* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘epiworldR’ ...
** this is package ‘epiworldR’ version ‘0.12.0.0’
** package ‘epiworldR’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.3.0-12) 14.3.0’
using C++17
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmphwVHKf/R.INSTALL3f332742c9217e/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 -Depiworld_double=double '-DEPI_CHECK_USER_INTERRUPT(a)=cpp11::check_user_interrupt()' -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 -Depiworld_double=double '-DEPI_CHECK_USER_INTERRUPT(a)=cpp11::check_user_interrupt()' -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 -Depiworld_double=double '-DEPI_CHECK_USER_INTERRUPT(a)=cpp11::check_user_interrupt()' -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 -Depiworld_double=double '-DEPI_CHECK_USER_INTERRUPT(a)=cpp11::check_user_interrupt()' -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 -Depiworld_double=double '-DEPI_CHECK_USER_INTERRUPT(a)=cpp11::check_user_interrupt()' -fpic -g -O2 -Wall -pedantic -mtune=native -c epimodels.cpp -o epimodels.o
In file included from ../inst/include/epiworld/epiworld.hpp:51,
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:1423:15,
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:2300:21,
inlined from ‘epiworld::epimodels::ModelSURV<TSeq>::ModelSURV(epiworld::epimodels::ModelSURV<TSeq>&, const std::string&, long long unsigned int, double, double, double, double, double, double, double, double, double, double, double) [with TSeq = int]’ at ../inst/include/epiworld/models/surveillance.hpp:366:24:
../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:60:
../inst/include/epiworld/database-meat.hpp: In constructor ‘epiworld::epimodels::ModelSURV<TSeq>::ModelSURV(epiworld::epimodels::ModelSURV<TSeq>&, const std::string&, long long unsigned int, double, double, double, double, double, double, double, double, double, double, double) [with TSeq = int]’:
../inst/include/epiworld/database-meat.hpp:1423:17: note: ‘<anonymous>’ declared here
1423 | 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 -Depiworld_double=double '-DEPI_CHECK_USER_INTERRUPT(a)=cpp11::check_user_interrupt()' -fpic -g -O2 -Wall -pedantic -mtune=native -c events.cpp -o events.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 -Depiworld_double=double '-DEPI_CHECK_USER_INTERRUPT(a)=cpp11::check_user_interrupt()' -fpic -g -O2 -Wall -pedantic -mtune=native -c lfmcmc.cpp -o lfmcmc.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 -Depiworld_double=double '-DEPI_CHECK_USER_INTERRUPT(a)=cpp11::check_user_interrupt()' -fpic -g -O2 -Wall -pedantic -mtune=native -c model-diagram.cpp -o model-diagram.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 -Depiworld_double=double '-DEPI_CHECK_USER_INTERRUPT(a)=cpp11::check_user_interrupt()' -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 -Depiworld_double=double '-DEPI_CHECK_USER_INTERRUPT(a)=cpp11::check_user_interrupt()' -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 -Depiworld_double=double '-DEPI_CHECK_USER_INTERRUPT(a)=cpp11::check_user_interrupt()' -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 agents.o cpp11.o db.o entities.o epimodels.o events.o lfmcmc.o model-diagram.o model.o tool.o virus.o -fopenmp -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmphwVHKf/R.INSTALL3f332742c9217e/epiworldR/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmphwVHKf/R.INSTALL3f332742c9217e/epiworldR/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmphwVHKf/R.INSTALL3f332742c9217e/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
LFMCMC html
ModelDiffNet html
ModelSEIR html
ModelSEIRCONN html
ModelSEIRD html
ModelSEIRDCONN html
ModelSEIRMixing html
ModelSEIRMixingQuarantine html
ModelSIR html
ModelSIRCONN html
ModelSIRD html
ModelSIRDCONN html
ModelSIRLogit html
ModelSIRMixing html
ModelSIS html
ModelSISD html
ModelSURV html
add_entities_from_dataframe html
agents html
agents_smallworld html
entities html
epiworld-gentime html
epiworld-history html
epiworld-hospitalizations html
epiworld-methods html
epiworld-model-diagram html
epiworld-repnum html
epiworld-summaries html
epiworld-transition html
epiworld-transmissions html
epiworldR-deprecated html
epiworldR-package html
global-events 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)