############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf bgx.buildbin-libdir && mkdir bgx.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh bgx_1.73.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R bgx.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=bgx.buildbin-libdir bgx_1.73.0.tar.gz' >>>>>>> * installing *source* package ‘bgx’ ... ** using staged installation checking for gcc... clang -arch x86_64 checking for C compiler default output file name... rm: a.out.dSYM: is a directory a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether clang -arch x86_64 accepts -g... yes checking for clang -arch x86_64 option to accept ISO C89... none needed checking for C compiler vendor... gnu checking whether C compiler accepts -ffast-math... yes checking whether C compiler accepts -O3... yes checking build system type... x86_64-apple-darwin21.6.0 checking host system type... x86_64-apple-darwin21.6.0 checking for gcc architecture flag... checking for x86 cpuid 0 output... 16:756e6547:6c65746e:49656e69 checking for x86 cpuid 1 output... 50657:25400800:7ffefbff:bfebfbff checking whether C compiler accepts -march=pentium2... no checking whether C compiler accepts -mcpu=pentium2... yes checking for gcc architecture flag... -mcpu=pentium2 checking for clang -arch x86_64 option to accept ISO C99... none needed checking for main in -lm... yes Untarring Boost header files... checking for an ANSI C-conforming const... yes checking for inline... inline configure: creating ./config.status config.status: creating src/Makevars ** 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 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I ../boostIncl -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -falign-functions=64 -Wall -g -O2 -ffast-math -O3 -DUSING_R -c bgx.cc -o bgx.o In file included from bgx.cc:32: ./rand.hh:51:11: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] #define R_NO_REMAP ^ :2:9: note: previous definition is here #define R_NO_REMAP 1 ^ bgx.cc:44:13: warning: 'FLUSH' macro redefined [-Wmacro-redefined] #define FLUSH {R_FlushConsole(); R_ProcessEvents();} ^ ./rand.hh:42:13: note: previous definition is here #define FLUSH R_FlushConsole(); ^ In file included from bgx.cc:36: ./bgx_updates.hh:47:8: warning: private field 'categories' is not used [-Wunused-private-field] int* categories; ^ ./bgx_updates.hh:310:8: warning: private field 'categories' is not used [-Wunused-private-field] int *categories; ^ ./bgx_updates.hh:311:7: warning: private field 'numberCategories' is not used [-Wunused-private-field] int numberCategories; ^ 5 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I ../boostIncl -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -falign-functions=64 -Wall -g -O2 -ffast-math -O3 -DUSING_R -c bgx_frontend.cc -o bgx_frontend.o bgx_frontend.cc:49:11: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] #define R_NO_REMAP ^ :2:9: note: previous definition is here #define R_NO_REMAP 1 ^ 1 warning generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I ../boostIncl -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -falign-functions=64 -Wall -g -O2 -mcpu=pentium2 -ffast-math -O3 -c qnorm.c -o qnorm.o clang: warning: argument unused during compilation: '-mcpu=pentium2' [-Wunused-command-line-argument] clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I ../boostIncl -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -falign-functions=64 -Wall -g -O2 -ffast-math -O3 -DUSING_R -c rundir.cc -o rundir.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I ../boostIncl -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -falign-functions=64 -Wall -g -O2 -ffast-math -O3 -DUSING_R -c sokal.cc -o sokal.o sokal.cc:46:11: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] #define R_NO_REMAP ^ :2:9: note: previous definition is here #define R_NO_REMAP 1 ^ 1 warning generated. 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 bgx.so bgx.o bgx_frontend.o qnorm.o rundir.o sokal.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation rm -r ../boostIncl installing to /Users/biocbuild/bbs-3.21-bioc/meat/bgx.buildbin-libdir/00LOCK-bgx/00new/bgx/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 (bgx) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR bgx.buildbin-libdir/bgx/libs/bgx.so >>>>>>> >>>>>>> Paths before fix: bgx.buildbin-libdir/bgx/libs/bgx.so: bgx.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0) /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) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgcc_s.1.1.dylib" "bgx.buildbin-libdir/bgx/libs/bgx.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "bgx.buildbin-libdir/bgx/libs/bgx.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "bgx.buildbin-libdir/bgx/libs/bgx.so" >>>>>>> Paths after fix: bgx.buildbin-libdir/bgx/libs/bgx.so: bgx.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0) /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)