Package: PWMEnrich

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PWMEnrich_1.2.0.tar.gz

StartedAt: 2013-03-09 00:53:24 -0800 (Sat, 09 Mar 2013)

EndedAt: 2013-03-09 00:55:34 -0800 (Sat, 09 Mar 2013)

EllapsedTime: 130.1 seconds

RetCode: 0

Status:  OK

CheckDir: PWMEnrich.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/PWMEnrich.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '1.2.0'
* 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 whether package 'PWMEnrich' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test-all.R'
 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	3.468	0.211	3.820
PWMUnscaled	0.973	0.104	1.198
getBackgroundFrequencies	0.001	0.000	0.000
makeBackground	0.005	0.003	0.010
makePWMCutoffBackground	0	0	0
makePWMEmpiricalBackground	0	0	0
makePWMGEVBackground	0	0	0
makePWMLognBackground	0.000	0.000	0.001
makePWMPvalCutoffBackground	0.001	0.000	0.000
makePriors	0.004	0.001	0.003
motifDiffEnrichment	0.830	0.010	0.887
motifEnrichment	0.829	0.009	0.863
motifIC	0.042	0.005	0.049
motifScores	0.899	0.011	0.929
motifSimilarity	0.104	0.007	0.119
plot-comma-PWM-comma-missing-dash-method	0.096	0.015	0.128
readMotifs	0.073	0.023	0.100
registerCoresPWMEnrich	0	0	0
reverseComplement-comma-PWM-dash-method	0.034	0.006	0.042
scanWithPWM	0.043	0.004	0.051