Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 11:55:04 -0400 (Tue, 09 Apr 2019).
Package 187/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
BSgenome 1.51.0 H. Pagès
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
Package: BSgenome |
Version: 1.51.0 |
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BSgenome.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings BSgenome_1.51.0.tar.gz |
StartedAt: 2019-04-09 01:29:22 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 01:45:38 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 976.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: BSgenome.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BSgenome.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings BSgenome_1.51.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/BSgenome.Rcheck' * using R Under development (unstable) (2019-03-09 r76216) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'BSgenome/DESCRIPTION' ... OK * this is package 'BSgenome' version '1.51.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... 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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-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' ... OK Examples with CPU or elapsed time > 5s user system elapsed XtraSNPlocs-class 94.79 18.97 155.59 BSgenome-utils 32.53 0.88 34.20 SNPlocs-class 31.29 1.61 59.90 BSgenome-class 23.72 0.92 37.49 BSgenomeViews-class 17.92 2.22 20.14 injectSNPs 18.14 0.64 39.39 bsapply 15.83 1.46 25.11 getSeq-methods 10.23 0.36 10.59 export-methods 8.53 0.99 9.51 BSgenomeForge 8.60 0.14 9.35 available.genomes 3.81 2.48 11.34 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed XtraSNPlocs-class 92.00 3.23 95.24 SNPlocs-class 58.81 2.44 61.25 BSgenome-utils 30.15 0.44 30.59 BSgenome-class 23.45 0.78 24.23 injectSNPs 16.75 2.00 18.75 BSgenomeViews-class 15.14 2.12 17.33 bsapply 14.80 0.56 15.79 export-methods 12.54 0.81 13.37 getSeq-methods 10.00 0.16 10.16 BSgenomeForge 7.01 0.10 7.11 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 5 NOTEs See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/BSgenome.Rcheck/00check.log' for details.
BSgenome.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/BSgenome_1.51.0.tar.gz && rm -rf BSgenome.buildbin-libdir && mkdir BSgenome.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BSgenome.buildbin-libdir BSgenome_1.51.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL BSgenome_1.51.0.zip && rm BSgenome_1.51.0.tar.gz BSgenome_1.51.0.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 5478k 100 5478k 0 0 49.6M 0 --:--:-- --:--:-- --:--:-- 53.4M install for i386 * installing *source* package 'BSgenome' ... ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'BSgenome' finding HTML links ... done BSParams-class html finding level-2 HTML links ... done BSgenome-class html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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 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link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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: 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package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/BSgenome/man/getSeq-methods.Rd:161: file link 'MaskedDNAString-class' in package 'Biostrings' does not exist and so has been treated as a topic injectSNPs html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/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-3.9-bioc/tmpdir/Rtmp6zis1M/R.INSTALL1068350b3e09/BSgenome/man/injectSNPs.Rd:106: file link '.inplaceReplaceLetterAt' in package 'Biostrings' does not exist and so has been treated as a topic ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'BSgenome' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'BSgenome' as BSgenome_1.51.0.zip * DONE (BSgenome) * installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library' package 'BSgenome' successfully unpacked and MD5 sums checked
BSgenome.Rcheck/examples_i386/BSgenome-Ex.timings
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BSgenome.Rcheck/examples_x64/BSgenome-Ex.timings
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