From unknown Wed Jun 18 00:25:56 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#57143 <57143@debbugs.gnu.org> To: bug#57143 <57143@debbugs.gnu.org> Subject: Status: python-dolfin-adjoint / FEniCS fails to build Reply-To: bug#57143 <57143@debbugs.gnu.org> Date: Wed, 18 Jun 2025 07:25:56 +0000 retitle 57143 python-dolfin-adjoint / FEniCS fails to build reassign 57143 guix submitter 57143 Andreas Enge severity 57143 normal thanks From debbugs-submit-bounces@debbugs.gnu.org Thu Aug 11 14:32:18 2022 Received: (at submit) by debbugs.gnu.org; 11 Aug 2022 18:32:18 +0000 Received: from localhost ([127.0.0.1]:54992 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oMCyf-0006Gk-Qx for submit@debbugs.gnu.org; Thu, 11 Aug 2022 14:32:18 -0400 Received: from lists.gnu.org ([209.51.188.17]:33792) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oMCyc-0006GM-DU for submit@debbugs.gnu.org; Thu, 11 Aug 2022 14:32:14 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:56532) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oMCyb-0001HF-Uv for bug-guix@gnu.org; Thu, 11 Aug 2022 14:32:14 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:38482) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oMCyZ-00048z-1R for bug-guix@gnu.org; Thu, 11 Aug 2022 14:32:12 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 4F57BC96; Thu, 11 Aug 2022 20:32:07 +0200 (CEST) X-Virus-Scanned: Debian amavisd-new at aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id zBTv6aQRjqW0; Thu, 11 Aug 2022 20:32:06 +0200 (CEST) Received: from jurong (unknown [IPv6:2001:861:c4:f2f0:1ce9:67cd:7487:edd5]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 9E31F3CE; Thu, 11 Aug 2022 20:32:06 +0200 (CEST) Date: Thu, 11 Aug 2022 20:32:02 +0200 From: Andreas Enge To: bug-guix@gnu.org Subject: python-dolfin-adjoint / FEniCS fails to build Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Received-SPF: pass client-ip=185.233.100.1; envelope-from=andreas@enge.fr; helo=hera.aquilenet.fr X-Spam_score_int: -18 X-Spam_score: -1.9 X-Spam_bar: - X-Spam_report: (-1.9 / 5.0 requ) BAYES_00=-1.9, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.6 (-) X-Debbugs-Envelope-To: submit Cc: Paul Garlick X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.6 (--) Hello, when updating python-sympy, I noticed that its dependent python-dolfin-adjoint fails to build. Probably this was also true before, since we do not have a substitute. I think the problem was in FEniCS, with an assertion failure, so my impression was that the code computed a wrong solution. It would be nice if someone with special knowledge could have a look; some of the packages in the family also have updates available (but not dolfin itself if I saw correctly). Andreas From debbugs-submit-bounces@debbugs.gnu.org Mon Jul 24 07:55:44 2023 Received: (at 57143) by debbugs.gnu.org; 24 Jul 2023 11:55:44 +0000 Received: from localhost ([127.0.0.1]:41986 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qNuAC-00007i-0X for submit@debbugs.gnu.org; Mon, 24 Jul 2023 07:55:44 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:58904) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qNuA7-00007L-Hd for 57143@debbugs.gnu.org; Mon, 24 Jul 2023 07:55:42 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 59206F92; Mon, 24 Jul 2023 13:55:33 +0200 (CEST) X-Virus-Scanned: Debian amavisd-new at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id qzRBxhnuAg61; Mon, 24 Jul 2023 13:55:32 +0200 (CEST) Received: from jurong (unknown [IPv6:2001:861:c4:f2f0::c64]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 83F5DEB; Mon, 24 Jul 2023 13:55:32 +0200 (CEST) Date: Mon, 24 Jul 2023 13:55:31 +0200 From: Andreas Enge To: 57143@debbugs.gnu.org Subject: Test failure in python-dolfin-adjoint Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 57143 Cc: Paul Garlick X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Hello, below are more details on the current test failure of python-dolfin-adjoint version 2019.1.0. Maybe an option would be to try to update to a newer version? There is 2019.1.2. Andreas =================================== FAILURES =================================== _____________________________ test_read_checkpoint _____________________________ def test_read_checkpoint(): with stop_annotating(): N = 15 mesh = UnitSquareMesh(N, N) V = FunctionSpace(mesh, "CG", 1) x = SpatialCoordinate(mesh) v = project(x[0]*x[1]*cos(x[1]), V) out = XDMFFile(file_from_curr_dir("scalar.xdmf")) out.write_checkpoint(v, "u", 0.0) out.close() exact = assemble(v*dx) mesh = UnitSquareMesh(N, N) V = FunctionSpace(mesh, "CG", 1) v = Function(V) c = Control(v) J = assemble(v*dx) infile = XDMFFile(file_from_curr_dir("scalar.xdmf")) u = Function(V) > infile.read_checkpoint(u,'u', -1) tests/fenics_adjoint/test_io.py:38: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = args = (Coefficient(FunctionSpace(Mesh(VectorElement(FiniteElement('Lagrange', triangle, 1), dim=2), 38754), FiniteElement('Lagrange', triangle, 1)), 38769), 'u', -1) kwargs = {}, annotate = True def XDMFFile_read_checkpoint(self, *args, **kwargs): annotate = annotate_tape(kwargs) > output = __XDMFFile_read_checkpoint__(self, *args, **kwargs) E RuntimeError: basic_string::_M_construct null not valid /gnu/store/p7hjddizapgmdk62dpvmrdkac0d4l3r9-python-dolfin-adjoint-2019.1.0/lib/python3.10/site-packages/fenics_adjoint/types/io.py:48: RuntimeError ----------------------------- Captured stdout call ----------------------------- Calling FFC just-in-time (JIT) compiler, this may take some time. ------------------------------ Captured log call ------------------------------- Level 25 FFC:log.py:127 Calling FFC just-in-time (JIT) compiler, this may take some time. INFO FFC:log.py:127 Compiling form ffc_form_e905624fad7a62b101d5d4bc784070d31ec0cc46 INFO FFC:log.py:127 Compiler stage 1: Analyzing form(s) INFO FFC:log.py:127 ----------------------------------- DEBUG FFC:log.py:127 Preprocessing form using 'uflacs' representation family. INFO FFC:log.py:127 INFO FFC:log.py:127 Geometric dimension: 2 Number of cell subdomains: 0 Rank: 1 Arguments: '(v_0)' Number of coefficients: 0 Coefficients: '[]' Unique elements: 'CG1(?,?), Vector<2 x CG1(?,?)>' Unique sub elements: 'CG1(?,?), Vector<2 x CG1(?,?)>' INFO FFC:log.py:127 representation: auto --> uflacs INFO FFC:log.py:127 quadrature_rule: auto --> default INFO FFC:log.py:127 quadrature_degree: auto --> 6 INFO FFC:log.py:127 quadrature_degree: 6 INFO FFC:log.py:127 INFO FFC:log.py:127 Compiler stage 1 finished in 0.00596237 seconds. INFO FFC:log.py:127 Compiler stage 2: Computing intermediate representation INFO FFC:log.py:127 ------------------------------------------------------- INFO FFC:log.py:127 Computing representation of 0 elements INFO FFC:log.py:127 Computing representation of 0 dofmaps INFO FFC:log.py:127 Computing representation of 0 coordinate mappings INFO FFC:log.py:127 Computing representation of integrals INFO FFC:log.py:127 Computing uflacs representation DEBUG FFC:log.py:127 Reusing element from cache DEBUG FFC:log.py:127 Reusing element from cache DEBUG FFC:log.py:127 Reusing element from cache DEBUG FFC:log.py:127 Reusing element from cache DEBUG FFC:log.py:127 Reusing element from cache DEBUG FFC:log.py:127 Reusing element from cache DEBUG FFC:log.py:127 Reusing element from cache DEBUG FFC:log.py:127 Reusing element from cache DEBUG FFC:log.py:127 Reusing element from cache DEBUG FFC:log.py:127 Reusing element from cache DEBUG FFC:log.py:127 Reusing element from cache DEBUG FFC:log.py:127 Reusing element from cache DEBUG FFC:log.py:127 Reusing element from cache DEBUG UFL:log.py:127 Blocks of each mode: 1 full INFO FFC:log.py:127 Computing representation of forms INFO FFC:log.py:127 INFO FFC:log.py:127 Compiler stage 2 finished in 0.0164835 seconds. INFO FFC:log.py:127 Compiler stage 3: Optimizing intermediate representation INFO FFC:log.py:127 -------------------------------------------------------- INFO FFC:log.py:127 Optimizing uflacs representation INFO FFC:log.py:127 INFO FFC:log.py:127 Compiler stage 3 finished in 0.000202894 seconds. INFO FFC:log.py:127 Compiler stage 4: Generating code INFO FFC:log.py:127 --------------------------------- INFO FFC:log.py:127 Generating code for 0 finite_element(s) INFO FFC:log.py:127 Generating code for 0 dofmap(s) INFO FFC:log.py:127 Generating code for 0 coordinate_mapping(s) INFO FFC:log.py:127 Generating code for integrals INFO FFC:log.py:127 Generating code from ffc.uflacs representation INFO FFC:log.py:127 Generating code for forms INFO FFC:log.py:127 INFO FFC:log.py:127 Compiler stage 4 finished in 0.00399137 seconds. INFO FFC:log.py:127 Compiler stage 4.1 finished in 9.53674e-07 seconds. INFO FFC:log.py:127 Compiler stage 5: Formatting code INFO FFC:log.py:127 --------------------------------- INFO FFC:log.py:127 INFO FFC:log.py:127 Compiler stage 5 finished in 0.000437498 seconds. INFO FFC:log.py:127 FFC finished in 0.0274181 seconds. =============================== warnings summary =============================== ../../../gnu/store/v36c8jmb0316czxkqajpkai70kjkmkfy-fenics-2019.1.0.post0/lib/python3.10/site-packages/dolfin_utils/test/fixtures.py:96 /gnu/store/v36c8jmb0316czxkqajpkai70kjkmkfy-fenics-2019.1.0.post0/lib/python3.10/site-packages/dolfin_utils/test/fixtures.py:96: PytestDeprecationWarning: @pytest.yield_fixture is deprecated. Use @pytest.fixture instead; they are the same. @pytest.yield_fixture(scope="function") ../../../gnu/store/v36c8jmb0316czxkqajpkai70kjkmkfy-fenics-2019.1.0.post0/lib/python3.10/site-packages/dolfin_utils/test/fixtures.py:230 /gnu/store/v36c8jmb0316czxkqajpkai70kjkmkfy-fenics-2019.1.0.post0/lib/python3.10/site-packages/dolfin_utils/test/fixtures.py:230: PytestDeprecationWarning: @pytest.yield_fixture is deprecated. Use @pytest.fixture instead; they are the same. @pytest.yield_fixture(scope="function") ../../../gnu/store/v36c8jmb0316czxkqajpkai70kjkmkfy-fenics-2019.1.0.post0/lib/python3.10/site-packages/dolfin_utils/test/fixtures.py:255 /gnu/store/v36c8jmb0316czxkqajpkai70kjkmkfy-fenics-2019.1.0.post0/lib/python3.10/site-packages/dolfin_utils/test/fixtures.py:255: PytestDeprecationWarning: @pytest.yield_fixture is deprecated. Use @pytest.fixture instead; they are the same. def pushpop_parameters(): -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ FAILED tests/fenics_adjoint/test_io.py::test_read_checkpoint - RuntimeError: ... = 1 failed, 125 passed, 9 skipped, 1 xfailed, 3 warnings in 839.66s (0:13:59) == From debbugs-submit-bounces@debbugs.gnu.org Mon Mar 31 17:55:29 2025 Received: (at 57143-done) by debbugs.gnu.org; 31 Mar 2025 21:55:29 +0000 Received: from localhost ([127.0.0.1]:43265 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tzN6O-0007Dt-D3 for submit@debbugs.gnu.org; Mon, 31 Mar 2025 17:55:28 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:45004) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tzN6E-0007AJ-Kj for 57143-done@debbugs.gnu.org; Mon, 31 Mar 2025 17:55:19 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 826523F4; Mon, 31 Mar 2025 23:55:12 +0200 (CEST) Authentication-Results: hera.aquilenet.fr; none X-Virus-Scanned: Debian amavis at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavis, port 10024) with ESMTP id rRItMYOZMt_u; Mon, 31 Mar 2025 23:55:12 +0200 (CEST) Received: from jurong (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 7E17E1B6; Mon, 31 Mar 2025 23:55:10 +0200 (CEST) Date: Mon, 31 Mar 2025 23:55:08 +0200 From: Andreas Enge To: 57143-done@debbugs.gnu.org Subject: Close Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline X-Rspamd-Queue-Id: 826523F4 X-Spamd-Result: default: False [8.40 / 15.00]; SPAM_FLAG(5.00)[]; NEURAL_SPAM(3.00)[0.999]; MID_RHS_NOT_FQDN(0.50)[]; MIME_GOOD(-0.10)[text/plain]; FROM_EQ_ENVFROM(0.00)[]; MIME_TRACE(0.00)[0:+]; RCPT_COUNT_ONE(0.00)[1]; ARC_NA(0.00)[]; TO_DN_NONE(0.00)[]; TO_MATCH_ENVRCPT_ALL(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; RCVD_VIA_SMTP_AUTH(0.00)[]; FROM_HAS_DN(0.00)[]; RCVD_TLS_ALL(0.00)[] X-Spam-Level: ******** X-Rspamd-Action: add header X-Spamd-Bar: ++++++++ X-Rspamd-Server: hera X-Spam: Yes X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 57143-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) This will be handled in https://issues.guix.gnu.org/77195 . Andreas From unknown Wed Jun 18 00:25:56 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Tue, 29 Apr 2025 11:24:18 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator