CRAN Package Check Results for Maintainer ‘Mao Tian <mtian at sbpdiscovery.org>’

Last updated on 2026-02-01 01:49:22 CET.

Package	ERROR	OK
iSubGen	6	7

Package iSubGen

Current CRAN status: ERROR: 6, OK: 7

Version: 1.0.4
Check: examples
Result: 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 Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0.4
Check: examples
Result: 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-gcc/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 Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.0.4
Check: examples
Result: 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-patched-gcc/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 Flavor: r-patched-linux-x86_64

Version: 1.0.4
Check: examples
Result: 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-release-gcc/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 Flavor: r-release-linux-x86_64

Version: 1.0.4
Check: package dependencies
Result: ERROR Package required but not available: ‘ConsensusClusterPlus’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. Flavors: r-release-macos-arm64, r-oldrel-macos-arm64