BioC 2.12: CHECK report for BSgenome on pelham

Package: BSgenome

Version: 1.27.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BSgenome_1.27.1.tar.gz

StartedAt: 2013-03-24 03:03:09 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 03:08:53 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 344.3 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 beta (2013-03-21 r62346)
* 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 '1.27.1'
* 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 ... [17s/18s] 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 ... [142s/171s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
BSgenome-utils    45.856  1.271  50.110
getSeq-methods    24.985  8.317  36.240
injectSNPs        24.271  1.785  26.805
bsapply           15.013  1.439  17.739
available.genomes  4.352  0.853  26.185
BSgenome-class     4.530  0.153   5.086
* 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
   'BSgenomeForge.Rnw' 
   'GenomeSearching.Rnw' 
** testing if installed package can be loaded
* DONE (BSgenome)

name	user	system	elapsed
BSgenome-class	4.530	0.153	5.086
BSgenome-utils	45.856	1.271	50.110
BSgenomeForge	0.033	0.020	0.115
GenomeData-class	0.020	0.015	0.035
GenomeDataList-class	0.026	0.006	0.034
GenomeDescription-class	0.057	0.015	0.102
available.genomes	4.352	0.853	26.185
bsapply	15.013	1.439	17.739
gdReduce	0.043	0.010	0.073
getSeq-methods	24.985	8.317	36.240
injectSNPs	24.271	1.785	26.805

Summary

Command output