Package: PWMEnrich

Version: 2.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PWMEnrich_2.2.0.tar.gz

StartedAt: 2013-05-01 09:41:18 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 09:44:45 -0700 (Wed, 01 May 2013)

EllapsedTime: 207.8 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 Patched (2013-04-08 r62531)
* 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 '2.2.0'
* 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 ... [13s/13s] 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 ... [56s/56s] OK
Examples with CPU or elapsed time > 5s
                                                                   user system
motifScores                                                      10.295  0.071
motifEnrichment                                                  10.266  0.077
PFMtoPWM                                                          8.039  0.638
motifDiffEnrichment                                               6.933  0.061
motifRankingForGroup-comma-MotifEnrichmentResults-dash-method     5.406  0.046
motifRankingForSequence-comma-MotifEnrichmentResults-dash-method  4.949  0.035
                                                                 elapsed
motifScores                                                       10.432
motifEnrichment                                                   10.456
PFMtoPWM                                                           8.870
motifDiffEnrichment                                                7.155
motifRankingForGroup-comma-MotifEnrichmentResults-dash-method      5.482
motifRankingForSequence-comma-MotifEnrichmentResults-dash-method   5.001
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test-all.R' [12s/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 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
** testing if installed package can be loaded
* DONE (PWMEnrich)

name	user	system	elapsed
PFMtoPWM	8.039	0.638	8.870
PWMUnscaled	1.158	0.049	1.219
getBackgroundFrequencies	0.010	0.003	0.013
makeBackground	0.017	0.007	0.024
makePWMCutoffBackground	0.011	0.005	0.016
makePWMEmpiricalBackground	0.011	0.005	0.016
makePWMGEVBackground	0.011	0.005	0.017
makePWMLognBackground	0.011	0.006	0.016
makePWMPvalCutoffBackground	0.011	0.005	0.017
makePriors	0.007	0.004	0.011
motifDiffEnrichment	6.933	0.061	7.155
motifEnrichment	10.266	0.077	10.456
motifIC	0.117	0.026	0.144
motifRankingForGroup-comma-MotifEnrichmentResults-dash-method	5.406	0.046	5.482
motifRankingForSequence-comma-MotifEnrichmentResults-dash-method	4.949	0.035	5.001
motifScores	10.295	0.071	10.432
motifSimilarity	0.168	0.016	0.183
plot-comma-PWM-comma-missing-dash-method	0.162	0.014	0.180
plotTopMotifsGroup-comma-MotifEnrichmentResults-dash-method	0.004	0.007	0.011
plotTopMotifsSequence-comma-MotifEnrichmentResults-dash-method	0.008	0.008	0.016
readMotifs	0.496	0.034	0.532
registerCoresPWMEnrich	0.006	0.006	0.013
reverseComplement-comma-PWM-dash-method	0.057	0.017	0.073
scanWithPWM	0.107	0.013	0.122
useBigMemoryPWMEnrich	0.006	0.004	0.011