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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD INSTALL survcomp
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* installing to library ‘/home/biocbuild/bbs-3.2-bioc/R/library’
* installing *source* package ‘survcomp’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c concordance.index.c -o concordance.index.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -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:12:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for( unsigned int i=0; i< size; ++i ) {
^
foo_mrmr_ensemble_surv.cpp:22:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for( unsigned int i=0; i< size; ++i ) {
^
foo_mrmr_ensemble_surv.cpp: In function ‘double returnConcordanceIndexC(int*, int*, double*, int*, double*, int*, double*, int*, int*, int*, int, int*)’:
foo_mrmr_ensemble_surv.cpp:106:10: warning: variable ‘uhs’ set but not used [-Wunused-but-set-variable]
double uhs[Ns];
^
foo_mrmr_ensemble_surv.cpp:107:10: warning: variable ‘rphs’ set but not used [-Wunused-but-set-variable]
double rphs[Ns];
^
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:202:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int i=0; i< size_subset; ++i){
^
foo_mrmr_ensemble_surv.cpp:203:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int j=0; j< (nvar-1); ++j){
^
foo_mrmr_ensemble_surv.cpp:214:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int i=0; i< nvar-1; ++i){
^
foo_mrmr_ensemble_surv.cpp:216:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int j=i+1; j< nvar-1; ++j){
^
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: In function ‘void bootstrap_tree(tree<int>&, tree<double>&, double*, int*, int, int, int, int*, int*, int*, double*, int*, double*, int*, int*, int*, int, int*)’:
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: 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:393:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int k=0; k< rep_boot; ++k){
^
foo_mrmr_ensemble_surv.cpp:396:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int i=1;i<= size_boot;++i){
^
foo_mrmr_ensemble_surv.cpp:400:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for( unsigned int i=0; i< size ; ++i ){
^
foo_mrmr_ensemble_surv.cpp:401:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for( unsigned int j=0; j< size ; ++j ){
^
foo_mrmr_ensemble_surv.cpp:412:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int i=0;i< rep_boot;++i){
^
foo_mrmr_ensemble_surv.cpp:419:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int i=0;i< rep_boot;++i){
^
foo_mrmr_ensemble_surv.cpp:387:10: warning: unused variable ‘mim’ [-Wunused-variable]
double *mim, *boot_val, *mat_info;
^
foo_mrmr_ensemble_surv.cpp: In function ‘double mrnet_onegene(double*, int, int, int*, int, int)’:
foo_mrmr_ensemble_surv.cpp:448:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int j=0;j< nbvar; j++){
^
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: In function ‘int verify_equivalentset_nparents(tree<int>&, tree<int>::pre_order_iterator, tree<int>::pre_order_iterator, tree<double>&, int)’:
foo_mrmr_ensemble_surv.cpp:467:7: warning: unused variable ‘found’ [-Wunused-variable]
bool found=false;
^
foo_mrmr_ensemble_surv.cpp: In function ‘void mrmr_ensemble_one_gene_remove(tree<int>&, tree<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:593:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int i=1;i<= nsamples;++i){
^
foo_mrmr_ensemble_surv.cpp:596:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for( unsigned int i=0; i< n; ++i ){
^
foo_mrmr_ensemble_surv.cpp:597:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for( unsigned int j=0; j< n; ++j ){
^
foo_mrmr_ensemble_surv.cpp:604:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int k=0;k< max_elements ;++k){
^
foo_mrmr_ensemble_surv.cpp:646:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (unsigned int i=0;i<=max_depth;++i){
^
foo_mrmr_ensemble_surv.cpp:654:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int k=0;k< n;++k){
^
foo_mrmr_ensemble_surv.cpp:657:69: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int k=0;k<=max(res_tmp_new.depth(it_local),max_depth) ;++k){
^
foo_mrmr_ensemble_surv.cpp:661:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int k=0;k< n;++k){
^
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: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: In function ‘SEXPREC* mrmr_cIndex_ensemble_remove(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
foo_mrmr_ensemble_surv.cpp:785:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int i=0;i< *npredn;++i){
^
foo_mrmr_ensemble_surv.cpp:819:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int k=0;k<length_res_old;k++){
^
foo_mrmr_ensemble_surv.cpp:833:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int k=0;k<length_res;k++){
^
foo_mrmr_ensemble_surv.cpp:838:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(i==(*npredn-1)){
^
foo_mrmr_ensemble_surv.cpp:842:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int k=0;k<length_res;k++){
^
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:858:9: warning: ‘Rres’ may be used uninitialized in this function [-Wmaybe-uninitialized]
return Rres;
^
foo_mrmr_ensemble_surv.cpp:820:25: warning: ‘res_old’ may be used uninitialized in this function [-Wmaybe-uninitialized]
res_all[k]=res_old[k];
^
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -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:12:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for( unsigned int i=0; i< size; ++i ) {
^
foo_mrmr_surv.cpp:22:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for( unsigned int i=0; i< size; ++i ) {
^
foo_mrmr_surv.cpp: In function ‘void build_mim_subset(double*, double*, int*, int, int, int*, int)’:
foo_mrmr_surv.cpp:49:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int i=0; i< size_subset; ++i){
^
foo_mrmr_surv.cpp:50:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int j=0; j< nvar; ++j){
^
foo_mrmr_surv.cpp:56:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int i=0; i< nvar; ++i){
^
foo_mrmr_surv.cpp:58:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int j=i+1; j< nvar; ++j){
^
foo_mrmr_surv.cpp: In function ‘double returnConcordanceIndexC(int*, int*, double*, int*, double*, int*, double*, int*, int*, int*, int*, int*)’:
foo_mrmr_surv.cpp:146:10: warning: variable ‘uhs’ set but not used [-Wunused-but-set-variable]
double uhs[Ns];
^
foo_mrmr_surv.cpp:147:10: warning: variable ‘rphs’ set but not used [-Wunused-but-set-variable]
double rphs[Ns];
^
foo_mrmr_surv.cpp: In function ‘SEXPREC* mrmr_cIndex(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
foo_mrmr_surv.cpp:300:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int i=0;i < *nsample; ++i){
^
foo_mrmr_surv.cpp:340:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for( int l=0; l<n; ++l )
^
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o survcomp.so concordance.index.o foo_mrmr_ensemble_surv.o foo_mrmr_surv.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/R/library/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)
