Last updated on 2025-03-19 08:52:48 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.3 | 5.86 | 67.38 | 73.24 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.2.3 | 4.40 | 49.75 | 54.15 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.2.3 | 105.92 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.2.3 | 113.26 | 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 | 7.00 | 94.00 | 101.00 | ERROR | |
| r-patched-linux-x86_64 | 1.2.3 | 6.04 | 62.98 | 69.02 | ERROR | |
| r-release-linux-x86_64 | 1.2.3 | 5.73 | 61.66 | 67.39 | 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 | 75.00 | 84.00 | 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 | 85.00 | 94.00 | 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 vignette.Rmd:198-237 [unnamed-chunk-18]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `$<-.data.frame`:
! replacement has 1 row, data has 0
---
Backtrace:
▆
1. ├─base::plot(ans, gene_sets = geneSets, as.network = TRUE)
2. └─massiveGST:::plot.mGST(ans, gene_sets = geneSets, as.network = TRUE)
3. └─massiveGST:::plot.network(...)
4. ├─base::`$<-`(`*tmp*`, "color", value = `<chr>`)
5. └─base::`$<-.data.frame`(`*tmp*`, "color", value = `<chr>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 vignette.Rmd:198-237 [unnamed-chunk-18]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `$<-.data.frame`:
! replacement has 1 row, data has 0
---
Backtrace:
▆
1. ├─base::plot(ans, gene_sets = geneSets, as.network = TRUE)
2. └─massiveGST:::plot.mGST(ans, gene_sets = geneSets, as.network = TRUE)
3. └─massiveGST:::plot.network(...)
4. ├─base::`$<-`(`*tmp*`, "color", value = `<chr>`)
5. └─base::`$<-.data.frame`(`*tmp*`, "color", value = `<chr>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 10.0.1
Warning: The `subcategory` argument of `msigdbr()` is deprecated as of msigdbr 10.0.0.
ℹ Please use the `subcollection` argument instead.
ℹ The deprecated feature was likely used in the massiveGST package.
Please report the issue to the authors.
The 'msigdbdf' package must be installed to access the full dataset.
Please run the following command to install the 'msigdbdf' package:
install.packages('msigdbdf', repos = 'https://igordot.r-universe.dev')
> 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
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 vignette.Rmd:198-237 [unnamed-chunk-18]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `$<-.data.frame`:
! replacement has 1 row, data has 0
---
Backtrace:
▆
1. ├─base::plot(ans, gene_sets = geneSets, as.network = TRUE)
2. └─massiveGST:::plot.mGST(ans, gene_sets = geneSets, as.network = TRUE)
3. └─massiveGST:::plot.network(...)
4. ├─base::`$<-`(`*tmp*`, "color", value = `<chr>`)
5. └─base::`$<-.data.frame`(`*tmp*`, "color", value = `<chr>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 vignette.Rmd:198-237 [unnamed-chunk-18]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `$<-.data.frame`:
! replacement has 1 row, data has 0
---
Backtrace:
▆
1. ├─base::plot(ans, gene_sets = geneSets, as.network = TRUE)
2. └─massiveGST:::plot.mGST(ans, gene_sets = geneSets, as.network = TRUE)
3. └─massiveGST:::plot.network(...)
4. ├─base::`$<-`(`*tmp*`, "color", value = `<chr>`)
5. └─base::`$<-.data.frame`(`*tmp*`, "color", value = `<chr>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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: 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-windows-x86_64, 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
ERROR: cannot open D:\temp\2025_03_17_01_26_54_17999\Rtmp8Wr4pA/WriteXLS/1.csv
. No such file or directory
Quitting from vignette.Rmd:198-237 [unnamed-chunk-18]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `$<-.data.frame`:
! replacement has 1 row, data has 0
---
Backtrace:
▆
1. ├─base::plot(ans, gene_sets = geneSets, as.network = TRUE)
2. └─massiveGST:::plot.mGST(ans, gene_sets = geneSets, as.network = TRUE)
3. └─massiveGST:::plot.network(...)
4. ├─base::`$<-`(`*tmp*`, "color", value = `<chr>`)
5. └─base::`$<-.data.frame`(`*tmp*`, "color", value = `<chr>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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-windows-x86_64
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 vignette.Rmd:198-237 [unnamed-chunk-18]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `$<-.data.frame`:
! replacement has 1 row, data has 0
---
Backtrace:
▆
1. ├─base::plot(ans, gene_sets = geneSets, as.network = TRUE)
2. └─massiveGST:::plot.mGST(ans, gene_sets = geneSets, as.network = TRUE)
3. └─massiveGST:::plot.network(...)
4. ├─base::`$<-`(`*tmp*`, "color", value = `<chr>`)
5. └─base::`$<-.data.frame`(`*tmp*`, "color", value = `<chr>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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_17_01_50_00_22525\RtmpOunZET/WriteXLS/1.csv
. No such file or directory
Quitting from vignette.Rmd:198-237 [unnamed-chunk-18]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `$<-.data.frame`:
! replacement has 1 row, data has 0
---
Backtrace:
▆
1. ├─base::plot(ans, gene_sets = geneSets, as.network = TRUE)
2. └─massiveGST:::plot.mGST(ans, gene_sets = geneSets, as.network = TRUE)
3. └─massiveGST:::plot.network(...)
4. ├─base::`$<-`(`*tmp*`, "color", value = `<chr>`)
5. └─base::`$<-.data.frame`(`*tmp*`, "color", value = `<chr>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
replacement has 1 row, data has 0
--- failed re-building 'vignette.Rmd'
SUMMARY: processing the following file failed:
'vignette.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-windows-x86_64
Version: 1.2.3
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'vignette.Rmd' using rmarkdown
ERROR: cannot open D:\temp\2025_03_17_01_50_00_22525\RtmpQ7qam6/WriteXLS/1.csv
. No such file or directory
Quitting from vignette.Rmd:198-237 [unnamed-chunk-18]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `$<-.data.frame`:
! replacement has 1 row, data has 0
---
Backtrace:
▆
1. ├─base::plot(ans, gene_sets = geneSets, as.network = TRUE)
2. └─massiveGST:::plot.mGST(ans, gene_sets = geneSets, as.network = TRUE)
3. └─massiveGST:::plot.network(...)
4. ├─base::`$<-`(`*tmp*`, "color", value = `<chr>`)
5. └─base::`$<-.data.frame`(`*tmp*`, "color", value = `<chr>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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