* installing *source* package ‘epiworldR’ ...
** this is package ‘epiworldR’ version ‘0.8.3.0’
** 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 clang++-20 -std=gnu++17 accepts -g... yes
checking for clang++-20 -std=gnu++17 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... clang++-20 -std=gnu++17 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether clang++-20 -std=gnu++17 accepts -g... (cached) yes
checking for clang++-20 -std=gnu++17 option to enable C++11 features... (cached) none needed
checking whether we have a suitable tempdir... /tmp/Rtmpa44JCp/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 20.1.7’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/epiworldR/src'
clang++-20 -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/cpp11/include' -isystem /usr/local/clang20/include -I/usr/local/clang/include   -fopenmp -I../inst/include/  -Dprintf_epiworld=Rprintf -Depiworld_double=double '-DEPI_CHECK_USER_INTERRUPT(a)=cpp11::check_user_interrupt()' -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c actions.cpp -o actions.o
clang++-20 -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/cpp11/include' -isystem /usr/local/clang20/include -I/usr/local/clang/include   -fopenmp -I../inst/include/  -Dprintf_epiworld=Rprintf -Depiworld_double=double '-DEPI_CHECK_USER_INTERRUPT(a)=cpp11::check_user_interrupt()' -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c agents.cpp -o agents.o
clang++-20 -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/cpp11/include' -isystem /usr/local/clang20/include -I/usr/local/clang/include   -fopenmp -I../inst/include/  -Dprintf_epiworld=Rprintf -Depiworld_double=double '-DEPI_CHECK_USER_INTERRUPT(a)=cpp11::check_user_interrupt()' -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c cpp11.cpp -o cpp11.o
clang++-20 -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/cpp11/include' -isystem /usr/local/clang20/include -I/usr/local/clang/include   -fopenmp -I../inst/include/  -Dprintf_epiworld=Rprintf -Depiworld_double=double '-DEPI_CHECK_USER_INTERRUPT(a)=cpp11::check_user_interrupt()' -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c db.cpp -o db.o
clang++-20 -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/cpp11/include' -isystem /usr/local/clang20/include -I/usr/local/clang/include   -fopenmp -I../inst/include/  -Dprintf_epiworld=Rprintf -Depiworld_double=double '-DEPI_CHECK_USER_INTERRUPT(a)=cpp11::check_user_interrupt()' -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c entities.cpp -o entities.o
clang++-20 -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/cpp11/include' -isystem /usr/local/clang20/include -I/usr/local/clang/include   -fopenmp -I../inst/include/  -Dprintf_epiworld=Rprintf -Depiworld_double=double '-DEPI_CHECK_USER_INTERRUPT(a)=cpp11::check_user_interrupt()' -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c epimodels.cpp -o epimodels.o
clang++-20 -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/cpp11/include' -isystem /usr/local/clang20/include -I/usr/local/clang/include   -fopenmp -I../inst/include/  -Dprintf_epiworld=Rprintf -Depiworld_double=double '-DEPI_CHECK_USER_INTERRUPT(a)=cpp11::check_user_interrupt()' -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c lfmcmc.cpp -o lfmcmc.o
clang++-20 -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/cpp11/include' -isystem /usr/local/clang20/include -I/usr/local/clang/include   -fopenmp -I../inst/include/  -Dprintf_epiworld=Rprintf -Depiworld_double=double '-DEPI_CHECK_USER_INTERRUPT(a)=cpp11::check_user_interrupt()' -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c model-diagram.cpp -o model-diagram.o
clang++-20 -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/cpp11/include' -isystem /usr/local/clang20/include -I/usr/local/clang/include   -fopenmp -I../inst/include/  -Dprintf_epiworld=Rprintf -Depiworld_double=double '-DEPI_CHECK_USER_INTERRUPT(a)=cpp11::check_user_interrupt()' -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c model.cpp -o model.o
clang++-20 -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/cpp11/include' -isystem /usr/local/clang20/include -I/usr/local/clang/include   -fopenmp -I../inst/include/  -Dprintf_epiworld=Rprintf -Depiworld_double=double '-DEPI_CHECK_USER_INTERRUPT(a)=cpp11::check_user_interrupt()' -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c tool.cpp -o tool.o
clang++-20 -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/cpp11/include' -isystem /usr/local/clang20/include -I/usr/local/clang/include   -fopenmp -I../inst/include/  -Dprintf_epiworld=Rprintf -Depiworld_double=double '-DEPI_CHECK_USER_INTERRUPT(a)=cpp11::check_user_interrupt()' -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c virus.cpp -o virus.o
clang++-20 -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang20/lib -L/usr/local/clang20/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -L/usr/local/clang20/lib/clang/20/lib/x86_64-unknown-linux-gnu -o epiworldR.so actions.o agents.o cpp11.o db.o entities.o epimodels.o lfmcmc.o model-diagram.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 -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)