• using R version 4.5.2 Patched (2026-01-31 r89382)
• using platform: aarch64-apple-darwin20
• R was compiled by     Apple clang version 16.0.0 (clang-1600.0.26.6)     GNU Fortran (GCC) 14.2.0
• running under: macOS Ventura 13.7.8
• using session charset: UTF-8
• 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 ... INFO Packages suggested but not available for checking:   'TxDb.Hsapiens.UCSC.hg38.knownGene',   'TxDb.Mmusculus.UCSC.mm10.knownGene'
• 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 ... [14s/22s] OK See the install log for details.
• used C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
• used C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
• used SDK: ‘MacOSX11.3.1.sdk’
• checking installed package size ... INFO   installed size is 6.6Mb
• 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 ... [4s/4s] OK
• checking whether the package can be loaded with stated dependencies ... [4s/4s] OK
• checking whether the package can be unloaded cleanly ... [4s/4s] OK
• checking whether the namespace can be loaded with stated dependencies ... [4s/4s] OK
• checking whether the namespace can be unloaded cleanly ... [4s/4s] OK
• checking loading without being on the library search path ... [4s/4s] 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/9s] OK
• checking Rd files ... [0s/0s] OK
• checking Rd metadata ... 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 compiled code ... OK
• checking examples ... [4s/4s] 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 ... [2s/2s] OK
• DONE Status: 1 ERROR
• using check arguments '--no-clean-on-error '