* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘pbdMPI’ ...
** package ‘pbdMPI’ successfully unpacked and MD5 sums checked
** using staged installation
checking for sed... /usr/bin/sed
checking for mpicc... mpicc
checking for ompi_info... ompi_info
checking for pkg-config... /usr/bin/pkg-config
Try sed, mpicc, and ompi_info ...
>> TMP_INC_DIRS = /usr/lib/x86_64-linux-gnu/openmpi/include /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi
Checking /usr/lib/x86_64-linux-gnu/openmpi/include ...
Found /usr/lib/x86_64-linux-gnu/openmpi/include/mpi.h ...
>> TMP_LIB_DIRS = /usr/lib/x86_64-linux-gnu/openmpi/lib
Checking /usr/lib/x86_64-linux-gnu/openmpi/lib ...
Found /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so ...
Found mpi.h and libmpi.so ... via mpicc --showme
>> TMP_INC = /usr/lib/x86_64-linux-gnu/openmpi/include
>> TMP_LIB = /usr/lib/x86_64-linux-gnu/openmpi/lib
>> TMP_FOUND = mpicc --showme
checking for openpty in -lutil... yes
checking for main in -lpthread... yes
******************* Results of pbdMPI package configure *****************
>> MPIRUN = /usr/bin/mpirun
>> MPIEXEC = /usr/bin/mpiexec
>> ORTERUN = /usr/bin/orterun
>> TMP_INC = /usr/lib/x86_64-linux-gnu/openmpi/include
>> TMP_LIB = /usr/lib/x86_64-linux-gnu/openmpi/lib
>> TMP_LIBNAME = libmpi.so
>> TMP_FOUND = mpicc --showme
>> MPI_ROOT =
>> MPITYPE = OPENMPI
>> MPI_INCLUDE_PATH = /usr/lib/x86_64-linux-gnu/openmpi/include
>> MPI_LIBPATH = /usr/lib/x86_64-linux-gnu/openmpi/lib
>> MPI_LIBNAME = libmpi.so
>> MPI_LIBS = -lutil -lpthread
>> MPI_DEFS = -DMPI2
>> MPI_INCL2 =
>> MPI_LDFLAGS =
>> PKG_CPPFLAGS = -I/usr/lib/x86_64-linux-gnu/openmpi/include -DMPI2 -DOPENMPI
>> PKG_LIBS = -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi -lutil -lpthread
>> PROF_LDFLAGS =
>> ENABLE_LD_LIBRARY_PATH = no
*************************************************************************
configure: creating ./config.status
config.status: creating src/Makevars
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/zzz.r
config.status: creating R/util_execmpi.r
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-13) 13.2.0’
make[1]: Entering directory '/tmp/RtmpioCEqL/R.INSTALL22f6726c447efc/pbdMPI/src'
echo "MPIRUN = /usr/bin/mpirun" > Makeconf
echo "MPIEXEC = /usr/bin/mpiexec" >> Makeconf
echo "ORTERUN = /usr/bin/orterun" >> Makeconf
echo "TMP_INC = /usr/lib/x86_64-linux-gnu/openmpi/include" >> Makeconf
echo "TMP_LIB = /usr/lib/x86_64-linux-gnu/openmpi/lib" >> Makeconf
echo "TMP_LIBNAME = libmpi.so" >> Makeconf
echo "TMP_FOUND = mpicc --showme" >> Makeconf
echo "MPI_ROOT = " >> Makeconf
echo "MPITYPE = OPENMPI" >> Makeconf
echo "MPI_INCLUDE_PATH = /usr/lib/x86_64-linux-gnu/openmpi/include" >> Makeconf
echo "MPI_LIBPATH = /usr/lib/x86_64-linux-gnu/openmpi/lib" >> Makeconf
echo "MPI_LIBNAME = libmpi.so" >> Makeconf
echo "MPI_LIBS = -lutil -lpthread" >> Makeconf
echo "MPI_DEFS = -DMPI2" >> Makeconf
echo "MPI_INCL2 = " >> Makeconf
echo "MPI_LDFLAGS = " >> Makeconf
echo "PKG_CPPFLAGS = -I/usr/lib/x86_64-linux-gnu/openmpi/include -DMPI2 -DOPENMPI" >> Makeconf
echo "PKG_LIBS = -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi -lutil -lpthread" >> Makeconf
echo "PROF_LDFLAGS = " >> Makeconf
echo "ENABLE_LD_LIBRARY_PATH = no" >> Makeconf
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/lib/x86_64-linux-gnu/openmpi/include -DMPI2 -DOPENMPI -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c comm_errors.c -o comm_errors.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/lib/x86_64-linux-gnu/openmpi/include -DMPI2 -DOPENMPI -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c comm_sort_double.c -o comm_sort_double.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/lib/x86_64-linux-gnu/openmpi/include -DMPI2 -DOPENMPI -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c comm_sort_integer.c -o comm_sort_integer.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/lib/x86_64-linux-gnu/openmpi/include -DMPI2 -DOPENMPI -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c pkg_dl.c -o pkg_dl.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/lib/x86_64-linux-gnu/openmpi/include -DMPI2 -DOPENMPI -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c pkg_tools.c -o pkg_tools.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/lib/x86_64-linux-gnu/openmpi/include -DMPI2 -DOPENMPI -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c spmd.c -o spmd.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/lib/x86_64-linux-gnu/openmpi/include -DMPI2 -DOPENMPI -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c spmd_allgather.c -o spmd_allgather.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/lib/x86_64-linux-gnu/openmpi/include -DMPI2 -DOPENMPI -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c spmd_allgatherv.c -o spmd_allgatherv.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/lib/x86_64-linux-gnu/openmpi/include -DMPI2 -DOPENMPI -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c spmd_allreduce.c -o spmd_allreduce.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/lib/x86_64-linux-gnu/openmpi/include -DMPI2 -DOPENMPI -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c spmd_alltoall.c -o spmd_alltoall.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/lib/x86_64-linux-gnu/openmpi/include -DMPI2 -DOPENMPI -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c spmd_alltoallv.c -o spmd_alltoallv.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/lib/x86_64-linux-gnu/openmpi/include -DMPI2 -DOPENMPI -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c spmd_bcast.c -o spmd_bcast.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/lib/x86_64-linux-gnu/openmpi/include -DMPI2 -DOPENMPI -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c spmd_communicator.c -o spmd_communicator.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/lib/x86_64-linux-gnu/openmpi/include -DMPI2 -DOPENMPI -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c spmd_communicator_spawn.c -o spmd_communicator_spawn.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/lib/x86_64-linux-gnu/openmpi/include -DMPI2 -DOPENMPI -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c spmd_gather.c -o spmd_gather.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/lib/x86_64-linux-gnu/openmpi/include -DMPI2 -DOPENMPI -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c spmd_gatherv.c -o spmd_gatherv.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/lib/x86_64-linux-gnu/openmpi/include -DMPI2 -DOPENMPI -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c spmd_info.c -o spmd_info.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/lib/x86_64-linux-gnu/openmpi/include -DMPI2 -DOPENMPI -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c spmd_recv.c -o spmd_recv.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/lib/x86_64-linux-gnu/openmpi/include -DMPI2 -DOPENMPI -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c spmd_reduce.c -o spmd_reduce.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/lib/x86_64-linux-gnu/openmpi/include -DMPI2 -DOPENMPI -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c spmd_scatter.c -o spmd_scatter.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/lib/x86_64-linux-gnu/openmpi/include -DMPI2 -DOPENMPI -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c spmd_scatterv.c -o spmd_scatterv.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/lib/x86_64-linux-gnu/openmpi/include -DMPI2 -DOPENMPI -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c spmd_send.c -o spmd_send.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/lib/x86_64-linux-gnu/openmpi/include -DMPI2 -DOPENMPI -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c spmd_sendrecv.c -o spmd_sendrecv.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/lib/x86_64-linux-gnu/openmpi/include -DMPI2 -DOPENMPI -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c spmd_sendrecv_replace.c -o spmd_sendrecv_replace.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/lib/x86_64-linux-gnu/openmpi/include -DMPI2 -DOPENMPI -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c spmd_tool.c -o spmd_tool.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/lib/x86_64-linux-gnu/openmpi/include -DMPI2 -DOPENMPI -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c spmd_utility.c -o spmd_utility.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/lib/x86_64-linux-gnu/openmpi/include -DMPI2 -DOPENMPI -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c spmd_wait.c -o spmd_wait.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/lib/x86_64-linux-gnu/openmpi/include -DMPI2 -DOPENMPI -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c zzz.c -o zzz.o
gcc-13 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o pbdMPI.so comm_errors.o comm_sort_double.o comm_sort_integer.o pkg_dl.o pkg_tools.o spmd.o spmd_allgather.o spmd_allgatherv.o spmd_allreduce.o spmd_alltoall.o spmd_alltoallv.o spmd_bcast.o spmd_communicator.o spmd_communicator_spawn.o spmd_gather.o spmd_gatherv.o spmd_info.o spmd_recv.o spmd_reduce.o spmd_scatter.o spmd_scatterv.o spmd_send.o spmd_sendrecv.o spmd_sendrecv_replace.o spmd_tool.o spmd_utility.o spmd_wait.o zzz.o -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi -lutil -lpthread -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpioCEqL/R.INSTALL22f6726c447efc/pbdMPI/src'
make[1]: Entering directory '/tmp/RtmpioCEqL/R.INSTALL22f6726c447efc/pbdMPI/src'
make[1]: Leaving directory '/tmp/RtmpioCEqL/R.INSTALL22f6726c447efc/pbdMPI/src'
installing via 'install.libs.R' to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-pbdMPI/00new/pbdMPI
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘pbdMPI’
finding HTML links ... done
00_pbdMPI-package html
11_d_control html
11_d_pbd_opt html
aa_allgather-method html
aa_allreduce-method html
aa_bcast-method html
aa_gather-method html
aa_reduce-method html
aa_scatter-method html
ab_recv-method html
ab_send-method html
ac_irecv-method html
ac_isend-method html
ad_sendrecv-method html
ad_sendrecv.replace-method html
ae_alltoall html
cc_arrange.mpi.apts html
cc_comm html
cc_comm.chunk html
dd_info html
dd_is.comm.null html
dd_prob html
dd_sourcetag html
dd_wait html
uu_execmpi html
vv_get_jid html
vv_print_cat html
vv_seed html
ww_comm_as_gbd html
ww_comm_balance html
ww_comm_read html
ww_comm_write html
xx_comm_Rprof html
xx_comm_allpairs html
xx_comm_any_all html
xx_comm_base html
xx_comm_dist html
xx_comm_match_arg html
xx_comm_pairwise html
xx_comm_range html
xx_comm_sort html
xx_comm_stop_warning html
xx_comm_timer html
xx_comm_which html
yy_api_apply html
yy_api_task_pull html
yy_get_conf_lib_winmpi html
yy_pkg_tools html
zz_comm_internal html
zz_spmd_control html
zz_spmd_internal html
** 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 (pbdMPI)