Package: BSgenome

Version: 1.20.1

Command: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch BSgenome_1.20.1.tar.gz

StartedAt: 2011-10-20 13:25:39 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 13:29:26 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 226.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: BSgenome.Rcheck

Warnings: 1

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/BSgenome.Rcheck'
* using R version 2.13.2 (2011-09-30)
* 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 '1.20.1'
* 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 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 examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... WARNING
Package vignette(s) without corresponding PDF:
   BSgenomeForge.Rnw
   GenomeSearching.Rnw

* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'D:/biocbld/bbs-2.8-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 ...
** testing if installed package can be loaded

* DONE (BSgenome)

name	user	system	elapsed
BSgenome-class	2.56	0.06	3.31
BSgenome-utils	36.32	0.44	38.38
BSgenomeForge	0.00	0.00	0.09
GenomeData-class	0.02	0.00	0.02
GenomeDataList-class	0.05	0.00	0.05
GenomeDescription-class	0.03	0.00	0.03
available.genomes	1.30	0.20	2.59
bsapply	8.89	0.44	9.59
gdreduce	0	0	0
getSeq	14.16	2.12	16.70
injectSNPs	19.03	2.46	37.36