Package: MethylSeekR

Version: 1.23.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MethylSeekR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MethylSeekR_1.23.0.tar.gz

StartedAt: 2019-04-09 03:29:34 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:39:16 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 581.2 seconds

RetCode: 0

Status:  OK

CheckDir: MethylSeekR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MethylSeekR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MethylSeekR_1.23.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/MethylSeekR.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MethylSeekR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MethylSeekR’ version ‘1.23.0’
* 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 ‘MethylSeekR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘parallel’
A package should be listed in only one of these fields.
* 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
Namespace in Imports field not imported from: ‘geneplotter’
  All declared Imports should be used.
Package in Depends field not imported from: ‘rtracklayer’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
PMDviterbiSegmentation : <anonymous>: no visible global function
  definition for ‘predict’
PMDviterbiSegmentation : <anonymous>: no visible global function
  definition for ‘Rle’
PMDviterbiSegmentation : <anonymous>: no visible global function
  definition for ‘runValue’
calculateAlphaDistr : <anonymous>: no visible global function
  definition for ‘Rle’
calculateFDRs: no visible global function definition for ‘queryHits’
calculateFDRs : <anonymous>: no visible global function definition for
  ‘Rle’
calculateFDRs : <anonymous>: no visible global function definition for
  ‘runValue’
createGRangesObjectPMDSegmentation : <anonymous>: no visible global
  function definition for ‘Rle’
createGRangesObjectPMDSegmentation : <anonymous>: no visible global
  function definition for ‘nrun’
createGRangesObjectPMDSegmentation : <anonymous>: no visible global
  function definition for ‘runValue’
plotFinalSegmentation: no visible global function definition for ‘Rle’
removeSNPs: no visible global function definition for ‘queryHits’
segmentUMRsLMRs : <anonymous>: no visible global function definition
  for ‘Rle’
segmentUMRsLMRs : <anonymous>: no visible global function definition
  for ‘runValue’
segmentUMRsLMRs: no visible global function definition for ‘queryHits’
segmentUMRsLMRs: no visible global function definition for
  ‘subjectHits’
segmentUMRsLMRs: no visible global function definition for ‘Rle’
segmentUMRsLMRs: no visible global function definition for ‘DataFrame’
segmentUMRsLMRs: no visible global function definition for
  ‘colorRampPalette’
Undefined global functions or variables:
  DataFrame Rle colorRampPalette nrun predict queryHits runValue
  subjectHits
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "predict")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
MethylSeekR-package         74.162 11.602 106.196
plotPMDSegmentation         47.731  7.189  59.054
savePMDSegments             39.917  6.092  46.294
segmentPMDs                 39.082  5.934  45.306
plotAlphaDistributionOneChr  9.707  1.433  12.076
calculateFDRs                7.879  2.993  23.430
* 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-3.9-bioc/meat/MethylSeekR.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MethylSeekR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘MethylSeekR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MethylSeekR)

name	user	system	elapsed
MethylSeekR-package	74.162	11.602	106.196
calculateFDRs	7.879	2.993	23.430
plotAlphaDistributionOneChr	9.707	1.433	12.076
plotFinalSegmentation	3.662	0.551	4.670
plotPMDSegmentation	47.731	7.189	59.054
readMethylome	0.561	0.074	0.662
readSNPTable	0.158	0.008	0.202
removeSNPs	0.703	0.119	0.900
savePMDSegments	39.917	6.092	46.294
saveUMRLMRSegments	1.561	0.290	1.851
segmentPMDs	39.082	5.934	45.306
segmentUMRsLMRs	1.590	0.294	1.885