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CHECK report for BSgenome on tokay1

This page was generated on 2020-04-15 12:17:39 -0400 (Wed, 15 Apr 2020).

Package 202/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BSgenome 1.54.0
H. Pag├Ęs
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/BSgenome
Branch: RELEASE_3_10
Last Commit: 58524c9
Last Changed Date: 2019-10-29 13:07:43 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: BSgenome
Version: 1.54.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BSgenome.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings BSgenome_1.54.0.tar.gz
StartedAt: 2020-04-15 01:43:52 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 01:59:27 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 934.7 seconds
RetCode: 1
Status:  ERROR  
CheckDir: BSgenome.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BSgenome.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings BSgenome_1.54.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/BSgenome.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.54.0'
* 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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/BSgenome/man/BSgenome-utils.Rd:41: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/BSgenome/man/BSgenome-utils.Rd:90: file link 'PDict' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/BSgenome/man/BSgenome-utils.Rd:90: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/BSgenome/man/BSgenome-utils.Rd:114: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/BSgenome/man/BSgenome-utils.Rd:118: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/BSgenome/man/BSgenome-utils.Rd:124: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/BSgenome/man/BSgenome-utils.Rd:132: file link 'matchPDict' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-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   5.8Mb
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'getSeq-methods':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'BSgenome-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bsapply
> ### Title: bsapply
> ### Aliases: bsapply
> ### Keywords: manip
> 
> ### ** Examples
> 
>   ## Load the Worm genome:
>   library("BSgenome.Celegans.UCSC.ce2")
> 
>   ## Count the alphabet frequencies for every chromosome but exclude
>   ## mitochrondrial and scaffold ones:
>   params <- new("BSParams", X = Celegans, FUN = alphabetFrequency,
+   exclude = c("M", "_"))
>   bsapply(params)
$chrI
      A       C       G       T       M       R       W       S       Y       K 
4838561 2697177 2693544 4851201       0       0       0       0       0       0 
      V       H       D       B       N       -       +       . 
      0       0       0       0       0       0       0       0 

$chrII
      A       C       G       T       M       R       W       S       Y       K 
4878194 2769208 2762193 4869710       0       0       0       0       0       0 
      V       H       D       B       N       -       +       . 
      0       0       0       0       3       0       0       0 

$chrIII
      A       C       G       T       M       R       W       S       Y       K 
4444527 2449074 2466260 4423447       0       0       0       0       0       0 
      V       H       D       B       N       -       +       . 
      0       0       0       0       5       0       0       0 

$chrIV
      A       C       G       T       M       R       W       S       Y       K 
5711041 3034771 3017009 5730970       0       0       0       0       0       0 
      V       H       D       B       N       -       +       . 
      0       0       0       0       0       0       0       0 

$chrV
      A       C       G       T       M       R       W       S       Y       K 
6749806 3711722 3700959 6759744       0       0       0       0       0       0 
      V       H       D       B       N       -       +       . 
      0       0       0       0       0       0       0       0 

$chrX
      A       C       G       T       M       R       W       S       Y       K 
5746418 3119282 3118284 5734865       0       0       0       0       0       0 
      V       H       D       B       N       -       +       . 
      0       0       0       0       0       0       0       0 

> 
>   ## Or we can do this same function with simplify = TRUE:
>   params <- new("BSParams", X = Celegans, FUN = alphabetFrequency,
+   exclude = c("M", "_"), simplify = TRUE)
>   bsapply(params)
     chrI   chrII  chrIII   chrIV    chrV    chrX
A 4838561 4878194 4444527 5711041 6749806 5746418
C 2697177 2769208 2449074 3034771 3711722 3119282
G 2693544 2762193 2466260 3017009 3700959 3118284
T 4851201 4869710 4423447 5730970 6759744 5734865
M       0       0       0       0       0       0
R       0       0       0       0       0       0
W       0       0       0       0       0       0
S       0       0       0       0       0       0
Y       0       0       0       0       0       0
K       0       0       0       0       0       0
V       0       0       0       0       0       0
H       0       0       0       0       0       0
D       0       0       0       0       0       0
B       0       0       0       0       0       0
N       0       3       5       0       0       0
-       0       0       0       0       0       0
+       0       0       0       0       0       0
.       0       0       0       0       0       0
> 
> 
>   ## Examples to show how we might look for a string (in this case an
>   ## ebox motif) across the whole genome.  
>   Ebox <- DNAStringSet("CACGTG")
>   pdict0 <- PDict(Ebox)
> 
>   params <- new("BSParams", X = Celegans, FUN = countPDict, simplify = TRUE)
>   bsapply(params, pdict = pdict0)
  chrI  chrII chrIII  chrIV   chrV   chrX   chrM 
  3369   2698   2612   2997   3588   2466      1 
> 
>   params@FUN <- matchPDict
>   bsapply(params, pdict = pdict0)
$chrI
MIndex object of length 1
[[1]]
IRanges object with 3369 ranges and 0 metadata columns:
             start       end     width
         <integer> <integer> <integer>
     [1]      2260      2265         6
     [2]      4920      4925         6
     [3]      8074      8079         6
     [4]     17729     17734         6
     [5]     18576     18581         6
     ...       ...       ...       ...
  [3365]  15062401  15062406         6
  [3366]  15065488  15065493         6
  [3367]  15066587  15066592         6
  [3368]  15066627  15066632         6
  [3369]  15074448  15074453         6


$chrII
MIndex object of length 1
[[1]]
IRanges object with 2698 ranges and 0 metadata columns:
             start       end     width
         <integer> <integer> <integer>
     [1]     28734     28739         6
     [2]     29032     29037         6
     [3]     35849     35854         6
     [4]     39084     39089         6
     [5]     43244     43249         6
     ...       ...       ...       ...
  [2694]  15271300  15271305         6
  [2695]  15273056  15273061         6
  [2696]  15273761  15273766         6
  [2697]  15275492  15275497         6
  [2698]  15277856  15277861         6


$chrIII
MIndex object of length 1
[[1]]
IRanges object with 2612 ranges and 0 metadata columns:
             start       end     width
         <integer> <integer> <integer>
     [1]      7323      7328         6
     [2]     11819     11824         6
     [3]     17156     17161         6
     [4]     24300     24305         6
     [5]     26324     26329         6
     ...       ...       ...       ...
  [2608]  13760197  13760202         6
  [2609]  13766607  13766612         6
  [2610]  13768348  13768353         6
  [2611]  13769745  13769750         6
  [2612]  13772637  13772642         6


$chrIV
MIndex object of length 1
[[1]]
IRanges object with 2997 ranges and 0 metadata columns:
             start       end     width
         <integer> <integer> <integer>
     [1]      5606      5611         6
     [2]      6675      6680         6
     [3]      8409      8414         6
     [4]      9438      9443         6
     [5]     18765     18770         6
     ...       ...       ...       ...
  [2993]  17458897  17458902         6
  [2994]  17479117  17479122         6
  [2995]  17488757  17488762         6
  [2996]  17490208  17490213         6
  [2997]  17490673  17490678         6


$chrV
MIndex object of length 1
[[1]]
IRanges object with 3588 ranges and 0 metadata columns:
             start       end     width
         <integer> <integer> <integer>
     [1]       605       610         6
     [2]      3531      3536         6
     [3]      5078      5083         6
     [4]      5128      5133         6
     [5]      6038      6043         6
     ...       ...       ...       ...
  [3584]  20891341  20891346         6
  [3585]  20894142  20894147         6
  [3586]  20897746  20897751         6
  [3587]  20899040  20899045         6
  [3588]  20921084  20921089         6


$chrX
MIndex object of length 1
[[1]]
IRanges object with 2466 ranges and 0 metadata columns:
             start       end     width
         <integer> <integer> <integer>
     [1]      7656      7661         6
     [2]     26993     26998         6
     [3]     37580     37585         6
     [4]     39506     39511         6
     [5]     56687     56692         6
     ...       ...       ...       ...
  [2462]  17708492  17708497         6
  [2463]  17708649  17708654         6
  [2464]  17709026  17709031         6
  [2465]  17712705  17712710         6
  [2466]  17716966  17716971         6


$chrM
MIndex object of length 1
[[1]]
IRanges object with 1 range and 0 metadata columns:
          start       end     width
      <integer> <integer> <integer>
  [1]      8767      8772         6


> 
>   ## And since its really overkill to use matchPDict to find a single pattern:
>   params@FUN <- matchPattern
>   bsapply(params, pattern = "CACGTG")
$chrI
  Views on a 15080483-letter DNAString subject
subject: GCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCT...AGGCTTAGGCTTAGGCTTAGGTTTAGGCTTAGGC
views:
          start      end width
   [1]     2260     2265     6 [CACGTG]
   [2]     4920     4925     6 [CACGTG]
   [3]     8074     8079     6 [CACGTG]
   [4]    17729    17734     6 [CACGTG]
   [5]    18576    18581     6 [CACGTG]
   ...      ...      ...   ... ...
[3365] 15062401 15062406     6 [CACGTG]
[3366] 15065488 15065493     6 [CACGTG]
[3367] 15066587 15066592     6 [CACGTG]
[3368] 15066627 15066632     6 [CACGTG]
[3369] 15074448 15074453     6 [CACGTG]

$chrII
  Views on a 15279308-letter DNAString subject
subject: CCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTA...TAGGCTGAGACTTAGGCTTAGGCTTAGGCTTAGT
views:
          start      end width
   [1]    28734    28739     6 [CACGTG]
   [2]    29032    29037     6 [CACGTG]
   [3]    35849    35854     6 [CACGTG]
   [4]    39084    39089     6 [CACGTG]
   [5]    43244    43249     6 [CACGTG]
   ...      ...      ...   ... ...
[2694] 15271300 15271305     6 [CACGTG]
[2695] 15273056 15273061     6 [CACGTG]
[2696] 15273761 15273766     6 [CACGTG]
[2697] 15275492 15275497     6 [CACGTG]
[2698] 15277856 15277861     6 [CACGTG]

$chrIII
  Views on a 13783313-letter DNAString subject
subject: CCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTA...TAGGCTTAGGCTTAGGCTTAGGCTTAGGCTTAGG
views:
          start      end width
   [1]     7323     7328     6 [CACGTG]
   [2]    11819    11824     6 [CACGTG]
   [3]    17156    17161     6 [CACGTG]
   [4]    24300    24305     6 [CACGTG]
   [5]    26324    26329     6 [CACGTG]
   ...      ...      ...   ... ...
[2608] 13760197 13760202     6 [CACGTG]
[2609] 13766607 13766612     6 [CACGTG]
[2610] 13768348 13768353     6 [CACGTG]
[2611] 13769745 13769750     6 [CACGTG]
[2612] 13772637 13772642     6 [CACGTG]

$chrIV
  Views on a 17493791-letter DNAString subject
subject: CCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTA...TAGGCTTAGGCTTAGGCTTAGGCTTAGGCTTAGG
views:
          start      end width
   [1]     5606     5611     6 [CACGTG]
   [2]     6675     6680     6 [CACGTG]
   [3]     8409     8414     6 [CACGTG]
   [4]     9438     9443     6 [CACGTG]
   [5]    18765    18770     6 [CACGTG]
   ...      ...      ...   ... ...
[2993] 17458897 17458902     6 [CACGTG]
[2994] 17479117 17479122     6 [CACGTG]
[2995] 17488757 17488762     6 [CACGTG]
[2996] 17490208 17490213     6 [CACGTG]
[2997] 17490673 17490678     6 [CACGTG]

$chrV
  Views on a 20922231-letter DNAString subject
subject: GAATTCCTAAGCCTAAGCCTAAGCCTAAGCCTAA...CTTAGGCTTAGGCTTAGGCTTAGGCTTAGGCTTA
views:
          start      end width
   [1]      605      610     6 [CACGTG]
   [2]     3531     3536     6 [CACGTG]
   [3]     5078     5083     6 [CACGTG]
   [4]     5128     5133     6 [CACGTG]
   [5]     6038     6043     6 [CACGTG]
   ...      ...      ...   ... ...
[3584] 20891341 20891346     6 [CACGTG]
[3585] 20894142 20894147     6 [CACGTG]
[3586] 20897746 20897751     6 [CACGTG]
[3587] 20899040 20899045     6 [CACGTG]
[3588] 20921084 20921089     6 [CACGTG]

$chrX
  Views on a 17718849-letter DNAString subject
subject: CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA...TAGGCTTAGGCTTAGGCTTAGGCTTAGGCTTAGG
views:
          start      end width
   [1]     7656     7661     6 [CACGTG]
   [2]    26993    26998     6 [CACGTG]
   [3]    37580    37585     6 [CACGTG]
   [4]    39506    39511     6 [CACGTG]
   [5]    56687    56692     6 [CACGTG]
   ...      ...      ...   ... ...
[2462] 17708492 17708497     6 [CACGTG]
[2463] 17708649 17708654     6 [CACGTG]
[2464] 17709026 17709031     6 [CACGTG]
[2465] 17712705 17712710     6 [CACGTG]
[2466] 17716966 17716971     6 [CACGTG]

$chrM
  Views on a 13794-letter DNAString subject
subject: CAGTAAATAGTTTAATAAAAATATAGCATTTGGG...TTTATAGATATATACTTTGTATATATCTATATTA
views:
    start  end width
[1]  8767 8772     6 [CACGTG]

> 
> 
>   ## Examples on how to use the masks
>   library(BSgenome.Hsapiens.UCSC.hg38.masked)
Loading required package: BSgenome.Hsapiens.UCSC.hg38
>   genome <- BSgenome.Hsapiens.UCSC.hg38.masked
>   ## I can make things verbose if I want to see the chromosomes getting processed.
>   options(verbose=TRUE)
>   ## For the 1st example, lets use default masks
>   params <- new("BSParams", X = genome, FUN = alphabetFrequency,
+   exclude = c(1:8,"M","X","_"), simplify = TRUE)
>   bsapply(params)
Warning in .local(con, format, text, ...) :
  needLargeMem: Out of memory - request size 34598680 bytes, errno: 12
Error in .local(con, format, text, ...) : UCSC library operation failed
Calls: bsapply ... .loadBSgenomeSequence -> [[ -> [[ -> import -> import -> .local
Execution halted
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
XtraSNPlocs-class   111.72   3.56  115.56
SNPlocs-class        52.33   2.23   55.14
BSgenome-utils       32.02   0.60   32.67
BSgenomeViews-class  22.36   2.61   25.05
injectSNPs           22.64   2.17   33.31
BSgenome-class       23.83   0.81   24.64
bsapply              12.79   0.26   16.19
getSeq-methods       10.19   0.08   10.26
export-methods        7.69   0.60    8.30
BSgenomeForge         6.20   0.11    6.31
* 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: 1 ERROR, 3 WARNINGs, 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/BSgenome.Rcheck/00check.log'
for details.


Installation output

BSgenome.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/BSgenome_1.54.0.tar.gz && rm -rf BSgenome.buildbin-libdir && mkdir BSgenome.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BSgenome.buildbin-libdir BSgenome_1.54.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL BSgenome_1.54.0.zip && rm BSgenome_1.54.0.tar.gz BSgenome_1.54.0.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 5476k  100 5476k    0     0  58.6M      0 --:--:-- --:--:-- --:--:-- 61.4M

install for i386

* installing *source* package 'BSgenome' ...
** using staged installation
** 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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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
    BSgenome-utils                          html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/BSgenome/man/BSgenome-utils.Rd:41: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/BSgenome/man/BSgenome-utils.Rd:90: file link 'PDict' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/BSgenome/man/BSgenome-utils.Rd:90: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/BSgenome/man/BSgenome-utils.Rd:114: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/BSgenome/man/BSgenome-utils.Rd:118: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/BSgenome/man/BSgenome-utils.Rd:124: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/BSgenome/man/BSgenome-utils.Rd:132: file link 'matchPDict' in package 'Biostrings' does not exist and so has been treated as a topic
    BSgenomeForge                           html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/BSgenome/man/BSgenomeForge.Rd:75: file link 'XString' in package 'Biostrings' does not exist and so has been treated as a topic
    BSgenomeViews-class                     html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/BSgenome/man/BSgenomeViews-class.Rd:281: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
    SNPlocs-class                           html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/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-3.10-bioc/tmpdir/Rtmpc1LM55/R.INSTALL3ec76741fe9/BSgenome/man/SNPlocs-class.Rd:112: file link 'subsetByOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
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    XtraSNPlocs-class                       html  
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    available.genomes                       html  
    bsapply                                 html  
    export-methods                          html  
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    getSeq-methods                          html  
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    injectSNPs                              html  
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** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'BSgenome' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BSgenome' as BSgenome_1.54.0.zip
* DONE (BSgenome)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'BSgenome' successfully unpacked and MD5 sums checked

Tests output


Example timings

BSgenome.Rcheck/examples_i386/BSgenome-Ex.timings

nameusersystemelapsed
BSgenome-class20.53 0.6538.10
BSgenome-utils26.72 0.8030.11
BSgenomeForge6.380.087.02
BSgenomeViews-class19.14 2.5923.91
SNPlocs-class21.23 1.4149.59
XtraSNPlocs-class 99.61 29.97159.09
available.genomes 3.69 2.2522.16

BSgenome.Rcheck/examples_x64/BSgenome-Ex.timings

nameusersystemelapsed
BSgenome-class23.83 0.8124.64
BSgenome-utils32.02 0.6032.67
BSgenomeForge6.200.116.31
BSgenomeViews-class22.36 2.6125.05
SNPlocs-class52.33 2.2355.14
XtraSNPlocs-class111.72 3.56115.56
available.genomes3.040.863.98
bsapply12.79 0.2616.19
export-methods7.690.608.30
getSeq-methods10.19 0.0810.26
injectSNPs22.64 2.1733.31