Package: bsseq

Version: 0.7.5

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings bsseq_0.7.5.tar.gz

StartedAt: 2013-03-25 00:27:53 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:32:23 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 269.5 seconds

RetCode: 0

Status:  OK

CheckDir: bsseq.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/bsseq.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bsseq/DESCRIPTION’ ... OK
* this is package ‘bsseq’ version ‘0.7.5’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘bsseq’ can be installed ... [20s/21s] OK
* checking installed package size ... OK
* checking package directory ... 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 ... NOTE
plotRegion: no visible binding for global variable ‘positions’
plotRegion: no visible binding for global variable ‘plotRange’
* 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 ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [44s/47s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
BSmooth.tstat 14.165  1.348  15.909
goodnessOfFit  4.068  0.364   5.065
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [11s/13s]
 [12s/13s] 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

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/bsseq.Rcheck/00check.log’
for details.

* installing *source* package ‘bsseq’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘bsseq.Rnw’ 
   ‘bsseq_analysis.Rnw’ 
** testing if installed package can be loaded
* DONE (bsseq)

name	user	system	elapsed
BS.chr22	1.912	0.080	2.257
BSmooth	0.000	0.004	0.007
BSmooth.tstat	14.165	1.348	15.909
BSseq-class	0.920	0.032	0.953
BSseq	0.312	0.000	0.311
data.frame2GRanges	0.040	0.000	0.041
dmrFinder	2.924	0.052	3.134
fisherTests	1.464	0.004	1.471
getCoverage	1.881	0.068	1.955
getMeth	1.624	0.676	2.348
getStats	2.204	0.080	2.663
goodnessOfFit	4.068	0.364	5.065
hasGRanges-class	0.012	0.000	0.011
read.bismark	0.008	0.000	0.005
read.umtab	0.008	0.000	0.008