From patchwork Fri Jan 27 15:06:37 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: =?utf-8?q?Tor-bj=C3=B6rn_Claesson?= X-Patchwork-Id: 46448 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id BF32927BBED; Fri, 27 Jan 2023 15:15:27 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-0.4 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_INVALID,DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI, RCVD_IN_MSPIKE_H2,RCVD_IN_SBL_CSS,SPF_HELO_PASS,URIBL_BLOCKED autolearn=no autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 3042127BBE9 for ; Fri, 27 Jan 2023 15:15:26 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pLQRU-00068a-QE; Fri, 27 Jan 2023 10:15:04 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pLQRS-00067t-CE for guix-patches@gnu.org; Fri, 27 Jan 2023 10:15:02 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pLQRS-0007GA-3v for guix-patches@gnu.org; Fri, 27 Jan 2023 10:15:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pLQRR-0006GR-R1 for guix-patches@gnu.org; Fri, 27 Jan 2023 10:15:01 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60640] Gnu: Add gdcm Resent-From: =?utf-8?q?Tor-bj=C3=B6rn?= Claesson Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 27 Jan 2023 15:15:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 60640 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Ludovic =?utf-8?q?Court=C3=A8s?= Cc: 60640@debbugs.gnu.org Received: via spool by 60640-submit@debbugs.gnu.org id=B60640.167483244223996 (code B ref 60640); Fri, 27 Jan 2023 15:15:01 +0000 Received: (at 60640) by debbugs.gnu.org; 27 Jan 2023 15:14:02 +0000 Received: from localhost ([127.0.0.1]:38256 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pLQQU-0006Ex-9O for submit@debbugs.gnu.org; Fri, 27 Jan 2023 10:14:02 -0500 Received: from mail-ej1-f48.google.com ([209.85.218.48]:46746) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pLQQP-0006EI-2I for 60640@debbugs.gnu.org; Fri, 27 Jan 2023 10:14:00 -0500 Received: by mail-ej1-f48.google.com with SMTP id p26so3307571ejx.13 for <60640@debbugs.gnu.org>; Fri, 27 Jan 2023 07:13:57 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=mime-version:message-id:in-reply-to:date:subject:cc:to:from :user-agent:references:from:to:cc:subject:date:message-id:reply-to; bh=K6FODux5SAPSRqhuJkUcYfXRKj1GqUOc0xodbZZ9jV4=; b=KHNqJZ9HNWbVHmSvXj0lt78V/ZA3ts2a3BSmYvYgcDnqVB09xbzILLP4491xJQq6TR v1JMno5OX3zK9SuTUL6iUT6L+aq0XTmq2CgwOTAfWPdVYAmpTlWijAnjjLAPGYEzsVlV m7P+ExZWfoprAdpbGfMbVVAcoctYxfJOvpgrphauyA1OEfUus7Cs1PhYIG8fNPs0DH37 FLsW7T/uP18tMe5gSgltJbFp6VsCGaki5PQ2SpiiHjettzQi+3IC0cb438OUD/zAjcI0 E/IuUv8QkjQv8Ekj+0VMBF1daOwztffMWs0kMAtQCLAX/C9X6D0lCpL54+3xXyPZ71Ru xTuQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=mime-version:message-id:in-reply-to:date:subject:cc:to:from :user-agent:references:x-gm-message-state:from:to:cc:subject:date :message-id:reply-to; bh=K6FODux5SAPSRqhuJkUcYfXRKj1GqUOc0xodbZZ9jV4=; b=HD84JSNTjcU4Rxpf/oMODkoLo1gjVfjaCQxu6AJ+IJWMLzffzQLnh1wZxPXuhlBqmM UKzZqKnp2Qz7T4O4eKdOBg5GQJ7zOVH8FPen0C8Rm2uzpM7rtmNSr8QtOm1iw74O2mKi Rweqr+J+49XFQHXDok2onb1yj//NKZlB92PI1FIaLwhsBfbo0qsdgqu8FGGUvFKQ60Sz Z+2UIhMzMDL93L4lQx6uPzv1rkGsYNNkOs37YHntw/SjVUICPmjRzKnkEQzk1kAJgQJR V81DETKtOAaurKInurIOh9p/PG42V7GfTNVJkqv6TUbJYRcedukFz56AXG/HjTSYt1A3 cnaw== X-Gm-Message-State: AFqh2kpdVsfXQhU9f0GnxhyBxqj2LT0GN5LUKmsw9QAuyd21RWrwF5bD gq6z1kKvoJpRP0hh2mkWDOXhMVf8i0E= X-Google-Smtp-Source: AMrXdXuK9H/8D7gw74kBqMkUhxTauSSrodsjZeAGBiBJedaZ4d30lwFjV3QSmYBPtOUqYX9ZE00Y8g== X-Received: by 2002:a17:906:1485:b0:7d3:c516:6ef4 with SMTP id x5-20020a170906148500b007d3c5166ef4mr42753926ejc.20.1674832429687; Fri, 27 Jan 2023 07:13:49 -0800 (PST) Received: from barbar ([193.64.204.56]) by smtp.gmail.com with ESMTPSA id l23-20020a50d6d7000000b004a0b1d7e39csm2467266edj.51.2023.01.27.07.13.48 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 27 Jan 2023 07:13:48 -0800 (PST) References: <877cxyp1wf.fsf@gmail.com> <87y1qdo3qq.fsf@gmail.com> <87wn5rfldh.fsf_-_@gnu.org> <875ydau2vf.fsf@gmail.com> <87wn5q9epc.fsf@gnu.org> <87bkn1m4dj.fsf@gmail.com> <875yd5i5v8.fsf@gnu.org> <878rhqrzzv.fsf@gnu.org> User-agent: mu4e 1.8.13; emacs 28.2 From: =?utf-8?q?Tor-bj=C3=B6rn?= Claesson Date: Fri, 27 Jan 2023 17:06:37 +0200 In-reply-to: <878rhqrzzv.fsf@gnu.org> Message-ID: <878rhoxb6c.fsf@gmail.com> MIME-Version: 1.0 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: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches Hi! Ludovic Courtès writes: > > The following tests FAILED: > 195 - TestStrictScanner1 (Failed) > 196 - TestStrictScanner2_1 (Failed) > 197 - TestStrictScanner2 (Failed) > 198 - TestStrictScanner2_2 (Failed) > Errors while running CTest > > Passing #:parallel-tests? #f doesn’t help. > > Could you take a look? The TestStrictScanner tests fail because they expect TestWriter to have run, but we disabled it. TestWriter, TestAnonymizer4, and TestPrinter1 are also reported as failing in the GDCM ctest dashboard (https://open.cdash.org/index.php?project=GDCM). It is strange that they passed previously in my local checkout (they fail now, some change in the toolchain?) I will try to look into this. For now, here is a patch to ignore the remaining failures, giving us an installable package, and also updated patches to add a bin output and use more system libraries. Investigating the remaining failing tests and using more system libraries feels like a fairly big, if fun, task possibly involving work on GDCM as well as this package. Should we close this bug report if we have a working package when the attached patches are applied? From 467a7b614ccafa2de51a8e56a6ecf384fb6fa07b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tor-bj=C3=B6rn=20Claesson?= Date: Fri, 27 Jan 2023 17:03:36 +0200 Subject: [PATCH 3/3] gnu: gdcm: Use more system libraries. gnu: gdcm: Use more system libraries. --- gnu/packages/bioinformatics.scm | 48 ++++++++++++++++++++++++++++++--- 1 file changed, 45 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9a3c0f7d42..77b3388f2e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -18082,7 +18082,28 @@ (define-public gdcm (file-name (git-file-name name version)) (sha256 (base32 - "1rf0p7dnakjry0fa6ax1h762bn0l5n6ibfdxn077mjvwgpqan51l")))) + "1rf0p7dnakjry0fa6ax1h762bn0l5n6ibfdxn077mjvwgpqan51l")) + (modules '((guix build utils) + (ice-9 ftw))) + (snippet + '(begin + (define (unbundle? file) + (member file '("dicom3tools" + "gdcmexpat" + "gdcmutfcpp" + "gdcmuuid" + "gdcmzlib" + "getopt" + "KWStyle" + "pvrg" + "Release" + "VTK"))) + (with-directory-excursion "Utilities" + (for-each (lambda (utility) + (delete-file-recursively utility) + (substitute* "CMakeLists.txt" + (((string-append ".*/" utility "/.*")) ""))) + (scandir "." unbundle?))))))) (build-system cmake-build-system) (outputs '("out" "bin" "doc")) (arguments @@ -18123,8 +18144,29 @@ (define-public gdcm "-DGDCM_PDF_DOCUMENTATION:BOOL=OFF" (string-append "-DGDCM_INSTALL_DOC_DIR=" #$output:doc "/share/doc/" #$name) - "-DGDCM_BUILD_DOCBOOK_MANPAGES:BOOL=OFF"))) ; TODO: need ‘xsl-ns’ - (native-inputs (list doxygen graphviz)) + "-DGDCM_BUILD_DOCBOOK_MANPAGES:BOOL=OFF" ; TODO: need ‘xsl-ns’ + ;; Libraries + "-DGDCM_USE_SYSTEM_EXPAT:BOOL=ON" + "-DGDCM_USE_SYSTEM_LIBXML2:BOOL=ON" + "-DGDCM_USE_SYSTEM_OPENSSL:BOOL=ON" + "-DGDCM_USE_SYSTEM_POPPLER:BOOL=ON" + "-DGDCM_USE_SYSTEM_UUID:BOOL=ON" + "-DGDCM_USE_SYSTEM_ZLIB:BOOL=ON" + ;; TODO: Unbundle these if possible. + "-DGDCM_USE_SYSTEM_CHARLS:BOOL=OFF" + "-DGDCM_USE_SYSTEM_JSON:BOOL=OFF" + "-DGDCM_USE_SYSTEM_LJPEG:BOOL=OFF" + "-DGDCM_USE_SYSTEM_OPENJPEG:BOOL=OFF" + "-DGDCM_USE_SYSTEM_PAPYRUS3:BOOL=OFF" + "-DGDCM_USE_SYSTEM_SOCKETXX:BOOL=OFF"))) + (inputs (list + expat + libxml2 + openssl + poppler + `(,util-linux "lib") + zlib)) + (native-inputs (list doxygen graphviz pkg-config)) (home-page "https://gdcm.sourceforge.net/wiki/index.php/Main_Page") (synopsis "Grassroots DICOM library") (description -- 2.39.1