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CHECK report for BSgenome on tokay2

This page was generated on 2018-10-17 08:32:51 -0400 (Wed, 17 Oct 2018).

Package 169/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BSgenome 1.48.0
H. Pagès
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/BSgenome
Branch: RELEASE_3_7
Last Commit: 092a1b9
Last Changed Date: 2018-04-30 10:35:05 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: BSgenome
Version: 1.48.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BSgenome.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings BSgenome_1.48.0.tar.gz
StartedAt: 2018-10-17 00:50:55 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 01:05:47 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 892.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: BSgenome.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BSgenome.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings BSgenome_1.48.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/BSgenome.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.48.0'
* 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-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenome-class.Rd:46: file link 'GenomeDescription' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenome-class.Rd:47: file link 'GenomeDescription' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenome-class.Rd:58: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenome-class.Rd:59: file link 'MaskedDNAString' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenome-class.Rd:68: file link 'length,XVector-method' in package 'XVector' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenome-class.Rd:69: file link 'length,MaskedXString-method' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenome-class.Rd:70: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenome-class.Rd:71: file link 'MaskedDNAString' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenome-class.Rd:73: file link 'MaskedXString' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenome-class.Rd:75: file link 'MaskedXString' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenome-class.Rd:83: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenome-class.Rd:143: file link 'BSgenome.Hsapiens.UCSC.hg38' in package 'BSgenome.Hsapiens.UCSC.hg38' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenome-class.Rd:155: file link 'DNAStringSet-class' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenome-class.Rd:156: file link 'MaskedDNAString-class' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenome-class.Rd:159: file link 'subseq,XVector-method' in package 'XVector' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenome-utils.Rd:46: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenome-utils.Rd:49: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenome-utils.Rd:108: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenome-utils.Rd:111: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenome-utils.Rd:113: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenome-utils.Rd:121: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenome-utils.Rd:133: file link 'matchPDict' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenomeForge.Rd:75: file link 'XString' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenomeViews-class.Rd:120: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenomeViews-class.Rd:135: file link 'alphabetFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenomeViews-class.Rd:136: file link 'oligonucleotideFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenomeViews-class.Rd:140: file link 'alphabetFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenomeViews-class.Rd:144: file link 'oligonucleotideFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenomeViews-class.Rd:148: file link 'consensusMatrix' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenomeViews-class.Rd:179: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenomeViews-class.Rd:215: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenomeViews-class.Rd:241: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenomeViews-class.Rd:245: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenomeViews-class.Rd:246: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenomeViews-class.Rd:249: file link 'seqtype' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenomeViews-class.Rd:250: file link 'nchar,XStringSet-method' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenomeViews-class.Rd:251: file link 'unlist,XStringSet-method' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenomeViews-class.Rd:252: file link 'alphabetFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenomeViews-class.Rd:253: file link 'hasOnlyBaseLetters' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenomeViews-class.Rd:254: file link 'uniqueLetters' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenomeViews-class.Rd:256: file link 'oligonucleotideFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenomeViews-class.Rd:257: file link 'nucleotideFrequencyAt' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenomeViews-class.Rd:258: file link 'consensusMatrix' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenomeViews-class.Rd:259: file link 'consensusString' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenomeViews-class.Rd:271: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenomeViews-class.Rd:274: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenomeViews-class.Rd:281: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/SNPlocs-class.Rd:111: file link 'subsetByOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/SNPlocs-class.Rd:112: file link 'subsetByOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/SNPlocs-class.Rd:113: file link 'subsetByOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/SNPlocs-class.Rd:116: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/SNPlocs-class.Rd:125: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/SNPlocs-class.Rd:125: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/SNPlocs-class.Rd:143: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/SNPlocs-class.Rd:156: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/SNPlocs-class.Rd:161: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/SNPlocs-class.Rd:171: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/SNPlocs-class.Rd:171: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/SNPlocs-class.Rd:178: file link 'subsetByOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/SNPlocs-class.Rd:180: file link 'subsetByOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/SNPlocs-class.Rd:183: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/XtraSNPlocs-class.Rd:93: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/XtraSNPlocs-class.Rd:94: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/XtraSNPlocs-class.Rd:97: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/XtraSNPlocs-class.Rd:106: file link 'subsetByOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/XtraSNPlocs-class.Rd:107: file link 'subsetByOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/XtraSNPlocs-class.Rd:108: file link 'subsetByOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/XtraSNPlocs-class.Rd:111: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/XtraSNPlocs-class.Rd:131: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/XtraSNPlocs-class.Rd:133: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/XtraSNPlocs-class.Rd:134: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/XtraSNPlocs-class.Rd:140: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/XtraSNPlocs-class.Rd:146: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/XtraSNPlocs-class.Rd:154: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/XtraSNPlocs-class.Rd:159: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/XtraSNPlocs-class.Rd:163: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/XtraSNPlocs-class.Rd:167: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/XtraSNPlocs-class.Rd:171: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/XtraSNPlocs-class.Rd:178: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/XtraSNPlocs-class.Rd:187: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/XtraSNPlocs-class.Rd:199: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/export-methods.Rd:33: file link 'FastaFile' in package 'rtracklayer' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/export-methods.Rd:33: file link 'TwoBitFile' in package 'rtracklayer' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/export-methods.Rd:61: file link 'TwoBitFile' in package 'rtracklayer' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/export-methods.Rd:71: file link 'FastaFile' in package 'rtracklayer' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/export-methods.Rd:71: file link 'TwoBitFile' in package 'rtracklayer' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:15: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:27: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:35: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:36: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:37: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:38: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:39: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:39: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:49: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:50: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:51: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:57: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:58: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:58: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:59: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:64: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:65: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:77: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:78: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:79: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:80: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:87: file link 'solveUserSEW' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:91: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:92: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:106: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:107: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:114: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:115: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:115: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:124: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:129: file link 'DNAStringSetList' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:130: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:132: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:133: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:135: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:136: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:136: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:137: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:149: file link 'MaskedDNAString-class' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:160: file link 'DNAStringSet-class' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:161: file link 'MaskedDNAString-class' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/injectSNPs.Rd:105: file link 'letterFrequencyInSlidingView' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/injectSNPs.Rd:106: file link '.inplaceReplaceLetterAt' in package 'Biostrings' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/BSgenome.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R         1.4Mb
    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'
  'IRanges:::unlist_as_integer' '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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
XtraSNPlocs-class   87.63  21.16  123.61
SNPlocs-class       29.32   1.97   69.77
BSgenome-utils      26.64   0.64   27.28
BSgenome-class      21.65   0.92   44.91
BSgenomeViews-class 16.56   1.97   18.55
bsapply             14.44   0.91   18.04
injectSNPs          14.42   0.73   30.08
getSeq-methods       7.25   0.70    7.95
export-methods       6.80   0.61    7.42
BSgenomeForge        6.81   0.11    6.92
available.genomes    3.64   1.33    7.31
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
XtraSNPlocs-class   95.52   2.98   98.58
SNPlocs-class       37.53   1.88   59.92
BSgenome-utils      23.28   0.37   23.65
injectSNPs          16.75   3.19   19.94
BSgenome-class      18.41   0.64   19.05
BSgenomeViews-class 13.64   1.54   15.19
bsapply             12.66   0.69   13.34
export-methods       9.21   0.72    9.94
getSeq-methods       7.85   0.20    8.04
BSgenomeForge        5.72   0.07    5.78
* 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-3.7-bioc/meat/BSgenome.Rcheck/00check.log'
for details.

Installation output

BSgenome.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/BSgenome_1.48.0.tar.gz && rm -rf BSgenome.buildbin-libdir && mkdir BSgenome.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BSgenome.buildbin-libdir BSgenome_1.48.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL BSgenome_1.48.0.zip && rm BSgenome_1.48.0.tar.gz BSgenome_1.48.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 5477k  100 5477k    0     0  48.8M      0 --:--:-- --:--:-- --:--:-- 51.4M

install for i386

* installing *source* package 'BSgenome' ...
** R
** inst
** byte-compile and prepare 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-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenome-class.Rd:46: file link 'GenomeDescription' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenome-class.Rd:47: file link 'GenomeDescription' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenome-class.Rd:58: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenome-class.Rd:59: file link 'MaskedDNAString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenome-class.Rd:68: file link 'length,XVector-method' in package 'XVector' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenome-class.Rd:69: file link 'length,MaskedXString-method' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenome-class.Rd:70: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenome-class.Rd:71: file link 'MaskedDNAString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/BSgenome-class.Rd:73: file link 'MaskedXString' in package 'Biostrings' does not exist and so has been treated as a topic
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Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:58: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:59: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:64: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:65: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:77: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:78: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:79: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:80: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:87: file link 'solveUserSEW' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:91: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:92: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:106: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:107: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:114: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:115: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:115: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:124: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:129: file link 'DNAStringSetList' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:130: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
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Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:133: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:135: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:136: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:136: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:137: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:149: file link 'MaskedDNAString-class' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:160: file link 'DNAStringSet-class' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/getSeq-methods.Rd:161: file link 'MaskedDNAString-class' in package 'Biostrings' does not exist and so has been treated as a topic
    injectSNPs                              html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/injectSNPs.Rd:105: file link 'letterFrequencyInSlidingView' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpCiIP9h/R.INSTALLf3c6e4668cb/BSgenome/man/injectSNPs.Rd:106: file link '.inplaceReplaceLetterAt' in package 'Biostrings' does not exist and so has been treated as a topic
** 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_1.48.0.zip
* DONE (BSgenome)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'BSgenome' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

Example timings

BSgenome.Rcheck/examples_i386/BSgenome-Ex.timings

nameusersystemelapsed
BSgenome-class21.65 0.9244.91
BSgenome-utils26.64 0.6427.28
BSgenomeForge6.810.116.92
BSgenomeViews-class16.56 1.9718.55
SNPlocs-class29.32 1.9769.77
XtraSNPlocs-class 87.63 21.16123.61
available.genomes3.641.337.31
bsapply14.44 0.9118.04
export-methods6.800.617.42
getSeq-methods7.250.707.95
injectSNPs14.42 0.7330.08

BSgenome.Rcheck/examples_x64/BSgenome-Ex.timings

nameusersystemelapsed
BSgenome-class18.41 0.6419.05
BSgenome-utils23.28 0.3723.65
BSgenomeForge5.720.075.78
BSgenomeViews-class13.64 1.5415.19
SNPlocs-class37.53 1.8859.92
XtraSNPlocs-class95.52 2.9898.58
available.genomes2.860.773.83
bsapply12.66 0.6913.34
export-methods9.210.729.94
getSeq-methods7.850.208.04
injectSNPs16.75 3.1919.94