Attachment 1444013 Details for Bug 1511600 – build.log

build.log

build.log (text/plain), 31.02 KB, created by Fedora Release Engineering on 2018-05-28 21:56:07 UTC

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Creator: Fedora Release Engineering

Created: 2018-05-28 21:56:07 UTC

Size: 31.02 KB

patch

obsolete

>Mock Version: 1.3.4
>Mock Version: 1.3.4
>ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target armv7hl --nodeps /builddir/build/SPECS/bionetgen.spec'], chrootPath='/var/lib/mock/f29-build-12476177-913638/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0xb5edaad0>timeout=172800uid=1000gid=425user='mockbuild'nspawn_args=[]printOutput=False)
>Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target armv7hl --nodeps /builddir/build/SPECS/bionetgen.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False
>sh: /usr/bin/perl: No such file or directory
>sh: /usr/bin/perl: No such file or directory
>sh: /usr/bin/perl: No such file or directory
>sh: /usr/bin/perl: No such file or directory
>sh: /usr/bin/perl: No such file or directory
>Building target platforms: armv7hl
>Building for target armv7hl
>Wrote: /builddir/build/SRPMS/bionetgen-2.3.0-7.fc29.src.rpm
>Child return code was: 0
>ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target armv7hl --nodeps /builddir/build/SPECS/bionetgen.spec'], chrootPath='/var/lib/mock/f29-build-12476177-913638/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0xb5edaad0>timeout=172800uid=1000gid=425user='mockbuild'nspawn_args=[]printOutput=False)
>Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target armv7hl --nodeps /builddir/build/SPECS/bionetgen.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False
>Building target platforms: armv7hl
>Building for target armv7hl
>Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.Qfn5tO
>+ umask 022
>+ cd /builddir/build/BUILD
>+ cd /builddir/build/BUILD
>+ rm -rf bionetgen-BioNetGen-2.3.0
>+ /usr/bin/gzip -dc /builddir/build/SOURCES/bionetgen-BioNetGen-2.3.0.tar.gz
>+ /usr/bin/tar -xof -
>+ STATUS=0
>+ '[' 0 -ne 0 ']'
>+ cd bionetgen-BioNetGen-2.3.0
>+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
>+ /usr/bin/cat /builddir/build/SOURCES/bionetgen-isnan.patch
>+ /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch
>+ rm bng2/libsource/Mathutils.tar.gz bng2/libsource/cvode-2.1.1.tar.gz bng2/libsource/cvode-2.6.0.tar.gz bng2/libsource/gsl-1.9.tar.gz bng2/libsource/muparser_v134.tar.gz bng2/libsource/muparser_v2_2_3.tar.gz bng2/libsource/muparser_v2_2_3.zip bng2/libsource/muparser_v2_2_4.tar.gz bng2/libsource/muparser_v2_2_4.zip
>+ pushd bng2/Network3
>~/build/BUILD/bionetgen-BioNetGen-2.3.0/bng2/Network3 ~/build/BUILD/bionetgen-BioNetGen-2.3.0
>+ sed -i 's/AC_PROG_LIBTOOL/AM_PROG_AR\nLT_INIT/' configure.ac
>+ sed -i 's/cvode-.*//; s/muparser_.*//' configure.ac Makefile.am
>+ sed -i -r 's/(run_network_LDADD =).*/\1 libmathutils.la -lmuparser -lsundials_nvecserial -lsundials_cvode/' src/Makefile.am
>+ exit 0
>Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.AavWsB
>+ umask 022
>+ cd /builddir/build/BUILD
>+ cd bionetgen-BioNetGen-2.3.0
>~/build/BUILD/bionetgen-BioNetGen-2.3.0/bng2/Network3 ~/build/BUILD/bionetgen-BioNetGen-2.3.0
>+ pushd bng2/Network3
>+ autoreconf -iv
>autoreconf: Entering directory `.'
>autoreconf: configure.ac: not using Gettext
>autoreconf: running: aclocal -I m4
>aclocal: warning: couldn't open directory 'm4': No such file or directory
>autoreconf: configure.ac: tracing
>autoreconf: running: libtoolize --copy
>libtoolize: putting auxiliary files in '.'.
>libtoolize: copying file './ltmain.sh'
>libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
>libtoolize: copying file 'm4/libtool.m4'
>libtoolize: copying file 'm4/ltoptions.m4'
>libtoolize: copying file 'm4/ltsugar.m4'
>libtoolize: copying file 'm4/ltversion.m4'
>libtoolize: copying file 'm4/lt~obsolete.m4'
>autoreconf: running: /usr/bin/autoconf
>autoreconf: running: /usr/bin/autoheader
>autoreconf: running: automake --add-missing --copy --no-force
>configure.ac:12: installing './ar-lib'
>configure.ac:12: installing './compile'
>configure.ac:16: installing './config.guess'
>configure.ac:16: installing './config.sub'
>configure.ac:6: installing './install-sh'
>configure.ac:6: installing './missing'
>src/Makefile.am: installing './depcomp'
>autoreconf: Leaving directory `.'
>+ . /etc/profile.d/modules.sh
>++ '[' -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 30440 -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_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-arm
>++ /usr/share/lmod/lmod/libexec/lmod sh load mpi/openmpi-arm
>+ eval '__LMOD_REF_COUNT_LD_LIBRARY_PATH="/usr/lib/openmpi/lib:1";' export '__LMOD_REF_COUNT_LD_LIBRARY_PATH;' 'LD_LIBRARY_PATH="/usr/lib/openmpi/lib";' export 'LD_LIBRARY_PATH;' '__LMOD_REF_COUNT_LOADEDMODULES="mpi/openmpi-arm:1";' export '__LMOD_REF_COUNT_LOADEDMODULES;' 'LOADEDMODULES="mpi/openmpi-arm";' export 'LOADEDMODULES;' '__LMOD_REF_COUNT_MANPATH="/usr/share/man/openmpi-arm:1;/usr/share/lmod/lmod/share/man:1";' export '__LMOD_REF_COUNT_MANPATH;' 'MANPATH="/usr/share/man/openmpi-arm:/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/lib/openmpi/bin";' export 'MPI_BIN;' 'MPI_COMPILER="openmpi-arm";' export 'MPI_COMPILER;' 'MPI_FORTRAN_MOD_DIR="/usr/lib/gfortran/modules/openmpi";' export 'MPI_FORTRAN_MOD_DIR;' 'MPI_HOME="/usr/lib/openmpi";' export 'MPI_HOME;' 'MPI_INCLUDE="/usr/include/openmpi-arm";' export 'MPI_INCLUDE;' 'MPI_LIB="/usr/lib/openmpi/lib";' export 'MPI_LIB;' 'MPI_MAN="/usr/share/man/openmpi-arm";' export 'MPI_MAN;' 'MPI_PYTHON2_SITEARCH="/usr/lib/python2.7/site-packages/openmpi";' export 'MPI_PYTHON2_SITEARCH;' 'MPI_PYTHON3_SITEARCH="/usr/lib/python3.6/site-packages/openmpi";' export 'MPI_PYTHON3_SITEARCH;' 'MPI_PYTHON_SITEARCH="/usr/lib/python2.7/site-packages/openmpi";' export 'MPI_PYTHON_SITEARCH;' 'MPI_SUFFIX="_openmpi";' export 'MPI_SUFFIX;' 'MPI_SYSCONFIG="/etc/openmpi-arm";' export 'MPI_SYSCONFIG;' '__LMOD_REF_COUNT_PATH="/usr/lib/openmpi/bin:1;/usr/bin:1;/bin:1;/usr/sbin:1;/sbin:1;/usr/local/sbin:1";' export '__LMOD_REF_COUNT_PATH;' 'PATH="/usr/lib/openmpi/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin";' export 'PATH;' '__LMOD_REF_COUNT_PKG_CONFIG_PATH="/usr/lib/openmpi/lib/pkgconfig:1;/usr/lib/pkgconfig:1;/usr/share/pkgconfig:1";' export '__LMOD_REF_COUNT_PKG_CONFIG_PATH;' 'PKG_CONFIG_PATH="/usr/lib/openmpi/lib/pkgconfig::/usr/lib/pkgconfig:/usr/share/pkgconfig";' export 'PKG_CONFIG_PATH;' '__LMOD_REF_COUNT__LMFILES_="/usr/share/modulefiles/mpi/openmpi-arm:1";' export '__LMOD_REF_COUNT__LMFILES_;' '_LMFILES_="/usr/share/modulefiles/mpi/openmpi-arm";' export '_LMFILES_;' '_ModuleTable001_="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";' export '_ModuleTable001_;' '_ModuleTable002_="aWxlcy9Db3JlIiwiL3Vzci9zaGFyZS9sbW9kL2xtb2QvbW9kdWxlZmlsZXMvQ29yZSIsfSxbInN5c3RlbUJhc2VNUEFUSCJdPSIvZXRjL21vZHVsZWZpbGVzOi91c3Ivc2hhcmUvbW9kdWxlZmlsZXM6L3Vzci9zaGFyZS9tb2R1bGVmaWxlcy9MaW51eDovdXNyL3NoYXJlL21vZHVsZWZpbGVzL0NvcmU6L3Vzci9zaGFyZS9sbW9kL2xtb2QvbW9kdWxlZmlsZXMvQ29yZSIsfQ==";' export '_ModuleTable002_;' '_ModuleTable_Sz_="2";' export '_ModuleTable_Sz_;'
>++ __LMOD_REF_COUNT_LD_LIBRARY_PATH=/usr/lib/openmpi/lib:1
>++ export __LMOD_REF_COUNT_LD_LIBRARY_PATH
>++ LD_LIBRARY_PATH=/usr/lib/openmpi/lib
>++ export LD_LIBRARY_PATH
>++ __LMOD_REF_COUNT_LOADEDMODULES=mpi/openmpi-arm:1
>++ export __LMOD_REF_COUNT_LOADEDMODULES
>++ LOADEDMODULES=mpi/openmpi-arm
>++ export LOADEDMODULES
>++ __LMOD_REF_COUNT_MANPATH='/usr/share/man/openmpi-arm:1;/usr/share/lmod/lmod/share/man:1'
>++ export __LMOD_REF_COUNT_MANPATH
>++ MANPATH=/usr/share/man/openmpi-arm:/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/lib/openmpi/bin
>++ export MPI_BIN
>++ MPI_COMPILER=openmpi-arm
>++ export MPI_COMPILER
>++ MPI_FORTRAN_MOD_DIR=/usr/lib/gfortran/modules/openmpi
>++ export MPI_FORTRAN_MOD_DIR
>++ MPI_HOME=/usr/lib/openmpi
>++ export MPI_HOME
>++ MPI_INCLUDE=/usr/include/openmpi-arm
>++ export MPI_INCLUDE
>++ MPI_LIB=/usr/lib/openmpi/lib
>++ export MPI_LIB
>++ MPI_MAN=/usr/share/man/openmpi-arm
>++ export MPI_MAN
>++ MPI_PYTHON2_SITEARCH=/usr/lib/python2.7/site-packages/openmpi
>++ export MPI_PYTHON2_SITEARCH
>++ MPI_PYTHON3_SITEARCH=/usr/lib/python3.6/site-packages/openmpi
>++ export MPI_PYTHON3_SITEARCH
>++ MPI_PYTHON_SITEARCH=/usr/lib/python2.7/site-packages/openmpi
>++ export MPI_PYTHON_SITEARCH
>++ MPI_SUFFIX=_openmpi
>++ export MPI_SUFFIX
>++ MPI_SYSCONFIG=/etc/openmpi-arm
>++ export MPI_SYSCONFIG
>++ __LMOD_REF_COUNT_PATH='/usr/lib/openmpi/bin:1;/usr/bin:1;/bin:1;/usr/sbin:1;/sbin:1;/usr/local/sbin:1'
>++ export __LMOD_REF_COUNT_PATH
>++ PATH=/usr/lib/openmpi/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
>++ export PATH
>++ __LMOD_REF_COUNT_PKG_CONFIG_PATH='/usr/lib/openmpi/lib/pkgconfig:1;/usr/lib/pkgconfig:1;/usr/share/pkgconfig:1'
>++ export __LMOD_REF_COUNT_PKG_CONFIG_PATH
>++ PKG_CONFIG_PATH=/usr/lib/openmpi/lib/pkgconfig::/usr/lib/pkgconfig:/usr/share/pkgconfig
>++ export PKG_CONFIG_PATH
>++ __LMOD_REF_COUNT__LMFILES_=/usr/share/modulefiles/mpi/openmpi-arm:1
>++ export __LMOD_REF_COUNT__LMFILES_
>++ _LMFILES_=/usr/share/modulefiles/mpi/openmpi-arm
>++ export _LMFILES_
>++ _ModuleTable001_=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
>++ export _ModuleTable001_
>++ _ModuleTable002_=aWxlcy9Db3JlIiwiL3Vzci9zaGFyZS9sbW9kL2xtb2QvbW9kdWxlZmlsZXMvQ29yZSIsfSxbInN5c3RlbUJhc2VNUEFUSCJdPSIvZXRjL21vZHVsZWZpbGVzOi91c3Ivc2hhcmUvbW9kdWxlZmlsZXM6L3Vzci9zaGFyZS9tb2R1bGVmaWxlcy9MaW51eDovdXNyL3NoYXJlL21vZHVsZWZpbGVzL0NvcmU6L3Vzci9zaGFyZS9sbW9kL2xtb2QvbW9kdWxlZmlsZXMvQ29yZSIsfQ==
>++ export _ModuleTable002_
>++ _ModuleTable_Sz_=2
>++ export _ModuleTable_Sz_
>+ CFLAGS='-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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard'
>+ export CFLAGS
>+ CXXFLAGS='-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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard'
>+ export CXXFLAGS
>+ FFLAGS='-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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -I/usr/lib/gfortran/modules'
>+ export FFLAGS
>+ FCFLAGS='-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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -I/usr/lib/gfortran/modules'
>+ export FCFLAGS
>+ LDFLAGS='-Wl,-z,relro  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld'
>+ export LDFLAGS
>+ '[' 1 = 1 ']'
>+++ dirname ./configure
>++ find . -name config.guess -o -name config.sub
>+ for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub)
>++ basename ./config.sub
>+ '[' -f /usr/lib/rpm/redhat/config.sub ']'
>+ /usr/bin/rm -f ./config.sub
>++ basename ./config.sub
>+ /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./config.sub
>'/usr/lib/rpm/redhat/config.sub' -> './config.sub'
>+ for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub)
>++ basename ./config.guess
>+ '[' -f /usr/lib/rpm/redhat/config.guess ']'
>+ /usr/bin/rm -f ./config.guess
>++ basename ./config.guess
>+ /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./config.guess
>'/usr/lib/rpm/redhat/config.guess' -> './config.guess'
>+ '[' 1 = 1 ']'
>+ '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']'
>++ find . -name ltmain.sh
>+ for i in $(find . -name ltmain.sh)
>+ /usr/bin/sed -i.backup -e 's~compiler_flags=$~compiler_flags="-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld"~' ./ltmain.sh
>+ ./configure --build=armv7hl-redhat-linux-gnu --host=armv7hl-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info
>checking for a BSD-compatible install... /usr/bin/install -c
>checking whether build environment is sane... yes
>checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
>checking for gawk... gawk
>checking whether make sets $(MAKE)... yes
>checking whether make supports nested variables... yes
>checking whether make supports the include directive... yes (GNU style)
>checking for armv7hl-redhat-linux-gnu-gcc... no
>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 whether gcc understands -c and -o together... yes
>checking dependency style of gcc... none
>checking for armv7hl-redhat-linux-gnu-ar... no
>checking for armv7hl-redhat-linux-gnu-lib... no
>checking for armv7hl-redhat-linux-gnu-link... no
>checking for ar... ar
>checking the archiver (ar) interface... ar
>checking for armv7hl-redhat-linux-gnu-ar... ar
>checking the archiver (ar) interface... (cached) ar
>checking build system type... armv7hl-redhat-linux-gnu
>checking host system type... armv7hl-redhat-linux-gnu
>checking how to print strings... printf
>checking for a sed that does not truncate output... /usr/bin/sed
>checking for grep that handles long lines and -e... /usr/bin/grep
>checking for egrep... /usr/bin/grep -E
>checking for fgrep... /usr/bin/grep -F
>checking for ld used by gcc... /usr/bin/ld
>checking if the linker (/usr/bin/ld) is GNU ld... yes
>checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
>checking the name lister (/usr/bin/nm -B) interface... BSD nm
>checking whether ln -s works... yes
>checking the maximum length of command line arguments... 1572864
>checking how to convert armv7hl-redhat-linux-gnu file names to armv7hl-redhat-linux-gnu format... func_convert_file_noop
>checking how to convert armv7hl-redhat-linux-gnu file names to toolchain format... func_convert_file_noop
>checking for /usr/bin/ld option to reload object files... -r
>checking for armv7hl-redhat-linux-gnu-objdump... no
>checking for objdump... objdump
>checking how to recognize dependent libraries... pass_all
>checking for armv7hl-redhat-linux-gnu-dlltool... no
>checking for dlltool... no
>checking how to associate runtime and link libraries... printf %s\n
>checking for armv7hl-redhat-linux-gnu-ar... (cached) ar
>checking for archiver @FILE support... @
>checking for armv7hl-redhat-linux-gnu-strip... no
>checking for strip... strip
>checking for armv7hl-redhat-linux-gnu-ranlib... no
>checking for ranlib... ranlib
>checking command to parse /usr/bin/nm -B output from gcc object... ok
>checking for sysroot... no
>checking for a working dd... /usr/bin/dd
>checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
>checking for armv7hl-redhat-linux-gnu-mt... no
>checking for mt... no
>checking if : is a manifest tool... no
>checking how to run the C preprocessor... gcc -E
>checking for ANSI C header files... yes
>checking for sys/types.h... yes
>checking for sys/stat.h... yes
>checking for stdlib.h... yes
>checking for string.h... yes
>checking for memory.h... yes
>checking for strings.h... yes
>checking for inttypes.h... yes
>checking for stdint.h... yes
>checking for unistd.h... yes
>checking for dlfcn.h... yes
>checking for objdir... .libs
>checking if gcc supports -fno-rtti -fno-exceptions... no
>checking for gcc option to produce PIC... -fPIC -DPIC
>checking if gcc PIC flag -fPIC -DPIC works... yes
>checking if gcc static flag -static works... no
>checking if gcc supports -c -o file.o... yes
>checking if gcc supports -c -o file.o... (cached) yes
>checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
>checking whether -lc should be explicitly linked in... no
>checking dynamic linker characteristics... GNU/Linux ld.so
>checking how to hardcode library paths into programs... immediate
>checking whether stripping libraries is possible... yes
>checking if libtool supports shared libraries... yes
>checking whether to build shared libraries... yes
>checking whether to build static libraries... yes
>checking for armv7hl-redhat-linux-gnu-g++... no
>checking for armv7hl-redhat-linux-gnu-c++... no
>checking for armv7hl-redhat-linux-gnu-gpp... no
>checking for armv7hl-redhat-linux-gnu-aCC... no
>checking for armv7hl-redhat-linux-gnu-CC... no
>checking for armv7hl-redhat-linux-gnu-cxx... no
>checking for armv7hl-redhat-linux-gnu-cc++... no
>checking for armv7hl-redhat-linux-gnu-cl.exe... no
>checking for armv7hl-redhat-linux-gnu-FCC... no
>checking for armv7hl-redhat-linux-gnu-KCC... no
>checking for armv7hl-redhat-linux-gnu-RCC... no
>checking for armv7hl-redhat-linux-gnu-xlC_r... no
>checking for armv7hl-redhat-linux-gnu-xlC... no
>checking for g++... g++
>checking whether we are using the GNU C++ compiler... yes
>checking whether g++ accepts -g... yes
>checking dependency style of g++... none
>checking how to run the C++ preprocessor... g++ -E
>checking for ld used by g++... /usr/bin/ld
>checking if the linker (/usr/bin/ld) is GNU ld... yes
>checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
>checking for g++ option to produce PIC... -fPIC -DPIC
>checking if g++ PIC flag -fPIC -DPIC works... yes
>checking if g++ static flag -static works... no
>checking if g++ supports -c -o file.o... yes
>checking if g++ supports -c -o file.o... (cached) yes
>checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
>checking dynamic linker characteristics... (cached) GNU/Linux ld.so
>checking how to hardcode library paths into programs... immediate
>checking for gawk... (cached) gawk
>checking for armv7hl-redhat-linux-gnu-gcc... gcc
>checking whether we are using the GNU C compiler... (cached) yes
>checking whether gcc accepts -g... (cached) yes
>checking for gcc option to accept ISO C89... (cached) none needed
>checking whether gcc understands -c and -o together... (cached) yes
>checking dependency style of gcc... (cached) none
>checking how to run the C preprocessor... gcc -E
>checking whether ln -s works... yes
>checking whether make sets $(MAKE)... (cached) yes
>checking limits.h usability... yes
>checking limits.h presence... yes
>checking for limits.h... yes
>checking for stdlib.h... (cached) yes
>checking for string.h... (cached) yes
>checking for unistd.h... (cached) yes
>checking for stdbool.h that conforms to C99... yes
>checking for _Bool... yes
>checking for inline... inline
>checking for size_t... yes
>checking for stdlib.h... (cached) yes
>checking for GNU libc compatible malloc... yes
>checking for stdlib.h... (cached) yes
>checking for GNU libc compatible realloc... yes
>checking for floor... no
>checking for pow... no
>checking for rint... no
>checking for sqrt... no
>checking for strchr... yes
>checking for strdup... yes
>checking for strpbrk... yes
>checking that generated files are newer than configure... done
>configure: creating ./config.status
>config.status: creating Makefile
>config.status: creating src/Makefile
>config.status: creating config.h
>config.status: executing depfiles commands
>config.status: executing libtool commands
>+ /usr/bin/make -O -j4 -C src
>make: Entering directory '/builddir/build/BUILD/bionetgen-BioNetGen-2.3.0/bng2/Network3/src'
>g++ -DHAVE_CONFIG_H -I. -I..  -I/usr/include -I../muparser_v2_2_4/include -I../cvode-2.6.0/include -Iutil/mathutils   -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -c -o run_network-network.o `test -f 'network.cpp' || echo './'`network.cpp
>make: Leaving directory '/builddir/build/BUILD/bionetgen-BioNetGen-2.3.0/bng2/Network3/src'
>network.cpp:2632:10: fatal error: cvode/cvode_dense.h: No such file or directory
> #include "cvode/cvode_dense.h"
>          ^~~~~~~~~~~~~~~~~~~~~
>compilation terminated.
>make: *** [Makefile:1293: run_network-network.o] Error 1
>make: *** Waiting for unfinished jobs....
>make: Entering directory '/builddir/build/BUILD/bionetgen-BioNetGen-2.3.0/bng2/Network3/src'
>g++ -DHAVE_CONFIG_H -I. -I..  -I/usr/include -I../muparser_v2_2_4/include -I../cvode-2.6.0/include -Iutil/mathutils   -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -c -o run_network-run_network.o `test -f 'run_network.cpp' || echo './'`run_network.cpp
>make: Leaving directory '/builddir/build/BUILD/bionetgen-BioNetGen-2.3.0/bng2/Network3/src'
>run_network.cpp: In function 'int main(int, char**)':
>run_network.cpp:431:13: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
>     sprintf(netfile_name_tmp, "%s%s", netfile_name_tmp, ".net");
>             ^~~~~~~~~~~~~~~~          ~~~~~~~~~~~~~~~~
>run_network.cpp:721:70: warning: variable 'n_deriv_calls_last' set but not used [-Wunused-but-set-variable]
>   long int /*n_steps = 0, n_steps_last = 0,*/ n_rate_calls_last = 0, n_deriv_calls_last = 0;
>                                                                      ^~~~~~~~~~~~~~~~~~
>In file included from network3.hh:12,
>                 from run_network.cpp:46:
>network.h: At global scope:
>network.h:257:23: warning: 'mu::value_type If(mu::value_type, mu::value_type, mu::value_type)' defined but not used [-Wunused-function]
> static mu::value_type If(mu::value_type v1, mu::value_type v2, mu::value_type v3){
>                       ^~
>In file included from run_network.cpp:39:
>util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable]
> static double dswap;
>               ^~~~~
>util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable]
> static int imarg1, imarg2;
>                    ^~~~~~
>util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable]
> static int imarg1, imarg2;
>            ^~~~~~
>util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable]
> static double marg1, marg2;
>                      ^~~~~
>util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable]
> static double marg1, marg2;
>               ^~~~~
>util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable]
> static int isqrarg;
>            ^~~~~~~
>util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable]
> static double sqrarg;
>               ^~~~~~
>run_network.cpp: In function 'int main(int, char**)':
>run_network.cpp:948:14: warning: 'derivs' may be used uninitialized in this function [-Wmaybe-uninitialized]
>     dx = NORM(derivs, n_species_network()) / n_species_network();
>          ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>run_network.cpp:943:17: warning: 'conc_last' may be used uninitialized in this function [-Wmaybe-uninitialized]
>     delta = sqrt(VECTOR_DIST(conc, conc_last, n_species_network())) / n_species_network();
>             ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>run_network.cpp:947:19: warning: 'conc' may be used uninitialized in this function [-Wmaybe-uninitialized]
>     derivs_network(t, conc, derivs);
>     ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
>run_network.cpp:691:29: warning: 'sample_time' may be used uninitialized in this function [-Wmaybe-uninitialized]
>    error = Network3::run_PLA(t,t_end,sample_time,
>            ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
>            step,maxSteps,stepInterval,
>            ~~~~~~~~~~~~~~~~~~~~~~~~~~~
>            pla_stop_condition,print_on_stop,
>            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>            outpre,
>            ~~~~~~~           
>            print_cdat,print_func,print_save_net,print_end_net,
>            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>            additional_pla_output,
>            ~~~~~~~~~~~~~~~~~~~~~~
>            verbose);
>            ~~~~~~~~          
>make: Entering directory '/builddir/build/BUILD/bionetgen-BioNetGen-2.3.0/bng2/Network3/src'
>g++ -DHAVE_CONFIG_H -I. -I..  -I/usr/include -I../muparser_v2_2_4/include -I../cvode-2.6.0/include -Iutil/mathutils   -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -c -o run_network-network3.o `test -f 'network3.cpp' || echo './'`network3.cpp
>make: Leaving directory '/builddir/build/BUILD/bionetgen-BioNetGen-2.3.0/bng2/Network3/src'
>In file included from network3.hh:12,
>                 from network3.cpp:8:
>network.h:257:23: warning: 'mu::value_type If(mu::value_type, mu::value_type, mu::value_type)' defined but not used [-Wunused-function]
> static mu::value_type If(mu::value_type v1, mu::value_type v2, mu::value_type v3){
>                       ^~
>In file included from /usr/include/c++/8/vector:69,
>                 from network.h:30,
>                 from network3.hh:12,
>                 from network3.cpp:8:
>/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
>/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
>       vector<_Tp, _Alloc>::
>       ^~~~~~~~~~~~~~~~~~~
>In file included from /usr/include/c++/8/vector:64,
>                 from network.h:30,
>                 from network3.hh:12,
>                 from network3.cpp:8:
>/usr/include/c++/8/bits/stl_vector.h: In static member function 'static void network3::Network3::read_Butcher_tableau(std::__cxx11::string, std::vector<std::vector<double> >&, std::vector<double>&, bool)':
>/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
>    _M_realloc_insert(end(), __x);
>    ^~~~~~~~~~~~~~~~~
>/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
>    _M_realloc_insert(end(), __x);
>    ^~~~~~~~~~~~~~~~~
>/usr/include/c++/8/bits/stl_vector.h: In static member function 'static void network3::Network3::init_Network3(double*, bool)':
>/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
>    _M_realloc_insert(end(), __x);
>    ^~~~~~~~~~~~~~~~~
>/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
>    _M_realloc_insert(end(), __x);
>    ^~~~~~~~~~~~~~~~~
>RPM build errors:
>error: Bad exit status from /var/tmp/rpm-tmp.AavWsB (%build)
>    Bad exit status from /var/tmp/rpm-tmp.AavWsB (%build)
>Child return code was: 1
>EXCEPTION: [Error()]
>Traceback (most recent call last):
>  File "/usr/lib/python3.6/site-packages/mockbuild/trace_decorator.py", line 89, in trace
>    result = func(*args, **kw)
>  File "/usr/lib/python3.6/site-packages/mockbuild/util.py", line 582, in do
>    raise exception.Error("Command failed. See logs for output.\n # %s" % (command,), child.returncode)
>mockbuild.exception.Error: Command failed. See logs for output.
> # bash --login -c /usr/bin/rpmbuild -bb --target armv7hl --nodeps /builddir/build/SPECS/bionetgen.spec

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Attachments on bug 1511600: 1444013 | 1444014 | 1444015