Pan Du
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/lumi |
| Branch: RELEASE_3_6 |
| Last Commit: de64da0 |
| Last Changed Date: 2017-10-30 12:39:19 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:18:31 -0400 (Thu, 12 Apr 2018).
| Package 763/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| lumi 2.30.0 Pan Du
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: lumi |
| Version: 2.30.0 |
| Command: rm -rf lumi.buildbin-libdir && mkdir lumi.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/lumi_2.30.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=lumi.buildbin-libdir --merge-multiarch lumi_2.30.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL lumi_2.30.0.zip && rm lumi_2.30.0.tar.gz lumi_2.30.0.zip |
| StartedAt: 2018-04-11 18:53:10 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 18:55:14 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 123.9 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### rm -rf lumi.buildbin-libdir && mkdir lumi.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/lumi_2.30.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=lumi.buildbin-libdir --merge-multiarch lumi_2.30.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL lumi_2.30.0.zip && rm lumi_2.30.0.tar.gz lumi_2.30.0.zip
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install for i386
* installing *source* package 'lumi' ...
** R
** data
** inst
** preparing 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-3.6-bioc/tmpdir/Rtmpcdkdty/R.INSTALLf3c32fb7f4e/lumi/man/LumiBatch-class.Rd:44: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcdkdty/R.INSTALLf3c32fb7f4e/lumi/man/LumiBatch-class.Rd:46: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcdkdty/R.INSTALLf3c32fb7f4e/lumi/man/LumiBatch-class.Rd:83: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcdkdty/R.INSTALLf3c32fb7f4e/lumi/man/LumiBatch-class.Rd:84: missing file link 'eSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcdkdty/R.INSTALLf3c32fb7f4e/lumi/man/LumiBatch-class.Rd:85: missing file link 'eSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcdkdty/R.INSTALLf3c32fb7f4e/lumi/man/LumiBatch-class.Rd:86: missing file link 'eSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcdkdty/R.INSTALLf3c32fb7f4e/lumi/man/LumiBatch-class.Rd:103: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcdkdty/R.INSTALLf3c32fb7f4e/lumi/man/LumiBatch-class.Rd:104: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcdkdty/R.INSTALLf3c32fb7f4e/lumi/man/LumiBatch-class.Rd:104: missing file link 'eSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcdkdty/R.INSTALLf3c32fb7f4e/lumi/man/LumiBatch-class.Rd:106: missing file link 'eSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcdkdty/R.INSTALLf3c32fb7f4e/lumi/man/LumiBatch-class.Rd:113: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcdkdty/R.INSTALLf3c32fb7f4e/lumi/man/LumiBatch-class.Rd:113: missing file link 'eSet'
MAplot-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcdkdty/R.INSTALLf3c32fb7f4e/lumi/man/MAplot-methods.Rd:16: missing file link 'ExpressionSet'
addAnnotationInfo html
addControlData2lumi html
addControlData2methyLumiM html
addNuID2lumi html
adjColorBias.quantile html
adjColorBias.ssn html
asBigMatrix-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcdkdty/R.INSTALLf3c32fb7f4e/lumi/man/asBigMatrix-methods.Rd:15: missing file link 'ExpressionSet'
beta2m html
bgAdjust html
bgAdjustMethylation html
boxplot-MethyLumiM-methods html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcdkdty/R.INSTALLf3c32fb7f4e/lumi/man/boxplot-MethyLumiM-methods.Rd:16: missing file link 'bwplot'
boxplot-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcdkdty/R.INSTALLf3c32fb7f4e/lumi/man/boxplot-methods.Rd:15: missing file link 'ExpressionSet'
boxplotColorBias html
colorBiasSummary html
density-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcdkdty/R.INSTALLf3c32fb7f4e/lumi/man/density-methods.Rd:17: missing file link 'ExpressionSet'
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-3.6-bioc/tmpdir/Rtmpcdkdty/R.INSTALLf3c32fb7f4e/lumi/man/getControlType.Rd:20: missing file link 'controlTypes'
getNuIDMappingInfo html
hist-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcdkdty/R.INSTALLf3c32fb7f4e/lumi/man/hist-methods.Rd:15: missing file link 'ExpressionSet'
id2seq html
importMethyIDAT html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcdkdty/R.INSTALLf3c32fb7f4e/lumi/man/importMethyIDAT.Rd:7: missing file link 'lumIDAT'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcdkdty/R.INSTALLf3c32fb7f4e/lumi/man/importMethyIDAT.Rd:20: missing file link 'lumIDAT'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcdkdty/R.INSTALLf3c32fb7f4e/lumi/man/importMethyIDAT.Rd:23: missing file link 'lumIDAT'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcdkdty/R.INSTALLf3c32fb7f4e/lumi/man/importMethyIDAT.Rd:37: missing file link 'lumIDAT'
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-3.6-bioc/tmpdir/Rtmpcdkdty/R.INSTALLf3c32fb7f4e/lumi/man/lumiN.Rd:19: file link 'vsn' in package 'vsn' does not exist and so has been treated as a topic
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-3.6-bioc/tmpdir/Rtmpcdkdty/R.INSTALLf3c32fb7f4e/lumi/man/pairs-methods.Rd:16: missing file link 'ExpressionSet'
plot-methods html
plotCDF html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcdkdty/R.INSTALLf3c32fb7f4e/lumi/man/plotCDF.Rd:17: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcdkdty/R.INSTALLf3c32fb7f4e/lumi/man/plotCDF.Rd:29: missing file link 'plot.ecdf'
plotColorBias1D html
plotColorBias2D html
plotControlData html
plotDensity html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpcdkdty/R.INSTALLf3c32fb7f4e/lumi/man/plotDensity.Rd:14: missing file link 'ExpressionSet'
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
In R CMD INSTALL
install for x64
* installing *source* package 'lumi' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'lumi' as lumi_2.30.0.zip
* DONE (lumi)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.6-bioc/R/library'
package 'lumi' successfully unpacked and MD5 sums checked
In R CMD INSTALL