BioC 2.12: CHECK report for BSgenome on pelham

Package: BSgenome

Version: 1.28.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BSgenome_1.28.0.tar.gz

StartedAt: 2013-05-01 03:09:00 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 03:15:50 -0700 (Wed, 01 May 2013)

EllapsedTime: 409.8 seconds

RetCode: 0

Status: WARNINGS

CheckDir: BSgenome.Rcheck

Warnings: 2

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/BSgenome.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'BSgenome/DESCRIPTION' ... OK
* this is package 'BSgenome' version '1.28.0'
* 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 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 for unstated dependencies in R code ... OK
* 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 installed files from 'inst/doc' ... OK
* checking examples ... [220s/240s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
BSgenome-utils    106.456  1.524 112.558
getSeq-methods     26.402  8.899  38.416
injectSNPs         27.933  1.898  33.443
bsapply            26.336  1.527  29.477
available.genomes   5.020  0.662  11.940
BSgenome-class      4.665  0.137   5.437
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 2 warnings.
NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/BSgenome.Rcheck/00check.log'
for details.

* installing *source* package 'BSgenome' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BSgenome)

name	user	system	elapsed
BSgenome-class	4.665	0.137	5.437
BSgenome-utils	106.456	1.524	112.558
BSgenomeForge	0.035	0.022	0.058
GenomeData-class	0.023	0.018	0.041
GenomeDataList-class	0.027	0.007	0.036
GenomeDescription-class	0.065	0.019	0.087
available.genomes	5.020	0.662	11.940
bsapply	26.336	1.527	29.477
gdReduce	0.038	0.010	0.049
getSeq-methods	26.402	8.899	38.416
injectSNPs	27.933	1.898	33.443

Summary

Command output