############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/IRISFGM_1.2.0.tar.gz && rm -rf IRISFGM.buildbin-libdir && mkdir IRISFGM.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IRISFGM.buildbin-libdir IRISFGM_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL IRISFGM_1.2.0.zip && rm IRISFGM_1.2.0.tar.gz IRISFGM_1.2.0.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 36 863k 36 316k 0 0 649k 0 0:00:01 --:--:-- 0:00:01 649k 100 863k 100 863k 0 0 699k 0 0:00:01 0:00:01 --:--:-- 699k install for i386 * installing *source* package 'IRISFGM' ... ** 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:/extsoft/include" -fopenmp -DVER=2.08 -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:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cluster.cpp -o cluster.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:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c expand.cpp -o expand.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:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c get_options.cpp -o get_options.o "C:/rtools40/mingw32/bin/"gcc -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:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getline.c -o getline.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:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c main.cpp -o main.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:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c make_graph.cpp -o make_graph.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:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_irisfgm.cpp -o rcpp_irisfgm.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:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_array.cpp -o read_array.o read_array.cpp: In function 'void discretize_new(const char*)': read_array.cpp:883:35: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] for (std::size_t j = 0; j < cols; j++) { ~~^~~~~~ read_array.cpp: In function 'void discretize_rpkm(const char*)': read_array.cpp:1377:35: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] for (std::size_t j = 0; j < cols; j++) { ~~^~~~~~ "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:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c struct.cpp -o struct.o struct.cpp: In function 'void uglyTime(const char*, ...)': struct.cpp:75:15: warning: variable 'lastTime' set but not used [-Wunused-but-set-variable] static long lastTime = 0; ^~~~~~~~ "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:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c write_block.cpp -o write_block.o C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o IRISFGM.dll tmp.def RcppExports.o cluster.o expand.o get_options.o getline.o main.o make_graph.o rcpp_irisfgm.o read_array.o struct.o write_block.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/IRISFGM.buildbin-libdir/00LOCK-IRISFGM/00new/IRISFGM/libs/i386 ** R ** data ** byte-compile and prepare package for lazy loading Creating a generic function from function 'ReadFrom10X_h5' in package 'IRISFGM' Creating a generic function from function 'ReadFrom10X_folder' in package 'IRISFGM' ** help *** installing help indices converting help for package 'IRISFGM' finding HTML links ... done AddMeta html BIC_LTMG html BIC_ZIMG html CLUSTERING html CalBinaryMultiSignal html CalBinarySingleSignal html CreateIRISFGMObject html DimReduce-class html DotPlotPathway html FindClassBasedOnMC html FindGlobalMarkers html finding level-2 HTML links ... done FindMarker html Fit_LTMG html GRAPH html GetBinaryMultiSignal html GetBinarySingleSignal html GetLTMGmatrix html Global_Zcut html IRISFGM-class html InverseMillsRatio html KS_LTMG html KS_ZIMG html LTMG html LogSeparateKRpkmNew html LogSeparateKRpkmNewLR html MCL html MINUS html MIN_return html Pi_Zj_Zcut_new html PlotDimension html PlotHeatmap html PlotMarkerHeatmap html PlotMeta html PlotModuleNetwork html PlotNetwork html ProcessData html Pure_CDF html ReadFrom10X_folder html ReadFrom10X_h5 html RunBicluster html RunClassification html RunDimensionReduction html RunDiscretization html RunLTMG html RunPathway html SC html SeparateKRpkmNew html SeparateKRpkmNew2 html SeparateKRpkmNewLR html SeparateKRpkmNewLRPlus html SeparateKRpkmNewp html State_return html SubsetData html dot-IDConvert html dot-RunGO html dot-RunKEGG html dot-generateNetObject html dot-getBlock html dot-runBiclusterBaseOnDiscretization html dot-runBiclusterBaseOnLTMG html dot-separateBic html example_object html getMeta html qubic 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 'IRISFGM' ... ** 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:/extsoft/include" -fopenmp -DVER=2.08 -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:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cluster.cpp -o cluster.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:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c expand.cpp -o expand.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:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c get_options.cpp -o get_options.o "C:/rtools40/mingw64/bin/"gcc -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:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c getline.c -o getline.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:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c main.cpp -o main.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:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c make_graph.cpp -o make_graph.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:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_irisfgm.cpp -o rcpp_irisfgm.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:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_array.cpp -o read_array.o read_array.cpp: In function 'void discretize_new(const char*)': read_array.cpp:882:21: warning: format '%d' expects argument of type 'int', but argument 4 has type '__gnu_cxx::__alloc_traits, long long unsigned int>::value_type' {aka 'long long unsigned int'} [-Wformat=] fprintf(F2, "%s_%d", genes_n[id], eflags[id][i]); ^~~~~~~ read_array.cpp:883:35: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] for (std::size_t j = 0; j < cols; j++) { ~~^~~~~~ read_array.cpp: In function 'void discretize_rpkm(const char*)': read_array.cpp:1376:21: warning: format '%d' expects argument of type 'int', but argument 4 has type '__gnu_cxx::__alloc_traits, long long unsigned int>::value_type' {aka 'long long unsigned int'} [-Wformat=] fprintf(F2, "%s_%d", genes_n[id], eflags[id][i]); ^~~~~~~ read_array.cpp:1377:35: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] for (std::size_t j = 0; j < cols; j++) { ~~^~~~~~ "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:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c struct.cpp -o struct.o struct.cpp: In function 'void uglyTime(const char*, ...)': struct.cpp:75:15: warning: variable 'lastTime' set but not used [-Wunused-but-set-variable] static long lastTime = 0; ^~~~~~~~ "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:/extsoft/include" -fopenmp -DVER=2.08 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c write_block.cpp -o write_block.o C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o IRISFGM.dll tmp.def RcppExports.o cluster.o expand.o get_options.o getline.o main.o make_graph.o rcpp_irisfgm.o read_array.o struct.o write_block.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/IRISFGM.buildbin-libdir/IRISFGM/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'IRISFGM' as IRISFGM_1.2.0.zip * DONE (IRISFGM) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'IRISFGM' successfully unpacked and MD5 sums checked