Package: PWMEnrich

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PWMEnrich_1.0.1.tar.gz

StartedAt: 2012-06-21 02:47:46 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 02:50:22 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 156.1 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 2.15.0 Patched (2012-04-26 r59216)
* 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 '1.0.1'
* 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 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	4.164	0.237	4.500
PWMUnscaled	1.209	0.101	1.343
getBackgroundFrequencies	0	0	0
makeBackground	0.005	0.001	0.007
makePWMCutoffBackground	0	0	0
makePWMEmpiricalBackground	0	0	0
makePWMGEVBackground	0.000	0.000	0.001
makePWMLognBackground	0	0	0
makePWMPvalCutoffBackground	0.000	0.001	0.000
makePriors	0.025	0.000	0.025
motifDiffEnrichment	1.016	0.012	1.050
motifEnrichment	1.339	0.015	1.374
motifIC	0.061	0.004	0.068
motifScores	1.211	0.010	1.234
motifSimilarity	0.133	0.003	0.136
plot-comma-PWM-comma-missing-dash-method	0.137	0.012	0.151
readMotifs	0.124	0.033	0.159
registerCoresPWMEnrich	0	0	0
reverseComplement-comma-PWM-dash-method	0.045	0.003	0.047
scanWithPWM	0.059	0.004	0.062