############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf iCARE.buildbin-libdir && mkdir iCARE.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh iCARE_1.34.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R iCARE.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=iCARE.buildbin-libdir iCARE_1.34.0.tar.gz' >>>>>>> * installing *source* package ‘iCARE’ ... ** 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:45:10: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] double * dVec_alloc(n, initFlag, initVal) ^ source.c:64:7: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] int * iVec_alloc(n, initFlag, initVal) ^ source.c:81:11: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] double ** dMat_alloc(nrow, ncol, initFlag, initVal) ^ source.c:98:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] void matrix_free(x, n) ^ source.c:114:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static int get_non_miss(vec, n, ovec) ^ source.c:135:13: 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 X_y(X, nr, nc, y, index, ni, ret) ^ source.c:155:13: 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 X_y2(X, nc, y, z, index, ni, ret) ^ source.c:185:15: 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 vec_mult(x, y, index, ni) ^ source.c:203:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static int vec_lteq_c(vec, n, c) ^ source.c:224:15: 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 mean_2val(vec, subvec, nsub, weights) ^ source.c:241:13: 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 mat_from_vec(vec, nr, nc, mat) ^ source.c:256:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static int quant_vecs(probs, nprobs, n, ivec, lo, hi, h) ^ source.c:284:13: 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 quantile(x, n, probs, nprobs, lo, hi, h, ivec, ni, qs) ^ source.c:338:15: 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 var_dvec(vec, n) ^ source.c:358:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static int get_cutpoints(quantiles, nq, ref_LP, nref) ^ source.c:406:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static int get_miss_perc(cutpoints, ncuts, miss_LP) ^ source.c:427:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static int vec_ab(x, n, a, b) ^ source.c:444:13: 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 get_newEndpoints(cutpoints, ncuts, miss_LP, miss_perc, ref_LP, nref, rcut1, rcut2) ^ source.c:471:12: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static int get_subs_2cut(x, n, a, b, ret) ^ source.c:493:13: 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 get_wgts(weights, subvec, nsub, retvec) ^ source.c:511:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] void ref_risk1(ref_risks, betavec, zmat, refmat, n_beta, nr_z, nc_z, nr_ref, nc_ref, ^ source.c:619:13: 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 get_int(nsub, age_new, t, aexp_rr, lambda, comp, zbeta, holder) ^ source.c:645:15: 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 finalVal(nsub, zbeta, expzbeta, age_new, age_int, lambda, loglambda, compRates, holder, tempv, weights) ^ source.c:684:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] void ref_risk2(betavec, zmat, refmat, n_beta, nr_z, nc_z, nr_ref, nc_ref, ^ 24 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 iCARE.so source.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/iCARE.buildbin-libdir/00LOCK-iCARE/00new/iCARE/libs ** R ** data *** moving datasets to lazyload DB ** 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 (iCARE) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR iCARE.buildbin-libdir/iCARE/libs/iCARE.so >>>>>>> >>>>>>> Paths before fix: iCARE.buildbin-libdir/iCARE/libs/iCARE.so: iCARE.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" "iCARE.buildbin-libdir/iCARE/libs/iCARE.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "iCARE.buildbin-libdir/iCARE/libs/iCARE.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "iCARE.buildbin-libdir/iCARE/libs/iCARE.so" >>>>>>> Paths after fix: iCARE.buildbin-libdir/iCARE/libs/iCARE.so: iCARE.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)