Mock Version: 2.11 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/R-pbdMPI.spec'], chrootPath='/var/lib/mock/epel-7-x86_64-1626866420.824101/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.84m0usk6:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True) Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.84m0usk6:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', 'dcc21939bb77407d80226bcb059609c6', '-D', '/var/lib/mock/epel-7-x86_64-1626866420.824101/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.84m0usk6:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/R-pbdMPI.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0'} and shell False Building target platforms: x86_64 Building for target x86_64 Wrote: /builddir/build/SRPMS/R-pbdMPI-0.4.3-3.el7.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/R-pbdMPI.spec'], chrootPath='/var/lib/mock/epel-7-x86_64-1626866420.824101/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.84m0usk6:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True) Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.84m0usk6:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '37970998d86a4311b9759d0a558214ae', '-D', '/var/lib/mock/epel-7-x86_64-1626866420.824101/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.84m0usk6:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/R-pbdMPI.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0'} and shell False Building target platforms: x86_64 Building for target x86_64 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.dWNCet + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf pbdMPI + /usr/bin/mkdir -p pbdMPI + cd pbdMPI + /usr/bin/gzip -dc /builddir/build/SOURCES/pbdMPI_0.4-3.tar.gz + /usr/bin/tar -xf - + STATUS=0 + '[' 0 -ne 0 ']' + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.vK8Ap6 + umask 022 + cd /builddir/build/BUILD + cd pbdMPI + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.4yA1AJ + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/R-pbdMPI-0.4.3-3.el7.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/R-pbdMPI-0.4.3-3.el7.x86_64 ++ dirname /builddir/build/BUILDROOT/R-pbdMPI-0.4.3-3.el7.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/R-pbdMPI-0.4.3-3.el7.x86_64 + cd pbdMPI + mkdir -p /builddir/build/BUILDROOT/R-pbdMPI-0.4.3-3.el7.x86_64/usr/lib64/R/library /builddir/build/BUILDROOT/R-pbdMPI-0.4.3-3.el7.x86_64/usr/lib64/openmpi/lib + . /etc/profile.d/modules.sh ++++ /bin/ps -p 31 -ocomm= +++ /bin/basename sh ++ shell=sh ++ '[' -f /usr/share/Modules/init/sh ']' ++ . /usr/share/Modules/init/sh +++ MODULESHOME=/usr/share/Modules +++ export MODULESHOME +++ '[' '' = '' ']' +++ LOADEDMODULES= +++ export LOADEDMODULES +++ '[' /usr/share/Modules/modulefiles:/etc/modulefiles = '' ']' + module load mpi/openmpi-x86_64 ++ /usr/bin/modulecmd sh load mpi/openmpi-x86_64 + eval LD_LIBRARY_PATH=/usr/lib64/openmpi/lib ';export' 'LD_LIBRARY_PATH;LOADEDMODULES=mpi/openmpi-x86_64' ';export' 'LOADEDMODULES;MANPATH=/usr/share/man/openmpi-x86_64:/usr/share/man:/usr/local/share/man' ';export' 'MANPATH;MPI_BIN=/usr/lib64/openmpi/bin' ';export' 'MPI_BIN;MPI_COMPILER=openmpi-x86_64' ';export' 'MPI_COMPILER;MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi-x86_64' ';export' 'MPI_FORTRAN_MOD_DIR;MPI_HOME=/usr/lib64/openmpi' ';export' 'MPI_HOME;MPI_INCLUDE=/usr/include/openmpi-x86_64' ';export' 'MPI_INCLUDE;MPI_LIB=/usr/lib64/openmpi/lib' ';export' 'MPI_LIB;MPI_MAN=/usr/share/man/openmpi-x86_64' ';export' 'MPI_MAN;MPI_PYTHON_SITEARCH=/usr/lib64/python2.7/site-packages/openmpi' ';export' 'MPI_PYTHON_SITEARCH;MPI_SUFFIX=_openmpi' ';export' 'MPI_SUFFIX;MPI_SYSCONFIG=/etc/openmpi-x86_64' ';export' 'MPI_SYSCONFIG;PATH=/usr/lib64/openmpi/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin:/builddir/.local/bin:/builddir/bin' ';export' 'PATH;PYTHONPATH=/usr/lib64/python2.7/site-packages/openmpi' ';export' 'PYTHONPATH;_LMFILES_=/etc/modulefiles/mpi/openmpi-x86_64' ';export' '_LMFILES_;' ++ LD_LIBRARY_PATH=/usr/lib64/openmpi/lib ++ export LD_LIBRARY_PATH ++ LOADEDMODULES=mpi/openmpi-x86_64 ++ export LOADEDMODULES ++ MANPATH=/usr/share/man/openmpi-x86_64:/usr/share/man:/usr/local/share/man ++ export MANPATH ++ MPI_BIN=/usr/lib64/openmpi/bin ++ export MPI_BIN ++ MPI_COMPILER=openmpi-x86_64 ++ export MPI_COMPILER ++ MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi-x86_64 ++ export MPI_FORTRAN_MOD_DIR ++ MPI_HOME=/usr/lib64/openmpi ++ export MPI_HOME ++ MPI_INCLUDE=/usr/include/openmpi-x86_64 ++ export MPI_INCLUDE ++ MPI_LIB=/usr/lib64/openmpi/lib ++ export MPI_LIB ++ MPI_MAN=/usr/share/man/openmpi-x86_64 ++ export MPI_MAN ++ MPI_PYTHON_SITEARCH=/usr/lib64/python2.7/site-packages/openmpi ++ export MPI_PYTHON_SITEARCH ++ MPI_SUFFIX=_openmpi ++ export MPI_SUFFIX ++ MPI_SYSCONFIG=/etc/openmpi-x86_64 ++ export MPI_SYSCONFIG ++ PATH=/usr/lib64/openmpi/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin:/builddir/.local/bin:/builddir/bin ++ export PATH ++ PYTHONPATH=/usr/lib64/python2.7/site-packages/openmpi ++ export PYTHONPATH ++ _LMFILES_=/etc/modulefiles/mpi/openmpi-x86_64 ++ export _LMFILES_ + export 'CFLAGS= -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic' + CFLAGS=' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic' + MPI_LIB_PATH=/usr/lib64/openmpi/lib + MPI_INCLUDE_PATH=/usr/include/openmpi-x86_64 + MPI_TYPE=OPENMPI + OMPI_MCA_rmaps_base_oversubscribe=1 + OMPI_MCA_orte_rsh_agent=/bin/false + /usr/bin/R CMD INSTALL -l /builddir/build/BUILDROOT/R-pbdMPI-0.4.3-3.el7.x86_64/usr/lib64/R/library pbdMPI * installing *source* package 'pbdMPI' ... ** package 'pbdMPI' successfully unpacked and MD5 sums checked ** using staged installation setting mpi include path from MPI_INCLUDE setting mpi lib path from MPI_LIB_PATH checking for sed... /usr/bin/sed checking for mpicc... mpicc checking for ompi_info... ompi_info checking for pkg-config... /usr/bin/pkg-config >> TMP_FOUND = Nothing found from mpicc --show & sed nor pkg-config ... 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 = >> TMP_LIB = >> TMP_LIBNAME = >> TMP_FOUND = Nothing found from mpicc --show & sed nor pkg-config ... >> MPI_ROOT = >> MPITYPE = OPENMPI >> MPI_INCLUDE_PATH = /usr/include/openmpi-x86_64 >> MPI_LIBPATH = /usr/lib64/openmpi/lib >> MPI_LIBNAME = >> 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 ** libs 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 = " >> Makeconf echo "TMP_LIB = " >> Makeconf echo "TMP_LIBNAME = " >> Makeconf echo "TMP_FOUND = Nothing found from mpicc --show & sed nor pkg-config ..." >> 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 = " >> 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 -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c comm_errors.c -o comm_errors.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c comm_sort_double.c -o comm_sort_double.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c comm_sort_integer.c -o comm_sort_integer.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c pkg_dl.c -o pkg_dl.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c pkg_tools.c -o pkg_tools.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c spmd.c -o spmd.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c spmd_allgather.c -o spmd_allgather.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c spmd_allgatherv.c -o spmd_allgatherv.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c spmd_allreduce.c -o spmd_allreduce.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c spmd_alltoall.c -o spmd_alltoall.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c spmd_alltoallv.c -o spmd_alltoallv.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c spmd_bcast.c -o spmd_bcast.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c spmd_communicator.c -o spmd_communicator.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c spmd_communicator_spawn.c -o spmd_communicator_spawn.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c spmd_gather.c -o spmd_gather.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c spmd_gatherv.c -o spmd_gatherv.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c spmd_info.c -o spmd_info.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c spmd_recv.c -o spmd_recv.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c spmd_reduce.c -o spmd_reduce.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c spmd_scatter.c -o spmd_scatter.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c spmd_scatterv.c -o spmd_scatterv.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c spmd_send.c -o spmd_send.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c spmd_sendrecv.c -o spmd_sendrecv.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c spmd_sendrecv_replace.c -o spmd_sendrecv_replace.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c spmd_tool.c -o spmd_tool.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c spmd_utility.c -o spmd_utility.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c spmd_wait.c -o spmd_wait.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c zzz.c -o zzz.o gcc -m64 -std=gnu99 -shared -L/usr/lib64/R/lib -Wl,-z,relro -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 -L/usr/lib64/R/lib -lR installing via 'install.libs.R' to /builddir/build/BUILDROOT/R-pbdMPI-0.4.3-3.el7.x86_64/usr/lib64/R/library/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 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 'pbdMPI-guide.Rnw' ** 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) + rm -rf /builddir/build/BUILDROOT/R-pbdMPI-0.4.3-3.el7.x86_64/usr/lib64/R/library/R.css + test -d pbdMPI/src + cd pbdMPI/src + rm -f 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 pbdMPI.so Makevars + /usr/lib/rpm/find-debuginfo.sh --strict-build-id -m --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 /builddir/build/BUILD/pbdMPI extracting debug info from /builddir/build/BUILDROOT/R-pbdMPI-0.4.3-3.el7.x86_64/usr/lib64/R/library/pbdMPI/libs/pbdMPI.so dwz: Too few files for multifile optimization /usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. 257 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-compress + /usr/lib/rpm/redhat/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/lib/rpm/redhat/brp-java-repack-jars Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.UK9pAM + umask 022 + cd /builddir/build/BUILD + cd pbdMPI + MPI_LIB_PATH= + MPI_INCLUDE_PATH= + MPI_TYPE=OPENMPI + OMPI_MCA_rmaps_base_oversubscribe=1 + OMPI_MCA_orte_rsh_agent=/bin/false + /usr/bin/R CMD check pbdMPI * using log directory '/builddir/build/BUILD/pbdMPI/pbdMPI.Rcheck' * using R version 3.6.0 (2019-04-26) * using platform: x86_64-redhat-linux-gnu (64-bit) * using session charset: ASCII * checking for file 'pbdMPI/DESCRIPTION' ... OK * this is package 'pbdMPI' version '0.4-3' * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.9/bioc/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.9/data/annotation/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.9/data/annotation/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.9/data/experiment/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.9/data/experiment/src/contrib/PACKAGES' NOTE Packages which this enhances but not available for checking: 'pbdPROF', 'pbdZMQ' * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package 'pbdMPI' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking compiled code ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... 'pbdMPI-guide.Rnw' ... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See '/builddir/build/BUILD/pbdMPI/pbdMPI.Rcheck/00check.log' for details. + exit 0 Processing files: R-pbdMPI-0.4.3-3.el7.x86_64 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.DGQOpI + umask 022 + cd /builddir/build/BUILD + cd pbdMPI + LICENSEDIR=/builddir/build/BUILDROOT/R-pbdMPI-0.4.3-3.el7.x86_64/usr/share/licenses/R-pbdMPI-0.4.3 + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/R-pbdMPI-0.4.3-3.el7.x86_64/usr/share/licenses/R-pbdMPI-0.4.3 + cp -pr pbdMPI/COPYING /builddir/build/BUILDROOT/R-pbdMPI-0.4.3-3.el7.x86_64/usr/share/licenses/R-pbdMPI-0.4.3 + exit 0 Provides: R-pbdMPI = 0.4.3-3.el7 R-pbdMPI(x86-64) = 0.4.3-3.el7 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /bin/sh libR.so()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.4)(64bit) libpthread.so.0()(64bit) libutil.so.1()(64bit) rtld(GNU_HASH) Processing files: R-pbdMPI-debuginfo-0.4.3-3.el7.x86_64 Provides: R-pbdMPI-debuginfo = 0.4.3-3.el7 R-pbdMPI-debuginfo(x86-64) = 0.4.3-3.el7 Requires(rpmlib): rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(CompressedFileNames) <= 3.0.4-1 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-pbdMPI-0.4.3-3.el7.x86_64 Wrote: /builddir/build/RPMS/R-pbdMPI-0.4.3-3.el7.x86_64.rpm Wrote: /builddir/build/RPMS/R-pbdMPI-debuginfo-0.4.3-3.el7.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.728IDz + umask 022 + cd /builddir/build/BUILD + cd pbdMPI + /usr/bin/rm -rf /builddir/build/BUILDROOT/R-pbdMPI-0.4.3-3.el7.x86_64 + exit 0 Child return code was: 0