Your message dated Tue, 12 May 2026 10:49:25 +0000
with message-id <[email protected]>
and subject line Bug#1136313: fixed in openstructure 2.11.1-3
has caused the Debian Bug report #1136313,
regarding openstructure: FTBFS with numpy 2
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1136313: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1136313
Debian Bug Tracking System
Contact [email protected] with problems
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Package: src:openstructure
Version: 2.11.1-2
Severity: important
Tags: sid forky ftbfs
User: [email protected]
Usertags: eigen3-5.0
Dear Maintainer,
your package depends on libeigen3-dev. The upstream released a
new major version of this mathematical library, 5.0.0. Some
basic information about new features and changes in this version
can be found here:
https://libeigen.gitlab.io/releases/5.0/
This is a major version change and may require code changes in packages
depending on eigen3. The key breaking changes include:
- Minimum required C++ standard is now C++14
- Changes in the build system integration
- Some API name changes
openstructure FTBFS with libeigen3-dev 5.0.1. The full build log is available
at:
https://debusine.debian.net/debian/developers-gladk-eigen3/artifact/3759854/raw/openstructure_2.11.1-2_amd64-2026-05-08T14:50:48Z.build
Here is the most probably relevant part of the failing build log:
===========================================
ResourceWarning: Enable tracemalloc to get the object allocation traceback
..........................................
======================================================================
ERROR: testCalcEnrichmentAUC (__main__.TestTable.testCalcEnrichmentAUC)
- ----------------------------------------------------------------------
Traceback (most recent call last):
File
"/build/reproducible-path/openstructure-2.11.1/modules/base/tests/test_table.py",
line 1275, in testCalcEnrichmentAUC
auc = tab.ComputeEnrichmentAUC(score_col='score', score_dir='-',
class_col='rmsd', class_cutoff=2.0,
class_dir='-')
File
"/build/reproducible-path/openstructure-2.11.1/obj-x86_64-linux-gnu/stage/lib/python3.13/dist-packages/ost/table.py",
line 2696, in ComputeEnrichmentAUC
return np.trapz(enr[1], enr[0])
^^^^^^^^
File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 792, in
__getattr__
raise AttributeError(f"module {__name__!r} has no attribute {attr!r}")
AttributeError: module 'numpy' has no attribute 'trapz'. Did you mean: 'trace'?
===========================================
libeigen3-dev_5.0.1-1 is available in experimental.
When this package version lands into unstable (probably at the beginning
of June 2026), this bug will be increased in severity to serious.
Thanks,
Anton
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--- Begin Message ---
Source: openstructure
Source-Version: 2.11.1-3
Done: Andrius Merkys <[email protected]>
We believe that the bug you reported is fixed in the latest version of
openstructure, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andrius Merkys <[email protected]> (supplier of updated openstructure package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
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Format: 1.8
Date: Tue, 12 May 2026 06:27:23 -0400
Source: openstructure
Architecture: source
Version: 2.11.1-3
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <[email protected]>
Changed-By: Andrius Merkys <[email protected]>
Closes: 1136313
Changes:
openstructure (2.11.1-3) unstable; urgency=medium
.
* Adjust numpy.trapz name change (Closes: #1136313)
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