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INSTALL report for BSgenome on tokay1

This page was generated on 2020-08-06 11:50:04 -0400 (Thu, 06 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BSgenome PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 202/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BSgenome 1.57.5
H. Pag├Ęs
Snapshot Date: 2020-08-05 14:50:59 -0400 (Wed, 05 Aug 2020)
URL: https://git.bioconductor.org/packages/BSgenome
Branch: master
Last Commit: 781c61d
Last Changed Date: 2020-07-20 17:17:06 -0400 (Mon, 20 Jul 2020)
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  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: BSgenome
Version: 1.57.5
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/BSgenome_1.57.5.tar.gz && rm -rf BSgenome.buildbin-libdir && mkdir BSgenome.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BSgenome.buildbin-libdir BSgenome_1.57.5.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BSgenome_1.57.5.zip && rm BSgenome_1.57.5.tar.gz BSgenome_1.57.5.zip
StartedAt: 2020-08-05 18:16:32 -0400 (Wed, 05 Aug 2020)
EndedAt: 2020-08-05 18:18:24 -0400 (Wed, 05 Aug 2020)
EllapsedTime: 112.8 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/BSgenome_1.57.5.tar.gz && rm -rf BSgenome.buildbin-libdir && mkdir BSgenome.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BSgenome.buildbin-libdir BSgenome_1.57.5.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BSgenome_1.57.5.zip && rm BSgenome_1.57.5.tar.gz BSgenome_1.57.5.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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100 5485k  100 5485k    0     0  47.0M      0 --:--:-- --:--:-- --:--:-- 48.6M

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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/BSgenome/man/BSgenome-class.Rd:81: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/BSgenome/man/BSgenome-class.Rd:82: file link 'MaskedDNAString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/BSgenome/man/BSgenome-class.Rd:91: 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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/BSgenome/man/BSgenome-class.Rd:92: 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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/BSgenome/man/BSgenome-class.Rd:93: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/BSgenome/man/BSgenome-class.Rd:94: file link 'MaskedDNAString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/BSgenome/man/BSgenome-class.Rd:96: file link 'MaskedXString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/BSgenome/man/BSgenome-class.Rd:98: file link 'MaskedXString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/BSgenome/man/BSgenome-class.Rd:106: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/BSgenome/man/BSgenome-class.Rd:166: 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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/BSgenome/man/BSgenome-class.Rd:178: file link 'DNAStringSet-class' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/BSgenome/man/BSgenome-class.Rd:179: file link 'MaskedDNAString-class' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/BSgenome/man/BSgenome-class.Rd:182: 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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/BSgenome/man/BSgenomeForge.Rd:120: 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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/BSgenome/man/SNPlocs-class.Rd:115: file link 'subsetByOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/BSgenome/man/SNPlocs-class.Rd:116: file link 'subsetByOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/BSgenome/man/SNPlocs-class.Rd:117: file link 'subsetByOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/BSgenome/man/SNPlocs-class.Rd:120: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/BSgenome/man/SNPlocs-class.Rd:139: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/BSgenome/man/SNPlocs-class.Rd:157: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
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Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/BSgenome/man/SNPlocs-class.Rd:196: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/BSgenome/man/SNPlocs-class.Rd:215: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/BSgenome/man/SNPlocs-class.Rd:220: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
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Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/BSgenome/man/SNPlocs-class.Rd:229: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/BSgenome/man/SNPlocs-class.Rd:242: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/BSgenome/man/SNPlocs-class.Rd:242: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/BSgenome/man/SNPlocs-class.Rd:249: file link 'subsetByOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
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Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/BSgenome/man/SNPlocs-class.Rd:254: 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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/BSgenome/man/XtraSNPlocs-class.Rd:93: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
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Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/BSgenome/man/XtraSNPlocs-class.Rd:108: file link 'subsetByOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
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Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/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-3.12-bioc/tmpdir/RtmpA9KUoG/R.INSTALL2460aa63084/BSgenome/man/XtraSNPlocs-class.Rd:140: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
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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_1.57.5.zip
* DONE (BSgenome)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'BSgenome' successfully unpacked and MD5 sums checked