############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf ternarynet.buildbin-libdir && mkdir ternarynet.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ternarynet_1.47.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R ternarynet.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ternarynet.buildbin-libdir ternarynet_1.47.2.tar.gz' >>>>>>> * installing *source* package ‘ternarynet’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c array.c -o array.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gn.c -o gn.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gn_Rwrap.c -o gn_Rwrap.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tnetfit.cc -o tnetfit.o tnetfit.cc:24:9: warning: variable 'perturbationType' set but not used [-Wunused-but-set-variable] int perturbationType, scoreType, backupStage, maxStage, maxTransition; ^ tnetfit.cc:24:27: warning: variable 'scoreType' set but not used [-Wunused-but-set-variable] int perturbationType, scoreType, backupStage, maxStage, maxTransition; ^ tnetfit.cc:24:38: warning: variable 'backupStage' set but not used [-Wunused-but-set-variable] int perturbationType, scoreType, backupStage, maxStage, maxTransition; ^ tnetfit.cc:73:39: warning: unused variable 'tempi' [-Wunused-variable] int nOutcomes=3, l0, stage_count, tempi, jtrans, nTransition; ^ 4 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tnetfuncs.cc -o tnetfuncs.o tnetfuncs.cc:435:5: warning: unused variable 'ipause' [-Wunused-variable] int ipause; ^ tnetfuncs.cc:427:5: warning: unused variable 'tableWidth' [-Wunused-variable] int tableWidth = powi(nOutcomes,maxDegree); ^ tnetfuncs.cc:521:16: warning: unused variable 'i' [-Wunused-variable] int m1, m2, i; ^ tnetfuncs.cc:517:6: warning: unused variable 'ipause' [-Wunused-variable] int ipause; ^ 4 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tnetpost.cc -o tnetpost.o tnetpost.cc:28:32: warning: variable 'minScore' set but not used [-Wunused-but-set-variable] double newScore, oldScore, minScore, finalScore; ^ tnetpost.cc:41:9: warning: variable 'Rf_beta' set but not used [-Wunused-but-set-variable] int beta; ^ /Library/Frameworks/R.framework/Resources/include/Rmath.h:210:15: note: expanded from macro 'beta' #define beta Rf_beta ^ tnetpost.cc:27:9: warning: unused variable 'm0fit' [-Wunused-variable] int m0fit; ^ tnetpost.cc:30:9: warning: unused variable 'l0' [-Wunused-variable] int l0, stage_count, tempi, jtrans, nTransition; ^ tnetpost.cc:40:12: warning: variable 'epsilon' set but not used [-Wunused-but-set-variable] double epsilon, chi0, delta, rho; ^ tnetpost.cc:40:21: warning: variable 'chi0' set but not used [-Wunused-but-set-variable] double epsilon, chi0, delta, rho; ^ tnetpost.cc:40:27: warning: variable 'delta' set but not used [-Wunused-but-set-variable] double epsilon, chi0, delta, rho; ^ tnetpost.cc:28:42: warning: unused variable 'finalScore' [-Wunused-variable] double newScore, oldScore, minScore, finalScore; ^ tnetpost.cc:40:34: warning: variable 'rho' set but not used [-Wunused-but-set-variable] double epsilon, chi0, delta, rho; ^ tnetpost.cc:30:41: warning: unused variable 'nTransition' [-Wunused-variable] int l0, stage_count, tempi, jtrans, nTransition; ^ tnetpost.cc:30:33: warning: unused variable 'jtrans' [-Wunused-variable] int l0, stage_count, tempi, jtrans, nTransition; ^ tnetpost.cc:30:26: warning: unused variable 'tempi' [-Wunused-variable] int l0, stage_count, tempi, jtrans, nTransition; ^ tnetpost.cc:30:13: warning: unused variable 'stage_count' [-Wunused-variable] int l0, stage_count, tempi, jtrans, nTransition; ^ tnetpost.cc:44:9: warning: variable 'ne' set but not used [-Wunused-but-set-variable] int ne, maxDegree; ^ tnetpost.cc:36:21: warning: variable 'xSeedFit' set but not used [-Wunused-but-set-variable] int m0, mdelta, xSeedFit; ^ tnetpost.cc:38:27: warning: variable 'scoreType' set but not used [-Wunused-but-set-variable] int perturbationType, scoreType, backupStage; ^ tnetpost.cc:38:9: warning: variable 'perturbationType' set but not used [-Wunused-but-set-variable] int perturbationType, scoreType, backupStage; ^ tnetpost.cc:25:9: warning: unused variable 'ipause' [-Wunused-variable] int ipause; ^ tnetpost.cc:39:19: warning: variable 'maxTransition' set but not used [-Wunused-but-set-variable] int maxStage, maxTransition; ^ tnetpost.cc:150:10: warning: variable 'minDump' set but not used [-Wunused-but-set-variable] bool minDump = true; ^ tnetpost.cc:39:9: warning: variable 'maxStage' set but not used [-Wunused-but-set-variable] int maxStage, maxTransition; ^ tnetpost.cc:38:38: warning: variable 'backupStage' set but not used [-Wunused-but-set-variable] int perturbationType, scoreType, backupStage; ^ 22 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c util.c -o util.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o ternarynet.so array.o gn.o gn_Rwrap.o init.o tnetfit.o tnetfuncs.o tnetpost.o util.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.19-bioc/meat/ternarynet.buildbin-libdir/00LOCK-ternarynet/00new/ternarynet/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 (ternarynet) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR ternarynet.buildbin-libdir/ternarynet/libs/ternarynet.so >>>>>>> >>>>>>> Paths before fix: ternarynet.buildbin-libdir/ternarynet/libs/ternarynet.so: ternarynet.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /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/4.4-x86_64/Resources/lib/libgcc_s.1.1.dylib" "ternarynet.buildbin-libdir/ternarynet/libs/ternarynet.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "ternarynet.buildbin-libdir/ternarynet/libs/ternarynet.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "ternarynet.buildbin-libdir/ternarynet/libs/ternarynet.so" >>>>>>> Paths after fix: ternarynet.buildbin-libdir/ternarynet/libs/ternarynet.so: ternarynet.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)