* 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)