BioC 2.14: BUILD BIN report for survcomp on petty

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf survcomp.buildbin-libdir && mkdir survcomp.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh survcomp_1.14.0.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_1.14.0.tar.gz'
>>>>>>> 

* installing *source* package ‘survcomp’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c concordance.index.c -o concordance.index.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c foo_mrmr_ensemble_surv.cpp -o foo_mrmr_ensemble_surv.o
foo_mrmr_ensemble_surv.cpp: In function ‘double get_correlation_ensemble(double*, int*, int, int, int)’:
foo_mrmr_ensemble_surv.cpp:12: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:22: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp: In function ‘void build_mim_cIndex_subset(double*, double*, int*, int, int, int*, int, int*, int*, int*, double*, int*, double*, int*, int*, int*, int*)’:
foo_mrmr_ensemble_surv.cpp:202: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:203: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:214: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:216: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:191: warning: unused variable ‘msurv_x’
foo_mrmr_ensemble_surv.cpp:191: warning: unused variable ‘ustrat_x’
foo_mrmr_ensemble_surv.cpp: In function ‘void bootstrap_tree(tree<int, std::allocator<tree_node_<int> > >&, tree<double, std::allocator<tree_node_<double> > >&, double*, int*, int, int, int, int*, int*, int*, double*, int*, double*, int*, int*, int*, int, int*)’:
foo_mrmr_ensemble_surv.cpp:351: warning: unused variable ‘cnt_back’
foo_mrmr_ensemble_surv.cpp:286: warning: unused variable ‘nsub’
foo_mrmr_ensemble_surv.cpp: In function ‘void bootstrap_mrmr(double&, double&, double*, int*, int, int, int, int, int, int, int, int*, int*, int*, int*, double*, int*, double*, int*, int*, int*, int, int*)’:
foo_mrmr_ensemble_surv.cpp:393: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:396: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:400: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:401: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:412: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:419: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:387: warning: unused variable ‘mim’
foo_mrmr_ensemble_surv.cpp: In function ‘double mrnet_onegene(double*, int, int, int*, int, int)’:
foo_mrmr_ensemble_surv.cpp:448: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:439: warning: unused variable ‘max_val’
foo_mrmr_ensemble_surv.cpp: In function ‘int verify_equivalentset_nparents(tree<int, std::allocator<tree_node_<int> > >&, tree<int, std::allocator<tree_node_<int> > >::pre_order_iterator, tree<int, std::allocator<tree_node_<int> > >::pre_order_iterator, tree<double, std::allocator<tree_node_<double> > >&, int)’:
foo_mrmr_ensemble_surv.cpp:467: warning: unused variable ‘found’
foo_mrmr_ensemble_surv.cpp: In function ‘void mrmr_ensemble_one_gene_remove(tree<int, std::allocator<tree_node_<int> > >&, tree<int, std::allocator<tree_node_<int> > >::pre_order_iterator, double*, int*, int, int, int, int, int, int, double, int*, int*, int*, double*, int*, double*, int*, int*, int*, int, int*)’:
foo_mrmr_ensemble_surv.cpp:593: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:596: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:597: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:604: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:646: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:654: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:657: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:661: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:578: warning: unused variable ‘nsamples_boot’
foo_mrmr_ensemble_surv.cpp:578: warning: unused variable ‘tmp_val_max_ind’
foo_mrmr_ensemble_surv.cpp:578: warning: unused variable ‘prev_sel_tmp’
foo_mrmr_ensemble_surv.cpp:579: warning: unused variable ‘vec_sort’
foo_mrmr_ensemble_surv.cpp: In function ‘SEXPREC* mrmr_cIndex_ensemble_remove(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
foo_mrmr_ensemble_surv.cpp:785: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:819: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:833: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:838: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:842: warning: comparison between signed and unsigned integer expressions
foo_mrmr_ensemble_surv.cpp:800: warning: unused variable ‘cnt2’
foo_mrmr_ensemble_surv.cpp:803: warning: unused variable ‘rootdepth’
foo_mrmr_ensemble_surv.cpp:816: warning: unused variable ‘ind’
foo_mrmr_ensemble_surv.cpp:732: warning: unused variable ‘res_all’
foo_mrmr_ensemble_surv.cpp:732: warning: unused variable ‘res_all2’
foo_mrmr_ensemble_surv.cpp:733: warning: unused variable ‘vec_tmp’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c foo_mrmr_surv.cpp -o foo_mrmr_surv.o
foo_mrmr_surv.cpp: In function ‘double get_correlation(double*, int*, int, int, int)’:
foo_mrmr_surv.cpp:12: warning: comparison between signed and unsigned integer expressions
foo_mrmr_surv.cpp:22: warning: comparison between signed and unsigned integer expressions
foo_mrmr_surv.cpp: In function ‘void build_mim_subset(double*, double*, int*, int, int, int*, int)’:
foo_mrmr_surv.cpp:49: warning: comparison between signed and unsigned integer expressions
foo_mrmr_surv.cpp:50: warning: comparison between signed and unsigned integer expressions
foo_mrmr_surv.cpp:56: warning: comparison between signed and unsigned integer expressions
foo_mrmr_surv.cpp:58: warning: comparison between signed and unsigned integer expressions
foo_mrmr_surv.cpp: In function ‘SEXPREC* mrmr_cIndex(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
foo_mrmr_surv.cpp:300: warning: comparison between signed and unsigned integer expressions
foo_mrmr_surv.cpp:340: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/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-2.14-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/3.1/Resources/lib/libgcc_s.1.dylib" "survcomp.buildbin-libdir/survcomp/libs//survcomp.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgfortran.2.dylib" "survcomp.buildbin-libdir/survcomp/libs//survcomp.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/lib/libreadline.dylib" "survcomp.buildbin-libdir/survcomp/libs//survcomp.so"
BioC 2.14: BUILD BIN report for survcomp on petty

Summary

Command output
