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###
### Running command:
###
###   rm -rf cisPath.buildbin-libdir && mkdir cisPath.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh cisPath_1.44.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R cisPath.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=cisPath.buildbin-libdir cisPath_1.44.0.tar.gz'
>>>>>>> 

* installing *source* package ‘cisPath’ ...
** using staged installation
** 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   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c cisPath.cpp -o cisPath.o
cisPath.cpp:714:9: warning: variable 'lineCount' set but not used [-Wunused-but-set-variable]
    int lineCount = 1;
        ^
cisPath.cpp:945:14: warning: explicitly assigning value of variable of type 'string' (aka 'basic_string<char, char_traits<char>, allocator<char>>') to itself [-Wself-assign-overloaded]
        Name = Name;
        ~~~~ ^ ~~~~
cisPath.cpp:3555:27: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
            PRINTFUNCTION(buffer);
                          ^~~~~~
cisPath.cpp:3555:27: note: treat the string as an argument to avoid this
            PRINTFUNCTION(buffer);
                          ^
                          "%s", 
3 warnings generated.
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 cisPath.so cisPath.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.19-bioc/meat/cisPath.buildbin-libdir/00LOCK-cisPath/00new/cisPath/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 (cisPath)


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

>>>>>>> Paths before fix:
cisPath.buildbin-libdir/cisPath/libs/cisPath.so:
	cisPath.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 4.4.0)
	/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-arm64/Resources/lib/libgcc_s.1.1.dylib" "cisPath.buildbin-libdir/cisPath/libs/cisPath.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "cisPath.buildbin-libdir/cisPath/libs/cisPath.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "cisPath.buildbin-libdir/cisPath/libs/cisPath.so"

>>>>>>> Paths after fix:
cisPath.buildbin-libdir/cisPath/libs/cisPath.so:
	cisPath.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 4.4.0)
	/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)