Package: PWMEnrich

Version: 2.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PWMEnrich_2.0.0.tar.gz

StartedAt: 2013-03-24 09:02:04 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 09:05:42 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 217.4 seconds

RetCode: 0

Status:  OK

CheckDir: PWMEnrich.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/PWMEnrich.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'PWMEnrich/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PWMEnrich' version '2.0.0'
* 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 'PWMEnrich' can be installed ... [14s/16s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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 examples ... [57s/57s] OK
Examples with CPU or elapsed time > 5s
                                                                   user system
motifEnrichment                                                  10.643  0.086
motifScores                                                      10.014  0.062
PFMtoPWM                                                          8.135  0.658
motifDiffEnrichment                                               6.672  0.050
motifRankingForSequence-comma-MotifEnrichmentResults-dash-method  5.900  0.047
motifRankingForGroup-comma-MotifEnrichmentResults-dash-method     5.619  0.045
                                                                 elapsed
motifEnrichment                                                   10.958
motifScores                                                       10.100
PFMtoPWM                                                           8.834
motifDiffEnrichment                                                6.755
motifRankingForSequence-comma-MotifEnrichmentResults-dash-method   6.014
motifRankingForGroup-comma-MotifEnrichmentResults-dash-method      5.772
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test-all.R' [12s/12s]
 [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 vignettes ... 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
   'PWMEnrich.Rnw' 
** testing if installed package can be loaded
* DONE (PWMEnrich)

name	user	system	elapsed
PFMtoPWM	8.135	0.658	8.834
PWMUnscaled	1.210	0.062	1.276
getBackgroundFrequencies	0.010	0.002	0.013
makeBackground	0.017	0.007	0.024
makePWMCutoffBackground	0.003	0.004	0.006
makePWMEmpiricalBackground	0.014	0.006	0.019
makePWMGEVBackground	0.003	0.004	0.007
makePWMLognBackground	0.012	0.004	0.016
makePWMPvalCutoffBackground	0.012	0.006	0.018
makePriors	0.018	0.004	0.023
motifDiffEnrichment	6.672	0.050	6.755
motifEnrichment	10.643	0.086	10.958
motifIC	0.120	0.020	0.151
motifRankingForGroup-comma-MotifEnrichmentResults-dash-method	5.619	0.045	5.772
motifRankingForSequence-comma-MotifEnrichmentResults-dash-method	5.900	0.047	6.014
motifScores	10.014	0.062	10.100
motifSimilarity	0.171	0.016	0.187
plot-comma-PWM-comma-missing-dash-method	0.169	0.018	0.186
plotTopMotifsGroup-comma-MotifEnrichmentResults-dash-method	0.013	0.010	0.023
plotTopMotifsSequence-comma-MotifEnrichmentResults-dash-method	0.011	0.011	0.023
readMotifs	0.175	0.028	0.203
registerCoresPWMEnrich	0.007	0.004	0.012
reverseComplement-comma-PWM-dash-method	0.061	0.013	0.075
scanWithPWM	0.107	0.013	0.121
useBigMemoryPWMEnrich	0.007	0.006	0.013