* 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 g++-14 -std=gnu++17 accepts -g... yes
checking for g++-14 -std=gnu++17 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... g++-14 -std=gnu++17 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether g++-14 -std=gnu++17 accepts -g... (cached) yes
checking for g++-14 -std=gnu++17 option to enable C++11 features... (cached) none needed
checking whether we have a suitable tempdir... /tmp/RtmpFv7H4P/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: ‘g++-14 (GCC) 14.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/epiworldR/src'
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/cpp11/include' -I/usr/local/include -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c actions.cpp -o actions.o
In file included from /data/gannet/ripley/R/test-dev/cpp11/include/cpp11.hpp:3,
from actions.cpp:2:
/data/gannet/ripley/R/test-dev/cpp11/include/cpp11/R.hpp:11:9: warning: "R_NO_REMAP" redefined
11 | #define R_NO_REMAP
| ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/cpp11/include' -I/usr/local/include -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c agents.cpp -o agents.o
In file included from /data/gannet/ripley/R/test-dev/cpp11/include/cpp11.hpp:3,
from agents.cpp:2:
/data/gannet/ripley/R/test-dev/cpp11/include/cpp11/R.hpp:11:9: warning: "R_NO_REMAP" redefined
11 | #define R_NO_REMAP
| ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/cpp11/include' -I/usr/local/include -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c cpp11.cpp -o cpp11.o
In file included from /data/gannet/ripley/R/test-dev/cpp11/include/cpp11.hpp:3,
from /data/gannet/ripley/R/test-dev/cpp11/include/cpp11/declarations.hpp:13,
from cpp11.cpp:5:
/data/gannet/ripley/R/test-dev/cpp11/include/cpp11/R.hpp:11:9: warning: "R_NO_REMAP" redefined
11 | #define R_NO_REMAP
| ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/cpp11/include' -I/usr/local/include -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c db.cpp -o db.o
In file included from /data/gannet/ripley/R/test-dev/cpp11/include/cpp11.hpp:3,
from db.cpp:2:
/data/gannet/ripley/R/test-dev/cpp11/include/cpp11/R.hpp:11:9: warning: "R_NO_REMAP" redefined
11 | #define R_NO_REMAP
| ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/cpp11/include' -I/usr/local/include -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c entities.cpp -o entities.o
In file included from /data/gannet/ripley/R/test-dev/cpp11/include/cpp11.hpp:3,
from entities.cpp:2:
/data/gannet/ripley/R/test-dev/cpp11/include/cpp11/R.hpp:11:9: warning: "R_NO_REMAP" redefined
11 | #define R_NO_REMAP
| ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/cpp11/include' -I/usr/local/include -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c epimodels.cpp -o epimodels.o
In file included from /data/gannet/ripley/R/test-dev/cpp11/include/cpp11.hpp:3,
from epimodels.cpp:2:
/data/gannet/ripley/R/test-dev/cpp11/include/cpp11/R.hpp:11:9: warning: "R_NO_REMAP" redefined
11 | #define R_NO_REMAP
| ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/cpp11/include' -I/usr/local/include -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c model.cpp -o model.o
In file included from /data/gannet/ripley/R/test-dev/cpp11/include/cpp11.hpp:3,
from model.cpp:1:
/data/gannet/ripley/R/test-dev/cpp11/include/cpp11/R.hpp:11:9: warning: "R_NO_REMAP" redefined
11 | #define R_NO_REMAP
| ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/cpp11/include' -I/usr/local/include -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c tool.cpp -o tool.o
In file included from /data/gannet/ripley/R/test-dev/cpp11/include/cpp11.hpp:3,
from tool.cpp:2:
/data/gannet/ripley/R/test-dev/cpp11/include/cpp11/R.hpp:11:9: warning: "R_NO_REMAP" redefined
11 | #define R_NO_REMAP
| ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/cpp11/include' -I/usr/local/include -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c virus.cpp -o virus.o
In file included from /data/gannet/ripley/R/test-dev/cpp11/include/cpp11.hpp:3,
from virus.cpp:2:
/data/gannet/ripley/R/test-dev/cpp11/include/cpp11/R.hpp:11:9: warning: "R_NO_REMAP" redefined
11 | #define R_NO_REMAP
| ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
In file included from ../inst/include/epiworld/epiworld.hpp:40,
from epiworld-common.h:4,
from epimodels.cpp:5:
In member function 'epiworld::UserData<int>& epiworld::UserData<int>::operator=(epiworld::UserData<int>&&)',
inlined from 'void epiworld::DataBase<TSeq>::set_user_data(std::vector<std::__cxx11::basic_string<char> >) [with TSeq = int]' at ../inst/include/epiworld/database-meat.hpp:1049:15,
inlined from 'void epiworld::Model<TSeq>::set_user_data(std::vector<std::__cxx11::basic_string<char> >) [with TSeq = int]' at ../inst/include/epiworld/model-meat.hpp:2172:21,
inlined from 'epiworld::epimodels::ModelSURV<TSeq>::ModelSURV(epiworld::epimodels::ModelSURV<TSeq>&, const std::string&, long long unsigned int, float, float, float, float, float, float, float, float, float, float, float) [with TSeq = int]' at ../inst/include/epiworld/models/surveillance.hpp:335:24:
../inst/include/epiworld/userdata-bones.hpp:16:7: warning: '<anonymous>.epiworld::UserData<int>::model' may be used uninitialized [-Wmaybe-uninitialized]
16 | class UserData
| ^~~~~~~~
In file included from ../inst/include/epiworld/epiworld.hpp:46:
../inst/include/epiworld/database-meat.hpp: In constructor 'epiworld::epimodels::ModelSURV<TSeq>::ModelSURV(epiworld::epimodels::ModelSURV<TSeq>&, const std::string&, long long unsigned int, float, float, float, float, float, float, float, float, float, float, float) [with TSeq = int]':
../inst/include/epiworld/database-meat.hpp:1049:17: note: '<anonymous>' declared here
1049 | user_data = UserData<TSeq>(names);
| ^~~~~~~~~~~~~~~~~~~~~
g++-14 -std=gnu++17 -shared -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o epiworldR.so actions.o agents.o cpp11.o db.o entities.o epimodels.o model.o tool.o virus.o -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath -fopenmp
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/epiworldR/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/epiworldR/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/epiworldR/src'
installing to /data/gannet/ripley/R/packages/tests-devel/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)