BioC 3.2: CHECK report for PWMEnrich on zin1

Package: PWMEnrich

Version: 4.5.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings PWMEnrich_4.5.0.tar.gz

StartedAt: 2015-08-24 02:49:05 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 02:50:45 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 99.8 seconds

RetCode: 0

Status:  OK

CheckDir: PWMEnrich.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings PWMEnrich_4.5.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/PWMEnrich.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-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 ‘4.5.0’
* 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 ... [6s/6s] OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    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 ... [31s/31s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [4s/4s]
 [4s/4s] 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
  ‘/home/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	2.184	0.180	2.373
PWMUnscaled	0.400	0.004	0.404
getBackgroundFrequencies	0	0	0
groupReport-commaMotifEnrichmentResults-method	2.329	0.000	2.327
makeBackground	0.004	0.000	0.004
makePWMCutoffBackground	0.001	0.000	0.000
makePWMEmpiricalBackground	0.000	0.000	0.001
makePWMGEVBackground	0.001	0.000	0.000
makePWMLognBackground	0.000	0.000	0.001
makePWMPvalCutoffBackground	0	0	0
makePWMPvalCutoffBackgroundFromSeq	0.000	0.000	0.001
makePriors	0.001	0.000	0.002
motifDiffEnrichment	2.423	0.000	2.421
motifEnrichment	3.549	0.000	3.566
motifIC	0.042	0.000	0.042
motifRankingForGroup-commaMotifEnrichmentResults-method	1.817	0.004	1.819
motifRankingForSequence-commaMotifEnrichmentResults-method	1.808	0.004	1.813
motifScores	3.635	0.008	3.645
motifSimilarity	0.064	0.000	0.065
plot	0.156	0.000	0.156
plotMotifScores	0.054	0.000	0.054
plotTopMotifsGroup-commaMotifEnrichmentResults-method	2.040	0.000	2.043
plotTopMotifsSequence-commaMotifEnrichmentResults-method	2.097	0.003	2.105
readMotifs	0.088	0.004	0.092
registerCoresPWMEnrich	0.000	0.000	0.001
reverseComplement	0.021	0.000	0.021
scanWithPWM	0.04	0.00	0.04
sequenceReport-commaMotifEnrichmentResults-method	2.659	0.016	2.680
toPWM	2.226	0.149	2.374
useBigMemoryPWMEnrich	0.001	0.000	0.001