• using R Under development (unstable) (2026-01-25 r89330)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 21.1.8 (1+b1)     Debian flang version 21.1.8 (1+b1)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘iSubGen/DESCRIPTION’ ... OK
• this is package ‘iSubGen’ version ‘1.0.4’
• checking CRAN incoming feasibility ... [1s/2s] 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 serialization versions ... OK
• checking whether package ‘iSubGen’ can be installed ... OK See the install log for details.
• 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 ... [3s/4s] OK
• checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
• checking whether the package can be unloaded cleanly ... [3s/3s] OK
• checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
• checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
• checking loading without being on the library search path ... [3s/3s] 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 ... [15s/20s] OK
• checking Rd files ... [0s/0s] 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 sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [4s/6s] ERROR Running examples in ‘iSubGen-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: write.scaling.factors > ### Title: Write scaling factors to file > ### Aliases: write.scaling.factors > > ### ** Examples > > > # load the aberration profiles for three data types > example.molecular.data.dir <- paste0(path.package('iSubGen'),'/exdata/'); > molecular.data <- list(); > for (i in c('cna','snv','methy')) { + molecular.data[[i]] <- load.molecular.aberration.data( + paste0(example.molecular.data.dir,i,'_profiles.txt'), + patients = c(paste0('EP00',1:9), paste0('EP0',10:30)) + ); + } > > # calculate scaling factors for all three data types > scaling.factors <- calculate.scaling(molecular.data); > > # save the scaling factors to file > write.scaling.factors(scaling.factors, example.molecular.data.dir); Warning in file(file, ifelse(append, "a", "w")) :   cannot open file '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/iSubGen/exdata/cna_gene_recenter.txt': Read-only file system Error in file(file, ifelse(append, "a", "w")) :   cannot open the connection Calls: write.scaling.factors -> write.table -> file Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [12s/15s] OK
• checking PDF version of manual ... [4s/6s] OK
• checking HTML version of manual ... [1s/1s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR