diff --git a/R/plot.common.R b/R/plot.common.R
index 754e9560aba..24f59288444 100644
--- a/R/plot.common.R
+++ b/R/plot.common.R
@@ -541,10 +541,16 @@ i.parse.plot.params <- function(graph, params) {
return(ret())
}
}
- 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 (!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]]
+ p[[type]][[name]][is.na(p[[type]][[name]])] <- i.default.values[[type]][[name]]
+ } else {
+ p[[type]][[name]][is.na(p[[type]][[name]])] <- ""
+ }
+ }
}
return(ret())
}
@@ -587,7 +593,8 @@ i.get.arrow.mode <- function(graph, arrow.mode = NULL) {
">" = 2,
"->" = 2,
"<>" = 3,
- "<->" = 3
+ "<->" = 3,
+ 0
)
}
)
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 [0;32mOK[0m
test-rehshape.R............... 24 tests [0;32mOK[0m
test-rehshape.R............... 25 tests [0;32mOK[0m
- test-rehshape.R............... 26 tests [0;32mOK[0m [0;34m2.8s[0m
+ test-rehshape.R............... 26 tests [0;32mOK[0m [0;34m2.9s[0m
test-remify-error-messages.R.. 1 tests [0;32mOK[0m
test-remify-error-messages.R.. 1 tests [0;32mOK[0m
@@ -1422,7 +993,7 @@ Run `revdepcheck::cloud_details(, "remify")` for more info
test-remify-methods.R......... 112 tests [0;31m10 fails[0m
test-remify-methods.R......... 112 tests [0;31m10 fails[0m
test-remify-methods.R......... 112 tests [0;31m10 fails[0m
- test-remify-methods.R......... 113 tests [0;31m10 fails[0m [0;34m10.9s[0m
+ test-remify-methods.R......... 113 tests [0;31m10 fails[0m [0;34m11.9s[0m
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 [0;32mOK[0m
test-remify-warning-messages.R 29 tests [0;32mOK[0m
test-remify-warning-messages.R 30 tests [0;32mOK[0m
- test-remify-warning-messages.R 31 tests [0;32mOK[0m [0;34m0.6s[0m
+ test-remify-warning-messages.R 31 tests [0;32mOK[0m [0;34m0.7s[0m
test-remify.R................. 0 tests
test-remify.R................. 1 tests [0;32mOK[0m
@@ -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
- ```
-