CRAN Package Check Results for Package massiveGST

Last updated on 2025-03-16 00:49:45 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.2.3 5.96 65.90 71.86 ERROR
r-devel-linux-x86_64-debian-gcc 1.2.3 4.04 48.63 52.67 ERROR
r-devel-linux-x86_64-fedora-clang 1.2.3 109.48 ERROR
r-devel-linux-x86_64-fedora-gcc 1.2.3 145.96 ERROR
r-devel-macos-arm64 1.2.3 96.00 OK
r-devel-macos-x86_64 1.2.3 200.00 OK
r-devel-windows-x86_64 1.2.3 8.00 215.00 223.00 NOTE
r-patched-linux-x86_64 1.2.3 5.24 62.47 67.71 ERROR
r-release-linux-x86_64 1.2.3 5.78 61.62 67.40 ERROR
r-release-macos-arm64 1.2.3 86.00 OK
r-release-macos-x86_64 1.2.3 149.00 OK
r-release-windows-x86_64 1.2.3 9.00 76.00 85.00 ERROR
r-oldrel-macos-arm64 1.2.3 OK
r-oldrel-macos-x86_64 1.2.3 173.00 OK
r-oldrel-windows-x86_64 1.2.3 9.00 224.00 233.00 ERROR

Additional issues

M1mac

Check Details

Version: 1.2.3
Check: Rd cross-references
Result: NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: get_geneSets_from_msigdbr.Rd: msigdbr plot.mGST.Rd: visOptions, visNetwork save_as_xls.Rd: WriteXLS Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64

Version: 1.2.3
Check: examples
Result: ERROR Running examples in ‘massiveGST-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: massiveORT > ### Title: A wrapper to fisher.test to get over representation analysis of > ### gene sets. > ### Aliases: massiveORT > > ### ** Examples > > library(massiveGST) > > # get the gene profile > fname <- system.file("extdata", package="massiveGST") > fname <- file.path(fname, "pre_ranked_list.txt") > geneProfile <- get_geneProfile(fname) > geneList <- names(head(geneProfile, 1000)) > > # get the gene-sets > geneSets <- get_geneSets_from_msigdbr(category = "C5", subcategory = "CC", what = "gene_symbol") msigdbr: R package version 10.0.0 The 'msigdbdf' package must be installed to access the full dataset. > geneSets <- geneSets[1:250] > > # run the function > ans <- massiveORT(geneList, geneSets) greater Error in data.frame(row.names = names(gene_sets), collection, universe_size = length(universe), : row names contain missing values Calls: massiveORT -> data.frame Execution halted Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.2.3
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘vignette.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/massiveGST.Rcheck/vign_test/massiveGST/vignettes/vignette_files/figure-html/bar-plot-1.png 3840x2496 pixels, 3x8 bits/pixel, RGB Input IDAT size = 555855 bytes Input file size = 556737 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 458793 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 458793 Output IDAT size = 458793 bytes (97062 bytes decrease) Output file size = 458871 bytes (97866 bytes = 17.58% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/massiveGST.Rcheck/vign_test/massiveGST/vignettes/vignette_files/figure-html/unnamed-chunk-17-1.png 3840x2496 pixels, 3x8 bits/pixel, RGB Input IDAT size = 262007 bytes Input file size = 262457 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 223212 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 223212 Output IDAT size = 223212 bytes (38795 bytes decrease) Output file size = 223290 bytes (39167 bytes = 14.92% decrease) Quitting from lines 199-237 [unnamed-chunk-18] (vignette.Rmd) Error: processing vignette 'vignette.Rmd' failed with diagnostics: replacement has 1 row, data has 0 --- failed re-building ‘vignette.Rmd’ SUMMARY: processing the following file failed: ‘vignette.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.2.3
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘vignette.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/massiveGST.Rcheck/vign_test/massiveGST/vignettes/vignette_files/figure-html/bar-plot-1.png 3840x2496 pixels, 3x8 bits/pixel, RGB Input IDAT size = 555855 bytes Input file size = 556737 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 458793 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 458793 Output IDAT size = 458793 bytes (97062 bytes decrease) Output file size = 458871 bytes (97866 bytes = 17.58% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/massiveGST.Rcheck/vign_test/massiveGST/vignettes/vignette_files/figure-html/unnamed-chunk-17-1.png 3840x2496 pixels, 3x8 bits/pixel, RGB Input IDAT size = 262007 bytes Input file size = 262457 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 223212 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 223212 Output IDAT size = 223212 bytes (38795 bytes decrease) Output file size = 223290 bytes (39167 bytes = 14.92% decrease) Quitting from lines 199-237 [unnamed-chunk-18] (vignette.Rmd) Error: processing vignette 'vignette.Rmd' failed with diagnostics: replacement has 1 row, data has 0 --- failed re-building ‘vignette.Rmd’ SUMMARY: processing the following file failed: ‘vignette.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.2.3
Check: examples
Result: ERROR Running examples in ‘massiveGST-Ex.R’ failed The error most likely occurred in: > ### Name: massiveORT > ### Title: A wrapper to fisher.test to get over representation analysis of > ### gene sets. > ### Aliases: massiveORT > > ### ** Examples > > library(massiveGST) > > # get the gene profile > fname <- system.file("extdata", package="massiveGST") > fname <- file.path(fname, "pre_ranked_list.txt") > geneProfile <- get_geneProfile(fname) > geneList <- names(head(geneProfile, 1000)) > > # get the gene-sets > geneSets <- get_geneSets_from_msigdbr(category = "C5", subcategory = "CC", what = "gene_symbol") msigdbr: R package version 10.0.0 The 'msigdbdf' package must be installed to access the full dataset. > geneSets <- geneSets[1:250] > > # run the function > ans <- massiveORT(geneList, geneSets) greater Error in data.frame(row.names = names(gene_sets), collection, universe_size = length(universe), : row names contain missing values Calls: massiveORT -> data.frame Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-windows-x86_64, r-oldrel-windows-x86_64

Version: 1.2.3
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘vignette.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-clang/massiveGST.Rcheck/vign_test/massiveGST/vignettes/vignette_files/figure-html/bar-plot-1.png 3840x2496 pixels, 3x8 bits/pixel, RGB Input IDAT size = 551717 bytes Input file size = 552599 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 442350 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 442350 Output IDAT size = 442350 bytes (109367 bytes decrease) Output file size = 442428 bytes (110171 bytes = 19.94% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/massiveGST.Rcheck/vign_test/massiveGST/vignettes/vignette_files/figure-html/unnamed-chunk-17-1.png 3840x2496 pixels, 3x8 bits/pixel, RGB Input IDAT size = 260307 bytes Input file size = 260757 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 214387 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 214387 Output IDAT size = 214387 bytes (45920 bytes decrease) Output file size = 214465 bytes (46292 bytes = 17.75% decrease) Quitting from lines 199-237 [unnamed-chunk-18] (vignette.Rmd) Error: processing vignette 'vignette.Rmd' failed with diagnostics: replacement has 1 row, data has 0 --- failed re-building ‘vignette.Rmd’ SUMMARY: processing the following file failed: ‘vignette.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.2.3
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘vignette.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-devel/massiveGST.Rcheck/vign_test/massiveGST/vignettes/vignette_files/figure-html/bar-plot-1.png 3840x2496 pixels, 3x8 bits/pixel, RGB Input IDAT size = 551717 bytes Input file size = 552599 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 442350 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 442350 Output IDAT size = 442350 bytes (109367 bytes decrease) Output file size = 442428 bytes (110171 bytes = 19.94% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/massiveGST.Rcheck/vign_test/massiveGST/vignettes/vignette_files/figure-html/unnamed-chunk-17-1.png 3840x2496 pixels, 3x8 bits/pixel, RGB Input IDAT size = 260307 bytes Input file size = 260757 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 214387 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 214387 Output IDAT size = 214387 bytes (45920 bytes decrease) Output file size = 214465 bytes (46292 bytes = 17.75% decrease) Quitting from lines 199-237 [unnamed-chunk-18] (vignette.Rmd) Error: processing vignette 'vignette.Rmd' failed with diagnostics: replacement has 1 row, data has 0 --- failed re-building ‘vignette.Rmd’ SUMMARY: processing the following file failed: ‘vignette.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.2.3
Check: whether package can be installed
Result: WARN Found the following significant warnings: Rd warning: get_geneSets_from_msigdbr.Rd:28: missing link ‘msigdbr’ Rd warning: plot.mGST.Rd:29: missing link ‘visOptions’ Rd warning: plot.mGST.Rd:30: missing link ‘visOptions’ Rd warning: plot.mGST.Rd:45: missing link ‘visNetwork’ Rd warning: plot.mGST.Rd:45: missing link ‘visOptions’ Rd warning: save_as_xls.Rd:20: missing link ‘WriteXLS’ Flavor: r-patched-linux-x86_64

Version: 1.2.3
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘vignette.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/massiveGST.Rcheck/vign_test/massiveGST/vignettes/vignette_files/figure-html/bar-plot-1.png 3840x2496 pixels, 3x8 bits/pixel, RGB Input IDAT size = 555855 bytes Input file size = 556737 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 458793 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 458793 Output IDAT size = 458793 bytes (97062 bytes decrease) Output file size = 458871 bytes (97866 bytes = 17.58% decrease) ** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/massiveGST.Rcheck/vign_test/massiveGST/vignettes/vignette_files/figure-html/unnamed-chunk-17-1.png 3840x2496 pixels, 3x8 bits/pixel, RGB Input IDAT size = 262007 bytes Input file size = 262457 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 223212 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 223212 Output IDAT size = 223212 bytes (38795 bytes decrease) Output file size = 223290 bytes (39167 bytes = 14.92% decrease) Quitting from lines 199-237 [unnamed-chunk-18] (vignette.Rmd) Error: processing vignette 'vignette.Rmd' failed with diagnostics: replacement has 1 row, data has 0 --- failed re-building ‘vignette.Rmd’ SUMMARY: processing the following file failed: ‘vignette.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-patched-linux-x86_64

Version: 1.2.3
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘vignette.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/massiveGST.Rcheck/vign_test/massiveGST/vignettes/vignette_files/figure-html/bar-plot-1.png 3840x2496 pixels, 3x8 bits/pixel, RGB Input IDAT size = 555855 bytes Input file size = 556737 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 458793 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 458793 Output IDAT size = 458793 bytes (97062 bytes decrease) Output file size = 458871 bytes (97866 bytes = 17.58% decrease) ** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/massiveGST.Rcheck/vign_test/massiveGST/vignettes/vignette_files/figure-html/unnamed-chunk-17-1.png 3840x2496 pixels, 3x8 bits/pixel, RGB Input IDAT size = 262007 bytes Input file size = 262457 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 223212 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 223212 Output IDAT size = 223212 bytes (38795 bytes decrease) Output file size = 223290 bytes (39167 bytes = 14.92% decrease) Quitting from lines 199-237 [unnamed-chunk-18] (vignette.Rmd) Error: processing vignette 'vignette.Rmd' failed with diagnostics: replacement has 1 row, data has 0 --- failed re-building ‘vignette.Rmd’ SUMMARY: processing the following file failed: ‘vignette.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-release-linux-x86_64

Version: 1.2.3
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building 'vignette.Rmd' using rmarkdown ERROR: cannot open D:\temp\2025_03_13_01_50_00_8052\RtmpMf5h7X/WriteXLS/1.csv . No such file or directory Quitting from lines 199-237 [unnamed-chunk-18] (vignette.Rmd) Error: processing vignette 'vignette.Rmd' failed with diagnostics: replacement has 1 row, data has 0 --- failed re-building 'vignette.Rmd' SUMMARY: processing the following file failed: 'vignette.Rmd' Error: Vignette re-building failed. Execution halted Flavor: r-release-windows-x86_64

Version: 1.2.3
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building 'vignette.Rmd' using rmarkdown ERROR: cannot open D:\temp\2025_03_14_01_50_00_28055\RtmpE3oBj4/WriteXLS/1.csv . No such file or directory Quitting from lines 199-237 [unnamed-chunk-18] (vignette.Rmd) Error: processing vignette 'vignette.Rmd' failed with diagnostics: replacement has 1 row, data has 0 --- failed re-building 'vignette.Rmd' SUMMARY: processing the following file failed: 'vignette.Rmd' Error: Vignette re-building failed. Execution halted Flavor: r-oldrel-windows-x86_64