BSgenome 1.30.0
H. Pages
| Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/BSgenome | | Last Changed Rev: 81642 / Revision: 88450 | | Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | WARNINGS | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ WARNINGS ] | OK |
* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/BSgenome.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.30.0’
* 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 ... [16s/16s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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:::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’ ‘newSNPlocs’ ‘referenceGenome’ ‘snpcount’
‘snpid2alleles’ ‘snpid2grange’ ‘snpid2loc’ ‘snplocs’
Undocumented S4 classes:
‘SNPlocs’
Undocumented S4 methods:
generic '[[' and siglist 'BSgenome,ANY,ANY'
generic '[[<-' and siglist 'BSgenome,ANY,ANY'
generic 'compatibleGenomes' and siglist 'SNPlocs'
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 'SNPlocs'
generic 'seqnames' and siglist 'GenomeDescription'
generic 'seqnames' and siglist 'SNPlocs'
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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
‘BSgenomeForge.Rnw’, ‘GenomeSearching.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [142s/149s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
BSgenome-utils 45.388 1.066 46.526
getSeq-methods 26.265 9.010 35.447
injectSNPs 18.914 1.590 20.757
bsapply 13.792 1.749 20.601
available.genomes 9.104 1.131 10.898
BSgenome-class 4.979 0.101 5.298
* 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-2.13-bioc/meat/BSgenome.Rcheck/00check.log’
for details.