From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp11.migadu.com ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms0.migadu.com with LMTPS id cCO7H4TUVGLsqgAAgWs5BA (envelope-from ) for ; Tue, 12 Apr 2022 03:23:16 +0200 Received: from aspmx1.migadu.com ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp11.migadu.com with LMTPS id KGYsHYTUVGIsWQEA9RJhRA (envelope-from ) for ; Tue, 12 Apr 2022 03:23:16 +0200 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id 7449332BCB for ; Tue, 12 Apr 2022 03:23:15 +0200 (CEST) Received: from localhost ([::1]:44210 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1ne5FS-0005Ps-KU for larch@yhetil.org; Mon, 11 Apr 2022 21:23:14 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:42132) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ne5FH-0005MJ-5i for guix-patches@gnu.org; Mon, 11 Apr 2022 21:23:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:52677) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1ne5FG-0001ef-TA for guix-patches@gnu.org; Mon, 11 Apr 2022 21:23:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1ne5FG-0003Vy-Ji for guix-patches@gnu.org; Mon, 11 Apr 2022 21:23:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#54869] [PATCH 0/5] gnu: python-vedo: Update to 2022.2.0 and sanity-check failures. Resent-From: "Paul A. Patience" Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 12 Apr 2022 01:23:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 54869 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 54869@debbugs.gnu.org Cc: "Paul A. Patience" X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.164972653213361 (code B ref -1); Tue, 12 Apr 2022 01:23:02 +0000 Received: (at submit) by debbugs.gnu.org; 12 Apr 2022 01:22:12 +0000 Received: from localhost ([127.0.0.1]:46552 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ne5ES-0003TP-61 for submit@debbugs.gnu.org; Mon, 11 Apr 2022 21:22:12 -0400 Received: from lists.gnu.org ([209.51.188.17]:58240) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ne5EQ-0003TA-Hu for submit@debbugs.gnu.org; Mon, 11 Apr 2022 21:22:10 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41776) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ne5EQ-0003st-8I for guix-patches@gnu.org; Mon, 11 Apr 2022 21:22:10 -0400 Received: from mail-40136.proton.ch ([185.70.40.136]:43874) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ne5EM-0001V2-HM for guix-patches@gnu.org; Mon, 11 Apr 2022 21:22:09 -0400 Date: Tue, 12 Apr 2022 01:21:57 +0000 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=apatience.com; s=protonmail2; t=1649726521; bh=ZLa0rdYLK3F85iwt/eaQbcs+edfsr5oxE4QB2GRbpW0=; h=Date:To:From:Cc:Reply-To:Subject:Message-ID:From:To:Cc:Date: Subject:Reply-To:Feedback-ID:Message-ID; b=gFGa0Ncr+jCD+D/ArowV5poT1Vz+1baNUN5jCZNz+KW1EUnSJAzUEx3ztsIjc8lbw K7sKn+KgRfpEHTkRJfm4poAMuBiasjKK2NoTjHES+oIERzv7WfqzPD6YkPGnnjGaNL QSEbHxwxZg9hwQOINwz23P9rJPEJCFm847UwaYNC6laVbaCOtNXMBkwpG4uG1+BRN1 2hTjt9TF8lIAEUJhSQvabBPYCHV3b6u3gT3/MimObxfjn1Qz5QxiTCYXZRpASv3x8F bDefKnDpgLNea1yvuTw/S83ShbEHwcS91rTS51KwK0euLOlCGFjk+8QL/rDR4iWfYW K39WtARDXPHng== From: "Paul A. Patience" Message-ID: <20220412012143.30573-1-paul@apatience.com> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Received-SPF: pass client-ip=185.70.40.136; envelope-from=paul@apatience.com; helo=mail-40136.proton.ch X-Spam_score_int: -19 X-Spam_score: -2.0 X-Spam_bar: -- X-Spam_report: (-2.0 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_MSPIKE_H4=0.001, RCVD_IN_MSPIKE_WL=0.001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01, URIBL_SBL_A=0.1 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Reply-To: "Paul A. Patience" Errors-To: guix-patches-bounces+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Migadu-Flow: FLOW_IN X-Migadu-To: larch@yhetil.org X-Migadu-Country: US ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1649726596; h=from:from:sender:sender:reply-to:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-type:content-type: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:list-id:list-help: list-unsubscribe:list-subscribe:list-post:dkim-signature; bh=ZLa0rdYLK3F85iwt/eaQbcs+edfsr5oxE4QB2GRbpW0=; b=kfbHgaNFPWsgWoi1bL6yrebsPHh/3kDy0F7dU40JV5Wx6puJdsJrsaKXJFpMH3Mf4fUZ5h TTxBvBFPrOafWYGTi9cUKSroMnH6NYyP/pDGQsTxP/qpva4+jkIn2yKi1OV1iQ6IyRaUXP UtdizrvUqM0bbH1JgF2dASfeJUBcm/vJUo7Ip81mh57OG412F6CiUxvjATjY2JYlaxcrQi Dbao26G52QkpYYABiuYVLX62bgiTkrb9khlSXoiy4eLWoPoDeIYH8+znMhX44JAPZgwcuc 6zgYeLroGsCNADwjaawtD4eS+eEezau4UlX0d0j11hOrxetFwdpX4eVumPpsew== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1649726596; a=rsa-sha256; cv=none; b=W7hhUB0Q5aY2sKnBPntjuwkNqITc5MhRBfZFKvl83oeeY+xxrYh7vVt5RfccsG4I/yy0vn FzMPZ684dxknFWQhjHcvDEsKDC3ACR1kEZxHnauhBr0IthnqUysCjvFzJIhzoaFuz0Qxop 4XutzA0q396Ln02/YxMa7e7NThBQQ3Y8QUNCaVorCFdKkbzLDNdsh0w22jhhY33eWEBwCx CqbRYk+VLVB54x8QMdTv3oFdBdAu2unxrP243yd7rgNIAzzFTTChAoaEqiISla1w54RzjT ru2CTrcs2KlLDAzuJz37P+M25fAb4mlGzDhsiooIGK5XSmAdQHCMA51bcrjV7w== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=apatience.com header.s=protonmail2 header.b=gFGa0Ncr; dmarc=none; spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: 3.23 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=apatience.com header.s=protonmail2 header.b=gFGa0Ncr; dmarc=none; spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: 7449332BCB X-Spam-Score: 3.23 X-Migadu-Scanner: scn1.migadu.com X-TUID: QQOstv4Ooqeg Hello, The following patch series updates python-vedo to its latest version, and also adds support for the #:tests? flag to fenics-dolfin, fenics and python-vedo. Unfortunately, I can't get fenics or python-vedo to build except by deleting the sanity-check phase, and this even before applying any of my patches. (I've confirmed that my patches are correct by testing the builds without sanity-checks, so applying them shouldn't be an issue.) The following is the sanity-check error obtained when building fenics: starting phase `sanity-check' validating 'fenics-dolfin' /gnu/store/lkb8mx8dk82znkzfgnx1k1mklaj9b34d-feni= cs-2019.1.0.post0/lib/python3.9/site-packages ...checking requirements: ERROR: fenics-dolfin=3D=3D2019.1.0 ContextualVers= ionConflict(pybind11 2.8.1 (/gnu/store/qmxw9dqqywrlllzlidv09f2nazirjwk7-pyb= ind11-2.8.1/lib/python3.9/site-packages), Requirement.parse('pybind11=3D=3D= 2.2.4'), {'fenics-dolfin'}) error: in phase 'sanity-check': uncaught exception: %exception #<&invoke-error program: "python" arguments: ("/gnu/store/35ix1m= 6m8a5s21j02ajhdyqxb2xkshfb-sanity-check.py" "/gnu/store/lkb8mx8dk82znkzfgnx= 1k1mklaj9b34d-fenics-2019.1.0.post0/lib/python3.9/site-packages") exit-stat= us: 1 term-signal: #f stop-signal: #f> phase `sanity-check' failed after 0.2 seconds Note that it complains that pybind11 is not at version 2.2.4, but when fenics was last updated (in commit 37bb0d1eafb3f08a204aed8c928cbf7cbc69cd19= ), the version of pybind11 at the time was 2.3.0, so this would appear to be either a new issue, or an issue specific to my machine (foreign distro). The sanity-check errors from vedo are similarly bizarre -- they complain about a missing vtk, but it is there in the propagated inputs. With old version of python-vedo: starting phase `sanity-check' validating 'vedo' /gnu/store/4h10widg2y0nhvacz8mricn187qzw9dq-python-vedo-2= 021.0.3/lib/python3.9/site-packages ...checking requirements: ERROR: vedo=3D=3D2021.0.3 DistributionNotFound(Re= quirement.parse('vtk'), {'vedo'}) error: in phase 'sanity-check': uncaught exception: %exception #<&invoke-error program: "python" arguments: ("/gnu/store/35ix1m= 6m8a5s21j02ajhdyqxb2xkshfb-sanity-check.py" "/gnu/store/4h10widg2y0nhvacz8m= ricn187qzw9dq-python-vedo-2021.0.3/lib/python3.9/site-packages") exit-statu= s: 1 term-signal: #f stop-signal: #f> phase `sanity-check' failed after 0.2 seconds With updated version of python-vedo (i.e., including the python-deprecated propagated input): starting phase `sanity-check' validating 'vedo' /gnu/store/a6g20gkvi1l70arh2rm53x7gm30dzqcp-python-vedo-2= 022.2.0/lib/python3.9/site-packages ...checking requirements: ERROR: vedo=3D=3D2022.2.0 DistributionNotFound(Re= quirement.parse('vtk<9.1.0'), {'vedo'}) error: in phase 'sanity-check': uncaught exception: %exception #<&invoke-error program: "python" arguments: ("/gnu/store/35ix1m= 6m8a5s21j02ajhdyqxb2xkshfb-sanity-check.py" "/gnu/store/a6g20gkvi1l70arh2rm= 53x7gm30dzqcp-python-vedo-2022.2.0/lib/python3.9/site-packages") exit-statu= s: 1 term-signal: #f stop-signal: #f> phase `sanity-check' failed after 0.2 seconds The latest commit of fenics (there isn't a newer release than the one included in Guix) no longer requires a specific version of pybind11 [1], and in addition, it seems the focus is on the dolfinx project [2] rather than dolfin (dolfin is already considered legacy [3]), so perhaps it would be worth updating the fenics package to the latest git commit. That wouldn't solve the problem python-vedo's sanity-check is encountering, though. Any help would be appreciated. Best regards, Paul [1]: https://bitbucket.org/fenics-project/dolfin/src/d29e24d19eab5200a55e43= a3e18e1f38214fb5a8/python/setup.py#lines-22) [2]: https://github.com/FEniCS/dolfinx [3]: https://fenicsproject.org/ Paul A. Patience (5): gnu: fenics-dolfin: Honor #:tests? flag. gnu: fenics: Honor #:tests? flag. gnu: python-vedo: Honor #:tests? flag. gnu: python-vedo: Remove input labels. gnu: python-vedo: Update to 2022.2.0. gnu/packages/python-science.scm | 35 ++++++++++++++++---------------- gnu/packages/simulation.scm | 36 +++++++++++++++++---------------- 2 files changed, 37 insertions(+), 34 deletions(-) -- 2.35.1