############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/NxtIRFcore_1.0.0.tar.gz && rm -rf NxtIRFcore.buildbin-libdir && mkdir NxtIRFcore.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=NxtIRFcore.buildbin-libdir NxtIRFcore_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL NxtIRFcore_1.0.0.zip && rm NxtIRFcore_1.0.0.tar.gz NxtIRFcore_1.0.0.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 50 826k 50 419k 0 0 591k 0 0:00:01 --:--:-- 0:00:01 591k 100 826k 100 826k 0 0 788k 0 0:00:01 0:00:01 --:--:-- 789k install for i386 * installing *source* package 'NxtIRFcore' ... ** 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:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppProgress/include' -I"C:/extsoft/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c BAM2blocks.cpp -o BAM2blocks.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppProgress/include' -I"C:/extsoft/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FastaReader.cpp -o FastaReader.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppProgress/include' -I"C:/extsoft/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FragmentBlocks.cpp -o FragmentBlocks.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppProgress/include' -I"C:/extsoft/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GZTools.cpp -o GZTools.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppProgress/include' -I"C:/extsoft/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c IRFinder.cpp -o IRFinder.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppProgress/include' -I"C:/extsoft/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppProgress/include' -I"C:/extsoft/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ReadBlockProcessor.cpp -o ReadBlockProcessor.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppProgress/include' -I"C:/extsoft/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ReadBlockProcessor_CoverageBlocks.cpp -o ReadBlockProcessor_CoverageBlocks.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppProgress/include' -I"C:/extsoft/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c covTools.cpp -o covTools.o C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o NxtIRFcore.dll tmp.def BAM2blocks.o FastaReader.o FragmentBlocks.o GZTools.o IRFinder.o RcppExports.o ReadBlockProcessor.o ReadBlockProcessor_CoverageBlocks.o covTools.o -fopenmp -DRNXTIRF -LC:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -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/NxtIRFcore.buildbin-libdir/00LOCK-NxtIRFcore/00new/NxtIRFcore/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'NxtIRFcore' finding HTML links ... done ASE-methods html BuildReference html CollateData html CoordToGR html Coverage html Find_Samples html IRFinder html IsCOV html MakeSE html Mappability-methods html NxtFilter-class html NxtIRFcore-package html NxtSE-class html finding level-2 HTML links ... done Plot_Coverage html Run_NxtIRF_Filters html STAR-methods html example-NxtIRF-data html make_plot_data html theme_white 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 'NxtIRFcore' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppProgress/include' -I"C:/extsoft/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c BAM2blocks.cpp -o BAM2blocks.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppProgress/include' -I"C:/extsoft/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FastaReader.cpp -o FastaReader.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppProgress/include' -I"C:/extsoft/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FragmentBlocks.cpp -o FragmentBlocks.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppProgress/include' -I"C:/extsoft/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GZTools.cpp -o GZTools.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppProgress/include' -I"C:/extsoft/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c IRFinder.cpp -o IRFinder.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppProgress/include' -I"C:/extsoft/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppProgress/include' -I"C:/extsoft/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ReadBlockProcessor.cpp -o ReadBlockProcessor.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppProgress/include' -I"C:/extsoft/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ReadBlockProcessor_CoverageBlocks.cpp -o ReadBlockProcessor_CoverageBlocks.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppProgress/include' -I"C:/extsoft/include" -fopenmp -DRNXTIRF -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c covTools.cpp -o covTools.o C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o NxtIRFcore.dll tmp.def BAM2blocks.o FastaReader.o FragmentBlocks.o GZTools.o IRFinder.o RcppExports.o ReadBlockProcessor.o ReadBlockProcessor_CoverageBlocks.o covTools.o -fopenmp -DRNXTIRF -LC:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -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/NxtIRFcore.buildbin-libdir/NxtIRFcore/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'NxtIRFcore' as NxtIRFcore_1.0.0.zip * DONE (NxtIRFcore) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'NxtIRFcore' successfully unpacked and MD5 sums checked