Package: missMethyl

Version: 1.18.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:missMethyl.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings missMethyl_1.18.0.tar.gz

StartedAt: 2019-10-16 03:15:28 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:23:11 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 463.1 seconds

RetCode: 0

Status:  OK

CheckDir: missMethyl.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:missMethyl.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings missMethyl_1.18.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/missMethyl.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.18.0’
* 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
':::' calls which should be '::':
  ‘limma:::alias2SymbolTable’ ‘limma:::tricubeMovingAverage’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  SWAN.MethyLumiSet SWAN.RGChannelSet SWAN.default varFit.DGEList
  varFit.MethylSet varFit.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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 : : 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’
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
topGSA             33.791  0.376  34.327
topRUV             31.674  0.128  31.803
RUVadj             30.537  0.615  31.163
SWAN               30.038  0.120  30.198
getAdj             26.629  0.208  26.853
RUVfit             24.020  0.092  24.124
densityByProbeType 11.959  0.032  11.991
* 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-3.9-bioc/meat/missMethyl.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL missMethyl
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘missMethyl’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (missMethyl)

name	user	system	elapsed
RUVadj	30.537	0.615	31.163
RUVfit	24.020	0.092	24.124
SWAN	30.038	0.120	30.198
contrasts.varFit	0.044	0.000	0.044
densityByProbeType	11.959	0.032	11.991
getAdj	26.629	0.208	26.853
getINCs	0.758	0.028	0.787
getLeveneResiduals	0.011	0.000	0.011
getMappedEntrezIDs	0.001	0.000	0.000
gometh	0.001	0.000	0.000
gsameth	0.000	0.000	0.001
topGSA	33.791	0.376	34.327
topRUV	31.674	0.128	31.803
topVar	0.015	0.000	0.015
varFit	0.014	0.000	0.014