Mock Version: 1.4.16 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/R-kazaam.spec'], chrootPath='/var/lib/mock/955910-fedora-30-x86_64-1562080551.258834/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': 'en_US.UTF-8'}shell=Falselogger=timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.m0bwv5__:/etc/resolv.conf']unshare_net=TrueprintOutput=True) Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.m0bwv5__:/etc/resolv.conf'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '6e2700cf5c2e4693a6f9cdb986befbd8', '-D', '/var/lib/mock/955910-fedora-30-x86_64-1562080551.258834/root', '-a', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.m0bwv5__:/etc/resolv.conf', '--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=en_US.UTF-8', '-u', 'mockbuild', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/R-kazaam.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': 'en_US.UTF-8'} and shell False Building target platforms: x86_64 Building for target x86_64 Wrote: /builddir/build/SRPMS/R-kazaam-0.2.0-1.fc30.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-kazaam.spec'], chrootPath='/var/lib/mock/955910-fedora-30-x86_64-1562080551.258834/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': 'en_US.UTF-8'}shell=Falselogger=timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.m0bwv5__:/etc/resolv.conf']unshare_net=TrueprintOutput=True) Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.m0bwv5__:/etc/resolv.conf'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '2e6baeb91d9f4c88bcad0e7260b0342d', '-D', '/var/lib/mock/955910-fedora-30-x86_64-1562080551.258834/root', '-a', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.m0bwv5__:/etc/resolv.conf', '--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=en_US.UTF-8', '-u', 'mockbuild', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/R-kazaam.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': 'en_US.UTF-8'} and shell False Building target platforms: x86_64 Building for target x86_64 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.IcxdgO + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf kazaam + /usr/bin/mkdir -p kazaam + cd kazaam + /usr/bin/gzip -dc /builddir/build/SOURCES/kazaam-0.2.0.tar.gz + /usr/bin/tar -xof - + 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.gKJgCI + umask 022 + cd /builddir/build/BUILD + cd kazaam + . /etc/profile.d/modules.sh BUILDSTDERR: ++ '[' -z '' ']' BUILDSTDERR: ++ '[' -z /usr/share/modulefiles ']' BUILDSTDERR: ++ PS_CMD=/usr/bin/ps BUILDSTDERR: ++ '[' '!' -x /usr/bin/ps ']' BUILDSTDERR: ++ EXPR_CMD=/usr/bin/expr BUILDSTDERR: ++ '[' '!' -x /usr/bin/expr ']' BUILDSTDERR: ++ BASENAME_CMD=/usr/bin/basename BUILDSTDERR: ++ '[' '!' -x /usr/bin/basename ']' BUILDSTDERR: +++ /usr/bin/ps -p 35 -ocomm= BUILDSTDERR: ++ my_shell=sh BUILDSTDERR: +++ /usr/bin/expr sh : '-*\(.*\)' BUILDSTDERR: ++ my_shell=sh BUILDSTDERR: +++ /usr/bin/basename sh BUILDSTDERR: ++ my_shell=sh BUILDSTDERR: ++ '[' -f /usr/share/lmod/lmod/init/sh ']' BUILDSTDERR: ++ . /usr/share/lmod/lmod/init/sh BUILDSTDERR: +++ LMOD_PKG=/usr/share/lmod/lmod BUILDSTDERR: +++ LMOD_DIR=/usr/share/lmod/lmod/libexec/ BUILDSTDERR: +++ LMOD_CMD=/usr/share/lmod/lmod/libexec/lmod BUILDSTDERR: +++ MODULESHOME=/usr/share/lmod/lmod BUILDSTDERR: +++ export LMOD_CMD BUILDSTDERR: +++ export LMOD_PKG BUILDSTDERR: +++ export LMOD_DIR BUILDSTDERR: +++ export MODULESHOME BUILDSTDERR: +++ export LMOD_DIR BUILDSTDERR: ++ unset my_shell PS_CMD EXPR_CMD BASENAME_CMD MODULEPATH_INIT + module load mpi/openmpi-x86_64 BUILDSTDERR: ++ /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/python2.7/site-packages/openmpi;' export 'MPI_PYTHON2_SITEARCH;' 'MPI_PYTHON3_SITEARCH=/usr/lib64/python3.7/site-packages/openmpi;' export 'MPI_PYTHON3_SITEARCH;' '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;' '__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_=/usr/share/modulefiles/mpi/openmpi-x86_64:1;' export '__LMOD_REF_COUNT__LMFILES_;' '_LMFILES_=/usr/share/modulefiles/mpi/openmpi-x86_64;' export '_LMFILES_;' '_ModuleTable001_=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;' export '_ModuleTable001_;' '_ModuleTable002_=ZS9tb2R1bGVmaWxlcy9Db3JlIiwiL3Vzci9zaGFyZS9sbW9kL2xtb2QvbW9kdWxlZmlsZXMvQ29yZSIsfSxbInN5c3RlbUJhc2VNUEFUSCJdPSIvZXRjL21vZHVsZWZpbGVzOi91c3Ivc2hhcmUvbW9kdWxlZmlsZXM6L3Vzci9zaGFyZS9tb2R1bGVmaWxlcy9MaW51eDovdXNyL3NoYXJlL21vZHVsZWZpbGVzL0NvcmU6L3Vzci9zaGFyZS9sbW9kL2xtb2QvbW9kdWxlZmlsZXMvQ29yZSIsfQ==;' export '_ModuleTable002_;' '_ModuleTable_Sz_=2;' export '_ModuleTable_Sz_;' BUILDSTDERR: ++ __LMOD_REF_COUNT_LD_LIBRARY_PATH=/usr/lib64/openmpi/lib:1 BUILDSTDERR: ++ export __LMOD_REF_COUNT_LD_LIBRARY_PATH BUILDSTDERR: ++ LD_LIBRARY_PATH=/usr/lib64/openmpi/lib BUILDSTDERR: ++ export LD_LIBRARY_PATH BUILDSTDERR: ++ __LMOD_REF_COUNT_LOADEDMODULES=mpi/openmpi-x86_64:1 BUILDSTDERR: ++ export __LMOD_REF_COUNT_LOADEDMODULES BUILDSTDERR: ++ LOADEDMODULES=mpi/openmpi-x86_64 BUILDSTDERR: ++ export LOADEDMODULES BUILDSTDERR: ++ __LMOD_REF_COUNT_MANPATH='/usr/share/man/openmpi-x86_64:1;/usr/share/lmod/lmod/share/man:1' BUILDSTDERR: ++ export __LMOD_REF_COUNT_MANPATH BUILDSTDERR: ++ MANPATH=/usr/share/man/openmpi-x86_64:/usr/share/lmod/lmod/share/man:: BUILDSTDERR: ++ export MANPATH BUILDSTDERR: ++ __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' BUILDSTDERR: ++ export __LMOD_REF_COUNT_MODULEPATH BUILDSTDERR: ++ MODULEPATH=/etc/modulefiles:/usr/share/modulefiles:/usr/share/modulefiles/Linux:/usr/share/modulefiles/Core:/usr/share/lmod/lmod/modulefiles/Core BUILDSTDERR: ++ export MODULEPATH BUILDSTDERR: ++ MPI_BIN=/usr/lib64/openmpi/bin BUILDSTDERR: ++ export MPI_BIN BUILDSTDERR: ++ MPI_COMPILER=openmpi-x86_64 BUILDSTDERR: ++ export MPI_COMPILER BUILDSTDERR: ++ MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi BUILDSTDERR: ++ export MPI_FORTRAN_MOD_DIR BUILDSTDERR: ++ MPI_HOME=/usr/lib64/openmpi BUILDSTDERR: ++ export MPI_HOME BUILDSTDERR: ++ MPI_INCLUDE=/usr/include/openmpi-x86_64 BUILDSTDERR: ++ export MPI_INCLUDE BUILDSTDERR: ++ MPI_LIB=/usr/lib64/openmpi/lib BUILDSTDERR: ++ export MPI_LIB BUILDSTDERR: ++ MPI_MAN=/usr/share/man/openmpi-x86_64 BUILDSTDERR: ++ export MPI_MAN BUILDSTDERR: ++ MPI_PYTHON2_SITEARCH=/usr/lib64/python2.7/site-packages/openmpi BUILDSTDERR: ++ export MPI_PYTHON2_SITEARCH BUILDSTDERR: ++ MPI_PYTHON3_SITEARCH=/usr/lib64/python3.7/site-packages/openmpi BUILDSTDERR: ++ export MPI_PYTHON3_SITEARCH BUILDSTDERR: ++ MPI_PYTHON_SITEARCH=/usr/lib64/python2.7/site-packages/openmpi BUILDSTDERR: ++ export MPI_PYTHON_SITEARCH BUILDSTDERR: ++ MPI_SUFFIX=_openmpi BUILDSTDERR: ++ export MPI_SUFFIX BUILDSTDERR: ++ MPI_SYSCONFIG=/etc/openmpi-x86_64 BUILDSTDERR: ++ export MPI_SYSCONFIG BUILDSTDERR: ++ __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' BUILDSTDERR: ++ export __LMOD_REF_COUNT_PATH BUILDSTDERR: ++ PATH=/usr/lib64/openmpi/bin:/builddir/.local/bin:/builddir/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin BUILDSTDERR: ++ export PATH BUILDSTDERR: ++ __LMOD_REF_COUNT_PKG_CONFIG_PATH='/usr/lib64/openmpi/lib/pkgconfig:1;/usr/lib64/pkgconfig:1;/usr/share/pkgconfig:1' BUILDSTDERR: ++ export __LMOD_REF_COUNT_PKG_CONFIG_PATH BUILDSTDERR: ++ PKG_CONFIG_PATH=/usr/lib64/openmpi/lib/pkgconfig::/usr/lib64/pkgconfig:/usr/share/pkgconfig BUILDSTDERR: ++ export PKG_CONFIG_PATH BUILDSTDERR: ++ __LMOD_REF_COUNT__LMFILES_=/usr/share/modulefiles/mpi/openmpi-x86_64:1 BUILDSTDERR: ++ export __LMOD_REF_COUNT__LMFILES_ BUILDSTDERR: ++ _LMFILES_=/usr/share/modulefiles/mpi/openmpi-x86_64 BUILDSTDERR: ++ export _LMFILES_ BUILDSTDERR: ++ _ModuleTable001_=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 BUILDSTDERR: ++ export _ModuleTable001_ BUILDSTDERR: ++ _ModuleTable002_=ZS9tb2R1bGVmaWxlcy9Db3JlIiwiL3Vzci9zaGFyZS9sbW9kL2xtb2QvbW9kdWxlZmlsZXMvQ29yZSIsfSxbInN5c3RlbUJhc2VNUEFUSCJdPSIvZXRjL21vZHVsZWZpbGVzOi91c3Ivc2hhcmUvbW9kdWxlZmlsZXM6L3Vzci9zaGFyZS9tb2R1bGVmaWxlcy9MaW51eDovdXNyL3NoYXJlL21vZHVsZWZpbGVzL0NvcmU6L3Vzci9zaGFyZS9sbW9kL2xtb2QvbW9kdWxlZmlsZXMvQ29yZSIsfQ== BUILDSTDERR: ++ export _ModuleTable002_ BUILDSTDERR: ++ _ModuleTable_Sz_=2 BUILDSTDERR: ++ export _ModuleTable_Sz_ + R CMD build kazaam-0.2-0 * checking for file 'kazaam-0.2-0/DESCRIPTION' ... OK * preparing 'kazaam': * checking DESCRIPTION meta-information ... OK * cleaning src * running 'cleanup' * installing the package to build vignettes * creating vignettes ... OK * cleaning src * running 'cleanup' * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories Removed empty directory 'kazaam/vignettes/cover/logo' * building 'kazaam_0.2-0.tar.gz' + tar fx kazaam_0.2-0.tar.gz + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.iOhfdp + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/R-kazaam-0.2.0-1.fc30.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/R-kazaam-0.2.0-1.fc30.x86_64 BUILDSTDERR: ++ dirname /builddir/build/BUILDROOT/R-kazaam-0.2.0-1.fc30.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/R-kazaam-0.2.0-1.fc30.x86_64 + cd kazaam + mkdir -p /builddir/build/BUILDROOT/R-kazaam-0.2.0-1.fc30.x86_64/usr/lib64/R/library + OMPI_MCA_orte_allocation_required=0 + OMPI_MCA_orte_rsh_agent=/bin/false + /usr/bin/R CMD INSTALL -l /builddir/build/BUILDROOT/R-kazaam-0.2.0-1.fc30.x86_64/usr/lib64/R/library kazaam BUILDSTDERR: * installing *source* package 'kazaam' ... BUILDSTDERR: ** using staged installation checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for gcc option to accept ISO C99... none needed ****************** Results of kazaam package configure ***************** >> 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 BUILDSTDERR: ** libs gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -fopenmp -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 crossprod.c -o crossprod.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -fopenmp -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 kazaam_native.c -o kazaam_native.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -fopenmp -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 kmeans.c -o kmeans.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -fopenmp -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 trsolve.c -o trsolve.o gcc -m64 -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o kazaam.so crossprod.o kazaam_native.o kmeans.o trsolve.o -L/usr/lib64/R/lib -lRlapack -L/usr/lib64/R/lib -lRblas -lgfortran -lm -lquadmath -L/usr/lib64/openmpi/lib -lmpi -lutil -lpthread -fopenmp -L/usr/lib64/R/lib -lR BUILDSTDERR: installing to /builddir/build/BUILDROOT/R-kazaam-0.2.0-1.fc30.x86_64/usr/lib64/R/library/00LOCK-kazaam/00new/kazaam/libs BUILDSTDERR: ** R BUILDSTDERR: ** inst BUILDSTDERR: ** byte-compile and prepare package for lazy loading Creating a generic function for 'nrow' from package 'base' in package 'kazaam' Creating a generic function for 'NROW' from package 'base' in package 'kazaam' Creating a generic function for 'ncol' from package 'base' in package 'kazaam' Creating a generic function for 'NCOL' from package 'base' in package 'kazaam' Creating a generic function for 'colSums' from package 'base' in package 'kazaam' Creating a generic function for 'colMeans' from package 'base' in package 'kazaam' Creating a generic function for 'cov' from package 'stats' in package 'kazaam' Creating a generic function for 'cor' from package 'stats' in package 'kazaam' Creating a generic function for 'crossprod' from package 'base' in package 'kazaam' Creating a generic function for 'norm' from package 'base' in package 'kazaam' Creating a generic function for 'rcond' from 'base' in package 'kazaam' (from the saved implicit definition) Creating a generic function for 'rcond' from package 'base' in package 'kazaam' Creating a generic function for 'svd' from 'base' in package 'kazaam' (from the saved implicit definition) Creating a generic function for 'svd' from package 'base' in package 'kazaam' BUILDSTDERR: ** help BUILDSTDERR: *** installing help indices converting help for package 'kazaam' BUILDSTDERR: finding HTML links ... done arithmetic html bracket html cbind.shaq html col_ops html collapse html cov html crossprod html expand html getters html glms html is.shaq html kazaam-package html km html lm_coefs html matmult html norm html prcomp html print html qr html ranshaq html rcond html rsvd html scale html setters html shaq-class html shaq html sum html svd html BUILDSTDERR: ** building package indices BUILDSTDERR: ** installing vignettes BUILDSTDERR: ** testing if installed package can be loaded from temporary location BUILDSTDERR: ** checking absolute paths in shared objects and dynamic libraries BUILDSTDERR: ** testing if installed package can be loaded from final location BUILDSTDERR: ** testing if installed package keeps a record of temporary installation path BUILDSTDERR: * DONE (kazaam) + test -d kazaam/src + cd kazaam/src + rm -f crossprod.o kazaam_native.o kmeans.o trsolve.o kazaam.so + rm -f /builddir/build/BUILDROOT/R-kazaam-0.2.0-1.fc30.x86_64/usr/lib64/R/library/R.css + /usr/lib/rpm/find-debuginfo.sh -j2 --strict-build-id -m -i --build-id-seed 0.2.0-1.fc30 --unique-debug-suffix -0.2.0-1.fc30.x86_64 --unique-debug-src-base R-kazaam-0.2.0-1.fc30.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/kazaam explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/R-kazaam-0.2.0-1.fc30.x86_64/usr/lib64/R/library/kazaam/libs/kazaam.so extracting debug info from /builddir/build/BUILDROOT/R-kazaam-0.2.0-1.fc30.x86_64/usr/lib64/R/library/kazaam/libs/kazaam.so /usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. BUILDSTDERR: 15 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1 0 + /usr/lib/rpm/brp-python-hardlink + /usr/lib/rpm/redhat/brp-mangle-shebangs mangling shebang in /usr/lib64/R/library/kazaam/batchtests/run from /bin/sh to #!/usr/bin/sh mangling shebang in /usr/lib64/R/library/kazaam/batchtests/allrun from /bin/sh to #!/usr/bin/sh Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.gOLMDE + umask 022 + cd /builddir/build/BUILD + cd kazaam + . /etc/profile.d/modules.sh BUILDSTDERR: ++ '[' -z '' ']' BUILDSTDERR: ++ '[' -z /usr/share/modulefiles ']' BUILDSTDERR: ++ PS_CMD=/usr/bin/ps BUILDSTDERR: ++ '[' '!' -x /usr/bin/ps ']' BUILDSTDERR: ++ EXPR_CMD=/usr/bin/expr BUILDSTDERR: ++ '[' '!' -x /usr/bin/expr ']' BUILDSTDERR: ++ BASENAME_CMD=/usr/bin/basename BUILDSTDERR: ++ '[' '!' -x /usr/bin/basename ']' BUILDSTDERR: +++ /usr/bin/ps -p 1606 -ocomm= BUILDSTDERR: ++ my_shell=sh BUILDSTDERR: +++ /usr/bin/expr sh : '-*\(.*\)' BUILDSTDERR: ++ my_shell=sh BUILDSTDERR: +++ /usr/bin/basename sh BUILDSTDERR: ++ my_shell=sh BUILDSTDERR: ++ '[' -f /usr/share/lmod/lmod/init/sh ']' BUILDSTDERR: ++ . /usr/share/lmod/lmod/init/sh BUILDSTDERR: +++ LMOD_PKG=/usr/share/lmod/lmod BUILDSTDERR: +++ LMOD_DIR=/usr/share/lmod/lmod/libexec/ BUILDSTDERR: +++ LMOD_CMD=/usr/share/lmod/lmod/libexec/lmod BUILDSTDERR: +++ MODULESHOME=/usr/share/lmod/lmod BUILDSTDERR: +++ export LMOD_CMD BUILDSTDERR: +++ export LMOD_PKG BUILDSTDERR: +++ export LMOD_DIR BUILDSTDERR: +++ export MODULESHOME BUILDSTDERR: +++ export LMOD_DIR BUILDSTDERR: ++ unset my_shell PS_CMD EXPR_CMD BASENAME_CMD MODULEPATH_INIT + module load mpi/openmpi-x86_64 BUILDSTDERR: ++ /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/python2.7/site-packages/openmpi;' export 'MPI_PYTHON2_SITEARCH;' 'MPI_PYTHON3_SITEARCH=/usr/lib64/python3.7/site-packages/openmpi;' export 'MPI_PYTHON3_SITEARCH;' '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;' '__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_=/usr/share/modulefiles/mpi/openmpi-x86_64:1;' export '__LMOD_REF_COUNT__LMFILES_;' '_LMFILES_=/usr/share/modulefiles/mpi/openmpi-x86_64;' export '_LMFILES_;' '_ModuleTable001_=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;' export '_ModuleTable001_;' '_ModuleTable002_=ZS9tb2R1bGVmaWxlcy9Db3JlIiwiL3Vzci9zaGFyZS9sbW9kL2xtb2QvbW9kdWxlZmlsZXMvQ29yZSIsfSxbInN5c3RlbUJhc2VNUEFUSCJdPSIvZXRjL21vZHVsZWZpbGVzOi91c3Ivc2hhcmUvbW9kdWxlZmlsZXM6L3Vzci9zaGFyZS9tb2R1bGVmaWxlcy9MaW51eDovdXNyL3NoYXJlL21vZHVsZWZpbGVzL0NvcmU6L3Vzci9zaGFyZS9sbW9kL2xtb2QvbW9kdWxlZmlsZXMvQ29yZSIsfQ==;' export '_ModuleTable002_;' '_ModuleTable_Sz_=2;' export '_ModuleTable_Sz_;' BUILDSTDERR: ++ __LMOD_REF_COUNT_LD_LIBRARY_PATH=/usr/lib64/openmpi/lib:1 BUILDSTDERR: ++ export __LMOD_REF_COUNT_LD_LIBRARY_PATH BUILDSTDERR: ++ LD_LIBRARY_PATH=/usr/lib64/openmpi/lib BUILDSTDERR: ++ export LD_LIBRARY_PATH BUILDSTDERR: ++ __LMOD_REF_COUNT_LOADEDMODULES=mpi/openmpi-x86_64:1 BUILDSTDERR: ++ export __LMOD_REF_COUNT_LOADEDMODULES BUILDSTDERR: ++ LOADEDMODULES=mpi/openmpi-x86_64 BUILDSTDERR: ++ export LOADEDMODULES BUILDSTDERR: ++ __LMOD_REF_COUNT_MANPATH='/usr/share/man/openmpi-x86_64:1;/usr/share/lmod/lmod/share/man:1' BUILDSTDERR: ++ export __LMOD_REF_COUNT_MANPATH BUILDSTDERR: ++ MANPATH=/usr/share/man/openmpi-x86_64:/usr/share/lmod/lmod/share/man:: BUILDSTDERR: ++ export MANPATH BUILDSTDERR: ++ __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' BUILDSTDERR: ++ export __LMOD_REF_COUNT_MODULEPATH BUILDSTDERR: ++ MODULEPATH=/etc/modulefiles:/usr/share/modulefiles:/usr/share/modulefiles/Linux:/usr/share/modulefiles/Core:/usr/share/lmod/lmod/modulefiles/Core BUILDSTDERR: ++ export MODULEPATH BUILDSTDERR: ++ MPI_BIN=/usr/lib64/openmpi/bin BUILDSTDERR: ++ export MPI_BIN BUILDSTDERR: ++ MPI_COMPILER=openmpi-x86_64 BUILDSTDERR: ++ export MPI_COMPILER BUILDSTDERR: ++ MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi BUILDSTDERR: ++ export MPI_FORTRAN_MOD_DIR BUILDSTDERR: ++ MPI_HOME=/usr/lib64/openmpi BUILDSTDERR: ++ export MPI_HOME BUILDSTDERR: ++ MPI_INCLUDE=/usr/include/openmpi-x86_64 BUILDSTDERR: ++ export MPI_INCLUDE BUILDSTDERR: ++ MPI_LIB=/usr/lib64/openmpi/lib BUILDSTDERR: ++ export MPI_LIB BUILDSTDERR: ++ MPI_MAN=/usr/share/man/openmpi-x86_64 BUILDSTDERR: ++ export MPI_MAN BUILDSTDERR: ++ MPI_PYTHON2_SITEARCH=/usr/lib64/python2.7/site-packages/openmpi BUILDSTDERR: ++ export MPI_PYTHON2_SITEARCH BUILDSTDERR: ++ MPI_PYTHON3_SITEARCH=/usr/lib64/python3.7/site-packages/openmpi BUILDSTDERR: ++ export MPI_PYTHON3_SITEARCH BUILDSTDERR: ++ MPI_PYTHON_SITEARCH=/usr/lib64/python2.7/site-packages/openmpi BUILDSTDERR: ++ export MPI_PYTHON_SITEARCH BUILDSTDERR: ++ MPI_SUFFIX=_openmpi BUILDSTDERR: ++ export MPI_SUFFIX BUILDSTDERR: ++ MPI_SYSCONFIG=/etc/openmpi-x86_64 BUILDSTDERR: ++ export MPI_SYSCONFIG BUILDSTDERR: ++ __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' BUILDSTDERR: ++ export __LMOD_REF_COUNT_PATH BUILDSTDERR: ++ PATH=/usr/lib64/openmpi/bin:/builddir/.local/bin:/builddir/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin BUILDSTDERR: ++ export PATH BUILDSTDERR: ++ __LMOD_REF_COUNT_PKG_CONFIG_PATH='/usr/lib64/openmpi/lib/pkgconfig:1;/usr/lib64/pkgconfig:1;/usr/share/pkgconfig:1' BUILDSTDERR: ++ export __LMOD_REF_COUNT_PKG_CONFIG_PATH BUILDSTDERR: ++ PKG_CONFIG_PATH=/usr/lib64/openmpi/lib/pkgconfig::/usr/lib64/pkgconfig:/usr/share/pkgconfig BUILDSTDERR: ++ export PKG_CONFIG_PATH BUILDSTDERR: ++ __LMOD_REF_COUNT__LMFILES_=/usr/share/modulefiles/mpi/openmpi-x86_64:1 BUILDSTDERR: ++ export __LMOD_REF_COUNT__LMFILES_ BUILDSTDERR: ++ _LMFILES_=/usr/share/modulefiles/mpi/openmpi-x86_64 BUILDSTDERR: ++ export _LMFILES_ BUILDSTDERR: ++ _ModuleTable001_=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 BUILDSTDERR: ++ export _ModuleTable001_ BUILDSTDERR: ++ _ModuleTable002_=ZS9tb2R1bGVmaWxlcy9Db3JlIiwiL3Vzci9zaGFyZS9sbW9kL2xtb2QvbW9kdWxlZmlsZXMvQ29yZSIsfSxbInN5c3RlbUJhc2VNUEFUSCJdPSIvZXRjL21vZHVsZWZpbGVzOi91c3Ivc2hhcmUvbW9kdWxlZmlsZXM6L3Vzci9zaGFyZS9tb2R1bGVmaWxlcy9MaW51eDovdXNyL3NoYXJlL21vZHVsZWZpbGVzL0NvcmU6L3Vzci9zaGFyZS9sbW9kL2xtb2QvbW9kdWxlZmlsZXMvQ29yZSIsfQ== BUILDSTDERR: ++ export _ModuleTable002_ BUILDSTDERR: ++ _ModuleTable_Sz_=2 BUILDSTDERR: ++ export _ModuleTable_Sz_ + OMPI_MCA_orte_allocation_required=0 + OMPI_MCA_orte_rsh_agent=/bin/false + /usr/bin/R CMD check kazaam * using log directory '/builddir/build/BUILD/kazaam/kazaam.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 'kazaam/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'kazaam' version '0.2-0' * checking package namespace information ... OK BUILDSTDERR: * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: BUILDSTDERR: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' BUILDSTDERR: Warning: unable to access index for repository https://bioconductor.org/packages/3.9/bioc/src/contrib: BUILDSTDERR: cannot open URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/PACKAGES' BUILDSTDERR: Warning: unable to access index for repository https://bioconductor.org/packages/3.9/data/annotation/src/contrib: BUILDSTDERR: cannot open URL 'https://bioconductor.org/packages/3.9/data/annotation/src/contrib/PACKAGES' BUILDSTDERR: Warning: unable to access index for repository https://bioconductor.org/packages/3.9/data/experiment/src/contrib: BUILDSTDERR: 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 'kazaam' can be installed ... OK * checking installed package size ... 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 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 compiled code ... OK * checking sizes of PDF files under 'inst/doc' ... 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 ... 'kazaam.Rnw' ... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE BUILDSTDERR: See BUILDSTDERR: '/builddir/build/BUILD/kazaam/kazaam.Rcheck/00check.log' BUILDSTDERR: for details. + exit 0 Processing files: R-kazaam-0.2.0-1.fc30.x86_64 Provides: R-kazaam = 0.2.0-1.fc30 R-kazaam(x86-64) = 0.2.0-1.fc30 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/sh libR.so()(64bit) libRblas.so()(64bit) libRlapack.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) libmpi.so.40()(64bit) rtld(GNU_HASH) Processing files: R-kazaam-debugsource-0.2.0-1.fc30.x86_64 Provides: R-kazaam-debugsource = 0.2.0-1.fc30 R-kazaam-debugsource(x86-64) = 0.2.0-1.fc30 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: R-kazaam-debuginfo-0.2.0-1.fc30.x86_64 Provides: R-kazaam-debuginfo = 0.2.0-1.fc30 R-kazaam-debuginfo(x86-64) = 0.2.0-1.fc30 debuginfo(build-id) = c83fb84eae0163fa7a079233e4ffabd9687c1e59 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: R-kazaam-debugsource(x86-64) = 0.2.0-1.fc30 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-kazaam-0.2.0-1.fc30.x86_64 Wrote: /builddir/build/RPMS/R-kazaam-0.2.0-1.fc30.x86_64.rpm Wrote: /builddir/build/RPMS/R-kazaam-debugsource-0.2.0-1.fc30.x86_64.rpm Wrote: /builddir/build/RPMS/R-kazaam-debuginfo-0.2.0-1.fc30.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.wOQMyK + umask 022 + cd /builddir/build/BUILD + cd kazaam + /usr/bin/rm -rf /builddir/build/BUILDROOT/R-kazaam-0.2.0-1.fc30.x86_64 + exit 0 Child return code was: 0