############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/chromstaR_1.20.2.tar.gz && rm -rf chromstaR.buildbin-libdir && mkdir chromstaR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=chromstaR.buildbin-libdir chromstaR_1.20.2.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL chromstaR_1.20.2.zip && rm chromstaR_1.20.2.tar.gz chromstaR_1.20.2.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 7 6684k 7 529k 0 0 593k 0 0:00:11 --:--:-- 0:00:11 593k 29 6684k 29 1961k 0 0 1038k 0 0:00:06 0:00:01 0:00:05 1038k 64 6684k 64 4295k 0 0 1489k 0 0:00:04 0:00:02 0:00:02 1489k 100 6684k 100 6684k 0 0 1843k 0 0:00:03 0:00:03 --:--:-- 1844k install for i386 * installing *source* package 'chromstaR' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_interface.cpp -o R_interface.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c densities.cpp -o densities.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.cpp -o init.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scalehmm.cpp -o scalehmm.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utility.cpp -o utility.o C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o chromstaR.dll tmp.def R_interface.o densities.o init.o scalehmm.o utility.o -fopenmp -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/chromstaR.buildbin-libdir/00LOCK-chromstaR/00new/chromstaR/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'chromstaR' finding HTML links ... done Chromstar html binReads html finding level-2 HTML links ... done binned.data html callPeaksMultivariate html callPeaksReplicates html callPeaksUnivariate html callPeaksUnivariateAllChr html changeMaxPostCutoff html changePostCutoff html chromstaR-objects html chromstaR-package html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/chromstaR.buildbin-libdir/00LOCK-chromstaR/00new/chromstaR/help/chromstaR.html collapseBins html combinatorialStates html combineMultivariates html combinedMultiHMM html conversion html enrichmentAtAnnotation html enrichment_analysis html experiment.table html exportFiles html exportGRangesAsBedFile html fixedWidthBins html genes_rn4 html genomicFrequencies html getCombinations html getDistinctColors html getStateColors html heatmapCombinations html heatmapCountCorrelation html heatmapTransitionProbs html loadHmmsFromFiles html mergeChroms html model.combined html model.multivariate html model.univariate html multiHMM html multivariateSegmentation html plotExpression html plotGenomeBrowser html plotHistogram html plotHistograms html plotting html print.combinedMultiHMM html print.multiHMM html print.uniHMM html readBamFileAsGRanges html readBedFileAsGRanges html readConfig html readCustomBedFile html removeCondition html scanBinsizes html scores html simulateMultivariate html simulateReadsFromCounts html simulateUnivariate html state.brewer html stateBrewer html subsample html transitionFrequencies html uniHMM html unis2pseudomulti html variableWidthBins html writeConfig html zinbinom 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 install for x64 * installing *source* package 'chromstaR' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_interface.cpp -o R_interface.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c densities.cpp -o densities.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.cpp -o init.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scalehmm.cpp -o scalehmm.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utility.cpp -o utility.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o chromstaR.dll tmp.def R_interface.o densities.o init.o scalehmm.o utility.o -fopenmp -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/chromstaR.buildbin-libdir/chromstaR/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'chromstaR' as chromstaR_1.20.2.zip * DONE (chromstaR) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'chromstaR' successfully unpacked and MD5 sums checked