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-epel-7-x86_64-1562080587.291118/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.vpoixjcm:/etc/resolv.conf']unshare_net=TrueprintOutput=True) Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.vpoixjcm:/etc/resolv.conf'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '785331e6d3704951a8ca783d31f4584d', '-D', '/var/lib/mock/955910-epel-7-x86_64-1562080587.291118/root', '-a', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.vpoixjcm:/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.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-kazaam.spec'], chrootPath='/var/lib/mock/955910-epel-7-x86_64-1562080587.291118/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.vpoixjcm:/etc/resolv.conf']unshare_net=TrueprintOutput=True) Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.vpoixjcm:/etc/resolv.conf'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '186571deeeb64c60bc0aac1ede923618', '-D', '/var/lib/mock/955910-epel-7-x86_64-1562080587.291118/root', '-a', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.vpoixjcm:/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.vI2UxV + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf kazaam + /usr/bin/mkdir -p kazaam + cd kazaam + /usr/bin/tar -xf - + /usr/bin/gzip -dc /builddir/build/SOURCES/kazaam-0.2.0.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.DwArFQ + umask 022 + cd /builddir/build/BUILD + cd kazaam + . /etc/profile.d/modules.sh BUILDSTDERR: ++++ /bin/ps -p 30 -ocomm= BUILDSTDERR: +++ /bin/basename sh BUILDSTDERR: ++ shell=sh BUILDSTDERR: ++ '[' -f /usr/share/Modules/init/sh ']' BUILDSTDERR: ++ . /usr/share/Modules/init/sh BUILDSTDERR: +++ MODULESHOME=/usr/share/Modules BUILDSTDERR: +++ export MODULESHOME BUILDSTDERR: +++ '[' '' = '' ']' BUILDSTDERR: +++ LOADEDMODULES= BUILDSTDERR: +++ export LOADEDMODULES BUILDSTDERR: +++ '[' /usr/share/Modules/modulefiles:/etc/modulefiles = '' ']' + module load mpi/openmpi-x86_64 BUILDSTDERR: ++ /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_;' BUILDSTDERR: ++ LD_LIBRARY_PATH=/usr/lib64/openmpi/lib BUILDSTDERR: ++ export LD_LIBRARY_PATH BUILDSTDERR: ++ LOADEDMODULES=mpi/openmpi-x86_64 BUILDSTDERR: ++ export LOADEDMODULES BUILDSTDERR: ++ MANPATH=/usr/share/man/openmpi-x86_64:/usr/share/man:/usr/local/share/man BUILDSTDERR: ++ export MANPATH 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-x86_64 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_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: ++ PATH=/usr/lib64/openmpi/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin:/builddir/.local/bin:/builddir/bin BUILDSTDERR: ++ export PATH BUILDSTDERR: ++ PYTHONPATH=/usr/lib64/python2.7/site-packages/openmpi BUILDSTDERR: ++ export PYTHONPATH BUILDSTDERR: ++ _LMFILES_=/etc/modulefiles/mpi/openmpi-x86_64 BUILDSTDERR: ++ export _LMFILES_ + export 'CFLAGS= -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic' + CFLAGS=' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic' + R CMD build 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.fUd0vo + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/R-kazaam-0.2.0-1.el7.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/R-kazaam-0.2.0-1.el7.x86_64 BUILDSTDERR: ++ dirname /builddir/build/BUILDROOT/R-kazaam-0.2.0-1.el7.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/R-kazaam-0.2.0-1.el7.x86_64 + cd kazaam + mkdir -p /builddir/build/BUILDROOT/R-kazaam-0.2.0-1.el7.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.el7.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... -std=gnu99 ****************** 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 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -fopenmp -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 crossprod.c -o crossprod.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -fopenmp -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 kazaam_native.c -o kazaam_native.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -fopenmp -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 kmeans.c -o kmeans.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -fopenmp -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 trsolve.c -o trsolve.o gcc -m64 -std=gnu99 -shared -L/usr/lib64/R/lib -Wl,-z,relro -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.el7.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.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/kazaam extracting debug info from /builddir/build/BUILDROOT/R-kazaam-0.2.0-1.el7.x86_64/usr/lib64/R/library/kazaam/libs/kazaam.so BUILDSTDERR: dwz: Too few files for multifile optimization /usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. BUILDSTDERR: 15 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.bEGBPo + umask 022 + cd /builddir/build/BUILD + cd kazaam + . /etc/profile.d/modules.sh BUILDSTDERR: ++++ /bin/ps -p 1503 -ocomm= BUILDSTDERR: +++ /bin/basename sh BUILDSTDERR: ++ shell=sh BUILDSTDERR: ++ '[' -f /usr/share/Modules/init/sh ']' BUILDSTDERR: ++ . /usr/share/Modules/init/sh BUILDSTDERR: +++ MODULESHOME=/usr/share/Modules BUILDSTDERR: +++ export MODULESHOME BUILDSTDERR: +++ '[' '' = '' ']' BUILDSTDERR: +++ LOADEDMODULES= BUILDSTDERR: +++ export LOADEDMODULES BUILDSTDERR: +++ '[' /usr/share/Modules/modulefiles:/etc/modulefiles = '' ']' + module load mpi/openmpi-x86_64 BUILDSTDERR: ++ /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_;' BUILDSTDERR: ++ LD_LIBRARY_PATH=/usr/lib64/openmpi/lib BUILDSTDERR: ++ export LD_LIBRARY_PATH BUILDSTDERR: ++ LOADEDMODULES=mpi/openmpi-x86_64 BUILDSTDERR: ++ export LOADEDMODULES BUILDSTDERR: ++ MANPATH=/usr/share/man/openmpi-x86_64:/usr/share/man:/usr/local/share/man BUILDSTDERR: ++ export MANPATH 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-x86_64 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_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: ++ PATH=/usr/lib64/openmpi/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin:/builddir/.local/bin:/builddir/bin BUILDSTDERR: ++ export PATH BUILDSTDERR: ++ PYTHONPATH=/usr/lib64/python2.7/site-packages/openmpi BUILDSTDERR: ++ export PYTHONPATH BUILDSTDERR: ++ _LMFILES_=/etc/modulefiles/mpi/openmpi-x86_64 BUILDSTDERR: ++ 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 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 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.el7.x86_64 Provides: R-kazaam = 0.2.0-1.el7 R-kazaam(x86-64) = 0.2.0-1.el7 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /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) libgfortran.so.3()(64bit) libgomp.so.1()(64bit) libm.so.6()(64bit) libmpi.so.12()(64bit) libpthread.so.0()(64bit) libquadmath.so.0()(64bit) libutil.so.1()(64bit) rtld(GNU_HASH) Processing files: R-kazaam-debuginfo-0.2.0-1.el7.x86_64 Provides: R-kazaam-debuginfo = 0.2.0-1.el7 R-kazaam-debuginfo(x86-64) = 0.2.0-1.el7 Requires(rpmlib): rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(CompressedFileNames) <= 3.0.4-1 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-kazaam-0.2.0-1.el7.x86_64 Wrote: /builddir/build/RPMS/R-kazaam-0.2.0-1.el7.x86_64.rpm Wrote: /builddir/build/RPMS/R-kazaam-debuginfo-0.2.0-1.el7.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.7snOQx + umask 022 + cd /builddir/build/BUILD + cd kazaam + /usr/bin/rm -rf /builddir/build/BUILDROOT/R-kazaam-0.2.0-1.el7.x86_64 + exit 0 Child return code was: 0