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[217.140.209.67]) by smtp.gmail.com with ESMTPSA id h21-20020a0565123c9500b004d468ed2ce3sm432205lfv.173.2023.01.14.14.00.20 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sat, 14 Jan 2023 14:00:20 -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 23:58:43 +0200 In-reply-to: <87wn5q9epc.fsf@gnu.org> Message-ID: <87358cn5e4.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=1673733676; a=rsa-sha256; cv=none; b=PZj6ZHXffmIqA/xvqzmM7HQXhVS023V9UvAdgwHC/7hd4xSnLOXs+owKA71p1O9uWZ4WSk BUYE+mA5IqjWyQ75RREabf4o9ecyt5r9Ig48XmsWER0s6t5YQxLwCKgYpfdxdnDP1J1Z/J 3Vf74w86jgYLFPO0TS6ApFkHNUakBZnxpGWDa8lv1FxoFE0VyWMgAe5SfOrXoaVjQSF1kY ov83h7QzJEgxLimy8v7Rzg3MLCgCTq+99IvmJ+B/i4zlY0fm+Im3CmHtVbPZm8Nuc25gmW 4SAL6nNYs08HyrhKyB6HkKrG5KR88lOe4vRiEuKPxRbV+0mUWlpNgygTGb5T0g== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=J75PtHsc; 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=1673733676; 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=zQnpxs6UKO5mVKO6eyCvUA4P0dxcC/I7nsO0P9G3mMg=; b=BMngB8Kq7OMN+LX9lfMn5A4Ns0m4WXlRtl4m7jhmnKSy8hwD9kI0zp+pl8A3H5rVlNrW9N bnbH1cgtO239eMyFnSSmAxDdM+JdnlFv2h+27EOJC6y2lwDy6XRmUnOVwSKKlmnpXWRHg3 nU8l9kVS4UXHMgm+dRjl9ItHjPYHXlw6bmcTJI9RI3f5p+QEwU6ADaD5UCVUM1A4+bDNFH shkzZVjK+bxLBohQ9fVPyBUo6/sq2Ty5mFOJWaO4sZMxoiQ94mRDvHIyh4j2MtzSagOPlL hnzk1NG+jlGbNdLLV7Doo55spzgC84Vt+otVbzX2/BYQp+bOUrJ88PEdEF5yDQ== X-Migadu-Spam-Score: -2.01 X-Spam-Score: -2.01 X-Migadu-Queue-Id: F2CA13EC8F 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=J75PtHsc; 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: GAKMNrernWzk --=-=-= Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable And here is the last patch, which uses system packages where possible. All nice things in these patches are thanks to the help of Tobias, any screwups are mine. Thanks! Tor-bj=C3=B6rn --=-=-= Content-Type: text/x-patch; charset=utf-8 Content-Disposition: attachment; filename=0001-gnu-gdcm-Use-system-packages-where-possible.patch Content-Transfer-Encoding: quoted-printable >From 77a7609eb727c53028846d0bf54204cdf9f58f9c Mon Sep 17 00:00:00 2001 From: =3D?UTF-8?q?Tor-bj=3DC3=3DB6rn=3D20Claesson?=3D Date: Sat, 14 Jan 2023 23:56:43 +0200 Subject: [PATCH] gnu: gdcm: Use system packages where possible. --- gnu/packages/bioinformatics.scm | 47 +++++++++++++++++++++++++++++++-- 1 file changed, 45 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.= scm index e45d33ec2b..41709fd9ed 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -17853,7 +17853,29 @@ (define-public gdcm (file-name (git-file-name name version)) (sha256 (base32 - "1w78cmm9q7aavs7svdkl4dgilcqk4yazci9m6x7icrssb7cj991i")))) + "1w78cmm9q7aavs7svdkl4dgilcqk4yazci9m6x7icrssb7cj991i")) + (modules '((guix build utils) + (ice-9 ftw))) + (snippet + '(begin + (define (unbundle? file) + (member file '("dicom3tools" + "gdcmexpat" + "gdcmutfcpp" + "gdcmuuid" + "gdcmzlib" + "getopt" + "KWStyle" + "pvrg" + "Release" + "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 @@ -17882,6 +17904,20 @@ (define-public gdcm "|gdcmscu-find-dicomserver" "|TestEcho" "|TestFind'") + ;; Libraries + "-DGDCM_USE_SYSTEM_EXPAT:BOOL=3DON" + "-DGDCM_USE_SYSTEM_JSON:BOOL=3DON" + "-DGDCM_USE_SYSTEM_LIBXML2:BOOL=3DON" + "-DGDCM_USE_SYSTEM_OPENSSL:BOOL=3DON" + "-DGDCM_USE_SYSTEM_POPPLER:BOOL=3DON" + "-DGDCM_USE_SYSTEM_UUID:BOOL=3DON" + "-DGDCM_USE_SYSTEM_ZLIB:BOOL=3DON" + ;; TODO: Unbundle these if possible. + "-DGDCM_USE_SYSTEM_CHARLS:BOOL=3DOFF" + "-DGDCM_USE_SYSTEM_LJPEG:BOOL=3DOFF" + "-DGDCM_USE_SYSTEM_OPENJPEG:BOOL=3DOFF" + "-DGDCM_USE_SYSTEM_PAPYRUS3:BOOL=3DOFF" + "-DGDCM_USE_SYSTEM_SOCKETXX:BOOL=3DOFF" ;; Documentation "-DGDCM_DOCUMENTATION:BOOL=3DON" "-DGDCM_PDF_DOCUMENTATION:BOOL=3DON" @@ -17890,7 +17926,14 @@ (define-public gdcm "-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)) + (inputs (list expat + json-c + libxml2 + openssl + poppler + `(,util-linux "lib") + zlib)) + (native-inputs (list doxygen ghostscript graphviz pkg-config texlive)) (home-page "https://gdcm.sourceforge.net/wiki/index.php/Main_Page") (synopsis "Grassroots DICOM library") (description --=20 2.38.1 --=-=-=--