* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’
* installing *source* package ‘SimInf’ ...
** this is package ‘SimInf’ version ‘11.1.0’
** package ‘SimInf’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... gcc-16
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-16 accepts -g... yes
checking for gcc-16 option to enable C11 features... none needed
checking for gcc-16 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-16 (Debian 16.2.0-4) 16.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpLraf61/R.INSTALL11160b1775a987/SimInf/src'
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-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-16 -I"/home/hornik/tmp/R.check/r-devel-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-16 -I"/home/hornik/tmp/R.check/r-devel-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_ssm.c -o solvers/SimInf_solver_ssm.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-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_aem.c -o solvers/SimInf_solver_aem.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-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_mssm.c -o solvers/SimInf_solver_mssm.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-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_mssm_crn.c -o solvers/SimInf_solver_mssm_crn.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-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-16 -I"/home/hornik/tmp/R.check/r-devel-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-16 -I"/home/hornik/tmp/R.check/r-devel-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-16 -I"/home/hornik/tmp/R.check/r-devel-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-16 -I"/home/hornik/tmp/R.check/r-devel-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-16 -I"/home/hornik/tmp/R.check/r-devel-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-16 -I"/home/hornik/tmp/R.check/r-devel-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-16 -I"/home/hornik/tmp/R.check/r-devel-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-16 -I"/home/hornik/tmp/R.check/r-devel-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-16 -I"/home/hornik/tmp/R.check/r-devel-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-16 -I"/home/hornik/tmp/R.check/r-devel-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-16 -I"/home/hornik/tmp/R.check/r-devel-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-16 -I"/home/hornik/tmp/R.check/r-devel-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_individual_events.c -o misc/SimInf_individual_events.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-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-16 -I"/home/hornik/tmp/R.check/r-devel-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-16 -I"/home/hornik/tmp/R.check/r-devel-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-16 -I"/home/hornik/tmp/R.check/r-devel-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_LambertW.c -o misc/SimInf_LambertW.o
gcc-16 -I"/home/hornik/tmp/R.check/r-devel-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-16 -I"/home/hornik/tmp/R.check/r-devel-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-16 -I"/home/hornik/tmp/R.check/r-devel-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-16 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -o SimInf.so SimInf.o solvers/SimInf_solver.o solvers/SimInf_solver_ssm.o solvers/SimInf_solver_aem.o solvers/SimInf_solver_mssm.o solvers/SimInf_solver_mssm_crn.o models/SISe3.o models/SISe3_sp.o models/SIS.o models/SEIR.o models/SISe_sp.o models/SISe.o models/SIR.o init.o misc/binheap.o misc/SimInf_local_spread.o misc/SimInf_arg.o misc/SimInf_forward_euler_linear_decay.o misc/SimInf_individual_events.o misc/SimInf_ldata.o misc/SimInf_openmp.o misc/SimInf_particle_filter.o misc/SimInf_LambertW.o misc/SimInf_trajectory.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-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpLraf61/R.INSTALL11160b1775a987/SimInf/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpLraf61/R.INSTALL11160b1775a987/SimInf/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpLraf61/R.INSTALL11160b1775a987/SimInf/src'
installing to /home/hornik/tmp/R.check/r-devel-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
creating formal generic function 'plot' in package 'SimInf'
creating formal generic function 'summary' in package 'SimInf'
creating formal generic function 'logLik' in package 'SimInf'
using implicit definition in package 'stats'
creating formal generic function 'boxplot' in package 'SimInf'
using implicit definition in package 'graphics'
creating formal generic function 'pairs' in package 'SimInf'
using implicit definition in package 'graphics'
** 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)