############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/runibic_1.16.0.tar.gz && rm -rf runibic.buildbin-libdir && mkdir runibic.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=runibic.buildbin-libdir runibic_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL runibic_1.16.0.zip && rm runibic_1.16.0.tar.gz runibic_1.16.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 34363 100 34363 0 0 289k 0 --:--:-- --:--:-- --:--:-- 291k install for i386 * installing *source* package 'runibic' ... ** 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" -I. -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GlobalDefs.cpp -o GlobalDefs.o GlobalDefs.cpp: In function 'bool check_seed(int, int, int, const std::vector&, int, int)': GlobalDefs.cpp:69:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (i=0; igenes.size(); i++){ ~^~~~~~~~~~~~~~~~~~~~~~~~~~ GlobalDefs.cpp:76:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (i=0; igenes.size(); i++){ ~^~~~~~~~~~~~~~~~~~~~~~~~~~ GlobalDefs.cpp: In function 'void block_init(int, int, int, BicBlock*, std::vector&, std::vector&, std::vector&, int, int*, std::vector&, Params*, std::vector >&, std::vector >*)': GlobalDefs.cpp:138:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (auto i = 0; i < (*inputData)[t0].size() ;i++){ ~~^~~~~~~~~~~~~~~~~~~~~~~~~ GlobalDefs.cpp:152:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for(auto i=0;i<(*inputData)[j].size();i++) ~^~~~~~~~~~~~~~~~~~~~~~~ GlobalDefs.cpp:117:7: warning: unused variable 'colNum' [-Wunused-variable] int colNum = gParameters.ColNumber; ^~~~~~ GlobalDefs.cpp: In function 'std::vector getGenesFullLCS(const std::vector&, const std::vector&)': GlobalDefs.cpp:240:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for(auto i=0;i::size_type' {aka 'unsigned int'} [-Wsign-compare] for(auto i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for(auto j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] for(auto i=1; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for(auto j=1; j::size_type' {aka 'unsigned int'} [-Wsign-compare] for (auto j=1;j::size_type' {aka 'unsigned int'} [-Wsign-compare] for (auto i=1;i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (auto j=1;j::size_type' {aka 'unsigned int'} [-Wsign-compare] for(auto i=0;i&, std::vector&, std::vector >&)': GlobalDefs.cpp:336:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (auto i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for (auto j=0; j::size_type' {aka 'unsigned int'} [-Wsign-compare] for(auto i=1; i::size_type' {aka 'unsigned int'} [-Wsign-compare] for(auto j=1; j&, std::vector&, std::vector&, int, int*, std::vector&, Params*, std::vector >&, std::vector >*)': GlobalDefs.cpp:192:15: warning: 'pvalue' may be used uninitialized in this function [-Wmaybe-uninitialized] pvalue=pvalue+poisson; ~~~~~~^~~~~~~~~~~~~~~ "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" -I. -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.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 fib.c -o fib.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" -I. -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c runibic.cpp -o runibic.o runibic.cpp: In function 'Rcpp::List calculateLCS(Rcpp::IntegerMatrix, bool)': runibic.cpp:329:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (auto i = 0; i < discreteInputData.size(); i++) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ runibic.cpp:358:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for(auto i = 0; i < out.size(); i++) ~~^~~~~~~~~~~~ runibic.cpp: In function 'Rcpp::List cluster(Rcpp::IntegerMatrix, Rcpp::IntegerMatrix, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, int, int)': runibic.cpp:417:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] for (auto i = 0; i < discreteInputData.size(); i++) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ runibic.cpp:498:18: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] for(k = 0; k < components; k++) { ~~^~~~~~~~~~~~ runibic.cpp:507:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] if(components > vecGenes.size()) ~~~~~~~~~~~^~~~~~~~~~~~~~~~~ runibic.cpp:513:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (auto ki=0; ki < vecGenes.size() ; ki++) { ~~~^~~~~~~~~~~~~~~~~ runibic.cpp:567:13: warning: unused variable 'temp' [-Wunused-variable] int temp; ^~~~ runibic.cpp:597:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (auto i = 0; i < discreteInputData[vecGenes[0]].size() ;i++){ ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runibic.cpp:621:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for (auto i = 0; i < discreteInputData[ki].size() ;i++){ ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runibic.cpp:700:26: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] if (arrBlocks.size() == gParameters.SchBlock) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ runibic.cpp:719:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] while (i < arrBlocks.size() && j < n) { ~~^~~~~~~~~~~~~~~~~~ runibic.cpp:755:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] for(auto ind =0; ind&, int, int)': GlobalDefs.cpp:69:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (i=0; igenes.size(); i++){ ~^~~~~~~~~~~~~~~~~~~~~~~~~~ GlobalDefs.cpp:76:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (i=0; igenes.size(); i++){ ~^~~~~~~~~~~~~~~~~~~~~~~~~~ GlobalDefs.cpp: In function 'void block_init(int, int, int, BicBlock*, std::vector&, std::vector&, std::vector&, int, int*, std::vector&, Params*, std::vector >&, std::vector >*)': GlobalDefs.cpp:138:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (auto i = 0; i < (*inputData)[t0].size() ;i++){ ~~^~~~~~~~~~~~~~~~~~~~~~~~~ GlobalDefs.cpp:152:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for(auto i=0;i<(*inputData)[j].size();i++) ~^~~~~~~~~~~~~~~~~~~~~~~ GlobalDefs.cpp:117:7: warning: unused variable 'colNum' [-Wunused-variable] int colNum = gParameters.ColNumber; ^~~~~~ GlobalDefs.cpp: In function 'std::vector getGenesFullLCS(const std::vector&, const std::vector&)': GlobalDefs.cpp:240:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for(auto i=0;i::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for(auto i=0; i::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for(auto j=0; j::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for(auto i=1; i::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for(auto j=1; j::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (auto j=1;j::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (auto i=1;i::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (auto j=1;j::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for(auto i=0;i&, std::vector&, std::vector >&)': GlobalDefs.cpp:336:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (auto i=0; i::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (auto j=0; j::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for(auto i=1; i::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for(auto j=1; j&, std::vector&, std::vector&, int, int*, std::vector&, Params*, std::vector >&, std::vector >*)': GlobalDefs.cpp:192:15: warning: 'pvalue' may be used uninitialized in this function [-Wmaybe-uninitialized] pvalue=pvalue+poisson; ~~~~~~^~~~~~~~~~~~~~~ "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" -I. -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.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 fib.c -o fib.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" -I. -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c runibic.cpp -o runibic.o runibic.cpp: In function 'Rcpp::List calculateLCS(Rcpp::IntegerMatrix, bool)': runibic.cpp:329:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (auto i = 0; i < discreteInputData.size(); i++) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ runibic.cpp:358:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for(auto i = 0; i < out.size(); i++) ~~^~~~~~~~~~~~ runibic.cpp: In function 'Rcpp::List cluster(Rcpp::IntegerMatrix, Rcpp::IntegerMatrix, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, int, int)': runibic.cpp:417:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (auto i = 0; i < discreteInputData.size(); i++) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ runibic.cpp:498:18: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] for(k = 0; k < components; k++) { ~~^~~~~~~~~~~~ runibic.cpp:507:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] if(components > vecGenes.size()) ~~~~~~~~~~~^~~~~~~~~~~~~~~~~ runibic.cpp:513:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (auto ki=0; ki < vecGenes.size() ; ki++) { ~~~^~~~~~~~~~~~~~~~~ runibic.cpp:567:13: warning: unused variable 'temp' [-Wunused-variable] int temp; ^~~~ runibic.cpp:597:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (auto i = 0; i < discreteInputData[vecGenes[0]].size() ;i++){ ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runibic.cpp:621:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for (auto i = 0; i < discreteInputData[ki].size() ;i++){ ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ runibic.cpp:700:26: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] if (arrBlocks.size() == gParameters.SchBlock) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ runibic.cpp:719:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] while (i < arrBlocks.size() && j < n) { ~~^~~~~~~~~~~~~~~~~~ runibic.cpp:755:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long long unsigned int'} [-Wsign-compare] for(auto ind =0; ind