BioC 2.14: CHECK report for PWMEnrich on morelia

Package: PWMEnrich

Version: 3.6.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PWMEnrich_3.6.1.tar.gz

StartedAt: 2014-10-08 00:52:18 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:55:07 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 168.3 seconds

RetCode: 0

Status:  OK

CheckDir: PWMEnrich.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PWMEnrich_3.6.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/PWMEnrich.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (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 ‘3.6.1’
* 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 ... [9s/9s] 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 files in ‘vignettes’ ... OK
* checking examples ... [53s/54s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
motifScores     6.628  0.029   6.799
PFMtoPWM        6.249  0.331   6.747
motifEnrichment 5.892  0.012   5.932
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [9s/9s]
 [9s/10s] 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

* 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	6.249	0.331	6.747
PWMUnscaled	1.106	0.022	1.129
getBackgroundFrequencies	0.001	0.001	0.001
groupReport-commaMotifEnrichmentResults-method	4.269	0.042	4.357
makeBackground	0.007	0.001	0.008
makePWMCutoffBackground	0.001	0.000	0.001
makePWMEmpiricalBackground	0	0	0
makePWMGEVBackground	0.001	0.001	0.001
makePWMLognBackground	0	0	0
makePWMPvalCutoffBackground	0.001	0.000	0.001
makePWMPvalCutoffBackgroundFromSeq	0.000	0.000	0.001
makePriors	0.003	0.000	0.004
motifDiffEnrichment	4.376	0.011	4.427
motifEnrichment	5.892	0.012	5.932
motifIC	0.064	0.002	0.089
motifRankingForGroup-commaMotifEnrichmentResults-method	3.151	0.007	3.161
motifRankingForSequence-commaMotifEnrichmentResults-method	3.224	0.007	3.253
motifScores	6.628	0.029	6.799
motifSimilarity	0.103	0.002	0.104
plot	0.207	0.005	0.211
plotMotifScores	0.096	0.003	0.099
plotTopMotifsGroup-commaMotifEnrichmentResults-method	3.736	0.023	3.794
plotTopMotifsSequence-commaMotifEnrichmentResults-method	3.918	0.019	4.015
readMotifs	0.149	0.013	0.161
registerCoresPWMEnrich	0	0	0
reverseComplement	0.030	0.001	0.031
scanWithPWM	0.049	0.002	0.051
sequenceReport-commaMotifEnrichmentResults-method	4.349	0.069	4.442
useBigMemoryPWMEnrich	0.001	0.000	0.000