| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:20:05 -0400 (Thu, 12 Apr 2018).
| Package 567/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GenomicRanges 1.30.3 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: GenomicRanges |
| Version: 1.30.3 |
| Command: rm -rf GenomicRanges.buildbin-libdir GenomicRanges.Rcheck && mkdir GenomicRanges.buildbin-libdir GenomicRanges.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicRanges.buildbin-libdir GenomicRanges_1.30.3.tar.gz >GenomicRanges.Rcheck\00install.out 2>&1 && cp GenomicRanges.Rcheck\00install.out GenomicRanges-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GenomicRanges.buildbin-libdir --install="check:GenomicRanges-install.out" --force-multiarch --no-vignettes --timings GenomicRanges_1.30.3.tar.gz |
| StartedAt: 2018-04-12 00:18:09 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 00:26:56 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 527.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GenomicRanges.Rcheck |
| Warnings: 2 |
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###
### Running command:
###
### rm -rf GenomicRanges.buildbin-libdir GenomicRanges.Rcheck && mkdir GenomicRanges.buildbin-libdir GenomicRanges.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicRanges.buildbin-libdir GenomicRanges_1.30.3.tar.gz >GenomicRanges.Rcheck\00install.out 2>&1 && cp GenomicRanges.Rcheck\00install.out GenomicRanges-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GenomicRanges.buildbin-libdir --install="check:GenomicRanges-install.out" --force-multiarch --no-vignettes --timings GenomicRanges_1.30.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicRanges.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomicRanges/DESCRIPTION' ... OK
* this is package 'GenomicRanges' version '1.30.3'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'GenomicRanges' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GNCList-class.Rd:46: missing file link 'NCList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GNCList-class.Rd:47: missing file link 'NCLists'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GNCList-class.Rd:48: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GNCList-class.Rd:49: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GNCList-class.Rd:55: missing file link 'NCList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GNCList-class.Rd:79: missing file link 'NCList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GNCList-class.Rd:79: missing file link 'NCLists'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:63: missing file link 'IPos'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:64: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:65: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:67: missing file link 'IPos'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:82: missing file link 'seqlevels'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:84: missing file link 'seqlengths'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:85: missing file link 'isCircular'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:86: missing file link 'genome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:134: missing file link 'Vector'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:152: missing file link 'IPos'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:171: missing file link 'snpsBySeqname'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:172: missing file link 'snpsByOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:173: missing file link 'snpsById'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:174: missing file link 'SNPlocs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:177: missing file link 'SummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:96: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:98: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:100: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:102: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:120: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:124: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:128: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:173: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:345: missing file link 'ManyToOneGrouping'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:523: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:524: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:527: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:527: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:537: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:575: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:577: missing file link 'Vector'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:577: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:578: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRangesList-class.Rd:208: missing file link 'IRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRangesList-class.Rd:368: missing file link 'RleList-class'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GenomicRanges-comparison.Rd:113: missing file link 'reduce'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GenomicRanges-comparison.Rd:113: missing file link 'disjoin'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GenomicRangesList-class.Rd:16: missing file link 'List'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/absoluteRanges.Rd:39: missing file link 'seqlengths'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/absoluteRanges.Rd:41: missing file link 'seqlengths'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/absoluteRanges.Rd:50: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/absoluteRanges.Rd:65: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/absoluteRanges.Rd:86: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/coverage-methods.Rd:12: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/coverage-methods.Rd:15: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/coverage-methods.Rd:16: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/coverage-methods.Rd:16: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/coverage-methods.Rd:18: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/coverage-methods.Rd:19: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/coverage-methods.Rd:45: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/coverage-methods.Rd:54: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/coverage-methods.Rd:67: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/coverage-methods.Rd:71: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/coverage-methods.Rd:82: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/coverage-methods.Rd:90: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/coverage-methods.Rd:95: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/findOverlaps-methods.Rd:26: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/findOverlaps-methods.Rd:27: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/findOverlaps-methods.Rd:27: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/findOverlaps-methods.Rd:29: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/findOverlaps-methods.Rd:30: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/findOverlaps-methods.Rd:31: missing file link 'GAlignmentsList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/findOverlaps-methods.Rd:59: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/findOverlaps-methods.Rd:99: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/findOverlaps-methods.Rd:113: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:16: missing file link 'ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:17: missing file link 'rglist'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:19: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:19: missing file link 'ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:21: missing file link 'IRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:21: missing file link 'rglist'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:32: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:33: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:34: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:35: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:36: missing file link 'GAlignmentsList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:37: missing file link 'Pairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:40: missing file link 'ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:46: missing file link 'ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:49: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:50: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:63: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:79: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:82: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:83: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomic-range-squeezers.Rd:84: missing file link 'GAlignmentsList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomicvars.Rd:20: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomicvars.Rd:49: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomicvars.Rd:60: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomicvars.Rd:80: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomicvars.Rd:91: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/genomicvars.Rd:105: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/inter-range-methods.Rd:104: missing file link 'reduce'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/inter-range-methods.Rd:112: missing file link 'gaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/inter-range-methods.Rd:121: missing file link 'disjoin'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/inter-range-methods.Rd:145: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/inter-range-methods.Rd:153: missing file link 'endoapply'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/intra-range-methods.Rd:53: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/intra-range-methods.Rd:54: missing file link 'GAlignmentsList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/intra-range-methods.Rd:118: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/intra-range-methods.Rd:122: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/intra-range-methods.Rd:126: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/intra-range-methods.Rd:194: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/intra-range-methods.Rd:196: missing file link 'endoapply'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/makeGRangesFromDataFrame.Rd:16: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/makeGRangesFromDataFrame.Rd:37: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/makeGRangesFromDataFrame.Rd:120: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/makeGRangesFromDataFrame.Rd:142: missing file link 'getTable'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/makeGRangesFromDataFrame.Rd:146: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/makeGRangesListFromDataFrame.Rd:15: missing file link 'split'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/nearest-methods.Rd:69: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/nearest-methods.Rd:141: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/nearest-methods.Rd:144: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/nearest-methods.Rd:157: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/nearest-methods.Rd:158: missing file link 'Hits'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/setops-methods.Rd:45: missing file link 'punion'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/setops-methods.Rd:45: missing file link 'pintersect'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/setops-methods.Rd:46: missing file link 'psetdiff'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/setops-methods.Rd:46: missing file link 'pgap'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/setops-methods.Rd:47: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/setops-methods.Rd:155: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/setops-methods.Rd:155: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/setops-methods.Rd:167: missing file link 'mendoapply'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/strand-utils.Rd:52: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/strand-utils.Rd:64: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/strand-utils.Rd:65: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/strand-utils.Rd:73: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/strand-utils.Rd:96: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/tile-methods.Rd:12: missing file link 'tile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/tile-methods.Rd:12: missing file link 'slidingWindows'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/tile-methods.Rd:30: missing file link 'tile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/tile-methods.Rd:35: missing file link 'tile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/tile-methods.Rd:65: missing file link 'tile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/tileGenome.Rd:68: missing file link 'IntegerList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/tileGenome.Rd:70: missing file link 'Views'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicRanges.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
poverlaps,GenomicRanges-GenomicRanges: no visible binding for global
variable 'minoverlaps'
Undefined global functions or variables:
minoverlaps
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'inter-range-methods':
\S4method{reduce}{GenomicRangesList}
Code: function(x, drop.empty.ranges = FALSE, ...)
Docs: function(x, drop.empty.ranges = FALSE, min.gapwidth = 1L,
with.inframe.attrib = FALSE, ignore.strand = FALSE)
Argument names in code not in docs:
...
Argument names in docs not in code:
min.gapwidth with.inframe.attrib ignore.strand
Mismatches in argument names:
Position: 3 Code: ... Docs: min.gapwidth
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicRanges.buildbin-libdir/GenomicRanges/libs/i386/GenomicRanges.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
genomicvars 52.69 15.04 67.86
GPos-class 32.17 6.14 42.75
makeGRangesFromDataFrame 0.97 0.00 19.77
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
genomicvars 61.88 18.47 80.40
GPos-class 31.07 5.84 36.91
makeGRangesFromDataFrame 2.11 0.01 20.89
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'run_unitTests.R'
OK
** running tests for arch 'x64' ...
Running 'run_unitTests.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicRanges.Rcheck/00check.log'
for details.
GenomicRanges.Rcheck/00install.out
install for i386
* installing *source* package 'GenomicRanges' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c transcript_utils.c -o transcript_utils.o
transcript_utils.c: In function 'tlocs2rlocs':
transcript_utils.c:143:38: warning: 'end' may be used uninitialized in this function [-Wmaybe-uninitialized]
return on_minus_strand ? end - tloc : start + tloc;
^
transcript_utils.c:120:24: note: 'end' was declared here
int nexons, j, start, end, width;
^
transcript_utils.c:143:38: warning: 'start' may be used uninitialized in this function [-Wmaybe-uninitialized]
return on_minus_strand ? end - tloc : start + tloc;
^
transcript_utils.c:120:17: note: 'start' was declared here
int nexons, j, start, end, width;
^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o GenomicRanges.dll tmp.def IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicRanges.buildbin-libdir/GenomicRanges/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'GenomicRanges'
finding HTML links ... done
DelegatingGenomicRanges-class html
GNCList-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GNCList-class.Rd:46: missing file link 'NCList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GNCList-class.Rd:47: missing file link 'NCLists'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GNCList-class.Rd:48: missing file link 'Ranges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GNCList-class.Rd:49: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GNCList-class.Rd:55: missing file link 'NCList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GNCList-class.Rd:79: missing file link 'NCList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GNCList-class.Rd:79: missing file link 'NCLists'
GPos-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:63: missing file link 'IPos'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:64: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:65: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:67: missing file link 'IPos'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:82: missing file link 'seqlevels'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:84: missing file link 'seqlengths'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:85: missing file link 'isCircular'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:86: missing file link 'genome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:134: missing file link 'Vector'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:152: missing file link 'IPos'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:171: missing file link 'snpsBySeqname'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:172: missing file link 'snpsByOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:173: missing file link 'snpsById'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:174: missing file link 'SNPlocs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GPos-class.Rd:177: missing file link 'SummarizedExperiment'
GRanges-class html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:96: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:98: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:100: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:102: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:120: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:124: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:128: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:173: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:345: missing file link 'ManyToOneGrouping'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:523: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:524: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:527: missing file link 'IRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:527: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpyM1mLg/R.INSTALL1e50589d161b/GenomicRanges/man/GRanges-class.Rd:537: missing file link 'DataFrame'
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GenomicRanges-comparison html
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GenomicRangesList-class html
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absoluteRanges html
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constraint html
coverage-methods html
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findOverlaps-methods html
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genomic-range-squeezers html
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genomicvars html
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inter-range-methods html
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intra-range-methods html
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makeGRangesFromDataFrame html
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makeGRangesListFromDataFrame html
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nearest-methods html
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phicoef html
setops-methods html
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strand-utils html
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tile-methods html
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tileGenome html
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** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'GenomicRanges' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c transcript_utils.c -o transcript_utils.o
transcript_utils.c: In function 'tlocs2rlocs':
transcript_utils.c:143:38: warning: 'end' may be used uninitialized in this function [-Wmaybe-uninitialized]
return on_minus_strand ? end - tloc : start + tloc;
^
transcript_utils.c:120:24: note: 'end' was declared here
int nexons, j, start, end, width;
^
transcript_utils.c:143:38: warning: 'start' may be used uninitialized in this function [-Wmaybe-uninitialized]
return on_minus_strand ? end - tloc : start + tloc;
^
transcript_utils.c:120:17: note: 'start' was declared here
int nexons, j, start, end, width;
^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o GenomicRanges.dll tmp.def IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicRanges.buildbin-libdir/GenomicRanges/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicRanges' as GenomicRanges_1.30.3.zip
* DONE (GenomicRanges)
In R CMD INSTALL
In R CMD INSTALL
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GenomicRanges.Rcheck/tests_i386/run_unitTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require("GenomicRanges") || stop("unable to load GenomicRanges package")
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
[1] TRUE
> GenomicRanges:::.test()
RUNIT TEST PROTOCOL -- Thu Apr 12 00:25:43 2018
***********************************************
Number of test functions: 70
Number of errors: 0
Number of failures: 0
1 Test Suite :
GenomicRanges RUnit Tests - 70 test functions, 0 errors, 0 failures
Number of test functions: 70
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
36.15 0.12 36.60
|
GenomicRanges.Rcheck/tests_x64/run_unitTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require("GenomicRanges") || stop("unable to load GenomicRanges package")
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
[1] TRUE
> GenomicRanges:::.test()
RUNIT TEST PROTOCOL -- Thu Apr 12 00:26:43 2018
***********************************************
Number of test functions: 70
Number of errors: 0
Number of failures: 0
1 Test Suite :
GenomicRanges RUnit Tests - 70 test functions, 0 errors, 0 failures
Number of test functions: 70
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
59.70 0.12 59.85
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GenomicRanges.Rcheck/examples_i386/GenomicRanges-Ex.timings
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GenomicRanges.Rcheck/examples_x64/GenomicRanges-Ex.timings
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