############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL BEclear ### ############################################################################## ############################################################################## * installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library' * installing *source* package 'BEclear' ... ** using staged installation ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c localLoss.cpp -o localLoss.o C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o BEclear.dll tmp.def RcppExports.o localLoss.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-BEclear/00new/BEclear/libs/x64 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help Loading required namespace: BEclear *** installing help indices converting help for package 'BEclear' finding HTML links ... done BEclear-example-methylation-data html BEclear-example-sample-data html BEclear-package html calcBatchEffects html calcBatchEffectsForBatch html calcBlockFrame html calcPositions html calcScore html calcSummary html clearBEgenes html combineBlocks html correctBatchEffect html countValuesToPredict html ex.corrected.data html findOutsideValues html gdepoch html imputeMissingData html imputeMissingDataForBlock html localLoss html loss html makeBoxplot html preprocessBEclear html replaceOutsideValues html runGradientDescent 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 * DONE (BEclear) Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") : DESCRIPTION file of package 'KBoost' is missing or broken done