• using R Under development (unstable) (2023-11-30 r85651)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-13 (Debian 13.2.0-5) 13.2.0     GNU Fortran (Debian 13.2.0-5) 13.2.0
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘PSCBS/DESCRIPTION’ ... OK
• this is package ‘PSCBS’ version ‘0.66.0’
• 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 ‘PSCBS’ 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 R files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [1s/1s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the package can be unloaded cleanly ... [1s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the namespace can be unloaded cleanly ... [0s/1s] OK
• checking loading without being on the library search path ... [1s/1s] OK
• checking whether startup messages can be suppressed ... [1s/1s] 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 ... [44s/71s] OK
• checking Rd files ... [1s/2s] 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 ... NOTE Documented arguments not in \usage in Rd file 'estimateDeltaLOH.PairedPSCBS.Rd':   ‘scale’ Documented arguments not in \usage in Rd file 'getLocusData.AbstractCBS.Rd':   ‘splitters’ Documented arguments not in \usage in Rd file 'getSegments.AbstractCBS.Rd':   ‘simplify’ ‘splitters’ Documented arguments not in \usage in Rd file 'mergeTwoSegments.AbstractCBS.Rd':   ‘left’ ‘update’ ‘verbose’ Documented arguments not in \usage in Rd file 'plotTracks.PairedPSCBS.Rd':   ‘x’ ‘tracks’ ‘scatter’ ‘calls’ ‘pch’ ‘col’ ‘cex’ ‘changepoints’   ‘grid’ ‘quantiles’ ‘xlim’ ‘Clim’ ‘Blim’ ‘xScale’ ‘add’ ‘subplots’   ‘verbose’ Documented arguments not in \usage in Rd file 'updateMeansTogether.AbstractCBS.Rd':   ‘idxList’ ‘verbose’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.
• 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 ... [6s/9s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [79s/151s] OK   Running ‘PairedPSCBS,boot.R’ [3s/6s]   Running ‘findLargeGaps.R’ [1s/1s]   Running ‘randomSeed.R’ [1s/2s]   Running ‘segmentByCBS,calls.R’ [0s/1s]   Running ‘segmentByCBS,futures.R’ [3s/12s]   Running ‘segmentByCBS,median.R’ [2s/4s]   Running ‘segmentByCBS,prune.R’ [2s/3s]   Running ‘segmentByCBS,report.R’ [0s/1s]   Running ‘segmentByCBS,shiftTCN.R’ [13s/18s]   Running ‘segmentByCBS,weights.R’ [4s/7s]   Running ‘segmentByCBS.R’ [4s/8s]   Running ‘segmentByNonPairedPSCBS,medianDH.R’ [3s/5s]   Running ‘segmentByPairedPSCBS,DH.R’ [4s/6s]   Running ‘segmentByPairedPSCBS,calls.R’ [6s/9s]   Running ‘segmentByPairedPSCBS,futures.R’ [10s/28s]   Running ‘segmentByPairedPSCBS,noNormalBAFs.R’ [4s/6s]   Running ‘segmentByPairedPSCBS,report.R’ [0s/1s]   Running ‘segmentByPairedPSCBS,seqOfSegmentsByDP.R’ [8s/13s]   Running ‘segmentByPairedPSCBS.R’ [8s/16s]   Running ‘weightedQuantile.R’ [2s/4s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking re-building of vignette outputs ... [67s/118s] OK
• checking PDF version of manual ... [11s/23s] OK
• checking HTML version of manual ... [4s/10s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 NOTE