* 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-13
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-13 accepts -g... yes
checking for gcc-13 option to enable C11 features... none needed
checking for gcc-13 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-13 (Debian 13.2.0-23) 13.2.0’
make[1]: Entering directory '/tmp/RtmpUNeeMP/R.INSTALL6c4fd2a341a7e/SimInf/src'
gcc-13 -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-13 -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-13 -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-13 -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-13 -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-13 -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-13 -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-13 -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-13 -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-13 -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-13 -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-13 -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-13 -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-13 -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-13 -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-13 -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-13 -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-13 -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-13 -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-13 -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-13 -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-13 -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-13 -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-13 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o SimInf.so SimInf.o init.o solvers/aem/SimInf_solver_aem.o solvers/SimInf_solver.o solvers/ssm/SimInf_solver_ssm.o models/SEIR.o models/SISe3.o models/SISe3_sp.o models/SIR.o models/SIS.o models/SISe.o models/SISe_sp.o misc/binheap.o misc/SimInf_forward_euler_linear_decay.o misc/SimInf_arg.o misc/SimInf_local_spread.o misc/SimInf_trajectory.o misc/SimInf_openmp.o misc/SimInf_particle_filter.o misc/SimInf_ldata.o misc/SimInf_clean_indiv_events.o misc/SimInf_distance_matrix.o misc/SimInf_abc.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 '/tmp/RtmpUNeeMP/R.INSTALL6c4fd2a341a7e/SimInf/src'
make[1]: Entering directory '/tmp/RtmpUNeeMP/R.INSTALL6c4fd2a341a7e/SimInf/src'
make[1]: Leaving directory '/tmp/RtmpUNeeMP/R.INSTALL6c4fd2a341a7e/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)