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This page was generated on 2024-02-28 11:37:23 -0500 (Wed, 28 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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 2081/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
survcomp 1.52.0  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2024-02-27 14:05:07 -0500 (Tue, 27 Feb 2024)
git_url: https://git.bioconductor.org/packages/survcomp
git_branch: RELEASE_3_18
git_last_commit: 6e3bbe2
git_last_commit_date: 2023-10-24 09:46:20 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

INSTALL results for survcomp on palomino4


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: 1.52.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL survcomp
StartedAt: 2024-02-27 16:47:29 -0500 (Tue, 27 Feb 2024)
EndedAt: 2024-02-27 16:47:48 -0500 (Tue, 27 Feb 2024)
EllapsedTime: 19.2 seconds
RetCode: 0
Status:   OK  

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL survcomp
###
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* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'survcomp' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.3.0'
using C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c concordance.index.c -o concordance.index.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 [-Wmaybe-uninitialized]
  859 |         return Rres;
      |                ^~~~
foo_mrmr_ensemble_surv.cpp:741:14: note: 'Rres' was declared here
  741 |         SEXP Rres;
      |              ^~~~
foo_mrmr_ensemble_surv.cpp:821:43: warning: 'res_old' may be used uninitialized [-Wmaybe-uninitialized]
  821 |                                 res_all[k]=res_old[k];
      |                                 ~~~~~~~~~~^~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:816:32: note: 'res_old' was declared here
  816 |                 int *res_all, *res_old;
      |                                ^~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG     -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c survcomp_init.cpp -o survcomp_init.o
g++ -std=gnu++17 -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:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.18-bioc/R/library/00LOCK-survcomp/00new/survcomp/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (survcomp)