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CHECK report for GenomicTuples on tokay1

This page was generated on 2019-04-13 11:24:30 -0400 (Sat, 13 Apr 2019).

Package 630/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicTuples 1.16.0
Peter Hickey
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/GenomicTuples
Branch: RELEASE_3_8
Last Commit: 3a2cd2b
Last Changed Date: 2018-10-30 11:41:55 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GenomicTuples
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicTuples.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GenomicTuples_1.16.0.tar.gz
StartedAt: 2019-04-13 02:33:42 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 02:37:57 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 254.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GenomicTuples.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicTuples.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GenomicTuples_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/GenomicTuples.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomicTuples/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GenomicTuples' version '1.16.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:75: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:82: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:86: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:91: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:94: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:101: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:109: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:132: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:139: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:151: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:214: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:238: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:267: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:275: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:278: file link 'DataTable' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:291: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:300: file link 'seqlevels' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:401: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:402: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:430: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:509: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:512: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:513: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:515: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:533: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:534: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:535: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:538: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:538: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:551: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-comparison.Rd:165: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:62: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:100: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:101: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:101: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:107: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:113: file link 'CompressedIRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:114: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:124: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:125: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:126: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:129: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:130: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:136: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:156: file link 'seqlevels' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:216: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:252: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:409: file link 'RleList-class' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/findOverlaps-methods.Rd:27: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/findOverlaps-methods.Rd:29: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/findOverlaps-methods.Rd:29: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/findOverlaps-methods.Rd:60: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/findOverlaps-methods.Rd:65: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/findOverlaps-methods.Rd:112: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/findOverlaps-methods.Rd:113: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/findOverlaps-methods.Rd:119: file link 'findOverlaps,GRangesList,GRangesList-method' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/findOverlaps-methods.Rd:132: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/findOverlaps-methods.Rd:133: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/findOverlaps-methods.Rd:147: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/findOverlaps-methods.Rd:172: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/findOverlaps-methods.Rd:173: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/illdefined-methods.Rd:56: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/illdefined-methods.Rd:57: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/intra-tuple-methods.Rd:43: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/nearest-methods.Rd:26: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/nearest-methods.Rd:70: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/nearest-methods.Rd:72: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/nearest-methods.Rd:147: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/nearest-methods.Rd:150: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/nearest-methods.Rd:165: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/nearest-methods.Rd:166: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/nearest-methods.Rd:167: file link 'IPosRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/nearest-methods.Rd:168: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/tuples-squeezers.Rd:13: file link 'granges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/tuples-squeezers.Rd:14: file link 'grglist' in package 'GenomicRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-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
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking 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-3.8-bioc/R/library/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 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, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/GenomicTuples.Rcheck/00check.log'
for details.

Installation output

GenomicTuples.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/GenomicTuples_1.16.0.tar.gz && rm -rf GenomicTuples.buildbin-libdir && mkdir GenomicTuples.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicTuples.buildbin-libdir GenomicTuples_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL GenomicTuples_1.16.0.zip && rm GenomicTuples_1.16.0.tar.gz GenomicTuples_1.16.0.zip
###
##############################################################################
##############################################################################


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100 77803  100 77803    0     0  1411k      0 --:--:-- --:--:-- --:--:-- 1519k

install for i386

* installing *source* package 'GenomicTuples' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c IPD.cpp -o IPD.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c allTuplesSorted.cpp -o allTuplesSorted.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/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:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/GenomicTuples.buildbin-libdir/GenomicTuples/libs/i386
** R
** inst
** byte-compile and prepare 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-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:75: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:82: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:86: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:91: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:94: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:101: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:109: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:132: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:139: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:151: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:214: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:238: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:267: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:275: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:278: file link 'DataTable' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:291: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:300: file link 'seqlevels' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:401: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:402: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:430: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:509: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:512: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:513: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:515: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:533: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:534: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:535: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:538: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:538: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-class.Rd:551: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
    GTuples-comparison                      html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuples-comparison.Rd:165: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
    GTuplesList-class                       html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:62: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:100: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:101: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:101: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:107: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:113: file link 'CompressedIRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:114: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:124: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:125: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:126: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:129: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:130: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:136: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:156: file link 'seqlevels' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:216: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:252: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/GTuplesList-class.Rd:409: file link 'RleList-class' in package 'IRanges' does not exist and so has been treated as a topic
    GenomicTuples-package                   html  
    findOverlaps-methods                    html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/findOverlaps-methods.Rd:27: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/findOverlaps-methods.Rd:29: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/findOverlaps-methods.Rd:29: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/findOverlaps-methods.Rd:60: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/findOverlaps-methods.Rd:65: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
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Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/findOverlaps-methods.Rd:132: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
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Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/findOverlaps-methods.Rd:147: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/findOverlaps-methods.Rd:172: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/findOverlaps-methods.Rd:173: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
    illdefined-methods                      html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/illdefined-methods.Rd:56: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/illdefined-methods.Rd:57: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
    intra-tuple-methods                     html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/intra-tuple-methods.Rd:43: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    nearest-methods                         html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/nearest-methods.Rd:26: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/nearest-methods.Rd:70: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/nearest-methods.Rd:72: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/nearest-methods.Rd:147: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/nearest-methods.Rd:150: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/nearest-methods.Rd:165: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/nearest-methods.Rd:166: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/nearest-methods.Rd:167: file link 'IPosRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/nearest-methods.Rd:168: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
    tuples-squeezers                        html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/tuples-squeezers.Rd:13: file link 'granges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpWMVYz6/R.INSTALL1f2046435140/GenomicTuples/man/tuples-squeezers.Rd:14: file link 'grglist' in package 'GenomicRanges' does not exist and so has been treated as a topic
** 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˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c IPD.cpp -o IPD.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c allTuplesSorted.cpp -o allTuplesSorted.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/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:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/GenomicTuples.buildbin-libdir/GenomicTuples/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicTuples' as GenomicTuples_1.16.0.zip
* DONE (GenomicTuples)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'GenomicTuples' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

GenomicTuples.Rcheck/tests_i386/testthat.Rout


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

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

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

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

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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
== testthat results  ===========================================================
OK: 1088 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  34.51    0.67   34.79

GenomicTuples.Rcheck/tests_x64/testthat.Rout


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

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

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

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

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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
== testthat results  ===========================================================
OK: 1088 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  38.17    1.01   38.92

Example timings

GenomicTuples.Rcheck/examples_i386/GenomicTuples-Ex.timings

nameusersystemelapsed
GTuples-class0.270.030.31
GTuples-comparison0.450.080.47
GTuplesList-class0.280.000.28
findOverlaps-methods0.410.010.39
illdefined-methods0.010.000.02
intra-tuple-methods0.060.020.08
nearest-methods0.380.000.37
tuples-squeezers000

GenomicTuples.Rcheck/examples_x64/GenomicTuples-Ex.timings

nameusersystemelapsed
GTuples-class0.390.030.45
GTuples-comparison0.560.030.59
GTuplesList-class0.370.000.38
findOverlaps-methods0.580.020.59
illdefined-methods0.010.000.01
intra-tuple-methods0.110.000.11
nearest-methods0.50.00.5
tuples-squeezers000