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###
### Running command:
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### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL predictionet
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘predictionet’ ...
** using staged installation
** libs
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.cpp -o foo_mrmr.o
foo_mrmr.cpp: In function ‘double get_correlation(double*, int*, int, int, int)’:
foo_mrmr.cpp:13:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
13 | for( unsigned int i=0; i< size; ++i ) {
| ~^~~~~~
foo_mrmr.cpp:23:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
23 | for( unsigned int i=0; i< size; ++i ) {
| ~^~~~~~
foo_mrmr.cpp: In function ‘void build_mim_subset(double*, double*, int*, int, int, int*, int)’:
foo_mrmr.cpp:50:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
50 | for(unsigned int i=0; i< size_subset; ++i){
| ~^~~~~~~~~~~~~
foo_mrmr.cpp:51:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
51 | for(unsigned int j=0; j< nvar; ++j){
| ~^~~~~~
foo_mrmr.cpp:57:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
57 | for(unsigned int i=0; i< nvar; ++i){
| ~^~~~~~
foo_mrmr.cpp:59:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
59 | for(unsigned int j=i+1; j< nvar; ++j){
| ~^~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c mrnet_adapted.cpp -o mrnet_adapted.o
mrnet_adapted.cpp: In function ‘SEXPREC* mrnet_adapted(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
mrnet_adapted.cpp:58:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare]
58 | for(unsigned int i=0;i < *nsample; ++i){
| ~~^~~~~~~~~~
mrnet_adapted.cpp:103:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
103 | for( int l=0; l<n; ++l )
| ~^~
mrnet_adapted.cpp:131:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare]
131 | for(unsigned int j=0; j< *npredn; ++j ) {
| ~^~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c mrnet_adapted2.cpp -o mrnet_adapted2.o
mrnet_adapted2.cpp: In function ‘SEXPREC* mrnet_adapted2(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
mrnet_adapted2.cpp:62:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare]
62 | for(unsigned int i=0;i < *nsample; ++i){
| ~~^~~~~~~~~~
mrnet_adapted2.cpp:121:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
121 | for( int l=0; l<n; ++l )
| ~^~
mrnet_adapted2.cpp:185:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare]
185 | for(unsigned int j=0; j< *npredn; ++j ) {
| ~^~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c mrnet_ensemble_standalone.cpp -o mrnet_ensemble_standalone.o
mrnet_ensemble_standalone.cpp: In function ‘void remove_equiv_subtrees(tree<int>&, tree<double>&)’:
mrnet_ensemble_standalone.cpp:24:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
24 | for(unsigned int j=0;j< length_vec;++j){
| ~^~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:42:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
42 | for(unsigned int j=0;j< length_vec;++j){
| ~^~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:47:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
47 | for(unsigned int j=0;j< (res.depth(it_main)-1);++j){
| ~^~~~~~~~~~~~~~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:60:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
60 | for(unsigned int j=0;j< length_vec;++j){
| ~^~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:65:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
65 | for(unsigned int j=0;j< length_vec && equiv;++j){
| ~^~~~~~~~~~~~
mrnet_ensemble_standalone.cpp: In function ‘int verify_equivalentset_nparents(tree<int>&, tree<int>::pre_order_iterator, tree<int>::pre_order_iterator, tree<double>&, int)’:
mrnet_ensemble_standalone.cpp:111:7: warning: unused variable ‘found’ [-Wunused-variable]
111 | bool found=false;
| ^~~~~
mrnet_ensemble_standalone.cpp: In function ‘int verify_equivalentset(tree<int>&, tree<int>::pre_order_iterator, tree<int>::pre_order_iterator, int, int*, int*)’:
mrnet_ensemble_standalone.cpp:223:6: warning: variable ‘to_remove’ set but not used [-Wunused-but-set-variable]
223 | int to_remove[number_leafs];
| ^~~~~~~~~
mrnet_ensemble_standalone.cpp:283:6: warning: unused variable ‘rootdepth’ [-Wunused-variable]
283 | int rootdepth=tr.depth(it);
| ^~~~~~~~~
mrnet_ensemble_standalone.cpp: In function ‘void build_tree_int(tree<int>&, tree<int>::pre_order_iterator, tree<int>::pre_order_iterator, int*, int, int)’:
mrnet_ensemble_standalone.cpp:304:6: warning: unused variable ‘rootdepth’ [-Wunused-variable]
304 | int rootdepth=tr.depth(it);
| ^~~~~~~~~
mrnet_ensemble_standalone.cpp: In function ‘void bootstrap_mrmr_fix(double&, double&, double*, int*, int, int, int, int, int, int, int, int*)’:
mrnet_ensemble_standalone.cpp:384:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
384 | for(unsigned int i=1;i<= nsamples;++i){
| ~^~~~~~~~~~~
mrnet_ensemble_standalone.cpp:377:16: warning: unused variable ‘boot_val’ [-Wunused-variable]
377 | double *mim, *boot_val;
| ^~~~~~~~
mrnet_ensemble_standalone.cpp: In function ‘void bootstrap_mrmr(double&, double&, double*, int*, int, int, int, int, int, int, int, int*)’:
mrnet_ensemble_standalone.cpp:414:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
414 | for(unsigned int k=0; k< rep_boot; ++k){
| ~^~~~~~~~~~
mrnet_ensemble_standalone.cpp:417:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
417 | for(unsigned int i=1;i<= size_boot;++i){
| ~^~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:426:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
426 | for(unsigned int i=0;i< rep_boot;++i){
| ~^~~~~~~~~~
mrnet_ensemble_standalone.cpp:433:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
433 | for(unsigned int i=0;i< rep_boot;++i){
| ~^~~~~~~~~~
mrnet_ensemble_standalone.cpp: In function ‘void bootstrap_tree(tree<int>&, tree<double>&, double*, int*, int, int, int)’:
mrnet_ensemble_standalone.cpp:507:7: warning: unused variable ‘cnt_back’ [-Wunused-variable]
507 | int cnt_back=cnt2;
| ^~~~~~~~
mrnet_ensemble_standalone.cpp:442:7: warning: unused variable ‘nsub’ [-Wunused-variable]
442 | int nsub, *prev_sel,nsamples_boot=nsamples,*to_remove;
| ^~~~
mrnet_ensemble_standalone.cpp: In function ‘double mrnet_onegene(double*, int, int, int*, int, int)’:
mrnet_ensemble_standalone.cpp:569:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
569 | for(unsigned int j=0;j< nbvar; j++){
| ~^~~~~~~
mrnet_ensemble_standalone.cpp:558:15: warning: variable ‘jmax’ set but not used [-Wunused-but-set-variable]
558 | unsigned int jmax;
| ^~~~
mrnet_ensemble_standalone.cpp:560:9: warning: unused variable ‘max_val’ [-Wunused-variable]
560 | double max_val=-1000;
| ^~~~~~~
mrnet_ensemble_standalone.cpp: In function ‘void mrmr_ensemble_one_gene(tree<int>&, tree<int>::pre_order_iterator, double*, int*, int, int, int, int, int, int, double)’:
mrnet_ensemble_standalone.cpp:600:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
600 | for(unsigned int k=0;k< max_elements ;++k){
| ~^~~~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:658:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
658 | for (unsigned int i=0;i<max_elements_tmp-1;++i){
| ~^~~~~~~~~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:665:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
665 | for(unsigned int k=0;k< n;++k){
| ~^~~
mrnet_ensemble_standalone.cpp:668:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
668 | for(unsigned int k=0;k<max_elements_tmp;++k){
| ~^~~~~~~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:672:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
672 | for(unsigned int k=0;k< n;++k){
| ~^~~
mrnet_ensemble_standalone.cpp:677:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
677 | if(k!=(nsub[0]-1) && vec_mean[k]>max_mrmr){
| ~^~~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:689:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
689 | for(unsigned int k=0;k< n;++k){
| ~^~~
mrnet_ensemble_standalone.cpp:586:48: warning: unused variable ‘nprev_sel’ [-Wunused-variable]
586 | int *nsub, *prev_sel,nsamples_boot=nsamples, nprev_sel=0;
| ^~~~~~~~~
mrnet_ensemble_standalone.cpp:587:10: warning: variable ‘res_vec’ set but not used [-Wunused-but-set-variable]
587 | double *res_vec, *vec_mean, *vec_sort, *vec_sd, *vec_local_max_mean, *vec_local_max_sd;;
| ^~~~~~~
mrnet_ensemble_standalone.cpp: In function ‘SEXPREC* mrmr_ensemble(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
mrnet_ensemble_standalone.cpp:760:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare]
760 | for(unsigned int i=0;i< *npredn;++i){
| ~^~~~~~~~~
mrnet_ensemble_standalone.cpp:799:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
799 | for(unsigned int k=0;k<length_res_old;k++){
| ~^~~~~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:813:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
813 | for(unsigned int k=0;k<length_res;k++){
| ~^~~~~~~~~~~
mrnet_ensemble_standalone.cpp:819:7: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
819 | if(i==(*npredn-1)){
| ~^~~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:822:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
822 | for(unsigned int k=0;k<length_res;k++){
| ~^~~~~~~~~~~
mrnet_ensemble_standalone.cpp:777:13: warning: unused variable ‘cnt2’ [-Wunused-variable]
777 | int cnt=1,cnt2=0;
| ^~~~
mrnet_ensemble_standalone.cpp:780:7: warning: unused variable ‘rootdepth’ [-Wunused-variable]
780 | int rootdepth=res_tree.depth(it_final);
| ^~~~~~~~~
mrnet_ensemble_standalone.cpp:794:7: warning: unused variable ‘ind’ [-Wunused-variable]
794 | int ind=0;
| ^~~
mrnet_ensemble_standalone.cpp:722:30: warning: unused variable ‘res_all’ [-Wunused-variable]
722 | int *predn, *rep_boot,*res,*res_all,*res_all2,*namat;
| ^~~~~~~
mrnet_ensemble_standalone.cpp:722:39: warning: unused variable ‘res_all2’ [-Wunused-variable]
722 | int *predn, *rep_boot,*res,*res_all,*res_all2,*namat;
| ^~~~~~~~
mrnet_ensemble_standalone.cpp:723:6: warning: unused variable ‘vec_tmp’ [-Wunused-variable]
723 | int vec_tmp;
| ^~~~~~~
mrnet_ensemble_standalone.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)’:
mrnet_ensemble_standalone.cpp:860:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
860 | for(unsigned int k=0;k< max_elements ;++k){
| ~^~~~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:904:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
904 | for (unsigned int i=0;i<=max_depth;++i){
| ~^~~~~~~~~~~
mrnet_ensemble_standalone.cpp:912:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
912 | for(unsigned int k=0;k< n;++k){
| ~^~~
mrnet_ensemble_standalone.cpp:915:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare]
915 | for(unsigned int k=0;k<=max(res_tmp_new.depth(it_local),max_depth) ;++k){
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:919:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
919 | for(unsigned int k=0;k< n;++k){
| ~^~~
mrnet_ensemble_standalone.cpp:848:48: warning: unused variable ‘tmp_val_max_ind’ [-Wunused-variable]
848 | int *nsub, *prev_sel,nsamples_boot=nsamples, tmp_val_max_ind, *prev_sel_tmp,*vec_sol_local,ndelete;
| ^~~~~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:848:66: warning: unused variable ‘prev_sel_tmp’ [-Wunused-variable]
848 | int *nsub, *prev_sel,nsamples_boot=nsamples, tmp_val_max_ind, *prev_sel_tmp,*vec_sol_local,ndelete;
| ^~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:849:21: warning: unused variable ‘vec_sort’ [-Wunused-variable]
849 | 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;
| ^~~~~~~~
mrnet_ensemble_standalone.cpp:849:63: warning: variable ‘vec_local_max_sd’ set but not used [-Wunused-but-set-variable]
849 | 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;
| ^~~~~~~~~~~~~~~~
mrnet_ensemble_standalone.cpp: In function ‘SEXPREC* mrmr_ensemble_remove(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
mrnet_ensemble_standalone.cpp:1029:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare]
1029 | for(unsigned int i=0;i< *npredn;++i){
| ~^~~~~~~~~
mrnet_ensemble_standalone.cpp:1066:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
1066 | for(unsigned int k=0;k<length_res_old;k++){
| ~^~~~~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:1080:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
1080 | for(unsigned int k=0;k<length_res;k++){
| ~^~~~~~~~~~~
mrnet_ensemble_standalone.cpp:1085:7: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
1085 | if(i==(*npredn-1)){
| ~^~~~~~~~~~~~~
mrnet_ensemble_standalone.cpp:1089:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
1089 | for(unsigned int k=0;k<length_res;k++){
| ~^~~~~~~~~~~
mrnet_ensemble_standalone.cpp:1046:13: warning: unused variable ‘cnt2’ [-Wunused-variable]
1046 | int cnt=1,cnt2=0;
| ^~~~
mrnet_ensemble_standalone.cpp:1049:7: warning: unused variable ‘rootdepth’ [-Wunused-variable]
1049 | int rootdepth=res_tree.depth(it_final);
| ^~~~~~~~~
mrnet_ensemble_standalone.cpp:1063:7: warning: unused variable ‘ind’ [-Wunused-variable]
1063 | int ind=0;
| ^~~
mrnet_ensemble_standalone.cpp:992:30: warning: unused variable ‘res_all’ [-Wunused-variable]
992 | int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
| ^~~~~~~
mrnet_ensemble_standalone.cpp:992:39: warning: unused variable ‘res_all2’ [-Wunused-variable]
992 | int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
| ^~~~~~~~
mrnet_ensemble_standalone.cpp:993:6: warning: unused variable ‘vec_tmp’ [-Wunused-variable]
993 | int vec_tmp;
| ^~~~~~~
mrnet_ensemble_standalone.cpp: In function ‘SEXPREC* mrmr_ensemble(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
mrnet_ensemble_standalone.cpp:840:9: warning: ‘Rres’ may be used uninitialized in this function [-Wmaybe-uninitialized]
840 | return Rres;
| ^~~~
mrnet_ensemble_standalone.cpp:800:25: warning: ‘res_old’ may be used uninitialized in this function [-Wmaybe-uninitialized]
800 | res_all[k]=res_old[k];
| ~~~~~~~~~^
mrnet_ensemble_standalone.cpp: In function ‘SEXPREC* mrmr_ensemble_remove(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
mrnet_ensemble_standalone.cpp:1105:9: warning: ‘Rres’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1105 | return Rres;
| ^~~~
mrnet_ensemble_standalone.cpp:1067:25: warning: ‘res_old’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1067 | res_all[k]=res_old[k];
| ~~~~~~~~~^
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o predictionet.so foo_mrmr.o mrnet_adapted.o mrnet_adapted2.o mrnet_ensemble_standalone.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-predictionet/00new/predictionet/libs
** R
** data
*** moving datasets to lazyload DB
** 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
Warning: Package 'predictionet' is deprecated and will be removed from
Bioconductor version 3.15
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: Package 'predictionet' is deprecated and will be removed from
Bioconductor version 3.15
** testing if installed package keeps a record of temporary installation path
* DONE (predictionet)
