[From nobody Sun May 24 13:21:05 2026 Received: (at submit) by bugs.debian.org; 25 Jun 2025 17:20:57 +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=-120.0 required=4.0 tests=BAYES_00, BODY_INCLUDES_PACKAGE,DKIMWL_WL_HIGH,DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU,DKIM_VALID_EF,FOURLA,FROMDEVELOPER,HAS_PACKAGE, RCVD_IN_DNSWL_MED,SPF_HELO_PASS,SPF_NONE,USER_IN_DKIM_WELCOMELIST, X_DEBBUGS_CC autolearn=ham autolearn_force=no version=4.0.1-bugs.debian.org_2005_01_02 X-Spam-Bayes: score:0.0000 Tokens: new, 29; hammy, 150; neutral, 130; spammy, 0. spammytokens: hammytokens:0.000-+--trixie, 0.000-+--armhf, 0.000-+--sk:buildd., 0.000-+--UD:buildd.debian.org, 0.000-+--buildddebianorg Return-path: <sanvila@debian.org> Received: from mitropoulos.debian.org ([2001:648:2ffc:deb:216:61ff:fe9d:958d]:36558) from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA, CN=mitropoulos.debian.org, EMAIL=hostmaster@mitropoulos.debian.org (verified) by buxtehude.debian.org with esmtps (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <sanvila@debian.org>) id 1uUTnt-001rPw-1k for submit@bugs.debian.org; Wed, 25 Jun 2025 17:20:57 +0000 Received: from paradis.debian.org ([2607:f8f0:614:1::1274:67]:49842) from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA, CN=paradis.debian.org, EMAIL=hostmaster@paradis.debian.org (verified) by mitropoulos.debian.org with esmtps (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.94.2) (envelope-from <sanvila@debian.org>) id 1uUTnr-008CvX-5m for submit@bugs.debian.org; Wed, 25 Jun 2025 17:20:55 +0000 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debian.org; s=smtpauto.paradis; h=Date:Message-Id:Subject:To:From:Reply-To:Cc: MIME-Version:Content-Type:Content-Transfer-Encoding:Content-ID: Content-Description:In-Reply-To:References; bh=GdzHxCV5Zmlb3HOb3wZVankrFl51IAdBAehFsfM9wi0=; b=dt4QUc24Lp5hmSxJZM3q0bOwce klIwY3pjVOo86gSUJ8kTOqh5MP9+BCOrGxO/9qcKHzLI/katEm6IbjTmbZ+sTNAwdaCnDz8D7ihmV LG03HtsEb8tJkbzGZp6sMIEQc3BqQQD16a1NZ6SngA9NMFe6LS5oCLhCpef5D8eO3YZtpKiMtrZib nkeW5pdYmO/Pr1VxPQwvfVjl8O3B4aA2TBjnZw3aZjRM6FHlsKF+0ZbOB/9Eq/oKqQBTaNXDmvJbb XF3mbu4+p4R9nTKMtLidSDcI8/TBnuFGOhCUh1HqO8KfjcapWVe3oN6hOpAm6k7hGNWx6IW7kCUz1 h6weuPKA==; Received: from sanvila by paradis.debian.org with local (Exim 4.96) (envelope-from <sanvila@debian.org>) id 1uUTno-007pRD-0i for submit@bugs.debian.org; Wed, 25 Jun 2025 17:20:52 +0000 From: Santiago Vila <sanvila@debian.org> To: Debian BTS <submit@bugs.debian.org> Subject: mdanalysis: FTBFS randomly: autobuilder hangs X-Debbugs-Cc: sanvila@debian.org Message-Id: <E1uUTno-007pRD-0i@paradis.debian.org> Date: Wed, 25 Jun 2025 17:20:52 +0000 Delivered-To: submit@bugs.debian.org Package: src:mdanalysis Version: 2.9.0-8 Severity: serious Tags: ftbfs trixie sid help Dear maintainer: During a rebuild of all packages in unstable, your package failed to build: -------------------------------------------------------------------------------- [...] testsuite/MDAnalysisTests/analysis/test_diffusionmap.py::test_long_traj PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_diffusionmap.py::test_updating_atomgroup PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_diffusionmap.py::test_not_universe_atomgroup_error PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_diffusionmap.py::test_DistanceMatrix_attr_warning PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestDihedral::test_dihedral[client_Dihedral0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestDihedral::test_dihedral_single_frame[client_Dihedral0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestDihedral::test_atomgroup_list[client_Dihedral0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestDihedral::test_enough_atoms[client_Dihedral0] PASSED [ 1%] testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestDihedral::test_dihedral_attr_warning[client_Dihedral0] E: Build killed with signal TERM after 30 minutes of inactivity -------------------------------------------------------------------------------- Notes: - The way it fails is not always the same. I've put a collection of different build logs here: https://people.debian.org/~sanvila/build-logs/202506/ - The build does not always fail, but the failure rate here is around 90% (tested on systems with 2 CPUs), which makes it not to be suitable for release. However, for some reason, the failure rate is only 20% on single-cpu systems, maybe this difference means something. - I believe, but I can't check anymore, that the failure rate raised a lot when I switched my autobuilders to trixie (i.e. when I started to use the kernel of trixie). - This failure where the autobuilder hangs also happens on the buildds. Please see: https://buildd.debian.org/status/fetch.php?pkg=mdanalysis&arch=all&ver=2.9.0-3&stamp=1744942413&raw=0 https://buildd.debian.org/status/fetch.php?pkg=mdanalysis&arch=amd64&ver=2.9.0-7&stamp=1745409028&raw=0 https://buildd.debian.org/status/fetch.php?pkg=mdanalysis&arch=arm64&ver=2.9.0-6&stamp=1745371276&raw=0 https://buildd.debian.org/status/fetch.php?pkg=mdanalysis&arch=armel&ver=2.9.0-8&stamp=1747011477&raw=0 https://buildd.debian.org/status/fetch.php?pkg=mdanalysis&arch=i386&ver=2.9.0-2&stamp=1744893854&raw=0 https://buildd.debian.org/status/fetch.php?pkg=mdanalysis&arch=mips64el&ver=2.9.0-4&stamp=1745023633&raw=0 all of which end with a message like this: E: Build killed with signal TERM after 150 minutes of inactivity (In my build logs, I lowered the value to 30 minutes because I know that in normal circumstances the package should take a lot less than that). - There are also similar failures (autobuilder hang) in the reproducible-builds site: https://tests.reproducible-builds.org/debian/rbuild/unstable/amd64/mdanalysis_2.9.0-8.rbuild.log.gz https://tests.reproducible-builds.org/debian/logs/unstable/armhf/mdanalysis_2.8.0-4.build2.log.gz - I have no idea of what's going on here, but as always, I can offer a VM to reproduce (contact me privately for details). Thanks. ]