BioC 3.2: CHECK report for PWMEnrich on perceval

Package: PWMEnrich

Version: 4.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PWMEnrich_4.6.0.tar.gz

StartedAt: 2015-10-27 11:15:45 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 11:18:23 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 158.4 seconds

RetCode: 0

Status:  OK

CheckDir: PWMEnrich.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PWMEnrich_4.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/PWMEnrich.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘4.6.0’
* 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 ... [10s/10s] OK
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       1.4Mb
    extdata   3.4Mb
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘parallel’ ‘PWMEnrich.Dmelanogaster.background’
  ‘PWMEnrich.Hsapiens.background’ ‘PWMEnrich.Mmusculus.background’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getPromoters: no visible global function definition for
  ‘providerVersion’
motifScores: no visible global function definition for ‘mclapply’
motifScoresBigMemory: no visible global function definition for
  ‘mclapply’
registerCoresPWMEnrich: no visible global function definition for
  ‘detectCores’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [49s/49s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
motifScores     5.906  0.028   5.934
motifEnrichment 5.299  0.009   5.328
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [6s/6s]
 [6s/6s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/PWMEnrich.Rcheck/00check.log’
for details.

* 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	3.130	0.387	3.580
PWMUnscaled	0.557	0.006	0.564
getBackgroundFrequencies	0	0	0
groupReport-commaMotifEnrichmentResults-method	3.580	0.038	3.633
makeBackground	0.005	0.001	0.005
makePWMCutoffBackground	0.001	0.000	0.000
makePWMEmpiricalBackground	0.001	0.000	0.001
makePWMGEVBackground	0.001	0.000	0.001
makePWMLognBackground	0.001	0.000	0.000
makePWMPvalCutoffBackground	0.001	0.000	0.001
makePWMPvalCutoffBackgroundFromSeq	0.002	0.000	0.002
makePriors	0.003	0.000	0.004
motifDiffEnrichment	3.928	0.006	3.934
motifEnrichment	5.299	0.009	5.328
motifIC	0.095	0.003	0.120
motifRankingForGroup-commaMotifEnrichmentResults-method	2.934	0.004	2.937
motifRankingForSequence-commaMotifEnrichmentResults-method	3.047	0.006	3.053
motifScores	5.906	0.028	5.934
motifSimilarity	0.128	0.001	0.129
plot	0.267	0.005	0.271
plotMotifScores	0.120	0.002	0.124
plotTopMotifsGroup-commaMotifEnrichmentResults-method	3.154	0.009	3.165
plotTopMotifsSequence-commaMotifEnrichmentResults-method	3.164	0.009	3.177
readMotifs	0.104	0.016	0.119
registerCoresPWMEnrich	0.000	0.000	0.001
reverseComplement	0.055	0.001	0.055
scanWithPWM	0.081	0.001	0.082
sequenceReport-commaMotifEnrichmentResults-method	4.097	0.084	4.304
toPWM	3.368	0.384	3.753
useBigMemoryPWMEnrich	0.001	0.000	0.001