[From nobody Tue Sep 29 08:53:05 2026 Received: (at submit) by bugs.debian.org; 3 Sep 2026 15:08:43 +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=-118.2 required=4.0 tests=ALL_TRUSTED,BAYES_00, BODY_INCLUDES_PACKAGE,DKIMWL_WL_HIGH,DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU,DKIM_VALID_EF,FROMDEVELOPER,HAS_PACKAGE,SPF_HELO_NONE, SPF_PASS,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, 60; hammy, 150; neutral, 108; 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: <maxy@debian.org> Received: from stravinsky.debian.org ([2001:41b8:202:deb::311:108]:52034) by buxtehude.debian.org with esmtps (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <maxy@debian.org>) id 1x293S-002rb5-1O for submit@bugs.debian.org; Thu, 03 Sep 2026 15:08:43 +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:MIME-Version:Message-ID: Subject:Cc:To:From:Date:Reply-To:Content-Transfer-Encoding:Content-ID: Content-Description:In-Reply-To:References; bh=vBuHa9AE4l77jX2waaT7JZVhxZz0XuPHl5Kiiw9uxF0=; b=gjORCBhb15/hZ0bixI9bMD2YFB VD1eC4oJ0U4peHQEZcP6lSDnXxzvPmMp2mFZ94M50i5BDnXFnQNpPyOAAuBWYD0UaxfPevI+/DXxH 16IsVP9eZhQqPLvIuWRn9b8UZr6mqR39ikj+ccW5EPkJov04uSdL01lYv5nFTH3Wdd0uni171s5LP CHGQQWSJeSBB4dn50abz7VQPFArTtgJLj/X0GxTiQODbypBl8Y8JE+JCPKFd2nvbrTaAhfrlhJGGF huf7xhMTND0m1fNJeX52H5klR2Yvl1hhL1wQYeaKZIkweZ/Vn9Elc3xdjFXm/BOjSAaW5Z4nIyMKM T0Ff+8eQ==; Received: from authenticated-user by stravinsky.debian.org with esmtpsa (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <maxy@debian.org>) id 1x293R-000dM9-0v; Thu, 03 Sep 2026 15:08:42 +0000 Date: Thu, 3 Sep 2026 17:08:40 +0200 From: Maximiliano Curia <maxy@debian.org> To: submit@bugs.debian.org Cc: debian-python@lists.debian.org Subject: rdkit: FTBFS against python 3.15rc1 Message-ID: <apmNeBubKGvbOjtV@hecuba.gnuservers.com.ar> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="mM6fBwnqoETPfkVt" Content-Disposition: inline X-Debian-User: maxy Delivered-To: submit@bugs.debian.org --mM6fBwnqoETPfkVt Content-Type: text/plain; charset=us-ascii; format=flowed Content-Disposition: inline Package: src:rdkit Version: 202603.4-1 User: debian-python@lists.debian.org Usertags: python3.15 Tags: patch, ftbfs, forky, sid Severity: serious Hi! While rebuilding the python related packages against the Python 3.15rc1 version we found that rdkit fails to build from source not only for 3.15 but also for 3.14 [1]. Error: testDistGeomHelpers: src/catch2/../catch2/internal/catch_output_redirect.hpp:40: void Catch::OutputRedirect::activate(): Assertion !m_redirectActive && "redirect is already active"' failed. This is because catch2 is not thread safe till release 3.12, but currently we have 3.7 in Debian, so the tests that depend on thread safety need workarounds. It's likely that this only started happening now, due to the new gcc version. I applied the fix in the sandbox [2] to be able to build the packages that depend on rdkit and it has built successfully, please consider applying the patch to get rdkit to build successfully. Happy hacking, [1]: https://debusine.debian.net/debian/r-python-python3.15/artifact/4587746/ [2]: https://debusine.debian.net/debian/r-python-python3.15/ -- "Can you imagine what I would do if I could do all I can?" -- Sun Tzu Saludos /\/\ /\ >< `/ --mM6fBwnqoETPfkVt Content-Type: text/x-diff; charset=us-ascii Content-Disposition: attachment; filename=fix_distgeom_threadsafety.patch Description: Avoid Catch2 assertions in multithreaded test helper Catch2 assertion macros are not thread-safe (prior catch2 3.12) and cause assertion failures in OutputRedirect when invoked concurrently across worker threads. Author: Maximiliano Curia <maxy@debian.org> Forwarded: no --- a/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp +++ b/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp @@ -943,17 +943,17 @@ void runblock(const std::vector<std::sha .useLegacyImplementation = legacyETKDG}; std::vector<int> cids = DGeomHelpers::EmbedMultipleConfs(*mol, 10, params); - REQUIRE(cids.size() == 10); + TEST_ASSERT(cids.size() == 10); std::unique_ptr<ForceFields::ForceField> field( UFF::constructForceField(*mol, 100, cids[0])); - REQUIRE(field); + TEST_ASSERT(field); field->initialize(); double eng = field->calcEnergy(); if (!feq(eng, energies[i])) { std::cerr << i << " iter " << j << " " << energies[i] << " != " << eng << std::endl; } - CHECK(feq(eng, energies[i])); + TEST_ASSERT(feq(eng, energies[i])); } } } --mM6fBwnqoETPfkVt Content-Type: text/x-diff; charset=us-ascii Content-Disposition: attachment; filename=fix_substruct_threadsafety.patch Description: Avoid Catch2 assertions in substruct multithreaded test helper Catch2 assertion macros are not thread-safe and cause assertion failures in OutputRedirect when invoked concurrently across worker threads. Author: Maximiliano Curia <maxy@debian.org> Forwarded: no --- a/Code/GraphMol/Substruct/testSubstructMatch.cpp +++ b/Code/GraphMol/Substruct/testSubstructMatch.cpp @@ -541,7 +541,7 @@ void runblock(const std::vector<std::uni MatchVectType matchV; bool found = SubstructMatch(*mol, *query, matchV); - CHECK(found == hits[i]); + TEST_ASSERT(found == hits[i]); } } } --mM6fBwnqoETPfkVt-- ]