From patchwork Sat Mar 29 09:21:31 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Andreas Enge X-Patchwork-Id: 40954 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 D986927BBEA; Sat, 29 Mar 2025 09:32:50 +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=-7.6 required=5.0 tests=BAYES_00,DKIMWL_WL_HIGH, DKIM_SIGNED,DKIM_VALID,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham 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 4BC4427BBE2 for ; Sat, 29 Mar 2025 09:32:50 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1tySYQ-0003Ga-T0; Sat, 29 Mar 2025 05:32:43 -0400 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 1tySW5-0002TT-CJ for guix-patches@gnu.org; Sat, 29 Mar 2025 05:30:19 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1tySW4-00070l-RM for guix-patches@gnu.org; Sat, 29 Mar 2025 05:30:13 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=wP483KLoGKmDvQ68CretTe36l9g0fuSilVPAr/GvP4A=; b=jJBWuuw/Jj7XY+SUAmPn8bPhVsxEu+jDGb+4MkbEgGkeeKk60OknuB9HcAly71jYBz/QYPjsPvxaisHxrK39oASw/hYJJnAkf8GPZx/GbrZUzNLvd4E4rDZV3c4weGYSM8e8ae2nsdlInTaD7WI7Hf0BaBhqIJcoqIxMyaQVGEBaBgW45NMUt1jvrHBz4OrTFhWx5ZRZT/DaCkvVCxY6D3Z3kXXAXlyks5Rpi63HjgylD5sEjOni6uowbxEETPXx8QP350U1o052hiitSq2KSWNQEfb8FVTT1YINJQelbS2RBO+jDBZ4BxdL3NUafzqx6vgeh/KssF+V9zs2yAr0hQ==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1tySVz-0004uo-Jp; Sat, 29 Mar 2025 05:30:07 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77287] [PATCH v2 7/8] gnu: hdf5: Make hdf@1.14 the default version. Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: andreas@enge.fr, bavier@posteo.net, laurent.gatto@gmail.com, rekado@elephly.net, sharlatanus@gmail.com, zimon.toutoune@gmail.com, guix-patches@gnu.org Resent-Date: Sat, 29 Mar 2025 09:30:07 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 77287 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 77287@debbugs.gnu.org Cc: rekado@elephly.net, Andreas Enge , Andreas Enge , Eric Bavier , Laurent Gatto , Ricardo Wurmus , Sharlatan Hellseher , Simon Tournier X-Debbugs-Original-Xcc: Andreas Enge , Eric Bavier , Laurent Gatto , Ricardo Wurmus , Sharlatan Hellseher , Simon Tournier Received: via spool by 77287-submit@debbugs.gnu.org id=B77287.174324057918757 (code B ref 77287); Sat, 29 Mar 2025 09:30:07 +0000 Received: (at 77287) by debbugs.gnu.org; 29 Mar 2025 09:29:39 +0000 Received: from localhost ([127.0.0.1]:56862 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tySVW-0004sQ-VZ for submit@debbugs.gnu.org; Sat, 29 Mar 2025 05:29:39 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:44914) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tySV6-0004qJ-12 for 77287@debbugs.gnu.org; Sat, 29 Mar 2025 05:29:12 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id BA0B6172; Sat, 29 Mar 2025 10:29:11 +0100 (CET) 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 6UWuLa0Svpzy; Sat, 29 Mar 2025 10:29:11 +0100 (CET) Received: from jurong.lan (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id B1A7DB2; Sat, 29 Mar 2025 10:29:09 +0100 (CET) From: Andreas Enge Date: Sat, 29 Mar 2025 10:21:31 +0100 Message-ID: X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 X-Rspamd-Queue-Id: BA0B6172 X-Spamd-Result: default: False [-6.45 / 15.00]; REPLY(-4.00)[]; BAYES_HAM(-3.00)[100.00%]; NEURAL_HAM(-2.85)[-0.951]; FORGED_RECIPIENTS(2.00)[m:andreas@enge.fr,s:andreas.enge@aquilenet.fr]; MID_CONTAINS_FROM(1.00)[]; R_MISSING_CHARSET(0.50)[]; MIME_GOOD(-0.10)[text/plain]; RCVD_TLS_ALL(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; MIME_TRACE(0.00)[0:+]; FROM_EQ_ENVFROM(0.00)[]; TO_MATCH_ENVRCPT_SOME(0.00)[]; RCPT_COUNT_THREE(0.00)[3]; TO_DN_SOME(0.00)[]; RCVD_VIA_SMTP_AUTH(0.00)[]; FROM_HAS_DN(0.00)[]; ARC_NA(0.00)[] X-Rspamd-Action: no action X-Spamd-Bar: ------ X-Rspamd-Server: hera 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 This replaces all inputs hdf5@1.10 by hdf5@1.14 unless explicitly specified otherwise. * gnu/packages/maths.scm (hdf5-1.14): Rename to... (hdf5): ...this, which was previously defined as hdf5-1.10. (hdf-eos5, hdf5-parallel-openmpi, scilab): Adapt variable names. (hdf-java)[inputs]: Keep hdf5-1.10. * gnu/packages/bioinformatics.scm (fast5, ncbi-vdb), gnu/packages/cran.scm (r-h5), gnu/packages/image.scm (vigra)[inputs]: Keep hdf5-1.10. Change-Id: Ie43a13ecbb4da597ec1d3f7c0428102b45881485 --- gnu/packages/bioinformatics.scm | 4 ++-- gnu/packages/cran.scm | 2 +- gnu/packages/image.scm | 2 +- gnu/packages/maths.scm | 16 ++++++---------- 4 files changed, 10 insertions(+), 14 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e8b585e495..8fd7789028 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7941,7 +7941,7 @@ (define-public fast5 (add-after 'unpack 'chdir (lambda _ (chdir "python")))))) - (inputs (list hdf5)) + (inputs (list hdf5-1.10)) (propagated-inputs (list python-dateutil)) (native-inputs @@ -11349,7 +11349,7 @@ (define-public ncbi-vdb (install-file "libs/kfg/default.kfg" target) (install-file "libs/kfg/certs.kfg" target))))))) (inputs - (list file hdf5 java-ngs libxml2 ngs-sdk )) + (list file hdf5-1.10 java-ngs libxml2 ngs-sdk )) (native-inputs (list perl)) ;; NCBI-VDB requires SSE capability. (supported-systems '("i686-linux" "x86_64-linux")) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8522eb07a5..4e96d70849 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -14934,7 +14934,7 @@ (define-public r-h5 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx")))) (build-system r-build-system) (inputs - (list zlib hdf5)) + (list zlib hdf5-1.10)) (native-inputs (list r-knitr r-testthat which)) (propagated-inputs diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index 89e7ef83e6..83b694b409 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -1389,7 +1389,7 @@ (define-public vigra `(("boost" ,boost) ("fftw" ,fftw) ("fftwf" ,fftwf) - ("hdf5" ,hdf5) + ("hdf5" ,hdf5-1.10) ("ilmbase" ,ilmbase) ; propagated by openexr, but needed explicitly ; to create a configure-flag ("libjpeg" ,libjpeg-turbo) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 017abecc00..f851937a7c 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1834,7 +1834,7 @@ (define-public hdf5-1.10 (base32 "14gih7kmjx4h3lc7pg4fwcl28hf1qqkf2x7rljpxqvzkjrqbxi00")) (patches (search-patches "hdf5-config-date.patch")))))) -(define-public hdf5-1.14 +(define-public hdf5 (package (inherit hdf5-1.8) (version "1.14.3") @@ -1872,10 +1872,6 @@ (define-public hdf5-1.14 (("@UNAME_INFO@") "Linux")))))))))) -(define-public hdf5 - ;; Default version of HDF5. - hdf5-1.10) - ;; Keep this in sync with the current hdf5 package. (define-public hdf-java (package @@ -1963,7 +1959,7 @@ (define-public hdf-java java-slf4j-simple)) (inputs (list hdf4 - hdf5 + hdf5-1.10 java-slf4j-api libjpeg-turbo zlib)) @@ -2041,7 +2037,7 @@ (define-public hdf-eos5 (list autoconf automake gfortran libtool)) (build-system gnu-build-system) (inputs - (list hdf5-1.14 zlib gctp)) + (list hdf5 zlib gctp)) (arguments (list #:configure-flags ''("--enable-install-include" "--enable-shared" @@ -2076,13 +2072,13 @@ (define-public hdf-eos5 (license (license:non-copyleft home-page)))) (define-public hdf5-parallel-openmpi - (package/inherit hdf5-1.14 ;use the latest + (package/inherit hdf5 (name "hdf5-parallel-openmpi") (inputs `(("mpi" ,openmpi) ,@(package-inputs hdf5))) (arguments - (substitute-keyword-arguments (package-arguments hdf5-1.14) + (substitute-keyword-arguments (package-arguments hdf5) ((#:configure-flags flags) #~(cons "--enable-parallel" (delete "--enable-cxx" @@ -10481,7 +10477,7 @@ (define-public scilab curl fftw gettext-minimal - hdf5-1.14 + hdf5 libarchive libx11 libxml2