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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:survcomp.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings survcomp_1.61.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/survcomp.Rcheck’
* using R Under development (unstable) (2026-03-20 r89666)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-03-21 05:47:10 UTC
* using option ‘--no-vignettes’
* checking for file ‘survcomp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘survcomp’ version ‘1.61.1’
* 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: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
* used C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
* used SDK: ‘MacOSX26.2.sdk’
* 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 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  metaplot.surv.Rd: meta.colors
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... INFO
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/survcomp.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL survcomp
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘survcomp’ ...
** this is package ‘survcomp’ version ‘1.61.1’
** using staged installation
** libs
using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c concordance.index.c -o concordance.index.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c foo_mrmr_ensemble_surv.cpp -o foo_mrmr_ensemble_surv.o
foo_mrmr_ensemble_surv.cpp:40:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
   40 |         double res_ch[lenStrat];
      |                       ^~~~~~~~
foo_mrmr_ensemble_surv.cpp:40:16: note: read of non-const variable 'lenStrat' is not allowed in a constant expression
foo_mrmr_ensemble_surv.cpp:38:6: note: declared here
   38 |         int lenStrat = lenS;
      |             ^
foo_mrmr_ensemble_surv.cpp:41:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
   41 |         double res_dh[lenStrat];
      |                       ^~~~~~~~
foo_mrmr_ensemble_surv.cpp:41:16: note: read of non-const variable 'lenStrat' is not allowed in a constant expression
foo_mrmr_ensemble_surv.cpp:38:6: note: declared here
   38 |         int lenStrat = lenS;
      |             ^
foo_mrmr_ensemble_surv.cpp:48:11: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
   48 |                 int ixs[lenStrat];
      |                         ^~~~~~~~
foo_mrmr_ensemble_surv.cpp:48:11: note: read of non-const variable 'lenStrat' is not allowed in a constant expression
foo_mrmr_ensemble_surv.cpp:38:6: note: declared here
   38 |         int lenStrat = lenS;
      |             ^
foo_mrmr_ensemble_surv.cpp:64:13: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
   64 |                 double xs[Ns];
      |                           ^~
foo_mrmr_ensemble_surv.cpp:64:13: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_ensemble_surv.cpp:46:6: note: declared here
   46 |         int Ns = 0;
      |             ^
foo_mrmr_ensemble_surv.cpp:72:11: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
   72 |                 int cls[Ns];
      |                         ^~
foo_mrmr_ensemble_surv.cpp:72:11: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_ensemble_surv.cpp:46:6: note: declared here
   46 |         int Ns = 0;
      |             ^
foo_mrmr_ensemble_surv.cpp:80:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
   80 |                 double sts[Ns];
      |                            ^~
foo_mrmr_ensemble_surv.cpp:80:14: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_ensemble_surv.cpp:46:6: note: declared here
   46 |         int Ns = 0;
      |             ^
foo_mrmr_ensemble_surv.cpp:88:11: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
   88 |                 int ses[Ns];
      |                         ^~
foo_mrmr_ensemble_surv.cpp:88:11: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_ensemble_surv.cpp:46:6: note: declared here
   46 |         int Ns = 0;
      |             ^
foo_mrmr_ensemble_surv.cpp:96:19: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
   96 |                 double weightss[Ns];
      |                                 ^~
foo_mrmr_ensemble_surv.cpp:96:19: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_ensemble_surv.cpp:46:6: note: declared here
   46 |         int Ns = 0;
      |             ^
foo_mrmr_ensemble_surv.cpp:104:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  104 |                 double chs[Ns];
      |                            ^~
foo_mrmr_ensemble_surv.cpp:104:14: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_ensemble_surv.cpp:46:6: note: declared here
   46 |         int Ns = 0;
      |             ^
foo_mrmr_ensemble_surv.cpp:105:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  105 |                 double dhs[Ns];
      |                            ^~
foo_mrmr_ensemble_surv.cpp:105:14: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_ensemble_surv.cpp:46:6: note: declared here
   46 |         int Ns = 0;
      |             ^
foo_mrmr_ensemble_surv.cpp:106:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  106 |                 double uhs[Ns];
      |                            ^~
foo_mrmr_ensemble_surv.cpp:106:14: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_ensemble_surv.cpp:46:6: note: declared here
   46 |         int Ns = 0;
      |             ^
foo_mrmr_ensemble_surv.cpp:107:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  107 |                 double rphs[Ns];
      |                             ^~
foo_mrmr_ensemble_surv.cpp:107:15: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_ensemble_surv.cpp:46:6: note: declared here
   46 |         int Ns = 0;
      |             ^
foo_mrmr_ensemble_surv.cpp:191:17: 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:191:27: 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:351:7: warning: unused variable 'cnt_back' [-Wunused-variable]
  351 |                 int cnt_back=cnt2;
      |                     ^~~~~~~~
foo_mrmr_ensemble_surv.cpp:286:7: warning: unused variable 'nsub' [-Wunused-variable]
  286 |         int  nsub, *prev_sel,nsamples_boot=nsamples,*to_remove;
      |              ^~~~
foo_mrmr_ensemble_surv.cpp:387:10: warning: unused variable 'mim' [-Wunused-variable]
  387 |         double *mim, *boot_val, *mat_info;
      |                 ^~~
foo_mrmr_ensemble_surv.cpp:437:15: warning: variable 'jmax' set but not used [-Wunused-but-set-variable]
  437 |         unsigned int jmax;
      |                      ^
foo_mrmr_ensemble_surv.cpp:439:9: warning: unused variable 'max_val' [-Wunused-variable]
  439 |         double max_val=-1000;
      |                ^~~~~~~
foo_mrmr_ensemble_surv.cpp:473:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  473 |         int vec_old[depth+1];
      |                     ^~~~~~~
foo_mrmr_ensemble_surv.cpp:473:14: note: read of non-const variable 'depth' is not allowed in a constant expression
foo_mrmr_ensemble_surv.cpp:471:6: note: declared here
  471 |         int depth=tr.depth(li);
      |             ^
foo_mrmr_ensemble_surv.cpp:474:43: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  474 |         int mat_res [power((maxnsol+1),(depth))][depth+2];
      |                                                  ^~~~~~~
foo_mrmr_ensemble_surv.cpp:474:43: note: read of non-const variable 'depth' is not allowed in a constant expression
foo_mrmr_ensemble_surv.cpp:471:6: note: declared here
  471 |         int depth=tr.depth(li);
      |             ^
foo_mrmr_ensemble_surv.cpp:474:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  474 |         int mat_res [power((maxnsol+1),(depth))][depth+2];
      |                      ^~~~~~~~~~~~~~~~~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:474:22: note: function parameter 'maxnsol' with unknown value cannot be used in a constant expression
  474 |         int mat_res [power((maxnsol+1),(depth))][depth+2];
      |                             ^
foo_mrmr_ensemble_surv.cpp:464:146: note: declared here
  464 | int verify_equivalentset_nparents (tree<int>& tr, tree<int>::pre_order_iterator it, tree<int>::pre_order_iterator end,tree<double>& tr_mrmr, int maxnsol){
      |                                                                                                                                                  ^
foo_mrmr_ensemble_surv.cpp:476:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  476 |         int to_remove[number_leafs];
      |                       ^~~~~~~~~~~~
foo_mrmr_ensemble_surv.cpp:476:16: note: read of non-const variable 'number_leafs' is not allowed in a constant expression
foo_mrmr_ensemble_surv.cpp:475:6: note: declared here
  475 |         int number_leafs=power((maxnsol+1),(depth));
      |             ^
foo_mrmr_ensemble_surv.cpp:467:7: warning: unused variable 'found' [-Wunused-variable]
  467 |         bool found=false;
      |              ^~~~~
foo_mrmr_ensemble_surv.cpp:578:24: 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:578:48: 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:578:66: 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:579:21: 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:579:63: 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:803:13: warning: unused variable 'cnt2' [-Wunused-variable]
  803 |                 int cnt=1,cnt2=0;
      |                           ^~~~
foo_mrmr_ensemble_surv.cpp:806:7: warning: unused variable 'rootdepth' [-Wunused-variable]
  806 |                 int rootdepth=res_tree.depth(it_final);
      |                     ^~~~~~~~~
foo_mrmr_ensemble_surv.cpp:819:7: warning: unused variable 'ind' [-Wunused-variable]
  819 |                 int ind=0;
      |                     ^~~
foo_mrmr_ensemble_surv.cpp:733:30: warning: unused variable 'res_all' [-Wunused-variable]
  733 |         int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
      |                                     ^~~~~~~
foo_mrmr_ensemble_surv.cpp:733:39: warning: unused variable 'res_all2' [-Wunused-variable]
  733 |         int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
      |                                              ^~~~~~~~
foo_mrmr_ensemble_surv.cpp:734:6: warning: unused variable 'vec_tmp' [-Wunused-variable]
  734 |         int vec_tmp;
      |             ^~~~~~~
35 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c foo_mrmr_surv.cpp -o foo_mrmr_surv.o
foo_mrmr_surv.cpp:80:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
   80 |         double res_ch[lenStrat];
      |                       ^~~~~~~~
foo_mrmr_surv.cpp:80:16: note: read of non-const variable 'lenStrat' is not allowed in a constant expression
foo_mrmr_surv.cpp:78:6: note: declared here
   78 |         int lenStrat = *lenS;
      |             ^
foo_mrmr_surv.cpp:81:16: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
   81 |         double res_dh[lenStrat];
      |                       ^~~~~~~~
foo_mrmr_surv.cpp:81:16: note: read of non-const variable 'lenStrat' is not allowed in a constant expression
foo_mrmr_surv.cpp:78:6: note: declared here
   78 |         int lenStrat = *lenS;
      |             ^
foo_mrmr_surv.cpp:88:11: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
   88 |                 int ixs[lenStrat];
      |                         ^~~~~~~~
foo_mrmr_surv.cpp:88:11: note: read of non-const variable 'lenStrat' is not allowed in a constant expression
foo_mrmr_surv.cpp:78:6: note: declared here
   78 |         int lenStrat = *lenS;
      |             ^
foo_mrmr_surv.cpp:104:13: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  104 |                 double xs[Ns];
      |                           ^~
foo_mrmr_surv.cpp:104:13: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_surv.cpp:86:6: note: declared here
   86 |         int Ns = 0;
      |             ^
foo_mrmr_surv.cpp:112:11: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  112 |                 int cls[Ns];
      |                         ^~
foo_mrmr_surv.cpp:112:11: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_surv.cpp:86:6: note: declared here
   86 |         int Ns = 0;
      |             ^
foo_mrmr_surv.cpp:120:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  120 |                 double sts[Ns];
      |                            ^~
foo_mrmr_surv.cpp:120:14: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_surv.cpp:86:6: note: declared here
   86 |         int Ns = 0;
      |             ^
foo_mrmr_surv.cpp:128:11: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  128 |                 int ses[Ns];
      |                         ^~
foo_mrmr_surv.cpp:128:11: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_surv.cpp:86:6: note: declared here
   86 |         int Ns = 0;
      |             ^
foo_mrmr_surv.cpp:136:19: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  136 |                 double weightss[Ns];
      |                                 ^~
foo_mrmr_surv.cpp:136:19: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_surv.cpp:86:6: note: declared here
   86 |         int Ns = 0;
      |             ^
foo_mrmr_surv.cpp:144:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  144 |                 double chs[Ns];
      |                            ^~
foo_mrmr_surv.cpp:144:14: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_surv.cpp:86:6: note: declared here
   86 |         int Ns = 0;
      |             ^
foo_mrmr_surv.cpp:145:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  145 |                 double dhs[Ns];
      |                            ^~
foo_mrmr_surv.cpp:145:14: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_surv.cpp:86:6: note: declared here
   86 |         int Ns = 0;
      |             ^
foo_mrmr_surv.cpp:146:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  146 |                 double uhs[Ns];
      |                            ^~
foo_mrmr_surv.cpp:146:14: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_surv.cpp:86:6: note: declared here
   86 |         int Ns = 0;
      |             ^
foo_mrmr_surv.cpp:147:15: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
  147 |                 double rphs[Ns];
      |                             ^~
foo_mrmr_surv.cpp:147:15: note: read of non-const variable 'Ns' is not allowed in a constant expression
foo_mrmr_surv.cpp:86:6: note: declared here
   86 |         int Ns = 0;
      |             ^
12 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c survcomp_init.cpp -o survcomp_init.o
clang++ -arch arm64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o survcomp.so concordance.index.o foo_mrmr_ensemble_surv.o foo_mrmr_surv.o survcomp_init.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6/Resources/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)