* installing *source* package ‘adapt3’ ...
** this is package ‘adapt3’ version ‘2.0.7’
** package ‘adapt3’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 21.1.8’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/adapt3/src'
/usr/local/clang21/bin/clang++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/lefko3/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include/ -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c RcppExports.cpp -o RcppExports.o
/usr/local/clang21/bin/clang++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/lefko3/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include/ -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c projection.cpp -o projection.o
/usr/local/clang21/bin/clang++ -std=gnu++20 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/BH/include' -I'/data/gannet/ripley/R/test-clang/lefko3/include' -isystem /usr/local/clang21/include -I/usr/local/clang/include -I../inst/include/ -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c utilities.cpp -o utilities.o
In file included from projection.cpp:10:
In file included from /data/gannet/ripley/R/test-clang/lefko3/include/LefkoUtils.h:8:
/data/gannet/ripley/R/test-clang/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};
| ^
/data/gannet/ripley/R/test-clang/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};
| ^
/data/gannet/ripley/R/test-clang/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:4474:9: warning: variable 'good_max_age_values' set but not used [-Wunused-but-set-variable]
4474 | int good_max_age_values {0};
| ^
In file included from projection.cpp:11:
In file included from ../inst/include/AdaptUtils.h:8:
../inst/include/basic_funcs/mats_utils.h:3699:9: warning: unused variable 'nostages_nounborn' [-Wunused-variable]
3699 | int nostages_nounborn = nostages - almostbornstages;
| ^~~~~~~~~~~~~~~~~
projection.cpp:5880:8: warning: variable 'pure_fleslie' set but not used [-Wunused-but-set-variable]
5880 | bool pure_fleslie {false}; // Are all function-based MPMs Leslie MPMs?
| ^
projection.cpp:5885:7: warning: variable 'stageframe_count' set but not used [-Wunused-but-set-variable]
5885 | int stageframe_count {0};
| ^
projection.cpp:5886:7: warning: variable 'stageframe_notNull_count' set but not used [-Wunused-but-set-variable]
5886 | int stageframe_notNull_count {0};
| ^
projection.cpp:5887:7: warning: variable 'supplement_count' set but not used [-Wunused-but-set-variable]
5887 | int supplement_count {0};
| ^
projection.cpp:5888:7: warning: variable 'equivalence_count' set but not used [-Wunused-but-set-variable]
5888 | int equivalence_count {0};
| ^
projection.cpp:5889:7: warning: variable 'start_count' set but not used [-Wunused-but-set-variable]
5889 | int start_count {0};
| ^
projection.cpp:5890:7: warning: variable 'tweights_count' set but not used [-Wunused-but-set-variable]
5890 | int tweights_count {0};
| ^
projection.cpp:5891:7: warning: variable 'density_count' set but not used [-Wunused-but-set-variable]
5891 | int density_count {0};
| ^
projection.cpp:5892:7: warning: variable 'entry_time_count' set but not used [-Wunused-but-set-variable]
5892 | int entry_time_count {0};
| ^
projection.cpp:5893:7: warning: variable 'density_vr_count' set but not used [-Wunused-but-set-variable]
5893 | int density_vr_count {0};
| ^
projection.cpp:5894:7: warning: variable 'sparse_vec_count' set but not used [-Wunused-but-set-variable]
5894 | int sparse_vec_count {0};
| ^
projection.cpp:5895:7: warning: variable 'found_fleslie' set but not used [-Wunused-but-set-variable]
5895 | int found_fleslie {0};
| ^
In file included from utilities.cpp:7:
In file included from /data/gannet/ripley/R/test-clang/lefko3/include/LefkoUtils.h:8:
/data/gannet/ripley/R/test-clang/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};
| ^
/data/gannet/ripley/R/test-clang/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};
| ^
/data/gannet/ripley/R/test-clang/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};
| ^
projection.cpp:7874:15: warning: variable 'maxage_NAs' set but not used [-Wunused-but-set-variable]
7874 | int maxage_NAs {0};
| ^
projection.cpp:6582:8: warning: unused variable 'sensitivity_bool' [-Wunused-variable]
6582 | bool sensitivity_bool {false};
| ^~~~~~~~~~~~~~~~
In file included from utilities.cpp:8:
In file included from ../inst/include/AdaptUtils.h:7:
../inst/include/basic_funcs/main_utils.h:4474:9: warning: variable 'good_max_age_values' set but not used [-Wunused-but-set-variable]
4474 | int good_max_age_values {0};
| ^
projection.cpp:12838:18: warning: unused variable 'res_fitness_test' [-Wunused-variable]
12838 | double res_fitness_test = current_round_fitness_values(0);
| ^~~~~~~~~~~~~~~~
projection.cpp:12468:12: warning: variable 'conv_test' set but not used [-Wunused-but-set-variable]
12468 | double conv_test {0.};
| ^
projection.cpp:12470:12: warning: variable 'xE' set but not used [-Wunused-but-set-variable]
12470 | double xE {0.}; // test value to keep in memory from previous expansion round
| ^
projection.cpp:12471:12: warning: variable 'xC_new' set but not used [-Wunused-but-set-variable]
12471 | double xC_new {0.}; // test value to keep in memory from previous contraction round
| ^
projection.cpp:13053:7: warning: unused variable 'optim_rows' [-Wunused-variable]
13053 | int optim_rows = static_cast<int>(final_output_df.nrows());
| ^~~~~~~~~~
projection.cpp:14893:18: warning: unused variable 'res_fitness_test' [-Wunused-variable]
14893 | double res_fitness_test = current_round_fitness_values(0);
| ^~~~~~~~~~~~~~~~
projection.cpp:14411:12: warning: variable 'conv_test' set but not used [-Wunused-but-set-variable]
14411 | double conv_test {0.};
| ^
projection.cpp:14413:12: warning: variable 'xE' set but not used [-Wunused-but-set-variable]
14413 | double xE {0.}; // test value to keep in memory from previous expansion round
| ^
projection.cpp:14414:12: warning: variable 'xC_new' set but not used [-Wunused-but-set-variable]
14414 | double xC_new {0.}; // test value to keep in memory from previous contraction round
| ^
projection.cpp:15110:7: warning: unused variable 'optim_rows' [-Wunused-variable]
15110 | int optim_rows = static_cast<int>(final_output_df.nrows());
| ^~~~~~~~~~
In file included from utilities.cpp:8:
In file included from ../inst/include/AdaptUtils.h:8:
../inst/include/basic_funcs/mats_utils.h:3699:9: warning: unused variable 'nostages_nounborn' [-Wunused-variable]
3699 | int nostages_nounborn = nostages - almostbornstages;
| ^~~~~~~~~~~~~~~~~
projection.cpp:19851:7: warning: unused variable 'stageframe_count' [-Wunused-variable]
19851 | int stageframe_count {0};
| ^~~~~~~~~~~~~~~~
projection.cpp:19852:7: warning: variable 'stageframe_notNull_count' set but not used [-Wunused-but-set-variable]
19852 | int stageframe_notNull_count {0};
| ^
projection.cpp:19853:7: warning: unused variable 'supplement_count' [-Wunused-variable]
19853 | int supplement_count {0};
| ^~~~~~~~~~~~~~~~
projection.cpp:19854:7: warning: variable 'equivalence_count' set but not used [-Wunused-but-set-variable]
19854 | int equivalence_count {0};
| ^
projection.cpp:19855:7: warning: variable 'start_count' set but not used [-Wunused-but-set-variable]
19855 | int start_count {0};
| ^
projection.cpp:19856:7: warning: variable 'tweights_count' set but not used [-Wunused-but-set-variable]
19856 | int tweights_count {0};
| ^
projection.cpp:19857:7: warning: variable 'density_count' set but not used [-Wunused-but-set-variable]
19857 | int density_count {0};
| ^
projection.cpp:19859:7: warning: variable 'entry_time_count' set but not used [-Wunused-but-set-variable]
19859 | int entry_time_count {0};
| ^
projection.cpp:19860:7: warning: variable 'density_vr_count' set but not used [-Wunused-but-set-variable]
19860 | int density_vr_count {0};
| ^
projection.cpp:19861:7: warning: variable 'sparse_vec_count' set but not used [-Wunused-but-set-variable]
19861 | int sparse_vec_count {0};
| ^
projection.cpp:19873:8: warning: variable 'prebreeding_bool' set but not used [-Wunused-but-set-variable]
19873 | bool prebreeding_bool {true};
| ^
5 warnings generated.
40 warnings generated.
/usr/local/clang21/bin/clang++ -std=gnu++20 -shared -L/usr/local/clang/lib64 -L/usr/local/clang21/lib -L/usr/local/clang21/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -o adapt3.so RcppExports.o projection.o utilities.o -fopenmp -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lflang_rt.runtime -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/adapt3/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/adapt3/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/adapt3/src'
installing to /data/gannet/ripley/R/packages/tests-clang/adapt3.Rcheck/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)