Back to Multiple platform build/check report for BioC 3.10
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

BUILD BIN 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. Pagès
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: 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
StartedAt: 2020-04-15 08:19:20 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 08:20:26 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 66.7 seconds
RetCode: 0
Status:  OK  
PackageFile: BSgenome_1.54.0.zip
PackageFileSize: 7.077 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   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
###
##############################################################################
##############################################################################



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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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-3.10-bioc/tmpdir/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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-3.10-bioc/tmpdir/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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-3.10-bioc/tmpdir/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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-3.10-bioc/tmpdir/RtmpGCBOSE/R.INSTALL14546dc812ed/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/RtmpGCBOSE/R.INSTALL14546dc812ed/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 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)