[Debichem-devel] Bug#1136313: openstructure: FTBFS with libeigen3-dev 5.0 (major version transition)

[Anton Gladky]

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Package: src:openstructure
Version: 2.11.1-2
Severity: important
Tags: sid forky ftbfs
User: debian-devel at lists.debian.org
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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