Back to Multiple platform build/check report for BioC 3.7
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

INSTALL report for BSgenome on tokay2

This page was generated on 2018-10-17 08:32:50 -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:\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
StartedAt: 2018-10-16 19:59:06 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 20:01:14 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 128.7 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
##############################################################################
###
### 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
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
    BSgenome-utils                          html  
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
    BSgenomeForge                           html  
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
    BSgenomeViews-class                     html  
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
    SNPlocs-class                           html  
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
    XtraSNPlocs-class                       html  
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
    available.genomes                       html  
    bsapply                                 html  
    export-methods                          html  
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
    getSeq-methods                          html  
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
    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