GNU bug report logs - #67630
Build python-phenograph.x86_64-linux on master is broken.

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Efraim Flashner <efraim <at> flashner.co.il>
Cc: tracker <at> debbugs.gnu.org
Subject: bug#67630: closed (Build python-phenograph.x86_64-linux on master
 is broken.)
Date: Tue, 16 Jul 2024 18:57:03 +0000

[Message part 1 (text/plain, inline)]

Your message dated Tue, 16 Jul 2024 21:55:15 +0300
with message-id <ZpbCE9mQSGZrE6gR <at> pbp>
and subject line Re: bug#67630: Build python-phenograph.x86_64-linux on master is broken.
has caused the debbugs.gnu.org bug report #67630,
regarding Build python-phenograph.x86_64-linux on master is broken.
to be marked as done.

(If you believe you have received this mail in error, please contact
help-debbugs <at> gnu.org.)


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67630: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=67630
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Contact help-debbugs <at> gnu.org with problems

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From: Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
To: bug-guix <bug-guix <at> gnu.org>
Subject: Re: Build python-phenograph.x86_64-linux on master is broken.
Date: Mon, 04 Dec 2023 17:05:43 -0500

Hi,

cuirass <at> gnu.org (Cuirass) writes:

> <p>The build <b>python-phenograph.x86_64-linux</b> for specification <b>master</b> is
> broken. You can find the detailed information about this build <a
> href="https://ci.guix.gnu.org/build/2736972/details">here</a>.</p>
>
> https://ci.guix.gnu.org/build/2736972/details

The failure reads:

--8<---------------cut here---------------start------------->8---
=================================== FAILURES ===================================
___________________________ test_classify_generated ____________________________

cluster_dataset_generated = <tests.conftest.GeneratedClusterDataset object at 0x7ffdcfdb90f0>

    def test_classify_generated(cluster_dataset_generated):
        output, _ = classify(
            cluster_dataset_generated.train_set, cluster_dataset_generated.test_set
        )
        actual = cluster_dataset_generated.test_labels
>       assert all([p == a for p, a in zip(output, actual)])
E       assert False
E        +  where False = all([True, True, False])

tests/test_classify.py:9: AssertionError
----------------------------- Captured stdout call -----------------------------
Finding 30 nearest neighbors using minkowski metric and 'auto' algorithm
=============================== warnings summary ===============================
phenograph/cluster.py:13
  /tmp/guix-build-python-phenograph-1.5.7.drv-0/PhenoGraph-1.5.7/phenograph/cluster.py:13: DeprecationWarning: Please use `spmatrix` from the `scipy.sparse` namespace, the `scipy.sparse.base` namespace is deprecated.
    from scipy.sparse.base import spmatrix

tests/test_classify.py::test_classify_generated
tests/test_classify.py::test_classify_generated
tests/test_classify.py::test_classify_generated
tests/test_classify.py::test_classify_fixed
tests/test_classify.py::test_classify_fixed
tests/test_classify.py::test_classify_fixed
tests/test_classify.py::test_random_walk_probabilities_fixed
tests/test_classify.py::test_random_walk_probabilities_fixed
tests/test_classify.py::test_random_walk_probabilities_fixed
  /tmp/guix-build-python-phenograph-1.5.7.drv-0/PhenoGraph-1.5.7/phenograph/classify.py:43: DeprecationWarning: Please use `bicgstab` from the `scipy.sparse.linalg` namespace, the `scipy.sparse.linalg.isolve` namespace is deprecated.
    sp.linalg.isolve.bicgstab(Lu, b.T.todense(), atol="legacy") for b in B.T

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED tests/test_classify.py::test_classify_generated - assert False
=================== 1 failed, 5 passed, 10 warnings in 3.48s ===================
--8<---------------cut here---------------end--------------->8---

The test is probably flaky and should be reported upstream and disabled
in our package meanwhile.

-- 
Thanks,
Maxim

[Message part 3 (message/rfc822, inline)]

From: Efraim Flashner <efraim <at> flashner.co.il>
To: Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
Cc: 67630-done <at> debbugs.gnu.org
Subject: Re: bug#67630: Build python-phenograph.x86_64-linux on master is
 broken.
Date: Tue, 16 Jul 2024 21:55:15 +0300

[Message part 4 (text/plain, inline)]

This package appears to be building correctly now.

-- 
Efraim Flashner   <efraim <at> flashner.co.il>   רנשלפ םירפא
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