From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp11.migadu.com ([2001:41d0:8:6d80::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms5.migadu.com with LMTPS id mPq0MN0Ew2OsTgEAbAwnHQ (envelope-from ) for ; Sat, 14 Jan 2023 20:39:09 +0100 Received: from aspmx1.migadu.com ([2001:41d0:8:6d80::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp11.migadu.com with LMTPS id sPa0MN0Ew2OfPAAA9RJhRA (envelope-from ) for ; Sat, 14 Jan 2023 20:39:09 +0100 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 660B9DD8C for ; Sat, 14 Jan 2023 20:39:09 +0100 (CET) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pGmMq-0008Hx-JQ; Sat, 14 Jan 2023 14:39:04 -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 1pGmMo-0008Hh-JI for guix-patches@gnu.org; Sat, 14 Jan 2023 14:39:02 -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 1pGmMo-0004En-8a for guix-patches@gnu.org; Sat, 14 Jan 2023 14:39:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pGmMn-0007KM-Td for guix-patches@gnu.org; Sat, 14 Jan 2023 14:39:01 -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: Sat, 14 Jan 2023 19:39:01 +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=B60640.167372509328092 (code B ref 60640); Sat, 14 Jan 2023 19:39:01 +0000 Received: (at 60640) by debbugs.gnu.org; 14 Jan 2023 19:38:13 +0000 Received: from localhost ([127.0.0.1]:55610 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pGmM1-0007J2-DP for submit@debbugs.gnu.org; Sat, 14 Jan 2023 14:38:13 -0500 Received: from mail-lf1-f46.google.com ([209.85.167.46]:43849) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pGmLz-0007Ij-P2 for 60640@debbugs.gnu.org; Sat, 14 Jan 2023 14:38:12 -0500 Received: by mail-lf1-f46.google.com with SMTP id f34so37547013lfv.10 for <60640@debbugs.gnu.org>; Sat, 14 Jan 2023 11:38:11 -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=H40FKu0OpkYCEUGHrzEcRMhsAgCoIHfjWJdvaU+A3+k=; b=I51+TJrcdWr0qveNwv5rHgKLqexIfR2B1YL1ZY6G6YOGToE0UInhJCiksxdu0zzw6o J61pKzQnHrtu5qw/LASNua6jsu0y69h92GKI1AcS8FZl2d6caPsk4y5SJ1e+BBc4VkyL VGM487V1Rb7W2vNtfreeePdfbOrF329BMKPgYra8+EzKUbBte04gJeWwwvoowxuRkXOF qRsmzI5zVr2I4WPiYvb5VKl6mtD+sG4GFjCuTNYDuJmlgD/m5VGpYCKr1GLsxZEY83gJ qoywA2mNygG+bTu/LJ66dGsrh7SwMkGooxKi5cTFnytrgkO+yiZNT2WouGT/nSmbxXgI uLKQ== 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=H40FKu0OpkYCEUGHrzEcRMhsAgCoIHfjWJdvaU+A3+k=; b=irB4JRUR0wnFJn3EU/IPVAjI3sd3bg5tJlG6KoBnvs6AxlHuaY/kB5R3gBVfinvfVy TcpJhjbKdtIyoeglIJeyb2/iZZ5XrKrveh5c6QVFr1dIAwibONv5G5vEvmsm5efMN1I7 J08dS/dRTllXCTmkpT8b/7EiX0kmaZHuRBe53qEW0xhtow03IrI6JfDXjqdaxM0HXG6d uAaTrLfg9SJ2xIXdkrez2454TIy46UIU9yuwXP7B+uRxaPbKLr5n/KLQ4yujQ6KtJSn0 TD1aUqUIP4197Os+6DPXASGW26hyU6kWXmNfIK31DCqdRs/IKGq58nt49tL7jVJXz4vp YHsQ== X-Gm-Message-State: AFqh2kpx6X4c0xPT5PA4UbW6fziKU/TXX+UBXXSa3JvGYU6JuDIV5+TS Tm/pBISOvR1E0RiwTO99JFmrVAQI1wo= X-Google-Smtp-Source: AMrXdXvInbt1jeUf+WYO02AfgVM78x9Kb2Elybrb8bbuSIlJ1x38LUqXluK40qRgppwMhrs6U+vBqQ== X-Received: by 2002:a19:a40b:0:b0:4b5:9183:5ad0 with SMTP id q11-20020a19a40b000000b004b591835ad0mr1367055lfc.63.1673725085244; Sat, 14 Jan 2023 11:38:05 -0800 (PST) Received: from barbar ([193.64.204.56]) by smtp.gmail.com with ESMTPSA id b21-20020a056512305500b004cf07a0051csm1082847lfb.228.2023.01.14.11.38.04 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sat, 14 Jan 2023 11:38:04 -0800 (PST) References: <877cxyp1wf.fsf@gmail.com> <87y1qdo3qq.fsf@gmail.com> <87wn5rfldh.fsf_-_@gnu.org> <875ydau2vf.fsf@gmail.com> <87wn5q9epc.fsf@gnu.org> User-agent: mu4e 1.8.13; emacs 28.2 From: =?UTF-8?Q?Tor-bj=C3=B6rn?= Claesson Date: Sat, 14 Jan 2023 21:34:44 +0200 In-reply-to: <87wn5q9epc.fsf@gnu.org> Message-ID: <877cxonbz7.fsf@gmail.com> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" 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+larch=yhetil.org@gnu.org Sender: guix-patches-bounces+larch=yhetil.org@gnu.org X-Migadu-Country: US X-Migadu-Flow: FLOW_IN ARC-Seal: i=1; s=key1; d=yhetil.org; t=1673725149; a=rsa-sha256; cv=none; b=WLjFWChP+KaXUp7if0Lno4x635X0RI2S40doe7TpU7+8Px8PmeAqWupV/39JFoE0GXZl17 b3oItR9AxuCIynKPOxJ3GAvUF0fAXHsQqJfeJrUrj7IE671IKgOcGj5ZgM2B4K0pdgxMBw fIuDkUku4jkfzGq+EAPYo24UhaGX0pGCaQDIERlioIDlDMmzRDSznJXt6bYQBZv7VqU9+H RNRnpPvErYinJoWWjdRMeW16De7FBK4LIG2AdQ71srW0l/AFa+CUUV51xiLi2plbkreU6t hIFB2aCd174D8DJdlCRVpjDXOcue6EelX9WcLatG3SwG0swrkDMsdTlIwc1O1A== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=I51+TJrc; 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"; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none) ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1673725149; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-type:content-type:resent-cc:resent-from:resent-sender: resent-message-id:in-reply-to:in-reply-to:references:references: list-id:list-help:list-unsubscribe:list-subscribe:list-post: dkim-signature; bh=H40FKu0OpkYCEUGHrzEcRMhsAgCoIHfjWJdvaU+A3+k=; b=OJYlWJ8uOzO9oMT4RjxrGoubiDXWQ7cEmDLRwDlAbvRqItcN2vzTd4J4CrGU0fuxO8PIVu wPQEauNj5uUtZkxXSVMPH5fT/iqBBVRcGTr63j9bYH80fT2cNaCiKvSMhfdsSZFMnvJycC OztUpkmc4+hJ6XutlvepqqlYGvDJV96beSTelBPp6t3zQlC0FWM+wtM8SN0Lwt7w7EJVlL Pg/6iGevpl8STtGDqseB3qmwmfnepSLcL485R+Dz7djQNqmlz1PM+JdjP2s3x5FueNXIwG HE6ybFTRKJjMLpLrdpKNu30ZhK+zM/J5x0DbeoFBxdffkPc/V5ClZCnwNcU0MQ== X-Migadu-Spam-Score: -0.71 X-Spam-Score: -0.71 X-Migadu-Queue-Id: 660B9DD8C X-Migadu-Scanner: scn1.migadu.com Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=I51+TJrc; 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"; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none) X-TUID: f6PM1/v9eYZ3 --=-=-= Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable And here is a patch which adds a "bin" output containing various utility-programs. Sorry for some slight spamming, but things suddenly start= ed working=3D) With this I think the package is functionally complete and I will move on to using system libraries. Cheers, Tor-bj=C3=B6rn Claesson --=-=-= Content-Type: text/x-patch; charset=utf-8 Content-Disposition: attachment; filename=0001-gnu-gdcm-Add-output-bin.patch Content-Transfer-Encoding: quoted-printable >From 1b680bf73c6a62efd40d608c25e9b7815f03d786 Mon Sep 17 00:00:00 2001 From: =3D?UTF-8?q?Tor-bj=3DC3=3DB6rn=3D20Claesson?=3D Date: Sat, 14 Jan 2023 21:17:23 +0200 Subject: [PATCH] gnu: gdcm: Add output "bin" --- gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++------ 1 file changed, 18 insertions(+), 6 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.= scm index aa54ec7ff7..e45d33ec2b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -17855,29 +17855,41 @@ (define-public gdcm (base32 "1w78cmm9q7aavs7svdkl4dgilcqk4yazci9m6x7icrssb7cj991i")))) (build-system cmake-build-system) - (outputs '("out" "doc")) + (outputs '("out" "bin" "doc")) (arguments (list #:phases #~(modify-phases %standard-phases (add-before 'build 'set-HOME - ;; The build spams =E2=80=98Fontconfig error: No writable= cache - ;; directories=E2=80=99 in a seemingly endless loop other= wise. - (lambda _ - (setenv "HOME" "/tmp")))) + ;; The build spams =E2=80=98Fontconfig error: No writable cache + ;; directories=E2=80=99 in a seemingly endless loop otherwise. + (lambda _ + (setenv "HOME" "/tmp"))) + (add-after 'install 'move-files + ;; Move utilities to bin output. + (lambda _ + (mkdir-p (string-append #$output:bin "/bin")) + (rename-file + (string-append #$output "/bin") + (string-append #$output:bin "/bin"))))) #:configure-flags #~(list "-DGDCM_BUILD_TESTING=3Dtrue" (string-append "-DCMAKE_CTEST_ARGUMENTS=3D-E;" "'TestFileMetaInformation" "|TestElement2" "|TestSCUValidation" + "|gdcmscu-echo-dicomserver" + "|gdcmscu-find-dicomserver" "|TestEcho" "|TestFind'") + ;; Documentation "-DGDCM_DOCUMENTATION:BOOL=3DON" "-DGDCM_PDF_DOCUMENTATION:BOOL=3DON" (string-append "-DGDCM_INSTALL_DOC_DIR=3D" #$output:doc "/share/doc/" #$name) - "-DGDCM_BUILD_DOCBOOK_MANPAGES:BOOL=3DOFF"))) ; TODO: need = =E2=80=98xsl-ns=E2=80=99 + "-DGDCM_BUILD_DOCBOOK_MANPAGES:BOOL=3DOFF" ;; TODO: need =E2= =80=98xsl-ns=E2=80=99 + ;; Utilities + "-DGDCM_BUILD_APPLICATIONS:BOOL=3DON"))) (native-inputs (list doxygen ghostscript graphviz texlive)) (home-page "https://gdcm.sourceforge.net/wiki/index.php/Main_Page") (synopsis "Grassroots DICOM library") --=20 2.38.1 --=-=-=--