- using R Under development (unstable) (2024-12-25 r87466)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
Debian clang version 19.1.6 (1)
Debian flang-new version 19.1.6 (1)
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘PSCBS/DESCRIPTION’ ... OK
- this is package ‘PSCBS’ version ‘0.67.0’
- 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 code 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 ... [1s/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/58s] OK
- checking Rd files ... [1s/2s] OK
- checking Rd metadata ... OK
- checking Rd line widths ... OK
- checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
as.CBS.DNAcopy.Rd: DNAcopy
as.DNAcopy.CBS.Rd: DNAcopy
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
- 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 ... [6s/10s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [81s/121s] OK
Running ‘PairedPSCBS,boot.R’ [3s/5s]
Running ‘findLargeGaps.R’ [1s/1s]
Running ‘randomSeed.R’ [1s/1s]
Running ‘segmentByCBS,calls.R’ [0s/0s]
Running ‘segmentByCBS,futures.R’ [3s/9s]
Running ‘segmentByCBS,median.R’ [3s/4s]
Running ‘segmentByCBS,prune.R’ [2s/3s]
Running ‘segmentByCBS,report.R’ [0s/0s]
Running ‘segmentByCBS,shiftTCN.R’ [15s/18s]
Running ‘segmentByCBS,weights.R’ [5s/6s]
Running ‘segmentByCBS.R’ [5s/7s]
Running ‘segmentByNonPairedPSCBS,medianDH.R’ [3s/5s]
Running ‘segmentByPairedPSCBS,DH.R’ [4s/5s]
Running ‘segmentByPairedPSCBS,calls.R’ [6s/8s]
Running ‘segmentByPairedPSCBS,futures.R’ [10s/22s]
Running ‘segmentByPairedPSCBS,noNormalBAFs.R’ [4s/5s]
Running ‘segmentByPairedPSCBS,report.R’ [0s/0s]
Running ‘segmentByPairedPSCBS,seqOfSegmentsByDP.R’ [8s/10s]
Running ‘segmentByPairedPSCBS.R’ [8s/11s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [59s/72s] OK
- checking PDF version of manual ... [9s/14s] OK
- checking HTML version of manual ... [4s/8s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 NOTE