Package: MethylSeekR

Version: 1.26.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:MethylSeekR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings MethylSeekR_1.26.0.tar.gz

StartedAt: 2020-04-15 01:35:49 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 01:42:43 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 414.5 seconds

RetCode: 0

Status:  OK

CheckDir: MethylSeekR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:MethylSeekR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings MethylSeekR_1.26.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/MethylSeekR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 ‘1.26.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
MethylSeekR-package         57.120  0.548  73.499
segmentPMDs                 34.852  0.132  35.078
plotPMDSegmentation         34.048  0.088  34.192
savePMDSegments             33.252  0.056  33.360
calculateFDRs                7.656  0.028  20.311
plotAlphaDistributionOneChr  7.092  0.044   7.147
* 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-3.10-bioc/meat/MethylSeekR.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL MethylSeekR
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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	57.120	0.548	73.499
calculateFDRs	7.656	0.028	20.311
plotAlphaDistributionOneChr	7.092	0.044	7.147
plotFinalSegmentation	2.212	0.024	2.236
plotPMDSegmentation	34.048	0.088	34.192
readMethylome	0.512	0.004	0.516
readSNPTable	0.132	0.004	0.137
removeSNPs	0.644	0.000	0.644
savePMDSegments	33.252	0.056	33.360
saveUMRLMRSegments	1.700	0.020	1.721
segmentPMDs	34.852	0.132	35.078
segmentUMRsLMRs	2.288	0.012	2.302