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INSTALL report for survcomp on tokay1

This page was generated on 2019-04-13 11:21:36 -0400 (Sat, 13 Apr 2019).

Package 1527/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
survcomp 1.32.0
Benjamin Haibe-Kains , Markus Schroeder , Catharina Olsen
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/survcomp
Branch: RELEASE_3_8
Last Commit: d23b602
Last Changed Date: 2018-10-30 11:41:47 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: survcomp
Version: 1.32.0
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/survcomp_1.32.0.tar.gz && rm -rf survcomp.buildbin-libdir && mkdir survcomp.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=survcomp.buildbin-libdir survcomp_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL survcomp_1.32.0.zip && rm survcomp_1.32.0.tar.gz survcomp_1.32.0.zip
StartedAt: 2019-04-12 19:26:09 -0400 (Fri, 12 Apr 2019)
EndedAt: 2019-04-12 19:28:37 -0400 (Fri, 12 Apr 2019)
EllapsedTime: 148.3 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/survcomp_1.32.0.tar.gz && rm -rf survcomp.buildbin-libdir && mkdir survcomp.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=survcomp.buildbin-libdir survcomp_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL survcomp_1.32.0.zip && rm survcomp_1.32.0.tar.gz survcomp_1.32.0.zip
###
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##############################################################################


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100  444k  100  444k    0     0  1883k      0 --:--:-- --:--:-- --:--:-- 1900k

install for i386

* installing *source* package 'survcomp' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c concordance.index.c -o concordance.index.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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 between signed and unsigned integer expressions [-Wsign-compare]
  for( unsigned int i=0; i< size; ++i ) {
                          ^
foo_mrmr_ensemble_surv.cpp:22:26: 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:202:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0; i< size_subset; ++i){
                         ^
foo_mrmr_ensemble_surv.cpp:203:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned int j=0; j< (nvar-1); ++j){
                          ^
foo_mrmr_ensemble_surv.cpp:214:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0; i< nvar-1; ++i){
                         ^
foo_mrmr_ensemble_surv.cpp:216:28: 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:393:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int k=0; k< rep_boot; ++k){
                         ^
foo_mrmr_ensemble_surv.cpp:396:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned int i=1;i<= size_boot;++i){
                         ^
foo_mrmr_ensemble_surv.cpp:400:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for( unsigned int i=0; i< size ; ++i ){
                           ^
foo_mrmr_ensemble_surv.cpp:401:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for( unsigned int j=0; j< size ; ++j ){
                            ^
foo_mrmr_ensemble_surv.cpp:412:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0;i< rep_boot;++i){
                        ^
foo_mrmr_ensemble_surv.cpp:419:24: 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:448:25: 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:593:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=1;i<= nsamples;++i){
                        ^
foo_mrmr_ensemble_surv.cpp:596:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for( unsigned int i=0; i< n; ++i ){
                          ^
foo_mrmr_ensemble_surv.cpp:597:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for( unsigned int j=0; j< n; ++j ){
                           ^
foo_mrmr_ensemble_surv.cpp:604:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int k=0;k< max_elements ;++k){
                        ^
foo_mrmr_ensemble_surv.cpp:646:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0;i<=max_depth;++i){
                           ^
foo_mrmr_ensemble_surv.cpp:654:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(unsigned int k=0;k< n;++k){
                          ^
foo_mrmr_ensemble_surv.cpp:657:26: 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){
                          ^
foo_mrmr_ensemble_surv.cpp:661:26: 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:786:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0;i< *npredn;++i){
                        ^
foo_mrmr_ensemble_surv.cpp:820:26: 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:834:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned int k=0;k<length_res;k++){
                         ^
foo_mrmr_ensemble_surv.cpp:839:7: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(i==(*npredn-1)){
       ^
foo_mrmr_ensemble_surv.cpp:843:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(unsigned int k=0;k<length_res;k++){
                          ^
foo_mrmr_ensemble_surv.cpp:801:13: warning: unused variable 'cnt2' [-Wunused-variable]
   int cnt=1,cnt2=0;
             ^
foo_mrmr_ensemble_surv.cpp:804:7: warning: unused variable 'rootdepth' [-Wunused-variable]
   int rootdepth=res_tree.depth(it_final);
       ^
foo_mrmr_ensemble_surv.cpp:817:7: warning: unused variable 'ind' [-Wunused-variable]
   int ind=0;
       ^
foo_mrmr_ensemble_surv.cpp:733:30: warning: unused variable 'res_all' [-Wunused-variable]
  int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
                              ^
foo_mrmr_ensemble_surv.cpp:733:39: warning: unused variable 'res_all2' [-Wunused-variable]
  int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
                                       ^
foo_mrmr_ensemble_surv.cpp:734:6: warning: unused variable 'vec_tmp' [-Wunused-variable]
  int vec_tmp;
      ^
foo_mrmr_ensemble_surv.cpp:859:9: warning: 'Rres' may be used uninitialized in this function [-Wmaybe-uninitialized]
  return Rres;
         ^
foo_mrmr_ensemble_surv.cpp:821:25: warning: 'res_old' may be used uninitialized in this function [-Wmaybe-uninitialized]
     res_all[k]=res_old[k];
                         ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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 between signed and unsigned integer expressions [-Wsign-compare]
  for( unsigned int i=0; i< size; ++i ) {
                          ^
foo_mrmr_surv.cpp:22:26: 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:49:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0; i< size_subset; ++i){
                         ^
foo_mrmr_surv.cpp:50:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned int j=0; j< nvar; ++j){
                          ^
foo_mrmr_surv.cpp:56:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0; i< nvar; ++i){
                         ^
foo_mrmr_surv.cpp:58:28: 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:301:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0;i < *nsample; ++i){
                         ^
foo_mrmr_surv.cpp:341:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for( int l=0; l<n; ++l )
                   ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c survcomp_init.cpp -o survcomp_init.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o survcomp.dll tmp.def concordance.index.o foo_mrmr_ensemble_surv.o foo_mrmr_surv.o survcomp_init.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/survcomp.buildbin-libdir/survcomp/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'survcomp'
    finding HTML links ... done
    D.index                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp2xh7ab/R.INSTALL13ac11af4970/survcomp/man/D.index.Rd:43: file link 'normOrder' in package 'SuppDists' does not exist and so has been treated as a topic
    balanced.hazard.ratio                   html  
    bhr.comp                                html  
    breastCancerData                        html  
    censor.time                             html  
    cindex.comp                             html  
    cindex.comp.meta                        html  
    combine.est                             html  
    combine.test                            html  
    concordance.index                       html  
    concordanceIndexC                       html  
    cvpl                                    html  
    dindex.comp                             html  
    dindex.comp.meta                        html  
    fisherz                                 html  
    forestplot.surv                         html  
    get_concordanceIndex_onevariable        html  
    getsurv2                                html  
    hazard.ratio                            html  
    hr.comp                                 html  
    hr.comp.meta                            html  
    hr.comp2                                html  
    iauc.comp                               html  
    ibsc.comp                               html  
    km.coxph.plot                           html  
    logpl                                   html  
    mainz7g                                 html  
    metaplot.surv                           html  
    finding level-2 HTML links ... done

    mrmr.cindex                             html  
    mrmr.cindex.ensemble                    html  
    mrmr_cIndex                             html  
    mrmr_cIndex_ensemble_remove             html  
    nki7g                                   html  
    no.at.risk                              html  
    sbrier.score2proba                      html  
    score2proba                             html  
    survcomp-package                        html  
    td.sens.spec                            html  
    tdrocc                                  html  
    test.hetero.est                         html  
    test.hetero.test                        html  
    transbig7g                              html  
    unt7g                                   html  
    upp7g                                   html  
    vdx7g                                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'survcomp' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c concordance.index.c -o concordance.index.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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 between signed and unsigned integer expressions [-Wsign-compare]
  for( unsigned int i=0; i< size; ++i ) {
                          ^
foo_mrmr_ensemble_surv.cpp:22:26: 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:202:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0; i< size_subset; ++i){
                         ^
foo_mrmr_ensemble_surv.cpp:203:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned int j=0; j< (nvar-1); ++j){
                          ^
foo_mrmr_ensemble_surv.cpp:214:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0; i< nvar-1; ++i){
                         ^
foo_mrmr_ensemble_surv.cpp:216:28: 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:393:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int k=0; k< rep_boot; ++k){
                         ^
foo_mrmr_ensemble_surv.cpp:396:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned int i=1;i<= size_boot;++i){
                         ^
foo_mrmr_ensemble_surv.cpp:400:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for( unsigned int i=0; i< size ; ++i ){
                           ^
foo_mrmr_ensemble_surv.cpp:401:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for( unsigned int j=0; j< size ; ++j ){
                            ^
foo_mrmr_ensemble_surv.cpp:412:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0;i< rep_boot;++i){
                        ^
foo_mrmr_ensemble_surv.cpp:419:24: 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:448:25: 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:593:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=1;i<= nsamples;++i){
                        ^
foo_mrmr_ensemble_surv.cpp:596:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for( unsigned int i=0; i< n; ++i ){
                          ^
foo_mrmr_ensemble_surv.cpp:597:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for( unsigned int j=0; j< n; ++j ){
                           ^
foo_mrmr_ensemble_surv.cpp:604:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int k=0;k< max_elements ;++k){
                        ^
foo_mrmr_ensemble_surv.cpp:646:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (unsigned int i=0;i<=max_depth;++i){
                           ^
foo_mrmr_ensemble_surv.cpp:654:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(unsigned int k=0;k< n;++k){
                          ^
foo_mrmr_ensemble_surv.cpp:657:26: 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){
                          ^
foo_mrmr_ensemble_surv.cpp:661:26: 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:786:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0;i< *npredn;++i){
                        ^
foo_mrmr_ensemble_surv.cpp:820:26: 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:834:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned int k=0;k<length_res;k++){
                         ^
foo_mrmr_ensemble_surv.cpp:839:7: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(i==(*npredn-1)){
       ^
foo_mrmr_ensemble_surv.cpp:843:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(unsigned int k=0;k<length_res;k++){
                          ^
foo_mrmr_ensemble_surv.cpp:801:13: warning: unused variable 'cnt2' [-Wunused-variable]
   int cnt=1,cnt2=0;
             ^
foo_mrmr_ensemble_surv.cpp:804:7: warning: unused variable 'rootdepth' [-Wunused-variable]
   int rootdepth=res_tree.depth(it_final);
       ^
foo_mrmr_ensemble_surv.cpp:817:7: warning: unused variable 'ind' [-Wunused-variable]
   int ind=0;
       ^
foo_mrmr_ensemble_surv.cpp:733:30: warning: unused variable 'res_all' [-Wunused-variable]
  int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
                              ^
foo_mrmr_ensemble_surv.cpp:733:39: warning: unused variable 'res_all2' [-Wunused-variable]
  int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
                                       ^
foo_mrmr_ensemble_surv.cpp:734:6: warning: unused variable 'vec_tmp' [-Wunused-variable]
  int vec_tmp;
      ^
foo_mrmr_ensemble_surv.cpp:859:9: warning: 'Rres' may be used uninitialized in this function [-Wmaybe-uninitialized]
  return Rres;
         ^
foo_mrmr_ensemble_surv.cpp:821:25: warning: 'res_old' may be used uninitialized in this function [-Wmaybe-uninitialized]
     res_all[k]=res_old[k];
                         ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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 between signed and unsigned integer expressions [-Wsign-compare]
  for( unsigned int i=0; i< size; ++i ) {
                          ^
foo_mrmr_surv.cpp:22:26: 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:49:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0; i< size_subset; ++i){
                         ^
foo_mrmr_surv.cpp:50:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(unsigned int j=0; j< nvar; ++j){
                          ^
foo_mrmr_surv.cpp:56:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0; i< nvar; ++i){
                         ^
foo_mrmr_surv.cpp:58:28: 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:301:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(unsigned int i=0;i < *nsample; ++i){
                         ^
foo_mrmr_surv.cpp:341:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for( int l=0; l<n; ++l )
                   ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c survcomp_init.cpp -o survcomp_init.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o survcomp.dll tmp.def concordance.index.o foo_mrmr_ensemble_surv.o foo_mrmr_surv.o survcomp_init.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/survcomp.buildbin-libdir/survcomp/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'survcomp' as survcomp_1.32.0.zip
* DONE (survcomp)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'survcomp' successfully unpacked and MD5 sums checked
In R CMD INSTALL