Mock Version: 1.4.14 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/R-pbdDEMO.spec'], chrootPath='/var/lib/mock/887114-epel-7-x86_64-1556059152.289673/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.s6t2zxdc:/etc/resolv.conf']unshare_net=TrueprintOutput=True) Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '08c5476f711140cf9e12028201ad1eac', '-D', '/var/lib/mock/887114-epel-7-x86_64-1556059152.289673/root', '-a', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.s6t2zxdc:/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-pbdDEMO.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-pbdDEMO-0.3.2-3.el7.src.rpm Child return code was: 0 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/R-pbdDEMO.spec'], chrootPath='/var/lib/mock/887114-epel-7-x86_64-1556059152.289673/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.s6t2zxdc:/etc/resolv.conf']unshare_net=TrueprintOutput=True) Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', 'ddbd56ff3afd4ff8b84fe5e5597047a4', '-D', '/var/lib/mock/887114-epel-7-x86_64-1556059152.289673/root', '-a', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.s6t2zxdc:/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-pbdDEMO.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.kK96Sd + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf pbdDEMO + /usr/bin/mkdir -p pbdDEMO + cd pbdDEMO + /usr/bin/gzip -dc /builddir/build/SOURCES/pbdDEMO-0.3.2.tar.gz + /usr/bin/tar -xf - + STATUS=0 + '[' 0 -ne 0 ']' + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + unzip /builddir/build/SOURCES/tocbibind.zip Archive: /builddir/build/SOURCES/tocbibind.zip creating: tocbibind/ inflating: tocbibind/README inflating: tocbibind/tocbibind.dtx inflating: tocbibind/tocbibind.ins inflating: tocbibind/tocbibind.pdf + cd tocbibind + latex tocbibind.ins This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013) restricted \write18 enabled. entering extended mode (./tocbibind.ins LaTeX2e <2011/06/27> Babel and hyphenation patterns for english, dumylang, nohyphenation, lo aded. (/usr/share/texlive/texmf-dist/tex/latex/base/docstrip.tex Utility: `docstrip' 2.5d <2005/07/29> English documentation <1999/03/31> ********************************************************** * This program converts documented macro-files into fast * * loadable files by stripping off (nearly) all comments! * ********************************************************** ******************************************************** * No Configuration file found, using default settings. * ******************************************************** (./tocbibind.ins *** Generating the LaTeX2e package files *** Generating file(s) ./tocbibind.sty Processing file tocbibind.dtx (usc) -> tocbibind.sty File tocbibind.dtx ended by \endinput. Lines processed: 1164 Comments removed: 860 Comments passed: 0 Codelines passed: 300 *********************************************************** * * To finish the installation you have to move the following * file(s) into a directory searched by TeX: * * tocbibind.sty * * * To produce the documentation run the files ending with * `.dtx' through LaTeX. * Process any name.idx file by: * makeindex -s gind.ist name * Process any name.glo file by: * makeindex -s gglo.ist -o name.gls name.glo * * Happy TeXing *********************************************************** ) ) ) No pages of output. Transcript written on tocbibind.log. + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.C2QGtd + umask 022 + cd /builddir/build/BUILD + cd pbdDEMO + . /etc/profile.d/modules.sh BUILDSTDERR: ++++ /bin/ps -p 32 -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' BUILDSTDERR: ++ dirname /builddir/build/SOURCES/algpseudocode.sty BUILDSTDERR: ++ pwd + TEXINPUTS=.:/builddir/build/SOURCES:/builddir/build/BUILD/pbdDEMO/tocbibind: + R CMD build pbdDEMO-0.3-2 * checking for file 'pbdDEMO-0.3-2/DESCRIPTION' ... OK * preparing 'pbdDEMO': * 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 * looking to see if a 'data/datalist' file should be added * building 'pbdDEMO_0.3-2.tar.gz' + tar fx pbdDEMO_0.3-2.tar.gz + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.IVEoz8 + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/R-pbdDEMO-0.3.2-3.el7.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/R-pbdDEMO-0.3.2-3.el7.x86_64 BUILDSTDERR: ++ dirname /builddir/build/BUILDROOT/R-pbdDEMO-0.3.2-3.el7.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/R-pbdDEMO-0.3.2-3.el7.x86_64 + cd pbdDEMO + mkdir -p /builddir/build/BUILDROOT/R-pbdDEMO-0.3.2-3.el7.x86_64/usr/lib64/R/library + . /etc/profile.d/modules.sh BUILDSTDERR: ++++ /bin/ps -p 800 -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 + R CMD INSTALL -l /builddir/build/BUILDROOT/R-pbdDEMO-0.3.2-3.el7.x86_64/usr/lib64/R/library pbdDEMO BUILDSTDERR: * installing *source* package 'pbdDEMO' ... BUILDSTDERR: ** libs gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -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 pbdDEMO_native.c -o pbdDEMO_native.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -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 wc.c -o wc.o gcc -m64 -std=gnu99 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o pbdDEMO.so pbdDEMO_native.o wc.o -L/usr/lib64/R/lib -lR BUILDSTDERR: installing to /builddir/build/BUILDROOT/R-pbdDEMO-0.3.2-3.el7.x86_64/usr/lib64/R/library/pbdDEMO/libs BUILDSTDERR: ** R BUILDSTDERR: ** data BUILDSTDERR: *** moving datasets to lazyload DB BUILDSTDERR: ** demo BUILDSTDERR: ** inst BUILDSTDERR: ** byte-compile and prepare package for lazy loading BUILDSTDERR: ** help BUILDSTDERR: *** installing help indices converting help for package 'pbdDEMO' BUILDSTDERR: finding HTML links ... done Temperature-at-Reference-Height html gbd_dmat html load_balance html mpi_example html ncvar html pbdDEMO-package html plot_dmat html read.csv.ddmatrix html timer html verify html BUILDSTDERR: ** building package indices BUILDSTDERR: ** installing vignettes BUILDSTDERR: ** testing if installed package can be loaded BUILDSTDERR: * DONE (pbdDEMO) + test -d pbdDEMO/src + cd pbdDEMO/src + rm -f pbdDEMO_native.o wc.o pbdDEMO.so + rm -f /builddir/build/BUILDROOT/R-pbdDEMO-0.3.2-3.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/pbdDEMO extracting debug info from /builddir/build/BUILDROOT/R-pbdDEMO-0.3.2-3.el7.x86_64/usr/lib64/R/library/pbdDEMO/libs/pbdDEMO.so BUILDSTDERR: dwz: Too few files for multifile optimization /usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. BUILDSTDERR: 3 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.Qttgin + umask 022 + cd /builddir/build/BUILD + cd pbdDEMO + . /etc/profile.d/modules.sh BUILDSTDERR: ++++ /bin/ps -p 939 -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 pbdDEMO * using log directory '/builddir/build/BUILD/pbdDEMO/pbdDEMO.Rcheck' * using R version 3.5.2 (2018-12-20) * using platform: x86_64-redhat-linux-gnu (64-bit) * using session charset: ASCII * checking for file 'pbdDEMO/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'pbdDEMO' version '0.3-2' * 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/3.8/bioc/src/contrib: BUILDSTDERR: cannot open URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/PACKAGES' BUILDSTDERR: Warning: unable to access index for repository https://bioconductor.org/packages/3.8/data/annotation/src/contrib: BUILDSTDERR: cannot open URL 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib/PACKAGES' BUILDSTDERR: Warning: unable to access index for repository https://bioconductor.org/packages/3.8/data/experiment/src/contrib: BUILDSTDERR: cannot open URL 'https://bioconductor.org/packages/3.8/data/experiment/src/contrib/PACKAGES' NOTE Packages which this enhances but not available for checking: 'maps' 'RColorBrewer' 'pbdNCDF4' 'pmclust' 'MixSim' 'EMCluster' 'phyclust' 'rjags' * 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 'pbdDEMO' 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... 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 ... 'pbdDEMO-guide.Rnw' ... OK NONE * checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : Running 'texi2dvi' on 'pbdDEMO-guide.tex' failed. LaTeX errors: ! LaTeX Error: File `algpseudocode.sty' not found. Type X to quit or to proceed, or enter new name. (Default extension: sty) ! Emergency stop. l.148 ^^M ! ==> Fatal error occurred, no output PDF file produced! Calls: buildVignettes -> texi2pdf -> texi2dvi Execution halted * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 1 NOTE BUILDSTDERR: See BUILDSTDERR: '/builddir/build/BUILD/pbdDEMO/pbdDEMO.Rcheck/00check.log' BUILDSTDERR: for details. + exit 0 Processing files: R-pbdDEMO-0.3.2-3.el7.x86_64 Provides: R-pbdDEMO = 0.3.2-3.el7 R-pbdDEMO(x86-64) = 0.3.2-3.el7 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libR.so()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.2.5)(64bit) rtld(GNU_HASH) Obsoletes: R-pbdDEMO < 0.3.2 Processing files: R-pbdDEMO-debuginfo-0.3.2-3.el7.x86_64 Provides: R-pbdDEMO-debuginfo = 0.3.2-3.el7 R-pbdDEMO-debuginfo(x86-64) = 0.3.2-3.el7 Requires(rpmlib): rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(CompressedFileNames) <= 3.0.4-1 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-pbdDEMO-0.3.2-3.el7.x86_64 Wrote: /builddir/build/RPMS/R-pbdDEMO-0.3.2-3.el7.x86_64.rpm Wrote: /builddir/build/RPMS/R-pbdDEMO-debuginfo-0.3.2-3.el7.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.UgBUuS + umask 022 + cd /builddir/build/BUILD + cd pbdDEMO + /usr/bin/rm -rf /builddir/build/BUILDROOT/R-pbdDEMO-0.3.2-3.el7.x86_64 + exit 0 Child return code was: 0