Package: BSgenome

Version: 1.21.0

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings BSgenome_1.21.0.tar.gz

StartedAt: 2011-05-09 15:26:26 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 15:33:23 -0700 (Mon, 09 May 2011)

EllapsedTime: 416.7 seconds

RetCode: 0

Status:  OK

CheckDir: BSgenome.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/BSgenome.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BSgenome/DESCRIPTION' ... OK
* this is package 'BSgenome' version '1.21.0'
* checking package name space 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 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 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

Attaching package: 'IRanges'

The following object(s) are masked from 'package:base':

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'BSgenomeForge.Rnw' 
   'GenomeSearching.Rnw' 
** testing if installed package can be loaded

* DONE (BSgenome)

name	user	system	elapsed
BSgenome-class	2.18	0.03	2.39
BSgenome-utils	35.91	0.53	37.78
BSgenomeForge	0.02	0.00	0.01
GenomeData-class	0.01	0.00	0.02
GenomeDataList-class	0.05	0.00	0.04
GenomeDescription-class	0.01	0.02	0.04
available.genomes	1.14	0.33	16.73
bsapply	8.86	0.55	11.05
gdreduce	0	0	0
getSeq	13.08	2.73	17.33
injectSNPs	18.69	2.91	157.01