• using R version 4.4.3 (2025-02-28 ucrt)
• using platform: x86_64-w64-mingw32
• R was compiled by     gcc.exe (GCC) 13.3.0     GNU Fortran (GCC) 13.3.0
• running under: Windows Server 2022 x64 (build 20348)
• 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 hidden files and directories ... OK
• checking for portable file names ... OK
• checking whether package 'massiveGST' can be installed ... 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 ... [1s] OK
• checking whether the package can be loaded with stated dependencies ... [1s] OK
• checking whether the package can be unloaded cleanly ... [1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s] OK
• checking whether the namespace can be unloaded cleanly ... [1s] OK
• checking loading without being on the library search path ... [1s] 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 ... [5s] OK
• checking Rd files ... [1s] OK
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• checking for unstated dependencies in examples ... OK
• checking installed files from 'inst/doc' ... OK
• checking files in 'vignettes' ... OK
• checking examples ... [4s] 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 ... [12s] 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
• checking PDF version of manual ... [21s] OK
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• DONE

Status: 2 ERRORs