BioC 2.11: CHECK report for BSgenome on perceval

Package: BSgenome

Version: 1.26.1

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BSgenome_1.26.1.tar.gz

StartedAt: 2013-03-24 22:48:39 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 22:53:12 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 273.2 seconds

RetCode: 0

Status: WARNINGS

CheckDir: BSgenome.Rcheck

Warnings: 2

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/BSgenome.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'BSgenome/DESCRIPTION' ... OK
* this is package 'BSgenome' version '1.26.1'
* 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 whether package 'BSgenome' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
BSgenome-utils    42.139  1.866  44.753
getSeq-methods    20.117 10.925  33.288
injectSNPs        23.016  1.869  25.933
bsapply           17.126  1.985  21.810
available.genomes  4.292  0.959   6.206
* 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.
See
  '/Users/biocbuild/bbs-2.11-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	2.926	0.097	3.084
BSgenome-utils	42.139	1.866	44.753
BSgenomeForge	0.025	0.004	0.030
GenomeData-class	0.01	0.00	0.01
GenomeDataList-class	0.022	0.000	0.023
GenomeDescription-class	0.044	0.007	0.050
available.genomes	4.292	0.959	6.206
bsapply	17.126	1.985	21.810
gdReduce	0.027	0.000	0.028
getSeq-methods	20.117	10.925	33.288
injectSNPs	23.016	1.869	25.933

Summary

Command output