| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:19:51 -0400 (Thu, 12 Apr 2018).
| Package 564/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GenomicFeatures 1.30.3 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK |
| Package: GenomicFeatures |
| Version: 1.30.3 |
| Command: rm -rf GenomicFeatures.buildbin-libdir GenomicFeatures.Rcheck && mkdir GenomicFeatures.buildbin-libdir GenomicFeatures.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicFeatures.buildbin-libdir GenomicFeatures_1.30.3.tar.gz >GenomicFeatures.Rcheck\00install.out 2>&1 && cp GenomicFeatures.Rcheck\00install.out GenomicFeatures-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GenomicFeatures.buildbin-libdir --install="check:GenomicFeatures-install.out" --force-multiarch --no-vignettes --timings GenomicFeatures_1.30.3.tar.gz |
| StartedAt: 2018-04-12 00:17:24 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 00:44:54 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 1649.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GenomicFeatures.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### rm -rf GenomicFeatures.buildbin-libdir GenomicFeatures.Rcheck && mkdir GenomicFeatures.buildbin-libdir GenomicFeatures.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicFeatures.buildbin-libdir GenomicFeatures_1.30.3.tar.gz >GenomicFeatures.Rcheck\00install.out 2>&1 && cp GenomicFeatures.Rcheck\00install.out GenomicFeatures-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GenomicFeatures.buildbin-libdir --install="check:GenomicFeatures-install.out" --force-multiarch --no-vignettes --timings GenomicFeatures_1.30.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicFeatures.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 'GenomicFeatures/DESCRIPTION' ... OK
* this is package 'GenomicFeatures' version '1.30.3'
* 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 ... OK
* 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-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/TxDb-class.Rd:97: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/TxDb-class.Rd:100: missing file link 'saveDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/TxDb-class.Rd:101: missing file link 'loadDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coordinate-mapping-methods.Rd:28: missing file link 'mapToAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coordinate-mapping-methods.Rd:225: missing file link 'mapToAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:25: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:25: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:26: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:27: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:28: missing file link 'GAlignmentsList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:32: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:33: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:35: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:38: missing file link 'grglist'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:43: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:55: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:70: missing file link 'grglist'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:71: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:72: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:74: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:75: missing file link 'grglist'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:80: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:81: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:102: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:105: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:108: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:114: missing file link 'findCompatibleOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/disjointExons.Rd:47: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/disjointExons.Rd:58: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/exonicParts.Rd:30: missing file link 'disjoin'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/exonicParts.Rd:36: missing file link 'disjoin'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/exonicParts.Rd:47: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/exonicParts.Rd:52: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/exonicParts.Rd:85: missing file link 'disjoin'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:26: missing file link 'DNAString'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:27: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:31: missing file link 'FaFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:40: missing file link 'DNAString'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:41: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:43: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:45: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:48: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:73: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:78: missing file link 'DNAString'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:80: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:83: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:86: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:92: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:102: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:124: missing file link 'DNAString'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:124: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:131: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:134: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractUpstreamSeqs.Rd:29: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractUpstreamSeqs.Rd:30: missing file link 'TwoBitFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractUpstreamSeqs.Rd:30: missing file link 'FaFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractUpstreamSeqs.Rd:39: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractUpstreamSeqs.Rd:57: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractUpstreamSeqs.Rd:59: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractUpstreamSeqs.Rd:61: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractUpstreamSeqs.Rd:65: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractUpstreamSeqs.Rd:109: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractUpstreamSeqs.Rd:116: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractUpstreamSeqs.Rd:116: missing file link 'TwoBitFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractUpstreamSeqs.Rd:117: missing file link 'FaFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractUpstreamSeqs.Rd:126: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractUpstreamSeqs.Rd:129: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/getPromoterSeq-methods.Rd:11: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/getPromoterSeq-methods.Rd:11: missing file link 'FaFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/getPromoterSeq-methods.Rd:21: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/getPromoterSeq-methods.Rd:21: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/getPromoterSeq-methods.Rd:24: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/getPromoterSeq-methods.Rd:24: missing file link 'FaFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/getPromoterSeq-methods.Rd:36: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/getPromoterSeq-methods.Rd:36: missing file link 'FaFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/getPromoterSeq-methods.Rd:45: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/getPromoterSeq-methods.Rd:46: missing file link 'DNAStringSetList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/makeTxDb.Rd:192: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/makeTxDb.Rd:197: missing file link 'saveDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/makeTxDb.Rd:198: missing file link 'loadDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/makeTxDbFromBiomart.Rd:141: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/makeTxDbFromEnsembl.Rd:62: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/makeTxDbFromGFF.Rd:29: missing file link 'GFF3File'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/makeTxDbFromGFF.Rd:30: missing file link 'GTFFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/makeTxDbFromGFF.Rd:99: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/makeTxDbFromGFF.Rd:101: missing file link 'import'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/makeTxDbFromGRanges.Rd:10: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/makeTxDbFromGRanges.Rd:20: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/makeTxDbFromGRanges.Rd:21: missing file link 'import'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/makeTxDbFromGRanges.Rd:57: missing file link 'import'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/makeTxDbFromGRanges.Rd:63: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/makeTxDbFromUCSC.Rd:96: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/mapIdsToRanges.Rd:24: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/mapRangesToIds.Rd:25: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/microRNAs.Rd:32: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcriptLengths.Rd:44: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcriptLengths.Rd:107: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcriptLocs2refLocs.Rd:36: missing file link 'IntegerList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcripts.Rd:80: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcripts.Rd:81: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcripts.Rd:84: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcripts.Rd:117: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcripts.Rd:119: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcriptsBy.Rd:49: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcriptsBy.Rd:52: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcriptsBy.Rd:54: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcriptsBy.Rd:79: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcriptsBy.Rd:89: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcriptsByOverlaps.Rd:46: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcriptsByOverlaps.Rd:49: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcriptsByOverlaps.Rd:59: missing file link 'findOverlaps'
See 'C:/Users/biocbuild/bbs-3.6-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 ... WARNING
Undocumented code objects:
'makePackageName'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* 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
coordinate-mapping-methods 45.19 1.76 109.85
makeFeatureDbFromUCSC 32.23 2.52 164.35
makeTxDbFromBiomart 30.75 1.13 117.40
coverageByTranscript 24.34 7.30 31.64
exonicParts 28.00 2.22 30.22
extractTranscriptSeqs 9.33 0.14 9.65
makeTxDbFromUCSC 8.74 0.17 46.29
makeTxDbFromGFF 5.60 0.04 5.91
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
coordinate-mapping-methods 42.61 1.45 44.11
makeFeatureDbFromUCSC 32.85 2.14 163.06
exonicParts 27.04 2.29 29.32
coverageByTranscript 23.71 5.40 29.18
makeTxDbFromBiomart 27.27 1.00 113.95
extractTranscriptSeqs 12.16 0.11 12.27
makeTxDbFromGFF 6.86 0.08 7.11
makeTxDbFromUCSC 6.89 0.05 44.99
transcriptLocs2refLocs 5.54 0.05 5.59
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'run_unitTests.R'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386/R" CMD BATCH --vanilla "run_unitTests.R" "run_unitTests.Rout"' had status 1
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'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64/R" CMD BATCH --vanilla "run_unitTests.R" "run_unitTests.Rout"' had status 1
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, 2 WARNINGs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/GenomicFeatures.Rcheck/00check.log'
for details.
GenomicFeatures.Rcheck/00install.out
install for i386
* installing *source* package 'GenomicFeatures' ...
** R
** inst
** preparing 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-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/TxDb-class.Rd:97: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/TxDb-class.Rd:100: missing file link 'saveDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/TxDb-class.Rd:101: missing file link 'loadDb'
as-format-methods html
coordinate-mapping-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coordinate-mapping-methods.Rd:28: missing file link 'mapToAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coordinate-mapping-methods.Rd:225: missing file link 'mapToAlignments'
coverageByTranscript html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:25: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:25: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:26: missing file link 'GAlignments'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:27: missing file link 'GAlignmentPairs'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:28: missing file link 'GAlignmentsList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:32: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:33: missing file link 'BamFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:35: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:38: missing file link 'grglist'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:43: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:55: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:70: missing file link 'grglist'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:71: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:72: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:74: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:75: missing file link 'grglist'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:80: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:81: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:102: missing file link 'RleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:105: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:108: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/coverageByTranscript.Rd:114: missing file link 'findCompatibleOverlaps'
disjointExons html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/disjointExons.Rd:47: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/disjointExons.Rd:58: missing file link 'GRanges'
exonicParts html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/exonicParts.Rd:30: missing file link 'disjoin'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/exonicParts.Rd:36: missing file link 'disjoin'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/exonicParts.Rd:47: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/exonicParts.Rd:52: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/exonicParts.Rd:85: missing file link 'disjoin'
extractTranscriptSeqs html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:26: missing file link 'DNAString'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:27: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:31: missing file link 'FaFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:40: missing file link 'DNAString'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:41: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:43: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:45: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:48: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:73: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:78: missing file link 'DNAString'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:80: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:83: missing file link 'Rle'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:86: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:92: missing file link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:102: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:124: missing file link 'DNAString'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:124: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:131: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractTranscriptSeqs.Rd:134: missing file link 'RangesList'
extractUpstreamSeqs html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractUpstreamSeqs.Rd:29: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractUpstreamSeqs.Rd:30: missing file link 'TwoBitFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractUpstreamSeqs.Rd:30: missing file link 'FaFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractUpstreamSeqs.Rd:39: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractUpstreamSeqs.Rd:57: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractUpstreamSeqs.Rd:59: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractUpstreamSeqs.Rd:61: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractUpstreamSeqs.Rd:65: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractUpstreamSeqs.Rd:109: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractUpstreamSeqs.Rd:116: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractUpstreamSeqs.Rd:116: missing file link 'TwoBitFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractUpstreamSeqs.Rd:117: missing file link 'FaFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractUpstreamSeqs.Rd:126: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/extractUpstreamSeqs.Rd:129: missing file link 'DNAStringSet'
features html
getPromoterSeq-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/getPromoterSeq-methods.Rd:11: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/getPromoterSeq-methods.Rd:11: missing file link 'FaFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/getPromoterSeq-methods.Rd:21: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/getPromoterSeq-methods.Rd:21: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/getPromoterSeq-methods.Rd:24: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/getPromoterSeq-methods.Rd:24: missing file link 'FaFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/getPromoterSeq-methods.Rd:36: missing file link 'BSgenome'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/getPromoterSeq-methods.Rd:36: missing file link 'FaFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/getPromoterSeq-methods.Rd:45: missing file link 'DNAStringSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/getPromoterSeq-methods.Rd:46: missing file link 'DNAStringSetList'
id2name html
makeFeatureDbFromUCSC html
makeTxDb html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/makeTxDb.Rd:192: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/makeTxDb.Rd:197: missing file link 'saveDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/makeTxDb.Rd:198: missing file link 'loadDb'
makeTxDbFromBiomart html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/makeTxDbFromBiomart.Rd:141: missing file link 'GRanges'
makeTxDbFromEnsembl html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/makeTxDbFromEnsembl.Rd:62: missing file link 'GRanges'
makeTxDbFromGFF html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/makeTxDbFromGFF.Rd:29: missing file link 'GFF3File'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/makeTxDbFromGFF.Rd:30: missing file link 'GTFFile'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/makeTxDbFromGFF.Rd:99: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/makeTxDbFromGFF.Rd:101: missing file link 'import'
makeTxDbFromGRanges html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/makeTxDbFromGRanges.Rd:10: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/makeTxDbFromGRanges.Rd:20: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/makeTxDbFromGRanges.Rd:21: missing file link 'import'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/makeTxDbFromGRanges.Rd:57: missing file link 'import'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/makeTxDbFromGRanges.Rd:63: missing file link 'GRanges'
makeTxDbFromUCSC html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/makeTxDbFromUCSC.Rd:96: missing file link 'GRanges'
makeTxDbPackage html
mapIdsToRanges html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/mapIdsToRanges.Rd:24: missing file link 'GRangesList'
mapRangesToIds html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/mapRangesToIds.Rd:25: missing file link 'DataFrame'
microRNAs html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/microRNAs.Rd:32: missing file link 'GRanges'
nearest-methods html
select-methods html
transcriptLengths html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcriptLengths.Rd:44: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcriptLengths.Rd:107: missing file link 'GRanges'
transcriptLocs2refLocs html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcriptLocs2refLocs.Rd:36: missing file link 'IntegerList'
transcripts html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcripts.Rd:80: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcripts.Rd:81: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcripts.Rd:84: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcripts.Rd:117: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcripts.Rd:119: missing file link 'GRangesList'
transcriptsBy html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcriptsBy.Rd:49: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcriptsBy.Rd:52: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcriptsBy.Rd:54: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcriptsBy.Rd:79: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcriptsBy.Rd:89: missing file link 'GRangesList'
transcriptsByOverlaps html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcriptsByOverlaps.Rd:46: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcriptsByOverlaps.Rd:49: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpAPdvJv/R.INSTALL253c5297406a/GenomicFeatures/man/transcriptsByOverlaps.Rd:59: missing file link 'findOverlaps'
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'GenomicFeatures' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicFeatures' as GenomicFeatures_1.30.3.zip
* DONE (GenomicFeatures)
In R CMD INSTALL
In R CMD INSTALL
|
GenomicFeatures.Rcheck/tests_i386/run_unitTests.Rout.fail
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("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, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
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: 12.35 0.84 25.81
Error in checkIdentical(TARGET_NEXONS_PER_TX, as.integer(nexons_per_tx)) :
FALSE
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
Extract the 'transcripts' data frame ... OK
Extract the 'splicings' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... 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 -- Thu Apr 12 00:41:55 2018
***********************************************
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 checkIdentical(TARGET_NEXONS_PER_TX, as.integer(nexons_per_tx)) :
FALSE
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 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("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, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
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: 10.7 0.33 25.08
Error in checkIdentical(TARGET_NEXONS_PER_TX, as.integer(nexons_per_tx)) :
FALSE
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
Extract the 'transcripts' data frame ... OK
Extract the 'splicings' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... 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 -- Thu Apr 12 00:44:46 2018
***********************************************
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 checkIdentical(TARGET_NEXONS_PER_TX, as.integer(nexons_per_tx)) :
FALSE
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
|
GenomicFeatures.Rcheck/examples_x64/GenomicFeatures-Ex.timings
|