Description of problem: Package python-biopython fails to build from source in Fedora Rawhide. Version-Release number of selected component (if applicable): 1.83-3.fc40 Steps to Reproduce: koji build --scratch f41 python-biopython-1.83-3.fc40.src.rpm Additional info: This package is tracked by Koschei. See: https://koschei.fedoraproject.org/package/python-biopython First failing Koschei build: https://koschei.fedoraproject.org/build/17470991 Reproducible: Always ====================================================================== ERROR: test_embl7 (test_SeqIO.TestSeqIO.test_embl7) ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.83/Tests/test_SeqIO.py", line 3406, in test_embl7 self.perform_test( File "/builddir/build/BUILD/biopython-1.83/Tests/test_SeqIO.py", line 625, in perform_test self.check_simple_write_read( File "/builddir/build/BUILD/biopython-1.83/Tests/test_SeqIO.py", line 362, in check_simple_write_read records2 = list(SeqIO.parse(handle=handle, format=fmt)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILDROOT/python-biopython-1.83-3.fc41.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO/Interfaces.py", line 85, in __next__ return next(self.records) ^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILDROOT/python-biopython-1.83-3.fc41.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO/SeqXmlIO.py", line 447, in iterate parser.close() File "/usr/lib64/python3.12/xml/sax/expatreader.py", line 234, in close self.feed(b"", isFinal=True) File "/usr/lib64/python3.12/xml/sax/expatreader.py", line 211, in feed self._parser.Parse(data, isFinal) File "/builddir/build/BUILD/Python-3.12.2/Modules/pyexpat.c", line 416, in StartElement File "/usr/lib64/python3.12/xml/sax/expatreader.py", line 363, in start_element_ns self._cont_handler.startElementNS(pair, None, File "/builddir/build/BUILDROOT/python-biopython-1.83-3.fc41.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO/SeqXmlIO.py", line 163, in startEntryFieldElement return self.startPropertyElement(attrs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILDROOT/python-biopython-1.83-3.fc41.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO/SeqXmlIO.py", line 339, in startPropertyElement record = self.records[-1] ~~~~~~~~~~~~^^^^ IndexError: list index out of range ====================================================================== ERROR: test_genbank8 (test_SeqIO.TestSeqIO.test_genbank8) ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.83/Tests/test_SeqIO.py", line 2803, in test_genbank8 self.perform_test( File "/builddir/build/BUILD/biopython-1.83/Tests/test_SeqIO.py", line 625, in perform_test self.check_simple_write_read( File "/builddir/build/BUILD/biopython-1.83/Tests/test_SeqIO.py", line 362, in check_simple_write_read records2 = list(SeqIO.parse(handle=handle, format=fmt)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILDROOT/python-biopython-1.83-3.fc41.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO/Interfaces.py", line 85, in __next__ return next(self.records) ^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILDROOT/python-biopython-1.83-3.fc41.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO/SeqXmlIO.py", line 447, in iterate parser.close() File "/usr/lib64/python3.12/xml/sax/expatreader.py", line 234, in close self.feed(b"", isFinal=True) File "/usr/lib64/python3.12/xml/sax/expatreader.py", line 211, in feed self._parser.Parse(data, isFinal) File "/builddir/build/BUILD/Python-3.12.2/Modules/pyexpat.c", line 416, in StartElement File "/usr/lib64/python3.12/xml/sax/expatreader.py", line 363, in start_element_ns self._cont_handler.startElementNS(pair, None, File "/builddir/build/BUILDROOT/python-biopython-1.83-3.fc41.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO/SeqXmlIO.py", line 163, in startEntryFieldElement return self.startPropertyElement(attrs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILDROOT/python-biopython-1.83-3.fc41.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO/SeqXmlIO.py", line 339, in startPropertyElement record = self.records[-1] ~~~~~~~~~~~~^^^^ IndexError: list index out of range ----------------------------------------------------------------------
I think this is probably related to the update from expat 2.5.0 to expat 2.6.0.
Found a matching upstream issue: https://github.com/biopython/biopython/issues/4640
https://src.fedoraproject.org/rpms/python-biopython/pull-request/7
FEDORA-2024-214bc7dd42 (python-biopython-1.83-4.fc41) has been submitted as an update to Fedora 41. https://bodhi.fedoraproject.org/updates/FEDORA-2024-214bc7dd42
FEDORA-2024-214bc7dd42 (python-biopython-1.83-4.fc41) has been pushed to the Fedora 41 stable repository. If problem still persists, please make note of it in this bug report.
FEDORA-2024-0949a9c696 (python-biopython-1.83-5.fc40) has been submitted as an update to Fedora 40. https://bodhi.fedoraproject.org/updates/FEDORA-2024-0949a9c696
FEDORA-2024-628f1fb666 (python-biopython-1.82-2.fc39) has been submitted as an update to Fedora 39. https://bodhi.fedoraproject.org/updates/FEDORA-2024-628f1fb666
FEDORA-2024-d9361f0861 (python-biopython-1.82-2.fc38) has been submitted as an update to Fedora 38. https://bodhi.fedoraproject.org/updates/FEDORA-2024-d9361f0861
FEDORA-2024-0949a9c696 has been pushed to the Fedora 40 testing repository. Soon you'll be able to install the update with the following command: `sudo dnf upgrade --enablerepo=updates-testing --refresh --advisory=FEDORA-2024-0949a9c696` You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2024-0949a9c696 See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.
FEDORA-2024-628f1fb666 has been pushed to the Fedora 39 testing repository. Soon you'll be able to install the update with the following command: `sudo dnf upgrade --enablerepo=updates-testing --refresh --advisory=FEDORA-2024-628f1fb666` You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2024-628f1fb666 See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.
FEDORA-2024-d9361f0861 has been pushed to the Fedora 38 testing repository. Soon you'll be able to install the update with the following command: `sudo dnf upgrade --enablerepo=updates-testing --refresh --advisory=FEDORA-2024-d9361f0861` You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2024-d9361f0861 See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.
FEDORA-2024-0949a9c696 (python-biopython-1.83-5.fc40) has been pushed to the Fedora 40 stable repository. If problem still persists, please make note of it in this bug report.
FEDORA-2024-628f1fb666 (python-biopython-1.82-2.fc39) has been pushed to the Fedora 39 stable repository. If problem still persists, please make note of it in this bug report.
FEDORA-2024-d9361f0861 (python-biopython-1.82-2.fc38) has been pushed to the Fedora 38 stable repository. If problem still persists, please make note of it in this bug report.