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###
### Running command:
###
###   rm -rf crlmm.buildbin-libdir && mkdir crlmm.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh crlmm_1.64.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R crlmm.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=crlmm.buildbin-libdir crlmm_1.64.0.tar.gz'
>>>>>>> 

* installing *source* package ‘crlmm’ ...
** 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'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c gtypeCaller.c -o gtypeCaller.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c init.c -o init.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c trimmed.c -o trimmed.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c utils.c -o utils.o
utils.c:81:13: warning: variable 'n1' set but not used [-Wunused-but-set-variable]
  int i, j, n1, n2, n3;
            ^
utils.c:81:17: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
  int i, j, n1, n2, n3;
                ^
utils.c:81:21: warning: variable 'n3' set but not used [-Wunused-but-set-variable]
  int i, j, n1, n2, n3;
                    ^
utils.c:207:13: warning: variable 'n1' set but not used [-Wunused-but-set-variable]
  int i, j, n1, n2, n3;
            ^
utils.c:207:17: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
  int i, j, n1, n2, n3;
                ^
utils.c:207:21: warning: variable 'n3' set but not used [-Wunused-but-set-variable]
  int i, j, n1, n2, n3;
                    ^
6 warnings generated.
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 crlmm.so gtypeCaller.o init.o trimmed.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/crlmm.buildbin-libdir/00LOCK-crlmm/00new/crlmm/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’
** testing if installed package keeps a record of temporary installation path
* DONE (crlmm)


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

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

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