Multiple platform build/check report for BioC 3.9 - CHECK report for missMethyl on tokay2

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:missMethyl.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings missMethyl_1.18.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/missMethyl.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
topRUV             34.16   4.24   38.41
topGSA             29.22   1.65   30.90
RUVadj             27.54   2.22   29.75
SWAN               26.14   2.60   28.73
getAdj             23.15   1.08   24.24
RUVfit             20.78   1.18   21.97
densityByProbeType 12.14   1.15   13.33
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
topRUV             40.73   1.51   42.44
RUVadj             31.69   1.84   33.53
SWAN               29.55   2.80   32.35
topGSA             29.30   1.72   31.01
getAdj             25.12   1.52   26.67
RUVfit             22.11   1.39   23.50
densityByProbeType 14.44   1.53   15.97
* 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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/missMethyl.Rcheck/00check.log'
for details.

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###
### Running command:
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###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/missMethyl_1.18.0.tar.gz && rm -rf missMethyl.buildbin-libdir && mkdir missMethyl.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=missMethyl.buildbin-libdir missMethyl_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL missMethyl_1.18.0.zip && rm missMethyl_1.18.0.tar.gz missMethyl_1.18.0.zip
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 43656  100 43656    0     0   680k      0 --:--:-- --:--:-- --:--:--  761k

install for i386

* installing *source* package 'missMethyl' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'missMethyl'
    finding HTML links ... done
    RUVadj                                  html  
    finding level-2 HTML links ... done

    RUVfit                                  html  
    SWAN                                    html  
    contrasts.varFit                        html  
    densityByProbeType                      html  
    getAdj                                  html  
    getINCs                                 html  
    getLeveneResiduals                      html  
    getMappedEntrezIDs                      html  
    gometh                                  html  
    gsameth                                 html  
    missMethyl-package                      html  
    topGSA                                  html  
    topRUV                                  html  
    topVar                                  html  
    varFit                                  html  
** 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

install for x64

* installing *source* package 'missMethyl' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'missMethyl' as missMethyl_1.18.0.zip
* DONE (missMethyl)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'missMethyl' successfully unpacked and MD5 sums checked

CHECK report for missMethyl on tokay2

Summary

Command output

Installation output

Tests output

Example timings