* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’
* installing *source* package ‘adapt3’ ...
** this is package ‘adapt3’ version ‘2.0.9’
** package ‘adapt3’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Debian clang version 22.1.8 (1)’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpp7g7v5/R.INSTALL1204491bdfcbbe/adapt3/src'
clang++-22 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/lefko3/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include/ -fpic -g -O3 -Wall -pedantic -c RcppExports.cpp -o RcppExports.o
clang++-22 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/lefko3/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include/ -fpic -g -O3 -Wall -pedantic -c projection.cpp -o projection.o
In file included from projection.cpp:10:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/lefko3/include/LefkoUtils.h:8:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/lefko3/include/basic_funcs/mat_stuff.h:1672:12: warning: variable 'esta2_used' set but not used [-Wunused-but-set-variable]
1672 | bool esta2_used {false};
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/lefko3/include/basic_funcs/mat_stuff.h:1478:9: warning: variable 'age_related_stages' set but not used [-Wunused-but-set-variable]
1478 | int age_related_stages {0};
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/lefko3/include/basic_funcs/mat_stuff.h:1479:9: warning: variable 'age_related_min_ages' set but not used [-Wunused-but-set-variable]
1479 | int age_related_min_ages {0};
| ^
In file included from projection.cpp:11:
In file included from ../inst/include/AdaptUtils.h:7:
../inst/include/basic_funcs/main_utils.h:4475:9: warning: variable 'good_max_age_values' set but not used [-Wunused-but-set-variable]
4475 | int good_max_age_values {0};
| ^
../inst/include/basic_funcs/main_utils.h:4551:9: warning: variable 'ce2_nas_length' set but not used [-Wunused-but-set-variable]
4551 | int ce2_nas_length {0};
| ^
In file included from projection.cpp:11:
In file included from ../inst/include/AdaptUtils.h:8:
../inst/include/basic_funcs/mats_utils.h:3763:9: warning: unused variable 'nostages_nounborn' [-Wunused-variable]
3763 | int nostages_nounborn = nostages - almostbornstages;
| ^~~~~~~~~~~~~~~~~
projection.cpp:5891:8: warning: variable 'pure_fleslie' set but not used [-Wunused-but-set-variable]
5891 | bool pure_fleslie {false}; // Are all function-based MPMs Leslie MPMs?
| ^
projection.cpp:5896:7: warning: variable 'stageframe_count' set but not used [-Wunused-but-set-variable]
5896 | int stageframe_count {0};
| ^
projection.cpp:5897:7: warning: variable 'stageframe_notNull_count' set but not used [-Wunused-but-set-variable]
5897 | int stageframe_notNull_count {0};
| ^
projection.cpp:5898:7: warning: variable 'supplement_count' set but not used [-Wunused-but-set-variable]
5898 | int supplement_count {0};
| ^
projection.cpp:5899:7: warning: variable 'equivalence_count' set but not used [-Wunused-but-set-variable]
5899 | int equivalence_count {0};
| ^
projection.cpp:5900:7: warning: variable 'start_count' set but not used [-Wunused-but-set-variable]
5900 | int start_count {0};
| ^
projection.cpp:5901:7: warning: variable 'tweights_count' set but not used [-Wunused-but-set-variable]
5901 | int tweights_count {0};
| ^
projection.cpp:5902:7: warning: variable 'density_count' set but not used [-Wunused-but-set-variable]
5902 | int density_count {0};
| ^
projection.cpp:5903:7: warning: variable 'entry_time_count' set but not used [-Wunused-but-set-variable]
5903 | int entry_time_count {0};
| ^
projection.cpp:5904:7: warning: variable 'density_vr_count' set but not used [-Wunused-but-set-variable]
5904 | int density_vr_count {0};
| ^
projection.cpp:5905:7: warning: variable 'sparse_vec_count' set but not used [-Wunused-but-set-variable]
5905 | int sparse_vec_count {0};
| ^
projection.cpp:5906:7: warning: variable 'found_fleslie' set but not used [-Wunused-but-set-variable]
5906 | int found_fleslie {0};
| ^
projection.cpp:7888:15: warning: variable 'maxage_NAs' set but not used [-Wunused-but-set-variable]
7888 | int maxage_NAs {0};
| ^
projection.cpp:8089:13: warning: unused variable 'current_supplement_rows' [-Wunused-variable]
8089 | int current_supplement_rows = static_cast<int>(current_supplement_df.nrows());
| ^~~~~~~~~~~~~~~~~~~~~~~
projection.cpp:6596:8: warning: unused variable 'sensitivity_bool' [-Wunused-variable]
6596 | bool sensitivity_bool {false};
| ^~~~~~~~~~~~~~~~
projection.cpp:12857:18: warning: unused variable 'res_fitness_test' [-Wunused-variable]
12857 | double res_fitness_test = current_round_fitness_values(0);
| ^~~~~~~~~~~~~~~~
projection.cpp:12487:12: warning: variable 'conv_test' set but not used [-Wunused-but-set-variable]
12487 | double conv_test {0.};
| ^
projection.cpp:12489:12: warning: variable 'xE' set but not used [-Wunused-but-set-variable]
12489 | double xE {0.}; // test value to keep in memory from previous expansion round
| ^
projection.cpp:12490:12: warning: variable 'xC_new' set but not used [-Wunused-but-set-variable]
12490 | double xC_new {0.}; // test value to keep in memory from previous contraction round
| ^
projection.cpp:13072:7: warning: unused variable 'optim_rows' [-Wunused-variable]
13072 | int optim_rows = static_cast<int>(final_output_df.nrows());
| ^~~~~~~~~~
projection.cpp:14912:18: warning: unused variable 'res_fitness_test' [-Wunused-variable]
14912 | double res_fitness_test = current_round_fitness_values(0);
| ^~~~~~~~~~~~~~~~
projection.cpp:14430:12: warning: variable 'conv_test' set but not used [-Wunused-but-set-variable]
14430 | double conv_test {0.};
| ^
projection.cpp:14432:12: warning: variable 'xE' set but not used [-Wunused-but-set-variable]
14432 | double xE {0.}; // test value to keep in memory from previous expansion round
| ^
projection.cpp:14433:12: warning: variable 'xC_new' set but not used [-Wunused-but-set-variable]
14433 | double xC_new {0.}; // test value to keep in memory from previous contraction round
| ^
projection.cpp:15129:7: warning: unused variable 'optim_rows' [-Wunused-variable]
15129 | int optim_rows = static_cast<int>(final_output_df.nrows());
| ^~~~~~~~~~
projection.cpp:19872:7: warning: unused variable 'stageframe_count' [-Wunused-variable]
19872 | int stageframe_count {0};
| ^~~~~~~~~~~~~~~~
projection.cpp:19873:7: warning: variable 'stageframe_notNull_count' set but not used [-Wunused-but-set-variable]
19873 | int stageframe_notNull_count {0};
| ^
projection.cpp:19874:7: warning: unused variable 'supplement_count' [-Wunused-variable]
19874 | int supplement_count {0};
| ^~~~~~~~~~~~~~~~
projection.cpp:19875:7: warning: variable 'equivalence_count' set but not used [-Wunused-but-set-variable]
19875 | int equivalence_count {0};
| ^
projection.cpp:19876:7: warning: variable 'start_count' set but not used [-Wunused-but-set-variable]
19876 | int start_count {0};
| ^
projection.cpp:19877:7: warning: variable 'tweights_count' set but not used [-Wunused-but-set-variable]
19877 | int tweights_count {0};
| ^
projection.cpp:19878:7: warning: variable 'density_count' set but not used [-Wunused-but-set-variable]
19878 | int density_count {0};
| ^
projection.cpp:19880:7: warning: variable 'entry_time_count' set but not used [-Wunused-but-set-variable]
19880 | int entry_time_count {0};
| ^
projection.cpp:19881:7: warning: variable 'density_vr_count' set but not used [-Wunused-but-set-variable]
19881 | int density_vr_count {0};
| ^
projection.cpp:19882:7: warning: variable 'sparse_vec_count' set but not used [-Wunused-but-set-variable]
19882 | int sparse_vec_count {0};
| ^
projection.cpp:19894:8: warning: variable 'prebreeding_bool' set but not used [-Wunused-but-set-variable]
19894 | bool prebreeding_bool {true};
| ^
42 warnings generated.
clang++-22 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/lefko3/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I../inst/include/ -fpic -g -O3 -Wall -pedantic -c utilities.cpp -o utilities.o
In file included from utilities.cpp:7:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/lefko3/include/LefkoUtils.h:8:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/lefko3/include/basic_funcs/mat_stuff.h:1672:12: warning: variable 'esta2_used' set but not used [-Wunused-but-set-variable]
1672 | bool esta2_used {false};
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/lefko3/include/basic_funcs/mat_stuff.h:1478:9: warning: variable 'age_related_stages' set but not used [-Wunused-but-set-variable]
1478 | int age_related_stages {0};
| ^
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/lefko3/include/basic_funcs/mat_stuff.h:1479:9: warning: variable 'age_related_min_ages' set but not used [-Wunused-but-set-variable]
1479 | int age_related_min_ages {0};
| ^
In file included from utilities.cpp:8:
In file included from ../inst/include/AdaptUtils.h:7:
../inst/include/basic_funcs/main_utils.h:4475:9: warning: variable 'good_max_age_values' set but not used [-Wunused-but-set-variable]
4475 | int good_max_age_values {0};
| ^
../inst/include/basic_funcs/main_utils.h:4551:9: warning: variable 'ce2_nas_length' set but not used [-Wunused-but-set-variable]
4551 | int ce2_nas_length {0};
| ^
In file included from utilities.cpp:8:
In file included from ../inst/include/AdaptUtils.h:8:
../inst/include/basic_funcs/mats_utils.h:3763:9: warning: unused variable 'nostages_nounborn' [-Wunused-variable]
3763 | int nostages_nounborn = nostages - almostbornstages;
| ^~~~~~~~~~~~~~~~~
6 warnings generated.
clang++-22 -std=gnu++20 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o adapt3.so RcppExports.o projection.o utilities.o -fopenmp -llapack -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lRblas -L/usr/lib/llvm-22/lib/clang/22/lib/linux -L/usr/lib/llvm-22/lib -lflang_rt.runtime -lm -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpp7g7v5/R.INSTALL1204491bdfcbbe/adapt3/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpp7g7v5/R.INSTALL1204491bdfcbbe/adapt3/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpp7g7v5/R.INSTALL1204491bdfcbbe/adapt3/src'
installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-adapt3/00new/adapt3/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (adapt3)