BioC 3.5: CHECK report for PWMEnrich on toluca2

Package: PWMEnrich

Version: 4.11.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PWMEnrich_4.11.0.tar.gz

StartedAt: 2017-04-23 08:21:51 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 08:24:08 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 136.8 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_4.11.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/PWMEnrich.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘4.11.0’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  5.3Mb
  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
colMedians: no visible binding for global variable ‘median’
getPromoters: no visible global function definition for
  ‘providerVersion’
getPromoters: no visible global function definition for ‘data’
gevPerSequence: no visible global function definition for ‘predict.lm’
logNormPval: no visible global function definition for ‘plnorm’
makePWMGEVBackground : <anonymous>: no visible global function
  definition for ‘lm’
makePWMLognBackground : dlnorm.lcen: no visible global function
  definition for ‘dlnorm’
makePWMLognBackground : dlnorm.lcen: no visible global function
  definition for ‘plnorm’
makePWMLognBackground: no visible global function definition for
  ‘quantile’
makePWMLognBackground: no visible global function definition for
  ‘median’
makePWMLognBackground: no visible global function definition for
  ‘optimize’
makePWMPvalCutoffBackground: no visible global function definition for
  ‘quantile’
makePWMPvalCutoffBackground: no visible global function definition for
  ‘ecdf’
makePWMPvalCutoffBackgroundFromSeq: no visible global function
  definition for ‘na.omit’
makePWMPvalCutoffBackgroundFromSeq: no visible global function
  definition for ‘quantile’
makePWMPvalCutoffBackgroundFromSeq: no visible global function
  definition for ‘ecdf’
motifEcdf : <anonymous>: no visible global function definition for
  ‘na.omit’
motifEcdf: no visible binding for global variable ‘ecdf’
motifEnrichment: no visible binding for global variable ‘qlnorm’
motifEnrichment : <anonymous>: no visible global function definition
  for ‘pchisq’
motifScores: no visible global function definition for ‘mclapply’
motifScoresBigMemory: no visible global function definition for
  ‘mclapply’
plotMotifScores: no visible global function definition for ‘palette’
plotMotifScores: no visible global function definition for ‘col2rgb’
plotMotifScores: no visible global function definition for ‘rgb’
plotMotifScores: no visible global function definition for ‘par’
plotMotifScores: no visible global function definition for ‘lines’
plotMotifScores: no visible global function definition for ‘polygon’
plotMotifScores: no visible global function definition for ‘rect’
plotMotifScores: no visible global function definition for ‘text’
registerCoresPWMEnrich: no visible global function definition for
  ‘detectCores’
tryAllMotifAlignments : <anonymous>: no visible global function
  definition for ‘cor’
Undefined global functions or variables:
  col2rgb cor data detectCores dlnorm ecdf lines lm mclapply median
  na.omit optimize palette par pchisq plnorm polygon predict.lm
  providerVersion qlnorm quantile rect rgb text
Consider adding
  importFrom("grDevices", "col2rgb", "palette", "rgb")
  importFrom("graphics", "lines", "par", "polygon", "rect", "text")
  importFrom("stats", "cor", "dlnorm", "ecdf", "lm", "median", "na.omit",
             "optimize", "pchisq", "plnorm", "predict.lm", "qlnorm",
             "quantile")
  importFrom("utils", "data")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
motifScores 5.143  0.036   5.215
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-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	2.887	0.363	3.283
PWMUnscaled	0.433	0.008	0.470
getBackgroundFrequencies	0.001	0.001	0.001
groupReport-commaMotifEnrichmentResults-method	3.676	0.046	3.762
makeBackground	0.005	0.001	0.005
makePWMCutoffBackground	0.001	0.000	0.000
makePWMEmpiricalBackground	0.000	0.000	0.001
makePWMGEVBackground	0.000	0.001	0.001
makePWMLognBackground	0.000	0.000	0.001
makePWMPvalCutoffBackground	0	0	0
makePWMPvalCutoffBackgroundFromSeq	0.000	0.000	0.001
makePriors	0.003	0.001	0.002
motifDiffEnrichment	3.706	0.012	3.737
motifEnrichment	4.836	0.016	4.908
motifIC	0.052	0.002	0.055
motifRankingForGroup-commaMotifEnrichmentResults-method	2.525	0.009	2.548
motifRankingForSequence-commaMotifEnrichmentResults-method	2.498	0.008	2.520
motifScores	5.143	0.036	5.215
motifSimilarity	0.158	0.002	0.159
plot	0.273	0.005	0.280
plotMotifScores	0.092	0.005	0.100
plotTopMotifsGroup-commaMotifEnrichmentResults-method	2.845	0.019	2.885
plotTopMotifsSequence-commaMotifEnrichmentResults-method	2.892	0.017	2.933
readMotifs	0.161	0.015	0.176
registerCoresPWMEnrich	0.001	0.000	0.000
reverseComplement	0.025	0.002	0.027
scanWithPWM	0.051	0.002	0.054
sequenceReport-commaMotifEnrichmentResults-method	3.684	0.075	3.788
toPWM	2.838	0.314	3.175
useBigMemoryPWMEnrich	0.001	0.000	0.001