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This page was generated on 2023-10-16 11:37:36 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 2045/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
survcomp 1.50.0  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/survcomp
git_branch: RELEASE_3_17
git_last_commit: 2e4fd3e
git_last_commit_date: 2023-04-25 10:19:21 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for survcomp on merida1


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: 1.50.0
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_1.50.0.tar.gz
StartedAt: 2023-10-16 07:48:21 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 07:50:59 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 157.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: survcomp.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### 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_1.50.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/survcomp.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘survcomp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘survcomp’ version ‘1.50.0’
* 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 ... WARNING
Found the following significant warnings:
  foo_mrmr_ensemble_surv.cpp:821:16: warning: variable 'res_old' is uninitialized when used here [-Wuninitialized]
  ./tree.h:505:18: warning: 'allocate' is deprecated [-Wdeprecated-declarations]
  ./tree.h:506:16: warning: 'allocate' is deprecated [-Wdeprecated-declarations]
  ./tree.h:1122:26: warning: 'allocate' is deprecated [-Wdeprecated-declarations]
  ./tree.h:998:26: warning: 'allocate' is deprecated [-Wdeprecated-declarations]
  ./tree.h:886:26: warning: 'allocate' is deprecated [-Wdeprecated-declarations]
See ‘/Users/biocbuild/bbs-3.17-bioc/meat/survcomp.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.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 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 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 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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



Installation output

survcomp.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL survcomp
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘survcomp’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c concordance.index.c -o concordance.index.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/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: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: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: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:387:10: warning: unused variable 'mim' [-Wunused-variable]
        double *mim, *boot_val, *mat_info;
                ^
foo_mrmr_ensemble_surv.cpp:439:9: warning: unused variable 'max_val' [-Wunused-variable]
        double max_val=-1000;
               ^
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:467:7: warning: unused variable 'found' [-Wunused-variable]
        bool found=false;
             ^
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: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:578:24: 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: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: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:817:7: warning: unused variable 'ind' [-Wunused-variable]
                int ind=0;
                    ^
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:734:6: warning: unused variable 'vec_tmp' [-Wunused-variable]
        int vec_tmp;
            ^
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:733:30: warning: unused variable 'res_all' [-Wunused-variable]
        int *predn, *rep_boot,*res,*res_all,*res_all2, *namat;
                                    ^
foo_mrmr_ensemble_surv.cpp:821:16: warning: variable 'res_old' is uninitialized when used here [-Wuninitialized]
                                res_all[k]=res_old[k];
                                           ^~~~~~~
foo_mrmr_ensemble_surv.cpp:816:25: note: initialize the variable 'res_old' to silence this warning
                int *res_all, *res_old;
                                      ^
                                       = nullptr
In file included from foo_mrmr_ensemble_surv.cpp:1:
In file included from ./foo_mrmr_ensemble_surv.h:10:
./tree.h:505:18: warning: 'allocate' is deprecated [-Wdeprecated-declarations]
   head = alloc_.allocate(1,0); // MSVC does not have default second argument 
                 ^
./tree.h:530:2: note: in instantiation of member function 'tree<int>::head_initialise_' requested here
        head_initialise_();
        ^
foo_mrmr_ensemble_surv.cpp:611:24: note: in instantiation of member function 'tree<int>::tree' requested here
        tree<int> res_tmp_new=res ;
                              ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1668:61: note: 'allocate' has been explicitly marked deprecated here
    _LIBCPP_NODISCARD_AFTER_CXX17 _LIBCPP_INLINE_VISIBILITY _LIBCPP_DEPRECATED_IN_CXX17
                                                            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1058:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
#  define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from foo_mrmr_ensemble_surv.cpp:1:
In file included from ./foo_mrmr_ensemble_surv.h:10:
./tree.h:506:16: warning: 'allocate' is deprecated [-Wdeprecated-declarations]
        feet = alloc_.allocate(1,0);
                      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1668:61: note: 'allocate' has been explicitly marked deprecated here
    _LIBCPP_NODISCARD_AFTER_CXX17 _LIBCPP_INLINE_VISIBILITY _LIBCPP_DEPRECATED_IN_CXX17
                                                            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1058:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
#  define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from foo_mrmr_ensemble_surv.cpp:1:
In file included from ./foo_mrmr_ensemble_surv.h:10:
./tree.h:1122:26: warning: 'allocate' is deprecated [-Wdeprecated-declarations]
        tree_node* tmp = alloc_.allocate(1,0);
                                ^
./tree.h:547:6: note: in instantiation of function template specialization 'tree<int>::replace<tree<int>::pre_order_iterator>' requested here
                to=replace(to, it);
                   ^
./tree.h:531:2: note: in instantiation of member function 'tree<int>::copy_' requested here
        copy_(other);
        ^
foo_mrmr_ensemble_surv.cpp:611:24: note: in instantiation of member function 'tree<int>::tree' requested here
        tree<int> res_tmp_new=res ;
                              ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1668:61: note: 'allocate' has been explicitly marked deprecated here
    _LIBCPP_NODISCARD_AFTER_CXX17 _LIBCPP_INLINE_VISIBILITY _LIBCPP_DEPRECATED_IN_CXX17
                                                            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1058:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
#  define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from foo_mrmr_ensemble_surv.cpp:1:
In file included from ./foo_mrmr_ensemble_surv.h:10:
./tree.h:505:18: warning: 'allocate' is deprecated [-Wdeprecated-declarations]
   head = alloc_.allocate(1,0); // MSVC does not have default second argument 
                 ^
./tree.h:476:2: note: in instantiation of member function 'tree<double>::head_initialise_' requested here
        head_initialise_();
        ^
foo_mrmr_ensemble_surv.cpp:620:15: note: in instantiation of member function 'tree<double>::tree' requested here
        tree<double> res_mrmr;
                     ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1668:61: note: 'allocate' has been explicitly marked deprecated here
    _LIBCPP_NODISCARD_AFTER_CXX17 _LIBCPP_INLINE_VISIBILITY _LIBCPP_DEPRECATED_IN_CXX17
                                                            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1058:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
#  define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from foo_mrmr_ensemble_surv.cpp:1:
In file included from ./foo_mrmr_ensemble_surv.h:10:
./tree.h:506:16: warning: 'allocate' is deprecated [-Wdeprecated-declarations]
        feet = alloc_.allocate(1,0);
                      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1668:61: note: 'allocate' has been explicitly marked deprecated here
    _LIBCPP_NODISCARD_AFTER_CXX17 _LIBCPP_INLINE_VISIBILITY _LIBCPP_DEPRECATED_IN_CXX17
                                                            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1058:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
#  define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from foo_mrmr_ensemble_surv.cpp:1:
In file included from ./foo_mrmr_ensemble_surv.h:10:
./tree.h:998:26: warning: 'allocate' is deprecated [-Wdeprecated-declarations]
        tree_node* tmp = alloc_.allocate(1,0);
                                ^
foo_mrmr_ensemble_surv.cpp:625:11: note: in instantiation of function template specialization 'tree<double>::insert<tree<double>::pre_order_iterator>' requested here
        res_mrmr.insert(top_mrmr, predn);
                 ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1668:61: note: 'allocate' has been explicitly marked deprecated here
    _LIBCPP_NODISCARD_AFTER_CXX17 _LIBCPP_INLINE_VISIBILITY _LIBCPP_DEPRECATED_IN_CXX17
                                                            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1058:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
#  define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from foo_mrmr_ensemble_surv.cpp:1:
In file included from ./foo_mrmr_ensemble_surv.h:10:
./tree.h:886:26: warning: 'allocate' is deprecated [-Wdeprecated-declarations]
        tree_node* tmp = alloc_.allocate(1,0);
                                ^
foo_mrmr_ensemble_surv.cpp:690:17: note: in instantiation of function template specialization 'tree<int>::append_child<tree<int>::pre_order_iterator>' requested here
                                res_tmp_new.append_child(it_local,vec_sol_local[k]);
                                            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1668:61: note: 'allocate' has been explicitly marked deprecated here
    _LIBCPP_NODISCARD_AFTER_CXX17 _LIBCPP_INLINE_VISIBILITY _LIBCPP_DEPRECATED_IN_CXX17
                                                            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1058:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
#  define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from foo_mrmr_ensemble_surv.cpp:1:
In file included from ./foo_mrmr_ensemble_surv.h:10:
./tree.h:886:26: warning: 'allocate' is deprecated [-Wdeprecated-declarations]
        tree_node* tmp = alloc_.allocate(1,0);
                                ^
foo_mrmr_ensemble_surv.cpp:691:14: note: in instantiation of function template specialization 'tree<double>::append_child<tree<double>::pre_order_iterator>' requested here
                                res_mrmr.append_child(it_mrmr_local,vec_sol_local_mrmr[k]);
                                         ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1668:61: note: 'allocate' has been explicitly marked deprecated here
    _LIBCPP_NODISCARD_AFTER_CXX17 _LIBCPP_INLINE_VISIBILITY _LIBCPP_DEPRECATED_IN_CXX17
                                                            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1058:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
#  define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from foo_mrmr_ensemble_surv.cpp:1:
In file included from ./foo_mrmr_ensemble_surv.h:10:
./tree.h:998:26: warning: 'allocate' is deprecated [-Wdeprecated-declarations]
        tree_node* tmp = alloc_.allocate(1,0);
                                ^
foo_mrmr_ensemble_surv.cpp:788:16: note: in instantiation of function template specialization 'tree<int>::insert<tree<int>::pre_order_iterator>' requested here
                one=res_tree.insert(top, predn[i]);
                             ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/memory:1668:61: note: 'allocate' has been explicitly marked deprecated here
    _LIBCPP_NODISCARD_AFTER_CXX17 _LIBCPP_INLINE_VISIBILITY _LIBCPP_DEPRECATED_IN_CXX17
                                                            ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1058:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX17'
#  define _LIBCPP_DEPRECATED_IN_CXX17 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
29 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c foo_mrmr_surv.cpp -o foo_mrmr_surv.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c survcomp_init.cpp -o survcomp_init.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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 -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-x86_64/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)

Tests output


Example timings

survcomp.Rcheck/survcomp-Ex.timings

nameusersystemelapsed
D.index0.0450.0170.079
balanced.hazard.ratio0.0240.0080.042
bhr.comp0.0210.0020.032
breastCancerData1.0150.0361.364
censor.time0.0010.0020.003
cindex.comp0.0040.0010.005
cindex.comp.meta0.0080.0010.009
combine.est0.0010.0010.002
combine.test0.0010.0010.002
concordance.index0.0050.0100.020
cvpl0.2770.0080.370
dindex.comp0.0190.0020.028
dindex.comp.meta0.0410.0020.054
fisherz0.0010.0010.002
forestplot.surv0.0610.0030.078
getsurv20.0070.0010.011
hazard.ratio0.0170.0070.034
hr.comp0.0190.0020.027
hr.comp.meta0.0400.0020.054
hr.comp20.0130.0010.015
iauc.comp0.5250.0340.696
ibsc.comp0.4560.0180.599
km.coxph.plot0.0810.0030.112
logpl0.0330.0020.046
mainz7g0.3290.0130.426
metaplot.surv0.0060.0010.011
mrmr.cindex0.0040.0010.008
nki7g0.3170.0120.404
no.at.risk0.0230.0010.030
sbrier.score2proba0.3750.0060.478
score2proba0.0310.0030.042
td.sens.spec0.0030.0000.004
tdrocc0.2010.0530.319
test.hetero.est0.0010.0010.002
test.hetero.test0.0010.0010.002
transbig7g0.3250.0120.429
unt7g0.3170.0130.417
upp7g0.3150.0120.408
vdx7g0.3200.0130.413