Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 11:57:30 -0400 (Tue, 09 Apr 2019).
Package 647/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
GenomicFeatures 1.35.9 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK |
Package: GenomicFeatures |
Version: 1.35.9 |
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicFeatures.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GenomicFeatures_1.35.9.tar.gz |
StartedAt: 2019-04-09 03:00:20 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 03:30:06 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 1786.2 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: GenomicFeatures.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicFeatures.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GenomicFeatures_1.35.9.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GenomicFeatures.Rcheck' * using R Under development (unstable) (2019-03-09 r76216) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'GenomicFeatures/DESCRIPTION' ... OK * this is package 'GenomicFeatures' version '1.35.9' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomeInfoDb', 'GenomicRanges', 'AnnotationDbi' Adding so many packages to the search path is excessive and importing selectively is preferable. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section 'Package structure' in the 'Writing R Extensions' manual. * checking for portable file names ... OK * checking whether package 'GenomicFeatures' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/TxDb-class.Rd:97: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/TxDb-class.Rd:100: file link 'saveDb' in package 'AnnotationDbi' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/TxDb-class.Rd:101: file link 'loadDb' in package 'AnnotationDbi' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coordinate-mapping-methods.Rd:28: file link 'mapToAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coordinate-mapping-methods.Rd:54: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coordinate-mapping-methods.Rd:58: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coordinate-mapping-methods.Rd:61: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coordinate-mapping-methods.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-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coordinate-mapping-methods.Rd:231: file link 'mapToAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:25: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:25: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:26: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:27: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:28: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:32: file link 'coverage' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:33: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:35: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:38: file link 'grglist' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:43: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:55: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:70: file link 'grglist' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:71: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:72: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:74: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:75: file link 'grglist' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:80: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:81: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:102: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:105: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:108: file link 'coverage' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:114: file link 'findCompatibleOverlaps' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/disjointExons.Rd:47: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/disjointExons.Rd:58: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/exonicParts.Rd:38: file link 'disjoin' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/exonicParts.Rd:44: file link 'disjoin' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/exonicParts.Rd:82: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/exonicParts.Rd:87: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/exonicParts.Rd:90: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/exonicParts.Rd:94: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/exonicParts.Rd:99: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/exonicParts.Rd:133: file link 'disjoin' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:26: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:27: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:31: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:40: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:41: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:44: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:46: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:49: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:74: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:79: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:81: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:84: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:87: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:93: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:103: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:125: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:125: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:132: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractTranscriptSeqs.Rd:135: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractUpstreamSeqs.Rd:29: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractUpstreamSeqs.Rd:30: file link 'TwoBitFile' in package 'rtracklayer' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractUpstreamSeqs.Rd:30: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractUpstreamSeqs.Rd:39: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractUpstreamSeqs.Rd:57: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractUpstreamSeqs.Rd:59: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractUpstreamSeqs.Rd:61: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractUpstreamSeqs.Rd:65: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractUpstreamSeqs.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-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractUpstreamSeqs.Rd:116: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractUpstreamSeqs.Rd:116: file link 'TwoBitFile' in package 'rtracklayer' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractUpstreamSeqs.Rd:117: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractUpstreamSeqs.Rd:126: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/extractUpstreamSeqs.Rd:129: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/getPromoterSeq-methods.Rd:11: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/getPromoterSeq-methods.Rd:11: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/getPromoterSeq-methods.Rd:21: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/getPromoterSeq-methods.Rd:21: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/getPromoterSeq-methods.Rd:24: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/getPromoterSeq-methods.Rd:24: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/getPromoterSeq-methods.Rd:36: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic Rd warning: 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file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/transcriptsBy.Rd:49: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/transcriptsBy.Rd:52: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/transcriptsBy.Rd:54: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/transcriptsBy.Rd:79: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/transcriptsBy.Rd:89: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/transcriptsByOverlaps.Rd:46: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/transcriptsByOverlaps.Rd:49: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/transcriptsByOverlaps.Rd:59: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GenomicFeatures.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 ':::' calls which should be '::': 'S4Vectors:::duplicatedIntegerPairs' 'S4Vectors:::matchIntegerPairs' 'S4Vectors:::orderIntegerPairs' See the note in ?`:::` about the use of this operator. Unexported objects imported by ':::' calls: 'biomaRt:::martBM' 'biomaRt:::martDataset' 'biomaRt:::martHost' 'rtracklayer:::resourceDescription' 'rtracklayer:::ucscTableOutputs' 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed exonicParts 67.83 4.34 75.98 makeTxDbFromBiomart 42.97 2.33 187.28 coverageByTranscript 33.11 6.77 39.88 makeFeatureDbFromUCSC 36.17 2.26 139.31 extractTranscriptSeqs 12.48 0.20 12.69 makeTxDbFromGFF 8.74 0.19 61.65 coordinate-mapping-methods 8.55 0.19 8.95 makeTxDbFromGRanges 2.23 0.01 8.74 mapIdsToRanges 0.59 0.00 35.36 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed coordinate-mapping-methods 51.55 2.07 188.83 exonicParts 50.78 2.72 53.51 makeFeatureDbFromUCSC 46.08 1.13 118.56 makeTxDbFromBiomart 43.46 2.22 147.93 coverageByTranscript 26.50 7.89 34.39 extractTranscriptSeqs 11.69 0.14 11.83 makeTxDbFromGFF 7.64 0.06 7.70 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'run_unitTests.R' ERROR Running the tests in 'tests/run_unitTests.R' failed. Last 13 lines of output: Error in BiocGenerics:::testPackage("GenomicFeatures") : unit tests failed for package GenomicFeatures Calls: <Anonymous> -> <Anonymous> In addition: Warning messages: 1: In .get_cds_IDX(type, phase) : The "phase" metadata column contains non-NA values for features of type exon. This information was ignored. 2: In .get_cds_IDX(type, phase) : The "phase" metadata column contains non-NA values for features of type stop_codon. This information was ignored. 3: In .get_cds_IDX(type, phase) : The "phase" metadata column contains non-NA values for features of type stop_codon. This information was ignored. Execution halted ** running tests for arch 'x64' ... Running 'run_unitTests.R' ERROR Running the tests in 'tests/run_unitTests.R' failed. Last 13 lines of output: Error in BiocGenerics:::testPackage("GenomicFeatures") : unit tests failed for package GenomicFeatures Calls: <Anonymous> -> <Anonymous> In addition: Warning messages: 1: In .get_cds_IDX(type, phase) : The "phase" metadata column contains non-NA values for features of type exon. This information was ignored. 2: In .get_cds_IDX(type, phase) : The "phase" metadata column contains non-NA values for features of type stop_codon. This information was ignored. 3: In .get_cds_IDX(type, phase) : The "phase" metadata column contains non-NA values for features of type stop_codon. This information was ignored. Execution halted * 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 ERRORs, 1 WARNING, 3 NOTEs See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GenomicFeatures.Rcheck/00check.log' for details.
GenomicFeatures.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/GenomicFeatures_1.35.9.tar.gz && rm -rf GenomicFeatures.buildbin-libdir && mkdir GenomicFeatures.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicFeatures.buildbin-libdir GenomicFeatures_1.35.9.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GenomicFeatures_1.35.9.zip && rm GenomicFeatures_1.35.9.tar.gz GenomicFeatures_1.35.9.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 1127k 100 1127k 0 0 4312k 0 --:--:-- --:--:-- --:--:-- 4420k install for i386 * installing *source* package 'GenomicFeatures' ... ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'GenomicFeatures' finding HTML links ... done DEFAULT_CIRC_SEQS html FeatureDb-class html finding level-2 HTML links ... done TxDb-class html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/TxDb-class.Rd:97: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/TxDb-class.Rd:100: file link 'saveDb' in package 'AnnotationDbi' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/TxDb-class.Rd:101: file link 'loadDb' in package 'AnnotationDbi' does not exist and so has been treated as a topic as-format-methods html coordinate-mapping-methods html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coordinate-mapping-methods.Rd:28: file link 'mapToAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coordinate-mapping-methods.Rd:54: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coordinate-mapping-methods.Rd:58: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coordinate-mapping-methods.Rd:61: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coordinate-mapping-methods.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-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coordinate-mapping-methods.Rd:231: file link 'mapToAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic coverageByTranscript html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:25: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:25: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:26: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:27: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:28: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:32: file link 'coverage' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:33: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:35: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:38: file link 'grglist' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/coverageByTranscript.Rd:43: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: 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C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/transcriptsBy.Rd:54: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/transcriptsBy.Rd:79: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/transcriptsBy.Rd:89: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic transcriptsByOverlaps html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/transcriptsByOverlaps.Rd:46: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/transcriptsByOverlaps.Rd:49: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUf73eW/R.INSTALL1a187a282f5f/GenomicFeatures/man/transcriptsByOverlaps.Rd:59: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'GenomicFeatures' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'GenomicFeatures' as GenomicFeatures_1.35.9.zip * DONE (GenomicFeatures) * installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library' package 'GenomicFeatures' successfully unpacked and MD5 sums checked
GenomicFeatures.Rcheck/tests_i386/run_unitTests.Rout.fail R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences" 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. > require("GenomicFeatures") || stop("unable to load GenomicFeatures package") Loading required package: GenomicFeatures 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, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: GenomeInfoDb Loading required package: GenomicRanges Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. [1] TRUE > GenomicFeatures:::.test() Loading required package: BSgenome Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: rtracklayer Download and preprocess the 'transcripts' data frame ... OK Download and preprocess the 'chrominfo' data frame ... OK Download and preprocess the 'splicings' data frame ... OK Download and preprocess the 'genes' data frame ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK Timing stopped at: 25.29 1.88 40.75 Error in checkTrue(GenomicFeatures:::compareTxDbs(target_txdb, current_txdb)) : Test not TRUE In addition: Warning messages: 1: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 3 out-of-bound ranges located on sequences a, b, and c. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. 2: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence c. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. 3: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence c. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. 4: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 4 out-of-bound ranges located on sequences 1, 2, 3, and 4. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns RUNIT TEST PROTOCOL -- Tue Apr 09 03:27:55 2019 *********************************************** Number of test functions: 75 Number of errors: 0 Number of failures: 1 1 Test Suite : GenomicFeatures RUnit Tests - 75 test functions, 0 errors, 1 failure FAILURE in test_makeTxDbFromBiomart: Error in checkTrue(GenomicFeatures:::compareTxDbs(target_txdb, current_txdb)) : Test not TRUE Test files with failing tests test_makeTxDbFromBiomart.R test_makeTxDbFromBiomart Error in BiocGenerics:::testPackage("GenomicFeatures") : unit tests failed for package GenomicFeatures Calls: <Anonymous> -> <Anonymous> In addition: Warning messages: 1: In .get_cds_IDX(type, phase) : The "phase" metadata column contains non-NA values for features of type exon. This information was ignored. 2: In .get_cds_IDX(type, phase) : The "phase" metadata column contains non-NA values for features of type stop_codon. This information was ignored. 3: In .get_cds_IDX(type, phase) : The "phase" metadata column contains non-NA values for features of type stop_codon. This information was ignored. Execution halted |
GenomicFeatures.Rcheck/tests_x64/run_unitTests.Rout.fail R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences" 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. > require("GenomicFeatures") || stop("unable to load GenomicFeatures package") Loading required package: GenomicFeatures 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, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: GenomeInfoDb Loading required package: GenomicRanges Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. [1] TRUE > GenomicFeatures:::.test() Loading required package: BSgenome Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: rtracklayer Download and preprocess the 'transcripts' data frame ... OK Download and preprocess the 'chrominfo' data frame ... Error in x$.self$finalize() : attempt to apply non-function In addition: Warning messages: 1: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 3 out-of-bound ranges located on sequences a, b, and c. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. 2: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence c. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. 3: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence c. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. 4: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 4 out-of-bound ranges located on sequences 1, 2, 3, and 4. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. OK Download and preprocess the 'splicings' data frame ... OK Download and preprocess the 'genes' data frame ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK Timing stopped at: 17.9 0.29 33.46 Error in checkTrue(GenomicFeatures:::compareTxDbs(target_txdb, current_txdb)) : Test not TRUE In addition: Warning message: call dbDisconnect() when finished working with a connection Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns RUNIT TEST PROTOCOL -- Tue Apr 09 03:29:58 2019 *********************************************** Number of test functions: 75 Number of errors: 0 Number of failures: 1 1 Test Suite : GenomicFeatures RUnit Tests - 75 test functions, 0 errors, 1 failure FAILURE in test_makeTxDbFromBiomart: Error in checkTrue(GenomicFeatures:::compareTxDbs(target_txdb, current_txdb)) : Test not TRUE Test files with failing tests test_makeTxDbFromBiomart.R test_makeTxDbFromBiomart Error in BiocGenerics:::testPackage("GenomicFeatures") : unit tests failed for package GenomicFeatures Calls: <Anonymous> -> <Anonymous> In addition: Warning messages: 1: In .get_cds_IDX(type, phase) : The "phase" metadata column contains non-NA values for features of type exon. This information was ignored. 2: In .get_cds_IDX(type, phase) : The "phase" metadata column contains non-NA values for features of type stop_codon. This information was ignored. 3: In .get_cds_IDX(type, phase) : The "phase" metadata column contains non-NA values for features of type stop_codon. This information was ignored. Execution halted |
GenomicFeatures.Rcheck/examples_i386/GenomicFeatures-Ex.timings
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GenomicFeatures.Rcheck/examples_x64/GenomicFeatures-Ex.timings
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