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INSTALL report for GenomicFeatures on tokay2

This page was generated on 2019-04-09 11:57:29 -0400 (Tue, 09 Apr 2019).

Package 647/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicFeatures 1.35.9
Bioconductor Package Maintainer
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/GenomicFeatures
Branch: master
Last Commit: aadeb64
Last Changed Date: 2019-03-25 10:43:18 -0400 (Mon, 25 Mar 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  ERROR  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 

Summary

Package: GenomicFeatures
Version: 1.35.9
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/GenomicFeatures_1.35.9.tar.gz && rm -rf GenomicFeatures.buildbin-libdir && mkdir GenomicFeatures.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicFeatures.buildbin-libdir GenomicFeatures_1.35.9.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GenomicFeatures_1.35.9.zip && rm GenomicFeatures_1.35.9.tar.gz GenomicFeatures_1.35.9.zip
StartedAt: 2019-04-08 20:01:54 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 20:03:35 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 100.5 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/GenomicFeatures_1.35.9.tar.gz && rm -rf GenomicFeatures.buildbin-libdir && mkdir GenomicFeatures.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicFeatures.buildbin-libdir GenomicFeatures_1.35.9.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GenomicFeatures_1.35.9.zip && rm GenomicFeatures_1.35.9.tar.gz GenomicFeatures_1.35.9.zip
###
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install for i386

* installing *source* package 'GenomicFeatures' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GenomicFeatures'
    finding HTML links ... done
    DEFAULT_CIRC_SEQS                       html  
    FeatureDb-class                         html  
    finding level-2 HTML links ... done

    TxDb-class                              html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/TxDb-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-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/TxDb-class.Rd:100: file link 'saveDb' in package 'AnnotationDbi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/TxDb-class.Rd:101: file link 'loadDb' in package 'AnnotationDbi' does not exist and so has been treated as a topic
    as-format-methods                       html  
    coordinate-mapping-methods              html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coordinate-mapping-methods.Rd:28: file link 'mapToAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coordinate-mapping-methods.Rd:54: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coordinate-mapping-methods.Rd:58: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coordinate-mapping-methods.Rd:61: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coordinate-mapping-methods.Rd:62: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coordinate-mapping-methods.Rd:231: file link 'mapToAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
    coverageByTranscript                    html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:25: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:25: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:26: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:27: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:28: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:32: file link 'coverage' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:33: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:35: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:38: file link 'grglist' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:43: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:55: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:70: file link 'grglist' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:71: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:72: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:74: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:75: file link 'grglist' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:80: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:81: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:102: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:105: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:108: file link 'coverage' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:114: file link 'findCompatibleOverlaps' in package 'GenomicAlignments' does not exist and so has been treated as a topic
    disjointExons                           html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/disjointExons.Rd:47: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/disjointExons.Rd:58: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    exonicParts                             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/exonicParts.Rd:38: file link 'disjoin' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/exonicParts.Rd:44: file link 'disjoin' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/exonicParts.Rd:82: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/exonicParts.Rd:87: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/exonicParts.Rd:90: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/exonicParts.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-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/exonicParts.Rd:99: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/exonicParts.Rd:133: file link 'disjoin' in package 'IRanges' does not exist and so has been treated as a topic
    extractTranscriptSeqs                   html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:26: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:27: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:31: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:40: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:41: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:44: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:46: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:49: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:74: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:79: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:81: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:84: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:87: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:93: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:103: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:125: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:125: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.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-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:135: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
    extractUpstreamSeqs                     html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractUpstreamSeqs.Rd:29: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractUpstreamSeqs.Rd:30: file link 'TwoBitFile' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractUpstreamSeqs.Rd:30: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractUpstreamSeqs.Rd:39: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractUpstreamSeqs.Rd:57: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractUpstreamSeqs.Rd:59: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractUpstreamSeqs.Rd:61: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractUpstreamSeqs.Rd:65: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractUpstreamSeqs.Rd:109: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractUpstreamSeqs.Rd:116: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractUpstreamSeqs.Rd:116: file link 'TwoBitFile' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractUpstreamSeqs.Rd:117: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractUpstreamSeqs.Rd:126: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractUpstreamSeqs.Rd:129: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
    features                                html  
    getPromoterSeq-methods                  html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/getPromoterSeq-methods.Rd:11: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/getPromoterSeq-methods.Rd:11: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/getPromoterSeq-methods.Rd:21: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/getPromoterSeq-methods.Rd:21: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/getPromoterSeq-methods.Rd:24: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/getPromoterSeq-methods.Rd:24: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/getPromoterSeq-methods.Rd:36: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/getPromoterSeq-methods.Rd:36: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/getPromoterSeq-methods.Rd:45: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/getPromoterSeq-methods.Rd:46: file link 'DNAStringSetList' in package 'Biostrings' does not exist and so has been treated as a topic
    id2name                                 html  
    makeFeatureDbFromUCSC                   html  
    makeTxDb                                html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/makeTxDb.Rd:201: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/makeTxDb.Rd:206: file link 'saveDb' in package 'AnnotationDbi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/makeTxDb.Rd:207: file link 'loadDb' in package 'AnnotationDbi' does not exist and so has been treated as a topic
    makeTxDbFromBiomart                     html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/makeTxDbFromBiomart.Rd:141: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    makeTxDbFromEnsembl                     html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/makeTxDbFromEnsembl.Rd:72: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    makeTxDbFromGFF                         html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/makeTxDbFromGFF.Rd:29: file link 'GFF3File' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/makeTxDbFromGFF.Rd:30: file link 'GTFFile' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/makeTxDbFromGFF.Rd:99: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/makeTxDbFromGFF.Rd:101: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
    makeTxDbFromGRanges                     html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/makeTxDbFromGRanges.Rd:10: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/makeTxDbFromGRanges.Rd:20: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/makeTxDbFromGRanges.Rd:21: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/makeTxDbFromGRanges.Rd:57: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/makeTxDbFromGRanges.Rd:63: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    makeTxDbFromUCSC                        html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/makeTxDbFromUCSC.Rd:99: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    makeTxDbPackage                         html  
    mapIdsToRanges                          html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/mapIdsToRanges.Rd:24: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
    mapRangesToIds                          html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/mapRangesToIds.Rd:25: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
    microRNAs                               html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/microRNAs.Rd:32: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    nearest-methods                         html  
    select-methods                          html  
    transcriptLengths                       html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/transcriptLengths.Rd:44: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/transcriptLengths.Rd:107: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    transcriptLocs2refLocs                  html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/transcriptLocs2refLocs.Rd:36: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
    transcripts                             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/transcripts.Rd:85: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/transcripts.Rd:86: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/transcripts.Rd:89: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/transcripts.Rd:122: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/transcripts.Rd:124: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
    transcriptsBy                           html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/transcriptsBy.Rd:49: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/transcriptsBy.Rd:52: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/transcriptsBy.Rd:54: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/transcriptsBy.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-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/transcriptsBy.Rd:89: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
    transcriptsByOverlaps                   html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/transcriptsByOverlaps.Rd:46: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/transcriptsByOverlaps.Rd:49: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/transcriptsByOverlaps.Rd:59: file link 'findOverlaps' in package 'IRanges' 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 'GenomicFeatures' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicFeatures' as GenomicFeatures_1.35.9.zip
* DONE (GenomicFeatures)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'GenomicFeatures' successfully unpacked and MD5 sums checked