############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf groHMM.buildbin-libdir && mkdir groHMM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh groHMM_1.34.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R groHMM.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=groHMM.buildbin-libdir groHMM_1.34.0.tar.gz' >>>>>>> * installing *source* package ‘groHMM’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c AnnotateProbes.c -o AnnotateProbes.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c DecayAlgorithm.c -o DecayAlgorithm.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c MLEfit.c -o MLEfit.o In file included from MLEfit.c:43: ./hmmHeader.h:281:16: warning: unused function 'MargainalizeSumLogProbOver' [-Wunused-function] static double MargainalizeSumLogProbOver(int state, int position, ^ ./hmmHeader.h:301:16: warning: unused function 'expSum' [-Wunused-function] static double expSum(double *logValues, int length) { ^ 2 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RegisterRRoutines.c -o RegisterRRoutines.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Windowing.c -o Windowing.o Windowing.c:146:6: warning: unused variable 'II' [-Wunused-variable] int II = 0; ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hmmEM.c -o hmmEM.o In file included from hmmEM.c:50: ./hmmHeader.h:281:16: warning: unused function 'MargainalizeSumLogProbOver' [-Wunused-function] static double MargainalizeSumLogProbOver(int state, int position, ^ ./hmmHeader.h:301:16: warning: unused function 'expSum' [-Wunused-function] static double expSum(double *logValues, int length) { ^ 2 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hmmFwBw.c -o hmmFwBw.o In file included from hmmFwBw.c:45: ./hmmHeader.h:281:16: warning: unused function 'MargainalizeSumLogProbOver' [-Wunused-function] static double MargainalizeSumLogProbOver(int state, int position, ^ ./hmmHeader.h:301:16: warning: unused function 'expSum' [-Wunused-function] static double expSum(double *logValues, int length) { ^ 2 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hmmMiscFunctions.c -o hmmMiscFunctions.o hmmMiscFunctions.c:384:10: warning: unused variable 'wi' [-Wunused-variable] double wi, *newEx; ^ hmmMiscFunctions.c:417:10: warning: unused variable 'epsilon' [-Wunused-variable] double epsilon=0.00001; ^ 2 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hmmViterbi.c -o hmmViterbi.o In file included from hmmViterbi.c:48: ./hmmHeader.h:281:16: warning: unused function 'MargainalizeSumLogProbOver' [-Wunused-function] static double MargainalizeSumLogProbOver(int state, int position, ^ ./hmmHeader.h:301:16: warning: unused function 'expSum' [-Wunused-function] static double expSum(double *logValues, int length) { ^ 2 warnings generated. clang -arch arm64 -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 groHMM.so AnnotateProbes.o DecayAlgorithm.o MLEfit.o RegisterRRoutines.o Windowing.o hmmEM.o hmmFwBw.o hmmMiscFunctions.o hmmViterbi.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/groHMM.buildbin-libdir/00LOCK-groHMM/00new/groHMM/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 (groHMM) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR groHMM.buildbin-libdir/groHMM/libs/groHMM.so >>>>>>> >>>>>>> Paths before fix: groHMM.buildbin-libdir/groHMM/libs/groHMM.so: groHMM.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "groHMM.buildbin-libdir/groHMM/libs/groHMM.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "groHMM.buildbin-libdir/groHMM/libs/groHMM.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "groHMM.buildbin-libdir/groHMM/libs/groHMM.so" >>>>>>> Paths after fix: groHMM.buildbin-libdir/groHMM/libs/groHMM.so: groHMM.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)