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BioC 3.5: BUILD BIN report for survcomp on toluca2

This page was generated on 2017-04-23 14:35:42 -0400 (Sun, 23 Apr 2017).

Package 1285/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
survcomp 1.25.0
Benjamin Haibe-Kains , Markus Schroeder , Catharina Olsen
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/survcomp
Last Changed Rev: 122712 / Revision: 129046
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK [ OK ]
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: survcomp
Version: 1.25.0
Command: rm -rf survcomp.buildbin-libdir && mkdir survcomp.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh survcomp_1.25.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R survcomp.buildbin-libdir
StartedAt: 2017-04-23 12:48:10 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 12:48:32 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 21.8 seconds
RetCode: 0
Status:  OK 
PackageFile: survcomp_1.25.0.tgz
PackageFileSize: 757.3 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf survcomp.buildbin-libdir && mkdir survcomp.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh survcomp_1.25.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R survcomp.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=survcomp.buildbin-libdir survcomp_1.25.0.tar.gz'
>>>>>>> 

* installing *source* package ‘survcomp’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c concordance.index.c -o concordance.index.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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:467:7: warning: unused variable 'found' [-Wunused-variable]
        bool found=false;
             ^
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: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: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:800:13: warning: unused variable 'cnt2' [-Wunused-variable]
                int cnt=1,cnt2=0;
                          ^
foo_mrmr_ensemble_surv.cpp:803:7: warning: unused variable 'rootdepth' [-Wunused-variable]
                int rootdepth=res_tree.depth(it_final);
                    ^
foo_mrmr_ensemble_surv.cpp:816:7: warning: unused variable 'ind' [-Wunused-variable]
                int ind=0;
                    ^
foo_mrmr_ensemble_surv.cpp:732:30: warning: unused variable 'res_all' [-Wunused-variable]
        int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
                                    ^
foo_mrmr_ensemble_surv.cpp:732:39: warning: unused variable 'res_all2' [-Wunused-variable]
        int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
                                             ^
foo_mrmr_ensemble_surv.cpp:733:6: warning: unused variable 'vec_tmp' [-Wunused-variable]
        int vec_tmp;
            ^
foo_mrmr_ensemble_surv.cpp:820:16: warning: variable 'res_old' is uninitialized when used here [-Wuninitialized]
                                res_all[k]=res_old[k];
                                           ^˜˜˜˜˜˜
foo_mrmr_ensemble_surv.cpp:815:25: note: initialize the variable 'res_old' to silence this warning
                int *res_all, *res_old;
                                      ^
                                       = NULL
18 warnings generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c foo_mrmr_surv.cpp -o foo_mrmr_surv.o
clang++ -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 survcomp.so concordance.index.o foo_mrmr_ensemble_surv.o foo_mrmr_surv.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/survcomp.buildbin-libdir/survcomp/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (survcomp)


>>>>>>> 
>>>>>>> FIXING LINKS FOR survcomp.buildbin-libdir/survcomp/libs//survcomp.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgcc_s.1.dylib" "survcomp.buildbin-libdir/survcomp/libs//survcomp.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "survcomp.buildbin-libdir/survcomp/libs//survcomp.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.5.2.dylib" "survcomp.buildbin-libdir/survcomp/libs//survcomp.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "survcomp.buildbin-libdir/survcomp/libs//survcomp.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "survcomp.buildbin-libdir/survcomp/libs//survcomp.so"