Mock Version: 2.12 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/R-pbdBASE.spec'], chrootPath='/var/lib/mock/epel-8-x86_64-1629815811.520923/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=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.2s99ph8n:/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.2s99ph8n:/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', '8132662ec8fa41469fb0a984756418da', '-D', '/var/lib/mock/epel-8-x86_64-1629815811.520923/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.2s99ph8n:/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-pbdBASE.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-pbdBASE-0.5.3-2.el8.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/R-pbdBASE.spec'], chrootPath='/var/lib/mock/epel-8-x86_64-1629815811.520923/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=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.2s99ph8n:/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.2s99ph8n:/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', 'aed443d5f49f490a8dbcee9a5ead9119', '-D', '/var/lib/mock/epel-8-x86_64-1629815811.520923/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.2s99ph8n:/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-pbdBASE.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.kFWdVu + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf pbdBASE + /usr/bin/mkdir -p pbdBASE + cd pbdBASE + /usr/bin/gzip -dc /builddir/build/SOURCES/pbdBASE_0.5-3.tar.gz + /usr/bin/tar -xof - + 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 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=latex) restricted \write18 enabled. kpathsea: Running mktexfmt latex.fmt mktexfmt: mktexfmt is using the following fmtutil.cnf files (in precedence order): mktexfmt: /usr/share/texlive/texmf-dist/web2c/fmtutil.cnf mktexfmt: mktexfmt is using the following fmtutil.cnf file for writing changes: mktexfmt: /builddir/.texlive2018/texmf-config/web2c/fmtutil.cnf mktexfmt [WARNING]: double mention of mf/mf-nowin in /usr/share/texlive/texmf-dist/web2c/fmtutil.cnf mktexfmt [WARNING]: double mention of tex/tex in /usr/share/texlive/texmf-dist/web2c/fmtutil.cnf mktexfmt [INFO]: writing formats under /builddir/.texlive2018/texmf-var/web2c mktexfmt [INFO]: --- remaking latex with pdftex mktexfmt: running `pdftex -ini -jobname=latex -progname=latex -translate-file=cp227.tcx *latex.ini' ... This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (INITEX) restricted \write18 enabled. (/usr/share/texlive/texmf-dist/web2c/cp227.tcx) entering extended mode (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/latex.ini (/usr/share/texlive/texmf-dist/tex/generic/tex-ini-files/pdftexconfig.tex) (/usr/share/texlive/texmf-dist/tex/latex/base/latex.ltx (/usr/share/texlive/texmf-dist/tex/latex/base/texsys.cfg) ./texsys.aux found \@currdir set to: ./. Assuming \openin and \input have the same search path. Defining UNIX/DOS style filename parser. catcodes, registers, parameters, LaTeX2e <2017-04-15> hacks, control, par, spacing, files, font encodings, lengths, ==================================== Local config file fonttext.cfg used ==================================== (/usr/share/texlive/texmf-dist/tex/latex/base/fonttext.cfg (/usr/share/texlive/texmf-dist/tex/latex/base/fonttext.ltx === Don't modify this file, use a .cfg file instead === (/usr/share/texlive/texmf-dist/tex/latex/base/omlenc.def) (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.def) (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1cmss.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1cmtt.fd))) ==================================== Local config file fontmath.cfg used ==================================== (/usr/share/texlive/texmf-dist/tex/latex/base/fontmath.cfg (/usr/share/texlive/texmf-dist/tex/latex/base/fontmath.ltx === Don't modify this file, use a .cfg file instead === (/usr/share/texlive/texmf-dist/tex/latex/base/omlcmm.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/omscmsy.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/omxcmex.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ucmr.fd))) ==================================== Local config file preload.cfg used ===================================== (/usr/share/texlive/texmf-dist/tex/latex/base/preload.cfg (/usr/share/texlive/texmf-dist/tex/latex/base/preload.ltx)) page nos., x-ref, environments, center, verbatim, math definitions, boxes, title, sectioning, contents, floats, footnotes, index, bibliography, output, =========================================== Local configuration file hyphen.cfg used =========================================== (/usr/share/texlive/texmf-dist/tex/generic/babel/hyphen.cfg (/usr/share/texlive/texmf-dist/tex/generic/babel/switch.def) (/usr/share/texlive/texmf-dist/tex/generic/hyphen/hyphen.tex) (/usr/share/texlive/texmf-dist/tex/generic/hyphen/dumyhyph.tex) (/usr/share/texlive/texmf-dist/tex/generic/hyphen/zerohyph.tex)) ) ) Beginning to dump on file latex.fmt (preloaded format=latex 2021.8.24) 5082 strings of total length 69275 44963 memory locations dumped; current usage is 144&44367 3423 multiletter control sequences \font\nullfont=nullfont \font\OMX/cmex/m/n/10=cmex10 \font\tenln=line10 \font\tenlnw=linew10 \font\tencirc=lcircle10 \font\tencircw=lcirclew10 \font\OT1/cmr/m/n/5=cmr5 \font\OT1/cmr/m/n/7=cmr7 \font\OT1/cmr/m/n/10=cmr10 \font\OML/cmm/m/it/5=cmmi5 \font\OML/cmm/m/it/7=cmmi7 \font\OML/cmm/m/it/10=cmmi10 \font\OMS/cmsy/m/n/5=cmsy5 \font\OMS/cmsy/m/n/7=cmsy7 \font\OMS/cmsy/m/n/10=cmsy10 3633 words of font info for 14 preloaded fonts 14 hyphenation exceptions Hyphenation trie of length 6081 has 183 ops out of 35111 2 for language 1 181 for language 0 0 words of pdfTeX memory 0 indirect objects No pages of output. Transcript written on latex.log. mktexfmt [INFO]: /builddir/.texlive2018/texmf-var/web2c/pdftex/latex.fmt installed. mktexfmt [INFO]: Disabled formats: 32 mktexfmt [INFO]: Successfully rebuilt formats: 1 mktexfmt [INFO]: Not selected formats: 15 mktexfmt [INFO]: Total formats: 48 mktexfmt [INFO]: exiting with status 0 entering extended mode (./tocbibind.ins LaTeX2e <2017-04-15> Babel <3.17> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/docstrip.tex Utility: `docstrip' 2.5e <2014/09/29> English documentation <2017/03/13> ********************************************************** * 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.l9Tu2u + umask 022 + cd /builddir/build/BUILD + cd pbdBASE + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.v9vozx + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/R-pbdBASE-0.5.3-2.el8.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/R-pbdBASE-0.5.3-2.el8.x86_64 ++ dirname /builddir/build/BUILDROOT/R-pbdBASE-0.5.3-2.el8.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/R-pbdBASE-0.5.3-2.el8.x86_64 + cd pbdBASE + mkdir -p /builddir/build/BUILDROOT/R-pbdBASE-0.5.3-2.el8.x86_64/usr/lib64/R/library + . /etc/profile.d/modules.sh ++ . /etc/profile.d/00-modulepath.sh +++ '[' -z /etc/modulefiles:/usr/share/modulefiles:/usr/share/modulefiles/Linux:/usr/share/modulefiles/Core:/usr/share/lmod/lmod/modulefiles/Core ']' +++ : ++ '[' -z '' ']' ++ '[' -z /usr/share/modulefiles ']' ++ PS_CMD=/usr/bin/ps ++ '[' '!' -x /usr/bin/ps ']' ++ EXPR_CMD=/usr/bin/expr ++ '[' '!' -x /usr/bin/expr ']' ++ BASENAME_CMD=/usr/bin/basename ++ '[' '!' -x /usr/bin/basename ']' +++ /usr/bin/ps -p 78 -ocomm= ++ my_shell=sh +++ /usr/bin/expr sh : '-*\(.*\)' ++ my_shell=sh +++ /usr/bin/basename sh ++ my_shell=sh ++ '[' -f /usr/share/lmod/lmod/init/sh ']' ++ . /usr/share/lmod/lmod/init/sh +++ LMOD_ROOT=/usr/share/lmod +++ LMOD_PKG=/usr/share/lmod/lmod +++ LMOD_DIR=/usr/share/lmod/lmod/libexec/ +++ LMOD_CMD=/usr/share/lmod/lmod/libexec/lmod +++ MODULESHOME=/usr/share/lmod/lmod +++ export LMOD_CMD +++ export LMOD_PKG +++ export LMOD_DIR +++ export MODULESHOME +++ export LMOD_DIR ++ unset my_shell PS_CMD EXPR_CMD BASENAME_CMD MODULEPATH_INIT + module load mpi/openmpi-x86_64 ++ /usr/share/lmod/lmod/libexec/lmod sh load mpi/openmpi-x86_64 + eval '__LMOD_REF_COUNT_LD_LIBRARY_PATH=/usr/lib64/openmpi/lib:1;' export '__LMOD_REF_COUNT_LD_LIBRARY_PATH;' 'LD_LIBRARY_PATH=/usr/lib64/openmpi/lib;' export 'LD_LIBRARY_PATH;' '__LMOD_REF_COUNT_LOADEDMODULES=mpi/openmpi-x86_64:1;' export '__LMOD_REF_COUNT_LOADEDMODULES;' 'LOADEDMODULES=mpi/openmpi-x86_64;' export 'LOADEDMODULES;' '__LMOD_REF_COUNT_MANPATH=/usr/share/man/openmpi-x86_64:1\;/usr/share/lmod/lmod/share/man:1;' export '__LMOD_REF_COUNT_MANPATH;' 'MANPATH=:/usr/share/man/openmpi-x86_64:/usr/share/lmod/lmod/share/man;' export 'MANPATH;' '__LMOD_REF_COUNT_MODULEPATH=/etc/modulefiles:1\;/usr/share/modulefiles:1\;/usr/share/modulefiles/Linux:1\;/usr/share/modulefiles/Core:1\;/usr/share/lmod/lmod/modulefiles/Core:1;' export '__LMOD_REF_COUNT_MODULEPATH;' 'MODULEPATH=/etc/modulefiles:/usr/share/modulefiles:/usr/share/modulefiles/Linux:/usr/share/modulefiles/Core:/usr/share/lmod/lmod/modulefiles/Core;' export 'MODULEPATH;' 'MPI_BIN=/usr/lib64/openmpi/bin;' export 'MPI_BIN;' 'MPI_COMPILER=openmpi-x86_64;' export 'MPI_COMPILER;' 'MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi;' export 'MPI_FORTRAN_MOD_DIR;' 'MPI_HOME=/usr/lib64/openmpi;' export 'MPI_HOME;' 'MPI_INCLUDE=/usr/include/openmpi-x86_64;' export 'MPI_INCLUDE;' 'MPI_LIB=/usr/lib64/openmpi/lib;' export 'MPI_LIB;' 'MPI_MAN=/usr/share/man/openmpi-x86_64;' export 'MPI_MAN;' 'MPI_PYTHON2_SITEARCH=/usr/lib64/python3.6/site-packages/openmpi;' export 'MPI_PYTHON2_SITEARCH;' 'MPI_PYTHON3_SITEARCH=/usr/lib64/python3.6/site-packages/openmpi;' export 'MPI_PYTHON3_SITEARCH;' 'MPI_PYTHON_SITEARCH=/usr/lib64/python3.6/site-packages/openmpi;' export 'MPI_PYTHON_SITEARCH;' 'MPI_SUFFIX=_openmpi;' export 'MPI_SUFFIX;' 'MPI_SYSCONFIG=/etc/openmpi-x86_64;' export 'MPI_SYSCONFIG;' '__LMOD_REF_COUNT_PATH=/usr/lib64/openmpi/bin:1\;/builddir/.local/bin:1\;/builddir/bin:1\;/usr/bin:1\;/bin:1\;/usr/sbin:1\;/sbin:1\;/usr/local/sbin:1;' export '__LMOD_REF_COUNT_PATH;' 'PATH=/usr/lib64/openmpi/bin:/builddir/.local/bin:/builddir/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin;' export 'PATH;' '__LMOD_REF_COUNT_PKG_CONFIG_PATH=/usr/lib64/openmpi/lib/pkgconfig:1\;/usr/lib64/pkgconfig:1\;/usr/share/pkgconfig:1;' export '__LMOD_REF_COUNT_PKG_CONFIG_PATH;' 'PKG_CONFIG_PATH=/usr/lib64/openmpi/lib/pkgconfig::/usr/lib64/pkgconfig:/usr/share/pkgconfig;' export 'PKG_CONFIG_PATH;' '__LMOD_REF_COUNT__LMFILES_=/etc/modulefiles/mpi/openmpi-x86_64:1;' export '__LMOD_REF_COUNT__LMFILES_;' '_LMFILES_=/etc/modulefiles/mpi/openmpi-x86_64;' export '_LMFILES_;' '_ModuleTable001_=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;' export '_ModuleTable001_;' '_ModuleTable002_=bGVmaWxlcy9Db3JlIiwiL3Vzci9zaGFyZS9sbW9kL2xtb2QvbW9kdWxlZmlsZXMvQ29yZSIsfSxbInN5c3RlbUJhc2VNUEFUSCJdPSIvZXRjL21vZHVsZWZpbGVzOi91c3Ivc2hhcmUvbW9kdWxlZmlsZXM6L3Vzci9zaGFyZS9tb2R1bGVmaWxlcy9MaW51eDovdXNyL3NoYXJlL21vZHVsZWZpbGVzL0NvcmU6L3Vzci9zaGFyZS9sbW9kL2xtb2QvbW9kdWxlZmlsZXMvQ29yZSIsfQ==;' export '_ModuleTable002_;' '_ModuleTable_Sz_=2;' export '_ModuleTable_Sz_;' ++ __LMOD_REF_COUNT_LD_LIBRARY_PATH=/usr/lib64/openmpi/lib:1 ++ export __LMOD_REF_COUNT_LD_LIBRARY_PATH ++ LD_LIBRARY_PATH=/usr/lib64/openmpi/lib ++ export LD_LIBRARY_PATH ++ __LMOD_REF_COUNT_LOADEDMODULES=mpi/openmpi-x86_64:1 ++ export __LMOD_REF_COUNT_LOADEDMODULES ++ LOADEDMODULES=mpi/openmpi-x86_64 ++ export LOADEDMODULES ++ __LMOD_REF_COUNT_MANPATH='/usr/share/man/openmpi-x86_64:1;/usr/share/lmod/lmod/share/man:1' ++ export __LMOD_REF_COUNT_MANPATH ++ MANPATH=:/usr/share/man/openmpi-x86_64:/usr/share/lmod/lmod/share/man ++ export MANPATH ++ __LMOD_REF_COUNT_MODULEPATH='/etc/modulefiles:1;/usr/share/modulefiles:1;/usr/share/modulefiles/Linux:1;/usr/share/modulefiles/Core:1;/usr/share/lmod/lmod/modulefiles/Core:1' ++ export __LMOD_REF_COUNT_MODULEPATH ++ MODULEPATH=/etc/modulefiles:/usr/share/modulefiles:/usr/share/modulefiles/Linux:/usr/share/modulefiles/Core:/usr/share/lmod/lmod/modulefiles/Core ++ export MODULEPATH ++ MPI_BIN=/usr/lib64/openmpi/bin ++ export MPI_BIN ++ MPI_COMPILER=openmpi-x86_64 ++ export MPI_COMPILER ++ MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi ++ export MPI_FORTRAN_MOD_DIR ++ MPI_HOME=/usr/lib64/openmpi ++ export MPI_HOME ++ MPI_INCLUDE=/usr/include/openmpi-x86_64 ++ export MPI_INCLUDE ++ MPI_LIB=/usr/lib64/openmpi/lib ++ export MPI_LIB ++ MPI_MAN=/usr/share/man/openmpi-x86_64 ++ export MPI_MAN ++ MPI_PYTHON2_SITEARCH=/usr/lib64/python3.6/site-packages/openmpi ++ export MPI_PYTHON2_SITEARCH ++ MPI_PYTHON3_SITEARCH=/usr/lib64/python3.6/site-packages/openmpi ++ export MPI_PYTHON3_SITEARCH ++ MPI_PYTHON_SITEARCH=/usr/lib64/python3.6/site-packages/openmpi ++ export MPI_PYTHON_SITEARCH ++ MPI_SUFFIX=_openmpi ++ export MPI_SUFFIX ++ MPI_SYSCONFIG=/etc/openmpi-x86_64 ++ export MPI_SYSCONFIG ++ __LMOD_REF_COUNT_PATH='/usr/lib64/openmpi/bin:1;/builddir/.local/bin:1;/builddir/bin:1;/usr/bin:1;/bin:1;/usr/sbin:1;/sbin:1;/usr/local/sbin:1' ++ export __LMOD_REF_COUNT_PATH ++ PATH=/usr/lib64/openmpi/bin:/builddir/.local/bin:/builddir/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin ++ export PATH ++ __LMOD_REF_COUNT_PKG_CONFIG_PATH='/usr/lib64/openmpi/lib/pkgconfig:1;/usr/lib64/pkgconfig:1;/usr/share/pkgconfig:1' ++ export __LMOD_REF_COUNT_PKG_CONFIG_PATH ++ PKG_CONFIG_PATH=/usr/lib64/openmpi/lib/pkgconfig::/usr/lib64/pkgconfig:/usr/share/pkgconfig ++ export PKG_CONFIG_PATH ++ __LMOD_REF_COUNT__LMFILES_=/etc/modulefiles/mpi/openmpi-x86_64:1 ++ export __LMOD_REF_COUNT__LMFILES_ ++ _LMFILES_=/etc/modulefiles/mpi/openmpi-x86_64 ++ export _LMFILES_ ++ _ModuleTable001_=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 ++ export _ModuleTable001_ ++ _ModuleTable002_=bGVmaWxlcy9Db3JlIiwiL3Vzci9zaGFyZS9sbW9kL2xtb2QvbW9kdWxlZmlsZXMvQ29yZSIsfSxbInN5c3RlbUJhc2VNUEFUSCJdPSIvZXRjL21vZHVsZWZpbGVzOi91c3Ivc2hhcmUvbW9kdWxlZmlsZXM6L3Vzci9zaGFyZS9tb2R1bGVmaWxlcy9MaW51eDovdXNyL3NoYXJlL21vZHVsZWZpbGVzL0NvcmU6L3Vzci9zaGFyZS9sbW9kL2xtb2QvbW9kdWxlZmlsZXMvQ29yZSIsfQ== ++ export _ModuleTable002_ ++ _ModuleTable_Sz_=2 ++ export _ModuleTable_Sz_ + OMPI_MCA_rmaps_base_oversubscribe=1 + OMPI_MCA_orte_rsh_agent=/bin/false ++ pwd + TEXINPUTS=.:/builddir/build/BUILD/pbdBASE/tocbibind: + R CMD INSTALL -l /builddir/build/BUILDROOT/R-pbdBASE-0.5.3-2.el8.x86_64/usr/lib64/R/library pbdBASE * installing *source* package 'pbdBASE' ... ** package 'pbdBASE' successfully unpacked and MD5 sums checked ** 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 Error in tools::file_path_as_absolute(system.file(lib.file, package = package)) : file '' does not exist Calls: get.lib -> Execution halted ****************** Results of pbdBASE package configure ***************** >> EXT_LDFLAGS = -lscalapack -lmpiblacs -lopenblas >> EXPORT_BLACS = export_blacs/pkg_tools.o >> R_SLAP = >> SLAP_LDFLAGS = -lscalapack -lmpiblacs -lopenblas >> SPMD_CPPFLAGS = -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI >> SPMD_LDFLAGS = -L/usr/lib64/openmpi/lib -lmpi -lutil -lpthread ************************************************************************* configure: creating ./config.status config.status: creating src/Makevars ** libs echo "SLAP_LDFLAGS = -lscalapack -lmpiblacs -lopenblas" >> Makeconf echo "SPMD_CPPFLAGS = -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI" >> Makeconf echo "SPMD_LDFLAGS = -L/usr/lib64/openmpi/lib -lmpi -lutil -lpthread" >> Makeconf echo "GFORTRAN_FLAGS = -DUSE_FC_LEN_T" >> Makeconf echo "PKG_CPPFLAGS = -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T" >> Makeconf echo "PKG_CFLAGS = " >> Makeconf echo "PKG_FFLAGS = " >> Makeconf echo "PKG_LIBS = -lscalapack -lmpiblacs -lopenblas -lgfortran -lm -lquadmath -L/usr/lib64/openmpi/lib -lmpi -lutil -lpthread" >> Makeconf gfortran -m64 -fno-optimize-sibling-calls -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules -c base/bprnt.f -o base/bprnt.o f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran base/bprnt.f:13:39: $ CMATNM, NOUT, WORK ) 1 Warning: Unused dummy argument 'nout' at (1) [-Wunused-dummy-argument] gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c base/bprnt_c.c -o base/bprnt_c.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c base/expm/pade_coefs.c -o base/expm/pade_coefs.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c base/expm/matexp.c -o base/expm/matexp.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c base/expm/p_matexp.c -o base/expm/p_matexp.o gfortran -m64 -fno-optimize-sibling-calls -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c base/linalg/norms.f90 -o base/linalg/norms.o f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran gfortran -m64 -fno-optimize-sibling-calls -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c base/linalg/pcrossprod.f90 -o base/linalg/pcrossprod.o f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran gfortran -m64 -fno-optimize-sibling-calls -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c base/linalg/pinverse.f90 -o base/linalg/pinverse.o f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran gfortran -m64 -fno-optimize-sibling-calls -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c base/linalg/prblas.f90 -o base/linalg/prblas.o f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran gfortran -m64 -fno-optimize-sibling-calls -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules -c base/linalg/plm.f -o base/linalg/plm.o f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran base/linalg/plm.f:447:0: IPW = IPN + NQ0 + NQ Warning: 'nq0' may be used uninitialized in this function [-Wmaybe-uninitialized] base/linalg/plm.f:401:0: $ NQ = NQ - ICOFF Warning: 'nq' may be used uninitialized in this function [-Wmaybe-uninitialized] base/linalg/plm.f:708:0: WORK( 1 ) = DBLE( LWMIN ) Warning: 'lwmin' may be used uninitialized in this function [-Wmaybe-uninitialized] base/linalg/plm.f:387:0: ELSE IF( LQUERY ) THEN Warning: 'lquery' may be used uninitialized in this function [-Wmaybe-uninitialized] base/linalg/plm.f:399:0: $ MP = MP - IROFF Warning: 'iroff' may be used uninitialized in this function [-Wmaybe-uninitialized] base/linalg/plm.f:401:0: $ NQ = NQ - ICOFF Warning: 'icoff' may be used uninitialized in this function [-Wmaybe-uninitialized] base/linalg/plm.f:264:0: WORK( 1 ) = DBLE( LWMIN ) Warning: 'lwmin' may be used uninitialized in this function [-Wmaybe-uninitialized] base/linalg/plm.f:180:0: ELSE IF( LQUERY ) THEN Warning: 'lquery' may be used uninitialized in this function [-Wmaybe-uninitialized] base/linalg/plm.f:954:0: IF( TPSD ) Warning: 'tpsd' may be used uninitialized in this function [-Wmaybe-uninitialized] base/linalg/plm.f:1052:0: WORK( 1 ) = DBLE( LWMIN ) Warning: 'lwmin' may be used uninitialized in this function [-Wmaybe-uninitialized] base/linalg/plm.f:987:0: $ TAU, WORK( IPW ), LWORK-LTAU, RANK, INFO) Warning: 'ltau' may be used uninitialized in this function [-Wmaybe-uninitialized] base/linalg/plm.f:907:0: ELSE IF( LQUERY ) THEN Warning: 'lquery' may be used uninitialized in this function [-Wmaybe-uninitialized] gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c coords.c -o coords.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c comm_utils.c -o comm_utils.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c export_blacs/pkg_tools.c -o export_blacs/pkg_tools.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c base_mpi_blacs.c -o base_mpi_blacs.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c base_mpi_blacs_reductions.c -o base_mpi_blacs_reductions.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c base_pblas_level3.c -o base_pblas_level3.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c base_plinalg.c -o base_plinalg.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c base_prblas.c -o base_prblas.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c base_putil.c -o base_putil.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c base_scalapack.c -o base_scalapack.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c base_variance.c -o base_variance.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c dims.c -o dims.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c lm.c -o lm.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c matexp.c -o matexp.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c pbdBASE_native.c -o pbdBASE_native.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qr.c -o qr.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c redist.c -o redist.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c svd.c -o svd.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c utility.c -o utility.o gfortran -m64 -fno-optimize-sibling-calls -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c base/stats/variance.f90 -o base/stats/variance.o f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran gfortran -m64 -fno-optimize-sibling-calls -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c utils/fpmod.f90 -o utils/fpmod.o f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran utils/fpmod.f90:10:0: ret = nan !ieee_value(1.0d0, ieee_quiet_nan) Warning: 'nan' may be used uninitialized in this function [-Wmaybe-uninitialized] gfortran -m64 -fno-optimize-sibling-calls -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c utils/swaps.f90 -o utils/swaps.o f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran gfortran -m64 -fno-optimize-sibling-calls -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c utils/quicksort_utils.f90 -o utils/quicksort_utils.o f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran gfortran -m64 -fno-optimize-sibling-calls -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c utils/signs.f90 -o utils/signs.o f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran gfortran -m64 -fno-optimize-sibling-calls -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c utils/sorts.f90 -o utils/sorts.o f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran gfortran -m64 -fno-optimize-sibling-calls -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c utils/strings.f90 -o utils/strings.o f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran gfortran -m64 -fno-optimize-sibling-calls -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c base/utils/blacs_util.f90 -o base/utils/blacs_util.o f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran gfortran -m64 -fno-optimize-sibling-calls -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules -c base/utils/dmat_redist.f -o base/utils/dmat_redist.o f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran gfortran -m64 -fno-optimize-sibling-calls -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c base/utils/indices.f90 -o base/utils/indices.o f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran gfortran -m64 -fno-optimize-sibling-calls -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules -c base/utils/putil.f -o base/utils/putil.o f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran base/utils/putil.f:307:30: SUBROUTINE PDGDGTK(X, IX, JX, DESCX, DIAG, RDEST, CDEST) 1 Warning: Unused dummy argument 'ix' at (1) [-Wunused-dummy-argument] base/utils/putil.f:307:34: SUBROUTINE PDGDGTK(X, IX, JX, DESCX, DIAG, RDEST, CDEST) 1 Warning: Unused dummy argument 'jx' at (1) [-Wunused-dummy-argument] base/utils/putil.f:357:31: SUBROUTINE PDDIAGMK(X, IX, JX, DESCX, DIAG, LDIAG) 1 Warning: Unused dummy argument 'ix' at (1) [-Wunused-dummy-argument] base/utils/putil.f:357:35: SUBROUTINE PDDIAGMK(X, IX, JX, DESCX, DIAG, LDIAG) 1 Warning: Unused dummy argument 'jx' at (1) [-Wunused-dummy-argument] gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c base/utils/redist.c -o base/utils/redist.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c base/utils/scale.c -o base/utils/scale.o gfortran -m64 -fno-optimize-sibling-calls -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c base/utils/special.f90 -o base/utils/special.o f951: Warning: '-Werror=' argument '-Werror=format-security' is not valid for Fortran gcc -m64 -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o pbdBASE.so base/bprnt.o base/bprnt_c.o base/expm/pade_coefs.o base/expm/matexp.o base/expm/p_matexp.o base/linalg/norms.o base/linalg/pcrossprod.o base/linalg/pinverse.o base/linalg/prblas.o base/linalg/plm.o coords.o comm_utils.o export_blacs/pkg_tools.o base_mpi_blacs.o base_mpi_blacs_reductions.o base_pblas_level3.o base_plinalg.o base_prblas.o base_putil.o base_scalapack.o base_variance.o dims.o lm.o matexp.o pbdBASE_native.o qr.o redist.o svd.o utility.o base/stats/variance.o utils/fpmod.o utils/quicksort_utils.o utils/signs.o utils/sorts.o utils/strings.o utils/swaps.o base/utils/blacs_util.o base/utils/dmat_redist.o base/utils/indices.o base/utils/putil.o base/utils/redist.o base/utils/scale.o base/utils/special.o -lscalapack -lmpiblacs -lopenblas -lgfortran -lm -lquadmath -L/usr/lib64/openmpi/lib -lmpi -lutil -lpthread -L/usr/lib64/R/lib -lR installing via 'install.libs.R' to /builddir/build/BUILDROOT/R-pbdBASE-0.5.3-2.el8.x86_64/usr/lib64/R/library/00LOCK-pbdBASE/00new/pbdBASE ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'pbdBASE' finding HTML links ... done BASE-Global-Environment html base.blacs_gridinit html base.crossprod html base.descinit html base.det html base.dhilbmk html base.dim0 html base.free_blacs_system_handle html base.indxg2p html base.matexp html base.maxdim html base.minctxt html base.nbd html base.numroc html base.ownany html base.p_matexp_pade_wrap html base.p_matpow_by_squaring_wrap html base.pdchtri html base.pdclvar html base.pdhilbmk html base.pdmkcpn1 html base.pdmvsum html base.pdsweep html base.procgrid html base.rcolcpy html base.rcolcpy2 html base.redist html base.rl2blas html base.rl2insert html base.rpdgecon html base.rpdgelqf html base.rpdgels html base.rpdgemm html base.rpdgemr2d html base.rpdgeqpf html base.rpdgesv html base.rpdgesvd html base.rpdgetrf html base.rpdgetri html base.rpdlange html base.rpdlaprnt html base.rpdorglq html base.rpdorgqr html base.rpdormqr html base.rpdpotrf html base.rpdsyevr html base.rpdsyevx html base.rpdtran html base.rpdtrcon html base.rrowcpy html base.rrowcpy2 html base.tri2zero html base.valid_context html blacs-max html blacs-min html blacs-p2p html blacs-sums html blacs_apts html blacsexit html coords html coordspair html diag html finalizer html g2l_coord html g2lcoord html get.comm.from.ICTXT html gridexit html gridinfo html gridinit html init.grid html l2g_coord html lclgblmat html numroc2 html pbdBASE-package html pcoords html sys2blacs.handle html ** building package indices ** installing vignettes 'pbdBASE-guide.Rnw' ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (pbdBASE) + test -d pbdBASE/src + cd pbdBASE/src + rm -f base_mpi_blacs.o base_mpi_blacs_reductions.o base_pblas_level3.o base_plinalg.o base_prblas.o base_putil.o base_scalapack.o base_variance.o comm_utils.o coords.o dims.o lm.o matexp.o pbdBASE_native.o qr.o redist.o svd.o utility.o pbdBASE.so + rm -f /builddir/build/BUILDROOT/R-pbdBASE-0.5.3-2.el8.x86_64/usr/lib64/R/library/R.css + /usr/lib/rpm/find-debuginfo.sh -j2 --strict-build-id -m -i --build-id-seed 0.5.3-2.el8 --unique-debug-suffix -0.5.3-2.el8.x86_64 --unique-debug-src-base R-pbdBASE-0.5.3-2.el8.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/pbdBASE extracting debug info from /builddir/build/BUILDROOT/R-pbdBASE-0.5.3-2.el8.x86_64/usr/lib64/R/library/pbdBASE/libs/pbdBASE.so /usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. cpio: pbdBASE/src/include/insertionsort_generic.inc: Cannot stat: No such file or directory cpio: pbdBASE/src/include/quicksort_median_of_3_generic.inc: Cannot stat: No such file or directory cpio: pbdBASE/src/include/quicksort_partition_generic.inc: Cannot stat: No such file or directory cpio: pbdBASE/src/include/quicksort_r_generic.inc: Cannot stat: No such file or directory cpio: pbdBASE/src/include/swap_generic.inc: Cannot stat: No such file or directory 486 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig /sbin/ldconfig: Warning: ignoring configuration file that cannot be opened: /etc/ld.so.conf: No such file or directory + /usr/lib/rpm/brp-compress + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/brp-python-bytecompile '' 1 + /usr/lib/rpm/brp-python-hardlink + PYTHON3=/usr/libexec/platform-python + /usr/lib/rpm/redhat/brp-mangle-shebangs Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.eIED5w + umask 022 + cd /builddir/build/BUILD + cd pbdBASE + . /etc/profile.d/modules.sh ++ . /etc/profile.d/00-modulepath.sh +++ '[' -z /etc/modulefiles:/usr/share/modulefiles:/usr/share/modulefiles/Linux:/usr/share/modulefiles/Core:/usr/share/lmod/lmod/modulefiles/Core ']' +++ : ++ '[' -z '' ']' ++ '[' -z /usr/share/modulefiles ']' ++ PS_CMD=/usr/bin/ps ++ '[' '!' -x /usr/bin/ps ']' ++ EXPR_CMD=/usr/bin/expr ++ '[' '!' -x /usr/bin/expr ']' ++ BASENAME_CMD=/usr/bin/basename ++ '[' '!' -x /usr/bin/basename ']' +++ /usr/bin/ps -p 869 -ocomm= ++ my_shell=sh +++ /usr/bin/expr sh : '-*\(.*\)' ++ my_shell=sh +++ /usr/bin/basename sh ++ my_shell=sh ++ '[' -f /usr/share/lmod/lmod/init/sh ']' ++ . /usr/share/lmod/lmod/init/sh +++ LMOD_ROOT=/usr/share/lmod +++ LMOD_PKG=/usr/share/lmod/lmod +++ LMOD_DIR=/usr/share/lmod/lmod/libexec/ +++ LMOD_CMD=/usr/share/lmod/lmod/libexec/lmod +++ MODULESHOME=/usr/share/lmod/lmod +++ export LMOD_CMD +++ export LMOD_PKG +++ export LMOD_DIR +++ export MODULESHOME +++ export LMOD_DIR ++ unset my_shell PS_CMD EXPR_CMD BASENAME_CMD MODULEPATH_INIT + module load mpi/openmpi-x86_64 ++ /usr/share/lmod/lmod/libexec/lmod sh load mpi/openmpi-x86_64 + eval '__LMOD_REF_COUNT_LD_LIBRARY_PATH=/usr/lib64/openmpi/lib:1;' export '__LMOD_REF_COUNT_LD_LIBRARY_PATH;' 'LD_LIBRARY_PATH=/usr/lib64/openmpi/lib;' export 'LD_LIBRARY_PATH;' '__LMOD_REF_COUNT_LOADEDMODULES=mpi/openmpi-x86_64:1;' export '__LMOD_REF_COUNT_LOADEDMODULES;' 'LOADEDMODULES=mpi/openmpi-x86_64;' export 'LOADEDMODULES;' '__LMOD_REF_COUNT_MANPATH=/usr/share/man/openmpi-x86_64:1\;/usr/share/lmod/lmod/share/man:1;' export '__LMOD_REF_COUNT_MANPATH;' 'MANPATH=:/usr/share/man/openmpi-x86_64:/usr/share/lmod/lmod/share/man;' export 'MANPATH;' '__LMOD_REF_COUNT_MODULEPATH=/etc/modulefiles:1\;/usr/share/modulefiles:1\;/usr/share/modulefiles/Linux:1\;/usr/share/modulefiles/Core:1\;/usr/share/lmod/lmod/modulefiles/Core:1;' export '__LMOD_REF_COUNT_MODULEPATH;' 'MODULEPATH=/etc/modulefiles:/usr/share/modulefiles:/usr/share/modulefiles/Linux:/usr/share/modulefiles/Core:/usr/share/lmod/lmod/modulefiles/Core;' export 'MODULEPATH;' 'MPI_BIN=/usr/lib64/openmpi/bin;' export 'MPI_BIN;' 'MPI_COMPILER=openmpi-x86_64;' export 'MPI_COMPILER;' 'MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi;' export 'MPI_FORTRAN_MOD_DIR;' 'MPI_HOME=/usr/lib64/openmpi;' export 'MPI_HOME;' 'MPI_INCLUDE=/usr/include/openmpi-x86_64;' export 'MPI_INCLUDE;' 'MPI_LIB=/usr/lib64/openmpi/lib;' export 'MPI_LIB;' 'MPI_MAN=/usr/share/man/openmpi-x86_64;' export 'MPI_MAN;' 'MPI_PYTHON2_SITEARCH=/usr/lib64/python3.6/site-packages/openmpi;' export 'MPI_PYTHON2_SITEARCH;' 'MPI_PYTHON3_SITEARCH=/usr/lib64/python3.6/site-packages/openmpi;' export 'MPI_PYTHON3_SITEARCH;' 'MPI_PYTHON_SITEARCH=/usr/lib64/python3.6/site-packages/openmpi;' export 'MPI_PYTHON_SITEARCH;' 'MPI_SUFFIX=_openmpi;' export 'MPI_SUFFIX;' 'MPI_SYSCONFIG=/etc/openmpi-x86_64;' export 'MPI_SYSCONFIG;' '__LMOD_REF_COUNT_PATH=/usr/lib64/openmpi/bin:1\;/builddir/.local/bin:1\;/builddir/bin:1\;/usr/bin:1\;/bin:1\;/usr/sbin:1\;/sbin:1\;/usr/local/sbin:1;' export '__LMOD_REF_COUNT_PATH;' 'PATH=/usr/lib64/openmpi/bin:/builddir/.local/bin:/builddir/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin;' export 'PATH;' '__LMOD_REF_COUNT_PKG_CONFIG_PATH=/usr/lib64/openmpi/lib/pkgconfig:1\;/usr/lib64/pkgconfig:1\;/usr/share/pkgconfig:1;' export '__LMOD_REF_COUNT_PKG_CONFIG_PATH;' 'PKG_CONFIG_PATH=/usr/lib64/openmpi/lib/pkgconfig::/usr/lib64/pkgconfig:/usr/share/pkgconfig;' export 'PKG_CONFIG_PATH;' '__LMOD_REF_COUNT__LMFILES_=/etc/modulefiles/mpi/openmpi-x86_64:1;' export '__LMOD_REF_COUNT__LMFILES_;' '_LMFILES_=/etc/modulefiles/mpi/openmpi-x86_64;' export '_LMFILES_;' '_ModuleTable001_=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;' export '_ModuleTable001_;' '_ModuleTable002_=bGVmaWxlcy9Db3JlIiwiL3Vzci9zaGFyZS9sbW9kL2xtb2QvbW9kdWxlZmlsZXMvQ29yZSIsfSxbInN5c3RlbUJhc2VNUEFUSCJdPSIvZXRjL21vZHVsZWZpbGVzOi91c3Ivc2hhcmUvbW9kdWxlZmlsZXM6L3Vzci9zaGFyZS9tb2R1bGVmaWxlcy9MaW51eDovdXNyL3NoYXJlL21vZHVsZWZpbGVzL0NvcmU6L3Vzci9zaGFyZS9sbW9kL2xtb2QvbW9kdWxlZmlsZXMvQ29yZSIsfQ==;' export '_ModuleTable002_;' '_ModuleTable_Sz_=2;' export '_ModuleTable_Sz_;' ++ __LMOD_REF_COUNT_LD_LIBRARY_PATH=/usr/lib64/openmpi/lib:1 ++ export __LMOD_REF_COUNT_LD_LIBRARY_PATH ++ LD_LIBRARY_PATH=/usr/lib64/openmpi/lib ++ export LD_LIBRARY_PATH ++ __LMOD_REF_COUNT_LOADEDMODULES=mpi/openmpi-x86_64:1 ++ export __LMOD_REF_COUNT_LOADEDMODULES ++ LOADEDMODULES=mpi/openmpi-x86_64 ++ export LOADEDMODULES ++ __LMOD_REF_COUNT_MANPATH='/usr/share/man/openmpi-x86_64:1;/usr/share/lmod/lmod/share/man:1' ++ export __LMOD_REF_COUNT_MANPATH ++ MANPATH=:/usr/share/man/openmpi-x86_64:/usr/share/lmod/lmod/share/man ++ export MANPATH ++ __LMOD_REF_COUNT_MODULEPATH='/etc/modulefiles:1;/usr/share/modulefiles:1;/usr/share/modulefiles/Linux:1;/usr/share/modulefiles/Core:1;/usr/share/lmod/lmod/modulefiles/Core:1' ++ export __LMOD_REF_COUNT_MODULEPATH ++ MODULEPATH=/etc/modulefiles:/usr/share/modulefiles:/usr/share/modulefiles/Linux:/usr/share/modulefiles/Core:/usr/share/lmod/lmod/modulefiles/Core ++ export MODULEPATH ++ MPI_BIN=/usr/lib64/openmpi/bin ++ export MPI_BIN ++ MPI_COMPILER=openmpi-x86_64 ++ export MPI_COMPILER ++ MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi ++ export MPI_FORTRAN_MOD_DIR ++ MPI_HOME=/usr/lib64/openmpi ++ export MPI_HOME ++ MPI_INCLUDE=/usr/include/openmpi-x86_64 ++ export MPI_INCLUDE ++ MPI_LIB=/usr/lib64/openmpi/lib ++ export MPI_LIB ++ MPI_MAN=/usr/share/man/openmpi-x86_64 ++ export MPI_MAN ++ MPI_PYTHON2_SITEARCH=/usr/lib64/python3.6/site-packages/openmpi ++ export MPI_PYTHON2_SITEARCH ++ MPI_PYTHON3_SITEARCH=/usr/lib64/python3.6/site-packages/openmpi ++ export MPI_PYTHON3_SITEARCH ++ MPI_PYTHON_SITEARCH=/usr/lib64/python3.6/site-packages/openmpi ++ export MPI_PYTHON_SITEARCH ++ MPI_SUFFIX=_openmpi ++ export MPI_SUFFIX ++ MPI_SYSCONFIG=/etc/openmpi-x86_64 ++ export MPI_SYSCONFIG ++ __LMOD_REF_COUNT_PATH='/usr/lib64/openmpi/bin:1;/builddir/.local/bin:1;/builddir/bin:1;/usr/bin:1;/bin:1;/usr/sbin:1;/sbin:1;/usr/local/sbin:1' ++ export __LMOD_REF_COUNT_PATH ++ PATH=/usr/lib64/openmpi/bin:/builddir/.local/bin:/builddir/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin ++ export PATH ++ __LMOD_REF_COUNT_PKG_CONFIG_PATH='/usr/lib64/openmpi/lib/pkgconfig:1;/usr/lib64/pkgconfig:1;/usr/share/pkgconfig:1' ++ export __LMOD_REF_COUNT_PKG_CONFIG_PATH ++ PKG_CONFIG_PATH=/usr/lib64/openmpi/lib/pkgconfig::/usr/lib64/pkgconfig:/usr/share/pkgconfig ++ export PKG_CONFIG_PATH ++ __LMOD_REF_COUNT__LMFILES_=/etc/modulefiles/mpi/openmpi-x86_64:1 ++ export __LMOD_REF_COUNT__LMFILES_ ++ _LMFILES_=/etc/modulefiles/mpi/openmpi-x86_64 ++ export _LMFILES_ ++ _ModuleTable001_=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 ++ export _ModuleTable001_ ++ _ModuleTable002_=bGVmaWxlcy9Db3JlIiwiL3Vzci9zaGFyZS9sbW9kL2xtb2QvbW9kdWxlZmlsZXMvQ29yZSIsfSxbInN5c3RlbUJhc2VNUEFUSCJdPSIvZXRjL21vZHVsZWZpbGVzOi91c3Ivc2hhcmUvbW9kdWxlZmlsZXM6L3Vzci9zaGFyZS9tb2R1bGVmaWxlcy9MaW51eDovdXNyL3NoYXJlL21vZHVsZWZpbGVzL0NvcmU6L3Vzci9zaGFyZS9sbW9kL2xtb2QvbW9kdWxlZmlsZXMvQ29yZSIsfQ== ++ export _ModuleTable002_ ++ _ModuleTable_Sz_=2 ++ export _ModuleTable_Sz_ + OMPI_MCA_rmaps_base_oversubscribe=1 + OMPI_MCA_orte_rsh_agent=/bin/false ++ pwd + TEXINPUTS=.:/builddir/build/BUILD/pbdBASE/tocbibind: + R CMD check pbdBASE * using log directory '/builddir/build/BUILD/pbdBASE/pbdBASE.Rcheck' * using R version 4.1.0 (2021-05-18) * using platform: x86_64-redhat-linux-gnu (64-bit) * using session charset: ASCII * checking for file 'pbdBASE/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'pbdBASE' version '0.5-3' * 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/3.13/bioc/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.13/bioc/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.13/data/annotation/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.13/data/annotation/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.13/data/experiment/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.13/data/experiment/src/contrib/PACKAGES' OK * checking if this is a source package ... NOTE Found the following apparent object files/libraries: src/base/bprnt.o src/base/bprnt_c.o src/base/expm/matexp.o src/base/expm/p_matexp.o src/base/expm/pade_coefs.o src/base/linalg/norms.o src/base/linalg/pcrossprod.o src/base/linalg/pinverse.o src/base/linalg/plm.o src/base/linalg/prblas.o src/base/stats/variance.o src/base/utils/blacs_util.o src/base/utils/dmat_redist.o src/base/utils/indices.o src/base/utils/putil.o src/base/utils/redist.o src/base/utils/scale.o src/base/utils/special.o src/export_blacs/pkg_tools.o src/utils/fpmod.o src/utils/quicksort_utils.o src/utils/signs.o src/utils/sorts.o src/utils/strings.o src/utils/swaps.o Object files/libraries should not be included in a source package. * 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 'pbdBASE' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... NOTE Package has both 'src/Makevars.in' and 'src/Makevars'. Installation with --no-configure' is unlikely to work. If you intended 'src/Makevars' to be used on Windows, rename it to 'src/Makevars.win' otherwise remove it. If 'configure' created 'src/Makevars', you need a 'cleanup' script. * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking 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 ... 'pbdBASE-guide.Rnw'... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See '/builddir/build/BUILD/pbdBASE/pbdBASE.Rcheck/00check.log' for details. + exit 0 Processing files: R-pbdBASE-0.5.3-2.el8.x86_64 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.xc9tbv + umask 022 + cd /builddir/build/BUILD + cd pbdBASE + LICENSEDIR=/builddir/build/BUILDROOT/R-pbdBASE-0.5.3-2.el8.x86_64/usr/share/licenses/R-pbdBASE + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/R-pbdBASE-0.5.3-2.el8.x86_64/usr/share/licenses/R-pbdBASE + cp -pr pbdBASE/COPYING /builddir/build/BUILDROOT/R-pbdBASE-0.5.3-2.el8.x86_64/usr/share/licenses/R-pbdBASE + exit 0 Provides: R(pbdBASE) = 0.5-3 R-pbdBASE = 0.5.3-2.el8 R-pbdBASE(x86-64) = 0.5.3-2.el8 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: R(methods) R(pbdMPI) >= 0.4-3 R(pbdSLAP) >= 0.2-9 R(utils) R-core >= 3.6.0 libR.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.5()(64bit) libgfortran.so.5(GFORTRAN_8)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libopenblas.so.0()(64bit) libpthread.so.0()(64bit) libquadmath.so.0()(64bit) libutil.so.1()(64bit) rtld(GNU_HASH) Processing files: R-pbdBASE-debugsource-0.5.3-2.el8.x86_64 Provides: R-pbdBASE-debugsource = 0.5.3-2.el8 R-pbdBASE-debugsource(x86-64) = 0.5.3-2.el8 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: R-pbdBASE-debuginfo-0.5.3-2.el8.x86_64 Provides: R-pbdBASE-debuginfo = 0.5.3-2.el8 R-pbdBASE-debuginfo(x86-64) = 0.5.3-2.el8 debuginfo(build-id) = 8a8653b62040e78297ac0f2a44a0a1877d31d108 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: R-pbdBASE-debugsource(x86-64) = 0.5.3-2.el8 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-pbdBASE-0.5.3-2.el8.x86_64 Wrote: /builddir/build/RPMS/R-pbdBASE-0.5.3-2.el8.x86_64.rpm Wrote: /builddir/build/RPMS/R-pbdBASE-debugsource-0.5.3-2.el8.x86_64.rpm Wrote: /builddir/build/RPMS/R-pbdBASE-debuginfo-0.5.3-2.el8.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.Uf1Rlu + umask 022 + cd /builddir/build/BUILD + cd pbdBASE + /usr/bin/rm -rf /builddir/build/BUILDROOT/R-pbdBASE-0.5.3-2.el8.x86_64 + exit 0 Child return code was: 0