BioC 2.14: CHECK report for PWMEnrich on zin2

Package: PWMEnrich

Version: 3.6.1

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings PWMEnrich_3.6.1.tar.gz

StartedAt: 2014-10-08 02:01:04 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 02:03:15 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 131.7 seconds

RetCode: 0

Status:  OK

CheckDir: PWMEnrich.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings PWMEnrich_3.6.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/PWMEnrich.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘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 ... [7s/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 files in ‘vignettes’ ... OK
* checking examples ... [42s/43s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
motifScores     5.597  0.008   5.615
motifEnrichment 5.297  0.000   5.303
PFMtoPWM        4.868  0.240   5.125
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [8s/8s]
 [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

* 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	4.868	0.240	5.125
PWMUnscaled	0.884	0.032	0.919
getBackgroundFrequencies	0.000	0.000	0.001
groupReport-commaMotifEnrichmentResults-method	3.328	0.004	3.393
makeBackground	0.004	0.000	0.005
makePWMCutoffBackground	0.000	0.000	0.001
makePWMEmpiricalBackground	0	0	0
makePWMGEVBackground	0	0	0
makePWMLognBackground	0.004	0.000	0.001
makePWMPvalCutoffBackground	0.000	0.000	0.001
makePWMPvalCutoffBackgroundFromSeq	0.000	0.000	0.001
makePriors	0.000	0.000	0.002
motifDiffEnrichment	3.384	0.000	3.391
motifEnrichment	5.297	0.000	5.303
motifIC	0.044	0.000	0.047
motifRankingForGroup-commaMotifEnrichmentResults-method	2.596	0.000	2.599
motifRankingForSequence-commaMotifEnrichmentResults-method	2.620	0.004	2.629
motifScores	5.597	0.008	5.615
motifSimilarity	0.088	0.000	0.091
plot	0.200	0.000	0.202
plotMotifScores	0.064	0.004	0.070
plotTopMotifsGroup-commaMotifEnrichmentResults-method	2.816	0.000	2.849
plotTopMotifsSequence-commaMotifEnrichmentResults-method	2.860	0.004	2.870
readMotifs	0.104	0.012	0.120
registerCoresPWMEnrich	0	0	0
reverseComplement	0.024	0.000	0.022
scanWithPWM	0.040	0.000	0.039
sequenceReport-commaMotifEnrichmentResults-method	3.632	0.000	3.641
useBigMemoryPWMEnrich	0.000	0.000	0.001