##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/GenomicFeatures_1.42.3.tar.gz && rm -rf GenomicFeatures.buildbin-libdir && mkdir GenomicFeatures.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicFeatures.buildbin-libdir GenomicFeatures_1.42.3.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL GenomicFeatures_1.42.3.zip && rm GenomicFeatures_1.42.3.tar.gz GenomicFeatures_1.42.3.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 1134k  100 1134k    0     0  42.5M      0 --:--:-- --:--:-- --:--:-- 44.3M

install for i386

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

    TxDb-class                              html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/exonicParts.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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/exonicParts.Rd:98: 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/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/exonicParts.Rd:102: 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/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/exonicParts.Rd:107: 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/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/exonicParts.Rd:141: 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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/makeTxDbFromBiomart.Rd:144: 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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/makeTxDbFromEnsembl.Rd:80: 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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/makeTxDbFromUCSC.Rd:51: 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/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/makeTxDbFromUCSC.Rd:52: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/makeTxDbFromUCSC.Rd:121: 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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcripts.Rd:84: 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/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcripts.Rd:90: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcripts.Rd:93: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcripts.Rd:126: 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/RtmpYrBg47/R.INSTALL16ac37f3609a/GenomicFeatures/man/transcripts.Rd:128: 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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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-3.12-bioc/tmpdir/RtmpYrBg47/R.INSTALL16ac37f3609a/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_1.42.3.zip
* DONE (GenomicFeatures)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'GenomicFeatures' successfully unpacked and MD5 sums checked