############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf BHC.buildbin-libdir && mkdir BHC.buildbin-libdir && F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL --build --library=BHC.buildbin-libdir BHC_1.52.0.tar.gz ### ############################################################################## ############################################################################## * installing *source* package 'BHC' ... ** using staged installation ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs using C++ compiler: 'G__~1.EXE (GCC) 12.2.0' g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/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 16 | #define NDEBUG | : note: this is the location of the previous definition g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/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 16 | #define NDEBUG | : note: this is the location of the previous definition g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/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 16 | #define NDEBUG | : note: this is the location of the previous definition g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/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 16 | #define NDEBUG | : note: this is the location of the previous definition DirichletProcessMixture.cpp:187: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 187 | #pragma omp parallel for default(shared) private(i) schedule(dynamic,1) | DirichletProcessMixture.cpp:272: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 272 | #pragma omp parallel for default(shared) private(i) schedule(dynamic,1) | DirichletProcessMixture.cpp:299: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 299 | #pragma omp parallel for default(shared) private(i,j) schedule(dynamic,1) | DirichletProcessMixture.cpp:375: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 375 | #pragma omp parallel for default(shared) private(j) schedule(dynamic,1) | g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/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 16 | #define NDEBUG | : note: this is the location of the previous definition g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/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 16 | #define NDEBUG | : note: this is the location of the previous definition g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/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 16 | #define NDEBUG | : note: this is the location of the previous definition g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/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 16 | #define NDEBUG | : note: this is the location of the previous definition g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/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 16 | #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] 339 | double currentLogEvidence, gridLogEvidence, | ^~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/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 16 | #define NDEBUG | : note: this is the location of the previous definition g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/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 16 | #define NDEBUG | : note: this is the location of the previous definition g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c gammaln.cpp -o gammaln.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/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 16 | #define NDEBUG | : note: this is the location of the previous definition g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c multinomial_CalculateHyperparameters.cpp -o multinomial_CalculateHyperparameters.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c multinomial_OutputDendrogramInformation.cpp -o multinomial_OutputDendrogramInformation.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c multinomial_ReadInData.cpp -o multinomial_ReadInData.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c multinomial_bayeslink_binf.cpp -o multinomial_bayeslink_binf.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c multinomial_binevidence.cpp -o multinomial_binevidence.o g++ -std=gnu++17 -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:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-bioc/meat/BHC.buildbin-libdir/00LOCK-BHC/00new/BHC/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * MD5 sums packaged installation of 'BHC' as BHC_1.52.0.zip * DONE (BHC)