Mock Version: 1.4.16 Mock Version: 1.4.16 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target i686 --nodeps /builddir/build/SPECS/bionetgen.spec'], chrootPath='/var/lib/mock/f31-build-16726714-1209593/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=172800uid=1000gid=425user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target i686 --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;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'} and shell False BUILDSTDERR: sh: /usr/bin/perl: No such file or directory Building target platforms: i686 Building for target i686 setting SOURCE_DATE_EPOCH=1561939200 Wrote: /builddir/build/SRPMS/bionetgen-2.5.0-3.fc31.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target i686 --nodeps /builddir/build/SPECS/bionetgen.spec'], chrootPath='/var/lib/mock/f31-build-16726714-1209593/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=172800uid=1000gid=425user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target i686 --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;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'} and shell False Building target platforms: i686 Building for target i686 setting SOURCE_DATE_EPOCH=1561939200 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.LywKF8 + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf bionetgen-2.5.0 + /usr/bin/mkdir -p bionetgen-2.5.0 + cd bionetgen-2.5.0 + /usr/bin/gzip -dc /builddir/build/SOURCES/bionetgen-BioNetGen-2.5.0.tar.gz + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + pushd bionetgen-BioNetGen-2.5.0 + rm -f bng2/libsource/gsl-1.9.tar.gz bng2/libsource/Mathutils.tar.gz bng2/libsource/muparser_v2_2_4.tar.gz bng2/libsource/muparser_v2_2_4.zip + tar -xvf bng2/libsource/cvode-2.6.0.tar.gz -C bng2/Network3 ~/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0 ~/build/BUILD/bionetgen-2.5.0 cvode-2.6.0/README cvode-2.6.0/INSTALL_NOTES cvode-2.6.0/LICENSE cvode-2.6.0/Makefile.in cvode-2.6.0/configure.ac cvode-2.6.0/acinclude.m4 cvode-2.6.0/config.hin cvode-2.6.0/configure cvode-2.6.0/CMakeLists.txt cvode-2.6.0/config/config.guess cvode-2.6.0/config/config.sub cvode-2.6.0/config/install-sh cvode-2.6.0/config/mkinstalldirs cvode-2.6.0/config/rminstalldirs cvode-2.6.0/config/ltmain.sh cvode-2.6.0/config/mod_c.m4 cvode-2.6.0/config/mod_fortran.m4 cvode-2.6.0/config/cust_general.m4 cvode-2.6.0/config/CheckFortranFunctionExists.cmake cvode-2.6.0/config/SundialsFortran.cmake cvode-2.6.0/config/SundialsLapack.cmake cvode-2.6.0/config/SundialsMPIC.cmake cvode-2.6.0/config/SundialsMPIF.cmake cvode-2.6.0/config/FindLAPACK.cmake cvode-2.6.0/config/FindBLAS.cmake cvode-2.6.0/config/FindMPI.cmake cvode-2.6.0/bin/sundials-config.in cvode-2.6.0/bin/fortran-update.in cvode-2.6.0/bin/makefile-update.in cvode-2.6.0/include/sundials/sundials_config.in cvode-2.6.0/include/sundials/sundials_types.h cvode-2.6.0/include/sundials/sundials_math.h cvode-2.6.0/include/sundials/sundials_nvector.h cvode-2.6.0/include/sundials/sundials_fnvector.h cvode-2.6.0/include/sundials/sundials_dense.h cvode-2.6.0/include/sundials/sundials_direct.h cvode-2.6.0/include/sundials/sundials_band.h cvode-2.6.0/include/sundials/sundials_lapack.h cvode-2.6.0/include/sundials/sundials_spgmr.h cvode-2.6.0/include/sundials/sundials_spbcgs.h cvode-2.6.0/include/sundials/sundials_sptfqmr.h cvode-2.6.0/include/sundials/sundials_iterative.h cvode-2.6.0/include/nvector/nvector_serial.h cvode-2.6.0/include/nvector/nvector_parallel.h cvode-2.6.0/src/sundials/README cvode-2.6.0/src/sundials/Makefile.in cvode-2.6.0/src/sundials/CMakeLists.txt cvode-2.6.0/src/sundials/sundials_math.c cvode-2.6.0/src/sundials/sundials_nvector.c cvode-2.6.0/src/sundials/sundials_dense.c cvode-2.6.0/src/sundials/sundials_direct.c cvode-2.6.0/src/sundials/sundials_band.c cvode-2.6.0/src/sundials/sundials_spgmr.c cvode-2.6.0/src/sundials/sundials_spbcgs.c cvode-2.6.0/src/sundials/sundials_sptfqmr.c cvode-2.6.0/src/sundials/sundials_iterative.c cvode-2.6.0/src/nvec_ser/README cvode-2.6.0/src/nvec_ser/Makefile.in cvode-2.6.0/src/nvec_ser/CMakeLists.txt cvode-2.6.0/src/nvec_ser/fnvector_serial.h cvode-2.6.0/src/nvec_ser/nvector_serial.c cvode-2.6.0/src/nvec_ser/fnvector_serial.c cvode-2.6.0/src/nvec_par/README cvode-2.6.0/src/nvec_par/Makefile.in cvode-2.6.0/src/nvec_par/CMakeLists.txt cvode-2.6.0/src/nvec_par/fnvector_parallel.h cvode-2.6.0/src/nvec_par/nvector_parallel.c cvode-2.6.0/src/nvec_par/fnvector_parallel.c cvode-2.6.0/examples/templates/cmakelists_parallel_C_ex.in cvode-2.6.0/examples/templates/cmakelists_parallel_F77_ex.in cvode-2.6.0/examples/templates/cmakelists_serial_C_ex.in cvode-2.6.0/examples/templates/cmakelists_serial_F77_ex.in cvode-2.6.0/examples/templates/makefile_parallel_C_ex.in cvode-2.6.0/examples/templates/makefile_parallel_F77_ex.in cvode-2.6.0/examples/templates/makefile_serial_C_ex.in cvode-2.6.0/examples/templates/makefile_serial_F77_ex.in cvode-2.6.0/doc/cvode/cv_guide.pdf cvode-2.6.0/doc/cvode/cv_examples.pdf cvode-2.6.0/include/cvode/cvode.h cvode-2.6.0/include/cvode/cvode_direct.h cvode-2.6.0/include/cvode/cvode_dense.h cvode-2.6.0/include/cvode/cvode_band.h cvode-2.6.0/include/cvode/cvode_lapack.h cvode-2.6.0/include/cvode/cvode_diag.h cvode-2.6.0/include/cvode/cvode_spgmr.h cvode-2.6.0/include/cvode/cvode_spbcgs.h cvode-2.6.0/include/cvode/cvode_sptfqmr.h cvode-2.6.0/include/cvode/cvode_spils.h cvode-2.6.0/include/cvode/cvode_bandpre.h cvode-2.6.0/include/cvode/cvode_bbdpre.h cvode-2.6.0/src/cvode/LICENSE cvode-2.6.0/src/cvode/README cvode-2.6.0/src/cvode/Makefile.in cvode-2.6.0/src/cvode/CMakeLists.txt cvode-2.6.0/src/cvode/cvode.c cvode-2.6.0/src/cvode/cvode_io.c cvode-2.6.0/src/cvode/cvode_direct.c cvode-2.6.0/src/cvode/cvode_dense.c cvode-2.6.0/src/cvode/cvode_band.c cvode-2.6.0/src/cvode/cvode_lapack.c cvode-2.6.0/src/cvode/cvode_diag.c BUILDSTDERR: cvode-2.6.0/src/cvode/cvode_sp+ popd + RPM_EC=0 BUILDSTDERR: ++ jobs -p + exit 0 ils.c cvode-2.6.0/src/cvode/cvode_spgmr.c cvode-2.6.0/src/cvode/cvode_spbcgs.c cvode-2.6.0/src/cvode/cvode_sptfqmr.c cvode-2.6.0/src/cvode/cvode_bandpre.c cvode-2.6.0/src/cvode/cvode_bbdpre.c cvode-2.6.0/src/cvode/cvode_impl.h cvode-2.6.0/src/cvode/cvode_direct_impl.h cvode-2.6.0/src/cvode/cvode_diag_impl.h cvode-2.6.0/src/cvode/cvode_spils_impl.h cvode-2.6.0/src/cvode/cvode_bandpre_impl.h cvode-2.6.0/src/cvode/cvode_bbdpre_impl.h cvode-2.6.0/src/cvode/fcmix/Makefile.in cvode-2.6.0/src/cvode/fcmix/CMakeLists.txt cvode-2.6.0/src/cvode/fcmix/fcvode.c cvode-2.6.0/src/cvode/fcmix/fcvewt.c cvode-2.6.0/src/cvode/fcmix/fcvpreco.c cvode-2.6.0/src/cvode/fcmix/fcvjtimes.c cvode-2.6.0/src/cvode/fcmix/fcvband.c cvode-2.6.0/src/cvode/fcmix/fcvdense.c cvode-2.6.0/src/cvode/fcmix/fcvlapack.c cvode-2.6.0/src/cvode/fcmix/fcvlapband.c cvode-2.6.0/src/cvode/fcmix/fcvlapdense.c cvode-2.6.0/src/cvode/fcmix/fcvbp.c cvode-2.6.0/src/cvode/fcmix/fcvbbd.c cvode-2.6.0/src/cvode/fcmix/fcvroot.c cvode-2.6.0/src/cvode/fcmix/fcvode.h cvode-2.6.0/src/cvode/fcmix/fcvbp.h cvode-2.6.0/src/cvode/fcmix/fcvbbd.h cvode-2.6.0/src/cvode/fcmix/fcvroot.h cvode-2.6.0/examples/cvode/serial/README cvode-2.6.0/examples/cvode/serial/Makefile.in cvode-2.6.0/examples/cvode/serial/CMakeLists.txt cvode-2.6.0/examples/cvode/serial/cvAdvDiff_bnd.c cvode-2.6.0/examples/cvode/serial/cvAdvDiff_bndL.c cvode-2.6.0/examples/cvode/serial/cvAdvDiff_bndL.out cvode-2.6.0/examples/cvode/serial/cvAdvDiff_bnd.out cvode-2.6.0/examples/cvode/serial/cvDirectDemo_ls.c cvode-2.6.0/examples/cvode/serial/cvDirectDemo_ls.out cvode-2.6.0/examples/cvode/serial/cvDiurnal_kry_bp.c cvode-2.6.0/examples/cvode/serial/cvDiurnal_kry_bp.out cvode-2.6.0/examples/cvode/serial/cvDiurnal_kry.c cvode-2.6.0/examples/cvode/serial/cvDiurnal_kry.out cvode-2.6.0/examples/cvode/serial/cvKrylovDemo_ls.c cvode-2.6.0/examples/cvode/serial/cvKrylovDemo_ls.out cvode-2.6.0/examples/cvode/serial/cvKrylovDemo_prec.c cvode-2.6.0/examples/cvode/serial/cvKrylovDemo_prec.out cvode-2.6.0/examples/cvode/serial/cvRoberts_dns.c cvode-2.6.0/examples/cvode/serial/cvRoberts_dnsL.c cvode-2.6.0/examples/cvode/serial/cvRoberts_dnsL.out cvode-2.6.0/examples/cvode/serial/cvRoberts_dns.out cvode-2.6.0/examples/cvode/serial/cvRoberts_dns_uw.c cvode-2.6.0/examples/cvode/serial/cvRoberts_dns_uw.out cvode-2.6.0/examples/cvode/fcmix_serial/README cvode-2.6.0/examples/cvode/fcmix_serial/Makefile.in cvode-2.6.0/examples/cvode/fcmix_serial/CMakeLists.txt cvode-2.6.0/examples/cvode/fcmix_serial/fcvAdvDiff_bnd.f cvode-2.6.0/examples/cvode/fcmix_serial/fcvAdvDiff_bnd.out cvode-2.6.0/examples/cvode/fcmix_serial/fcvDiurnal_kry_bp.f cvode-2.6.0/examples/cvode/fcmix_serial/fcvDiurnal_kry_bp.out cvode-2.6.0/examples/cvode/fcmix_serial/fcvDiurnal_kry.f cvode-2.6.0/examples/cvode/fcmix_serial/fcvDiurnal_kry.out cvode-2.6.0/examples/cvode/fcmix_serial/fcvRoberts_dns.f cvode-2.6.0/examples/cvode/fcmix_serial/fcvRoberts_dnsL.f cvode-2.6.0/examples/cvode/fcmix_serial/fcvRoberts_dnsL.out cvode-2.6.0/examples/cvode/fcmix_serial/fcvRoberts_dns.out cvode-2.6.0/examples/cvode/parallel/README cvode-2.6.0/examples/cvode/parallel/Makefile.in cvode-2.6.0/examples/cvode/parallel/CMakeLists.txt cvode-2.6.0/examples/cvode/parallel/cvAdvDiff_non_p.c cvode-2.6.0/examples/cvode/parallel/cvAdvDiff_non_p.out cvode-2.6.0/examples/cvode/parallel/cvDiurnal_kry_bbd_p.c cvode-2.6.0/examples/cvode/parallel/cvDiurnal_kry_bbd_p.out cvode-2.6.0/examples/cvode/parallel/cvDiurnal_kry_p.c cvode-2.6.0/examples/cvode/parallel/cvDiurnal_kry_p.out cvode-2.6.0/examples/cvode/fcmix_parallel/README cvode-2.6.0/examples/cvode/fcmix_parallel/Makefile.in cvode-2.6.0/examples/cvode/fcmix_parallel/CMakeLists.txt cvode-2.6.0/examples/cvode/fcmix_parallel/fcvDiag_non_p.f cvode-2.6.0/examples/cvode/fcmix_parallel/fcvDiag_non_p.out cvode-2.6.0/examples/cvode/fcmix_parallel/fcvDiag_kry_bbd_p.f cvode-2.6.0/examples/cvode/fcmix_parallel/fcvDiag_kry_bbd_p.out cvode-2.6.0/examples/cvode/fcmix_parallel/fcvDiag_kry_p.f cvode-2.6.0/examples/cvode/fcmix_parallel/fcvDiag_kry_p.out ~/build/BUILD/bionetgen-2.5.0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.EXLBE5 + umask 022 + cd /builddir/build/BUILD + cd bionetgen-2.5.0 + pushd bionetgen-BioNetGen-2.5.0/bng2/Network3 + sed -i 's/AC_PROG_LIBTOOL/AM_PROG_AR\nLT_INIT/' configure.ac + sed -i 's/AC_PROG_LIBTOOL/AM_PROG_AR\nLT_INIT/' cvode-2.6.0/configure.ac + sed -i 's/muparser_.*//' configure.ac Makefile.am + sed -i -r 's!(run_network_LDADD =).*!\1 libmathutils.la ../cvode-2.6.0/src/nvec_ser/libsundials_nvecserial.la ../cvode-2.6.0/src/cvode/libsundials_cvode.la -lmuparser!' src/Makefile.am + autoreconf -iv --no-recursive BUILDSTDERR: autoreconf: Entering directory `.' BUILDSTDERR: autoreconf: configure.ac: not using Gettext BUILDSTDERR: autoreconf: running: aclocal -I m4 BUILDSTDERR: aclocal: warning: couldn't open directory 'm4': No such file or directory BUILDSTDERR: autoreconf: configure.ac: tracing BUILDSTDERR: autoreconf: running: libtoolize --copy BUILDSTDERR: autoreconf: running: /usr/bin/autoconf BUILDSTDERR: autoreconf: running: /usr/bin/autoheader BUILDSTDERR: autoreconf: running: automake --add-missing --copy --no-force BUILDSTDERR: configure.ac:12: installing './ar-lib' BUILDSTDERR: configure.ac:12: installing './compile' BUILDSTDERR: configure.ac:16: installing './config.guess' BUILDSTDERR: configure.ac:16: installing './config.sub' BUILDSTDERR: configure.ac:6: installing './install-sh' BUILDSTDERR: configure.ac:6: installing './missing' BUILDSTDERR: src/Makefile.am: installing './depcomp' BUILDSTDERR: autoreconf: Leaving directory `.' + warnings='-Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized' + 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' + export LDFLAGS + '[' 1 = 1 ']' BUILDSTDERR: +++ dirname ./configure BUILDSTDERR: ++ find . -name config.guess -o -name config.sub + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) BUILDSTDERR: ++ basename ./config.guess + '[' -f /usr/lib/rpm/redhat/config.guess ']' + /usr/bin/rm -f ./config.guess BUILDSTDERR: ++ basename ./config.guess + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./config.guess + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) BUILDSTDERR: ++ basename ./config.sub + '[' -f /usr/lib/rpm/redhat/config.sub ']' + /usr/bin/rm -f ./config.sub BUILDSTDERR: ++ basename ./config.sub + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./config.sub + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) BUILDSTDERR: ++ basename ./cvode-2.6.0/config/config.guess + '[' -f /usr/lib/rpm/redhat/config.guess ']' + /usr/bin/rm -f ./cvode-2.6.0/config/config.guess BUILDSTDERR: ++ basename ./cvode-2.6.0/config/config.guess + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./cvode-2.6.0/config/config.guess + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) BUILDSTDERR: ++ basename ./cvode-2.6.0/config/config.sub + '[' -f /usr/lib/rpm/redhat/config.sub ']' + /usr/bin/rm -f ./cvode-2.6.0/config/config.sub BUILDSTDERR: ++ basename ./cvode-2.6.0/config/config.sub + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./cvode-2.6.0/config/config.sub + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']' BUILDSTDERR: ++ 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 + 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"~' ./cvode-2.6.0/config/ltmain.sh + ./configure --build=i686-redhat-linux-gnu --host=i686-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 CC=gcc CXX=g++ F77=gfortran ~/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3 ~/build/BUILD/bionetgen-2.5.0 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' '/usr/lib/rpm/redhat/config.guess' -> './config.guess' '/usr/lib/rpm/redhat/config.sub' -> './config.sub' '/usr/lib/rpm/redhat/config.guess' -> './cvode-2.6.0/config/config.guess' '/usr/lib/rpm/redhat/config.sub' -> './cvode-2.6.0/config/config.sub' 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 i686-redhat-linux-gnu-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 i686-redhat-linux-gnu-ar... no checking for i686-redhat-linux-gnu-lib... no checking for i686-redhat-linux-gnu-link... no checking for ar... ar checking the archiver (ar) interface... ar checking for i686-redhat-linux-gnu-ar... ar checking the archiver (ar) interface... (cached) ar checking build system type... i686-redhat-linux-gnu checking host system type... i686-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 i686-redhat-linux-gnu file names to i686-redhat-linux-gnu format... func_convert_file_noop checking how to convert i686-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 i686-redhat-linux-gnu-objdump... no checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for i686-redhat-linux-gnu-dlltool... no checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for i686-redhat-linux-gnu-ar... (cached) ar checking for archiver @FILE support... @ checking for i686-redhat-linux-gnu-strip... no checking for strip... strip checking for i686-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 i686-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 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 i686-redhat-linux-gnu-gcc... (cached) 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 === configuring in cvode-2.6.0 (/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0) configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr' '--build=i686-redhat-linux-gnu' '--host=i686-redhat-linux-gnu' '--program-prefix=' '--disable-dependency-tracking' '--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' 'CC=gcc' 'CXX=g++' 'F77=gfortran' 'build_alias=i686-redhat-linux-gnu' 'host_alias=i686-redhat-linux-gnu' '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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' '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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' --cache-file=/dev/null --srcdir=. --------------------------------- Running SUNDIALS Configure Script --------------------------------- Initialization -------------- checking build system type... i686-redhat-linux-gnu checking host system type... i686-redhat-linux-gnu checking whether make sets $(MAKE)... yes checking for a BSD-compatible install... /usr/bin/install -c C Compiler Settings ------------------- checking for i686-redhat-linux-gnu-cc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... 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 grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E 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 floating-point data type to use... double checking for C compiler flags... none checking how to run the C preprocessor... gcc -E checking for C/C++ preprocessor flags... none checking for linker flags... none checking for extra libraries... none checking for ANSI C header files... yes checking for stdlib.h... (cached) yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking math.h usability... yes checking math.h presence... yes checking for math.h... yes checking for abs in -lm... yes checking for fabs in -lm... yes checking for pow in -lm... yes checking for sqrt in -lm... yes checking for additional required C libraries... -lm checking for int... yes checking size of int... 4 checking for long int... yes checking size of long int... 4 checking for double... yes checking size of double... 8 checking for egrep... (cached) /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking if gcc is a C++ compiler... no Fortran Settings ---------------- checking for i686-redhat-linux-gnu-f77... gfortran checking whether we are using the GNU Fortran 77 compiler... yes checking whether gfortran accepts -g... yes checking for extra Fortran compiler flags... none checking how to get verbose linking output from gfortran... -v checking for Fortran 77 libraries of gfortran... -L/usr/lib/gcc/i686-redhat-linux/9 -L/usr/lib/gcc/i686-redhat-linux/9/../../.. -lgfortran -lm -lquadmath checking which linker to use... gfortran checking for Fortran name-mangling scheme of C identifiers... lower case + one underscore checking for Fortran name-mangling scheme of C identifiers with underscores... lower case + one underscore checking for dgemm_... no checking for dgemm_ in -lcxml... no checking for dgemm_ in -ldxml... no checking for dgemm_ in -lscs... no checking for dgemm_ in -lcomplib.sgimath... no checking for dgemm_ in -lblas... no checking for dgemm_ in -lblas... (cached) no checking for Blas/Lapack library linkage... "no" Unable to determine Blas/Lapack library linkage. Try using --with-blas and --with-lapack. Disabling compilation of Blas/Lapack interfaces... MPI-C Settings -------------- checking if using MPI-C script... yes BUILDSTDERR: checking if absolute path configure: WARNING: cannot find MPI-C compiler to mpicc was given... no checking for mpicc... none Unable to find a functional MPI-C compiler. Try using --with-mpicc to specify a MPI-C compiler script, --with-mpi-incdir, --with-mpi-libdir and --with-mpi-libs to specify the locations of all relevant MPI files, or --with-mpi-root to specify the base installation directory of the MPI implementation to be used. Disabling the parallel NVECTOR module and all parallel examples... Libtool Settings ---------------- checking for a sed that does not truncate output... /usr/bin/sed checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking whether ln -s works... yes checking how to recognize dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking how to run the C++ preprocessor... g++ -E checking the maximum length of command line arguments... 1572864 checking command to parse /usr/bin/nm -B output from gcc object... ok checking for objdir... .libs checking for i686-redhat-linux-gnu-ar... no checking for ar... ar checking for i686-redhat-linux-gnu-ranlib... no checking for ranlib... ranlib checking for i686-redhat-linux-gnu-strip... no checking for strip... strip checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC checking if gcc PIC flag -fPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes 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... no checking whether to build static libraries... yes configure: creating libtool appending configuration tag "CXX" to libtool 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 checking if g++ PIC flag -fPIC works... yes checking if g++ static flag -static works... no checking if g++ supports -c -o file.o... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate appending configuration tag "F77" to libtool checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking for gfortran option to produce PIC... -fPIC checking if gfortran PIC flag -fPIC works... yes checking if gfortran static flag -static works... no checking if gfortran supports -c -o file.o... yes checking whether the gfortran linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate Create Makefiles and configuration files ---------------------------------------- configure: creating ./config.status config.status: creating Makefile config.status: creating src/sundials/Makefile config.status: creating src/nvec_ser/Makefile config.status: creating src/cvode/Makefile config.status: creating src/cvode/fcmix/Makefile config.status: creating include/sundials/sundials_config.h config.status: creating bin/sundials-config config.status: creating config.h *************** * WARNING * *************** At least one warning was issued. Some features were disabled. Review the configure output and/or the contents of config.log before proceeding with the build. BUILDSTDERR: -------------------------++ echo '-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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' BUILDSTDERR: ++ sed -e s/-Werror=format-security/-Wno-error=format-security/g + SETOPT_FLAGS='-O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + /usr/bin/make -O -j48 V=1 VERBOSE=1 -C cvode-2.6.0 V=1 CC=gcc CXX=g++ F77=gfortran 'CXXFLAGS=-O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized' 'CFLAGS=-O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized' ----- SUNDIALS Configuration Summary ------------------------------ Configuration ------------- Host System: i686-redhat-linux-gnu Build System: i686-redhat-linux-gnu C Preprocessor: gcc -E C Preprocessor Flags: C Compiler: gcc C Compiler Flags -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection C Linker: gcc Linker Flags: -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld Libraries: -lm Fortran Compiler: gfortran Fortran Compiler Flags: -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules Fortran Linker: gfortran Extra Fortran Libraries: -L/usr/lib/gcc/i686-redhat-linux/9 -L/usr/lib/gcc/i686-redhat-linux/9/../../.. -lgfortran -lm -lquadmath srcdir: /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0 builddir: /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0 prefix: /usr exec_prefix: /usr includedir: /usr/include libdir: /usr/lib Modules ------- CVODE FCVODE Type 'make' and then 'make install' to build and install SUNDIALS 2.4.0. ---------------------------------- Finished SUNDIALS Configure Script ---------------------------------- ---------------------- Make src/sundials... ---------------------- make[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/sundials' make[2]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/sundials' make[2]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/sundials' make[2]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/sundials' /bin/sh ../../libtool --mode=compile gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./sundials_direct.c gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./sundials_direct.c -o sundials_direct.o /bin/sh ../../libtool --mode=compile gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./sundials_band.c gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./sundials_band.c -o sundials_band.o /bin/sh ../../libtool --mode=compile gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./sundials_dense.c gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./sundials_dense.c -o sundials_dense.o /bin/sh ../../libtool --mode=compile gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./sundials_iterative.c gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./sundials_iterative.c -o sundials_iterative.o /bin/sh ../../libtool --mode=compile gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./sundials_math.c gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./sundials_math.c -o sundials_math.o /bin/sh ../../libtool --mode=compile gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./sundials_nvector.c gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./sundials_nvector.c -o sundials_nvector.o /bin/sh ../../libtool --mode=compile gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./sundials_spgmr.c gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./sundials_spgmr.c -o sundials_spgmr.o /bin/sh ../../libtool --mode=compile gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./sundials_spbcgs.c gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./sundials_spbcgs.c -o sundials_spbcgs.o BUILDSTDERR: /bin/sh ../../libtool --mode=compile gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mmake[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. BUILDSTDERR: make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. stackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./sundials_sptfqmr.c gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./sundials_sptfqmr.c -o sundials_sptfqmr.o make[2]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/sundials' make[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/sundials' ---------------------- Make src/nvec_ser... ---------------------- make[2]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/sundials' make[3]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/sundials' make[3]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/sundials' make[3]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/sundials' make[3]: Nothing to be done for 'lib_without_bl'. make[3]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/sundials' make[2]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/sundials' make[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/nvec_ser' /bin/sh ../../libtool --mode=compile gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./fnvector_serial.c gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./fnvector_serial.c -o fnvector_serial.o make[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/nvec_ser' make[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/nvec_ser' /bin/sh ../../libtool --mode=compile gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./nvector_serial.c BUILDSTDERR: gcc -I./../../include -Imake[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. ../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./nvector_serial.c -o nvector_serial.o make[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/nvec_ser' make[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/nvec_ser' /bin/sh ../../libtool --mode=link gcc -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -o libsundials_fnvecserial.la fnvector_serial.lo ../../src/sundials/sundials_math.lo -rpath /usr/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -lm -version-info 0:2:0 mkdir .libs ar cru .libs/libsundials_fnvecserial.a fnvector_serial.o ../../src/sundials/sundials_math.o ranlib .libs/libsundials_fnvecserial.a creating libsundials_fnvecserial.la (cd .libs && rm -f libsundials_fnvecserial.la && ln -s ../libsundials_fnvecserial.la libsundials_fnvecserial.la) make[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/nvec_ser' make[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/nvec_ser' /bin/sh ../../libtool --mode=link gcc -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -o libsundials_nvecserial.la nvector_serial.lo ../../src/sundials/sundials_math.lo -rpath /usr/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -lm -version-info 0:2:0 ar cru .libs/libsundials_nvecserial.a nvector_serial.o ../../src/sundials/sundials_math.o ranlib .libs/libsundials_nvecserial.a creating libsundials_nvecserial.la (cd .libs && rm -f libsundials_nvecserial.la && ln -s ../libsundials_nvecserial.la libsundials_nvecserial.la) make[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/nvec_ser' ---------------------- Make src/cvode... ---------------------- make[2]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/sundials' make[3]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/sundials' make[3]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/sundials' make[3]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/sundials' make[3]: Nothing to be done for 'lib_without_bl'. make[3]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/sundials' make[2]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/sundials' make[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode' /bin/sh ../../libtool --mode=compile gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./cvode_dense.c gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./cvode_dense.c -o cvode_dense.o make[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode' make[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode' /bin/sh ../../libtool --mode=compile gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./cvode_band.c gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./cvode_band.c -o cvode_band.o make[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode' make[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode' /bin/sh ../../libtool --mode=compile gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./cvode_sptfqmr.c gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./cvode_sptfqmr.c -o cvode_sptfqmr.o make[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode' make[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode' /bin/sh ../../libtool --mode=compile gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./cvode_spbcgs.c gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./cvode_spbcgs.c -o cvode_spbcgs.o make[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode' make[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode' /bin/sh ../../libtool --mode=compile gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./cvode_spgmr.c gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./cvode_spgmr.c -o cvode_spgmr.o make[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode' make[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode' /bin/sh ../../libtool --mode=compile gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./cvode_diag.c gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./cvode_diag.c -o cvode_diag.o make[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode' make[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode' /bin/sh ../../libtool --mode=compile gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./cvode_direct.c gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./cvode_direct.c -o cvode_direct.o make[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode' make[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode' /bin/sh ../../libtool --mode=compile gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./cvode_spils.c gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./cvode_spils.c -o cvode_spils.o make[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode' make[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode' /bin/sh ../../libtool --mode=compile gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./cvode_bandpre.c gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./cvode_bandpre.c -o cvode_bandpre.o make[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode' make[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode' /bin/sh ../../libtool --mode=compile gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./cvode_bbdpre.c gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./cvode_bbdpre.c -o cvode_bbdpre.o make[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode' make[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode' /bin/sh ../../libtool --mode=compile gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./cvode_io.c gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./cvode_io.c -o cvode_io.o make[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode' make[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode' /bin/sh ../../libtool --mode=compile gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./cvode.c BUILDSTDERR: gcc -I./../../include -I../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtumake[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. ne=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./cvode.c -o cvode.o make[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode' make[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode' make[2]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode' make[2]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode' make[2]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode' make[3]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/sundials' make[4]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/sundials' make[4]: Nothing to be done for 'lib_without_bl'. make[4]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/sundials' make[3]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/sundials' /bin/sh ../../libtool --mode=link gcc -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -o libsundials_cvode.la cvode.lo cvode_io.lo cvode_direct.lo cvode_band.lo cvode_dense.lo cvode_diag.lo cvode_spils.lo cvode_spbcgs.lo cvode_spgmr.lo cvode_sptfqmr.lo cvode_bandpre.lo cvode_bbdpre.lo ../../src/sundials/sundials_band.lo ../../src/sundials/sundials_dense.lo ../../src/sundials/sundials_direct.lo ../../src/sundials/sundials_iterative.lo ../../src/sundials/sundials_spgmr.lo ../../src/sundials/sundials_spbcgs.lo ../../src/sundials/sundials_sptfqmr.lo ../../src/sundials/sundials_math.lo ../../src/sundials/sundials_nvector.lo -rpath /usr/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -lm -version-info 1:0:0 mkdir .libs ar cru .libs/libsundials_cvode.a cvode.o cvode_io.o cvode_direct.o cvode_band.o cvode_dense.o cvode_diag.o cvode_spils.o cvode_spbcgs.o cvode_spgmr.o cvode_sptfqmr.o cvode_bandpre.o cvode_bbdpre.o ../../src/sundials/sundials_band.o ../../src/sundials/sundials_dense.o ../../src/sundials/sundials_direct.o ../../src/sundials/sundials_iterative.o ../../src/sundials/sundials_spgmr.o ../../src/sundials/sundials_spbcgs.o ../../src/sundials/sundials_sptfqmr.o ../../src/sundials/sundials_math.o ../../src/sundials/sundials_nvector.o ranlib .libs/libsundials_cvode.a creating libsundials_cvode.la (cd .libs && rm -f libsundials_cvode.la && ln -s ../libsundials_cvode.la libsundials_cvode.la) make[2]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode' make[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode' ---------------------- Make src/cvode/fcmix... ---------------------- make[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix' /bin/sh ../../../libtool --mode=compile gcc -I./../../../include -I./../../../src/cvode -I../../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./fcvbp.c gcc -I./../../../include -I./../../../src/cvode -I../../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./fcvbp.c -o fcvbp.o make[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix' make[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix' /bin/sh ../../../libtool --mode=compile gcc -I./../../../include -I./../../../src/cvode -I../../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./fcvroot.c gcc -I./../../../include -I./../../../src/cvode -I../../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./fcvroot.c -o fcvroot.o make[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix' make[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix' /bin/sh ../../../libtool --mode=compile gcc -I./../../../include -I./../../../src/cvode -I../../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./fcvjtimes.c gcc -I./../../../include -I./../../../src/cvode -I../../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./fcvjtimes.c -o fcvjtimes.o make[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix' make[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix' /bin/sh ../../../libtool --mode=compile gcc -I./../../../include -I./../../../src/cvode -I../../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./fcvband.c gcc -I./../../../include -I./../../../src/cvode -I../../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./fcvband.c -o fcvband.o make[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix' make[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix' /bin/sh ../../../libtool --mode=compile gcc -I./../../../include -I./../../../src/cvode -I../../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./fcvbbd.c gcc -I./../../../include -I./../../../src/cvode -I../../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./fcvbbd.c -o fcvbbd.o make[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix' make[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix' /bin/sh ../../../libtool --mode=compile gcc -I./../../../include -I./../../../src/cvode -I../../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./fcvpreco.c gcc -I./../../../include -I./../../../src/cvode -I../../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./fcvpreco.c -o fcvpreco.o make[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix' make[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix' /bin/sh ../../../libtool --mode=compile gcc -I./../../../include -I./../../../src/cvode -I../../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./fcvewt.c gcc -I./../../../include -I./../../../src/cvode -I../../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./fcvewt.c -o fcvewt.o make[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix' make[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix' /bin/sh ../../../libtool --mode=compile gcc -I./../../../include -I./../../../src/cvode -I../../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./fcvdense.c gcc -I./../../../include -I./../../../src/cvode -I../../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./fcvdense.c -o fcvdense.o make[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix' make[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix' /bin/sh ../../../libtool --mode=compile gcc -I./../../../include -I./../../../src/cvode -I../../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./fcvode.c BUILDSTDERR: gcc -I./../../../include -I./../../../src/cvode -I../../../include -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=imake[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. + /usr/bin/make -O -j48 V=1 VERBOSE=1 -C src V=1 CC=gcc CXX=g++ F77=gfortran '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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized' 686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c ./fcvode.c -o fcvode.o make[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix' make[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix' make[2]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix' make[2]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix' make[2]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix' /bin/sh ../../../libtool --mode=link gcc -O2 -g -pipe -Wall -Wno-error=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -o libsundials_fcvode.la fcvode.lo fcvband.lo fcvdense.lo fcvjtimes.lo fcvpreco.lo fcvbbd.lo fcvbp.lo fcvroot.lo fcvewt.lo -rpath /usr/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -lm -static -version-info 0:1:0 mkdir .libs ar cru .libs/libsundials_fcvode.a fcvode.o fcvband.o fcvdense.o fcvjtimes.o fcvpreco.o fcvbbd.o fcvbp.o fcvroot.o fcvewt.o ranlib .libs/libsundials_fcvode.a creating libsundials_fcvode.la (cd .libs && rm -f libsundials_fcvode.la && ln -s ../libsundials_fcvode.la libsundials_fcvode.la) make[2]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix' make[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/cvode-2.6.0/src/cvode/fcmix' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o pla/base/run_network-firingGenerator.o `test -f 'pla/base/firingGenerator.cpp' || echo './'`pla/base/firingGenerator.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o pla/base/run_network-postleapChecker.o `test -f 'pla/base/postleapChecker.cpp' || echo './'`pla/base/postleapChecker.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o pla/base/run_network-tauCalculator.o `test -f 'pla/base/tauCalculator.cpp' || echo './'`pla/base/tauCalculator.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o pla/base/run_network-rxnClassifier.o `test -f 'pla/base/rxnClassifier.cpp' || echo './'`pla/base/rxnClassifier.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o pla/util/run_network-preleap_TC.o `test -f 'pla/util/preleap_TC.cpp' || echo './'`pla/util/preleap_TC.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o model/run_network-simpleSpecies.o `test -f 'model/simpleSpecies.cpp' || echo './'`model/simpleSpecies.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o pla/util/run_network-negPopChecker.o `test -f 'pla/util/negPopChecker.cpp' || echo './'`pla/util/negPopChecker.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o pla/fEuler/run_network-fEulerRB_TC_PL.o `test -f 'pla/fEuler/fEulerRB_TC_PL.cpp' || echo './'`pla/fEuler/fEulerRB_TC_PL.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o util/MTrand/run_network-mtrand.o `test -f 'util/MTrand/mtrand.cpp' || echo './'`util/MTrand/mtrand.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o pla/fEuler/run_network-fEulerSB_TC_PL.o `test -f 'pla/fEuler/fEulerSB_TC_PL.cpp' || echo './'`pla/fEuler/fEulerSB_TC_PL.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o pla/fEuler/run_network-fEuler_RC.o `test -f 'pla/fEuler/fEuler_RC.cpp' || echo './'`pla/fEuler/fEuler_RC.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o pla/util/run_network-sbChecker.o `test -f 'pla/util/sbChecker.cpp' || echo './'`pla/util/sbChecker.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o pla/util/run_network-rbChecker.o `test -f 'pla/util/rbChecker.cpp' || echo './'`pla/util/rbChecker.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o model/run_network-rateExpression.o `test -f 'model/rateExpression.cpp' || echo './'`model/rateExpression.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o util/rand2/run_network-rand2.o `test -f 'util/rand2/rand2.cpp' || echo './'`util/rand2/rand2.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o util/run_network-rand.o `test -f 'util/rand.cpp' || echo './'`util/rand.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o pla/fEuler/run_network-fEulerPreleapSB_TC.o `test -f 'pla/fEuler/fEulerPreleapSB_TC.cpp' || echo './'`pla/fEuler/fEulerPreleapSB_TC.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o pla/eRungeKutta/util/run_network-binomialCorrector_RK.o `test -f 'pla/eRungeKutta/util/binomialCorrector_RK.cpp' || echo './'`pla/eRungeKutta/util/binomialCorrector_RK.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o pla/fEuler/run_network-fEuler_FG.o `test -f 'pla/fEuler/fEuler_FG.cpp' || echo './'`pla/fEuler/fEuler_FG.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' BUILDSTDERR: 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/redhatIn file included from util/mathutils/cabs.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: In file included from util/mathutils/cadd.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: In file included from util/mathutils/complex_zero.c:2: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ -annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o model/run_network-function.o `test -f 'model/function.cpp' || echo './'`model/function.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/cabs.lo util/mathutils/cabs.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/cabs.c -fPIC -DPIC -o util/mathutils/.libs/cabs.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/cabs.c -o util/mathutils/cabs.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/cadd.lo util/mathutils/cadd.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/cadd.c -fPIC -DPIC -o util/mathutils/.libs/cadd.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/cadd.c -o util/mathutils/cadd.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/complex_zero.lo util/mathutils/complex_zero.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/complex_zero.c -fPIC -DPIC -o util/mathutils/.libs/complex_zero.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/complex_zero.c -o util/mathutils/complex_zero.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o pla/fEuler/run_network-fEulerSB_PL.o `test -f 'pla/fEuler/fEulerSB_PL.cpp' || echo './'`pla/fEuler/fEulerSB_PL.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/cmult.lo util/mathutils/cmult.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/cmult.c -fPIC -DPIC -o util/mathutils/.libs/cmult.o BUILDSTDERR: libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/cmIn file included from util/mathutils/cmult.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: In file included from util/mathutils/cconj.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: In file included from util/mathutils/copy_vector.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ ult.c -o util/mathutils/cmult.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/cconj.lo util/mathutils/cconj.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/cconj.c -fPIC -DPIC -o util/mathutils/.libs/cconj.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/cconj.c -o util/mathutils/cconj.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/copy_vector.lo util/mathutils/copy_vector.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/copy_vector.c -fPIC -DPIC -o util/mathutils/.libs/copy_vector.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/copy_vector.c -o util/mathutils/copy_vector.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' BUILDSTDERR: 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=/usrIn file included from util/mathutils/cprob.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: In file included from util/mathutils/csub.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ /lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o pla/fEuler/run_network-fEulerPreleapRB_TC.o `test -f 'pla/fEuler/fEulerPreleapRB_TC.cpp' || echo './'`pla/fEuler/fEulerPreleapRB_TC.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/cprob.lo util/mathutils/cprob.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/cprob.c -fPIC -DPIC -o util/mathutils/.libs/cprob.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/cprob.c -o util/mathutils/cprob.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o pla/eRungeKutta/run_network-eRungeKutta_preTC_RC_FG_sbPL.o `test -f 'pla/eRungeKutta/eRungeKutta_preTC_RC_FG_sbPL.cpp' || echo './'`pla/eRungeKutta/eRungeKutta_preTC_RC_FG_sbPL.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/csub.lo util/mathutils/csub.c BUILDSTDERR: libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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/rIn file included from util/mathutils/dotp.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ edhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/csub.c -fPIC -DPIC -o util/mathutils/.libs/csub.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/csub.c -o util/mathutils/csub.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o pla/eRungeKutta/run_network-eRungeKutta_preTC_RC_FG_rbPL.o `test -f 'pla/eRungeKutta/eRungeKutta_preTC_RC_FG_rbPL.cpp' || echo './'`pla/eRungeKutta/eRungeKutta_preTC_RC_FG_rbPL.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o pla/eRungeKutta/run_network-eRungeKutta_preTC_RC_FG_negPL.o `test -f 'pla/eRungeKutta/eRungeKutta_preTC_RC_FG_negPL.cpp' || echo './'`pla/eRungeKutta/eRungeKutta_preTC_RC_FG_negPL.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/dotp.lo util/mathutils/dotp.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/dotp.c -fPIC -DPIC -o util/mathutils/.libs/dotp.o BUILDSTDERR: libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-secuIn file included from util/mathutils/expi.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ rity -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/dotp.c -o util/mathutils/dotp.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o model/rateExpressions/run_network-rateMM.o `test -f 'model/rateExpressions/rateMM.cpp' || echo './'`model/rateExpressions/rateMM.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/expi.lo util/mathutils/expi.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/expi.c -fPIC -DPIC -o util/mathutils/.libs/expi.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/expi.c -o util/mathutils/expi.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o model/run_network-observable.o `test -f 'model/observable.cpp' || echo './'`model/observable.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o pla/eRungeKutta/run_network-eRungeKutta_postTC_RC_FG_sbPL.o `test -f 'pla/eRungeKutta/eRungeKutta_postTC_RC_FG_sbPL.cpp' || echo './'`pla/eRungeKutta/eRungeKutta_postTC_RC_FG_sbPL.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o pla/fEuler/run_network-fEulerRB_PL.o `test -f 'pla/fEuler/fEulerRB_PL.cpp' || echo './'`pla/fEuler/fEulerRB_PL.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o model/rateExpressions/run_network-rateElementary.o `test -f 'model/rateExpressions/rateElementary.cpp' || echo './'`model/rateExpressions/rateElementary.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/eigensystem.lo util/mathutils/eigensystem.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/eigensystem.c -fPIC -DPIC -o util/mathutils/.libs/eigensystem.o BUILDSTDERR: libtool: cIn file included from util/mathutils/eigensystem.c:1: BUILDSTDERR: util/mathutils/eigensystem.c: In function 'SYM_EIGENSYSTEM': BUILDSTDERR: util/mathutils/eigensystem.c:27:11: warning: implicit declaration of function 'dsyev' [-Wimplicit-function-declaration] BUILDSTDERR: 27 | FNAME(dsyev)(&jobz, &uplo, &N, A[0], &N, evals, work, &lwork, &info); BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:18:20: note: in definition of macro 'FNAME' BUILDSTDERR: 18 | #define FNAME(fun) fun BUILDSTDERR: | ^~~ BUILDSTDERR: util/mathutils/eigensystem.c: In function 'GEN_SYM_EIGENSYSTEM': BUILDSTDERR: util/mathutils/eigensystem.c:58:11: warning: implicit declaration of function 'dsygv' [-Wimplicit-function-declaration] BUILDSTDERR: 58 | FNAME(dsygv)(&itype, &jobz, &uplo, &N, A[0], &N, B[0], &N, evals, work, BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:18:20: note: in definition of macro 'FNAME' BUILDSTDERR: 18 | #define FNAME(fun) fun BUILDSTDERR: | ^~~ BUILDSTDERR: At top level: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: In file included from util/mathutils/herm_matrix_mult.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ ompile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/eigensystem.c -o util/mathutils/eigensystem.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o pla/eRungeKutta/run_network-eRungeKutta_postTC_RC_FG_rbPL.o `test -f 'pla/eRungeKutta/eRungeKutta_postTC_RC_FG_rbPL.cpp' || echo './'`pla/eRungeKutta/eRungeKutta_postTC_RC_FG_rbPL.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/herm_matrix_mult.lo util/mathutils/herm_matrix_mult.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/herm_matrix_mult.c -fPIC -DPIC -o util/mathutils/.libs/herm_matrix_mult.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/herm_matrix_mult.c -o util/mathutils/herm_matrix_mult.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/allocate.lo util/mathutils/allocate.c BUILDSTDERR: libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -O2 -gutil/mathutils/allocate.c: In function 'ALLOC_MATRIX': BUILDSTDERR: util/mathutils/allocate.c:9:20: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: 9 | register int i,j; BUILDSTDERR: | ^ BUILDSTDERR: util/mathutils/allocate.c: In function 'IALLOC_MATRIX': BUILDSTDERR: util/mathutils/allocate.c:100:20: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: 100 | register int i,j; BUILDSTDERR: | ^ BUILDSTDERR: util/mathutils/allocate.c: In function 'ZALLOC_MATRIX': BUILDSTDERR: util/mathutils/allocate.c:191:20: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: 191 | register int i,j; BUILDSTDERR: | ^ BUILDSTDERR: In file included from util/mathutils/allocate.c:1: BUILDSTDERR: At top level: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: In file included from util/mathutils/gram_schmidt.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/allocate.c -fPIC -DPIC -o util/mathutils/.libs/allocate.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/allocate.c -o util/mathutils/allocate.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/gram_schmidt.lo util/mathutils/gram_schmidt.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/gram_schmidt.c -fPIC -DPIC -o util/mathutils/.libs/gram_schmidt.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/gram_schmidt.c -o util/mathutils/gram_schmidt.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/icmult.lo util/mathutils/icmult.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/icmult.c -fPIC -DPIC -o util/mathutils/.libs/icmult.o BUILDSTDERR: libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIn file included from util/mathutils/icmult.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: In file included from util/mathutils/herm_matrix_vector_mult.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: In file included from util/mathutils/init.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ IBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/icmult.c -o util/mathutils/icmult.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/herm_matrix_vector_mult.lo util/mathutils/herm_matrix_vector_mult.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/herm_matrix_vector_mult.c -fPIC -DPIC -o util/mathutils/.libs/herm_matrix_vector_mult.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/herm_matrix_vector_mult.c -o util/mathutils/herm_matrix_vector_mult.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o util/run_network-misc.o `test -f 'util/misc.cpp' || echo './'`util/misc.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/init.lo util/mathutils/init.c BUILDSTDERR: libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -speIn file included from util/mathutils/matherr.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ cs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/init.c -fPIC -DPIC -o util/mathutils/.libs/init.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/init.c -o util/mathutils/init.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/matherr.lo util/mathutils/matherr.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/matherr.c -fPIC -DPIC -o util/mathutils/.libs/matherr.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/matherr.c -o util/mathutils/matherr.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/matrix_elt.lo util/mathutils/matrix_elt.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/matrix_elt.c -fPIC -DPIC -o util/mathutils/.libs/matrix_elt.o BUILDSTDERR: libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstacIn file included from util/mathutils/matrix_elt.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/linsolve.c: In function 'LINSOLVE': BUILDSTDERR: util/mathutils/linsolve.c:16:20: warning: unused variable 'j' [-Wunused-variable] BUILDSTDERR: 16 | register int i,j; BUILDSTDERR: | ^ BUILDSTDERR: util/mathutils/linsolve.c:16:18: warning: unused variable 'i' [-Wunused-variable] BUILDSTDERR: 16 | register int i,j; BUILDSTDERR: | ^ BUILDSTDERR: In file included from util/mathutils/linsolve.c:1: BUILDSTDERR: At top level: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: In file included from util/mathutils/matrix_add.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ krealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/matrix_elt.c -o util/mathutils/matrix_elt.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/linsolve.lo util/mathutils/linsolve.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/linsolve.c -fPIC -DPIC -o util/mathutils/.libs/linsolve.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/linsolve.c -o util/mathutils/linsolve.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/matrix_add.lo util/mathutils/matrix_add.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/matrix_add.c -fPIC -DPIC -o util/mathutils/.libs/matrix_add.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/matrix_add.c -o util/mathutils/matrix_add.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o pla/util/run_network-fixed_TC.o `test -f 'pla/util/fixed_TC.cpp' || echo './'`pla/util/fixed_TC.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o pla/util/run_network-g_Getter.o `test -f 'pla/util/g_Getter.cpp' || echo './'`pla/util/g_Getter.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o pla/eRungeKutta/util/run_network-butcherTableau.o `test -f 'pla/eRungeKutta/util/butcherTableau.cpp' || echo './'`pla/eRungeKutta/util/butcherTableau.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/matrix_mult.lo util/mathutils/matrix_mult.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/matrix_mult.c -fPIC -DPIC -o util/mathutils/.libs/matrix_mult.o BUILDSTDERR: libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/In file included from util/mathutils/matrix_mult.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: In file included from util/mathutils/matrix_sub.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ matrix_mult.c -o util/mathutils/matrix_mult.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o model/rateExpressions/run_network-rateHill.o `test -f 'model/rateExpressions/rateHill.cpp' || echo './'`model/rateExpressions/rateHill.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/matrix_sub.lo util/mathutils/matrix_sub.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/matrix_sub.c -fPIC -DPIC -o util/mathutils/.libs/matrix_sub.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/matrix_sub.c -o util/mathutils/matrix_sub.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/matrix_transpose.lo util/mathutils/matrix_transpose.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/matrix_transpose.c -fPIC -DPIC -o util/mathutils/.libs/matrix_transpose.o BUILDSTDERR: libtool: compile: gcc -DHAVE_CONFIn file included from util/mathutils/matrix_transpose.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: In file included from util/mathutils/matrix_vector_mult.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/normsq.c: In function 'NORMSQ': BUILDSTDERR: util/mathutils/normsq.c:13:12: warning: unused variable 'norm' [-Wunused-variable] BUILDSTDERR: 13 | double norm; BUILDSTDERR: | ^~~~ BUILDSTDERR: In file included from util/mathutils/normsq.c:1: BUILDSTDERR: At top level: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ IG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/matrix_transpose.c -o util/mathutils/matrix_transpose.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o model/rateExpressions/run_network-rateMuParser.o `test -f 'model/rateExpressions/rateMuParser.cpp' || echo './'`model/rateExpressions/rateMuParser.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/matrix_vector_mult.lo util/mathutils/matrix_vector_mult.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/matrix_vector_mult.c -fPIC -DPIC -o util/mathutils/.libs/matrix_vector_mult.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/matrix_vector_mult.c -o util/mathutils/matrix_vector_mult.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/normsq.lo util/mathutils/normsq.c BUILDSTDERR: libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -WIn file included from util/mathutils/rcmult.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: In file included from util/mathutils/random.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ p,-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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/normsq.c -fPIC -DPIC -o util/mathutils/.libs/normsq.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/normsq.c -o util/mathutils/normsq.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/rcmult.lo util/mathutils/rcmult.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/rcmult.c -fPIC -DPIC -o util/mathutils/.libs/rcmult.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/rcmult.c -o util/mathutils/rcmult.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/random.lo util/mathutils/random.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/random.c -fPIC -DPIC -o util/mathutils/.libs/random.o BUILDSTDERR: libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specsIn file included from util/mathutils/integration.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: In file included from util/mathutils/project.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/rect_transpose.c: In function 'RECT_TRANSPOSE': BUILDSTDERR: util/mathutils/rect_transpose.c:5:26: warning: unused variable 'Atptr' [-Wunused-variable] BUILDSTDERR: 5 | double **At, *Aptr, *Atptr; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/rect_transpose.c:5:19: warning: unused variable 'Aptr' [-Wunused-variable] BUILDSTDERR: 5 | double **At, *Aptr, *Atptr; BUILDSTDERR: | ^~~~ BUILDSTDERR: In file included from util/mathutils/rect_transpose.c:1: BUILDSTDERR: At top level: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ =/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/random.c -o util/mathutils/random.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/integration.lo util/mathutils/integration.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/integration.c -fPIC -DPIC -o util/mathutils/.libs/integration.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/integration.c -o util/mathutils/integration.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/project.lo util/mathutils/project.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/project.c -fPIC -DPIC -o util/mathutils/.libs/project.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/project.c -o util/mathutils/project.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/rect_transpose.lo util/mathutils/rect_transpose.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/rect_transpose.c -fPIC -DPIC -o util/mathutils/.libs/rect_transpose.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/rect_transpose.c -o util/mathutils/rect_transpose.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/scale_vector.lo util/mathutils/scale_vector.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/scale_vector.c -fPIC -DPIC -o util/mathutils/.libs/scale_vector.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/scale_vector.c -o util/mathutils/scale_vector.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/norm.lo util/mathutils/norm.c BUILDSTDERR: libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -In file included from util/mathutils/scale_vector.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/norm.c: In function 'NORM': BUILDSTDERR: util/mathutils/norm.c:14:12: warning: unused variable 'norm' [-Wunused-variable] BUILDSTDERR: 14 | double norm; BUILDSTDERR: | ^~~~ BUILDSTDERR: In file included from util/mathutils/norm.c:1: BUILDSTDERR: At top level: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: In file included from util/mathutils/matrixexp.c:5: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/norm.c -fPIC -DPIC -o util/mathutils/.libs/norm.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/norm.c -o util/mathutils/norm.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/matrixexp.lo util/mathutils/matrixexp.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/matrixexp.c -fPIC -DPIC -o util/mathutils/.libs/matrixexp.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/matrixexp.c -o util/mathutils/matrixexp.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o model/rateExpressions/run_network-rateSaturation.o `test -f 'model/rateExpressions/rateSaturation.cpp' || echo './'`model/rateExpressions/rateSaturation.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' BUILDSTDERR: 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-protectoIn file included from util/mathutils/sum_vector.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ r-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o util/run_network-conversion.o `test -f 'util/conversion.cpp' || echo './'`util/conversion.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o pla/eRungeKutta/base/run_network-eRungeKutta_TC_RC_FG_sbPL.o `test -f 'pla/eRungeKutta/base/eRungeKutta_TC_RC_FG_sbPL.cpp' || echo './'`pla/eRungeKutta/base/eRungeKutta_TC_RC_FG_sbPL.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/sum_vector.lo util/mathutils/sum_vector.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/sum_vector.c -fPIC -DPIC -o util/mathutils/.libs/sum_vector.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/sum_vector.c -o util/mathutils/sum_vector.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/sym_matrix_mult.lo util/mathutils/sym_matrix_mult.c BUILDSTDERR: libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -WIn file included from util/mathutils/sym_matrix_mult.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: In file included from util/mathutils/sym_linsolve.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ p,-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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/sym_matrix_mult.c -fPIC -DPIC -o util/mathutils/.libs/sym_matrix_mult.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/sym_matrix_mult.c -o util/mathutils/sym_matrix_mult.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/sym_linsolve.lo util/mathutils/sym_linsolve.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/sym_linsolve.c -fPIC -DPIC -o util/mathutils/.libs/sym_linsolve.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/sym_linsolve.c -o util/mathutils/sym_linsolve.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/sym_matrix_vector_mult.lo util/mathutils/sym_matrix_vector_mult.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/sym_matrix_vector_mult.c -fPIC -DPIC -o util/mathutils/.libs/sym_matrix_vector_mult.o BUILDSTDERR: libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,In file included from util/mathutils/sym_matrix_vector_mult.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: In file included from util/mathutils/sympos_linsolve.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: In file included from util/mathutils/roots.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/roots.c: In function 'ROOT_FIND': BUILDSTDERR: util/mathutils/roots.c:69:17: warning: 'e' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: 69 | min2=fabs(e*q); BUILDSTDERR: | ~^~ -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/sym_matrix_vector_mult.c -o util/mathutils/sym_matrix_vector_mult.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/sympos_linsolve.lo util/mathutils/sympos_linsolve.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/sympos_linsolve.c -fPIC -DPIC -o util/mathutils/.libs/sympos_linsolve.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/sympos_linsolve.c -o util/mathutils/sympos_linsolve.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/roots.lo util/mathutils/roots.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/roots.c -fPIC -DPIC -o util/mathutils/.libs/roots.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/roots.c -o util/mathutils/roots.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' BUILDSTDERR: make: Entering directoryutil/mathutils/testdummy.c:3:1: warning: return type defaults to 'int' [-Wimplicit-int] BUILDSTDERR: 3 | main(){ BUILDSTDERR: | ^~~~ BUILDSTDERR: util/mathutils/testdummy.c: In function 'main': BUILDSTDERR: util/mathutils/testdummy.c:5:9: warning: unused variable 'incx' [-Wunused-variable] BUILDSTDERR: 5 | int incx=1; BUILDSTDERR: | ^~~~ BUILDSTDERR: util/mathutils/testdummy.c:9:5: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 9 | scanf("%d", &n); BUILDSTDERR: | ^~~~~~~~~~~~~~~ BUILDSTDERR: util/mathutils/testdummy.c:15:2: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: 15 | scanf("%lf", x+i); BUILDSTDERR: | ^~~~~~~~~~~~~~~~~ BUILDSTDERR: In file included from util/mathutils/testdummy.c:1: BUILDSTDERR: At top level: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o pla/eRungeKutta/base/run_network-eRungeKutta_TC_RC_FG_rbPL.o `test -f 'pla/eRungeKutta/base/eRungeKutta_TC_RC_FG_rbPL.cpp' || echo './'`pla/eRungeKutta/base/eRungeKutta_TC_RC_FG_rbPL.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/testdummy.lo util/mathutils/testdummy.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/testdummy.c -fPIC -DPIC -o util/mathutils/.libs/testdummy.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/testdummy.c -o util/mathutils/testdummy.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/test_transpose.lo util/mathutils/test_transpose.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/test_transpose.c -fPIC -DPIC -o util/mathutils/.libs/test_transpose.o BUILDSTDERR: libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-swutil/mathutils/test_transpose.c:3:1: warning: return type defaults to 'int' [-Wimplicit-int] BUILDSTDERR: 3 | main() BUILDSTDERR: | ^~~~ BUILDSTDERR: In file included from util/mathutils/test_transpose.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/testspline.c:7:1: warning: return type defaults to 'int' [-Wimplicit-int] BUILDSTDERR: 7 | main() BUILDSTDERR: | ^~~~ BUILDSTDERR: In file included from util/mathutils/testspline.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: In file included from util/mathutils/splines.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ itches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/test_transpose.c -o util/mathutils/test_transpose.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/testspline.lo util/mathutils/testspline.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/testspline.c -fPIC -DPIC -o util/mathutils/.libs/testspline.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/testspline.c -o util/mathutils/testspline.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/splines.lo util/mathutils/splines.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/splines.c -fPIC -DPIC -o util/mathutils/.libs/splines.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/splines.c -o util/mathutils/splines.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' BUILDSTDERR: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I.In file included from util/mathutils/vector_dist.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ ./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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o pla/eRungeKutta/base/run_network-eRungeKutta_TC_RC_FG_PL.o `test -f 'pla/eRungeKutta/base/eRungeKutta_TC_RC_FG_PL.cpp' || echo './'`pla/eRungeKutta/base/eRungeKutta_TC_RC_FG_PL.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/vector_dist.lo util/mathutils/vector_dist.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/vector_dist.c -fPIC -DPIC -o util/mathutils/.libs/vector_dist.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/vector_dist.c -o util/mathutils/vector_dist.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o model/reactions/run_network-elementaryRxn.o `test -f 'model/reactions/elementaryRxn.cpp' || echo './'`model/reactions/elementaryRxn.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' BUILDSTDERR: /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tablIn file included from util/mathutils/zdotc.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ es -fstack-clash-protection -fcf-protection -c -o util/mathutils/zdotc.lo util/mathutils/zdotc.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/zdotc.c -fPIC -DPIC -o util/mathutils/.libs/zdotc.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/zdotc.c -o util/mathutils/zdotc.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o model/reactions/run_network-michaelisMentenRxn.o `test -f 'model/reactions/michaelisMentenRxn.cpp' || echo './'`model/reactions/michaelisMentenRxn.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o model/reactions/run_network-functionalRxn.o `test -f 'model/reactions/functionalRxn.cpp' || echo './'`model/reactions/functionalRxn.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/zmatrix_add.lo util/mathutils/zmatrix_add.c BUILDSTDERR: libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -In file included from util/mathutils/zmatrix_add.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: In file included from util/mathutils/vector_add.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/zmatrix_add.c -fPIC -DPIC -o util/mathutils/.libs/zmatrix_add.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/zmatrix_add.c -o util/mathutils/zmatrix_add.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/vector_add.lo util/mathutils/vector_add.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/vector_add.c -fPIC -DPIC -o util/mathutils/.libs/vector_add.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/vector_add.c -o util/mathutils/vector_add.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/zcopy_vector.lo util/mathutils/zcopy_vector.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/zcopy_vector.c -fPIC -DPIC -o util/mathutils/.libs/zcopy_vector.o BUILDSTDERR: libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronoIn file included from util/mathutils/zcopy_vector.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: In file included from util/mathutils/zmatrix_mult.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: In file included from util/mathutils/zdotu.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ us-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/zcopy_vector.c -o util/mathutils/zcopy_vector.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/zmatrix_mult.lo util/mathutils/zmatrix_mult.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/zmatrix_mult.c -fPIC -DPIC -o util/mathutils/.libs/zmatrix_mult.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/zmatrix_mult.c -o util/mathutils/zmatrix_mult.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/zdotu.lo util/mathutils/zdotu.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/zdotu.c -fPIC -DPIC -o util/mathutils/.libs/zdotu.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/zdotu.c -o util/mathutils/zdotu.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' BUILDSTDERR: 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 -fstackIn file included from util/mathutils/znormsq.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/minimum.c: In function 'MIN_BRACKET': BUILDSTDERR: util/mathutils/minimum.c:17:26: warning: unused variable 'dum' [-Wunused-variable] BUILDSTDERR: 17 | double ulim,u,r,q,fu,dum; BUILDSTDERR: | ^~~ BUILDSTDERR: In file included from util/mathutils/minimum.c:3: BUILDSTDERR: At top level: BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/minimum.c: In function 'MIN_FIND': BUILDSTDERR: util/mathutils/minimum.c:117:31: warning: 'e' may be used uninitialized in this function [-Wmaybe-uninitialized] BUILDSTDERR: 117 | if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) BUILDSTDERR: | ~~~~~^~~~~~ -protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o model/reactions/run_network-hillRxn.o `test -f 'model/reactions/hillRxn.cpp' || echo './'`model/reactions/hillRxn.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/znormsq.lo util/mathutils/znormsq.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/znormsq.c -fPIC -DPIC -o util/mathutils/.libs/znormsq.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/znormsq.c -o util/mathutils/znormsq.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/minimum.lo util/mathutils/minimum.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/minimum.c -fPIC -DPIC -o util/mathutils/.libs/minimum.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/minimum.c -o util/mathutils/minimum.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' BUILDSTDERR: make: EnIn file included from util/mathutils/zmatrix_sub.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: In file included from util/mathutils/znorm.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ tering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/zmatrix_sub.lo util/mathutils/zmatrix_sub.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/zmatrix_sub.c -fPIC -DPIC -o util/mathutils/.libs/zmatrix_sub.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/zmatrix_sub.c -o util/mathutils/zmatrix_sub.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/znorm.lo util/mathutils/znorm.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/znorm.c -fPIC -DPIC -o util/mathutils/.libs/znorm.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/znorm.c -o util/mathutils/znorm.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' BUILDSTDERR: /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/runge-kuttIn file included from util/mathutils/runge-kutta.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: In file included from util/mathutils/zrscale_vector.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: In file included from util/mathutils/zsum_vector.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ a.lo util/mathutils/runge-kutta.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/runge-kutta.c -fPIC -DPIC -o util/mathutils/.libs/runge-kutta.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/runge-kutta.c -o util/mathutils/runge-kutta.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/zrscale_vector.lo util/mathutils/zrscale_vector.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/zrscale_vector.c -fPIC -DPIC -o util/mathutils/.libs/zrscale_vector.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/zrscale_vector.c -o util/mathutils/zrscale_vector.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/zsum_vector.lo util/mathutils/zsum_vector.c BUILDSTDERR: libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/zsum_vector.c -fPIC -DPIC -o util/mathutils/.libs/zsum_vIn file included from util/mathutils/zmatrix_transpose.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ ector.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/zsum_vector.c -o util/mathutils/zsum_vector.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/zmatrix_transpose.lo util/mathutils/zmatrix_transpose.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/zmatrix_transpose.c -fPIC -DPIC -o util/mathutils/.libs/zmatrix_transpose.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/zmatrix_transpose.c -o util/mathutils/zmatrix_transpose.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/zmatrix_vector_mult.lo util/mathutils/zmatrix_vector_mult.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/zmatrix_vector_mult.c -fPIC -DPIC -o util/mathutils/.libs/zmatrix_vector_mult.o BUILDSTDERR: libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/zmatrix_vector_mult.c -o util/matIn file included from util/mathutils/zmatrix_vector_mult.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: In file included from util/mathutils/zsym_linsolve.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: In file included from util/mathutils/zscale_vector.c:1: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ hutils/zmatrix_vector_mult.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/zsym_linsolve.lo util/mathutils/zsym_linsolve.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/zsym_linsolve.c -fPIC -DPIC -o util/mathutils/.libs/zsym_linsolve.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/zsym_linsolve.c -o util/mathutils/zsym_linsolve.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/zscale_vector.lo util/mathutils/zscale_vector.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/zscale_vector.c -fPIC -DPIC -o util/mathutils/.libs/zscale_vector.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/zscale_vector.c -o util/mathutils/zscale_vector.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' BUILDSTDERR: /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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-hardenutil/mathutils/testgram.c:3:1: warning: return type defaults to 'int' [-Wimplicit-int] BUILDSTDERR: 3 | main(int argc, char *argv[]){ BUILDSTDERR: | ^~~~ BUILDSTDERR: util/mathutils/testgram.c: In function 'main': BUILDSTDERR: util/mathutils/testgram.c:7:63: warning: unused variable 'V' [-Wunused-variable] BUILDSTDERR: 7 | double **A, **At, **G, **Gt, **GtG, **U, **Ut, **UtU, *w, **V, norm; BUILDSTDERR: | ^ BUILDSTDERR: util/mathutils/testgram.c:7:58: warning: unused variable 'w' [-Wunused-variable] BUILDSTDERR: 7 | double **A, **At, **G, **Gt, **GtG, **U, **Ut, **UtU, *w, **V, norm; BUILDSTDERR: | ^ BUILDSTDERR: util/mathutils/testgram.c:7:52: warning: unused variable 'UtU' [-Wunused-variable] BUILDSTDERR: 7 | double **A, **At, **G, **Gt, **GtG, **U, **Ut, **UtU, *w, **V, norm; BUILDSTDERR: | ^~~ BUILDSTDERR: util/mathutils/testgram.c:7:46: warning: unused variable 'Ut' [-Wunused-variable] BUILDSTDERR: 7 | double **A, **At, **G, **Gt, **GtG, **U, **Ut, **UtU, *w, **V, norm; BUILDSTDERR: | ^~ BUILDSTDERR: util/mathutils/testgram.c:5:7: warning: unused variable 'nr' [-Wunused-variable] BUILDSTDERR: 5 | int nr, n_run; BUILDSTDERR: | ^~ BUILDSTDERR: In file included from util/mathutils/testgram.c:1: BUILDSTDERR: At top level: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/testsvd.c:3:1: warning: return type defaults to 'int' [-Wimplicit-int] BUILDSTDERR: 3 | main(int argc, char *argv[]){ BUILDSTDERR: | ^~~~ BUILDSTDERR: util/mathutils/testsvd.c: In function 'main': BUILDSTDERR: util/mathutils/testsvd.c:7:28: warning: unused variable 'GtG' [-Wunused-variable] BUILDSTDERR: 7 | double **A, **G, **Gt, **GtG, **U, **Ut, **UtU, *w, **V, norm; BUILDSTDERR: | ^~~ BUILDSTDERR: util/mathutils/testsvd.c:7:22: warning: unused variable 'Gt' [-Wunused-variable] BUILDSTDERR: 7 | double **A, **G, **Gt, **GtG, **U, **Ut, **UtU, *w, **V, norm; BUILDSTDERR: | ^~ BUILDSTDERR: util/mathutils/testsvd.c:7:17: warning: unused variable 'G' [-Wunused-variable] BUILDSTDERR: 7 | double **A, **G, **Gt, **GtG, **U, **Ut, **UtU, *w, **V, norm; BUILDSTDERR: | ^ BUILDSTDERR: In file included from util/mathutils/testsvd.c:1: BUILDSTDERR: At top level: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ ed-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/testgram.lo util/mathutils/testgram.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/testgram.c -fPIC -DPIC -o util/mathutils/.libs/testgram.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/testgram.c -o util/mathutils/testgram.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/testsvd.lo util/mathutils/testsvd.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/testsvd.c -fPIC -DPIC -o util/mathutils/.libs/testsvd.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/testsvd.c -o util/mathutils/testsvd.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o model/reactions/run_network-bioNetGenRxn.o `test -f 'model/reactions/bioNetGenRxn.cpp' || echo './'`model/reactions/bioNetGenRxn.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' BUILDSTDERR: make: Entering directory '/bIn file included from util/mathutils/svd.c:2: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ uilddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o pla/run_network-PLA.o `test -f 'pla/PLA.cpp' || echo './'`pla/PLA.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o model/reactions/run_network-saturationRxn.o `test -f 'model/reactions/saturationRxn.cpp' || echo './'`model/reactions/saturationRxn.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/svd.lo util/mathutils/svd.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/svd.c -fPIC -DPIC -o util/mathutils/.libs/svd.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/svd.c -o util/mathutils/svd.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' BUILDSTDERR: 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unutil/mathutils/testutils.c:6:1: warning: return type defaults to 'int' [-Wimplicit-int] BUILDSTDERR: 6 | main (int argc, char *argv[]) BUILDSTDERR: | ^~~~ BUILDSTDERR: util/mathutils/testutils.c: In function 'main': BUILDSTDERR: util/mathutils/testutils.c:15:12: warning: unused variable 'z1' [-Wunused-variable] BUILDSTDERR: 15 | dcomplex z1; BUILDSTDERR: | ^~ BUILDSTDERR: util/mathutils/testutils.c:10:7: warning: unused variable 'seed' [-Wunused-variable] BUILDSTDERR: 10 | int seed; BUILDSTDERR: | ^~~~ BUILDSTDERR: util/mathutils/testutils.c:8:11: warning: unused variable 'k' [-Wunused-variable] BUILDSTDERR: 8 | int i,j,k; BUILDSTDERR: | ^ BUILDSTDERR: In file included from util/mathutils/testutils.c:2: BUILDSTDERR: At top level: BUILDSTDERR: util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] BUILDSTDERR: 364 | static double dswap; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] BUILDSTDERR: 359 | static int imarg1, imarg2; BUILDSTDERR: | ^~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] BUILDSTDERR: 356 | static double marg1, marg2; BUILDSTDERR: | ^~~~~ BUILDSTDERR: util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 354 | static int isqrarg; BUILDSTDERR: | ^~~~~~~ BUILDSTDERR: util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] BUILDSTDERR: 352 | static double sqrarg; BUILDSTDERR: | ^~~~~~ wind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o pla/eRungeKutta/util/run_network-aEff_Calculator.o `test -f 'pla/eRungeKutta/util/aEff_Calculator.cpp' || echo './'`pla/eRungeKutta/util/aEff_Calculator.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o model/run_network-reaction.o `test -f 'model/reaction.cpp' || echo './'`model/reaction.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o util/mathutils/testutils.lo util/mathutils/testutils.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/testutils.c -fPIC -DPIC -o util/mathutils/.libs/testutils.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c util/mathutils/testutils.c -o util/mathutils/testutils.o >/dev/null 2>&1 make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CC --mode=link gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o libmathutils.la util/mathutils/allocate.lo util/mathutils/cabs.lo util/mathutils/cadd.lo util/mathutils/cconj.lo util/mathutils/cmult.lo util/mathutils/complex_zero.lo util/mathutils/copy_vector.lo util/mathutils/cprob.lo util/mathutils/csub.lo util/mathutils/dotp.lo util/mathutils/eigensystem.lo util/mathutils/expi.lo util/mathutils/gram_schmidt.lo util/mathutils/herm_matrix_mult.lo util/mathutils/herm_matrix_vector_mult.lo util/mathutils/icmult.lo util/mathutils/init.lo util/mathutils/integration.lo util/mathutils/linsolve.lo util/mathutils/matherr.lo util/mathutils/matrix_add.lo util/mathutils/matrix_elt.lo util/mathutils/matrix_mult.lo util/mathutils/matrix_sub.lo util/mathutils/matrix_transpose.lo util/mathutils/matrix_vector_mult.lo util/mathutils/matrixexp.lo util/mathutils/minimum.lo util/mathutils/norm.lo util/mathutils/normsq.lo util/mathutils/project.lo util/mathutils/random.lo util/mathutils/rcmult.lo util/mathutils/rect_transpose.lo util/mathutils/roots.lo util/mathutils/runge-kutta.lo util/mathutils/scale_vector.lo util/mathutils/splines.lo util/mathutils/sum_vector.lo util/mathutils/svd.lo util/mathutils/sym_linsolve.lo util/mathutils/sym_matrix_mult.lo util/mathutils/sym_matrix_vector_mult.lo util/mathutils/sympos_linsolve.lo util/mathutils/test_transpose.lo util/mathutils/testdummy.lo util/mathutils/testgram.lo util/mathutils/testspline.lo util/mathutils/testsvd.lo util/mathutils/testutils.lo util/mathutils/vector_add.lo util/mathutils/vector_dist.lo util/mathutils/zcopy_vector.lo util/mathutils/zdotc.lo util/mathutils/zdotu.lo util/mathutils/zmatrix_add.lo util/mathutils/zmatrix_mult.lo util/mathutils/zmatrix_sub.lo util/mathutils/zmatrix_transpose.lo util/mathutils/zmatrix_vector_mult.lo util/mathutils/znorm.lo util/mathutils/znormsq.lo util/mathutils/zrscale_vector.lo util/mathutils/zscale_vector.lo util/mathutils/zsum_vector.lo util/mathutils/zsym_linsolve.lo libtool: link: ar cru .libs/libmathutils.a util/mathutils/.libs/allocate.o util/mathutils/.libs/cabs.o util/mathutils/.libs/cadd.o util/mathutils/.libs/cconj.o util/mathutils/.libs/cmult.o util/mathutils/.libs/complex_zero.o util/mathutils/.libs/copy_vector.o util/mathutils/.libs/cprob.o util/mathutils/.libs/csub.o util/mathutils/.libs/dotp.o util/mathutils/.libs/eigensystem.o util/mathutils/.libs/expi.o util/mathutils/.libs/gram_schmidt.o util/mathutils/.libs/herm_matrix_mult.o util/mathutils/.libs/herm_matrix_vector_mult.o util/mathutils/.libs/icmult.o util/mathutils/.libs/init.o util/mathutils/.libs/integration.o util/mathutils/.libs/linsolve.o util/mathutils/.libs/matherr.o util/mathutils/.libs/matrix_add.o util/mathutils/.libs/matrix_elt.o util/mathutils/.libs/matrix_mult.o util/mathutils/.libs/matrix_sub.o util/mathutils/.libs/matrix_transpose.o util/mathutils/.libs/matrix_vector_mult.o util/mathutils/.libs/matrixexp.o util/mathutils/.libs/minimum.o util/mathutils/.libs/norm.o util/mathutils/.libs/normsq.o util/mathutils/.libs/project.o util/mathutils/.libs/random.o util/mathutils/.libs/rcmult.o util/mathutils/.libs/rect_transpose.o util/mathutils/.libs/roots.o util/mathutils/.libs/runge-kutta.o util/mathutils/.libs/scale_vector.o util/mathutils/.libs/splines.o util/mathutils/.libs/sum_vector.o util/mathutils/.libs/svd.o util/mathutils/.libs/sym_linsolve.o util/mathutils/.libs/sym_matrix_mult.o util/mathutils/.libs/sym_matrix_vector_mult.o util/mathutils/.libs/sympos_linsolve.o util/mathutils/.libs/test_transpose.o util/mathutils/.libs/testdummy.o util/mathutils/.libs/testgram.o util/mathutils/.libs/testspline.o util/mathutils/.libs/testsvd.o util/mathutils/.libs/testutils.o util/mathutils/.libs/vector_add.o util/mathutils/.libs/vector_dist.o util/mathutils/.libs/zcopy_vector.o util/mathutils/.libs/zdotc.o util/mathutils/.libs/zdotu.o util/mathutils/.libs/zmatrix_add.o util/mathutils/.libs/zmatrix_mult.o util/mathutils/.libs/zmatrix_sub.o util/mathutils/.libs/zmatrix_transpose.o util/mathutils/.libs/zmatrix_vector_mult.o util/mathutils/.libs/znorm.o util/mathutils/.libs/znormsq.o util/mathutils/.libs/zrscale_vector.o util/mathutils/.libs/zscale_vector.o util/mathutils/.libs/zsum_vector.o util/mathutils/.libs/zsym_linsolve.o libtool: link: ranlib .libs/libmathutils.a libtool: link: ( cd ".libs" && rm -f "libmathutils.la" && ln -s "../libmathutils.la" "libmathutils.la" ) make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o run_network-run_network.o `test -f 'run_network.cpp' || echo './'`run_network.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o run_network-network.o `test -f 'network.cpp' || echo './'`network.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -c -o run_network-network3.o `test -f 'network3.cpp' || echo './'`network3.cpp make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /bin/sh ../libtool --tag=CXX --mode=link g++ -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o run_network run_network-network3.o run_network-network.o run_network-run_network.o model/run_network-function.o model/run_network-observable.o model/run_network-rateExpression.o model/run_network-reaction.o model/run_network-simpleSpecies.o model/rateExpressions/run_network-rateElementary.o model/rateExpressions/run_network-rateHill.o model/rateExpressions/run_network-rateMM.o model/rateExpressions/run_network-rateMuParser.o model/rateExpressions/run_network-rateSaturation.o model/reactions/run_network-bioNetGenRxn.o model/reactions/run_network-elementaryRxn.o model/reactions/run_network-functionalRxn.o model/reactions/run_network-hillRxn.o model/reactions/run_network-michaelisMentenRxn.o model/reactions/run_network-saturationRxn.o pla/run_network-PLA.o pla/base/run_network-firingGenerator.o pla/base/run_network-postleapChecker.o pla/base/run_network-rxnClassifier.o pla/base/run_network-tauCalculator.o pla/eRungeKutta/run_network-eRungeKutta_postTC_RC_FG_rbPL.o pla/eRungeKutta/run_network-eRungeKutta_postTC_RC_FG_sbPL.o pla/eRungeKutta/run_network-eRungeKutta_preTC_RC_FG_negPL.o pla/eRungeKutta/run_network-eRungeKutta_preTC_RC_FG_rbPL.o pla/eRungeKutta/run_network-eRungeKutta_preTC_RC_FG_sbPL.o pla/eRungeKutta/base/run_network-eRungeKutta_TC_RC_FG_PL.o pla/eRungeKutta/base/run_network-eRungeKutta_TC_RC_FG_rbPL.o pla/eRungeKutta/base/run_network-eRungeKutta_TC_RC_FG_sbPL.o pla/eRungeKutta/util/run_network-aEff_Calculator.o pla/eRungeKutta/util/run_network-binomialCorrector_RK.o pla/eRungeKutta/util/run_network-butcherTableau.o pla/fEuler/run_network-fEuler_FG.o pla/fEuler/run_network-fEulerPreleapRB_TC.o pla/fEuler/run_network-fEulerPreleapSB_TC.o pla/fEuler/run_network-fEulerRB_PL.o pla/fEuler/run_network-fEulerRB_TC_PL.o pla/fEuler/run_network-fEuler_RC.o pla/fEuler/run_network-fEulerSB_PL.o pla/fEuler/run_network-fEulerSB_TC_PL.o pla/util/run_network-g_Getter.o pla/util/run_network-negPopChecker.o pla/util/run_network-preleap_TC.o pla/util/run_network-rbChecker.o pla/util/run_network-sbChecker.o pla/util/run_network-fixed_TC.o util/run_network-conversion.o util/run_network-rand.o util/MTrand/run_network-mtrand.o util/rand2/run_network-rand2.o util/run_network-misc.o libmathutils.la ../cvode-2.6.0/src/nvec_ser/libsundials_nvecserial.la ../cvode-2.6.0/src/cvode/libsundials_cvode.la -lmuparser BUILDSTDERR: libtool: link: g++ -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Wno-unused-variable -Wno-unused-function -Wno-unused-but-set-variable -Wno-maybe-uninitialized -Wl,-z -Wl,relro -Wl,--as-needed -Wl,-z -Wl,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o run_network run_network-network3.o run_network-network.o run_network-run_network.o model/run_network-function.o model/run_network-observable.o model/run_network-rateExpression.o model/run_network-reaction.o model/run_network-simpleSpecies.o model/rateExpressions/run_network-rateElementary.o model/rateExpressions/run_network-rateHill.o model/rateExpressions/run_network-rateMM.o model/rateExpressions/run_network-rateMuParser.o model/rateExpressions/run_network-rateSaturation.o model/reactions/run_network-bioNetGenRxn.o model/reactions/run_network-elementaryRxn.o model/reactions/run_network-functionalRxn.o model/reactions/run_network-hillRxn.o model/reactions/run_network-michaelisMentenRxn.o model/reactions/run_network-saturationRxn.o pla/run_network-PLA.o pla/base/run_network-firingGenerator.o pla/base/run_network-postleapChecker.o pla/base/run_network-rxnClassifier.o pla/base/run_network-tauCalculator.o pla/eRungeKutta/run_network-eRungeKutta_postTC_RC_FG_rbPL.o pla/eRungeKutta/run_network-eRungeKutta_postTC_RC_FG_sbPL.o pla/eRungeKutta/run_network-eRungeKutta_preTC_RC_FG_negPL.o pla/eRungeKutta/run_network-eRungeKutta_preTC_RC_FG_rbPL.o pla/eRungeKutta/run_network-eRungeKutta_preTC_RC_FG_sbPL.o pla/eRungeKutta/base/run_network-eRungeKutta_TC_RC_FG_PL.o pla/eRungeKutta/base/run_network-eRungeKutta_TC_RC_FG_rbPL.o pla/eRungeKutta/base/run_network-eRungeKutta_TC_RC_FG_sbPL.o pla/eRungeKutta/util/run_network-aEff_Calculator.o pla/eRungeKutta/util/run_network-binomialCorrector_RK.o pla/eRungeKutta/util/run_network-butcherTableau.o pla/fEuler/run_network-fEuler_FG.o pla/fEuler/run_network-fEulerPreleapRB_TC.o pla/fEuler/run_network-fEulerPreleapSB_TC.o pla/fEuler/run_network-fEulerRB_PL.o pla/fEuler/run_network-fEulerRB_TC_PL.o pla/fEuler/run_network-fEuler_RC.o pla/fEuler/run_network-fEulerSB_PL.o pla/fEuler/run_network-fEulerSB_TC_PL.o pla/util/run_ne+ popd + RPM_EC=0 BUILDSTDERR: ++ jobs -p + exit 0 twork-g_Getter.o pla/util/run_network-negPopChecker.o pla/util/run_network-preleap_TC.o pla/util/run_network-rbChecker.o pla/util/run_network-sbChecker.o pla/util/run_network-fixed_TC.o util/run_network-conversion.o util/run_network-rand.o util/MTrand/run_network-mtrand.o util/rand2/run_network-rand2.o util/run_network-misc.o ./.libs/libmathutils.a ../cvode-2.6.0/src/nvec_ser/.libs/libsundials_nvecserial.a ../cvode-2.6.0/src/cvode/.libs/libsundials_cvode.a -lm -lmuparser make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' ~/build/BUILD/bionetgen-2.5.0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.B8vbg5 + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/bionetgen-2.5.0-3.fc31.i386 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/bionetgen-2.5.0-3.fc31.i386 BUILDSTDERR: ++ dirname /builddir/build/BUILDROOT/bionetgen-2.5.0-3.fc31.i386 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/bionetgen-2.5.0-3.fc31.i386 + cd bionetgen-2.5.0 + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/bionetgen-2.5.0-3.fc31.i386 'INSTALL=/usr/bin/install -p' -C bionetgen-BioNetGen-2.5.0/bng2/Network3/src + mkdir -vp /builddir/build/BUILDROOT/bionetgen-2.5.0-3.fc31.i386/usr/share/perl5/vendor_perl/BioNetGen + cp -r bionetgen-BioNetGen-2.5.0/bng2/Perl2 /builddir/build/BUILDROOT/bionetgen-2.5.0-3.fc31.i386/usr/share/perl5/vendor_perl/BioNetGen/ + cp -r bionetgen-BioNetGen-2.5.0/bng2/BNG2.pl /builddir/build/BUILDROOT/bionetgen-2.5.0-3.fc31.i386/usr/share/perl5/vendor_perl/BioNetGen/ + cp -a bionetgen-BioNetGen-2.5.0/bng2/Models2 /builddir/build/BUILDROOT/bionetgen-2.5.0-3.fc31.i386/usr/share/perl5/vendor_perl/BioNetGen/ + rm -f /builddir/build/BUILDROOT/bionetgen-2.5.0-3.fc31.i386/usr/share/perl5/vendor_perl/BioNetGen/Models2/bin/run_network_i386-linux + rm -f /builddir/build/BUILDROOT/bionetgen-2.5.0-3.fc31.i386/usr/share/perl5/vendor_perl/BioNetGen/Models2/run_network + /usr/lib/rpm/find-debuginfo.sh -j48 --strict-build-id -m -i --build-id-seed 2.5.0-3.fc31 --unique-debug-suffix -2.5.0-3.fc31.i386 --unique-debug-src-base bionetgen-2.5.0-3.fc31.i386 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/bionetgen-2.5.0 BUILDSTDERR: 1829 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1 0 + /usr/lib/rpm/brp-python-hardlink + /usr/lib/rpm/redhat/brp-mangle-shebangs make: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/bionetgen-2.5.0-3.fc31.i386/usr/bin' /bin/sh ../libtool --mode=install /usr/bin/install -p run_network '/builddir/build/BUILDROOT/bionetgen-2.5.0-3.fc31.i386/usr/bin' libtool: install: /usr/bin/install -p run_network /builddir/build/BUILDROOT/bionetgen-2.5.0-3.fc31.i386/usr/bin/run_network make[1]: Nothing to be done for 'install-data-am'. make[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' make: Leaving directory '/builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Network3/src' mkdir: created directory '/builddir/build/BUILDROOT/bionetgen-2.5.0-3.fc31.i386/usr/share' mkdir: created directory '/builddir/build/BUILDROOT/bionetgen-2.5.0-3.fc31.i386/usr/share/perl5' mkdir: created directory '/builddir/build/BUILDROOT/bionetgen-2.5.0-3.fc31.i386/usr/share/perl5/vendor_perl' mkdir: created directory '/builddir/build/BUILDROOT/bionetgen-2.5.0-3.fc31.i386/usr/share/perl5/vendor_perl/BioNetGen' explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/bionetgen-2.5.0-3.fc31.i386/usr/bin/run_network extracting debug info from /builddir/build/BUILDROOT/bionetgen-2.5.0-3.fc31.i386/usr/bin/run_network original debug info size: 10344kB, size after compression: 8076kB /usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.bxyRy6 + umask 022 + cd /builddir/build/BUILD + cd bionetgen-2.5.0 + pushd bionetgen-BioNetGen-2.5.0/bng2/Models2 + install -pm 755 ../Network3/src/run_network -D ./bin/run_network_i686-linux + install -pm 755 ../Network3/src/run_network -D ../bin/run_network_i686-linux + echo 'Running some tests ...' + ../BNG2.pl CaOscillate_Func.bngl CaOscillate_Sat.bngl catalysis.bngl egfr_net.bngl egfr_net_red.bngl egfr_path.bngl energy_example1.bngl fceri_ji.bngl test_continue.bngl BUILDSTDERR: Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Perl2/BNGAction.pm line 547. ~/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Models2 ~/build/BUILD/bionetgen-2.5.0 Running some tests ... BioNetGen version 2.5.0 Reading from file CaOscillate_Func.bngl (level 0) Read 17 parameters. Read 4 molecule types. Read 4 species. Read 4 observable(s). Read 8 reaction rule(s). ACTION: generate_network( CaOscillate_Func ) Iteration 0: 4 species 0 rxns 0.00e+00 CPU s Iteration 1: 4 species 8 rxns 0.00e+00 CPU s Cumulative CPU time for each rule Rule 1: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 2: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 3: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 4: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 5: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 6: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 7: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 8: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Total : 8 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Wrote network in net format to ./CaOscillate_Func.net. CPU TIME: generate_network 0.00 s. ACTION: simulate( method=>"cvode" ) Network simulation using cvode WARNING: writeFile(): Overwriting existing file ./CaOscillate_Func.net. Wrote network in net format to ./CaOscillate_Func.net. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/bin/run_network_i686-linux -o ./CaOscillate_Func -p cvode -a 1e-12 -r 1e-12 --cdat 1 --fdat 0 -v -g ./CaOscillate_Func.net ./CaOscillate_Func.net 0.1 200 [simulation PID is: 4058] run_network 3.0 Read 17 parameters from ./CaOscillate_Func.net Read 4 species from ./CaOscillate_Func.net Read 4 group(s) from ./CaOscillate_Func.net Read 4 function(s) from ./CaOscillate_Func.net Read 8 reaction(s) from ./CaOscillate_Func.net 8 reaction(s) have nonzero rate Initialization took 0.00 CPU seconds Propagating with cvode using dense LU time n_steps n_deriv_calls 0.00 0 0 0.10 717 850 0.20 741 879 0.30 765 904 0.40 790 930 0.50 814 960 0.60 838 985 0.70 863 1015 0.80 887 1040 0.90 912 1067 1.00 936 1099 1.10 961 1129 1.20 993 1171 1.30 1025 1207 1.40 1063 1260 1.50 1105 1310 1.60 1152 1368 1.70 1208 1436 1.80 1281 1523 1.90 1354 1611 2.00 1434 1704 2.10 1509 1792 2.20 1584 1871 2.30 1638 1932 2.40 1688 1984 2.50 1741 2047 2.60 1880 2222 2.70 2351 2772 2.80 2453 2892 2.90 2501 2946 3.00 2552 3007 3.10 2616 3078 3.20 2672 3143 3.30 2730 3208 3.40 2789 3271 3.50 2847 3333 3.60 2903 3395 3.70 2956 3464 3.80 3084 3620 3.90 3240 3799 4.00 3350 3920 4.10 3415 3990 4.20 3465 4046 4.30 3516 4103 4.40 3563 4151 4.50 3599 4196 4.60 3644 4249 4.70 3690 4304 4.80 3746 4371 4.90 3802 4441 5.00 3856 4498 5.10 3895 4545 5.20 3929 4585 5.30 3961 4618 5.40 3984 4642 5.50 4007 4671 5.60 4031 4697 5.70 4054 4722 5.80 4075 4750 5.90 4095 4773 6.00 4115 4795 6.10 4136 4821 6.20 4155 4841 6.30 4168 4854 6.40 4181 4872 6.50 4194 4885 6.60 4207 4898 6.70 4220 4911 6.80 4231 4927 6.90 4239 4935 7.00 4248 4945 7.10 4257 4954 7.20 4265 4963 7.30 4274 4972 7.40 4283 4982 7.50 4292 4996 7.60 4300 5004 7.70 4309 5015 7.80 4318 5024 7.90 4329 5044 8.00 4341 5059 8.10 4352 5077 8.20 4364 5090 8.30 4377 5108 8.40 4396 5135 8.50 4423 5174 8.60 4453 5207 8.70 4492 5256 8.80 4549 5327 8.90 4658 5465 9.00 4979 5847 9.10 5283 6181 9.20 5392 6300 9.30 5431 6345 9.40 5447 6363 9.50 5460 6376 9.60 5473 6389 9.70 5485 6405 9.80 5498 6418 9.90 5511 6431 10.00 5524 6445 10.10 5537 6458 10.20 5549 6475 10.30 5562 6489 10.40 5575 6502 10.50 5588 6516 10.60 5601 6534 10.70 5613 6547 10.80 5626 6562 10.90 5639 6575 11.00 5652 6590 11.10 5664 6608 11.20 5677 6621 11.30 5690 6638 11.40 5708 6656 11.50 5725 6674 11.60 5742 6696 11.70 5759 6714 11.80 5777 6733 11.90 5794 6755 12.00 5811 6773 12.10 5829 6791 12.20 5846 6809 12.30 5863 6832 12.40 5880 6851 12.50 5898 6871 12.60 5915 6894 12.70 5934 6915 12.80 5958 6940 12.90 5981 6969 13.00 6004 6994 13.10 6031 7026 13.20 6063 7065 13.30 6095 7100 13.40 6129 7145 13.50 6172 7196 13.60 6218 7252 13.70 6272 7316 13.80 6345 7398 13.90 6417 7485 14.00 6498 7583 14.10 6573 7669 14.20 6648 7748 14.30 6704 7810 14.40 6754 7867 14.50 6806 7929 14.60 6933 8086 14.70 7384 8613 14.80 7501 8742 14.90 7554 8801 15.00 7603 8864 15.10 7665 8933 15.20 7720 8999 15.30 7776 9062 15.40 7833 9124 15.50 7889 9184 15.60 7946 9241 15.70 8003 9314 15.80 8128 9466 15.90 8283 9646 16.00 8394 9768 16.10 8459 9838 16.20 8509 9895 16.30 8559 9951 16.40 8606 10003 16.50 8642 10044 16.60 8687 10097 16.70 8732 10151 16.80 8787 10212 16.90 8843 10286 17.00 8897 10344 17.10 8937 10391 17.20 8973 10433 17.30 9007 10468 17.40 9030 10495 17.50 9054 10522 17.60 9077 10547 17.70 9101 10577 17.80 9123 10602 17.90 9142 10625 18.00 9162 10651 18.10 9183 10673 18.20 9202 10697 18.30 9212 10712 18.40 9223 10723 18.50 9233 10734 18.60 9243 10744 18.70 9253 10754 18.80 9263 10764 18.90 9274 10779 19.00 9284 10789 19.10 9294 10799 19.20 9304 10809 19.30 9315 10820 19.40 9325 10830 19.50 9335 10845 19.60 9345 10855 19.70 9355 10866 19.80 9366 10877 19.90 9376 10889 20.00 9386 10908 Time course of concentrations written to file ./CaOscillate_Func.cdat. Time course of groups written to file ./CaOscillate_Func.gdat. Propagation took 2.00e-02 CPU seconds Program times: 0.02 CPU s 0.00 clock s Updating species concentrations from ./CaOscillate_Func.cdat CPU TIME: simulate 0.03 s. Finished processing file CaOscillate_Func.bngl. CPU TIME: total 0.04 s. BioNetGen version 2.5.0 Reading from file CaOscillate_Sat.bngl (level 0) Read 17 parameters. Read 4 molecule types. Read 4 species. Read 4 observable(s). Read 8 reaction rule(s). ACTION: generate_network( CaOscillate_Sat ) Iteration 0: 4 species 0 rxns 0.00e+00 CPU s Iteration 1: 4 species 8 rxns 1.00e-02 CPU s Cumulative CPU time for each rule Rule 1: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 2: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 3: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 4: 1 reactions 1.00e-02 CPU s 1.00e-02 CPU s/rxn Rule 5: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 6: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 7: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 8: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Total : 8 reactions 1.00e-02 CPU s 1.25e-03 CPU s/rxn Wrote network in net format to ./CaOscillate_Sat.net. CPU TIME: generate_network 0.01 s. ACTION: simulate( method=>"cvode" ) Network simulation using cvode BUILDSTDERR: WARNCan't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Perl2/BNGAction.pm line 547. ING: writeFile(): Overwriting existing file ./CaOscillate_Sat.net. Wrote network in net format to ./CaOscillate_Sat.net. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/bin/run_network_i686-linux -o ./CaOscillate_Sat -p cvode -a 1e-12 -r 1e-12 --cdat 1 --fdat 0 -v -g ./CaOscillate_Sat.net ./CaOscillate_Sat.net 0.1 200 [simulation PID is: 4060] run_network 3.0 Read 17 parameters from ./CaOscillate_Sat.net Read 4 species from ./CaOscillate_Sat.net Read 4 group(s) from ./CaOscillate_Sat.net Read 0 function(s) from ./CaOscillate_Sat.net Read 8 reaction(s) from ./CaOscillate_Sat.net 8 reaction(s) have nonzero rate Initialization took 0.00 CPU seconds Propagating with cvode using dense LU time n_steps n_deriv_calls 0.00 0 0 0.10 719 851 0.20 753 889 0.30 788 924 0.40 819 960 0.50 842 984 0.60 865 1008 0.70 888 1036 0.80 911 1060 0.90 934 1091 1.00 957 1116 1.10 983 1146 1.20 1014 1184 1.30 1046 1218 1.40 1079 1259 1.50 1122 1310 1.60 1169 1362 1.70 1226 1428 1.80 1296 1512 1.90 1370 1605 2.00 1450 1698 2.10 1526 1787 2.20 1601 1866 2.30 1655 1927 2.40 1705 1979 2.50 1759 2043 2.60 1897 2217 2.70 2371 2794 2.80 2470 2900 2.90 2528 2962 3.00 2575 3020 3.10 2628 3083 3.20 2680 3143 3.30 2732 3204 3.40 2784 3261 3.50 2836 3315 3.60 2888 3373 3.70 2941 3438 3.80 3067 3595 3.90 3224 3777 4.00 3337 3901 4.10 3402 3971 4.20 3456 4029 4.30 3510 4087 4.40 3558 4140 4.50 3594 4180 4.60 3640 4236 4.70 3688 4292 4.80 3746 4359 4.90 3805 4430 5.00 3862 4493 5.10 3903 4540 5.20 3941 4580 5.30 3975 4619 5.40 4000 4645 5.50 4025 4675 5.60 4051 4705 5.70 4076 4735 5.80 4099 4760 5.90 4119 4782 6.00 4140 4808 6.10 4162 4831 6.20 4181 4855 6.30 4192 4871 6.40 4204 4883 6.50 4216 4896 6.60 4228 4908 6.70 4240 4920 6.80 4252 4936 6.90 4264 4948 7.00 4276 4960 7.10 4288 4972 7.20 4299 4983 7.30 4311 4999 7.40 4323 5011 7.50 4335 5023 7.60 4347 5035 7.70 4359 5047 7.80 4371 5063 7.90 4383 5075 8.00 4395 5087 8.10 4407 5099 8.20 4419 5113 8.30 4434 5143 8.40 4450 5161 8.50 4471 5189 8.60 4498 5230 8.70 4533 5272 8.80 4592 5345 8.90 4696 5473 9.00 5025 5862 9.10 5314 6183 9.20 5422 6298 9.30 5462 6344 9.40 5475 6364 9.50 5485 6378 9.60 5494 6387 9.70 5503 6402 9.80 5513 6412 9.90 5522 6423 10.00 5532 6433 10.10 5541 6444 10.20 5551 6454 10.30 5562 6471 10.40 5575 6485 10.50 5588 6498 10.60 5600 6511 10.70 5613 6525 10.80 5626 6544 10.90 5638 6558 11.00 5651 6571 11.10 5664 6586 11.20 5677 6605 11.30 5691 6621 11.40 5708 6639 11.50 5725 6661 11.60 5742 6678 11.70 5760 6697 11.80 5777 6715 11.90 5794 6737 12.00 5811 6755 12.10 5828 6773 12.20 5845 6795 12.30 5862 6813 12.40 5880 6833 12.50 5897 6852 12.60 5914 6875 12.70 5934 6897 12.80 5957 6921 12.90 5980 6950 13.00 6003 6975 13.10 6031 7008 13.20 6063 7047 13.30 6094 7086 13.40 6128 7126 13.50 6171 7177 13.60 6218 7234 13.70 6273 7301 13.80 6345 7381 13.90 6417 7472 14.00 6501 7568 14.10 6578 7655 14.20 6655 7740 14.30 6708 7800 14.40 6759 7858 14.50 6813 7917 14.60 6940 8079 14.70 7388 8611 14.80 7506 8741 14.90 7559 8800 15.00 7608 8861 15.10 7668 8930 15.20 7728 8997 15.30 7788 9063 15.40 7848 9127 15.50 7908 9191 15.60 7965 9253 15.70 8017 9318 15.80 8141 9471 15.90 8281 9636 16.00 8398 9764 16.10 8466 9837 16.20 8522 9897 16.30 8578 9957 16.40 8626 10010 16.50 8664 10052 16.60 8708 10105 16.70 8758 10161 BUILDSTDERR: Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Perl2/BNGAction.pm line 547. 16.80 8816 10230 16.90 8876 10295 17.00 8934 10360 17.10 8976 10408 17.20 9014 10452 17.30 9048 10487 17.40 9073 10516 17.50 9099 10543 17.60 9124 10576 17.70 9149 10602 17.80 9172 10627 17.90 9192 10653 18.00 9213 10675 18.10 9234 10697 18.20 9253 10721 18.30 9265 10738 18.40 9275 10748 18.50 9285 10759 18.60 9295 10769 18.70 9305 10783 18.80 9315 10793 18.90 9325 10803 19.00 9335 10813 19.10 9345 10823 19.20 9354 10832 19.30 9364 10846 19.40 9374 10856 19.50 9384 10868 19.60 9394 10878 19.70 9404 10889 19.80 9414 10901 19.90 9424 10919 20.00 9434 10929 Time course of concentrations written to file ./CaOscillate_Sat.cdat. Time course of groups written to file ./CaOscillate_Sat.gdat. Propagation took 2.00e-02 CPU seconds Program times: 0.02 CPU s 0.00 clock s Updating species concentrations from ./CaOscillate_Sat.cdat CPU TIME: simulate 0.02 s. Finished processing file CaOscillate_Sat.bngl. CPU TIME: total 0.04 s. BioNetGen version 2.5.0 Reading from file catalysis.bngl (level 0) CPU TIME: version 0.00 s. Read 17 parameters. Read 1 compartments. Read 5 molecule types. Read 5 species. Read 4 reaction rule(s). Read 4 energy patterns(s). Read 6 observable(s). ACTION: generate_network( catalysis ) Iteration 0: 5 species 0 rxns 0.00e+00 CPU s Iteration 1: 7 species 2 rxns 0.00e+00 CPU s Iteration 2: 9 species 6 rxns 1.00e-02 CPU s Iteration 3: 10 species 10 rxns 0.00e+00 CPU s Iteration 4: 10 species 12 rxns 0.00e+00 CPU s Cumulative CPU time for each rule Rule 1: 4 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 2: 4 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 3: 2 reactions 1.00e-02 CPU s 5.00e-03 CPU s/rxn Rule 4: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Total : 12 reactions 1.00e-02 CPU s 8.33e-04 CPU s/rxn Wrote network in net format to ./catalysis.net. CPU TIME: generate_network 0.02 s. ACTION: simulate( method=>"cvode" ) Network simulation using cvode WARNING: writeFile(): Overwriting existing file ./catalysis.net. Wrote network in net format to ./catalysis.net. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/bin/run_network_i686-linux -o ./catalysis -p cvode -a 0.001 -r 1e-07 --cdat 1 --fdat 0 -g ./catalysis.net ./catalysis.net 30 120 [simulation PID is: 4062] run_network 3.0 Read 30 parameters from ./catalysis.net @C::$ATP() is a fixed (boundaryCondition) variable @C::$ADP() is a fixed (boundaryCondition) variable Read 10 species from ./catalysis.net Read 6 group(s) from ./catalysis.net Read 0 function(s) from ./catalysis.net Read 12 reaction(s) from ./catalysis.net 12 reaction(s) have nonzero rate Initialization took 0.00 CPU seconds Propagating with cvode using dense LU Time course of concentrations written to file ./catalysis.cdat. Time course of groups written to file ./catalysis.gdat. Propagation took 1.00e-02 CPU seconds Program times: 0.01 CPU s 0.00 clock s Updating species concentrations from ./catalysis.cdat CPU TIME: simulate 0.02 s. Finished processing file catalysis.bngl. CPU TIME: total 0.06 s. BioNetGen version 2.5.0 Reading from file egfr_net.bngl (level 0) Read 48 parameters. BUILDSTDERR: RCan't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Perl2/BNGAction.pm line 547. ead 5 molecule types. Read 6 species. Read 23 reaction rule(s). Read 15 observable(s). ACTION: generate_network( egfr_net ) Iteration 0: 6 species 0 rxns 0.00e+00 CPU s Iteration 1: 7 species 3 rxns 1.00e-02 CPU s Iteration 2: 8 species 5 rxns 0.00e+00 CPU s Iteration 3: 10 species 8 rxns 1.00e-02 CPU s Iteration 4: 19 species 21 rxns 2.00e-02 CPU s Iteration 5: 37 species 76 rxns 1.00e-01 CPU s Iteration 6: 69 species 213 rxns 2.20e-01 CPU s Iteration 7: 131 species 494 rxns 4.90e-01 CPU s Iteration 8: 295 species 1260 rxns 1.54e+00 CPU s Iteration 9: 356 species 3088 rxns 4.00e+00 CPU s Iteration 10: 356 species 3749 rxns 1.84e+00 CPU s Cumulative CPU time for each rule Rule 1: 48 reactions 9.00e-02 CPU s 1.88e-03 CPU s/rxn Rule 2: 600 reactions 2.04e+00 CPU s 3.40e-03 CPU s/rxn Rule 3: 144 reactions 2.40e-01 CPU s 1.67e-03 CPU s/rxn Rule 4: 96 reactions 1.70e-01 CPU s 1.77e-03 CPU s/rxn Rule 5: 156 reactions 2.00e-01 CPU s 1.28e-03 CPU s/rxn Rule 6: 104 reactions 1.40e-01 CPU s 1.35e-03 CPU s/rxn Rule 7: 96 reactions 1.80e-01 CPU s 1.87e-03 CPU s/rxn Rule 8: 104 reactions 1.70e-01 CPU s 1.63e-03 CPU s/rxn Rule 9: 312 reactions 5.50e-01 CPU s 1.76e-03 CPU s/rxn Rule 10: 312 reactions 6.10e-01 CPU s 1.96e-03 CPU s/rxn Rule 11: 312 reactions 6.20e-01 CPU s 1.99e-03 CPU s/rxn Rule 12: 208 reactions 3.60e-01 CPU s 1.73e-03 CPU s/rxn Rule 13: 208 reactions 3.70e-01 CPU s 1.78e-03 CPU s/rxn Rule 14: 208 reactions 4.70e-01 CPU s 2.26e-03 CPU s/rxn Rule 15: 208 reactions 5.10e-01 CPU s 2.45e-03 CPU s/rxn Rule 16: 208 reactions 4.50e-01 CPU s 2.16e-03 CPU s/rxn Rule 17: 208 reactions 4.80e-01 CPU s 2.31e-03 CPU s/rxn Rule 18: 208 reactions 4.50e-01 CPU s 2.16e-03 CPU s/rxn Rule 19: 2 reactions 4.00e-02 CPU s 2.00e-02 CPU s/rxn Rule 20: 2 reactions 2.00e-02 CPU s 1.00e-02 CPU s/rxn Rule 21: 1 reactions 2.00e-02 CPU s 2.00e-02 CPU s/rxn Rule 22: 2 reactions 2.00e-02 CPU s 1.00e-02 CPU s/rxn Rule 23: 2 reactions 3.00e-02 CPU s 1.50e-02 CPU s/rxn Total : 3749 reactions 8.23e+00 CPU s 2.20e-03 CPU s/rxn Wrote network in net format to ./egfr_net.net. CPU TIME: generate_network 8.36 s. ACTION: simulate( method=>"cvode" ) Network simulation using cvode WARNING: writeFile(): Overwriting existing file ./egfr_net.net. Wrote network in net format to ./egfr_net.net. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/bin/run_network_i686-linux -o ./egfr_net -p cvode -a 1e-08 -r 1e-08 -b --cdat 1 --fdat 0 -g ./egfr_net.net ./egfr_net.net 0.8 50 [simulation PID is: 4064] run_network 3.0 Read 48 parameters from ./egfr_net.net Read 356 species from ./egfr_net.net Read 15 group(s) from ./egfr_net.net Read 0 function(s) from ./egfr_net.net Read 3749 reaction(s) from ./egfr_net.net 3749 reaction(s) have nonzero rate Initialization took 0.03 CPU seconds Propagating with cvode using GMRES Time course of concentrations written to file ./egfr_net.cdat. Time course of groups written to file ./egfr_net.gdat. Propagation took 1.10e-01 CPU seconds Program times: 0.14 CPU s 0.00 clock s Updating species concentrations from ./egfr_net.cdat CPU TIME: simulate 0.27 s. Finished processing file egfr_net.bngl. CPU TIME: total 8.69 s. BioNetGen version 2.5.0 Reading from file egfr_net_red.bngl (level 0) Read 48 parameters. Read 7 molecule types. Read 7 species. Read 14 observable(s). Read 26 reaction rule(s). ACTION: generate_network( egfr_net_red ) Iteration 0: 7 species 0 rxns 0.00e+00 CPU s Iteration 1: 11 species 4 rxns 1.00e-02 CPU s Iteration 2: 13 species 10 rxns 1.00e-02 CPU s Iteration 3: 15 species 14 rxns 1.00e-02 CPU s Iteration 4: 20 species 21 rxns 1.00e-02 CPU s Iteration 5: 26 species 39 rxns 3.00e-02 CPU s Iteration 6: 33 species 62 rxns 3.00e-02 CPU s Iteration 7: 38 species 90 rxns 3.00e-02 CPU s BUILDSTDERR: Iteration 8: Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Perl2/BNGAction.pm line 547. BUILDSTDERR: Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Perl2/BNGAction.pm line 547. 40 species 115 rxns 3.00e-02 CPU s Iteration 9: 40 species 123 rxns 2.00e-02 CPU s Cumulative CPU time for each rule Rule 1: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 2: 8 reactions 1.00e-02 CPU s 1.25e-03 CPU s/rxn Rule 3: 12 reactions 2.00e-02 CPU s 1.67e-03 CPU s/rxn Rule 4: 8 reactions 2.00e-02 CPU s 2.50e-03 CPU s/rxn Rule 5: 12 reactions 2.00e-02 CPU s 1.67e-03 CPU s/rxn Rule 6: 1 reactions 1.00e-02 CPU s 1.00e-02 CPU s/rxn Rule 7: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 8: 3 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 9: 3 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 10: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 11: 3 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 12: 6 reactions 2.00e-02 CPU s 3.33e-03 CPU s/rxn Rule 13: 6 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 14: 6 reactions 1.00e-02 CPU s 1.67e-03 CPU s/rxn Rule 15: 6 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 16: 6 reactions 1.00e-02 CPU s 1.67e-03 CPU s/rxn Rule 17: 6 reactions 1.00e-02 CPU s 1.67e-03 CPU s/rxn Rule 18: 6 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 19: 6 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 20: 6 reactions 3.00e-02 CPU s 5.00e-03 CPU s/rxn Rule 21: 6 reactions 1.00e-02 CPU s 1.67e-03 CPU s/rxn Rule 22: 2 reactions 1.00e-02 CPU s 5.00e-03 CPU s/rxn Rule 23: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 24: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 25: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 26: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Total : 123 reactions 1.80e-01 CPU s 1.46e-03 CPU s/rxn Wrote network in net format to ./egfr_net_red.net. CPU TIME: generate_network 0.18 s. Set concentration of species egf(r) to value 0 CPU TIME: setConcentration 0.00 s. ACTION: simulate( method=>"cvode" ) Network simulation using cvode WARNING: writeFile(): Overwriting existing file ./egfr_net_red.net. Wrote network in net format to ./egfr_net_red.net. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/bin/run_network_i686-linux -o ./egfr_net_red -p cvode -a 1e-08 -r 1e-08 -b -c --cdat 1 --fdat 0 -g ./egfr_net_red.net ./egfr_net_red.net 10000 10 [simulation PID is: 4066] run_network 3.0 Read 48 parameters from ./egfr_net_red.net Read 40 species from ./egfr_net_red.net Read 14 group(s) from ./egfr_net_red.net Read 3 function(s) from ./egfr_net_red.net Read 123 reaction(s) from ./egfr_net_red.net 123 reaction(s) have nonzero rate Initialization took 0.00 CPU seconds Propagating with cvode using GMRES Time course of concentrations written to file ./egfr_net_red.cdat. Time course of groups written to file ./egfr_net_red.gdat. Propagation took 0.00e+00 CPU seconds Program times: 0.00 CPU s 0.00 clock s Simulation reached steady state by t_end=100000 Updating species concentrations from ./egfr_net_red.cdat CPU TIME: simulate 0.03 s. Set concentration of species egf(r) to value egf_tot CPU TIME: setConcentration 0.00 s. ACTION: simulate( method=>"cvode" ) Network simulation using cvode WARNING: writeFile(): Overwriting existing file ./egfr_net_red.net. Wrote network in net format to ./egfr_net_red.net. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/bin/run_network_i686-linux -o ./egfr_net_red -p cvode -a 1e-08 -r 1e-08 -b --cdat 1 --fdat 0 -g ./egfr_net_red.net ./egfr_net_red.net 1 120 [simulation PID is: 4068] run_network 3.0 Read 48 parameters from ./egfr_net_red.net Read 40 species from ./egfr_net_red.net Read 14 group(s) from ./egfr_net_red.net Read 3 function(s) from ./egfr_net_red.net Read 123 reaction(s) from ./egfr_net_red.net 123 reaction(s) have nonzero rate Initialization took 0.00 CPU seconds Propagating with cvode using GMRES Time course of concentrations written to file ./egfr_net_red.cdat. Time course of groups written to file ./egfr_net_red.gdat. BUILDSTDERR: Propagation took 1.00e-02 CPU secondCan't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Perl2/BNGAction.pm line 547. BUILDSTDERR: Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Perl2/BNGAction.pm line 547. s Program times: 0.01 CPU s 0.00 clock s Updating species concentrations from ./egfr_net_red.cdat CPU TIME: simulate 0.03 s. Finished processing file egfr_net_red.bngl. CPU TIME: total 0.30 s. BioNetGen version 2.5.0 Reading from file egfr_path.bngl (level 0) Read 48 parameters. Read 18 species. Read 19 reaction rule(s). Read 11 observable(s). ACTION: generate_network( egfr_path ) Iteration 0: 18 species 0 rxns 0.00e+00 CPU s Iteration 1: 18 species 37 rxns 2.00e-02 CPU s Cumulative CPU time for each rule Rule 1: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 2: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 3: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 4: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 5: 2 reactions 1.00e-02 CPU s 5.00e-03 CPU s/rxn Rule 6: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 7: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 8: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 9: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 10: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 11: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 12: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 13: 2 reactions 1.00e-02 CPU s 5.00e-03 CPU s/rxn Rule 14: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 15: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 16: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 17: 1 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 18: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 19: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Total : 37 reactions 2.00e-02 CPU s 5.41e-04 CPU s/rxn Wrote network in net format to ./egfr_path.net. CPU TIME: generate_network 0.04 s. Set concentration of species EGF() to value 0 CPU TIME: setConcentration 0.00 s. ACTION: simulate( method=>"cvode" ) Network simulation using cvode WARNING: writeFile(): Overwriting existing file ./egfr_path.net. Wrote network in net format to ./egfr_path.net. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/bin/run_network_i686-linux -o ./egfr_path -p cvode -a 1e-08 -r 1e-08 -c --cdat 1 --fdat 0 -g ./egfr_path.net ./egfr_path.net 10000 10 [simulation PID is: 4070] run_network 3.0 Read 48 parameters from ./egfr_path.net Read 18 species from ./egfr_path.net Read 11 group(s) from ./egfr_path.net Read 0 function(s) from ./egfr_path.net Read 37 reaction(s) from ./egfr_path.net 37 reaction(s) have nonzero rate Initialization took 0.00 CPU seconds Propagating with cvode using dense LU Time course of concentrations written to file ./egfr_path.cdat. Time course of groups written to file ./egfr_path.gdat. Propagation took 0.00e+00 CPU seconds Program times: 0.00 CPU s 0.00 clock s Simulation reached steady state by t_end=100000 Updating species concentrations from ./egfr_path.cdat CPU TIME: simulate 0.02 s. Set concentration of species EGF() to value EGF_tot CPU TIME: setConcentration 0.00 s. ACTION: simulate( method=>"cvode" ) Network simulation using cvode WARNING: writeFile(): Overwriting existing file ./egfr_path.net. Wrote network in net format to ./egfr_path.net. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/bin/run_network_i686-linux -o ./egfr_path -p cvode -a 1e-08 -r 1e-08 --cdat 1 --fdat 0 -g ./egfr_path.net ./egfr_path.net 1 120 [simulation PID is: 4072] run_network 3.0 Read 48 parameters from ./egfr_path.net Read 18 species from ./egfr_path.net Read 11 group(s) from ./egfr_path.net Read 0 function(s) from ./egfr_path.net Read 37 reaction(s) from ./egfr_path.net 37 reaction(s) have nonzero rate Initialization took 0.00 CPU seconds Propagating with cvode using dense LU Time course of concentrations written to file ./egfr_path.cdat. Time course of groups written to file ./egfr_path.gdat. Propagation took 1.00e-02 CPU seconds Program times: 0.01 CPU s 0.00 clock s Updating species concentrations from ./egfr_path.cdat BUILDSTDERR: CPU Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Perl2/BNGAction.pm line 547. TIME: simulate 0.02 s. Finished processing file egfr_path.bngl. CPU TIME: total 0.12 s. BioNetGen version 2.5.0 Reading from file energy_example1.bngl (level 0) CPU TIME: version 0.00 s. Read 19 parameters. Read 1 compartments. Read 4 molecule types. Read 4 species. Read 6 energy patterns(s). Read 11 observable(s). Read 3 reaction rule(s). ACTION: generate_network( energy_example1 ) Iteration 0: 4 species 0 rxns 0.00e+00 CPU s Iteration 1: 7 species 3 rxns 1.00e-02 CPU s Iteration 2: 10 species 12 rxns 1.00e-02 CPU s Iteration 3: 11 species 21 rxns 2.00e-02 CPU s Iteration 4: 11 species 24 rxns 0.00e+00 CPU s Cumulative CPU time for each rule Rule 1: 8 reactions 2.00e-02 CPU s 2.50e-03 CPU s/rxn Rule 2: 8 reactions 1.00e-02 CPU s 1.25e-03 CPU s/rxn Rule 3: 8 reactions 1.00e-02 CPU s 1.25e-03 CPU s/rxn Total : 24 reactions 4.00e-02 CPU s 1.67e-03 CPU s/rxn Wrote network in net format to ./energy_example1.net. CPU TIME: generate_network 0.05 s. Wrote SBML to ./energy_example1_sbml.xml. CPU TIME: writeSBML 0.01 s. Finished processing file energy_example1.bngl. CPU TIME: total 0.08 s. BioNetGen version 2.5.0 Reading from file fceri_ji.bngl (level 0) Read 26 parameters. Read 4 species. Adding pY as allowed state of component b of molecule Rec Adding pY as allowed state of component g of molecule Rec Adding pY as allowed state of component l of molecule Syk Adding pY as allowed state of component a of molecule Syk Read 19 reaction rule(s). Read 10 observable(s). ACTION: generate_network( fceri_ji ) Iteration 0: 4 species 0 rxns 0.00e+00 CPU s Iteration 1: 6 species 2 rxns 0.00e+00 CPU s Iteration 2: 9 species 8 rxns 1.00e-02 CPU s Iteration 3: 12 species 20 rxns 2.00e-02 CPU s Iteration 4: 22 species 36 rxns 2.00e-02 CPU s Iteration 5: 43 species 100 rxns 8.00e-02 CPU s Iteration 6: 78 species 255 rxns 1.90e-01 CPU s Iteration 7: 139 species 586 rxns 4.40e-01 CPU s Iteration 8: 199 species 1190 rxns 8.40e-01 CPU s Iteration 9: 303 species 1841 rxns 1.04e+00 CPU s Iteration 10: 354 species 3143 rxns 1.81e+00 CPU s Iteration 11: 354 species 3680 rxns 7.80e-01 CPU s Cumulative CPU time for each rule Rule 1: 48 reactions 1.00e-01 CPU s 2.08e-03 CPU s/rxn Rule 2: 1152 reactions 1.47e+00 CPU s 1.28e-03 CPU s/rxn Rule 3: 312 reactions 4.40e-01 CPU s 1.41e-03 CPU s/rxn Rule 4: 36 reactions 8.00e-02 CPU s 2.22e-03 CPU s/rxn Rule 5: 24 reactions 9.00e-02 CPU s 3.75e-03 CPU s/rxn Rule 6: 312 reactions 4.30e-01 CPU s 1.38e-03 CPU s/rxn Rule 7: 36 reactions 1.00e-01 CPU s 2.78e-03 CPU s/rxn Rule 8: 24 reactions 5.00e-02 CPU s 2.08e-03 CPU s/rxn Rule 9: 832 reactions 1.09e+00 CPU s 1.31e-03 CPU s/rxn Rule 10: 48 reactions 1.10e-01 CPU s 2.29e-03 CPU s/rxn Rule 11: 48 reactions 1.10e-01 CPU s 2.29e-03 CPU s/rxn Rule 12: 64 reactions 1.90e-01 CPU s 2.97e-03 CPU s/rxn Rule 13: 64 reactions 1.50e-01 CPU s 2.34e-03 CPU s/rxn Rule 14: 156 reactions 1.70e-01 CPU s 1.09e-03 CPU s/rxn Rule 15: 104 reactions 1.10e-01 CPU s 1.06e-03 CPU s/rxn Rule 16: 208 reactions 2.60e-01 CPU s 1.25e-03 CPU s/rxn Rule 17: 208 reactions 2.40e-01 CPU s 1.15e-03 CPU s/rxn Rule 18: 2 reactions 3.00e-02 CPU s 1.50e-02 CPU s/rxn Rule 19: 2 reactions 1.00e-02 CPU s 5.00e-03 CPU s/rxn Total : 3680 reactions 5.23e+00 CPU s 1.42e-03 CPU s/rxn Wrote network in net format to ./fceri_ji.net. CPU TIME: generate_network 5.35 s. ACTION: simulate( method=>"cvode" ) Network simulation using cvode WARNING: writeFile(): Overwriting existing file ./fceri_ji.net. Wrote network in net format to ./fceri_ji.net. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/bin/run_network_i686-linux -o ./fceri_ji -p cvode -a 1e-08 -r 1e-08 --cdat 1 --fdat 0 -g ./fceri_ji.net ./fceri_ji.net 60 10 [simulation PID is: 4074] run_network 3.0 Read 26 parameters from ./fceri_ji.net BUILDSTDERR: Read 354 spCan't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Perl2/BNGAction.pm line 547. BUILDSTDERR: Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Perl2/BNGAction.pm line 547. ecies from ./fceri_ji.net Read 10 group(s) from ./fceri_ji.net Read 0 function(s) from ./fceri_ji.net Read 3680 reaction(s) from ./fceri_ji.net Removed 600 reactions with zero rate 3080 reaction(s) have nonzero rate Initialization took 0.03 CPU seconds Propagating with cvode using dense LU Time course of concentrations written to file ./fceri_ji.cdat. Time course of groups written to file ./fceri_ji.gdat. Propagation took 9.90e-01 CPU seconds Program times: 1.02 CPU s 1.00 clock s Updating species concentrations from ./fceri_ji.cdat CPU TIME: simulate 1.13 s. Finished processing file fceri_ji.bngl. CPU TIME: total 6.51 s. BioNetGen version 2.5.0 Reading from file test_continue.bngl (level 0) Read 19 parameters. Read 5 molecule types. Read 4 species. Read 6 observable(s). Read 6 reaction rule(s). ACTION: generate_network( test_continue ) Iteration 0: 4 species 0 rxns 0.00e+00 CPU s Iteration 1: 6 species 2 rxns 0.00e+00 CPU s Iteration 2: 7 species 5 rxns 1.00e-02 CPU s Iteration 3: 8 species 7 rxns 0.00e+00 CPU s Iteration 4: 12 species 12 rxns 1.00e-02 CPU s Iteration 5: 17 species 30 rxns 2.00e-02 CPU s Iteration 6: 22 species 59 rxns 4.00e-02 CPU s Iteration 7: 22 species 76 rxns 3.00e-02 CPU s Cumulative CPU time for each rule Rule 1: 8 reactions 1.00e-02 CPU s 1.25e-03 CPU s/rxn Rule 2: 20 reactions 5.00e-02 CPU s 2.50e-03 CPU s/rxn Rule 3: 4 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 4: 6 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 5: 24 reactions 4.00e-02 CPU s 1.67e-03 CPU s/rxn Rule 6: 14 reactions 1.00e-02 CPU s 7.14e-04 CPU s/rxn Total : 76 reactions 1.10e-01 CPU s 1.45e-03 CPU s/rxn Wrote network in net format to ./test_continue.net. CPU TIME: generate_network 0.12 s. Set concentration of species EGF(R) to value EGF_init CPU TIME: setConcentration 0.00 s. ACTION: simulate( method=>"cvode" ) Network simulation using cvode WARNING: writeFile(): Overwriting existing file ./test_continue.net. Wrote network in net format to ./test_continue.net. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/bin/run_network_i686-linux -o ./test_continue -p cvode -a 1e-08 -r 1e-08 --cdat 1 --fdat 0 -g ./test_continue.net ./test_continue.net 2.5 40 [simulation PID is: 4076] run_network 3.0 Read 19 parameters from ./test_continue.net Read 22 species from ./test_continue.net Read 6 group(s) from ./test_continue.net Read 0 function(s) from ./test_continue.net Read 76 reaction(s) from ./test_continue.net 76 reaction(s) have nonzero rate Initialization took 0.00 CPU seconds Propagating with cvode using dense LU Time course of concentrations written to file ./test_continue.cdat. Time course of groups written to file ./test_continue.gdat. Propagation took 0.00e+00 CPU seconds Program times: 0.00 CPU s 0.00 clock s Updating species concentrations from ./test_continue.cdat CPU TIME: simulate 0.01 s. Set concentration of species EGF(R) to value 10*EGF_init CPU TIME: setConcentration 0.00 s. ACTION: simulate( method=>"cvode" ) Network simulation using cvode WARNING: writeFile(): Overwriting existing file ./test_continue.net. Wrote network in net format to ./test_continue.net. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/bin/run_network_i686-linux -o ./test_continue -p cvode -a 1e-08 -r 1e-08 --cdat 1 --fdat 0 -x -i 1.000000000000e+02 -g ./test_continue.net ./test_continue.net 2.5 40 [simulation PID is: 4078] run_network 3.0 Read 20 parameters from ./test_continue.net Read 22 species from ./test_continue.net Read 6 group(s) from ./test_continue.net Read 0 function(s) from ./test_continue.net Read 76 reaction(s) from ./test_continue.net 76 reaction(s) have nonzero rate Initialization took 0.00 CPU seconds Propagating with cvode using dense LU Time course of concentrations written to file ./test_continue.cdat. Time course of groups written to file ./test_continue.gdat. BUILDSTDERR: Propagation took 0.00eCan't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Perl2/BNGAction.pm line 547. BUILDSTDERR: Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Perl2/BNGAction.pm line 547. BUILDSTDERR: Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Perl2/BNGAction.pm line 547. +00 CPU seconds Program times: 0.00 CPU s 0.00 clock s Updating species concentrations from ./test_continue.cdat CPU TIME: simulate 0.04 s. Set concentration of species EGF(R) to value 0.1*EGF_init CPU TIME: setConcentration 0.00 s. ACTION: simulate( method=>"cvode" ) Network simulation using cvode WARNING: writeFile(): Overwriting existing file ./test_continue.net. Wrote network in net format to ./test_continue.net. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/bin/run_network_i686-linux -o ./test_continue -p cvode -a 1e-08 -r 1e-08 --cdat 1 --fdat 0 -x -i 2.000000000000e+02 -g ./test_continue.net ./test_continue.net 2.5 40 [simulation PID is: 4080] run_network 3.0 Read 21 parameters from ./test_continue.net Read 22 species from ./test_continue.net Read 6 group(s) from ./test_continue.net Read 0 function(s) from ./test_continue.net Read 76 reaction(s) from ./test_continue.net 76 reaction(s) have nonzero rate Initialization took 0.00 CPU seconds Propagating with cvode using dense LU Time course of concentrations written to file ./test_continue.cdat. Time course of groups written to file ./test_continue.gdat. Propagation took 0.00e+00 CPU seconds Program times: 0.00 CPU s 0.00 clock s Updating species concentrations from ./test_continue.cdat CPU TIME: simulate 0.01 s. Reset species concentrations to "DEFAULT" saved values. CPU TIME: resetConcentrations 0.00 s. Set concentration of species EGF(R) to value EGF_init CPU TIME: setConcentration 0.00 s. ACTION: simulate( method=>"ssa" ) Network simulation using ssa Wrote network in net format to ./test_continue_ssa.net. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/bin/run_network_i686-linux -o ./test_continue_ssa -p ssa -h 797375363 --cdat 1 --fdat 0 -g ./test_continue_ssa.net ./test_continue_ssa.net 2.5 40 [simulation PID is: 4082] run_network 3.0 Read 21 parameters from ./test_continue_ssa.net Read 22 species from ./test_continue_ssa.net Read 6 group(s) from ./test_continue_ssa.net Read 0 function(s) from ./test_continue_ssa.net Read 76 reaction(s) from ./test_continue_ssa.net 76 reaction(s) have nonzero rate rxn_rate_update_interval=1 Average number of update rxns is 14.17 Initialization took 0.00 CPU seconds Stochastic simulation using direct Gillespie algorithm TOTAL STEPS: 70848 Time course of concentrations written to file ./test_continue_ssa.cdat. Time course of groups written to file ./test_continue_ssa.gdat. Propagation took 2.00e-02 CPU seconds Program times: 0.02 CPU s 0.00 clock s Updating species concentrations from ./test_continue_ssa.cdat CPU TIME: simulate 0.03 s. Set concentration of species EGF(R) to value 10*EGF_init CPU TIME: setConcentration 0.01 s. ACTION: simulate( method=>"ssa" ) Network simulation using ssa WARNING: writeFile(): Overwriting existing file ./test_continue_ssa.net. Wrote network in net format to ./test_continue_ssa.net. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/bin/run_network_i686-linux -o ./test_continue_ssa -p ssa -h 1233171060 --cdat 1 --fdat 0 -x -i 1.000000000000e+02 -g ./test_continue_ssa.net ./test_continue_ssa.net 2.5 40 [simulation PID is: 4084] run_network 3.0 Read 22 parameters from ./test_continue_ssa.net Read 22 species from ./test_continue_ssa.net Read 6 group(s) from ./test_continue_ssa.net Read 0 function(s) from ./test_continue_ssa.net Read 76 reaction(s) from ./test_continue_ssa.net 76 reaction(s) have nonzero rate rxn_rate_update_interval=1 Average number of update rxns is 14.17 Initialization took 0.00 CPU seconds Stochastic simulation using direct Gillespie algorithm TOTAL STEPS: 130338 Time course of concentrations written to file ./test_continue_ssa.cdat. Time course of groups written to file ./test_continue_ssa.gdat. Propagation took 3.00e-02 CPU seconds Program times: 0.03 CPU s 0.00 clock s Updating species concentrations from ./test_continue_ssa.cdat CPU TIME: simulate 0.04 s. BUILDSTDERR: Set concentration of speCan't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/Perl2/BNGAction.pm line 547. + echo 'Tests finished.' + RPM_EC=0 BUILDSTDERR: ++ jobs -p + exit 0 cies EGF(R) to value 0.1*EGF_init CPU TIME: setConcentration 0.00 s. ACTION: simulate( method=>"ssa" ) Network simulation using ssa WARNING: writeFile(): Overwriting existing file ./test_continue_ssa.net. Wrote network in net format to ./test_continue_ssa.net. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.5.0/bionetgen-BioNetGen-2.5.0/bng2/bin/run_network_i686-linux -o ./test_continue_ssa -p ssa -h 244299810 --cdat 1 --fdat 0 -x -i 2.000000000000e+02 -g ./test_continue_ssa.net ./test_continue_ssa.net 2.5 40 [simulation PID is: 4086] run_network 3.0 Read 23 parameters from ./test_continue_ssa.net Read 22 species from ./test_continue_ssa.net Read 6 group(s) from ./test_continue_ssa.net Read 0 function(s) from ./test_continue_ssa.net Read 76 reaction(s) from ./test_continue_ssa.net 76 reaction(s) have nonzero rate rxn_rate_update_interval=1 Average number of update rxns is 14.17 Initialization took 0.00 CPU seconds Stochastic simulation using direct Gillespie algorithm TOTAL STEPS: 106471 Time course of concentrations written to file ./test_continue_ssa.cdat. Time course of groups written to file ./test_continue_ssa.gdat. Propagation took 3.00e-02 CPU seconds Program times: 0.03 CPU s 0.00 clock s Updating species concentrations from ./test_continue_ssa.cdat CPU TIME: simulate 0.06 s. Finished processing file test_continue.bngl. CPU TIME: total 0.36 s. Tests finished. Processing files: bionetgen-2.5.0-3.fc31.i686 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.M9TRw6 + umask 022 + cd /builddir/build/BUILD + cd bionetgen-2.5.0 + DOCDIR=/builddir/build/BUILDROOT/bionetgen-2.5.0-3.fc31.i386/usr/share/doc/bionetgen + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/bionetgen-2.5.0-3.fc31.i386/usr/share/doc/bionetgen + cp -pr bionetgen-BioNetGen-2.5.0/README.md /builddir/build/BUILDROOT/bionetgen-2.5.0-3.fc31.i386/usr/share/doc/bionetgen + cp -pr bionetgen-BioNetGen-2.5.0/bng2/CREDITS.txt /builddir/build/BUILDROOT/bionetgen-2.5.0-3.fc31.i386/usr/share/doc/bionetgen + cp -pr bionetgen-BioNetGen-2.5.0/bng2/CHANGES.txt /builddir/build/BUILDROOT/bionetgen-2.5.0-3.fc31.i386/usr/share/doc/bionetgen + cp -pr bionetgen-BioNetGen-2.5.0/bng2/VERSION /builddir/build/BUILDROOT/bionetgen-2.5.0-3.fc31.i386/usr/share/doc/bionetgen + RPM_EC=0 BUILDSTDERR: ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.beU9S5 + umask 022 + cd /builddir/build/BUILD + cd bionetgen-2.5.0 + LICENSEDIR=/builddir/build/BUILDROOT/bionetgen-2.5.0-3.fc31.i386/usr/share/licenses/bionetgen + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/bionetgen-2.5.0-3.fc31.i386/usr/share/licenses/bionetgen + cp -pr bionetgen-BioNetGen-2.5.0/LICENSE /builddir/build/BUILDROOT/bionetgen-2.5.0-3.fc31.i386/usr/share/licenses/bionetgen + RPM_EC=0 BUILDSTDERR: ++ jobs -p + exit 0 Provides: bionetgen = 2.5.0-3.fc31 bionetgen(x86-32) = 2.5.0-3.fc31 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libc.so.6 libc.so.6(GLIBC_2.0) libc.so.6(GLIBC_2.1) libc.so.6(GLIBC_2.1.3) libc.so.6(GLIBC_2.3.4) libc.so.6(GLIBC_2.4) libc.so.6(GLIBC_2.7) libgcc_s.so.1 libgcc_s.so.1(GCC_3.0) libm.so.6 libm.so.6(GLIBC_2.0) libm.so.6(GLIBC_2.29) libmuparser.so.2 libstdc++.so.6 libstdc++.so.6(CXXABI_1.3) libstdc++.so.6(CXXABI_1.3.8) libstdc++.so.6(CXXABI_1.3.9) libstdc++.so.6(GLIBCXX_3.4) libstdc++.so.6(GLIBCXX_3.4.11) libstdc++.so.6(GLIBCXX_3.4.20) libstdc++.so.6(GLIBCXX_3.4.21) libstdc++.so.6(GLIBCXX_3.4.9) rtld(GNU_HASH) Processing files: bionetgen-perl-2.5.0-3.fc31.noarch Provides: bionetgen-perl = 2.5.0-3.fc31 perl(Viz) Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/perl perl(Carp) perl(Class::Struct) perl(Config) perl(Cwd) perl(Data::Dumper) perl(Exporter) perl(File::Basename) perl(File::Path) perl(File::Spec) perl(File::Spec::Win32) perl(FindBin) perl(Getopt::Long) perl(IO::Handle) perl(IO::Select) perl(IPC::Open3) perl(List::Util) perl(Math::Trig) perl(POSIX) perl(Scalar::Util) perl(Storable) perl(Symbol) perl(constant) perl(lib) perl(strict) perl(vars) perl(warnings) Processing files: bionetgen-debugsource-2.5.0-3.fc31.i686 Provides: bionetgen-debugsource = 2.5.0-3.fc31 bionetgen-debugsource(x86-32) = 2.5.0-3.fc31 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: bionetgen-debuginfo-2.5.0-3.fc31.i686 Provides: bionetgen-debuginfo = 2.5.0-3.fc31 bionetgen-debuginfo(x86-32) = 2.5.0-3.fc31 debuginfo(build-id) = b1b1ab872db75b2985163ba18548adf737430241 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: bionetgen-debugsource(x86-32) = 2.5.0-3.fc31 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/bionetgen-2.5.0-3.fc31.i386 Wrote: /builddir/build/RPMS/bionetgen-debugsource-2.5.0-3.fc31.i686.rpm Wrote: /builddir/build/RPMS/bionetgen-2.5.0-3.fc31.i686.rpm Wrote: /builddir/build/RPMS/bionetgen-perl-2.5.0-3.fc31.noarch.rpm Wrote: /builddir/build/RPMS/bionetgen-debuginfo-2.5.0-3.fc31.i686.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.5hVj45 + umask 022 + cd /builddir/build/BUILD + cd bionetgen-2.5.0 + /usr/bin/rm -rf /builddir/build/BUILDROOT/bionetgen-2.5.0-3.fc31.i386 + RPM_EC=0 BUILDSTDERR: ++ jobs -p + exit 0 Child return code was: 0