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: 2013-03-25 04:10:08 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:13:10 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 182.6 seconds

RetCode: 0

Status:  OK

CheckDir: PWMEnrich.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/PWMEnrich.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-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 ... [12s/12s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [45s/45s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
motifEnrichment     8.332  0.028   8.360
motifScores         8.199  0.032   8.231
PFMtoPWM            6.487  0.502   7.034
motifDiffEnrichment 5.580  0.026   5.627
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test-all.R' [12s/12s]
 [12s/12s] 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	6.487	0.502	7.034
PWMUnscaled	1.145	0.080	1.231
getBackgroundFrequencies	0.006	0.004	0.011
makeBackground	0.008	0.009	0.017
makePWMCutoffBackground	0.149	0.008	0.158
makePWMEmpiricalBackground	0.005	0.008	0.013
makePWMGEVBackground	0.006	0.008	0.014
makePWMLognBackground	0.002	0.005	0.008
makePWMPvalCutoffBackground	0.004	0.006	0.009
makePriors	0.006	0.004	0.010
motifDiffEnrichment	5.580	0.026	5.627
motifEnrichment	8.332	0.028	8.360
motifIC	0.113	0.013	0.137
motifRankingForGroup-comma-MotifEnrichmentResults-dash-method	4.608	0.021	4.633
motifRankingForSequence-comma-MotifEnrichmentResults-dash-method	4.210	0.018	4.228
motifScores	8.199	0.032	8.231
motifSimilarity	0.143	0.010	0.154
plot-comma-PWM-comma-missing-dash-method	0.133	0.014	0.147
plotTopMotifsGroup-comma-MotifEnrichmentResults-dash-method	0.005	0.007	0.013
plotTopMotifsSequence-comma-MotifEnrichmentResults-dash-method	0.006	0.007	0.012
readMotifs	0.139	0.025	0.164
registerCoresPWMEnrich	0.004	0.005	0.009
reverseComplement-comma-PWM-dash-method	0.046	0.007	0.054
scanWithPWM	0.090	0.010	0.101
useBigMemoryPWMEnrich	0.005	0.004	0.008