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CHECK report for BSgenome on tokay1

This page was generated on 2018-04-12 13:18:17 -0400 (Thu, 12 Apr 2018).

Package 162/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BSgenome 1.46.0
H. Pagès
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/BSgenome
Branch: RELEASE_3_6
Last Commit: bdfbd6d
Last Changed Date: 2017-10-30 12:39:17 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: BSgenome
Version: 1.46.0
Command: rm -rf BSgenome.buildbin-libdir BSgenome.Rcheck && mkdir BSgenome.buildbin-libdir BSgenome.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BSgenome.buildbin-libdir BSgenome_1.46.0.tar.gz >BSgenome.Rcheck\00install.out 2>&1 && cp BSgenome.Rcheck\00install.out BSgenome-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BSgenome.buildbin-libdir --install="check:BSgenome-install.out" --force-multiarch --no-vignettes --timings BSgenome_1.46.0.tar.gz
StartedAt: 2018-04-11 22:37:32 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:53:30 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 958.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: BSgenome.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   rm -rf BSgenome.buildbin-libdir BSgenome.Rcheck && mkdir BSgenome.buildbin-libdir BSgenome.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BSgenome.buildbin-libdir BSgenome_1.46.0.tar.gz >BSgenome.Rcheck\00install.out 2>&1 && cp BSgenome.Rcheck\00install.out BSgenome-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BSgenome.buildbin-libdir --install="check:BSgenome-install.out" --force-multiarch --no-vignettes --timings BSgenome_1.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/BSgenome.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BSgenome/DESCRIPTION' ... OK
* this is package 'BSgenome' version '1.46.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics' 'S4Vectors' 'IRanges' 'GenomeInfoDb' 'GenomicRanges'
  'Biostrings' 'rtracklayer'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... NOTE
Found the following non-portable file path:
  BSgenome/inst/extdata/GentlemanLab/1000genomes/BSgenome.Hsapiens.1000g.b36female-tools/split_human_b36_female.sh

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking whether package 'BSgenome' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-class.Rd:46: missing file link 'GenomeDescription'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-class.Rd:47: missing file link 'GenomeDescription'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-class.Rd:58: missing file link 'DNAString'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-class.Rd:59: missing file link 'MaskedDNAString'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-class.Rd:68: missing file link 'length,XVector-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-class.Rd:69: missing file link 'length,MaskedXString-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-class.Rd:70: missing file link 'DNAString'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-class.Rd:71: missing file link 'MaskedDNAString'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-class.Rd:73: missing file link 'MaskedXString'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-class.Rd:75: missing file link 'MaskedXString'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-class.Rd:83: missing file link 'DNAStringSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-class.Rd:143: missing file link 'BSgenome.Hsapiens.UCSC.hg38'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-class.Rd:155: missing file link 'DNAStringSet-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-class.Rd:156: missing file link 'MaskedDNAString-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-class.Rd:159: missing file link 'subseq,XVector-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-utils.Rd:46: missing file link 'DNAString'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-utils.Rd:49: missing file link 'DNAStringSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-utils.Rd:108: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-utils.Rd:111: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-utils.Rd:113: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-utils.Rd:121: missing file link 'DataFrame'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-utils.Rd:133: missing file link 'matchPDict'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeForge.Rd:75: missing file link 'XString'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:120: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:135: missing file link 'alphabetFrequency'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:136: missing file link 'oligonucleotideFrequency'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:140: missing file link 'alphabetFrequency'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:144: missing file link 'oligonucleotideFrequency'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:148: missing file link 'consensusMatrix'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:179: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:215: missing file link 'DNAStringSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:241: missing file link 'DNAStringSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:245: missing file link 'DNAStringSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:246: missing file link 'DNAStringSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:249: missing file link 'seqtype'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:250: missing file link 'nchar,XStringSet-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:251: missing file link 'unlist,XStringSet-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:252: missing file link 'alphabetFrequency'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:253: missing file link 'hasOnlyBaseLetters'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:254: missing file link 'uniqueLetters'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:256: missing file link 'oligonucleotideFrequency'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:257: missing file link 'nucleotideFrequencyAt'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:258: missing file link 'consensusMatrix'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:259: missing file link 'consensusString'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:271: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:274: missing file link 'DNAStringSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:281: missing file link 'TxDb'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/SNPlocs-class.Rd:111: missing file link 'subsetByOverlaps'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/SNPlocs-class.Rd:112: missing file link 'subsetByOverlaps'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/SNPlocs-class.Rd:113: missing file link 'subsetByOverlaps'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/SNPlocs-class.Rd:116: missing file link 'GenomicRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/SNPlocs-class.Rd:125: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/SNPlocs-class.Rd:125: missing file link 'GPos'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/SNPlocs-class.Rd:143: missing file link 'GPos'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/SNPlocs-class.Rd:156: missing file link 'GPos'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/SNPlocs-class.Rd:161: missing file link 'GPos'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/SNPlocs-class.Rd:171: missing file link 'GPos'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/SNPlocs-class.Rd:171: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/SNPlocs-class.Rd:178: missing file link 'subsetByOverlaps'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/SNPlocs-class.Rd:180: missing file link 'subsetByOverlaps'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/SNPlocs-class.Rd:183: missing file link 'GenomicRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:93: missing file link 'DataFrame'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:94: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:97: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:106: missing file link 'subsetByOverlaps'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:107: missing file link 'subsetByOverlaps'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:108: missing file link 'subsetByOverlaps'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:111: missing file link 'GenomicRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:131: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:133: missing file link 'DataFrame'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:134: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:140: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:146: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:154: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:159: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:163: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:167: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:171: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:178: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:187: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:199: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/export-methods.Rd:33: missing file link 'FastaFile'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/export-methods.Rd:33: missing file link 'TwoBitFile'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/export-methods.Rd:61: missing file link 'TwoBitFile'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/export-methods.Rd:71: missing file link 'FastaFile'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/export-methods.Rd:71: missing file link 'TwoBitFile'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:15: missing file link 'XStringSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:27: missing file link 'XStringSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:35: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:36: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:37: missing file link 'RangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:38: missing file link 'Ranges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:39: missing file link 'RangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:39: missing file link 'Ranges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:49: missing file link 'XStringSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:50: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:51: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:57: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:58: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:58: missing file link 'RangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:59: missing file link 'Ranges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:64: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:65: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:77: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:78: missing file link 'Ranges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:79: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:80: missing file link 'RangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:87: missing file link 'solveUserSEW'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:91: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:92: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:106: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:107: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:114: missing file link 'XStringSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:115: missing file link 'GenomicRanges-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:116: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:125: missing file link 'DNAStringSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:130: missing file link 'DNAStringSetList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:131: missing file link 'CharacterList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:133: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:134: missing file link 'DNAString'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:136: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:137: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:137: missing file link 'RangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:138: missing file link 'Ranges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:150: missing file link 'MaskedDNAString-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:161: missing file link 'DNAStringSet-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:162: missing file link 'MaskedDNAString-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/injectSNPs.Rd:105: missing file link 'letterFrequencyInSlidingView'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/injectSNPs.Rd:106: missing file link '.inplaceReplaceLetterAt'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/BSgenome.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' 'BiocGenerics' 'S4Vectors' 'IRanges' 'GenomeInfoDb' 'GenomicRanges' 'Biostrings' 'rtracklayer'
A package should be listed in only one of these fields.
* 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
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'GenomeInfoDb:::compactPrintNamedAtomicVector'
  'GenomeInfoDb:::showGenomeDescription' 'IRanges:::.normargSEW'
  'S4Vectors:::anyMissing' 'S4Vectors:::anyMissingOrOutside'
  'S4Vectors:::decodeRle' 'S4Vectors:::diffWithInitialZero'
  'S4Vectors:::makeClassinfoRowForCompactPrinting'
  'S4Vectors:::makePrettyMatrixForCompactPrinting'
  'S4Vectors:::make_zero_col_DataFrame' 'S4Vectors:::quick_unlist'
  'S4Vectors:::quick_unsplit' 'S4Vectors:::recycleVector'
  'rtracklayer:::.DNAString_to_twoBit' 'rtracklayer:::.TwoBits_export'
  'rtracklayer:::checkArgFormat' 'rtracklayer:::twoBitPath'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'MaskedBSgenome' 'OnDiskLongTable' 'OnDiskLongTable_old'
  'as.data.frame.BSgenomeViews' 'batchsizes' 'blocksizes' 'breakpoints'
  'forgeMaskedBSgenomeDataPkg'
  'getBatchesByOverlapsFromOnDiskLongTable'
  'getBatchesBySeqnameFromOnDiskLongTable'
  'getBatchesFromOnDiskLongTable' 'getBatchesFromOnDiskLongTable_old'
  'getRowsByIdFromOnDiskLongTable' 'getRowsByIdFromOnDiskLongTable_old'
  'getRowsByIndexFromOnDiskLongTable_old' 'getRowsFromOnDiskLongTable'
  'rowids' 'saveAsOnDiskLongTable_old'
  'saveRowidsForOnDiskLongTable_old' 'spatialIndex'
  'writeOnDiskLongTable' 'writeOnDiskLongTableRowids'
Undocumented S4 classes:
  'OnDiskLongTable_old' 'OnDiskLongTable' 'MaskedBSgenome'
  'GRanges_OR_NULL'
Undocumented S4 methods:
  generic '[' and siglist 'XStringSet,GRangesList,ANY,ANY'
  generic '[' and siglist 'XStringSet,GenomicRanges,ANY,ANY'
  generic '[[' and siglist 'BSgenome,ANY,ANY'
  generic '[[' and siglist 'FastaNamedSequences,ANY,ANY'
  generic '[[' and siglist 'RdaNamedSequences,ANY,ANY'
  generic '[[' and siglist 'TwobitNamedSequences,ANY,ANY'
  generic 'batchsizes' and siglist 'OnDiskLongTable'
  generic 'blocksizes' and siglist 'OnDiskLongTable_old'
  generic 'breakpoints' and siglist 'OnDiskLongTable'
  generic 'breakpoints' and siglist 'OnDiskLongTable_old'
  generic 'dim' and siglist 'OnDiskLongTable'
  generic 'dim' and siglist 'OnDiskLongTable_old'
  generic 'dimnames' and siglist 'OnDiskLongTable'
  generic 'dimnames' and siglist 'OnDiskLongTable_old'
  generic 'dimnames' and siglist 'XtraSNPlocs'
  generic 'forgeMaskedBSgenomeDataPkg' and siglist
    'MaskedBSgenomeDataPkgSeed'
  generic 'forgeMaskedBSgenomeDataPkg' and siglist 'character'
  generic 'forgeMaskedBSgenomeDataPkg' and siglist 'list'
  generic 'length' and siglist 'OnDiskNamedSequences'
  generic 'names' and siglist 'FastaNamedSequences'
  generic 'names' and siglist 'TwobitNamedSequences'
  generic 'rowids' and siglist 'OnDiskLongTable'
  generic 'rowids' and siglist 'OnDiskLongTable_old'
  generic 'seqinfo' and siglist 'FastaNamedSequences'
  generic 'seqinfo' and siglist 'RdaNamedSequences'
  generic 'seqinfo' and siglist 'TwobitNamedSequences'
  generic 'seqnames' and siglist 'OnDiskNamedSequences'
  generic 'show' and siglist 'OnDiskLongTable'
  generic 'show' and siglist 'OnDiskLongTable_old'
  generic 'show' and siglist 'OnDiskNamedSequences'
  generic 'spatialIndex' and siglist 'OnDiskLongTable'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
XtraSNPlocs-class   122.39  15.86  157.83
SNPlocs-class        26.51   1.97   58.76
BSgenome-utils       26.36   0.57   31.98
BSgenome-class       16.95   0.69   21.84
injectSNPs           12.95   1.07   79.12
BSgenomeViews-class  11.56   1.17   53.17
bsapply               9.22   0.39   14.73
export-methods        7.61   0.65    8.27
BSgenomeForge         6.78   0.08    6.86
getSeq-methods        6.40   0.35    6.76
available.genomes     3.38   0.51   10.36
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
XtraSNPlocs-class   116.98   3.13  120.20
SNPlocs-class        41.32   2.16   43.47
BSgenome-utils       26.66   0.32   27.00
BSgenome-class       18.89   0.64   19.54
injectSNPs           15.41   1.41   16.82
BSgenomeViews-class  11.25   1.42   12.70
bsapply               8.89   0.41    9.30
export-methods        7.49   0.70    8.19
getSeq-methods        6.78   0.12    6.90
BSgenomeForge         5.91   0.08    5.98
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/BSgenome.Rcheck/00check.log'
for details.

Installation output

BSgenome.Rcheck/00install.out


install for i386

* installing *source* package 'BSgenome' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'BSgenome'
    finding HTML links ... done
    BSParams-class                          html  
    finding level-2 HTML links ... done

    BSgenome-class                          html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-class.Rd:46: missing file link 'GenomeDescription'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-class.Rd:47: missing file link 'GenomeDescription'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-class.Rd:58: missing file link 'DNAString'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-class.Rd:59: missing file link 'MaskedDNAString'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-class.Rd:68: missing file link 'length,XVector-method'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-class.Rd:69: missing file link 'length,MaskedXString-method'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-class.Rd:70: missing file link 'DNAString'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-class.Rd:71: missing file link 'MaskedDNAString'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-class.Rd:73: missing file link 'MaskedXString'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-class.Rd:75: missing file link 'MaskedXString'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-class.Rd:83: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-class.Rd:143: missing file link 'BSgenome.Hsapiens.UCSC.hg38'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-class.Rd:155: missing file link 'DNAStringSet-class'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-class.Rd:156: missing file link 'MaskedDNAString-class'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-class.Rd:159: missing file link 'subseq,XVector-method'
    BSgenome-utils                          html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-utils.Rd:46: missing file link 'DNAString'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-utils.Rd:49: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-utils.Rd:108: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-utils.Rd:111: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-utils.Rd:113: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-utils.Rd:121: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenome-utils.Rd:133: missing file link 'matchPDict'
    BSgenomeForge                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeForge.Rd:75: missing file link 'XString'
    BSgenomeViews-class                     html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:120: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:135: missing file link 'alphabetFrequency'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:136: missing file link 'oligonucleotideFrequency'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:140: missing file link 'alphabetFrequency'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:144: missing file link 'oligonucleotideFrequency'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:148: missing file link 'consensusMatrix'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:179: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:215: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:241: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:245: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:246: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:249: missing file link 'seqtype'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:250: missing file link 'nchar,XStringSet-method'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:251: missing file link 'unlist,XStringSet-method'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:252: missing file link 'alphabetFrequency'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:253: missing file link 'hasOnlyBaseLetters'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:254: missing file link 'uniqueLetters'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:256: missing file link 'oligonucleotideFrequency'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:257: missing file link 'nucleotideFrequencyAt'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:258: missing file link 'consensusMatrix'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:259: missing file link 'consensusString'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:271: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:274: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/BSgenomeViews-class.Rd:281: missing file link 'TxDb'
    SNPlocs-class                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/SNPlocs-class.Rd:111: missing file link 'subsetByOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/SNPlocs-class.Rd:112: missing file link 'subsetByOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/SNPlocs-class.Rd:113: missing file link 'subsetByOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/SNPlocs-class.Rd:116: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/SNPlocs-class.Rd:125: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/SNPlocs-class.Rd:125: missing file link 'GPos'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/SNPlocs-class.Rd:143: missing file link 'GPos'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/SNPlocs-class.Rd:156: missing file link 'GPos'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/SNPlocs-class.Rd:161: missing file link 'GPos'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/SNPlocs-class.Rd:171: missing file link 'GPos'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/SNPlocs-class.Rd:171: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/SNPlocs-class.Rd:178: missing file link 'subsetByOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/SNPlocs-class.Rd:180: missing file link 'subsetByOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/SNPlocs-class.Rd:183: missing file link 'GenomicRanges'
    XtraSNPlocs-class                       html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:93: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:94: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:97: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:106: missing file link 'subsetByOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:107: missing file link 'subsetByOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:108: missing file link 'subsetByOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:111: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:131: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:133: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:134: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:140: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:146: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:154: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:159: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:163: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:167: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:171: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:178: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:187: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/XtraSNPlocs-class.Rd:199: missing file link 'GRanges'
    available.genomes                       html  
    bsapply                                 html  
    export-methods                          html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/export-methods.Rd:33: missing file link 'FastaFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/export-methods.Rd:33: missing file link 'TwoBitFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/export-methods.Rd:61: missing file link 'TwoBitFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/export-methods.Rd:71: missing file link 'FastaFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/export-methods.Rd:71: missing file link 'TwoBitFile'
    getSeq-methods                          html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:15: missing file link 'XStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:27: missing file link 'XStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:35: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:36: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:37: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:38: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:39: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:39: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:49: missing file link 'XStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:50: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:51: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:57: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:58: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:58: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:59: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:64: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:65: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:77: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:78: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:79: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:80: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:87: missing file link 'solveUserSEW'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:91: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:92: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:106: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:107: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:114: missing file link 'XStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:115: missing file link 'GenomicRanges-class'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:116: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:125: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:130: missing file link 'DNAStringSetList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:131: missing file link 'CharacterList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:133: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:134: missing file link 'DNAString'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:136: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:137: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:137: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:138: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:150: missing file link 'MaskedDNAString-class'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:161: missing file link 'DNAStringSet-class'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/getSeq-methods.Rd:162: missing file link 'MaskedDNAString-class'
    injectSNPs                              html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/injectSNPs.Rd:105: missing file link 'letterFrequencyInSlidingView'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpIrV06G/R.INSTALLd3c6f983864/BSgenome/man/injectSNPs.Rd:106: missing file link '.inplaceReplaceLetterAt'
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'BSgenome' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BSgenome' as BSgenome_1.46.0.zip
* DONE (BSgenome)
In R CMD INSTALL
In R CMD INSTALL

Tests output

Example timings

BSgenome.Rcheck/examples_i386/BSgenome-Ex.timings

nameusersystemelapsed
BSgenome-class16.95 0.6921.84
BSgenome-utils26.36 0.5731.98
BSgenomeForge6.780.086.86
BSgenomeViews-class11.56 1.1753.17
SNPlocs-class26.51 1.9758.76
XtraSNPlocs-class122.39 15.86157.83
available.genomes 3.38 0.5110.36
bsapply 9.22 0.3914.73
export-methods7.610.658.27
getSeq-methods6.400.356.76
injectSNPs12.95 1.0779.12

BSgenome.Rcheck/examples_x64/BSgenome-Ex.timings

nameusersystemelapsed
BSgenome-class18.89 0.6419.54
BSgenome-utils26.66 0.3227.00
BSgenomeForge5.910.085.98
BSgenomeViews-class11.25 1.4212.70
SNPlocs-class41.32 2.1643.47
XtraSNPlocs-class116.98 3.13120.20
available.genomes1.920.342.42
bsapply8.890.419.30
export-methods7.490.708.19
getSeq-methods6.780.126.90
injectSNPs15.41 1.4116.82