BioC 2.13: CHECK report for PWMEnrich on zin1

Package: PWMEnrich

Version: 2.6.2

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings PWMEnrich_2.6.2.tar.gz

StartedAt: 2014-04-05 03:15:44 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:18:01 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 136.8 seconds

RetCode: 0

Status:  OK

CheckDir: PWMEnrich.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/PWMEnrich.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PWMEnrich/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PWMEnrich’ version ‘2.6.2’
* 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 ‘PWMEnrich’ can be installed ... [8s/8s] OK
* checking installed package size ... OK
* 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 ... 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘PWMEnrich.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [44s/45s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
motifEnrichment 5.548  0.000   5.571
motifScores     5.309  0.008   5.336
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [7s/7s]
 [8s/8s] 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 was 1 note.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/PWMEnrich.Rcheck/00check.log’
for details.

* installing *source* package ‘PWMEnrich’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (PWMEnrich)

name	user	system	elapsed
PFMtoPWM	4.752	0.176	4.977
PWMUnscaled	0.792	0.012	0.806
getBackgroundFrequencies	0.004	0.000	0.004
groupReport-commaMotifEnrichmentResults-method	3.456	0.000	3.511
makeBackground	0.008	0.004	0.013
makePWMCutoffBackground	0.004	0.000	0.004
makePWMEmpiricalBackground	0.004	0.000	0.004
makePWMGEVBackground	0.004	0.000	0.004
makePWMLognBackground	0.004	0.000	0.004
makePWMPvalCutoffBackground	0.004	0.000	0.004
makePWMPvalCutoffBackgroundFromSeq	0.004	0.000	0.003
makePriors	0.004	0.000	0.004
motifDiffEnrichment	3.609	0.000	3.614
motifEnrichment	5.548	0.000	5.571
motifIC	0.048	0.000	0.048
motifRankingForGroup-commaMotifEnrichmentResults-method	2.708	0.004	2.714
motifRankingForSequence-commaMotifEnrichmentResults-method	2.872	0.000	2.874
motifScores	5.309	0.008	5.336
motifSimilarity	0.088	0.000	0.090
plot	0.184	0.004	0.190
plotMotifScores	0.072	0.000	0.074
plotTopMotifsGroup-commaMotifEnrichmentResults-method	3.036	0.008	3.047
plotTopMotifsSequence-commaMotifEnrichmentResults-method	3.224	0.000	3.232
readMotifs	0.100	0.012	0.114
registerCoresPWMEnrich	0.004	0.000	0.001
reverseComplement	0.028	0.004	0.028
scanWithPWM	0.044	0.008	0.051
sequenceReport-commaMotifEnrichmentResults-method	3.904	0.020	3.992
useBigMemoryPWMEnrich	0.000	0.000	0.001