libsbml-5.11.0-11.fc23 fails to build in F23 because tested code crashed: Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.vjfdDy + umask 022 ~/build/BUILD/libSBML-5.11.0-Source/build2 ~/build/BUILD/libSBML-5.11.0-Source + cd /builddir/build/BUILD + cd libSBML-5.11.0-Source + pushd build2 + ctest -V -j4 UpdateCTestConfiguration from :/builddir/build/BUILD/libSBML-5.11.0-Source/build2/DartConfiguration.tcl Parse Config file:/builddir/build/BUILD/libSBML-5.11.0-Source/build2/DartConfiguration.tcl UpdateCTestConfiguration from :/builddir/build/BUILD/libSBML-5.11.0-Source/build2/DartConfiguration.tcl Parse Config file:/builddir/build/BUILD/libSBML-5.11.0-Source/build2/DartConfiguration.tcl Test project /builddir/build/BUILD/libSBML-5.11.0-Source/build2 Constructing a list of tests Done constructing a list of tests Checking test dependency graph... Checking test dependency graph end test 1 Start 1: test_sbml_package_fbc_run 1: Test command: /builddir/build/BUILD/libSBML-5.11.0-Source/build2/src/sbml/packages/fbc/extension/test/test_sbml_package_fbc 1: Test timeout computed to be: 1500 test 2 Start 2: test_fbc_validator_run 2: Test command: /builddir/build/BUILD/libSBML-5.11.0-Source/build2/src/sbml/packages/fbc/validator/test/test_fbc_validator "/builddir/build/BUILD/libSBML-5.11.0-Source/src/sbml/packages/fbc/validator/test" 2: Test timeout computed to be: 1500 test 3 Start 3: test_sbml_package_layout_run 3: Test command: /builddir/build/BUILD/libSBML-5.11.0-Source/build2/src/sbml/packages/layout/sbml/test/test_sbml_package_layout 3: Test timeout computed to be: 1500 test 4 Start 4: test_layout_validator_run 4: Test command: /builddir/build/BUILD/libSBML-5.11.0-Source/build2/src/sbml/packages/layout/validator/test/test_layout_validator "/builddir/build/BUILD/libSBML-5.11.0-Source/src/sbml/packages/layout/validator/test" 4: Test timeout computed to be: 1500 1: Running suite(s): FbcExtension 1: *** Error in `/builddir/build/BUILD/libSBML-5.11.0-Source/build2/src/sbml/packages/fbc/extension/test/test_sbml_package_fbc': free(): invalid pointer: 0x00007fff27f469b8 *** 1: ======= Backtrace: ========= 1: /lib64/libc.so.6(+0x7a0bd)[0x7fa1d2b210bd] 1: /lib64/libc.so.6(+0x819c4)[0x7fa1d2b289c4] 1: /lib64/libc.so.6(cfree+0x4c)[0x7fa1d2b2d51c] 1: /builddir/build/BUILD/libSBML-5.11.0-Source/build2/src/sbml/packages/fbc/extension/test/test_sbml_package_fbc(_ZN8XMLTokenD1Ev+0x2f)[0x7fa1d47e775f] 1: /builddir/build/BUILD/libSBML-5.11.0-Source/build2/src/sbml/packages/fbc/extension/test/test_sbml_package_fbc(_ZN7XMLNodeC2ER14XMLInputStream+0x12d)[0x7fa1d47dcfad] 1: /builddir/build/BUILD/libSBML-5.11.0-Source/build2/src/sbml/packages/fbc/extension/test/test_sbml_package_fbc(_ZN7XMLNodeC2ER14XMLInputStream+0x11a)[0x7fa1d47dcf9a] 1: /builddir/build/BUILD/libSBML-5.11.0-Source/build2/src/sbml/packages/fbc/extension/test/test_sbml_package_fbc(_ZN7XMLNodeC2ER14XMLInputStream+0x11a)[0x7fa1d47dcf9a] 1: /builddir/build/BUILD/libSBML-5.11.0-Source/build2/src/sbml/packages/fbc/extension/test/test_sbml_package_fbc(_ZN5Model12readOtherXMLER14XMLInputStream+0xe4)[0x7fa1d47012d4] 1: /builddir/build/BUILD/libSBML-5.11.0-Source/build2/src/sbml/packages/fbc/extension/test/test_sbml_package_fbc(_ZN5SBase4readER14XMLInputStream+0x631)[0x7fa1d474ecc1] 1: /builddir/build/BUILD/libSBML-5.11.0-Source/build2/src/sbml/packages/fbc/extension/test/test_sbml_package_fbc(_ZN5SBase4readER14XMLInputStream+0x2c8)[0x7fa1d474e958] 1: /builddir/build/BUILD/libSBML-5.11.0-Source/build2/src/sbml/packages/fbc/extension/test/test_sbml_package_fbc(_ZN10SBMLReader12readInternalEPKcb+0xe3)[0x7fa1d4775343] 1: /builddir/build/BUILD/libSBML-5.11.0-Source/build2/src/sbml/packages/fbc/extension/test/test_sbml_package_fbc(_ZN10SBMLReader18readSBMLFromStringERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0xed)[0x7fa1d47762fd] 1: /builddir/build/BUILD/libSBML-5.11.0-Source/build2/src/sbml/packages/fbc/extension/test/test_sbml_package_fbc(readSBMLFromString+0x5c)[0x7fa1d477653c] 1: /builddir/build/BUILD/libSBML-5.11.0-Source/build2/src/sbml/packages/fbc/extension/test/test_sbml_package_fbc(+0x1db1ac)[0x7fa1d46b21ac] 1: /lib64/libcheck.so.0(srunner_run+0x7f5)[0x7fa1d40ad025] 1: /builddir/build/BUILD/libSBML-5.11.0-Source/build2/src/sbml/packages/fbc/extension/test/test_sbml_package_fbc(main+0x65)[0x7fa1d46a79e5] 1: /lib64/libc.so.6(__libc_start_main+0xf0)[0x7fa1d2ac7840] 1: /builddir/build/BUILD/libSBML-5.11.0-Source/build2/src/sbml/packages/fbc/extension/test/test_sbml_package_fbc(_start+0x29)[0x7fa1d46b0f59] [...]
This issue has already been submitted to the upstream maintainer. Unfortunately he needs to work on check code compiled with GCC-5.0.0 and has not available a Fedora 22 workable at the present moment.
This bug appears to have been reported against 'rawhide' during the Fedora 23 development cycle. Changing version to '23'. (As we did not run this process for some time, it could affect also pre-Fedora 23 development cycle bugs. We are very sorry. It will help us with cleanup during Fedora 23 End Of Life. Thank you.) More information and reason for this action is here: https://fedoraproject.org/wiki/BugZappers/HouseKeeping/Fedora23
Same issue on aarch64. F22 has gcc 5.0.0 and is able to build package from rawhide: Zapisano: /builddir/build/RPMS/libsbml-5.11.5-0.11.20150528svn22272.fc22.aarch64.rpm Zapisano: /builddir/build/RPMS/libsbml-devel-5.11.5-0.11.20150528svn22272.fc22.aarch64.rpm Zapisano: /builddir/build/RPMS/python-libsbml-5.11.5-0.11.20150528svn22272.fc22.aarch64.rpm Zapisano: /builddir/build/RPMS/python3-libsbml-5.11.5-0.11.20150528svn22272.fc22.aarch64.rpm Zapisano: /builddir/build/RPMS/perl-LibSBML-5.11.5-0.11.20150528svn22272.fc22.aarch64.rpm Zapisano: /builddir/build/RPMS/ruby-SBML-5.11.5-0.11.20150528svn22272.fc22.aarch64.rpm Zapisano: /builddir/build/RPMS/octave-SBML-5.11.5-0.11.20150528svn22272.fc22.aarch64.rpm Zapisano: /builddir/build/RPMS/R-libSBML-5.11.5-0.11.20150528svn22272.fc22.aarch64.rpm
Did one more check. First built gcc 5.2.1-1.fc23 with gcc4 compatibility and then used it to build libsbml. Build went fine.
libsbml-5.11.6-2.fc24 builds on aarch64 due to disabled tests. When tests are enabled it goes like this: gmake[4]: Entering directory '/builddir/build/BUILD/libsbml-5.11.6/build2' Running tests... /usr/bin/ctest --force-new-ctest-process Test project /builddir/build/BUILD/libsbml-5.11.6/build2 Start 1: test_sbml_package_render_run 1/13 Test #1: test_sbml_package_render_run .....***Exception: Other 1.80 sec Start 2: test_sbml_package_layout_run 2/13 Test #2: test_sbml_package_layout_run .....***Exception: Other 0.10 sec Start 3: test_layout_validator_run 3/13 Test #3: test_layout_validator_run ........***Exception: Other 0.64 sec Start 4: test_sbml_annotation_run 4/13 Test #4: test_sbml_annotation_run .........***Exception: Other 0.06 sec Start 5: test_sbml_conversion_run 5/13 Test #5: test_sbml_conversion_run .........***Exception: Other 0.82 sec Start 6: test_sbml_extension_run 6/13 Test #6: test_sbml_extension_run ..........***Exception: Other 0.09 sec Start 7: test_sbml_math_run 7/13 Test #7: test_sbml_math_run ...............***Exception: Other 0.74 sec Start 8: test_sbml_sbml_run 8/13 Test #8: test_sbml_sbml_run ...............***Exception: Other 0.17 sec Start 9: test_sbml_units_run 9/13 Test #9: test_sbml_units_run .............. Passed 2.21 sec Start 10: test_sbml_util_run 10/13 Test #10: test_sbml_util_run ............... Passed 0.07 sec Start 11: test_sbml_validator_run 11/13 Test #11: test_sbml_validator_run ..........***Exception: Other 0.42 sec Start 12: test_sbml_xml_run 12/13 Test #12: test_sbml_xml_run ................***Exception: Other 0.06 sec Start 13: test_python_binding 13/13 Test #13: test_python_binding ..............***Exception: Other 3.20 sec 15% tests passed, 11 tests failed out of 13 Total Test time (real) = 10.41 sec The following tests FAILED: 1 - test_sbml_package_render_run (OTHER_FAULT) 2 - test_sbml_package_layout_run (OTHER_FAULT) 3 - test_layout_validator_run (OTHER_FAULT) 4 - test_sbml_annotation_run (OTHER_FAULT) 5 - test_sbml_conversion_run (OTHER_FAULT) 6 - test_sbml_extension_run (OTHER_FAULT) 7 - test_sbml_math_run (OTHER_FAULT) 8 - test_sbml_sbml_run (OTHER_FAULT) 11 - test_sbml_validator_run (OTHER_FAULT) 12 - test_sbml_xml_run (OTHER_FAULT) 13 - test_python_binding (OTHER_FAULT) Errors while running CTest Makefile:152: recipe for target 'test' failed gmake[4]: Leaving directory '/builddir/build/BUILD/libsbml-5.11.6/build2' just fyi
(In reply to Marcin Juszkiewicz from comment #5) > libsbml-5.11.6-2.fc24 builds on aarch64 due to disabled tests. > > When tests are enabled it goes like this: > > gmake[4]: Entering directory '/builddir/build/BUILD/libsbml-5.11.6/build2' > Running tests... > /usr/bin/ctest --force-new-ctest-process > Test project /builddir/build/BUILD/libsbml-5.11.6/build2 > Start 1: test_sbml_package_render_run > 1/13 Test #1: test_sbml_package_render_run .....***Exception: Other 1.80 > sec > Start 2: test_sbml_package_layout_run > 2/13 Test #2: test_sbml_package_layout_run .....***Exception: Other 0.10 > sec > Start 3: test_layout_validator_run > 3/13 Test #3: test_layout_validator_run ........***Exception: Other 0.64 > sec > Start 4: test_sbml_annotation_run > 4/13 Test #4: test_sbml_annotation_run .........***Exception: Other 0.06 > sec > Start 5: test_sbml_conversion_run > 5/13 Test #5: test_sbml_conversion_run .........***Exception: Other 0.82 > sec > Start 6: test_sbml_extension_run > 6/13 Test #6: test_sbml_extension_run ..........***Exception: Other 0.09 > sec > Start 7: test_sbml_math_run > 7/13 Test #7: test_sbml_math_run ...............***Exception: Other 0.74 > sec > Start 8: test_sbml_sbml_run > 8/13 Test #8: test_sbml_sbml_run ...............***Exception: Other 0.17 > sec > Start 9: test_sbml_units_run > 9/13 Test #9: test_sbml_units_run .............. Passed 2.21 sec > Start 10: test_sbml_util_run > 10/13 Test #10: test_sbml_util_run ............... Passed 0.07 sec > Start 11: test_sbml_validator_run > 11/13 Test #11: test_sbml_validator_run ..........***Exception: Other 0.42 > sec > Start 12: test_sbml_xml_run > 12/13 Test #12: test_sbml_xml_run ................***Exception: Other 0.06 > sec > Start 13: test_python_binding > 13/13 Test #13: test_python_binding ..............***Exception: Other 3.20 > sec > > 15% tests passed, 11 tests failed out of 13 > > Total Test time (real) = 10.41 sec > > The following tests FAILED: > 1 - test_sbml_package_render_run (OTHER_FAULT) > 2 - test_sbml_package_layout_run (OTHER_FAULT) > 3 - test_layout_validator_run (OTHER_FAULT) > 4 - test_sbml_annotation_run (OTHER_FAULT) > 5 - test_sbml_conversion_run (OTHER_FAULT) > 6 - test_sbml_extension_run (OTHER_FAULT) > 7 - test_sbml_math_run (OTHER_FAULT) > 8 - test_sbml_sbml_run (OTHER_FAULT) > 11 - test_sbml_validator_run (OTHER_FAULT) > 12 - test_sbml_xml_run (OTHER_FAULT) > 13 - test_python_binding (OTHER_FAULT) > Errors while running CTest > Makefile:152: recipe for target 'test' failed > gmake[4]: Leaving directory '/builddir/build/BUILD/libsbml-5.11.6/build2' > > > just fyi Yes, i know; unfortunately aarch64 is one of arches which are not supported by upstream or, at least, it is hard to manage by upstream.
libsbml-5.11.6-6.fc23 has been submitted as an update to Fedora 23. https://bodhi.fedoraproject.org/updates/FEDORA-2015-1263dac701
libsbml-5.11.6-5.fc22 has been submitted as an update to Fedora 22. https://bodhi.fedoraproject.org/updates/FEDORA-2015-cd01a15f6f
libsbml-5.11.6-6.fc23 has been pushed to the Fedora 23 testing repository. If problems still persist, please make note of it in this bug report. If you want to test the update, you can install it with $ su -c 'dnf --enablerepo=updates-testing update libsbml' You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2015-1263dac701
libsbml-5.11.6-5.fc22 has been pushed to the Fedora 22 testing repository. If problems still persist, please make note of it in this bug report. If you want to test the update, you can install it with $ su -c 'dnf --enablerepo=updates-testing update libsbml' You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2015-cd01a15f6f
libsbml-5.11.6-5.fc21 has been pushed to the Fedora 21 testing repository. If problems still persist, please make note of it in this bug report. If you want to test the update, you can install it with $ su -c 'dnf --enablerepo=updates-testing update libsbml' You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2015-f64c540a93
libsbml-5.11.6-6.fc23 has been pushed to the Fedora 23 stable repository. If problems still persist, please make note of it in this bug report.
libsbml-5.11.6-5.fc22 has been pushed to the Fedora 22 stable repository. If problems still persist, please make note of it in this bug report.
libsbml-5.11.6-5.fc21 has been pushed to the Fedora 21 stable repository. If problems still persist, please make note of it in this bug report.