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 |
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