############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf REBET.buildbin-libdir && mkdir REBET.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh REBET_1.24.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R REBET.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=REBET.buildbin-libdir REBET_1.24.0.tar.gz' >>>>>>> * installing *source* package ‘REBET’ ... ** using staged installation ** libs 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 -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-3.20-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 4.4.2) /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 4.4.2) /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)