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CHECK report for IRanges on tokay1

This page was generated on 2018-04-12 13:17:25 -0400 (Thu, 12 Apr 2018).

Package 712/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IRanges 2.12.0
Bioconductor Package Maintainer
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/IRanges
Branch: RELEASE_3_6
Last Commit: 1b17486
Last Changed Date: 2017-10-30 12:39:00 -0400 (Mon, 30 Oct 2017)
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: IRanges
Version: 2.12.0
Command: rm -rf IRanges.buildbin-libdir IRanges.Rcheck && mkdir IRanges.buildbin-libdir IRanges.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IRanges.buildbin-libdir IRanges_2.12.0.tar.gz >IRanges.Rcheck\00install.out 2>&1 && cp IRanges.Rcheck\00install.out IRanges-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=IRanges.buildbin-libdir --install="check:IRanges-install.out" --force-multiarch --no-vignettes --timings IRanges_2.12.0.tar.gz
StartedAt: 2018-04-12 00:53:02 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:59:37 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 394.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: IRanges.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   rm -rf IRanges.buildbin-libdir IRanges.Rcheck && mkdir IRanges.buildbin-libdir IRanges.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IRanges.buildbin-libdir IRanges_2.12.0.tar.gz >IRanges.Rcheck\00install.out 2>&1 && cp IRanges.Rcheck\00install.out IRanges-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=IRanges.buildbin-libdir --install="check:IRanges-install.out" --force-multiarch --no-vignettes --timings IRanges_2.12.0.tar.gz
###
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##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/IRanges.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 'IRanges/DESCRIPTION' ... OK
* this is package 'IRanges' version '2.12.0'
* 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 'IRanges' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/AtomicList-class.Rd:307: missing file link 'List'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:42: missing file link 'SimpleList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:43: missing file link 'List'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:48: missing file link 'SimpleList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:53: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:54: missing file link 'GAlignmentsList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:64: missing file link 'SimpleList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:70: missing file link 'SimpleList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:85: missing file link 'List'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:88: missing file link 'SimpleList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:91: missing file link 'List'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:93: missing file link 'SimpleList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:99: missing file link 'List'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:104: missing file link 'List'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:109: missing file link 'List'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:114: missing file link 'List'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:122: missing file link 'classNameForDisplay'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:128: missing file link 'List'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:131: missing file link 'SimpleList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/Hits-class-leftovers.Rd:31: missing file link 'Hits'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/Hits-class-leftovers.Rd:68: missing file link 'Hits'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/IPos-class.Rd:109: missing file link 'Vector'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/IPos-class.Rd:123: missing file link 'GPos'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/List-class-leftovers.Rd:11: missing file link 'List'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/List-class-leftovers.Rd:35: missing file link 'List'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/MaskCollection-class.Rd:206: missing file link 'alphabetFrequency'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/NCList-class.Rd:77: missing file link 'GNCList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/NCList-class.Rd:97: missing file link 'GNCList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/NCList-class.Rd:98: missing file link 'GenomicRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/NCList-class.Rd:106: missing file link 'GenomicRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/NCList-class.Rd:121: missing file link 'GenomicRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/NCList-class.Rd:123: missing file link 'GNCList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/NCList-class.Rd:126: missing file link 'GNCList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/NCList-class.Rd:150: missing file link 'GNCList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/RangedData-class.Rd:78: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/RangedData-class.Rd:78: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/RangedData-class.Rd:80: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/RangedData-class.Rd:80: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/RangedData-class.Rd:84: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/RangedData-class.Rd:85: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/Ranges-class.Rd:243: missing file link 'Hits'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/Ranges-class.Rd:243: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/Ranges-class.Rd:244: missing file link 'GPos'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/Ranges-class.Rd:244: missing file link 'GAlignments'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/Ranges-class.Rd:245: missing file link 'XStringSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/Ranges-comparison.Rd:161: missing file link 'GenomicRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/Rle-class-leftovers.Rd:22: missing file link 'Rle'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/Rle-class-leftovers.Rd:71: missing file link 'Rle'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/Vector-class-leftovers.Rd:34: missing file link 'Vector'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/Vector-class-leftovers.Rd:159: missing file link 'Vector'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/Views-class.Rd:45: missing file link 'XIntegerViews'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/Views-class.Rd:46: missing file link 'XStringViews'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/Views-class.Rd:155: missing file link 'XVector'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/extractList.Rd:24: missing file link 'split'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/extractList.Rd:95: missing file link 'relistToClass'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/extractList.Rd:149: missing file link 'relistToClass'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/extractList.Rd:160: missing file link 'unsplit'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/extractList.Rd:163: missing file link 'split'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/extractList.Rd:166: missing file link 'Vector'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/extractList.Rd:166: missing file link 'List'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/extractList.Rd:167: missing file link 'Rle'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/extractList.Rd:167: missing file link 'DataFrame'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/extractList.Rd:169: missing file link 'relistToClass'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/extractList.Rd:170: missing file link 'List'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:82: missing file link 'findOverlaps,GenomicRanges,GenomicRanges-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:84: missing file link 'GenomicRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:84: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:193: missing file link 'Hits'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:201: missing file link 'HitsList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:213: missing file link 'Hits'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:213: missing file link 'HitsList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:270: missing file link 'Hits'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:270: missing file link 'HitsList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:278: missing file link 'Hits'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:279: missing file link 'HitsList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:310: missing file link 'Hits'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:310: missing file link 'HitsList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:314: missing file link 'findOverlaps,GenomicRanges,GenomicRanges-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:316: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:316: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/inter-range-methods.Rd:266: missing file link 'endoapply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/intra-range-methods.Rd:281: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/intra-range-methods.Rd:282: missing file link 'promoters,GenomicRanges-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/intra-range-methods.Rd:337: missing file link 'endoapply'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/nearest-methods.Rd:147: missing file link 'breakTies'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/nearest-methods.Rd:173: missing file link 'GenomicRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/nearest-methods.Rd:174: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/nearest-methods.Rd:187: missing file link 'precede,GenomicRanges,GenomicRanges-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:15: missing file link 'granges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:16: missing file link 'grglist'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:18: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:19: missing file link 'granges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:20: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:21: missing file link 'grglist'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:32: missing file link 'GenomicRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:33: missing file link 'RangedSummarizedExperiment'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:34: missing file link 'GAlignments'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:35: missing file link 'GAlignmentPairs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:36: missing file link 'GAlignmentsList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:37: missing file link 'Pairs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:63: missing file link 'GAlignments'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:64: missing file link 'GAlignmentPairs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:77: missing file link 'GAlignments'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:93: missing file link 'RangedSummarizedExperiment'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:96: missing file link 'GAlignments'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:97: missing file link 'GAlignmentPairs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:98: missing file link 'GAlignmentsList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/setops-methods.Rd:90: missing file link 'Pairs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/setops-methods.Rd:115: missing file link 'Pairs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/setops-methods.Rd:165: missing file link 'mendoapply'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/IRanges.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
setCompressedListSummaryMethod : <anonymous>: no visible binding for
  global variable 'C_fun'
setCompressedListWhichSummaryMethod : def: no visible binding for
  global variable 'C_fun'
overlapsAny,RangesList-RangedData: no visible global function
  definition for '.wmsg'
overlapsAny,RangesList-RangedData: no visible binding for global
  variable 'overlapsAny_RangedData_deprecation_msg'
Undefined global functions or variables:
  .wmsg C_fun overlapsAny_RangedData_deprecation_msg
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  '%poutside%' '%pover%' '%pwithin%' 'slidingIRanges' 'slidingViews'
Undocumented S4 methods:
  generic 'anyDuplicated' and siglist 'RangesNSBS'
  generic 'as.factor' and siglist 'ManyToOneGrouping'
  generic 'c' and siglist 'SimpleList'
  generic 'cbind' and siglist 'Rle'
  generic 'cbind' and siglist 'RleList'
  generic 'coerce' and siglist 'AtomicList,RleViews'
  generic 'coerce' and siglist 'PartitioningByEnd,PartitioningMap'
  generic 'coerce' and siglist 'factor,ManyToOneGrouping'
  generic 'colnames' and siglist 'SDFLWrapperForTransform'
  generic 'colnames' and siglist 'SplitDataFrameList'
  generic 'ifelse2' and siglist 'ANY,List,List'
  generic 'is.unsorted' and siglist 'CompressedIntegerList'
  generic 'is.unsorted' and siglist 'CompressedLogicalList'
  generic 'is.unsorted' and siglist 'CompressedNumericList'
  generic 'length' and siglist 'RangesNSBS'
  generic 'pcompareRecursively' and siglist 'Ranges'
  generic 'relist' and siglist 'grouping,missing'
  generic 'showAsCell' and siglist 'Views'
  generic 'splitAsList' and siglist 'ANY'
  generic 'stack' and siglist 'matrix'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'nearest-methods':
  'hits'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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/IRanges.buildbin-libdir/IRanges/libs/i386/IRanges.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
IPos-class 7.42    0.3    7.73
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
IPos-class 7.59   0.26    7.86
* 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: 3 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/IRanges.Rcheck/00check.log'
for details.

Installation output

IRanges.Rcheck/00install.out


install for i386

* installing *source* package 'IRanges' ...
** 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:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.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:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c CompressedIRangesList_class.c -o CompressedIRangesList_class.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:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c CompressedList_class.c -o CompressedList_class.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:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c Grouping_class.c -o Grouping_class.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:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c IRanges_class.c -o IRanges_class.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:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c IRanges_constructor.c -o IRanges_constructor.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:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c NCList.c -o NCList.o
NCList.c:202:22: warning: 'next_top_down' defined but not used [-Wunused-function]
 static const NCList *next_top_down(const NCList *nclist)
                      ^
NCList.c:1173:13: warning: 'NCList_get_y_overlaps_rec' defined but not used [-Wunused-function]
 static void NCList_get_y_overlaps_rec(const NCList *x_nclist,
             ^
NCList.c: In function 'NCList_find_overlaps':
NCList.c:1465:7: warning: 'ans' may be used uninitialized in this function [-Wmaybe-uninitialized]
  SEXP ans;
       ^
NCList.c: In function 'NCList_find_overlaps_in_groups':
NCList.c:1545:7: warning: 'ans' may be used uninitialized in this function [-Wmaybe-uninitialized]
  SEXP ans;
       ^
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:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_IRanges.c -o R_init_IRanges.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:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c Ranges_class.c -o Ranges_class.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:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c Ranges_comparison.c -o Ranges_comparison.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:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c RleViews_utils.c -o RleViews_utils.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:/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:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c SimpleRangesList_class.c -o SimpleRangesList_class.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:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c coverage_methods.c -o coverage_methods.o
coverage_methods.c: In function 'compute_coverage_from_IRanges_holder':
coverage_methods.c:503:28: warning: 'x_end' may be used uninitialized in this function [-Wmaybe-uninitialized]
  if (*out_ranges_are_tiles && x_end != cvg_len)
                            ^
coverage_methods.c:419:21: note: 'x_end' was declared here
      i, j, x_start, x_end, shift_elt, tmp;
                     ^
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:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c inter_range_methods.c -o inter_range_methods.o
inter_range_methods.c: In function 'Ranges_reduce':
inter_range_methods.c:154:11: warning: 'gapwidth' may be used uninitialized in this function [-Wmaybe-uninitialized]
     delta += gapwidth;
           ^
inter_range_methods.c:102:31: note: 'gapwidth' was declared here
      append_or_drop, max_end, gapwidth, delta, width_inc;
                               ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o IRanges.dll tmp.def CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o Ranges_comparison.o RleViews_utils.o S4Vectors_stubs.o SimpleRangesList_class.o coverage_methods.o inter_range_methods.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/IRanges.buildbin-libdir/IRanges/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'drop' from package 'base' in package 'IRanges'
Creating a generic function for 'smoothEnds' from package 'stats' in package 'IRanges'
Creating a generic function for 'runmed' from package 'stats' in package 'IRanges'
Creating a generic function for 'chartr' from package 'base' in package 'IRanges'
Creating a generic function for 'tolower' from package 'base' in package 'IRanges'
Creating a generic function for 'toupper' from package 'base' in package 'IRanges'
Creating a generic function for 'sub' from package 'base' in package 'IRanges'
Creating a generic function for 'gsub' from package 'base' in package 'IRanges'
** help
*** installing help indices
  converting help for package 'IRanges'
    finding HTML links ... done
    AtomicList-class                        html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/AtomicList-class.Rd:307: missing file link 'List'
    AtomicList-utils                        html  
    CompressedHitsList-class                html  
    CompressedList-class                    html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:42: missing file link 'SimpleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:43: missing file link 'List'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:48: missing file link 'SimpleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:53: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:54: missing file link 'GAlignmentsList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:64: missing file link 'SimpleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:70: missing file link 'SimpleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:85: missing file link 'List'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:88: missing file link 'SimpleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:91: missing file link 'List'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:93: missing file link 'SimpleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:99: missing file link 'List'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:104: missing file link 'List'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:109: missing file link 'List'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:114: missing file link 'List'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:122: missing file link 'classNameForDisplay'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:128: missing file link 'List'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/CompressedList-class.Rd:131: missing file link 'SimpleList'
    DataFrame-utils                         html  
    DataFrameList-class                     html  
    Grouping-class                          html  
    Hits-class-leftovers                    html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/Hits-class-leftovers.Rd:31: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/Hits-class-leftovers.Rd:68: missing file link 'Hits'
    IPos-class                              html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/IPos-class.Rd:109: missing file link 'Vector'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/IPos-class.Rd:123: missing file link 'GPos'
    IRanges-class                           html  
    IRanges-constructor                     html  
    IRanges-internals                       html  
    IRanges-utils                           html  
    IRangesList-class                       html  
    List-class-leftovers                    html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/List-class-leftovers.Rd:11: missing file link 'List'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/List-class-leftovers.Rd:35: missing file link 'List'
    MaskCollection-class                    html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/MaskCollection-class.Rd:206: missing file link 'alphabetFrequency'
    NCList-class                            html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/NCList-class.Rd:77: missing file link 'GNCList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/NCList-class.Rd:97: missing file link 'GNCList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/NCList-class.Rd:98: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/NCList-class.Rd:106: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/NCList-class.Rd:121: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/NCList-class.Rd:123: missing file link 'GNCList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/NCList-class.Rd:126: missing file link 'GNCList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/NCList-class.Rd:150: missing file link 'GNCList'
    RangedData-class                        html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/RangedData-class.Rd:78: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/RangedData-class.Rd:78: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/RangedData-class.Rd:80: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/RangedData-class.Rd:80: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/RangedData-class.Rd:84: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/RangedData-class.Rd:85: missing file link 'GRangesList'
    RangedSelection-class                   html  
    Ranges-class                            html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/Ranges-class.Rd:243: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/Ranges-class.Rd:243: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/Ranges-class.Rd:244: missing file link 'GPos'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/Ranges-class.Rd:244: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/Ranges-class.Rd:245: missing file link 'XStringSet'
    Ranges-comparison                       html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/Ranges-comparison.Rd:161: missing file link 'GenomicRanges'
    RangesList-class                        html  
    Rle-class-leftovers                     html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/Rle-class-leftovers.Rd:22: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/Rle-class-leftovers.Rd:71: missing file link 'Rle'
    RleViews-class                          html  
    RleViewsList-class                      html  
    Vector-class-leftovers                  html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/Vector-class-leftovers.Rd:34: missing file link 'Vector'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/Vector-class-leftovers.Rd:159: missing file link 'Vector'
    Views-class                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/Views-class.Rd:45: missing file link 'XIntegerViews'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/Views-class.Rd:46: missing file link 'XStringViews'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/Views-class.Rd:155: missing file link 'XVector'
    ViewsList-class                         html  
    coverage-methods                        html  
    extractList                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/extractList.Rd:24: missing file link 'split'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/extractList.Rd:95: missing file link 'relistToClass'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/extractList.Rd:149: missing file link 'relistToClass'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/extractList.Rd:160: missing file link 'unsplit'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/extractList.Rd:163: missing file link 'split'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/extractList.Rd:166: missing file link 'Vector'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/extractList.Rd:166: missing file link 'List'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/extractList.Rd:167: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/extractList.Rd:167: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/extractList.Rd:169: missing file link 'relistToClass'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/extractList.Rd:170: missing file link 'List'
    findOverlaps-methods                    html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:82: missing file link 'findOverlaps,GenomicRanges,GenomicRanges-method'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:84: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:84: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:193: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:201: missing file link 'HitsList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:213: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:213: missing file link 'HitsList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:270: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:270: missing file link 'HitsList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:278: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:279: missing file link 'HitsList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:310: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:310: missing file link 'HitsList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:314: missing file link 'findOverlaps,GenomicRanges,GenomicRanges-method'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:316: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/findOverlaps-methods.Rd:316: missing file link 'GRangesList'
    inter-range-methods                     html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/inter-range-methods.Rd:266: missing file link 'endoapply'
    intra-range-methods                     html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/intra-range-methods.Rd:281: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/intra-range-methods.Rd:282: missing file link 'promoters,GenomicRanges-method'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/intra-range-methods.Rd:337: missing file link 'endoapply'
    multisplit                              html  
    nearest-methods                         html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/nearest-methods.Rd:147: missing file link 'breakTies'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/nearest-methods.Rd:173: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/nearest-methods.Rd:174: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/nearest-methods.Rd:187: missing file link 'precede,GenomicRanges,GenomicRanges-method'
    range-squeezers                         html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:15: missing file link 'granges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:16: missing file link 'grglist'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:18: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:19: missing file link 'granges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:20: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:21: missing file link 'grglist'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:32: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:33: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:34: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:35: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:36: missing file link 'GAlignmentsList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:37: missing file link 'Pairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:63: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:64: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:77: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:93: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:96: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:97: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/range-squeezers.Rd:98: missing file link 'GAlignmentsList'
    read.Mask                               html  
    reverse-methods                         html  
    seqapply                                html  
    setops-methods                          html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/setops-methods.Rd:90: missing file link 'Pairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/setops-methods.Rd:115: missing file link 'Pairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpozrFIt/R.INSTALL1d284d273365/IRanges/man/setops-methods.Rd:165: missing file link 'mendoapply'
    slice-methods                           html  
    view-summarization-methods              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'IRanges' ...
** 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:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.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:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c CompressedIRangesList_class.c -o CompressedIRangesList_class.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:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c CompressedList_class.c -o CompressedList_class.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:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Grouping_class.c -o Grouping_class.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:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c IRanges_class.c -o IRanges_class.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:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c IRanges_constructor.c -o IRanges_constructor.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:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c NCList.c -o NCList.o
NCList.c:202:22: warning: 'next_top_down' defined but not used [-Wunused-function]
 static const NCList *next_top_down(const NCList *nclist)
                      ^
NCList.c:1173:13: warning: 'NCList_get_y_overlaps_rec' defined but not used [-Wunused-function]
 static void NCList_get_y_overlaps_rec(const NCList *x_nclist,
             ^
NCList.c: In function 'NCList_find_overlaps_in_groups':
NCList.c:1545:7: warning: 'ans' may be used uninitialized in this function [-Wmaybe-uninitialized]
  SEXP ans;
       ^
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:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_IRanges.c -o R_init_IRanges.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:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Ranges_class.c -o Ranges_class.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:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Ranges_comparison.c -o Ranges_comparison.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:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c RleViews_utils.c -o RleViews_utils.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:/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:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c SimpleRangesList_class.c -o SimpleRangesList_class.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:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c coverage_methods.c -o coverage_methods.o
coverage_methods.c: In function 'compute_coverage_from_IRanges_holder':
coverage_methods.c:503:28: warning: 'x_end' may be used uninitialized in this function [-Wmaybe-uninitialized]
  if (*out_ranges_are_tiles && x_end != cvg_len)
                            ^
coverage_methods.c:419:21: note: 'x_end' was declared here
      i, j, x_start, x_end, shift_elt, tmp;
                     ^
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:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c inter_range_methods.c -o inter_range_methods.o
inter_range_methods.c: In function 'reduce_ranges':
inter_range_methods.c:165:5: warning: 'revmap_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
     IntAE_insert_at(revmap_elt,
     ^
inter_range_methods.c:154:11: warning: 'delta' may be used uninitialized in this function [-Wmaybe-uninitialized]
     delta += gapwidth;
           ^
inter_range_methods.c:154:11: warning: 'gapwidth' may be used uninitialized in this function [-Wmaybe-uninitialized]
inter_range_methods.c:156:14: warning: 'max_end' may be used uninitialized in this function [-Wmaybe-uninitialized]
    width_inc = end_j - max_end;
              ^
inter_range_methods.c:131:6: warning: 'append_or_drop' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (append_or_drop) {
      ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o IRanges.dll tmp.def CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o Ranges_comparison.o RleViews_utils.o S4Vectors_stubs.o SimpleRangesList_class.o coverage_methods.o inter_range_methods.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/IRanges.buildbin-libdir/IRanges/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IRanges' as IRanges_2.12.0.zip
* DONE (IRanges)
In R CMD INSTALL
In R CMD INSTALL

Tests output

IRanges.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("IRanges") || stop("unable to load IRanges package")
Loading required package: IRanges
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
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

[1] TRUE
> IRanges:::.test()


RUNIT TEST PROTOCOL -- Thu Apr 12 00:57:10 2018 
*********************************************** 
Number of test functions: 89 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
IRanges RUnit Tests - 89 test functions, 0 errors, 0 failures
Number of test functions: 89 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  99.85    0.10   99.95

IRanges.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("IRanges") || stop("unable to load IRanges package")
Loading required package: IRanges
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
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

[1] TRUE
> IRanges:::.test()


RUNIT TEST PROTOCOL -- Thu Apr 12 00:59:29 2018 
*********************************************** 
Number of test functions: 89 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
IRanges RUnit Tests - 89 test functions, 0 errors, 0 failures
Number of test functions: 89 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 138.57    0.21  138.84

Example timings

IRanges.Rcheck/examples_i386/IRanges-Ex.timings

nameusersystemelapsed
AtomicList-class0.430.000.42
AtomicList-utils0.040.000.05
CompressedList-class0.010.000.02
DataFrame-utils0.240.000.23
Grouping-class0.110.000.11
Hits-class-leftovers0.110.010.13
IPos-class7.420.307.73
IRanges-class2.030.132.16
IRanges-constructor0.060.000.06
IRanges-utils2.000.072.08
IRangesList-class0.050.000.05
List-class-leftovers0.030.000.03
MaskCollection-class0.090.000.10
NCList-class0.060.020.08
RangedData-class1.140.001.14
RangedSelection-class0.020.010.03
Ranges-class0.060.000.06
Ranges-comparison0.080.000.08
RangesList-class0.030.000.03
Rle-class-leftovers000
RleViews-class0.060.000.06
RleViewsList-class0.070.000.06
Views-class0.060.000.06
ViewsList-class000
coverage-methods0.190.000.19
extractList0.040.000.05
findOverlaps-methods0.330.000.33
inter-range-methods0.520.000.51
intra-range-methods0.230.000.24
multisplit0.020.000.01
nearest-methods0.070.000.08
range-squeezers000
read.Mask0.080.000.08
reverse-methods0.050.000.04
setops-methods0.190.000.19
slice-methods000
view-summarization-methods0.030.000.03

IRanges.Rcheck/examples_x64/IRanges-Ex.timings

nameusersystemelapsed
AtomicList-class0.470.020.49
AtomicList-utils0.030.000.03
CompressedList-class0.020.000.01
DataFrame-utils0.230.000.24
Grouping-class0.140.000.14
Hits-class-leftovers0.130.000.12
IPos-class7.590.267.86
IRanges-class2.380.072.44
IRanges-constructor0.060.000.06
IRanges-utils2.410.062.47
IRangesList-class0.060.000.06
List-class-leftovers0.030.000.03
MaskCollection-class0.130.000.13
NCList-class0.070.000.08
RangedData-class1.280.001.28
RangedSelection-class0.040.000.03
Ranges-class0.090.000.09
Ranges-comparison0.110.000.11
RangesList-class0.050.000.05
Rle-class-leftovers000
RleViews-class0.070.000.08
RleViewsList-class0.100.000.09
Views-class0.080.000.08
ViewsList-class000
coverage-methods0.200.000.21
extractList0.070.000.06
findOverlaps-methods0.390.000.39
inter-range-methods0.670.000.67
intra-range-methods0.290.000.30
multisplit0.030.000.03
nearest-methods0.130.000.12
range-squeezers000
read.Mask0.090.000.10
reverse-methods0.060.000.06
setops-methods0.230.000.24
slice-methods000
view-summarization-methods0.040.000.03