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This page was generated on 2023-04-19 11:01:58 -0400 (Wed, 19 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnsonmacOS 13.0 Venturaarm644.2.2 (2022-10-31) -- "Innocent and Trusting" 4256
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BUILD BIN results for survcomp on kjohnson


To the developers/maintainers of the survcomp package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1997/2183HostnameOS / ArchINSTALLBUILDBUILD BIN
survcomp 1.48.0  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2023-04-12 13:00:02 -0400 (Wed, 12 Apr 2023)
git_url: https://git.bioconductor.org/packages/survcomp
git_branch: RELEASE_3_16
git_last_commit: 85135e0
git_last_commit_date: 2022-11-01 11:05:46 -0400 (Tue, 01 Nov 2022)
kjohnsonmacOS 13.0 Ventura / arm64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: survcomp
Version: 1.48.0
Command: rm -rf survcomp.buildbin-libdir && mkdir survcomp.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh survcomp_1.48.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R survcomp.buildbin-libdir
StartedAt: 2023-04-18 20:00:00 -0400 (Tue, 18 Apr 2023)
EndedAt: 2023-04-18 20:00:31 -0400 (Tue, 18 Apr 2023)
EllapsedTime: 31.4 seconds
RetCode: 0
Status:   OK  
PackageFile: survcomp_1.48.0.tgz
PackageFileSize: 822.8 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf survcomp.buildbin-libdir && mkdir survcomp.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh survcomp_1.48.0.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_1.48.0.tar.gz'
>>>>>>> 

* installing *source* package ‘survcomp’ ...
** using staged installation
** libs
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c concordance.index.c -o concordance.index.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -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:439:9: warning: unused variable 'max_val' [-Wunused-variable]
        double max_val=-1000;
               ^
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:467:7: warning: unused variable 'found' [-Wunused-variable]
        bool found=false;
             ^
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: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: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:578:66: 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: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:804:7: warning: unused variable 'rootdepth' [-Wunused-variable]
                int rootdepth=res_tree.depth(it_final);
                    ^
foo_mrmr_ensemble_surv.cpp:817:7: warning: unused variable 'ind' [-Wunused-variable]
                int ind=0;
                    ^
foo_mrmr_ensemble_surv.cpp:801:13: warning: unused variable 'cnt2' [-Wunused-variable]
                int cnt=1,cnt2=0;
                          ^
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:733:30: warning: unused variable 'res_all' [-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
20 warnings generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c foo_mrmr_surv.cpp -o foo_mrmr_surv.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c survcomp_init.cpp -o survcomp_init.o
clang++ -arch arm64 -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/opt/R/arm64/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
ld: warning: -undefined dynamic_lookup may not work with chained fixups
installing to /Volumes/External/bbs-3.16-bioc-m1/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 LINKS FOR survcomp.buildbin-libdir/survcomp/libs/survcomp.so
>>>>>>> 

install_name_tool -change "/opt/R/arm64/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgcc_s.1.1.dylib" "survcomp.buildbin-libdir/survcomp/libs/survcomp.so"
install_name_tool -change "/opt/R/arm64/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgfortran.5.dylib" "survcomp.buildbin-libdir/survcomp/libs/survcomp.so"
install_name_tool -change "/opt/R/arm64/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libquadmath.0.dylib" "survcomp.buildbin-libdir/survcomp/libs/survcomp.so"