BioC 2.13: CHECK report for PWMEnrich on perceval

Package: PWMEnrich

Version: 2.6.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PWMEnrich_2.6.2.tar.gz

StartedAt: 2014-04-05 03:35:08 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:39:00 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 231.9 seconds

RetCode: 0

Status:  OK

CheckDir: PWMEnrich.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/PWMEnrich.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 ‘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 ... [13s/14s] 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 sizes of PDF files under ‘inst/doc’ ... 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 ... [65s/66s] OK
Examples with CPU or elapsed time > 5s
                                                   user system elapsed
PFMtoPWM                                          7.607  0.530   8.390
motifScores                                       7.807  0.056   7.981
motifEnrichment                                   7.422  0.057   7.612
sequenceReport-commaMotifEnrichmentResults-method 5.161  0.161   5.389
motifDiffEnrichment                               5.277  0.029   5.384
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [13s/13s]
 [13s/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 was 1 note.
See
  ‘/Users/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	7.607	0.530	8.390
PWMUnscaled	1.386	0.054	1.457
getBackgroundFrequencies	0.012	0.003	0.016
groupReport-commaMotifEnrichmentResults-method	4.658	0.048	4.800
makeBackground	0.017	0.007	0.024
makePWMCutoffBackground	0.009	0.004	0.013
makePWMEmpiricalBackground	0.011	0.006	0.017
makePWMGEVBackground	0.012	0.005	0.017
makePWMLognBackground	0.010	0.005	0.016
makePWMPvalCutoffBackground	0.013	0.006	0.020
makePWMPvalCutoffBackgroundFromSeq	0.013	0.005	0.018
makePriors	0.005	0.003	0.009
motifDiffEnrichment	5.277	0.029	5.384
motifEnrichment	7.422	0.057	7.612
motifIC	0.105	0.010	0.117
motifRankingForGroup-commaMotifEnrichmentResults-method	3.840	0.032	3.912
motifRankingForSequence-commaMotifEnrichmentResults-method	3.775	0.022	3.816
motifScores	7.807	0.056	7.981
motifSimilarity	0.146	0.009	0.156
plot	0.296	0.017	0.313
plotMotifScores	0.113	0.013	0.126
plotTopMotifsGroup-commaMotifEnrichmentResults-method	3.994	0.057	4.105
plotTopMotifsSequence-commaMotifEnrichmentResults-method	4.195	0.044	4.270
readMotifs	0.153	0.026	0.181
registerCoresPWMEnrich	0.002	0.003	0.006
reverseComplement	0.057	0.005	0.063
scanWithPWM	0.088	0.007	0.096
sequenceReport-commaMotifEnrichmentResults-method	5.161	0.161	5.389
useBigMemoryPWMEnrich	0.002	0.003	0.005