BioC 2.12: CHECK report for PWMEnrich on george2

Package: PWMEnrich

Version: 2.2.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings PWMEnrich_2.2.0.tar.gz

StartedAt: 2013-10-09 04:12:47 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 04:16:51 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 244.3 seconds

RetCode: 0

Status:  OK

CheckDir: PWMEnrich.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/PWMEnrich.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘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 ... [17s/18s] 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 ... [58s/58s] OK
Examples with CPU or elapsed time > 5s
                                                                   user system
PFMtoPWM                                                         10.285  0.384
motifEnrichment                                                   9.749  0.028
motifScores                                                       8.637  0.028
motifDiffEnrichment                                               7.724  0.000
motifRankingForSequence-comma-MotifEnrichmentResults-dash-method  5.868  0.004
motifRankingForGroup-comma-MotifEnrichmentResults-dash-method     5.056  0.004
                                                                 elapsed
PFMtoPWM                                                          10.712
motifEnrichment                                                    9.831
motifScores                                                        8.713
motifDiffEnrichment                                                7.746
motifRankingForSequence-comma-MotifEnrichmentResults-dash-method   5.877
motifRankingForGroup-comma-MotifEnrichmentResults-dash-method      5.070
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [15s/16s]
 [15s/16s] 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	10.285	0.384	10.712
PWMUnscaled	1.472	0.064	1.539
getBackgroundFrequencies	0.056	0.004	0.060
makeBackground	0.064	0.000	0.065
makePWMCutoffBackground	0.040	0.000	0.038
makePWMEmpiricalBackground	0.020	0.000	0.022
makePWMGEVBackground	0.020	0.000	0.021
makePWMLognBackground	0.024	0.000	0.021
makePWMPvalCutoffBackground	0.020	0.000	0.021
makePriors	0.008	0.000	0.010
motifDiffEnrichment	7.724	0.000	7.746
motifEnrichment	9.749	0.028	9.831
motifIC	0.068	0.004	0.078
motifRankingForGroup-comma-MotifEnrichmentResults-dash-method	5.056	0.004	5.070
motifRankingForSequence-comma-MotifEnrichmentResults-dash-method	5.868	0.004	5.877
motifScores	8.637	0.028	8.713
motifSimilarity	0.140	0.004	0.146
plot-comma-PWM-comma-missing-dash-method	0.132	0.000	0.133
plotTopMotifsGroup-comma-MotifEnrichmentResults-dash-method	0.020	0.000	0.019
plotTopMotifsSequence-comma-MotifEnrichmentResults-dash-method	0.020	0.000	0.016
readMotifs	0.180	0.020	0.202
registerCoresPWMEnrich	0.012	0.000	0.011
reverseComplement-comma-PWM-dash-method	0.048	0.000	0.050
scanWithPWM	0.092	0.000	0.094
useBigMemoryPWMEnrich	0.004	0.000	0.004