[From nobody Fri Oct 23 16:53:05 2026 Received: (at submit) by bugs.debian.org; 30 Dec 2024 12:40:29 +0000 X-Spam-Checker-Version: SpamAssassin 3.4.6-bugs.debian.org_2005_01_02 (2021-04-09) on buxtehude.debian.org X-Spam-Level: X-Spam-Status: No, score=-107.3 required=4.0 tests=BAYES_00,DKIMWL_WL_HIGH, DKIM_SIGNED,DKIM_VALID,DKIM_VALID_AU,DKIM_VALID_EF,FOURLA, FROMDEVELOPER,FUZZY_CPILL,SPF_HELO_NONE,SPF_NONE,UNPARSEABLE_RELAY, USER_IN_DKIM_WELCOMELIST,USER_IN_DKIM_WHITELIST autolearn=ham autolearn_force=no version=3.4.6-bugs.debian.org_2005_01_02 X-Spam-Bayes: score:0.0000 Tokens: new, 51; hammy, 148; neutral, 30; 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: <ginggs@debian.org> Received: from stravinsky.debian.org ([2001:41b8:202:deb::311:108]:53152) from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA, CN=stravinsky.debian.org, EMAIL=hostmaster@stravinsky.debian.org (verified) by buxtehude.debian.org with esmtps (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.94.2) (envelope-from <ginggs@debian.org>) id 1tSF4O-002ymP-QF for submit@bugs.debian.org; Mon, 30 Dec 2024 12:40:28 +0000 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debian.org; s=smtpauto.stravinsky; h=X-Debian-User:Content-Type:To:Subject:Message-ID: Date:From:MIME-Version:Reply-To:Cc:Content-Transfer-Encoding:Content-ID: Content-Description:In-Reply-To:References; bh=wRMLvylejuOvBqtebkPG7ev1aZiXGrjPCQDGzzvdYro=; b=R0djGspyQUl2tm0thgafVgnNPh Ncv7SobxFiuM22DY4iJJErXCJIfuc3LFvpIFM1WXoJcjfYQhgNbz3Yw6XmVwGxZBupYb12vX02iAJ HnOkSE2Zx+YPqVr7SKXrzPNaTgqT1jTLnVwaMgLTRDX52/92tnG4Z6XmJfdS2k8Hr30rrD3hlkQGC 6A317sMRZguIuhr1ImzyJdk9xcnTFrHwkQ4TdyR1b/Hh9HEPG/gbELEZkdq5aq24UBrbPGKmRu1xm 2q8x/w4Eadru4hHoEe4VACDc1BA0ufaLMDgo9vRkVV4MDvBdnC2S6zyI1nB69T1pJd84oz1NYiDye DcoH6pJg==; Received: from authenticated user by stravinsky.debian.org with esmtpsa (TLS1.3:ECDHE_X25519__RSA_PSS_RSAE_SHA256__AES_128_GCM:128) (Exim 4.94.2) (envelope-from <ginggs@debian.org>) id 1tSF4M-005yf1-8m for submit@bugs.debian.org; Mon, 30 Dec 2024 12:40:27 +0000 Received: by mail-vk1-f181.google.com with SMTP id 71dfb90a1353d-518988b41a1so259652e0c.0 for <submit@bugs.debian.org>; Mon, 30 Dec 2024 04:40:26 -0800 (PST) X-Gm-Message-State: AOJu0Yxhvkv4MjH/PdU8hOybnCw+tUWnTbt6ve3Rfg46xt8B1mUjUV7M 7ZXxvGKsVUtAvrCFDPGPDahKII4Wtn77chzN6mVdDmCHUoA4s1utK+xR9N2/H+uSptJ5PI5ELMT ydLomBi07wY2Trj7pwFB4+vQ/IK8= X-Google-Smtp-Source: AGHT+IFWfxprDM9R55eG6/ci/nAN6UNFt8Qcfq5tSzzu/N0M5PW1rEzhpt9SAQ/CvkiW2RdWetxPacOrHXLKG6gVzbg= X-Received: by 2002:a05:6122:2905:b0:516:20fe:d5d8 with SMTP id 71dfb90a1353d-51b75d39651mr8443142e0c.2.1735562424655; Mon, 30 Dec 2024 04:40:24 -0800 (PST) MIME-Version: 1.0 From: Graham Inggs <ginggs@debian.org> Date: Mon, 30 Dec 2024 11:40:13 -0100 X-Gmail-Original-Message-ID: <CAM8zJQvjdD03vf+mCGHJFA+W246_DCk5ron2NnPPNmBguDFDDQ@mail.gmail.com> Message-ID: <CAM8zJQvjdD03vf+mCGHJFA+W246_DCk5ron2NnPPNmBguDFDDQ@mail.gmail.com> Subject: pbsuite: autopkgtest regression in testing To: Debian Bug Tracking System <submit@bugs.debian.org> Content-Type: text/plain; charset="UTF-8" X-Debian-User: ginggs Delivered-To: submit@bugs.debian.org Source: pbsuite Version: 15.8.24+dfsg-8 Severity: serious User: debian-ci@lists.debian.org Usertags: regression Hi Maintainer Sometime around 2024-12-26, pbsuite's autopkgtest regressed in testing [1]. I've copied what I hope is the relevant part of the log below. This regression allowed blasr/5.3.5+dfsg-7 to migrate to testing. Regards Graham [1] https://ci.debian.net/packages/p/pbsuite/testing/amd64/ 74s 2024-12-26 05:20:04,185 [INFO] Running /usr/bin/Honey spots --reference lambda_modified.fasta mappingFinal.bam 74s Traceback (most recent call last): 74s File "/usr/bin/Honey", line 51, in <module> 74s parseArgs() 74s File "/usr/bin/Honey", line 48, in parseArgs 74s STAGES[args.stage](args.options) 74s File "/usr/lib/python3/dist-packages/pbsuite/honey/HSpots.py", line 1092, in run 74s bam = pysam.Samfile(args.bam) 74s ^^^^^^^^^^^^^^^^^^^^^^^ 74s File "pysam/libcalignmentfile.pyx", line 751, in pysam.libcalignmentfile.AlignmentFile.__cinit__ 74s File "pysam/libcalignmentfile.pyx", line 956, in pysam.libcalignmentfile.AlignmentFile._open 74s ValueError: file does not contain alignment data ]