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CHECK report for missMethyl on malbec1

This page was generated on 2018-04-12 13:12:29 -0400 (Thu, 12 Apr 2018).

Package 874/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
missMethyl 1.12.0
Belinda Phipson
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/missMethyl
Branch: RELEASE_3_6
Last Commit: 4cb904f
Last Changed Date: 2017-10-30 12:40:20 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: missMethyl
Version: 1.12.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings missMethyl_1.12.0.tar.gz
StartedAt: 2018-04-12 01:11:01 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 01:17:24 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 382.9 seconds
RetCode: 0
Status:  OK 
CheckDir: missMethyl.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings missMethyl_1.12.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/missMethyl.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.12.0’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
gometh             49.168  0.560  54.307
SWAN               28.780  0.216  29.015
getMappedEntrezIDs 17.952  0.292  18.268
RUVadj             16.300  0.452  16.764
gsameth            14.276  0.028  14.312
topGSA             14.084  0.008  14.100
densityByProbeType 13.604  0.036  13.646
topRUV             11.256  0.088  11.352
RUVfit              9.540  0.024   9.571
* 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-3.6-bioc/meat/missMethyl.Rcheck/00check.log’
for details.



Installation output

missMethyl.Rcheck/00install.out

* installing *source* package ‘missMethyl’ ...
** R
** inst
** preparing 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
RUVadj16.300 0.45216.764
RUVfit9.5400.0249.571
SWAN28.780 0.21629.015
contrasts.varFit0.3120.0000.311
densityByProbeType13.604 0.03613.646
getINCs0.6800.0080.686
getLeveneResiduals0.0080.0000.009
getMappedEntrezIDs17.952 0.29218.268
gometh49.168 0.56054.307
gsameth14.276 0.02814.312
topGSA14.084 0.00814.100
topRUV11.256 0.08811.352
topVar0.0560.0000.056
varFit0.0080.0000.010