From a9c88529ebe57ec9ad8327c5ffe8e0b18ba79454 Mon Sep 17 00:00:00 2001 From: schochastics Date: Fri, 4 Apr 2025 15:17:42 +0200 Subject: [PATCH 1/5] fix NA replacement for labels --- R/plot.common.R | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/R/plot.common.R b/R/plot.common.R index 754e9560aba..027560da811 100644 --- a/R/plot.common.R +++ b/R/plot.common.R @@ -542,9 +542,14 @@ i.parse.plot.params <- function(graph, params) { } } if (any(is.na(p[[type]][[name]]))) { - cli::cli_warn("{type} attribute {name} contains NAs. Replacing with default value {i.default.values[[type]][[name]] + if (name != "label") { + cli::cli_warn("{type} attribute {name} contains NAs. Replacing with default value {i.default.values[[type]][[name]] }") - p[[type]][[name]][is.na(p[[type]][[name]])] <- i.default.values[[type]][[name]] + p[[type]][[name]][is.na(p[[type]][[name]])] <- i.default.values[[type]][[name]] + } else { + cli::cli_warn("{type} attribute {name} contains NAs. Replacing with empty string") + p[[type]][[name]][is.na(p[[type]][[name]])] <- "" + } } return(ret()) } From 5354835314d990630dc792144d8990a2b304ff81 Mon Sep 17 00:00:00 2001 From: schochastics Date: Fri, 4 Apr 2025 15:46:13 +0200 Subject: [PATCH 2/5] fix case where parameter is function --- R/plot.common.R | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/R/plot.common.R b/R/plot.common.R index 027560da811..b9a2707a2b7 100644 --- a/R/plot.common.R +++ b/R/plot.common.R @@ -541,14 +541,16 @@ i.parse.plot.params <- function(graph, params) { return(ret()) } } - if (any(is.na(p[[type]][[name]]))) { - if (name != "label") { - cli::cli_warn("{type} attribute {name} contains NAs. Replacing with default value {i.default.values[[type]][[name]] + if (!is.function(p[[type]][[name]])) { + if (any(is.na(p[[type]][[name]]))) { + if (name != "label") { + cli::cli_warn("{type} attribute {name} contains NAs. Replacing with default value {i.default.values[[type]][[name]] }") - p[[type]][[name]][is.na(p[[type]][[name]])] <- i.default.values[[type]][[name]] - } else { - cli::cli_warn("{type} attribute {name} contains NAs. Replacing with empty string") - p[[type]][[name]][is.na(p[[type]][[name]])] <- "" + p[[type]][[name]][is.na(p[[type]][[name]])] <- i.default.values[[type]][[name]] + } else { + cli::cli_warn("{type} attribute {name} contains NAs. Replacing with empty string") + p[[type]][[name]][is.na(p[[type]][[name]])] <- "" + } } } return(ret()) From 1bc0b06f0499a60c77fc9619da6ea7b4f110911c Mon Sep 17 00:00:00 2001 From: schochastics Date: Fri, 4 Apr 2025 16:00:59 +0200 Subject: [PATCH 3/5] dont warn for labels --- R/plot.common.R | 1 - 1 file changed, 1 deletion(-) diff --git a/R/plot.common.R b/R/plot.common.R index b9a2707a2b7..f6cb15c3fe9 100644 --- a/R/plot.common.R +++ b/R/plot.common.R @@ -548,7 +548,6 @@ i.parse.plot.params <- function(graph, params) { }") p[[type]][[name]][is.na(p[[type]][[name]])] <- i.default.values[[type]][[name]] } else { - cli::cli_warn("{type} attribute {name} contains NAs. Replacing with empty string") p[[type]][[name]][is.na(p[[type]][[name]])] <- "" } } From fbb740c960a0901edf11ed6809a1876e4993237f Mon Sep 17 00:00:00 2001 From: schochastics Date: Fri, 4 Apr 2025 16:13:21 +0200 Subject: [PATCH 4/5] added default arrow.mode --- R/plot.common.R | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/R/plot.common.R b/R/plot.common.R index f6cb15c3fe9..24f59288444 100644 --- a/R/plot.common.R +++ b/R/plot.common.R @@ -593,7 +593,8 @@ i.get.arrow.mode <- function(graph, arrow.mode = NULL) { ">" = 2, "->" = 2, "<>" = 3, - "<->" = 3 + "<->" = 3, + 0 ) } ) From 04b944ddb9a091fe6cf03480b8b9392e2c7af5ed Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Kirill=20M=C3=BCller?= Date: Fri, 4 Apr 2025 16:54:13 +0200 Subject: [PATCH 5/5] Winning! --- revdep/README.md | 16 +- revdep/cran.md | 34 +-- revdep/problems.md | 592 ++------------------------------------------- 3 files changed, 19 insertions(+), 623 deletions(-) diff --git a/revdep/README.md b/revdep/README.md index 4f9ff1e47a4..09c739a30c2 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -8,31 +8,21 @@ |datapack |1.4.1 |1 | | | |streamDAG |? | | | | -## New problems (23) +## New problems (13) -|package |version |error |warning |note | -|:-------------|:-------|:------|:-------|:----| -|[alakazam](problems.md#alakazam)|1.3.0 |__+1__ | |1 | -|[arulesViz](problems.md#arulesviz)|1.5.3 |__+1__ | | | +|package |version |error |warning |note | +|:------------|:-------|:------|:-------|:----| |[ccTensor](problems.md#cctensor)|1.0.2 |__+1__ | |2 | |[corpustools](problems.md#corpustools)|0.5.1 |__+1__ | |2 | -|[discourseGT](problems.md#discoursegt)|1.2.0 |__+1__ | | | |[dosearch](problems.md#dosearch)|1.0.11 |__+1__ | |1 | |[GMPro](problems.md#gmpro)|0.1.0 |__+2__ | |1 | -|[gsbm](problems.md#gsbm)|0.2.2 |__+1__ | |1 | |[incidentally](problems.md#incidentally)|1.0.2 |__+1__ | | | |[klassR](problems.md#klassr)|1.0.2 |__+1__ | |1 | |[manynet](problems.md#manynet)|1.3.2 |__+1__ | |3 | |[MetaNet](problems.md#metanet)|0.1.2 |__+1__ | | | -|[multivariance](problems.md#multivariance)|2.4.1 |__+1__ | | | |[mwcsr](problems.md#mwcsr)|0.1.9 |__+2__ | |1 | -|[nett](problems.md#nett)|1.0.0 |__+1__ | |1 | -|[POSetR](problems.md#posetr)|1.1.4 |__+1__ | |1 | |[remify](problems.md#remify)|3.2.8 |__+1__ | |1 | |[SEMID](problems.md#semid)|0.4.1 |__+2__ | | | -|[sglasso](problems.md#sglasso)|1.2.6 |__+1__ | | | -|[simdata](problems.md#simdata)|0.4.1 |__+1__ | | | |[ssifs](problems.md#ssifs)|1.0.4 |__+2__ | | | |[tilemaps](problems.md#tilemaps)|0.2.0 |__+2__ | |1 | -|[wpa](problems.md#wpa)|1.9.1 |__+1__ | | | diff --git a/revdep/cran.md b/revdep/cran.md index ee13425e7b6..e635997c8b7 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,8 +1,8 @@ ## revdepcheck results -We checked 27 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. +We checked 26 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. - * We saw 23 new problems + * We saw 13 new problems * We failed to check 3 packages Issues with CRAN packages are summarised below. @@ -10,21 +10,12 @@ Issues with CRAN packages are summarised below. ### New problems (This reports the first line of each new failure) -* alakazam - checking re-building of vignette outputs ... ERROR - -* arulesViz - checking examples ... ERROR - * ccTensor checking examples ... ERROR * corpustools checking examples ... ERROR -* discourseGT - checking tests ... ERROR - * dosearch checking tests ... ERROR @@ -32,9 +23,6 @@ Issues with CRAN packages are summarised below. checking examples ... ERROR checking tests ... ERROR -* gsbm - checking re-building of vignette outputs ... ERROR - * incidentally checking re-building of vignette outputs ... ERROR @@ -47,19 +35,10 @@ Issues with CRAN packages are summarised below. * MetaNet checking examples ... ERROR -* multivariance - checking examples ... ERROR - * mwcsr checking examples ... ERROR checking tests ... ERROR -* nett - checking re-building of vignette outputs ... ERROR - -* POSetR - checking examples ... ERROR - * remify checking tests ... ERROR @@ -67,12 +46,6 @@ Issues with CRAN packages are summarised below. checking examples ... ERROR checking tests ... ERROR -* sglasso - checking examples ... ERROR - -* simdata - checking re-building of vignette outputs ... ERROR - * ssifs checking examples ... ERROR checking re-building of vignette outputs ... ERROR @@ -81,9 +54,6 @@ Issues with CRAN packages are summarised below. checking examples ... ERROR checking re-building of vignette outputs ... ERROR -* wpa - checking examples ... ERROR - ### Failed to check * bnlearn (NA) diff --git a/revdep/problems.md b/revdep/problems.md index 68888d06fb9..7ca00a8a73d 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1,196 +1,3 @@ -# alakazam - -
- -* Version: 1.3.0 -* GitHub: NA -* Source code: https://github.com/cran/alakazam -* Date/Publication: 2023-09-30 01:12:40 UTC -* Number of recursive dependencies: 119 - -Run `revdepcheck::cloud_details(, "alakazam")` for more info - -
- -## Newly broken - -* checking re-building of vignette outputs ... ERROR - ``` - Error(s) in re-building vignettes: - --- re-building ‘AminoAcids-Vignette.Rmd’ using rmarkdown - --- finished re-building ‘AminoAcids-Vignette.Rmd’ - - --- re-building ‘Diversity-Vignette.Rmd’ using rmarkdown - --- finished re-building ‘Diversity-Vignette.Rmd’ - - --- re-building ‘Fastq-Vignette.Rmd’ using rmarkdown - --- finished re-building ‘Fastq-Vignette.Rmd’ - - --- re-building ‘Files-Vignette.Rmd’ using rmarkdown - --- finished re-building ‘Files-Vignette.Rmd’ - - --- re-building ‘GeneUsage-Vignette.Rmd’ using rmarkdown - --- finished re-building ‘GeneUsage-Vignette.Rmd’ - - --- re-building ‘Lineage-Vignette.Rmd’ using rmarkdown - - Quitting from Lineage-Vignette.Rmd:149-165 [unnamed-chunk-7] - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - - Error in `paste0()`: - ! cannot coerce type 'closure' to vector of type 'character' - --- - Backtrace: - x - 1. +-base::plot(...) - 2. +-base::plot(...) - 3. +-igraph::plot.igraph(...) - 4. | \-igraph (local) params("vertex", "label") - 5. | \-cli::cli_warn("{type} attribute {name} contains NAs. Replacing with default value {i.default.values[[type]][[name]]\n }") - 6. | +-rlang::warn(format_warning(message, .envir = .envir), ...) - 7. | | \-rlang:::validate_signal_args(...) - 8. | \-cli::format_warning(message, .envir = .envir) - 9. | \-cli::cli_fmt(...) - 10. | \-cli:::cli__fmt(rec, collapse, strip_newline) - 11. | +-base::do.call(app[[msg$type]], msg$args) - 12. | \-cli (local) ``(text = ``, id = "cli-151-3", class = NULL) - 13. | \-cli:::clii_bullets(app, text, id, class) - 14. | \-base::lapply(...) - 15. | \-cli (local) FUN(X[[i]], ...) - 16. | \-app$text(text[[i]]) - 17. | \-cli:::clii_text(app, text) - 18. | \-app$xtext(text) - 19. | \-cli:::clii__xtext(...) - 20. | \-app$inline(text, .list = .list) - 21. | \-cli:::clii__inline(app, text, .list = .list) - 22. | \-base::lapply(...) - 23. | \-cli (local) FUN(X[[i]], ...) - 24. | \-cli:::glue(...) - 25. \-cli (local) ``("v7") - 26. +-.transformer(expr, .envir) %||% character() - 27. \-cli (local) .transformer(expr, .envir) - 28. +-cli:::inline_collapse(...) - 29. | \-cli::ansi_collapse(...) - 30. | \-cli:::collapse_both_ends(x, sep, sep2, last, trunc, width, ellipsis) - 31. \-cli:::inline_generic(app, val, style = style) - 32. \-base::paste0(before, x, after) - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - - Error: processing vignette 'Lineage-Vignette.Rmd' failed with diagnostics: - cannot coerce type 'closure' to vector of type 'character' - --- failed re-building ‘Lineage-Vignette.Rmd’ - - --- re-building ‘Topology-Vignette.Rmd’ using rmarkdown - --- finished re-building ‘Topology-Vignette.Rmd’ - - SUMMARY: processing the following file failed: - ‘Lineage-Vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -## In both - -* checking Rd files ... NOTE - ``` - checkRd: (-1) buildPhylipLineage.Rd:61: Lost braces; missing escapes or markup? - 61 | names with the format {"Inferred1", "Inferred2", ...}. - | ^ - ``` - -# arulesViz - -
- -* Version: 1.5.3 -* GitHub: https://github.com/mhahsler/arulesViz -* Source code: https://github.com/cran/arulesViz -* Date/Publication: 2024-04-26 09:20:02 UTC -* Number of recursive dependencies: 124 - -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: associations2igraph - > ### Title: Convert rules or itemsets into a graph - > ### Aliases: associations2igraph saveAsGraph graph igraph tidygraph - > ### Keywords: file - > - > ### ** Examples - > - > - > data("Groceries") - > rules <- apriori(Groceries, parameter = list(support = 0.01, confidence = 0.5)) - Apriori - - Parameter specification: - confidence minval smax arem aval originalSupport maxtime support minlen - 0.5 0.1 1 none FALSE TRUE 5 0.01 1 - maxlen target ext - 10 rules TRUE - - Algorithmic control: - filter tree heap memopt load sort verbose - 0.1 TRUE TRUE FALSE TRUE 2 TRUE - - Absolute minimum support count: 98 - - set item appearances ...[0 item(s)] done [0.00s]. - set transactions ...[169 item(s), 9835 transaction(s)] done [0.00s]. - sorting and recoding items ... [88 item(s)] done [0.00s]. - creating transaction tree ... done [0.00s]. - checking subsets of size 1 2 3 4 done [0.00s]. - writing ... [15 rule(s)] done [0.00s]. - creating S4 object ... done [0.00s]. - > - > # convert rules into a graph with rules as nodes - > library("igraph") - - Attaching package: ‘igraph’ - - The following object is masked from ‘package:arules’: - - union - - The following objects are masked from ‘package:stats’: - - decompose, spectrum - - The following object is masked from ‘package:base’: - - union - - > g <- associations2igraph(rules) - > g - IGRAPH ff25a0a DN-B 27 45 -- - + attr: name (v/c), label (v/c), index (v/n), type (v/n), support - | (v/n), confidence (v/n), coverage (v/n), lift (v/n), count (v/n) - + edges from ff25a0a (vertex names): - [1] 27 ->assoc1 30 ->assoc1 23 ->assoc2 26 ->assoc2 - [5] 23 ->assoc3 55 ->assoc3 30 ->assoc4 31 ->assoc4 - [9] 23 ->assoc5 31 ->assoc5 16 ->assoc6 23 ->assoc6 - [13] 14 ->assoc7 20 ->assoc7 15 ->assoc8 20 ->assoc8 - [17] 15 ->assoc9 20 ->assoc9 15 ->assoc10 30 ->assoc10 - [21] 20 ->assoc11 30 ->assoc11 20 ->assoc12 30 ->assoc12 - [25] 20 ->assoc13 56 ->assoc13 20 ->assoc14 56 ->assoc14 - + ... omitted several edges - > - > plot(g) - Error in paste0(before, x, after) : - cannot coerce type 'closure' to vector of type 'character' - Calls: plot ... ansi_collapse -> collapse_both_ends -> inline_generic -> paste0 - Execution halted - ``` - # ccTensor
@@ -340,58 +147,6 @@ Run `revdepcheck::cloud_details(, "corpustools")` for more info Note: found 438 marked UTF-8 strings ``` -# discourseGT - -
- -* Version: 1.2.0 -* GitHub: NA -* Source code: https://github.com/cran/discourseGT -* Date/Publication: 2023-07-19 07:20:02 UTC -* Number of recursive dependencies: 128 - -Run `revdepcheck::cloud_details(, "discourseGT")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > # This file is part of the standard setup for testthat. - > # It is recommended that you do not modify it. - > # - > # Where should you do additional test configuration? - > # Learn more about the roles of various files in: - > # * https://r-pkgs.org/tests.html - > # * https://testthat.r-lib.org/reference/test_package.html#special-files - > - > library(testthat) - > library(discourseGT) - > - > test_check("discourseGT") - [ FAIL 5 | WARN 14 | SKIP 0 | PASS 30 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Failure ('test-basicPlot.R:12:3'): basicPlot works ────────────────────────── - `basicPlot(ginp, graph_selection_input = 0)` produced warnings. - ── Failure ('test-basicPlot.R:15:3'): basicPlot works ────────────────────────── - `basicPlot(ginp, graph_selection_input = 1)` produced warnings. - ── Failure ('test-basicPlot.R:18:3'): basicPlot works ────────────────────────── - `basicPlot(ginp, graph_selection_input = 2)` produced warnings. - ── Failure ('test-basicPlot.R:21:3'): basicPlot works ────────────────────────── - `basicPlot(...)` produced warnings. - ── Failure ('test-basicPlot.R:27:3'): basicPlot works ────────────────────────── - `basicPlot(ginp, graph_selection_input = 0, scaledEdgeLines = FALSE)` produced warnings. - - [ FAIL 5 | WARN 14 | SKIP 0 | PASS 30 ] - Error: Test failures - Execution halted - ``` - # dosearch
@@ -643,52 +398,6 @@ Run `revdepcheck::cloud_details(, "GMPro")` for more info 'LazyData' is specified without a 'data' directory ``` -# gsbm - -
- -* Version: 0.2.2 -* GitHub: NA -* Source code: https://github.com/cran/gsbm -* Date/Publication: 2022-09-20 08:16:14 UTC -* Number of recursive dependencies: 105 - -Run `revdepcheck::cloud_details(, "gsbm")` for more info - -
- -## Newly broken - -* checking re-building of vignette outputs ... ERROR - ``` - Error(s) in re-building vignettes: - --- re-building ‘PrimarySchool.Rmd’ using rmarkdown - ``` - -## In both - -* checking Rd files ... NOTE - ``` - checkRd: (-1) crossval.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly - checkRd: (-1) crossval.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly - checkRd: (-1) crossval.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly - checkRd: (-1) crossval.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly - checkRd: (-1) crossval.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly - checkRd: (-1) crossval.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly - checkRd: (-1) gsbm_mcgd.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly - checkRd: (-1) gsbm_mcgd.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly - checkRd: (-1) gsbm_mcgd.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly - checkRd: (-1) gsbm_mcgd.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly - checkRd: (-1) gsbm_mcgd.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly - checkRd: (-1) gsbm_mcgd.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly - checkRd: (-1) gsbm_mcgd_parallel.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly - checkRd: (-1) gsbm_mcgd_parallel.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly - checkRd: (-1) gsbm_mcgd_parallel.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly - checkRd: (-1) gsbm_mcgd_parallel.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly - checkRd: (-1) gsbm_mcgd_parallel.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly - checkRd: (-1) gsbm_mcgd_parallel.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly - ``` - # incidentally
@@ -784,7 +493,7 @@ Run `revdepcheck::cloud_details(, "klassR")` for more info * GitHub: https://github.com/stocnet/manynet * Source code: https://github.com/cran/manynet * Date/Publication: 2024-11-05 20:50:02 UTC -* Number of recursive dependencies: 144 +* Number of recursive dependencies: 145 Run `revdepcheck::cloud_details(, "manynet")` for more info @@ -909,63 +618,6 @@ Run `revdepcheck::cloud_details(, "MetaNet")` for more info Execution halted ``` -# 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: 32 - -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 - > y = coins(N,2) - > x = cbind(y,y,y) - > - > ds = dependence.structure(x,structure.type = "clustered") - - 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 - - 2-tuples x 36: max. multivariance: 200.000; min. p-value (unadjusted): 0 - New cluster detected. Not all vertices are in one cluster. - 2-tuples x 3: max. multivariance: 0.504; min. p-value (unadjusted): 0.477634223802113 - 3-tuples x 1: max. multivariance: 199.392; min. p-value (unadjusted): 0 - All vertices are in one cluster. - - total number of tests: 40, groups of tests: 3 - - Same structure for any significance level in (0,1) - - Conservative estimate of the type I error probability: 0.143 - > plot(clean.graph(ds$graph)) - Error in paste0(before, x, after) : - cannot coerce type 'closure' to vector of type 'character' - Calls: plot ... ansi_collapse -> collapse_both_ends -> inline_generic -> paste0 - Execution halted - ``` - # mwcsr
@@ -1067,87 +719,6 @@ Run `revdepcheck::cloud_details(, "mwcsr")` for more info libs 10.5Mb ``` -# 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: 96 - -Run `revdepcheck::cloud_details(, "nett")` for more info - -
- -## Newly broken - -* checking re-building of vignette outputs ... ERROR - ``` - Error(s) in re-building vignettes: - --- re-building ‘Community_Detection.Rmd’ using rmarkdown - ``` - -## In both - -* checking Rd files ... NOTE - ``` - checkRd: (-1) spec_clust.Rd:33: Lost braces; missing escapes or markup? - 33 | A label vector of size n x 1 with elements in {1,2,...,K} - | ^ - ``` - -# POSetR - -
- -* Version: 1.1.4 -* GitHub: NA -* Source code: https://github.com/cran/POSetR -* Date/Publication: 2023-12-04 15:20:15 UTC -* Number of recursive dependencies: 14 - -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 vapply(.x, .f, .mold, ..., USE.NAMES = FALSE) : - values must be length 1, - but FUN(X[[1]]) result is length 0 - Calls: plot ... i.get.arrow.mode -> map_dbl -> .rlang_purrr_map_mold -> vapply - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 19.3Mb - sub-directories of 1Mb or more: - libs 19.2Mb - ``` - # remify
@@ -1207,7 +778,7 @@ Run `revdepcheck::cloud_details(, "remify")` for more info test-rehshape.R............... 24 tests OK test-rehshape.R............... 24 tests OK test-rehshape.R............... 25 tests OK - test-rehshape.R............... 26 tests OK 2.8s + test-rehshape.R............... 26 tests OK 2.9s test-remify-error-messages.R.. 1 tests OK test-remify-error-messages.R.. 1 tests OK @@ -1422,7 +993,7 @@ Run `revdepcheck::cloud_details(, "remify")` for more info test-remify-methods.R......... 112 tests 10 fails test-remify-methods.R......... 112 tests 10 fails test-remify-methods.R......... 112 tests 10 fails - test-remify-methods.R......... 113 tests 10 fails 10.9s + test-remify-methods.R......... 113 tests 10 fails 11.9s test-remify-warning-messages.R 0 tests test-remify-warning-messages.R 0 tests @@ -1492,7 +1063,7 @@ Run `revdepcheck::cloud_details(, "remify")` for more info test-remify-warning-messages.R 29 tests OK test-remify-warning-messages.R 29 tests OK test-remify-warning-messages.R 30 tests OK - test-remify-warning-messages.R 31 tests OK 0.6s + test-remify-warning-messages.R 31 tests OK 0.7s test-remify.R................. 0 tests test-remify.R................. 1 tests OK @@ -1628,46 +1199,46 @@ Run `revdepcheck::cloud_details(, "remify")` for more info ----- FAILED[xcpt]: test-remify-methods.R<349--349> call| expect_silent(plot(x = out)) diff| Execution was not silent. A warning was thrown with message - diff| 'is.na() applied to non-(list or vector) of type 'closure'' + diff| 'vertex attribute frame.color contains NAs. Replacing with default value black' ----- FAILED[xcpt]: test-remify-methods.R<350--350> call| expect_silent(plot(x = out, breaks = NULL, palette = NULL, n_intervals = NULL, call| --> rev = NULL, actors = NULL, pch.degree = NULL, igraph.edge.color = NULL, call| --> igraph.vertex.color = NULL)) diff| Execution was not silent. A warning was thrown with message - diff| 'is.na() applied to non-(list or vector) of type 'closure'' + diff| 'vertex attribute frame.color contains NAs. Replacing with default value black' ----- FAILED[xcpt]: test-remify-methods.R<351--351> call| expect_silent(plot(x = out, pch.degree = -1)) diff| Execution was not silent. A warning was thrown with message - diff| 'is.na() applied to non-(list or vector) of type 'closure'' + diff| 'vertex attribute frame.color contains NAs. Replacing with default value black' ----- FAILED[xcpt]: test-remify-methods.R<352--352> call| expect_silent(plot(x = out, igraph.edge.color = "#000000000", call| --> igraph.vertex.color = "#000000000")) diff| Execution was not silent. A warning was thrown with message - diff| 'is.na() applied to non-(list or vector) of type 'closure'' + diff| 'vertex attribute frame.color contains NAs. Replacing with default value black' ----- FAILED[xcpt]: test-remify-methods.R<353--353> call| expect_silent(plot(x = out, igraph.edge.color = "magenta", igraph.vertex.color = "cyan4")) diff| Execution was not silent. A warning was thrown with message - diff| 'is.na() applied to non-(list or vector) of type 'closure'' + diff| 'vertex attribute frame.color contains NAs. Replacing with default value black' ----- FAILED[xcpt]: test-remify-methods.R<354--354> call| expect_silent(plot(x = out, n_intervals = 5)) diff| Execution was not silent. A warning was thrown with message - diff| 'is.na() applied to non-(list or vector) of type 'closure'' + diff| 'vertex attribute frame.color contains NAs. Replacing with default value black' ----- FAILED[xcpt]: test-remify-methods.R<355--355> call| expect_silent(plot(x = out, actors = attr(out, "dictionary")$actors$actorName[1:5])) diff| Execution was not silent. A warning was thrown with message - diff| 'is.na() applied to non-(list or vector) of type 'closure'' + diff| 'vertex attribute frame.color contains NAs. Replacing with default value black' ----- FAILED[xcpt]: test-remify-methods.R<362--362> call| expect_silent(plot(x = out)) diff| Execution was not silent. A warning was thrown with message - diff| 'is.na() applied to non-(list or vector) of type 'closure'' + diff| 'vertex attribute frame.color contains NAs. Replacing with default value black' ----- FAILED[xcpt]: test-remify-methods.R<363--363> call| expect_silent(plot(x = out, n_intervals = 5)) diff| Execution was not silent. A warning was thrown with message - diff| 'is.na() applied to non-(list or vector) of type 'closure'' + diff| 'vertex attribute frame.color contains NAs. Replacing with default value black' ----- FAILED[xcpt]: test-remify-methods.R<364--364> call| expect_silent(plot(x = out, actors = attr(out, "dictionary")$actors$actorName[1:5])) diff| Execution was not silent. A warning was thrown with message - diff| 'is.na() applied to non-(list or vector) of type 'closure'' + diff| 'vertex attribute frame.color contains NAs. Replacing with default value black' Error: 10 out of 254 tests failed Execution halted ``` @@ -2013,71 +1584,6 @@ Run `revdepcheck::cloud_details(, "SEMID")` for more info Execution halted ``` -# sglasso - -
- -* Version: 1.2.6 -* GitHub: NA -* Source code: https://github.com/cran/sglasso -* Date/Publication: 2023-12-03 08:40:02 UTC -* Number of recursive dependencies: 11 - -Run `revdepcheck::cloud_details(, "sglasso")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘sglasso-Ex.R’ failed - The error most likely occurred in: - - > ### Name: gplot.fglasso - > ### Title: Plotting Sparse Factorial Dynamic Gaussian Graphical Model - > ### Aliases: gplot.fglasso - > ### Keywords: models - > - > ### ** Examples - > - > N <- 50 - > tp <- 3 - > p <- 3 - > X <- matrix(rnorm(N * p * tp), N, tp * p) - > S <- crossprod(X) / N - > model <- list(lag0 = c(s = "c", n = "ut"), lag1 = c(s = "t", n = "t")) - > out.fglasso <- fglasso(S = S, model = model, tp = tp, p = p) - > gplot(out.fglasso, rhoid = 50, sub.tp1 = "First graph", - + sub.tp2 = "Second graph") - Error in paste0(before, x, after) : - cannot coerce type 'closure' to vector of type 'character' - Calls: gplot ... ansi_collapse -> collapse_both_ends -> inline_generic -> paste0 - Execution halted - ``` - -# simdata - -
- -* Version: 0.4.1 -* GitHub: https://github.com/matherealize/simdata -* Source code: https://github.com/cran/simdata -* Date/Publication: 2024-12-03 23:10:07 UTC -* Number of recursive dependencies: 92 - -Run `revdepcheck::cloud_details(, "simdata")` for more info - -
- -## Newly broken - -* checking re-building of vignette outputs ... ERROR - ``` - Error(s) in re-building vignettes: - --- re-building ‘Demo.Rmd’ using rmarkdown - ``` - # ssifs
@@ -2243,73 +1749,3 @@ Run `revdepcheck::cloud_details(, "tilemaps")` for more info All declared Imports should be used. ``` -# wpa - -
- -* Version: 1.9.1 -* GitHub: https://github.com/microsoft/wpa -* Source code: https://github.com/cran/wpa -* Date/Publication: 2024-06-06 13:20:02 UTC -* Number of recursive dependencies: 120 - -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_p2p - > ### Title: Perform network analysis with the person-to-person query - > ### Aliases: network_p2p - > - > ### ** Examples - > - > p2p_df <- p2p_data_sim(dim = 1, size = 100) - > - > # default - ggraph visual - > network_p2p(data = p2p_df, style = "ggraph") - > - > # return vertex table - > network_p2p(data = p2p_df, return = "table") - # A tibble: 6 × 2 - Organization n - - 1 Org A 14 - 2 Org B 14 - 3 Org C 15 - 4 Org D 11 - 5 Org E 12 - 6 Org F 34 - > - > # return vertex table with community detection - > network_p2p(data = p2p_df, community = "leiden", return = "table") - # A tibble: 100 × 3 - Organization cluster n - - 1 Org A 12 1 - 2 Org A 25 1 - 3 Org A 32 1 - 4 Org A 38 1 - 5 Org A 44 1 - 6 Org A 51 1 - 7 Org A 58 1 - 8 Org A 6 1 - 9 Org A 65 1 - 10 Org A 71 1 - # ℹ 90 more rows - > - > # leiden - igraph style with custom resolution parameters - > network_p2p(data = p2p_df, community = "leiden", comm_args = list("resolution" = 0.1)) - Error in vapply(.x, .f, .mold, ..., USE.NAMES = FALSE) : - values must be length 1, - but FUN(X[[1]]) result is length 0 - Calls: network_p2p ... i.get.arrow.mode -> map_dbl -> .rlang_purrr_map_mold -> vapply - Execution halted - ``` -