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CHECK report for lumi on tokay2

This page was generated on 2019-04-09 11:55:29 -0400 (Tue, 09 Apr 2019).

Package 878/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
lumi 2.35.0
Pan Du , Lei Huang , Gang Feng
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/lumi
Branch: master
Last Commit: fe6ee8a
Last Changed Date: 2018-10-30 11:54:27 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: lumi
Version: 2.35.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:lumi.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings lumi_2.35.0.tar.gz
StartedAt: 2019-04-09 03:54:12 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 04:05:28 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 675.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: lumi.Rcheck
Warnings: 4

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:lumi.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings lumi_2.35.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/lumi.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'lumi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'lumi' version '2.35.0'
* 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 'lumi' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/LumiBatch-class.Rd:44: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/LumiBatch-class.Rd:46: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/LumiBatch-class.Rd:83: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/LumiBatch-class.Rd:84: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/LumiBatch-class.Rd:85: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/LumiBatch-class.Rd:86: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/LumiBatch-class.Rd:103: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/LumiBatch-class.Rd:104: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/LumiBatch-class.Rd:104: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/LumiBatch-class.Rd:106: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/LumiBatch-class.Rd:113: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/LumiBatch-class.Rd:113: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/MAplot-methods.Rd:16: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/asBigMatrix-methods.Rd:15: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/boxplot-MethyLumiM-methods.Rd:16: file link 'bwplot' in package 'lattice' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/boxplot-methods.Rd:15: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/density-methods.Rd:17: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/getControlType.Rd:20: file link 'controlTypes' in package 'methylumi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/hist-methods.Rd:15: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/importMethyIDAT.Rd:7: file link 'lumIDAT' in package 'methylumi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/importMethyIDAT.Rd:20: file link 'lumIDAT' in package 'methylumi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/importMethyIDAT.Rd:23: file link 'lumIDAT' in package 'methylumi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/importMethyIDAT.Rd:37: file link 'lumIDAT' in package 'methylumi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/lumiN.Rd:19: missing file link 'vsn'
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/pairs-methods.Rd:16: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/plotCDF.Rd:17: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/plotCDF.Rd:29: file link 'plot.ecdf' in package 'stats' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/plotDensity.Rd:14: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/lumi.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   3.6Mb
* checking package 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 ... WARNING
'::' or ':::' imports not declared from:
  'IRanges' 'bigmemoryExtras'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Packages unavailable to check Rd xrefs: 'bigmemoryExtras', 'hdrcde'
Missing link or links in documentation object 'lumiN.Rd':
  '[vsn]{vsn}'

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  'IlluminaAnnotation.R', 'IlluminaAnnotation.pdf', 'lumi.R',
    'lumi.pdf', 'lumi_VST_evaluation.R', 'lumi_VST_evaluation.pdf',
    'methylationAnalysis.R', 'methylationAnalysis.pdf'
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
lumiMethyStatus 46.76   0.25   47.01
getChipInfo      6.50   0.10   43.14
MAplot-methods   6.08   0.10    6.17
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
lumiMethyStatus 47.62   0.06   47.72
getChipInfo      5.85   0.14    5.98
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/lumi.Rcheck/00check.log'
for details.



Installation output

lumi.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/lumi_2.35.0.tar.gz && rm -rf lumi.buildbin-libdir && mkdir lumi.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=lumi.buildbin-libdir lumi_2.35.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL lumi_2.35.0.zip && rm lumi_2.35.0.tar.gz lumi_2.35.0.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 8225k  100 8225k    0     0  17.9M      0 --:--:-- --:--:-- --:--:-- 18.2M

install for i386

* installing *source* package 'lumi' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'lumi'
    finding HTML links ... done
    IlluminaID2nuID                         html  
    LumiBatch-class                         html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/LumiBatch-class.Rd:44: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/LumiBatch-class.Rd:46: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/LumiBatch-class.Rd:83: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/LumiBatch-class.Rd:84: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/LumiBatch-class.Rd:85: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/LumiBatch-class.Rd:86: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/LumiBatch-class.Rd:103: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/LumiBatch-class.Rd:104: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/LumiBatch-class.Rd:104: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/LumiBatch-class.Rd:106: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/LumiBatch-class.Rd:113: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/LumiBatch-class.Rd:113: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
    MAplot-methods                          html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/MAplot-methods.Rd:16: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
    addAnnotationInfo                       html  
    addControlData2lumi                     html  
    addControlData2methyLumiM               html  
    addNuID2lumi                            html  
    adjColorBias.quantile                   html  
    adjColorBias.ssn                        html  
    asBigMatrix-methods                     html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/asBigMatrix-methods.Rd:15: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
    beta2m                                  html  
    bgAdjust                                html  
    bgAdjustMethylation                     html  
    boxplot-MethyLumiM-methods              html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/boxplot-MethyLumiM-methods.Rd:16: file link 'bwplot' in package 'lattice' does not exist and so has been treated as a topic
    boxplot-methods                         html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/boxplot-methods.Rd:15: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
    boxplotColorBias                        html  
    colorBiasSummary                        html  
    density-methods                         html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/density-methods.Rd:17: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
    detectOutlier                           html  
    detectionCall                           html  
    estimateBeta                            html  
    estimateIntensity                       html  
    estimateLumiCV                          html  
    estimateM                               html  
    estimateMethylationBG                   html  
    example.lumi                            html  
    example.lumiMethy                       html  
    example.methyTitration                  html  
    gammaFitEM                              html  
    getChipInfo                             html  
    getChrInfo                              html  
    getControlData                          html  
    getControlProbe                         html  
    getControlType                          html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/getControlType.Rd:20: file link 'controlTypes' in package 'methylumi' does not exist and so has been treated as a topic
    getNuIDMappingInfo                      html  
    hist-methods                            html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/hist-methods.Rd:15: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
    id2seq                                  html  
    importMethyIDAT                         html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/importMethyIDAT.Rd:7: file link 'lumIDAT' in package 'methylumi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/importMethyIDAT.Rd:20: file link 'lumIDAT' in package 'methylumi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/importMethyIDAT.Rd:23: file link 'lumIDAT' in package 'methylumi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/importMethyIDAT.Rd:37: file link 'lumIDAT' in package 'methylumi' does not exist and so has been treated as a topic
    inverseVST                              html  
    is.nuID                                 html  
    lumi.package                            html  
    lumiB                                   html  
    lumiExpresso                            html  
    lumiMethyB                              html  
    lumiMethyC                              html  
    lumiMethyN                              html  
    lumiMethyR                              html  
    lumiMethyStatus                         html  
    lumiN                                   html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/lumiN.Rd:19: missing file link 'vsn'
    lumiQ                                   html  
    lumiR                                   html  
    lumiR.batch                             html  
    lumiT                                   html  
    m2beta                                  html  
    methylationCall                         html  
    monoSmu                                 html  
    monoSpline                              html  
    normalizeMethylation.quantile           html  
    normalizeMethylation.ssn                html  
    nuID2EntrezID                           html  
    nuID2IlluminaID                         html  
    nuID2RefSeqID                           html  
    nuID2probeID                            html  
    nuID2targetID                           html  
    pairs-methods                           html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/pairs-methods.Rd:16: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
    plot-methods                            html  
    plotCDF                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/plotCDF.Rd:17: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/plotCDF.Rd:29: file link 'plot.ecdf' in package 'stats' does not exist and so has been treated as a topic
    plotColorBias1D                         html  
    plotColorBias2D                         html  
    plotControlData                         html  
    plotDensity                             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpG4nqed/R.INSTALL24c4665a1c2/lumi/man/plotDensity.Rd:14: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
    plotGammaFit                            html  
    plotHousekeepingGene                    html  
    plotSampleRelation                      html  
    plotStringencyGene                      html  
    plotVST                                 html  
    probeID2nuID                            html  
    produceGEOPlatformFile                  html  
    produceGEOSampleInfoTemplate            html  
    produceGEOSubmissionFile                html  
    produceMethylationGEOSubmissionFile     html  
    rankinvariant                           html  
    rsn                                     html  
    seq2id                                  html  
    smoothQuantileNormalization             html  
    ssn                                     html  
    targetID2nuID                           html  
    vst                                     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 'lumi' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'lumi' as lumi_2.35.0.zip
* DONE (lumi)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'lumi' successfully unpacked and MD5 sums checked

Tests output


Example timings

lumi.Rcheck/examples_i386/lumi-Ex.timings

nameusersystemelapsed
LumiBatch-class1.550.421.97
MAplot-methods6.080.106.17
addAnnotationInfo0.060.000.07
addControlData2lumi000
addNuID2lumi000
adjColorBias.quantile1.690.061.75
adjColorBias.ssn0.620.010.64
bgAdjust0.130.020.14
bgAdjustMethylation0.240.020.25
boxplot-MethyLumiM-methods0.780.000.78
boxplot-methods0.110.000.11
boxplotColorBias0.140.000.14
density-methods0.110.000.11
detectOutlier0.110.000.11
detectionCall0.180.010.21
estimateBeta0.160.000.15
estimateIntensity0.190.020.21
estimateLumiCV0.120.000.12
estimateM0.660.000.66
estimateMethylationBG0.140.010.15
example.lumi0.090.000.10
example.lumiMethy0.060.000.07
example.methyTitration0.250.000.25
gammaFitEM2.780.073.12
getChipInfo 6.50 0.1043.14
getControlData000
getControlProbe000
getControlType000
getNuIDMappingInfo1.120.082.61
hist-methods0.250.000.25
id2seq000
inverseVST0.450.000.45
is.nuID000
lumiB0.110.000.11
lumiExpresso0.340.030.38
lumiMethyB0.100.000.09
lumiMethyC1.150.051.21
lumiMethyN0.100.020.11
lumiMethyStatus46.76 0.2547.01
lumiN0.430.010.44
lumiQ0.280.030.31
lumiR000
lumiR.batch000
lumiT0.390.000.39
methylationCall2.360.002.36
normalizeMethylation.quantile0.170.000.17
normalizeMethylation.ssn0.120.020.14
nuID2EntrezID0.720.010.74
nuID2IlluminaID3.140.023.15
nuID2RefSeqID1.470.021.49
nuID2probeID2.60.02.6
nuID2targetID3.290.023.31
pairs-methods1.000.011.02
plot-methods1.820.001.81
plotCDF0.260.000.26
plotColorBias1D0.240.020.25
plotColorBias2D0.180.000.19
plotControlData000
plotDensity0.140.010.16
plotGammaFit3.100.023.11
plotHousekeepingGene000
plotSampleRelation0.650.050.70
plotStringencyGene000
plotVST0.550.010.56
probeID2nuID4.580.024.60
produceGEOPlatformFile000
produceGEOSubmissionFile000
produceMethylationGEOSubmissionFile000
seq2id000
targetID2nuID4.840.014.86
vst0.400.000.41

lumi.Rcheck/examples_x64/lumi-Ex.timings

nameusersystemelapsed
LumiBatch-class1.960.112.07
MAplot-methods4.250.044.38
addAnnotationInfo0.070.000.06
addControlData2lumi000
addNuID2lumi000
adjColorBias.quantile1.870.001.88
adjColorBias.ssn0.530.000.53
bgAdjust0.110.020.12
bgAdjustMethylation0.240.000.24
boxplot-MethyLumiM-methods0.950.030.98
boxplot-methods0.120.020.14
boxplotColorBias0.220.000.22
density-methods0.140.000.14
detectOutlier0.140.010.16
detectionCall0.290.000.28
estimateBeta0.280.020.29
estimateIntensity0.310.030.35
estimateLumiCV0.160.010.17
estimateM0.760.050.83
estimateMethylationBG0.160.000.15
example.lumi0.090.000.10
example.lumiMethy0.060.000.06
example.methyTitration0.210.000.20
gammaFitEM2.810.003.00
getChipInfo5.850.145.98
getControlData000
getControlProbe000
getControlType000
getNuIDMappingInfo1.390.031.42
hist-methods0.160.030.18
id2seq000
inverseVST0.580.020.60
is.nuID000
lumiB0.120.010.14
lumiExpresso0.380.030.41
lumiMethyB0.050.020.06
lumiMethyC1.280.001.28
lumiMethyN0.140.000.14
lumiMethyStatus47.62 0.0647.72
lumiN0.460.000.47
lumiQ0.280.020.29
lumiR000
lumiR.batch000
lumiT0.520.000.52
methylationCall2.940.002.93
normalizeMethylation.quantile0.180.010.21
normalizeMethylation.ssn0.240.000.23
nuID2EntrezID1.000.051.05
nuID2IlluminaID4.150.024.17
nuID2RefSeqID2.340.022.36
nuID2probeID3.940.013.95
nuID2targetID3.500.023.52
pairs-methods1.060.031.09
plot-methods2.250.002.25
plotCDF0.210.010.22
plotColorBias1D0.390.000.39
plotColorBias2D0.260.000.27
plotControlData000
plotDensity0.190.000.18
plotGammaFit4.060.024.08
plotHousekeepingGene000
plotSampleRelation0.770.020.78
plotStringencyGene000
plotVST0.550.010.57
probeID2nuID3.790.003.79
produceGEOPlatformFile000
produceGEOSubmissionFile000
produceMethylationGEOSubmissionFile000
seq2id000
targetID2nuID3.880.033.91
vst0.450.020.47