Mock Version: 3.5 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/bionetgen.spec'], chrootPath='/var/lib/mock/fedora-rawhide-x86_64-1671798894.085067/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.o93qj4y_:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True) Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.o93qj4y_:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '50ceac5208c74972a5a39fa294582e3c', '-D', '/var/lib/mock/fedora-rawhide-x86_64-1671798894.085067/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.o93qj4y_:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/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', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False sh: line 1: /usr/bin/perl: No such file or directory Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1670716800 Wrote: /builddir/build/SRPMS/bionetgen-2.8.4-3.fc38.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/bionetgen.spec'], chrootPath='/var/lib/mock/fedora-rawhide-x86_64-1671798894.085067/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.o93qj4y_:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True) Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.o93qj4y_:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '0a9717e6af7345d3a237c57308d0f32a', '-D', '/var/lib/mock/fedora-rawhide-x86_64-1671798894.085067/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.o93qj4y_:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/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', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1670716800 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.KRSzYW + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf bionetgen-2.8.4 + /usr/bin/mkdir -p bionetgen-2.8.4 + cd bionetgen-2.8.4 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/bionetgen-BioNetGen-2.8.4.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + pushd bionetgen-BioNetGen-2.8.4 ~/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4 ~/build/BUILD/bionetgen-2.8.4 + rm -f bng2/libsource/gsl-1.9.tar.gz bng2/libsource/Mathutils.tar.gz bng2/libsource/muparser_v2_2_4.zip + tar -xvf bng2/libsource/cvode-2.6.0.tar.gz -C bng2/Network3 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 cvode-2.6.0/src/cvode/cvode_spils.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 + tar -xvf bng2/libsource/muparser_v2_2_4.tar.gz -C bng2/Network3 muparser_v2_2_4/._Changes.txt muparser_v2_2_4/Changes.txt muparser_v2_2_4/._Install.txt muparser_v2_2_4/Install.txt muparser_v2_2_4/._License.txt muparser_v2_2_4/License.txt muparser_v2_2_4/._Makefile.in muparser_v2_2_4/Makefile.in muparser_v2_2_4/._build muparser_v2_2_4/build/ muparser_v2_2_4/build/._autoconf muparser_v2_2_4/build/autoconf/ muparser_v2_2_4/build/._bakefiles muparser_v2_2_4/build/bakefiles/ muparser_v2_2_4/build/._makefile.mingw muparser_v2_2_4/build/makefile.mingw muparser_v2_2_4/build/._makefile.vc muparser_v2_2_4/build/makefile.vc muparser_v2_2_4/build/._msvc2013 muparser_v2_2_4/build/msvc2013/ muparser_v2_2_4/build/._obj muparser_v2_2_4/build/obj/ muparser_v2_2_4/build/msvc2013/._muparser.sln muparser_v2_2_4/build/msvc2013/muparser.sln muparser_v2_2_4/build/msvc2013/._muparser_example1.vcxproj muparser_v2_2_4/build/msvc2013/muparser_example1.vcxproj muparser_v2_2_4/build/msvc2013/._muparser_example1.vcxproj.filters muparser_v2_2_4/build/msvc2013/muparser_example1.vcxproj.filters muparser_v2_2_4/build/msvc2013/._muparser_example2.vcxproj muparser_v2_2_4/build/msvc2013/muparser_example2.vcxproj muparser_v2_2_4/build/msvc2013/._muparser_example2.vcxproj.filters muparser_v2_2_4/build/msvc2013/muparser_example2.vcxproj.filters muparser_v2_2_4/build/msvc2013/._muparser_muParser.vcxproj muparser_v2_2_4/build/msvc2013/muparser_muParser.vcxproj muparser_v2_2_4/build/msvc2013/._muparser_muParser.vcxproj.filters muparser_v2_2_4/build/msvc2013/muparser_muParser.vcxproj.filters muparser_v2_2_4/build/bakefiles/._Bakefiles.bkgen muparser_v2_2_4/build/bakefiles/Bakefiles.bkgen muparser_v2_2_4/build/bakefiles/._howto.txt muparser_v2_2_4/build/bakefiles/howto.txt muparser_v2_2_4/build/bakefiles/._muparser.bkl muparser_v2_2_4/build/bakefiles/muparser.bkl muparser_v2_2_4/build/bakefiles/._presets muparser_v2_2_4/build/bakefiles/presets/ muparser_v2_2_4/build/bakefiles/presets/._debugopt.bkl muparser_v2_2_4/build/bakefiles/presets/debugopt.bkl muparser_v2_2_4/build/bakefiles/presets/._setbuilddir.bkl muparser_v2_2_4/build/bakefiles/presets/setbuilddir.bkl muparser_v2_2_4/build/bakefiles/presets/._sharedopt.bkl muparser_v2_2_4/build/bakefiles/presets/sharedopt.bkl muparser_v2_2_4/build/bakefiles/presets/._unicodeopt.bkl muparser_v2_2_4/build/bakefiles/presets/unicodeopt.bkl muparser_v2_2_4/build/autoconf/._aclocal.m4 muparser_v2_2_4/build/autoconf/aclocal.m4 muparser_v2_2_4/build/autoconf/._acregen.sh muparser_v2_2_4/build/autoconf/acregen.sh muparser_v2_2_4/build/autoconf/._autoconf_inc.m4 muparser_v2_2_4/build/autoconf/autoconf_inc.m4 muparser_v2_2_4/build/autoconf/._bakefile-presets.m4 muparser_v2_2_4/build/autoconf/bakefile-presets.m4 muparser_v2_2_4/build/autoconf/._config.guess muparser_v2_2_4/build/autoconf/config.guess muparser_v2_2_4/build/autoconf/._config.sub muparser_v2_2_4/build/autoconf/config.sub muparser_v2_2_4/build/autoconf/._configure.ac muparser_v2_2_4/build/autoconf/configure.ac muparser_v2_2_4/build/autoconf/._install-sh muparser_v2_2_4/build/autoconf/install-sh muparser_v2_2_4/build/autoconf/._muparser.pc.in muparser_v2_2_4/build/autoconf/muparser.pc.in muparser_v2_2_4/._configure muparser_v2_2_4/configure muparser_v2_2_4/._docs muparser_v2_2_4/docs/ muparser_v2_2_4/docs/._Doxyfile muparser_v2_2_4/docs/Doxyfile muparser_v2_2_4/docs/._muparser_doc.html muparser_v2_2_4/docs/muparser_doc.html muparser_v2_2_4/._include muparser_v2_2_4/include/ muparser_v2_2_4/include/._muParser.h muparser_v2_2_4/include/muParser.h muparser_v2_2_4/include/._muParserBase.h muparser_v2_2_4/include/muParserBase.h muparser_v2_2_4/include/._muParserBytecode.h muparser_v2_2_4/include/muParserBytecode.h muparser_v2_2_4/include/._muParserCallback.h muparser_v2_2_4/include/muParserCallback.h muparser_v2_2_4/include/._muParserDef.h muparser_v2_2_4/include/muParserDef.h muparser_v2_2_4/include/._muParserDLL.h muparser_v2_2_4/include/muParserDLL.h muparser_v2_2_4/include/._muParserError.h muparser_v2_2_4/include/muParserError.h muparser_v2_2_4/include/._muParserFixes.h muparser_v2_2_4/include/muParserFixes.h muparser_v2_2_4/include/._muParserInt.h muparser_v2_2_4/include/muParserInt.h muparser_v2_2_4/include/._muParserStack.h muparser_v2_2_4/include/muParserStack.h muparser_v2_2_4/include/._muParserTemplateMagic.h muparser_v2_2_4/include/muParserTemplateMagic.h muparser_v2_2_4/include/._muParserTest.h muparser_v2_2_4/include/muParserTest.h muparser_v2_2_4/include/._muParserToken.h muparser_v2_2_4/include/muParserToken.h muparser_v2_2_4/include/._muParserTokenReader.h muparser_v2_2_4/include/muParserTokenReader.h muparser_v2_2_4/._lib muparser_v2_2_4/lib/ muparser_v2_2_4/lib/._Readme.txt muparser_v2_2_4/lib/Readme.txt muparser_v2_2_4/._samples muparser_v2_2_4/samples/ muparser_v2_2_4/samples/._example1 muparser_v2_2_4/samples/example1/ muparser_v2_2_4/samples/._example2 muparser_v2_2_4/samples/example2/ muparser_v2_2_4/samples/example2/._example2.c muparser_v2_2_4/samples/example2/example2.c muparser_v2_2_4/samples/example2/._muparser32.dll muparser_v2_2_4/samples/example2/muparser32.dll muparser_v2_2_4/samples/example2/._muparser32.lib muparser_v2_2_4/samples/example2/muparser32.lib muparser_v2_2_4/samples/example2/._muparser64.dll muparser_v2_2_4/samples/example2/muparser64.dll muparser_v2_2_4/samples/example2/._muparser64.lib muparser_v2_2_4/samples/example2/muparser64.lib muparser_v2_2_4/samples/example2/._muparserd32.dll muparser_v2_2_4/samples/example2/muparserd32.dll muparser_v2_2_4/samples/example2/._muparserd32.lib muparser_v2_2_4/samples/example2/muparserd32.lib muparser_v2_2_4/samples/example2/._muparserd64.dll muparser_v2_2_4/samples/example2/muparserd64.dll muparser_v2_2_4/samples/example2/._muparserd64.lib muparser_v2_2_4/samples/example2/muparserd64.lib muparser_v2_2_4/samples/example2/._Readme.txt muparser_v2_2_4/samples/example2/Readme.txt muparser_v2_2_4/samples/example1/._example1.cpp muparser_v2_2_4/samples/example1/example1.cpp muparser_v2_2_4/._src muparser_v2_2_4/src/ muparser_v2_2_4/src/._muParser.cpp muparser_v2_2_4/src/muParser.cpp muparser_v2_2_4/src/._muParserBase.cpp muparser_v2_2_4/src/muParserBase.cpp muparser_v2_2_4/src/._muParserBytecode.cpp muparser_v2_2_4/src/muParserBytecode.cpp muparser_v2_2_4/src/._muParserCallback.cpp muparser_v2_2_4/src/muParserCallback.cpp muparser_v2_2_4/src/._muParserDLL.cpp muparser_v2_2_4/src/muParserDLL.cpp muparser_v2_2_4/src/._muParserError.cpp muparser_v2_2_4/src/muParserError.cpp muparser_v2_2_4/src/._muParserInt.cpp muparser_v2_2_4/src/muParserInt.cpp muparser_v2_2_4/src/._muParserTest.cpp muparser_v2_2_4/src/muParserTest.cpp muparser_v2_2_4/src/._muParserTokenReader.cpp muparser_v2_2_4/src/muParserTokenReader.cpp Patch #0 (bionetgen-fix_linker.patch): + echo 'Patch #0 (bionetgen-fix_linker.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .backup --fuzz=0 patching file bng2/Network3/CMakeLists.txt Patch #1 (bionetgen-fix_cmake_minimum.patch): + echo 'Patch #1 (bionetgen-fix_cmake_minimum.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .backup --fuzz=0 patching file bng2/Network3/CMakeLists.txt patching file bng2/Network3/cvode-2.6.0/CMakeLists.txt Patch #2 (bionetgen-cmake-c99.patch): + echo 'Patch #2 (bionetgen-cmake-c99.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .c99 --fuzz=0 patching file bng2/Network3/cvode-2.6.0/config/SundialsFortran.cmake + rm -f bng2/libsource/cvode-2.6.0.tar.gz bng2/libsource/muparser_v2_2_4.tar.gz + popd ~/build/BUILD/bionetgen-2.8.4 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.SniVvf + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS ~/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3 ~/build/BUILD/bionetgen-2.8.4 + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd bionetgen-2.8.4 + pushd bionetgen-BioNetGen-2.8.4/bng2/Network3 + cd muparser_v2_2_4 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + '[' '-flto=auto -ffat-lto-objectsx' '!=' x ']' ++ find . -type f -name configure -print + for file in $(find . -type f -name configure -print) + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + '[' 1 = 1 ']' +++ dirname ./configure ++ find . -name config.guess -o -name config.sub + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./build/autoconf/config.sub + '[' -f /usr/lib/rpm/redhat/config.sub ']' + /usr/bin/rm -f ./build/autoconf/config.sub ++ basename ./build/autoconf/config.sub + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./build/autoconf/config.sub '/usr/lib/rpm/redhat/config.sub' -> './build/autoconf/config.sub' + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./build/autoconf/config.guess + '[' -f /usr/lib/rpm/redhat/config.guess ']' + /usr/bin/rm -f ./build/autoconf/config.guess ++ basename ./build/autoconf/config.guess + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./build/autoconf/config.guess '/usr/lib/rpm/redhat/config.guess' -> './build/autoconf/config.guess' + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']' ++ find . -name ltmain.sh ++ grep -q runstatedir=DIR ./configure + ./configure --build=x86_64-redhat-linux-gnu --host=x86_64-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/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared=no --enable-static=yes --enable-samples=no configure: WARNING: unrecognized options: --enable-static checking build system type... x86_64-redhat-linux-gnu checking host system type... x86_64-redhat-linux-gnu checking target system type... x86_64-redhat-linux-gnu checking for gawk... gawk checking for a BSD-compatible install... /usr/bin/install -c checking whether ln -s works... yes checking for x86_64-redhat-linux-gnu-ranlib... no checking for ranlib... ranlib checking for x86_64-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 we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking how to run the C++ preprocessor... g++ -E checking for the --enable-debug option... no checking for the --enable-shared option... no checking for the --enable-samples option... no checking whether we are using the Intel C compiler... no checking whether we are using the Intel C++ compiler... no checking whether we are using the Sun C++ compiler... no checking for x86_64-redhat-linux-gnu-ranlib... ranlib checking whether ln -s works... yes checking whether make sets $(MAKE)... yes checking for x86_64-redhat-linux-gnu-ar... no checking for ar... ar checking for x86_64-redhat-linux-gnu-strip... no checking for strip... strip checking for x86_64-redhat-linux-gnu-nm... no checking for nm... nm checking for command to install directories... /usr/bin/install -c -d checking if make is GNU make... egrep: warning: egrep is obsolescent; using grep -E yes checking for dependency tracking method... disabled configure: creating ./config.status config.status: creating Makefile config.status: creating build/autoconf/muparser.pc configure: WARNING: unrecognized options: --enable-static ---------------------------------------------------------------- Configuration for muparser 2.2.4 successfully completed. Summary of main configuration settings for muparser: - STATIC mode - RELEASE build - SAMPLES disabled Now, just run make. ---------------------------------------------------------------- + /usr/bin/make -O -j2 V=1 VERBOSE=1 g++ -c -o muParser_lib_muParser.o -DNDEBUG -I./include -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection ./src/muParser.cpp In file included from ./include/muParserStack.h:35, from ./include/muParserBase.h:39, from ./include/muParser.h:32, from ./src/muParser.cpp:26: ./include/muParserToken.h:72:12: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from ./include/muParserBase.h:33: /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ ./include/muParserBase.h:291:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ g++ -c -o muParser_lib_muParserBytecode.o -DNDEBUG -I./include -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection ./src/muParserBytecode.cpp In file included from ./include/muParserBytecode.h:35, from ./src/muParserBytecode.cpp:26: ./include/muParserToken.h:72:12: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from ./include/muParserError.h:34, from ./include/muParserBytecode.h:34: /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ ./src/muParserBytecode.cpp: In member function 'void mu::ParserByteCode::AddOp(mu::ECmdCode)': ./src/muParserBytecode.cpp:213:15: warning: enumeration value 'cmLE' not handled in switch [-Wswitch] 213 | switch(a_Oprt) | ^ ./src/muParserBytecode.cpp:213:15: warning: enumeration value 'cmGE' not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value 'cmNEQ' not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value 'cmEQ' not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value 'cmLT' not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value 'cmGT' not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value 'cmLAND' not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value 'cmLOR' not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value 'cmASSIGN' not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value 'cmBO' not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value 'cmBC' not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value 'cmIF' not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value 'cmELSE' not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value 'cmENDIF' not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value 'cmARG_SEP' not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value 'cmVAR' not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value 'cmVAL' not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value 'cmVARPOW2' not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value 'cmVARPOW3' not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value 'cmVARPOW4' not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value 'cmVARMUL' not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value 'cmPOW2' not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value 'cmFUNC' not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value 'cmFUNC_STR' not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value 'cmFUNC_BULK' not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value 'cmSTRING' not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value 'cmOPRT_BIN' not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value 'cmOPRT_POSTFIX' not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value 'cmOPRT_INFIX' not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value 'cmEND' not handled in switch [-Wswitch] ./src/muParserBytecode.cpp:213:15: warning: enumeration value 'cmUNKNOWN' not handled in switch [-Wswitch] g++ -c -o muParser_lib_muParserCallback.o -DNDEBUG -I./include -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection ./src/muParserCallback.cpp g++ -c -o muParser_lib_muParserDLL.o -DNDEBUG -I./include -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection ./src/muParserDLL.cpp g++ -c -o muParser_lib_muParserError.o -DNDEBUG -I./include -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection ./src/muParserError.cpp g++ -c -o muParser_lib_muParserBase.o -DNDEBUG -I./include -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection ./src/muParserBase.cpp In file included from ./include/muParserStack.h:35, from ./include/muParserBase.h:39, from ./src/muParserBase.cpp:26: ./include/muParserToken.h:72:12: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from ./include/muParserBase.h:33: /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ ./include/muParserBase.h:291:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ ./src/muParserBase.cpp: In member function 'void mu::ParserBase::ApplyFunc(mu::ParserStack > >&, mu::ParserStack > >&, int) const': ./src/muParserBase.cpp:838:11: warning: enumeration value 'cmLE' not handled in switch [-Wswitch] 838 | switch(funTok.GetCode()) | ^ ./src/muParserBase.cpp:838:11: warning: enumeration value 'cmGE' not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value 'cmNEQ' not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value 'cmEQ' not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value 'cmLT' not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value 'cmGT' not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value 'cmADD' not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value 'cmSUB' not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value 'cmMUL' not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value 'cmDIV' not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value 'cmPOW' not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value 'cmLAND' not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value 'cmLOR' not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value 'cmASSIGN' not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value 'cmBO' not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value 'cmBC' not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value 'cmIF' not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value 'cmELSE' not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value 'cmENDIF' not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value 'cmARG_SEP' not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value 'cmVAR' not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value 'cmVAL' not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value 'cmVARPOW2' not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value 'cmVARPOW3' not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value 'cmVARPOW4' not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value 'cmVARMUL' not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value 'cmPOW2' not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value 'cmSTRING' not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value 'cmEND' not handled in switch [-Wswitch] ./src/muParserBase.cpp:838:11: warning: enumeration value 'cmUNKNOWN' not handled in switch [-Wswitch] g++ -c -o muParser_lib_muParserInt.o -DNDEBUG -I./include -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection ./src/muParserInt.cpp In file included from ./include/muParserStack.h:35, from ./include/muParserBase.h:39, from ./include/muParserInt.h:29, from ./src/muParserInt.cpp:26: ./include/muParserToken.h:72:12: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from ./include/muParserBase.h:33: /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ ./include/muParserBase.h:291:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ g++ -c -o muParser_lib_muParserTokenReader.o -DNDEBUG -I./include -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection ./src/muParserTokenReader.cpp In file included from ./include/muParserTokenReader.h:39, from ./src/muParserTokenReader.cpp:32: ./include/muParserToken.h:72:12: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from ./include/muParserTokenReader.h:34: /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ In file included from ./src/muParserTokenReader.cpp:33: ./include/muParserBase.h:291:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ ./src/muParserTokenReader.cpp: In member function 'mu::ParserTokenReader* mu::ParserTokenReader::Clone(mu::ParserBase*) const': ./src/muParserTokenReader.cpp:150:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 150 | std::auto_ptr ptr(new ParserTokenReader(*this)); | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ g++ -c -o muParser_lib_muParserTest.o -DNDEBUG -I./include -O2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection ./src/muParserTest.cpp ./src/muParserTest.cpp:1387: warning: ignoring '#pragma warning ' [-Wunknown-pragmas] 1387 | #pragma warning(push) | ./src/muParserTest.cpp:1388: warning: ignoring '#pragma warning ' [-Wunknown-pragmas] 1388 | #pragma warning(disable:4127) | ./src/muParserTest.cpp:1390: warning: ignoring '#pragma warning ' [-Wunknown-pragmas] 1390 | #pragma warning(pop) | In file included from ./include/muParserStack.h:35, from ./include/muParserBase.h:39, from ./include/muParser.h:32, from ./include/muParserTest.h:32, from ./src/muParserTest.cpp:26: ./include/muParserToken.h:72:12: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from ./include/muParserBase.h:33: /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ ./include/muParserBase.h:291:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ ./src/muParserTest.cpp: In member function 'int mu::Test::ParserTester::EqnTest(const mu::string_type&, double, bool)': ./src/muParserTest.cpp:1261:14: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1261 | std::auto_ptr p1; | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ rm -f lib/libmuparser.a ar rcu lib/libmuparser.a muParser_lib_muParser.o muParser_lib_muParserBase.o muParser_lib_muParserBytecode.o muParser_lib_muParserCallback.o muParser_lib_muParserDLL.o muParser_lib_muParserError.o muParser_lib_muParserInt.o muParser_lib_muParserTest.o muParser_lib_muParserTokenReader.o ranlib lib/libmuparser.a + cd ../ + make -j1 -C src/util/mathutils make: Entering directory '/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/mathutils' gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o allocate.o allocate.c allocate.c: In function 'ALLOC_MATRIX': allocate.c:9:20: warning: unused variable 'j' [-Wunused-variable] 9 | register int i,j; | ^ allocate.c: In function 'IALLOC_MATRIX': allocate.c:100:20: warning: unused variable 'j' [-Wunused-variable] 100 | register int i,j; | ^ allocate.c: In function 'ZALLOC_MATRIX': allocate.c:191:20: warning: unused variable 'j' [-Wunused-variable] 191 | register int i,j; | ^ In file included from allocate.c:1: mathutils.h: At top level: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a allocate.o ar: creating libmathutils.a a - allocate.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o cabs.o cabs.c In file included from cabs.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a cabs.o a - cabs.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o cadd.o cadd.c In file included from cadd.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a cadd.o a - cadd.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o cconj.o cconj.c In file included from cconj.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a cconj.o a - cconj.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o cmult.o cmult.c In file included from cmult.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a cmult.o a - cmult.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o complex_zero.o complex_zero.c In file included from complex_zero.c:2: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a complex_zero.o a - complex_zero.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o copy_vector.o copy_vector.c In file included from copy_vector.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a copy_vector.o a - copy_vector.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o cprob.o cprob.c In file included from cprob.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a cprob.o a - cprob.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o csub.o csub.c In file included from csub.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a csub.o a - csub.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o dotp.o dotp.c In file included from dotp.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a dotp.o a - dotp.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o eigensystem.o eigensystem.c In file included from eigensystem.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a eigensystem.o a - eigensystem.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o expi.o expi.c In file included from expi.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a expi.o a - expi.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o gram_schmidt.o gram_schmidt.c In file included from gram_schmidt.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a gram_schmidt.o a - gram_schmidt.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o herm_matrix_mult.o herm_matrix_mult.c In file included from herm_matrix_mult.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a herm_matrix_mult.o a - herm_matrix_mult.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o herm_matrix_vector_mult.o herm_matrix_vector_mult.c In file included from herm_matrix_vector_mult.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a herm_matrix_vector_mult.o a - herm_matrix_vector_mult.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o icmult.o icmult.c In file included from icmult.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a icmult.o a - icmult.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o init.o init.c In file included from init.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a init.o a - init.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o integration.o integration.c In file included from integration.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a integration.o a - integration.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o linsolve.o linsolve.c linsolve.c: In function 'LINSOLVE': linsolve.c:16:20: warning: unused variable 'j' [-Wunused-variable] 16 | register int i,j; | ^ linsolve.c:16:18: warning: unused variable 'i' [-Wunused-variable] 16 | register int i,j; | ^ In file included from linsolve.c:1: mathutils.h: At top level: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a linsolve.o a - linsolve.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o matherr.o matherr.c In file included from matherr.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a matherr.o a - matherr.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o matrix_add.o matrix_add.c In file included from matrix_add.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a matrix_add.o a - matrix_add.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o matrix_elt.o matrix_elt.c In file included from matrix_elt.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a matrix_elt.o a - matrix_elt.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o matrix_mult.o matrix_mult.c In file included from matrix_mult.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a matrix_mult.o a - matrix_mult.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o matrix_sub.o matrix_sub.c In file included from matrix_sub.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a matrix_sub.o a - matrix_sub.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o matrix_transpose.o matrix_transpose.c In file included from matrix_transpose.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a matrix_transpose.o a - matrix_transpose.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o matrix_vector_mult.o matrix_vector_mult.c In file included from matrix_vector_mult.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a matrix_vector_mult.o a - matrix_vector_mult.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o matrixexp.o matrixexp.c In file included from matrixexp.c:5: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a matrixexp.o a - matrixexp.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o minimum.o minimum.c minimum.c: In function 'MIN_BRACKET': minimum.c:17:26: warning: unused variable 'dum' [-Wunused-variable] 17 | double ulim,u,r,q,fu,dum; | ^~~ In file included from minimum.c:3: mathutils.h: At top level: mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a minimum.o a - minimum.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o norm.o norm.c norm.c: In function 'NORM': norm.c:14:12: warning: unused variable 'norm' [-Wunused-variable] 14 | double norm; | ^~~~ In file included from norm.c:1: mathutils.h: At top level: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a norm.o a - norm.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o normsq.o normsq.c normsq.c: In function 'NORMSQ': normsq.c:13:12: warning: unused variable 'norm' [-Wunused-variable] 13 | double norm; | ^~~~ In file included from normsq.c:1: mathutils.h: At top level: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a normsq.o a - normsq.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o project.o project.c In file included from project.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a project.o a - project.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o random.o random.c In file included from random.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a random.o a - random.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o rcmult.o rcmult.c In file included from rcmult.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a rcmult.o a - rcmult.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o rect_transpose.o rect_transpose.c rect_transpose.c: In function 'RECT_TRANSPOSE': rect_transpose.c:5:26: warning: unused variable 'Atptr' [-Wunused-variable] 5 | double **At, *Aptr, *Atptr; | ^~~~~ rect_transpose.c:5:19: warning: unused variable 'Aptr' [-Wunused-variable] 5 | double **At, *Aptr, *Atptr; | ^~~~ In file included from rect_transpose.c:1: mathutils.h: At top level: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a rect_transpose.o a - rect_transpose.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o roots.o roots.c In file included from roots.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ roots.c: In function 'ROOT_FIND': roots.c:55:13: warning: 'e' may be used uninitialized [-Wmaybe-uninitialized] 55 | if (fabs(e) >= tol1 && fabs(fa) > fabs(fb)) { | ^~~~~~~ roots.c:32:29: note: 'e' was declared here 32 | double a=x1,b=x2,c=x2,d,e,min1,min2; | ^ ar rv libmathutils.a roots.o a - roots.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o runge-kutta.o runge-kutta.c In file included from runge-kutta.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a runge-kutta.o a - runge-kutta.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o scale_vector.o scale_vector.c In file included from scale_vector.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a scale_vector.o a - scale_vector.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o splines.o splines.c In file included from splines.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a splines.o a - splines.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o sum_vector.o sum_vector.c In file included from sum_vector.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a sum_vector.o a - sum_vector.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o svd.o svd.c In file included from svd.c:2: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ ar rv libmathutils.a svd.o a - svd.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o sym_linsolve.o sym_linsolve.c In file included from sym_linsolve.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a sym_linsolve.o a - sym_linsolve.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o sym_matrix_mult.o sym_matrix_mult.c In file included from sym_matrix_mult.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a sym_matrix_mult.o a - sym_matrix_mult.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o sym_matrix_vector_mult.o sym_matrix_vector_mult.c In file included from sym_matrix_vector_mult.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a sym_matrix_vector_mult.o a - sym_matrix_vector_mult.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o sympos_linsolve.o sympos_linsolve.c In file included from sympos_linsolve.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a sympos_linsolve.o a - sympos_linsolve.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o vector_add.o vector_add.c In file included from vector_add.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a vector_add.o a - vector_add.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o vector_dist.o vector_dist.c In file included from vector_dist.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a vector_dist.o a - vector_dist.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o zcopy_vector.o zcopy_vector.c In file included from zcopy_vector.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a zcopy_vector.o a - zcopy_vector.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o zdotc.o zdotc.c In file included from zdotc.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a zdotc.o a - zdotc.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o zdotu.o zdotu.c In file included from zdotu.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a zdotu.o a - zdotu.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o zmatrix_mult.o zmatrix_mult.c In file included from zmatrix_mult.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a zmatrix_mult.o a - zmatrix_mult.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o zmatrix_transpose.o zmatrix_transpose.c In file included from zmatrix_transpose.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a zmatrix_transpose.o a - zmatrix_transpose.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o zmatrix_vector_mult.o zmatrix_vector_mult.c In file included from zmatrix_vector_mult.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a zmatrix_vector_mult.o a - zmatrix_vector_mult.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o znorm.o znorm.c In file included from znorm.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a znorm.o a - znorm.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o znormsq.o znormsq.c In file included from znormsq.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a znormsq.o a - znormsq.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o zrscale_vector.o zrscale_vector.c In file included from zrscale_vector.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a zrscale_vector.o a - zrscale_vector.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o zscale_vector.o zscale_vector.c In file included from zscale_vector.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a zscale_vector.o a - zscale_vector.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o zsum_vector.o zsum_vector.c In file included from zsum_vector.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a zsum_vector.o a - zsum_vector.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o zsym_linsolve.o zsym_linsolve.c In file included from zsym_linsolve.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a zsym_linsolve.o a - zsym_linsolve.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o zmatrix_add.o zmatrix_add.c In file included from zmatrix_add.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a zmatrix_add.o a - zmatrix_add.o gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c -o zmatrix_sub.o zmatrix_sub.c In file included from zmatrix_sub.c:1: mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ ar rv libmathutils.a zmatrix_sub.o a - zmatrix_sub.o ranlib ./libmathutils.a make: Leaving directory '/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/mathutils' ++ echo '-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' ++ sed -e s/-Werror=format-security/-Wno-error=format-security/g + SETOPT_FLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + mkdir -p cvode-2.6.0/build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + /usr/bin/cmake -S . -B cvode-2.6.0/build -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -S cvode-2.6.0 -B cvode-2.6.0/build '-DCMAKE_MODULE_LINKER_FLAGS:STRING=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' -DCMAKE_INSTALL_PREFIX=/usr -DEXAMPLES_ENABLE=OFF -DEXAMPLES_INSTALL=OFF -DBUILD_SHARED_LIBS:BOOL=OFF -DBUILD_STATIC_LIBS:BOOL=ON -DMPI_ENABLE:BOOL=OFF -DFCMIX_ENABLE:BOOL=ON CMake Warning: Ignoring extra path from command line: "/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3" -- The C compiler identification is GNU 13.0.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- The Fortran compiler identification is GNU 13.0.0 -- Searching for a Fortran compiler... /usr/bin/gfortran -- Trying to compile and link a simple Fortran program... OK CMake Warning (dev) in /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/FortranTest/CMakeLists.txt: No cmake_minimum_required command is present. A line of code such as cmake_minimum_required(VERSION 3.25) should be added at the top of the file. The version specified may be lower if you wish to support older CMake versions for this project. For more information run "cmake --help-policy CMP0000". This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) in /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/FortranTest/CMakeLists.txt: No cmake_minimum_required command is present. A line of code such as cmake_minimum_required(VERSION 3.25) should be added at the top of the file. The version specified may be lower if you wish to support older CMake versions for this project. For more information run "cmake --help-policy CMP0000". This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) in /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/FortranTest/CMakeLists.txt: No cmake_minimum_required command is present. A line of code such as cmake_minimum_required(VERSION 3.25) should be added at the top of the file. The version specified may be lower if you wish to support older CMake versions for this project. For more information run "cmake --help-policy CMP0000". This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) in /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/FortranTest/CMakeLists.txt: No cmake_minimum_required command is present. A line of code such as cmake_minimum_required(VERSION 3.25) should be added at the top of the file. The version specified may be lower if you wish to support older CMake versions for this project. For more information run "cmake --help-policy CMP0000". This warning is for project developers. Use -Wno-dev to suppress it. -- Determining Fortran name-mangling scheme... OK -- Added NVECTOR_SERIAL module -- Added CVODE module -- Added CVODE FCMIX module -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_CXX_FLAGS_RELEASE CMAKE_INSTALL_DO_STRIP CMAKE_MODULE_LINKER_FLAGS INCLUDE_INSTALL_DIR LIB_INSTALL_DIR LIB_SUFFIX SHARE_INSTALL_PREFIX SYSCONF_INSTALL_DIR -- Build files have been written to: /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build + /usr/bin/cmake --build cvode-2.6.0/build -j2 --verbose /usr/bin/cmake -S/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0 -B/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/CMakeFiles /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build//CMakeFiles/progress.marks /usr/bin/gmake -f CMakeFiles/Makefile2 all gmake[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build' /usr/bin/gmake -f src/nvec_ser/CMakeFiles/sundials_nvecserial_static.dir/build.make src/nvec_ser/CMakeFiles/sundials_nvecserial_static.dir/depend /usr/bin/gmake -f src/nvec_ser/CMakeFiles/sundials_fnvecserial_static.dir/build.make src/nvec_ser/CMakeFiles/sundials_fnvecserial_static.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build' cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0 /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/nvec_ser /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/nvec_ser /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/nvec_ser/CMakeFiles/sundials_nvecserial_static.dir/DependInfo.cmake --color= gmake[2]: Entering directory '/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build' cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0 /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/nvec_ser /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/nvec_ser /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/nvec_ser/CMakeFiles/sundials_fnvecserial_static.dir/DependInfo.cmake --color= gmake[2]: Leaving directory '/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build' /usr/bin/gmake -f src/nvec_ser/CMakeFiles/sundials_nvecserial_static.dir/build.make src/nvec_ser/CMakeFiles/sundials_nvecserial_static.dir/build gmake[2]: Leaving directory '/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build' /usr/bin/gmake -f src/nvec_ser/CMakeFiles/sundials_fnvecserial_static.dir/build.make src/nvec_ser/CMakeFiles/sundials_fnvecserial_static.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build' gmake[2]: Entering directory '/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build' [ 2%] Building C object src/nvec_ser/CMakeFiles/sundials_nvecserial_static.dir/nvector_serial.c.o cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/nvec_ser && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/nvec_ser/. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -MD -MT src/nvec_ser/CMakeFiles/sundials_nvecserial_static.dir/nvector_serial.c.o -MF CMakeFiles/sundials_nvecserial_static.dir/nvector_serial.c.o.d -o CMakeFiles/sundials_nvecserial_static.dir/nvector_serial.c.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/nvec_ser/nvector_serial.c [ 5%] Building C object src/nvec_ser/CMakeFiles/sundials_fnvecserial_static.dir/fnvector_serial.c.o cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/nvec_ser && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/nvec_ser/. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -MD -MT src/nvec_ser/CMakeFiles/sundials_fnvecserial_static.dir/fnvector_serial.c.o -MF CMakeFiles/sundials_fnvecserial_static.dir/fnvector_serial.c.o.d -o CMakeFiles/sundials_fnvecserial_static.dir/fnvector_serial.c.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/nvec_ser/fnvector_serial.c [ 8%] Linking C static library libsundials_fnvecserial.a cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/nvec_ser && /usr/bin/cmake -P CMakeFiles/sundials_fnvecserial_static.dir/cmake_clean_target.cmake cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/nvec_ser && /usr/bin/cmake -E cmake_link_script CMakeFiles/sundials_fnvecserial_static.dir/link.txt --verbose=1 /usr/bin/ar qc libsundials_fnvecserial.a CMakeFiles/sundials_fnvecserial_static.dir/fnvector_serial.c.o /usr/bin/ranlib libsundials_fnvecserial.a gmake[2]: Leaving directory '/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build' [ 8%] Built target sundials_fnvecserial_static /usr/bin/gmake -f src/cvode/CMakeFiles/sundials_cvode_static.dir/build.make src/cvode/CMakeFiles/sundials_cvode_static.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build' cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0 /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode/CMakeFiles/sundials_cvode_static.dir/DependInfo.cmake --color= gmake[2]: Leaving directory '/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build' /usr/bin/gmake -f src/cvode/CMakeFiles/sundials_cvode_static.dir/build.make src/cvode/CMakeFiles/sundials_cvode_static.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build' [ 10%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode.c.o cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode.c.o -MF CMakeFiles/sundials_cvode_static.dir/cvode.c.o.d -o CMakeFiles/sundials_cvode_static.dir/cvode.c.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/cvode.c [ 13%] Building C object src/nvec_ser/CMakeFiles/sundials_nvecserial_static.dir/__/sundials/sundials_math.c.o cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/nvec_ser && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/nvec_ser/. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -MD -MT src/nvec_ser/CMakeFiles/sundials_nvecserial_static.dir/__/sundials/sundials_math.c.o -MF CMakeFiles/sundials_nvecserial_static.dir/__/sundials/sundials_math.c.o.d -o CMakeFiles/sundials_nvecserial_static.dir/__/sundials/sundials_math.c.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/sundials/sundials_math.c [ 16%] Linking C static library libsundials_nvecserial.a cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/nvec_ser && /usr/bin/cmake -P CMakeFiles/sundials_nvecserial_static.dir/cmake_clean_target.cmake cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/nvec_ser && /usr/bin/cmake -E cmake_link_script CMakeFiles/sundials_nvecserial_static.dir/link.txt --verbose=1 /usr/bin/ar qc libsundials_nvecserial.a CMakeFiles/sundials_nvecserial_static.dir/nvector_serial.c.o CMakeFiles/sundials_nvecserial_static.dir/__/sundials/sundials_math.c.o /usr/bin/ranlib libsundials_nvecserial.a gmake[2]: Leaving directory '/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build' [ 16%] Built target sundials_nvecserial_static /usr/bin/gmake -f src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/build.make src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build' cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0 /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode/fcmix /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/DependInfo.cmake --color= gmake[2]: Leaving directory '/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build' /usr/bin/gmake -f src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/build.make src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build' [ 18%] Building C object src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvband.c.o cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode/fcmix && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/. -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -MD -MT src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvband.c.o -MF CMakeFiles/sundials_fcvode_static.dir/fcvband.c.o.d -o CMakeFiles/sundials_fcvode_static.dir/fcvband.c.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvband.c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvband.c: In function 'fcvbandsetjac_': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvband.c:48:12: warning: variable 'cv_mem' set but not used [-Wunused-but-set-variable] 48 | CVodeMem cv_mem; | ^~~~~~ [ 21%] Building C object src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvbbd.c.o cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode/fcmix && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/. -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -MD -MT src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvbbd.c.o -MF CMakeFiles/sundials_fcvode_static.dir/fcvbbd.c.o.d -o CMakeFiles/sundials_fcvode_static.dir/fcvbbd.c.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvbbd.c [ 24%] Building C object src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvbp.c.o cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode/fcmix && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/. -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -MD -MT src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvbp.c.o -MF CMakeFiles/sundials_fcvode_static.dir/fcvbp.c.o.d -o CMakeFiles/sundials_fcvode_static.dir/fcvbp.c.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvbp.c [ 27%] Building C object src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvdense.c.o cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode/fcmix && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/. -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -MD -MT src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvdense.c.o -MF CMakeFiles/sundials_fcvode_static.dir/fcvdense.c.o.d -o CMakeFiles/sundials_fcvode_static.dir/fcvdense.c.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvdense.c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvdense.c: In function 'fcvdensesetjac_': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvdense.c:48:12: warning: variable 'cv_mem' set but not used [-Wunused-but-set-variable] 48 | CVodeMem cv_mem; | ^~~~~~ [ 29%] Building C object src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvewt.c.o cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode/fcmix && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/. -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -MD -MT src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvewt.c.o -MF CMakeFiles/sundials_fcvode_static.dir/fcvewt.c.o.d -o CMakeFiles/sundials_fcvode_static.dir/fcvewt.c.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvewt.c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvewt.c: In function 'fcvewtset_': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvewt.c:46:12: warning: variable 'cv_mem' set but not used [-Wunused-but-set-variable] 46 | CVodeMem cv_mem; | ^~~~~~ [ 32%] Building C object src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvjtimes.c.o cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode/fcmix && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/. -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -MD -MT src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvjtimes.c.o -MF CMakeFiles/sundials_fcvode_static.dir/fcvjtimes.c.o.d -o CMakeFiles/sundials_fcvode_static.dir/fcvjtimes.c.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvjtimes.c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvjtimes.c: In function 'fcvspilssetjac_': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvjtimes.c:52:12: warning: variable 'cv_mem' set but not used [-Wunused-but-set-variable] 52 | CVodeMem cv_mem; | ^~~~~~ [ 35%] Building C object src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvode.c.o cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode/fcmix && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/. -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -MD -MT src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvode.c.o -MF CMakeFiles/sundials_fcvode_static.dir/fcvode.c.o.d -o CMakeFiles/sundials_fcvode_static.dir/fcvode.c.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvode.c [ 37%] Building C object src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvpreco.c.o cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode/fcmix && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/. -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -MD -MT src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvpreco.c.o -MF CMakeFiles/sundials_fcvode_static.dir/fcvpreco.c.o.d -o CMakeFiles/sundials_fcvode_static.dir/fcvpreco.c.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvpreco.c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvpreco.c: In function 'fcvspilssetprec_': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvpreco.c:59:12: warning: variable 'cv_mem' set but not used [-Wunused-but-set-variable] 59 | CVodeMem cv_mem; | ^~~~~~ [ 40%] Building C object src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvroot.c.o cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode/fcmix && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/. -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/.. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -MD -MT src/cvode/fcmix/CMakeFiles/sundials_fcvode_static.dir/fcvroot.c.o -MF CMakeFiles/sundials_fcvode_static.dir/fcvroot.c.o.d -o CMakeFiles/sundials_fcvode_static.dir/fcvroot.c.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvroot.c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvroot.c: In function 'fcvrootinit_': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/fcmix/fcvroot.c:44:12: warning: variable 'cv_mem' set but not used [-Wunused-but-set-variable] 44 | CVodeMem cv_mem; | ^~~~~~ [ 43%] Linking C static library libsundials_fcvode.a cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode/fcmix && /usr/bin/cmake -P CMakeFiles/sundials_fcvode_static.dir/cmake_clean_target.cmake cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode/fcmix && /usr/bin/cmake -E cmake_link_script CMakeFiles/sundials_fcvode_static.dir/link.txt --verbose=1 /usr/bin/ar qc libsundials_fcvode.a CMakeFiles/sundials_fcvode_static.dir/fcvband.c.o CMakeFiles/sundials_fcvode_static.dir/fcvbbd.c.o CMakeFiles/sundials_fcvode_static.dir/fcvbp.c.o CMakeFiles/sundials_fcvode_static.dir/fcvdense.c.o CMakeFiles/sundials_fcvode_static.dir/fcvewt.c.o CMakeFiles/sundials_fcvode_static.dir/fcvjtimes.c.o CMakeFiles/sundials_fcvode_static.dir/fcvode.c.o CMakeFiles/sundials_fcvode_static.dir/fcvpreco.c.o CMakeFiles/sundials_fcvode_static.dir/fcvroot.c.o /usr/bin/ranlib libsundials_fcvode.a gmake[2]: Leaving directory '/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build' [ 43%] Built target sundials_fcvode_static [ 45%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_io.c.o cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_io.c.o -MF CMakeFiles/sundials_cvode_static.dir/cvode_io.c.o.d -o CMakeFiles/sundials_cvode_static.dir/cvode_io.c.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/cvode_io.c [ 48%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_direct.c.o cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_direct.c.o -MF CMakeFiles/sundials_cvode_static.dir/cvode_direct.c.o.d -o CMakeFiles/sundials_cvode_static.dir/cvode_direct.c.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/cvode_direct.c [ 51%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_band.c.o cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_band.c.o -MF CMakeFiles/sundials_cvode_static.dir/cvode_band.c.o.d -o CMakeFiles/sundials_cvode_static.dir/cvode_band.c.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/cvode_band.c [ 54%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_dense.c.o cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables 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-I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_diag.c.o -MF CMakeFiles/sundials_cvode_static.dir/cvode_diag.c.o.d -o CMakeFiles/sundials_cvode_static.dir/cvode_diag.c.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/cvode_diag.c [ 59%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_spils.c.o cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_spils.c.o -MF CMakeFiles/sundials_cvode_static.dir/cvode_spils.c.o.d -o CMakeFiles/sundials_cvode_static.dir/cvode_spils.c.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/cvode_spils.c [ 62%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_spbcgs.c.o cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_spbcgs.c.o -MF CMakeFiles/sundials_cvode_static.dir/cvode_spbcgs.c.o.d -o CMakeFiles/sundials_cvode_static.dir/cvode_spbcgs.c.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/cvode_spbcgs.c [ 64%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_spgmr.c.o cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_spgmr.c.o -MF CMakeFiles/sundials_cvode_static.dir/cvode_spgmr.c.o.d -o CMakeFiles/sundials_cvode_static.dir/cvode_spgmr.c.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/cvode_spgmr.c [ 67%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_sptfqmr.c.o cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_sptfqmr.c.o -MF CMakeFiles/sundials_cvode_static.dir/cvode_sptfqmr.c.o.d -o CMakeFiles/sundials_cvode_static.dir/cvode_sptfqmr.c.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/cvode_sptfqmr.c [ 70%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_bandpre.c.o cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_bandpre.c.o -MF CMakeFiles/sundials_cvode_static.dir/cvode_bandpre.c.o.d -o CMakeFiles/sundials_cvode_static.dir/cvode_bandpre.c.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/cvode_bandpre.c [ 72%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_bbdpre.c.o cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/cvode_bbdpre.c.o -MF CMakeFiles/sundials_cvode_static.dir/cvode_bbdpre.c.o.d -o CMakeFiles/sundials_cvode_static.dir/cvode_bbdpre.c.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/cvode_bbdpre.c [ 75%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_nvector.c.o cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic 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-I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_math.c.o -MF CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_math.c.o.d -o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_math.c.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/sundials/sundials_math.c [ 81%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_direct.c.o cd 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src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_direct.c.o -MF CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_direct.c.o.d -o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_direct.c.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/sundials/sundials_direct.c [ 83%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_band.c.o cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_band.c.o -MF CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_band.c.o.d -o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_band.c.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/sundials/sundials_band.c [ 86%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_dense.c.o cd 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src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_dense.c.o -MF CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_dense.c.o.d -o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_dense.c.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/sundials/sundials_dense.c [ 89%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_iterative.c.o cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_iterative.c.o -MF CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_iterative.c.o.d -o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_iterative.c.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/sundials/sundials_iterative.c [ 91%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_spbcgs.c.o cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_spbcgs.c.o -MF CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_spbcgs.c.o.d -o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_spbcgs.c.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/sundials/sundials_spbcgs.c [ 94%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_spgmr.c.o cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_spgmr.c.o -MF CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_spgmr.c.o.d -o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_spgmr.c.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/sundials/sundials_spgmr.c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/sundials/sundials_spgmr.c: In function 'SpgmrFree': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/sundials/sundials_spgmr.c:439:29: warning: variable 'yg' set but not used [-Wunused-but-set-variable] 439 | realtype **Hes, *givens, *yg; | ^~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/sundials/sundials_spgmr.c:439:20: warning: variable 'givens' set but not used [-Wunused-but-set-variable] 439 | realtype **Hes, *givens, *yg; | ^~~~~~ [ 97%] Building C object src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_sptfqmr.c.o cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/gcc -DBUILD_SUNDIALS_LIBRARY -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/. -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/cvode/../sundials -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -MD -MT src/cvode/CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_sptfqmr.c.o -MF CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_sptfqmr.c.o.d -o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_sptfqmr.c.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/src/sundials/sundials_sptfqmr.c [100%] Linking C static library libsundials_cvode.a cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/cmake -P CMakeFiles/sundials_cvode_static.dir/cmake_clean_target.cmake cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/src/cvode && /usr/bin/cmake -E cmake_link_script CMakeFiles/sundials_cvode_static.dir/link.txt --verbose=1 /usr/bin/ar qc libsundials_cvode.a CMakeFiles/sundials_cvode_static.dir/cvode.c.o CMakeFiles/sundials_cvode_static.dir/cvode_io.c.o CMakeFiles/sundials_cvode_static.dir/cvode_direct.c.o CMakeFiles/sundials_cvode_static.dir/cvode_band.c.o CMakeFiles/sundials_cvode_static.dir/cvode_dense.c.o CMakeFiles/sundials_cvode_static.dir/cvode_diag.c.o CMakeFiles/sundials_cvode_static.dir/cvode_spils.c.o CMakeFiles/sundials_cvode_static.dir/cvode_spbcgs.c.o CMakeFiles/sundials_cvode_static.dir/cvode_spgmr.c.o CMakeFiles/sundials_cvode_static.dir/cvode_sptfqmr.c.o CMakeFiles/sundials_cvode_static.dir/cvode_bandpre.c.o CMakeFiles/sundials_cvode_static.dir/cvode_bbdpre.c.o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_nvector.c.o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_math.c.o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_direct.c.o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_band.c.o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_dense.c.o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_iterative.c.o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_spbcgs.c.o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_spgmr.c.o CMakeFiles/sundials_cvode_static.dir/__/sundials/sundials_sptfqmr.c.o /usr/bin/ranlib libsundials_cvode.a gmake[2]: Leaving directory '/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build' [100%] Built target sundials_cvode_static gmake[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/cvode-2.6.0/build/CMakeFiles 0 ++ echo '-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' ++ sed -e s/-Werror=format-security/-Wno-error=format-security/g + SETOPT_FLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src/util/mathutils -I../cvode-2.6.0/include -I../muparser_v2_2_4/include' + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src/util/mathutils -I../cvode-2.6.0/include -I../muparser_v2_2_4/include' + export 'CXXFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser' + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser' + mkdir -p build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src/util/mathutils -I../cvode-2.6.0/include -I../muparser_v2_2_4/include' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + /usr/bin/cmake -S . -B build -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DBUILD_SHARED_LIBS:BOOL=OFF -DBUILD_STATIC_LIBS:BOOL=ON -- The C compiler identification is GNU 13.0.0 -- The CXX compiler identification is GNU 13.0.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: BUILD_SHARED_LIBS BUILD_STATIC_LIBS CMAKE_CXX_FLAGS_RELEASE CMAKE_C_FLAGS_RELEASE CMAKE_Fortran_FLAGS_RELEASE CMAKE_INSTALL_DO_STRIP CMAKE_SKIP_INSTALL_RPATH INCLUDE_INSTALL_DIR LIB_INSTALL_DIR LIB_SUFFIX SHARE_INSTALL_PREFIX SYSCONF_INSTALL_DIR -- Build files have been written to: /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/build + /usr/bin/cmake --build build -j2 --verbose /usr/bin/cmake -S/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3 -B/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/build/CMakeFiles /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/build//CMakeFiles/progress.marks /usr/bin/gmake -f CMakeFiles/Makefile2 all gmake[1]: Entering directory '/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/build' /usr/bin/gmake -f CMakeFiles/run_network.dir/build.make CMakeFiles/run_network.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/build' cd /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3 /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3 /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/build /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/build /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/build/CMakeFiles/run_network.dir/DependInfo.cmake --color= gmake[2]: Leaving directory '/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/build' /usr/bin/gmake -f CMakeFiles/run_network.dir/build.make CMakeFiles/run_network.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/build' [ 3%] Building CXX object CMakeFiles/run_network.dir/src/network3.cpp.o [ 3%] Building CXX object CMakeFiles/run_network.dir/src/network.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/network.cpp.o -MF CMakeFiles/run_network.dir/src/network.cpp.o.d -o CMakeFiles/run_network.dir/src/network.cpp.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/network3.cpp.o -MF CMakeFiles/run_network.dir/src/network3.cpp.o.d -o CMakeFiles/run_network.dir/src/network3.cpp.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network3.cpp In file included from ../muparser_v2_2_4/include/muParserStack.h:35, from ../muparser_v2_2_4/include/muParserBase.h:39, from ../muparser_v2_2_4/include/muParser.h:32, from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.h:36, from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network3.hh:12, from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network3.cpp:8: ../muparser_v2_2_4/include/muParserToken.h:72:12: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from ../muparser_v2_2_4/include/muParserStack.h:35, from ../muparser_v2_2_4/include/muParserBase.h:39, from ../muparser_v2_2_4/include/muParser.h:32, from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.h:36, from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:54: ../muparser_v2_2_4/include/muParserToken.h:72:12: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from ../muparser_v2_2_4/include/muParserBase.h:33: /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from ../muparser_v2_2_4/include/muParserBase.h:33: /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ ../muparser_v2_2_4/include/muParserBase.h:291:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ ../muparser_v2_2_4/include/muParserBase.h:291:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp: In function 'void read_functions_array(const char*, Elt_array*&, std::map, double*>&, std::map, int>, std::map, int>, double*)': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:440:13: warning: variable 'index' set but not used [-Wunused-but-set-variable] 440 | int index; | ^~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp: In function 'Rxn* new_Rxn(int, int, int, int*, int*, int, int, int*, double, Elt_array*)': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:1132:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1132 | register int i; | ^ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp: In function 'int* read_indices_Rxn(char*, int*, Elt_array*, int)': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:1543:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1543 | register int i; | ^ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp: In function 'void print_Rxn_array(FILE*, Rxn_array*, Elt_array*, Elt_array*)': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:1925:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1925 | register int i; | ^ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:1927:15: warning: variable 'sarr' set but not used [-Wunused-but-set-variable] 1927 | Elt **sarr, **rarr; | ^~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp: In function 'int n_species_active()': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:2068:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2068 | register int i; | ^ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp: In function 'int get_conc_network(double*)': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:2088:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2088 | register int i; | ^ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp: In function 'int set_conc_network(double*)': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:2110:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2110 | register int i, n_species; | ^ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:2110:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2110 | register int i, n_species; | ^~~~~~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp: In function 'int rxn_rates_network(double*, int)': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:2729:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2729 | register int i; | ^ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp: In function 'void derivs_network(double, double*, double*)': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:2782:15: warning: unused variable 'rarray' [-Wunused-variable] 2782 | Rxn **rarray, *rxn; | ^~~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:2783:15: warning: variable 'rates' set but not used [-Wunused-but-set-variable] 2783 | Elt** rates; | ^~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp: In function 'int print_derivs_network(FILE*)': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:2957:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2957 | register int i/*,j*/; | ^ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp: In function 'int print_derivs_species_network(FILE*)': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:2990:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2990 | register int i/*,j*/; | ^ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp: In function 'int print_rates_network(FILE*, int)': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:3019:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 3019 | register int i; | ^ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp: In function 'void sparse_jac_matlab(FILE*)': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:3198:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 3198 | register int i, j, r, n; | ^ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:3198:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 3198 | register int i, j, r, n; | ^ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:3198:28: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 3198 | register int i, j, r, n; | ^ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:3198:31: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 3198 | register int i, j, r, n; | ^ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:3204:15: warning: variable 'rates' set but not used [-Wunused-but-set-variable] 3204 | Elt** rates; | ^~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp: In function 'void CVjac_network(long int, DlsMat, realtype, N_Vector, N_Vector, void*, N_Vector, N_Vector, N_Vector)': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:3272:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 3272 | register int i, j, r, n; | ^ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:3272:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 3272 | register int i, j, r, n; | ^ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:3272:28: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 3272 | register int i, j, r, n; | ^ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:3272:31: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 3272 | register int i, j, r, n; | ^ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:3277:15: warning: variable 'rates' set but not used [-Wunused-but-set-variable] 3277 | Elt** rates; | ^~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp: In function 'int CVjtimes(N_Vector, N_Vector, realtype, N_Vector, N_Vector, void*, N_Vector)': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:3333:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 3333 | register int i, j, r, n; | ^ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:3333:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 3333 | register int i, j, r, n; | ^ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:3333:28: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 3333 | register int i, j, r, n; | ^ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:3333:31: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 3333 | register int i, j, r, n; | ^ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:3338:15: warning: variable 'rates' set but not used [-Wunused-but-set-variable] 3338 | Elt** rates; | ^~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp: In function 'int print_flux_network(FILE*, double, int)': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:4037:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 4037 | register int i; | ^ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp: In function 'void print_rxn_update_list(FILE*)': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:4376:29: warning: variable 'rxn' set but not used [-Wunused-but-set-variable] 4376 | Rxn /* **rarray,*/ *rxn; | ^~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp: In function 'void print_as_reactant_list(FILE*)': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:4410:13: warning: variable 'offset' set but not used [-Wunused-but-set-variable] 4410 | int offset; | ^~~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp: In function 'int create_update_lists()': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:4757:37: warning: unused variable 'pp' [-Wunused-variable] 4757 | int pp = GSP.func_param_affect.at(ff)-1; | ^~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp: In function 'int init_gillespie_direct_network(int, int)': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:4837:15: warning: unused variable 'rarray' [-Wunused-variable] 4837 | Rxn** rarray; | ^~~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp: In function 'int init_adaptive_scaling_network(int, int, double, bool)': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:4905:15: warning: unused variable 'rarray' [-Wunused-variable] 4905 | Rxn** rarray; | ^~~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp: In function 'int update_gillespie_direct_network(int, int)': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:4978:13: warning: unused variable 'ip' [-Wunused-variable] 4978 | int ip, ir, is, irxn; | ^~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:4978:17: warning: unused variable 'ir' [-Wunused-variable] 4978 | int ip, ir, is, irxn; | ^~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:4978:21: warning: unused variable 'is' [-Wunused-variable] 4978 | int ip, ir, is, irxn; | ^~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:4978:25: warning: unused variable 'irxn' [-Wunused-variable] 4978 | int ip, ir, is, irxn; | ^~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:4980:14: warning: unused variable 'rxn_dep' [-Wunused-variable] 4980 | int *rxn_dep/*, *rxn_dep2, *rxn_dep3*/; /* boolean arrays to keep track of dependent | ^~~~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:4983:17: warning: unused variable 'arl' [-Wunused-variable] 4983 | iarray *arl, *apl, *rul; /* species and reaction update lists */ | ^~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:4983:23: warning: unused variable 'apl' [-Wunused-variable] 4983 | iarray *arl, *apl, *rul; /* species and reaction update lists */ | ^~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:4983:29: warning: unused variable 'rul' [-Wunused-variable] 4983 | iarray *arl, *apl, *rul; /* species and reaction update lists */ | ^~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:4984:13: warning: unused variable 'offset' [-Wunused-variable] 4984 | int offset, r_index, p_index; | ^~~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:4984:21: warning: unused variable 'r_index' [-Wunused-variable] 4984 | int offset, r_index, p_index; | ^~~~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:4984:30: warning: unused variable 'p_index' [-Wunused-variable] 4984 | int offset, r_index, p_index; | ^~~~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:4985:15: warning: unused variable 'rarray' [-Wunused-variable] 4985 | Rxn **rarray, *rxn; | ^~~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:4985:24: warning: unused variable 'rxn' [-Wunused-variable] 4985 | Rxn **rarray, *rxn; | ^~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp: In function 'int update_adaptive_scaling_network(int, int)': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:5160:13: warning: unused variable 'ip' [-Wunused-variable] 5160 | int ip, ir, is, irxn; | ^~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:5160:17: warning: unused variable 'ir' [-Wunused-variable] 5160 | int ip, ir, is, irxn; | ^~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:5160:21: warning: unused variable 'is' [-Wunused-variable] 5160 | int ip, ir, is, irxn; | ^~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:5160:25: warning: unused variable 'irxn' [-Wunused-variable] 5160 | int ip, ir, is, irxn; | ^~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:5162:14: warning: unused variable 'rxn_dep' [-Wunused-variable] 5162 | int *rxn_dep/*, *rxn_dep2, *rxn_dep3*/; /* boolean arrays to keep track of dependent | ^~~~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:5165:17: warning: unused variable 'arl' [-Wunused-variable] 5165 | iarray *arl, *apl, *rul; /* species and reaction update lists */ | ^~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:5165:23: warning: unused variable 'apl' [-Wunused-variable] 5165 | iarray *arl, *apl, *rul; /* species and reaction update lists */ | ^~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:5165:29: warning: unused variable 'rul' [-Wunused-variable] 5165 | iarray *arl, *apl, *rul; /* species and reaction update lists */ | ^~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:5166:13: warning: unused variable 'offset' [-Wunused-variable] 5166 | int offset, r_index, p_index; | ^~~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:5166:21: warning: unused variable 'r_index' [-Wunused-variable] 5166 | int offset, r_index, p_index; | ^~~~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:5166:30: warning: unused variable 'p_index' [-Wunused-variable] 5166 | int offset, r_index, p_index; | ^~~~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:5167:15: warning: unused variable 'rarray' [-Wunused-variable] 5167 | Rxn **rarray, *rxn; | ^~~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:5167:24: warning: unused variable 'rxn' [-Wunused-variable] 5167 | Rxn **rarray, *rxn; | ^~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp: In function 'void update_rxn_rates(int)': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:5683:27: warning: variable 'c' set but not used [-Wunused-but-set-variable] 5683 | double *a, anew, *c; | ^ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp: In function 'void update_rxn_rates_has(int, double, bool)': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:5747:27: warning: variable 'c' set but not used [-Wunused-but-set-variable] 5747 | double *a, anew, *c; | ^ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp: At global scope: /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:3332:12: warning: 'int CVjtimes(N_Vector, N_Vector, realtype, N_Vector, N_Vector, void*, N_Vector)' defined but not used [-Wunused-function] 3332 | static int CVjtimes(N_Vector v, N_Vector Jv, realtype t, N_Vector y, N_Vector fy, void* jac_data, N_Vector tmp) { | ^~~~~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:3270:13: warning: 'void CVjac_network(long int, DlsMat, realtype, N_Vector, N_Vector, void*, N_Vector, N_Vector, N_Vector)' defined but not used [-Wunused-function] 3270 | static void CVjac_network(long int N, DlsMat J, realtype t, N_Vector y, N_Vector fy, void* jac_data, N_Vector tmp1, N_Vector tmp2, | ^~~~~~~~~~~~~ In file included from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:38: ../src/util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ ../src/util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ ../src/util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ ../src/util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ ../src/util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.h:262:23: warning: 'mu::value_type Mratio(mu::value_type, mu::value_type, mu::value_type)' defined but not used [-Wunused-function] 262 | static mu::value_type Mratio(mu::value_type a, mu::value_type b, mu::value_type z){ | ^~~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.h:258:23: warning: 'mu::value_type If(mu::value_type, mu::value_type, mu::value_type)' defined but not used [-Wunused-function] 258 | static mu::value_type If(mu::value_type v1, mu::value_type v2, mu::value_type v3){ | ^~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp: In function 'rxn_rate_scaled(RXN*, double*, int, double&, double, bool) [clone .constprop.0]': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:2703:22: warning: 'rate' may be used uninitialized [-Wmaybe-uninitialized] 2703 | if (discrete && rate < 0.0){ | ~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:2328:16: note: 'rate' was declared here 2328 | double rate; | ^~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp: In function 'rxn_rate(RXN*, double*, int)': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:2303:22: warning: 'rate' may be used uninitialized [-Wmaybe-uninitialized] 2303 | if (discrete && rate < 0.0){ | ~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:2126:16: note: 'rate' was declared here 2126 | double rate; | ^~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp: In function 'create_update_lists()': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:4474:27: warning: 'rarray' may be used uninitialized [-Wmaybe-uninitialized] 4474 | if (!(rxn = rarray[i])) | ~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.cpp:4459:15: note: 'rarray' was declared here 4459 | Rxn **rarray, *rxn; | ^~~~~~ [ 5%] Building CXX object CMakeFiles/run_network.dir/src/run_network.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/run_network.cpp.o -MF CMakeFiles/run_network.dir/src/run_network.cpp.o.d -o CMakeFiles/run_network.dir/src/run_network.cpp.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/run_network.cpp In file included from ../muparser_v2_2_4/include/muParserStack.h:35, from ../muparser_v2_2_4/include/muParserBase.h:39, from ../muparser_v2_2_4/include/muParser.h:32, from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.h:36, from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network3.hh:12, from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/run_network.cpp:46: ../muparser_v2_2_4/include/muParserToken.h:72:12: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from ../muparser_v2_2_4/include/muParserBase.h:33: /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ ../muparser_v2_2_4/include/muParserBase.h:291:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/run_network.cpp: In function 'int main(int, char**)': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/run_network.cpp:95:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 95 | register int i/*, j*/; | ^ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/run_network.cpp:735:84: warning: variable 'n_deriv_calls_last' set but not used [-Wunused-but-set-variable] 735 | long int /*n_steps = 0, n_steps_last = 0,*/ n_rate_calls_last = 0, n_deriv_calls_last = 0; | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.h: At global scope: /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.h:262:23: warning: 'mu::value_type Mratio(mu::value_type, mu::value_type, mu::value_type)' defined but not used [-Wunused-function] 262 | static mu::value_type Mratio(mu::value_type a, mu::value_type b, mu::value_type z){ | ^~~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/network.h:258:23: warning: 'mu::value_type If(mu::value_type, mu::value_type, mu::value_type)' defined but not used [-Wunused-function] 258 | static mu::value_type If(mu::value_type v1, mu::value_type v2, mu::value_type v3){ | ^~ In file included from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/run_network.cpp:39: ../src/util/mathutils/mathutils.h:364:15: warning: 'dswap' defined but not used [-Wunused-variable] 364 | static double dswap; | ^~~~~ ../src/util/mathutils/mathutils.h:359:20: warning: 'imarg2' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ ../src/util/mathutils/mathutils.h:359:12: warning: 'imarg1' defined but not used [-Wunused-variable] 359 | static int imarg1, imarg2; | ^~~~~~ ../src/util/mathutils/mathutils.h:356:22: warning: 'marg2' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ ../src/util/mathutils/mathutils.h:356:15: warning: 'marg1' defined but not used [-Wunused-variable] 356 | static double marg1, marg2; | ^~~~~ ../src/util/mathutils/mathutils.h:354:12: warning: 'isqrarg' defined but not used [-Wunused-variable] 354 | static int isqrarg; | ^~~~~~~ ../src/util/mathutils/mathutils.h:352:15: warning: 'sqrarg' defined but not used [-Wunused-variable] 352 | static double sqrarg; | ^~~~~~ [ 7%] Building CXX object CMakeFiles/run_network.dir/src/model/function.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/model/function.cpp.o -MF CMakeFiles/run_network.dir/src/model/function.cpp.o.d -o CMakeFiles/run_network.dir/src/model/function.cpp.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/function.cpp In file included from ../muparser_v2_2_4/include/muParserStack.h:35, from ../muparser_v2_2_4/include/muParserBase.h:39, from ../muparser_v2_2_4/include/muParser.h:32, from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/function.hh:12, from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/function.cpp:8: ../muparser_v2_2_4/include/muParserToken.h:72:12: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from ../muparser_v2_2_4/include/muParserBase.h:33: /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ ../muparser_v2_2_4/include/muParserBase.h:291:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ [ 9%] Building CXX object CMakeFiles/run_network.dir/src/model/observable.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/model/observable.cpp.o -MF CMakeFiles/run_network.dir/src/model/observable.cpp.o.d -o CMakeFiles/run_network.dir/src/model/observable.cpp.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/observable.cpp /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/run_network.cpp: In function 'main': /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/run_network.cpp:588:48: warning: 'sample_time' may be used uninitialized [-Wmaybe-uninitialized] 588 | else t_end = t_start + (double)n_sample*sample_time; | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/run_network.cpp:106:12: note: 'sample_time' was declared here 106 | double sample_time, *sample_times = 0x0/*, *st, t1*/; | ^~~~~~~~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/run_network.cpp:1014:47: warning: 'derivs' may be used uninitialized [-Wmaybe-uninitialized] 1014 | derivs_network(t, conc, derivs); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/run_network.cpp:117:32: note: 'derivs' was declared here 117 | double *conc, *conc_last, *derivs; | ^~~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/run_network.cpp:1009:49: warning: 'conc' may be used uninitialized [-Wmaybe-uninitialized] 1009 | get_conc_network(conc); | ~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/run_network.cpp:117:13: note: 'conc' was declared here 117 | double *conc, *conc_last, *derivs; | ^~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/run_network.cpp:1010:45: warning: 'conc_last' may be used uninitialized [-Wmaybe-uninitialized] 1010 | delta = sqrt(VECTOR_DIST(conc, conc_last, n_species_network())) / n_species_network(); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/run_network.cpp:117:20: note: 'conc_last' was declared here 117 | double *conc, *conc_last, *derivs; | ^~~~~~~~~ [ 10%] Building CXX object CMakeFiles/run_network.dir/src/model/rateExpression.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/model/rateExpression.cpp.o -MF CMakeFiles/run_network.dir/src/model/rateExpression.cpp.o.d -o CMakeFiles/run_network.dir/src/model/rateExpression.cpp.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/rateExpression.cpp [ 12%] Building CXX object CMakeFiles/run_network.dir/src/model/reaction.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/base 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-I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic 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-I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/model/rateExpressions/rateMM.cpp.o -MF CMakeFiles/run_network.dir/src/model/rateExpressions/rateMM.cpp.o.d -o CMakeFiles/run_network.dir/src/model/rateExpressions/rateMM.cpp.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/rateExpressions/rateMM.cpp [ 29%] Building CXX object CMakeFiles/run_network.dir/src/model/rateExpressions/rateMuParser.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/ssa 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-I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/model/rateExpressions/rateMuParser.cpp.o -MF CMakeFiles/run_network.dir/src/model/rateExpressions/rateMuParser.cpp.o.d -o CMakeFiles/run_network.dir/src/model/rateExpressions/rateMuParser.cpp.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/rateExpressions/rateMuParser.cpp In file included from ../muparser_v2_2_4/include/../include/muParserStack.h:35, from ../muparser_v2_2_4/include/../include/muParserBase.h:39, from ../muparser_v2_2_4/include/../include/muParser.h:32, from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/rateExpressions/rateMuParser.hh:12, from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/rateExpressions/rateMuParser.cpp:8: ../muparser_v2_2_4/include/../include/muParserToken.h:72:12: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from ../muparser_v2_2_4/include/../include/muParserBase.h:33: /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ ../muparser_v2_2_4/include/../include/muParserBase.h:291:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ [ 30%] Building CXX object CMakeFiles/run_network.dir/src/model/rateExpressions/rateSaturation.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/model/rateExpressions/rateSaturation.cpp.o -MF CMakeFiles/run_network.dir/src/model/rateExpressions/rateSaturation.cpp.o.d -o CMakeFiles/run_network.dir/src/model/rateExpressions/rateSaturation.cpp.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/rateExpressions/rateSaturation.cpp [ 32%] Building CXX object CMakeFiles/run_network.dir/src/model/reactions/bioNetGenRxn.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/model/reactions/bioNetGenRxn.cpp.o -MF CMakeFiles/run_network.dir/src/model/reactions/bioNetGenRxn.cpp.o.d -o CMakeFiles/run_network.dir/src/model/reactions/bioNetGenRxn.cpp.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions/bioNetGenRxn.cpp In file included from ../muparser_v2_2_4/include/muParserStack.h:35, from ../muparser_v2_2_4/include/muParserBase.h:39, from ../muparser_v2_2_4/include/muParser.h:32, from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions/../function.hh:12, from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions/bioNetGenRxn.hh:12, from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions/bioNetGenRxn.cpp:8: ../muparser_v2_2_4/include/muParserToken.h:72:12: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from ../muparser_v2_2_4/include/muParserBase.h:33: /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ ../muparser_v2_2_4/include/muParserBase.h:291:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ [ 34%] Building CXX object CMakeFiles/run_network.dir/src/model/reactions/elementaryRxn.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/model/reactions/elementaryRxn.cpp.o -MF CMakeFiles/run_network.dir/src/model/reactions/elementaryRxn.cpp.o.d -o CMakeFiles/run_network.dir/src/model/reactions/elementaryRxn.cpp.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions/elementaryRxn.cpp In file included from ../muparser_v2_2_4/include/muParserStack.h:35, from ../muparser_v2_2_4/include/muParserBase.h:39, from ../muparser_v2_2_4/include/muParser.h:32, from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions/../function.hh:12, from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions/bioNetGenRxn.hh:12, from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions/elementaryRxn.cpp:8: ../muparser_v2_2_4/include/muParserToken.h:72:12: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from ../muparser_v2_2_4/include/muParserBase.h:33: /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ ../muparser_v2_2_4/include/muParserBase.h:291:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ [ 36%] Building CXX object CMakeFiles/run_network.dir/src/model/reactions/functionalRxn.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/model/reactions/functionalRxn.cpp.o -MF CMakeFiles/run_network.dir/src/model/reactions/functionalRxn.cpp.o.d -o CMakeFiles/run_network.dir/src/model/reactions/functionalRxn.cpp.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions/functionalRxn.cpp [ 38%] Building CXX object CMakeFiles/run_network.dir/src/model/reactions/hillRxn.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/model/reactions/hillRxn.cpp.o -MF CMakeFiles/run_network.dir/src/model/reactions/hillRxn.cpp.o.d -o CMakeFiles/run_network.dir/src/model/reactions/hillRxn.cpp.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions/hillRxn.cpp In file included from ../muparser_v2_2_4/include/muParserStack.h:35, from ../muparser_v2_2_4/include/muParserBase.h:39, from ../muparser_v2_2_4/include/muParser.h:32, from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions/../function.hh:12, from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions/bioNetGenRxn.hh:12, from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions/functionalRxn.cpp:8: ../muparser_v2_2_4/include/muParserToken.h:72:12: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from ../muparser_v2_2_4/include/muParserBase.h:33: /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ ../muparser_v2_2_4/include/muParserBase.h:291:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ In file included from ../muparser_v2_2_4/include/muParserStack.h:35, from ../muparser_v2_2_4/include/muParserBase.h:39, from ../muparser_v2_2_4/include/muParser.h:32, from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions/../function.hh:12, from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions/bioNetGenRxn.hh:12, from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions/hillRxn.cpp:8: ../muparser_v2_2_4/include/muParserToken.h:72:12: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from ../muparser_v2_2_4/include/muParserBase.h:33: /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ ../muparser_v2_2_4/include/muParserBase.h:291:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ [ 40%] Building CXX object CMakeFiles/run_network.dir/src/model/reactions/michaelisMentenRxn.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util 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-flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/model/reactions/michaelisMentenRxn.cpp.o -MF CMakeFiles/run_network.dir/src/model/reactions/michaelisMentenRxn.cpp.o.d -o CMakeFiles/run_network.dir/src/model/reactions/michaelisMentenRxn.cpp.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions/michaelisMentenRxn.cpp [ 41%] Building CXX object CMakeFiles/run_network.dir/src/model/reactions/saturationRxn.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla 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-I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/model/reactions/saturationRxn.cpp.o -MF CMakeFiles/run_network.dir/src/model/reactions/saturationRxn.cpp.o.d -o CMakeFiles/run_network.dir/src/model/reactions/saturationRxn.cpp.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions/saturationRxn.cpp In file included from ../muparser_v2_2_4/include/muParserStack.h:35, from ../muparser_v2_2_4/include/muParserBase.h:39, from ../muparser_v2_2_4/include/muParser.h:32, from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions/../function.hh:12, from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions/bioNetGenRxn.hh:12, from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions/michaelisMentenRxn.cpp:8: ../muparser_v2_2_4/include/muParserToken.h:72:12: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from ../muparser_v2_2_4/include/muParserBase.h:33: /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ ../muparser_v2_2_4/include/muParserBase.h:291:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ In file included from ../muparser_v2_2_4/include/muParserStack.h:35, from ../muparser_v2_2_4/include/muParserBase.h:39, from ../muparser_v2_2_4/include/muParser.h:32, from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions/../function.hh:12, from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions/bioNetGenRxn.hh:12, from /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions/saturationRxn.cpp:8: ../muparser_v2_2_4/include/muParserToken.h:72:12: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 72 | std::auto_ptr m_pCallback; | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from ../muparser_v2_2_4/include/muParserBase.h:33: /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ ../muparser_v2_2_4/include/muParserBase.h:291:10: warning: 'template class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 291 | std::auto_ptr m_pTokenReader; ///< Managed pointer to the token reader object. | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:66:28: note: declared here 66 | template class auto_ptr; | ^~~~~~~~ [ 43%] Building CXX object CMakeFiles/run_network.dir/src/pla/base/firingGenerator.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util 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-I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/util/MTrand/mtrand.cpp.o -MF CMakeFiles/run_network.dir/src/util/MTrand/mtrand.cpp.o.d -o CMakeFiles/run_network.dir/src/util/MTrand/mtrand.cpp.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/MTrand/mtrand.cpp [ 98%] Building CXX object CMakeFiles/run_network.dir/src/util/rand2/rand2.cpp.o /usr/bin/g++ -DRUN_NETWORK_VERSION=\"3.0\" -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3 -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/cvode -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/nvector -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/include/sundials -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/ssa -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/rateExpressions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/model/reactions -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/base -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/fEuler -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta/base -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/pla/eRungeKutta/util -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/MTrand -I/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/rand2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -MD -MT CMakeFiles/run_network.dir/src/util/rand2/rand2.cpp.o -MF CMakeFiles/run_network.dir/src/util/rand2/rand2.cpp.o.d -o CMakeFiles/run_network.dir/src/util/rand2/rand2.cpp.o -c /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/src/util/rand2/rand2.cpp [100%] Linking CXX executable run_network /usr/bin/cmake -E cmake_link_script CMakeFiles/run_network.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-error=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src/util/mathutils -I../cvode-2.6.0/include -I../cvode-2.6.0/include/cvode -I../cvode-2.6.0/build/include -I../cvode-2.6.0/src/cvode/fcmix -L../src/util/mathutils -I../muparser_v2_2_4/include -L../muparser_v2_2_4/lib -L../cvode-2.6.0/build/src/cvode/fcmix -L../cvode-2.6.0/build/src/sundials -L../cvode-2.6.0/build/src/cvode -L../cvode-2.6.0/build/src/nvec_ser -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes CMakeFiles/run_network.dir/src/network.cpp.o CMakeFiles/run_network.dir/src/network3.cpp.o CMakeFiles/run_network.dir/src/run_network.cpp.o CMakeFiles/run_network.dir/src/model/function.cpp.o CMakeFiles/run_network.dir/src/model/observable.cpp.o CMakeFiles/run_network.dir/src/model/rateExpression.cpp.o CMakeFiles/run_network.dir/src/model/reaction.cpp.o CMakeFiles/run_network.dir/src/model/simpleSpecies.cpp.o CMakeFiles/run_network.dir/src/pla/PLA.cpp.o CMakeFiles/run_network.dir/src/util/conversion.cpp.o CMakeFiles/run_network.dir/src/util/misc.cpp.o CMakeFiles/run_network.dir/src/util/rand.cpp.o CMakeFiles/run_network.dir/src/model/rateExpressions/rateElementary.cpp.o CMakeFiles/run_network.dir/src/model/rateExpressions/rateHill.cpp.o CMakeFiles/run_network.dir/src/model/rateExpressions/rateMM.cpp.o CMakeFiles/run_network.dir/src/model/rateExpressions/rateMuParser.cpp.o CMakeFiles/run_network.dir/src/model/rateExpressions/rateSaturation.cpp.o CMakeFiles/run_network.dir/src/model/reactions/bioNetGenRxn.cpp.o CMakeFiles/run_network.dir/src/model/reactions/elementaryRxn.cpp.o CMakeFiles/run_network.dir/src/model/reactions/functionalRxn.cpp.o CMakeFiles/run_network.dir/src/model/reactions/hillRxn.cpp.o CMakeFiles/run_network.dir/src/model/reactions/michaelisMentenRxn.cpp.o CMakeFiles/run_network.dir/src/model/reactions/saturationRxn.cpp.o CMakeFiles/run_network.dir/src/pla/base/firingGenerator.cpp.o CMakeFiles/run_network.dir/src/pla/base/postleapChecker.cpp.o CMakeFiles/run_network.dir/src/pla/base/rxnClassifier.cpp.o CMakeFiles/run_network.dir/src/pla/base/tauCalculator.cpp.o CMakeFiles/run_network.dir/src/pla/eRungeKutta/eRungeKutta_postTC_RC_FG_rbPL.cpp.o CMakeFiles/run_network.dir/src/pla/eRungeKutta/eRungeKutta_postTC_RC_FG_sbPL.cpp.o CMakeFiles/run_network.dir/src/pla/eRungeKutta/eRungeKutta_preTC_RC_FG_negPL.cpp.o CMakeFiles/run_network.dir/src/pla/eRungeKutta/eRungeKutta_preTC_RC_FG_rbPL.cpp.o CMakeFiles/run_network.dir/src/pla/eRungeKutta/eRungeKutta_preTC_RC_FG_sbPL.cpp.o CMakeFiles/run_network.dir/src/pla/fEuler/fEulerPreleapRB_TC.cpp.o CMakeFiles/run_network.dir/src/pla/fEuler/fEulerPreleapSB_TC.cpp.o CMakeFiles/run_network.dir/src/pla/fEuler/fEulerRB_PL.cpp.o CMakeFiles/run_network.dir/src/pla/fEuler/fEulerRB_TC_PL.cpp.o CMakeFiles/run_network.dir/src/pla/fEuler/fEulerSB_PL.cpp.o CMakeFiles/run_network.dir/src/pla/fEuler/fEulerSB_TC_PL.cpp.o CMakeFiles/run_network.dir/src/pla/fEuler/fEuler_FG.cpp.o CMakeFiles/run_network.dir/src/pla/fEuler/fEuler_RC.cpp.o CMakeFiles/run_network.dir/src/pla/util/fixed_TC.cpp.o CMakeFiles/run_network.dir/src/pla/util/g_Getter.cpp.o CMakeFiles/run_network.dir/src/pla/util/negPopChecker.cpp.o CMakeFiles/run_network.dir/src/pla/util/preleap_TC.cpp.o CMakeFiles/run_network.dir/src/pla/util/rbChecker.cpp.o CMakeFiles/run_network.dir/src/pla/util/sbChecker.cpp.o CMakeFiles/run_network.dir/src/pla/eRungeKutta/base/eRungeKutta_TC_RC_FG_PL.cpp.o CMakeFiles/run_network.dir/src/pla/eRungeKutta/base/eRungeKutta_TC_RC_FG_rbPL.cpp.o CMakeFiles/run_network.dir/src/pla/eRungeKutta/base/eRungeKutta_TC_RC_FG_sbPL.cpp.o CMakeFiles/run_network.dir/src/pla/eRungeKutta/util/aEff_Calculator.cpp.o CMakeFiles/run_network.dir/src/pla/eRungeKutta/util/binomialCorrector_RK.cpp.o CMakeFiles/run_network.dir/src/pla/eRungeKutta/util/butcherTableau.cpp.o CMakeFiles/run_network.dir/src/util/MTrand/mtrand.cpp.o CMakeFiles/run_network.dir/src/util/rand2/rand2.cpp.o -o run_network -L/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/lib -Wl,-Bstatic -lmathutils -lmuparser -lsundials_cvode -lsundials_fcvode -lsundials_nvecserial -Wl,-Bdynamic gmake[2]: Leaving directory '/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/build' [100%] Built target run_network gmake[1]: Leaving directory '/builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/build' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/build/CMakeFiles 0 + popd ~/build/BUILD/bionetgen-2.8.4 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.d8wfz3 + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/bionetgen-2.8.4-3.fc38.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/bionetgen-2.8.4-3.fc38.x86_64 ++ dirname /builddir/build/BUILDROOT/bionetgen-2.8.4-3.fc38.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/bionetgen-2.8.4-3.fc38.x86_64 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH ~/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Network3/build ~/build/BUILD/bionetgen-2.8.4 + CC=gcc + export CC + CXX=g++ + export CXX + cd bionetgen-2.8.4 + pushd bionetgen-BioNetGen-2.8.4/bng2/Network3/build + mkdir -vp /builddir/build/BUILDROOT/bionetgen-2.8.4-3.fc38.x86_64/usr/bin mkdir: created directory '/builddir/build/BUILDROOT/bionetgen-2.8.4-3.fc38.x86_64/usr' mkdir: created directory '/builddir/build/BUILDROOT/bionetgen-2.8.4-3.fc38.x86_64/usr/bin' + install -pm 755 run_network /builddir/build/BUILDROOT/bionetgen-2.8.4-3.fc38.x86_64/usr/bin/ + popd ~/build/BUILD/bionetgen-2.8.4 + mkdir -vp /builddir/build/BUILDROOT/bionetgen-2.8.4-3.fc38.x86_64/usr/share/perl5/vendor_perl/BioNetGen mkdir: created directory '/builddir/build/BUILDROOT/bionetgen-2.8.4-3.fc38.x86_64/usr/share' mkdir: created directory '/builddir/build/BUILDROOT/bionetgen-2.8.4-3.fc38.x86_64/usr/share/perl5' mkdir: created directory '/builddir/build/BUILDROOT/bionetgen-2.8.4-3.fc38.x86_64/usr/share/perl5/vendor_perl' mkdir: created directory '/builddir/build/BUILDROOT/bionetgen-2.8.4-3.fc38.x86_64/usr/share/perl5/vendor_perl/BioNetGen' + cp -r bionetgen-BioNetGen-2.8.4/bng2/Perl2 /builddir/build/BUILDROOT/bionetgen-2.8.4-3.fc38.x86_64/usr/share/perl5/vendor_perl/BioNetGen/ + cp -r bionetgen-BioNetGen-2.8.4/bng2/BNG2.pl /builddir/build/BUILDROOT/bionetgen-2.8.4-3.fc38.x86_64/usr/share/perl5/vendor_perl/BioNetGen/ + cp -a bionetgen-BioNetGen-2.8.4/bng2/Models2 /builddir/build/BUILDROOT/bionetgen-2.8.4-3.fc38.x86_64/usr/share/perl5/vendor_perl/BioNetGen/ + rm -f /builddir/build/BUILDROOT/bionetgen-2.8.4-3.fc38.x86_64/usr/share/perl5/vendor_perl/BioNetGen/Models2/bin/run_network_x86_64-linux + rm -f /builddir/build/BUILDROOT/bionetgen-2.8.4-3.fc38.x86_64/usr/share/perl5/vendor_perl/BioNetGen/Models2/run_network + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 2.8.4-3.fc38 --unique-debug-suffix -2.8.4-3.fc38.x86_64 --unique-debug-src-base bionetgen-2.8.4-3.fc38.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/bionetgen-2.8.4 extracting debug info from /builddir/build/BUILDROOT/bionetgen-2.8.4-3.fc38.x86_64/usr/bin/run_network original debug info size: 8940kB, size after compression: 6872kB /usr/bin/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. 2296 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.k2cbIz + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS ~/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Models2 ~/build/BUILD/bionetgen-2.8.4 + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd bionetgen-2.8.4 + pushd bionetgen-BioNetGen-2.8.4/bng2/Models2 + install -pm 755 ../Network3/build/run_network -D ./bin/run_network_x86_64-linux + install -pm 755 ../Network3/build/run_network -D ../bin/run_network_x86_64-linux Running some tests ... + 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 BioNetGen version 2.8.4 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. Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Perl2/BNGAction.pm line 548. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/bin/run_network_x86_64-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: 3066] 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 7392 8627 14.80 7505 8764 14.90 7557 8822 15.00 7606 8884 15.10 7667 8954 15.20 7727 9021 15.30 7788 9088 15.40 7849 9153 15.50 7910 9218 15.60 7968 9281 15.70 8020 9346 15.80 8144 9498 15.90 8284 9667 16.00 8401 9791 16.10 8469 9868 16.20 8525 9928 16.30 8581 9988 16.40 8629 10037 16.50 8666 10082 16.60 8711 10136 16.70 8761 10188 16.80 8819 10257 16.90 8879 10326 17.00 8937 10391 17.10 8976 10441 17.20 9012 10480 17.30 9045 10518 17.40 9069 10542 17.50 9092 10572 17.60 9115 10597 17.70 9139 10623 17.80 9160 10651 17.90 9180 10674 18.00 9200 10696 18.10 9221 10722 18.20 9240 10742 18.30 9251 10758 18.40 9262 10769 18.50 9273 10785 18.60 9284 10796 18.70 9295 10807 18.80 9306 10818 18.90 9316 10828 19.00 9327 10839 19.10 9338 10854 19.20 9349 10865 19.30 9360 10876 19.40 9371 10887 19.50 9382 10898 19.60 9393 10913 19.70 9404 10924 19.80 9415 10935 19.90 9426 10946 20.00 9437 10959 Time course of concentrations written to file ./CaOscillate_Func.cdat. Time course of groups written to file ./CaOscillate_Func.gdat. Propagation took 1.00e-02 CPU seconds Program times: 0.01 CPU s 0.00 clock s Updating species concentrations from ./CaOscillate_Func.cdat CPU TIME: simulate 0.01 s. Finished processing file CaOscillate_Func.bngl. CPU TIME: total 0.02 s. BioNetGen version 2.8.4 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 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_Sat.net. CPU TIME: generate_network 0.00 s. ACTION: simulate( method=>"cvode" ) Network simulation using cvode WARNING: writeFile(): Overwriting existing file ./CaOscillate_Sat.net. Wrote network in net format to ./CaOscillate_Sat.net. Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Perl2/BNGAction.pm line 548. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/bin/run_network_x86_64-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: 3068] 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 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 0.00e+00 CPU seconds Program times: 0.00 CPU s 0.00 clock s Updating species concentrations from ./CaOscillate_Sat.cdat CPU TIME: simulate 0.01 s. Finished processing file CaOscillate_Sat.bngl. CPU TIME: total 0.03 s. BioNetGen version 2.8.4 Reading from file catalysis.bngl (level 0) CPU TIME: version 0.00 s. Warning: Parameter Gf_S_kinase is set to a negative value: -41.5 Warning: Parameter Gf_S_pptase is set to a negative value: -41.5 Warning: Parameter Ea0_S_kinase is set to a negative value: -7.7 Warning: Parameter Ea0_S_pptase is set to a negative value: -7.7 Warning: Parameter Ea0_cat_kinase is set to a negative value: -11.9 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 0.00e+00 CPU s Iteration 3: 10 species 10 rxns 1.00e-02 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 1.00e-02 CPU s 2.50e-03 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 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 0.01 s. ACTION: simulate( method=>"cvode" ) Network simulation using cvode WARNING: writeFile(): Overwriting existing file ./catalysis.net. Wrote network in net format to ./catalysis.net. Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Perl2/BNGAction.pm line 548. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/bin/run_network_x86_64-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: 3070] 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 0.00e+00 CPU seconds Program times: 0.00 CPU s 0.00 clock s Updating species concentrations from ./catalysis.cdat CPU TIME: simulate 0.00 s. Finished processing file catalysis.bngl. CPU TIME: total 0.03 s. BioNetGen version 2.8.4 Reading from file egfr_net.bngl (level 0) Read 48 parameters. Read 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 0.00e+00 CPU s Iteration 2: 8 species 5 rxns 1.00e-02 CPU s Iteration 3: 10 species 8 rxns 0.00e+00 CPU s Iteration 4: 19 species 21 rxns 2.00e-02 CPU s Iteration 5: 37 species 76 rxns 5.00e-02 CPU s Iteration 6: 69 species 213 rxns 1.30e-01 CPU s Iteration 7: 131 species 494 rxns 2.90e-01 CPU s Iteration 8: 295 species 1260 rxns 9.00e-01 CPU s Iteration 9: 356 species 3088 rxns 2.36e+00 CPU s Iteration 10: 356 species 3749 rxns 1.08e+00 CPU s Cumulative CPU time for each rule Rule 1: 48 reactions 6.00e-02 CPU s 1.25e-03 CPU s/rxn Rule 2: 600 reactions 1.17e+00 CPU s 1.95e-03 CPU s/rxn Rule 3: 144 reactions 1.40e-01 CPU s 9.72e-04 CPU s/rxn Rule 4: 96 reactions 1.00e-01 CPU s 1.04e-03 CPU s/rxn Rule 5: 156 reactions 1.10e-01 CPU s 7.05e-04 CPU s/rxn Rule 6: 104 reactions 9.00e-02 CPU s 8.65e-04 CPU s/rxn Rule 7: 96 reactions 1.00e-01 CPU s 1.04e-03 CPU s/rxn Rule 8: 104 reactions 9.00e-02 CPU s 8.65e-04 CPU s/rxn Rule 9: 312 reactions 3.40e-01 CPU s 1.09e-03 CPU s/rxn Rule 10: 312 reactions 3.50e-01 CPU s 1.12e-03 CPU s/rxn Rule 11: 312 reactions 3.50e-01 CPU s 1.12e-03 CPU s/rxn Rule 12: 208 reactions 2.50e-01 CPU s 1.20e-03 CPU s/rxn Rule 13: 208 reactions 2.00e-01 CPU s 9.62e-04 CPU s/rxn Rule 14: 208 reactions 2.80e-01 CPU s 1.35e-03 CPU s/rxn Rule 15: 208 reactions 3.00e-01 CPU s 1.44e-03 CPU s/rxn Rule 16: 208 reactions 2.60e-01 CPU s 1.25e-03 CPU s/rxn Rule 17: 208 reactions 2.90e-01 CPU s 1.39e-03 CPU s/rxn Rule 18: 208 reactions 2.80e-01 CPU s 1.35e-03 CPU s/rxn Rule 19: 2 reactions 1.00e-02 CPU s 5.00e-03 CPU s/rxn Rule 20: 2 reactions 2.00e-02 CPU s 1.00e-02 CPU s/rxn Rule 21: 1 reactions 1.00e-02 CPU s 1.00e-02 CPU s/rxn Rule 22: 2 reactions 2.00e-02 CPU s 1.00e-02 CPU s/rxn Rule 23: 2 reactions 2.00e-02 CPU s 1.00e-02 CPU s/rxn Total : 3749 reactions 4.84e+00 CPU s 1.29e-03 CPU s/rxn Wrote network in net format to ./egfr_net.net. CPU TIME: generate_network 4.91 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. Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Perl2/BNGAction.pm line 548. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/bin/run_network_x86_64-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: 3072] 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 0.01 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 6.00e-02 CPU seconds Program times: 0.07 CPU s 0.00 clock s Updating species concentrations from ./egfr_net.cdat CPU TIME: simulate 0.16 s. Finished processing file egfr_net.bngl. CPU TIME: total 5.11 s. BioNetGen version 2.8.4 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 0.00e+00 CPU s Iteration 2: 13 species 10 rxns 1.00e-02 CPU s Iteration 3: 15 species 14 rxns 0.00e+00 CPU s Iteration 4: 20 species 21 rxns 1.00e-02 CPU s Iteration 5: 26 species 39 rxns 2.00e-02 CPU s Iteration 6: 33 species 62 rxns 2.00e-02 CPU s Iteration 7: 38 species 90 rxns 2.00e-02 CPU s Iteration 8: 40 species 115 rxns 2.00e-02 CPU s Iteration 9: 40 species 123 rxns 1.00e-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 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 3: 12 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 4: 8 reactions 1.00e-02 CPU s 1.25e-03 CPU s/rxn Rule 5: 12 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: 3 reactions 1.00e-02 CPU s 3.33e-03 CPU s/rxn Rule 9: 3 reactions 1.00e-02 CPU s 3.33e-03 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 1.00e-02 CPU s 1.67e-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 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 17: 6 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 18: 6 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 19: 6 reactions 1.00e-02 CPU s 1.67e-03 CPU s/rxn Rule 20: 6 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 21: 6 reactions 3.00e-02 CPU s 5.00e-03 CPU s/rxn Rule 22: 2 reactions 0.00e+00 CPU s 0.00e+00 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 1.00e-02 CPU s 5.00e-03 CPU s/rxn Total : 123 reactions 1.00e-01 CPU s 8.13e-04 CPU s/rxn Wrote network in net format to ./egfr_net_red.net. CPU TIME: generate_network 0.12 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. Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Perl2/BNGAction.pm line 548. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/bin/run_network_x86_64-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: 3074] 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 0.01 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. Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Perl2/BNGAction.pm line 548. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/bin/run_network_x86_64-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: 3076] 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 Updating species concentrations from ./egfr_net_red.cdat CPU TIME: simulate 0.01 s. Finished processing file egfr_net_red.bngl. CPU TIME: total 0.18 s. BioNetGen version 2.8.4 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 1.00e-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 0.00e+00 CPU s 0.00e+00 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 1.00e-02 CPU s 5.00e-03 CPU s/rxn Rule 13: 2 reactions 0.00e+00 CPU s 0.00e+00 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 1.00e-02 CPU s 2.70e-04 CPU s/rxn Wrote network in net format to ./egfr_path.net. CPU TIME: generate_network 0.03 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. Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Perl2/BNGAction.pm line 548. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/bin/run_network_x86_64-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: 3078] 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. Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Perl2/BNGAction.pm line 548. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/bin/run_network_x86_64-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: 3080] 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 Updating species concentrations from ./egfr_path.cdat CPU TIME: simulate 0.00 s. Finished processing file egfr_path.bngl. CPU TIME: total 0.07 s. BioNetGen version 2.8.4 Reading from file energy_example1.bngl (level 0) CPU TIME: version 0.00 s. Warning: Parameter Gf_SA is set to a negative value: -47.5 Warning: Parameter Gf_SB is set to a negative value: -47.5 Warning: Parameter Gf_SC is set to a negative value: -47.5 Warning: Parameter Gf_SBC is set to a negative value: -5.9 Warning: Parameter Gf_SABC is set to a negative value: -1.8 Warning: Parameter Ea0_SA is set to a negative value: -17.8 Warning: Parameter Ea0_SB is set to a negative value: -17.8 Warning: Parameter Ea0_SC is set to a negative value: -17.8 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 0.00e+00 CPU s Iteration 2: 10 species 12 rxns 1.00e-02 CPU s Iteration 3: 11 species 21 rxns 1.00e-02 CPU s Iteration 4: 11 species 24 rxns 1.00e-02 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 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 3: 8 reactions 1.00e-02 CPU s 1.25e-03 CPU s/rxn Total : 24 reactions 3.00e-02 CPU s 1.25e-03 CPU s/rxn Wrote network in net format to ./energy_example1.net. CPU TIME: generate_network 0.03 s. Wrote SBML to ./energy_example1_sbml.xml. CPU TIME: writeSBML 0.00 s. Finished processing file energy_example1.bngl. CPU TIME: total 0.04 s. BioNetGen version 2.8.4 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 1.00e-02 CPU s Iteration 2: 9 species 8 rxns 0.00e+00 CPU s Iteration 3: 12 species 20 rxns 1.00e-02 CPU s Iteration 4: 22 species 36 rxns 2.00e-02 CPU s Iteration 5: 43 species 100 rxns 4.00e-02 CPU s Iteration 6: 78 species 255 rxns 1.20e-01 CPU s Iteration 7: 139 species 586 rxns 2.50e-01 CPU s Iteration 8: 199 species 1190 rxns 5.00e-01 CPU s Iteration 9: 303 species 1841 rxns 6.20e-01 CPU s Iteration 10: 354 species 3143 rxns 1.10e+00 CPU s Iteration 11: 354 species 3680 rxns 4.60e-01 CPU s Cumulative CPU time for each rule Rule 1: 48 reactions 6.00e-02 CPU s 1.25e-03 CPU s/rxn Rule 2: 1152 reactions 8.70e-01 CPU s 7.55e-04 CPU s/rxn Rule 3: 312 reactions 2.70e-01 CPU s 8.65e-04 CPU s/rxn Rule 4: 36 reactions 5.00e-02 CPU s 1.39e-03 CPU s/rxn Rule 5: 24 reactions 4.00e-02 CPU s 1.67e-03 CPU s/rxn Rule 6: 312 reactions 2.60e-01 CPU s 8.33e-04 CPU s/rxn Rule 7: 36 reactions 6.00e-02 CPU s 1.67e-03 CPU s/rxn Rule 8: 24 reactions 3.00e-02 CPU s 1.25e-03 CPU s/rxn Rule 9: 832 reactions 6.80e-01 CPU s 8.17e-04 CPU s/rxn Rule 10: 48 reactions 7.00e-02 CPU s 1.46e-03 CPU s/rxn Rule 11: 48 reactions 6.00e-02 CPU s 1.25e-03 CPU s/rxn Rule 12: 64 reactions 1.20e-01 CPU s 1.87e-03 CPU s/rxn Rule 13: 64 reactions 8.00e-02 CPU s 1.25e-03 CPU s/rxn Rule 14: 156 reactions 1.10e-01 CPU s 7.05e-04 CPU s/rxn Rule 15: 104 reactions 4.00e-02 CPU s 3.85e-04 CPU s/rxn Rule 16: 208 reactions 1.60e-01 CPU s 7.69e-04 CPU s/rxn Rule 17: 208 reactions 1.60e-01 CPU s 7.69e-04 CPU s/rxn Rule 18: 2 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 19: 2 reactions 1.00e-02 CPU s 5.00e-03 CPU s/rxn Total : 3680 reactions 3.13e+00 CPU s 8.51e-04 CPU s/rxn Wrote network in net format to ./fceri_ji.net. CPU TIME: generate_network 3.20 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. Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Perl2/BNGAction.pm line 548. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/bin/run_network_x86_64-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: 3082] run_network 3.0 Read 26 parameters from ./fceri_ji.net Read 354 species 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 0.01 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 6.20e-01 CPU seconds Program times: 0.63 CPU s 0.00 clock s Updating species concentrations from ./fceri_ji.cdat CPU TIME: simulate 0.72 s. Finished processing file fceri_ji.bngl. CPU TIME: total 3.94 s. BioNetGen version 2.8.4 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 0.00e+00 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 1.00e-02 CPU s Iteration 6: 22 species 59 rxns 3.00e-02 CPU s Iteration 7: 22 species 76 rxns 2.00e-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 1.00e-02 CPU s 5.00e-04 CPU s/rxn Rule 3: 4 reactions 2.00e-02 CPU s 5.00e-03 CPU s/rxn Rule 4: 6 reactions 0.00e+00 CPU s 0.00e+00 CPU s/rxn Rule 5: 24 reactions 2.00e-02 CPU s 8.33e-04 CPU s/rxn Rule 6: 14 reactions 1.00e-02 CPU s 7.14e-04 CPU s/rxn Total : 76 reactions 7.00e-02 CPU s 9.21e-04 CPU s/rxn Wrote network in net format to ./test_continue.net. CPU TIME: generate_network 0.08 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. Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Perl2/BNGAction.pm line 548. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/bin/run_network_x86_64-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: 3084] 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. Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Perl2/BNGAction.pm line 548. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/bin/run_network_x86_64-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: 3086] 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. 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 0.02 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. Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Perl2/BNGAction.pm line 548. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/bin/run_network_x86_64-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: 3088] 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. Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Perl2/BNGAction.pm line 548. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/bin/run_network_x86_64-linux -o ./test_continue_ssa -p ssa -h 1761416253 --cdat 1 --fdat 0 -g ./test_continue_ssa.net ./test_continue_ssa.net 2.5 40 [simulation PID is: 3090] 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: 71903 Time course of concentrations written to file ./test_continue_ssa.cdat. Time course of groups written to file ./test_continue_ssa.gdat. Propagation took 1.00e-02 CPU seconds Program times: 0.01 CPU s 0.00 clock s Updating species concentrations from ./test_continue_ssa.cdat CPU TIME: simulate 0.02 s. Set concentration of species EGF(R) to value 10*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. Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Perl2/BNGAction.pm line 548. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/bin/run_network_x86_64-linux -o ./test_continue_ssa -p ssa -h 50455151 --cdat 1 --fdat 0 -x -i 1.000000000000e+02 -g ./test_continue_ssa.net ./test_continue_ssa.net 2.5 40 [simulation PID is: 3092] 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: 130065 Time course of concentrations written to file ./test_continue_ssa.cdat. Time course of groups written to file ./test_continue_ssa.gdat. Propagation took 1.00e-02 CPU seconds Program times: 0.01 CPU s 0.00 clock s Updating species concentrations from ./test_continue_ssa.cdat CPU TIME: simulate 0.02 s. Set concentration of species 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. Can't exec "hostname": No such file or directory at /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/Perl2/BNGAction.pm line 548. Running run_network on full command: /builddir/build/BUILD/bionetgen-2.8.4/bionetgen-BioNetGen-2.8.4/bng2/bin/run_network_x86_64-linux -o ./test_continue_ssa -p ssa -h 1887902519 --cdat 1 --fdat 0 -x -i 2.000000000000e+02 -g ./test_continue_ssa.net ./test_continue_ssa.net 2.5 40 [simulation PID is: 3094] 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: 107592 Time course of concentrations written to file ./test_continue_ssa.cdat. Time course of groups written to file ./test_continue_ssa.gdat. Propagation took 1.00e-02 CPU seconds Program times: 0.01 CPU s 0.00 clock s Updating species concentrations from ./test_continue_ssa.cdat CPU TIME: simulate 0.01 s. Finished processing file test_continue.bngl. CPU TIME: total 0.18 s. Tests finished. + echo 'Tests finished.' + RPM_EC=0 ++ jobs -p + exit 0 Processing files: bionetgen-2.8.4-3.fc38.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.Gsfoa3 + umask 022 + cd /builddir/build/BUILD + cd bionetgen-2.8.4 + DOCDIR=/builddir/build/BUILDROOT/bionetgen-2.8.4-3.fc38.x86_64/usr/share/doc/bionetgen + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/bionetgen-2.8.4-3.fc38.x86_64/usr/share/doc/bionetgen + cp -pr bionetgen-BioNetGen-2.8.4/README.md /builddir/build/BUILDROOT/bionetgen-2.8.4-3.fc38.x86_64/usr/share/doc/bionetgen + cp -pr bionetgen-BioNetGen-2.8.4/bng2/CREDITS.txt /builddir/build/BUILDROOT/bionetgen-2.8.4-3.fc38.x86_64/usr/share/doc/bionetgen + cp -pr bionetgen-BioNetGen-2.8.4/bng2/CHANGES.txt /builddir/build/BUILDROOT/bionetgen-2.8.4-3.fc38.x86_64/usr/share/doc/bionetgen + cp -pr bionetgen-BioNetGen-2.8.4/bng2/VERSION /builddir/build/BUILDROOT/bionetgen-2.8.4-3.fc38.x86_64/usr/share/doc/bionetgen + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.OJ3XVT + umask 022 + cd /builddir/build/BUILD + cd bionetgen-2.8.4 + LICENSEDIR=/builddir/build/BUILDROOT/bionetgen-2.8.4-3.fc38.x86_64/usr/share/licenses/bionetgen + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/bionetgen-2.8.4-3.fc38.x86_64/usr/share/licenses/bionetgen + cp -pr bionetgen-BioNetGen-2.8.4/LICENSE /builddir/build/BUILDROOT/bionetgen-2.8.4-3.fc38.x86_64/usr/share/licenses/bionetgen + RPM_EC=0 ++ jobs -p + exit 0 Provides: bionetgen = 2.8.4-3.fc38 bionetgen(x86-64) = 2.8.4-3.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.26)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) rtld(GNU_HASH) Processing files: bionetgen-perl-2.8.4-3.fc38.noarch Provides: bionetgen-perl = 2.8.4-3.fc38 bundled(XML-TreePP) = 0.41 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-2.8.4-3.fc38.x86_64 Provides: bionetgen-debugsource = 2.8.4-3.fc38 bionetgen-debugsource(x86-64) = 2.8.4-3.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: bionetgen-debuginfo-2.8.4-3.fc38.x86_64 Provides: bionetgen-debuginfo = 2.8.4-3.fc38 bionetgen-debuginfo(x86-64) = 2.8.4-3.fc38 debuginfo(build-id) = 2ba833be8e057e797cd8048e4651dc1fcf1b8e19 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: bionetgen-debugsource(x86-64) = 2.8.4-3.fc38 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/bionetgen-2.8.4-3.fc38.x86_64 Wrote: /builddir/build/RPMS/bionetgen-perl-2.8.4-3.fc38.noarch.rpm Wrote: /builddir/build/RPMS/bionetgen-debugsource-2.8.4-3.fc38.x86_64.rpm Wrote: /builddir/build/RPMS/bionetgen-2.8.4-3.fc38.x86_64.rpm Wrote: /builddir/build/RPMS/bionetgen-debuginfo-2.8.4-3.fc38.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.eHUvSQ + umask 022 + cd /builddir/build/BUILD + cd bionetgen-2.8.4 + /usr/bin/rm -rf /builddir/build/BUILDROOT/bionetgen-2.8.4-3.fc38.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.9F92OF + umask 022 + cd /builddir/build/BUILD + rm -rf bionetgen-2.8.4 bionetgen-2.8.4.gemspec + RPM_EC=0 ++ jobs -p + exit 0 Child return code was: 0