Back to Multiple platform build/check report for BioC 3.8 |
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This page was generated on 2019-04-13 11:20:06 -0400 (Sat, 13 Apr 2019).
Package 854/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
lumi 2.34.0 Pan Du
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | [ OK ] | |||||||
merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
Package: lumi |
Version: 2.34.0 |
Command: rm -rf lumi.buildbin-libdir && mkdir lumi.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=lumi.buildbin-libdir lumi_2.34.0.tar.gz |
StartedAt: 2019-04-13 07:35:38 -0400 (Sat, 13 Apr 2019) |
EndedAt: 2019-04-13 07:36:46 -0400 (Sat, 13 Apr 2019) |
EllapsedTime: 68.0 seconds |
RetCode: 0 |
Status: OK |
PackageFile: lumi_2.34.0.zip |
PackageFileSize: 4.829 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf lumi.buildbin-libdir && mkdir lumi.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=lumi.buildbin-libdir lumi_2.34.0.tar.gz ### ############################################################################## ############################################################################## 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-3.8-bioc/tmpdir/Rtmpw3LlRi/R.INSTALL211447ac1ba7/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-3.8-bioc/tmpdir/Rtmpw3LlRi/R.INSTALL211447ac1ba7/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-3.8-bioc/tmpdir/Rtmpw3LlRi/R.INSTALL211447ac1ba7/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-3.8-bioc/tmpdir/Rtmpw3LlRi/R.INSTALL211447ac1ba7/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-3.8-bioc/tmpdir/Rtmpw3LlRi/R.INSTALL211447ac1ba7/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-3.8-bioc/tmpdir/Rtmpw3LlRi/R.INSTALL211447ac1ba7/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-3.8-bioc/tmpdir/Rtmpw3LlRi/R.INSTALL211447ac1ba7/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-3.8-bioc/tmpdir/Rtmpw3LlRi/R.INSTALL211447ac1ba7/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-3.8-bioc/tmpdir/Rtmpw3LlRi/R.INSTALL211447ac1ba7/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-3.8-bioc/tmpdir/Rtmpw3LlRi/R.INSTALL211447ac1ba7/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-3.8-bioc/tmpdir/Rtmpw3LlRi/R.INSTALL211447ac1ba7/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-3.8-bioc/tmpdir/Rtmpw3LlRi/R.INSTALL211447ac1ba7/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-3.8-bioc/tmpdir/Rtmpw3LlRi/R.INSTALL211447ac1ba7/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-3.8-bioc/tmpdir/Rtmpw3LlRi/R.INSTALL211447ac1ba7/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-3.8-bioc/tmpdir/Rtmpw3LlRi/R.INSTALL211447ac1ba7/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-3.8-bioc/tmpdir/Rtmpw3LlRi/R.INSTALL211447ac1ba7/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-3.8-bioc/tmpdir/Rtmpw3LlRi/R.INSTALL211447ac1ba7/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-3.8-bioc/tmpdir/Rtmpw3LlRi/R.INSTALL211447ac1ba7/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-3.8-bioc/tmpdir/Rtmpw3LlRi/R.INSTALL211447ac1ba7/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-3.8-bioc/tmpdir/Rtmpw3LlRi/R.INSTALL211447ac1ba7/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-3.8-bioc/tmpdir/Rtmpw3LlRi/R.INSTALL211447ac1ba7/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-3.8-bioc/tmpdir/Rtmpw3LlRi/R.INSTALL211447ac1ba7/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-3.8-bioc/tmpdir/Rtmpw3LlRi/R.INSTALL211447ac1ba7/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-3.8-bioc/tmpdir/Rtmpw3LlRi/R.INSTALL211447ac1ba7/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-3.8-bioc/tmpdir/Rtmpw3LlRi/R.INSTALL211447ac1ba7/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-3.8-bioc/tmpdir/Rtmpw3LlRi/R.INSTALL211447ac1ba7/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-3.8-bioc/tmpdir/Rtmpw3LlRi/R.INSTALL211447ac1ba7/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-3.8-bioc/tmpdir/Rtmpw3LlRi/R.INSTALL211447ac1ba7/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 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_2.34.0.zip * DONE (lumi) In R CMD INSTALL In R CMD INSTALL