H. Pagès
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/BSgenome |
| Branch: RELEASE_3_11 |
| Last Commit: 8364a0f |
| Last Changed Date: 2020-04-27 14:13:21 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:11 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE BSgenome PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 207/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BSgenome 1.56.0 H. Pagès
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| Package: BSgenome |
| Version: 1.56.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BSgenome.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings BSgenome_1.56.0.tar.gz |
| StartedAt: 2020-10-17 02:07:47 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 02:27:22 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 1175.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BSgenome.Rcheck |
| Warnings: 3 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BSgenome.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings BSgenome_1.56.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/BSgenome.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.56.0'
* 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 ... OK
* checking whether package 'BSgenome' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/BSgenome/man/BSgenome-utils.Rd:41: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/BSgenome/man/BSgenome-utils.Rd:90: file link 'PDict' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/BSgenome/man/BSgenome-utils.Rd:90: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/BSgenome/man/BSgenome-utils.Rd:114: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/BSgenome/man/BSgenome-utils.Rd:118: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/BSgenome/man/BSgenome-utils.Rd:124: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/BSgenome/man/BSgenome-utils.Rd:132: file link 'matchPDict' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/BSgenome/man/BSgenomeForge.Rd:111: file link 'XString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/BSgenome/man/SNPlocs-class.Rd:115: file link 'subsetByOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/BSgenome/man/SNPlocs-class.Rd:116: file link 'subsetByOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/BSgenome/man/SNPlocs-class.Rd:117: file link 'subsetByOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/BSgenome/man/SNPlocs-class.Rd:120: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/BSgenome/man/SNPlocs-class.Rd:139: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/BSgenome/man/SNPlocs-class.Rd:157: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/BSgenome/man/SNPlocs-class.Rd:157: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/BSgenome/man/SNPlocs-class.Rd:169: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/BSgenome/man/SNPlocs-class.Rd:196: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/BSgenome/man/SNPlocs-class.Rd:215: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/BSgenome/man/SNPlocs-class.Rd:220: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/BSgenome/man/SNPlocs-class.Rd:226: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/BSgenome/man/SNPlocs-class.Rd:229: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/BSgenome/man/SNPlocs-class.Rd:242: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/BSgenome/man/SNPlocs-class.Rd:242: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/BSgenome/man/SNPlocs-class.Rd:249: file link 'subsetByOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/BSgenome/man/SNPlocs-class.Rd:251: file link 'subsetByOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/BSgenome/man/SNPlocs-class.Rd:254: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/meat/BSgenome.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 7.8Mb
sub-directories of 1Mb or more:
R 1.7Mb
extdata 5.8Mb
* 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
':::' call which should be '::': 'S4Vectors:::makePrettyMatrixForCompactPrinting'
See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
'GenomeInfoDb:::compactPrintNamedAtomicVector'
'GenomeInfoDb:::showGenomeDescription'
'GenomicRanges:::get_out_of_bound_index' 'IRanges:::.normargSEW'
'IRanges:::unlist_as_integer' 'S4Vectors:::anyMissing'
'S4Vectors:::anyMissingOrOutside' 'S4Vectors:::decodeRle'
'S4Vectors:::diffWithInitialZero'
'S4Vectors:::makeClassinfoRowForCompactPrinting'
'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 'extractAt' and siglist 'BSgenome'
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 ... WARNING
Documented arguments not in \usage in documentation object 'getSeq-methods':
'...'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 (user + system) or elapsed time > 5s
user system elapsed
XtraSNPlocs-class 76.61 17.83 212.08
SNPlocs-class 37.58 3.38 90.12
BSgenome-utils 26.64 0.73 27.38
BSgenome-class 24.49 0.94 57.22
BSgenomeViews-class 21.92 3.18 28.27
injectSNPs 17.14 0.64 139.06
bsapply 16.83 0.56 17.99
getSeq-methods 7.24 0.44 7.68
export-methods 6.57 0.59 7.17
BSgenomeForge 6.63 0.05 6.92
available.genomes 2.51 0.47 23.39
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
XtraSNPlocs-class 68.90 2.45 71.47
SNPlocs-class 53.36 3.25 56.67
BSgenome-utils 30.30 0.41 30.70
BSgenomeViews-class 20.52 2.58 27.33
BSgenome-class 21.25 0.69 21.94
injectSNPs 16.72 1.71 18.42
bsapply 8.20 0.22 8.42
BSgenomeForge 7.22 0.09 7.73
getSeq-methods 7.18 0.04 7.23
export-methods 5.38 0.47 5.85
* 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: 3 WARNINGs, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-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/3.11/bioc/src/contrib/BSgenome_1.56.0.tar.gz && rm -rf BSgenome.buildbin-libdir && mkdir BSgenome.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BSgenome.buildbin-libdir BSgenome_1.56.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL BSgenome_1.56.0.zip && rm BSgenome_1.56.0.tar.gz BSgenome_1.56.0.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 5483k 100 5483k 0 0 28.7M 0 --:--:-- --:--:-- --:--:-- 29.9M
install for i386
* installing *source* package 'BSgenome' ...
** using staged installation
** 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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/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
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SNPlocs-class html
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injectSNPs html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpwjw0D0/R.INSTALL24cca4c64d1/BSgenome/man/injectSNPs.Rd:105: file link 'letterFrequencyInSlidingView' in package 'Biostrings' does not exist and so has been treated as a topic
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** 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_1.56.0.zip
* DONE (BSgenome)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'BSgenome' successfully unpacked and MD5 sums checked
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BSgenome.Rcheck/examples_i386/BSgenome-Ex.timings
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BSgenome.Rcheck/examples_x64/BSgenome-Ex.timings
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