Mock Version: 5.5 Mock Version: 5.5 Mock Version: 5.5 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --noclean --target aarch64 --nodeps /builddir/build/SPECS/smoldyn.spec'], chrootPath='/var/lib/mock/f41-build-50456496-6038281/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=201600uid=1000gid=425user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.ymzyd3q0:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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=False) Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.ymzyd3q0:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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', 'd3ea424f6cc3457ca1bb0a512b07a20b', '-D', '/var/lib/mock/f41-build-50456496-6038281/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.ymzyd3q0:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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 --noclean --target aarch64 --nodeps /builddir/build/SPECS/smoldyn.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: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1706313600 Wrote: /builddir/build/SRPMS/smoldyn-2.72-3.fc41.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --noclean --target aarch64 --nodeps /builddir/build/SPECS/smoldyn.spec'], chrootPath='/var/lib/mock/f41-build-50456496-6038281/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=201600uid=1000gid=425user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.ymzyd3q0:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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=False) Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.ymzyd3q0:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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', '8bbb633c630b44899d4fd4839bf75174', '-D', '/var/lib/mock/f41-build-50456496-6038281/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.ymzyd3q0:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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 --noclean --target aarch64 --nodeps /builddir/build/SPECS/smoldyn.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: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1706313600 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.2ckRlh + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf Smoldyn-2.72 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/Smoldyn-2.72.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd Smoldyn-2.72 + rm -rf /builddir/build/BUILD/Smoldyn-2.72-SPECPARTS + /usr/bin/mkdir -p /builddir/build/BUILD/Smoldyn-2.72-SPECPARTS + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . Patch #0 (smoldyn-fix_libpaths.patch): + echo 'Patch #0 (smoldyn-fix_libpaths.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p0 -b --suffix .fix_libpaths --fuzz=0 patching file CMakeLists.txt Patch #1 (smoldyn-freeglut.patch): + echo 'Patch #1 (smoldyn-freeglut.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p0 -b --suffix .freeglut --fuzz=0 patching file CMakeLists.txt Hunk #1 succeeded at 370 (offset 44 lines). Patch #2 (smoldyn-create_soname.patch): + echo 'Patch #2 (smoldyn-create_soname.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p0 -b --suffix .create_soname --fuzz=0 patching file CMakeLists.txt Hunk #1 succeeded at 490 (offset 5 lines). Hunk #2 succeeded at 522 (offset 52 lines). Patch #3 (smoldyn-avoid_automatic_wheel.patch): + echo 'Patch #3 (smoldyn-avoid_automatic_wheel.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p0 -b --suffix .avoid_automatic_wheel --fuzz=0 patching file source/python/CMakeLists.txt Hunk #1 succeeded at 20 (offset -3 lines). + rm -rf source/MSVClibs + rm -rf source/pybind11 + rm -rf source/BioNetGen source/MinGWlibs Toolchain-mingw32.cmake + rm -rf source/vcell/SimpleMesh.cpp source/vcell/SimpleMesh.h source/vcell/SimpleValueProvider.cpp source/vcell/SimpleValueProvider.h source/vcell/zconf.h source/vcell/zlib.h source/vcell/zlib.lib source/NextSubVolume/Eigen + rm -rf source/NextSubVolume/boost_include + rm -f 'source/vtk/*' + find . -type f -name '*.h' -exec chmod 0644 '{}' ';' + find . -type f -name '*.c' -exec chmod 0644 '{}' ';' + find . -type f -name '*.pdf' -exec chmod 0644 '{}' ';' + find . -type f -name '*.txt' -exec chmod 0644 '{}' ';' + find . -type f -name '*.txt' -exec sed -i 's/\r$//' '{}' ';' + sed -e 's|../../../source/BioNetGen/BNG2.pl|/usr/share/perl5/vendor_perl/BioNetGen/BNG2.pl|g' -i examples/S95_regression/lrmsim.txt examples/S12_bionetgen/lrm/lrmsim.txt examples/S12_bionetgen/abba/abbasim.txt examples/S94_archive/Andrews_2016/BioNetGen/lrm/lrmsim.txt examples/S94_archive/Andrews_2016/BioNetGen/abba/abbasim.txt + cp -p source/libSteve/SFMT/LICENSE.txt source/libSteve/SFMT/SFMT-LICENSE.txt + cp -p source/libSteve/SFMT/README.txt source/libSteve/SFMT/SFMT-README.txt + find -name '*.pyc' -delete + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.6e0x1E + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 Smoldyn-2.72 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 redhat-linux-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 -Wno-dev -DCPACK_BINARY_STGZ:BOOL=OFF -DCPACK_BINARY_TGZ:BOOL=OFF -DCPACK_BINARY_TZ:BOOL=OFF -DCPACK_SOURCE_TBZ2:BOOL=OFF -DCPACK_SOURCE_TGZ:BOOL=OFF -DCPACK_SOURCE_TXZ:BOOL=OFF -DCPACK_SOURCE_TZ:BOOL=OFF -DOPTION_VCELL:BOOL=OFF -DOPTION_VTK:BOOL=OFF -DBUILD_SHARED_LIBS:BOOL=ON -DSMOLDYN_VERSION:STRING=2.72 -DSMOLDYN_VERSION_MAJOR:STRING=2 -DOPTION_TARGET_LIBSMOLDYN:BOOL=ON -DOPTION_STATIC:BOOL=OFF -DOPTION_PYTHON:BOOL=ON -DPYBIND11_FINDPYTHON:BOOL=ON -Dpybind11_DIR:PATH=/usr/share/cmake/pybind11 -DOPTION_USE_ZLIB:BOOL=ON -DOPTION_PDE:BOOL=ON -DPERL_VENDORLIB:PATH=/usr/share/perl5/vendor_perl -DCMAKE_BUILD_TYPE:STRING=Release -DCMAKE_INSTALL_LIBDIR:PATH=/usr/lib64 -DCMAKE_INSTALL_PREFIX:PATH=/usr -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE -DCMAKE_COLOR_MAKEFILE:BOOL=ON -DCMAKE_SKIP_RPATH:BOOL=YES -DHAVE_GL_FREEGLUT_H=TRUE -DOPTION_EXAMPLES:BOOL=OFF -DOPTION_DOCS:BOOL=OFF -- The CXX compiler identification is GNU 14.0.1 -- The C compiler identification is GNU 14.0.1 -- 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 -- 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 -- Smoldyn version is set to: '2.72' -- Compiling for Smoldyn: ON -- Compiling for Libsmoldyn: ON -- Option to compile Smoldyn for VCell: OFF -- Option to cross-compile for Windows using MinGW: OFF -- Option to include NextSubvolume: ON -- Option to include VTK: OFF -- Option to compile with static libraries: OFF -- Option to include OpenGL support: ON -- Option to include LibTiff: ON -- Option to include Zlib: ON -- Option to incude Python module: ON -- Option to run Libsmoldyn examples: OFF -- Option to build documentation: OFF -- Performing Test C_FLAG_EXISTS -- Performing Test C_FLAG_EXISTS - Success -- Performing Test CXX_FLAG_EXISTS -- Performing Test CXX_FLAG_EXISTS - Success -- [COMPILER] Adding -Wno-unused-parameter -- Build type: Release -- Compiling on a Linux computer -- CMAKE_CXX_FLAGS variable: '-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' -- BioNetGen path: '/usr/share/perl5/vendor_perl/BioNetGen/BNG2.pl' -- Found OpenGL: /usr/lib64/libOpenGL.so -- OpenGL found: '/usr/include', '/usr/lib64/libGL.so;/usr/lib64/libGLU.so' -- Found GLUT: /usr/lib64/libglut.so -- Found TIFF: /usr/lib64/libtiff.so (found version "4.6.0") -- Found Libtiff: '/usr/include', '/usr/lib64/libtiff.so' -- Found Zlib: '/usr/include', '/usr/lib64/libz.so' -- Boost headers found: '/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume/boost_include' -- Found Python3: /usr/bin/python3.12 (found version "3.12.3") found components: Interpreter Development Development.Module Development.Embed -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Found pybind11: /usr/include (found version "2.12.0") -- [TEST] Found 15 test scripts -- Configuring done (2.7s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_Fortran_FLAGS_RELEASE CMAKE_INSTALL_DO_STRIP LIB_INSTALL_DIR SHARE_INSTALL_PREFIX SYSCONF_INSTALL_DIR -- Build files have been written to: /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build + /usr/bin/cmake --build redhat-linux-build -j12 --verbose Change Dir: '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' Run Build Command(s): /usr/bin/cmake -E env VERBOSE=1 /usr/bin/gmake -f Makefile -j12 /usr/bin/cmake -S/builddir/build/BUILD/Smoldyn-2.72 -B/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/CMakeFiles /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build//CMakeFiles/progress.marks /usr/bin/gmake -f CMakeFiles/Makefile2 all gmake[1]: Entering directory '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' /usr/bin/gmake -f source/NextSubVolume/CMakeFiles/nsv.dir/build.make source/NextSubVolume/CMakeFiles/nsv.dir/depend /usr/bin/gmake -f source/libSteve/CMakeFiles/Steve.dir/build.make source/libSteve/CMakeFiles/Steve.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/Smoldyn-2.72 /builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/NextSubVolume /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/NextSubVolume/CMakeFiles/nsv.dir/DependInfo.cmake "--color=" gmake[2]: Entering directory '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/Smoldyn-2.72 /builddir/build/BUILD/Smoldyn-2.72/source/libSteve /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/libSteve /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/libSteve/CMakeFiles/Steve.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' gmake[2]: Leaving directory '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' /usr/bin/gmake -f source/NextSubVolume/CMakeFiles/nsv.dir/build.make source/NextSubVolume/CMakeFiles/nsv.dir/build /usr/bin/gmake -f source/libSteve/CMakeFiles/Steve.dir/build.make source/libSteve/CMakeFiles/Steve.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' gmake[2]: Entering directory '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' [ 9%] Building CXX object source/NextSubVolume/CMakeFiles/nsv.dir/Species.cpp.o [ 7%] Building C object source/libSteve/CMakeFiles/Steve.dir/math2.c.o [ 12%] Building C object source/libSteve/CMakeFiles/Steve.dir/List.c.o [ 12%] Building CXX object source/NextSubVolume/CMakeFiles/nsv.dir/NextSubvolumeMethod.cpp.o [ 6%] Building C object source/libSteve/CMakeFiles/Steve.dir/queue.c.o [ 8%] Building C object source/libSteve/CMakeFiles/Steve.dir/opengl2.c.o [ 6%] Building C object source/libSteve/CMakeFiles/Steve.dir/parse.c.o [ 8%] Building CXX object source/NextSubVolume/CMakeFiles/nsv.dir/Kairos.cpp.o [ 12%] Building CXX object source/NextSubVolume/CMakeFiles/nsv.dir/ReactionEquation.cpp.o [ 12%] Building CXX object source/NextSubVolume/CMakeFiles/nsv.dir/StructuredGrid.cpp.o [ 13%] Building CXX object source/NextSubVolume/CMakeFiles/nsv.dir/Io.cpp.o [ 14%] Building C object source/libSteve/CMakeFiles/Steve.dir/Geometry.c.o cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/NextSubVolume && /usr/bin/g++ -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -isystem /builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume/boost_include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/NextSubVolume/CMakeFiles/nsv.dir/Species.cpp.o -MF CMakeFiles/nsv.dir/Species.cpp.o.d -o CMakeFiles/nsv.dir/Species.cpp.o -c /builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume/Species.cpp cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/libSteve && /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve/../Smoldyn -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/libSteve/CMakeFiles/Steve.dir/math2.c.o -MF CMakeFiles/Steve.dir/math2.c.o.d -o CMakeFiles/Steve.dir/math2.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/libSteve/math2.c cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/libSteve && /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve/../Smoldyn -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/libSteve/CMakeFiles/Steve.dir/List.c.o -MF CMakeFiles/Steve.dir/List.c.o.d -o CMakeFiles/Steve.dir/List.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/libSteve/List.c cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/NextSubVolume && /usr/bin/g++ -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -isystem /builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume/boost_include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/NextSubVolume/CMakeFiles/nsv.dir/NextSubvolumeMethod.cpp.o -MF CMakeFiles/nsv.dir/NextSubvolumeMethod.cpp.o.d -o CMakeFiles/nsv.dir/NextSubvolumeMethod.cpp.o -c /builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume/NextSubvolumeMethod.cpp cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/libSteve && /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve/../Smoldyn -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/libSteve/CMakeFiles/Steve.dir/parse.c.o -MF CMakeFiles/Steve.dir/parse.c.o.d -o CMakeFiles/Steve.dir/parse.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/libSteve/parse.c cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/NextSubVolume && /usr/bin/g++ -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -isystem /builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume/boost_include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/NextSubVolume/CMakeFiles/nsv.dir/ReactionEquation.cpp.o -MF CMakeFiles/nsv.dir/ReactionEquation.cpp.o.d -o CMakeFiles/nsv.dir/ReactionEquation.cpp.o -c /builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume/ReactionEquation.cpp cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/libSteve && /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve/../Smoldyn -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/libSteve/CMakeFiles/Steve.dir/opengl2.c.o -MF CMakeFiles/Steve.dir/opengl2.c.o.d -o CMakeFiles/Steve.dir/opengl2.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/libSteve/opengl2.c cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/NextSubVolume && /usr/bin/g++ -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -isystem /builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume/boost_include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/NextSubVolume/CMakeFiles/nsv.dir/StructuredGrid.cpp.o -MF CMakeFiles/nsv.dir/StructuredGrid.cpp.o.d -o CMakeFiles/nsv.dir/StructuredGrid.cpp.o -c /builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume/StructuredGrid.cpp cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/NextSubVolume && /usr/bin/g++ -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -isystem /builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume/boost_include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/NextSubVolume/CMakeFiles/nsv.dir/Kairos.cpp.o -MF CMakeFiles/nsv.dir/Kairos.cpp.o.d -o CMakeFiles/nsv.dir/Kairos.cpp.o -c /builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume/Kairos.cpp cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/libSteve && /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve/../Smoldyn -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/libSteve/CMakeFiles/Steve.dir/Geometry.c.o -MF CMakeFiles/Steve.dir/Geometry.c.o.d -o CMakeFiles/Steve.dir/Geometry.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/libSteve/Geometry.c cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/NextSubVolume && /usr/bin/g++ -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -isystem /builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume/boost_include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/NextSubVolume/CMakeFiles/nsv.dir/Io.cpp.o -MF CMakeFiles/nsv.dir/Io.cpp.o.d -o CMakeFiles/nsv.dir/Io.cpp.o -c /builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume/Io.cpp cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/libSteve && /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve/../Smoldyn -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/libSteve/CMakeFiles/Steve.dir/queue.c.o -MF CMakeFiles/Steve.dir/queue.c.o.d -o CMakeFiles/Steve.dir/queue.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/libSteve/queue.c [ 16%] Building CXX object source/NextSubVolume/CMakeFiles/nsv.dir/Geometry.cpp.o cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/NextSubVolume && /usr/bin/g++ -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -isystem /builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume/boost_include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/NextSubVolume/CMakeFiles/nsv.dir/Geometry.cpp.o -MF CMakeFiles/nsv.dir/Geometry.cpp.o.d -o CMakeFiles/nsv.dir/Geometry.cpp.o -c /builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume/Geometry.cpp /builddir/build/BUILD/Smoldyn-2.72/source/libSteve/parse.c: In function ‘Parse_ReadLine’: /builddir/build/BUILD/Smoldyn-2.72/source/libSteve/parse.c:382:60: warning: comparison is always true due to limited range of data type [-Wtype-limits] 382 | while((ch=fgetc(pfp->fptr))!=EOF && ch!='\n' && ch!='\r'); | ^~ [ 17%] Building C object source/libSteve/CMakeFiles/Steve.dir/random2.c.o cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/libSteve && /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve/../Smoldyn -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/libSteve/CMakeFiles/Steve.dir/random2.c.o -MF CMakeFiles/Steve.dir/random2.c.o.d -o CMakeFiles/Steve.dir/random2.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/libSteve/random2.c [ 18%] Building C object source/libSteve/CMakeFiles/Steve.dir/Rn.c.o cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/libSteve && /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve/../Smoldyn -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/libSteve/CMakeFiles/Steve.dir/Rn.c.o -MF CMakeFiles/Steve.dir/Rn.c.o.d -o CMakeFiles/Steve.dir/Rn.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/libSteve/Rn.c [ 19%] Building C object source/libSteve/CMakeFiles/Steve.dir/RnSort.c.o cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/libSteve && /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve/../Smoldyn -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/libSteve/CMakeFiles/Steve.dir/RnSort.c.o -MF CMakeFiles/Steve.dir/RnSort.c.o.d -o CMakeFiles/Steve.dir/RnSort.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/libSteve/RnSort.c [ 20%] Building C object source/libSteve/CMakeFiles/Steve.dir/rxnparam.c.o cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/libSteve && /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve/../Smoldyn -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/libSteve/CMakeFiles/Steve.dir/rxnparam.c.o -MF CMakeFiles/Steve.dir/rxnparam.c.o.d -o CMakeFiles/Steve.dir/rxnparam.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/libSteve/rxnparam.c [ 22%] Building CXX object source/NextSubVolume/CMakeFiles/nsv.dir/nsvc.cpp.o cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/NextSubVolume && /usr/bin/g++ -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -isystem /builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume/boost_include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/NextSubVolume/CMakeFiles/nsv.dir/nsvc.cpp.o -MF CMakeFiles/nsv.dir/nsvc.cpp.o.d -o CMakeFiles/nsv.dir/nsvc.cpp.o -c /builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume/nsvc.cpp [ 23%] Building C object source/libSteve/CMakeFiles/Steve.dir/SimCommand.c.o cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/libSteve && 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-mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/libSteve/CMakeFiles/Steve.dir/string2.c.o -MF CMakeFiles/Steve.dir/string2.c.o.d -o CMakeFiles/Steve.dir/string2.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/libSteve/string2.c [ 27%] Building C object source/libSteve/CMakeFiles/Steve.dir/SurfaceParam.c.o cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/libSteve && /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve/../Smoldyn -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security 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-I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve/../Smoldyn -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/libSteve/CMakeFiles/Steve.dir/Zn.c.o -MF CMakeFiles/Steve.dir/Zn.c.o.d -o CMakeFiles/Steve.dir/Zn.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/libSteve/Zn.c [ 29%] Building C object source/libSteve/CMakeFiles/Steve.dir/SFMT/SFMT.c.o cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/libSteve && /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve/../Smoldyn -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT source/libSteve/CMakeFiles/Steve.dir/SFMT/SFMT.c.o -MF CMakeFiles/Steve.dir/SFMT/SFMT.c.o.d -o CMakeFiles/Steve.dir/SFMT/SFMT.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/libSteve/SFMT/SFMT.c /builddir/build/BUILD/Smoldyn-2.72/source/libSteve/string2.c: In function ‘strmatheval’: /builddir/build/BUILD/Smoldyn-2.72/source/libSteve/string2.c:1415:9: warning: ‘strncpy’ specified bound 512 equals destination size [-Wstringop-truncation] 1415 | strncpy(expr,expression,STRCHAR); | ^ gmake[2]: Leaving directory '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' [ 29%] Built target Steve gmake[2]: Leaving directory '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' [ 29%] Built target nsv /usr/bin/gmake -f CMakeFiles/smoldyn_static.dir/build.make CMakeFiles/smoldyn_static.dir/depend /usr/bin/gmake -f CMakeFiles/smoldyn_shared.dir/build.make CMakeFiles/smoldyn_shared.dir/depend /usr/bin/gmake -f source/python/CMakeFiles/_pysmoldyn.dir/build.make source/python/CMakeFiles/_pysmoldyn.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' gmake[2]: Entering directory '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build && /usr/bin/cmake -E cmake_depends "Unix 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CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolcomparts.c.o.d -o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolcomparts.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolcomparts.c /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolbng.c.o -MF CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolbng.c.o.d -o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolbng.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c /usr/bin/gcc -Dsmoldyn_shared_EXPORTS -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolcmd.c.o -MF CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolcmd.c.o.d -o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolcmd.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolcmd.c cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -I/usr/include/python3.12 -I/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -DENABLE_PYTHON_CALLBACK -DCOMPILE_AS_PY_MODULE -MD -MT source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolcmd.c.o -MF CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolcmd.c.o.d -o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolcmd.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolcmd.c /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolboxes.c.o -MF CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolboxes.c.o.d -o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolboxes.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolboxes.c /usr/bin/gcc -Dsmoldyn_shared_EXPORTS -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolboxes.c.o -MF CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolboxes.c.o.d -o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolboxes.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolboxes.c /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolcomparts.c.o -MF CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolcomparts.c.o.d -o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolcomparts.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolcomparts.c cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -I/usr/include/python3.12 -I/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -DENABLE_PYTHON_CALLBACK -DCOMPILE_AS_PY_MODULE -MD -MT source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolbng.c.o -MF CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolbng.c.o.d -o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolbng.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c /usr/bin/gcc -Dsmoldyn_shared_EXPORTS -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolbng.c.o -MF CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolbng.c.o.d -o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolbng.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -I/usr/include/python3.12 -I/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -DENABLE_PYTHON_CALLBACK -DCOMPILE_AS_PY_MODULE -MD -MT source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolboxes.c.o -MF CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolboxes.c.o.d -o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolboxes.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolboxes.c cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -I/usr/include/python3.12 -I/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -DENABLE_PYTHON_CALLBACK -DCOMPILE_AS_PY_MODULE -MD -MT source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolcomparts.c.o -MF CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolcomparts.c.o.d -o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolcomparts.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolcomparts.c In file included from /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolcomparts.c:18: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolcomparts.c: In function ‘compartreadstring’: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolcomparts.c:894:29: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4082 [-Wformat-truncation=] 894 | CHECKS(s>=0,"surface name '%s' not recognized",nm); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolcomparts.c:894:44: note: format string is defined here 894 | CHECKS(s>=0,"surface name '%s' not recognized",nm); | ^~ In file included from /usr/include/stdio.h:980, from /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolcomparts.c:9: In function ‘snprintf’, inlined from ‘compartreadstring’ at /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolcomparts.c:894:3: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 31 and 4126 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolcomparts.c:18: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolcomparts.c: In function ‘compartreadstring’: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolcomparts.c:894:29: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4082 [-Wformat-truncation=] 894 | CHECKS(s>=0,"surface name '%s' not recognized",nm); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolcomparts.c:894:44: note: format string is defined here 894 | CHECKS(s>=0,"surface name '%s' not recognized",nm); | ^~ In file included from /usr/include/stdio.h:980, from /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolcomparts.c:9: In function ‘snprintf’, inlined from ‘compartreadstring’ at /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolcomparts.c:894:3: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 31 and 4126 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolcomparts.c:18: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolcomparts.c: In function ‘compartreadstring’: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolcomparts.c:894:29: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4082 [-Wformat-truncation=] 894 | CHECKS(s>=0,"surface name '%s' not recognized",nm); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolcomparts.c:894:44: note: format string is defined here 894 | CHECKS(s>=0,"surface name '%s' not recognized",nm); | ^~ In file included from /usr/include/stdio.h:980, from /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolcomparts.c:9: In function ‘snprintf’, inlined from ‘compartreadstring’ at /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolcomparts.c:894:3: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 31 and 4126 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolboxes.c: In function ‘boxesupdatelists’: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolboxes.c:783:55: warning: argument 1 range [18446744071562067968, 18446744073709551614] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 783 | bptr->neigh=(boxptr*) calloc(nneigh,sizeof(boxptr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/Smoldyn-2.72/source/libSteve/random2.h:17, from /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolboxes.c:13: /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolboxes.c: In function ‘boxesupdatelists’: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolboxes.c:783:55: warning: argument 1 range [18446744071562067968, 18446744073709551614] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 783 | bptr->neigh=(boxptr*) calloc(nneigh,sizeof(boxptr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/Smoldyn-2.72/source/libSteve/random2.h:17, from /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolboxes.c:13: /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ [ 45%] Building C object source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolfilament.c.o cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -I/usr/include/python3.12 -I/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -DENABLE_PYTHON_CALLBACK -DCOMPILE_AS_PY_MODULE -MD -MT source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolfilament.c.o -MF CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolfilament.c.o.d -o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolfilament.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolfilament.c [ 46%] Building C object CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolfilament.c.o /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolfilament.c.o -MF CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolfilament.c.o.d -o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolfilament.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolfilament.c [ 48%] Building C object CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolfilament.c.o /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolboxes.c: In function ‘boxesupdatelists’: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolboxes.c:783:55: warning: argument 1 range [18446744071562067968, 18446744073709551614] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 783 | bptr->neigh=(boxptr*) calloc(nneigh,sizeof(boxptr)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/Smoldyn-2.72/source/libSteve/random2.h:17, from /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolboxes.c:13: /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ /usr/bin/gcc -Dsmoldyn_shared_EXPORTS -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolfilament.c.o -MF CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolfilament.c.o.d -o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolfilament.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolfilament.c [ 49%] Building C object source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolgraphics.c.o cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -I/usr/include/python3.12 -I/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -DENABLE_PYTHON_CALLBACK -DCOMPILE_AS_PY_MODULE -MD -MT source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolgraphics.c.o -MF CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolgraphics.c.o.d -o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolgraphics.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolgraphics.c [ 50%] Building C object CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolgraphics.c.o /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolgraphics.c.o -MF CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolgraphics.c.o.d -o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolgraphics.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolgraphics.c [ 51%] Building C object CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolmolec.c.o /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolmolec.c.o -MF CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolmolec.c.o.d -o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolmolec.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolmolec.c In file included from /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:14: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1496:30: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4066 [-Wformat-truncation=] 1496 | CHECKS(er!=3,"Error reading BioNetGen file '%s'. Try again with '-v' flag for more information.",str1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1496:61: note: format string is defined here 1496 | CHECKS(er!=3,"Error reading BioNetGen file '%s'. Try again with '-v' flag for more information.",str1); | ^~ In file included from /usr/include/stdio.h:980, from /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:8: In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1496:3: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 80 and 4175 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1495:30: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4080 [-Wformat-truncation=] 1495 | CHECKS(er!=2,"BioNetGen file '%s' not found",str1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1495:47: note: format string is defined here 1495 | CHECKS(er!=2,"BioNetGen file '%s' not found",str1); | ^~ In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1495:3: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 28 and 4123 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1450:31: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4087 [-Wformat-truncation=] 1450 | CHECKS(er!=-2,"invalid '%s' monomer name",str1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1450:41: note: format string is defined here 1450 | CHECKS(er!=-2,"invalid '%s' monomer name",str1); | ^~ In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1450:3: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 24 and 4119 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1442:36: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4075 [-Wformat-truncation=] 1442 | CHECKS(!er,"error adding monomer %s",str1); }} | ^~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1442:58: note: format string is defined here 1442 | CHECKS(!er,"error adding monomer %s",str1); }} | ^~ In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1442:4: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 22 and 4117 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1441:39: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4082 [-Wformat-truncation=] 1441 | CHECKS(er!=-2,"monomer name '%s' is not permitted",str1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1441:54: note: format string is defined here 1441 | CHECKS(er!=-2,"monomer name '%s' is not permitted",str1); | ^~ In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1441:4: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 33 and 4128 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1440:39: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4067 [-Wformat-truncation=] 1440 | CHECKS(er!=-1,"out of memory adding monomer %s",str1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1440:69: note: format string is defined here 1440 | CHECKS(er!=-1,"out of memory adding monomer %s",str1); | ^~ In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1440:4: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 30 and 4125 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:14: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1496:30: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4066 [-Wformat-truncation=] 1496 | CHECKS(er!=3,"Error reading BioNetGen file '%s'. Try again with '-v' flag for more information.",str1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1496:61: note: format string is defined here 1496 | CHECKS(er!=3,"Error reading BioNetGen file '%s'. Try again with '-v' flag for more information.",str1); | ^~ In file included from /usr/include/stdio.h:980, from /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:8: In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1496:3: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 80 and 4175 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1495:30: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4080 [-Wformat-truncation=] 1495 | CHECKS(er!=2,"BioNetGen file '%s' not found",str1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1495:47: note: format string is defined here 1495 | CHECKS(er!=2,"BioNetGen file '%s' not found",str1); | ^~ In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1495:3: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 28 and 4123 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1450:31: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4087 [-Wformat-truncation=] 1450 | CHECKS(er!=-2,"invalid '%s' monomer name",str1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1450:41: note: format string is defined here 1450 | CHECKS(er!=-2,"invalid '%s' monomer name",str1); | ^~ In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1450:3: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 24 and 4119 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1442:36: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4075 [-Wformat-truncation=] 1442 | CHECKS(!er,"error adding monomer %s",str1); }} | ^~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1442:58: note: format string is defined here 1442 | CHECKS(!er,"error adding monomer %s",str1); }} | ^~ In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1442:4: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 22 and 4117 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1441:39: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4082 [-Wformat-truncation=] 1441 | CHECKS(er!=-2,"monomer name '%s' is not permitted",str1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1441:54: note: format string is defined here 1441 | CHECKS(er!=-2,"monomer name '%s' is not permitted",str1); | ^~ In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1441:4: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 33 and 4128 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1440:39: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4067 [-Wformat-truncation=] 1440 | CHECKS(er!=-1,"out of memory adding monomer %s",str1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1440:69: note: format string is defined here 1440 | CHECKS(er!=-1,"out of memory adding monomer %s",str1); | ^~ In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1440:4: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 30 and 4125 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:14: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1496:30: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4066 [-Wformat-truncation=] 1496 | CHECKS(er!=3,"Error reading BioNetGen file '%s'. Try again with '-v' flag for more information.",str1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1496:61: note: format string is defined here 1496 | CHECKS(er!=3,"Error reading BioNetGen file '%s'. Try again with '-v' flag for more information.",str1); | ^~ In file included from /usr/include/stdio.h:980, from /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:8: In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1496:3: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 80 and 4175 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1495:30: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4080 [-Wformat-truncation=] 1495 | CHECKS(er!=2,"BioNetGen file '%s' not found",str1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1495:47: note: format string is defined here 1495 | CHECKS(er!=2,"BioNetGen file '%s' not found",str1); | ^~ In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1495:3: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 28 and 4123 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1450:31: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4087 [-Wformat-truncation=] 1450 | CHECKS(er!=-2,"invalid '%s' monomer name",str1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1450:41: note: format string is defined here 1450 | CHECKS(er!=-2,"invalid '%s' monomer name",str1); | ^~ In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1450:3: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 24 and 4119 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1442:36: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4075 [-Wformat-truncation=] 1442 | CHECKS(!er,"error adding monomer %s",str1); }} | ^~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1442:58: note: format string is defined here 1442 | CHECKS(!er,"error adding monomer %s",str1); }} | ^~ In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1442:4: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 22 and 4117 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1441:39: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4082 [-Wformat-truncation=] 1441 | CHECKS(er!=-2,"monomer name '%s' is not permitted",str1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1441:54: note: format string is defined here 1441 | CHECKS(er!=-2,"monomer name '%s' is not permitted",str1); | ^~ In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1441:4: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 33 and 4128 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c: In function ‘bngreadstring’: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1440:39: warning: ‘%s’ directive output may be truncated writing up to 4095 bytes into a region of size 4067 [-Wformat-truncation=] 1440 | CHECKS(er!=-1,"out of memory adding monomer %s",str1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1440:69: note: format string is defined here 1440 | CHECKS(er!=-1,"out of memory adding monomer %s",str1); | ^~ In function ‘snprintf’, inlined from ‘bngreadstring’ at /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolbng.c:1440:4: /usr/include/bits/stdio2.h:68:10: note: ‘__snprintf_chk’ output between 30 and 4125 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 53%] Building C object CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolgraphics.c.o /usr/bin/gcc -Dsmoldyn_shared_EXPORTS -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolgraphics.c.o -MF CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolgraphics.c.o.d -o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolgraphics.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolgraphics.c [ 54%] Building C object CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolport.c.o /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolport.c.o -MF CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolport.c.o.d -o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolport.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolport.c [ 55%] Building C object source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolmolec.c.o cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -I/usr/include/python3.12 -I/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -DENABLE_PYTHON_CALLBACK -DCOMPILE_AS_PY_MODULE -MD -MT source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolmolec.c.o -MF CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolmolec.c.o.d -o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolmolec.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolmolec.c [ 56%] Building C object CMakeFiles/smoldyn_static.dir/source/Smoldyn/smollattice.c.o /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_static.dir/source/Smoldyn/smollattice.c.o -MF CMakeFiles/smoldyn_static.dir/source/Smoldyn/smollattice.c.o.d -o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smollattice.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smollattice.c [ 58%] Building C object source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolport.c.o cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -I/usr/include/python3.12 -I/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -DENABLE_PYTHON_CALLBACK -DCOMPILE_AS_PY_MODULE -MD -MT source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolport.c.o -MF CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolport.c.o.d -o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolport.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolport.c [ 59%] Building C object CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolreact.c.o /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolreact.c.o -MF CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolreact.c.o.d -o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolreact.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolreact.c [ 60%] Building C object CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolmolec.c.o /usr/bin/gcc -Dsmoldyn_shared_EXPORTS -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolmolec.c.o -MF CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolmolec.c.o.d -o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolmolec.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolmolec.c [ 61%] Building C object CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolrule.c.o /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolrule.c.o -MF CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolrule.c.o.d -o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolrule.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolrule.c [ 62%] Building C object source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smollattice.c.o cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -I/usr/include/python3.12 -I/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -DENABLE_PYTHON_CALLBACK -DCOMPILE_AS_PY_MODULE -MD -MT source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smollattice.c.o -MF CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smollattice.c.o.d -o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smollattice.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smollattice.c [ 64%] Building C object source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolreact.c.o cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -I/usr/include/python3.12 -I/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -DENABLE_PYTHON_CALLBACK -DCOMPILE_AS_PY_MODULE -MD -MT source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolreact.c.o -MF CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolreact.c.o.d -o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolreact.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolreact.c [ 66%] Building C object CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolport.c.o [ 66%] Building CXX object CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolsim.cpp.o /usr/bin/gcc -Dsmoldyn_shared_EXPORTS -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolport.c.o -MF CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolport.c.o.d -o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolport.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolport.c /usr/bin/g++ -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolsim.cpp.o -MF CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolsim.cpp.o.d -o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolsim.cpp.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolsim.cpp [ 67%] Building C object source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolrule.c.o cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -I/usr/include/python3.12 -I/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -DENABLE_PYTHON_CALLBACK -DCOMPILE_AS_PY_MODULE -MD -MT source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolrule.c.o -MF CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolrule.c.o.d -o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolrule.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolrule.c [ 69%] Building CXX object source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolsim.cpp.o cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/g++ -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -I/usr/include/python3.12 -I/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -Wno-unused-parameter -Wall -Wextra -DENABLE_PYTHON_CALLBACK -DCOMPILE_AS_PY_MODULE -MD -MT source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolsim.cpp.o -MF CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolsim.cpp.o.d -o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolsim.cpp.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolsim.cpp [ 70%] Building C object CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smollattice.c.o /usr/bin/gcc -Dsmoldyn_shared_EXPORTS -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smollattice.c.o -MF CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smollattice.c.o.d -o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smollattice.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smollattice.c [ 71%] Building C object source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolsurface.c.o cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -I/usr/include/python3.12 -I/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -DENABLE_PYTHON_CALLBACK -DCOMPILE_AS_PY_MODULE -MD -MT source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolsurface.c.o -MF CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolsurface.c.o.d -o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolsurface.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolsurface.c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolsim.cpp: In function ‘simParseError’: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolsim.cpp:166:58: warning: ‘%s’ directive writing up to 4095 bytes into a region of size between 603 and 4698 [-Wformat-overflow=] 166 | sprintf(ErrorLineAndString,"%s\nMessage: %s",parseerrstr,ErrorString); | ^~ ~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from /usr/include/c++/14/cstdio:42, from /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolsim.cpp:12: In function ‘sprintf’, inlined from ‘simParseError’ at /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolsim.cpp:166:10: /usr/include/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 11 and 8201 bytes into a destination of size 4708 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 72%] Building C object source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolwall.c.o cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -I/usr/include/python3.12 -I/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -DENABLE_PYTHON_CALLBACK -DCOMPILE_AS_PY_MODULE -MD -MT source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolwall.c.o -MF CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolwall.c.o.d -o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolwall.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolwall.c [ 74%] Building C object CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolreact.c.o /usr/bin/gcc -Dsmoldyn_shared_EXPORTS -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolreact.c.o -MF CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolreact.c.o.d -o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolreact.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolreact.c [ 75%] Building CXX object source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/libsmoldyn.cpp.o cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/g++ -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -I/usr/include/python3.12 -I/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -Wno-unused-parameter -Wall -Wextra -DENABLE_PYTHON_CALLBACK -DCOMPILE_AS_PY_MODULE -MD -MT source/python/CMakeFiles/_pysmoldyn.dir/__/Smoldyn/libsmoldyn.cpp.o -MF CMakeFiles/_pysmoldyn.dir/__/Smoldyn/libsmoldyn.cpp.o.d -o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/libsmoldyn.cpp.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/libsmoldyn.cpp [ 76%] Building C object CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolrule.c.o /usr/bin/gcc -Dsmoldyn_shared_EXPORTS -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolrule.c.o -MF CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolrule.c.o.d -o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolrule.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolrule.c In file included from /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smoldyn.h:15, from /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolsim.cpp:27: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/../python/CallbackFunc.h:20:7: warning: ‘CallbackFunc’ declared with greater visibility than the type of its field ‘CallbackFunc::func_’ [-Wattributes] 20 | class CallbackFunc | ^~~~~~~~~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/../python/CallbackFunc.h:20:7: warning: ‘CallbackFunc’ declared with greater visibility than the type of its field ‘CallbackFunc::target_’ [-Wattributes] /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/../python/CallbackFunc.h:20:7: warning: ‘CallbackFunc’ declared with greater visibility than the type of its field ‘CallbackFunc::args_’ [-Wattributes] [ 77%] Building CXX object CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolsim.cpp.o /usr/bin/g++ -Dsmoldyn_shared_EXPORTS -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolsim.cpp.o -MF CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolsim.cpp.o.d -o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolsim.cpp.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolsim.cpp [ 79%] Building C object CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolsurface.c.o /usr/bin/gcc -Dsmoldyn_shared_EXPORTS -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolsurface.c.o -MF CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolsurface.c.o.d -o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolsurface.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolsurface.c [ 80%] Building C object CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolwall.c.o /usr/bin/gcc -Dsmoldyn_shared_EXPORTS -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolwall.c.o -MF CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolwall.c.o.d -o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolwall.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolwall.c [ 81%] Building CXX object CMakeFiles/smoldyn_shared.dir/source/Smoldyn/libsmoldyn.cpp.o /usr/bin/g++ -Dsmoldyn_shared_EXPORTS -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_shared.dir/source/Smoldyn/libsmoldyn.cpp.o -MF CMakeFiles/smoldyn_shared.dir/source/Smoldyn/libsmoldyn.cpp.o.d -o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/libsmoldyn.cpp.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/libsmoldyn.cpp [ 82%] Building C object CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolsurface.c.o /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolsurface.c.o -MF CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolsurface.c.o.d -o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolsurface.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolsurface.c [ 83%] Building C object CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolwall.c.o /usr/bin/gcc -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu11 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolwall.c.o -MF CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolwall.c.o.d -o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolwall.c.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolwall.c [ 85%] Building CXX object CMakeFiles/smoldyn_static.dir/source/Smoldyn/libsmoldyn.cpp.o /usr/bin/g++ -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn_static.dir/source/Smoldyn/libsmoldyn.cpp.o -MF CMakeFiles/smoldyn_static.dir/source/Smoldyn/libsmoldyn.cpp.o.d -o CMakeFiles/smoldyn_static.dir/source/Smoldyn/libsmoldyn.cpp.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/libsmoldyn.cpp In file included from /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smoldyn.h:15, from /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/libsmoldyn.cpp:15: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/../python/CallbackFunc.h:20:7: warning: ‘CallbackFunc’ declared with greater visibility than the type of its field ‘CallbackFunc::func_’ [-Wattributes] 20 | class CallbackFunc | ^~~~~~~~~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/../python/CallbackFunc.h:20:7: warning: ‘CallbackFunc’ declared with greater visibility than the type of its field ‘CallbackFunc::target_’ [-Wattributes] /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/../python/CallbackFunc.h:20:7: warning: ‘CallbackFunc’ declared with greater visibility than the type of its field ‘CallbackFunc::args_’ [-Wattributes] /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolsim.cpp: In function ‘simParseError’: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolsim.cpp:166:58: warning: ‘%s’ directive writing up to 4095 bytes into a region of size between 603 and 4698 [-Wformat-overflow=] 166 | sprintf(ErrorLineAndString,"%s\nMessage: %s",parseerrstr,ErrorString); | ^~ ~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from /usr/include/c++/14/cstdio:42, from /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolsim.cpp:12: In function ‘sprintf’, inlined from ‘simParseError’ at /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolsim.cpp:166:10: /usr/include/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 11 and 8201 bytes into a destination of size 4708 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolsim.cpp: In function ‘simParseError’: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolsim.cpp:166:58: warning: ‘%s’ directive writing up to 4095 bytes into a region of size between 603 and 4698 [-Wformat-overflow=] 166 | sprintf(ErrorLineAndString,"%s\nMessage: %s",parseerrstr,ErrorString); | ^~ ~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from /usr/include/c++/14/cstdio:42, from /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolsim.cpp:12: In function ‘sprintf’, inlined from ‘simParseError’ at /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolsim.cpp:166:10: /usr/include/bits/stdio2.h:30:34: note: ‘__sprintf_chk’ output between 11 and 8201 bytes into a destination of size 4708 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 86%] Linking CXX shared library libsmoldyn_shared.so /usr/bin/cmake -E cmake_link_script CMakeFiles/smoldyn_shared.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 -shared -Wl,-soname,libsmoldyn_shared.so.2 -o libsmoldyn_shared.so.2.72 CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolbng.c.o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolboxes.c.o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolcmd.c.o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolcomparts.c.o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolfilament.c.o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolgraphics.c.o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolmolec.c.o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolport.c.o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smollattice.c.o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolreact.c.o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolrule.c.o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolsim.cpp.o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolsurface.c.o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/smolwall.c.o CMakeFiles/smoldyn_shared.dir/source/Smoldyn/libsmoldyn.cpp.o source/libSteve/CMakeFiles/Steve.dir/Geometry.c.o source/libSteve/CMakeFiles/Steve.dir/List.c.o source/libSteve/CMakeFiles/Steve.dir/math2.c.o source/libSteve/CMakeFiles/Steve.dir/opengl2.c.o source/libSteve/CMakeFiles/Steve.dir/parse.c.o source/libSteve/CMakeFiles/Steve.dir/queue.c.o source/libSteve/CMakeFiles/Steve.dir/random2.c.o source/libSteve/CMakeFiles/Steve.dir/Rn.c.o source/libSteve/CMakeFiles/Steve.dir/RnSort.c.o source/libSteve/CMakeFiles/Steve.dir/rxnparam.c.o source/libSteve/CMakeFiles/Steve.dir/SimCommand.c.o source/libSteve/CMakeFiles/Steve.dir/Sphere.c.o source/libSteve/CMakeFiles/Steve.dir/string2.c.o source/libSteve/CMakeFiles/Steve.dir/SurfaceParam.c.o source/libSteve/CMakeFiles/Steve.dir/Zn.c.o source/libSteve/CMakeFiles/Steve.dir/SFMT/SFMT.c.o source/NextSubVolume/CMakeFiles/nsv.dir/StructuredGrid.cpp.o source/NextSubVolume/CMakeFiles/nsv.dir/Species.cpp.o source/NextSubVolume/CMakeFiles/nsv.dir/ReactionEquation.cpp.o source/NextSubVolume/CMakeFiles/nsv.dir/NextSubvolumeMethod.cpp.o source/NextSubVolume/CMakeFiles/nsv.dir/Kairos.cpp.o source/NextSubVolume/CMakeFiles/nsv.dir/Io.cpp.o source/NextSubVolume/CMakeFiles/nsv.dir/Geometry.cpp.o source/NextSubVolume/CMakeFiles/nsv.dir/nsvc.cpp.o /usr/lib64/libGL.so /usr/lib64/libGLU.so -lglut /usr/lib64/libtiff.so /usr/lib64/libz.so /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smoldyn.h:714:16: warning: type ‘struct latticestruct’ violates the C++ One Definition Rule [-Wodr] 714 | typedef struct latticestruct | ^ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smoldyn.h:714:16: note: a different type is defined in another translation unit 714 | typedef struct latticestruct | ^ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smoldyn.h:739:26: note: the first difference of corresponding definitions is field ‘nsv’ 739 | NextSubvolumeMethod* nsv; // nsv class | ^ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smoldyn.h:739:26: note: a field of same name but different type is defined in another translation unit 739 | NextSubvolumeMethod* nsv; // nsv class | ^ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smoldyn.h:714:16: note: type name ‘NextSubvolumeMethod’ should match type name ‘Kairos::NextSubvolumeMethod’ 714 | typedef struct latticestruct | ^ /builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume/NextSubvolumeMethod.h:137:7: note: the incompatible type is defined here 137 | class NextSubvolumeMethod | ^ [ 87%] Linking CXX static library libsmoldyn_static.a /usr/bin/cmake -P CMakeFiles/smoldyn_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/smoldyn_static.dir/link.txt --verbose=1 /usr/bin/ar qc libsmoldyn_static.a CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolbng.c.o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolboxes.c.o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolcmd.c.o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolcomparts.c.o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolfilament.c.o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolgraphics.c.o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolmolec.c.o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolport.c.o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smollattice.c.o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolreact.c.o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolrule.c.o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolsim.cpp.o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolsurface.c.o CMakeFiles/smoldyn_static.dir/source/Smoldyn/smolwall.c.o CMakeFiles/smoldyn_static.dir/source/Smoldyn/libsmoldyn.cpp.o source/libSteve/CMakeFiles/Steve.dir/Geometry.c.o source/libSteve/CMakeFiles/Steve.dir/List.c.o source/libSteve/CMakeFiles/Steve.dir/math2.c.o source/libSteve/CMakeFiles/Steve.dir/opengl2.c.o source/libSteve/CMakeFiles/Steve.dir/parse.c.o source/libSteve/CMakeFiles/Steve.dir/queue.c.o source/libSteve/CMakeFiles/Steve.dir/random2.c.o source/libSteve/CMakeFiles/Steve.dir/Rn.c.o source/libSteve/CMakeFiles/Steve.dir/RnSort.c.o source/libSteve/CMakeFiles/Steve.dir/rxnparam.c.o source/libSteve/CMakeFiles/Steve.dir/SimCommand.c.o source/libSteve/CMakeFiles/Steve.dir/Sphere.c.o source/libSteve/CMakeFiles/Steve.dir/string2.c.o source/libSteve/CMakeFiles/Steve.dir/SurfaceParam.c.o source/libSteve/CMakeFiles/Steve.dir/Zn.c.o source/libSteve/CMakeFiles/Steve.dir/SFMT/SFMT.c.o source/NextSubVolume/CMakeFiles/nsv.dir/StructuredGrid.cpp.o source/NextSubVolume/CMakeFiles/nsv.dir/Species.cpp.o source/NextSubVolume/CMakeFiles/nsv.dir/ReactionEquation.cpp.o source/NextSubVolume/CMakeFiles/nsv.dir/NextSubvolumeMethod.cpp.o source/NextSubVolume/CMakeFiles/nsv.dir/Kairos.cpp.o source/NextSubVolume/CMakeFiles/nsv.dir/Io.cpp.o source/NextSubVolume/CMakeFiles/nsv.dir/Geometry.cpp.o source/NextSubVolume/CMakeFiles/nsv.dir/nsvc.cpp.o /usr/bin/ranlib libsmoldyn_static.a gmake[2]: Leaving directory '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' [ 87%] Built target smoldyn_static /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolboxes.c: In function ‘boxesupdatelists’: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolboxes.c:783:55: warning: argument 1 range [18446744071562067968, 18446744073709551614] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 783 | bptr->neigh=(boxptr*) calloc(nneigh,sizeof(boxptr)); | ^ /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^ /usr/bin/cmake -E cmake_symlink_library libsmoldyn_shared.so.2.72 libsmoldyn_shared.so.2 libsmoldyn_shared.so gmake[2]: Leaving directory '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' [ 87%] Built target smoldyn_shared /usr/bin/gmake -f CMakeFiles/smoldyn.dir/build.make CMakeFiles/smoldyn.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/Smoldyn-2.72 /builddir/build/BUILD/Smoldyn-2.72 /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/CMakeFiles/smoldyn.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' /usr/bin/gmake -f CMakeFiles/smoldyn.dir/build.make CMakeFiles/smoldyn.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' [ 88%] Building CXX object CMakeFiles/smoldyn.dir/source/Smoldyn/smoldyn.cpp.o /usr/bin/g++ -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -Wno-unused-parameter -Wall -Wextra -MD -MT CMakeFiles/smoldyn.dir/source/Smoldyn/smoldyn.cpp.o -MF CMakeFiles/smoldyn.dir/source/Smoldyn/smoldyn.cpp.o.d -o CMakeFiles/smoldyn.dir/source/Smoldyn/smoldyn.cpp.o -c /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smoldyn.cpp [ 90%] Linking CXX executable smoldyn /usr/bin/cmake -E cmake_link_script CMakeFiles/smoldyn.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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/smoldyn.dir/source/Smoldyn/smoldyn.cpp.o -o smoldyn libsmoldyn_shared.so.2.72 /usr/lib64/libGL.so /usr/lib64/libGLU.so -lglut /usr/lib64/libtiff.so /usr/lib64/libz.so gmake[2]: Leaving directory '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' [ 90%] Built target smoldyn [ 91%] Linking CXX static library lib_pysmoldyn.a cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/cmake -P CMakeFiles/_pysmoldyn.dir/cmake_clean_target.cmake cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/cmake -E cmake_link_script CMakeFiles/_pysmoldyn.dir/link.txt --verbose=1 /usr/bin/ar qc lib_pysmoldyn.a CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolbng.c.o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolboxes.c.o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolcmd.c.o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolcomparts.c.o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolfilament.c.o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolgraphics.c.o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolmolec.c.o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolport.c.o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smollattice.c.o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolreact.c.o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolrule.c.o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolsim.cpp.o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolsurface.c.o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/smolwall.c.o CMakeFiles/_pysmoldyn.dir/__/Smoldyn/libsmoldyn.cpp.o ../libSteve/CMakeFiles/Steve.dir/Geometry.c.o ../libSteve/CMakeFiles/Steve.dir/List.c.o ../libSteve/CMakeFiles/Steve.dir/math2.c.o ../libSteve/CMakeFiles/Steve.dir/opengl2.c.o ../libSteve/CMakeFiles/Steve.dir/parse.c.o ../libSteve/CMakeFiles/Steve.dir/queue.c.o ../libSteve/CMakeFiles/Steve.dir/random2.c.o ../libSteve/CMakeFiles/Steve.dir/Rn.c.o ../libSteve/CMakeFiles/Steve.dir/RnSort.c.o ../libSteve/CMakeFiles/Steve.dir/rxnparam.c.o ../libSteve/CMakeFiles/Steve.dir/SimCommand.c.o ../libSteve/CMakeFiles/Steve.dir/Sphere.c.o ../libSteve/CMakeFiles/Steve.dir/string2.c.o ../libSteve/CMakeFiles/Steve.dir/SurfaceParam.c.o ../libSteve/CMakeFiles/Steve.dir/Zn.c.o ../libSteve/CMakeFiles/Steve.dir/SFMT/SFMT.c.o ../NextSubVolume/CMakeFiles/nsv.dir/StructuredGrid.cpp.o ../NextSubVolume/CMakeFiles/nsv.dir/Species.cpp.o ../NextSubVolume/CMakeFiles/nsv.dir/ReactionEquation.cpp.o ../NextSubVolume/CMakeFiles/nsv.dir/NextSubvolumeMethod.cpp.o ../NextSubVolume/CMakeFiles/nsv.dir/Kairos.cpp.o ../NextSubVolume/CMakeFiles/nsv.dir/Io.cpp.o ../NextSubVolume/CMakeFiles/nsv.dir/Geometry.cpp.o ../NextSubVolume/CMakeFiles/nsv.dir/nsvc.cpp.o /usr/bin/ranlib lib_pysmoldyn.a gmake[2]: Leaving directory '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' [ 91%] Built target _pysmoldyn /usr/bin/gmake -f source/python/CMakeFiles/_smoldyn.dir/build.make source/python/CMakeFiles/_smoldyn.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/Smoldyn-2.72 /builddir/build/BUILD/Smoldyn-2.72/source/python /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python/CMakeFiles/_smoldyn.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' /usr/bin/gmake -f source/python/CMakeFiles/_smoldyn.dir/build.make source/python/CMakeFiles/_smoldyn.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' [ 96%] Building CXX object source/python/CMakeFiles/_smoldyn.dir/module.cpp.o [ 96%] Building CXX object source/python/CMakeFiles/_smoldyn.dir/Simulation.cpp.o [ 96%] Building CXX object source/python/CMakeFiles/_smoldyn.dir/Command.cpp.o [ 96%] Building CXX object source/python/CMakeFiles/_smoldyn.dir/CallbackFunc.cpp.o cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/g++ -D_smoldyn_EXPORTS -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/Smoldyn-2.72/source/external/pybind11/include -isystem /usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -fvisibility=hidden -Wno-unused-parameter -Wall -Wextra -DSMOLDYN_VERSION=2.72 -DENABLE_PYTHON_CALLBACK -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT source/python/CMakeFiles/_smoldyn.dir/module.cpp.o -MF CMakeFiles/_smoldyn.dir/module.cpp.o.d -o CMakeFiles/_smoldyn.dir/module.cpp.o -c /builddir/build/BUILD/Smoldyn-2.72/source/python/module.cpp cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/g++ -D_smoldyn_EXPORTS -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/Smoldyn-2.72/source/external/pybind11/include -isystem /usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -fvisibility=hidden -Wno-unused-parameter -Wall -Wextra -DSMOLDYN_VERSION=2.72 -DENABLE_PYTHON_CALLBACK -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT source/python/CMakeFiles/_smoldyn.dir/Command.cpp.o -MF CMakeFiles/_smoldyn.dir/Command.cpp.o.d -o CMakeFiles/_smoldyn.dir/Command.cpp.o -c /builddir/build/BUILD/Smoldyn-2.72/source/python/Command.cpp cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/g++ -D_smoldyn_EXPORTS -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/Smoldyn-2.72/source/external/pybind11/include -isystem /usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -fvisibility=hidden -Wno-unused-parameter -Wall -Wextra -DSMOLDYN_VERSION=2.72 -DENABLE_PYTHON_CALLBACK -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT source/python/CMakeFiles/_smoldyn.dir/CallbackFunc.cpp.o -MF CMakeFiles/_smoldyn.dir/CallbackFunc.cpp.o.d -o CMakeFiles/_smoldyn.dir/CallbackFunc.cpp.o -c /builddir/build/BUILD/Smoldyn-2.72/source/python/CallbackFunc.cpp cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/g++ -D_smoldyn_EXPORTS -I/builddir/build/BUILD/Smoldyn-2.72/source/libSteve -I/builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn -I/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build -I/usr/include/GL -I/builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume -I/builddir/build/BUILD/Smoldyn-2.72/source/external/pybind11/include -isystem /usr/include/python3.12 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -std=gnu++14 -fPIC -fvisibility=hidden -Wno-unused-parameter -Wall -Wextra -DSMOLDYN_VERSION=2.72 -DENABLE_PYTHON_CALLBACK -fvisibility=hidden -flto -fno-fat-lto-objects -MD -MT source/python/CMakeFiles/_smoldyn.dir/Simulation.cpp.o -MF CMakeFiles/_smoldyn.dir/Simulation.cpp.o.d -o CMakeFiles/_smoldyn.dir/Simulation.cpp.o -c /builddir/build/BUILD/Smoldyn-2.72/source/python/Simulation.cpp [ 97%] Linking CXX shared module /builddir/build/BUILD/Smoldyn-2.72/source/python/smoldyn/_smoldyn.cpython-312-aarch64-linux-gnu.so cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/cmake -E cmake_link_script CMakeFiles/_smoldyn.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -flto -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 -shared -o /builddir/build/BUILD/Smoldyn-2.72/source/python/smoldyn/_smoldyn.cpython-312-aarch64-linux-gnu.so CMakeFiles/_smoldyn.dir/CallbackFunc.cpp.o CMakeFiles/_smoldyn.dir/Command.cpp.o CMakeFiles/_smoldyn.dir/Simulation.cpp.o CMakeFiles/_smoldyn.dir/module.cpp.o lib_pysmoldyn.a /usr/lib64/libGL.so /usr/lib64/libGLU.so -lglut /usr/lib64/libtiff.so /usr/lib64/libz.so /builddir/build/BUILD/Smoldyn-2.72/source/python/../Smoldyn/smoldyn.h:1045:16: warning: type ‘struct simstruct’ violates the C++ One Definition Rule [-Wodr] 1045 | typedef struct simstruct | ^ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smoldyn.h:1045:16: note: a different type is defined in another translation unit 1045 | typedef struct simstruct | ^ /builddir/build/BUILD/Smoldyn-2.72/source/python/../Smoldyn/smoldyn.h:1106:19: note: the first difference of corresponding definitions is field ‘callbacks’ 1106 | CallbackFunc* callbacks[MAX_PY_CALLBACK]; // Python callback. | ^ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smoldyn.h:1045:16: note: a type with different number of fields is defined in another translation unit 1045 | typedef struct simstruct | ^ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smoldyn.h:714:16: warning: type ‘struct latticestruct’ violates the C++ One Definition Rule [-Wodr] 714 | typedef struct latticestruct | ^ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smoldyn.h:714:16: note: a different type is defined in another translation unit 714 | typedef struct latticestruct | ^ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smoldyn.h:739:26: note: the first difference of corresponding definitions is field ‘nsv’ 739 | NextSubvolumeMethod* nsv; // nsv class | ^ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smoldyn.h:739:26: note: a field of same name but different type is defined in another translation unit 739 | NextSubvolumeMethod* nsv; // nsv class | ^ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smoldyn.h:714:16: note: type name ‘NextSubvolumeMethod’ should match type name ‘Kairos::NextSubvolumeMethod’ 714 | typedef struct latticestruct | ^ /builddir/build/BUILD/Smoldyn-2.72/source/NextSubVolume/NextSubvolumeMethod.h:137:7: note: the incompatible type is defined here 137 | class NextSubvolumeMethod | ^ /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolboxes.c: In function ‘boxesupdatelists’: /builddir/build/BUILD/Smoldyn-2.72/source/Smoldyn/smolboxes.c:783:55: warning: argument 1 range [18446744071562067968, 18446744073709551614] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 783 | bptr->neigh=(boxptr*) calloc(nneigh,sizeof(boxptr)); | ^ /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^ cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/strip /builddir/build/BUILD/Smoldyn-2.72/source/python/smoldyn/_smoldyn.cpython-312-aarch64-linux-gnu.so gmake[2]: Leaving directory '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' [ 97%] Built target _smoldyn /usr/bin/gmake -f source/python/CMakeFiles/copy_python_tree.dir/build.make source/python/CMakeFiles/copy_python_tree.dir/depend /usr/bin/gmake -f source/python/CMakeFiles/wheel.dir/build.make source/python/CMakeFiles/wheel.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' gmake[2]: Entering directory '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/Smoldyn-2.72 /builddir/build/BUILD/Smoldyn-2.72/source/python /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python/CMakeFiles/wheel.dir/DependInfo.cmake "--color=" cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/Smoldyn-2.72 /builddir/build/BUILD/Smoldyn-2.72/source/python /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python/CMakeFiles/copy_python_tree.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' gmake[2]: Leaving directory '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' /usr/bin/gmake -f source/python/CMakeFiles/wheel.dir/build.make source/python/CMakeFiles/wheel.dir/build /usr/bin/gmake -f source/python/CMakeFiles/copy_python_tree.dir/build.make source/python/CMakeFiles/copy_python_tree.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' gmake[2]: Entering directory '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' [100%] Generating wheel in /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build [100%] Copying python source tree to binary directory cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/py && /usr/bin/python3.12 setup.py bdist_wheel -d /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build cd /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python && /usr/bin/cmake -E copy_directory /builddir/build/BUILD/Smoldyn-2.72/source/python/smoldyn /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/py/smoldyn gmake[2]: Leaving directory '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' [100%] Built target copy_python_tree running bdist_wheel running build running build_py creating build creating build/lib.linux-aarch64-cpython-312 creating build/lib.linux-aarch64-cpython-312/smoldyn copying smoldyn/__init__.py -> build/lib.linux-aarch64-cpython-312/smoldyn copying smoldyn/__main__.py -> build/lib.linux-aarch64-cpython-312/smoldyn copying smoldyn/smoldyn.py -> build/lib.linux-aarch64-cpython-312/smoldyn copying smoldyn/types.py -> build/lib.linux-aarch64-cpython-312/smoldyn copying smoldyn/utils.py -> build/lib.linux-aarch64-cpython-312/smoldyn creating build/lib.linux-aarch64-cpython-312/smoldyn/biosimulators copying smoldyn/biosimulators/__init__.py -> build/lib.linux-aarch64-cpython-312/smoldyn/biosimulators copying smoldyn/biosimulators/__main__.py -> build/lib.linux-aarch64-cpython-312/smoldyn/biosimulators copying smoldyn/biosimulators/_version.py -> build/lib.linux-aarch64-cpython-312/smoldyn/biosimulators copying smoldyn/biosimulators/combine.py -> build/lib.linux-aarch64-cpython-312/smoldyn/biosimulators copying smoldyn/biosimulators/data_model.py -> build/lib.linux-aarch64-cpython-312/smoldyn/biosimulators copying smoldyn/biosimulators/utils.py -> build/lib.linux-aarch64-cpython-312/smoldyn/biosimulators copying smoldyn/_smoldyn.cpython-312-aarch64-linux-gnu.so -> build/lib.linux-aarch64-cpython-312/smoldyn running build_ext /usr/lib/python3.12/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. Follow the current Python packaging guidelines when building Python RPM packages. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html and https://docs.fedoraproject.org/en-US/packaging-guidelines/Python/ for details. ******************************************************************************** !! self.initialize_options() installing to build/bdist.linux-aarch64/wheel running install running install_lib creating build/bdist.linux-aarch64 creating build/bdist.linux-aarch64/wheel creating build/bdist.linux-aarch64/wheel/smoldyn copying build/lib.linux-aarch64-cpython-312/smoldyn/__init__.py -> build/bdist.linux-aarch64/wheel/smoldyn copying build/lib.linux-aarch64-cpython-312/smoldyn/__main__.py -> build/bdist.linux-aarch64/wheel/smoldyn copying build/lib.linux-aarch64-cpython-312/smoldyn/smoldyn.py -> build/bdist.linux-aarch64/wheel/smoldyn copying build/lib.linux-aarch64-cpython-312/smoldyn/types.py -> build/bdist.linux-aarch64/wheel/smoldyn copying build/lib.linux-aarch64-cpython-312/smoldyn/utils.py -> build/bdist.linux-aarch64/wheel/smoldyn creating build/bdist.linux-aarch64/wheel/smoldyn/biosimulators copying build/lib.linux-aarch64-cpython-312/smoldyn/biosimulators/__init__.py -> build/bdist.linux-aarch64/wheel/smoldyn/biosimulators copying build/lib.linux-aarch64-cpython-312/smoldyn/biosimulators/__main__.py -> build/bdist.linux-aarch64/wheel/smoldyn/biosimulators copying build/lib.linux-aarch64-cpython-312/smoldyn/biosimulators/_version.py -> build/bdist.linux-aarch64/wheel/smoldyn/biosimulators copying build/lib.linux-aarch64-cpython-312/smoldyn/biosimulators/combine.py -> build/bdist.linux-aarch64/wheel/smoldyn/biosimulators copying build/lib.linux-aarch64-cpython-312/smoldyn/biosimulators/data_model.py -> build/bdist.linux-aarch64/wheel/smoldyn/biosimulators copying build/lib.linux-aarch64-cpython-312/smoldyn/biosimulators/utils.py -> build/bdist.linux-aarch64/wheel/smoldyn/biosimulators copying build/lib.linux-aarch64-cpython-312/smoldyn/_smoldyn.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/smoldyn running install_egg_info running egg_info creating smoldyn.egg-info writing smoldyn.egg-info/PKG-INFO writing dependency_links to smoldyn.egg-info/dependency_links.txt writing requirements to smoldyn.egg-info/requires.txt writing top-level names to smoldyn.egg-info/top_level.txt writing manifest file 'smoldyn.egg-info/SOURCES.txt' reading manifest file 'smoldyn.egg-info/SOURCES.txt' writing manifest file 'smoldyn.egg-info/SOURCES.txt' Copying smoldyn.egg-info to build/bdist.linux-aarch64/wheel/smoldyn-2.72-py3.12.egg-info running install_scripts creating build/bdist.linux-aarch64/wheel/smoldyn-2.72.dist-info/WHEEL creating '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/smoldyn-2.72-cp312-cp312-linux_aarch64.whl' and adding 'build/bdist.linux-aarch64/wheel' to it adding 'smoldyn/__init__.py' adding 'smoldyn/__main__.py' adding 'smoldyn/_smoldyn.cpython-312-aarch64-linux-gnu.so' adding 'smoldyn/smoldyn.py' adding 'smoldyn/types.py' adding 'smoldyn/utils.py' adding 'smoldyn/biosimulators/__init__.py' adding 'smoldyn/biosimulators/__main__.py' adding 'smoldyn/biosimulators/_version.py' adding 'smoldyn/biosimulators/combine.py' adding 'smoldyn/biosimulators/data_model.py' adding 'smoldyn/biosimulators/utils.py' adding 'smoldyn-2.72.dist-info/METADATA' adding 'smoldyn-2.72.dist-info/WHEEL' adding 'smoldyn-2.72.dist-info/top_level.txt' adding 'smoldyn-2.72.dist-info/RECORD' removing build/bdist.linux-aarch64/wheel gmake[2]: Leaving directory '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' [100%] Built target wheel gmake[1]: Leaving directory '/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/CMakeFiles 0 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.7Gvug6 + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64 ++ dirname /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 Smoldyn-2.72 + DESTDIR=/builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64 + /usr/bin/cmake --install redhat-linux-build -- Install configuration: "Release" -- Installing: /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/bin/smoldyn -- Installing: /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/lib64/libsmoldyn_shared.so.2.72 -- Installing: /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/lib64/libsmoldyn_shared.so.2 -- Installing: /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/lib64/libsmoldyn_shared.so -- Installing: /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/lib64/libsmoldyn_static.a -- Installing: /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/include/smoldyn/libsmoldyn.h -- Installing: /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/include/smoldyn/smoldyn.h -- Installing: /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/include/smoldyn/smoldynconfigure.h + pushd redhat-linux-build/py ~/build/BUILD/Smoldyn-2.72/redhat-linux-build/py ~/build/BUILD/Smoldyn-2.72 + mkdir -p /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/lib64/python3.12/site-packages + cp -a smoldyn smoldyn.egg-info /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/lib64/python3.12/site-packages/ + popd ~/build/BUILD/Smoldyn-2.72 + /usr/bin/find-debuginfo -j12 --strict-build-id -m -i --build-id-seed 2.72-3.fc41 --unique-debug-suffix -2.72-3.fc41.aarch64 --unique-debug-src-base smoldyn-2.72-3.fc41.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/Smoldyn-2.72 find-debuginfo: starting Extracting debug info from 2 files DWARF-compressing 2 files sepdebugcrcfix: Updated 2 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/smoldyn-2.72-3.fc41.aarch64 3558 blocks find-debuginfo: done + /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 + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j12 Bytecompiling .py files below /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/lib64/python3.12 using python3.12 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.PfxT4V + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' ~/build/BUILD/Smoldyn-2.72/redhat-linux-build ~/build/BUILD/Smoldyn-2.72 + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 Smoldyn-2.72 + pushd redhat-linux-build + export LD_LIBRARY_PATH=/builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/lib64 + LD_LIBRARY_PATH=/builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/lib64 + export PYTHONPATH=/builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/lib64/python3.12/site-packages + xvfb-run ctest -j1 -VV -R 'test_api|test_sanity|test_biosimulator' --output-on-failure --debug /builddir/build/BUILD/cmake-3.28.3/Source/cmCTest.cxx:425 Here: 425 /builddir/build/BUILD/cmake-3.28.3/Source/cmCTest.cxx:710 UpdateCTestConfiguration from :/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/DartConfiguration.tcl /builddir/build/BUILD/cmake-3.28.3/Source/cmCTest.cxx:437 Here: 437 /builddir/build/BUILD/cmake-3.28.3/Source/cmCTest.cxx:3036 * Read custom CTest configuration directory: /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build /builddir/build/BUILD/cmake-3.28.3/Source/cmCTest.cxx:3041 * Check for file: /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/CTestCustom.cmake /builddir/build/BUILD/cmake-3.28.3/Source/cmCTest.cxx:3061 * Check for file: /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/CTestCustom.ctest /builddir/build/BUILD/cmake-3.28.3/Source/cmCTest.cxx:710 UpdateCTestConfiguration from :/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/DartConfiguration.tcl /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:407 Test project /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:1770 Constructing a list of tests /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2431 Add test: test_actions /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2474 Set test directory: /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2431 Add test: test_api /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2474 Set test directory: /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2431 Add test: test_biosimulators /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2474 Set test directory: /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2431 Add test: test_concurrent_simulation /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2474 Set test directory: /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2431 Add test: test_connect_func /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2474 Set test directory: /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2431 Add test: test_connect_var /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2474 Set test directory: /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2431 Add test: test_data_in_array /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2474 Set test directory: /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2431 Add test: test_data_outputfile /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2474 Set test directory: /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2431 Add test: test_getters /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2474 Set test directory: /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2431 Add test: test_issue_118 /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2474 Set test directory: /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2431 Add test: test_libsmoldyn /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2474 Set test directory: /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2431 Add test: test_multiple_iterations /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2474 Set test directory: /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2431 Add test: test_prd_placement /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2474 Set test directory: /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2431 Add test: test_sanity /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2474 Set test directory: /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2431 Add test: test_sim_from_file /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:2474 Set test directory: /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/source/python /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:1821 Done constructing a list of tests /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:984 Updating test list for fixtures /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:1207 Added 0 tests to meet fixture requirements /builddir/build/BUILD/cmake-3.28.3/Source/cmCTest.cxx:310 Current_Time: Apr 22 07:26 UTC /builddir/build/BUILD/cmake-3.28.3/Source/cmCTest.cxx:310 Current_Time: Apr 22 07:26 UTC /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestMultiProcessHandler.cxx:1418 Checking test dependency graph... /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestMultiProcessHandler.cxx:1447 Checking test dependency graph end /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestMultiProcessHandler.cxx:172 test 2 /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:549 Start 2: test_api /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:710 2: Test command: /usr/bin/python3.12 "/builddir/build/BUILD/Smoldyn-2.72/tests/test_api.py" /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:718 2: Working Directory: /builddir/build/BUILD/Smoldyn-2.72/tests /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:726 2: Environment variables: /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:731 2: PYTHONPATH=/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/py /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:731 2: SMOLDYN_NO_PROMPT=1 /builddir/build/BUILD/cmake-3.28.3/Source/cmCTest.cxx:310 Current_Time: Apr 22 07:26 UTC /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:830 2: Test timeout computed to be: 10000000 /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:1009 1/3 Test #2: test_api ......................... /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:1012 Testing test_api ... /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:268 Passed 0.38 sec /builddir/build/BUILD/cmake-3.28.3/Source/cmCTest.cxx:310 Current_Time: Apr 22 07:26 UTC /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestMultiProcessHandler.cxx:172 test 3 /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:549 Start 3: test_biosimulators /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:710 3: Test command: /usr/bin/python3.12 "/builddir/build/BUILD/Smoldyn-2.72/tests/test_biosimulators.py" /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:718 3: Working Directory: /builddir/build/BUILD/Smoldyn-2.72/tests /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:726 3: Environment variables: /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:731 3: PYTHONPATH=/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/py /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:731 3: SMOLDYN_NO_PROMPT=1 /builddir/build/BUILD/cmake-3.28.3/Source/cmCTest.cxx:310 Current_Time: Apr 22 07:26 UTC /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:830 3: Test timeout computed to be: 10000000 /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:39 3: ssssssssssssssssssssssss /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:39 3: ---------------------------------------------------------------------- /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:39 3: Ran 24 tests in 0.000s /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:39 3: /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:39 3: OK (skipped=24) /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:1009 2/3 Test #3: test_biosimulators ............... /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:1012 Testing test_biosimulators ... /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:268 Passed 0.41 sec /builddir/build/BUILD/cmake-3.28.3/Source/cmCTest.cxx:310 Current_Time: Apr 22 07:26 UTC /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestMultiProcessHandler.cxx:172 test 14 /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:549 Start 14: test_sanity /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:710 14: Test command: /usr/bin/python3.12 "/builddir/build/BUILD/Smoldyn-2.72/tests/test_sanity.py" /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:718 14: Working Directory: /builddir/build/BUILD/Smoldyn-2.72/tests /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:726 14: Environment variables: /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:731 14: PYTHONPATH=/builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/py /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:731 14: SMOLDYN_NO_PROMPT=1 /builddir/build/BUILD/cmake-3.28.3/Source/cmCTest.cxx:310 Current_Time: Apr 22 07:26 UTC /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:830 14: Test timeout computed to be: 10000000 /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:39 14: Using smoldyn from /builddir/build/BUILD/Smoldyn-2.72/redhat-linux-build/py/smoldyn/__init__.py /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:39 14: test_newcursim /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:39 14: /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:39 14: Testing test_get_err /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:39 14: (, '') /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:1009 3/3 Test #14: test_sanity ...................... /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:1012 Testing test_sanity ... /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestRunTest.cxx:268 Passed 0.33 sec /builddir/build/BUILD/cmake-3.28.3/Source/cmCTest.cxx:310 Current_Time: Apr 22 07:26 UTC /builddir/build/BUILD/cmake-3.28.3/Source/cmCTest.cxx:310 Current_Time: Apr 22 07:26 UTC /builddir/build/BUILD/cmake-3.28.3/Source/cmCTest.cxx:310 Current_Time: Apr 22 07:26 UTC /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:446 The following tests passed: /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:451 test_api /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:451 test_biosimulators /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:451 test_sanity /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:612 100% tests passed, 0 tests failed out of 3 /builddir/build/BUILD/cmake-3.28.3/Source/CTest/cmCTestTestHandler.cxx:628 Total Test time (real) = 1.13 sec ~/build/BUILD/Smoldyn-2.72 + popd + RPM_EC=0 ++ jobs -p + exit 0 Processing files: smoldyn-2.72-3.fc41.aarch64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.6dyvpC + umask 022 + cd /builddir/build/BUILD + cd Smoldyn-2.72 + DOCDIR=/builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/doc/smoldyn + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/doc/smoldyn + cp -pr /builddir/build/BUILD/Smoldyn-2.72/Using-Smoldyn-with-SED-ML-COMBINE-BioSimulators.md /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/doc/smoldyn + cp -pr /builddir/build/BUILD/Smoldyn-2.72/README.md /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/doc/smoldyn + RPM_EC=0 ++ jobs -p + exit 0 Provides: bundled(SFMT) = 1.3.3 smoldyn = 2.72-3.fc41 smoldyn(aarch-64) = 2.72-3.fc41 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.34)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libsmoldyn_shared.so.2()(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) rtld(GNU_HASH) Processing files: smoldyn-doc-2.72-3.fc41.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.r9NwCb + umask 022 + cd /builddir/build/BUILD + cd Smoldyn-2.72 + DOCDIR=/builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/doc/smoldyn-doc + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/Smoldyn-2.72/docs/BioNetGen /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/Smoldyn-2.72/docs/CMakeLists.txt /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/Smoldyn-2.72/docs/Doxyfile.in /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/Smoldyn-2.72/docs/README.md /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/Smoldyn-2.72/docs/SmolCrowd /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/Smoldyn-2.72/docs/SmolEmulate /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/Smoldyn-2.72/docs/Smoldyn /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/Smoldyn-2.72/docs/_static /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/Smoldyn-2.72/docs/build_doxygen /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/Smoldyn-2.72/docs/conf.py /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/Smoldyn-2.72/docs/doxygen /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/Smoldyn-2.72/docs/examples /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/Smoldyn-2.72/docs/index.rst /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/Smoldyn-2.72/docs/libSteve /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/Smoldyn-2.72/docs/python /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/Smoldyn-2.72/docs/requirements.txt /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/Smoldyn-2.72/docs/tikz /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/Smoldyn-2.72/docs/user /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/doc/smoldyn-doc + cp -pr /builddir/build/BUILD/Smoldyn-2.72/docs/wrl2smol /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/doc/smoldyn-doc + RPM_EC=0 ++ jobs -p + exit 0 Provides: smoldyn-doc = 2.72-3.fc41 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: smoldyn-libs-2.72-3.fc41.aarch64 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.qVAXVt + umask 022 + cd /builddir/build/BUILD + cd Smoldyn-2.72 + LICENSEDIR=/builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/licenses/smoldyn-libs + export LC_ALL= + LC_ALL= + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/licenses/smoldyn-libs + cp -pr /builddir/build/BUILD/Smoldyn-2.72/License.txt /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/licenses/smoldyn-libs + cp -pr /builddir/build/BUILD/Smoldyn-2.72/source/libSteve/SFMT/SFMT-LICENSE.txt /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/licenses/smoldyn-libs + cp -pr /builddir/build/BUILD/Smoldyn-2.72/LICENSE /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/licenses/smoldyn-libs + RPM_EC=0 ++ jobs -p + exit 0 Provides: libsmoldyn_shared.so.2()(64bit) smoldyn-libs = 2.72-3.fc41 smoldyn-libs(aarch-64) = 2.72-3.fc41 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libGL.so.1()(64bit) libGLU.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.38)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libglut.so.3()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(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_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.32)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) libtiff.so.6()(64bit) libtiff.so.6(LIBTIFF_4.0)(64bit) rtld(GNU_HASH) Processing files: smoldyn-libs-devel-2.72-3.fc41.aarch64 Provides: smoldyn-libs-devel = 2.72-3.fc41 smoldyn-libs-devel(aarch-64) = 2.72-3.fc41 smoldyn-libs-static = 0:2.72-3.fc41 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libsmoldyn_shared.so.2()(64bit) Processing files: python3-smoldyn-2.72-3.fc41.aarch64 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.zEMPpP + umask 022 + cd /builddir/build/BUILD + cd Smoldyn-2.72 + LICENSEDIR=/builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/licenses/python3-smoldyn + export LC_ALL= + LC_ALL= + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/licenses/python3-smoldyn + cp -pr /builddir/build/BUILD/Smoldyn-2.72/License.txt /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/licenses/python3-smoldyn + cp -pr /builddir/build/BUILD/Smoldyn-2.72/source/libSteve/SFMT/SFMT-LICENSE.txt /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/licenses/python3-smoldyn + cp -pr /builddir/build/BUILD/Smoldyn-2.72/LICENSE /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64/usr/share/licenses/python3-smoldyn + RPM_EC=0 ++ jobs -p + exit 0 Provides: python-smoldyn = 2.72-3.fc41 python3-smoldyn = 2.72-3.fc41 python3-smoldyn(aarch-64) = 2.72-3.fc41 python3.12-smoldyn = 2.72-3.fc41 python3.12dist(smoldyn) = 2.72 python3dist(smoldyn) = 2.72 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libGL.so.1()(64bit) libGLU.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.38)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libglut.so.3()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.13)(64bit) libstdc++.so.6(CXXABI_1.3.15)(64bit) libstdc++.so.6(CXXABI_1.3.2)(64bit) libstdc++.so.6(CXXABI_1.3.3)(64bit) libstdc++.so.6(CXXABI_1.3.5)(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_3.4.18)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.32)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) libtiff.so.6()(64bit) libtiff.so.6(LIBTIFF_4.0)(64bit) python(abi) = 3.12 rtld(GNU_HASH) Obsoletes: python-smoldyn < 2.72-3.fc41 Processing files: smoldyn-debugsource-2.72-3.fc41.aarch64 Provides: smoldyn-debugsource = 2.72-3.fc41 smoldyn-debugsource(aarch-64) = 2.72-3.fc41 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: smoldyn-debuginfo-2.72-3.fc41.aarch64 Provides: debuginfo(build-id) = c8dfe16349d4998bde60dc80c895b93eacd281d3 smoldyn-debuginfo = 2.72-3.fc41 smoldyn-debuginfo(aarch-64) = 2.72-3.fc41 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: smoldyn-debugsource(aarch-64) = 2.72-3.fc41 Processing files: smoldyn-libs-debuginfo-2.72-3.fc41.aarch64 Provides: debuginfo(build-id) = bf1cb24762458308a4b32063e89c48ff57d9e61c libsmoldyn_shared.so.2.72-2.72-3.fc41.aarch64.debug()(64bit) smoldyn-libs-debuginfo = 2.72-3.fc41 smoldyn-libs-debuginfo(aarch-64) = 2.72-3.fc41 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: smoldyn-debugsource(aarch-64) = 2.72-3.fc41 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/smoldyn-2.72-3.fc41.aarch64 Wrote: /builddir/build/RPMS/smoldyn-2.72-3.fc41.aarch64.rpm Wrote: /builddir/build/RPMS/smoldyn-debuginfo-2.72-3.fc41.aarch64.rpm Wrote: /builddir/build/RPMS/smoldyn-libs-2.72-3.fc41.aarch64.rpm Wrote: /builddir/build/RPMS/smoldyn-debugsource-2.72-3.fc41.aarch64.rpm Wrote: /builddir/build/RPMS/python3-smoldyn-2.72-3.fc41.aarch64.rpm Wrote: /builddir/build/RPMS/smoldyn-libs-devel-2.72-3.fc41.aarch64.rpm Wrote: /builddir/build/RPMS/smoldyn-libs-debuginfo-2.72-3.fc41.aarch64.rpm Wrote: /builddir/build/RPMS/smoldyn-doc-2.72-3.fc41.noarch.rpm Child return code was: 0