############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf BHC.buildbin-libdir && mkdir BHC.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BHC_1.50.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R BHC.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=BHC.buildbin-libdir BHC_1.50.0.tar.gz' >>>>>>> * installing *source* package ‘BHC’ ... ** using staged installation checking for gcc... clang -arch arm64 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether clang -arch arm64 accepts -g... yes checking for clang -arch arm64 option to accept ISO C89... none needed checking for clang -arch arm64 option to support OpenMP... unsupported configure: WARNING: No OpenMP support. If using GCC, upgrade to >= 4.2 configure: creating ./config.status config.status: creating src/Makevars ** libs clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c BlockCovarianceMatrix.cpp -o BlockCovarianceMatrix.o In file included from BlockCovarianceMatrix.cpp:15: In file included from ./BlockCovarianceMatrix.h:16: ./header.h:16:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CubicSplineTimecourseDataSet.cpp -o CubicSplineTimecourseDataSet.o In file included from CubicSplineTimecourseDataSet.cpp:15: In file included from ./CubicSplineTimecourseDataSet.h:20: In file included from ./TimecourseDataSet.h:20: In file included from ./DataSet.h:16: ./header.h:16:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ In file included from CubicSplineTimecourseDataSet.cpp:15: ./CubicSplineTimecourseDataSet.h:29:10: warning: 'CubicSplineTimecourseDataSet::GetMLIINoise' hides overloaded virtual function [-Woverloaded-virtual] double GetMLIINoise(const vector& itemIndex); ^ ./TimecourseDataSet.h:36:10: note: hidden overloaded virtual function 'TimecourseDataSet::GetMLIINoise' declared here: type mismatch at 1st parameter ('vector' vs 'const vector &') double GetMLIINoise(vector itemIndex); ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c DataSet.cpp -o DataSet.o In file included from DataSet.cpp:13: In file included from ./DataSet.h:16: ./header.h:16:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ DataSet.cpp:36:48: warning: if statement has empty body [-Wempty-body] if(!system("PAUSE")) /* could not pause */ ; ^ DataSet.cpp:36:48: note: put the semicolon on a separate line to silence this warning 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c DirichletProcessMixture.cpp -o DirichletProcessMixture.o In file included from DirichletProcessMixture.cpp:15: In file included from ./DirichletProcessMixture.h:4: ./header.h:16:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ DirichletProcessMixture.cpp:164:12: warning: 'random_shuffle>' is deprecated [-Wdeprecated-declarations] std::random_shuffle(random_id.begin(), random_id.end()); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/shuffle.h:60:1: note: 'random_shuffle>' has been explicitly marked deprecated here _LIBCPP_DEPRECATED_IN_CXX14 void ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1060:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX14' # define _LIBCPP_DEPRECATED_IN_CXX14 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1043:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MultinomialDataSet.cpp -o MultinomialDataSet.o In file included from MultinomialDataSet.cpp:1: In file included from ./MultinomialDataSet.h:4: In file included from ./DataSet.h:16: ./header.h:16:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ In file included from MultinomialDataSet.cpp:1: ./MultinomialDataSet.h:19:10: warning: 'MultinomialDataSet::SingleClusterLogEvidence' hides overloaded virtual function [-Woverloaded-virtual] double SingleClusterLogEvidence(vector itemIndex); // returns the log-evidence for a cluster that contains data items defined by itemIndex ^ ./DataSet.h:29:18: note: hidden overloaded virtual function 'DataSet::SingleClusterLogEvidence' declared here: different number of parameters (5 vs 1) virtual double SingleClusterLogEvidence(const vector& itemIndex, ^ MultinomialDataSet.cpp:77:43: warning: if statement has empty body [-Wempty-body] if(!system("PAUSE"))/* didn't pause */; ^ MultinomialDataSet.cpp:77:43: note: put the semicolon on a separate line to silence this warning 3 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Node.cpp -o Node.o In file included from Node.cpp:13: In file included from ./Node.h:16: ./header.h:16:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RobustCubicSplineTimecourseDataSet.cpp -o RobustCubicSplineTimecourseDataSet.o In file included from RobustCubicSplineTimecourseDataSet.cpp:15: In file included from ./RobustCubicSplineTimecourseDataSet.h:20: In file included from ./CubicSplineTimecourseDataSet.h:20: In file included from ./TimecourseDataSet.h:20: In file included from ./DataSet.h:16: ./header.h:16:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ In file included from RobustCubicSplineTimecourseDataSet.cpp:15: In file included from ./RobustCubicSplineTimecourseDataSet.h:20: ./CubicSplineTimecourseDataSet.h:29:10: warning: 'CubicSplineTimecourseDataSet::GetMLIINoise' hides overloaded virtual function [-Woverloaded-virtual] double GetMLIINoise(const vector& itemIndex); ^ ./TimecourseDataSet.h:36:10: note: hidden overloaded virtual function 'TimecourseDataSet::GetMLIINoise' declared here: type mismatch at 1st parameter ('vector' vs 'const vector &') double GetMLIINoise(vector itemIndex); ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RobustSquaredExponentialTimecourseDataSet.cpp -o RobustSquaredExponentialTimecourseDataSet.o In file included from RobustSquaredExponentialTimecourseDataSet.cpp:15: In file included from ./RobustSquaredExponentialTimecourseDataSet.h:20: In file included from ./SquaredExponentialTimecourseDataSet.h:20: ./header.h:16:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SquaredExponentialTimecourseDataSet.cpp -o SquaredExponentialTimecourseDataSet.o In file included from SquaredExponentialTimecourseDataSet.cpp:15: In file included from ./SquaredExponentialTimecourseDataSet.h:20: ./header.h:16:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ SquaredExponentialTimecourseDataSet.cpp:339:30: warning: variable 'gridLogEvidence' set but not used [-Wunused-but-set-variable] double currentLogEvidence, gridLogEvidence, ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c TimecourseDataSet.cpp -o TimecourseDataSet.o In file included from TimecourseDataSet.cpp:13: In file included from ./TimecourseDataSet.h:20: In file included from ./DataSet.h:16: ./header.h:16:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ TimecourseDataSet.cpp:80:40: warning: if statement has empty body [-Wempty-body] if(!system("PAUSE"))/*didn't work*/; ^ TimecourseDataSet.cpp:80:40: note: put the semicolon on a separate line to silence this warning TimecourseDataSet.cpp:143:40: warning: if statement has empty body [-Wempty-body] if(!system("PAUSE"))/*didn't work*/; ^ TimecourseDataSet.cpp:143:40: note: put the semicolon on a separate line to silence this warning 3 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bhc.cpp -o bhc.o In file included from bhc.cpp:17: ./header.h:16:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ In file included from bhc.cpp:20: ./CubicSplineTimecourseDataSet.h:29:10: warning: 'CubicSplineTimecourseDataSet::GetMLIINoise' hides overloaded virtual function [-Woverloaded-virtual] double GetMLIINoise(const vector& itemIndex); ^ ./TimecourseDataSet.h:36:10: note: hidden overloaded virtual function 'TimecourseDataSet::GetMLIINoise' declared here: type mismatch at 1st parameter ('vector' vs 'const vector &') double GetMLIINoise(vector itemIndex); ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gammaln.cpp -o gammaln.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c header.cpp -o header.o In file included from header.cpp:1: ./header.h:16:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c multinomial_CalculateHyperparameters.cpp -o multinomial_CalculateHyperparameters.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c multinomial_OutputDendrogramInformation.cpp -o multinomial_OutputDendrogramInformation.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c multinomial_ReadInData.cpp -o multinomial_ReadInData.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c multinomial_bayeslink_binf.cpp -o multinomial_bayeslink_binf.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c multinomial_binevidence.cpp -o multinomial_binevidence.o clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o BHC.so 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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: -undefined dynamic_lookup may not work with chained fixups installing to /Volumes/External/bbs-3.16-bioc-m1/meat/BHC.buildbin-libdir/00LOCK-BHC/00new/BHC/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BHC) >>>>>>> >>>>>>> FIXING LINKS FOR BHC.buildbin-libdir/BHC/libs/BHC.so >>>>>>> install_name_tool -change "/opt/R/arm64/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgcc_s.1.1.dylib" "BHC.buildbin-libdir/BHC/libs/BHC.so" install_name_tool -change "/opt/R/arm64/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgfortran.5.dylib" "BHC.buildbin-libdir/BHC/libs/BHC.so" install_name_tool -change "/opt/R/arm64/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libquadmath.0.dylib" "BHC.buildbin-libdir/BHC/libs/BHC.so"