############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/BHC_1.46.0.tar.gz && rm -rf BHC.buildbin-libdir && mkdir BHC.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BHC.buildbin-libdir BHC_1.46.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL BHC_1.46.0.zip && rm BHC_1.46.0.tar.gz BHC_1.46.0.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 79942 100 79942 0 0 176k 0 --:--:-- --:--:-- --:--:-- 176k install for i386 * installing *source* package 'BHC' ... ** using staged installation ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** 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" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c BlockCovarianceMatrix.cpp -o BlockCovarianceMatrix.o In file included from BlockCovarianceMatrix.h:16, from BlockCovarianceMatrix.cpp:15: header.h:16: warning: "NDEBUG" redefined #define NDEBUG : note: this is the location of the previous definition "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CubicSplineTimecourseDataSet.cpp -o CubicSplineTimecourseDataSet.o In file included from DataSet.h:16, from TimecourseDataSet.h:20, from CubicSplineTimecourseDataSet.h:20, from CubicSplineTimecourseDataSet.cpp:15: header.h:16: warning: "NDEBUG" redefined #define NDEBUG : note: this is the location of the previous definition "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DataSet.cpp -o DataSet.o In file included from DataSet.h:16, from DataSet.cpp:13: header.h:16: warning: "NDEBUG" redefined #define NDEBUG : note: this is the location of the previous definition "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DirichletProcessMixture.cpp -o DirichletProcessMixture.o In file included from DirichletProcessMixture.h:4, from DirichletProcessMixture.cpp:15: header.h:16: warning: "NDEBUG" redefined #define NDEBUG : note: this is the location of the previous definition DirichletProcessMixture.cpp:187: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for default(shared) private(i) schedule(dynamic,1) DirichletProcessMixture.cpp:272: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for default(shared) private(i) schedule(dynamic,1) DirichletProcessMixture.cpp:299: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for default(shared) private(i,j) schedule(dynamic,1) DirichletProcessMixture.cpp:375: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for default(shared) private(j) schedule(dynamic,1) "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MultinomialDataSet.cpp -o MultinomialDataSet.o In file included from DataSet.h:16, from MultinomialDataSet.h:4, from MultinomialDataSet.cpp:1: header.h:16: warning: "NDEBUG" redefined #define NDEBUG : note: this is the location of the previous definition "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Node.cpp -o Node.o In file included from Node.h:16, from Node.cpp:13: header.h:16: warning: "NDEBUG" redefined #define NDEBUG : note: this is the location of the previous definition "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RobustCubicSplineTimecourseDataSet.cpp -o RobustCubicSplineTimecourseDataSet.o In file included from DataSet.h:16, from TimecourseDataSet.h:20, from CubicSplineTimecourseDataSet.h:20, from RobustCubicSplineTimecourseDataSet.h:20, from RobustCubicSplineTimecourseDataSet.cpp:15: header.h:16: warning: "NDEBUG" redefined #define NDEBUG : note: this is the location of the previous definition "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RobustSquaredExponentialTimecourseDataSet.cpp -o RobustSquaredExponentialTimecourseDataSet.o In file included from SquaredExponentialTimecourseDataSet.h:20, from RobustSquaredExponentialTimecourseDataSet.h:20, from RobustSquaredExponentialTimecourseDataSet.cpp:15: header.h:16: warning: "NDEBUG" redefined #define NDEBUG : note: this is the location of the previous definition "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SquaredExponentialTimecourseDataSet.cpp -o SquaredExponentialTimecourseDataSet.o In file included from SquaredExponentialTimecourseDataSet.h:20, from SquaredExponentialTimecourseDataSet.cpp:15: header.h:16: warning: "NDEBUG" redefined #define NDEBUG : note: this is the location of the previous definition SquaredExponentialTimecourseDataSet.cpp: In member function 'void SquaredExponentialTimecourseDataSet::OptimiseHyperparametersEstimatedNoise(std::vector, double&, double&, double&, double)': SquaredExponentialTimecourseDataSet.cpp:339:30: warning: variable 'gridLogEvidence' set but not used [-Wunused-but-set-variable] double currentLogEvidence, gridLogEvidence, ^~~~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c TimecourseDataSet.cpp -o TimecourseDataSet.o In file included from DataSet.h:16, from TimecourseDataSet.h:20, from TimecourseDataSet.cpp:13: header.h:16: warning: "NDEBUG" redefined #define NDEBUG : note: this is the location of the previous definition "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bhc.cpp -o bhc.o In file included from bhc.cpp:17: header.h:16: warning: "NDEBUG" redefined #define NDEBUG : note: this is the location of the previous definition "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c gammaln.cpp -o gammaln.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" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c header.cpp -o header.o In file included from header.cpp:1: header.h:16: warning: "NDEBUG" redefined #define NDEBUG : note: this is the location of the previous definition "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c multinomial_CalculateHyperparameters.cpp -o multinomial_CalculateHyperparameters.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" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c multinomial_OutputDendrogramInformation.cpp -o multinomial_OutputDendrogramInformation.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" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c multinomial_ReadInData.cpp -o multinomial_ReadInData.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" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c multinomial_bayeslink_binf.cpp -o multinomial_bayeslink_binf.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" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c multinomial_binevidence.cpp -o multinomial_binevidence.o C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o BHC.dll tmp.def BlockCovarianceMatrix.o CubicSplineTimecourseDataSet.o DataSet.o DirichletProcessMixture.o MultinomialDataSet.o Node.o RobustCubicSplineTimecourseDataSet.o RobustSquaredExponentialTimecourseDataSet.o SquaredExponentialTimecourseDataSet.o TimecourseDataSet.o bhc.o gammaln.o header.o multinomial_CalculateHyperparameters.o multinomial_OutputDendrogramInformation.o multinomial_ReadInData.o multinomial_bayeslink_binf.o multinomial_binevidence.o -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/BHC.buildbin-libdir/00LOCK-BHC/00new/BHC/libs/i386 ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'BHC' finding HTML links ... done BHC 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 'BHC' ... ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** 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" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c BlockCovarianceMatrix.cpp -o BlockCovarianceMatrix.o In file included from BlockCovarianceMatrix.h:16, from BlockCovarianceMatrix.cpp:15: header.h:16: warning: "NDEBUG" redefined #define NDEBUG : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CubicSplineTimecourseDataSet.cpp -o CubicSplineTimecourseDataSet.o In file included from DataSet.h:16, from TimecourseDataSet.h:20, from CubicSplineTimecourseDataSet.h:20, from CubicSplineTimecourseDataSet.cpp:15: header.h:16: warning: "NDEBUG" redefined #define NDEBUG : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DataSet.cpp -o DataSet.o In file included from DataSet.h:16, from DataSet.cpp:13: header.h:16: warning: "NDEBUG" redefined #define NDEBUG : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DirichletProcessMixture.cpp -o DirichletProcessMixture.o In file included from DirichletProcessMixture.h:4, from DirichletProcessMixture.cpp:15: header.h:16: warning: "NDEBUG" redefined #define NDEBUG : note: this is the location of the previous definition DirichletProcessMixture.cpp:187: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for default(shared) private(i) schedule(dynamic,1) DirichletProcessMixture.cpp:272: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for default(shared) private(i) schedule(dynamic,1) DirichletProcessMixture.cpp:299: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for default(shared) private(i,j) schedule(dynamic,1) DirichletProcessMixture.cpp:375: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for default(shared) private(j) schedule(dynamic,1) "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MultinomialDataSet.cpp -o MultinomialDataSet.o In file included from DataSet.h:16, from MultinomialDataSet.h:4, from MultinomialDataSet.cpp:1: header.h:16: warning: "NDEBUG" redefined #define NDEBUG : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Node.cpp -o Node.o In file included from Node.h:16, from Node.cpp:13: header.h:16: warning: "NDEBUG" redefined #define NDEBUG : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RobustCubicSplineTimecourseDataSet.cpp -o RobustCubicSplineTimecourseDataSet.o In file included from DataSet.h:16, from TimecourseDataSet.h:20, from CubicSplineTimecourseDataSet.h:20, from RobustCubicSplineTimecourseDataSet.h:20, from RobustCubicSplineTimecourseDataSet.cpp:15: header.h:16: warning: "NDEBUG" redefined #define NDEBUG : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RobustSquaredExponentialTimecourseDataSet.cpp -o RobustSquaredExponentialTimecourseDataSet.o In file included from SquaredExponentialTimecourseDataSet.h:20, from RobustSquaredExponentialTimecourseDataSet.h:20, from RobustSquaredExponentialTimecourseDataSet.cpp:15: header.h:16: warning: "NDEBUG" redefined #define NDEBUG : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SquaredExponentialTimecourseDataSet.cpp -o SquaredExponentialTimecourseDataSet.o In file included from SquaredExponentialTimecourseDataSet.h:20, from SquaredExponentialTimecourseDataSet.cpp:15: header.h:16: warning: "NDEBUG" redefined #define NDEBUG : note: this is the location of the previous definition SquaredExponentialTimecourseDataSet.cpp: In member function 'void SquaredExponentialTimecourseDataSet::OptimiseHyperparametersEstimatedNoise(std::vector, double&, double&, double&, double)': SquaredExponentialTimecourseDataSet.cpp:339:30: warning: variable 'gridLogEvidence' set but not used [-Wunused-but-set-variable] double currentLogEvidence, gridLogEvidence, ^~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c TimecourseDataSet.cpp -o TimecourseDataSet.o In file included from DataSet.h:16, from TimecourseDataSet.h:20, from TimecourseDataSet.cpp:13: header.h:16: warning: "NDEBUG" redefined #define NDEBUG : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bhc.cpp -o bhc.o In file included from bhc.cpp:17: header.h:16: warning: "NDEBUG" redefined #define NDEBUG : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c gammaln.cpp -o gammaln.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" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c header.cpp -o header.o In file included from header.cpp:1: header.h:16: warning: "NDEBUG" redefined #define NDEBUG : note: this is the location of the previous definition "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c multinomial_CalculateHyperparameters.cpp -o multinomial_CalculateHyperparameters.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" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c multinomial_OutputDendrogramInformation.cpp -o multinomial_OutputDendrogramInformation.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" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c multinomial_ReadInData.cpp -o multinomial_ReadInData.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" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c multinomial_bayeslink_binf.cpp -o multinomial_bayeslink_binf.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" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c multinomial_binevidence.cpp -o multinomial_binevidence.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o BHC.dll tmp.def BlockCovarianceMatrix.o CubicSplineTimecourseDataSet.o DataSet.o DirichletProcessMixture.o MultinomialDataSet.o Node.o RobustCubicSplineTimecourseDataSet.o RobustSquaredExponentialTimecourseDataSet.o SquaredExponentialTimecourseDataSet.o TimecourseDataSet.o bhc.o gammaln.o header.o multinomial_CalculateHyperparameters.o multinomial_OutputDendrogramInformation.o multinomial_ReadInData.o multinomial_bayeslink_binf.o multinomial_binevidence.o -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/BHC.buildbin-libdir/BHC/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'BHC' as BHC_1.46.0.zip * DONE (BHC) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'BHC' successfully unpacked and MD5 sums checked