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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2092/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
survcomp 1.56.0  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/survcomp
git_branch: RELEASE_3_20
git_last_commit: 1e00a05
git_last_commit_date: 2024-10-29 09:36:33 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for survcomp on nebbiolo2

To the developers/maintainers of the survcomp package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/survcomp.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: survcomp
Version: 1.56.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:survcomp.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings survcomp_1.56.0.tar.gz
StartedAt: 2024-12-20 06:00:24 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 06:01:22 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 58.0 seconds
RetCode: 0
Status:   OK  
CheckDir: survcomp.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:survcomp.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings survcomp_1.56.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/survcomp.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘survcomp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘survcomp’ version ‘1.56.0’
* 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 13.3.0-6ubuntu2~24.04) 13.3.0’
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* 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 ... OK
* 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/survcomp.Rcheck/00check.log’
for details.


Installation output

survcomp.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL survcomp
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘survcomp’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c concordance.index.c -o concordance.index.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-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:832:27: warning: ‘res_old’ may be used uninitialized [-Wmaybe-uninitialized]
  832 |                 delete [] res_old;
      |                           ^~~~~~~
foo_mrmr_ensemble_surv.cpp:816:32: note: ‘res_old’ was declared here
  816 |                 int *res_all, *res_old;
      |                                ^~~~~~~
foo_mrmr_ensemble_surv.cpp:859:16: warning: ‘Rres’ may be used uninitialized [-Wmaybe-uninitialized]
  859 |         return Rres;
      |                ^~~~
foo_mrmr_ensemble_surv.cpp:741:14: note: ‘Rres’ was declared here
  741 |         SEXP Rres;
      |              ^~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-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++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c survcomp_init.cpp -o survcomp_init.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-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-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-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)

Tests output


Example timings

survcomp.Rcheck/survcomp-Ex.timings

nameusersystemelapsed
D.index0.0210.0000.021
balanced.hazard.ratio0.0080.0000.009
bhr.comp0.0110.0010.011
breastCancerData0.4570.0130.471
censor.time000
cindex.comp0.0020.0000.002
cindex.comp.meta0.0040.0000.003
combine.est0.0010.0000.000
combine.test0.0010.0000.001
concordance.index0.0020.0000.002
cvpl0.1150.0000.115
dindex.comp0.0090.0010.010
dindex.comp.meta0.0160.0030.018
fisherz000
forestplot.surv0.0470.0020.049
getsurv20.0050.0000.005
hazard.ratio0.0070.0000.009
hr.comp0.0090.0000.009
hr.comp.meta0.0190.0000.019
hr.comp20.0060.0000.005
iauc.comp0.1720.0150.187
ibsc.comp0.2060.0050.210
km.coxph.plot0.0390.0010.039
logpl0.0100.0000.011
mainz7g0.1750.0060.182
metaplot.surv0.0030.0000.003
mrmr.cindex0.0020.0000.002
nki7g0.1740.0070.181
no.at.risk0.0080.0000.008
sbrier.score2proba0.1470.0000.147
score2proba0.0140.0000.014
td.sens.spec0.0020.0000.001
tdrocc0.0650.0130.078
test.hetero.est000
test.hetero.test000
transbig7g0.1670.0020.169
unt7g0.1760.0060.182
upp7g0.1820.0020.184
vdx7g0.1620.0030.164