* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘Rmpi’ ...
** package ‘Rmpi’ 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 we are using the GNU C compiler... yes
checking whether gcc-13 accepts -g... yes
checking for gcc-13 option to accept ISO C89... none needed
checking for pkg-config... /usr/bin/pkg-config
checking if pkg-config knows about OpenMPI... yes
checking for orted... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-13) 13.2.0’
make[1]: Entering directory '/tmp/RtmpY6bJy9/R.INSTALL1f06f42501a3dc/Rmpi/src'
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -DMPI2 -DOPENMPI -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Rmpi.c -o Rmpi.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -DMPI2 -DOPENMPI -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c conversion.c -o conversion.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/fortran/gfortran-mod-15/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -DMPI2 -DOPENMPI -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c internal.c -o internal.o
internal.c: In function ‘mpi_errhandler’:
internal.c:26:14: warning: unused variable ‘errmsg’ [-Wunused-variable]
26 | char errmsg[MPI_MAX_ERROR_STRING];
| ^~~~~~
internal.c:25:13: warning: unused variable ‘errmsglen’ [-Wunused-variable]
25 | int errmsglen;
| ^~~~~~~~~
gcc-13 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o Rmpi.so Rmpi.o conversion.o internal.o -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpY6bJy9/R.INSTALL1f06f42501a3dc/Rmpi/src'
make[1]: Entering directory '/tmp/RtmpY6bJy9/R.INSTALL1f06f42501a3dc/Rmpi/src'
make[1]: Leaving directory '/tmp/RtmpY6bJy9/R.INSTALL1f06f42501a3dc/Rmpi/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Rmpi/00new/Rmpi/libs
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘Rmpi’
finding HTML links ... done
hosts html
internal html
mpi.abort html
mpi.apply html
mpi.barrier html
mpi.bcast html
mpi.bcast.Robj html
mpi.bcast.cmd html
mpi.cart.coords html
mpi.cart.create html
mpi.cart.get html
mpi.cart.rank html
mpi.cart.shift html
mpi.cartdim.get html
mpi.comm html
mpi.comm.disconnect html
mpi.comm.free html
mpi.comm.inter html
mpi.comm.set.errhandler html
mpi.comm.spawn html
mpi.const html
mpi.dims.create html
mpi.exit html
mpi.finalize html
mpi.gather html
mpi.gather.Robj html
mpi.get.count html
mpi.get.processor.name html
mpi.get.sourcetag html
mpi.iapply html
mpi.info html
mpi.intercomm.merge html
mpi.parSim html
mpi.parapply html
mpi.probe html
mpi.realloc html
mpi.reduce html
mpi.remote.exec html
mpi.scatter html
mpi.scatter.Robj html
mpi.send html
mpi.send.Robj html
mpi.sendrecv html
mpi.setup.rng html
mpi.spawn.Rslaves html
mpi.universe.size html
mpi.wait html
** building package indices
** 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 (Rmpi)