BSgenome 1.50.0
H. Pagès
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/BSgenome |
| Branch: RELEASE_3_8 |
| Last Commit: 4391075 |
| Last Changed Date: 2018-10-30 11:41:43 -0400 (Tue, 30 Oct 2018) |
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BSgenome.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings BSgenome_1.50.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/BSgenome.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BSgenome/DESCRIPTION' ... OK
* this is package 'BSgenome' version '1.50.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
NOTE
Depends: includes the non-default packages:
'BiocGenerics' 'S4Vectors' 'IRanges' 'GenomeInfoDb' 'GenomicRanges'
'Biostrings' 'rtracklayer'
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 ... NOTE
Found the following non-portable file path:
BSgenome/inst/extdata/GentlemanLab/1000genomes/BSgenome.Hsapiens.1000g.b36female-tools/split_human_b36_female.sh
Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking whether package 'BSgenome' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenome-class.Rd:46: file link 'GenomeDescription' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenome-class.Rd:47: file link 'GenomeDescription' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenome-class.Rd:58: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenome-class.Rd:59: file link 'MaskedDNAString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenome-class.Rd:68: file link 'length,XVector-method' in package 'XVector' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenome-class.Rd:69: file link 'length,MaskedXString-method' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenome-class.Rd:70: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenome-class.Rd:71: file link 'MaskedDNAString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenome-class.Rd:73: file link 'MaskedXString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenome-class.Rd:75: file link 'MaskedXString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenome-class.Rd:83: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenome-class.Rd:143: file link 'BSgenome.Hsapiens.UCSC.hg38' in package 'BSgenome.Hsapiens.UCSC.hg38' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenome-class.Rd:155: file link 'DNAStringSet-class' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenome-class.Rd:156: file link 'MaskedDNAString-class' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenome-class.Rd:159: file link 'subseq,XVector-method' in package 'XVector' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenome-utils.Rd:46: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenome-utils.Rd:49: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenome-utils.Rd:108: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenome-utils.Rd:111: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenome-utils.Rd:113: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenome-utils.Rd:121: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenome-utils.Rd:133: file link 'matchPDict' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenomeForge.Rd:75: file link 'XString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenomeViews-class.Rd:120: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenomeViews-class.Rd:135: file link 'alphabetFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenomeViews-class.Rd:136: file link 'oligonucleotideFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenomeViews-class.Rd:140: file link 'alphabetFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenomeViews-class.Rd:144: file link 'oligonucleotideFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenomeViews-class.Rd:148: file link 'consensusMatrix' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenomeViews-class.Rd:179: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenomeViews-class.Rd:215: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenomeViews-class.Rd:241: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenomeViews-class.Rd:245: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenomeViews-class.Rd:246: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenomeViews-class.Rd:249: file link 'seqtype' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenomeViews-class.Rd:250: file link 'nchar,XStringSet-method' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenomeViews-class.Rd:251: file link 'unlist,XStringSet-method' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenomeViews-class.Rd:252: file link 'alphabetFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenomeViews-class.Rd:253: file link 'hasOnlyBaseLetters' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenomeViews-class.Rd:254: file link 'uniqueLetters' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenomeViews-class.Rd:256: file link 'oligonucleotideFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenomeViews-class.Rd:257: file link 'nucleotideFrequencyAt' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenomeViews-class.Rd:258: file link 'consensusMatrix' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenomeViews-class.Rd:259: file link 'consensusString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenomeViews-class.Rd:271: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenomeViews-class.Rd:274: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/BSgenomeViews-class.Rd:281: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/SNPlocs-class.Rd:111: file link 'subsetByOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/SNPlocs-class.Rd:112: file link 'subsetByOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/SNPlocs-class.Rd:113: file link 'subsetByOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/SNPlocs-class.Rd:116: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/SNPlocs-class.Rd:125: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/SNPlocs-class.Rd:125: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/SNPlocs-class.Rd:143: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/SNPlocs-class.Rd:156: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/SNPlocs-class.Rd:161: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/SNPlocs-class.Rd:171: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/SNPlocs-class.Rd:171: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/SNPlocs-class.Rd:178: file link 'subsetByOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/SNPlocs-class.Rd:180: file link 'subsetByOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/SNPlocs-class.Rd:183: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/XtraSNPlocs-class.Rd:93: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/XtraSNPlocs-class.Rd:94: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/XtraSNPlocs-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-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/XtraSNPlocs-class.Rd:106: file link 'subsetByOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/XtraSNPlocs-class.Rd:107: file link 'subsetByOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/XtraSNPlocs-class.Rd:108: file link 'subsetByOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/XtraSNPlocs-class.Rd:111: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/XtraSNPlocs-class.Rd:131: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/XtraSNPlocs-class.Rd:133: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/XtraSNPlocs-class.Rd:134: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/XtraSNPlocs-class.Rd:140: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/XtraSNPlocs-class.Rd:146: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/XtraSNPlocs-class.Rd:154: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/XtraSNPlocs-class.Rd:159: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/XtraSNPlocs-class.Rd:163: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/XtraSNPlocs-class.Rd:167: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/XtraSNPlocs-class.Rd:171: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/XtraSNPlocs-class.Rd:178: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/XtraSNPlocs-class.Rd:187: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/XtraSNPlocs-class.Rd:199: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/export-methods.Rd:33: file link 'FastaFile' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/export-methods.Rd:33: file link 'TwoBitFile' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/export-methods.Rd:61: file link 'TwoBitFile' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/export-methods.Rd:71: file link 'FastaFile' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/export-methods.Rd:71: file link 'TwoBitFile' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:15: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:27: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:35: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:36: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:37: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:38: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:39: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:39: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:49: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:50: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:51: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:57: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:58: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:58: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:59: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:64: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:65: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:77: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:78: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.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-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:80: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:87: file link 'solveUserSEW' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:91: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:92: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:106: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:107: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:114: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:115: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:115: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:124: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:129: file link 'DNAStringSetList' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:130: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.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-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:133: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:135: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:136: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:136: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:137: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:149: file link 'MaskedDNAString-class' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:160: file link 'DNAStringSet-class' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/getSeq-methods.Rd:161: file link 'MaskedDNAString-class' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/injectSNPs.Rd:105: file link 'letterFrequencyInSlidingView' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8yjlZz/R.INSTALL20e857767caa/BSgenome/man/injectSNPs.Rd:106: file link '.inplaceReplaceLetterAt' in package 'Biostrings' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/BSgenome.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 7.5Mb
sub-directories of 1Mb or more:
R 1.4Mb
extdata 5.7Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
'methods' 'BiocGenerics' 'S4Vectors' 'IRanges' 'GenomeInfoDb' 'GenomicRanges' 'Biostrings' 'rtracklayer'
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
'GenomeInfoDb:::compactPrintNamedAtomicVector'
'GenomeInfoDb:::showGenomeDescription' 'IRanges:::.normargSEW'
'IRanges:::unlist_as_integer' 'S4Vectors:::anyMissing'
'S4Vectors:::anyMissingOrOutside' 'S4Vectors:::decodeRle'
'S4Vectors:::diffWithInitialZero'
'S4Vectors:::makeClassinfoRowForCompactPrinting'
'S4Vectors:::makePrettyMatrixForCompactPrinting'
'S4Vectors:::make_zero_col_DataFrame' 'S4Vectors:::quick_unlist'
'S4Vectors:::quick_unsplit' 'S4Vectors:::recycleVector'
'rtracklayer:::.DNAString_to_twoBit' 'rtracklayer:::.TwoBits_export'
'rtracklayer:::checkArgFormat' 'rtracklayer:::twoBitPath'
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:
'MaskedBSgenome' 'OnDiskLongTable' 'OnDiskLongTable_old'
'as.data.frame.BSgenomeViews' 'batchsizes' 'blocksizes' 'breakpoints'
'forgeMaskedBSgenomeDataPkg'
'getBatchesByOverlapsFromOnDiskLongTable'
'getBatchesBySeqnameFromOnDiskLongTable'
'getBatchesFromOnDiskLongTable' 'getBatchesFromOnDiskLongTable_old'
'getRowsByIdFromOnDiskLongTable' 'getRowsByIdFromOnDiskLongTable_old'
'getRowsByIndexFromOnDiskLongTable_old' 'getRowsFromOnDiskLongTable'
'rowids' 'saveAsOnDiskLongTable_old'
'saveRowidsForOnDiskLongTable_old' 'spatialIndex'
'writeOnDiskLongTable' 'writeOnDiskLongTableRowids'
Undocumented S4 classes:
'OnDiskLongTable_old' 'OnDiskLongTable' 'MaskedBSgenome'
'GRanges_OR_NULL'
Undocumented S4 methods:
generic '[' and siglist 'XStringSet,GRangesList,ANY,ANY'
generic '[' and siglist 'XStringSet,GenomicRanges,ANY,ANY'
generic '[[' and siglist 'BSgenome,ANY,ANY'
generic '[[' and siglist 'FastaNamedSequences,ANY,ANY'
generic '[[' and siglist 'RdaNamedSequences,ANY,ANY'
generic '[[' and siglist 'TwobitNamedSequences,ANY,ANY'
generic 'batchsizes' and siglist 'OnDiskLongTable'
generic 'blocksizes' and siglist 'OnDiskLongTable_old'
generic 'breakpoints' and siglist 'OnDiskLongTable'
generic 'breakpoints' and siglist 'OnDiskLongTable_old'
generic 'dim' and siglist 'OnDiskLongTable'
generic 'dim' and siglist 'OnDiskLongTable_old'
generic 'dimnames' and siglist 'OnDiskLongTable'
generic 'dimnames' and siglist 'OnDiskLongTable_old'
generic 'dimnames' and siglist 'XtraSNPlocs'
generic 'forgeMaskedBSgenomeDataPkg' and siglist
'MaskedBSgenomeDataPkgSeed'
generic 'forgeMaskedBSgenomeDataPkg' and siglist 'character'
generic 'forgeMaskedBSgenomeDataPkg' and siglist 'list'
generic 'length' and siglist 'OnDiskNamedSequences'
generic 'names' and siglist 'FastaNamedSequences'
generic 'names' and siglist 'TwobitNamedSequences'
generic 'rowids' and siglist 'OnDiskLongTable'
generic 'rowids' and siglist 'OnDiskLongTable_old'
generic 'seqinfo' and siglist 'FastaNamedSequences'
generic 'seqinfo' and siglist 'RdaNamedSequences'
generic 'seqinfo' and siglist 'TwobitNamedSequences'
generic 'seqnames' and siglist 'OnDiskNamedSequences'
generic 'show' and siglist 'OnDiskLongTable'
generic 'show' and siglist 'OnDiskLongTable_old'
generic 'show' and siglist 'OnDiskNamedSequences'
generic 'spatialIndex' and siglist 'OnDiskLongTable'
All user-level objects in a package (including S4 classes and methods)
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 'BSgenome-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bsapply
> ### Title: bsapply
> ### Aliases: bsapply
> ### Keywords: manip
>
> ### ** Examples
>
> ## Load the Worm genome:
> library("BSgenome.Celegans.UCSC.ce2")
>
> ## Count the alphabet frequencies for every chromosome but exclude
> ## mitochrondrial and scaffold ones:
> params <- new("BSParams", X = Celegans, FUN = alphabetFrequency,
+ exclude = c("M", "_"))
> bsapply(params)
$chrI
A C G T M R W S Y K
4838561 2697177 2693544 4851201 0 0 0 0 0 0
V H D B N - + .
0 0 0 0 0 0 0 0
$chrII
A C G T M R W S Y K
4878194 2769208 2762193 4869710 0 0 0 0 0 0
V H D B N - + .
0 0 0 0 3 0 0 0
$chrIII
A C G T M R W S Y K
4444527 2449074 2466260 4423447 0 0 0 0 0 0
V H D B N - + .
0 0 0 0 5 0 0 0
$chrIV
A C G T M R W S Y K
5711041 3034771 3017009 5730970 0 0 0 0 0 0
V H D B N - + .
0 0 0 0 0 0 0 0
$chrV
A C G T M R W S Y K
6749806 3711722 3700959 6759744 0 0 0 0 0 0
V H D B N - + .
0 0 0 0 0 0 0 0
$chrX
A C G T M R W S Y K
5746418 3119282 3118284 5734865 0 0 0 0 0 0
V H D B N - + .
0 0 0 0 0 0 0 0
>
> ## Or we can do this same function with simplify = TRUE:
> params <- new("BSParams", X = Celegans, FUN = alphabetFrequency,
+ exclude = c("M", "_"), simplify = TRUE)
> bsapply(params)
chrI chrII chrIII chrIV chrV chrX
A 4838561 4878194 4444527 5711041 6749806 5746418
C 2697177 2769208 2449074 3034771 3711722 3119282
G 2693544 2762193 2466260 3017009 3700959 3118284
T 4851201 4869710 4423447 5730970 6759744 5734865
M 0 0 0 0 0 0
R 0 0 0 0 0 0
W 0 0 0 0 0 0
S 0 0 0 0 0 0
Y 0 0 0 0 0 0
K 0 0 0 0 0 0
V 0 0 0 0 0 0
H 0 0 0 0 0 0
D 0 0 0 0 0 0
B 0 0 0 0 0 0
N 0 3 5 0 0 0
- 0 0 0 0 0 0
+ 0 0 0 0 0 0
. 0 0 0 0 0 0
>
>
> ## Examples to show how we might look for a string (in this case an
> ## ebox motif) across the whole genome.
> Ebox <- DNAStringSet("CACGTG")
> pdict0 <- PDict(Ebox)
>
> params <- new("BSParams", X = Celegans, FUN = countPDict, simplify = TRUE)
> bsapply(params, pdict = pdict0)
chrI chrII chrIII chrIV chrV chrX chrM
3369 2698 2612 2997 3588 2466 1
>
> params@FUN <- matchPDict
> bsapply(params, pdict = pdict0)
$chrI
MIndex object of length 1
[[1]]
IRanges object with 3369 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 2260 2265 6
[2] 4920 4925 6
[3] 8074 8079 6
[4] 17729 17734 6
[5] 18576 18581 6
... ... ... ...
[3365] 15062401 15062406 6
[3366] 15065488 15065493 6
[3367] 15066587 15066592 6
[3368] 15066627 15066632 6
[3369] 15074448 15074453 6
$chrII
MIndex object of length 1
[[1]]
IRanges object with 2698 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 28734 28739 6
[2] 29032 29037 6
[3] 35849 35854 6
[4] 39084 39089 6
[5] 43244 43249 6
... ... ... ...
[2694] 15271300 15271305 6
[2695] 15273056 15273061 6
[2696] 15273761 15273766 6
[2697] 15275492 15275497 6
[2698] 15277856 15277861 6
$chrIII
MIndex object of length 1
[[1]]
IRanges object with 2612 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 7323 7328 6
[2] 11819 11824 6
[3] 17156 17161 6
[4] 24300 24305 6
[5] 26324 26329 6
... ... ... ...
[2608] 13760197 13760202 6
[2609] 13766607 13766612 6
[2610] 13768348 13768353 6
[2611] 13769745 13769750 6
[2612] 13772637 13772642 6
$chrIV
MIndex object of length 1
[[1]]
IRanges object with 2997 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 5606 5611 6
[2] 6675 6680 6
[3] 8409 8414 6
[4] 9438 9443 6
[5] 18765 18770 6
... ... ... ...
[2993] 17458897 17458902 6
[2994] 17479117 17479122 6
[2995] 17488757 17488762 6
[2996] 17490208 17490213 6
[2997] 17490673 17490678 6
$chrV
MIndex object of length 1
[[1]]
IRanges object with 3588 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 605 610 6
[2] 3531 3536 6
[3] 5078 5083 6
[4] 5128 5133 6
[5] 6038 6043 6
... ... ... ...
[3584] 20891341 20891346 6
[3585] 20894142 20894147 6
[3586] 20897746 20897751 6
[3587] 20899040 20899045 6
[3588] 20921084 20921089 6
$chrX
MIndex object of length 1
[[1]]
IRanges object with 2466 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 7656 7661 6
[2] 26993 26998 6
[3] 37580 37585 6
[4] 39506 39511 6
[5] 56687 56692 6
... ... ... ...
[2462] 17708492 17708497 6
[2463] 17708649 17708654 6
[2464] 17709026 17709031 6
[2465] 17712705 17712710 6
[2466] 17716966 17716971 6
$chrM
MIndex object of length 1
[[1]]
IRanges object with 1 range and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 8767 8772 6
>
> ## And since its really overkill to use matchPDict to find a single pattern:
> params@FUN <- matchPattern
> bsapply(params, pattern = "CACGTG")
$chrI
Views on a 15080483-letter DNAString subject
subject: GCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCT...AGGCTTAGGCTTAGGCTTAGGTTTAGGCTTAGGC
views:
start end width
[1] 2260 2265 6 [CACGTG]
[2] 4920 4925 6 [CACGTG]
[3] 8074 8079 6 [CACGTG]
[4] 17729 17734 6 [CACGTG]
[5] 18576 18581 6 [CACGTG]
... ... ... ... ...
[3365] 15062401 15062406 6 [CACGTG]
[3366] 15065488 15065493 6 [CACGTG]
[3367] 15066587 15066592 6 [CACGTG]
[3368] 15066627 15066632 6 [CACGTG]
[3369] 15074448 15074453 6 [CACGTG]
$chrII
Views on a 15279308-letter DNAString subject
subject: CCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTA...TAGGCTGAGACTTAGGCTTAGGCTTAGGCTTAGT
views:
start end width
[1] 28734 28739 6 [CACGTG]
[2] 29032 29037 6 [CACGTG]
[3] 35849 35854 6 [CACGTG]
[4] 39084 39089 6 [CACGTG]
[5] 43244 43249 6 [CACGTG]
... ... ... ... ...
[2694] 15271300 15271305 6 [CACGTG]
[2695] 15273056 15273061 6 [CACGTG]
[2696] 15273761 15273766 6 [CACGTG]
[2697] 15275492 15275497 6 [CACGTG]
[2698] 15277856 15277861 6 [CACGTG]
$chrIII
Views on a 13783313-letter DNAString subject
subject: CCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTA...TAGGCTTAGGCTTAGGCTTAGGCTTAGGCTTAGG
views:
start end width
[1] 7323 7328 6 [CACGTG]
[2] 11819 11824 6 [CACGTG]
[3] 17156 17161 6 [CACGTG]
[4] 24300 24305 6 [CACGTG]
[5] 26324 26329 6 [CACGTG]
... ... ... ... ...
[2608] 13760197 13760202 6 [CACGTG]
[2609] 13766607 13766612 6 [CACGTG]
[2610] 13768348 13768353 6 [CACGTG]
[2611] 13769745 13769750 6 [CACGTG]
[2612] 13772637 13772642 6 [CACGTG]
$chrIV
Views on a 17493791-letter DNAString subject
subject: CCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTA...TAGGCTTAGGCTTAGGCTTAGGCTTAGGCTTAGG
views:
start end width
[1] 5606 5611 6 [CACGTG]
[2] 6675 6680 6 [CACGTG]
[3] 8409 8414 6 [CACGTG]
[4] 9438 9443 6 [CACGTG]
[5] 18765 18770 6 [CACGTG]
... ... ... ... ...
[2993] 17458897 17458902 6 [CACGTG]
[2994] 17479117 17479122 6 [CACGTG]
[2995] 17488757 17488762 6 [CACGTG]
[2996] 17490208 17490213 6 [CACGTG]
[2997] 17490673 17490678 6 [CACGTG]
$chrV
Views on a 20922231-letter DNAString subject
subject: GAATTCCTAAGCCTAAGCCTAAGCCTAAGCCTAA...CTTAGGCTTAGGCTTAGGCTTAGGCTTAGGCTTA
views:
start end width
[1] 605 610 6 [CACGTG]
[2] 3531 3536 6 [CACGTG]
[3] 5078 5083 6 [CACGTG]
[4] 5128 5133 6 [CACGTG]
[5] 6038 6043 6 [CACGTG]
... ... ... ... ...
[3584] 20891341 20891346 6 [CACGTG]
[3585] 20894142 20894147 6 [CACGTG]
[3586] 20897746 20897751 6 [CACGTG]
[3587] 20899040 20899045 6 [CACGTG]
[3588] 20921084 20921089 6 [CACGTG]
$chrX
Views on a 17718849-letter DNAString subject
subject: CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA...TAGGCTTAGGCTTAGGCTTAGGCTTAGGCTTAGG
views:
start end width
[1] 7656 7661 6 [CACGTG]
[2] 26993 26998 6 [CACGTG]
[3] 37580 37585 6 [CACGTG]
[4] 39506 39511 6 [CACGTG]
[5] 56687 56692 6 [CACGTG]
... ... ... ... ...
[2462] 17708492 17708497 6 [CACGTG]
[2463] 17708649 17708654 6 [CACGTG]
[2464] 17709026 17709031 6 [CACGTG]
[2465] 17712705 17712710 6 [CACGTG]
[2466] 17716966 17716971 6 [CACGTG]
$chrM
Views on a 13794-letter DNAString subject
subject: CAGTAAATAGTTTAATAAAAATATAGCATTTGGG...TTTATAGATATATACTTTGTATATATCTATATTA
views:
start end width
[1] 8767 8772 6 [CACGTG]
>
>
> ## Examples on how to use the masks
> library(BSgenome.Hsapiens.UCSC.hg38.masked)
Loading required package: BSgenome.Hsapiens.UCSC.hg38
> genome <- BSgenome.Hsapiens.UCSC.hg38.masked
> ## I can make things verbose if I want to see the chromosomes getting processed.
> options(verbose=TRUE)
> ## For the 1st example, lets use default masks
> params <- new("BSParams", X = genome, FUN = alphabetFrequency,
+ exclude = c(1:8,"M","X","_"), simplify = TRUE)
> bsapply(params)
Warning in .local(con, format, text, ...) :
needLargeMem: Out of memory - request size 138394718 bytes, errno: 12
Error in .local(con, format, text, ...) : UCSC library operation failed
Calls: bsapply ... .loadBSgenomeSequence -> [[ -> [[ -> import -> import -> .local
Execution halted
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
XtraSNPlocs-class 90.34 3.40 93.75
SNPlocs-class 52.89 2.17 55.32
BSgenome-utils 25.06 0.41 25.48
BSgenome-class 18.66 0.78 19.46
injectSNPs 15.49 1.52 30.89
BSgenomeViews-class 13.09 1.89 15.00
bsapply 12.82 0.47 14.26
export-methods 11.97 1.02 12.99
getSeq-methods 7.71 0.37 8.09
BSgenomeForge 6.15 0.16 6.29
* 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, 5 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/BSgenome.Rcheck/00check.log'
for details.