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CHECK report for GenomicFeatures on tokay1

This page was generated on 2019-04-13 11:21:04 -0400 (Sat, 13 Apr 2019).

Package 625/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicFeatures 1.34.8
Bioconductor Package Maintainer
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/GenomicFeatures
Branch: RELEASE_3_8
Last Commit: c798b3b
Last Changed Date: 2019-04-09 22:45:15 -0400 (Tue, 09 Apr 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GenomicFeatures
Version: 1.34.8
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicFeatures.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GenomicFeatures_1.34.8.tar.gz
StartedAt: 2019-04-13 02:32:57 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 02:53:45 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 1248.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GenomicFeatures.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicFeatures.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GenomicFeatures_1.34.8.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/GenomicFeatures.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomicFeatures/DESCRIPTION' ... OK
* this is package 'GenomicFeatures' version '1.34.8'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 NOTE
Depends: includes the non-default packages:
  'BiocGenerics' 'S4Vectors' 'IRanges' 'GenomeInfoDb' 'GenomicRanges'
  'AnnotationDbi'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'GenomicFeatures' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/GenomicFeatures/man/TxDb-class.Rd:101: file link 'loadDb' in package 'AnnotationDbi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/GenomicFeatures/man/coordinate-mapping-methods.Rd:231: file link 'mapToAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/GenomicFeatures/man/coverageByTranscript.Rd:114: file link 'findCompatibleOverlaps' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/GenomicFeatures/man/disjointExons.Rd:58: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/GenomicFeatures/man/exonicParts.Rd:30: file link 'disjoin' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/GenomicFeatures/man/exonicParts.Rd:36: file link 'disjoin' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/GenomicFeatures/man/exonicParts.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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/GenomicFeatures/man/exonicParts.Rd:52: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/GenomicFeatures/man/exonicParts.Rd:85: file link 'disjoin' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/GenomicFeatures/man/extractTranscriptSeqs.Rd:135: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/GenomicFeatures/man/extractUpstreamSeqs.Rd:129: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/GenomicFeatures/man/getPromoterSeq-methods.Rd:46: file link 'DNAStringSetList' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/GenomicFeatures/man/makeTxDb.Rd:207: file link 'loadDb' in package 'AnnotationDbi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/GenomicFeatures/man/makeTxDbFromBiomart.Rd:141: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/GenomicFeatures/man/makeTxDbFromEnsembl.Rd:72: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/GenomicFeatures/man/makeTxDbFromGFF.Rd:101: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/GenomicFeatures/man/makeTxDbFromGRanges.Rd:63: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/GenomicFeatures/man/makeTxDbFromUCSC.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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/GenomicFeatures/man/mapIdsToRanges.Rd:24: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/GenomicFeatures/man/mapRangesToIds.Rd:25: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/GenomicFeatures/man/microRNAs.Rd:32: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/GenomicFeatures/man/transcriptLengths.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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/GenomicFeatures/man/transcriptLocs2refLocs.Rd:36: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/GenomicFeatures/man/transcripts.Rd:124: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/GenomicFeatures/man/transcriptsBy.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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/GenomicFeatures/man/transcriptsByOverlaps.Rd:59: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/GenomicFeatures.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
':::' calls which should be '::':
  'S4Vectors:::duplicatedIntegerPairs' 'S4Vectors:::matchIntegerPairs'
  'S4Vectors:::orderIntegerPairs'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'biomaRt:::martBM' 'biomaRt:::martDataset' 'biomaRt:::martHost'
  'rtracklayer:::resourceDescription' 'rtracklayer:::ucscTableOutputs'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
makeFeatureDbFromUCSC      44.17   4.08  142.61
coverageByTranscript       28.70   6.85   35.55
exonicParts                24.85   3.14   27.98
makeTxDbFromGFF             9.51   1.84   21.19
extractTranscriptSeqs       9.54   0.12    9.68
coordinate-mapping-methods  7.98   0.17    8.51
makeTxDbPackage             0.20   0.00   45.19
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
makeFeatureDbFromUCSC      65.33   1.25  138.09
coverageByTranscript       33.80   6.86   40.82
exonicParts                32.24   2.43   34.66
extractTranscriptSeqs      16.37   0.21   16.59
transcriptLocs2refLocs     12.03   0.14   12.17
makeTxDbFromGFF            10.69   0.24   10.92
coordinate-mapping-methods  7.51   0.25    8.47
makeTxDbFromGRanges         5.56   0.04    5.61
transcriptLengths           5.32   0.17    5.48
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'run_unitTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'run_unitTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/GenomicFeatures.Rcheck/00check.log'
for details.



Installation output

GenomicFeatures.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/GenomicFeatures_1.34.8.tar.gz && rm -rf GenomicFeatures.buildbin-libdir && mkdir GenomicFeatures.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicFeatures.buildbin-libdir GenomicFeatures_1.34.8.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL GenomicFeatures_1.34.8.zip && rm GenomicFeatures_1.34.8.tar.gz GenomicFeatures_1.34.8.zip
###
##############################################################################
##############################################################################


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100 1126k  100 1126k    0     0  22.9M      0 --:--:-- --:--:-- --:--:-- 25.0M

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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/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-3.8-bioc/tmpdir/Rtmp4KAS08/R.INSTALL227829a363a6/GenomicFeatures/man/exonicParts.Rd:30: file link 'disjoin' in package 'IRanges' does not exist and so has been treated as a topic
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    extractTranscriptSeqs                   html  
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    extractUpstreamSeqs                     html  
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    features                                html  
    getPromoterSeq-methods                  html  
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    id2name                                 html  
    makeFeatureDbFromUCSC                   html  
    makeTxDb                                html  
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    makeTxDbFromBiomart                     html  
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    makeTxDbFromEnsembl                     html  
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    makeTxDbFromGFF                         html  
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    makeTxDbFromGRanges                     html  
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    makeTxDbFromUCSC                        html  
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    makeTxDbPackage                         html  
    mapIdsToRanges                          html  
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    mapRangesToIds                          html  
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    microRNAs                               html  
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    nearest-methods                         html  
    select-methods                          html  
    transcriptLengths                       html  
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    transcriptLocs2refLocs                  html  
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    transcripts                             html  
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    transcriptsBy                           html  
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    transcriptsByOverlaps                   html  
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** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'GenomicFeatures' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicFeatures' as GenomicFeatures_1.34.8.zip
* DONE (GenomicFeatures)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'GenomicFeatures' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

GenomicFeatures.Rcheck/tests_i386/run_unitTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("GenomicFeatures") || stop("unable to load GenomicFeatures package")
Loading required package: GenomicFeatures
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

[1] TRUE
> GenomicFeatures:::.test()
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: rtracklayer
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns


RUNIT TEST PROTOCOL -- Sat Apr 13 02:50:32 2019 
*********************************************** 
Number of test functions: 75 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GenomicFeatures RUnit Tests - 75 test functions, 0 errors, 0 failures
Number of test functions: 75 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 3 out-of-bound ranges located on sequences a,
  b, and c. Note that ranges located on a sequence whose length is
  unknown (NA) or on a circular sequence are not considered out-of-bound
  (use seqlengths() and isCircular() to get the lengths and circularity
  flags of the underlying sequences). You can use trim() to trim these
  ranges. See ?`trim,GenomicRanges-method` for more information.
2: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 1 out-of-bound range located on sequence c.
  Note that ranges located on a sequence whose length is unknown (NA) or
  on a circular sequence are not considered out-of-bound (use
  seqlengths() and isCircular() to get the lengths and circularity flags
  of the underlying sequences). You can use trim() to trim these ranges.
  See ?`trim,GenomicRanges-method` for more information.
3: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 1 out-of-bound range located on sequence c.
  Note that ranges located on a sequence whose length is unknown (NA) or
  on a circular sequence are not considered out-of-bound (use
  seqlengths() and isCircular() to get the lengths and circularity flags
  of the underlying sequences). You can use trim() to trim these ranges.
  See ?`trim,GenomicRanges-method` for more information.
4: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 4 out-of-bound ranges located on sequences 1,
  2, 3, and 4. Note that ranges located on a sequence whose length is
  unknown (NA) or on a circular sequence are not considered out-of-bound
  (use seqlengths() and isCircular() to get the lengths and circularity
  flags of the underlying sequences). You can use trim() to trim these
  ranges. See ?`trim,GenomicRanges-method` for more information.
5: In .get_cds_IDX(type, phase) :
  The "phase" metadata column contains non-NA values for features of type
  exon. This information was ignored.
6: In .get_cds_IDX(type, phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
7: In .get_cds_IDX(type, phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
> 
> proc.time()
   user  system elapsed 
 103.96    3.64  125.39 

GenomicFeatures.Rcheck/tests_x64/run_unitTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("GenomicFeatures") || stop("unable to load GenomicFeatures package")
Loading required package: GenomicFeatures
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

[1] TRUE
> GenomicFeatures:::.test()
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: rtracklayer
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns


RUNIT TEST PROTOCOL -- Sat Apr 13 02:53:35 2019 
*********************************************** 
Number of test functions: 75 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GenomicFeatures RUnit Tests - 75 test functions, 0 errors, 0 failures
Number of test functions: 75 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 3 out-of-bound ranges located on sequences a,
  b, and c. Note that ranges located on a sequence whose length is
  unknown (NA) or on a circular sequence are not considered out-of-bound
  (use seqlengths() and isCircular() to get the lengths and circularity
  flags of the underlying sequences). You can use trim() to trim these
  ranges. See ?`trim,GenomicRanges-method` for more information.
2: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 1 out-of-bound range located on sequence c.
  Note that ranges located on a sequence whose length is unknown (NA) or
  on a circular sequence are not considered out-of-bound (use
  seqlengths() and isCircular() to get the lengths and circularity flags
  of the underlying sequences). You can use trim() to trim these ranges.
  See ?`trim,GenomicRanges-method` for more information.
3: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 1 out-of-bound range located on sequence c.
  Note that ranges located on a sequence whose length is unknown (NA) or
  on a circular sequence are not considered out-of-bound (use
  seqlengths() and isCircular() to get the lengths and circularity flags
  of the underlying sequences). You can use trim() to trim these ranges.
  See ?`trim,GenomicRanges-method` for more information.
4: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 4 out-of-bound ranges located on sequences 1,
  2, 3, and 4. Note that ranges located on a sequence whose length is
  unknown (NA) or on a circular sequence are not considered out-of-bound
  (use seqlengths() and isCircular() to get the lengths and circularity
  flags of the underlying sequences). You can use trim() to trim these
  ranges. See ?`trim,GenomicRanges-method` for more information.
5: In .get_cds_IDX(type, phase) :
  The "phase" metadata column contains non-NA values for features of type
  exon. This information was ignored.
6: In .get_cds_IDX(type, phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
7: In .get_cds_IDX(type, phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
> 
> proc.time()
   user  system elapsed 
 165.70    2.20  182.53 

Example timings

GenomicFeatures.Rcheck/examples_i386/GenomicFeatures-Ex.timings

nameusersystemelapsed
DEFAULT_CIRC_SEQS000
FeatureDb-class0.070.010.30
TxDb-class0.530.060.60
as-format-methods0.970.031.00
coordinate-mapping-methods7.980.178.51
coverageByTranscript28.70 6.8535.55
disjointExons000
exonicParts24.85 3.1427.98
extractTranscriptSeqs9.540.129.68
extractUpstreamSeqs1.440.071.50
features0.030.000.03
getPromoterSeq-methods0.630.030.65
id2name0.140.000.14
makeFeatureDbFromUCSC 44.17 4.08142.61
makeTxDb0.060.040.11
makeTxDbFromBiomart0.020.000.02
makeTxDbFromEnsembl000
makeTxDbFromGFF 9.51 1.8421.19
makeTxDbFromGRanges3.10.14.2
makeTxDbFromUCSC000
makeTxDbPackage 0.20 0.0045.19
mapIdsToRanges1.750.004.63
mapRangesToIds0.450.000.45
microRNAs000
nearest-methods0.470.030.50
select-methods0.410.000.41
transcriptLengths3.840.344.18
transcriptLocs2refLocs4.080.194.27
transcripts1.840.031.87
transcriptsBy0.500.010.52
transcriptsByOverlaps0.330.020.34

GenomicFeatures.Rcheck/examples_x64/GenomicFeatures-Ex.timings

nameusersystemelapsed
DEFAULT_CIRC_SEQS000
FeatureDb-class0.060.000.06
TxDb-class0.700.020.72
as-format-methods1.600.041.64
coordinate-mapping-methods7.510.258.47
coverageByTranscript33.80 6.8640.82
disjointExons000
exonicParts32.24 2.4334.66
extractTranscriptSeqs16.37 0.2116.59
extractUpstreamSeqs2.070.082.14
features0.070.000.08
getPromoterSeq-methods0.990.051.04
id2name0.280.000.31
makeFeatureDbFromUCSC 65.33 1.25138.09
makeTxDb0.110.000.11
makeTxDbFromBiomart0.010.000.02
makeTxDbFromEnsembl000
makeTxDbFromGFF10.69 0.2410.92
makeTxDbFromGRanges5.560.045.61
makeTxDbFromUCSC000
makeTxDbPackage0.390.003.11
mapIdsToRanges0.780.000.78
mapRangesToIds1.520.001.52
microRNAs000
nearest-methods0.670.000.67
select-methods0.280.000.29
transcriptLengths5.320.175.48
transcriptLocs2refLocs12.03 0.1412.17
transcripts2.680.062.75
transcriptsBy0.830.020.85
transcriptsByOverlaps0.220.010.23