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Bug 2274533

Summary: python-biopython: FTBFS in Fedora Rawhide (and F38/F39/F40!)
Product: [Fedora] Fedora Reporter: Ben Beasley <code>
Component: python-biopythonAssignee: Luis Bazan <bazanluis20>
Status: CLOSED ERRATA QA Contact: Fedora Extras Quality Assurance <extras-qa>
Severity: medium Docs Contact:
Priority: unspecified    
Version: rawhideCC: alex, bazanluis20, jaruga, neuro-sig, trpost
Target Milestone: ---   
Target Release: ---   
Hardware: Unspecified   
OS: Linux   
URL: https://koschei.fedoraproject.org/package/python-biopython
Whiteboard:
Fixed In Version: python-biopython-1.83-4.fc41 python-biopython-1.83-5.fc40 python-biopython-1.82-2.fc39 python-biopython-1.82-2.fc38 Doc Type: If docs needed, set a value
Doc Text:
Story Points: ---
Clone Of: Environment:
Last Closed: 2024-04-13 12:21:25 UTC Type: ---
Regression: --- Mount Type: ---
Documentation: --- CRM:
Verified Versions: Category: ---
oVirt Team: --- RHEL 7.3 requirements from Atomic Host:
Cloudforms Team: --- Target Upstream Version:
Embargoed:

Description Ben Beasley 2024-04-11 14:00:57 UTC 
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
----------------------------------------------------------------------
Comment 1 Ben Beasley 2024-04-11 14:01:34 UTC 
I think this is probably related to the update from expat 2.5.0 to expat 2.6.0.
Comment 2 Ben Beasley 2024-04-11 14:02:49 UTC 
Found a matching upstream issue: https://github.com/biopython/biopython/issues/4640
Comment 3 Ben Beasley 2024-04-11 14:13:46 UTC 
https://src.fedoraproject.org/rpms/python-biopython/pull-request/7
Comment 4 Fedora Update System 2024-04-13 12:17:09 UTC 
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
Comment 5 Fedora Update System 2024-04-13 12:21:25 UTC 
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.
Comment 6 Fedora Update System 2024-04-13 13:30:49 UTC 
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
Comment 7 Fedora Update System 2024-04-13 16:08:40 UTC 
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
Comment 8 Fedora Update System 2024-04-13 17:14:04 UTC 
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
Comment 9 Fedora Update System 2024-04-14 02:05:55 UTC 
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.
Comment 10 Fedora Update System 2024-04-14 02:44:27 UTC 
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.
Comment 11 Fedora Update System 2024-04-14 02:58:34 UTC 
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.
Comment 12 Fedora Update System 2024-04-22 00:58:30 UTC 
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.
Comment 13 Fedora Update System 2024-04-22 01:28:16 UTC 
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.
Comment 14 Fedora Update System 2024-04-22 02:34:24 UTC 
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.