############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf ternarynet.buildbin-libdir && mkdir ternarynet.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ternarynet_1.41.0.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_1.41.0.tar.gz' >>>>>>> * installing *source* package ‘ternarynet’ ... ** using staged installation ** libs clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c array.c -o array.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 gn.c -o gn.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 gn_Rwrap.c -o gn_Rwrap.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 init.c -o init.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 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:24:38: warning: variable 'backupStage' 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:73:39: warning: unused variable 'tempi' [-Wunused-variable] int nOutcomes=3, l0, stage_count, tempi, jtrans, nTransition; ^ 4 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 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 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 tnetpost.cc -o tnetpost.o tnetpost.cc:30:26: warning: unused variable 'tempi' [-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:30:33: warning: unused variable 'jtrans' [-Wunused-variable] int l0, stage_count, tempi, jtrans, nTransition; ^ tnetpost.cc:30:9: warning: unused variable 'l0' [-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:30:41: warning: unused variable 'nTransition' [-Wunused-variable] int l0, stage_count, tempi, jtrans, nTransition; ^ tnetpost.cc:36:21: warning: variable 'xSeedFit' set but not used [-Wunused-but-set-variable] int m0, mdelta, xSeedFit; ^ tnetpost.cc:38:9: warning: variable 'perturbationType' set but not used [-Wunused-but-set-variable] int perturbationType, scoreType, backupStage; ^ 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:25:9: warning: unused variable 'ipause' [-Wunused-variable] int ipause; ^ tnetpost.cc:38:38: warning: variable 'backupStage' set but not used [-Wunused-but-set-variable] int perturbationType, scoreType, backupStage; ^ tnetpost.cc:38:27: warning: variable 'scoreType' set but not used [-Wunused-but-set-variable] int perturbationType, scoreType, backupStage; ^ tnetpost.cc:40:27: warning: variable 'delta' 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:27:9: warning: unused variable 'm0fit' [-Wunused-variable] int m0fit; ^ tnetpost.cc:40:12: warning: variable 'epsilon' set but not used [-Wunused-but-set-variable] double epsilon, chi0, delta, rho; ^ tnetpost.cc:39:19: warning: variable 'maxTransition' set but not used [-Wunused-but-set-variable] int maxStage, maxTransition; ^ 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:28:32: warning: variable 'minScore' set but not used [-Wunused-but-set-variable] double newScore, oldScore, minScore, finalScore; ^ 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; ^ 22 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 util.c -o util.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 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-3.16-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 LINKS FOR ternarynet.buildbin-libdir/ternarynet/libs/ternarynet.so >>>>>>> ERROR: R installation problem: File /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib not found!