* 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/include/openmpi-x86_64 Checking /usr/include/openmpi-x86_64 ... Found /usr/include/openmpi-x86_64/mpi.h ... >> TMP_LIB_DIRS = /usr/lib64/openmpi/lib Checking /usr/lib64/openmpi/lib ... Found /usr/lib64/openmpi/lib/libmpi.so ... Found mpi.h and libmpi.so ... via mpicc --showme >> TMP_INC = /usr/include/openmpi-x86_64 >> TMP_LIB = /usr/lib64/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/lib64/openmpi/bin/mpirun >> MPIEXEC = /usr/lib64/openmpi/bin/mpiexec >> ORTERUN = /usr/lib64/openmpi/bin/orterun >> TMP_INC = /usr/include/openmpi-x86_64 >> TMP_LIB = /usr/lib64/openmpi/lib >> TMP_LIBNAME = libmpi.so >> TMP_FOUND = mpicc --showme >> MPI_ROOT = >> MPITYPE = OPENMPI >> MPI_INCLUDE_PATH = /usr/include/openmpi-x86_64 >> MPI_LIBPATH = /usr/lib64/openmpi/lib >> MPI_LIBNAME = libmpi.so >> MPI_LIBS = -lutil -lpthread >> MPI_DEFS = -DMPI2 >> MPI_INCL2 = >> MPI_LDFLAGS = >> PKG_CPPFLAGS = -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI >> PKG_LIBS = -L/usr/lib64/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-14 (GCC) 14.2.0’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/pbdMPI/src' echo "MPIRUN = /usr/lib64/openmpi/bin/mpirun" > Makeconf echo "MPIEXEC = /usr/lib64/openmpi/bin/mpiexec" >> Makeconf echo "ORTERUN = /usr/lib64/openmpi/bin/orterun" >> Makeconf echo "TMP_INC = /usr/include/openmpi-x86_64" >> Makeconf echo "TMP_LIB = /usr/lib64/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/include/openmpi-x86_64" >> Makeconf echo "MPI_LIBPATH = /usr/lib64/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/include/openmpi-x86_64 -DMPI2 -DOPENMPI" >> Makeconf echo "PKG_LIBS = -L/usr/lib64/openmpi/lib -lmpi -lutil -lpthread" >> Makeconf echo "PROF_LDFLAGS = " >> Makeconf echo "ENABLE_LD_LIBRARY_PATH = no" >> Makeconf gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c comm_errors.c -o comm_errors.o gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c comm_sort_double.c -o comm_sort_double.o gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c comm_sort_integer.c -o comm_sort_integer.o gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c pkg_dl.c -o pkg_dl.o gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c pkg_tools.c -o pkg_tools.o gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c spmd.c -o spmd.o gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c spmd_allgather.c -o spmd_allgather.o gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c spmd_allgatherv.c -o spmd_allgatherv.o gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c spmd_allreduce.c -o spmd_allreduce.o gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c spmd_alltoall.c -o spmd_alltoall.o gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c spmd_alltoallv.c -o spmd_alltoallv.o gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c spmd_bcast.c -o spmd_bcast.o gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c spmd_communicator.c -o spmd_communicator.o gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c spmd_communicator_spawn.c -o spmd_communicator_spawn.o gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c spmd_gather.c -o spmd_gather.o gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c spmd_gatherv.c -o spmd_gatherv.o gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c spmd_info.c -o spmd_info.o gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c spmd_recv.c -o spmd_recv.o gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c spmd_reduce.c -o spmd_reduce.o gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c spmd_scatter.c -o spmd_scatter.o gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c spmd_scatterv.c -o spmd_scatterv.o gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c spmd_send.c -o spmd_send.o gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c spmd_sendrecv.c -o spmd_sendrecv.o gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c spmd_sendrecv_replace.c -o spmd_sendrecv_replace.o gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c spmd_tool.c -o spmd_tool.o gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c spmd_utility.c -o spmd_utility.o gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c spmd_wait.c -o spmd_wait.o gcc-14 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c zzz.c -o zzz.o gcc-14 -shared -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -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/lib64/openmpi/lib -lmpi -lutil -lpthread make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/pbdMPI/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/pbdMPI/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/pbdMPI/src' installing via 'install.libs.R' to /data/gannet/ripley/R/packages/tests-devel/pbdMPI.Rcheck/00LOCK-pbdMPI/00new/pbdMPI ** R ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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)