* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* 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... /home/hornik/tmp/scratch
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 (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpzrxeqX/R.INSTALL1b56596558c13/epiworldR/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/cpp11/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O2 -Wall -pedantic -mtune=native -c actions.cpp -o actions.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/cpp11/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O2 -Wall -pedantic -mtune=native -c agents.cpp -o agents.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/cpp11/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O2 -Wall -pedantic -mtune=native -c cpp11.cpp -o cpp11.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/cpp11/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O2 -Wall -pedantic -mtune=native -c db.cpp -o db.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/cpp11/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O2 -Wall -pedantic -mtune=native -c entities.cpp -o entities.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/cpp11/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O2 -Wall -pedantic -mtune=native -c epimodels.cpp -o epimodels.o
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 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/cpp11/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O2 -Wall -pedantic -mtune=native -c model.cpp -o model.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/cpp11/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O2 -Wall -pedantic -mtune=native -c tool.cpp -o tool.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/cpp11/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O2 -Wall -pedantic -mtune=native -c virus.cpp -o virus.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o epiworldR.so actions.o agents.o cpp11.o db.o entities.o epimodels.o model.o tool.o virus.o -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpzrxeqX/R.INSTALL1b56596558c13/epiworldR/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpzrxeqX/R.INSTALL1b56596558c13/epiworldR/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpzrxeqX/R.INSTALL1b56596558c13/epiworldR/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-epiworldR/00new/epiworldR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘epiworldR’
finding HTML links ... done
ModelDiffNet html
ModelSEIR html
ModelSEIRCONN html
ModelSEIRD html
ModelSEIRDCONN html
ModelSEIRMixing html
ModelSIR html
ModelSIRCONN html
ModelSIRD html
ModelSIRDCONN html
ModelSIRLogit html
ModelSIRMixing html
ModelSIS html
ModelSISD html
ModelSURV html
agents html
agents_smallworld html
entities html
epiworld-data html
epiworld-methods html
epiworldR-deprecated html
epiworldR-package html
global-actions html
run_multiple html
tool html
virus html
*** 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)