Package: BSgenome

Version: 1.20.1

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BSgenome_1.20.1.tar.gz

StartedAt: 2011-10-20 13:53:39 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 13:58:39 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 300.4 seconds

RetCode: 0

Status:  OK

CheckDir: BSgenome.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/BSgenome.Rcheck'
* using R version 2.13.2 (2011-09-30)
* 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 '1.20.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... 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 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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... NOTE
'library' or 'require' call not declared from: BSgenome.Scerevisiae.UCSC.sacCer1
* checking sizes of PDF files under inst/doc ... OK
* checking examples ... OK
* 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

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

* DONE (BSgenome)

name	user	system	elapsed
BSgenome-class	2.181	0.094	3.162
BSgenome-utils	52.687	1.912	59.294
BSgenomeForge	0.026	0.003	0.038
GenomeData-class	0.020	0.000	0.029
GenomeDataList-class	0.064	0.001	0.071
GenomeDescription-class	0.050	0.003	0.054
available.genomes	1.868	0.390	8.842
bsapply	18.581	1.688	24.050
gdreduce	0.002	0.000	0.002
getSeq	16.640	7.697	31.904
injectSNPs	17.794	1.142	23.225