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BioC 3.4: CHECK report for MethylSeekR on zin1

This page was generated on 2016-09-21 03:38:11 -0700 (Wed, 21 Sep 2016).

Package 739/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MethylSeekR 1.13.0
Lukas Burger
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MethylSeekR
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MethylSeekR
Version: 1.13.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings MethylSeekR_1.13.0.tar.gz
StartedAt: 2016-09-20 09:16:42 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 09:22:18 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 336.1 seconds
RetCode: 0
Status:  OK 
CheckDir: MethylSeekR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings MethylSeekR_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/MethylSeekR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.13.0’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
MethylSeekR-package         53.968  0.288  70.730
plotPMDSegmentation         35.648  0.068  35.720
savePMDSegments             33.844  0.056  33.904
segmentPMDs                 31.808  0.068  31.876
plotAlphaDistributionOneChr  8.048  0.004   8.051
calculateFDRs                6.588  0.020  21.052
* 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-3.4-bioc/meat/MethylSeekR.Rcheck/00check.log’
for details.


MethylSeekR.Rcheck/00install.out:

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

MethylSeekR.Rcheck/MethylSeekR-Ex.timings:

nameusersystemelapsed
MethylSeekR-package53.968 0.28870.730
calculateFDRs 6.588 0.02021.052
plotAlphaDistributionOneChr8.0480.0048.051
plotFinalSegmentation3.0120.0123.025
plotPMDSegmentation35.648 0.06835.720
readMethylome0.4920.0000.493
readSNPTable0.0760.0000.075
removeSNPs0.6240.0120.635
savePMDSegments33.844 0.05633.904
saveUMRLMRSegments1.5000.0161.517
segmentPMDs31.808 0.06831.876
segmentUMRsLMRs1.6960.0121.710