* installing *source* package ‘SimInf’ ...
** package ‘SimInf’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... /usr/local/clang18/bin/clang
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 /usr/local/clang18/bin/clang accepts -g... yes
checking for /usr/local/clang18/bin/clang option to enable C11 features... none needed
checking for /usr/local/clang18/bin/clang 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 -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS
PKG_CFLAGS................: -fopenmp
PKG_LIBS..................: -fopenmp -lgsl -lgslcblas -lm
Have support for OpenMP...: yes
--------------------------------------------------
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘clang version 18.1.4’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/SimInf/src'
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c misc/binheap.c -o misc/binheap.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c misc/SimInf_particle_filter.c -o misc/SimInf_particle_filter.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c misc/SimInf_openmp.c -o misc/SimInf_openmp.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c misc/SimInf_arg.c -o misc/SimInf_arg.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c misc/SimInf_forward_euler_linear_decay.c -o misc/SimInf_forward_euler_linear_decay.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c misc/SimInf_distance_matrix.c -o misc/SimInf_distance_matrix.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c misc/SimInf_trajectory.c -o misc/SimInf_trajectory.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c misc/SimInf_abc.c -o misc/SimInf_abc.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c misc/SimInf_ldata.c -o misc/SimInf_ldata.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c misc/SimInf_local_spread.c -o misc/SimInf_local_spread.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c misc/SimInf_clean_indiv_events.c -o misc/SimInf_clean_indiv_events.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c models/SISe_sp.c -o models/SISe_sp.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c models/SEIR.c -o models/SEIR.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c models/SIS.c -o models/SIS.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c models/SISe3_sp.c -o models/SISe3_sp.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c models/SISe3.c -o models/SISe3.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c models/SIR.c -o models/SIR.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c models/SISe.c -o models/SISe.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c init.c -o init.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c solvers/SimInf_solver.c -o solvers/SimInf_solver.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c solvers/aem/SimInf_solver_aem.c -o solvers/aem/SimInf_solver_aem.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c solvers/ssm/SimInf_solver_ssm.c -o solvers/ssm/SimInf_solver_ssm.o
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I../inst/include -isystem /usr/local/clang18/include -I/usr/local/clang/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c SimInf.c -o SimInf.o
/usr/local/clang18/bin/clang -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o SimInf.so misc/binheap.o misc/SimInf_particle_filter.o misc/SimInf_openmp.o misc/SimInf_arg.o misc/SimInf_forward_euler_linear_decay.o misc/SimInf_distance_matrix.o misc/SimInf_trajectory.o misc/SimInf_abc.o misc/SimInf_ldata.o misc/SimInf_local_spread.o misc/SimInf_clean_indiv_events.o models/SISe_sp.o models/SEIR.o models/SIS.o models/SISe3_sp.o models/SISe3.o models/SIR.o models/SISe.o init.o solvers/SimInf_solver.o solvers/aem/SimInf_solver_aem.o solvers/ssm/SimInf_solver_ssm.o SimInf.o -fopenmp -lgsl -lgslcblas -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/SimInf/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/SimInf/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/SimInf/src'
installing to /data/gannet/ripley/R/packages/tests-clang/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)