* installing *source* package ‘epiworldR’ ... ** 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 clang++-19 -stdlib=libc++ -std=gnu++17 accepts -g... yes checking for clang++-19 -stdlib=libc++ -std=gnu++17 option to enable C++11 features... none needed checking how to run the C++ preprocessor... clang++-19 -stdlib=libc++ -std=gnu++17 -E checking whether the compiler supports GNU C++... (cached) yes checking whether clang++-19 -stdlib=libc++ -std=gnu++17 accepts -g... (cached) yes checking for clang++-19 -stdlib=libc++ -std=gnu++17 option to enable C++11 features... (cached) none needed checking whether we have a suitable tempdir... /home/hornik/tmp/scratch/Rtmpp6s71U/working_dir checking whether R CMD SHLIB can already compile programs using OpenMP... no checking whether g++ version is sufficient... almost configure: WARNING: Compiler self-identifies as being compliant with GNUC extensions but is not g++. checking for macOS... no 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: ‘Debian clang version 19.1.1 (1)’ clang++-19 -stdlib=libc++ -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-lcxx/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c actions.cpp -o actions.o In file included from actions.cpp:2: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11.hpp:3: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/R.hpp:11:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] 11 | #define R_NO_REMAP | ^ :6:9: note: previous definition is here 6 | #define R_NO_REMAP 1 | ^ In file included from actions.cpp:2: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11.hpp:3: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/R.hpp:12:9: warning: 'STRICT_R_HEADERS' macro redefined [-Wmacro-redefined] 12 | #define STRICT_R_HEADERS | ^ :4:9: note: previous definition is here 4 | #define STRICT_R_HEADERS 1 | ^ 2 warnings generated. clang++-19 -stdlib=libc++ -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-lcxx/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c agents.cpp -o agents.o In file included from agents.cpp:2: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11.hpp:3: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/R.hpp:11:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] 11 | #define R_NO_REMAP | ^ :6:9: note: previous definition is here 6 | #define R_NO_REMAP 1 | ^ In file included from agents.cpp:2: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11.hpp:3: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/R.hpp:12:9: warning: 'STRICT_R_HEADERS' macro redefined [-Wmacro-redefined] 12 | #define STRICT_R_HEADERS | ^ :4:9: note: previous definition is here 4 | #define STRICT_R_HEADERS 1 | ^ 2 warnings generated. clang++-19 -stdlib=libc++ -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-lcxx/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c cpp11.cpp -o cpp11.o In file included from cpp11.cpp:5: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/declarations.hpp:13: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11.hpp:3: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/R.hpp:11:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] 11 | #define R_NO_REMAP | ^ :6:9: note: previous definition is here 6 | #define R_NO_REMAP 1 | ^ In file included from cpp11.cpp:5: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/declarations.hpp:13: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11.hpp:3: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/R.hpp:12:9: warning: 'STRICT_R_HEADERS' macro redefined [-Wmacro-redefined] 12 | #define STRICT_R_HEADERS | ^ :4:9: note: previous definition is here 4 | #define STRICT_R_HEADERS 1 | ^ 2 warnings generated. clang++-19 -stdlib=libc++ -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-lcxx/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c db.cpp -o db.o In file included from db.cpp:2: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11.hpp:3: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/R.hpp:11:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] 11 | #define R_NO_REMAP | ^ :6:9: note: previous definition is here 6 | #define R_NO_REMAP 1 | ^ In file included from db.cpp:2: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11.hpp:3: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/R.hpp:12:9: warning: 'STRICT_R_HEADERS' macro redefined [-Wmacro-redefined] 12 | #define STRICT_R_HEADERS | ^ :4:9: note: previous definition is here 4 | #define STRICT_R_HEADERS 1 | ^ 2 warnings generated. clang++-19 -stdlib=libc++ -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-lcxx/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c entities.cpp -o entities.o In file included from entities.cpp:2: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11.hpp:3: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/R.hpp:11:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] 11 | #define R_NO_REMAP | ^ :6:9: note: previous definition is here 6 | #define R_NO_REMAP 1 | ^ In file included from entities.cpp:2: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11.hpp:3: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/R.hpp:12:9: warning: 'STRICT_R_HEADERS' macro redefined [-Wmacro-redefined] 12 | #define STRICT_R_HEADERS | ^ :4:9: note: previous definition is here 4 | #define STRICT_R_HEADERS 1 | ^ 2 warnings generated. clang++-19 -stdlib=libc++ -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-lcxx/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c epimodels.cpp -o epimodels.o In file included from epimodels.cpp:2: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11.hpp:3: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/R.hpp:11:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] 11 | #define R_NO_REMAP | ^ :6:9: note: previous definition is here 6 | #define R_NO_REMAP 1 | ^ In file included from epimodels.cpp:2: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11.hpp:3: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/R.hpp:12:9: warning: 'STRICT_R_HEADERS' macro redefined [-Wmacro-redefined] 12 | #define STRICT_R_HEADERS | ^ :4:9: note: previous definition is here 4 | #define STRICT_R_HEADERS 1 | ^ 2 warnings generated. clang++-19 -stdlib=libc++ -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-lcxx/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c model.cpp -o model.o In file included from model.cpp:1: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11.hpp:3: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/R.hpp:11:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] 11 | #define R_NO_REMAP | ^ :6:9: note: previous definition is here 6 | #define R_NO_REMAP 1 | ^ In file included from model.cpp:1: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11.hpp:3: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/R.hpp:12:9: warning: 'STRICT_R_HEADERS' macro redefined [-Wmacro-redefined] 12 | #define STRICT_R_HEADERS | ^ :4:9: note: previous definition is here 4 | #define STRICT_R_HEADERS 1 | ^ 2 warnings generated. clang++-19 -stdlib=libc++ -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-lcxx/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c tool.cpp -o tool.o In file included from tool.cpp:2: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11.hpp:3: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/R.hpp:11:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] 11 | #define R_NO_REMAP | ^ :6:9: note: previous definition is here 6 | #define R_NO_REMAP 1 | ^ In file included from tool.cpp:2: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11.hpp:3: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/R.hpp:12:9: warning: 'STRICT_R_HEADERS' macro redefined [-Wmacro-redefined] 12 | #define STRICT_R_HEADERS | ^ :4:9: note: previous definition is here 4 | #define STRICT_R_HEADERS 1 | ^ 2 warnings generated. clang++-19 -stdlib=libc++ -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-lcxx/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DSTRICT_R_HEADERS=1 -I../inst/include/ -Dprintf_epiworld=Rprintf -fpic -g -O3 -Wall -pedantic -DR_NO_REMAP -c virus.cpp -o virus.o In file included from virus.cpp:2: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11.hpp:3: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/R.hpp:11:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined] 11 | #define R_NO_REMAP | ^ :6:9: note: previous definition is here 6 | #define R_NO_REMAP 1 | ^ In file included from virus.cpp:2: In file included from /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11.hpp:3: /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/cpp11/include/cpp11/R.hpp:12:9: warning: 'STRICT_R_HEADERS' macro redefined [-Wmacro-redefined] 12 | #define STRICT_R_HEADERS | ^ :4:9: note: previous definition is here 4 | #define STRICT_R_HEADERS 1 | ^ 2 warnings generated. clang++-19 -stdlib=libc++ -std=gnu++17 -shared -L/home/hornik/tmp/R-d-clang-lcxx/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-d-clang-lcxx/lib -lRblas -lFortranRuntime -lFortranDecimal -lm -L/home/hornik/tmp/R-d-clang-lcxx/lib -lR installing to /home/hornik/tmp/CRAN_special_clang19/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)