############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf SUITOR.buildbin-libdir && mkdir SUITOR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SUITOR_1.6.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SUITOR.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SUITOR.buildbin-libdir SUITOR_1.6.0.tar.gz' >>>>>>> * installing *source* package ‘SUITOR’ ... ** 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 SUITOR_init.c -o SUITOR_init.o 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:166:17: 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:185:14: 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 * iVec_alloc(n, initFlag, initVal) ^ source.c:203:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] static char * cVec_alloc(n, initFlag, initVal) ^ source.c:222:13: 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 copy_dVec(v, n, ret) ^ source.c:233:13: 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 matrixMult(m1, m1_nr, m1_nc, m2, m2_nc, ret) ^ 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 which_max(v, n) ^ source.c:280:13: 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 which_max_cols(mat, nr, nc, ret) ^ source.c:292:12: 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 update_cons(cons, cons_len, index, nc) ^ source.c:323:12: 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 myStopFun(cons, cons_len, inc, hMat, hnr, hnc, maxIndex) ^ source.c:348:13: 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_runif_vec(v, n, a, b) ^ source.c:359:12: 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_idxMat0(idx, nr, nc, k, kfold) ^ source.c:385:15: 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 loglike(input, log_input, input_k_hat, idxMat, delta_denom, len, which_idx) ^ source.c:416:13: 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 replaceZeroVal_dVec(v, n, minval) ^ source.c:428:15: 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 get_delta_denom(v, n) ^ source.c:444:15: 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 get_max(v, n) ^ source.c:460:13: 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 my_update_H(pV, w, h, wnr, wnc, hnc) ^ source.c:539:13: 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 my_update_W(pV, w, h, wnr, wnc, hnc) ^ source.c:611:13: 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 my_update_brunet(i, x, w, h, str) ^ source.c:636:13: 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_init_WH(runifVec, w, h, wlen, hlen, maxval) ^ source.c:655:13: 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 call_nmf(mat, str) ^ source.c:714:13: 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 update_x_k(x_k, x_k_hat, idxMat, n) ^ source.c:838:15: 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 get_median(v, n) ^ source.c:863:13: 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_init_x_k(x, x_k, idxMat, nr, nc, tmpvec, minvalue) ^ source.c:916:13: 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_colsums(x, nr, nc, ret) ^ source.c:934:13: 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 transpose(v, nr, nc, ret) ^ source.c:949:13: 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 ECM_update_h(h1, h0, w0, x_k, hnr, hnc, wnr, wnc, xnr, xnc, vM, vN, vN2) ^ source.c:983:13: 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 ECM_update_w(w1, h1, w0, x_k, hnr, hnc, wnr, wnc, xnr, xnc, vM, vN, vN2) ^ source.c:1017:12: 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 ECM_alg(str) ^ source.c:1093:13: 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 init_wh_rank(str, rank) ^ source.c:1119:13: 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 suitor_main(str) ^ source.c:1203:13: 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 init_logx(x, logx, n) ^ source.c:1221:13: 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 NMFSTR_init(str, iargs, dargs, xmat) ^ source.c:1311:13: 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 NMFSTR_free(str, EMflag) ^ source.c:1339:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] void C_call_nmf(mat, iargs, dargs, retW, retH) ^ source.c:1361:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] void C_call_suitor(mat, iargs, dargs, rankVec, kVec, ret_train, ret_test, ret_convVec, ret_EM_niterVec) ^ 35 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 SUITOR.so SUITOR_init.o source.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.19-bioc/meat/SUITOR.buildbin-libdir/00LOCK-SUITOR/00new/SUITOR/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 (SUITOR) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR SUITOR.buildbin-libdir/SUITOR/libs/SUITOR.so >>>>>>> >>>>>>> Paths before fix: SUITOR.buildbin-libdir/SUITOR/libs/SUITOR.so: SUITOR.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" "SUITOR.buildbin-libdir/SUITOR/libs/SUITOR.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "SUITOR.buildbin-libdir/SUITOR/libs/SUITOR.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "SUITOR.buildbin-libdir/SUITOR/libs/SUITOR.so" >>>>>>> Paths after fix: SUITOR.buildbin-libdir/SUITOR/libs/SUITOR.so: SUITOR.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)