• using R Under development (unstable) (2025-03-10 r87922)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 19.1.7 (1+b1)     Debian flang-new version 19.1.7 (1+b1)
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• 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 ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [2s/2s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the package can be unloaded cleanly ... [1s/2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the namespace can be unloaded cleanly ... [1s/2s] OK
• checking loading without being on the library search path ... [1s/2s] 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 ... [9s/13s] OK
• checking Rd files ... [0s/1s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... 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.
• 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 ... [3s/5s] 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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [20s/29s] 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
• checking PDF version of manual ... [4s/6s] OK
• checking HTML version of manual ... [0s/1s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs, 1 NOTE