Mock Version: 2.12 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/R-pbdDMAT.spec'], chrootPath='/var/lib/mock/epel-7-x86_64-1630678720.359684/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.wgev5kwf:/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.wgev5kwf:/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', 'e32f5eb65dec41f3a297a7040a7036e5', '-D', '/var/lib/mock/epel-7-x86_64-1630678720.359684/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.wgev5kwf:/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-pbdDMAT.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-pbdDMAT-0.5.1-3.gitb170a3c.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-pbdDMAT.spec'], chrootPath='/var/lib/mock/epel-7-x86_64-1630678720.359684/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.wgev5kwf:/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.wgev5kwf:/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', '3ffe923258524f46a6b570bb15201376', '-D', '/var/lib/mock/epel-7-x86_64-1630678720.359684/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.wgev5kwf:/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-pbdDMAT.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.XluKe8 + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf R-pbdDMAT-0.5.1 + /usr/bin/mkdir -p R-pbdDMAT-0.5.1 + cd R-pbdDMAT-0.5.1 + /usr/bin/tar -xf - + /usr/bin/gzip -dc /builddir/build/SOURCES/pbdDMAT-b170a3c.tar.gz + 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.nXjZjZ + umask 022 + cd /builddir/build/BUILD + cd R-pbdDMAT-0.5.1 + . /etc/profile.d/modules.sh ++++ /bin/ps -p 31 -ocomm= +++ /bin/basename sh ++ shell=sh ++ '[' -f /usr/share/Modules/init/sh ']' ++ . /usr/share/Modules/init/sh +++ MODULESHOME=/usr/share/Modules +++ export MODULESHOME +++ '[' '' = '' ']' +++ LOADEDMODULES= +++ export LOADEDMODULES +++ '[' /usr/share/Modules/modulefiles:/etc/modulefiles = '' ']' + module load mpi/openmpi-x86_64 ++ /usr/bin/modulecmd sh load mpi/openmpi-x86_64 + eval LD_LIBRARY_PATH=/usr/lib64/openmpi/lib ';export' 'LD_LIBRARY_PATH;LOADEDMODULES=mpi/openmpi-x86_64' ';export' 'LOADEDMODULES;MANPATH=/usr/share/man/openmpi-x86_64:/usr/share/man:/usr/local/share/man' ';export' 'MANPATH;MPI_BIN=/usr/lib64/openmpi/bin' ';export' 'MPI_BIN;MPI_COMPILER=openmpi-x86_64' ';export' 'MPI_COMPILER;MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi-x86_64' ';export' 'MPI_FORTRAN_MOD_DIR;MPI_HOME=/usr/lib64/openmpi' ';export' 'MPI_HOME;MPI_INCLUDE=/usr/include/openmpi-x86_64' ';export' 'MPI_INCLUDE;MPI_LIB=/usr/lib64/openmpi/lib' ';export' 'MPI_LIB;MPI_MAN=/usr/share/man/openmpi-x86_64' ';export' 'MPI_MAN;MPI_PYTHON_SITEARCH=/usr/lib64/python2.7/site-packages/openmpi' ';export' 'MPI_PYTHON_SITEARCH;MPI_SUFFIX=_openmpi' ';export' 'MPI_SUFFIX;MPI_SYSCONFIG=/etc/openmpi-x86_64' ';export' 'MPI_SYSCONFIG;PATH=/usr/lib64/openmpi/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin:/builddir/.local/bin:/builddir/bin' ';export' 'PATH;PYTHONPATH=/usr/lib64/python2.7/site-packages/openmpi' ';export' 'PYTHONPATH;_LMFILES_=/etc/modulefiles/mpi/openmpi-x86_64' ';export' '_LMFILES_;' ++ LD_LIBRARY_PATH=/usr/lib64/openmpi/lib ++ export LD_LIBRARY_PATH ++ LOADEDMODULES=mpi/openmpi-x86_64 ++ export LOADEDMODULES ++ MANPATH=/usr/share/man/openmpi-x86_64:/usr/share/man:/usr/local/share/man ++ export MANPATH ++ MPI_BIN=/usr/lib64/openmpi/bin ++ export MPI_BIN ++ MPI_COMPILER=openmpi-x86_64 ++ export MPI_COMPILER ++ MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi-x86_64 ++ export MPI_FORTRAN_MOD_DIR ++ MPI_HOME=/usr/lib64/openmpi ++ export MPI_HOME ++ MPI_INCLUDE=/usr/include/openmpi-x86_64 ++ export MPI_INCLUDE ++ MPI_LIB=/usr/lib64/openmpi/lib ++ export MPI_LIB ++ MPI_MAN=/usr/share/man/openmpi-x86_64 ++ export MPI_MAN ++ MPI_PYTHON_SITEARCH=/usr/lib64/python2.7/site-packages/openmpi ++ export MPI_PYTHON_SITEARCH ++ MPI_SUFFIX=_openmpi ++ export MPI_SUFFIX ++ MPI_SYSCONFIG=/etc/openmpi-x86_64 ++ export MPI_SYSCONFIG ++ PATH=/usr/lib64/openmpi/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin:/builddir/.local/bin:/builddir/bin ++ export PATH ++ PYTHONPATH=/usr/lib64/python2.7/site-packages/openmpi ++ export PYTHONPATH ++ _LMFILES_=/etc/modulefiles/mpi/openmpi-x86_64 ++ export _LMFILES_ + export 'CFLAGS= -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic' + CFLAGS=' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic' ++ dirname /builddir/build/SOURCES/tocbibind.sty + export TEXINPUTS=/builddir/build/SOURCES: + TEXINPUTS=/builddir/build/SOURCES: + R CMD build pbdDMAT-b170a3c590592950a902b0febf1bad8b97dbca2e * checking for file 'pbdDMAT-b170a3c590592950a902b0febf1bad8b97dbca2e/DESCRIPTION' ... OK * preparing 'pbdDMAT': * 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 * building 'pbdDMAT_0.5-1.tar.gz' + tar fx pbdDMAT_0.5-1.tar.gz + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.6a6Lzl + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/R-pbdDMAT-0.5.1-3.gitb170a3c.el7.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/R-pbdDMAT-0.5.1-3.gitb170a3c.el7.x86_64 ++ dirname /builddir/build/BUILDROOT/R-pbdDMAT-0.5.1-3.gitb170a3c.el7.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/R-pbdDMAT-0.5.1-3.gitb170a3c.el7.x86_64 + cd R-pbdDMAT-0.5.1 + . /etc/profile.d/modules.sh ++++ /bin/ps -p 756 -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' ++ dirname /builddir/build/SOURCES/tocbibind.sty + export TEXINPUTS=/builddir/build/SOURCES: + TEXINPUTS=/builddir/build/SOURCES: + mkdir -p /builddir/build/BUILDROOT/R-pbdDMAT-0.5.1-3.gitb170a3c.el7.x86_64/usr/lib64/R/library + OMPI_MCA_orte_allocation_required=0 + OMPI_MCA_orte_rsh_agent=/bin/false + R CMD INSTALL -l /builddir/build/BUILDROOT/R-pbdDMAT-0.5.1-3.gitb170a3c.el7.x86_64/usr/lib64/R/library pbdDMAT * installing *source* package 'pbdDMAT' ... ** using staged installation ** libs gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I../inst/RNACI -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 converters.c -o converters.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I../inst/RNACI -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 pbdDMAT_native.c -o pbdDMAT_native.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I../inst/RNACI -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 sparse_utils.c -o sparse_utils.o In file included from dmat.h:7:0, from sparse_utils.c:2: ../inst/RNACI/RNACI.h:86:21: warning: 'RNACI_ptct' defined but not used [-Wunused-variable] static unsigned int RNACI_ptct = 0; ^ gcc -m64 -std=gnu99 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o pbdDMAT.so converters.o pbdDMAT_native.o sparse_utils.o -L/usr/lib64/R/lib -lR installing to /builddir/build/BUILDROOT/R-pbdDMAT-0.5.1-3.gitb170a3c.el7.x86_64/usr/lib64/R/library/00LOCK-pbdDMAT/00new/pbdDMAT/libs ** R ** demo ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for 'as.vector' in package 'pbdDMAT' Creating a generic function for 'chol2inv' from 'base' in package 'pbdDMAT' (from the saved implicit definition) Creating a generic function for 'chol2inv' from package 'base' in package 'pbdDMAT' Creating a generic function for 'rcond' from 'base' in package 'pbdDMAT' (from the saved implicit definition) Creating a generic function for 'rcond' from package 'base' in package 'pbdDMAT' Creating a generic function for 'cov' from package 'stats' in package 'pbdDMAT' Creating a generic function for 'var' from package 'stats' in package 'pbdDMAT' Creating a generic function for 'cor' from package 'stats' in package 'pbdDMAT' Creating a generic function for 'cov2cor' from package 'stats' in package 'pbdDMAT' Creating a generic function for 'det' from package 'base' in package 'pbdDMAT' Creating a generic function for 'crossprod' from package 'base' in package 'pbdDMAT' Creating a generic function for 'tcrossprod' from package 'base' in package 'pbdDMAT' Creating a generic function for 'norm' from package 'base' in package 'pbdDMAT' Creating a generic function for 'rowSums' from package 'base' in package 'pbdDMAT' Creating a generic function for 'colSums' from package 'base' in package 'pbdDMAT' Creating a generic function for 'rowMeans' from package 'base' in package 'pbdDMAT' Creating a generic function for 'colMeans' from package 'base' in package 'pbdDMAT' ** help *** installing help indices converting help for package 'pbdDMAT' finding HTML links ... done Comparators html Hilbert html accessors html arithmetic html as.ddmatrix html as.matrix html as.rowcyclic html as.vector html binds html chol2inv html companion html condnums html control html covariance html ddmatrix-apply html ddmatrix-chol html ddmatrix-class html ddmatrix-constructors html ddmatrix-eigen html ddmatrix-lu html ddmatrix-norm html ddmatrix-prcomp html ddmatrix-print html ddmatrix-scale html ddmatrix-solve html ddmatrix-summary html ddmatrix-sumstats html ddmatrix-svd html det html diag-constructors html eigen2 html expm html extract html getLocal html headsortails html insert html isSymmetric html isdot html lm.fit html math html matmult html na html pbdDMAT-package html qr html redistribute html reductions html rounding html sd html sparsity html sweep html transpose html ** building package indices ** installing vignettes ** 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 (pbdDMAT) + test -d pbdDMAT/src + cd pbdDMAT/src + rm -f converters.o pbdDMAT_native.o sparse_utils.o pbdDMAT.so + rm -f /builddir/build/BUILDROOT/R-pbdDMAT-0.5.1-3.gitb170a3c.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/R-pbdDMAT-0.5.1 extracting debug info from /builddir/build/BUILDROOT/R-pbdDMAT-0.5.1-3.gitb170a3c.el7.x86_64/usr/lib64/R/library/pbdDMAT/libs/pbdDMAT.so dwz: Too few files for multifile optimization /usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. 33 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.RjfIr6 + umask 022 + cd /builddir/build/BUILD + cd R-pbdDMAT-0.5.1 + . /etc/profile.d/modules.sh ++++ /bin/ps -p 934 -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 + R CMD check pbdDMAT * using log directory '/builddir/build/BUILD/R-pbdDMAT-0.5.1/pbdDMAT.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 'pbdDMAT/DESCRIPTION' ... OK * this is package 'pbdDMAT' version '0.5-1' * 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 'pbdDMAT' 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 ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking compiled code ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... 'pbdDMAT-guide.Rnw' ... OK NONE * checking re-building of vignette outputs ... WARNING Error(s) in re-building vignettes: ... --- re-building 'pbdDMAT-guide.Rnw' using Sweave Error: processing vignette 'pbdDMAT-guide.Rnw' failed with diagnostics: Running 'texi2dvi' on 'pbdDMAT-guide.tex' failed. LaTeX errors: ! LaTeX Error: File `tocbibind.sty' not found. Type X to quit or to proceed, or enter new name. (Default extension: sty) ! Emergency stop. l.262 \usepackage [authoryear,round]{natbib}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building 'pbdDMAT-guide.Rnw' SUMMARY: processing the following file failed: 'pbdDMAT-guide.Rnw' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 WARNING See '/builddir/build/BUILD/R-pbdDMAT-0.5.1/pbdDMAT.Rcheck/00check.log' for details. + exit 0 Processing files: R-pbdDMAT-0.5.1-3.gitb170a3c.el7.x86_64 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.rkvLs6 + umask 022 + cd /builddir/build/BUILD + cd R-pbdDMAT-0.5.1 + LICENSEDIR=/builddir/build/BUILDROOT/R-pbdDMAT-0.5.1-3.gitb170a3c.el7.x86_64/usr/share/licenses/R-pbdDMAT-0.5.1 + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/R-pbdDMAT-0.5.1-3.gitb170a3c.el7.x86_64/usr/share/licenses/R-pbdDMAT-0.5.1 + cp -pr pbdDMAT/COPYING /builddir/build/BUILDROOT/R-pbdDMAT-0.5.1-3.gitb170a3c.el7.x86_64/usr/share/licenses/R-pbdDMAT-0.5.1 + exit 0 Provides: R-pbdDMAT = 0.5.1-3.gitb170a3c.el7 R-pbdDMAT(x86-64) = 0.5.1-3.gitb170a3c.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) rtld(GNU_HASH) Processing files: R-pbdDMAT-debuginfo-0.5.1-3.gitb170a3c.el7.x86_64 Provides: R-pbdDMAT-debuginfo = 0.5.1-3.gitb170a3c.el7 R-pbdDMAT-debuginfo(x86-64) = 0.5.1-3.gitb170a3c.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-pbdDMAT-0.5.1-3.gitb170a3c.el7.x86_64 Wrote: /builddir/build/RPMS/R-pbdDMAT-0.5.1-3.gitb170a3c.el7.x86_64.rpm Wrote: /builddir/build/RPMS/R-pbdDMAT-debuginfo-0.5.1-3.gitb170a3c.el7.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.QLyY18 + umask 022 + cd /builddir/build/BUILD + cd R-pbdDMAT-0.5.1 + /usr/bin/rm -rf /builddir/build/BUILDROOT/R-pbdDMAT-0.5.1-3.gitb170a3c.el7.x86_64 + exit 0 Child return code was: 0