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CHECK report for missMethyl on merida1

This page was generated on 2019-04-16 11:57:49 -0400 (Tue, 16 Apr 2019).

Package 977/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
missMethyl 1.16.0
Belinda Phipson
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/missMethyl
Branch: RELEASE_3_8
Last Commit: de46e07
Last Changed Date: 2018-10-30 11:41:54 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: missMethyl
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:missMethyl.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings missMethyl_1.16.0.tar.gz
StartedAt: 2019-04-16 01:20:46 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:28:11 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 444.8 seconds
RetCode: 0
Status:  OK 
CheckDir: missMethyl.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:missMethyl.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings missMethyl_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/missMethyl.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘missMethyl/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘missMethyl’ version ‘1.16.0’
* 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 ‘missMethyl’ 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 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
.aveQuantile: no visible global function definition for ‘approx’
.getFlatAnnotation: no visible binding for global variable
  ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
.getFlatAnnotation: no visible binding for global variable
  ‘IlluminaHumanMethylationEPICanno.ilm10b4.hg19’
.plotBias: no visible global function definition for ‘par’
.plotBias: no visible global function definition for ‘plot’
.plotBias: no visible global function definition for ‘lines’
.plotBias: no visible global function definition for ‘lowess’
.subsetQuantileNorm: no visible global function definition for ‘approx’
SWAN.MethyLumiSet: no visible global function definition for
  ‘DataFrame’
SWAN.MethyLumiSet: no visible global function definition for
  ‘phenoData’
SWAN.MethyLumiSet: no visible global function definition for
  ‘packageVersion’
SWAN.default: no visible binding for global variable
  ‘IlluminaHumanMethylation450kmanifest’
SWAN.default: no visible binding for global variable
  ‘IlluminaHumanMethylationEPICmanifest’
SWAN.default: no visible global function definition for ‘colData’
SWAN.default: no visible global function definition for
  ‘packageVersion’
densityByProbeType: no visible binding for global variable
  ‘IlluminaHumanMethylation450kmanifest’
densityByProbeType: no visible binding for global variable
  ‘IlluminaHumanMethylationEPICmanifest’
densityByProbeType : <anonymous>: no visible global function definition
  for ‘density’
densityByProbeType: no visible global function definition for ‘plot’
densityByProbeType: no visible global function definition for ‘density’
densityByProbeType: no visible global function definition for ‘lines’
densityByProbeType: no visible global function definition for ‘legend’
gometh: no visible global function definition for ‘p.adjust’
gsameth: no visible global function definition for ‘phyper’
gsameth: no visible global function definition for ‘p.adjust’
topVar: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  DataFrame IlluminaHumanMethylation450kanno.ilmn12.hg19
  IlluminaHumanMethylation450kmanifest
  IlluminaHumanMethylationEPICanno.ilm10b4.hg19
  IlluminaHumanMethylationEPICmanifest approx colData density legend
  lines lowess p.adjust packageVersion par phenoData phyper plot
Consider adding
  importFrom("graphics", "legend", "lines", "par", "plot")
  importFrom("stats", "approx", "density", "lowess", "p.adjust",
             "phyper")
  importFrom("utils", "packageVersion")
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
SWAN               33.676  4.922  39.585
topGSA             34.586  2.127  37.477
densityByProbeType 18.016  2.672  21.117
RUVadj             17.372  1.472  19.042
topRUV             14.691  1.345  16.183
getAdjusted        13.231  1.375  14.927
RUVfit             10.274  1.229  11.591
* 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-3.8-bioc/meat/missMethyl.Rcheck/00check.log’
for details.



Installation output

missMethyl.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL missMethyl
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘missMethyl’ ...
** 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
* DONE (missMethyl)

Tests output


Example timings

missMethyl.Rcheck/missMethyl-Ex.timings

nameusersystemelapsed
RUVadj17.372 1.47219.042
RUVfit10.274 1.22911.591
SWAN33.676 4.92239.585
contrasts.varFit0.0690.0020.071
densityByProbeType18.016 2.67221.117
getAdjusted13.231 1.37514.927
getINCs1.8590.2432.163
getLeveneResiduals0.0110.0010.016
getMappedEntrezIDs0.0010.0000.004
gometh0.0000.0000.001
gsameth0.0000.0000.001
topGSA34.586 2.12737.477
topRUV14.691 1.34516.183
topVar0.0140.0010.016
varFit0.0140.0010.015