• using R Under development (unstable) (2025-03-12 r87947)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 20.1.0     flang version 20.1.0
• running under: Fedora Linux 40 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘massiveGST/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘massiveGST’ version ‘1.2.3’
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘massiveGST’ can be installed ... [10s/17s] OK See the install log for details.
• checking installed package size ... OK
• checking package directory ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [15s/25s] OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [6s/10s] 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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [22s/30s] 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
• checking PDF version of manual ... OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 2 ERRORs