From patchwork Sun Oct 25 10:35:06 2020 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Christopher Baines X-Patchwork-Id: 24801 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 4125727BBF1; Sun, 25 Oct 2020 10:36:20 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.9 required=5.0 tests=BAYES_00,MAILING_LIST_MULTI, RCVD_IN_MSPIKE_H4,RCVD_IN_MSPIKE_WL,UNPARSEABLE_RELAY,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 3127727BBF0 for ; Sun, 25 Oct 2020 10:36:19 +0000 (GMT) Received: from localhost ([::1]:55634 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kWdNq-0003vo-Bu for patchwork@mira.cbaines.net; Sun, 25 Oct 2020 06:36:18 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:48078) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kWdNb-0003ve-3N for guix-patches@gnu.org; Sun, 25 Oct 2020 06:36:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:52497) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1kWdNa-0004N1-PB for guix-patches@gnu.org; Sun, 25 Oct 2020 06:36:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1kWdNa-0003ar-NE for guix-patches@gnu.org; Sun, 25 Oct 2020 06:36:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#44208] [PATCH 1/3] gnu: netcdf: Update to 4.7.4. Resent-From: Christopher Baines Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 25 Oct 2020 10:36:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 44208 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 44208@debbugs.gnu.org Received: via spool by 44208-submit@debbugs.gnu.org id=B44208.160362212113733 (code B ref 44208); Sun, 25 Oct 2020 10:36:02 +0000 Received: (at 44208) by debbugs.gnu.org; 25 Oct 2020 10:35:21 +0000 Received: from localhost ([127.0.0.1]:35808 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kWdMs-0003ZP-T5 for submit@debbugs.gnu.org; Sun, 25 Oct 2020 06:35:21 -0400 Received: from mira.cbaines.net ([212.71.252.8]:33498) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kWdMm-0003Yi-1q for 44208@debbugs.gnu.org; Sun, 25 Oct 2020 06:35:15 -0400 Received: from localhost (92.41.179.191.threembb.co.uk [92.41.179.191]) by mira.cbaines.net (Postfix) with ESMTPSA id A999E27BBF0 for <44208@debbugs.gnu.org>; Sun, 25 Oct 2020 10:35:10 +0000 (GMT) Received: from localhost (localhost [local]) by localhost (OpenSMTPD) with ESMTPA id 7bc3508a for <44208@debbugs.gnu.org>; Sun, 25 Oct 2020 10:35:08 +0000 (UTC) From: Christopher Baines Date: Sun, 25 Oct 2020 10:35:06 +0000 Message-Id: <20201025103508.6845-1-mail@cbaines.net> X-Mailer: git-send-email 2.28.0 In-Reply-To: <87lffua9ct.fsf@cbaines.net> References: <87lffua9ct.fsf@cbaines.net> 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" X-getmail-retrieved-from-mailbox: Patches This will fix an issue building qgis. * gnu/packages/maths.scm (netcdf): Update to 4.7.4. [source]: Remove the netcdf-tst_h_par.patch. [inputs]: Update hdf5 and add curl. * gnu/packages/patches/netcdf-tst_h_par.patch: Delete. * gnu/local.mk (dist_patch_DATA): Remove deleted patch. --- gnu/local.mk | 1 - gnu/packages/maths.scm | 18 ++++++++---------- gnu/packages/patches/netcdf-date-time.patch | 6 +++--- gnu/packages/patches/netcdf-tst_h_par.patch | 21 --------------------- 4 files changed, 11 insertions(+), 35 deletions(-) delete mode 100644 gnu/packages/patches/netcdf-tst_h_par.patch diff --git a/gnu/local.mk b/gnu/local.mk index 1a01360d72..0ada3b727b 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1355,7 +1355,6 @@ dist_patch_DATA = \ %D%/packages/patches/m4-gnulib-libio.patch \ %D%/packages/patches/ncompress-fix-softlinks.patch \ %D%/packages/patches/netcdf-date-time.patch \ - %D%/packages/patches/netcdf-tst_h_par.patch \ %D%/packages/patches/netpbm-CVE-2017-2586.patch \ %D%/packages/patches/netpbm-CVE-2017-2587.patch \ %D%/packages/patches/netsurf-message-timestamp.patch \ diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index f7565dd885..d2631501aa 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1538,17 +1538,17 @@ similar to MATLAB, GNU Octave or SciPy.") (define-public netcdf (package (name "netcdf") - (version "4.4.1.1") + (version "4.7.4") (source (origin (method url-fetch) - (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/" - "netcdf-" version ".tar.gz")) + (uri (string-append + "https://www.unidata.ucar.edu/downloads/netcdf/ftp/" + "netcdf-c-" version ".tar.gz")) (sha256 (base32 - "1blc7ik5yin7i0ls2kag0a9xjk12m0dzx6v1x88az3ras3scci2d")) - (patches (search-patches "netcdf-date-time.patch" - "netcdf-tst_h_par.patch")))) + "1a2fpp15a2rl1m50gcvvzd9y6bavl6vjf9zzf63sz5gdmq06yiqf")) + (patches (search-patches "netcdf-date-time.patch")))) (build-system gnu-build-system) (native-inputs `(("m4" ,m4) @@ -1556,10 +1556,8 @@ similar to MATLAB, GNU Octave or SciPy.") ("graphviz" ,graphviz))) (inputs `(("hdf4" ,hdf4-alt) - - ;; XXX: The 'tst_nccopy4.sh' test fails when using hdf5-1.10. - ("hdf5" ,hdf5-1.8) - + ("hdf5" ,hdf5) + ("curl" ,curl) ("zlib" ,zlib) ("libjpeg" ,libjpeg-turbo))) (arguments diff --git a/gnu/packages/patches/netcdf-date-time.patch b/gnu/packages/patches/netcdf-date-time.patch index a4e7925aa1..0bdfc55299 100644 --- a/gnu/packages/patches/netcdf-date-time.patch +++ b/gnu/packages/patches/netcdf-date-time.patch @@ -3,9 +3,9 @@ @@ -13,7 +13,7 @@ #endif - /* Tell the user the version of netCDF. */ + /** @internal The version string for the library, used by + * nc_inq_libvers(). */ -static const char nc_libvers[] = PACKAGE_VERSION " of "__DATE__" "__TIME__" $"; -+static const char nc_libvers[] = PACKAGE_VERSION" $"; ++static const char nc_libvers[] = PACKAGE_VERSION " $"; /** - \defgroup lib_version Library Version diff --git a/gnu/packages/patches/netcdf-tst_h_par.patch b/gnu/packages/patches/netcdf-tst_h_par.patch deleted file mode 100644 index ac14a4c0a2..0000000000 --- a/gnu/packages/patches/netcdf-tst_h_par.patch +++ /dev/null @@ -1,21 +0,0 @@ -From a83702834938b23cc2e843589aa223e2024a7e6f Mon Sep 17 00:00:00 2001 -From: Orion Poplawski -Date: Tue, 29 Nov 2016 11:48:01 -0700 -Subject: [PATCH] Add missing #include "err_macros.h" to tst_h_par.c - ---- - h5_test/tst_h_par.c | 1 + - 1 file changed, 1 insertion(+) - -diff --git a/h5_test/tst_h_par.c b/h5_test/tst_h_par.c -index c3da7f4..a419d55 100644 ---- a/h5_test/tst_h_par.c -+++ b/h5_test/tst_h_par.c -@@ -11,6 +11,7 @@ - $Id: tst_h_par.c,v 1.15 2010/05/25 13:53:04 ed Exp $ - */ - #include -+#include "err_macros.h" - #include - - /* Defining USE_MPE causes the MPE trace library to be used (and you From patchwork Sun Oct 25 10:35:07 2020 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Christopher Baines X-Patchwork-Id: 24802 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 731DA27BBF0; Sun, 25 Oct 2020 10:36:20 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.9 required=5.0 tests=BAYES_00,MAILING_LIST_MULTI, RCVD_IN_MSPIKE_H4,RCVD_IN_MSPIKE_WL,UNPARSEABLE_RELAY autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 59D3D27BBF2 for ; Sun, 25 Oct 2020 10:36:19 +0000 (GMT) Received: from localhost ([::1]:55636 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kWdNq-0003vx-HY for patchwork@mira.cbaines.net; Sun, 25 Oct 2020 06:36:18 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:48074) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kWdNa-0003vY-Mk for guix-patches@gnu.org; Sun, 25 Oct 2020 06:36:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:52496) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1kWdNa-0004Me-DH for guix-patches@gnu.org; Sun, 25 Oct 2020 06:36:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1kWdNa-0003ak-B3 for guix-patches@gnu.org; Sun, 25 Oct 2020 06:36:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#44208] [PATCH 2/3] gnu: netcdf-fortran: Update to 4.5.3. Resent-From: Christopher Baines Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 25 Oct 2020 10:36:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 44208 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 44208@debbugs.gnu.org Received: via spool by 44208-submit@debbugs.gnu.org id=B44208.160362211413710 (code B ref 44208); Sun, 25 Oct 2020 10:36:02 +0000 Received: (at 44208) by debbugs.gnu.org; 25 Oct 2020 10:35:14 +0000 Received: from localhost ([127.0.0.1]:35806 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kWdMn-0003Yy-Ic for submit@debbugs.gnu.org; Sun, 25 Oct 2020 06:35:13 -0400 Received: from mira.cbaines.net ([212.71.252.8]:33500) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kWdMl-0003Yj-Ik for 44208@debbugs.gnu.org; Sun, 25 Oct 2020 06:35:12 -0400 Received: from localhost (92.41.179.191.threembb.co.uk [92.41.179.191]) by mira.cbaines.net (Postfix) with ESMTPSA id BE89A27BBF1 for <44208@debbugs.gnu.org>; Sun, 25 Oct 2020 10:35:10 +0000 (GMT) Received: from localhost (localhost [local]) by localhost (OpenSMTPD) with ESMTPA id e3a706f8 for <44208@debbugs.gnu.org>; Sun, 25 Oct 2020 10:35:08 +0000 (UTC) From: Christopher Baines Date: Sun, 25 Oct 2020 10:35:07 +0000 Message-Id: <20201025103508.6845-2-mail@cbaines.net> X-Mailer: git-send-email 2.28.0 In-Reply-To: <20201025103508.6845-1-mail@cbaines.net> References: <87lffua9ct.fsf@cbaines.net> <20201025103508.6845-1-mail@cbaines.net> 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" X-getmail-retrieved-from-mailbox: Patches This allows the package to build with netcdf 4.7.4. * gnu/packages/maths.scm (netcdf-fortran): Update to 4.5.3. --- gnu/packages/maths.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index d2631501aa..ba46937f9a 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1619,7 +1619,7 @@ sharing of scientific data.") (define-public netcdf-fortran (package (name "netcdf-fortran") - (version "4.4.4") + (version "4.5.3") (source (origin (method url-fetch) (uri (string-append @@ -1627,7 +1627,7 @@ sharing of scientific data.") version ".tar.gz")) (sha256 (base32 - "0xaxdcg1p83zmypwml3swsnr3ccn38inwldyr1l3wa4dbwbrblxj")))) + "0x4acvfhbsx1q79dkkwrwbgfhm0w5ngnp4zj5kk92s1khihmqfhj")))) (build-system gnu-build-system) (arguments `(#:parallel-tests? #f)) From patchwork Sun Oct 25 10:35:08 2020 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Christopher Baines X-Patchwork-Id: 24800 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 AB61327BBF3; Sun, 25 Oct 2020 10:36:19 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.9 required=5.0 tests=BAYES_00,MAILING_LIST_MULTI, RCVD_IN_MSPIKE_H4,RCVD_IN_MSPIKE_WL,UNPARSEABLE_RELAY autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 39E8D27BBF1 for ; Sun, 25 Oct 2020 10:36:19 +0000 (GMT) Received: from localhost ([::1]:55632 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kWdNq-0003vn-D0 for patchwork@mira.cbaines.net; Sun, 25 Oct 2020 06:36:18 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:48066) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kWdNa-0003vR-BB for guix-patches@gnu.org; Sun, 25 Oct 2020 06:36:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:52495) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1kWdNa-0004MA-0N for guix-patches@gnu.org; Sun, 25 Oct 2020 06:36:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1kWdNZ-0003ac-UG for guix-patches@gnu.org; Sun, 25 Oct 2020 06:36:01 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#44208] [PATCH 3/3] gnu: python2-netcdf4: Remove package. Resent-From: Christopher Baines Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 25 Oct 2020 10:36:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 44208 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 44208@debbugs.gnu.org Received: via spool by 44208-submit@debbugs.gnu.org id=B44208.160362211313703 (code B ref 44208); Sun, 25 Oct 2020 10:36:01 +0000 Received: (at 44208) by debbugs.gnu.org; 25 Oct 2020 10:35:13 +0000 Received: from localhost ([127.0.0.1]:35804 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kWdMn-0003Yw-Aa for submit@debbugs.gnu.org; Sun, 25 Oct 2020 06:35:13 -0400 Received: from mira.cbaines.net ([212.71.252.8]:33496) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kWdMl-0003Yh-Jl for 44208@debbugs.gnu.org; Sun, 25 Oct 2020 06:35:12 -0400 Received: from localhost (92.41.179.191.threembb.co.uk [92.41.179.191]) by mira.cbaines.net (Postfix) with ESMTPSA id CFBF127BBF2 for <44208@debbugs.gnu.org>; Sun, 25 Oct 2020 10:35:10 +0000 (GMT) Received: from localhost (localhost [local]) by localhost (OpenSMTPD) with ESMTPA id c54e6cbf for <44208@debbugs.gnu.org>; Sun, 25 Oct 2020 10:35:08 +0000 (UTC) From: Christopher Baines Date: Sun, 25 Oct 2020 10:35:08 +0000 Message-Id: <20201025103508.6845-3-mail@cbaines.net> X-Mailer: git-send-email 2.28.0 In-Reply-To: <20201025103508.6845-1-mail@cbaines.net> References: <87lffua9ct.fsf@cbaines.net> <20201025103508.6845-1-mail@cbaines.net> 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" X-getmail-retrieved-from-mailbox: Patches This fails to build, and as it's the Python 2 variant, I think it can be removed. * gnu/packages/python-xyz.scm (python2-netcdf4): Remove variable. --- gnu/packages/python-xyz.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 0fe4703a27..4695869bc9 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -958,9 +958,6 @@ to users of that module.") ;; by the Expat license. (license (list license:isc license:expat)))) -(define-public python2-netcdf4 - (package-with-python2 python-netcdf4)) - (define-public python-license-expression (package (name "python-license-expression")