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###
### Running command:
###
###   rm -rf fmcsR.buildbin-libdir && mkdir fmcsR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh fmcsR_1.47.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R fmcsR.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=fmcsR.buildbin-libdir fmcsR_1.47.1.tar.gz'
>>>>>>> 

* installing *source* package ‘fmcsR’ ...
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -arch arm64 -std=gnu++17 accepts -g... yes
checking for gcc... clang -arch arm64
checking whether we are using the GNU C compiler... yes
checking whether clang -arch arm64 accepts -g... yes
checking for clang -arch arm64 option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -arch arm64 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for inline... inline
checking for size_t... yes
checking for alarm... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating config.h
config.status: config.h is unchanged
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c MCS.cpp -o MCS.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c MCSCompound.cpp -o MCSCompound.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c MCSMap.cpp -o MCSMap.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c MCSRingDetector.cpp -o MCSRingDetector.o
MCSRingDetector.cpp:175:13: warning: unused variable 'aromaticCount' [-Wunused-variable]
        int aromaticCount = 0;
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c fmcs_R_wrap.cpp -o fmcs_R_wrap.o
fmcs_R_wrap.cpp:47:13: warning: variable 'matchType' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
            default: 
            ^~~~~~~
fmcs_R_wrap.cpp:74:13: note: uninitialized use occurs here
            matchType, runningMode, *timeout);
            ^~~~~~~~~
fmcs_R_wrap.cpp:42:6: note: variable 'matchType' is declared here
        MCS::MatchType matchType;
        ^
fmcs_R_wrap.cpp:56:13: warning: variable 'runningMode' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
            default:
            ^~~~~~~
fmcs_R_wrap.cpp:74:24: note: uninitialized use occurs here
            matchType, runningMode, *timeout);
                       ^~~~~~~~~~~
fmcs_R_wrap.cpp:52:9: note: variable 'runningMode' is declared here
        MCS::RunningMode runningMode;
        ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DSTRICT_R_HEADERS -DR_NO_REMAP  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c util.cpp -o util.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o fmcsR.so MCS.o MCSCompound.o MCSMap.o MCSRingDetector.o fmcs_R_wrap.o util.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/fmcsR.buildbin-libdir/00LOCK-fmcsR/00new/fmcsR/libs
** R
** data
** 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 (fmcsR)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR fmcsR.buildbin-libdir/fmcsR/libs/fmcsR.so
>>>>>>> 

>>>>>>> Paths before fix:
fmcsR.buildbin-libdir/fmcsR/libs/fmcsR.so:
	fmcsR.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
	/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-arm64/Resources/lib/libgcc_s.1.1.dylib" "fmcsR.buildbin-libdir/fmcsR/libs/fmcsR.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "fmcsR.buildbin-libdir/fmcsR/libs/fmcsR.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "fmcsR.buildbin-libdir/fmcsR/libs/fmcsR.so"

>>>>>>> Paths after fix:
fmcsR.buildbin-libdir/fmcsR/libs/fmcsR.so:
	fmcsR.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
	/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)