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###
### Running command:
###
###   rm -rf REBET.buildbin-libdir && mkdir REBET.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh REBET_1.22.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R REBET.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=REBET.buildbin-libdir REBET_1.22.0.tar.gz'
>>>>>>> 

* installing *source* package ‘REBET’ ...
** 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 source.c -o source.o
source.c:58:17: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static double * dVec_alloc(n, initFlag, initVal)
                ^
source.c:76:18: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static double ** dMat_alloc(nrow, ncol, initFlag, initVal)
                 ^
source.c:92:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void matrix_free(x, n)
            ^
source.c:105:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void vecIntoMat(vec, nrow, ncol, ret)
            ^
source.c:123:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void mult_stVec_stVec(X, invXtX, n, m, ret)
            ^
source.c:149:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void mult_stVec_scalar(X, n, col, c, ret)
            ^
source.c:165:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static void mult_vec_TstVec(vec, TstVec, n, m, ret)
            ^
source.c:189:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
static double dotProd(v1, v2, n)
              ^
source.c:205:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
void SIGMA2_cont(G, p_nsub, p_nsnp, X, p_ncov, invXtX, p_tildeSigma, ret)
     ^
source.c:297:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
void SIGMA2_binary(G, p_nsub, p_nsnp, X, p_ncov, invXtX, d, ret)
     ^
source.c:388:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
void computeXtDX(X, d, p_nsub, p_ncov, ret)
     ^
11 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 REBET.so source.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.19-bioc/meat/REBET.buildbin-libdir/00LOCK-REBET/00new/REBET/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 (REBET)


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

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

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