* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/HiCociety.Rcheck’
* using R Under development (unstable) (2026-03-07 r89567)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)
    GNU Fortran (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)
* running under: Fedora Linux 42 (Workstation Edition)
* using session charset: UTF-8
* current time: 2026-03-07 15:06:23 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘HiCociety/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiCociety’ version ‘0.1.39’
* 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 ‘HiCociety’ can be installed ... [86s/81s] OK
* used C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’
* used C++ compiler: ‘g++ (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’
* checking package 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 ... [23s/23s] OK
* checking whether the package can be loaded with stated dependencies ... [22s/23s] OK
* checking whether the package can be unloaded cleanly ... [23s/23s] OK
* checking whether the namespace can be loaded with stated dependencies ... [22s/22s] OK
* checking whether the namespace can be unloaded cleanly ... [23s/23s] OK
* checking loading without being on the library search path ... [24s/25s] 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 ... [96s/97s] 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 line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... [27s/27s] ERROR
Running examples in ‘HiCociety-Ex.R’ failed
The error most likely occurred in:

> ### Name: add_Genes
> ### Title: Add gene information
> ### Aliases: add_Genes
> 
> ### ** Examples
> 
> modulefile = system.file('extdata','mouse_naiveCD4T_Vahedi_short.rds',
+ package = 'HiCocietyExample')
> mycom = readRDS(modulefile)
> mycom$ModuleSummary = add_Genes(mycom$ModuleSummary,
+ 'TxDb.Mmusculus.UCSC.mm10.knownGene')
Error in add_Genes(mycom$ModuleSummary, "TxDb.Mmusculus.UCSC.mm10.knownGene") : 
  Package TxDb.Mmusculus.UCSC.mm10.knownGene not found
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: 1 ERROR
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/HiCociety.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 10:13.63, 580.68 + 31.99