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###
### Running command:
###
###   rm -rf matter.buildbin-libdir && mkdir matter.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh matter_2.5.4.tar.gz /Library/Frameworks/R.framework/Resources/bin/R matter.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=matter.buildbin-libdir matter_2.5.4.tar.gz'
>>>>>>> 

* installing *source* package ‘matter’ ...
** using staged installation
** libs
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/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c altrep.cpp -o altrep.o
altrep.cpp:112:65: warning: format specifies type 'int' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
        Rprintf("matter array (mode=%d, len=%d, mem=%d)\n", xm.type(), xm.length(), mem);
                                            ~~                         ^~~~~~~~~~~
                                            %td
altrep.cpp:242:67: warning: format specifies type 'int' but the argument has type 'R_xlen_t' (aka 'long') [-Wformat]
        Rprintf("matter strings (mode=%d, len=%d, mem=%d)\n", xm.type(), xm.length(), mem);
                                              ~~                         ^~~~~~~~~~~
                                              %td
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c init.cpp -o init.o
In file included from init.cpp:3:
In file included from ./matterExports.h:13:
./signal2.h:153:24: warning: variable 'lo' set but not used [-Wunused-but-set-variable]
        index_t ii, jj, prev, lo, hi;
                              ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c matterExports.cpp -o matterExports.o
In file included from matterExports.cpp:2:
In file included from ./matterExports.h:13:
./signal2.h:153:24: warning: variable 'lo' set but not used [-Wunused-but-set-variable]
        index_t ii, jj, prev, lo, hi;
                              ^
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 matter.so altrep.o init.o matterExports.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.19-bioc/meat/matter.buildbin-libdir/00LOCK-matter/00new/matter/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 (matter)


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

>>>>>>> Paths before fix:
matter.buildbin-libdir/matter/libs/matter.so:
	matter.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/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-x86_64/Resources/lib/libgcc_s.1.1.dylib" "matter.buildbin-libdir/matter/libs/matter.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "matter.buildbin-libdir/matter/libs/matter.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "matter.buildbin-libdir/matter/libs/matter.so"

>>>>>>> Paths after fix:
matter.buildbin-libdir/matter/libs/matter.so:
	matter.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/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)