Your message dated Sun, 12 Oct 2025 21:47:00 +0000
with message-id <[email protected]>
and subject line Bug#1109955: fixed in scikit-learn 1.7.2+dfsg-1
has caused the Debian Bug report #1109955,
regarding scikit-learn: deprecated API fails with scipy 1.16
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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--
1109955: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1109955
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: scikit-learn
Version: 1.4.2+dfsg-8
Severity: normal
Control: tags -1 fixed-upstream
scikit-learn uses a deprecated scipy API which causes
test_linalg_warning_with_newton_solver (test_glm) to fail with
scipy 1.16 (from experimental)
test_logistic_regression_path_convergence_fail also fails
176s FAILED
../../../../usr/lib/python3/dist-packages/sklearn/linear_model/_glm/tests/test_glm.py::test_linalg_warning_with_newton_solver[42]
176s FAILED
../../../../usr/lib/python3/dist-packages/sklearn/linear_model/tests/test_logistic.py::test_logistic_regression_path_convergence_fail
176s = 2 failed, 29255 passed, 3388 skipped, 88 xfailed, 45 xpassed, 15607
warnings in 128.24s (0:02:08) =
In the case of the test_glm failure the problem is
176s E DeprecationWarning: scipy.optimize: The `disp` and `iprint`
options of the L-BFGS-B solver are deprecated and will be removed in SciPy
1.18.0.
176s
176s /usr/lib/python3/dist-packages/scipy/optimize/_lbfgsb_py.py:387:
DeprecationWarning
The problem is fixed upstream
https://github.com/scikit-learn/scikit-learn/pull/31642
in upstream release 1.7.1.
The second error is:
176s ________________ test_logistic_regression_path_convergence_fail
________________
176s [gw14] linux -- Python 3.13.5 /usr/bin/python3.13
176s
176s def test_logistic_regression_path_convergence_fail():
176s rng = np.random.RandomState(0)
176s X = np.concatenate((rng.randn(100, 2) + [1, 1], rng.randn(100, 2)))
176s y = [1] * 100 + [-1] * 100
176s Cs = [1e3]
176s
176s # Check that the convergence message points to both a model
agnostic
176s # advice (scaling the data) and to the logistic regression specific
176s # documentation that includes hints on the solver configuration.
176s with pytest.warns(ConvergenceWarning) as record:
176s _logistic_regression_path(
176s X, y, Cs=Cs, tol=0.0, max_iter=1, random_state=0, verbose=0
176s )
176s
176s > assert len(record) == 1
176s E assert 2 == 1
176s E + where 2 = len(WarningsChecker(record=True))
176s
176s
/usr/lib/python3/dist-packages/sklearn/linear_model/tests/test_logistic.py:437:
AssertionError
I can't say if it's fixed in the later upstream release, but likely so
since thay have been testing scipy 1.16.
Best way to fix the bug is to upload the new upstream release.
This bug will become RC serious later, once scipy 1.16 is uploaded to
unstable.
-- System Information:
Debian Release: 13.0
APT prefers unstable-debug
APT policy: (500, 'unstable-debug'), (500, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 6.12.38+deb13-amd64 (SMP w/8 CPU threads; PREEMPT)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_WARN, TAINT_OOT_MODULE
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8),
LANGUAGE=en_AU:en
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
--- End Message ---
--- Begin Message ---
Source: scikit-learn
Source-Version: 1.7.2+dfsg-1
Done: Timo Röhling <[email protected]>
We believe that the bug you reported is fixed in the latest version of
scikit-learn, 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.
Timo Röhling <[email protected]> (supplier of updated scikit-learn 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])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sun, 12 Oct 2025 23:07:39 +0200
Source: scikit-learn
Architecture: source
Version: 1.7.2+dfsg-1
Distribution: experimental
Urgency: medium
Maintainer: Debian Science Maintainers
<[email protected]>
Changed-By: Timo Röhling <[email protected]>
Closes: 1074234 1088346 1088593 1109955
Changes:
scikit-learn (1.7.2+dfsg-1) experimental; urgency=medium
.
* Team upload.
* Migrate debian/watch to version 5 format
* New upstream version 1.7.2+dfsg
- Fix FTBFS with SciPy 1.16 (Closes: #1109955)
- Fix CVE-2024-5206: Potential data leakage from TF-IDF vectorizer
(Closes: #1074234)
* Update Debian patches
* Update d/copyright
* Wrap and sort Debian package files
* Update build dependencies
- Stop using twitter-bootstrap (Closes: #1088346, #1088593)
* Clean up d/rules
* Migrate to autopkgtest-pkg-pybuild
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