Package: BSgenome

Version: 1.26.1

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings BSgenome_1.26.1.tar.gz

StartedAt: 2013-03-24 23:49:12 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 23:53:58 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 286.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: BSgenome.Rcheck

Warnings: 2

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/BSgenome.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
injectSNPs        23.454 22.477  50.292
BSgenome-utils    33.802  0.280  34.564
getSeq-methods    19.945  0.560  20.991
available.genomes 16.096  0.896  26.240
bsapply            9.093  0.444   9.620
* 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
  ‘/loc/home/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	3.864	0.044	4.086
BSgenome-utils	33.802	0.280	34.564
BSgenomeForge	0.020	0.000	0.024
GenomeData-class	0.008	0.000	0.011
GenomeDataList-class	0.028	0.000	0.028
GenomeDescription-class	0.032	0.004	0.037
available.genomes	16.096	0.896	26.240
bsapply	9.093	0.444	9.620
gdReduce	0.032	0.000	0.033
getSeq-methods	19.945	0.560	20.991
injectSNPs	23.454	22.477	50.292