BioC 2.13: CHECK report for bsseq on perceval

Package: bsseq

Version: 0.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch bsseq_0.10.0.tar.gz

StartedAt: 2014-04-04 23:56:20 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-05 00:00:27 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 246.5 seconds

RetCode: 0

Status:  OK

CheckDir: bsseq.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/bsseq.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bsseq/DESCRIPTION’ ... OK
* this is package ‘bsseq’ version ‘0.10.0’
* 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 ... [21s/21s] OK
* checking installed package size ... NOTE
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.bsGetCol’ ‘.bsPlotLines’ ‘.bsPlotTitle’ ‘.plotSmoothData’
  ‘plotAnnoTrack’ ‘read.bsmoothDirRaw’ ‘regionFinder3’
  ‘sampleRawToBSseq’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... [39s/43s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
BSmooth.tstat 10.154  3.503  16.954
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [9s/12s]
 [10s/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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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	2.125	0.142	2.270
BSmooth	0.002	0.004	0.006
BSmooth.tstat	10.154	3.503	16.954
BSseq-class	0.418	0.090	0.508
BSseq	0.346	0.008	0.354
data.frame2GRanges	0.049	0.005	0.054
dmrFinder	2.495	0.932	4.133
fisherTests	0.221	0.016	0.242
getCoverage	1.628	0.677	2.335
getMeth	1.751	1.449	3.205
getStats	0.817	0.378	1.197
goodnessOfFit	2.111	0.819	3.108
hasGRanges-class	0.006	0.008	0.014
read.bismark	0.002	0.004	0.007
read.umtab	0.003	0.005	0.008