############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf methimpute.buildbin-libdir && mkdir methimpute.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh methimpute_1.20.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R methimpute.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=methimpute.buildbin-libdir methimpute_1.20.0.tar.gz' >>>>>>> * installing *source* package ‘methimpute’ ... ** using staged installation ** libs clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c densities.cpp -o densities.o In file included from densities.cpp:1: In file included from ./densities.h:1: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from densities.cpp:1: ./densities.h:98:10: warning: 'BinomialTest::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual] double getLogDensityAt(int test, int total); ^ ./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: different number of parameters (1 vs 2) virtual double getLogDensityAt(int) { return(0); }; ^ ./densities.h:224:10: warning: 'Beta::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual] double getLogDensityAt(double x); ^ ./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: type mismatch at 1st parameter ('int' vs 'double') virtual double getLogDensityAt(int) { return(0); }; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fitHMM.cpp -o fitHMM.o In file included from fitHMM.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from fitHMM.cpp:2: In file included from ./scalehmm.h:4: ./densities.h:98:10: warning: 'BinomialTest::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual] double getLogDensityAt(int test, int total); ^ ./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: different number of parameters (1 vs 2) virtual double getLogDensityAt(int) { return(0); }; ^ ./densities.h:224:10: warning: 'Beta::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual] double getLogDensityAt(double x); ^ ./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: type mismatch at 1st parameter ('int' vs 'double') virtual double getLogDensityAt(int) { return(0); }; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fitHMM_context.cpp -o fitHMM_context.o In file included from fitHMM_context.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from fitHMM_context.cpp:2: In file included from ./hmm_context.h:4: ./densities.h:98:10: warning: 'BinomialTest::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual] double getLogDensityAt(int test, int total); ^ ./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: different number of parameters (1 vs 2) virtual double getLogDensityAt(int) { return(0); }; ^ ./densities.h:224:10: warning: 'Beta::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual] double getLogDensityAt(double x); ^ ./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: type mismatch at 1st parameter ('int' vs 'double') virtual double getLogDensityAt(int) { return(0); }; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hmm_context.cpp -o hmm_context.o In file included from hmm_context.cpp:1: In file included from ./hmm_context.h:4: In file included from ./densities.h:1: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from hmm_context.cpp:1: In file included from ./hmm_context.h:4: ./densities.h:98:10: warning: 'BinomialTest::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual] double getLogDensityAt(int test, int total); ^ ./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: different number of parameters (1 vs 2) virtual double getLogDensityAt(int) { return(0); }; ^ ./densities.h:224:10: warning: 'Beta::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual] double getLogDensityAt(double x); ^ ./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: type mismatch at 1st parameter ('int' vs 'double') virtual double getLogDensityAt(int) { return(0); }; ^ 3 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c methimpute_init.c -o methimpute_init.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c scalehmm.cpp -o scalehmm.o In file included from scalehmm.cpp:1: In file included from ./scalehmm.h:4: In file included from ./densities.h:1: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ In file included from scalehmm.cpp:1: In file included from ./scalehmm.h:4: ./densities.h:98:10: warning: 'BinomialTest::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual] double getLogDensityAt(int test, int total); ^ ./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: different number of parameters (1 vs 2) virtual double getLogDensityAt(int) { return(0); }; ^ ./densities.h:224:10: warning: 'Beta::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual] double getLogDensityAt(double x); ^ ./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: type mismatch at 1st parameter ('int' vs 'double') virtual double getLogDensityAt(int) { return(0); }; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++11 -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 methimpute.so RcppExports.o densities.o fitHMM.o fitHMM_context.o hmm_context.o methimpute_init.o scalehmm.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/methimpute.buildbin-libdir/00LOCK-methimpute/00new/methimpute/libs ** R ** data ** 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 (methimpute) >>>>>>> >>>>>>> FIXING LINKS FOR methimpute.buildbin-libdir/methimpute/libs/methimpute.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" "methimpute.buildbin-libdir/methimpute/libs/methimpute.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" "methimpute.buildbin-libdir/methimpute/libs/methimpute.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" "methimpute.buildbin-libdir/methimpute/libs/methimpute.so"