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CHECK report for missMethyl on tokay1

This page was generated on 2019-04-13 11:24:09 -0400 (Sat, 13 Apr 2019).

Package 977/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
missMethyl 1.16.0
Belinda Phipson
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/missMethyl
Branch: RELEASE_3_8
Last Commit: de46e07
Last Changed Date: 2018-10-30 11:41:54 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 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
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: missMethyl
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:missMethyl.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings missMethyl_1.16.0.tar.gz
StartedAt: 2019-04-13 03:54:18 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:04:50 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 632.3 seconds
RetCode: 0
Status:  OK  
CheckDir: missMethyl.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:missMethyl.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings missMethyl_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/missMethyl.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.16.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... OK
* 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'
.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'
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.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
SWAN               26.52   2.64   29.15
topGSA             26.48   2.58   29.06
RUVadj             17.64   1.73   19.38
topRUV             15.55   2.15   17.74
densityByProbeType 12.59   1.05   13.66
getAdjusted        10.67   0.85   11.52
RUVfit              9.68   1.00   10.69
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
topGSA             29.36   1.30   30.65
SWAN               27.48   1.69   29.20
RUVadj             19.76   1.08   20.87
topRUV             12.81   0.74   13.54
densityByProbeType 12.08   0.92   13.05
getAdjusted         9.67   0.74   10.43
RUVfit              9.59   0.79   10.39
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/missMethyl.Rcheck/00check.log'
for details.

Installation output

missMethyl.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/missMethyl_1.16.0.tar.gz && rm -rf missMethyl.buildbin-libdir && mkdir missMethyl.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=missMethyl.buildbin-libdir missMethyl_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL missMethyl_1.16.0.zip && rm missMethyl_1.16.0.tar.gz missMethyl_1.16.0.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 41265  100 41265    0     0   720k      0 --:--:-- --:--:-- --:--:--  774k

install for i386

* installing *source* package 'missMethyl' ...
** 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  
    getAdjusted                             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
In R CMD INSTALL

install for x64

* installing *source* package 'missMethyl' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'missMethyl' as missMethyl_1.16.0.zip
* DONE (missMethyl)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'missMethyl' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

Example timings

missMethyl.Rcheck/examples_i386/missMethyl-Ex.timings

nameusersystemelapsed
RUVadj17.64 1.7319.38
RUVfit 9.68 1.0010.69
SWAN26.52 2.6429.15
contrasts.varFit0.050.000.04
densityByProbeType12.59 1.0513.66
getAdjusted10.67 0.8511.52
getINCs0.590.090.69
getLeveneResiduals0.020.000.02
getMappedEntrezIDs000
gometh000
gsameth000
topGSA26.48 2.5829.06
topRUV15.55 2.1517.74
topVar0.010.000.01
varFit0.020.000.02

missMethyl.Rcheck/examples_x64/missMethyl-Ex.timings

nameusersystemelapsed
RUVadj19.76 1.0820.87
RUVfit 9.59 0.7910.39
SWAN27.48 1.6929.20
contrasts.varFit0.050.000.05
densityByProbeType12.08 0.9213.05
getAdjusted 9.67 0.7410.43
getINCs1.580.151.73
getLeveneResiduals0.010.000.02
getMappedEntrezIDs000
gometh000
gsameth000
topGSA29.36 1.3030.65
topRUV12.81 0.7413.54
topVar000
varFit0.010.000.02