* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/GeneNMF.Rcheck’
* using R Under development (unstable) (2024-04-19 r86451)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-13 (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘GeneNMF/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneNMF’ version ‘0.4.0’
* package encoding: UTF-8
* 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 ‘GeneNMF’ can be installed ... [59s/115s] 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 ... [15s/24s] OK
* checking whether the package can be loaded with stated dependencies ... [13s/20s] OK
* checking whether the package can be unloaded cleanly ... [13s/20s] OK
* checking whether the namespace can be loaded with stated dependencies ... [13s/21s] OK
* checking whether the namespace can be unloaded cleanly ... [14s/25s] OK
* checking loading without being on the library search path ... [14s/22s] 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 ... [60s/79s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [13s/17s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [51s/68s] ERROR
Running examples in ‘GeneNMF-Ex.R’ failed
The error most likely occurred in:

> ### Name: runGSEA
> ### Title: Run Gene set enrichment analysis
> ### Aliases: runGSEA
> 
> ### ** Examples
> 
> data(sampleObj)
> geneset <- c("BANK1","CD22","CD79A","CD19","IGHD","IGHG3","IGHM")
> gsea_res <- runGSEA(geneset, universe=rownames(sampleObj), category = "C8")
Error: Function 'runGSEA' requires the 'fgsea' and 'msigdbr' packages.
            Please install them.
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [8s/11s] 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: 1 ERROR
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/GeneNMF.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 11:16.02, 416.78 + 34.23