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###
### Running command:
###
###   rm -rf Repitools.buildbin-libdir && mkdir Repitools.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Repitools_1.50.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Repitools.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Repitools.buildbin-libdir Repitools_1.50.0.tar.gz'
>>>>>>> 

* installing *source* package ‘Repitools’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -D R_NO_REMAP -I. -fPIC  -falign-functions=64 -Wall -g -O2  -c const.c -o const.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -D R_NO_REMAP -I. -fPIC  -falign-functions=64 -Wall -g -O2  -c hyp2f1.c -o hyp2f1.o
hyp2f1.c:126:8: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
double hyp2f1( a, b, c, x )
       ^
hyp2f1.c:294:9: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
 double hyt2f1( a, b, c, x, loss )
        ^
hyp2f1.c:438:9: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
 double hys2f1( a, b, c, x, loss )
        ^
3 warnings generated.
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 mmeansd.cpp -o mmeansd.o
mmeansd.cpp:33:24: warning: variable 'is' set but not used [-Wunused-but-set-variable]
    int * x, nval, hs, is, i;
                       ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -D R_NO_REMAP -I. -fPIC  -falign-functions=64 -Wall -g -O2  -c mtherr.c -o mtherr.o
mtherr.c:77:5: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
int mtherr( name, code )
    ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -D R_NO_REMAP -I. -fPIC  -falign-functions=64 -Wall -g -O2  -c ringo_stuff.c -o ringo_stuff.o
ringo_stuff.c:13:24: warning: unused variable 'Ringo_calls' [-Wunused-variable]
static R_CallMethodDef Ringo_calls[] = {
                       ^
1 warning 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 Repitools.so const.o hyp2f1.o mmeansd.o mtherr.o ringo_stuff.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.19-bioc/meat/Repitools.buildbin-libdir/00LOCK-Repitools/00new/Repitools/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 (Repitools)


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

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

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