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CHECK report for GenomicRanges on tokay1

This page was generated on 2018-04-12 13:20:05 -0400 (Thu, 12 Apr 2018).

Package 567/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicRanges 1.30.3
Bioconductor Package Maintainer
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/GenomicRanges
Branch: RELEASE_3_6
Last Commit: e999790
Last Changed Date: 2018-02-21 12:07:02 -0400 (Wed, 21 Feb 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: GenomicRanges
Version: 1.30.3
Command: rm -rf GenomicRanges.buildbin-libdir GenomicRanges.Rcheck && mkdir GenomicRanges.buildbin-libdir GenomicRanges.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicRanges.buildbin-libdir GenomicRanges_1.30.3.tar.gz >GenomicRanges.Rcheck\00install.out 2>&1 && cp GenomicRanges.Rcheck\00install.out GenomicRanges-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GenomicRanges.buildbin-libdir --install="check:GenomicRanges-install.out" --force-multiarch --no-vignettes --timings GenomicRanges_1.30.3.tar.gz
StartedAt: 2018-04-12 00:18:09 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:26:56 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 527.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GenomicRanges.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   rm -rf GenomicRanges.buildbin-libdir GenomicRanges.Rcheck && mkdir GenomicRanges.buildbin-libdir GenomicRanges.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicRanges.buildbin-libdir GenomicRanges_1.30.3.tar.gz >GenomicRanges.Rcheck\00install.out 2>&1 && cp GenomicRanges.Rcheck\00install.out GenomicRanges-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GenomicRanges.buildbin-libdir --install="check:GenomicRanges-install.out" --force-multiarch --no-vignettes --timings GenomicRanges_1.30.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicRanges.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomicRanges/DESCRIPTION' ... OK
* this is package 'GenomicRanges' version '1.30.3'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'GenomicRanges' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GNCList-class.Rd:46: missing file link 'NCList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GNCList-class.Rd:47: missing file link 'NCLists'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GNCList-class.Rd:48: missing file link 'Ranges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GNCList-class.Rd:49: missing file link 'RangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GNCList-class.Rd:55: missing file link 'NCList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GNCList-class.Rd:79: missing file link 'NCList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GNCList-class.Rd:79: missing file link 'NCLists'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:63: missing file link 'IPos'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:64: missing file link 'IRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:65: missing file link 'IRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:67: missing file link 'IPos'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:82: missing file link 'seqlevels'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:84: missing file link 'seqlengths'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:85: missing file link 'isCircular'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:86: missing file link 'genome'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:134: missing file link 'Vector'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:152: missing file link 'IPos'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:171: missing file link 'snpsBySeqname'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:172: missing file link 'snpsByOverlaps'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:173: missing file link 'snpsById'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:174: missing file link 'SNPlocs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:177: missing file link 'SummarizedExperiment'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:96: missing file link 'Rle'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:98: missing file link 'IRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:100: missing file link 'Rle'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:102: missing file link 'DataFrame'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:120: missing file link 'Rle'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:124: missing file link 'IRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:128: missing file link 'Rle'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:173: missing file link 'Rle'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:345: missing file link 'ManyToOneGrouping'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:523: missing file link 'GAlignments'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:524: missing file link 'GAlignmentPairs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:527: missing file link 'IRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:527: missing file link 'DNAStringSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:537: missing file link 'DataFrame'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:575: missing file link 'Ranges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:577: missing file link 'Vector'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:577: missing file link 'Rle'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:578: missing file link 'DataFrame'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRangesList-class.Rd:208: missing file link 'IRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRangesList-class.Rd:368: missing file link 'RleList-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GenomicRanges-comparison.Rd:113: missing file link 'reduce'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GenomicRanges-comparison.Rd:113: missing file link 'disjoin'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GenomicRangesList-class.Rd:16: missing file link 'List'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/absoluteRanges.Rd:39: missing file link 'seqlengths'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/absoluteRanges.Rd:41: missing file link 'seqlengths'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/absoluteRanges.Rd:50: missing file link 'IRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/absoluteRanges.Rd:65: missing file link 'IRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/absoluteRanges.Rd:86: missing file link 'IRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/coverage-methods.Rd:12: missing file link 'coverage'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/coverage-methods.Rd:15: missing file link 'coverage'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/coverage-methods.Rd:16: missing file link 'Ranges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/coverage-methods.Rd:16: missing file link 'RangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/coverage-methods.Rd:18: missing file link 'GAlignments'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/coverage-methods.Rd:19: missing file link 'GAlignmentPairs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/coverage-methods.Rd:45: missing file link 'coverage'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/coverage-methods.Rd:54: missing file link 'coverage'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/coverage-methods.Rd:67: missing file link 'coverage'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/coverage-methods.Rd:71: missing file link 'coverage'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/coverage-methods.Rd:82: missing file link 'RleList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/coverage-methods.Rd:90: missing file link 'coverage'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/coverage-methods.Rd:95: missing file link 'RleList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/findOverlaps-methods.Rd:26: missing file link 'findOverlaps'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/findOverlaps-methods.Rd:27: missing file link 'Ranges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/findOverlaps-methods.Rd:27: missing file link 'RangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/findOverlaps-methods.Rd:29: missing file link 'GAlignments'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/findOverlaps-methods.Rd:30: missing file link 'GAlignmentPairs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/findOverlaps-methods.Rd:31: missing file link 'GAlignmentsList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/findOverlaps-methods.Rd:59: missing file link 'findOverlaps'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/findOverlaps-methods.Rd:99: missing file link 'Hits'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/findOverlaps-methods.Rd:113: missing file link 'findOverlaps'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:16: missing file link 'ranges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:17: missing file link 'rglist'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:19: missing file link 'IRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:19: missing file link 'ranges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:21: missing file link 'IRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:21: missing file link 'rglist'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:32: missing file link 'GenomicRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:33: missing file link 'RangedSummarizedExperiment'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:34: missing file link 'GAlignments'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:35: missing file link 'GAlignmentPairs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:36: missing file link 'GAlignmentsList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:37: missing file link 'Pairs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:40: missing file link 'ranges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:46: missing file link 'ranges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:49: missing file link 'GAlignments'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:50: missing file link 'GAlignmentPairs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:63: missing file link 'GAlignments'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:79: missing file link 'RangedSummarizedExperiment'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:82: missing file link 'GAlignments'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:83: missing file link 'GAlignmentPairs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:84: missing file link 'GAlignmentsList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomicvars.Rd:20: missing file link 'RleList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomicvars.Rd:49: missing file link 'RleList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomicvars.Rd:60: missing file link 'RleList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomicvars.Rd:80: missing file link 'Rle'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomicvars.Rd:91: missing file link 'RleList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomicvars.Rd:105: missing file link 'RleList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/inter-range-methods.Rd:104: missing file link 'reduce'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/inter-range-methods.Rd:112: missing file link 'gaps'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/inter-range-methods.Rd:121: missing file link 'disjoin'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/inter-range-methods.Rd:145: missing file link 'Ranges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/inter-range-methods.Rd:153: missing file link 'endoapply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/intra-range-methods.Rd:53: missing file link 'GAlignments'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/intra-range-methods.Rd:54: missing file link 'GAlignmentsList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/intra-range-methods.Rd:118: missing file link 'Ranges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/intra-range-methods.Rd:122: missing file link 'Ranges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/intra-range-methods.Rd:126: missing file link 'Ranges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/intra-range-methods.Rd:194: missing file link 'Ranges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/intra-range-methods.Rd:196: missing file link 'endoapply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/makeGRangesFromDataFrame.Rd:16: missing file link 'DataFrame'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/makeGRangesFromDataFrame.Rd:37: missing file link 'DataFrame'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/makeGRangesFromDataFrame.Rd:120: missing file link 'DataFrame'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/makeGRangesFromDataFrame.Rd:142: missing file link 'getTable'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/makeGRangesFromDataFrame.Rd:146: missing file link 'DataFrame'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/makeGRangesListFromDataFrame.Rd:15: missing file link 'split'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/nearest-methods.Rd:69: missing file link 'Hits'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/nearest-methods.Rd:141: missing file link 'Hits'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/nearest-methods.Rd:144: missing file link 'Hits'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/nearest-methods.Rd:157: missing file link 'Ranges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/nearest-methods.Rd:158: missing file link 'Hits'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/setops-methods.Rd:45: missing file link 'punion'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/setops-methods.Rd:45: missing file link 'pintersect'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/setops-methods.Rd:46: missing file link 'psetdiff'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/setops-methods.Rd:46: missing file link 'pgap'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/setops-methods.Rd:47: missing file link 'Ranges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/setops-methods.Rd:155: missing file link 'Ranges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/setops-methods.Rd:155: missing file link 'RangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/setops-methods.Rd:167: missing file link 'mendoapply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/strand-utils.Rd:52: missing file link 'Rle'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/strand-utils.Rd:64: missing file link 'Rle'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/strand-utils.Rd:65: missing file link 'Rle'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/strand-utils.Rd:73: missing file link 'Rle'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/strand-utils.Rd:96: missing file link 'Rle'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/tile-methods.Rd:12: missing file link 'tile'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/tile-methods.Rd:12: missing file link 'slidingWindows'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/tile-methods.Rd:30: missing file link 'tile'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/tile-methods.Rd:35: missing file link 'tile'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/tile-methods.Rd:65: missing file link 'tile'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/tileGenome.Rd:68: missing file link 'IntegerList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/tileGenome.Rd:70: missing file link 'Views'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicRanges.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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
poverlaps,GenomicRanges-GenomicRanges: no visible binding for global
  variable 'minoverlaps'
Undefined global functions or variables:
  minoverlaps
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'inter-range-methods':
\S4method{reduce}{GenomicRangesList}
  Code: function(x, drop.empty.ranges = FALSE, ...)
  Docs: function(x, drop.empty.ranges = FALSE, min.gapwidth = 1L,
                 with.inframe.attrib = FALSE, ignore.strand = FALSE)
  Argument names in code not in docs:
    ...
  Argument names in docs not in code:
    min.gapwidth with.inframe.attrib ignore.strand
  Mismatches in argument names:
    Position: 3 Code: ... Docs: min.gapwidth

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicRanges.buildbin-libdir/GenomicRanges/libs/i386/GenomicRanges.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
genomicvars              52.69  15.04   67.86
GPos-class               32.17   6.14   42.75
makeGRangesFromDataFrame  0.97   0.00   19.77
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
genomicvars              61.88  18.47   80.40
GPos-class               31.07   5.84   36.91
makeGRangesFromDataFrame  2.11   0.01   20.89
* 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: 2 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicRanges.Rcheck/00check.log'
for details.

Installation output

GenomicRanges.Rcheck/00install.out


install for i386

* installing *source* package 'GenomicRanges' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c transcript_utils.c -o transcript_utils.o
transcript_utils.c: In function 'tlocs2rlocs':
transcript_utils.c:143:38: warning: 'end' may be used uninitialized in this function [-Wmaybe-uninitialized]
  return on_minus_strand ? end - tloc : start + tloc;
                                      ^
transcript_utils.c:120:24: note: 'end' was declared here
  int nexons, j, start, end, width;
                        ^
transcript_utils.c:143:38: warning: 'start' may be used uninitialized in this function [-Wmaybe-uninitialized]
  return on_minus_strand ? end - tloc : start + tloc;
                                      ^
transcript_utils.c:120:17: note: 'start' was declared here
  int nexons, j, start, end, width;
                 ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o GenomicRanges.dll tmp.def IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicRanges.buildbin-libdir/GenomicRanges/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'GenomicRanges'
    finding HTML links ... done
    DelegatingGenomicRanges-class           html  
    GNCList-class                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GNCList-class.Rd:46: missing file link 'NCList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GNCList-class.Rd:47: missing file link 'NCLists'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GNCList-class.Rd:48: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GNCList-class.Rd:49: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GNCList-class.Rd:55: missing file link 'NCList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GNCList-class.Rd:79: missing file link 'NCList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GNCList-class.Rd:79: missing file link 'NCLists'
    GPos-class                              html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:63: missing file link 'IPos'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:64: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:65: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:67: missing file link 'IPos'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:82: missing file link 'seqlevels'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:84: missing file link 'seqlengths'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:85: missing file link 'isCircular'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:86: missing file link 'genome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:134: missing file link 'Vector'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:152: missing file link 'IPos'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:171: missing file link 'snpsBySeqname'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:172: missing file link 'snpsByOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:173: missing file link 'snpsById'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:174: missing file link 'SNPlocs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:177: missing file link 'SummarizedExperiment'
    GRanges-class                           html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:96: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:98: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:100: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:102: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:120: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:124: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:128: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:173: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:345: missing file link 'ManyToOneGrouping'
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    constraint                              html  
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    findOverlaps-methods                    html  
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    genomic-range-squeezers                 html  
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    genomicvars                             html  
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    inter-range-methods                     html  
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    intra-range-methods                     html  
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    makeGRangesFromDataFrame                html  
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    makeGRangesListFromDataFrame            html  
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    nearest-methods                         html  
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    phicoef                                 html  
    setops-methods                          html  
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    strand-utils                            html  
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    tile-methods                            html  
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Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/tile-methods.Rd:65: missing file link 'tile'
    tileGenome                              html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/tileGenome.Rd:68: missing file link 'IntegerList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/tileGenome.Rd:70: missing file link 'Views'
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'GenomicRanges' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c transcript_utils.c -o transcript_utils.o
transcript_utils.c: In function 'tlocs2rlocs':
transcript_utils.c:143:38: warning: 'end' may be used uninitialized in this function [-Wmaybe-uninitialized]
  return on_minus_strand ? end - tloc : start + tloc;
                                      ^
transcript_utils.c:120:24: note: 'end' was declared here
  int nexons, j, start, end, width;
                        ^
transcript_utils.c:143:38: warning: 'start' may be used uninitialized in this function [-Wmaybe-uninitialized]
  return on_minus_strand ? end - tloc : start + tloc;
                                      ^
transcript_utils.c:120:17: note: 'start' was declared here
  int nexons, j, start, end, width;
                 ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o GenomicRanges.dll tmp.def IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicRanges.buildbin-libdir/GenomicRanges/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicRanges' as GenomicRanges_1.30.3.zip
* DONE (GenomicRanges)
In R CMD INSTALL
In R CMD INSTALL

Tests output

GenomicRanges.Rcheck/tests_i386/run_unitTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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("GenomicRanges") || stop("unable to load GenomicRanges package")
Loading required package: GenomicRanges
Loading required package: stats4
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, cbind, colMeans, colSums, colnames, 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

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
[1] TRUE
> GenomicRanges:::.test()


RUNIT TEST PROTOCOL -- Thu Apr 12 00:25:43 2018 
*********************************************** 
Number of test functions: 70 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GenomicRanges RUnit Tests - 70 test functions, 0 errors, 0 failures
Number of test functions: 70 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  36.15    0.12   36.60

GenomicRanges.Rcheck/tests_x64/run_unitTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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("GenomicRanges") || stop("unable to load GenomicRanges package")
Loading required package: GenomicRanges
Loading required package: stats4
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, cbind, colMeans, colSums, colnames, 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

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
[1] TRUE
> GenomicRanges:::.test()


RUNIT TEST PROTOCOL -- Thu Apr 12 00:26:43 2018 
*********************************************** 
Number of test functions: 70 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GenomicRanges RUnit Tests - 70 test functions, 0 errors, 0 failures
Number of test functions: 70 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  59.70    0.12   59.85

Example timings

GenomicRanges.Rcheck/examples_i386/GenomicRanges-Ex.timings

nameusersystemelapsed
GNCList-class0.950.000.95
GPos-class32.17 6.1442.75
GRanges-class2.030.252.28
GRangesList-class0.560.000.56
GenomicRanges-comparison0.320.000.31
absoluteRanges1.890.112.00
constraint1.630.081.70
coverage-methods0.340.000.34
findOverlaps-methods1.50.01.5
genomic-range-squeezers000
genomicvars52.6915.0467.86
inter-range-methods1.980.412.39
intra-range-methods0.360.000.36
makeGRangesFromDataFrame 0.97 0.0019.77
makeGRangesListFromDataFrame0.080.000.08
nearest-methods0.590.000.59
phicoef0.030.000.03
setops-methods1.860.031.89
strand-utils0.080.000.08
tile-methods0.080.000.08
tileGenome0.270.000.26

GenomicRanges.Rcheck/examples_x64/GenomicRanges-Ex.timings

nameusersystemelapsed
GNCList-class1.170.021.19
GPos-class31.07 5.8436.91
GRanges-class1.810.111.92
GRangesList-class0.610.000.61
GenomicRanges-comparison0.320.000.31
absoluteRanges1.540.131.67
constraint1.570.011.58
coverage-methods0.250.000.25
findOverlaps-methods1.210.001.22
genomic-range-squeezers000
genomicvars61.8818.4780.40
inter-range-methods3.920.414.33
intra-range-methods0.780.000.78
makeGRangesFromDataFrame 2.11 0.0120.89
makeGRangesListFromDataFrame0.110.000.11
nearest-methods0.920.000.92
phicoef0.030.000.03
setops-methods2.390.002.39
strand-utils0.130.000.13
tile-methods0.070.000.07
tileGenome0.250.020.27