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BioC 3.5: CHECK report for missMethyl on malbec2

This page was generated on 2017-08-16 13:15:54 -0400 (Wed, 16 Aug 2017).

Package 833/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
missMethyl 1.10.0
Belinda Phipson
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/missMethyl
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
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
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: missMethyl
Version: 1.10.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings missMethyl_1.10.0.tar.gz
StartedAt: 2017-08-16 00:41:53 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:48:35 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 401.9 seconds
RetCode: 0
Status:  OK 
CheckDir: missMethyl.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings missMethyl_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/missMethyl.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.10.0’
* 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             55.300  1.616  62.878
SWAN               33.864  0.916  34.805
getMappedEntrezIDs 16.956  1.344  18.348
densityByProbeType 17.136  0.116  17.263
topGSA             16.856  0.004  16.868
RUVadj             15.072  1.556  16.638
gsameth            15.056  0.032  15.182
topRUV              9.400  0.572   9.976
RUVfit              7.648  0.268   7.927
* 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-3.5-bioc/meat/missMethyl.Rcheck/00check.log’
for details.


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)

missMethyl.Rcheck/missMethyl-Ex.timings:

nameusersystemelapsed
RUVadj15.072 1.55616.638
RUVfit7.6480.2687.927
SWAN33.864 0.91634.805
contrasts.varFit0.3160.0000.315
densityByProbeType17.136 0.11617.263
getINCs0.4760.0680.548
getLeveneResiduals0.0080.0000.008
getMappedEntrezIDs16.956 1.34418.348
gometh55.300 1.61662.878
gsameth15.056 0.03215.182
topGSA16.856 0.00416.868
topRUV9.4000.5729.976
topVar0.0560.0000.054
varFit0.0080.0000.009