Install log for 'epiworldR'

* installing to library ‘/home/hornik/tmp/R.check/r-devel-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++-13 -std=gnu++17 accepts -g... yes
checking for g++-13 -std=gnu++17 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... g++-13 -std=gnu++17 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether g++-13 -std=gnu++17 accepts -g... (cached) yes
checking for g++-13 -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++-13 (Debian 13.2.0-23) 13.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp0LCafG/R.INSTALLda9243dc43ce3/epiworldR/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-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:31,
                 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:2391:21,
    inlined from ‘epiworld::epimodels::ModelSURV<TSeq>::ModelSURV(epiworld::epimodels::ModelSURV<TSeq>&, 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:37:
../inst/include/epiworld/database-meat.hpp: In constructor ‘epiworld::epimodels::ModelSURV<TSeq>::ModelSURV(epiworld::epimodels::ModelSURV<TSeq>&, 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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-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++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -o epiworldR.so actions.o agents.o cpp11.o db.o epimodels.o model.o tool.o virus.o -llapack -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp0LCafG/R.INSTALLda9243dc43ce3/epiworldR/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp0LCafG/R.INSTALLda9243dc43ce3/epiworldR/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp0LCafG/R.INSTALLda9243dc43ce3/epiworldR/src'
installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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
* creating tarball
packaged installation of ‘epiworldR’ as ‘epiworldR_0.1-0_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (epiworldR)