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CHECK report for GenomicTuples on tokay1

This page was generated on 2018-04-12 13:25:10 -0400 (Thu, 12 Apr 2018).

Package 569/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicTuples 1.12.0
Peter Hickey
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/GenomicTuples
Branch: RELEASE_3_6
Last Commit: 4db6e6d
Last Changed Date: 2017-10-30 12:40:42 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GenomicTuples
Version: 1.12.0
Command: rm -rf GenomicTuples.buildbin-libdir GenomicTuples.Rcheck && mkdir GenomicTuples.buildbin-libdir GenomicTuples.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicTuples.buildbin-libdir GenomicTuples_1.12.0.tar.gz >GenomicTuples.Rcheck\00install.out 2>&1 && cp GenomicTuples.Rcheck\00install.out GenomicTuples-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GenomicTuples.buildbin-libdir --install="check:GenomicTuples-install.out" --force-multiarch --no-vignettes --timings GenomicTuples_1.12.0.tar.gz
StartedAt: 2018-04-12 00:18:55 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:23:14 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 258.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GenomicTuples.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   rm -rf GenomicTuples.buildbin-libdir GenomicTuples.Rcheck && mkdir GenomicTuples.buildbin-libdir GenomicTuples.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicTuples.buildbin-libdir GenomicTuples_1.12.0.tar.gz >GenomicTuples.Rcheck\00install.out 2>&1 && cp GenomicTuples.Rcheck\00install.out GenomicTuples-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GenomicTuples.buildbin-libdir --install="check:GenomicTuples-install.out" --force-multiarch --no-vignettes --timings GenomicTuples_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicTuples.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 'GenomicTuples/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GenomicTuples' version '1.12.0'
* 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 'GenomicTuples' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:75: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:82: missing file link 'Rle'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:86: missing file link 'IRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:91: missing file link 'Rle'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:94: missing file link 'DataFrame'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:101: missing file link 'DataFrame'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:109: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:132: missing file link 'Rle'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:139: missing file link 'Rle'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:151: missing file link 'DataFrame'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:214: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:238: missing file link 'Rle'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:267: missing file link 'Rle'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:275: missing file link 'DataFrame'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:278: missing file link 'DataTable'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:291: missing file link 'DataFrame'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:300: missing file link 'seqlevels'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:401: missing file link 'DataFrame'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:402: missing file link 'DataFrame'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:430: missing file link 'Rle'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:509: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:512: missing file link 'IRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:513: missing file link 'GenomicRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:515: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:533: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:534: missing file link 'GAlignments'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:535: missing file link 'GAlignmentPairs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:538: missing file link 'IRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:538: missing file link 'DNAStringSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:552: missing file link 'DataFrame'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-comparison.Rd:165: missing file link 'Hits'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:62: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:100: missing file link 'RleList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:101: missing file link 'RleList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:101: missing file link 'CharacterList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:107: missing file link 'SimpleList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:113: missing file link 'CompressedIRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:114: missing file link 'RangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:124: missing file link 'RleList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:125: missing file link 'RleList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:126: missing file link 'CharacterList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:129: missing file link 'RleList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:130: missing file link 'CharacterList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:136: missing file link 'DataFrame'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:156: missing file link 'seqlevels'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:216: missing file link 'SimpleList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:252: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:409: missing file link 'RleList-class'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:102: missing file link 'findOverlaps'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:103: missing file link 'Ranges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:103: missing file link 'RangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:105: missing file link 'GenomicRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:106: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:108: missing file link 'GAlignments'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:109: missing file link 'GAlignmentPairs'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:110: missing file link 'GAlignmentsList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:140: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:141: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:141: missing file link 'RangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:142: missing file link 'RangedData'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:149: missing file link 'findOverlaps'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:153: missing file link 'findOverlaps'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:157: missing file link 'findOverlaps'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:201: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:202: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:208: missing file link 'findOverlaps,GRangesList,GRangesList-method'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:221: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:222: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:236: missing file link 'Hits'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:267: missing file link 'findOverlaps'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:268: missing file link 'findOverlaps'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/illdefined-methods.Rd:56: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/illdefined-methods.Rd:57: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/intra-tuple-methods.Rd:43: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/nearest-methods.Rd:26: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/nearest-methods.Rd:70: missing file link 'Hits'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/nearest-methods.Rd:72: missing file link 'Hits'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/nearest-methods.Rd:147: missing file link 'Hits'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/nearest-methods.Rd:150: missing file link 'Hits'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/nearest-methods.Rd:165: missing file link 'GenomicRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/nearest-methods.Rd:166: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/nearest-methods.Rd:167: missing file link 'Ranges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/nearest-methods.Rd:168: missing file link 'Hits'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/tuples-squeezers.Rd:13: missing file link 'granges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/tuples-squeezers.Rd:14: missing file link 'grglist'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicTuples.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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'GenomicRanges:::clone' 'GenomicRanges:::extraColumnSlotNames'
  'GenomicRanges:::extraColumnSlots'
  'GenomicRanges:::extraColumnSlotsAsDF' 'GenomicRanges:::showList'
  'S4Vectors:::VH_recycle' 'S4Vectors:::decodeRle'
  'S4Vectors:::makePrettyMatrixForCompactPrinting'
  'S4Vectors:::orderBy'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
coerce<-,GTuplesList-GRangesList: no visible global function definition
  for 'slot<-'
coerce<-,GTuplesList-GRangesList: no visible global function definition
  for 'slot'
Undefined global functions or variables:
  slot slot<-
Consider adding
  importFrom("methods", "slot", "slot<-")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking 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/GenomicTuples.buildbin-libdir/GenomicTuples/libs/i386/GenomicTuples.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicTuples.Rcheck/00check.log'
for details.

Installation output

GenomicTuples.Rcheck/00install.out


install for i386

* installing *source* package 'GenomicTuples' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c IPD.cpp -o IPD.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c allTuplesSorted.cpp -o allTuplesSorted.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c pcompareGTuples.cpp -o pcompareGTuples.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o GenomicTuples.dll tmp.def IPD.o RcppExports.o allTuplesSorted.o pcompareGTuples.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/GenomicTuples.buildbin-libdir/GenomicTuples/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'GenomicTuples'
    finding HTML links ... done
    GTuples-class                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:75: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:82: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:86: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:91: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:94: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:101: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:109: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:132: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:139: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:151: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:214: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:238: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:267: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:275: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:278: missing file link 'DataTable'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:291: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:300: missing file link 'seqlevels'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:401: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:402: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:430: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:509: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:512: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:513: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:515: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:533: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:534: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:535: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:538: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:538: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-class.Rd:552: missing file link 'DataFrame'
    GTuples-comparison                      html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuples-comparison.Rd:165: missing file link 'Hits'
    GTuplesList-class                       html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:62: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:100: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:101: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:101: missing file link 'CharacterList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:107: missing file link 'SimpleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:113: missing file link 'CompressedIRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:114: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:124: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:125: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:126: missing file link 'CharacterList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:129: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:130: missing file link 'CharacterList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:136: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:156: missing file link 'seqlevels'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:216: missing file link 'SimpleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:252: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/GTuplesList-class.Rd:409: missing file link 'RleList-class'
    GenomicTuples-package                   html  
    findOverlaps-methods                    html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:102: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:103: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:103: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:105: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:106: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:108: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:109: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:110: missing file link 'GAlignmentsList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:140: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:141: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:141: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:142: missing file link 'RangedData'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:149: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:153: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:157: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:201: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:202: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:208: missing file link 'findOverlaps,GRangesList,GRangesList-method'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:221: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:222: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:236: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:267: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/findOverlaps-methods.Rd:268: missing file link 'findOverlaps'
    illdefined-methods                      html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/illdefined-methods.Rd:56: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/illdefined-methods.Rd:57: missing file link 'GRangesList'
    intra-tuple-methods                     html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/intra-tuple-methods.Rd:43: missing file link 'GRanges'
    nearest-methods                         html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/nearest-methods.Rd:26: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/nearest-methods.Rd:70: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/nearest-methods.Rd:72: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/nearest-methods.Rd:147: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/nearest-methods.Rd:150: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/nearest-methods.Rd:165: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/nearest-methods.Rd:166: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/nearest-methods.Rd:167: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/nearest-methods.Rd:168: missing file link 'Hits'
    tuples-squeezers                        html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/tuples-squeezers.Rd:13: missing file link 'granges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpU1NYBw/R.INSTALL1e80766f7e18/GenomicTuples/man/tuples-squeezers.Rd:14: missing file link 'grglist'
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'GenomicTuples' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c IPD.cpp -o IPD.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c allTuplesSorted.cpp -o allTuplesSorted.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c pcompareGTuples.cpp -o pcompareGTuples.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o GenomicTuples.dll tmp.def IPD.o RcppExports.o allTuplesSorted.o pcompareGTuples.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/GenomicTuples.buildbin-libdir/GenomicTuples/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicTuples' as GenomicTuples_1.12.0.zip
* DONE (GenomicTuples)
In R CMD INSTALL
In R CMD INSTALL

Tests output

GenomicTuples.Rcheck/tests_i386/testthat.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.

> library(testthat)
> test_check("GenomicTuples")
Loading required package: GenomicTuples
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
== testthat results  ===========================================================
OK: 1088 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  33.10    0.25   33.28

GenomicTuples.Rcheck/tests_x64/testthat.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.

> library(testthat)
> test_check("GenomicTuples")
Loading required package: GenomicTuples
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
== testthat results  ===========================================================
OK: 1088 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  41.70    0.21   41.90

Example timings

GenomicTuples.Rcheck/examples_i386/GenomicTuples-Ex.timings

nameusersystemelapsed
GTuples-class0.810.000.81
GTuples-comparison0.580.000.58
GTuplesList-class0.70.00.7
findOverlaps-methods0.770.000.76
illdefined-methods0.010.000.02
intra-tuple-methods0.100.000.09
nearest-methods0.700.000.71
tuples-squeezers000

GenomicTuples.Rcheck/examples_x64/GenomicTuples-Ex.timings

nameusersystemelapsed
GTuples-class1.110.051.15
GTuples-comparison0.710.000.72
GTuplesList-class0.800.010.81
findOverlaps-methods0.620.020.64
illdefined-methods000
intra-tuple-methods0.080.000.07
nearest-methods0.840.000.85
tuples-squeezers000