BioC 3.2: CHECK report for PWMEnrich on oaxaca

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: 2016-04-23 03:21:25 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 03:23:51 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 146.1 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 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (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 ... [8s/9s] 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:
  ‘PWMEnrich.Dmelanogaster.background’ ‘PWMEnrich.Hsapiens.background’
  ‘PWMEnrich.Mmusculus.background’ ‘parallel’
  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 ... [42s/44s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
motifScores 4.991  0.029   5.416
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [5s/5s]
 [5s/5s] 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	3.108	0.373	3.593
PWMUnscaled	0.438	0.008	0.447
getBackgroundFrequencies	0	0	0
groupReport-commaMotifEnrichmentResults-method	3.148	0.040	3.211
makeBackground	0.005	0.000	0.005
makePWMCutoffBackground	0.001	0.000	0.001
makePWMEmpiricalBackground	0.000	0.000	0.001
makePWMGEVBackground	0	0	0
makePWMLognBackground	0	0	0
makePWMPvalCutoffBackground	0.000	0.000	0.001
makePWMPvalCutoffBackgroundFromSeq	0.001	0.000	0.001
makePriors	0.003	0.000	0.003
motifDiffEnrichment	3.645	0.011	3.657
motifEnrichment	4.532	0.014	4.574
motifIC	0.059	0.004	0.079
motifRankingForGroup-commaMotifEnrichmentResults-method	2.919	0.009	2.933
motifRankingForSequence-commaMotifEnrichmentResults-method	2.347	0.004	2.352
motifScores	4.991	0.029	5.416
motifSimilarity	0.091	0.001	0.144
plot	0.210	0.006	0.406
plotMotifScores	0.067	0.003	0.293
plotTopMotifsGroup-commaMotifEnrichmentResults-method	2.889	0.015	2.914
plotTopMotifsSequence-commaMotifEnrichmentResults-method	2.652	0.011	2.667
readMotifs	0.266	0.020	0.287
registerCoresPWMEnrich	0.001	0.000	0.001
reverseComplement	0.032	0.001	0.034
scanWithPWM	0.059	0.002	0.061
sequenceReport-commaMotifEnrichmentResults-method	3.124	0.060	3.334
toPWM	2.684	0.313	3.381
useBigMemoryPWMEnrich	0.000	0.000	0.001