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Bug 1197715
| Summary: | libsbml-5.11.0-11.fc23 FTBFS: test_sbml_package_fbc': free(): invalid pointer | ||
|---|---|---|---|
| Product: | [Fedora] Fedora | Reporter: | Petr Pisar <ppisar> |
| Component: | libsbml | Assignee: | Zbigniew Jędrzejewski-Szmek <zbyszek> |
| Status: | CLOSED ERRATA | QA Contact: | Fedora Extras Quality Assurance <extras-qa> |
| Severity: | unspecified | Docs Contact: | |
| Priority: | unspecified | ||
| Version: | 23 | CC: | anto.trande, mjuszkie, zbyszek |
| Target Milestone: | --- | ||
| Target Release: | --- | ||
| Hardware: | Unspecified | ||
| OS: | Unspecified | ||
| URL: | http://koji.fedoraproject.org/koji/taskinfo?taskID=9118285 | ||
| Whiteboard: | |||
| Fixed In Version: | libsbml-5.11.6-6.fc23 libsbml-5.11.6-5.fc22 libsbml-5.11.6-5.fc21 | Doc Type: | Bug Fix |
| Doc Text: | Story Points: | --- | |
| Clone Of: | Environment: | ||
| Last Closed: | 2015-11-09 21:53:13 UTC | Type: | Bug |
| Regression: | --- | Mount Type: | --- |
| Documentation: | --- | CRM: | |
| Verified Versions: | Category: | --- | |
| oVirt Team: | --- | RHEL 7.3 requirements from Atomic Host: | |
| Cloudforms Team: | --- | Target Upstream Version: | |
| Embargoed: | |||
| Bug Depends On: | |||
| Bug Blocks: | 922257 | ||
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. |
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] [...]