Package: BSgenome

Version: 1.18.3

Command: E:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings BSgenome_1.18.3.tar.gz

StartedAt: 2011-04-07 06:18:32 -0700 (Thu, 07 Apr 2011)

EndedAt: 2011-04-07 06:21:49 -0700 (Thu, 07 Apr 2011)

EllapsedTime: 197.2 seconds

RetCode: 0

Status:  OK

CheckDir: BSgenome.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.7-bioc/meat/BSgenome.Rcheck'
* using R version 2.12.2 (2011-02-25)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BSgenome/DESCRIPTION' ... OK
* this is package 'BSgenome' version '1.18.3'
* 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 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 package vignettes in 'inst/doc' ... 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, mapply, order, paste, pmax, pmax.int, pmin,
    pmin.int, rbind, rep.int, table

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (BSgenome)

name	user	system	elapsed
BSgenome-class	1.98	0.06	2.10
BSgenome-utils	32.08	0.34	32.75
BSgenomeForge	0.01	0.00	0.01
GenomeData-class	0.02	0.00	0.02
GenomeDataList-class	0.05	0.00	0.04
GenomeDescription-class	0.01	0.02	0.04
available.genomes	7.47	0.25	9.32
bsapply	8.57	0.39	9.42
gdreduce	0	0	0
getSeq	12.72	2.33	15.31
injectSNPs	13.00	0.26	13.97