| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:34:25 -0400 (Wed, 17 Oct 2018).
| Package 594/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GenomicFeatures 1.32.3 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: GenomicFeatures |
| Version: 1.32.3 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicFeatures.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings GenomicFeatures_1.32.3.tar.gz |
| StartedAt: 2018-10-17 02:15:26 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 02:35:26 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 1200.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GenomicFeatures.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicFeatures.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings GenomicFeatures_1.32.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/GenomicFeatures.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.32.3'
* 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 ... 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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/coordinate-mapping-methods.Rd:227: file link 'mapToAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/exonicParts.Rd:30: file link 'disjoin' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/exonicParts.Rd:36: file link 'disjoin' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/exonicParts.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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/exonicParts.Rd:52: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/exonicParts.Rd:85: file link 'disjoin' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/getPromoterSeq-methods.Rd:36: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/getPromoterSeq-methods.Rd:45: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/getPromoterSeq-methods.Rd:46: file link 'DNAStringSetList' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/makeTxDb.Rd:192: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/makeTxDb.Rd:197: file link 'saveDb' in package 'AnnotationDbi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/makeTxDb.Rd:198: file link 'loadDb' in package 'AnnotationDbi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/makeTxDbFromBiomart.Rd:141: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/makeTxDbFromEnsembl.Rd:72: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/makeTxDbFromGFF.Rd:29: file link 'GFF3File' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/makeTxDbFromGFF.Rd:30: file link 'GTFFile' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/makeTxDbFromGFF.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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/makeTxDbFromGFF.Rd:101: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/makeTxDbFromGRanges.Rd:10: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/makeTxDbFromGRanges.Rd:20: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/makeTxDbFromGRanges.Rd:21: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/makeTxDbFromGRanges.Rd:57: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/makeTxDbFromGRanges.Rd:63: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/makeTxDbFromUCSC.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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/mapIdsToRanges.Rd:24: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/mapRangesToIds.Rd:25: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/microRNAs.Rd:32: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/transcriptLengths.Rd:44: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/transcriptLengths.Rd:107: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/transcriptLocs2refLocs.Rd:36: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/transcripts.Rd:85: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/transcripts.Rd:86: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/transcripts.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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/transcripts.Rd:122: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/transcripts.Rd:124: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'GenomicFeatures-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mapToTranscripts
> ### Title: Map range coordinates between transcripts and genome space
> ### Aliases: coordinate-mapping mapToTranscripts
> ### mapToTranscripts,GenomicRanges,GenomicRanges-method
> ### mapToTranscripts,GenomicRanges,GRangesList-method
> ### mapToTranscripts,ANY,TxDb-method pmapToTranscripts
> ### pmapToTranscripts,GenomicRanges,GenomicRanges-method
> ### pmapToTranscripts,GenomicRanges,GRangesList-method
> ### pmapToTranscripts,GRangesList,GRangesList-method mapFromTranscripts
> ### mapFromTranscripts,GenomicRanges,GenomicRanges-method
> ### mapFromTranscripts,GenomicRanges,GRangesList-method
> ### pmapFromTranscripts
> ### pmapFromTranscripts,IntegerRanges,GenomicRanges-method
> ### pmapFromTranscripts,IntegerRanges,GRangesList-method
> ### pmapFromTranscripts,GenomicRanges,GenomicRanges-method
> ### pmapFromTranscripts,GenomicRanges,GRangesList-method
> ### Keywords: methods utilities
>
> ### ** Examples
>
>
> ## ---------------------------------------------------------------------
> ## A. Basic Use
> ## ---------------------------------------------------------------------
>
> ## Gene "Dgkb" has ENTREZID "217480":
> library(org.Mm.eg.db)
> library(TxDb.Mmusculus.UCSC.mm10.knownGene)
> geneid <- select(org.Mm.eg.db, "Dgkb", "ENTREZID", "SYMBOL")
'select()' returned 1:1 mapping between keys and columns
> geneid
SYMBOL ENTREZID
1 Dgkb 217480
>
> ## The gene is on the positive strand, chromosome 12:
> txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene
> genes(txdb)[geneid[,"ENTREZID"]]
GRanges object with 1 range and 1 metadata column:
seqnames ranges strand | gene_id
<Rle> <IRanges> <Rle> | <character>
217480 chr12 37880174-38633410 + | 217480
-------
seqinfo: 66 sequences (1 circular) from mm10 genome
>
> ## Transcripts in the gene:
> tx_names <- transcriptsBy(txdb, "gene")[[geneid[,"ENTREZID"]]]$tx_name
> tx_names
[1] "uc007nki.1" "uc007nkj.1" "uc007nkk.1" "uc007nkl.1" "uc007nkm.1"
[6] "uc007nkn.1"
>
> ## Map CDS location '4' to the genome:
> coord <- GRanges("chr12", IRanges(4, width=1))
> cdsbytx <- cdsBy(txdb, "tx", use.name=TRUE)[tx_names]
> ## A prerequesite of the mapping from transcript space to genome space
> ## is that seqnames in 'x' match names in 'transcripts'.
> names(cdsbytx) <- rep(seqnames(coord), length(cdsbytx))
> ## There are 6 results, one for each transcript.
> mapFromTranscripts(coord, cdsbytx)
GRanges object with 6 ranges and 2 metadata columns:
seqnames ranges strand | xHits transcriptsHits
<Rle> <IRanges> <Rle> | <integer> <integer>
[1] chr12 37981944 + | 1 1
[2] chr12 37981944 + | 1 2
[3] chr12 37981944 + | 1 3
[4] chr12 37981944 + | 1 4
[5] chr12 38100397 + | 1 5
[6] chr12 38100397 + | 1 6
-------
seqinfo: 66 sequences from an unspecified genome; no seqlengths
>
> ## Map exon location '100' to genome:
> coord <- GRanges("chr12", IRanges(100, width=1))
> exonsbytx <- exonsBy(txdb, "tx", use.name=TRUE)[tx_names]
> names(exonsbytx) <- rep(seqnames(coord), length(exonsbytx))
> ## Again the output has 6 results, one for each transcript.
> mapFromTranscripts(coord, exonsbytx)
GRanges object with 6 ranges and 2 metadata columns:
seqnames ranges strand | xHits transcriptsHits
<Rle> <IRanges> <Rle> | <integer> <integer>
[1] chr12 37880273 + | 1 1
[2] chr12 37880273 + | 1 2
[3] chr12 37880804 + | 1 3
[4] chr12 37880804 + | 1 4
[5] chr12 38019279 + | 1 5
[6] chr12 38100365 + | 1 6
-------
seqinfo: 66 sequences from an unspecified genome; no seqlengths
>
> ## Going in the reverse direction, genomic position 37981944 maps
> ## to CDS position 4:
> coord <- GRanges("chr12", IRanges(37981944, width=1))
> mapToTranscripts(coord, cdsbytx)
GRanges object with 4 ranges and 2 metadata columns:
seqnames ranges strand | xHits transcriptsHits
<Rle> <IRanges> <Rle> | <integer> <integer>
[1] chr12 4 + | 1 1
[2] chr12 4 + | 1 2
[3] chr12 4 + | 1 3
[4] chr12 4 + | 1 4
-------
seqinfo: 1 sequence from an unspecified genome
>
> ## Genomic position 37880273 maps back to position 100 in the exon region:
> coord <- GRanges("chr12", IRanges(37880273, width=1))
> mapToTranscripts(coord, exonsbytx)
GRanges object with 2 ranges and 2 metadata columns:
seqnames ranges strand | xHits transcriptsHits
<Rle> <IRanges> <Rle> | <integer> <integer>
[1] chr12 100 + | 1 1
[2] chr12 100 + | 1 2
-------
seqinfo: 1 sequence from an unspecified genome
>
> ## ---------------------------------------------------------------------
> ## B. Map sequence locations in exons to the genome
> ## ---------------------------------------------------------------------
>
> ## NAGNAG alternative splicing plays an essential role in biological processes
> ## and represents a highly adaptable system for posttranslational regulation
> ## of gene function. The majority of NAGNAG studies largely focus on messenger
> ## RNA. A study by Sun, Lin, and Yan
> ## (http://www.hindawi.com/journals/bmri/2014/736798/) demonstrated that
> ## NAGNAG splicing is also operative in large intergenic noncoding RNA
> ## (lincRNA).
>
> ## One finding of interest was that linc-POLR3G-10 exhibited two NAGNAG
> ## acceptors located in two distinct transcripts: TCONS_00010012 and
> ## TCONS_00010010.
>
> ## Extract the exon coordinates of TCONS_00010012 and TCONS_00010010:
> lincrna <- c("TCONS_00010012", "TCONS_00010010")
> library(TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts)
> txdb <- TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts
> exons <- exonsBy(txdb, by="tx", use.names=TRUE)[lincrna]
> exons
GRangesList object of length 2:
$TCONS_00010012
GRanges object with 5 ranges and 3 metadata columns:
seqnames ranges strand | exon_id exon_name exon_rank
<Rle> <IRanges> <Rle> | <integer> <character> <integer>
[1] chr5 87577501-87577923 + | 16943 <NA> 1
[2] chr5 87578532-87578683 + | 16947 <NA> 2
[3] chr5 87578827-87578903 + | 16950 <NA> 3
[4] chr5 87581561-87581668 + | 16953 <NA> 4
[5] chr5 87583253-87583828 + | 16957 <NA> 5
$TCONS_00010010
GRanges object with 2 ranges and 3 metadata columns:
seqnames ranges strand | exon_id exon_name exon_rank
[1] chr5 87577114-87578683 + | 16941 <NA> 1
[2] chr5 87581558-87581668 + | 16952 <NA> 2
-------
seqinfo: 93 sequences (1 circular) from hg19 genome
>
> ## The two NAGNAG acceptors were identified in the upstream region of
> ## the fourth and fifth exons located in TCONS_00010012.
> ## Extract the sequences for transcript TCONS_00010012:
> library(BSgenome.Hsapiens.UCSC.hg19)
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
> genome <- BSgenome.Hsapiens.UCSC.hg19
> exons_seq <- getSeq(genome, exons[[1]])
>
> ## TCONS_00010012 has 4 exons:
> exons_seq
A DNAStringSet instance of length 5
width seq
[1] 423 CAAGAGAGAAGCAGAAGCCACCATGGTTTTTTAT...TGCTGGTGCCGTGCTTCTACAGCCTGCAGAACT
[2] 152 GAAGGACTTTACAGCTTCTCTTTCGCATATCCAA...TGATAACCAAGAAGTCTACTAAGTGACTAACAG
[3] 77 TTAATATTTTTGGACATGAGGTGACTGCAGTTAA...GGAAAGCAAACCCATAGATAAAGGGATACTATG
[4] 108 AGCAACTGGGAACCTAATTCTGACCAAAAAGGAG...AAGCAACCGCATACCAAGGATAATTATAAGAAG
[5] 576 AAGAGAAGACATGGAGAAGAGGAGGGAGTAGTTG...CTAGGGACTTTCCAAGAGGATGACCAAAGAAGG
>
> ## The most common triplet among the lincRNA sequences was CAG. Identify
> ## the location of this pattern in all exons.
> cag_loc <- vmatchPattern("CAG", exons_seq)
>
> ## Convert the first occurance of CAG in each exon back to genome coordinates.
> first_loc <- do.call(c, sapply(cag_loc, "[", 1, simplify=TRUE))
> pmapFromTranscripts(first_loc, exons[[1]])
GRanges object with 5 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr5 87577512-87577514 +
[2] chr5 87578543-87578545 +
[3] chr5 87578854-87578856 +
[4] chr5 87581620-87581622 +
[5] chr5 87583299-87583301 +
-------
seqinfo: 93 sequences from an unspecified genome; no seqlengths
>
> ## -----------------------------------------------------------------------
> ## C. Map dbSNP variants to CDS or cDNA coordinates
> ## -----------------------------------------------------------------------
>
> ## The GIPR gene encodes a G-protein coupled receptor for gastric inhibitory
> ## polypeptide (GIP). Originally GIP was identified to inhibited gastric acid
> ## secretion and gastrin release but was later demonstrated to stimulate
> ## insulin release in the presence of elevated glucose.
>
> ## In this example 5 SNPs located in the GIPR gene are mapped to cDNA
> ## coordinates. A list of SNPs in GIPR can be downloaded from dbSNP or NCBI.
> rsids <- c("rs4803846", "rs139322374", "rs7250736", "rs7250754", "rs9749185")
>
> ## Extract genomic coordinates with a SNPlocs package.
> library(SNPlocs.Hsapiens.dbSNP144.GRCh38)
> snps <- snpsById(SNPlocs.Hsapiens.dbSNP144.GRCh38, rsids)
Error: cannot allocate vector of size 1024.0 Mb
Execution halted
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
makeTxDbFromBiomart 63.83 1.39 221.03
coordinate-mapping-methods 52.98 2.39 77.76
makeFeatureDbFromUCSC 44.04 1.89 155.71
coverageByTranscript 20.54 4.83 25.38
exonicParts 23.04 1.26 24.32
extractTranscriptSeqs 11.44 0.21 11.64
makeTxDbFromGFF 8.28 0.00 10.44
transcriptLocs2refLocs 6.75 0.13 6.87
transcriptLengths 5.30 0.06 5.36
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'run_unitTests.R'
OK
** running tests for arch 'x64' ...
Running 'run_unitTests.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 WARNINGs, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.7-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/3.7/bioc/src/contrib/GenomicFeatures_1.32.3.tar.gz && rm -rf GenomicFeatures.buildbin-libdir && mkdir GenomicFeatures.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicFeatures.buildbin-libdir GenomicFeatures_1.32.3.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL GenomicFeatures_1.32.3.zip && rm GenomicFeatures_1.32.3.tar.gz GenomicFeatures_1.32.3.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 1124k 100 1124k 0 0 15.6M 0 --:--:-- --:--:-- --:--:-- 17.4M
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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/coordinate-mapping-methods.Rd:227: 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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/coverageByTranscript.Rd:114: file link 'findCompatibleOverlaps' in package 'GenomicAlignments' does not exist and so has been treated as a topic
disjointExons html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/disjointExons.Rd:58: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
exonicParts html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/exonicParts.Rd:30: file link 'disjoin' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/exonicParts.Rd:36: file link 'disjoin' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/exonicParts.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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/exonicParts.Rd:52: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/exonicParts.Rd:85: file link 'disjoin' in package 'IRanges' does not exist and so has been treated as a topic
extractTranscriptSeqs html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/extractTranscriptSeqs.Rd:135: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
extractUpstreamSeqs html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/extractUpstreamSeqs.Rd:129: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
features html
getPromoterSeq-methods html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/getPromoterSeq-methods.Rd:36: file link 'FaFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/getPromoterSeq-methods.Rd:45: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/getPromoterSeq-methods.Rd:46: file link 'DNAStringSetList' in package 'Biostrings' does not exist and so has been treated as a topic
id2name html
makeFeatureDbFromUCSC html
makeTxDb html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/makeTxDb.Rd:192: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/makeTxDb.Rd:197: file link 'saveDb' in package 'AnnotationDbi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/makeTxDb.Rd:198: file link 'loadDb' in package 'AnnotationDbi' does not exist and so has been treated as a topic
makeTxDbFromBiomart html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/makeTxDbFromBiomart.Rd:141: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
makeTxDbFromEnsembl html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/makeTxDbFromEnsembl.Rd:72: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
makeTxDbFromGFF html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/makeTxDbFromGFF.Rd:29: file link 'GFF3File' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/makeTxDbFromGFF.Rd:30: file link 'GTFFile' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/makeTxDbFromGFF.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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/makeTxDbFromGFF.Rd:101: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
makeTxDbFromGRanges html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/makeTxDbFromGRanges.Rd:10: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/makeTxDbFromGRanges.Rd:20: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/makeTxDbFromGRanges.Rd:21: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/makeTxDbFromGRanges.Rd:57: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/makeTxDbFromGRanges.Rd:63: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
makeTxDbFromUCSC html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/makeTxDbFromUCSC.Rd:99: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
makeTxDbPackage html
mapIdsToRanges html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/mapIdsToRanges.Rd:24: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
mapRangesToIds html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/mapRangesToIds.Rd:25: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
microRNAs html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/microRNAs.Rd:32: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
nearest-methods html
select-methods html
transcriptLengths html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/transcriptLengths.Rd:44: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/transcriptLengths.Rd:107: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
transcriptLocs2refLocs html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/transcriptLocs2refLocs.Rd:36: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
transcripts html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/transcripts.Rd:85: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/transcripts.Rd:86: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/transcripts.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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/transcripts.Rd:122: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/GenomicFeatures/man/transcripts.Rd:124: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
transcriptsBy html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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-3.7-bioc/tmpdir/Rtmp0aC8Bd/R.INSTALL20541e0e7863/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
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_1.32.3.zip
* DONE (GenomicFeatures)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'GenomicFeatures' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
GenomicFeatures.Rcheck/tests_i386/run_unitTests.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
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
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 -- Wed Oct 17 02:32:34 2018
***********************************************
Number of test functions: 74
Number of errors: 0
Number of failures: 0
1 Test Suite :
GenomicFeatures RUnit Tests - 74 test functions, 0 errors, 0 failures
Number of test functions: 74
Number of errors: 0
Number of failures: 0
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.
5: In .get_cds_IDX(type, phase) :
The "phase" metadata column contains non-NA values for features of type
exon. This information was ignored.
6: In .get_cds_IDX(type, phase) :
The "phase" metadata column contains non-NA values for features of type
stop_codon. This information was ignored.
7: In .get_cds_IDX(type, phase) :
The "phase" metadata column contains non-NA values for features of type
stop_codon. This information was ignored.
>
> proc.time()
user system elapsed
124.82 4.46 144.75
|
GenomicFeatures.Rcheck/tests_x64/run_unitTests.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
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
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 -- Wed Oct 17 02:35:19 2018
***********************************************
Number of test functions: 74
Number of errors: 0
Number of failures: 0
1 Test Suite :
GenomicFeatures RUnit Tests - 74 test functions, 0 errors, 0 failures
Number of test functions: 74
Number of errors: 0
Number of failures: 0
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.
5: In .get_cds_IDX(type, phase) :
The "phase" metadata column contains non-NA values for features of type
exon. This information was ignored.
6: In .get_cds_IDX(type, phase) :
The "phase" metadata column contains non-NA values for features of type
stop_codon. This information was ignored.
7: In .get_cds_IDX(type, phase) :
The "phase" metadata column contains non-NA values for features of type
stop_codon. This information was ignored.
>
> proc.time()
user system elapsed
150.60 2.25 164.48
|
|
GenomicFeatures.Rcheck/examples_i386/GenomicFeatures-Ex.timings
|
GenomicFeatures.Rcheck/examples_x64/GenomicFeatures-Ex.timings
|