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### Running command:
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### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL survcomp
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘survcomp’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c concordance.index.c -o concordance.index.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-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:12:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
12 | for( unsigned int i=0; i< size; ++i ) {
| ~^~~~~~
foo_mrmr_ensemble_surv.cpp:22:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
22 | 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]
106 | double uhs[Ns];
| ^~~
foo_mrmr_ensemble_surv.cpp:107:10: warning: variable ‘rphs’ set but not used [-Wunused-but-set-variable]
107 | 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:202:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
202 | for(unsigned int i=0; i< size_subset; ++i){
| ~^~~~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:203:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
203 | for(unsigned int j=0; j< (nvar-1); ++j){
| ~^~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:214:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
214 | for(unsigned int i=0; i< nvar-1; ++i){
| ~^~~~~~~~
foo_mrmr_ensemble_surv.cpp:216:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
216 | for(unsigned int j=i+1; j< nvar-1; ++j){
| ~^~~~~~~~
foo_mrmr_ensemble_surv.cpp:191:17: warning: unused variable ‘msurv_x’ [-Wunused-variable]
191 | 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]
191 | 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]
351 | int cnt_back=cnt2;
| ^~~~~~~~
foo_mrmr_ensemble_surv.cpp:286:7: warning: unused variable ‘nsub’ [-Wunused-variable]
286 | 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:393:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
393 | for(unsigned int k=0; k< rep_boot; ++k){
| ~^~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:396:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
396 | for(unsigned int i=1;i<= size_boot;++i){
| ~^~~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:400:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
400 | for( unsigned int i=0; i< size ; ++i ){
| ~^~~~~~
foo_mrmr_ensemble_surv.cpp:401:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
401 | for( unsigned int j=0; j< size ; ++j ){
| ~^~~~~~
foo_mrmr_ensemble_surv.cpp:412:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
412 | for(unsigned int i=0;i< rep_boot;++i){
| ~^~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:419:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
419 | for(unsigned int i=0;i< rep_boot;++i){
| ~^~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:387:10: warning: unused variable ‘mim’ [-Wunused-variable]
387 | 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:448:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
448 | 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]
437 | unsigned int jmax;
| ^~~~
foo_mrmr_ensemble_surv.cpp:439:9: warning: unused variable ‘max_val’ [-Wunused-variable]
439 | 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]
467 | 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:593:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
593 | for(unsigned int i=1;i<= nsamples;++i){
| ~^~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:596:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
596 | for( unsigned int i=0; i< n; ++i ){
| ~^~~
foo_mrmr_ensemble_surv.cpp:597:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
597 | for( unsigned int j=0; j< n; ++j ){
| ~^~~
foo_mrmr_ensemble_surv.cpp:604:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
604 | for(unsigned int k=0;k< max_elements ;++k){
| ~^~~~~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:646:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
646 | for (unsigned int i=0;i<=max_depth;++i){
| ~^~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:654:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
654 | for(unsigned int k=0;k< n;++k){
| ~^~~
foo_mrmr_ensemble_surv.cpp:657:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare]
657 | for(unsigned int k=0;k<=max(res_tmp_new.depth(it_local),max_depth) ;++k){
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:661:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
661 | for(unsigned int k=0;k< n;++k){
| ~^~~
foo_mrmr_ensemble_surv.cpp:578:24: warning: unused variable ‘nsamples_boot’ [-Wunused-variable]
578 | 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]
578 | 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]
578 | 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]
579 | 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]
579 | 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:786:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare]
786 | for(unsigned int i=0;i< *npredn;++i){
| ~^~~~~~~~~
foo_mrmr_ensemble_surv.cpp:820:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
820 | for(unsigned int k=0;k<length_res_old;k++){
| ~^~~~~~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:834:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
834 | for(unsigned int k=0;k<length_res;k++){
| ~^~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:839:7: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
839 | if(i==(*npredn-1)){
| ~^~~~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:843:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
843 | for(unsigned int k=0;k<length_res;k++){
| ~^~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:801:13: warning: unused variable ‘cnt2’ [-Wunused-variable]
801 | int cnt=1,cnt2=0;
| ^~~~
foo_mrmr_ensemble_surv.cpp:804:7: warning: unused variable ‘rootdepth’ [-Wunused-variable]
804 | int rootdepth=res_tree.depth(it_final);
| ^~~~~~~~~
foo_mrmr_ensemble_surv.cpp:817:7: warning: unused variable ‘ind’ [-Wunused-variable]
817 | int ind=0;
| ^~~
foo_mrmr_ensemble_surv.cpp:733:30: warning: unused variable ‘res_all’ [-Wunused-variable]
733 | int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
| ^~~~~~~
foo_mrmr_ensemble_surv.cpp:733:39: warning: unused variable ‘res_all2’ [-Wunused-variable]
733 | int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
| ^~~~~~~~
foo_mrmr_ensemble_surv.cpp:734:6: warning: unused variable ‘vec_tmp’ [-Wunused-variable]
734 | int vec_tmp;
| ^~~~~~~
foo_mrmr_ensemble_surv.cpp:859:9: warning: ‘Rres’ may be used uninitialized in this function [-Wmaybe-uninitialized]
859 | return Rres;
| ^~~~
foo_mrmr_ensemble_surv.cpp:821:25: warning: ‘res_old’ may be used uninitialized in this function [-Wmaybe-uninitialized]
821 | res_all[k]=res_old[k];
| ~~~~~~~~~^
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-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:12:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
12 | for( unsigned int i=0; i< size; ++i ) {
| ~^~~~~~
foo_mrmr_surv.cpp:22:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
22 | 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:49:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
49 | for(unsigned int i=0; i< size_subset; ++i){
| ~^~~~~~~~~~~~~
foo_mrmr_surv.cpp:50:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
50 | for(unsigned int j=0; j< nvar; ++j){
| ~^~~~~~
foo_mrmr_surv.cpp:56:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
56 | for(unsigned int i=0; i< nvar; ++i){
| ~^~~~~~
foo_mrmr_surv.cpp:58:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
58 | 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]
146 | double uhs[Ns];
| ^~~
foo_mrmr_surv.cpp:147:10: warning: variable ‘rphs’ set but not used [-Wunused-but-set-variable]
147 | double rphs[Ns];
| ^~~~
foo_mrmr_surv.cpp: In function ‘SEXPREC* mrmr_cIndex(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
foo_mrmr_surv.cpp:301:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare]
301 | for(unsigned int i=0;i < *nsample; ++i){
| ~~^~~~~~~~~~
foo_mrmr_surv.cpp:341:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
341 | for( int l=0; l<n; ++l )
| ~^~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c survcomp_init.cpp -o survcomp_init.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o survcomp.so concordance.index.o foo_mrmr_ensemble_surv.o foo_mrmr_surv.o survcomp_init.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/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)
