Back to Multiple platform build/check report for BioC 3.6 |
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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 |
############################################################################## ############################################################################## ### ### Running 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 ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 21 8225k 21 1744k 0 0 34.8M 0 --:--:-- --:--:-- --:--:-- 36.2M 100 8225k 100 8225k 0 0 66.5M 0 --:--:-- --:--:-- --:--:-- 68.0M 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