* installing *source* package ‘epiworldR’ ... ** 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 clang++-16 -std=gnu++17 accepts -g... yes checking for clang++-16 -std=gnu++17 option to enable C++11 features... none needed checking how to run the C++ preprocessor... clang++-16 -std=gnu++17 -E checking whether the compiler supports GNU C++... (cached) yes checking whether clang++-16 -std=gnu++17 accepts -g... (cached) yes checking for clang++-16 -std=gnu++17 option to enable C++11 features... (cached) none needed checking whether we have a suitable tempdir... /tmp/RtmpIHUoRB/working_dir checking whether R CMD SHLIB can already compile programs using OpenMP... yes configure: creating ./config.status config.status: creating src/Makevars ** libs using C++ compiler: ‘Debian clang version 16.0.6 (11)’ clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O3 -Wall -pedantic -c actions.cpp -o actions.o clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O3 -Wall -pedantic -c agents.cpp -o agents.o clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O3 -Wall -pedantic -c cpp11.cpp -o cpp11.o clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O3 -Wall -pedantic -c db.cpp -o db.o clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O3 -Wall -pedantic -c epimodels.cpp -o epimodels.o In file included from epimodels.cpp:5: In file included from ./epiworld-common.h:4: In file included from ../inst/include/epiworld/epiworld.hpp:72: In file included from ../inst/include/epiworld/models/models.hpp:15: ../inst/include/epiworld/models/seird.hpp:67:10: warning: unused variable 'state' [-Wunused-variable] auto state = p->get_state(); ^ ../inst/include/epiworld/models/seird.hpp:38:3: note: in instantiation of default member initializer 'epiworld::epimodels::ModelSEIRD<>::update_infected' requested here ModelSEIRD( ^ epimodels.cpp:218:13: note: in instantiation of member function 'epiworld::epimodels::ModelSEIRD<>::ModelSEIRD' requested here new epiworld::epimodels::ModelSEIRD<>( ^ 1 warning generated. clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O3 -Wall -pedantic -c model.cpp -o model.o clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O3 -Wall -pedantic -c tool.cpp -o tool.o In file included from tool.cpp:4: In file included from ./epiworld-common.h:4: In file included from ../inst/include/epiworld/epiworld.hpp:59: ../inst/include/epiworld/tool-meat.hpp:69:9: 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] #pragma omp simd reduction(+:res) ^ 1 warning generated. clang++-16 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O3 -Wall -pedantic -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] VirusFun fun_infect = [coefs_f,vars,logit]( ^ virus.cpp:108:11: note: in instantiation of function template specialization 'epiworld::virus_fun_logit' requested here virus_fun_logit( ^ 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:68:9: 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] #pragma omp simd reduction(+:res) ^ 2 warnings generated. clang++-16 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o epiworldR.so actions.o agents.o cpp11.o db.o epimodels.o model.o tool.o virus.o -llapack -L/home/hornik/tmp/R/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/hornik/tmp/R/lib -lR installing to /srv/hornik/tmp/CRAN/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)