[From nobody Tue Sep 8 11:26:09 2026 Received: (at submit) by bugs.debian.org; 6 Sep 2026 10:05:34 +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,GMAIL,HAS_PACKAGE, MD5_SHA1_SUM,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, 54; hammy, 150; neutral, 126; 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]:60944) 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 1x39kj-002mAo-3C for submit@bugs.debian.org; Sun, 06 Sep 2026 10:05:34 +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:To:From:Date:Reply-To:Cc:Content-Transfer-Encoding:Content-ID: Content-Description:In-Reply-To:References; bh=TPLKL/xadE/KTTI6fYxNQmdnz39599N7wL6UoyCeXzk=; b=F/V+ARdGVbn0Vxc7Vx2U2t0mYh 7lOKtIGcg9CEkEcqsDV/NQHbZeuBmt4My7oDtPD6FNc9VOBUfjNzwlHAsz6IlN6Y7ikA4XE+rXAiw zepY7ScSQJzy2qT93I4asANqj7E0/odeTN/oM+lGqNLyEMHVMhq1+p6QMgK2kfUT+l+hay1mDu6ch Q67293CwA4npez3z5pyoOND9RvgWBY78oqUvikDR0k3ZRTgliYkZX92LhZaaw7VLIuV402aEFbUEJ f8yBBTiJrdC34dJfwhmiYlVs5mWer7ximEUuh1nuBnWoNnLg/OPXu1R9G3AYP3Z6HtT3MiM36xE9s uiRzOF1A==; 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 1x39kh-000evF-0e for submit@bugs.debian.org; Sun, 06 Sep 2026 10:05:32 +0000 Date: Sun, 6 Sep 2026 12:05:23 +0200 From: Maximiliano Curia <maxy@debian.org> To: submit@bugs.debian.org Subject: rdkit: FTBFS with new eigen3 and also fails in arm64 Message-ID: <ap064ypy5c5EBOm3@hecuba.gnuservers.com.ar> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="aAdYj61fnbEhkwUL" Content-Disposition: inline X-Debian-User: maxy Delivered-To: submit@bugs.debian.org --aAdYj61fnbEhkwUL 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 [1], now because it fails to detect a newer eigen3. Upstream commit d8ce92b61ce356bc2764e13f0d4b9a5df48094c5 [2] improved handling of finding eigen and solves the problem. After applying this fix, I found that it also fails on arm64 architecture [3], due to a different reason. This one can be fixed with upstream commit fab08afd7000ac6000358a7c79e95cc1940e1c39 [4] test: increase DistGeomHelpers compareConfs tolerance to 0.1 Please consider applying these patches as well as the one reported on #1146588, to get rdkit to build successfully. Happy hacking, [1]: https://debusine.debian.net/debian/r-python-python3.15/artifact/4631477/ [2]: https://github.com/rdkit/rdkit/commit/d8ce92b61ce356bc2764e13f0d4b9a5df48094c5 [3]: https://debusine.debian.net/debian/r-python-python3.15/artifact/4632989/ [4]: https://github.com/rdkit/rdkit/commit/fab08afd7000ac6000358a7c79e95cc1940e1c39 -- "Can you imagine what I would do if I could do all I can?" -- Sun Tzu Saludos /\/\ /\ >< `/ --aAdYj61fnbEhkwUL Content-Type: text/x-diff; charset=us-ascii Content-Disposition: attachment; filename=improved_handling_of_finding_eigen.patch Content-Transfer-Encoding: quoted-printable =46rom: Greg Landrum <greg.landrum@gmail.com> Date: Wed, 2 Sep 2026 18:10:13 +0200 Subject: improved handling of finding eigen (#9543) Origin: upstream, https://github.com/rdkit/rdkit/commit/d8ce92b61ce356bc276= 4e13f0d4b9a5df48094c5 * improved handling of finding eigen Fixes #8896 --- CMakeLists.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -407,9 +407,9 @@ else(RDK_BUILD_PYTHON_WRAPPERS) find_package(Boost ${RDK_BOOST_VERSION} REQUIRED CONFIG) endif(RDK_BUILD_PYTHON_WRAPPERS) =20 -find_package(Eigen3) +find_package(Eigen3 NO_MODULE) if(RDK_BUILD_DESCRIPTORS3D) - if(NOT EIGEN3_FOUND) + if(NOT TARGET Eigen3::Eigen) add_subdirectory(External/Eigen) endif() target_compile_definitions(rdkit_base INTERFACE "-DRDK_BUILD_DESCRIPTORS= 3D") --aAdYj61fnbEhkwUL Content-Type: text/x-diff; charset=us-ascii Content-Disposition: attachment; filename=increase-compareconfs-tolerance.patch Content-Transfer-Encoding: quoted-printable =46rom: younes ouzza <166823313+younesouzza@users.noreply.github.com> Date: Wed, 22 Jul 2026 11:16:03 +0100 Subject: test: increase DistGeomHelpers compareConfs tolerance to 0.1 (#941= 3) Origin: upstream, https://github.com/rdkit/rdkit/commit/fab08afd7000ac60003= 58a7c79e95cc1940e1c39 This prevents false test failures on systems using -march=3Dnative, where compiler optimizations cause tiny, harmless math differences. (See issue #[9406]) --- Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) --- a/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp +++ b/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp @@ -135,7 +135,7 @@ void compareConfs(const RWMol *m, const =20 RDGeom::Point3D pt1i =3D conf1.getAtomPos(i); RDGeom::Point3D pt2i =3D conf2.getAtomPos(i); - CHECK((pt1i - pt2i).length() < 0.05); + CHECK((pt1i - pt2i).length() < 0.1); } } } // namespace --aAdYj61fnbEhkwUL-- ]