* using log directory ‘/srv/hornik/tmp/CRAN_pretest/massiveGST.Rcheck’ * using R Under development (unstable) (2025-03-24 r88048) * 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 ‘1.2.4’ * checking CRAN incoming feasibility ... [4s/8s] OK * 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 ... [3s/3s] OK * 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... NOTE Mismatches for apparent methods not registered: plot: function(x, ...) plot.network: function(ttable, gs, eps, similarity_threshold, manipulation, autoResize, use.clustering, edges.color, ...) See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [4s/4s] OK * checking Rd files ... [0s/0s] 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 ... [2s/2s] 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 10.0.1 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 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [12s/12s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘vignette.Rmd’ using rmarkdown ** Processing: /srv/hornik/tmp/CRAN_pretest/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: /srv/hornik/tmp/CRAN_pretest/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 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 = ``) 5. └─base::`$<-.data.frame`(`*tmp*`, "color", value = ``) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs, 2 NOTEs