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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:survcomp.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings survcomp_1.49.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/survcomp.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘survcomp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘survcomp’ version ‘1.49.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘survcomp’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
concordance:
  function(object, ...)
concordance.index:
  function(x, surv.time, surv.event, cl, weights, comppairs, strat,
           alpha, outx, method, alternative, na.rm)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.

Found the following apparent S3 methods exported but not registered:
  concordance.index
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in documentation object 'concordance.index':
  ‘concordance.index’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘survcomp.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/survcomp.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL survcomp
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘survcomp’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-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-3.17-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:12:33: 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:22:33: 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:106:24: warning: variable ‘uhs’ set but not used [-Wunused-but-set-variable]
  106 |                 double uhs[Ns];
      |                        ^~~
foo_mrmr_ensemble_surv.cpp:107:24: 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:202:32: 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:203:40: 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:214:32: 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:216:42: 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:191:24: 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:191:34: 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:351:21: warning: unused variable ‘cnt_back’ [-Wunused-variable]
  351 |                 int cnt_back=cnt2;
      |                     ^~~~~~~~
foo_mrmr_ensemble_surv.cpp:286:14: 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:393:32: 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:396:39: 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:400:41: 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:401:49: 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:412:31: 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:419:31: 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:387:17: 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:448:39: 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:437:22: warning: variable ‘jmax’ set but not used [-Wunused-but-set-variable]
  437 |         unsigned int jmax;
      |                      ^~~~
foo_mrmr_ensemble_surv.cpp:439:16: 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:467:14: 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:593:31: 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:596:33: 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:597:41: 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:604:31: 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:646:48: 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:654:47: 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:657:47: 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:661:47: 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:578:31: 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:578:55: 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:578:73: 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:579:28: 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:579:70: 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:786:31: 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:820:47: 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:834:39: 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:839:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  839 |                 if(i==(*npredn-1)){
      |                    ~^~~~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:843:47: 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:801:27: warning: unused variable ‘cnt2’ [-Wunused-variable]
  801 |                 int cnt=1,cnt2=0;
      |                           ^~~~
foo_mrmr_ensemble_surv.cpp:804:21: warning: unused variable ‘rootdepth’ [-Wunused-variable]
  804 |                 int rootdepth=res_tree.depth(it_final);
      |                     ^~~~~~~~~
foo_mrmr_ensemble_surv.cpp:817:21: warning: unused variable ‘ind’ [-Wunused-variable]
  817 |                 int ind=0;
      |                     ^~~
foo_mrmr_ensemble_surv.cpp:733:37: warning: unused variable ‘res_all’ [-Wunused-variable]
  733 |         int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
      |                                     ^~~~~~~
foo_mrmr_ensemble_surv.cpp:733:46: warning: unused variable ‘res_all2’ [-Wunused-variable]
  733 |         int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
      |                                              ^~~~~~~~
foo_mrmr_ensemble_surv.cpp:734:13: warning: unused variable ‘vec_tmp’ [-Wunused-variable]
  734 |         int vec_tmp;
      |             ^~~~~~~
foo_mrmr_ensemble_surv.cpp:859:16: warning: ‘Rres’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  859 |         return Rres;
      |                ^~~~
foo_mrmr_ensemble_surv.cpp:821:43: 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-3.17-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:12:33: 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:22:33: 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:49:32: 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:50:40: 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:56:32: 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:58:42: 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:146:24: warning: variable ‘uhs’ set but not used [-Wunused-but-set-variable]
  146 |                 double uhs[Ns];
      |                        ^~~
foo_mrmr_surv.cpp:147:24: 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:301:32: 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:341:40: 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-3.17-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-3.17-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-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-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)