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###
### Running command:
###
###   rm -rf rqubic.buildbin-libdir && mkdir rqubic.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh rqubic_1.50.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R rqubic.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=rqubic.buildbin-libdir rqubic_1.50.0.tar.gz'
>>>>>>> 

* installing *source* package ‘rqubic’ ...
** 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 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bicluster.c -o bicluster.o
bicluster.c:354:15: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
      if (flag=ss) (*m_cnt)++;
          ~~~~^~~
bicluster.c:354:15: note: place parentheses around the assignment to silence this warning
      if (flag=ss) (*m_cnt)++;
              ^
          (      )
bicluster.c:354:15: note: use '==' to turn this assignment into an equality comparison
      if (flag=ss) (*m_cnt)++;
              ^
              ==
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c discretize.c -o discretize.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c fib.c -o fib.o
fib.c:170:13: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion]
        n->fh_keys = 1;
                   ^ ~
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c graph.c -o graph.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rqubic.c -o rqubic.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o rqubic.so bicluster.o discretize.o fib.o graph.o rqubic.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/rqubic.buildbin-libdir/00LOCK-rqubic/00new/rqubic/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 (rqubic)


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

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

>>>>>>> Paths after fix:
rqubic.buildbin-libdir/rqubic/libs/rqubic.so:
	rqubic.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/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)