* installing *source* package ‘epiworldR’ ...
** package ‘epiworldR’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether /usr/local/clang18/bin/clang++ -std=gnu++17 accepts -g... yes
checking for /usr/local/clang18/bin/clang++ -std=gnu++17 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... /usr/local/clang18/bin/clang++ -std=gnu++17 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether /usr/local/clang18/bin/clang++ -std=gnu++17 accepts -g... (cached) yes
checking for /usr/local/clang18/bin/clang++ -std=gnu++17 option to enable C++11 features... (cached) none needed
checking whether we have a suitable tempdir... /tmp/RtmpTsrAly/working_dir
checking whether R CMD SHLIB can already compile programs using OpenMP... yes
checking whether to build the dev version... configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/epiworldR-package.R
** libs
using C++ compiler: ‘clang version 18.1.4’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/epiworldR/src'
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/cpp11/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c actions.cpp -o actions.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/cpp11/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c agents.cpp -o agents.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/cpp11/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c cpp11.cpp -o cpp11.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/cpp11/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c db.cpp -o db.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/cpp11/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c epimodels.cpp -o epimodels.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/cpp11/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c model.cpp -o model.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/cpp11/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c tool.cpp -o tool.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/cpp11/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c virus.cpp -o virus.o
In file included from virus.cpp:4:
In file included from ./epiworld-common.h:4:
In file included from ../inst/include/epiworld/epiworld.hpp:54:
../inst/include/epiworld/virus-meat.hpp:59:47: warning: lambda capture 'logit' is not used [-Wunused-lambda-capture]
59 | VirusFun<TSeq> fun_infect = [coefs_f,vars,logit](
| ^
virus.cpp:108:11: note: in instantiation of function template specialization 'epiworld::virus_fun_logit<int>' requested here
108 | virus_fun_logit(
| ^
In file included from tool.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11.hpp:3:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:27:
In file included from /usr/local/clang18/bin/../include/c++/v1/type_traits:445:
/usr/local/clang18/bin/../include/c++/v1/__type_traits/invoke.h:342:1: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
342 | __invoke(_Fp&& __f, _Args&&... __args)
| ^
1 warning generated.
In file included from virus.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11.hpp:3:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:27:
In file included from /usr/local/clang18/bin/../include/c++/v1/type_traits:445:
/usr/local/clang18/bin/../include/c++/v1/__type_traits/invoke.h:410:67: warning: loop not vectorized: the optimizer was unable to perform the requested transformation; the transformation might be disabled or specified as part of an unsupported transformation ordering [-Wpass-failed=transform-warning]
410 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX20 static _Ret __call(_Args&&... __args) {
| ^
2 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o epiworldR.so actions.o agents.o cpp11.o db.o epimodels.o model.o tool.o virus.o -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lFortran_main -lFortranRuntime -lFortranDecimal -lm -fopenmp
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/epiworldR/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/epiworldR/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/epiworldR/src'
installing to /data/gannet/ripley/R/packages/tests-clang/epiworldR.Rcheck/00LOCK-epiworldR/00new/epiworldR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (epiworldR)