* installing *source* package ‘SimInf’ ... ** using staged installation checking for gcc... clang-18 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-18 accepts -g... yes checking for clang-18 option to enable C11 features... none needed checking for clang-18 option to support OpenMP... -fopenmp checking whether OpenMP will work in a package... yes checking for gsl-config... /usr/bin/gsl-config ---- Results for the SimInf package configure ---- PKG_CPPFLAGS..............: -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS PKG_CFLAGS................: -fopenmp PKG_LIBS..................: -fopenmp -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm Have support for OpenMP...: yes -------------------------------------------------- configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘Debian clang version 18.1.6 (1)’ clang-18 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -c init.c -o init.o clang-18 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -c models/SISe_sp.c -o models/SISe_sp.o clang-18 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -c models/SISe3.c -o models/SISe3.o clang-18 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -c models/SEIR.c -o models/SEIR.o clang-18 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -c models/SIR.c -o models/SIR.o clang-18 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -c models/SISe.c -o models/SISe.o clang-18 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -c models/SISe3_sp.c -o models/SISe3_sp.o clang-18 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -c models/SIS.c -o models/SIS.o clang-18 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -c solvers/aem/SimInf_solver_aem.c -o solvers/aem/SimInf_solver_aem.o clang-18 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -c solvers/SimInf_solver.c -o solvers/SimInf_solver.o clang-18 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -c solvers/ssm/SimInf_solver_ssm.c -o solvers/ssm/SimInf_solver_ssm.o clang-18 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -c misc/SimInf_clean_indiv_events.c -o misc/SimInf_clean_indiv_events.o clang-18 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -c misc/SimInf_arg.c -o misc/SimInf_arg.o clang-18 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -c misc/SimInf_particle_filter.c -o misc/SimInf_particle_filter.o clang-18 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -c misc/SimInf_ldata.c -o misc/SimInf_ldata.o clang-18 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -c misc/SimInf_abc.c -o misc/SimInf_abc.o clang-18 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -c misc/SimInf_trajectory.c -o misc/SimInf_trajectory.o clang-18 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -c misc/SimInf_openmp.c -o misc/SimInf_openmp.o clang-18 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -c misc/SimInf_local_spread.c -o misc/SimInf_local_spread.o clang-18 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -c misc/binheap.c -o misc/binheap.o clang-18 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -c misc/SimInf_forward_euler_linear_decay.c -o misc/SimInf_forward_euler_linear_decay.o clang-18 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -c misc/SimInf_distance_matrix.c -o misc/SimInf_distance_matrix.o clang-18 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O3 -Wall -pedantic -c SimInf.c -o SimInf.o clang-18 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o SimInf.so init.o models/SISe_sp.o models/SISe3.o models/SEIR.o models/SIR.o models/SISe.o models/SISe3_sp.o models/SIS.o solvers/aem/SimInf_solver_aem.o solvers/SimInf_solver.o solvers/ssm/SimInf_solver_ssm.o misc/SimInf_clean_indiv_events.o misc/SimInf_arg.o misc/SimInf_particle_filter.o misc/SimInf_ldata.o misc/SimInf_abc.o misc/SimInf_trajectory.o misc/SimInf_openmp.o misc/SimInf_local_spread.o misc/binheap.o misc/SimInf_forward_euler_linear_decay.o misc/SimInf_distance_matrix.o SimInf.o -fopenmp -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm -L/home/hornik/tmp/R/lib -lR installing to /srv/hornik/tmp/CRAN/SimInf.Rcheck/00LOCK-SimInf/00new/SimInf/libs ** R ** data *** moving datasets to lazyload DB ** 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 (SimInf)