Bug 1913346
| Summary: | libsbml fails to build with Python 3.10: Imports the removed formatter module | ||
|---|---|---|---|
| Product: | [Fedora] Fedora | Reporter: | Tomáš Hrnčiar <thrnciar> |
| Component: | libsbml | Assignee: | Zbigniew Jędrzejewski-Szmek <zbyszek> |
| Status: | CLOSED RAWHIDE | QA Contact: | |
| Severity: | unspecified | Docs Contact: | |
| Priority: | unspecified | ||
| Version: | rawhide | CC: | mhroncok, neuro-sig, thrnciar, trpost, zbyszek |
| Target Milestone: | --- | ||
| Target Release: | --- | ||
| Hardware: | Unspecified | ||
| OS: | Unspecified | ||
| Whiteboard: | |||
| Fixed In Version: | Doc Type: | If docs needed, set a value | |
| Doc Text: | Story Points: | --- | |
| Clone Of: | Environment: | ||
| Last Closed: | 2021-01-21 08:25:32 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: | 1890881 | ||
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[ 70%] Swig Python source
cd /builddir/build/BUILD/libSBML-5.18.0-Source/build/src/bindings/python && /usr/bin/python3 /builddir/build/BUILD/libSBML-5.18.0-Source/src/bindings/python/../swig/swigdoc.py --language python --top /builddir/build/BUILD/libSBML-5.18.0-Source --master /builddir/build/BUILD/libSBML-5.18.0-Source/src/bindings/python/../swig/libsbml.i --output /builddir/build/BUILD/libSBML-5.18.0-Source/build/src/bindings/python/pydoc-doxygen.i --define USE_COMP --define USE_FBC --define USE_GROUPS --define USE_L3V2EXTENDEDMATH --define USE_LAYOUT --define USE_MULTI --define USE_QUAL --define USE_RENDER --define USE_COMP --define USE_FBC --define USE_GROUPS --define USE_L3V2EXTENDEDMATH --define USE_MULTI --define USE_QUAL --define USE_RENDER
cd /builddir/build/BUILD/libSBML-5.18.0-Source/build/src/bindings/python && /usr/bin/python3 /builddir/build/BUILD/libSBML-5.18.0-Source/build/src/bindings/python/generate-class-name-list.py /builddir/build/BUILD/libSBML-5.18.0-Source/src > /builddir/build/BUILD/libSBML-5.18.0-Source/build/src/bindings/python/class-list.txt
cd /builddir/build/BUILD/libSBML-5.18.0-Source/build/src/bindings/python && /usr/bin/python3 /builddir/build/BUILD/libSBML-5.18.0-Source/build/src/bindings/python/generate-converters-list.py /builddir/build/BUILD/libSBML-5.18.0-Source/build/src/bindings/python/class-list.txt > /builddir/build/BUILD/libSBML-5.18.0-Source/build/src/bindings/python/libsbml-converters.txt
cd /builddir/build/BUILD/libSBML-5.18.0-Source/build/src/bindings/python && /usr/bin/python3 /builddir/build/BUILD/libSBML-5.18.0-Source/src/bindings/python/doc-converter/rewrite_pydoc.py -f /builddir/build/BUILD/libSBML-5.18.0-Source/build/src/bindings/python/pydoc-doxygen.i -o /builddir/build/BUILD/libSBML-5.18.0-Source/build/src/bindings/python/pydoc-normal.i -i /builddir/build/BUILD/libSBML-5.18.0-Source/src/bindings/python/../../../docs/src/common-text -g /builddir/build/BUILD/libSBML-5.18.0-Source/src/bindings/python/../../../docs/src/common-graphics
Traceback (most recent call last):
File "/builddir/build/BUILD/libSBML-5.18.0-Source/src/bindings/python/doc-converter/rewrite_pydoc.py", line 121, in <module>
from formatter import NullWriter, AbstractFormatter
ModuleNotFoundError: No module named 'formatter'
Yes, that is the actual error. Do you know where is the formatter module suppose to come from? formatter: Deprecated since version 3.4: Due to lack of usage, the formatter module has been deprecated. https://docs.python.org/3.10/whatsnew/3.10.html#removed Removed the formatter module, which was deprecated in Python 3.4. It is somewhat obsolete, little used, and not tested. It was originally scheduled to be removed in Python 3.6, but such removals were delayed until after Python 2.7 EOL. Existing users should copy whatever classes they use into their code. (Contributed by Dong-hee Na and Terry J. Reedy in https://bugs.python.org/issue42299.) @Zbigniew, i was about to open a bug ticket for upstream; do you prefer to patch libsbml for this issue? There's a bunch of issues. I had it building already, but then upgrades in rawhide caused more issues. So I want to figure it out all the way, and then file a bug upstream. |
libsbml fails to build with Python 3.10.0a4. cd /builddir/build/BUILD/libSBML-5.18.0-Source/build/src && /usr/bin/cmake -E cmake_symlink_library libsbml.so.5.18.0 libsbml.so.5 libsbml.so make[2]: Leaving directory '/builddir/build/BUILD/libSBML-5.18.0-Source/build' In function 'strncpy', inlined from '__ct_base ' at /builddir/build/BUILD/libSBML-5.18.0-Source/src/sbml/xml/XMLMemoryBuffer.cpp:62:10: /usr/include/bits/string_fortified.h:91:34: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] 91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ /builddir/build/BUILD/libSBML-5.18.0-Source/src/sbml/xml/XMLMemoryBuffer.cpp: In member function '__ct_base ': /builddir/build/BUILD/libSBML-5.18.0-Source/src/sbml/xml/XMLMemoryBuffer.cpp:59:27: note: length computed here 59 | size_t bufsize = strlen(buffer); | ^ In function 'strncpy', inlined from 'file_build_ioposix' at /builddir/build/BUILD/libSBML-5.18.0-Source/src/sbml/compress/ioapi.c:123:5, inlined from 'fopen_file_func' at /builddir/build/BUILD/libSBML-5.18.0-Source/src/sbml/compress/ioapi.c:141:16: /usr/include/bits/string_fortified.h:91:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] 91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ /builddir/build/BUILD/libSBML-5.18.0-Source/src/sbml/compress/ioapi.c: In function 'fopen_file_func': /builddir/build/BUILD/libSBML-5.18.0-Source/src/sbml/compress/ioapi.c:121:31: note: length computed here 121 | ioposix->filenameLength = strlen(filename) + 1; | ^ make[1]: Entering directory '/builddir/build/BUILD/libSBML-5.18.0-Source/build' [ 70%] Built target sbml make[1]: Leaving directory '/builddir/build/BUILD/libSBML-5.18.0-Source/build' make: *** [Makefile:185: all] Error 2 error: Bad exit status from /var/tmp/rpm-tmp.oEPHut (%build) For the build logs, see: https://copr-be.cloud.fedoraproject.org/results/@python/python3.10/fedora-rawhide-x86_64/01859884-libsbml/ For all our attempts to build libsbml with Python 3.10, see: https://copr.fedorainfracloud.org/coprs/g/python/python3.10/package/libsbml/ Testing and mass rebuild of packages is happening in copr. You can follow these instructions to test locally in mock if your package builds with Python 3.10: https://copr.fedorainfracloud.org/coprs/g/python/python3.10/ Let us know here if you have any questions. Python 3.10 will be included in Fedora 35. To make that update smoother, we're building Fedora packages with early pre-releases of Python 3.10. A build failure prevents us from testing all dependent packages (transitive [Build]Requires), so if this package is required a lot, it's important for us to get it fixed soon. We'd appreciate help from the people who know this package best, but if you don't want to work on this now, let us know so we can try to work around it on our side.