' failed with diagnostics: + LaTeX failed to compile /tmp/workdir/secrlinear/new/secrlinear.Rcheck/vign_test/secrlinear/vignettes/secrlinear-vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See secrlinear-vignette.log for more info. + --- failed re-building ‘secrlinear-vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘secrlinear-vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# shazam
-* Version: 0.4.1 -* GitHub: https://github.com/DominikRafacz/deepdep -* Source code: https://github.com/cran/deepdep -* Date/Publication: 2021-12-20 16:20:02 UTC -* Number of recursive dependencies: 144 +* Version: 1.1.2 +* GitHub: NA +* Source code: https://github.com/cran/shazam +* Date/Publication: 2022-10-01 07:30:02 UTC +* Number of recursive dependencies: 124 -Run `revdepcheck::cloud_details(, "deepdep")` for more info +Run `revdepcheck::cloud_details(, "shazam")` for more info
## Newly broken -* checking tests ... ERROR +* checking examples ... ERROR ``` - Running ‘spelling.R’ - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 6. └─ggraph:::create_layout.default(graph, layout, ...) - 7. ├─ggraph::create_layout(graph, layout, ...) - 8. └─ggraph:::create_layout.tbl_graph(graph, layout, ...) - 9. ├─dplyr::mutate(ungroup(activate(graph, "nodes")), .ggraph.orig_index = seq_len(graph_order())) - 10. └─tidygraph:::mutate.tbl_graph(...) - 11. └─tidygraph::mutate_as_tbl(.data, !!!dot) - 12. ├─tidygraph:::set_graph_data(.data, d_tmp) - 13. └─tidygraph:::set_graph_data.tbl_graph(.data, d_tmp) - 14. └─tidygraph:::set_node_attributes(x, value) - 15. └─igraph::`vertex_attr<-`(`*tmp*`, value = as.list(value)) - 16. └─igraph::`vertex.attributes<-`(graph, index = index, value = value) - - [ FAIL 9 | WARN 0 | SKIP 2 | PASS 25 ] - Error: Test failures - Execution halted + Running examples in ‘shazam-Ex.R’ failed + The error most likely occurred in: + + > ### Name: makeGraphDf + > ### Title: Build a data.frame from a ChangeoClone and an igraph object + > ### containing a clonal lineage + > ### Aliases: makeGraphDf + > + > ### ** Examples + > + > # Load and subset example data + > data(ExampleDb, package = "alakazam") + > data(ExampleTrees, package = "alakazam") + > graph <- ExampleTrees[[17]] + > db <- subset(ExampleDb, clone_id == graph$clone) + Error in graph_attr(x, name) : + VECTOR_ELT() can only be applied to a 'list', not a 'environment' + Calls: subset ... subset.data.frame -> eval -> eval -> $ -> $.igraph -> graph_attr + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘Baseline-Vignette.Rmd’ using rmarkdown + A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TinyTeX with tinytex::reinstall_tinytex(repository = "illinois"). + + tlmgr: Local TeX Live (2022) is older than remote repository (2023). + Cross release updates are only supported with + update-tlmgr-latest(.sh/.exe) --update + See https://tug.org/texlive/upgrade.html for details. + Warning in system2("tlmgr", args, ...) : + running command ''tlmgr' search --file --global '/grffile.sty'' had status 1 + ... + LaTeX failed to compile /tmp/workdir/shazam/new/shazam.Rcheck/vign_test/shazam/vignettes/Targeting-Vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Targeting-Vignette.log for more info. + --- failed re-building ‘Targeting-Vignette.Rmd’ + + SUMMARY: processing the following files failed: + ‘Baseline-Vignette.Rmd’ ‘DistToNearest-Vignette.Rmd’ + ‘Mutation-Vignette.Rmd’ ‘Shmulate-Vignette.Rmd’ + ‘Targeting-Vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted ``` -# egor +# sigmajs
-* Version: 1.22.12 -* GitHub: https://github.com/tilltnet/egor -* Source code: https://github.com/cran/egor -* Date/Publication: 2022-12-20 06:20:02 UTC -* Number of recursive dependencies: 89 +* Version: 0.1.5 +* GitHub: https://github.com/JohnCoene/sigmajs +* Source code: https://github.com/cran/sigmajs +* Date/Publication: 2020-06-18 18:10:02 UTC +* Number of recursive dependencies: 76 -Run `revdepcheck::cloud_details(, "egor")` for more info +Run `revdepcheck::cloud_details(, "sigmajs")` for more info
@@ -96,34 +3164,41 @@ Run `revdepcheck::cloud_details(, "egor")` for more info Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: - Sorting data by egoID: Transforming alters data to long format: Transforming wide dyad data to edgelist: Sorting data by egoID: Transforming alters data to long format: Transforming wide dyad data to edgelist: Filtering out empty alter entries using provided network size values: Sorting data by egoID: Transforming alters data to long format: Transforming wide dyad data to edgelist: [ FAIL 1 | WARN 7 | SKIP 15 | PASS 205 ] - - ══ Skipped tests ═══════════════════════════════════════════════════════════════ - • On CRAN (15) + > test_check("sigmajs") + Found # 4 clusters + [ FAIL 1 | WARN 8 | SKIP 0 | PASS 64 ] ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Failure ('test-clustered_graphs.R:55'): Methods work (properly) with grouping variable being completly NA. ── - igraph::V(clustered_graphs(mpf, "country")[[1]])$grp.size is not NULL - - `actual` is a double vector () - `expected` is NULL + ── Error ('test-formats.R:21:3'): igraph ─────────────────────────────────────── + Error in `vcount(graph)`: REAL() can only be applied to a 'numeric', not a 'logical' + Backtrace: + ▆ + 1. └─igraph::layout_with_fr(lesmis_igraph) at test-formats.R:21:2 + 2. └─igraph::vcount(graph) - [ FAIL 1 | WARN 7 | SKIP 15 | PASS 205 ] + [ FAIL 1 | WARN 8 | SKIP 0 | PASS 64 ] Error: Test failures Execution halted ``` -# GREMLINS +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 28 marked UTF-8 strings + ``` + +# signnet
-* Version: 0.2.0 -* GitHub: https://github.com/demiperimetre/GREMLINS -* Source code: https://github.com/cran/GREMLINS -* Date/Publication: 2020-11-25 13:50:04 UTC -* Number of recursive dependencies: 62 +* Version: 1.0.1 +* GitHub: https://github.com/schochastics/signnet +* Source code: https://github.com/cran/signnet +* Date/Publication: 2023-01-27 13:40:02 UTC +* Number of recursive dependencies: 104 -Run `revdepcheck::cloud_details(, "GREMLINS")` for more info +Run `revdepcheck::cloud_details(, "signnet")` for more info
@@ -131,47 +3206,71 @@ Run `revdepcheck::cloud_details(, "GREMLINS")` for more info * checking examples ... ERROR ``` - Running examples in ‘GREMLINS-Ex.R’ failed + Running examples in ‘signnet-Ex.R’ failed The error most likely occurred in: - > ### Name: plotMBM - > ### Title: Plot the mesoscopic view of the estimated MBM - > ### Aliases: plotMBM + > ### Name: eigen_centrality_signed + > ### Title: Signed Eigenvector centrality + > ### Aliases: eigen_centrality_signed > > ### ** Examples > - > namesFG <- c('A','B') + > library(igraph) ... - [1] "gaussian" "bernoulli" - [1] "-------------------------------------------------------------------" - [1] " ------ Searching the numbers of blocks starting from [ 2 2 ] blocks" - [1] "ICL : -2028.78 . Nb of blocks: [ 2 2 ]" - [1] "Best model------ ICL : -2028.78 . Nb of clusters: [ 2 2 ] for [ A , B ] respectively" - > plotMBM(res_MBMsimu) - Error in i_set_edge_attr(graph = graph, name = name, value = value, check = FALSE) : - Length of new attribute value must be 1 or 0, the number of target edges, not 8 - Calls: plotMBM -> %>% -> set_edge_attr -> i_set_edge_attr + The following object is masked from ‘package:base’: + + union + + > data("tribes") + > eigen_centrality_signed(tribes) + Error in igraph::edge_attr_names(g) : + VECTOR_ELT() can only be applied to a 'list', not a 'environment' + Calls: eigen_centrality_signed -> is_signed -> %in% -> Execution halted ``` +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 2. └─signnet::is_signed(g) + 3. ├─"sign" %in% igraph::edge_attr_names(g) + 4. └─igraph::edge_attr_names(g) + ── Error ('test-blockmodel.R:25:3'): general blockmodeling works ─────────────── + Error in `igraph::edge_attr_names(g)`: VECTOR_ELT() can only be applied to a 'list', not a 'environment' + Backtrace: + ▆ + 1. └─signnet::signed_blockmodel_general(...) at test-blockmodel.R:25:2 + 2. └─signnet::is_signed(g) + 3. ├─"sign" %in% igraph::edge_attr_names(g) + 4. └─igraph::edge_attr_names(g) + + [ FAIL 3 | WARN 0 | SKIP 0 | PASS 86 ] + Error: Test failures + Execution halted + ``` + * checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: - ... - --- re-building ‘EcologicalNetwork.Rmd’ using rmarkdown - Quitting from lines 130-131 (EcologicalNetwork.Rmd) - Error: processing vignette 'EcologicalNetwork.Rmd' failed with diagnostics: - Length of new attribute value must be 1 or 0, the number of target edges, not 14 - --- failed re-building ‘EcologicalNetwork.Rmd’ + --- re-building ‘blockmodeling.Rmd’ using rmarkdown + Quitting from lines 56-61 (blockmodeling.Rmd) + Error: processing vignette 'blockmodeling.Rmd' failed with diagnostics: + VECTOR_ELT() can only be applied to a 'list', not a 'environment' + --- failed re-building ‘blockmodeling.Rmd’ - --- re-building ‘Introduction.Rmd’ using rmarkdown - --- finished re-building ‘Introduction.Rmd’ + --- re-building ‘centrality.Rmd’ using rmarkdown + --- finished re-building ‘centrality.Rmd’ - --- re-building ‘SimulatedNetwork.Rmd’ using rmarkdown - --- finished re-building ‘SimulatedNetwork.Rmd’ + ... + Quitting from lines 79-83 (structural_balance.Rmd) + Error: processing vignette 'structural_balance.Rmd' failed with diagnostics: + VECTOR_ELT() can only be applied to a 'list', not a 'environment' + --- failed re-building ‘structural_balance.Rmd’ - SUMMARY: processing the following file failed: - ‘EcologicalNetwork.Rmd’ + SUMMARY: processing the following files failed: + ‘blockmodeling.Rmd’ ‘signed_networks.Rmd’ ‘structural_balance.Rmd’ Error: Vignette re-building failed. Execution halted @@ -179,64 +3278,124 @@ Run `revdepcheck::cloud_details(, "GREMLINS")` for more info ## In both -* checking dependencies in R code ... NOTE +* checking installed package size ... NOTE ``` - Namespace in Imports field not imported from: ‘mclust’ - All declared Imports should be used. + installed size is 7.7Mb + sub-directories of 1Mb or more: + libs 6.1Mb ``` -# incidentally +# SNscan
-* Version: 1.0.1 -* GitHub: https://github.com/zpneal/incidentally -* Source code: https://github.com/cran/incidentally -* Date/Publication: 2022-08-05 22:40:09 UTC -* Number of recursive dependencies: 37 +* Version: 1.0 +* GitHub: NA +* Source code: https://github.com/cran/SNscan +* Date/Publication: 2016-01-19 13:09:28 +* Number of recursive dependencies: 11 + +Run `revdepcheck::cloud_details(, "SNscan")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘SNscan-Ex.R’ failed + The error most likely occurred in: + + > ### Name: network.scan + > ### Title: Network Scan Statistic + > ### Aliases: network.scan + > ### Keywords: scanning method + > + > ### ** Examples + > + > data(karate) + > + > ks=network.scan(g=karate,radius=3,attribute=NULL, + + model="pois.stat",pattern="structure") + Error in is_directed(graph) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: network.scan -> shortest.paths -> is_directed + Execution halted + ``` + +# SOMbrero + +
-Run `revdepcheck::cloud_details(, "incidentally")` for more info +* Version: 1.4-1 +* GitHub: https://github.com/tuxette/sombrero +* Source code: https://github.com/cran/SOMbrero +* Date/Publication: 2022-01-03 17:10:08 UTC +* Number of recursive dependencies: 110 + +Run `revdepcheck::cloud_details(, "SOMbrero")` for more info
## Newly broken +* checking examples ... ERROR + ``` + Running examples in ‘SOMbrero-Ex.R’ failed + The error most likely occurred in: + + > ### Name: projectIGraph + > ### Title: Compute the projection of a graph on a grid + > ### Aliases: projectIGraph projectIGraph.somRes + > + > ### ** Examples + > + > data(lesmis) + > set.seed(7383) + > mis.som <- trainSOM(x.data=dissim.lesmis, type="relational", nb.save=10) + > proj.lesmis <- projectIGraph(mis.som, lesmis) + Error in gorder(init.graph) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: projectIGraph -> projectIGraph.somRes -> gorder + Execution halted + ``` + * checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: - ... - --- re-building ‘congress.Rmd’ using rmarkdown - trying URL 'https://www.govinfo.gov/bulkdata/BILLSTATUS/115/sres/BILLSTATUS-115-sres.zip' - Content type 'application/zip' length 2070239 bytes (2.0 MB) - ================================================== - downloaded 2.0 MB + --- re-building ‘a-doc-SOMbrero-package.Rmd’ using knitr + --- finished re-building ‘a-doc-SOMbrero-package.Rmd’ - trying URL 'https://www.govinfo.gov/bulkdata/BILLSTATUS/115/sres/BILLSTATUS-115-sres.zip' - Content type 'application/zip' length 2070239 bytes (2.0 MB) - ... - --- failed re-building ‘congress.Rmd’ + --- re-building ‘b-doc-grids.Rmd’ using knitr + --- finished re-building ‘b-doc-grids.Rmd’ - --- re-building ‘incidentally.Rmd’ using rmarkdown - --- finished re-building ‘incidentally.Rmd’ + --- re-building ‘c-doc-numericSOM.Rmd’ using knitr + Warning in wordcloud_boxes(data_points = points_valid_first, boxes = boxes, : + Some words could not fit on page. They have been placed at their original positions. + ... + Quitting from lines 41-100 (e-doc-relationalSOM.Rmd) + Error: processing vignette 'e-doc-relationalSOM.Rmd' failed with diagnostics: + REAL() can only be applied to a 'numeric', not a 'logical' + --- failed re-building ‘e-doc-relationalSOM.Rmd’ SUMMARY: processing the following file failed: - ‘congress.Rmd’ + ‘e-doc-relationalSOM.Rmd’ Error: Vignette re-building failed. Execution halted ``` -# mstknnclust +# spreadr
-* Version: 0.3.1 +* Version: 0.2.0 * GitHub: NA -* Source code: https://github.com/cran/mstknnclust -* Date/Publication: 2020-09-17 12:20:03 UTC -* Number of recursive dependencies: 34 +* Source code: https://github.com/cran/spreadr +* Date/Publication: 2021-05-11 06:50:02 UTC +* Number of recursive dependencies: 94 -Run `revdepcheck::cloud_details(, "mstknnclust")` for more info +Run `revdepcheck::cloud_details(, "spreadr")` for more info
@@ -246,80 +3405,101 @@ Run `revdepcheck::cloud_details(, "mstknnclust")` for more info ``` Error(s) in re-building vignettes: ... - --- re-building ‘guide.Rmd’ using rmarkdown - Quitting from lines 103-110 (guide.Rmd) - Error: processing vignette 'guide.Rmd' failed with diagnostics: - Length of new attribute value must be 1 or 84, the number of target vertices, not 2 - --- failed re-building ‘guide.Rmd’ + --- re-building ‘spreadr_vignette.Rmd’ using rmarkdown + Quitting from lines 78-81 (spreadr_vignette.Rmd) + Error: processing vignette 'spreadr_vignette.Rmd' failed with diagnostics: + REAL() can only be applied to a 'numeric', not a 'logical' + --- failed re-building ‘spreadr_vignette.Rmd’ SUMMARY: processing the following file failed: - ‘guide.Rmd’ + ‘spreadr_vignette.Rmd’ Error: Vignette re-building failed. Execution halted ``` -# nat +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘extrafont’ ‘ggplot2’ + All declared Imports should be used. + ``` + +# SubpathwayLNCE
-* Version: 1.8.19 -* GitHub: https://github.com/natverse/nat -* Source code: https://github.com/cran/nat -* Date/Publication: 2022-04-06 11:50:02 UTC -* Number of recursive dependencies: 87 +* Version: 1.0 +* GitHub: NA +* Source code: https://github.com/cran/SubpathwayLNCE +* Date/Publication: 2016-01-19 08:17:59 +* Number of recursive dependencies: 13 -Run `revdepcheck::cloud_details(, "nat")` for more info +Run `revdepcheck::cloud_details(, "SubpathwayLNCE")` for more info
## Newly broken -* checking tests ... ERROR +* checking running R code from vignettes ... ERROR ``` - Running ‘test-all.R’ - Running the tests in ‘tests/test-all.R’ failed. - Last 13 lines of output: - ▆ - 1. ├─testthat::expect_warning(...) at test-ngraph.R:147:2 - 2. │ └─testthat:::quasi_capture(...) - 3. │ ├─testthat (local) .capture(...) - 4. │ │ └─base::withCallingHandlers(...) - 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) - 6. ├─nat::as.ngraph(testd, graph.attributes = gatts, vertex.attributes = list(X = testd$X[-1])) - 7. └─nat:::as.ngraph.data.frame(testd, graph.attributes = gatts, vertex.attributes = list(X = testd$X[-1])) - 8. └─nat::ngraph(...) - 9. └─igraph::set.vertex.attribute(g, name = n, value = vertex.attributes[[n]]) - 10. └─igraph:::i_set_vertex_attr(...) - - [ FAIL 1 | WARN 420 | SKIP 5 | PASS 787 ] - Error: Test failures - Execution halted + Errors in running code in vignettes: + when running code in ‘SubpathwayLNCE.Rnw’ + ... + + > g2 <- GetExampleData(exampleData = "g2") + + > LncGenePairs <- GetExampleData(exampleData = "LncGenePairs") + + > interUMGraph <- getInteGraphList(g2[42:45], LncGenePairs) + + When sourcing ‘SubpathwayLNCE.R’: + Error: REAL() can only be applied to a 'numeric', not a 'logical' + Execution halted + + ‘SubpathwayLNCE.Rnw’... failed ``` ## In both -* checking examples ... WARNING +* checking re-building of vignette outputs ... NOTE ``` - Found the following significant warnings: + Error(s) in re-building vignettes: + --- re-building ‘SubpathwayLNCE.Rnw’ using Sweave + Loading required package: igraph + + Attaching package: ‘igraph’ - Warning: 'rgl.close' is deprecated. - Deprecated functions may be defunct as soon as of the next release of - R. - See ?Deprecated. + The following objects are masked from ‘package:stats’: + + decompose, spectrum + + ... + Error in vcount(graphList[[t]]) : + REAL() can only be applied to a 'numeric', not a 'logical' + + --- failed re-building ‘SubpathwayLNCE.Rnw’ + + SUMMARY: processing the following file failed: + ‘SubpathwayLNCE.Rnw’ + + Error: Vignette re-building failed. + Execution halted ``` -# netmeta +# SubtypeDrug
-* Version: 2.7-0 -* GitHub: https://github.com/guido-s/netmeta -* Source code: https://github.com/cran/netmeta -* Date/Publication: 2022-12-22 09:30:02 UTC -* Number of recursive dependencies: 90 +* Version: 0.1.5 +* GitHub: https://github.com/hanjunwei-lab/SubtypeDrug +* Source code: https://github.com/cran/SubtypeDrug +* Date/Publication: 2021-05-17 08:50:03 UTC +* Number of recursive dependencies: 126 -Run `revdepcheck::cloud_details(, "netmeta")` for more info +Run `revdepcheck::cloud_details(, "SubtypeDrug")` for more info
@@ -327,158 +3507,166 @@ Run `revdepcheck::cloud_details(, "netmeta")` for more info * checking examples ... ERROR ``` - Running examples in ‘netmeta-Ex.R’ failed + Running examples in ‘SubtypeDrug-Ex.R’ failed The error most likely occurred in: - > ### Name: netcontrib - > ### Title: Contribution matrix in network meta-analysis - > ### Aliases: netcontrib print.netcontrib - > ### Keywords: contribution + > ### Name: plotSpwNetGraph + > ### Title: Polt a subpathway network graph + > ### Aliases: plotSpwNetGraph > > ### ** Examples > + > require(igraph) ... - > # Use the Woods dataset - > # - > data("Woods2010") - > p1 <- pairwise(treatment, event = r, n = N, - + studlab = author, data = Woods2010, sm = "OR") - > - > net1 <- netmeta(p1) - > cm <- netcontrib(net1) - Error: C stack usage 9968708 is too close to the limit + The following object is masked from ‘package:base’: + + union + + > # plot network graph of the subpathway 00020_4. + > plotSpwNetGraph(spwid="00020_4") + Error in vcount(graph) : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: plotSpwNetGraph -> plot -> plot.igraph -> vcount Execution halted ``` -## In both - -* checking data for non-ASCII characters ... NOTE +* checking re-building of vignette outputs ... WARNING ``` - Note: found 2 marked UTF-8 strings + Error(s) in re-building vignettes: + ... + --- re-building ‘vignette.Rmd’ using rmarkdown + Quitting from lines 182-185 (vignette.Rmd) + Error: processing vignette 'vignette.Rmd' failed with diagnostics: + REAL() can only be applied to a 'numeric', not a 'logical' + --- failed re-building ‘vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted ``` -# NetOrigin +# tgver
-* Version: 1.1-4 -* GitHub: https://github.com/jmanitz/NetOrigin -* Source code: https://github.com/cran/NetOrigin -* Date/Publication: 2022-01-20 08:32:42 UTC -* Number of recursive dependencies: 77 +* Version: 0.3.0 +* GitHub: https://github.com/tgve/tgver +* Source code: https://github.com/cran/tgver +* Date/Publication: 2022-09-30 15:20:03 UTC +* Number of recursive dependencies: 157 -Run `revdepcheck::cloud_details(, "NetOrigin")` for more info +Run `revdepcheck::cloud_details(, "tgver")` for more info
## Newly broken -* checking examples ... ERROR +* checking re-building of vignette outputs ... WARNING ``` - Running examples in ‘NetOrigin-Ex.R’ failed - The error most likely occurred in: + Error(s) in re-building vignettes: + ... + --- re-building ‘dev-plan.Rmd’ using rmarkdown + --- finished re-building ‘dev-plan.Rmd’ - > ### Name: origin - > ### Title: Origin Estimation for Propagation Processes on Complex Networks - > ### Aliases: origin origin_edm origin_backtracking origin_centrality - > ### origin_bayesian - > - > ### ** Examples - > - ... - > performance(om, start=1, graph=ptnGoe) - start est hitt rank spj dist - 1 X.Adolf.Hoyer.Strasse X.Gotthelf.Leimbach.Strasse FALSE 2 2 1332 - > - > # backtracking origin estimation (Manitz et al., 2016) - > ob <- origin(events=delayGoe[10,-c(1:2)], type='backtracking', graph=ptnGoe) - Error in if (V(graph)[current_node]$events > 0 | !start_with_event_node) { : - argument is of length zero - Calls: origin -> origin_backtracking + --- re-building ‘r-and-js.Rmd’ using rmarkdown + Quitting from lines 31-67 (r-and-js.Rmd) + Error: processing vignette 'r-and-js.Rmd' failed with diagnostics: + REAL() can only be applied to a 'numeric', not a 'logical' + --- failed re-building ‘r-and-js.Rmd’ + + --- re-building ‘tgver.Rmd’ using rmarkdown + --- finished re-building ‘tgver.Rmd’ + + SUMMARY: processing the following file failed: + ‘r-and-js.Rmd’ + + Error: Vignette re-building failed. Execution halted ``` -# poppr +# threejs
-* Version: 2.9.3 -* GitHub: https://github.com/grunwaldlab/poppr -* Source code: https://github.com/cran/poppr -* Date/Publication: 2021-09-07 07:00:02 UTC -* Number of recursive dependencies: 97 +* Version: 0.3.3 +* GitHub: https://github.com/bwlewis/rthreejs +* Source code: https://github.com/cran/threejs +* Date/Publication: 2020-01-21 15:50:03 UTC +* Number of recursive dependencies: 40 -Run `revdepcheck::cloud_details(, "poppr")` for more info +Run `revdepcheck::cloud_details(, "threejs")` for more info
## Newly broken +* checking examples ... ERROR + ``` + Running examples in ‘threejs-Ex.R’ failed + The error most likely occurred in: + + > ### Name: graphjs + > ### Title: Interactive 3D Graph Visualization + > ### Aliases: graphjs + > + > ### ** Examples + > + > set.seed(1) + ... + > l3 = light_ambient(color = "#555555") + > (graphjs(g, vertex.color="gray", vertex.shape="sphere", lights=list(l1, l2, l3))) + > + > # Les Miserables Character Co-appearance Data + > data("LeMis") + > (graphjs(LeMis)) + Error in adjacent_vertices(x, i, mode = if (directed) "out" else "all") : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: graphjs -> [[ -> [[.igraph -> adjacent_vertices + Execution halted + ``` + * checking tests ... ERROR ``` - Running ‘test-all.R’ - Running the tests in ‘tests/test-all.R’ failed. + Running ‘threejs.R’ + Running the tests in ‘tests/threejs.R’ failed. Last 13 lines of output: - Attributes: < Modes: list, NULL > - Attributes: < Lengths: 2, 0 > - Attributes: < names for target but not for current > - Attributes: < current is not list-like > - target is table, current is numeric - Backtrace: - ▆ - 1. └─poppr (local) expect_vertex_size_scale(pmsn, as.integer(table(mll(pc)))) at test-msn.R:439:2 - 2. ├─base::eval(...) at test-msn.R:105:2 - 3. │ └─base::eval(...) - 4. └─testthat::expect_equal(...) - - [ FAIL 2 | WARN 0 | SKIP 181 | PASS 378 ] - Error: Test failures + > frequent_destinations <- names(freq)[1:10] + > idx <- dest %in% frequent_destinations + > frequent_flights <- flights[idx, ] + > ll <- unique(frequent_flights[, 3:4]) + > globejs(lat=ll[, 1], long=ll[, 2], arcs=frequent_flights, + + arcsHeight=0.3, arcsLwd=2, arcsColor="#ffff00", arcsOpacity=0.15, + + atmosphere=TRUE, color="#00aaff", pointsize=0.5) + > + > # graphs + > data(LeMis, package="threejs") + > g <- graphjs(LeMis, main="Les Misérables") + Error in adjacent_vertices(x, i, mode = if (directed) "out" else "all") : + REAL() can only be applied to a 'numeric', not a 'logical' + Calls: graphjs -> [[ -> [[.igraph -> adjacent_vertices Execution halted ``` ## In both -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘algo.Rnw’ using knitr - Error: processing vignette 'algo.Rnw' failed with diagnostics: - Running 'texi2dvi' on 'algo.tex' failed. - LaTeX errors: - ! LaTeX Error: File `colortbl.sty' not found. - - Type X to quit or to proceed, - or enter new name. (Default extension: sty) - ... - l.270 \long - \def\@secondoffive#1#2#3#4#5{#2}^^M - ! ==> Fatal error occurred, no output PDF file produced! - --- failed re-building ‘algo.Rnw’ - - SUMMARY: processing the following file failed: - ‘algo.Rnw’ - - Error: Vignette re-building failed. - Execution halted - ``` - * checking package dependencies ... NOTE ``` - Package suggested but not available for checking: ‘RClone’ + Package which this enhances but not available for checking: ‘shiny’ ``` -# sfnetworks +# tosr
-* Version: 0.6.1 -* GitHub: https://github.com/luukvdmeer/sfnetworks -* Source code: https://github.com/cran/sfnetworks -* Date/Publication: 2022-10-27 15:10:02 UTC -* Number of recursive dependencies: 146 +* Version: 0.1.2 +* GitHub: https://github.com/coreofscience/tosr +* Source code: https://github.com/cran/tosr +* Date/Publication: 2023-01-13 23:50:02 UTC +* Number of recursive dependencies: 182 -Run `revdepcheck::cloud_details(, "sfnetworks")` for more info +Run `revdepcheck::cloud_details(, "tosr")` for more info
@@ -489,34 +3677,34 @@ Run `revdepcheck::cloud_details(, "sfnetworks")` for more info Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: - > library(sfnetworks) - > - > test_check("sfnetworks") - [ FAIL 1 | WARN 1 | SKIP 0 | PASS 277 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Failure ('test_paths.R:242'): ... is passed correcly onto igraph::distances ── - isTRUE(all.equal(cost_dijkstra, cost_johnson)) is not FALSE - - `actual`: TRUE - `expected`: FALSE + ▆ + 1. ├─testthat::expect_equal(...) at test-tosr_load.R:4:2 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. ├─base::nrow(tosSAP(my_tosr_load$graph, my_tosr_load$df, my_tosr_load$nodes)) + 5. ├─tosr::tosSAP(my_tosr_load$graph, my_tosr_load$df, my_tosr_load$nodes) + 6. │ └─tibble::tibble(...) + 7. │ └─tibble:::tibble_quos(xs, .rows, .name_repair) + 8. │ └─rlang::eval_tidy(xs[[j]], mask) + 9. └─igraph::V(graph) + 10. └─igraph::vcount(graph) - [ FAIL 1 | WARN 1 | SKIP 0 | PASS 277 ] + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] Error: Test failures Execution halted ``` -# signnet +# webSDM
-* Version: 1.0.0 -* GitHub: https://github.com/schochastics/signnet -* Source code: https://github.com/cran/signnet -* Date/Publication: 2022-12-22 15:10:02 UTC -* Number of recursive dependencies: 101 +* Version: 1.1-3 +* GitHub: https://github.com/giopogg/webSDM +* Source code: https://github.com/cran/webSDM +* Date/Publication: 2023-03-14 13:50:02 UTC +* Number of recursive dependencies: 190 -Run `revdepcheck::cloud_details(, "signnet")` for more info +Run `revdepcheck::cloud_details(, "webSDM")` for more info
@@ -524,35 +3712,30 @@ Run `revdepcheck::cloud_details(, "signnet")` for more info * checking examples ... ERROR ``` - Running examples in ‘signnet-Ex.R’ failed + Running examples in ‘webSDM-Ex.R’ failed The error most likely occurred in: - > ### Name: triad_census_signed - > ### Title: signed triad census - > ### Aliases: triad_census_signed + > ### Name: SDMfit + > ### Title: Fitting a single-species SDM + > ### Aliases: SDMfit > > ### ** Examples > - > library(igraph) - ... - The following object is masked from ‘package:base’: - - union - - > g <- graph.full(4, directed = TRUE) - > E(g)$sign <- c(-1, 1, 1, -1, -1, 1) - Error in i_set_edge_attr(x, attr(value, "name"), index = value, value = attr(value, : - Length of new attribute value must be 1 or 12, the number of target edges, not 6 - Calls: E<- -> i_set_edge_attr + > data(Y,X,G) + > # Run a local model (i.e. a SDM) for species Y6 + > mySDM = SDMfit("Y6", Y, X, G, "~X_1 + X_2", mode = "prey", + + method = "stan_glm", family = binomial(link = "logit")) + Error in vertex_attr_names(graph) : + VECTOR_ELT() can only be applied to a 'list', not a 'environment' + Calls: SDMfit ... neighbors -> as.igraph.vs -> %in% -> vertex_attr_names Execution halted ``` ## In both -* checking installed package size ... NOTE +* checking dependencies in R code ... NOTE ``` - installed size is 7.8Mb - sub-directories of 1Mb or more: - libs 6.1Mb + Namespace in Imports field not imported from: ‘Matrix’ + All declared Imports should be used. ``` From 263135c1bf5df29b3788c81b83eaf856f2e8a57a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Kirill=20M=C3=BCller?= Date: Tue, 16 May 2023 15:31:01 +0200 Subject: [PATCH 2/8] New check results --- revdep/README.md | 118 +- revdep/cran.md | 224 +-- revdep/failures.md | 162 +- revdep/problems.md | 3825 +++++--------------------------------------- 4 files changed, 590 insertions(+), 3739 deletions(-) diff --git a/revdep/README.md b/revdep/README.md index f040817e449..958b6b44465 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,91 +1,39 @@ # Revdeps -## Failed to check (11) +## Failed to check (13) -|package |version |error |warning |note | -|:---------|:-------|:-----|:-------|:----| -|beadplexr |? | | | | -|NA |? | | | | -|DRviaSPCN |? | | | | -|genekitr |? | | | | -|immcp |? | | | | -|MACP |? | | | | -|numbat |? | | | | -|NA |? | | | | -|NA |? | | | | -|tidySEM |? | | | | -|vivid |? | | | | +|package |version |error |warning |note | +|:---------------|:-------|:-----|:-------|:----| +|beadplexr |? | | | | +|NA |? | | | | +|DRviaSPCN |? | | | | +|genekitr |? | | | | +|HospitalNetwork |0.9.3 |1 | | | +|immcp |? | | | | +|MACP |? | | | | +|numbat |? | | | | +|NA |? | | | | +|Platypus |? | | | | +|NA |? | | | | +|tidySEM |? | | | | +|vivid |? | | | | -## New problems (68) +## New problems (14) -|package |version |error |warning |note | -|:--------------|:--------|:------|:-------|:--------| -|[alakazam](problems.md#alakazam)|1.2.1 |__+1__ |1 | | -|[aniSNA](problems.md#anisna)|1.0 |__+1__ | | | -|[bc3net](problems.md#bc3net)|1.0.4 |__+1__ | | | -|[bio3d](problems.md#bio3d)|2.4-4 |__+1__ | |1 | -|[causaloptim](problems.md#causaloptim)|0.9.7 |__+1__ | | | -|[chemodiv](problems.md#chemodiv)|0.2.0 |__+1__ | | | -|[CINNA](problems.md#cinna)|1.2.0 |__+1__ |__+1__ |1 | -|[clustAnalytics](problems.md#clustanalytics)|0.5.2 |__+2__ |__+1__ |1 | -|[crosstalkr](problems.md#crosstalkr)|1.0.1 | |__+1__ | | -|[dnet](problems.md#dnet)|1.1.7 |__+1__ | | | -|[DrDimont](problems.md#drdimont)|0.1.4 |__+1__ |__+1__ | | -|[DTSEA](problems.md#dtsea)|0.0.3 |__+1__ |__+1__ | | -|[dynwrap](problems.md#dynwrap)|1.2.3 |__+1__ | | | -|[edgebundle](problems.md#edgebundle)|0.4.1 |__+1__ | |1 | -|[einet](problems.md#einet)|0.1.0 |__+1__ | | | -|[emba](problems.md#emba)|0.1.8 | |__+1__ |1 | -|[etree](problems.md#etree)|0.1.0 |__+1__ | | | -|[gemtc](problems.md#gemtc)|1.0-1 |__+1__ | | | -|[geonetwork](problems.md#geonetwork)|0.5.0 |__+1__ | | | -|[GISSB](problems.md#gissb)|1.1 |__+1__ | |1 | -|[grand](problems.md#grand)|0.9.0 |__+1__ |__+1__ | | -|[graph4lg](problems.md#graph4lg)|1.8.0 |__+1__ |__+1__ |1 __+1__ | -|[graphkernels](problems.md#graphkernels)|1.6.1 |__+1__ | |1 | -|[graphlayouts](problems.md#graphlayouts)|0.8.4 |__+2__ | |1 | -|[graphsim](problems.md#graphsim)|1.0.3 |__+1__ | | | -|[iGraphMatch](problems.md#igraphmatch)|2.0.1 |__+1__ |__+1__ | | -|[influenceR](problems.md#influencer)|0.1.0.1 |__+1__ | | | -|[intergraph](problems.md#intergraph)|2.0-2 |__+1__ | | | -|[invertiforms](problems.md#invertiforms)|0.1.1 |__+2__ | | | -|[ITNr](problems.md#itnr)|0.7.0 |__+1__ | | | -|[LEANR](problems.md#leanr)|1.4.9 |__+1__ | | | -|[leiden](problems.md#leiden)|0.4.3 |__+1__ |__+1__ |1 | -|[leidenAlg](problems.md#leidenalg)|1.0.5 |__+2__ | |1 | -|[leidenbase](problems.md#leidenbase)|0.1.18 |__+2__ |__+1__ |1 | -|[meconetcomp](problems.md#meconetcomp)|0.2.0 |__+1__ | | | -|[metanetwork](problems.md#metanetwork)|0.7.0 |__+2__ | | | -|[migraph](problems.md#migraph)|0.13.2 |__+2__ | | | -|[missSBM](problems.md#misssbm)|1.0.3 |__+2__ |__+1__ |1 | -|[molnet](problems.md#molnet)|0.1.0 |__+1__ |__+1__ | | -|[motifr](problems.md#motifr)|1.0.0 |__+1__ | | | -|[multinets](problems.md#multinets)|0.2.2 |__+2__ | | | -|[mwcsr](problems.md#mwcsr)|0.1.6 |__+2__ |__+1__ |1 | -|[nda](problems.md#nda)|0.1.6 |__+1__ | | | -|[netplot](problems.md#netplot)|0.1-1 |__+1__ |__+1__ | | -|[netrankr](problems.md#netrankr)|1.2.0 |__+2__ |__+1__ |1 | -|[netseg](problems.md#netseg)|1.0-1 |__+2__ |__+1__ | | -|[nett](problems.md#nett)|1.0.0 |__+1__ |__+1__ | | -|[poppr](problems.md#poppr)|2.9.4 |__+1__ |1 | | -|[psSubpathway](problems.md#pssubpathway)|0.1.1 |__+1__ |__+1__ | | -|[rmonad](problems.md#rmonad)|0.7.0 |__+1__ | | | -|[rsetse](problems.md#rsetse)|0.5.0 |__+1__ |__+1__ | | -|[rSpectral](problems.md#rspectral)|1.0.0.10 |__+2__ | |1 | -|[sbm](problems.md#sbm)|0.4.5 |__+1__ |__+1__ | | -|[sccore](problems.md#sccore)|1.0.3 |__+2__ | |1 | -|[ScorePlus](problems.md#scoreplus)|0.1 |__+1__ | |1 | -|[secrlinear](problems.md#secrlinear)|1.1.4 |__+1__ |1 | | -|[shazam](problems.md#shazam)|1.1.2 |__+1__ |1 | | -|[sigmajs](problems.md#sigmajs)|0.1.5 |__+1__ | |1 | -|[signnet](problems.md#signnet)|1.0.1 |__+2__ |__+1__ |1 | -|[SNscan](problems.md#snscan)|1.0 |__+1__ | | | -|[SOMbrero](problems.md#sombrero)|1.4-1 |__+1__ |__+1__ | | -|[spreadr](problems.md#spreadr)|0.2.0 | |__+1__ |1 | -|[SubpathwayLNCE](problems.md#subpathwaylnce)|1.0 |__+1__ | |1 | -|[SubtypeDrug](problems.md#subtypedrug)|0.1.5 |__+1__ |__+1__ | | -|[tgver](problems.md#tgver)|0.3.0 | |__+1__ | | -|[threejs](problems.md#threejs)|0.3.3 |__+2__ | |1 | -|[tosr](problems.md#tosr)|0.1.2 |__+1__ | | | -|[webSDM](problems.md#websdm)|1.1-3 |__+1__ | |1 | +|package |version |error |warning |note | +|:--------------|:-------|:------|:-------|:----| +|[causaloptim](problems.md#causaloptim)|0.9.7 |__+1__ | | | +|[clustAnalytics](problems.md#clustanalytics)|0.5.2 | |__+1__ |1 | +|[dnet](problems.md#dnet)|1.1.7 |__+1__ | | | +|[drake](problems.md#drake)|7.13.5 |__+1__ | | | +|[gemtc](problems.md#gemtc)|1.0-1 |__+1__ | | | +|[leidenAlg](problems.md#leidenalg)|1.0.5 |__+2__ | |1 | +|[leidenbase](problems.md#leidenbase)|0.1.18 |__+2__ |__+1__ |1 | +|[metanetwork](problems.md#metanetwork)|0.7.0 |__+1__ | | | +|[migraph](problems.md#migraph)|0.13.2 |__+1__ | | | +|[nda](problems.md#nda)|0.1.6 |__+1__ | | | +|[netseg](problems.md#netseg)|1.0-1 |__+2__ |__+1__ | | +|[SEMgraph](problems.md#semgraph)|1.2.0 |__+1__ | | | +|[shazam](problems.md#shazam)|1.1.2 |__+1__ |1 | | +|[SNscan](problems.md#snscan)|1.0 |__+1__ | | | diff --git a/revdep/cran.md b/revdep/cran.md index c358ecf8f9e..ef98085c26c 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,123 +1,30 @@ ## revdepcheck results -We checked 778 reverse dependencies (775 from CRAN + 3 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. +We checked 781 reverse dependencies (778 from CRAN + 3 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. - * We saw 68 new problems - * We failed to check 8 packages + * We saw 14 new problems + * We failed to check 10 packages Issues with CRAN packages are summarised below. ### New problems (This reports the first line of each new failure) -* alakazam - checking examples ... ERROR - -* aniSNA - checking examples ... ERROR - -* bc3net - checking examples ... ERROR - -* bio3d - checking examples ... ERROR - * causaloptim checking tests ... ERROR -* chemodiv - checking examples ... ERROR - -* CINNA - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - * clustAnalytics - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* crosstalkr checking re-building of vignette outputs ... WARNING * dnet checking examples ... ERROR -* DrDimont - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* DTSEA - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* dynwrap - checking examples ... ERROR - -* edgebundle - checking examples ... ERROR - -* einet - checking tests ... ERROR - -* emba - checking re-building of vignette outputs ... WARNING - -* etree +* drake checking tests ... ERROR * gemtc checking tests ... ERROR -* geonetwork - checking examples ... ERROR - -* GISSB - checking examples ... ERROR - -* grand - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* graph4lg - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - checking data for non-ASCII characters ... NOTE - -* graphkernels - checking examples ... ERROR - -* graphlayouts - checking examples ... ERROR - checking tests ... ERROR - -* graphsim - checking examples ... ERROR - -* iGraphMatch - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* influenceR - checking tests ... ERROR - -* intergraph - checking examples ... ERROR - -* invertiforms - checking examples ... ERROR - checking tests ... ERROR - -* ITNr - checking examples ... ERROR - -* LEANR - checking tests ... ERROR - -* leiden - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - * leidenAlg checking examples ... ERROR checking tests ... ERROR @@ -127,139 +34,38 @@ Issues with CRAN packages are summarised below. checking tests ... ERROR checking re-building of vignette outputs ... WARNING -* meconetcomp - checking examples ... ERROR - * metanetwork - checking examples ... ERROR checking tests ... ERROR * migraph - checking examples ... ERROR - checking tests ... ERROR - -* missSBM - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* molnet - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* motifr - checking examples ... ERROR - -* multinets - checking examples ... ERROR checking tests ... ERROR -* mwcsr - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - * nda checking examples ... ERROR -* netplot - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* netrankr - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - * netseg checking examples ... ERROR checking tests ... ERROR checking re-building of vignette outputs ... WARNING -* nett - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* poppr - checking tests ... ERROR - -* psSubpathway - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* rmonad - checking examples ... ERROR - -* rsetse - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* rSpectral - checking examples ... ERROR - checking tests ... ERROR - -* sbm - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* sccore - checking examples ... ERROR - checking tests ... ERROR - -* ScorePlus - checking examples ... ERROR - -* secrlinear +* SEMgraph checking examples ... ERROR * shazam checking examples ... ERROR -* sigmajs - checking tests ... ERROR - -* signnet - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - * SNscan checking examples ... ERROR -* SOMbrero - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* spreadr - checking re-building of vignette outputs ... WARNING - -* SubpathwayLNCE - checking running R code from vignettes ... ERROR - -* SubtypeDrug - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* tgver - checking re-building of vignette outputs ... WARNING - -* threejs - checking examples ... ERROR - checking tests ... ERROR - -* tosr - checking tests ... ERROR - -* webSDM - checking examples ... ERROR - ### Failed to check -* beadplexr (NA) -* DRviaSPCN (NA) -* genekitr (NA) -* immcp (NA) -* MACP (NA) -* numbat (NA) -* tidySEM (NA) -* vivid (NA) +* beadplexr (NA) +* DRviaSPCN (NA) +* genekitr (NA) +* HospitalNetwork (NA) +* immcp (NA) +* MACP (NA) +* numbat (NA) +* Platypus (NA) +* tidySEM (NA) +* vivid (NA) diff --git a/revdep/failures.md b/revdep/failures.md index cf2b04aead8..2a59f74adcd 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -244,6 +244,66 @@ Status: 1 ERROR +``` +# HospitalNetwork + +
+ +* Version: 0.9.3 +* GitHub: https://github.com/PascalCrepey/HospitalNetwork +* Source code: https://github.com/cran/HospitalNetwork +* Date/Publication: 2023-02-27 08:22:43 UTC +* Number of recursive dependencies: 115 + +Run `revdepcheck::cloud_details(, "HospitalNetwork")` for more info + +
+ +## In both + +* checking whether package ‘HospitalNetwork’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/HospitalNetwork/new/HospitalNetwork.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘HospitalNetwork’ ... +** package ‘HospitalNetwork’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + there is no package called ‘graphlayouts’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘HospitalNetwork’ +* removing ‘/tmp/workdir/HospitalNetwork/new/HospitalNetwork.Rcheck/HospitalNetwork’ + + +``` +### CRAN + +``` +* installing *source* package ‘HospitalNetwork’ ... +** package ‘HospitalNetwork’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + there is no package called ‘graphlayouts’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘HospitalNetwork’ +* removing ‘/tmp/workdir/HospitalNetwork/old/HospitalNetwork.Rcheck/HospitalNetwork’ + + ``` # immcp @@ -487,6 +547,82 @@ Run `revdepcheck::cloud_details(, "NA")` for more info +``` +# Platypus + +
+ +* Version: 3.4.1 +* GitHub: NA +* Source code: https://github.com/cran/Platypus +* Date/Publication: 2022-08-15 07:20:20 UTC +* Number of recursive dependencies: 354 + +Run `revdepcheck::cloud_details(, "Platypus")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/Platypus/new/Platypus.Rcheck’ +* using R version 4.1.1 (2021-08-10) +* using platform: x86_64-pc-linux-gnu (64-bit) +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘Platypus/DESCRIPTION’ ... OK +* checking extension type ... Package +* this is package ‘Platypus’ version ‘3.4.1’ +* package encoding: UTF-8 +* checking package namespace information ... OK +... +Package required but not available: ‘ggtree’ + +Packages suggested but not available for checking: + 'Matrix.utils', 'monocle3', 'ProjecTILs', 'SeuratWrappers', + 'vanddraabe' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/Platypus/old/Platypus.Rcheck’ +* using R version 4.1.1 (2021-08-10) +* using platform: x86_64-pc-linux-gnu (64-bit) +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘Platypus/DESCRIPTION’ ... OK +* checking extension type ... Package +* this is package ‘Platypus’ version ‘3.4.1’ +* package encoding: UTF-8 +* checking package namespace information ... OK +... +Package required but not available: ‘ggtree’ + +Packages suggested but not available for checking: + 'Matrix.utils', 'monocle3', 'ProjecTILs', 'SeuratWrappers', + 'vanddraabe' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + ``` # NA @@ -527,11 +663,11 @@ Run `revdepcheck::cloud_details(, "NA")` for more info
-* Version: 0.2.3 +* Version: 0.2.4 * GitHub: https://github.com/cjvanlissa/tidySEM * Source code: https://github.com/cran/tidySEM -* Date/Publication: 2022-04-14 17:50:02 UTC -* Number of recursive dependencies: 173 +* Date/Publication: 2023-05-01 20:00:06 UTC +* Number of recursive dependencies: 190 Run `revdepcheck::cloud_details(, "tidySEM")` for more info @@ -549,16 +685,16 @@ Run `revdepcheck::cloud_details(, "tidySEM")` for more info * using option ‘--no-manual’ * checking for file ‘tidySEM/DESCRIPTION’ ... OK * checking extension type ... Package -* this is package ‘tidySEM’ version ‘0.2.3’ +* this is package ‘tidySEM’ version ‘0.2.4’ * package encoding: UTF-8 * checking package namespace information ... OK ... -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... NONE - ‘Generating_syntax.Rmd’ using ‘UTF-8’... OK ‘Plotting_graphs.Rmd’ using ‘UTF-8’... OK ‘Tabulating_results.Rmd’ using ‘UTF-8’... OK + ‘lca_confirmatory.Rmd’ using ‘UTF-8’... OK + ‘lca_exploratory.Rmd’ using ‘UTF-8’... OK + ‘lca_lcga.Rmd’ using ‘UTF-8’... OK + ‘lca_ordinal.Rmd’ using ‘UTF-8’... OK ‘sem_graph.Rmd’ using ‘UTF-8’... OK * checking re-building of vignette outputs ... OK * DONE @@ -579,16 +715,16 @@ Status: 1 NOTE * using option ‘--no-manual’ * checking for file ‘tidySEM/DESCRIPTION’ ... OK * checking extension type ... Package -* this is package ‘tidySEM’ version ‘0.2.3’ +* this is package ‘tidySEM’ version ‘0.2.4’ * package encoding: UTF-8 * checking package namespace information ... OK ... -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... NONE - ‘Generating_syntax.Rmd’ using ‘UTF-8’... OK ‘Plotting_graphs.Rmd’ using ‘UTF-8’... OK ‘Tabulating_results.Rmd’ using ‘UTF-8’... OK + ‘lca_confirmatory.Rmd’ using ‘UTF-8’... OK + ‘lca_exploratory.Rmd’ using ‘UTF-8’... OK + ‘lca_lcga.Rmd’ using ‘UTF-8’... OK + ‘lca_ordinal.Rmd’ using ‘UTF-8’... OK ‘sem_graph.Rmd’ using ‘UTF-8’... OK * checking re-building of vignette outputs ... OK * DONE diff --git a/revdep/problems.md b/revdep/problems.md index 4251463aae3..e16ae3b03fb 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1,162 +1,102 @@ -# alakazam +# causaloptim
-* Version: 1.2.1 -* GitHub: NA -* Source code: https://github.com/cran/alakazam -* Date/Publication: 2022-09-20 22:10:02 UTC -* Number of recursive dependencies: 117 +* Version: 0.9.7 +* GitHub: https://github.com/sachsmc/causaloptim +* Source code: https://github.com/cran/causaloptim +* Date/Publication: 2023-03-24 12:00:15 UTC +* Number of recursive dependencies: 63 -Run `revdepcheck::cloud_details(, "alakazam")` for more info +Run `revdepcheck::cloud_details(, "causaloptim")` for more info
## Newly broken -* checking examples ... ERROR - ``` - Running examples in ‘alakazam-Ex.R’ failed - The error most likely occurred in: - - > ### Name: getMRCA - > ### Title: Retrieve the first non-root node of a lineage tree - > ### Aliases: getMRCA - > - > ### ** Examples - > - > # Define example graph - ... - > - > # Use unweighted path length and do not exclude any nodes - > getMRCA(graph, path="steps", root="Germline") - This graph was created by an old(er) igraph version. - Call upgrade_graph() on it to use with the current igraph version - For now we convert it on the fly... - Error in vcount(graph) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: getMRCA -> getPathLengths -> data.frame -> V -> vcount - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING +* checking tests ... ERROR ``` - Error(s) in re-building vignettes: - --- re-building ‘AminoAcids-Vignette.Rmd’ using rmarkdown - A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TinyTeX with tinytex::reinstall_tinytex(repository = "illinois"). - - tlmgr: Local TeX Live (2022) is older than remote repository (2023). - Cross release updates are only supported with - update-tlmgr-latest(.sh/.exe) --update - See https://tug.org/texlive/upgrade.html for details. - Warning in system2("tlmgr", args, ...) : - running command ''tlmgr' search --file --global '/grffile.sty'' had status 1 - ... - REAL() can only be applied to a 'numeric', not a 'logical' - --- failed re-building ‘Topology-Vignette.Rmd’ - - SUMMARY: processing the following files failed: - ‘AminoAcids-Vignette.Rmd’ ‘Diversity-Vignette.Rmd’ - ‘Fastq-Vignette.Rmd’ ‘Files-Vignette.Rmd’ ‘GeneUsage-Vignette.Rmd’ - ‘Lineage-Vignette.Rmd’ ‘Topology-Vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + decompose, spectrum + + The following object is masked from 'package:base': + + union + + > + > test_check("causaloptim") + ERROR: Unable to successfully parse objective function. + qNA + + *** caught segfault *** + address 0x2b0000005d, cause 'memory not mapped' + An irrecoverable exception occurred. R is aborting now ... + Segmentation fault (core dumped) ``` -# aniSNA +# clustAnalytics
-* Version: 1.0 +* Version: 0.5.2 * GitHub: NA -* Source code: https://github.com/cran/aniSNA -* Date/Publication: 2023-02-17 09:50:09 UTC -* Number of recursive dependencies: 58 +* Source code: https://github.com/cran/clustAnalytics +* Date/Publication: 2022-11-09 11:50:09 UTC +* Number of recursive dependencies: 71 -Run `revdepcheck::cloud_details(, "aniSNA")` for more info +Run `revdepcheck::cloud_details(, "clustAnalytics")` for more info
## Newly broken -* checking examples ... ERROR +* checking re-building of vignette outputs ... WARNING ``` - Running examples in ‘aniSNA-Ex.R’ failed - The error most likely occurred in: + Error(s) in re-building vignettes: + --- re-building ‘cluster_stability.Rmd’ using rmarkdown + --- finished re-building ‘cluster_stability.Rmd’ - > ### Name: elk_network_2010 - > ### Title: An igraph object depicting the network obtained from - > ### elk_interactions_2010 - > ### Aliases: elk_network_2010 - > ### Keywords: datasets - > - > ### ** Examples - > - > igraph::E(elk_network_2010) - This graph was created by an old(er) igraph version. - Call upgrade_graph() on it to use with the current igraph version - For now we convert it on the fly... - Error in ecount(graph) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: -> ecount + --- re-building ‘graph_rewiring_functions.Rmd’ using rmarkdown + --- finished re-building ‘graph_rewiring_functions.Rmd’ + + --- re-building ‘other_functions.Rmd’ using rmarkdown + --- finished re-building ‘other_functions.Rmd’ + + ... + 28: tryCatchList(expr, classes, parentenv, handlers) + 29: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))}) + 30: tools:::.buildOneVignette("stability_significance_examples.Rmd", "/tmp/workdir/clustAnalytics/new/clustAnalytics.Rcheck/vign_test/clustAnalytics", TRUE, FALSE, "stability_significance_examples", "UTF-8", "/tmp/RtmparyCh1/file35332ad0ed20.rds") + An irrecoverable exception occurred. R is aborting now ... + Segmentation fault (core dumped) + SUMMARY: processing the following file failed: + ‘stability_significance_examples.Rmd’ + + Error: Vignette re-building failed. Execution halted ``` -# bc3net - -
- -* Version: 1.0.4 -* GitHub: NA -* Source code: https://github.com/cran/bc3net -* Date/Publication: 2016-11-28 08:21:04 -* Number of recursive dependencies: 9 - -Run `revdepcheck::cloud_details(, "bc3net")` for more info - -
- -## Newly broken +## In both -* checking examples ... ERROR +* checking installed package size ... NOTE ``` - Running examples in ‘bc3net-Ex.R’ failed - The error most likely occurred in: - - > ### Name: enrichment - > ### Title: Function that performs a functional enrichment analysis based on - > ### a one-sided Fisher's exact teset (hypergeometric test). - > ### Aliases: enrichment - > - > ### ** Examples - > - ... - > # as a reference list. - > - > data(exanet) - > data(exgensets) - > - > candidate=V(getgcc(exanet))$name - Error in clusters(net) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: V -> is_igraph -> %in% -> getgcc -> clusters - Execution halted + installed size is 6.6Mb + sub-directories of 1Mb or more: + libs 6.1Mb ``` -# bio3d +# dnet
-* Version: 2.4-4 -* GitHub: NA -* Source code: https://github.com/cran/bio3d -* Date/Publication: 2022-10-26 22:45:06 UTC -* Number of recursive dependencies: 77 +* Version: 1.1.7 +* GitHub: https://github.com/hfang-bristol/dnet +* Source code: https://github.com/cran/dnet +* Date/Publication: 2020-02-20 10:10:07 UTC +* Number of recursive dependencies: 51 -Run `revdepcheck::cloud_details(, "bio3d")` for more info +Run `revdepcheck::cloud_details(, "dnet")` for more info
@@ -164,49 +104,40 @@ Run `revdepcheck::cloud_details(, "bio3d")` for more info * checking examples ... ERROR ``` - Running examples in ‘bio3d-Ex.R’ failed + Running examples in ‘dnet-Ex.R’ failed The error most likely occurred in: - > ### Name: print.cna - > ### Title: Summarize and Print Features of a cna Network Graph - > ### Aliases: print.cna summary.cna - > ### Keywords: utilities + > ### Name: dDAGlevel + > ### Title: Function to define/calculate the level of nodes in a direct + > ### acyclic graph (DAG) + > ### Aliases: dDAGlevel > > ### ** Examples > ... - + x<- summary(net) - + x$members[[2]] - + - + detach(hivp) - + - + } - Error in igraph::ecount(x$network) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: print -> print.cna -> paste -> + > + > # 4) calculate the node levels + > # 4a) definition based on the longest path + > dDAGlevel(subg, level.mode="longest_path") + Warning in dDAGlevel(subg, level.mode = "longest_path") : + The input DAG has multiple roots; recalculate the root after being reversed. + + Error in dDAGlevel(subg, level.mode = "longest_path") : + Even after automatic reversing, the input DAG still has multiple roots; check the eligibility of the input DAG. Execution halted ``` -## In both - -* checking installed package size ... NOTE - ``` - installed size is 11.0Mb - sub-directories of 1Mb or more: - libs 7.3Mb - ``` - -# causaloptim +# drake
-* Version: 0.9.7 -* GitHub: https://github.com/sachsmc/causaloptim -* Source code: https://github.com/cran/causaloptim -* Date/Publication: 2023-03-24 12:00:15 UTC -* Number of recursive dependencies: 63 +* Version: 7.13.5 +* GitHub: https://github.com/ropensci/drake +* Source code: https://github.com/cran/drake +* Date/Publication: 2023-03-24 13:10:02 UTC +* Number of recursive dependencies: 164 -Run `revdepcheck::cloud_details(, "causaloptim")` for more info +Run `revdepcheck::cloud_details(, "drake")` for more info
@@ -217,75 +148,72 @@ Run `revdepcheck::cloud_details(, "causaloptim")` for more info Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: - Error in `vcount(graph)`: REAL() can only be applied to a 'numeric', not a 'logical' - Backtrace: - ▆ - 1. └─igraph::V(`*tmp*`) at test-known-bounds.R:57:4 - 2. └─igraph::vcount(graph) - ── Error ('test-known-bounds.R:144:5'): Mediator ─────────────────────────────── - Error in `vcount(graph)`: REAL() can only be applied to a 'numeric', not a 'logical' - Backtrace: - ▆ - 1. └─igraph::V(`*tmp*`) at test-known-bounds.R:144:4 - 2. └─igraph::vcount(graph) + ── 9. Failure ('test-4-imports.R:65:3'): responses to imported objects and funct + justbuilt(config) not equal to `builds`. + Lengths differ: 5 is not 4 + + ── 10. Failure ('test-4-imports.R:75:3'): responses to imported objects and func + justbuilt(config) not equal to `builds`. + Lengths differ: 1 is not 4 + ... and 16 more - [ FAIL 4 | WARN 0 | SKIP 0 | PASS 7 ] + + Maximum number of 10 failures reached, some test results may be missing. + + ══ DONE ════════════════════════════════════════════════════════════════════════ Error: Test failures Execution halted ``` -# chemodiv +# gemtc
-* Version: 0.2.0 -* GitHub: https://github.com/hpetren/chemodiv -* Source code: https://github.com/cran/chemodiv -* Date/Publication: 2023-01-12 09:30:06 UTC -* Number of recursive dependencies: 168 +* Version: 1.0-1 +* GitHub: https://github.com/gertvv/gemtc +* Source code: https://github.com/cran/gemtc +* Date/Publication: 2021-05-14 23:20:02 UTC +* Number of recursive dependencies: 58 -Run `revdepcheck::cloud_details(, "chemodiv")` for more info +Run `revdepcheck::cloud_details(, "gemtc")` for more info
## Newly broken -* checking examples ... ERROR +* checking tests ... ERROR ``` - Running examples in ‘chemodiv-Ex.R’ failed - The error most likely occurred in: - - > ### Name: molNetPlot - > ### Title: Plot molecular networks - > ### Aliases: molNetPlot - > - > ### ** Examples - > - > data(minimalSampData) - ... - > data(minimalNPCTable) - > data(minimalMolNet) - > groups <- c("A", "A", "B", "B") - > molNetPlot(minimalSampData, minimalMolNet) - It is recommended to include an npcTable for an improved - network visualization. - Error in vertex.attributes(graph) : - VECTOR_ELT() can only be applied to a 'list', not a 'environment' - Calls: molNetPlot ... node_tibble -> as_tibble -> vertex_attr -> vertex.attributes - Execution halted + Running ‘test.R’ + Running the tests in ‘tests/test.R’ failed. + Last 13 lines of output: + 5. └─testthat:::compare.default(act$val, exp$val, ...) + 6. ├─base::all.equal(x, y, ...) + 7. └─base::all.equal.default(x, y, ...) + 8. └─base::all.equal.list(target, current, ...) + 9. ├─base::all.equal(...) + 10. └─base::all.equal.default(...) + 11. └─base::all.equal.list(target, current, ...) + 12. └─base::attr.all.equal(target, current, ...) + 13. ├─base::length(target) + 14. └─igraph:::length.igraph(target) + 15. └─igraph::vcount(x) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 376 ] + Error: Test failures + Execution halted ``` -# CINNA +# leidenAlg
-* Version: 1.2.0 -* GitHub: NA -* Source code: https://github.com/cran/CINNA -* Date/Publication: 2022-04-07 15:12:31 UTC -* Number of recursive dependencies: 143 +* Version: 1.0.5 +* GitHub: https://github.com/kharchenkolab/leidenAlg +* Source code: https://github.com/cran/leidenAlg +* Date/Publication: 2022-09-30 07:20:02 UTC +* Number of recursive dependencies: 68 -Run `revdepcheck::cloud_details(, "CINNA")` for more info +Run `revdepcheck::cloud_details(, "leidenAlg")` for more info
@@ -293,60 +221,61 @@ Run `revdepcheck::cloud_details(, "CINNA")` for more info * checking examples ... ERROR ``` - Running examples in ‘CINNA-Ex.R’ failed + Running examples in ‘leidenAlg-Ex.R’ failed The error most likely occurred in: - > ### Name: calculate_centralities - > ### Title: Centrality measure calculation - > ### Aliases: calculate_centralities + > ### Name: as.dendrogram.fakeCommunities + > ### Title: Returns pre-calculated dendrogram + > ### Aliases: as.dendrogram.fakeCommunities > > ### ** Examples > - > - > data("zachary") - > p <- proper_centralities(zachary) - Error in is_directed(x) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: proper_centralities -> is_directed + > rLeidenComm = suppressWarnings(rleiden.community(exampleGraph, n.cores=1)) + Error in find_partition(graph, igraph::E(graph)$weight, resolution, n.iterations) : + REAL() can only be applied to a 'numeric', not a 'NULL' Execution halted ``` -* checking re-building of vignette outputs ... WARNING +* checking tests ... ERROR ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘CINNA.Rmd’ using rmarkdown - Quitting from lines 67-71 (CINNA.Rmd) - Error: processing vignette 'CINNA.Rmd' failed with diagnostics: - REAL() can only be applied to a 'numeric', not a 'logical' - --- failed re-building ‘CINNA.Rmd’ - - SUMMARY: processing the following file failed: - ‘CINNA.Rmd’ - - Error: Vignette re-building failed. - Execution halted + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Backtrace: + ▆ + 1. ├─base::suppressWarnings(rleiden.community(exampleGraph, n.cores = 1)) at test_functions.R:19:8 + 2. │ └─base::withCallingHandlers(...) + 3. └─leidenAlg::rleiden.community(exampleGraph, n.cores = 1) + 4. └─sccore::plapply(...) + 5. └─base::lapply(...) + 6. └─leidenAlg (local) FUN(X[[i]], ...) + 7. └─leidenAlg::rleiden.community(...) + 8. └─leidenAlg::leiden.community(graph, resolution = res, ...) + 9. └─leidenAlg::find_partition(...) + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 3 ] + Error: Test failures + Execution halted ``` ## In both -* checking dependencies in R code ... NOTE +* checking for GNU extensions in Makefiles ... NOTE ``` - Namespace in Imports field not imported from: ‘circlize’ - All declared Imports should be used. + GNU make is a SystemRequirements. ``` -# clustAnalytics +# leidenbase
-* Version: 0.5.2 -* GitHub: NA -* Source code: https://github.com/cran/clustAnalytics -* Date/Publication: 2022-11-09 11:50:09 UTC -* Number of recursive dependencies: 71 +* Version: 0.1.18 +* GitHub: https://github.com/cole-trapnell-lab/leidenbase +* Source code: https://github.com/cran/leidenbase +* Date/Publication: 2023-04-15 09:20:02 UTC +* Number of recursive dependencies: 54 -Run `revdepcheck::cloud_details(, "clustAnalytics")` for more info +Run `revdepcheck::cloud_details(, "leidenbase")` for more info
@@ -354,20 +283,26 @@ Run `revdepcheck::cloud_details(, "clustAnalytics")` for more info * checking examples ... ERROR ``` - Running examples in ‘clustAnalytics-Ex.R’ failed + Running examples in ‘leidenbase-Ex.R’ failed The error most likely occurred in: - > ### Name: FOMD - > ### Title: FOMD (Fraction Over Median Degree) - > ### Aliases: FOMD + > ### Name: leiden_find_partition + > ### Title: Leiden find partition community detection function + > ### Aliases: leiden_find_partition > > ### ** Examples > - > data(karate, package="igraphdata") - > FOMD(karate, membership(cluster_louvain(karate))) - Error in matrix(.Call(R_igraph_get_edgelist, graph, TRUE), ncol = 2) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: FOMD ... igraph_to_edgelist -> cbind -> as_edgelist -> matrix + > library(igraph) + ... + + > fpath <- system.file( 'testdata', 'igraph_n1500_edgelist.txt.gz', package = 'leidenbase' ) + > zfp <- gzfile(fpath) + > igraph <- read_graph( file = zfp, format='edgelist', n=1500 ) + > res <- leiden_find_partition(igraph=igraph, + + partition_type='CPMVertexPartition', + + resolution_parameter=1e-5) + Error in leiden_find_partition(igraph = igraph, partition_type = "CPMVertexPartition", : + REAL() can only be applied to a 'numeric', not a 'NULL' Execution halted ``` @@ -376,19 +311,19 @@ Run `revdepcheck::cloud_details(, "clustAnalytics")` for more info Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: - ── Error ('test_scoring_functions.R:8:5'): test scoring functions ────────────── - Error in `edge.attributes(g)`: VECTOR_ELT() can only be applied to a 'list', not a 'environment' + Error in `leidenbase::leiden_find_partition(igraph, partition_type = "RBConfigurationVertexPartition", + node_sizes = nodsiz, seed = 123456, resolution_parameter = 0.5)`: REAL() can only be applied to a 'numeric', not a 'NULL' + Backtrace: + ▆ + 1. └─leidenbase::leiden_find_partition(...) at test-leidenbase.R:224:2 + ── Error ('test-leidenbase.R:245:3'): modularity and significance return values ── + Error in `leidenbase::leiden_find_partition(igraph, partition_type = "CPMVertexPartition", + seed = 123456, resolution_parameter = 0.1)`: REAL() can only be applied to a 'numeric', not a 'NULL' Backtrace: ▆ - 1. ├─testthat::expect_equal_to_reference(...) at test_scoring_functions.R:8:4 - 2. │ └─testthat::expect_known_value(..., update = update) - 3. │ └─testthat::quasi_label(enquo(object), label, arg = "object") - 4. │ └─rlang::eval_bare(expr, quo_get_env(quo)) - 5. └─clustAnalytics::scoring_functions(...) - 6. ├─"weight" %in% names(edge.attributes(g)) - 7. └─igraph::edge.attributes(g) + 1. └─leidenbase::leiden_find_partition(...) at test-leidenbase.R:245:2 - [ FAIL 3 | WARN 0 | SKIP 0 | PASS 0 ] + [ FAIL 11 | WARN 0 | SKIP 0 | PASS 6 ] Error: Test failures Execution halted ``` @@ -396,23 +331,15 @@ Run `revdepcheck::cloud_details(, "clustAnalytics")` for more info * checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: - --- re-building ‘cluster_stability.Rmd’ using rmarkdown - Quitting from lines 24-29 (cluster_stability.Rmd) - Error: processing vignette 'cluster_stability.Rmd' failed with diagnostics: - VECTOR_ELT() can only be applied to a 'list', not a 'environment' - --- failed re-building ‘cluster_stability.Rmd’ - - --- re-building ‘graph_rewiring_functions.Rmd’ using rmarkdown - Quitting from lines 30-32 (graph_rewiring_functions.Rmd) - Error: processing vignette 'graph_rewiring_functions.Rmd' failed with diagnostics: - ... - VECTOR_ELT() can only be applied to a 'list', not a 'environment' - --- failed re-building ‘stability_significance_examples.Rmd’ + ... + --- re-building ‘leidenbase.Rmd’ using rmarkdown + Quitting from lines 87-92 (leidenbase.Rmd) + Error: processing vignette 'leidenbase.Rmd' failed with diagnostics: + REAL() can only be applied to a 'numeric', not a 'NULL' + --- failed re-building ‘leidenbase.Rmd’ - SUMMARY: processing the following files failed: - ‘cluster_stability.Rmd’ ‘graph_rewiring_functions.Rmd’ - ‘other_functions.Rmd’ ‘scoring_functions.Rmd’ - ‘stability_significance_examples.Rmd’ + SUMMARY: processing the following file failed: + ‘leidenbase.Rmd’ Error: Vignette re-building failed. Execution halted @@ -422,96 +349,98 @@ Run `revdepcheck::cloud_details(, "clustAnalytics")` for more info * checking installed package size ... NOTE ``` - installed size is 6.6Mb + installed size is 19.1Mb sub-directories of 1Mb or more: - libs 6.1Mb + libs 18.8Mb ``` -# crosstalkr +# metanetwork
-* Version: 1.0.1 -* GitHub: NA -* Source code: https://github.com/cran/crosstalkr -* Date/Publication: 2023-01-31 09:00:07 UTC -* Number of recursive dependencies: 167 +* Version: 0.7.0 +* GitHub: https://github.com/MarcOhlmann/metanetwork +* Source code: https://github.com/cran/metanetwork +* Date/Publication: 2022-12-05 14:10:02 UTC +* Number of recursive dependencies: 106 -Run `revdepcheck::cloud_details(, "crosstalkr")` for more info +Run `revdepcheck::cloud_details(, "metanetwork")` for more info
## Newly broken -* checking re-building of vignette outputs ... WARNING +* checking tests ... ERROR ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘crosstalkr_vignette.Rmd’ using rmarkdown - Quitting from lines 72-77 (crosstalkr_vignette.Rmd) - Error: processing vignette 'crosstalkr_vignette.Rmd' failed with diagnostics: - REAL() can only be applied to a 'numeric', not a 'logical' - --- failed re-building ‘crosstalkr_vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘crosstalkr_vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Epoch: Iteration #300 error is: 199.576452337934 + x_max = 1692.55352861469 + y_max = 336.30631387777 + [ FAIL 1 | WARN 22 | SKIP 0 | PASS 73 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-compute_TL.R:25:3'): Computation of trophic levels of norway dataset ── + V(meta0$metaweb)$TL (`actual`) not equal to V(meta_angola$metaweb)$TL (`expected`). + + `actual`: 1.2 1.4 0.9 0.5 0.8 0.8 0.2 0.8 0.9 1.8 and 18 more... + `expected`: 1.6 1.3 1.8 2.3 1.9 1.9 2.6 1.9 1.9 1.0 ... + + [ FAIL 1 | WARN 22 | SKIP 0 | PASS 73 ] + Error: Test failures + Execution halted ``` -# dnet +# migraph
-* Version: 1.1.7 -* GitHub: https://github.com/hfang-bristol/dnet -* Source code: https://github.com/cran/dnet -* Date/Publication: 2020-02-20 10:10:07 UTC -* Number of recursive dependencies: 51 +* Version: 0.13.2 +* GitHub: https://github.com/snlab-ch/migraph +* Source code: https://github.com/cran/migraph +* Date/Publication: 2022-12-20 16:20:02 UTC +* Number of recursive dependencies: 138 -Run `revdepcheck::cloud_details(, "dnet")` for more info +Run `revdepcheck::cloud_details(, "migraph")` for more info
## Newly broken -* checking examples ... ERROR +* checking tests ... ERROR ``` - Running examples in ‘dnet-Ex.R’ failed - The error most likely occurred in: - - > ### Name: dDAGancestor - > ### Title: Function to find common ancestors of two terms/nodes from a - > ### direct acyclic graph (DAG) - > ### Aliases: dDAGancestor - > - > ### ** Examples - > - ... - > - > # 2) randomly give two terms - > term1 <- sample(V(g)$name,1) - This graph was created by an old(er) igraph version. - Call upgrade_graph() on it to use with the current igraph version - For now we convert it on the fly... - Error in vcount(graph) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: sample -> V -> vcount - Execution halted + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + round(unname(tidys$estimate[1]), 3) not equal to -8.47. + 1/1 mismatches + [1] -3.79 - -8.47 == 4.68 + ── Failure ('test-model_regression.R:35:3'): glance works correctly for network_reg ── + round(glances$r.squared, 4) not equal to 0.0575. + 1/1 mismatches + [1] 0.064 - 0.0575 == 0.0065 + ── Failure ('test-motif_census.R:7:3'): node tie census works ────────────────── + test[1:4] not equal to rep(0, 4). + 1/4 mismatches + [2] 1 - 0 == 1 + + [ FAIL 9 | WARN 0 | SKIP 0 | PASS 544 ] + Error: Test failures + Execution halted ``` -# DrDimont +# nda
-* Version: 0.1.4 -* GitHub: NA -* Source code: https://github.com/cran/DrDimont -* Date/Publication: 2022-09-23 15:40:02 UTC -* Number of recursive dependencies: 127 +* Version: 0.1.6 +* GitHub: https://github.com/kzst/nda +* Source code: https://github.com/cran/nda +* Date/Publication: 2022-10-14 13:10:02 UTC +* Number of recursive dependencies: 81 -Run `revdepcheck::cloud_details(, "DrDimont")` for more info +Run `revdepcheck::cloud_details(, "nda")` for more info
@@ -519,57 +448,40 @@ Run `revdepcheck::cloud_details(, "DrDimont")` for more info * checking examples ... ERROR ``` - Running examples in ‘DrDimont-Ex.R’ failed + Running examples in ‘nda-Ex.R’ failed The error most likely occurred in: - > ### Name: compute_drug_response_scores - > ### Title: Calculate drug response score - > ### Aliases: compute_drug_response_scores + > ### Name: biplot.nda + > ### Title: Biplot function for Network-based Dimensionality Reduction and + > ### Analysis (NDA) + > ### Aliases: biplot.nda + > ### Keywords: plot > > ### ** Examples - > - > data(drug_target_edges_example) ... - > example_drug_response_scores <- compute_drug_response_scores( - + differential_graph=differential_graph_example, - + drug_targets=drug_target_edges_example$targets, - + settings=example_settings) - [23-04-21 14:50:48] Computing drug response scores based on the mean of the differential scores ... - - Error in matrix(.Call(R_igraph_get_edgelist, graph, TRUE), ncol = 2) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: compute_drug_response_scores -> -> as_edgelist -> matrix - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘DrDimont_Vignette.Rmd’ using rmarkdown - Quitting from lines 400-409 (DrDimont_Vignette.Rmd) - Error: processing vignette 'DrDimont_Vignette.Rmd' failed with diagnostics: - VECTOR_ELT() can only be applied to a 'list', not a 'environment' - --- failed re-building ‘DrDimont_Vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘DrDimont_Vignette.Rmd’ - - Error: Vignette re-building failed. + > + > # Biplot function without feature selection + > + > data("CrimesUSA1990.X") + > df<-CrimesUSA1990.X + > p<-ndr(df) + Error in find_partition(graph, igraph::E(graph)$weight, resolution, n.iterations) : + REAL() can only be applied to a 'numeric', not a 'NULL' + Calls: ndr -> -> find_partition Execution halted ``` -# DTSEA +# netseg
-* Version: 0.0.3 -* GitHub: NA -* Source code: https://github.com/cran/DTSEA -* Date/Publication: 2022-11-06 13:20:02 UTC -* Number of recursive dependencies: 72 +* Version: 1.0-1 +* GitHub: https://github.com/mbojan/netseg +* Source code: https://github.com/cran/netseg +* Date/Publication: 2022-08-25 12:10:06 UTC +* Number of recursive dependencies: 61 -Run `revdepcheck::cloud_details(, "DTSEA")` for more info +Run `revdepcheck::cloud_details(, "netseg")` for more info
@@ -577,57 +489,80 @@ Run `revdepcheck::cloud_details(, "DTSEA")` for more info * checking examples ... ERROR ``` - Running examples in ‘DTSEA-Ex.R’ failed + Running examples in ‘netseg-Ex.R’ failed The error most likely occurred in: - > ### Name: calculate_p0 - > ### Title: Function to calculate the p0 vector used in Random Walk with - > ### Restart (RwR) - > ### Aliases: calculate_p0 + > ### Name: ssi + > ### Title: Spectral Segregation Index for Social Networks + > ### Aliases: ssi > > ### ** Examples > + > if(requireNamespace("igraph", quietly = TRUE)) { ... - > - > # Compute the p0 vector - > p0 <- calculate_p0(nodes = example_ppi, disease = example_disease_list) - This graph was created by an old(er) igraph version. - Call upgrade_graph() on it to use with the current igraph version - For now we convert it on the fly... - Error in vcount(graph) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: calculate_p0 -> V -> vcount + + vertex.color= gray(k), + + vertex.shape=c("circle", "csquare")[a], + + vertex.label.color="black") + + legend( "topleft", legend=c("Men", "Women"), pch=c(0,1), col=1) + + } + Error in igraph::induced.subgraph(g, which(ids == b)) : + At core/core/vector.pmt:1030 : Assertion failed: v->stor_begin != NULL. This is an unexpected igraph error; please report this as a bug, along with the steps to reproduce it. + Please restart your R session to avoid crashes or other surprising behavior. + Calls: ssi -> unlist -> lapply -> FUN -> ssib -> Execution halted ``` +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ── Error ('test-ssi.R:4:3'): values of ssi for EF3 data correspond to values from the paper ── + Error in `igraph::induced.subgraph(g, which(ids == b))`: At core/core/vector.pmt:1030 : Assertion failed: v->stor_begin != NULL. This is an unexpected igraph error; please report this as a bug, along with the steps to reproduce it. + Please restart your R session to avoid crashes or other surprising behavior. + Backtrace: + ▆ + 1. └─netseg::ssi(EF3, "race") at test-ssi.R:4:2 + 2. ├─base::unlist(...) + 3. └─base::lapply(...) + 4. └─netseg (local) FUN(X[[i]], ...) + 5. └─netseg:::ssib(g = gg, vattr = vattr, b = val) + 6. └─igraph::induced.subgraph(g, which(ids == b)) + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 72 ] + Error: Test failures + Execution halted + ``` + * checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: ... - --- re-building ‘DTSEA.Rmd’ using rmarkdown - Quitting from lines 54-67 (DTSEA.Rmd) - Error: processing vignette 'DTSEA.Rmd' failed with diagnostics: - REAL() can only be applied to a 'numeric', not a 'logical' - --- failed re-building ‘DTSEA.Rmd’ + --- re-building ‘netseg.Rmd’ using rmarkdown + Quitting from lines 252-253 (netseg.Rmd) + Error: processing vignette 'netseg.Rmd' failed with diagnostics: + At core/core/vector.pmt:483 : Assertion failed: v->stor_begin != NULL. This is an unexpected igraph error; please report this as a bug, along with the steps to reproduce it. + Please restart your R session to avoid crashes or other surprising behavior. + --- failed re-building ‘netseg.Rmd’ SUMMARY: processing the following file failed: - ‘DTSEA.Rmd’ + ‘netseg.Rmd’ Error: Vignette re-building failed. Execution halted ``` -# dynwrap +# SEMgraph
-* Version: 1.2.3 -* GitHub: https://github.com/dynverse/dynwrap -* Source code: https://github.com/cran/dynwrap -* Date/Publication: 2023-03-01 17:10:02 UTC -* Number of recursive dependencies: 97 +* Version: 1.2.0 +* GitHub: https://github.com/fernandoPalluzzi/SEMgraph +* Source code: https://github.com/cran/SEMgraph +* Date/Publication: 2023-05-04 16:00:02 UTC +* Number of recursive dependencies: 51 -Run `revdepcheck::cloud_details(, "dynwrap")` for more info +Run `revdepcheck::cloud_details(, "SEMgraph")` for more info
@@ -635,37 +570,40 @@ Run `revdepcheck::cloud_details(, "dynwrap")` for more info * checking examples ... ERROR ``` - Running examples in ‘dynwrap-Ex.R’ failed + Running examples in ‘SEMgraph-Ex.R’ failed The error most likely occurred in: - > ### Name: trajectory_type_dag - > ### Title: A DAG connecting different trajectory types - > ### Aliases: trajectory_type_dag - > ### Keywords: create_ti_method + > ### Name: SEMdag + > ### Title: Estimate a DAG from an input (or empty) graph + > ### Aliases: SEMdag > > ### ** Examples > - > trajectory_type_dag - This graph was created by an old(er) igraph version. - Call upgrade_graph() on it to use with the current igraph version - For now we convert it on the fly... - Error in is_directed(object) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: ... print.igraph -> .print.header -> paste0 -> is_directed + > + ... + > + > # DAG estimation (default values) + > dag0 <- SEMdag(ig, X) + WARNING: input graph is not acyclic ! + Applying graph -> DAG conversion... + DAG conversion : TRUE + Node Linear Ordering with TO setting + + Error: from glmnet C++ code (error code 10000); All penalty factors are <= 0 Execution halted ``` -# edgebundle +# shazam
-* Version: 0.4.1 -* GitHub: https://github.com/schochastics/edgebundle -* Source code: https://github.com/cran/edgebundle -* Date/Publication: 2022-11-22 07:00:02 UTC -* Number of recursive dependencies: 55 +* Version: 1.1.2 +* GitHub: NA +* Source code: https://github.com/cran/shazam +* Date/Publication: 2022-10-01 07:30:02 UTC +* Number of recursive dependencies: 124 -Run `revdepcheck::cloud_details(, "edgebundle")` for more info +Run `revdepcheck::cloud_details(, "shazam")` for more info
@@ -673,2635 +611,73 @@ Run `revdepcheck::cloud_details(, "edgebundle")` for more info * checking examples ... ERROR ``` - Running examples in ‘edgebundle-Ex.R’ failed + Running examples in ‘shazam-Ex.R’ failed The error most likely occurred in: - > ### Name: metro_multicriteria - > ### Title: Metro Map Layout - > ### Aliases: metro_multicriteria + > ### Name: makeGraphDf + > ### Title: Build a data.frame from a ChangeoClone and an igraph object + > ### containing a clonal lineage + > ### Aliases: makeGraphDf > > ### ** Examples > - > # the algorithm has problems with parallel edges ... - decompose, spectrum - - The following object is masked from ‘package:base’: - - union - - > g <- simplify(metro_berlin) - Error in simplify(metro_berlin) : - REAL() can only be applied to a 'numeric', not a 'logical' + > data(ExampleDb, package = "alakazam") + > data(ExampleTrees, package = "alakazam") + > graph <- ExampleTrees[[17]] + > db <- subset(ExampleDb, clone_id == graph$clone) + > clone <- alakazam::makeChangeoClone(db) + > + > # Extend data with lineage information + > df <- makeGraphDf(graph, clone) + Error: Expecting a single string value: [type=character; extent=0]. Execution halted ``` ## In both -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 22 marked UTF-8 strings - ``` - -# einet - -
- -* Version: 0.1.0 -* GitHub: https://github.com/travisbyrum/einet -* Source code: https://github.com/cran/einet -* Date/Publication: 2020-04-23 17:20:03 UTC -* Number of recursive dependencies: 67 - -Run `revdepcheck::cloud_details(, "einet")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 1. ├─testthat::expect_lte(effective_information(karate) - 2.35, MAX_ERROR) at test_effective_information.R:76:2 - 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") - 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) - 4. ├─einet::effective_information(karate) - 5. ├─einet:::effective_information.igraph(karate) - 6. │ └─einet:::check_network(graph) - 7. │ └─graph %>% igraph::simplify(remove.loops = FALSE) %>% ... - 8. ├─igraph::as.directed(.) - 9. │ └─igraph::is_igraph(graph) - 10. │ └─"igraph" %in% class(graph) - 11. └─igraph::simplify(., remove.loops = FALSE) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 12 ] - Error: Test failures - Execution halted - ``` - -# emba - -
- -* Version: 0.1.8 -* GitHub: https://github.com/bblodfon/emba -* Source code: https://github.com/cran/emba -* Date/Publication: 2021-01-07 04:00:02 UTC -* Number of recursive dependencies: 76 - -Run `revdepcheck::cloud_details(, "emba")` for more info - -
- -## Newly broken - * checking re-building of vignette outputs ... WARNING ``` Error(s) in re-building vignettes: - ... - --- re-building ‘emba.Rmd’ using rmarkdown - Quitting from lines 208-210 (emba.Rmd) - Error: processing vignette 'emba.Rmd' failed with diagnostics: - REAL() can only be applied to a 'numeric', not a 'logical' - --- failed re-building ‘emba.Rmd’ + --- re-building ‘Baseline-Vignette.Rmd’ using rmarkdown + A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TinyTeX with tinytex::reinstall_tinytex(repository = "illinois"). - SUMMARY: processing the following file failed: - ‘emba.Rmd’ + tlmgr: Local TeX Live (2022) is older than remote repository (2023). + Cross release updates are only supported with + update-tlmgr-latest(.sh/.exe) --update + See https://tug.org/texlive/upgrade.html for details. + Warning in system2("tlmgr", args, ...) : + running command ''tlmgr' search --file --global '/grffile.sty'' had status 1 + ... + LaTeX failed to compile /tmp/workdir/shazam/new/shazam.Rcheck/vign_test/shazam/vignettes/Targeting-Vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Targeting-Vignette.log for more info. + --- failed re-building ‘Targeting-Vignette.Rmd’ + + SUMMARY: processing the following files failed: + ‘Baseline-Vignette.Rmd’ ‘DistToNearest-Vignette.Rmd’ + ‘Mutation-Vignette.Rmd’ ‘Shmulate-Vignette.Rmd’ + ‘Targeting-Vignette.Rmd’ Error: Vignette re-building failed. Execution halted ``` -## In both - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# etree - -
- -* Version: 0.1.0 -* GitHub: https://github.com/ricgbl/etree -* Source code: https://github.com/cran/etree -* Date/Publication: 2022-07-16 08:30:02 UTC -* Number of recursive dependencies: 128 - -Run `revdepcheck::cloud_details(, "etree")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 3. │ └─testthat:::quasi_capture(...) - 4. │ ├─testthat (local) .capture(...) - 5. │ │ └─base::withCallingHandlers(...) - 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) - 7. └─etree::etree(resp_cls, covs_cls, split_type = "cluster") - 8. └─base::lapply(covariates, dist_comp) - 9. └─etree (local) FUN(X[[i]], ...) - 10. └─base::sapply(x, function(i) is.null(igraph::edge.attributes(i)$weight)) - 11. └─base::lapply(X = X, FUN = FUN, ...) - 12. └─etree (local) FUN(X[[i]], ...) - 13. └─igraph::edge.attributes(i) - - [ FAIL 25 | WARN 1 | SKIP 0 | PASS 46 ] - Error: Test failures - Execution halted - ``` - -# gemtc +# SNscan
-* Version: 1.0-1 -* GitHub: https://github.com/gertvv/gemtc -* Source code: https://github.com/cran/gemtc -* Date/Publication: 2021-05-14 23:20:02 UTC -* Number of recursive dependencies: 58 +* Version: 1.0 +* GitHub: NA +* Source code: https://github.com/cran/SNscan +* Date/Publication: 2016-01-19 13:09:28 +* Number of recursive dependencies: 11 -Run `revdepcheck::cloud_details(, "gemtc")` for more info +Run `revdepcheck::cloud_details(, "SNscan")` for more info
## Newly broken -* checking tests ... ERROR - ``` - Running ‘test.R’ - Running the tests in ‘tests/test.R’ failed. - Last 13 lines of output: - 5. └─testthat:::compare.default(act$val, exp$val, ...) - 6. ├─base::all.equal(x, y, ...) - 7. └─base::all.equal.default(x, y, ...) - 8. └─base::all.equal.list(target, current, ...) - 9. ├─base::all.equal(...) - 10. └─base::all.equal.default(...) - 11. └─base::all.equal.list(target, current, ...) - 12. └─base::attr.all.equal(target, current, ...) - 13. ├─base::length(target) - 14. └─igraph:::length.igraph(target) - 15. └─igraph::vcount(x) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 376 ] - Error: Test failures - Execution halted - ``` - -# geonetwork - -
- -* Version: 0.5.0 -* GitHub: NA -* Source code: https://github.com/cran/geonetwork -* Date/Publication: 2023-04-14 08:30:02 UTC -* Number of recursive dependencies: 156 - -Run `revdepcheck::cloud_details(, "geonetwork")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘geonetwork-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plot.geonetwork - > ### Title: Plot a geonetwork - > ### Aliases: plot.geonetwork - > - > ### ** Examples - > - > plot(eurodist, axes = TRUE, type = "n") - Error in vertex.attributes(graph) : - VECTOR_ELT() can only be applied to a 'list', not a 'environment' - Calls: plot ... plot.geonetwork -> -> vertex_attr -> vertex.attributes - Execution halted - ``` - -# GISSB - -
- -* Version: 1.1 -* GitHub: NA -* Source code: https://github.com/cran/GISSB -* Date/Publication: 2023-01-10 18:33:14 UTC -* Number of recursive dependencies: 114 - -Run `revdepcheck::cloud_details(, "GISSB")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘GISSB-Ex.R’ failed - The error most likely occurred in: - - > ### Name: path_leaflet - > ### Title: Visualize the shortest path with Leaflet - > ### Aliases: path_leaflet - > - > ### ** Examples - > - > - ... - > shortest_path_igraph(from_node_ID = 25, - + to_node_ID = 33, - + unit = "minutes", - + path = TRUE, - + graph_object = graph_sampledata) %>% - + path_leaflet(graph_object = graph_sampledata) - Error in edge.attributes(graph) : - VECTOR_ELT() can only be applied to a 'list', not a 'environment' - Calls: %>% ... edge_tibble -> as_tibble -> edge_attr -> edge.attributes - Execution halted - ``` - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 866 marked UTF-8 strings - ``` - -# grand - -
- -* Version: 0.9.0 -* GitHub: https://github.com/zpneal/grand -* Source code: https://github.com/cran/grand -* Date/Publication: 2023-02-10 10:30:02 UTC -* Number of recursive dependencies: 36 - -Run `revdepcheck::cloud_details(, "grand")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘grand-Ex.R’ failed - The error most likely occurred in: - - > ### Name: grand - > ### Title: Apply Guidelines for Reporting About Network Data (GRAND) to an - > ### igraph object - > ### Aliases: grand - > - > ### ** Examples - > - > data(airport) #Load example data - > airport <- grand(airport) #Apply GRAND interactively - Error in igraph::is_simple(G) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: grand -> - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘grand.Rmd’ using rmarkdown - Quitting from lines 167-178 (grand.Rmd) - Error: processing vignette 'grand.Rmd' failed with diagnostics: - REAL() can only be applied to a 'numeric', not a 'logical' - --- failed re-building ‘grand.Rmd’ - - SUMMARY: processing the following file failed: - ‘grand.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# graph4lg - -
- -* Version: 1.8.0 -* GitHub: NA -* Source code: https://github.com/cran/graph4lg -* Date/Publication: 2023-01-30 14:00:05 UTC -* Number of recursive dependencies: 119 - -Run `revdepcheck::cloud_details(, "graph4lg")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘graph4lg-Ex.R’ failed - The error most likely occurred in: - - > ### Name: add_nodes_attr - > ### Title: Add attributes to the nodes of a graph - > ### Aliases: add_nodes_attr - > - > ### ** Examples - > - > data("data_tuto") - ... - > graph <- data_tuto[[3]] - > df_nodes <- data.frame(Id = igraph::V(graph)$name, - + Area = runif(50, min = 10, max = 60)) - This graph was created by an old(er) igraph version. - Call upgrade_graph() on it to use with the current igraph version - For now we convert it on the fly... - Error in vcount(graph) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: data.frame -> -> vcount - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘genetic_graph_2.Rmd’ using rmarkdown - Quitting from lines 227-228 (genetic_graph_2.Rmd) - Error: processing vignette 'genetic_graph_2.Rmd' failed with diagnostics: - REAL() can only be applied to a 'numeric', not a 'logical' - --- failed re-building ‘genetic_graph_2.Rmd’ - - --- re-building ‘graph_comparisons_4.Rmd’ using rmarkdown - --- finished re-building ‘graph_comparisons_4.Rmd’ - ... - Quitting from lines 426-430 (landscape_graph_3.Rmd) - Error: processing vignette 'landscape_graph_3.Rmd' failed with diagnostics: - REAL() can only be applied to a 'numeric', not a 'logical' - --- failed re-building ‘landscape_graph_3.Rmd’ - - SUMMARY: processing the following files failed: - ‘genetic_graph_2.Rmd’ ‘landscape_graph_3.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Error loading dataset 'data_tuto': - Error in vcount(x) : - REAL() can only be applied to a 'numeric', not a 'logical' - - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘Rdpack’ - All declared Imports should be used. - ``` - -# graphkernels - -
- -* Version: 1.6.1 -* GitHub: NA -* Source code: https://github.com/cran/graphkernels -* Date/Publication: 2021-12-20 09:00:02 UTC -* Number of recursive dependencies: 9 - -Run `revdepcheck::cloud_details(, "graphkernels")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘graphkernels-Ex.R’ failed - The error most likely occurred in: - - > ### Name: CalculateConnectedGraphletKernel - > ### Title: Connected graphlet kernel - > ### Aliases: CalculateConnectedGraphletKernel - > ### Keywords: graph kernel graphlet - > - > ### ** Examples - > - > data(mutag) - > K <- CalculateConnectedGraphletKernel(mutag, 4) - Error in is_directed(graph) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: CalculateConnectedGraphletKernel -> as_adj_list -> is_directed - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 15.6Mb - sub-directories of 1Mb or more: - libs 15.4Mb - ``` - -# graphlayouts - -
- -* Version: 0.8.4 -* GitHub: https://github.com/schochastics/graphlayouts -* Source code: https://github.com/cran/graphlayouts -* Date/Publication: 2022-11-24 06:20:02 UTC -* Number of recursive dependencies: 93 - -Run `revdepcheck::cloud_details(, "graphlayouts")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘graphlayouts-Ex.R’ failed - The error most likely occurred in: - - > ### Name: layout_multilevel - > ### Title: multilevel layout - > ### Aliases: layout_multilevel layout_as_multilevel - > ### layout_igraph_multilevel - > - > ### ** Examples - > - ... - union - - > data("multilvl_ex") - > - > # compute a layout for the whole network - > xy <- layout_as_multilevel(multilvl_ex,type = "all", alpha = 25, beta = 45) - Error in igraph::vertex_attr_names(g) : - VECTOR_ELT() can only be applied to a 'list', not a 'environment' - Calls: layout_as_multilevel -> %in% -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Error ('test-layout_multilevel.R:3:3'): layout_mulitlevel works ───────────── - Error in `igraph::vertex_attr_names(g)`: VECTOR_ELT() can only be applied to a 'list', not a 'environment' - Backtrace: - ▆ - 1. ├─testthat::expect_is(...) at test-layout_multilevel.R:3:2 - 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") - 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) - 4. └─graphlayouts::layout_as_multilevel(...) - 5. ├─"lvl" %in% igraph::vertex_attr_names(g) - 6. └─igraph::vertex_attr_names(g) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 71 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 9.1Mb - sub-directories of 1Mb or more: - help 2.4Mb - libs 6.5Mb - ``` - -# graphsim - -
- -* Version: 1.0.3 -* GitHub: https://github.com/TomKellyGenetics/graphsim -* Source code: https://github.com/cran/graphsim -* Date/Publication: 2022-09-12 06:12:54 UTC -* Number of recursive dependencies: 121 - -Run `revdepcheck::cloud_details(, "graphsim")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘graphsim-Ex.R’ failed - The error most likely occurred in: - - > ### Name: generate_expression - > ### Title: Generate Simulated Expression - > ### Aliases: generate_expression generate_expression_mat - > ### Keywords: graph igraph mvtnorm network simulation - > - > ### ** Examples - > - ... - > # absolute = FALSE (geometric distance by default) - > # compute states directly from graph attributes for TGF-\eqn{\Beta} pathway - > TGFBeta_Smad_state <- E(TGFBeta_Smad_graph)$state - This graph was created by an old(er) igraph version. - Call upgrade_graph() on it to use with the current igraph version - For now we convert it on the fly... - Error in ecount(graph) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: E -> ecount - Execution halted - ``` - -# iGraphMatch - -
- -* Version: 2.0.1 -* GitHub: https://github.com/dpmcsuss/iGraphMatch -* Source code: https://github.com/cran/iGraphMatch -* Date/Publication: 2022-09-13 18:30:02 UTC -* Number of recursive dependencies: 80 - -Run `revdepcheck::cloud_details(, "iGraphMatch")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘iGraphMatch-Ex.R’ failed - The error most likely occurred in: - - > ### Name: C.Elegans - > ### Title: Chemical synapses and electrical synapses networks of roundworm - > ### Aliases: C.Elegans - > ### Keywords: datasets - > - > ### ** Examples - > - > data(C.Elegans) - > g1 <- C.Elegans[[1]] - > g2 <- C.Elegans[[2]] - > plot(g1, g2) - Error in igraph::vcount(x) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: plot -> plot -> .local -> identity_match -> - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘iGraphMatch.Rmd’ using rmarkdown - Quitting from lines 951-987 (iGraphMatch.Rmd) - Error: processing vignette 'iGraphMatch.Rmd' failed with diagnostics: - REAL() can only be applied to a 'numeric', not a 'logical' - --- failed re-building ‘iGraphMatch.Rmd’ - - SUMMARY: processing the following file failed: - ‘iGraphMatch.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# influenceR - -
- -* Version: 0.1.0.1 -* GitHub: https://github.com/rcc-uchicago/influenceR -* Source code: https://github.com/cran/influenceR -* Date/Publication: 2021-09-25 10:15:40 UTC -* Number of recursive dependencies: 35 - -Run `revdepcheck::cloud_details(, "influenceR")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 4. │ └─rlang::eval_bare(expr, quo_get_env(quo)) - 5. └─influenceR::betweenness(flo_graph) - 6. └─igraph::get.edgelist(g, names = F) - 7. └─base::matrix(.Call(R_igraph_get_edgelist, graph, TRUE), ncol = 2) - ── Error ('test_reference.R:72:3'): bridging matches reference function ──────── - Error in `vcount(graph)`: REAL() can only be applied to a 'numeric', not a 'logical' - Backtrace: - ▆ - 1. └─influenceR (local) bridge_test(flo_graph) at test_reference.R:72:2 - 2. └─igraph::V(g) at test_reference.R:26:2 - 3. └─igraph::vcount(graph) - - [ FAIL 5 | WARN 2 | SKIP 0 | PASS 0 ] - Error: Test failures - Execution halted - ``` - -# intergraph - -
- -* Version: 2.0-2 -* GitHub: NA -* Source code: https://github.com/cran/intergraph -* Date/Publication: 2016-12-05 18:28:47 -* Number of recursive dependencies: 49 - -Run `revdepcheck::cloud_details(, "intergraph")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘intergraph-Ex.R’ failed - The error most likely occurred in: - - > ### Name: asDF - > ### Title: Convert network to data frame(s) - > ### Aliases: asDF asDF.igraph asDF.network - > - > ### ** Examples - > - > # using method for 'network' objects - ... - ..$ label : chr [1:15] "a" "b" "c" "d" ... - ..$ na : logi [1:15] FALSE FALSE FALSE FALSE FALSE FALSE ... - ..$ vertex.names : chr [1:15] "a" "b" "c" "d" ... - > - > # using method for 'igraph' objects - > d2 <- asDF(exIgraph) - Error in matrix(.Call(R_igraph_get_edgelist, graph, TRUE), ncol = 2) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: asDF ... asDF.igraph -> as.data.frame -> -> matrix - Execution halted - ``` - -# invertiforms - -
- -* Version: 0.1.1 -* GitHub: https://github.com/RoheLab/invertiforms -* Source code: https://github.com/cran/invertiforms -* Date/Publication: 2022-11-25 12:40:10 UTC -* Number of recursive dependencies: 50 - -Run `revdepcheck::cloud_details(, "invertiforms")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘invertiforms-Ex.R’ failed - The error most likely occurred in: - - > ### Name: DoubleCenter - > ### Title: Construct and use DoubleCenter transformations - > ### Aliases: DoubleCenter transform,DoubleCenter,sparseMatrix-method - > ### inverse_transform,DoubleCenter,sparseLRMatrix-method - > ### inverse_transform,DoubleCenter,vsp_fa-method - > - > ### ** Examples - ... - - > library(igraphdata) - > - > data("karate", package = "igraphdata") - > - > A <- get.adjacency(karate) - Error in vcount(graph) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: get.adjacency -> get.adjacency.sparse -> vcount - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ▆ - 1. └─igraph::get.adjacency(karate) at test-PerturbedLaplacian.R:6:0 - 2. └─igraph:::get.adjacency.sparse(...) - 3. └─igraph::vcount(graph) - ── Error ('test-RegularizedLaplacian.R:6:1'): (code run outside of `test_that()`) ── - Error in `vcount(graph)`: REAL() can only be applied to a 'numeric', not a 'logical' - Backtrace: - ▆ - 1. └─igraph::get.adjacency(karate) at test-RegularizedLaplacian.R:6:0 - 2. └─igraph:::get.adjacency.sparse(...) - 3. └─igraph::vcount(graph) - - [ FAIL 4 | WARN 0 | SKIP 0 | PASS 0 ] - Error: Test failures - Execution halted - ``` - -# ITNr - -
- -* Version: 0.7.0 -* GitHub: NA -* Source code: https://github.com/cran/ITNr -* Date/Publication: 2023-03-31 14:10:11 UTC -* Number of recursive dependencies: 82 - -Run `revdepcheck::cloud_details(, "ITNr")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ITNr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: ITNproperties - > ### Title: ITN Properties - > ### Aliases: ITNproperties - > - > ### ** Examples - > - > ##Load the network - > data(ELEnet16) - > - > ##Calculate the network properties - > ITNPROP<-ITNproperties(ELEnet16,TRUE) - Error in matrix(.Call(R_igraph_get_edgelist, graph, TRUE), ncol = 2) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: ITNproperties -> cbind -> -> matrix - Execution halted - ``` - -# LEANR - -
- -* Version: 1.4.9 -* GitHub: NA -* Source code: https://github.com/cran/LEANR -* Date/Publication: 2016-11-12 15:47:01 -* Number of recursive dependencies: 64 - -Run `revdepcheck::cloud_details(, "LEANR")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ── Error ('test_output.R:8:1'): (code run outside of `test_that()`) ──────────── - Error in `vcount(graph)`: REAL() can only be applied to a 'numeric', not a 'logical' - Backtrace: - ▆ - 1. └─LEANR::run.lean(...) at test_output.R:8:0 - 2. └─LEANR:::reduce.graph.fromdata(g, ranking, add.scored.genes, keep.nodes.without.scores) - 3. ├─base::intersect(V(g)$name, gene.list.char) - 4. │ ├─base::unique(y[match(as.vector(x), y, 0L)]) - 5. │ └─base::as.vector(x) - 6. └─igraph::V(g) - 7. └─igraph::vcount(graph) - - [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ] - Error: Test failures - Execution halted - ``` - -# leiden - -
- -* Version: 0.4.3 -* GitHub: https://github.com/TomKellyGenetics/leiden -* Source code: https://github.com/cran/leiden -* Date/Publication: 2022-09-10 17:22:53 UTC -* Number of recursive dependencies: 147 - -Run `revdepcheck::cloud_details(, "leiden")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘spelling.R’ - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 16: test_code(NULL, exprs, env) - 17: source_file(path, child_env(env), wrap = wrap) - 18: FUN(X[[i]], ...) - 19: lapply(test_paths, test_one_file, env = env, wrap = wrap) - 20: doTryCatch(return(expr), name, parentenv, handler) - 21: tryCatchOne(expr, names, parentenv, handlers[[1L]]) - 22: tryCatchList(expr, classes, parentenv, handlers) - 23: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL}) - 24: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, wrap = wrap)) - 25: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package) - 26: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package, parallel = parallel) - 27: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed") - 28: test_check("leiden") - An irrecoverable exception occurred. R is aborting now ... - Segmentation fault (core dumped) - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘benchmarking.Rmd’ using knitr - Warning: The closing backticks on line 337 ("```") in benchmarking.Rmd do not match the opening backticks "````" on line 334. You are recommended to fix either the opening or closing delimiter of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). - Warning: The closing backticks on line 400 ("```") in benchmarking.Rmd do not match the opening backticks "````" on line 396. You are recommended to fix either the opening or closing delimiter of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). - Warning: The closing backticks on line 408 ("```") in benchmarking.Rmd do not match the opening backticks "````" on line 404. You are recommended to fix either the opening or closing delimiter of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote). - --- finished re-building ‘benchmarking.Rmd’ - - --- re-building ‘run_bipartite.Rmd’ using knitr - - *** caught segfault *** - ... - zero-length arrow is of indeterminate angle and so skipped - Warning in doTryCatch(return(expr), name, parentenv, handler) : - zero-length arrow is of indeterminate angle and so skipped - --- finished re-building ‘run_multiplex.Rmd’ - - SUMMARY: processing the following file failed: - ‘run_bipartite.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.0Mb - sub-directories of 1Mb or more: - doc 5.9Mb - ``` - -# leidenAlg - -
- -* Version: 1.0.5 -* GitHub: https://github.com/kharchenkolab/leidenAlg -* Source code: https://github.com/cran/leidenAlg -* Date/Publication: 2022-09-30 07:20:02 UTC -* Number of recursive dependencies: 68 - -Run `revdepcheck::cloud_details(, "leidenAlg")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘leidenAlg-Ex.R’ failed - The error most likely occurred in: - - > ### Name: as.dendrogram.fakeCommunities - > ### Title: Returns pre-calculated dendrogram - > ### Aliases: as.dendrogram.fakeCommunities - > - > ### ** Examples - > - > rLeidenComm = suppressWarnings(rleiden.community(exampleGraph, n.cores=1)) - Error in edge_attr_names(graph) : - VECTOR_ELT() can only be applied to a 'list', not a 'environment' - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 2. └─igraph::is_weighted(graph) - 3. ├─"weight" %in% edge_attr_names(graph) - 4. └─igraph::edge_attr_names(graph) - ── Error ('test_functions.R:25:2'): membership.fakeCommunities() functionality ── - Error in `edge_attr_names(graph)`: VECTOR_ELT() can only be applied to a 'list', not a 'environment' - Backtrace: - ▆ - 1. └─leidenAlg::leiden.community(exampleGraph) at test_functions.R:25:8 - 2. └─igraph::is_weighted(graph) - 3. ├─"weight" %in% edge_attr_names(graph) - 4. └─igraph::edge_attr_names(graph) - - [ FAIL 4 | WARN 0 | SKIP 0 | PASS 0 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking for GNU extensions in Makefiles ... NOTE - ``` - GNU make is a SystemRequirements. - ``` - -# leidenbase - -
- -* Version: 0.1.18 -* GitHub: https://github.com/cole-trapnell-lab/leidenbase -* Source code: https://github.com/cran/leidenbase -* Date/Publication: 2023-04-15 09:20:02 UTC -* Number of recursive dependencies: 54 - -Run `revdepcheck::cloud_details(, "leidenbase")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘leidenbase-Ex.R’ failed - The error most likely occurred in: - - > ### Name: leiden_find_partition - > ### Title: Leiden find partition community detection function - > ### Aliases: leiden_find_partition - > - > ### ** Examples - > - > library(igraph) - ... - - > fpath <- system.file( 'testdata', 'igraph_n1500_edgelist.txt.gz', package = 'leidenbase' ) - > zfp <- gzfile(fpath) - > igraph <- read_graph( file = zfp, format='edgelist', n=1500 ) - > res <- leiden_find_partition(igraph=igraph, - + partition_type='CPMVertexPartition', - + resolution_parameter=1e-5) - Error in leiden_find_partition(igraph = igraph, partition_type = "CPMVertexPartition", : - REAL() can only be applied to a 'numeric', not a 'NULL' - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Error in `leidenbase::leiden_find_partition(igraph, partition_type = "RBConfigurationVertexPartition", - node_sizes = nodsiz, seed = 123456, resolution_parameter = 0.5)`: REAL() can only be applied to a 'numeric', not a 'NULL' - Backtrace: - ▆ - 1. └─leidenbase::leiden_find_partition(...) at test-leidenbase.R:224:2 - ── Error ('test-leidenbase.R:245:3'): modularity and significance return values ── - Error in `leidenbase::leiden_find_partition(igraph, partition_type = "CPMVertexPartition", - seed = 123456, resolution_parameter = 0.1)`: REAL() can only be applied to a 'numeric', not a 'NULL' - Backtrace: - ▆ - 1. └─leidenbase::leiden_find_partition(...) at test-leidenbase.R:245:2 - - [ FAIL 11 | WARN 0 | SKIP 0 | PASS 6 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘leidenbase.Rmd’ using rmarkdown - Quitting from lines 87-92 (leidenbase.Rmd) - Error: processing vignette 'leidenbase.Rmd' failed with diagnostics: - REAL() can only be applied to a 'numeric', not a 'NULL' - --- failed re-building ‘leidenbase.Rmd’ - - SUMMARY: processing the following file failed: - ‘leidenbase.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 19.1Mb - sub-directories of 1Mb or more: - libs 18.8Mb - ``` - -# meconetcomp - -
- -* Version: 0.2.0 -* GitHub: https://github.com/ChiLiubio/meconetcomp -* Source code: https://github.com/cran/meconetcomp -* Date/Publication: 2022-10-05 15:20:02 UTC -* Number of recursive dependencies: 147 - -Run `revdepcheck::cloud_details(, "meconetcomp")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘meconetcomp-Ex.R’ failed - The error most likely occurred in: - - > ### Name: cal_module - > ### Title: Assign modules to each network - > ### Aliases: cal_module - > - > ### ** Examples - > - > data(soil_amp_network) - > soil_amp_network <- cal_module(soil_amp_network) - Error in is_directed(network_list[[i]]$res_network) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: cal_module -> is_directed - Execution halted - ``` - -# metanetwork - -
- -* Version: 0.7.0 -* GitHub: https://github.com/MarcOhlmann/metanetwork -* Source code: https://github.com/cran/metanetwork -* Date/Publication: 2022-12-05 14:10:02 UTC -* Number of recursive dependencies: 106 - -Run `revdepcheck::cloud_details(, "metanetwork")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘metanetwork-Ex.R’ failed - The error most likely occurred in: - - > ### Name: append_agg_nets - > ### Title: append aggregated networks - > ### Aliases: append_agg_nets append_agg_nets.metanetwork - > - > ### ** Examples - > - > library(metanetwork) - > data(meta_angola) - > meta_angola = append_agg_nets(meta_angola) - Error in graph_attr(x, name) : - VECTOR_ELT() can only be applied to a 'list', not a 'environment' - Calls: append_agg_nets ... sapply -> lapply -> FUN -> $ -> $.igraph -> graph_attr - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Error in `graph_attr(x, name)`: VECTOR_ELT() can only be applied to a 'list', not a 'environment' - Backtrace: - ▆ - 1. ├─testthat::expect_is(...) at test-vismetaNetwork.R:34:2 - 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") - 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) - 4. └─metanetwork::diff_plot(...) - 5. ├─c(g1$name, g2$name) %in% ... - 6. ├─g1$name - 7. └─igraph:::`$.igraph`(g1, "name") - 8. └─igraph::graph_attr(x, name) - - [ FAIL 16 | WARN 8 | SKIP 0 | PASS 32 ] - Error: Test failures - Execution halted - ``` - -# migraph - -
- -* Version: 0.13.2 -* GitHub: https://github.com/snlab-ch/migraph -* Source code: https://github.com/cran/migraph -* Date/Publication: 2022-12-20 16:20:02 UTC -* Number of recursive dependencies: 138 - -Run `revdepcheck::cloud_details(, "migraph")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘migraph-Ex.R’ failed - The error most likely occurred in: - - > ### Name: add - > ### Title: Adding and copying attributes from one graph to another - > ### Aliases: add add_node_attribute add_tie_attribute copy_node_attributes - > ### join_ties - > - > ### ** Examples - > - > add_node_attribute(mpn_elite_mex, "wealth", 1:35) - Error in igraph::vcount(as_igraph(object)) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: add_node_attribute -> network_nodes -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 8. └─igraph::vertex_attr_names(graph) - ── Error ('test-viz_layout_partition.R:20:3'): concentric layout works ───────── - Error in `vertex_attr_names(graph)`: VECTOR_ELT() can only be applied to a 'list', not a 'environment' - Backtrace: - ▆ - 1. └─migraph::layout_tbl_graph_concentric(ison_southern_women) at test-viz_layout_partition.R:20:2 - 2. ├─migraph::is_twomode(object) - 3. └─migraph:::is_twomode.igraph(object) - 4. └─igraph::is.bipartite(object) - 5. ├─"type" %in% vertex_attr_names(graph) - 6. └─igraph::vertex_attr_names(graph) - - [ FAIL 74 | WARN 0 | SKIP 0 | PASS 99 ] - Error: Test failures - Execution halted - ``` - -# missSBM - -
- -* Version: 1.0.3 -* GitHub: https://github.com/grossSBM/missSBM -* Source code: https://github.com/cran/missSBM -* Date/Publication: 2022-08-23 12:10:06 UTC -* Number of recursive dependencies: 113 - -Run `revdepcheck::cloud_details(, "missSBM")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘missSBM-Ex.R’ failed - The error most likely occurred in: - - > ### Name: frenchblog2007 - > ### Title: Political Blogosphere network prior to 2007 French presidential - > ### election - > ### Aliases: frenchblog2007 - > ### Keywords: datasets - > - > ### ** Examples - ... - > - > data(frenchblog2007) - > igraph::V(frenchblog2007)$party - This graph was created by an old(er) igraph version. - Call upgrade_graph() on it to use with the current igraph version - For now we convert it on the fly... - Error in vcount(graph) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: -> vcount - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘spelling.R’ - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 396 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Error ('test-consistency-on-fully-observed-network.R:9:3'): SimpleSBM_fit_missSBM and missSBMfit are coherent ── - Error in `vcount(graph)`: REAL() can only be applied to a 'numeric', not a 'logical' - Backtrace: - ▆ - 1. ├─war$belligerent %>% igraph::as_adj() at test-consistency-on-fully-observed-network.R:9:2 - 2. └─igraph::as_adj(.) - 3. └─igraph:::get.adjacency.sparse(...) - 4. └─igraph::vcount(graph) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 396 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘case_study_war_networks.Rmd’ using rmarkdown - Quitting from lines 60-65 (case_study_war_networks.Rmd) - Error: processing vignette 'case_study_war_networks.Rmd' failed with diagnostics: - REAL() can only be applied to a 'numeric', not a 'logical' - --- failed re-building ‘case_study_war_networks.Rmd’ - - SUMMARY: processing the following file failed: - ‘case_study_war_networks.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 10.6Mb - sub-directories of 1Mb or more: - libs 8.6Mb - ``` - -# molnet - -
- -* Version: 0.1.0 -* GitHub: NA -* Source code: https://github.com/cran/molnet -* Date/Publication: 2021-08-06 08:30:02 UTC -* Number of recursive dependencies: 123 - -Run `revdepcheck::cloud_details(, "molnet")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘molnet-Ex.R’ failed - The error most likely occurred in: - - > ### Name: determine_drug_targets - > ### Title: Determine drug target nodes in network - > ### Aliases: determine_drug_targets - > - > ### ** Examples - > - > data(drug_gene_interactions) - ... - + combined_graphs[["annotations"]], - + drug_target_interaction, - + settings) - This graph was created by an old(er) igraph version. - Call upgrade_graph() on it to use with the current igraph version - For now we convert it on the fly... - Error in vcount(graph) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: determine_drug_targets -> find_targets -> %in% -> -> vcount - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘Molnet_Vignette.Rmd’ using rmarkdown - Quitting from lines 310-312 (Molnet_Vignette.Rmd) - Error: processing vignette 'Molnet_Vignette.Rmd' failed with diagnostics: - VECTOR_ELT() can only be applied to a 'list', not a 'environment' - --- failed re-building ‘Molnet_Vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘Molnet_Vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# motifr - -
- -* Version: 1.0.0 -* GitHub: https://github.com/marioangst/motifr -* Source code: https://github.com/cran/motifr -* Date/Publication: 2020-12-10 15:40:02 UTC -* Number of recursive dependencies: 121 - -Run `revdepcheck::cloud_details(, "motifr")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘motifr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: directed_dummy_net - > ### Title: Two-level directed network dummy example - > ### Aliases: directed_dummy_net - > ### Keywords: datasets - > - > ### ** Examples - > - > plot_mnet(directed_dummy_net) - Error in vertex.attributes(graph) : - VECTOR_ELT() can only be applied to a 'list', not a 'environment' - Calls: plot_mnet ... node_tibble -> as_tibble -> vertex_attr -> vertex.attributes - Execution halted - ``` - -# multinets - -
- -* Version: 0.2.2 -* GitHub: https://github.com/neylsoncrepalde/multinets -* Source code: https://github.com/cran/multinets -* Date/Publication: 2019-12-14 17:20:03 UTC -* Number of recursive dependencies: 72 - -Run `revdepcheck::cloud_details(, "multinets")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘multinets-Ex.R’ failed - The error most likely occurred in: - - > ### Name: extract_highlevel - > ### Title: Extract the high level of a multilevel network - > ### Aliases: extract_highlevel - > - > ### ** Examples - > - > organizations <- extract_highlevel(linked_sim) - Error in vertex_attr_names(graph) : - VECTOR_ELT() can only be applied to a 'list', not a 'environment' - Calls: extract_highlevel ... is_multilevel -> -> %in% -> vertex_attr_names - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 11. └─igraph::is_bipartite(x) - 12. ├─"type" %in% vertex_attr_names(graph) - 13. └─igraph::vertex_attr_names(graph) - ── Error ('test-mode_transformation.R:15:3'): mode transformation works without specifying 'which' ── - Error in `vertex_attr_names(graph)`: VECTOR_ELT() can only be applied to a 'list', not a 'environment' - Backtrace: - ▆ - 1. └─igraph::bipartite_projection(g.bip) at test-mode_transformation.R:15:2 - 2. └─igraph:::handle_vertex_type_arg(types, graph) - 3. ├─"type" %in% vertex_attr_names(graph) - 4. └─igraph::vertex_attr_names(graph) - - [ FAIL 4 | WARN 0 | SKIP 0 | PASS 10 ] - Error: Test failures - Execution halted - ``` - -# mwcsr - -
- -* Version: 0.1.6 -* GitHub: https://github.com/ctlab/mwcsr -* Source code: https://github.com/cran/mwcsr -* Date/Publication: 2022-07-12 17:50:02 UTC -* Number of recursive dependencies: 91 - -Run `revdepcheck::cloud_details(, "mwcsr")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘mwcsr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: get_instance_type - > ### Title: Check the type and the validity of an MWCS instance - > ### Aliases: get_instance_type - > - > ### ** Examples - > - > data(mwcs_example) - > get_instance_type(mwcs_example) - Error in igraph::is_directed(g) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: get_instance_type -> check_graph -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ▆ - 1. └─mwcsr::solve_mwcsp(solver, sgmwcs_small_instance) at test_virgo.R:48:4 - 2. └─mwcsr:::check_graph(instance) - 3. └─igraph::is_directed(g) - ── Error ('test_virgo.R:80:5'): heuristic virgo_solver works on SGMWCS ───────── - Error in `graph_attr(x, name)`: VECTOR_ELT() can only be applied to a 'list', not a 'environment' - Backtrace: - ▆ - 1. ├─si$signals at test_virgo.R:80:4 - 2. └─igraph:::`$.igraph`(si, signals) at test_virgo.R:80:4 - 3. └─igraph::graph_attr(x, name) - - [ FAIL 9 | WARN 1 | SKIP 6 | PASS 30 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘tutorial.Rmd’ using rmarkdown - Quitting from lines 43-46 (tutorial.Rmd) - Error: processing vignette 'tutorial.Rmd' failed with diagnostics: - REAL() can only be applied to a 'numeric', not a 'logical' - --- failed re-building ‘tutorial.Rmd’ - - SUMMARY: processing the following file failed: - ‘tutorial.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 17.4Mb - sub-directories of 1Mb or more: - java 2.5Mb - libs 14.2Mb - ``` - -# nda - -
- -* Version: 0.1.6 -* GitHub: https://github.com/kzst/nda -* Source code: https://github.com/cran/nda -* Date/Publication: 2022-10-14 13:10:02 UTC -* Number of recursive dependencies: 81 - -Run `revdepcheck::cloud_details(, "nda")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘nda-Ex.R’ failed - The error most likely occurred in: - - > ### Name: biplot.nda - > ### Title: Biplot function for Network-based Dimensionality Reduction and - > ### Analysis (NDA) - > ### Aliases: biplot.nda - > ### Keywords: plot - > - > ### ** Examples - ... - > - > # Biplot function without feature selection - > - > data("CrimesUSA1990.X") - > df<-CrimesUSA1990.X - > p<-ndr(df) - Error in find_partition(graph, igraph::E(graph)$weight, resolution, n.iterations) : - REAL() can only be applied to a 'numeric', not a 'NULL' - Calls: ndr -> -> find_partition - Execution halted - ``` - -# netplot - -
- -* Version: 0.1-1 -* GitHub: https://github.com/USCCANA/netplot -* Source code: https://github.com/cran/netplot -* Date/Publication: 2021-06-16 07:10:02 UTC -* Number of recursive dependencies: 82 - -Run `revdepcheck::cloud_details(, "netplot")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘netplot-Ex.R’ failed - The error most likely occurred in: - - > ### Name: make_colors - > ### Title: Create a vector of colors for vertices and edges - > ### Aliases: make_colors make_edges_colors make_vertex_colors - > - > ### ** Examples - > - > - > data(UKfaculty, package="igraphdata") - > col <- make_vertex_colors(UKfaculty, "Group") - Error in igraph::vertex_attr(x, attr) : - VECTOR_ELT() can only be applied to a 'list', not a 'environment' - Calls: make_vertex_colors -> get_vertex_attr -> - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘base-and-grid.Rmd’ using rmarkdown - --- finished re-building ‘base-and-grid.Rmd’ - - --- re-building ‘examples.Rmd’ using rmarkdown - Quitting from lines 32-43 (examples.Rmd) - Error: processing vignette 'examples.Rmd' failed with diagnostics: - REAL() can only be applied to a 'numeric', not a 'logical' - --- failed re-building ‘examples.Rmd’ - - SUMMARY: processing the following file failed: - ‘examples.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# netrankr - -
- -* Version: 1.2.0 -* GitHub: https://github.com/schochastics/netrankr -* Source code: https://github.com/cran/netrankr -* Date/Publication: 2022-09-26 21:00:02 UTC -* Number of recursive dependencies: 65 - -Run `revdepcheck::cloud_details(, "netrankr")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘netrankr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: aggregate_positions - > ### Title: Quantification of (indirect) relations - > ### Aliases: aggregate_positions - > - > ### ** Examples - > - > library(igraph) - ... - > - > data("dbces11") - > # degree - > dbces11 %>% - + indirect_relations(type = "adjacency") %>% - + aggregate_positions(type = "sum") - Error in igraph::is_directed(g) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: %>% ... aggregate_positions -> indirect_relations -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Error ('test_dominance.R:11:3'): neighborhood-inclusion is correct ────────── - Error in `igraph::is_directed(g)`: REAL() can only be applied to a 'numeric', not a 'logical' - Backtrace: - ▆ - 1. ├─testthat::expect_equal(...) at test_dominance.R:11:2 - 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") - 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) - 4. └─netrankr::neighborhood_inclusion(dbces11, sparse = FALSE) - 5. └─igraph::is_directed(g) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 78 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘benchmarks.Rmd’ using rmarkdown - --- finished re-building ‘benchmarks.Rmd’ - - --- re-building ‘centrality_indices.Rmd’ using rmarkdown - --- finished re-building ‘centrality_indices.Rmd’ - - --- re-building ‘indirect_relations.Rmd’ using rmarkdown - Quitting from lines 61-79 (indirect_relations.Rmd) - Error: processing vignette 'indirect_relations.Rmd' failed with diagnostics: - ... - REAL() can only be applied to a 'numeric', not a 'logical' - --- failed re-building ‘use_case.Rmd’ - - SUMMARY: processing the following files failed: - ‘indirect_relations.Rmd’ ‘neighborhood_inclusion.Rmd’ - ‘partial_centrality.Rmd’ ‘positional_dominance.Rmd’ - ‘probabilistic_cent.Rmd’ ‘threshold_graph.Rmd’ ‘use_case.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 12.5Mb - sub-directories of 1Mb or more: - doc 1.6Mb - libs 10.6Mb - ``` - -# netseg - -
- -* Version: 1.0-1 -* GitHub: https://github.com/mbojan/netseg -* Source code: https://github.com/cran/netseg -* Date/Publication: 2022-08-25 12:10:06 UTC -* Number of recursive dependencies: 61 - -Run `revdepcheck::cloud_details(, "netseg")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘netseg-Ex.R’ failed - The error most likely occurred in: - - > ### Name: EF3 - > ### Title: Example data from Figure III of Echenique and Fryer (2006) - > ### Aliases: EF3 - > ### Keywords: datasets - > - > ### ** Examples - > - ... - + vertex.color = igraph::V(EF3)$type+1, - + vertex.label.family = "", - + sub = "Source: Echenique & Fryer (2006)", - + main = "Neighborhood racial segregation\n in a fictional city" - + ) - + } - Error in vcount(graph) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: plot -> plot.igraph -> vcount - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 7. │ │ └─base::withVisible(code) - 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) - 9. ├─netseg::smi(as.directed(WhiteKinship), "gender") - 10. └─igraph::as.directed(WhiteKinship) - ── Error ('test-ssi.R:4:3'): values of ssi for EF3 data correspond to values from the paper ── - Error in `igraph::is.directed(g)`: REAL() can only be applied to a 'numeric', not a 'logical' - Backtrace: - ▆ - 1. └─netseg::ssi(EF3, "race") at test-ssi.R:4:2 - 2. ├─base::stopifnot(!igraph::is.directed(g), !igraph::any_multiple(g)) - 3. └─igraph::is.directed(g) - - [ FAIL 15 | WARN 0 | SKIP 0 | PASS 59 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘netseg.Rmd’ using rmarkdown - Quitting from lines 46-47 (netseg.Rmd) - Error: processing vignette 'netseg.Rmd' failed with diagnostics: - REAL() can only be applied to a 'numeric', not a 'logical' - --- failed re-building ‘netseg.Rmd’ - - SUMMARY: processing the following file failed: - ‘netseg.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# nett - -
- -* Version: 1.0.0 -* GitHub: https://github.com/aaamini/nett -* Source code: https://github.com/cran/nett -* Date/Publication: 2022-11-09 10:50:05 UTC -* Number of recursive dependencies: 97 - -Run `revdepcheck::cloud_details(, "nett")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘nett-Ex.R’ failed - The error most likely occurred in: - - > ### Name: fast_cpl - > ### Title: CPL algorithm for community detection (fast) - > ### Aliases: fast_cpl - > ### Keywords: comm_detect - > - > ### ** Examples - > - > head(fast_cpl(igraph::as_adj(polblogs), 2), 50) - Error in vcount(graph) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: head ... spec_repr -> -> get.adjacency.sparse -> vcount - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘Community_Detection.Rmd’ using rmarkdown - --- finished re-building ‘Community_Detection.Rmd’ - - --- re-building ‘Visualization.Rmd’ using rmarkdown - Quitting from lines 99-105 (Visualization.Rmd) - Error: processing vignette 'Visualization.Rmd' failed with diagnostics: - REAL() can only be applied to a 'numeric', not a 'logical' - --- failed re-building ‘Visualization.Rmd’ - ... - --- finished re-building ‘explore-comm.Rmd’ - - --- re-building ‘hard_dcsbm_testing.Rmd’ using rmarkdown - --- finished re-building ‘hard_dcsbm_testing.Rmd’ - - SUMMARY: processing the following file failed: - ‘Visualization.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# poppr - -
- -* Version: 2.9.4 -* GitHub: https://github.com/grunwaldlab/poppr -* Source code: https://github.com/cran/poppr -* Date/Publication: 2023-03-23 03:20:02 UTC -* Number of recursive dependencies: 98 - -Run `revdepcheck::cloud_details(, "poppr")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘test-all.R’ - Running the tests in ‘tests/test-all.R’ failed. - Last 13 lines of output: - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Failure ('test-msn.R:445:3'): Minimum spanning networks can subset populations ── - ucl(bmsn) not identical to ucl(pmsn). - Component 10: Component 3: 1 string mismatch - ── Failure ('test-msn.R:449:3'): Minimum spanning networks can subset populations ── - ucl(bmsn12) not identical to ucl(pmsn12). - Component 10: Component 3: 1 string mismatch - ── Failure ('test-msn.R:453:3'): Minimum spanning networks can subset populations ── - ucl(bmsn1) not identical to ucl(pmsn1). - Component 10: Component 3: 1 string mismatch - - [ FAIL 3 | WARN 0 | SKIP 181 | PASS 375 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘algo.Rnw’ using knitr - Error: processing vignette 'algo.Rnw' failed with diagnostics: - Running 'texi2dvi' on 'algo.tex' failed. - LaTeX errors: - ! LaTeX Error: File `colortbl.sty' not found. - - Type X to quit or to proceed, - or enter new name. (Default extension: sty) - ... - l.270 \long - \def\@secondoffive#1#2#3#4#5{#2}^^M - ! ==> Fatal error occurred, no output PDF file produced! - --- failed re-building ‘algo.Rnw’ - - SUMMARY: processing the following file failed: - ‘algo.Rnw’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# psSubpathway - -
- -* Version: 0.1.1 -* GitHub: NA -* Source code: https://github.com/cran/psSubpathway -* Date/Publication: 2019-10-02 12:40:02 UTC -* Number of recursive dependencies: 105 - -Run `revdepcheck::cloud_details(, "psSubpathway")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘psSubpathway-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plotSpwNetmap - > ### Title: Polt a subpathway network map - > ### Aliases: plotSpwNetmap - > - > ### ** Examples - > - > # load depend package. - ... - The following object is masked from ‘package:base’: - - union - - > # plot network graph of the subpathway 00982_2 - > plotSpwNetmap(spwid="00982_2",layout=layout_nicely) - Error in vcount(graph) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: plotSpwNetmap -> plot -> plot.igraph -> vcount - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘vignette.Rmd’ using rmarkdown - Quitting from lines 173-178 (vignette.Rmd) - Error: processing vignette 'vignette.Rmd' failed with diagnostics: - REAL() can only be applied to a 'numeric', not a 'logical' - --- failed re-building ‘vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# rmonad - -
- -* Version: 0.7.0 -* GitHub: https://github.com/arendsee/rmonad -* Source code: https://github.com/cran/rmonad -* Date/Publication: 2020-02-14 07:00:02 UTC -* Number of recursive dependencies: 81 - -Run `revdepcheck::cloud_details(, "rmonad")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘rmonad-Ex.R’ failed - The error most likely occurred in: - - > ### Name: missues - > ### Title: Tabulates all errors, warnings and notes - > ### Aliases: missues - > - > ### ** Examples - > - > data(gff) - > m <- gff$good_result - > missues(m) - This graph was created by an old(er) igraph version. - Call upgrade_graph() on it to use with the current igraph version - For now we convert it on the fly... - Error in vcount(graph) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: missues ... .process_tag_and_index -> .get_ids -> -> vcount - Execution halted - ``` - -# rsetse - -
- -* Version: 0.5.0 -* GitHub: https://github.com/JonnoB/rSETSe -* Source code: https://github.com/cran/rsetse -* Date/Publication: 2021-06-11 10:00:02 UTC -* Number of recursive dependencies: 81 - -Run `revdepcheck::cloud_details(, "rsetse")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘rsetse-Ex.R’ failed - The error most likely occurred in: - - > ### Name: calc_tension_strain_hd - > ### Title: Calculate line tension and strain from the topology and node - > ### embeddings for high dimensional feature networks - > ### Aliases: calc_tension_strain_hd - > - > ### ** Examples - > - ... - > g <- biconnected_network %>% - + prepare_edges(., k = 1000) %>% - + #prepare the continuous features as normal - + prepare_continuous_force(., node_names = "name", force_var = "force") %>% - + #prepare the categorical features as normal - + prepare_categorical_force(., node_names = "name", force_var = "group") - Error in igraph::as_data_frame(g, what = "both") : - VECTOR_ELT() can only be applied to a 'list', not a 'environment' - Calls: %>% ... prepare_continuous_force -> prepare_edges -> - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘Categorical-and-continuous-features.Rmd’ using rmarkdown - Quitting from lines 31-35 (Categorical-and-continuous-features.Rmd) - Error: processing vignette 'Categorical-and-continuous-features.Rmd' failed with diagnostics: - VECTOR_ELT() can only be applied to a 'list', not a 'environment' - --- failed re-building ‘Categorical-and-continuous-features.Rmd’ - - --- re-building ‘separate-peels-quintet.Rmd’ using rmarkdown - --- finished re-building ‘separate-peels-quintet.Rmd’ - - SUMMARY: processing the following file failed: - ‘Categorical-and-continuous-features.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# rSpectral - -
- -* Version: 1.0.0.10 -* GitHub: https://github.com/cmclean5/rSpectral -* Source code: https://github.com/cran/rSpectral -* Date/Publication: 2023-01-18 12:00:02 UTC -* Number of recursive dependencies: 44 - -Run `revdepcheck::cloud_details(, "rSpectral")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘rSpectral-Ex.R’ failed - The error most likely occurred in: - - > ### Name: spectral_igraph_communities - > ### Title: Spectral clustering for 'igraph' objects - > ### Aliases: spectral_igraph_communities - > - > ### ** Examples - > - > data(karate,package='igraphdata') - > c<-spectral_igraph_communities(karate) - Error in matrix(.Call(R_igraph_get_edgelist, graph, TRUE), ncol = 2) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: spectral_igraph_communities ... spectral_igraph_membership -> as.data.frame -> -> matrix - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 4. └─igraph::get.edgelist(g, names = TRUE) - 5. └─base::matrix(.Call(R_igraph_get_edgelist, graph, TRUE), ncol = 2) - ── Error ('test-igraph.R:24:3'): membership fix_neig=1 is correct ────────────── - Error in `matrix(.Call(R_igraph_get_edgelist, graph, TRUE), ncol = 2)`: REAL() can only be applied to a 'numeric', not a 'logical' - Backtrace: - ▆ - 1. └─rSpectral::spectral_igraph_communities(karate, fix_neig = 1) at test-igraph.R:24:2 - 2. └─rSpectral::spectral_igraph_membership(...) - 3. ├─base::as.data.frame(igraph::get.edgelist(g, names = TRUE)) - 4. └─igraph::get.edgelist(g, names = TRUE) - 5. └─base::matrix(.Call(R_igraph_get_edgelist, graph, TRUE), ncol = 2) - - [ FAIL 3 | WARN 0 | SKIP 0 | PASS 4 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.9Mb - sub-directories of 1Mb or more: - libs 5.2Mb - ``` - -# sbm - -
- -* Version: 0.4.5 -* GitHub: https://github.com/GrossSBM/sbm -* Source code: https://github.com/cran/sbm -* Date/Publication: 2023-01-09 10:30:02 UTC -* Number of recursive dependencies: 108 - -Run `revdepcheck::cloud_details(, "sbm")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘sbm-Ex.R’ failed - The error most likely occurred in: - - > ### Name: war - > ### Title: War data set - > ### Aliases: war - > ### Keywords: datasets - > - > ### ** Examples - > - > data(war) - > class(war$belligerent) - [1] "igraph" - > igraph::gorder(war$alliance) - Error in igraph::gorder(war$alliance) : - REAL() can only be applied to a 'numeric', not a 'logical' - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘Multipartite_EcologicalNetwork.Rmd’ using rmarkdown - --- finished re-building ‘Multipartite_EcologicalNetwork.Rmd’ - - --- re-building ‘MultiplexNetwork_principle.Rmd’ using rmarkdown - --- finished re-building ‘MultiplexNetwork_principle.Rmd’ - - --- re-building ‘Multiplex_allianceNwar_case_study.Rmd’ using rmarkdown - Quitting from lines 56-59 (Multiplex_allianceNwar_case_study.Rmd) - ... - --- failed re-building ‘Multiplex_allianceNwar_case_study.Rmd’ - - --- re-building ‘SBM_fungus_tree_network.Rmd’ using rmarkdown - --- finished re-building ‘SBM_fungus_tree_network.Rmd’ - - SUMMARY: processing the following file failed: - ‘Multiplex_allianceNwar_case_study.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# sccore - -
- -* Version: 1.0.3 -* GitHub: https://github.com/kharchenkolab/sccore -* Source code: https://github.com/cran/sccore -* Date/Publication: 2023-03-13 00:00:02 UTC -* Number of recursive dependencies: 76 - -Run `revdepcheck::cloud_details(, "sccore")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘sccore-Ex.R’ failed - The error most likely occurred in: - - > ### Name: graphToAdjList - > ### Title: Convert igraph graph into an adjacency list - > ### Aliases: graphToAdjList - > - > ### ** Examples - > - > library(dplyr) - ... - - The following objects are masked from ‘package:base’: - - intersect, setdiff, setequal, union - - > edge.list.fact <- igraph::as_edgelist(conosGraph) %>% as_factor() - Error in matrix(.Call(R_igraph_get_edgelist, graph, TRUE), ncol = 2) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: %>% -> as_factor -> -> matrix - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 2. ├─sccore::as_factor(.) - 3. └─igraph::as_edgelist(conosGraph) - 4. └─base::matrix(.Call(R_igraph_get_edgelist, graph, TRUE), ncol = 2) - ── Error ('test_helpers.R:43:2'): graphToAdjList() functionality ─────────────── - Error in `matrix(.Call(R_igraph_get_edgelist, graph, TRUE), ncol = 2)`: REAL() can only be applied to a 'numeric', not a 'logical' - Backtrace: - ▆ - 1. ├─igraph::as_edgelist(conosGraph) %>% as_factor() at test_helpers.R:43:8 - 2. ├─sccore::as_factor(.) - 3. └─igraph::as_edgelist(conosGraph) - 4. └─base::matrix(.Call(R_igraph_get_edgelist, graph, TRUE), ncol = 2) - - [ FAIL 4 | WARN 0 | SKIP 0 | PASS 2 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 7.9Mb - sub-directories of 1Mb or more: - libs 7.1Mb - ``` - -# ScorePlus - -
- -* Version: 0.1 -* GitHub: NA -* Source code: https://github.com/cran/ScorePlus -* Date/Publication: 2019-06-14 08:40:03 UTC -* Number of recursive dependencies: 16 - -Run `revdepcheck::cloud_details(, "ScorePlus")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ScorePlus-Ex.R’ failed - The error most likely occurred in: - - > ### Name: SCORE - > ### Title: community detection method called SCORE Spectral Clustering On - > ### Ratios-of-Eigenvectors (SCORE) - > ### Aliases: SCORE - > - > ### ** Examples - > - ... - The following object is masked from ‘package:base’: - - union - - > data('karate') - > A = get.adjacency(karate) - Error in vcount(graph) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: get.adjacency -> get.adjacency.sparse -> vcount - Execution halted - ``` - -## In both - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# secrlinear - -
- -* Version: 1.1.4 -* GitHub: NA -* Source code: https://github.com/cran/secrlinear -* Date/Publication: 2021-05-04 04:50:05 UTC -* Number of recursive dependencies: 69 - -Run `revdepcheck::cloud_details(, "secrlinear")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘secrlinear-Ex.R’ failed - The error most likely occurred in: - - > ### Name: Arvicola - > ### Title: Water Vole Capture Dataset - > ### Aliases: arvicola - > ### Keywords: datasets - > - > ### ** Examples - > - ... - > - > ## for speed, pre-compute distance matrix - > userd <- networkdistance (traps(arvicola), glymemask, glymemask) - This graph was created by an old(er) igraph version. - Call upgrade_graph() on it to use with the current igraph version - For now we convert it on the fly... - Error in vcount(graph) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: networkdistance -> cbind -> V -> vcount - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘secrlinear-vignette.Rmd’ using rmarkdown - A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TinyTeX with tinytex::reinstall_tinytex(repository = "illinois"). - - tlmgr: Local TeX Live (2022) is older than remote repository (2023). - Cross release updates are only supported with - update-tlmgr-latest(.sh/.exe) --update - See https://tug.org/texlive/upgrade.html for details. - Warning in system2("tlmgr", args, ...) : - ... - - Error: processing vignette 'secrlinear-vignette.Rmd' failed with diagnostics: - LaTeX failed to compile /tmp/workdir/secrlinear/new/secrlinear.Rcheck/vign_test/secrlinear/vignettes/secrlinear-vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See secrlinear-vignette.log for more info. - --- failed re-building ‘secrlinear-vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘secrlinear-vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# shazam - -
- -* Version: 1.1.2 -* GitHub: NA -* Source code: https://github.com/cran/shazam -* Date/Publication: 2022-10-01 07:30:02 UTC -* Number of recursive dependencies: 124 - -Run `revdepcheck::cloud_details(, "shazam")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘shazam-Ex.R’ failed - The error most likely occurred in: - - > ### Name: makeGraphDf - > ### Title: Build a data.frame from a ChangeoClone and an igraph object - > ### containing a clonal lineage - > ### Aliases: makeGraphDf - > - > ### ** Examples - > - > # Load and subset example data - > data(ExampleDb, package = "alakazam") - > data(ExampleTrees, package = "alakazam") - > graph <- ExampleTrees[[17]] - > db <- subset(ExampleDb, clone_id == graph$clone) - Error in graph_attr(x, name) : - VECTOR_ELT() can only be applied to a 'list', not a 'environment' - Calls: subset ... subset.data.frame -> eval -> eval -> $ -> $.igraph -> graph_attr - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘Baseline-Vignette.Rmd’ using rmarkdown - A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TinyTeX with tinytex::reinstall_tinytex(repository = "illinois"). - - tlmgr: Local TeX Live (2022) is older than remote repository (2023). - Cross release updates are only supported with - update-tlmgr-latest(.sh/.exe) --update - See https://tug.org/texlive/upgrade.html for details. - Warning in system2("tlmgr", args, ...) : - running command ''tlmgr' search --file --global '/grffile.sty'' had status 1 - ... - LaTeX failed to compile /tmp/workdir/shazam/new/shazam.Rcheck/vign_test/shazam/vignettes/Targeting-Vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Targeting-Vignette.log for more info. - --- failed re-building ‘Targeting-Vignette.Rmd’ - - SUMMARY: processing the following files failed: - ‘Baseline-Vignette.Rmd’ ‘DistToNearest-Vignette.Rmd’ - ‘Mutation-Vignette.Rmd’ ‘Shmulate-Vignette.Rmd’ - ‘Targeting-Vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# sigmajs - -
- -* Version: 0.1.5 -* GitHub: https://github.com/JohnCoene/sigmajs -* Source code: https://github.com/cran/sigmajs -* Date/Publication: 2020-06-18 18:10:02 UTC -* Number of recursive dependencies: 76 - -Run `revdepcheck::cloud_details(, "sigmajs")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - > test_check("sigmajs") - Found # 4 clusters - [ FAIL 1 | WARN 8 | SKIP 0 | PASS 64 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Error ('test-formats.R:21:3'): igraph ─────────────────────────────────────── - Error in `vcount(graph)`: REAL() can only be applied to a 'numeric', not a 'logical' - Backtrace: - ▆ - 1. └─igraph::layout_with_fr(lesmis_igraph) at test-formats.R:21:2 - 2. └─igraph::vcount(graph) - - [ FAIL 1 | WARN 8 | SKIP 0 | PASS 64 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 28 marked UTF-8 strings - ``` - -# signnet - -
- -* Version: 1.0.1 -* GitHub: https://github.com/schochastics/signnet -* Source code: https://github.com/cran/signnet -* Date/Publication: 2023-01-27 13:40:02 UTC -* Number of recursive dependencies: 104 - -Run `revdepcheck::cloud_details(, "signnet")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘signnet-Ex.R’ failed - The error most likely occurred in: - - > ### Name: eigen_centrality_signed - > ### Title: Signed Eigenvector centrality - > ### Aliases: eigen_centrality_signed - > - > ### ** Examples - > - > library(igraph) - ... - The following object is masked from ‘package:base’: - - union - - > data("tribes") - > eigen_centrality_signed(tribes) - Error in igraph::edge_attr_names(g) : - VECTOR_ELT() can only be applied to a 'list', not a 'environment' - Calls: eigen_centrality_signed -> is_signed -> %in% -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 2. └─signnet::is_signed(g) - 3. ├─"sign" %in% igraph::edge_attr_names(g) - 4. └─igraph::edge_attr_names(g) - ── Error ('test-blockmodel.R:25:3'): general blockmodeling works ─────────────── - Error in `igraph::edge_attr_names(g)`: VECTOR_ELT() can only be applied to a 'list', not a 'environment' - Backtrace: - ▆ - 1. └─signnet::signed_blockmodel_general(...) at test-blockmodel.R:25:2 - 2. └─signnet::is_signed(g) - 3. ├─"sign" %in% igraph::edge_attr_names(g) - 4. └─igraph::edge_attr_names(g) - - [ FAIL 3 | WARN 0 | SKIP 0 | PASS 86 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘blockmodeling.Rmd’ using rmarkdown - Quitting from lines 56-61 (blockmodeling.Rmd) - Error: processing vignette 'blockmodeling.Rmd' failed with diagnostics: - VECTOR_ELT() can only be applied to a 'list', not a 'environment' - --- failed re-building ‘blockmodeling.Rmd’ - - --- re-building ‘centrality.Rmd’ using rmarkdown - --- finished re-building ‘centrality.Rmd’ - - ... - Quitting from lines 79-83 (structural_balance.Rmd) - Error: processing vignette 'structural_balance.Rmd' failed with diagnostics: - VECTOR_ELT() can only be applied to a 'list', not a 'environment' - --- failed re-building ‘structural_balance.Rmd’ - - SUMMARY: processing the following files failed: - ‘blockmodeling.Rmd’ ‘signed_networks.Rmd’ ‘structural_balance.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 7.7Mb - sub-directories of 1Mb or more: - libs 6.1Mb - ``` - -# SNscan - -
- -* Version: 1.0 -* GitHub: NA -* Source code: https://github.com/cran/SNscan -* Date/Publication: 2016-01-19 13:09:28 -* Number of recursive dependencies: 11 - -Run `revdepcheck::cloud_details(, "SNscan")` for more info - -
- -## Newly broken - -* checking examples ... ERROR +* checking examples ... ERROR ``` Running examples in ‘SNscan-Ex.R’ failed The error most likely occurred in: @@ -3318,424 +694,9 @@ Run `revdepcheck::cloud_details(, "SNscan")` for more info > ks=network.scan(g=karate,radius=3,attribute=NULL, + model="pois.stat",pattern="structure") Error in is_directed(graph) : - REAL() can only be applied to a 'numeric', not a 'logical' + This graph was created by a now unsupported old igraph version. + Call upgrade_version() before using igraph functions on that object. Calls: network.scan -> shortest.paths -> is_directed Execution halted ``` -# SOMbrero - -
- -* Version: 1.4-1 -* GitHub: https://github.com/tuxette/sombrero -* Source code: https://github.com/cran/SOMbrero -* Date/Publication: 2022-01-03 17:10:08 UTC -* Number of recursive dependencies: 110 - -Run `revdepcheck::cloud_details(, "SOMbrero")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘SOMbrero-Ex.R’ failed - The error most likely occurred in: - - > ### Name: projectIGraph - > ### Title: Compute the projection of a graph on a grid - > ### Aliases: projectIGraph projectIGraph.somRes - > - > ### ** Examples - > - > data(lesmis) - > set.seed(7383) - > mis.som <- trainSOM(x.data=dissim.lesmis, type="relational", nb.save=10) - > proj.lesmis <- projectIGraph(mis.som, lesmis) - Error in gorder(init.graph) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: projectIGraph -> projectIGraph.somRes -> gorder - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘a-doc-SOMbrero-package.Rmd’ using knitr - --- finished re-building ‘a-doc-SOMbrero-package.Rmd’ - - --- re-building ‘b-doc-grids.Rmd’ using knitr - --- finished re-building ‘b-doc-grids.Rmd’ - - --- re-building ‘c-doc-numericSOM.Rmd’ using knitr - Warning in wordcloud_boxes(data_points = points_valid_first, boxes = boxes, : - Some words could not fit on page. They have been placed at their original positions. - ... - Quitting from lines 41-100 (e-doc-relationalSOM.Rmd) - Error: processing vignette 'e-doc-relationalSOM.Rmd' failed with diagnostics: - REAL() can only be applied to a 'numeric', not a 'logical' - --- failed re-building ‘e-doc-relationalSOM.Rmd’ - - SUMMARY: processing the following file failed: - ‘e-doc-relationalSOM.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# spreadr - -
- -* Version: 0.2.0 -* GitHub: NA -* Source code: https://github.com/cran/spreadr -* Date/Publication: 2021-05-11 06:50:02 UTC -* Number of recursive dependencies: 94 - -Run `revdepcheck::cloud_details(, "spreadr")` for more info - -
- -## Newly broken - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘spreadr_vignette.Rmd’ using rmarkdown - Quitting from lines 78-81 (spreadr_vignette.Rmd) - Error: processing vignette 'spreadr_vignette.Rmd' failed with diagnostics: - REAL() can only be applied to a 'numeric', not a 'logical' - --- failed re-building ‘spreadr_vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘spreadr_vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘extrafont’ ‘ggplot2’ - All declared Imports should be used. - ``` - -# SubpathwayLNCE - -
- -* Version: 1.0 -* GitHub: NA -* Source code: https://github.com/cran/SubpathwayLNCE -* Date/Publication: 2016-01-19 08:17:59 -* Number of recursive dependencies: 13 - -Run `revdepcheck::cloud_details(, "SubpathwayLNCE")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘SubpathwayLNCE.Rnw’ - ... - - > g2 <- GetExampleData(exampleData = "g2") - - > LncGenePairs <- GetExampleData(exampleData = "LncGenePairs") - - > interUMGraph <- getInteGraphList(g2[42:45], LncGenePairs) - - When sourcing ‘SubpathwayLNCE.R’: - Error: REAL() can only be applied to a 'numeric', not a 'logical' - Execution halted - - ‘SubpathwayLNCE.Rnw’... failed - ``` - -## In both - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘SubpathwayLNCE.Rnw’ using Sweave - Loading required package: igraph - - Attaching package: ‘igraph’ - - The following objects are masked from ‘package:stats’: - - decompose, spectrum - - ... - Error in vcount(graphList[[t]]) : - REAL() can only be applied to a 'numeric', not a 'logical' - - --- failed re-building ‘SubpathwayLNCE.Rnw’ - - SUMMARY: processing the following file failed: - ‘SubpathwayLNCE.Rnw’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# SubtypeDrug - -
- -* Version: 0.1.5 -* GitHub: https://github.com/hanjunwei-lab/SubtypeDrug -* Source code: https://github.com/cran/SubtypeDrug -* Date/Publication: 2021-05-17 08:50:03 UTC -* Number of recursive dependencies: 126 - -Run `revdepcheck::cloud_details(, "SubtypeDrug")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘SubtypeDrug-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plotSpwNetGraph - > ### Title: Polt a subpathway network graph - > ### Aliases: plotSpwNetGraph - > - > ### ** Examples - > - > require(igraph) - ... - The following object is masked from ‘package:base’: - - union - - > # plot network graph of the subpathway 00020_4. - > plotSpwNetGraph(spwid="00020_4") - Error in vcount(graph) : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: plotSpwNetGraph -> plot -> plot.igraph -> vcount - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘vignette.Rmd’ using rmarkdown - Quitting from lines 182-185 (vignette.Rmd) - Error: processing vignette 'vignette.Rmd' failed with diagnostics: - REAL() can only be applied to a 'numeric', not a 'logical' - --- failed re-building ‘vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# tgver - -
- -* Version: 0.3.0 -* GitHub: https://github.com/tgve/tgver -* Source code: https://github.com/cran/tgver -* Date/Publication: 2022-09-30 15:20:03 UTC -* Number of recursive dependencies: 157 - -Run `revdepcheck::cloud_details(, "tgver")` for more info - -
- -## Newly broken - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘dev-plan.Rmd’ using rmarkdown - --- finished re-building ‘dev-plan.Rmd’ - - --- re-building ‘r-and-js.Rmd’ using rmarkdown - Quitting from lines 31-67 (r-and-js.Rmd) - Error: processing vignette 'r-and-js.Rmd' failed with diagnostics: - REAL() can only be applied to a 'numeric', not a 'logical' - --- failed re-building ‘r-and-js.Rmd’ - - --- re-building ‘tgver.Rmd’ using rmarkdown - --- finished re-building ‘tgver.Rmd’ - - SUMMARY: processing the following file failed: - ‘r-and-js.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# threejs - -
- -* Version: 0.3.3 -* GitHub: https://github.com/bwlewis/rthreejs -* Source code: https://github.com/cran/threejs -* Date/Publication: 2020-01-21 15:50:03 UTC -* Number of recursive dependencies: 40 - -Run `revdepcheck::cloud_details(, "threejs")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘threejs-Ex.R’ failed - The error most likely occurred in: - - > ### Name: graphjs - > ### Title: Interactive 3D Graph Visualization - > ### Aliases: graphjs - > - > ### ** Examples - > - > set.seed(1) - ... - > l3 = light_ambient(color = "#555555") - > (graphjs(g, vertex.color="gray", vertex.shape="sphere", lights=list(l1, l2, l3))) - > - > # Les Miserables Character Co-appearance Data - > data("LeMis") - > (graphjs(LeMis)) - Error in adjacent_vertices(x, i, mode = if (directed) "out" else "all") : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: graphjs -> [[ -> [[.igraph -> adjacent_vertices - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘threejs.R’ - Running the tests in ‘tests/threejs.R’ failed. - Last 13 lines of output: - > frequent_destinations <- names(freq)[1:10] - > idx <- dest %in% frequent_destinations - > frequent_flights <- flights[idx, ] - > ll <- unique(frequent_flights[, 3:4]) - > globejs(lat=ll[, 1], long=ll[, 2], arcs=frequent_flights, - + arcsHeight=0.3, arcsLwd=2, arcsColor="#ffff00", arcsOpacity=0.15, - + atmosphere=TRUE, color="#00aaff", pointsize=0.5) - > - > # graphs - > data(LeMis, package="threejs") - > g <- graphjs(LeMis, main="Les Misérables") - Error in adjacent_vertices(x, i, mode = if (directed) "out" else "all") : - REAL() can only be applied to a 'numeric', not a 'logical' - Calls: graphjs -> [[ -> [[.igraph -> adjacent_vertices - Execution halted - ``` - -## In both - -* checking package dependencies ... NOTE - ``` - Package which this enhances but not available for checking: ‘shiny’ - ``` - -# tosr - -
- -* Version: 0.1.2 -* GitHub: https://github.com/coreofscience/tosr -* Source code: https://github.com/cran/tosr -* Date/Publication: 2023-01-13 23:50:02 UTC -* Number of recursive dependencies: 182 - -Run `revdepcheck::cloud_details(, "tosr")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ▆ - 1. ├─testthat::expect_equal(...) at test-tosr_load.R:4:2 - 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") - 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) - 4. ├─base::nrow(tosSAP(my_tosr_load$graph, my_tosr_load$df, my_tosr_load$nodes)) - 5. ├─tosr::tosSAP(my_tosr_load$graph, my_tosr_load$df, my_tosr_load$nodes) - 6. │ └─tibble::tibble(...) - 7. │ └─tibble:::tibble_quos(xs, .rows, .name_repair) - 8. │ └─rlang::eval_tidy(xs[[j]], mask) - 9. └─igraph::V(graph) - 10. └─igraph::vcount(graph) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] - Error: Test failures - Execution halted - ``` - -# webSDM - -
- -* Version: 1.1-3 -* GitHub: https://github.com/giopogg/webSDM -* Source code: https://github.com/cran/webSDM -* Date/Publication: 2023-03-14 13:50:02 UTC -* Number of recursive dependencies: 190 - -Run `revdepcheck::cloud_details(, "webSDM")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘webSDM-Ex.R’ failed - The error most likely occurred in: - - > ### Name: SDMfit - > ### Title: Fitting a single-species SDM - > ### Aliases: SDMfit - > - > ### ** Examples - > - > data(Y,X,G) - > # Run a local model (i.e. a SDM) for species Y6 - > mySDM = SDMfit("Y6", Y, X, G, "~X_1 + X_2", mode = "prey", - + method = "stan_glm", family = binomial(link = "logit")) - Error in vertex_attr_names(graph) : - VECTOR_ELT() can only be applied to a 'list', not a 'environment' - Calls: SDMfit ... neighbors -> as.igraph.vs -> %in% -> vertex_attr_names - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘Matrix’ - All declared Imports should be used. - ``` - From df9c3bcef49fe1d80fb61453b0d7ab65a243a6ae Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Kirill=20M=C3=BCller?= Date: Sun, 21 May 2023 19:30:32 +0200 Subject: [PATCH 3/8] New results, minus two packages still being tested --- revdep/README.md | 44 +++--- revdep/cran.md | 48 ++----- revdep/failures.md | 174 +++------------------- revdep/problems.md | 352 --------------------------------------------- 4 files changed, 45 insertions(+), 573 deletions(-) diff --git a/revdep/README.md b/revdep/README.md index 958b6b44465..6d2163f386b 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,39 +1,29 @@ # Revdeps -## Failed to check (13) +## Failed to check (11) -|package |version |error |warning |note | -|:---------------|:-------|:-----|:-------|:----| -|beadplexr |? | | | | -|NA |? | | | | -|DRviaSPCN |? | | | | -|genekitr |? | | | | -|HospitalNetwork |0.9.3 |1 | | | -|immcp |? | | | | -|MACP |? | | | | -|numbat |? | | | | -|NA |? | | | | -|Platypus |? | | | | -|NA |? | | | | -|tidySEM |? | | | | -|vivid |? | | | | +|package |version |error |warning |note | +|:---------|:-------|:-----|:-------|:----| +|NA |? | | | | +|DRviaSPCN |? | | | | +|genekitr |? | | | | +|immcp |? | | | | +|MACP |? | | | | +|numbat |? | | | | +|NA |? | | | | +|Platypus |? | | | | +|NA |? | | | | +|tidySEM |? | | | | +|vivid |? | | | | -## New problems (14) +## New problems (6) -|package |version |error |warning |note | -|:--------------|:-------|:------|:-------|:----| -|[causaloptim](problems.md#causaloptim)|0.9.7 |__+1__ | | | -|[clustAnalytics](problems.md#clustanalytics)|0.5.2 | |__+1__ |1 | -|[dnet](problems.md#dnet)|1.1.7 |__+1__ | | | -|[drake](problems.md#drake)|7.13.5 |__+1__ | | | +|package |version |error |warning |note | +|:----------|:-------|:------|:-------|:----| |[gemtc](problems.md#gemtc)|1.0-1 |__+1__ | | | |[leidenAlg](problems.md#leidenalg)|1.0.5 |__+2__ | |1 | |[leidenbase](problems.md#leidenbase)|0.1.18 |__+2__ |__+1__ |1 | -|[metanetwork](problems.md#metanetwork)|0.7.0 |__+1__ | | | -|[migraph](problems.md#migraph)|0.13.2 |__+1__ | | | |[nda](problems.md#nda)|0.1.6 |__+1__ | | | |[netseg](problems.md#netseg)|1.0-1 |__+2__ |__+1__ | | -|[SEMgraph](problems.md#semgraph)|1.2.0 |__+1__ | | | -|[shazam](problems.md#shazam)|1.1.2 |__+1__ |1 | | |[SNscan](problems.md#snscan)|1.0 |__+1__ | | | diff --git a/revdep/cran.md b/revdep/cran.md index ef98085c26c..4a6e4dfcd03 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,27 +1,15 @@ ## revdepcheck results -We checked 781 reverse dependencies (778 from CRAN + 3 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. +We checked 777 reverse dependencies (774 from CRAN + 3 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. - * We saw 14 new problems - * We failed to check 10 packages + * We saw 6 new problems + * We failed to check 8 packages Issues with CRAN packages are summarised below. ### New problems (This reports the first line of each new failure) -* causaloptim - checking tests ... ERROR - -* clustAnalytics - checking re-building of vignette outputs ... WARNING - -* dnet - checking examples ... ERROR - -* drake - checking tests ... ERROR - * gemtc checking tests ... ERROR @@ -34,12 +22,6 @@ Issues with CRAN packages are summarised below. checking tests ... ERROR checking re-building of vignette outputs ... WARNING -* metanetwork - checking tests ... ERROR - -* migraph - checking tests ... ERROR - * nda checking examples ... ERROR @@ -48,24 +30,16 @@ Issues with CRAN packages are summarised below. checking tests ... ERROR checking re-building of vignette outputs ... WARNING -* SEMgraph - checking examples ... ERROR - -* shazam - checking examples ... ERROR - * SNscan checking examples ... ERROR ### Failed to check -* beadplexr (NA) -* DRviaSPCN (NA) -* genekitr (NA) -* HospitalNetwork (NA) -* immcp (NA) -* MACP (NA) -* numbat (NA) -* Platypus (NA) -* tidySEM (NA) -* vivid (NA) +* DRviaSPCN (NA) +* genekitr (NA) +* immcp (NA) +* MACP (NA) +* numbat (NA) +* Platypus (NA) +* tidySEM (NA) +* vivid (NA) diff --git a/revdep/failures.md b/revdep/failures.md index 2a59f74adcd..233d3ba695a 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -1,79 +1,3 @@ -# beadplexr - -
- -* Version: 0.4.1 -* GitHub: NA -* Source code: https://github.com/cran/beadplexr -* Date/Publication: 2022-03-05 13:50:02 UTC -* Number of recursive dependencies: 128 - -Run `revdepcheck::cloud_details(, "beadplexr")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/beadplexr/new/beadplexr.Rcheck’ -* using R version 4.1.1 (2021-08-10) -* using platform: x86_64-pc-linux-gnu (64-bit) -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘beadplexr/DESCRIPTION’ ... OK -* checking extension type ... Package -* this is package ‘beadplexr’ version ‘0.4.1’ -* package encoding: UTF-8 -* checking package namespace information ... OK -... - Running ‘testthat.R’ -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... NONE - ‘cba_macsplex_example.Rmd’ using ‘UTF-8’... OK - ‘legendplex_analysis.Rmd’ using ‘UTF-8’... OK - ‘preparing_flow_data.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 NOTE - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/beadplexr/old/beadplexr.Rcheck’ -* using R version 4.1.1 (2021-08-10) -* using platform: x86_64-pc-linux-gnu (64-bit) -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘beadplexr/DESCRIPTION’ ... OK -* checking extension type ... Package -* this is package ‘beadplexr’ version ‘0.4.1’ -* package encoding: UTF-8 -* checking package namespace information ... OK -... - Running ‘testthat.R’ -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... NONE - ‘cba_macsplex_example.Rmd’ using ‘UTF-8’... OK - ‘legendplex_analysis.Rmd’ using ‘UTF-8’... OK - ‘preparing_flow_data.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 NOTE - - - - - -``` # NA
@@ -244,66 +168,6 @@ Status: 1 ERROR -``` -# HospitalNetwork - -
- -* Version: 0.9.3 -* GitHub: https://github.com/PascalCrepey/HospitalNetwork -* Source code: https://github.com/cran/HospitalNetwork -* Date/Publication: 2023-02-27 08:22:43 UTC -* Number of recursive dependencies: 115 - -Run `revdepcheck::cloud_details(, "HospitalNetwork")` for more info - -
- -## In both - -* checking whether package ‘HospitalNetwork’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/HospitalNetwork/new/HospitalNetwork.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘HospitalNetwork’ ... -** package ‘HospitalNetwork’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - there is no package called ‘graphlayouts’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: lazy loading failed for package ‘HospitalNetwork’ -* removing ‘/tmp/workdir/HospitalNetwork/new/HospitalNetwork.Rcheck/HospitalNetwork’ - - -``` -### CRAN - -``` -* installing *source* package ‘HospitalNetwork’ ... -** package ‘HospitalNetwork’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - there is no package called ‘graphlayouts’ -Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: lazy loading failed for package ‘HospitalNetwork’ -* removing ‘/tmp/workdir/HospitalNetwork/old/HospitalNetwork.Rcheck/HospitalNetwork’ - - ``` # immcp @@ -667,7 +531,7 @@ Run `revdepcheck::cloud_details(, "NA")` for more info * GitHub: https://github.com/cjvanlissa/tidySEM * Source code: https://github.com/cran/tidySEM * Date/Publication: 2023-05-01 20:00:06 UTC -* Number of recursive dependencies: 190 +* Number of recursive dependencies: 189 Run `revdepcheck::cloud_details(, "tidySEM")` for more info @@ -688,17 +552,15 @@ Run `revdepcheck::cloud_details(, "tidySEM")` for more info * this is package ‘tidySEM’ version ‘0.2.4’ * package encoding: UTF-8 * checking package namespace information ... OK -... - ‘Plotting_graphs.Rmd’ using ‘UTF-8’... OK - ‘Tabulating_results.Rmd’ using ‘UTF-8’... OK - ‘lca_confirmatory.Rmd’ using ‘UTF-8’... OK - ‘lca_exploratory.Rmd’ using ‘UTF-8’... OK - ‘lca_lcga.Rmd’ using ‘UTF-8’... OK - ‘lca_ordinal.Rmd’ using ‘UTF-8’... OK - ‘sem_graph.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘blavaan’ + +Package suggested but not available for checking: ‘umx’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. * DONE -Status: 1 NOTE +Status: 1 ERROR @@ -718,17 +580,15 @@ Status: 1 NOTE * this is package ‘tidySEM’ version ‘0.2.4’ * package encoding: UTF-8 * checking package namespace information ... OK -... - ‘Plotting_graphs.Rmd’ using ‘UTF-8’... OK - ‘Tabulating_results.Rmd’ using ‘UTF-8’... OK - ‘lca_confirmatory.Rmd’ using ‘UTF-8’... OK - ‘lca_exploratory.Rmd’ using ‘UTF-8’... OK - ‘lca_lcga.Rmd’ using ‘UTF-8’... OK - ‘lca_ordinal.Rmd’ using ‘UTF-8’... OK - ‘sem_graph.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘blavaan’ + +Package suggested but not available for checking: ‘umx’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. * DONE -Status: 1 NOTE +Status: 1 ERROR diff --git a/revdep/problems.md b/revdep/problems.md index e16ae3b03fb..90c0b9833ba 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1,170 +1,3 @@ -# causaloptim - -
- -* Version: 0.9.7 -* GitHub: https://github.com/sachsmc/causaloptim -* Source code: https://github.com/cran/causaloptim -* Date/Publication: 2023-03-24 12:00:15 UTC -* Number of recursive dependencies: 63 - -Run `revdepcheck::cloud_details(, "causaloptim")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - decompose, spectrum - - The following object is masked from 'package:base': - - union - - > - > test_check("causaloptim") - ERROR: Unable to successfully parse objective function. - qNA - - *** caught segfault *** - address 0x2b0000005d, cause 'memory not mapped' - An irrecoverable exception occurred. R is aborting now ... - Segmentation fault (core dumped) - ``` - -# clustAnalytics - -
- -* Version: 0.5.2 -* GitHub: NA -* Source code: https://github.com/cran/clustAnalytics -* Date/Publication: 2022-11-09 11:50:09 UTC -* Number of recursive dependencies: 71 - -Run `revdepcheck::cloud_details(, "clustAnalytics")` for more info - -
- -## Newly broken - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘cluster_stability.Rmd’ using rmarkdown - --- finished re-building ‘cluster_stability.Rmd’ - - --- re-building ‘graph_rewiring_functions.Rmd’ using rmarkdown - --- finished re-building ‘graph_rewiring_functions.Rmd’ - - --- re-building ‘other_functions.Rmd’ using rmarkdown - --- finished re-building ‘other_functions.Rmd’ - - ... - 28: tryCatchList(expr, classes, parentenv, handlers) - 29: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))}) - 30: tools:::.buildOneVignette("stability_significance_examples.Rmd", "/tmp/workdir/clustAnalytics/new/clustAnalytics.Rcheck/vign_test/clustAnalytics", TRUE, FALSE, "stability_significance_examples", "UTF-8", "/tmp/RtmparyCh1/file35332ad0ed20.rds") - An irrecoverable exception occurred. R is aborting now ... - Segmentation fault (core dumped) - SUMMARY: processing the following file failed: - ‘stability_significance_examples.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.6Mb - sub-directories of 1Mb or more: - libs 6.1Mb - ``` - -# dnet - -
- -* Version: 1.1.7 -* GitHub: https://github.com/hfang-bristol/dnet -* Source code: https://github.com/cran/dnet -* Date/Publication: 2020-02-20 10:10:07 UTC -* Number of recursive dependencies: 51 - -Run `revdepcheck::cloud_details(, "dnet")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘dnet-Ex.R’ failed - The error most likely occurred in: - - > ### Name: dDAGlevel - > ### Title: Function to define/calculate the level of nodes in a direct - > ### acyclic graph (DAG) - > ### Aliases: dDAGlevel - > - > ### ** Examples - > - ... - > - > # 4) calculate the node levels - > # 4a) definition based on the longest path - > dDAGlevel(subg, level.mode="longest_path") - Warning in dDAGlevel(subg, level.mode = "longest_path") : - The input DAG has multiple roots; recalculate the root after being reversed. - - Error in dDAGlevel(subg, level.mode = "longest_path") : - Even after automatic reversing, the input DAG still has multiple roots; check the eligibility of the input DAG. - Execution halted - ``` - -# drake - -
- -* Version: 7.13.5 -* GitHub: https://github.com/ropensci/drake -* Source code: https://github.com/cran/drake -* Date/Publication: 2023-03-24 13:10:02 UTC -* Number of recursive dependencies: 164 - -Run `revdepcheck::cloud_details(, "drake")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ── 9. Failure ('test-4-imports.R:65:3'): responses to imported objects and funct - justbuilt(config) not equal to `builds`. - Lengths differ: 5 is not 4 - - ── 10. Failure ('test-4-imports.R:75:3'): responses to imported objects and func - justbuilt(config) not equal to `builds`. - Lengths differ: 1 is not 4 - ... and 16 more - - - Maximum number of 10 failures reached, some test results may be missing. - - ══ DONE ════════════════════════════════════════════════════════════════════════ - Error: Test failures - Execution halted - ``` - # gemtc
@@ -354,82 +187,6 @@ Run `revdepcheck::cloud_details(, "leidenbase")` for more info libs 18.8Mb ``` -# metanetwork - -
- -* Version: 0.7.0 -* GitHub: https://github.com/MarcOhlmann/metanetwork -* Source code: https://github.com/cran/metanetwork -* Date/Publication: 2022-12-05 14:10:02 UTC -* Number of recursive dependencies: 106 - -Run `revdepcheck::cloud_details(, "metanetwork")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Epoch: Iteration #300 error is: 199.576452337934 - x_max = 1692.55352861469 - y_max = 336.30631387777 - [ FAIL 1 | WARN 22 | SKIP 0 | PASS 73 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Failure ('test-compute_TL.R:25:3'): Computation of trophic levels of norway dataset ── - V(meta0$metaweb)$TL (`actual`) not equal to V(meta_angola$metaweb)$TL (`expected`). - - `actual`: 1.2 1.4 0.9 0.5 0.8 0.8 0.2 0.8 0.9 1.8 and 18 more... - `expected`: 1.6 1.3 1.8 2.3 1.9 1.9 2.6 1.9 1.9 1.0 ... - - [ FAIL 1 | WARN 22 | SKIP 0 | PASS 73 ] - Error: Test failures - Execution halted - ``` - -# migraph - -
- -* Version: 0.13.2 -* GitHub: https://github.com/snlab-ch/migraph -* Source code: https://github.com/cran/migraph -* Date/Publication: 2022-12-20 16:20:02 UTC -* Number of recursive dependencies: 138 - -Run `revdepcheck::cloud_details(, "migraph")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - round(unname(tidys$estimate[1]), 3) not equal to -8.47. - 1/1 mismatches - [1] -3.79 - -8.47 == 4.68 - ── Failure ('test-model_regression.R:35:3'): glance works correctly for network_reg ── - round(glances$r.squared, 4) not equal to 0.0575. - 1/1 mismatches - [1] 0.064 - 0.0575 == 0.0065 - ── Failure ('test-motif_census.R:7:3'): node tie census works ────────────────── - test[1:4] not equal to rep(0, 4). - 1/4 mismatches - [2] 1 - 0 == 1 - - [ FAIL 9 | WARN 0 | SKIP 0 | PASS 544 ] - Error: Test failures - Execution halted - ``` - # nda
@@ -552,115 +309,6 @@ Run `revdepcheck::cloud_details(, "netseg")` for more info Execution halted ``` -# SEMgraph - -
- -* Version: 1.2.0 -* GitHub: https://github.com/fernandoPalluzzi/SEMgraph -* Source code: https://github.com/cran/SEMgraph -* Date/Publication: 2023-05-04 16:00:02 UTC -* Number of recursive dependencies: 51 - -Run `revdepcheck::cloud_details(, "SEMgraph")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘SEMgraph-Ex.R’ failed - The error most likely occurred in: - - > ### Name: SEMdag - > ### Title: Estimate a DAG from an input (or empty) graph - > ### Aliases: SEMdag - > - > ### ** Examples - > - > - ... - > - > # DAG estimation (default values) - > dag0 <- SEMdag(ig, X) - WARNING: input graph is not acyclic ! - Applying graph -> DAG conversion... - DAG conversion : TRUE - Node Linear Ordering with TO setting - - Error: from glmnet C++ code (error code 10000); All penalty factors are <= 0 - Execution halted - ``` - -# shazam - -
- -* Version: 1.1.2 -* GitHub: NA -* Source code: https://github.com/cran/shazam -* Date/Publication: 2022-10-01 07:30:02 UTC -* Number of recursive dependencies: 124 - -Run `revdepcheck::cloud_details(, "shazam")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘shazam-Ex.R’ failed - The error most likely occurred in: - - > ### Name: makeGraphDf - > ### Title: Build a data.frame from a ChangeoClone and an igraph object - > ### containing a clonal lineage - > ### Aliases: makeGraphDf - > - > ### ** Examples - > - ... - > data(ExampleDb, package = "alakazam") - > data(ExampleTrees, package = "alakazam") - > graph <- ExampleTrees[[17]] - > db <- subset(ExampleDb, clone_id == graph$clone) - > clone <- alakazam::makeChangeoClone(db) - > - > # Extend data with lineage information - > df <- makeGraphDf(graph, clone) - Error: Expecting a single string value: [type=character; extent=0]. - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘Baseline-Vignette.Rmd’ using rmarkdown - A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TinyTeX with tinytex::reinstall_tinytex(repository = "illinois"). - - tlmgr: Local TeX Live (2022) is older than remote repository (2023). - Cross release updates are only supported with - update-tlmgr-latest(.sh/.exe) --update - See https://tug.org/texlive/upgrade.html for details. - Warning in system2("tlmgr", args, ...) : - running command ''tlmgr' search --file --global '/grffile.sty'' had status 1 - ... - LaTeX failed to compile /tmp/workdir/shazam/new/shazam.Rcheck/vign_test/shazam/vignettes/Targeting-Vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Targeting-Vignette.log for more info. - --- failed re-building ‘Targeting-Vignette.Rmd’ - - SUMMARY: processing the following files failed: - ‘Baseline-Vignette.Rmd’ ‘DistToNearest-Vignette.Rmd’ - ‘Mutation-Vignette.Rmd’ ‘Shmulate-Vignette.Rmd’ - ‘Targeting-Vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - # SNscan
From 07ac7ca57d079d7613dd7dfa663f5765dcef5a67 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Kirill=20M=C3=BCller?= Date: Mon, 12 Jun 2023 20:36:56 +0200 Subject: [PATCH 4/8] Problems --- revdep/README.md | 476 +- revdep/cran.md | 1571 ++- revdep/failures.md | 199 +- revdep/problems.md | 24867 ++++++++++++++++++++++++++++++++++++++++++- 4 files changed, 27069 insertions(+), 44 deletions(-) diff --git a/revdep/README.md b/revdep/README.md index 2652759ea90..869365d61a2 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,18 +1,466 @@ # Revdeps -## Failed to check (11) +## Failed to check (13) -|package |version |error |warning |note | -|:---------|:-------|:-----|:-------|:----| -|NA |? | | | | -|DRviaSPCN |? | | | | -|genekitr |? | | | | -|immcp |? | | | | -|MACP |? | | | | -|numbat |? | | | | -|NA |? | | | | -|Platypus |? | | | | -|NA |? | | | | -|tidySEM |? | | | | -|vivid |? | | | | +|package |version |error |warning |note | +|:---------|:-------|:------|:-------|:----| +|NA |? | | | | +|DRviaSPCN |? | | | | +|FinNet |0.1.1 |1 | | | +|genekitr |? | | | | +|immcp |? | | | | +|MACP |? | | | | +|numbat |? | | | | +|NA |? | | | | +|Platypus |? | | | | +|[R6causal](failures.md#r6causal)|0.7.0 |__+1__ |-1 | | +|NA |? | | | | +|tidySEM |? | | | | +|vivid |? | | | | + +## New problems (441) + +|package |version |error |warning |note | +|:--------------------|:---------|:--------|:-------|:--------| +|[adegenet](problems.md#adegenet)|2.1.10 |__+1__ | | | +|[AHPWR](problems.md#ahpwr)|0.1.0 |__+1__ |__+1__ | | +|[akc](problems.md#akc)|0.9.9 |__+2__ |__+1__ | | +|[alakazam](problems.md#alakazam)|1.2.1 |__+1__ |1 | | +|[AnimalHabitatNetwork](problems.md#animalhabitatnetwork)|0.1.0 |__+1__ | | | +|[aniSNA](problems.md#anisna)|1.0 |__+1__ | | | +|[anocva](problems.md#anocva)|0.1.1 |__+1__ | | | +|[archeofrag](problems.md#archeofrag)|0.8.2 |__+2__ |__+1__ | | +|[arulesViz](problems.md#arulesviz)|1.5-2 |__+2__ | |1 | +|[autoharp](problems.md#autoharp)|0.0.10 |__+1__ | | | +|[autostats](problems.md#autostats)|0.4.0 | |__+1__ | | +|[backbone](problems.md#backbone)|2.1.2 |__+2__ |__+1__ | | +|[backShift](problems.md#backshift)|0.1.4.3 |__+2__ |__+1__ |1 | +|[BallMapper](problems.md#ballmapper)|0.2.0 |__+1__ | |2 | +|[bamm](problems.md#bamm)|0.4.3 |__+2__ |__+1__ | | +|[BASiNET](problems.md#basinet)|0.0.5 | |__+1__ | | +|[BASiNETEntropy](problems.md#basinetentropy)|0.99.5 |__+1__ | | | +|[basket](problems.md#basket)|0.10.11 |__+1__ | | | +|[BayesMallows](problems.md#bayesmallows)|1.3.0 |__+2__ | |1 | +|[BayesMRA](problems.md#bayesmra)|1.0.0 |__+2__ | |1 | +|[BayesNetBP](problems.md#bayesnetbp)|1.6.1 |__+1__ | | | +|[BayesSUR](problems.md#bayessur)|2.1-3 |__+1__ | |1 | +|[bcgam](problems.md#bcgam)|1.0 |__+1__ | | | +|[BCT](problems.md#bct)|1.2 |__+1__ | | | +|[BDgraph](problems.md#bdgraph)|2.72 |__+1__ |__+1__ |1 | +|[beam](problems.md#beam)|2.0.2 |__+1__ | |1 | +|[bibliometrix](problems.md#bibliometrix)|4.1.2 |__+1__ | | | +|[bifurcatingr](problems.md#bifurcatingr)|1.0.0 |__+1__ | | | +|[bio3d](problems.md#bio3d)|2.4-4 |__+1__ | |1 | +|[Bioi](problems.md#bioi)|0.2.10 |__+1__ | |1 | +|[bioregion](problems.md#bioregion)|1.0.0 |__+1__ | |1 | +|[Bios2cor](problems.md#bios2cor)|2.2.1 |__+1__ | | | +|[bipartite](problems.md#bipartite)|2.18 |__+1__ | |1 | +|[bnma](problems.md#bnma)|1.5.0 |__+1__ | | | +|[bnviewer](problems.md#bnviewer)|0.1.6 |__+2__ | |2 | +|[BoolNet](problems.md#boolnet)|2.1.8 |__+1__ | |1 | +|[bootnet](problems.md#bootnet)|1.5.3 |__+1__ | | | +|[BSBT](problems.md#bsbt)|1.2.1 |__+2__ | | | +|[btergm](problems.md#btergm)|1.10.10 |__+1__ | | | +|[bwsTools](problems.md#bwstools)|1.2.0 |__+1__ | | | +|[Canek](problems.md#canek)|0.2.2 |__+2__ |__+1__ | | +|[cape](problems.md#cape)|3.1.1 | |__+1__ | | +|[CARlasso](problems.md#carlasso)|0.1.2 |__+1__ | |1 | +|[cartograflow](problems.md#cartograflow)|1.0.3 |__+1__ | | | +|[cassowaryr](problems.md#cassowaryr)|2.0.0 |__+2__ |__+1__ | | +|[causact](problems.md#causact)|0.4.2 |__+2__ | | | +|[causalDisco](problems.md#causaldisco)|0.9.1 |__+1__ | | | +|[ccTensor](problems.md#cctensor)|1.0.2 |__+1__ | |1 | +|[CePa](problems.md#cepa)|0.8.0 |__+1__ |1 | | +|[CeRNASeek](problems.md#cernaseek)|2.1.3 |__+1__ | | | +|[cfid](problems.md#cfid)|0.1.4 |__+1__ | | | +|[chemodiv](problems.md#chemodiv)|0.2.0 |__+2__ |__+1__ | | +|[cholera](problems.md#cholera)|0.8.0 |__+1__ |__+1__ |1 | +|[CKMRpop](problems.md#ckmrpop)|0.1.3 |__+1__ |__+1__ |1 | +|[CliquePercolation](problems.md#cliquepercolation)|0.4.0 |__+1__ |__+1__ | | +|[ClustAssess](problems.md#clustassess)|0.3.0 |__+1__ |__+1__ | | +|[ClusTorus](problems.md#clustorus)|0.2.2 |__+1__ |__+1__ | | +|[clustree](problems.md#clustree)|0.5.0 |__+2__ |__+1__ | | +|[clustringr](problems.md#clustringr)|1.0 |__+1__ | |2 | +|[CoDiNA](problems.md#codina)|1.1.2 |__+1__ | | | +|[comato](problems.md#comato)|1.1 |__+1__ | | | +|[concatipede](problems.md#concatipede)|1.0.1 |__+2__ |__+1__ | | 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+|[DemoKin](problems.md#demokin)|1.0.3 | |__+1__ |1 | +|[dexterMST](problems.md#dextermst)|0.9.3 |__+1__ | |1 | +|[DiagrammeR](problems.md#diagrammer)|1.0.10 |__+2__ | |1 | +|[diffeRenTES](problems.md#differentes)|0.3.2 |__+2__ |__+1__ | | +|[diffudist](problems.md#diffudist)|1.0.1 |__+1__ | |1 | +|[diffusr](problems.md#diffusr)|0.1.4 |__+2__ |__+1__ |3 | +|[dimRed](problems.md#dimred)|0.2.6 |__+2__ |1 | | +|[discourseGT](problems.md#discoursegt)|1.1.8 |__+1__ | | | +|[discretecdAlgorithm](problems.md#discretecdalgorithm)|0.0.7 |__+2__ | |2 | +|[dm](problems.md#dm) |1.0.5 |__+2__ | | | +|[dnapath](problems.md#dnapath)|0.7.4 |__+1__ |__+1__ | | +|[dnr](problems.md#dnr)|0.3.5 |__+1__ |1 | | +|[dodgr](problems.md#dodgr)|0.2.21 |__+2__ |__+1__ |2 | +|[dosearch](problems.md#dosearch)|1.0.8 |__+1__ | |1 | +|[dragon](problems.md#dragon)|1.2.1 |__+1__ | |1 | +|[drake](problems.md#drake)|7.13.5 |__+2__ | | | +|[DrDimont](problems.md#drdimont)|0.1.4 |__+1__ |__+1__ | | +|[DTSEA](problems.md#dtsea)|0.0.3 |__+1__ |__+1__ | | +|[dyndimred](problems.md#dyndimred)|1.0.4 |__+1__ | |2 | +|[dynetNLAResistance](problems.md#dynetnlaresistance)|0.1.0 |__+2__ | |1 | +|[dyngen](problems.md#dyngen)|1.0.5 |__+1__ | | | +|[dynplot](problems.md#dynplot)|1.1.2 |__+1__ |__+1__ | | +|[dynwrap](problems.md#dynwrap)|1.2.3 |__+2__ |__+1__ | | +|[ecoCopula](problems.md#ecocopula)|1.0.2 |__+2__ |__+1__ | | +|[ECoL](problems.md#ecol)|0.3.0 |__+2__ | |1 | +|[econet](problems.md#econet)|1.0.0 |__+1__ |1 | | +|[EcoNetGen](problems.md#econetgen)|0.2.3 |__+1__ | |1 | +|[economiccomplexity](problems.md#economiccomplexity)|1.4.0 |__+2__ | |1 | +|[econullnetr](problems.md#econullnetr)|0.2.1 |__+1__ |__+1__ | | +|[EcotoneFinder](problems.md#ecotonefinder)|0.2.3 |__+1__ | |2 | +|[ecpc](problems.md#ecpc)|3.1.1 |__+1__ | | | +|[edgebundle](problems.md#edgebundle)|0.4.1 |__+2__ | |1 | +|[edmcr](problems.md#edmcr)|0.2.0 |__+1__ | | | +|[EDOIF](problems.md#edoif)|0.1.3 |__+1__ |__+1__ | | 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+|[handwriter](problems.md#handwriter)|1.0.1 |__+1__ | |1 | +|[hero](problems.md#hero)|0.4.7 |__+1__ | | | +|[HLSM](problems.md#hlsm)|0.9.0 |__+1__ | | | +|[HospitalNetwork](problems.md#hospitalnetwork)|0.9.3 |__+2__ |__+1__ | | +|[HTT](problems.md#htt)|0.1.2 |__+1__ |__+1__ |1 | +|[huge](problems.md#huge)|1.3.5 |__+1__ |1 |1 | +|[ICDS](problems.md#icds)|0.1.2 |__+1__ |__+1__ | | +|[iconr](problems.md#iconr)|0.1.0 |__+1__ | |1 | +|[icosa](problems.md#icosa)|0.11.0 |__+1__ |__+1__ |1 | +|[idopNetwork](problems.md#idopnetwork)|0.1.2 | |__+1__ | | +|[iGraphMatch](problems.md#igraphmatch)|2.0.1 |__+2__ |__+1__ | | +|[IMEC](problems.md#imec)|0.2.0 |__+2__ | |1 | +|[immunarch](problems.md#immunarch)|0.9.0 |__+1__ | |1 | +|[immuneSIM](problems.md#immunesim)|0.8.7 |__+1__ | |1 | +|[imsig](problems.md#imsig)|1.1.3 |__+1__ | | | +|[incidentally](problems.md#incidentally)|1.0.2 |__+1__ | | | +|[influenceR](problems.md#influencer)|0.1.5 |__+2__ | | | +|[influential](problems.md#influential)|2.2.7 |__+1__ |__+1__ | | +|[intergraph](problems.md#intergraph)|2.0-2 |__+1__ | | | +|[IOHanalyzer](problems.md#iohanalyzer)|0.1.6.3 |__+1__ | |2 | +|[isa2](problems.md#isa2)|0.3.6 |__+1__ | | | +|[isotracer](problems.md#isotracer)|1.1.4 |__+2__ | |3 | +|[ITNr](problems.md#itnr)|0.7.0 |__+1__ | | | +|[IxPopDyMod](problems.md#ixpopdymod)|0.2.0 |__+1__ | | | +|[jewel](problems.md#jewel)|2.0.0 |__+1__ | | | +|[jti](problems.md#jti)|0.8.4 |__+1__ | |1 | +|[kangar00](problems.md#kangar00)|1.4.1 |__+1__ | | | +|[Karen](problems.md#karen)|1.0 |__+1__ |1 | | +|[keyplayer](problems.md#keyplayer)|1.0.3 |__+1__ | | | +|[kknn](problems.md#kknn)|1.3.1 |__+1__ | | | +|[l1spectral](problems.md#l1spectral)|0.99.6 |__+1__ | | | +|[lconnect](problems.md#lconnect)|0.1.1 |__+1__ | |1 | +|[leidenAlg](problems.md#leidenalg)|1.0.5 |__+2__ | |1 | +|[leidenbase](problems.md#leidenbase)|0.1.18 |__+2__ |__+1__ |1 | +|[lexRankr](problems.md#lexrankr)|0.5.2 |__+2__ | | | +|[linkprediction](problems.md#linkprediction)|1.0-0 |__+2__ | |1 | +|[LoopDetectR](problems.md#loopdetectr)|0.1.2 |__+1__ |__+1__ | | +|[LSVAR](problems.md#lsvar)|1.2 |__+1__ | | | +|[lvm4net](problems.md#lvm4net)|0.3 |__+1__ | | | +|[macrosyntR](problems.md#macrosyntr)|0.2.19 |__+1__ |__+1__ | | +|[madrat](problems.md#madrat)|3.3.0 |__+2__ |__+1__ | | +|[malan](problems.md#malan)|1.0.2 |__+1__ |__+1__ |1 | +|[manymome](problems.md#manymome)|0.1.10 |1 __+1__ | | | +|[manynet](problems.md#manynet)|0.1.1 |1 __+1__ | | | +|[matrixcut](problems.md#matrixcut)|0.0.1 |__+1__ | |1 | +|[maxmatching](problems.md#maxmatching)|0.1.0 |__+1__ | |1 | +|[mazeGen](problems.md#mazegen)|0.1.3 |__+1__ | | | +|[MBNMAdose](problems.md#mbnmadose)|0.4.1 |__+1__ |__+1__ |1 | +|[MBNMAtime](problems.md#mbnmatime)|0.2.3 |__+1__ |__+1__ | | +|[mcMST](problems.md#mcmst)|1.1.1 |__+1__ | | | +|[mcvis](problems.md#mcvis)|1.0.8 |__+2__ |__+1__ | | +|[meconetcomp](problems.md#meconetcomp)|0.2.0 |__+1__ | | | +|[Mercator](problems.md#mercator)|1.1.2 |__+1__ |__+1__ | | +|[metacoder](problems.md#metacoder)|0.3.6 |__+2__ | |1 | +|[metanetwork](problems.md#metanetwork)|0.7.0 |__+1__ | | | +|[MetricGraph](problems.md#metricgraph)|1.1.1 |__+2__ | |1 | +|[mfpp](problems.md#mfpp)|0.0.4 |__+1__ | | | +|[migraph](problems.md#migraph)|0.13.2 |__+2__ | | | +|[miniCRAN](problems.md#minicran)|0.2.16 |__+1__ |__+1__ | | +|[missSBM](problems.md#misssbm)|1.0.3 |__+1__ | |1 | +|[mlmts](problems.md#mlmts)|1.1.1 |__+1__ | |1 | +|[mnda](problems.md#mnda)|1.0.9 |__+1__ | |1 | +|[modnets](problems.md#modnets)|0.9.0 |__+1__ | | | +|[molnet](problems.md#molnet)|0.1.0 |__+1__ |__+1__ | | +|[moranajp](problems.md#moranajp)|0.9.6 |__+1__ | | | +|[motifcluster](problems.md#motifcluster)|0.2.3 |__+2__ |1 | | +|[motifr](problems.md#motifr)|1.0.0 |__+1__ | | | +|[mppR](problems.md#mppr)|1.4.0 |__+2__ |__+1__ | | +|[MRFcov](problems.md#mrfcov)|1.0.39 |__+1__ |__+1__ | | +|[MRReg](problems.md#mrreg)|0.1.5 |__+1__ |__+1__ | | +|[MRS](problems.md#mrs)|1.2.4 |__+1__ | |1 | +|[mstknnclust](problems.md#mstknnclust)|0.3.2 |__+1__ |__+1__ | | +|[MTA](problems.md#mta)|0.4.1 |__+1__ |__+1__ | | +|[mully](problems.md#mully)|2.1.38 |__+1__ |1 | | +|[multilaterals](problems.md#multilaterals)|1.0 |__+1__ | | | +|[multilink](problems.md#multilink)|0.1.1 |__+1__ | |1 | +|[multinets](problems.md#multinets)|0.2.2 |__+2__ | | | +|[multinma](problems.md#multinma)|0.5.1 |__+2__ | |2 | +|[MultIS](problems.md#multis)|0.6.2 | |__+1__ |1 | +|[multivariance](problems.md#multivariance)|2.4.1 |__+2__ | | | +|[mverse](problems.md#mverse)|0.1.0 | |__+1__ | | +|[mwcsr](problems.md#mwcsr)|0.1.7 |__+2__ | |1 | +|[nat](problems.md#nat)|1.8.22 |__+2__ |__+1__ | | +|[nbTransmission](problems.md#nbtransmission)|1.1.2 |__+1__ |__+1__ | | +|[nda](problems.md#nda)|0.1.6 |__+1__ | | | +|[neat](problems.md#neat)|1.2.3 |__+1__ |__+1__ | | +|[neatmaps](problems.md#neatmaps)|2.1.0 |__+1__ | |1 | +|[Neighboot](problems.md#neighboot)|1.0.1 |__+1__ | | | +|[netCoin](problems.md#netcoin)|2.0.48 |__+1__ | |1 | +|[netcom](problems.md#netcom)|2.1.6 |__+1__ | |1 | +|[NetCoupler](problems.md#netcoupler)|0.1.0 |__+2__ |__+1__ | | +|[netdiffuseR](problems.md#netdiffuser)|1.22.5 |__+2__ |__+1__ |1 | +|[NetFACS](problems.md#netfacs)|0.5.0 |__+1__ |__+1__ | | +|[netgsa](problems.md#netgsa)|4.0.4 | |__+1__ |1 | +|[netjack](problems.md#netjack)|1.2.0 |__+1__ |__+1__ |1 | +|[netmap](problems.md#netmap)|0.1.2 |__+1__ | | | +|[netmeta](problems.md#netmeta)|2.8-2 |__+1__ | |2 | +|[NetMix](problems.md#netmix)|0.2.0.1 |__+1__ | |1 | +|[netplot](problems.md#netplot)|0.1-1 |__+1__ | | | +|[netrankr](problems.md#netrankr)|1.2.0 |__+1__ | |1 | +|[netropy](problems.md#netropy)|0.1.0 |__+1__ |__+1__ | | +|[NetSci](problems.md#netsci)|1.0.0 |__+1__ | | | +|[netseg](problems.md#netseg)|1.0-1 |__+2__ | | | +|[nett](problems.md#nett)|1.0.0 |__+1__ | | | +|[netUtils](problems.md#netutils)|0.8.1 |__+1__ | | | +|[NetworkExtinction](problems.md#networkextinction)|1.0.3 |__+2__ |__+1__ | | +|[networkGen](problems.md#networkgen)|0.1.1 |__+1__ | |2 | +|[NetworkInference](problems.md#networkinference)|1.2.4 |__+1__ |__+1__ | | +|[NetworkToolbox](problems.md#networktoolbox)|1.4.2 |__+1__ | | | +|[networktools](problems.md#networktools)|1.5.0 |__+1__ | | | +|[NIMAA](problems.md#nimaa)|0.2.1 |__+2__ |__+1__ |2 | +|[nimble](problems.md#nimble)|1.0.0 |__+1__ | |1 | +|[nlnet](problems.md#nlnet)|1.4 |__+1__ | | | +|[nlrx](problems.md#nlrx)|0.4.4 |__+1__ | | | +|[node2vec](problems.md#node2vec)|0.1.0 |__+1__ | | | +|[nutriNetwork](problems.md#nutrinetwork)|0.1.1 |__+1__ | | | +|[OCNet](problems.md#ocnet)|1.0.1 |__+1__ | |1 | +|[oddnet](problems.md#oddnet)|0.1.0 |__+1__ | | | +|[ohun](problems.md#ohun)|0.1.0 |__+1__ | | | +|[OpenRepGrid](problems.md#openrepgrid)|0.1.14 |__+1__ | | | +|[OpenRepGrid.ic](problems.md#openrepgridic)|0.6.1 |__+1__ | | | +|[OrdCD](problems.md#ordcd)|1.1.2 |__+1__ | | | +|[PAC](problems.md#pac)|1.1.4 | |__+1__ | | +|[PAFit](problems.md#pafit)|1.2.5 |__+2__ | | | +|[PairViz](problems.md#pairviz)|1.3.6 | |__+1__ | | +|[pald](problems.md#pald)|0.0.2 |__+2__ | | | +|[PANACEA](problems.md#panacea)|1.0.0 |__+1__ | | | +|[paramlink](problems.md#paramlink)|1.1-5 |__+1__ | | | +|[particles](problems.md#particles)|0.2.3 |__+1__ |__+1__ | | +|[pathfindR](problems.md#pathfindr)|2.1.0 |__+2__ |__+1__ | | +|[pcalg](problems.md#pcalg)|2.7-8 |__+3__ | |3 | +|[pcFactorStan](problems.md#pcfactorstan)|1.5.3 |__+2__ | |3 | +|[pedtools](problems.md#pedtools)|2.2.0 |1 __+1__ | | | +|[perturbR](problems.md#perturbr)|0.1.3 |__+1__ | | | +|[pGRN](problems.md#pgrn)|0.3.5 |__+1__ | | | +|[phangorn](problems.md#phangorn)|2.11.1 |__+1__ |__+1__ |1 | +|[PhaseTypeR](problems.md#phasetyper)|1.0.4 |__+1__ | | | +|[phyloseqGraphTest](problems.md#phyloseqgraphtest)|0.1.0 |__+1__ |__+1__ |2 | +|[phylosignal](problems.md#phylosignal)|1.3 |__+1__ | |1 | +|[phyloTop](problems.md#phylotop)|2.1.2 |__+2__ | | | +|[pkggraph](problems.md#pkggraph)|0.2.3 |__+1__ | | | +|[PlackettLuce](problems.md#plackettluce)|0.4.2 |1 __+1__ |__+1__ | | +|[plantTracker](problems.md#planttracker)|1.1.0 |__+2__ |__+1__ | | +|[plinkQC](problems.md#plinkqc)|0.3.4 |__+1__ |1 | | +|[PLNmodels](problems.md#plnmodels)|1.0.1 |__+1__ |__+1__ |1 | +|[pmd](problems.md#pmd)|0.2.1 |__+1__ |__+1__ |1 | +|[PNAR](problems.md#pnar)|1.4 |__+1__ | | | +|[polymapR](problems.md#polymapr)|1.1.3 |__+1__ |__+1__ |1 | +|[polyqtlR](problems.md#polyqtlr)|0.0.9 |__+1__ |__+1__ |1 | +|[pomdp](problems.md#pomdp)|1.1.0 |2 |__+1__ |1 | +|[pop](problems.md#pop)|0.1 |__+2__ | |1 | +|[poppr](problems.md#poppr)|2.9.4 |__+2__ |1 | | +|[POSetR](problems.md#posetr)|1.1.1 |__+1__ | |2 | +|[ProjectManagement](problems.md#projectmanagement)|1.4.7 |__+1__ | | | +|[provGraphR](problems.md#provgraphr)|1.0.1 |__+2__ | | | +|[ptools](problems.md#ptools)|2.0.0 |__+2__ | | | +|[qdap](problems.md#qdap)|2.4.6 |__+1__ | |1 | +|[qgraph](problems.md#qgraph)|1.9.5 |__+1__ | | | +|[R.temis](problems.md#rtemis)|0.1.3 |__+1__ | |1 | +|[RaceID](problems.md#raceid)|0.3.0 |__+1__ |__+1__ |1 | +|[rags2ridges](problems.md#rags2ridges)|2.2.6 |__+1__ | |1 | +|[RavenR](problems.md#ravenr)|2.2.0 |__+1__ |__+1__ | | +|[rcrimeanalysis](problems.md#rcrimeanalysis)|0.5.0 |__+1__ |__+1__ | | +|[rD3plot](problems.md#rd3plot)|1.0.68 |__+1__ | | | +|[RDS](problems.md#rds)|0.9-6 |__+2__ | | | +|[readsdr](problems.md#readsdr)|0.2.0 |__+1__ | |1 | +|[ReDaMoR](problems.md#redamor)|0.7.1 |__+1__ |__+1__ | | +|[refdb](problems.md#refdb)|0.1.1 |__+2__ |__+1__ | | +|[RepertoiR](problems.md#repertoir)|0.0.1 |__+2__ | |1 | +|[repo](problems.md#repo)|2.1.5 |__+1__ | | | +|[ResIN](problems.md#resin)|0.1.0 |__+1__ |__+1__ | | +|[RevEcoR](problems.md#revecor)|0.99.3 |__+1__ | | | +|[rflexscan](problems.md#rflexscan)|1.1.0 |__+1__ | | | +|[rgexf](problems.md#rgexf)|0.16.2 |__+2__ |__+1__ | | +|[rgraph6](problems.md#rgraph6)|2.0-2 |__+2__ |__+1__ | | +|[rhcoclust](problems.md#rhcoclust)|2.0.0 |__+1__ | | | +|[rmangal](problems.md#rmangal)|2.1.3 |__+1__ | | | +|[rmcfs](problems.md#rmcfs)|1.3.5 |__+1__ | | | +|[rmonad](problems.md#rmonad)|0.7.0 |__+2__ |__+1__ | | +|[roads](problems.md#roads)|1.1.0 |__+2__ |__+1__ | | +|[robber](problems.md#robber)|0.2.3 |__+2__ | | | +|[robin](problems.md#robin)|1.1.1 |__+1__ | | | +|[RobustIV](problems.md#robustiv)|0.2.5 |__+1__ | | | +|[robustrao](problems.md#robustrao)|1.0-5 |__+1__ | | | +|[roprov](problems.md#roprov)|0.1.2 |__+1__ | | | +|[RPANDA](problems.md#rpanda)|2.2 |__+1__ | | | +|[rquery](problems.md#rquery)|1.4.9 |__+1__ | | | +|[rscc](problems.md#rscc)|0.2.1 |__+1__ | | | +|[RScelestial](problems.md#rscelestial)|1.0.3 |__+1__ | |1 | +|[rsetse](problems.md#rsetse)|0.5.0 |__+1__ | | | +|[rSpectral](problems.md#rspectral)|1.0.0.10 |__+2__ | |1 | +|[rsppfp](problems.md#rsppfp)|1.0.4 |__+1__ | |1 | +|[rvinecopulib](problems.md#rvinecopulib)|0.6.3.1.1 |__+2__ | |1 | +|[safedata](problems.md#safedata)|1.1.3 |__+1__ |__+1__ | | +|[saotd](problems.md#saotd)|0.3.0 |__+1__ |__+1__ | | +|[sBIC](problems.md#sbic)|0.2.0 |__+1__ | | | +|[sbm](problems.md#sbm)|0.4.5 |__+2__ |__+1__ | | +|[SBN](problems.md#sbn)|1.0.0 |__+1__ | | | +|[sccore](problems.md#sccore)|1.0.3 |__+2__ | |1 | +|[scDHA](problems.md#scdha)|1.2.1 |__+1__ | |1 | +|[scDiffCom](problems.md#scdiffcom)|0.1.0 |__+1__ | |1 | +|[SCORPION](problems.md#scorpion)|1.0.1 |__+1__ | |1 | +|[scRNAtools](problems.md#scrnatools)|1.0 |__+1__ | | | +|[secrlinear](problems.md#secrlinear)|1.2.1 |__+2__ |1 | | +|[SelectBoost](problems.md#selectboost)|2.2.2 |__+1__ | | | +|[SEMID](problems.md#semid)|0.4.0 |__+2__ | | | +|[sensitivity](problems.md#sensitivity)|1.28.1 |__+1__ | |1 | +|[SeqDetect](problems.md#seqdetect)|1.0.7 |__+2__ | |2 | +|[seqHMM](problems.md#seqhmm)|1.2.4 |__+1__ |1 |1 | +|[SeqNet](problems.md#seqnet)|1.1.3 |__+2__ | |2 | +|[SetRank](problems.md#setrank)|1.1.0 |__+1__ |1 | | +|[sfcr](problems.md#sfcr)|0.2.1 |__+2__ |__+1__ | | +|[sfdep](problems.md#sfdep)|0.2.3 |__+1__ | | | +|[sfnetworks](problems.md#sfnetworks)|0.6.3 |__+2__ |__+1__ | | +|[SFSI](problems.md#sfsi)|1.2.0 |__+1__ | | | +|[sharp](problems.md#sharp)|1.4.2 |__+1__ |1 | | +|[sharpshootR](problems.md#sharpshootr)|2.1 |__+1__ | | | +|[shazam](problems.md#shazam)|1.1.2 |__+1__ |1 | | +|[shock](problems.md#shock)|1.0 |__+1__ | | | +|[sidier](problems.md#sidier)|4.1.0 |__+1__ | | | +|[sigmajs](problems.md#sigmajs)|0.1.5 |__+2__ | |1 | +|[signnet](problems.md#signnet)|1.0.1 |__+2__ | |1 | +|[simcausal](problems.md#simcausal)|0.5.6 |__+2__ |1 | | +|[simer](problems.md#simer)|0.9.0.2 |__+1__ | |1 | +|[simPATHy](problems.md#simpathy)|0.6 |__+1__ |__+1__ | | +|[simplifyNet](problems.md#simplifynet)|0.0.1 |__+1__ | | | +|[SIRE](problems.md#sire)|1.1.0 |__+1__ | |1 | +|[sirt](problems.md#sirt)|3.12-66 |__+1__ | |1 | +|[SITH](problems.md#sith)|1.1.0 | |__+1__ | | +|[skynet](problems.md#skynet)|1.4.3 |__+2__ |__+1__ |1 | +|[SmCCNet](problems.md#smccnet)|0.99.0 |__+1__ | | | +|[smotefamily](problems.md#smotefamily)|1.3.1 |__+1__ | | | +|[snowboot](problems.md#snowboot)|1.0.2 |__+1__ | | | +|[SNscan](problems.md#snscan)|1.0 |__+1__ | | | +|[SOAs](problems.md#soas)|1.3 |__+1__ | |1 | +|[SoilR](problems.md#soilr)|1.2.105 |__+1__ | | | +|[solitude](problems.md#solitude)|1.1.3 |__+1__ | |1 | +|[SourceSet](problems.md#sourceset)|0.1.5 |__+1__ |__+1__ |1 | +|[spacejamr](problems.md#spacejamr)|0.2.1 |__+2__ | | | +|[sparsebnUtils](problems.md#sparsebnutils)|0.0.8 |__+1__ | |1 | +|[spathial](problems.md#spathial)|0.1.2 |__+1__ |__+1__ |2 | +|[spatsoc](problems.md#spatsoc)|0.1.16 |__+2__ |__+1__ |1 | +|[specr](problems.md#specr)|1.0.0 |__+2__ |__+1__ | | +|[spinner](problems.md#spinner)|1.1.0 |__+1__ | | | +|[spNetwork](problems.md#spnetwork)|0.4.3.7 |__+2__ |__+1__ |1 | +|[spqdep](problems.md#spqdep)|0.1.2 |__+1__ |__+1__ |2 | +|[SSN](problems.md#ssn)|1.1.17 |__+1__ |1 | | +|[stagedtrees](problems.md#stagedtrees)|2.2.1 |__+1__ | | | +|[statGraph](problems.md#statgraph)|0.5.0 |__+1__ | | | +|[stemmatology](problems.md#stemmatology)|0.3.2 |__+2__ |1 | | +|[stm](problems.md#stm)|1.3.6 |1 __+1__ | |2 | +|[stplanr](problems.md#stplanr)|1.0.2 |__+1__ |__+1__ | | +|[SurvHiDim](problems.md#survhidim)|0.1.1 |__+1__ | |1 | +|[targets](problems.md#targets)|1.1.3 |__+1__ | | | +|[TDA](problems.md#tda)|1.9 |__+2__ | |4 | +|[text2map](problems.md#text2map)|0.1.6 |1 __+1__ | |1 | +|[textrank](problems.md#textrank)|0.3.1 |__+1__ |__+1__ | | +|[tidygraph](problems.md#tidygraph)|1.2.3 |__+2__ | | | +|[tilemaps](problems.md#tilemaps)|0.2.0 |__+1__ |__+1__ |1 | +|[tip](problems.md#tip)|0.1.0 |__+1__ |__+1__ | | +|[Tlasso](problems.md#tlasso)|1.0.2 |__+1__ |__+1__ | | +|[TOHM](problems.md#tohm)|1.4 |__+1__ | | | +|[TreeDimensionTest](problems.md#treedimensiontest)|0.0.2 | |__+1__ | | +|[treefit](problems.md#treefit)|1.0.2 |__+1__ |__+1__ | | +|[treemap](problems.md#treemap)|2.4-4 |__+1__ | | | +|[VARDetect](problems.md#vardetect)|0.1.6 |__+1__ | |1 | +|[vennLasso](problems.md#vennlasso)|0.1.6 |__+1__ |1 |2 | +|[VertexSimilarity](problems.md#vertexsimilarity)|0.1 |__+1__ | |1 | +|[vivainsights](problems.md#vivainsights)|0.3.1 |__+1__ | |1 | +|[wdnet](problems.md#wdnet)|1.1.0 |__+2__ | |1 | +|[webtrackR](problems.md#webtrackr)|0.0.1 |__+2__ | |1 | +|[whitechapelR](problems.md#whitechapelr)|0.3.0 |__+2__ | | | +|[wpa](problems.md#wpa)|1.8.1 |__+1__ | | | +|[xgboost](problems.md#xgboost)|1.7.5.1 |__+2__ | |2 | diff --git a/revdep/cran.md b/revdep/cran.md index c6bdb020b30..de4bf328e67 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,19 +1,1584 @@ ## revdepcheck results -We checked 778 reverse dependencies (775 from CRAN + 3 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. +We checked 786 reverse dependencies (783 from CRAN + 3 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. - * We saw 0 new problems - * We failed to check 8 packages + * We saw 441 new problems + * We failed to check 10 packages Issues with CRAN packages are summarised below. +### New problems +(This reports the first line of each new failure) + +* adegenet + checking examples ... ERROR + +* AHPWR + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* akc + checking examples ... ERROR + checking tests ... ERROR + checking re-building of vignette outputs ... WARNING + +* alakazam + checking examples ... ERROR + +* AnimalHabitatNetwork + checking examples ... ERROR + +* aniSNA + checking examples ... ERROR + +* anocva + checking examples ... ERROR + +* archeofrag + checking examples ... ERROR + checking tests ... ERROR + checking re-building of vignette outputs ... WARNING + +* arulesViz + checking examples ... ERROR + checking running R code from vignettes ... ERROR + +* autoharp + checking examples ... ERROR + +* autostats + checking re-building of vignette outputs ... WARNING + +* backbone + checking examples ... ERROR + checking tests ... ERROR + checking re-building of vignette outputs ... WARNING + +* backShift + checking examples ... ERROR + checking tests ... ERROR + checking re-building of vignette outputs ... 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ERROR + checking data for non-ASCII characters ... NOTE + +* graphclust + checking examples ... ERROR + +* graphicalExtremes + checking examples ... ERROR + +* graphlayouts + checking tests ... ERROR + +* graphseg + checking examples ... ERROR + +* graphTweets + checking examples ... ERROR + checking tests ... ERROR + +* gRbase + checking examples ... ERROR + checking tests ... ERROR + +* gRim + checking examples ... ERROR + checking running R code from vignettes ... ERROR + +* handwriter + checking examples ... ERROR + +* hero + checking examples ... ERROR + +* HLSM + checking examples ... ERROR + +* HospitalNetwork + checking examples ... ERROR + checking tests ... ERROR + checking re-building of vignette outputs ... WARNING + +* HTT + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* huge + checking examples ... ERROR + +* ICDS + checking examples ... ERROR + checking re-building of vignette outputs ... 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ERROR + +* ITNr + checking examples ... ERROR + +* IxPopDyMod + checking examples ... ERROR + +* jewel + checking examples ... ERROR + +* jti + checking examples ... ERROR + +* kangar00 + checking examples ... ERROR + +* Karen + checking examples ... ERROR + +* keyplayer + checking examples ... ERROR + +* kknn + checking examples ... ERROR + +* l1spectral + checking examples ... ERROR + +* lconnect + checking examples ... ERROR + +* leidenAlg + checking examples ... ERROR + checking tests ... ERROR + +* leidenbase + checking examples ... ERROR + checking tests ... ERROR + checking re-building of vignette outputs ... WARNING + +* lexRankr + checking examples ... ERROR + checking tests ... ERROR + +* linkprediction + checking examples ... ERROR + checking tests ... ERROR + +* LoopDetectR + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* LSVAR + checking examples ... ERROR + +* lvm4net + checking examples ... 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ERROR + checking re-building of vignette outputs ... WARNING + +* pathfindR + checking examples ... ERROR + checking tests ... ERROR + checking re-building of vignette outputs ... WARNING + +* pcalg + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + +* pcFactorStan + checking examples ... ERROR + checking tests ... ERROR + +* pedtools + checking examples ... ERROR + +* perturbR + checking examples ... ERROR + +* pGRN + checking examples ... ERROR + +* phangorn + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* PhaseTypeR + checking tests ... ERROR + +* phyloseqGraphTest + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* phylosignal + checking examples ... ERROR + +* phyloTop + checking examples ... ERROR + checking tests ... ERROR + +* pkggraph + checking examples ... ERROR + +* PlackettLuce + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* plantTracker + checking examples ... ERROR + checking tests ... ERROR + checking re-building of vignette outputs ... WARNING + +* plinkQC + checking tests ... ERROR + +* PLNmodels + checking tests ... ERROR + checking re-building of vignette outputs ... WARNING + +* pmd + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* PNAR + checking examples ... ERROR + +* polymapR + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* polyqtlR + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* pomdp + checking re-building of vignette outputs ... WARNING + +* pop + checking examples ... ERROR + checking tests ... ERROR + +* poppr + checking examples ... ERROR + checking tests ... ERROR + +* POSetR + checking examples ... ERROR + +* ProjectManagement + checking examples ... ERROR + +* provGraphR + checking examples ... ERROR + checking tests ... ERROR + +* ptools + checking examples ... ERROR + checking tests ... ERROR + +* qdap + checking tests ... ERROR + +* qgraph + checking examples ... ERROR + +* R.temis + checking examples ... ERROR + +* RaceID + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* rags2ridges + checking examples ... ERROR + +* RavenR + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* rcrimeanalysis + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* rD3plot + checking examples ... ERROR + +* RDS + checking examples ... ERROR + checking tests ... ERROR + +* readsdr + checking tests ... ERROR + +* ReDaMoR + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* refdb + checking examples ... ERROR + checking tests ... ERROR + checking re-building of vignette outputs ... WARNING + +* RepertoiR + checking examples ... ERROR + checking tests ... ERROR + +* repo + checking examples ... ERROR + +* ResIN + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* RevEcoR + checking examples ... ERROR + +* rflexscan + checking examples ... ERROR + +* rgexf + checking examples ... ERROR + checking tests ... ERROR + checking re-building of vignette outputs ... WARNING + +* rgraph6 + checking examples ... ERROR + checking tests ... ERROR + checking re-building of vignette outputs ... WARNING + +* rhcoclust + checking examples ... ERROR + +* rmangal + checking tests ... ERROR + +* rmcfs + checking tests ... ERROR + +* rmonad + checking examples ... ERROR + checking tests ... ERROR + checking re-building of vignette outputs ... WARNING + +* roads + checking examples ... ERROR + checking tests ... ERROR + checking re-building of vignette outputs ... WARNING + +* robber + checking examples ... ERROR + checking tests ... ERROR + +* robin + checking examples ... ERROR + +* RobustIV + checking examples ... ERROR + +* robustrao + checking examples ... ERROR + +* roprov + checking examples ... ERROR + +* RPANDA + checking examples ... ERROR + +* rquery + checking examples ... ERROR + +* rscc + checking examples ... ERROR + +* RScelestial + checking examples ... ERROR + +* rsetse + checking examples ... ERROR + +* rSpectral + checking examples ... ERROR + checking tests ... ERROR + +* rsppfp + checking examples ... ERROR + +* rvinecopulib + checking examples ... ERROR + checking tests ... ERROR + +* safedata + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* saotd + checking tests ... ERROR + checking re-building of vignette outputs ... WARNING + +* sBIC + checking tests ... ERROR + +* sbm + checking examples ... ERROR + checking tests ... ERROR + checking re-building of vignette outputs ... WARNING + +* SBN + checking examples ... ERROR + +* sccore + checking examples ... ERROR + checking tests ... ERROR + +* scDHA + checking tests ... ERROR + +* scDiffCom + checking tests ... ERROR + +* SCORPION + checking examples ... ERROR + +* scRNAtools + checking examples ... ERROR + +* secrlinear + checking examples ... ERROR + checking tests ... ERROR + +* SelectBoost + checking examples ... ERROR + +* SEMID + checking examples ... ERROR + checking tests ... ERROR + +* sensitivity + checking examples ... ERROR + +* SeqDetect + checking examples ... ERROR + checking running R code from vignettes ... ERROR + +* seqHMM + checking examples ... ERROR + +* SeqNet + checking examples ... ERROR + checking tests ... ERROR + +* SetRank + checking examples ... ERROR + +* sfcr + checking examples ... ERROR + checking tests ... ERROR + checking re-building of vignette outputs ... WARNING + +* sfdep + checking examples ... ERROR + +* sfnetworks + checking examples ... ERROR + checking tests ... ERROR + checking re-building of vignette outputs ... WARNING + +* SFSI + checking examples ... ERROR + +* sharp + checking examples ... ERROR + +* sharpshootR + checking examples ... ERROR + +* shazam + checking examples ... ERROR + +* shock + checking examples ... ERROR + +* sidier + checking examples ... ERROR + +* sigmajs + checking examples ... ERROR + checking tests ... ERROR + +* signnet + checking examples ... ERROR + checking tests ... ERROR + +* simcausal + checking examples ... ERROR + checking tests ... ERROR + +* simer + checking examples ... ERROR + +* simPATHy + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* simplifyNet + checking examples ... ERROR + +* SIRE + checking examples ... ERROR + +* sirt + checking examples ... ERROR + +* SITH + checking re-building of vignette outputs ... WARNING + +* skynet + checking examples ... ERROR + checking tests ... ERROR + checking re-building of vignette outputs ... WARNING + +* SmCCNet + checking examples ... ERROR + +* smotefamily + checking examples ... ERROR + +* snowboot + checking examples ... ERROR + +* SNscan + checking examples ... ERROR + +* SOAs + checking tests ... ERROR + +* SoilR + checking examples ... ERROR + +* solitude + checking examples ... ERROR + +* SourceSet + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* spacejamr + checking examples ... ERROR + checking tests ... ERROR + +* sparsebnUtils + checking tests ... ERROR + +* spathial + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* spatsoc + checking examples ... ERROR + checking tests ... ERROR + checking re-building of vignette outputs ... WARNING + +* specr + checking examples ... ERROR + checking tests ... ERROR + checking re-building of vignette outputs ... WARNING + +* spinner + checking tests ... ERROR + +* spNetwork + checking examples ... ERROR + checking tests ... ERROR + checking re-building of vignette outputs ... WARNING + +* spqdep + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* SSN + checking examples ... ERROR + +* stagedtrees + checking tests ... ERROR + +* statGraph + checking examples ... ERROR + +* stemmatology + checking examples ... ERROR + checking tests ... ERROR + +* stm + checking running R code from vignettes ... ERROR + +* stplanr + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* SurvHiDim + checking examples ... ERROR + +* targets + checking tests ... ERROR + +* TDA + checking examples ... ERROR + checking running R code from vignettes ... ERROR + +* text2map + checking examples ... ERROR + +* textrank + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* tidygraph + checking examples ... ERROR + checking tests ... ERROR + +* tilemaps + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* tip + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* Tlasso + checking examples ... ERROR + checking re-building of vignette outputs ... WARNING + +* TOHM + checking examples ... ERROR + +* TreeDimensionTest + checking re-building of vignette outputs ... WARNING + +* treefit + checking tests ... ERROR + checking re-building of vignette outputs ... WARNING + +* treemap + checking examples ... ERROR + +* VARDetect + checking examples ... ERROR + +* vennLasso + checking examples ... ERROR + +* VertexSimilarity + checking examples ... ERROR + +* vivainsights + checking examples ... ERROR + +* wdnet + checking examples ... ERROR + checking tests ... ERROR + +* webtrackR + checking examples ... ERROR + checking tests ... ERROR + +* whitechapelR + checking examples ... ERROR + checking tests ... ERROR + +* wpa + checking examples ... ERROR + +* xgboost + checking examples ... ERROR + checking tests ... ERROR + ### Failed to check * DRviaSPCN (NA) +* FinNet (NA) * genekitr (NA) * immcp (NA) * MACP (NA) * numbat (NA) * Platypus (NA) +* R6causal (NA) * tidySEM (NA) * vivid (NA) diff --git a/revdep/failures.md b/revdep/failures.md index 233d3ba695a..f6939cdc6f3 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -100,15 +100,73 @@ Status: 1 ERROR +``` +# FinNet + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/FATelarico/FinNet +* Source code: https://github.com/cran/FinNet +* Date/Publication: 2023-06-01 13:00:02 UTC +* Number of recursive dependencies: 42 + +Run `revdepcheck::cloud_details(, "FinNet")` for more info + +
+ +## In both + +* checking whether package ‘FinNet’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/FinNet/new/FinNet.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘FinNet’ ... +** package ‘FinNet’ successfully unpacked and MD5 sums checked +** using staged installation +** R +Error in parse(outFile) : + /tmp/workdir/FinNet/new/FinNet.Rcheck/00_pkg_src/FinNet/R/00.helpers.R:172:21: unexpected input +171: y <- rep(clrs[1], 3)|> paste0(collapse = '')|> +172: paste0('#', x = _ + ^ +ERROR: unable to collate and parse R files for package ‘FinNet’ +* removing ‘/tmp/workdir/FinNet/new/FinNet.Rcheck/FinNet’ + + +``` +### CRAN + +``` +* installing *source* package ‘FinNet’ ... +** package ‘FinNet’ successfully unpacked and MD5 sums checked +** using staged installation +** R +Error in parse(outFile) : + /tmp/workdir/FinNet/old/FinNet.Rcheck/00_pkg_src/FinNet/R/00.helpers.R:172:21: unexpected input +171: y <- rep(clrs[1], 3)|> paste0(collapse = '')|> +172: paste0('#', x = _ + ^ +ERROR: unable to collate and parse R files for package ‘FinNet’ +* removing ‘/tmp/workdir/FinNet/old/FinNet.Rcheck/FinNet’ + + ``` # genekitr
-* Version: 1.1.9 +* Version: 1.2.2 * GitHub: https://github.com/GangLiLab/genekitr * Source code: https://github.com/cran/genekitr -* Date/Publication: 2023-04-15 07:50:02 UTC +* Date/Publication: 2023-05-24 04:00:02 UTC * Number of recursive dependencies: 206 Run `revdepcheck::cloud_details(, "genekitr")` for more info @@ -127,7 +185,7 @@ Run `revdepcheck::cloud_details(, "genekitr")` for more info * using option ‘--no-manual’ * checking for file ‘genekitr/DESCRIPTION’ ... OK * checking extension type ... Package -* this is package ‘genekitr’ version ‘1.1.9’ +* this is package ‘genekitr’ version ‘1.2.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR @@ -153,7 +211,7 @@ Status: 1 ERROR * using option ‘--no-manual’ * checking for file ‘genekitr/DESCRIPTION’ ... OK * checking extension type ... Package -* this is package ‘genekitr’ version ‘1.1.9’ +* this is package ‘genekitr’ version ‘1.2.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR @@ -265,16 +323,16 @@ Run `revdepcheck::cloud_details(, "MACP")` for more info * package encoding: UTF-8 * checking package namespace information ... OK ... -* checking installed files from ‘inst/doc’ ... OK -* checking files in ‘vignettes’ ... OK -* checking examples ... OK -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... NONE - ‘MACP_tutorial.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK +--- failed re-building ‘MACP_tutorial.Rmd’ + +SUMMARY: processing the following file failed: + ‘MACP_tutorial.Rmd’ + +Error: Vignette re-building failed. +Execution halted + * DONE -Status: 3 NOTEs +Status: 1 ERROR, 1 WARNING, 3 NOTEs @@ -315,10 +373,10 @@ Status: 3 NOTEs
-* Version: 1.3.0 +* Version: 1.3.2 * GitHub: https://github.com/kharchenkolab/numbat * Source code: https://github.com/cran/numbat -* Date/Publication: 2023-04-02 17:50:03 UTC +* Date/Publication: 2023-06-06 16:40:02 UTC * Number of recursive dependencies: 132 Run `revdepcheck::cloud_details(, "numbat")` for more info @@ -336,7 +394,7 @@ Run `revdepcheck::cloud_details(, "numbat")` for more info * using session charset: UTF-8 * using option ‘--no-manual’ * checking for file ‘numbat/DESCRIPTION’ ... OK -* this is package ‘numbat’ version ‘1.3.0’ +* this is package ‘numbat’ version ‘1.3.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR @@ -361,7 +419,7 @@ Status: 1 ERROR * using session charset: UTF-8 * using option ‘--no-manual’ * checking for file ‘numbat/DESCRIPTION’ ... OK -* this is package ‘numbat’ version ‘1.3.0’ +* this is package ‘numbat’ version ‘1.3.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR @@ -487,6 +545,95 @@ Status: 1 ERROR +``` +# R6causal + +
+ +* Version: 0.7.0 +* GitHub: NA +* Source code: https://github.com/cran/R6causal +* Date/Publication: 2022-11-04 08:00:02 UTC +* Number of recursive dependencies: 98 + +Run `revdepcheck::cloud_details(, "R6causal")` for more info + +
+ +## Newly broken + +* checking whether package ‘R6causal’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/R6causal/new/R6causal.Rcheck/00install.out’ for details. + ``` + +## Newly fixed + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘using_R6causal.Rmd’ using rmarkdown + A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TinyTeX with tinytex::reinstall_tinytex(repository = "illinois"). + + tlmgr: Local TeX Live (2022) is older than remote repository (2023). + Cross release updates are only supported with + update-tlmgr-latest(.sh/.exe) --update + See https://tug.org/texlive/upgrade.html for details. + Warning in system2("tlmgr", args, ...) : + ... + + Error: processing vignette 'using_R6causal.Rmd' failed with diagnostics: + LaTeX failed to compile /tmp/workdir/R6causal/old/R6causal.Rcheck/vign_test/R6causal/vignettes/using_R6causal.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See using_R6causal.log for more info. + --- failed re-building ‘using_R6causal.Rmd’ + + SUMMARY: processing the following file failed: + ‘using_R6causal.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘R6causal’ ... +** package ‘R6causal’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" +Error: unable to load R code in package ‘R6causal’ +Execution halted +ERROR: lazy loading failed for package ‘R6causal’ +* removing ‘/tmp/workdir/R6causal/new/R6causal.Rcheck/R6causal’ + + +``` +### CRAN + +``` +* installing *source* package ‘R6causal’ ... +** package ‘R6causal’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +** help +*** installing help indices +** building package indices +** installing vignettes +** testing if installed package can be loaded from temporary location +** testing if installed package can be loaded from final location +** testing if installed package keeps a record of temporary installation path +* DONE (R6causal) + + ``` # NA @@ -625,16 +772,16 @@ Run `revdepcheck::cloud_details(, "vivid")` for more info * checking package namespace information ... OK * checking package dependencies ... NOTE ... -* checking installed files from ‘inst/doc’ ... OK -* checking files in ‘vignettes’ ... OK -* checking examples ... OK -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... NONE - ‘vividVignette.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK +--- failed re-building ‘vividVignette.Rmd’ + +SUMMARY: processing the following file failed: + ‘vividVignette.Rmd’ + +Error: Vignette re-building failed. +Execution halted + * DONE -Status: 1 NOTE +Status: 1 WARNING, 1 NOTE diff --git a/revdep/problems.md b/revdep/problems.md index 9a207363396..be5022953b2 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1 +1,24866 @@ -*Wow, no problems at all. :)* \ No newline at end of file +# adegenet + +
+ +* Version: 2.1.10 +* GitHub: https://github.com/thibautjombart/adegenet +* Source code: https://github.com/cran/adegenet +* Date/Publication: 2023-01-26 22:00:23 UTC +* Number of recursive dependencies: 132 + +Run `revdepcheck::cloud_details(, "adegenet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘adegenet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: gengraph + > ### Title: Genetic transitive graphs + > ### Aliases: gengraph gengraph.default gengraph.matrix gengraph.dist + > ### gengraph.genind gengraph.genpop gengraph.DNAbin + > + > ### ** Examples + > + ... + + g <- gengraph(woodmouse, cutoff=5) + + g + + plot(g$graph) + + + + } + Loading required package: ape + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: gengraph ... gengraph.matrix -> graph.adjacency -> graph.adjacency.dense + Execution halted + ``` + +# AHPWR + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/AHPWR +* Date/Publication: 2022-12-06 17:02:46 UTC +* Number of recursive dependencies: 96 + +Run `revdepcheck::cloud_details(, "AHPWR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘AHPWR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: flow_chart + > ### Title: creates a hierarchical structure + > ### Aliases: flow_chart + > + > ### ** Examples + > + > p=flow_chart(names=NULL, a=2, c=2) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: flow_chart -> -> make_empty_graph + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Intro_to_AHP.Rmd’ using rmarkdown + + Quitting from lines 45-47 [unnamed-chunk-2] (Intro_to_AHP.Rmd) + Error: processing vignette 'Intro_to_AHP.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘Intro_to_AHP.Rmd’ + + SUMMARY: processing the following file failed: + ‘Intro_to_AHP.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# akc + +
+ +* Version: 0.9.9 +* GitHub: https://github.com/hope-data-science/akc +* Source code: https://github.com/cran/akc +* Date/Publication: 2023-01-06 08:00:02 UTC +* Number of recursive dependencies: 118 + +Run `revdepcheck::cloud_details(, "akc")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘akc-Ex.R’ failed + The error most likely occurred in: + + > ### Name: doc_group + > ### Title: Construct network of documents based on keyword co-occurrence + > ### Aliases: doc_group + > + > ### ** Examples + > + > library(akc) + > bibli_data_table %>% + + keyword_clean(id = "id",keyword = "keyword") %>% + + doc_group(id = "id",keyword = "keyword") -> grouped_doc + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: %>% ... as_tbl_graph -> graph_from_data_frame -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 5. ├─dplyr::pull(., 2) + 6. ├─akc::keyword_table(.) + 7. │ └─tidygraph::is.tbl_graph(tibble_graph) + 8. ├─akc::keyword_group(., id = "id", keyword = "keyword") + 9. │ └─... %>% mutate(group = com_detect_fun()) + 10. ├─dplyr::mutate(., group = com_detect_fun()) + 11. ├─dplyr::rename(., freq = n) + 12. ├─dplyr::inner_join(., freq_table, by = c(name = "keyword")) + 13. ├─tidygraph::as_tbl_graph(.) + 14. └─igraph::graph_from_data_frame(., directed = FALSE) + 15. └─igraph::make_empty_graph(n = 0, directed = directed) + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 4 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Benchmarking.Rmd’ using rmarkdown + --- finished re-building ‘Benchmarking.Rmd’ + + --- re-building ‘akc_vignette.Rmd’ using rmarkdown + + Quitting from lines 75-79 [unnamed-chunk-5] (akc_vignette.Rmd) + Error: processing vignette 'akc_vignette.Rmd' failed with diagnostics: + could not find function ".igraph.status" + ... + Quitting from lines 63-65 [unnamed-chunk-6] (tutorial_raw_text.Rmd) + Error: processing vignette 'tutorial_raw_text.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘tutorial_raw_text.Rmd’ + + SUMMARY: processing the following files failed: + ‘akc_vignette.Rmd’ ‘tutorial_raw_text.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# alakazam + +
+ +* Version: 1.2.1 +* GitHub: NA +* Source code: https://github.com/cran/alakazam +* Date/Publication: 2022-09-20 22:10:02 UTC +* Number of recursive dependencies: 117 + +Run `revdepcheck::cloud_details(, "alakazam")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘alakazam-Ex.R’ failed + The error most likely occurred in: + + > ### Name: getMRCA + > ### Title: Retrieve the first non-root node of a lineage tree + > ### Aliases: getMRCA + > + > ### ** Examples + > + > # Define example graph + > graph <- ExampleTrees[[23]] + > + > # Use unweighted path length and do not exclude any nodes + > getMRCA(graph, path="steps", root="Germline") + Error in .igraph.status("Restore graph external pointer.\n") : + could not find function ".igraph.status" + Calls: getMRCA ... data.frame -> V -> ensure_igraph -> is_igraph -> warn_version + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘AminoAcids-Vignette.Rmd’ using rmarkdown + A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TinyTeX with tinytex::reinstall_tinytex(repository = "illinois"). + + tlmgr: Local TeX Live (2022) is older than remote repository (2023). + Cross release updates are only supported with + update-tlmgr-latest(.sh/.exe) --update + See https://tug.org/texlive/upgrade.html for details. + Warning in system2("tlmgr", args, ...) : + running command ''tlmgr' search --file --global '/grffile.sty'' had status 1 + ... + LaTeX failed to compile /tmp/workdir/alakazam/new/alakazam.Rcheck/vign_test/alakazam/vignettes/Topology-Vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Topology-Vignette.log for more info. + --- failed re-building ‘Topology-Vignette.Rmd’ + + SUMMARY: processing the following files failed: + ‘AminoAcids-Vignette.Rmd’ ‘Diversity-Vignette.Rmd’ + ‘Fastq-Vignette.Rmd’ ‘Files-Vignette.Rmd’ ‘GeneUsage-Vignette.Rmd’ + ‘Lineage-Vignette.Rmd’ ‘Topology-Vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# AnimalHabitatNetwork + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/AnimalHabitatNetwork +* Date/Publication: 2019-11-25 19:40:02 UTC +* Number of recursive dependencies: 30 + +Run `revdepcheck::cloud_details(, "AnimalHabitatNetwork")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘AnimalHabitatNetwork-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ahn_gen + > ### Title: Generate networks characterising habitat physical configurations + > ### Aliases: ahn_gen + > + > ### ** Examples + > + > # generate a connected and weighted network + > ahn_gen(N = 10, L = 5, mu = 1, lamda = 5) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: ahn_gen ... graph_from_adjacency_matrix -> graph.adjacency.dense + Execution halted + ``` + +# aniSNA + +
+ +* Version: 1.0 +* GitHub: NA +* Source code: https://github.com/cran/aniSNA +* Date/Publication: 2023-02-17 09:50:09 UTC +* Number of recursive dependencies: 58 + +Run `revdepcheck::cloud_details(, "aniSNA")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘aniSNA-Ex.R’ failed + The error most likely occurred in: + + > ### Name: elk_network_2010 + > ### Title: An igraph object depicting the network obtained from + > ### elk_interactions_2010 + > ### Aliases: elk_network_2010 + > ### Keywords: datasets + > + > ### ** Examples + > + > igraph::E(elk_network_2010) + Error in .igraph.status("Restore graph external pointer.\n") : + could not find function ".igraph.status" + Calls: -> ensure_igraph -> is_igraph -> warn_version + Execution halted + ``` + +# anocva + +
+ +* Version: 0.1.1 +* GitHub: NA +* Source code: https://github.com/cran/anocva +* Date/Publication: 2017-11-10 04:27:50 UTC +* Number of recursive dependencies: 9 + +Run `revdepcheck::cloud_details(, "anocva")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘anocva-Ex.R’ failed + The error most likely occurred in: + + > ### Name: spectralClustering + > ### Title: Spectral clustering + > ### Aliases: spectralClustering + > + > ### ** Examples + > + > # Install igraph if necessary + ... + + # Cluster the tree graph in to four clusters + + cluster = spectralClustering(adj, 4) + + + + # See the result clustering + + plot(treeGraph, vertex.size=10, vertex.color = cluster, vertex.label = NA) + + } + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: + Execution halted + ``` + +# archeofrag + +
+ +* Version: 0.8.2 +* GitHub: https://github.com/sebastien-plutniak/archeofrag +* Source code: https://github.com/cran/archeofrag +* Date/Publication: 2022-09-11 22:02:59 UTC +* Number of recursive dependencies: 68 + +Run `revdepcheck::cloud_details(, "archeofrag")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘archeofrag-Ex.R’ failed + The error most likely occurred in: + + > ### Name: frag.cycles + > ### Title: Count the k-cycles in a graph, for cycles =< k + > ### Aliases: frag.cycles + > ### Keywords: measurement + > + > ### ** Examples + > + > g <- frag.simul.process(n.components=20, vertices=50, disturbance=.15) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: frag.simul.process -> .main -> -> do.call -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 2. └─archeofrag::make_cr_graph(g) + 3. └─igraph::graph_from_data_frame(...) + 4. └─igraph::make_empty_graph(n = 0, directed = directed) + ── Error ('test.frag.get.parameters.R:15:3'): retrieved parameters are correct ── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. ├─archeofrag::make_cr_graph(g) at test.frag.get.parameters.R:15:2 + 2. └─archeofrag::make_cr_graph(g) + 3. └─igraph::graph_from_data_frame(...) + 4. └─igraph::make_empty_graph(n = 0, directed = directed) + + [ FAIL 31 | WARN 0 | SKIP 0 | PASS 4 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘archeofrag-vignette.Rmd’ using rmarkdown + + Quitting from lines 61-65 [make-empirical-graph] (archeofrag-vignette.Rmd) + Error: processing vignette 'archeofrag-vignette.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘archeofrag-vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘archeofrag-vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# arulesViz + +
+ +* Version: 1.5-2 +* GitHub: https://github.com/mhahsler/arulesViz +* Source code: https://github.com/cran/arulesViz +* Date/Publication: 2023-03-07 16:50:02 UTC +* Number of recursive dependencies: 111 + +Run `revdepcheck::cloud_details(, "arulesViz")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘arulesViz-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot + > ### Title: Visualize Association Rules and Itemsets + > ### Aliases: plot plot.itemsets plot.rules plot.grouped_matrix plotly + > ### guide_edge_colourbar + > ### Keywords: hplot + > + > ### ** Examples + ... + > + > ## Graph representation + > # Default engine is ggplot2 with ggraph. Associations are represented as nodes. + > # We limit the number of rules to the 10 with the larges + > # lift (measure used for shading) + > plot(subrules, method = "graph", limit = 10) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot ... associations2igraph_nodes -> -> make_empty_graph + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘arulesViz.Rnw’ + ... + + > plot(rules, method = "grouped", control = list(k = 50)) + + > subrules2 <- head(rules, n = 10, by = "lift") + + > plot(subrules2, method = "graph") + + When sourcing ‘arulesViz.R’: + Error: could not find function ".igraph.status" + Execution halted + + ‘arulesViz.Rnw’ using ‘UTF-8’... failed + ``` + +## In both + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘arulesViz.Rnw’ using Sweave + Loading required package: arules + Loading required package: Matrix + + Attaching package: ‘arules’ + + The following objects are masked from ‘package:base’: + + abbreviate, write + ... + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + + --- failed re-building ‘arulesViz.Rnw’ + + SUMMARY: processing the following file failed: + ‘arulesViz.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# autoharp + +
+ +* Version: 0.0.10 +* GitHub: NA +* Source code: https://github.com/cran/autoharp +* Date/Publication: 2021-11-12 22:50:02 UTC +* Number of recursive dependencies: 92 + +Run `revdepcheck::cloud_details(, "autoharp")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘autoharp-Ex.R’ failed + The error most likely occurred in: + + > ### Name: carve_subtree + > ### Title: Carve out branches to form a new tree. + > ### Aliases: carve_subtree + > + > ### ** Examples + > + > th3 <- list(a= c(2L,3L,4L), b=NULL, c=c(5L, 6L), d=7L, e=NULL, f=NULL, g=NULL) + > carve_subtree(TreeHarp(th3), c(1,0,0,0,0,0,0)) + a + > st <- subtree_at(TreeHarp(th3), 4) + > plot(st) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot -> plot -> + Execution halted + ``` + +# autostats + +
+ +* Version: 0.4.0 +* GitHub: https://github.com/Harrison4192/autostats +* Source code: https://github.com/cran/autostats +* Date/Publication: 2022-11-07 10:20:06 UTC +* Number of recursive dependencies: 229 + +Run `revdepcheck::cloud_details(, "autostats")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘autostats.Rmd’ using rmarkdown + --- finished re-building ‘autostats.Rmd’ + + --- re-building ‘tidyXgboost.Rmd’ using rmarkdown + + Quitting from lines 187-189 [unnamed-chunk-15] (tidyXgboost.Rmd) + Error: processing vignette 'tidyXgboost.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘tidyXgboost.Rmd’ + + SUMMARY: processing the following file failed: + ‘tidyXgboost.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# backbone + +
+ +* Version: 2.1.2 +* GitHub: https://github.com/zpneal/backbone +* Source code: https://github.com/cran/backbone +* Date/Publication: 2023-02-13 21:20:02 UTC +* Number of recursive dependencies: 38 + +Run `revdepcheck::cloud_details(, "backbone")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘backbone-Ex.R’ failed + The error most likely occurred in: + + > ### Name: disparity + > ### Title: Extract backbone using the Disparity Filter + > ### Aliases: disparity + > + > ### ** Examples + > + > #A network with heterogeneous (i.e. multiscale) weights + ... + + 0,0,0,0,0,100,0,10,10,10, + + 0,0,0,0,0,100,10,0,10,10, + + 0,0,0,0,0,100,10,10,0,10, + + 0,0,0,0,0,100,10,10,10,0),10) + > + > net <- igraph::graph_from_adjacency_matrix(net, mode = "undirected", weighted = TRUE) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: -> graph.adjacency.dense + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘tinytest.R’ + Running the tests in ‘tests/tinytest.R’ failed. + Last 13 lines of output: + test_backbone.R............... 22 tests OK + test_backbone.R............... 23 tests OK + test_backbone.R............... 24 tests OK + test_backbone.R............... 25 tests OK + test_backbone.R............... 25 tests OK + test_backbone.R............... 25 tests OK + test_backbone.R............... 25 tests OK + test_backbone.R............... 26 tests OK + test_backbone.R............... 27 tests OK + test_backbone.R............... 28 tests OK + test_backbone.R............... 29 tests OK + test_backbone.R............... 30 tests OK Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: ... run_test_dir -> lapply -> FUN -> eval -> eval -> + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘backbone.Rmd’ using rmarkdown + + Quitting from lines 132-134 [unnamed-chunk-5] (backbone.Rmd) + Error: processing vignette 'backbone.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘backbone.Rmd’ + + SUMMARY: processing the following file failed: + ‘backbone.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# backShift + +
+ +* Version: 0.1.4.3 +* GitHub: https://github.com/christinaheinze/backShift +* Source code: https://github.com/cran/backShift +* Date/Publication: 2020-05-06 11:30:03 UTC +* Number of recursive dependencies: 97 + +Run `revdepcheck::cloud_details(, "backShift")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘backShift-Ex.R’ failed + The error most likely occurred in: + + > ### Name: exampleAdjacencyMatrix + > ### Title: Example adjacency matrix + > ### Aliases: exampleAdjacencyMatrix + > ### Keywords: datasets + > + > ### ** Examples + > + > data("exampleAdjacencyMatrix") + > plotGraphEdgeAttr(estimate = exampleAdjacencyMatrix, plotStabSelec = FALSE, + + labels = colnames(exampleAdjacencyMatrix), + + thres.point = 0, thres.stab = NULL, main = "True graph") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plotGraphEdgeAttr -> graph.data.frame -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. ├─testthat::expect_is(...) at test_backShift.R:67:12 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. └─backShift::backShift(...) + 5. └─backShift:::permuteAndScale(estimatedB, verbose) + 6. └─backShift:::hasCPsmallerOne(Dhat, returnCycleNodes = FALSE) + 7. └─igraph::graph.adjacency(Ahat.larger.1, mode = "directed", weighted = "a") + 8. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 32 | WARN 7 | SKIP 0 | PASS 0 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘exampleBackShift.Rmd’ using rmarkdown + + Quitting from lines 180-184 [unnamed-chunk-7] (exampleBackShift.Rmd) + Error: processing vignette 'exampleBackShift.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘exampleBackShift.Rmd’ + + SUMMARY: processing the following file failed: + ‘exampleBackShift.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking Rd cross-references ... NOTE + ``` + Packages unavailable to check Rd xrefs: ‘InvariantCausalPrediction’, ‘CompareCausalNetworks’ + ``` + +# BallMapper + +
+ +* Version: 0.2.0 +* GitHub: NA +* Source code: https://github.com/cran/BallMapper +* Date/Publication: 2019-08-20 21:20:17 UTC +* Number of recursive dependencies: 75 + +Run `revdepcheck::cloud_details(, "BallMapper")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘BallMapper-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ColorIgraphPlot + > ### Title: Produce a static color visualization of the Ball Mapper graph. + > ### It is based on the output from BallMapper function. + > ### Aliases: ColorIgraphPlot + > + > ### ** Examples + > + ... + > var <- seq(from=0,to=6.3,by=0.1) + > points <- as.data.frame( cbind( sin(var),cos(var) ) ) + > values <- as.data.frame( sin(var) ) + > epsilon <- 0.25 + > l <- BallMapper(points,values,epsilon) + > ColorIgraphPlot(l) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: ColorIgraphPlot -> -> make_empty_graph + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘testthat’ + All declared Imports should be used. + ``` + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# bamm + +
+ +* Version: 0.4.3 +* GitHub: https://github.com/luismurao/bamm +* Source code: https://github.com/cran/bamm +* Date/Publication: 2022-12-20 11:10:05 UTC +* Number of recursive dependencies: 110 + +Run `revdepcheck::cloud_details(, "bamm")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘bamm-Ex.R’ failed + The error most likely occurred in: + + > ### Name: bam_clusters + > ### Title: bam_clusters: Function to estimate the connectivity of suitable + > ### areas + > ### Aliases: bam_clusters + > + > ### ** Examples + > + ... + > set.seed(891) + > model_path <- system.file("extdata/Lepus_californicus_cont.tif", + + package = "bamm") + > model <- raster::raster(model_path) + > model <- model > 0.7 + > clusterin <- bamm::bam_clusters(model,ngbs=1,plot_model=TRUE) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: -> -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Backtrace: + ▆ + 1. ├─bamm::csd_estimate(model, dispersal_steps = c(1, 2)) at test-bam.R:230:2 + 2. │ └─... %>% ... + 3. ├─dplyr::summarise(., Clusters = max(clusterID), mean_area = mean(nclust)) + 4. ├─dplyr::group_by(., d) + 5. ├─dplyr::summarise(., nclust = dplyr::n()) + 6. ├─dplyr::group_by(., d, clusterID) + 7. └─dplyr:::group_by.data.frame(., d, clusterID) + 8. └─dplyr::group_by_prepare(.data, ..., .add = .add, error_call = current_env()) + 9. └─rlang::abort(bullets, call = error_call) + + [ FAIL 4 | WARN 0 | SKIP 0 | PASS 63 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘bam.Rmd’ using rmarkdown + + Quitting from lines 97-99 [unnamed-chunk-6] (bam.Rmd) + Error: processing vignette 'bam.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘bam.Rmd’ + + SUMMARY: processing the following file failed: + ‘bam.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# BASiNET + +
+ +* Version: 0.0.5 +* GitHub: NA +* Source code: https://github.com/cran/BASiNET +* Date/Publication: 2022-08-19 08:50:25 UTC +* Number of recursive dependencies: 78 + +Run `revdepcheck::cloud_details(, "BASiNET")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘BASiNET.Rmd’ using rmarkdown + + Quitting from lines 69-73 [unnamed-chunk-1] (BASiNET.Rmd) + Error: processing vignette 'BASiNET.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘BASiNET.Rmd’ + + SUMMARY: processing the following file failed: + ‘BASiNET.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# BASiNETEntropy + +
+ +* Version: 0.99.5 +* GitHub: NA +* Source code: https://github.com/cran/BASiNETEntropy +* Date/Publication: 2022-08-26 14:44:34 UTC +* Number of recursive dependencies: 48 + +Run `revdepcheck::cloud_details(, "BASiNETEntropy")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘BASiNETEntropy-Ex.R’ failed + The error most likely occurred in: + + > ### Name: classify + > ### Title: Performs the classification methodology using complex network + > ### and entropy theories + > ### Aliases: classify + > + > ### ** Examples + > + ... + 6 + 7 + 8 + 9 + 10 + [INFO] Filtering the graphs + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: classify ... graph_from_edgelist -> make_graph -> do.call -> + Execution halted + ``` + +# basket + +
+ +* Version: 0.10.11 +* GitHub: https://github.com/kaneplusplus/basket +* Source code: https://github.com/cran/basket +* Date/Publication: 2021-10-16 23:30:22 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "basket")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 4. └─igraph::graph_from_adjacency_matrix(...) + 5. └─igraph:::graph.adjacency.dense(...) + ── Error ('test-plot.r:7:5'): Plotting works. ────────────────────────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─basket::mem_mcmc(...) at test-plot.r:7:4 + 2. └─basket:::cluster_comp(ret, cluster_function) + 3. └─basket (local) cluster_function(map) + 4. └─igraph::graph_from_adjacency_matrix(...) + 5. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 3 | WARN 0 | SKIP 3 | PASS 15 ] + Error: Test failures + Execution halted + ``` + +# BayesMallows + +
+ +* Version: 1.3.0 +* GitHub: https://github.com/ocbe-uio/BayesMallows +* Source code: https://github.com/cran/BayesMallows +* Date/Publication: 2023-03-10 16:20:17 UTC +* Number of recursive dependencies: 94 + +Run `revdepcheck::cloud_details(, "BayesMallows")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘BayesMallows-Ex.R’ failed + The error most likely occurred in: + + > ### Name: generate_constraints + > ### Title: Generate Constraint Set from Pairwise Comparisons + > ### Aliases: generate_constraints + > + > ### ** Examples + > + > # Here is an example with the beach preference data. + > # First, generate the transitive closure. + > beach_tc <- generate_transitive_closure(beach_preferences) + > + > # Next, generate an initial ranking. + > beach_init_rank <- generate_initial_ranking(beach_tc) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: generate_initial_ranking ... -> make_graph -> do.call -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Backtrace: + ▆ + 1. └─BayesMallows::generate_initial_ranking(beach_tc) at test-plot_top_k.R:6:0 + 2. ├─base::do.call(...) + 3. └─base::lapply(...) + 4. └─BayesMallows (local) FUN(X[[i]], ...) + 5. └─BayesMallows:::create_ranks(as.matrix(x), y, sr, r) + 6. └─igraph::graph_from_edgelist(as.matrix(mat)) + 7. └─igraph::make_graph(t(el), directed = directed) + 8. ├─base::do.call(old_graph, args) + 9. └─igraph (local) ``(``, directed = TRUE) + + [ FAIL 6 | WARN 0 | SKIP 0 | PASS 509 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 47.4Mb + sub-directories of 1Mb or more: + doc 1.7Mb + libs 44.9Mb + ``` + +# BayesMRA + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/jtipton25/BayesMRA +* Source code: https://github.com/cran/BayesMRA +* Date/Publication: 2020-08-18 09:52:11 UTC +* Number of recursive dependencies: 93 + +Run `revdepcheck::cloud_details(, "BayesMRA")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘BayesMRA-Ex.R’ failed + The error most likely occurred in: + + > ### Name: make_Q_alpha_2d + > ### Title: Generate CAR precision matrix + > ### Aliases: make_Q_alpha_2d + > + > ### ** Examples + > + > n_dims <- c(4, 8) + > phi <- c(0.8, 0.9) + > Q_alpha <- make_Q_alpha_2d(n_dims, phi) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: make_Q_alpha_2d ... as_adjacency_matrix -> ensure_igraph -> make_lattice + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 5. ├─igraph::as_adjacency_matrix(...) + 6. │ └─igraph:::ensure_igraph(graph) + 7. └─igraph::make_lattice(length = n_dims[[m]], dim = 2) + ── Error ('test-precision-matrices.R:84:5'): make_Q_alpha_tau2 ───────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─BayesMRA::make_Q_alpha_2d(n_dims, phi) at test-precision-matrices.R:84:4 + 2. ├─igraph::as_adjacency_matrix(...) + 3. │ └─igraph:::ensure_igraph(graph) + 4. └─igraph::make_lattice(length = n_dims[[m]], dim = 2) + + [ FAIL 3 | WARN 0 | SKIP 0 | PASS 121 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.2Mb + sub-directories of 1Mb or more: + doc 2.8Mb + libs 2.3Mb + ``` + +# BayesNetBP + +
+ +* Version: 1.6.1 +* GitHub: https://github.com/hyu-ub/BayesNetBP +* Source code: https://github.com/cran/BayesNetBP +* Date/Publication: 2022-05-08 17:40:02 UTC +* Number of recursive dependencies: 128 + +Run `revdepcheck::cloud_details(, "BayesNetBP")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘BayesNetBP-Ex.R’ failed + The error most likely occurred in: + + > ### Name: AbsorbEvidence + > ### Title: Absorb evidence into the model + > ### Aliases: AbsorbEvidence + > + > ### ** Examples + > + > + > data(liver) + > tree.init.p <- Initializer(dag=liver$dag, data=liver$data, + + node.class=liver$node.class, + + propagate = TRUE) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: Initializer ... EliminationOrder -> igraph.from.graphNEL -> graph_from_adj_list + Execution halted + ``` + +# BayesSUR + +
+ +* Version: 2.1-3 +* GitHub: NA +* Source code: https://github.com/cran/BayesSUR +* Date/Publication: 2023-01-28 17:00:02 UTC +* Number of recursive dependencies: 47 + +Run `revdepcheck::cloud_details(, "BayesSUR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘BayesSUR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.BayesSUR + > ### Title: create a selection of plots + > ### Aliases: plot.BayesSUR + > + > ### ** Examples + > + > data("exampleEQTL", package = "BayesSUR") + ... + > + > ## plot heatmaps of the estimated beta, gamma and Gy + > plot(fit, estimator = c("beta", "gamma", "Gy"), type = "heatmap") + > + > ## plot estimated graph of responses Gy + > plot(fit, estimator = "Gy", type = "graph") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot ... graph_from_adjacency_matrix -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 32.1Mb + sub-directories of 1Mb or more: + data 1.5Mb + libs 29.8Mb + ``` + +# bcgam + +
+ +* Version: 1.0 +* GitHub: NA +* Source code: https://github.com/cran/bcgam +* Date/Publication: 2018-03-18 22:06:50 UTC +* Number of recursive dependencies: 39 + +Run `revdepcheck::cloud_details(, "bcgam")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('testthat.R:3:1'): (code run outside of `test_that()`) ─────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─bcgam::bcgam(...) at testthat.R:3:0 + 2. └─bcgam:::bcgam.fit(...) + 3. └─nimble::nimbleModel(...) + 4. └─md$setupModel(...) + 5. └─nimble (local) genExpandedNodeAndParentNames3(debug = debug) + 6. └─igraph::graph.empty() + + [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ] + Error: Test failures + Execution halted + ``` + +# BCT + +
+ +* Version: 1.2 +* GitHub: NA +* Source code: https://github.com/cran/BCT +* Date/Publication: 2022-05-12 14:00:05 UTC +* Number of recursive dependencies: 14 + +Run `revdepcheck::cloud_details(, "BCT")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘BCT-Ex.R’ failed + The error most likely occurred in: + + > ### Name: draw_models + > ### Title: Plot the results of the BCT and kBCT functions + > ### Aliases: draw_models + > + > ### ** Examples + > + > + > # Use the pewee dataset as an example: + > q <- BCT(pewee, 5) # maximum depth of 5 + > + > draw_models(q) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: draw_models -> show_tree -> + Execution halted + ``` + +# BDgraph + +
+ +* Version: 2.72 +* GitHub: NA +* Source code: https://github.com/cran/BDgraph +* Date/Publication: 2022-12-25 07:20:14 UTC +* Number of recursive dependencies: 72 + +Run `revdepcheck::cloud_details(, "BDgraph")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘BDgraph-Ex.R’ failed + The error most likely occurred in: + + > ### Name: adj2link + > ### Title: Extract links from an adjacency matrix + > ### Aliases: adj2link + > ### Keywords: graphs + > + > ### ** Examples + > + > # Generating a 'random' graph + > adj <- graph.sim( p = 6, vis = TRUE ) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: graph.sim ... -> -> graph.adjacency.dense + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘BDgraph-Examples.Rmd’ using rmarkdown + + Quitting from lines 46-49 [unnamed-chunk-2] (BDgraph-Examples.Rmd) + Error: processing vignette 'BDgraph-Examples.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘BDgraph-Examples.Rmd’ + + --- re-building ‘Introduction-BDgraph.Rmd’ using rmarkdown + ... + Quitting from lines 200-201 [unnamed-chunk-13] (Introduction-BDgraph.Rmd) + Error: processing vignette 'Introduction-BDgraph.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘Introduction-BDgraph.Rmd’ + + SUMMARY: processing the following files failed: + ‘BDgraph-Examples.Rmd’ ‘Introduction-BDgraph.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 11.0Mb + sub-directories of 1Mb or more: + libs 9.5Mb + ``` + +# beam + +
+ +* Version: 2.0.2 +* GitHub: https://github.com/gleday/beam +* Source code: https://github.com/cran/beam +* Date/Publication: 2020-05-28 23:20:18 UTC +* Number of recursive dependencies: 53 + +Run `revdepcheck::cloud_details(, "beam")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.r’ + Running the tests in ‘tests/testthat.r’ failed. + Last 13 lines of output: + ── Error ('test_beam.r:227:3'): NlowerthanP ──────────────────────────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. ├─testthat::expect_equal(class(bgraph(fit)), "igraph") at test_beam.r:227:2 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. ├─beam::bgraph(fit) + 5. └─beam::bgraph(fit) + 6. └─igraph::graph_from_data_frame(d = edges, directed = FALSE) + 7. └─igraph::make_empty_graph(n = 0, directed = directed) + + [ FAIL 2 | WARN 9 | SKIP 0 | PASS 51 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.5Mb + sub-directories of 1Mb or more: + libs 5.8Mb + ``` + +# bibliometrix + +
+ +* Version: 4.1.2 +* GitHub: https://github.com/massimoaria/bibliometrix +* Source code: https://github.com/cran/bibliometrix +* Date/Publication: 2023-03-07 16:00:03 UTC +* Number of recursive dependencies: 150 + +Run `revdepcheck::cloud_details(, "bibliometrix")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘bibliometrix-Ex.R’ failed + The error most likely occurred in: + + > ### Name: biblioNetwork + > ### Title: Creating Bibliographic networks + > ### Aliases: biblioNetwork + > + > ### ** Examples + > + > # EXAMPLE 1: Authors collaboration network + ... + > data(scientometrics, package = "bibliometrixData") + > + > NetMatrix <- biblioNetwork(scientometrics, analysis = "co-citation", + + network = "references", sep = ";") + > + > net <- networkPlot(NetMatrix, n = 30, type = "kamada", Title = "Co-Citation",labelsize=0.5) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: networkPlot ... graph.adjacency.sparse -> make_graph -> do.call -> + Execution halted + ``` + +# bifurcatingr + +
+ +* Version: 1.0.0 +* GitHub: NA +* Source code: https://github.com/cran/bifurcatingr +* Date/Publication: 2021-02-15 17:10:02 UTC +* Number of recursive dependencies: 37 + +Run `revdepcheck::cloud_details(, "bifurcatingr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘bifurcatingr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: bfa.tree.plot + > ### Title: Plotting Bifurcating Autoregressive Trees + > ### Aliases: bfa.tree.plot + > + > ### ** Examples + > + > z <- bfa.tree.gen(31, 1, 1, 1, 0.5, 0.5, 0, 10, c(0.7)) + > bfa.tree.plot(z) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: bfa.tree.plot -> + Execution halted + ``` + +# bio3d + +
+ +* Version: 2.4-4 +* GitHub: NA +* Source code: https://github.com/cran/bio3d +* Date/Publication: 2022-10-26 22:45:06 UTC +* Number of recursive dependencies: 77 + +Run `revdepcheck::cloud_details(, "bio3d")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘bio3d-Ex.R’ failed + The error most likely occurred in: + + > ### Name: print.cna + > ### Title: Summarize and Print Features of a cna Network Graph + > ### Aliases: print.cna summary.cna + > ### Keywords: utilities + > + > ### ** Examples + > + ... + + x<- summary(net) + + x$members[[2]] + + + + detach(hivp) + + + + } + Error in .igraph.status("Restore graph external pointer.\n") : + could not find function ".igraph.status" + Calls: print ... -> ensure_igraph -> is_igraph -> warn_version + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 11.0Mb + sub-directories of 1Mb or more: + libs 7.3Mb + ``` + +# Bioi + +
+ +* Version: 0.2.10 +* GitHub: NA +* Source code: https://github.com/cran/Bioi +* Date/Publication: 2019-12-08 01:30:08 UTC +* Number of recursive dependencies: 72 + +Run `revdepcheck::cloud_details(, "Bioi")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Backtrace: + ▆ + 1. ├─testthat::expect_true(...) at test.euclidean_linker_cpp.R:7:4 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. └─Bioi::euclidean_linker(input, crit_dist) at test.euclidean_linker_cpp.R:11:6 + 5. └─Bioi::.perform_partitioning(...) + 6. ├─igraph::components(...) + 7. │ └─igraph:::ensure_igraph(graph) + 8. └─igraph::graph.data.frame(pOne_dict, directed = FALSE) + 9. └─igraph::make_empty_graph(n = 0, directed = directed) + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 20 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# bioregion + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/bioRgeo/bioregion +* Source code: https://github.com/cran/bioregion +* Date/Publication: 2023-04-14 19:30:02 UTC +* Number of recursive dependencies: 119 + +Run `revdepcheck::cloud_details(, "bioregion")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘bioregion-Ex.R’ failed + The error most likely occurred in: + + > ### Name: map_clusters + > ### Title: Create a map of bioregions + > ### Aliases: map_clusters + > + > ### ** Examples + > + > data(fishmat) + > data(fishsf) + > + > net <- similarity(fishmat, metric = "Simpson") + > clu <- netclu_greedy(net) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: netclu_greedy -> -> make_empty_graph + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.1Mb + sub-directories of 1Mb or more: + data 1.7Mb + doc 1.1Mb + help 1.1Mb + ``` + +# Bios2cor + +
+ +* Version: 2.2.1 +* GitHub: NA +* Source code: https://github.com/cran/Bios2cor +* Date/Publication: 2022-07-08 09:25:23 UTC +* Number of recursive dependencies: 16 + +Run `revdepcheck::cloud_details(, "Bios2cor")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘Bios2cor-Ex.R’ failed + The error most likely occurred in: + + > ### Name: network.plot + > ### Title: Creates network structure of top elements + > ### Aliases: network.plot + > + > ### ** Examples + > + > #File path for output file + ... + > + > #Analyzing pairs with top scores and creating 'top_pairs' object + > top_pairs <- top_pairs_analysis(omes, top = 25, file) + > + > #Plotting the network structure of top pairs in pdf file + > network.plot(top_pairs, file) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: network.plot -> graph_from_data_frame -> make_empty_graph + Execution halted + ``` + +# bipartite + +
+ +* Version: 2.18 +* GitHub: https://github.com/biometry/bipartite +* Source code: https://github.com/cran/bipartite +* Date/Publication: 2022-10-18 23:35:14 UTC +* Number of recursive dependencies: 48 + +Run `revdepcheck::cloud_details(, "bipartite")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘bipartite-Ex.R’ failed + The error most likely occurred in: + + > ### Name: betweenness_w + > ### Title: Betweenness centrality in a weighted network + > ### Aliases: betweenness_w + > + > ### ** Examples + > + > ## Load sample data + ... + + c(3,4,10), + + c(4,2,6), + + c(4,3,10)) + > + > ## Run the programme + > betweenness_w(sampledata) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: betweenness_w ... -> make_graph -> do.call -> + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Intro2bipartite.Rnw’ using Sweave + Loading required package: vegan + Loading required package: permute + Loading required package: lattice + This is vegan 2.6-4 + Loading required package: sna + Loading required package: statnet.common + + Attaching package: ‘statnet.common’ + + The following objects are masked from ‘package:base’: + + attr, order + + Loading required package: network + + ‘network’ 1.18.1 (2023-01-24), part of the Statnet Project + ``` + +# bnma + +
+ +* Version: 1.5.0 +* GitHub: NA +* Source code: https://github.com/cran/bnma +* Date/Publication: 2022-01-03 13:40:08 UTC +* Number of recursive dependencies: 56 + +Run `revdepcheck::cloud_details(, "bnma")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘bnma-Ex.R’ failed + The error most likely occurred in: + + > ### Name: draw.network.graph + > ### Title: Draws network graph using igraph package + > ### Aliases: draw.network.graph + > + > ### ** Examples + > + > #cardiovascular + > network <- with(thrombolytic, { + + network.data(Outcomes, Study, Treat, N=N, response = "binomial") + + }) + > draw.network.graph(network) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: draw.network.graph ... -> make_graph -> do.call -> + Execution halted + ``` + +# bnviewer + +
+ +* Version: 0.1.6 +* GitHub: NA +* Source code: https://github.com/cran/bnviewer +* Date/Publication: 2020-09-14 06:00:03 UTC +* Number of recursive dependencies: 109 + +Run `revdepcheck::cloud_details(, "bnviewer")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘bnviewer-Ex.R’ failed + The error most likely occurred in: + + > ### Name: model.to.structure + > ### Title: Model to Bayesian Network Structure + > ### Aliases: model.to.structure + > + > ### ** Examples + > + > + ... + + bayesianNetwork.layout = "layout_on_grid", + + node.colors = list(background = "#f4bafd", + + border = "#2b7ce9", + + highlight = list(background = "#97c2fc", + + border = "#2b7ce9")) + + ) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: viewer -> -> -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘alarm.R’ + Running the tests in ‘tests/alarm.R’ failed. + Last 13 lines of output: + + bayesianNetwork.title="Discrete Bayesian Network - Coronary", + + bayesianNetwork.subtitle = "Coronary heart disease data set", + + bayesianNetwork.footer = "Fig. 1 - Layout on grid", + + edges.smooth = TRUE, + + edges.shadow = TRUE, + + edges.width = 1.5, + + node.colors = list(background = "#f4bafd", + + border = "#2b7ce9", + + highlight = "#97c2fc") + + + + ) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: viewer -> -> -> make_empty_graph + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘caret’ ‘e1071’ + All declared Imports should be used. + ``` + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# BoolNet + +
+ +* Version: 2.1.8 +* GitHub: NA +* Source code: https://github.com/cran/BoolNet +* Date/Publication: 2023-02-27 13:52:30 UTC +* Number of recursive dependencies: 8 + +Run `revdepcheck::cloud_details(, "BoolNet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘BoolNet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: BoolNet-package + > ### Title: Construction, Simulation and Analysis of Boolean Networks + > ### Aliases: BoolNet-package BoolNet + > + > ### ** Examples + > + > ################################## + ... + > + > # identifies asynchronous attractors + > attractors <- getAttractors(cellcycle, + + type="asynchronous", startStates=100) + > + > plotAttractors(attractors, mode="graph") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plotAttractors ... lapply -> FUN -> graph.data.frame -> make_empty_graph + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘BoolNet_package_vignette.Snw’ using Sweave + Error: processing vignette 'BoolNet_package_vignette.Snw' failed with diagnostics: + Running 'texi2dvi' on 'BoolNet_package_vignette.tex' failed. + LaTeX errors: + ! LaTeX Error: File `a4wide.sty' not found. + + Type X to quit or to proceed, + or enter new name. (Default extension: sty) + ... + l.7 ^^M + + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘BoolNet_package_vignette.Snw’ + + SUMMARY: processing the following file failed: + ‘BoolNet_package_vignette.Snw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# bootnet + +
+ +* Version: 1.5.3 +* GitHub: NA +* Source code: https://github.com/cran/bootnet +* Date/Publication: 2023-06-05 12:30:02 UTC +* Number of recursive dependencies: 190 + +Run `revdepcheck::cloud_details(, "bootnet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘bootnet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: bootnet + > ### Title: Bootstrapped network estimation + > ### Aliases: bootnet + > + > ### ** Examples + > + > # BFI Extraversion data from psychTools package: + ... + Warning in EBICglassoCore(S = S, n = n, gamma = gamma, penalize.diagonal = penalize.diagonal, : + A dense regularized network was selected (lambda < 0.1 * lambda.max). Recent work indicates a possible drop in specificity. Interpret the presence of the smallest edges with care. Setting threshold = TRUE will enforce higher specificity, at the cost of sensitivity. + > + > # Centrality indices: + > library("qgraph") + > centralityPlot(Network) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: centralityPlot ... FUN -> centrality -> -> graph.adjacency.dense + Execution halted + ``` + +# BSBT + +
+ +* Version: 1.2.1 +* GitHub: https://github.com/rowlandseymour/BSBT +* Source code: https://github.com/cran/BSBT +* Date/Publication: 2022-08-09 09:10:02 UTC +* Number of recursive dependencies: 86 + +Run `revdepcheck::cloud_details(, "BSBT")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘BSBT-Ex.R’ failed + The error most likely occurred in: + + > ### Name: constrained_adjacency_covariance_function + > ### Title: Construct a constrained covariance matrix from the adjacency + > ### matrix + > ### Aliases: constrained_adjacency_covariance_function + > + > ### ** Examples + > + > #Construct covariance matrix of Dar es Salaam, Tanzania, using network metric + > data(dar.adj.matrix, package = "BSBT") #load dar es salaam adjacency matrix + > k <- constrained_adjacency_covariance_function(dar.adj.matrix, type = "sqexp", + + hyperparameters = c(1, 1), rep(1, dim(dar.adj.matrix)[1]), 0) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: constrained_adjacency_covariance_function -> -> graph.adjacency.dense + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ▆ + 1. └─BSBT::constrained_adjacency_covariance_function(...) at test-mcmc_functions.R:32:2 + 2. └─igraph::graph.adjacency(adj.matrix, weighted = TRUE) + 3. └─igraph:::graph.adjacency.dense(...) + ── Error ('test-mcmc_functions.R:42:3'): asymmetric MCMC function works ──────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─BSBT::constrained_adjacency_covariance_function(...) at test-mcmc_functions.R:42:2 + 2. └─igraph::graph.adjacency(adj.matrix, weighted = TRUE) + 3. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 6 | WARN 0 | SKIP 0 | PASS 19 ] + Error: Test failures + Execution halted + ``` + +# btergm + +
+ +* Version: 1.10.10 +* GitHub: https://github.com/leifeld/btergm +* Source code: https://github.com/cran/btergm +* Date/Publication: 2023-04-24 12:40:14 UTC +* Number of recursive dependencies: 100 + +Run `revdepcheck::cloud_details(, "btergm")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + + [ FAIL 1 | WARN 0 | SKIP 8 | PASS 51 ] + + ══ Skipped tests ═══════════════════════════════════════════════════════════════ + • On CRAN (8) + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-gof.R:24:3'): basic GOF functionality works ────────────────── + length(g) not equal to 7. + 1/1 mismatches + [1] 6 - 7 == -1 + + [ FAIL 1 | WARN 0 | SKIP 8 | PASS 51 ] + Error: Test failures + Execution halted + ``` + +# bwsTools + +
+ +* Version: 1.2.0 +* GitHub: https://github.com/markhwhiteii/bwsTools +* Source code: https://github.com/cran/bwsTools +* Date/Publication: 2020-08-26 22:40:03 UTC +* Number of recursive dependencies: 75 + +Run `revdepcheck::cloud_details(, "bwsTools")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 6. └─igraph:::graph.adjacency.dense(...) + ── Error ('test_walkscoring.R:4:1'): (code run outside of `test_that()`) ─────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─bwsTools::walkscoring(...) at test_walkscoring.R:4:0 + 2. └─base::lapply(...) + 3. └─bwsTools (local) FUN(X[[i]], ...) + 4. └─bwsTools:::get_walkscores(...) + 5. └─igraph::graph_from_adjacency_matrix(M, mode = "directed", weighted = TRUE) + 6. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 4 | WARN 3 | SKIP 0 | PASS 96 ] + Error: Test failures + Execution halted + ``` + +# Canek + +
+ +* Version: 0.2.2 +* GitHub: https://github.com/MartinLoza/Canek +* Source code: https://github.com/cran/Canek +* Date/Publication: 2023-05-31 04:50:02 UTC +* Number of recursive dependencies: 214 + +Run `revdepcheck::cloud_details(, "Canek")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘Canek-Ex.R’ failed + The error most likely occurred in: + + > ### Name: CorrectBatch + > ### Title: CorrectBatch + > ### Aliases: CorrectBatch + > + > ### ** Examples + > + > x <- SimBatches$batches[[1]] + > y <- SimBatches$batches[[2]] + > z <- CorrectBatch(x, y) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: CorrectBatch ... neighborsToSNNGraph -> make_graph -> do.call -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ▆ + 1. ├─Canek::RunCanek(x, "orig.ident") at test_RunCanek.R:12:0 + 2. └─Canek:::RunCanek.Seurat(x, "orig.ident") + 3. └─Canek::CorrectBatches(counts, debug = debug, ...) + 4. └─Canek::CorrectBatch(...) + 5. └─Canek:::ClusterLouvain(pcaQue[, 1:10], k = kNN, verbose = verbose) + 6. └─bluster::makeSNNGraph(x, k = k) + 7. └─bluster::neighborsToSNNGraph(nn.out$index, type = match.arg(type)) + 8. └─igraph::make_graph(edges, directed = FALSE) + 9. ├─base::do.call(old_graph, args) + 10. └─igraph (local) ``(``, directed = FALSE) + + [ FAIL 7 | WARN 0 | SKIP 0 | PASS 33 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘toy_example.Rmd’ using rmarkdown + + Quitting from lines 79-80 [unnamed-chunk-5] (toy_example.Rmd) + Error: processing vignette 'toy_example.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘toy_example.Rmd’ + + SUMMARY: processing the following file failed: + ‘toy_example.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# cape + +
+ +* Version: 3.1.1 +* GitHub: NA +* Source code: https://github.com/cran/cape +* Date/Publication: 2022-05-19 13:40:02 UTC +* Number of recursive dependencies: 97 + +Run `revdepcheck::cloud_details(, "cape")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘cape.Rmd’ using rmarkdown + + Quitting from lines 481-483 [run_cape] (cape.Rmd) + Error: processing vignette 'cape.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘cape.Rmd’ + + SUMMARY: processing the following file failed: + ‘cape.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# CARlasso + +
+ +* Version: 0.1.2 +* GitHub: https://github.com/YunyiShen/CAR-LASSO +* Source code: https://github.com/cran/CARlasso +* Date/Publication: 2021-08-11 19:00:02 UTC +* Number of recursive dependencies: 87 + +Run `revdepcheck::cloud_details(, "CARlasso")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘CARlasso-Ex.R’ failed + The error most likely occurred in: + + > ### Name: CARlasso + > ### Title: Gibbs sampler for Conditional Autoregressive LASSO and + > ### extensions + > ### Aliases: CARlasso + > + > ### ** Examples + > + ... + [----|----|----|----|----|----|----|----|----|----| + **************************************************| + + done + + > plot(car_res,tol = 0.05) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot ... plot.carlasso_out -> graph.data.frame -> make_empty_graph + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 22.9Mb + sub-directories of 1Mb or more: + libs 22.6Mb + ``` + +# cartograflow + +
+ +* Version: 1.0.3 +* GitHub: https://github.com/fbahoken/cartogRaflow +* Source code: https://github.com/cran/cartograflow +* Date/Publication: 2020-07-19 19:50:02 UTC +* Number of recursive dependencies: 105 + +Run `revdepcheck::cloud_details(, "cartograflow")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘cartograflow-Ex.R’ failed + The error most likely occurred in: + + > ### Name: flowcontig + > ### Title: Builds an ordinal distance matrices from a spatial features + > ### background + > ### Aliases: flowcontig + > + > ### ** Examples + > + ... + Simple feature collection with 12 features and 14 fields + Geometry type: POLYGON + Dimension: XY + Bounding box: xmin: 637297.4 ymin: 6838629 xmax: 671752.1 ymax: 6879246 + Projected CRS: Lambert_Conformal_Conic + > graph_ckij_1 <- flowcontig(bkg = map, code = "EPT_NUM", k = 1, algo = "automatic") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: flowcontig -> -> make_empty_graph + Execution halted + ``` + +# cassowaryr + +
+ +* Version: 2.0.0 +* GitHub: https://github.com/numbats/cassowaryr +* Source code: https://github.com/cran/cassowaryr +* Date/Publication: 2022-08-09 12:30:02 UTC +* Number of recursive dependencies: 106 + +Run `revdepcheck::cloud_details(, "cassowaryr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘cassowaryr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: calc_scags + > ### Title: Compute selected scagnostics on subsets + > ### Aliases: calc_scags + > + > ### ** Examples + > + > # Calculate selected scagnostics on a single pair + > calc_scags(anscombe$x1, anscombe$y1, scags=c("monotonic", "outlying")) + The legacy packages maptools, rgdal, and rgeos, underpinning this package + will retire shortly. Please refer to R-spatial evolution reports on + https://r-spatial.org/r/2023/05/15/evolution4.html for details. + This package is now running under evolution status 0 + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: calc_scags ... -> make_graph -> do.call -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 1. ├─testthat::expect_equal(sc_striated2(x1, y1), 1) at test_mst.R:98:2 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. ├─cassowaryr::sc_striated2(x1, y1) + 5. └─cassowaryr:::sc_striated2.default(x1, y1) + 6. └─cassowaryr:::sc_striated2.scree(sc) + 7. └─cassowaryr:::gen_mst(x$del, x$weights) + 8. └─igraph::graph_from_edgelist(edges, directed = FALSE) + 9. └─igraph::make_graph(t(el), directed = directed) + 10. ├─base::do.call(old_graph, args) + 11. └─igraph (local) ``(``, directed = FALSE) + + [ FAIL 7 | WARN 0 | SKIP 0 | PASS 3 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘cassowaryr.Rmd’ using rmarkdown + + Quitting from lines 67-69 [unnamed-chunk-2] (cassowaryr.Rmd) + Error: processing vignette 'cassowaryr.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘cassowaryr.Rmd’ + + SUMMARY: processing the following file failed: + ‘cassowaryr.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# causact + +
+ +* Version: 0.4.2 +* GitHub: https://github.com/flyaflya/causact +* Source code: https://github.com/cran/causact +* Date/Publication: 2022-06-14 16:00:02 UTC +* Number of recursive dependencies: 118 + +Run `revdepcheck::cloud_details(, "causact")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘causact-Ex.R’ failed + The error most likely occurred in: + + > ### Name: dag_diagrammer + > ### Title: Convert graph to Diagrammer object for visualization + > ### Aliases: dag_diagrammer + > + > ### ** Examples + > + > library("DiagrammeR") + ... + > dag_create() %>% + + dag_node("Get Card","y", + + rhs = bernoulli(theta), + + data = carModelDF$getCard) %>% + + dag_diagrammer() %>% + + render_graph(title = "DiagrammeR Version of causact_graph") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: %>% ... -> ensure_igraph -> -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 2. ├─causact::dag_render(.) + 3. │ └─... %>% generate_dot2() + 4. ├─causact::generate_dot2(.) + 5. ├─causact::dag_diagrammer(., shortLabel = sLabel, wrapWidth = ww) + 6. │ └─graph %>% dag_dim() + 7. ├─causact:::dag_dim(.) + 8. │ ├─... %>% as.integer() + 9. │ └─igraph::graph_from_data_frame(...) + 10. │ └─igraph::make_empty_graph(n = 0, directed = directed) + 11. └─igraph::topo_sort(., mode = "in") + 12. └─igraph:::ensure_igraph(graph) + + [ FAIL 4 | WARN 17 | SKIP 0 | PASS 21 ] + Error: Test failures + Execution halted + ``` + +# causalDisco + +
+ +* Version: 0.9.1 +* GitHub: https://github.com/annennenne/causalDisco +* Source code: https://github.com/cran/causalDisco +* Date/Publication: 2022-05-12 07:50:06 UTC +* Number of recursive dependencies: 41 + +Run `revdepcheck::cloud_details(, "causalDisco")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘causalDisco-Ex.R’ failed + The error most likely occurred in: + + > ### Name: probmat2amat + > ### Title: Convert a matrix of probabilities into an adjacency matrix + > ### Aliases: probmat2amat + > + > ### ** Examples + > + > #Make random probability matrix that can be + ... + > #converted into adjancency matrix + > pmat <- matrix(runif(25, 0, 1), 5, 5) + > diag(pmat) <- 0 + > + > #Convert to adjacency matrix using cutoff-method (threshold = 0.5) + > probmat2amat(pmat, threshold = 0.5) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: probmat2amat ... ensure_igraph -> graph.adjacency -> graph.adjacency.dense + Execution halted + ``` + +# ccTensor + +
+ +* Version: 1.0.2 +* GitHub: https://github.com/rikenbit/ccTensor +* Source code: https://github.com/cran/ccTensor +* Date/Publication: 2021-08-12 04:30:07 UTC +* Number of recursive dependencies: 60 + +Run `revdepcheck::cloud_details(, "ccTensor")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ccTensor-Ex.R’ failed + The error most likely occurred in: + + > ### Name: CUR + > ### Title: CUR Matrix Decomposition + > ### Aliases: CUR + > ### Keywords: methods + > + > ### ** Examples + > + ... + > library("ccTensor") + > library("nnTensor") + > # Test data + > matdata <- toyModel(model = "NMF") + > # Simple usage + > out <- CUR(matdata, c.rank=3, r.rank=4) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: CUR ... graph_from_incidence_matrix -> graph.incidence.dense -> make_empty_graph + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘fields’ + All declared Imports should be used. + ``` + +# CePa + +
+ +* Version: 0.8.0 +* GitHub: https://github.com/jokergoo/CePa +* Source code: https://github.com/cran/CePa +* Date/Publication: 2022-06-11 21:30:06 UTC +* Number of recursive dependencies: 10 + +Run `revdepcheck::cloud_details(, "CePa")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘CePa-Ex.R’ failed + The error most likely occurred in: + + > ### Name: generate.pathway + > ### Title: Generate igraph object from edge list + > ### Aliases: generate.pathway + > + > ### ** Examples + > + > edgelist = rbind(c("a", "b"), c("a", "b"), c("a", "c")) + > g = generate.pathway(edgelist) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: generate.pathway ... graph.edgelist -> make_graph -> do.call -> + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘CePa.Rnw’ using Sweave + Error: processing vignette 'CePa.Rnw' failed with diagnostics: + Running 'texi2dvi' on 'CePa.tex' failed. + LaTeX errors: + ! LaTeX Error: File `ae.sty' not found. + + Type X to quit or to proceed, + or enter new name. (Default extension: sty) + + ... + l.30 \ifthenelse + {\boolean{Sweave@inconsolata}}{%^^M + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘parsing-PID-pathway-data.Rnw’ + + SUMMARY: processing the following files failed: + ‘CePa.Rnw’ ‘analysis-p53.Rnw’ ‘parsing-PID-pathway-data.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# CeRNASeek + +
+ +* Version: 2.1.3 +* GitHub: NA +* Source code: https://github.com/cran/CeRNASeek +* Date/Publication: 2020-04-29 08:00:02 UTC +* Number of recursive dependencies: 9 + +Run `revdepcheck::cloud_details(, "CeRNASeek")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘CeRNASeek-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ceRNA.Net + > ### Title: visualize and analyze the identified ceRNA-ceRNA network using + > ### ceRNA.Net function + > ### Aliases: ceRNA.Net + > ### Keywords: ceRNA.Net + > + > ### ** Examples + ... + > ##file identified by the ceRNA.cmi function. + > ##Here we apply the ceRNA list in the example file for CMI identification to + > ##display the network and analyze the network topology properties. + > ceRNA.Net(as.matrix(dataset[["Pre.ceRNA"]]),net_direct=TRUE,vertex_size=20,v.label = TRUE, + + node_shape="circle",n_color = "orange",E_weight=TRUE,ity=1,label_cex=2, + + label_color="black",edge_color="gray",n_frame.color = "gray") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: ceRNA.Net ... graph.edgelist -> make_graph -> do.call -> + Execution halted + ``` + +# cfid + +
+ +* Version: 0.1.4 +* GitHub: https://github.com/santikka/cfid +* Source code: https://github.com/cran/cfid +* Date/Publication: 2022-10-26 15:35:07 UTC +* Number of recursive dependencies: 51 + +Run `revdepcheck::cloud_details(, "cfid")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 1. └─igraph::graph.formula(X - +Y) at test-graphs.R:175:2 + 2. └─igraph:::graph_from_literal_i(mf) + 3. └─igraph::make_graph(unname(ids[edges]), n = length(v), directed = directed) + 4. ├─base::do.call(old_graph, args) + 5. └─igraph (local) ``(``, n = 2L, directed = TRUE) + ── Error ('test-graphs.R:212:3'): causaleffect sanity ────────────────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─cfid::export_graph(g, "causaleffect") at test-graphs.R:212:2 + 2. └─igraph::make_empty_graph(n = sum(!lat)) + + [ FAIL 4 | WARN 0 | SKIP 0 | PASS 183 ] + Error: Test failures + Execution halted + ``` + +# chemodiv + +
+ +* Version: 0.2.0 +* GitHub: https://github.com/hpetren/chemodiv +* Source code: https://github.com/cran/chemodiv +* Date/Publication: 2023-01-12 09:30:06 UTC +* Number of recursive dependencies: 168 + +Run `revdepcheck::cloud_details(, "chemodiv")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘chemodiv-Ex.R’ failed + The error most likely occurred in: + + > ### Name: molNet + > ### Title: Generate a molecular network with some properties + > ### Aliases: molNet + > + > ### ** Examples + > + > data(minimalCompDis) + > data(minimalNPCTable) + > molNet(minimalCompDis, minimalNPCTable, cutOff = 0) + Using cut-off value = 0 + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: molNet ... graph_from_edgelist -> make_graph -> do.call -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Backtrace: + ▆ + 1. └─chemodiv::molNet(testCompDis) at test-molNetPlot.R:15:0 + 2. └─tidygraph::tbl_graph(nodes = nodes, edges = links) + 3. ├─tidygraph::as_tbl_graph(...) + 4. └─tidygraph:::as_tbl_graph.list(...) + 5. └─tidygraph:::as_graph_node_edge(x, directed = directed, node_key = node_key) + 6. └─igraph::graph_from_edgelist(as.matrix(edges[, 1:2]), directed = directed) + 7. └─igraph::make_graph(t(el), directed = directed) + 8. ├─base::do.call(old_graph, args) + 9. └─igraph (local) ``(``, directed = TRUE) + + [ FAIL 2 | WARN 0 | SKIP 3 | PASS 75 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘chemodiv-vignette.Rmd’ using rmarkdown + + Quitting from lines 313-318 [unnamed-chunk-16] (chemodiv-vignette.Rmd) + Error: processing vignette 'chemodiv-vignette.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘chemodiv-vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘chemodiv-vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# cholera + +
+ +* Version: 0.8.0 +* GitHub: https://github.com/lindbrook/cholera +* Source code: https://github.com/cran/cholera +* Date/Publication: 2023-03-01 12:40:02 UTC +* Number of recursive dependencies: 97 + +Run `revdepcheck::cloud_details(, "cholera")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘cholera-Ex.R’ failed + The error most likely occurred in: + + > ### Name: addWalkingPath + > ### Title: Add the shortest walking path between a selected cases or pumps. + > ### Aliases: addWalkingPath + > + > ### ** Examples + > + > streetNameLocator("broad street", zoom = TRUE, highlight = FALSE, + + add.subtitle = FALSE) + > addWalkingPath(447) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: addWalkingPath ... do.call -> nodeData -> -> make_empty_graph + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘duplicate.missing.cases.Rmd’ using rmarkdown + --- finished re-building ‘duplicate.missing.cases.Rmd’ + + --- re-building ‘kernel.density.Rmd’ using rmarkdown + + Quitting from lines 40-42 [unnamed-chunk-5] (kernel.density.Rmd) + Error: processing vignette 'kernel.density.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘kernel.density.Rmd’ + ... + --- finished re-building ‘time.series.Rmd’ + + --- re-building ‘unstacking.bars.Rmd’ using rmarkdown + --- finished re-building ‘unstacking.bars.Rmd’ + + SUMMARY: processing the following file failed: + ‘kernel.density.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.5Mb + sub-directories of 1Mb or more: + data 1.0Mb + doc 1.5Mb + help 2.2Mb + ``` + +# CKMRpop + +
+ +* Version: 0.1.3 +* GitHub: NA +* Source code: https://github.com/cran/CKMRpop +* Date/Publication: 2021-07-17 10:00:06 UTC +* Number of recursive dependencies: 120 + +Run `revdepcheck::cloud_details(, "CKMRpop")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘CKMRpop-Ex.R’ failed + The error most likely occurred in: + + > ### Name: compile_related_pairs + > ### Title: compile pairwise relationships from the samples + > ### Aliases: compile_related_pairs + > + > ### ** Examples + > + > C <- compile_related_pairs(three_pops_with_mig_slurped_results$samples) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: compile_related_pairs ... -> ensure_igraph -> -> make_empty_graph + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘about_spip.Rmd’ using rmarkdown + --- finished re-building ‘about_spip.Rmd’ + + --- re-building ‘simple-example-with-migration.Rmd’ using rmarkdown + + Quitting from lines 241-262 [unnamed-chunk-14] (simple-example-with-migration.Rmd) + Error: processing vignette 'simple-example-with-migration.Rmd' failed with diagnostics: + could not find function ".igraph.status" + ... + Quitting from lines 306-307 [unnamed-chunk-20] (species_1_simulation.Rmd) + Error: processing vignette 'species_1_simulation.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘species_1_simulation.Rmd’ + + SUMMARY: processing the following files failed: + ‘simple-example-with-migration.Rmd’ ‘species_1_simulation.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 8.3Mb + sub-directories of 1Mb or more: + data 1.1Mb + doc 3.6Mb + help 1.0Mb + libs 2.4Mb + ``` + +# CliquePercolation + +
+ +* Version: 0.4.0 +* GitHub: NA +* Source code: https://github.com/cran/CliquePercolation +* Date/Publication: 2022-11-09 08:40:37 UTC +* Number of recursive dependencies: 115 + +Run `revdepcheck::cloud_details(, "CliquePercolation")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘CliquePercolation-Ex.R’ failed + The error most likely occurred in: + + > ### Name: FuzzyMod + > ### Title: Fuzzy Modularity of a community structure of a graph + > ### Aliases: FuzzyMod + > + > ### ** Examples + > + > g <- igraph::disjoint_union(igraph::make_full_graph(5),igraph::make_full_graph(4)) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: -> unlist -> lapply -> + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘CliquePercolation.Rmd’ using rmarkdown + + Quitting from lines 110-112 [unnamed-chunk-5] (CliquePercolation.Rmd) + Error: processing vignette 'CliquePercolation.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘CliquePercolation.Rmd’ + + SUMMARY: processing the following file failed: + ‘CliquePercolation.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# ClustAssess + +
+ +* Version: 0.3.0 +* GitHub: https://github.com/Core-Bioinformatics/ClustAssess +* Source code: https://github.com/cran/ClustAssess +* Date/Publication: 2022-01-26 16:52:46 UTC +* Number of recursive dependencies: 160 + +Run `revdepcheck::cloud_details(, "ClustAssess")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ClustAssess-Ex.R’ failed + The error most likely occurred in: + + > ### Name: element_sim + > ### Title: The Element-Centric Clustering Similarity + > ### Aliases: element_sim + > + > ### ** Examples + > + > km.res = kmeans(mtcars, 3)$cluster + > hc.res = hclust(dist(mtcars)) + > element_sim(km.res, hc.res) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: element_sim ... make_cielg_hierarchical -> -> graph.adjacency.dense + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘ClustAssess.Rmd’ using rmarkdown + --- finished re-building ‘ClustAssess.Rmd’ + + --- re-building ‘comparing-soft-and-hierarchical.Rmd’ using rmarkdown + + Quitting from lines 76-100 [ecs] (comparing-soft-and-hierarchical.Rmd) + Error: processing vignette 'comparing-soft-and-hierarchical.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘comparing-soft-and-hierarchical.Rmd’ + + SUMMARY: processing the following file failed: + ‘comparing-soft-and-hierarchical.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# ClusTorus + +
+ +* Version: 0.2.2 +* GitHub: https://github.com/sungkyujung/ClusTorus +* Source code: https://github.com/cran/ClusTorus +* Date/Publication: 2022-01-04 10:10:05 UTC +* Number of recursive dependencies: 131 + +Run `revdepcheck::cloud_details(, "ClusTorus")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ClusTorus-Ex.R’ failed + The error most likely occurred in: + + > ### Name: cluster.assign.torus + > ### Title: Clustering by connected components of ellipsoids + > ### Aliases: cluster.assign.torus plot.cluster.obj + > + > ### ** Examples + > + > data <- toydata1[, 1:2] + ... + + kmeansfitmethod = "general", + + J = 4, concentration = 25) + ellip.kmeans.torus: fitting appr. mixture, J = 4, option = general.Done + > level <- 0.1 + > + > cluster.assign.torus(icp.torus, level = level) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: cluster.assign.torus ... conn.comp.ellipse -> -> graph.adjacency.dense + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘ClusTorus.Rmd’ using rmarkdown + + Quitting from lines 59-62 [unnamed-chunk-4] (ClusTorus.Rmd) + Error: processing vignette 'ClusTorus.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘ClusTorus.Rmd’ + + SUMMARY: processing the following file failed: + ‘ClusTorus.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# clustree + +
+ +* Version: 0.5.0 +* GitHub: https://github.com/lazappi/clustree +* Source code: https://github.com/cran/clustree +* Date/Publication: 2022-06-25 20:50:02 UTC +* Number of recursive dependencies: 185 + +Run `revdepcheck::cloud_details(, "clustree")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘clustree-Ex.R’ failed + The error most likely occurred in: + + > ### Name: clustree + > ### Title: Plot a clustering tree + > ### Aliases: clustree clustree.matrix clustree.data.frame + > ### clustree.SingleCellExperiment clustree.seurat clustree.Seurat + > + > ### ** Examples + > + > data(nba_clusts) + > clustree(nba_clusts, prefix = "K") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: clustree ... graph_from_edgelist -> make_graph -> do.call -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 6. ├─clustree::clustree(...) + 7. └─clustree:::clustree.matrix(...) + 8. └─clustree:::build_tree_graph(...) + 9. └─tidygraph::tbl_graph(nodes = nodes, edges = edges) + 10. ├─tidygraph::as_tbl_graph(...) + 11. └─tidygraph:::as_tbl_graph.list(...) + 12. └─tidygraph:::as_graph_node_edge(x, directed = directed, node_key = node_key) + 13. └─igraph::graph_from_edgelist(as.matrix(edges[, 1:2]), directed = directed) + 14. └─igraph::make_graph(t(el), directed = directed) + 15. ├─base::do.call(old_graph, args) + 16. └─igraph (local) ``(``, directed = TRUE) + + [ FAIL 59 | WARN 4 | SKIP 0 | PASS 13 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘clustree.Rmd’ using rmarkdown + + Quitting from lines 81-82 [nba-plot] (clustree.Rmd) + Error: processing vignette 'clustree.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘clustree.Rmd’ + + SUMMARY: processing the following file failed: + ‘clustree.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# clustringr + +
+ +* Version: 1.0 +* GitHub: NA +* Source code: https://github.com/cran/clustringr +* Date/Publication: 2019-03-30 16:10:03 UTC +* Number of recursive dependencies: 54 + +Run `revdepcheck::cloud_details(, "clustringr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘clustringr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: cluster_plot + > ### Title: Plot string clusters as graph. + > ### Aliases: cluster_plot + > + > ### ** Examples + > + > s_vec <- c("alcool","alcohol","alcoholic","brandy","brandie","cachaça") + > s_clust <- cluster_strings(s_vec,method="lv",max_dist=3,algo="cc") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: cluster_strings ... graph_from_adjacency_matrix -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘stringi’ + All declared Imports should be used. + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 5626 marked UTF-8 strings + ``` + +# CoDiNA + +
+ +* Version: 1.1.2 +* GitHub: NA +* Source code: https://github.com/cran/CoDiNA +* Date/Publication: 2020-07-15 12:30:02 UTC +* Number of recursive dependencies: 50 + +Run `revdepcheck::cloud_details(, "CoDiNA")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘CoDiNA-Ex.R’ failed + The error most likely occurred in: + + > ### Name: as.igraph + > ### Title: as.igraph + > ### Aliases: as.igraph + > + > ### ** Examples + > + > suppressWarnings(RNGversion("3.5.0")) + ... + Coding the groups. + Recode is done! + > Graph = plot(x = DiffNet, + + layout = NULL, smooth.edges = TRUE, + + path = NULL, MakeGroups = FALSE, Cluster = FALSE, + + legend = TRUE, manipulation = FALSE, sort.by.Phi = FALSE) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot -> plot.CoDiNA -> -> make_empty_graph + Execution halted + ``` + +# comato + +
+ +* Version: 1.1 +* GitHub: NA +* Source code: https://github.com/cran/comato +* Date/Publication: 2018-03-02 16:36:47 UTC +* Number of recursive dependencies: 22 + +Run `revdepcheck::cloud_details(, "comato")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘comato-Ex.R’ failed + The error most likely occurred in: + + > ### Name: as.matrix.conceptmaps + > ### Title: Convert a conceptmaps object to a matrix + > ### Aliases: as.matrix.conceptmaps + > + > ### ** Examples + > + > data = rbind( + ... + Error in .igraph.status("Free graph external pointer.\n") : + could not find function ".igraph.status" + Error in .igraph.status("Free graph external pointer.\n") : + could not find function ".igraph.status" + Error in .igraph.status("Free graph external pointer.\n") : + could not find function ".igraph.status" + Error in .igraph.status("Free graph external pointer.\n") : + could not find function ".igraph.status" + Error in .igraph.status("Free graph external pointer.\n") : + could not find function ".igraph.status" + ``` + +# concatipede + +
+ +* Version: 1.0.1 +* GitHub: https://github.com/tardipede/concatipede +* Source code: https://github.com/cran/concatipede +* Date/Publication: 2021-08-06 18:10:05 UTC +* Number of recursive dependencies: 128 + +Run `revdepcheck::cloud_details(, "concatipede")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘concatipede-Ex.R’ failed + The error most likely occurred in: + + > ### Name: auto_match_seqs + > ### Title: Build a template table with automatically matched sequence names + > ### Aliases: auto_match_seqs + > + > ### ** Examples + > + > xlsx_file <- concatipede_example("sequences-test-matching.xlsx") + > xlsx_template <- readxl::read_xlsx(xlsx_file) + > auto_match_seqs(xlsx_template) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: auto_match_seqs -> -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 7. └─igraph::make_empty_graph(n = 0, directed = directed) + ── Error ('test-integration.R:61:5'): Functions work well together (medium pipeline 2) ── + Error in `eval(code, test_env)`: !file.exists("my-template.xlsx") is not TRUE + Backtrace: + ▆ + 1. └─base::stopifnot(!file.exists("my-template.xlsx")) at test-integration.R:61:4 + ── Error ('test-integration.R:80:5'): Functions work well together (long pipeline) ── + Error in `eval(code, test_env)`: !file.exists("my-template.xlsx") is not TRUE + Backtrace: + ▆ + 1. └─base::stopifnot(!file.exists("my-template.xlsx")) at test-integration.R:80:4 + + [ FAIL 5 | WARN 0 | SKIP 0 | PASS 31 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Package-usage.Rmd’ using rmarkdown + Warning in in_dir(input_dir(), expr) : + You changed the working directory to /tmp/workdir/concatipede/new/concatipede.Rcheck/vign_test/concatipede/vignettes/concatipede_test (probably via setwd()). It will be restored to /tmp/workdir/concatipede/new/concatipede.Rcheck/vign_test/concatipede/vignettes. See the Note section in ?knitr::knit + + Quitting from lines 173-181 [unnamed-chunk-15] (Package-usage.Rmd) + Error: processing vignette 'Package-usage.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘Package-usage.Rmd’ + + SUMMARY: processing the following file failed: + ‘Package-usage.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# concorR + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/ATraxLab/concorR +* Source code: https://github.com/cran/concorR +* Date/Publication: 2020-11-25 20:30:07 UTC +* Number of recursive dependencies: 19 + +Run `revdepcheck::cloud_details(, "concorR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘concorR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: concor_igraph_apply + > ### Title: Find CONCOR partition and add to a list of 'igraph' objects + > ### Aliases: concor_igraph_apply + > + > ### ** Examples + > + > a <- matrix(c(0, 0, 0, 1, 1, 0, 1, 0, 1, 1, 0, 1, 1, 0, 1, 0), ncol = 4) + > rownames(a) <- c("a", "b", "c", "d") + > colnames(a) <- c("a", "b", "c", "d") + > a.igraph <- igraph::graph_from_adjacency_matrix(a) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: -> graph.adjacency.dense + Execution halted + ``` + +# CoNI + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/CoNI +* Date/Publication: 2021-09-30 09:10:02 UTC +* Number of recursive dependencies: 128 + +Run `revdepcheck::cloud_details(, "CoNI")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘CoNI-Ex.R’ failed + The error most likely occurred in: + + > ### Name: NetStats + > ### Title: Network Statistics + > ### Aliases: NetStats + > + > ### ** Examples + > + > #Load color nodes table + ... + > HFDNetwork<-generate_network(ResultsCoNI = CoNIResultsHFDToy, + + colorVertexNetwork = TRUE, + + colorVertexTable = MetColorTable, + + outputDir = "./", + + outputFileName = "HFD", + + saveFiles = FALSE) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: generate_network -> -> make_empty_graph + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Full_RunCoNI.Rmd’ using rmarkdown + + Quitting from lines 133-138 [network_chow] (Full_RunCoNI.Rmd) + Error: processing vignette 'Full_RunCoNI.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘Full_RunCoNI.Rmd’ + + SUMMARY: processing the following file failed: + ‘Full_RunCoNI.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# corTest + +
+ +* Version: 1.0.7 +* GitHub: NA +* Source code: https://github.com/cran/corTest +* Date/Publication: 2020-09-25 15:30:02 UTC +* Number of recursive dependencies: 33 + +Run `revdepcheck::cloud_details(, "corTest")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘corTest-Ex.R’ failed + The error most likely occurred in: + + > ### Name: construct_network + > ### Title: Construct Differential Correlation Network + > ### Aliases: construct_network + > ### Keywords: correlation test + > + > ### ** Examples + > + ... + + cor_method = "st5", + + pseudo_adjust_cutoff = FALSE, + + var.grp = "grp", + + pAdjMethod = 'fdr', + + cutoff = 0.05, + + nPseudo = 25) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: construct_network -> -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘graphics’ + All declared Imports should be used. + ``` + +# countland + +
+ +* Version: 0.1.1 +* GitHub: NA +* Source code: https://github.com/cran/countland +* Date/Publication: 2022-08-17 06:40:06 UTC +* Number of recursive dependencies: 194 + +Run `revdepcheck::cloud_details(, "countland")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘countland-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Cluster + > ### Title: Perform spectral clustering on dot products. + > ### Aliases: Cluster + > + > ### ** Examples + > + > gold_path <- system.file("testdata", package = "countland", mustWork = TRUE) + ... + the fraction of entries that are nonzero is 0.4074 + > C <- Dot(C) + Calculating dot products between rows... + done. + > C <- Embed(C,n_components=5) + Performing spectral embedding on dot products... + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: Embed ... -> graph.adjacency.sparse -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ── Error ('test-countland_shared_counts.R:13:3'): function PlotSharedCounts, returns plot object ── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─countland::SharedCounts(C, n_clusters = 2, n_cells = 10, subsample = F) at test-countland_shared_counts.R:13:2 + 2. └─countland:::ScikitManifoldSpectralEmbedding(C@sharedcounts, n_clusters) + 3. ├─igraph::as.undirected(igraph::graph.adjacency(A, weighted = T)) + 4. │ └─igraph:::ensure_igraph(graph) + 5. └─igraph::graph.adjacency(A, weighted = T) + 6. └─igraph:::graph.adjacency.sparse(...) + 7. └─igraph::make_empty_graph(n = vc, directed = (mode == "directed")) + + [ FAIL 4 | WARN 0 | SKIP 0 | PASS 59 ] + Error: Test failures + Execution halted + ``` + +# cppRouting + +
+ +* Version: 3.1 +* GitHub: https://github.com/vlarmet/cppRouting +* Source code: https://github.com/cran/cppRouting +* Date/Publication: 2022-12-01 13:20:02 UTC +* Number of recursive dependencies: 40 + +Run `revdepcheck::cloud_details(, "cppRouting")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘cppRouting-Ex.R’ failed + The error most likely occurred in: + + > ### Name: cpp_simplify + > ### Title: Reduce the number of edges by removing non-intersection nodes, + > ### duplicated edges and isolated loops in the graph. + > ### Aliases: cpp_simplify + > + > ### ** Examples + > + ... + > + > #Plot + > if(requireNamespace("igraph",quietly = TRUE)){ + + igr<-igraph::graph_from_data_frame(edges) + + plot(igr) + + } + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: -> make_empty_graph + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 16.4Mb + sub-directories of 1Mb or more: + libs 16.2Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘RcppProgress’ + All declared Imports should be used. + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# crandep + +
+ +* Version: 0.3.1 +* GitHub: https://github.com/clement-lee/crandep +* Source code: https://github.com/cran/crandep +* Date/Publication: 2022-06-03 08:30:10 UTC +* Number of recursive dependencies: 70 + +Run `revdepcheck::cloud_details(, "crandep")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘crandep-Ex.R’ failed + The error most likely occurred in: + + > ### Name: df_to_graph + > ### Title: Construct the giant component of the network from two data + > ### frames + > ### Aliases: df_to_graph + > + > ### ** Examples + > + > from <- c("1", "2", "4") + > to <- c("2", "3", "5") + > edges <- data.frame(from = from, to = to, stringsAsFactors = FALSE) + > nodes <- data.frame(name = c("1", "2", "3", "4", "5"), stringsAsFactors = FALSE) + > df_to_graph(edges, nodes) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: df_to_graph -> -> make_empty_graph + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.1Mb + sub-directories of 1Mb or more: + data 1.2Mb + doc 2.3Mb + libs 3.5Mb + ``` + +# cranly + +
+ +* Version: 0.6.0 +* GitHub: https://github.com/ikosmidis/cranly +* Source code: https://github.com/cran/cranly +* Date/Publication: 2022-08-26 22:14:41 UTC +* Number of recursive dependencies: 64 + +Run `revdepcheck::cloud_details(, "cranly")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘cranly.Rmd’ using rmarkdown + + Quitting from lines 63-65 [unnamed-chunk-7] (cranly.Rmd) + Error: processing vignette 'cranly.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘cranly.Rmd’ + + --- re-building ‘dependence_trees.Rmd’ using rmarkdown + ... + --- failed re-building ‘dependence_trees.Rmd’ + + --- re-building ‘extractors.Rmd’ using rmarkdown + --- finished re-building ‘extractors.Rmd’ + + SUMMARY: processing the following files failed: + ‘cranly.Rmd’ ‘dependence_trees.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.4Mb + sub-directories of 1Mb or more: + doc 5.1Mb + ``` + +# criticalpath + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/rubens2005/criticalpath +* Source code: https://github.com/cran/criticalpath +* Date/Publication: 2022-03-13 22:40:10 UTC +* Number of recursive dependencies: 88 + +Run `revdepcheck::cloud_details(, "criticalpath")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘criticalpath-Ex.R’ failed + The error most likely occurred in: + + > ### Name: sch_activities + > ### Title: Activities + > ### Aliases: sch_activities + > + > ### ** Examples + > + > sch <- sch_new() %>% + ... + + sch_add_activity( 10L, "a10", 3L, 12) %>% + + sch_add_activity( 11L, "a11", 3L, 12) %>% + + sch_add_activity( 12L, "a12", 0L) %>% + + sch_plan() + Error in sch_plan(.) : + The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + Calls: %>% -> sch_plan + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Backtrace: + ▆ + 1. ├─testthat::expect_silent(sch1 <- sch_plan(sch)) at test-cpt-validate_schedule.R:17:2 + 2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise) + 3. │ ├─testthat (local) .capture(...) + 4. │ │ ├─withr::with_output_sink(...) + 5. │ │ │ └─base::force(code) + 6. │ │ ├─base::withCallingHandlers(...) + 7. │ │ └─base::withVisible(code) + 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 9. └─criticalpath::sch_plan(sch) + + [ FAIL 98 | WARN 0 | SKIP 0 | PASS 162 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘criticalpath-introduction.Rmd’ using rmarkdown + + Quitting from lines 95-117 [unnamed-chunk-2] (criticalpath-introduction.Rmd) + Error: processing vignette 'criticalpath-introduction.Rmd' failed with diagnostics: + The schedule is invalid!!! To view the problem, execute: + + `validation <- sch_validate(sch)` + --- failed re-building ‘criticalpath-introduction.Rmd’ + + SUMMARY: processing the following file failed: + ‘criticalpath-introduction.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# crosstalkr + +
+ +* Version: 1.0.2 +* GitHub: NA +* Source code: https://github.com/cran/crosstalkr +* Date/Publication: 2023-05-18 17:50:02 UTC +* Number of recursive dependencies: 167 + +Run `revdepcheck::cloud_details(, "crosstalkr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘crosstalkr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: compute_crosstalk + > ### Title: Identify proteins with a statistically significant relationship + > ### to user-provided seeds. + > ### Aliases: compute_crosstalk + > + > ### ** Examples + > + > #2) Also works for any other kind of graph- just specify g (must be igraph formatted as of now) + > g <- igraph::sample_gnp(n = 1000, p = 10/1000) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─igraph::graph_from_adjacency_matrix(w) at test-filter.R:11:0 + 2. └─igraph:::graph.adjacency.dense(...) + ── Error ('test-plot.R:11:1'): (code run outside of `test_that()`) ───────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─igraph::graph_from_adjacency_matrix(w) at test-plot.R:11:0 + 2. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 4 | WARN 0 | SKIP 11 | PASS 36 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘crosstalkr_vignette.Rmd’ using rmarkdown + + Quitting from lines 79-84 [filter] (crosstalkr_vignette.Rmd) + Error: processing vignette 'crosstalkr_vignette.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘crosstalkr_vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘crosstalkr_vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# cytometree + +
+ +* Version: 2.0.2 +* GitHub: https://github.com/sistm/Cytometree +* Source code: https://github.com/cran/cytometree +* Date/Publication: 2019-12-04 22:20:19 UTC +* Number of recursive dependencies: 63 + +Run `revdepcheck::cloud_details(, "cytometree")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘cytometree-Ex.R’ failed + The error most likely occurred in: + + > ### Name: CytomeTree + > ### Title: Binary tree algorithm for cytometry data analysis. + > ### Aliases: CytomeTree + > + > ### ** Examples + > + > head(DLBCL) + ... + > # Choose a node to plot + > plot_nodes(Tree,"FL4.1") + > + > # Plot a graph of the tree + > par(mfrow=c(1,1)) + > plot_graph(Tree,edge.arrow.size=.3, Vcex =.5, vertex.size = 30) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot_graph -> graph.data.frame -> make_empty_graph + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘autogating_cytometree.Rmd’ using rmarkdown + + Quitting from lines 80-82 [unnamed-chunk-4] (autogating_cytometree.Rmd) + Error: processing vignette 'autogating_cytometree.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘autogating_cytometree.Rmd’ + + --- re-building ‘cytoftree.Rmd’ using rmarkdown + --- finished re-building ‘cytoftree.Rmd’ + + SUMMARY: processing the following file failed: + ‘autogating_cytometree.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# d3po + +
+ +* Version: 0.3.4 +* GitHub: https://github.com/pachadotdev/d3po +* Source code: https://github.com/cran/d3po +* Date/Publication: 2023-03-03 20:20:02 UTC +* Number of recursive dependencies: 56 + +Run `revdepcheck::cloud_details(, "d3po")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘d3po-Ex.R’ failed + The error most likely occurred in: + + > ### Name: d3po_graph + > ### Title: Graph + > ### Aliases: d3po_graph po_nodes po_edges po_layout + > + > ### ** Examples + > + > tr <- igraph::make_tree(40, children = 3, mode = "undirected") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: + Execution halted + ``` + +# dartR + +
+ +* Version: 2.9.7 +* GitHub: NA +* Source code: https://github.com/cran/dartR +* Date/Publication: 2023-06-07 10:40:02 UTC +* Number of recursive dependencies: 285 + +Run `revdepcheck::cloud_details(, "dartR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘dartR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: gl.grm.network + > ### Title: Represents a genomic relationship matrix (GRM) as a network + > ### Aliases: gl.grm.network + > + > ### ** Examples + > + > if (requireNamespace("igraph", quietly = TRUE) & requireNamespace("rrBLUP", + ... + Completed: gl.subsample.loci + Starting gl.grm + Processing genlight object with SNP data + Completed: gl.grm + Starting gl.grm.network + Processing genlight object with SNP data + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: gl.grm.network -> -> make_empty_graph + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘dartRTutorials.Rmd’ using rmarkdown + A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TinyTeX with tinytex::reinstall_tinytex(repository = "illinois"). + + tlmgr: Local TeX Live (2022) is older than remote repository (2023). + Cross release updates are only supported with + update-tlmgr-latest(.sh/.exe) --update + See https://tug.org/texlive/upgrade.html for details. + Warning in system2("tlmgr", args, ...) : + ... + + Error: processing vignette 'dartRTutorials.Rmd' failed with diagnostics: + LaTeX failed to compile /tmp/workdir/dartR/new/dartR.Rcheck/vign_test/dartR/vignettes/dartRTutorials.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See dartRTutorials.log for more info. + --- failed re-building ‘dartRTutorials.Rmd’ + + SUMMARY: processing the following file failed: + ‘dartRTutorials.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# data.tree + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/gluc/data.tree +* Source code: https://github.com/cran/data.tree +* Date/Publication: 2020-08-03 15:50:02 UTC +* Number of recursive dependencies: 122 + +Run `revdepcheck::cloud_details(, "data.tree")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ▆ + 1. └─data.tree::as.igraph.Node(acme, "p", c("level", "isLeaf"), directed = FALSE) at test-treeConversionigraph.R:6:2 + 2. └─igraph::graph_from_data_frame(data, directed = directed, vertices = vert) + 3. └─igraph::make_empty_graph(n = 0, directed = directed) + ── Error ('test-treeConversionigraph.R:15:3'): as.Node.igraph directed ───────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─data.tree::as.igraph.Node(acme, "p", c("level", "isLeaf"), directed = TRUE) at test-treeConversionigraph.R:15:2 + 2. └─igraph::graph_from_data_frame(data, directed = directed, vertices = vert) + 3. └─igraph::make_empty_graph(n = 0, directed = directed) + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 370 ] + Error: Test failures + Execution halted + ``` + +# DDPNA + +
+ +* Version: 0.3.1 +* GitHub: https://github.com/liukf10/DDPNA +* Source code: https://github.com/cran/DDPNA +* Date/Publication: 2022-05-17 12:20:02 UTC +* Number of recursive dependencies: 155 + +Run `revdepcheck::cloud_details(, "DDPNA")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘DDPNA-Ex.R’ failed + The error most likely occurred in: + + > ### Name: getmoduleHub + > ### Title: getmoduleHub + > ### Aliases: getmoduleHub + > + > ### ** Examples + > + > data(net) + ... + > data <- imputedData + > logD <- data$log2_value + > rownames(logD) <- data$inf$ori.ID + > group <- gsub("[0-9]+","", colnames(logD)) + > Module <- Module_inf(net, data$inf) + > Mod10 <- getmoduleHub(logD, Module, 10, coln = "ori.ID", adjustp = FALSE) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: getmoduleHub -> graph.data.frame -> make_empty_graph + Execution halted + ``` + +# deaR + +
+ +* Version: 1.4.1 +* GitHub: NA +* Source code: https://github.com/cran/deaR +* Date/Publication: 2023-05-02 09:20:02 UTC +* Number of recursive dependencies: 75 + +Run `revdepcheck::cloud_details(, "deaR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘deaR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.dea + > ### Title: Plot for DEA models. + > ### Aliases: plot.dea + > + > ### ** Examples + > + > data_example <- make_deadata(datadea = Fortune500, + + inputs = 2:4, + + outputs = 5:6) + > result <- model_basic(data_example) + > plot(result) + Press [enter] to continue + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot ... plot.dea -> graph.adjacency -> graph.adjacency.dense + Execution halted + ``` + +# deepdep + +
+ +* Version: 0.4.2 +* GitHub: https://github.com/DominikRafacz/deepdep +* Source code: https://github.com/cran/deepdep +* Date/Publication: 2023-02-21 00:10:05 UTC +* Number of recursive dependencies: 145 + +Run `revdepcheck::cloud_details(, "deepdep")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ── Error ('test-plot.R:17:1'): (code run outside of `test_that()`) ───────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. ├─vcr::use_cassette(...) at test-plot.R:17:0 + 2. │ └─cassette$call_block(...) + 3. ├─deepdep::plot_dependencies(dd_rlang) at test-plot.R:19:2 + 4. └─deepdep:::plot_dependencies.deepdep(dd_rlang) + 5. └─igraph::make_graph(edges = c(), n = 1) + 6. ├─base::do.call(old_graph, args) + 7. └─igraph (local) ``(``, n = 1) + + [ FAIL 3 | WARN 0 | SKIP 1 | PASS 23 ] + Error: Test failures + Execution halted + ``` + +# degreenet + +
+ +* Version: 1.3-3 +* GitHub: NA +* Source code: https://github.com/cran/degreenet +* Date/Publication: 2018-03-26 07:38:43 UTC +* Number of recursive dependencies: 18 + +Run `revdepcheck::cloud_details(, "degreenet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘degreenet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: reedmolloy + > ### Title: Generate a (non-random) network with a given degree sequence + > ### Aliases: reedmolloy + > ### Keywords: models + > + > ### ** Examples + > + ... + > s4 <- simpln(n=100, v=c(-1,1)) + > table(s4) + s4 + 1 2 3 4 5 6 + 65 18 7 4 4 2 + > # + > simr <- reedmolloy(s4) + Error in reedmolloy(s4) : + The reedmolloy function failed to form a valid network from the passed degree sequence. + Execution halted + ``` + +# delayed + +
+ +* Version: 0.4.0 +* GitHub: https://github.com/tlverse/delayed +* Source code: https://github.com/cran/delayed +* Date/Publication: 2022-10-19 22:25:09 UTC +* Number of recursive dependencies: 81 + +Run `revdepcheck::cloud_details(, "delayed")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘delayed-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.Delayed + > ### Title: Plot Method for Delayed Objects + > ### Aliases: plot.Delayed + > + > ### ** Examples + > + > adder <- function(x, y) { + ... + > delayed_adder <- delayed_fun(adder) + > z <- delayed_adder(3, 4) + > z2 <- delayed_adder(z, 4) + > z2$sequential <- TRUE + > z3 <- delayed_adder(z2, z) + > plot(z3) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot -> plot.Delayed -> make_graph -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + • empty test (1) + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test_make_graph.R:18:3'): can plot graph ──────────────────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. ├─base::plot(z3) at test_make_graph.R:18:2 + 2. └─delayed:::plot.Delayed(z3) + 3. └─delayed:::make_graph(x) + 4. └─igraph::make_empty_graph() + + [ FAIL 1 | WARN 0 | SKIP 1 | PASS 12 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘delayed.Rmd’ using rmarkdown + + Quitting from lines 97-98 [unnamed-chunk-2] (delayed.Rmd) + Error: processing vignette 'delayed.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘delayed.Rmd’ + + SUMMARY: processing the following file failed: + ‘delayed.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# DemoKin + +
+ +* Version: 1.0.3 +* GitHub: https://github.com/IvanWilli/DemoKin +* Source code: https://github.com/cran/DemoKin +* Date/Publication: 2023-06-05 09:00:02 UTC +* Number of recursive dependencies: 77 + +Run `revdepcheck::cloud_details(, "DemoKin")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Reference_OneSex.Rmd’ using rmarkdown + + Quitting from lines 119-123 [unnamed-chunk-10] (Reference_OneSex.Rmd) + Error: processing vignette 'Reference_OneSex.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘Reference_OneSex.Rmd’ + + --- re-building ‘Reference_TwoSex.Rmd’ using rmarkdown + --- finished re-building ‘Reference_TwoSex.Rmd’ + + SUMMARY: processing the following file failed: + ‘Reference_OneSex.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.8Mb + sub-directories of 1Mb or more: + data 1.2Mb + doc 3.1Mb + help 1.3Mb + ``` + +# dexterMST + +
+ +* Version: 0.9.3 +* GitHub: https://github.com/dexter-psychometrics/dexter +* Source code: https://github.com/cran/dexterMST +* Date/Publication: 2022-02-14 19:40:13 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "dexterMST")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘dexterMST-Ex.R’ failed + The error most likely occurred in: + + > ### Name: create_mst_test + > ### Title: Define a new multi stage test + > ### Aliases: create_mst_test + > + > ### ** Examples + > + > # extended example + ... + > + > add_response_data_mst(db, dat) + Added 90000 responses for 3000 administrations + > + > + > design_plot(db) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: design_plot ... ensure_igraph -> graph.data.frame -> make_empty_graph + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.3Mb + sub-directories of 1Mb or more: + libs 5.7Mb + ``` + +# DiagrammeR + +
+ +* Version: 1.0.10 +* GitHub: https://github.com/rich-iannone/DiagrammeR +* Source code: https://github.com/cran/DiagrammeR +* Date/Publication: 2023-05-18 14:30:07 UTC +* Number of recursive dependencies: 99 + +Run `revdepcheck::cloud_details(, "DiagrammeR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘DiagrammeR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: add_full_graph + > ### Title: Add a fully connected graph + > ### Aliases: add_full_graph + > + > ### ** Examples + > + > # Create a new graph object + ... + > # and to themselves + > graph <- + + create_graph() %>% + + add_full_graph( + + n = 3, keep_loops = TRUE + + ) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: %>% ... from_adj_matrix -> -> graph.adjacency.dense + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ── Error ('test-write_graph_backup.R:922:3'): Graph backups for `recode_node_attrs()` works ── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. ├─... %>% ... at test-write_graph_backup.R:922:2 + 2. ├─DiagrammeR::recode_node_attrs(...) + 3. │ └─DiagrammeR:::graph_object_valid(graph) + 4. │ └─... %in% names(graph) + 5. ├─DiagrammeR::set_node_attrs(...) + 6. └─DiagrammeR::add_gnm_graph(., n = 5, m = 10, set_seed = 23) + 7. └─igraph::sample_gnm(n = n, m = m, directed = graph_directed, loops = loops) + + [ FAIL 109 | WARN 3 | SKIP 0 | PASS 1373 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 1 marked UTF-8 string + ``` + +# diffeRenTES + +
+ +* Version: 0.3.2 +* GitHub: NA +* Source code: https://github.com/cran/diffeRenTES +* Date/Publication: 2022-04-28 07:20:04 UTC +* Number of recursive dependencies: 60 + +Run `revdepcheck::cloud_details(, "diffeRenTES")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘diffeRenTES-Ex.R’ failed + The error most likely occurred in: + + > ### Name: getTESs + > ### Title: Compute TES + > ### Aliases: getTESs + > + > ### ** Examples + > + > + > net <- BoolNet::generateRandomNKNetwork(10, 2) + > attractors <- BoolNet::getAttractors(net) + > ATM <- getATM(net, attractors) + > getTESs(ATM) + In the ATM there is no threshold value equal to 0, it will be added for the calculation of TESs + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: getTESs -> -> graph.adjacency.dense + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Loading required package: diffeRenTES + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 20 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('tests-atm.R:17:3'): TES tests working ─────────────────────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─diffeRenTES::getTESs(a) at tests-atm.R:17:2 + 2. └─igraph::graph_from_adjacency_matrix(adj_mtrx, mode = "directed") + 3. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 20 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘diffeRenTES_vignette.Rmd’ using rmarkdown + + Quitting from lines 67-75 [unnamed-chunk-5] (diffeRenTES_vignette.Rmd) + Error: processing vignette 'diffeRenTES_vignette.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘diffeRenTES_vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘diffeRenTES_vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# diffudist + +
+ +* Version: 1.0.1 +* GitHub: https://github.com/gbertagnolli/diffudist +* Source code: https://github.com/cran/diffudist +* Date/Publication: 2023-02-27 19:42:40 UTC +* Number of recursive dependencies: 74 + +Run `revdepcheck::cloud_details(, "diffudist")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘diffudist-Ex.R’ failed + The error most likely occurred in: + + > ### Name: get_distance_matrix + > ### Title: Diffusion Distance Matrix + > ### Aliases: get_distance_matrix getDistanceMatrix get_DDM + > ### Keywords: diffusion distance + > + > ### ** Examples + > + > g <- igraph::sample_pa(10, directed = FALSE) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.1Mb + sub-directories of 1Mb or more: + libs 4.1Mb + ``` + +# diffusr + +
+ +* Version: 0.1.4 +* GitHub: https://github.com/dirmeier/diffusr +* Source code: https://github.com/cran/diffusr +* Date/Publication: 2018-05-17 21:01:21 UTC +* Number of recursive dependencies: 65 + +Run `revdepcheck::cloud_details(, "diffusr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘diffusr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: random.walk + > ### Title: Graph diffusion using a Markov random walk + > ### Aliases: random.walk random.walk,numeric,matrix-method + > ### random.walk,matrix,matrix-method + > + > ### ** Examples + > + ... + > # adjacency matrix (either normalized or not) + > graph <- matrix(abs(rnorm(n*n)), n, n) + > # computation of stationary distribution + > pt <- random.walk(p0, graph) + setting diag of graph to zero + normalizing column vectors! + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: random.walk ... .is.ergodic -> -> graph.adjacency.dense + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Backtrace: + ▆ + 1. └─igraph::graph_from_adjacency_matrix(adja) at test_mrw.R:24:0 + 2. └─igraph:::graph.adjacency.dense(...) + ── Error ('test_util.R:24:1'): (code run outside of `test_that()`) ───────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─igraph::make_graph(c(1, 2, 2, 3, 3, 4, 4, 5), directed = FALSE) at test_util.R:24:0 + 2. ├─base::do.call(old_graph, args) + 3. └─igraph (local) ``(``, directed = FALSE) + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 21 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘diffusr.Rmd’ using rmarkdown + + Quitting from lines 34-42 [unnamed-chunk-2] (diffusr.Rmd) + Error: processing vignette 'diffusr.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘diffusr.Rmd’ + + SUMMARY: processing the following file failed: + ‘diffusr.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 15.8Mb + sub-directories of 1Mb or more: + libs 14.8Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘methods’ + All declared Imports should be used. + ``` + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# dimRed + +
+ +* Version: 0.2.6 +* GitHub: https://github.com/gdkrmr/dimRed +* Source code: https://github.com/cran/dimRed +* Date/Publication: 2022-07-11 12:40:06 UTC +* Number of recursive dependencies: 132 + +Run `revdepcheck::cloud_details(, "dimRed")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘dimRed-Ex.R’ failed + The error most likely occurred in: + + > ### Name: FruchtermanReingold-class + > ### Title: Fruchterman Reingold Graph Layout + > ### Aliases: FruchtermanReingold-class FruchtermanReingold + > + > ### ** Examples + > + > if(requireNamespace(c("igraph", "coRanking"), quietly = TRUE)) { + ... + + + + dat <- loadDataSet("Swiss Roll", n = 100) + + emb <- embed(dat, "FruchtermanReingold") + + plot(emb, type = "2vars") + + + + } + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: embed ... construct_knn_graph -> -> graph.adjacency.dense + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ── Error ('test_isomap.R:49:3'): check other.data ────────────────────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. ├─dimRed::embed(a, "Isomap", knn = 8, ndim = 2, get_geod = TRUE) at test_isomap.R:49:2 + 2. └─dimRed::embed(a, "Isomap", knn = 8, ndim = 2, get_geod = TRUE) + 3. └─dimRed (local) .local(.data, ...) + 4. ├─base::do.call(methodObject@fun, args) + 5. └─dimRed (local) ``(data = ``, keep.org.data = TRUE, pars = ``) + 6. └─dimRed:::makeKNNgraph(x = indata, k = pars$knn, eps = pars$eps) + 7. └─igraph::make_empty_graph(M, directed = TRUE) + + [ FAIL 3 | WARN 8 | SKIP 7 | PASS 166 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking for unstated dependencies in examples ... WARNING + ``` + 'library' or 'require' calls not declared from: + ‘MASS’ ‘Matrix’ ‘NNMF’ ‘RANN’ ‘RSpectra’ ‘c’ ‘coRanking’ ‘ggplot’ + ‘igraph’ ‘loe’ ‘scales’ ‘tidyr’ + ``` + +# discourseGT + +
+ +* Version: 1.1.8 +* GitHub: NA +* Source code: https://github.com/cran/discourseGT +* Date/Publication: 2022-10-27 23:25:10 UTC +* Number of recursive dependencies: 119 + +Run `revdepcheck::cloud_details(, "discourseGT")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘discourseGT-Ex.R’ failed + The error most likely occurred in: + + > ### Name: basicPlot + > ### Title: Plot Graphs + > ### Aliases: basicPlot + > + > ### ** Examples + > + > + > df <- sampleData1 + > prepNet <- tabulate_edges(df, iscsvfile = FALSE, silentNodes = 0) + > baseNet <- prepareGraphs(prepNet, project_title = "Sample Data 1", weightedGraph = TRUE) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: prepareGraphs -> -> make_empty_graph + Execution halted + ``` + +# discretecdAlgorithm + +
+ +* Version: 0.0.7 +* GitHub: NA +* Source code: https://github.com/cran/discretecdAlgorithm +* Date/Publication: 2020-03-12 06:40:02 UTC +* Number of recursive dependencies: 39 + +Run `revdepcheck::cloud_details(, "discretecdAlgorithm")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘discretecdAlgorithm-Ex.R’ failed + The error most likely occurred in: + + > ### Name: generate_discrete_data + > ### Title: generate_discrete_data + > ### Aliases: generate_discrete_data + > + > ### ** Examples + > + > + ... + > nlevels <- c(3, 5, 2, 2, 3) + > gr.params <- coef_gen(edge_list = gr, n_levels = nlevels) + > data.obs <- discretecdAlgorithm::generate_discrete_data(graph = gr, + + n = 100, + + n_levels = nlevels, + + params = gr.params) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: ... datGen_call -> -> graph.adjacency.dense + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 2. └─discretecdAlgorithm:::datGen_call(...) + 3. └─igraph::graph.adjacency(as.matrix(adj_matrix)) + 4. └─igraph:::graph.adjacency.dense(...) + ── Error ('test-generate_discrete_data.R:41:3'): Check output ────────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─discretecdAlgorithm::generate_discrete_data(...) at test-generate_discrete_data.R:41:2 + 2. └─discretecdAlgorithm:::datGen_call(...) + 3. └─igraph::graph.adjacency(as.matrix(adj_matrix)) + 4. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 9 | WARN 0 | SKIP 0 | PASS 544 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 14.3Mb + sub-directories of 1Mb or more: + libs 14.2Mb + ``` + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# dm + +
+ +* Version: 1.0.5 +* GitHub: https://github.com/cynkra/dm +* Source code: https://github.com/cran/dm +* Date/Publication: 2023-03-16 17:10:02 UTC +* Number of recursive dependencies: 134 + +Run `revdepcheck::cloud_details(, "dm")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘dm-Ex.R’ failed + The error most likely occurred in: + + > ### Name: copy_dm_to + > ### Title: Copy data model to data source + > ### Aliases: copy_dm_to + > + > ### ** Examples + > + > ## Don't show: + ... + + + + DBI::dbDisconnect(con) + + ## Don't show: + + }) # examplesIf + > con <- DBI::dbConnect(RSQLite::SQLite()) + > temp_dm <- copy_dm_to(con, dm_nycflights13(), set_key_constraints = FALSE) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: ... create_graph_from_dm -> %>% -> -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ▆ + 1. ├─dm::copy_dm_to(...) at test_dm_from_con.R:46:2 + 2. │ └─dm:::build_copy_queries(...) + 3. │ └─dm:::create_graph_from_dm(dm, directed = TRUE) + 4. │ └─... %>% ... + 5. └─igraph::graph_from_data_frame(., directed = directed, vertices = def$table) + 6. └─igraph::make_empty_graph(n = 0, directed = directed) + ── Error ('test-zoom.R:135:3'): zoom output for compound keys ────────────────── + `{ ... }` threw an unexpected error. + Message: could not find function ".igraph.status" + Class: simpleError/error/condition + + [ FAIL 41 | WARN 2 | SKIP 192 | PASS 1176 ] + Error: Test failures + Execution halted + ``` + +# dnapath + +
+ +* Version: 0.7.4 +* GitHub: NA +* Source code: https://github.com/cran/dnapath +* Date/Publication: 2022-05-09 09:00:05 UTC +* Number of recursive dependencies: 149 + +Run `revdepcheck::cloud_details(, "dnapath")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘dnapath-Ex.R’ failed + The error most likely occurred in: + + > ### Name: dnapath + > ### Title: Differential Network Analysis Using Gene Pathways + > ### Aliases: dnapath + > + > ### ** Examples + > + > data(meso) + ... + 7 Regulation of TP53 Degradation … 983 0.141 0.0909 8.49 8.56 + 8 Regulation of TP53 Degradation … 7157 0.221 0.182 11.1 10.8 + 9 Regulation of TP53 Degradation … 80196 0.214 0.182 9.37 9.36 + 10 Regulation of TP53 Degradation … 5519 0.177 0.182 9.14 9.20 + # ℹ 27 more rows + > plot(results[[1]]) # Plot of the differential network for pathway 1. + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot ... -> -> graph.adjacency.dense + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘introduction_to_dnapath.Rmd’ using rmarkdown + + Quitting from lines 164-165 [unnamed-chunk-3] (introduction_to_dnapath.Rmd) + Error: processing vignette 'introduction_to_dnapath.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘introduction_to_dnapath.Rmd’ + + --- re-building ‘package_data.Rmd’ using rmarkdown + --- finished re-building ‘package_data.Rmd’ + + SUMMARY: processing the following file failed: + ‘introduction_to_dnapath.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# dnr + +
+ +* Version: 0.3.5 +* GitHub: NA +* Source code: https://github.com/cran/dnr +* Date/Publication: 2020-11-30 17:10:03 UTC +* Number of recursive dependencies: 73 + +Run `revdepcheck::cloud_details(, "dnr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘dnr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: clustCoef + > ### Title: clustCoef + > ### Aliases: clustCoef + > + > ### ** Examples + > + > clustCoef(beach[[1]][, ]) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: clustCoef ... ensure_igraph -> -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘dnr_vignette.Rnw’ using knitr + Warning: 'mode(width)' differs between new and previous + ==> NOT changing 'width' + Warning: 'mode(width)' differs between new and previous + ==> NOT changing 'width' + Warning: 'mode(width)' differs between new and previous + ==> NOT changing 'width' + Warning: 'mode(width)' differs between new and previous + ... + Quitting from lines 126-133 [beach-vertex-model-fit] (dnr_vignette.Rnw) + Error: processing vignette 'dnr_vignette.Rnw' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘dnr_vignette.Rnw’ + + SUMMARY: processing the following file failed: + ‘dnr_vignette.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# dodgr + +
+ +* Version: 0.2.21 +* GitHub: https://github.com/ATFutures/dodgr +* Source code: https://github.com/cran/dodgr +* Date/Publication: 2023-06-02 11:40:02 UTC +* Number of recursive dependencies: 110 + +Run `revdepcheck::cloud_details(, "dodgr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘dodgr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: dodgr_centrality + > ### Title: Calculate betweenness centrality for a 'dodgr' network. + > ### Aliases: dodgr_centrality + > + > ### ** Examples + > + > graph_full <- weight_streetnet (hampi) + ... + Graph has duplicated edges. Only the first will be used here, + but it is better to remove them first with the 'dodgr_deduplicate_graph() function. + > # 'graph' is then the contracted graph with an additional 'centrality' column + > # Same calculation via 'igraph': + > igr <- dodgr_to_igraph (graph) + Loading required namespace: igraph + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: dodgr_to_igraph -> -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘sc-conversion-fns.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 3. └─igraph::make_empty_graph(n = 0, directed = directed) + ── Error ('test-graph-conversion.R:25:5'): tidyraph ──────────────────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. ├─dodgr::dodgr_to_tidygraph(graph) at test-graph-conversion.R:25:4 + 2. │ ├─dodgr_to_igraph(graph) %>% tidygraph::as_tbl_graph() + 3. │ └─dodgr::dodgr_to_igraph(graph) + 4. │ └─igraph::graph_from_data_frame(graph, directed = TRUE, vertices = v) + 5. │ └─igraph::make_empty_graph(n = 0, directed = directed) + 6. └─tidygraph::as_tbl_graph(.) + + [ FAIL 2 | WARN 0 | SKIP 11 | PASS 242 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘dists-categorical.Rmd’ using rmarkdown + --- finished re-building ‘dists-categorical.Rmd’ + + --- re-building ‘dodgr.Rmd’ using rmarkdown + + Quitting from lines 501-502 [compare-heaps] (dodgr.Rmd) + Error: processing vignette 'dodgr.Rmd' failed with diagnostics: + could not find function ".igraph.status" + ... + --- finished re-building ‘parallel.Rmd’ + + --- re-building ‘times.Rmd’ using rmarkdown + --- finished re-building ‘times.Rmd’ + + SUMMARY: processing the following file failed: + ‘dodgr.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 35.2Mb + sub-directories of 1Mb or more: + doc 6.5Mb + libs 28.1Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# dosearch + +
+ +* Version: 1.0.8 +* GitHub: NA +* Source code: https://github.com/cran/dosearch +* Date/Publication: 2021-08-19 16:40:02 UTC +* Number of recursive dependencies: 15 + +Run `revdepcheck::cloud_details(, "dosearch")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘dosearch-Ex.R’ failed + The error most likely occurred in: + + > ### Name: dosearch + > ### Title: Identify a causal effect from arbitrary experiments and + > ### observations + > ### Aliases: dosearch + > + > ### ** Examples + > + ... + > ## Graph input using 'igraph' in the 'causaleffect' syntax + > if (requireNamespace("igraph", quietly = TRUE)) { + + g_igraph <- igraph::graph.formula(x -+ z, z -+ y, x -+ y, y -+ x) + + g_igraph <- igraph::set.edge.attribute(g_igraph, "description", 3:4, "U") + + dosearch(data2, query2, g_igraph) + + } + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: ... graph_from_literal_i -> make_graph -> do.call -> + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.4Mb + sub-directories of 1Mb or more: + libs 6.2Mb + ``` + +# dragon + +
+ +* Version: 1.2.1 +* GitHub: https://github.com/sjspielman/dragon +* Source code: https://github.com/cran/dragon +* Date/Publication: 2022-04-08 08:42:33 UTC +* Number of recursive dependencies: 130 + +Run `revdepcheck::cloud_details(, "dragon")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 5. │ └─testthat:::test_files_setup_state(...) + 6. │ └─testthat::source_test_setup(".", env) + 7. │ └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE) + 8. │ └─base::lapply(...) + 9. │ └─testthat (local) FUN(X[[i]], ...) + 10. │ └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap) + 11. │ ├─base::withCallingHandlers(...) + 12. │ └─base::eval(exprs, env) + 13. │ └─base::eval(exprs, env) + 14. │ └─igraph::read_graph("graph_by_redox.igraph", format = "ncol") at tests/testthat/setup_test-settings.R:8:0 + 15. │ └─igraph:::read.graph.ncol(file, ...) + 16. └─base::.handleSimpleError(...) + 17. └─testthat (local) h(simpleError(msg, call)) + 18. └─rlang::abort(...) + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘htmltools’ + All declared Imports should be used. + ``` + +# drake + +
+ +* Version: 7.13.5 +* GitHub: https://github.com/ropensci/drake +* Source code: https://github.com/cran/drake +* Date/Publication: 2023-03-24 13:10:02 UTC +* Number of recursive dependencies: 164 + +Run `revdepcheck::cloud_details(, "drake")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘drake-Ex.R’ failed + The error most likely occurred in: + + > ### Name: code_to_plan + > ### Title: Turn an R script file or 'knitr' / R Markdown report into a + > ### 'drake' plan. *[Questioning]* + > ### Aliases: code_to_plan + > + > ### ** Examples + > + ... + + hist = create_plot(data), + + fit = lm(Ozone ~ Temp + Wind, data) + + ) + > file <- tempfile() + > # Turn the plan into an R script a the given file path. + > plan_to_code(plan, file) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plan_to_code ... cdg_finalize_graph -> -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Backtrace: + 1. drake::drake_config(...) + at test-4-rng.R:301:2 + 2. drake:::create_drake_graph(...) + 5. drake:::cdg_finalize_graph(edges, targets, args) + 6. igraph::graph_from_data_frame(edges) + 7. igraph::make_empty_graph(n = 0, directed = directed) + ... and 41 more + + + Maximum number of 10 failures reached, some test results may be missing. + + ══ DONE ════════════════════════════════════════════════════════════════════════ + Error: Test failures + Execution halted + ``` + +# DrDimont + +
+ +* Version: 0.1.4 +* GitHub: NA +* Source code: https://github.com/cran/DrDimont +* Date/Publication: 2022-09-23 15:40:02 UTC +* Number of recursive dependencies: 127 + +Run `revdepcheck::cloud_details(, "DrDimont")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘DrDimont-Ex.R’ failed + The error most likely occurred in: + + > ### Name: compute_drug_response_scores + > ### Title: Calculate drug response score + > ### Aliases: compute_drug_response_scores + > + > ### ** Examples + > + > data(drug_target_edges_example) + ... + > example_drug_response_scores <- compute_drug_response_scores( + + differential_graph=differential_graph_example, + + drug_targets=drug_target_edges_example$targets, + + settings=example_settings) + [23-06-11 21:55:10] Computing drug response scores based on the mean of the differential scores ... + + Error in .igraph.status("Restore graph external pointer.\n") : + could not find function ".igraph.status" + Calls: compute_drug_response_scores ... -> ensure_igraph -> is_igraph -> warn_version + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘DrDimont_Vignette.Rmd’ using rmarkdown + + Quitting from lines 328-333 [Individual graphs] (DrDimont_Vignette.Rmd) + Error: processing vignette 'DrDimont_Vignette.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘DrDimont_Vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘DrDimont_Vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# DTSEA + +
+ +* Version: 0.0.3 +* GitHub: NA +* Source code: https://github.com/cran/DTSEA +* Date/Publication: 2022-11-06 13:20:02 UTC +* Number of recursive dependencies: 72 + +Run `revdepcheck::cloud_details(, "DTSEA")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘DTSEA-Ex.R’ failed + The error most likely occurred in: + + > ### Name: calculate_p0 + > ### Title: Function to calculate the p0 vector used in Random Walk with + > ### Restart (RwR) + > ### Aliases: calculate_p0 + > + > ### ** Examples + > + ... + > data("example_disease_list", package = "DTSEA") + > data("example_drug_target_list", package = "DTSEA") + > data("example_ppi", package = "DTSEA") + > + > # Compute the p0 vector + > p0 <- calculate_p0(nodes = example_ppi, disease = example_disease_list) + Error in .igraph.status("Restore graph external pointer.\n") : + could not find function ".igraph.status" + Calls: calculate_p0 -> is.igraph -> warn_version + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘DTSEA.Rmd’ using rmarkdown + + Quitting from lines 54-67 [unnamed-chunk-2] (DTSEA.Rmd) + Error: processing vignette 'DTSEA.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘DTSEA.Rmd’ + + SUMMARY: processing the following file failed: + ‘DTSEA.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# dyndimred + +
+ +* Version: 1.0.4 +* GitHub: https://github.com/dynverse/dyndimred +* Source code: https://github.com/cran/dyndimred +* Date/Publication: 2021-03-23 08:30:06 UTC +* Number of recursive dependencies: 160 + +Run `revdepcheck::cloud_details(, "dyndimred")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 4. └─igraph::graph_from_data_frame(kdf, vertices = seq_len(nrow(x))) + 5. └─igraph::make_empty_graph(n = 0, directed = directed) + ── Error ('test-dimred.R:70:7'): Check sparse capable knn_fr ─────────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. ├─utils::capture.output(...) at test-dimred.R:70:6 + 2. │ └─base::withVisible(...elt(i)) + 3. └─dyndimred (local) dr_fun(sparse_expr) at test-dimred.R:74:8 + 4. └─igraph::graph_from_data_frame(kdf, vertices = seq_len(nrow(x))) + 5. └─igraph::make_empty_graph(n = 0, directed = directed) + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 131 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘lle’ + ``` + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# dynetNLAResistance + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/dynetNLAResistance +* Date/Publication: 2016-11-25 14:14:30 +* Number of recursive dependencies: 39 + +Run `revdepcheck::cloud_details(, "dynetNLAResistance")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘dynetNLAResistance-Ex.R’ failed + The error most likely occurred in: + + > ### Name: draw.graph + > ### Title: Draw a graph contains vertexs with sensitive or unsensitive + > ### label + > ### Aliases: draw.graph + > + > ### ** Examples + > + > dynet <- make.virtual.dynamic.network() + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: make.virtual.dynamic.network -> graph.data.frame -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + > test_check("dynetNLAResistance") + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('testmain.R:5:3'): mvdn ────────────────────────────────────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─dynetNLAResistance::make.virtual.dynamic.network(prop.init = 0.03) at testmain.R:5:2 + 2. └─igraph::graph.data.frame(network, directed = F) + 3. └─igraph::make_empty_graph(n = 0, directed = directed) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘graphics’ + All declared Imports should be used. + ``` + +# dyngen + +
+ +* Version: 1.0.5 +* GitHub: https://github.com/dynverse/dyngen +* Source code: https://github.com/cran/dyngen +* Date/Publication: 2022-10-12 15:22:39 UTC +* Number of recursive dependencies: 203 + +Run `revdepcheck::cloud_details(, "dyngen")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 14. │ │ └─base::withCallingHandlers(...) + 15. │ ├─purrr:::call_with_cleanup(...) + 16. │ └─dyngen (local) .f(start = .l[[1L]][[i]], stop = .l[[2L]][[i]], ...) + 17. │ └─dyngen:::.feature_network_sample_downstream(...) + 18. │ └─... %>% ... + 19. ├─igraph::graph_from_data_frame(., vertices = colnames(realnet)) + 20. │ └─igraph::make_empty_graph(n = 0, directed = directed) + 21. └─base::.handleSimpleError(...) + 22. └─purrr (local) h(simpleError(msg, call)) + 23. └─cli::cli_abort(...) + 24. └─rlang::abort(...) + + [ FAIL 1 | WARN 17 | SKIP 0 | PASS 64 ] + Error: Test failures + Execution halted + ``` + +# dynplot + +
+ +* Version: 1.1.2 +* GitHub: https://github.com/dynverse/dynplot +* Source code: https://github.com/cran/dynplot +* Date/Publication: 2021-12-07 19:00:02 UTC +* Number of recursive dependencies: 134 + +Run `revdepcheck::cloud_details(, "dynplot")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘dynplot-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_dendro + > ### Title: Plot a trajectory as a dendrogram + > ### Aliases: plot_dendro + > ### Keywords: plot_trajectory + > + > ### ** Examples + > + > data(example_tree) + > plot_dendro(example_tree) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot_dendro ... as_graph_edge_df -> graph_from_data_frame -> make_empty_graph + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘plotting-a-toy.Rmd’ using rmarkdown + + Quitting from lines 40-41 [dendro] (plotting-a-toy.Rmd) + Error: processing vignette 'plotting-a-toy.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘plotting-a-toy.Rmd’ + + SUMMARY: processing the following file failed: + ‘plotting-a-toy.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# dynwrap + +
+ +* Version: 1.2.3 +* GitHub: https://github.com/dynverse/dynwrap +* Source code: https://github.com/cran/dynwrap +* Date/Publication: 2023-03-01 17:10:02 UTC +* Number of recursive dependencies: 95 + +Run `revdepcheck::cloud_details(, "dynwrap")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘dynwrap-Ex.R’ failed + The error most likely occurred in: + + > ### Name: add_branch_trajectory + > ### Title: Construct a trajectory given its branch network and the + > ### pseudotime of the cells on one of the branches. + > ### Aliases: add_branch_trajectory + > ### Keywords: create_trajectory + > + > ### ** Examples + ... + > trajectory <- add_branch_trajectory( + + dataset, + + branch_network, + + branches, + + branch_progressions + + ) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: add_branch_trajectory ... -> ensure_igraph -> -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 1. ├─wrap_data(id = id, cell_ids = cell_ids) %>% ... at test-wrap_label_milestones.R:28:0 + 2. ├─dynwrap::add_trajectory(...) + 3. │ └─dynwrap:::changed_topology(dataset) + 4. │ └─dynwrap::classify_milestone_network(trajectory$milestone_network) + 5. │ └─... %>% simplify_igraph_network() + 6. ├─dynwrap::simplify_igraph_network(.) + 7. │ ├─base::paste0("#M#", igraph::V(gr)$name) + 8. │ └─igraph::V(gr) + 9. │ └─igraph:::ensure_igraph(graph) + 10. └─igraph::graph_from_data_frame(., directed = is_directed) + 11. └─igraph::make_empty_graph(n = 0, directed = directed) + + [ FAIL 108 | WARN 11 | SKIP 1 | PASS 137 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘create_ti_method_container.Rmd’ using rmarkdown + --- finished re-building ‘create_ti_method_container.Rmd’ + + --- re-building ‘create_ti_method_definition.Rmd’ using rmarkdown + running: bash -c 'chmod +x run.R' + --- finished re-building ‘create_ti_method_definition.Rmd’ + + --- re-building ‘create_ti_method_r.Rmd’ using rmarkdown + + ... + Quitting from lines 77-83 [unnamed-chunk-5] (create_ti_method_wrappers.Rmd) + Error: processing vignette 'create_ti_method_wrappers.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘create_ti_method_wrappers.Rmd’ + + SUMMARY: processing the following files failed: + ‘create_ti_method_r.Rmd’ ‘create_ti_method_wrappers.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# ecoCopula + +
+ +* Version: 1.0.2 +* GitHub: NA +* Source code: https://github.com/cran/ecoCopula +* Date/Publication: 2022-03-02 00:20:02 UTC +* Number of recursive dependencies: 114 + +Run `revdepcheck::cloud_details(, "ecoCopula")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ecoCopula-Ex.R’ failed + The error most likely occurred in: + + > ### Name: cgr + > ### Title: Fitting Gaussian copula graphical lasso to co-occurrence data + > ### Aliases: cgr + > + > ### ** Examples + > + > abund <- spider$abund[,1:5] + > spider_mod <- stackedsdm(abund,~1, data = spider$x, ncores=2) + > spid_graph=cgr(spider_mod) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: cgr ... ensure_igraph -> -> graph.adjacency.dense + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Backtrace: + ▆ + 1. ├─testthat::expect_is(cgr(spider.mod), "cgr") at test_try.R:13:2 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. └─ecoCopula::cgr(spider.mod) + 5. └─ecoCopula:::graph_from_partial(part_cor) + 6. ├─igraph::as_data_frame(...) + 7. │ └─igraph:::ensure_igraph(x) + 8. └─igraph::graph_from_adjacency_matrix(...) + 9. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 77 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘the_basics.Rmd’ using rmarkdown + + Quitting from lines 117-123 [unnamed-chunk-10] (the_basics.Rmd) + Error: processing vignette 'the_basics.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘the_basics.Rmd’ + + SUMMARY: processing the following file failed: + ‘the_basics.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# ECoL + +
+ +* Version: 0.3.0 +* GitHub: https://github.com/lpfgarcia/ECoL +* Source code: https://github.com/cran/ECoL +* Date/Publication: 2019-11-05 05:10:02 UTC +* Number of recursive dependencies: 41 + +Run `revdepcheck::cloud_details(, "ECoL")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ECoL-Ex.R’ failed + The error most likely occurred in: + + > ### Name: complexity + > ### Title: Extract the complexity measures from datasets + > ### Aliases: complexity complexity.default complexity.formula + > + > ### ** Examples + > + > ## Extract all complexity measures for classification task + > data(iris) + > complexity(Species ~ ., iris) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: complexity ... eval -> c.N1 -> -> graph.adjacency.dense + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 1. ├─ECoL::smoothness(speed ~ ., cars, measures = "S1", summary = "mean") at test_smoothness.R:5:2 + 2. └─ECoL:::smoothness.formula(speed ~ ., cars, measures = "S1", summary = "mean") + 3. └─ECoL:::smoothness.default(...) + 4. └─base::sapply(...) + 5. └─base::lapply(X = X, FUN = FUN, ...) + 6. └─ECoL (local) FUN(X[[i]], ...) + 7. ├─base::eval(call(paste("r", f, sep = "."), d = d, x = x, y = y)) + 8. │ └─base::eval(call(paste("r", f, sep = "."), d = d, x = x, y = y)) + 9. └─ECoL:::r.S1(d = ``, x = ``, y = ``) + 10. └─igraph::graph.adjacency(d, mode = "undirected", weighted = TRUE) + 11. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 6 | WARN 0 | SKIP 0 | PASS 83 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# econet + +
+ +* Version: 1.0.0 +* GitHub: NA +* Source code: https://github.com/cran/econet +* Date/Publication: 2022-04-28 00:00:02 UTC +* Number of recursive dependencies: 64 + +Run `revdepcheck::cloud_details(, "econet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘econet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: horse_race + > ### Title: Compare the explanatory power of parameter.dependent network + > ### centrality measures with those of standard measures of network + > ### centrality. + > ### Aliases: horse_race + > + > ### ** Examples + ... + + data = db_model, unobservables = NULL, G = G_model, + + model = "model_A", estimation = "NLLS", + + start.val = c(alpha = -0.31055275, + + beta_dw = 1.50666982, + + beta_betweenness = 0.09666742, + + phi = 16.13035695)) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: horse_race ... compute_centralities -> -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘econet.tex’ using tex + Error: processing vignette 'econet.tex' failed with diagnostics: + Running 'texi2dvi' on 'econet.tex' failed. + LaTeX errors: + ! LaTeX Error: File `ae.sty' not found. + + Type X to quit or to proceed, + or enter new name. (Default extension: sty) + ... + l.55 \RequirePackage + [T1]{fontenc}^^M + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘econet.tex’ + + SUMMARY: processing the following file failed: + ‘econet.tex’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# EcoNetGen + +
+ +* Version: 0.2.3 +* GitHub: https://github.com/cboettig/EcoNetGen +* Source code: https://github.com/cran/EcoNetGen +* Date/Publication: 2019-07-13 23:30:14 UTC +* Number of recursive dependencies: 85 + +Run `revdepcheck::cloud_details(, "EcoNetGen")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ▆ + 1. └─EcoNetGen:::netgen_v1() at test-netsample.R:10:2 + 2. └─igraph::graph_from_adjacency_matrix(M) + 3. └─igraph:::graph.adjacency.dense(...) + ── Error ('test-netsample.R:22:3'): net sample works with other settings ─────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─EcoNetGen:::netgen_v1() at test-netsample.R:22:2 + 2. └─igraph::graph_from_adjacency_matrix(M) + 3. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 7 | WARN 0 | SKIP 0 | PASS 10 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# economiccomplexity + +
+ +* Version: 1.4.0 +* GitHub: https://github.com/pachadotdev/economiccomplexity +* Source code: https://github.com/cran/economiccomplexity +* Date/Publication: 2022-09-04 07:00:02 UTC +* Number of recursive dependencies: 95 + +Run `revdepcheck::cloud_details(, "economiccomplexity")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘economiccomplexity-Ex.R’ failed + The error most likely occurred in: + + > ### Name: projections + > ### Title: Projections of a Country-Product Network + > ### Aliases: projections + > ### Keywords: functions + > + > ### ** Examples + > + ... + + economiccomplexity_output$proximity$proximity_product, + + avg_links = 10, + + tolerance = 0.1 + + ) + computing product projection... + -------------------------------------------------- + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: projections ... graph_from_adjacency_matrix -> graph.adjacency.sparse -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ▆ + 1. ├─testthat::expect_warning(...) at test-projections.R:51:2 + 2. │ └─testthat:::quasi_capture(...) + 3. │ ├─testthat (local) .capture(...) + 4. │ │ └─base::withCallingHandlers(...) + 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 6. └─economiccomplexity::projections(...) + 7. └─economiccomplexity (local) trim_network(proximity_product, avg_links) + 8. └─igraph::graph_from_adjacency_matrix(...) + 9. └─igraph:::graph.adjacency.sparse(...) + 10. └─igraph::make_empty_graph(n = vc, directed = (mode == "directed")) + + [ FAIL 4 | WARN 0 | SKIP 0 | PASS 80 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘Rdpack’ + All declared Imports should be used. + ``` + +# econullnetr + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/ivaughan/econullnetr +* Source code: https://github.com/cran/econullnetr +* Date/Publication: 2021-06-02 08:10:05 UTC +* Number of recursive dependencies: 97 + +Run `revdepcheck::cloud_details(, "econullnetr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘econullnetr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: generate_edgelist + > ### Title: Export null modelling results + > ### Aliases: generate_edgelist + > + > ### ** Examples + > + > set.seed(1234) + ... + + + + igraph::plot.igraph(net.1, layout = igraph::layout_in_circle, + + edge.color = igraph::E(net.1)$edge.cols, + + edge.width = sqrt(igraph::E(net.1)$obs.str), + + edge.arrow.size = .4) + + } + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: -> make_graph -> do.call -> + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘econullnetr-intro.Rmd’ using rmarkdown + + Quitting from lines 183-198 [unnamed-chunk-13] (econullnetr-intro.Rmd) + Error: processing vignette 'econullnetr-intro.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘econullnetr-intro.Rmd’ + + SUMMARY: processing the following file failed: + ‘econullnetr-intro.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# EcotoneFinder + +
+ +* Version: 0.2.3 +* GitHub: NA +* Source code: https://github.com/cran/EcotoneFinder +* Date/Publication: 2021-02-16 23:00:02 UTC +* Number of recursive dependencies: 113 + +Run `revdepcheck::cloud_details(, "EcotoneFinder")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘EcotoneFinder-Ex.R’ failed + The error most likely occurred in: + + > ### Name: DistEco + > ### Title: Tools for internal data structure exploration + > ### Aliases: DistEco + > + > ### ** Examples + > + > ### Artificial data: + ... + > + > ## Network of species, with raw spinglass groups: + > DistEco(SyntheticTrial[,2:ncol(SyntheticTrial)], transpose = TRUE, + + plot = c("network"), spinglass = TRUE, run = 10, + + spinglass.groups = c("raw")) + Metric: 'inner_product'; comparing: 21 vectors. + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: DistEco ... graph.edgelist -> make_graph -> do.call -> + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘Rmisc’ ‘rlang’ + All declared Imports should be used. + ``` + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# ecpc + +
+ +* Version: 3.1.1 +* GitHub: NA +* Source code: https://github.com/cran/ecpc +* Date/Publication: 2023-02-27 21:12:30 UTC +* Number of recursive dependencies: 145 + +Run `revdepcheck::cloud_details(, "ecpc")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ecpc-Ex.R’ failed + The error most likely occurred in: + + > ### Name: visualiseGroupset + > ### Title: Visualise a group set + > ### Aliases: visualiseGroupset + > + > ### ** Examples + > + > #groups without hierarchical constraints + > groupset <- list("Group1"=c(1:20),"Group2"=c(15,30)) + > visualiseGroupset(groupset,c(0.5,2)) + Loading required namespace: ggraph + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: visualiseGroupset -> -> make_empty_graph + Execution halted + ``` + +# edgebundle + +
+ +* Version: 0.4.1 +* GitHub: https://github.com/schochastics/edgebundle +* Source code: https://github.com/cran/edgebundle +* Date/Publication: 2022-11-22 07:00:02 UTC +* Number of recursive dependencies: 55 + +Run `revdepcheck::cloud_details(, "edgebundle")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘edgebundle-Ex.R’ failed + The error most likely occurred in: + + > ### Name: tnss_smooth + > ### Title: Smooth a Steiner tree + > ### Aliases: tnss_smooth + > + > ### ** Examples + > + > xy <- cbind(state.center$x,state.center$y)[!state.name%in%c("Alaska","Hawaii"),] + ... + > xy_dummy <- tnss_dummies(xy,root = 4) + > gtree <- tnss_tree(cali2010,xy,xy_dummy,root = 4,gamma = 0.9) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: tnss_tree ... -> make_graph -> do.call -> + Execution halted + Error in .igraph.status("Free graph external pointer.\n") : + could not find function ".igraph.status" + Error in .igraph.status("Free graph external pointer.\n") : + could not find function ".igraph.status" + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Backtrace: + ▆ + 1. └─igraph::graph_from_edgelist(...) at test-bundle_test.R:2:2 + 2. └─igraph::make_graph(t(el), directed = directed) + 3. ├─base::do.call(old_graph, args) + 4. └─igraph (local) ``(``, directed = FALSE) + ── Error ('test-bundle_test.R:9:4'): stub bundle works ───────────────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─igraph::graph.star(10, "undirected") at test-bundle_test.R:9:3 + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 22 marked UTF-8 strings + ``` + +# edmcr + +
+ +* Version: 0.2.0 +* GitHub: https://github.com/great-northern-diver/edmcr +* Source code: https://github.com/cran/edmcr +* Date/Publication: 2021-09-10 10:40:06 UTC +* Number of recursive dependencies: 46 + +Run `revdepcheck::cloud_details(, "edmcr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘edmcr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: dpf + > ### Title: Dissimilarity Parameterization Formulation + > ### Aliases: dpf + > + > ### ** Examples + > + > set.seed(1337) + ... + + 4,1,0,5,NA,5, + + 3,NA,5,0,1,NA, + + 4,5,NA,1,0,5, + + 3,NA,5,NA,5,0),byrow=TRUE, nrow=6) + > + > edmc(D, method="dpf", d=3, toler=1e-8) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: edmc ... dpf -> mstUB -> graph.data.frame -> make_empty_graph + Execution halted + ``` + +# EDOIF + +
+ +* Version: 0.1.3 +* GitHub: https://github.com/DarkEyes/EDOIF +* Source code: https://github.com/cran/EDOIF +* Date/Publication: 2021-03-28 06:20:05 UTC +* Number of recursive dependencies: 61 + +Run `revdepcheck::cloud_details(, "EDOIF")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘EDOIF-Ex.R’ failed + The error most likely occurred in: + + > ### Name: EDOIF + > ### Title: Empirical Distribution Ordering Inference Framework (EDOIF) + > ### Aliases: EDOIF + > + > ### ** Examples + > + > # Generate simulation data + ... + > simData1$Values<-c(simData1$Values,rnorm(nInv,mean=initMean+4*stepMean,sd=std) ) + > simData1$Group<-c(simData1$Group, rep(c("C5"),times=nInv) ) + > + > # Performing ordering infernce from simData1 + > + > resultObj<-EDOIF(simData1$Values,simData1$Group) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: EDOIF ... graph_from_adjacency_matrix -> graph.adjacency.dense + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘EDOIF_demo.Rmd’ using knitr + + Quitting from lines 34-45 [unnamed-chunk-1] (EDOIF_demo.Rmd) + Error: processing vignette 'EDOIF_demo.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘EDOIF_demo.Rmd’ + + SUMMARY: processing the following file failed: + ‘EDOIF_demo.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# eff2 + +
+ +* Version: 1.0.1 +* GitHub: https://github.com/richardkwo/eff2 +* Source code: https://github.com/cran/eff2 +* Date/Publication: 2021-09-30 20:40:02 UTC +* Number of recursive dependencies: 115 + +Run `revdepcheck::cloud_details(, "eff2")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘eff2-Ex.R’ failed + The error most likely occurred in: + + > ### Name: estimateEffect + > ### Title: Estimate the total causal effect + > ### Aliases: estimateEffect + > + > ### ** Examples + > + > data("ex1") + > result <- estimateEffect(ex1$data, c(5,3), 7, ex1$amat.cpdag, bootstrap=TRUE) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: estimateEffect ... ensure_igraph -> graph.adjacency -> graph.adjacency.dense + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ▆ + 1. └─eff2::estimateEffect(ex1$data, .x, .y, ex1$amat.cpdag, bootstrap = FALSE) at test_ex1.R:26:4 + 2. └─eff2:::.estimateEffect(stats::cov(data), x, y, amat) + 3. └─eff2:::getBucketDecomp(x, y, amat) + 4. ├─base::stopifnot(pcalg::isValidGraph(amat, type = "pdag")) + 5. └─pcalg::isValidGraph(amat, type = "pdag") + 6. └─pcalg:::chordalComponents(corresp.cpdag) + 7. ├─igraph::graph.dfs(...) + 8. │ └─igraph:::ensure_igraph(graph) + 9. └─igraph::graph.adjacency(amat.undir, mode = "undirected") + 10. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 5 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘eff2-doc.Rmd’ using rmarkdown + + Quitting from lines 62-63 [unnamed-chunk-4] (eff2-doc.Rmd) + Error: processing vignette 'eff2-doc.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘eff2-doc.Rmd’ + + SUMMARY: processing the following file failed: + ‘eff2-doc.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# EGAnet + +
+ +* Version: 1.2.3 +* GitHub: NA +* Source code: https://github.com/cran/EGAnet +* Date/Publication: 2022-09-05 15:50:02 UTC +* Number of recursive dependencies: 160 + +Run `revdepcheck::cloud_details(, "EGAnet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘EGAnet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: convert2igraph + > ### Title: Convert networks to 'igraph' + > ### Aliases: convert2igraph + > + > ### ** Examples + > + > convert2igraph(ega.wmt$network) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: convert2igraph + Execution halted + ``` + +# egor + +
+ +* Version: 1.23.3 +* GitHub: https://github.com/tilltnet/egor +* Source code: https://github.com/cran/egor +* Date/Publication: 2023-03-16 04:40:02 UTC +* Number of recursive dependencies: 89 + +Run `revdepcheck::cloud_details(, "egor")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘egor-Ex.R’ failed + The error most likely occurred in: + + > ### Name: as_igraph + > ### Title: Convert 'egor' object to 'network' or 'igraph' objects + > ### Aliases: as_igraph as_igraph.nested_egor as.igraph.egor as_network + > ### as.network.egor + > + > ### ** Examples + > + > e <- make_egor(3, 22) + > as_igraph(e) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: as_igraph ... mapply -> -> -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 7. ├─egor:::rotate_to_equilibrium(.) + 8. ├─igraph::layout_as_star(.) + 9. │ └─igraph:::ensure_igraph(graph) + 10. ├─egor::as_igraph(.) + 11. └─egor:::as_igraph.egor(.) + 12. ├─egor::as_igraph(...) + 13. └─egor:::as_igraph.nested_egor(...) + 14. └─base::mapply(...) + 15. └─egor (local) ``(dots[[1L]][[1L]], dots[[2L]][[1L]]) + 16. └─igraph::graph.data.frame(...) + 17. └─igraph::make_empty_graph(n = 0, directed = directed) + + [ FAIL 48 | WARN 8 | SKIP 15 | PASS 152 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘egor_allbus.Rmd’ using rmarkdown + + Quitting from lines 179-181 [unnamed-chunk-11] (egor_allbus.Rmd) + Error: processing vignette 'egor_allbus.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘egor_allbus.Rmd’ + + --- re-building ‘qualtrics.Rmd’ using rmarkdown + ... + Quitting from lines 222-241 [unnamed-chunk-16] (using_egor.Rmd) + Error: processing vignette 'using_egor.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘using_egor.Rmd’ + + SUMMARY: processing the following files failed: + ‘egor_allbus.Rmd’ ‘using_egor.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# eicm + +
+ +* Version: 1.0.3 +* GitHub: https://github.com/miguel-porto/eicm +* Source code: https://github.com/cran/eicm +* Date/Publication: 2023-05-05 23:10:02 UTC +* Number of recursive dependencies: 48 + +Run `revdepcheck::cloud_details(, "eicm")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘eicm-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plotNetworkFromMatrix + > ### Title: Plot graphs from adjacency matrices + > ### Aliases: plotNetworkFromMatrix + > + > ### ** Examples + > + > # generate two adjacency matrices with 15 species and 10 interactions + ... + > + > # set the species names + > rownames(A) <- rownames(B) <- + + colnames(A) <- colnames(B) <- paste0("S", 1:15) + > + > plotNetworkFromMatrix(A, B) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plotNetworkFromMatrix -> -> graph.adjacency.dense + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘eicm.Rmd’ using rmarkdown + + Quitting from lines 185-187 [unnamed-chunk-7] (eicm.Rmd) + Error: processing vignette 'eicm.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘eicm.Rmd’ + + SUMMARY: processing the following file failed: + ‘eicm.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘snow’ + All declared Imports should be used. + ``` + +# einet + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/travisbyrum/einet +* Source code: https://github.com/cran/einet +* Date/Publication: 2020-04-23 17:20:03 UTC +* Number of recursive dependencies: 67 + +Run `revdepcheck::cloud_details(, "einet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘einet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: causal_emergence + > ### Title: Causal Emergence + > ### Aliases: causal_emergence + > + > ### ** Examples + > + > graph <- matrix( + ... + + c(0.0, 0.0, 0.0, 1.0), + + c(0.0, 0.0, 0.0, 0.0) + + ), + + nrow = 4 + + ) %>% + + igraph::graph.adjacency(mode = "directed") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: %>% -> -> graph.adjacency.dense + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 5. └─einet:::effective_information.igraph(karate) + 6. ├─assertthat::assert_that(igraph::is.igraph(graph)) + 7. │ └─assertthat::see_if(..., env = env, msg = msg) + 8. │ ├─base::tryCatch(...) + 9. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) + 10. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) + 11. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) + 12. │ └─base::eval(assertion, env) + 13. │ └─base::eval(assertion, env) + 14. └─igraph::is.igraph(graph) + 15. └─igraph:::warn_version(graph) + + [ FAIL 5 | WARN 0 | SKIP 0 | PASS 0 ] + Error: Test failures + Execution halted + ``` + +# EmbedSOM + +
+ +* Version: 2.1.2 +* GitHub: https://github.com/exaexa/EmbedSOM +* Source code: https://github.com/cran/EmbedSOM +* Date/Publication: 2022-07-05 10:20:02 UTC +* Number of recursive dependencies: 75 + +Run `revdepcheck::cloud_details(, "EmbedSOM")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘EmbedSOM-Ex.R’ failed + The error most likely occurred in: + + > ### Name: RandomMap + > ### Title: Create a map by randomly selecting points + > ### Aliases: RandomMap + > + > ### ** Examples + > + > d <- iris[,1:4] + ... + > EmbedSOM::PlotEmbed( + + EmbedSOM::EmbedSOM( + + data = d, + + map = EmbedSOM::RandomMap(d, 30, EmbedSOM::GraphCoords())), + + pch=19, clust=iris[,5] + + ) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: ... ensure_igraph -> -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘Matrix’ ‘Rtsne’ ‘uwot’ + All declared Imports should be used. + ``` + +# enviGCMS + +
+ +* Version: 0.7.1 +* GitHub: https://github.com/yufree/enviGCMS +* Source code: https://github.com/cran/enviGCMS +* Date/Publication: 2023-02-06 08:42:34 UTC +* Number of recursive dependencies: 150 + +Run `revdepcheck::cloud_details(, "enviGCMS")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘enviGCMS-Ex.R’ failed + The error most likely occurred in: + + > ### Name: getalign2 + > ### Title: Align mass to charge ratio and/or retention time to remove + > ### redundancy + > ### Aliases: getalign2 + > + > ### ** Examples + > + > mz <- c(221.1171, 221.1170, 229.1546, 233.1497, 271.0790 ) + > rt <- c(590.8710, 587.3820, 102.9230, 85.8850, 313.8240) + > getalign2(mz,rt) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: getalign2 -> -> make_empty_graph + Execution halted + ``` + +# epicontacts + +
+ +* Version: 1.1.3 +* GitHub: https://github.com/reconhub/epicontacts +* Source code: https://github.com/cran/epicontacts +* Date/Publication: 2023-03-28 13:10:12 UTC +* Number of recursive dependencies: 88 + +Run `revdepcheck::cloud_details(, "epicontacts")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘epicontacts-Ex.R’ failed + The error most likely occurred in: + + > ### Name: get_clusters + > ### Title: Assign cluster IDs to epicontacts data + > ### Aliases: get_clusters + > + > ### ** Examples + > + > if (require(outbreaks)) { + ... + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: get_clusters ... as.igraph.epicontacts -> -> make_empty_graph + Execution halted + Error in .igraph.status("Free graph external pointer.\n") : + could not find function ".igraph.status" + Error in .igraph.status("Free graph external pointer.\n") : + could not find function ".igraph.status" + Error in .igraph.status("Free graph external pointer.\n") : + could not find function ".igraph.status" + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘epicontacts.Rmd’ using rmarkdown + + Quitting from lines 128-130 [unnamed-chunk-9] (epicontacts.Rmd) + Error: processing vignette 'epicontacts.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘epicontacts.Rmd’ + + --- re-building ‘epicontacts_class.Rmd’ using rmarkdown + --- finished re-building ‘epicontacts_class.Rmd’ + + SUMMARY: processing the following file failed: + ‘epicontacts.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘colorspace’ + All declared Imports should be used. + ``` + +# EpiILMCT + +
+ +* Version: 1.1.7 +* GitHub: https://github.com/waleedalmutiry/EpiILMCT +* Source code: https://github.com/cran/EpiILMCT +* Date/Publication: 2021-06-29 06:10:06 UTC +* Number of recursive dependencies: 8 + +Run `revdepcheck::cloud_details(, "EpiILMCT")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘EpiILMCT-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.contactnet + > ### Title: Plot the contact network of 'contactnet' object + > ### Aliases: plot.contactnet + > ### Keywords: plot + > + > ### ** Examples + > + ... + > net1<- contactnet(type = "powerlaw", location = loc, beta = 1.5, nu = 0.5) + > plot(net1) + > net2<- contactnet(type = "Cauchy", location = loc, beta = 0.5) + > plot(net2) + > net3<- contactnet(type = "random", num.id = 50, beta = 0.08) + > plot(net3) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot ... plot.contactnet -> -> do.call -> + Execution halted + ``` + +# epinetr + +
+ +* Version: 0.96 +* GitHub: https://github.com/diondetterer/epinetr +* Source code: https://github.com/cran/epinetr +* Date/Publication: 2022-03-10 10:30:02 UTC +* Number of recursive dependencies: 87 + +Run `revdepcheck::cloud_details(, "epinetr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘epinetr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: getEpiNet + > ### Title: Epistatic network retrieval. + > ### Aliases: getEpiNet + > + > ### ** Examples + > + > # Create population and attach an epistatic network + ... + Estimating heritability... + Estimating SNP effects... + > + > # Plot epistatic network + > epiNet <- getEpiNet(pop) + > plot(epiNet) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot ... plot.EpiNet -> -> do.call -> + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘epinetr-vignette.Rmd’ using rmarkdown + + Quitting from lines 36-51 [unnamed-chunk-2] (epinetr-vignette.Rmd) + Error: processing vignette 'epinetr-vignette.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘epinetr-vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘epinetr-vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# espadon + +
+ +* Version: 1.3.2 +* GitHub: NA +* Source code: https://github.com/cran/espadon +* Date/Publication: 2023-04-04 07:50:06 UTC +* Number of recursive dependencies: 75 + +Run `revdepcheck::cloud_details(, "espadon")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘espadon-Ex.R’ failed + The error most likely occurred in: + + > ### Name: display.obj.links + > ### Title: Display patient objects links + > ### Aliases: display.obj.links + > + > ### ** Examples + > + > # loading of toy-patient objects + > patient <- toy.load.patient (dxyz = c (5, 5, 5), beam.nb = 1) + > display.obj.links (patient, group.by.connected.FoR = FALSE) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: display.obj.links ... graph_from_adjacency_matrix -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 8.0Mb + sub-directories of 1Mb or more: + libs 6.5Mb + ``` + +# ess + +
+ +* Version: 1.1.2 +* GitHub: https://github.com/mlindsk/ess +* Source code: https://github.com/cran/ess +* Date/Publication: 2021-05-31 07:40:08 UTC +* Number of recursive dependencies: 9 + +Run `revdepcheck::cloud_details(, "ess")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ess-Ex.R’ failed + The error most likely occurred in: + + > ### Name: fit_graph + > ### Title: Fit a decomposable graphical model + > ### Aliases: fit_graph + > + > ### ** Examples + > + > + ... + - max: 2 + - min: 2 + - avg: 2 + + ------------------------- + > plot(g) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot ... plot.gengraph -> -> graph.adjacency.dense + Execution halted + ``` + +# etree + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/ricgbl/etree +* Source code: https://github.com/cran/etree +* Date/Publication: 2022-07-16 08:30:02 UTC +* Number of recursive dependencies: 128 + +Run `revdepcheck::cloud_details(, "etree")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘etree-Ex.R’ failed + The error most likely occurred in: + + > ### Name: dist_comp + > ### Title: Distances + > ### Aliases: dist_comp + > + > ### ** Examples + > + > + ... + > obj <- fda.usc::rproc2fdata(nobs, seq(0, 1, len = 100), sigma = 1) + > d <- dist_comp(obj) + Warning: executing %dopar% sequentially: no parallel backend registered + > + > ## Graphs + > obj <- lapply(1:nobs, function(j) igraph::sample_gnp(100, 0.2)) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: lapply -> FUN -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 7. └─etree::etree(resp_cls, covs_cls, split_type = "cluster") + 8. └─base::lapply(covariates, dist_comp) + 9. └─etree (local) FUN(X[[i]], ...) + 10. └─base::sapply(x, function(i) is.null(igraph::edge.attributes(i)$weight)) + 11. └─base::lapply(X = X, FUN = FUN, ...) + 12. └─etree (local) FUN(X[[i]], ...) + 13. └─igraph::edge.attributes(i) + 14. └─igraph:::ensure_igraph(graph) + 15. └─igraph::is_igraph(graph) + 16. └─igraph:::warn_version(graph) + + [ FAIL 28 | WARN 1 | SKIP 0 | PASS 37 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘etree-vignette-eforest.Rmd’ using rmarkdown + + Quitting from lines 148-170 [unnamed-chunk-4] (etree-vignette-eforest.Rmd) + Error: processing vignette 'etree-vignette-eforest.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘etree-vignette-eforest.Rmd’ + + --- re-building ‘etree-vignette.Rmd’ using rmarkdown + ... + Quitting from lines 142-164 [unnamed-chunk-4] (etree-vignette.Rmd) + Error: processing vignette 'etree-vignette.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘etree-vignette.Rmd’ + + SUMMARY: processing the following files failed: + ‘etree-vignette-eforest.Rmd’ ‘etree-vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# fairadapt + +
+ +* Version: 0.2.5 +* GitHub: https://github.com/dplecko/fairadapt +* Source code: https://github.com/cran/fairadapt +* Date/Publication: 2023-03-23 15:02:04 UTC +* Number of recursive dependencies: 103 + +Run `revdepcheck::cloud_details(, "fairadapt")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘fairadapt-Ex.R’ failed + The error most likely occurred in: + + > ### Name: fairTwins + > ### Title: Fair Twin Inspection convenience function. + > ### Aliases: fairTwins + > + > ### ** Examples + > + > n_samp <- 200 + ... + > uni_ada <- fairadapt(score ~ ., + + train.data = head(uni_admission, n = n_samp), + + test.data = tail(uni_admission, n = n_samp), + + adj.mat = uni_adj, + + prot.attr = "gender" + + ) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: fairadapt ... graph_from_adjacency_matrix -> graph.adjacency.dense + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + • generics/fttrn_cts.csv + • generics/fttrn_lin.csv + • generics/fttrn_rf.csv + • generics/graph_cts.png + • generics/graph_lin.png + • generics/graph_rf.png + • generics/plot_cts.png + • generics/plot_lin.png + • generics/plot_rf.png + • generics/predi_cts.csv + • generics/predi_disc.csv + • generics/predi_lin.csv + • generics/predi_rf.csv + Error: Test failures + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘jss.Rmd’ using rmarkdown + Error: processing vignette 'jss.Rmd' failed with diagnostics: + pandoc version 2.7 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available). + --- failed re-building ‘jss.Rmd’ + + SUMMARY: processing the following file failed: + ‘jss.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# FAIRmaterials + +
+ +* Version: 0.3.0 +* GitHub: NA +* Source code: https://github.com/cran/FAIRmaterials +* Date/Publication: 2023-02-11 07:10:07 UTC +* Number of recursive dependencies: 69 + +Run `revdepcheck::cloud_details(, "FAIRmaterials")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘FAIRmaterials-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_json_graph + > ### Title: Plot an igraph visualization of a JSON document + > ### Aliases: plot_json_graph + > + > ### ** Examples + > + > json_file <- '{ + ... + + "name": "Jane Doe", + + "jobTitle": "Professor", + + "telephone": "(425) 123-4567", + + "url": "http://www.janedoe.com"}' + > + > plot_json_graph(json_file) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot_json_graph -> -> make_empty_graph + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.5Mb + sub-directories of 1Mb or more: + doc 5.3Mb + ``` + +# fake + +
+ +* Version: 1.4.0 +* GitHub: NA +* Source code: https://github.com/cran/fake +* Date/Publication: 2023-04-13 22:30:24 UTC +* Number of recursive dependencies: 41 + +Run `revdepcheck::cloud_details(, "fake")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘fake-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ExpectedCommunities + > ### Title: Expected community structure + > ### Aliases: ExpectedCommunities + > + > ### ** Examples + > + > # Simulation parameters + ... + [1] 40 + > + > # Comparing observed and expected modularity + > igraph::modularity(igraph::graph_from_adjacency_matrix(theta, mode = "undirected"), + + membership = rep.int(1:length(pk), times = pk) + + ) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: -> -> graph.adjacency.dense + Execution halted + ``` + +# fastnet + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/networkgroupR/fastnet +* Source code: https://github.com/cran/fastnet +* Date/Publication: 2020-12-01 07:40:02 UTC +* Number of recursive dependencies: 29 + +Run `revdepcheck::cloud_details(, "fastnet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘fastnet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: from.adjacency + > ### Title: Adjacency Matrix to 'fastnet' + > ### Aliases: from.adjacency + > + > ### ** Examples + > + > adj.mat <- matrix(c(0,1,0,0,1,0,0,0,0,0,0,1,0,0,1,0), nrow = 4, ncol = 4) + > g <- from.adjacency(adj.mat) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: from.adjacency ... ensure_igraph -> -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# fbnet + +
+ +* Version: 1.0.2 +* GitHub: https://github.com/MarsicoFL/fbnet +* Source code: https://github.com/cran/fbnet +* Date/Publication: 2023-02-27 22:02:35 UTC +* Number of recursive dependencies: 10 + +Run `revdepcheck::cloud_details(, "fbnet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘fbnet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: buildBN + > ### Title: buildBN: a function for building the bayesian network. + > ### Aliases: buildBN + > + > ### ** Examples + > + > bnet <- buildBN(pbn,QP=3) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: buildBN -> graph_from_data_frame -> make_empty_graph + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘Rsolnp’ ‘assertthat’ ‘utils’ + All declared Imports should be used. + ``` + +# FCMapper + +
+ +* Version: 1.1 +* GitHub: NA +* Source code: https://github.com/cran/FCMapper +* Date/Publication: 2016-02-12 07:40:47 +* Number of recursive dependencies: 7 + +Run `revdepcheck::cloud_details(, "FCMapper")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘FCMapper-Ex.R’ failed + The error most likely occurred in: + + > ### Name: graph.fcm + > ### Title: Fuzzy cognitive map graph + > ### Aliases: graph.fcm + > + > ### ** Examples + > + > + ... + > matrix[7,] = c(0,0,0,-0.5,0,0,1) + > concept.names = c("A","B","C","D","E","F","G") + > + > results = nochanges.scenario(matrix,iter=25,concept.names) + > + > graph.fcm(matrix,concept.sizes=results$Equilibrium_value,concept.names) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: graph.fcm -> -> graph.adjacency.dense + Execution halted + ``` + +# FindIt + +
+ +* Version: 1.2.0 +* GitHub: NA +* Source code: https://github.com/cran/FindIt +* Date/Publication: 2019-11-20 21:50:02 UTC +* Number of recursive dependencies: 60 + +Run `revdepcheck::cloud_details(, "FindIt")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘FindIt-Ex.R’ failed + The error most likely occurred in: + + > ### Name: CausalANOVA + > ### Title: Estimating the AMEs and AMIEs with the CausalANOVA. + > ### Aliases: CausalANOVA + > + > ### ** Examples + > + > + ... + 1 newRecordF promise + 2 newRecordF coeth_voting + 3 promise relevantdegree + + ***** Collapsing ***** + > summary(fit.r2) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: summary ... graph_from_adjacency_matrix -> graph.adjacency.dense + Execution halted + ``` + +# fnets + +
+ +* Version: 0.1.3 +* GitHub: NA +* Source code: https://github.com/cran/fnets +* Date/Publication: 2023-06-08 15:10:02 UTC +* Number of recursive dependencies: 59 + +Run `revdepcheck::cloud_details(, "fnets")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. ├─base::plot(out, type = "pc", display = "network") at test-omega.R:21:0 + 2. └─fnets:::plot.fnets(out, type = "pc", display = "network") + 3. ├─base::suppressWarnings(...) + 4. │ └─base::withCallingHandlers(...) + 5. ├─fnets::network(...) + 6. └─fnets:::network.fnets(...) + 7. └─igraph::graph_from_adjacency_matrix(...) + 8. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 1 | WARN 3 | SKIP 16 | PASS 2 ] + Error: Test failures + Execution halted + ``` + +# foodingraph + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/vgasque/foodingraph +* Source code: https://github.com/cran/foodingraph +* Date/Publication: 2019-10-06 11:30:08 UTC +* Number of recursive dependencies: 60 + +Run `revdepcheck::cloud_details(, "foodingraph")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘foodingraph-Ex.R’ failed + The error most likely occurred in: + + > ### Name: graph_from_links_nodes + > ### Title: Display a graph from a list of links and nodes + > ### Aliases: graph_from_links_nodes + > + > ### ** Examples + > + > adj_matrix <- cor(iris[,-5]) + > legend <- data.frame(name = colnames(iris[,-5]), + + title = colnames(iris[,-5])) + > graph_iris <- links_nodes_from_mat(adj_matrix, legend) + > graph_from_links_nodes(graph_iris, main_title = "Iris graph") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: graph_from_links_nodes -> graph_from_data_frame -> make_empty_graph + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘grid’ + All declared Imports should be used. + ``` + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# ForestGapR + +
+ +* Version: 0.1.7 +* GitHub: NA +* Source code: https://github.com/cran/ForestGapR +* Date/Publication: 2023-03-31 20:50:18 UTC +* Number of recursive dependencies: 50 + +Run `revdepcheck::cloud_details(, "ForestGapR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ForestGapR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: GapSPDF + > ### Title: Forest Canopy Gaps as Spatial Polygons + > ### Aliases: GapSPDF + > + > ### ** Examples + > + > # Loading raster and viridis libraries + ... + > # set height thresholds (e.g. 10 meters) + > threshold <- 10 + > size <- c(1, 10^4) # m2 + > + > # Detecting forest gaps + > gaps_duc <- getForestGaps(chm_layer = ALS_CHM_DUC, threshold = threshold, size = size) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: getForestGaps ... ensure_igraph -> -> do.call -> + Execution halted + ``` + +# forestRK + +
+ +* Version: 0.0-5 +* GitHub: NA +* Source code: https://github.com/cran/forestRK +* Date/Publication: 2019-07-19 10:50:02 UTC +* Number of recursive dependencies: 57 + +Run `revdepcheck::cloud_details(, "forestRK")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘forestRK-Ex.R’ failed + The error most likely occurred in: + + > ### Name: draw.treeRK + > ### Title: Creates a 'igraph' plot of a 'rktree' + > ### Aliases: draw.treeRK + > ### Keywords: plot treeRK tree.plot + > + > ### ** Examples + > + ... + > + > # Plot the tree + > draw.treeRK(tree.entropy, y.factor.levels, font="Times", + + node.colour = "black", text.colour = "white", text.size = 0.7, + + tree.vertex.size = 100, tree.title = "Decision Tree", + + title.colour = "dark green") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: draw.treeRK -> make_empty_graph + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘pkgKitten’ + All declared Imports should be used. + ``` + +# fossilbrush + +
+ +* Version: 1.0.3 +* GitHub: NA +* Source code: https://github.com/cran/fossilbrush +* Date/Publication: 2022-07-21 15:50:02 UTC +* Number of recursive dependencies: 40 + +Run `revdepcheck::cloud_details(, "fossilbrush")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘fossilbrush-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_taxa + > ### Title: plot_taxa + > ### Aliases: plot_taxa + > + > ### ** Examples + > + > # load dataset + > data("brachios") + > # define ranks in dataset + > b_ranks <- c("phylum", "class", "order", "family", "genus") + > # plot taxon + > plot_taxa(brachios, "Atrypa", trank = "genus", ranks = b_ranks, mode = "parent") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot_taxa ... -> make_graph -> do.call -> + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘fossilbrush_vignette.Rmd’ using rmarkdown + + Quitting from lines 92-99 [unnamed-chunk-5] (fossilbrush_vignette.Rmd) + Error: processing vignette 'fossilbrush_vignette.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘fossilbrush_vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘fossilbrush_vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 31 marked UTF-8 strings + ``` + +# FrF2 + +
+ +* Version: 2.3 +* GitHub: NA +* Source code: https://github.com/cran/FrF2 +* Date/Publication: 2023-05-07 23:00:02 UTC +* Number of recursive dependencies: 34 + +Run `revdepcheck::cloud_details(, "FrF2")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘FrF2-Ex.R’ failed + The error most likely occurred in: + + > ### Name: CIG + > ### Title: Clear interactions graph from catlg entry + > ### Aliases: CIGstatic CIG gen2CIG + > ### Keywords: design + > + > ### ** Examples + > + ... + > ##D ## look up its id number in the title bar of the graph window and use it for id + > ##D par(xpd=TRUE) + > ##D CIGstatic(ex.CIG, id=1) + > ## End(Not run) + > + > graph1 <- CIG("9-4.2", plot=FALSE) ### create graph object from design name + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: CIG -> graph.empty + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘FrF2test.R’ + Running the tests in ‘tests/FrF2test.R’ failed. + Last 13 lines of output: + ..$ replications : num 1 + ..$ repeat.only : logi FALSE + ..$ randomize : logi FALSE + ..$ seed : NULL + ..$ creator : language FrF2(64, 7, blocks = 32, alias.block.2fis = TRUE, randomize = FALSE) + > + > ## godolphin with estimable + > str.wover(FrF2(64,9,blocks=16,factor.names=Letters[15:23], + + estimable=compromise(9,3)$requirement, + + alias.block.2fis=TRUE,randomize=FALSE)) + a clear design requires at least 32 runs + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: str.wover -> FrF2 -> estimable -> mapcalc -> graph.empty + Execution halted + ``` + +# fssemR + +
+ +* Version: 0.1.8 +* GitHub: https://github.com/Ivis4ml/fssemR +* Source code: https://github.com/cran/fssemR +* Date/Publication: 2022-02-11 13:00:02 UTC +* Number of recursive dependencies: 88 + +Run `revdepcheck::cloud_details(, "fssemR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘fssemR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: fssemR + > ### Title: Solving Sparse Structural Equation Model + > ### Aliases: fssemR package-fssemR + > + > ### ** Examples + > + > seed = as.numeric(Sys.time()) + ... + > Ns = 1 # sparse ratio + > sigma2 = 0.01 # sigma2 + > set.seed(seed) + > library(fssemR) + > data = randomFSSEMdata(n = N, p = Ng, k = Nk, sparse = Ns, df = 0.3, sigma2 = sigma2, + + u = 5, type = "DG", nhub = 1, dag = TRUE) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: randomFSSEMdata ... graph_from_adjacency_matrix -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘fssemR.Rmd’ using rmarkdown + + Quitting from lines 45-57 [unnamed-chunk-2] (fssemR.Rmd) + Error: processing vignette 'fssemR.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘fssemR.Rmd’ + + SUMMARY: processing the following file failed: + ‘fssemR.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +* checking installed package size ... NOTE + ``` + installed size is 18.2Mb + sub-directories of 1Mb or more: + libs 17.5Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘qpdf’ + All declared Imports should be used. + ``` + +# gDefrag + +
+ +* Version: 0.3 +* GitHub: NA +* Source code: https://github.com/cran/gDefrag +* Date/Publication: 2020-09-02 20:00:03 UTC +* Number of recursive dependencies: 12 + +Run `revdepcheck::cloud_details(, "gDefrag")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘gDefrag-Ex.R’ failed + The error most likely occurred in: + + > ### Name: prioritize + > ### Title: Prioritizing connectivity corridors + > ### Aliases: prioritize + > + > ### ** Examples + > + > data(road_P) + ... + > + > #Prioritize + > out3 <- prioritize(nodes = out1, edges = out2, + + method = "value")#Raster value + > out4 <- prioritize(nodes = out1, edges = out2, + + method = "between")#Betweenness + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: prioritize -> graph_from_data_frame -> make_empty_graph + Execution halted + ``` + +# gemtc + +
+ +* Version: 1.0-1 +* GitHub: https://github.com/gertvv/gemtc +* Source code: https://github.com/cran/gemtc +* Date/Publication: 2021-05-14 23:20:02 UTC +* Number of recursive dependencies: 58 + +Run `revdepcheck::cloud_details(, "gemtc")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘gemtc-Ex.R’ failed + The error most likely occurred in: + + > ### Name: atrialFibrillation + > ### Title: Prevention of stroke in atrial fibrillation patients + > ### Aliases: atrialFibrillation + > + > ### ** Examples + > + > # Build a model similar to Model 4(b) from Cooper et al. (2009): + ... + + classes=classes) + > + > model <- mtc.model(atrialFibrillation, + + type="regression", + + regressor=regressor, + + om.scale=10) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: mtc.model ... ensure_igraph -> mtc.network.graph -> graph.create -> graph.empty + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘test.R’ + Running the tests in ‘tests/test.R’ failed. + Last 13 lines of output: + 5. └─igraph::graph.empty() + ── Error ('test-unit-relative.effect.table.R:5:3'): it works for the smoking example ── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─gemtc::relative.effect.table(smoking_result) at test-unit-relative.effect.table.R:5:2 + 2. ├─base::as.matrix(...) + 3. └─gemtc::relative.effect(...) + 4. └─gemtc:::spanning.tree.mtc.result(result) + 5. └─gemtc:::graph.create(...) + 6. └─igraph::graph.empty() + + [ FAIL 48 | WARN 0 | SKIP 0 | PASS 221 ] + Error: Test failures + Execution halted + ``` + +# genscore + +
+ +* Version: 1.0.2.1 +* GitHub: https://github.com/sqyu/genscore +* Source code: https://github.com/cran/genscore +* Date/Publication: 2023-05-12 06:57:06 UTC +* Number of recursive dependencies: 45 + +Run `revdepcheck::cloud_details(, "genscore")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘genscore-Ex.R’ failed + The error most likely occurred in: + + > ### Name: cov_cons + > ### Title: Random generator of inverse covariance matrices. + > ### Aliases: cov_cons + > + > ### ** Examples + > + > p <- 100 + > K1 <- cov_cons("random", p, seed = 1, spars = 0.05, eig = 0.1) + > K2 <- cov_cons("sub", p, seed = 2, spars = 0.5, eig = 0.1, subgraphs=10) + > K3 <- cov_cons("er", p, seed = 3, spars = 0.05, eig = 0.1) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: cov_cons ... as.matrix -> -> ensure_igraph -> + Execution halted + ``` + +# geonetwork + +
+ +* Version: 0.5.0 +* GitHub: NA +* Source code: https://github.com/cran/geonetwork +* Date/Publication: 2023-04-14 08:30:02 UTC +* Number of recursive dependencies: 156 + +Run `revdepcheck::cloud_details(, "geonetwork")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘geonetwork-Ex.R’ failed + The error most likely occurred in: + + > ### Name: geonetwork + > ### Title: Create geographic networks + > ### Aliases: geonetwork + > + > ### ** Examples + > + > e <- data.frame(from = c("A", "A"), to = c("B", "C")) + > n <- data.frame(id = LETTERS[1:3], x = c(0, 0, 1), y = c(0, 1, 0)) + > geonetwork(e, n) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: geonetwork -> -> make_empty_graph + Execution halted + ``` + +# ggdag + +
+ +* Version: 0.2.10 +* GitHub: https://github.com/r-causal/ggdag +* Source code: https://github.com/cran/ggdag +* Date/Publication: 2023-05-28 23:30:02 UTC +* Number of recursive dependencies: 102 + +Run `revdepcheck::cloud_details(, "ggdag")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggdag-Ex.R’ failed + The error most likely occurred in: + + > ### Name: activate_collider_paths + > ### Title: Activate paths opened by stratifying on a collider + > ### Aliases: activate_collider_paths + > + > ### ** Examples + > + > dag <- dagify(m ~ x + y, x ~ y) + > + > collided_dag <- activate_collider_paths(dag, adjust_for = "m") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: activate_collider_paths ... tidy_dagitty -> %>% -> -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 7. │ └─testthat::source_dir(path, "^helper.*\\.[rR]$", env = env, wrap = FALSE) + 8. │ └─base::lapply(...) + 9. │ └─testthat (local) FUN(X[[i]], ...) + 10. │ └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap) + 11. │ ├─base::withCallingHandlers(...) + 12. │ └─base::eval(exprs, env) + 13. │ └─base::eval(exprs, env) + 14. │ └─ggdag::tidy_dagitty(test_dag) at tests/testthat/helper-load_dag.R:13:0 + 15. │ └─... %>% ... + 16. ├─igraph::graph_from_data_frame(., vertices = names(.dagitty)) + 17. │ └─igraph::make_empty_graph(n = 0, directed = directed) + 18. └─base::.handleSimpleError(...) + 19. └─testthat (local) h(simpleError(msg, call)) + 20. └─rlang::abort(...) + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘bias-structures.Rmd’ using rmarkdown + + Quitting from lines 44-46 [unnamed-chunk-1] (bias-structures.Rmd) + Error: processing vignette 'bias-structures.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘bias-structures.Rmd’ + + --- re-building ‘intro-to-dags.Rmd’ using rmarkdown + + ... + Quitting from lines 35-41 [dagitty] (intro-to-ggdag.Rmd) + Error: processing vignette 'intro-to-ggdag.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘intro-to-ggdag.Rmd’ + + SUMMARY: processing the following files failed: + ‘bias-structures.Rmd’ ‘intro-to-dags.Rmd’ ‘intro-to-ggdag.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# ggenealogy + +
+ +* Version: 1.0.1 +* GitHub: NA +* Source code: https://github.com/cran/ggenealogy +* Date/Publication: 2020-03-04 09:40:14 UTC +* Number of recursive dependencies: 82 + +Run `revdepcheck::cloud_details(, "ggenealogy")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggenealogy-Ex.R’ failed + The error most likely occurred in: + + > ### Name: getBasicStatistics + > ### Title: Determine basic statistics of the graph object + > ### Aliases: getBasicStatistics + > + > ### ** Examples + > + > data(sbGeneal) + > ig <- dfToIG(sbGeneal) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: dfToIG -> -> make_empty_graph + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggenealogy.Rnw’ + ... + + for iGraph information + + + + > ig <- dfToIG(sbGeneal) + + When sourcing ‘ggenealogy.R’: + Error: could not find function ".igraph.status" + Execution halted + + ‘ggenealogy.Rnw’ using ‘UTF-8’... failed + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘tibble’ + All declared Imports should be used. + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 2356 marked UTF-8 strings + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘ggenealogy.Rnw’ using Sweave + dfToIG package:ggenealogy R Documentation + + _P_r_o_c_e_s_s _t_h_e _g_e_n_e_a_l_o_g_y _g_r_a_p_h + + _D_e_s_c_r_i_p_t_i_o_n: + + Processes the genealogy into an igraph object with appropriate + vertex information, graph type, and edge weights. + ... + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + + --- failed re-building ‘ggenealogy.Rnw’ + + SUMMARY: processing the following file failed: + ‘ggenealogy.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# ggflowchart + +
+ +* Version: 1.0.0 +* GitHub: NA +* Source code: https://github.com/cran/ggflowchart +* Date/Publication: 2023-05-11 10:10:05 UTC +* Number of recursive dependencies: 60 + +Run `revdepcheck::cloud_details(, "ggflowchart")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggflowchart-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ggflowchart + > ### Title: Generate a flowchart in ggplot2 + > ### Aliases: ggflowchart + > + > ### ** Examples + > + > data <- tibble::tibble(from = c("A", "A", "A", "B", "C", "F"), to = c("B", "C", "D", "E", "F", "G")) + > ggflowchart(data) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: ggflowchart -> get_layout -> -> make_empty_graph + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘decision-tree-example.Rmd’ using rmarkdown + + Quitting from lines 64-65 [flowchart] (decision-tree-example.Rmd) + Error: processing vignette 'decision-tree-example.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘decision-tree-example.Rmd’ + + --- re-building ‘minimal-example.Rmd’ using rmarkdown + ... + Quitting from lines 31-32 [flowchart] (minimal-example.Rmd) + Error: processing vignette 'minimal-example.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘minimal-example.Rmd’ + + SUMMARY: processing the following files failed: + ‘decision-tree-example.Rmd’ ‘minimal-example.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# ggm + +
+ +* Version: 2.5 +* GitHub: NA +* Source code: https://github.com/cran/ggm +* Date/Publication: 2020-02-16 14:00:02 UTC +* Number of recursive dependencies: 9 + +Run `revdepcheck::cloud_details(, "ggm")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggm-Ex.R’ failed + The error most likely occurred in: + + > ### Name: AG + > ### Title: Ancestral graph + > ### Aliases: AG + > ### Keywords: graphs ancestral graph directed acyclic graph marginalization + > ### and conditioning + > + > ### ** Examples + ... + + 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, + + 1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0, + + 0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0),16,16,byrow=TRUE) + > M <- c(3,5,6,15,16) + > C <- c(4,7) + > AG(ex, M, C, plot = TRUE) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: AG -> plotfun -> graph -> do.call -> + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘graph’ + All declared Imports should be used. + ``` + +# ggnetwork + +
+ +* Version: 0.5.12 +* GitHub: https://github.com/briatte/ggnetwork +* Source code: https://github.com/cran/ggnetwork +* Date/Publication: 2023-03-06 20:00:02 UTC +* Number of recursive dependencies: 73 + +Run `revdepcheck::cloud_details(, "ggnetwork")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ── Error ('test-fortify-network.R:13:1'): (code run outside of `test_that()`) ── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─igraph::random.graph.game(n = 1, p.or.m = 0) at test-fortify-network.R:13:0 + ── Error ('test-ggnetwork.R:7:3'): ggnetwork works ───────────────────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─igraph::graph_from_adjacency_matrix(as.matrix(emon[[1]])) at test-ggnetwork.R:7:2 + 2. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 3 | WARN 0 | SKIP 0 | PASS 25 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘sna’ ‘utils’ + All declared Imports should be used. + ``` + +# ggraph + +
+ +* Version: 2.1.0 +* GitHub: https://github.com/thomasp85/ggraph +* Source code: https://github.com/cran/ggraph +* Date/Publication: 2022-10-09 20:33:19 UTC +* Number of recursive dependencies: 98 + +Run `revdepcheck::cloud_details(, "ggraph")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggraph-Ex.R’ failed + The error most likely occurred in: + + > ### Name: autograph + > ### Title: Quickplot wrapper for networks + > ### Aliases: autograph autograph.default + > + > ### ** Examples + > + > library(tidygraph) + ... + + filter + + > gr <- create_notable('herschel') %>% + + mutate(class = sample(letters[1:3], n(), TRUE)) %E>% + + mutate(weight = runif(n())) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: %E>% ... create_notable -> as_tbl_graph -> make_graph -> make_famous_graph + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘Edges.Rmd’ using rmarkdown + + Quitting from lines 40-75 [unnamed-chunk-2] (Edges.Rmd) + Error: processing vignette 'Edges.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘Edges.Rmd’ + + --- re-building ‘Layouts.Rmd’ using rmarkdown + + ... + Quitting from lines 67-77 [unnamed-chunk-2] (tidygraph.Rmd) + Error: processing vignette 'tidygraph.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘tidygraph.Rmd’ + + SUMMARY: processing the following files failed: + ‘Edges.Rmd’ ‘Layouts.Rmd’ ‘Nodes.Rmd’ ‘tidygraph.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 10.7Mb + sub-directories of 1Mb or more: + doc 3.5Mb + libs 5.9Mb + ``` + +# ghypernet + +
+ +* Version: 1.1.0 +* GitHub: NA +* Source code: https://github.com/cran/ghypernet +* Date/Publication: 2021-10-15 13:30:05 UTC +* Number of recursive dependencies: 98 + +Run `revdepcheck::cloud_details(, "ghypernet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ghypernet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: CreateIgGraphs + > ### Title: Convert a list of adjacency matrices to a list of igraph graphs. + > ### Aliases: CreateIgGraphs + > + > ### ** Examples + > + > data('adj_karate') + > adj_list <- list(adj_karate) + > glist <- CreateIgGraphs(adj_list, FALSE, FALSE) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: CreateIgGraphs -> lapply -> FUN -> graph.adjacency.dense + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Significantlinks.Rmd’ using rmarkdown + --- finished re-building ‘Significantlinks.Rmd’ + + --- re-building ‘Tutorial_NRM.Rmd’ using rmarkdown + + Quitting from lines 643-649 [unnamed-chunk-39] (Tutorial_NRM.Rmd) + Error: processing vignette 'Tutorial_NRM.Rmd' failed with diagnostics: + No layout function defined for objects of class + ... + --- failed re-building ‘Tutorial_NRM.Rmd’ + + --- re-building ‘tutorial.Rmd’ using rmarkdown + --- finished re-building ‘tutorial.Rmd’ + + SUMMARY: processing the following file failed: + ‘Tutorial_NRM.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘methods’ + All declared Imports should be used. + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 11 marked UTF-8 strings + ``` + +# GISSB + +
+ +* Version: 1.1 +* GitHub: NA +* Source code: https://github.com/cran/GISSB +* Date/Publication: 2023-01-10 18:33:14 UTC +* Number of recursive dependencies: 114 + +Run `revdepcheck::cloud_details(, "GISSB")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘GISSB-Ex.R’ failed + The error most likely occurred in: + + > ### Name: path_leaflet + > ### Title: Visualize the shortest path with Leaflet + > ### Aliases: path_leaflet + > + > ### ** Examples + > + > + ... + > shortest_path_igraph(from_node_ID = 25, + + to_node_ID = 33, + + unit = "minutes", + + path = TRUE, + + graph_object = graph_sampledata) %>% + + path_leaflet(graph_object = graph_sampledata) + Error in .igraph.status("Restore graph external pointer.\n") : + could not find function ".igraph.status" + Calls: %>% ... -> ensure_igraph -> is_igraph -> warn_version + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 12. │ └─base::eval(exprs, env) + 13. │ └─base::eval(exprs, env) + 14. │ └─GISSB::vegnett_to_R(...) at tests/testthat/helper_files.R:4:0 + 15. │ └─tidygraph::tbl_graph(...) + 16. │ ├─tidygraph::as_tbl_graph(...) + 17. │ └─tidygraph:::as_tbl_graph.list(...) + 18. │ └─tidygraph:::as_graph_node_edge(x, directed = directed, node_key = node_key) + 19. │ └─igraph::graph_from_edgelist(as.matrix(edges[, 1:2]), directed = directed) + 20. │ └─igraph::make_graph(t(el), directed = directed) + 21. │ ├─base::do.call(old_graph, args) + 22. │ └─igraph (local) ``(``, directed = TRUE) + 23. └─base::.handleSimpleError(...) + 24. └─testthat (local) h(simpleError(msg, call)) + 25. └─rlang::abort(...) + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 866 marked UTF-8 strings + ``` + +# gmat + +
+ +* Version: 0.2.2 +* GitHub: https://github.com/gherardovarando/gmat +* Source code: https://github.com/cran/gmat +* Date/Publication: 2020-08-30 01:00:18 UTC +* Number of recursive dependencies: 55 + +Run `revdepcheck::cloud_details(, "gmat")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘gmat-Ex.R’ failed + The error most likely occurred in: + + > ### Name: dag-constrained correlation matrices + > ### Title: Simulation of correlation matrices + > ### Aliases: 'dag-constrained correlation matrices' chol_mh chol_iid + > + > ### ** Examples + > + > ## Cholesky sampling via Metropolis-Hastings + ... + [2,] -0.7183196 1.0000000 0.9953518 + [3,] -0.7542058 0.9953518 1.0000000 + + > + > # Generate a matrix with a percentage of zeros + > chol_mh(d = 0.5) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: chol_mh -> rgraph -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─gmat::rgraph(p = p, d = d) at test_utils.R:98:2 + 2. └─igraph::sample_gnp(n = p, p = d) + ── Error ('test_utils.R:113:3'): the oriented dag does not contain v-structures ── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─gmat::rgraph(p = p, d = d) at test_utils.R:113:2 + 2. └─igraph::sample_gnp(n = p, p = d) + + [ FAIL 16 | WARN 0 | SKIP 0 | PASS 45 ] + Error: Test failures + Execution halted + ``` + +# GMPro + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/GMPro +* Date/Publication: 2020-06-25 14:00:02 UTC +* Number of recursive dependencies: 40 + +Run `revdepcheck::cloud_details(, "GMPro")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘GMPro-Ex.R’ failed + The error most likely occurred in: + + > ### Name: DP_SBM + > ### Title: Degree profile graph matching with community detection. + > ### Aliases: DP_SBM + > + > ### ** Examples + > + > ### Here we use graphs under stochastic block model(SBM). + ... + > dB[lower.tri(dB)] = t(dB)[lower.tri(dB)] + > B1 = G*dB + > indB = sample(1:n, n, replace = FALSE) + > labelB = l[indB] + > B = B1[indB, indB] + > DP_SBM(A = A, B = B, K = 2, fun = "EEpost", rep = 10, d = 3) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: DP_SBM ... graph.incidence -> graph.incidence.dense -> make_empty_graph + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# GOxploreR + +
+ +* Version: 1.2.6 +* GitHub: NA +* Source code: https://github.com/cran/GOxploreR +* Date/Publication: 2022-04-19 14:02:33 UTC +* Number of recursive dependencies: 114 + +Run `revdepcheck::cloud_details(, "GOxploreR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘GOxploreR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: prioritizedGOTerms + > ### Title: prioritization of a lists of GO-terms + > ### Aliases: prioritizedGOTerms + > + > ### ** Examples + > + > + > Terms <-c("GO:0000278", "GO:0006414","GO:0022403","GO:0006415","GO:0006614", + + "GO:0045047","GO:0022411","GO:0001775","GO:0046649","GO:045321") + > prioritizedGOTerms(Terms, organism = "Human", sp=TRUE, domain = "BP") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: prioritizedGOTerms ... graph.edgelist -> make_graph -> do.call -> + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘GOxploreR.Rmd’ using rmarkdown + + Quitting from lines 355-366 [unnamed-chunk-16] (GOxploreR.Rmd) + Error: processing vignette 'GOxploreR.Rmd' failed with diagnostics: + error in evaluating the argument 'x' in selecting a method for function 'head': No layout function defined for objects of class + --- failed re-building ‘GOxploreR.Rmd’ + + SUMMARY: processing the following file failed: + ‘GOxploreR.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +* checking installed package size ... NOTE + ``` + installed size is 6.7Mb + sub-directories of 1Mb or more: + R 6.2Mb + ``` + +# gRain + +
+ +* Version: 1.3.13 +* GitHub: NA +* Source code: https://github.com/cran/gRain +* Date/Publication: 2023-03-09 16:20:02 UTC +* Number of recursive dependencies: 59 + +Run `revdepcheck::cloud_details(, "gRain")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘gRain-Ex.R’ failed + The error most likely occurred in: + + > ### Name: chest + > ### Title: Chest clinic example + > ### Aliases: chest chest_cpt + > ### Keywords: datasets + > + > ### ** Examples + > + ... + > b.s <- cptable(~bronc|smoke, values=c(6,4,3,7), levels=yn) + > e.lt <- cptable(~either|lung:tub,values=c(1,0,1,0,1,0,0,1),levels=yn) + > x.e <- cptable(~xray|either, values=c(98,2,5,95), levels=yn) + > d.be <- cptable(~dysp|bronc:either, values=c(9,1,7,3,8,2,1,9), levels=yn) + > + > grain(compileCPT(a, t.a, s, l.s, b.s, e.lt, x.e, d.be)) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: grain ... asMethod -> g_gn2ig_ -> -> graph_from_adj_list + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testhat.R’ + Running the tests in ‘tests/testhat.R’ failed. + Last 13 lines of output: + 8. │ └─gRbase:::topo_sortMAT_(amat) + 9. └─methods::as(object, "dgCMatrix") + 10. └─gRbase (local) asMethod(object) + 11. └─gRbase::g_gn2sm_(from) + 12. ├─igraph::as_adjacency_matrix(as(object, "igraph")) + 13. │ └─igraph:::ensure_igraph(graph) + 14. └─methods::as(object, "igraph") + 15. └─gRbase (local) asMethod(object) + 16. └─gRbase::g_gn2ig_(from) + 17. └─igraph::igraph.from.graphNEL(object) + 18. └─igraph::graph_from_adj_list(al, mode = mode, duplicate = TRUE) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘grain-intro.Rnw’ using knitr + + Quitting from lines 121-134 [unnamed-chunk-3] (grain-intro.Rnw) + Error: processing vignette 'grain-intro.Rnw' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘grain-intro.Rnw’ + + SUMMARY: processing the following file failed: + ‘grain-intro.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# grainscape + +
+ +* Version: 0.4.4 +* GitHub: https://github.com/achubaty/grainscape +* Source code: https://github.com/cran/grainscape +* Date/Publication: 2023-04-20 08:40:02 UTC +* Number of recursive dependencies: 96 + +Run `revdepcheck::cloud_details(, "grainscape")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘grainscape-Ex.R’ failed + The error most likely occurred in: + + > ### Name: GOC + > ### Title: Produce a grains of connectivity model at multiple scales + > ### (patch-based or lattice GOC) + > ### Aliases: GOC GOC,mpg-method + > + > ### ** Examples + > + ... + > tiny <- raster::raster(system.file("extdata/tiny.asc", package = "grainscape")) + > + > ## Create a resistance surface from a raster using an is-becomes reclassification + > tinyCost <- raster::reclassify(tiny, rcl = cbind(c(1, 2, 3, 4), c(1, 5, 10, 12))) + > ## Produce a patch-based MPG where patches are resistance features=1 + > tinyPatchMPG <- MPG(cost = tinyCost, patch = tinyCost == 1) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: MPG -> MPG -> graph_from_data_frame -> make_empty_graph + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘MPG_algorithm.Rmd’ using rmarkdown + A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TinyTeX with tinytex::reinstall_tinytex(repository = "illinois"). + + tlmgr: Local TeX Live (2022) is older than remote repository (2023). + Cross release updates are only supported with + update-tlmgr-latest(.sh/.exe) --update + See https://tug.org/texlive/upgrade.html for details. + Warning in system2("tlmgr", args, ...) : + running command ''tlmgr' search --file --global '/grffile.sty'' had status 1 + ... + + Error: processing vignette 'grainscape_vignette.Rmd' failed with diagnostics: + LaTeX failed to compile /tmp/workdir/grainscape/new/grainscape.Rcheck/vign_test/grainscape/vignettes/grainscape_vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See grainscape_vignette.log for more info. + --- failed re-building ‘grainscape_vignette.Rmd’ + + SUMMARY: processing the following files failed: + ‘MPG_algorithm.Rmd’ ‘grainscape_vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +* checking installed package size ... NOTE + ``` + installed size is 5.2Mb + sub-directories of 1Mb or more: + doc 1.5Mb + libs 2.3Mb + ``` + +# grand + +
+ +* Version: 0.9.0 +* GitHub: https://github.com/zpneal/grand +* Source code: https://github.com/cran/grand +* Date/Publication: 2023-02-10 10:30:02 UTC +* Number of recursive dependencies: 36 + +Run `revdepcheck::cloud_details(, "grand")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘grand-Ex.R’ failed + The error most likely occurred in: + + > ### Name: grand + > ### Title: Apply Guidelines for Reporting About Network Data (GRAND) to an + > ### igraph object + > ### Aliases: grand + > + > ### ** Examples + > + > data(airport) #Load example data + > airport <- grand(airport) #Apply GRAND interactively + Error in .igraph.status("Restore graph external pointer.\n") : + could not find function ".igraph.status" + Calls: grand ... -> ensure_igraph -> is_igraph -> warn_version + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘grand.Rmd’ using rmarkdown + + Quitting from lines 167-178 [unnamed-chunk-3] (grand.Rmd) + Error: processing vignette 'grand.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘grand.Rmd’ + + SUMMARY: processing the following file failed: + ‘grand.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# graph4lg + +
+ +* Version: 1.8.0 +* GitHub: NA +* Source code: https://github.com/cran/graph4lg +* Date/Publication: 2023-01-30 14:00:05 UTC +* Number of recursive dependencies: 119 + +Run `revdepcheck::cloud_details(, "graph4lg")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘graph4lg-Ex.R’ failed + The error most likely occurred in: + + > ### Name: add_nodes_attr + > ### Title: Add attributes to the nodes of a graph + > ### Aliases: add_nodes_attr + > + > ### ** Examples + > + > data("data_tuto") + > graph <- data_tuto[[3]] + > df_nodes <- data.frame(Id = igraph::V(graph)$name, + + Area = runif(50, min = 10, max = 60)) + Error in .igraph.status("Restore graph external pointer.\n") : + could not find function ".igraph.status" + Calls: data.frame ... -> ensure_igraph -> is_igraph -> warn_version + Execution halted + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Error loading dataset 'data_tuto': + Error in .igraph.status("Restore graph external pointer.\n") : + could not find function ".igraph.status" + + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘Rdpack’ + All declared Imports should be used. + ``` + +# graphclust + +
+ +* Version: 1.3 +* GitHub: NA +* Source code: https://github.com/cran/graphclust +* Date/Publication: 2023-06-07 16:50:02 UTC +* Number of recursive dependencies: 15 + +Run `revdepcheck::cloud_details(, "graphclust")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘graphclust-Ex.R’ failed + The error most likely occurred in: + + > ### Name: metagraph + > ### Title: Plot the metagraph of the parameter of the stochastic block + > ### model associated with one of the estimated graph clusters + > ### Aliases: metagraph + > + > ### ** Examples + > + ... + + initialization of DelatICL... + + clustering algorithm... + + > metagraph(1, res) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: metagraph ... graph_from_adjacency_matrix -> graph.adjacency.dense + Execution halted + ``` + +# graphicalExtremes + +
+ +* Version: 0.2.0 +* GitHub: https://github.com/sebastian-engelke/graphicalExtremes +* Source code: https://github.com/cran/graphicalExtremes +* Date/Publication: 2022-12-02 12:20:04 UTC +* Number of recursive dependencies: 94 + +Run `revdepcheck::cloud_details(, "graphicalExtremes")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘graphicalExtremes-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Gamma2graph + > ### Title: Transformation of matrix to graph object + > ### Aliases: Gamma2graph Theta2graph + > + > ### ** Examples + > + > Gamma <- cbind( + ... + + c(1.5, 0, 2, 1.5), + + c(1.5, 2, 0, 1.5), + + c(2, 1.5, 1.5, 0) + + ) + > + > Gamma2graph(Gamma) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: Gamma2graph ... Theta2graph -> -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘glasso’ + ``` + +# graphlayouts + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/schochastics/graphlayouts +* Source code: https://github.com/cran/graphlayouts +* Date/Publication: 2023-05-01 08:00:02 UTC +* Number of recursive dependencies: 93 + +Run `revdepcheck::cloud_details(, "graphlayouts")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─igraph::make_full_graph(3) at test-graph_manipulate.R:2:3 + ── Error ('test-layout_backbone.R:2:3'): backbone layout works ───────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. ├─graphlayouts::layout_as_backbone(igraph::graph.full(10)) at test-layout_backbone.R:2:2 + 2. │ └─igraph::is.igraph(g) + 3. └─igraph::graph.full(10) + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 113 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 11.1Mb + sub-directories of 1Mb or more: + doc 1.9Mb + help 2.4Mb + libs 6.5Mb + ``` + +# graphseg + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/goepp/graphseg +* Source code: https://github.com/cran/graphseg +* Date/Publication: 2023-05-02 08:10:06 UTC +* Number of recursive dependencies: 67 + +Run `revdepcheck::cloud_details(, "graphseg")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘graphseg-Ex.R’ failed + The error most likely occurred in: + + > ### Name: utrecht_district + > ### Title: Administrative areas of the Netherlands aroung the city of + > ### Utrecht + > ### Aliases: utrecht_district graph_utrecht_district + > ### Keywords: datasets + > + > ### ** Examples + ... + old-style crs object detected; please recreate object with a recent sf::st_crs() + old-style crs object detected; please recreate object with a recent sf::st_crs() + Warning: st_crs<- : replacing crs does not reproject data; use st_transform for that + > adj_municip <- as(as(igraph::as_adjacency_matrix(graph_utrecht_district, type = "both"), + + "symmetricMatrix"), + + "TsparseMatrix") + Error in .igraph.status("Restore graph external pointer.\n") : + could not find function ".igraph.status" + Calls: as ... -> ensure_igraph -> is_igraph -> warn_version + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 14768 marked UTF-8 strings + ``` + +# graphTweets + +
+ +* Version: 0.5.3 +* GitHub: https://github.com/JohnCoene/graphTweets +* Source code: https://github.com/cran/graphTweets +* Date/Publication: 2020-01-08 09:00:08 UTC +* Number of recursive dependencies: 58 + +Run `revdepcheck::cloud_details(, "graphTweets")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘graphTweets-Ex.R’ failed + The error most likely occurred in: + + > ### Name: gt_graph + > ### Title: Graph + > ### Aliases: gt_graph + > + > ### ** Examples + > + > # simulate dataset + ... + + ) + > + > tweets %>% + + gt_edges(text, screen_name, status_id) %>% + + gt_nodes() %>% + + gt_graph() -> net + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: %>% -> gt_graph -> -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ── Error ('test_overhaul.R:53:3'): nodes & edges & dyn ───────────────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. ├─testthat::expect_is(...) at test_overhaul.R:53:2 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. ├─... %>% gt_graph() + 5. └─graphTweets::gt_graph(.) + 6. └─igraph::graph.data.frame(gt[["edges"]], directed = TRUE, vertices = gt[["nodes"]]) + 7. └─igraph::make_empty_graph(n = 0, directed = directed) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 11 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘utils’ + All declared Imports should be used. + ``` + +# gRbase + +
+ +* Version: 1.8.9 +* GitHub: NA +* Source code: https://github.com/cran/gRbase +* Date/Publication: 2022-11-10 10:40:02 UTC +* Number of recursive dependencies: 49 + +Run `revdepcheck::cloud_details(, "gRbase")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘gRbase-Ex.R’ failed + The error most likely occurred in: + + > ### Name: dag2chol + > ### Title: Create regression matrix matrix from DAG A DAG can be + > ### represented as a triangular matrix of regression coefficients. + > ### Aliases: dag2chol + > + > ### ** Examples + > + > + > g <- dag(~x2|x1 + x3|x1:x2 + x4|x3) + > gi <- as(g, "igraph") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: as ... asMethod -> g_gn2ig_ -> -> graph_from_adj_list + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testhat.R’ + Running the tests in ‘tests/testhat.R’ failed. + Last 13 lines of output: + 9. └─gRbase (local) asMethod(object) + 10. └─gRbase::g_gn2dm_(from) + 11. ├─methods::as(...) + 12. │ └─methods:::.class1(object) + 13. ├─igraph::as_adjacency_matrix(as(object, "igraph")) + 14. │ └─igraph:::ensure_igraph(graph) + 15. └─methods::as(object, "igraph") + 16. └─gRbase (local) asMethod(object) + 17. └─gRbase::g_gn2ig_(from) + 18. └─igraph::igraph.from.graphNEL(object) + 19. └─igraph::graph_from_adj_list(al, mode = mode, duplicate = TRUE) + + [ FAIL 4 | WARN 0 | SKIP 0 | PASS 52 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘arrays.Rnw’ using knitr + Error: processing vignette 'arrays.Rnw' failed with diagnostics: + Running 'texi2dvi' on 'arrays.tex' failed. + LaTeX errors: + ! LaTeX Error: File `boxedminipage.sty' not found. + + Type X to quit or to proceed, + or enter new name. (Default extension: sty) + + ... + Quitting from lines 369-377 [unnamed-chunk-15] (graphs.Rnw) + Error: processing vignette 'graphs.Rnw' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘graphs.Rnw’ + + SUMMARY: processing the following files failed: + ‘arrays.Rnw’ ‘graphs.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +* checking installed package size ... NOTE + ``` + installed size is 25.7Mb + sub-directories of 1Mb or more: + libs 23.6Mb + ``` + +# gRim + +
+ +* Version: 0.2.10 +* GitHub: NA +* Source code: https://github.com/cran/gRim +* Date/Publication: 2022-10-15 22:22:35 UTC +* Number of recursive dependencies: 55 + +Run `revdepcheck::cloud_details(, "gRim")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘gRim-Ex.R’ failed + The error most likely occurred in: + + > ### Name: getEdges + > ### Title: Find edges in a graph or edges not in an undirected graph. + > ### Aliases: getEdges getEdges.list getEdges.graphNEL getEdges.matrix + > ### getInEdges getOutEdges getEdgesMAT getInEdgesMAT getOutEdgesMAT + > ### Keywords: utilities + > + > ### ** Examples + > + > + > gg <- ug(~a:b:d + a:c:d + c:e) + > glist <- getCliques(gg) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: getCliques ... asMethod -> g_gn2ig_ -> -> graph_from_adj_list + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘grim.Rnw’ + ... + + "mental", "phys")), data = reinis, interactions = 2) + + > formula(dm3) + ~smoke * mental + smoke * phys + mental * phys + smoke * systol + + > iplot(dm1) + + When sourcing ‘grim.R’: + Error: could not find function ".igraph.status" + Execution halted + + ‘grim.Rnw’ using ‘latin1’... failed + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.7Mb + sub-directories of 1Mb or more: + libs 4.9Mb + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘grim.Rnw’ using Sweave + Loading required package: gRbase + Warning in dir.create("figures") : 'figures' already exists + Loading required package: graph + Loading required package: BiocGenerics + + Attaching package: ‘BiocGenerics’ + + The following objects are masked from ‘package:stats’: + ... + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + + --- failed re-building ‘grim.Rnw’ + + SUMMARY: processing the following file failed: + ‘grim.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# handwriter + +
+ +* Version: 1.0.1 +* GitHub: NA +* Source code: https://github.com/cran/handwriter +* Date/Publication: 2021-08-16 16:20:02 UTC +* Number of recursive dependencies: 64 + +Run `revdepcheck::cloud_details(, "handwriter")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘handwriter-Ex.R’ failed + The error most likely occurred in: + + > ### Name: AddLetterImages + > ### Title: AddLetterImages + > ### Aliases: AddLetterImages + > + > ### ** Examples + > + > twoSent_document = list() + > twoSent_document$image = twoSent + > twoSent_document$thin = thinImage(twoSent_document$image) + > twoSent_processList = processHandwriting(twoSent_document$thin, dim(twoSent_document$image)) + Starting Processing... + Getting Nodes...Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: processHandwriting -> graph_from_data_frame -> make_empty_graph + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.6Mb + sub-directories of 1Mb or more: + libs 4.5Mb + ``` + +# hero + +
+ +* Version: 0.4.7 +* GitHub: NA +* Source code: https://github.com/cran/hero +* Date/Publication: 2020-01-24 22:00:02 UTC +* Number of recursive dependencies: 148 + +Run `revdepcheck::cloud_details(, "hero")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘hero-Ex.R’ failed + The error most likely occurred in: + + > ### Name: adjacent + > ### Title: Determine adjacent points + > ### Aliases: adjacent + > + > ### ** Examples + > + > # basic coordinates + ... + > coords = expand.grid(1:4, 1:4) + > # plot coordinates to see relationships + > plot(coords, type = "n") + > text(coords) + > a = adjacent(coords, digits = 1) + > plot(a) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot ... graph.adjacency.sparse -> make_graph -> do.call -> + Execution halted + ``` + +# HLSM + +
+ +* Version: 0.9.0 +* GitHub: NA +* Source code: https://github.com/cran/HLSM +* Date/Publication: 2021-12-06 13:00:02 UTC +* Number of recursive dependencies: 10 + +Run `revdepcheck::cloud_details(, "HLSM")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘HLSM-Ex.R’ failed + The error most likely occurred in: + + > ### Name: HLSMrandomEF + > ### Title: Function to run the MCMC sampler in random effects latent space + > ### model, HLSMfixedEF for fixed effects model, or LSM for single network + > ### latent space model) + > ### Aliases: HLSMrandomEF HLSMfixedEF LSM print.HLSM print.summary.HLSM + > ### summary.HLSM getIntercept getLS getLikelihood getBeta + > + ... + > + > #Fixed effect HLSM on Pitt and Spillane data + > + > fixed.fit = HLSMfixedEF(Y = ps.advice.mat, senderCov=ps.node.df, + + initialVals = initialVals,priors = priors, + + tune = tune,tuneIn = FALSE,dd = 2,niter = niter) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: HLSMfixedEF ... lapply -> FUN -> graph.adjacency -> graph.adjacency.dense + Execution halted + ``` + +# HospitalNetwork + +
+ +* Version: 0.9.3 +* GitHub: https://github.com/PascalCrepey/HospitalNetwork +* Source code: https://github.com/cran/HospitalNetwork +* Date/Publication: 2023-02-27 08:22:43 UTC +* Number of recursive dependencies: 115 + +Run `revdepcheck::cloud_details(, "HospitalNetwork")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘HospitalNetwork-Ex.R’ failed + The error most likely occurred in: + + > ### Name: HospiNet + > ### Title: Class providing the HospiNet object with its methods + > ### Aliases: HospiNet + > ### Keywords: data + > + > ### ** Examples + > + ... + + condition = "dates" + + ) + Checking for missing values... + Checking for duplicated records... + Removed 0 duplicates + Done. + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: hospinet_from_subject_database ... checkClass -> -> -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 9. │ └─checkmate::checkClass(x, classes, ordered, null.ok) + 10. └─HospitalNetwork (local) ``() + 11. └─igraph::graph_from_data_frame(self$edgelist) + 12. └─igraph::make_empty_graph(n = 0, directed = directed) + + [ FAIL 2 | WARN 0 | SKIP 2 | PASS 55 ] + Deleting unused snapshots: + • HospiNet/clmat100.svg + • HospiNet/clustdeg500.svg + • HospiNet/clustmatclust500.svg + • HospiNet/deg100.svg + • HospiNet/mat100.svg + • HospiNet/matclust500.svg + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘HospitalNetwork-Workflow.Rmd’ using rmarkdown + + Quitting from lines 154-157 [setup2] (HospitalNetwork-Workflow.Rmd) + Error: processing vignette 'HospitalNetwork-Workflow.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘HospitalNetwork-Workflow.Rmd’ + + SUMMARY: processing the following file failed: + ‘HospitalNetwork-Workflow.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# HTT + +
+ +* Version: 0.1.2 +* GitHub: NA +* Source code: https://github.com/cran/HTT +* Date/Publication: 2023-03-12 14:30:02 UTC +* Number of recursive dependencies: 72 + +Run `revdepcheck::cloud_details(, "HTT")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘HTT-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Hypothesis Testing Tree + > ### Title: Hypothesis Testing Tree + > ### Aliases: HTT + > ### Keywords: HTT + > + > ### ** Examples + > + > ## regression + > data("Boston", package = "MASS") + > Bostonhtt <- HTT(medv ~ . , data = Boston, controls = htt_control(R = 99)) + > plot(Bostonhtt) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot ... plot.htt -> graph_from_data_frame -> make_empty_graph + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Intro.Rmd’ using rmarkdown + + Quitting from lines 24-32 [unnamed-chunk-2] (Intro.Rmd) + Error: processing vignette 'Intro.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘Intro.Rmd’ + + SUMMARY: processing the following file failed: + ‘Intro.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.1Mb + sub-directories of 1Mb or more: + libs 6.5Mb + ``` + +# huge + +
+ +* Version: 1.3.5 +* GitHub: NA +* Source code: https://github.com/cran/huge +* Date/Publication: 2021-06-30 20:20:02 UTC +* Number of recursive dependencies: 10 + +Run `revdepcheck::cloud_details(, "huge")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘huge-Ex.R’ failed + The error most likely occurred in: + + > ### Name: huge + > ### Title: High-dimensional undirected graph estimation + > ### Aliases: huge + > + > ### ** Examples + > + > #generate data + ... + Model: Meinshausen & Buhlmann graph estimation (mb) + Input: The Data Matrix + Path length: 10 + Graph dimension: 12 + Sparsity level: 0 -----> 0.6969697 + > plot(out1) #Not aligned + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot ... plot.huge -> graph.adjacency -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘vignette.Rnw’ using Sweave + Error: processing vignette 'vignette.Rnw' failed with diagnostics: + Running 'texi2dvi' on 'vignette.tex' failed. + LaTeX errors: + ! LaTeX Error: File `pdfpages.sty' not found. + + Type X to quit or to proceed, + or enter new name. (Default extension: sty) + ... + l.8 \usepackage + {Sweave}^^M + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘vignette.Rnw’ + + SUMMARY: processing the following file failed: + ‘vignette.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +* checking installed package size ... NOTE + ``` + installed size is 13.5Mb + sub-directories of 1Mb or more: + libs 12.0Mb + ``` + +# ICDS + +
+ +* Version: 0.1.2 +* GitHub: NA +* Source code: https://github.com/cran/ICDS +* Date/Publication: 2021-07-15 11:30:10 UTC +* Number of recursive dependencies: 93 + +Run `revdepcheck::cloud_details(, "ICDS")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ICDS-Ex.R’ failed + The error most likely occurred in: + + > ### Name: opt_subpath + > ### Title: opt_subpath + > ### Aliases: opt_subpath + > + > ### ** Examples + > + > zz<-GetExampleData("zzz") + > subpathdata<-GetExampleData("subpathdata") + > optsubpath<-opt_subpath(subpathdata,zz,overlap=0.6) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: opt_subpath ... overlapSPMatrix -> graph.adjacency -> graph.adjacency.dense + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘ICDS.Rmd’ using rmarkdown + + Quitting from lines 137-140 [unnamed-chunk-10] (ICDS.Rmd) + Error: processing vignette 'ICDS.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘ICDS.Rmd’ + + SUMMARY: processing the following file failed: + ‘ICDS.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# iconr + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/zoometh/iconr +* Source code: https://github.com/cran/iconr +* Date/Publication: 2021-02-16 09:10:05 UTC +* Number of recursive dependencies: 81 + +Run `revdepcheck::cloud_details(, "iconr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘iconr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: contemp_nds + > ### Title: Select Contemporaneous Nodes + > ### Aliases: contemp_nds + > ### Keywords: ~kwd1 graphs + > + > ### ** Examples + > + ... + > eds.df <- read_eds(site = "Ibahernando", + + decor = "Ibahernando", + + dir = dataDir) + > + > # Extract the subgraph contemporaneous to the node 2 + > l_dec_df <- contemp_nds(nds.df, eds.df, selected.nd = 2) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: contemp_nds -> -> make_empty_graph + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# icosa + +
+ +* Version: 0.11.0 +* GitHub: https://github.com/adamkocsis/icosa +* Source code: https://github.com/cran/icosa +* Date/Publication: 2023-03-23 14:42:09 UTC +* Number of recursive dependencies: 52 + +Run `revdepcheck::cloud_details(, "icosa")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘icosa-Ex.R’ failed + The error most likely occurred in: + + > ### Name: SpPolygons + > ### Title: Spatial polygons from an icosahedral grid + > ### Aliases: SpPolygons SpPolygons,trigrid-method + > ### SpPolygons,hexagrid-method + > + > ### ** Examples + > + > a <- trigrid() + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: trigrid ... .local -> do.call -> -> make_empty_graph + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘icosa_cran.Rmd’ using rmarkdown + + Quitting from lines 17-20 [unnamed-chunk-1] (icosa_cran.Rmd) + Error: processing vignette 'icosa_cran.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘icosa_cran.Rmd’ + + SUMMARY: processing the following file failed: + ‘icosa_cran.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.9Mb + sub-directories of 1Mb or more: + libs 4.3Mb + ``` + +# idopNetwork + +
+ +* Version: 0.1.2 +* GitHub: https://github.com/cxzdsa2332/idopNetwork +* Source code: https://github.com/cran/idopNetwork +* Date/Publication: 2023-04-18 06:50:02 UTC +* Number of recursive dependencies: 78 + +Run `revdepcheck::cloud_details(, "idopNetwork")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘idopNetwork_vignette.Rmd’ using rmarkdown + + Quitting from lines 309-311 [unnamed-chunk-36] (idopNetwork_vignette.Rmd) + Error: processing vignette 'idopNetwork_vignette.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘idopNetwork_vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘idopNetwork_vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# iGraphMatch + +
+ +* Version: 2.0.1 +* GitHub: https://github.com/dpmcsuss/iGraphMatch +* Source code: https://github.com/cran/iGraphMatch +* Date/Publication: 2022-09-13 18:30:02 UTC +* Number of recursive dependencies: 80 + +Run `revdepcheck::cloud_details(, "iGraphMatch")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘iGraphMatch-Ex.R’ failed + The error most likely occurred in: + + > ### Name: C.Elegans + > ### Title: Chemical synapses and electrical synapses networks of roundworm + > ### Aliases: C.Elegans + > ### Keywords: datasets + > + > ### ** Examples + > + > data(C.Elegans) + > g1 <- C.Elegans[[1]] + > g2 <- C.Elegans[[2]] + > plot(g1, g2) + Error in .igraph.status("Restore graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot ... .local -> identity_match -> is.igraph -> warn_version + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─igraph::sample_gnm(20, 60) at test-split_igraph.R:1:0 + ── Error ('test-umeyama.R:5:1'): (code run outside of `test_that()`) ─────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─iGraphMatch::sample_correlated_gnp_pair(10, 0.9, 0.5) at test-umeyama.R:5:0 + 2. └─iGraphMatch:::sample_correlated_gnp_pair_no_junk(...) + 3. └─igraph::sample_gnp(n, p, ...) + + [ FAIL 22 | WARN 0 | SKIP 1 | PASS 25 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘iGraphMatch.Rmd’ using rmarkdown + + Quitting from lines 648-654 [sample_graph] (iGraphMatch.Rmd) + Error: processing vignette 'iGraphMatch.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘iGraphMatch.Rmd’ + + SUMMARY: processing the following file failed: + ‘iGraphMatch.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# IMEC + +
+ +* Version: 0.2.0 +* GitHub: NA +* Source code: https://github.com/cran/IMEC +* Date/Publication: 2020-11-27 10:10:03 UTC +* Number of recursive dependencies: 103 + +Run `revdepcheck::cloud_details(, "IMEC")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘IMEC-Ex.R’ failed + The error most likely occurred in: + + > ### Name: computeIMEC + > ### Title: Computes the Ising model of explanatory coherence. + > ### Aliases: computeIMEC + > + > ### ** Examples + > + > # simple example comparing two hypotheses one of them with more explanatory breadth## + ... + > coherence <- computeIMEC(explanations, Thresholds, Phenomena, T1) + > summary(coherence) + T1 EC_T1 + 1 H1 0.8673686 + 2 H2 0.1347264 + > plot(coherence) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot -> plot.IMEC -> -> graph.adjacency.dense + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 2. └─IMEC:::plot.IMEC(IMEC) + 3. └─igraph::graph_from_adjacency_matrix(...) + 4. └─igraph:::graph.adjacency.dense(...) + ── Error ('test-0-basictests.R:58:3'): analytic way of calculating coherence works for 1 theory ── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. ├─base::plot(IMEC) at test-0-basictests.R:58:2 + 2. └─IMEC:::plot.IMEC(IMEC) + 3. └─igraph::graph_from_adjacency_matrix(...) + 4. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 2 | WARN 0 | SKIP 1 | PASS 2 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# immunarch + +
+ +* Version: 0.9.0 +* GitHub: https://github.com/immunomind/immunarch +* Source code: https://github.com/cran/immunarch +* Date/Publication: 2022-12-15 15:00:05 UTC +* Number of recursive dependencies: 194 + +Run `revdepcheck::cloud_details(, "immunarch")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘immunarch-Ex.R’ failed + The error most likely occurred in: + + > ### Name: seqCluster + > ### Title: Function for assigning clusters based on sequences similarity + > ### Aliases: seqCluster + > + > ### ** Examples + > + > + ... + 18. ├─reshape2::melt(.) + 19. ├─igraph::clusters(.) + 20. │ └─igraph:::ensure_igraph(graph) + 21. ├─igraph::graph_from_data_frame(.) + 22. │ └─igraph::make_empty_graph(n = 0, directed = directed) + 23. └─base::.handleSimpleError(...) + 24. └─purrr (local) h(simpleError(msg, call)) + 25. └─cli::cli_abort(...) + 26. └─rlang::abort(...) + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.4Mb + sub-directories of 1Mb or more: + data 3.3Mb + doc 1.6Mb + ``` + +# immuneSIM + +
+ +* Version: 0.8.7 +* GitHub: https://github.com/GreiffLab/immuneSIM +* Source code: https://github.com/cran/immuneSIM +* Date/Publication: 2019-09-27 10:30:06 UTC +* Number of recursive dependencies: 66 + +Run `revdepcheck::cloud_details(, "immuneSIM")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘immuneSIM-Ex.R’ failed + The error most likely occurred in: + + > ### Name: hub_seqs_exclusion + > ### Title: Deletes top hub sequences from repertoire, changing the network + > ### architecture. + > ### Aliases: hub_seqs_exclusion + > + > ### ** Examples + > + > repertoire <- list_example_repertoires[["example_repertoire_A"]] + > rep_excluded_hubs <- hub_seqs_exclusion(repertoire, top_x = 0.005, output_dir = "") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: hub_seqs_exclusion -> -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# imsig + +
+ +* Version: 1.1.3 +* GitHub: https://github.com/ajitjohnson/imsig +* Source code: https://github.com/cran/imsig +* Date/Publication: 2021-01-10 01:00:02 UTC +* Number of recursive dependencies: 52 + +Run `revdepcheck::cloud_details(, "imsig")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘imsig-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_network + > ### Title: Network graph of ImSig genes + > ### Aliases: plot_network + > + > ### ** Examples + > + > plot_network (exp = example_data, r = 0.7) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot_network ... graph_from_adjacency_matrix -> graph.adjacency.dense + Execution halted + ``` + +# incidentally + +
+ +* Version: 1.0.2 +* GitHub: https://github.com/zpneal/incidentally +* Source code: https://github.com/cran/incidentally +* Date/Publication: 2023-02-15 21:00:02 UTC +* Number of recursive dependencies: 39 + +Run `revdepcheck::cloud_details(, "incidentally")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘incidentally-Ex.R’ failed + The error most likely occurred in: + + > ### Name: add.blocks + > ### Title: Adds a block structure to an incidence matrix + > ### Aliases: add.blocks + > + > ### ** Examples + > + > I <- incidence.from.probability(R = 100, C = 100, P = .1) + ... + > all(rowSums(I)==rowSums(blocked)) + [1] TRUE + > all(colSums(I)==colSums(blocked)) + [1] TRUE + > + > B <- igraph::sample_bipartite(100, 100, p=.1) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: + Execution halted + ``` + +# influenceR + +
+ +* Version: 0.1.5 +* GitHub: https://github.com/khanna-lab/influenceR +* Source code: https://github.com/cran/influenceR +* Date/Publication: 2023-05-18 10:00:02 UTC +* Number of recursive dependencies: 35 + +Run `revdepcheck::cloud_details(, "influenceR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘influenceR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: betweenness + > ### Title: Vertex Betweenness centrality measure. + > ### Aliases: betweenness + > + > ### ** Examples + > + > ig.ex <- igraph::erdos.renyi.game(100, p.or.m=0.3) # generate an undirected 'igraph' object + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 6. └─igraph::is_igraph(g) + 7. └─igraph:::warn_version(graph) + ── Error ('test_reference.R:72:3'): bridging matches reference function ──────── + Error in `.igraph.status("Restore graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─influenceR (local) bridge_test(flo_graph) at test_reference.R:72:2 + 2. └─igraph::V(g) at test_reference.R:26:2 + 3. └─igraph:::ensure_igraph(graph) + 4. └─igraph::is_igraph(graph) + 5. └─igraph:::warn_version(graph) + + [ FAIL 5 | WARN 2 | SKIP 0 | PASS 0 ] + Error: Test failures + Execution halted + ``` + +# influential + +
+ +* Version: 2.2.7 +* GitHub: https://github.com/asalavaty/influential +* Source code: https://github.com/cran/influential +* Date/Publication: 2023-05-16 05:10:02 UTC +* Number of recursive dependencies: 187 + +Run `revdepcheck::cloud_details(, "influential")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘influential-Ex.R’ failed + The error most likely occurred in: + + > ### Name: V + > ### Title: Vertices of an igraph graph + > ### Aliases: V vertices + > ### Keywords: graph_vertices + > + > ### ** Examples + > + > MyData <- coexpression.data + > My_graph <- graph_from_data_frame(MyData) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: graph_from_data_frame -> make_empty_graph + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Vignettes.Rmd’ using rmarkdown + + Quitting from lines 140-145 [g_dataframe] (Vignettes.Rmd) + Error: processing vignette 'Vignettes.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘Vignettes.Rmd’ + + SUMMARY: processing the following file failed: + ‘Vignettes.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# intergraph + +
+ +* Version: 2.0-2 +* GitHub: NA +* Source code: https://github.com/cran/intergraph +* Date/Publication: 2016-12-05 18:28:47 +* Number of recursive dependencies: 49 + +Run `revdepcheck::cloud_details(, "intergraph")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘intergraph-Ex.R’ failed + The error most likely occurred in: + + > ### Name: asDF + > ### Title: Convert network to data frame(s) + > ### Aliases: asDF asDF.igraph asDF.network + > + > ### ** Examples + > + > # using method for 'network' objects + ... + ..$ label : chr [1:15] "a" "b" "c" "d" ... + ..$ na : logi [1:15] FALSE FALSE FALSE FALSE FALSE FALSE ... + ..$ vertex.names : chr [1:15] "a" "b" "c" "d" ... + > + > # using method for 'igraph' objects + > d2 <- asDF(exIgraph) + Error in .igraph.status("Restore graph external pointer.\n") : + could not find function ".igraph.status" + Calls: asDF ... -> ensure_igraph -> is_igraph -> warn_version + Execution halted + ``` + +# IOHanalyzer + +
+ +* Version: 0.1.6.3 +* GitHub: https://github.com/IOHprofiler/IOHAnalyzer +* Source code: https://github.com/cran/IOHanalyzer +* Date/Publication: 2022-03-09 08:20:12 UTC +* Number of recursive dependencies: 132 + +Run `revdepcheck::cloud_details(, "IOHanalyzer")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘IOHanalyzer-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Plot.Stats.Significance_Graph + > ### Title: Plot a network graph showing the statistically different + > ### algorithms + > ### Aliases: Plot.Stats.Significance_Graph + > ### Plot.Stats.Significance_Graph.DataSetList + > + > ### ** Examples + > + > Plot.Stats.Significance_Graph(subset(dsl, funcId == 2), 16) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: Plot.Stats.Significance_Graph ... Plot.Stats.Significance_Graph.DataSetList -> -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.3Mb + sub-directories of 1Mb or more: + data 1.4Mb + libs 4.1Mb + shiny-server 1.0Mb + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 102 marked UTF-8 strings + ``` + +# isa2 + +
+ +* Version: 0.3.6 +* GitHub: https://github.com/gaborcsardi/ISA +* Source code: https://github.com/cran/isa2 +* Date/Publication: 2023-02-21 21:30:02 UTC +* Number of recursive dependencies: 42 + +Run `revdepcheck::cloud_details(, "isa2")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘isa2-Ex.R’ failed + The error most likely occurred in: + + > ### Name: isa.sweep + > ### Title: Create a hierarchical structure of ISA biclusters + > ### Aliases: isa.sweep isa.sweep,matrix-method sweep.graph + > ### sweep.graph,list-method + > ### Keywords: cluster + > + > ### ** Examples + ... + DONE + Calculating ISA robustness + DONE + DONE + > network <- sweep.graph(isa.tree) + Loading required namespace: igraph + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: sweep.graph ... sweep.graph.default -> -> do.call -> + Execution halted + ``` + +# isotracer + +
+ +* Version: 1.1.4 +* GitHub: NA +* Source code: https://github.com/cran/isotracer +* Date/Publication: 2023-03-21 14:10:02 UTC +* Number of recursive dependencies: 157 + +Run `revdepcheck::cloud_details(, "isotracer")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘isotracer-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ggflows + > ### Title: A quick-and-dirty way of visualizing relative flows in a network + > ### Aliases: ggflows + > + > ### ** Examples + > + > if (requireNamespace("ggraph")) { + ... + 13. │ └─tidygraph:::as_tbl_graph.data.frame(graph) + 14. │ └─tidygraph:::as_graph_edge_df(x, directed) + 15. │ └─igraph::graph_from_data_frame(x, directed = directed) + 16. │ └─igraph::make_empty_graph(n = 0, directed = directed) + 17. └─base::.handleSimpleError(...) + 18. └─rlang (local) h(simpleError(msg, call)) + 19. └─handlers[[1L]](cnd) + 20. └─cli::cli_abort("No layout function defined for objects of class {.cls {class(graph)[1]}}") + 21. └─rlang::abort(...) + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 2. │ └─testthat:::quasi_capture(...) + 3. │ ├─testthat (local) .capture(...) + 4. │ │ └─base::withCallingHandlers(...) + 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 6. └─isotracer::sankey(r, debug = TRUE, edge_f = 0.2, node_s = "prop") + 7. └─isotracer:::sankey_place_nodes(...) + 8. └─isotracer:::sankey_calc_nodes_locations(topo, layout) + 9. ├─isotracer::as_tbl_graph(x) + 10. └─isotracer:::as_tbl_graph.topology(x) + 11. └─igraph::graph_from_adjacency_matrix(t(x)) + 12. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 9 | WARN 0 | SKIP 0 | PASS 284 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 89.6Mb + sub-directories of 1Mb or more: + data 1.8Mb + doc 2.3Mb + libs 84.4Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘rstantools’ + All declared Imports should be used. + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# ITNr + +
+ +* Version: 0.7.0 +* GitHub: NA +* Source code: https://github.com/cran/ITNr +* Date/Publication: 2023-03-31 14:10:11 UTC +* Number of recursive dependencies: 82 + +Run `revdepcheck::cloud_details(, "ITNr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ITNr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ITNproperties + > ### Title: ITN Properties + > ### Aliases: ITNproperties + > + > ### ** Examples + > + > ##Load the network + ... + Error in .igraph.status("Restore graph external pointer.\n") : + could not find function ".igraph.status" + Calls: ITNproperties ... -> ensure_igraph -> is_igraph -> warn_version + Execution halted + Error in .igraph.status("Free graph external pointer.\n") : + could not find function ".igraph.status" + Error in .igraph.status("Free graph external pointer.\n") : + could not find function ".igraph.status" + Error in .igraph.status("Free graph external pointer.\n") : + could not find function ".igraph.status" + ``` + +# IxPopDyMod + +
+ +* Version: 0.2.0 +* GitHub: https://github.com/dallenmidd/IxPopDyMod +* Source code: https://github.com/cran/IxPopDyMod +* Date/Publication: 2022-02-08 07:30:05 UTC +* Number of recursive dependencies: 69 + +Run `revdepcheck::cloud_details(, "IxPopDyMod")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘IxPopDyMod-Ex.R’ failed + The error most likely occurred in: + + > ### Name: graph_lifecycle + > ### Title: Visualize transitions as a life cycle graph + > ### Aliases: graph_lifecycle + > + > ### ** Examples + > + > graph_lifecycle(config_ex_1$transitions) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: graph_lifecycle ... %>% -> plot -> graph_from_data_frame -> make_empty_graph + Execution halted + ``` + +# jewel + +
+ +* Version: 2.0.0 +* GitHub: https://github.com/annaplaksienko/jewel +* Source code: https://github.com/cran/jewel +* Date/Publication: 2023-05-12 14:30:08 UTC +* Number of recursive dependencies: 45 + +Run `revdepcheck::cloud_details(, "jewel")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘jewel-Ex.R’ failed + The error most likely occurred in: + + > ### Name: constructWeights + > ### Title: Construct weights for _jewel_ minimization problem from prior + > ### information on vertices degrees. + > ### Aliases: constructWeights + > + > ### ** Examples + > + ... + + G_list_true <- data$Graphs + + true_degrees <- rowSums(G_list_true[[1]]) + + cut <- sort(true_degrees, decreasing = TRUE)[ceiling(p * 0.03)] + + apriori_hubs <- ifelse(true_degrees >= cut, 10, 1) + + W <- constructWeights(apriori_hubs, K = K) + + } + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: generateData_rewire -> barabasi.game + Execution halted + ``` + +# jti + +
+ +* Version: 0.8.4 +* GitHub: https://github.com/mlindsk/jti +* Source code: https://github.com/cran/jti +* Date/Publication: 2022-04-12 07:12:38 UTC +* Number of recursive dependencies: 41 + +Run `revdepcheck::cloud_details(, "jti")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘jti-Ex.R’ failed + The error most likely occurred in: + + > ### Name: compile + > ### Title: Compile information + > ### Aliases: compile compile.cpt_list + > + > ### ** Examples + > + > cptl <- cpt_list(asia2) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: cpt_list ... cpt_list.list -> graph_from_cpt_list -> + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.1Mb + sub-directories of 1Mb or more: + libs 5.3Mb + ``` + +# kangar00 + +
+ +* Version: 1.4.1 +* GitHub: NA +* Source code: https://github.com/cran/kangar00 +* Date/Publication: 2022-12-06 08:40:06 UTC +* Number of recursive dependencies: 95 + +Run `revdepcheck::cloud_details(, "kangar00")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘kangar00-Ex.R’ failed + The error most likely occurred in: + + > ### Name: pathway + > ### Title: An S4 class to represent a gene-gene interaction network + > ### Aliases: pathway pathway,ANY-method show,pathway-method + > ### show,pathway,ANY-method summary,pathway-method + > ### summary,pathway,ANY-method pathway2igraph,pathway-method + > ### pathway2igraph ANY-method analyze,pathway-method analyze + > ### get_genes,pathway-method get_genes plot,pathway,missing-method + ... + ..$ adj : int [1:180, 1:180] 0 0 0 0 0 0 0 0 0 0 ... + .. ..- attr(*, "dimnames")=List of 2 + .. .. ..$ : chr [1:180] "ITPKA" "ITPKB" "ITPKC" "ADCY1" ... + .. .. ..$ : chr [1:180] "ITPKA" "ITPKB" "ITPKC" "ADCY1" ... + ..$ sign: int [1:594] 1 1 1 1 1 1 1 1 1 1 ... + > g <- pathway2igraph(hsa04020) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: pathway2igraph ... pathway2igraph -> .local -> -> graph.adjacency.dense + Execution halted + ``` + +# Karen + +
+ +* Version: 1.0 +* GitHub: NA +* Source code: https://github.com/cran/Karen +* Date/Publication: 2022-09-15 07:40:02 UTC +* Number of recursive dependencies: 39 + +Run `revdepcheck::cloud_details(, "Karen")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘Karen-Ex.R’ failed + The error most likely occurred in: + + > ### Name: get.cdn + > ### Title: Get the cell differentiation network from a fitted Kalman + > ### Reaction Network. + > ### Aliases: get.cdn + > + > ### ** Examples + > + ... + DONE + Smoothing step... DONE + Exporting new initial conditions to the cluster... DONE + > parallel::stopCluster(cl) + > + > get.cdn(res.fit) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: get.cdn ... graph_from_adjacency_matrix -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Karen.ltx’ using tex + Error: processing vignette 'Karen.ltx' failed with diagnostics: + Running 'texi2dvi' on 'Karen.ltx' failed. + LaTeX errors: + ! LaTeX Error: File `realboxes.sty' not found. + + Type X to quit or to proceed, + or enter new name. (Default extension: sty) + ... + l.12 \usepackage + {amssymb}^^M + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘Karen.ltx’ + + SUMMARY: processing the following file failed: + ‘Karen.ltx’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# keyplayer + +
+ +* Version: 1.0.3 +* GitHub: NA +* Source code: https://github.com/cran/keyplayer +* Date/Publication: 2016-04-16 10:33:52 +* Number of recursive dependencies: 20 + +Run `revdepcheck::cloud_details(, "keyplayer")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘keyplayer-Ex.R’ failed + The error most likely occurred in: + + > ### Name: fragment + > ### Title: Compute the Fragmentation Centrality Score in a Netwrok + > ### Aliases: fragment + > + > ### ** Examples + > + > # Create a 5x5 weighted and directed adjacency matrix, where edge values + ... + > # Transform the edge value to distance interpretaion + > A <- W + > A[W!=0] <- 1/W[W!=0] + > + > # List the fragmentation centrality scores for every node + > fragment(A) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: fragment -> -> graph.adjacency.dense + Execution halted + ``` + +# kknn + +
+ +* Version: 1.3.1 +* GitHub: https://github.com/KlausVigo/kknn +* Source code: https://github.com/cran/kknn +* Date/Publication: 2016-03-26 22:02:21 +* Number of recursive dependencies: 7 + +Run `revdepcheck::cloud_details(, "kknn")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘kknn-Ex.R’ failed + The error most likely occurred in: + + > ### Name: specClust + > ### Title: Spectral Clustering + > ### Aliases: specClust plot.specClust + > ### Keywords: cluster + > + > ### ** Examples + > + > data(iris) + > cl <- specClust(iris[,1:4], 3, nn=5) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: specClust -> graph -> do.call -> + Execution halted + ``` + +# l1spectral + +
+ +* Version: 0.99.6 +* GitHub: NA +* Source code: https://github.com/cran/l1spectral +* Date/Publication: 2022-01-26 17:12:46 UTC +* Number of recursive dependencies: 84 + +Run `revdepcheck::cloud_details(, "l1spectral")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘l1spectral-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ComputePerformances + > ### Title: Compute the performances of the l1-spectral clustering algorithm + > ### Aliases: ComputePerformances + > + > ### ** Examples + > + > ############################################################# + ... + > ############################################################# + > + > data(ToyData) + > + > results <- l1_spectralclustering(A = ToyData$A_hat, pen = "lasso", + + k=2, elements = c(1,4)) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: l1_spectralclustering ... graph_from_adjacency_matrix -> graph.adjacency.dense + Execution halted + ``` + +# lconnect + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/FMestre1/lconnect +* Source code: https://github.com/cran/lconnect +* Date/Publication: 2021-02-06 16:10:02 UTC +* Number of recursive dependencies: 19 + +Run `revdepcheck::cloud_details(, "lconnect")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘lconnect-Ex.R’ failed + The error most likely occurred in: + + > ### Name: patch_imp + > ### Title: Prioritization of patches + > ### Aliases: patch_imp + > + > ### ** Examples + > + > vec_path <- system.file("extdata/vec_projected.shp", package = "lconnect") + > landscape <- upload_land(vec_path, bound_path = NULL, + + habitat = 1, max_dist = 500) + > importance <- patch_imp(landscape, metric = "IIC") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: patch_imp -> con_metric -> -> make_empty_graph + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# leidenAlg + +
+ +* Version: 1.0.5 +* GitHub: https://github.com/kharchenkolab/leidenAlg +* Source code: https://github.com/cran/leidenAlg +* Date/Publication: 2022-09-30 07:20:02 UTC +* Number of recursive dependencies: 68 + +Run `revdepcheck::cloud_details(, "leidenAlg")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘leidenAlg-Ex.R’ failed + The error most likely occurred in: + + > ### Name: as.dendrogram.fakeCommunities + > ### Title: Returns pre-calculated dendrogram + > ### Aliases: as.dendrogram.fakeCommunities + > + > ### ** Examples + > + > rLeidenComm = suppressWarnings(rleiden.community(exampleGraph, n.cores=1)) + Error in .igraph.status("Restore graph external pointer.\n") : + could not find function ".igraph.status" + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 4. └─igraph::is_igraph(graph) + 5. └─igraph:::warn_version(graph) + ── Error ('test_functions.R:25:2'): membership.fakeCommunities() functionality ── + Error in `.igraph.status("Restore graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─leidenAlg::leiden.community(exampleGraph) at test_functions.R:25:8 + 2. └─igraph::is_weighted(graph) + 3. └─igraph:::ensure_igraph(graph) + 4. └─igraph::is_igraph(graph) + 5. └─igraph:::warn_version(graph) + + [ FAIL 4 | WARN 0 | SKIP 0 | PASS 0 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# leidenbase + +
+ +* Version: 0.1.18 +* GitHub: https://github.com/cole-trapnell-lab/leidenbase +* Source code: https://github.com/cran/leidenbase +* Date/Publication: 2023-04-15 09:20:02 UTC +* Number of recursive dependencies: 54 + +Run `revdepcheck::cloud_details(, "leidenbase")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘leidenbase-Ex.R’ failed + The error most likely occurred in: + + > ### Name: leiden_find_partition + > ### Title: Leiden find partition community detection function + > ### Aliases: leiden_find_partition + > + > ### ** Examples + > + > library(igraph) + ... + + > fpath <- system.file( 'testdata', 'igraph_n1500_edgelist.txt.gz', package = 'leidenbase' ) + > zfp <- gzfile(fpath) + > igraph <- read_graph( file = zfp, format='edgelist', n=1500 ) + > res <- leiden_find_partition(igraph=igraph, + + partition_type='CPMVertexPartition', + + resolution_parameter=1e-5) + Error in leiden_find_partition(igraph = igraph, partition_type = "CPMVertexPartition", : + REAL() can only be applied to a 'numeric', not a 'NULL' + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + > testthat::test_check("leidenbase") + Loading required package: leidenbase + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-leidenbase.R:27:3'): (code run outside of `test_that()`) ─────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─igraph::read_graph(file = zfp, format = "edgelist", n = 1500) at test-leidenbase.R:27:2 + 2. └─igraph:::read.graph.edgelist(file, ...) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘leidenbase.Rmd’ using rmarkdown + + Quitting from lines 87-92 [unnamed-chunk-1] (leidenbase.Rmd) + Error: processing vignette 'leidenbase.Rmd' failed with diagnostics: + REAL() can only be applied to a 'numeric', not a 'NULL' + --- failed re-building ‘leidenbase.Rmd’ + + SUMMARY: processing the following file failed: + ‘leidenbase.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 19.1Mb + sub-directories of 1Mb or more: + libs 18.8Mb + ``` + +# lexRankr + +
+ +* Version: 0.5.2 +* GitHub: https://github.com/AdamSpannbauer/lexRankr +* Source code: https://github.com/cran/lexRankr +* Date/Publication: 2019-03-17 21:00:03 UTC +* Number of recursive dependencies: 52 + +Run `revdepcheck::cloud_details(, "lexRankr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘lexRankr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: lexRank + > ### Title: Extractive text summarization with LexRank + > ### Aliases: lexRank + > + > ### ** Examples + > + > lexRank(c("This is a test.","Tests are fun.", + + "Do you think the exam will be hard?","Is an exam the same as a test?", + + "How many questions are going to be on the exam?")) + Parsing text into sentences and tokens...DONE + Calculating pairwise sentence similarities...DONE + Applying LexRank...Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: lexRank ... lexRankFromSimil -> -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ▆ + 1. └─lexRankr::lexRankFromSimil(similDf$sent1, similDf$sent2, similDf$similVal) at test-lexRankFromSimil.R:14:2 + 2. └─igraph::graph_from_data_frame(edges, directed = FALSE) + 3. └─igraph::make_empty_graph(n = 0, directed = directed) + ── Error ('test-lexRankFromSimil.R:52:3'): object out value ──────────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─lexRankr::lexRankFromSimil(similDf$sent1, similDf$sent2, similDf$similVal) at test-lexRankFromSimil.R:52:2 + 2. └─igraph::graph_from_data_frame(edges, directed = FALSE) + 3. └─igraph::make_empty_graph(n = 0, directed = directed) + + [ FAIL 8 | WARN 0 | SKIP 0 | PASS 112 ] + Error: Test failures + Execution halted + ``` + +# linkprediction + +
+ +* Version: 1.0-0 +* GitHub: https://github.com/recon-icm/linkprediction +* Source code: https://github.com/cran/linkprediction +* Date/Publication: 2018-10-19 13:40:03 UTC +* Number of recursive dependencies: 43 + +Run `revdepcheck::cloud_details(, "linkprediction")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘linkprediction-Ex.R’ failed + The error most likely occurred in: + + > ### Name: proxfun + > ### Title: Vertex proximity indexes + > ### Aliases: proxfun proxfun.igraph proxfun.network + > + > ### ** Examples + > + > if(requireNamespace("igraph")) { + ... + + proxfun(g, method="aa", value="edgelist") + + + + # Random Walk with Restart + + proxfun(g, method="rwr", value="edgelist") + + } + Loading required namespace: igraph + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: ... graph_from_literal_i -> make_graph -> do.call -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ▆ + 1. └─igraph::graph(c(1, 2, 1, 3, 1, 4, 2, 4, 1, 5, 2, 5, 4, 5), directed = FALSE) at test_check_vertices.R:3:0 + 2. ├─base::do.call(old_graph, args) + 3. └─igraph (local) ``(``, directed = FALSE) + ── Error ('test_proxfun.R:3:1'): (code run outside of `test_that()`) ─────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─igraph::graph(c(1, 2, 1, 3, 1, 4, 2, 4, 1, 5, 2, 5, 4, 5), directed = FALSE) at test_proxfun.R:3:0 + 2. ├─base::do.call(old_graph, args) + 3. └─igraph (local) ``(``, directed = FALSE) + + [ FAIL 3 | WARN 0 | SKIP 0 | PASS 0 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# LoopDetectR + +
+ +* Version: 0.1.2 +* GitHub: NA +* Source code: https://github.com/cran/LoopDetectR +* Date/Publication: 2020-07-20 09:20:12 UTC +* Number of recursive dependencies: 41 + +Run `revdepcheck::cloud_details(, "LoopDetectR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘LoopDetectR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: compare_loop_list + > ### Title: Compare two loop lists + > ### Aliases: compare_loop_list + > + > ### ** Examples + > + > #sample Jacobian matrix of a system with 4 variables + > jac_matrix <- rbind(c(-1,0,0,-1),c(1,-1,0,1),c(0,1,-1,0),c(0,0,1,-1)) + > #find the feedback loops of the system + > loop_list <- find_loops(jac_matrix,10) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: find_loops -> -> graph.adjacency.dense + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘workflow_LoopDetectR.Rmd’ using knitr + + Quitting from lines 53-73 [quick_example] (workflow_LoopDetectR.Rmd) + Error: processing vignette 'workflow_LoopDetectR.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘workflow_LoopDetectR.Rmd’ + + SUMMARY: processing the following file failed: + ‘workflow_LoopDetectR.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# LSVAR + +
+ +* Version: 1.2 +* GitHub: NA +* Source code: https://github.com/cran/LSVAR +* Date/Publication: 2021-05-26 12:00:02 UTC +* Number of recursive dependencies: 38 + +Run `revdepcheck::cloud_details(, "LSVAR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘LSVAR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: fista.LpS + > ### Title: A function to solve low rank plus sparse model estimation using + > ### FISTA algorithm + > ### Aliases: fista.LpS + > + > ### ** Examples + > + > n <- 300 + > p <- 20 + > try <- testVAR(n, p, struct = "LS", signal = 0.75, rank = 2, + + singular_vals = c(1, 0.8)) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: testVAR -> erdos.renyi.game + Execution halted + ``` + +# lvm4net + +
+ +* Version: 0.3 +* GitHub: https://github.com/igollini/lvm4net +* Source code: https://github.com/cran/lvm4net +* Date/Publication: 2019-06-13 15:40:07 UTC +* Number of recursive dependencies: 67 + +Run `revdepcheck::cloud_details(, "lvm4net")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘lvm4net-Ex.R’ failed + The error most likely occurred in: + + > ### Name: boxroc + > ### Title: Boxplot and ROC Curves + > ### Aliases: boxroc + > + > ### ** Examples + > + > + > N <- 20 + > Y <- network(N, directed = FALSE)[,] + > + > modLSM <- lsm(Y, D = 2) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: lsm ... make_call -> graph.adjacency -> graph.adjacency.dense + Execution halted + ``` + +# macrosyntR + +
+ +* Version: 0.2.19 +* GitHub: https://github.com/SamiLhll/macrosyntR +* Source code: https://github.com/cran/macrosyntR +* Date/Publication: 2023-03-29 13:30:16 UTC +* Number of recursive dependencies: 63 + +Run `revdepcheck::cloud_details(, "macrosyntR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘macrosyntR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: reorder_macrosynteny + > ### Title: Reorder the mbh_df before plotting + > ### Aliases: reorder_macrosynteny + > + > ### ** Examples + > + > # basic usage of reorder_macrosynteny : + ... + > + > orthologs_table <- system.file("extdata","my_orthologs.tab",package="macrosyntR") + > + > my_orthologs <- read.table(orthologs_table,header=TRUE) + > + > my_orthologs_reordered <- reorder_macrosynteny(my_orthologs) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: reorder_macrosynteny -> -> make_empty_graph + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘macrosyntR.Rmd’ using rmarkdown + + Quitting from lines 210-221 [unnamed-chunk-12] (macrosyntR.Rmd) + Error: processing vignette 'macrosyntR.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘macrosyntR.Rmd’ + + SUMMARY: processing the following file failed: + ‘macrosyntR.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# madrat + +
+ +* Version: 3.3.0 +* GitHub: https://github.com/pik-piam/madrat +* Source code: https://github.com/cran/madrat +* Date/Publication: 2023-05-02 11:10:02 UTC +* Number of recursive dependencies: 81 + +Run `revdepcheck::cloud_details(, "madrat")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘madrat-Ex.R’ failed + The error most likely occurred in: + + > ### Name: cacheGet + > ### Title: Tool: cacheGet + > ### Aliases: cacheGet + > + > ### ** Examples + > + > madrat:::cacheGet("calc", "TauTotal", packages = "madrat") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: ... fingerprint -> getDependencies -> -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 9. ├─madrat:::withMadratLogging(do.call(cfg$functionCode, cfg$fullNow)) + 10. │ └─base::withCallingHandlers(...) + 11. ├─base::do.call(cfg$functionCode, cfg$fullNow) + 12. └─madrat (local) ``() + 13. └─madrat::calcOutput("WarningTest", aggregate = FALSE) at test-retrieveData.R:105:4 + 14. └─madrat:::cacheGet(prefix = "calc", type = type, args = args) + 15. └─madrat:::cacheName(...) + 16. └─madrat:::fingerprint(...) + 17. └─madrat::getDependencies(...) + 18. └─igraph::graph_from_data_frame(graph) + 19. └─igraph::make_empty_graph(n = 0, directed = directed) + + [ FAIL 12 | WARN 0 | SKIP 8 | PASS 524 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘madrat-caching.Rmd’ using rmarkdown + + Quitting from lines 37-38 [unnamed-chunk-3] (madrat-caching.Rmd) + Error: processing vignette 'madrat-caching.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘madrat-caching.Rmd’ + + --- re-building ‘madrat-puc.Rmd’ using rmarkdown + ... + --- finished re-building ‘madrat-puc.Rmd’ + + --- re-building ‘madrat.Rmd’ using rmarkdown + --- finished re-building ‘madrat.Rmd’ + + SUMMARY: processing the following file failed: + ‘madrat-caching.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# malan + +
+ +* Version: 1.0.2 +* GitHub: https://github.com/mikldk/malan +* Source code: https://github.com/cran/malan +* Date/Publication: 2020-06-25 12:00:06 UTC +* Number of recursive dependencies: 89 + +Run `revdepcheck::cloud_details(, "malan")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘malan-Ex.R’ failed + The error most likely occurred in: + + > ### Name: from_igraph + > ### Title: Convert igraph to population + > ### Aliases: from_igraph + > + > ### ** Examples + > + > g <- igraph::graph_from_literal( 2 +- 1 -+ 3, 4 -+ 5 ) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: ... graph_from_literal_i -> make_graph -> do.call -> + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘case-study-partial.Rmd’ using rmarkdown + + Quitting from lines 76-78 [unnamed-chunk-8] (case-study-partial.Rmd) + Error: processing vignette 'case-study-partial.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘case-study-partial.Rmd’ + + --- re-building ‘introduction.Rmd’ using rmarkdown + ... + Quitting from lines 52-53 [unnamed-chunk-6] (introduction.Rmd) + Error: processing vignette 'introduction.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘introduction.Rmd’ + + SUMMARY: processing the following files failed: + ‘case-study-partial.Rmd’ ‘introduction.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 22.8Mb + sub-directories of 1Mb or more: + libs 21.8Mb + ``` + +# manymome + +
+ +* Version: 0.1.10 +* GitHub: https://github.com/sfcheung/manymome +* Source code: https://github.com/cran/manymome +* Date/Publication: 2023-06-08 15:30:03 UTC +* Number of recursive dependencies: 157 + +Run `revdepcheck::cloud_details(, "manymome")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘manymome-Ex.R’ failed + The error most likely occurred in: + + > ### Name: all_indirect_paths + > ### Title: Enumerate All Indirect Effects in a Model + > ### Aliases: all_indirect_paths all_paths_to_df + > + > ### ** Examples + > + > library(lavaan) + ... + + y ~ m12 + m2 + m11 + x + c1 + c2 + + " + > fit <- sem(mod, data_serial_parallel, + + fixed.x = FALSE) + > # All indirect paths + > out1 <- all_indirect_paths(fit) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: all_indirect_paths -> -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─manymome::all_indirect_paths(fit) at test_all_indirect_paths_lv.R:28:0 + 2. └─igraph::graph_from_adjacency_matrix(adj, mode = "directed") + 3. └─igraph:::graph.adjacency.dense(...) + ── Failure ('test_lavaan2lm_list.R:51:5'): lm_from_lavaan: predict ───────────── + predict(fit_list[["y"]], dat[3:5, ]) (`actual`) not equal to predict(lm_y, dat[3:5, ]) - coef(lm_y)[1] (`expected`). + + `actual`: 15.544720 15.345482 15.139308 + `expected`: 15.544747 15.345493 15.139317 + + [ FAIL 2 | WARN 0 | SKIP 22 | PASS 392 ] + Error: Test failures + Execution halted + ``` + +# manynet + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/snlab-ch/manynet +* Source code: https://github.com/cran/manynet +* Date/Publication: 2023-06-10 14:10:02 UTC +* Number of recursive dependencies: 89 + +Run `revdepcheck::cloud_details(, "manynet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘manynet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: add + > ### Title: Adding nodes and ties and their attributes + > ### Aliases: add add_nodes add_ties add_node_attribute add_tie_attribute + > + > ### ** Examples + > + > other <- create_filled(4) %>% mutate(name = c("A", "B", "C", "D")) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: %>% ... create_filled -> -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 5. ├─dplyr::mutate(ungroup(activate(graph, "nodes")), .ggraph.orig_index = seq_len(graph_order())) + 6. └─tidygraph:::mutate.tbl_graph(...) + 7. └─tidygraph::mutate_as_tbl(.data, !!!dot) + 8. ├─tibble::as_tibble(.data) + 9. └─tidygraph:::as_tibble.tbl_graph(.data) + 10. └─tidygraph:::node_tibble(x) + 11. ├─tibble::as_tibble(vertex_attr(x)) + 12. └─igraph::vertex_attr(x) + 13. └─igraph:::ensure_igraph(graph) + 14. └─igraph::is_igraph(graph) + 15. └─igraph:::warn_version(graph) + + [ FAIL 45 | WARN 0 | SKIP 0 | PASS 12 ] + Error: Test failures + Execution halted + ``` + +# matrixcut + +
+ +* Version: 0.0.1 +* GitHub: NA +* Source code: https://github.com/cran/matrixcut +* Date/Publication: 2023-03-24 16:30:02 UTC +* Number of recursive dependencies: 8 + +Run `revdepcheck::cloud_details(, "matrixcut")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘matrixcut-Ex.R’ failed + The error most likely occurred in: + + > ### Name: componentplot + > ### Title: Draws a Plot Showing the Number of Components as a Function of + > ### the Cutoff Value. + > ### Aliases: componentplot + > + > ### ** Examples + > + > componentplot(xenarthra,0.75,0.9) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: componentplot -> -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘stats’ + All declared Imports should be used. + ``` + +# maxmatching + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/maxmatching +* Date/Publication: 2017-01-15 09:51:07 +* Number of recursive dependencies: 7 + +Run `revdepcheck::cloud_details(, "maxmatching")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘maxmatching-Ex.R’ failed + The error most likely occurred in: + + > ### Name: maxmatching + > ### Title: Maximum Matching + > ### Aliases: maxmatching + > + > ### ** Examples + > + > # Unweighted general graph + > G1 <- igraph::graph(c(1, 2, 1, 3, 1, 4, 3, 4, 3, 5, + + 5, 6, 6, 7, 7, 8, 8, 9, 3, 8, 5, 8), directed = FALSE) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: -> do.call -> + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# mazeGen + +
+ +* Version: 0.1.3 +* GitHub: NA +* Source code: https://github.com/cran/mazeGen +* Date/Publication: 2017-12-04 17:34:53 UTC +* Number of recursive dependencies: 7 + +Run `revdepcheck::cloud_details(, "mazeGen")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘mazeGen-Ex.R’ failed + The error most likely occurred in: + + > ### Name: genEMLseed + > ### Title: Generate Equal Minimum Legs Seed + > ### Aliases: genEMLseed + > + > ### ** Examples + > + > + ... + > seed <- 1 + > + > #Search for just one unique path + > justOne <- genEMLseed(path=1,rank=rank,satPercent=satPercent,seed=seed) + > nodePosition <- np(rank,satPercent,seed=justOne) + > mazeEst(nodePosition) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: mazeEst -> graph -> do.call -> + Execution halted + ``` + +# MBNMAdose + +
+ +* Version: 0.4.1 +* GitHub: NA +* Source code: https://github.com/cran/MBNMAdose +* Date/Publication: 2022-02-24 11:40:02 UTC +* Number of recursive dependencies: 95 + +Run `revdepcheck::cloud_details(, "MBNMAdose")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘MBNMAdose-Ex.R’ failed + The error most likely occurred in: + + > ### Name: MBNMAdose-package + > ### Title: MBNMAdose for dose-response Model-Based Network Meta-Analysis + > ### Aliases: MBNMAdose MBNMAdose-package + > ### Keywords: internal + > + > ### ** Examples + > + ... + > network <- mbnma.network(triptans) + Values for `agent` with dose = 0 have been recoded to `Placebo` + agent is being recoded to enforce sequential numbering and allow inclusion of `Placebo` + > + > # Generate a network plot at the dose/treatment level + > plot(network, level="treatment") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot -> plot.mbnma.network -> + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘mbnmadose.Rmd’ using rmarkdown + Warning in eng_r(options) : + Failed to tidy R code in chunk 'unnamed-chunk-2'. Reason: + Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. + + Warning in eng_r(options) : + Failed to tidy R code in chunk 'unnamed-chunk-6'. Reason: + Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. + ... + Quitting from lines 112-115 [unnamed-chunk-6] (mbnmadose.Rmd) + Error: processing vignette 'mbnmadose.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘mbnmadose.Rmd’ + + SUMMARY: processing the following file failed: + ‘mbnmadose.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 6 marked Latin-1 strings + ``` + +# MBNMAtime + +
+ +* Version: 0.2.3 +* GitHub: NA +* Source code: https://github.com/cran/MBNMAtime +* Date/Publication: 2023-03-17 12:30:13 UTC +* Number of recursive dependencies: 108 + +Run `revdepcheck::cloud_details(, "MBNMAtime")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘MBNMAtime-Ex.R’ failed + The error most likely occurred in: + + > ### Name: inconsistency.loops + > ### Title: Identify comparisons in loops that fulfil criteria for + > ### node-splitting + > ### Aliases: inconsistency.loops + > + > ### ** Examples + > + ... + > data <- data.frame(studyID=c(1,1,2,2,3,3,4,4,5,5,5), + + treatment=c(1,2,1,3,2,3,3,4,1,2,4) + + ) + > + > # Identify comparisons informed by direct and indirect evidence + > inconsistency.loops(data) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: inconsistency.loops -> + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘MBNMAtime.Rmd’ using rmarkdown + + Quitting from lines 146-151 [unnamed-chunk-6] (MBNMAtime.Rmd) + Error: processing vignette 'MBNMAtime.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘MBNMAtime.Rmd’ + + SUMMARY: processing the following file failed: + ‘MBNMAtime.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# mcMST + +
+ +* Version: 1.1.1 +* GitHub: https://github.com/jakobbossek/mcMST +* Source code: https://github.com/cran/mcMST +* Date/Publication: 2023-03-13 19:00:02 UTC +* Number of recursive dependencies: 138 + +Run `revdepcheck::cloud_details(, "mcMST")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘mcMST-Ex.R’ failed + The error most likely occurred in: + + > ### Name: mcMSTEmoaBG + > ### Title: Subgraph EMOA for the multi-criteria MST problem. + > ### Aliases: mcMSTEmoaBG + > + > ### ** Examples + > + > inst = genRandomMCGP(10) + > res = mcMSTEmoaBG(inst, mu = 20L, max.iter = 100L) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: mcMSTEmoaBG ... -> make_graph -> do.call -> + Execution halted + ``` + +# mcvis + +
+ +* Version: 1.0.8 +* GitHub: NA +* Source code: https://github.com/cran/mcvis +* Date/Publication: 2021-07-30 08:20:05 UTC +* Number of recursive dependencies: 92 + +Run `revdepcheck::cloud_details(, "mcvis")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘mcvis-Ex.R’ failed + The error most likely occurred in: + + > ### Name: alt_mcvis + > ### Title: Multi-collinearity Visualization plots + > ### Aliases: alt_mcvis ggplot_mcvis igraph_mcvis plot.mcvis + > + > ### ** Examples + > + > set.seed(1) + ... + > n = 100 + > X = matrix(rnorm(n*p), ncol = p) + > X[,1] = X[,2] + rnorm(n, 0, 0.1) + > mcvis_result = mcvis(X) + > plot(mcvis_result) + > plot(mcvis_result, type = "igraph") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot ... igraph_mcvis -> -> graph.incidence.dense + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-plot-mcvis.R:10:1'): (code run outside of `test_that()`) ─────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. ├─base::plot(mcvis_result, type = "igraph") at test-plot-mcvis.R:10:0 + 2. └─mcvis:::plot.mcvis(mcvis_result, type = "igraph") + 3. └─mcvis::igraph_mcvis(mcvis_result = x, eig_max = eig_max, var_max = var_max) + 4. └─igraph::graph_from_incidence_matrix(M) + 5. └─igraph:::graph.incidence.dense(...) + + [ FAIL 1 | WARN 1 | SKIP 0 | PASS 3 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘mcvis.Rmd’ using rmarkdown + + Quitting from lines 71-72 [unnamed-chunk-4] (mcvis.Rmd) + Error: processing vignette 'mcvis.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘mcvis.Rmd’ + + SUMMARY: processing the following file failed: + ‘mcvis.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# meconetcomp + +
+ +* Version: 0.2.0 +* GitHub: https://github.com/ChiLiubio/meconetcomp +* Source code: https://github.com/cran/meconetcomp +* Date/Publication: 2022-10-05 15:20:02 UTC +* Number of recursive dependencies: 147 + +Run `revdepcheck::cloud_details(, "meconetcomp")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘meconetcomp-Ex.R’ failed + The error most likely occurred in: + + > ### Name: cal_module + > ### Title: Assign modules to each network + > ### Aliases: cal_module + > + > ### ** Examples + > + > data(soil_amp_network) + > soil_amp_network <- cal_module(soil_amp_network) + Error in .igraph.status("Restore graph external pointer.\n") : + could not find function ".igraph.status" + Calls: cal_module ... is_directed -> ensure_igraph -> is_igraph -> warn_version + Execution halted + ``` + +# Mercator + +
+ +* Version: 1.1.2 +* GitHub: NA +* Source code: https://github.com/cran/Mercator +* Date/Publication: 2022-06-30 16:20:02 UTC +* Number of recursive dependencies: 98 + +Run `revdepcheck::cloud_details(, "Mercator")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘test-01Metrics.R’ + Comparing ‘test-01Metrics.Rout’ to ‘test-01Metrics.Rout.save’ ... OK + Running ‘test-02binmat.R’ + Comparing ‘test-02binmat.Rout’ to ‘test-02binmat.Rout.save’ ... OK + Running ‘test-03thresh.R’ + Comparing ‘test-03thresh.Rout’ to ‘test-03thresh.Rout.save’ ... OK + Running ‘test-04vis.R’ + Running the tests in ‘tests/test-04vis.R’ failed. + Last 13 lines of output: + > vis1 <- addVisualization(vis1, "tsne", perplexity=30) + ... + > ## hclust + > vis1 <- addVisualization(vis1, "hclust") + > plot(vis1, view = "hclust") + > + > ## now test the igraph part + > vis1 <- addVisualization(vis1, "graph") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: addVisualization ... createGraph -> graph_from_data_frame -> make_empty_graph + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘mercVis.Rmd’ using rmarkdown + + Quitting from lines 118-124 [igraph] (mercVis.Rmd) + Error: processing vignette 'mercVis.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘mercVis.Rmd’ + + --- re-building ‘mercator.Rmd’ using rmarkdown + ... + --- failed re-building ‘mercator.Rmd’ + + --- re-building ‘umap-som.Rmd’ using rmarkdown + --- finished re-building ‘umap-som.Rmd’ + + SUMMARY: processing the following files failed: + ‘mercVis.Rmd’ ‘mercator.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# metacoder + +
+ +* Version: 0.3.6 +* GitHub: https://github.com/grunwaldlab/metacoder +* Source code: https://github.com/cran/metacoder +* Date/Publication: 2023-04-04 02:20:02 UTC +* Number of recursive dependencies: 201 + +Run `revdepcheck::cloud_details(, "metacoder")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘metacoder-Ex.R’ failed + The error most likely occurred in: + + > ### Name: layout_functions + > ### Title: Layout functions + > ### Aliases: layout_functions + > + > ### ** Examples + > + > # List available function names: + ... + [4] "gem" "graphopt" "mds" + [7] "fruchterman-reingold" "kamada-kawai" "large-graph" + [10] "drl" + > + > # Execute layout function on graph: + > layout_functions("davidson-harel", igraph::make_ring(5)) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: layout_functions -> -> ensure_igraph -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 6. ├─metacoder::heat_tree(...) + 7. └─metacoder:::heat_tree.Taxmap(...) + 8. ├─base::do.call(heat_tree, arguments) + 9. ├─metacoder (local) ``(...) + 10. └─metacoder:::heat_tree.default(...) + 11. └─base::lapply(sub_graph_taxa, get_sub_graphs) + 12. └─metacoder (local) FUN(X[[i]], ...) + 13. └─igraph::graph_from_edgelist(edgelist) + 14. └─igraph::make_graph(unname(ids[t(el)]), directed = directed) + 15. ├─base::do.call(old_graph, args) + 16. └─igraph (local) ``(``, directed = TRUE) + + [ FAIL 3 | WARN 0 | SKIP 3 | PASS 533 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘R6’ + All declared Imports should be used. + ``` + +# metanetwork + +
+ +* Version: 0.7.0 +* GitHub: https://github.com/MarcOhlmann/metanetwork +* Source code: https://github.com/cran/metanetwork +* Date/Publication: 2022-12-05 14:10:02 UTC +* Number of recursive dependencies: 106 + +Run `revdepcheck::cloud_details(, "metanetwork")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘metanetwork-Ex.R’ failed + The error most likely occurred in: + + > ### Name: append_agg_nets + > ### Title: append aggregated networks + > ### Aliases: append_agg_nets append_agg_nets.metanetwork + > + > ### ** Examples + > + > library(metanetwork) + > data(meta_angola) + > meta_angola = append_agg_nets(meta_angola) + Error in .igraph.status("Restore graph external pointer.\n") : + could not find function ".igraph.status" + Calls: append_agg_nets ... graph_attr -> ensure_igraph -> is_igraph -> warn_version + Execution halted + ``` + +# MetricGraph + +
+ +* Version: 1.1.1 +* GitHub: https://github.com/davidbolin/MetricGraph +* Source code: https://github.com/cran/MetricGraph +* Date/Publication: 2023-06-01 12:00:11 UTC +* Number of recursive dependencies: 124 + +Run `revdepcheck::cloud_details(, "MetricGraph")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘MetricGraph-Ex.R’ failed + The error most likely occurred in: + + > ### Name: graph_components + > ### Title: Connected components of metric graph + > ### Aliases: graph_components + > + > ### ** Examples + > + > library(sp) + ... + > line2 <- Line(rbind(c(1, 0), c(2, 0))) + > line3 <- Line(rbind(c(1, 1), c(2, 1))) + > Lines <- SpatialLines(list(Lines(list(line1), ID = "1"), + + Lines(list(line2), ID = "2"), + + Lines(list(line3), ID = "3"))) + > graphs <- graph_components$new(Lines) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: -> initialize -> graph -> do.call -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 4. ├─base::do.call(old_graph, args) + 5. └─igraph (local) ``(``, directed = FALSE) + ── Error ('test_split_line.R:12:1'): Testing if splitting edges, and adding obsevations casuse error ── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─metric_graph$new(lines = Lines) at test_split_line.R:12:0 + 2. └─MetricGraph (local) initialize(...) + 3. └─igraph::graph(edges = c(t(self$E)), directed = FALSE) + 4. ├─base::do.call(old_graph, args) + 5. └─igraph (local) ``(``, directed = FALSE) + + [ FAIL 12 | WARN 0 | SKIP 1 | PASS 8 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 19.9Mb + sub-directories of 1Mb or more: + libs 19.0Mb + ``` + +# mfpp + +
+ +* Version: 0.0.4 +* GitHub: https://github.com/kzst/mfpp +* Source code: https://github.com/cran/mfpp +* Date/Publication: 2022-08-22 10:20:02 UTC +* Number of recursive dependencies: 65 + +Run `revdepcheck::cloud_details(, "mfpp")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘mfpp-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.mfpp + > ### Title: Plot function for Matrix-Based Flexible Project Planning + > ### Aliases: plot.PDM_matrix plot.PDM_list plot.Set_PDM_matrix + > ### plot.Set_PDM_list plot.TPT + > + > ### ** Examples + > + ... + > + > # Generation of PDM list for TCTP a project scenario using MFPP package. + > + > PDM<-generatepdm(N,ff,cf,mTD,mCD,mRD,w,nR,nW,scale,lst=TRUE) + > + > plot(PDM) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot ... plot.PDM_matrix -> -> graph.adjacency.dense + Execution halted + ``` + +# migraph + +
+ +* Version: 0.13.2 +* GitHub: https://github.com/snlab-ch/migraph +* Source code: https://github.com/cran/migraph +* Date/Publication: 2022-12-20 16:20:02 UTC +* Number of recursive dependencies: 138 + +Run `revdepcheck::cloud_details(, "migraph")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘migraph-Ex.R’ failed + The error most likely occurred in: + + > ### Name: add + > ### Title: Adding and copying attributes from one graph to another + > ### Aliases: add add_node_attribute add_tie_attribute copy_node_attributes + > ### join_ties + > + > ### ** Examples + > + > add_node_attribute(mpn_elite_mex, "wealth", 1:35) + Error in .igraph.status("Restore graph external pointer.\n") : + could not find function ".igraph.status" + Calls: add_node_attribute ... -> ensure_igraph -> is_igraph -> warn_version + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ── Error ('test-viz_layout_partition.R:20:3'): concentric layout works ───────── + Error in `.igraph.status("Restore graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─migraph::layout_tbl_graph_concentric(ison_southern_women) at test-viz_layout_partition.R:20:2 + 2. ├─migraph::is_twomode(object) + 3. └─migraph:::is_twomode.igraph(object) + 4. └─igraph::is.bipartite(object) + 5. └─igraph:::ensure_igraph(graph) + 6. └─igraph::is_igraph(graph) + 7. └─igraph:::warn_version(graph) + + [ FAIL 85 | WARN 0 | SKIP 0 | PASS 12 ] + Error: Test failures + Execution halted + ``` + +# miniCRAN + +
+ +* Version: 0.2.16 +* GitHub: https://github.com/andrie/miniCRAN +* Source code: https://github.com/cran/miniCRAN +* Date/Publication: 2022-02-14 09:00:05 UTC +* Number of recursive dependencies: 108 + +Run `revdepcheck::cloud_details(, "miniCRAN")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘test-all.R’ + Running the tests in ‘tests/test-all.R’ failed. + Last 13 lines of output: + ── Error ('test-2-makeDepGraph.R:66:3'): makeDepGraph and pgkDep gives similar results for MASS ── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. ├─testthat::expect_true(checkPkgDepFunctions(tag)) at test-2-makeDepGraph.R:66:2 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. └─miniCRAN (local) checkPkgDepFunctions(tag) + 5. └─miniCRAN::makeDepGraph(...) at test-2-makeDepGraph.R:12:2 + 6. └─igraph::graph.data.frame(d = edges, directed = TRUE, vertices = vert) + 7. └─igraph::make_empty_graph(n = 0, directed = directed) + + [ FAIL 2 | WARN 3 | SKIP 28 | PASS 32 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘miniCRAN-dependency-graph.rmd’ using rmarkdown + + Quitting from lines 55-58 [makeDepGraph] (miniCRAN-dependency-graph.rmd) + Error: processing vignette 'miniCRAN-dependency-graph.rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘miniCRAN-dependency-graph.rmd’ + + --- re-building ‘miniCRAN-introduction.rmd’ using rmarkdown + ... + --- finished re-building ‘miniCRAN-introduction.rmd’ + + --- re-building ‘miniCRAN-non-CRAN-repos.rmd’ using rmarkdown + --- finished re-building ‘miniCRAN-non-CRAN-repos.rmd’ + + SUMMARY: processing the following file failed: + ‘miniCRAN-dependency-graph.rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# missSBM + +
+ +* Version: 1.0.3 +* GitHub: https://github.com/grossSBM/missSBM +* Source code: https://github.com/cran/missSBM +* Date/Publication: 2022-08-23 12:10:06 UTC +* Number of recursive dependencies: 113 + +Run `revdepcheck::cloud_details(, "missSBM")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘missSBM-Ex.R’ failed + The error most likely occurred in: + + > ### Name: estimateMissSBM + > ### Title: Estimation of simple SBMs with missing data + > ### Aliases: estimateMissSBM + > + > ### ** Examples + > + > ## SBM parameters + ... + + > + > myModel <- collection$bestModel + > plot(myModel, "expected") + > plot(myModel, "imputed") + > plot(myModel, "meso") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot ... -> plotMeso -> -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 10.6Mb + sub-directories of 1Mb or more: + libs 8.6Mb + ``` + +# mlmts + +
+ +* Version: 1.1.1 +* GitHub: NA +* Source code: https://github.com/cran/mlmts +* Date/Publication: 2023-01-22 21:30:02 UTC +* Number of recursive dependencies: 236 + +Run `revdepcheck::cloud_details(, "mlmts")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘mlmts-Ex.R’ failed + The error most likely occurred in: + + > ### Name: dis_mcc + > ### Title: Constructs a pairwise distance matrix based on maximal + > ### cross-correlations + > ### Aliases: dis_mcc + > + > ### ** Examples + > + > reduced_dataset <- dis_mcc(RacketSports$data[1], features = TRUE) # Reducing + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: dis_mcc ... lapply -> FUN -> -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘ClusterR’ ‘MASS’ ‘Rdpack’ ‘multiwave’ ‘randomForest’ ‘ranger’ + All declared Imports should be used. + ``` + +# mnda + +
+ +* Version: 1.0.9 +* GitHub: NA +* Source code: https://github.com/cran/mnda +* Date/Publication: 2023-01-25 08:30:02 UTC +* Number of recursive dependencies: 89 + +Run `revdepcheck::cloud_details(, "mnda")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘mnda-Ex.R’ failed + The error most likely occurred in: + + > ### Name: EDNN + > ### Title: Encoder decoder neural network (EDNN) function + > ### Aliases: EDNN + > + > ### ** Examples + > + > myNet = network_gen(N_nodes = 50) + > graphData = myNet[["data_graph"]] + > edge.list = graphData[,1:2] + > edge.weight = graphData[,3:4] + > XY = ednn_IOprepare(edge.list, edge.weight) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: ednn_IOprepare ... graph_from_edgelist -> make_graph -> do.call -> + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘MASS’ ‘Matrix’ ‘magrittr’ ‘reticulate’ ‘tensorflow’ ‘usethis’ + All declared Imports should be used. + ``` + +# modnets + +
+ +* Version: 0.9.0 +* GitHub: https://github.com/tswanson222/modnets +* Source code: https://github.com/cran/modnets +* Date/Publication: 2021-10-01 08:20:02 UTC +* Number of recursive dependencies: 136 + +Run `revdepcheck::cloud_details(, "modnets")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘modnets-Ex.R’ failed + The error most likely occurred in: + + > ### Name: CentClust + > ### Title: Node centrality, clustering coefficients, and shortest path + > ### lengths + > ### Aliases: CentClust centAuto clustAuto + > + > ### ** Examples + > + > x <- fitNetwork(ggmDat, 'M') + > + > clustAuto(x) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: clustAuto -> -> graph.adjacency.dense + Execution halted + ``` + +# molnet + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/molnet +* Date/Publication: 2021-08-06 08:30:02 UTC +* Number of recursive dependencies: 123 + +Run `revdepcheck::cloud_details(, "molnet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘molnet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: determine_drug_targets + > ### Title: Determine drug target nodes in network + > ### Aliases: determine_drug_targets + > + > ### ** Examples + > + > data(drug_gene_interactions) + ... + + interaction_table=drug_gene_interactions, + + match_on='gene_name') + > drug_targets <- determine_drug_targets(combined_graphs[["graphs"]], + + combined_graphs[["annotations"]], + + drug_target_interaction, + + settings) + Error in .igraph.status("Restore graph external pointer.\n") : + could not find function ".igraph.status" + Calls: determine_drug_targets ... -> ensure_igraph -> is_igraph -> warn_version + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Molnet_Vignette.Rmd’ using rmarkdown + + Quitting from lines 255-256 [Individual Graphs] (Molnet_Vignette.Rmd) + Error: processing vignette 'Molnet_Vignette.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘Molnet_Vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘Molnet_Vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# moranajp + +
+ +* Version: 0.9.6 +* GitHub: https://github.com/matutosi/moranajp +* Source code: https://github.com/cran/moranajp +* Date/Publication: 2023-02-28 05:12:29 UTC +* Number of recursive dependencies: 129 + +Run `revdepcheck::cloud_details(, "moranajp")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘moranajp-Ex.R’ failed + The error most likely occurred in: + + > ### Name: draw_bigram_network + > ### Title: Draw bigram network using morphological analysis data. + > ### Aliases: draw_bigram_network bigram bigram_depend bigram_network + > ### word_freq bigram_network_plot + > + > ### ** Examples + > + ... + + clean_up(use_common_data = TRUE, synonym_df = synonym) + Joining with `by = join_by(原形)` + > + > bigram_neko <- + + neko_mecab %>% + + draw_bigram_network() + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: %>% ... bigram_network -> %>% -> -> make_empty_graph + Execution halted + ``` + +# motifcluster + +
+ +* Version: 0.2.3 +* GitHub: https://github.com/wgunderwood/motifcluster +* Source code: https://github.com/cran/motifcluster +* Date/Publication: 2022-11-18 08:10:02 UTC +* Number of recursive dependencies: 66 + +Run `revdepcheck::cloud_details(, "motifcluster")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘motifcluster-Ex.R’ failed + The error most likely occurred in: + + > ### Name: get_largest_component + > ### Title: Get largest connected component + > ### Aliases: get_largest_component + > + > ### ** Examples + > + > adj_mat <- matrix(c(0, 1, 0, 0, 0, 0, 0, 0, 0), nrow = 3) + > get_largest_component(adj_mat) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: get_largest_component ... graph_from_adjacency_matrix -> graph.adjacency.dense + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 5. └─igraph::make_empty_graph(n = vc, directed = (mode == "directed")) + ── Error ('test_utils.R:65:3'): get_largest_component returns correct indices ── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. ├─testthat::expect_equal(...) at test_utils.R:65:2 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. └─motifcluster::get_largest_component(adj_mat_dense) + 5. └─igraph::graph_from_adjacency_matrix(...) + 6. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 4 | WARN 0 | SKIP 0 | PASS 478 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘motifcluster_vignette.Rmd’ using rmarkdown + + Quitting from lines 424-429 [unnamed-chunk-23] (motifcluster_vignette.Rmd) + Error: processing vignette 'motifcluster_vignette.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘motifcluster_vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘motifcluster_vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# motifr + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/marioangst/motifr +* Source code: https://github.com/cran/motifr +* Date/Publication: 2020-12-10 15:40:02 UTC +* Number of recursive dependencies: 121 + +Run `revdepcheck::cloud_details(, "motifr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘motifr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: directed_dummy_net + > ### Title: Two-level directed network dummy example + > ### Aliases: directed_dummy_net + > ### Keywords: datasets + > + > ### ** Examples + > + > plot_mnet(directed_dummy_net) + Error in .igraph.status("Restore graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot_mnet ... vertex_attr -> ensure_igraph -> is_igraph -> warn_version + Execution halted + ``` + +# mppR + +
+ +* Version: 1.4.0 +* GitHub: https://github.com/vincentgarin/mppR +* Source code: https://github.com/cran/mppR +* Date/Publication: 2023-01-05 20:50:02 UTC +* Number of recursive dependencies: 71 + +Run `revdepcheck::cloud_details(, "mppR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘mppR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: MQE_gen_effects + > ### Title: QTL genetic effects multi-QTL effect model + > ### Aliases: MQE_gen_effects + > + > ### ** Examples + > + > + ... + > + > SIM <- mpp_SIM(mppData = mppData) + > QTL <- QTL_select(SIM) + > + > QTL.eff <- MQE_gen_effects(mppData = mppData, QTL = QTL[, 1], + + Q.eff = c("anc", "par", "biall")) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: MQE_gen_effects ... graph_from_edgelist -> make_graph -> do.call -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ▆ + 1. └─mppR::mpp_proc(...) at test_mpp_proc.R:32:2 + 2. └─mppR::QTL_gen_effects(...) + 3. └─base::mapply(...) + 4. └─mppR (local) ``(...) + 5. └─mppR::design_connectivity(...) + 6. └─igraph::graph(vertices) + 7. └─igraph::graph_from_edgelist(el, directed = directed) + 8. └─igraph::make_graph(unname(ids[t(el)]), directed = directed) + 9. ├─base::do.call(old_graph, args) + 10. └─igraph (local) ``(``, directed = TRUE) + + [ FAIL 3 | WARN 0 | SKIP 0 | PASS 24 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘MPP_ME_QTL_detect.Rmd’ using rmarkdown + + Quitting from lines 126-129 [setup] (MPP_ME_QTL_detect.Rmd) + Error: processing vignette 'MPP_ME_QTL_detect.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘MPP_ME_QTL_detect.Rmd’ + + --- re-building ‘mppR_gen_vignette.Rmd’ using rmarkdown + ... + Quitting from lines 355-360 [design_connectivity] (mppR_gen_vignette.Rmd) + Error: processing vignette 'mppR_gen_vignette.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘mppR_gen_vignette.Rmd’ + + SUMMARY: processing the following files failed: + ‘MPP_ME_QTL_detect.Rmd’ ‘mppR_gen_vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# MRFcov + +
+ +* Version: 1.0.39 +* GitHub: https://github.com/nicholasjclark/MRFcov +* Source code: https://github.com/cran/MRFcov +* Date/Publication: 2023-04-06 10:13:19 UTC +* Number of recursive dependencies: 115 + +Run `revdepcheck::cloud_details(, "MRFcov")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘MRFcov-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plotMRF_hm + > ### Title: Plot MRF interaction parameters as a heatmap + > ### Aliases: plotMRF_hm + > + > ### ** Examples + > + > + ... + ℹ Please use one dimensional logical vectors instead. + ℹ The deprecated feature was likely used in the MRFcov package. + Please report the issue to the authors. + > + > #To plot as an igraph network instead, we can simply extract the adjacency matrix + > net <- igraph::graph.adjacency(CRFmod$graph, weighted = TRUE, mode = "undirected") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: -> graph.adjacency.dense + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Bird_Parasite_CRF.Rmd’ using rmarkdown + + Quitting from lines 52-58 [unnamed-chunk-6] (Bird_Parasite_CRF.Rmd) + Error: processing vignette 'Bird_Parasite_CRF.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘Bird_Parasite_CRF.Rmd’ + + --- re-building ‘CRF_data_prep.Rmd’ using rmarkdown + ... + --- finished re-building ‘CRF_data_prep.Rmd’ + + --- re-building ‘Gaussian_Poisson_CRFs.Rmd’ using rmarkdown + --- finished re-building ‘Gaussian_Poisson_CRFs.Rmd’ + + SUMMARY: processing the following file failed: + ‘Bird_Parasite_CRF.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# MRReg + +
+ +* Version: 0.1.5 +* GitHub: https://github.com/DarkEyes/MRReg +* Source code: https://github.com/cran/MRReg +* Date/Publication: 2022-08-19 15:30:02 UTC +* Number of recursive dependencies: 99 + +Run `revdepcheck::cloud_details(, "MRReg")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘MRReg-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plotOptimalClustersTree + > ### Title: plotOptimalClustersTree + > ### Aliases: plotOptimalClustersTree + > + > ### ** Examples + > + > # Running FindMaxHomoOptimalPartitions using simulation data + ... + Warning in summary.lm(submodels[[inx2]]) : + essentially perfect fit: summary may be unreliable + Warning in summary.lm(submodels[[inx2]]) : + essentially perfect fit: summary may be unreliable + > # Plotting the result + > plotOptimalClustersTree(obj) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plotOptimalClustersTree ... graph_from_adjacency_matrix -> graph.adjacency.dense + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘MDLResFramework_Demo.Rmd’ using knitr + + Quitting from lines 51-52 [unnamed-chunk-2] (MDLResFramework_Demo.Rmd) + Error: processing vignette 'MDLResFramework_Demo.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘MDLResFramework_Demo.Rmd’ + + SUMMARY: processing the following file failed: + ‘MDLResFramework_Demo.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# MRS + +
+ +* Version: 1.2.4 +* GitHub: NA +* Source code: https://github.com/cran/MRS +* Date/Publication: 2018-01-23 09:10:10 UTC +* Number of recursive dependencies: 10 + +Run `revdepcheck::cloud_details(, "MRS")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘MRS-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plotTree + > ### Title: Plot nodes of the representative tree + > ### Aliases: plotTree + > + > ### ** Examples + > + > set.seed(1) + ... + > X = rbind(X1, X2) + > colnames(X) = c(1,2) + > G = c(rep(1, n1), rep(2,n2)) + > + > ans = mrs(X, G, K=8) + > plotTree(ans, type = "prob", legend = TRUE) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plotTree -> -> do.call -> + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.2Mb + sub-directories of 1Mb or more: + libs 7.1Mb + ``` + +# mstknnclust + +
+ +* Version: 0.3.2 +* GitHub: NA +* Source code: https://github.com/cran/mstknnclust +* Date/Publication: 2023-01-27 14:10:02 UTC +* Number of recursive dependencies: 36 + +Run `revdepcheck::cloud_details(, "mstknnclust")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘mstknnclust-Ex.R’ failed + The error most likely occurred in: + + > ### Name: compute.costs.proximity.graph + > ### Title: Computes the edge costs sum of a proximity graph + > ### Aliases: compute.costs.proximity.graph + > ### Keywords: internal + > + > ### ** Examples + > + ... + > ##Generates complete graph (CG) + > + > cg <- generate.complete.graph(1:nrow(x),d) + > + > ##Generates a proximity graph (MST) + > mstree <- generate.mst(cg) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: generate.mst -> -> make_empty_graph + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘guide.Rmd’ using rmarkdown + + Quitting from lines 77-79 [unnamed-chunk-4] (guide.Rmd) + Error: processing vignette 'guide.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘guide.Rmd’ + + SUMMARY: processing the following file failed: + ‘guide.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# MTA + +
+ +* Version: 0.4.1 +* GitHub: https://github.com/riatelab/MTA +* Source code: https://github.com/cran/MTA +* Date/Publication: 2022-06-03 16:00:02 UTC +* Number of recursive dependencies: 51 + +Run `revdepcheck::cloud_details(, "MTA")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘MTA-Ex.R’ failed + The error most likely occurred in: + + > ### Name: map_mst + > ### Title: Map Multiscalar Typology (3 deviations) + > ### Aliases: map_mst + > + > ### ** Examples + > + > # Load data + ... + > ept <- st_read(system.file("metroparis.gpkg", package = "MTA"), layer = "ept", quiet = TRUE) + > + > # Prerequisites - Compute the 3 deviations + > com$gdev <- gdev(x = com, var1 = "INC", var2 = "TH") + > com$tdev <- tdev(x = com, var1 = "INC", var2 = "TH", key = "EPT") + > com$sdev <- sdev(x = com, var1 = "INC", var2 = "TH", order = 1) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: sdev ... contiguityMat -> -> graph.adjacency.dense + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘MTA.Rmd’ using rmarkdown + --- finished re-building ‘MTA.Rmd’ + + --- re-building ‘MTA_Scenario.Rmd’ using rmarkdown + + Quitting from lines 439-473 [localdevrel_plot] (MTA_Scenario.Rmd) + Error: processing vignette 'MTA_Scenario.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘MTA_Scenario.Rmd’ + + SUMMARY: processing the following file failed: + ‘MTA_Scenario.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# mully + +
+ +* Version: 2.1.38 +* GitHub: https://github.com/frankkramer-lab/mully +* Source code: https://github.com/cran/mully +* Date/Publication: 2023-02-22 17:00:03 UTC +* Number of recursive dependencies: 51 + +Run `revdepcheck::cloud_details(, "mully")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘mully-Ex.R’ failed + The error most likely occurred in: + + > ### Name: addEdge + > ### Title: Add an edge + > ### Aliases: addEdge + > + > ### ** Examples + > + > g=mully::demo() + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: -> mully -> graph.empty + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘mully-pdf.Rmd’ using rmarkdown + A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TinyTeX with tinytex::reinstall_tinytex(repository = "illinois"). + + tlmgr: Local TeX Live (2022) is older than remote repository (2023). + Cross release updates are only supported with + update-tlmgr-latest(.sh/.exe) --update + See https://tug.org/texlive/upgrade.html for details. + Warning in system2("tlmgr", args, ...) : + running command ''tlmgr' search --file --global '/grffile.sty'' had status 1 + ... + --- failed re-building ‘mully-pdf.Rmd’ + + --- re-building ‘mully-vignette.Rmd’ using rmarkdown + --- finished re-building ‘mully-vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘mully-pdf.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# multilaterals + +
+ +* Version: 1.0 +* GitHub: NA +* Source code: https://github.com/cran/multilaterals +* Date/Publication: 2017-09-07 15:23:58 UTC +* Number of recursive dependencies: 11 + +Run `revdepcheck::cloud_details(, "multilaterals")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘multilaterals-Ex.R’ failed + The error most likely occurred in: + + > ### Name: multilaterals + > ### Title: Transitive Index Numbers for Cross-Sections and Panel Data + > ### Aliases: multilaterals-package multilaterals + > ### Keywords: package + > + > ### ** Examples + > + ... + Error in .igraph.status("Free graph external pointer.\n") : + could not find function ".igraph.status" + Error in .igraph.status("Free graph external pointer.\n") : + could not find function ".igraph.status" + Error in .igraph.status("Free graph external pointer.\n") : + could not find function ".igraph.status" + Error in .igraph.status("Free graph external pointer.\n") : + could not find function ".igraph.status" + Error in .igraph.status("Free graph external pointer.\n") : + could not find function ".igraph.status" + ``` + +# multilink + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/aleshing/multilink +* Source code: https://github.com/cran/multilink +* Date/Publication: 2023-06-09 14:20:07 UTC +* Number of recursive dependencies: 57 + +Run `revdepcheck::cloud_details(, "multilink")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘multilink-Ex.R’ failed + The error most likely occurred in: + + > ### Name: find_bayes_estimate + > ### Title: Find the Bayes Estimate of a Partition + > ### Aliases: find_bayes_estimate + > + > ### ** Examples + > + > # Example with small no duplicate dataset + ... + > # The following line corresponds to only keeping pairs of records as + > # potential matches in the initialization for which neither gname nor fname + > # disagree at the highest level + > pairs_to_keep <- (comparison_list$comparisons[, "gname_DL_3"] != TRUE) & + + (comparison_list$comparisons[, "fname_DL_3"] != TRUE) + > Z_init <- initialize_partition(comparison_list, pairs_to_keep, seed = 42) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: initialize_partition ... -> make_graph -> do.call -> + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 8.7Mb + sub-directories of 1Mb or more: + libs 8.4Mb + ``` + +# multinets + +
+ +* Version: 0.2.2 +* GitHub: https://github.com/neylsoncrepalde/multinets +* Source code: https://github.com/cran/multinets +* Date/Publication: 2019-12-14 17:20:03 UTC +* Number of recursive dependencies: 73 + +Run `revdepcheck::cloud_details(, "multinets")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘multinets-Ex.R’ failed + The error most likely occurred in: + + > ### Name: extract_highlevel + > ### Title: Extract the high level of a multilevel network + > ### Aliases: extract_highlevel + > + > ### ** Examples + > + > organizations <- extract_highlevel(linked_sim) + Error in .igraph.status("Restore graph external pointer.\n") : + could not find function ".igraph.status" + Calls: extract_highlevel ... -> ensure_igraph -> is_igraph -> warn_version + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 12. └─igraph:::ensure_igraph(graph) + 13. └─igraph::is_igraph(graph) + 14. └─igraph:::warn_version(graph) + ── Error ('test-mode_transformation.R:15:3'): mode transformation works without specifying 'which' ── + Error in `.igraph.status("Restore graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─igraph::bipartite_projection(g.bip) at test-mode_transformation.R:15:2 + 2. └─igraph:::ensure_igraph(graph) + 3. └─igraph::is_igraph(graph) + 4. └─igraph:::warn_version(graph) + + [ FAIL 4 | WARN 0 | SKIP 0 | PASS 10 ] + Error: Test failures + Execution halted + ``` + +# multinma + +
+ +* Version: 0.5.1 +* GitHub: https://github.com/dmphillippo/multinma +* Source code: https://github.com/cran/multinma +* Date/Publication: 2023-05-24 11:20:02 UTC +* Number of recursive dependencies: 139 + +Run `revdepcheck::cloud_details(, "multinma")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘multinma-Ex.R’ failed + The error most likely occurred in: + + > ### Name: example_pso_mlnmr + > ### Title: Example plaque psoriasis ML-NMR + > ### Aliases: example_pso_mlnmr + > ### Keywords: examples + > + > ### ** Examples + > + ... + + study = studyc, + + trt = trtc, + + r = pasi75_r, + + n = pasi75_n, + + trt_class = trtclass) + + ) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: combine_network ... as.igraph.nma_data -> -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─multinma::nma(...) at test-relative_effects.R:10:0 + 2. └─multinma::is_network_connected(network) + 3. ├─igraph::is_connected(igraph::as.igraph(network)) + 4. │ └─igraph:::ensure_igraph(graph) + 5. ├─igraph::as.igraph(network) + 6. └─multinma:::as.igraph.nma_data(network) + 7. └─igraph::graph_from_data_frame(e_all, directed = FALSE, vertices = v_all) + 8. └─igraph::make_empty_graph(n = 0, directed = directed) + + [ FAIL 26 | WARN 0 | SKIP 12 | PASS 320 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 286.7Mb + sub-directories of 1Mb or more: + doc 4.0Mb + libs 281.3Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# MultIS + +
+ +* Version: 0.6.2 +* GitHub: NA +* Source code: https://github.com/cran/MultIS +* Date/Publication: 2021-08-06 11:10:02 UTC +* Number of recursive dependencies: 81 + +Run `revdepcheck::cloud_details(, "MultIS")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘QuickStart.Rmd’ using knitr + + Quitting from lines 189-203 [QS-clusteringC3] (QuickStart.Rmd) + Error: processing vignette 'QuickStart.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘QuickStart.Rmd’ + + SUMMARY: processing the following file failed: + ‘QuickStart.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘poweRlaw’ ‘rmutil’ + All declared Imports should be used. + ``` + +# multivariance + +
+ +* Version: 2.4.1 +* GitHub: NA +* Source code: https://github.com/cran/multivariance +* Date/Publication: 2021-10-06 15:50:05 UTC +* Number of recursive dependencies: 37 + +Run `revdepcheck::cloud_details(, "multivariance")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘multivariance-Ex.R’ failed + The error most likely occurred in: + + > ### Name: clean.graph + > ### Title: cleanup dependence structure graph + > ### Aliases: clean.graph + > + > ### ** Examples + > + > N = 200 + ... + Dependence structure detection + + data: 'x' with 200 samples of 9 variables + structure: clustered + detection method: test -- method for p-values: conservative -- significance level: 0.05 + + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: dependence.structure -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + > + > test_check("multivariance") + [ FAIL 1 | WARN 34 | SKIP 0 | PASS 160 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('testmultivariances.R:341:1'): (code run outside of `test_that()`) ─── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─multivariance::dependence.structure(...) at testmultivariances.R:341:0 + 2. └─igraph::graph.empty(, directed = FALSE) + + [ FAIL 1 | WARN 34 | SKIP 0 | PASS 160 ] + Error: Test failures + Execution halted + ``` + +# mverse + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/mverseanalysis/mverse +* Source code: https://github.com/cran/mverse +* Date/Publication: 2022-05-23 08:10:02 UTC +* Number of recursive dependencies: 149 + +Run `revdepcheck::cloud_details(, "mverse")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘mverse_gettingstarted.Rmd’ using rmarkdown + --- finished re-building ‘mverse_gettingstarted.Rmd’ + + --- re-building ‘mverse_intro_glmmodelling.Rmd’ using rmarkdown + + Quitting from lines 210-211 [unnamed-chunk-8] (mverse_intro_glmmodelling.Rmd) + Error: processing vignette 'mverse_intro_glmmodelling.Rmd' failed with diagnostics: + could not find function ".igraph.status" + ... + --- failed re-building ‘mverse_intro_glmmodelling.Rmd’ + + --- re-building ‘mverse_intro_regressionmodelling.Rmd’ using rmarkdown + --- finished re-building ‘mverse_intro_regressionmodelling.Rmd’ + + SUMMARY: processing the following file failed: + ‘mverse_intro_glmmodelling.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# mwcsr + +
+ +* Version: 0.1.7 +* GitHub: https://github.com/ctlab/mwcsr +* Source code: https://github.com/cran/mwcsr +* Date/Publication: 2023-05-16 11:10:05 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "mwcsr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘mwcsr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: get_instance_type + > ### Title: Check the type and the validity of an MWCS instance + > ### Aliases: get_instance_type + > + > ### ** Examples + > + > data(mwcs_example) + > get_instance_type(mwcs_example) + Error in .igraph.status("Restore graph external pointer.\n") : + could not find function ".igraph.status" + Calls: get_instance_type -> check_graph -> -> warn_version + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Backtrace: + ▆ + 1. └─mwcsr::solve_mwcsp(solver, gam_example) at test_rmwcs.R:55:4 + 2. └─mwcsr:::check_graph(instance) + 3. └─igraph::is.igraph(g) + 4. └─igraph:::warn_version(graph) + ── Error ('test_rmwcs.R:61:5'): rmwcs solver works with empty solutions ──────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─igraph::graph.ring(10) at test_rmwcs.R:61:4 + + [ FAIL 5 | WARN 1 | SKIP 5 | PASS 32 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 17.4Mb + sub-directories of 1Mb or more: + java 2.5Mb + libs 14.3Mb + ``` + +# nat + +
+ +* Version: 1.8.22 +* GitHub: https://github.com/natverse/nat +* Source code: https://github.com/cran/nat +* Date/Publication: 2023-06-07 14:50:05 UTC +* Number of recursive dependencies: 90 + +Run `revdepcheck::cloud_details(, "nat")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘nat-Ex.R’ failed + The error most likely occurred in: + + > ### Name: neuron + > ### Title: neuron: class to represent traced neurons + > ### Aliases: neuron is.neuron as.neuron as.neuron.data.frame + > ### as.neuron.ngraph as.neuron.igraph as.neuron.default + > + > ### ** Examples + > + ... + [25] xform xyzmatrix xyzmatrix<- + see '?methods' for accessing help and source code + > + > ## Neurons as graphs + > # convert to graph and find longest paths by number of nodes + > ng=as.ngraph(n) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: as.ngraph ... as.ngraph.data.frame -> ngraph -> -> do.call -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘test-all.R’ + Running the tests in ‘tests/test-all.R’ failed. + Last 13 lines of output: + Backtrace: + ▆ + 1. ├─nat::as.neuron(testd) at test-neuron.R:13:0 + 2. └─nat:::as.neuron.data.frame(testd) + 3. ├─nat::as.neuron(as.ngraph(x), vertexData = x, ...) + 4. ├─nat::as.ngraph(x) + 5. └─nat:::as.ngraph.data.frame(x) + 6. └─nat::ngraph(...) + 7. └─igraph::graph(rawel, n = length(vertexlabels), directed = directed) + 8. ├─base::do.call(old_graph, args) + 9. └─igraph (local) ``(``, n = 6L, directed = TRUE) + + [ FAIL 30 | WARN 2 | SKIP 4 | PASS 633 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Installation.Rmd’ using rmarkdown + --- finished re-building ‘Installation.Rmd’ + + --- re-building ‘neurons-intro.Rmd’ using rmarkdown + + Quitting from lines 200-207 [unnamed-chunk-14] (neurons-intro.Rmd) + Error: processing vignette 'neurons-intro.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘neurons-intro.Rmd’ + + SUMMARY: processing the following file failed: + ‘neurons-intro.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# nbTransmission + +
+ +* Version: 1.1.2 +* GitHub: https://github.com/sarahleavitt/nbTransmission +* Source code: https://github.com/cran/nbTransmission +* Date/Publication: 2021-01-06 19:50:03 UTC +* Number of recursive dependencies: 123 + +Run `revdepcheck::cloud_details(, "nbTransmission")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Backtrace: + ▆ + 1. ├─testthat::expect_message(...) at test_visualizeResults.R:167:2 + 2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages) + 3. │ ├─testthat (local) .capture(...) + 4. │ │ └─base::withCallingHandlers(...) + 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 6. └─nbTransmission (local) createNetworkWrapper(nbResults, probBreaks = c(0.01, 0.05, 1)) + 7. └─nbTransmission:::createNetwork(...) at test_visualizeResults.R:48:2 + 8. └─igraph::graph_from_data_frame(d = edges, vertices = nodes, directed = T) + 9. └─igraph::make_empty_graph(n = 0, directed = directed) + + [ FAIL 4 | WARN 5 | SKIP 0 | PASS 124 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘nbTransmission-vignette.Rmd’ using rmarkdown + + Quitting from lines 266-269 [networkFull] (nbTransmission-vignette.Rmd) + Error: processing vignette 'nbTransmission-vignette.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘nbTransmission-vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘nbTransmission-vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# nda + +
+ +* Version: 0.1.6 +* GitHub: https://github.com/kzst/nda +* Source code: https://github.com/cran/nda +* Date/Publication: 2022-10-14 13:10:02 UTC +* Number of recursive dependencies: 81 + +Run `revdepcheck::cloud_details(, "nda")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘nda-Ex.R’ failed + The error most likely occurred in: + + > ### Name: biplot.nda + > ### Title: Biplot function for Network-based Dimensionality Reduction and + > ### Analysis (NDA) + > ### Aliases: biplot.nda + > ### Keywords: plot + > + > ### ** Examples + ... + > + > # Biplot function without feature selection + > + > data("CrimesUSA1990.X") + > df<-CrimesUSA1990.X + > p<-ndr(df) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: ndr ... ensure_igraph -> -> graph.adjacency.dense + Execution halted + ``` + +# neat + +
+ +* Version: 1.2.3 +* GitHub: NA +* Source code: https://github.com/cran/neat +* Date/Publication: 2021-01-07 06:00:02 UTC +* Number of recursive dependencies: 36 + +Run `revdepcheck::cloud_details(, "neat")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘neat-Ex.R’ failed + The error most likely occurred in: + + > ### Name: neat + > ### Title: Performs neat for lists of gene sets + > ### Aliases: neat pvalue neatc + > ### Keywords: htest + > + > ### ** Examples + > + ... + > blist = list('set 3' = set3) + > + > # test without multiple testing correction + > test1 = neat(alist = alist, blist = blist, network=A, + + nettype='directed', nodes=labels, + + alpha=0.05, mtc.type = 'none') + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: neat ... networkmatrix -> -> graph.adjacency.dense + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘neat.Rmd’ using rmarkdown + + Quitting from lines 158-159 [unnamed-chunk-13] (neat.Rmd) + Error: processing vignette 'neat.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘neat.Rmd’ + + SUMMARY: processing the following file failed: + ‘neat.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# neatmaps + +
+ +* Version: 2.1.0 +* GitHub: https://github.com/PhilBoileau/neatmaps +* Source code: https://github.com/cran/neatmaps +* Date/Publication: 2019-05-12 19:10:03 UTC +* Number of recursive dependencies: 98 + +Run `revdepcheck::cloud_details(, "neatmaps")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘neatmaps-Ex.R’ failed + The error most likely occurred in: + + > ### Name: consClustResTable + > ### Title: Consensus Cluster Results in a Table + > ### Aliases: consClustResTable + > + > ### ** Examples + > + > # create the data frame using the network, node and edge attributes + > df <- netsDataFrame(network_attr_df, + + node_attr_df, + + edge_df) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: netsDataFrame ... -> make_graph -> do.call -> + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.3Mb + ``` + +# Neighboot + +
+ +* Version: 1.0.1 +* GitHub: NA +* Source code: https://github.com/cran/Neighboot +* Date/Publication: 2022-05-31 23:20:08 UTC +* Number of recursive dependencies: 92 + +Run `revdepcheck::cloud_details(, "Neighboot")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘Neighboot-Ex.R’ failed + The error most likely occurred in: + + > ### Name: neighb + > ### Title: Compute standard errors and confidence intervals + > ### Aliases: neighb + > + > ### ** Examples + > + > #Load the synthetic population network dataset. + ... + Loading required package: RDStreeboot + > RDS.samp <- sample.RDS(pop.network$traits, pop.network$adj.mat, 200, 10, + + 3, c(1/6,1/3,1/3,1/6), FALSE) + > + > #Compute 95% confidence intervals using the percentile method + > neighb(RDS.data=RDS.samp, quant=c(0.025, 0.975),method="percentile", B=100) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: neighb -> .Nb -> -> make_empty_graph + Execution halted + ``` + +# netCoin + +
+ +* Version: 2.0.48 +* GitHub: https://github.com/Modesto-Escobar/netCoin-2.x +* Source code: https://github.com/cran/netCoin +* Date/Publication: 2023-03-23 22:40:02 UTC +* Number of recursive dependencies: 73 + +Run `revdepcheck::cloud_details(, "netCoin")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘netCoin-Ex.R’ failed + The error most likely occurred in: + + > ### Name: addDescription + > ### Title: Adds a description to a 'netCoin' object. + > ### Aliases: addDescription + > + > ### ** Examples + > + > data(finches) + ... + > + > Net<-allNet(Galapagos,nodes=finches, criteria="hyp", maxL=.05, + + lwidth ="Haberman",lweight="Haberman", + + size="frequency", color="species", layout="mds", + + main="Species coincidences in Galapagos Islands", + + note="Data source: Sanderson (2000)") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: allNet ... ensure_igraph -> rd3_toIgraph -> -> make_empty_graph + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 21 marked UTF-8 strings + ``` + +# netcom + +
+ +* Version: 2.1.6 +* GitHub: https://github.com/langendorfr/netcom +* Source code: https://github.com/cran/netcom +* Date/Publication: 2022-07-21 17:40:06 UTC +* Number of recursive dependencies: 102 + +Run `revdepcheck::cloud_details(, "netcom")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘netcom-Ex.R’ failed + The error most likely occurred in: + + > ### Name: align + > ### Title: Network Alignment + > ### Aliases: align + > + > ### ** Examples + > + > # The two networks to be aligned + > net_one <- matrix(stats::runif(25,0,1), nrow=5, ncol=5) + > net_two <- matrix(stats::runif(25,0,1), nrow=5, ncol=5) + > + > align(net_one, net_two) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: align ... ensure_igraph -> -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘ggfortify’ ‘ggplot2’ ‘ggraph’ ‘reshape2’ + All declared Imports should be used. + ``` + +# NetCoupler + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/NetCoupler/NetCoupler +* Source code: https://github.com/cran/NetCoupler +* Date/Publication: 2022-04-08 09:02:33 UTC +* Number of recursive dependencies: 101 + +Run `revdepcheck::cloud_details(, "NetCoupler")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘NetCoupler-Ex.R’ failed + The error most likely occurred in: + + > ### Name: nc_estimate_links + > ### Title: Compute model estimates between an external (exposure or + > ### outcome) variable and a network. + > ### Aliases: nc_estimate_links nc_estimate_exposure_links + > ### nc_estimate_outcome_links + > + > ### ** Examples + ... + + nc_standardize(starts_with("metabolite")) + > + > metabolite_network <- simulated_data %>% + + nc_standardize(starts_with("metabolite"), + + regressed_on = "age") %>% + + nc_estimate_network(starts_with("metabolite")) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: %>% ... %>% -> -> -> graph_from_adj_list + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 11. │ ├─base::withCallingHandlers(...) + 12. │ └─base::eval(exprs, env) + 13. │ └─base::eval(exprs, env) + 14. │ └─... %>% nc_estimate_network(starts_with("metabolite")) at tests/testthat/helpers-test-prep.R:6:0 + 15. ├─NetCoupler::nc_estimate_network(., starts_with("metabolite")) + 16. │ └─subset_data %>% pc_estimate_undirected_graph(alpha) %>% ... + 17. ├─NetCoupler:::as_tbl_graph.pcAlgo(.) + 18. │ └─... %>% tidygraph::as_tbl_graph() + 19. ├─tidygraph::as_tbl_graph(.) + 20. ├─igraph::graph_from_graphnel(.) + 21. │ └─igraph::graph_from_adj_list(al, mode = mode, duplicate = TRUE) + 22. └─base::.handleSimpleError(...) + 23. └─testthat (local) h(simpleError(msg, call)) + 24. └─rlang::abort(...) + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘NetCoupler.Rmd’ using rmarkdown + + Quitting from lines 175-178 [create-network] (NetCoupler.Rmd) + Error: processing vignette 'NetCoupler.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘NetCoupler.Rmd’ + + SUMMARY: processing the following file failed: + ‘NetCoupler.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# netdiffuseR + +
+ +* Version: 1.22.5 +* GitHub: https://github.com/USCCANA/netdiffuseR +* Source code: https://github.com/cran/netdiffuseR +* Date/Publication: 2022-12-02 16:20:02 UTC +* Number of recursive dependencies: 86 + +Run `revdepcheck::cloud_details(, "netdiffuseR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘netdiffuseR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: approx_geodesic + > ### Title: Approximate Geodesic Distances + > ### Aliases: approx_geodesic Geodesic Shortest-Path approx_geodist + > + > ### ** Examples + > + > # A very simple example ----------------------------------------------------- + ... + [9,] 1 1 2 2 2 3 3 3 0 1 + [10,] 1 1 1 2 2 2 3 3 3 0 + > igraph::distances( + + igraph::graph_from_adjacency_matrix(g, mode = "directed"), + + mode = "out" + + ) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: ... graph.adjacency.sparse -> make_graph -> do.call -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 4. base::with.default(...) + 5. base::eval(substitute(expr), data, enclos = parent.frame()) + 6. base::eval(substitute(expr), data, enclos = parent.frame()) + 7. netdiffuseR:::diffusionMap.default(graph[[slice]], toa, ...) + 8. igraph::graph_from_adjacency_matrix(graph, weighted = TRUE) + 9. igraph:::graph.adjacency.sparse(...) + 10. igraph::make_empty_graph(n = vc, directed = (mode == "directed")) + ... and 1 more + + + Maximum number of 10 failures reached, some test results may be missing. + + ══ DONE ════════════════════════════════════════════════════════════════════════ + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘analyzing-medical-innovation-data.Rmd’ using rmarkdown + + Quitting from lines 85-88 [Checking-the-methods] (analyzing-medical-innovation-data.Rmd) + Error: processing vignette 'analyzing-medical-innovation-data.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘analyzing-medical-innovation-data.Rmd’ + + --- re-building ‘introduction-to-netdiffuser.Rmd’ using rmarkdown + + ... + + --- re-building ‘time_discount_suscep_infect.Rmd’ using rmarkdown + --- finished re-building ‘time_discount_suscep_infect.Rmd’ + + SUMMARY: processing the following files failed: + ‘analyzing-medical-innovation-data.Rmd’ + ‘introduction-to-netdiffuser.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 16.7Mb + sub-directories of 1Mb or more: + doc 2.5Mb + libs 12.4Mb + ``` + +# NetFACS + +
+ +* Version: 0.5.0 +* GitHub: NA +* Source code: https://github.com/cran/NetFACS +* Date/Publication: 2022-12-06 17:32:35 UTC +* Number of recursive dependencies: 100 + +Run `revdepcheck::cloud_details(, "NetFACS")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘NetFACS-Ex.R’ failed + The error most likely occurred in: + + > ### Name: multiple_netfacs_network + > ### Title: Creates network objects out of the netfacs data + > ### Aliases: multiple_netfacs_network multiple.netfacs.network + > + > ### ** Examples + > + > data(emotions_set) + ... + + condition = emotions_set[[2]]$emotion, + + ran.trials = 10, # only for example + + combination.size = 2 + + ) + > + > emo.nets <- multiple_netfacs_network(emo.faces) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: multiple_netfacs_network ... %>% -> -> -> make_empty_graph + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘netfacs_tutorial.Rmd’ using rmarkdown + + Quitting from lines 286-297 [overlap] (netfacs_tutorial.Rmd) + Error: processing vignette 'netfacs_tutorial.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘netfacs_tutorial.Rmd’ + + SUMMARY: processing the following file failed: + ‘netfacs_tutorial.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# netgsa + +
+ +* Version: 4.0.4 +* GitHub: https://github.com/mikehellstern/netgsa +* Source code: https://github.com/cran/netgsa +* Date/Publication: 2022-10-25 06:02:36 UTC +* Number of recursive dependencies: 113 + +Run `revdepcheck::cloud_details(, "netgsa")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘netgsa.Rmd’ using rmarkdown + + Quitting from lines 150-154 [unnamed-chunk-6] (netgsa.Rmd) + Error: processing vignette 'netgsa.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘netgsa.Rmd’ + + SUMMARY: processing the following file failed: + ‘netgsa.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 28.1Mb + sub-directories of 1Mb or more: + doc 2.8Mb + libs 24.4Mb + ``` + +# netjack + +
+ +* Version: 1.2.0 +* GitHub: NA +* Source code: https://github.com/cran/netjack +* Date/Publication: 2019-07-07 17:50:03 UTC +* Number of recursive dependencies: 64 + +Run `revdepcheck::cloud_details(, "netjack")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘netjack-Ex.R’ failed + The error most likely occurred in: + + > ### Name: diff_test + > ### Title: Test for differences from original statistic + > ### Aliases: diff_test + > + > ### ** Examples + > + > data(GroupA) + > GroupA_Net = as_NetSample(GroupA, 1:20, node.variables = list(community = c(rep(1, 10), rep(2,10))), + + sample.variables = list(group = c(rep(1, 10), rep(2,10)))) + > Jackknife_GroupA_Net = net_apply(GroupA_Net, node_jackknife) + > GlobEff_GroupA_Net = net_stat_apply(Jackknife_GroupA_Net, global_efficiency) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: net_stat_apply ... -> -> graph.adjacency.dense + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘developingNetjack.Rmd’ using rmarkdown + --- finished re-building ‘developingNetjack.Rmd’ + + --- re-building ‘netjackIntro.Rmd’ using rmarkdown + + Quitting from lines 114-124 [unnamed-chunk-6] (netjackIntro.Rmd) + Error: processing vignette 'netjackIntro.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘netjackIntro.Rmd’ + + SUMMARY: processing the following file failed: + ‘netjackIntro.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘Rdpack’ + All declared Imports should be used. + ``` + +# netmap + +
+ +* Version: 0.1.2 +* GitHub: https://github.com/artod83/netmap +* Source code: https://github.com/cran/netmap +* Date/Publication: 2023-03-06 14:40:02 UTC +* Number of recursive dependencies: 84 + +Run `revdepcheck::cloud_details(, "netmap")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + id or vertex.names not found in lookup table + Invalid network/igraph object supplied + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 20 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-ggcentrality.R:34:3'): ggconn_area returns the correct connected areas for am igraph object ── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─igraph::graph_from_adjacency_matrix(...) at test-ggcentrality.R:34:2 + 2. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 20 ] + Error: Test failures + Execution halted + ``` + +# netmeta + +
+ +* Version: 2.8-2 +* GitHub: https://github.com/guido-s/netmeta +* Source code: https://github.com/cran/netmeta +* Date/Publication: 2023-05-06 10:10:05 UTC +* Number of recursive dependencies: 98 + +Run `revdepcheck::cloud_details(, "netmeta")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘netmeta-Ex.R’ failed + The error most likely occurred in: + + > ### Name: netcontrib + > ### Title: Contribution matrix in network meta-analysis + > ### Aliases: netcontrib print.netcontrib + > ### Keywords: contribution + > + > ### ** Examples + > + ... + > data("Woods2010") + > p1 <- pairwise(treatment, event = r, n = N, + + studlab = author, data = Woods2010, sm = "OR") + > + > net1 <- netmeta(p1) + > cm <- netcontrib(net1) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: netcontrib ... -> make_graph -> do.call -> + Execution halted + ``` + +## In both + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘crossnma’ + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 2 marked UTF-8 strings + ``` + +# NetMix + +
+ +* Version: 0.2.0.1 +* GitHub: https://github.com/solivella/NetMix +* Source code: https://github.com/cran/NetMix +* Date/Publication: 2022-11-16 16:34:41 UTC +* Number of recursive dependencies: 59 + +Run `revdepcheck::cloud_details(, "NetMix")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘NetMix-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.mmsbm + > ### Title: Various visualization tools for 'mmsbm' objects + > ### Aliases: plot.mmsbm + > + > ### ** Examples + > + > library(NetMix) + ... + + mmsbm.control = list(seed = 123, + + conv_tol = 1e-2, + + hessian = FALSE)) + > + > ## Plot blockmodel as network + > plot(lazega_mmsbm) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot -> plot.mmsbm -> -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.1Mb + sub-directories of 1Mb or more: + libs 5.8Mb + ``` + +# netplot + +
+ +* Version: 0.1-1 +* GitHub: https://github.com/USCCANA/netplot +* Source code: https://github.com/cran/netplot +* Date/Publication: 2021-06-16 07:10:02 UTC +* Number of recursive dependencies: 82 + +Run `revdepcheck::cloud_details(, "netplot")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘netplot-Ex.R’ failed + The error most likely occurred in: + + > ### Name: make_colors + > ### Title: Create a vector of colors for vertices and edges + > ### Aliases: make_colors make_edges_colors make_vertex_colors + > + > ### ** Examples + > + > + > data(UKfaculty, package="igraphdata") + > col <- make_vertex_colors(UKfaculty, "Group") + Error in .igraph.status("Restore graph external pointer.\n") : + could not find function ".igraph.status" + Calls: make_vertex_colors ... -> ensure_igraph -> is_igraph -> warn_version + Execution halted + ``` + +# netrankr + +
+ +* Version: 1.2.0 +* GitHub: https://github.com/schochastics/netrankr +* Source code: https://github.com/cran/netrankr +* Date/Publication: 2022-09-26 21:00:02 UTC +* Number of recursive dependencies: 65 + +Run `revdepcheck::cloud_details(, "netrankr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘netrankr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: approx_rank_expected + > ### Title: Approximation of expected ranks + > ### Aliases: approx_rank_expected + > + > ### ** Examples + > + > P <- matrix(c(0, 0, 1, 1, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, rep(0, 10)), 5, 5, byrow = TRUE) + > # Exact result + > exact_rank_prob(P)$expected.rank + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: exact_rank_prob ... ensure_igraph -> -> graph.adjacency.dense + Execution halted + Error in .igraph.status("Free graph external pointer.\n") : + could not find function ".igraph.status" + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 12.5Mb + sub-directories of 1Mb or more: + doc 1.6Mb + libs 10.6Mb + ``` + +# netropy + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/netropy +* Date/Publication: 2022-02-02 08:20:02 UTC +* Number of recursive dependencies: 85 + +Run `revdepcheck::cloud_details(, "netropy")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘netropy-Ex.R’ failed + The error most likely occurred in: + + > ### Name: assoc_graph + > ### Title: Association Graphs + > ### Aliases: assoc_graph + > + > ### ** Examples + > + > library(ggraph) + ... + + ifelse(df.att$age<=45,1,2)), + + practice = df.att$practice, + + lawschool= df.att$lawschool-1) + > + > # association graph based on cutoff 0.15 + > assoc_graph(df.att.ed, 0.15) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: assoc_graph -> -> graph.adjacency.dense + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘joint_entropies.Rmd’ using rmarkdown + + Quitting from lines 96-98 [assoc_g] (joint_entropies.Rmd) + Error: processing vignette 'joint_entropies.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘joint_entropies.Rmd’ + + --- re-building ‘prediction_power.Rmd’ using rmarkdown + ... + --- finished re-building ‘univariate_bivariate_trivariate.Rmd’ + + --- re-building ‘variable_domains.Rmd’ using rmarkdown + --- finished re-building ‘variable_domains.Rmd’ + + SUMMARY: processing the following file failed: + ‘joint_entropies.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# NetSci + +
+ +* Version: 1.0.0 +* GitHub: NA +* Source code: https://github.com/cran/NetSci +* Date/Publication: 2022-07-03 18:00:02 UTC +* Number of recursive dependencies: 61 + +Run `revdepcheck::cloud_details(, "NetSci")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘NetSci-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Histogram_LCC + > ### Title: Histogram_LCC + > ### Aliases: Histogram_LCC + > + > ### ** Examples + > + > set.seed(666) + ... + + Node.2 = sample(LETTERS[1:10], 15, replace = TRUE)) + > net$value = 1 + > net = CoDiNA::OrderNames(net) + > net = unique(net) + > + > g <- igraph::graph_from_data_frame(net, directed = FALSE ) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: -> make_empty_graph + Execution halted + ``` + +# netseg + +
+ +* Version: 1.0-1 +* GitHub: https://github.com/mbojan/netseg +* Source code: https://github.com/cran/netseg +* Date/Publication: 2022-08-25 12:10:06 UTC +* Number of recursive dependencies: 61 + +Run `revdepcheck::cloud_details(, "netseg")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘netseg-Ex.R’ failed + The error most likely occurred in: + + > ### Name: EF3 + > ### Title: Example data from Figure III of Echenique and Fryer (2006) + > ### Aliases: EF3 + > ### Keywords: datasets + > + > ### ** Examples + > + ... + + vertex.color = igraph::V(EF3)$type+1, + + vertex.label.family = "", + + sub = "Source: Echenique & Fryer (2006)", + + main = "Neighborhood racial segregation\n in a fictional city" + + ) + + } + Error in .igraph.status("Restore graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot ... plot.igraph -> ensure_igraph -> is_igraph -> warn_version + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ▆ + 1. ├─netseg::assort(WhiteKinship, "gender") at test-assort.R:11:10 + 2. └─netseg:::assort.igraph(WhiteKinship, "gender") + 3. ├─netseg::mixingm(object, vattr) + 4. └─netseg:::mixingm.igraph(object, vattr) + 5. └─igraph::any_multiple(object) + 6. └─igraph:::ensure_igraph(graph) + 7. └─igraph::is_igraph(graph) + 8. └─igraph:::warn_version(graph) + ── Failure ('test-smi.R:5:3'): SMI works ─────────────────────────────────────── + `smi(as.directed(WhiteKinship), "gender")` produced messages. + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 72 ] + Error: Test failures + Execution halted + ``` + +# nett + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/aaamini/nett +* Source code: https://github.com/cran/nett +* Date/Publication: 2022-11-09 10:50:05 UTC +* Number of recursive dependencies: 97 + +Run `revdepcheck::cloud_details(, "nett")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘nett-Ex.R’ failed + The error most likely occurred in: + + > ### Name: fast_cpl + > ### Title: CPL algorithm for community detection (fast) + > ### Aliases: fast_cpl + > ### Keywords: comm_detect + > + > ### ** Examples + > + > head(fast_cpl(igraph::as_adj(polblogs), 2), 50) + Error in .igraph.status("Restore graph external pointer.\n") : + could not find function ".igraph.status" + Calls: head ... -> ensure_igraph -> is_igraph -> warn_version + Execution halted + ``` + +# netUtils + +
+ +* Version: 0.8.1 +* GitHub: https://github.com/schochastics/netUtils +* Source code: https://github.com/cran/netUtils +* Date/Publication: 2022-12-19 21:00:02 UTC +* Number of recursive dependencies: 52 + +Run `revdepcheck::cloud_details(, "netUtils")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘netUtils-Ex.R’ failed + The error most likely occurred in: + + > ### Name: core_periphery + > ### Title: Discrete core-periphery model + > ### Aliases: core_periphery + > + > ### ** Examples + > + > set.seed(121) + ... + Error in .igraph.status("Free graph external pointer.\n") : + could not find function ".igraph.status" + Error in .igraph.status("Free graph external pointer.\n") : + could not find function ".igraph.status" + Error in .igraph.status("Free graph external pointer.\n") : + could not find function ".igraph.status" + Error in .igraph.status("Free graph external pointer.\n") : + could not find function ".igraph.status" + Error in .igraph.status("Free graph external pointer.\n") : + could not find function ".igraph.status" + ``` + +# NetworkExtinction + +
+ +* Version: 1.0.3 +* GitHub: NA +* Source code: https://github.com/cran/NetworkExtinction +* Date/Publication: 2023-03-31 11:40:02 UTC +* Number of recursive dependencies: 100 + +Run `revdepcheck::cloud_details(, "NetworkExtinction")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘NetworkExtinction-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ExtinctionPlot + > ### Title: Plots the extinctions history of a network + > ### Aliases: ExtinctionPlot + > + > ### ** Examples + > + > # If you don't specify the y variable it will plot the secondary extinctions + > # by default + > data("net") + > history <- SimulateExtinctions(Network = net, Method = "Mostconnected") + + | + | | 0%Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: SimulateExtinctions ... withCallingHandlers -> -> graph.adjacency.dense + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 2. │ └─testthat:::expect_condition_matching(...) + 3. │ └─testthat:::quasi_capture(...) + 4. │ ├─testthat (local) .capture(...) + 5. │ │ └─base::withCallingHandlers(...) + 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 7. └─NetworkExtinction::SimulateExtinctions(Network = net, Method = "Mostconnected") + 8. └─NetworkExtinction::ExtinctionOrder(...) + 9. ├─base::suppressMessages(...) + 10. │ └─base::withCallingHandlers(...) + 11. └─igraph::graph_from_adjacency_matrix(net, mode = "directed", weighted = TRUE) + 12. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 2 | WARN 0 | SKIP 3 | PASS 2 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘NetworkExtinction.Rmd’ using rmarkdown + + Quitting from lines 136-141 [mostconnected2] (NetworkExtinction.Rmd) + Error: processing vignette 'NetworkExtinction.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘NetworkExtinction.Rmd’ + + SUMMARY: processing the following file failed: + ‘NetworkExtinction.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# networkGen + +
+ +* Version: 0.1.1 +* GitHub: NA +* Source code: https://github.com/cran/networkGen +* Date/Publication: 2017-12-04 17:31:37 UTC +* Number of recursive dependencies: 9 + +Run `revdepcheck::cloud_details(, "networkGen")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘networkGen-Ex.R’ failed + The error most likely occurred in: + + > ### Name: check.graph + > ### Title: check.graph + > ### Aliases: check.graph + > + > ### ** Examples + > + > check.graph(nodeLogic(value = 1, type= "circuit", itemFamily= 1)) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: check.graph ... graph_from_literal_i -> make_graph -> do.call -> + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘mgcv’ ‘stats’ + All declared Imports should be used. + ``` + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# NetworkInference + +
+ +* Version: 1.2.4 +* GitHub: https://github.com/desmarais-lab/NetworkInference +* Source code: https://github.com/cran/NetworkInference +* Date/Publication: 2019-02-28 05:50:06 UTC +* Number of recursive dependencies: 77 + +Run `revdepcheck::cloud_details(, "NetworkInference")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘NetworkInference-Ex.R’ failed + The error most likely occurred in: + + > ### Name: simulate_cascades + > ### Title: Simulate cascades from a diffusion network + > ### Aliases: simulate_cascades + > + > ### ** Examples + > + > + ... + **************************************************| + Inferring 5 edges... + 0% 10 20 30 40 50 60 70 80 90 100% + [----|----|----|----|----|----|----|----|----|----| + **************************************************| + > simulated_cascades <- simulate_cascades(out, nsim = 10) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: simulate_cascades ... lapply -> FUN -> -> graph.adjacency.dense + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘quickstart_vignette.Rmd’ using rmarkdown + --- finished re-building ‘quickstart_vignette.Rmd’ + + --- re-building ‘tutorial_vignette.Rmd’ using rmarkdown + Warning: ggrepel: 16 unlabeled data points (too many overlaps). Consider increasing max.overlaps + + Quitting from lines 278-284 [unnamed-chunk-29] (tutorial_vignette.Rmd) + Error: processing vignette 'tutorial_vignette.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘tutorial_vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘tutorial_vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# NetworkToolbox + +
+ +* Version: 1.4.2 +* GitHub: NA +* Source code: https://github.com/cran/NetworkToolbox +* Date/Publication: 2021-05-28 11:40:06 UTC +* Number of recursive dependencies: 111 + +Run `revdepcheck::cloud_details(, "NetworkToolbox")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘NetworkToolbox-Ex.R’ failed + The error most likely occurred in: + + > ### Name: comcat + > ### Title: Communicating Nodes + > ### Aliases: comcat + > + > ### ** Examples + > + > # Pearson's correlation only for CRAN checks + > A <- TMFG(neoOpen, normal = FALSE)$A + > + > communicating <- comcat(A, comm = "walktrap", cent = "strength", metric = "across") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: comcat ... graph.edgelist -> make_graph -> do.call -> + Execution halted + ``` + +# networktools + +
+ +* Version: 1.5.0 +* GitHub: https://github.com/paytonjjones/networktools +* Source code: https://github.com/cran/networktools +* Date/Publication: 2022-06-03 22:20:02 UTC +* Number of recursive dependencies: 158 + +Run `revdepcheck::cloud_details(, "networktools")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + > + > test_check("networktools") + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-networktools.R:7:1'): (code run outside of `test_that()`) ────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─igraph::graph_from_adjacency_matrix(dep_cor, mode = "undirected") at test-networktools.R:7:0 + 2. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] + Error: Test failures + Execution halted + ``` + +# NIMAA + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/jafarilab/NIMAA +* Source code: https://github.com/cran/NIMAA +* Date/Publication: 2022-04-11 14:12:45 UTC +* Number of recursive dependencies: 173 + +Run `revdepcheck::cloud_details(, "NIMAA")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘NIMAA-Ex.R’ failed + The error most likely occurred in: + + > ### Name: analyseNetwork + > ### Title: General properties of the network + > ### Aliases: analyseNetwork + > + > ### ** Examples + > + > # generate a toy graph + > g1 <- igraph::make_graph(c(1, 2, 3, 4, 1, 3), directed = FALSE) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: -> do.call -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 1. └─igraph::make_graph(c(1, 2, 3, 4, 1, 3), directed = FALSE) at test-analyse-network.R:2:2 + 2. ├─base::do.call(old_graph, args) + 3. └─igraph (local) ``(``, directed = FALSE) + ── Error ('test-find-cluster.R:5:3'): find cluster works ─────────────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─NIMAA::findCluster(...) at test-find-cluster.R:5:2 + 2. └─NIMAA:::projectGraph(inc_mat, dim = part) + 3. └─igraph::graph_from_adjacency_matrix(...) + 4. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 2 | WARN 6 | SKIP 0 | PASS 8 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘NIMAA-vignette.Rmd’ using rmarkdown + + Quitting from lines 70-74 [plotBipartite] (NIMAA-vignette.Rmd) + Error: processing vignette 'NIMAA-vignette.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘NIMAA-vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘NIMAA-vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.2Mb + sub-directories of 1Mb or more: + doc 4.0Mb + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 24 marked UTF-8 strings + ``` + +# nimble + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/nimble-dev/nimble +* Source code: https://github.com/cran/nimble +* Date/Publication: 2023-05-23 19:42:03 UTC +* Number of recursive dependencies: 38 + +Run `revdepcheck::cloud_details(, "nimble")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘nimble-Ex.R’ failed + The error most likely occurred in: + + > ### Name: MCMCconf-class + > ### Title: Class 'MCMCconf' + > ### Aliases: MCMCconf-class MCMCconf addSampler removeSamplers setSamplers + > ### printSamplers getSamplers setSamplerExecutionOrder + > ### getSamplerExecutionOrder addMonitors addMonitors2 setMonitors + > ### setMonitors2 resetMonitors getMonitors getMonitors2 printMonitors + > ### setThin setThin2 + ... + > code <- nimbleCode({ + + mu ~ dnorm(0, 1) + + x ~ dnorm(mu, 1) + + }) + > Rmodel <- nimbleModel(code) + Defining model + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: nimbleModel ... -> genExpandedNodeAndParentNames3 -> graph.empty + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 45.2Mb + sub-directories of 1Mb or more: + CppCode 2.6Mb + R 7.4Mb + classic-bugs 1.6Mb + include 10.6Mb + libs 22.1Mb + ``` + +# nlnet + +
+ +* Version: 1.4 +* GitHub: NA +* Source code: https://github.com/cran/nlnet +* Date/Publication: 2020-10-19 23:10:05 UTC +* Number of recursive dependencies: 38 + +Run `revdepcheck::cloud_details(, "nlnet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘nlnet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: nlnet + > ### Title: Non-Linear Network reconstruction from expression matrix + > ### Aliases: nlnet + > + > ### ** Examples + > + > + ... + > ## now input includes data matrix and hiden clusters, so get the matrix as input. + > input<-input$data + > ##change the ploting method + > result<-nlnet(input,plot.method="graph") + ------fdr cutoff aimed 7.426061e-16 ------- + ------fdr cutoff real 0.05 ------- + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: nlnet -> graph.adjacency -> graph.adjacency.dense + Execution halted + ``` + +# nlrx + +
+ +* Version: 0.4.4 +* GitHub: https://github.com/ropensci/nlrx +* Source code: https://github.com/cran/nlrx +* Date/Publication: 2023-05-16 14:40:02 UTC +* Number of recursive dependencies: 155 + +Run `revdepcheck::cloud_details(, "nlrx")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat-class.R’ + Running ‘testthat-exe1.R’ + Running ‘testthat-exe2.R’ + Running ‘testthat-exe3.R’ + Running ‘testthat-nldoc.R’ + Running the tests in ‘tests/testthat-nldoc.R’ failed. + Last 13 lines of output: + [1] "File successfully compiled!" + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 2 ] + + ... + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─nlrx::nldoc_network(modelfiles) at test-nldoc.R:51:4 + 2. └─igraph::graph_from_data_frame(nw) + 3. └─igraph::make_empty_graph(n = 0, directed = directed) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 2 ] + Error: Test failures + Execution halted + ``` + +# node2vec + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/node2vec +* Date/Publication: 2021-01-14 09:00:02 UTC +* Number of recursive dependencies: 34 + +Run `revdepcheck::cloud_details(, "node2vec")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘node2vec-Ex.R’ failed + The error most likely occurred in: + + > ### Name: node2vecR + > ### Title: Algorithmic Framework for Representational Learning on Graphs + > ### Aliases: node2vecR + > + > ### ** Examples + > + > #Parameters can be customized as needed + > data(gene_edges) + > use_data<-gene_edges + > emb<-node2vecR(use_data,p=2,q=1,num_walks=5,walk_length=5,dim=10) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: node2vecR -> graph_from_data_frame -> make_empty_graph + Execution halted + ``` + +# nutriNetwork + +
+ +* Version: 0.1.1 +* GitHub: NA +* Source code: https://github.com/cran/nutriNetwork +* Date/Publication: 2019-04-26 10:00:02 UTC +* Number of recursive dependencies: 17 + +Run `revdepcheck::cloud_details(, "nutriNetwork")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘nutriNetwork-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.nutriNetwork + > ### Title: plot for S3 class "nutriNetwork" + > ### Aliases: plot.nutriNetwork + > + > ### ** Examples + > + > ## Don't show: + ... + > out <- nutriNetwork(vfit, method = "npn") + Network reconstruction is in progress ... + + Network reconstruction is done. + + > plot(out) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot ... plot.nutriNetwork -> graph.adjacency -> graph.adjacency.dense + Execution halted + ``` + +# OCNet + +
+ +* Version: 1.0.1 +* GitHub: NA +* Source code: https://github.com/cran/OCNet +* Date/Publication: 2023-04-25 13:50:02 UTC +* Number of recursive dependencies: 77 + +Run `revdepcheck::cloud_details(, "OCNet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘OCNet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: OCN_to_SSN + > ### Title: Transform OCN into SSN object + > ### Aliases: OCN_to_SSN + > + > ### ** Examples + > + > # transform a 20x20 single-outlet OCN (aggregated at the AG level) + > # into a SSN object and plot it + > OCN <- aggregate_OCN(landscape_OCN(OCN_20), thrA = 4) + > ssn1 <- OCN_to_SSN(OCN, "AG", obsDesign = SSN::poissonDesign(10), + + path=paste(tempdir(),"/OCN.ssn", sep = ""), importToR = TRUE) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: OCN_to_SSN ... graph.adjacency.sparse -> make_graph -> do.call -> + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 8.1Mb + sub-directories of 1Mb or more: + data 2.6Mb + libs 4.4Mb + ``` + +# oddnet + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/oddnet +* Date/Publication: 2022-12-22 20:10:01 UTC +* Number of recursive dependencies: 85 + +Run `revdepcheck::cloud_details(, "oddnet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘oddnet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: anomalous_networks + > ### Title: Identifies anomalous networks from a series of temporal + > ### networks. + > ### Aliases: anomalous_networks + > + > ### ** Examples + > + ... + > p.or.m.seq <- rep(0.1, 50) + > p.or.m.seq[20] <- 0.3 # anomalous network at 20 + > for(i in 1:50){ + + gr <- igraph::erdos.renyi.game(50, p.or.m = p.or.m.seq[i]) + + networks[[i]] <- igraph::as_adjacency_matrix(gr) + + } + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: + Execution halted + ``` + +# ohun + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/maRce10/ohun +* Source code: https://github.com/cran/ohun +* Date/Publication: 2022-12-19 09:30:02 UTC +* Number of recursive dependencies: 89 + +Run `revdepcheck::cloud_details(, "ohun")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ohun-Ex.R’ failed + The error most likely occurred in: + + > ### Name: label_detection + > ### Title: Label detections from a sound event detection procedure + > ### Aliases: label_detection + > + > ### ** Examples + > + > { + ... + + label_detection(reference = lbh_reference, detection = Y) + + + + # remove split to get only merge + + Y <- Y[-2, ] + + label_detection(reference = lbh_reference, detection = Y) + + } + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: label_detection ... lapply -> FUN -> -> graph.incidence.dense + Execution halted + ``` + +# OpenRepGrid + +
+ +* Version: 0.1.14 +* GitHub: https://github.com/markheckmann/OpenRepGrid +* Source code: https://github.com/cran/OpenRepGrid +* Date/Publication: 2023-05-16 15:00:11 UTC +* Number of recursive dependencies: 86 + +Run `revdepcheck::cloud_details(, "OpenRepGrid")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘OpenRepGrid-Ex.R’ failed + The error most likely occurred in: + + > ### Name: indexDilemma + > ### Title: Detect implicative dilemmas (conflicts). + > ### Aliases: indexDilemma + > + > ### ** Examples + > + > id <- indexDilemma(boeker, self = 1, ideal = 2) + ... + R = Correlation including Self & Ideal + RexSI = Correlation excluding Self & Ideal + R was used as criterion> + > # plot dilemmas as network graph (see ?plot.indexDilemma for help) + > # set a seed for reproducibility + > plot(id, layout = "rows") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot ... plot.indexDilemma -> -> graph.adjacency.dense + Execution halted + ``` + +# OpenRepGrid.ic + +
+ +* Version: 0.6.1 +* GitHub: https://github.com/markheckmann/OpenRepGrid.ic +* Source code: https://github.com/cran/OpenRepGrid.ic +* Date/Publication: 2022-10-25 18:57:49 UTC +* Number of recursive dependencies: 148 + +Run `revdepcheck::cloud_details(, "OpenRepGrid.ic")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ▆ + 1. └─OpenRepGrid.ic::network_graph_images(...) at test-excel.R:15:2 + 2. └─igraph::graph_from_adjacency_matrix(MM, diag = FALSE, mode = "undirected") + 3. └─igraph:::graph.adjacency.dense(...) + ── Error ('test-excel.R:57:3'): Excel output file gets created ───────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─OpenRepGrid.ic::network_graph_images(...) at test-excel.R:57:2 + 2. └─igraph::graph_from_adjacency_matrix(MM, diag = FALSE, mode = "undirected") + 3. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 29 ] + Error: Test failures + Execution halted + ``` + +# OrdCD + +
+ +* Version: 1.1.2 +* GitHub: https://github.com/nySTAT/OrdCD +* Source code: https://github.com/cran/OrdCD +* Date/Publication: 2023-05-17 21:40:11 UTC +* Number of recursive dependencies: 19 + +Run `revdepcheck::cloud_details(, "OrdCD")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘OrdCD-Ex.R’ failed + The error most likely occurred in: + + > ### Name: OrdCD + > ### Title: Causal Discovery for Ordinal Categorical Data + > ### Aliases: OrdCD + > + > ### ** Examples + > + > set.seed(2020) + ... + > for (j in 1:q){ + + y[,j]=as.factor(y[,j]) + + } + > + > time=proc.time() + > G=OrdCD(y) #estimated DAG adjacency matrix + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: OrdCD ... -> -> graph.adjacency.dense + Execution halted + ``` + +# PAC + +
+ +* Version: 1.1.4 +* GitHub: NA +* Source code: https://github.com/cran/PAC +* Date/Publication: 2021-02-18 07:00:02 UTC +* Number of recursive dependencies: 62 + +Run `revdepcheck::cloud_details(, "PAC")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘intro.Rmd’ using rmarkdown + + Quitting from lines 42-43 [PAC and Network Inference] (intro.Rmd) + Error: processing vignette 'intro.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘intro.Rmd’ + + SUMMARY: processing the following file failed: + ‘intro.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# PAFit + +
+ +* Version: 1.2.5 +* GitHub: https://github.com/thongphamthe/PAFit +* Source code: https://github.com/cran/PAFit +* Date/Publication: 2022-01-11 10:02:48 UTC +* Number of recursive dependencies: 61 + +Run `revdepcheck::cloud_details(, "PAFit")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘PAFit-Ex.R’ failed + The error most likely occurred in: + + > ### Name: from_igraph + > ### Title: Convert an igraph object to a PAFit_net object + > ### Aliases: from_igraph + > + > ### ** Examples + > + > library("PAFit") + > # a network from Bianconi-Barabasi model + > net <- generate_BB(N = 50 , m = 10 , s = 10) + > igraph_graph <- to_igraph(net) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: to_igraph -> graph.data.frame -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘fit_node_no_new_edge.R’ + Running ‘loop_generate.R’ + Running ‘loop_joint_estimate.R’ + Running ‘loop_overall.R’ + Running ‘loop_test_Newman_Kong.R’ + Running ‘test_GenerateNet_final_padding.R’ + Running ‘test_GetStatistics_compress_2.R’ + Running ‘test_GetStatistics_undirected.R’ + Running ‘test_Newman_Kong.R’ + Running ‘test_PAFit_oneshot.R’ + ... + > library(PAFit) + > + > net <- generate_BA(N = 100, multiple_node = 20, m = 1) + > + > system.time(b <- to_igraph(net)) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: system.time -> to_igraph -> graph.data.frame -> make_empty_graph + Timing stopped at: 0.002 0 0.002 + Execution halted + ``` + +# PairViz + +
+ +* Version: 1.3.6 +* GitHub: NA +* Source code: https://github.com/cran/PairViz +* Date/Publication: 2022-08-12 15:00:05 UTC +* Number of recursive dependencies: 109 + +Run `revdepcheck::cloud_details(, "PairViz")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘MultipleComparisons.Rmd’ using rmarkdown + + Quitting from lines 146-160 [unnamed-chunk-11] (MultipleComparisons.Rmd) + Error: processing vignette 'MultipleComparisons.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘MultipleComparisons.Rmd’ + + --- re-building ‘PairVizIntroduction.Rmd’ using rmarkdown + + ... + Quitting from lines 370-371 [unnamed-chunk-29] (pcp.Rmd) + Error: processing vignette 'pcp.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘pcp.Rmd’ + + SUMMARY: processing the following files failed: + ‘MultipleComparisons.Rmd’ ‘PairVizIntroduction.Rmd’ ‘pcp.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# pald + +
+ +* Version: 0.0.2 +* GitHub: https://github.com/LucyMcGowan/pald +* Source code: https://github.com/cran/pald +* Date/Publication: 2022-06-03 08:30:02 UTC +* Number of recursive dependencies: 35 + +Run `revdepcheck::cloud_details(, "pald")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘pald-Ex.R’ failed + The error most likely occurred in: + + > ### Name: cohesion_strong + > ### Title: Cohesion Matrix: Strong Ties + > ### Aliases: cohesion_strong + > + > ### ** Examples + > + > C <- cohesion_matrix(dist(exdata2)) + ... + > if (requireNamespace("igraph", quietly = TRUE)) { + + G_strong <- igraph::simplify( + + igraph::graph.adjacency(CS, weighted = TRUE, mode = "undirected") + + ) + + plot(G_strong) + + } + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: ... ensure_igraph -> -> graph.adjacency.dense + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-pald_functions.R:59:3'): community_clusters works ────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─pald::community_clusters(C) at test-pald_functions.R:59:2 + 2. └─pald::community_graphs(c) + 3. ├─igraph::simplify(...) + 4. │ └─igraph:::ensure_igraph(graph) + 5. └─igraph::graph.adjacency(c_symmetric, weighted = TRUE, mode = "undirected") + 6. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 11 ] + Error: Test failures + Execution halted + ``` + +# PANACEA + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/egeulgen/PANACEA +* Source code: https://github.com/cran/PANACEA +* Date/Publication: 2023-05-02 21:10:05 UTC +* Number of recursive dependencies: 86 + +Run `revdepcheck::cloud_details(, "PANACEA")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘PANACEA-Ex.R’ failed + The error most likely occurred in: + + > ### Name: score_drugs + > ### Title: Scoring of Drugs via Network-based Methods + > ### Aliases: score_drugs + > + > ### ** Examples + > + > toy_data <- data.frame( + ... + + driveR_res = toy_data, + + drug_interactions_df = toy_interactions, # leave blank for default + + W_mat = toy_W_mat, # leave blank for default + + method = "distance-based", + + verbose = FALSE + + ) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: score_drugs ... score_drugs_distance_based -> -> graph.adjacency.dense + Execution halted + ``` + +# paramlink + +
+ +* Version: 1.1-5 +* GitHub: https://github.com/magnusdv/paramlink +* Source code: https://github.com/cran/paramlink +* Date/Publication: 2022-04-15 08:10:02 UTC +* Number of recursive dependencies: 21 + +Run `revdepcheck::cloud_details(, "paramlink")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘paramlink-Ex.R’ failed + The error most likely occurred in: + + > ### Name: pedigreeLoops + > ### Title: Pedigree loops + > ### Aliases: pedigreeLoops breakLoops tieLoops findLoopBreakers + > ### findLoopBreakers2 + > + > ### ** Examples + > + ... + > if(requireNamespace("igraph", quietly = TRUE)) { + + y = doubleCousins(1, 1, child=TRUE) + + findLoopBreakers(y) # --> 9 + + findLoopBreakers2(y) # --> 9 and 4 + + breakLoops(y) # uses both 9 and 4 + + } + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: findLoopBreakers2 ... -> make_graph -> do.call -> + Execution halted + ``` + +# particles + +
+ +* Version: 0.2.3 +* GitHub: https://github.com/thomasp85/particles +* Source code: https://github.com/cran/particles +* Date/Publication: 2022-08-19 12:20:05 UTC +* Number of recursive dependencies: 81 + +Run `revdepcheck::cloud_details(, "particles")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘particles-Ex.R’ failed + The error most likely occurred in: + + > ### Name: evolve + > ### Title: Move the simulation forward one or more steps + > ### Aliases: evolve + > + > ### ** Examples + > + > graph <- tidygraph::create_notable('folkman') + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: -> as_tbl_graph -> make_graph -> make_famous_graph + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘intro.Rmd’ using rmarkdown + + Quitting from lines 61-71 [unnamed-chunk-1] (intro.Rmd) + Error: processing vignette 'intro.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘intro.Rmd’ + + SUMMARY: processing the following file failed: + ‘intro.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# pathfindR + +
+ +* Version: 2.1.0 +* GitHub: https://github.com/egeulgen/pathfindR +* Source code: https://github.com/cran/pathfindR +* Date/Publication: 2023-05-12 07:10:03 UTC +* Number of recursive dependencies: 143 + +Run `revdepcheck::cloud_details(, "pathfindR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘pathfindR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: combine_pathfindR_results + > ### Title: Combine 2 pathfindR Results + > ### Aliases: combine_pathfindR_results + > + > ### ** Examples + > + > combined_results <- combine_pathfindR_results(example_pathfindR_output, example_comparison_output) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: combine_pathfindR_results ... combined_results_graph -> -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat-active_snw.R’ + Running ‘testthat-clustering.R’ + Running the tests in ‘tests/testthat-clustering.R’ failed. + Last 13 lines of output: + with the additional columns `Cluster` and `Status` ── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─pathfindR::cluster_enriched_terms(...) at test-clustering.R:419:2 + 2. ├─R.utils::doCall(...) + 3. ├─R.utils::doCall.default(...) + 4. │ └─base::do.call(.fcn, args = args, envir = envir) + 5. └─pathfindR::cluster_graph_vis(...) + 6. └─igraph::graph_from_adjacency_matrix(kappa_mat2, weighted = TRUE) + 7. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 3 | WARN 0 | SKIP 1 | PASS 45 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘comparing_results.Rmd’ using rmarkdown + + Quitting from lines 34-35 [compare_graph1] (comparing_results.Rmd) + Error: processing vignette 'comparing_results.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘comparing_results.Rmd’ + + --- re-building ‘intro_vignette.Rmd’ using rmarkdown + --- finished re-building ‘intro_vignette.Rmd’ + ... + Quitting from lines 122-123 [term_gene1] (visualization_vignette.Rmd) + Error: processing vignette 'visualization_vignette.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘visualization_vignette.Rmd’ + + SUMMARY: processing the following files failed: + ‘comparing_results.Rmd’ ‘visualization_vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# pcalg + +
+ +* Version: 2.7-8 +* GitHub: NA +* Source code: https://github.com/cran/pcalg +* Date/Publication: 2022-12-21 00:20:05 UTC +* Number of recursive dependencies: 58 + +Run `revdepcheck::cloud_details(, "pcalg")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘pcalg-Ex.R’ failed + The error most likely occurred in: + + > ### Name: addBgKnowledge + > ### Title: Add background knowledge to a CPDAG or PDAG + > ### Aliases: addBgKnowledge + > ### Keywords: models + > + > ### ** Examples + > + > ## a -- b -- c + > amat <- matrix(c(0,1,0, 1,0,1, 0,1,0), 3,3) + > colnames(amat) <- rownames(amat) <- letters[1:3] + > ## plot(as(t(amat), "graphNEL")) + > addBgKnowledge(gInput = amat) ## amat is a valid CPDAG + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: addBgKnowledge ... ensure_igraph -> graph.adjacency -> graph.adjacency.dense + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘test_LINGAM.R’ + Running ‘test_addBgKnowledge.R’ + Running the tests in ‘tests/test_addBgKnowledge.R’ failed. + Last 13 lines of output: + duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, + lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, + pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, + tapply, union, unique, unsplit, which.max, which.min + + > cpdag <- dag2cpdag(g) + > ## plot(cpdag) + > cpdag.mat <- t(as(cpdag,"matrix")) ## has correct encoding + > + > ## test 1: using graph, valid + > g1 <- addBgKnowledge(gInput = cpdag, x = 3, y = 5) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: addBgKnowledge ... ensure_igraph -> graph.adjacency -> graph.adjacency.dense + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘vignette2018.Rnw’ + ... + + > amat <- matrix(c(0, 1, 0, 1, 0, 1, 0, 1, 0), 3, 3) + + > colnames(amat) <- rownames(amat) <- letters[1:3] + + > bg <- addBgKnowledge(gInput = amat, x = "a", y = "b") + + When sourcing 'vignette2018.R': + Error: could not find function ".igraph.status" + Execution halted + + ‘vignette2018.Rnw’ using ‘UTF-8’... failed + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 16.7Mb + sub-directories of 1Mb or more: + data 2.1Mb + libs 11.9Mb + ``` + +* checking Rd cross-references ... NOTE + ``` + Packages unavailable to check Rd xrefs: ‘combinat’, ‘unifDAG’ + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘vignette2018.Rnw’ using Sweave + Loading required package: Rgraphviz + Loading required package: graph + Loading required package: BiocGenerics + + Attaching package: 'BiocGenerics' + + The following objects are masked from 'package:stats': + + ... + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + + --- failed re-building 'vignette2018.Rnw' + + SUMMARY: processing the following file failed: + 'vignette2018.Rnw' + + Error: Vignette re-building failed. + Execution halted + ``` + +# pcFactorStan + +
+ +* Version: 1.5.3 +* GitHub: https://github.com/jpritikin/pcFactorStan +* Source code: https://github.com/cran/pcFactorStan +* Date/Publication: 2021-09-25 15:50:02 UTC +* Number of recursive dependencies: 126 + +Run `revdepcheck::cloud_details(, "pcFactorStan")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘pcFactorStan-Ex.R’ failed + The error most likely occurred in: + + > ### Name: filterGraph + > ### Title: Filter graph to remove vertices that are not well connected + > ### Aliases: filterGraph + > + > ### ** Examples + > + > df <- filterGraph(phyActFlowPropensity[,c(paste0('pa',1:2),'predict')]) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: filterGraph ... graph_from_edgelist -> make_graph -> do.call -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 6. └─igraph (local) ``(``, directed = FALSE) + ── Error ('test-7report.R:62:3'): parInterval+parDistributionFor ─────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─pcFactorStan::prepData(phyActFlowPropensity[, c(1, 2, 3)]) at test-7report.R:62:2 + 2. └─pcFactorStan::filterGraph(df) + 3. └─igraph::graph_from_edgelist(el, directed = FALSE) + 4. └─igraph::make_graph(unname(ids[t(el)]), directed = directed) + 5. ├─base::do.call(old_graph, args) + 6. └─igraph (local) ``(``, directed = FALSE) + + [ FAIL 5 | WARN 0 | SKIP 5 | PASS 53 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 300.1Mb + sub-directories of 1Mb or more: + doc 2.9Mb + libs 296.5Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘rstantools’ + All declared Imports should be used. + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# pedtools + +
+ +* Version: 2.2.0 +* GitHub: https://github.com/magnusdv/pedtools +* Source code: https://github.com/cran/pedtools +* Date/Publication: 2023-05-25 10:40:02 UTC +* Number of recursive dependencies: 77 + +Run `revdepcheck::cloud_details(, "pedtools")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘pedtools-Ex.R’ failed + The error most likely occurred in: + + > ### Name: inbreedingLoops + > ### Title: Pedigree loops + > ### Aliases: inbreedingLoops breakLoops tieLoops findLoopBreakers + > ### findLoopBreakers2 + > + > ### ** Examples + > + ... + + plot(y2) + + + + # Or loop breakers chosen by user + + y3 = breakLoops(y, 6:7) + + plot(y3) + + } + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: findLoopBreakers2 ... -> make_graph -> do.call -> + Execution halted + ``` + +## In both + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-founder-inbreeding.R:24:3'): setFounderInbreeding works on lists ── + fi(y1) not equal to c(`1` = 1, `2` = 1, `4` = 1). + 3/3 mismatches (average diff: 1) + [1] 0 - 1 == -1 + [2] 0 - 1 == -1 + [3] 0 - 1 == -1 + ── Failure ('test-founder-inbreeding.R:27:3'): setFounderInbreeding works on lists ── + fi(y2) not equal to c(`1` = 0, `2` = 1, `4` = 0). + 1/3 mismatches + [2] 0 - 1 == -1 + + [ FAIL 2 | WARN 0 | SKIP 2 | PASS 595 ] + Error: Test failures + Execution halted + ``` + +# perturbR + +
+ +* Version: 0.1.3 +* GitHub: NA +* Source code: https://github.com/cran/perturbR +* Date/Publication: 2019-02-19 09:30:03 UTC +* Number of recursive dependencies: 54 + +Run `revdepcheck::cloud_details(, "perturbR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘perturbR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: perturbR + > ### Title: Perturb networks and evaluate subgroup structures. + > ### Aliases: perturbR evalClust + > + > ### ** Examples + > + > perturbR(exampledata, plot=FALSE, resolution=0.10, reps=1, errbars = FALSE) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: perturbR -> graph.adjacency -> graph.adjacency.dense + Execution halted + ``` + +# pGRN + +
+ +* Version: 0.3.5 +* GitHub: NA +* Source code: https://github.com/cran/pGRN +* Date/Publication: 2023-01-17 17:20:02 UTC +* Number of recursive dependencies: 94 + +Run `revdepcheck::cloud_details(, "pGRN")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘pGRN-Ex.R’ failed + The error most likely occurred in: + + > ### Name: get_networks + > ### Title: Get the list of sub-networks + > ### Aliases: get_networks + > + > ### ** Examples + > + > example_data <- pGRNDB + ... + > pseudotime_list <- example_data[["ptime"]]$PseudoTime + > dtw_dist_matrix <- get_dtw_dist_mat(expression_matrix, + + pseudotime_list, + + cores=1) + > adj_df <- matrix2adj(dtw_dist_matrix) + > get_networks(adj_df,network_min_genes=5) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: get_networks ... as_graph_edge_df -> graph_from_data_frame -> make_empty_graph + Execution halted + ``` + +# phangorn + +
+ +* Version: 2.11.1 +* GitHub: https://github.com/KlausVigo/phangorn +* Source code: https://github.com/cran/phangorn +* Date/Publication: 2023-01-23 10:10:02 UTC +* Number of recursive dependencies: 67 + +Run `revdepcheck::cloud_details(, "phangorn")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘phangorn-Ex.R’ failed + The error most likely occurred in: + + > ### Name: addConfidences + > ### Title: Compare splits and add support values to an object + > ### Aliases: addConfidences addConfidences.phylo presenceAbsence + > ### createLabel + > ### Keywords: cluster + > + > ### ** Examples + ... + + "extdata/trees/RAxML_bootstrap.woodmouse", package="phangorn")) + > boot_trees <- read.tree(tmpfile) + > + > dm <- dist.ml(woodmouse) + > tree <- upgma(dm) + > nnet <- neighborNet(dm) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: neighborNet ... as.networx.splits -> circNetwork -> graph -> do.call -> + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘AdvancedFeatures.Rmd’ using rmarkdown + --- finished re-building ‘AdvancedFeatures.Rmd’ + + --- re-building ‘Ancestral.Rmd’ using rmarkdown + --- finished re-building ‘Ancestral.Rmd’ + + --- re-building ‘IntertwiningTreesAndNetworks.Rmd’ using rmarkdown + + Quitting from lines 76-101 [unnamed-chunk-3] (IntertwiningTreesAndNetworks.Rmd) + ... + Error: processing vignette 'Trees.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘Trees.Rmd’ + + SUMMARY: processing the following files failed: + ‘IntertwiningTreesAndNetworks.Rmd’ ‘MLbyHand.Rmd’ ‘Networx.Rmd’ + ‘Trees.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 9.8Mb + sub-directories of 1Mb or more: + doc 1.5Mb + libs 5.8Mb + ``` + +# PhaseTypeR + +
+ +* Version: 1.0.4 +* GitHub: https://github.com/rivasiker/PhaseTypeR +* Source code: https://github.com/cran/PhaseTypeR +* Date/Publication: 2022-07-21 16:20:05 UTC +* Number of recursive dependencies: 62 + +Run `revdepcheck::cloud_details(, "PhaseTypeR")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Backtrace: + ▆ + 1. ├─testthat::expect_warning(...) at test-phase_type_to_network.R:33:4 + 2. │ └─testthat:::expect_condition_matching(...) + 3. │ └─testthat:::quasi_capture(...) + 4. │ ├─testthat (local) .capture(...) + 5. │ │ └─base::withCallingHandlers(...) + 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 7. └─PhaseTypeR::phase_type_to_network(disc_phase_type, 3) + 8. └─igraph::graph_from_data_frame(...) + 9. └─igraph::make_empty_graph(n = 0, directed = directed) + + [ FAIL 5 | WARN 0 | SKIP 8 | PASS 102 ] + Error: Test failures + Execution halted + ``` + +# phyloseqGraphTest + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/jfukuyama/phyloseqGraphTest +* Source code: https://github.com/cran/phyloseqGraphTest +* Date/Publication: 2020-02-07 16:30:02 UTC +* Number of recursive dependencies: 95 + +Run `revdepcheck::cloud_details(, "phyloseqGraphTest")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘phyloseqGraphTest-Ex.R’ failed + The error most likely occurred in: + + > ### Name: graph_perm_test + > ### Title: Performs graph-based permutation tests + > ### Aliases: graph_perm_test + > + > ### ** Examples + > + > library(phyloseq) + > data(enterotype) + > gt = graph_perm_test(enterotype, sampletype = "SeqTech", type = "mst") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: graph_perm_test -> graph.adjacency -> graph.adjacency.dense + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘gt_vignette.Rmd’ using rmarkdown + + Quitting from lines 128-134 [unnamed-chunk-4] (gt_vignette.Rmd) + Error: processing vignette 'gt_vignette.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘gt_vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘gt_vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘intergraph’ + All declared Imports should be used. + ``` + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# phylosignal + +
+ +* Version: 1.3 +* GitHub: NA +* Source code: https://github.com/cran/phylosignal +* Date/Publication: 2020-02-03 20:40:07 UTC +* Number of recursive dependencies: 110 + +Run `revdepcheck::cloud_details(, "phylosignal")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘phylosignal-Ex.R’ failed + The error most likely occurred in: + + > ### Name: graphClust + > ### Title: Phylogenetically constrained clustering + > ### Aliases: graphClust + > + > ### ** Examples + > + > data(navic) + > gC <- graphClust(navic, lim.phylo = 1, lim.trait = 2, scale.lim = FALSE) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: graphClust -> -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.7Mb + sub-directories of 1Mb or more: + help 1.6Mb + libs 2.9Mb + ``` + +# phyloTop + +
+ +* Version: 2.1.2 +* GitHub: https://github.com/MichelleKendall/phyloTop +* Source code: https://github.com/cran/phyloTop +* Date/Publication: 2023-01-24 15:20:02 UTC +* Number of recursive dependencies: 93 + +Run `revdepcheck::cloud_details(, "phyloTop")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘phyloTop-Ex.R’ failed + The error most likely occurred in: + + > ### Name: avgLadder + > ### Title: Average ladder size + > ### Aliases: avgLadder + > + > ### ** Examples + > + > ## Find the average ladder size in a random tree with 20 tips: + > tree <- rtree(20) + > plot(tree) + > avgLadder(tree) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: avgLadder ... graph_from_edgelist -> make_graph -> do.call -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('testbasics.R:11:1'): (code run outside of `test_that()`) ──────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─phyloTop::phyloTop(trees) at testbasics.R:11:0 + 2. └─phyloTop::ladderSizes(treeList[[i]]) + 3. └─igraph::graph_from_edgelist(chEL) + 4. └─igraph::make_graph(unname(ids[t(el)]), directed = directed) + 5. ├─base::do.call(old_graph, args) + 6. └─igraph (local) ``(``, directed = TRUE) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] + Error: Test failures + Execution halted + ``` + +# pkggraph + +
+ +* Version: 0.2.3 +* GitHub: https://github.com/talegari/pkggraph +* Source code: https://github.com/cran/pkggraph +* Date/Publication: 2018-11-15 09:50:03 UTC +* Number of recursive dependencies: 71 + +Run `revdepcheck::cloud_details(, "pkggraph")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘pkggraph-Ex.R’ failed + The error most likely occurred in: + + > ### Name: make_neighborhood_graph + > ### Title: make_neighborhood_graph + > ### Aliases: make_neighborhood_graph + > + > ### ** Examples + > + > pkggraph::init(local = TRUE) + Using 'local' data ... + To fetch data from CRAN over internet, run:`pkggraph::init(local = FALSE)` + Done! + > graph_object <- pkggraph::get_neighborhood("caret") + > pkggraph::make_neighborhood_graph(graph_object) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: -> -> make_empty_graph + Execution halted + ``` + +# PlackettLuce + +
+ +* Version: 0.4.2 +* GitHub: https://github.com/hturner/PlackettLuce +* Source code: https://github.com/cran/PlackettLuce +* Date/Publication: 2022-08-15 07:50:05 UTC +* Number of recursive dependencies: 184 + +Run `revdepcheck::cloud_details(, "PlackettLuce")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘PlackettLuce-Ex.R’ failed + The error most likely occurred in: + + > ### Name: PlackettLuce + > ### Title: Fit a Plackett-Luce Model + > ### Aliases: PlackettLuce + > + > ### ** Examples + > + > # Six partial rankings of four objects, 1 is top rank, e.g + ... + > + > # create rankings object + > R <- as.rankings(R) + > + > # Standard maximum likelihood estimates + > mod_mle <- PlackettLuce(R, npseudo = 0) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: PlackettLuce ... graph_from_adjacency_matrix -> graph.adjacency.dense + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Overview.Rmd’ using rmarkdown + + Quitting from lines 489-491 [unnamed-chunk-7] (Overview.Rmd) + Error: processing vignette 'Overview.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘Overview.Rmd’ + + --- re-building ‘PLADMM.Rmd’ using rmarkdown + ... + Quitting from lines 124-126 [unnamed-chunk-5] (PLADMM.Rmd) + Error: processing vignette 'PLADMM.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘PLADMM.Rmd’ + + SUMMARY: processing the following files failed: + ‘Overview.Rmd’ ‘PLADMM.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 2. └─PlackettLuce::connectivity(X, verbose = FALSE) + 3. └─igraph::graph_from_adjacency_matrix(x > 0L) + 4. └─igraph:::graph.adjacency.dense(...) + ── Error ('test-weights.R:35:5'): (code run outside of `test_that()`) ────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─PlackettLuce::PlackettLuce(R, npseudo = 0) at test-weights.R:35:4 + 2. └─PlackettLuce::connectivity(X, verbose = FALSE) + 3. └─igraph::graph_from_adjacency_matrix(x > 0L) + 4. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 19 | WARN 0 | SKIP 11 | PASS 104 ] + Error: Test failures + Execution halted + ``` + +# plantTracker + +
+ +* Version: 1.1.0 +* GitHub: https://github.com/aestears/plantTracker +* Source code: https://github.com/cran/plantTracker +* Date/Publication: 2023-05-05 18:20:02 UTC +* Number of recursive dependencies: 86 + +Run `revdepcheck::cloud_details(, "plantTracker")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘plantTracker-Ex.R’ failed + The error most likely occurred in: + + > ### Name: aggregateByGenet + > ### Title: aggregateByGenet + > ### Aliases: aggregateByGenet + > + > ### ** Examples + > + > dat <- grasslandData[grasslandData$Site == c("AZ") & + ... + + aggByGenet = FALSE + + ) + Site: AZ + + -- Quadrat: SG2 + + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: trackSpp ... graph.adjacency.sparse -> make_graph -> do.call -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 1. └─plantTracker::trackSpp(...) at test-trackSpp.R:5:0 + 2. └─plantTracker:::assign(...) + 3. └─plantTracker (local) ifClonal(cloneDat = tempPreviousYear, clonal = clonal, buffGenet = buffGenet) + 4. └─plantTracker::groupByGenet(cloneDat, buffGenet) + 5. ├─igraph::clusters(...) + 6. │ └─igraph:::ensure_igraph(graph) + 7. └─igraph::graph_from_adjacency_matrix(methods::as(connects, "lMatrix")) + 8. └─igraph:::graph.adjacency.sparse(...) + 9. └─igraph::make_graph(n = vc, edges, directed = (mode == "directed")) + 10. ├─base::do.call(old_graph, args) + 11. └─igraph (local) ``(``, n = 11L, directed = TRUE) + + [ FAIL 9 | WARN 0 | SKIP 0 | PASS 3 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘Suggested_plantTracker_Workflow.Rmd’ using rmarkdown + Warning in check_pandoc_version(minimum = "2.0.0", recommend = "2.7.2") : + minidown supports Pandoc >= 2.7.2 Pandoc with older versions may result in unexpected behaviors. + Warning in options[opts_class] <- Map(code_folding_class, options[opts_class], : + number of items to replace is not a multiple of replacement length + Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr], : + number of items to replace is not a multiple of replacement length + Warning in options[opts_class] <- Map(code_folding_class, options[opts_class], : + number of items to replace is not a multiple of replacement length + ... + Error: processing vignette 'Using_the_plantTracker_trackSpp_function.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘Using_the_plantTracker_trackSpp_function.Rmd’ + + SUMMARY: processing the following files failed: + ‘Suggested_plantTracker_Workflow.Rmd’ + ‘Using_the_plantTracker_trackSpp_function.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# plinkQC + +
+ +* Version: 0.3.4 +* GitHub: https://github.com/meyer-lab-cshl/plinkQC +* Source code: https://github.com/cran/plinkQC +* Date/Publication: 2021-07-15 15:40:02 UTC +* Number of recursive dependencies: 90 + +Run `revdepcheck::cloud_details(, "plinkQC")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 4. └─igraph::graph_from_data_frame(combination, directed = FALSE) + 5. └─igraph::make_empty_graph(n = 0, directed = directed) + ── Error ('test-utils.R:165:5'): relatednessFilter only returns one fail ID for 4-way relatedness ── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─plinkQC::relatednessFilter(...) at test-utils.R:165:4 + 2. └─base::lapply(...) + 3. └─plinkQC (local) FUN(X[[i]], ...) + 4. └─igraph::graph_from_data_frame(combination, directed = FALSE) + 5. └─igraph::make_empty_graph(n = 0, directed = directed) + + [ FAIL 5 | WARN 8 | SKIP 0 | PASS 69 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘AncestryCheck.Rmd’ using rmarkdown + A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TinyTeX with tinytex::reinstall_tinytex(repository = "illinois"). + + tlmgr: Local TeX Live (2022) is older than remote repository (2023). + Cross release updates are only supported with + update-tlmgr-latest(.sh/.exe) --update + See https://tug.org/texlive/upgrade.html for details. + Warning in system2("tlmgr", args, ...) : + running command ''tlmgr' search --file --global '/grffile.sty'' had status 1 + ... + + Error: processing vignette 'plinkQC.Rmd' failed with diagnostics: + LaTeX failed to compile /tmp/workdir/plinkQC/new/plinkQC.Rcheck/vign_test/plinkQC/vignettes/plinkQC.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See plinkQC.log for more info. + --- failed re-building ‘plinkQC.Rmd’ + + SUMMARY: processing the following files failed: + ‘AncestryCheck.Rmd’ ‘Genomes1000.Rmd’ ‘HapMap.Rmd’ ‘plinkQC.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# PLNmodels + +
+ +* Version: 1.0.1 +* GitHub: https://github.com/pln-team/PLNmodels +* Source code: https://github.com/cran/PLNmodels +* Date/Publication: 2023-02-12 14:42:07 UTC +* Number of recursive dependencies: 147 + +Run `revdepcheck::cloud_details(, "PLNmodels")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. ├─testthat::expect_true(...) at test-plnnetworkfit.R:45:2 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. ├─igraph::is.igraph(myPLNfit$plot_network(output = "igraph", plot = FALSE)) + 5. └─myPLNfit$plot_network(output = "igraph", plot = FALSE) + 6. └─igraph::graph_from_adjacency_matrix(...) + 7. └─igraph:::graph.adjacency.sparse(...) + 8. └─igraph::make_empty_graph(n = vc, directed = (mode == "directed")) + + [ FAIL 1 | WARN 4 | SKIP 0 | PASS 716 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘Import_data.Rmd’ using rmarkdown + --- finished re-building ‘Import_data.Rmd’ + + --- re-building ‘PLN.Rmd’ using rmarkdown + --- finished re-building ‘PLN.Rmd’ + + --- re-building ‘PLNLDA.Rmd’ using rmarkdown + --- finished re-building ‘PLNLDA.Rmd’ + + ... + --- failed re-building ‘PLNnetwork.Rmd’ + + --- re-building ‘Trichoptera.Rmd’ using rmarkdown + --- finished re-building ‘Trichoptera.Rmd’ + + SUMMARY: processing the following file failed: + ‘PLNnetwork.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 25.2Mb + sub-directories of 1Mb or more: + doc 2.2Mb + libs 21.6Mb + ``` + +# pmd + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/yufree/pmd +* Source code: https://github.com/cran/pmd +* Date/Publication: 2021-01-21 23:20:08 UTC +* Number of recursive dependencies: 122 + +Run `revdepcheck::cloud_details(, "pmd")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘pmd-Ex.R’ failed + The error most likely occurred in: + + > ### Name: getcda + > ### Title: Perform correlation directed analysis for peaks list. + > ### Aliases: getcda + > + > ### ** Examples + > + > data(spmeinvivo) + > cluster <- getcorcluster(spmeinvivo) + 75 retention time cluster found. + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: getcorcluster -> -> make_empty_graph + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘globalstd.Rmd’ using rmarkdown + + Quitting from lines 151-161 [comp] (globalstd.Rmd) + Error: processing vignette 'globalstd.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘globalstd.Rmd’ + + --- re-building ‘reactomics.Rmd’ using rmarkdown + --- finished re-building ‘reactomics.Rmd’ + + SUMMARY: processing the following file failed: + ‘globalstd.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 62 marked UTF-8 strings + ``` + +# PNAR + +
+ +* Version: 1.4 +* GitHub: NA +* Source code: https://github.com/cran/PNAR +* Date/Publication: 2023-05-12 07:20:06 UTC +* Number of recursive dependencies: 47 + +Run `revdepcheck::cloud_details(, "PNAR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘PNAR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: adja + > ### Title: Generation of a network from the Stochastic Block Model + > ### Aliases: adja + > + > ### ** Examples + > + > W <- adja(N = 20, K = 5, alpha = 0.1) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: adja -> + Execution halted + ``` + +# polymapR + +
+ +* Version: 1.1.3 +* GitHub: NA +* Source code: https://github.com/cran/polymapR +* Date/Publication: 2023-03-13 17:20:02 UTC +* Number of recursive dependencies: 198 + +Run `revdepcheck::cloud_details(, "polymapR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘polymapR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: bridgeHomologues + > ### Title: Use bridge markers to cluster homologues into linkage groups + > ### Aliases: bridgeHomologues assembleDuplexLinks + > + > ### ** Examples + > + > data("P1_homologues", "P2_homologues", "SN_DN_P1", "SN_SS_P1", "SN_SS_P2") + ... + > ChHomDf<-bridgeHomologues(cluster_stack = P1_homologues[["5"]], + + linkage_df=SN_DN_P1, + + LOD_threshold=4, + + automatic_clustering=TRUE, + + LG_number=5, + + parentname="P1") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: bridgeHomologues -> -> make_empty_graph + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Vignette_genotype_probabilities.Rmd’ using rmarkdown + --- finished re-building ‘Vignette_genotype_probabilities.Rmd’ + + --- re-building ‘Vignette_polymapR.Rmd’ using rmarkdown + + Quitting from lines 242-246 [unnamed-chunk-18] (Vignette_polymapR.Rmd) + Error: processing vignette 'Vignette_polymapR.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘Vignette_polymapR.Rmd’ + + SUMMARY: processing the following file failed: + ‘Vignette_polymapR.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 12.2Mb + sub-directories of 1Mb or more: + R 6.5Mb + data 4.6Mb + ``` + +# polyqtlR + +
+ +* Version: 0.0.9 +* GitHub: NA +* Source code: https://github.com/cran/polyqtlR +* Date/Publication: 2022-02-02 16:40:02 UTC +* Number of recursive dependencies: 182 + +Run `revdepcheck::cloud_details(, "polyqtlR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘polyqtlR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: visualisePairing + > ### Title: Visualise pairing of parental homologues + > ### Aliases: visualisePairing + > + > ### ** Examples + > + > data("mr.ls") + > visualisePairing(meiosis_report.ls = mr.ls, + + parent = "P1", + + datawidemax = 3) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: visualisePairing ... setNames -> lapply -> FUN -> -> make_empty_graph + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘polyqtlR_vignette.rmd’ using rmarkdown + + Quitting from lines 694-698 [unnamed-chunk-63] (polyqtlR_vignette.rmd) + Error: processing vignette 'polyqtlR_vignette.rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘polyqtlR_vignette.rmd’ + + SUMMARY: processing the following file failed: + ‘polyqtlR_vignette.rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.0Mb + sub-directories of 1Mb or more: + data 2.6Mb + doc 1.7Mb + libs 2.2Mb + ``` + +# pomdp + +
+ +* Version: 1.1.0 +* GitHub: https://github.com/mhahsler/pomdp +* Source code: https://github.com/cran/pomdp +* Date/Publication: 2023-01-24 15:40:10 UTC +* Number of recursive dependencies: 77 + +Run `revdepcheck::cloud_details(, "pomdp")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘POMDP.Rmd’ using rmarkdown + + Quitting from lines 376-377 [unnamed-chunk-11] (POMDP.Rmd) + Error: processing vignette 'POMDP.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘POMDP.Rmd’ + + SUMMARY: processing the following file failed: + ‘POMDP.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking examples ... ERROR + ``` + Running examples in ‘pomdp-Ex.R’ failed + The error most likely occurred in: + + > ### Name: MDP + > ### Title: Define an MDP Problem + > ### Aliases: MDP MDP2POMDP is_solved_MDP + > + > ### ** Examples + > + > # Michael's Sleepy Tiger Problem is like the POMDP Tiger problem, but + ... + Horizon: Inf epochs + Size: 2 states / 3 actions + + List components: ‘name’, ‘discount’, ‘horizon’, ‘states’, ‘actions’, + ‘transition_prob’, ‘reward’, ‘start’ + > + > sol <- solve_MDP(STiger, eps = 1e-7) + Error in P[[a]][s, ] : no 'dimnames' attribute for array + Calls: solve_MDP ... MDP_value_iteration_inf_horizon -> outer -> FUN -> do.call -> mapply -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─pomdp::plot_policy_graph(sol) at test-solve_POMDP.R:9:0 + 2. └─pomdp:::.plot.igraph(...) + 3. └─pomdp::policy_graph(...) + 4. └─pomdp:::policy_graph_converged(...) + 5. └─igraph::graph.edgelist(as.matrix(l[, 1:2])) + 6. └─igraph::make_graph(t(el), directed = directed) + 7. ├─base::do.call(old_graph, args) + 8. └─igraph (local) ``(``, directed = TRUE) + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 58 ] + Error: Test failures + Execution halted + ``` + +* checking installed package size ... NOTE + ``` + installed size is 6.5Mb + sub-directories of 1Mb or more: + libs 5.6Mb + ``` + +# pop + +
+ +* Version: 0.1 +* GitHub: NA +* Source code: https://github.com/cran/pop +* Date/Publication: 2016-06-07 06:26:35 +* Number of recursive dependencies: 40 + +Run `revdepcheck::cloud_details(, "pop")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘pop-Ex.R’ failed + The error most likely occurred in: + + > ### Name: dynamic + > ### Title: dynamic objects + > ### Aliases: as.matrix.dynamic dynamic is.dynamic parameters.dynamic + > ### parameters<-.dynamic plot.dynamic print.dynamic states + > + > ### ** Examples + > + ... + > # combine these into one dynamic (the same as listing all the transitions + > # separately) + > all <- dynamic(stasis, growth, reproduction) + > + > # plot these + > plot(stasis) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot ... plot.dynamic -> graph.adjacency -> graph.adjacency.dense + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘test-all.R’ + Running the tests in ‘tests/test-all.R’ failed. + Last 13 lines of output: + • On CRAN (1) + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test_dynamic_class.R:143:3'): dynamic classes work ────────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. ├─base::plot(stasis) at test_dynamic_class.R:143:2 + 2. └─pop:::plot.dynamic(stasis) + 3. └─igraph::graph.adjacency(linkmat, weighted = TRUE) + 4. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 1 | WARN 0 | SKIP 1 | PASS 212 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# poppr + +
+ +* Version: 2.9.4 +* GitHub: https://github.com/grunwaldlab/poppr +* Source code: https://github.com/cran/poppr +* Date/Publication: 2023-03-23 03:20:02 UTC +* Number of recursive dependencies: 98 + +Run `revdepcheck::cloud_details(, "poppr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘poppr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: bruvo.msn + > ### Title: Create minimum spanning network of selected populations using + > ### Bruvo's distance. + > ### Aliases: bruvo.msn msn.bruvo + > + > ### ** Examples + > + ... + > # Load the data set. + > data(nancycats) + > + > # View populations 8 and 9 with default colors. + > bruvo.msn(nancycats, replen = rep(2, 9), sublist=8:9, vertex.label="inds", + + vertex.label.cex=0.7, vertex.label.dist=0.4) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: bruvo.msn ... msn_constructor -> graph.adjacency -> graph.adjacency.dense + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘test-all.R’ + Running the tests in ‘tests/test-all.R’ failed. + Last 13 lines of output: + 2. └─poppr:::msn_constructor(...) + 3. └─igraph::graph.adjacency(indist, weighted = TRUE, mode = "undirected") + 4. └─igraph:::graph.adjacency.dense(...) + ── Error ('test-msn.R:118:1'): (code run outside of `test_that()`) ───────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─poppr::bruvo.msn(gend, replen = c(1, 1), showplot = FALSE) at test-msn.R:118:0 + 2. └─poppr:::msn_constructor(...) + 3. └─igraph::graph.adjacency(indist, weighted = TRUE, mode = "undirected") + 4. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 2 | WARN 0 | SKIP 166 | PASS 332 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘algo.Rnw’ using knitr + Error: processing vignette 'algo.Rnw' failed with diagnostics: + Running 'texi2dvi' on 'algo.tex' failed. + LaTeX errors: + ! LaTeX Error: File `colortbl.sty' not found. + + Type X to quit or to proceed, + or enter new name. (Default extension: sty) + ... + l.270 \long + \def\@secondoffive#1#2#3#4#5{#2}^^M + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘algo.Rnw’ + + SUMMARY: processing the following file failed: + ‘algo.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# POSetR + +
+ +* Version: 1.1.1 +* GitHub: NA +* Source code: https://github.com/cran/POSetR +* Date/Publication: 2023-01-17 10:40:02 UTC +* Number of recursive dependencies: 10 + +Run `revdepcheck::cloud_details(, "POSetR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘POSetR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: intersection + > ### Title: Intersection of two posets + > ### Aliases: intersection %it% + > + > ### ** Examples + > + > dom <- matrix(c( + ... + + "a", "b", + + "c", "b", + + "b", "d" + + ), ncol = 2, byrow = TRUE) + > p <- poset(x = dom) + > plot(p) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot -> plot.poset -> -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 26.0Mb + sub-directories of 1Mb or more: + libs 25.8Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘Rdpack’ + All declared Imports should be used. + ``` + +# ProjectManagement + +
+ +* Version: 1.4.7 +* GitHub: NA +* Source code: https://github.com/cran/ProjectManagement +* Date/Publication: 2022-09-19 08:26:16 UTC +* Number of recursive dependencies: 83 + +Run `revdepcheck::cloud_details(, "ProjectManagement")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ProjectManagement-Ex.R’ failed + The error most likely occurred in: + + > ### Name: dag.plot + > ### Title: DAG plot + > ### Aliases: dag.plot + > + > ### ** Examples + > + > + > prec1and2<-matrix(c(0,1,0,2,0,0,0,0,0,1,0,0,0,1,0,0,0,0,0,0,0,0,0,2,0),nrow=5,ncol=5,byrow=TRUE) + > prec3and4<-matrix(0,nrow=5,ncol=5) + > prec3and4[3,1]<-3 + > dag.plot(prec1and2,prec3and4) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: dag.plot ... graph_from_adjacency_matrix -> graph.adjacency.dense + Execution halted + ``` + +# provGraphR + +
+ +* Version: 1.0.1 +* GitHub: NA +* Source code: https://github.com/cran/provGraphR +* Date/Publication: 2022-08-17 15:30:02 UTC +* Number of recursive dependencies: 36 + +Run `revdepcheck::cloud_details(, "provGraphR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘provGraphR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: get.lineage + > ### Title: Calculate lineage of a node + > ### Aliases: get.lineage + > + > ### ** Examples + > + > adj.graph <- create.graph(system.file("testdata", "basic.json", package = "provGraphR")) + > get.lineage (adj.graph, "d24") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: get.lineage ... graph.adjacency.sparse -> make_graph -> do.call -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 9. └─igraph (local) ``(``, n = 56L, directed = TRUE) + ── Error ('test_provGraphR.R:115:7'): order ──────────────────────────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─provGraphR::get.lineage(adj.graph, "d4") at test_provGraphR.R:115:6 + 2. └─igraph::graph_from_adjacency_matrix(adj.graph) + 3. └─igraph:::graph.adjacency.sparse(...) + 4. └─igraph::make_graph(n = vc, edges, directed = (mode == "directed")) + 5. ├─base::do.call(old_graph, args) + 6. └─igraph (local) ``(``, n = 10L, directed = TRUE) + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 47 ] + Error: Test failures + Execution halted + ``` + +# ptools + +
+ +* Version: 2.0.0 +* GitHub: https://github.com/apwheele/ptools +* Source code: https://github.com/cran/ptools +* Date/Publication: 2023-02-07 19:02:30 UTC +* Number of recursive dependencies: 82 + +Run `revdepcheck::cloud_details(, "ptools")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ptools-Ex.R’ failed + The error most likely occurred in: + + > ### Name: near_strings1 + > ### Title: Strings of Near Repeats + > ### Aliases: near_strings1 + > + > ### ** Examples + > + > # Simplified example showing two clusters + ... + > s <- c(0,0,0,4,4) + > ccheck <- c(1,1,1,2,2) + > dat <- data.frame(x=1:5,y=0, + + ti=s, + + id=1:5) + > res1 <- near_strings1(dat,'id','x','y','ti',2,1) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: near_strings1 -> -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ▆ + 1. └─ptools::near_strings1(dat, "id", "x", "y", "ti", 1, 1) at test-nearstring.R:34:2 + 2. └─igraph::graph_from_data_frame(...) + 3. └─igraph::make_empty_graph(n = 0, directed = directed) + ── Error ('test-nearstring.R:46:3'): Checking two components ─────────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─ptools::near_strings1(dat, "id", "x", "y", "ti", 2, 1) at test-nearstring.R:46:2 + 2. └─igraph::graph_from_data_frame(...) + 3. └─igraph::make_empty_graph(n = 0, directed = directed) + + [ FAIL 4 | WARN 0 | SKIP 0 | PASS 40 ] + Error: Test failures + Execution halted + ``` + +# qdap + +
+ +* Version: 2.4.6 +* GitHub: https://github.com/trinker/qdap +* Source code: https://github.com/cran/qdap +* Date/Publication: 2023-05-11 06:10:02 UTC +* Number of recursive dependencies: 98 + +Run `revdepcheck::cloud_details(, "qdap")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + |======================================================================| 100% + [ FAIL 1 | WARN 1 | SKIP 0 | PASS 216 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-phrase_net.R:19:5'): phrase_net gives a `phrase_net` and `igraph` object ── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─qdap::phrase_net(sents, r = 0.5) at test-phrase_net.R:19:4 + 2. └─igraph::graph.data.frame(X2, directed = FALSE) + 3. └─igraph::make_empty_graph(n = 0, directed = directed) + + [ FAIL 1 | WARN 1 | SKIP 0 | PASS 216 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘gplots’ + ``` + +# qgraph + +
+ +* Version: 1.9.5 +* GitHub: https://github.com/SachaEpskamp/qgraph +* Source code: https://github.com/cran/qgraph +* Date/Publication: 2023-05-16 10:10:02 UTC +* Number of recursive dependencies: 89 + +Run `revdepcheck::cloud_details(, "qgraph")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘qgraph-Ex.R’ failed + The error most likely occurred in: + + > ### Name: centrality + > ### Title: Centrality statistics of graphs + > ### Aliases: centrality + > ### Keywords: graphs + > + > ### ** Examples + > + > set.seed(1) + > adj <- matrix(sample(0:1,10^2,TRUE,prob=c(0.8,0.2)),nrow=10,ncol=10) + > Q <- qgraph(adj) + > + > centrality(Q) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: centrality -> -> graph.adjacency.dense + Execution halted + ``` + +# R.temis + +
+ +* Version: 0.1.3 +* GitHub: https://github.com/nalimilan/R.TeMiS +* Source code: https://github.com/cran/R.temis +* Date/Publication: 2021-05-12 19:02:12 UTC +* Number of recursive dependencies: 135 + +Run `revdepcheck::cloud_details(, "R.temis")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘R.temis-Ex.R’ failed + The error most likely occurred in: + + > ### Name: terms_graph + > ### Title: terms_graph + > ### Aliases: terms_graph + > + > ### ** Examples + > + > + > file <- system.file("texts", "reut21578-factiva.xml", package="tm.plugin.factiva") + > corpus <- import_corpus(file, "factiva", language="en") + > dtm <- build_dtm(corpus) + > terms_graph(dtm, 100, 3) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: terms_graph -> -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘testthat’ + All declared Imports should be used. + ``` + +# R6causal + +
+ +* Version: 0.7.0 +* GitHub: NA +* Source code: https://github.com/cran/R6causal +* Date/Publication: 2022-11-04 08:00:02 UTC +* Number of recursive dependencies: 98 + +Run `revdepcheck::cloud_details(, "R6causal")` for more info + +
+ +## Newly broken + +* checking whether package ‘R6causal’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/R6causal/new/R6causal.Rcheck/00install.out’ for details. + ``` + +## Newly fixed + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘using_R6causal.Rmd’ using rmarkdown + A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TinyTeX with tinytex::reinstall_tinytex(repository = "illinois"). + + tlmgr: Local TeX Live (2022) is older than remote repository (2023). + Cross release updates are only supported with + update-tlmgr-latest(.sh/.exe) --update + See https://tug.org/texlive/upgrade.html for details. + Warning in system2("tlmgr", args, ...) : + ... + + Error: processing vignette 'using_R6causal.Rmd' failed with diagnostics: + LaTeX failed to compile /tmp/workdir/R6causal/old/R6causal.Rcheck/vign_test/R6causal/vignettes/using_R6causal.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See using_R6causal.log for more info. + --- failed re-building ‘using_R6causal.Rmd’ + + SUMMARY: processing the following file failed: + ‘using_R6causal.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘R6causal’ ... +** package ‘R6causal’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" +Error: unable to load R code in package ‘R6causal’ +Execution halted +ERROR: lazy loading failed for package ‘R6causal’ +* removing ‘/tmp/workdir/R6causal/new/R6causal.Rcheck/R6causal’ + + +``` +### CRAN + +``` +* installing *source* package ‘R6causal’ ... +** package ‘R6causal’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +** help +*** installing help indices +** building package indices +** installing vignettes +** testing if installed package can be loaded from temporary location +** testing if installed package can be loaded from final location +** testing if installed package keeps a record of temporary installation path +* DONE (R6causal) + + +``` +# RaceID + +
+ +* Version: 0.3.0 +* GitHub: NA +* Source code: https://github.com/cran/RaceID +* Date/Publication: 2023-03-13 12:10:02 UTC +* Number of recursive dependencies: 157 + +Run `revdepcheck::cloud_details(, "RaceID")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘RaceID-Ex.R’ failed + The error most likely occurred in: + + > ### Name: compfr + > ### Title: Computation of a two dimensional Fruchterman-Rheingold + > ### representation + > ### Aliases: compfr + > + > ### ** Examples + > + ... + determine final clustering partition 2 + determine final clustering partition 3 + determine final clustering partition 4 + determine final clustering partition 5 + determine final clustering partition 6 + > sc <- compfr(sc) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: compfr ... graph_from_adjacency_matrix -> graph.adjacency.dense + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘RaceID.Rmd’ using rmarkdown + + Quitting from lines 119-120 [unnamed-chunk-17] (RaceID.Rmd) + Error: processing vignette 'RaceID.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘RaceID.Rmd’ + + SUMMARY: processing the following file failed: + ‘RaceID.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 12.1Mb + sub-directories of 1Mb or more: + data 2.1Mb + doc 6.6Mb + libs 2.6Mb + ``` + +# rags2ridges + +
+ +* Version: 2.2.6 +* GitHub: https://github.com/CFWP/rags2ridges +* Source code: https://github.com/cran/rags2ridges +* Date/Publication: 2022-05-01 14:40:02 UTC +* Number of recursive dependencies: 103 + +Run `revdepcheck::cloud_details(, "rags2ridges")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘rags2ridges-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Communities + > ### Title: Search and visualize community-structures + > ### Aliases: Communities + > + > ### ** Examples + > + > + ... + - Retained elements: 11 + - Corresponding to 3.67 % of possible edges + + > + > ## Search and visualize communities + > Commy <- Communities(PC0) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: Communities -> graph.adjacency -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.6Mb + sub-directories of 1Mb or more: + libs 6.4Mb + ``` + +# RavenR + +
+ +* Version: 2.2.0 +* GitHub: https://github.com/rchlumsk/RavenR +* Source code: https://github.com/cran/RavenR +* Date/Publication: 2022-10-28 21:02:50 UTC +* Number of recursive dependencies: 141 + +Run `revdepcheck::cloud_details(, "RavenR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘RavenR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: rvn_calc_runoff_coeff + > ### Title: Generate runoff coefficients upstream of gauges + > ### Aliases: rvn_calc_runoff_coeff + > + > ### ** Examples + > + > myrvh <- system.file("extdata","Nith.rvh", package="RavenR") + > mycust <- system.file("extdata", "run1_PRECIP_Daily_Average_BySubbasin.csv", package="RavenR") + > myhyd <- system.file("extdata", "run1_Hydrographs.csv", package="RavenR") + > + > rcs <- rvn_calc_runoff_coeff(myrvh, mycust, myhyd, correct=TRUE) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: rvn_calc_runoff_coeff ... rvn_rvh_read -> graph_from_data_frame -> make_empty_graph + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Introduction_to_RavenR.Rmd’ using rmarkdown + + Quitting from lines 213-217 [RVI connection plot example] (Introduction_to_RavenR.Rmd) + Error: processing vignette 'Introduction_to_RavenR.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘Introduction_to_RavenR.Rmd’ + + SUMMARY: processing the following file failed: + ‘Introduction_to_RavenR.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# rcrimeanalysis + +
+ +* Version: 0.5.0 +* GitHub: NA +* Source code: https://github.com/cran/rcrimeanalysis +* Date/Publication: 2023-05-18 21:50:02 UTC +* Number of recursive dependencies: 104 + +Run `revdepcheck::cloud_details(, "rcrimeanalysis")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘rcrimeanalysis-Ex.R’ failed + The error most likely occurred in: + + > ### Name: near_repeat_analysis + > ### Title: Near Repeat Analysis of Crime Incidents with Crime Linkage + > ### Output + > ### Aliases: near_repeat_analysis + > ### Keywords: spatial + > + > ### ** Examples + > + > data(crimes) + > nr_data <- head(crimes, n = 1000) #truncate dataset for near repeat analysis + > out <- near_repeat_analysis(data=nr_data,tz="America/Chicago",epsg="32616") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: near_repeat_analysis -> -> graph.adjacency.dense + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘rcrimeanalysis.Rmd’ using rmarkdown + + Quitting from lines 157-162 [unnamed-chunk-8] (rcrimeanalysis.Rmd) + Error: processing vignette 'rcrimeanalysis.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘rcrimeanalysis.Rmd’ + + SUMMARY: processing the following file failed: + ‘rcrimeanalysis.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# rD3plot + +
+ +* Version: 1.0.68 +* GitHub: NA +* Source code: https://github.com/cran/rD3plot +* Date/Publication: 2023-03-22 16:50:10 UTC +* Number of recursive dependencies: 49 + +Run `revdepcheck::cloud_details(, "rD3plot")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘rD3plot-Ex.R’ failed + The error most likely occurred in: + + > ### Name: rd3_fromIgraph + > ### Title: Produce interactive networks from 'igraph' objects. + > ### Aliases: rd3_fromIgraph + > + > ### ** Examples + > + > g <- igraph::make_ring(10) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: + Execution halted + ``` + +# RDS + +
+ +* Version: 0.9-6 +* GitHub: NA +* Source code: https://github.com/cran/RDS +* Date/Publication: 2023-02-10 18:20:02 UTC +* Number of recursive dependencies: 106 + +Run `revdepcheck::cloud_details(, "RDS")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘RDS-Ex.R’ failed + The error most likely occurred in: + + > ### Name: read.rdsat + > ### Title: Import data from the 'RDSAT' format as an 'rds.data.frame' + > ### Aliases: read.rdsat + > + > ### ** Examples + > + > fn <- paste0(path.package("RDS"),"/extdata/nyjazz.rdsat") + > rd <- read.rdsat(fn) + > plot(rd) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot ... -> make_graph -> do.call -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘tests.R’ + Running the tests in ‘tests/tests.R’ failed. + Complete output: + > + > + > library(testthat) + > library(RDS) + > + > test_check("RDS") + Killed + ``` + +# readsdr + +
+ +* Version: 0.2.0 +* GitHub: https://github.com/jandraor/readsdr +* Source code: https://github.com/cran/readsdr +* Date/Publication: 2021-01-08 16:00:02 UTC +* Number of recursive dependencies: 74 + +Run `revdepcheck::cloud_details(, "readsdr")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + > + > test_check("readsdr") + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 252 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-generate_igraph_inputs.R:28:3'): get_igraph_inputs() valid inputs for igraph ── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─igraph::graph_from_data_frame(...) at test-generate_igraph_inputs.R:28:2 + 2. └─igraph::make_empty_graph(n = 0, directed = directed) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 252 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# ReDaMoR + +
+ +* Version: 0.7.1 +* GitHub: https://github.com/patzaw/ReDaMoR +* Source code: https://github.com/cran/ReDaMoR +* Date/Publication: 2022-10-19 13:47:56 UTC +* Number of recursive dependencies: 86 + +Run `revdepcheck::cloud_details(, "ReDaMoR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ReDaMoR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: df_to_model + > ### Title: Create a RelDataModel object from column names of data frames + > ### Aliases: df_to_model + > + > ### ** Examples + > + > ## Read data files ---- + ... + + list=names(hpo_tables), envir=as.environment(hpo_tables) + + ) + > ## Plot the model ---- + > new_model %>% + + auto_layout(lengthMultiplier=250) %>% + + plot() + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: %>% ... %>% -> -> -> make_empty_graph + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘ReDaMoR.Rmd’ using rmarkdown + + Quitting from lines 383-390 [unnamed-chunk-12] (ReDaMoR.Rmd) + Error: processing vignette 'ReDaMoR.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘ReDaMoR.Rmd’ + + SUMMARY: processing the following file failed: + ‘ReDaMoR.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# refdb + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/fkeck/refdb +* Source code: https://github.com/cran/refdb +* Date/Publication: 2022-09-22 17:00:05 UTC +* Number of recursive dependencies: 163 + +Run `revdepcheck::cloud_details(, "refdb")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘refdb-Ex.R’ failed + The error most likely occurred in: + + > ### Name: refdb_plot_tax_tree + > ### Title: Reference database taxonomy tree + > ### Aliases: refdb_plot_tax_tree + > + > ### ** Examples + > + > lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb")) + ... + Selected rank column for the color: species_name + Warning: There was 1 warning in `dplyr::group_by()`. + ℹ In argument: `dplyr::across()`. + Caused by warning: + ! Using `across()` without supplying `.cols` was deprecated in dplyr 1.1.0. + ℹ Please supply `.cols` instead. + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: refdb_plot_tax_tree ... igraph_from_taxo -> -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ══ Skipped tests ═══════════════════════════════════════════════════════════════ + • On CRAN (1) + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test_plots.R:7:3'): Test plot functions ───────────────────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─refdb:::igraph_from_taxo(test) at test_plots.R:7:2 + 2. └─igraph::graph_from_data_frame(graph_def_edges, vertices = res_tidy) + 3. └─igraph::make_empty_graph(n = 0, directed = directed) + + [ FAIL 1 | WARN 16 | SKIP 1 | PASS 123 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘intro_refdb.Rmd’ using rmarkdown + + Quitting from lines 227-228 [unnamed-chunk-17] (intro_refdb.Rmd) + Error: processing vignette 'intro_refdb.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘intro_refdb.Rmd’ + + --- re-building ‘ncbi_bold.Rmd’ using rmarkdown + --- finished re-building ‘ncbi_bold.Rmd’ + + SUMMARY: processing the following file failed: + ‘intro_refdb.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# RepertoiR + +
+ +* Version: 0.0.1 +* GitHub: https://github.com/systemsbiomed/RepertoiR +* Source code: https://github.com/cran/RepertoiR +* Date/Publication: 2021-10-25 07:00:21 UTC +* Number of recursive dependencies: 45 + +Run `revdepcheck::cloud_details(, "RepertoiR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘RepertoiR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: network + > ### Title: Sequences distance network + > ### Aliases: network + > + > ### ** Examples + > + > + ... + + } + > + > rownames(data) <- aavec + > colnames(data) <- LETTERS[1:ncol(data)] + > + > network(data, by = 3, nrow = 100) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: network ... ensure_igraph -> graph.data.frame -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 9. └─igraph::make_empty_graph(n = 0, directed = directed) + ── Error ('test-sunflower.R:5:3'): check no error has occurred ───────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. ├─testthat::expect_identical(sunflower(data), NULL) at test-sunflower.R:5:2 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. ├─RepertoiR::sunflower(data) + 5. └─RepertoiR:::sunflower.default(data) + 6. └─igraph::make_empty_graph(length(mat)) + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘stringi’ + All declared Imports should be used. + ``` + +# repo + +
+ +* Version: 2.1.5 +* GitHub: NA +* Source code: https://github.com/cran/repo +* Date/Publication: 2020-02-08 16:20:02 UTC +* Number of recursive dependencies: 58 + +Run `revdepcheck::cloud_details(, "repo")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘repo-Ex.R’ failed + The error most likely occurred in: + + > ### Name: repo_dependencies + > ### Title: Build and/or plots a dependency graph + > ### Aliases: repo_dependencies + > + > ### ** Examples + > + > ## Repository creation + ... + item1 0 0 0 0 + item2 1 0 0 0 + item3 1 1 0 0 + temp.pdf 2 0 0 0 + > ## The matrix can be plotted as a graph (requires igraph package) + > rp$dependencies() + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: -> -> graph.adjacency.dense + Execution halted + ``` + +# ResIN + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/pwarncke77/ResIN +* Source code: https://github.com/cran/ResIN +* Date/Publication: 2023-05-10 13:50:06 UTC +* Number of recursive dependencies: 94 + +Run `revdepcheck::cloud_details(, "ResIN")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ResIN-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ResIN + > ### Title: ResIN + > ### Aliases: ResIN + > + > ### ** Examples + > + > + ... + > ## Load the 12-item simulated Likert-type ResIN toy dataset + > data(lik_data) + > library(ggplot2) + > + > # Apply the ResIN function to toy Likert data: + > output <- ResIN(lik_data, cor_method = "spearman", network_stats = TRUE) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: ResIN -> -> graph.adjacency.dense + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘ResIN-VIGNETTE.Rmd’ using rmarkdown + + Quitting from lines 61-65 [run ResIN] (ResIN-VIGNETTE.Rmd) + Error: processing vignette 'ResIN-VIGNETTE.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘ResIN-VIGNETTE.Rmd’ + + SUMMARY: processing the following file failed: + ‘ResIN-VIGNETTE.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# RevEcoR + +
+ +* Version: 0.99.3 +* GitHub: NA +* Source code: https://github.com/cran/RevEcoR +* Date/Publication: 2016-04-03 17:14:01 +* Number of recursive dependencies: 23 + +Run `revdepcheck::cloud_details(, "RevEcoR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘RevEcoR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: reconstructGsMN + > ### Title: Reconstuction of the specific-organism genome-scale metabolic + > ### network + > ### Aliases: reconstructGsMN + > + > ### ** Examples + > + ... + > ## species detected in a human microbiome + > annodir <- system.file("extdata","koanno.tab",package = "RevEcoR") + > metabolic.data <- read.delim2(file=annodir,stringsAsFactors=FALSE) + > ##load the reference metabolic data + > data(RefDbcache) + > g2 <- reconstructGsMN(metabolic.data, RefData = RefDbcache) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: reconstructGsMN -> graph.adjacency -> graph.adjacency.dense + Execution halted + ``` + +# rflexscan + +
+ +* Version: 1.1.0 +* GitHub: NA +* Source code: https://github.com/cran/rflexscan +* Date/Publication: 2023-03-01 08:52:30 UTC +* Number of recursive dependencies: 53 + +Run `revdepcheck::cloud_details(, "rflexscan")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘rflexscan-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.rflexscan + > ### Title: Graph plotting of flexscan results + > ### Aliases: plot.rflexscan + > + > ### ** Examples + > + > # load sample data (North Carolina SIDS data) + ... + + name = rownames(nc.sids), + + clustersize = 10, + + nb = ncCR85.nb) + > + > # display all clusters + > plot(fls) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot ... graph_from_adjacency_matrix -> graph.adjacency.dense + Execution halted + ``` + +# rgexf + +
+ +* Version: 0.16.2 +* GitHub: https://github.com/gvegayon/rgexf +* Source code: https://github.com/cran/rgexf +* Date/Publication: 2021-08-12 21:30:02 UTC +* Number of recursive dependencies: 53 + +Run `revdepcheck::cloud_details(, "rgexf")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘rgexf-Ex.R’ failed + The error most likely occurred in: + + > ### Name: igraph.to.gexf + > ### Title: Converting between 'gexf' and 'igraph' classes + > ### Aliases: igraph.to.gexf gexf.to.igraph + > ### Keywords: manip + > + > ### ** Examples + > + ... + + demo(gexfigraph) + + } + > + > fn <- system.file("gexf-graphs/lesmiserables.gexf", package = "rgexf") + > gexf1 <- read.gexf(fn) + > igraph1 <- gexf.to.igraph(gexf1) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: gexf.to.igraph -> -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘tinytest.R’ + Running the tests in ‘tests/tinytest.R’ failed. + Complete output: + > + > if ( requireNamespace("tinytest", quietly=TRUE) ){ + + tinytest::test_package("rgexf") + + } + + test-bugs.r................... 0 tests Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: ... run_test_dir -> lapply -> FUN -> eval -> eval -> + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘rgexf.Rmd’ using rmarkdown + + Quitting from lines 52-58 [igraph-plot] (rgexf.Rmd) + Error: processing vignette 'rgexf.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘rgexf.Rmd’ + + SUMMARY: processing the following file failed: + ‘rgexf.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# rgraph6 + +
+ +* Version: 2.0-2 +* GitHub: https://github.com/mbojan/rgraph6 +* Source code: https://github.com/cran/rgraph6 +* Date/Publication: 2022-08-25 12:10:02 UTC +* Number of recursive dependencies: 58 + +Run `revdepcheck::cloud_details(, "rgraph6")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘rgraph6-Ex.R’ failed + The error most likely occurred in: + + > ### Name: adjacency_from_text + > ### Title: Create adjacency matrices from 'graph6', 'sparse6', or + > ### 'digraph6' symbols + > ### Aliases: adjacency_from_text + > + > ### ** Examples + > + ... + + > + > # Sparse6 symbols + > s6 <- c(":DgXI@G~", ":DgWCgCb") + > adjacency_from_text(s6) + Loading required namespace: igraph + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: adjacency_from_text ... igraph_from_sparse6 -> lapply -> FUN -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 4. │ │ ├─withr::with_output_sink(...) + 5. │ │ │ └─base::force(code) + 6. │ │ ├─base::withCallingHandlers(...) + 7. │ │ └─base::withVisible(code) + 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 9. └─rgraph6::read_file6(...) + 10. └─rgraph6::adjacency_from_text(txt) + 11. └─rgraph6::igraph_from_sparse6(object[fmt == "sparse6"]) + 12. └─base::lapply(ellist, my_graph_from_edgelist) + 13. └─rgraph6 (local) FUN(X[[i]], ...) + 14. └─igraph::make_empty_graph(attr(el, "gorder"), directed = FALSE) + + [ FAIL 10 | WARN 0 | SKIP 0 | PASS 199 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘rgraph6.Rmd’ using rmarkdown + + Quitting from lines 31-38 [unnamed-chunk-1] (rgraph6.Rmd) + Error: processing vignette 'rgraph6.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘rgraph6.Rmd’ + + SUMMARY: processing the following file failed: + ‘rgraph6.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# rhcoclust + +
+ +* Version: 2.0.0 +* GitHub: NA +* Source code: https://github.com/cran/rhcoclust +* Date/Publication: 2023-01-29 03:40:02 UTC +* Number of recursive dependencies: 36 + +Run `revdepcheck::cloud_details(, "rhcoclust")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘rhcoclust-Ex.R’ failed + The error most likely occurred in: + + > ### Name: rhcoclust_internet + > ### Title: Interaction network (internet) of the 'rhcoclust' objects + > ### Aliases: rhcoclust_internet + > + > ### ** Examples + > + > # Load necessary library + ... + > # Plot interaction network (internet) + > # Please use dev.off() to avoid the figure margin from previous plot + > # mar order: bottom, left, top, and right + > # please use par(mar=c(5,2,5,2)) or modify when necessary to best fit for the plot + > Netrhcoclust <- rhcoclust_internet(data, CoClustObj = CoClustObj, + + CoClust.sig = FALSE, cex.nodes = 0.7, edge.width = 1) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: rhcoclust_internet ... graph_from_edgelist -> make_graph -> do.call -> + Execution halted + ``` + +# rmangal + +
+ +* Version: 2.1.3 +* GitHub: https://github.com/ropensci/rmangal +* Source code: https://github.com/cran/rmangal +* Date/Publication: 2023-03-30 14:10:02 UTC +* Number of recursive dependencies: 140 + +Run `revdepcheck::cloud_details(, "rmangal")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 78 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-get_network_by_id.R:9:3'): get_network_by_id() works ─────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. ├─igraph::as.igraph(mg100) at test-get_network_by_id.R:9:2 + 2. └─rmangal:::as.igraph.mgNetwork(mg100) + 3. └─igraph::graph_from_data_frame(...) + 4. └─igraph::make_empty_graph(n = 0, directed = directed) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 78 ] + Error: Test failures + Execution halted + ``` + +# rmcfs + +
+ +* Version: 1.3.5 +* GitHub: NA +* Source code: https://github.com/cran/rmcfs +* Date/Publication: 2021-09-18 13:30:02 UTC +* Number of recursive dependencies: 65 + +Run `revdepcheck::cloud_details(, "rmcfs")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘test-all.R’ + Running the tests in ‘tests/test-all.R’ failed. + Last 13 lines of output: + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─rmcfs::build.idgraph(result) at test-man.mcfs.R:57:2 + 2. └─igraph::graph.empty() + ── Error ('test-man.plot.idgraph.R:19:3'): man build.idgraph ─────────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─rmcfs::build.idgraph(result, size = 6, size_ID = 12, orphan_nodes = TRUE) at test-man.plot.idgraph.R:19:2 + 2. └─igraph::graph.empty() + + [ FAIL 3 | WARN 4 | SKIP 0 | PASS 35 ] + Error: Test failures + Execution halted + ``` + +# rmonad + +
+ +* Version: 0.7.0 +* GitHub: https://github.com/arendsee/rmonad +* Source code: https://github.com/cran/rmonad +* Date/Publication: 2020-02-14 07:00:02 UTC +* Number of recursive dependencies: 81 + +Run `revdepcheck::cloud_details(, "rmonad")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘rmonad-Ex.R’ failed + The error most likely occurred in: + + > ### Name: clear_cache + > ### Title: Clear cached values and delete temporary files + > ### Aliases: clear_cache + > + > ### ** Examples + > + > 256 %v>% sqrt %>>% sqrt %>>% sqrt -> m + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: %>>% ... as_monad -> Rmonad -> .new_rmonad_graph -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 6. └─igraph::make_empty_graph(directed = TRUE, n = 1) + ── Error (???): view handles failure ─────────────────────────────────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─rmonad (local) ``(as_monad("hi") %>>% sqrt %>% tag("a/f"), log) + 2. └─rmonad (local) entry_lhs_transform(x, f, desc = lhs_str) + 3. └─rmonad::as_monad(m, lossy = TRUE, ...) + 4. └─rmonad:::Rmonad(node_id = paste(key, collapse = "")) + 5. └─rmonad:::.new_rmonad_graph(m, node_id = node_id) + 6. └─igraph::make_empty_graph(directed = TRUE, n = 1) + + [ FAIL 73 | WARN 0 | SKIP 1 | PASS 79 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘cheatsheet.Rmd’ using rmarkdown + --- finished re-building ‘cheatsheet.Rmd’ + + --- re-building ‘gff-processing.Rmd’ using rmarkdown + + Quitting from lines 563-566 [unnamed-chunk-8] (gff-processing.Rmd) + Error: processing vignette 'gff-processing.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘gff-processing.Rmd’ + ... + --- failed re-building ‘introduction.Rmd’ + + --- re-building ‘nozzle.Rmd’ using rmarkdown + --- finished re-building ‘nozzle.Rmd’ + + SUMMARY: processing the following files failed: + ‘gff-processing.Rmd’ ‘introduction.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# roads + +
+ +* Version: 1.1.0 +* GitHub: https://github.com/LandSciTech/roads +* Source code: https://github.com/cran/roads +* Date/Publication: 2023-02-02 16:10:02 UTC +* Number of recursive dependencies: 113 + +Run `revdepcheck::cloud_details(, "roads")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘roads-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plotRoads + > ### Title: Plot projected roads + > ### Aliases: plotRoads + > + > ### ** Examples + > + > + > prRes <- projectRoads(CLUSexample$landings, CLUSexample$cost, CLUSexample$roads) + 0s detected in cost raster, these will be considered as existing roads + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: projectRoads ... -> make_graph -> do.call -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 3. │ ├─testthat (local) .capture(...) + 4. │ │ └─base::withCallingHandlers(...) + 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 6. └─roads::rasterToLineSegments(roadRast) + 7. ├─roads::projectRoads(...) + 8. └─roads::projectRoads(...) + 9. └─roads:::getGraph(sim, neighbourhood) + 10. └─igraph::graph.edgelist(edge_mat, dir = FALSE) + 11. └─igraph::make_graph(t(el), directed = directed) + 12. ├─base::do.call(old_graph, args) + 13. └─igraph (local) ``(``, directed = FALSE) + + [ FAIL 5 | WARN 0 | SKIP 0 | PASS 11 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘ReconstructRoadHistory.Rmd’ using rmarkdown + + Quitting from lines 43-55 [unnamed-chunk-2] (ReconstructRoadHistory.Rmd) + Error: processing vignette 'ReconstructRoadHistory.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘ReconstructRoadHistory.Rmd’ + + --- re-building ‘roads-vignette.Rmd’ using rmarkdown + ... + Quitting from lines 133-147 [unnamed-chunk-4] (roads-vignette.Rmd) + Error: processing vignette 'roads-vignette.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘roads-vignette.Rmd’ + + SUMMARY: processing the following files failed: + ‘ReconstructRoadHistory.Rmd’ ‘roads-vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# robber + +
+ +* Version: 0.2.3 +* GitHub: https://github.com/Chabert-Liddell/robber +* Source code: https://github.com/cran/robber +* Date/Publication: 2023-02-28 08:32:35 UTC +* Number of recursive dependencies: 144 + +Run `revdepcheck::cloud_details(, "robber")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘robber-Ex.R’ failed + The error most likely occurred in: + + > ### Name: simulate_lbm + > ### Title: Simulate a bipartite interaction network using block model + > ### Aliases: simulate_lbm + > + > ### ** Examples + > + > # For a random number of interactions and blocks sizes + ... + > con <- matrix(c(.5,.3,.3,.1), 2, 2) + > pi <- c(.25,.75) + > rho <- c(1/3, 2/3) + > nr <- 50 + > nc <- 30 + > simulate_lbm(con, pi, rho, nr, nc, method = "gnp") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: simulate_lbm -> -> ensure_igraph -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 5. ├─igraph::as_incidence_matrix(...) + 6. │ └─igraph:::ensure_igraph(graph) + 7. └─igraph::sample_bipartite(...) + ── Error ('test-simulate_bm.R:29:1'): (code run outside of `test_that()`) ────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─robber::simulate_lbm(con, pi, rho, nr, nc, method = "gnm") at test-simulate_bm.R:29:0 + 2. ├─igraph::as_incidence_matrix(...) + 3. │ └─igraph:::ensure_igraph(graph) + 4. └─igraph::sample_bipartite(...) + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 41 ] + Error: Test failures + Execution halted + ``` + +# robin + +
+ +* Version: 1.1.1 +* GitHub: https://github.com/ValeriaPolicastro/robin +* Source code: https://github.com/cran/robin +* Date/Publication: 2022-05-16 18:30:02 UTC +* Number of recursive dependencies: 156 + +Run `revdepcheck::cloud_details(, "robin")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘robin-Ex.R’ failed + The error most likely occurred in: + + > ### Name: robinCompareFast + > ### Title: robinCompareFast + > ### Aliases: robinCompareFast + > + > ### ** Examples + > + > my_file <- system.file("example/football.gml", package="robin") + > graph <- prepGraph(file=my_file, file.format="gml") + > robinCompareFast(graph=graph, method1="louvain", + + method2="fastGreedy", measure="vi") + Detecting robin method independent type, wait it can take time it depends on the size of the network. + Error in checkForRemoteErrors(val) : + 12 nodes produced errors; first error: could not find function ".igraph.status" + Calls: robinCompareFast ... -> staticClusterApply -> checkForRemoteErrors + Execution halted + ``` + +# RobustIV + +
+ +* Version: 0.2.5 +* GitHub: https://github.com/zijguo/RobustIV +* Source code: https://github.com/cran/RobustIV +* Date/Publication: 2022-12-20 01:10:02 UTC +* Number of recursive dependencies: 26 + +Run `revdepcheck::cloud_details(, "RobustIV")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘RobustIV-Ex.R’ failed + The error most likely occurred in: + + > ### Name: TSHT + > ### Title: Two-Stage Hard Thresholding + > ### Aliases: TSHT + > + > ### ** Examples + > + > data("lineardata") + > Y <- lineardata[,"Y"] + > D <- lineardata[,"D"] + > Z <- as.matrix(lineardata[,c("Z.1","Z.2","Z.3","Z.4","Z.5","Z.6","Z.7","Z.8")]) + > X <- as.matrix(lineardata[,c("age","sex")]) + > TSHT.model <- TSHT(Y=Y,D=D,Z=Z,X=X) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: TSHT ... ensure_igraph -> -> graph.adjacency.dense + Execution halted + ``` + +# robustrao + +
+ +* Version: 1.0-5 +* GitHub: NA +* Source code: https://github.com/cran/robustrao +* Date/Publication: 2020-01-24 21:50:08 UTC +* Number of recursive dependencies: 16 + +Run `revdepcheck::cloud_details(, "robustrao")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘robustrao-Ex.R’ failed + The error most likely occurred in: + + > ### Name: LowerIndexBound + > ### Title: Lower bound of the uncertainty interval of the Rao-Stirling + > ### diversity index. + > ### Aliases: LowerIndexBound + > + > ### ** Examples + > + ... + > #Get number of uncategorized references in the publication + > uncat <- pd1.uncat.refs[1] + > + > #Get vector of permissible disciplines. + > logic.disciplines <- counts > 0 + > permissible <- PruneDisciplines(logic.disciplines, 0.233, pd1.similarity) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: PruneDisciplines -> graph.adjacency -> graph.adjacency.dense + Execution halted + ``` + +# roprov + +
+ +* Version: 0.1.2 +* GitHub: NA +* Source code: https://github.com/cran/roprov +* Date/Publication: 2018-11-06 09:10:03 UTC +* Number of recursive dependencies: 13 + +Run `revdepcheck::cloud_details(, "roprov")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘roprov-Ex.R’ failed + The error most likely occurred in: + + > ### Name: fullprovgraph + > ### Title: Create the full (multiple values per variable) provenance graph + > ### for a cache + > ### Aliases: fullprovgraph fullprovgraph,ProvStoreDF-method + > ### fullprovgraph,ProvStoreDF fullprovgraph,data.frame-method + > ### fullprovgraph,data.frame + > + ... + + invarhashes = invarhashes, + + invarclasses = invarclasses, + + code = code, + + agent = "coolguyorgirl") + > + > plot(fullprovgraph(ps)) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot ... graph_from_edgelist -> make_graph -> do.call -> + Execution halted + ``` + +# RPANDA + +
+ +* Version: 2.2 +* GitHub: https://github.com/hmorlon/PANDA +* Source code: https://github.com/cran/RPANDA +* Date/Publication: 2022-10-24 15:28:00 UTC +* Number of recursive dependencies: 129 + +Run `revdepcheck::cloud_details(, "RPANDA")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘RPANDA-Ex.R’ failed + The error most likely occurred in: + + > ### Name: JSDtree + > ### Title: Jensen-Shannon distance between phylogenies + > ### Aliases: JSDtree + > + > ### ** Examples + > + > trees<-TESS::tess.sim.age(n=20,age=10,0.15,0.05,MRCA=TRUE) + > JSDtree(trees) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: JSDtree -> lapply -> FUN -> graph.adjacency.dense + Execution halted + ``` + +# rquery + +
+ +* Version: 1.4.9 +* GitHub: https://github.com/WinVector/rquery +* Source code: https://github.com/cran/rquery +* Date/Publication: 2022-02-28 18:00:02 UTC +* Number of recursive dependencies: 46 + +Run `revdepcheck::cloud_details(, "rquery")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘rquery-Ex.R’ failed + The error most likely occurred in: + + > ### Name: topo_sort_tables + > ### Title: Topologically sort join plan so values are available before + > ### uses. + > ### Aliases: topo_sort_tables + > + > ### ** Examples + > + ... + + inspect_join_plan(tDesc, sorted$columnJoinPlan))) + + print(plot(sorted$dependencyGraph)) + + DBI::dbDisconnect(my_db) + + my_db <- NULL + + } + [1] "problems: key col(s) ( dept ) not contained in result cols of previous table(s) for table: revenue" + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: topo_sort_tables -> + Execution halted + ``` + +# rscc + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/sigbertklinke/rscc +* Source code: https://github.com/cran/rscc +* Date/Publication: 2022-01-20 12:02:42 UTC +* Number of recursive dependencies: 45 + +Run `revdepcheck::cloud_details(, "rscc")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘rscc-Ex.R’ failed + The error most likely occurred in: + + > ### Name: as_igraph + > ### Title: as.igraph + > ### Aliases: as_igraph + > + > ### ** Examples + > + > files <- list.files(path=system.file("examples", package="rscc"), pattern="*.R$", full.names = TRUE) + ... + /tmp/workdir/rscc/new/rscc.Rcheck/rscc/examples/kwantyle1.R + /tmp/workdir/rscc/new/rscc.Rcheck/rscc/examples/kwantyle1_variables.R + > docs <- documents(prgs) + > simm <- similarities(docs) + > # a similarity coefficients equal to zero does not create an edge! + > g <- as_igraph(simm, diag=FALSE) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: as_igraph -> do.call -> -> graph.adjacency.dense + Execution halted + ``` + +# RScelestial + +
+ +* Version: 1.0.3 +* GitHub: NA +* Source code: https://github.com/cran/RScelestial +* Date/Publication: 2021-12-09 22:20:02 UTC +* Number of recursive dependencies: 45 + +Run `revdepcheck::cloud_details(, "RScelestial")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘RScelestial-Ex.R’ failed + The error most likely occurred in: + + > ### Name: scelestial + > ### Title: Infer the single-cell phylogenetic tree + > ### Aliases: scelestial + > + > ### ** Examples + > + > ## simulates tumor evolution + > S = synthesis(10, 10, 2, seed=7) + > ## convert to 10-state matrix + > seq = as.ten.state.matrix(S$seqeunce) + > ## runs the scelestial to generate 4-restricted Steiner trees. It represents the tree and graph + > SP = scelestial(seq, mink=3, maxk=4, return.graph = TRUE) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: scelestial ... graph_from_edgelist -> make_graph -> do.call -> + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.2Mb + sub-directories of 1Mb or more: + libs 4.9Mb + ``` + +# rsetse + +
+ +* Version: 0.5.0 +* GitHub: https://github.com/JonnoB/rSETSe +* Source code: https://github.com/cran/rsetse +* Date/Publication: 2021-06-11 10:00:02 UTC +* Number of recursive dependencies: 81 + +Run `revdepcheck::cloud_details(, "rsetse")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘rsetse-Ex.R’ failed + The error most likely occurred in: + + > ### Name: calc_tension_strain + > ### Title: Calculate line tension and strain from the topology and node + > ### embeddings + > ### Aliases: calc_tension_strain + > + > ### ** Examples + > + ... + Error in .igraph.status("Free graph external pointer.\n") : + could not find function ".igraph.status" + Error in .igraph.status("Free graph external pointer.\n") : + could not find function ".igraph.status" + Error in .igraph.status("Free graph external pointer.\n") : + could not find function ".igraph.status" + Error in .igraph.status("Free graph external pointer.\n") : + could not find function ".igraph.status" + Error in .igraph.status("Free graph external pointer.\n") : + could not find function ".igraph.status" + ``` + +# rSpectral + +
+ +* Version: 1.0.0.10 +* GitHub: https://github.com/cmclean5/rSpectral +* Source code: https://github.com/cran/rSpectral +* Date/Publication: 2023-01-18 12:00:02 UTC +* Number of recursive dependencies: 44 + +Run `revdepcheck::cloud_details(, "rSpectral")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘rSpectral-Ex.R’ failed + The error most likely occurred in: + + > ### Name: spectral_igraph_communities + > ### Title: Spectral clustering for 'igraph' objects + > ### Aliases: spectral_igraph_communities + > + > ### ** Examples + > + > data(karate,package='igraphdata') + > c<-spectral_igraph_communities(karate) + Error in .igraph.status("Restore graph external pointer.\n") : + could not find function ".igraph.status" + Calls: spectral_igraph_communities ... -> ensure_igraph -> is_igraph -> warn_version + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ── Error ('test-igraph.R:24:3'): membership fix_neig=1 is correct ────────────── + Error in `.igraph.status("Restore graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─rSpectral::spectral_igraph_communities(karate, fix_neig = 1) at test-igraph.R:24:2 + 2. └─rSpectral::spectral_igraph_membership(...) + 3. ├─base::as.data.frame(igraph::get.edgelist(g, names = TRUE)) + 4. └─igraph::get.edgelist(g, names = TRUE) + 5. └─igraph:::ensure_igraph(graph) + 6. └─igraph::is_igraph(graph) + 7. └─igraph:::warn_version(graph) + + [ FAIL 3 | WARN 0 | SKIP 0 | PASS 4 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.9Mb + sub-directories of 1Mb or more: + libs 5.2Mb + ``` + +# rsppfp + +
+ +* Version: 1.0.4 +* GitHub: https://github.com/melvidoni/rsppfp +* Source code: https://github.com/cran/rsppfp +* Date/Publication: 2019-02-19 15:10:03 UTC +* Number of recursive dependencies: 84 + +Run `revdepcheck::cloud_details(, "rsppfp")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘rsppfp-Ex.R’ failed + The error most likely occurred in: + + > ### Name: get_shortest_path + > ### Title: igraph Shortest Path + > ### Aliases: get_shortest_path + > + > ### ** Examples + > + > # Given a specific gStar graph: + ... + 16 s|u s|u|v 4 + 17 u u|v 4 + 18 u|v u|v|y 3 + > + > # Obtain the shortest path + > get_shortest_path(gStar, "s", "v", "weight") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: get_shortest_path -> graph_from_data_frame -> make_empty_graph + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# rvinecopulib + +
+ +* Version: 0.6.3.1.1 +* GitHub: https://github.com/vinecopulib/rvinecopulib +* Source code: https://github.com/cran/rvinecopulib +* Date/Publication: 2023-02-23 11:50:02 UTC +* Number of recursive dependencies: 75 + +Run `revdepcheck::cloud_details(, "rvinecopulib")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘rvinecopulib-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.rvine_structure + > ### Title: Plotting R-vine structures + > ### Aliases: plot.rvine_structure plot.rvine_matrix + > + > ### ** Examples + > + > plot(cvine_structure(1:5)) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot ... lapply -> FUN -> -> graph.adjacency.dense + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 4. │ │ ├─withr::with_output_sink(...) + 5. │ │ │ └─base::force(code) + 6. │ │ ├─base::withCallingHandlers(...) + 7. │ │ └─base::withVisible(code) + 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 9. ├─base::plot(vc, edge_labels = "family", var_names = "legend") + 10. └─rvinecopulib:::plot.vinecop_dist(...) + 11. └─base::lapply(tree, get_graph, vc = x, edge_labels = edge_labels) + 12. └─rvinecopulib (local) FUN(X[[i]], ...) + 13. └─igraph::graph_from_adjacency_matrix(I, mode = "undirected") + 14. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 290 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 76.5Mb + sub-directories of 1Mb or more: + include 5.0Mb + libs 71.1Mb + ``` + +# safedata + +
+ +* Version: 1.1.3 +* GitHub: https://github.com/ImperialCollegeLondon/safedata +* Source code: https://github.com/cran/safedata +* Date/Publication: 2023-05-05 15:00:02 UTC +* Number of recursive dependencies: 80 + +Run `revdepcheck::cloud_details(, "safedata")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘safedata-Ex.R’ failed + The error most likely occurred in: + + > ### Name: get_taxon_graph + > ### Title: Get a graph of the taxa in a dataset + > ### Aliases: get_taxon_graph + > + > ### ** Examples + > + > set_example_safe_dir() + Loading and caching index + Validating directory + > beetle_graph <- get_taxon_graph(1400562) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: get_taxon_graph -> -> make_empty_graph + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘overview.Rmd’ using rmarkdown + --- finished re-building ‘overview.Rmd’ + + --- re-building ‘using_safe_data.Rmd’ using rmarkdown + + Quitting from lines 513-516 [get_phylo] (using_safe_data.Rmd) + Error: processing vignette 'using_safe_data.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘using_safe_data.Rmd’ + + SUMMARY: processing the following file failed: + ‘using_safe_data.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# saotd + +
+ +* Version: 0.3.0 +* GitHub: https://github.com/evan-l-munson/saotd +* Source code: https://github.com/cran/saotd +* Date/Publication: 2021-10-13 09:50:02 UTC +* Number of recursive dependencies: 121 + +Run `revdepcheck::cloud_details(, "saotd")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ── Error ('test_word_corr_network.R:68:1'): (code run outside of `test_that()`) ── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. ├─saotd::word_corr_network(WordCorr = test, Correlation = 0.1) at test_word_corr_network.R:68:0 + 2. │ └─... %>% ggraph::ggraph(layout = layout) + 3. ├─ggraph::ggraph(., layout = layout) + 4. │ ├─ggplot2::ggplot(data = create_layout(graph, layout, ...), environment = envir) + 5. │ └─ggraph::create_layout(graph, layout, ...) + 6. └─igraph::graph_from_data_frame(.) + 7. └─igraph::make_empty_graph(n = 0, directed = directed) + + [ FAIL 2 | WARN 1 | SKIP 0 | PASS 59 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘saotd.Rmd’ using rmarkdown + + Quitting from lines 171-181 [bigram_network] (saotd.Rmd) + Error: processing vignette 'saotd.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘saotd.Rmd’ + + SUMMARY: processing the following file failed: + ‘saotd.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# sBIC + +
+ +* Version: 0.2.0 +* GitHub: https://github.com/Lucaweihs/sBIC +* Source code: https://github.com/cran/sBIC +* Date/Publication: 2016-10-01 14:31:14 +* Number of recursive dependencies: 52 + +Run `revdepcheck::cloud_details(, "sBIC")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 1. ├─testthat::expect_equal(...) at test_LatentForests.R:379:2 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. ├─sBIC:::forestDepth(...) + 5. │ ├─base::unique(igraph::clusters(forest)$membership[1:numLeaves]) + 6. │ └─igraph::clusters(forest) + 7. │ └─igraph:::ensure_igraph(graph) + 8. └─igraph::graph.edgelist(...) + 9. └─igraph::make_graph(t(el), directed = directed) + 10. ├─base::do.call(old_graph, args) + 11. └─igraph (local) ``(``, directed = FALSE) + + [ FAIL 11 | WARN 0 | SKIP 0 | PASS 12 ] + Error: Test failures + Execution halted + ``` + +# sbm + +
+ +* Version: 0.4.5 +* GitHub: https://github.com/GrossSBM/sbm +* Source code: https://github.com/cran/sbm +* Date/Publication: 2023-01-09 10:30:02 UTC +* Number of recursive dependencies: 108 + +Run `revdepcheck::cloud_details(, "sbm")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘sbm-Ex.R’ failed + The error most likely occurred in: + + > ### Name: estimateSimpleSBM + > ### Title: Estimation of Simple SBMs + > ### Aliases: estimateSimpleSBM + > + > ### ** Examples + > + > ### ======================================= + ... + -> For 2 groups + > plot(mySimpleSBM, 'data', ordered = FALSE) + > plot(mySimpleSBM, 'data') + > plot(mySimpleSBM, 'expected', ordered = FALSE) + > plot(mySimpleSBM, 'expected') + > plot(mySimpleSBM, 'meso') + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot ... -> plotMeso -> -> graph.adjacency.dense + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ...6c6 + < NULL + --- + > All Done! + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 4. │ │ ├─withr::with_output_sink(...) + 5. │ │ │ └─base::force(code) + ... + 9. ├─base::plot(myMBM, type = "meso") + 10. └─sbm:::plot.SBM(myMBM, type = "meso") + 11. └─x$plot(type, ordered, plotOptions) + 12. └─sbm:::plotMesoMultipartite(...) + 13. └─igraph::graph.adjacency(...) + 14. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1045 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘Multipartite_EcologicalNetwork.Rmd’ using rmarkdown + + Quitting from lines 152-158 [plot meso] (Multipartite_EcologicalNetwork.Rmd) + Error: processing vignette 'Multipartite_EcologicalNetwork.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘Multipartite_EcologicalNetwork.Rmd’ + + --- re-building ‘MultiplexNetwork_principle.Rmd’ using rmarkdown + --- finished re-building ‘MultiplexNetwork_principle.Rmd’ + ... + Quitting from lines 114-115 [simpleSBMfit plotmeso] (SBM_fungus_tree_network.Rmd) + Error: processing vignette 'SBM_fungus_tree_network.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘SBM_fungus_tree_network.Rmd’ + + SUMMARY: processing the following files failed: + ‘Multipartite_EcologicalNetwork.Rmd’ ‘SBM_fungus_tree_network.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# SBN + +
+ +* Version: 1.0.0 +* GitHub: NA +* Source code: https://github.com/cran/SBN +* Date/Publication: 2022-01-17 19:42:42 UTC +* Number of recursive dependencies: 7 + +Run `revdepcheck::cloud_details(, "SBN")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘SBN-Ex.R’ failed + The error most likely occurred in: + + > ### Name: sbn_change_dir + > ### Title: Change the upstream/downstream direction of an SBN + > ### Aliases: sbn_change_dir + > + > ### ** Examples + > + > g <- sbn_create(10, 0.7) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: sbn_create -> -> graph.adjacency.dense + Execution halted + ``` + +# sccore + +
+ +* Version: 1.0.3 +* GitHub: https://github.com/kharchenkolab/sccore +* Source code: https://github.com/cran/sccore +* Date/Publication: 2023-03-13 00:00:02 UTC +* Number of recursive dependencies: 76 + +Run `revdepcheck::cloud_details(, "sccore")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘sccore-Ex.R’ failed + The error most likely occurred in: + + > ### Name: graphToAdjList + > ### Title: Convert igraph graph into an adjacency list + > ### Aliases: graphToAdjList + > + > ### ** Examples + > + > library(dplyr) + ... + + The following objects are masked from ‘package:base’: + + intersect, setdiff, setequal, union + + > edge.list.fact <- igraph::as_edgelist(conosGraph) %>% as_factor() + Error in .igraph.status("Restore graph external pointer.\n") : + could not find function ".igraph.status" + Calls: %>% ... -> ensure_igraph -> is_igraph -> warn_version + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 6. └─igraph:::warn_version(graph) + ── Error ('test_helpers.R:43:2'): graphToAdjList() functionality ─────────────── + Error in `.igraph.status("Restore graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. ├─igraph::as_edgelist(conosGraph) %>% as_factor() at test_helpers.R:43:8 + 2. ├─sccore::as_factor(.) + 3. └─igraph::as_edgelist(conosGraph) + 4. └─igraph:::ensure_igraph(graph) + 5. └─igraph::is_igraph(graph) + 6. └─igraph:::warn_version(graph) + + [ FAIL 4 | WARN 0 | SKIP 0 | PASS 2 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.9Mb + sub-directories of 1Mb or more: + libs 7.1Mb + ``` + +# scDHA + +
+ +* Version: 1.2.1 +* GitHub: https://github.com/duct317/scDHA +* Source code: https://github.com/cran/scDHA +* Date/Publication: 2023-04-04 12:10:02 UTC +* Number of recursive dependencies: 62 + +Run `revdepcheck::cloud_details(, "scDHA")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ══ Skipped tests ═══════════════════════════════════════════════════════════════ + • On CRAN (2) + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-scDHA.R:33:3'): scDHA.pt can run ─────────────────────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─scDHA::scDHA.pt(result, start.point = 1, ncores = 2, seed = 1) at test-scDHA.R:33:2 + 2. └─igraph::graph_from_adjacency_matrix(adj, weighted = TRUE, mode = "undirected") + 3. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 1 | WARN 0 | SKIP 2 | PASS 3 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 8.3Mb + sub-directories of 1Mb or more: + data 3.2Mb + libs 4.7Mb + ``` + +# scDiffCom + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/scDiffCom +* Date/Publication: 2021-08-17 07:20:05 UTC +* Number of recursive dependencies: 245 + +Run `revdepcheck::cloud_details(, "scDiffCom")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 13. └─igraph::graph_from_data_frame(...) + 14. └─igraph::make_empty_graph(n = 0, directed = directed) + ── Error ('test-everything.R:1023:1'): (code run outside of `test_that()`) ───── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─scDiffCom:::build_interactive_network(...) at test-everything.R:1023:0 + 2. └─scDiffCom:::interactive_from_igraph(...) + 3. └─scDiffCom:::build_igraph(...) + 4. └─igraph::graph_from_data_frame(...) + 5. └─igraph::make_empty_graph(n = 0, directed = directed) + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 80 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘future’ ‘utils’ + All declared Imports should be used. + ``` + +# SCORPION + +
+ +* Version: 1.0.1 +* GitHub: NA +* Source code: https://github.com/cran/SCORPION +* Date/Publication: 2022-09-22 09:30:02 UTC +* Number of recursive dependencies: 12 + +Run `revdepcheck::cloud_details(, "SCORPION")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘SCORPION-Ex.R’ failed + The error most likely occurred in: + + > ### Name: scorpion + > ### Title: Constructs PANDA gene regulatory networks from single-cell gene + > ### expression data + > ### Aliases: scorpion + > + > ### ** Examples + > + ... + > scorpionOutput <- scorpion(tfMotifs = scorpionTest$tf, + + gexMatrix = scorpionTest$gex, + + ppiNet = scorpionTest$ppi, + + alphaValue = 0.8) + + ── SCORPION ──────────────────────────────────────────────────────────────────── + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: scorpion ... makeSuperCells -> buildKNN -> buildNN2 -> + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘RhpcBLASctl’ + All declared Imports should be used. + ``` + +# scRNAtools + +
+ +* Version: 1.0 +* GitHub: NA +* Source code: https://github.com/cran/scRNAtools +* Date/Publication: 2018-07-05 14:00:03 UTC +* Number of recursive dependencies: 131 + +Run `revdepcheck::cloud_details(, "scRNAtools")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘scRNAtools-Ex.R’ failed + The error most likely occurred in: + + > ### Name: scRNAtools_inter_net + > ### Title: Construction of interactive network in scRNA sequencing data + > ### Aliases: scRNAtools_inter_net + > + > ### ** Examples + > + > data(corr_re) + ... + > p<-0.05 + > r<-0.9 + > size<-5 #nodes size + > color<-"#00B2EE" ##Color of nodes. + > pdf(file=file.path(tempdir(), "interact_net.pdf")) + > scRNAtools_inter_net(corr_re,p,r,size,color) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: scRNAtools_inter_net -> graph.data.frame -> make_empty_graph + Execution halted + ``` + +# secrlinear + +
+ +* Version: 1.2.1 +* GitHub: https://github.com/MurrayEfford/secrlinear +* Source code: https://github.com/cran/secrlinear +* Date/Publication: 2023-05-19 04:10:02 UTC +* Number of recursive dependencies: 83 + +Run `revdepcheck::cloud_details(, "secrlinear")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘secrlinear-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Arvicola + > ### Title: Water Vole Capture Dataset + > ### Aliases: arvicola + > ### Keywords: datasets + > + > ### ** Examples + > + ... + 20.B 163.85 629.66 + 40.A 164.88 649.19 + 40.B 164.88 649.19 + > + > ## for speed, pre-compute distance matrix + > userd <- networkdistance (traps(arvicola), glymemask, glymemask) + Error in .igraph.status("Restore graph external pointer.\n") : + could not find function ".igraph.status" + Calls: networkdistance ... cbind -> V -> ensure_igraph -> is_igraph -> warn_version + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-secrlinear.R:14:1'): (code run outside of `test_that()`) ─────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─secrlinear::read.linearmask(data = xy, spacing = 20) at test-secrlinear.R:14:0 + 2. └─secrlinear:::make.linearmask(...) + 3. └─secrlinear::asgraph(mask) + 4. └─igraph::graph.adjacency(tempdist, mode = "lower") + 5. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘secrlinear-vignette.Rmd’ using rmarkdown + + Quitting from lines 71-73 [readglyme] (secrlinear-vignette.Rmd) + Error: processing vignette 'secrlinear-vignette.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘secrlinear-vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘secrlinear-vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# SelectBoost + +
+ +* Version: 2.2.2 +* GitHub: https://github.com/fbertran/SelectBoost +* Source code: https://github.com/cran/SelectBoost +* Date/Publication: 2022-11-30 09:10:06 UTC +* Number of recursive dependencies: 114 + +Run `revdepcheck::cloud_details(, "SelectBoost")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘SelectBoost-Ex.R’ failed + The error most likely occurred in: + + > ### Name: boost + > ### Title: Boost step by step functions + > ### Aliases: boost boost.normalize boost.compcorrs boost.correlation_sign + > ### boost.findgroups boost.Xpass boost.adjust boost.random boost.apply + > ### boost.select + > + > ### ** Examples + ... + > xran_corr<- boost.compcorrs(xran_norm) + > + > xran_corr_sign <- boost.correlation_sign(xran_corr) + > + > xran_groups <- boost.findgroups(xran_corr, group=group_func_1, .3) + > xran_groups_2 <- boost.findgroups(xran_corr, group=group_func_2, .3) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: boost.findgroups ... group2 -> group -> graph.adjacency -> graph.adjacency.dense + Execution halted + ``` + +# SEMID + +
+ +* Version: 0.4.0 +* GitHub: https://github.com/Lucaweihs/SEMID +* Source code: https://github.com/cran/SEMID +* Date/Publication: 2022-01-13 15:12:43 UTC +* Number of recursive dependencies: 38 + +Run `revdepcheck::cloud_details(, "SEMID")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘SEMID-Ex.R’ failed + The error most likely occurred in: + + > ### Name: SEMID-package + > ### Title: SEMID package documentation. + > ### Aliases: SEMID-package SEMID + > + > ### ** Examples + > + > ### + ... + + 0, 0, 0, 0, 0, + + 0, 0, 0, 0, 0, + + 0, 0, 0, 0, 0), 5, 5)); O=O+t(O) + > + > # Create a mixed graph object + > graph = MixedGraph(L, O) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: MixedGraph ... LatentDigraphFixedOrder -> -> graph.adjacency.dense + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ── Error ('test_edgewiseID.R:43:9'): TO DELETE ───────────────────────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─SEMID::MixedGraph(L, O) at test_edgewiseID.R:43:8 + 2. ├─R.oo::extend(...) + 3. ├─R.oo::extend.Object(...) + 4. └─SEMID::LatentDigraph(...) + 5. └─SEMID::LatentDigraphFixedOrder(L, length(observedNodes)) + 6. └─igraph::graph.adjacency(L, mode = "directed") + 7. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 11 | WARN 641 | SKIP 0 | PASS 478 ] + Error: Test failures + Execution halted + ``` + +# sensitivity + +
+ +* Version: 1.28.1 +* GitHub: NA +* Source code: https://github.com/cran/sensitivity +* Date/Publication: 2023-03-19 19:10:02 UTC +* Number of recursive dependencies: 124 + +Run `revdepcheck::cloud_details(, "sensitivity")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘sensitivity-Ex.R’ failed + The error most likely occurred in: + + > ### Name: shapleyBlockEstimation + > ### Title: Computation of the Shapley effects in the Gaussian linear + > ### framework with an unknown block-diagonal covariance matrix + > ### Aliases: shapleyBlockEstimation shapleyBlockEstimationS + > ### shapleyBlockEstimationX + > + > ### ** Examples + ... + + cex.main=3,ylab = "", xlab = "",axes=FALSE) + > box() + > + > + > Beta_ord=3*runif(p)+1 + > eta_ord=shapleyLinearGaussian(Beta=Beta_ord, Sigma=Sigma_ord) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: shapleyLinearGaussian ... ensure_igraph -> -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 9.0Mb + sub-directories of 1Mb or more: + R 2.2Mb + libs 6.2Mb + ``` + +# SeqDetect + +
+ +* Version: 1.0.7 +* GitHub: NA +* Source code: https://github.com/cran/SeqDetect +* Date/Publication: 2020-03-02 14:30:05 UTC +* Number of recursive dependencies: 23 + +Run `revdepcheck::cloud_details(, "SeqDetect")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘SeqDetect-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plotMachines,HybridSequenceClassifier-method + > ### Title: Sequence Detector Method: plot machines (ETTs) + > ### Aliases: plotMachines,HybridSequenceClassifier-method + > + > ### ** Examples + > + > ldf1 <- data.frame(product=c("P1","P1","P1","P1"),sequence_id=c(1,3,5,7), + ... + + + + > hsc$cleanKeys() + > hsc$mergeMachines() + > hsc$plotMachines() + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: -> graph_from_data_frame -> make_empty_graph + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘SequentialDetector.Rnw’ + ... + Transition(278bf27b866ebd1b659a) to:H_REL Symbols:[H_REL] Input state: Output state: Population:1 + Patterns:[Hospital release] + ========= + -==***************************************==- + + > seq_detector$plotMachines() + + When sourcing ‘SequentialDetector.R’: + Error: could not find function ".igraph.status" + Execution halted + + ‘SequentialDetector.Rnw’ using ‘UTF-8’... failed + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 18.1Mb + sub-directories of 1Mb or more: + libs 16.8Mb + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘SequentialDetector.Rnw’ using Sweave + Loading required package: Rcpp + Loading required package: eventdataR + + Attaching package: ‘dplyr’ + + The following objects are masked from ‘package:stats’: + + filter, lag + ... + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + + --- failed re-building ‘SequentialDetector.Rnw’ + + SUMMARY: processing the following file failed: + ‘SequentialDetector.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# seqHMM + +
+ +* Version: 1.2.4 +* GitHub: https://github.com/helske/seqHMM +* Source code: https://github.com/cran/seqHMM +* Date/Publication: 2023-01-09 11:20:02 UTC +* Number of recursive dependencies: 64 + +Run `revdepcheck::cloud_details(, "seqHMM")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘seqHMM-Ex.R’ failed + The error most likely occurred in: + + > ### Name: hmm_biofam + > ### Title: Hidden Markov model for the biofam data + > ### Aliases: hmm_biofam + > ### Keywords: datasets + > + > ### ** Examples + > + > + > # Plotting the model + > plot(hmm_biofam) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot ... plot.hmm -> graph.adjacency -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘seqHMM.Rnw’ using knitr + + Quitting from lines 495-498 [plottingHMM] (seqHMM.Rnw) + Error: processing vignette 'seqHMM.Rnw' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘seqHMM.Rnw’ + + --- re-building ‘seqHMM_algorithms.Rnw’ using knitr + Error: processing vignette 'seqHMM_algorithms.Rnw' failed with diagnostics: + ... + Quitting from lines 112-128 [HMMplot] (seqHMM_visualization.Rnw) + Error: processing vignette 'seqHMM_visualization.Rnw' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘seqHMM_visualization.Rnw’ + + SUMMARY: processing the following files failed: + ‘seqHMM.Rnw’ ‘seqHMM_algorithms.Rnw’ ‘seqHMM_visualization.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +* checking installed package size ... NOTE + ``` + installed size is 34.4Mb + sub-directories of 1Mb or more: + doc 6.4Mb + libs 27.2Mb + ``` + +# SeqNet + +
+ +* Version: 1.1.3 +* GitHub: NA +* Source code: https://github.com/cran/SeqNet +* Date/Publication: 2021-07-09 08:20:08 UTC +* Number of recursive dependencies: 74 + +Run `revdepcheck::cloud_details(, "SeqNet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘SeqNet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: add_random_module_to_network + > ### Title: Adds a random module of a given size to the network + > ### Aliases: add_random_module_to_network + > + > ### ** Examples + > + > # This function provides an alternative way to iteratively add random + > # modules to the network. It uses a weighted sampling of nodes, where + > # nodes that haven't been selected for a module have a higher probability + > # of being sampled for the new module. + > nw <- create_empty_network(100) + > plot(nw) # An empty network of 100 nodes. + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot ... plot_network -> -> graph.adjacency.dense + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + > test_check("SeqNet") + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 36 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test_network_structure.R:12:3'): networks have appropriate structure. ── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─SeqNet::get_network_characteristics(network) at test_network_structure.R:12:2 + 2. └─igraph::graph_from_adjacency_matrix(adj, mode = "undirected") + 3. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 36 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.0Mb + sub-directories of 1Mb or more: + data 4.7Mb + libs 1.8Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘Rdpack’ + All declared Imports should be used. + ``` + +# SetRank + +
+ +* Version: 1.1.0 +* GitHub: NA +* Source code: https://github.com/cran/SetRank +* Date/Publication: 2016-05-11 12:06:23 +* Number of recursive dependencies: 15 + +Run `revdepcheck::cloud_details(, "SetRank")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘SetRank-Ex.R’ failed + The error most likely occurred in: + + > ### Name: setRankAnalysis + > ### Title: Advanced gene set enrichment analysis. + > ### Aliases: setRankAnalysis + > + > ### ** Examples + > + > options(mc.cores=1) + ... + 1 gene set DBs, 9 initial gene sets, 9 sets remaining and 50 genes in collection + 7 intersections to test...Pre-calculating critical Fisher-test values... + > genes = reference[sample(c(TRUE, FALSE), 50, TRUE)] + > network = setRankAnalysis(genes, collection, TRUE) + 2023-06-11 21:50:07 - calculating primary set p-values + 2023-06-11 21:50:07 - 0 significant sets + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: setRankAnalysis ... buildSetNet -> add.vertices -> ensure_igraph -> graph.empty + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘vignette.ltx’ using tex + Error: processing vignette 'vignette.ltx' failed with diagnostics: + Running 'texi2dvi' on 'vignette.ltx' failed. + LaTeX errors: + ! LaTeX Error: File `beramono.sty' not found. + + Type X to quit or to proceed, + or enter new name. (Default extension: sty) + ... + l.7 \usepackage + [T1]{fontenc}^^M + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘vignette.ltx’ + + SUMMARY: processing the following file failed: + ‘vignette.ltx’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# sfcr + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/joaomacalos/sfcr +* Source code: https://github.com/cran/sfcr +* Date/Publication: 2021-10-11 08:00:02 UTC +* Number of recursive dependencies: 140 + +Run `revdepcheck::cloud_details(, "sfcr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘sfcr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: sfcr_baseline + > ### Title: Simulate the baseline scenario of a stock-flow consistent model + > ### Aliases: sfcr_baseline + > + > ### ** Examples + > + > eqs <- sfcr_set( + ... + > + > external <- sfcr_set(Gd ~ 20, W ~ 1, alpha1 ~ 0.6, alpha2 ~ 0.4, theta ~ 0.2) + > + > # Periods is set to 10 to run faster. A usual model should run at + > # least 50 periods to find a steady state + > sfcr_baseline(equations = eqs, external = external, periods = 10) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: sfcr_baseline ... .find_blocks -> -> graph.adjacency.dense + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 4. └─igraph::graph.adjacency(adjmatrix = t(adj), mode = "directed") + 5. └─igraph:::graph.adjacency.dense(...) + ── Error ('test-sfcr_scenario.R:25:1'): (code run outside of `test_that()`) ──── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─sfcr::sfcr_baseline(...) at test-sfcr_scenario.R:25:0 + 2. └─sfcr:::.sfcr_find_order(equations) + 3. └─sfcr:::.find_blocks(km) + 4. └─igraph::graph.adjacency(adjmatrix = t(adj), mode = "directed") + 5. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 17 | WARN 0 | SKIP 0 | PASS 11 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘sfcr_multis.Rmd’ using rmarkdown + + Quitting from lines 50-51 [unnamed-chunk-2] (sfcr_multis.Rmd) + Error: processing vignette 'sfcr_multis.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘sfcr_multis.Rmd’ + + SUMMARY: processing the following file failed: + ‘sfcr_multis.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# sfdep + +
+ +* Version: 0.2.3 +* GitHub: https://github.com/josiahparry/sfdep +* Source code: https://github.com/cran/sfdep +* Date/Publication: 2023-01-11 06:30:02 UTC +* Number of recursive dependencies: 100 + +Run `revdepcheck::cloud_details(, "sfdep")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘sfdep-Ex.R’ failed + The error most likely occurred in: + + > ### Name: st_as_graph + > ### Title: Create an sfnetwork + > ### Aliases: st_as_graph st_as_graph.sf st_as_graph.sfc + > + > ### ** Examples + > + > library(magrittr) + > + > guerry_nb %>% + + st_as_graph(nb, wt) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: %>% ... graph_from_edgelist -> make_graph -> do.call -> + Execution halted + ``` + +# sfnetworks + +
+ +* Version: 0.6.3 +* GitHub: https://github.com/luukvdmeer/sfnetworks +* Source code: https://github.com/cran/sfnetworks +* Date/Publication: 2023-03-22 16:40:02 UTC +* Number of recursive dependencies: 106 + +Run `revdepcheck::cloud_details(, "sfnetworks")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘sfnetworks-Ex.R’ failed + The error most likely occurred in: + + > ### Name: as_sfnetwork + > ### Title: Convert a foreign object to a sfnetwork + > ### Aliases: as_sfnetwork as_sfnetwork.default as_sfnetwork.sf + > ### as_sfnetwork.linnet as_sfnetwork.psp as_sfnetwork.sfc + > ### as_sfnetwork.sfNetwork as_sfnetwork.sfnetwork as_sfnetwork.tbl_graph + > + > ### ** Examples + ... + > # From an sf object. + > library(sf, quietly = TRUE) + Linking to GEOS 3.8.0, GDAL 3.0.4, PROJ 6.3.1; sf_use_s2() is TRUE + > + > # With LINESTRING geometries. + > as_sfnetwork(roxel) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: as_sfnetwork ... graph_from_edgelist -> make_graph -> do.call -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 1. ├─sfnetworks::as_sfnetwork(rdm_rox) at test_bbox.R:5:2 + 2. └─sfnetworks:::as_sfnetwork.sf(rdm_rox) + 3. └─sfnetworks::sfnetwork(...) + 4. └─tidygraph::tbl_graph(nodes, edges_df, directed, node_key) + 5. ├─tidygraph::as_tbl_graph(...) + 6. └─tidygraph:::as_tbl_graph.list(...) + 7. └─tidygraph:::as_graph_node_edge(x, directed = directed, node_key = node_key) + 8. └─igraph::graph_from_edgelist(as.matrix(edges[, 1:2]), directed = directed) + 9. └─igraph::make_graph(t(el), directed = directed) + 10. ├─base::do.call(old_graph, args) + 11. └─igraph (local) ``(``, directed = TRUE) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 269 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘sfn01_structure.Rmd’ using rmarkdown + --- finished re-building ‘sfn01_structure.Rmd’ + + --- re-building ‘sfn02_preprocess_clean.Rmd’ using rmarkdown + --- finished re-building ‘sfn02_preprocess_clean.Rmd’ + + --- re-building ‘sfn03_join_filter.Rmd’ using rmarkdown + --- finished re-building ‘sfn03_join_filter.Rmd’ + ... + --- failed re-building ‘sfn04_routing.Rmd’ + + --- re-building ‘sfn05_morphers.Rmd’ using rmarkdown + --- finished re-building ‘sfn05_morphers.Rmd’ + + SUMMARY: processing the following file failed: + ‘sfn04_routing.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# SFSI + +
+ +* Version: 1.2.0 +* GitHub: NA +* Source code: https://github.com/cran/SFSI +* Date/Publication: 2022-08-16 15:40:09 UTC +* Number of recursive dependencies: 62 + +Run `revdepcheck::cloud_details(, "SFSI")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘SFSI-Ex.R’ failed + The error most likely occurred in: + + > ### Name: net.plot + > ### Title: Network plot + > ### Aliases: net.plot + > + > ### ** Examples + > + > require(SFSI) + ... + |==================================================================== | 96% + | + |======================================================================| 100% + > + > # Basic setting + > net.plot(fm) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: net.plot -> get_net -> + Execution halted + ``` + +# sharp + +
+ +* Version: 1.4.2 +* GitHub: https://github.com/barbarabodinier/sharp +* Source code: https://github.com/cran/sharp +* Date/Publication: 2023-06-09 16:20:02 UTC +* Number of recursive dependencies: 150 + +Run `revdepcheck::cloud_details(, "sharp")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘sharp-Ex.R’ failed + The error most likely occurred in: + + > ### Name: GraphComparison + > ### Title: Edge-wise comparison of two graphs + > ### Aliases: GraphComparison + > + > ### ** Examples + > + > # Data simulation + ... + > + > # Edge-wise comparison of the two graphs + > mygraph <- GraphComparison( + + graph1 = simul1, + + graph2 = simul2 + + ) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: GraphComparison ... -> -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘overview.Rnw’ using Sweave + Error: processing vignette 'overview.Rnw' failed with diagnostics: + Running 'texi2dvi' on 'overview.tex' failed. + LaTeX errors: + ! LaTeX Error: File `pdfpages.sty' not found. + + Type X to quit or to proceed, + or enter new name. (Default extension: sty) + ... + l.4 ^^M + + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘overview.Rnw’ + + SUMMARY: processing the following file failed: + ‘overview.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# sharpshootR + +
+ +* Version: 2.1 +* GitHub: https://github.com/ncss-tech/sharpshootR +* Source code: https://github.com/cran/sharpshootR +* Date/Publication: 2023-03-22 16:50:05 UTC +* Number of recursive dependencies: 149 + +Run `revdepcheck::cloud_details(, "sharpshootR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘sharpshootR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: component.adj.matrix + > ### Title: Create an adjacency matrix from a data.frame of component data + > ### Aliases: component.adj.matrix + > ### Keywords: manip + > + > ### ** Examples + > + ... + + m <- component.adj.matrix(amador) + + + + # plot network diagram, with Amador soil highlighted + + plotSoilRelationGraph(m, s = 'amador') + + } + Loading required namespace: igraph + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plotSoilRelationGraph -> -> graph.adjacency.dense + Execution halted + ``` + +# shazam + +
+ +* Version: 1.1.2 +* GitHub: NA +* Source code: https://github.com/cran/shazam +* Date/Publication: 2022-10-01 07:30:02 UTC +* Number of recursive dependencies: 124 + +Run `revdepcheck::cloud_details(, "shazam")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘shazam-Ex.R’ failed + The error most likely occurred in: + + > ### Name: distToNearest + > ### Title: Distance to nearest neighbor + > ### Aliases: distToNearest + > + > ### ** Examples + > + > # Subset example data to one sample as a demo + ... + > # Use genotyped V assignments, Hamming distance, and normalize by junction length + > # First partition based on V and J assignments, then by junction length + > # Take into consideration ambiguous V and J annotations + > dist <- distToNearest(db, sequenceColumn="junction", + + vCallColumn="v_call_genotyped", jCallColumn="j_call", + + model="ham", first=FALSE, VJthenLen=TRUE, normalize="len") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: distToNearest ... graph.adjacency.sparse -> make_graph -> do.call -> + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘Baseline-Vignette.Rmd’ using rmarkdown + A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TinyTeX with tinytex::reinstall_tinytex(repository = "illinois"). + + tlmgr: Local TeX Live (2022) is older than remote repository (2023). + Cross release updates are only supported with + update-tlmgr-latest(.sh/.exe) --update + See https://tug.org/texlive/upgrade.html for details. + Warning in system2("tlmgr", args, ...) : + running command ''tlmgr' search --file --global '/grffile.sty'' had status 1 + ... + LaTeX failed to compile /tmp/workdir/shazam/new/shazam.Rcheck/vign_test/shazam/vignettes/Targeting-Vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Targeting-Vignette.log for more info. + --- failed re-building ‘Targeting-Vignette.Rmd’ + + SUMMARY: processing the following files failed: + ‘Baseline-Vignette.Rmd’ ‘DistToNearest-Vignette.Rmd’ + ‘Mutation-Vignette.Rmd’ ‘Shmulate-Vignette.Rmd’ + ‘Targeting-Vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# shock + +
+ +* Version: 1.0 +* GitHub: NA +* Source code: https://github.com/cran/shock +* Date/Publication: 2015-12-24 14:45:29 +* Number of recursive dependencies: 14 + +Run `revdepcheck::cloud_details(, "shock")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘shock-Ex.R’ failed + The error most likely occurred in: + + > ### Name: computeLoglikeFromPartition + > ### Title: Compute the log-likelihood of the model + > ### Aliases: computeLoglikeFromPartition + > + > ### ** Examples + > + > ## load data to test + > data(dataTest) + > + > ## threshold of absS matrix + > myLABELS <- thresholdAbsSPath(dataTest)$partitionList + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: thresholdAbsSPath -> graph.adjacency -> graph.adjacency.dense + Execution halted + ``` + +# sidier + +
+ +* Version: 4.1.0 +* GitHub: NA +* Source code: https://github.com/cran/sidier +* Date/Publication: 2021-06-25 11:50:02 UTC +* Number of recursive dependencies: 58 + +Run `revdepcheck::cloud_details(, "sidier")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘sidier-Ex.R’ failed + The error most likely occurred in: + + > ### Name: zero.thr + > ### Title: Zero distance networks + > ### Aliases: zero.thr + > + > ### ** Examples + > + > + ... + Pop9 0.640 0.360 0.800 0.64 0.840 0.56 0.000 0.62 0.465 + Pop10 0.010 0.330 0.940 0.88 0.760 0.81 0.620 0.00 0.920 + Pop4-Pop5 0.555 0.875 0.715 0.54 0.295 0.27 0.465 0.92 0.000 + > # It is now possible to estimate a percolation threshold + > perc.thr(dis=Dis1_Merged,ptPDF=FALSE, estimPDF=FALSE, estimOutfile=FALSE) + [1] "Threshold value:0 Range to test: from 0 to 1" + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: perc.thr -> graph.adjacency -> graph.adjacency.dense + Execution halted + ``` + +# sigmajs + +
+ +* Version: 0.1.5 +* GitHub: https://github.com/JohnCoene/sigmajs +* Source code: https://github.com/cran/sigmajs +* Date/Publication: 2020-06-18 18:10:02 UTC +* Number of recursive dependencies: 76 + +Run `revdepcheck::cloud_details(, "sigmajs")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘sigmajs-Ex.R’ failed + The error most likely occurred in: + + > ### Name: sg_cluster + > ### Title: Cluster + > ### Aliases: sg_cluster sg_get_cluster + > + > ### ** Examples + > + > nodes <- sg_make_nodes() + ... + > + > sigmajs() %>% + + sg_nodes(nodes, id, size) %>% + + sg_edges(edges, id, source, target) %>% + + sg_layout() %>% + + sg_cluster() + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: %>% ... sg_get_layout -> .build_igraph -> -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 4. └─sigmajs:::.build_igraph(edges, directed = directed, nodes, save = save_igraph) + 5. └─igraph::graph_from_data_frame(edges, directed, nodes) + 6. └─igraph::make_empty_graph(n = 0, directed = directed) + ── Error ('test-formats.R:21:3'): igraph ─────────────────────────────────────── + Error in `.igraph.status("Restore graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─igraph::layout_with_fr(lesmis_igraph) at test-formats.R:21:2 + 2. └─igraph:::ensure_igraph(graph) + 3. └─igraph::is_igraph(graph) + 4. └─igraph:::warn_version(graph) + + [ FAIL 3 | WARN 8 | SKIP 0 | PASS 57 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 28 marked UTF-8 strings + ``` + +# signnet + +
+ +* Version: 1.0.1 +* GitHub: https://github.com/schochastics/signnet +* Source code: https://github.com/cran/signnet +* Date/Publication: 2023-01-27 13:40:02 UTC +* Number of recursive dependencies: 104 + +Run `revdepcheck::cloud_details(, "signnet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘signnet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: as_complex_edges + > ### Title: Convert Signed Network to Complex + > ### Aliases: as_complex_edges + > + > ### ** Examples + > + > g <- sample_islands_signed(2,10,1,10) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: sample_islands_signed ... -> make_graph -> do.call -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ▆ + 1. └─igraph::graph.full(5, directed = T) at test-signed_triangles.R:106:2 + ── Error ('test-utils.R:9:3'): from_edgelist works ───────────────────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─signnet::graph_from_edgelist_signed(el, signs) at test-utils.R:9:2 + 2. └─igraph::graph_from_edgelist(el, directed = directed) + 3. └─igraph::make_graph(unname(ids[t(el)]), directed = directed) + 4. ├─base::do.call(old_graph, args) + 5. └─igraph (local) ``(``, directed = FALSE) + + [ FAIL 65 | WARN 0 | SKIP 0 | PASS 23 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.7Mb + sub-directories of 1Mb or more: + libs 6.1Mb + ``` + +# simcausal + +
+ +* Version: 0.5.6 +* GitHub: https://github.com/osofr/simcausal +* Source code: https://github.com/cran/simcausal +* Date/Publication: 2022-10-28 11:52:27 UTC +* Number of recursive dependencies: 84 + +Run `revdepcheck::cloud_details(, "simcausal")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘simcausal-Ex.R’ failed + The error most likely occurred in: + + > ### Name: network + > ### Title: Define a Network Generator + > ### Aliases: network + > + > ### ** Examples + > + > #-------------------------------------------------------------------------------------------------- + ... + node W3, order:4 + node A, order:5 + node Y, order:6 + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Error in sampleNodeDistr(newNodeParams = newNodeParams, distr = distr, : + failed while sampling node 'ER.net', from distribution 'gen.ER' + Error in set.DAG(D, n.test = 100) : + ...attempt to simulate data from DAG failed... + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘test-all.R’ + Running the tests in ‘tests/test-all.R’ failed. + Last 13 lines of output: + ERROR in test.set.DAG_DAG2b_newactions: Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + ERROR in test.networkgen1: Error in set.DAG(D) : + ...attempt to simulate data from DAG failed... + ERROR in test.networkgen_time: Error in set.DAG(D) : + ...attempt to simulate data from DAG failed... + ERROR in test.tKmaxnet: Error in set.DAG(D, n.test = 200) : + ...attempt to simulate data from DAG failed... + ERROR in test.MV: Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Error: + + unit testing failed (#test failures: 0, #R errors: 7) + + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘simcausal_vignette.Rnw’ using knitr + + Quitting from lines 963-966 [DAG1t] (simcausal_vignette.Rnw) + Error: processing vignette 'simcausal_vignette.Rnw' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘simcausal_vignette.Rnw’ + + SUMMARY: processing the following file failed: + ‘simcausal_vignette.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# simer + +
+ +* Version: 0.9.0.2 +* GitHub: https://github.com/xiaolei-lab/SIMER +* Source code: https://github.com/cran/simer +* Date/Publication: 2022-08-08 13:30:02 UTC +* Number of recursive dependencies: 21 + +Run `revdepcheck::cloud_details(, "simer")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘simer-Ex.R’ failed + The error most likely occurred in: + + > ### Name: GxG.network + > ### Title: Genetic interaction network + > ### Aliases: GxG.network + > + > ### ** Examples + > + > pop.map <- generate.map(pop.marker = 1e4) + > GxG.net <- GxG.network(pop.map) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: GxG.network -> ba.game + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 9.5Mb + sub-directories of 1Mb or more: + libs 8.6Mb + ``` + +# simPATHy + +
+ +* Version: 0.6 +* GitHub: NA +* Source code: https://github.com/cran/simPATHy +* Date/Publication: 2021-11-23 09:50:02 UTC +* Number of recursive dependencies: 150 + +Run `revdepcheck::cloud_details(, "simPATHy")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘simPATHy-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plotCorGraph + > ### Title: Plot correlation or partial correlation matrix + > ### Aliases: plotCorGraph + > + > ### ** Examples + > + > if( require(gRbase) & require(graph)){ + ... + as.data.frame, basename, cbind, colnames, dirname, do.call, + duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, + lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, + pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, + tapply, union, unique, unsplit, which.max, which.min + + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: fitSgraph ... asMethod -> g_gn2ig_ -> -> graph_from_adj_list + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘simPATHy.Rmd’ using rmarkdown + + Quitting from lines 54-56 [unnamed-chunk-6] (simPATHy.Rmd) + Error: processing vignette 'simPATHy.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘simPATHy.Rmd’ + + SUMMARY: processing the following file failed: + ‘simPATHy.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# simplifyNet + +
+ +* Version: 0.0.1 +* GitHub: NA +* Source code: https://github.com/cran/simplifyNet +* Date/Publication: 2022-11-15 16:30:02 UTC +* Number of recursive dependencies: 23 + +Run `revdepcheck::cloud_details(, "simplifyNet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘simplifyNet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: EffRSparse + > ### Title: Sparsification through edge sampling via effective resistances + > ### Aliases: EffRSparse + > + > ### ** Examples + > + > #Generate random ER graph with uniformly random edge weights + > g = igraph::erdos.renyi.game(100, 0.1) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: + Execution halted + ``` + +# SIRE + +
+ +* Version: 1.1.0 +* GitHub: NA +* Source code: https://github.com/cran/SIRE +* Date/Publication: 2019-04-11 16:32:41 UTC +* Number of recursive dependencies: 79 + +Run `revdepcheck::cloud_details(, "SIRE")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘SIRE-Ex.R’ failed + The error most likely occurred in: + + > ### Name: causal_decompose + > ### Title: Estimation and decomposition of simultaneous equation model + > ### Aliases: causal_decompose + > + > ### ** Examples + > + > data("macroIT") + ... + > + > causal_decompose(data = macroIT, + + eq.system = eq.system, + + resid.est = "noDfCor", + + instruments = instruments, + + sigma.in = NULL) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: causal_decompose -> -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘dplyr’ ‘magrittr’ ‘psych’ ‘stringr’ + All declared Imports should be used. + ``` + +# sirt + +
+ +* Version: 3.12-66 +* GitHub: https://github.com/alexanderrobitzsch/sirt +* Source code: https://github.com/cran/sirt +* Date/Publication: 2022-05-17 09:10:05 UTC +* Number of recursive dependencies: 110 + +Run `revdepcheck::cloud_details(, "sirt")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘sirt-Ex.R’ failed + The error most likely occurred in: + + > ### Name: sia.sirt + > ### Title: Statistical Implicative Analysis (SIA) + > ### Aliases: sia.sirt + > + > ### ** Examples + > + > ############################################################################# + ... + > ############################################################################# + > + > data(data.read) + > dat <- data.read + > + > res <- sirt::sia.sirt(dat, significance=.85 ) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: ... -> make_graph -> do.call -> + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 22.0Mb + sub-directories of 1Mb or more: + R 2.1Mb + libs 17.8Mb + ``` + +# SITH + +
+ +* Version: 1.1.0 +* GitHub: https://github.com/phillipnicol/SITH +* Source code: https://github.com/cran/SITH +* Date/Publication: 2021-01-05 15:10:02 UTC +* Number of recursive dependencies: 58 + +Run `revdepcheck::cloud_details(, "SITH")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘SITH.Rmd’ using rmarkdown + Warning in snapshot3d(paste0(name, ".png")) : + webshot = TRUE requires the webshot2 package and Chrome browser; using rgl.snapshot() instead + Warning in rgl.snapshot(filename, fmt, top) : + this build of rgl does not support snapshots + Warning in snapshot3d(paste0(name, ".png")) : + webshot = TRUE requires the webshot2 package and Chrome browser; using rgl.snapshot() instead + Warning in rgl.snapshot(filename, fmt, top) : + ... + Quitting from lines 296-304 [unnamed-chunk-17] (SITH.Rmd) + Error: processing vignette 'SITH.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘SITH.Rmd’ + + SUMMARY: processing the following file failed: + ‘SITH.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# skynet + +
+ +* Version: 1.4.3 +* GitHub: https://github.com/ropensci/skynet +* Source code: https://github.com/cran/skynet +* Date/Publication: 2022-06-17 13:00:02 UTC +* Number of recursive dependencies: 105 + +Run `revdepcheck::cloud_details(, "skynet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘skynet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: summary.skynet + > ### Title: Displays a summary of a skynet object + > ### Aliases: summary.skynet + > + > ### ** Examples + > + > net <- make_net_dir(OD_Sample) + ... + + # Auto named with `tibble::lst()`: tibble::lst(mean, median) + + # Using lambdas list(~ mean(., trim = .2), ~ median(., na.rm = TRUE)) + ℹ The deprecated feature was likely used in the skynet package. + Please report the issue at . + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: make_net_dir -> -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 1. └─skynet::make_net_dir(OD_Sample) at test_smallerfunctions.R:21:2 + 2. └─igraph::graph_from_data_frame(netDir_all, directed = TRUE, vertices = nodes) + 3. └─igraph::make_empty_graph(n = 0, directed = directed) + ── Error ('test_smallerfunctions.R:33:3'): Plot Map ──────────────────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. ├─skynet::net_map(make_net_dir(OD_Sample)) at test_smallerfunctions.R:33:2 + 2. └─skynet::make_net_dir(OD_Sample) + 3. └─igraph::graph_from_data_frame(netDir_all, directed = TRUE, vertices = nodes) + 4. └─igraph::make_empty_graph(n = 0, directed = directed) + + [ FAIL 14 | WARN 14 | SKIP 4 | PASS 20 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘skynet.Rmd’ using rmarkdown + + Quitting from lines 97-101 [unnamed-chunk-4] (skynet.Rmd) + Error: processing vignette 'skynet.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘skynet.Rmd’ + + SUMMARY: processing the following file failed: + ‘skynet.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘maps’ + All declared Imports should be used. + ``` + +# SmCCNet + +
+ +* Version: 0.99.0 +* GitHub: https://github.com/KechrisLab/SmCCNet +* Source code: https://github.com/cran/SmCCNet +* Date/Publication: 2019-03-04 16:50:03 UTC +* Number of recursive dependencies: 9 + +Run `revdepcheck::cloud_details(, "SmCCNet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘SmCCNet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plotMultiOmicsNetwork + > ### Title: Plot multi-omics module networks. + > ### Aliases: plotMultiOmicsNetwork + > + > ### ** Examples + > + > set.seed(123) + ... + > abar <- getAbar(w, P1 = 2, FeatureLabel = NULL) + > modules <- getMultiOmicsModules(abar, P1 = 2, CutHeight = 0.5) + > x <- cbind(geneExpr[ ,seq_len(2)], mirnaExpr[ , seq_len(3)]) + > corr <- cor(x) + > + > plotMultiOmicsNetwork(abar, corr, modules, ModuleIdx = 1, P1 = 2) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plotMultiOmicsNetwork -> -> graph.adjacency.dense + Execution halted + ``` + +# smotefamily + +
+ +* Version: 1.3.1 +* GitHub: NA +* Source code: https://github.com/cran/smotefamily +* Date/Publication: 2019-05-30 07:30:02 UTC +* Number of recursive dependencies: 10 + +Run `revdepcheck::cloud_details(, "smotefamily")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘smotefamily-Ex.R’ failed + The error most likely occurred in: + + > ### Name: DBSMOTE + > ### Title: Density-based SMOTE + > ### Aliases: DBSMOTE + > ### Keywords: manip methods + > + > ### ** Examples + > + > data_example = sample_generator(5000,ratio = 0.90) + > genData = DBSMOTE(data_example[,-3],data_example[,3]) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: DBSMOTE -> -> graph.adjacency.dense + Execution halted + ``` + +# snowboot + +
+ +* Version: 1.0.2 +* GitHub: NA +* Source code: https://github.com/cran/snowboot +* Date/Publication: 2020-04-25 18:30:03 UTC +* Number of recursive dependencies: 10 + +Run `revdepcheck::cloud_details(, "snowboot")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘snowboot-Ex.R’ failed + The error most likely occurred in: + + > ### Name: igraph_to_network + > ### Title: Create a "Network" Object from an igraph Object + > ### Aliases: igraph_to_network + > + > ### ** Examples + > + > hex_ring <- igraph::make_ring(6, directed = FALSE, mutual = FALSE, circular = TRUE) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: + Execution halted + ``` + +# SNscan + +
+ +* Version: 1.0 +* GitHub: NA +* Source code: https://github.com/cran/SNscan +* Date/Publication: 2016-01-19 13:09:28 +* Number of recursive dependencies: 11 + +Run `revdepcheck::cloud_details(, "SNscan")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘SNscan-Ex.R’ failed + The error most likely occurred in: + + > ### Name: group.graph + > ### Title: Generate igraph Objects with Different Connection + > ### Characteristics. + > ### Aliases: group.graph + > ### Keywords: graph sampling + > + > ### ** Examples + ... + > + > group.graph(V=10, cv =1:3 , p1=1/10, p2 = 1/2) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: group.graph -> graph.adjacency -> graph.adjacency.dense + Execution halted + Error in .igraph.status("Free graph external pointer.\n") : + could not find function ".igraph.status" + Error in .igraph.status("Free graph external pointer.\n") : + could not find function ".igraph.status" + ``` + +# SOAs + +
+ +* Version: 1.3 +* GitHub: https://github.com/bertcarnell/SOAs +* Source code: https://github.com/cran/SOAs +* Date/Publication: 2022-10-03 11:30:02 UTC +* Number of recursive dependencies: 58 + +Run `revdepcheck::cloud_details(, "SOAs")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 8. └─igraph (local) ``(``, directed = TRUE) + ── Error ('test-utilitiesCreate.R:3:1'): utilitiesCreate ─────────────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─SOAs:::createAB(3) at test-utilitiesCreate.R:3:0 + 2. └─SOAs:::BcolsFromBcolllist(Bcollist) + 3. └─igraph::graph_from_edgelist(el) + 4. └─igraph::make_graph(t(el), directed = directed) + 5. ├─base::do.call(old_graph, args) + 6. └─igraph (local) ``(``, directed = TRUE) + + [ FAIL 3 | WARN 0 | SKIP 14 | PASS 1036 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘iterators’ ‘itertools’ + All declared Imports should be used. + ``` + +# SoilR + +
+ +* Version: 1.2.105 +* GitHub: NA +* Source code: https://github.com/cran/SoilR +* Date/Publication: 2022-01-23 16:12:42 UTC +* Number of recursive dependencies: 49 + +Run `revdepcheck::cloud_details(, "SoilR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘SoilR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: WangThreePoolNonAutonomous_sym + > ### Title: A non-autonomous version of the original Wang 3 pool model + > ### Aliases: WangThreePoolNonAutonomous_sym + > + > ### ** Examples + > + > # This is a working example which demostrates some of the new functionality. + > require('SoilR',quietly =TRUE) + > smod <- WangThreePoolNonAutonomous_sym() + > # (look at the source code of WangThreePoolNonAutonomous_sym ) + > plotPoolGraph(smod) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plotPoolGraph ... plotPoolGraphFromTupleLists -> graph_from_data_frame -> make_empty_graph + Execution halted + ``` + +# solitude + +
+ +* Version: 1.1.3 +* GitHub: https://github.com/talegari/solitude +* Source code: https://github.com/cran/solitude +* Date/Publication: 2021-07-29 20:00:02 UTC +* Number of recursive dependencies: 131 + +Run `revdepcheck::cloud_details(, "solitude")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘solitude-Ex.R’ failed + The error most likely occurred in: + + > ### Name: terminalNodesDepth + > ### Title: Depth of each terminal node of all trees in a ranger model + > ### Aliases: terminalNodesDepth + > + > ### ** Examples + > + > rf = ranger::ranger(Species ~ ., data = iris, num.trees = 100) + > terminalNodesDepth(rf) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: terminalNodesDepth ... resolve.list -> signalConditionsASAP -> signalConditions + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘R6’ ‘lgr’ + All declared Imports should be used. + ``` + +# SourceSet + +
+ +* Version: 0.1.5 +* GitHub: NA +* Source code: https://github.com/cran/SourceSet +* Date/Publication: 2022-11-21 11:30:02 UTC +* Number of recursive dependencies: 106 + +Run `revdepcheck::cloud_details(, "SourceSet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘SourceSet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: infoSource + > ### Title: Get summary statistics on graphs and variables + > ### Aliases: infoSource + > + > ### ** Examples + > + > ## Load the SourceSetObj obtained from the source set analysis of ALL dataset + ... + as.data.frame, basename, cbind, colnames, dirname, do.call, + duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, + lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, + pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, + tapply, union, unique, unsplit, which.max, which.min + + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: infoSource ... ensure_igraph -> -> graph_from_adj_list + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘SourceSet.Rmd’ using rmarkdown + + Quitting from lines 151-158 [unnamed-chunk-5] (SourceSet.Rmd) + Error: processing vignette 'SourceSet.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘SourceSet.Rmd’ + + SUMMARY: processing the following file failed: + ‘SourceSet.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘r2cytoscape’ + ``` + +# spacejamr + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/dscolby/spacejamr +* Source code: https://github.com/cran/spacejamr +* Date/Publication: 2022-04-01 20:10:02 UTC +* Number of recursive dependencies: 138 + +Run `revdepcheck::cloud_details(, "spacejamr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘spacejamr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: NetSim + > ### Title: Simulate a network from a point process or sequence + > ### Aliases: NetSim + > + > ### ** Examples + > + > # Load spacejamr object + ... + + power = -2.4) + Warning: There was 1 warning in `dplyr::mutate()`. + ℹ In argument: `dplyr::across(...)`. + Caused by warning: + ! Using `across()` without supplying `.cols` was deprecated in dplyr 1.1.0. + ℹ Please supply `.cols` instead. + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: NetSim ... ensure_igraph -> -> graph.adjacency.dense + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. ├─spacejamr::NetSim(ri_points) at test-generics.R:6:0 + 2. │ └─spacejamr:::new_NetSim(...) + 3. │ └─spacejamr:::validate_NetSim(...) + 4. │ ├─... %>% igraph::simplify() + 5. │ └─igraph::graph_from_adjacency_matrix(distances, mode = "undirected") + 6. │ └─igraph:::graph.adjacency.dense(...) + 7. └─igraph::simplify(.) + 8. └─igraph:::ensure_igraph(graph) + + [ FAIL 3 | WARN 1 | SKIP 0 | PASS 10 ] + Error: Test failures + Execution halted + ``` + +# sparsebnUtils + +
+ +* Version: 0.0.8 +* GitHub: https://github.com/itsrainingdata/sparsebnUtils +* Source code: https://github.com/cran/sparsebnUtils +* Date/Publication: 2021-01-27 06:30:02 UTC +* Number of recursive dependencies: 69 + +Run `revdepcheck::cloud_details(, "sparsebnUtils")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. ├─sparsebnUtils::to_edgeList(to_graphNEL(to_network(to_igraph(sbf.empty)))) + 5. ├─sparsebnUtils::to_graphNEL(to_network(to_igraph(sbf.empty))) + 6. ├─sparsebnUtils::to_network(to_igraph(sbf.empty)) + 7. ├─sparsebnUtils::to_igraph(sbf.empty) + 8. └─sparsebnUtils:::to_igraph.sparsebnFit(sbf.empty) + 9. ├─sparsebnUtils::to_igraph(x$edges) + 10. └─sparsebnUtils:::to_igraph.edgeList(x$edges) + 11. └─igraph::graph.adjacency(as.matrix(x)) + 12. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 8 | WARN 0 | SKIP 1 | PASS 284 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking Rd cross-references ... NOTE + ``` + Unknown package ‘sparsebn’ in Rd xrefs + ``` + +# spathial + +
+ +* Version: 0.1.2 +* GitHub: NA +* Source code: https://github.com/cran/spathial +* Date/Publication: 2020-04-10 18:20:02 UTC +* Number of recursive dependencies: 43 + +Run `revdepcheck::cloud_details(, "spathial")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘spathial-Ex.R’ failed + The error most likely occurred in: + + > ### Name: spathialPrefiltering + > ### Title: Prefilter data + > ### Aliases: spathialPrefiltering + > + > ### ** Examples + > + > # Load data matrix X + ... + > boundaryRes <- spathialBoundaryIds(X, X_labels, mode=2, from=3, to=6) + > X <- boundaryRes$X + > X_labels <- boundaryRes$X_labels + > boundary_ids <- boundaryRes$boundary_ids + > # Run spathial spathialPrefilterinh with the output of the function spathialBoundaryIds + > filterRes <- spathialPrefiltering(X, boundary_ids) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: spathialPrefiltering ... rkm_prefilter -> -> graph.adjacency.dense + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘vignette.rmd’ using rmarkdown + + Quitting from lines 178-186 [unnamed-chunk-15] (vignette.rmd) + Error: processing vignette 'vignette.rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘vignette.rmd’ + + SUMMARY: processing the following file failed: + ‘vignette.rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘irlba’ ‘knitr’ ‘rmarkdown’ + All declared Imports should be used. + ``` + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# spatsoc + +
+ +* Version: 0.1.16 +* GitHub: https://github.com/ropensci/spatsoc +* Source code: https://github.com/cran/spatsoc +* Date/Publication: 2021-02-24 06:50:02 UTC +* Number of recursive dependencies: 70 + +Run `revdepcheck::cloud_details(, "spatsoc")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘spatsoc-Ex.R’ failed + The error most likely occurred in: + + > ### Name: get_gbi + > ### Title: Generate group by individual matrix + > ### Aliases: get_gbi + > + > ### ** Examples + > + > # Load data.table + ... + Please note that rgeos will be retired during October 2023, + plan transition to sf or terra functions using GEOS at your earliest convenience. + See https://r-spatial.org/r/2023/05/15/evolution4.html for details. + Linking to sp version: 1.6-1 + Polygon checking: TRUE + + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: group_polys ... [.data.table -> -> graph.adjacency.dense + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 7. └─igraph::graph_from_adjacency_matrix(distMatrix <= threshold) + 8. └─igraph:::graph.adjacency.dense(...) + ── Error ('test-random.R:11:1'): (code run outside of `test_that()`) ─────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. ├─spatsoc::group_pts(...) at test-random.R:11:0 + 2. │ ├─...[] + 3. │ └─data.table:::`[.data.table`(...) + 4. └─igraph::graph_from_adjacency_matrix(distMatrix <= threshold) + 5. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 26 | WARN 7 | SKIP 0 | PASS 184 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘using-edge-and-dyad.Rmd’ using rmarkdown + --- finished re-building ‘using-edge-and-dyad.Rmd’ + + --- re-building ‘faq.Rmd’ using knitr + + Quitting from lines 32-53 [unnamed-chunk-1] (faq.Rmd) + Error: processing vignette 'faq.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘faq.Rmd’ + ... + --- failed re-building ‘intro-spatsoc.Rmd’ + + --- re-building ‘using-in-sna.Rmd’ using knitr + --- finished re-building ‘using-in-sna.Rmd’ + + SUMMARY: processing the following files failed: + ‘faq.Rmd’ ‘intro-spatsoc.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# specr + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/masurp/specr +* Source code: https://github.com/cran/specr +* Date/Publication: 2023-01-20 13:50:02 UTC +* Number of recursive dependencies: 152 + +Run `revdepcheck::cloud_details(, "specr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘specr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_decisiontree + > ### Title: Plot decision tree + > ### Aliases: plot_decisiontree + > + > ### ** Examples + > + > results <- run_specs(df = example_data, + ... + + controls = c("c1", "c2")) + > + > # Basic, non-labelled decisions tree + > plot_decisiontree(results) + Warning: `plot_decisiontree()` was deprecated in specr 1.0.0. + ℹ Please use `plot.specr.setup()` instead. + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot_decisiontree ... create_layout -> graph_from_data_frame -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. ├─base::plot(specs) at test-generics.R:13:2 + 2. ├─specr:::plot.specr.setup(specs) + 3. │ └─edge_list %>% graph_from_data_frame %>% ... + 4. ├─ggraph::ggraph(., layout = layout, circular = circular) + 5. │ ├─ggplot2::ggplot(data = create_layout(graph, layout, ...), environment = envir) + 6. │ └─ggraph::create_layout(graph, layout, ...) + 7. └─igraph::graph_from_data_frame(.) + 8. └─igraph::make_empty_graph(n = 0, directed = directed) + + [ FAIL 1 | WARN 8 | SKIP 0 | PASS 25 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘custom-plot.rmd’ using rmarkdown + --- finished re-building ‘custom-plot.rmd’ + + --- re-building ‘different-specifications.Rmd’ using rmarkdown + --- finished re-building ‘different-specifications.Rmd’ + + --- re-building ‘getting-started.rmd’ using rmarkdown + + Quitting from lines 75-76 [unnamed-chunk-5] (getting-started.rmd) + ... + --- finished re-building ‘parallel-bayesian-models.Rmd’ + + --- re-building ‘parallelization.Rmd’ using rmarkdown + --- finished re-building ‘parallelization.Rmd’ + + SUMMARY: processing the following file failed: + ‘getting-started.rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# spinner + +
+ +* Version: 1.1.0 +* GitHub: NA +* Source code: https://github.com/cran/spinner +* Date/Publication: 2023-03-21 06:10:02 UTC +* Number of recursive dependencies: 76 + +Run `revdepcheck::cloud_details(, "spinner")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + > library(spinner) + > + > test_check("spinner") + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test.R:1:1'): (code run outside of `test_that()`) ─────────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─igraph::random.graph.game(20, 0.3) at test.R:1:0 + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] + Error: Test failures + Execution halted + ``` + +# spNetwork + +
+ +* Version: 0.4.3.7 +* GitHub: https://github.com/JeremyGelb/spNetwork +* Source code: https://github.com/cran/spNetwork +* Date/Publication: 2023-04-11 15:50:02 UTC +* Number of recursive dependencies: 150 + +Run `revdepcheck::cloud_details(, "spNetwork")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘spNetwork-Ex.R’ failed + The error most likely occurred in: + + > ### Name: build_graph + > ### Title: Network generation + > ### Aliases: build_graph + > + > ### ** Examples + > + > data(mtl_network) + > mtl_network$length <- as.numeric(sf::st_length(mtl_network)) + > graph_result <- build_graph(mtl_network, 2, "length", attrs = TRUE) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: build_graph -> -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ── Error ('test_tnkde_sf.R:285:3'): Testing the multicore version of the function TNKDE ── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─spNetwork::tnkde(...) at test_tnkde_sf.R:285:2 + 2. └─base::lapply(...) + 3. └─spNetwork (local) FUN(X[[i]], ...) + 4. └─spNetwork:::tnkde_worker(...) + 5. └─spNetwork::build_graph(lines, digits = digits, line_weight = "length") + 6. └─igraph::graph_from_data_frame(linelist, directed = FALSE, vertices = NULL) + 7. └─igraph::make_empty_graph(n = 0, directed = directed) + + [ FAIL 56 | WARN 0 | SKIP 0 | PASS 18 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘Isochrones.Rmd’ using rmarkdown + + Quitting from lines 66-72 [unnamed-chunk-2] (Isochrones.Rmd) + Error: processing vignette 'Isochrones.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘Isochrones.Rmd’ + + --- re-building ‘KNetworkFunctions.Rmd’ using rmarkdown + --- finished re-building ‘KNetworkFunctions.Rmd’ + ... + --- finished re-building ‘SpatialWeightMatrices.Rmd’ + + --- re-building ‘TNKDE.Rmd’ using rmarkdown + --- finished re-building ‘TNKDE.Rmd’ + + SUMMARY: processing the following file failed: + ‘Isochrones.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 30.6Mb + sub-directories of 1Mb or more: + doc 1.1Mb + extdata 2.6Mb + libs 25.5Mb + ``` + +# spqdep + +
+ +* Version: 0.1.2 +* GitHub: NA +* Source code: https://github.com/cran/spqdep +* Date/Publication: 2022-03-28 16:20:02 UTC +* Number of recursive dependencies: 114 + +Run `revdepcheck::cloud_details(, "spqdep")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘spqdep-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Q.map.test + > ### Title: Compute the QE and QI tests of Equivalence and Independence + > ### between maps + > ### Aliases: Q.map.test + > + > ### ** Examples + > + ... + + attr(,"class") + [1] "qmap" "list" + > plot(qmap) + > plot(qmap, ci=.6) + > plot(qmap[[1]]$mh) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot ... plot.m_surr -> graph.adjacency -> graph.adjacency.dense + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘spq_userguide.Rmd’ using rmarkdown + + Quitting from lines 137-138 [plot mh] (spq_userguide.Rmd) + Error: processing vignette 'spq_userguide.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘spq_userguide.Rmd’ + + SUMMARY: processing the following file failed: + ‘spq_userguide.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘lwgeom’ ‘rgeoda’ + All declared Imports should be used. + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 4 marked UTF-8 strings + ``` + +# SSN + +
+ +* Version: 1.1.17 +* GitHub: NA +* Source code: https://github.com/cran/SSN +* Date/Publication: 2023-02-27 08:22:38 UTC +* Number of recursive dependencies: 27 + +Run `revdepcheck::cloud_details(, "SSN")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘SSN-Ex.R’ failed + The error most likely occurred in: + + > ### Name: SimulateOnSSN + > ### Title: Simulating Data on Spatial Stream Networks + > ### Aliases: SimulateOnSSN + > + > ### ** Examples + > + > ####################################### + ... + > library(SSN) + > set.seed(101) + > ## simulate a SpatialStreamNetwork object + > raw1.ssn <- createSSN(n = c(10,10), + + obsDesign = binomialDesign(c(50,50)), predDesign = binomialDesign(c(100,100)), + + importToR = TRUE, path = paste(tempdir(),"/sim1", sep = "")) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: createSSN + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘SSN.Rnw’ using Sweave + Error: processing vignette 'SSN.Rnw' failed with diagnostics: + Running 'texi2dvi' on 'SSN.tex' failed. + LaTeX errors: + ! LaTeX Error: File `ae.sty' not found. + + Type X to quit or to proceed, + or enter new name. (Default extension: sty) + + ... + l.30 \ifthenelse + {\boolean{Sweave@inconsolata}}{%^^M + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘STARS.Rnw’ + + SUMMARY: processing the following files failed: + ‘SSN.Rnw’ ‘STARS.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# stagedtrees + +
+ +* Version: 2.2.1 +* GitHub: https://github.com/gherardovarando/stagedtrees +* Source code: https://github.com/cran/stagedtrees +* Date/Publication: 2022-04-28 23:10:02 UTC +* Number of recursive dependencies: 48 + +Run `revdepcheck::cloud_details(, "stagedtrees")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise) + 3. │ ├─testthat (local) .capture(...) + 4. │ │ ├─withr::with_output_sink(...) + 5. │ │ │ └─base::force(code) + 6. │ │ ├─base::withCallingHandlers(...) + 7. │ │ └─base::withVisible(code) + 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 9. ├─base::plot(ceg(mod), col = "stages") + 10. └─stagedtrees:::plot.ceg(ceg(mod), col = "stages") + 11. └─igraph::graph_from_adjacency_matrix(A) + 12. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 1037 ] + Error: Test failures + Execution halted + ``` + +# statGraph + +
+ +* Version: 0.5.0 +* GitHub: NA +* Source code: https://github.com/cran/statGraph +* Date/Publication: 2021-05-19 07:00:06 UTC +* Number of recursive dependencies: 17 + +Run `revdepcheck::cloud_details(, "statGraph")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘statGraph-Ex.R’ failed + The error most likely occurred in: + + > ### Name: GIC + > ### Title: Graph Information Criterion (GIC) + > ### Aliases: GIC + > ### Keywords: graph_information_criterion + > + > ### ** Examples + > + > set.seed(1) + > G <- as.matrix(igraph::get.adjacency(igraph::sample_gnp(n=50, p=0.5))) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: as.matrix -> -> ensure_igraph -> + Execution halted + ``` + +# stemmatology + +
+ +* Version: 0.3.2 +* GitHub: https://github.com/Jean-Baptiste-Camps/stemmatology +* Source code: https://github.com/cran/stemmatology +* Date/Publication: 2019-04-10 15:52:51 UTC +* Number of recursive dependencies: 64 + +Run `revdepcheck::cloud_details(, "stemmatology")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘stemmatology-Ex.R’ failed + The error most likely occurred in: + + > ### Name: PCC.Exploratory + > ### Title: PCC Exploratory methods + > ### Aliases: PCC.Exploratory + > ### Keywords: stemmatology + > + > ### ** Examples + > + ... + > ## Don't show: + > # subsetting for exec time + > fournival = fournival[1:50,c(-5,-8)] + > ## End(Don't show) + > # Non interactive mode + > PCC.Exploratory(fournival, ask = FALSE, threshold = 0.06) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: PCC.Exploratory ... -> make_graph -> do.call -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. ├─testthat::expect_equal(...) at test-layout_as_stemma.R:11:2 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. └─stemmatology::layout_as_stemma(edgelist) + 5. └─igraph::graph_from_edgelist(edgelist[, 1:2], directed = TRUE) + 6. └─igraph::make_graph(unname(ids[t(el)]), directed = directed) + 7. ├─base::do.call(old_graph, args) + 8. └─igraph (local) ``(``, directed = TRUE) + + [ FAIL 13 | WARN 0 | SKIP 4 | PASS 43 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘stemmatology.Rnw’ using Sweave + Error: processing vignette 'stemmatology.Rnw' failed with diagnostics: + Running 'texi2dvi' on 'stemmatology.tex' failed. + LaTeX errors: + ! LaTeX Error: File `ae.sty' not found. + + Type X to quit or to proceed, + or enter new name. (Default extension: sty) + ... + l.55 \RequirePackage + [T1]{fontenc}^^M + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘stemmatology.Rnw’ + + SUMMARY: processing the following file failed: + ‘stemmatology.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# stm + +
+ +* Version: 1.3.6 +* GitHub: https://github.com/bstewart/stm +* Source code: https://github.com/cran/stm +* Date/Publication: 2020-09-18 13:50:02 UTC +* Number of recursive dependencies: 86 + +Run `revdepcheck::cloud_details(, "stm")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘stmVignette.Rnw’ + ... + + > cloud(poliblogPrevFit, topic = 7, scale = c(2, 0.25)) + + > mod.out.corr <- topicCorr(poliblogPrevFit) + + > plot(mod.out.corr) + + When sourcing 'stmVignette.R': + Error: could not find function ".igraph.status" + Execution halted + + ‘stmVignette.Rnw’ using ‘UTF-8’... failed + ``` + +## In both + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Error in `if (...length() && any(...names() == "Dimnames")) .Object@Dimnames <- fixupDN(.Object@Dimnames)`: missing value where TRUE/FALSE needed + Backtrace: + ▆ + 1. ├─quanteda::dfm(...) at test-quanteda-stm.R:9:4 + 2. └─quanteda:::dfm.corpus(...) + 3. └─(function(x, tolower = TRUE, remove_padding = FALSE, stem = NULL, ... + 4. └─quanteda:::dfm.tokens(...) + 5. └─quanteda:::build_dfm(...) + 6. └─methods::new(...) + 7. ├─methods::initialize(value, ...) + 8. └─Matrix (local) initialize(value, ...) + + [ FAIL 1 | WARN 3 | SKIP 0 | PASS 8 ] + Error: Test failures + Execution halted + ``` + +* checking installed package size ... NOTE + ``` + installed size is 6.3Mb + sub-directories of 1Mb or more: + data 1.7Mb + libs 3.4Mb + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘stmVignette.Rnw’ using Sweave + stm v1.3.6 successfully loaded. See ?stm for help. + Papers, resources, and other materials at structuraltopicmodel.com + + Error: processing vignette 'stmVignette.Rnw' failed with diagnostics: + chunk 27 + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + + --- failed re-building 'stmVignette.Rnw' + + SUMMARY: processing the following file failed: + 'stmVignette.Rnw' + + Error: Vignette re-building failed. + Execution halted + ``` + +# stplanr + +
+ +* Version: 1.0.2 +* GitHub: https://github.com/ropensci/stplanr +* Source code: https://github.com/cran/stplanr +* Date/Publication: 2022-11-08 12:40:02 UTC +* Number of recursive dependencies: 167 + +Run `revdepcheck::cloud_details(, "stplanr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘stplanr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: rnet_group + > ### Title: Assign segments in a route network to groups + > ### Aliases: rnet_group rnet_group.default rnet_group.sfc rnet_group.sf + > + > ### ** Examples + > + > rnet <- rnet_breakup_vertices(stplanr::osm_net_example) + > rnet$group <- rnet_group(rnet) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: rnet_group ... rnet_group.sf -> rnet_group -> rnet_group.sfc -> + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘stplanr-od.Rmd’ using rmarkdown + --- finished re-building ‘stplanr-od.Rmd’ + + --- re-building ‘stplanr-paper.Rmd’ using rmarkdown + --- finished re-building ‘stplanr-paper.Rmd’ + + --- re-building ‘stplanr-parallel.Rmd’ using rmarkdown + --- finished re-building ‘stplanr-parallel.Rmd’ + + ... + --- finished re-building ‘stplanr-routing.Rmd’ + + --- re-building ‘stplanr.Rmd’ using rmarkdown + --- finished re-building ‘stplanr.Rmd’ + + SUMMARY: processing the following file failed: + ‘stplanr-route-nets.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# SurvHiDim + +
+ +* Version: 0.1.1 +* GitHub: NA +* Source code: https://github.com/cran/SurvHiDim +* Date/Publication: 2021-06-26 15:40:02 UTC +* Number of recursive dependencies: 171 + +Run `revdepcheck::cloud_details(, "SurvHiDim")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘SurvHiDim-Ex.R’ failed + The error most likely occurred in: + + > ### Name: hdNetwork + > ### Title: hdNetwork + > ### Aliases: hdNetwork + > + > ### ** Examples + > + > ## + > data(hnscc) + > hdNetwork(7,105,0.05,0.2,ID="id",OS="os",Death="death",PFS="pfs",Prog="prog",hnscc) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: hdNetwork ... graph_from_adjacency_matrix -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘readr’ + All declared Imports should be used. + ``` + +# targets + +
+ +* Version: 1.1.3 +* GitHub: https://github.com/ropensci/targets +* Source code: https://github.com/cran/targets +* Date/Publication: 2023-05-23 14:10:02 UTC +* Number of recursive dependencies: 177 + +Run `revdepcheck::cloud_details(, "targets")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ──────────────────────────────────────────────────────────────────────────────── + Maximum number of failures exceeded; quitting at end of file. + ℹ Increase this number with (e.g.) `testthat::set_max_fails(Inf)` + + ══ Results ═════════════════════════════════════════════════════════════════════ + Duration: 4.7 s + + ── Skipped tests ────────────────────────────────────────────────────────────── + • On CRAN (44) + • version of crew, mirai, or nanonext is too low (6) + + [ FAIL 36 | WARN 0 | SKIP 50 | PASS 202 ] + ══ Terminated early ════════════════════════════════════════════════════════════ + Error: Test failures + Execution halted + ``` + +# TDA + +
+ +* Version: 1.9 +* GitHub: NA +* Source code: https://github.com/cran/TDA +* Date/Publication: 2023-02-04 18:42:30 UTC +* Number of recursive dependencies: 59 + +Run `revdepcheck::cloud_details(, "TDA")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘TDA-Ex.R’ failed + The error most likely occurred in: + + > ### Name: clusterTree + > ### Title: Density clustering: the cluster tree + > ### Aliases: clusterTree print.clusterTree + > ### Keywords: nonparametric + > + > ### ** Examples + > + ... + > X <- rbind(X1, X2, X3) + > + > k <- 100 #parameter of knn + > + > ## Density clustering using knn and kde + > Tree <- clusterTree(X, k, density = "knn") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: clusterTree -> -> graph.adjacency.dense + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘article.Rnw’ + ... + > X3 <- cbind(rnorm(300, 6, 1), rnorm(300, 1, 1)) + + > XX <- rbind(X1, X2, X3) + + > Tree <- clusterTree(XX, k = 100, density = "knn", + + printProgress = FALSE) + + When sourcing ‘article.R’: + Error: could not find function ".igraph.status" + Execution halted + + ‘article.Rnw’ using ‘UTF-8’... failed + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 51.4Mb + sub-directories of 1Mb or more: + libs 50.2Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘scales’ + All declared Imports should be used. + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘article.Rnw’ using Sweave + + Error: processing vignette 'article.Rnw' failed with diagnostics: + chunk 48 (label = eq18b) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + + --- failed re-building ‘article.Rnw’ + + SUMMARY: processing the following file failed: + ‘article.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# text2map + +
+ +* Version: 0.1.6 +* GitHub: NA +* Source code: https://github.com/cran/text2map +* Date/Publication: 2022-08-17 22:20:02 UTC +* Number of recursive dependencies: 133 + +Run `revdepcheck::cloud_details(, "text2map")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘text2map-Ex.R’ failed + The error most likely occurred in: + + > ### Name: CoCA + > ### Title: Performs Concept Class Analysis (CoCA) + > ### Aliases: CoCA + > + > ### ** Examples + > + > + ... + + wv = ft_wv_sample, + + directions = sem_dirs, + + filter_sig = TRUE, + + filter_value = 0.05, + + zero_action = "drop" + + ) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: CoCA ... .get_cor_class -> -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 13. │ └─base::eval(exprs, env) + 14. │ └─text2map:::tidytext_dfm(corpus) at tests/testthat/helper-data.R:184:0 + 15. │ └─... %>% tidytext::cast_dfm(doc_id, word, n) at tests/testthat/helper-data.R:162:12 + 16. ├─tidytext::cast_dfm(., doc_id, word, n) + 17. │ ├─quanteda::as.dfm(m) + 18. │ └─quanteda:::as.dfm.Matrix(m) + 19. │ └─quanteda:::matrix2dfm(x) + 20. │ └─quanteda:::build_dfm(...) + 21. │ └─methods::new(...) + 22. │ ├─methods::initialize(value, ...) + 23. │ └─Matrix (local) initialize(value, ...) + 24. └─base::.handleSimpleError(...) + 25. └─testthat (local) h(simpleError(msg, call)) + 26. └─rlang::abort(...) + Execution halted + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 3 marked UTF-8 strings + ``` + +# textrank + +
+ +* Version: 0.3.1 +* GitHub: https://github.com/bnosac/textrank +* Source code: https://github.com/cran/textrank +* Date/Publication: 2020-10-12 11:50:02 UTC +* Number of recursive dependencies: 54 + +Run `revdepcheck::cloud_details(, "textrank")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘textrank-Ex.R’ failed + The error most likely occurred in: + + > ### Name: textrank_candidates_lsh + > ### Title: Use locality-sensitive hashing to get combinations of sentences + > ### which contain words which are in the same minhash bucket + > ### Aliases: textrank_candidates_lsh + > + > ### ** Examples + > + ... + + textrank_candidates = candidates) + + summary(tr, n = 2) + + ## Don't show: + + } # End of main if statement running only if the required packages are installed + Loading required package: udpipe + Loading required package: textreuse + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: textrank_sentences -> -> make_empty_graph + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘textrank.Rmd’ using rmarkdown + + Quitting from lines 78-81 [unnamed-chunk-4] (textrank.Rmd) + Error: processing vignette 'textrank.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘textrank.Rmd’ + + SUMMARY: processing the following file failed: + ‘textrank.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# tidygraph + +
+ +* Version: 1.2.3 +* GitHub: https://github.com/thomasp85/tidygraph +* Source code: https://github.com/cran/tidygraph +* Date/Publication: 2023-02-01 21:10:02 UTC +* Number of recursive dependencies: 77 + +Run `revdepcheck::cloud_details(, "tidygraph")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘tidygraph-Ex.R’ failed + The error most likely occurred in: + + > ### Name: activate + > ### Title: Determine the context of subsequent manipulations + > ### Aliases: activate active %N>% %E>% + > + > ### ** Examples + > + > gr <- create_complete(5) %>% + + activate(nodes) %>% + + mutate(class = sample(c('a', 'b'), 5, TRUE)) %>% + + activate(edges) %>% + + arrange(from) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: %>% ... activate -> create_complete -> as_tbl_graph -> make_full_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 2. ├─tidygraph::as_tbl_graph(make_tree(n, children, mode)) + 3. └─igraph::make_tree(n, children, mode) + ── Error ('test-search.R:33:3'): search requires active nodes ────────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. ├─create_tree(10, 2) %>% activate(edges) at test-search.R:33:2 + 2. ├─tidygraph::activate(., edges) + 3. └─tidygraph::create_tree(10, 2) + 4. ├─tidygraph::as_tbl_graph(make_tree(n, children, mode)) + 5. └─igraph::make_tree(n, children, mode) + + [ FAIL 54 | WARN 0 | SKIP 0 | PASS 3 ] + Error: Test failures + Execution halted + ``` + +# tilemaps + +
+ +* Version: 0.2.0 +* GitHub: https://github.com/kaerosen/tilemaps +* Source code: https://github.com/cran/tilemaps +* Date/Publication: 2020-07-10 04:20:02 UTC +* Number of recursive dependencies: 75 + +Run `revdepcheck::cloud_details(, "tilemaps")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘tilemaps-Ex.R’ failed + The error most likely occurred in: + + > ### Name: create_island + > ### Title: Create a Tile for an Island + > ### Aliases: create_island + > + > ### ** Examples + > + > library(sf) + Linking to GEOS 3.8.0, GDAL 3.0.4, PROJ 6.3.1; sf_use_s2() is TRUE + > northeast <- governors[c(6,7,17,18,19,27,28,30,36,37,43),] + > tile_map <- generate_map(northeast$geometry, square = FALSE) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: generate_map -> -> graph.adjacency.dense + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘tilemaps.Rmd’ using rmarkdown + + Quitting from lines 33-41 [unnamed-chunk-2] (tilemaps.Rmd) + Error: processing vignette 'tilemaps.Rmd' failed with diagnostics: + ℹ In argument: `tile_map = generate_map(geometry, square = FALSE, + flat_topped = TRUE)`. + Caused by error in `.igraph.status()`: + ! could not find function ".igraph.status" + --- failed re-building ‘tilemaps.Rmd’ + + SUMMARY: processing the following file failed: + ‘tilemaps.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘lwgeom’ + All declared Imports should be used. + ``` + +# tip + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/tip +* Date/Publication: 2022-11-14 17:30:02 UTC +* Number of recursive dependencies: 100 + +Run `revdepcheck::cloud_details(, "tip")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘tip-Ex.R’ failed + The error most likely occurred in: + + > ### Name: partition_undirected_graph + > ### Title: Partition an undirected graph + > ### Aliases: partition_undirected_graph + > + > ### ** Examples + > + > # Import the tip library + ... + + } + > + > # Generate a one-cluster graph (i.e., partitioned_graph_matrix) + > partition_undirected_graph(.graph_matrix = posterior_prob_matrix, + + .num_components = 1, + + .step_size = 0.001) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: partition_undirected_graph -> -> graph.adjacency.dense + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘matrix-CONSTANT-simulated-vignette.Rmd’ using rmarkdown + + Quitting from lines 113-117 [unnamed-chunk-6] (matrix-CONSTANT-simulated-vignette.Rmd) + Error: processing vignette 'matrix-CONSTANT-simulated-vignette.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘matrix-CONSTANT-simulated-vignette.Rmd’ + + --- re-building ‘matrix-MNIW-simulated-vignette.Rmd’ using rmarkdown + + ... + --- failed re-building ‘vector-NIW-usarrests-vignette.Rmd’ + + SUMMARY: processing the following files failed: + ‘matrix-CONSTANT-simulated-vignette.Rmd’ + ‘matrix-MNIW-simulated-vignette.Rmd’ + ‘tensor-CONSTANT-simulated-vignette.Rmd’ + ‘vector-NIW-iris-vignette.Rmd’ ‘vector-NIW-usarrests-vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# Tlasso + +
+ +* Version: 1.0.2 +* GitHub: NA +* Source code: https://github.com/cran/Tlasso +* Date/Publication: 2022-02-01 08:20:08 UTC +* Number of recursive dependencies: 42 + +Run `revdepcheck::cloud_details(, "Tlasso")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘Tlasso-Ex.R’ failed + The error most likely occurred in: + + > ### Name: graph.pattern + > ### Title: Graph Pattern Visualization + > ### Aliases: graph.pattern + > + > ### ** Examples + > + > + > graph.pattern(ChainOmega(5, sd = 13)) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: graph.pattern -> graph.adjacency -> graph.adjacency.dense + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Tlasso.Rmd’ using rmarkdown + + Quitting from lines 319-327 [unnamed-chunk-10] (Tlasso.Rmd) + Error: processing vignette 'Tlasso.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘Tlasso.Rmd’ + + SUMMARY: processing the following file failed: + ‘Tlasso.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# TOHM + +
+ +* Version: 1.4 +* GitHub: NA +* Source code: https://github.com/cran/TOHM +* Date/Publication: 2021-03-09 20:30:05 UTC +* Number of recursive dependencies: 40 + +Run `revdepcheck::cloud_details(, "TOHM")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘TOHM-Ex.R’ failed + The error most likely occurred in: + + > ### Name: EC_LRT + > ### Title: Compute the Euler characteristic for the generalized Likelihood + > ### Ratio Test field + > ### Aliases: EC_LRT + > ### Keywords: Euler characteristic generalized Likelihood Ratio random + > ### field + > + ... + > THETA_sel<-THETA2[(THETA2[,2]<=(28+sqrt(30^2-(THETA2[,1]- + + 195)^2)))&(THETA2[,2]>=(28-sqrt(30^2-(THETA2[,1]-195)^2))),] + > + > EC_LRT(ck=c(1,8),x=data,mll=mll,null0=0,init=c(0.1), + + lowlim=c(0),uplim=c(1), THETA_sel) + Evaluating LRT for each point of the grid... + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: EC_LRT ... graph_from_adjacency_matrix -> graph.adjacency.dense + Execution halted + ``` + +# TreeDimensionTest + +
+ +* Version: 0.0.2 +* GitHub: NA +* Source code: https://github.com/cran/TreeDimensionTest +* Date/Publication: 2022-03-12 10:30:07 UTC +* Number of recursive dependencies: 68 + +Run `revdepcheck::cloud_details(, "TreeDimensionTest")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Tutorial.Rmd’ using rmarkdown + + Quitting from lines 46-56 [unnamed-chunk-5] (Tutorial.Rmd) + Error: processing vignette 'Tutorial.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘Tutorial.Rmd’ + + SUMMARY: processing the following file failed: + ‘Tutorial.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# treefit + +
+ +* Version: 1.0.2 +* GitHub: https://github.com/hayamizu-lab/treefit-r +* Source code: https://github.com/cran/treefit +* Date/Publication: 2022-01-18 07:50:02 UTC +* Number of recursive dependencies: 154 + +Run `revdepcheck::cloud_details(, "treefit")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─treefit::treefit(list(expression = star), "tree-like") at test-treefit.R:142:2 + 2. └─treefit:::calculate_eigenvectors_list(...) + 3. └─base::lapply(...) + 4. └─treefit (local) FUN(X[[i]], ...) + 5. └─treefit:::do_build_tree(original, target, build_tree) + 6. └─treefit:::calculate_mst(target) + 7. └─igraph::graph_from_adjacency_matrix(...) + 8. └─igraph:::graph.adjacency.dense(...) + + [ FAIL 5 | WARN 0 | SKIP 0 | PASS 7 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘treefit.Rmd’ using rmarkdown + + Quitting from lines 100-105 [estimate-tree-like-data] (treefit.Rmd) + Error: processing vignette 'treefit.Rmd' failed with diagnostics: + could not find function ".igraph.status" + --- failed re-building ‘treefit.Rmd’ + + --- re-building ‘working-with-seurat.Rmd’ using rmarkdown + ... + ================================================== + downloaded 6.0 MB + + --- finished re-building ‘working-with-seurat.Rmd’ + + SUMMARY: processing the following file failed: + ‘treefit.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# treemap + +
+ +* Version: 2.4-4 +* GitHub: NA +* Source code: https://github.com/cran/treemap +* Date/Publication: 2023-05-25 15:20:02 UTC +* Number of recursive dependencies: 62 + +Run `revdepcheck::cloud_details(, "treemap")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘treemap-Ex.R’ failed + The error most likely occurred in: + + > ### Name: treegraph + > ### Title: Create a tree graph + > ### Aliases: treegraph + > + > ### ** Examples + > + > data(business) + > treegraph(business, index=c("NACE1", "NACE2", "NACE3", "NACE4"), show.labels=FALSE) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: treegraph -> graph.data.frame -> make_empty_graph + Execution halted + ``` + +# VARDetect + +
+ +* Version: 0.1.6 +* GitHub: NA +* Source code: https://github.com/cran/VARDetect +* Date/Publication: 2022-05-10 08:00:06 UTC +* Number of recursive dependencies: 85 + +Run `revdepcheck::cloud_details(, "VARDetect")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘VARDetect-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.VARDetect.result + > ### Title: Plotting the output from VARDetect.result class + > ### Aliases: plot.VARDetect.result + > + > ### ** Examples + > + > nob <- 1000 + ... + [1] 341 682 + [1] "second.brk.points:" + [1] 341 682 + no refit for the parameter estimation> plot(fit, display = "cp") + > plot(fit, display = "param") + > plot(fit, display = "granger", threshold = 0.2, layout = "nicely") + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plot ... plot_granger -> graph.adjacency -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.5Mb + sub-directories of 1Mb or more: + libs 6.0Mb + ``` + +# vennLasso + +
+ +* Version: 0.1.6 +* GitHub: https://github.com/jaredhuling/vennLasso +* Source code: https://github.com/cran/vennLasso +* Date/Publication: 2020-06-03 08:50:02 UTC +* Number of recursive dependencies: 51 + +Run `revdepcheck::cloud_details(, "vennLasso")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘vennLasso-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plotCoefs + > ### Title: plotting function to investigate estimated coefficients + > ### Aliases: plotCoefs + > + > ### ** Examples + > + > set.seed(123) + ... + > + > dat.sim <- genHierSparseData(ncats = 3, nvars = 25, nobs = 200) + > + > fit <- vennLasso(x = dat.sim$x, y = dat.sim$y, groups = dat.sim$group.ind) + > + > plotCoefs(fit, s = fit$lambda[22]) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: plotCoefs ... %in% -> visIgraphLayout -> -> make_empty_graph + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘using_the_vennLasso_package.Rmd’ using rmarkdown + A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TinyTeX with tinytex::reinstall_tinytex(repository = "illinois"). + + tlmgr: Local TeX Live (2022) is older than remote repository (2023). + Cross release updates are only supported with + update-tlmgr-latest(.sh/.exe) --update + See https://tug.org/texlive/upgrade.html for details. + Warning in system2("tlmgr", args, ...) : + ... + + Error: processing vignette 'using_the_vennLasso_package.Rmd' failed with diagnostics: + LaTeX failed to compile /tmp/workdir/vennLasso/new/vennLasso.Rcheck/vign_test/vennLasso/vignettes/using_the_vennLasso_package.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See using_the_vennLasso_package.log for more info. + --- failed re-building ‘using_the_vennLasso_package.Rmd’ + + SUMMARY: processing the following file failed: + ‘using_the_vennLasso_package.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +* checking installed package size ... NOTE + ``` + installed size is 36.1Mb + sub-directories of 1Mb or more: + libs 35.5Mb + ``` + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# VertexSimilarity + +
+ +* Version: 0.1 +* GitHub: NA +* Source code: https://github.com/cran/VertexSimilarity +* Date/Publication: 2016-01-24 21:37:10 +* Number of recursive dependencies: 7 + +Run `revdepcheck::cloud_details(, "VertexSimilarity")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘VertexSimilarity-Ex.R’ failed + The error most likely occurred in: + + > ### Name: VertexSimilarity + > ### Title: Vertex Similarity + > ### Aliases: VertexSimilarity + > + > ### ** Examples + > + > m <- matrix(c(1,0,0,0,0,1,1,1,1),ncol=3,nrow=3,byrow=TRUE) + > SimilarityMatrix <- VertexSimilarity(m,alpha=0.85) + Loading required namespace: igraph + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: VertexSimilarity -> -> graph.adjacency.dense + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# vivainsights + +
+ +* Version: 0.3.1 +* GitHub: NA +* Source code: https://github.com/cran/vivainsights +* Date/Publication: 2023-05-22 13:10:02 UTC +* Number of recursive dependencies: 98 + +Run `revdepcheck::cloud_details(, "vivainsights")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘vivainsights-Ex.R’ failed + The error most likely occurred in: + + > ### Name: tm_cooc + > ### Title: Analyse word co-occurrence in subject lines and return a network + > ### plot + > ### Aliases: tm_cooc + > + > ### ** Examples + > + > # Demo using a subset of `mt_data` + > mt_data %>% + + dplyr::slice(1:20) %>% + + tm_cooc(lmult = 0.01) + Selecting by n + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: %>% ... ggplot -> create_layout -> -> make_empty_graph + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 52 marked UTF-8 strings + ``` + +# wdnet + +
+ +* Version: 1.1.0 +* GitHub: NA +* Source code: https://github.com/cran/wdnet +* Date/Publication: 2023-05-17 10:10:02 UTC +* Number of recursive dependencies: 54 + +Run `revdepcheck::cloud_details(, "wdnet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘wdnet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: adj_to_wdnet + > ### Title: Creates a 'wdnet' object using an adjacency matrix + > ### Aliases: adj_to_wdnet + > + > ### ** Examples + > + > adj <- matrix(c(0, 1, 2, 0), nrow = 2, ncol = 2, byrow = TRUE) + > adj_to_wdnet(adj = adj, directed = TRUE, weighted = FALSE) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: adj_to_wdnet ... adj_to_edgelist -> -> graph.adjacency.dense + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 5. └─igraph::graph_from_adjacency_matrix(...) + 6. └─igraph:::graph.adjacency.dense(...) + ── Error ('test-wdnet-igraph.R:4:3'): multiplication works ───────────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─wdnet::wdnet_to_igraph(netwk0) at test-wdnet-igraph.R:4:2 + 2. └─igraph::graph_from_edgelist(netwk$edgelist, directed = netwk$directed) + 3. └─igraph::make_graph(t(el), directed = directed) + 4. ├─base::do.call(old_graph, args) + 5. └─igraph (local) ``(``, directed = TRUE) + + [ FAIL 5 | WARN 0 | SKIP 0 | PASS 16 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 9.3Mb + sub-directories of 1Mb or more: + libs 9.0Mb + ``` + +# webtrackR + +
+ +* Version: 0.0.1 +* GitHub: https://github.com/schochastics/webtrackR +* Source code: https://github.com/cran/webtrackR +* Date/Publication: 2023-03-13 13:30:02 UTC +* Number of recursive dependencies: 40 + +Run `revdepcheck::cloud_details(, "webtrackR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘webtrackR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: audience_incidence + > ### Title: Create incidence matrix for audience-outlet network + > ### Aliases: audience_incidence + > + > ### ** Examples + > + > data("test_data") + > wt <- as.wt_dt(test_data) + > wt <- add_duration(wt) + > wt <- extract_domain(wt) + > audience_incidence(wt) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: audience_incidence -> -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-audience_networks.R:6:3'): audience_incidence ────────────────── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. └─webtrackR::audience_incidence(wt) at test-audience_networks.R:6:2 + 2. └─igraph::graph_from_data_frame(el, directed = FALSE) + 3. └─igraph::make_empty_graph(n = 0, directed = directed) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 14 marked UTF-8 strings + ``` + +# whitechapelR + +
+ +* Version: 0.3.0 +* GitHub: NA +* Source code: https://github.com/cran/whitechapelR +* Date/Publication: 2018-10-02 17:40:03 UTC +* Number of recursive dependencies: 47 + +Run `revdepcheck::cloud_details(, "whitechapelR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘whitechapelR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: show_board + > ### Title: Display game board representation + > ### Aliases: show_board + > + > ### ** Examples + > + > possibilities = start_round(64) + ... + > possibilities = take_a_step(possibilities,roads) + > possibilities = take_a_step(possibilities,roads,blocked=list(c(63,82),c(63,65))) + > possibilities = take_a_step(possibilities,alley) + > show_board(paths=possibilities,hideouts=NULL,roads,alley,node_locations) + Warning in v$color[as.numeric(names(tbl))] <- to_replace : + number of items to replace is not a multiple of replacement length + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: show_board -> -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test_whitechapel.R:77:3'): Expect plot generates without errors ───── + Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Backtrace: + ▆ + 1. ├─testthat::expect_null(...) at test_whitechapel.R:77:2 + 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. └─whitechapelR::show_board(list(69), c(45, 46), roads, alley, node_locations) + 5. └─igraph::graph_from_data_frame(...) + 6. └─igraph::make_empty_graph(n = 0, directed = directed) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 13 ] + Error: Test failures + Execution halted + ``` + +# wpa + +
+ +* Version: 1.8.1 +* GitHub: https://github.com/microsoft/wpa +* Source code: https://github.com/cran/wpa +* Date/Publication: 2023-01-30 15:00:02 UTC +* Number of recursive dependencies: 121 + +Run `revdepcheck::cloud_details(, "wpa")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘wpa-Ex.R’ failed + The error most likely occurred in: + + > ### Name: network_describe + > ### Title: Uncover HR attributes which best represent a population for a + > ### Person to Person query + > ### Aliases: network_describe + > + > ### ** Examples + > + > # Simulate a P2P edge list + > sim_data <- p2p_data_sim() + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: p2p_data_sim ... as.data.frame -> -> ensure_igraph -> + Execution halted + ``` + +# xgboost + +
+ +* Version: 1.7.5.1 +* GitHub: https://github.com/dmlc/xgboost +* Source code: https://github.com/cran/xgboost +* Date/Publication: 2023-03-30 19:40:02 UTC +* Number of recursive dependencies: 107 + +Run `revdepcheck::cloud_details(, "xgboost")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘xgboost-Ex.R’ failed + The error most likely occurred in: + + > ### Name: xgb.ggplot.deepness + > ### Title: Plot model trees deepness + > ### Aliases: xgb.ggplot.deepness xgb.plot.deepness + > + > ### ** Examples + > + > + ... + [47] train-logloss:0.009265 + [48] train-logloss:0.008787 + [49] train-logloss:0.008370 + [50] train-logloss:0.007953 + > + > xgb.plot.deepness(bst) + Error in .igraph.status("Make graph external pointer.\n") : + could not find function ".igraph.status" + Calls: xgb.plot.deepness ... [ -> [.data.table -> -> make_empty_graph + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + ⠇ | 9 | update trees in an existing model [22:10:17] WARNING: src/gbm/gbtree.cc:84: DANGER AHEAD: You have manually specified `updater` parameter. The `tree_method` parameter will be ignored. Incorrect sequence of updaters will produce undefined behavior. For common uses, we recommend using `tree_method` parameter instead. + [22:10:17] WARNING: src/gbm/gbtree.cc:84: DANGER AHEAD: You have manually specified `updater` parameter. The `tree_method` parameter will be ignored. Incorrect sequence of updaters will produce undefined behavior. For common uses, we recommend using `tree_method` parameter instead. + + ⠏ | 20 | update trees in an existing model + ✔ | 22 | update trees in an existing model [0.4s] + + ══ Results ═════════════════════════════════════════════════════════════════════ + Duration: 45.3 s + + ── Skipped tests ────────────────────────────────────────────────────────────── + • empty test (1) + + [ FAIL 1 | WARN 2 | SKIP 1 | PASS 1325 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 134.1Mb + sub-directories of 1Mb or more: + libs 133.2Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + From cb29dbcc4149ca6c15c0f4f4b1119fbd38bcd15a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Kirill=20M=C3=BCller?= Date: Mon, 12 Jun 2023 22:48:36 +0200 Subject: [PATCH 5/8] Intermediate results --- revdep/README.md | 474 +- revdep/cran.md | 1564 +-- revdep/failures.md | 821 +- revdep/problems.md | 24905 +------------------------------------------ 4 files changed, 213 insertions(+), 27551 deletions(-) diff --git a/revdep/README.md b/revdep/README.md index 869365d61a2..88be88e4bcc 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,466 +1,14 @@ # Revdeps -## Failed to check (13) - -|package |version |error |warning |note | -|:---------|:-------|:------|:-------|:----| -|NA |? | | | | -|DRviaSPCN |? | | | | -|FinNet |0.1.1 |1 | | | -|genekitr |? | | | | -|immcp |? | | | | -|MACP |? | | | | -|numbat |? | | | | -|NA |? | | | | -|Platypus |? | | | | -|[R6causal](failures.md#r6causal)|0.7.0 |__+1__ |-1 | | -|NA |? | | | | -|tidySEM |? | | | | -|vivid |? | | | | - -## New problems (441) - -|package |version |error |warning |note | -|:--------------------|:---------|:--------|:-------|:--------| -|[adegenet](problems.md#adegenet)|2.1.10 |__+1__ | | | -|[AHPWR](problems.md#ahpwr)|0.1.0 |__+1__ |__+1__ | | -|[akc](problems.md#akc)|0.9.9 |__+2__ |__+1__ | | -|[alakazam](problems.md#alakazam)|1.2.1 |__+1__ |1 | | -|[AnimalHabitatNetwork](problems.md#animalhabitatnetwork)|0.1.0 |__+1__ | | | -|[aniSNA](problems.md#anisna)|1.0 |__+1__ | | | -|[anocva](problems.md#anocva)|0.1.1 |__+1__ | | | -|[archeofrag](problems.md#archeofrag)|0.8.2 |__+2__ |__+1__ | | -|[arulesViz](problems.md#arulesviz)|1.5-2 |__+2__ | |1 | -|[autoharp](problems.md#autoharp)|0.0.10 |__+1__ | | | -|[autostats](problems.md#autostats)|0.4.0 | |__+1__ | | -|[backbone](problems.md#backbone)|2.1.2 |__+2__ |__+1__ | | -|[backShift](problems.md#backshift)|0.1.4.3 |__+2__ |__+1__ |1 | -|[BallMapper](problems.md#ballmapper)|0.2.0 |__+1__ | |2 | -|[bamm](problems.md#bamm)|0.4.3 |__+2__ |__+1__ | | -|[BASiNET](problems.md#basinet)|0.0.5 | |__+1__ | | -|[BASiNETEntropy](problems.md#basinetentropy)|0.99.5 |__+1__ | | | -|[basket](problems.md#basket)|0.10.11 |__+1__ | | | -|[BayesMallows](problems.md#bayesmallows)|1.3.0 |__+2__ | |1 | -|[BayesMRA](problems.md#bayesmra)|1.0.0 |__+2__ | |1 | -|[BayesNetBP](problems.md#bayesnetbp)|1.6.1 |__+1__ | | | -|[BayesSUR](problems.md#bayessur)|2.1-3 |__+1__ | |1 | -|[bcgam](problems.md#bcgam)|1.0 |__+1__ | | | -|[BCT](problems.md#bct)|1.2 |__+1__ | | | -|[BDgraph](problems.md#bdgraph)|2.72 |__+1__ |__+1__ |1 | -|[beam](problems.md#beam)|2.0.2 |__+1__ | |1 | -|[bibliometrix](problems.md#bibliometrix)|4.1.2 |__+1__ | | | -|[bifurcatingr](problems.md#bifurcatingr)|1.0.0 |__+1__ | | | -|[bio3d](problems.md#bio3d)|2.4-4 |__+1__ | |1 | -|[Bioi](problems.md#bioi)|0.2.10 |__+1__ | |1 | -|[bioregion](problems.md#bioregion)|1.0.0 |__+1__ | |1 | -|[Bios2cor](problems.md#bios2cor)|2.2.1 |__+1__ | | | -|[bipartite](problems.md#bipartite)|2.18 |__+1__ | |1 | -|[bnma](problems.md#bnma)|1.5.0 |__+1__ | | | -|[bnviewer](problems.md#bnviewer)|0.1.6 |__+2__ | |2 | -|[BoolNet](problems.md#boolnet)|2.1.8 |__+1__ | |1 | -|[bootnet](problems.md#bootnet)|1.5.3 |__+1__ | | | -|[BSBT](problems.md#bsbt)|1.2.1 |__+2__ | | | -|[btergm](problems.md#btergm)|1.10.10 |__+1__ | | | -|[bwsTools](problems.md#bwstools)|1.2.0 |__+1__ | | | -|[Canek](problems.md#canek)|0.2.2 |__+2__ |__+1__ | | -|[cape](problems.md#cape)|3.1.1 | |__+1__ | | -|[CARlasso](problems.md#carlasso)|0.1.2 |__+1__ | |1 | -|[cartograflow](problems.md#cartograflow)|1.0.3 |__+1__ | | | -|[cassowaryr](problems.md#cassowaryr)|2.0.0 |__+2__ |__+1__ | | -|[causact](problems.md#causact)|0.4.2 |__+2__ | | | -|[causalDisco](problems.md#causaldisco)|0.9.1 |__+1__ | | | -|[ccTensor](problems.md#cctensor)|1.0.2 |__+1__ | |1 | -|[CePa](problems.md#cepa)|0.8.0 |__+1__ |1 | | -|[CeRNASeek](problems.md#cernaseek)|2.1.3 |__+1__ | | | -|[cfid](problems.md#cfid)|0.1.4 |__+1__ | | | -|[chemodiv](problems.md#chemodiv)|0.2.0 |__+2__ |__+1__ | | -|[cholera](problems.md#cholera)|0.8.0 |__+1__ |__+1__ |1 | -|[CKMRpop](problems.md#ckmrpop)|0.1.3 |__+1__ |__+1__ |1 | -|[CliquePercolation](problems.md#cliquepercolation)|0.4.0 |__+1__ |__+1__ | | -|[ClustAssess](problems.md#clustassess)|0.3.0 |__+1__ |__+1__ | | -|[ClusTorus](problems.md#clustorus)|0.2.2 |__+1__ |__+1__ | | -|[clustree](problems.md#clustree)|0.5.0 |__+2__ |__+1__ | | -|[clustringr](problems.md#clustringr)|1.0 |__+1__ | |2 | -|[CoDiNA](problems.md#codina)|1.1.2 |__+1__ | | | -|[comato](problems.md#comato)|1.1 |__+1__ | | | -|[concatipede](problems.md#concatipede)|1.0.1 |__+2__ |__+1__ | | -|[concorR](problems.md#concorr)|0.2.1 |__+1__ | | | -|[CoNI](problems.md#coni)|0.1.0 |__+1__ |__+1__ | | -|[corTest](problems.md#cortest)|1.0.7 |__+1__ | |1 | -|[countland](problems.md#countland)|0.1.1 |__+2__ | | | -|[cppRouting](problems.md#cpprouting)|3.1 |__+1__ | |3 | -|[crandep](problems.md#crandep)|0.3.1 |__+1__ | |1 | -|[cranly](problems.md#cranly)|0.6.0 | |__+1__ |1 | -|[criticalpath](problems.md#criticalpath)|0.2.1 |__+2__ |__+1__ | | -|[crosstalkr](problems.md#crosstalkr)|1.0.2 |__+2__ |__+1__ | | -|[cytometree](problems.md#cytometree)|2.0.2 |__+1__ |__+1__ | | -|[d3po](problems.md#d3po)|0.3.4 |__+1__ | | | -|[dartR](problems.md#dartr)|2.9.7 |__+1__ |1 | | -|[data.tree](problems.md#datatree)|1.0.0 |__+1__ | | | -|[DDPNA](problems.md#ddpna)|0.3.1 |__+1__ | | | -|[deaR](problems.md#dear)|1.4.1 |__+1__ | | | -|[deepdep](problems.md#deepdep)|0.4.2 |__+1__ | | | -|[degreenet](problems.md#degreenet)|1.3-3 |__+1__ | | | -|[delayed](problems.md#delayed)|0.4.0 |__+2__ |__+1__ | | -|[DemoKin](problems.md#demokin)|1.0.3 | |__+1__ |1 | -|[dexterMST](problems.md#dextermst)|0.9.3 |__+1__ | |1 | -|[DiagrammeR](problems.md#diagrammer)|1.0.10 |__+2__ | |1 | -|[diffeRenTES](problems.md#differentes)|0.3.2 |__+2__ |__+1__ | | -|[diffudist](problems.md#diffudist)|1.0.1 |__+1__ | |1 | -|[diffusr](problems.md#diffusr)|0.1.4 |__+2__ |__+1__ |3 | -|[dimRed](problems.md#dimred)|0.2.6 |__+2__ |1 | | -|[discourseGT](problems.md#discoursegt)|1.1.8 |__+1__ | | | -|[discretecdAlgorithm](problems.md#discretecdalgorithm)|0.0.7 |__+2__ | |2 | -|[dm](problems.md#dm) |1.0.5 |__+2__ | | | -|[dnapath](problems.md#dnapath)|0.7.4 |__+1__ |__+1__ | | -|[dnr](problems.md#dnr)|0.3.5 |__+1__ |1 | | -|[dodgr](problems.md#dodgr)|0.2.21 |__+2__ |__+1__ |2 | -|[dosearch](problems.md#dosearch)|1.0.8 |__+1__ | |1 | -|[dragon](problems.md#dragon)|1.2.1 |__+1__ | |1 | -|[drake](problems.md#drake)|7.13.5 |__+2__ | | | -|[DrDimont](problems.md#drdimont)|0.1.4 |__+1__ |__+1__ | | -|[DTSEA](problems.md#dtsea)|0.0.3 |__+1__ |__+1__ | | -|[dyndimred](problems.md#dyndimred)|1.0.4 |__+1__ | |2 | -|[dynetNLAResistance](problems.md#dynetnlaresistance)|0.1.0 |__+2__ | |1 | -|[dyngen](problems.md#dyngen)|1.0.5 |__+1__ | | | -|[dynplot](problems.md#dynplot)|1.1.2 |__+1__ |__+1__ | | -|[dynwrap](problems.md#dynwrap)|1.2.3 |__+2__ |__+1__ | | -|[ecoCopula](problems.md#ecocopula)|1.0.2 |__+2__ |__+1__ | | -|[ECoL](problems.md#ecol)|0.3.0 |__+2__ | |1 | -|[econet](problems.md#econet)|1.0.0 |__+1__ |1 | | -|[EcoNetGen](problems.md#econetgen)|0.2.3 |__+1__ | |1 | -|[economiccomplexity](problems.md#economiccomplexity)|1.4.0 |__+2__ | |1 | -|[econullnetr](problems.md#econullnetr)|0.2.1 |__+1__ |__+1__ | | -|[EcotoneFinder](problems.md#ecotonefinder)|0.2.3 |__+1__ | |2 | -|[ecpc](problems.md#ecpc)|3.1.1 |__+1__ | | | -|[edgebundle](problems.md#edgebundle)|0.4.1 |__+2__ | |1 | -|[edmcr](problems.md#edmcr)|0.2.0 |__+1__ | | | -|[EDOIF](problems.md#edoif)|0.1.3 |__+1__ |__+1__ | | -|[eff2](problems.md#eff2)|1.0.1 |__+2__ |__+1__ | | -|[EGAnet](problems.md#eganet)|1.2.3 |__+1__ | | | -|[egor](problems.md#egor)|1.23.3 |__+2__ |__+1__ | | -|[eicm](problems.md#eicm)|1.0.3 |__+1__ |__+1__ |1 | -|[einet](problems.md#einet)|0.1.0 |__+2__ | | | -|[EmbedSOM](problems.md#embedsom)|2.1.2 |__+1__ | |1 | -|[enviGCMS](problems.md#envigcms)|0.7.1 |__+1__ | | | -|[epicontacts](problems.md#epicontacts)|1.1.3 |__+1__ |__+1__ |1 | -|[EpiILMCT](problems.md#epiilmct)|1.1.7 |__+1__ | | | -|[epinetr](problems.md#epinetr)|0.96 |__+1__ |__+1__ | | -|[espadon](problems.md#espadon)|1.3.2 |__+1__ | |1 | -|[ess](problems.md#ess)|1.1.2 |__+1__ | | | -|[etree](problems.md#etree)|0.1.0 |__+2__ |__+1__ | | -|[fairadapt](problems.md#fairadapt)|0.2.5 |__+2__ |1 | | -|[FAIRmaterials](problems.md#fairmaterials)|0.3.0 |__+1__ | |1 | -|[fake](problems.md#fake)|1.4.0 |__+1__ | | | -|[fastnet](problems.md#fastnet)|1.0.0 |__+1__ | |1 | -|[fbnet](problems.md#fbnet)|1.0.2 |__+1__ | |1 | -|[FCMapper](problems.md#fcmapper)|1.1 |__+1__ | | | -|[FindIt](problems.md#findit)|1.2.0 |__+1__ | | | -|[fnets](problems.md#fnets)|0.1.3 |__+1__ | | | -|[foodingraph](problems.md#foodingraph)|0.1.0 |__+1__ | |2 | -|[ForestGapR](problems.md#forestgapr)|0.1.7 |__+1__ | | | -|[forestRK](problems.md#forestrk)|0.0-5 |__+1__ | |1 | -|[fossilbrush](problems.md#fossilbrush)|1.0.3 |__+1__ |1 |1 | -|[FrF2](problems.md#frf2)|2.3 |__+2__ | | | -|[fssemR](problems.md#fssemr)|0.1.8 |__+1__ |1 |2 | -|[gDefrag](problems.md#gdefrag)|0.3 |__+1__ | | | -|[gemtc](problems.md#gemtc)|1.0-1 |__+2__ | | | -|[genscore](problems.md#genscore)|1.0.2.1 |__+1__ | | | -|[geonetwork](problems.md#geonetwork)|0.5.0 |__+1__ | | | -|[ggdag](problems.md#ggdag)|0.2.10 |__+2__ |__+1__ | | -|[ggenealogy](problems.md#ggenealogy)|1.0.1 |__+2__ | |3 | -|[ggflowchart](problems.md#ggflowchart)|1.0.0 |__+1__ |__+1__ | | -|[ggm](problems.md#ggm)|2.5 |__+1__ | |1 | -|[ggnetwork](problems.md#ggnetwork)|0.5.12 |__+1__ | |1 | -|[ggraph](problems.md#ggraph)|2.1.0 |__+1__ |__+1__ |1 | -|[ghypernet](problems.md#ghypernet)|1.1.0 |__+1__ |__+1__ |2 | -|[GISSB](problems.md#gissb)|1.1 |__+2__ | |1 | -|[gmat](problems.md#gmat)|0.2.2 |__+2__ | | | -|[GMPro](problems.md#gmpro)|0.1.0 |__+1__ | |1 | -|[GOxploreR](problems.md#goxplorer)|1.2.6 |__+1__ |1 |1 | -|[gRain](problems.md#grain)|1.3.13 |__+2__ |1 | | -|[grainscape](problems.md#grainscape)|0.4.4 |__+1__ |1 |1 | -|[grand](problems.md#grand)|0.9.0 |__+1__ |__+1__ | | -|[graph4lg](problems.md#graph4lg)|1.8.0 |__+1__ | |1 __+1__ | -|[graphclust](problems.md#graphclust)|1.3 |__+1__ | | | -|[graphicalExtremes](problems.md#graphicalextremes)|0.2.0 |__+1__ | |1 | -|[graphlayouts](problems.md#graphlayouts)|1.0.0 |__+1__ | |1 | -|[graphseg](problems.md#graphseg)|0.1.0 |__+1__ | |1 | -|[graphTweets](problems.md#graphtweets)|0.5.3 |__+2__ | |1 | -|[gRbase](problems.md#grbase)|1.8.9 |__+2__ |1 |1 | -|[gRim](problems.md#grim)|0.2.10 |__+2__ | |2 | -|[handwriter](problems.md#handwriter)|1.0.1 |__+1__ | |1 | -|[hero](problems.md#hero)|0.4.7 |__+1__ | | | -|[HLSM](problems.md#hlsm)|0.9.0 |__+1__ | | | -|[HospitalNetwork](problems.md#hospitalnetwork)|0.9.3 |__+2__ |__+1__ | | -|[HTT](problems.md#htt)|0.1.2 |__+1__ |__+1__ |1 | -|[huge](problems.md#huge)|1.3.5 |__+1__ |1 |1 | -|[ICDS](problems.md#icds)|0.1.2 |__+1__ |__+1__ | | -|[iconr](problems.md#iconr)|0.1.0 |__+1__ | |1 | -|[icosa](problems.md#icosa)|0.11.0 |__+1__ |__+1__ |1 | -|[idopNetwork](problems.md#idopnetwork)|0.1.2 | |__+1__ | | -|[iGraphMatch](problems.md#igraphmatch)|2.0.1 |__+2__ |__+1__ | | -|[IMEC](problems.md#imec)|0.2.0 |__+2__ | |1 | -|[immunarch](problems.md#immunarch)|0.9.0 |__+1__ | |1 | -|[immuneSIM](problems.md#immunesim)|0.8.7 |__+1__ | |1 | -|[imsig](problems.md#imsig)|1.1.3 |__+1__ | | | -|[incidentally](problems.md#incidentally)|1.0.2 |__+1__ | | | -|[influenceR](problems.md#influencer)|0.1.5 |__+2__ | | | -|[influential](problems.md#influential)|2.2.7 |__+1__ |__+1__ | | -|[intergraph](problems.md#intergraph)|2.0-2 |__+1__ | | | -|[IOHanalyzer](problems.md#iohanalyzer)|0.1.6.3 |__+1__ | |2 | -|[isa2](problems.md#isa2)|0.3.6 |__+1__ | | | -|[isotracer](problems.md#isotracer)|1.1.4 |__+2__ | |3 | -|[ITNr](problems.md#itnr)|0.7.0 |__+1__ | | | -|[IxPopDyMod](problems.md#ixpopdymod)|0.2.0 |__+1__ | | | -|[jewel](problems.md#jewel)|2.0.0 |__+1__ | | | -|[jti](problems.md#jti)|0.8.4 |__+1__ | |1 | -|[kangar00](problems.md#kangar00)|1.4.1 |__+1__ | | | -|[Karen](problems.md#karen)|1.0 |__+1__ |1 | | -|[keyplayer](problems.md#keyplayer)|1.0.3 |__+1__ | | | -|[kknn](problems.md#kknn)|1.3.1 |__+1__ | | | -|[l1spectral](problems.md#l1spectral)|0.99.6 |__+1__ | | | -|[lconnect](problems.md#lconnect)|0.1.1 |__+1__ | |1 | -|[leidenAlg](problems.md#leidenalg)|1.0.5 |__+2__ | |1 | -|[leidenbase](problems.md#leidenbase)|0.1.18 |__+2__ |__+1__ |1 | -|[lexRankr](problems.md#lexrankr)|0.5.2 |__+2__ | | | -|[linkprediction](problems.md#linkprediction)|1.0-0 |__+2__ | |1 | -|[LoopDetectR](problems.md#loopdetectr)|0.1.2 |__+1__ |__+1__ | | -|[LSVAR](problems.md#lsvar)|1.2 |__+1__ | | | -|[lvm4net](problems.md#lvm4net)|0.3 |__+1__ | | | -|[macrosyntR](problems.md#macrosyntr)|0.2.19 |__+1__ |__+1__ | | -|[madrat](problems.md#madrat)|3.3.0 |__+2__ |__+1__ | | -|[malan](problems.md#malan)|1.0.2 |__+1__ |__+1__ |1 | -|[manymome](problems.md#manymome)|0.1.10 |1 __+1__ | | | -|[manynet](problems.md#manynet)|0.1.1 |1 __+1__ | | | -|[matrixcut](problems.md#matrixcut)|0.0.1 |__+1__ | |1 | -|[maxmatching](problems.md#maxmatching)|0.1.0 |__+1__ | |1 | -|[mazeGen](problems.md#mazegen)|0.1.3 |__+1__ | | | -|[MBNMAdose](problems.md#mbnmadose)|0.4.1 |__+1__ |__+1__ |1 | -|[MBNMAtime](problems.md#mbnmatime)|0.2.3 |__+1__ |__+1__ | | -|[mcMST](problems.md#mcmst)|1.1.1 |__+1__ | | | -|[mcvis](problems.md#mcvis)|1.0.8 |__+2__ |__+1__ | | -|[meconetcomp](problems.md#meconetcomp)|0.2.0 |__+1__ | | | -|[Mercator](problems.md#mercator)|1.1.2 |__+1__ |__+1__ | | -|[metacoder](problems.md#metacoder)|0.3.6 |__+2__ | |1 | -|[metanetwork](problems.md#metanetwork)|0.7.0 |__+1__ | | | -|[MetricGraph](problems.md#metricgraph)|1.1.1 |__+2__ | |1 | -|[mfpp](problems.md#mfpp)|0.0.4 |__+1__ | | | -|[migraph](problems.md#migraph)|0.13.2 |__+2__ | | | -|[miniCRAN](problems.md#minicran)|0.2.16 |__+1__ |__+1__ | | -|[missSBM](problems.md#misssbm)|1.0.3 |__+1__ | |1 | -|[mlmts](problems.md#mlmts)|1.1.1 |__+1__ | |1 | -|[mnda](problems.md#mnda)|1.0.9 |__+1__ | |1 | -|[modnets](problems.md#modnets)|0.9.0 |__+1__ | | | -|[molnet](problems.md#molnet)|0.1.0 |__+1__ |__+1__ | | -|[moranajp](problems.md#moranajp)|0.9.6 |__+1__ | | | -|[motifcluster](problems.md#motifcluster)|0.2.3 |__+2__ |1 | | -|[motifr](problems.md#motifr)|1.0.0 |__+1__ | | | -|[mppR](problems.md#mppr)|1.4.0 |__+2__ |__+1__ | | -|[MRFcov](problems.md#mrfcov)|1.0.39 |__+1__ |__+1__ | | -|[MRReg](problems.md#mrreg)|0.1.5 |__+1__ |__+1__ | | -|[MRS](problems.md#mrs)|1.2.4 |__+1__ | |1 | -|[mstknnclust](problems.md#mstknnclust)|0.3.2 |__+1__ |__+1__ | | -|[MTA](problems.md#mta)|0.4.1 |__+1__ |__+1__ | | -|[mully](problems.md#mully)|2.1.38 |__+1__ |1 | | -|[multilaterals](problems.md#multilaterals)|1.0 |__+1__ | | | -|[multilink](problems.md#multilink)|0.1.1 |__+1__ | |1 | -|[multinets](problems.md#multinets)|0.2.2 |__+2__ | | | -|[multinma](problems.md#multinma)|0.5.1 |__+2__ | |2 | -|[MultIS](problems.md#multis)|0.6.2 | |__+1__ |1 | -|[multivariance](problems.md#multivariance)|2.4.1 |__+2__ | | | -|[mverse](problems.md#mverse)|0.1.0 | |__+1__ | | -|[mwcsr](problems.md#mwcsr)|0.1.7 |__+2__ | |1 | -|[nat](problems.md#nat)|1.8.22 |__+2__ |__+1__ | | -|[nbTransmission](problems.md#nbtransmission)|1.1.2 |__+1__ |__+1__ | | -|[nda](problems.md#nda)|0.1.6 |__+1__ | | | -|[neat](problems.md#neat)|1.2.3 |__+1__ |__+1__ | | -|[neatmaps](problems.md#neatmaps)|2.1.0 |__+1__ | |1 | -|[Neighboot](problems.md#neighboot)|1.0.1 |__+1__ | | | -|[netCoin](problems.md#netcoin)|2.0.48 |__+1__ | |1 | -|[netcom](problems.md#netcom)|2.1.6 |__+1__ | |1 | -|[NetCoupler](problems.md#netcoupler)|0.1.0 |__+2__ |__+1__ | | -|[netdiffuseR](problems.md#netdiffuser)|1.22.5 |__+2__ |__+1__ |1 | -|[NetFACS](problems.md#netfacs)|0.5.0 |__+1__ |__+1__ | | -|[netgsa](problems.md#netgsa)|4.0.4 | |__+1__ |1 | -|[netjack](problems.md#netjack)|1.2.0 |__+1__ |__+1__ |1 | -|[netmap](problems.md#netmap)|0.1.2 |__+1__ | | | -|[netmeta](problems.md#netmeta)|2.8-2 |__+1__ | |2 | -|[NetMix](problems.md#netmix)|0.2.0.1 |__+1__ | |1 | -|[netplot](problems.md#netplot)|0.1-1 |__+1__ | | | -|[netrankr](problems.md#netrankr)|1.2.0 |__+1__ | |1 | -|[netropy](problems.md#netropy)|0.1.0 |__+1__ |__+1__ | | -|[NetSci](problems.md#netsci)|1.0.0 |__+1__ | | | -|[netseg](problems.md#netseg)|1.0-1 |__+2__ | | | -|[nett](problems.md#nett)|1.0.0 |__+1__ | | | -|[netUtils](problems.md#netutils)|0.8.1 |__+1__ | | | -|[NetworkExtinction](problems.md#networkextinction)|1.0.3 |__+2__ |__+1__ | | -|[networkGen](problems.md#networkgen)|0.1.1 |__+1__ | |2 | -|[NetworkInference](problems.md#networkinference)|1.2.4 |__+1__ |__+1__ | | -|[NetworkToolbox](problems.md#networktoolbox)|1.4.2 |__+1__ | | | -|[networktools](problems.md#networktools)|1.5.0 |__+1__ | | | -|[NIMAA](problems.md#nimaa)|0.2.1 |__+2__ |__+1__ |2 | -|[nimble](problems.md#nimble)|1.0.0 |__+1__ | |1 | -|[nlnet](problems.md#nlnet)|1.4 |__+1__ | | | -|[nlrx](problems.md#nlrx)|0.4.4 |__+1__ | | | -|[node2vec](problems.md#node2vec)|0.1.0 |__+1__ | | | -|[nutriNetwork](problems.md#nutrinetwork)|0.1.1 |__+1__ | | | -|[OCNet](problems.md#ocnet)|1.0.1 |__+1__ | |1 | -|[oddnet](problems.md#oddnet)|0.1.0 |__+1__ | | | -|[ohun](problems.md#ohun)|0.1.0 |__+1__ | | | -|[OpenRepGrid](problems.md#openrepgrid)|0.1.14 |__+1__ | | | -|[OpenRepGrid.ic](problems.md#openrepgridic)|0.6.1 |__+1__ | | | -|[OrdCD](problems.md#ordcd)|1.1.2 |__+1__ | | | -|[PAC](problems.md#pac)|1.1.4 | |__+1__ | | -|[PAFit](problems.md#pafit)|1.2.5 |__+2__ | | | -|[PairViz](problems.md#pairviz)|1.3.6 | |__+1__ | | -|[pald](problems.md#pald)|0.0.2 |__+2__ | | | -|[PANACEA](problems.md#panacea)|1.0.0 |__+1__ | | | -|[paramlink](problems.md#paramlink)|1.1-5 |__+1__ | | | -|[particles](problems.md#particles)|0.2.3 |__+1__ |__+1__ | | -|[pathfindR](problems.md#pathfindr)|2.1.0 |__+2__ |__+1__ | | -|[pcalg](problems.md#pcalg)|2.7-8 |__+3__ | |3 | -|[pcFactorStan](problems.md#pcfactorstan)|1.5.3 |__+2__ | |3 | -|[pedtools](problems.md#pedtools)|2.2.0 |1 __+1__ | | | -|[perturbR](problems.md#perturbr)|0.1.3 |__+1__ | | | -|[pGRN](problems.md#pgrn)|0.3.5 |__+1__ | | | -|[phangorn](problems.md#phangorn)|2.11.1 |__+1__ |__+1__ |1 | -|[PhaseTypeR](problems.md#phasetyper)|1.0.4 |__+1__ | | | -|[phyloseqGraphTest](problems.md#phyloseqgraphtest)|0.1.0 |__+1__ |__+1__ |2 | -|[phylosignal](problems.md#phylosignal)|1.3 |__+1__ | |1 | -|[phyloTop](problems.md#phylotop)|2.1.2 |__+2__ | | | -|[pkggraph](problems.md#pkggraph)|0.2.3 |__+1__ | | | -|[PlackettLuce](problems.md#plackettluce)|0.4.2 |1 __+1__ |__+1__ | | -|[plantTracker](problems.md#planttracker)|1.1.0 |__+2__ |__+1__ | | -|[plinkQC](problems.md#plinkqc)|0.3.4 |__+1__ |1 | | -|[PLNmodels](problems.md#plnmodels)|1.0.1 |__+1__ |__+1__ |1 | -|[pmd](problems.md#pmd)|0.2.1 |__+1__ |__+1__ |1 | -|[PNAR](problems.md#pnar)|1.4 |__+1__ | | | -|[polymapR](problems.md#polymapr)|1.1.3 |__+1__ |__+1__ |1 | -|[polyqtlR](problems.md#polyqtlr)|0.0.9 |__+1__ |__+1__ |1 | -|[pomdp](problems.md#pomdp)|1.1.0 |2 |__+1__ |1 | -|[pop](problems.md#pop)|0.1 |__+2__ | |1 | -|[poppr](problems.md#poppr)|2.9.4 |__+2__ |1 | | -|[POSetR](problems.md#posetr)|1.1.1 |__+1__ | |2 | -|[ProjectManagement](problems.md#projectmanagement)|1.4.7 |__+1__ | | | -|[provGraphR](problems.md#provgraphr)|1.0.1 |__+2__ | | | -|[ptools](problems.md#ptools)|2.0.0 |__+2__ | | | -|[qdap](problems.md#qdap)|2.4.6 |__+1__ | |1 | -|[qgraph](problems.md#qgraph)|1.9.5 |__+1__ | | | -|[R.temis](problems.md#rtemis)|0.1.3 |__+1__ | |1 | -|[RaceID](problems.md#raceid)|0.3.0 |__+1__ |__+1__ |1 | -|[rags2ridges](problems.md#rags2ridges)|2.2.6 |__+1__ | |1 | -|[RavenR](problems.md#ravenr)|2.2.0 |__+1__ |__+1__ | | -|[rcrimeanalysis](problems.md#rcrimeanalysis)|0.5.0 |__+1__ |__+1__ | | -|[rD3plot](problems.md#rd3plot)|1.0.68 |__+1__ | | | -|[RDS](problems.md#rds)|0.9-6 |__+2__ | | | -|[readsdr](problems.md#readsdr)|0.2.0 |__+1__ | |1 | -|[ReDaMoR](problems.md#redamor)|0.7.1 |__+1__ |__+1__ | | -|[refdb](problems.md#refdb)|0.1.1 |__+2__ |__+1__ | | -|[RepertoiR](problems.md#repertoir)|0.0.1 |__+2__ | |1 | -|[repo](problems.md#repo)|2.1.5 |__+1__ | | | -|[ResIN](problems.md#resin)|0.1.0 |__+1__ |__+1__ | | -|[RevEcoR](problems.md#revecor)|0.99.3 |__+1__ | | | -|[rflexscan](problems.md#rflexscan)|1.1.0 |__+1__ | | | -|[rgexf](problems.md#rgexf)|0.16.2 |__+2__ |__+1__ | | -|[rgraph6](problems.md#rgraph6)|2.0-2 |__+2__ |__+1__ | | -|[rhcoclust](problems.md#rhcoclust)|2.0.0 |__+1__ | | | -|[rmangal](problems.md#rmangal)|2.1.3 |__+1__ | | | -|[rmcfs](problems.md#rmcfs)|1.3.5 |__+1__ | | | -|[rmonad](problems.md#rmonad)|0.7.0 |__+2__ |__+1__ | | -|[roads](problems.md#roads)|1.1.0 |__+2__ |__+1__ | | -|[robber](problems.md#robber)|0.2.3 |__+2__ | | | -|[robin](problems.md#robin)|1.1.1 |__+1__ | | | -|[RobustIV](problems.md#robustiv)|0.2.5 |__+1__ | | | -|[robustrao](problems.md#robustrao)|1.0-5 |__+1__ | | | -|[roprov](problems.md#roprov)|0.1.2 |__+1__ | | | -|[RPANDA](problems.md#rpanda)|2.2 |__+1__ | | | -|[rquery](problems.md#rquery)|1.4.9 |__+1__ | | | -|[rscc](problems.md#rscc)|0.2.1 |__+1__ | | | -|[RScelestial](problems.md#rscelestial)|1.0.3 |__+1__ | |1 | -|[rsetse](problems.md#rsetse)|0.5.0 |__+1__ | | | -|[rSpectral](problems.md#rspectral)|1.0.0.10 |__+2__ | |1 | -|[rsppfp](problems.md#rsppfp)|1.0.4 |__+1__ | |1 | -|[rvinecopulib](problems.md#rvinecopulib)|0.6.3.1.1 |__+2__ | |1 | -|[safedata](problems.md#safedata)|1.1.3 |__+1__ |__+1__ | | -|[saotd](problems.md#saotd)|0.3.0 |__+1__ |__+1__ | | -|[sBIC](problems.md#sbic)|0.2.0 |__+1__ | | | -|[sbm](problems.md#sbm)|0.4.5 |__+2__ |__+1__ | | -|[SBN](problems.md#sbn)|1.0.0 |__+1__ | | | -|[sccore](problems.md#sccore)|1.0.3 |__+2__ | |1 | -|[scDHA](problems.md#scdha)|1.2.1 |__+1__ | |1 | -|[scDiffCom](problems.md#scdiffcom)|0.1.0 |__+1__ | |1 | -|[SCORPION](problems.md#scorpion)|1.0.1 |__+1__ | |1 | -|[scRNAtools](problems.md#scrnatools)|1.0 |__+1__ | | | -|[secrlinear](problems.md#secrlinear)|1.2.1 |__+2__ |1 | | -|[SelectBoost](problems.md#selectboost)|2.2.2 |__+1__ | | | -|[SEMID](problems.md#semid)|0.4.0 |__+2__ | | | -|[sensitivity](problems.md#sensitivity)|1.28.1 |__+1__ | |1 | -|[SeqDetect](problems.md#seqdetect)|1.0.7 |__+2__ | |2 | -|[seqHMM](problems.md#seqhmm)|1.2.4 |__+1__ |1 |1 | -|[SeqNet](problems.md#seqnet)|1.1.3 |__+2__ | |2 | -|[SetRank](problems.md#setrank)|1.1.0 |__+1__ |1 | | -|[sfcr](problems.md#sfcr)|0.2.1 |__+2__ |__+1__ | | -|[sfdep](problems.md#sfdep)|0.2.3 |__+1__ | | | -|[sfnetworks](problems.md#sfnetworks)|0.6.3 |__+2__ |__+1__ | | -|[SFSI](problems.md#sfsi)|1.2.0 |__+1__ | | | -|[sharp](problems.md#sharp)|1.4.2 |__+1__ |1 | | -|[sharpshootR](problems.md#sharpshootr)|2.1 |__+1__ | | | -|[shazam](problems.md#shazam)|1.1.2 |__+1__ |1 | | -|[shock](problems.md#shock)|1.0 |__+1__ | | | -|[sidier](problems.md#sidier)|4.1.0 |__+1__ | | | -|[sigmajs](problems.md#sigmajs)|0.1.5 |__+2__ | |1 | -|[signnet](problems.md#signnet)|1.0.1 |__+2__ | |1 | -|[simcausal](problems.md#simcausal)|0.5.6 |__+2__ |1 | | -|[simer](problems.md#simer)|0.9.0.2 |__+1__ | |1 | -|[simPATHy](problems.md#simpathy)|0.6 |__+1__ |__+1__ | | -|[simplifyNet](problems.md#simplifynet)|0.0.1 |__+1__ | | | -|[SIRE](problems.md#sire)|1.1.0 |__+1__ | |1 | -|[sirt](problems.md#sirt)|3.12-66 |__+1__ | |1 | -|[SITH](problems.md#sith)|1.1.0 | |__+1__ | | -|[skynet](problems.md#skynet)|1.4.3 |__+2__ |__+1__ |1 | -|[SmCCNet](problems.md#smccnet)|0.99.0 |__+1__ | | | -|[smotefamily](problems.md#smotefamily)|1.3.1 |__+1__ | | | -|[snowboot](problems.md#snowboot)|1.0.2 |__+1__ | | | -|[SNscan](problems.md#snscan)|1.0 |__+1__ | | | -|[SOAs](problems.md#soas)|1.3 |__+1__ | |1 | -|[SoilR](problems.md#soilr)|1.2.105 |__+1__ | | | -|[solitude](problems.md#solitude)|1.1.3 |__+1__ | |1 | -|[SourceSet](problems.md#sourceset)|0.1.5 |__+1__ |__+1__ |1 | -|[spacejamr](problems.md#spacejamr)|0.2.1 |__+2__ | | | -|[sparsebnUtils](problems.md#sparsebnutils)|0.0.8 |__+1__ | |1 | -|[spathial](problems.md#spathial)|0.1.2 |__+1__ |__+1__ |2 | -|[spatsoc](problems.md#spatsoc)|0.1.16 |__+2__ |__+1__ |1 | -|[specr](problems.md#specr)|1.0.0 |__+2__ |__+1__ | | -|[spinner](problems.md#spinner)|1.1.0 |__+1__ | | | -|[spNetwork](problems.md#spnetwork)|0.4.3.7 |__+2__ |__+1__ |1 | -|[spqdep](problems.md#spqdep)|0.1.2 |__+1__ |__+1__ |2 | -|[SSN](problems.md#ssn)|1.1.17 |__+1__ |1 | | -|[stagedtrees](problems.md#stagedtrees)|2.2.1 |__+1__ | | | -|[statGraph](problems.md#statgraph)|0.5.0 |__+1__ | | | -|[stemmatology](problems.md#stemmatology)|0.3.2 |__+2__ |1 | | -|[stm](problems.md#stm)|1.3.6 |1 __+1__ | |2 | -|[stplanr](problems.md#stplanr)|1.0.2 |__+1__ |__+1__ | | -|[SurvHiDim](problems.md#survhidim)|0.1.1 |__+1__ | |1 | -|[targets](problems.md#targets)|1.1.3 |__+1__ | | | -|[TDA](problems.md#tda)|1.9 |__+2__ | |4 | -|[text2map](problems.md#text2map)|0.1.6 |1 __+1__ | |1 | -|[textrank](problems.md#textrank)|0.3.1 |__+1__ |__+1__ | | -|[tidygraph](problems.md#tidygraph)|1.2.3 |__+2__ | | | -|[tilemaps](problems.md#tilemaps)|0.2.0 |__+1__ |__+1__ |1 | -|[tip](problems.md#tip)|0.1.0 |__+1__ |__+1__ | | -|[Tlasso](problems.md#tlasso)|1.0.2 |__+1__ |__+1__ | | -|[TOHM](problems.md#tohm)|1.4 |__+1__ | | | -|[TreeDimensionTest](problems.md#treedimensiontest)|0.0.2 | |__+1__ | | -|[treefit](problems.md#treefit)|1.0.2 |__+1__ |__+1__ | | -|[treemap](problems.md#treemap)|2.4-4 |__+1__ | | | -|[VARDetect](problems.md#vardetect)|0.1.6 |__+1__ | |1 | -|[vennLasso](problems.md#vennlasso)|0.1.6 |__+1__ |1 |2 | -|[VertexSimilarity](problems.md#vertexsimilarity)|0.1 |__+1__ | |1 | -|[vivainsights](problems.md#vivainsights)|0.3.1 |__+1__ | |1 | -|[wdnet](problems.md#wdnet)|1.1.0 |__+2__ | |1 | -|[webtrackR](problems.md#webtrackr)|0.0.1 |__+2__ | |1 | -|[whitechapelR](problems.md#whitechapelr)|0.3.0 |__+2__ | | | -|[wpa](problems.md#wpa)|1.8.1 |__+1__ | | | -|[xgboost](problems.md#xgboost)|1.7.5.1 |__+2__ | |2 | +## New problems (7) + +|package |version |error |warning |note | +|:----------|:-------|:------|:-------|:----| +|[gemtc](problems.md#gemtc)|1.0-1 |__+1__ | | | +|[leidenAlg](problems.md#leidenalg)|1.0.5 |__+2__ | |1 | +|[leidenbase](problems.md#leidenbase)|0.1.18 |__+2__ |__+1__ |1 | +|[nda](problems.md#nda)|0.1.6 |__+1__ | | | +|[netseg](problems.md#netseg)|1.0-1 |__+1__ | | | +|[SNscan](problems.md#snscan)|1.0 |__+1__ | | | +|[tidygraph](problems.md#tidygraph)|1.2.3 |__+1__ | | | diff --git a/revdep/cran.md b/revdep/cran.md index de4bf328e67..7ebaec4067a 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,1584 +1,36 @@ ## revdepcheck results -We checked 786 reverse dependencies (783 from CRAN + 3 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. +We checked 438 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. - * We saw 441 new problems - * We failed to check 10 packages + * We saw 7 new problems + * We failed to check 0 packages Issues with CRAN packages are summarised below. ### New problems (This reports the first line of each new failure) -* adegenet - checking examples ... ERROR - -* AHPWR - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* akc - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* alakazam - checking examples ... ERROR - -* AnimalHabitatNetwork - checking examples ... ERROR - -* aniSNA - checking examples ... ERROR - -* anocva - checking examples ... ERROR - -* archeofrag - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* arulesViz - checking examples ... ERROR - checking running R code from vignettes ... ERROR - -* autoharp - checking examples ... ERROR - -* autostats - checking re-building of vignette outputs ... WARNING - -* backbone - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* backShift - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* BallMapper - checking examples ... ERROR - -* bamm - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* BASiNET - checking re-building of vignette outputs ... WARNING - -* BASiNETEntropy - checking examples ... ERROR - -* basket - checking tests ... ERROR - -* BayesMallows - checking examples ... ERROR - checking tests ... ERROR - -* BayesMRA - checking examples ... ERROR - checking tests ... ERROR - -* BayesNetBP - checking examples ... ERROR - -* BayesSUR - checking examples ... ERROR - -* bcgam - checking tests ... ERROR - -* BCT - checking examples ... ERROR - -* BDgraph - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* beam - checking tests ... ERROR - -* bibliometrix - checking examples ... ERROR - -* bifurcatingr - checking examples ... ERROR - -* bio3d - checking examples ... ERROR - -* Bioi - checking tests ... ERROR - -* bioregion - checking examples ... ERROR - -* Bios2cor - checking examples ... ERROR - -* bipartite - checking examples ... ERROR - -* bnma - checking examples ... ERROR - -* bnviewer - checking examples ... ERROR - checking tests ... ERROR - -* BoolNet - checking examples ... ERROR - -* bootnet - checking examples ... ERROR - -* BSBT - checking examples ... ERROR - checking tests ... ERROR - -* btergm - checking tests ... ERROR - -* bwsTools - checking tests ... ERROR - -* Canek - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* cape - checking re-building of vignette outputs ... WARNING - -* CARlasso - checking examples ... ERROR - -* cartograflow - checking examples ... ERROR - -* cassowaryr - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* causact - checking examples ... ERROR - checking tests ... ERROR - -* causalDisco - checking examples ... ERROR - -* ccTensor - checking examples ... ERROR - -* CePa - checking examples ... ERROR - -* CeRNASeek - checking examples ... ERROR - -* cfid - checking tests ... ERROR - -* chemodiv - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* cholera - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* CKMRpop - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* CliquePercolation - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* ClustAssess - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* ClusTorus - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* clustree - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* clustringr - checking examples ... ERROR - -* CoDiNA - checking examples ... ERROR - -* comato - checking examples ... ERROR - -* concatipede - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* concorR - checking examples ... ERROR - -* CoNI - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* corTest - checking examples ... ERROR - -* countland - checking examples ... ERROR - checking tests ... ERROR - -* cppRouting - checking examples ... ERROR - -* crandep - checking examples ... ERROR - -* cranly - checking re-building of vignette outputs ... WARNING - -* criticalpath - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* crosstalkr - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* cytometree - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* d3po - checking examples ... ERROR - -* dartR - checking examples ... ERROR - -* data.tree - checking tests ... ERROR - -* DDPNA - checking examples ... ERROR - -* deaR - checking examples ... ERROR - -* deepdep - checking tests ... ERROR - -* degreenet - checking examples ... ERROR - -* delayed - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* DemoKin - checking re-building of vignette outputs ... WARNING - -* dexterMST - checking examples ... ERROR - -* DiagrammeR - checking examples ... ERROR - checking tests ... ERROR - -* diffeRenTES - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* diffudist - checking examples ... ERROR - -* diffusr - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* dimRed - checking examples ... ERROR - checking tests ... ERROR - -* discourseGT - checking examples ... ERROR - -* discretecdAlgorithm - checking examples ... ERROR - checking tests ... ERROR - -* dm - checking examples ... ERROR - checking tests ... ERROR - -* dnapath - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* dnr - checking examples ... ERROR - -* dodgr - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* dosearch - checking examples ... ERROR - -* dragon - checking tests ... ERROR - -* drake - checking examples ... ERROR - checking tests ... ERROR - -* DrDimont - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* DTSEA - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* dyndimred - checking tests ... ERROR - -* dynetNLAResistance - checking examples ... ERROR - checking tests ... ERROR - -* dyngen - checking tests ... ERROR - -* dynplot - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* dynwrap - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* ecoCopula - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* ECoL - checking examples ... ERROR - checking tests ... ERROR - -* econet - checking examples ... ERROR - -* EcoNetGen - checking tests ... ERROR - -* economiccomplexity - checking examples ... ERROR - checking tests ... ERROR - -* econullnetr - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* EcotoneFinder - checking examples ... ERROR - -* ecpc - checking examples ... ERROR - -* edgebundle - checking examples ... ERROR - checking tests ... ERROR - -* edmcr - checking examples ... ERROR - -* EDOIF - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* eff2 - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* EGAnet - checking examples ... ERROR - -* egor - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* eicm - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* einet - checking examples ... ERROR - checking tests ... ERROR - -* EmbedSOM - checking examples ... ERROR - -* enviGCMS - checking examples ... ERROR - -* epicontacts - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* EpiILMCT - checking examples ... ERROR - -* epinetr - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* espadon - checking examples ... ERROR - -* ess - checking examples ... ERROR - -* etree - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* fairadapt - checking examples ... ERROR - checking tests ... ERROR - -* FAIRmaterials - checking examples ... ERROR - -* fake - checking examples ... ERROR - -* fastnet - checking examples ... ERROR - -* fbnet - checking examples ... ERROR - -* FCMapper - checking examples ... ERROR - -* FindIt - checking examples ... ERROR - -* fnets - checking tests ... ERROR - -* foodingraph - checking examples ... ERROR - -* ForestGapR - checking examples ... ERROR - -* forestRK - checking examples ... ERROR - -* fossilbrush - checking examples ... ERROR - -* FrF2 - checking examples ... ERROR - checking tests ... ERROR - -* fssemR - checking examples ... ERROR - -* gDefrag - checking examples ... ERROR - -* gemtc - checking examples ... ERROR - checking tests ... ERROR - -* genscore - checking examples ... ERROR - -* geonetwork - checking examples ... ERROR - -* ggdag - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* ggenealogy - checking examples ... ERROR - checking running R code from vignettes ... ERROR - -* ggflowchart - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* ggm - checking examples ... ERROR - -* ggnetwork - checking tests ... ERROR - -* ggraph - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* ghypernet - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* GISSB - checking examples ... ERROR - checking tests ... ERROR - -* gmat - checking examples ... ERROR - checking tests ... ERROR - -* GMPro - checking examples ... ERROR - -* GOxploreR - checking examples ... ERROR - -* gRain - checking examples ... ERROR - checking tests ... ERROR - -* grainscape - checking examples ... ERROR - -* grand - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* graph4lg - checking examples ... ERROR - checking data for non-ASCII characters ... NOTE - -* graphclust - checking examples ... ERROR - -* graphicalExtremes - checking examples ... ERROR - -* graphlayouts - checking tests ... ERROR - -* graphseg - checking examples ... ERROR - -* graphTweets - checking examples ... ERROR - checking tests ... ERROR - -* gRbase - checking examples ... ERROR - checking tests ... ERROR - -* gRim - checking examples ... ERROR - checking running R code from vignettes ... ERROR - -* handwriter - checking examples ... ERROR - -* hero - checking examples ... ERROR - -* HLSM - checking examples ... ERROR - -* HospitalNetwork - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* HTT - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* huge - checking examples ... ERROR - -* ICDS - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* iconr - checking examples ... ERROR - -* icosa - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* idopNetwork - checking re-building of vignette outputs ... WARNING - -* iGraphMatch - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* IMEC - checking examples ... ERROR - checking tests ... ERROR - -* immunarch - checking examples ... ERROR - -* immuneSIM - checking examples ... ERROR - -* imsig - checking examples ... ERROR - -* incidentally - checking examples ... ERROR - -* influenceR - checking examples ... ERROR - checking tests ... ERROR - -* influential - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* intergraph - checking examples ... ERROR - -* IOHanalyzer - checking examples ... ERROR - -* isa2 - checking examples ... ERROR - -* isotracer - checking examples ... ERROR - checking tests ... ERROR - -* ITNr - checking examples ... ERROR - -* IxPopDyMod - checking examples ... ERROR - -* jewel - checking examples ... ERROR - -* jti - checking examples ... ERROR - -* kangar00 - checking examples ... ERROR - -* Karen - checking examples ... ERROR - -* keyplayer - checking examples ... ERROR - -* kknn - checking examples ... ERROR - -* l1spectral - checking examples ... ERROR - -* lconnect - checking examples ... ERROR - -* leidenAlg - checking examples ... ERROR - checking tests ... ERROR - -* leidenbase - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* lexRankr - checking examples ... ERROR - checking tests ... ERROR - -* linkprediction - checking examples ... ERROR - checking tests ... ERROR - -* LoopDetectR - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* LSVAR - checking examples ... ERROR - -* lvm4net - checking examples ... ERROR - -* macrosyntR - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* madrat - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* malan - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* manymome - checking examples ... ERROR - -* manynet - checking examples ... ERROR - -* matrixcut - checking examples ... ERROR - -* maxmatching - checking examples ... ERROR - -* mazeGen - checking examples ... ERROR - -* MBNMAdose - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* MBNMAtime - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* mcMST - checking examples ... ERROR - -* mcvis - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* meconetcomp - checking examples ... ERROR - -* Mercator - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* metacoder - checking examples ... ERROR - checking tests ... ERROR - -* metanetwork - checking examples ... ERROR - -* MetricGraph - checking examples ... ERROR - checking tests ... ERROR - -* mfpp - checking examples ... ERROR - -* migraph - checking examples ... ERROR - checking tests ... ERROR - -* miniCRAN - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* missSBM - checking examples ... ERROR - -* mlmts - checking examples ... ERROR - -* mnda - checking examples ... ERROR - -* modnets - checking examples ... ERROR - -* molnet - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* moranajp - checking examples ... ERROR - -* motifcluster - checking examples ... ERROR - checking tests ... ERROR - -* motifr - checking examples ... ERROR - -* mppR - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* MRFcov - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* MRReg - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* MRS - checking examples ... ERROR - -* mstknnclust - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* MTA - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* mully - checking examples ... ERROR - -* multilaterals - checking examples ... ERROR - -* multilink - checking examples ... ERROR - -* multinets - checking examples ... ERROR - checking tests ... ERROR - -* multinma - checking examples ... ERROR - checking tests ... ERROR - -* MultIS - checking re-building of vignette outputs ... WARNING - -* multivariance - checking examples ... ERROR - checking tests ... ERROR - -* mverse - checking re-building of vignette outputs ... WARNING - -* mwcsr - checking examples ... ERROR - checking tests ... ERROR - -* nat - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* nbTransmission - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* nda - checking examples ... ERROR - -* neat - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* neatmaps - checking examples ... ERROR - -* Neighboot - checking examples ... ERROR - -* netCoin - checking examples ... ERROR - -* netcom - checking examples ... ERROR - -* NetCoupler - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* netdiffuseR - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* NetFACS - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* netgsa - checking re-building of vignette outputs ... WARNING - -* netjack - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* netmap - checking tests ... ERROR - -* netmeta - checking examples ... ERROR - -* NetMix - checking examples ... ERROR - -* netplot - checking examples ... ERROR - -* netrankr - checking examples ... ERROR - -* netropy - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* NetSci - checking examples ... ERROR - -* netseg - checking examples ... ERROR - checking tests ... ERROR - -* nett - checking examples ... ERROR - -* netUtils - checking examples ... ERROR - -* NetworkExtinction - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* networkGen - checking examples ... ERROR - -* NetworkInference - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* NetworkToolbox - checking examples ... ERROR - -* networktools - checking tests ... ERROR - -* NIMAA - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* nimble - checking examples ... ERROR - -* nlnet - checking examples ... ERROR - -* nlrx - checking tests ... ERROR - -* node2vec - checking examples ... ERROR - -* nutriNetwork - checking examples ... ERROR - -* OCNet - checking examples ... ERROR - -* oddnet - checking examples ... ERROR - -* ohun - checking examples ... ERROR - -* OpenRepGrid - checking examples ... ERROR - -* OpenRepGrid.ic - checking tests ... ERROR - -* OrdCD - checking examples ... ERROR - -* PAC - checking re-building of vignette outputs ... WARNING - -* PAFit - checking examples ... ERROR - checking tests ... ERROR - -* PairViz - checking re-building of vignette outputs ... WARNING - -* pald - checking examples ... ERROR - checking tests ... ERROR - -* PANACEA - checking examples ... ERROR - -* paramlink - checking examples ... ERROR - -* particles - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* pathfindR - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* pcalg - checking examples ... ERROR - checking tests ... ERROR - checking running R code from vignettes ... ERROR - -* pcFactorStan - checking examples ... ERROR - checking tests ... ERROR - -* pedtools - checking examples ... ERROR - -* perturbR - checking examples ... ERROR - -* pGRN - checking examples ... ERROR - -* phangorn - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* PhaseTypeR - checking tests ... ERROR - -* phyloseqGraphTest - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* phylosignal - checking examples ... ERROR - -* phyloTop - checking examples ... ERROR - checking tests ... ERROR - -* pkggraph - checking examples ... ERROR - -* PlackettLuce - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* plantTracker - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* plinkQC - checking tests ... ERROR - -* PLNmodels - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* pmd - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* PNAR - checking examples ... ERROR - -* polymapR - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* polyqtlR - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* pomdp - checking re-building of vignette outputs ... WARNING - -* pop - checking examples ... ERROR - checking tests ... ERROR - -* poppr - checking examples ... ERROR - checking tests ... ERROR - -* POSetR - checking examples ... ERROR - -* ProjectManagement - checking examples ... ERROR - -* provGraphR - checking examples ... ERROR - checking tests ... ERROR - -* ptools - checking examples ... ERROR - checking tests ... ERROR - -* qdap - checking tests ... ERROR - -* qgraph - checking examples ... ERROR - -* R.temis - checking examples ... ERROR - -* RaceID - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* rags2ridges - checking examples ... ERROR - -* RavenR - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* rcrimeanalysis - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* rD3plot - checking examples ... ERROR - -* RDS - checking examples ... ERROR - checking tests ... ERROR - -* readsdr - checking tests ... ERROR - -* ReDaMoR - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* refdb - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* RepertoiR - checking examples ... ERROR - checking tests ... ERROR - -* repo - checking examples ... ERROR - -* ResIN - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* RevEcoR - checking examples ... ERROR - -* rflexscan - checking examples ... ERROR - -* rgexf - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* rgraph6 - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* rhcoclust - checking examples ... ERROR - -* rmangal - checking tests ... ERROR - -* rmcfs - checking tests ... ERROR - -* rmonad - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* roads - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* robber - checking examples ... ERROR - checking tests ... ERROR - -* robin - checking examples ... ERROR - -* RobustIV - checking examples ... ERROR - -* robustrao - checking examples ... ERROR - -* roprov - checking examples ... ERROR - -* RPANDA - checking examples ... ERROR - -* rquery - checking examples ... ERROR - -* rscc - checking examples ... ERROR - -* RScelestial - checking examples ... ERROR - -* rsetse - checking examples ... ERROR - -* rSpectral - checking examples ... ERROR - checking tests ... ERROR - -* rsppfp - checking examples ... ERROR - -* rvinecopulib - checking examples ... ERROR - checking tests ... ERROR - -* safedata - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* saotd - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* sBIC - checking tests ... ERROR - -* sbm - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* SBN - checking examples ... ERROR - -* sccore - checking examples ... ERROR - checking tests ... ERROR - -* scDHA - checking tests ... ERROR - -* scDiffCom - checking tests ... ERROR - -* SCORPION - checking examples ... ERROR - -* scRNAtools - checking examples ... ERROR - -* secrlinear - checking examples ... ERROR - checking tests ... ERROR - -* SelectBoost - checking examples ... ERROR - -* SEMID - checking examples ... ERROR - checking tests ... ERROR - -* sensitivity - checking examples ... ERROR - -* SeqDetect - checking examples ... ERROR - checking running R code from vignettes ... ERROR - -* seqHMM - checking examples ... ERROR - -* SeqNet - checking examples ... ERROR - checking tests ... ERROR - -* SetRank - checking examples ... ERROR - -* sfcr - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* sfdep - checking examples ... ERROR - -* sfnetworks - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* SFSI - checking examples ... ERROR - -* sharp - checking examples ... ERROR - -* sharpshootR - checking examples ... ERROR - -* shazam - checking examples ... ERROR - -* shock - checking examples ... ERROR - -* sidier - checking examples ... ERROR - -* sigmajs - checking examples ... ERROR +* gemtc checking tests ... ERROR -* signnet +* leidenAlg checking examples ... ERROR checking tests ... ERROR -* simcausal +* leidenbase checking examples ... ERROR checking tests ... ERROR - -* simer - checking examples ... ERROR - -* simPATHy - checking examples ... ERROR checking re-building of vignette outputs ... WARNING -* simplifyNet - checking examples ... ERROR - -* SIRE - checking examples ... ERROR - -* sirt +* nda checking examples ... ERROR -* SITH - checking re-building of vignette outputs ... WARNING - -* skynet - checking examples ... ERROR +* netseg checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* SmCCNet - checking examples ... ERROR - -* smotefamily - checking examples ... ERROR - -* snowboot - checking examples ... ERROR * SNscan checking examples ... ERROR -* SOAs - checking tests ... ERROR - -* SoilR - checking examples ... ERROR - -* solitude - checking examples ... ERROR - -* SourceSet - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* spacejamr - checking examples ... ERROR - checking tests ... ERROR - -* sparsebnUtils - checking tests ... ERROR - -* spathial - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* spatsoc - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* specr - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* spinner - checking tests ... ERROR - -* spNetwork - checking examples ... ERROR - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* spqdep - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* SSN - checking examples ... ERROR - -* stagedtrees - checking tests ... ERROR - -* statGraph - checking examples ... ERROR - -* stemmatology - checking examples ... ERROR - checking tests ... ERROR - -* stm - checking running R code from vignettes ... ERROR - -* stplanr - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* SurvHiDim - checking examples ... ERROR - -* targets - checking tests ... ERROR - -* TDA - checking examples ... ERROR - checking running R code from vignettes ... ERROR - -* text2map - checking examples ... ERROR - -* textrank - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - * tidygraph - checking examples ... ERROR - checking tests ... ERROR - -* tilemaps - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* tip - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* Tlasso - checking examples ... ERROR - checking re-building of vignette outputs ... WARNING - -* TOHM - checking examples ... ERROR - -* TreeDimensionTest - checking re-building of vignette outputs ... WARNING - -* treefit - checking tests ... ERROR - checking re-building of vignette outputs ... WARNING - -* treemap - checking examples ... ERROR - -* VARDetect - checking examples ... ERROR - -* vennLasso - checking examples ... ERROR - -* VertexSimilarity - checking examples ... ERROR - -* vivainsights - checking examples ... ERROR - -* wdnet - checking examples ... ERROR - checking tests ... ERROR - -* webtrackR - checking examples ... ERROR - checking tests ... ERROR - -* whitechapelR - checking examples ... ERROR - checking tests ... ERROR - -* wpa - checking examples ... ERROR - -* xgboost - checking examples ... ERROR checking tests ... ERROR -### Failed to check - -* DRviaSPCN (NA) -* FinNet (NA) -* genekitr (NA) -* immcp (NA) -* MACP (NA) -* numbat (NA) -* Platypus (NA) -* R6causal (NA) -* tidySEM (NA) -* vivid (NA) diff --git a/revdep/failures.md b/revdep/failures.md index f6939cdc6f3..9a207363396 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -1,820 +1 @@ -# NA - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/NA -* Number of recursive dependencies: 0 - -Run `revdepcheck::cloud_details(, "NA")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# DRviaSPCN - -
- -* Version: 0.1.2 -* GitHub: NA -* Source code: https://github.com/cran/DRviaSPCN -* Date/Publication: 2022-03-03 16:00:02 UTC -* Number of recursive dependencies: 170 - -Run `revdepcheck::cloud_details(, "DRviaSPCN")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/DRviaSPCN/new/DRviaSPCN.Rcheck’ -* using R version 4.1.1 (2021-08-10) -* using platform: x86_64-pc-linux-gnu (64-bit) -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘DRviaSPCN/DESCRIPTION’ ... OK -* checking extension type ... Package -* this is package ‘DRviaSPCN’ version ‘0.1.2’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘clusterProfiler’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/DRviaSPCN/old/DRviaSPCN.Rcheck’ -* using R version 4.1.1 (2021-08-10) -* using platform: x86_64-pc-linux-gnu (64-bit) -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘DRviaSPCN/DESCRIPTION’ ... OK -* checking extension type ... Package -* this is package ‘DRviaSPCN’ version ‘0.1.2’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘clusterProfiler’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -# FinNet - -
- -* Version: 0.1.1 -* GitHub: https://github.com/FATelarico/FinNet -* Source code: https://github.com/cran/FinNet -* Date/Publication: 2023-06-01 13:00:02 UTC -* Number of recursive dependencies: 42 - -Run `revdepcheck::cloud_details(, "FinNet")` for more info - -
- -## In both - -* checking whether package ‘FinNet’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/FinNet/new/FinNet.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘FinNet’ ... -** package ‘FinNet’ successfully unpacked and MD5 sums checked -** using staged installation -** R -Error in parse(outFile) : - /tmp/workdir/FinNet/new/FinNet.Rcheck/00_pkg_src/FinNet/R/00.helpers.R:172:21: unexpected input -171: y <- rep(clrs[1], 3)|> paste0(collapse = '')|> -172: paste0('#', x = _ - ^ -ERROR: unable to collate and parse R files for package ‘FinNet’ -* removing ‘/tmp/workdir/FinNet/new/FinNet.Rcheck/FinNet’ - - -``` -### CRAN - -``` -* installing *source* package ‘FinNet’ ... -** package ‘FinNet’ successfully unpacked and MD5 sums checked -** using staged installation -** R -Error in parse(outFile) : - /tmp/workdir/FinNet/old/FinNet.Rcheck/00_pkg_src/FinNet/R/00.helpers.R:172:21: unexpected input -171: y <- rep(clrs[1], 3)|> paste0(collapse = '')|> -172: paste0('#', x = _ - ^ -ERROR: unable to collate and parse R files for package ‘FinNet’ -* removing ‘/tmp/workdir/FinNet/old/FinNet.Rcheck/FinNet’ - - -``` -# genekitr - -
- -* Version: 1.2.2 -* GitHub: https://github.com/GangLiLab/genekitr -* Source code: https://github.com/cran/genekitr -* Date/Publication: 2023-05-24 04:00:02 UTC -* Number of recursive dependencies: 206 - -Run `revdepcheck::cloud_details(, "genekitr")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/genekitr/new/genekitr.Rcheck’ -* using R version 4.1.1 (2021-08-10) -* using platform: x86_64-pc-linux-gnu (64-bit) -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘genekitr/DESCRIPTION’ ... OK -* checking extension type ... Package -* this is package ‘genekitr’ version ‘1.2.2’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘clusterProfiler’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/genekitr/old/genekitr.Rcheck’ -* using R version 4.1.1 (2021-08-10) -* using platform: x86_64-pc-linux-gnu (64-bit) -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘genekitr/DESCRIPTION’ ... OK -* checking extension type ... Package -* this is package ‘genekitr’ version ‘1.2.2’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘clusterProfiler’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -# immcp - -
- -* Version: 1.0.3 -* GitHub: https://github.com/YuanlongHu/immcp -* Source code: https://github.com/cran/immcp -* Date/Publication: 2022-05-12 05:50:02 UTC -* Number of recursive dependencies: 195 - -Run `revdepcheck::cloud_details(, "immcp")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/immcp/new/immcp.Rcheck’ -* using R version 4.1.1 (2021-08-10) -* using platform: x86_64-pc-linux-gnu (64-bit) -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘immcp/DESCRIPTION’ ... OK -* this is package ‘immcp’ version ‘1.0.3’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘clusterProfiler’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/immcp/old/immcp.Rcheck’ -* using R version 4.1.1 (2021-08-10) -* using platform: x86_64-pc-linux-gnu (64-bit) -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘immcp/DESCRIPTION’ ... OK -* this is package ‘immcp’ version ‘1.0.3’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘clusterProfiler’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -# MACP - -
- -* Version: 0.1.0 -* GitHub: https://github.com/mrbakhsh/MACP -* Source code: https://github.com/cran/MACP -* Date/Publication: 2023-02-28 17:32:30 UTC -* Number of recursive dependencies: 234 - -Run `revdepcheck::cloud_details(, "MACP")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/MACP/new/MACP.Rcheck’ -* using R version 4.1.1 (2021-08-10) -* using platform: x86_64-pc-linux-gnu (64-bit) -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘MACP/DESCRIPTION’ ... OK -* checking extension type ... Package -* this is package ‘MACP’ version ‘0.1.0’ -* package encoding: UTF-8 -* checking package namespace information ... OK -... ---- failed re-building ‘MACP_tutorial.Rmd’ - -SUMMARY: processing the following file failed: - ‘MACP_tutorial.Rmd’ - -Error: Vignette re-building failed. -Execution halted - -* DONE -Status: 1 ERROR, 1 WARNING, 3 NOTEs - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/MACP/old/MACP.Rcheck’ -* using R version 4.1.1 (2021-08-10) -* using platform: x86_64-pc-linux-gnu (64-bit) -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘MACP/DESCRIPTION’ ... OK -* checking extension type ... Package -* this is package ‘MACP’ version ‘0.1.0’ -* package encoding: UTF-8 -* checking package namespace information ... OK -... -* checking installed files from ‘inst/doc’ ... OK -* checking files in ‘vignettes’ ... OK -* checking examples ... OK -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... NONE - ‘MACP_tutorial.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 3 NOTEs - - - - - -``` -# numbat - -
- -* Version: 1.3.2 -* GitHub: https://github.com/kharchenkolab/numbat -* Source code: https://github.com/cran/numbat -* Date/Publication: 2023-06-06 16:40:02 UTC -* Number of recursive dependencies: 132 - -Run `revdepcheck::cloud_details(, "numbat")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/numbat/new/numbat.Rcheck’ -* using R version 4.1.1 (2021-08-10) -* using platform: x86_64-pc-linux-gnu (64-bit) -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘numbat/DESCRIPTION’ ... OK -* this is package ‘numbat’ version ‘1.3.2’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'ggtree', 'scistreer' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/numbat/old/numbat.Rcheck’ -* using R version 4.1.1 (2021-08-10) -* using platform: x86_64-pc-linux-gnu (64-bit) -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘numbat/DESCRIPTION’ ... OK -* this is package ‘numbat’ version ‘1.3.2’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Packages required but not available: 'ggtree', 'scistreer' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -# NA - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/NA -* Number of recursive dependencies: 0 - -Run `revdepcheck::cloud_details(, "NA")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# Platypus - -
- -* Version: 3.4.1 -* GitHub: NA -* Source code: https://github.com/cran/Platypus -* Date/Publication: 2022-08-15 07:20:20 UTC -* Number of recursive dependencies: 354 - -Run `revdepcheck::cloud_details(, "Platypus")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/Platypus/new/Platypus.Rcheck’ -* using R version 4.1.1 (2021-08-10) -* using platform: x86_64-pc-linux-gnu (64-bit) -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘Platypus/DESCRIPTION’ ... OK -* checking extension type ... Package -* this is package ‘Platypus’ version ‘3.4.1’ -* package encoding: UTF-8 -* checking package namespace information ... OK -... -Package required but not available: ‘ggtree’ - -Packages suggested but not available for checking: - 'Matrix.utils', 'monocle3', 'ProjecTILs', 'SeuratWrappers', - 'vanddraabe' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/Platypus/old/Platypus.Rcheck’ -* using R version 4.1.1 (2021-08-10) -* using platform: x86_64-pc-linux-gnu (64-bit) -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘Platypus/DESCRIPTION’ ... OK -* checking extension type ... Package -* this is package ‘Platypus’ version ‘3.4.1’ -* package encoding: UTF-8 -* checking package namespace information ... OK -... -Package required but not available: ‘ggtree’ - -Packages suggested but not available for checking: - 'Matrix.utils', 'monocle3', 'ProjecTILs', 'SeuratWrappers', - 'vanddraabe' - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -# R6causal - -
- -* Version: 0.7.0 -* GitHub: NA -* Source code: https://github.com/cran/R6causal -* Date/Publication: 2022-11-04 08:00:02 UTC -* Number of recursive dependencies: 98 - -Run `revdepcheck::cloud_details(, "R6causal")` for more info - -
- -## Newly broken - -* checking whether package ‘R6causal’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/R6causal/new/R6causal.Rcheck/00install.out’ for details. - ``` - -## Newly fixed - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘using_R6causal.Rmd’ using rmarkdown - A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TinyTeX with tinytex::reinstall_tinytex(repository = "illinois"). - - tlmgr: Local TeX Live (2022) is older than remote repository (2023). - Cross release updates are only supported with - update-tlmgr-latest(.sh/.exe) --update - See https://tug.org/texlive/upgrade.html for details. - Warning in system2("tlmgr", args, ...) : - ... - - Error: processing vignette 'using_R6causal.Rmd' failed with diagnostics: - LaTeX failed to compile /tmp/workdir/R6causal/old/R6causal.Rcheck/vign_test/R6causal/vignettes/using_R6causal.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See using_R6causal.log for more info. - --- failed re-building ‘using_R6causal.Rmd’ - - SUMMARY: processing the following file failed: - ‘using_R6causal.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘R6causal’ ... -** package ‘R6causal’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" -Error: unable to load R code in package ‘R6causal’ -Execution halted -ERROR: lazy loading failed for package ‘R6causal’ -* removing ‘/tmp/workdir/R6causal/new/R6causal.Rcheck/R6causal’ - - -``` -### CRAN - -``` -* installing *source* package ‘R6causal’ ... -** package ‘R6causal’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -** help -*** installing help indices -** building package indices -** installing vignettes -** testing if installed package can be loaded from temporary location -** testing if installed package can be loaded from final location -** testing if installed package keeps a record of temporary installation path -* DONE (R6causal) - - -``` -# NA - -
- -* Version: NA -* GitHub: NA -* Source code: https://github.com/cran/NA -* Number of recursive dependencies: 0 - -Run `revdepcheck::cloud_details(, "NA")` for more info - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# tidySEM - -
- -* Version: 0.2.4 -* GitHub: https://github.com/cjvanlissa/tidySEM -* Source code: https://github.com/cran/tidySEM -* Date/Publication: 2023-05-01 20:00:06 UTC -* Number of recursive dependencies: 189 - -Run `revdepcheck::cloud_details(, "tidySEM")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/tidySEM/new/tidySEM.Rcheck’ -* using R version 4.1.1 (2021-08-10) -* using platform: x86_64-pc-linux-gnu (64-bit) -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘tidySEM/DESCRIPTION’ ... OK -* checking extension type ... Package -* this is package ‘tidySEM’ version ‘0.2.4’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘blavaan’ - -Package suggested but not available for checking: ‘umx’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/tidySEM/old/tidySEM.Rcheck’ -* using R version 4.1.1 (2021-08-10) -* using platform: x86_64-pc-linux-gnu (64-bit) -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘tidySEM/DESCRIPTION’ ... OK -* checking extension type ... Package -* this is package ‘tidySEM’ version ‘0.2.4’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... ERROR -Package required but not available: ‘blavaan’ - -Package suggested but not available for checking: ‘umx’ - -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -# vivid - -
- -* Version: 0.2.7 -* GitHub: NA -* Source code: https://github.com/cran/vivid -* Date/Publication: 2023-04-11 13:50:02 UTC -* Number of recursive dependencies: 209 - -Run `revdepcheck::cloud_details(, "vivid")` for more info - -
- -## Error before installation - -### Devel - -``` -* using log directory ‘/tmp/workdir/vivid/new/vivid.Rcheck’ -* using R version 4.1.1 (2021-08-10) -* using platform: x86_64-pc-linux-gnu (64-bit) -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘vivid/DESCRIPTION’ ... OK -* this is package ‘vivid’ version ‘0.2.7’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... NOTE -... ---- failed re-building ‘vividVignette.Rmd’ - -SUMMARY: processing the following file failed: - ‘vividVignette.Rmd’ - -Error: Vignette re-building failed. -Execution halted - -* DONE -Status: 1 WARNING, 1 NOTE - - - - - -``` -### CRAN - -``` -* using log directory ‘/tmp/workdir/vivid/old/vivid.Rcheck’ -* using R version 4.1.1 (2021-08-10) -* using platform: x86_64-pc-linux-gnu (64-bit) -* using session charset: UTF-8 -* using option ‘--no-manual’ -* checking for file ‘vivid/DESCRIPTION’ ... OK -* this is package ‘vivid’ version ‘0.2.7’ -* package encoding: UTF-8 -* checking package namespace information ... OK -* checking package dependencies ... NOTE -... -* checking installed files from ‘inst/doc’ ... OK -* checking files in ‘vignettes’ ... OK -* checking examples ... OK -* checking for unstated dependencies in vignettes ... OK -* checking package vignettes in ‘inst/doc’ ... OK -* checking running R code from vignettes ... NONE - ‘vividVignette.Rmd’ using ‘UTF-8’... OK -* checking re-building of vignette outputs ... OK -* DONE -Status: 1 NOTE - - - - - -``` +*Wow, no problems at all. :)* \ No newline at end of file diff --git a/revdep/problems.md b/revdep/problems.md index be5022953b2..2dc1184fa38 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1,24482 +1,52 @@ -# adegenet - -
- -* Version: 2.1.10 -* GitHub: https://github.com/thibautjombart/adegenet -* Source code: https://github.com/cran/adegenet -* Date/Publication: 2023-01-26 22:00:23 UTC -* Number of recursive dependencies: 132 - -Run `revdepcheck::cloud_details(, "adegenet")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘adegenet-Ex.R’ failed - The error most likely occurred in: - - > ### Name: gengraph - > ### Title: Genetic transitive graphs - > ### Aliases: gengraph gengraph.default gengraph.matrix gengraph.dist - > ### gengraph.genind gengraph.genpop gengraph.DNAbin - > - > ### ** Examples - > - ... - + g <- gengraph(woodmouse, cutoff=5) - + g - + plot(g$graph) - + - + } - Loading required package: ape - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: gengraph ... gengraph.matrix -> graph.adjacency -> graph.adjacency.dense - Execution halted - ``` - -# AHPWR - -
- -* Version: 0.1.0 -* GitHub: NA -* Source code: https://github.com/cran/AHPWR -* Date/Publication: 2022-12-06 17:02:46 UTC -* Number of recursive dependencies: 96 - -Run `revdepcheck::cloud_details(, "AHPWR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘AHPWR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: flow_chart - > ### Title: creates a hierarchical structure - > ### Aliases: flow_chart - > - > ### ** Examples - > - > p=flow_chart(names=NULL, a=2, c=2) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: flow_chart -> -> make_empty_graph - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘Intro_to_AHP.Rmd’ using rmarkdown - - Quitting from lines 45-47 [unnamed-chunk-2] (Intro_to_AHP.Rmd) - Error: processing vignette 'Intro_to_AHP.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘Intro_to_AHP.Rmd’ - - SUMMARY: processing the following file failed: - ‘Intro_to_AHP.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# akc - -
- -* Version: 0.9.9 -* GitHub: https://github.com/hope-data-science/akc -* Source code: https://github.com/cran/akc -* Date/Publication: 2023-01-06 08:00:02 UTC -* Number of recursive dependencies: 118 - -Run `revdepcheck::cloud_details(, "akc")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘akc-Ex.R’ failed - The error most likely occurred in: - - > ### Name: doc_group - > ### Title: Construct network of documents based on keyword co-occurrence - > ### Aliases: doc_group - > - > ### ** Examples - > - > library(akc) - > bibli_data_table %>% - + keyword_clean(id = "id",keyword = "keyword") %>% - + doc_group(id = "id",keyword = "keyword") -> grouped_doc - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: %>% ... as_tbl_graph -> graph_from_data_frame -> make_empty_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 5. ├─dplyr::pull(., 2) - 6. ├─akc::keyword_table(.) - 7. │ └─tidygraph::is.tbl_graph(tibble_graph) - 8. ├─akc::keyword_group(., id = "id", keyword = "keyword") - 9. │ └─... %>% mutate(group = com_detect_fun()) - 10. ├─dplyr::mutate(., group = com_detect_fun()) - 11. ├─dplyr::rename(., freq = n) - 12. ├─dplyr::inner_join(., freq_table, by = c(name = "keyword")) - 13. ├─tidygraph::as_tbl_graph(.) - 14. └─igraph::graph_from_data_frame(., directed = FALSE) - 15. └─igraph::make_empty_graph(n = 0, directed = directed) - - [ FAIL 2 | WARN 0 | SKIP 0 | PASS 4 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘Benchmarking.Rmd’ using rmarkdown - --- finished re-building ‘Benchmarking.Rmd’ - - --- re-building ‘akc_vignette.Rmd’ using rmarkdown - - Quitting from lines 75-79 [unnamed-chunk-5] (akc_vignette.Rmd) - Error: processing vignette 'akc_vignette.Rmd' failed with diagnostics: - could not find function ".igraph.status" - ... - Quitting from lines 63-65 [unnamed-chunk-6] (tutorial_raw_text.Rmd) - Error: processing vignette 'tutorial_raw_text.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘tutorial_raw_text.Rmd’ - - SUMMARY: processing the following files failed: - ‘akc_vignette.Rmd’ ‘tutorial_raw_text.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# alakazam - -
- -* Version: 1.2.1 -* GitHub: NA -* Source code: https://github.com/cran/alakazam -* Date/Publication: 2022-09-20 22:10:02 UTC -* Number of recursive dependencies: 117 - -Run `revdepcheck::cloud_details(, "alakazam")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘alakazam-Ex.R’ failed - The error most likely occurred in: - - > ### Name: getMRCA - > ### Title: Retrieve the first non-root node of a lineage tree - > ### Aliases: getMRCA - > - > ### ** Examples - > - > # Define example graph - > graph <- ExampleTrees[[23]] - > - > # Use unweighted path length and do not exclude any nodes - > getMRCA(graph, path="steps", root="Germline") - Error in .igraph.status("Restore graph external pointer.\n") : - could not find function ".igraph.status" - Calls: getMRCA ... data.frame -> V -> ensure_igraph -> is_igraph -> warn_version - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘AminoAcids-Vignette.Rmd’ using rmarkdown - A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TinyTeX with tinytex::reinstall_tinytex(repository = "illinois"). - - tlmgr: Local TeX Live (2022) is older than remote repository (2023). - Cross release updates are only supported with - update-tlmgr-latest(.sh/.exe) --update - See https://tug.org/texlive/upgrade.html for details. - Warning in system2("tlmgr", args, ...) : - running command ''tlmgr' search --file --global '/grffile.sty'' had status 1 - ... - LaTeX failed to compile /tmp/workdir/alakazam/new/alakazam.Rcheck/vign_test/alakazam/vignettes/Topology-Vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Topology-Vignette.log for more info. - --- failed re-building ‘Topology-Vignette.Rmd’ - - SUMMARY: processing the following files failed: - ‘AminoAcids-Vignette.Rmd’ ‘Diversity-Vignette.Rmd’ - ‘Fastq-Vignette.Rmd’ ‘Files-Vignette.Rmd’ ‘GeneUsage-Vignette.Rmd’ - ‘Lineage-Vignette.Rmd’ ‘Topology-Vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# AnimalHabitatNetwork - -
- -* Version: 0.1.0 -* GitHub: NA -* Source code: https://github.com/cran/AnimalHabitatNetwork -* Date/Publication: 2019-11-25 19:40:02 UTC -* Number of recursive dependencies: 30 - -Run `revdepcheck::cloud_details(, "AnimalHabitatNetwork")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘AnimalHabitatNetwork-Ex.R’ failed - The error most likely occurred in: - - > ### Name: ahn_gen - > ### Title: Generate networks characterising habitat physical configurations - > ### Aliases: ahn_gen - > - > ### ** Examples - > - > # generate a connected and weighted network - > ahn_gen(N = 10, L = 5, mu = 1, lamda = 5) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: ahn_gen ... graph_from_adjacency_matrix -> graph.adjacency.dense - Execution halted - ``` - -# aniSNA - -
- -* Version: 1.0 -* GitHub: NA -* Source code: https://github.com/cran/aniSNA -* Date/Publication: 2023-02-17 09:50:09 UTC -* Number of recursive dependencies: 58 - -Run `revdepcheck::cloud_details(, "aniSNA")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘aniSNA-Ex.R’ failed - The error most likely occurred in: - - > ### Name: elk_network_2010 - > ### Title: An igraph object depicting the network obtained from - > ### elk_interactions_2010 - > ### Aliases: elk_network_2010 - > ### Keywords: datasets - > - > ### ** Examples - > - > igraph::E(elk_network_2010) - Error in .igraph.status("Restore graph external pointer.\n") : - could not find function ".igraph.status" - Calls: -> ensure_igraph -> is_igraph -> warn_version - Execution halted - ``` - -# anocva - -
- -* Version: 0.1.1 -* GitHub: NA -* Source code: https://github.com/cran/anocva -* Date/Publication: 2017-11-10 04:27:50 UTC -* Number of recursive dependencies: 9 - -Run `revdepcheck::cloud_details(, "anocva")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘anocva-Ex.R’ failed - The error most likely occurred in: - - > ### Name: spectralClustering - > ### Title: Spectral clustering - > ### Aliases: spectralClustering - > - > ### ** Examples - > - > # Install igraph if necessary - ... - + # Cluster the tree graph in to four clusters - + cluster = spectralClustering(adj, 4) - + - + # See the result clustering - + plot(treeGraph, vertex.size=10, vertex.color = cluster, vertex.label = NA) - + } - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: - Execution halted - ``` - -# archeofrag - -
- -* Version: 0.8.2 -* GitHub: https://github.com/sebastien-plutniak/archeofrag -* Source code: https://github.com/cran/archeofrag -* Date/Publication: 2022-09-11 22:02:59 UTC -* Number of recursive dependencies: 68 - -Run `revdepcheck::cloud_details(, "archeofrag")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘archeofrag-Ex.R’ failed - The error most likely occurred in: - - > ### Name: frag.cycles - > ### Title: Count the k-cycles in a graph, for cycles =< k - > ### Aliases: frag.cycles - > ### Keywords: measurement - > - > ### ** Examples - > - > g <- frag.simul.process(n.components=20, vertices=50, disturbance=.15) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: frag.simul.process -> .main -> -> do.call -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 2. └─archeofrag::make_cr_graph(g) - 3. └─igraph::graph_from_data_frame(...) - 4. └─igraph::make_empty_graph(n = 0, directed = directed) - ── Error ('test.frag.get.parameters.R:15:3'): retrieved parameters are correct ── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. ├─archeofrag::make_cr_graph(g) at test.frag.get.parameters.R:15:2 - 2. └─archeofrag::make_cr_graph(g) - 3. └─igraph::graph_from_data_frame(...) - 4. └─igraph::make_empty_graph(n = 0, directed = directed) - - [ FAIL 31 | WARN 0 | SKIP 0 | PASS 4 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘archeofrag-vignette.Rmd’ using rmarkdown - - Quitting from lines 61-65 [make-empirical-graph] (archeofrag-vignette.Rmd) - Error: processing vignette 'archeofrag-vignette.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘archeofrag-vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘archeofrag-vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# arulesViz - -
- -* Version: 1.5-2 -* GitHub: https://github.com/mhahsler/arulesViz -* Source code: https://github.com/cran/arulesViz -* Date/Publication: 2023-03-07 16:50:02 UTC -* Number of recursive dependencies: 111 - -Run `revdepcheck::cloud_details(, "arulesViz")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘arulesViz-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plot - > ### Title: Visualize Association Rules and Itemsets - > ### Aliases: plot plot.itemsets plot.rules plot.grouped_matrix plotly - > ### guide_edge_colourbar - > ### Keywords: hplot - > - > ### ** Examples - ... - > - > ## Graph representation - > # Default engine is ggplot2 with ggraph. Associations are represented as nodes. - > # We limit the number of rules to the 10 with the larges - > # lift (measure used for shading) - > plot(subrules, method = "graph", limit = 10) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot ... associations2igraph_nodes -> -> make_empty_graph - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘arulesViz.Rnw’ - ... - - > plot(rules, method = "grouped", control = list(k = 50)) - - > subrules2 <- head(rules, n = 10, by = "lift") - - > plot(subrules2, method = "graph") - - When sourcing ‘arulesViz.R’: - Error: could not find function ".igraph.status" - Execution halted - - ‘arulesViz.Rnw’ using ‘UTF-8’... failed - ``` - -## In both - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘arulesViz.Rnw’ using Sweave - Loading required package: arules - Loading required package: Matrix - - Attaching package: ‘arules’ - - The following objects are masked from ‘package:base’: - - abbreviate, write - ... - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - - --- failed re-building ‘arulesViz.Rnw’ - - SUMMARY: processing the following file failed: - ‘arulesViz.Rnw’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# autoharp - -
- -* Version: 0.0.10 -* GitHub: NA -* Source code: https://github.com/cran/autoharp -* Date/Publication: 2021-11-12 22:50:02 UTC -* Number of recursive dependencies: 92 - -Run `revdepcheck::cloud_details(, "autoharp")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘autoharp-Ex.R’ failed - The error most likely occurred in: - - > ### Name: carve_subtree - > ### Title: Carve out branches to form a new tree. - > ### Aliases: carve_subtree - > - > ### ** Examples - > - > th3 <- list(a= c(2L,3L,4L), b=NULL, c=c(5L, 6L), d=7L, e=NULL, f=NULL, g=NULL) - > carve_subtree(TreeHarp(th3), c(1,0,0,0,0,0,0)) - a - > st <- subtree_at(TreeHarp(th3), 4) - > plot(st) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot -> plot -> - Execution halted - ``` - -# autostats - -
- -* Version: 0.4.0 -* GitHub: https://github.com/Harrison4192/autostats -* Source code: https://github.com/cran/autostats -* Date/Publication: 2022-11-07 10:20:06 UTC -* Number of recursive dependencies: 229 - -Run `revdepcheck::cloud_details(, "autostats")` for more info - -
- -## Newly broken - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘autostats.Rmd’ using rmarkdown - --- finished re-building ‘autostats.Rmd’ - - --- re-building ‘tidyXgboost.Rmd’ using rmarkdown - - Quitting from lines 187-189 [unnamed-chunk-15] (tidyXgboost.Rmd) - Error: processing vignette 'tidyXgboost.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘tidyXgboost.Rmd’ - - SUMMARY: processing the following file failed: - ‘tidyXgboost.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# backbone - -
- -* Version: 2.1.2 -* GitHub: https://github.com/zpneal/backbone -* Source code: https://github.com/cran/backbone -* Date/Publication: 2023-02-13 21:20:02 UTC -* Number of recursive dependencies: 38 - -Run `revdepcheck::cloud_details(, "backbone")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘backbone-Ex.R’ failed - The error most likely occurred in: - - > ### Name: disparity - > ### Title: Extract backbone using the Disparity Filter - > ### Aliases: disparity - > - > ### ** Examples - > - > #A network with heterogeneous (i.e. multiscale) weights - ... - + 0,0,0,0,0,100,0,10,10,10, - + 0,0,0,0,0,100,10,0,10,10, - + 0,0,0,0,0,100,10,10,0,10, - + 0,0,0,0,0,100,10,10,10,0),10) - > - > net <- igraph::graph_from_adjacency_matrix(net, mode = "undirected", weighted = TRUE) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: -> graph.adjacency.dense - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘tinytest.R’ - Running the tests in ‘tests/tinytest.R’ failed. - Last 13 lines of output: - test_backbone.R............... 22 tests OK - test_backbone.R............... 23 tests OK - test_backbone.R............... 24 tests OK - test_backbone.R............... 25 tests OK - test_backbone.R............... 25 tests OK - test_backbone.R............... 25 tests OK - test_backbone.R............... 25 tests OK - test_backbone.R............... 26 tests OK - test_backbone.R............... 27 tests OK - test_backbone.R............... 28 tests OK - test_backbone.R............... 29 tests OK - test_backbone.R............... 30 tests OK Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: ... run_test_dir -> lapply -> FUN -> eval -> eval -> - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘backbone.Rmd’ using rmarkdown - - Quitting from lines 132-134 [unnamed-chunk-5] (backbone.Rmd) - Error: processing vignette 'backbone.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘backbone.Rmd’ - - SUMMARY: processing the following file failed: - ‘backbone.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# backShift - -
- -* Version: 0.1.4.3 -* GitHub: https://github.com/christinaheinze/backShift -* Source code: https://github.com/cran/backShift -* Date/Publication: 2020-05-06 11:30:03 UTC -* Number of recursive dependencies: 97 - -Run `revdepcheck::cloud_details(, "backShift")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘backShift-Ex.R’ failed - The error most likely occurred in: - - > ### Name: exampleAdjacencyMatrix - > ### Title: Example adjacency matrix - > ### Aliases: exampleAdjacencyMatrix - > ### Keywords: datasets - > - > ### ** Examples - > - > data("exampleAdjacencyMatrix") - > plotGraphEdgeAttr(estimate = exampleAdjacencyMatrix, plotStabSelec = FALSE, - + labels = colnames(exampleAdjacencyMatrix), - + thres.point = 0, thres.stab = NULL, main = "True graph") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plotGraphEdgeAttr -> graph.data.frame -> make_empty_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. ├─testthat::expect_is(...) at test_backShift.R:67:12 - 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") - 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) - 4. └─backShift::backShift(...) - 5. └─backShift:::permuteAndScale(estimatedB, verbose) - 6. └─backShift:::hasCPsmallerOne(Dhat, returnCycleNodes = FALSE) - 7. └─igraph::graph.adjacency(Ahat.larger.1, mode = "directed", weighted = "a") - 8. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 32 | WARN 7 | SKIP 0 | PASS 0 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘exampleBackShift.Rmd’ using rmarkdown - - Quitting from lines 180-184 [unnamed-chunk-7] (exampleBackShift.Rmd) - Error: processing vignette 'exampleBackShift.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘exampleBackShift.Rmd’ - - SUMMARY: processing the following file failed: - ‘exampleBackShift.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking Rd cross-references ... NOTE - ``` - Packages unavailable to check Rd xrefs: ‘InvariantCausalPrediction’, ‘CompareCausalNetworks’ - ``` - -# BallMapper - -
- -* Version: 0.2.0 -* GitHub: NA -* Source code: https://github.com/cran/BallMapper -* Date/Publication: 2019-08-20 21:20:17 UTC -* Number of recursive dependencies: 75 - -Run `revdepcheck::cloud_details(, "BallMapper")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘BallMapper-Ex.R’ failed - The error most likely occurred in: - - > ### Name: ColorIgraphPlot - > ### Title: Produce a static color visualization of the Ball Mapper graph. - > ### It is based on the output from BallMapper function. - > ### Aliases: ColorIgraphPlot - > - > ### ** Examples - > - ... - > var <- seq(from=0,to=6.3,by=0.1) - > points <- as.data.frame( cbind( sin(var),cos(var) ) ) - > values <- as.data.frame( sin(var) ) - > epsilon <- 0.25 - > l <- BallMapper(points,values,epsilon) - > ColorIgraphPlot(l) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: ColorIgraphPlot -> -> make_empty_graph - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘testthat’ - All declared Imports should be used. - ``` - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# bamm - -
- -* Version: 0.4.3 -* GitHub: https://github.com/luismurao/bamm -* Source code: https://github.com/cran/bamm -* Date/Publication: 2022-12-20 11:10:05 UTC -* Number of recursive dependencies: 110 - -Run `revdepcheck::cloud_details(, "bamm")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘bamm-Ex.R’ failed - The error most likely occurred in: - - > ### Name: bam_clusters - > ### Title: bam_clusters: Function to estimate the connectivity of suitable - > ### areas - > ### Aliases: bam_clusters - > - > ### ** Examples - > - ... - > set.seed(891) - > model_path <- system.file("extdata/Lepus_californicus_cont.tif", - + package = "bamm") - > model <- raster::raster(model_path) - > model <- model > 0.7 - > clusterin <- bamm::bam_clusters(model,ngbs=1,plot_model=TRUE) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: -> -> make_empty_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Backtrace: - ▆ - 1. ├─bamm::csd_estimate(model, dispersal_steps = c(1, 2)) at test-bam.R:230:2 - 2. │ └─... %>% ... - 3. ├─dplyr::summarise(., Clusters = max(clusterID), mean_area = mean(nclust)) - 4. ├─dplyr::group_by(., d) - 5. ├─dplyr::summarise(., nclust = dplyr::n()) - 6. ├─dplyr::group_by(., d, clusterID) - 7. └─dplyr:::group_by.data.frame(., d, clusterID) - 8. └─dplyr::group_by_prepare(.data, ..., .add = .add, error_call = current_env()) - 9. └─rlang::abort(bullets, call = error_call) - - [ FAIL 4 | WARN 0 | SKIP 0 | PASS 63 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘bam.Rmd’ using rmarkdown - - Quitting from lines 97-99 [unnamed-chunk-6] (bam.Rmd) - Error: processing vignette 'bam.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘bam.Rmd’ - - SUMMARY: processing the following file failed: - ‘bam.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# BASiNET - -
- -* Version: 0.0.5 -* GitHub: NA -* Source code: https://github.com/cran/BASiNET -* Date/Publication: 2022-08-19 08:50:25 UTC -* Number of recursive dependencies: 78 - -Run `revdepcheck::cloud_details(, "BASiNET")` for more info - -
- -## Newly broken - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘BASiNET.Rmd’ using rmarkdown - - Quitting from lines 69-73 [unnamed-chunk-1] (BASiNET.Rmd) - Error: processing vignette 'BASiNET.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘BASiNET.Rmd’ - - SUMMARY: processing the following file failed: - ‘BASiNET.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# BASiNETEntropy - -
- -* Version: 0.99.5 -* GitHub: NA -* Source code: https://github.com/cran/BASiNETEntropy -* Date/Publication: 2022-08-26 14:44:34 UTC -* Number of recursive dependencies: 48 - -Run `revdepcheck::cloud_details(, "BASiNETEntropy")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘BASiNETEntropy-Ex.R’ failed - The error most likely occurred in: - - > ### Name: classify - > ### Title: Performs the classification methodology using complex network - > ### and entropy theories - > ### Aliases: classify - > - > ### ** Examples - > - ... - 6 - 7 - 8 - 9 - 10 - [INFO] Filtering the graphs - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: classify ... graph_from_edgelist -> make_graph -> do.call -> - Execution halted - ``` - -# basket - -
- -* Version: 0.10.11 -* GitHub: https://github.com/kaneplusplus/basket -* Source code: https://github.com/cran/basket -* Date/Publication: 2021-10-16 23:30:22 UTC -* Number of recursive dependencies: 91 - -Run `revdepcheck::cloud_details(, "basket")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 4. └─igraph::graph_from_adjacency_matrix(...) - 5. └─igraph:::graph.adjacency.dense(...) - ── Error ('test-plot.r:7:5'): Plotting works. ────────────────────────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─basket::mem_mcmc(...) at test-plot.r:7:4 - 2. └─basket:::cluster_comp(ret, cluster_function) - 3. └─basket (local) cluster_function(map) - 4. └─igraph::graph_from_adjacency_matrix(...) - 5. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 3 | WARN 0 | SKIP 3 | PASS 15 ] - Error: Test failures - Execution halted - ``` - -# BayesMallows - -
- -* Version: 1.3.0 -* GitHub: https://github.com/ocbe-uio/BayesMallows -* Source code: https://github.com/cran/BayesMallows -* Date/Publication: 2023-03-10 16:20:17 UTC -* Number of recursive dependencies: 94 - -Run `revdepcheck::cloud_details(, "BayesMallows")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘BayesMallows-Ex.R’ failed - The error most likely occurred in: - - > ### Name: generate_constraints - > ### Title: Generate Constraint Set from Pairwise Comparisons - > ### Aliases: generate_constraints - > - > ### ** Examples - > - > # Here is an example with the beach preference data. - > # First, generate the transitive closure. - > beach_tc <- generate_transitive_closure(beach_preferences) - > - > # Next, generate an initial ranking. - > beach_init_rank <- generate_initial_ranking(beach_tc) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: generate_initial_ranking ... -> make_graph -> do.call -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Backtrace: - ▆ - 1. └─BayesMallows::generate_initial_ranking(beach_tc) at test-plot_top_k.R:6:0 - 2. ├─base::do.call(...) - 3. └─base::lapply(...) - 4. └─BayesMallows (local) FUN(X[[i]], ...) - 5. └─BayesMallows:::create_ranks(as.matrix(x), y, sr, r) - 6. └─igraph::graph_from_edgelist(as.matrix(mat)) - 7. └─igraph::make_graph(t(el), directed = directed) - 8. ├─base::do.call(old_graph, args) - 9. └─igraph (local) ``(``, directed = TRUE) - - [ FAIL 6 | WARN 0 | SKIP 0 | PASS 509 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 47.4Mb - sub-directories of 1Mb or more: - doc 1.7Mb - libs 44.9Mb - ``` - -# BayesMRA - -
- -* Version: 1.0.0 -* GitHub: https://github.com/jtipton25/BayesMRA -* Source code: https://github.com/cran/BayesMRA -* Date/Publication: 2020-08-18 09:52:11 UTC -* Number of recursive dependencies: 93 - -Run `revdepcheck::cloud_details(, "BayesMRA")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘BayesMRA-Ex.R’ failed - The error most likely occurred in: - - > ### Name: make_Q_alpha_2d - > ### Title: Generate CAR precision matrix - > ### Aliases: make_Q_alpha_2d - > - > ### ** Examples - > - > n_dims <- c(4, 8) - > phi <- c(0.8, 0.9) - > Q_alpha <- make_Q_alpha_2d(n_dims, phi) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: make_Q_alpha_2d ... as_adjacency_matrix -> ensure_igraph -> make_lattice - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 5. ├─igraph::as_adjacency_matrix(...) - 6. │ └─igraph:::ensure_igraph(graph) - 7. └─igraph::make_lattice(length = n_dims[[m]], dim = 2) - ── Error ('test-precision-matrices.R:84:5'): make_Q_alpha_tau2 ───────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─BayesMRA::make_Q_alpha_2d(n_dims, phi) at test-precision-matrices.R:84:4 - 2. ├─igraph::as_adjacency_matrix(...) - 3. │ └─igraph:::ensure_igraph(graph) - 4. └─igraph::make_lattice(length = n_dims[[m]], dim = 2) - - [ FAIL 3 | WARN 0 | SKIP 0 | PASS 121 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.2Mb - sub-directories of 1Mb or more: - doc 2.8Mb - libs 2.3Mb - ``` - -# BayesNetBP - -
- -* Version: 1.6.1 -* GitHub: https://github.com/hyu-ub/BayesNetBP -* Source code: https://github.com/cran/BayesNetBP -* Date/Publication: 2022-05-08 17:40:02 UTC -* Number of recursive dependencies: 128 - -Run `revdepcheck::cloud_details(, "BayesNetBP")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘BayesNetBP-Ex.R’ failed - The error most likely occurred in: - - > ### Name: AbsorbEvidence - > ### Title: Absorb evidence into the model - > ### Aliases: AbsorbEvidence - > - > ### ** Examples - > - > - > data(liver) - > tree.init.p <- Initializer(dag=liver$dag, data=liver$data, - + node.class=liver$node.class, - + propagate = TRUE) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: Initializer ... EliminationOrder -> igraph.from.graphNEL -> graph_from_adj_list - Execution halted - ``` - -# BayesSUR - -
- -* Version: 2.1-3 -* GitHub: NA -* Source code: https://github.com/cran/BayesSUR -* Date/Publication: 2023-01-28 17:00:02 UTC -* Number of recursive dependencies: 47 - -Run `revdepcheck::cloud_details(, "BayesSUR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘BayesSUR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plot.BayesSUR - > ### Title: create a selection of plots - > ### Aliases: plot.BayesSUR - > - > ### ** Examples - > - > data("exampleEQTL", package = "BayesSUR") - ... - > - > ## plot heatmaps of the estimated beta, gamma and Gy - > plot(fit, estimator = c("beta", "gamma", "Gy"), type = "heatmap") - > - > ## plot estimated graph of responses Gy - > plot(fit, estimator = "Gy", type = "graph") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot ... graph_from_adjacency_matrix -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 32.1Mb - sub-directories of 1Mb or more: - data 1.5Mb - libs 29.8Mb - ``` - -# bcgam - -
- -* Version: 1.0 -* GitHub: NA -* Source code: https://github.com/cran/bcgam -* Date/Publication: 2018-03-18 22:06:50 UTC -* Number of recursive dependencies: 39 - -Run `revdepcheck::cloud_details(, "bcgam")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Error ('testthat.R:3:1'): (code run outside of `test_that()`) ─────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─bcgam::bcgam(...) at testthat.R:3:0 - 2. └─bcgam:::bcgam.fit(...) - 3. └─nimble::nimbleModel(...) - 4. └─md$setupModel(...) - 5. └─nimble (local) genExpandedNodeAndParentNames3(debug = debug) - 6. └─igraph::graph.empty() - - [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ] - Error: Test failures - Execution halted - ``` - -# BCT - -
- -* Version: 1.2 -* GitHub: NA -* Source code: https://github.com/cran/BCT -* Date/Publication: 2022-05-12 14:00:05 UTC -* Number of recursive dependencies: 14 - -Run `revdepcheck::cloud_details(, "BCT")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘BCT-Ex.R’ failed - The error most likely occurred in: - - > ### Name: draw_models - > ### Title: Plot the results of the BCT and kBCT functions - > ### Aliases: draw_models - > - > ### ** Examples - > - > - > # Use the pewee dataset as an example: - > q <- BCT(pewee, 5) # maximum depth of 5 - > - > draw_models(q) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: draw_models -> show_tree -> - Execution halted - ``` - -# BDgraph - -
- -* Version: 2.72 -* GitHub: NA -* Source code: https://github.com/cran/BDgraph -* Date/Publication: 2022-12-25 07:20:14 UTC -* Number of recursive dependencies: 72 - -Run `revdepcheck::cloud_details(, "BDgraph")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘BDgraph-Ex.R’ failed - The error most likely occurred in: - - > ### Name: adj2link - > ### Title: Extract links from an adjacency matrix - > ### Aliases: adj2link - > ### Keywords: graphs - > - > ### ** Examples - > - > # Generating a 'random' graph - > adj <- graph.sim( p = 6, vis = TRUE ) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: graph.sim ... -> -> graph.adjacency.dense - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘BDgraph-Examples.Rmd’ using rmarkdown - - Quitting from lines 46-49 [unnamed-chunk-2] (BDgraph-Examples.Rmd) - Error: processing vignette 'BDgraph-Examples.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘BDgraph-Examples.Rmd’ - - --- re-building ‘Introduction-BDgraph.Rmd’ using rmarkdown - ... - Quitting from lines 200-201 [unnamed-chunk-13] (Introduction-BDgraph.Rmd) - Error: processing vignette 'Introduction-BDgraph.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘Introduction-BDgraph.Rmd’ - - SUMMARY: processing the following files failed: - ‘BDgraph-Examples.Rmd’ ‘Introduction-BDgraph.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 11.0Mb - sub-directories of 1Mb or more: - libs 9.5Mb - ``` - -# beam - -
- -* Version: 2.0.2 -* GitHub: https://github.com/gleday/beam -* Source code: https://github.com/cran/beam -* Date/Publication: 2020-05-28 23:20:18 UTC -* Number of recursive dependencies: 53 - -Run `revdepcheck::cloud_details(, "beam")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.r’ - Running the tests in ‘tests/testthat.r’ failed. - Last 13 lines of output: - ── Error ('test_beam.r:227:3'): NlowerthanP ──────────────────────────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. ├─testthat::expect_equal(class(bgraph(fit)), "igraph") at test_beam.r:227:2 - 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") - 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) - 4. ├─beam::bgraph(fit) - 5. └─beam::bgraph(fit) - 6. └─igraph::graph_from_data_frame(d = edges, directed = FALSE) - 7. └─igraph::make_empty_graph(n = 0, directed = directed) - - [ FAIL 2 | WARN 9 | SKIP 0 | PASS 51 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.5Mb - sub-directories of 1Mb or more: - libs 5.8Mb - ``` - -# bibliometrix - -
- -* Version: 4.1.2 -* GitHub: https://github.com/massimoaria/bibliometrix -* Source code: https://github.com/cran/bibliometrix -* Date/Publication: 2023-03-07 16:00:03 UTC -* Number of recursive dependencies: 150 - -Run `revdepcheck::cloud_details(, "bibliometrix")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘bibliometrix-Ex.R’ failed - The error most likely occurred in: - - > ### Name: biblioNetwork - > ### Title: Creating Bibliographic networks - > ### Aliases: biblioNetwork - > - > ### ** Examples - > - > # EXAMPLE 1: Authors collaboration network - ... - > data(scientometrics, package = "bibliometrixData") - > - > NetMatrix <- biblioNetwork(scientometrics, analysis = "co-citation", - + network = "references", sep = ";") - > - > net <- networkPlot(NetMatrix, n = 30, type = "kamada", Title = "Co-Citation",labelsize=0.5) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: networkPlot ... graph.adjacency.sparse -> make_graph -> do.call -> - Execution halted - ``` - -# bifurcatingr - -
- -* Version: 1.0.0 -* GitHub: NA -* Source code: https://github.com/cran/bifurcatingr -* Date/Publication: 2021-02-15 17:10:02 UTC -* Number of recursive dependencies: 37 - -Run `revdepcheck::cloud_details(, "bifurcatingr")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘bifurcatingr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: bfa.tree.plot - > ### Title: Plotting Bifurcating Autoregressive Trees - > ### Aliases: bfa.tree.plot - > - > ### ** Examples - > - > z <- bfa.tree.gen(31, 1, 1, 1, 0.5, 0.5, 0, 10, c(0.7)) - > bfa.tree.plot(z) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: bfa.tree.plot -> - Execution halted - ``` - -# bio3d - -
- -* Version: 2.4-4 -* GitHub: NA -* Source code: https://github.com/cran/bio3d -* Date/Publication: 2022-10-26 22:45:06 UTC -* Number of recursive dependencies: 77 - -Run `revdepcheck::cloud_details(, "bio3d")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘bio3d-Ex.R’ failed - The error most likely occurred in: - - > ### Name: print.cna - > ### Title: Summarize and Print Features of a cna Network Graph - > ### Aliases: print.cna summary.cna - > ### Keywords: utilities - > - > ### ** Examples - > - ... - + x<- summary(net) - + x$members[[2]] - + - + detach(hivp) - + - + } - Error in .igraph.status("Restore graph external pointer.\n") : - could not find function ".igraph.status" - Calls: print ... -> ensure_igraph -> is_igraph -> warn_version - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 11.0Mb - sub-directories of 1Mb or more: - libs 7.3Mb - ``` - -# Bioi - -
- -* Version: 0.2.10 -* GitHub: NA -* Source code: https://github.com/cran/Bioi -* Date/Publication: 2019-12-08 01:30:08 UTC -* Number of recursive dependencies: 72 - -Run `revdepcheck::cloud_details(, "Bioi")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Backtrace: - ▆ - 1. ├─testthat::expect_true(...) at test.euclidean_linker_cpp.R:7:4 - 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") - 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) - 4. └─Bioi::euclidean_linker(input, crit_dist) at test.euclidean_linker_cpp.R:11:6 - 5. └─Bioi::.perform_partitioning(...) - 6. ├─igraph::components(...) - 7. │ └─igraph:::ensure_igraph(graph) - 8. └─igraph::graph.data.frame(pOne_dict, directed = FALSE) - 9. └─igraph::make_empty_graph(n = 0, directed = directed) - - [ FAIL 2 | WARN 0 | SKIP 0 | PASS 20 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# bioregion - -
- -* Version: 1.0.0 -* GitHub: https://github.com/bioRgeo/bioregion -* Source code: https://github.com/cran/bioregion -* Date/Publication: 2023-04-14 19:30:02 UTC -* Number of recursive dependencies: 119 - -Run `revdepcheck::cloud_details(, "bioregion")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘bioregion-Ex.R’ failed - The error most likely occurred in: - - > ### Name: map_clusters - > ### Title: Create a map of bioregions - > ### Aliases: map_clusters - > - > ### ** Examples - > - > data(fishmat) - > data(fishsf) - > - > net <- similarity(fishmat, metric = "Simpson") - > clu <- netclu_greedy(net) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: netclu_greedy -> -> make_empty_graph - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.1Mb - sub-directories of 1Mb or more: - data 1.7Mb - doc 1.1Mb - help 1.1Mb - ``` - -# Bios2cor - -
- -* Version: 2.2.1 -* GitHub: NA -* Source code: https://github.com/cran/Bios2cor -* Date/Publication: 2022-07-08 09:25:23 UTC -* Number of recursive dependencies: 16 - -Run `revdepcheck::cloud_details(, "Bios2cor")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘Bios2cor-Ex.R’ failed - The error most likely occurred in: - - > ### Name: network.plot - > ### Title: Creates network structure of top elements - > ### Aliases: network.plot - > - > ### ** Examples - > - > #File path for output file - ... - > - > #Analyzing pairs with top scores and creating 'top_pairs' object - > top_pairs <- top_pairs_analysis(omes, top = 25, file) - > - > #Plotting the network structure of top pairs in pdf file - > network.plot(top_pairs, file) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: network.plot -> graph_from_data_frame -> make_empty_graph - Execution halted - ``` - -# bipartite - -
- -* Version: 2.18 -* GitHub: https://github.com/biometry/bipartite -* Source code: https://github.com/cran/bipartite -* Date/Publication: 2022-10-18 23:35:14 UTC -* Number of recursive dependencies: 48 - -Run `revdepcheck::cloud_details(, "bipartite")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘bipartite-Ex.R’ failed - The error most likely occurred in: - - > ### Name: betweenness_w - > ### Title: Betweenness centrality in a weighted network - > ### Aliases: betweenness_w - > - > ### ** Examples - > - > ## Load sample data - ... - + c(3,4,10), - + c(4,2,6), - + c(4,3,10)) - > - > ## Run the programme - > betweenness_w(sampledata) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: betweenness_w ... -> make_graph -> do.call -> - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘Intro2bipartite.Rnw’ using Sweave - Loading required package: vegan - Loading required package: permute - Loading required package: lattice - This is vegan 2.6-4 - Loading required package: sna - Loading required package: statnet.common - - Attaching package: ‘statnet.common’ - - The following objects are masked from ‘package:base’: - - attr, order - - Loading required package: network - - ‘network’ 1.18.1 (2023-01-24), part of the Statnet Project - ``` - -# bnma - -
- -* Version: 1.5.0 -* GitHub: NA -* Source code: https://github.com/cran/bnma -* Date/Publication: 2022-01-03 13:40:08 UTC -* Number of recursive dependencies: 56 - -Run `revdepcheck::cloud_details(, "bnma")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘bnma-Ex.R’ failed - The error most likely occurred in: - - > ### Name: draw.network.graph - > ### Title: Draws network graph using igraph package - > ### Aliases: draw.network.graph - > - > ### ** Examples - > - > #cardiovascular - > network <- with(thrombolytic, { - + network.data(Outcomes, Study, Treat, N=N, response = "binomial") - + }) - > draw.network.graph(network) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: draw.network.graph ... -> make_graph -> do.call -> - Execution halted - ``` - -# bnviewer - -
- -* Version: 0.1.6 -* GitHub: NA -* Source code: https://github.com/cran/bnviewer -* Date/Publication: 2020-09-14 06:00:03 UTC -* Number of recursive dependencies: 109 - -Run `revdepcheck::cloud_details(, "bnviewer")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘bnviewer-Ex.R’ failed - The error most likely occurred in: - - > ### Name: model.to.structure - > ### Title: Model to Bayesian Network Structure - > ### Aliases: model.to.structure - > - > ### ** Examples - > - > - ... - + bayesianNetwork.layout = "layout_on_grid", - + node.colors = list(background = "#f4bafd", - + border = "#2b7ce9", - + highlight = list(background = "#97c2fc", - + border = "#2b7ce9")) - + ) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: viewer -> -> -> make_empty_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘alarm.R’ - Running the tests in ‘tests/alarm.R’ failed. - Last 13 lines of output: - + bayesianNetwork.title="Discrete Bayesian Network - Coronary", - + bayesianNetwork.subtitle = "Coronary heart disease data set", - + bayesianNetwork.footer = "Fig. 1 - Layout on grid", - + edges.smooth = TRUE, - + edges.shadow = TRUE, - + edges.width = 1.5, - + node.colors = list(background = "#f4bafd", - + border = "#2b7ce9", - + highlight = "#97c2fc") - + - + ) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: viewer -> -> -> make_empty_graph - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘caret’ ‘e1071’ - All declared Imports should be used. - ``` - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# BoolNet - -
- -* Version: 2.1.8 -* GitHub: NA -* Source code: https://github.com/cran/BoolNet -* Date/Publication: 2023-02-27 13:52:30 UTC -* Number of recursive dependencies: 8 - -Run `revdepcheck::cloud_details(, "BoolNet")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘BoolNet-Ex.R’ failed - The error most likely occurred in: - - > ### Name: BoolNet-package - > ### Title: Construction, Simulation and Analysis of Boolean Networks - > ### Aliases: BoolNet-package BoolNet - > - > ### ** Examples - > - > ################################## - ... - > - > # identifies asynchronous attractors - > attractors <- getAttractors(cellcycle, - + type="asynchronous", startStates=100) - > - > plotAttractors(attractors, mode="graph") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plotAttractors ... lapply -> FUN -> graph.data.frame -> make_empty_graph - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘BoolNet_package_vignette.Snw’ using Sweave - Error: processing vignette 'BoolNet_package_vignette.Snw' failed with diagnostics: - Running 'texi2dvi' on 'BoolNet_package_vignette.tex' failed. - LaTeX errors: - ! LaTeX Error: File `a4wide.sty' not found. - - Type X to quit or to proceed, - or enter new name. (Default extension: sty) - ... - l.7 ^^M - - ! ==> Fatal error occurred, no output PDF file produced! - --- failed re-building ‘BoolNet_package_vignette.Snw’ - - SUMMARY: processing the following file failed: - ‘BoolNet_package_vignette.Snw’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# bootnet - -
- -* Version: 1.5.3 -* GitHub: NA -* Source code: https://github.com/cran/bootnet -* Date/Publication: 2023-06-05 12:30:02 UTC -* Number of recursive dependencies: 190 - -Run `revdepcheck::cloud_details(, "bootnet")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘bootnet-Ex.R’ failed - The error most likely occurred in: - - > ### Name: bootnet - > ### Title: Bootstrapped network estimation - > ### Aliases: bootnet - > - > ### ** Examples - > - > # BFI Extraversion data from psychTools package: - ... - Warning in EBICglassoCore(S = S, n = n, gamma = gamma, penalize.diagonal = penalize.diagonal, : - A dense regularized network was selected (lambda < 0.1 * lambda.max). Recent work indicates a possible drop in specificity. Interpret the presence of the smallest edges with care. Setting threshold = TRUE will enforce higher specificity, at the cost of sensitivity. - > - > # Centrality indices: - > library("qgraph") - > centralityPlot(Network) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: centralityPlot ... FUN -> centrality -> -> graph.adjacency.dense - Execution halted - ``` - -# BSBT - -
- -* Version: 1.2.1 -* GitHub: https://github.com/rowlandseymour/BSBT -* Source code: https://github.com/cran/BSBT -* Date/Publication: 2022-08-09 09:10:02 UTC -* Number of recursive dependencies: 86 - -Run `revdepcheck::cloud_details(, "BSBT")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘BSBT-Ex.R’ failed - The error most likely occurred in: - - > ### Name: constrained_adjacency_covariance_function - > ### Title: Construct a constrained covariance matrix from the adjacency - > ### matrix - > ### Aliases: constrained_adjacency_covariance_function - > - > ### ** Examples - > - > #Construct covariance matrix of Dar es Salaam, Tanzania, using network metric - > data(dar.adj.matrix, package = "BSBT") #load dar es salaam adjacency matrix - > k <- constrained_adjacency_covariance_function(dar.adj.matrix, type = "sqexp", - + hyperparameters = c(1, 1), rep(1, dim(dar.adj.matrix)[1]), 0) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: constrained_adjacency_covariance_function -> -> graph.adjacency.dense - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ▆ - 1. └─BSBT::constrained_adjacency_covariance_function(...) at test-mcmc_functions.R:32:2 - 2. └─igraph::graph.adjacency(adj.matrix, weighted = TRUE) - 3. └─igraph:::graph.adjacency.dense(...) - ── Error ('test-mcmc_functions.R:42:3'): asymmetric MCMC function works ──────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─BSBT::constrained_adjacency_covariance_function(...) at test-mcmc_functions.R:42:2 - 2. └─igraph::graph.adjacency(adj.matrix, weighted = TRUE) - 3. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 6 | WARN 0 | SKIP 0 | PASS 19 ] - Error: Test failures - Execution halted - ``` - -# btergm - -
- -* Version: 1.10.10 -* GitHub: https://github.com/leifeld/btergm -* Source code: https://github.com/cran/btergm -* Date/Publication: 2023-04-24 12:40:14 UTC -* Number of recursive dependencies: 100 - -Run `revdepcheck::cloud_details(, "btergm")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - - [ FAIL 1 | WARN 0 | SKIP 8 | PASS 51 ] - - ══ Skipped tests ═══════════════════════════════════════════════════════════════ - • On CRAN (8) - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Failure ('test-gof.R:24:3'): basic GOF functionality works ────────────────── - length(g) not equal to 7. - 1/1 mismatches - [1] 6 - 7 == -1 - - [ FAIL 1 | WARN 0 | SKIP 8 | PASS 51 ] - Error: Test failures - Execution halted - ``` - -# bwsTools - -
- -* Version: 1.2.0 -* GitHub: https://github.com/markhwhiteii/bwsTools -* Source code: https://github.com/cran/bwsTools -* Date/Publication: 2020-08-26 22:40:03 UTC -* Number of recursive dependencies: 75 - -Run `revdepcheck::cloud_details(, "bwsTools")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 6. └─igraph:::graph.adjacency.dense(...) - ── Error ('test_walkscoring.R:4:1'): (code run outside of `test_that()`) ─────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─bwsTools::walkscoring(...) at test_walkscoring.R:4:0 - 2. └─base::lapply(...) - 3. └─bwsTools (local) FUN(X[[i]], ...) - 4. └─bwsTools:::get_walkscores(...) - 5. └─igraph::graph_from_adjacency_matrix(M, mode = "directed", weighted = TRUE) - 6. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 4 | WARN 3 | SKIP 0 | PASS 96 ] - Error: Test failures - Execution halted - ``` - -# Canek - -
- -* Version: 0.2.2 -* GitHub: https://github.com/MartinLoza/Canek -* Source code: https://github.com/cran/Canek -* Date/Publication: 2023-05-31 04:50:02 UTC -* Number of recursive dependencies: 214 - -Run `revdepcheck::cloud_details(, "Canek")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘Canek-Ex.R’ failed - The error most likely occurred in: - - > ### Name: CorrectBatch - > ### Title: CorrectBatch - > ### Aliases: CorrectBatch - > - > ### ** Examples - > - > x <- SimBatches$batches[[1]] - > y <- SimBatches$batches[[2]] - > z <- CorrectBatch(x, y) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: CorrectBatch ... neighborsToSNNGraph -> make_graph -> do.call -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ▆ - 1. ├─Canek::RunCanek(x, "orig.ident") at test_RunCanek.R:12:0 - 2. └─Canek:::RunCanek.Seurat(x, "orig.ident") - 3. └─Canek::CorrectBatches(counts, debug = debug, ...) - 4. └─Canek::CorrectBatch(...) - 5. └─Canek:::ClusterLouvain(pcaQue[, 1:10], k = kNN, verbose = verbose) - 6. └─bluster::makeSNNGraph(x, k = k) - 7. └─bluster::neighborsToSNNGraph(nn.out$index, type = match.arg(type)) - 8. └─igraph::make_graph(edges, directed = FALSE) - 9. ├─base::do.call(old_graph, args) - 10. └─igraph (local) ``(``, directed = FALSE) - - [ FAIL 7 | WARN 0 | SKIP 0 | PASS 33 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘toy_example.Rmd’ using rmarkdown - - Quitting from lines 79-80 [unnamed-chunk-5] (toy_example.Rmd) - Error: processing vignette 'toy_example.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘toy_example.Rmd’ - - SUMMARY: processing the following file failed: - ‘toy_example.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# cape - -
- -* Version: 3.1.1 -* GitHub: NA -* Source code: https://github.com/cran/cape -* Date/Publication: 2022-05-19 13:40:02 UTC -* Number of recursive dependencies: 97 - -Run `revdepcheck::cloud_details(, "cape")` for more info - -
- -## Newly broken - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘cape.Rmd’ using rmarkdown - - Quitting from lines 481-483 [run_cape] (cape.Rmd) - Error: processing vignette 'cape.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘cape.Rmd’ - - SUMMARY: processing the following file failed: - ‘cape.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# CARlasso - -
- -* Version: 0.1.2 -* GitHub: https://github.com/YunyiShen/CAR-LASSO -* Source code: https://github.com/cran/CARlasso -* Date/Publication: 2021-08-11 19:00:02 UTC -* Number of recursive dependencies: 87 - -Run `revdepcheck::cloud_details(, "CARlasso")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘CARlasso-Ex.R’ failed - The error most likely occurred in: - - > ### Name: CARlasso - > ### Title: Gibbs sampler for Conditional Autoregressive LASSO and - > ### extensions - > ### Aliases: CARlasso - > - > ### ** Examples - > - ... - [----|----|----|----|----|----|----|----|----|----| - **************************************************| - - done - - > plot(car_res,tol = 0.05) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot ... plot.carlasso_out -> graph.data.frame -> make_empty_graph - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 22.9Mb - sub-directories of 1Mb or more: - libs 22.6Mb - ``` - -# cartograflow - -
- -* Version: 1.0.3 -* GitHub: https://github.com/fbahoken/cartogRaflow -* Source code: https://github.com/cran/cartograflow -* Date/Publication: 2020-07-19 19:50:02 UTC -* Number of recursive dependencies: 105 - -Run `revdepcheck::cloud_details(, "cartograflow")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘cartograflow-Ex.R’ failed - The error most likely occurred in: - - > ### Name: flowcontig - > ### Title: Builds an ordinal distance matrices from a spatial features - > ### background - > ### Aliases: flowcontig - > - > ### ** Examples - > - ... - Simple feature collection with 12 features and 14 fields - Geometry type: POLYGON - Dimension: XY - Bounding box: xmin: 637297.4 ymin: 6838629 xmax: 671752.1 ymax: 6879246 - Projected CRS: Lambert_Conformal_Conic - > graph_ckij_1 <- flowcontig(bkg = map, code = "EPT_NUM", k = 1, algo = "automatic") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: flowcontig -> -> make_empty_graph - Execution halted - ``` - -# cassowaryr - -
- -* Version: 2.0.0 -* GitHub: https://github.com/numbats/cassowaryr -* Source code: https://github.com/cran/cassowaryr -* Date/Publication: 2022-08-09 12:30:02 UTC -* Number of recursive dependencies: 106 - -Run `revdepcheck::cloud_details(, "cassowaryr")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘cassowaryr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: calc_scags - > ### Title: Compute selected scagnostics on subsets - > ### Aliases: calc_scags - > - > ### ** Examples - > - > # Calculate selected scagnostics on a single pair - > calc_scags(anscombe$x1, anscombe$y1, scags=c("monotonic", "outlying")) - The legacy packages maptools, rgdal, and rgeos, underpinning this package - will retire shortly. Please refer to R-spatial evolution reports on - https://r-spatial.org/r/2023/05/15/evolution4.html for details. - This package is now running under evolution status 0 - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: calc_scags ... -> make_graph -> do.call -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 1. ├─testthat::expect_equal(sc_striated2(x1, y1), 1) at test_mst.R:98:2 - 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") - 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) - 4. ├─cassowaryr::sc_striated2(x1, y1) - 5. └─cassowaryr:::sc_striated2.default(x1, y1) - 6. └─cassowaryr:::sc_striated2.scree(sc) - 7. └─cassowaryr:::gen_mst(x$del, x$weights) - 8. └─igraph::graph_from_edgelist(edges, directed = FALSE) - 9. └─igraph::make_graph(t(el), directed = directed) - 10. ├─base::do.call(old_graph, args) - 11. └─igraph (local) ``(``, directed = FALSE) - - [ FAIL 7 | WARN 0 | SKIP 0 | PASS 3 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘cassowaryr.Rmd’ using rmarkdown - - Quitting from lines 67-69 [unnamed-chunk-2] (cassowaryr.Rmd) - Error: processing vignette 'cassowaryr.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘cassowaryr.Rmd’ - - SUMMARY: processing the following file failed: - ‘cassowaryr.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# causact - -
- -* Version: 0.4.2 -* GitHub: https://github.com/flyaflya/causact -* Source code: https://github.com/cran/causact -* Date/Publication: 2022-06-14 16:00:02 UTC -* Number of recursive dependencies: 118 - -Run `revdepcheck::cloud_details(, "causact")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘causact-Ex.R’ failed - The error most likely occurred in: - - > ### Name: dag_diagrammer - > ### Title: Convert graph to Diagrammer object for visualization - > ### Aliases: dag_diagrammer - > - > ### ** Examples - > - > library("DiagrammeR") - ... - > dag_create() %>% - + dag_node("Get Card","y", - + rhs = bernoulli(theta), - + data = carModelDF$getCard) %>% - + dag_diagrammer() %>% - + render_graph(title = "DiagrammeR Version of causact_graph") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: %>% ... -> ensure_igraph -> -> make_empty_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 2. ├─causact::dag_render(.) - 3. │ └─... %>% generate_dot2() - 4. ├─causact::generate_dot2(.) - 5. ├─causact::dag_diagrammer(., shortLabel = sLabel, wrapWidth = ww) - 6. │ └─graph %>% dag_dim() - 7. ├─causact:::dag_dim(.) - 8. │ ├─... %>% as.integer() - 9. │ └─igraph::graph_from_data_frame(...) - 10. │ └─igraph::make_empty_graph(n = 0, directed = directed) - 11. └─igraph::topo_sort(., mode = "in") - 12. └─igraph:::ensure_igraph(graph) - - [ FAIL 4 | WARN 17 | SKIP 0 | PASS 21 ] - Error: Test failures - Execution halted - ``` - -# causalDisco - -
- -* Version: 0.9.1 -* GitHub: https://github.com/annennenne/causalDisco -* Source code: https://github.com/cran/causalDisco -* Date/Publication: 2022-05-12 07:50:06 UTC -* Number of recursive dependencies: 41 - -Run `revdepcheck::cloud_details(, "causalDisco")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘causalDisco-Ex.R’ failed - The error most likely occurred in: - - > ### Name: probmat2amat - > ### Title: Convert a matrix of probabilities into an adjacency matrix - > ### Aliases: probmat2amat - > - > ### ** Examples - > - > #Make random probability matrix that can be - ... - > #converted into adjancency matrix - > pmat <- matrix(runif(25, 0, 1), 5, 5) - > diag(pmat) <- 0 - > - > #Convert to adjacency matrix using cutoff-method (threshold = 0.5) - > probmat2amat(pmat, threshold = 0.5) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: probmat2amat ... ensure_igraph -> graph.adjacency -> graph.adjacency.dense - Execution halted - ``` - -# ccTensor - -
- -* Version: 1.0.2 -* GitHub: https://github.com/rikenbit/ccTensor -* Source code: https://github.com/cran/ccTensor -* Date/Publication: 2021-08-12 04:30:07 UTC -* Number of recursive dependencies: 60 - -Run `revdepcheck::cloud_details(, "ccTensor")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ccTensor-Ex.R’ failed - The error most likely occurred in: - - > ### Name: CUR - > ### Title: CUR Matrix Decomposition - > ### Aliases: CUR - > ### Keywords: methods - > - > ### ** Examples - > - ... - > library("ccTensor") - > library("nnTensor") - > # Test data - > matdata <- toyModel(model = "NMF") - > # Simple usage - > out <- CUR(matdata, c.rank=3, r.rank=4) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: CUR ... graph_from_incidence_matrix -> graph.incidence.dense -> make_empty_graph - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘fields’ - All declared Imports should be used. - ``` - -# CePa - -
- -* Version: 0.8.0 -* GitHub: https://github.com/jokergoo/CePa -* Source code: https://github.com/cran/CePa -* Date/Publication: 2022-06-11 21:30:06 UTC -* Number of recursive dependencies: 10 - -Run `revdepcheck::cloud_details(, "CePa")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘CePa-Ex.R’ failed - The error most likely occurred in: - - > ### Name: generate.pathway - > ### Title: Generate igraph object from edge list - > ### Aliases: generate.pathway - > - > ### ** Examples - > - > edgelist = rbind(c("a", "b"), c("a", "b"), c("a", "c")) - > g = generate.pathway(edgelist) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: generate.pathway ... graph.edgelist -> make_graph -> do.call -> - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘CePa.Rnw’ using Sweave - Error: processing vignette 'CePa.Rnw' failed with diagnostics: - Running 'texi2dvi' on 'CePa.tex' failed. - LaTeX errors: - ! LaTeX Error: File `ae.sty' not found. - - Type X to quit or to proceed, - or enter new name. (Default extension: sty) - - ... - l.30 \ifthenelse - {\boolean{Sweave@inconsolata}}{%^^M - ! ==> Fatal error occurred, no output PDF file produced! - --- failed re-building ‘parsing-PID-pathway-data.Rnw’ - - SUMMARY: processing the following files failed: - ‘CePa.Rnw’ ‘analysis-p53.Rnw’ ‘parsing-PID-pathway-data.Rnw’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# CeRNASeek - -
- -* Version: 2.1.3 -* GitHub: NA -* Source code: https://github.com/cran/CeRNASeek -* Date/Publication: 2020-04-29 08:00:02 UTC -* Number of recursive dependencies: 9 - -Run `revdepcheck::cloud_details(, "CeRNASeek")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘CeRNASeek-Ex.R’ failed - The error most likely occurred in: - - > ### Name: ceRNA.Net - > ### Title: visualize and analyze the identified ceRNA-ceRNA network using - > ### ceRNA.Net function - > ### Aliases: ceRNA.Net - > ### Keywords: ceRNA.Net - > - > ### ** Examples - ... - > ##file identified by the ceRNA.cmi function. - > ##Here we apply the ceRNA list in the example file for CMI identification to - > ##display the network and analyze the network topology properties. - > ceRNA.Net(as.matrix(dataset[["Pre.ceRNA"]]),net_direct=TRUE,vertex_size=20,v.label = TRUE, - + node_shape="circle",n_color = "orange",E_weight=TRUE,ity=1,label_cex=2, - + label_color="black",edge_color="gray",n_frame.color = "gray") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: ceRNA.Net ... graph.edgelist -> make_graph -> do.call -> - Execution halted - ``` - -# cfid - -
- -* Version: 0.1.4 -* GitHub: https://github.com/santikka/cfid -* Source code: https://github.com/cran/cfid -* Date/Publication: 2022-10-26 15:35:07 UTC -* Number of recursive dependencies: 51 - -Run `revdepcheck::cloud_details(, "cfid")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 1. └─igraph::graph.formula(X - +Y) at test-graphs.R:175:2 - 2. └─igraph:::graph_from_literal_i(mf) - 3. └─igraph::make_graph(unname(ids[edges]), n = length(v), directed = directed) - 4. ├─base::do.call(old_graph, args) - 5. └─igraph (local) ``(``, n = 2L, directed = TRUE) - ── Error ('test-graphs.R:212:3'): causaleffect sanity ────────────────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─cfid::export_graph(g, "causaleffect") at test-graphs.R:212:2 - 2. └─igraph::make_empty_graph(n = sum(!lat)) - - [ FAIL 4 | WARN 0 | SKIP 0 | PASS 183 ] - Error: Test failures - Execution halted - ``` - -# chemodiv - -
- -* Version: 0.2.0 -* GitHub: https://github.com/hpetren/chemodiv -* Source code: https://github.com/cran/chemodiv -* Date/Publication: 2023-01-12 09:30:06 UTC -* Number of recursive dependencies: 168 - -Run `revdepcheck::cloud_details(, "chemodiv")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘chemodiv-Ex.R’ failed - The error most likely occurred in: - - > ### Name: molNet - > ### Title: Generate a molecular network with some properties - > ### Aliases: molNet - > - > ### ** Examples - > - > data(minimalCompDis) - > data(minimalNPCTable) - > molNet(minimalCompDis, minimalNPCTable, cutOff = 0) - Using cut-off value = 0 - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: molNet ... graph_from_edgelist -> make_graph -> do.call -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Backtrace: - ▆ - 1. └─chemodiv::molNet(testCompDis) at test-molNetPlot.R:15:0 - 2. └─tidygraph::tbl_graph(nodes = nodes, edges = links) - 3. ├─tidygraph::as_tbl_graph(...) - 4. └─tidygraph:::as_tbl_graph.list(...) - 5. └─tidygraph:::as_graph_node_edge(x, directed = directed, node_key = node_key) - 6. └─igraph::graph_from_edgelist(as.matrix(edges[, 1:2]), directed = directed) - 7. └─igraph::make_graph(t(el), directed = directed) - 8. ├─base::do.call(old_graph, args) - 9. └─igraph (local) ``(``, directed = TRUE) - - [ FAIL 2 | WARN 0 | SKIP 3 | PASS 75 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘chemodiv-vignette.Rmd’ using rmarkdown - - Quitting from lines 313-318 [unnamed-chunk-16] (chemodiv-vignette.Rmd) - Error: processing vignette 'chemodiv-vignette.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘chemodiv-vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘chemodiv-vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# cholera - -
- -* Version: 0.8.0 -* GitHub: https://github.com/lindbrook/cholera -* Source code: https://github.com/cran/cholera -* Date/Publication: 2023-03-01 12:40:02 UTC -* Number of recursive dependencies: 97 - -Run `revdepcheck::cloud_details(, "cholera")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘cholera-Ex.R’ failed - The error most likely occurred in: - - > ### Name: addWalkingPath - > ### Title: Add the shortest walking path between a selected cases or pumps. - > ### Aliases: addWalkingPath - > - > ### ** Examples - > - > streetNameLocator("broad street", zoom = TRUE, highlight = FALSE, - + add.subtitle = FALSE) - > addWalkingPath(447) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: addWalkingPath ... do.call -> nodeData -> -> make_empty_graph - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘duplicate.missing.cases.Rmd’ using rmarkdown - --- finished re-building ‘duplicate.missing.cases.Rmd’ - - --- re-building ‘kernel.density.Rmd’ using rmarkdown - - Quitting from lines 40-42 [unnamed-chunk-5] (kernel.density.Rmd) - Error: processing vignette 'kernel.density.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘kernel.density.Rmd’ - ... - --- finished re-building ‘time.series.Rmd’ - - --- re-building ‘unstacking.bars.Rmd’ using rmarkdown - --- finished re-building ‘unstacking.bars.Rmd’ - - SUMMARY: processing the following file failed: - ‘kernel.density.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.5Mb - sub-directories of 1Mb or more: - data 1.0Mb - doc 1.5Mb - help 2.2Mb - ``` - -# CKMRpop - -
- -* Version: 0.1.3 -* GitHub: NA -* Source code: https://github.com/cran/CKMRpop -* Date/Publication: 2021-07-17 10:00:06 UTC -* Number of recursive dependencies: 120 - -Run `revdepcheck::cloud_details(, "CKMRpop")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘CKMRpop-Ex.R’ failed - The error most likely occurred in: - - > ### Name: compile_related_pairs - > ### Title: compile pairwise relationships from the samples - > ### Aliases: compile_related_pairs - > - > ### ** Examples - > - > C <- compile_related_pairs(three_pops_with_mig_slurped_results$samples) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: compile_related_pairs ... -> ensure_igraph -> -> make_empty_graph - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘about_spip.Rmd’ using rmarkdown - --- finished re-building ‘about_spip.Rmd’ - - --- re-building ‘simple-example-with-migration.Rmd’ using rmarkdown - - Quitting from lines 241-262 [unnamed-chunk-14] (simple-example-with-migration.Rmd) - Error: processing vignette 'simple-example-with-migration.Rmd' failed with diagnostics: - could not find function ".igraph.status" - ... - Quitting from lines 306-307 [unnamed-chunk-20] (species_1_simulation.Rmd) - Error: processing vignette 'species_1_simulation.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘species_1_simulation.Rmd’ - - SUMMARY: processing the following files failed: - ‘simple-example-with-migration.Rmd’ ‘species_1_simulation.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 8.3Mb - sub-directories of 1Mb or more: - data 1.1Mb - doc 3.6Mb - help 1.0Mb - libs 2.4Mb - ``` - -# CliquePercolation - -
- -* Version: 0.4.0 -* GitHub: NA -* Source code: https://github.com/cran/CliquePercolation -* Date/Publication: 2022-11-09 08:40:37 UTC -* Number of recursive dependencies: 115 - -Run `revdepcheck::cloud_details(, "CliquePercolation")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘CliquePercolation-Ex.R’ failed - The error most likely occurred in: - - > ### Name: FuzzyMod - > ### Title: Fuzzy Modularity of a community structure of a graph - > ### Aliases: FuzzyMod - > - > ### ** Examples - > - > g <- igraph::disjoint_union(igraph::make_full_graph(5),igraph::make_full_graph(4)) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: -> unlist -> lapply -> - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘CliquePercolation.Rmd’ using rmarkdown - - Quitting from lines 110-112 [unnamed-chunk-5] (CliquePercolation.Rmd) - Error: processing vignette 'CliquePercolation.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘CliquePercolation.Rmd’ - - SUMMARY: processing the following file failed: - ‘CliquePercolation.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# ClustAssess - -
- -* Version: 0.3.0 -* GitHub: https://github.com/Core-Bioinformatics/ClustAssess -* Source code: https://github.com/cran/ClustAssess -* Date/Publication: 2022-01-26 16:52:46 UTC -* Number of recursive dependencies: 160 - -Run `revdepcheck::cloud_details(, "ClustAssess")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ClustAssess-Ex.R’ failed - The error most likely occurred in: - - > ### Name: element_sim - > ### Title: The Element-Centric Clustering Similarity - > ### Aliases: element_sim - > - > ### ** Examples - > - > km.res = kmeans(mtcars, 3)$cluster - > hc.res = hclust(dist(mtcars)) - > element_sim(km.res, hc.res) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: element_sim ... make_cielg_hierarchical -> -> graph.adjacency.dense - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘ClustAssess.Rmd’ using rmarkdown - --- finished re-building ‘ClustAssess.Rmd’ - - --- re-building ‘comparing-soft-and-hierarchical.Rmd’ using rmarkdown - - Quitting from lines 76-100 [ecs] (comparing-soft-and-hierarchical.Rmd) - Error: processing vignette 'comparing-soft-and-hierarchical.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘comparing-soft-and-hierarchical.Rmd’ - - SUMMARY: processing the following file failed: - ‘comparing-soft-and-hierarchical.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# ClusTorus - -
- -* Version: 0.2.2 -* GitHub: https://github.com/sungkyujung/ClusTorus -* Source code: https://github.com/cran/ClusTorus -* Date/Publication: 2022-01-04 10:10:05 UTC -* Number of recursive dependencies: 131 - -Run `revdepcheck::cloud_details(, "ClusTorus")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ClusTorus-Ex.R’ failed - The error most likely occurred in: - - > ### Name: cluster.assign.torus - > ### Title: Clustering by connected components of ellipsoids - > ### Aliases: cluster.assign.torus plot.cluster.obj - > - > ### ** Examples - > - > data <- toydata1[, 1:2] - ... - + kmeansfitmethod = "general", - + J = 4, concentration = 25) - ellip.kmeans.torus: fitting appr. mixture, J = 4, option = general.Done - > level <- 0.1 - > - > cluster.assign.torus(icp.torus, level = level) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: cluster.assign.torus ... conn.comp.ellipse -> -> graph.adjacency.dense - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘ClusTorus.Rmd’ using rmarkdown - - Quitting from lines 59-62 [unnamed-chunk-4] (ClusTorus.Rmd) - Error: processing vignette 'ClusTorus.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘ClusTorus.Rmd’ - - SUMMARY: processing the following file failed: - ‘ClusTorus.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# clustree - -
- -* Version: 0.5.0 -* GitHub: https://github.com/lazappi/clustree -* Source code: https://github.com/cran/clustree -* Date/Publication: 2022-06-25 20:50:02 UTC -* Number of recursive dependencies: 185 - -Run `revdepcheck::cloud_details(, "clustree")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘clustree-Ex.R’ failed - The error most likely occurred in: - - > ### Name: clustree - > ### Title: Plot a clustering tree - > ### Aliases: clustree clustree.matrix clustree.data.frame - > ### clustree.SingleCellExperiment clustree.seurat clustree.Seurat - > - > ### ** Examples - > - > data(nba_clusts) - > clustree(nba_clusts, prefix = "K") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: clustree ... graph_from_edgelist -> make_graph -> do.call -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘spelling.R’ - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 6. ├─clustree::clustree(...) - 7. └─clustree:::clustree.matrix(...) - 8. └─clustree:::build_tree_graph(...) - 9. └─tidygraph::tbl_graph(nodes = nodes, edges = edges) - 10. ├─tidygraph::as_tbl_graph(...) - 11. └─tidygraph:::as_tbl_graph.list(...) - 12. └─tidygraph:::as_graph_node_edge(x, directed = directed, node_key = node_key) - 13. └─igraph::graph_from_edgelist(as.matrix(edges[, 1:2]), directed = directed) - 14. └─igraph::make_graph(t(el), directed = directed) - 15. ├─base::do.call(old_graph, args) - 16. └─igraph (local) ``(``, directed = TRUE) - - [ FAIL 59 | WARN 4 | SKIP 0 | PASS 13 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘clustree.Rmd’ using rmarkdown - - Quitting from lines 81-82 [nba-plot] (clustree.Rmd) - Error: processing vignette 'clustree.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘clustree.Rmd’ - - SUMMARY: processing the following file failed: - ‘clustree.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# clustringr - -
- -* Version: 1.0 -* GitHub: NA -* Source code: https://github.com/cran/clustringr -* Date/Publication: 2019-03-30 16:10:03 UTC -* Number of recursive dependencies: 54 - -Run `revdepcheck::cloud_details(, "clustringr")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘clustringr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: cluster_plot - > ### Title: Plot string clusters as graph. - > ### Aliases: cluster_plot - > - > ### ** Examples - > - > s_vec <- c("alcool","alcohol","alcoholic","brandy","brandie","cachaça") - > s_clust <- cluster_strings(s_vec,method="lv",max_dist=3,algo="cc") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: cluster_strings ... graph_from_adjacency_matrix -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘stringi’ - All declared Imports should be used. - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 5626 marked UTF-8 strings - ``` - -# CoDiNA - -
- -* Version: 1.1.2 -* GitHub: NA -* Source code: https://github.com/cran/CoDiNA -* Date/Publication: 2020-07-15 12:30:02 UTC -* Number of recursive dependencies: 50 - -Run `revdepcheck::cloud_details(, "CoDiNA")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘CoDiNA-Ex.R’ failed - The error most likely occurred in: - - > ### Name: as.igraph - > ### Title: as.igraph - > ### Aliases: as.igraph - > - > ### ** Examples - > - > suppressWarnings(RNGversion("3.5.0")) - ... - Coding the groups. - Recode is done! - > Graph = plot(x = DiffNet, - + layout = NULL, smooth.edges = TRUE, - + path = NULL, MakeGroups = FALSE, Cluster = FALSE, - + legend = TRUE, manipulation = FALSE, sort.by.Phi = FALSE) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot -> plot.CoDiNA -> -> make_empty_graph - Execution halted - ``` - -# comato - -
- -* Version: 1.1 -* GitHub: NA -* Source code: https://github.com/cran/comato -* Date/Publication: 2018-03-02 16:36:47 UTC -* Number of recursive dependencies: 22 - -Run `revdepcheck::cloud_details(, "comato")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘comato-Ex.R’ failed - The error most likely occurred in: - - > ### Name: as.matrix.conceptmaps - > ### Title: Convert a conceptmaps object to a matrix - > ### Aliases: as.matrix.conceptmaps - > - > ### ** Examples - > - > data = rbind( - ... - Error in .igraph.status("Free graph external pointer.\n") : - could not find function ".igraph.status" - Error in .igraph.status("Free graph external pointer.\n") : - could not find function ".igraph.status" - Error in .igraph.status("Free graph external pointer.\n") : - could not find function ".igraph.status" - Error in .igraph.status("Free graph external pointer.\n") : - could not find function ".igraph.status" - Error in .igraph.status("Free graph external pointer.\n") : - could not find function ".igraph.status" - ``` - -# concatipede - -
- -* Version: 1.0.1 -* GitHub: https://github.com/tardipede/concatipede -* Source code: https://github.com/cran/concatipede -* Date/Publication: 2021-08-06 18:10:05 UTC -* Number of recursive dependencies: 128 - -Run `revdepcheck::cloud_details(, "concatipede")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘concatipede-Ex.R’ failed - The error most likely occurred in: - - > ### Name: auto_match_seqs - > ### Title: Build a template table with automatically matched sequence names - > ### Aliases: auto_match_seqs - > - > ### ** Examples - > - > xlsx_file <- concatipede_example("sequences-test-matching.xlsx") - > xlsx_template <- readxl::read_xlsx(xlsx_file) - > auto_match_seqs(xlsx_template) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: auto_match_seqs -> -> make_empty_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 7. └─igraph::make_empty_graph(n = 0, directed = directed) - ── Error ('test-integration.R:61:5'): Functions work well together (medium pipeline 2) ── - Error in `eval(code, test_env)`: !file.exists("my-template.xlsx") is not TRUE - Backtrace: - ▆ - 1. └─base::stopifnot(!file.exists("my-template.xlsx")) at test-integration.R:61:4 - ── Error ('test-integration.R:80:5'): Functions work well together (long pipeline) ── - Error in `eval(code, test_env)`: !file.exists("my-template.xlsx") is not TRUE - Backtrace: - ▆ - 1. └─base::stopifnot(!file.exists("my-template.xlsx")) at test-integration.R:80:4 - - [ FAIL 5 | WARN 0 | SKIP 0 | PASS 31 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘Package-usage.Rmd’ using rmarkdown - Warning in in_dir(input_dir(), expr) : - You changed the working directory to /tmp/workdir/concatipede/new/concatipede.Rcheck/vign_test/concatipede/vignettes/concatipede_test (probably via setwd()). It will be restored to /tmp/workdir/concatipede/new/concatipede.Rcheck/vign_test/concatipede/vignettes. See the Note section in ?knitr::knit - - Quitting from lines 173-181 [unnamed-chunk-15] (Package-usage.Rmd) - Error: processing vignette 'Package-usage.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘Package-usage.Rmd’ - - SUMMARY: processing the following file failed: - ‘Package-usage.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# concorR - -
- -* Version: 0.2.1 -* GitHub: https://github.com/ATraxLab/concorR -* Source code: https://github.com/cran/concorR -* Date/Publication: 2020-11-25 20:30:07 UTC -* Number of recursive dependencies: 19 - -Run `revdepcheck::cloud_details(, "concorR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘concorR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: concor_igraph_apply - > ### Title: Find CONCOR partition and add to a list of 'igraph' objects - > ### Aliases: concor_igraph_apply - > - > ### ** Examples - > - > a <- matrix(c(0, 0, 0, 1, 1, 0, 1, 0, 1, 1, 0, 1, 1, 0, 1, 0), ncol = 4) - > rownames(a) <- c("a", "b", "c", "d") - > colnames(a) <- c("a", "b", "c", "d") - > a.igraph <- igraph::graph_from_adjacency_matrix(a) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: -> graph.adjacency.dense - Execution halted - ``` - -# CoNI - -
- -* Version: 0.1.0 -* GitHub: NA -* Source code: https://github.com/cran/CoNI -* Date/Publication: 2021-09-30 09:10:02 UTC -* Number of recursive dependencies: 128 - -Run `revdepcheck::cloud_details(, "CoNI")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘CoNI-Ex.R’ failed - The error most likely occurred in: - - > ### Name: NetStats - > ### Title: Network Statistics - > ### Aliases: NetStats - > - > ### ** Examples - > - > #Load color nodes table - ... - > HFDNetwork<-generate_network(ResultsCoNI = CoNIResultsHFDToy, - + colorVertexNetwork = TRUE, - + colorVertexTable = MetColorTable, - + outputDir = "./", - + outputFileName = "HFD", - + saveFiles = FALSE) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: generate_network -> -> make_empty_graph - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘Full_RunCoNI.Rmd’ using rmarkdown - - Quitting from lines 133-138 [network_chow] (Full_RunCoNI.Rmd) - Error: processing vignette 'Full_RunCoNI.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘Full_RunCoNI.Rmd’ - - SUMMARY: processing the following file failed: - ‘Full_RunCoNI.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# corTest - -
- -* Version: 1.0.7 -* GitHub: NA -* Source code: https://github.com/cran/corTest -* Date/Publication: 2020-09-25 15:30:02 UTC -* Number of recursive dependencies: 33 - -Run `revdepcheck::cloud_details(, "corTest")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘corTest-Ex.R’ failed - The error most likely occurred in: - - > ### Name: construct_network - > ### Title: Construct Differential Correlation Network - > ### Aliases: construct_network - > ### Keywords: correlation test - > - > ### ** Examples - > - ... - + cor_method = "st5", - + pseudo_adjust_cutoff = FALSE, - + var.grp = "grp", - + pAdjMethod = 'fdr', - + cutoff = 0.05, - + nPseudo = 25) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: construct_network -> -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘graphics’ - All declared Imports should be used. - ``` - -# countland - -
- -* Version: 0.1.1 -* GitHub: NA -* Source code: https://github.com/cran/countland -* Date/Publication: 2022-08-17 06:40:06 UTC -* Number of recursive dependencies: 194 - -Run `revdepcheck::cloud_details(, "countland")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘countland-Ex.R’ failed - The error most likely occurred in: - - > ### Name: Cluster - > ### Title: Perform spectral clustering on dot products. - > ### Aliases: Cluster - > - > ### ** Examples - > - > gold_path <- system.file("testdata", package = "countland", mustWork = TRUE) - ... - the fraction of entries that are nonzero is 0.4074 - > C <- Dot(C) - Calculating dot products between rows... - done. - > C <- Embed(C,n_components=5) - Performing spectral embedding on dot products... - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: Embed ... -> graph.adjacency.sparse -> make_empty_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ── Error ('test-countland_shared_counts.R:13:3'): function PlotSharedCounts, returns plot object ── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─countland::SharedCounts(C, n_clusters = 2, n_cells = 10, subsample = F) at test-countland_shared_counts.R:13:2 - 2. └─countland:::ScikitManifoldSpectralEmbedding(C@sharedcounts, n_clusters) - 3. ├─igraph::as.undirected(igraph::graph.adjacency(A, weighted = T)) - 4. │ └─igraph:::ensure_igraph(graph) - 5. └─igraph::graph.adjacency(A, weighted = T) - 6. └─igraph:::graph.adjacency.sparse(...) - 7. └─igraph::make_empty_graph(n = vc, directed = (mode == "directed")) - - [ FAIL 4 | WARN 0 | SKIP 0 | PASS 59 ] - Error: Test failures - Execution halted - ``` - -# cppRouting - -
- -* Version: 3.1 -* GitHub: https://github.com/vlarmet/cppRouting -* Source code: https://github.com/cran/cppRouting -* Date/Publication: 2022-12-01 13:20:02 UTC -* Number of recursive dependencies: 40 - -Run `revdepcheck::cloud_details(, "cppRouting")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘cppRouting-Ex.R’ failed - The error most likely occurred in: - - > ### Name: cpp_simplify - > ### Title: Reduce the number of edges by removing non-intersection nodes, - > ### duplicated edges and isolated loops in the graph. - > ### Aliases: cpp_simplify - > - > ### ** Examples - > - ... - > - > #Plot - > if(requireNamespace("igraph",quietly = TRUE)){ - + igr<-igraph::graph_from_data_frame(edges) - + plot(igr) - + } - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: -> make_empty_graph - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 16.4Mb - sub-directories of 1Mb or more: - libs 16.2Mb - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘RcppProgress’ - All declared Imports should be used. - ``` - -* checking for GNU extensions in Makefiles ... NOTE - ``` - GNU make is a SystemRequirements. - ``` - -# crandep - -
- -* Version: 0.3.1 -* GitHub: https://github.com/clement-lee/crandep -* Source code: https://github.com/cran/crandep -* Date/Publication: 2022-06-03 08:30:10 UTC -* Number of recursive dependencies: 70 - -Run `revdepcheck::cloud_details(, "crandep")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘crandep-Ex.R’ failed - The error most likely occurred in: - - > ### Name: df_to_graph - > ### Title: Construct the giant component of the network from two data - > ### frames - > ### Aliases: df_to_graph - > - > ### ** Examples - > - > from <- c("1", "2", "4") - > to <- c("2", "3", "5") - > edges <- data.frame(from = from, to = to, stringsAsFactors = FALSE) - > nodes <- data.frame(name = c("1", "2", "3", "4", "5"), stringsAsFactors = FALSE) - > df_to_graph(edges, nodes) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: df_to_graph -> -> make_empty_graph - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 7.1Mb - sub-directories of 1Mb or more: - data 1.2Mb - doc 2.3Mb - libs 3.5Mb - ``` - -# cranly - -
- -* Version: 0.6.0 -* GitHub: https://github.com/ikosmidis/cranly -* Source code: https://github.com/cran/cranly -* Date/Publication: 2022-08-26 22:14:41 UTC -* Number of recursive dependencies: 64 - -Run `revdepcheck::cloud_details(, "cranly")` for more info - -
- -## Newly broken - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘cranly.Rmd’ using rmarkdown - - Quitting from lines 63-65 [unnamed-chunk-7] (cranly.Rmd) - Error: processing vignette 'cranly.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘cranly.Rmd’ - - --- re-building ‘dependence_trees.Rmd’ using rmarkdown - ... - --- failed re-building ‘dependence_trees.Rmd’ - - --- re-building ‘extractors.Rmd’ using rmarkdown - --- finished re-building ‘extractors.Rmd’ - - SUMMARY: processing the following files failed: - ‘cranly.Rmd’ ‘dependence_trees.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.4Mb - sub-directories of 1Mb or more: - doc 5.1Mb - ``` - -# criticalpath - -
- -* Version: 0.2.1 -* GitHub: https://github.com/rubens2005/criticalpath -* Source code: https://github.com/cran/criticalpath -* Date/Publication: 2022-03-13 22:40:10 UTC -* Number of recursive dependencies: 88 - -Run `revdepcheck::cloud_details(, "criticalpath")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘criticalpath-Ex.R’ failed - The error most likely occurred in: - - > ### Name: sch_activities - > ### Title: Activities - > ### Aliases: sch_activities - > - > ### ** Examples - > - > sch <- sch_new() %>% - ... - + sch_add_activity( 10L, "a10", 3L, 12) %>% - + sch_add_activity( 11L, "a11", 3L, 12) %>% - + sch_add_activity( 12L, "a12", 0L) %>% - + sch_plan() - Error in sch_plan(.) : - The schedule is invalid!!! To view the problem, execute: - - `validation <- sch_validate(sch)` - Calls: %>% -> sch_plan - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Backtrace: - ▆ - 1. ├─testthat::expect_silent(sch1 <- sch_plan(sch)) at test-cpt-validate_schedule.R:17:2 - 2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise) - 3. │ ├─testthat (local) .capture(...) - 4. │ │ ├─withr::with_output_sink(...) - 5. │ │ │ └─base::force(code) - 6. │ │ ├─base::withCallingHandlers(...) - 7. │ │ └─base::withVisible(code) - 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) - 9. └─criticalpath::sch_plan(sch) - - [ FAIL 98 | WARN 0 | SKIP 0 | PASS 162 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘criticalpath-introduction.Rmd’ using rmarkdown - - Quitting from lines 95-117 [unnamed-chunk-2] (criticalpath-introduction.Rmd) - Error: processing vignette 'criticalpath-introduction.Rmd' failed with diagnostics: - The schedule is invalid!!! To view the problem, execute: - - `validation <- sch_validate(sch)` - --- failed re-building ‘criticalpath-introduction.Rmd’ - - SUMMARY: processing the following file failed: - ‘criticalpath-introduction.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# crosstalkr - -
- -* Version: 1.0.2 -* GitHub: NA -* Source code: https://github.com/cran/crosstalkr -* Date/Publication: 2023-05-18 17:50:02 UTC -* Number of recursive dependencies: 167 - -Run `revdepcheck::cloud_details(, "crosstalkr")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘crosstalkr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: compute_crosstalk - > ### Title: Identify proteins with a statistically significant relationship - > ### to user-provided seeds. - > ### Aliases: compute_crosstalk - > - > ### ** Examples - > - > #2) Also works for any other kind of graph- just specify g (must be igraph formatted as of now) - > g <- igraph::sample_gnp(n = 1000, p = 10/1000) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─igraph::graph_from_adjacency_matrix(w) at test-filter.R:11:0 - 2. └─igraph:::graph.adjacency.dense(...) - ── Error ('test-plot.R:11:1'): (code run outside of `test_that()`) ───────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─igraph::graph_from_adjacency_matrix(w) at test-plot.R:11:0 - 2. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 4 | WARN 0 | SKIP 11 | PASS 36 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘crosstalkr_vignette.Rmd’ using rmarkdown - - Quitting from lines 79-84 [filter] (crosstalkr_vignette.Rmd) - Error: processing vignette 'crosstalkr_vignette.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘crosstalkr_vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘crosstalkr_vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# cytometree - -
- -* Version: 2.0.2 -* GitHub: https://github.com/sistm/Cytometree -* Source code: https://github.com/cran/cytometree -* Date/Publication: 2019-12-04 22:20:19 UTC -* Number of recursive dependencies: 63 - -Run `revdepcheck::cloud_details(, "cytometree")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘cytometree-Ex.R’ failed - The error most likely occurred in: - - > ### Name: CytomeTree - > ### Title: Binary tree algorithm for cytometry data analysis. - > ### Aliases: CytomeTree - > - > ### ** Examples - > - > head(DLBCL) - ... - > # Choose a node to plot - > plot_nodes(Tree,"FL4.1") - > - > # Plot a graph of the tree - > par(mfrow=c(1,1)) - > plot_graph(Tree,edge.arrow.size=.3, Vcex =.5, vertex.size = 30) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot_graph -> graph.data.frame -> make_empty_graph - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘autogating_cytometree.Rmd’ using rmarkdown - - Quitting from lines 80-82 [unnamed-chunk-4] (autogating_cytometree.Rmd) - Error: processing vignette 'autogating_cytometree.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘autogating_cytometree.Rmd’ - - --- re-building ‘cytoftree.Rmd’ using rmarkdown - --- finished re-building ‘cytoftree.Rmd’ - - SUMMARY: processing the following file failed: - ‘autogating_cytometree.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# d3po - -
- -* Version: 0.3.4 -* GitHub: https://github.com/pachadotdev/d3po -* Source code: https://github.com/cran/d3po -* Date/Publication: 2023-03-03 20:20:02 UTC -* Number of recursive dependencies: 56 - -Run `revdepcheck::cloud_details(, "d3po")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘d3po-Ex.R’ failed - The error most likely occurred in: - - > ### Name: d3po_graph - > ### Title: Graph - > ### Aliases: d3po_graph po_nodes po_edges po_layout - > - > ### ** Examples - > - > tr <- igraph::make_tree(40, children = 3, mode = "undirected") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: - Execution halted - ``` - -# dartR - -
- -* Version: 2.9.7 -* GitHub: NA -* Source code: https://github.com/cran/dartR -* Date/Publication: 2023-06-07 10:40:02 UTC -* Number of recursive dependencies: 285 - -Run `revdepcheck::cloud_details(, "dartR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘dartR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: gl.grm.network - > ### Title: Represents a genomic relationship matrix (GRM) as a network - > ### Aliases: gl.grm.network - > - > ### ** Examples - > - > if (requireNamespace("igraph", quietly = TRUE) & requireNamespace("rrBLUP", - ... - Completed: gl.subsample.loci - Starting gl.grm - Processing genlight object with SNP data - Completed: gl.grm - Starting gl.grm.network - Processing genlight object with SNP data - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: gl.grm.network -> -> make_empty_graph - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘dartRTutorials.Rmd’ using rmarkdown - A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TinyTeX with tinytex::reinstall_tinytex(repository = "illinois"). - - tlmgr: Local TeX Live (2022) is older than remote repository (2023). - Cross release updates are only supported with - update-tlmgr-latest(.sh/.exe) --update - See https://tug.org/texlive/upgrade.html for details. - Warning in system2("tlmgr", args, ...) : - ... - - Error: processing vignette 'dartRTutorials.Rmd' failed with diagnostics: - LaTeX failed to compile /tmp/workdir/dartR/new/dartR.Rcheck/vign_test/dartR/vignettes/dartRTutorials.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See dartRTutorials.log for more info. - --- failed re-building ‘dartRTutorials.Rmd’ - - SUMMARY: processing the following file failed: - ‘dartRTutorials.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# data.tree - -
- -* Version: 1.0.0 -* GitHub: https://github.com/gluc/data.tree -* Source code: https://github.com/cran/data.tree -* Date/Publication: 2020-08-03 15:50:02 UTC -* Number of recursive dependencies: 122 - -Run `revdepcheck::cloud_details(, "data.tree")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ▆ - 1. └─data.tree::as.igraph.Node(acme, "p", c("level", "isLeaf"), directed = FALSE) at test-treeConversionigraph.R:6:2 - 2. └─igraph::graph_from_data_frame(data, directed = directed, vertices = vert) - 3. └─igraph::make_empty_graph(n = 0, directed = directed) - ── Error ('test-treeConversionigraph.R:15:3'): as.Node.igraph directed ───────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─data.tree::as.igraph.Node(acme, "p", c("level", "isLeaf"), directed = TRUE) at test-treeConversionigraph.R:15:2 - 2. └─igraph::graph_from_data_frame(data, directed = directed, vertices = vert) - 3. └─igraph::make_empty_graph(n = 0, directed = directed) - - [ FAIL 2 | WARN 0 | SKIP 0 | PASS 370 ] - Error: Test failures - Execution halted - ``` - -# DDPNA - -
- -* Version: 0.3.1 -* GitHub: https://github.com/liukf10/DDPNA -* Source code: https://github.com/cran/DDPNA -* Date/Publication: 2022-05-17 12:20:02 UTC -* Number of recursive dependencies: 155 - -Run `revdepcheck::cloud_details(, "DDPNA")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘DDPNA-Ex.R’ failed - The error most likely occurred in: - - > ### Name: getmoduleHub - > ### Title: getmoduleHub - > ### Aliases: getmoduleHub - > - > ### ** Examples - > - > data(net) - ... - > data <- imputedData - > logD <- data$log2_value - > rownames(logD) <- data$inf$ori.ID - > group <- gsub("[0-9]+","", colnames(logD)) - > Module <- Module_inf(net, data$inf) - > Mod10 <- getmoduleHub(logD, Module, 10, coln = "ori.ID", adjustp = FALSE) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: getmoduleHub -> graph.data.frame -> make_empty_graph - Execution halted - ``` - -# deaR - -
- -* Version: 1.4.1 -* GitHub: NA -* Source code: https://github.com/cran/deaR -* Date/Publication: 2023-05-02 09:20:02 UTC -* Number of recursive dependencies: 75 - -Run `revdepcheck::cloud_details(, "deaR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘deaR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plot.dea - > ### Title: Plot for DEA models. - > ### Aliases: plot.dea - > - > ### ** Examples - > - > data_example <- make_deadata(datadea = Fortune500, - + inputs = 2:4, - + outputs = 5:6) - > result <- model_basic(data_example) - > plot(result) - Press [enter] to continue - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot ... plot.dea -> graph.adjacency -> graph.adjacency.dense - Execution halted - ``` - -# deepdep - -
- -* Version: 0.4.2 -* GitHub: https://github.com/DominikRafacz/deepdep -* Source code: https://github.com/cran/deepdep -* Date/Publication: 2023-02-21 00:10:05 UTC -* Number of recursive dependencies: 145 - -Run `revdepcheck::cloud_details(, "deepdep")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘spelling.R’ - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ── Error ('test-plot.R:17:1'): (code run outside of `test_that()`) ───────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. ├─vcr::use_cassette(...) at test-plot.R:17:0 - 2. │ └─cassette$call_block(...) - 3. ├─deepdep::plot_dependencies(dd_rlang) at test-plot.R:19:2 - 4. └─deepdep:::plot_dependencies.deepdep(dd_rlang) - 5. └─igraph::make_graph(edges = c(), n = 1) - 6. ├─base::do.call(old_graph, args) - 7. └─igraph (local) ``(``, n = 1) - - [ FAIL 3 | WARN 0 | SKIP 1 | PASS 23 ] - Error: Test failures - Execution halted - ``` - -# degreenet - -
- -* Version: 1.3-3 -* GitHub: NA -* Source code: https://github.com/cran/degreenet -* Date/Publication: 2018-03-26 07:38:43 UTC -* Number of recursive dependencies: 18 - -Run `revdepcheck::cloud_details(, "degreenet")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘degreenet-Ex.R’ failed - The error most likely occurred in: - - > ### Name: reedmolloy - > ### Title: Generate a (non-random) network with a given degree sequence - > ### Aliases: reedmolloy - > ### Keywords: models - > - > ### ** Examples - > - ... - > s4 <- simpln(n=100, v=c(-1,1)) - > table(s4) - s4 - 1 2 3 4 5 6 - 65 18 7 4 4 2 - > # - > simr <- reedmolloy(s4) - Error in reedmolloy(s4) : - The reedmolloy function failed to form a valid network from the passed degree sequence. - Execution halted - ``` - -# delayed - -
- -* Version: 0.4.0 -* GitHub: https://github.com/tlverse/delayed -* Source code: https://github.com/cran/delayed -* Date/Publication: 2022-10-19 22:25:09 UTC -* Number of recursive dependencies: 81 - -Run `revdepcheck::cloud_details(, "delayed")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘delayed-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plot.Delayed - > ### Title: Plot Method for Delayed Objects - > ### Aliases: plot.Delayed - > - > ### ** Examples - > - > adder <- function(x, y) { - ... - > delayed_adder <- delayed_fun(adder) - > z <- delayed_adder(3, 4) - > z2 <- delayed_adder(z, 4) - > z2$sequential <- TRUE - > z3 <- delayed_adder(z2, z) - > plot(z3) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot -> plot.Delayed -> make_graph -> make_empty_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - • empty test (1) - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Error ('test_make_graph.R:18:3'): can plot graph ──────────────────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. ├─base::plot(z3) at test_make_graph.R:18:2 - 2. └─delayed:::plot.Delayed(z3) - 3. └─delayed:::make_graph(x) - 4. └─igraph::make_empty_graph() - - [ FAIL 1 | WARN 0 | SKIP 1 | PASS 12 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘delayed.Rmd’ using rmarkdown - - Quitting from lines 97-98 [unnamed-chunk-2] (delayed.Rmd) - Error: processing vignette 'delayed.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘delayed.Rmd’ - - SUMMARY: processing the following file failed: - ‘delayed.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# DemoKin - -
- -* Version: 1.0.3 -* GitHub: https://github.com/IvanWilli/DemoKin -* Source code: https://github.com/cran/DemoKin -* Date/Publication: 2023-06-05 09:00:02 UTC -* Number of recursive dependencies: 77 - -Run `revdepcheck::cloud_details(, "DemoKin")` for more info - -
- -## Newly broken - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘Reference_OneSex.Rmd’ using rmarkdown - - Quitting from lines 119-123 [unnamed-chunk-10] (Reference_OneSex.Rmd) - Error: processing vignette 'Reference_OneSex.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘Reference_OneSex.Rmd’ - - --- re-building ‘Reference_TwoSex.Rmd’ using rmarkdown - --- finished re-building ‘Reference_TwoSex.Rmd’ - - SUMMARY: processing the following file failed: - ‘Reference_OneSex.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.8Mb - sub-directories of 1Mb or more: - data 1.2Mb - doc 3.1Mb - help 1.3Mb - ``` - -# dexterMST - -
- -* Version: 0.9.3 -* GitHub: https://github.com/dexter-psychometrics/dexter -* Source code: https://github.com/cran/dexterMST -* Date/Publication: 2022-02-14 19:40:13 UTC -* Number of recursive dependencies: 91 - -Run `revdepcheck::cloud_details(, "dexterMST")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘dexterMST-Ex.R’ failed - The error most likely occurred in: - - > ### Name: create_mst_test - > ### Title: Define a new multi stage test - > ### Aliases: create_mst_test - > - > ### ** Examples - > - > # extended example - ... - > - > add_response_data_mst(db, dat) - Added 90000 responses for 3000 administrations - > - > - > design_plot(db) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: design_plot ... ensure_igraph -> graph.data.frame -> make_empty_graph - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.3Mb - sub-directories of 1Mb or more: - libs 5.7Mb - ``` - -# DiagrammeR - -
- -* Version: 1.0.10 -* GitHub: https://github.com/rich-iannone/DiagrammeR -* Source code: https://github.com/cran/DiagrammeR -* Date/Publication: 2023-05-18 14:30:07 UTC -* Number of recursive dependencies: 99 - -Run `revdepcheck::cloud_details(, "DiagrammeR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘DiagrammeR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: add_full_graph - > ### Title: Add a fully connected graph - > ### Aliases: add_full_graph - > - > ### ** Examples - > - > # Create a new graph object - ... - > # and to themselves - > graph <- - + create_graph() %>% - + add_full_graph( - + n = 3, keep_loops = TRUE - + ) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: %>% ... from_adj_matrix -> -> graph.adjacency.dense - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ── Error ('test-write_graph_backup.R:922:3'): Graph backups for `recode_node_attrs()` works ── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. ├─... %>% ... at test-write_graph_backup.R:922:2 - 2. ├─DiagrammeR::recode_node_attrs(...) - 3. │ └─DiagrammeR:::graph_object_valid(graph) - 4. │ └─... %in% names(graph) - 5. ├─DiagrammeR::set_node_attrs(...) - 6. └─DiagrammeR::add_gnm_graph(., n = 5, m = 10, set_seed = 23) - 7. └─igraph::sample_gnm(n = n, m = m, directed = graph_directed, loops = loops) - - [ FAIL 109 | WARN 3 | SKIP 0 | PASS 1373 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 1 marked UTF-8 string - ``` - -# diffeRenTES - -
- -* Version: 0.3.2 -* GitHub: NA -* Source code: https://github.com/cran/diffeRenTES -* Date/Publication: 2022-04-28 07:20:04 UTC -* Number of recursive dependencies: 60 - -Run `revdepcheck::cloud_details(, "diffeRenTES")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘diffeRenTES-Ex.R’ failed - The error most likely occurred in: - - > ### Name: getTESs - > ### Title: Compute TES - > ### Aliases: getTESs - > - > ### ** Examples - > - > - > net <- BoolNet::generateRandomNKNetwork(10, 2) - > attractors <- BoolNet::getAttractors(net) - > ATM <- getATM(net, attractors) - > getTESs(ATM) - In the ATM there is no threshold value equal to 0, it will be added for the calculation of TESs - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: getTESs -> -> graph.adjacency.dense - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Loading required package: diffeRenTES - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 20 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Error ('tests-atm.R:17:3'): TES tests working ─────────────────────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─diffeRenTES::getTESs(a) at tests-atm.R:17:2 - 2. └─igraph::graph_from_adjacency_matrix(adj_mtrx, mode = "directed") - 3. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 20 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘diffeRenTES_vignette.Rmd’ using rmarkdown - - Quitting from lines 67-75 [unnamed-chunk-5] (diffeRenTES_vignette.Rmd) - Error: processing vignette 'diffeRenTES_vignette.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘diffeRenTES_vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘diffeRenTES_vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# diffudist - -
- -* Version: 1.0.1 -* GitHub: https://github.com/gbertagnolli/diffudist -* Source code: https://github.com/cran/diffudist -* Date/Publication: 2023-02-27 19:42:40 UTC -* Number of recursive dependencies: 74 - -Run `revdepcheck::cloud_details(, "diffudist")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘diffudist-Ex.R’ failed - The error most likely occurred in: - - > ### Name: get_distance_matrix - > ### Title: Diffusion Distance Matrix - > ### Aliases: get_distance_matrix getDistanceMatrix get_DDM - > ### Keywords: diffusion distance - > - > ### ** Examples - > - > g <- igraph::sample_pa(10, directed = FALSE) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.1Mb - sub-directories of 1Mb or more: - libs 4.1Mb - ``` - -# diffusr - -
- -* Version: 0.1.4 -* GitHub: https://github.com/dirmeier/diffusr -* Source code: https://github.com/cran/diffusr -* Date/Publication: 2018-05-17 21:01:21 UTC -* Number of recursive dependencies: 65 - -Run `revdepcheck::cloud_details(, "diffusr")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘diffusr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: random.walk - > ### Title: Graph diffusion using a Markov random walk - > ### Aliases: random.walk random.walk,numeric,matrix-method - > ### random.walk,matrix,matrix-method - > - > ### ** Examples - > - ... - > # adjacency matrix (either normalized or not) - > graph <- matrix(abs(rnorm(n*n)), n, n) - > # computation of stationary distribution - > pt <- random.walk(p0, graph) - setting diag of graph to zero - normalizing column vectors! - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: random.walk ... .is.ergodic -> -> graph.adjacency.dense - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Backtrace: - ▆ - 1. └─igraph::graph_from_adjacency_matrix(adja) at test_mrw.R:24:0 - 2. └─igraph:::graph.adjacency.dense(...) - ── Error ('test_util.R:24:1'): (code run outside of `test_that()`) ───────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─igraph::make_graph(c(1, 2, 2, 3, 3, 4, 4, 5), directed = FALSE) at test_util.R:24:0 - 2. ├─base::do.call(old_graph, args) - 3. └─igraph (local) ``(``, directed = FALSE) - - [ FAIL 2 | WARN 0 | SKIP 0 | PASS 21 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘diffusr.Rmd’ using rmarkdown - - Quitting from lines 34-42 [unnamed-chunk-2] (diffusr.Rmd) - Error: processing vignette 'diffusr.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘diffusr.Rmd’ - - SUMMARY: processing the following file failed: - ‘diffusr.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 15.8Mb - sub-directories of 1Mb or more: - libs 14.8Mb - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘methods’ - All declared Imports should be used. - ``` - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# dimRed - -
- -* Version: 0.2.6 -* GitHub: https://github.com/gdkrmr/dimRed -* Source code: https://github.com/cran/dimRed -* Date/Publication: 2022-07-11 12:40:06 UTC -* Number of recursive dependencies: 132 - -Run `revdepcheck::cloud_details(, "dimRed")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘dimRed-Ex.R’ failed - The error most likely occurred in: - - > ### Name: FruchtermanReingold-class - > ### Title: Fruchterman Reingold Graph Layout - > ### Aliases: FruchtermanReingold-class FruchtermanReingold - > - > ### ** Examples - > - > if(requireNamespace(c("igraph", "coRanking"), quietly = TRUE)) { - ... - + - + dat <- loadDataSet("Swiss Roll", n = 100) - + emb <- embed(dat, "FruchtermanReingold") - + plot(emb, type = "2vars") - + - + } - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: embed ... construct_knn_graph -> -> graph.adjacency.dense - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ── Error ('test_isomap.R:49:3'): check other.data ────────────────────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. ├─dimRed::embed(a, "Isomap", knn = 8, ndim = 2, get_geod = TRUE) at test_isomap.R:49:2 - 2. └─dimRed::embed(a, "Isomap", knn = 8, ndim = 2, get_geod = TRUE) - 3. └─dimRed (local) .local(.data, ...) - 4. ├─base::do.call(methodObject@fun, args) - 5. └─dimRed (local) ``(data = ``, keep.org.data = TRUE, pars = ``) - 6. └─dimRed:::makeKNNgraph(x = indata, k = pars$knn, eps = pars$eps) - 7. └─igraph::make_empty_graph(M, directed = TRUE) - - [ FAIL 3 | WARN 8 | SKIP 7 | PASS 166 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking for unstated dependencies in examples ... WARNING - ``` - 'library' or 'require' calls not declared from: - ‘MASS’ ‘Matrix’ ‘NNMF’ ‘RANN’ ‘RSpectra’ ‘c’ ‘coRanking’ ‘ggplot’ - ‘igraph’ ‘loe’ ‘scales’ ‘tidyr’ - ``` - -# discourseGT - -
- -* Version: 1.1.8 -* GitHub: NA -* Source code: https://github.com/cran/discourseGT -* Date/Publication: 2022-10-27 23:25:10 UTC -* Number of recursive dependencies: 119 - -Run `revdepcheck::cloud_details(, "discourseGT")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘discourseGT-Ex.R’ failed - The error most likely occurred in: - - > ### Name: basicPlot - > ### Title: Plot Graphs - > ### Aliases: basicPlot - > - > ### ** Examples - > - > - > df <- sampleData1 - > prepNet <- tabulate_edges(df, iscsvfile = FALSE, silentNodes = 0) - > baseNet <- prepareGraphs(prepNet, project_title = "Sample Data 1", weightedGraph = TRUE) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: prepareGraphs -> -> make_empty_graph - Execution halted - ``` - -# discretecdAlgorithm - -
- -* Version: 0.0.7 -* GitHub: NA -* Source code: https://github.com/cran/discretecdAlgorithm -* Date/Publication: 2020-03-12 06:40:02 UTC -* Number of recursive dependencies: 39 - -Run `revdepcheck::cloud_details(, "discretecdAlgorithm")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘discretecdAlgorithm-Ex.R’ failed - The error most likely occurred in: - - > ### Name: generate_discrete_data - > ### Title: generate_discrete_data - > ### Aliases: generate_discrete_data - > - > ### ** Examples - > - > - ... - > nlevels <- c(3, 5, 2, 2, 3) - > gr.params <- coef_gen(edge_list = gr, n_levels = nlevels) - > data.obs <- discretecdAlgorithm::generate_discrete_data(graph = gr, - + n = 100, - + n_levels = nlevels, - + params = gr.params) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: ... datGen_call -> -> graph.adjacency.dense - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 2. └─discretecdAlgorithm:::datGen_call(...) - 3. └─igraph::graph.adjacency(as.matrix(adj_matrix)) - 4. └─igraph:::graph.adjacency.dense(...) - ── Error ('test-generate_discrete_data.R:41:3'): Check output ────────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─discretecdAlgorithm::generate_discrete_data(...) at test-generate_discrete_data.R:41:2 - 2. └─discretecdAlgorithm:::datGen_call(...) - 3. └─igraph::graph.adjacency(as.matrix(adj_matrix)) - 4. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 9 | WARN 0 | SKIP 0 | PASS 544 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 14.3Mb - sub-directories of 1Mb or more: - libs 14.2Mb - ``` - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# dm - -
- -* Version: 1.0.5 -* GitHub: https://github.com/cynkra/dm -* Source code: https://github.com/cran/dm -* Date/Publication: 2023-03-16 17:10:02 UTC -* Number of recursive dependencies: 134 - -Run `revdepcheck::cloud_details(, "dm")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘dm-Ex.R’ failed - The error most likely occurred in: - - > ### Name: copy_dm_to - > ### Title: Copy data model to data source - > ### Aliases: copy_dm_to - > - > ### ** Examples - > - > ## Don't show: - ... - + - + DBI::dbDisconnect(con) - + ## Don't show: - + }) # examplesIf - > con <- DBI::dbConnect(RSQLite::SQLite()) - > temp_dm <- copy_dm_to(con, dm_nycflights13(), set_key_constraints = FALSE) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: ... create_graph_from_dm -> %>% -> -> make_empty_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ▆ - 1. ├─dm::copy_dm_to(...) at test_dm_from_con.R:46:2 - 2. │ └─dm:::build_copy_queries(...) - 3. │ └─dm:::create_graph_from_dm(dm, directed = TRUE) - 4. │ └─... %>% ... - 5. └─igraph::graph_from_data_frame(., directed = directed, vertices = def$table) - 6. └─igraph::make_empty_graph(n = 0, directed = directed) - ── Error ('test-zoom.R:135:3'): zoom output for compound keys ────────────────── - `{ ... }` threw an unexpected error. - Message: could not find function ".igraph.status" - Class: simpleError/error/condition - - [ FAIL 41 | WARN 2 | SKIP 192 | PASS 1176 ] - Error: Test failures - Execution halted - ``` - -# dnapath - -
- -* Version: 0.7.4 -* GitHub: NA -* Source code: https://github.com/cran/dnapath -* Date/Publication: 2022-05-09 09:00:05 UTC -* Number of recursive dependencies: 149 - -Run `revdepcheck::cloud_details(, "dnapath")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘dnapath-Ex.R’ failed - The error most likely occurred in: - - > ### Name: dnapath - > ### Title: Differential Network Analysis Using Gene Pathways - > ### Aliases: dnapath - > - > ### ** Examples - > - > data(meso) - ... - 7 Regulation of TP53 Degradation … 983 0.141 0.0909 8.49 8.56 - 8 Regulation of TP53 Degradation … 7157 0.221 0.182 11.1 10.8 - 9 Regulation of TP53 Degradation … 80196 0.214 0.182 9.37 9.36 - 10 Regulation of TP53 Degradation … 5519 0.177 0.182 9.14 9.20 - # ℹ 27 more rows - > plot(results[[1]]) # Plot of the differential network for pathway 1. - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot ... -> -> graph.adjacency.dense - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘introduction_to_dnapath.Rmd’ using rmarkdown - - Quitting from lines 164-165 [unnamed-chunk-3] (introduction_to_dnapath.Rmd) - Error: processing vignette 'introduction_to_dnapath.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘introduction_to_dnapath.Rmd’ - - --- re-building ‘package_data.Rmd’ using rmarkdown - --- finished re-building ‘package_data.Rmd’ - - SUMMARY: processing the following file failed: - ‘introduction_to_dnapath.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# dnr - -
- -* Version: 0.3.5 -* GitHub: NA -* Source code: https://github.com/cran/dnr -* Date/Publication: 2020-11-30 17:10:03 UTC -* Number of recursive dependencies: 73 - -Run `revdepcheck::cloud_details(, "dnr")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘dnr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: clustCoef - > ### Title: clustCoef - > ### Aliases: clustCoef - > - > ### ** Examples - > - > clustCoef(beach[[1]][, ]) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: clustCoef ... ensure_igraph -> -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘dnr_vignette.Rnw’ using knitr - Warning: 'mode(width)' differs between new and previous - ==> NOT changing 'width' - Warning: 'mode(width)' differs between new and previous - ==> NOT changing 'width' - Warning: 'mode(width)' differs between new and previous - ==> NOT changing 'width' - Warning: 'mode(width)' differs between new and previous - ... - Quitting from lines 126-133 [beach-vertex-model-fit] (dnr_vignette.Rnw) - Error: processing vignette 'dnr_vignette.Rnw' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘dnr_vignette.Rnw’ - - SUMMARY: processing the following file failed: - ‘dnr_vignette.Rnw’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# dodgr - -
- -* Version: 0.2.21 -* GitHub: https://github.com/ATFutures/dodgr -* Source code: https://github.com/cran/dodgr -* Date/Publication: 2023-06-02 11:40:02 UTC -* Number of recursive dependencies: 110 - -Run `revdepcheck::cloud_details(, "dodgr")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘dodgr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: dodgr_centrality - > ### Title: Calculate betweenness centrality for a 'dodgr' network. - > ### Aliases: dodgr_centrality - > - > ### ** Examples - > - > graph_full <- weight_streetnet (hampi) - ... - Graph has duplicated edges. Only the first will be used here, - but it is better to remove them first with the 'dodgr_deduplicate_graph() function. - > # 'graph' is then the contracted graph with an additional 'centrality' column - > # Same calculation via 'igraph': - > igr <- dodgr_to_igraph (graph) - Loading required namespace: igraph - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: dodgr_to_igraph -> -> make_empty_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘sc-conversion-fns.R’ - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 3. └─igraph::make_empty_graph(n = 0, directed = directed) - ── Error ('test-graph-conversion.R:25:5'): tidyraph ──────────────────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. ├─dodgr::dodgr_to_tidygraph(graph) at test-graph-conversion.R:25:4 - 2. │ ├─dodgr_to_igraph(graph) %>% tidygraph::as_tbl_graph() - 3. │ └─dodgr::dodgr_to_igraph(graph) - 4. │ └─igraph::graph_from_data_frame(graph, directed = TRUE, vertices = v) - 5. │ └─igraph::make_empty_graph(n = 0, directed = directed) - 6. └─tidygraph::as_tbl_graph(.) - - [ FAIL 2 | WARN 0 | SKIP 11 | PASS 242 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘dists-categorical.Rmd’ using rmarkdown - --- finished re-building ‘dists-categorical.Rmd’ - - --- re-building ‘dodgr.Rmd’ using rmarkdown - - Quitting from lines 501-502 [compare-heaps] (dodgr.Rmd) - Error: processing vignette 'dodgr.Rmd' failed with diagnostics: - could not find function ".igraph.status" - ... - --- finished re-building ‘parallel.Rmd’ - - --- re-building ‘times.Rmd’ using rmarkdown - --- finished re-building ‘times.Rmd’ - - SUMMARY: processing the following file failed: - ‘dodgr.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 35.2Mb - sub-directories of 1Mb or more: - doc 6.5Mb - libs 28.1Mb - ``` - -* checking for GNU extensions in Makefiles ... NOTE - ``` - GNU make is a SystemRequirements. - ``` - -# dosearch - -
- -* Version: 1.0.8 -* GitHub: NA -* Source code: https://github.com/cran/dosearch -* Date/Publication: 2021-08-19 16:40:02 UTC -* Number of recursive dependencies: 15 - -Run `revdepcheck::cloud_details(, "dosearch")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘dosearch-Ex.R’ failed - The error most likely occurred in: - - > ### Name: dosearch - > ### Title: Identify a causal effect from arbitrary experiments and - > ### observations - > ### Aliases: dosearch - > - > ### ** Examples - > - ... - > ## Graph input using 'igraph' in the 'causaleffect' syntax - > if (requireNamespace("igraph", quietly = TRUE)) { - + g_igraph <- igraph::graph.formula(x -+ z, z -+ y, x -+ y, y -+ x) - + g_igraph <- igraph::set.edge.attribute(g_igraph, "description", 3:4, "U") - + dosearch(data2, query2, g_igraph) - + } - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: ... graph_from_literal_i -> make_graph -> do.call -> - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.4Mb - sub-directories of 1Mb or more: - libs 6.2Mb - ``` - -# dragon - -
- -* Version: 1.2.1 -* GitHub: https://github.com/sjspielman/dragon -* Source code: https://github.com/cran/dragon -* Date/Publication: 2022-04-08 08:42:33 UTC -* Number of recursive dependencies: 130 - -Run `revdepcheck::cloud_details(, "dragon")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 5. │ └─testthat:::test_files_setup_state(...) - 6. │ └─testthat::source_test_setup(".", env) - 7. │ └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE) - 8. │ └─base::lapply(...) - 9. │ └─testthat (local) FUN(X[[i]], ...) - 10. │ └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap) - 11. │ ├─base::withCallingHandlers(...) - 12. │ └─base::eval(exprs, env) - 13. │ └─base::eval(exprs, env) - 14. │ └─igraph::read_graph("graph_by_redox.igraph", format = "ncol") at tests/testthat/setup_test-settings.R:8:0 - 15. │ └─igraph:::read.graph.ncol(file, ...) - 16. └─base::.handleSimpleError(...) - 17. └─testthat (local) h(simpleError(msg, call)) - 18. └─rlang::abort(...) - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘htmltools’ - All declared Imports should be used. - ``` - -# drake - -
- -* Version: 7.13.5 -* GitHub: https://github.com/ropensci/drake -* Source code: https://github.com/cran/drake -* Date/Publication: 2023-03-24 13:10:02 UTC -* Number of recursive dependencies: 164 - -Run `revdepcheck::cloud_details(, "drake")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘drake-Ex.R’ failed - The error most likely occurred in: - - > ### Name: code_to_plan - > ### Title: Turn an R script file or 'knitr' / R Markdown report into a - > ### 'drake' plan. *[Questioning]* - > ### Aliases: code_to_plan - > - > ### ** Examples - > - ... - + hist = create_plot(data), - + fit = lm(Ozone ~ Temp + Wind, data) - + ) - > file <- tempfile() - > # Turn the plan into an R script a the given file path. - > plan_to_code(plan, file) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plan_to_code ... cdg_finalize_graph -> -> make_empty_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Backtrace: - 1. drake::drake_config(...) - at test-4-rng.R:301:2 - 2. drake:::create_drake_graph(...) - 5. drake:::cdg_finalize_graph(edges, targets, args) - 6. igraph::graph_from_data_frame(edges) - 7. igraph::make_empty_graph(n = 0, directed = directed) - ... and 41 more - - - Maximum number of 10 failures reached, some test results may be missing. - - ══ DONE ════════════════════════════════════════════════════════════════════════ - Error: Test failures - Execution halted - ``` - -# DrDimont - -
- -* Version: 0.1.4 -* GitHub: NA -* Source code: https://github.com/cran/DrDimont -* Date/Publication: 2022-09-23 15:40:02 UTC -* Number of recursive dependencies: 127 - -Run `revdepcheck::cloud_details(, "DrDimont")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘DrDimont-Ex.R’ failed - The error most likely occurred in: - - > ### Name: compute_drug_response_scores - > ### Title: Calculate drug response score - > ### Aliases: compute_drug_response_scores - > - > ### ** Examples - > - > data(drug_target_edges_example) - ... - > example_drug_response_scores <- compute_drug_response_scores( - + differential_graph=differential_graph_example, - + drug_targets=drug_target_edges_example$targets, - + settings=example_settings) - [23-06-11 21:55:10] Computing drug response scores based on the mean of the differential scores ... - - Error in .igraph.status("Restore graph external pointer.\n") : - could not find function ".igraph.status" - Calls: compute_drug_response_scores ... -> ensure_igraph -> is_igraph -> warn_version - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘DrDimont_Vignette.Rmd’ using rmarkdown - - Quitting from lines 328-333 [Individual graphs] (DrDimont_Vignette.Rmd) - Error: processing vignette 'DrDimont_Vignette.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘DrDimont_Vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘DrDimont_Vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# DTSEA - -
- -* Version: 0.0.3 -* GitHub: NA -* Source code: https://github.com/cran/DTSEA -* Date/Publication: 2022-11-06 13:20:02 UTC -* Number of recursive dependencies: 72 - -Run `revdepcheck::cloud_details(, "DTSEA")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘DTSEA-Ex.R’ failed - The error most likely occurred in: - - > ### Name: calculate_p0 - > ### Title: Function to calculate the p0 vector used in Random Walk with - > ### Restart (RwR) - > ### Aliases: calculate_p0 - > - > ### ** Examples - > - ... - > data("example_disease_list", package = "DTSEA") - > data("example_drug_target_list", package = "DTSEA") - > data("example_ppi", package = "DTSEA") - > - > # Compute the p0 vector - > p0 <- calculate_p0(nodes = example_ppi, disease = example_disease_list) - Error in .igraph.status("Restore graph external pointer.\n") : - could not find function ".igraph.status" - Calls: calculate_p0 -> is.igraph -> warn_version - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘DTSEA.Rmd’ using rmarkdown - - Quitting from lines 54-67 [unnamed-chunk-2] (DTSEA.Rmd) - Error: processing vignette 'DTSEA.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘DTSEA.Rmd’ - - SUMMARY: processing the following file failed: - ‘DTSEA.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# dyndimred - -
- -* Version: 1.0.4 -* GitHub: https://github.com/dynverse/dyndimred -* Source code: https://github.com/cran/dyndimred -* Date/Publication: 2021-03-23 08:30:06 UTC -* Number of recursive dependencies: 160 - -Run `revdepcheck::cloud_details(, "dyndimred")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 4. └─igraph::graph_from_data_frame(kdf, vertices = seq_len(nrow(x))) - 5. └─igraph::make_empty_graph(n = 0, directed = directed) - ── Error ('test-dimred.R:70:7'): Check sparse capable knn_fr ─────────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. ├─utils::capture.output(...) at test-dimred.R:70:6 - 2. │ └─base::withVisible(...elt(i)) - 3. └─dyndimred (local) dr_fun(sparse_expr) at test-dimred.R:74:8 - 4. └─igraph::graph_from_data_frame(kdf, vertices = seq_len(nrow(x))) - 5. └─igraph::make_empty_graph(n = 0, directed = directed) - - [ FAIL 2 | WARN 0 | SKIP 0 | PASS 131 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘lle’ - ``` - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# dynetNLAResistance - -
- -* Version: 0.1.0 -* GitHub: NA -* Source code: https://github.com/cran/dynetNLAResistance -* Date/Publication: 2016-11-25 14:14:30 -* Number of recursive dependencies: 39 - -Run `revdepcheck::cloud_details(, "dynetNLAResistance")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘dynetNLAResistance-Ex.R’ failed - The error most likely occurred in: - - > ### Name: draw.graph - > ### Title: Draw a graph contains vertexs with sensitive or unsensitive - > ### label - > ### Aliases: draw.graph - > - > ### ** Examples - > - > dynet <- make.virtual.dynamic.network() - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: make.virtual.dynamic.network -> graph.data.frame -> make_empty_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - > test_check("dynetNLAResistance") - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Error ('testmain.R:5:3'): mvdn ────────────────────────────────────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─dynetNLAResistance::make.virtual.dynamic.network(prop.init = 0.03) at testmain.R:5:2 - 2. └─igraph::graph.data.frame(network, directed = F) - 3. └─igraph::make_empty_graph(n = 0, directed = directed) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘graphics’ - All declared Imports should be used. - ``` - -# dyngen - -
- -* Version: 1.0.5 -* GitHub: https://github.com/dynverse/dyngen -* Source code: https://github.com/cran/dyngen -* Date/Publication: 2022-10-12 15:22:39 UTC -* Number of recursive dependencies: 203 - -Run `revdepcheck::cloud_details(, "dyngen")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 14. │ │ └─base::withCallingHandlers(...) - 15. │ ├─purrr:::call_with_cleanup(...) - 16. │ └─dyngen (local) .f(start = .l[[1L]][[i]], stop = .l[[2L]][[i]], ...) - 17. │ └─dyngen:::.feature_network_sample_downstream(...) - 18. │ └─... %>% ... - 19. ├─igraph::graph_from_data_frame(., vertices = colnames(realnet)) - 20. │ └─igraph::make_empty_graph(n = 0, directed = directed) - 21. └─base::.handleSimpleError(...) - 22. └─purrr (local) h(simpleError(msg, call)) - 23. └─cli::cli_abort(...) - 24. └─rlang::abort(...) - - [ FAIL 1 | WARN 17 | SKIP 0 | PASS 64 ] - Error: Test failures - Execution halted - ``` - -# dynplot - -
- -* Version: 1.1.2 -* GitHub: https://github.com/dynverse/dynplot -* Source code: https://github.com/cran/dynplot -* Date/Publication: 2021-12-07 19:00:02 UTC -* Number of recursive dependencies: 134 - -Run `revdepcheck::cloud_details(, "dynplot")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘dynplot-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plot_dendro - > ### Title: Plot a trajectory as a dendrogram - > ### Aliases: plot_dendro - > ### Keywords: plot_trajectory - > - > ### ** Examples - > - > data(example_tree) - > plot_dendro(example_tree) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot_dendro ... as_graph_edge_df -> graph_from_data_frame -> make_empty_graph - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘plotting-a-toy.Rmd’ using rmarkdown - - Quitting from lines 40-41 [dendro] (plotting-a-toy.Rmd) - Error: processing vignette 'plotting-a-toy.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘plotting-a-toy.Rmd’ - - SUMMARY: processing the following file failed: - ‘plotting-a-toy.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# dynwrap - -
- -* Version: 1.2.3 -* GitHub: https://github.com/dynverse/dynwrap -* Source code: https://github.com/cran/dynwrap -* Date/Publication: 2023-03-01 17:10:02 UTC -* Number of recursive dependencies: 95 - -Run `revdepcheck::cloud_details(, "dynwrap")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘dynwrap-Ex.R’ failed - The error most likely occurred in: - - > ### Name: add_branch_trajectory - > ### Title: Construct a trajectory given its branch network and the - > ### pseudotime of the cells on one of the branches. - > ### Aliases: add_branch_trajectory - > ### Keywords: create_trajectory - > - > ### ** Examples - ... - > trajectory <- add_branch_trajectory( - + dataset, - + branch_network, - + branches, - + branch_progressions - + ) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: add_branch_trajectory ... -> ensure_igraph -> -> make_empty_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 1. ├─wrap_data(id = id, cell_ids = cell_ids) %>% ... at test-wrap_label_milestones.R:28:0 - 2. ├─dynwrap::add_trajectory(...) - 3. │ └─dynwrap:::changed_topology(dataset) - 4. │ └─dynwrap::classify_milestone_network(trajectory$milestone_network) - 5. │ └─... %>% simplify_igraph_network() - 6. ├─dynwrap::simplify_igraph_network(.) - 7. │ ├─base::paste0("#M#", igraph::V(gr)$name) - 8. │ └─igraph::V(gr) - 9. │ └─igraph:::ensure_igraph(graph) - 10. └─igraph::graph_from_data_frame(., directed = is_directed) - 11. └─igraph::make_empty_graph(n = 0, directed = directed) - - [ FAIL 108 | WARN 11 | SKIP 1 | PASS 137 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘create_ti_method_container.Rmd’ using rmarkdown - --- finished re-building ‘create_ti_method_container.Rmd’ - - --- re-building ‘create_ti_method_definition.Rmd’ using rmarkdown - running: bash -c 'chmod +x run.R' - --- finished re-building ‘create_ti_method_definition.Rmd’ - - --- re-building ‘create_ti_method_r.Rmd’ using rmarkdown - - ... - Quitting from lines 77-83 [unnamed-chunk-5] (create_ti_method_wrappers.Rmd) - Error: processing vignette 'create_ti_method_wrappers.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘create_ti_method_wrappers.Rmd’ - - SUMMARY: processing the following files failed: - ‘create_ti_method_r.Rmd’ ‘create_ti_method_wrappers.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# ecoCopula - -
- -* Version: 1.0.2 -* GitHub: NA -* Source code: https://github.com/cran/ecoCopula -* Date/Publication: 2022-03-02 00:20:02 UTC -* Number of recursive dependencies: 114 - -Run `revdepcheck::cloud_details(, "ecoCopula")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ecoCopula-Ex.R’ failed - The error most likely occurred in: - - > ### Name: cgr - > ### Title: Fitting Gaussian copula graphical lasso to co-occurrence data - > ### Aliases: cgr - > - > ### ** Examples - > - > abund <- spider$abund[,1:5] - > spider_mod <- stackedsdm(abund,~1, data = spider$x, ncores=2) - > spid_graph=cgr(spider_mod) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: cgr ... ensure_igraph -> -> graph.adjacency.dense - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Backtrace: - ▆ - 1. ├─testthat::expect_is(cgr(spider.mod), "cgr") at test_try.R:13:2 - 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") - 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) - 4. └─ecoCopula::cgr(spider.mod) - 5. └─ecoCopula:::graph_from_partial(part_cor) - 6. ├─igraph::as_data_frame(...) - 7. │ └─igraph:::ensure_igraph(x) - 8. └─igraph::graph_from_adjacency_matrix(...) - 9. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 77 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘the_basics.Rmd’ using rmarkdown - - Quitting from lines 117-123 [unnamed-chunk-10] (the_basics.Rmd) - Error: processing vignette 'the_basics.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘the_basics.Rmd’ - - SUMMARY: processing the following file failed: - ‘the_basics.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# ECoL - -
- -* Version: 0.3.0 -* GitHub: https://github.com/lpfgarcia/ECoL -* Source code: https://github.com/cran/ECoL -* Date/Publication: 2019-11-05 05:10:02 UTC -* Number of recursive dependencies: 41 - -Run `revdepcheck::cloud_details(, "ECoL")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ECoL-Ex.R’ failed - The error most likely occurred in: - - > ### Name: complexity - > ### Title: Extract the complexity measures from datasets - > ### Aliases: complexity complexity.default complexity.formula - > - > ### ** Examples - > - > ## Extract all complexity measures for classification task - > data(iris) - > complexity(Species ~ ., iris) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: complexity ... eval -> c.N1 -> -> graph.adjacency.dense - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 1. ├─ECoL::smoothness(speed ~ ., cars, measures = "S1", summary = "mean") at test_smoothness.R:5:2 - 2. └─ECoL:::smoothness.formula(speed ~ ., cars, measures = "S1", summary = "mean") - 3. └─ECoL:::smoothness.default(...) - 4. └─base::sapply(...) - 5. └─base::lapply(X = X, FUN = FUN, ...) - 6. └─ECoL (local) FUN(X[[i]], ...) - 7. ├─base::eval(call(paste("r", f, sep = "."), d = d, x = x, y = y)) - 8. │ └─base::eval(call(paste("r", f, sep = "."), d = d, x = x, y = y)) - 9. └─ECoL:::r.S1(d = ``, x = ``, y = ``) - 10. └─igraph::graph.adjacency(d, mode = "undirected", weighted = TRUE) - 11. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 6 | WARN 0 | SKIP 0 | PASS 83 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# econet - -
- -* Version: 1.0.0 -* GitHub: NA -* Source code: https://github.com/cran/econet -* Date/Publication: 2022-04-28 00:00:02 UTC -* Number of recursive dependencies: 64 - -Run `revdepcheck::cloud_details(, "econet")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘econet-Ex.R’ failed - The error most likely occurred in: - - > ### Name: horse_race - > ### Title: Compare the explanatory power of parameter.dependent network - > ### centrality measures with those of standard measures of network - > ### centrality. - > ### Aliases: horse_race - > - > ### ** Examples - ... - + data = db_model, unobservables = NULL, G = G_model, - + model = "model_A", estimation = "NLLS", - + start.val = c(alpha = -0.31055275, - + beta_dw = 1.50666982, - + beta_betweenness = 0.09666742, - + phi = 16.13035695)) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: horse_race ... compute_centralities -> -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘econet.tex’ using tex - Error: processing vignette 'econet.tex' failed with diagnostics: - Running 'texi2dvi' on 'econet.tex' failed. - LaTeX errors: - ! LaTeX Error: File `ae.sty' not found. - - Type X to quit or to proceed, - or enter new name. (Default extension: sty) - ... - l.55 \RequirePackage - [T1]{fontenc}^^M - ! ==> Fatal error occurred, no output PDF file produced! - --- failed re-building ‘econet.tex’ - - SUMMARY: processing the following file failed: - ‘econet.tex’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# EcoNetGen - -
- -* Version: 0.2.3 -* GitHub: https://github.com/cboettig/EcoNetGen -* Source code: https://github.com/cran/EcoNetGen -* Date/Publication: 2019-07-13 23:30:14 UTC -* Number of recursive dependencies: 85 - -Run `revdepcheck::cloud_details(, "EcoNetGen")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘spelling.R’ - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ▆ - 1. └─EcoNetGen:::netgen_v1() at test-netsample.R:10:2 - 2. └─igraph::graph_from_adjacency_matrix(M) - 3. └─igraph:::graph.adjacency.dense(...) - ── Error ('test-netsample.R:22:3'): net sample works with other settings ─────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─EcoNetGen:::netgen_v1() at test-netsample.R:22:2 - 2. └─igraph::graph_from_adjacency_matrix(M) - 3. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 7 | WARN 0 | SKIP 0 | PASS 10 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# economiccomplexity - -
- -* Version: 1.4.0 -* GitHub: https://github.com/pachadotdev/economiccomplexity -* Source code: https://github.com/cran/economiccomplexity -* Date/Publication: 2022-09-04 07:00:02 UTC -* Number of recursive dependencies: 95 - -Run `revdepcheck::cloud_details(, "economiccomplexity")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘economiccomplexity-Ex.R’ failed - The error most likely occurred in: - - > ### Name: projections - > ### Title: Projections of a Country-Product Network - > ### Aliases: projections - > ### Keywords: functions - > - > ### ** Examples - > - ... - + economiccomplexity_output$proximity$proximity_product, - + avg_links = 10, - + tolerance = 0.1 - + ) - computing product projection... - -------------------------------------------------- - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: projections ... graph_from_adjacency_matrix -> graph.adjacency.sparse -> make_empty_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ▆ - 1. ├─testthat::expect_warning(...) at test-projections.R:51:2 - 2. │ └─testthat:::quasi_capture(...) - 3. │ ├─testthat (local) .capture(...) - 4. │ │ └─base::withCallingHandlers(...) - 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) - 6. └─economiccomplexity::projections(...) - 7. └─economiccomplexity (local) trim_network(proximity_product, avg_links) - 8. └─igraph::graph_from_adjacency_matrix(...) - 9. └─igraph:::graph.adjacency.sparse(...) - 10. └─igraph::make_empty_graph(n = vc, directed = (mode == "directed")) - - [ FAIL 4 | WARN 0 | SKIP 0 | PASS 80 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘Rdpack’ - All declared Imports should be used. - ``` - -# econullnetr - -
- -* Version: 0.2.1 -* GitHub: https://github.com/ivaughan/econullnetr -* Source code: https://github.com/cran/econullnetr -* Date/Publication: 2021-06-02 08:10:05 UTC -* Number of recursive dependencies: 97 - -Run `revdepcheck::cloud_details(, "econullnetr")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘econullnetr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: generate_edgelist - > ### Title: Export null modelling results - > ### Aliases: generate_edgelist - > - > ### ** Examples - > - > set.seed(1234) - ... - + - + igraph::plot.igraph(net.1, layout = igraph::layout_in_circle, - + edge.color = igraph::E(net.1)$edge.cols, - + edge.width = sqrt(igraph::E(net.1)$obs.str), - + edge.arrow.size = .4) - + } - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: -> make_graph -> do.call -> - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘econullnetr-intro.Rmd’ using rmarkdown - - Quitting from lines 183-198 [unnamed-chunk-13] (econullnetr-intro.Rmd) - Error: processing vignette 'econullnetr-intro.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘econullnetr-intro.Rmd’ - - SUMMARY: processing the following file failed: - ‘econullnetr-intro.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# EcotoneFinder - -
- -* Version: 0.2.3 -* GitHub: NA -* Source code: https://github.com/cran/EcotoneFinder -* Date/Publication: 2021-02-16 23:00:02 UTC -* Number of recursive dependencies: 113 - -Run `revdepcheck::cloud_details(, "EcotoneFinder")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘EcotoneFinder-Ex.R’ failed - The error most likely occurred in: - - > ### Name: DistEco - > ### Title: Tools for internal data structure exploration - > ### Aliases: DistEco - > - > ### ** Examples - > - > ### Artificial data: - ... - > - > ## Network of species, with raw spinglass groups: - > DistEco(SyntheticTrial[,2:ncol(SyntheticTrial)], transpose = TRUE, - + plot = c("network"), spinglass = TRUE, run = 10, - + spinglass.groups = c("raw")) - Metric: 'inner_product'; comparing: 21 vectors. - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: DistEco ... graph.edgelist -> make_graph -> do.call -> - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘Rmisc’ ‘rlang’ - All declared Imports should be used. - ``` - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# ecpc - -
- -* Version: 3.1.1 -* GitHub: NA -* Source code: https://github.com/cran/ecpc -* Date/Publication: 2023-02-27 21:12:30 UTC -* Number of recursive dependencies: 145 - -Run `revdepcheck::cloud_details(, "ecpc")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ecpc-Ex.R’ failed - The error most likely occurred in: - - > ### Name: visualiseGroupset - > ### Title: Visualise a group set - > ### Aliases: visualiseGroupset - > - > ### ** Examples - > - > #groups without hierarchical constraints - > groupset <- list("Group1"=c(1:20),"Group2"=c(15,30)) - > visualiseGroupset(groupset,c(0.5,2)) - Loading required namespace: ggraph - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: visualiseGroupset -> -> make_empty_graph - Execution halted - ``` - -# edgebundle - -
- -* Version: 0.4.1 -* GitHub: https://github.com/schochastics/edgebundle -* Source code: https://github.com/cran/edgebundle -* Date/Publication: 2022-11-22 07:00:02 UTC -* Number of recursive dependencies: 55 - -Run `revdepcheck::cloud_details(, "edgebundle")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘edgebundle-Ex.R’ failed - The error most likely occurred in: - - > ### Name: tnss_smooth - > ### Title: Smooth a Steiner tree - > ### Aliases: tnss_smooth - > - > ### ** Examples - > - > xy <- cbind(state.center$x,state.center$y)[!state.name%in%c("Alaska","Hawaii"),] - ... - > xy_dummy <- tnss_dummies(xy,root = 4) - > gtree <- tnss_tree(cali2010,xy,xy_dummy,root = 4,gamma = 0.9) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: tnss_tree ... -> make_graph -> do.call -> - Execution halted - Error in .igraph.status("Free graph external pointer.\n") : - could not find function ".igraph.status" - Error in .igraph.status("Free graph external pointer.\n") : - could not find function ".igraph.status" - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Backtrace: - ▆ - 1. └─igraph::graph_from_edgelist(...) at test-bundle_test.R:2:2 - 2. └─igraph::make_graph(t(el), directed = directed) - 3. ├─base::do.call(old_graph, args) - 4. └─igraph (local) ``(``, directed = FALSE) - ── Error ('test-bundle_test.R:9:4'): stub bundle works ───────────────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─igraph::graph.star(10, "undirected") at test-bundle_test.R:9:3 - - [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 22 marked UTF-8 strings - ``` - -# edmcr - -
- -* Version: 0.2.0 -* GitHub: https://github.com/great-northern-diver/edmcr -* Source code: https://github.com/cran/edmcr -* Date/Publication: 2021-09-10 10:40:06 UTC -* Number of recursive dependencies: 46 - -Run `revdepcheck::cloud_details(, "edmcr")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘edmcr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: dpf - > ### Title: Dissimilarity Parameterization Formulation - > ### Aliases: dpf - > - > ### ** Examples - > - > set.seed(1337) - ... - + 4,1,0,5,NA,5, - + 3,NA,5,0,1,NA, - + 4,5,NA,1,0,5, - + 3,NA,5,NA,5,0),byrow=TRUE, nrow=6) - > - > edmc(D, method="dpf", d=3, toler=1e-8) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: edmc ... dpf -> mstUB -> graph.data.frame -> make_empty_graph - Execution halted - ``` - -# EDOIF - -
- -* Version: 0.1.3 -* GitHub: https://github.com/DarkEyes/EDOIF -* Source code: https://github.com/cran/EDOIF -* Date/Publication: 2021-03-28 06:20:05 UTC -* Number of recursive dependencies: 61 - -Run `revdepcheck::cloud_details(, "EDOIF")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘EDOIF-Ex.R’ failed - The error most likely occurred in: - - > ### Name: EDOIF - > ### Title: Empirical Distribution Ordering Inference Framework (EDOIF) - > ### Aliases: EDOIF - > - > ### ** Examples - > - > # Generate simulation data - ... - > simData1$Values<-c(simData1$Values,rnorm(nInv,mean=initMean+4*stepMean,sd=std) ) - > simData1$Group<-c(simData1$Group, rep(c("C5"),times=nInv) ) - > - > # Performing ordering infernce from simData1 - > - > resultObj<-EDOIF(simData1$Values,simData1$Group) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: EDOIF ... graph_from_adjacency_matrix -> graph.adjacency.dense - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘EDOIF_demo.Rmd’ using knitr - - Quitting from lines 34-45 [unnamed-chunk-1] (EDOIF_demo.Rmd) - Error: processing vignette 'EDOIF_demo.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘EDOIF_demo.Rmd’ - - SUMMARY: processing the following file failed: - ‘EDOIF_demo.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# eff2 - -
- -* Version: 1.0.1 -* GitHub: https://github.com/richardkwo/eff2 -* Source code: https://github.com/cran/eff2 -* Date/Publication: 2021-09-30 20:40:02 UTC -* Number of recursive dependencies: 115 - -Run `revdepcheck::cloud_details(, "eff2")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘eff2-Ex.R’ failed - The error most likely occurred in: - - > ### Name: estimateEffect - > ### Title: Estimate the total causal effect - > ### Aliases: estimateEffect - > - > ### ** Examples - > - > data("ex1") - > result <- estimateEffect(ex1$data, c(5,3), 7, ex1$amat.cpdag, bootstrap=TRUE) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: estimateEffect ... ensure_igraph -> graph.adjacency -> graph.adjacency.dense - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ▆ - 1. └─eff2::estimateEffect(ex1$data, .x, .y, ex1$amat.cpdag, bootstrap = FALSE) at test_ex1.R:26:4 - 2. └─eff2:::.estimateEffect(stats::cov(data), x, y, amat) - 3. └─eff2:::getBucketDecomp(x, y, amat) - 4. ├─base::stopifnot(pcalg::isValidGraph(amat, type = "pdag")) - 5. └─pcalg::isValidGraph(amat, type = "pdag") - 6. └─pcalg:::chordalComponents(corresp.cpdag) - 7. ├─igraph::graph.dfs(...) - 8. │ └─igraph:::ensure_igraph(graph) - 9. └─igraph::graph.adjacency(amat.undir, mode = "undirected") - 10. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 5 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘eff2-doc.Rmd’ using rmarkdown - - Quitting from lines 62-63 [unnamed-chunk-4] (eff2-doc.Rmd) - Error: processing vignette 'eff2-doc.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘eff2-doc.Rmd’ - - SUMMARY: processing the following file failed: - ‘eff2-doc.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# EGAnet - -
- -* Version: 1.2.3 -* GitHub: NA -* Source code: https://github.com/cran/EGAnet -* Date/Publication: 2022-09-05 15:50:02 UTC -* Number of recursive dependencies: 160 - -Run `revdepcheck::cloud_details(, "EGAnet")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘EGAnet-Ex.R’ failed - The error most likely occurred in: - - > ### Name: convert2igraph - > ### Title: Convert networks to 'igraph' - > ### Aliases: convert2igraph - > - > ### ** Examples - > - > convert2igraph(ega.wmt$network) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: convert2igraph - Execution halted - ``` - -# egor - -
- -* Version: 1.23.3 -* GitHub: https://github.com/tilltnet/egor -* Source code: https://github.com/cran/egor -* Date/Publication: 2023-03-16 04:40:02 UTC -* Number of recursive dependencies: 89 - -Run `revdepcheck::cloud_details(, "egor")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘egor-Ex.R’ failed - The error most likely occurred in: - - > ### Name: as_igraph - > ### Title: Convert 'egor' object to 'network' or 'igraph' objects - > ### Aliases: as_igraph as_igraph.nested_egor as.igraph.egor as_network - > ### as.network.egor - > - > ### ** Examples - > - > e <- make_egor(3, 22) - > as_igraph(e) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: as_igraph ... mapply -> -> -> make_empty_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 7. ├─egor:::rotate_to_equilibrium(.) - 8. ├─igraph::layout_as_star(.) - 9. │ └─igraph:::ensure_igraph(graph) - 10. ├─egor::as_igraph(.) - 11. └─egor:::as_igraph.egor(.) - 12. ├─egor::as_igraph(...) - 13. └─egor:::as_igraph.nested_egor(...) - 14. └─base::mapply(...) - 15. └─egor (local) ``(dots[[1L]][[1L]], dots[[2L]][[1L]]) - 16. └─igraph::graph.data.frame(...) - 17. └─igraph::make_empty_graph(n = 0, directed = directed) - - [ FAIL 48 | WARN 8 | SKIP 15 | PASS 152 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘egor_allbus.Rmd’ using rmarkdown - - Quitting from lines 179-181 [unnamed-chunk-11] (egor_allbus.Rmd) - Error: processing vignette 'egor_allbus.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘egor_allbus.Rmd’ - - --- re-building ‘qualtrics.Rmd’ using rmarkdown - ... - Quitting from lines 222-241 [unnamed-chunk-16] (using_egor.Rmd) - Error: processing vignette 'using_egor.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘using_egor.Rmd’ - - SUMMARY: processing the following files failed: - ‘egor_allbus.Rmd’ ‘using_egor.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# eicm - -
- -* Version: 1.0.3 -* GitHub: https://github.com/miguel-porto/eicm -* Source code: https://github.com/cran/eicm -* Date/Publication: 2023-05-05 23:10:02 UTC -* Number of recursive dependencies: 48 - -Run `revdepcheck::cloud_details(, "eicm")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘eicm-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plotNetworkFromMatrix - > ### Title: Plot graphs from adjacency matrices - > ### Aliases: plotNetworkFromMatrix - > - > ### ** Examples - > - > # generate two adjacency matrices with 15 species and 10 interactions - ... - > - > # set the species names - > rownames(A) <- rownames(B) <- - + colnames(A) <- colnames(B) <- paste0("S", 1:15) - > - > plotNetworkFromMatrix(A, B) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plotNetworkFromMatrix -> -> graph.adjacency.dense - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘eicm.Rmd’ using rmarkdown - - Quitting from lines 185-187 [unnamed-chunk-7] (eicm.Rmd) - Error: processing vignette 'eicm.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘eicm.Rmd’ - - SUMMARY: processing the following file failed: - ‘eicm.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘snow’ - All declared Imports should be used. - ``` - -# einet - -
- -* Version: 0.1.0 -* GitHub: https://github.com/travisbyrum/einet -* Source code: https://github.com/cran/einet -* Date/Publication: 2020-04-23 17:20:03 UTC -* Number of recursive dependencies: 67 - -Run `revdepcheck::cloud_details(, "einet")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘einet-Ex.R’ failed - The error most likely occurred in: - - > ### Name: causal_emergence - > ### Title: Causal Emergence - > ### Aliases: causal_emergence - > - > ### ** Examples - > - > graph <- matrix( - ... - + c(0.0, 0.0, 0.0, 1.0), - + c(0.0, 0.0, 0.0, 0.0) - + ), - + nrow = 4 - + ) %>% - + igraph::graph.adjacency(mode = "directed") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: %>% -> -> graph.adjacency.dense - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 5. └─einet:::effective_information.igraph(karate) - 6. ├─assertthat::assert_that(igraph::is.igraph(graph)) - 7. │ └─assertthat::see_if(..., env = env, msg = msg) - 8. │ ├─base::tryCatch(...) - 9. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) - 10. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) - 11. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) - 12. │ └─base::eval(assertion, env) - 13. │ └─base::eval(assertion, env) - 14. └─igraph::is.igraph(graph) - 15. └─igraph:::warn_version(graph) - - [ FAIL 5 | WARN 0 | SKIP 0 | PASS 0 ] - Error: Test failures - Execution halted - ``` - -# EmbedSOM - -
- -* Version: 2.1.2 -* GitHub: https://github.com/exaexa/EmbedSOM -* Source code: https://github.com/cran/EmbedSOM -* Date/Publication: 2022-07-05 10:20:02 UTC -* Number of recursive dependencies: 75 - -Run `revdepcheck::cloud_details(, "EmbedSOM")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘EmbedSOM-Ex.R’ failed - The error most likely occurred in: - - > ### Name: RandomMap - > ### Title: Create a map by randomly selecting points - > ### Aliases: RandomMap - > - > ### ** Examples - > - > d <- iris[,1:4] - ... - > EmbedSOM::PlotEmbed( - + EmbedSOM::EmbedSOM( - + data = d, - + map = EmbedSOM::RandomMap(d, 30, EmbedSOM::GraphCoords())), - + pch=19, clust=iris[,5] - + ) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: ... ensure_igraph -> -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘Matrix’ ‘Rtsne’ ‘uwot’ - All declared Imports should be used. - ``` - -# enviGCMS - -
- -* Version: 0.7.1 -* GitHub: https://github.com/yufree/enviGCMS -* Source code: https://github.com/cran/enviGCMS -* Date/Publication: 2023-02-06 08:42:34 UTC -* Number of recursive dependencies: 150 - -Run `revdepcheck::cloud_details(, "enviGCMS")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘enviGCMS-Ex.R’ failed - The error most likely occurred in: - - > ### Name: getalign2 - > ### Title: Align mass to charge ratio and/or retention time to remove - > ### redundancy - > ### Aliases: getalign2 - > - > ### ** Examples - > - > mz <- c(221.1171, 221.1170, 229.1546, 233.1497, 271.0790 ) - > rt <- c(590.8710, 587.3820, 102.9230, 85.8850, 313.8240) - > getalign2(mz,rt) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: getalign2 -> -> make_empty_graph - Execution halted - ``` - -# epicontacts - -
- -* Version: 1.1.3 -* GitHub: https://github.com/reconhub/epicontacts -* Source code: https://github.com/cran/epicontacts -* Date/Publication: 2023-03-28 13:10:12 UTC -* Number of recursive dependencies: 88 - -Run `revdepcheck::cloud_details(, "epicontacts")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘epicontacts-Ex.R’ failed - The error most likely occurred in: - - > ### Name: get_clusters - > ### Title: Assign cluster IDs to epicontacts data - > ### Aliases: get_clusters - > - > ### ** Examples - > - > if (require(outbreaks)) { - ... - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: get_clusters ... as.igraph.epicontacts -> -> make_empty_graph - Execution halted - Error in .igraph.status("Free graph external pointer.\n") : - could not find function ".igraph.status" - Error in .igraph.status("Free graph external pointer.\n") : - could not find function ".igraph.status" - Error in .igraph.status("Free graph external pointer.\n") : - could not find function ".igraph.status" - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘epicontacts.Rmd’ using rmarkdown - - Quitting from lines 128-130 [unnamed-chunk-9] (epicontacts.Rmd) - Error: processing vignette 'epicontacts.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘epicontacts.Rmd’ - - --- re-building ‘epicontacts_class.Rmd’ using rmarkdown - --- finished re-building ‘epicontacts_class.Rmd’ - - SUMMARY: processing the following file failed: - ‘epicontacts.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘colorspace’ - All declared Imports should be used. - ``` - -# EpiILMCT - -
- -* Version: 1.1.7 -* GitHub: https://github.com/waleedalmutiry/EpiILMCT -* Source code: https://github.com/cran/EpiILMCT -* Date/Publication: 2021-06-29 06:10:06 UTC -* Number of recursive dependencies: 8 - -Run `revdepcheck::cloud_details(, "EpiILMCT")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘EpiILMCT-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plot.contactnet - > ### Title: Plot the contact network of 'contactnet' object - > ### Aliases: plot.contactnet - > ### Keywords: plot - > - > ### ** Examples - > - ... - > net1<- contactnet(type = "powerlaw", location = loc, beta = 1.5, nu = 0.5) - > plot(net1) - > net2<- contactnet(type = "Cauchy", location = loc, beta = 0.5) - > plot(net2) - > net3<- contactnet(type = "random", num.id = 50, beta = 0.08) - > plot(net3) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot ... plot.contactnet -> -> do.call -> - Execution halted - ``` - -# epinetr - -
- -* Version: 0.96 -* GitHub: https://github.com/diondetterer/epinetr -* Source code: https://github.com/cran/epinetr -* Date/Publication: 2022-03-10 10:30:02 UTC -* Number of recursive dependencies: 87 - -Run `revdepcheck::cloud_details(, "epinetr")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘epinetr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: getEpiNet - > ### Title: Epistatic network retrieval. - > ### Aliases: getEpiNet - > - > ### ** Examples - > - > # Create population and attach an epistatic network - ... - Estimating heritability... - Estimating SNP effects... - > - > # Plot epistatic network - > epiNet <- getEpiNet(pop) - > plot(epiNet) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot ... plot.EpiNet -> -> do.call -> - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘epinetr-vignette.Rmd’ using rmarkdown - - Quitting from lines 36-51 [unnamed-chunk-2] (epinetr-vignette.Rmd) - Error: processing vignette 'epinetr-vignette.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘epinetr-vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘epinetr-vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# espadon - -
- -* Version: 1.3.2 -* GitHub: NA -* Source code: https://github.com/cran/espadon -* Date/Publication: 2023-04-04 07:50:06 UTC -* Number of recursive dependencies: 75 - -Run `revdepcheck::cloud_details(, "espadon")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘espadon-Ex.R’ failed - The error most likely occurred in: - - > ### Name: display.obj.links - > ### Title: Display patient objects links - > ### Aliases: display.obj.links - > - > ### ** Examples - > - > # loading of toy-patient objects - > patient <- toy.load.patient (dxyz = c (5, 5, 5), beam.nb = 1) - > display.obj.links (patient, group.by.connected.FoR = FALSE) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: display.obj.links ... graph_from_adjacency_matrix -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 8.0Mb - sub-directories of 1Mb or more: - libs 6.5Mb - ``` - -# ess - -
- -* Version: 1.1.2 -* GitHub: https://github.com/mlindsk/ess -* Source code: https://github.com/cran/ess -* Date/Publication: 2021-05-31 07:40:08 UTC -* Number of recursive dependencies: 9 - -Run `revdepcheck::cloud_details(, "ess")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ess-Ex.R’ failed - The error most likely occurred in: - - > ### Name: fit_graph - > ### Title: Fit a decomposable graphical model - > ### Aliases: fit_graph - > - > ### ** Examples - > - > - ... - - max: 2 - - min: 2 - - avg: 2 - - ------------------------- - > plot(g) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot ... plot.gengraph -> -> graph.adjacency.dense - Execution halted - ``` - -# etree - -
- -* Version: 0.1.0 -* GitHub: https://github.com/ricgbl/etree -* Source code: https://github.com/cran/etree -* Date/Publication: 2022-07-16 08:30:02 UTC -* Number of recursive dependencies: 128 - -Run `revdepcheck::cloud_details(, "etree")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘etree-Ex.R’ failed - The error most likely occurred in: - - > ### Name: dist_comp - > ### Title: Distances - > ### Aliases: dist_comp - > - > ### ** Examples - > - > - ... - > obj <- fda.usc::rproc2fdata(nobs, seq(0, 1, len = 100), sigma = 1) - > d <- dist_comp(obj) - Warning: executing %dopar% sequentially: no parallel backend registered - > - > ## Graphs - > obj <- lapply(1:nobs, function(j) igraph::sample_gnp(100, 0.2)) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: lapply -> FUN -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) - 7. └─etree::etree(resp_cls, covs_cls, split_type = "cluster") - 8. └─base::lapply(covariates, dist_comp) - 9. └─etree (local) FUN(X[[i]], ...) - 10. └─base::sapply(x, function(i) is.null(igraph::edge.attributes(i)$weight)) - 11. └─base::lapply(X = X, FUN = FUN, ...) - 12. └─etree (local) FUN(X[[i]], ...) - 13. └─igraph::edge.attributes(i) - 14. └─igraph:::ensure_igraph(graph) - 15. └─igraph::is_igraph(graph) - 16. └─igraph:::warn_version(graph) - - [ FAIL 28 | WARN 1 | SKIP 0 | PASS 37 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘etree-vignette-eforest.Rmd’ using rmarkdown - - Quitting from lines 148-170 [unnamed-chunk-4] (etree-vignette-eforest.Rmd) - Error: processing vignette 'etree-vignette-eforest.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘etree-vignette-eforest.Rmd’ - - --- re-building ‘etree-vignette.Rmd’ using rmarkdown - ... - Quitting from lines 142-164 [unnamed-chunk-4] (etree-vignette.Rmd) - Error: processing vignette 'etree-vignette.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘etree-vignette.Rmd’ - - SUMMARY: processing the following files failed: - ‘etree-vignette-eforest.Rmd’ ‘etree-vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# fairadapt - -
- -* Version: 0.2.5 -* GitHub: https://github.com/dplecko/fairadapt -* Source code: https://github.com/cran/fairadapt -* Date/Publication: 2023-03-23 15:02:04 UTC -* Number of recursive dependencies: 103 - -Run `revdepcheck::cloud_details(, "fairadapt")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘fairadapt-Ex.R’ failed - The error most likely occurred in: - - > ### Name: fairTwins - > ### Title: Fair Twin Inspection convenience function. - > ### Aliases: fairTwins - > - > ### ** Examples - > - > n_samp <- 200 - ... - > uni_ada <- fairadapt(score ~ ., - + train.data = head(uni_admission, n = n_samp), - + test.data = tail(uni_admission, n = n_samp), - + adj.mat = uni_adj, - + prot.attr = "gender" - + ) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: fairadapt ... graph_from_adjacency_matrix -> graph.adjacency.dense - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - • generics/fttrn_cts.csv - • generics/fttrn_lin.csv - • generics/fttrn_rf.csv - • generics/graph_cts.png - • generics/graph_lin.png - • generics/graph_rf.png - • generics/plot_cts.png - • generics/plot_lin.png - • generics/plot_rf.png - • generics/predi_cts.csv - • generics/predi_disc.csv - • generics/predi_lin.csv - • generics/predi_rf.csv - Error: Test failures - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘jss.Rmd’ using rmarkdown - Error: processing vignette 'jss.Rmd' failed with diagnostics: - pandoc version 2.7 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available). - --- failed re-building ‘jss.Rmd’ - - SUMMARY: processing the following file failed: - ‘jss.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# FAIRmaterials - -
- -* Version: 0.3.0 -* GitHub: NA -* Source code: https://github.com/cran/FAIRmaterials -* Date/Publication: 2023-02-11 07:10:07 UTC -* Number of recursive dependencies: 69 - -Run `revdepcheck::cloud_details(, "FAIRmaterials")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘FAIRmaterials-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plot_json_graph - > ### Title: Plot an igraph visualization of a JSON document - > ### Aliases: plot_json_graph - > - > ### ** Examples - > - > json_file <- '{ - ... - + "name": "Jane Doe", - + "jobTitle": "Professor", - + "telephone": "(425) 123-4567", - + "url": "http://www.janedoe.com"}' - > - > plot_json_graph(json_file) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot_json_graph -> -> make_empty_graph - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.5Mb - sub-directories of 1Mb or more: - doc 5.3Mb - ``` - -# fake - -
- -* Version: 1.4.0 -* GitHub: NA -* Source code: https://github.com/cran/fake -* Date/Publication: 2023-04-13 22:30:24 UTC -* Number of recursive dependencies: 41 - -Run `revdepcheck::cloud_details(, "fake")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘fake-Ex.R’ failed - The error most likely occurred in: - - > ### Name: ExpectedCommunities - > ### Title: Expected community structure - > ### Aliases: ExpectedCommunities - > - > ### ** Examples - > - > # Simulation parameters - ... - [1] 40 - > - > # Comparing observed and expected modularity - > igraph::modularity(igraph::graph_from_adjacency_matrix(theta, mode = "undirected"), - + membership = rep.int(1:length(pk), times = pk) - + ) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: -> -> graph.adjacency.dense - Execution halted - ``` - -# fastnet - -
- -* Version: 1.0.0 -* GitHub: https://github.com/networkgroupR/fastnet -* Source code: https://github.com/cran/fastnet -* Date/Publication: 2020-12-01 07:40:02 UTC -* Number of recursive dependencies: 29 - -Run `revdepcheck::cloud_details(, "fastnet")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘fastnet-Ex.R’ failed - The error most likely occurred in: - - > ### Name: from.adjacency - > ### Title: Adjacency Matrix to 'fastnet' - > ### Aliases: from.adjacency - > - > ### ** Examples - > - > adj.mat <- matrix(c(0,1,0,0,1,0,0,0,0,0,0,1,0,0,1,0), nrow = 4, ncol = 4) - > g <- from.adjacency(adj.mat) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: from.adjacency ... ensure_igraph -> -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# fbnet - -
- -* Version: 1.0.2 -* GitHub: https://github.com/MarsicoFL/fbnet -* Source code: https://github.com/cran/fbnet -* Date/Publication: 2023-02-27 22:02:35 UTC -* Number of recursive dependencies: 10 - -Run `revdepcheck::cloud_details(, "fbnet")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘fbnet-Ex.R’ failed - The error most likely occurred in: - - > ### Name: buildBN - > ### Title: buildBN: a function for building the bayesian network. - > ### Aliases: buildBN - > - > ### ** Examples - > - > bnet <- buildBN(pbn,QP=3) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: buildBN -> graph_from_data_frame -> make_empty_graph - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘Rsolnp’ ‘assertthat’ ‘utils’ - All declared Imports should be used. - ``` - -# FCMapper - -
- -* Version: 1.1 -* GitHub: NA -* Source code: https://github.com/cran/FCMapper -* Date/Publication: 2016-02-12 07:40:47 -* Number of recursive dependencies: 7 - -Run `revdepcheck::cloud_details(, "FCMapper")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘FCMapper-Ex.R’ failed - The error most likely occurred in: - - > ### Name: graph.fcm - > ### Title: Fuzzy cognitive map graph - > ### Aliases: graph.fcm - > - > ### ** Examples - > - > - ... - > matrix[7,] = c(0,0,0,-0.5,0,0,1) - > concept.names = c("A","B","C","D","E","F","G") - > - > results = nochanges.scenario(matrix,iter=25,concept.names) - > - > graph.fcm(matrix,concept.sizes=results$Equilibrium_value,concept.names) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: graph.fcm -> -> graph.adjacency.dense - Execution halted - ``` - -# FindIt - -
- -* Version: 1.2.0 -* GitHub: NA -* Source code: https://github.com/cran/FindIt -* Date/Publication: 2019-11-20 21:50:02 UTC -* Number of recursive dependencies: 60 - -Run `revdepcheck::cloud_details(, "FindIt")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘FindIt-Ex.R’ failed - The error most likely occurred in: - - > ### Name: CausalANOVA - > ### Title: Estimating the AMEs and AMIEs with the CausalANOVA. - > ### Aliases: CausalANOVA - > - > ### ** Examples - > - > - ... - 1 newRecordF promise - 2 newRecordF coeth_voting - 3 promise relevantdegree - - ***** Collapsing ***** - > summary(fit.r2) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: summary ... graph_from_adjacency_matrix -> graph.adjacency.dense - Execution halted - ``` - -# fnets - -
- -* Version: 0.1.3 -* GitHub: NA -* Source code: https://github.com/cran/fnets -* Date/Publication: 2023-06-08 15:10:02 UTC -* Number of recursive dependencies: 59 - -Run `revdepcheck::cloud_details(, "fnets")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. ├─base::plot(out, type = "pc", display = "network") at test-omega.R:21:0 - 2. └─fnets:::plot.fnets(out, type = "pc", display = "network") - 3. ├─base::suppressWarnings(...) - 4. │ └─base::withCallingHandlers(...) - 5. ├─fnets::network(...) - 6. └─fnets:::network.fnets(...) - 7. └─igraph::graph_from_adjacency_matrix(...) - 8. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 1 | WARN 3 | SKIP 16 | PASS 2 ] - Error: Test failures - Execution halted - ``` - -# foodingraph - -
- -* Version: 0.1.0 -* GitHub: https://github.com/vgasque/foodingraph -* Source code: https://github.com/cran/foodingraph -* Date/Publication: 2019-10-06 11:30:08 UTC -* Number of recursive dependencies: 60 - -Run `revdepcheck::cloud_details(, "foodingraph")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘foodingraph-Ex.R’ failed - The error most likely occurred in: - - > ### Name: graph_from_links_nodes - > ### Title: Display a graph from a list of links and nodes - > ### Aliases: graph_from_links_nodes - > - > ### ** Examples - > - > adj_matrix <- cor(iris[,-5]) - > legend <- data.frame(name = colnames(iris[,-5]), - + title = colnames(iris[,-5])) - > graph_iris <- links_nodes_from_mat(adj_matrix, legend) - > graph_from_links_nodes(graph_iris, main_title = "Iris graph") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: graph_from_links_nodes -> graph_from_data_frame -> make_empty_graph - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘grid’ - All declared Imports should be used. - ``` - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# ForestGapR - -
- -* Version: 0.1.7 -* GitHub: NA -* Source code: https://github.com/cran/ForestGapR -* Date/Publication: 2023-03-31 20:50:18 UTC -* Number of recursive dependencies: 50 - -Run `revdepcheck::cloud_details(, "ForestGapR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ForestGapR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: GapSPDF - > ### Title: Forest Canopy Gaps as Spatial Polygons - > ### Aliases: GapSPDF - > - > ### ** Examples - > - > # Loading raster and viridis libraries - ... - > # set height thresholds (e.g. 10 meters) - > threshold <- 10 - > size <- c(1, 10^4) # m2 - > - > # Detecting forest gaps - > gaps_duc <- getForestGaps(chm_layer = ALS_CHM_DUC, threshold = threshold, size = size) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: getForestGaps ... ensure_igraph -> -> do.call -> - Execution halted - ``` - -# forestRK - -
- -* Version: 0.0-5 -* GitHub: NA -* Source code: https://github.com/cran/forestRK -* Date/Publication: 2019-07-19 10:50:02 UTC -* Number of recursive dependencies: 57 - -Run `revdepcheck::cloud_details(, "forestRK")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘forestRK-Ex.R’ failed - The error most likely occurred in: - - > ### Name: draw.treeRK - > ### Title: Creates a 'igraph' plot of a 'rktree' - > ### Aliases: draw.treeRK - > ### Keywords: plot treeRK tree.plot - > - > ### ** Examples - > - ... - > - > # Plot the tree - > draw.treeRK(tree.entropy, y.factor.levels, font="Times", - + node.colour = "black", text.colour = "white", text.size = 0.7, - + tree.vertex.size = 100, tree.title = "Decision Tree", - + title.colour = "dark green") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: draw.treeRK -> make_empty_graph - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘pkgKitten’ - All declared Imports should be used. - ``` - -# fossilbrush - -
- -* Version: 1.0.3 -* GitHub: NA -* Source code: https://github.com/cran/fossilbrush -* Date/Publication: 2022-07-21 15:50:02 UTC -* Number of recursive dependencies: 40 - -Run `revdepcheck::cloud_details(, "fossilbrush")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘fossilbrush-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plot_taxa - > ### Title: plot_taxa - > ### Aliases: plot_taxa - > - > ### ** Examples - > - > # load dataset - > data("brachios") - > # define ranks in dataset - > b_ranks <- c("phylum", "class", "order", "family", "genus") - > # plot taxon - > plot_taxa(brachios, "Atrypa", trank = "genus", ranks = b_ranks, mode = "parent") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot_taxa ... -> make_graph -> do.call -> - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘fossilbrush_vignette.Rmd’ using rmarkdown - - Quitting from lines 92-99 [unnamed-chunk-5] (fossilbrush_vignette.Rmd) - Error: processing vignette 'fossilbrush_vignette.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘fossilbrush_vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘fossilbrush_vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 31 marked UTF-8 strings - ``` - -# FrF2 - -
- -* Version: 2.3 -* GitHub: NA -* Source code: https://github.com/cran/FrF2 -* Date/Publication: 2023-05-07 23:00:02 UTC -* Number of recursive dependencies: 34 - -Run `revdepcheck::cloud_details(, "FrF2")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘FrF2-Ex.R’ failed - The error most likely occurred in: - - > ### Name: CIG - > ### Title: Clear interactions graph from catlg entry - > ### Aliases: CIGstatic CIG gen2CIG - > ### Keywords: design - > - > ### ** Examples - > - ... - > ##D ## look up its id number in the title bar of the graph window and use it for id - > ##D par(xpd=TRUE) - > ##D CIGstatic(ex.CIG, id=1) - > ## End(Not run) - > - > graph1 <- CIG("9-4.2", plot=FALSE) ### create graph object from design name - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: CIG -> graph.empty - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘FrF2test.R’ - Running the tests in ‘tests/FrF2test.R’ failed. - Last 13 lines of output: - ..$ replications : num 1 - ..$ repeat.only : logi FALSE - ..$ randomize : logi FALSE - ..$ seed : NULL - ..$ creator : language FrF2(64, 7, blocks = 32, alias.block.2fis = TRUE, randomize = FALSE) - > - > ## godolphin with estimable - > str.wover(FrF2(64,9,blocks=16,factor.names=Letters[15:23], - + estimable=compromise(9,3)$requirement, - + alias.block.2fis=TRUE,randomize=FALSE)) - a clear design requires at least 32 runs - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: str.wover -> FrF2 -> estimable -> mapcalc -> graph.empty - Execution halted - ``` - -# fssemR - -
- -* Version: 0.1.8 -* GitHub: https://github.com/Ivis4ml/fssemR -* Source code: https://github.com/cran/fssemR -* Date/Publication: 2022-02-11 13:00:02 UTC -* Number of recursive dependencies: 88 - -Run `revdepcheck::cloud_details(, "fssemR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘fssemR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: fssemR - > ### Title: Solving Sparse Structural Equation Model - > ### Aliases: fssemR package-fssemR - > - > ### ** Examples - > - > seed = as.numeric(Sys.time()) - ... - > Ns = 1 # sparse ratio - > sigma2 = 0.01 # sigma2 - > set.seed(seed) - > library(fssemR) - > data = randomFSSEMdata(n = N, p = Ng, k = Nk, sparse = Ns, df = 0.3, sigma2 = sigma2, - + u = 5, type = "DG", nhub = 1, dag = TRUE) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: randomFSSEMdata ... graph_from_adjacency_matrix -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘fssemR.Rmd’ using rmarkdown - - Quitting from lines 45-57 [unnamed-chunk-2] (fssemR.Rmd) - Error: processing vignette 'fssemR.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘fssemR.Rmd’ - - SUMMARY: processing the following file failed: - ‘fssemR.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -* checking installed package size ... NOTE - ``` - installed size is 18.2Mb - sub-directories of 1Mb or more: - libs 17.5Mb - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘qpdf’ - All declared Imports should be used. - ``` - -# gDefrag - -
- -* Version: 0.3 -* GitHub: NA -* Source code: https://github.com/cran/gDefrag -* Date/Publication: 2020-09-02 20:00:03 UTC -* Number of recursive dependencies: 12 - -Run `revdepcheck::cloud_details(, "gDefrag")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘gDefrag-Ex.R’ failed - The error most likely occurred in: - - > ### Name: prioritize - > ### Title: Prioritizing connectivity corridors - > ### Aliases: prioritize - > - > ### ** Examples - > - > data(road_P) - ... - > - > #Prioritize - > out3 <- prioritize(nodes = out1, edges = out2, - + method = "value")#Raster value - > out4 <- prioritize(nodes = out1, edges = out2, - + method = "between")#Betweenness - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: prioritize -> graph_from_data_frame -> make_empty_graph - Execution halted - ``` - -# gemtc - -
- -* Version: 1.0-1 -* GitHub: https://github.com/gertvv/gemtc -* Source code: https://github.com/cran/gemtc -* Date/Publication: 2021-05-14 23:20:02 UTC -* Number of recursive dependencies: 58 - -Run `revdepcheck::cloud_details(, "gemtc")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘gemtc-Ex.R’ failed - The error most likely occurred in: - - > ### Name: atrialFibrillation - > ### Title: Prevention of stroke in atrial fibrillation patients - > ### Aliases: atrialFibrillation - > - > ### ** Examples - > - > # Build a model similar to Model 4(b) from Cooper et al. (2009): - ... - + classes=classes) - > - > model <- mtc.model(atrialFibrillation, - + type="regression", - + regressor=regressor, - + om.scale=10) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: mtc.model ... ensure_igraph -> mtc.network.graph -> graph.create -> graph.empty - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘test.R’ - Running the tests in ‘tests/test.R’ failed. - Last 13 lines of output: - 5. └─igraph::graph.empty() - ── Error ('test-unit-relative.effect.table.R:5:3'): it works for the smoking example ── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─gemtc::relative.effect.table(smoking_result) at test-unit-relative.effect.table.R:5:2 - 2. ├─base::as.matrix(...) - 3. └─gemtc::relative.effect(...) - 4. └─gemtc:::spanning.tree.mtc.result(result) - 5. └─gemtc:::graph.create(...) - 6. └─igraph::graph.empty() - - [ FAIL 48 | WARN 0 | SKIP 0 | PASS 221 ] - Error: Test failures - Execution halted - ``` - -# genscore - -
- -* Version: 1.0.2.1 -* GitHub: https://github.com/sqyu/genscore -* Source code: https://github.com/cran/genscore -* Date/Publication: 2023-05-12 06:57:06 UTC -* Number of recursive dependencies: 45 - -Run `revdepcheck::cloud_details(, "genscore")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘genscore-Ex.R’ failed - The error most likely occurred in: - - > ### Name: cov_cons - > ### Title: Random generator of inverse covariance matrices. - > ### Aliases: cov_cons - > - > ### ** Examples - > - > p <- 100 - > K1 <- cov_cons("random", p, seed = 1, spars = 0.05, eig = 0.1) - > K2 <- cov_cons("sub", p, seed = 2, spars = 0.5, eig = 0.1, subgraphs=10) - > K3 <- cov_cons("er", p, seed = 3, spars = 0.05, eig = 0.1) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: cov_cons ... as.matrix -> -> ensure_igraph -> - Execution halted - ``` - -# geonetwork - -
- -* Version: 0.5.0 -* GitHub: NA -* Source code: https://github.com/cran/geonetwork -* Date/Publication: 2023-04-14 08:30:02 UTC -* Number of recursive dependencies: 156 - -Run `revdepcheck::cloud_details(, "geonetwork")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘geonetwork-Ex.R’ failed - The error most likely occurred in: - - > ### Name: geonetwork - > ### Title: Create geographic networks - > ### Aliases: geonetwork - > - > ### ** Examples - > - > e <- data.frame(from = c("A", "A"), to = c("B", "C")) - > n <- data.frame(id = LETTERS[1:3], x = c(0, 0, 1), y = c(0, 1, 0)) - > geonetwork(e, n) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: geonetwork -> -> make_empty_graph - Execution halted - ``` - -# ggdag - -
- -* Version: 0.2.10 -* GitHub: https://github.com/r-causal/ggdag -* Source code: https://github.com/cran/ggdag -* Date/Publication: 2023-05-28 23:30:02 UTC -* Number of recursive dependencies: 102 - -Run `revdepcheck::cloud_details(, "ggdag")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ggdag-Ex.R’ failed - The error most likely occurred in: - - > ### Name: activate_collider_paths - > ### Title: Activate paths opened by stratifying on a collider - > ### Aliases: activate_collider_paths - > - > ### ** Examples - > - > dag <- dagify(m ~ x + y, x ~ y) - > - > collided_dag <- activate_collider_paths(dag, adjust_for = "m") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: activate_collider_paths ... tidy_dagitty -> %>% -> -> make_empty_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘spelling.R’ - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 7. │ └─testthat::source_dir(path, "^helper.*\\.[rR]$", env = env, wrap = FALSE) - 8. │ └─base::lapply(...) - 9. │ └─testthat (local) FUN(X[[i]], ...) - 10. │ └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap) - 11. │ ├─base::withCallingHandlers(...) - 12. │ └─base::eval(exprs, env) - 13. │ └─base::eval(exprs, env) - 14. │ └─ggdag::tidy_dagitty(test_dag) at tests/testthat/helper-load_dag.R:13:0 - 15. │ └─... %>% ... - 16. ├─igraph::graph_from_data_frame(., vertices = names(.dagitty)) - 17. │ └─igraph::make_empty_graph(n = 0, directed = directed) - 18. └─base::.handleSimpleError(...) - 19. └─testthat (local) h(simpleError(msg, call)) - 20. └─rlang::abort(...) - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘bias-structures.Rmd’ using rmarkdown - - Quitting from lines 44-46 [unnamed-chunk-1] (bias-structures.Rmd) - Error: processing vignette 'bias-structures.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘bias-structures.Rmd’ - - --- re-building ‘intro-to-dags.Rmd’ using rmarkdown - - ... - Quitting from lines 35-41 [dagitty] (intro-to-ggdag.Rmd) - Error: processing vignette 'intro-to-ggdag.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘intro-to-ggdag.Rmd’ - - SUMMARY: processing the following files failed: - ‘bias-structures.Rmd’ ‘intro-to-dags.Rmd’ ‘intro-to-ggdag.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# ggenealogy - -
- -* Version: 1.0.1 -* GitHub: NA -* Source code: https://github.com/cran/ggenealogy -* Date/Publication: 2020-03-04 09:40:14 UTC -* Number of recursive dependencies: 82 - -Run `revdepcheck::cloud_details(, "ggenealogy")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ggenealogy-Ex.R’ failed - The error most likely occurred in: - - > ### Name: getBasicStatistics - > ### Title: Determine basic statistics of the graph object - > ### Aliases: getBasicStatistics - > - > ### ** Examples - > - > data(sbGeneal) - > ig <- dfToIG(sbGeneal) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: dfToIG -> -> make_empty_graph - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘ggenealogy.Rnw’ - ... - - for iGraph information - - - - > ig <- dfToIG(sbGeneal) - - When sourcing ‘ggenealogy.R’: - Error: could not find function ".igraph.status" - Execution halted - - ‘ggenealogy.Rnw’ using ‘UTF-8’... failed - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘tibble’ - All declared Imports should be used. - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 2356 marked UTF-8 strings - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘ggenealogy.Rnw’ using Sweave - dfToIG package:ggenealogy R Documentation - - _P_r_o_c_e_s_s _t_h_e _g_e_n_e_a_l_o_g_y _g_r_a_p_h - - _D_e_s_c_r_i_p_t_i_o_n: - - Processes the genealogy into an igraph object with appropriate - vertex information, graph type, and edge weights. - ... - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - - --- failed re-building ‘ggenealogy.Rnw’ - - SUMMARY: processing the following file failed: - ‘ggenealogy.Rnw’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# ggflowchart - -
- -* Version: 1.0.0 -* GitHub: NA -* Source code: https://github.com/cran/ggflowchart -* Date/Publication: 2023-05-11 10:10:05 UTC -* Number of recursive dependencies: 60 - -Run `revdepcheck::cloud_details(, "ggflowchart")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ggflowchart-Ex.R’ failed - The error most likely occurred in: - - > ### Name: ggflowchart - > ### Title: Generate a flowchart in ggplot2 - > ### Aliases: ggflowchart - > - > ### ** Examples - > - > data <- tibble::tibble(from = c("A", "A", "A", "B", "C", "F"), to = c("B", "C", "D", "E", "F", "G")) - > ggflowchart(data) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: ggflowchart -> get_layout -> -> make_empty_graph - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘decision-tree-example.Rmd’ using rmarkdown - - Quitting from lines 64-65 [flowchart] (decision-tree-example.Rmd) - Error: processing vignette 'decision-tree-example.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘decision-tree-example.Rmd’ - - --- re-building ‘minimal-example.Rmd’ using rmarkdown - ... - Quitting from lines 31-32 [flowchart] (minimal-example.Rmd) - Error: processing vignette 'minimal-example.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘minimal-example.Rmd’ - - SUMMARY: processing the following files failed: - ‘decision-tree-example.Rmd’ ‘minimal-example.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# ggm - -
- -* Version: 2.5 -* GitHub: NA -* Source code: https://github.com/cran/ggm -* Date/Publication: 2020-02-16 14:00:02 UTC -* Number of recursive dependencies: 9 - -Run `revdepcheck::cloud_details(, "ggm")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ggm-Ex.R’ failed - The error most likely occurred in: - - > ### Name: AG - > ### Title: Ancestral graph - > ### Aliases: AG - > ### Keywords: graphs ancestral graph directed acyclic graph marginalization - > ### and conditioning - > - > ### ** Examples - ... - + 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, - + 1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0, - + 0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0),16,16,byrow=TRUE) - > M <- c(3,5,6,15,16) - > C <- c(4,7) - > AG(ex, M, C, plot = TRUE) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: AG -> plotfun -> graph -> do.call -> - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘graph’ - All declared Imports should be used. - ``` - -# ggnetwork - -
- -* Version: 0.5.12 -* GitHub: https://github.com/briatte/ggnetwork -* Source code: https://github.com/cran/ggnetwork -* Date/Publication: 2023-03-06 20:00:02 UTC -* Number of recursive dependencies: 73 - -Run `revdepcheck::cloud_details(, "ggnetwork")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ── Error ('test-fortify-network.R:13:1'): (code run outside of `test_that()`) ── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─igraph::random.graph.game(n = 1, p.or.m = 0) at test-fortify-network.R:13:0 - ── Error ('test-ggnetwork.R:7:3'): ggnetwork works ───────────────────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─igraph::graph_from_adjacency_matrix(as.matrix(emon[[1]])) at test-ggnetwork.R:7:2 - 2. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 3 | WARN 0 | SKIP 0 | PASS 25 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘sna’ ‘utils’ - All declared Imports should be used. - ``` - -# ggraph - -
- -* Version: 2.1.0 -* GitHub: https://github.com/thomasp85/ggraph -* Source code: https://github.com/cran/ggraph -* Date/Publication: 2022-10-09 20:33:19 UTC -* Number of recursive dependencies: 98 - -Run `revdepcheck::cloud_details(, "ggraph")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ggraph-Ex.R’ failed - The error most likely occurred in: - - > ### Name: autograph - > ### Title: Quickplot wrapper for networks - > ### Aliases: autograph autograph.default - > - > ### ** Examples - > - > library(tidygraph) - ... - - filter - - > gr <- create_notable('herschel') %>% - + mutate(class = sample(letters[1:3], n(), TRUE)) %E>% - + mutate(weight = runif(n())) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: %E>% ... create_notable -> as_tbl_graph -> make_graph -> make_famous_graph - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘Edges.Rmd’ using rmarkdown - - Quitting from lines 40-75 [unnamed-chunk-2] (Edges.Rmd) - Error: processing vignette 'Edges.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘Edges.Rmd’ - - --- re-building ‘Layouts.Rmd’ using rmarkdown - - ... - Quitting from lines 67-77 [unnamed-chunk-2] (tidygraph.Rmd) - Error: processing vignette 'tidygraph.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘tidygraph.Rmd’ - - SUMMARY: processing the following files failed: - ‘Edges.Rmd’ ‘Layouts.Rmd’ ‘Nodes.Rmd’ ‘tidygraph.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 10.7Mb - sub-directories of 1Mb or more: - doc 3.5Mb - libs 5.9Mb - ``` - -# ghypernet - -
- -* Version: 1.1.0 -* GitHub: NA -* Source code: https://github.com/cran/ghypernet -* Date/Publication: 2021-10-15 13:30:05 UTC -* Number of recursive dependencies: 98 - -Run `revdepcheck::cloud_details(, "ghypernet")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ghypernet-Ex.R’ failed - The error most likely occurred in: - - > ### Name: CreateIgGraphs - > ### Title: Convert a list of adjacency matrices to a list of igraph graphs. - > ### Aliases: CreateIgGraphs - > - > ### ** Examples - > - > data('adj_karate') - > adj_list <- list(adj_karate) - > glist <- CreateIgGraphs(adj_list, FALSE, FALSE) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: CreateIgGraphs -> lapply -> FUN -> graph.adjacency.dense - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘Significantlinks.Rmd’ using rmarkdown - --- finished re-building ‘Significantlinks.Rmd’ - - --- re-building ‘Tutorial_NRM.Rmd’ using rmarkdown - - Quitting from lines 643-649 [unnamed-chunk-39] (Tutorial_NRM.Rmd) - Error: processing vignette 'Tutorial_NRM.Rmd' failed with diagnostics: - No layout function defined for objects of class - ... - --- failed re-building ‘Tutorial_NRM.Rmd’ - - --- re-building ‘tutorial.Rmd’ using rmarkdown - --- finished re-building ‘tutorial.Rmd’ - - SUMMARY: processing the following file failed: - ‘Tutorial_NRM.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘methods’ - All declared Imports should be used. - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 11 marked UTF-8 strings - ``` - -# GISSB - -
- -* Version: 1.1 -* GitHub: NA -* Source code: https://github.com/cran/GISSB -* Date/Publication: 2023-01-10 18:33:14 UTC -* Number of recursive dependencies: 114 - -Run `revdepcheck::cloud_details(, "GISSB")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘GISSB-Ex.R’ failed - The error most likely occurred in: - - > ### Name: path_leaflet - > ### Title: Visualize the shortest path with Leaflet - > ### Aliases: path_leaflet - > - > ### ** Examples - > - > - ... - > shortest_path_igraph(from_node_ID = 25, - + to_node_ID = 33, - + unit = "minutes", - + path = TRUE, - + graph_object = graph_sampledata) %>% - + path_leaflet(graph_object = graph_sampledata) - Error in .igraph.status("Restore graph external pointer.\n") : - could not find function ".igraph.status" - Calls: %>% ... -> ensure_igraph -> is_igraph -> warn_version - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 12. │ └─base::eval(exprs, env) - 13. │ └─base::eval(exprs, env) - 14. │ └─GISSB::vegnett_to_R(...) at tests/testthat/helper_files.R:4:0 - 15. │ └─tidygraph::tbl_graph(...) - 16. │ ├─tidygraph::as_tbl_graph(...) - 17. │ └─tidygraph:::as_tbl_graph.list(...) - 18. │ └─tidygraph:::as_graph_node_edge(x, directed = directed, node_key = node_key) - 19. │ └─igraph::graph_from_edgelist(as.matrix(edges[, 1:2]), directed = directed) - 20. │ └─igraph::make_graph(t(el), directed = directed) - 21. │ ├─base::do.call(old_graph, args) - 22. │ └─igraph (local) ``(``, directed = TRUE) - 23. └─base::.handleSimpleError(...) - 24. └─testthat (local) h(simpleError(msg, call)) - 25. └─rlang::abort(...) - Execution halted - ``` - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 866 marked UTF-8 strings - ``` - -# gmat - -
- -* Version: 0.2.2 -* GitHub: https://github.com/gherardovarando/gmat -* Source code: https://github.com/cran/gmat -* Date/Publication: 2020-08-30 01:00:18 UTC -* Number of recursive dependencies: 55 - -Run `revdepcheck::cloud_details(, "gmat")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘gmat-Ex.R’ failed - The error most likely occurred in: - - > ### Name: dag-constrained correlation matrices - > ### Title: Simulation of correlation matrices - > ### Aliases: 'dag-constrained correlation matrices' chol_mh chol_iid - > - > ### ** Examples - > - > ## Cholesky sampling via Metropolis-Hastings - ... - [2,] -0.7183196 1.0000000 0.9953518 - [3,] -0.7542058 0.9953518 1.0000000 - - > - > # Generate a matrix with a percentage of zeros - > chol_mh(d = 0.5) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: chol_mh -> rgraph -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─gmat::rgraph(p = p, d = d) at test_utils.R:98:2 - 2. └─igraph::sample_gnp(n = p, p = d) - ── Error ('test_utils.R:113:3'): the oriented dag does not contain v-structures ── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─gmat::rgraph(p = p, d = d) at test_utils.R:113:2 - 2. └─igraph::sample_gnp(n = p, p = d) - - [ FAIL 16 | WARN 0 | SKIP 0 | PASS 45 ] - Error: Test failures - Execution halted - ``` - -# GMPro - -
- -* Version: 0.1.0 -* GitHub: NA -* Source code: https://github.com/cran/GMPro -* Date/Publication: 2020-06-25 14:00:02 UTC -* Number of recursive dependencies: 40 - -Run `revdepcheck::cloud_details(, "GMPro")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘GMPro-Ex.R’ failed - The error most likely occurred in: - - > ### Name: DP_SBM - > ### Title: Degree profile graph matching with community detection. - > ### Aliases: DP_SBM - > - > ### ** Examples - > - > ### Here we use graphs under stochastic block model(SBM). - ... - > dB[lower.tri(dB)] = t(dB)[lower.tri(dB)] - > B1 = G*dB - > indB = sample(1:n, n, replace = FALSE) - > labelB = l[indB] - > B = B1[indB, indB] - > DP_SBM(A = A, B = B, K = 2, fun = "EEpost", rep = 10, d = 3) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: DP_SBM ... graph.incidence -> graph.incidence.dense -> make_empty_graph - Execution halted - ``` - -## In both - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# GOxploreR - -
- -* Version: 1.2.6 -* GitHub: NA -* Source code: https://github.com/cran/GOxploreR -* Date/Publication: 2022-04-19 14:02:33 UTC -* Number of recursive dependencies: 114 - -Run `revdepcheck::cloud_details(, "GOxploreR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘GOxploreR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: prioritizedGOTerms - > ### Title: prioritization of a lists of GO-terms - > ### Aliases: prioritizedGOTerms - > - > ### ** Examples - > - > - > Terms <-c("GO:0000278", "GO:0006414","GO:0022403","GO:0006415","GO:0006614", - + "GO:0045047","GO:0022411","GO:0001775","GO:0046649","GO:045321") - > prioritizedGOTerms(Terms, organism = "Human", sp=TRUE, domain = "BP") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: prioritizedGOTerms ... graph.edgelist -> make_graph -> do.call -> - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘GOxploreR.Rmd’ using rmarkdown - - Quitting from lines 355-366 [unnamed-chunk-16] (GOxploreR.Rmd) - Error: processing vignette 'GOxploreR.Rmd' failed with diagnostics: - error in evaluating the argument 'x' in selecting a method for function 'head': No layout function defined for objects of class - --- failed re-building ‘GOxploreR.Rmd’ - - SUMMARY: processing the following file failed: - ‘GOxploreR.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -* checking installed package size ... NOTE - ``` - installed size is 6.7Mb - sub-directories of 1Mb or more: - R 6.2Mb - ``` - -# gRain - -
- -* Version: 1.3.13 -* GitHub: NA -* Source code: https://github.com/cran/gRain -* Date/Publication: 2023-03-09 16:20:02 UTC -* Number of recursive dependencies: 59 - -Run `revdepcheck::cloud_details(, "gRain")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘gRain-Ex.R’ failed - The error most likely occurred in: - - > ### Name: chest - > ### Title: Chest clinic example - > ### Aliases: chest chest_cpt - > ### Keywords: datasets - > - > ### ** Examples - > - ... - > b.s <- cptable(~bronc|smoke, values=c(6,4,3,7), levels=yn) - > e.lt <- cptable(~either|lung:tub,values=c(1,0,1,0,1,0,0,1),levels=yn) - > x.e <- cptable(~xray|either, values=c(98,2,5,95), levels=yn) - > d.be <- cptable(~dysp|bronc:either, values=c(9,1,7,3,8,2,1,9), levels=yn) - > - > grain(compileCPT(a, t.a, s, l.s, b.s, e.lt, x.e, d.be)) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: grain ... asMethod -> g_gn2ig_ -> -> graph_from_adj_list - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testhat.R’ - Running the tests in ‘tests/testhat.R’ failed. - Last 13 lines of output: - 8. │ └─gRbase:::topo_sortMAT_(amat) - 9. └─methods::as(object, "dgCMatrix") - 10. └─gRbase (local) asMethod(object) - 11. └─gRbase::g_gn2sm_(from) - 12. ├─igraph::as_adjacency_matrix(as(object, "igraph")) - 13. │ └─igraph:::ensure_igraph(graph) - 14. └─methods::as(object, "igraph") - 15. └─gRbase (local) asMethod(object) - 16. └─gRbase::g_gn2ig_(from) - 17. └─igraph::igraph.from.graphNEL(object) - 18. └─igraph::graph_from_adj_list(al, mode = mode, duplicate = TRUE) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘grain-intro.Rnw’ using knitr - - Quitting from lines 121-134 [unnamed-chunk-3] (grain-intro.Rnw) - Error: processing vignette 'grain-intro.Rnw' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘grain-intro.Rnw’ - - SUMMARY: processing the following file failed: - ‘grain-intro.Rnw’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# grainscape - -
- -* Version: 0.4.4 -* GitHub: https://github.com/achubaty/grainscape -* Source code: https://github.com/cran/grainscape -* Date/Publication: 2023-04-20 08:40:02 UTC -* Number of recursive dependencies: 96 - -Run `revdepcheck::cloud_details(, "grainscape")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘grainscape-Ex.R’ failed - The error most likely occurred in: - - > ### Name: GOC - > ### Title: Produce a grains of connectivity model at multiple scales - > ### (patch-based or lattice GOC) - > ### Aliases: GOC GOC,mpg-method - > - > ### ** Examples - > - ... - > tiny <- raster::raster(system.file("extdata/tiny.asc", package = "grainscape")) - > - > ## Create a resistance surface from a raster using an is-becomes reclassification - > tinyCost <- raster::reclassify(tiny, rcl = cbind(c(1, 2, 3, 4), c(1, 5, 10, 12))) - > ## Produce a patch-based MPG where patches are resistance features=1 - > tinyPatchMPG <- MPG(cost = tinyCost, patch = tinyCost == 1) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: MPG -> MPG -> graph_from_data_frame -> make_empty_graph - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘MPG_algorithm.Rmd’ using rmarkdown - A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TinyTeX with tinytex::reinstall_tinytex(repository = "illinois"). - - tlmgr: Local TeX Live (2022) is older than remote repository (2023). - Cross release updates are only supported with - update-tlmgr-latest(.sh/.exe) --update - See https://tug.org/texlive/upgrade.html for details. - Warning in system2("tlmgr", args, ...) : - running command ''tlmgr' search --file --global '/grffile.sty'' had status 1 - ... - - Error: processing vignette 'grainscape_vignette.Rmd' failed with diagnostics: - LaTeX failed to compile /tmp/workdir/grainscape/new/grainscape.Rcheck/vign_test/grainscape/vignettes/grainscape_vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See grainscape_vignette.log for more info. - --- failed re-building ‘grainscape_vignette.Rmd’ - - SUMMARY: processing the following files failed: - ‘MPG_algorithm.Rmd’ ‘grainscape_vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -* checking installed package size ... NOTE - ``` - installed size is 5.2Mb - sub-directories of 1Mb or more: - doc 1.5Mb - libs 2.3Mb - ``` - -# grand - -
- -* Version: 0.9.0 -* GitHub: https://github.com/zpneal/grand -* Source code: https://github.com/cran/grand -* Date/Publication: 2023-02-10 10:30:02 UTC -* Number of recursive dependencies: 36 - -Run `revdepcheck::cloud_details(, "grand")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘grand-Ex.R’ failed - The error most likely occurred in: - - > ### Name: grand - > ### Title: Apply Guidelines for Reporting About Network Data (GRAND) to an - > ### igraph object - > ### Aliases: grand - > - > ### ** Examples - > - > data(airport) #Load example data - > airport <- grand(airport) #Apply GRAND interactively - Error in .igraph.status("Restore graph external pointer.\n") : - could not find function ".igraph.status" - Calls: grand ... -> ensure_igraph -> is_igraph -> warn_version - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘grand.Rmd’ using rmarkdown - - Quitting from lines 167-178 [unnamed-chunk-3] (grand.Rmd) - Error: processing vignette 'grand.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘grand.Rmd’ - - SUMMARY: processing the following file failed: - ‘grand.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# graph4lg - -
- -* Version: 1.8.0 -* GitHub: NA -* Source code: https://github.com/cran/graph4lg -* Date/Publication: 2023-01-30 14:00:05 UTC -* Number of recursive dependencies: 119 - -Run `revdepcheck::cloud_details(, "graph4lg")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘graph4lg-Ex.R’ failed - The error most likely occurred in: - - > ### Name: add_nodes_attr - > ### Title: Add attributes to the nodes of a graph - > ### Aliases: add_nodes_attr - > - > ### ** Examples - > - > data("data_tuto") - > graph <- data_tuto[[3]] - > df_nodes <- data.frame(Id = igraph::V(graph)$name, - + Area = runif(50, min = 10, max = 60)) - Error in .igraph.status("Restore graph external pointer.\n") : - could not find function ".igraph.status" - Calls: data.frame ... -> ensure_igraph -> is_igraph -> warn_version - Execution halted - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Error loading dataset 'data_tuto': - Error in .igraph.status("Restore graph external pointer.\n") : - could not find function ".igraph.status" - - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘Rdpack’ - All declared Imports should be used. - ``` - -# graphclust - -
- -* Version: 1.3 -* GitHub: NA -* Source code: https://github.com/cran/graphclust -* Date/Publication: 2023-06-07 16:50:02 UTC -* Number of recursive dependencies: 15 - -Run `revdepcheck::cloud_details(, "graphclust")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘graphclust-Ex.R’ failed - The error most likely occurred in: - - > ### Name: metagraph - > ### Title: Plot the metagraph of the parameter of the stochastic block - > ### model associated with one of the estimated graph clusters - > ### Aliases: metagraph - > - > ### ** Examples - > - ... - - initialization of DelatICL... - - clustering algorithm... - - > metagraph(1, res) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: metagraph ... graph_from_adjacency_matrix -> graph.adjacency.dense - Execution halted - ``` - -# graphicalExtremes - -
- -* Version: 0.2.0 -* GitHub: https://github.com/sebastian-engelke/graphicalExtremes -* Source code: https://github.com/cran/graphicalExtremes -* Date/Publication: 2022-12-02 12:20:04 UTC -* Number of recursive dependencies: 94 - -Run `revdepcheck::cloud_details(, "graphicalExtremes")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘graphicalExtremes-Ex.R’ failed - The error most likely occurred in: - - > ### Name: Gamma2graph - > ### Title: Transformation of matrix to graph object - > ### Aliases: Gamma2graph Theta2graph - > - > ### ** Examples - > - > Gamma <- cbind( - ... - + c(1.5, 0, 2, 1.5), - + c(1.5, 2, 0, 1.5), - + c(2, 1.5, 1.5, 0) - + ) - > - > Gamma2graph(Gamma) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: Gamma2graph ... Theta2graph -> -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘glasso’ - ``` - -# graphlayouts - -
- -* Version: 1.0.0 -* GitHub: https://github.com/schochastics/graphlayouts -* Source code: https://github.com/cran/graphlayouts -* Date/Publication: 2023-05-01 08:00:02 UTC -* Number of recursive dependencies: 93 - -Run `revdepcheck::cloud_details(, "graphlayouts")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─igraph::make_full_graph(3) at test-graph_manipulate.R:2:3 - ── Error ('test-layout_backbone.R:2:3'): backbone layout works ───────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. ├─graphlayouts::layout_as_backbone(igraph::graph.full(10)) at test-layout_backbone.R:2:2 - 2. │ └─igraph::is.igraph(g) - 3. └─igraph::graph.full(10) - - [ FAIL 2 | WARN 0 | SKIP 0 | PASS 113 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 11.1Mb - sub-directories of 1Mb or more: - doc 1.9Mb - help 2.4Mb - libs 6.5Mb - ``` - -# graphseg - -
- -* Version: 0.1.0 -* GitHub: https://github.com/goepp/graphseg -* Source code: https://github.com/cran/graphseg -* Date/Publication: 2023-05-02 08:10:06 UTC -* Number of recursive dependencies: 67 - -Run `revdepcheck::cloud_details(, "graphseg")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘graphseg-Ex.R’ failed - The error most likely occurred in: - - > ### Name: utrecht_district - > ### Title: Administrative areas of the Netherlands aroung the city of - > ### Utrecht - > ### Aliases: utrecht_district graph_utrecht_district - > ### Keywords: datasets - > - > ### ** Examples - ... - old-style crs object detected; please recreate object with a recent sf::st_crs() - old-style crs object detected; please recreate object with a recent sf::st_crs() - Warning: st_crs<- : replacing crs does not reproject data; use st_transform for that - > adj_municip <- as(as(igraph::as_adjacency_matrix(graph_utrecht_district, type = "both"), - + "symmetricMatrix"), - + "TsparseMatrix") - Error in .igraph.status("Restore graph external pointer.\n") : - could not find function ".igraph.status" - Calls: as ... -> ensure_igraph -> is_igraph -> warn_version - Execution halted - ``` - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 14768 marked UTF-8 strings - ``` - -# graphTweets - -
- -* Version: 0.5.3 -* GitHub: https://github.com/JohnCoene/graphTweets -* Source code: https://github.com/cran/graphTweets -* Date/Publication: 2020-01-08 09:00:08 UTC -* Number of recursive dependencies: 58 - -Run `revdepcheck::cloud_details(, "graphTweets")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘graphTweets-Ex.R’ failed - The error most likely occurred in: - - > ### Name: gt_graph - > ### Title: Graph - > ### Aliases: gt_graph - > - > ### ** Examples - > - > # simulate dataset - ... - + ) - > - > tweets %>% - + gt_edges(text, screen_name, status_id) %>% - + gt_nodes() %>% - + gt_graph() -> net - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: %>% -> gt_graph -> -> make_empty_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ── Error ('test_overhaul.R:53:3'): nodes & edges & dyn ───────────────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. ├─testthat::expect_is(...) at test_overhaul.R:53:2 - 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") - 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) - 4. ├─... %>% gt_graph() - 5. └─graphTweets::gt_graph(.) - 6. └─igraph::graph.data.frame(gt[["edges"]], directed = TRUE, vertices = gt[["nodes"]]) - 7. └─igraph::make_empty_graph(n = 0, directed = directed) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 11 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘utils’ - All declared Imports should be used. - ``` - -# gRbase - -
- -* Version: 1.8.9 -* GitHub: NA -* Source code: https://github.com/cran/gRbase -* Date/Publication: 2022-11-10 10:40:02 UTC -* Number of recursive dependencies: 49 - -Run `revdepcheck::cloud_details(, "gRbase")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘gRbase-Ex.R’ failed - The error most likely occurred in: - - > ### Name: dag2chol - > ### Title: Create regression matrix matrix from DAG A DAG can be - > ### represented as a triangular matrix of regression coefficients. - > ### Aliases: dag2chol - > - > ### ** Examples - > - > - > g <- dag(~x2|x1 + x3|x1:x2 + x4|x3) - > gi <- as(g, "igraph") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: as ... asMethod -> g_gn2ig_ -> -> graph_from_adj_list - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testhat.R’ - Running the tests in ‘tests/testhat.R’ failed. - Last 13 lines of output: - 9. └─gRbase (local) asMethod(object) - 10. └─gRbase::g_gn2dm_(from) - 11. ├─methods::as(...) - 12. │ └─methods:::.class1(object) - 13. ├─igraph::as_adjacency_matrix(as(object, "igraph")) - 14. │ └─igraph:::ensure_igraph(graph) - 15. └─methods::as(object, "igraph") - 16. └─gRbase (local) asMethod(object) - 17. └─gRbase::g_gn2ig_(from) - 18. └─igraph::igraph.from.graphNEL(object) - 19. └─igraph::graph_from_adj_list(al, mode = mode, duplicate = TRUE) - - [ FAIL 4 | WARN 0 | SKIP 0 | PASS 52 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘arrays.Rnw’ using knitr - Error: processing vignette 'arrays.Rnw' failed with diagnostics: - Running 'texi2dvi' on 'arrays.tex' failed. - LaTeX errors: - ! LaTeX Error: File `boxedminipage.sty' not found. - - Type X to quit or to proceed, - or enter new name. (Default extension: sty) - - ... - Quitting from lines 369-377 [unnamed-chunk-15] (graphs.Rnw) - Error: processing vignette 'graphs.Rnw' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘graphs.Rnw’ - - SUMMARY: processing the following files failed: - ‘arrays.Rnw’ ‘graphs.Rnw’ - - Error: Vignette re-building failed. - Execution halted - ``` - -* checking installed package size ... NOTE - ``` - installed size is 25.7Mb - sub-directories of 1Mb or more: - libs 23.6Mb - ``` - -# gRim - -
- -* Version: 0.2.10 -* GitHub: NA -* Source code: https://github.com/cran/gRim -* Date/Publication: 2022-10-15 22:22:35 UTC -* Number of recursive dependencies: 55 - -Run `revdepcheck::cloud_details(, "gRim")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘gRim-Ex.R’ failed - The error most likely occurred in: - - > ### Name: getEdges - > ### Title: Find edges in a graph or edges not in an undirected graph. - > ### Aliases: getEdges getEdges.list getEdges.graphNEL getEdges.matrix - > ### getInEdges getOutEdges getEdgesMAT getInEdgesMAT getOutEdgesMAT - > ### Keywords: utilities - > - > ### ** Examples - > - > - > gg <- ug(~a:b:d + a:c:d + c:e) - > glist <- getCliques(gg) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: getCliques ... asMethod -> g_gn2ig_ -> -> graph_from_adj_list - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘grim.Rnw’ - ... - + "mental", "phys")), data = reinis, interactions = 2) - - > formula(dm3) - ~smoke * mental + smoke * phys + mental * phys + smoke * systol - - > iplot(dm1) - - When sourcing ‘grim.R’: - Error: could not find function ".igraph.status" - Execution halted - - ‘grim.Rnw’ using ‘latin1’... failed - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.7Mb - sub-directories of 1Mb or more: - libs 4.9Mb - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘grim.Rnw’ using Sweave - Loading required package: gRbase - Warning in dir.create("figures") : 'figures' already exists - Loading required package: graph - Loading required package: BiocGenerics - - Attaching package: ‘BiocGenerics’ - - The following objects are masked from ‘package:stats’: - ... - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - - --- failed re-building ‘grim.Rnw’ - - SUMMARY: processing the following file failed: - ‘grim.Rnw’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# handwriter - -
- -* Version: 1.0.1 -* GitHub: NA -* Source code: https://github.com/cran/handwriter -* Date/Publication: 2021-08-16 16:20:02 UTC -* Number of recursive dependencies: 64 - -Run `revdepcheck::cloud_details(, "handwriter")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘handwriter-Ex.R’ failed - The error most likely occurred in: - - > ### Name: AddLetterImages - > ### Title: AddLetterImages - > ### Aliases: AddLetterImages - > - > ### ** Examples - > - > twoSent_document = list() - > twoSent_document$image = twoSent - > twoSent_document$thin = thinImage(twoSent_document$image) - > twoSent_processList = processHandwriting(twoSent_document$thin, dim(twoSent_document$image)) - Starting Processing... - Getting Nodes...Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: processHandwriting -> graph_from_data_frame -> make_empty_graph - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.6Mb - sub-directories of 1Mb or more: - libs 4.5Mb - ``` - -# hero - -
- -* Version: 0.4.7 -* GitHub: NA -* Source code: https://github.com/cran/hero -* Date/Publication: 2020-01-24 22:00:02 UTC -* Number of recursive dependencies: 148 - -Run `revdepcheck::cloud_details(, "hero")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘hero-Ex.R’ failed - The error most likely occurred in: - - > ### Name: adjacent - > ### Title: Determine adjacent points - > ### Aliases: adjacent - > - > ### ** Examples - > - > # basic coordinates - ... - > coords = expand.grid(1:4, 1:4) - > # plot coordinates to see relationships - > plot(coords, type = "n") - > text(coords) - > a = adjacent(coords, digits = 1) - > plot(a) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot ... graph.adjacency.sparse -> make_graph -> do.call -> - Execution halted - ``` - -# HLSM - -
- -* Version: 0.9.0 -* GitHub: NA -* Source code: https://github.com/cran/HLSM -* Date/Publication: 2021-12-06 13:00:02 UTC -* Number of recursive dependencies: 10 - -Run `revdepcheck::cloud_details(, "HLSM")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘HLSM-Ex.R’ failed - The error most likely occurred in: - - > ### Name: HLSMrandomEF - > ### Title: Function to run the MCMC sampler in random effects latent space - > ### model, HLSMfixedEF for fixed effects model, or LSM for single network - > ### latent space model) - > ### Aliases: HLSMrandomEF HLSMfixedEF LSM print.HLSM print.summary.HLSM - > ### summary.HLSM getIntercept getLS getLikelihood getBeta - > - ... - > - > #Fixed effect HLSM on Pitt and Spillane data - > - > fixed.fit = HLSMfixedEF(Y = ps.advice.mat, senderCov=ps.node.df, - + initialVals = initialVals,priors = priors, - + tune = tune,tuneIn = FALSE,dd = 2,niter = niter) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: HLSMfixedEF ... lapply -> FUN -> graph.adjacency -> graph.adjacency.dense - Execution halted - ``` - -# HospitalNetwork - -
- -* Version: 0.9.3 -* GitHub: https://github.com/PascalCrepey/HospitalNetwork -* Source code: https://github.com/cran/HospitalNetwork -* Date/Publication: 2023-02-27 08:22:43 UTC -* Number of recursive dependencies: 115 - -Run `revdepcheck::cloud_details(, "HospitalNetwork")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘HospitalNetwork-Ex.R’ failed - The error most likely occurred in: - - > ### Name: HospiNet - > ### Title: Class providing the HospiNet object with its methods - > ### Aliases: HospiNet - > ### Keywords: data - > - > ### ** Examples - > - ... - + condition = "dates" - + ) - Checking for missing values... - Checking for duplicated records... - Removed 0 duplicates - Done. - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: hospinet_from_subject_database ... checkClass -> -> -> make_empty_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 9. │ └─checkmate::checkClass(x, classes, ordered, null.ok) - 10. └─HospitalNetwork (local) ``() - 11. └─igraph::graph_from_data_frame(self$edgelist) - 12. └─igraph::make_empty_graph(n = 0, directed = directed) - - [ FAIL 2 | WARN 0 | SKIP 2 | PASS 55 ] - Deleting unused snapshots: - • HospiNet/clmat100.svg - • HospiNet/clustdeg500.svg - • HospiNet/clustmatclust500.svg - • HospiNet/deg100.svg - • HospiNet/mat100.svg - • HospiNet/matclust500.svg - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘HospitalNetwork-Workflow.Rmd’ using rmarkdown - - Quitting from lines 154-157 [setup2] (HospitalNetwork-Workflow.Rmd) - Error: processing vignette 'HospitalNetwork-Workflow.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘HospitalNetwork-Workflow.Rmd’ - - SUMMARY: processing the following file failed: - ‘HospitalNetwork-Workflow.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# HTT - -
- -* Version: 0.1.2 -* GitHub: NA -* Source code: https://github.com/cran/HTT -* Date/Publication: 2023-03-12 14:30:02 UTC -* Number of recursive dependencies: 72 - -Run `revdepcheck::cloud_details(, "HTT")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘HTT-Ex.R’ failed - The error most likely occurred in: - - > ### Name: Hypothesis Testing Tree - > ### Title: Hypothesis Testing Tree - > ### Aliases: HTT - > ### Keywords: HTT - > - > ### ** Examples - > - > ## regression - > data("Boston", package = "MASS") - > Bostonhtt <- HTT(medv ~ . , data = Boston, controls = htt_control(R = 99)) - > plot(Bostonhtt) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot ... plot.htt -> graph_from_data_frame -> make_empty_graph - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘Intro.Rmd’ using rmarkdown - - Quitting from lines 24-32 [unnamed-chunk-2] (Intro.Rmd) - Error: processing vignette 'Intro.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘Intro.Rmd’ - - SUMMARY: processing the following file failed: - ‘Intro.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 7.1Mb - sub-directories of 1Mb or more: - libs 6.5Mb - ``` - -# huge - -
- -* Version: 1.3.5 -* GitHub: NA -* Source code: https://github.com/cran/huge -* Date/Publication: 2021-06-30 20:20:02 UTC -* Number of recursive dependencies: 10 - -Run `revdepcheck::cloud_details(, "huge")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘huge-Ex.R’ failed - The error most likely occurred in: - - > ### Name: huge - > ### Title: High-dimensional undirected graph estimation - > ### Aliases: huge - > - > ### ** Examples - > - > #generate data - ... - Model: Meinshausen & Buhlmann graph estimation (mb) - Input: The Data Matrix - Path length: 10 - Graph dimension: 12 - Sparsity level: 0 -----> 0.6969697 - > plot(out1) #Not aligned - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot ... plot.huge -> graph.adjacency -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘vignette.Rnw’ using Sweave - Error: processing vignette 'vignette.Rnw' failed with diagnostics: - Running 'texi2dvi' on 'vignette.tex' failed. - LaTeX errors: - ! LaTeX Error: File `pdfpages.sty' not found. - - Type X to quit or to proceed, - or enter new name. (Default extension: sty) - ... - l.8 \usepackage - {Sweave}^^M - ! ==> Fatal error occurred, no output PDF file produced! - --- failed re-building ‘vignette.Rnw’ - - SUMMARY: processing the following file failed: - ‘vignette.Rnw’ - - Error: Vignette re-building failed. - Execution halted - ``` - -* checking installed package size ... NOTE - ``` - installed size is 13.5Mb - sub-directories of 1Mb or more: - libs 12.0Mb - ``` - -# ICDS - -
- -* Version: 0.1.2 -* GitHub: NA -* Source code: https://github.com/cran/ICDS -* Date/Publication: 2021-07-15 11:30:10 UTC -* Number of recursive dependencies: 93 - -Run `revdepcheck::cloud_details(, "ICDS")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ICDS-Ex.R’ failed - The error most likely occurred in: - - > ### Name: opt_subpath - > ### Title: opt_subpath - > ### Aliases: opt_subpath - > - > ### ** Examples - > - > zz<-GetExampleData("zzz") - > subpathdata<-GetExampleData("subpathdata") - > optsubpath<-opt_subpath(subpathdata,zz,overlap=0.6) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: opt_subpath ... overlapSPMatrix -> graph.adjacency -> graph.adjacency.dense - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘ICDS.Rmd’ using rmarkdown - - Quitting from lines 137-140 [unnamed-chunk-10] (ICDS.Rmd) - Error: processing vignette 'ICDS.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘ICDS.Rmd’ - - SUMMARY: processing the following file failed: - ‘ICDS.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# iconr - -
- -* Version: 0.1.0 -* GitHub: https://github.com/zoometh/iconr -* Source code: https://github.com/cran/iconr -* Date/Publication: 2021-02-16 09:10:05 UTC -* Number of recursive dependencies: 81 - -Run `revdepcheck::cloud_details(, "iconr")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘iconr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: contemp_nds - > ### Title: Select Contemporaneous Nodes - > ### Aliases: contemp_nds - > ### Keywords: ~kwd1 graphs - > - > ### ** Examples - > - ... - > eds.df <- read_eds(site = "Ibahernando", - + decor = "Ibahernando", - + dir = dataDir) - > - > # Extract the subgraph contemporaneous to the node 2 - > l_dec_df <- contemp_nds(nds.df, eds.df, selected.nd = 2) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: contemp_nds -> -> make_empty_graph - Execution halted - ``` - -## In both - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# icosa - -
- -* Version: 0.11.0 -* GitHub: https://github.com/adamkocsis/icosa -* Source code: https://github.com/cran/icosa -* Date/Publication: 2023-03-23 14:42:09 UTC -* Number of recursive dependencies: 52 - -Run `revdepcheck::cloud_details(, "icosa")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘icosa-Ex.R’ failed - The error most likely occurred in: - - > ### Name: SpPolygons - > ### Title: Spatial polygons from an icosahedral grid - > ### Aliases: SpPolygons SpPolygons,trigrid-method - > ### SpPolygons,hexagrid-method - > - > ### ** Examples - > - > a <- trigrid() - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: trigrid ... .local -> do.call -> -> make_empty_graph - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘icosa_cran.Rmd’ using rmarkdown - - Quitting from lines 17-20 [unnamed-chunk-1] (icosa_cran.Rmd) - Error: processing vignette 'icosa_cran.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘icosa_cran.Rmd’ - - SUMMARY: processing the following file failed: - ‘icosa_cran.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.9Mb - sub-directories of 1Mb or more: - libs 4.3Mb - ``` - -# idopNetwork - -
- -* Version: 0.1.2 -* GitHub: https://github.com/cxzdsa2332/idopNetwork -* Source code: https://github.com/cran/idopNetwork -* Date/Publication: 2023-04-18 06:50:02 UTC -* Number of recursive dependencies: 78 - -Run `revdepcheck::cloud_details(, "idopNetwork")` for more info - -
- -## Newly broken - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘idopNetwork_vignette.Rmd’ using rmarkdown - - Quitting from lines 309-311 [unnamed-chunk-36] (idopNetwork_vignette.Rmd) - Error: processing vignette 'idopNetwork_vignette.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘idopNetwork_vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘idopNetwork_vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# iGraphMatch - -
- -* Version: 2.0.1 -* GitHub: https://github.com/dpmcsuss/iGraphMatch -* Source code: https://github.com/cran/iGraphMatch -* Date/Publication: 2022-09-13 18:30:02 UTC -* Number of recursive dependencies: 80 - -Run `revdepcheck::cloud_details(, "iGraphMatch")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘iGraphMatch-Ex.R’ failed - The error most likely occurred in: - - > ### Name: C.Elegans - > ### Title: Chemical synapses and electrical synapses networks of roundworm - > ### Aliases: C.Elegans - > ### Keywords: datasets - > - > ### ** Examples - > - > data(C.Elegans) - > g1 <- C.Elegans[[1]] - > g2 <- C.Elegans[[2]] - > plot(g1, g2) - Error in .igraph.status("Restore graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot ... .local -> identity_match -> is.igraph -> warn_version - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘spelling.R’ - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─igraph::sample_gnm(20, 60) at test-split_igraph.R:1:0 - ── Error ('test-umeyama.R:5:1'): (code run outside of `test_that()`) ─────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─iGraphMatch::sample_correlated_gnp_pair(10, 0.9, 0.5) at test-umeyama.R:5:0 - 2. └─iGraphMatch:::sample_correlated_gnp_pair_no_junk(...) - 3. └─igraph::sample_gnp(n, p, ...) - - [ FAIL 22 | WARN 0 | SKIP 1 | PASS 25 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘iGraphMatch.Rmd’ using rmarkdown - - Quitting from lines 648-654 [sample_graph] (iGraphMatch.Rmd) - Error: processing vignette 'iGraphMatch.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘iGraphMatch.Rmd’ - - SUMMARY: processing the following file failed: - ‘iGraphMatch.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# IMEC - -
- -* Version: 0.2.0 -* GitHub: NA -* Source code: https://github.com/cran/IMEC -* Date/Publication: 2020-11-27 10:10:03 UTC -* Number of recursive dependencies: 103 - -Run `revdepcheck::cloud_details(, "IMEC")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘IMEC-Ex.R’ failed - The error most likely occurred in: - - > ### Name: computeIMEC - > ### Title: Computes the Ising model of explanatory coherence. - > ### Aliases: computeIMEC - > - > ### ** Examples - > - > # simple example comparing two hypotheses one of them with more explanatory breadth## - ... - > coherence <- computeIMEC(explanations, Thresholds, Phenomena, T1) - > summary(coherence) - T1 EC_T1 - 1 H1 0.8673686 - 2 H2 0.1347264 - > plot(coherence) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot -> plot.IMEC -> -> graph.adjacency.dense - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 2. └─IMEC:::plot.IMEC(IMEC) - 3. └─igraph::graph_from_adjacency_matrix(...) - 4. └─igraph:::graph.adjacency.dense(...) - ── Error ('test-0-basictests.R:58:3'): analytic way of calculating coherence works for 1 theory ── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. ├─base::plot(IMEC) at test-0-basictests.R:58:2 - 2. └─IMEC:::plot.IMEC(IMEC) - 3. └─igraph::graph_from_adjacency_matrix(...) - 4. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 2 | WARN 0 | SKIP 1 | PASS 2 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# immunarch - -
- -* Version: 0.9.0 -* GitHub: https://github.com/immunomind/immunarch -* Source code: https://github.com/cran/immunarch -* Date/Publication: 2022-12-15 15:00:05 UTC -* Number of recursive dependencies: 194 - -Run `revdepcheck::cloud_details(, "immunarch")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘immunarch-Ex.R’ failed - The error most likely occurred in: - - > ### Name: seqCluster - > ### Title: Function for assigning clusters based on sequences similarity - > ### Aliases: seqCluster - > - > ### ** Examples - > - > - ... - 18. ├─reshape2::melt(.) - 19. ├─igraph::clusters(.) - 20. │ └─igraph:::ensure_igraph(graph) - 21. ├─igraph::graph_from_data_frame(.) - 22. │ └─igraph::make_empty_graph(n = 0, directed = directed) - 23. └─base::.handleSimpleError(...) - 24. └─purrr (local) h(simpleError(msg, call)) - 25. └─cli::cli_abort(...) - 26. └─rlang::abort(...) - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 7.4Mb - sub-directories of 1Mb or more: - data 3.3Mb - doc 1.6Mb - ``` - -# immuneSIM - -
- -* Version: 0.8.7 -* GitHub: https://github.com/GreiffLab/immuneSIM -* Source code: https://github.com/cran/immuneSIM -* Date/Publication: 2019-09-27 10:30:06 UTC -* Number of recursive dependencies: 66 - -Run `revdepcheck::cloud_details(, "immuneSIM")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘immuneSIM-Ex.R’ failed - The error most likely occurred in: - - > ### Name: hub_seqs_exclusion - > ### Title: Deletes top hub sequences from repertoire, changing the network - > ### architecture. - > ### Aliases: hub_seqs_exclusion - > - > ### ** Examples - > - > repertoire <- list_example_repertoires[["example_repertoire_A"]] - > rep_excluded_hubs <- hub_seqs_exclusion(repertoire, top_x = 0.005, output_dir = "") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: hub_seqs_exclusion -> -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# imsig - -
- -* Version: 1.1.3 -* GitHub: https://github.com/ajitjohnson/imsig -* Source code: https://github.com/cran/imsig -* Date/Publication: 2021-01-10 01:00:02 UTC -* Number of recursive dependencies: 52 - -Run `revdepcheck::cloud_details(, "imsig")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘imsig-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plot_network - > ### Title: Network graph of ImSig genes - > ### Aliases: plot_network - > - > ### ** Examples - > - > plot_network (exp = example_data, r = 0.7) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot_network ... graph_from_adjacency_matrix -> graph.adjacency.dense - Execution halted - ``` - -# incidentally - -
- -* Version: 1.0.2 -* GitHub: https://github.com/zpneal/incidentally -* Source code: https://github.com/cran/incidentally -* Date/Publication: 2023-02-15 21:00:02 UTC -* Number of recursive dependencies: 39 - -Run `revdepcheck::cloud_details(, "incidentally")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘incidentally-Ex.R’ failed - The error most likely occurred in: - - > ### Name: add.blocks - > ### Title: Adds a block structure to an incidence matrix - > ### Aliases: add.blocks - > - > ### ** Examples - > - > I <- incidence.from.probability(R = 100, C = 100, P = .1) - ... - > all(rowSums(I)==rowSums(blocked)) - [1] TRUE - > all(colSums(I)==colSums(blocked)) - [1] TRUE - > - > B <- igraph::sample_bipartite(100, 100, p=.1) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: - Execution halted - ``` - -# influenceR - -
- -* Version: 0.1.5 -* GitHub: https://github.com/khanna-lab/influenceR -* Source code: https://github.com/cran/influenceR -* Date/Publication: 2023-05-18 10:00:02 UTC -* Number of recursive dependencies: 35 - -Run `revdepcheck::cloud_details(, "influenceR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘influenceR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: betweenness - > ### Title: Vertex Betweenness centrality measure. - > ### Aliases: betweenness - > - > ### ** Examples - > - > ig.ex <- igraph::erdos.renyi.game(100, p.or.m=0.3) # generate an undirected 'igraph' object - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 6. └─igraph::is_igraph(g) - 7. └─igraph:::warn_version(graph) - ── Error ('test_reference.R:72:3'): bridging matches reference function ──────── - Error in `.igraph.status("Restore graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─influenceR (local) bridge_test(flo_graph) at test_reference.R:72:2 - 2. └─igraph::V(g) at test_reference.R:26:2 - 3. └─igraph:::ensure_igraph(graph) - 4. └─igraph::is_igraph(graph) - 5. └─igraph:::warn_version(graph) - - [ FAIL 5 | WARN 2 | SKIP 0 | PASS 0 ] - Error: Test failures - Execution halted - ``` - -# influential - -
- -* Version: 2.2.7 -* GitHub: https://github.com/asalavaty/influential -* Source code: https://github.com/cran/influential -* Date/Publication: 2023-05-16 05:10:02 UTC -* Number of recursive dependencies: 187 - -Run `revdepcheck::cloud_details(, "influential")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘influential-Ex.R’ failed - The error most likely occurred in: - - > ### Name: V - > ### Title: Vertices of an igraph graph - > ### Aliases: V vertices - > ### Keywords: graph_vertices - > - > ### ** Examples - > - > MyData <- coexpression.data - > My_graph <- graph_from_data_frame(MyData) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: graph_from_data_frame -> make_empty_graph - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘Vignettes.Rmd’ using rmarkdown - - Quitting from lines 140-145 [g_dataframe] (Vignettes.Rmd) - Error: processing vignette 'Vignettes.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘Vignettes.Rmd’ - - SUMMARY: processing the following file failed: - ‘Vignettes.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# intergraph - -
- -* Version: 2.0-2 -* GitHub: NA -* Source code: https://github.com/cran/intergraph -* Date/Publication: 2016-12-05 18:28:47 -* Number of recursive dependencies: 49 - -Run `revdepcheck::cloud_details(, "intergraph")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘intergraph-Ex.R’ failed - The error most likely occurred in: - - > ### Name: asDF - > ### Title: Convert network to data frame(s) - > ### Aliases: asDF asDF.igraph asDF.network - > - > ### ** Examples - > - > # using method for 'network' objects - ... - ..$ label : chr [1:15] "a" "b" "c" "d" ... - ..$ na : logi [1:15] FALSE FALSE FALSE FALSE FALSE FALSE ... - ..$ vertex.names : chr [1:15] "a" "b" "c" "d" ... - > - > # using method for 'igraph' objects - > d2 <- asDF(exIgraph) - Error in .igraph.status("Restore graph external pointer.\n") : - could not find function ".igraph.status" - Calls: asDF ... -> ensure_igraph -> is_igraph -> warn_version - Execution halted - ``` - -# IOHanalyzer - -
- -* Version: 0.1.6.3 -* GitHub: https://github.com/IOHprofiler/IOHAnalyzer -* Source code: https://github.com/cran/IOHanalyzer -* Date/Publication: 2022-03-09 08:20:12 UTC -* Number of recursive dependencies: 132 - -Run `revdepcheck::cloud_details(, "IOHanalyzer")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘IOHanalyzer-Ex.R’ failed - The error most likely occurred in: - - > ### Name: Plot.Stats.Significance_Graph - > ### Title: Plot a network graph showing the statistically different - > ### algorithms - > ### Aliases: Plot.Stats.Significance_Graph - > ### Plot.Stats.Significance_Graph.DataSetList - > - > ### ** Examples - > - > Plot.Stats.Significance_Graph(subset(dsl, funcId == 2), 16) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: Plot.Stats.Significance_Graph ... Plot.Stats.Significance_Graph.DataSetList -> -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 7.3Mb - sub-directories of 1Mb or more: - data 1.4Mb - libs 4.1Mb - shiny-server 1.0Mb - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 102 marked UTF-8 strings - ``` - -# isa2 - -
- -* Version: 0.3.6 -* GitHub: https://github.com/gaborcsardi/ISA -* Source code: https://github.com/cran/isa2 -* Date/Publication: 2023-02-21 21:30:02 UTC -* Number of recursive dependencies: 42 - -Run `revdepcheck::cloud_details(, "isa2")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘isa2-Ex.R’ failed - The error most likely occurred in: - - > ### Name: isa.sweep - > ### Title: Create a hierarchical structure of ISA biclusters - > ### Aliases: isa.sweep isa.sweep,matrix-method sweep.graph - > ### sweep.graph,list-method - > ### Keywords: cluster - > - > ### ** Examples - ... - DONE - Calculating ISA robustness - DONE - DONE - > network <- sweep.graph(isa.tree) - Loading required namespace: igraph - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: sweep.graph ... sweep.graph.default -> -> do.call -> - Execution halted - ``` - -# isotracer - -
- -* Version: 1.1.4 -* GitHub: NA -* Source code: https://github.com/cran/isotracer -* Date/Publication: 2023-03-21 14:10:02 UTC -* Number of recursive dependencies: 157 - -Run `revdepcheck::cloud_details(, "isotracer")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘isotracer-Ex.R’ failed - The error most likely occurred in: - - > ### Name: ggflows - > ### Title: A quick-and-dirty way of visualizing relative flows in a network - > ### Aliases: ggflows - > - > ### ** Examples - > - > if (requireNamespace("ggraph")) { - ... - 13. │ └─tidygraph:::as_tbl_graph.data.frame(graph) - 14. │ └─tidygraph:::as_graph_edge_df(x, directed) - 15. │ └─igraph::graph_from_data_frame(x, directed = directed) - 16. │ └─igraph::make_empty_graph(n = 0, directed = directed) - 17. └─base::.handleSimpleError(...) - 18. └─rlang (local) h(simpleError(msg, call)) - 19. └─handlers[[1L]](cnd) - 20. └─cli::cli_abort("No layout function defined for objects of class {.cls {class(graph)[1]}}") - 21. └─rlang::abort(...) - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 2. │ └─testthat:::quasi_capture(...) - 3. │ ├─testthat (local) .capture(...) - 4. │ │ └─base::withCallingHandlers(...) - 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) - 6. └─isotracer::sankey(r, debug = TRUE, edge_f = 0.2, node_s = "prop") - 7. └─isotracer:::sankey_place_nodes(...) - 8. └─isotracer:::sankey_calc_nodes_locations(topo, layout) - 9. ├─isotracer::as_tbl_graph(x) - 10. └─isotracer:::as_tbl_graph.topology(x) - 11. └─igraph::graph_from_adjacency_matrix(t(x)) - 12. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 9 | WARN 0 | SKIP 0 | PASS 284 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 89.6Mb - sub-directories of 1Mb or more: - data 1.8Mb - doc 2.3Mb - libs 84.4Mb - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘rstantools’ - All declared Imports should be used. - ``` - -* checking for GNU extensions in Makefiles ... NOTE - ``` - GNU make is a SystemRequirements. - ``` - -# ITNr - -
- -* Version: 0.7.0 -* GitHub: NA -* Source code: https://github.com/cran/ITNr -* Date/Publication: 2023-03-31 14:10:11 UTC -* Number of recursive dependencies: 82 - -Run `revdepcheck::cloud_details(, "ITNr")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ITNr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: ITNproperties - > ### Title: ITN Properties - > ### Aliases: ITNproperties - > - > ### ** Examples - > - > ##Load the network - ... - Error in .igraph.status("Restore graph external pointer.\n") : - could not find function ".igraph.status" - Calls: ITNproperties ... -> ensure_igraph -> is_igraph -> warn_version - Execution halted - Error in .igraph.status("Free graph external pointer.\n") : - could not find function ".igraph.status" - Error in .igraph.status("Free graph external pointer.\n") : - could not find function ".igraph.status" - Error in .igraph.status("Free graph external pointer.\n") : - could not find function ".igraph.status" - ``` - -# IxPopDyMod - -
- -* Version: 0.2.0 -* GitHub: https://github.com/dallenmidd/IxPopDyMod -* Source code: https://github.com/cran/IxPopDyMod -* Date/Publication: 2022-02-08 07:30:05 UTC -* Number of recursive dependencies: 69 - -Run `revdepcheck::cloud_details(, "IxPopDyMod")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘IxPopDyMod-Ex.R’ failed - The error most likely occurred in: - - > ### Name: graph_lifecycle - > ### Title: Visualize transitions as a life cycle graph - > ### Aliases: graph_lifecycle - > - > ### ** Examples - > - > graph_lifecycle(config_ex_1$transitions) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: graph_lifecycle ... %>% -> plot -> graph_from_data_frame -> make_empty_graph - Execution halted - ``` - -# jewel - -
- -* Version: 2.0.0 -* GitHub: https://github.com/annaplaksienko/jewel -* Source code: https://github.com/cran/jewel -* Date/Publication: 2023-05-12 14:30:08 UTC -* Number of recursive dependencies: 45 - -Run `revdepcheck::cloud_details(, "jewel")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘jewel-Ex.R’ failed - The error most likely occurred in: - - > ### Name: constructWeights - > ### Title: Construct weights for _jewel_ minimization problem from prior - > ### information on vertices degrees. - > ### Aliases: constructWeights - > - > ### ** Examples - > - ... - + G_list_true <- data$Graphs - + true_degrees <- rowSums(G_list_true[[1]]) - + cut <- sort(true_degrees, decreasing = TRUE)[ceiling(p * 0.03)] - + apriori_hubs <- ifelse(true_degrees >= cut, 10, 1) - + W <- constructWeights(apriori_hubs, K = K) - + } - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: generateData_rewire -> barabasi.game - Execution halted - ``` - -# jti - -
- -* Version: 0.8.4 -* GitHub: https://github.com/mlindsk/jti -* Source code: https://github.com/cran/jti -* Date/Publication: 2022-04-12 07:12:38 UTC -* Number of recursive dependencies: 41 - -Run `revdepcheck::cloud_details(, "jti")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘jti-Ex.R’ failed - The error most likely occurred in: - - > ### Name: compile - > ### Title: Compile information - > ### Aliases: compile compile.cpt_list - > - > ### ** Examples - > - > cptl <- cpt_list(asia2) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: cpt_list ... cpt_list.list -> graph_from_cpt_list -> - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.1Mb - sub-directories of 1Mb or more: - libs 5.3Mb - ``` - -# kangar00 - -
- -* Version: 1.4.1 -* GitHub: NA -* Source code: https://github.com/cran/kangar00 -* Date/Publication: 2022-12-06 08:40:06 UTC -* Number of recursive dependencies: 95 - -Run `revdepcheck::cloud_details(, "kangar00")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘kangar00-Ex.R’ failed - The error most likely occurred in: - - > ### Name: pathway - > ### Title: An S4 class to represent a gene-gene interaction network - > ### Aliases: pathway pathway,ANY-method show,pathway-method - > ### show,pathway,ANY-method summary,pathway-method - > ### summary,pathway,ANY-method pathway2igraph,pathway-method - > ### pathway2igraph ANY-method analyze,pathway-method analyze - > ### get_genes,pathway-method get_genes plot,pathway,missing-method - ... - ..$ adj : int [1:180, 1:180] 0 0 0 0 0 0 0 0 0 0 ... - .. ..- attr(*, "dimnames")=List of 2 - .. .. ..$ : chr [1:180] "ITPKA" "ITPKB" "ITPKC" "ADCY1" ... - .. .. ..$ : chr [1:180] "ITPKA" "ITPKB" "ITPKC" "ADCY1" ... - ..$ sign: int [1:594] 1 1 1 1 1 1 1 1 1 1 ... - > g <- pathway2igraph(hsa04020) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: pathway2igraph ... pathway2igraph -> .local -> -> graph.adjacency.dense - Execution halted - ``` - -# Karen - -
- -* Version: 1.0 -* GitHub: NA -* Source code: https://github.com/cran/Karen -* Date/Publication: 2022-09-15 07:40:02 UTC -* Number of recursive dependencies: 39 - -Run `revdepcheck::cloud_details(, "Karen")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘Karen-Ex.R’ failed - The error most likely occurred in: - - > ### Name: get.cdn - > ### Title: Get the cell differentiation network from a fitted Kalman - > ### Reaction Network. - > ### Aliases: get.cdn - > - > ### ** Examples - > - ... - DONE - Smoothing step... DONE - Exporting new initial conditions to the cluster... DONE - > parallel::stopCluster(cl) - > - > get.cdn(res.fit) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: get.cdn ... graph_from_adjacency_matrix -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘Karen.ltx’ using tex - Error: processing vignette 'Karen.ltx' failed with diagnostics: - Running 'texi2dvi' on 'Karen.ltx' failed. - LaTeX errors: - ! LaTeX Error: File `realboxes.sty' not found. - - Type X to quit or to proceed, - or enter new name. (Default extension: sty) - ... - l.12 \usepackage - {amssymb}^^M - ! ==> Fatal error occurred, no output PDF file produced! - --- failed re-building ‘Karen.ltx’ - - SUMMARY: processing the following file failed: - ‘Karen.ltx’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# keyplayer - -
- -* Version: 1.0.3 -* GitHub: NA -* Source code: https://github.com/cran/keyplayer -* Date/Publication: 2016-04-16 10:33:52 -* Number of recursive dependencies: 20 - -Run `revdepcheck::cloud_details(, "keyplayer")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘keyplayer-Ex.R’ failed - The error most likely occurred in: - - > ### Name: fragment - > ### Title: Compute the Fragmentation Centrality Score in a Netwrok - > ### Aliases: fragment - > - > ### ** Examples - > - > # Create a 5x5 weighted and directed adjacency matrix, where edge values - ... - > # Transform the edge value to distance interpretaion - > A <- W - > A[W!=0] <- 1/W[W!=0] - > - > # List the fragmentation centrality scores for every node - > fragment(A) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: fragment -> -> graph.adjacency.dense - Execution halted - ``` - -# kknn - -
- -* Version: 1.3.1 -* GitHub: https://github.com/KlausVigo/kknn -* Source code: https://github.com/cran/kknn -* Date/Publication: 2016-03-26 22:02:21 -* Number of recursive dependencies: 7 - -Run `revdepcheck::cloud_details(, "kknn")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘kknn-Ex.R’ failed - The error most likely occurred in: - - > ### Name: specClust - > ### Title: Spectral Clustering - > ### Aliases: specClust plot.specClust - > ### Keywords: cluster - > - > ### ** Examples - > - > data(iris) - > cl <- specClust(iris[,1:4], 3, nn=5) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: specClust -> graph -> do.call -> - Execution halted - ``` - -# l1spectral - -
- -* Version: 0.99.6 -* GitHub: NA -* Source code: https://github.com/cran/l1spectral -* Date/Publication: 2022-01-26 17:12:46 UTC -* Number of recursive dependencies: 84 - -Run `revdepcheck::cloud_details(, "l1spectral")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘l1spectral-Ex.R’ failed - The error most likely occurred in: - - > ### Name: ComputePerformances - > ### Title: Compute the performances of the l1-spectral clustering algorithm - > ### Aliases: ComputePerformances - > - > ### ** Examples - > - > ############################################################# - ... - > ############################################################# - > - > data(ToyData) - > - > results <- l1_spectralclustering(A = ToyData$A_hat, pen = "lasso", - + k=2, elements = c(1,4)) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: l1_spectralclustering ... graph_from_adjacency_matrix -> graph.adjacency.dense - Execution halted - ``` - -# lconnect - -
- -* Version: 0.1.1 -* GitHub: https://github.com/FMestre1/lconnect -* Source code: https://github.com/cran/lconnect -* Date/Publication: 2021-02-06 16:10:02 UTC -* Number of recursive dependencies: 19 - -Run `revdepcheck::cloud_details(, "lconnect")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘lconnect-Ex.R’ failed - The error most likely occurred in: - - > ### Name: patch_imp - > ### Title: Prioritization of patches - > ### Aliases: patch_imp - > - > ### ** Examples - > - > vec_path <- system.file("extdata/vec_projected.shp", package = "lconnect") - > landscape <- upload_land(vec_path, bound_path = NULL, - + habitat = 1, max_dist = 500) - > importance <- patch_imp(landscape, metric = "IIC") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: patch_imp -> con_metric -> -> make_empty_graph - Execution halted - ``` - -## In both - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# leidenAlg - -
- -* Version: 1.0.5 -* GitHub: https://github.com/kharchenkolab/leidenAlg -* Source code: https://github.com/cran/leidenAlg -* Date/Publication: 2022-09-30 07:20:02 UTC -* Number of recursive dependencies: 68 - -Run `revdepcheck::cloud_details(, "leidenAlg")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘leidenAlg-Ex.R’ failed - The error most likely occurred in: - - > ### Name: as.dendrogram.fakeCommunities - > ### Title: Returns pre-calculated dendrogram - > ### Aliases: as.dendrogram.fakeCommunities - > - > ### ** Examples - > - > rLeidenComm = suppressWarnings(rleiden.community(exampleGraph, n.cores=1)) - Error in .igraph.status("Restore graph external pointer.\n") : - could not find function ".igraph.status" - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 4. └─igraph::is_igraph(graph) - 5. └─igraph:::warn_version(graph) - ── Error ('test_functions.R:25:2'): membership.fakeCommunities() functionality ── - Error in `.igraph.status("Restore graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─leidenAlg::leiden.community(exampleGraph) at test_functions.R:25:8 - 2. └─igraph::is_weighted(graph) - 3. └─igraph:::ensure_igraph(graph) - 4. └─igraph::is_igraph(graph) - 5. └─igraph:::warn_version(graph) - - [ FAIL 4 | WARN 0 | SKIP 0 | PASS 0 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking for GNU extensions in Makefiles ... NOTE - ``` - GNU make is a SystemRequirements. - ``` - -# leidenbase - -
- -* Version: 0.1.18 -* GitHub: https://github.com/cole-trapnell-lab/leidenbase -* Source code: https://github.com/cran/leidenbase -* Date/Publication: 2023-04-15 09:20:02 UTC -* Number of recursive dependencies: 54 - -Run `revdepcheck::cloud_details(, "leidenbase")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘leidenbase-Ex.R’ failed - The error most likely occurred in: - - > ### Name: leiden_find_partition - > ### Title: Leiden find partition community detection function - > ### Aliases: leiden_find_partition - > - > ### ** Examples - > - > library(igraph) - ... - - > fpath <- system.file( 'testdata', 'igraph_n1500_edgelist.txt.gz', package = 'leidenbase' ) - > zfp <- gzfile(fpath) - > igraph <- read_graph( file = zfp, format='edgelist', n=1500 ) - > res <- leiden_find_partition(igraph=igraph, - + partition_type='CPMVertexPartition', - + resolution_parameter=1e-5) - Error in leiden_find_partition(igraph = igraph, partition_type = "CPMVertexPartition", : - REAL() can only be applied to a 'numeric', not a 'NULL' - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - > testthat::test_check("leidenbase") - Loading required package: leidenbase - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Error ('test-leidenbase.R:27:3'): (code run outside of `test_that()`) ─────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─igraph::read_graph(file = zfp, format = "edgelist", n = 1500) at test-leidenbase.R:27:2 - 2. └─igraph:::read.graph.edgelist(file, ...) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘leidenbase.Rmd’ using rmarkdown - - Quitting from lines 87-92 [unnamed-chunk-1] (leidenbase.Rmd) - Error: processing vignette 'leidenbase.Rmd' failed with diagnostics: - REAL() can only be applied to a 'numeric', not a 'NULL' - --- failed re-building ‘leidenbase.Rmd’ - - SUMMARY: processing the following file failed: - ‘leidenbase.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 19.1Mb - sub-directories of 1Mb or more: - libs 18.8Mb - ``` - -# lexRankr - -
- -* Version: 0.5.2 -* GitHub: https://github.com/AdamSpannbauer/lexRankr -* Source code: https://github.com/cran/lexRankr -* Date/Publication: 2019-03-17 21:00:03 UTC -* Number of recursive dependencies: 52 - -Run `revdepcheck::cloud_details(, "lexRankr")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘lexRankr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: lexRank - > ### Title: Extractive text summarization with LexRank - > ### Aliases: lexRank - > - > ### ** Examples - > - > lexRank(c("This is a test.","Tests are fun.", - + "Do you think the exam will be hard?","Is an exam the same as a test?", - + "How many questions are going to be on the exam?")) - Parsing text into sentences and tokens...DONE - Calculating pairwise sentence similarities...DONE - Applying LexRank...Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: lexRank ... lexRankFromSimil -> -> make_empty_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ▆ - 1. └─lexRankr::lexRankFromSimil(similDf$sent1, similDf$sent2, similDf$similVal) at test-lexRankFromSimil.R:14:2 - 2. └─igraph::graph_from_data_frame(edges, directed = FALSE) - 3. └─igraph::make_empty_graph(n = 0, directed = directed) - ── Error ('test-lexRankFromSimil.R:52:3'): object out value ──────────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─lexRankr::lexRankFromSimil(similDf$sent1, similDf$sent2, similDf$similVal) at test-lexRankFromSimil.R:52:2 - 2. └─igraph::graph_from_data_frame(edges, directed = FALSE) - 3. └─igraph::make_empty_graph(n = 0, directed = directed) - - [ FAIL 8 | WARN 0 | SKIP 0 | PASS 112 ] - Error: Test failures - Execution halted - ``` - -# linkprediction - -
- -* Version: 1.0-0 -* GitHub: https://github.com/recon-icm/linkprediction -* Source code: https://github.com/cran/linkprediction -* Date/Publication: 2018-10-19 13:40:03 UTC -* Number of recursive dependencies: 43 - -Run `revdepcheck::cloud_details(, "linkprediction")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘linkprediction-Ex.R’ failed - The error most likely occurred in: - - > ### Name: proxfun - > ### Title: Vertex proximity indexes - > ### Aliases: proxfun proxfun.igraph proxfun.network - > - > ### ** Examples - > - > if(requireNamespace("igraph")) { - ... - + proxfun(g, method="aa", value="edgelist") - + - + # Random Walk with Restart - + proxfun(g, method="rwr", value="edgelist") - + } - Loading required namespace: igraph - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: ... graph_from_literal_i -> make_graph -> do.call -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ▆ - 1. └─igraph::graph(c(1, 2, 1, 3, 1, 4, 2, 4, 1, 5, 2, 5, 4, 5), directed = FALSE) at test_check_vertices.R:3:0 - 2. ├─base::do.call(old_graph, args) - 3. └─igraph (local) ``(``, directed = FALSE) - ── Error ('test_proxfun.R:3:1'): (code run outside of `test_that()`) ─────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─igraph::graph(c(1, 2, 1, 3, 1, 4, 2, 4, 1, 5, 2, 5, 4, 5), directed = FALSE) at test_proxfun.R:3:0 - 2. ├─base::do.call(old_graph, args) - 3. └─igraph (local) ``(``, directed = FALSE) - - [ FAIL 3 | WARN 0 | SKIP 0 | PASS 0 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# LoopDetectR - -
- -* Version: 0.1.2 -* GitHub: NA -* Source code: https://github.com/cran/LoopDetectR -* Date/Publication: 2020-07-20 09:20:12 UTC -* Number of recursive dependencies: 41 - -Run `revdepcheck::cloud_details(, "LoopDetectR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘LoopDetectR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: compare_loop_list - > ### Title: Compare two loop lists - > ### Aliases: compare_loop_list - > - > ### ** Examples - > - > #sample Jacobian matrix of a system with 4 variables - > jac_matrix <- rbind(c(-1,0,0,-1),c(1,-1,0,1),c(0,1,-1,0),c(0,0,1,-1)) - > #find the feedback loops of the system - > loop_list <- find_loops(jac_matrix,10) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: find_loops -> -> graph.adjacency.dense - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘workflow_LoopDetectR.Rmd’ using knitr - - Quitting from lines 53-73 [quick_example] (workflow_LoopDetectR.Rmd) - Error: processing vignette 'workflow_LoopDetectR.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘workflow_LoopDetectR.Rmd’ - - SUMMARY: processing the following file failed: - ‘workflow_LoopDetectR.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# LSVAR - -
- -* Version: 1.2 -* GitHub: NA -* Source code: https://github.com/cran/LSVAR -* Date/Publication: 2021-05-26 12:00:02 UTC -* Number of recursive dependencies: 38 - -Run `revdepcheck::cloud_details(, "LSVAR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘LSVAR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: fista.LpS - > ### Title: A function to solve low rank plus sparse model estimation using - > ### FISTA algorithm - > ### Aliases: fista.LpS - > - > ### ** Examples - > - > n <- 300 - > p <- 20 - > try <- testVAR(n, p, struct = "LS", signal = 0.75, rank = 2, - + singular_vals = c(1, 0.8)) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: testVAR -> erdos.renyi.game - Execution halted - ``` - -# lvm4net - -
- -* Version: 0.3 -* GitHub: https://github.com/igollini/lvm4net -* Source code: https://github.com/cran/lvm4net -* Date/Publication: 2019-06-13 15:40:07 UTC -* Number of recursive dependencies: 67 - -Run `revdepcheck::cloud_details(, "lvm4net")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘lvm4net-Ex.R’ failed - The error most likely occurred in: - - > ### Name: boxroc - > ### Title: Boxplot and ROC Curves - > ### Aliases: boxroc - > - > ### ** Examples - > - > - > N <- 20 - > Y <- network(N, directed = FALSE)[,] - > - > modLSM <- lsm(Y, D = 2) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: lsm ... make_call -> graph.adjacency -> graph.adjacency.dense - Execution halted - ``` - -# macrosyntR - -
- -* Version: 0.2.19 -* GitHub: https://github.com/SamiLhll/macrosyntR -* Source code: https://github.com/cran/macrosyntR -* Date/Publication: 2023-03-29 13:30:16 UTC -* Number of recursive dependencies: 63 - -Run `revdepcheck::cloud_details(, "macrosyntR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘macrosyntR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: reorder_macrosynteny - > ### Title: Reorder the mbh_df before plotting - > ### Aliases: reorder_macrosynteny - > - > ### ** Examples - > - > # basic usage of reorder_macrosynteny : - ... - > - > orthologs_table <- system.file("extdata","my_orthologs.tab",package="macrosyntR") - > - > my_orthologs <- read.table(orthologs_table,header=TRUE) - > - > my_orthologs_reordered <- reorder_macrosynteny(my_orthologs) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: reorder_macrosynteny -> -> make_empty_graph - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘macrosyntR.Rmd’ using rmarkdown - - Quitting from lines 210-221 [unnamed-chunk-12] (macrosyntR.Rmd) - Error: processing vignette 'macrosyntR.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘macrosyntR.Rmd’ - - SUMMARY: processing the following file failed: - ‘macrosyntR.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# madrat - -
- -* Version: 3.3.0 -* GitHub: https://github.com/pik-piam/madrat -* Source code: https://github.com/cran/madrat -* Date/Publication: 2023-05-02 11:10:02 UTC -* Number of recursive dependencies: 81 - -Run `revdepcheck::cloud_details(, "madrat")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘madrat-Ex.R’ failed - The error most likely occurred in: - - > ### Name: cacheGet - > ### Title: Tool: cacheGet - > ### Aliases: cacheGet - > - > ### ** Examples - > - > madrat:::cacheGet("calc", "TauTotal", packages = "madrat") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: ... fingerprint -> getDependencies -> -> make_empty_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 9. ├─madrat:::withMadratLogging(do.call(cfg$functionCode, cfg$fullNow)) - 10. │ └─base::withCallingHandlers(...) - 11. ├─base::do.call(cfg$functionCode, cfg$fullNow) - 12. └─madrat (local) ``() - 13. └─madrat::calcOutput("WarningTest", aggregate = FALSE) at test-retrieveData.R:105:4 - 14. └─madrat:::cacheGet(prefix = "calc", type = type, args = args) - 15. └─madrat:::cacheName(...) - 16. └─madrat:::fingerprint(...) - 17. └─madrat::getDependencies(...) - 18. └─igraph::graph_from_data_frame(graph) - 19. └─igraph::make_empty_graph(n = 0, directed = directed) - - [ FAIL 12 | WARN 0 | SKIP 8 | PASS 524 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘madrat-caching.Rmd’ using rmarkdown - - Quitting from lines 37-38 [unnamed-chunk-3] (madrat-caching.Rmd) - Error: processing vignette 'madrat-caching.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘madrat-caching.Rmd’ - - --- re-building ‘madrat-puc.Rmd’ using rmarkdown - ... - --- finished re-building ‘madrat-puc.Rmd’ - - --- re-building ‘madrat.Rmd’ using rmarkdown - --- finished re-building ‘madrat.Rmd’ - - SUMMARY: processing the following file failed: - ‘madrat-caching.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# malan - -
- -* Version: 1.0.2 -* GitHub: https://github.com/mikldk/malan -* Source code: https://github.com/cran/malan -* Date/Publication: 2020-06-25 12:00:06 UTC -* Number of recursive dependencies: 89 - -Run `revdepcheck::cloud_details(, "malan")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘malan-Ex.R’ failed - The error most likely occurred in: - - > ### Name: from_igraph - > ### Title: Convert igraph to population - > ### Aliases: from_igraph - > - > ### ** Examples - > - > g <- igraph::graph_from_literal( 2 +- 1 -+ 3, 4 -+ 5 ) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: ... graph_from_literal_i -> make_graph -> do.call -> - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘case-study-partial.Rmd’ using rmarkdown - - Quitting from lines 76-78 [unnamed-chunk-8] (case-study-partial.Rmd) - Error: processing vignette 'case-study-partial.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘case-study-partial.Rmd’ - - --- re-building ‘introduction.Rmd’ using rmarkdown - ... - Quitting from lines 52-53 [unnamed-chunk-6] (introduction.Rmd) - Error: processing vignette 'introduction.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘introduction.Rmd’ - - SUMMARY: processing the following files failed: - ‘case-study-partial.Rmd’ ‘introduction.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 22.8Mb - sub-directories of 1Mb or more: - libs 21.8Mb - ``` - -# manymome - -
- -* Version: 0.1.10 -* GitHub: https://github.com/sfcheung/manymome -* Source code: https://github.com/cran/manymome -* Date/Publication: 2023-06-08 15:30:03 UTC -* Number of recursive dependencies: 157 - -Run `revdepcheck::cloud_details(, "manymome")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘manymome-Ex.R’ failed - The error most likely occurred in: - - > ### Name: all_indirect_paths - > ### Title: Enumerate All Indirect Effects in a Model - > ### Aliases: all_indirect_paths all_paths_to_df - > - > ### ** Examples - > - > library(lavaan) - ... - + y ~ m12 + m2 + m11 + x + c1 + c2 - + " - > fit <- sem(mod, data_serial_parallel, - + fixed.x = FALSE) - > # All indirect paths - > out1 <- all_indirect_paths(fit) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: all_indirect_paths -> -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─manymome::all_indirect_paths(fit) at test_all_indirect_paths_lv.R:28:0 - 2. └─igraph::graph_from_adjacency_matrix(adj, mode = "directed") - 3. └─igraph:::graph.adjacency.dense(...) - ── Failure ('test_lavaan2lm_list.R:51:5'): lm_from_lavaan: predict ───────────── - predict(fit_list[["y"]], dat[3:5, ]) (`actual`) not equal to predict(lm_y, dat[3:5, ]) - coef(lm_y)[1] (`expected`). - - `actual`: 15.544720 15.345482 15.139308 - `expected`: 15.544747 15.345493 15.139317 - - [ FAIL 2 | WARN 0 | SKIP 22 | PASS 392 ] - Error: Test failures - Execution halted - ``` - -# manynet - -
- -* Version: 0.1.1 -* GitHub: https://github.com/snlab-ch/manynet -* Source code: https://github.com/cran/manynet -* Date/Publication: 2023-06-10 14:10:02 UTC -* Number of recursive dependencies: 89 - -Run `revdepcheck::cloud_details(, "manynet")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘manynet-Ex.R’ failed - The error most likely occurred in: - - > ### Name: add - > ### Title: Adding nodes and ties and their attributes - > ### Aliases: add add_nodes add_ties add_node_attribute add_tie_attribute - > - > ### ** Examples - > - > other <- create_filled(4) %>% mutate(name = c("A", "B", "C", "D")) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: %>% ... create_filled -> -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 5. ├─dplyr::mutate(ungroup(activate(graph, "nodes")), .ggraph.orig_index = seq_len(graph_order())) - 6. └─tidygraph:::mutate.tbl_graph(...) - 7. └─tidygraph::mutate_as_tbl(.data, !!!dot) - 8. ├─tibble::as_tibble(.data) - 9. └─tidygraph:::as_tibble.tbl_graph(.data) - 10. └─tidygraph:::node_tibble(x) - 11. ├─tibble::as_tibble(vertex_attr(x)) - 12. └─igraph::vertex_attr(x) - 13. └─igraph:::ensure_igraph(graph) - 14. └─igraph::is_igraph(graph) - 15. └─igraph:::warn_version(graph) - - [ FAIL 45 | WARN 0 | SKIP 0 | PASS 12 ] - Error: Test failures - Execution halted - ``` - -# matrixcut - -
- -* Version: 0.0.1 -* GitHub: NA -* Source code: https://github.com/cran/matrixcut -* Date/Publication: 2023-03-24 16:30:02 UTC -* Number of recursive dependencies: 8 - -Run `revdepcheck::cloud_details(, "matrixcut")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘matrixcut-Ex.R’ failed - The error most likely occurred in: - - > ### Name: componentplot - > ### Title: Draws a Plot Showing the Number of Components as a Function of - > ### the Cutoff Value. - > ### Aliases: componentplot - > - > ### ** Examples - > - > componentplot(xenarthra,0.75,0.9) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: componentplot -> -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘stats’ - All declared Imports should be used. - ``` - -# maxmatching - -
- -* Version: 0.1.0 -* GitHub: NA -* Source code: https://github.com/cran/maxmatching -* Date/Publication: 2017-01-15 09:51:07 -* Number of recursive dependencies: 7 - -Run `revdepcheck::cloud_details(, "maxmatching")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘maxmatching-Ex.R’ failed - The error most likely occurred in: - - > ### Name: maxmatching - > ### Title: Maximum Matching - > ### Aliases: maxmatching - > - > ### ** Examples - > - > # Unweighted general graph - > G1 <- igraph::graph(c(1, 2, 1, 3, 1, 4, 3, 4, 3, 5, - + 5, 6, 6, 7, 7, 8, 8, 9, 3, 8, 5, 8), directed = FALSE) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: -> do.call -> - Execution halted - ``` - -## In both - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# mazeGen - -
- -* Version: 0.1.3 -* GitHub: NA -* Source code: https://github.com/cran/mazeGen -* Date/Publication: 2017-12-04 17:34:53 UTC -* Number of recursive dependencies: 7 - -Run `revdepcheck::cloud_details(, "mazeGen")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘mazeGen-Ex.R’ failed - The error most likely occurred in: - - > ### Name: genEMLseed - > ### Title: Generate Equal Minimum Legs Seed - > ### Aliases: genEMLseed - > - > ### ** Examples - > - > - ... - > seed <- 1 - > - > #Search for just one unique path - > justOne <- genEMLseed(path=1,rank=rank,satPercent=satPercent,seed=seed) - > nodePosition <- np(rank,satPercent,seed=justOne) - > mazeEst(nodePosition) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: mazeEst -> graph -> do.call -> - Execution halted - ``` - -# MBNMAdose - -
- -* Version: 0.4.1 -* GitHub: NA -* Source code: https://github.com/cran/MBNMAdose -* Date/Publication: 2022-02-24 11:40:02 UTC -* Number of recursive dependencies: 95 - -Run `revdepcheck::cloud_details(, "MBNMAdose")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘MBNMAdose-Ex.R’ failed - The error most likely occurred in: - - > ### Name: MBNMAdose-package - > ### Title: MBNMAdose for dose-response Model-Based Network Meta-Analysis - > ### Aliases: MBNMAdose MBNMAdose-package - > ### Keywords: internal - > - > ### ** Examples - > - ... - > network <- mbnma.network(triptans) - Values for `agent` with dose = 0 have been recoded to `Placebo` - agent is being recoded to enforce sequential numbering and allow inclusion of `Placebo` - > - > # Generate a network plot at the dose/treatment level - > plot(network, level="treatment") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot -> plot.mbnma.network -> - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘mbnmadose.Rmd’ using rmarkdown - Warning in eng_r(options) : - Failed to tidy R code in chunk 'unnamed-chunk-2'. Reason: - Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. - - Warning in eng_r(options) : - Failed to tidy R code in chunk 'unnamed-chunk-6'. Reason: - Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. - ... - Quitting from lines 112-115 [unnamed-chunk-6] (mbnmadose.Rmd) - Error: processing vignette 'mbnmadose.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘mbnmadose.Rmd’ - - SUMMARY: processing the following file failed: - ‘mbnmadose.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 6 marked Latin-1 strings - ``` - -# MBNMAtime - -
- -* Version: 0.2.3 -* GitHub: NA -* Source code: https://github.com/cran/MBNMAtime -* Date/Publication: 2023-03-17 12:30:13 UTC -* Number of recursive dependencies: 108 - -Run `revdepcheck::cloud_details(, "MBNMAtime")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘MBNMAtime-Ex.R’ failed - The error most likely occurred in: - - > ### Name: inconsistency.loops - > ### Title: Identify comparisons in loops that fulfil criteria for - > ### node-splitting - > ### Aliases: inconsistency.loops - > - > ### ** Examples - > - ... - > data <- data.frame(studyID=c(1,1,2,2,3,3,4,4,5,5,5), - + treatment=c(1,2,1,3,2,3,3,4,1,2,4) - + ) - > - > # Identify comparisons informed by direct and indirect evidence - > inconsistency.loops(data) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: inconsistency.loops -> - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘MBNMAtime.Rmd’ using rmarkdown - - Quitting from lines 146-151 [unnamed-chunk-6] (MBNMAtime.Rmd) - Error: processing vignette 'MBNMAtime.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘MBNMAtime.Rmd’ - - SUMMARY: processing the following file failed: - ‘MBNMAtime.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# mcMST - -
- -* Version: 1.1.1 -* GitHub: https://github.com/jakobbossek/mcMST -* Source code: https://github.com/cran/mcMST -* Date/Publication: 2023-03-13 19:00:02 UTC -* Number of recursive dependencies: 138 - -Run `revdepcheck::cloud_details(, "mcMST")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘mcMST-Ex.R’ failed - The error most likely occurred in: - - > ### Name: mcMSTEmoaBG - > ### Title: Subgraph EMOA for the multi-criteria MST problem. - > ### Aliases: mcMSTEmoaBG - > - > ### ** Examples - > - > inst = genRandomMCGP(10) - > res = mcMSTEmoaBG(inst, mu = 20L, max.iter = 100L) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: mcMSTEmoaBG ... -> make_graph -> do.call -> - Execution halted - ``` - -# mcvis - -
- -* Version: 1.0.8 -* GitHub: NA -* Source code: https://github.com/cran/mcvis -* Date/Publication: 2021-07-30 08:20:05 UTC -* Number of recursive dependencies: 92 - -Run `revdepcheck::cloud_details(, "mcvis")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘mcvis-Ex.R’ failed - The error most likely occurred in: - - > ### Name: alt_mcvis - > ### Title: Multi-collinearity Visualization plots - > ### Aliases: alt_mcvis ggplot_mcvis igraph_mcvis plot.mcvis - > - > ### ** Examples - > - > set.seed(1) - ... - > n = 100 - > X = matrix(rnorm(n*p), ncol = p) - > X[,1] = X[,2] + rnorm(n, 0, 0.1) - > mcvis_result = mcvis(X) - > plot(mcvis_result) - > plot(mcvis_result, type = "igraph") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot ... igraph_mcvis -> -> graph.incidence.dense - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Error ('test-plot-mcvis.R:10:1'): (code run outside of `test_that()`) ─────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. ├─base::plot(mcvis_result, type = "igraph") at test-plot-mcvis.R:10:0 - 2. └─mcvis:::plot.mcvis(mcvis_result, type = "igraph") - 3. └─mcvis::igraph_mcvis(mcvis_result = x, eig_max = eig_max, var_max = var_max) - 4. └─igraph::graph_from_incidence_matrix(M) - 5. └─igraph:::graph.incidence.dense(...) - - [ FAIL 1 | WARN 1 | SKIP 0 | PASS 3 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘mcvis.Rmd’ using rmarkdown - - Quitting from lines 71-72 [unnamed-chunk-4] (mcvis.Rmd) - Error: processing vignette 'mcvis.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘mcvis.Rmd’ - - SUMMARY: processing the following file failed: - ‘mcvis.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# meconetcomp - -
- -* Version: 0.2.0 -* GitHub: https://github.com/ChiLiubio/meconetcomp -* Source code: https://github.com/cran/meconetcomp -* Date/Publication: 2022-10-05 15:20:02 UTC -* Number of recursive dependencies: 147 - -Run `revdepcheck::cloud_details(, "meconetcomp")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘meconetcomp-Ex.R’ failed - The error most likely occurred in: - - > ### Name: cal_module - > ### Title: Assign modules to each network - > ### Aliases: cal_module - > - > ### ** Examples - > - > data(soil_amp_network) - > soil_amp_network <- cal_module(soil_amp_network) - Error in .igraph.status("Restore graph external pointer.\n") : - could not find function ".igraph.status" - Calls: cal_module ... is_directed -> ensure_igraph -> is_igraph -> warn_version - Execution halted - ``` - -# Mercator - -
- -* Version: 1.1.2 -* GitHub: NA -* Source code: https://github.com/cran/Mercator -* Date/Publication: 2022-06-30 16:20:02 UTC -* Number of recursive dependencies: 98 - -Run `revdepcheck::cloud_details(, "Mercator")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘test-01Metrics.R’ - Comparing ‘test-01Metrics.Rout’ to ‘test-01Metrics.Rout.save’ ... OK - Running ‘test-02binmat.R’ - Comparing ‘test-02binmat.Rout’ to ‘test-02binmat.Rout.save’ ... OK - Running ‘test-03thresh.R’ - Comparing ‘test-03thresh.Rout’ to ‘test-03thresh.Rout.save’ ... OK - Running ‘test-04vis.R’ - Running the tests in ‘tests/test-04vis.R’ failed. - Last 13 lines of output: - > vis1 <- addVisualization(vis1, "tsne", perplexity=30) - ... - > ## hclust - > vis1 <- addVisualization(vis1, "hclust") - > plot(vis1, view = "hclust") - > - > ## now test the igraph part - > vis1 <- addVisualization(vis1, "graph") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: addVisualization ... createGraph -> graph_from_data_frame -> make_empty_graph - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘mercVis.Rmd’ using rmarkdown - - Quitting from lines 118-124 [igraph] (mercVis.Rmd) - Error: processing vignette 'mercVis.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘mercVis.Rmd’ - - --- re-building ‘mercator.Rmd’ using rmarkdown - ... - --- failed re-building ‘mercator.Rmd’ - - --- re-building ‘umap-som.Rmd’ using rmarkdown - --- finished re-building ‘umap-som.Rmd’ - - SUMMARY: processing the following files failed: - ‘mercVis.Rmd’ ‘mercator.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# metacoder - -
- -* Version: 0.3.6 -* GitHub: https://github.com/grunwaldlab/metacoder -* Source code: https://github.com/cran/metacoder -* Date/Publication: 2023-04-04 02:20:02 UTC -* Number of recursive dependencies: 201 - -Run `revdepcheck::cloud_details(, "metacoder")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘metacoder-Ex.R’ failed - The error most likely occurred in: - - > ### Name: layout_functions - > ### Title: Layout functions - > ### Aliases: layout_functions - > - > ### ** Examples - > - > # List available function names: - ... - [4] "gem" "graphopt" "mds" - [7] "fruchterman-reingold" "kamada-kawai" "large-graph" - [10] "drl" - > - > # Execute layout function on graph: - > layout_functions("davidson-harel", igraph::make_ring(5)) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: layout_functions -> -> ensure_igraph -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 6. ├─metacoder::heat_tree(...) - 7. └─metacoder:::heat_tree.Taxmap(...) - 8. ├─base::do.call(heat_tree, arguments) - 9. ├─metacoder (local) ``(...) - 10. └─metacoder:::heat_tree.default(...) - 11. └─base::lapply(sub_graph_taxa, get_sub_graphs) - 12. └─metacoder (local) FUN(X[[i]], ...) - 13. └─igraph::graph_from_edgelist(edgelist) - 14. └─igraph::make_graph(unname(ids[t(el)]), directed = directed) - 15. ├─base::do.call(old_graph, args) - 16. └─igraph (local) ``(``, directed = TRUE) - - [ FAIL 3 | WARN 0 | SKIP 3 | PASS 533 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘R6’ - All declared Imports should be used. - ``` - -# metanetwork - -
- -* Version: 0.7.0 -* GitHub: https://github.com/MarcOhlmann/metanetwork -* Source code: https://github.com/cran/metanetwork -* Date/Publication: 2022-12-05 14:10:02 UTC -* Number of recursive dependencies: 106 - -Run `revdepcheck::cloud_details(, "metanetwork")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘metanetwork-Ex.R’ failed - The error most likely occurred in: - - > ### Name: append_agg_nets - > ### Title: append aggregated networks - > ### Aliases: append_agg_nets append_agg_nets.metanetwork - > - > ### ** Examples - > - > library(metanetwork) - > data(meta_angola) - > meta_angola = append_agg_nets(meta_angola) - Error in .igraph.status("Restore graph external pointer.\n") : - could not find function ".igraph.status" - Calls: append_agg_nets ... graph_attr -> ensure_igraph -> is_igraph -> warn_version - Execution halted - ``` - -# MetricGraph - -
- -* Version: 1.1.1 -* GitHub: https://github.com/davidbolin/MetricGraph -* Source code: https://github.com/cran/MetricGraph -* Date/Publication: 2023-06-01 12:00:11 UTC -* Number of recursive dependencies: 124 - -Run `revdepcheck::cloud_details(, "MetricGraph")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘MetricGraph-Ex.R’ failed - The error most likely occurred in: - - > ### Name: graph_components - > ### Title: Connected components of metric graph - > ### Aliases: graph_components - > - > ### ** Examples - > - > library(sp) - ... - > line2 <- Line(rbind(c(1, 0), c(2, 0))) - > line3 <- Line(rbind(c(1, 1), c(2, 1))) - > Lines <- SpatialLines(list(Lines(list(line1), ID = "1"), - + Lines(list(line2), ID = "2"), - + Lines(list(line3), ID = "3"))) - > graphs <- graph_components$new(Lines) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: -> initialize -> graph -> do.call -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 4. ├─base::do.call(old_graph, args) - 5. └─igraph (local) ``(``, directed = FALSE) - ── Error ('test_split_line.R:12:1'): Testing if splitting edges, and adding obsevations casuse error ── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─metric_graph$new(lines = Lines) at test_split_line.R:12:0 - 2. └─MetricGraph (local) initialize(...) - 3. └─igraph::graph(edges = c(t(self$E)), directed = FALSE) - 4. ├─base::do.call(old_graph, args) - 5. └─igraph (local) ``(``, directed = FALSE) - - [ FAIL 12 | WARN 0 | SKIP 1 | PASS 8 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 19.9Mb - sub-directories of 1Mb or more: - libs 19.0Mb - ``` - -# mfpp - -
- -* Version: 0.0.4 -* GitHub: https://github.com/kzst/mfpp -* Source code: https://github.com/cran/mfpp -* Date/Publication: 2022-08-22 10:20:02 UTC -* Number of recursive dependencies: 65 - -Run `revdepcheck::cloud_details(, "mfpp")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘mfpp-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plot.mfpp - > ### Title: Plot function for Matrix-Based Flexible Project Planning - > ### Aliases: plot.PDM_matrix plot.PDM_list plot.Set_PDM_matrix - > ### plot.Set_PDM_list plot.TPT - > - > ### ** Examples - > - ... - > - > # Generation of PDM list for TCTP a project scenario using MFPP package. - > - > PDM<-generatepdm(N,ff,cf,mTD,mCD,mRD,w,nR,nW,scale,lst=TRUE) - > - > plot(PDM) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot ... plot.PDM_matrix -> -> graph.adjacency.dense - Execution halted - ``` - -# migraph - -
- -* Version: 0.13.2 -* GitHub: https://github.com/snlab-ch/migraph -* Source code: https://github.com/cran/migraph -* Date/Publication: 2022-12-20 16:20:02 UTC -* Number of recursive dependencies: 138 - -Run `revdepcheck::cloud_details(, "migraph")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘migraph-Ex.R’ failed - The error most likely occurred in: - - > ### Name: add - > ### Title: Adding and copying attributes from one graph to another - > ### Aliases: add add_node_attribute add_tie_attribute copy_node_attributes - > ### join_ties - > - > ### ** Examples - > - > add_node_attribute(mpn_elite_mex, "wealth", 1:35) - Error in .igraph.status("Restore graph external pointer.\n") : - could not find function ".igraph.status" - Calls: add_node_attribute ... -> ensure_igraph -> is_igraph -> warn_version - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ── Error ('test-viz_layout_partition.R:20:3'): concentric layout works ───────── - Error in `.igraph.status("Restore graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─migraph::layout_tbl_graph_concentric(ison_southern_women) at test-viz_layout_partition.R:20:2 - 2. ├─migraph::is_twomode(object) - 3. └─migraph:::is_twomode.igraph(object) - 4. └─igraph::is.bipartite(object) - 5. └─igraph:::ensure_igraph(graph) - 6. └─igraph::is_igraph(graph) - 7. └─igraph:::warn_version(graph) - - [ FAIL 85 | WARN 0 | SKIP 0 | PASS 12 ] - Error: Test failures - Execution halted - ``` - -# miniCRAN - -
- -* Version: 0.2.16 -* GitHub: https://github.com/andrie/miniCRAN -* Source code: https://github.com/cran/miniCRAN -* Date/Publication: 2022-02-14 09:00:05 UTC -* Number of recursive dependencies: 108 - -Run `revdepcheck::cloud_details(, "miniCRAN")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘spelling.R’ - Running ‘test-all.R’ - Running the tests in ‘tests/test-all.R’ failed. - Last 13 lines of output: - ── Error ('test-2-makeDepGraph.R:66:3'): makeDepGraph and pgkDep gives similar results for MASS ── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. ├─testthat::expect_true(checkPkgDepFunctions(tag)) at test-2-makeDepGraph.R:66:2 - 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") - 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) - 4. └─miniCRAN (local) checkPkgDepFunctions(tag) - 5. └─miniCRAN::makeDepGraph(...) at test-2-makeDepGraph.R:12:2 - 6. └─igraph::graph.data.frame(d = edges, directed = TRUE, vertices = vert) - 7. └─igraph::make_empty_graph(n = 0, directed = directed) - - [ FAIL 2 | WARN 3 | SKIP 28 | PASS 32 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘miniCRAN-dependency-graph.rmd’ using rmarkdown - - Quitting from lines 55-58 [makeDepGraph] (miniCRAN-dependency-graph.rmd) - Error: processing vignette 'miniCRAN-dependency-graph.rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘miniCRAN-dependency-graph.rmd’ - - --- re-building ‘miniCRAN-introduction.rmd’ using rmarkdown - ... - --- finished re-building ‘miniCRAN-introduction.rmd’ - - --- re-building ‘miniCRAN-non-CRAN-repos.rmd’ using rmarkdown - --- finished re-building ‘miniCRAN-non-CRAN-repos.rmd’ - - SUMMARY: processing the following file failed: - ‘miniCRAN-dependency-graph.rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# missSBM - -
- -* Version: 1.0.3 -* GitHub: https://github.com/grossSBM/missSBM -* Source code: https://github.com/cran/missSBM -* Date/Publication: 2022-08-23 12:10:06 UTC -* Number of recursive dependencies: 113 - -Run `revdepcheck::cloud_details(, "missSBM")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘missSBM-Ex.R’ failed - The error most likely occurred in: - - > ### Name: estimateMissSBM - > ### Title: Estimation of simple SBMs with missing data - > ### Aliases: estimateMissSBM - > - > ### ** Examples - > - > ## SBM parameters - ... - - > - > myModel <- collection$bestModel - > plot(myModel, "expected") - > plot(myModel, "imputed") - > plot(myModel, "meso") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot ... -> plotMeso -> -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 10.6Mb - sub-directories of 1Mb or more: - libs 8.6Mb - ``` - -# mlmts - -
- -* Version: 1.1.1 -* GitHub: NA -* Source code: https://github.com/cran/mlmts -* Date/Publication: 2023-01-22 21:30:02 UTC -* Number of recursive dependencies: 236 - -Run `revdepcheck::cloud_details(, "mlmts")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘mlmts-Ex.R’ failed - The error most likely occurred in: - - > ### Name: dis_mcc - > ### Title: Constructs a pairwise distance matrix based on maximal - > ### cross-correlations - > ### Aliases: dis_mcc - > - > ### ** Examples - > - > reduced_dataset <- dis_mcc(RacketSports$data[1], features = TRUE) # Reducing - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: dis_mcc ... lapply -> FUN -> -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘ClusterR’ ‘MASS’ ‘Rdpack’ ‘multiwave’ ‘randomForest’ ‘ranger’ - All declared Imports should be used. - ``` - -# mnda - -
- -* Version: 1.0.9 -* GitHub: NA -* Source code: https://github.com/cran/mnda -* Date/Publication: 2023-01-25 08:30:02 UTC -* Number of recursive dependencies: 89 - -Run `revdepcheck::cloud_details(, "mnda")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘mnda-Ex.R’ failed - The error most likely occurred in: - - > ### Name: EDNN - > ### Title: Encoder decoder neural network (EDNN) function - > ### Aliases: EDNN - > - > ### ** Examples - > - > myNet = network_gen(N_nodes = 50) - > graphData = myNet[["data_graph"]] - > edge.list = graphData[,1:2] - > edge.weight = graphData[,3:4] - > XY = ednn_IOprepare(edge.list, edge.weight) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: ednn_IOprepare ... graph_from_edgelist -> make_graph -> do.call -> - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘MASS’ ‘Matrix’ ‘magrittr’ ‘reticulate’ ‘tensorflow’ ‘usethis’ - All declared Imports should be used. - ``` - -# modnets - -
- -* Version: 0.9.0 -* GitHub: https://github.com/tswanson222/modnets -* Source code: https://github.com/cran/modnets -* Date/Publication: 2021-10-01 08:20:02 UTC -* Number of recursive dependencies: 136 - -Run `revdepcheck::cloud_details(, "modnets")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘modnets-Ex.R’ failed - The error most likely occurred in: - - > ### Name: CentClust - > ### Title: Node centrality, clustering coefficients, and shortest path - > ### lengths - > ### Aliases: CentClust centAuto clustAuto - > - > ### ** Examples - > - > x <- fitNetwork(ggmDat, 'M') - > - > clustAuto(x) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: clustAuto -> -> graph.adjacency.dense - Execution halted - ``` - -# molnet - -
- -* Version: 0.1.0 -* GitHub: NA -* Source code: https://github.com/cran/molnet -* Date/Publication: 2021-08-06 08:30:02 UTC -* Number of recursive dependencies: 123 - -Run `revdepcheck::cloud_details(, "molnet")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘molnet-Ex.R’ failed - The error most likely occurred in: - - > ### Name: determine_drug_targets - > ### Title: Determine drug target nodes in network - > ### Aliases: determine_drug_targets - > - > ### ** Examples - > - > data(drug_gene_interactions) - ... - + interaction_table=drug_gene_interactions, - + match_on='gene_name') - > drug_targets <- determine_drug_targets(combined_graphs[["graphs"]], - + combined_graphs[["annotations"]], - + drug_target_interaction, - + settings) - Error in .igraph.status("Restore graph external pointer.\n") : - could not find function ".igraph.status" - Calls: determine_drug_targets ... -> ensure_igraph -> is_igraph -> warn_version - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘Molnet_Vignette.Rmd’ using rmarkdown - - Quitting from lines 255-256 [Individual Graphs] (Molnet_Vignette.Rmd) - Error: processing vignette 'Molnet_Vignette.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘Molnet_Vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘Molnet_Vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# moranajp - -
- -* Version: 0.9.6 -* GitHub: https://github.com/matutosi/moranajp -* Source code: https://github.com/cran/moranajp -* Date/Publication: 2023-02-28 05:12:29 UTC -* Number of recursive dependencies: 129 - -Run `revdepcheck::cloud_details(, "moranajp")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘moranajp-Ex.R’ failed - The error most likely occurred in: - - > ### Name: draw_bigram_network - > ### Title: Draw bigram network using morphological analysis data. - > ### Aliases: draw_bigram_network bigram bigram_depend bigram_network - > ### word_freq bigram_network_plot - > - > ### ** Examples - > - ... - + clean_up(use_common_data = TRUE, synonym_df = synonym) - Joining with `by = join_by(原形)` - > - > bigram_neko <- - + neko_mecab %>% - + draw_bigram_network() - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: %>% ... bigram_network -> %>% -> -> make_empty_graph - Execution halted - ``` - -# motifcluster - -
- -* Version: 0.2.3 -* GitHub: https://github.com/wgunderwood/motifcluster -* Source code: https://github.com/cran/motifcluster -* Date/Publication: 2022-11-18 08:10:02 UTC -* Number of recursive dependencies: 66 - -Run `revdepcheck::cloud_details(, "motifcluster")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘motifcluster-Ex.R’ failed - The error most likely occurred in: - - > ### Name: get_largest_component - > ### Title: Get largest connected component - > ### Aliases: get_largest_component - > - > ### ** Examples - > - > adj_mat <- matrix(c(0, 1, 0, 0, 0, 0, 0, 0, 0), nrow = 3) - > get_largest_component(adj_mat) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: get_largest_component ... graph_from_adjacency_matrix -> graph.adjacency.dense - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 5. └─igraph::make_empty_graph(n = vc, directed = (mode == "directed")) - ── Error ('test_utils.R:65:3'): get_largest_component returns correct indices ── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. ├─testthat::expect_equal(...) at test_utils.R:65:2 - 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") - 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) - 4. └─motifcluster::get_largest_component(adj_mat_dense) - 5. └─igraph::graph_from_adjacency_matrix(...) - 6. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 4 | WARN 0 | SKIP 0 | PASS 478 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘motifcluster_vignette.Rmd’ using rmarkdown - - Quitting from lines 424-429 [unnamed-chunk-23] (motifcluster_vignette.Rmd) - Error: processing vignette 'motifcluster_vignette.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘motifcluster_vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘motifcluster_vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# motifr - -
- -* Version: 1.0.0 -* GitHub: https://github.com/marioangst/motifr -* Source code: https://github.com/cran/motifr -* Date/Publication: 2020-12-10 15:40:02 UTC -* Number of recursive dependencies: 121 - -Run `revdepcheck::cloud_details(, "motifr")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘motifr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: directed_dummy_net - > ### Title: Two-level directed network dummy example - > ### Aliases: directed_dummy_net - > ### Keywords: datasets - > - > ### ** Examples - > - > plot_mnet(directed_dummy_net) - Error in .igraph.status("Restore graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot_mnet ... vertex_attr -> ensure_igraph -> is_igraph -> warn_version - Execution halted - ``` - -# mppR - -
- -* Version: 1.4.0 -* GitHub: https://github.com/vincentgarin/mppR -* Source code: https://github.com/cran/mppR -* Date/Publication: 2023-01-05 20:50:02 UTC -* Number of recursive dependencies: 71 - -Run `revdepcheck::cloud_details(, "mppR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘mppR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: MQE_gen_effects - > ### Title: QTL genetic effects multi-QTL effect model - > ### Aliases: MQE_gen_effects - > - > ### ** Examples - > - > - ... - > - > SIM <- mpp_SIM(mppData = mppData) - > QTL <- QTL_select(SIM) - > - > QTL.eff <- MQE_gen_effects(mppData = mppData, QTL = QTL[, 1], - + Q.eff = c("anc", "par", "biall")) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: MQE_gen_effects ... graph_from_edgelist -> make_graph -> do.call -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ▆ - 1. └─mppR::mpp_proc(...) at test_mpp_proc.R:32:2 - 2. └─mppR::QTL_gen_effects(...) - 3. └─base::mapply(...) - 4. └─mppR (local) ``(...) - 5. └─mppR::design_connectivity(...) - 6. └─igraph::graph(vertices) - 7. └─igraph::graph_from_edgelist(el, directed = directed) - 8. └─igraph::make_graph(unname(ids[t(el)]), directed = directed) - 9. ├─base::do.call(old_graph, args) - 10. └─igraph (local) ``(``, directed = TRUE) - - [ FAIL 3 | WARN 0 | SKIP 0 | PASS 24 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘MPP_ME_QTL_detect.Rmd’ using rmarkdown - - Quitting from lines 126-129 [setup] (MPP_ME_QTL_detect.Rmd) - Error: processing vignette 'MPP_ME_QTL_detect.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘MPP_ME_QTL_detect.Rmd’ - - --- re-building ‘mppR_gen_vignette.Rmd’ using rmarkdown - ... - Quitting from lines 355-360 [design_connectivity] (mppR_gen_vignette.Rmd) - Error: processing vignette 'mppR_gen_vignette.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘mppR_gen_vignette.Rmd’ - - SUMMARY: processing the following files failed: - ‘MPP_ME_QTL_detect.Rmd’ ‘mppR_gen_vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# MRFcov - -
- -* Version: 1.0.39 -* GitHub: https://github.com/nicholasjclark/MRFcov -* Source code: https://github.com/cran/MRFcov -* Date/Publication: 2023-04-06 10:13:19 UTC -* Number of recursive dependencies: 115 - -Run `revdepcheck::cloud_details(, "MRFcov")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘MRFcov-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plotMRF_hm - > ### Title: Plot MRF interaction parameters as a heatmap - > ### Aliases: plotMRF_hm - > - > ### ** Examples - > - > - ... - ℹ Please use one dimensional logical vectors instead. - ℹ The deprecated feature was likely used in the MRFcov package. - Please report the issue to the authors. - > - > #To plot as an igraph network instead, we can simply extract the adjacency matrix - > net <- igraph::graph.adjacency(CRFmod$graph, weighted = TRUE, mode = "undirected") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: -> graph.adjacency.dense - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘Bird_Parasite_CRF.Rmd’ using rmarkdown - - Quitting from lines 52-58 [unnamed-chunk-6] (Bird_Parasite_CRF.Rmd) - Error: processing vignette 'Bird_Parasite_CRF.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘Bird_Parasite_CRF.Rmd’ - - --- re-building ‘CRF_data_prep.Rmd’ using rmarkdown - ... - --- finished re-building ‘CRF_data_prep.Rmd’ - - --- re-building ‘Gaussian_Poisson_CRFs.Rmd’ using rmarkdown - --- finished re-building ‘Gaussian_Poisson_CRFs.Rmd’ - - SUMMARY: processing the following file failed: - ‘Bird_Parasite_CRF.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# MRReg - -
- -* Version: 0.1.5 -* GitHub: https://github.com/DarkEyes/MRReg -* Source code: https://github.com/cran/MRReg -* Date/Publication: 2022-08-19 15:30:02 UTC -* Number of recursive dependencies: 99 - -Run `revdepcheck::cloud_details(, "MRReg")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘MRReg-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plotOptimalClustersTree - > ### Title: plotOptimalClustersTree - > ### Aliases: plotOptimalClustersTree - > - > ### ** Examples - > - > # Running FindMaxHomoOptimalPartitions using simulation data - ... - Warning in summary.lm(submodels[[inx2]]) : - essentially perfect fit: summary may be unreliable - Warning in summary.lm(submodels[[inx2]]) : - essentially perfect fit: summary may be unreliable - > # Plotting the result - > plotOptimalClustersTree(obj) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plotOptimalClustersTree ... graph_from_adjacency_matrix -> graph.adjacency.dense - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘MDLResFramework_Demo.Rmd’ using knitr - - Quitting from lines 51-52 [unnamed-chunk-2] (MDLResFramework_Demo.Rmd) - Error: processing vignette 'MDLResFramework_Demo.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘MDLResFramework_Demo.Rmd’ - - SUMMARY: processing the following file failed: - ‘MDLResFramework_Demo.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# MRS - -
- -* Version: 1.2.4 -* GitHub: NA -* Source code: https://github.com/cran/MRS -* Date/Publication: 2018-01-23 09:10:10 UTC -* Number of recursive dependencies: 10 - -Run `revdepcheck::cloud_details(, "MRS")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘MRS-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plotTree - > ### Title: Plot nodes of the representative tree - > ### Aliases: plotTree - > - > ### ** Examples - > - > set.seed(1) - ... - > X = rbind(X1, X2) - > colnames(X) = c(1,2) - > G = c(rep(1, n1), rep(2,n2)) - > - > ans = mrs(X, G, K=8) - > plotTree(ans, type = "prob", legend = TRUE) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plotTree -> -> do.call -> - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 7.2Mb - sub-directories of 1Mb or more: - libs 7.1Mb - ``` - -# mstknnclust - -
- -* Version: 0.3.2 -* GitHub: NA -* Source code: https://github.com/cran/mstknnclust -* Date/Publication: 2023-01-27 14:10:02 UTC -* Number of recursive dependencies: 36 - -Run `revdepcheck::cloud_details(, "mstknnclust")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘mstknnclust-Ex.R’ failed - The error most likely occurred in: - - > ### Name: compute.costs.proximity.graph - > ### Title: Computes the edge costs sum of a proximity graph - > ### Aliases: compute.costs.proximity.graph - > ### Keywords: internal - > - > ### ** Examples - > - ... - > ##Generates complete graph (CG) - > - > cg <- generate.complete.graph(1:nrow(x),d) - > - > ##Generates a proximity graph (MST) - > mstree <- generate.mst(cg) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: generate.mst -> -> make_empty_graph - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘guide.Rmd’ using rmarkdown - - Quitting from lines 77-79 [unnamed-chunk-4] (guide.Rmd) - Error: processing vignette 'guide.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘guide.Rmd’ - - SUMMARY: processing the following file failed: - ‘guide.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# MTA - -
- -* Version: 0.4.1 -* GitHub: https://github.com/riatelab/MTA -* Source code: https://github.com/cran/MTA -* Date/Publication: 2022-06-03 16:00:02 UTC -* Number of recursive dependencies: 51 - -Run `revdepcheck::cloud_details(, "MTA")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘MTA-Ex.R’ failed - The error most likely occurred in: - - > ### Name: map_mst - > ### Title: Map Multiscalar Typology (3 deviations) - > ### Aliases: map_mst - > - > ### ** Examples - > - > # Load data - ... - > ept <- st_read(system.file("metroparis.gpkg", package = "MTA"), layer = "ept", quiet = TRUE) - > - > # Prerequisites - Compute the 3 deviations - > com$gdev <- gdev(x = com, var1 = "INC", var2 = "TH") - > com$tdev <- tdev(x = com, var1 = "INC", var2 = "TH", key = "EPT") - > com$sdev <- sdev(x = com, var1 = "INC", var2 = "TH", order = 1) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: sdev ... contiguityMat -> -> graph.adjacency.dense - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘MTA.Rmd’ using rmarkdown - --- finished re-building ‘MTA.Rmd’ - - --- re-building ‘MTA_Scenario.Rmd’ using rmarkdown - - Quitting from lines 439-473 [localdevrel_plot] (MTA_Scenario.Rmd) - Error: processing vignette 'MTA_Scenario.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘MTA_Scenario.Rmd’ - - SUMMARY: processing the following file failed: - ‘MTA_Scenario.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# mully - -
- -* Version: 2.1.38 -* GitHub: https://github.com/frankkramer-lab/mully -* Source code: https://github.com/cran/mully -* Date/Publication: 2023-02-22 17:00:03 UTC -* Number of recursive dependencies: 51 - -Run `revdepcheck::cloud_details(, "mully")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘mully-Ex.R’ failed - The error most likely occurred in: - - > ### Name: addEdge - > ### Title: Add an edge - > ### Aliases: addEdge - > - > ### ** Examples - > - > g=mully::demo() - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: -> mully -> graph.empty - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘mully-pdf.Rmd’ using rmarkdown - A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TinyTeX with tinytex::reinstall_tinytex(repository = "illinois"). - - tlmgr: Local TeX Live (2022) is older than remote repository (2023). - Cross release updates are only supported with - update-tlmgr-latest(.sh/.exe) --update - See https://tug.org/texlive/upgrade.html for details. - Warning in system2("tlmgr", args, ...) : - running command ''tlmgr' search --file --global '/grffile.sty'' had status 1 - ... - --- failed re-building ‘mully-pdf.Rmd’ - - --- re-building ‘mully-vignette.Rmd’ using rmarkdown - --- finished re-building ‘mully-vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘mully-pdf.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# multilaterals - -
- -* Version: 1.0 -* GitHub: NA -* Source code: https://github.com/cran/multilaterals -* Date/Publication: 2017-09-07 15:23:58 UTC -* Number of recursive dependencies: 11 - -Run `revdepcheck::cloud_details(, "multilaterals")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘multilaterals-Ex.R’ failed - The error most likely occurred in: - - > ### Name: multilaterals - > ### Title: Transitive Index Numbers for Cross-Sections and Panel Data - > ### Aliases: multilaterals-package multilaterals - > ### Keywords: package - > - > ### ** Examples - > - ... - Error in .igraph.status("Free graph external pointer.\n") : - could not find function ".igraph.status" - Error in .igraph.status("Free graph external pointer.\n") : - could not find function ".igraph.status" - Error in .igraph.status("Free graph external pointer.\n") : - could not find function ".igraph.status" - Error in .igraph.status("Free graph external pointer.\n") : - could not find function ".igraph.status" - Error in .igraph.status("Free graph external pointer.\n") : - could not find function ".igraph.status" - ``` - -# multilink - -
- -* Version: 0.1.1 -* GitHub: https://github.com/aleshing/multilink -* Source code: https://github.com/cran/multilink -* Date/Publication: 2023-06-09 14:20:07 UTC -* Number of recursive dependencies: 57 - -Run `revdepcheck::cloud_details(, "multilink")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘multilink-Ex.R’ failed - The error most likely occurred in: - - > ### Name: find_bayes_estimate - > ### Title: Find the Bayes Estimate of a Partition - > ### Aliases: find_bayes_estimate - > - > ### ** Examples - > - > # Example with small no duplicate dataset - ... - > # The following line corresponds to only keeping pairs of records as - > # potential matches in the initialization for which neither gname nor fname - > # disagree at the highest level - > pairs_to_keep <- (comparison_list$comparisons[, "gname_DL_3"] != TRUE) & - + (comparison_list$comparisons[, "fname_DL_3"] != TRUE) - > Z_init <- initialize_partition(comparison_list, pairs_to_keep, seed = 42) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: initialize_partition ... -> make_graph -> do.call -> - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 8.7Mb - sub-directories of 1Mb or more: - libs 8.4Mb - ``` - -# multinets - -
- -* Version: 0.2.2 -* GitHub: https://github.com/neylsoncrepalde/multinets -* Source code: https://github.com/cran/multinets -* Date/Publication: 2019-12-14 17:20:03 UTC -* Number of recursive dependencies: 73 - -Run `revdepcheck::cloud_details(, "multinets")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘multinets-Ex.R’ failed - The error most likely occurred in: - - > ### Name: extract_highlevel - > ### Title: Extract the high level of a multilevel network - > ### Aliases: extract_highlevel - > - > ### ** Examples - > - > organizations <- extract_highlevel(linked_sim) - Error in .igraph.status("Restore graph external pointer.\n") : - could not find function ".igraph.status" - Calls: extract_highlevel ... -> ensure_igraph -> is_igraph -> warn_version - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 12. └─igraph:::ensure_igraph(graph) - 13. └─igraph::is_igraph(graph) - 14. └─igraph:::warn_version(graph) - ── Error ('test-mode_transformation.R:15:3'): mode transformation works without specifying 'which' ── - Error in `.igraph.status("Restore graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─igraph::bipartite_projection(g.bip) at test-mode_transformation.R:15:2 - 2. └─igraph:::ensure_igraph(graph) - 3. └─igraph::is_igraph(graph) - 4. └─igraph:::warn_version(graph) - - [ FAIL 4 | WARN 0 | SKIP 0 | PASS 10 ] - Error: Test failures - Execution halted - ``` - -# multinma - -
- -* Version: 0.5.1 -* GitHub: https://github.com/dmphillippo/multinma -* Source code: https://github.com/cran/multinma -* Date/Publication: 2023-05-24 11:20:02 UTC -* Number of recursive dependencies: 139 - -Run `revdepcheck::cloud_details(, "multinma")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘multinma-Ex.R’ failed - The error most likely occurred in: - - > ### Name: example_pso_mlnmr - > ### Title: Example plaque psoriasis ML-NMR - > ### Aliases: example_pso_mlnmr - > ### Keywords: examples - > - > ### ** Examples - > - ... - + study = studyc, - + trt = trtc, - + r = pasi75_r, - + n = pasi75_n, - + trt_class = trtclass) - + ) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: combine_network ... as.igraph.nma_data -> -> make_empty_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─multinma::nma(...) at test-relative_effects.R:10:0 - 2. └─multinma::is_network_connected(network) - 3. ├─igraph::is_connected(igraph::as.igraph(network)) - 4. │ └─igraph:::ensure_igraph(graph) - 5. ├─igraph::as.igraph(network) - 6. └─multinma:::as.igraph.nma_data(network) - 7. └─igraph::graph_from_data_frame(e_all, directed = FALSE, vertices = v_all) - 8. └─igraph::make_empty_graph(n = 0, directed = directed) - - [ FAIL 26 | WARN 0 | SKIP 12 | PASS 320 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 286.7Mb - sub-directories of 1Mb or more: - doc 4.0Mb - libs 281.3Mb - ``` - -* checking for GNU extensions in Makefiles ... NOTE - ``` - GNU make is a SystemRequirements. - ``` - -# MultIS - -
- -* Version: 0.6.2 -* GitHub: NA -* Source code: https://github.com/cran/MultIS -* Date/Publication: 2021-08-06 11:10:02 UTC -* Number of recursive dependencies: 81 - -Run `revdepcheck::cloud_details(, "MultIS")` for more info - -
- -## Newly broken - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘QuickStart.Rmd’ using knitr - - Quitting from lines 189-203 [QS-clusteringC3] (QuickStart.Rmd) - Error: processing vignette 'QuickStart.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘QuickStart.Rmd’ - - SUMMARY: processing the following file failed: - ‘QuickStart.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘poweRlaw’ ‘rmutil’ - All declared Imports should be used. - ``` - -# multivariance - -
- -* Version: 2.4.1 -* GitHub: NA -* Source code: https://github.com/cran/multivariance -* Date/Publication: 2021-10-06 15:50:05 UTC -* Number of recursive dependencies: 37 - -Run `revdepcheck::cloud_details(, "multivariance")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘multivariance-Ex.R’ failed - The error most likely occurred in: - - > ### Name: clean.graph - > ### Title: cleanup dependence structure graph - > ### Aliases: clean.graph - > - > ### ** Examples - > - > N = 200 - ... - Dependence structure detection - - data: 'x' with 200 samples of 9 variables - structure: clustered - detection method: test -- method for p-values: conservative -- significance level: 0.05 - - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: dependence.structure -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - > - > test_check("multivariance") - [ FAIL 1 | WARN 34 | SKIP 0 | PASS 160 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Error ('testmultivariances.R:341:1'): (code run outside of `test_that()`) ─── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─multivariance::dependence.structure(...) at testmultivariances.R:341:0 - 2. └─igraph::graph.empty(, directed = FALSE) - - [ FAIL 1 | WARN 34 | SKIP 0 | PASS 160 ] - Error: Test failures - Execution halted - ``` - -# mverse - -
- -* Version: 0.1.0 -* GitHub: https://github.com/mverseanalysis/mverse -* Source code: https://github.com/cran/mverse -* Date/Publication: 2022-05-23 08:10:02 UTC -* Number of recursive dependencies: 149 - -Run `revdepcheck::cloud_details(, "mverse")` for more info - -
- -## Newly broken - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘mverse_gettingstarted.Rmd’ using rmarkdown - --- finished re-building ‘mverse_gettingstarted.Rmd’ - - --- re-building ‘mverse_intro_glmmodelling.Rmd’ using rmarkdown - - Quitting from lines 210-211 [unnamed-chunk-8] (mverse_intro_glmmodelling.Rmd) - Error: processing vignette 'mverse_intro_glmmodelling.Rmd' failed with diagnostics: - could not find function ".igraph.status" - ... - --- failed re-building ‘mverse_intro_glmmodelling.Rmd’ - - --- re-building ‘mverse_intro_regressionmodelling.Rmd’ using rmarkdown - --- finished re-building ‘mverse_intro_regressionmodelling.Rmd’ - - SUMMARY: processing the following file failed: - ‘mverse_intro_glmmodelling.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# mwcsr - -
- -* Version: 0.1.7 -* GitHub: https://github.com/ctlab/mwcsr -* Source code: https://github.com/cran/mwcsr -* Date/Publication: 2023-05-16 11:10:05 UTC -* Number of recursive dependencies: 91 - -Run `revdepcheck::cloud_details(, "mwcsr")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘mwcsr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: get_instance_type - > ### Title: Check the type and the validity of an MWCS instance - > ### Aliases: get_instance_type - > - > ### ** Examples - > - > data(mwcs_example) - > get_instance_type(mwcs_example) - Error in .igraph.status("Restore graph external pointer.\n") : - could not find function ".igraph.status" - Calls: get_instance_type -> check_graph -> -> warn_version - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Backtrace: - ▆ - 1. └─mwcsr::solve_mwcsp(solver, gam_example) at test_rmwcs.R:55:4 - 2. └─mwcsr:::check_graph(instance) - 3. └─igraph::is.igraph(g) - 4. └─igraph:::warn_version(graph) - ── Error ('test_rmwcs.R:61:5'): rmwcs solver works with empty solutions ──────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─igraph::graph.ring(10) at test_rmwcs.R:61:4 - - [ FAIL 5 | WARN 1 | SKIP 5 | PASS 32 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 17.4Mb - sub-directories of 1Mb or more: - java 2.5Mb - libs 14.3Mb - ``` - -# nat - -
- -* Version: 1.8.22 -* GitHub: https://github.com/natverse/nat -* Source code: https://github.com/cran/nat -* Date/Publication: 2023-06-07 14:50:05 UTC -* Number of recursive dependencies: 90 - -Run `revdepcheck::cloud_details(, "nat")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘nat-Ex.R’ failed - The error most likely occurred in: - - > ### Name: neuron - > ### Title: neuron: class to represent traced neurons - > ### Aliases: neuron is.neuron as.neuron as.neuron.data.frame - > ### as.neuron.ngraph as.neuron.igraph as.neuron.default - > - > ### ** Examples - > - ... - [25] xform xyzmatrix xyzmatrix<- - see '?methods' for accessing help and source code - > - > ## Neurons as graphs - > # convert to graph and find longest paths by number of nodes - > ng=as.ngraph(n) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: as.ngraph ... as.ngraph.data.frame -> ngraph -> -> do.call -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘test-all.R’ - Running the tests in ‘tests/test-all.R’ failed. - Last 13 lines of output: - Backtrace: - ▆ - 1. ├─nat::as.neuron(testd) at test-neuron.R:13:0 - 2. └─nat:::as.neuron.data.frame(testd) - 3. ├─nat::as.neuron(as.ngraph(x), vertexData = x, ...) - 4. ├─nat::as.ngraph(x) - 5. └─nat:::as.ngraph.data.frame(x) - 6. └─nat::ngraph(...) - 7. └─igraph::graph(rawel, n = length(vertexlabels), directed = directed) - 8. ├─base::do.call(old_graph, args) - 9. └─igraph (local) ``(``, n = 6L, directed = TRUE) - - [ FAIL 30 | WARN 2 | SKIP 4 | PASS 633 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘Installation.Rmd’ using rmarkdown - --- finished re-building ‘Installation.Rmd’ - - --- re-building ‘neurons-intro.Rmd’ using rmarkdown - - Quitting from lines 200-207 [unnamed-chunk-14] (neurons-intro.Rmd) - Error: processing vignette 'neurons-intro.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘neurons-intro.Rmd’ - - SUMMARY: processing the following file failed: - ‘neurons-intro.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# nbTransmission - -
- -* Version: 1.1.2 -* GitHub: https://github.com/sarahleavitt/nbTransmission -* Source code: https://github.com/cran/nbTransmission -* Date/Publication: 2021-01-06 19:50:03 UTC -* Number of recursive dependencies: 123 - -Run `revdepcheck::cloud_details(, "nbTransmission")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Backtrace: - ▆ - 1. ├─testthat::expect_message(...) at test_visualizeResults.R:167:2 - 2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages) - 3. │ ├─testthat (local) .capture(...) - 4. │ │ └─base::withCallingHandlers(...) - 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) - 6. └─nbTransmission (local) createNetworkWrapper(nbResults, probBreaks = c(0.01, 0.05, 1)) - 7. └─nbTransmission:::createNetwork(...) at test_visualizeResults.R:48:2 - 8. └─igraph::graph_from_data_frame(d = edges, vertices = nodes, directed = T) - 9. └─igraph::make_empty_graph(n = 0, directed = directed) - - [ FAIL 4 | WARN 5 | SKIP 0 | PASS 124 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘nbTransmission-vignette.Rmd’ using rmarkdown - - Quitting from lines 266-269 [networkFull] (nbTransmission-vignette.Rmd) - Error: processing vignette 'nbTransmission-vignette.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘nbTransmission-vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘nbTransmission-vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# nda - -
- -* Version: 0.1.6 -* GitHub: https://github.com/kzst/nda -* Source code: https://github.com/cran/nda -* Date/Publication: 2022-10-14 13:10:02 UTC -* Number of recursive dependencies: 81 - -Run `revdepcheck::cloud_details(, "nda")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘nda-Ex.R’ failed - The error most likely occurred in: - - > ### Name: biplot.nda - > ### Title: Biplot function for Network-based Dimensionality Reduction and - > ### Analysis (NDA) - > ### Aliases: biplot.nda - > ### Keywords: plot - > - > ### ** Examples - ... - > - > # Biplot function without feature selection - > - > data("CrimesUSA1990.X") - > df<-CrimesUSA1990.X - > p<-ndr(df) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: ndr ... ensure_igraph -> -> graph.adjacency.dense - Execution halted - ``` - -# neat - -
- -* Version: 1.2.3 -* GitHub: NA -* Source code: https://github.com/cran/neat -* Date/Publication: 2021-01-07 06:00:02 UTC -* Number of recursive dependencies: 36 - -Run `revdepcheck::cloud_details(, "neat")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘neat-Ex.R’ failed - The error most likely occurred in: - - > ### Name: neat - > ### Title: Performs neat for lists of gene sets - > ### Aliases: neat pvalue neatc - > ### Keywords: htest - > - > ### ** Examples - > - ... - > blist = list('set 3' = set3) - > - > # test without multiple testing correction - > test1 = neat(alist = alist, blist = blist, network=A, - + nettype='directed', nodes=labels, - + alpha=0.05, mtc.type = 'none') - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: neat ... networkmatrix -> -> graph.adjacency.dense - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘neat.Rmd’ using rmarkdown - - Quitting from lines 158-159 [unnamed-chunk-13] (neat.Rmd) - Error: processing vignette 'neat.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘neat.Rmd’ - - SUMMARY: processing the following file failed: - ‘neat.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# neatmaps - -
- -* Version: 2.1.0 -* GitHub: https://github.com/PhilBoileau/neatmaps -* Source code: https://github.com/cran/neatmaps -* Date/Publication: 2019-05-12 19:10:03 UTC -* Number of recursive dependencies: 98 - -Run `revdepcheck::cloud_details(, "neatmaps")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘neatmaps-Ex.R’ failed - The error most likely occurred in: - - > ### Name: consClustResTable - > ### Title: Consensus Cluster Results in a Table - > ### Aliases: consClustResTable - > - > ### ** Examples - > - > # create the data frame using the network, node and edge attributes - > df <- netsDataFrame(network_attr_df, - + node_attr_df, - + edge_df) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: netsDataFrame ... -> make_graph -> do.call -> - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.3Mb - ``` - -# Neighboot - -
- -* Version: 1.0.1 -* GitHub: NA -* Source code: https://github.com/cran/Neighboot -* Date/Publication: 2022-05-31 23:20:08 UTC -* Number of recursive dependencies: 92 - -Run `revdepcheck::cloud_details(, "Neighboot")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘Neighboot-Ex.R’ failed - The error most likely occurred in: - - > ### Name: neighb - > ### Title: Compute standard errors and confidence intervals - > ### Aliases: neighb - > - > ### ** Examples - > - > #Load the synthetic population network dataset. - ... - Loading required package: RDStreeboot - > RDS.samp <- sample.RDS(pop.network$traits, pop.network$adj.mat, 200, 10, - + 3, c(1/6,1/3,1/3,1/6), FALSE) - > - > #Compute 95% confidence intervals using the percentile method - > neighb(RDS.data=RDS.samp, quant=c(0.025, 0.975),method="percentile", B=100) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: neighb -> .Nb -> -> make_empty_graph - Execution halted - ``` - -# netCoin - -
- -* Version: 2.0.48 -* GitHub: https://github.com/Modesto-Escobar/netCoin-2.x -* Source code: https://github.com/cran/netCoin -* Date/Publication: 2023-03-23 22:40:02 UTC -* Number of recursive dependencies: 73 - -Run `revdepcheck::cloud_details(, "netCoin")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘netCoin-Ex.R’ failed - The error most likely occurred in: - - > ### Name: addDescription - > ### Title: Adds a description to a 'netCoin' object. - > ### Aliases: addDescription - > - > ### ** Examples - > - > data(finches) - ... - > - > Net<-allNet(Galapagos,nodes=finches, criteria="hyp", maxL=.05, - + lwidth ="Haberman",lweight="Haberman", - + size="frequency", color="species", layout="mds", - + main="Species coincidences in Galapagos Islands", - + note="Data source: Sanderson (2000)") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: allNet ... ensure_igraph -> rd3_toIgraph -> -> make_empty_graph - Execution halted - ``` - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 21 marked UTF-8 strings - ``` - -# netcom - -
- -* Version: 2.1.6 -* GitHub: https://github.com/langendorfr/netcom -* Source code: https://github.com/cran/netcom -* Date/Publication: 2022-07-21 17:40:06 UTC -* Number of recursive dependencies: 102 - -Run `revdepcheck::cloud_details(, "netcom")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘netcom-Ex.R’ failed - The error most likely occurred in: - - > ### Name: align - > ### Title: Network Alignment - > ### Aliases: align - > - > ### ** Examples - > - > # The two networks to be aligned - > net_one <- matrix(stats::runif(25,0,1), nrow=5, ncol=5) - > net_two <- matrix(stats::runif(25,0,1), nrow=5, ncol=5) - > - > align(net_one, net_two) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: align ... ensure_igraph -> -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘ggfortify’ ‘ggplot2’ ‘ggraph’ ‘reshape2’ - All declared Imports should be used. - ``` - -# NetCoupler - -
- -* Version: 0.1.0 -* GitHub: https://github.com/NetCoupler/NetCoupler -* Source code: https://github.com/cran/NetCoupler -* Date/Publication: 2022-04-08 09:02:33 UTC -* Number of recursive dependencies: 101 - -Run `revdepcheck::cloud_details(, "NetCoupler")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘NetCoupler-Ex.R’ failed - The error most likely occurred in: - - > ### Name: nc_estimate_links - > ### Title: Compute model estimates between an external (exposure or - > ### outcome) variable and a network. - > ### Aliases: nc_estimate_links nc_estimate_exposure_links - > ### nc_estimate_outcome_links - > - > ### ** Examples - ... - + nc_standardize(starts_with("metabolite")) - > - > metabolite_network <- simulated_data %>% - + nc_standardize(starts_with("metabolite"), - + regressed_on = "age") %>% - + nc_estimate_network(starts_with("metabolite")) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: %>% ... %>% -> -> -> graph_from_adj_list - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘spelling.R’ - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 11. │ ├─base::withCallingHandlers(...) - 12. │ └─base::eval(exprs, env) - 13. │ └─base::eval(exprs, env) - 14. │ └─... %>% nc_estimate_network(starts_with("metabolite")) at tests/testthat/helpers-test-prep.R:6:0 - 15. ├─NetCoupler::nc_estimate_network(., starts_with("metabolite")) - 16. │ └─subset_data %>% pc_estimate_undirected_graph(alpha) %>% ... - 17. ├─NetCoupler:::as_tbl_graph.pcAlgo(.) - 18. │ └─... %>% tidygraph::as_tbl_graph() - 19. ├─tidygraph::as_tbl_graph(.) - 20. ├─igraph::graph_from_graphnel(.) - 21. │ └─igraph::graph_from_adj_list(al, mode = mode, duplicate = TRUE) - 22. └─base::.handleSimpleError(...) - 23. └─testthat (local) h(simpleError(msg, call)) - 24. └─rlang::abort(...) - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘NetCoupler.Rmd’ using rmarkdown - - Quitting from lines 175-178 [create-network] (NetCoupler.Rmd) - Error: processing vignette 'NetCoupler.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘NetCoupler.Rmd’ - - SUMMARY: processing the following file failed: - ‘NetCoupler.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# netdiffuseR - -
- -* Version: 1.22.5 -* GitHub: https://github.com/USCCANA/netdiffuseR -* Source code: https://github.com/cran/netdiffuseR -* Date/Publication: 2022-12-02 16:20:02 UTC -* Number of recursive dependencies: 86 - -Run `revdepcheck::cloud_details(, "netdiffuseR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘netdiffuseR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: approx_geodesic - > ### Title: Approximate Geodesic Distances - > ### Aliases: approx_geodesic Geodesic Shortest-Path approx_geodist - > - > ### ** Examples - > - > # A very simple example ----------------------------------------------------- - ... - [9,] 1 1 2 2 2 3 3 3 0 1 - [10,] 1 1 1 2 2 2 3 3 3 0 - > igraph::distances( - + igraph::graph_from_adjacency_matrix(g, mode = "directed"), - + mode = "out" - + ) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: ... graph.adjacency.sparse -> make_graph -> do.call -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 4. base::with.default(...) - 5. base::eval(substitute(expr), data, enclos = parent.frame()) - 6. base::eval(substitute(expr), data, enclos = parent.frame()) - 7. netdiffuseR:::diffusionMap.default(graph[[slice]], toa, ...) - 8. igraph::graph_from_adjacency_matrix(graph, weighted = TRUE) - 9. igraph:::graph.adjacency.sparse(...) - 10. igraph::make_empty_graph(n = vc, directed = (mode == "directed")) - ... and 1 more - - - Maximum number of 10 failures reached, some test results may be missing. - - ══ DONE ════════════════════════════════════════════════════════════════════════ - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘analyzing-medical-innovation-data.Rmd’ using rmarkdown - - Quitting from lines 85-88 [Checking-the-methods] (analyzing-medical-innovation-data.Rmd) - Error: processing vignette 'analyzing-medical-innovation-data.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘analyzing-medical-innovation-data.Rmd’ - - --- re-building ‘introduction-to-netdiffuser.Rmd’ using rmarkdown - - ... - - --- re-building ‘time_discount_suscep_infect.Rmd’ using rmarkdown - --- finished re-building ‘time_discount_suscep_infect.Rmd’ - - SUMMARY: processing the following files failed: - ‘analyzing-medical-innovation-data.Rmd’ - ‘introduction-to-netdiffuser.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 16.7Mb - sub-directories of 1Mb or more: - doc 2.5Mb - libs 12.4Mb - ``` - -# NetFACS - -
- -* Version: 0.5.0 -* GitHub: NA -* Source code: https://github.com/cran/NetFACS -* Date/Publication: 2022-12-06 17:32:35 UTC -* Number of recursive dependencies: 100 - -Run `revdepcheck::cloud_details(, "NetFACS")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘NetFACS-Ex.R’ failed - The error most likely occurred in: - - > ### Name: multiple_netfacs_network - > ### Title: Creates network objects out of the netfacs data - > ### Aliases: multiple_netfacs_network multiple.netfacs.network - > - > ### ** Examples - > - > data(emotions_set) - ... - + condition = emotions_set[[2]]$emotion, - + ran.trials = 10, # only for example - + combination.size = 2 - + ) - > - > emo.nets <- multiple_netfacs_network(emo.faces) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: multiple_netfacs_network ... %>% -> -> -> make_empty_graph - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘netfacs_tutorial.Rmd’ using rmarkdown - - Quitting from lines 286-297 [overlap] (netfacs_tutorial.Rmd) - Error: processing vignette 'netfacs_tutorial.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘netfacs_tutorial.Rmd’ - - SUMMARY: processing the following file failed: - ‘netfacs_tutorial.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# netgsa - -
- -* Version: 4.0.4 -* GitHub: https://github.com/mikehellstern/netgsa -* Source code: https://github.com/cran/netgsa -* Date/Publication: 2022-10-25 06:02:36 UTC -* Number of recursive dependencies: 113 - -Run `revdepcheck::cloud_details(, "netgsa")` for more info - -
- -## Newly broken - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘netgsa.Rmd’ using rmarkdown - - Quitting from lines 150-154 [unnamed-chunk-6] (netgsa.Rmd) - Error: processing vignette 'netgsa.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘netgsa.Rmd’ - - SUMMARY: processing the following file failed: - ‘netgsa.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 28.1Mb - sub-directories of 1Mb or more: - doc 2.8Mb - libs 24.4Mb - ``` - -# netjack - -
- -* Version: 1.2.0 -* GitHub: NA -* Source code: https://github.com/cran/netjack -* Date/Publication: 2019-07-07 17:50:03 UTC -* Number of recursive dependencies: 64 - -Run `revdepcheck::cloud_details(, "netjack")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘netjack-Ex.R’ failed - The error most likely occurred in: - - > ### Name: diff_test - > ### Title: Test for differences from original statistic - > ### Aliases: diff_test - > - > ### ** Examples - > - > data(GroupA) - > GroupA_Net = as_NetSample(GroupA, 1:20, node.variables = list(community = c(rep(1, 10), rep(2,10))), - + sample.variables = list(group = c(rep(1, 10), rep(2,10)))) - > Jackknife_GroupA_Net = net_apply(GroupA_Net, node_jackknife) - > GlobEff_GroupA_Net = net_stat_apply(Jackknife_GroupA_Net, global_efficiency) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: net_stat_apply ... -> -> graph.adjacency.dense - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘developingNetjack.Rmd’ using rmarkdown - --- finished re-building ‘developingNetjack.Rmd’ - - --- re-building ‘netjackIntro.Rmd’ using rmarkdown - - Quitting from lines 114-124 [unnamed-chunk-6] (netjackIntro.Rmd) - Error: processing vignette 'netjackIntro.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘netjackIntro.Rmd’ - - SUMMARY: processing the following file failed: - ‘netjackIntro.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘Rdpack’ - All declared Imports should be used. - ``` - -# netmap - -
- -* Version: 0.1.2 -* GitHub: https://github.com/artod83/netmap -* Source code: https://github.com/cran/netmap -* Date/Publication: 2023-03-06 14:40:02 UTC -* Number of recursive dependencies: 84 - -Run `revdepcheck::cloud_details(, "netmap")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - id or vertex.names not found in lookup table - Invalid network/igraph object supplied - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 20 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Error ('test-ggcentrality.R:34:3'): ggconn_area returns the correct connected areas for am igraph object ── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─igraph::graph_from_adjacency_matrix(...) at test-ggcentrality.R:34:2 - 2. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 20 ] - Error: Test failures - Execution halted - ``` - -# netmeta - -
- -* Version: 2.8-2 -* GitHub: https://github.com/guido-s/netmeta -* Source code: https://github.com/cran/netmeta -* Date/Publication: 2023-05-06 10:10:05 UTC -* Number of recursive dependencies: 98 - -Run `revdepcheck::cloud_details(, "netmeta")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘netmeta-Ex.R’ failed - The error most likely occurred in: - - > ### Name: netcontrib - > ### Title: Contribution matrix in network meta-analysis - > ### Aliases: netcontrib print.netcontrib - > ### Keywords: contribution - > - > ### ** Examples - > - ... - > data("Woods2010") - > p1 <- pairwise(treatment, event = r, n = N, - + studlab = author, data = Woods2010, sm = "OR") - > - > net1 <- netmeta(p1) - > cm <- netcontrib(net1) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: netcontrib ... -> make_graph -> do.call -> - Execution halted - ``` - -## In both - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘crossnma’ - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 2 marked UTF-8 strings - ``` - -# NetMix - -
- -* Version: 0.2.0.1 -* GitHub: https://github.com/solivella/NetMix -* Source code: https://github.com/cran/NetMix -* Date/Publication: 2022-11-16 16:34:41 UTC -* Number of recursive dependencies: 59 - -Run `revdepcheck::cloud_details(, "NetMix")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘NetMix-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plot.mmsbm - > ### Title: Various visualization tools for 'mmsbm' objects - > ### Aliases: plot.mmsbm - > - > ### ** Examples - > - > library(NetMix) - ... - + mmsbm.control = list(seed = 123, - + conv_tol = 1e-2, - + hessian = FALSE)) - > - > ## Plot blockmodel as network - > plot(lazega_mmsbm) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot -> plot.mmsbm -> -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.1Mb - sub-directories of 1Mb or more: - libs 5.8Mb - ``` - -# netplot - -
- -* Version: 0.1-1 -* GitHub: https://github.com/USCCANA/netplot -* Source code: https://github.com/cran/netplot -* Date/Publication: 2021-06-16 07:10:02 UTC -* Number of recursive dependencies: 82 - -Run `revdepcheck::cloud_details(, "netplot")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘netplot-Ex.R’ failed - The error most likely occurred in: - - > ### Name: make_colors - > ### Title: Create a vector of colors for vertices and edges - > ### Aliases: make_colors make_edges_colors make_vertex_colors - > - > ### ** Examples - > - > - > data(UKfaculty, package="igraphdata") - > col <- make_vertex_colors(UKfaculty, "Group") - Error in .igraph.status("Restore graph external pointer.\n") : - could not find function ".igraph.status" - Calls: make_vertex_colors ... -> ensure_igraph -> is_igraph -> warn_version - Execution halted - ``` - -# netrankr - -
- -* Version: 1.2.0 -* GitHub: https://github.com/schochastics/netrankr -* Source code: https://github.com/cran/netrankr -* Date/Publication: 2022-09-26 21:00:02 UTC -* Number of recursive dependencies: 65 - -Run `revdepcheck::cloud_details(, "netrankr")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘netrankr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: approx_rank_expected - > ### Title: Approximation of expected ranks - > ### Aliases: approx_rank_expected - > - > ### ** Examples - > - > P <- matrix(c(0, 0, 1, 1, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, rep(0, 10)), 5, 5, byrow = TRUE) - > # Exact result - > exact_rank_prob(P)$expected.rank - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: exact_rank_prob ... ensure_igraph -> -> graph.adjacency.dense - Execution halted - Error in .igraph.status("Free graph external pointer.\n") : - could not find function ".igraph.status" - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 12.5Mb - sub-directories of 1Mb or more: - doc 1.6Mb - libs 10.6Mb - ``` - -# netropy - -
- -* Version: 0.1.0 -* GitHub: NA -* Source code: https://github.com/cran/netropy -* Date/Publication: 2022-02-02 08:20:02 UTC -* Number of recursive dependencies: 85 - -Run `revdepcheck::cloud_details(, "netropy")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘netropy-Ex.R’ failed - The error most likely occurred in: - - > ### Name: assoc_graph - > ### Title: Association Graphs - > ### Aliases: assoc_graph - > - > ### ** Examples - > - > library(ggraph) - ... - + ifelse(df.att$age<=45,1,2)), - + practice = df.att$practice, - + lawschool= df.att$lawschool-1) - > - > # association graph based on cutoff 0.15 - > assoc_graph(df.att.ed, 0.15) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: assoc_graph -> -> graph.adjacency.dense - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘joint_entropies.Rmd’ using rmarkdown - - Quitting from lines 96-98 [assoc_g] (joint_entropies.Rmd) - Error: processing vignette 'joint_entropies.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘joint_entropies.Rmd’ - - --- re-building ‘prediction_power.Rmd’ using rmarkdown - ... - --- finished re-building ‘univariate_bivariate_trivariate.Rmd’ - - --- re-building ‘variable_domains.Rmd’ using rmarkdown - --- finished re-building ‘variable_domains.Rmd’ - - SUMMARY: processing the following file failed: - ‘joint_entropies.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# NetSci - -
- -* Version: 1.0.0 -* GitHub: NA -* Source code: https://github.com/cran/NetSci -* Date/Publication: 2022-07-03 18:00:02 UTC -* Number of recursive dependencies: 61 - -Run `revdepcheck::cloud_details(, "NetSci")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘NetSci-Ex.R’ failed - The error most likely occurred in: - - > ### Name: Histogram_LCC - > ### Title: Histogram_LCC - > ### Aliases: Histogram_LCC - > - > ### ** Examples - > - > set.seed(666) - ... - + Node.2 = sample(LETTERS[1:10], 15, replace = TRUE)) - > net$value = 1 - > net = CoDiNA::OrderNames(net) - > net = unique(net) - > - > g <- igraph::graph_from_data_frame(net, directed = FALSE ) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: -> make_empty_graph - Execution halted - ``` - -# netseg - -
- -* Version: 1.0-1 -* GitHub: https://github.com/mbojan/netseg -* Source code: https://github.com/cran/netseg -* Date/Publication: 2022-08-25 12:10:06 UTC -* Number of recursive dependencies: 61 - -Run `revdepcheck::cloud_details(, "netseg")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘netseg-Ex.R’ failed - The error most likely occurred in: - - > ### Name: EF3 - > ### Title: Example data from Figure III of Echenique and Fryer (2006) - > ### Aliases: EF3 - > ### Keywords: datasets - > - > ### ** Examples - > - ... - + vertex.color = igraph::V(EF3)$type+1, - + vertex.label.family = "", - + sub = "Source: Echenique & Fryer (2006)", - + main = "Neighborhood racial segregation\n in a fictional city" - + ) - + } - Error in .igraph.status("Restore graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot ... plot.igraph -> ensure_igraph -> is_igraph -> warn_version - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ▆ - 1. ├─netseg::assort(WhiteKinship, "gender") at test-assort.R:11:10 - 2. └─netseg:::assort.igraph(WhiteKinship, "gender") - 3. ├─netseg::mixingm(object, vattr) - 4. └─netseg:::mixingm.igraph(object, vattr) - 5. └─igraph::any_multiple(object) - 6. └─igraph:::ensure_igraph(graph) - 7. └─igraph::is_igraph(graph) - 8. └─igraph:::warn_version(graph) - ── Failure ('test-smi.R:5:3'): SMI works ─────────────────────────────────────── - `smi(as.directed(WhiteKinship), "gender")` produced messages. - - [ FAIL 2 | WARN 0 | SKIP 0 | PASS 72 ] - Error: Test failures - Execution halted - ``` - -# nett - -
- -* Version: 1.0.0 -* GitHub: https://github.com/aaamini/nett -* Source code: https://github.com/cran/nett -* Date/Publication: 2022-11-09 10:50:05 UTC -* Number of recursive dependencies: 97 - -Run `revdepcheck::cloud_details(, "nett")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘nett-Ex.R’ failed - The error most likely occurred in: - - > ### Name: fast_cpl - > ### Title: CPL algorithm for community detection (fast) - > ### Aliases: fast_cpl - > ### Keywords: comm_detect - > - > ### ** Examples - > - > head(fast_cpl(igraph::as_adj(polblogs), 2), 50) - Error in .igraph.status("Restore graph external pointer.\n") : - could not find function ".igraph.status" - Calls: head ... -> ensure_igraph -> is_igraph -> warn_version - Execution halted - ``` - -# netUtils - -
- -* Version: 0.8.1 -* GitHub: https://github.com/schochastics/netUtils -* Source code: https://github.com/cran/netUtils -* Date/Publication: 2022-12-19 21:00:02 UTC -* Number of recursive dependencies: 52 - -Run `revdepcheck::cloud_details(, "netUtils")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘netUtils-Ex.R’ failed - The error most likely occurred in: - - > ### Name: core_periphery - > ### Title: Discrete core-periphery model - > ### Aliases: core_periphery - > - > ### ** Examples - > - > set.seed(121) - ... - Error in .igraph.status("Free graph external pointer.\n") : - could not find function ".igraph.status" - Error in .igraph.status("Free graph external pointer.\n") : - could not find function ".igraph.status" - Error in .igraph.status("Free graph external pointer.\n") : - could not find function ".igraph.status" - Error in .igraph.status("Free graph external pointer.\n") : - could not find function ".igraph.status" - Error in .igraph.status("Free graph external pointer.\n") : - could not find function ".igraph.status" - ``` - -# NetworkExtinction - -
- -* Version: 1.0.3 -* GitHub: NA -* Source code: https://github.com/cran/NetworkExtinction -* Date/Publication: 2023-03-31 11:40:02 UTC -* Number of recursive dependencies: 100 - -Run `revdepcheck::cloud_details(, "NetworkExtinction")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘NetworkExtinction-Ex.R’ failed - The error most likely occurred in: - - > ### Name: ExtinctionPlot - > ### Title: Plots the extinctions history of a network - > ### Aliases: ExtinctionPlot - > - > ### ** Examples - > - > # If you don't specify the y variable it will plot the secondary extinctions - > # by default - > data("net") - > history <- SimulateExtinctions(Network = net, Method = "Mostconnected") - - | - | | 0%Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: SimulateExtinctions ... withCallingHandlers -> -> graph.adjacency.dense - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 2. │ └─testthat:::expect_condition_matching(...) - 3. │ └─testthat:::quasi_capture(...) - 4. │ ├─testthat (local) .capture(...) - 5. │ │ └─base::withCallingHandlers(...) - 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) - 7. └─NetworkExtinction::SimulateExtinctions(Network = net, Method = "Mostconnected") - 8. └─NetworkExtinction::ExtinctionOrder(...) - 9. ├─base::suppressMessages(...) - 10. │ └─base::withCallingHandlers(...) - 11. └─igraph::graph_from_adjacency_matrix(net, mode = "directed", weighted = TRUE) - 12. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 2 | WARN 0 | SKIP 3 | PASS 2 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘NetworkExtinction.Rmd’ using rmarkdown - - Quitting from lines 136-141 [mostconnected2] (NetworkExtinction.Rmd) - Error: processing vignette 'NetworkExtinction.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘NetworkExtinction.Rmd’ - - SUMMARY: processing the following file failed: - ‘NetworkExtinction.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# networkGen - -
- -* Version: 0.1.1 -* GitHub: NA -* Source code: https://github.com/cran/networkGen -* Date/Publication: 2017-12-04 17:31:37 UTC -* Number of recursive dependencies: 9 - -Run `revdepcheck::cloud_details(, "networkGen")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘networkGen-Ex.R’ failed - The error most likely occurred in: - - > ### Name: check.graph - > ### Title: check.graph - > ### Aliases: check.graph - > - > ### ** Examples - > - > check.graph(nodeLogic(value = 1, type= "circuit", itemFamily= 1)) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: check.graph ... graph_from_literal_i -> make_graph -> do.call -> - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘mgcv’ ‘stats’ - All declared Imports should be used. - ``` - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# NetworkInference - -
- -* Version: 1.2.4 -* GitHub: https://github.com/desmarais-lab/NetworkInference -* Source code: https://github.com/cran/NetworkInference -* Date/Publication: 2019-02-28 05:50:06 UTC -* Number of recursive dependencies: 77 - -Run `revdepcheck::cloud_details(, "NetworkInference")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘NetworkInference-Ex.R’ failed - The error most likely occurred in: - - > ### Name: simulate_cascades - > ### Title: Simulate cascades from a diffusion network - > ### Aliases: simulate_cascades - > - > ### ** Examples - > - > - ... - **************************************************| - Inferring 5 edges... - 0% 10 20 30 40 50 60 70 80 90 100% - [----|----|----|----|----|----|----|----|----|----| - **************************************************| - > simulated_cascades <- simulate_cascades(out, nsim = 10) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: simulate_cascades ... lapply -> FUN -> -> graph.adjacency.dense - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘quickstart_vignette.Rmd’ using rmarkdown - --- finished re-building ‘quickstart_vignette.Rmd’ - - --- re-building ‘tutorial_vignette.Rmd’ using rmarkdown - Warning: ggrepel: 16 unlabeled data points (too many overlaps). Consider increasing max.overlaps - - Quitting from lines 278-284 [unnamed-chunk-29] (tutorial_vignette.Rmd) - Error: processing vignette 'tutorial_vignette.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘tutorial_vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘tutorial_vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# NetworkToolbox - -
- -* Version: 1.4.2 -* GitHub: NA -* Source code: https://github.com/cran/NetworkToolbox -* Date/Publication: 2021-05-28 11:40:06 UTC -* Number of recursive dependencies: 111 - -Run `revdepcheck::cloud_details(, "NetworkToolbox")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘NetworkToolbox-Ex.R’ failed - The error most likely occurred in: - - > ### Name: comcat - > ### Title: Communicating Nodes - > ### Aliases: comcat - > - > ### ** Examples - > - > # Pearson's correlation only for CRAN checks - > A <- TMFG(neoOpen, normal = FALSE)$A - > - > communicating <- comcat(A, comm = "walktrap", cent = "strength", metric = "across") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: comcat ... graph.edgelist -> make_graph -> do.call -> - Execution halted - ``` - -# networktools - -
- -* Version: 1.5.0 -* GitHub: https://github.com/paytonjjones/networktools -* Source code: https://github.com/cran/networktools -* Date/Publication: 2022-06-03 22:20:02 UTC -* Number of recursive dependencies: 158 - -Run `revdepcheck::cloud_details(, "networktools")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - > - > test_check("networktools") - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Error ('test-networktools.R:7:1'): (code run outside of `test_that()`) ────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─igraph::graph_from_adjacency_matrix(dep_cor, mode = "undirected") at test-networktools.R:7:0 - 2. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] - Error: Test failures - Execution halted - ``` - -# NIMAA - -
- -* Version: 0.2.1 -* GitHub: https://github.com/jafarilab/NIMAA -* Source code: https://github.com/cran/NIMAA -* Date/Publication: 2022-04-11 14:12:45 UTC -* Number of recursive dependencies: 173 - -Run `revdepcheck::cloud_details(, "NIMAA")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘NIMAA-Ex.R’ failed - The error most likely occurred in: - - > ### Name: analyseNetwork - > ### Title: General properties of the network - > ### Aliases: analyseNetwork - > - > ### ** Examples - > - > # generate a toy graph - > g1 <- igraph::make_graph(c(1, 2, 3, 4, 1, 3), directed = FALSE) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: -> do.call -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 1. └─igraph::make_graph(c(1, 2, 3, 4, 1, 3), directed = FALSE) at test-analyse-network.R:2:2 - 2. ├─base::do.call(old_graph, args) - 3. └─igraph (local) ``(``, directed = FALSE) - ── Error ('test-find-cluster.R:5:3'): find cluster works ─────────────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─NIMAA::findCluster(...) at test-find-cluster.R:5:2 - 2. └─NIMAA:::projectGraph(inc_mat, dim = part) - 3. └─igraph::graph_from_adjacency_matrix(...) - 4. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 2 | WARN 6 | SKIP 0 | PASS 8 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘NIMAA-vignette.Rmd’ using rmarkdown - - Quitting from lines 70-74 [plotBipartite] (NIMAA-vignette.Rmd) - Error: processing vignette 'NIMAA-vignette.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘NIMAA-vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘NIMAA-vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.2Mb - sub-directories of 1Mb or more: - doc 4.0Mb - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 24 marked UTF-8 strings - ``` - -# nimble - -
- -* Version: 1.0.0 -* GitHub: https://github.com/nimble-dev/nimble -* Source code: https://github.com/cran/nimble -* Date/Publication: 2023-05-23 19:42:03 UTC -* Number of recursive dependencies: 38 - -Run `revdepcheck::cloud_details(, "nimble")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘nimble-Ex.R’ failed - The error most likely occurred in: - - > ### Name: MCMCconf-class - > ### Title: Class 'MCMCconf' - > ### Aliases: MCMCconf-class MCMCconf addSampler removeSamplers setSamplers - > ### printSamplers getSamplers setSamplerExecutionOrder - > ### getSamplerExecutionOrder addMonitors addMonitors2 setMonitors - > ### setMonitors2 resetMonitors getMonitors getMonitors2 printMonitors - > ### setThin setThin2 - ... - > code <- nimbleCode({ - + mu ~ dnorm(0, 1) - + x ~ dnorm(mu, 1) - + }) - > Rmodel <- nimbleModel(code) - Defining model - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: nimbleModel ... -> genExpandedNodeAndParentNames3 -> graph.empty - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 45.2Mb - sub-directories of 1Mb or more: - CppCode 2.6Mb - R 7.4Mb - classic-bugs 1.6Mb - include 10.6Mb - libs 22.1Mb - ``` - -# nlnet - -
- -* Version: 1.4 -* GitHub: NA -* Source code: https://github.com/cran/nlnet -* Date/Publication: 2020-10-19 23:10:05 UTC -* Number of recursive dependencies: 38 - -Run `revdepcheck::cloud_details(, "nlnet")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘nlnet-Ex.R’ failed - The error most likely occurred in: - - > ### Name: nlnet - > ### Title: Non-Linear Network reconstruction from expression matrix - > ### Aliases: nlnet - > - > ### ** Examples - > - > - ... - > ## now input includes data matrix and hiden clusters, so get the matrix as input. - > input<-input$data - > ##change the ploting method - > result<-nlnet(input,plot.method="graph") - ------fdr cutoff aimed 7.426061e-16 ------- - ------fdr cutoff real 0.05 ------- - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: nlnet -> graph.adjacency -> graph.adjacency.dense - Execution halted - ``` - -# nlrx - -
- -* Version: 0.4.4 -* GitHub: https://github.com/ropensci/nlrx -* Source code: https://github.com/cran/nlrx -* Date/Publication: 2023-05-16 14:40:02 UTC -* Number of recursive dependencies: 155 - -Run `revdepcheck::cloud_details(, "nlrx")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat-class.R’ - Running ‘testthat-exe1.R’ - Running ‘testthat-exe2.R’ - Running ‘testthat-exe3.R’ - Running ‘testthat-nldoc.R’ - Running the tests in ‘tests/testthat-nldoc.R’ failed. - Last 13 lines of output: - [1] "File successfully compiled!" - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 2 ] - - ... - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─nlrx::nldoc_network(modelfiles) at test-nldoc.R:51:4 - 2. └─igraph::graph_from_data_frame(nw) - 3. └─igraph::make_empty_graph(n = 0, directed = directed) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 2 ] - Error: Test failures - Execution halted - ``` - -# node2vec - -
- -* Version: 0.1.0 -* GitHub: NA -* Source code: https://github.com/cran/node2vec -* Date/Publication: 2021-01-14 09:00:02 UTC -* Number of recursive dependencies: 34 - -Run `revdepcheck::cloud_details(, "node2vec")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘node2vec-Ex.R’ failed - The error most likely occurred in: - - > ### Name: node2vecR - > ### Title: Algorithmic Framework for Representational Learning on Graphs - > ### Aliases: node2vecR - > - > ### ** Examples - > - > #Parameters can be customized as needed - > data(gene_edges) - > use_data<-gene_edges - > emb<-node2vecR(use_data,p=2,q=1,num_walks=5,walk_length=5,dim=10) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: node2vecR -> graph_from_data_frame -> make_empty_graph - Execution halted - ``` - -# nutriNetwork - -
- -* Version: 0.1.1 -* GitHub: NA -* Source code: https://github.com/cran/nutriNetwork -* Date/Publication: 2019-04-26 10:00:02 UTC -* Number of recursive dependencies: 17 - -Run `revdepcheck::cloud_details(, "nutriNetwork")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘nutriNetwork-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plot.nutriNetwork - > ### Title: plot for S3 class "nutriNetwork" - > ### Aliases: plot.nutriNetwork - > - > ### ** Examples - > - > ## Don't show: - ... - > out <- nutriNetwork(vfit, method = "npn") - Network reconstruction is in progress ... - - Network reconstruction is done. - - > plot(out) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot ... plot.nutriNetwork -> graph.adjacency -> graph.adjacency.dense - Execution halted - ``` - -# OCNet - -
- -* Version: 1.0.1 -* GitHub: NA -* Source code: https://github.com/cran/OCNet -* Date/Publication: 2023-04-25 13:50:02 UTC -* Number of recursive dependencies: 77 - -Run `revdepcheck::cloud_details(, "OCNet")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘OCNet-Ex.R’ failed - The error most likely occurred in: - - > ### Name: OCN_to_SSN - > ### Title: Transform OCN into SSN object - > ### Aliases: OCN_to_SSN - > - > ### ** Examples - > - > # transform a 20x20 single-outlet OCN (aggregated at the AG level) - > # into a SSN object and plot it - > OCN <- aggregate_OCN(landscape_OCN(OCN_20), thrA = 4) - > ssn1 <- OCN_to_SSN(OCN, "AG", obsDesign = SSN::poissonDesign(10), - + path=paste(tempdir(),"/OCN.ssn", sep = ""), importToR = TRUE) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: OCN_to_SSN ... graph.adjacency.sparse -> make_graph -> do.call -> - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 8.1Mb - sub-directories of 1Mb or more: - data 2.6Mb - libs 4.4Mb - ``` - -# oddnet - -
- -* Version: 0.1.0 -* GitHub: NA -* Source code: https://github.com/cran/oddnet -* Date/Publication: 2022-12-22 20:10:01 UTC -* Number of recursive dependencies: 85 - -Run `revdepcheck::cloud_details(, "oddnet")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘oddnet-Ex.R’ failed - The error most likely occurred in: - - > ### Name: anomalous_networks - > ### Title: Identifies anomalous networks from a series of temporal - > ### networks. - > ### Aliases: anomalous_networks - > - > ### ** Examples - > - ... - > p.or.m.seq <- rep(0.1, 50) - > p.or.m.seq[20] <- 0.3 # anomalous network at 20 - > for(i in 1:50){ - + gr <- igraph::erdos.renyi.game(50, p.or.m = p.or.m.seq[i]) - + networks[[i]] <- igraph::as_adjacency_matrix(gr) - + } - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: - Execution halted - ``` - -# ohun - -
- -* Version: 0.1.0 -* GitHub: https://github.com/maRce10/ohun -* Source code: https://github.com/cran/ohun -* Date/Publication: 2022-12-19 09:30:02 UTC -* Number of recursive dependencies: 89 - -Run `revdepcheck::cloud_details(, "ohun")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ohun-Ex.R’ failed - The error most likely occurred in: - - > ### Name: label_detection - > ### Title: Label detections from a sound event detection procedure - > ### Aliases: label_detection - > - > ### ** Examples - > - > { - ... - + label_detection(reference = lbh_reference, detection = Y) - + - + # remove split to get only merge - + Y <- Y[-2, ] - + label_detection(reference = lbh_reference, detection = Y) - + } - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: label_detection ... lapply -> FUN -> -> graph.incidence.dense - Execution halted - ``` - -# OpenRepGrid - -
- -* Version: 0.1.14 -* GitHub: https://github.com/markheckmann/OpenRepGrid -* Source code: https://github.com/cran/OpenRepGrid -* Date/Publication: 2023-05-16 15:00:11 UTC -* Number of recursive dependencies: 86 - -Run `revdepcheck::cloud_details(, "OpenRepGrid")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘OpenRepGrid-Ex.R’ failed - The error most likely occurred in: - - > ### Name: indexDilemma - > ### Title: Detect implicative dilemmas (conflicts). - > ### Aliases: indexDilemma - > - > ### ** Examples - > - > id <- indexDilemma(boeker, self = 1, ideal = 2) - ... - R = Correlation including Self & Ideal - RexSI = Correlation excluding Self & Ideal - R was used as criterion> - > # plot dilemmas as network graph (see ?plot.indexDilemma for help) - > # set a seed for reproducibility - > plot(id, layout = "rows") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot ... plot.indexDilemma -> -> graph.adjacency.dense - Execution halted - ``` - -# OpenRepGrid.ic - -
- -* Version: 0.6.1 -* GitHub: https://github.com/markheckmann/OpenRepGrid.ic -* Source code: https://github.com/cran/OpenRepGrid.ic -* Date/Publication: 2022-10-25 18:57:49 UTC -* Number of recursive dependencies: 148 - -Run `revdepcheck::cloud_details(, "OpenRepGrid.ic")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ▆ - 1. └─OpenRepGrid.ic::network_graph_images(...) at test-excel.R:15:2 - 2. └─igraph::graph_from_adjacency_matrix(MM, diag = FALSE, mode = "undirected") - 3. └─igraph:::graph.adjacency.dense(...) - ── Error ('test-excel.R:57:3'): Excel output file gets created ───────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─OpenRepGrid.ic::network_graph_images(...) at test-excel.R:57:2 - 2. └─igraph::graph_from_adjacency_matrix(MM, diag = FALSE, mode = "undirected") - 3. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 2 | WARN 0 | SKIP 0 | PASS 29 ] - Error: Test failures - Execution halted - ``` - -# OrdCD - -
- -* Version: 1.1.2 -* GitHub: https://github.com/nySTAT/OrdCD -* Source code: https://github.com/cran/OrdCD -* Date/Publication: 2023-05-17 21:40:11 UTC -* Number of recursive dependencies: 19 - -Run `revdepcheck::cloud_details(, "OrdCD")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘OrdCD-Ex.R’ failed - The error most likely occurred in: - - > ### Name: OrdCD - > ### Title: Causal Discovery for Ordinal Categorical Data - > ### Aliases: OrdCD - > - > ### ** Examples - > - > set.seed(2020) - ... - > for (j in 1:q){ - + y[,j]=as.factor(y[,j]) - + } - > - > time=proc.time() - > G=OrdCD(y) #estimated DAG adjacency matrix - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: OrdCD ... -> -> graph.adjacency.dense - Execution halted - ``` - -# PAC - -
- -* Version: 1.1.4 -* GitHub: NA -* Source code: https://github.com/cran/PAC -* Date/Publication: 2021-02-18 07:00:02 UTC -* Number of recursive dependencies: 62 - -Run `revdepcheck::cloud_details(, "PAC")` for more info - -
- -## Newly broken - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘intro.Rmd’ using rmarkdown - - Quitting from lines 42-43 [PAC and Network Inference] (intro.Rmd) - Error: processing vignette 'intro.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘intro.Rmd’ - - SUMMARY: processing the following file failed: - ‘intro.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# PAFit - -
- -* Version: 1.2.5 -* GitHub: https://github.com/thongphamthe/PAFit -* Source code: https://github.com/cran/PAFit -* Date/Publication: 2022-01-11 10:02:48 UTC -* Number of recursive dependencies: 61 - -Run `revdepcheck::cloud_details(, "PAFit")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘PAFit-Ex.R’ failed - The error most likely occurred in: - - > ### Name: from_igraph - > ### Title: Convert an igraph object to a PAFit_net object - > ### Aliases: from_igraph - > - > ### ** Examples - > - > library("PAFit") - > # a network from Bianconi-Barabasi model - > net <- generate_BB(N = 50 , m = 10 , s = 10) - > igraph_graph <- to_igraph(net) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: to_igraph -> graph.data.frame -> make_empty_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘fit_node_no_new_edge.R’ - Running ‘loop_generate.R’ - Running ‘loop_joint_estimate.R’ - Running ‘loop_overall.R’ - Running ‘loop_test_Newman_Kong.R’ - Running ‘test_GenerateNet_final_padding.R’ - Running ‘test_GetStatistics_compress_2.R’ - Running ‘test_GetStatistics_undirected.R’ - Running ‘test_Newman_Kong.R’ - Running ‘test_PAFit_oneshot.R’ - ... - > library(PAFit) - > - > net <- generate_BA(N = 100, multiple_node = 20, m = 1) - > - > system.time(b <- to_igraph(net)) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: system.time -> to_igraph -> graph.data.frame -> make_empty_graph - Timing stopped at: 0.002 0 0.002 - Execution halted - ``` - -# PairViz - -
- -* Version: 1.3.6 -* GitHub: NA -* Source code: https://github.com/cran/PairViz -* Date/Publication: 2022-08-12 15:00:05 UTC -* Number of recursive dependencies: 109 - -Run `revdepcheck::cloud_details(, "PairViz")` for more info - -
- -## Newly broken - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘MultipleComparisons.Rmd’ using rmarkdown - - Quitting from lines 146-160 [unnamed-chunk-11] (MultipleComparisons.Rmd) - Error: processing vignette 'MultipleComparisons.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘MultipleComparisons.Rmd’ - - --- re-building ‘PairVizIntroduction.Rmd’ using rmarkdown - - ... - Quitting from lines 370-371 [unnamed-chunk-29] (pcp.Rmd) - Error: processing vignette 'pcp.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘pcp.Rmd’ - - SUMMARY: processing the following files failed: - ‘MultipleComparisons.Rmd’ ‘PairVizIntroduction.Rmd’ ‘pcp.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# pald - -
- -* Version: 0.0.2 -* GitHub: https://github.com/LucyMcGowan/pald -* Source code: https://github.com/cran/pald -* Date/Publication: 2022-06-03 08:30:02 UTC -* Number of recursive dependencies: 35 - -Run `revdepcheck::cloud_details(, "pald")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘pald-Ex.R’ failed - The error most likely occurred in: - - > ### Name: cohesion_strong - > ### Title: Cohesion Matrix: Strong Ties - > ### Aliases: cohesion_strong - > - > ### ** Examples - > - > C <- cohesion_matrix(dist(exdata2)) - ... - > if (requireNamespace("igraph", quietly = TRUE)) { - + G_strong <- igraph::simplify( - + igraph::graph.adjacency(CS, weighted = TRUE, mode = "undirected") - + ) - + plot(G_strong) - + } - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: ... ensure_igraph -> -> graph.adjacency.dense - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Error ('test-pald_functions.R:59:3'): community_clusters works ────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─pald::community_clusters(C) at test-pald_functions.R:59:2 - 2. └─pald::community_graphs(c) - 3. ├─igraph::simplify(...) - 4. │ └─igraph:::ensure_igraph(graph) - 5. └─igraph::graph.adjacency(c_symmetric, weighted = TRUE, mode = "undirected") - 6. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 11 ] - Error: Test failures - Execution halted - ``` - -# PANACEA - -
- -* Version: 1.0.0 -* GitHub: https://github.com/egeulgen/PANACEA -* Source code: https://github.com/cran/PANACEA -* Date/Publication: 2023-05-02 21:10:05 UTC -* Number of recursive dependencies: 86 - -Run `revdepcheck::cloud_details(, "PANACEA")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘PANACEA-Ex.R’ failed - The error most likely occurred in: - - > ### Name: score_drugs - > ### Title: Scoring of Drugs via Network-based Methods - > ### Aliases: score_drugs - > - > ### ** Examples - > - > toy_data <- data.frame( - ... - + driveR_res = toy_data, - + drug_interactions_df = toy_interactions, # leave blank for default - + W_mat = toy_W_mat, # leave blank for default - + method = "distance-based", - + verbose = FALSE - + ) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: score_drugs ... score_drugs_distance_based -> -> graph.adjacency.dense - Execution halted - ``` - -# paramlink - -
- -* Version: 1.1-5 -* GitHub: https://github.com/magnusdv/paramlink -* Source code: https://github.com/cran/paramlink -* Date/Publication: 2022-04-15 08:10:02 UTC -* Number of recursive dependencies: 21 - -Run `revdepcheck::cloud_details(, "paramlink")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘paramlink-Ex.R’ failed - The error most likely occurred in: - - > ### Name: pedigreeLoops - > ### Title: Pedigree loops - > ### Aliases: pedigreeLoops breakLoops tieLoops findLoopBreakers - > ### findLoopBreakers2 - > - > ### ** Examples - > - ... - > if(requireNamespace("igraph", quietly = TRUE)) { - + y = doubleCousins(1, 1, child=TRUE) - + findLoopBreakers(y) # --> 9 - + findLoopBreakers2(y) # --> 9 and 4 - + breakLoops(y) # uses both 9 and 4 - + } - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: findLoopBreakers2 ... -> make_graph -> do.call -> - Execution halted - ``` - -# particles - -
- -* Version: 0.2.3 -* GitHub: https://github.com/thomasp85/particles -* Source code: https://github.com/cran/particles -* Date/Publication: 2022-08-19 12:20:05 UTC -* Number of recursive dependencies: 81 - -Run `revdepcheck::cloud_details(, "particles")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘particles-Ex.R’ failed - The error most likely occurred in: - - > ### Name: evolve - > ### Title: Move the simulation forward one or more steps - > ### Aliases: evolve - > - > ### ** Examples - > - > graph <- tidygraph::create_notable('folkman') - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: -> as_tbl_graph -> make_graph -> make_famous_graph - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘intro.Rmd’ using rmarkdown - - Quitting from lines 61-71 [unnamed-chunk-1] (intro.Rmd) - Error: processing vignette 'intro.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘intro.Rmd’ - - SUMMARY: processing the following file failed: - ‘intro.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# pathfindR - -
- -* Version: 2.1.0 -* GitHub: https://github.com/egeulgen/pathfindR -* Source code: https://github.com/cran/pathfindR -* Date/Publication: 2023-05-12 07:10:03 UTC -* Number of recursive dependencies: 143 - -Run `revdepcheck::cloud_details(, "pathfindR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘pathfindR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: combine_pathfindR_results - > ### Title: Combine 2 pathfindR Results - > ### Aliases: combine_pathfindR_results - > - > ### ** Examples - > - > combined_results <- combine_pathfindR_results(example_pathfindR_output, example_comparison_output) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: combine_pathfindR_results ... combined_results_graph -> -> make_empty_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat-active_snw.R’ - Running ‘testthat-clustering.R’ - Running the tests in ‘tests/testthat-clustering.R’ failed. - Last 13 lines of output: - with the additional columns `Cluster` and `Status` ── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─pathfindR::cluster_enriched_terms(...) at test-clustering.R:419:2 - 2. ├─R.utils::doCall(...) - 3. ├─R.utils::doCall.default(...) - 4. │ └─base::do.call(.fcn, args = args, envir = envir) - 5. └─pathfindR::cluster_graph_vis(...) - 6. └─igraph::graph_from_adjacency_matrix(kappa_mat2, weighted = TRUE) - 7. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 3 | WARN 0 | SKIP 1 | PASS 45 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘comparing_results.Rmd’ using rmarkdown - - Quitting from lines 34-35 [compare_graph1] (comparing_results.Rmd) - Error: processing vignette 'comparing_results.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘comparing_results.Rmd’ - - --- re-building ‘intro_vignette.Rmd’ using rmarkdown - --- finished re-building ‘intro_vignette.Rmd’ - ... - Quitting from lines 122-123 [term_gene1] (visualization_vignette.Rmd) - Error: processing vignette 'visualization_vignette.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘visualization_vignette.Rmd’ - - SUMMARY: processing the following files failed: - ‘comparing_results.Rmd’ ‘visualization_vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# pcalg - -
- -* Version: 2.7-8 -* GitHub: NA -* Source code: https://github.com/cran/pcalg -* Date/Publication: 2022-12-21 00:20:05 UTC -* Number of recursive dependencies: 58 - -Run `revdepcheck::cloud_details(, "pcalg")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘pcalg-Ex.R’ failed - The error most likely occurred in: - - > ### Name: addBgKnowledge - > ### Title: Add background knowledge to a CPDAG or PDAG - > ### Aliases: addBgKnowledge - > ### Keywords: models - > - > ### ** Examples - > - > ## a -- b -- c - > amat <- matrix(c(0,1,0, 1,0,1, 0,1,0), 3,3) - > colnames(amat) <- rownames(amat) <- letters[1:3] - > ## plot(as(t(amat), "graphNEL")) - > addBgKnowledge(gInput = amat) ## amat is a valid CPDAG - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: addBgKnowledge ... ensure_igraph -> graph.adjacency -> graph.adjacency.dense - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘test_LINGAM.R’ - Running ‘test_addBgKnowledge.R’ - Running the tests in ‘tests/test_addBgKnowledge.R’ failed. - Last 13 lines of output: - duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, - lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, - pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, - tapply, union, unique, unsplit, which.max, which.min - - > cpdag <- dag2cpdag(g) - > ## plot(cpdag) - > cpdag.mat <- t(as(cpdag,"matrix")) ## has correct encoding - > - > ## test 1: using graph, valid - > g1 <- addBgKnowledge(gInput = cpdag, x = 3, y = 5) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: addBgKnowledge ... ensure_igraph -> graph.adjacency -> graph.adjacency.dense - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘vignette2018.Rnw’ - ... - - > amat <- matrix(c(0, 1, 0, 1, 0, 1, 0, 1, 0), 3, 3) - - > colnames(amat) <- rownames(amat) <- letters[1:3] - - > bg <- addBgKnowledge(gInput = amat, x = "a", y = "b") - - When sourcing 'vignette2018.R': - Error: could not find function ".igraph.status" - Execution halted - - ‘vignette2018.Rnw’ using ‘UTF-8’... failed - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 16.7Mb - sub-directories of 1Mb or more: - data 2.1Mb - libs 11.9Mb - ``` - -* checking Rd cross-references ... NOTE - ``` - Packages unavailable to check Rd xrefs: ‘combinat’, ‘unifDAG’ - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘vignette2018.Rnw’ using Sweave - Loading required package: Rgraphviz - Loading required package: graph - Loading required package: BiocGenerics - - Attaching package: 'BiocGenerics' - - The following objects are masked from 'package:stats': - - ... - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - - --- failed re-building 'vignette2018.Rnw' - - SUMMARY: processing the following file failed: - 'vignette2018.Rnw' - - Error: Vignette re-building failed. - Execution halted - ``` - -# pcFactorStan - -
- -* Version: 1.5.3 -* GitHub: https://github.com/jpritikin/pcFactorStan -* Source code: https://github.com/cran/pcFactorStan -* Date/Publication: 2021-09-25 15:50:02 UTC -* Number of recursive dependencies: 126 - -Run `revdepcheck::cloud_details(, "pcFactorStan")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘pcFactorStan-Ex.R’ failed - The error most likely occurred in: - - > ### Name: filterGraph - > ### Title: Filter graph to remove vertices that are not well connected - > ### Aliases: filterGraph - > - > ### ** Examples - > - > df <- filterGraph(phyActFlowPropensity[,c(paste0('pa',1:2),'predict')]) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: filterGraph ... graph_from_edgelist -> make_graph -> do.call -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 6. └─igraph (local) ``(``, directed = FALSE) - ── Error ('test-7report.R:62:3'): parInterval+parDistributionFor ─────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─pcFactorStan::prepData(phyActFlowPropensity[, c(1, 2, 3)]) at test-7report.R:62:2 - 2. └─pcFactorStan::filterGraph(df) - 3. └─igraph::graph_from_edgelist(el, directed = FALSE) - 4. └─igraph::make_graph(unname(ids[t(el)]), directed = directed) - 5. ├─base::do.call(old_graph, args) - 6. └─igraph (local) ``(``, directed = FALSE) - - [ FAIL 5 | WARN 0 | SKIP 5 | PASS 53 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 300.1Mb - sub-directories of 1Mb or more: - doc 2.9Mb - libs 296.5Mb - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘rstantools’ - All declared Imports should be used. - ``` - -* checking for GNU extensions in Makefiles ... NOTE - ``` - GNU make is a SystemRequirements. - ``` - -# pedtools - -
- -* Version: 2.2.0 -* GitHub: https://github.com/magnusdv/pedtools -* Source code: https://github.com/cran/pedtools -* Date/Publication: 2023-05-25 10:40:02 UTC -* Number of recursive dependencies: 77 - -Run `revdepcheck::cloud_details(, "pedtools")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘pedtools-Ex.R’ failed - The error most likely occurred in: - - > ### Name: inbreedingLoops - > ### Title: Pedigree loops - > ### Aliases: inbreedingLoops breakLoops tieLoops findLoopBreakers - > ### findLoopBreakers2 - > - > ### ** Examples - > - ... - + plot(y2) - + - + # Or loop breakers chosen by user - + y3 = breakLoops(y, 6:7) - + plot(y3) - + } - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: findLoopBreakers2 ... -> make_graph -> do.call -> - Execution halted - ``` - -## In both - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Failure ('test-founder-inbreeding.R:24:3'): setFounderInbreeding works on lists ── - fi(y1) not equal to c(`1` = 1, `2` = 1, `4` = 1). - 3/3 mismatches (average diff: 1) - [1] 0 - 1 == -1 - [2] 0 - 1 == -1 - [3] 0 - 1 == -1 - ── Failure ('test-founder-inbreeding.R:27:3'): setFounderInbreeding works on lists ── - fi(y2) not equal to c(`1` = 0, `2` = 1, `4` = 0). - 1/3 mismatches - [2] 0 - 1 == -1 - - [ FAIL 2 | WARN 0 | SKIP 2 | PASS 595 ] - Error: Test failures - Execution halted - ``` - -# perturbR - -
- -* Version: 0.1.3 -* GitHub: NA -* Source code: https://github.com/cran/perturbR -* Date/Publication: 2019-02-19 09:30:03 UTC -* Number of recursive dependencies: 54 - -Run `revdepcheck::cloud_details(, "perturbR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘perturbR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: perturbR - > ### Title: Perturb networks and evaluate subgroup structures. - > ### Aliases: perturbR evalClust - > - > ### ** Examples - > - > perturbR(exampledata, plot=FALSE, resolution=0.10, reps=1, errbars = FALSE) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: perturbR -> graph.adjacency -> graph.adjacency.dense - Execution halted - ``` - -# pGRN - -
- -* Version: 0.3.5 -* GitHub: NA -* Source code: https://github.com/cran/pGRN -* Date/Publication: 2023-01-17 17:20:02 UTC -* Number of recursive dependencies: 94 - -Run `revdepcheck::cloud_details(, "pGRN")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘pGRN-Ex.R’ failed - The error most likely occurred in: - - > ### Name: get_networks - > ### Title: Get the list of sub-networks - > ### Aliases: get_networks - > - > ### ** Examples - > - > example_data <- pGRNDB - ... - > pseudotime_list <- example_data[["ptime"]]$PseudoTime - > dtw_dist_matrix <- get_dtw_dist_mat(expression_matrix, - + pseudotime_list, - + cores=1) - > adj_df <- matrix2adj(dtw_dist_matrix) - > get_networks(adj_df,network_min_genes=5) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: get_networks ... as_graph_edge_df -> graph_from_data_frame -> make_empty_graph - Execution halted - ``` - -# phangorn - -
- -* Version: 2.11.1 -* GitHub: https://github.com/KlausVigo/phangorn -* Source code: https://github.com/cran/phangorn -* Date/Publication: 2023-01-23 10:10:02 UTC -* Number of recursive dependencies: 67 - -Run `revdepcheck::cloud_details(, "phangorn")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘phangorn-Ex.R’ failed - The error most likely occurred in: - - > ### Name: addConfidences - > ### Title: Compare splits and add support values to an object - > ### Aliases: addConfidences addConfidences.phylo presenceAbsence - > ### createLabel - > ### Keywords: cluster - > - > ### ** Examples - ... - + "extdata/trees/RAxML_bootstrap.woodmouse", package="phangorn")) - > boot_trees <- read.tree(tmpfile) - > - > dm <- dist.ml(woodmouse) - > tree <- upgma(dm) - > nnet <- neighborNet(dm) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: neighborNet ... as.networx.splits -> circNetwork -> graph -> do.call -> - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘AdvancedFeatures.Rmd’ using rmarkdown - --- finished re-building ‘AdvancedFeatures.Rmd’ - - --- re-building ‘Ancestral.Rmd’ using rmarkdown - --- finished re-building ‘Ancestral.Rmd’ - - --- re-building ‘IntertwiningTreesAndNetworks.Rmd’ using rmarkdown - - Quitting from lines 76-101 [unnamed-chunk-3] (IntertwiningTreesAndNetworks.Rmd) - ... - Error: processing vignette 'Trees.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘Trees.Rmd’ - - SUMMARY: processing the following files failed: - ‘IntertwiningTreesAndNetworks.Rmd’ ‘MLbyHand.Rmd’ ‘Networx.Rmd’ - ‘Trees.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 9.8Mb - sub-directories of 1Mb or more: - doc 1.5Mb - libs 5.8Mb - ``` - -# PhaseTypeR - -
- -* Version: 1.0.4 -* GitHub: https://github.com/rivasiker/PhaseTypeR -* Source code: https://github.com/cran/PhaseTypeR -* Date/Publication: 2022-07-21 16:20:05 UTC -* Number of recursive dependencies: 62 - -Run `revdepcheck::cloud_details(, "PhaseTypeR")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Backtrace: - ▆ - 1. ├─testthat::expect_warning(...) at test-phase_type_to_network.R:33:4 - 2. │ └─testthat:::expect_condition_matching(...) - 3. │ └─testthat:::quasi_capture(...) - 4. │ ├─testthat (local) .capture(...) - 5. │ │ └─base::withCallingHandlers(...) - 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) - 7. └─PhaseTypeR::phase_type_to_network(disc_phase_type, 3) - 8. └─igraph::graph_from_data_frame(...) - 9. └─igraph::make_empty_graph(n = 0, directed = directed) - - [ FAIL 5 | WARN 0 | SKIP 8 | PASS 102 ] - Error: Test failures - Execution halted - ``` - -# phyloseqGraphTest - -
- -* Version: 0.1.0 -* GitHub: https://github.com/jfukuyama/phyloseqGraphTest -* Source code: https://github.com/cran/phyloseqGraphTest -* Date/Publication: 2020-02-07 16:30:02 UTC -* Number of recursive dependencies: 95 - -Run `revdepcheck::cloud_details(, "phyloseqGraphTest")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘phyloseqGraphTest-Ex.R’ failed - The error most likely occurred in: - - > ### Name: graph_perm_test - > ### Title: Performs graph-based permutation tests - > ### Aliases: graph_perm_test - > - > ### ** Examples - > - > library(phyloseq) - > data(enterotype) - > gt = graph_perm_test(enterotype, sampletype = "SeqTech", type = "mst") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: graph_perm_test -> graph.adjacency -> graph.adjacency.dense - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘gt_vignette.Rmd’ using rmarkdown - - Quitting from lines 128-134 [unnamed-chunk-4] (gt_vignette.Rmd) - Error: processing vignette 'gt_vignette.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘gt_vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘gt_vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘intergraph’ - All declared Imports should be used. - ``` - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# phylosignal - -
- -* Version: 1.3 -* GitHub: NA -* Source code: https://github.com/cran/phylosignal -* Date/Publication: 2020-02-03 20:40:07 UTC -* Number of recursive dependencies: 110 - -Run `revdepcheck::cloud_details(, "phylosignal")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘phylosignal-Ex.R’ failed - The error most likely occurred in: - - > ### Name: graphClust - > ### Title: Phylogenetically constrained clustering - > ### Aliases: graphClust - > - > ### ** Examples - > - > data(navic) - > gC <- graphClust(navic, lim.phylo = 1, lim.trait = 2, scale.lim = FALSE) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: graphClust -> -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.7Mb - sub-directories of 1Mb or more: - help 1.6Mb - libs 2.9Mb - ``` - -# phyloTop - -
- -* Version: 2.1.2 -* GitHub: https://github.com/MichelleKendall/phyloTop -* Source code: https://github.com/cran/phyloTop -* Date/Publication: 2023-01-24 15:20:02 UTC -* Number of recursive dependencies: 93 - -Run `revdepcheck::cloud_details(, "phyloTop")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘phyloTop-Ex.R’ failed - The error most likely occurred in: - - > ### Name: avgLadder - > ### Title: Average ladder size - > ### Aliases: avgLadder - > - > ### ** Examples - > - > ## Find the average ladder size in a random tree with 20 tips: - > tree <- rtree(20) - > plot(tree) - > avgLadder(tree) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: avgLadder ... graph_from_edgelist -> make_graph -> do.call -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Error ('testbasics.R:11:1'): (code run outside of `test_that()`) ──────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─phyloTop::phyloTop(trees) at testbasics.R:11:0 - 2. └─phyloTop::ladderSizes(treeList[[i]]) - 3. └─igraph::graph_from_edgelist(chEL) - 4. └─igraph::make_graph(unname(ids[t(el)]), directed = directed) - 5. ├─base::do.call(old_graph, args) - 6. └─igraph (local) ``(``, directed = TRUE) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] - Error: Test failures - Execution halted - ``` - -# pkggraph - -
- -* Version: 0.2.3 -* GitHub: https://github.com/talegari/pkggraph -* Source code: https://github.com/cran/pkggraph -* Date/Publication: 2018-11-15 09:50:03 UTC -* Number of recursive dependencies: 71 - -Run `revdepcheck::cloud_details(, "pkggraph")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘pkggraph-Ex.R’ failed - The error most likely occurred in: - - > ### Name: make_neighborhood_graph - > ### Title: make_neighborhood_graph - > ### Aliases: make_neighborhood_graph - > - > ### ** Examples - > - > pkggraph::init(local = TRUE) - Using 'local' data ... - To fetch data from CRAN over internet, run:`pkggraph::init(local = FALSE)` - Done! - > graph_object <- pkggraph::get_neighborhood("caret") - > pkggraph::make_neighborhood_graph(graph_object) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: -> -> make_empty_graph - Execution halted - ``` - -# PlackettLuce - -
- -* Version: 0.4.2 -* GitHub: https://github.com/hturner/PlackettLuce -* Source code: https://github.com/cran/PlackettLuce -* Date/Publication: 2022-08-15 07:50:05 UTC -* Number of recursive dependencies: 184 - -Run `revdepcheck::cloud_details(, "PlackettLuce")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘PlackettLuce-Ex.R’ failed - The error most likely occurred in: - - > ### Name: PlackettLuce - > ### Title: Fit a Plackett-Luce Model - > ### Aliases: PlackettLuce - > - > ### ** Examples - > - > # Six partial rankings of four objects, 1 is top rank, e.g - ... - > - > # create rankings object - > R <- as.rankings(R) - > - > # Standard maximum likelihood estimates - > mod_mle <- PlackettLuce(R, npseudo = 0) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: PlackettLuce ... graph_from_adjacency_matrix -> graph.adjacency.dense - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘Overview.Rmd’ using rmarkdown - - Quitting from lines 489-491 [unnamed-chunk-7] (Overview.Rmd) - Error: processing vignette 'Overview.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘Overview.Rmd’ - - --- re-building ‘PLADMM.Rmd’ using rmarkdown - ... - Quitting from lines 124-126 [unnamed-chunk-5] (PLADMM.Rmd) - Error: processing vignette 'PLADMM.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘PLADMM.Rmd’ - - SUMMARY: processing the following files failed: - ‘Overview.Rmd’ ‘PLADMM.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 2. └─PlackettLuce::connectivity(X, verbose = FALSE) - 3. └─igraph::graph_from_adjacency_matrix(x > 0L) - 4. └─igraph:::graph.adjacency.dense(...) - ── Error ('test-weights.R:35:5'): (code run outside of `test_that()`) ────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─PlackettLuce::PlackettLuce(R, npseudo = 0) at test-weights.R:35:4 - 2. └─PlackettLuce::connectivity(X, verbose = FALSE) - 3. └─igraph::graph_from_adjacency_matrix(x > 0L) - 4. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 19 | WARN 0 | SKIP 11 | PASS 104 ] - Error: Test failures - Execution halted - ``` - -# plantTracker - -
- -* Version: 1.1.0 -* GitHub: https://github.com/aestears/plantTracker -* Source code: https://github.com/cran/plantTracker -* Date/Publication: 2023-05-05 18:20:02 UTC -* Number of recursive dependencies: 86 - -Run `revdepcheck::cloud_details(, "plantTracker")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘plantTracker-Ex.R’ failed - The error most likely occurred in: - - > ### Name: aggregateByGenet - > ### Title: aggregateByGenet - > ### Aliases: aggregateByGenet - > - > ### ** Examples - > - > dat <- grasslandData[grasslandData$Site == c("AZ") & - ... - + aggByGenet = FALSE - + ) - Site: AZ - - -- Quadrat: SG2 - - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: trackSpp ... graph.adjacency.sparse -> make_graph -> do.call -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘spelling.R’ - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 1. └─plantTracker::trackSpp(...) at test-trackSpp.R:5:0 - 2. └─plantTracker:::assign(...) - 3. └─plantTracker (local) ifClonal(cloneDat = tempPreviousYear, clonal = clonal, buffGenet = buffGenet) - 4. └─plantTracker::groupByGenet(cloneDat, buffGenet) - 5. ├─igraph::clusters(...) - 6. │ └─igraph:::ensure_igraph(graph) - 7. └─igraph::graph_from_adjacency_matrix(methods::as(connects, "lMatrix")) - 8. └─igraph:::graph.adjacency.sparse(...) - 9. └─igraph::make_graph(n = vc, edges, directed = (mode == "directed")) - 10. ├─base::do.call(old_graph, args) - 11. └─igraph (local) ``(``, n = 11L, directed = TRUE) - - [ FAIL 9 | WARN 0 | SKIP 0 | PASS 3 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘Suggested_plantTracker_Workflow.Rmd’ using rmarkdown - Warning in check_pandoc_version(minimum = "2.0.0", recommend = "2.7.2") : - minidown supports Pandoc >= 2.7.2 Pandoc with older versions may result in unexpected behaviors. - Warning in options[opts_class] <- Map(code_folding_class, options[opts_class], : - number of items to replace is not a multiple of replacement length - Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr], : - number of items to replace is not a multiple of replacement length - Warning in options[opts_class] <- Map(code_folding_class, options[opts_class], : - number of items to replace is not a multiple of replacement length - ... - Error: processing vignette 'Using_the_plantTracker_trackSpp_function.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘Using_the_plantTracker_trackSpp_function.Rmd’ - - SUMMARY: processing the following files failed: - ‘Suggested_plantTracker_Workflow.Rmd’ - ‘Using_the_plantTracker_trackSpp_function.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# plinkQC - -
- -* Version: 0.3.4 -* GitHub: https://github.com/meyer-lab-cshl/plinkQC -* Source code: https://github.com/cran/plinkQC -* Date/Publication: 2021-07-15 15:40:02 UTC -* Number of recursive dependencies: 90 - -Run `revdepcheck::cloud_details(, "plinkQC")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 4. └─igraph::graph_from_data_frame(combination, directed = FALSE) - 5. └─igraph::make_empty_graph(n = 0, directed = directed) - ── Error ('test-utils.R:165:5'): relatednessFilter only returns one fail ID for 4-way relatedness ── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─plinkQC::relatednessFilter(...) at test-utils.R:165:4 - 2. └─base::lapply(...) - 3. └─plinkQC (local) FUN(X[[i]], ...) - 4. └─igraph::graph_from_data_frame(combination, directed = FALSE) - 5. └─igraph::make_empty_graph(n = 0, directed = directed) - - [ FAIL 5 | WARN 8 | SKIP 0 | PASS 69 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘AncestryCheck.Rmd’ using rmarkdown - A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TinyTeX with tinytex::reinstall_tinytex(repository = "illinois"). - - tlmgr: Local TeX Live (2022) is older than remote repository (2023). - Cross release updates are only supported with - update-tlmgr-latest(.sh/.exe) --update - See https://tug.org/texlive/upgrade.html for details. - Warning in system2("tlmgr", args, ...) : - running command ''tlmgr' search --file --global '/grffile.sty'' had status 1 - ... - - Error: processing vignette 'plinkQC.Rmd' failed with diagnostics: - LaTeX failed to compile /tmp/workdir/plinkQC/new/plinkQC.Rcheck/vign_test/plinkQC/vignettes/plinkQC.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See plinkQC.log for more info. - --- failed re-building ‘plinkQC.Rmd’ - - SUMMARY: processing the following files failed: - ‘AncestryCheck.Rmd’ ‘Genomes1000.Rmd’ ‘HapMap.Rmd’ ‘plinkQC.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# PLNmodels - -
- -* Version: 1.0.1 -* GitHub: https://github.com/pln-team/PLNmodels -* Source code: https://github.com/cran/PLNmodels -* Date/Publication: 2023-02-12 14:42:07 UTC -* Number of recursive dependencies: 147 - -Run `revdepcheck::cloud_details(, "PLNmodels")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. ├─testthat::expect_true(...) at test-plnnetworkfit.R:45:2 - 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") - 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) - 4. ├─igraph::is.igraph(myPLNfit$plot_network(output = "igraph", plot = FALSE)) - 5. └─myPLNfit$plot_network(output = "igraph", plot = FALSE) - 6. └─igraph::graph_from_adjacency_matrix(...) - 7. └─igraph:::graph.adjacency.sparse(...) - 8. └─igraph::make_empty_graph(n = vc, directed = (mode == "directed")) - - [ FAIL 1 | WARN 4 | SKIP 0 | PASS 716 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘Import_data.Rmd’ using rmarkdown - --- finished re-building ‘Import_data.Rmd’ - - --- re-building ‘PLN.Rmd’ using rmarkdown - --- finished re-building ‘PLN.Rmd’ - - --- re-building ‘PLNLDA.Rmd’ using rmarkdown - --- finished re-building ‘PLNLDA.Rmd’ - - ... - --- failed re-building ‘PLNnetwork.Rmd’ - - --- re-building ‘Trichoptera.Rmd’ using rmarkdown - --- finished re-building ‘Trichoptera.Rmd’ - - SUMMARY: processing the following file failed: - ‘PLNnetwork.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 25.2Mb - sub-directories of 1Mb or more: - doc 2.2Mb - libs 21.6Mb - ``` - -# pmd - -
- -* Version: 0.2.1 -* GitHub: https://github.com/yufree/pmd -* Source code: https://github.com/cran/pmd -* Date/Publication: 2021-01-21 23:20:08 UTC -* Number of recursive dependencies: 122 - -Run `revdepcheck::cloud_details(, "pmd")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘pmd-Ex.R’ failed - The error most likely occurred in: - - > ### Name: getcda - > ### Title: Perform correlation directed analysis for peaks list. - > ### Aliases: getcda - > - > ### ** Examples - > - > data(spmeinvivo) - > cluster <- getcorcluster(spmeinvivo) - 75 retention time cluster found. - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: getcorcluster -> -> make_empty_graph - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘globalstd.Rmd’ using rmarkdown - - Quitting from lines 151-161 [comp] (globalstd.Rmd) - Error: processing vignette 'globalstd.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘globalstd.Rmd’ - - --- re-building ‘reactomics.Rmd’ using rmarkdown - --- finished re-building ‘reactomics.Rmd’ - - SUMMARY: processing the following file failed: - ‘globalstd.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 62 marked UTF-8 strings - ``` - -# PNAR - -
- -* Version: 1.4 -* GitHub: NA -* Source code: https://github.com/cran/PNAR -* Date/Publication: 2023-05-12 07:20:06 UTC -* Number of recursive dependencies: 47 - -Run `revdepcheck::cloud_details(, "PNAR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘PNAR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: adja - > ### Title: Generation of a network from the Stochastic Block Model - > ### Aliases: adja - > - > ### ** Examples - > - > W <- adja(N = 20, K = 5, alpha = 0.1) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: adja -> - Execution halted - ``` - -# polymapR - -
- -* Version: 1.1.3 -* GitHub: NA -* Source code: https://github.com/cran/polymapR -* Date/Publication: 2023-03-13 17:20:02 UTC -* Number of recursive dependencies: 198 - -Run `revdepcheck::cloud_details(, "polymapR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘polymapR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: bridgeHomologues - > ### Title: Use bridge markers to cluster homologues into linkage groups - > ### Aliases: bridgeHomologues assembleDuplexLinks - > - > ### ** Examples - > - > data("P1_homologues", "P2_homologues", "SN_DN_P1", "SN_SS_P1", "SN_SS_P2") - ... - > ChHomDf<-bridgeHomologues(cluster_stack = P1_homologues[["5"]], - + linkage_df=SN_DN_P1, - + LOD_threshold=4, - + automatic_clustering=TRUE, - + LG_number=5, - + parentname="P1") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: bridgeHomologues -> -> make_empty_graph - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘Vignette_genotype_probabilities.Rmd’ using rmarkdown - --- finished re-building ‘Vignette_genotype_probabilities.Rmd’ - - --- re-building ‘Vignette_polymapR.Rmd’ using rmarkdown - - Quitting from lines 242-246 [unnamed-chunk-18] (Vignette_polymapR.Rmd) - Error: processing vignette 'Vignette_polymapR.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘Vignette_polymapR.Rmd’ - - SUMMARY: processing the following file failed: - ‘Vignette_polymapR.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 12.2Mb - sub-directories of 1Mb or more: - R 6.5Mb - data 4.6Mb - ``` - -# polyqtlR - -
- -* Version: 0.0.9 -* GitHub: NA -* Source code: https://github.com/cran/polyqtlR -* Date/Publication: 2022-02-02 16:40:02 UTC -* Number of recursive dependencies: 182 - -Run `revdepcheck::cloud_details(, "polyqtlR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘polyqtlR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: visualisePairing - > ### Title: Visualise pairing of parental homologues - > ### Aliases: visualisePairing - > - > ### ** Examples - > - > data("mr.ls") - > visualisePairing(meiosis_report.ls = mr.ls, - + parent = "P1", - + datawidemax = 3) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: visualisePairing ... setNames -> lapply -> FUN -> -> make_empty_graph - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘polyqtlR_vignette.rmd’ using rmarkdown - - Quitting from lines 694-698 [unnamed-chunk-63] (polyqtlR_vignette.rmd) - Error: processing vignette 'polyqtlR_vignette.rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘polyqtlR_vignette.rmd’ - - SUMMARY: processing the following file failed: - ‘polyqtlR_vignette.rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 7.0Mb - sub-directories of 1Mb or more: - data 2.6Mb - doc 1.7Mb - libs 2.2Mb - ``` - -# pomdp - -
- -* Version: 1.1.0 -* GitHub: https://github.com/mhahsler/pomdp -* Source code: https://github.com/cran/pomdp -* Date/Publication: 2023-01-24 15:40:10 UTC -* Number of recursive dependencies: 77 - -Run `revdepcheck::cloud_details(, "pomdp")` for more info - -
- -## Newly broken - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘POMDP.Rmd’ using rmarkdown - - Quitting from lines 376-377 [unnamed-chunk-11] (POMDP.Rmd) - Error: processing vignette 'POMDP.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘POMDP.Rmd’ - - SUMMARY: processing the following file failed: - ‘POMDP.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking examples ... ERROR - ``` - Running examples in ‘pomdp-Ex.R’ failed - The error most likely occurred in: - - > ### Name: MDP - > ### Title: Define an MDP Problem - > ### Aliases: MDP MDP2POMDP is_solved_MDP - > - > ### ** Examples - > - > # Michael's Sleepy Tiger Problem is like the POMDP Tiger problem, but - ... - Horizon: Inf epochs - Size: 2 states / 3 actions - - List components: ‘name’, ‘discount’, ‘horizon’, ‘states’, ‘actions’, - ‘transition_prob’, ‘reward’, ‘start’ - > - > sol <- solve_MDP(STiger, eps = 1e-7) - Error in P[[a]][s, ] : no 'dimnames' attribute for array - Calls: solve_MDP ... MDP_value_iteration_inf_horizon -> outer -> FUN -> do.call -> mapply -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─pomdp::plot_policy_graph(sol) at test-solve_POMDP.R:9:0 - 2. └─pomdp:::.plot.igraph(...) - 3. └─pomdp::policy_graph(...) - 4. └─pomdp:::policy_graph_converged(...) - 5. └─igraph::graph.edgelist(as.matrix(l[, 1:2])) - 6. └─igraph::make_graph(t(el), directed = directed) - 7. ├─base::do.call(old_graph, args) - 8. └─igraph (local) ``(``, directed = TRUE) - - [ FAIL 2 | WARN 0 | SKIP 0 | PASS 58 ] - Error: Test failures - Execution halted - ``` - -* checking installed package size ... NOTE - ``` - installed size is 6.5Mb - sub-directories of 1Mb or more: - libs 5.6Mb - ``` - -# pop - -
- -* Version: 0.1 -* GitHub: NA -* Source code: https://github.com/cran/pop -* Date/Publication: 2016-06-07 06:26:35 -* Number of recursive dependencies: 40 - -Run `revdepcheck::cloud_details(, "pop")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘pop-Ex.R’ failed - The error most likely occurred in: - - > ### Name: dynamic - > ### Title: dynamic objects - > ### Aliases: as.matrix.dynamic dynamic is.dynamic parameters.dynamic - > ### parameters<-.dynamic plot.dynamic print.dynamic states - > - > ### ** Examples - > - ... - > # combine these into one dynamic (the same as listing all the transitions - > # separately) - > all <- dynamic(stasis, growth, reproduction) - > - > # plot these - > plot(stasis) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot ... plot.dynamic -> graph.adjacency -> graph.adjacency.dense - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘test-all.R’ - Running the tests in ‘tests/test-all.R’ failed. - Last 13 lines of output: - • On CRAN (1) - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Error ('test_dynamic_class.R:143:3'): dynamic classes work ────────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. ├─base::plot(stasis) at test_dynamic_class.R:143:2 - 2. └─pop:::plot.dynamic(stasis) - 3. └─igraph::graph.adjacency(linkmat, weighted = TRUE) - 4. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 1 | WARN 0 | SKIP 1 | PASS 212 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# poppr - -
- -* Version: 2.9.4 -* GitHub: https://github.com/grunwaldlab/poppr -* Source code: https://github.com/cran/poppr -* Date/Publication: 2023-03-23 03:20:02 UTC -* Number of recursive dependencies: 98 - -Run `revdepcheck::cloud_details(, "poppr")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘poppr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: bruvo.msn - > ### Title: Create minimum spanning network of selected populations using - > ### Bruvo's distance. - > ### Aliases: bruvo.msn msn.bruvo - > - > ### ** Examples - > - ... - > # Load the data set. - > data(nancycats) - > - > # View populations 8 and 9 with default colors. - > bruvo.msn(nancycats, replen = rep(2, 9), sublist=8:9, vertex.label="inds", - + vertex.label.cex=0.7, vertex.label.dist=0.4) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: bruvo.msn ... msn_constructor -> graph.adjacency -> graph.adjacency.dense - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘test-all.R’ - Running the tests in ‘tests/test-all.R’ failed. - Last 13 lines of output: - 2. └─poppr:::msn_constructor(...) - 3. └─igraph::graph.adjacency(indist, weighted = TRUE, mode = "undirected") - 4. └─igraph:::graph.adjacency.dense(...) - ── Error ('test-msn.R:118:1'): (code run outside of `test_that()`) ───────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─poppr::bruvo.msn(gend, replen = c(1, 1), showplot = FALSE) at test-msn.R:118:0 - 2. └─poppr:::msn_constructor(...) - 3. └─igraph::graph.adjacency(indist, weighted = TRUE, mode = "undirected") - 4. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 2 | WARN 0 | SKIP 166 | PASS 332 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘algo.Rnw’ using knitr - Error: processing vignette 'algo.Rnw' failed with diagnostics: - Running 'texi2dvi' on 'algo.tex' failed. - LaTeX errors: - ! LaTeX Error: File `colortbl.sty' not found. - - Type X to quit or to proceed, - or enter new name. (Default extension: sty) - ... - l.270 \long - \def\@secondoffive#1#2#3#4#5{#2}^^M - ! ==> Fatal error occurred, no output PDF file produced! - --- failed re-building ‘algo.Rnw’ - - SUMMARY: processing the following file failed: - ‘algo.Rnw’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# POSetR - -
- -* Version: 1.1.1 -* GitHub: NA -* Source code: https://github.com/cran/POSetR -* Date/Publication: 2023-01-17 10:40:02 UTC -* Number of recursive dependencies: 10 - -Run `revdepcheck::cloud_details(, "POSetR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘POSetR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: intersection - > ### Title: Intersection of two posets - > ### Aliases: intersection %it% - > - > ### ** Examples - > - > dom <- matrix(c( - ... - + "a", "b", - + "c", "b", - + "b", "d" - + ), ncol = 2, byrow = TRUE) - > p <- poset(x = dom) - > plot(p) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot -> plot.poset -> -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 26.0Mb - sub-directories of 1Mb or more: - libs 25.8Mb - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘Rdpack’ - All declared Imports should be used. - ``` - -# ProjectManagement - -
- -* Version: 1.4.7 -* GitHub: NA -* Source code: https://github.com/cran/ProjectManagement -* Date/Publication: 2022-09-19 08:26:16 UTC -* Number of recursive dependencies: 83 - -Run `revdepcheck::cloud_details(, "ProjectManagement")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ProjectManagement-Ex.R’ failed - The error most likely occurred in: - - > ### Name: dag.plot - > ### Title: DAG plot - > ### Aliases: dag.plot - > - > ### ** Examples - > - > - > prec1and2<-matrix(c(0,1,0,2,0,0,0,0,0,1,0,0,0,1,0,0,0,0,0,0,0,0,0,2,0),nrow=5,ncol=5,byrow=TRUE) - > prec3and4<-matrix(0,nrow=5,ncol=5) - > prec3and4[3,1]<-3 - > dag.plot(prec1and2,prec3and4) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: dag.plot ... graph_from_adjacency_matrix -> graph.adjacency.dense - Execution halted - ``` - -# provGraphR - -
- -* Version: 1.0.1 -* GitHub: NA -* Source code: https://github.com/cran/provGraphR -* Date/Publication: 2022-08-17 15:30:02 UTC -* Number of recursive dependencies: 36 - -Run `revdepcheck::cloud_details(, "provGraphR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘provGraphR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: get.lineage - > ### Title: Calculate lineage of a node - > ### Aliases: get.lineage - > - > ### ** Examples - > - > adj.graph <- create.graph(system.file("testdata", "basic.json", package = "provGraphR")) - > get.lineage (adj.graph, "d24") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: get.lineage ... graph.adjacency.sparse -> make_graph -> do.call -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 9. └─igraph (local) ``(``, n = 56L, directed = TRUE) - ── Error ('test_provGraphR.R:115:7'): order ──────────────────────────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─provGraphR::get.lineage(adj.graph, "d4") at test_provGraphR.R:115:6 - 2. └─igraph::graph_from_adjacency_matrix(adj.graph) - 3. └─igraph:::graph.adjacency.sparse(...) - 4. └─igraph::make_graph(n = vc, edges, directed = (mode == "directed")) - 5. ├─base::do.call(old_graph, args) - 6. └─igraph (local) ``(``, n = 10L, directed = TRUE) - - [ FAIL 2 | WARN 0 | SKIP 0 | PASS 47 ] - Error: Test failures - Execution halted - ``` - -# ptools - -
- -* Version: 2.0.0 -* GitHub: https://github.com/apwheele/ptools -* Source code: https://github.com/cran/ptools -* Date/Publication: 2023-02-07 19:02:30 UTC -* Number of recursive dependencies: 82 - -Run `revdepcheck::cloud_details(, "ptools")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ptools-Ex.R’ failed - The error most likely occurred in: - - > ### Name: near_strings1 - > ### Title: Strings of Near Repeats - > ### Aliases: near_strings1 - > - > ### ** Examples - > - > # Simplified example showing two clusters - ... - > s <- c(0,0,0,4,4) - > ccheck <- c(1,1,1,2,2) - > dat <- data.frame(x=1:5,y=0, - + ti=s, - + id=1:5) - > res1 <- near_strings1(dat,'id','x','y','ti',2,1) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: near_strings1 -> -> make_empty_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ▆ - 1. └─ptools::near_strings1(dat, "id", "x", "y", "ti", 1, 1) at test-nearstring.R:34:2 - 2. └─igraph::graph_from_data_frame(...) - 3. └─igraph::make_empty_graph(n = 0, directed = directed) - ── Error ('test-nearstring.R:46:3'): Checking two components ─────────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─ptools::near_strings1(dat, "id", "x", "y", "ti", 2, 1) at test-nearstring.R:46:2 - 2. └─igraph::graph_from_data_frame(...) - 3. └─igraph::make_empty_graph(n = 0, directed = directed) - - [ FAIL 4 | WARN 0 | SKIP 0 | PASS 40 ] - Error: Test failures - Execution halted - ``` - -# qdap - -
- -* Version: 2.4.6 -* GitHub: https://github.com/trinker/qdap -* Source code: https://github.com/cran/qdap -* Date/Publication: 2023-05-11 06:10:02 UTC -* Number of recursive dependencies: 98 - -Run `revdepcheck::cloud_details(, "qdap")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - |======================================================================| 100% - [ FAIL 1 | WARN 1 | SKIP 0 | PASS 216 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Error ('test-phrase_net.R:19:5'): phrase_net gives a `phrase_net` and `igraph` object ── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─qdap::phrase_net(sents, r = 0.5) at test-phrase_net.R:19:4 - 2. └─igraph::graph.data.frame(X2, directed = FALSE) - 3. └─igraph::make_empty_graph(n = 0, directed = directed) - - [ FAIL 1 | WARN 1 | SKIP 0 | PASS 216 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘gplots’ - ``` - -# qgraph - -
- -* Version: 1.9.5 -* GitHub: https://github.com/SachaEpskamp/qgraph -* Source code: https://github.com/cran/qgraph -* Date/Publication: 2023-05-16 10:10:02 UTC -* Number of recursive dependencies: 89 - -Run `revdepcheck::cloud_details(, "qgraph")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘qgraph-Ex.R’ failed - The error most likely occurred in: - - > ### Name: centrality - > ### Title: Centrality statistics of graphs - > ### Aliases: centrality - > ### Keywords: graphs - > - > ### ** Examples - > - > set.seed(1) - > adj <- matrix(sample(0:1,10^2,TRUE,prob=c(0.8,0.2)),nrow=10,ncol=10) - > Q <- qgraph(adj) - > - > centrality(Q) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: centrality -> -> graph.adjacency.dense - Execution halted - ``` - -# R.temis - -
- -* Version: 0.1.3 -* GitHub: https://github.com/nalimilan/R.TeMiS -* Source code: https://github.com/cran/R.temis -* Date/Publication: 2021-05-12 19:02:12 UTC -* Number of recursive dependencies: 135 - -Run `revdepcheck::cloud_details(, "R.temis")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘R.temis-Ex.R’ failed - The error most likely occurred in: - - > ### Name: terms_graph - > ### Title: terms_graph - > ### Aliases: terms_graph - > - > ### ** Examples - > - > - > file <- system.file("texts", "reut21578-factiva.xml", package="tm.plugin.factiva") - > corpus <- import_corpus(file, "factiva", language="en") - > dtm <- build_dtm(corpus) - > terms_graph(dtm, 100, 3) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: terms_graph -> -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘testthat’ - All declared Imports should be used. - ``` - -# R6causal - -
- -* Version: 0.7.0 -* GitHub: NA -* Source code: https://github.com/cran/R6causal -* Date/Publication: 2022-11-04 08:00:02 UTC -* Number of recursive dependencies: 98 - -Run `revdepcheck::cloud_details(, "R6causal")` for more info - -
- -## Newly broken - -* checking whether package ‘R6causal’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/R6causal/new/R6causal.Rcheck/00install.out’ for details. - ``` - -## Newly fixed - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘using_R6causal.Rmd’ using rmarkdown - A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TinyTeX with tinytex::reinstall_tinytex(repository = "illinois"). - - tlmgr: Local TeX Live (2022) is older than remote repository (2023). - Cross release updates are only supported with - update-tlmgr-latest(.sh/.exe) --update - See https://tug.org/texlive/upgrade.html for details. - Warning in system2("tlmgr", args, ...) : - ... - - Error: processing vignette 'using_R6causal.Rmd' failed with diagnostics: - LaTeX failed to compile /tmp/workdir/R6causal/old/R6causal.Rcheck/vign_test/R6causal/vignettes/using_R6causal.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See using_R6causal.log for more info. - --- failed re-building ‘using_R6causal.Rmd’ - - SUMMARY: processing the following file failed: - ‘using_R6causal.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘R6causal’ ... -** package ‘R6causal’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" -Error: unable to load R code in package ‘R6causal’ -Execution halted -ERROR: lazy loading failed for package ‘R6causal’ -* removing ‘/tmp/workdir/R6causal/new/R6causal.Rcheck/R6causal’ - - -``` -### CRAN - -``` -* installing *source* package ‘R6causal’ ... -** package ‘R6causal’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -** help -*** installing help indices -** building package indices -** installing vignettes -** testing if installed package can be loaded from temporary location -** testing if installed package can be loaded from final location -** testing if installed package keeps a record of temporary installation path -* DONE (R6causal) - - -``` -# RaceID - -
- -* Version: 0.3.0 -* GitHub: NA -* Source code: https://github.com/cran/RaceID -* Date/Publication: 2023-03-13 12:10:02 UTC -* Number of recursive dependencies: 157 - -Run `revdepcheck::cloud_details(, "RaceID")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘RaceID-Ex.R’ failed - The error most likely occurred in: - - > ### Name: compfr - > ### Title: Computation of a two dimensional Fruchterman-Rheingold - > ### representation - > ### Aliases: compfr - > - > ### ** Examples - > - ... - determine final clustering partition 2 - determine final clustering partition 3 - determine final clustering partition 4 - determine final clustering partition 5 - determine final clustering partition 6 - > sc <- compfr(sc) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: compfr ... graph_from_adjacency_matrix -> graph.adjacency.dense - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘RaceID.Rmd’ using rmarkdown - - Quitting from lines 119-120 [unnamed-chunk-17] (RaceID.Rmd) - Error: processing vignette 'RaceID.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘RaceID.Rmd’ - - SUMMARY: processing the following file failed: - ‘RaceID.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 12.1Mb - sub-directories of 1Mb or more: - data 2.1Mb - doc 6.6Mb - libs 2.6Mb - ``` - -# rags2ridges - -
- -* Version: 2.2.6 -* GitHub: https://github.com/CFWP/rags2ridges -* Source code: https://github.com/cran/rags2ridges -* Date/Publication: 2022-05-01 14:40:02 UTC -* Number of recursive dependencies: 103 - -Run `revdepcheck::cloud_details(, "rags2ridges")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘rags2ridges-Ex.R’ failed - The error most likely occurred in: - - > ### Name: Communities - > ### Title: Search and visualize community-structures - > ### Aliases: Communities - > - > ### ** Examples - > - > - ... - - Retained elements: 11 - - Corresponding to 3.67 % of possible edges - - > - > ## Search and visualize communities - > Commy <- Communities(PC0) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: Communities -> graph.adjacency -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 7.6Mb - sub-directories of 1Mb or more: - libs 6.4Mb - ``` - -# RavenR - -
- -* Version: 2.2.0 -* GitHub: https://github.com/rchlumsk/RavenR -* Source code: https://github.com/cran/RavenR -* Date/Publication: 2022-10-28 21:02:50 UTC -* Number of recursive dependencies: 141 - -Run `revdepcheck::cloud_details(, "RavenR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘RavenR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: rvn_calc_runoff_coeff - > ### Title: Generate runoff coefficients upstream of gauges - > ### Aliases: rvn_calc_runoff_coeff - > - > ### ** Examples - > - > myrvh <- system.file("extdata","Nith.rvh", package="RavenR") - > mycust <- system.file("extdata", "run1_PRECIP_Daily_Average_BySubbasin.csv", package="RavenR") - > myhyd <- system.file("extdata", "run1_Hydrographs.csv", package="RavenR") - > - > rcs <- rvn_calc_runoff_coeff(myrvh, mycust, myhyd, correct=TRUE) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: rvn_calc_runoff_coeff ... rvn_rvh_read -> graph_from_data_frame -> make_empty_graph - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘Introduction_to_RavenR.Rmd’ using rmarkdown - - Quitting from lines 213-217 [RVI connection plot example] (Introduction_to_RavenR.Rmd) - Error: processing vignette 'Introduction_to_RavenR.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘Introduction_to_RavenR.Rmd’ - - SUMMARY: processing the following file failed: - ‘Introduction_to_RavenR.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# rcrimeanalysis - -
- -* Version: 0.5.0 -* GitHub: NA -* Source code: https://github.com/cran/rcrimeanalysis -* Date/Publication: 2023-05-18 21:50:02 UTC -* Number of recursive dependencies: 104 - -Run `revdepcheck::cloud_details(, "rcrimeanalysis")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘rcrimeanalysis-Ex.R’ failed - The error most likely occurred in: - - > ### Name: near_repeat_analysis - > ### Title: Near Repeat Analysis of Crime Incidents with Crime Linkage - > ### Output - > ### Aliases: near_repeat_analysis - > ### Keywords: spatial - > - > ### ** Examples - > - > data(crimes) - > nr_data <- head(crimes, n = 1000) #truncate dataset for near repeat analysis - > out <- near_repeat_analysis(data=nr_data,tz="America/Chicago",epsg="32616") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: near_repeat_analysis -> -> graph.adjacency.dense - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘rcrimeanalysis.Rmd’ using rmarkdown - - Quitting from lines 157-162 [unnamed-chunk-8] (rcrimeanalysis.Rmd) - Error: processing vignette 'rcrimeanalysis.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘rcrimeanalysis.Rmd’ - - SUMMARY: processing the following file failed: - ‘rcrimeanalysis.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# rD3plot - -
- -* Version: 1.0.68 -* GitHub: NA -* Source code: https://github.com/cran/rD3plot -* Date/Publication: 2023-03-22 16:50:10 UTC -* Number of recursive dependencies: 49 - -Run `revdepcheck::cloud_details(, "rD3plot")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘rD3plot-Ex.R’ failed - The error most likely occurred in: - - > ### Name: rd3_fromIgraph - > ### Title: Produce interactive networks from 'igraph' objects. - > ### Aliases: rd3_fromIgraph - > - > ### ** Examples - > - > g <- igraph::make_ring(10) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: - Execution halted - ``` - -# RDS - -
- -* Version: 0.9-6 -* GitHub: NA -* Source code: https://github.com/cran/RDS -* Date/Publication: 2023-02-10 18:20:02 UTC -* Number of recursive dependencies: 106 - -Run `revdepcheck::cloud_details(, "RDS")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘RDS-Ex.R’ failed - The error most likely occurred in: - - > ### Name: read.rdsat - > ### Title: Import data from the 'RDSAT' format as an 'rds.data.frame' - > ### Aliases: read.rdsat - > - > ### ** Examples - > - > fn <- paste0(path.package("RDS"),"/extdata/nyjazz.rdsat") - > rd <- read.rdsat(fn) - > plot(rd) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot ... -> make_graph -> do.call -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘tests.R’ - Running the tests in ‘tests/tests.R’ failed. - Complete output: - > - > - > library(testthat) - > library(RDS) - > - > test_check("RDS") - Killed - ``` - -# readsdr - -
- -* Version: 0.2.0 -* GitHub: https://github.com/jandraor/readsdr -* Source code: https://github.com/cran/readsdr -* Date/Publication: 2021-01-08 16:00:02 UTC -* Number of recursive dependencies: 74 - -Run `revdepcheck::cloud_details(, "readsdr")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - > - > test_check("readsdr") - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 252 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Error ('test-generate_igraph_inputs.R:28:3'): get_igraph_inputs() valid inputs for igraph ── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─igraph::graph_from_data_frame(...) at test-generate_igraph_inputs.R:28:2 - 2. └─igraph::make_empty_graph(n = 0, directed = directed) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 252 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# ReDaMoR - -
- -* Version: 0.7.1 -* GitHub: https://github.com/patzaw/ReDaMoR -* Source code: https://github.com/cran/ReDaMoR -* Date/Publication: 2022-10-19 13:47:56 UTC -* Number of recursive dependencies: 86 - -Run `revdepcheck::cloud_details(, "ReDaMoR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ReDaMoR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: df_to_model - > ### Title: Create a RelDataModel object from column names of data frames - > ### Aliases: df_to_model - > - > ### ** Examples - > - > ## Read data files ---- - ... - + list=names(hpo_tables), envir=as.environment(hpo_tables) - + ) - > ## Plot the model ---- - > new_model %>% - + auto_layout(lengthMultiplier=250) %>% - + plot() - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: %>% ... %>% -> -> -> make_empty_graph - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘ReDaMoR.Rmd’ using rmarkdown - - Quitting from lines 383-390 [unnamed-chunk-12] (ReDaMoR.Rmd) - Error: processing vignette 'ReDaMoR.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘ReDaMoR.Rmd’ - - SUMMARY: processing the following file failed: - ‘ReDaMoR.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# refdb - -
- -* Version: 0.1.1 -* GitHub: https://github.com/fkeck/refdb -* Source code: https://github.com/cran/refdb -* Date/Publication: 2022-09-22 17:00:05 UTC -* Number of recursive dependencies: 163 - -Run `revdepcheck::cloud_details(, "refdb")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘refdb-Ex.R’ failed - The error most likely occurred in: - - > ### Name: refdb_plot_tax_tree - > ### Title: Reference database taxonomy tree - > ### Aliases: refdb_plot_tax_tree - > - > ### ** Examples - > - > lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb")) - ... - Selected rank column for the color: species_name - Warning: There was 1 warning in `dplyr::group_by()`. - ℹ In argument: `dplyr::across()`. - Caused by warning: - ! Using `across()` without supplying `.cols` was deprecated in dplyr 1.1.0. - ℹ Please supply `.cols` instead. - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: refdb_plot_tax_tree ... igraph_from_taxo -> -> make_empty_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ══ Skipped tests ═══════════════════════════════════════════════════════════════ - • On CRAN (1) - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Error ('test_plots.R:7:3'): Test plot functions ───────────────────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─refdb:::igraph_from_taxo(test) at test_plots.R:7:2 - 2. └─igraph::graph_from_data_frame(graph_def_edges, vertices = res_tidy) - 3. └─igraph::make_empty_graph(n = 0, directed = directed) - - [ FAIL 1 | WARN 16 | SKIP 1 | PASS 123 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘intro_refdb.Rmd’ using rmarkdown - - Quitting from lines 227-228 [unnamed-chunk-17] (intro_refdb.Rmd) - Error: processing vignette 'intro_refdb.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘intro_refdb.Rmd’ - - --- re-building ‘ncbi_bold.Rmd’ using rmarkdown - --- finished re-building ‘ncbi_bold.Rmd’ - - SUMMARY: processing the following file failed: - ‘intro_refdb.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# RepertoiR - -
- -* Version: 0.0.1 -* GitHub: https://github.com/systemsbiomed/RepertoiR -* Source code: https://github.com/cran/RepertoiR -* Date/Publication: 2021-10-25 07:00:21 UTC -* Number of recursive dependencies: 45 - -Run `revdepcheck::cloud_details(, "RepertoiR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘RepertoiR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: network - > ### Title: Sequences distance network - > ### Aliases: network - > - > ### ** Examples - > - > - ... - + } - > - > rownames(data) <- aavec - > colnames(data) <- LETTERS[1:ncol(data)] - > - > network(data, by = 3, nrow = 100) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: network ... ensure_igraph -> graph.data.frame -> make_empty_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 9. └─igraph::make_empty_graph(n = 0, directed = directed) - ── Error ('test-sunflower.R:5:3'): check no error has occurred ───────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. ├─testthat::expect_identical(sunflower(data), NULL) at test-sunflower.R:5:2 - 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") - 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) - 4. ├─RepertoiR::sunflower(data) - 5. └─RepertoiR:::sunflower.default(data) - 6. └─igraph::make_empty_graph(length(mat)) - - [ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘stringi’ - All declared Imports should be used. - ``` - -# repo - -
- -* Version: 2.1.5 -* GitHub: NA -* Source code: https://github.com/cran/repo -* Date/Publication: 2020-02-08 16:20:02 UTC -* Number of recursive dependencies: 58 - -Run `revdepcheck::cloud_details(, "repo")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘repo-Ex.R’ failed - The error most likely occurred in: - - > ### Name: repo_dependencies - > ### Title: Build and/or plots a dependency graph - > ### Aliases: repo_dependencies - > - > ### ** Examples - > - > ## Repository creation - ... - item1 0 0 0 0 - item2 1 0 0 0 - item3 1 1 0 0 - temp.pdf 2 0 0 0 - > ## The matrix can be plotted as a graph (requires igraph package) - > rp$dependencies() - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: -> -> graph.adjacency.dense - Execution halted - ``` - -# ResIN - -
- -* Version: 0.1.0 -* GitHub: https://github.com/pwarncke77/ResIN -* Source code: https://github.com/cran/ResIN -* Date/Publication: 2023-05-10 13:50:06 UTC -* Number of recursive dependencies: 94 - -Run `revdepcheck::cloud_details(, "ResIN")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ResIN-Ex.R’ failed - The error most likely occurred in: - - > ### Name: ResIN - > ### Title: ResIN - > ### Aliases: ResIN - > - > ### ** Examples - > - > - ... - > ## Load the 12-item simulated Likert-type ResIN toy dataset - > data(lik_data) - > library(ggplot2) - > - > # Apply the ResIN function to toy Likert data: - > output <- ResIN(lik_data, cor_method = "spearman", network_stats = TRUE) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: ResIN -> -> graph.adjacency.dense - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘ResIN-VIGNETTE.Rmd’ using rmarkdown - - Quitting from lines 61-65 [run ResIN] (ResIN-VIGNETTE.Rmd) - Error: processing vignette 'ResIN-VIGNETTE.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘ResIN-VIGNETTE.Rmd’ - - SUMMARY: processing the following file failed: - ‘ResIN-VIGNETTE.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# RevEcoR - -
- -* Version: 0.99.3 -* GitHub: NA -* Source code: https://github.com/cran/RevEcoR -* Date/Publication: 2016-04-03 17:14:01 -* Number of recursive dependencies: 23 - -Run `revdepcheck::cloud_details(, "RevEcoR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘RevEcoR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: reconstructGsMN - > ### Title: Reconstuction of the specific-organism genome-scale metabolic - > ### network - > ### Aliases: reconstructGsMN - > - > ### ** Examples - > - ... - > ## species detected in a human microbiome - > annodir <- system.file("extdata","koanno.tab",package = "RevEcoR") - > metabolic.data <- read.delim2(file=annodir,stringsAsFactors=FALSE) - > ##load the reference metabolic data - > data(RefDbcache) - > g2 <- reconstructGsMN(metabolic.data, RefData = RefDbcache) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: reconstructGsMN -> graph.adjacency -> graph.adjacency.dense - Execution halted - ``` - -# rflexscan - -
- -* Version: 1.1.0 -* GitHub: NA -* Source code: https://github.com/cran/rflexscan -* Date/Publication: 2023-03-01 08:52:30 UTC -* Number of recursive dependencies: 53 - -Run `revdepcheck::cloud_details(, "rflexscan")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘rflexscan-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plot.rflexscan - > ### Title: Graph plotting of flexscan results - > ### Aliases: plot.rflexscan - > - > ### ** Examples - > - > # load sample data (North Carolina SIDS data) - ... - + name = rownames(nc.sids), - + clustersize = 10, - + nb = ncCR85.nb) - > - > # display all clusters - > plot(fls) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot ... graph_from_adjacency_matrix -> graph.adjacency.dense - Execution halted - ``` - -# rgexf - -
- -* Version: 0.16.2 -* GitHub: https://github.com/gvegayon/rgexf -* Source code: https://github.com/cran/rgexf -* Date/Publication: 2021-08-12 21:30:02 UTC -* Number of recursive dependencies: 53 - -Run `revdepcheck::cloud_details(, "rgexf")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘rgexf-Ex.R’ failed - The error most likely occurred in: - - > ### Name: igraph.to.gexf - > ### Title: Converting between 'gexf' and 'igraph' classes - > ### Aliases: igraph.to.gexf gexf.to.igraph - > ### Keywords: manip - > - > ### ** Examples - > - ... - + demo(gexfigraph) - + } - > - > fn <- system.file("gexf-graphs/lesmiserables.gexf", package = "rgexf") - > gexf1 <- read.gexf(fn) - > igraph1 <- gexf.to.igraph(gexf1) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: gexf.to.igraph -> -> make_empty_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘tinytest.R’ - Running the tests in ‘tests/tinytest.R’ failed. - Complete output: - > - > if ( requireNamespace("tinytest", quietly=TRUE) ){ - + tinytest::test_package("rgexf") - + } - - test-bugs.r................... 0 tests Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: ... run_test_dir -> lapply -> FUN -> eval -> eval -> - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘rgexf.Rmd’ using rmarkdown - - Quitting from lines 52-58 [igraph-plot] (rgexf.Rmd) - Error: processing vignette 'rgexf.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘rgexf.Rmd’ - - SUMMARY: processing the following file failed: - ‘rgexf.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# rgraph6 - -
- -* Version: 2.0-2 -* GitHub: https://github.com/mbojan/rgraph6 -* Source code: https://github.com/cran/rgraph6 -* Date/Publication: 2022-08-25 12:10:02 UTC -* Number of recursive dependencies: 58 - -Run `revdepcheck::cloud_details(, "rgraph6")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘rgraph6-Ex.R’ failed - The error most likely occurred in: - - > ### Name: adjacency_from_text - > ### Title: Create adjacency matrices from 'graph6', 'sparse6', or - > ### 'digraph6' symbols - > ### Aliases: adjacency_from_text - > - > ### ** Examples - > - ... - - > - > # Sparse6 symbols - > s6 <- c(":DgXI@G~", ":DgWCgCb") - > adjacency_from_text(s6) - Loading required namespace: igraph - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: adjacency_from_text ... igraph_from_sparse6 -> lapply -> FUN -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 4. │ │ ├─withr::with_output_sink(...) - 5. │ │ │ └─base::force(code) - 6. │ │ ├─base::withCallingHandlers(...) - 7. │ │ └─base::withVisible(code) - 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) - 9. └─rgraph6::read_file6(...) - 10. └─rgraph6::adjacency_from_text(txt) - 11. └─rgraph6::igraph_from_sparse6(object[fmt == "sparse6"]) - 12. └─base::lapply(ellist, my_graph_from_edgelist) - 13. └─rgraph6 (local) FUN(X[[i]], ...) - 14. └─igraph::make_empty_graph(attr(el, "gorder"), directed = FALSE) - - [ FAIL 10 | WARN 0 | SKIP 0 | PASS 199 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘rgraph6.Rmd’ using rmarkdown - - Quitting from lines 31-38 [unnamed-chunk-1] (rgraph6.Rmd) - Error: processing vignette 'rgraph6.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘rgraph6.Rmd’ - - SUMMARY: processing the following file failed: - ‘rgraph6.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# rhcoclust - -
- -* Version: 2.0.0 -* GitHub: NA -* Source code: https://github.com/cran/rhcoclust -* Date/Publication: 2023-01-29 03:40:02 UTC -* Number of recursive dependencies: 36 - -Run `revdepcheck::cloud_details(, "rhcoclust")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘rhcoclust-Ex.R’ failed - The error most likely occurred in: - - > ### Name: rhcoclust_internet - > ### Title: Interaction network (internet) of the 'rhcoclust' objects - > ### Aliases: rhcoclust_internet - > - > ### ** Examples - > - > # Load necessary library - ... - > # Plot interaction network (internet) - > # Please use dev.off() to avoid the figure margin from previous plot - > # mar order: bottom, left, top, and right - > # please use par(mar=c(5,2,5,2)) or modify when necessary to best fit for the plot - > Netrhcoclust <- rhcoclust_internet(data, CoClustObj = CoClustObj, - + CoClust.sig = FALSE, cex.nodes = 0.7, edge.width = 1) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: rhcoclust_internet ... graph_from_edgelist -> make_graph -> do.call -> - Execution halted - ``` - -# rmangal - -
- -* Version: 2.1.3 -* GitHub: https://github.com/ropensci/rmangal -* Source code: https://github.com/cran/rmangal -* Date/Publication: 2023-03-30 14:10:02 UTC -* Number of recursive dependencies: 140 - -Run `revdepcheck::cloud_details(, "rmangal")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘spelling.R’ - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 78 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Error ('test-get_network_by_id.R:9:3'): get_network_by_id() works ─────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. ├─igraph::as.igraph(mg100) at test-get_network_by_id.R:9:2 - 2. └─rmangal:::as.igraph.mgNetwork(mg100) - 3. └─igraph::graph_from_data_frame(...) - 4. └─igraph::make_empty_graph(n = 0, directed = directed) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 78 ] - Error: Test failures - Execution halted - ``` - -# rmcfs - -
- -* Version: 1.3.5 -* GitHub: NA -* Source code: https://github.com/cran/rmcfs -* Date/Publication: 2021-09-18 13:30:02 UTC -* Number of recursive dependencies: 65 - -Run `revdepcheck::cloud_details(, "rmcfs")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘test-all.R’ - Running the tests in ‘tests/test-all.R’ failed. - Last 13 lines of output: - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─rmcfs::build.idgraph(result) at test-man.mcfs.R:57:2 - 2. └─igraph::graph.empty() - ── Error ('test-man.plot.idgraph.R:19:3'): man build.idgraph ─────────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─rmcfs::build.idgraph(result, size = 6, size_ID = 12, orphan_nodes = TRUE) at test-man.plot.idgraph.R:19:2 - 2. └─igraph::graph.empty() - - [ FAIL 3 | WARN 4 | SKIP 0 | PASS 35 ] - Error: Test failures - Execution halted - ``` - -# rmonad - -
- -* Version: 0.7.0 -* GitHub: https://github.com/arendsee/rmonad -* Source code: https://github.com/cran/rmonad -* Date/Publication: 2020-02-14 07:00:02 UTC -* Number of recursive dependencies: 81 - -Run `revdepcheck::cloud_details(, "rmonad")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘rmonad-Ex.R’ failed - The error most likely occurred in: - - > ### Name: clear_cache - > ### Title: Clear cached values and delete temporary files - > ### Aliases: clear_cache - > - > ### ** Examples - > - > 256 %v>% sqrt %>>% sqrt %>>% sqrt -> m - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: %>>% ... as_monad -> Rmonad -> .new_rmonad_graph -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 6. └─igraph::make_empty_graph(directed = TRUE, n = 1) - ── Error (???): view handles failure ─────────────────────────────────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─rmonad (local) ``(as_monad("hi") %>>% sqrt %>% tag("a/f"), log) - 2. └─rmonad (local) entry_lhs_transform(x, f, desc = lhs_str) - 3. └─rmonad::as_monad(m, lossy = TRUE, ...) - 4. └─rmonad:::Rmonad(node_id = paste(key, collapse = "")) - 5. └─rmonad:::.new_rmonad_graph(m, node_id = node_id) - 6. └─igraph::make_empty_graph(directed = TRUE, n = 1) - - [ FAIL 73 | WARN 0 | SKIP 1 | PASS 79 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘cheatsheet.Rmd’ using rmarkdown - --- finished re-building ‘cheatsheet.Rmd’ - - --- re-building ‘gff-processing.Rmd’ using rmarkdown - - Quitting from lines 563-566 [unnamed-chunk-8] (gff-processing.Rmd) - Error: processing vignette 'gff-processing.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘gff-processing.Rmd’ - ... - --- failed re-building ‘introduction.Rmd’ - - --- re-building ‘nozzle.Rmd’ using rmarkdown - --- finished re-building ‘nozzle.Rmd’ - - SUMMARY: processing the following files failed: - ‘gff-processing.Rmd’ ‘introduction.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# roads - -
- -* Version: 1.1.0 -* GitHub: https://github.com/LandSciTech/roads -* Source code: https://github.com/cran/roads -* Date/Publication: 2023-02-02 16:10:02 UTC -* Number of recursive dependencies: 113 - -Run `revdepcheck::cloud_details(, "roads")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘roads-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plotRoads - > ### Title: Plot projected roads - > ### Aliases: plotRoads - > - > ### ** Examples - > - > - > prRes <- projectRoads(CLUSexample$landings, CLUSexample$cost, CLUSexample$roads) - 0s detected in cost raster, these will be considered as existing roads - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: projectRoads ... -> make_graph -> do.call -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 3. │ ├─testthat (local) .capture(...) - 4. │ │ └─base::withCallingHandlers(...) - 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) - 6. └─roads::rasterToLineSegments(roadRast) - 7. ├─roads::projectRoads(...) - 8. └─roads::projectRoads(...) - 9. └─roads:::getGraph(sim, neighbourhood) - 10. └─igraph::graph.edgelist(edge_mat, dir = FALSE) - 11. └─igraph::make_graph(t(el), directed = directed) - 12. ├─base::do.call(old_graph, args) - 13. └─igraph (local) ``(``, directed = FALSE) - - [ FAIL 5 | WARN 0 | SKIP 0 | PASS 11 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘ReconstructRoadHistory.Rmd’ using rmarkdown - - Quitting from lines 43-55 [unnamed-chunk-2] (ReconstructRoadHistory.Rmd) - Error: processing vignette 'ReconstructRoadHistory.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘ReconstructRoadHistory.Rmd’ - - --- re-building ‘roads-vignette.Rmd’ using rmarkdown - ... - Quitting from lines 133-147 [unnamed-chunk-4] (roads-vignette.Rmd) - Error: processing vignette 'roads-vignette.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘roads-vignette.Rmd’ - - SUMMARY: processing the following files failed: - ‘ReconstructRoadHistory.Rmd’ ‘roads-vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# robber - -
- -* Version: 0.2.3 -* GitHub: https://github.com/Chabert-Liddell/robber -* Source code: https://github.com/cran/robber -* Date/Publication: 2023-02-28 08:32:35 UTC -* Number of recursive dependencies: 144 - -Run `revdepcheck::cloud_details(, "robber")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘robber-Ex.R’ failed - The error most likely occurred in: - - > ### Name: simulate_lbm - > ### Title: Simulate a bipartite interaction network using block model - > ### Aliases: simulate_lbm - > - > ### ** Examples - > - > # For a random number of interactions and blocks sizes - ... - > con <- matrix(c(.5,.3,.3,.1), 2, 2) - > pi <- c(.25,.75) - > rho <- c(1/3, 2/3) - > nr <- 50 - > nc <- 30 - > simulate_lbm(con, pi, rho, nr, nc, method = "gnp") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: simulate_lbm -> -> ensure_igraph -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘spelling.R’ - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 5. ├─igraph::as_incidence_matrix(...) - 6. │ └─igraph:::ensure_igraph(graph) - 7. └─igraph::sample_bipartite(...) - ── Error ('test-simulate_bm.R:29:1'): (code run outside of `test_that()`) ────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─robber::simulate_lbm(con, pi, rho, nr, nc, method = "gnm") at test-simulate_bm.R:29:0 - 2. ├─igraph::as_incidence_matrix(...) - 3. │ └─igraph:::ensure_igraph(graph) - 4. └─igraph::sample_bipartite(...) - - [ FAIL 2 | WARN 0 | SKIP 0 | PASS 41 ] - Error: Test failures - Execution halted - ``` - -# robin - -
- -* Version: 1.1.1 -* GitHub: https://github.com/ValeriaPolicastro/robin -* Source code: https://github.com/cran/robin -* Date/Publication: 2022-05-16 18:30:02 UTC -* Number of recursive dependencies: 156 - -Run `revdepcheck::cloud_details(, "robin")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘robin-Ex.R’ failed - The error most likely occurred in: - - > ### Name: robinCompareFast - > ### Title: robinCompareFast - > ### Aliases: robinCompareFast - > - > ### ** Examples - > - > my_file <- system.file("example/football.gml", package="robin") - > graph <- prepGraph(file=my_file, file.format="gml") - > robinCompareFast(graph=graph, method1="louvain", - + method2="fastGreedy", measure="vi") - Detecting robin method independent type, wait it can take time it depends on the size of the network. - Error in checkForRemoteErrors(val) : - 12 nodes produced errors; first error: could not find function ".igraph.status" - Calls: robinCompareFast ... -> staticClusterApply -> checkForRemoteErrors - Execution halted - ``` - -# RobustIV - -
- -* Version: 0.2.5 -* GitHub: https://github.com/zijguo/RobustIV -* Source code: https://github.com/cran/RobustIV -* Date/Publication: 2022-12-20 01:10:02 UTC -* Number of recursive dependencies: 26 - -Run `revdepcheck::cloud_details(, "RobustIV")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘RobustIV-Ex.R’ failed - The error most likely occurred in: - - > ### Name: TSHT - > ### Title: Two-Stage Hard Thresholding - > ### Aliases: TSHT - > - > ### ** Examples - > - > data("lineardata") - > Y <- lineardata[,"Y"] - > D <- lineardata[,"D"] - > Z <- as.matrix(lineardata[,c("Z.1","Z.2","Z.3","Z.4","Z.5","Z.6","Z.7","Z.8")]) - > X <- as.matrix(lineardata[,c("age","sex")]) - > TSHT.model <- TSHT(Y=Y,D=D,Z=Z,X=X) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: TSHT ... ensure_igraph -> -> graph.adjacency.dense - Execution halted - ``` - -# robustrao - -
- -* Version: 1.0-5 -* GitHub: NA -* Source code: https://github.com/cran/robustrao -* Date/Publication: 2020-01-24 21:50:08 UTC -* Number of recursive dependencies: 16 - -Run `revdepcheck::cloud_details(, "robustrao")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘robustrao-Ex.R’ failed - The error most likely occurred in: - - > ### Name: LowerIndexBound - > ### Title: Lower bound of the uncertainty interval of the Rao-Stirling - > ### diversity index. - > ### Aliases: LowerIndexBound - > - > ### ** Examples - > - ... - > #Get number of uncategorized references in the publication - > uncat <- pd1.uncat.refs[1] - > - > #Get vector of permissible disciplines. - > logic.disciplines <- counts > 0 - > permissible <- PruneDisciplines(logic.disciplines, 0.233, pd1.similarity) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: PruneDisciplines -> graph.adjacency -> graph.adjacency.dense - Execution halted - ``` - -# roprov - -
- -* Version: 0.1.2 -* GitHub: NA -* Source code: https://github.com/cran/roprov -* Date/Publication: 2018-11-06 09:10:03 UTC -* Number of recursive dependencies: 13 - -Run `revdepcheck::cloud_details(, "roprov")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘roprov-Ex.R’ failed - The error most likely occurred in: - - > ### Name: fullprovgraph - > ### Title: Create the full (multiple values per variable) provenance graph - > ### for a cache - > ### Aliases: fullprovgraph fullprovgraph,ProvStoreDF-method - > ### fullprovgraph,ProvStoreDF fullprovgraph,data.frame-method - > ### fullprovgraph,data.frame - > - ... - + invarhashes = invarhashes, - + invarclasses = invarclasses, - + code = code, - + agent = "coolguyorgirl") - > - > plot(fullprovgraph(ps)) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot ... graph_from_edgelist -> make_graph -> do.call -> - Execution halted - ``` - -# RPANDA - -
- -* Version: 2.2 -* GitHub: https://github.com/hmorlon/PANDA -* Source code: https://github.com/cran/RPANDA -* Date/Publication: 2022-10-24 15:28:00 UTC -* Number of recursive dependencies: 129 - -Run `revdepcheck::cloud_details(, "RPANDA")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘RPANDA-Ex.R’ failed - The error most likely occurred in: - - > ### Name: JSDtree - > ### Title: Jensen-Shannon distance between phylogenies - > ### Aliases: JSDtree - > - > ### ** Examples - > - > trees<-TESS::tess.sim.age(n=20,age=10,0.15,0.05,MRCA=TRUE) - > JSDtree(trees) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: JSDtree -> lapply -> FUN -> graph.adjacency.dense - Execution halted - ``` - -# rquery - -
- -* Version: 1.4.9 -* GitHub: https://github.com/WinVector/rquery -* Source code: https://github.com/cran/rquery -* Date/Publication: 2022-02-28 18:00:02 UTC -* Number of recursive dependencies: 46 - -Run `revdepcheck::cloud_details(, "rquery")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘rquery-Ex.R’ failed - The error most likely occurred in: - - > ### Name: topo_sort_tables - > ### Title: Topologically sort join plan so values are available before - > ### uses. - > ### Aliases: topo_sort_tables - > - > ### ** Examples - > - ... - + inspect_join_plan(tDesc, sorted$columnJoinPlan))) - + print(plot(sorted$dependencyGraph)) - + DBI::dbDisconnect(my_db) - + my_db <- NULL - + } - [1] "problems: key col(s) ( dept ) not contained in result cols of previous table(s) for table: revenue" - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: topo_sort_tables -> - Execution halted - ``` - -# rscc - -
- -* Version: 0.2.1 -* GitHub: https://github.com/sigbertklinke/rscc -* Source code: https://github.com/cran/rscc -* Date/Publication: 2022-01-20 12:02:42 UTC -* Number of recursive dependencies: 45 - -Run `revdepcheck::cloud_details(, "rscc")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘rscc-Ex.R’ failed - The error most likely occurred in: - - > ### Name: as_igraph - > ### Title: as.igraph - > ### Aliases: as_igraph - > - > ### ** Examples - > - > files <- list.files(path=system.file("examples", package="rscc"), pattern="*.R$", full.names = TRUE) - ... - /tmp/workdir/rscc/new/rscc.Rcheck/rscc/examples/kwantyle1.R - /tmp/workdir/rscc/new/rscc.Rcheck/rscc/examples/kwantyle1_variables.R - > docs <- documents(prgs) - > simm <- similarities(docs) - > # a similarity coefficients equal to zero does not create an edge! - > g <- as_igraph(simm, diag=FALSE) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: as_igraph -> do.call -> -> graph.adjacency.dense - Execution halted - ``` - -# RScelestial - -
- -* Version: 1.0.3 -* GitHub: NA -* Source code: https://github.com/cran/RScelestial -* Date/Publication: 2021-12-09 22:20:02 UTC -* Number of recursive dependencies: 45 - -Run `revdepcheck::cloud_details(, "RScelestial")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘RScelestial-Ex.R’ failed - The error most likely occurred in: - - > ### Name: scelestial - > ### Title: Infer the single-cell phylogenetic tree - > ### Aliases: scelestial - > - > ### ** Examples - > - > ## simulates tumor evolution - > S = synthesis(10, 10, 2, seed=7) - > ## convert to 10-state matrix - > seq = as.ten.state.matrix(S$seqeunce) - > ## runs the scelestial to generate 4-restricted Steiner trees. It represents the tree and graph - > SP = scelestial(seq, mink=3, maxk=4, return.graph = TRUE) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: scelestial ... graph_from_edgelist -> make_graph -> do.call -> - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.2Mb - sub-directories of 1Mb or more: - libs 4.9Mb - ``` - -# rsetse - -
- -* Version: 0.5.0 -* GitHub: https://github.com/JonnoB/rSETSe -* Source code: https://github.com/cran/rsetse -* Date/Publication: 2021-06-11 10:00:02 UTC -* Number of recursive dependencies: 81 - -Run `revdepcheck::cloud_details(, "rsetse")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘rsetse-Ex.R’ failed - The error most likely occurred in: - - > ### Name: calc_tension_strain - > ### Title: Calculate line tension and strain from the topology and node - > ### embeddings - > ### Aliases: calc_tension_strain - > - > ### ** Examples - > - ... - Error in .igraph.status("Free graph external pointer.\n") : - could not find function ".igraph.status" - Error in .igraph.status("Free graph external pointer.\n") : - could not find function ".igraph.status" - Error in .igraph.status("Free graph external pointer.\n") : - could not find function ".igraph.status" - Error in .igraph.status("Free graph external pointer.\n") : - could not find function ".igraph.status" - Error in .igraph.status("Free graph external pointer.\n") : - could not find function ".igraph.status" - ``` - -# rSpectral - -
- -* Version: 1.0.0.10 -* GitHub: https://github.com/cmclean5/rSpectral -* Source code: https://github.com/cran/rSpectral -* Date/Publication: 2023-01-18 12:00:02 UTC -* Number of recursive dependencies: 44 - -Run `revdepcheck::cloud_details(, "rSpectral")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘rSpectral-Ex.R’ failed - The error most likely occurred in: - - > ### Name: spectral_igraph_communities - > ### Title: Spectral clustering for 'igraph' objects - > ### Aliases: spectral_igraph_communities - > - > ### ** Examples - > - > data(karate,package='igraphdata') - > c<-spectral_igraph_communities(karate) - Error in .igraph.status("Restore graph external pointer.\n") : - could not find function ".igraph.status" - Calls: spectral_igraph_communities ... -> ensure_igraph -> is_igraph -> warn_version - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ── Error ('test-igraph.R:24:3'): membership fix_neig=1 is correct ────────────── - Error in `.igraph.status("Restore graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─rSpectral::spectral_igraph_communities(karate, fix_neig = 1) at test-igraph.R:24:2 - 2. └─rSpectral::spectral_igraph_membership(...) - 3. ├─base::as.data.frame(igraph::get.edgelist(g, names = TRUE)) - 4. └─igraph::get.edgelist(g, names = TRUE) - 5. └─igraph:::ensure_igraph(graph) - 6. └─igraph::is_igraph(graph) - 7. └─igraph:::warn_version(graph) - - [ FAIL 3 | WARN 0 | SKIP 0 | PASS 4 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.9Mb - sub-directories of 1Mb or more: - libs 5.2Mb - ``` - -# rsppfp - -
- -* Version: 1.0.4 -* GitHub: https://github.com/melvidoni/rsppfp -* Source code: https://github.com/cran/rsppfp -* Date/Publication: 2019-02-19 15:10:03 UTC -* Number of recursive dependencies: 84 - -Run `revdepcheck::cloud_details(, "rsppfp")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘rsppfp-Ex.R’ failed - The error most likely occurred in: - - > ### Name: get_shortest_path - > ### Title: igraph Shortest Path - > ### Aliases: get_shortest_path - > - > ### ** Examples - > - > # Given a specific gStar graph: - ... - 16 s|u s|u|v 4 - 17 u u|v 4 - 18 u|v u|v|y 3 - > - > # Obtain the shortest path - > get_shortest_path(gStar, "s", "v", "weight") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: get_shortest_path -> graph_from_data_frame -> make_empty_graph - Execution halted - ``` - -## In both - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# rvinecopulib - -
- -* Version: 0.6.3.1.1 -* GitHub: https://github.com/vinecopulib/rvinecopulib -* Source code: https://github.com/cran/rvinecopulib -* Date/Publication: 2023-02-23 11:50:02 UTC -* Number of recursive dependencies: 75 - -Run `revdepcheck::cloud_details(, "rvinecopulib")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘rvinecopulib-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plot.rvine_structure - > ### Title: Plotting R-vine structures - > ### Aliases: plot.rvine_structure plot.rvine_matrix - > - > ### ** Examples - > - > plot(cvine_structure(1:5)) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot ... lapply -> FUN -> -> graph.adjacency.dense - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 4. │ │ ├─withr::with_output_sink(...) - 5. │ │ │ └─base::force(code) - 6. │ │ ├─base::withCallingHandlers(...) - 7. │ │ └─base::withVisible(code) - 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) - 9. ├─base::plot(vc, edge_labels = "family", var_names = "legend") - 10. └─rvinecopulib:::plot.vinecop_dist(...) - 11. └─base::lapply(tree, get_graph, vc = x, edge_labels = edge_labels) - 12. └─rvinecopulib (local) FUN(X[[i]], ...) - 13. └─igraph::graph_from_adjacency_matrix(I, mode = "undirected") - 14. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 2 | WARN 0 | SKIP 0 | PASS 290 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 76.5Mb - sub-directories of 1Mb or more: - include 5.0Mb - libs 71.1Mb - ``` - -# safedata - -
- -* Version: 1.1.3 -* GitHub: https://github.com/ImperialCollegeLondon/safedata -* Source code: https://github.com/cran/safedata -* Date/Publication: 2023-05-05 15:00:02 UTC -* Number of recursive dependencies: 80 - -Run `revdepcheck::cloud_details(, "safedata")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘safedata-Ex.R’ failed - The error most likely occurred in: - - > ### Name: get_taxon_graph - > ### Title: Get a graph of the taxa in a dataset - > ### Aliases: get_taxon_graph - > - > ### ** Examples - > - > set_example_safe_dir() - Loading and caching index - Validating directory - > beetle_graph <- get_taxon_graph(1400562) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: get_taxon_graph -> -> make_empty_graph - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘overview.Rmd’ using rmarkdown - --- finished re-building ‘overview.Rmd’ - - --- re-building ‘using_safe_data.Rmd’ using rmarkdown - - Quitting from lines 513-516 [get_phylo] (using_safe_data.Rmd) - Error: processing vignette 'using_safe_data.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘using_safe_data.Rmd’ - - SUMMARY: processing the following file failed: - ‘using_safe_data.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# saotd - -
- -* Version: 0.3.0 -* GitHub: https://github.com/evan-l-munson/saotd -* Source code: https://github.com/cran/saotd -* Date/Publication: 2021-10-13 09:50:02 UTC -* Number of recursive dependencies: 121 - -Run `revdepcheck::cloud_details(, "saotd")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ── Error ('test_word_corr_network.R:68:1'): (code run outside of `test_that()`) ── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. ├─saotd::word_corr_network(WordCorr = test, Correlation = 0.1) at test_word_corr_network.R:68:0 - 2. │ └─... %>% ggraph::ggraph(layout = layout) - 3. ├─ggraph::ggraph(., layout = layout) - 4. │ ├─ggplot2::ggplot(data = create_layout(graph, layout, ...), environment = envir) - 5. │ └─ggraph::create_layout(graph, layout, ...) - 6. └─igraph::graph_from_data_frame(.) - 7. └─igraph::make_empty_graph(n = 0, directed = directed) - - [ FAIL 2 | WARN 1 | SKIP 0 | PASS 59 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘saotd.Rmd’ using rmarkdown - - Quitting from lines 171-181 [bigram_network] (saotd.Rmd) - Error: processing vignette 'saotd.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘saotd.Rmd’ - - SUMMARY: processing the following file failed: - ‘saotd.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# sBIC - -
- -* Version: 0.2.0 -* GitHub: https://github.com/Lucaweihs/sBIC -* Source code: https://github.com/cran/sBIC -* Date/Publication: 2016-10-01 14:31:14 -* Number of recursive dependencies: 52 - -Run `revdepcheck::cloud_details(, "sBIC")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 1. ├─testthat::expect_equal(...) at test_LatentForests.R:379:2 - 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") - 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) - 4. ├─sBIC:::forestDepth(...) - 5. │ ├─base::unique(igraph::clusters(forest)$membership[1:numLeaves]) - 6. │ └─igraph::clusters(forest) - 7. │ └─igraph:::ensure_igraph(graph) - 8. └─igraph::graph.edgelist(...) - 9. └─igraph::make_graph(t(el), directed = directed) - 10. ├─base::do.call(old_graph, args) - 11. └─igraph (local) ``(``, directed = FALSE) - - [ FAIL 11 | WARN 0 | SKIP 0 | PASS 12 ] - Error: Test failures - Execution halted - ``` - -# sbm - -
- -* Version: 0.4.5 -* GitHub: https://github.com/GrossSBM/sbm -* Source code: https://github.com/cran/sbm -* Date/Publication: 2023-01-09 10:30:02 UTC -* Number of recursive dependencies: 108 - -Run `revdepcheck::cloud_details(, "sbm")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘sbm-Ex.R’ failed - The error most likely occurred in: - - > ### Name: estimateSimpleSBM - > ### Title: Estimation of Simple SBMs - > ### Aliases: estimateSimpleSBM - > - > ### ** Examples - > - > ### ======================================= - ... - -> For 2 groups - > plot(mySimpleSBM, 'data', ordered = FALSE) - > plot(mySimpleSBM, 'data') - > plot(mySimpleSBM, 'expected', ordered = FALSE) - > plot(mySimpleSBM, 'expected') - > plot(mySimpleSBM, 'meso') - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot ... -> plotMeso -> -> graph.adjacency.dense - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘spelling.R’ - Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ...6c6 - < NULL - --- - > All Done! - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 4. │ │ ├─withr::with_output_sink(...) - 5. │ │ │ └─base::force(code) - ... - 9. ├─base::plot(myMBM, type = "meso") - 10. └─sbm:::plot.SBM(myMBM, type = "meso") - 11. └─x$plot(type, ordered, plotOptions) - 12. └─sbm:::plotMesoMultipartite(...) - 13. └─igraph::graph.adjacency(...) - 14. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1045 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘Multipartite_EcologicalNetwork.Rmd’ using rmarkdown - - Quitting from lines 152-158 [plot meso] (Multipartite_EcologicalNetwork.Rmd) - Error: processing vignette 'Multipartite_EcologicalNetwork.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘Multipartite_EcologicalNetwork.Rmd’ - - --- re-building ‘MultiplexNetwork_principle.Rmd’ using rmarkdown - --- finished re-building ‘MultiplexNetwork_principle.Rmd’ - ... - Quitting from lines 114-115 [simpleSBMfit plotmeso] (SBM_fungus_tree_network.Rmd) - Error: processing vignette 'SBM_fungus_tree_network.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘SBM_fungus_tree_network.Rmd’ - - SUMMARY: processing the following files failed: - ‘Multipartite_EcologicalNetwork.Rmd’ ‘SBM_fungus_tree_network.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# SBN - -
- -* Version: 1.0.0 -* GitHub: NA -* Source code: https://github.com/cran/SBN -* Date/Publication: 2022-01-17 19:42:42 UTC -* Number of recursive dependencies: 7 - -Run `revdepcheck::cloud_details(, "SBN")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘SBN-Ex.R’ failed - The error most likely occurred in: - - > ### Name: sbn_change_dir - > ### Title: Change the upstream/downstream direction of an SBN - > ### Aliases: sbn_change_dir - > - > ### ** Examples - > - > g <- sbn_create(10, 0.7) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: sbn_create -> -> graph.adjacency.dense - Execution halted - ``` - -# sccore - -
- -* Version: 1.0.3 -* GitHub: https://github.com/kharchenkolab/sccore -* Source code: https://github.com/cran/sccore -* Date/Publication: 2023-03-13 00:00:02 UTC -* Number of recursive dependencies: 76 - -Run `revdepcheck::cloud_details(, "sccore")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘sccore-Ex.R’ failed - The error most likely occurred in: - - > ### Name: graphToAdjList - > ### Title: Convert igraph graph into an adjacency list - > ### Aliases: graphToAdjList - > - > ### ** Examples - > - > library(dplyr) - ... - - The following objects are masked from ‘package:base’: - - intersect, setdiff, setequal, union - - > edge.list.fact <- igraph::as_edgelist(conosGraph) %>% as_factor() - Error in .igraph.status("Restore graph external pointer.\n") : - could not find function ".igraph.status" - Calls: %>% ... -> ensure_igraph -> is_igraph -> warn_version - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 6. └─igraph:::warn_version(graph) - ── Error ('test_helpers.R:43:2'): graphToAdjList() functionality ─────────────── - Error in `.igraph.status("Restore graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. ├─igraph::as_edgelist(conosGraph) %>% as_factor() at test_helpers.R:43:8 - 2. ├─sccore::as_factor(.) - 3. └─igraph::as_edgelist(conosGraph) - 4. └─igraph:::ensure_igraph(graph) - 5. └─igraph::is_igraph(graph) - 6. └─igraph:::warn_version(graph) - - [ FAIL 4 | WARN 0 | SKIP 0 | PASS 2 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 7.9Mb - sub-directories of 1Mb or more: - libs 7.1Mb - ``` - -# scDHA - -
- -* Version: 1.2.1 -* GitHub: https://github.com/duct317/scDHA -* Source code: https://github.com/cran/scDHA -* Date/Publication: 2023-04-04 12:10:02 UTC -* Number of recursive dependencies: 62 - -Run `revdepcheck::cloud_details(, "scDHA")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ══ Skipped tests ═══════════════════════════════════════════════════════════════ - • On CRAN (2) - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Error ('test-scDHA.R:33:3'): scDHA.pt can run ─────────────────────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─scDHA::scDHA.pt(result, start.point = 1, ncores = 2, seed = 1) at test-scDHA.R:33:2 - 2. └─igraph::graph_from_adjacency_matrix(adj, weighted = TRUE, mode = "undirected") - 3. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 1 | WARN 0 | SKIP 2 | PASS 3 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 8.3Mb - sub-directories of 1Mb or more: - data 3.2Mb - libs 4.7Mb - ``` - -# scDiffCom - -
- -* Version: 0.1.0 -* GitHub: NA -* Source code: https://github.com/cran/scDiffCom -* Date/Publication: 2021-08-17 07:20:05 UTC -* Number of recursive dependencies: 245 - -Run `revdepcheck::cloud_details(, "scDiffCom")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘spelling.R’ - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 13. └─igraph::graph_from_data_frame(...) - 14. └─igraph::make_empty_graph(n = 0, directed = directed) - ── Error ('test-everything.R:1023:1'): (code run outside of `test_that()`) ───── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─scDiffCom:::build_interactive_network(...) at test-everything.R:1023:0 - 2. └─scDiffCom:::interactive_from_igraph(...) - 3. └─scDiffCom:::build_igraph(...) - 4. └─igraph::graph_from_data_frame(...) - 5. └─igraph::make_empty_graph(n = 0, directed = directed) - - [ FAIL 2 | WARN 0 | SKIP 0 | PASS 80 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘future’ ‘utils’ - All declared Imports should be used. - ``` - -# SCORPION - -
- -* Version: 1.0.1 -* GitHub: NA -* Source code: https://github.com/cran/SCORPION -* Date/Publication: 2022-09-22 09:30:02 UTC -* Number of recursive dependencies: 12 - -Run `revdepcheck::cloud_details(, "SCORPION")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘SCORPION-Ex.R’ failed - The error most likely occurred in: - - > ### Name: scorpion - > ### Title: Constructs PANDA gene regulatory networks from single-cell gene - > ### expression data - > ### Aliases: scorpion - > - > ### ** Examples - > - ... - > scorpionOutput <- scorpion(tfMotifs = scorpionTest$tf, - + gexMatrix = scorpionTest$gex, - + ppiNet = scorpionTest$ppi, - + alphaValue = 0.8) - - ── SCORPION ──────────────────────────────────────────────────────────────────── - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: scorpion ... makeSuperCells -> buildKNN -> buildNN2 -> - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘RhpcBLASctl’ - All declared Imports should be used. - ``` - -# scRNAtools - -
- -* Version: 1.0 -* GitHub: NA -* Source code: https://github.com/cran/scRNAtools -* Date/Publication: 2018-07-05 14:00:03 UTC -* Number of recursive dependencies: 131 - -Run `revdepcheck::cloud_details(, "scRNAtools")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘scRNAtools-Ex.R’ failed - The error most likely occurred in: - - > ### Name: scRNAtools_inter_net - > ### Title: Construction of interactive network in scRNA sequencing data - > ### Aliases: scRNAtools_inter_net - > - > ### ** Examples - > - > data(corr_re) - ... - > p<-0.05 - > r<-0.9 - > size<-5 #nodes size - > color<-"#00B2EE" ##Color of nodes. - > pdf(file=file.path(tempdir(), "interact_net.pdf")) - > scRNAtools_inter_net(corr_re,p,r,size,color) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: scRNAtools_inter_net -> graph.data.frame -> make_empty_graph - Execution halted - ``` - -# secrlinear - -
- -* Version: 1.2.1 -* GitHub: https://github.com/MurrayEfford/secrlinear -* Source code: https://github.com/cran/secrlinear -* Date/Publication: 2023-05-19 04:10:02 UTC -* Number of recursive dependencies: 83 - -Run `revdepcheck::cloud_details(, "secrlinear")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘secrlinear-Ex.R’ failed - The error most likely occurred in: - - > ### Name: Arvicola - > ### Title: Water Vole Capture Dataset - > ### Aliases: arvicola - > ### Keywords: datasets - > - > ### ** Examples - > - ... - 20.B 163.85 629.66 - 40.A 164.88 649.19 - 40.B 164.88 649.19 - > - > ## for speed, pre-compute distance matrix - > userd <- networkdistance (traps(arvicola), glymemask, glymemask) - Error in .igraph.status("Restore graph external pointer.\n") : - could not find function ".igraph.status" - Calls: networkdistance ... cbind -> V -> ensure_igraph -> is_igraph -> warn_version - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Error ('test-secrlinear.R:14:1'): (code run outside of `test_that()`) ─────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─secrlinear::read.linearmask(data = xy, spacing = 20) at test-secrlinear.R:14:0 - 2. └─secrlinear:::make.linearmask(...) - 3. └─secrlinear::asgraph(mask) - 4. └─igraph::graph.adjacency(tempdist, mode = "lower") - 5. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘secrlinear-vignette.Rmd’ using rmarkdown - - Quitting from lines 71-73 [readglyme] (secrlinear-vignette.Rmd) - Error: processing vignette 'secrlinear-vignette.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘secrlinear-vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘secrlinear-vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# SelectBoost - -
- -* Version: 2.2.2 -* GitHub: https://github.com/fbertran/SelectBoost -* Source code: https://github.com/cran/SelectBoost -* Date/Publication: 2022-11-30 09:10:06 UTC -* Number of recursive dependencies: 114 - -Run `revdepcheck::cloud_details(, "SelectBoost")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘SelectBoost-Ex.R’ failed - The error most likely occurred in: - - > ### Name: boost - > ### Title: Boost step by step functions - > ### Aliases: boost boost.normalize boost.compcorrs boost.correlation_sign - > ### boost.findgroups boost.Xpass boost.adjust boost.random boost.apply - > ### boost.select - > - > ### ** Examples - ... - > xran_corr<- boost.compcorrs(xran_norm) - > - > xran_corr_sign <- boost.correlation_sign(xran_corr) - > - > xran_groups <- boost.findgroups(xran_corr, group=group_func_1, .3) - > xran_groups_2 <- boost.findgroups(xran_corr, group=group_func_2, .3) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: boost.findgroups ... group2 -> group -> graph.adjacency -> graph.adjacency.dense - Execution halted - ``` - -# SEMID - -
- -* Version: 0.4.0 -* GitHub: https://github.com/Lucaweihs/SEMID -* Source code: https://github.com/cran/SEMID -* Date/Publication: 2022-01-13 15:12:43 UTC -* Number of recursive dependencies: 38 - -Run `revdepcheck::cloud_details(, "SEMID")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘SEMID-Ex.R’ failed - The error most likely occurred in: - - > ### Name: SEMID-package - > ### Title: SEMID package documentation. - > ### Aliases: SEMID-package SEMID - > - > ### ** Examples - > - > ### - ... - + 0, 0, 0, 0, 0, - + 0, 0, 0, 0, 0, - + 0, 0, 0, 0, 0), 5, 5)); O=O+t(O) - > - > # Create a mixed graph object - > graph = MixedGraph(L, O) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: MixedGraph ... LatentDigraphFixedOrder -> -> graph.adjacency.dense - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ── Error ('test_edgewiseID.R:43:9'): TO DELETE ───────────────────────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─SEMID::MixedGraph(L, O) at test_edgewiseID.R:43:8 - 2. ├─R.oo::extend(...) - 3. ├─R.oo::extend.Object(...) - 4. └─SEMID::LatentDigraph(...) - 5. └─SEMID::LatentDigraphFixedOrder(L, length(observedNodes)) - 6. └─igraph::graph.adjacency(L, mode = "directed") - 7. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 11 | WARN 641 | SKIP 0 | PASS 478 ] - Error: Test failures - Execution halted - ``` - -# sensitivity - -
- -* Version: 1.28.1 -* GitHub: NA -* Source code: https://github.com/cran/sensitivity -* Date/Publication: 2023-03-19 19:10:02 UTC -* Number of recursive dependencies: 124 - -Run `revdepcheck::cloud_details(, "sensitivity")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘sensitivity-Ex.R’ failed - The error most likely occurred in: - - > ### Name: shapleyBlockEstimation - > ### Title: Computation of the Shapley effects in the Gaussian linear - > ### framework with an unknown block-diagonal covariance matrix - > ### Aliases: shapleyBlockEstimation shapleyBlockEstimationS - > ### shapleyBlockEstimationX - > - > ### ** Examples - ... - + cex.main=3,ylab = "", xlab = "",axes=FALSE) - > box() - > - > - > Beta_ord=3*runif(p)+1 - > eta_ord=shapleyLinearGaussian(Beta=Beta_ord, Sigma=Sigma_ord) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: shapleyLinearGaussian ... ensure_igraph -> -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 9.0Mb - sub-directories of 1Mb or more: - R 2.2Mb - libs 6.2Mb - ``` - -# SeqDetect - -
- -* Version: 1.0.7 -* GitHub: NA -* Source code: https://github.com/cran/SeqDetect -* Date/Publication: 2020-03-02 14:30:05 UTC -* Number of recursive dependencies: 23 - -Run `revdepcheck::cloud_details(, "SeqDetect")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘SeqDetect-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plotMachines,HybridSequenceClassifier-method - > ### Title: Sequence Detector Method: plot machines (ETTs) - > ### Aliases: plotMachines,HybridSequenceClassifier-method - > - > ### ** Examples - > - > ldf1 <- data.frame(product=c("P1","P1","P1","P1"),sequence_id=c(1,3,5,7), - ... - - - - > hsc$cleanKeys() - > hsc$mergeMachines() - > hsc$plotMachines() - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: -> graph_from_data_frame -> make_empty_graph - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘SequentialDetector.Rnw’ - ... - Transition(278bf27b866ebd1b659a) to:H_REL Symbols:[H_REL] Input state: Output state: Population:1 - Patterns:[Hospital release] - ========= - -==***************************************==- - - > seq_detector$plotMachines() - - When sourcing ‘SequentialDetector.R’: - Error: could not find function ".igraph.status" - Execution halted - - ‘SequentialDetector.Rnw’ using ‘UTF-8’... failed - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 18.1Mb - sub-directories of 1Mb or more: - libs 16.8Mb - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘SequentialDetector.Rnw’ using Sweave - Loading required package: Rcpp - Loading required package: eventdataR - - Attaching package: ‘dplyr’ - - The following objects are masked from ‘package:stats’: - - filter, lag - ... - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - - --- failed re-building ‘SequentialDetector.Rnw’ - - SUMMARY: processing the following file failed: - ‘SequentialDetector.Rnw’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# seqHMM - -
- -* Version: 1.2.4 -* GitHub: https://github.com/helske/seqHMM -* Source code: https://github.com/cran/seqHMM -* Date/Publication: 2023-01-09 11:20:02 UTC -* Number of recursive dependencies: 64 - -Run `revdepcheck::cloud_details(, "seqHMM")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘seqHMM-Ex.R’ failed - The error most likely occurred in: - - > ### Name: hmm_biofam - > ### Title: Hidden Markov model for the biofam data - > ### Aliases: hmm_biofam - > ### Keywords: datasets - > - > ### ** Examples - > - > - > # Plotting the model - > plot(hmm_biofam) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot ... plot.hmm -> graph.adjacency -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘seqHMM.Rnw’ using knitr - - Quitting from lines 495-498 [plottingHMM] (seqHMM.Rnw) - Error: processing vignette 'seqHMM.Rnw' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘seqHMM.Rnw’ - - --- re-building ‘seqHMM_algorithms.Rnw’ using knitr - Error: processing vignette 'seqHMM_algorithms.Rnw' failed with diagnostics: - ... - Quitting from lines 112-128 [HMMplot] (seqHMM_visualization.Rnw) - Error: processing vignette 'seqHMM_visualization.Rnw' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘seqHMM_visualization.Rnw’ - - SUMMARY: processing the following files failed: - ‘seqHMM.Rnw’ ‘seqHMM_algorithms.Rnw’ ‘seqHMM_visualization.Rnw’ - - Error: Vignette re-building failed. - Execution halted - ``` - -* checking installed package size ... NOTE - ``` - installed size is 34.4Mb - sub-directories of 1Mb or more: - doc 6.4Mb - libs 27.2Mb - ``` - -# SeqNet - -
- -* Version: 1.1.3 -* GitHub: NA -* Source code: https://github.com/cran/SeqNet -* Date/Publication: 2021-07-09 08:20:08 UTC -* Number of recursive dependencies: 74 - -Run `revdepcheck::cloud_details(, "SeqNet")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘SeqNet-Ex.R’ failed - The error most likely occurred in: - - > ### Name: add_random_module_to_network - > ### Title: Adds a random module of a given size to the network - > ### Aliases: add_random_module_to_network - > - > ### ** Examples - > - > # This function provides an alternative way to iteratively add random - > # modules to the network. It uses a weighted sampling of nodes, where - > # nodes that haven't been selected for a module have a higher probability - > # of being sampled for the new module. - > nw <- create_empty_network(100) - > plot(nw) # An empty network of 100 nodes. - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot ... plot_network -> -> graph.adjacency.dense - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - > test_check("SeqNet") - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 36 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Error ('test_network_structure.R:12:3'): networks have appropriate structure. ── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─SeqNet::get_network_characteristics(network) at test_network_structure.R:12:2 - 2. └─igraph::graph_from_adjacency_matrix(adj, mode = "undirected") - 3. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 36 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 7.0Mb - sub-directories of 1Mb or more: - data 4.7Mb - libs 1.8Mb - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘Rdpack’ - All declared Imports should be used. - ``` - -# SetRank - -
- -* Version: 1.1.0 -* GitHub: NA -* Source code: https://github.com/cran/SetRank -* Date/Publication: 2016-05-11 12:06:23 -* Number of recursive dependencies: 15 - -Run `revdepcheck::cloud_details(, "SetRank")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘SetRank-Ex.R’ failed - The error most likely occurred in: - - > ### Name: setRankAnalysis - > ### Title: Advanced gene set enrichment analysis. - > ### Aliases: setRankAnalysis - > - > ### ** Examples - > - > options(mc.cores=1) - ... - 1 gene set DBs, 9 initial gene sets, 9 sets remaining and 50 genes in collection - 7 intersections to test...Pre-calculating critical Fisher-test values... - > genes = reference[sample(c(TRUE, FALSE), 50, TRUE)] - > network = setRankAnalysis(genes, collection, TRUE) - 2023-06-11 21:50:07 - calculating primary set p-values - 2023-06-11 21:50:07 - 0 significant sets - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: setRankAnalysis ... buildSetNet -> add.vertices -> ensure_igraph -> graph.empty - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘vignette.ltx’ using tex - Error: processing vignette 'vignette.ltx' failed with diagnostics: - Running 'texi2dvi' on 'vignette.ltx' failed. - LaTeX errors: - ! LaTeX Error: File `beramono.sty' not found. - - Type X to quit or to proceed, - or enter new name. (Default extension: sty) - ... - l.7 \usepackage - [T1]{fontenc}^^M - ! ==> Fatal error occurred, no output PDF file produced! - --- failed re-building ‘vignette.ltx’ - - SUMMARY: processing the following file failed: - ‘vignette.ltx’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# sfcr - -
- -* Version: 0.2.1 -* GitHub: https://github.com/joaomacalos/sfcr -* Source code: https://github.com/cran/sfcr -* Date/Publication: 2021-10-11 08:00:02 UTC -* Number of recursive dependencies: 140 - -Run `revdepcheck::cloud_details(, "sfcr")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘sfcr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: sfcr_baseline - > ### Title: Simulate the baseline scenario of a stock-flow consistent model - > ### Aliases: sfcr_baseline - > - > ### ** Examples - > - > eqs <- sfcr_set( - ... - > - > external <- sfcr_set(Gd ~ 20, W ~ 1, alpha1 ~ 0.6, alpha2 ~ 0.4, theta ~ 0.2) - > - > # Periods is set to 10 to run faster. A usual model should run at - > # least 50 periods to find a steady state - > sfcr_baseline(equations = eqs, external = external, periods = 10) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: sfcr_baseline ... .find_blocks -> -> graph.adjacency.dense - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 4. └─igraph::graph.adjacency(adjmatrix = t(adj), mode = "directed") - 5. └─igraph:::graph.adjacency.dense(...) - ── Error ('test-sfcr_scenario.R:25:1'): (code run outside of `test_that()`) ──── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─sfcr::sfcr_baseline(...) at test-sfcr_scenario.R:25:0 - 2. └─sfcr:::.sfcr_find_order(equations) - 3. └─sfcr:::.find_blocks(km) - 4. └─igraph::graph.adjacency(adjmatrix = t(adj), mode = "directed") - 5. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 17 | WARN 0 | SKIP 0 | PASS 11 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘sfcr_multis.Rmd’ using rmarkdown - - Quitting from lines 50-51 [unnamed-chunk-2] (sfcr_multis.Rmd) - Error: processing vignette 'sfcr_multis.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘sfcr_multis.Rmd’ - - SUMMARY: processing the following file failed: - ‘sfcr_multis.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# sfdep - -
- -* Version: 0.2.3 -* GitHub: https://github.com/josiahparry/sfdep -* Source code: https://github.com/cran/sfdep -* Date/Publication: 2023-01-11 06:30:02 UTC -* Number of recursive dependencies: 100 - -Run `revdepcheck::cloud_details(, "sfdep")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘sfdep-Ex.R’ failed - The error most likely occurred in: - - > ### Name: st_as_graph - > ### Title: Create an sfnetwork - > ### Aliases: st_as_graph st_as_graph.sf st_as_graph.sfc - > - > ### ** Examples - > - > library(magrittr) - > - > guerry_nb %>% - + st_as_graph(nb, wt) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: %>% ... graph_from_edgelist -> make_graph -> do.call -> - Execution halted - ``` - -# sfnetworks - -
- -* Version: 0.6.3 -* GitHub: https://github.com/luukvdmeer/sfnetworks -* Source code: https://github.com/cran/sfnetworks -* Date/Publication: 2023-03-22 16:40:02 UTC -* Number of recursive dependencies: 106 - -Run `revdepcheck::cloud_details(, "sfnetworks")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘sfnetworks-Ex.R’ failed - The error most likely occurred in: - - > ### Name: as_sfnetwork - > ### Title: Convert a foreign object to a sfnetwork - > ### Aliases: as_sfnetwork as_sfnetwork.default as_sfnetwork.sf - > ### as_sfnetwork.linnet as_sfnetwork.psp as_sfnetwork.sfc - > ### as_sfnetwork.sfNetwork as_sfnetwork.sfnetwork as_sfnetwork.tbl_graph - > - > ### ** Examples - ... - > # From an sf object. - > library(sf, quietly = TRUE) - Linking to GEOS 3.8.0, GDAL 3.0.4, PROJ 6.3.1; sf_use_s2() is TRUE - > - > # With LINESTRING geometries. - > as_sfnetwork(roxel) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: as_sfnetwork ... graph_from_edgelist -> make_graph -> do.call -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 1. ├─sfnetworks::as_sfnetwork(rdm_rox) at test_bbox.R:5:2 - 2. └─sfnetworks:::as_sfnetwork.sf(rdm_rox) - 3. └─sfnetworks::sfnetwork(...) - 4. └─tidygraph::tbl_graph(nodes, edges_df, directed, node_key) - 5. ├─tidygraph::as_tbl_graph(...) - 6. └─tidygraph:::as_tbl_graph.list(...) - 7. └─tidygraph:::as_graph_node_edge(x, directed = directed, node_key = node_key) - 8. └─igraph::graph_from_edgelist(as.matrix(edges[, 1:2]), directed = directed) - 9. └─igraph::make_graph(t(el), directed = directed) - 10. ├─base::do.call(old_graph, args) - 11. └─igraph (local) ``(``, directed = TRUE) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 269 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘sfn01_structure.Rmd’ using rmarkdown - --- finished re-building ‘sfn01_structure.Rmd’ - - --- re-building ‘sfn02_preprocess_clean.Rmd’ using rmarkdown - --- finished re-building ‘sfn02_preprocess_clean.Rmd’ - - --- re-building ‘sfn03_join_filter.Rmd’ using rmarkdown - --- finished re-building ‘sfn03_join_filter.Rmd’ - ... - --- failed re-building ‘sfn04_routing.Rmd’ - - --- re-building ‘sfn05_morphers.Rmd’ using rmarkdown - --- finished re-building ‘sfn05_morphers.Rmd’ - - SUMMARY: processing the following file failed: - ‘sfn04_routing.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# SFSI - -
- -* Version: 1.2.0 -* GitHub: NA -* Source code: https://github.com/cran/SFSI -* Date/Publication: 2022-08-16 15:40:09 UTC -* Number of recursive dependencies: 62 - -Run `revdepcheck::cloud_details(, "SFSI")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘SFSI-Ex.R’ failed - The error most likely occurred in: - - > ### Name: net.plot - > ### Title: Network plot - > ### Aliases: net.plot - > - > ### ** Examples - > - > require(SFSI) - ... - |==================================================================== | 96% - | - |======================================================================| 100% - > - > # Basic setting - > net.plot(fm) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: net.plot -> get_net -> - Execution halted - ``` - -# sharp - -
- -* Version: 1.4.2 -* GitHub: https://github.com/barbarabodinier/sharp -* Source code: https://github.com/cran/sharp -* Date/Publication: 2023-06-09 16:20:02 UTC -* Number of recursive dependencies: 150 - -Run `revdepcheck::cloud_details(, "sharp")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘sharp-Ex.R’ failed - The error most likely occurred in: - - > ### Name: GraphComparison - > ### Title: Edge-wise comparison of two graphs - > ### Aliases: GraphComparison - > - > ### ** Examples - > - > # Data simulation - ... - > - > # Edge-wise comparison of the two graphs - > mygraph <- GraphComparison( - + graph1 = simul1, - + graph2 = simul2 - + ) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: GraphComparison ... -> -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘overview.Rnw’ using Sweave - Error: processing vignette 'overview.Rnw' failed with diagnostics: - Running 'texi2dvi' on 'overview.tex' failed. - LaTeX errors: - ! LaTeX Error: File `pdfpages.sty' not found. - - Type X to quit or to proceed, - or enter new name. (Default extension: sty) - ... - l.4 ^^M - - ! ==> Fatal error occurred, no output PDF file produced! - --- failed re-building ‘overview.Rnw’ - - SUMMARY: processing the following file failed: - ‘overview.Rnw’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# sharpshootR - -
- -* Version: 2.1 -* GitHub: https://github.com/ncss-tech/sharpshootR -* Source code: https://github.com/cran/sharpshootR -* Date/Publication: 2023-03-22 16:50:05 UTC -* Number of recursive dependencies: 149 - -Run `revdepcheck::cloud_details(, "sharpshootR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘sharpshootR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: component.adj.matrix - > ### Title: Create an adjacency matrix from a data.frame of component data - > ### Aliases: component.adj.matrix - > ### Keywords: manip - > - > ### ** Examples - > - ... - + m <- component.adj.matrix(amador) - + - + # plot network diagram, with Amador soil highlighted - + plotSoilRelationGraph(m, s = 'amador') - + } - Loading required namespace: igraph - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plotSoilRelationGraph -> -> graph.adjacency.dense - Execution halted - ``` - -# shazam - -
- -* Version: 1.1.2 -* GitHub: NA -* Source code: https://github.com/cran/shazam -* Date/Publication: 2022-10-01 07:30:02 UTC -* Number of recursive dependencies: 124 - -Run `revdepcheck::cloud_details(, "shazam")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘shazam-Ex.R’ failed - The error most likely occurred in: - - > ### Name: distToNearest - > ### Title: Distance to nearest neighbor - > ### Aliases: distToNearest - > - > ### ** Examples - > - > # Subset example data to one sample as a demo - ... - > # Use genotyped V assignments, Hamming distance, and normalize by junction length - > # First partition based on V and J assignments, then by junction length - > # Take into consideration ambiguous V and J annotations - > dist <- distToNearest(db, sequenceColumn="junction", - + vCallColumn="v_call_genotyped", jCallColumn="j_call", - + model="ham", first=FALSE, VJthenLen=TRUE, normalize="len") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: distToNearest ... graph.adjacency.sparse -> make_graph -> do.call -> - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘Baseline-Vignette.Rmd’ using rmarkdown - A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TinyTeX with tinytex::reinstall_tinytex(repository = "illinois"). - - tlmgr: Local TeX Live (2022) is older than remote repository (2023). - Cross release updates are only supported with - update-tlmgr-latest(.sh/.exe) --update - See https://tug.org/texlive/upgrade.html for details. - Warning in system2("tlmgr", args, ...) : - running command ''tlmgr' search --file --global '/grffile.sty'' had status 1 - ... - LaTeX failed to compile /tmp/workdir/shazam/new/shazam.Rcheck/vign_test/shazam/vignettes/Targeting-Vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Targeting-Vignette.log for more info. - --- failed re-building ‘Targeting-Vignette.Rmd’ - - SUMMARY: processing the following files failed: - ‘Baseline-Vignette.Rmd’ ‘DistToNearest-Vignette.Rmd’ - ‘Mutation-Vignette.Rmd’ ‘Shmulate-Vignette.Rmd’ - ‘Targeting-Vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# shock - -
- -* Version: 1.0 -* GitHub: NA -* Source code: https://github.com/cran/shock -* Date/Publication: 2015-12-24 14:45:29 -* Number of recursive dependencies: 14 - -Run `revdepcheck::cloud_details(, "shock")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘shock-Ex.R’ failed - The error most likely occurred in: - - > ### Name: computeLoglikeFromPartition - > ### Title: Compute the log-likelihood of the model - > ### Aliases: computeLoglikeFromPartition - > - > ### ** Examples - > - > ## load data to test - > data(dataTest) - > - > ## threshold of absS matrix - > myLABELS <- thresholdAbsSPath(dataTest)$partitionList - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: thresholdAbsSPath -> graph.adjacency -> graph.adjacency.dense - Execution halted - ``` - -# sidier - -
- -* Version: 4.1.0 -* GitHub: NA -* Source code: https://github.com/cran/sidier -* Date/Publication: 2021-06-25 11:50:02 UTC -* Number of recursive dependencies: 58 - -Run `revdepcheck::cloud_details(, "sidier")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘sidier-Ex.R’ failed - The error most likely occurred in: - - > ### Name: zero.thr - > ### Title: Zero distance networks - > ### Aliases: zero.thr - > - > ### ** Examples - > - > - ... - Pop9 0.640 0.360 0.800 0.64 0.840 0.56 0.000 0.62 0.465 - Pop10 0.010 0.330 0.940 0.88 0.760 0.81 0.620 0.00 0.920 - Pop4-Pop5 0.555 0.875 0.715 0.54 0.295 0.27 0.465 0.92 0.000 - > # It is now possible to estimate a percolation threshold - > perc.thr(dis=Dis1_Merged,ptPDF=FALSE, estimPDF=FALSE, estimOutfile=FALSE) - [1] "Threshold value:0 Range to test: from 0 to 1" - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: perc.thr -> graph.adjacency -> graph.adjacency.dense - Execution halted - ``` - -# sigmajs - -
- -* Version: 0.1.5 -* GitHub: https://github.com/JohnCoene/sigmajs -* Source code: https://github.com/cran/sigmajs -* Date/Publication: 2020-06-18 18:10:02 UTC -* Number of recursive dependencies: 76 - -Run `revdepcheck::cloud_details(, "sigmajs")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘sigmajs-Ex.R’ failed - The error most likely occurred in: - - > ### Name: sg_cluster - > ### Title: Cluster - > ### Aliases: sg_cluster sg_get_cluster - > - > ### ** Examples - > - > nodes <- sg_make_nodes() - ... - > - > sigmajs() %>% - + sg_nodes(nodes, id, size) %>% - + sg_edges(edges, id, source, target) %>% - + sg_layout() %>% - + sg_cluster() - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: %>% ... sg_get_layout -> .build_igraph -> -> make_empty_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 4. └─sigmajs:::.build_igraph(edges, directed = directed, nodes, save = save_igraph) - 5. └─igraph::graph_from_data_frame(edges, directed, nodes) - 6. └─igraph::make_empty_graph(n = 0, directed = directed) - ── Error ('test-formats.R:21:3'): igraph ─────────────────────────────────────── - Error in `.igraph.status("Restore graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─igraph::layout_with_fr(lesmis_igraph) at test-formats.R:21:2 - 2. └─igraph:::ensure_igraph(graph) - 3. └─igraph::is_igraph(graph) - 4. └─igraph:::warn_version(graph) - - [ FAIL 3 | WARN 8 | SKIP 0 | PASS 57 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 28 marked UTF-8 strings - ``` - -# signnet - -
- -* Version: 1.0.1 -* GitHub: https://github.com/schochastics/signnet -* Source code: https://github.com/cran/signnet -* Date/Publication: 2023-01-27 13:40:02 UTC -* Number of recursive dependencies: 104 - -Run `revdepcheck::cloud_details(, "signnet")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘signnet-Ex.R’ failed - The error most likely occurred in: - - > ### Name: as_complex_edges - > ### Title: Convert Signed Network to Complex - > ### Aliases: as_complex_edges - > - > ### ** Examples - > - > g <- sample_islands_signed(2,10,1,10) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: sample_islands_signed ... -> make_graph -> do.call -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ▆ - 1. └─igraph::graph.full(5, directed = T) at test-signed_triangles.R:106:2 - ── Error ('test-utils.R:9:3'): from_edgelist works ───────────────────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─signnet::graph_from_edgelist_signed(el, signs) at test-utils.R:9:2 - 2. └─igraph::graph_from_edgelist(el, directed = directed) - 3. └─igraph::make_graph(unname(ids[t(el)]), directed = directed) - 4. ├─base::do.call(old_graph, args) - 5. └─igraph (local) ``(``, directed = FALSE) - - [ FAIL 65 | WARN 0 | SKIP 0 | PASS 23 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 7.7Mb - sub-directories of 1Mb or more: - libs 6.1Mb - ``` - -# simcausal - -
- -* Version: 0.5.6 -* GitHub: https://github.com/osofr/simcausal -* Source code: https://github.com/cran/simcausal -* Date/Publication: 2022-10-28 11:52:27 UTC -* Number of recursive dependencies: 84 - -Run `revdepcheck::cloud_details(, "simcausal")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘simcausal-Ex.R’ failed - The error most likely occurred in: - - > ### Name: network - > ### Title: Define a Network Generator - > ### Aliases: network - > - > ### ** Examples - > - > #-------------------------------------------------------------------------------------------------- - ... - node W3, order:4 - node A, order:5 - node Y, order:6 - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Error in sampleNodeDistr(newNodeParams = newNodeParams, distr = distr, : - failed while sampling node 'ER.net', from distribution 'gen.ER' - Error in set.DAG(D, n.test = 100) : - ...attempt to simulate data from DAG failed... - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘test-all.R’ - Running the tests in ‘tests/test-all.R’ failed. - Last 13 lines of output: - ERROR in test.set.DAG_DAG2b_newactions: Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - ERROR in test.networkgen1: Error in set.DAG(D) : - ...attempt to simulate data from DAG failed... - ERROR in test.networkgen_time: Error in set.DAG(D) : - ...attempt to simulate data from DAG failed... - ERROR in test.tKmaxnet: Error in set.DAG(D, n.test = 200) : - ...attempt to simulate data from DAG failed... - ERROR in test.MV: Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Error: - - unit testing failed (#test failures: 0, #R errors: 7) - - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘simcausal_vignette.Rnw’ using knitr - - Quitting from lines 963-966 [DAG1t] (simcausal_vignette.Rnw) - Error: processing vignette 'simcausal_vignette.Rnw' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘simcausal_vignette.Rnw’ - - SUMMARY: processing the following file failed: - ‘simcausal_vignette.Rnw’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# simer - -
- -* Version: 0.9.0.2 -* GitHub: https://github.com/xiaolei-lab/SIMER -* Source code: https://github.com/cran/simer -* Date/Publication: 2022-08-08 13:30:02 UTC -* Number of recursive dependencies: 21 - -Run `revdepcheck::cloud_details(, "simer")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘simer-Ex.R’ failed - The error most likely occurred in: - - > ### Name: GxG.network - > ### Title: Genetic interaction network - > ### Aliases: GxG.network - > - > ### ** Examples - > - > pop.map <- generate.map(pop.marker = 1e4) - > GxG.net <- GxG.network(pop.map) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: GxG.network -> ba.game - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 9.5Mb - sub-directories of 1Mb or more: - libs 8.6Mb - ``` - -# simPATHy - -
- -* Version: 0.6 -* GitHub: NA -* Source code: https://github.com/cran/simPATHy -* Date/Publication: 2021-11-23 09:50:02 UTC -* Number of recursive dependencies: 150 - -Run `revdepcheck::cloud_details(, "simPATHy")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘simPATHy-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plotCorGraph - > ### Title: Plot correlation or partial correlation matrix - > ### Aliases: plotCorGraph - > - > ### ** Examples - > - > if( require(gRbase) & require(graph)){ - ... - as.data.frame, basename, cbind, colnames, dirname, do.call, - duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, - lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, - pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, - tapply, union, unique, unsplit, which.max, which.min - - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: fitSgraph ... asMethod -> g_gn2ig_ -> -> graph_from_adj_list - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘simPATHy.Rmd’ using rmarkdown - - Quitting from lines 54-56 [unnamed-chunk-6] (simPATHy.Rmd) - Error: processing vignette 'simPATHy.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘simPATHy.Rmd’ - - SUMMARY: processing the following file failed: - ‘simPATHy.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# simplifyNet - -
- -* Version: 0.0.1 -* GitHub: NA -* Source code: https://github.com/cran/simplifyNet -* Date/Publication: 2022-11-15 16:30:02 UTC -* Number of recursive dependencies: 23 - -Run `revdepcheck::cloud_details(, "simplifyNet")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘simplifyNet-Ex.R’ failed - The error most likely occurred in: - - > ### Name: EffRSparse - > ### Title: Sparsification through edge sampling via effective resistances - > ### Aliases: EffRSparse - > - > ### ** Examples - > - > #Generate random ER graph with uniformly random edge weights - > g = igraph::erdos.renyi.game(100, 0.1) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: - Execution halted - ``` - -# SIRE - -
- -* Version: 1.1.0 -* GitHub: NA -* Source code: https://github.com/cran/SIRE -* Date/Publication: 2019-04-11 16:32:41 UTC -* Number of recursive dependencies: 79 - -Run `revdepcheck::cloud_details(, "SIRE")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘SIRE-Ex.R’ failed - The error most likely occurred in: - - > ### Name: causal_decompose - > ### Title: Estimation and decomposition of simultaneous equation model - > ### Aliases: causal_decompose - > - > ### ** Examples - > - > data("macroIT") - ... - > - > causal_decompose(data = macroIT, - + eq.system = eq.system, - + resid.est = "noDfCor", - + instruments = instruments, - + sigma.in = NULL) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: causal_decompose -> -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘dplyr’ ‘magrittr’ ‘psych’ ‘stringr’ - All declared Imports should be used. - ``` - -# sirt - -
- -* Version: 3.12-66 -* GitHub: https://github.com/alexanderrobitzsch/sirt -* Source code: https://github.com/cran/sirt -* Date/Publication: 2022-05-17 09:10:05 UTC -* Number of recursive dependencies: 110 - -Run `revdepcheck::cloud_details(, "sirt")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘sirt-Ex.R’ failed - The error most likely occurred in: - - > ### Name: sia.sirt - > ### Title: Statistical Implicative Analysis (SIA) - > ### Aliases: sia.sirt - > - > ### ** Examples - > - > ############################################################################# - ... - > ############################################################################# - > - > data(data.read) - > dat <- data.read - > - > res <- sirt::sia.sirt(dat, significance=.85 ) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: ... -> make_graph -> do.call -> - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 22.0Mb - sub-directories of 1Mb or more: - R 2.1Mb - libs 17.8Mb - ``` - -# SITH - -
- -* Version: 1.1.0 -* GitHub: https://github.com/phillipnicol/SITH -* Source code: https://github.com/cran/SITH -* Date/Publication: 2021-01-05 15:10:02 UTC -* Number of recursive dependencies: 58 - -Run `revdepcheck::cloud_details(, "SITH")` for more info - -
- -## Newly broken - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘SITH.Rmd’ using rmarkdown - Warning in snapshot3d(paste0(name, ".png")) : - webshot = TRUE requires the webshot2 package and Chrome browser; using rgl.snapshot() instead - Warning in rgl.snapshot(filename, fmt, top) : - this build of rgl does not support snapshots - Warning in snapshot3d(paste0(name, ".png")) : - webshot = TRUE requires the webshot2 package and Chrome browser; using rgl.snapshot() instead - Warning in rgl.snapshot(filename, fmt, top) : - ... - Quitting from lines 296-304 [unnamed-chunk-17] (SITH.Rmd) - Error: processing vignette 'SITH.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘SITH.Rmd’ - - SUMMARY: processing the following file failed: - ‘SITH.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# skynet - -
- -* Version: 1.4.3 -* GitHub: https://github.com/ropensci/skynet -* Source code: https://github.com/cran/skynet -* Date/Publication: 2022-06-17 13:00:02 UTC -* Number of recursive dependencies: 105 - -Run `revdepcheck::cloud_details(, "skynet")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘skynet-Ex.R’ failed - The error most likely occurred in: - - > ### Name: summary.skynet - > ### Title: Displays a summary of a skynet object - > ### Aliases: summary.skynet - > - > ### ** Examples - > - > net <- make_net_dir(OD_Sample) - ... - - # Auto named with `tibble::lst()`: tibble::lst(mean, median) - - # Using lambdas list(~ mean(., trim = .2), ~ median(., na.rm = TRUE)) - ℹ The deprecated feature was likely used in the skynet package. - Please report the issue at . - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: make_net_dir -> -> make_empty_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 1. └─skynet::make_net_dir(OD_Sample) at test_smallerfunctions.R:21:2 - 2. └─igraph::graph_from_data_frame(netDir_all, directed = TRUE, vertices = nodes) - 3. └─igraph::make_empty_graph(n = 0, directed = directed) - ── Error ('test_smallerfunctions.R:33:3'): Plot Map ──────────────────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. ├─skynet::net_map(make_net_dir(OD_Sample)) at test_smallerfunctions.R:33:2 - 2. └─skynet::make_net_dir(OD_Sample) - 3. └─igraph::graph_from_data_frame(netDir_all, directed = TRUE, vertices = nodes) - 4. └─igraph::make_empty_graph(n = 0, directed = directed) - - [ FAIL 14 | WARN 14 | SKIP 4 | PASS 20 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘skynet.Rmd’ using rmarkdown - - Quitting from lines 97-101 [unnamed-chunk-4] (skynet.Rmd) - Error: processing vignette 'skynet.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘skynet.Rmd’ - - SUMMARY: processing the following file failed: - ‘skynet.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘maps’ - All declared Imports should be used. - ``` - -# SmCCNet - -
- -* Version: 0.99.0 -* GitHub: https://github.com/KechrisLab/SmCCNet -* Source code: https://github.com/cran/SmCCNet -* Date/Publication: 2019-03-04 16:50:03 UTC -* Number of recursive dependencies: 9 - -Run `revdepcheck::cloud_details(, "SmCCNet")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘SmCCNet-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plotMultiOmicsNetwork - > ### Title: Plot multi-omics module networks. - > ### Aliases: plotMultiOmicsNetwork - > - > ### ** Examples - > - > set.seed(123) - ... - > abar <- getAbar(w, P1 = 2, FeatureLabel = NULL) - > modules <- getMultiOmicsModules(abar, P1 = 2, CutHeight = 0.5) - > x <- cbind(geneExpr[ ,seq_len(2)], mirnaExpr[ , seq_len(3)]) - > corr <- cor(x) - > - > plotMultiOmicsNetwork(abar, corr, modules, ModuleIdx = 1, P1 = 2) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plotMultiOmicsNetwork -> -> graph.adjacency.dense - Execution halted - ``` - -# smotefamily - -
- -* Version: 1.3.1 -* GitHub: NA -* Source code: https://github.com/cran/smotefamily -* Date/Publication: 2019-05-30 07:30:02 UTC -* Number of recursive dependencies: 10 - -Run `revdepcheck::cloud_details(, "smotefamily")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘smotefamily-Ex.R’ failed - The error most likely occurred in: - - > ### Name: DBSMOTE - > ### Title: Density-based SMOTE - > ### Aliases: DBSMOTE - > ### Keywords: manip methods - > - > ### ** Examples - > - > data_example = sample_generator(5000,ratio = 0.90) - > genData = DBSMOTE(data_example[,-3],data_example[,3]) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: DBSMOTE -> -> graph.adjacency.dense - Execution halted - ``` - -# snowboot - -
- -* Version: 1.0.2 -* GitHub: NA -* Source code: https://github.com/cran/snowboot -* Date/Publication: 2020-04-25 18:30:03 UTC -* Number of recursive dependencies: 10 - -Run `revdepcheck::cloud_details(, "snowboot")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘snowboot-Ex.R’ failed - The error most likely occurred in: - - > ### Name: igraph_to_network - > ### Title: Create a "Network" Object from an igraph Object - > ### Aliases: igraph_to_network - > - > ### ** Examples - > - > hex_ring <- igraph::make_ring(6, directed = FALSE, mutual = FALSE, circular = TRUE) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: - Execution halted - ``` - -# SNscan - -
- -* Version: 1.0 -* GitHub: NA -* Source code: https://github.com/cran/SNscan -* Date/Publication: 2016-01-19 13:09:28 -* Number of recursive dependencies: 11 - -Run `revdepcheck::cloud_details(, "SNscan")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘SNscan-Ex.R’ failed - The error most likely occurred in: - - > ### Name: group.graph - > ### Title: Generate igraph Objects with Different Connection - > ### Characteristics. - > ### Aliases: group.graph - > ### Keywords: graph sampling - > - > ### ** Examples - ... - > - > group.graph(V=10, cv =1:3 , p1=1/10, p2 = 1/2) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: group.graph -> graph.adjacency -> graph.adjacency.dense - Execution halted - Error in .igraph.status("Free graph external pointer.\n") : - could not find function ".igraph.status" - Error in .igraph.status("Free graph external pointer.\n") : - could not find function ".igraph.status" - ``` - -# SOAs - -
- -* Version: 1.3 -* GitHub: https://github.com/bertcarnell/SOAs -* Source code: https://github.com/cran/SOAs -* Date/Publication: 2022-10-03 11:30:02 UTC -* Number of recursive dependencies: 58 - -Run `revdepcheck::cloud_details(, "SOAs")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 8. └─igraph (local) ``(``, directed = TRUE) - ── Error ('test-utilitiesCreate.R:3:1'): utilitiesCreate ─────────────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─SOAs:::createAB(3) at test-utilitiesCreate.R:3:0 - 2. └─SOAs:::BcolsFromBcolllist(Bcollist) - 3. └─igraph::graph_from_edgelist(el) - 4. └─igraph::make_graph(t(el), directed = directed) - 5. ├─base::do.call(old_graph, args) - 6. └─igraph (local) ``(``, directed = TRUE) - - [ FAIL 3 | WARN 0 | SKIP 14 | PASS 1036 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘iterators’ ‘itertools’ - All declared Imports should be used. - ``` - -# SoilR - -
- -* Version: 1.2.105 -* GitHub: NA -* Source code: https://github.com/cran/SoilR -* Date/Publication: 2022-01-23 16:12:42 UTC -* Number of recursive dependencies: 49 - -Run `revdepcheck::cloud_details(, "SoilR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘SoilR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: WangThreePoolNonAutonomous_sym - > ### Title: A non-autonomous version of the original Wang 3 pool model - > ### Aliases: WangThreePoolNonAutonomous_sym - > - > ### ** Examples - > - > # This is a working example which demostrates some of the new functionality. - > require('SoilR',quietly =TRUE) - > smod <- WangThreePoolNonAutonomous_sym() - > # (look at the source code of WangThreePoolNonAutonomous_sym ) - > plotPoolGraph(smod) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plotPoolGraph ... plotPoolGraphFromTupleLists -> graph_from_data_frame -> make_empty_graph - Execution halted - ``` - -# solitude - -
- -* Version: 1.1.3 -* GitHub: https://github.com/talegari/solitude -* Source code: https://github.com/cran/solitude -* Date/Publication: 2021-07-29 20:00:02 UTC -* Number of recursive dependencies: 131 - -Run `revdepcheck::cloud_details(, "solitude")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘solitude-Ex.R’ failed - The error most likely occurred in: - - > ### Name: terminalNodesDepth - > ### Title: Depth of each terminal node of all trees in a ranger model - > ### Aliases: terminalNodesDepth - > - > ### ** Examples - > - > rf = ranger::ranger(Species ~ ., data = iris, num.trees = 100) - > terminalNodesDepth(rf) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: terminalNodesDepth ... resolve.list -> signalConditionsASAP -> signalConditions - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘R6’ ‘lgr’ - All declared Imports should be used. - ``` - -# SourceSet - -
- -* Version: 0.1.5 -* GitHub: NA -* Source code: https://github.com/cran/SourceSet -* Date/Publication: 2022-11-21 11:30:02 UTC -* Number of recursive dependencies: 106 - -Run `revdepcheck::cloud_details(, "SourceSet")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘SourceSet-Ex.R’ failed - The error most likely occurred in: - - > ### Name: infoSource - > ### Title: Get summary statistics on graphs and variables - > ### Aliases: infoSource - > - > ### ** Examples - > - > ## Load the SourceSetObj obtained from the source set analysis of ALL dataset - ... - as.data.frame, basename, cbind, colnames, dirname, do.call, - duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, - lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, - pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, - tapply, union, unique, unsplit, which.max, which.min - - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: infoSource ... ensure_igraph -> -> graph_from_adj_list - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘SourceSet.Rmd’ using rmarkdown - - Quitting from lines 151-158 [unnamed-chunk-5] (SourceSet.Rmd) - Error: processing vignette 'SourceSet.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘SourceSet.Rmd’ - - SUMMARY: processing the following file failed: - ‘SourceSet.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘r2cytoscape’ - ``` - -# spacejamr - -
- -* Version: 0.2.1 -* GitHub: https://github.com/dscolby/spacejamr -* Source code: https://github.com/cran/spacejamr -* Date/Publication: 2022-04-01 20:10:02 UTC -* Number of recursive dependencies: 138 - -Run `revdepcheck::cloud_details(, "spacejamr")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘spacejamr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: NetSim - > ### Title: Simulate a network from a point process or sequence - > ### Aliases: NetSim - > - > ### ** Examples - > - > # Load spacejamr object - ... - + power = -2.4) - Warning: There was 1 warning in `dplyr::mutate()`. - ℹ In argument: `dplyr::across(...)`. - Caused by warning: - ! Using `across()` without supplying `.cols` was deprecated in dplyr 1.1.0. - ℹ Please supply `.cols` instead. - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: NetSim ... ensure_igraph -> -> graph.adjacency.dense - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. ├─spacejamr::NetSim(ri_points) at test-generics.R:6:0 - 2. │ └─spacejamr:::new_NetSim(...) - 3. │ └─spacejamr:::validate_NetSim(...) - 4. │ ├─... %>% igraph::simplify() - 5. │ └─igraph::graph_from_adjacency_matrix(distances, mode = "undirected") - 6. │ └─igraph:::graph.adjacency.dense(...) - 7. └─igraph::simplify(.) - 8. └─igraph:::ensure_igraph(graph) - - [ FAIL 3 | WARN 1 | SKIP 0 | PASS 10 ] - Error: Test failures - Execution halted - ``` - -# sparsebnUtils - -
- -* Version: 0.0.8 -* GitHub: https://github.com/itsrainingdata/sparsebnUtils -* Source code: https://github.com/cran/sparsebnUtils -* Date/Publication: 2021-01-27 06:30:02 UTC -* Number of recursive dependencies: 69 - -Run `revdepcheck::cloud_details(, "sparsebnUtils")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected") - 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) - 4. ├─sparsebnUtils::to_edgeList(to_graphNEL(to_network(to_igraph(sbf.empty)))) - 5. ├─sparsebnUtils::to_graphNEL(to_network(to_igraph(sbf.empty))) - 6. ├─sparsebnUtils::to_network(to_igraph(sbf.empty)) - 7. ├─sparsebnUtils::to_igraph(sbf.empty) - 8. └─sparsebnUtils:::to_igraph.sparsebnFit(sbf.empty) - 9. ├─sparsebnUtils::to_igraph(x$edges) - 10. └─sparsebnUtils:::to_igraph.edgeList(x$edges) - 11. └─igraph::graph.adjacency(as.matrix(x)) - 12. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 8 | WARN 0 | SKIP 1 | PASS 284 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking Rd cross-references ... NOTE - ``` - Unknown package ‘sparsebn’ in Rd xrefs - ``` - -# spathial - -
- -* Version: 0.1.2 -* GitHub: NA -* Source code: https://github.com/cran/spathial -* Date/Publication: 2020-04-10 18:20:02 UTC -* Number of recursive dependencies: 43 - -Run `revdepcheck::cloud_details(, "spathial")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘spathial-Ex.R’ failed - The error most likely occurred in: - - > ### Name: spathialPrefiltering - > ### Title: Prefilter data - > ### Aliases: spathialPrefiltering - > - > ### ** Examples - > - > # Load data matrix X - ... - > boundaryRes <- spathialBoundaryIds(X, X_labels, mode=2, from=3, to=6) - > X <- boundaryRes$X - > X_labels <- boundaryRes$X_labels - > boundary_ids <- boundaryRes$boundary_ids - > # Run spathial spathialPrefilterinh with the output of the function spathialBoundaryIds - > filterRes <- spathialPrefiltering(X, boundary_ids) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: spathialPrefiltering ... rkm_prefilter -> -> graph.adjacency.dense - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘vignette.rmd’ using rmarkdown - - Quitting from lines 178-186 [unnamed-chunk-15] (vignette.rmd) - Error: processing vignette 'vignette.rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘vignette.rmd’ - - SUMMARY: processing the following file failed: - ‘vignette.rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘irlba’ ‘knitr’ ‘rmarkdown’ - All declared Imports should be used. - ``` - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# spatsoc - -
- -* Version: 0.1.16 -* GitHub: https://github.com/ropensci/spatsoc -* Source code: https://github.com/cran/spatsoc -* Date/Publication: 2021-02-24 06:50:02 UTC -* Number of recursive dependencies: 70 - -Run `revdepcheck::cloud_details(, "spatsoc")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘spatsoc-Ex.R’ failed - The error most likely occurred in: - - > ### Name: get_gbi - > ### Title: Generate group by individual matrix - > ### Aliases: get_gbi - > - > ### ** Examples - > - > # Load data.table - ... - Please note that rgeos will be retired during October 2023, - plan transition to sf or terra functions using GEOS at your earliest convenience. - See https://r-spatial.org/r/2023/05/15/evolution4.html for details. - Linking to sp version: 1.6-1 - Polygon checking: TRUE - - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: group_polys ... [.data.table -> -> graph.adjacency.dense - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 7. └─igraph::graph_from_adjacency_matrix(distMatrix <= threshold) - 8. └─igraph:::graph.adjacency.dense(...) - ── Error ('test-random.R:11:1'): (code run outside of `test_that()`) ─────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. ├─spatsoc::group_pts(...) at test-random.R:11:0 - 2. │ ├─...[] - 3. │ └─data.table:::`[.data.table`(...) - 4. └─igraph::graph_from_adjacency_matrix(distMatrix <= threshold) - 5. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 26 | WARN 7 | SKIP 0 | PASS 184 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘using-edge-and-dyad.Rmd’ using rmarkdown - --- finished re-building ‘using-edge-and-dyad.Rmd’ - - --- re-building ‘faq.Rmd’ using knitr - - Quitting from lines 32-53 [unnamed-chunk-1] (faq.Rmd) - Error: processing vignette 'faq.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘faq.Rmd’ - ... - --- failed re-building ‘intro-spatsoc.Rmd’ - - --- re-building ‘using-in-sna.Rmd’ using knitr - --- finished re-building ‘using-in-sna.Rmd’ - - SUMMARY: processing the following files failed: - ‘faq.Rmd’ ‘intro-spatsoc.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# specr - -
- -* Version: 1.0.0 -* GitHub: https://github.com/masurp/specr -* Source code: https://github.com/cran/specr -* Date/Publication: 2023-01-20 13:50:02 UTC -* Number of recursive dependencies: 152 - -Run `revdepcheck::cloud_details(, "specr")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘specr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plot_decisiontree - > ### Title: Plot decision tree - > ### Aliases: plot_decisiontree - > - > ### ** Examples - > - > results <- run_specs(df = example_data, - ... - + controls = c("c1", "c2")) - > - > # Basic, non-labelled decisions tree - > plot_decisiontree(results) - Warning: `plot_decisiontree()` was deprecated in specr 1.0.0. - ℹ Please use `plot.specr.setup()` instead. - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot_decisiontree ... create_layout -> graph_from_data_frame -> make_empty_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. ├─base::plot(specs) at test-generics.R:13:2 - 2. ├─specr:::plot.specr.setup(specs) - 3. │ └─edge_list %>% graph_from_data_frame %>% ... - 4. ├─ggraph::ggraph(., layout = layout, circular = circular) - 5. │ ├─ggplot2::ggplot(data = create_layout(graph, layout, ...), environment = envir) - 6. │ └─ggraph::create_layout(graph, layout, ...) - 7. └─igraph::graph_from_data_frame(.) - 8. └─igraph::make_empty_graph(n = 0, directed = directed) - - [ FAIL 1 | WARN 8 | SKIP 0 | PASS 25 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘custom-plot.rmd’ using rmarkdown - --- finished re-building ‘custom-plot.rmd’ - - --- re-building ‘different-specifications.Rmd’ using rmarkdown - --- finished re-building ‘different-specifications.Rmd’ - - --- re-building ‘getting-started.rmd’ using rmarkdown - - Quitting from lines 75-76 [unnamed-chunk-5] (getting-started.rmd) - ... - --- finished re-building ‘parallel-bayesian-models.Rmd’ - - --- re-building ‘parallelization.Rmd’ using rmarkdown - --- finished re-building ‘parallelization.Rmd’ - - SUMMARY: processing the following file failed: - ‘getting-started.rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# spinner - -
- -* Version: 1.1.0 -* GitHub: NA -* Source code: https://github.com/cran/spinner -* Date/Publication: 2023-03-21 06:10:02 UTC -* Number of recursive dependencies: 76 - -Run `revdepcheck::cloud_details(, "spinner")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - > library(spinner) - > - > test_check("spinner") - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Error ('test.R:1:1'): (code run outside of `test_that()`) ─────────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─igraph::random.graph.game(20, 0.3) at test.R:1:0 - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] - Error: Test failures - Execution halted - ``` - -# spNetwork - -
- -* Version: 0.4.3.7 -* GitHub: https://github.com/JeremyGelb/spNetwork -* Source code: https://github.com/cran/spNetwork -* Date/Publication: 2023-04-11 15:50:02 UTC -* Number of recursive dependencies: 150 - -Run `revdepcheck::cloud_details(, "spNetwork")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘spNetwork-Ex.R’ failed - The error most likely occurred in: - - > ### Name: build_graph - > ### Title: Network generation - > ### Aliases: build_graph - > - > ### ** Examples - > - > data(mtl_network) - > mtl_network$length <- as.numeric(sf::st_length(mtl_network)) - > graph_result <- build_graph(mtl_network, 2, "length", attrs = TRUE) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: build_graph -> -> make_empty_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ── Error ('test_tnkde_sf.R:285:3'): Testing the multicore version of the function TNKDE ── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─spNetwork::tnkde(...) at test_tnkde_sf.R:285:2 - 2. └─base::lapply(...) - 3. └─spNetwork (local) FUN(X[[i]], ...) - 4. └─spNetwork:::tnkde_worker(...) - 5. └─spNetwork::build_graph(lines, digits = digits, line_weight = "length") - 6. └─igraph::graph_from_data_frame(linelist, directed = FALSE, vertices = NULL) - 7. └─igraph::make_empty_graph(n = 0, directed = directed) - - [ FAIL 56 | WARN 0 | SKIP 0 | PASS 18 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘Isochrones.Rmd’ using rmarkdown - - Quitting from lines 66-72 [unnamed-chunk-2] (Isochrones.Rmd) - Error: processing vignette 'Isochrones.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘Isochrones.Rmd’ - - --- re-building ‘KNetworkFunctions.Rmd’ using rmarkdown - --- finished re-building ‘KNetworkFunctions.Rmd’ - ... - --- finished re-building ‘SpatialWeightMatrices.Rmd’ - - --- re-building ‘TNKDE.Rmd’ using rmarkdown - --- finished re-building ‘TNKDE.Rmd’ - - SUMMARY: processing the following file failed: - ‘Isochrones.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 30.6Mb - sub-directories of 1Mb or more: - doc 1.1Mb - extdata 2.6Mb - libs 25.5Mb - ``` - -# spqdep - -
- -* Version: 0.1.2 -* GitHub: NA -* Source code: https://github.com/cran/spqdep -* Date/Publication: 2022-03-28 16:20:02 UTC -* Number of recursive dependencies: 114 - -Run `revdepcheck::cloud_details(, "spqdep")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘spqdep-Ex.R’ failed - The error most likely occurred in: - - > ### Name: Q.map.test - > ### Title: Compute the QE and QI tests of Equivalence and Independence - > ### between maps - > ### Aliases: Q.map.test - > - > ### ** Examples - > - ... - - attr(,"class") - [1] "qmap" "list" - > plot(qmap) - > plot(qmap, ci=.6) - > plot(qmap[[1]]$mh) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot ... plot.m_surr -> graph.adjacency -> graph.adjacency.dense - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘spq_userguide.Rmd’ using rmarkdown - - Quitting from lines 137-138 [plot mh] (spq_userguide.Rmd) - Error: processing vignette 'spq_userguide.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘spq_userguide.Rmd’ - - SUMMARY: processing the following file failed: - ‘spq_userguide.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘lwgeom’ ‘rgeoda’ - All declared Imports should be used. - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 4 marked UTF-8 strings - ``` - -# SSN - -
- -* Version: 1.1.17 -* GitHub: NA -* Source code: https://github.com/cran/SSN -* Date/Publication: 2023-02-27 08:22:38 UTC -* Number of recursive dependencies: 27 - -Run `revdepcheck::cloud_details(, "SSN")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘SSN-Ex.R’ failed - The error most likely occurred in: - - > ### Name: SimulateOnSSN - > ### Title: Simulating Data on Spatial Stream Networks - > ### Aliases: SimulateOnSSN - > - > ### ** Examples - > - > ####################################### - ... - > library(SSN) - > set.seed(101) - > ## simulate a SpatialStreamNetwork object - > raw1.ssn <- createSSN(n = c(10,10), - + obsDesign = binomialDesign(c(50,50)), predDesign = binomialDesign(c(100,100)), - + importToR = TRUE, path = paste(tempdir(),"/sim1", sep = "")) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: createSSN - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘SSN.Rnw’ using Sweave - Error: processing vignette 'SSN.Rnw' failed with diagnostics: - Running 'texi2dvi' on 'SSN.tex' failed. - LaTeX errors: - ! LaTeX Error: File `ae.sty' not found. - - Type X to quit or to proceed, - or enter new name. (Default extension: sty) - - ... - l.30 \ifthenelse - {\boolean{Sweave@inconsolata}}{%^^M - ! ==> Fatal error occurred, no output PDF file produced! - --- failed re-building ‘STARS.Rnw’ - - SUMMARY: processing the following files failed: - ‘SSN.Rnw’ ‘STARS.Rnw’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# stagedtrees - -
- -* Version: 2.2.1 -* GitHub: https://github.com/gherardovarando/stagedtrees -* Source code: https://github.com/cran/stagedtrees -* Date/Publication: 2022-04-28 23:10:02 UTC -* Number of recursive dependencies: 48 - -Run `revdepcheck::cloud_details(, "stagedtrees")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise) - 3. │ ├─testthat (local) .capture(...) - 4. │ │ ├─withr::with_output_sink(...) - 5. │ │ │ └─base::force(code) - 6. │ │ ├─base::withCallingHandlers(...) - 7. │ │ └─base::withVisible(code) - 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) - 9. ├─base::plot(ceg(mod), col = "stages") - 10. └─stagedtrees:::plot.ceg(ceg(mod), col = "stages") - 11. └─igraph::graph_from_adjacency_matrix(A) - 12. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 2 | WARN 0 | SKIP 0 | PASS 1037 ] - Error: Test failures - Execution halted - ``` - -# statGraph - -
- -* Version: 0.5.0 -* GitHub: NA -* Source code: https://github.com/cran/statGraph -* Date/Publication: 2021-05-19 07:00:06 UTC -* Number of recursive dependencies: 17 - -Run `revdepcheck::cloud_details(, "statGraph")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘statGraph-Ex.R’ failed - The error most likely occurred in: - - > ### Name: GIC - > ### Title: Graph Information Criterion (GIC) - > ### Aliases: GIC - > ### Keywords: graph_information_criterion - > - > ### ** Examples - > - > set.seed(1) - > G <- as.matrix(igraph::get.adjacency(igraph::sample_gnp(n=50, p=0.5))) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: as.matrix -> -> ensure_igraph -> - Execution halted - ``` - -# stemmatology - -
- -* Version: 0.3.2 -* GitHub: https://github.com/Jean-Baptiste-Camps/stemmatology -* Source code: https://github.com/cran/stemmatology -* Date/Publication: 2019-04-10 15:52:51 UTC -* Number of recursive dependencies: 64 - -Run `revdepcheck::cloud_details(, "stemmatology")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘stemmatology-Ex.R’ failed - The error most likely occurred in: - - > ### Name: PCC.Exploratory - > ### Title: PCC Exploratory methods - > ### Aliases: PCC.Exploratory - > ### Keywords: stemmatology - > - > ### ** Examples - > - ... - > ## Don't show: - > # subsetting for exec time - > fournival = fournival[1:50,c(-5,-8)] - > ## End(Don't show) - > # Non interactive mode - > PCC.Exploratory(fournival, ask = FALSE, threshold = 0.06) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: PCC.Exploratory ... -> make_graph -> do.call -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. ├─testthat::expect_equal(...) at test-layout_as_stemma.R:11:2 - 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") - 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) - 4. └─stemmatology::layout_as_stemma(edgelist) - 5. └─igraph::graph_from_edgelist(edgelist[, 1:2], directed = TRUE) - 6. └─igraph::make_graph(unname(ids[t(el)]), directed = directed) - 7. ├─base::do.call(old_graph, args) - 8. └─igraph (local) ``(``, directed = TRUE) - - [ FAIL 13 | WARN 0 | SKIP 4 | PASS 43 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘stemmatology.Rnw’ using Sweave - Error: processing vignette 'stemmatology.Rnw' failed with diagnostics: - Running 'texi2dvi' on 'stemmatology.tex' failed. - LaTeX errors: - ! LaTeX Error: File `ae.sty' not found. - - Type X to quit or to proceed, - or enter new name. (Default extension: sty) - ... - l.55 \RequirePackage - [T1]{fontenc}^^M - ! ==> Fatal error occurred, no output PDF file produced! - --- failed re-building ‘stemmatology.Rnw’ - - SUMMARY: processing the following file failed: - ‘stemmatology.Rnw’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# stm - -
- -* Version: 1.3.6 -* GitHub: https://github.com/bstewart/stm -* Source code: https://github.com/cran/stm -* Date/Publication: 2020-09-18 13:50:02 UTC -* Number of recursive dependencies: 86 - -Run `revdepcheck::cloud_details(, "stm")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘stmVignette.Rnw’ - ... - - > cloud(poliblogPrevFit, topic = 7, scale = c(2, 0.25)) - - > mod.out.corr <- topicCorr(poliblogPrevFit) - - > plot(mod.out.corr) - - When sourcing 'stmVignette.R': - Error: could not find function ".igraph.status" - Execution halted - - ‘stmVignette.Rnw’ using ‘UTF-8’... failed - ``` - -## In both - -* checking tests ... ERROR - ``` - Running ‘spelling.R’ - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Error in `if (...length() && any(...names() == "Dimnames")) .Object@Dimnames <- fixupDN(.Object@Dimnames)`: missing value where TRUE/FALSE needed - Backtrace: - ▆ - 1. ├─quanteda::dfm(...) at test-quanteda-stm.R:9:4 - 2. └─quanteda:::dfm.corpus(...) - 3. └─(function(x, tolower = TRUE, remove_padding = FALSE, stem = NULL, ... - 4. └─quanteda:::dfm.tokens(...) - 5. └─quanteda:::build_dfm(...) - 6. └─methods::new(...) - 7. ├─methods::initialize(value, ...) - 8. └─Matrix (local) initialize(value, ...) - - [ FAIL 1 | WARN 3 | SKIP 0 | PASS 8 ] - Error: Test failures - Execution halted - ``` - -* checking installed package size ... NOTE - ``` - installed size is 6.3Mb - sub-directories of 1Mb or more: - data 1.7Mb - libs 3.4Mb - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘stmVignette.Rnw’ using Sweave - stm v1.3.6 successfully loaded. See ?stm for help. - Papers, resources, and other materials at structuraltopicmodel.com - - Error: processing vignette 'stmVignette.Rnw' failed with diagnostics: - chunk 27 - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - - --- failed re-building 'stmVignette.Rnw' - - SUMMARY: processing the following file failed: - 'stmVignette.Rnw' - - Error: Vignette re-building failed. - Execution halted - ``` - -# stplanr - -
- -* Version: 1.0.2 -* GitHub: https://github.com/ropensci/stplanr -* Source code: https://github.com/cran/stplanr -* Date/Publication: 2022-11-08 12:40:02 UTC -* Number of recursive dependencies: 167 - -Run `revdepcheck::cloud_details(, "stplanr")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘stplanr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: rnet_group - > ### Title: Assign segments in a route network to groups - > ### Aliases: rnet_group rnet_group.default rnet_group.sfc rnet_group.sf - > - > ### ** Examples - > - > rnet <- rnet_breakup_vertices(stplanr::osm_net_example) - > rnet$group <- rnet_group(rnet) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: rnet_group ... rnet_group.sf -> rnet_group -> rnet_group.sfc -> - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘stplanr-od.Rmd’ using rmarkdown - --- finished re-building ‘stplanr-od.Rmd’ - - --- re-building ‘stplanr-paper.Rmd’ using rmarkdown - --- finished re-building ‘stplanr-paper.Rmd’ - - --- re-building ‘stplanr-parallel.Rmd’ using rmarkdown - --- finished re-building ‘stplanr-parallel.Rmd’ - - ... - --- finished re-building ‘stplanr-routing.Rmd’ - - --- re-building ‘stplanr.Rmd’ using rmarkdown - --- finished re-building ‘stplanr.Rmd’ - - SUMMARY: processing the following file failed: - ‘stplanr-route-nets.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# SurvHiDim - -
- -* Version: 0.1.1 -* GitHub: NA -* Source code: https://github.com/cran/SurvHiDim -* Date/Publication: 2021-06-26 15:40:02 UTC -* Number of recursive dependencies: 171 - -Run `revdepcheck::cloud_details(, "SurvHiDim")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘SurvHiDim-Ex.R’ failed - The error most likely occurred in: - - > ### Name: hdNetwork - > ### Title: hdNetwork - > ### Aliases: hdNetwork - > - > ### ** Examples - > - > ## - > data(hnscc) - > hdNetwork(7,105,0.05,0.2,ID="id",OS="os",Death="death",PFS="pfs",Prog="prog",hnscc) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: hdNetwork ... graph_from_adjacency_matrix -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘readr’ - All declared Imports should be used. - ``` - -# targets - -
- -* Version: 1.1.3 -* GitHub: https://github.com/ropensci/targets -* Source code: https://github.com/cran/targets -* Date/Publication: 2023-05-23 14:10:02 UTC -* Number of recursive dependencies: 177 - -Run `revdepcheck::cloud_details(, "targets")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ──────────────────────────────────────────────────────────────────────────────── - Maximum number of failures exceeded; quitting at end of file. - ℹ Increase this number with (e.g.) `testthat::set_max_fails(Inf)` - - ══ Results ═════════════════════════════════════════════════════════════════════ - Duration: 4.7 s - - ── Skipped tests ────────────────────────────────────────────────────────────── - • On CRAN (44) - • version of crew, mirai, or nanonext is too low (6) - - [ FAIL 36 | WARN 0 | SKIP 50 | PASS 202 ] - ══ Terminated early ════════════════════════════════════════════════════════════ - Error: Test failures - Execution halted - ``` - -# TDA - -
- -* Version: 1.9 -* GitHub: NA -* Source code: https://github.com/cran/TDA -* Date/Publication: 2023-02-04 18:42:30 UTC -* Number of recursive dependencies: 59 - -Run `revdepcheck::cloud_details(, "TDA")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘TDA-Ex.R’ failed - The error most likely occurred in: - - > ### Name: clusterTree - > ### Title: Density clustering: the cluster tree - > ### Aliases: clusterTree print.clusterTree - > ### Keywords: nonparametric - > - > ### ** Examples - > - ... - > X <- rbind(X1, X2, X3) - > - > k <- 100 #parameter of knn - > - > ## Density clustering using knn and kde - > Tree <- clusterTree(X, k, density = "knn") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: clusterTree -> -> graph.adjacency.dense - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘article.Rnw’ - ... - > X3 <- cbind(rnorm(300, 6, 1), rnorm(300, 1, 1)) - - > XX <- rbind(X1, X2, X3) - - > Tree <- clusterTree(XX, k = 100, density = "knn", - + printProgress = FALSE) - - When sourcing ‘article.R’: - Error: could not find function ".igraph.status" - Execution halted - - ‘article.Rnw’ using ‘UTF-8’... failed - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 51.4Mb - sub-directories of 1Mb or more: - libs 50.2Mb - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘scales’ - All declared Imports should be used. - ``` - -* checking for GNU extensions in Makefiles ... NOTE - ``` - GNU make is a SystemRequirements. - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘article.Rnw’ using Sweave - - Error: processing vignette 'article.Rnw' failed with diagnostics: - chunk 48 (label = eq18b) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - - --- failed re-building ‘article.Rnw’ - - SUMMARY: processing the following file failed: - ‘article.Rnw’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# text2map - -
- -* Version: 0.1.6 -* GitHub: NA -* Source code: https://github.com/cran/text2map -* Date/Publication: 2022-08-17 22:20:02 UTC -* Number of recursive dependencies: 133 - -Run `revdepcheck::cloud_details(, "text2map")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘text2map-Ex.R’ failed - The error most likely occurred in: - - > ### Name: CoCA - > ### Title: Performs Concept Class Analysis (CoCA) - > ### Aliases: CoCA - > - > ### ** Examples - > - > - ... - + wv = ft_wv_sample, - + directions = sem_dirs, - + filter_sig = TRUE, - + filter_value = 0.05, - + zero_action = "drop" - + ) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: CoCA ... .get_cor_class -> -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 13. │ └─base::eval(exprs, env) - 14. │ └─text2map:::tidytext_dfm(corpus) at tests/testthat/helper-data.R:184:0 - 15. │ └─... %>% tidytext::cast_dfm(doc_id, word, n) at tests/testthat/helper-data.R:162:12 - 16. ├─tidytext::cast_dfm(., doc_id, word, n) - 17. │ ├─quanteda::as.dfm(m) - 18. │ └─quanteda:::as.dfm.Matrix(m) - 19. │ └─quanteda:::matrix2dfm(x) - 20. │ └─quanteda:::build_dfm(...) - 21. │ └─methods::new(...) - 22. │ ├─methods::initialize(value, ...) - 23. │ └─Matrix (local) initialize(value, ...) - 24. └─base::.handleSimpleError(...) - 25. └─testthat (local) h(simpleError(msg, call)) - 26. └─rlang::abort(...) - Execution halted - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 3 marked UTF-8 strings - ``` - -# textrank - -
- -* Version: 0.3.1 -* GitHub: https://github.com/bnosac/textrank -* Source code: https://github.com/cran/textrank -* Date/Publication: 2020-10-12 11:50:02 UTC -* Number of recursive dependencies: 54 - -Run `revdepcheck::cloud_details(, "textrank")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘textrank-Ex.R’ failed - The error most likely occurred in: - - > ### Name: textrank_candidates_lsh - > ### Title: Use locality-sensitive hashing to get combinations of sentences - > ### which contain words which are in the same minhash bucket - > ### Aliases: textrank_candidates_lsh - > - > ### ** Examples - > - ... - + textrank_candidates = candidates) - + summary(tr, n = 2) - + ## Don't show: - + } # End of main if statement running only if the required packages are installed - Loading required package: udpipe - Loading required package: textreuse - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: textrank_sentences -> -> make_empty_graph - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘textrank.Rmd’ using rmarkdown - - Quitting from lines 78-81 [unnamed-chunk-4] (textrank.Rmd) - Error: processing vignette 'textrank.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘textrank.Rmd’ - - SUMMARY: processing the following file failed: - ‘textrank.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# tidygraph - -
- -* Version: 1.2.3 -* GitHub: https://github.com/thomasp85/tidygraph -* Source code: https://github.com/cran/tidygraph -* Date/Publication: 2023-02-01 21:10:02 UTC -* Number of recursive dependencies: 77 - -Run `revdepcheck::cloud_details(, "tidygraph")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘tidygraph-Ex.R’ failed - The error most likely occurred in: - - > ### Name: activate - > ### Title: Determine the context of subsequent manipulations - > ### Aliases: activate active %N>% %E>% - > - > ### ** Examples - > - > gr <- create_complete(5) %>% - + activate(nodes) %>% - + mutate(class = sample(c('a', 'b'), 5, TRUE)) %>% - + activate(edges) %>% - + arrange(from) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: %>% ... activate -> create_complete -> as_tbl_graph -> make_full_graph - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 2. ├─tidygraph::as_tbl_graph(make_tree(n, children, mode)) - 3. └─igraph::make_tree(n, children, mode) - ── Error ('test-search.R:33:3'): search requires active nodes ────────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. ├─create_tree(10, 2) %>% activate(edges) at test-search.R:33:2 - 2. ├─tidygraph::activate(., edges) - 3. └─tidygraph::create_tree(10, 2) - 4. ├─tidygraph::as_tbl_graph(make_tree(n, children, mode)) - 5. └─igraph::make_tree(n, children, mode) - - [ FAIL 54 | WARN 0 | SKIP 0 | PASS 3 ] - Error: Test failures - Execution halted - ``` - -# tilemaps - -
- -* Version: 0.2.0 -* GitHub: https://github.com/kaerosen/tilemaps -* Source code: https://github.com/cran/tilemaps -* Date/Publication: 2020-07-10 04:20:02 UTC -* Number of recursive dependencies: 75 - -Run `revdepcheck::cloud_details(, "tilemaps")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘tilemaps-Ex.R’ failed - The error most likely occurred in: - - > ### Name: create_island - > ### Title: Create a Tile for an Island - > ### Aliases: create_island - > - > ### ** Examples - > - > library(sf) - Linking to GEOS 3.8.0, GDAL 3.0.4, PROJ 6.3.1; sf_use_s2() is TRUE - > northeast <- governors[c(6,7,17,18,19,27,28,30,36,37,43),] - > tile_map <- generate_map(northeast$geometry, square = FALSE) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: generate_map -> -> graph.adjacency.dense - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘tilemaps.Rmd’ using rmarkdown - - Quitting from lines 33-41 [unnamed-chunk-2] (tilemaps.Rmd) - Error: processing vignette 'tilemaps.Rmd' failed with diagnostics: - ℹ In argument: `tile_map = generate_map(geometry, square = FALSE, - flat_topped = TRUE)`. - Caused by error in `.igraph.status()`: - ! could not find function ".igraph.status" - --- failed re-building ‘tilemaps.Rmd’ - - SUMMARY: processing the following file failed: - ‘tilemaps.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘lwgeom’ - All declared Imports should be used. - ``` - -# tip - -
- -* Version: 0.1.0 -* GitHub: NA -* Source code: https://github.com/cran/tip -* Date/Publication: 2022-11-14 17:30:02 UTC -* Number of recursive dependencies: 100 - -Run `revdepcheck::cloud_details(, "tip")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘tip-Ex.R’ failed - The error most likely occurred in: - - > ### Name: partition_undirected_graph - > ### Title: Partition an undirected graph - > ### Aliases: partition_undirected_graph - > - > ### ** Examples - > - > # Import the tip library - ... - + } - > - > # Generate a one-cluster graph (i.e., partitioned_graph_matrix) - > partition_undirected_graph(.graph_matrix = posterior_prob_matrix, - + .num_components = 1, - + .step_size = 0.001) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: partition_undirected_graph -> -> graph.adjacency.dense - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - --- re-building ‘matrix-CONSTANT-simulated-vignette.Rmd’ using rmarkdown - - Quitting from lines 113-117 [unnamed-chunk-6] (matrix-CONSTANT-simulated-vignette.Rmd) - Error: processing vignette 'matrix-CONSTANT-simulated-vignette.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘matrix-CONSTANT-simulated-vignette.Rmd’ - - --- re-building ‘matrix-MNIW-simulated-vignette.Rmd’ using rmarkdown - - ... - --- failed re-building ‘vector-NIW-usarrests-vignette.Rmd’ - - SUMMARY: processing the following files failed: - ‘matrix-CONSTANT-simulated-vignette.Rmd’ - ‘matrix-MNIW-simulated-vignette.Rmd’ - ‘tensor-CONSTANT-simulated-vignette.Rmd’ - ‘vector-NIW-iris-vignette.Rmd’ ‘vector-NIW-usarrests-vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# Tlasso - -
- -* Version: 1.0.2 -* GitHub: NA -* Source code: https://github.com/cran/Tlasso -* Date/Publication: 2022-02-01 08:20:08 UTC -* Number of recursive dependencies: 42 - -Run `revdepcheck::cloud_details(, "Tlasso")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘Tlasso-Ex.R’ failed - The error most likely occurred in: - - > ### Name: graph.pattern - > ### Title: Graph Pattern Visualization - > ### Aliases: graph.pattern - > - > ### ** Examples - > - > - > graph.pattern(ChainOmega(5, sd = 13)) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: graph.pattern -> graph.adjacency -> graph.adjacency.dense - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘Tlasso.Rmd’ using rmarkdown - - Quitting from lines 319-327 [unnamed-chunk-10] (Tlasso.Rmd) - Error: processing vignette 'Tlasso.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘Tlasso.Rmd’ - - SUMMARY: processing the following file failed: - ‘Tlasso.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# TOHM - -
- -* Version: 1.4 -* GitHub: NA -* Source code: https://github.com/cran/TOHM -* Date/Publication: 2021-03-09 20:30:05 UTC -* Number of recursive dependencies: 40 - -Run `revdepcheck::cloud_details(, "TOHM")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘TOHM-Ex.R’ failed - The error most likely occurred in: - - > ### Name: EC_LRT - > ### Title: Compute the Euler characteristic for the generalized Likelihood - > ### Ratio Test field - > ### Aliases: EC_LRT - > ### Keywords: Euler characteristic generalized Likelihood Ratio random - > ### field - > - ... - > THETA_sel<-THETA2[(THETA2[,2]<=(28+sqrt(30^2-(THETA2[,1]- - + 195)^2)))&(THETA2[,2]>=(28-sqrt(30^2-(THETA2[,1]-195)^2))),] - > - > EC_LRT(ck=c(1,8),x=data,mll=mll,null0=0,init=c(0.1), - + lowlim=c(0),uplim=c(1), THETA_sel) - Evaluating LRT for each point of the grid... - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: EC_LRT ... graph_from_adjacency_matrix -> graph.adjacency.dense - Execution halted - ``` - -# TreeDimensionTest - -
- -* Version: 0.0.2 -* GitHub: NA -* Source code: https://github.com/cran/TreeDimensionTest -* Date/Publication: 2022-03-12 10:30:07 UTC -* Number of recursive dependencies: 68 - -Run `revdepcheck::cloud_details(, "TreeDimensionTest")` for more info - -
- -## Newly broken - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘Tutorial.Rmd’ using rmarkdown - - Quitting from lines 46-56 [unnamed-chunk-5] (Tutorial.Rmd) - Error: processing vignette 'Tutorial.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘Tutorial.Rmd’ - - SUMMARY: processing the following file failed: - ‘Tutorial.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# treefit - -
- -* Version: 1.0.2 -* GitHub: https://github.com/hayamizu-lab/treefit-r -* Source code: https://github.com/cran/treefit -* Date/Publication: 2022-01-18 07:50:02 UTC -* Number of recursive dependencies: 154 - -Run `revdepcheck::cloud_details(, "treefit")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─treefit::treefit(list(expression = star), "tree-like") at test-treefit.R:142:2 - 2. └─treefit:::calculate_eigenvectors_list(...) - 3. └─base::lapply(...) - 4. └─treefit (local) FUN(X[[i]], ...) - 5. └─treefit:::do_build_tree(original, target, build_tree) - 6. └─treefit:::calculate_mst(target) - 7. └─igraph::graph_from_adjacency_matrix(...) - 8. └─igraph:::graph.adjacency.dense(...) - - [ FAIL 5 | WARN 0 | SKIP 0 | PASS 7 ] - Error: Test failures - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘treefit.Rmd’ using rmarkdown - - Quitting from lines 100-105 [estimate-tree-like-data] (treefit.Rmd) - Error: processing vignette 'treefit.Rmd' failed with diagnostics: - could not find function ".igraph.status" - --- failed re-building ‘treefit.Rmd’ - - --- re-building ‘working-with-seurat.Rmd’ using rmarkdown - ... - ================================================== - downloaded 6.0 MB - - --- finished re-building ‘working-with-seurat.Rmd’ - - SUMMARY: processing the following file failed: - ‘treefit.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# treemap - -
- -* Version: 2.4-4 -* GitHub: NA -* Source code: https://github.com/cran/treemap -* Date/Publication: 2023-05-25 15:20:02 UTC -* Number of recursive dependencies: 62 - -Run `revdepcheck::cloud_details(, "treemap")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘treemap-Ex.R’ failed - The error most likely occurred in: - - > ### Name: treegraph - > ### Title: Create a tree graph - > ### Aliases: treegraph - > - > ### ** Examples - > - > data(business) - > treegraph(business, index=c("NACE1", "NACE2", "NACE3", "NACE4"), show.labels=FALSE) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: treegraph -> graph.data.frame -> make_empty_graph - Execution halted - ``` - -# VARDetect - -
- -* Version: 0.1.6 -* GitHub: NA -* Source code: https://github.com/cran/VARDetect -* Date/Publication: 2022-05-10 08:00:06 UTC -* Number of recursive dependencies: 85 - -Run `revdepcheck::cloud_details(, "VARDetect")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘VARDetect-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plot.VARDetect.result - > ### Title: Plotting the output from VARDetect.result class - > ### Aliases: plot.VARDetect.result - > - > ### ** Examples - > - > nob <- 1000 - ... - [1] 341 682 - [1] "second.brk.points:" - [1] 341 682 - no refit for the parameter estimation> plot(fit, display = "cp") - > plot(fit, display = "param") - > plot(fit, display = "granger", threshold = 0.2, layout = "nicely") - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plot ... plot_granger -> graph.adjacency -> graph.adjacency.dense - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.5Mb - sub-directories of 1Mb or more: - libs 6.0Mb - ``` - -# vennLasso +# gemtc
-* Version: 0.1.6 -* GitHub: https://github.com/jaredhuling/vennLasso -* Source code: https://github.com/cran/vennLasso -* Date/Publication: 2020-06-03 08:50:02 UTC -* Number of recursive dependencies: 51 +* Version: 1.0-1 +* GitHub: https://github.com/gertvv/gemtc +* Source code: https://github.com/cran/gemtc +* Date/Publication: 2021-05-14 23:20:02 UTC +* Number of recursive dependencies: 58 -Run `revdepcheck::cloud_details(, "vennLasso")` for more info +Run `revdepcheck::cloud_details(, "gemtc")` for more info
## Newly broken -* checking examples ... ERROR - ``` - Running examples in ‘vennLasso-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plotCoefs - > ### Title: plotting function to investigate estimated coefficients - > ### Aliases: plotCoefs - > - > ### ** Examples - > - > set.seed(123) - ... - > - > dat.sim <- genHierSparseData(ncats = 3, nvars = 25, nobs = 200) - > - > fit <- vennLasso(x = dat.sim$x, y = dat.sim$y, groups = dat.sim$group.ind) - > - > plotCoefs(fit, s = fit$lambda[22]) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: plotCoefs ... %in% -> visIgraphLayout -> -> make_empty_graph - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘using_the_vennLasso_package.Rmd’ using rmarkdown - A new version of TeX Live has been released. If you need to install or update any LaTeX packages, you have to upgrade TinyTeX with tinytex::reinstall_tinytex(repository = "illinois"). - - tlmgr: Local TeX Live (2022) is older than remote repository (2023). - Cross release updates are only supported with - update-tlmgr-latest(.sh/.exe) --update - See https://tug.org/texlive/upgrade.html for details. - Warning in system2("tlmgr", args, ...) : - ... - - Error: processing vignette 'using_the_vennLasso_package.Rmd' failed with diagnostics: - LaTeX failed to compile /tmp/workdir/vennLasso/new/vennLasso.Rcheck/vign_test/vennLasso/vignettes/using_the_vennLasso_package.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See using_the_vennLasso_package.log for more info. - --- failed re-building ‘using_the_vennLasso_package.Rmd’ - - SUMMARY: processing the following file failed: - ‘using_the_vennLasso_package.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -* checking installed package size ... NOTE - ``` - installed size is 36.1Mb - sub-directories of 1Mb or more: - libs 35.5Mb - ``` - -* checking LazyData ... NOTE +* checking tests ... ERROR ``` - 'LazyData' is specified without a 'data' directory + Running ‘test.R’ + Running the tests in ‘tests/test.R’ failed. + Last 13 lines of output: + 8. └─base::all.equal.list(target, current, ...) + 9. ├─base::all.equal(...) + 10. └─base::all.equal.default(...) + 11. └─base::all.equal.list(target, current, ...) + 12. └─base::attr.all.equal(target, current, ...) + 13. ├─base::length(target) + 14. └─igraph:::length.igraph(target) + 15. └─igraph::vcount(x) + 16. └─igraph:::ensure_igraph(graph) + 17. └─igraph::is_igraph(graph) + 18. └─igraph:::warn_version(graph) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 376 ] + Error: Test failures + Execution halted ``` -# VertexSimilarity +# leidenAlg
-* Version: 0.1 -* GitHub: NA -* Source code: https://github.com/cran/VertexSimilarity -* Date/Publication: 2016-01-24 21:37:10 -* Number of recursive dependencies: 7 +* Version: 1.0.5 +* GitHub: https://github.com/kharchenkolab/leidenAlg +* Source code: https://github.com/cran/leidenAlg +* Date/Publication: 2022-09-30 07:20:02 UTC +* Number of recursive dependencies: 68 -Run `revdepcheck::cloud_details(, "VertexSimilarity")` for more info +Run `revdepcheck::cloud_details(, "leidenAlg")` for more info
@@ -24484,88 +54,64 @@ Run `revdepcheck::cloud_details(, "VertexSimilarity")` for more info * checking examples ... ERROR ``` - Running examples in ‘VertexSimilarity-Ex.R’ failed + Running examples in ‘leidenAlg-Ex.R’ failed The error most likely occurred in: - > ### Name: VertexSimilarity - > ### Title: Vertex Similarity - > ### Aliases: VertexSimilarity + > ### Name: as.dendrogram.fakeCommunities + > ### Title: Returns pre-calculated dendrogram + > ### Aliases: as.dendrogram.fakeCommunities > > ### ** Examples > - > m <- matrix(c(1,0,0,0,0,1,1,1,1),ncol=3,nrow=3,byrow=TRUE) - > SimilarityMatrix <- VertexSimilarity(m,alpha=0.85) - Loading required namespace: igraph - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: VertexSimilarity -> -> graph.adjacency.dense + > rLeidenComm = suppressWarnings(rleiden.community(exampleGraph, n.cores=1)) + This graph was created by an old(er) igraph version. + Call upgrade_graph() on it to use with the current igraph version + For now we convert it on the fly... + Error in find_partition(graph, igraph::E(graph)$weight, resolution, n.iterations) : + REAL() can only be applied to a 'numeric', not a 'NULL' Execution halted ``` -## In both - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# vivainsights - -
- -* Version: 0.3.1 -* GitHub: NA -* Source code: https://github.com/cran/vivainsights -* Date/Publication: 2023-05-22 13:10:02 UTC -* Number of recursive dependencies: 98 - -Run `revdepcheck::cloud_details(, "vivainsights")` for more info - -
- -## Newly broken - -* checking examples ... ERROR +* checking tests ... ERROR ``` - Running examples in ‘vivainsights-Ex.R’ failed - The error most likely occurred in: - - > ### Name: tm_cooc - > ### Title: Analyse word co-occurrence in subject lines and return a network - > ### plot - > ### Aliases: tm_cooc - > - > ### ** Examples - > - > # Demo using a subset of `mt_data` - > mt_data %>% - + dplyr::slice(1:20) %>% - + tm_cooc(lmult = 0.01) - Selecting by n - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: %>% ... ggplot -> create_layout -> -> make_empty_graph - Execution halted + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + Backtrace: + ▆ + 1. ├─base::suppressWarnings(rleiden.community(exampleGraph, n.cores = 1)) at test_functions.R:19:8 + 2. │ └─base::withCallingHandlers(...) + 3. └─leidenAlg::rleiden.community(exampleGraph, n.cores = 1) + 4. └─sccore::plapply(...) + 5. └─base::lapply(...) + 6. └─leidenAlg (local) FUN(X[[i]], ...) + 7. └─leidenAlg::rleiden.community(...) + 8. └─leidenAlg::leiden.community(graph, resolution = res, ...) + 9. └─leidenAlg::find_partition(...) + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 3 ] + Error: Test failures + Execution halted ``` ## In both -* checking data for non-ASCII characters ... NOTE +* checking for GNU extensions in Makefiles ... NOTE ``` - Note: found 52 marked UTF-8 strings + GNU make is a SystemRequirements. ``` -# wdnet +# leidenbase
-* Version: 1.1.0 -* GitHub: NA -* Source code: https://github.com/cran/wdnet -* Date/Publication: 2023-05-17 10:10:02 UTC +* Version: 0.1.18 +* GitHub: https://github.com/cole-trapnell-lab/leidenbase +* Source code: https://github.com/cran/leidenbase +* Date/Publication: 2023-04-15 09:20:02 UTC * Number of recursive dependencies: 54 -Run `revdepcheck::cloud_details(, "wdnet")` for more info +Run `revdepcheck::cloud_details(, "leidenbase")` for more info
@@ -24573,20 +119,26 @@ Run `revdepcheck::cloud_details(, "wdnet")` for more info * checking examples ... ERROR ``` - Running examples in ‘wdnet-Ex.R’ failed + Running examples in ‘leidenbase-Ex.R’ failed The error most likely occurred in: - > ### Name: adj_to_wdnet - > ### Title: Creates a 'wdnet' object using an adjacency matrix - > ### Aliases: adj_to_wdnet + > ### Name: leiden_find_partition + > ### Title: Leiden find partition community detection function + > ### Aliases: leiden_find_partition > > ### ** Examples > - > adj <- matrix(c(0, 1, 2, 0), nrow = 2, ncol = 2, byrow = TRUE) - > adj_to_wdnet(adj = adj, directed = TRUE, weighted = FALSE) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: adj_to_wdnet ... adj_to_edgelist -> -> graph.adjacency.dense + > library(igraph) + ... + + > fpath <- system.file( 'testdata', 'igraph_n1500_edgelist.txt.gz', package = 'leidenbase' ) + > zfp <- gzfile(fpath) + > igraph <- read_graph( file = zfp, format='edgelist', n=1500 ) + > res <- leiden_find_partition(igraph=igraph, + + partition_type='CPMVertexPartition', + + resolution_parameter=1e-5) + Error in leiden_find_partition(igraph = igraph, partition_type = "CPMVertexPartition", : + REAL() can only be applied to a 'numeric', not a 'NULL' Execution halted ``` @@ -24595,43 +147,61 @@ Run `revdepcheck::cloud_details(, "wdnet")` for more info Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: - 5. └─igraph::graph_from_adjacency_matrix(...) - 6. └─igraph:::graph.adjacency.dense(...) - ── Error ('test-wdnet-igraph.R:4:3'): multiplication works ───────────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" + Error in `leidenbase::leiden_find_partition(igraph, partition_type = "RBConfigurationVertexPartition", + node_sizes = nodsiz, seed = 123456, resolution_parameter = 0.5)`: REAL() can only be applied to a 'numeric', not a 'NULL' + Backtrace: + ▆ + 1. └─leidenbase::leiden_find_partition(...) at test-leidenbase.R:224:2 + ── Error ('test-leidenbase.R:245:3'): modularity and significance return values ── + Error in `leidenbase::leiden_find_partition(igraph, partition_type = "CPMVertexPartition", + seed = 123456, resolution_parameter = 0.1)`: REAL() can only be applied to a 'numeric', not a 'NULL' Backtrace: ▆ - 1. └─wdnet::wdnet_to_igraph(netwk0) at test-wdnet-igraph.R:4:2 - 2. └─igraph::graph_from_edgelist(netwk$edgelist, directed = netwk$directed) - 3. └─igraph::make_graph(t(el), directed = directed) - 4. ├─base::do.call(old_graph, args) - 5. └─igraph (local) ``(``, directed = TRUE) + 1. └─leidenbase::leiden_find_partition(...) at test-leidenbase.R:245:2 - [ FAIL 5 | WARN 0 | SKIP 0 | PASS 16 ] + [ FAIL 11 | WARN 0 | SKIP 0 | PASS 6 ] Error: Test failures Execution halted ``` +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘leidenbase.Rmd’ using rmarkdown + + Quitting from lines 87-92 [unnamed-chunk-1] (leidenbase.Rmd) + Error: processing vignette 'leidenbase.Rmd' failed with diagnostics: + REAL() can only be applied to a 'numeric', not a 'NULL' + --- failed re-building ‘leidenbase.Rmd’ + + SUMMARY: processing the following file failed: + ‘leidenbase.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + ## In both * checking installed package size ... NOTE ``` - installed size is 9.3Mb + installed size is 19.1Mb sub-directories of 1Mb or more: - libs 9.0Mb + libs 18.8Mb ``` -# webtrackR +# nda
-* Version: 0.0.1 -* GitHub: https://github.com/schochastics/webtrackR -* Source code: https://github.com/cran/webtrackR -* Date/Publication: 2023-03-13 13:30:02 UTC -* Number of recursive dependencies: 40 +* Version: 0.1.6 +* GitHub: https://github.com/kzst/nda +* Source code: https://github.com/cran/nda +* Date/Publication: 2022-10-14 13:10:02 UTC +* Number of recursive dependencies: 81 -Run `revdepcheck::cloud_details(, "webtrackR")` for more info +Run `revdepcheck::cloud_details(, "nda")` for more info
@@ -24639,129 +209,76 @@ Run `revdepcheck::cloud_details(, "webtrackR")` for more info * checking examples ... ERROR ``` - Running examples in ‘webtrackR-Ex.R’ failed + Running examples in ‘nda-Ex.R’ failed The error most likely occurred in: - > ### Name: audience_incidence - > ### Title: Create incidence matrix for audience-outlet network - > ### Aliases: audience_incidence + > ### Name: biplot.nda + > ### Title: Biplot function for Network-based Dimensionality Reduction and + > ### Analysis (NDA) + > ### Aliases: biplot.nda + > ### Keywords: plot > > ### ** Examples + ... + > + > # Biplot function without feature selection > - > data("test_data") - > wt <- as.wt_dt(test_data) - > wt <- add_duration(wt) - > wt <- extract_domain(wt) - > audience_incidence(wt) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: audience_incidence -> -> make_empty_graph + > data("CrimesUSA1990.X") + > df<-CrimesUSA1990.X + > p<-ndr(df) + Error in find_partition(graph, igraph::E(graph)$weight, resolution, n.iterations) : + REAL() can only be applied to a 'numeric', not a 'NULL' + Calls: ndr -> -> find_partition Execution halted ``` -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Error ('test-audience_networks.R:6:3'): audience_incidence ────────────────── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. └─webtrackR::audience_incidence(wt) at test-audience_networks.R:6:2 - 2. └─igraph::graph_from_data_frame(el, directed = FALSE) - 3. └─igraph::make_empty_graph(n = 0, directed = directed) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 14 marked UTF-8 strings - ``` - -# whitechapelR +# netseg
-* Version: 0.3.0 -* GitHub: NA -* Source code: https://github.com/cran/whitechapelR -* Date/Publication: 2018-10-02 17:40:03 UTC -* Number of recursive dependencies: 47 +* Version: 1.0-1 +* GitHub: https://github.com/mbojan/netseg +* Source code: https://github.com/cran/netseg +* Date/Publication: 2022-08-25 12:10:06 UTC +* Number of recursive dependencies: 61 -Run `revdepcheck::cloud_details(, "whitechapelR")` for more info +Run `revdepcheck::cloud_details(, "netseg")` for more info
## Newly broken -* checking examples ... ERROR - ``` - Running examples in ‘whitechapelR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: show_board - > ### Title: Display game board representation - > ### Aliases: show_board - > - > ### ** Examples - > - > possibilities = start_round(64) - ... - > possibilities = take_a_step(possibilities,roads) - > possibilities = take_a_step(possibilities,roads,blocked=list(c(63,82),c(63,65))) - > possibilities = take_a_step(possibilities,alley) - > show_board(paths=possibilities,hideouts=NULL,roads,alley,node_locations) - Warning in v$color[as.numeric(names(tbl))] <- to_replace : - number of items to replace is not a multiple of replacement length - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: show_board -> -> make_empty_graph - Execution halted - ``` - * checking tests ... ERROR ``` Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: + Complete output: + > library(testthat) + > library(netseg) + > + > test_check("netseg") + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 73 ] + ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Error ('test_whitechapel.R:77:3'): Expect plot generates without errors ───── - Error in `.igraph.status("Make graph external pointer.\n")`: could not find function ".igraph.status" - Backtrace: - ▆ - 1. ├─testthat::expect_null(...) at test_whitechapel.R:77:2 - 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") - 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) - 4. └─whitechapelR::show_board(list(69), c(45, 46), roads, alley, node_locations) - 5. └─igraph::graph_from_data_frame(...) - 6. └─igraph::make_empty_graph(n = 0, directed = directed) + ── Failure ('test-smi.R:5:3'): SMI works ─────────────────────────────────────── + `smi(as.directed(WhiteKinship), "gender")` produced messages. - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 13 ] + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 73 ] Error: Test failures Execution halted ``` -# wpa +# SNscan
-* Version: 1.8.1 -* GitHub: https://github.com/microsoft/wpa -* Source code: https://github.com/cran/wpa -* Date/Publication: 2023-01-30 15:00:02 UTC -* Number of recursive dependencies: 121 +* Version: 1.0 +* GitHub: NA +* Source code: https://github.com/cran/SNscan +* Date/Publication: 2016-01-19 13:09:28 +* Number of recursive dependencies: 11 -Run `revdepcheck::cloud_details(, "wpa")` for more info +Run `revdepcheck::cloud_details(, "SNscan")` for more info
@@ -24769,98 +286,62 @@ Run `revdepcheck::cloud_details(, "wpa")` for more info * checking examples ... ERROR ``` - Running examples in ‘wpa-Ex.R’ failed + Running examples in ‘SNscan-Ex.R’ failed The error most likely occurred in: - > ### Name: network_describe - > ### Title: Uncover HR attributes which best represent a population for a - > ### Person to Person query - > ### Aliases: network_describe + > ### Name: network.scan + > ### Title: Network Scan Statistic + > ### Aliases: network.scan + > ### Keywords: scanning method > > ### ** Examples > - > # Simulate a P2P edge list - > sim_data <- p2p_data_sim() - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: p2p_data_sim ... as.data.frame -> -> ensure_igraph -> + > data(karate) + > + > ks=network.scan(g=karate,radius=3,attribute=NULL, + + model="pois.stat",pattern="structure") + Error in warn_version(graph) : + This graph was created by a now unsupported old igraph version. + Call upgrade_version() before using igraph functions on that object. + Calls: network.scan ... shortest.paths -> ensure_igraph -> is_igraph -> warn_version Execution halted ``` -# xgboost +# tidygraph
-* Version: 1.7.5.1 -* GitHub: https://github.com/dmlc/xgboost -* Source code: https://github.com/cran/xgboost -* Date/Publication: 2023-03-30 19:40:02 UTC -* Number of recursive dependencies: 107 +* Version: 1.2.3 +* GitHub: https://github.com/thomasp85/tidygraph +* Source code: https://github.com/cran/tidygraph +* Date/Publication: 2023-02-01 21:10:02 UTC +* Number of recursive dependencies: 77 -Run `revdepcheck::cloud_details(, "xgboost")` for more info +Run `revdepcheck::cloud_details(, "tidygraph")` for more info
## Newly broken -* checking examples ... ERROR - ``` - Running examples in ‘xgboost-Ex.R’ failed - The error most likely occurred in: - - > ### Name: xgb.ggplot.deepness - > ### Title: Plot model trees deepness - > ### Aliases: xgb.ggplot.deepness xgb.plot.deepness - > - > ### ** Examples - > - > - ... - [47] train-logloss:0.009265 - [48] train-logloss:0.008787 - [49] train-logloss:0.008370 - [50] train-logloss:0.007953 - > - > xgb.plot.deepness(bst) - Error in .igraph.status("Make graph external pointer.\n") : - could not find function ".igraph.status" - Calls: xgb.plot.deepness ... [ -> [.data.table -> -> make_empty_graph - Execution halted - ``` - * checking tests ... ERROR ``` Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: - ⠇ | 9 | update trees in an existing model [22:10:17] WARNING: src/gbm/gbtree.cc:84: DANGER AHEAD: You have manually specified `updater` parameter. The `tree_method` parameter will be ignored. Incorrect sequence of updaters will produce undefined behavior. For common uses, we recommend using `tree_method` parameter instead. - [22:10:17] WARNING: src/gbm/gbtree.cc:84: DANGER AHEAD: You have manually specified `updater` parameter. The `tree_method` parameter will be ignored. Incorrect sequence of updaters will produce undefined behavior. For common uses, we recommend using `tree_method` parameter instead. - - ⠏ | 20 | update trees in an existing model - ✔ | 22 | update trees in an existing model [0.4s] - - ══ Results ═════════════════════════════════════════════════════════════════════ - Duration: 45.3 s - - ── Skipped tests ────────────────────────────────────────────────────────────── - • empty test (1) + 15. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by) + 16. │ ├─base::withCallingHandlers(...) + 17. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns) + 18. │ └─mask$eval_all_mutate(quo) + 19. │ └─dplyr (local) eval() + 20. ├─tidygraph::group_leading_eigen(n_groups = 32) + 21. │ └─igraph::cut_at(group, no = n_groups) + 22. │ └─base::stop("Not a hierarchical communitity structure") + 23. └─base::.handleSimpleError(...) + 24. └─dplyr (local) h(simpleError(msg, call)) + 25. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) - [ FAIL 1 | WARN 2 | SKIP 1 | PASS 1325 ] + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 278 ] Error: Test failures Execution halted ``` -## In both - -* checking installed package size ... NOTE - ``` - installed size is 134.1Mb - sub-directories of 1Mb or more: - libs 133.2Mb - ``` - -* checking for GNU extensions in Makefiles ... NOTE - ``` - GNU make is a SystemRequirements. - ``` - From 32a7f802948120ec6fb29c2182f87ffd30e6b0d6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Kirill=20M=C3=BCller?= Date: Tue, 13 Jun 2023 05:50:40 +0200 Subject: [PATCH 6/8] Final results --- revdep/cran.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/revdep/cran.md b/revdep/cran.md index 7ebaec4067a..feaabbeac80 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,6 +1,6 @@ ## revdepcheck results -We checked 438 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. +We checked 440 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. * We saw 7 new problems * We failed to check 0 packages From fac5e6f4bf6d0eadbd41c6fc622cba293bd9d17b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Kirill=20M=C3=BCller?= Date: Tue, 13 Jun 2023 06:03:37 +0200 Subject: [PATCH 7/8] Revert "fix: Compatibility with tidyselect, mitigate #797" This reverts commit 1320b18453bac9ba0be413998e4410bf59abe0fe. --- R/community.R | 4 ---- 1 file changed, 4 deletions(-) diff --git a/R/community.R b/R/community.R index eff965942a8..4627d8cd847 100644 --- a/R/community.R +++ b/R/community.R @@ -1691,10 +1691,6 @@ cluster_leading_eigen <- function(graph, steps = -1, weights = NULL, res$vcount <- vcount(graph) res$membership <- res$membership + 1 res$cluster.merges <- res$cluster.merges + 1 - - # tidygraph compatibility - res$merges <- res$cluster.merges - res$history <- res$history + 1 class(res) <- "communities" res From c0aa474beb28cbc9dc2f3f12fc8cde9bf5ea6ab9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Kirill=20M=C3=BCller?= Date: Tue, 13 Jun 2023 08:36:39 +0200 Subject: [PATCH 8/8] tidygraph fixed --- revdep/README.md | 3 +-- revdep/cran.md | 7 ++----- revdep/problems.md | 38 -------------------------------------- 3 files changed, 3 insertions(+), 45 deletions(-) diff --git a/revdep/README.md b/revdep/README.md index 88be88e4bcc..aac941620ae 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,6 +1,6 @@ # Revdeps -## New problems (7) +## New problems (6) |package |version |error |warning |note | |:----------|:-------|:------|:-------|:----| @@ -10,5 +10,4 @@ |[nda](problems.md#nda)|0.1.6 |__+1__ | | | |[netseg](problems.md#netseg)|1.0-1 |__+1__ | | | |[SNscan](problems.md#snscan)|1.0 |__+1__ | | | -|[tidygraph](problems.md#tidygraph)|1.2.3 |__+1__ | | | diff --git a/revdep/cran.md b/revdep/cran.md index feaabbeac80..484ff096ea7 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,8 +1,8 @@ ## revdepcheck results -We checked 440 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. +We checked 7 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. - * We saw 7 new problems + * We saw 6 new problems * We failed to check 0 packages Issues with CRAN packages are summarised below. @@ -31,6 +31,3 @@ Issues with CRAN packages are summarised below. * SNscan checking examples ... ERROR -* tidygraph - checking tests ... ERROR - diff --git a/revdep/problems.md b/revdep/problems.md index 2dc1184fa38..a9208860476 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -307,41 +307,3 @@ Run `revdepcheck::cloud_details(, "SNscan")` for more info Execution halted ``` -# tidygraph - -
- -* Version: 1.2.3 -* GitHub: https://github.com/thomasp85/tidygraph -* Source code: https://github.com/cran/tidygraph -* Date/Publication: 2023-02-01 21:10:02 UTC -* Number of recursive dependencies: 77 - -Run `revdepcheck::cloud_details(, "tidygraph")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 15. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by) - 16. │ ├─base::withCallingHandlers(...) - 17. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns) - 18. │ └─mask$eval_all_mutate(quo) - 19. │ └─dplyr (local) eval() - 20. ├─tidygraph::group_leading_eigen(n_groups = 32) - 21. │ └─igraph::cut_at(group, no = n_groups) - 22. │ └─base::stop("Not a hierarchical communitity structure") - 23. └─base::.handleSimpleError(...) - 24. └─dplyr (local) h(simpleError(msg, call)) - 25. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 278 ] - Error: Test failures - Execution halted - ``` -