##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL predictionet
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘predictionet’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-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 between signed and unsigned integer expressions [-Wsign-compare]
for( unsigned int i=0; i< size; ++i ) {
˜^˜˜˜˜˜
foo_mrmr.cpp:23:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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 between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int i=0; i< size_subset; ++i){
˜^˜˜˜˜˜˜˜˜˜˜˜˜
foo_mrmr.cpp:51:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int j=0; j< nvar; ++j){
˜^˜˜˜˜˜
foo_mrmr.cpp:57:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int i=0; i< nvar; ++i){
˜^˜˜˜˜˜
foo_mrmr.cpp:59:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int j=i+1; j< nvar; ++j){
˜^˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-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 between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int i=0;i < *nsample; ++i){
˜˜^˜˜˜˜˜˜˜˜˜
mrnet_adapted.cpp:103:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for( int l=0; l<n; ++l )
˜^˜
mrnet_adapted.cpp:131:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int j=0; j< *npredn; ++j ) {
˜^˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-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 between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int i=0;i < *nsample; ++i){
˜˜^˜˜˜˜˜˜˜˜˜
mrnet_adapted2.cpp:121:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for( int l=0; l<n; ++l )
˜^˜
mrnet_adapted2.cpp:185:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int j=0; j< *npredn; ++j ) {
˜^˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-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 between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int j=0;j< length_vec;++j){
˜^˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:42:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int j=0;j< length_vec;++j){
˜^˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:47:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int j=0;j< (res.depth(it_main)-1);++j){
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:60:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int j=0;j< length_vec;++j){
˜^˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:65:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
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]
int to_remove[number_leafs];
^˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:283:6: warning: unused variable ‘rootdepth’ [-Wunused-variable]
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]
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 between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int i=1;i<= nsamples;++i){
˜^˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:377:16: warning: unused variable ‘boot_val’ [-Wunused-variable]
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 between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int k=0; k< rep_boot; ++k){
˜^˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:417:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int i=1;i<= size_boot;++i){
˜^˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:426:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int i=0;i< rep_boot;++i){
˜^˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:433:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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]
int cnt_back=cnt2;
^˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:442:7: warning: unused variable ‘nsub’ [-Wunused-variable]
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 between signed and unsigned integer expressions [-Wsign-compare]
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]
unsigned int jmax;
^˜˜˜
mrnet_ensemble_standalone.cpp:560:9: warning: unused variable ‘max_val’ [-Wunused-variable]
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 between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int k=0;k< max_elements ;++k){
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:658:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (unsigned int i=0;i<max_elements_tmp-1;++i){
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:665:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int k=0;k< n;++k){
˜^˜˜
mrnet_ensemble_standalone.cpp:668:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int k=0;k<max_elements_tmp;++k){
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:672:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int k=0;k< n;++k){
˜^˜˜
mrnet_ensemble_standalone.cpp:677:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(k!=(nsub[0]-1) && vec_mean[k]>max_mrmr){
˜^˜˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:689:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int k=0;k< n;++k){
˜^˜˜
mrnet_ensemble_standalone.cpp:586:48: warning: unused variable ‘nprev_sel’ [-Wunused-variable]
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]
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 between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int i=0;i< *npredn;++i){
˜^˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:799:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int k=0;k<length_res_old;k++){
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:813:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int k=0;k<length_res;k++){
˜^˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:819:7: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(i==(*npredn-1)){
˜^˜˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:822:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int k=0;k<length_res;k++){
˜^˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:777:13: warning: unused variable ‘cnt2’ [-Wunused-variable]
int cnt=1,cnt2=0;
^˜˜˜
mrnet_ensemble_standalone.cpp:780:7: warning: unused variable ‘rootdepth’ [-Wunused-variable]
int rootdepth=res_tree.depth(it_final);
^˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:794:7: warning: unused variable ‘ind’ [-Wunused-variable]
int ind=0;
^˜˜
mrnet_ensemble_standalone.cpp:722:30: warning: unused variable ‘res_all’ [-Wunused-variable]
int *predn, *rep_boot,*res,*res_all,*res_all2,*namat;
^˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:722:39: warning: unused variable ‘res_all2’ [-Wunused-variable]
int *predn, *rep_boot,*res,*res_all,*res_all2,*namat;
^˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:723:6: warning: unused variable ‘vec_tmp’ [-Wunused-variable]
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 between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int k=0;k< max_elements ;++k){
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:904:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (unsigned int i=0;i<=max_depth;++i){
˜^˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:912:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int k=0;k< n;++k){
˜^˜˜
mrnet_ensemble_standalone.cpp:915:26: 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){
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:919:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int k=0;k< n;++k){
˜^˜˜
mrnet_ensemble_standalone.cpp:848:48: 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;
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:848:66: 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;
^˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:849:21: 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;
^˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:849:63: 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;
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
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 between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int i=0;i< *npredn;++i){
˜^˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:1066:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int k=0;k<length_res_old;k++){
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:1080:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int k=0;k<length_res;k++){
˜^˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:1085:7: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(i==(*npredn-1)){
˜^˜˜˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:1089:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(unsigned int k=0;k<length_res;k++){
˜^˜˜˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:1046:13: warning: unused variable ‘cnt2’ [-Wunused-variable]
int cnt=1,cnt2=0;
^˜˜˜
mrnet_ensemble_standalone.cpp:1049:7: warning: unused variable ‘rootdepth’ [-Wunused-variable]
int rootdepth=res_tree.depth(it_final);
^˜˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:1063:7: warning: unused variable ‘ind’ [-Wunused-variable]
int ind=0;
^˜˜
mrnet_ensemble_standalone.cpp:992:30: warning: unused variable ‘res_all’ [-Wunused-variable]
int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
^˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:992:39: warning: unused variable ‘res_all2’ [-Wunused-variable]
int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
^˜˜˜˜˜˜˜
mrnet_ensemble_standalone.cpp:993:6: warning: unused variable ‘vec_tmp’ [-Wunused-variable]
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]
return Rres;
^˜˜˜
mrnet_ensemble_standalone.cpp:800:25: warning: ‘res_old’ may be used uninitialized in this function [-Wmaybe-uninitialized]
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]
return Rres;
^˜˜˜
mrnet_ensemble_standalone.cpp:1067:25: warning: ‘res_old’ may be used uninitialized in this function [-Wmaybe-uninitialized]
res_all[k]=res_old[k];
˜˜˜˜˜˜˜˜˜^
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-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-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-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
** 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 (predictionet)
