Package: missMethyl

Version: 1.20.4

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:missMethyl.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings missMethyl_1.20.4.tar.gz

StartedAt: 2020-04-15 02:21:20 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 02:29:53 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 513.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: missMethyl.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:missMethyl.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings missMethyl_1.20.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/missMethyl.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.20.4’
* 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 ... WARNING
'library' or 'require' calls not declared from:
  ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
  ‘IlluminaHumanMethylationEPICanno.ilm10b4.hg19’
'library' or 'require' calls in package code:
  ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
  ‘IlluminaHumanMethylationEPICanno.ilm10b4.hg19’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' 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 : <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’
goregion: no visible binding for global variable
  ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
goregion: no visible binding for global variable
  ‘IlluminaHumanMethylationEPICanno.ilm10b4.hg19’
goregion: no visible global function definition for ‘GRanges’
goregion: no visible global function definition for ‘IRanges’
goregion: no visible global function definition for ‘findOverlaps’
goregion: no visible global function definition for ‘from’
gsaregion: no visible binding for global variable
  ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
gsaregion: no visible binding for global variable
  ‘IlluminaHumanMethylationEPICanno.ilm10b4.hg19’
gsaregion: no visible global function definition for ‘GRanges’
gsaregion: no visible global function definition for ‘IRanges’
gsaregion: no visible global function definition for ‘findOverlaps’
gsaregion: no visible global function definition for ‘from’
topVar: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  DataFrame GRanges IRanges
  IlluminaHumanMethylation450kanno.ilmn12.hg19
  IlluminaHumanMethylation450kmanifest
  IlluminaHumanMethylationEPICanno.ilm10b4.hg19
  IlluminaHumanMethylationEPICmanifest approx colData density
  findOverlaps from legend lines lowess p.adjust packageVersion par
  phenoData plot
Consider adding
  importFrom("graphics", "legend", "lines", "par", "plot")
  importFrom("stats", "approx", "density", "lowess", "p.adjust")
  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
RUVadj             36.608  0.784  38.005
topGSA             35.700  0.372  37.094
SWAN               32.340  0.192  33.423
topRUV             30.300  0.300  30.670
RUVfit             27.952  0.040  28.108
getAdj             27.808  0.116  27.978
densityByProbeType 14.152  0.012  14.240
* 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 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/missMethyl.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL missMethyl
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* installing to library ‘/home/biocbuild/bbs-3.10-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	36.608	0.784	38.005
RUVfit	27.952	0.040	28.108
SWAN	32.340	0.192	33.423
contrasts.varFit	0.072	0.000	0.074
densityByProbeType	14.152	0.012	14.240
getAdj	27.808	0.116	27.978
getINCs	0.732	0.008	0.743
getLeveneResiduals	0.004	0.004	0.010
getMappedEntrezIDs	0	0	0
gometh	0	0	0
goregion	0.000	0.000	0.001
gsameth	0	0	0
gsaregion	0	0	0
topGSA	35.700	0.372	37.094
topRUV	30.30	0.30	30.67
topVar	0.008	0.000	0.009
varFit	0.012	0.000	0.009