BSgenome 1.32.0
H. Pages
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/BSgenome | | Last Changed Rev: 88838 / Revision: 95116 | | Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ WARNINGS ] | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BSgenome_1.32.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/BSgenome.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BSgenome/DESCRIPTION’ ... OK
* this is package ‘BSgenome’ version ‘1.32.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘BSgenome’ can be installed ... [23s/24s] OK
* checking installed package size ... OK
* 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’ ‘IRanges’ ‘GenomicRanges’ ‘Biostrings’
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
* 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:
‘BiocGenerics:::labeledLine’
‘GenomicRanges:::compactPrintNamedAtomicVector’
‘GenomicRanges:::showSeqlengths’ ‘IRanges:::.normargSEW’
‘IRanges:::anyMissing’ ‘IRanges:::recycleVector’
See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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:
‘compatibleGenomes’ ‘forgeMaskedBSgenomeDataPkg’ ‘MaskedBSgenome’
‘newSNPlocs’ ‘referenceGenome’ ‘snpcount’ ‘snpid2alleles’
‘snpid2grange’ ‘snpid2loc’ ‘snplocs’
Undocumented S4 classes:
‘MaskedBSgenome’ ‘SNPlocs’
Undocumented S4 methods:
generic '[[' and siglist 'BSgenome,ANY,ANY'
generic '[[' and siglist 'FastaNamedSequences,ANY,ANY'
generic '[[' and siglist 'RdaNamedSequences,ANY,ANY'
generic '[[<-' and siglist 'BSgenome,ANY,ANY'
generic 'compatibleGenomes' and siglist 'SNPlocs'
generic 'forgeMaskedBSgenomeDataPkg' and siglist 'character'
generic 'forgeMaskedBSgenomeDataPkg' and siglist 'list'
generic 'forgeMaskedBSgenomeDataPkg' and siglist
'MaskedBSgenomeDataPkgSeed'
generic 'length' and siglist 'OnDiskNamedSequences'
generic 'names' and siglist 'FastaNamedSequences'
generic 'organism' and siglist 'SNPlocs'
generic 'provider' and siglist 'SNPlocs'
generic 'providerVersion' and siglist 'SNPlocs'
generic 'referenceGenome' and siglist 'SNPlocs'
generic 'releaseDate' and siglist 'SNPlocs'
generic 'releaseName' and siglist 'SNPlocs'
generic 'seqinfo' and siglist 'FastaNamedSequences'
generic 'seqinfo' and siglist 'RdaNamedSequences'
generic 'seqinfo' and siglist 'SNPlocs'
generic 'seqnames' and siglist 'GenomeDescription'
generic 'seqnames' and siglist 'OnDiskNamedSequences'
generic 'seqnames' and siglist 'SNPlocs'
generic 'show' and siglist 'OnDiskNamedSequences'
generic 'show' and siglist 'SNPlocs'
generic 'snpcount' and siglist 'SNPlocs'
generic 'snpid2alleles' and siglist 'SNPlocs'
generic 'snpid2grange' and siglist 'SNPlocs'
generic 'snpid2loc' and siglist 'SNPlocs'
generic 'snplocs' and siglist 'SNPlocs'
generic 'species' and siglist 'SNPlocs'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the 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 ... WARNING
'library' or 'require' call not declared from: ‘BSgenome.Scerevisiae.UCSC.sacCer1’
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [166s/179s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
BSgenome-utils 63.828 0.741 65.357
injectSNPs 25.701 1.312 27.899
getSeq-methods 23.103 3.737 28.520
bsapply 17.152 1.165 18.715
available.genomes 13.053 1.304 22.966
* 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
WARNING: There were 2 warnings.
NOTE: There were 3 notes.
See
‘/Users/biocbuild/bbs-2.14-bioc/meat/BSgenome.Rcheck/00check.log’
for details.