############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf survcomp.buildbin-libdir && mkdir survcomp.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh survcomp_1.57.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R survcomp.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=survcomp.buildbin-libdir survcomp_1.57.0.tar.gz' >>>>>>> * installing *source* package ‘survcomp’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c concordance.index.c -o concordance.index.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c foo_mrmr_ensemble_surv.cpp -o foo_mrmr_ensemble_surv.o foo_mrmr_ensemble_surv.cpp:191:17: warning: unused variable 'msurv_x' [-Wunused-variable] int *namat_x, *msurv_x, *ustrat_x, *cl2_x, *se_x, *strat_x; ^ foo_mrmr_ensemble_surv.cpp:191:27: warning: unused variable 'ustrat_x' [-Wunused-variable] int *namat_x, *msurv_x, *ustrat_x, *cl2_x, *se_x, *strat_x; ^ foo_mrmr_ensemble_surv.cpp:351:7: warning: unused variable 'cnt_back' [-Wunused-variable] int cnt_back=cnt2; ^ foo_mrmr_ensemble_surv.cpp:286:7: warning: unused variable 'nsub' [-Wunused-variable] int nsub, *prev_sel,nsamples_boot=nsamples,*to_remove; ^ foo_mrmr_ensemble_surv.cpp:387:10: warning: unused variable 'mim' [-Wunused-variable] double *mim, *boot_val, *mat_info; ^ foo_mrmr_ensemble_surv.cpp:437:15: warning: variable 'jmax' set but not used [-Wunused-but-set-variable] unsigned int jmax; ^ foo_mrmr_ensemble_surv.cpp:439:9: warning: unused variable 'max_val' [-Wunused-variable] double max_val=-1000; ^ foo_mrmr_ensemble_surv.cpp:467:7: warning: unused variable 'found' [-Wunused-variable] bool found=false; ^ foo_mrmr_ensemble_surv.cpp:579:21: warning: unused variable 'vec_sort' [-Wunused-variable] double *vec_mean, *vec_sort, *vec_sd, *vec_local_max_mean, *vec_local_max_sd,tmp_val_max, *mrmr_vec_sort,*vec_sol_local_mrmr; ^ foo_mrmr_ensemble_surv.cpp:579:63: warning: variable 'vec_local_max_sd' set but not used [-Wunused-but-set-variable] double *vec_mean, *vec_sort, *vec_sd, *vec_local_max_mean, *vec_local_max_sd,tmp_val_max, *mrmr_vec_sort,*vec_sol_local_mrmr; ^ foo_mrmr_ensemble_surv.cpp:578:24: warning: unused variable 'nsamples_boot' [-Wunused-variable] int *nsub, *prev_sel,nsamples_boot=nsamples, tmp_val_max_ind, *prev_sel_tmp,*vec_sol_local,ndelete; ^ foo_mrmr_ensemble_surv.cpp:578:48: warning: unused variable 'tmp_val_max_ind' [-Wunused-variable] int *nsub, *prev_sel,nsamples_boot=nsamples, tmp_val_max_ind, *prev_sel_tmp,*vec_sol_local,ndelete; ^ foo_mrmr_ensemble_surv.cpp:578:66: warning: unused variable 'prev_sel_tmp' [-Wunused-variable] int *nsub, *prev_sel,nsamples_boot=nsamples, tmp_val_max_ind, *prev_sel_tmp,*vec_sol_local,ndelete; ^ foo_mrmr_ensemble_surv.cpp:801:13: warning: unused variable 'cnt2' [-Wunused-variable] int cnt=1,cnt2=0; ^ foo_mrmr_ensemble_surv.cpp:817:7: warning: unused variable 'ind' [-Wunused-variable] int ind=0; ^ foo_mrmr_ensemble_surv.cpp:804:7: warning: unused variable 'rootdepth' [-Wunused-variable] int rootdepth=res_tree.depth(it_final); ^ foo_mrmr_ensemble_surv.cpp:733:30: warning: unused variable 'res_all' [-Wunused-variable] int *predn, *rep_boot,*res,*res_all,*res_all2, *namat; ^ foo_mrmr_ensemble_surv.cpp:733:39: warning: unused variable 'res_all2' [-Wunused-variable] int *predn, *rep_boot,*res,*res_all,*res_all2, *namat; ^ foo_mrmr_ensemble_surv.cpp:734:6: warning: unused variable 'vec_tmp' [-Wunused-variable] int vec_tmp; ^ foo_mrmr_ensemble_surv.cpp:821:16: warning: variable 'res_old' is uninitialized when used here [-Wuninitialized] res_all[k]=res_old[k]; ^~~~~~~ foo_mrmr_ensemble_surv.cpp:816:25: note: initialize the variable 'res_old' to silence this warning int *res_all, *res_old; ^ = nullptr In file included from foo_mrmr_ensemble_surv.cpp:1: In file included from ./foo_mrmr_ensemble_surv.h:10: ./tree.h:505:18: warning: 'allocate' is deprecated [-Wdeprecated-declarations] head = alloc_.allocate(1,0); // MSVC does not have default second argument ^ ./tree.h:530:2: note: in instantiation of member function 'tree::head_initialise_' requested here head_initialise_(); ^ foo_mrmr_ensemble_surv.cpp:611:24: note: in instantiation of member function 'tree::tree' requested here tree res_tmp_new=res ; ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1668:61: note: 'allocate' has been explicitly marked deprecated here _LIBCPP_NODISCARD_AFTER_CXX17 _LIBCPP_INLINE_VISIBILITY _LIBCPP_DEPRECATED_IN_CXX17 ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1058:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from foo_mrmr_ensemble_surv.cpp:1: In file included from ./foo_mrmr_ensemble_surv.h:10: ./tree.h:506:16: warning: 'allocate' is deprecated [-Wdeprecated-declarations] feet = alloc_.allocate(1,0); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1668:61: note: 'allocate' has been explicitly marked deprecated here _LIBCPP_NODISCARD_AFTER_CXX17 _LIBCPP_INLINE_VISIBILITY _LIBCPP_DEPRECATED_IN_CXX17 ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1058:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from foo_mrmr_ensemble_surv.cpp:1: In file included from ./foo_mrmr_ensemble_surv.h:10: ./tree.h:1122:26: warning: 'allocate' is deprecated [-Wdeprecated-declarations] tree_node* tmp = alloc_.allocate(1,0); ^ ./tree.h:547:6: note: in instantiation of function template specialization 'tree::replace::pre_order_iterator>' requested here to=replace(to, it); ^ ./tree.h:531:2: note: in instantiation of member function 'tree::copy_' requested here copy_(other); ^ foo_mrmr_ensemble_surv.cpp:611:24: note: in instantiation of member function 'tree::tree' requested here tree res_tmp_new=res ; ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1668:61: note: 'allocate' has been explicitly marked deprecated here _LIBCPP_NODISCARD_AFTER_CXX17 _LIBCPP_INLINE_VISIBILITY _LIBCPP_DEPRECATED_IN_CXX17 ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1058:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from foo_mrmr_ensemble_surv.cpp:1: In file included from ./foo_mrmr_ensemble_surv.h:10: ./tree.h:505:18: warning: 'allocate' is deprecated [-Wdeprecated-declarations] head = alloc_.allocate(1,0); // MSVC does not have default second argument ^ ./tree.h:476:2: note: in instantiation of member function 'tree::head_initialise_' requested here head_initialise_(); ^ foo_mrmr_ensemble_surv.cpp:620:15: note: in instantiation of member function 'tree::tree' requested here tree res_mrmr; ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1668:61: note: 'allocate' has been explicitly marked deprecated here _LIBCPP_NODISCARD_AFTER_CXX17 _LIBCPP_INLINE_VISIBILITY _LIBCPP_DEPRECATED_IN_CXX17 ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1058:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from foo_mrmr_ensemble_surv.cpp:1: In file included from ./foo_mrmr_ensemble_surv.h:10: ./tree.h:506:16: warning: 'allocate' is deprecated [-Wdeprecated-declarations] feet = alloc_.allocate(1,0); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1668:61: note: 'allocate' has been explicitly marked deprecated here _LIBCPP_NODISCARD_AFTER_CXX17 _LIBCPP_INLINE_VISIBILITY _LIBCPP_DEPRECATED_IN_CXX17 ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1058:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from foo_mrmr_ensemble_surv.cpp:1: In file included from ./foo_mrmr_ensemble_surv.h:10: ./tree.h:998:26: warning: 'allocate' is deprecated [-Wdeprecated-declarations] tree_node* tmp = alloc_.allocate(1,0); ^ foo_mrmr_ensemble_surv.cpp:625:11: note: in instantiation of function template specialization 'tree::insert::pre_order_iterator>' requested here res_mrmr.insert(top_mrmr, predn); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1668:61: note: 'allocate' has been explicitly marked deprecated here _LIBCPP_NODISCARD_AFTER_CXX17 _LIBCPP_INLINE_VISIBILITY _LIBCPP_DEPRECATED_IN_CXX17 ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1058:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from foo_mrmr_ensemble_surv.cpp:1: In file included from ./foo_mrmr_ensemble_surv.h:10: ./tree.h:886:26: warning: 'allocate' is deprecated [-Wdeprecated-declarations] tree_node* tmp = alloc_.allocate(1,0); ^ foo_mrmr_ensemble_surv.cpp:690:17: note: in instantiation of function template specialization 'tree::append_child::pre_order_iterator>' requested here res_tmp_new.append_child(it_local,vec_sol_local[k]); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1668:61: note: 'allocate' has been explicitly marked deprecated here _LIBCPP_NODISCARD_AFTER_CXX17 _LIBCPP_INLINE_VISIBILITY _LIBCPP_DEPRECATED_IN_CXX17 ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1058:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from foo_mrmr_ensemble_surv.cpp:1: In file included from ./foo_mrmr_ensemble_surv.h:10: ./tree.h:886:26: warning: 'allocate' is deprecated [-Wdeprecated-declarations] tree_node* tmp = alloc_.allocate(1,0); ^ foo_mrmr_ensemble_surv.cpp:691:14: note: in instantiation of function template specialization 'tree::append_child::pre_order_iterator>' requested here res_mrmr.append_child(it_mrmr_local,vec_sol_local_mrmr[k]); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1668:61: note: 'allocate' has been explicitly marked deprecated here _LIBCPP_NODISCARD_AFTER_CXX17 _LIBCPP_INLINE_VISIBILITY _LIBCPP_DEPRECATED_IN_CXX17 ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1058:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ In file included from foo_mrmr_ensemble_surv.cpp:1: In file included from ./foo_mrmr_ensemble_surv.h:10: ./tree.h:998:26: warning: 'allocate' is deprecated [-Wdeprecated-declarations] tree_node* tmp = alloc_.allocate(1,0); ^ foo_mrmr_ensemble_surv.cpp:788:16: note: in instantiation of function template specialization 'tree::insert::pre_order_iterator>' requested here one=res_tree.insert(top, predn[i]); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1668:61: note: 'allocate' has been explicitly marked deprecated here _LIBCPP_NODISCARD_AFTER_CXX17 _LIBCPP_INLINE_VISIBILITY _LIBCPP_DEPRECATED_IN_CXX17 ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1058:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17' # define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED' # define _LIBCPP_DEPRECATED __attribute__ ((deprecated)) ^ 29 warnings generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c foo_mrmr_surv.cpp -o foo_mrmr_surv.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c survcomp_init.cpp -o survcomp_init.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o survcomp.so concordance.index.o foo_mrmr_ensemble_surv.o foo_mrmr_surv.o survcomp_init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.21-bioc/meat/survcomp.buildbin-libdir/00LOCK-survcomp/00new/survcomp/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 (survcomp) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR survcomp.buildbin-libdir/survcomp/libs/survcomp.so >>>>>>> >>>>>>> Paths before fix: survcomp.buildbin-libdir/survcomp/libs/survcomp.so: survcomp.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0) /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/4.5-x86_64/Resources/lib/libgcc_s.1.1.dylib" "survcomp.buildbin-libdir/survcomp/libs/survcomp.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "survcomp.buildbin-libdir/survcomp/libs/survcomp.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "survcomp.buildbin-libdir/survcomp/libs/survcomp.so" >>>>>>> Paths after fix: survcomp.buildbin-libdir/survcomp/libs/survcomp.so: survcomp.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0) /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)