############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/GeoDiff_1.0.0.tar.gz && rm -rf GeoDiff.buildbin-libdir && mkdir GeoDiff.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeoDiff.buildbin-libdir GeoDiff_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL GeoDiff_1.0.0.zip && rm GeoDiff_1.0.0.tar.gz GeoDiff_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 23 4363k 23 1045k 0 0 1120k 0 0:00:03 --:--:-- 0:00:03 1120k 71 4363k 71 3140k 0 0 1625k 0 0:00:02 0:00:01 0:00:01 1625k 100 4363k 100 4363k 0 0 1835k 0 0:00:02 0:00:02 --:--:-- 1836k install for i386 * installing *source* package 'GeoDiff' ... ** 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/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/roptim/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c NBthDEOptPara.cpp -o NBthDEOptPara.o NBthDEOptPara.cpp: In member function 'virtual double NBthDE_paranll::operator()(const vec&)': NBthDEOptPara.cpp:34:9: warning: unused variable 'm' [-Wunused-variable] int m = y.n_elem; ^ NBthDEOptPara.cpp: In member function 'virtual void NBthDE_paranll::Gradient(const vec&, arma::vec&)': NBthDEOptPara.cpp:85:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for(int k = 0; k < y.n_elem; k++){ ~~^~~~~~~~~~ NBthDEOptPara.cpp:58:9: warning: unused variable 'm' [-Wunused-variable] int m = y.n_elem; ^ "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/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/roptim/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c NBthmDEGrad.cpp -o NBthmDEGrad.o NBthmDEGrad.cpp: In function 'arma::vec NBthmDE_grad(arma::vec&, arma::mat&, arma::mat&, arma::vec&, arma::vec&, arma::vec&, arma::vec&, arma::mat&, double, double)': NBthmDEGrad.cpp:34:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for(int i = 0; i < y.n_elem; i++){ ~~^~~~~~~~~~ NBthmDEGrad.cpp: In function 'arma::mat NBthmDE_gradM(arma::vec&, arma::mat&, arma::mat&, arma::vec&, arma::mat&, arma::vec&, arma::vec&, arma::mat&, double, double)': NBthmDEGrad.cpp:90:24: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for(int k = 0; k < y.n_elem; k++){ ~~^~~~~~~~~~ "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/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/roptim/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c NBthmDEMH.cpp -o NBthmDEMH.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/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/roptim/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c NBthmDEOptPara.cpp -o NBthmDEOptPara.o NBthmDEOptPara.cpp: In member function 'virtual void NBthmDE_fparanll::Gradient(const vec&, arma::vec&)': NBthmDEOptPara.cpp:107:24: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for(int k = 0; k < y.n_elem; k++){ ~~^~~~~~~~~~ "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/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/roptim/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c NBthmDEOptU.cpp -o NBthmDEOptU.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/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/roptim/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PoisthNormOptPara.cpp -o PoisthNormOptPara.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/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/roptim/include' -I"C:/extsoft/include" -fopenmp -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/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/roptim/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dnbinom_mu_vec.cpp -o dnbinom_mu_vec.o C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o GeoDiff.dll tmp.def NBthDEOptPara.o NBthmDEGrad.o NBthmDEMH.o NBthmDEOptPara.o NBthmDEOptU.o PoisthNormOptPara.o RcppExports.o dnbinom_mu_vec.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -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/GeoDiff.buildbin-libdir/00LOCK-GeoDiff/00new/GeoDiff/libs/i386 ** R ** data ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'GeoDiff' finding HTML links ... done BGScoreTest-methods html BGScoreTest_sp-methods html DENBth-methods html NBthDEmod2 html NBthmDEmod2 html NBthmDEmod2slope html QuanRange-methods html aggreprobe-methods html coefNBth-methods html contrastNBth-methods html demoData html diagPoisBG-methods html fitNBth-methods html fitNBthDE-methods html fitNBthmDE-methods html fitPoisBG-methods html fitPoisBG_sp-methods html fitPoisthNorm-methods html fitPoisthNorm_sp-methods html kidney 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 'GeoDiff' ... ** 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/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/roptim/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c NBthDEOptPara.cpp -o NBthDEOptPara.o NBthDEOptPara.cpp: In member function 'virtual double NBthDE_paranll::operator()(const vec&)': NBthDEOptPara.cpp:34:9: warning: unused variable 'm' [-Wunused-variable] int m = y.n_elem; ^ NBthDEOptPara.cpp: In member function 'virtual void NBthDE_paranll::Gradient(const vec&, arma::vec&)': NBthDEOptPara.cpp:85:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for(int k = 0; k < y.n_elem; k++){ ~~^~~~~~~~~~ NBthDEOptPara.cpp:58:9: warning: unused variable 'm' [-Wunused-variable] int m = y.n_elem; ^ "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/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/roptim/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c NBthmDEGrad.cpp -o NBthmDEGrad.o NBthmDEGrad.cpp: In function 'arma::vec NBthmDE_grad(arma::vec&, arma::mat&, arma::mat&, arma::vec&, arma::vec&, arma::vec&, arma::vec&, arma::mat&, double, double)': NBthmDEGrad.cpp:34:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for(int i = 0; i < y.n_elem; i++){ ~~^~~~~~~~~~ NBthmDEGrad.cpp: In function 'arma::mat NBthmDE_gradM(arma::vec&, arma::mat&, arma::mat&, arma::vec&, arma::mat&, arma::vec&, arma::vec&, arma::mat&, double, double)': NBthmDEGrad.cpp:90:24: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for(int k = 0; k < y.n_elem; k++){ ~~^~~~~~~~~~ "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/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/roptim/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c NBthmDEMH.cpp -o NBthmDEMH.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/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/roptim/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c NBthmDEOptPara.cpp -o NBthmDEOptPara.o NBthmDEOptPara.cpp: In member function 'virtual void NBthmDE_fparanll::Gradient(const vec&, arma::vec&)': NBthmDEOptPara.cpp:107:24: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare] for(int k = 0; k < y.n_elem; k++){ ~~^~~~~~~~~~ "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/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/roptim/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c NBthmDEOptU.cpp -o NBthmDEOptU.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/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/roptim/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PoisthNormOptPara.cpp -o PoisthNormOptPara.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/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/roptim/include' -I"C:/extsoft/include" -fopenmp -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/RcppArmadillo/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/roptim/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dnbinom_mu_vec.cpp -o dnbinom_mu_vec.o C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o GeoDiff.dll tmp.def NBthDEOptPara.o NBthmDEGrad.o NBthmDEMH.o NBthmDEOptPara.o NBthmDEOptU.o PoisthNormOptPara.o RcppExports.o dnbinom_mu_vec.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -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/GeoDiff.buildbin-libdir/GeoDiff/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'GeoDiff' as GeoDiff_1.0.0.zip * DONE (GeoDiff) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'GeoDiff' successfully unpacked and MD5 sums checked