Mock Version: 2.12
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/R-pbdSLAP.spec'], chrootPath='/var/lib/mock/epel-7-x86_64-1629809713.002170/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7f11e8dbf580>timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.pefo8n0t:/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.pefo8n0t:/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', '37ec91d6780f4d2e9f7c89c7373cab22', '-D', '/var/lib/mock/epel-7-x86_64-1629809713.002170/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.pefo8n0t:/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;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\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-pbdSLAP.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\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-pbdSLAP-0.3.0-3.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-pbdSLAP.spec'], chrootPath='/var/lib/mock/epel-7-x86_64-1629809713.002170/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7f11e8dbf580>timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.pefo8n0t:/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.pefo8n0t:/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', 'f320cfd73a8b46a19aefa7022732dca3', '-D', '/var/lib/mock/epel-7-x86_64-1629809713.002170/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.pefo8n0t:/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;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\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-pbdSLAP.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\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.G54Mbi
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf pbdSLAP
+ /usr/bin/mkdir -p pbdSLAP
+ cd pbdSLAP
+ /usr/bin/gzip -dc /builddir/build/SOURCES/pbdSLAP_0.3-0.tar.gz
+ /usr/bin/tar -xf -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ echo 'Patch #1 (R-pbdSLAP-conf.patch):'
Patch #1 (R-pbdSLAP-conf.patch):
+ /usr/bin/patch -p1 --fuzz=0
+ /usr/bin/cat /builddir/build/SOURCES/R-pbdSLAP-conf.patch
patching file pbdSLAP/inst/test_intface/00_make.sh
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.ZiIpaL
+ umask 022
+ cd /builddir/build/BUILD
+ cd pbdSLAP
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.ymnq9d
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/R-pbdSLAP-0.3.0-3.el7.x86_64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/R-pbdSLAP-0.3.0-3.el7.x86_64
++ dirname /builddir/build/BUILDROOT/R-pbdSLAP-0.3.0-3.el7.x86_64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/R-pbdSLAP-0.3.0-3.el7.x86_64
+ cd pbdSLAP
+ mkdir -p /builddir/build/BUILDROOT/R-pbdSLAP-0.3.0-3.el7.x86_64/usr/lib64/R/library
+ . /etc/profile.d/modules.sh
++++ /bin/ps -p 33 -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
+ OMPI_MCA_orte_rsh_agent=/bin/false
+ /usr/bin/R CMD INSTALL -l /builddir/build/BUILDROOT/R-pbdSLAP-0.3.0-3.el7.x86_64/usr/lib64/R/library pbdSLAP '--configure-vars=EXT_LDFLAGS='\''-lscalapack -lmpiblacs -lopenblas'\'''
* installing *source* package 'pbdSLAP' ...
file 'inst/test_intface/00_make.sh' has the wrong MD5 checksum
** using staged installation
 
****************** Results of pbdSLAP package configure *****************
 
>> CC = gcc -m64 -std=gnu99
>> F77 = gfortran -m64
>> FC = gfortran -m64
>> EXT_LDFLAGS = -lscalapack -lmpiblacs -lopenblas
>> EXT_OBJS = 
>> EXT_LIBS = 
>> CDEFS = -DAdd_
>> CDEFS_CHECK = TRUE
>> SPMD_CPPFLAGS = -I/usr/include/openmpi-x86_64  -DMPI2 -DOPENMPI
>> SPMD_LDFLAGS = -L/usr/lib64/openmpi/lib -lmpi  -lutil -lpthread
 
*************************************************************************
 
configure: creating ./config.status
config.status: creating src/Makevars
** libs
echo "CC = gcc -m64 -std=gnu99" > Makeconf
echo "F77 = gfortran -m64" >> Makeconf
echo "FC = gfortran -m64" >> Makeconf
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 "EXT_LDFLAGS = -lscalapack -lmpiblacs -lopenblas" >> Makeconf
echo "CDEFS = -DAdd_" >> Makeconf
echo "CDEFS_CHECK = TRUE" >> Makeconf
echo "PKG_CPPFLAGS = -I/usr/include/openmpi-x86_64  -DMPI2 -DOPENMPI -DUSE_FC_LEN_T" >> Makeconf
echo "PKG_CFLAGS = " >> Makeconf
echo "PKG_FFLAGS = " >> Makeconf
echo "PKG_LIBS = -lscalapack -lmpiblacs -lopenblas -lgfortran -lm -lquadmath -L/usr/lib64/openmpi/lib -lmpi  -lutil -lpthread" >> Makeconf
echo "SLAP_FFLAGS =  -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 -I/usr/lib64/gfortran/modules -msse2 -mfpmath=sse" >> Makeconf
echo "R_SLAP = lib/libslap.a" >> Makeconf
gfortran -m64  -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 -I/usr/lib64/gfortran/modules -msse2 -mfpmath=sse -c -o slap_blacs.o slap_blacs.f
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64  -DMPI2 -DOPENMPI -DUSE_FC_LEN_T  -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 pbdSLAP.so slap_blacs.o zzz.o -lscalapack -lmpiblacs -lopenblas -lgfortran -lm -lquadmath -L/usr/lib64/openmpi/lib -lmpi -lutil -lpthread -lgfortran -lm -lquadmath -L/usr/lib64/R/lib -lR
installing via 'install.libs.R' to /builddir/build/BUILDROOT/R-pbdSLAP-0.3.0-3.el7.x86_64/usr/lib64/R/library/00LOCK-pbdSLAP/00new/pbdSLAP
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'pbdSLAP'
    finding HTML links ... done
    00_pbdSLAP-package                      html  
    slap_gridinfo                           html  
** building package indices
** installing vignettes
   'pbdSLAP-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 (pbdSLAP)
+ test -d pbdSLAP/src
+ cd pbdSLAP/src
+ rm -f slap_blacs.o zzz.o pbdSLAP.so
+ rm -f /builddir/build/BUILDROOT/R-pbdSLAP-0.3.0-3.el7.x86_64/usr/lib64/R/library/R.css
+ rm -rf /builddir/build/BUILDROOT/R-pbdSLAP-0.3.0-3.el7.x86_64/usr/lib64/R/library/pbdSLAP/test_intface
+ rm -rf /builddir/build/BUILDROOT/R-pbdSLAP-0.3.0-3.el7.x86_64/usr/lib64/R/library/pbdSLAP/lib/libslap.a
+ /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/pbdSLAP
extracting debug info from /builddir/build/BUILDROOT/R-pbdSLAP-0.3.0-3.el7.x86_64/usr/lib64/R/library/pbdSLAP/libs/pbdSLAP.so
dwz: Too few files for multifile optimization
/usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match.
4 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.6o1h7R
+ umask 022
+ cd /builddir/build/BUILD
+ cd pbdSLAP
+ . /etc/profile.d/modules.sh
++++ /bin/ps -p 605 -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
+ OMPI_MCA_orte_rsh_agent=/bin/false
+ /usr/bin/R CMD check pbdSLAP
* using log directory '/builddir/build/BUILD/pbdSLAP/pbdSLAP.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 'pbdSLAP/DESCRIPTION' ... OK
* this is package 'pbdSLAP' version '0.3-0'
* 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'
 OK
* 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 'pbdSLAP' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.4Mb
  sub-directories of 1Mb or more:
    lib  11.0Mb
* 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 ... 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 include directives in Makefiles ... 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 ...
   'pbdSLAP-guide.Rnw' ... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
  '/builddir/build/BUILD/pbdSLAP/pbdSLAP.Rcheck/00check.log'
for details.
+ exit 0
Processing files: R-pbdSLAP-0.3.0-3.el7.x86_64
Provides: R-pbdSLAP = 0.3.0-3.el7 R-pbdSLAP(x86-64) = 0.3.0-3.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_2.4)(64bit) libgfortran.so.3()(64bit) libm.so.6()(64bit) libopenblas.so.0()(64bit) libpthread.so.0()(64bit) libquadmath.so.0()(64bit) libutil.so.1()(64bit) rtld(GNU_HASH)
Processing files: R-pbdSLAP-debuginfo-0.3.0-3.el7.x86_64
Provides: R-pbdSLAP-debuginfo = 0.3.0-3.el7 R-pbdSLAP-debuginfo(x86-64) = 0.3.0-3.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-pbdSLAP-0.3.0-3.el7.x86_64
Wrote: /builddir/build/RPMS/R-pbdSLAP-0.3.0-3.el7.x86_64.rpm
Wrote: /builddir/build/RPMS/R-pbdSLAP-debuginfo-0.3.0-3.el7.x86_64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.S0gdIu
+ umask 022
+ cd /builddir/build/BUILD
+ cd pbdSLAP
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/R-pbdSLAP-0.3.0-3.el7.x86_64
+ exit 0
Child return code was: 0