* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’ * installing *source* package ‘SimInf’ ... ** package ‘SimInf’ successfully unpacked and MD5 sums checked ** using staged installation checking for gcc... gcc-14 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 gcc-14 accepts -g... yes checking for gcc-14 option to enable C11 features... none needed checking for gcc-14 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: ‘gcc-14 (Debian 14.2.0-6) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpvwqeSu/R.INSTALL19f16a4e110693/SimInf/src' gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c models/SISe_sp.c -o models/SISe_sp.o gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c models/SISe3_sp.c -o models/SISe3_sp.o gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c models/SIS.c -o models/SIS.o gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c models/SIR.c -o models/SIR.o gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c models/SISe3.c -o models/SISe3.o gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c models/SEIR.c -o models/SEIR.o gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c models/SISe.c -o models/SISe.o gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c misc/SimInf_forward_euler_linear_decay.c -o misc/SimInf_forward_euler_linear_decay.o gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c misc/SimInf_ldata.c -o misc/SimInf_ldata.o gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c misc/binheap.c -o misc/binheap.o gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c misc/SimInf_clean_indiv_events.c -o misc/SimInf_clean_indiv_events.o gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c misc/SimInf_arg.c -o misc/SimInf_arg.o gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c misc/SimInf_local_spread.c -o misc/SimInf_local_spread.o gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c misc/SimInf_openmp.c -o misc/SimInf_openmp.o gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c misc/SimInf_abc.c -o misc/SimInf_abc.o gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c misc/SimInf_particle_filter.c -o misc/SimInf_particle_filter.o gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c misc/SimInf_distance_matrix.c -o misc/SimInf_distance_matrix.o gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c misc/SimInf_trajectory.c -o misc/SimInf_trajectory.o gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c SimInf.c -o SimInf.o gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c solvers/ssm/SimInf_solver_ssm.c -o solvers/ssm/SimInf_solver_ssm.o gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c solvers/SimInf_solver.c -o solvers/SimInf_solver.o gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I. -I../inst/include -I/usr/local/include -I/usr/include -DR_NO_REMAP -DSTRICT_R_HEADERS -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c solvers/aem/SimInf_solver_aem.c -o solvers/aem/SimInf_solver_aem.o gcc-14 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o SimInf.so models/SISe_sp.o models/SISe3_sp.o models/SIS.o models/SIR.o models/SISe3.o models/SEIR.o models/SISe.o misc/SimInf_forward_euler_linear_decay.o misc/SimInf_ldata.o misc/binheap.o misc/SimInf_clean_indiv_events.o misc/SimInf_arg.o misc/SimInf_local_spread.o misc/SimInf_openmp.o misc/SimInf_abc.o misc/SimInf_particle_filter.o misc/SimInf_distance_matrix.o misc/SimInf_trajectory.o init.o SimInf.o solvers/ssm/SimInf_solver_ssm.o solvers/SimInf_solver.o solvers/aem/SimInf_solver_aem.o -fopenmp -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpvwqeSu/R.INSTALL19f16a4e110693/SimInf/src' make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpvwqeSu/R.INSTALL19f16a4e110693/SimInf/src' make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpvwqeSu/R.INSTALL19f16a4e110693/SimInf/src' installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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 converting help for package ‘SimInf’ finding HTML links ... done C_code html SEIR-class html SEIR html SIR-class html SIR html SIS-class html SIS html SISe-class html SISe html SISe3-class html SISe3 html SISe3_sp-class html SISe3_sp html SISe_sp-class html SISe_sp html SimInf html SimInf_abc-class html SimInf_events-class html SimInf_events html SimInf_indiv_events-class html SimInf_model-class html SimInf_model html SimInf_pfilter-class html abc html as.data.frame.SimInf_abc html as.data.frame.SimInf_events html as.data.frame.SimInf_indiv_events html boxplot-SimInf_model-method html continue html distance_matrix html edge_properties_to_matrix html events html events_SEIR html events_SIR html events_SIS html events_SISe html events_SISe3 html gdata-set html gdata html get_individuals html indegree html individual_events html ldata html logLik-SimInf_pfilter-method html mparse html n_generations html n_nodes html node_events html nodes html outdegree html package_skeleton html pairs-SimInf_model-method html pfilter html plot-SimInf_abc-method html plot-SimInf_events-method html plot-SimInf_indiv_events-method html plot-SimInf_pfilter-method html plot html prevalence-SimInf_model-method html prevalence-SimInf_pfilter-method html prevalence html punchcard-set html run html select_matrix-set html select_matrix html set_num_threads html shift_matrix-set html shift_matrix html show-SimInf_abc-method html show-SimInf_events-method html show-SimInf_indiv_events-method html show-SimInf_model-method html show-SimInf_pfilter-method html summary-SimInf_abc-method html summary-SimInf_events-method html summary-SimInf_indiv_events-method html summary-SimInf_model-method html summary-SimInf_pfilter-method html trajectory-SimInf_model-method html trajectory-SimInf_pfilter-method html trajectory html u0-set html u0 html u0_SEIR html u0_SIR html u0_SIS html u0_SISe html u0_SISe3 html v0-set html *** 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)