[From nobody Tue May 12 11:51:05 2026 Received: (at maintonly) by bugs.debian.org; 11 May 2026 20:31:08 +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=-15.3 required=4.0 tests=BAYES_00, BODY_INCLUDES_PACKAGE,DKIM_SIGNED,DKIM_VALID,DKIM_VALID_EF, FREEMAIL_FORGED_FROMDOMAIN,FREEMAIL_FROM,FROMDEVELOPER, FVGT_m_MULTI_ODD,HEADER_FROM_DIFFERENT_DOMAINS,MONEY,PGPSIGNATURE, RCVD_IN_DNSWL_NONE,SPF_HELO_NONE,SPF_PASS autolearn=ham autolearn_force=no version=4.0.1-bugs.debian.org_2005_01_02 X-Spam-Bayes: score:0.0000 Tokens: new, 90; hammy, 150; neutral, 154; spammy, 0. spammytokens: hammytokens:0.000-+--sk:iQIzBAE, 0.000-+--sk:iqizbae, 0.000-+--python3, 0.000-+--forky, 0.000-+--sk:objx86 Return-path: <gladky.anton@gmail.com> Received: from mail-wr1-x42e.google.com ([2a00:1450:4864:20::42e]:60705) by buxtehude.debian.org with esmtps (TLS1.3:ECDHE_X25519__RSA_PSS_RSAE_SHA256__AES_128_GCM:128) (Exim 4.96) (envelope-from <gladky.anton@gmail.com>) id 1wMXHO-0071cy-1N for maintonly@bugs.debian.org; Mon, 11 May 2026 20:31:08 +0000 Received: by mail-wr1-x42e.google.com with SMTP id ffacd0b85a97d-44b330c5cc6so3470073f8f.1 for <maintonly@bugs.debian.org>; Mon, 11 May 2026 13:31:05 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20251104; t=1778531463; x=1779136263; darn=bugs.debian.org; h=date:message-id:subject:from:to:sender:from:to:cc:subject:date :message-id:reply-to; bh=dN0TUrG+vddEhUqaipgaCbAEUKN34x32hTaAaf41d54=; b=p+vrQnc4zlGJoWIcEIQ6ER4dLghYFys19V8lEDqcz5LkCPQtC1+96IHEcm1Veadu0x qjtuvaZvrUq/ybMLGmpq/IJEvf7iMn7rpgYmG467jHmVIXtOuUzg88TbcOzXMQ09/7mH 9OxGjfdbqJ063xdRto1f+C53q/RhDtLApn8v1eXWwPUqABD0WcRAN/TSZhA5PqnUh2QV 0W0n517nXPaBfsHCpU3ZhbPoLb3t81F168I2jlrMzgkkfgC0c3SjE20wXkJJXsTcsXMk eCJ5Qb6QrR93C5q2KvNN+b6EVQvu3EY3v6l0q4HxgE2EXe6C6bsVEtVM77CxKEeSPsvO g1bw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20251104; t=1778531463; x=1779136263; h=date:message-id:subject:from:to:sender:x-gm-gg:x-gm-message-state :from:to:cc:subject:date:message-id:reply-to; bh=dN0TUrG+vddEhUqaipgaCbAEUKN34x32hTaAaf41d54=; b=m/N1WWvu4LCfKRvtYYDJMnDVWH6Ev8FnyOUpbKPfjJ/BTgUZQc6km0UWrUrKFWnO/i seZZHbcylTJSyqtvhXPE0XxJQiTJ6JCaZ8XwqwXcZhDqCWY7HUmJ7uTh8Dl0dayzGp+A bb/esRUsfqWvHNuzB9WVBWBDowqRToHLW3IsNet/2ejmxE8yVsZBzgmanKnJc86z5eA8 snLxtYk9JWWC5sUf/4BWppPDnpeTFZ1XgNLtJ8couJXQo4j2ogQzvTU5CcTrGn/LPPyI N0ioM3/bXJpGnhiqryx6OUtgY7/LBKVhmb4Z0XD4Cv4p+XVCSPbSppPTDTRGJYa5PBZP cspw== X-Gm-Message-State: AOJu0YynBfRC7R9+QVae/Jkr/iDg3HHI2EWl/h5uqOEXX1oEiNEyL11w A6rnmYk8jOTv+NVwPVGwmfnGTYgdGm1FA1biE51pXk71XR3d9UzPIcVMZsFxQg== X-Gm-Gg: Acq92OFPKHkxycwC2ocjqKKmA+Lilf7KVZF8MoIYw9iBEno9UZI/1DGnmGFFNv7060A noZHC9/6/qF7LZhnZaU924ylwcQUWDTuqrezIQFVhl8q0cred9kSaVTGp818RNofOB+cZCCfD0I XcRbh1nuBzYFqfwUUHbilfgPw8PLYupXmc6cahkm29UZS8Rfjg7kzOON+y5weGpu5LVNlePQ34G cIm2widU2I04ccrZ8XOsiY0QqXgdjfla2c6OTA2JAVlDVPhkiOyX7iBBuVvrwrrgvnCRHK1mPHq rwoIbtIHXq33SziN+J8hnr9YhgYMFTfiPW2hZ1YF84UMwU36iC3FDE/1AJctUh4ijxkDsCbUQnj Wk92RiE6isSHTfhHEWFbOCNe4O7CQPpG/9rfGuRVd8QGkfltNrxyo7QjtfBpdhWafu8dV4YaPQJ TStIme/D64KTKFHeXrwSl23q56SoepcD0wTHRsUmhA4xecdaxnf/k= X-Received: by 2002:a05:6000:22c6:b0:437:711c:8754 with SMTP id ffacd0b85a97d-4515b056c9bmr39745108f8f.7.1778531462937; Mon, 11 May 2026 13:31:02 -0700 (PDT) Received: from MacBook-Air-von-Anton.local ([2a01:239:200:7f00::1]) by smtp.gmail.com with ESMTPSA id ffacd0b85a97d-45491ca383asm27135819f8f.28.2026.05.11.13.31.02 for <maintonly@bugs.debian.org> (version=TLS1_3 cipher=TLS_CHACHA20_POLY1305_SHA256 bits=256/256); Mon, 11 May 2026 13:31:02 -0700 (PDT) Sender: Anton Gladky <gladky.anton@gmail.com> Received: by MacBook-Air-von-Anton.local (Postfix, from userid 501) id 719C1BE5C10; Mon, 11 May 2026 22:31:01 +0200 (CEST) To: maintonly@bugs.debian.org From: Anton Gladky <gladk@debian.org> Subject: openstructure: FTBFS with libeigen3-dev 5.0 (major version transition) Message-Id: <20260511203101.719C1BE5C10@MacBook-Air-von-Anton.local> Date: Mon, 11 May 2026 22:31:01 +0200 (CEST) Delivered-To: maintonly@bugs.debian.org -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Package: src:openstructure Version: 2.11.1-2 Severity: important Tags: sid forky ftbfs User: debian-devel@lists.debian.org Usertags: eigen3-5.0 Dear Maintainer, your package depends on libeigen3-dev. The upstream released a new major version of this mathematical library, 5.0.0. Some basic information about new features and changes in this version can be found here: https://libeigen.gitlab.io/releases/5.0/ This is a major version change and may require code changes in packages depending on eigen3. The key breaking changes include: - Minimum required C++ standard is now C++14 - Changes in the build system integration - Some API name changes openstructure FTBFS with libeigen3-dev 5.0.1. The full build log is available at: https://debusine.debian.net/debian/developers-gladk-eigen3/artifact/3759854/raw/openstructure_2.11.1-2_amd64-2026-05-08T14:50:48Z.build Here is the most probably relevant part of the failing build log: =========================================== ResourceWarning: Enable tracemalloc to get the object allocation traceback .......................................... ====================================================================== ERROR: testCalcEnrichmentAUC (__main__.TestTable.testCalcEnrichmentAUC) - ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/openstructure-2.11.1/modules/base/tests/test_table.py", line 1275, in testCalcEnrichmentAUC auc = tab.ComputeEnrichmentAUC(score_col='score', score_dir='-', class_col='rmsd', class_cutoff=2.0, class_dir='-') File "/build/reproducible-path/openstructure-2.11.1/obj-x86_64-linux-gnu/stage/lib/python3.13/dist-packages/ost/table.py", line 2696, in ComputeEnrichmentAUC return np.trapz(enr[1], enr[0]) ^^^^^^^^ File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 792, in __getattr__ raise AttributeError(f"module {__name__!r} has no attribute {attr!r}") AttributeError: module 'numpy' has no attribute 'trapz'. Did you mean: 'trace'? =========================================== libeigen3-dev_5.0.1-1 is available in experimental. When this package version lands into unstable (probably at the beginning of June 2026), this bug will be increased in severity to serious. Thanks, Anton -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEu71F6oGKuG/2fnKF0+Fzg8+n/wYFAmoCPIUACgkQ0+Fzg8+n /wbWdA/8DCGkOVcRm6w6LNo04CgZKVUhehj3uQ5b5TT35qtkE3vHuVairThpbTJF G9+X852SlssE3iTYTUhlkEjSA8zQXpDmQClaTHtjlEOF7XBeNLVB53NvFGYgS+AV wZLlLY2iCjBBHqE4fnIC0TtQ58zc57EsgjD30kOWAbeATWT1cdcj0ZvxvcuOtfGO fnzRfow+UoEnODrgC+XqfjDBsserpKaGRvbZQOdtQqqESpIjMDUSA9eW3COEWde2 NEKcOOQzgl/HA+U7IOC8w+oWn/Gror81xsct2QThle/2iLhG6U7gQQd4VGe43361 eiA7aZwLv4eUC9+w5hprLuTrXjttNnuvBwJep9Tcxc606P24anEMXYexxwhtDgKl eSwGYa0geaqRACSMradH1T3nk31cP0gtGwZvEppa+AlwNpzqHimss5oGaO2fIAeS jeY27wwvAFPZXBQA6cfLoL64NlAUdF8ZKjI5aFJDjB2cip3IVjaRaOszEH9TyOZf OeFnedKmprcacZbK6GAzLoyjqdoP0XkyC2grAe87PydXH2aXmFgAprJ+stSun1Ei lfoBlFQSRGL0JKeLbJvzcBU4VbD4D4QIFQhdTfX9+OGKLFdmDa5GVzuK2DsoRxm3 g2BkAiyqgh2A/CQU99EycNuHJwvDedltgIhitPGOJ4nII+bhonU= =csyw -----END PGP SIGNATURE----- ]