BioC 2.12: CHECK report for PWMEnrich on petty

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: 2013-10-08 23:32:32 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:36:44 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 252.7 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 3.0.1 (2013-05-16)
* 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 ... [16s/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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [67s/68s] OK
Examples with CPU or elapsed time > 5s
                                                                   user system
motifEnrichment                                                  12.924  0.060
motifScores                                                      12.259  0.058
PFMtoPWM                                                          9.631  0.564
motifDiffEnrichment                                               8.454  0.036
motifRankingForGroup-comma-MotifEnrichmentResults-dash-method     6.492  0.028
motifRankingForSequence-comma-MotifEnrichmentResults-dash-method  6.312  0.022
                                                                 elapsed
motifEnrichment                                                   13.074
motifScores                                                       12.388
PFMtoPWM                                                          10.503
motifDiffEnrichment                                                8.612
motifRankingForGroup-comma-MotifEnrichmentResults-dash-method      6.648
motifRankingForSequence-comma-MotifEnrichmentResults-dash-method   6.377
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test-all.R' [14s/14s]
 [15s/15s] 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	9.631	0.564	10.503
PWMUnscaled	1.342	0.061	1.408
getBackgroundFrequencies	0.010	0.002	0.012
makeBackground	0.018	0.006	0.024
makePWMCutoffBackground	0.010	0.004	0.014
makePWMEmpiricalBackground	0.010	0.005	0.016
makePWMGEVBackground	0.011	0.004	0.015
makePWMLognBackground	0.010	0.004	0.015
makePWMPvalCutoffBackground	0.011	0.005	0.016
makePriors	0.009	0.004	0.012
motifDiffEnrichment	8.454	0.036	8.612
motifEnrichment	12.924	0.060	13.074
motifIC	0.110	0.017	0.134
motifRankingForGroup-comma-MotifEnrichmentResults-dash-method	6.492	0.028	6.648
motifRankingForSequence-comma-MotifEnrichmentResults-dash-method	6.312	0.022	6.377
motifScores	12.259	0.058	12.388
motifSimilarity	0.201	0.011	0.214
plot-comma-PWM-comma-missing-dash-method	0.168	0.012	0.181
plotTopMotifsGroup-comma-MotifEnrichmentResults-dash-method	0.010	0.007	0.017
plotTopMotifsSequence-comma-MotifEnrichmentResults-dash-method	0.008	0.006	0.014
readMotifs	0.221	0.030	0.251
registerCoresPWMEnrich	0.002	0.002	0.005
reverseComplement-comma-PWM-dash-method	0.061	0.007	0.067
scanWithPWM	0.108	0.007	0.115
useBigMemoryPWMEnrich	0.006	0.004	0.011