Package: MethylSeekR

Version: 1.18.0

Command: rm -rf MethylSeekR.buildbin-libdir MethylSeekR.Rcheck && mkdir MethylSeekR.buildbin-libdir MethylSeekR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MethylSeekR.buildbin-libdir MethylSeekR_1.18.0.tar.gz >MethylSeekR.Rcheck\00install.out 2>&1 && cp MethylSeekR.Rcheck\00install.out MethylSeekR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=MethylSeekR.buildbin-libdir --install="check:MethylSeekR-install.out" --force-multiarch --no-vignettes --timings MethylSeekR_1.18.0.tar.gz

StartedAt: 2018-04-12 01:23:21 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:35:24 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 722.8 seconds

RetCode: 0

Status:  OK

CheckDir: MethylSeekR.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf MethylSeekR.buildbin-libdir MethylSeekR.Rcheck && mkdir MethylSeekR.buildbin-libdir MethylSeekR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MethylSeekR.buildbin-libdir MethylSeekR_1.18.0.tar.gz >MethylSeekR.Rcheck\00install.out 2>&1 && cp MethylSeekR.Rcheck\00install.out MethylSeekR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=MethylSeekR.buildbin-libdir --install="check:MethylSeekR-install.out" --force-multiarch --no-vignettes --timings MethylSeekR_1.18.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/MethylSeekR.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MethylSeekR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MethylSeekR' version '1.18.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
MethylSeekR-package         71.59   3.86   93.47
plotPMDSegmentation         44.98   2.05   47.03
savePMDSegments             41.90   1.72   43.61
segmentPMDs                 40.94   1.73   42.67
plotAlphaDistributionOneChr 13.48   0.47   13.96
calculateFDRs                8.80   1.03   28.07
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
MethylSeekR-package         55.80   3.94   77.86
segmentPMDs                 32.61   1.38   33.99
savePMDSegments             32.08   1.84   33.94
plotPMDSegmentation         31.75   1.44   33.18
calculateFDRs                7.04   0.79   26.17
plotAlphaDistributionOneChr  6.91   0.22    7.12
* 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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/MethylSeekR.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'MethylSeekR' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'MethylSeekR'
    finding HTML links ... done
    MethylSeekR-package                     html  
    calculateFDRs                           html  
    plotAlphaDistributionOneChr             html  
    plotFinalSegmentation                   html  
    plotPMDSegmentation                     html  
    readMethylome                           html  
    readSNPTable                            html  
    removeSNPs                              html  
    savePMDSegments                         html  
    saveUMRLMRSegments                      html  
    segmentPMDs                             html  
    segmentUMRsLMRs                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'MethylSeekR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MethylSeekR' as MethylSeekR_1.18.0.zip
* DONE (MethylSeekR)
In R CMD INSTALL
In R CMD INSTALL