From patchwork Fri Jul 12 09:48:59 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Luca Cirrottola X-Patchwork-Id: 29216 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 C2F5F27BBE9; Fri, 12 Jul 2024 10:50:23 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable 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 31FAA27BBE2 for ; Fri, 12 Jul 2024 10:50:22 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1sSCul-0005rn-4e; Fri, 12 Jul 2024 05:50:09 -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 1sSCug-0005d3-Pe for guix-patches@gnu.org; Fri, 12 Jul 2024 05:50:04 -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 1sSCug-00030X-5p for guix-patches@gnu.org; Fri, 12 Jul 2024 05:50:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1sSCug-0006Qa-8y for guix-patches@gnu.org; Fri, 12 Jul 2024 05:50:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#72071] [PATCH 1/2] Solve issue https://issues.guix.gnu.org/68313 by updating HDF5 version to 1.14.3 (containing the official fix https://github.com/HDFGroup/hdf5/pull/3421). References: <20240712094059.15538-1-luca.cirrottola@inria.fr> In-Reply-To: <20240712094059.15538-1-luca.cirrottola@inria.fr> Resent-From: Luca Cirrottola Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 12 Jul 2024 09:50:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 72071 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 72071@debbugs.gnu.org Cc: Luca Cirrottola Received: via spool by 72071-submit@debbugs.gnu.org id=B72071.172077777524648 (code B ref 72071); Fri, 12 Jul 2024 09:50:02 +0000 Received: (at 72071) by debbugs.gnu.org; 12 Jul 2024 09:49:35 +0000 Received: from localhost ([127.0.0.1]:53211 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sSCuF-0006PT-5a for submit@debbugs.gnu.org; Fri, 12 Jul 2024 05:49:35 -0400 Received: from mail2-relais-roc.national.inria.fr ([192.134.164.83]:55721) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sSCuB-0006PD-NC for 72071@debbugs.gnu.org; Fri, 12 Jul 2024 05:49:34 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=inria.fr; s=dc; h=from:to:cc:subject:date:message-id:mime-version: content-transfer-encoding; bh=hWzeB/x69sldhDHehxVVITAhnSe9zab23c2Th37uLm8=; b=MXFeWNvjY8r9VJuVuzzKSlspfdSzNsn4DHy6RLNqKA49ufGyCH8uwbey CMbCtgOVj0jZIzpSx+K6UreqQDpcX1VSxUfhzVf9WRlcJs9bpqODzkVhn W1rED6KSUG/+V9wEkgDUCPf2hZ40v8N9RoBc7x8gaYjAd2OIaJOCjSfev E=; Authentication-Results: mail2-relais-roc.national.inria.fr; dkim=none (message not signed) header.i=none; spf=SoftFail smtp.mailfrom=luca.cirrottola@inria.fr; dmarc=fail (p=none dis=none) d=inria.fr X-IronPort-AV: E=Sophos;i="6.09,202,1716242400"; d="scan'208";a="175208152" Received: from unknown (HELO canard.bordeaux.inria.fr) ([193.50.110.114]) by mail2-relais-roc.national.inria.fr with ESMTP/TLS/ECDHE-RSA-AES256-GCM-SHA384; 12 Jul 2024 11:49:25 +0200 From: Luca Cirrottola Date: Fri, 12 Jul 2024 11:48:59 +0200 Message-Id: <20240712094900.15964-1-luca.cirrottola@inria.fr> X-Mailer: git-send-email 2.34.1 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 --- gnu/packages/maths.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 391c11891e..8116569bca 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1814,7 +1814,7 @@ (define-public hdf5-1.10 (define-public hdf5-1.14 (package (inherit hdf5-1.8) - (version "1.14.0") + (version "1.14.3") (source (origin (method url-fetch) @@ -1828,7 +1828,7 @@ (define-public hdf5-1.14 (take (string-split version #\.) 2)) "/src/hdf5-" version ".tar.bz2"))) (sha256 - (base32 "181bdh8hp7v9xqwcby3lknr92lxlicc2hqscba3f5nhf8lrr9rz4")) + (base32 "05zr11y3bivfwrbvzbky1q2gjf6r7n92cvvdnh5jilbmxljg49cl")) (patches (search-patches "hdf5-config-date.patch")))))) (define-public hdf5 @@ -2069,7 +2069,7 @@ (define-public hdf-eos5 (license (license:non-copyleft home-page)))) (define-public hdf5-parallel-openmpi - (package/inherit hdf5-1.10 ;use the latest + (package/inherit hdf5-1.14 ;use the latest (name "hdf5-parallel-openmpi") (inputs `(("mpi" ,openmpi) From patchwork Fri Jul 12 09:49:00 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Luca Cirrottola X-Patchwork-Id: 29217 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 1CFD927BBEA; Fri, 12 Jul 2024 10:50:30 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,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 7F1A927BBE2 for ; Fri, 12 Jul 2024 10:50:29 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1sSCul-0005rm-Ix; Fri, 12 Jul 2024 05:50:09 -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 1sSCug-0005dW-Tn for guix-patches@gnu.org; Fri, 12 Jul 2024 05:50:04 -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 1sSCug-00030d-Jx for guix-patches@gnu.org; Fri, 12 Jul 2024 05:50:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1sSCug-0006Qh-NH for guix-patches@gnu.org; Fri, 12 Jul 2024 05:50:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#72071] [PATCH 2/2] Fix broken HDF5 test: Do not modify the file src/libhdf5.settings generated by the configure script, as it will be checked against a new version generated by the test code in test/test_check_version.sh.in. Resent-From: Luca Cirrottola Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 12 Jul 2024 09:50:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 72071 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 72071@debbugs.gnu.org Cc: Luca Cirrottola Received: via spool by 72071-submit@debbugs.gnu.org id=B72071.172077777824663 (code B ref 72071); Fri, 12 Jul 2024 09:50:02 +0000 Received: (at 72071) by debbugs.gnu.org; 12 Jul 2024 09:49:38 +0000 Received: from localhost ([127.0.0.1]:53213 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sSCuI-0006Pi-H0 for submit@debbugs.gnu.org; Fri, 12 Jul 2024 05:49:38 -0400 Received: from mail2-relais-roc.national.inria.fr ([192.134.164.83]:55721) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sSCuE-0006PD-Ij for 72071@debbugs.gnu.org; Fri, 12 Jul 2024 05:49:36 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=inria.fr; s=dc; h=from:to:cc:subject:date:message-id:in-reply-to: references:mime-version:content-transfer-encoding; bh=7gMVERNtj6/fDKyfhvn3ugeF0LS+f5u+KH0EprwU1c0=; b=KLhVZZrITKPao70qHjqqTGtjTU0OAXBKt4r3vmNxF3W17PBJhjR7Hbhv lj8+ajqyBGZiqlAZJ6PNubFQj+pqAQ+Rpsx03ehSUKtfLMcr2oVNzv/ks WBWqo6FNxiwKUrQoVZ4pDi0JCN5VbGunaJLRNcYKi0ZW9LE2XocHeUzit g=; Authentication-Results: mail2-relais-roc.national.inria.fr; dkim=none (message not signed) header.i=none; spf=SoftFail smtp.mailfrom=luca.cirrottola@inria.fr; dmarc=fail (p=none dis=none) d=inria.fr X-IronPort-AV: E=Sophos;i="6.09,202,1716242400"; d="scan'208";a="175208177" Received: from unknown (HELO canard.bordeaux.inria.fr) ([193.50.110.114]) by mail2-relais-roc.national.inria.fr with ESMTP/TLS/ECDHE-RSA-AES256-GCM-SHA384; 12 Jul 2024 11:49:32 +0200 From: Luca Cirrottola Date: Fri, 12 Jul 2024 11:49:00 +0200 Message-Id: <20240712094900.15964-2-luca.cirrottola@inria.fr> X-Mailer: git-send-email 2.34.1 In-Reply-To: <20240712094900.15964-1-luca.cirrottola@inria.fr> References: <20240712094900.15964-1-luca.cirrottola@inria.fr> 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 --- gnu/packages/maths.scm | 13 ------------- 1 file changed, 13 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 8116569bca..2f12deba3b 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1729,19 +1729,6 @@ (define-public hdf5-1.8 (("libhdf5hl_fortran_la_LDFLAGS =") (string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath=" (assoc-ref outputs "fortran") "/lib"))))) - (add-after 'configure 'patch-settings - (lambda _ - ;; libhdf5.settings contains the full path of the - ;; compilers used, and its contents are included in - ;; libhdf5.so. We truncate the hashes to avoid - ;; unnecessary store references to those compilers: - (substitute* "src/libhdf5.settings" - (("(/gnu/store/)([a-zA-Z0-9]*)" all prefix hash) - (string-append prefix (string-take hash 10) "...")) - ;; Don't record the build-time kernel version to make the - ;; settings file reproducible. - (("Uname information:.*") - "Uname information: Linux\n")))) (add-after 'install 'patch-references (lambda* (#:key inputs outputs #:allow-other-keys) (let ((bin (string-append (assoc-ref outputs "out") "/bin"))