Mock Version: 2.4 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-8-x86_64-1597138489.258765/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.j9vqj2da:/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.j9vqj2da:/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', 'c19b9887c7de41dabe34219f444bd97c', '-D', '/var/lib/mock/epel-8-x86_64-1597138489.258765/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.j9vqj2da:/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', '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;\\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-pbdSLAP-0.2.5-3.el8.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-8-x86_64-1597138489.258765/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.j9vqj2da:/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.j9vqj2da:/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', '905294f278af4bd5a5a49c532a722a56', '-D', '/var/lib/mock/epel-8-x86_64-1597138489.258765/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.j9vqj2da:/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', '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;\\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.dtqeXQ + 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_0.2-5.tar.gz + /usr/bin/tar -xof - + 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 --no-backup-if-mismatch -p1 --fuzz=0 patching file pbdSLAP/inst/test_intface/00_make.sh + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.b3Mk0C + umask 022 + cd /builddir/build/BUILD + cd pbdSLAP + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.xJnj4o + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/R-pbdSLAP-0.2.5-3.el8.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/R-pbdSLAP-0.2.5-3.el8.x86_64 ++ dirname /builddir/build/BUILDROOT/R-pbdSLAP-0.2.5-3.el8.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/R-pbdSLAP-0.2.5-3.el8.x86_64 + cd pbdSLAP + mkdir -p /builddir/build/BUILDROOT/R-pbdSLAP-0.2.5-3.el8.x86_64/usr/lib64/R/library + . /etc/profile.d/modules.sh ++ . /etc/profile.d/00-modulepath.sh +++ '[' -z /etc/modulefiles:/usr/share/modulefiles:/usr/share/modulefiles/Linux:/usr/share/modulefiles/Core:/usr/share/lmod/lmod/modulefiles/Core ']' +++ : ++ '[' -z '' ']' ++ '[' -z /usr/share/modulefiles ']' ++ PS_CMD=/usr/bin/ps ++ '[' '!' -x /usr/bin/ps ']' ++ EXPR_CMD=/usr/bin/expr ++ '[' '!' -x /usr/bin/expr ']' ++ BASENAME_CMD=/usr/bin/basename ++ '[' '!' -x /usr/bin/basename ']' +++ /usr/bin/ps -p 58 -ocomm= ++ my_shell=sh +++ /usr/bin/expr sh : '-*\(.*\)' ++ my_shell=sh +++ /usr/bin/basename sh ++ my_shell=sh ++ '[' -f /usr/share/lmod/lmod/init/sh ']' ++ . /usr/share/lmod/lmod/init/sh +++ LMOD_ROOT=/usr/share/lmod +++ LMOD_PKG=/usr/share/lmod/lmod +++ LMOD_DIR=/usr/share/lmod/lmod/libexec/ +++ LMOD_CMD=/usr/share/lmod/lmod/libexec/lmod +++ MODULESHOME=/usr/share/lmod/lmod +++ export LMOD_CMD +++ export LMOD_PKG +++ export LMOD_DIR +++ export MODULESHOME +++ export LMOD_DIR ++ unset my_shell PS_CMD EXPR_CMD BASENAME_CMD MODULEPATH_INIT + module load mpi/openmpi-x86_64 ++ /usr/share/lmod/lmod/libexec/lmod sh load mpi/openmpi-x86_64 + eval '__LMOD_REF_COUNT_LD_LIBRARY_PATH=/usr/lib64/openmpi/lib:1;' export '__LMOD_REF_COUNT_LD_LIBRARY_PATH;' 'LD_LIBRARY_PATH=/usr/lib64/openmpi/lib;' export 'LD_LIBRARY_PATH;' '__LMOD_REF_COUNT_LOADEDMODULES=mpi/openmpi-x86_64:1;' export '__LMOD_REF_COUNT_LOADEDMODULES;' 'LOADEDMODULES=mpi/openmpi-x86_64;' export 'LOADEDMODULES;' '__LMOD_REF_COUNT_MANPATH=/usr/share/man/openmpi-x86_64:1\;/usr/share/lmod/lmod/share/man:1;' export '__LMOD_REF_COUNT_MANPATH;' 'MANPATH=/usr/share/man/openmpi-x86_64:/usr/share/lmod/lmod/share/man::;' export 'MANPATH;' '__LMOD_REF_COUNT_MODULEPATH=/etc/modulefiles:1\;/usr/share/modulefiles:1\;/usr/share/modulefiles/Linux:1\;/usr/share/modulefiles/Core:1\;/usr/share/lmod/lmod/modulefiles/Core:1;' export '__LMOD_REF_COUNT_MODULEPATH;' 'MODULEPATH=/etc/modulefiles:/usr/share/modulefiles:/usr/share/modulefiles/Linux:/usr/share/modulefiles/Core:/usr/share/lmod/lmod/modulefiles/Core;' export 'MODULEPATH;' '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;' 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_PYTHON2_SITEARCH=/usr/lib64/python3.6/site-packages/openmpi;' export 'MPI_PYTHON2_SITEARCH;' 'MPI_PYTHON3_SITEARCH=/usr/lib64/python3.6/site-packages/openmpi;' export 'MPI_PYTHON3_SITEARCH;' 'MPI_PYTHON_SITEARCH=/usr/lib64/python3.6/site-packages/openmpi;' export 'MPI_PYTHON_SITEARCH;' 'MPI_SUFFIX=_openmpi;' export 'MPI_SUFFIX;' 'MPI_SYSCONFIG=/etc/openmpi-x86_64;' export 'MPI_SYSCONFIG;' '__LMOD_REF_COUNT_PATH=/usr/lib64/openmpi/bin:1\;/builddir/.local/bin:1\;/builddir/bin:1\;/usr/bin:1\;/bin:1\;/usr/sbin:1\;/sbin:1\;/usr/local/sbin:1;' export '__LMOD_REF_COUNT_PATH;' 'PATH=/usr/lib64/openmpi/bin:/builddir/.local/bin:/builddir/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin;' export 'PATH;' '__LMOD_REF_COUNT_PKG_CONFIG_PATH=/usr/lib64/openmpi/lib/pkgconfig:1\;/usr/lib64/pkgconfig:1\;/usr/share/pkgconfig:1;' export '__LMOD_REF_COUNT_PKG_CONFIG_PATH;' 'PKG_CONFIG_PATH=/usr/lib64/openmpi/lib/pkgconfig::/usr/lib64/pkgconfig:/usr/share/pkgconfig;' export 'PKG_CONFIG_PATH;' '__LMOD_REF_COUNT__LMFILES_=/etc/modulefiles/mpi/openmpi-x86_64:1;' export '__LMOD_REF_COUNT__LMFILES_;' '_LMFILES_=/etc/modulefiles/mpi/openmpi-x86_64;' export '_LMFILES_;' '_ModuleTable001_=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;' export '_ModuleTable001_;' '_ModuleTable002_=bGVmaWxlcy9Db3JlIiwiL3Vzci9zaGFyZS9sbW9kL2xtb2QvbW9kdWxlZmlsZXMvQ29yZSIsfSxbInN5c3RlbUJhc2VNUEFUSCJdPSIvZXRjL21vZHVsZWZpbGVzOi91c3Ivc2hhcmUvbW9kdWxlZmlsZXM6L3Vzci9zaGFyZS9tb2R1bGVmaWxlcy9MaW51eDovdXNyL3NoYXJlL21vZHVsZWZpbGVzL0NvcmU6L3Vzci9zaGFyZS9sbW9kL2xtb2QvbW9kdWxlZmlsZXMvQ29yZSIsfQ==;' export '_ModuleTable002_;' '_ModuleTable_Sz_=2;' export '_ModuleTable_Sz_;' ++ __LMOD_REF_COUNT_LD_LIBRARY_PATH=/usr/lib64/openmpi/lib:1 ++ export __LMOD_REF_COUNT_LD_LIBRARY_PATH ++ LD_LIBRARY_PATH=/usr/lib64/openmpi/lib ++ export LD_LIBRARY_PATH ++ __LMOD_REF_COUNT_LOADEDMODULES=mpi/openmpi-x86_64:1 ++ export __LMOD_REF_COUNT_LOADEDMODULES ++ LOADEDMODULES=mpi/openmpi-x86_64 ++ export LOADEDMODULES ++ __LMOD_REF_COUNT_MANPATH='/usr/share/man/openmpi-x86_64:1;/usr/share/lmod/lmod/share/man:1' ++ export __LMOD_REF_COUNT_MANPATH ++ MANPATH=/usr/share/man/openmpi-x86_64:/usr/share/lmod/lmod/share/man:: ++ export MANPATH ++ __LMOD_REF_COUNT_MODULEPATH='/etc/modulefiles:1;/usr/share/modulefiles:1;/usr/share/modulefiles/Linux:1;/usr/share/modulefiles/Core:1;/usr/share/lmod/lmod/modulefiles/Core:1' ++ export __LMOD_REF_COUNT_MODULEPATH ++ MODULEPATH=/etc/modulefiles:/usr/share/modulefiles:/usr/share/modulefiles/Linux:/usr/share/modulefiles/Core:/usr/share/lmod/lmod/modulefiles/Core ++ export MODULEPATH ++ 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 ++ 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_PYTHON2_SITEARCH=/usr/lib64/python3.6/site-packages/openmpi ++ export MPI_PYTHON2_SITEARCH ++ MPI_PYTHON3_SITEARCH=/usr/lib64/python3.6/site-packages/openmpi ++ export MPI_PYTHON3_SITEARCH ++ MPI_PYTHON_SITEARCH=/usr/lib64/python3.6/site-packages/openmpi ++ export MPI_PYTHON_SITEARCH ++ MPI_SUFFIX=_openmpi ++ export MPI_SUFFIX ++ MPI_SYSCONFIG=/etc/openmpi-x86_64 ++ export MPI_SYSCONFIG ++ __LMOD_REF_COUNT_PATH='/usr/lib64/openmpi/bin:1;/builddir/.local/bin:1;/builddir/bin:1;/usr/bin:1;/bin:1;/usr/sbin:1;/sbin:1;/usr/local/sbin:1' ++ export __LMOD_REF_COUNT_PATH ++ PATH=/usr/lib64/openmpi/bin:/builddir/.local/bin:/builddir/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin ++ export PATH ++ __LMOD_REF_COUNT_PKG_CONFIG_PATH='/usr/lib64/openmpi/lib/pkgconfig:1;/usr/lib64/pkgconfig:1;/usr/share/pkgconfig:1' ++ export __LMOD_REF_COUNT_PKG_CONFIG_PATH ++ PKG_CONFIG_PATH=/usr/lib64/openmpi/lib/pkgconfig::/usr/lib64/pkgconfig:/usr/share/pkgconfig ++ export PKG_CONFIG_PATH ++ __LMOD_REF_COUNT__LMFILES_=/etc/modulefiles/mpi/openmpi-x86_64:1 ++ export __LMOD_REF_COUNT__LMFILES_ ++ _LMFILES_=/etc/modulefiles/mpi/openmpi-x86_64 ++ export _LMFILES_ ++ _ModuleTable001_=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 ++ export _ModuleTable001_ ++ _ModuleTable002_=bGVmaWxlcy9Db3JlIiwiL3Vzci9zaGFyZS9sbW9kL2xtb2QvbW9kdWxlZmlsZXMvQ29yZSIsfSxbInN5c3RlbUJhc2VNUEFUSCJdPSIvZXRjL21vZHVsZWZpbGVzOi91c3Ivc2hhcmUvbW9kdWxlZmlsZXM6L3Vzci9zaGFyZS9tb2R1bGVmaWxlcy9MaW51eDovdXNyL3NoYXJlL21vZHVsZWZpbGVzL0NvcmU6L3Vzci9zaGFyZS9sbW9kL2xtb2QvbW9kdWxlZmlsZXMvQ29yZSIsfQ== ++ export _ModuleTable002_ ++ _ModuleTable_Sz_=2 ++ export _ModuleTable_Sz_ + OMPI_MCA_rmaps_base_oversubscribe=1 + OMPI_MCA_orte_rsh_agent=/bin/false + /usr/bin/R CMD INSTALL -l /builddir/build/BUILDROOT/R-pbdSLAP-0.2.5-3.el8.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 >> 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" > 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" >> 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 = -fno-optimize-sibling-calls -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules -msse2 -mfpmath=sse" >> Makeconf echo "R_SLAP = lib/libslap.a" >> Makeconf gfortran -m64 -fno-optimize-sibling-calls -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules -msse2 -mfpmath=sse -c -o slap_blacs.o slap_blacs.f f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c zzz.c -o zzz.o gcc -m64 -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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-0.2.5-3.el8.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-0.2.5-3.el8.x86_64/usr/lib64/R/library/R.css + rm -rf /builddir/build/BUILDROOT/R-pbdSLAP-0.2.5-3.el8.x86_64/usr/lib64/R/library/pbdSLAP/test_intface + rm -rf /builddir/build/BUILDROOT/R-pbdSLAP-0.2.5-3.el8.x86_64/usr/lib64/R/library/pbdSLAP/lib/libslap.a + /usr/lib/rpm/find-debuginfo.sh -j2 --strict-build-id -m -i --build-id-seed 0.2.5-3.el8 --unique-debug-suffix -0.2.5-3.el8.x86_64 --unique-debug-src-base R-pbdSLAP-0.2.5-3.el8.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/pbdSLAP extracting debug info from /builddir/build/BUILDROOT/R-pbdSLAP-0.2.5-3.el8.x86_64/usr/lib64/R/library/pbdSLAP/libs/pbdSLAP.so /usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. 4 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig /sbin/ldconfig: Warning: ignoring configuration file that cannot be opened: /etc/ld.so.conf: No such file or directory + /usr/lib/rpm/brp-compress + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/brp-python-bytecompile '' 1 + /usr/lib/rpm/brp-python-hardlink + PYTHON3=/usr/libexec/platform-python + /usr/lib/rpm/redhat/brp-mangle-shebangs Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.qRSX8p + umask 022 + cd /builddir/build/BUILD + cd pbdSLAP + OMPI_MCA_rmaps_base_oversubscribe=1 + 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 4.0.2 (2020-06-22) * using platform: x86_64-redhat-linux-gnu (64-bit) * using session charset: ASCII * checking for file 'pbdSLAP/DESCRIPTION' ... OK * this is package 'pbdSLAP' version '0.2-5' * 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/3.11/bioc/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.11/bioc/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.11/data/annotation/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.11/data/experiment/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.11/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 16.0Mb sub-directories of 1Mb or more: lib 15.5Mb * 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 use of PKG_*FLAGS in Makefiles ... 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-0.2.5-3.el8.x86_64 Provides: R(pbdSLAP) = 0.2-5 R-pbdSLAP = 0.2.5-3.el8 R-pbdSLAP(x86-64) = 0.2.5-3.el8 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: R(methods) R(pbdMPI) >= 0.3-1 R(rlecuyer) R-core >= 3.5.0 libR.so()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.4)(64bit) libgfortran.so.5()(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-debugsource-0.2.5-3.el8.x86_64 Provides: R-pbdSLAP-debugsource = 0.2.5-3.el8 R-pbdSLAP-debugsource(x86-64) = 0.2.5-3.el8 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: R-pbdSLAP-debuginfo-0.2.5-3.el8.x86_64 Provides: R-pbdSLAP-debuginfo = 0.2.5-3.el8 R-pbdSLAP-debuginfo(x86-64) = 0.2.5-3.el8 debuginfo(build-id) = a31710020444595210c3391b90ec6b73b79c2aed Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: R-pbdSLAP-debugsource(x86-64) = 0.2.5-3.el8 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-pbdSLAP-0.2.5-3.el8.x86_64 Wrote: /builddir/build/RPMS/R-pbdSLAP-0.2.5-3.el8.x86_64.rpm Wrote: /builddir/build/RPMS/R-pbdSLAP-debugsource-0.2.5-3.el8.x86_64.rpm Wrote: /builddir/build/RPMS/R-pbdSLAP-debuginfo-0.2.5-3.el8.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.vxhU2j + umask 022 + cd /builddir/build/BUILD + cd pbdSLAP + /usr/bin/rm -rf /builddir/build/BUILDROOT/R-pbdSLAP-0.2.5-3.el8.x86_64 + exit 0 Child return code was: 0