[From nobody Wed May 13 15:41:09 2026 Received: (at maintonly) by bugs.debian.org; 17 Mar 2026 10:46:18 +0000 X-Spam-Checker-Version: SpamAssassin 4.0.1-bugs.debian.org_2005_01_02 (2024-03-25) on buxtehude.debian.org X-Spam-Level: X-Spam-Status: No, score=-105.1 required=4.0 tests=BAYES_00,DKIMWL_WL_HIGH, DKIM_SIGNED,DKIM_VALID,DKIM_VALID_AU,DKIM_VALID_EF,FOURLA, FROMDEVELOPER,SPF_HELO_NONE,SPF_NONE,UNPARSEABLE_RELAY, USER_IN_DKIM_WELCOMELIST autolearn=ham autolearn_force=no version=4.0.1-bugs.debian.org_2005_01_02 X-Spam-Bayes: score:0.0000 Tokens: new, 44; hammy, 146; neutral, 23; spammy, 0. spammytokens: hammytokens:0.000-+--Hx-spam-relays-external:sk:stravin, 0.000-+--H*RT:sk:stravin, 0.000-+--Hx-spam-relays-external:311, 0.000-+--H*RT:311, 0.000-+--H*RT:108 Return-path: <roehling@debian.org> Received: from stravinsky.debian.org ([2001:41b8:202:deb::311:108]:58872) by buxtehude.debian.org with esmtps (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <roehling@debian.org>) id 1w2RwI-00DNyF-1F for maintonly@bugs.debian.org; Tue, 17 Mar 2026 10:46:18 +0000 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debian.org; s=smtpauto.stravinsky; h=X-Debian-User:Date:Subject:To:From:Message-ID: Reply-To:Cc:MIME-Version:Content-Type:Content-Transfer-Encoding:Content-ID: Content-Description:In-Reply-To:References; bh=9uvqrhy4LykmK5406C0gG3uGT01PEppWy9QTKU/ozHQ=; b=OPTiN6Vva5FyHzbmx/NxIMHoy4 3MgPPetfr6cWpYoRYgRik4MhQfyHDxZgAwUyCPzES5Ecfskhs5n0ID2UiVnV1LnwlCigqq/k4LbUU lmXut5mpOYmo/miZW9JwaVvpBxpgNuVIqX92GspBbpWLn5vRAJ71QqcFaJgP/cm8Ji6lR88NRUrmS Wsjg1NJu4vmEvILvcnAjQhO6tVTSzzUBiHQq1geXpdqe/7Q8Kg9MDUgsm/dQDRwDVpG+rmcJBKJCM pHPDJxDEQP0hjgV2sJZUkFsE11cOJm99ZmpUWjfaTXXCYtrU8CFUidpWi86t9JoZ5Hsijdpjm4HqT ilMR/n5g==; Received: from authenticated user by stravinsky.debian.org with esmtpsa (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.94.2) (envelope-from <roehling@debian.org>) id 1w2RwI-002pUy-3j for maintonly@bugs.debian.org; Tue, 17 Mar 2026 10:46:16 +0000 Message-ID: <d057665ff2e1c0d5f23a27844c6dc3f7@debian.org> From: roehling@debian.org To: maintonly@bugs.debian.org Subject: python-biopython: autopkgtest regression with NumPy 2.4 Date: Tue, 17 Mar 2026 11:46:15 +0100 X-Generator: mass-bug from devscripts 2.26.6 X-Debian-User: roehling Delivered-To: maintonly@bugs.debian.org Source: python-biopython Version: 1.86+dfsg-1 Severity: important User: debian-python@lists.debian.org Usertags: numpy2.4 Dear maintainer, According to https://ci.debian.net data, your package python-biopython has an autopkgtest regression with numpy. The following architectures failed: amd64, arm64. Hopefully relevant excerpt from https://ci.debian.net/packages/p/python-biopython/unstable/amd64/69506848/ follows: 129s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 152s test_PDB_binary_cif ... skipping. Error: Install msgpack to use Bio.PDB.binaryCIF (e.g. pip install msgpack) 152s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 152s FAIL 220s ERROR: test_coord_space (test_PDB_vectors.VectorTests.test_coord_space) 220s TypeError: only 0-dimensional arrays can be converted to Python scalars 220s ValueError: setting an array element with a sequence. 220s FAILED (failures = 1) 258s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 282s test_PDB_binary_cif ... skipping. Error: Install msgpack to use Bio.PDB.binaryCIF (e.g. pip install msgpack) 282s test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) 282s FAIL 337s ERROR: test_coord_space (test_PDB_vectors.VectorTests.test_coord_space) 337s TypeError: only 0-dimensional arrays can be converted to Python scalars 337s ValueError: setting an array element with a sequence. 337s FAILED (failures = 1) 338s dependencies FAIL non-zero exit status 1 561s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 584s FAIL 688s ERROR: test_coord_space (test_PDB_vectors.VectorTests.test_coord_space) 688s TypeError: only 0-dimensional arrays can be converted to Python scalars 688s ValueError: setting an array element with a sequence. 688s FAILED (failures = 1) 724s xml.parsers.expat.ExpatError: unclosed token: line 320, column 0 753s FAIL 853s ERROR: test_coord_space (test_PDB_vectors.VectorTests.test_coord_space) 853s TypeError: only 0-dimensional arrays can be converted to Python scalars 853s ValueError: setting an array element with a sequence. 853s FAILED (failures = 1) 855s full_suite FAIL non-zero exit status 1 855s dependencies FAIL non-zero exit status 1 855s full_suite FAIL non-zero exit status 1 ]