############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/lumi_2.46.0.tar.gz && rm -rf lumi.buildbin-libdir && mkdir lumi.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=lumi.buildbin-libdir lumi_2.46.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL lumi_2.46.0.zip && rm lumi_2.46.0.tar.gz lumi_2.46.0.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 16 8225k 16 1386k 0 0 1549k 0 0:00:05 --:--:-- 0:00:05 1549k 48 8225k 48 3953k 0 0 2119k 0 0:00:03 0:00:01 0:00:02 2119k 90 8225k 90 7448k 0 0 2598k 0 0:00:03 0:00:02 0:00:01 2598k 100 8225k 100 8225k 0 0 2692k 0 0:00:03 0:00:03 --:--:-- 2693k install for i386 * installing *source* package 'lumi' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi' ** help *** installing help indices converting help for package 'lumi' finding HTML links ... done IlluminaID2nuID html LumiBatch-class html MAplot-methods html addAnnotationInfo html addControlData2lumi html addControlData2methyLumiM html addNuID2lumi html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/lumi.buildbin-libdir/00LOCK-lumi/00new/lumi/help/addNuId2lumi.html adjColorBias.quantile html adjColorBias.ssn html asBigMatrix-methods html beta2m html bgAdjust html bgAdjustMethylation html boxplot-MethyLumiM-methods html finding level-2 HTML links ... done boxplot-methods html boxplotColorBias html colorBiasSummary html density-methods html 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 getNuIDMappingInfo html hist-methods html id2seq html importMethyIDAT html inverseVST html is.nuID html lumi.package html lumiB html lumiExpresso html lumiMethyB html lumiMethyC html lumiMethyN html lumiMethyR html lumiMethyStatus html lumiN html 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 plot-methods html plotCDF html plotColorBias1D html plotColorBias2D html plotControlData html plotDensity html 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 No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi' ** testing if installed package can be loaded from final location No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi' ** 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 No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi' * MD5 sums packaged installation of 'lumi' as lumi_2.46.0.zip * DONE (lumi) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'lumi' successfully unpacked and MD5 sums checked