From unknown Sat Jun 21 10:40:45 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#67630 <67630@debbugs.gnu.org> To: bug#67630 <67630@debbugs.gnu.org> Subject: Status: Build python-phenograph.x86_64-linux on master is broken. Reply-To: bug#67630 <67630@debbugs.gnu.org> Date: Sat, 21 Jun 2025 17:40:45 +0000 retitle 67630 Build python-phenograph.x86_64-linux on master is broken. reassign 67630 guix submitter 67630 Maxim Cournoyer severity 67630 normal thanks From debbugs-submit-bounces@debbugs.gnu.org Mon Dec 04 17:06:10 2023 Received: (at submit) by debbugs.gnu.org; 4 Dec 2023 22:06:10 +0000 Received: from localhost ([127.0.0.1]:35978 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rAH4s-0006v4-Ak for submit@debbugs.gnu.org; Mon, 04 Dec 2023 17:06:10 -0500 Received: from lists.gnu.org ([2001:470:142::17]:34320) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rAH4q-0006uS-0U for submit@debbugs.gnu.org; Mon, 04 Dec 2023 17:06:08 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1rAH4Y-0006bb-DT for bug-guix@gnu.org; Mon, 04 Dec 2023 17:05:50 -0500 Received: from mail-qv1-xf30.google.com ([2607:f8b0:4864:20::f30]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1rAH4U-0007IX-Lh for bug-guix@gnu.org; Mon, 04 Dec 2023 17:05:49 -0500 Received: by mail-qv1-xf30.google.com with SMTP id 6a1803df08f44-67ad891ff36so3461756d6.1 for ; Mon, 04 Dec 2023 14:05:46 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20230601; t=1701727545; x=1702332345; darn=gnu.org; h=mime-version:message-id:date:user-agent:references:in-reply-to :subject:to:from:from:to:cc:subject:date:message-id:reply-to; bh=u7pe3vPekf/Jxg7w+36DtUn9udQoE1mPA/DptvHuO8k=; b=KLKaJtICdxyWMn9Xerh6ESBVCVm8kVBUUzMfBerox8xzBGKsckSnMMcxHuhVsnySIC 1JAjuuaIq+98e4crIkK8LcLliOdCF93PRmBbZvKEwFEal/I7/2uuI5VpjkcD/U0PB6hy uPwDR5aIFxNSN1TrujEOfnkpMvEzrpasVJaK2AACEAhjcyaXEHuYTWUv0iyOvGCRUWR8 lSQQOFlg/nwXmFXuNYrWXb1PTYW2Y+VROVAhN8FbcbvMPTBX2lShXTIDP9pmCZ7J8TLH 9VIUEoGHZB2kflOhcUIJbVWn57h8iFc+ydl9g6A29xArwXpfC5U9qoXjyW723kyt1deJ 9ecg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20230601; t=1701727545; x=1702332345; h=mime-version:message-id:date:user-agent:references:in-reply-to :subject:to:from:x-gm-message-state:from:to:cc:subject:date :message-id:reply-to; bh=u7pe3vPekf/Jxg7w+36DtUn9udQoE1mPA/DptvHuO8k=; b=u4x8tS9ba53Fy0JHpm/SD4iSjNAZ0DfiwxAkBDYSUbJZtave5/m3Br8bG9Sg8mSxfN 0dd7vGCYdbyQAB5yxd6epJROHVYeEB3V9fjfvM1bN6hx7Rhnabw2MYzM+wjNTBHpxTIl yQFbcSfWZV2Lm49QJ6ehU1oyrS+MNY9WgC38bF4P1holrKS2U5tEceomoa/woVdPzDju q4m0iP7INw/rnDPy/QHPfIRSSGylwsIJVh5cPPhHAYXD7m1j8iaIMWJ70drgRWbBDrUB nsmDA2k8GtRL0l+BOVhFpohuuBG/ubmAgF5chK71ny+PoV6yi4upmtsIkGKWGVI98HP7 bSBA== X-Gm-Message-State: AOJu0YxVCDnBm5Ss+dcTUsQOJqr11TU77GXapenb4ZLsx48dxqFVZC7+ jRUEhpsktRB4PzS9tZIhHGGritg6xgn3Ow== X-Google-Smtp-Source: AGHT+IETXeC7KwEJtTx+X3BXqEcw0zu7LetLNQKNw85O5zB8KJEN0GAOqkq+/3hFgGA/R3NMLdixEQ== X-Received: by 2002:ad4:59c6:0:b0:67a:d7d5:9512 with SMTP id el6-20020ad459c6000000b0067ad7d59512mr246983qvb.126.1701727545315; Mon, 04 Dec 2023 14:05:45 -0800 (PST) Received: from hurd (dsl-141-198.b2b2c.ca. [66.158.141.198]) by smtp.gmail.com with ESMTPSA id z6-20020a0cf006000000b0067a17c8696esm3009554qvk.82.2023.12.04.14.05.44 for (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 04 Dec 2023 14:05:44 -0800 (PST) From: Maxim Cournoyer To: bug-guix Subject: Re: Build python-phenograph.x86_64-linux on master is broken. In-Reply-To: <2246@guix-ci.nnrss> (cuirass@gnu.org's message of "Sat, 02 Dec 2023 13:31:37 +0000") References: <2246@guix-ci.nnrss> User-Agent: Gnus/5.13 (Gnus v5.13) Date: Mon, 04 Dec 2023 17:05:43 -0500 Message-ID: <87zfypr5c8.fsf@gmail.com> MIME-Version: 1.0 Content-Type: text/plain Received-SPF: pass client-ip=2607:f8b0:4864:20::f30; envelope-from=maxim.cournoyer@gmail.com; helo=mail-qv1-xf30.google.com X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01, WEIRD_PORT=0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.0 (/) Hi, cuirass@gnu.org (Cuirass) writes: >

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

> > https://ci.guix.gnu.org/build/2736972/details The failure reads: --8<---------------cut here---------------start------------->8--- =================================== FAILURES =================================== ___________________________ test_classify_generated ____________________________ cluster_dataset_generated = 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 From debbugs-submit-bounces@debbugs.gnu.org Tue Jul 16 14:56:30 2024 Received: (at 67630-done) by debbugs.gnu.org; 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[173.3.146.22]) by smtp.gmail.com with ESMTPSA id d75a77b69052e-44f5b7fce1esm37988311cf.55.2024.07.16.11.55.16 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 16 Jul 2024 11:55:17 -0700 (PDT) Date: Tue, 16 Jul 2024 21:55:15 +0300 From: Efraim Flashner To: Maxim Cournoyer Subject: Re: bug#67630: Build python-phenograph.x86_64-linux on master is broken. Message-ID: Mail-Followup-To: Efraim Flashner , Maxim Cournoyer , 67630-done@debbugs.gnu.org References: <2246@guix-ci.nnrss> <87zfypr5c8.fsf@gmail.com> MIME-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha256; protocol="application/pgp-signature"; boundary="rqBfclggcHXkYjA4" Content-Disposition: inline In-Reply-To: <87zfypr5c8.fsf@gmail.com> X-PGP-Key-ID: 0x41AAE7DCCA3D8351 X-PGP-Key: https://flashner.co.il/~efraim/efraim_flashner.asc X-PGP-Fingerprint: A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 67630-done Cc: 67630-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) --rqBfclggcHXkYjA4 Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable This package appears to be building correctly now. --=20 Efraim Flashner =D7=A8=D7=A0=D7=A9=D7=9C=D7=A4 = =D7=9D=D7=99=D7=A8=D7=A4=D7=90 GPG key =3D A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 Confidentiality cannot be guaranteed on emails sent or received unencrypted --rqBfclggcHXkYjA4 Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAABCAAdFiEEoov0DD5VE3JmLRT3Qarn3Mo9g1EFAmaWwgkACgkQQarn3Mo9 g1HthA//dhzfCEI7NQsZkFWy6jEe+0IR3iagffMUWQI0X9rp7Ddc2fweExVgiz49 jgleeLchMN+zW8gUCAEbTfCH22tFaVYuxWeaCdvlh2OiMV7rU8vMYhKauJLEpP0K GYDgqQklUeGPIHo4Dv0BOZgXQaSYtVo/Bk1ieAPijY6WcOybBM92E8QadjAp80aZ lETsHeQsP7hND2e0aY0cIifWfwp7ZMC3ltlWvgwxfBx0iARNZ5bo4dnZ/92a/Yb8 I56qf7Frol1vrdqt8IOsrSSFBOO9SSk+PlttDRo+o52Vri7KEW7VPcSWU9PWd5Pn wLE2eT/+vSpDRDFxc0aB49/FSPXn9rVqHz+SJlwhxUmqkV6uWGIVosaaSMSZ91a7 3NTSq5fisRhElj9iAwd9CveHTy/ziIYRpcpAHWvydq15Pym1boOfjVDawlAPgDgV aPjhGC1fNdYHFiTapDqVZj3RXNjjCe5GNNCZJ4hfwljjzbS142nrRIfvBJavRu96 GMt1nPXN4I3OQoJaKaST8dEZb0KmrDWQPmmK9Cd3XCa4nRT8QjOo+hTN5AIG3Yb7 dhLsI5eS9VgxV4a7DqBkHaJC6iqiFbzWF+sS/EG+d9cyiB3mczR0tN7/d+lPX6DO JN805zODU6R4w1E+5cIa0DAL7WXQjHiLjgnQJtMWqPe3tyATvtI= =vXs0 -----END PGP SIGNATURE----- --rqBfclggcHXkYjA4-- From unknown Sat Jun 21 10:40:45 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. 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