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###
### Running command:
###
###   rm -rf bgx.buildbin-libdir && mkdir bgx.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh bgx_1.68.3.tar.gz /Library/Frameworks/R.framework/Resources/bin/R bgx.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=bgx.buildbin-libdir bgx_1.68.3.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... 50657:14400800:7ffefbff: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/4.3-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  -ffast-math -O3 -DUSING_R -c bgx.cc -o bgx.o
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;
      ^
4 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/4.3-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  -ffast-math -O3 -DUSING_R -c bgx_frontend.cc -o bgx_frontend.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I ../boostIncl -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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  -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/4.3-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  -ffast-math -O3 -DUSING_R -c sokal.cc -o sokal.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 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-3.18-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/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.2)
	/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/4.3-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/4.3-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/4.3-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/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.2)
	/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)