* using log directory ‘/srv/hornik/tmp/CRAN/CleanBSequences.Rcheck’
* using R Under development (unstable) (2024-05-06 r86526)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.4 (1)
    Debian flang-new version 18.1.4 (1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘CleanBSequences/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CleanBSequences’ version ‘2.2.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/5s] Note_to_CRAN_maintainers
Maintainer: ‘Florencia I. Pozzi <florenciapoz@hotmail.com>’
* 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 ‘CleanBSequences’ can be installed ... [6s/6s] WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘Biostrings::pairwiseAlignment’ by ‘pwalign::pairwiseAlignment’ when loading ‘CleanBSequences’
  Warning: replacing previous import ‘Biostrings::nindel’ by ‘pwalign::nindel’ when loading ‘CleanBSequences’
  Warning: replacing previous import ‘Biostrings::errorSubstitutionMatrices’ by ‘pwalign::errorSubstitutionMatrices’ when loading ‘CleanBSequences’
  Warning: replacing previous import ‘Biostrings::alignedPattern’ by ‘pwalign::alignedPattern’ when loading ‘CleanBSequences’
  Warning: replacing previous import ‘Biostrings::alignedSubject’ by ‘pwalign::alignedSubject’ when loading ‘CleanBSequences’
  Warning: replacing previous import ‘Biostrings::stringDist’ by ‘pwalign::stringDist’ when loading ‘CleanBSequences’
  Warning: replacing previous import ‘Biostrings::pid’ by ‘pwalign::pid’ when loading ‘CleanBSequences’
  Warning: replacing previous import ‘Biostrings::nedit’ by ‘pwalign::nedit’ when loading ‘CleanBSequences’
  Warning: replacing previous import ‘Biostrings::mismatchSummary’ by ‘pwalign::mismatchSummary’ when loading ‘CleanBSequences’
  Warning: replacing previous import ‘Biostrings::writePairwiseAlignments’ by ‘pwalign::writePairwiseAlignments’ when loading ‘CleanBSequences’
  Warning: replacing previous import ‘Biostrings::mismatchTable’ by ‘pwalign::mismatchTable’ when loading ‘CleanBSequences’
  Warning: replacing previous import ‘Biostrings::nucleotideSubstitutionMatrix’ by ‘pwalign::nucleotideSubstitutionMatrix’ when loading ‘CleanBSequences’
  Warning: replacing previous import ‘Biostrings::PairwiseAlignments’ by ‘pwalign::PairwiseAlignments’ when loading ‘CleanBSequences’
  Warning: replacing previous import ‘Biostrings::qualitySubstitutionMatrices’ by ‘pwalign::qualitySubstitutionMatrices’ when loading ‘CleanBSequences’
  Warning: replacing previous import ‘Biostrings::compareStrings’ by ‘pwalign::compareStrings’ when loading ‘CleanBSequences’
  Warning: replacing previous import ‘Biostrings::deletion’ by ‘pwalign::deletion’ when loading ‘CleanBSequences’
  Warning: replacing previous import ‘Biostrings::unaligned’ by ‘pwalign::unaligned’ when loading ‘CleanBSequences’
  Warning: replacing previous import ‘Biostrings::indel’ by ‘pwalign::indel’ when loading ‘CleanBSequences’
  Warning: replacing previous import ‘Biostrings::insertion’ by ‘pwalign::insertion’ when loading ‘CleanBSequences’
  Warning: replacing previous import ‘Biostrings::PairwiseAlignmentsSingleSubject’ by ‘pwalign::PairwiseAlignmentsSingleSubject’ when loading ‘CleanBSequences’
  Warning: replacing previous import ‘Biostrings::aligned’ by ‘pwalign::aligned’ when loading ‘CleanBSequences’
See ‘/srv/hornik/tmp/CRAN/CleanBSequences.Rcheck/00install.out’ for details.
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] 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 ... [9s/9s] 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 examples ... [4s/4s] OK
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 WARNING