From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp1 ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms0.migadu.com with LMTPS id cMyXCGxH52D2GwEAgWs5BA (envelope-from ) for ; Thu, 08 Jul 2021 20:43:56 +0200 Received: from aspmx1.migadu.com ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp1 with LMTPS id QEs0BGxH52ByNgAAbx9fmQ (envelope-from ) for ; Thu, 08 Jul 2021 18:43:56 +0000 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id 440941124F for ; Thu, 8 Jul 2021 20:43:55 +0200 (CEST) Received: from localhost ([::1]:46382 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1m1Z06-0002B8-B2 for larch@yhetil.org; Thu, 08 Jul 2021 14:43:54 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:59000) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1m1YDq-0002E6-GO for bug-guix@gnu.org; Thu, 08 Jul 2021 13:54:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:45882) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1m1YDq-0005mI-4m for bug-guix@gnu.org; Thu, 08 Jul 2021 13:54:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1m1YDq-0002YE-53 for bug-guix@gnu.org; Thu, 08 Jul 2021 13:54:02 -0400 X-Loop: help-debbugs@gnu.org Subject: bug#49467: python-scanpy 1.7.2 tests failing with SIGILL Resent-From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Original-Sender: "Debbugs-submit" Resent-CC: bug-guix@gnu.org Resent-Date: Thu, 08 Jul 2021 17:54:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 49467 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: 49467@debbugs.gnu.org X-Debbugs-Original-To: bug-guix@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.16257668289751 (code B ref -1); Thu, 08 Jul 2021 17:54:01 +0000 Received: (at submit) by debbugs.gnu.org; 8 Jul 2021 17:53:48 +0000 Received: from localhost ([127.0.0.1]:57428 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1m1YDR-0002Ww-OC for submit@debbugs.gnu.org; Thu, 08 Jul 2021 13:53:48 -0400 Received: from lists.gnu.org ([209.51.188.17]:55244) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1m1YDH-0002Wf-6D for submit@debbugs.gnu.org; Thu, 08 Jul 2021 13:53:36 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:58916) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1m1YDG-00015G-RQ for bug-guix@gnu.org; Thu, 08 Jul 2021 13:53:26 -0400 Received: from mail3-relais-sop.national.inria.fr ([192.134.164.104]:40516) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1m1YDD-0005ar-NF for bug-guix@gnu.org; Thu, 08 Jul 2021 13:53:26 -0400 IronPort-HdrOrdr: A9a23:kV/ED6rKjnc/il9QAiIjoNYaV5oyeYIsimQD101hICG9Afbo9PxG/c566faaslkssR0b8+xoW5PgfZq/z/JICOAqVN+ftWLd1VdAQrsI0WKv+VPdJxE= X-IronPort-AV: E=Sophos;i="5.84,224,1620684000"; d="scan'208";a="387512713" Received: from 91-160-117-201.subs.proxad.net (HELO ribbon) ([91.160.117.201]) by mail3-relais-sop.national.inria.fr with ESMTP/TLS/DHE-RSA-AES256-GCM-SHA384; 08 Jul 2021 19:53:20 +0200 From: Ludovic =?UTF-8?Q?Court=C3=A8s?= X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 20 Messidor an 229 de la =?UTF-8?Q?R=C3=A9volution?= X-PGP-Key-ID: 0x090B11993D9AEBB5 X-PGP-Key: http://www.fdn.fr/~lcourtes/ludovic.asc X-PGP-Fingerprint: 3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5 X-OS: x86_64-pc-linux-gnu Date: Thu, 08 Jul 2021 19:53:19 +0200 Message-ID: <8735solmk0.fsf@inria.fr> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/27.2 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Received-SPF: pass client-ip=192.134.164.104; envelope-from=ludovic.courtes@inria.fr; helo=mail3-relais-sop.national.inria.fr X-Spam_score_int: -41 X-Spam_score: -4.2 X-Spam_bar: ---- X-Spam_report: (-4.2 / 5.0 requ) BAYES_00=-1.9, RCVD_IN_DNSWL_MED=-2.3, RCVD_IN_MSPIKE_H3=0.001, RCVD_IN_MSPIKE_WL=0.001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: bug-guix@gnu.org List-Id: Bug reports for GNU Guix List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: bug-guix-bounces+larch=yhetil.org@gnu.org Sender: "bug-Guix" X-Migadu-Flow: FLOW_IN ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1625769835; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:mime-version:mime-version: content-type:content-type: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:list-id:list-help: list-unsubscribe:list-subscribe:list-post; bh=4ioyAvSHHH9O9ruCU2sYL5Juf0Xb0wFRUbwDqTyYRko=; b=LK+E8IRmlxf0q6Tn+Ip/d2k5r/0tB2t73LWRjkVy2IqgDiY/1ZcOb1Eup/ZuroxAV14Gez oXvsQCrNJCiK8x1nhWfa5VO1yp1Dntu5wpfOYBrwSTXw291ijnsMCJgyhERwqlBi81wN0Z p35auYI8KvfEfZ6H/zzn2RTWdbDxkmydaezr8NXTVfLEiXDE2Fzr377x16eacmqZvZcnRc ikY5IDkdlqEM4a/wJ+XvkrP9yXcE1XPclp2u+8+I2syS1f9m2p0CGcNOFuvKnYiqbY0xDd l7QFSwykeq03iFfAVIzGpumhpARmY2LKGf7GpnzrD7cz2Ky+U+VKu7EdaeWCmg== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1625769835; a=rsa-sha256; cv=none; b=Kw73xfBLVzvij1G9F1/YgFf9J46b7iaGIdHllrZdQGVXeT9YgoB+3yNwf82jmB51zKZhbJ nqqFpFKfwgWDN944CZQv/KUBsZubIjjLgalLMJ1j/lrZ5sBpmSrarYkCNJkuooS2/ZuVdW bS4SYu0QzfT7N04097fvFI2VEJpGJL6K9Jnpw4Nayut3bDm7YURdIYgsDQt4fsqovtyJwa lwIlPt2njw0feSHqBRMola6LuRL3Gasbqf3SedBAzhWaPnc1VGaCuthKjT/kTf+SoX73TW QrCp03ShzLN7SVpnBRB9AKGXxNryKhTqs7wQfGMq9OzqEQX+3imSwcEj2bVbkA== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=none; spf=pass (aspmx1.migadu.com: domain of bug-guix-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=bug-guix-bounces@gnu.org X-Migadu-Spam-Score: -2.41 Authentication-Results: aspmx1.migadu.com; dkim=none; dmarc=none; spf=pass (aspmx1.migadu.com: domain of bug-guix-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=bug-guix-bounces@gnu.org X-Migadu-Queue-Id: 440941124F X-Spam-Score: -2.41 X-Migadu-Scanner: scn0.migadu.com X-TUID: KPT3TBsRzYrZ On an x86_64 machine, I=E2=80=99ve seen this: --8<---------------cut here---------------start------------->8--- $ guix build python-scanpy --no-grafts --check [=E2=80=A6] starting phase `check' =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D test session starts =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D platform linux -- Python 3.8.2, pytest-5.3.5, py-1.8.1, pluggy-0.13.1 rootdir: /tmp/guix-build-python-scanpy-1.7.2.drv-0/scanpy-1.7.2 plugins: hypothesis-5.4.1, cov-2.8.1, black-0.3.8 Fatal Python error: Illegal instruction Current thread 0x00007ffff785c300 (most recent call first): File "", line 219 in _call_with_frames_remov= ed File "", line 1109 in exec_module File "", line 671 in _load_unlocked File "", line 975 in _find_and_load_unlocked File "", line 991 in _find_and_load File "", line 219 in _call_with_frames_remov= ed File "", line 1042 in _handle_fromlist File "/gnu/store/368d0i579ga5sbc3mms4bg7bd4lzj6km-python-numcodecs-0.6.4/= lib/python3.8/site-packages/numcodecs/__init __.py", line 45 in File "", line 219 in _call_with_frames_remov= ed File "", line 783 in exec_module File "", line 671 in _load_unlocked File "", line 975 in _find_and_load_unlocked File "", line 991 in _find_and_load File "/gnu/store/cjclqalblsxf8l6cn1l1r4qmyjab0di3-python-zarr-2.4.0/lib/p= ython3.8/site-packages/zarr/codecs.py", line 3 in File "", line 219 in _call_with_frames_remov= ed File "", line 783 in exec_module File "", line 671 in _load_unlocked File "", line 975 in _find_and_load_unlocked File "", line 991 in _find_and_load File "/gnu/store/cjclqalblsxf8l6cn1l1r4qmyjab0di3-python-zarr-2.4.0/lib/p= ython3.8/site-packages/zarr/__init__.py", li ne 3 in File "", line 219 in _call_with_frames_remov= ed File "", line 783 in exec_module File "", line 671 in _load_unlocked File "", line 975 in _find_and_load_unlocked File "", line 991 in _find_and_load File "", line 219 in _call_with_frames_remov= ed File "", line 961 in _find_and_load_unlocked File "", line 991 in _find_and_load File "/gnu/store/hynk61vdvgv3ha41lki2z1f4daqyn6b4-python-anndata-0.7.6/li= b/python3.8/site-packages/anndata/compat/__i nit__.py", line 19 in File "", line 219 in _call_with_frames_remov= ed File "", line 783 in exec_module File "", line 671 in _load_unlocked File "", line 975 in _find_and_load_unlocked File "", line 991 in _find_and_load File "/gnu/store/hynk61vdvgv3ha41lki2z1f4daqyn6b4-python-anndata-0.7.6/li= b/python3.8/site-packages/anndata/_core/views.py", line 13 in File "", line 219 in _call_with_frames_remov= ed File "", line 783 in exec_module File "", line 671 in _load_unlocked File "", line 975 in _find_and_load_unlocked File "", line 991 in _find_and_load File "/gnu/store/hynk61vdvgv3ha41lki2z1f4daqyn6b4-python-anndata-0.7.6/li= b/python3.8/site-packages/anndata/_core/aligned_mapping.py", line 13 in File "", line 219 in _call_with_frames_remov= ed File "", line 783 in exec_module File "", line 671 in _load_unlocked File "", line 975 in _find_and_load_unlocked File "", line 991 in _find_and_load File "/gnu/store/hynk61vdvgv3ha41lki2z1f4daqyn6b4-python-anndata-0.7.6/li= b/python3.8/site-packages/anndata/_core/raw.py", line 11 in File "", line 219 in _call_with_frames_remov= ed File "", line 783 in exec_module File "", line 671 in _load_unlocked File "", line 975 in _find_and_load_unlocked File "", line 991 in _find_and_load File "/gnu/store/hynk61vdvgv3ha41lki2z1f4daqyn6b4-python-anndata-0.7.6/li= b/python3.8/site-packages/anndata/_core/anndata.py", line 26 in File "", line 219 in _call_with_frames_remov= ed File "", line 783 in exec_module File "", line 671 in _load_unlocked File "", line 975 in _find_and_load_unlocked File "", line 991 in _find_and_load File "/gnu/store/hynk61vdvgv3ha41lki2z1f4daqyn6b4-python-anndata-0.7.6/li= b/python3.8/site-packages/anndata/__init__.py", line 7 in File "", line 219 in _call_with_frames_remov= ed File "", line 783 in exec_module File "", line 671 in _load_unlocked File "", line 975 in _find_and_load_unlocked File "", line 991 in _find_and_load File "/tmp/guix-build-python-scanpy-1.7.2.drv-0/scanpy-1.7.2/scanpy/_util= s.py", line 18 in File "", line 219 in _call_with_frames_remov= ed File "", line 783 in exec_module File "", line 671 in _load_unlocked File "", line 975 in _find_and_load_unlocked File "", line 991 in _find_and_load File "/tmp/guix-build-python-scanpy-1.7.2.drv-0/scanpy-1.7.2/scanpy/__ini= t__.py", line 5 in File "", line 219 in _call_with_frames_remov= ed File "", line 783 in exec_module File "", line 671 in _load_unlocked File "", line 975 in _find_and_load_unlocked File "", line 991 in _find_and_load File "/tmp/guix-build-python-scanpy-1.7.2.drv-0/scanpy-1.7.2/scanpy/tests= /conftest.py", line 11 in File "/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib= /python3.8/site-packages/_pytest/assertion/rewrite.py", line 143 in exec_mo= dule File "", line 671 in _load_unlocked File "", line 975 in _find_and_load_unlocked File "", line 991 in _find_and_load File "/gnu/store/avj1ma4bvfjnw86pd9ys64899b627f0x-python-py-1.8.1/lib/pyt= hon3.8/site-packages/py/_path/local.py", line 701 in pyimport File "/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib= /python3.8/site-packages/_pytest/config/__init__.py", line 465 in _importco= nftest File "/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib= /python3.8/site-packages/_pytest/config/__init__.py", line 437 in _getconft= estmodules File "/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib= /python3.8/site-packages/_pytest/main.py", line 445 in gethookproxy File "/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib= /python3.8/site-packages/_pytest/main.py", line 626 in _recurse File "/gnu/store/avj1ma4bvfjnw86pd9ys64899b627f0x-python-py-1.8.1/lib/pyt= hon3.8/site-packages/py/_path/common.py", line 425 in File "/gnu/store/avj1ma4bvfjnw86pd9ys64899b627f0x-python-py-1.8.1/lib/pyt= hon3.8/site-packages/py/_path/common.py", line 424 in gen File "/gnu/store/avj1ma4bvfjnw86pd9ys64899b627f0x-python-py-1.8.1/lib/pyt= hon3.8/site-packages/py/_path/common.py", line 435 in gen File "/gnu/store/avj1ma4bvfjnw86pd9ys64899b627f0x-python-py-1.8.1/lib/pyt= hon3.8/site-packages/py/_path/common.py", line 383 in visit File "/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib= /python3.8/site-packages/_pytest/main.py", line 545 in _collect File "/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib= /python3.8/site-packages/_pytest/main.py", line 504 in collect File "/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib= /python3.8/site-packages/_pytest/runner.py", line 257 in File "/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib= /python3.8/site-packages/_pytest/runner.py", line 237 in from_call File "/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib= /python3.8/site-packages/_pytest/runner.py", line 257 in pytest_make_collec= t_report File "/gnu/store/nqi6xqx8h2fxldi3xbigkc24wfzzsy5j-python-pluggy-0.13.1/li= b/python3.8/site-packages/pluggy/callers.py", line 187 in _multicall File "/gnu/store/nqi6xqx8h2fxldi3xbigkc24wfzzsy5j-python-pluggy-0.13.1/li= b/python3.8/site-packages/pluggy/manager.py", line 84 in File "/gnu/store/nqi6xqx8h2fxldi3xbigkc24wfzzsy5j-python-pluggy-0.13.1/li= b/python3.8/site-packages/pluggy/manager.py", line 93 in _hookexec File "/gnu/store/nqi6xqx8h2fxldi3xbigkc24wfzzsy5j-python-pluggy-0.13.1/li= b/python3.8/site-packages/pluggy/hooks.py", line 286 in __call__ File "/gnu/store/436410968f8mpdlsn1pw456mpgwmbh4m-python-pytest-5.3.5/lib= /python3.8/site-packages/_pytest/runner.py", line 379 in collect_one_node ... command "pytest" failed with signal 4 builder for `/gnu/store/xdqc4a2xhkiknasj8rk36gl3gr5iswr8-python-scanpy-1.7.= 2.drv' failed with exit code 1 build of /gnu/store/xdqc4a2xhkiknasj8rk36gl3gr5iswr8-python-scanpy-1.7.2.dr= v failed --8<---------------cut here---------------end--------------->8--- It would seem that one of these dependencies has code using x86_64 ISA extensions that this particular CPU doesn=E2=80=99t support. Thoughts? Ludo=E2=80=99.