* 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 fun_infect = [coefs_f,vars,logit]( | ^ virus.cpp:108:11: note: in instantiation of function template specialization 'epiworld::virus_fun_logit' 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)