* installing *source* package ‘epiworldR’ ...
** this is package ‘epiworldR’ version ‘0.6.1.0’
** 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 /usr/local/clang20/bin/clang++ -stdlib=libc++ -std=gnu++17 accepts -g... yes
checking for /usr/local/clang20/bin/clang++ -stdlib=libc++ -std=gnu++17 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... /usr/local/clang20/bin/clang++ -stdlib=libc++ -std=gnu++17 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether /usr/local/clang20/bin/clang++ -stdlib=libc++ -std=gnu++17 accepts -g... (cached) yes
checking for /usr/local/clang20/bin/clang++ -stdlib=libc++ -std=gnu++17 option to enable C++11 features... (cached) none needed
checking whether we have a suitable tempdir... /tmp/Rtmp4hBbq1/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 20.1.0-rc2’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/epiworldR/src'
/usr/local/clang20/bin/clang++ -stdlib=libc++ -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 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c actions.cpp -o actions.o
In file included from actions.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11.hpp:3:
/data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
52 | constexpr R_xlen_t operator"" _xl(unsigned long long int value) { return value; }
| ~~~~~~~~~~~^~~
| operator""_xl
In file included from actions.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11.hpp:7:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/data_frame.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/list.hpp:9:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/r_vector.hpp:19:
/data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
42 | inline named_arg operator"" _nm(const char* name, std::size_t) { return named_arg(name); }
| ~~~~~~~~~~~^~~
| operator""_nm
/usr/local/clang20/bin/clang++ -stdlib=libc++ -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 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c agents.cpp -o agents.o
In file included from agents.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11.hpp:3:
/data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
52 | constexpr R_xlen_t operator"" _xl(unsigned long long int value) { return value; }
| ~~~~~~~~~~~^~~
| operator""_xl
In file included from agents.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11.hpp:7:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/data_frame.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/list.hpp:9:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/r_vector.hpp:19:
/data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
42 | inline named_arg operator"" _nm(const char* name, std::size_t) { return named_arg(name); }
| ~~~~~~~~~~~^~~
| operator""_nm
2 warnings generated.
2 warnings generated.
/usr/local/clang20/bin/clang++ -stdlib=libc++ -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 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c cpp11.cpp -o cpp11.o
In file included from cpp11.cpp:5:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/declarations.hpp:13:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11.hpp:3:
/data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
52 | constexpr R_xlen_t operator"" _xl(unsigned long long int value) { return value; }
| ~~~~~~~~~~~^~~
| operator""_xl
In file included from cpp11.cpp:5:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/declarations.hpp:13:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11.hpp:7:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/data_frame.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/list.hpp:9:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/r_vector.hpp:19:
/data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
42 | inline named_arg operator"" _nm(const char* name, std::size_t) { return named_arg(name); }
| ~~~~~~~~~~~^~~
| operator""_nm
2 warnings generated.
/usr/local/clang20/bin/clang++ -stdlib=libc++ -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 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c db.cpp -o db.o
In file included from db.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11.hpp:3:
/data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
52 | constexpr R_xlen_t operator"" _xl(unsigned long long int value) { return value; }
| ~~~~~~~~~~~^~~
| operator""_xl
In file included from db.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11.hpp:7:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/data_frame.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/list.hpp:9:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/r_vector.hpp:19:
/data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
42 | inline named_arg operator"" _nm(const char* name, std::size_t) { return named_arg(name); }
| ~~~~~~~~~~~^~~
| operator""_nm
/usr/local/clang20/bin/clang++ -stdlib=libc++ -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 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c entities.cpp -o entities.o
In file included from entities.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11.hpp:3:
/data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
52 | constexpr R_xlen_t operator"" _xl(unsigned long long int value) { return value; }
| ~~~~~~~~~~~^~~
| operator""_xl
In file included from entities.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11.hpp:7:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/data_frame.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/list.hpp:9:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/r_vector.hpp:19:
/data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
42 | inline named_arg operator"" _nm(const char* name, std::size_t) { return named_arg(name); }
| ~~~~~~~~~~~^~~
| operator""_nm
/usr/local/clang20/bin/clang++ -stdlib=libc++ -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 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c epimodels.cpp -o epimodels.o
In file included from epimodels.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11.hpp:3:
/data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
52 | constexpr R_xlen_t operator"" _xl(unsigned long long int value) { return value; }
| ~~~~~~~~~~~^~~
| operator""_xl
In file included from epimodels.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11.hpp:7:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/data_frame.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/list.hpp:9:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/r_vector.hpp:19:
/data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
42 | inline named_arg operator"" _nm(const char* name, std::size_t) { return named_arg(name); }
| ~~~~~~~~~~~^~~
| operator""_nm
/usr/local/clang20/bin/clang++ -stdlib=libc++ -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 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c lfmcmc.cpp -o lfmcmc.o
In file included from lfmcmc.cpp:1:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11.hpp:3:
/data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
52 | constexpr R_xlen_t operator"" _xl(unsigned long long int value) { return value; }
| ~~~~~~~~~~~^~~
| operator""_xl
2 warnings generated.
In file included from lfmcmc.cpp:1:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11.hpp:7:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/data_frame.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/list.hpp:9:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/r_vector.hpp:19:
/data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
42 | inline named_arg operator"" _nm(const char* name, std::size_t) { return named_arg(name); }
| ~~~~~~~~~~~^~~
| operator""_nm
/usr/local/clang20/bin/clang++ -stdlib=libc++ -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 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c model.cpp -o model.o
In file included from model.cpp:1:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11.hpp:3:
/data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
52 | constexpr R_xlen_t operator"" _xl(unsigned long long int value) { return value; }
| ~~~~~~~~~~~^~~
| operator""_xl
2 warnings generated.
/usr/local/clang20/bin/clang++ -stdlib=libc++ -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 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c tool.cpp -o tool.o
In file included from tool.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11.hpp:3:
/data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
52 | constexpr R_xlen_t operator"" _xl(unsigned long long int value) { return value; }
| ~~~~~~~~~~~^~~
| operator""_xl
In file included from model.cpp:1:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11.hpp:7:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/data_frame.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/list.hpp:9:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/r_vector.hpp:19:
/data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
42 | inline named_arg operator"" _nm(const char* name, std::size_t) { return named_arg(name); }
| ~~~~~~~~~~~^~~
| operator""_nm
In file included from tool.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11.hpp:7:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/data_frame.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/list.hpp:9:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/r_vector.hpp:19:
/data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
42 | inline named_arg operator"" _nm(const char* name, std::size_t) { return named_arg(name); }
| ~~~~~~~~~~~^~~
| operator""_nm
2 warnings generated.
/usr/local/clang20/bin/clang++ -stdlib=libc++ -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 -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw -c virus.cpp -o virus.o
In file included from virus.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11.hpp:3:
/data/gannet/ripley/R/test-clang/cpp11/include/cpp11/R.hpp:52:31: warning: identifier '_xl' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
52 | constexpr R_xlen_t operator"" _xl(unsigned long long int value) { return value; }
| ~~~~~~~~~~~^~~
| operator""_xl
In file included from virus.cpp:2:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11.hpp:7:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/data_frame.hpp:12:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/list.hpp:9:
In file included from /data/gannet/ripley/R/test-clang/cpp11/include/cpp11/r_vector.hpp:19:
/data/gannet/ripley/R/test-clang/cpp11/include/cpp11/named_arg.hpp:42:29: warning: identifier '_nm' preceded by whitespace in a literal operator declaration is deprecated [-Wdeprecated-literal-operator]
42 | inline named_arg operator"" _nm(const char* name, std::size_t) { return named_arg(name); }
| ~~~~~~~~~~~^~~
| operator""_nm
2 warnings generated.
2 warnings generated.
2 warnings generated.
2 warnings generated.
/usr/local/clang20/bin/clang++ -stdlib=libc++ -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 -o epiworldR.so actions.o agents.o cpp11.o db.o entities.o epimodels.o lfmcmc.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)