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CHECK report for missMethyl on malbec2

This page was generated on 2018-10-17 08:26:27 -0400 (Wed, 17 Oct 2018).

Package 924/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
missMethyl 1.14.0
Belinda Phipson
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/missMethyl
Branch: RELEASE_3_7
Last Commit: 6b9a65d
Last Changed Date: 2018-04-30 10:35:33 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: missMethyl
Version: 1.14.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:missMethyl.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings missMethyl_1.14.0.tar.gz
StartedAt: 2018-10-16 02:05:21 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 02:15:04 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 583.4 seconds
RetCode: 0
Status:  OK 
CheckDir: missMethyl.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:missMethyl.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings missMethyl_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/missMethyl.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (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 ‘1.14.0’
* 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 ... NOTE
Namespace in Imports field not imported from: ‘IlluminaHumanMethylationEPICmanifest’
  All declared Imports should be used.
* 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’
.flattenAnn: no visible binding for global variable
  ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
.flattenAnn: no visible binding for global variable
  ‘IlluminaHumanMethylationEPICanno.ilm10b2.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.ilm10b2.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
topGSA             319.408  0.524 320.149
SWAN                23.576  0.196  23.783
RUVadj              14.768  0.496  15.272
densityByProbeType  10.400  0.020  10.422
topRUV              10.048  0.176  10.230
RUVfit               8.304  0.060   8.371
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/missMethyl.Rcheck/00check.log’
for details.



Installation output

missMethyl.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL missMethyl
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/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
RUVadj14.768 0.49615.272
RUVfit8.3040.0608.371
SWAN23.576 0.19623.783
contrasts.varFit0.0440.0000.046
densityByProbeType10.400 0.02010.422
getINCs0.4640.0160.479
getLeveneResiduals0.0080.0000.008
getMappedEntrezIDs0.0000.0000.001
gometh0.0000.0000.001
gsameth0.0000.0000.001
topGSA319.408 0.524320.149
topRUV10.048 0.17610.230
topVar0.0080.0000.010
varFit0.0120.0000.010