############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf predictionet.buildbin-libdir && mkdir predictionet.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh predictionet_1.38.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R predictionet.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=predictionet.buildbin-libdir predictionet_1.38.0.tar.gz' >>>>>>> * installing *source* package ‘predictionet’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c foo_mrmr.cpp -o foo_mrmr.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c mrnet_adapted.cpp -o mrnet_adapted.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c mrnet_adapted2.cpp -o mrnet_adapted2.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c mrnet_ensemble_standalone.cpp -o mrnet_ensemble_standalone.o mrnet_ensemble_standalone.cpp:111:7: warning: unused variable 'found' [-Wunused-variable] bool found=false; ^ mrnet_ensemble_standalone.cpp:283:6: warning: unused variable 'rootdepth' [-Wunused-variable] int rootdepth=tr.depth(it); ^ mrnet_ensemble_standalone.cpp:304:6: warning: unused variable 'rootdepth' [-Wunused-variable] int rootdepth=tr.depth(it); ^ mrnet_ensemble_standalone.cpp:377:16: warning: unused variable 'boot_val' [-Wunused-variable] double *mim, *boot_val; ^ mrnet_ensemble_standalone.cpp:507:7: warning: unused variable 'cnt_back' [-Wunused-variable] int cnt_back=cnt2; ^ mrnet_ensemble_standalone.cpp:442:7: warning: unused variable 'nsub' [-Wunused-variable] int nsub, *prev_sel,nsamples_boot=nsamples,*to_remove; ^ mrnet_ensemble_standalone.cpp:560:9: warning: unused variable 'max_val' [-Wunused-variable] double max_val=-1000; ^ mrnet_ensemble_standalone.cpp:586:48: warning: unused variable 'nprev_sel' [-Wunused-variable] int *nsub, *prev_sel,nsamples_boot=nsamples, nprev_sel=0; ^ mrnet_ensemble_standalone.cpp:777:13: warning: unused variable 'cnt2' [-Wunused-variable] int cnt=1,cnt2=0; ^ mrnet_ensemble_standalone.cpp:780:7: warning: unused variable 'rootdepth' [-Wunused-variable] int rootdepth=res_tree.depth(it_final); ^ mrnet_ensemble_standalone.cpp:794:7: warning: unused variable 'ind' [-Wunused-variable] int ind=0; ^ mrnet_ensemble_standalone.cpp:723:6: warning: unused variable 'vec_tmp' [-Wunused-variable] int vec_tmp; ^ mrnet_ensemble_standalone.cpp:722:39: warning: unused variable 'res_all2' [-Wunused-variable] int *predn, *rep_boot,*res,*res_all,*res_all2,*namat; ^ mrnet_ensemble_standalone.cpp:722:30: warning: unused variable 'res_all' [-Wunused-variable] int *predn, *rep_boot,*res,*res_all,*res_all2,*namat; ^ mrnet_ensemble_standalone.cpp:800:16: warning: variable 'res_old' is uninitialized when used here [-Wuninitialized] res_all[k]=res_old[k]; ^~~~~~~ mrnet_ensemble_standalone.cpp:793:25: note: initialize the variable 'res_old' to silence this warning int *res_all, *res_old; ^ = nullptr mrnet_ensemble_standalone.cpp:849:21: 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; ^ mrnet_ensemble_standalone.cpp:848:66: 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; ^ mrnet_ensemble_standalone.cpp:848:48: 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; ^ mrnet_ensemble_standalone.cpp:1046:13: warning: unused variable 'cnt2' [-Wunused-variable] int cnt=1,cnt2=0; ^ mrnet_ensemble_standalone.cpp:1049:7: warning: unused variable 'rootdepth' [-Wunused-variable] int rootdepth=res_tree.depth(it_final); ^ mrnet_ensemble_standalone.cpp:1063:7: warning: unused variable 'ind' [-Wunused-variable] int ind=0; ^ mrnet_ensemble_standalone.cpp:993:6: warning: unused variable 'vec_tmp' [-Wunused-variable] int vec_tmp; ^ mrnet_ensemble_standalone.cpp:992:30: warning: unused variable 'res_all' [-Wunused-variable] int *predn, *rep_boot,*res,*res_all,*res_all2, *namat; ^ mrnet_ensemble_standalone.cpp:992:39: warning: unused variable 'res_all2' [-Wunused-variable] int *predn, *rep_boot,*res,*res_all,*res_all2, *namat; ^ mrnet_ensemble_standalone.cpp:1067:16: warning: variable 'res_old' is uninitialized when used here [-Wuninitialized] res_all[k]=res_old[k]; ^~~~~~~ mrnet_ensemble_standalone.cpp:1062:25: note: initialize the variable 'res_old' to silence this warning int *res_all, *res_old; ^ = nullptr 25 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o predictionet.so foo_mrmr.o mrnet_adapted.o mrnet_adapted2.o mrnet_ensemble_standalone.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.13-bioc/meat/predictionet.buildbin-libdir/00LOCK-predictionet/00new/predictionet/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 (predictionet) >>>>>>> >>>>>>> FIXING LINKS FOR predictionet.buildbin-libdir/predictionet/libs/predictionet.so >>>>>>> install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgcc_s.1.dylib" "predictionet.buildbin-libdir/predictionet/libs/predictionet.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgfortran.5.dylib" "predictionet.buildbin-libdir/predictionet/libs/predictionet.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libquadmath.0.dylib" "predictionet.buildbin-libdir/predictionet/libs/predictionet.so"