From unknown Sun Jun 22 00:49:53 2025 X-Loop: help-debbugs@gnu.org Subject: bug#67630: Build python-phenograph.x86_64-linux on master is broken. Resent-From: Maxim Cournoyer Original-Sender: "Debbugs-submit" Resent-CC: bug-guix@gnu.org Resent-Date: Mon, 04 Dec 2023 22:07:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 67630 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: 67630@debbugs.gnu.org X-Debbugs-Original-To: bug-guix Received: via spool by submit@debbugs.gnu.org id=B.170172757026608 (code B ref -1); Mon, 04 Dec 2023 22:07:02 +0000 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 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-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 unknown Sun Jun 22 00:49:53 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: Maxim Cournoyer Subject: bug#67630: closed (Re: bug#67630: Build python-phenograph.x86_64-linux on master is broken.) Message-ID: References: <87zfypr5c8.fsf@gmail.com> X-Gnu-PR-Message: they-closed 67630 X-Gnu-PR-Package: guix Reply-To: 67630@debbugs.gnu.org Date: Tue, 16 Jul 2024 18:57:03 +0000 Content-Type: multipart/mixed; boundary="----------=_1721156223-2394-1" This is a multi-part message in MIME format... ------------=_1721156223-2394-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #67630: Build python-phenograph.x86_64-linux on master is broken. which was filed against the guix package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 67630@debbugs.gnu.org. --=20 67630: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D67630 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1721156223-2394-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 67630-done) by debbugs.gnu.org; 16 Jul 2024 18:56:30 +0000 Received: from localhost ([127.0.0.1]:34366 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sTnLi-0000ak-8m for submit@debbugs.gnu.org; Tue, 16 Jul 2024 14:56:30 -0400 Received: from mail-qt1-f180.google.com ([209.85.160.180]:53647) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sTnLe-0000aV-D4 for 67630-done@debbugs.gnu.org; Tue, 16 Jul 2024 14:56:28 -0400 Received: by mail-qt1-f180.google.com with SMTP id d75a77b69052e-44d5f487556so31833871cf.3 for <67630-done@debbugs.gnu.org>; Tue, 16 Jul 2024 11:56:23 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20230601; t=1721156118; x=1721760918; darn=debbugs.gnu.org; h=in-reply-to:content-disposition:mime-version:references :mail-followup-to:message-id:subject:cc:to:from:date:sender:from:to :cc:subject:date:message-id:reply-to; bh=cPd4eQTSCSGcz8IYK48Qk2MGtfVdV2tE7GM0gUT0lVE=; b=Cf5AtAlcCNyrITqRD+09Jy3uTIoMM5B8ZOw5M14vdpKmsFQ1KATgm0rvMj/l9MitZ5 yNoKRJm3AJwMNr5UngN+TS4YHMbwZ/tCiI+nQp+UTNevlRLft480COuDo73sOgfqXqwl 8CsHgBkjbEfVjJXUN6CS4wf8GphLRoxiwx/dVgY/rAvdxEUmxljPYMkwkoxcG2ynrH+L yvCfmdAZ4NkWBf4/vHvs2YMTIBp6K5gpzgaAdCm3NZABd/EO+Yhl/ceX9nGFzWHNr83t xbxixrH2P/HcNmm2t787LwYNUrekndp17tbimLXn/AfVkg6f9h/JoJh8WYnNJ24K1abc Zcxw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20230601; t=1721156118; x=1721760918; h=in-reply-to:content-disposition:mime-version:references :mail-followup-to:message-id:subject:cc:to:from:date:sender :x-gm-message-state:from:to:cc:subject:date:message-id:reply-to; bh=cPd4eQTSCSGcz8IYK48Qk2MGtfVdV2tE7GM0gUT0lVE=; b=FEwEWzwyaEGgSfWfQspa0H5gQV8QYBCpI60Zlq7Wq90xyafDLW1z2jykNX3ICR06S6 oO67YXc4en2Z1NeyGM0AXHVV15t+q/Kz4vmM0QaUDx7F8vmgjwSdCfSQDfMQ7oTljdeI kC+Ushs+88ryvqm3bqgJIALKcDCcxFL/hY38N/aPGlPg3tCXSI1Q1Dr4J3t1EGjIAgH6 HA3rYJv6yRaJszjrlLTeTXdRB99tuJQ3zvyMbYXLX2Ka8WW1uA8AxkpCDYkV97Ejxs0e wT5CXmKS8EECF0XpEqV4iPe9ixtPNjltSkfRntBioN1JiYkIcXgxhlc2IrhDUW9hcwxG yjkQ== X-Gm-Message-State: AOJu0YzejnUq/O6ScmoOBS3474cGWZWFW4Dr0zAGyilbC6mTfA3IiAwZ KgAMs05KmyiIBIunvUam4OL7pO55Qd+M3cj20pqUHagSFhJnRhrb X-Google-Smtp-Source: AGHT+IHE0haOtoRSi03Mq8yo3RbQRMvtkAcowi785jxtmht/7x+a0l/s9AW74UuDx60z7AWYwRXIQw== X-Received: by 2002:a05:622a:5cd:b0:446:56d4:4d6c with SMTP id d75a77b69052e-44f7ace35a8mr36257211cf.40.1721156117610; Tue, 16 Jul 2024 11:55:17 -0700 (PDT) Received: from localhost (ool-ad039216.dyn.optonline.net. [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; 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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 ------------=_1721156223-2394-1--