BioC 2.12: CHECK report for bsseq on petty

Package: bsseq

Version: 0.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch bsseq_0.8.0.tar.gz

StartedAt: 2013-10-08 21:46:17 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 21:50:50 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 272.9 seconds

RetCode: 0

Status:  OK

CheckDir: bsseq.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/bsseq.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'bsseq/DESCRIPTION' ... OK
* this is package 'bsseq' version '0.8.0'
* 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 ... [22s/22s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [45s/47s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
BSmooth.tstat 13.685  2.743  16.667
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'runTests.R' [11s/12s]
 [12s/12s] 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
  '/Users/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
** testing if installed package can be loaded
* DONE (bsseq)

name	user	system	elapsed
BS.chr22	1.470	0.087	1.563
BSmooth	0.002	0.006	0.008
BSmooth.tstat	13.685	2.743	16.667
BSseq-class	0.841	0.189	1.033
BSseq	0.385	0.035	0.423
data.frame2GRanges	0.053	0.005	0.059
dmrFinder	3.162	0.688	4.108
fisherTests	1.033	0.027	1.065
getCoverage	1.859	0.313	2.178
getMeth	1.842	1.264	3.159
getStats	1.825	0.295	2.140
goodnessOfFit	3.663	0.454	4.491
hasGRanges-class	0.006	0.007	0.013
read.bismark	0.002	0.004	0.008
read.umtab	0.003	0.005	0.007