BioC 3.3: CHECK report for DMRcaller on oaxaca

Package: DMRcaller

Version: 1.4.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DMRcaller_1.4.2.tar.gz

StartedAt: 2016-10-13 00:58:26 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 01:04:12 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 345.6 seconds

RetCode: 0

Status:  OK

CheckDir: DMRcaller.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 DMRcaller_1.4.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/DMRcaller.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DMRcaller/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DMRcaller’ version ‘1.4.2’
* 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 ‘DMRcaller’ can be installed ... OK
* checking installed package size ... OK
* 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 loading without being on the library search path ... OK
* checking 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 ... NOTE
.computeAdjuestedPValues: no visible global function definition for
  ‘p.adjust’
.computeaAjustedPValuesInDMRs: no visible global function definition
  for ‘p.adjust’
.fisherTestPValue: no visible global function definition for
  ‘fisher.test’
.isColor: no visible global function definition for ‘colors’
.plotGeneticElements: no visible global function definition for ‘text’
.plotGeneticElements: no visible global function definition for ‘lines’
.plotGeneticElements: no visible global function definition for
  ‘segments’
.plotGeneticElements: no visible global function definition for ‘rect’
.scoreTest: no visible global function definition for ‘pnorm’
plotLocalMethylationProfile: no visible global function definition for
  ‘colorRampPalette’
plotLocalMethylationProfile: no visible global function definition for
  ‘plot’
plotLocalMethylationProfile: no visible global function definition for
  ‘axis’
plotLocalMethylationProfile: no visible global function definition for
  ‘points’
plotLocalMethylationProfile: no visible global function definition for
  ‘legend’
plotLocalMethylationProfile: no visible global function definition for
  ‘segments’
plotLocalMethylationProfile: no visible global function definition for
  ‘rect’
plotLocalMethylationProfile: no visible global function definition for
  ‘text’
plotLocalMethylationProfile: no visible global function definition for
  ‘par’
plotLocalMethylationProfile: no visible global function definition for
  ‘mtext’
plotMethylationDataCoverage: no visible global function definition for
  ‘rainbow’
plotMethylationDataCoverage: no visible global function definition for
  ‘par’
plotMethylationDataCoverage: no visible global function definition for
  ‘plot’
plotMethylationDataCoverage: no visible global function definition for
  ‘lines’
plotMethylationDataCoverage: no visible global function definition for
  ‘axis’
plotMethylationDataCoverage: no visible global function definition for
  ‘legend’
plotMethylationDataCoverage: no visible global function definition for
  ‘mtext’
plotMethylationProfile: no visible global function definition for
  ‘rainbow’
plotMethylationProfile: no visible global function definition for
  ‘plot’
plotMethylationProfile: no visible global function definition for
  ‘lines’
plotMethylationProfile: no visible global function definition for
  ‘legend’
plotMethylationProfile: no visible global function definition for
  ‘mtext’
plotMethylationProfile: no visible global function definition for
  ‘axis’
plotMethylationProfileFromData: no visible global function definition
  for ‘rainbow’
plotMethylationProfileFromData: no visible global function definition
  for ‘par’
plotOverlapProfile: no visible global function definition for
  ‘colorRampPalette’
plotOverlapProfile: no visible global function definition for ‘par’
plotOverlapProfile: no visible global function definition for ‘plot’
plotOverlapProfile: no visible global function definition for ‘rect’
plotOverlapProfile: no visible global function definition for ‘mtext’
plotOverlapProfile: no visible global function definition for ‘text’
saveBismark: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  axis colorRampPalette colors fisher.test legend lines mtext p.adjust
  par plot pnorm points rainbow rect segments text write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "colors", "rainbow")
  importFrom("graphics", "axis", "legend", "lines", "mtext", "par",
             "plot", "points", "rect", "segments", "text")
  importFrom("stats", "fisher.test", "p.adjust", "pnorm")
  importFrom("utils", "write.table")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
plotMethylationProfileFromData 86.971  0.449  87.607
plotMethylationProfile         42.912  0.207  43.246
computeMethylationProfile      42.476  0.252  44.686
readBismarkPool                11.060  0.650  11.919
computeDMRs                     6.909  0.161   7.732
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/DMRcaller.Rcheck/00check.log’
for details.

* installing *source* package ‘DMRcaller’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DMRcaller)

name	user	system	elapsed
DMRcaller	0.005	0.001	0.006
analyseReadsInsideRegionsForCondition	1.752	0.092	2.111
computeDMRs	6.909	0.161	7.732
computeMethylationDataCoverage	1.101	0.193	1.596
computeMethylationProfile	42.476	0.252	44.686
computeOverlapProfile	1.193	0.037	1.251
filterDMRs	2.384	0.163	2.549
getWholeChromosomes	0.552	0.078	0.630
mergeDMRsIteratively	4.317	0.112	4.438
plotLocalMethylationProfile	2.504	0.212	2.721
plotMethylationDataCoverage	1.555	0.255	1.833
plotMethylationProfile	42.912	0.207	43.246
plotMethylationProfileFromData	86.971	0.449	87.607
plotOverlapProfile	1.680	0.040	1.724
poolMethylationDatasets	2.228	0.316	2.551
poolTwoMethylationDatasets	1.702	0.194	1.899
readBismark	4.647	0.246	4.910
readBismarkPool	11.060	0.650	11.919
saveBismark	2.054	0.130	2.195