* installing *source* package ‘lefko3’ ...
** this is package ‘lefko3’ version ‘6.7.1’
** package ‘lefko3’ 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/lefko3/src'
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_USE_CURRENT -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' -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 DataManagement.cpp -o DataManagement.o
In file included from DataManagement.cpp:5:
In file included from ../inst/include/LefkoUtils.h:8:
../inst/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};
      |            ^
../inst/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};
      |         ^
../inst/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};
      |         ^
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_USE_CURRENT -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' -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 ErrorChecks.cpp -o ErrorChecks.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_USE_CURRENT -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' -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 ExtraFunctions.cpp -o ExtraFunctions.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_USE_CURRENT -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' -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 Mats2.cpp -o Mats2.o
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_USE_CURRENT -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' -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 MatsNProj.cpp -o MatsNProj.o
In file included from Mats2.cpp:3:
In file included from ../inst/include/LefkoUtils.h:8:
../inst/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};
      |            ^
../inst/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};
      |         ^
../inst/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};
      |         ^
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_USE_CURRENT -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' -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 ModelSelection.cpp -o ModelSelection.o
In file included from MatsNProj.cpp:7:
In file included from ../inst/include/LefkoUtils.h:8:
../inst/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};
      |            ^
../inst/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};
      |         ^
../inst/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};
      |         ^
3 warnings generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_USE_CURRENT -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' -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 PopChar.cpp -o PopChar.o
In file included from ModelSelection.cpp:2:
In file included from ../inst/include/LefkoUtils.h:8:
../inst/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};
      |            ^
../inst/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};
      |         ^
../inst/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};
      |         ^
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_USE_CURRENT -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' -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 PopDyn2.cpp -o PopDyn2.o
In file included from PopChar.cpp:3:
In file included from ../inst/include/LefkoUtils.h:8:
../inst/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};
      |            ^
../inst/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};
      |         ^
../inst/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};
      |         ^
/usr/local/clang21/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DARMA_USE_CURRENT -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' -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
3 warnings generated.
In file included from PopDyn2.cpp:3:
In file included from ../inst/include/LefkoUtils.h:8:
../inst/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};
      |            ^
../inst/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};
      |         ^
../inst/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};
      |         ^
3 warnings generated.
3 warnings generated.
3 warnings generated.
3 warnings generated.
/usr/local/clang21/bin/clang++ -std=gnu++17 -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 lefko3.so DataManagement.o ErrorChecks.o ExtraFunctions.o Mats2.o MatsNProj.o ModelSelection.o PopChar.o PopDyn2.o RcppExports.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/lefko3/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/lefko3/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/lefko3/src'
installing to /data/gannet/ripley/R/packages/tests-clang/lefko3.Rcheck/00LOCK-lefko3/00new/lefko3/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 (lefko3)