Mock Version: 2.10 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/R-pbdNCDF4.spec'], chrootPath='/var/lib/mock/epel-7-x86_64-1621975664.654919/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=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.w6qoyb0m:/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.w6qoyb0m:/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', 'fe2b92e89f134d19bd51dca9196a585b', '-D', '/var/lib/mock/epel-7-x86_64-1621975664.654919/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.w6qoyb0m:/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-pbdNCDF4.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-pbdNCDF4-0.1.6-1.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-pbdNCDF4.spec'], chrootPath='/var/lib/mock/epel-7-x86_64-1621975664.654919/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=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.w6qoyb0m:/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.w6qoyb0m:/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', '15aff902a38c4594ba1db6fc3c9c401a', '-D', '/var/lib/mock/epel-7-x86_64-1621975664.654919/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.w6qoyb0m:/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-pbdNCDF4.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.bmZ0Zs + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf pbdNCDF4 + /usr/bin/mkdir -p pbdNCDF4 + cd pbdNCDF4 + /usr/bin/gzip -dc /builddir/build/SOURCES/pbdNCDF4-9b59aae.tar.gz + /usr/bin/tar -xf - + STATUS=0 + '[' 0 -ne 0 ']' + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + mv pbdNCDF4-9b59aaef205518d52c3e4d3a5065a57c57999823 pbdNCDF4 + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.B1Hf8z + umask 022 + cd /builddir/build/BUILD + cd pbdNCDF4 + . /etc/profile.d/modules.sh ++++ /bin/ps -p 29 -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' + R CMD build pbdNCDF4 * checking for file 'pbdNCDF4/DESCRIPTION' ... OK * preparing 'pbdNCDF4': * checking DESCRIPTION meta-information ... OK * cleaning src * running 'cleanup' * installing the package to build vignettes * creating vignettes ... OK Warning: 'inst/doc' files 'pbdNCDF4-guide.Rnw', 'pbdNCDF4-guide.pdf' ignored as vignettes have been rebuilt. Run R CMD build with --no-build-vignettes to prevent rebuilding. * cleaning src * running 'cleanup' * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building 'pbdNCDF4_0.1-6.tar.gz' + tar fx pbdNCDF4_0.1-6.tar.gz + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.F8Xiw2 + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/R-pbdNCDF4-0.1.6-1.el7.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/R-pbdNCDF4-0.1.6-1.el7.x86_64 ++ dirname /builddir/build/BUILDROOT/R-pbdNCDF4-0.1.6-1.el7.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/R-pbdNCDF4-0.1.6-1.el7.x86_64 + cd pbdNCDF4 + mkdir -p /builddir/build/BUILDROOT/R-pbdNCDF4-0.1.6-1.el7.x86_64/usr/lib64/R/library + . /etc/profile.d/modules.sh ++++ /bin/ps -p 1125 -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' + sed -i -e 's|^NETCDF_HEADER=.*|NETCDF_HEADER=/usr/include/openmpi-x86_64/netcdf_par.h|' pbdNCDF4/configure + OMPI_MCA_orte_allocation_required=0 + /usr/bin/R CMD INSTALL --no-test-load '--configure-args=--enable-parallel --with-nc-config=/usr/lib64/openmpi/bin/nc-config' -l /builddir/build/BUILDROOT/R-pbdNCDF4-0.1.6-1.el7.x86_64/usr/lib64/R/library pbdNCDF4 * installing *source* package 'pbdNCDF4' ... ** using staged installation user specified nc-config is /usr/lib64/openmpi/bin/nc-config checking for nc-config... yes Netcdf library version: netCDF 4.3.3.1 Netcdf library has version 4 interface present: yes Netcdf library was compiled with C compiler: mpicc configure: creating ./config.status config.status: creating src/Makevars configure: creating ./config.status config.status: creating src/Makevars config.status: creating R/zzz.R ****************** Results of ncdf4 package configure ******************* SPMD_CPPFLAGS = -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI SPMD_LDFLAGS = -L/usr/lib64/openmpi/lib -lmpi -lutil -lpthread NETCDF_HEADER = /usr/include/openmpi-x86_64/netcdf_par.h NETCDF_INCLUDE = 1 NETCDF_PAR = TRUE NETCDF_PAR_OBJS = pncdf4.o netCDF v4 CPP flags = -I/usr/include -I/usr/include/hdf netCDF v4 LD flags = -lnetcdf netCDF v4 runtime path = ************************************************************************* ** libs echo "SPMD_CPPFLAGS = -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI" > Makeconf echo "SPMD_LDFLAGS = -L/usr/lib64/openmpi/lib -lmpi -lutil -lpthread" >> Makeconf echo "NETCDF_HEADER = /usr/include/openmpi-x86_64/netcdf_par.h" >> Makeconf echo "NETCDF_INCLUDE = 1" >> Makeconf echo "NETCDF_PAR = TRUE" >> Makeconf echo "NETCDF_PAR_OBJS = pncdf4.o" >> Makeconf echo "NETCDF_CPPFLAGS = -I/usr/include -I/usr/include/hdf -DNETCDF_INCLUDE=1" >> Makeconf echo "NETCDF_LDFLAGS = -lnetcdf " >> Makeconf echo "NETCDF_RPATH = " >> Makeconf echo "HAVE_NETCDF = TRUE" >> Makeconf echo "PKG_CPPFLAGS = -I/usr/include -I/usr/include/hdf -DNETCDF_INCLUDE=1 -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI" >> Makeconf echo "PKG_LIBS = -lnetcdf -L/usr/lib64/openmpi/lib -lmpi -lutil -lpthread" >> Makeconf gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include -I/usr/include/hdf -DNETCDF_INCLUDE=1 -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 ncdf2.c -o ncdf2.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include -I/usr/include/hdf -DNETCDF_INCLUDE=1 -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 ncdf3.c -o ncdf3.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include -I/usr/include/hdf -DNETCDF_INCLUDE=1 -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 ncdf.c -o ncdf.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include -I/usr/include/hdf -DNETCDF_INCLUDE=1 -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 src_ncdf4.c -o src_ncdf4.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include -I/usr/include/hdf -DNETCDF_INCLUDE=1 -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 pncdf4.c -o pncdf4.o pncdf4.c: In function 'R_nc4_open_par': pncdf4.c:25:6: warning: variable 'nc_mode' set but not used [-Wunused-but-set-variable] int nc_mode; ^ gcc -m64 -std=gnu99 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o pbdNCDF4.so ncdf2.o ncdf3.o ncdf.o src_ncdf4.o pncdf4.o -lnetcdf -L/usr/lib64/openmpi/lib -lmpi -lutil -lpthread -L/usr/lib64/R/lib -lR installing via 'install.libs.R' to /builddir/build/BUILDROOT/R-pbdNCDF4-0.1.6-1.el7.x86_64/usr/lib64/R/library/00LOCK-pbdNCDF4/00new/pbdNCDF4 ** R ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'pbdNCDF4' finding HTML links ... done 00_pbdNCDF4-package html 01_nc_create_par html 01_nc_open_par html 01_nc_var_par_access html 02_ncdump html ancdf4 html ancvar_put html nc_close html nc_create html nc_enddef html nc_open html nc_redef html nc_sync html nc_version html ncatt_get html ncatt_put html ncdf4-internal html ncdim_def html ncvar_add html ncvar_change_missval html ncvar_def html ncvar_get html ncvar_rename html print.ncdf4 html ** building package indices ** installing vignettes ** checking absolute paths in shared objects and dynamic libraries * DONE (pbdNCDF4) + test -d pbdNCDF4/src + cd pbdNCDF4/src + rm -f ncdf.o ncdf2.o ncdf3.o pncdf4.o src_ncdf4.o pbdNCDF4.so + rm -f /builddir/build/BUILDROOT/R-pbdNCDF4-0.1.6-1.el7.x86_64/usr/lib64/R/library/R.css + /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/pbdNCDF4 extracting debug info from /builddir/build/BUILDROOT/R-pbdNCDF4-0.1.6-1.el7.x86_64/usr/lib64/R/library/pbdNCDF4/libs/pbdNCDF4.so dwz: Too few files for multifile optimization /usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. 133 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.rbcg5H + umask 022 + cd /builddir/build/BUILD + cd pbdNCDF4 + . /etc/profile.d/modules.sh ++++ /bin/ps -p 1759 -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' + OMPI_MCA_orte_allocation_required=0 + /usr/bin/R CMD check --no-install pbdNCDF4 * using log directory '/builddir/build/BUILD/pbdNCDF4/pbdNCDF4.Rcheck' * using R version 3.6.0 (2019-04-26) * using platform: x86_64-redhat-linux-gnu (64-bit) * using session charset: ASCII * using option '--no-install' * checking for file 'pbdNCDF4/DESCRIPTION' ... OK * this is package 'pbdNCDF4' version '0.1-6' * 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 ... NOTE Found the following hidden files and directories: .gitignore These were most likely included in error. See section 'Package structure' in the 'Writing R Extensions' manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking package directory ... OK * checking 'build' 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 dependencies in R code ... NOTE Package in Depends field not imported from: 'pbdMPI' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * 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 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 ... NOTE Package has both 'src/Makevars.in' and 'src/Makevars'. Installation with --no-configure' is unlikely to work. If you intended 'src/Makevars' to be used on Windows, rename it to 'src/Makevars.win' otherwise remove it. If 'configure' created 'src/Makevars', you need a 'cleanup' script. * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking files in 'vignettes' ... OK * checking examples ... SKIPPED * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See '/builddir/build/BUILD/pbdNCDF4/pbdNCDF4.Rcheck/00check.log' for details. + exit 0 Processing files: R-pbdNCDF4-0.1.6-1.el7.x86_64 Provides: R-pbdNCDF4 = 0.1.6-1.el7 R-pbdNCDF4(x86-64) = 0.1.6-1.el7 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libR.so()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libmpi.so.12()(64bit) libnetcdf.so.7()(64bit) libpthread.so.0()(64bit) libutil.so.1()(64bit) rtld(GNU_HASH) Processing files: R-pbdNCDF4-debuginfo-0.1.6-1.el7.x86_64 Provides: R-pbdNCDF4-debuginfo = 0.1.6-1.el7 R-pbdNCDF4-debuginfo(x86-64) = 0.1.6-1.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-pbdNCDF4-0.1.6-1.el7.x86_64 Wrote: /builddir/build/RPMS/R-pbdNCDF4-0.1.6-1.el7.x86_64.rpm Wrote: /builddir/build/RPMS/R-pbdNCDF4-debuginfo-0.1.6-1.el7.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.RdWjBL + umask 022 + cd /builddir/build/BUILD + cd pbdNCDF4 + /usr/bin/rm -rf /builddir/build/BUILDROOT/R-pbdNCDF4-0.1.6-1.el7.x86_64 + exit 0 Child return code was: 0