From unknown Sat Sep 20 13:00:05 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#60039 <60039@debbugs.gnu.org> To: bug#60039 <60039@debbugs.gnu.org> Subject: Status: Update GDAL and NetCDF and include lz4 and openjpeg support Reply-To: bug#60039 <60039@debbugs.gnu.org> Date: Sat, 20 Sep 2025 20:00:05 +0000 retitle 60039 Update GDAL and NetCDF and include lz4 and openjpeg support reassign 60039 guix-patches submitter 60039 Roman Scherer severity 60039 normal thanks From debbugs-submit-bounces@debbugs.gnu.org Tue Dec 13 13:05:22 2022 Received: (at submit) by debbugs.gnu.org; 13 Dec 2022 18:05:22 +0000 Received: from localhost ([127.0.0.1]:33739 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p59eb-0003J3-Uh for submit@debbugs.gnu.org; Tue, 13 Dec 2022 13:05:22 -0500 Received: from lists.gnu.org ([209.51.188.17]:47200) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p59ea-0003Ix-55 for submit@debbugs.gnu.org; Tue, 13 Dec 2022 13:05:20 -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 1p59eL-00085Z-PZ for guix-patches@gnu.org; Tue, 13 Dec 2022 13:05:12 -0500 Received: from mail-ej1-x62f.google.com ([2a00:1450:4864:20::62f]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1p59eI-0002Pn-7s for guix-patches@gnu.org; Tue, 13 Dec 2022 13:05:05 -0500 Received: by mail-ej1-x62f.google.com with SMTP id tz12so15853122ejc.9 for ; Tue, 13 Dec 2022 10:05:01 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=burningswell-com.20210112.gappssmtp.com; s=20210112; h=mime-version:message-id:date:subject:to:from:user-agent:from:to:cc :subject:date:message-id:reply-to; bh=DYr7tmb3rJJy9ZGG1naac4c7ZYrMpS8OOscOmr+R+yw=; b=DPkIrGI73oiIE3h5jVuvBtUflVf9X+uv+L9jx0ZV8qBEld3mvhNZwij/l/sCp+3PTw xUNDuYgh8uFiGuTfriWdntilZwXqKWA5IplwTXMszU/27Ru9t/nkqtpLSSfIqqXCXYIe F9kEQusjt/XqzmDOmyAevqAR0L9RFMowmhxMOJxXLmcYORSPtLbZovOTqWoL0lEuZArj MeUUYddBEKXhujQ/EI39JwleCPtVZOVWphkw2fQAgx/d2iwhc0/YN+HkUIVg1/hDvqYX tRCE3iKqbtmkcvA70GvSPGvoYeJNMXfv9/hM6Fk0xMtS7TLCUTmByxqb9ijZ4A0fJgKy Z8LQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=mime-version:message-id:date:subject:to:from:user-agent :x-gm-message-state:from:to:cc:subject:date:message-id:reply-to; bh=DYr7tmb3rJJy9ZGG1naac4c7ZYrMpS8OOscOmr+R+yw=; b=AgIHwZythiiFjoSgw7jA5p8x2Y9swRUHry36f4eV8pIH2NZa5dXVm4dqdUbBmLeuLB VISnpC6KmLC0qT7Ml2sphHdTgrR0/wfmZju2jmqIaC34VumPMz4jdZersOsNVRw4a0y3 vtQPK8l03xzSYFT8SLeDOK+KRTk7bCCu6bbmLIA72cHNMfbh3zqRMTutrJ/5WqclpAJC K4rqklkvuA80a6gyKlRViQ9cLFcYnJJvnuIGOlMlXnY6Mm4tjsPa1Z1e5D8XkVbEhgJs chv/MglF0S7Q4cMwf1uXaoxZRiLLxP9Hen48jCwT/JlECO2ZL4j6fMDXvN5WmUjWucXv 7TVQ== X-Gm-Message-State: ANoB5plJXorAIHZ1/OvVZpu1kjOKP7pL+7P1gk39rGmHbyGPE0vf2nqy XCoxvTLHKZjD4R99yHTjF/G28b4cZnPBl3Ft4O8= X-Google-Smtp-Source: AA0mqf4PGHghxYupEW/yMZ8Kjz/8RSqcWZxZGm1H2/BS1jX9v7rvYe+bXbTAcjD1MC/fNEr5YotzVA== X-Received: by 2002:a17:906:859a:b0:7c1:4bb2:f62c with SMTP id v26-20020a170906859a00b007c14bb2f62cmr15529848ejx.40.1670954699855; Tue, 13 Dec 2022 10:04:59 -0800 (PST) Received: from precision (tmo-117-8.customers.d1-online.com. [80.187.117.8]) by smtp.gmail.com with ESMTPSA id b10-20020a17090630ca00b0073dbaeb50f6sm4832482ejb.169.2022.12.13.10.04.59 for (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 13 Dec 2022 10:04:59 -0800 (PST) User-agent: mu4e 1.8.11; emacs 29.0.50 From: Roman Scherer To: guix-patches@gnu.org Subject: Update GDAL and NetCDF and include lz4 and openjpeg support Date: Tue, 13 Dec 2022 19:00:32 +0100 Message-ID: <86mt7rp4c5.fsf@burningswell.com> MIME-Version: 1.0 Content-Type: multipart/signed; boundary="==-=-="; micalg=pgp-sha256; protocol="application/pgp-signature" Received-SPF: none client-ip=2a00:1450:4864:20::62f; envelope-from=roman.scherer@burningswell.com; helo=mail-ej1-x62f.google.com X-Spam_score_int: -6 X-Spam_score: -0.7 X-Spam_bar: / X-Spam_report: (-0.7 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_NONE=0.001, URI_DOTEDU=1.213 autolearn=no autolearn_force=no X-Spam_action: no action X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) --==-=-= Content-Type: multipart/mixed; boundary="=-=-=" --=-=-= Content-Type: text/plain Hello Guix, this patch series updates the GDAL, Netcdf and libtiff packages. It also adds support for lz4 and openjpeg to GDAL. Could you please review it? Thanks, Roman. --=-=-= Content-Type: text/x-diff Content-Disposition: attachment; filename=0001-gnu-gdal-Update-to-3.6.0.patch Content-Transfer-Encoding: quoted-printable From=200fcc8aa4999271d0f50aac8bed9a9c826c88a392 Mon Sep 17 00:00:00 2001 From: r0man Date: Sat, 3 Dec 2022 18:15:04 +0100 Subject: [PATCH 1/4] gnu: gdal: Update to 3.6.0. * gnu/packages/geo.scm (gdal): Update to 3.6.0. =2D-- gnu/packages/geo.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index abfa5963b9..bfce9399c3 100644 =2D-- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -1043,7 +1043,7 @@ (define-public spatialite-gui (define-public gdal (package (name "gdal") =2D (version "3.5.1") + (version "3.6.0") (source (origin (method url-fetch) (uri (string-append @@ -1051,7 +1051,7 @@ (define-public gdal version ".tar.gz")) (sha256 (base32 =2D "1l93q7xf6qx9ck5axfkf3ygmvclxkvrjd8x00ckn7j0d0750ci3w")) + "1nri6p495chlm63dcylq2wwmvlf90pn2kr3jf5ybkby6q3p7jshd")) (modules '((guix build utils))) (snippet `(begin =2D-=20 2.38.1 --=-=-= Content-Type: text/x-diff Content-Disposition: attachment; filename=0002-gnu-gdal-Add-support-for-lz4-and-openjpeg.patch Content-Transfer-Encoding: quoted-printable From=20d740188e07a5368fd0e01a8aa24a6e515ecebc9e Mon Sep 17 00:00:00 2001 From: r0man Date: Sat, 3 Dec 2022 18:59:02 +0100 Subject: [PATCH 2/4] gnu: gdal: Add support for lz4 and openjpeg. * gnu/packages/geo.scm (gdal): Add support for lz4 and openjpeg. =2D-- gnu/packages/geo.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index bfce9399c3..ba348dbb7d 100644 =2D-- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -1084,8 +1084,10 @@ (define-public gdal libpng libtiff libwebp + lz4 netcdf openssl + openjpeg pcre2 postgresql ; libpq proj =2D-=20 2.38.1 --=-=-= Content-Type: text/x-diff Content-Disposition: attachment; filename=0003-gnu-libtiff-Update-to-4.4.0.patch Content-Transfer-Encoding: quoted-printable From=20a6deb05aabbbea9b0e0ccb79887e524ddd99e589 Mon Sep 17 00:00:00 2001 From: r0man Date: Sat, 10 Dec 2022 12:16:21 +0100 Subject: [PATCH 3/4] gnu: libtiff: Update to 4.4.0. * gnu/packages/image.scm (libtiff): Update to 4.4.0. =2D-- gnu/packages/image.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index bc1f25627b..9427d022d9 100644 =2D-- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -569,7 +569,7 @@ (define-public libicns (define-public libtiff (package (name "libtiff") =2D (version "4.3.0") + (version "4.4.0") (source (origin (method url-fetch) @@ -577,7 +577,7 @@ (define-public libtiff version ".tar.gz")) (sha256 (base32 =2D "1j3snghqjbhwmnm5vz3dr1zm68dj15mgbx1wqld7vkl7n2nfaihf")))) + "1vdbk3sc497c58kxmp02irl6nqkfm9rjs3br7g59m59qfnrj6wli")))) (build-system gnu-build-system) (outputs '("out" "doc")) ;1.8 MiB of HTML documenta= tion =2D-=20 2.38.1 --=-=-= Content-Type: text/x-diff Content-Disposition: attachment; filename=0004-gnu-netcdf-Update-to-4.9.0.patch Content-Transfer-Encoding: quoted-printable From=204ab999dfcab8b999d6256e328667a07aa7cb5e76 Mon Sep 17 00:00:00 2001 From: r0man Date: Sat, 10 Dec 2022 12:18:20 +0100 Subject: [PATCH 4/4] gnu: netcdf: Update to 4.9.0. * gnu/packages/maths.scm (netcdf): Update to 4.9.0. * gnu/packages/patches/netcdf-4.9.0-fix-cmake-typo.patch =2D-- gnu/packages/maths.scm | 46 +++++++++++++------ .../patches/netcdf-4.9.0-fix-cmake-typo.patch | 23 ++++++++++ 2 files changed, 55 insertions(+), 14 deletions(-) create mode 100644 gnu/packages/patches/netcdf-4.9.0-fix-cmake-typo.patch diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index aee050735e..057e9651c2 100644 =2D-- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1850,16 +1850,16 @@ (define-public itpp (define-public netcdf (package (name "netcdf") =2D (version "4.7.4") + (version "4.9.0") (source (origin (method url-fetch) (uri (string-append =2D "https://www.unidata.ucar.edu/downloads/netcdf/ftp/" =2D "netcdf-c-" version ".tar.gz")) + "https://downloads.unidata.ucar.edu/netcdf-c/" version + "/netcdf-c-" version ".tar.gz")) (sha256 (base32 =2D "1a2fpp15a2rl1m50gcvvzd9y6bavl6vjf9zzf63sz5gdmq06yiqf")) + "0j8b814mjdqvqanzmrxpq8hn33n22cdzb3gf9vhya24wnwi615ac")) (modules '((guix build utils))) (snippet ;; Make sure this variable is defined only once. Failing to do so @@ -1867,20 +1867,35 @@ (define-public netcdf ;; multiple-definition link error with GCC 10. '(substitute* "ncdump/ocprint.c" (("^int ocdebug") "static int ocdebug"))) =2D (patches (search-patches "netcdf-date-time.patch")))) =2D (build-system gnu-build-system) + (patches (search-patches "netcdf-date-time.patch" + "netcdf-4.9.0-fix-cmake-typo.patch")))) + (build-system cmake-build-system) (native-inputs =2D (list m4 doxygen graphviz)) + (list m4 doxygen graphviz unzip)) (inputs `(("hdf4" ,hdf4-alt) =2D ("hdf5" ,hdf5) + ("hdf5" ,hdf5-1.12) ("curl" ,curl) ("zlib" ,zlib) =2D ("libjpeg" ,libjpeg-turbo))) + ("libjpeg" ,libjpeg-turbo) + ("libxml2" ,libxml2))) (arguments =2D `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-h= df4") =2D =2D #:phases (modify-phases %standard-phases + `(#:configure-flags + '("-DENABLE_BYTERANGE=3DON" + "-DENABLE_CDF5=3DON" + "-DENABLE_DAP_LONG_TESTS=3DOFF" + "-DENABLE_DAP_REMOTE_TESTS=3DOFF" + "-DENABLE_EXAMPLE_TESTS=3DOFF" + "-DENABLE_EXTRA_TESTS=3DOFF" + "-DENABLE_FILTER_TESTING=3DOFF" + "-DENABLE_LARGE_FILE_TESTS=3DOFF" + "-DENABLE_UNIT_TESTS=3DOFF" + "-DSOURCE_DATE_EPOCH=3D0") + #:phases + (modify-phases %standard-phases + (add-before 'configure 'disable-nc-byterange-test + (lambda _ + (invoke "sed" "-i" "/test_byterange/d" "nc_test/CMakeLists.tx= t"))) (add-before 'configure 'fix-source-date (lambda _ ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build @@ -1900,8 +1915,11 @@ (define-public netcdf (substitute* "libnetcdf.settings" (("(/gnu/store/)([0-9A-Za-z]*)" all prefix hash) (string-append prefix (string-take hash 10) "..."))) =2D #t))) =2D + #t)) + (add-before 'check 'fix-test-rcmerge + (lambda _ + ;; Set HOME, to fix the test-rcmerge. + (setenv "HOME" "/tmp")))) #:parallel-tests? #f)) ;various race conditions (home-page "https://www.unidata.ucar.edu/software/netcdf/") (synopsis "Library for scientific data") diff --git a/gnu/packages/patches/netcdf-4.9.0-fix-cmake-typo.patch b/gnu/p= ackages/patches/netcdf-4.9.0-fix-cmake-typo.patch new file mode 100644 index 0000000000..b9c0ed5c10 =2D-- /dev/null +++ b/gnu/packages/patches/netcdf-4.9.0-fix-cmake-typo.patch @@ -0,0 +1,23 @@ +From 80a6611cfca98a5979c5ac69cba56a49af8c1e48 Mon Sep 17 00:00:00 2001 +From: Yuriy Chernyshov +Date: Sun, 19 Jun 2022 19:29:20 +0300 +Subject: [PATCH] Fix typo in CMakeLists.txt + +At the time generated dynamic library is named `libnetcdf.so.19}` which lo= oks like a typo. +--- + CMakeLists.txt | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 7bf8641bec..18366d24ad 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -39,5 +39,5 @@ SET(NC_VERSION ${netCDF_VERSION}) + SET(PACKAGE_VERSION ${VERSION}) + + # These values should match those in configure.ac +-SET(netCDF_LIB_VERSION 19}) ++SET(netCDF_LIB_VERSION 19) + SET(netCDF_SO_VERSION 19) + + # Version of the dispatch table. This must match the value in =2D-=20 2.38.1 --=-=-=-- --==-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQFTBAEBCAA9FiEE0iajOdjfRIFd3gygPdpSUn0qwZkFAmOYvsofHHJvbWFuLnNj aGVyZXJAYnVybmluZ3N3ZWxsLmNvbQAKCRA92lJSfSrBmQS/B/9HfL9wgvHo9uqJ bmTtuF8YRxUBA7kwbdx4xBcaBopLUMDyQj/i7na4mbK8cin4/SuEn/lgjhTrSuE/ n8tA2dzPtJfNVHp7fYwHDybvKCN+dbNRcYmc09k0FEXIcgFpOdcnpvIqoYKODpS9 ParfRzF8RgCADuj+LfsMsCjPR/HEXlcBnRBy4/QGWygSu3+7tU4lKXheI5qv0tFt aLZKwQrqWkva/Y6N+XTzshWo4rxdZkhlTGJzQaQq0KWv2QoRv9vhg0qjzU8I7od8 kJV9XziJCx/DuJr9Ts7e8+zpyIU+6GTV8I8qE1l97oTbLjsgt39wkmuT/+0fxNFG lMmtjff5 =tSN9 -----END PGP SIGNATURE----- --==-=-=-- From debbugs-submit-bounces@debbugs.gnu.org Tue Dec 20 12:27:05 2022 Received: (at 60039) by debbugs.gnu.org; 20 Dec 2022 17:27:05 +0000 Received: from localhost ([127.0.0.1]:46131 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p7gOM-0007Ea-2R for submit@debbugs.gnu.org; Tue, 20 Dec 2022 12:27:05 -0500 Received: from mout01.posteo.de ([185.67.36.65]:48393) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p7gOG-0007ED-5a for 60039@debbugs.gnu.org; Tue, 20 Dec 2022 12:27:01 -0500 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 3024E240028 for <60039@debbugs.gnu.org>; Tue, 20 Dec 2022 18:26:49 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1671557209; bh=r9nf6rtWXBxRU1BSUu1GpMLbOA2aul5IaM+oE4sfiCI=; h=From:To:Cc:Subject:Date:From; b=c+r7RtgwhdaSEpWUMYEKLmPnvdDe2tA5z/Kt3N2p7HUiRGiK6Se7oH8EHH8Zd5d+M EVC/mSd970nazGI1ApxkblPbBeyrJ5JDGFA5oL9NZMSqWsgYlNIpHzCqUbAB7vxLkf sNO8yzYNZbb6QS9lu6ZIsXtObyqmN7FlCTXu7PnDkK+zJEqZEOTdJQkc6gACp5kycz e+84VN5hQME6Ie4eipATq7OrjoHY7jv3uavyHKEZIsaGI88aS75yKVqcopuXvVD2T7 4gT35EzoPduD/85xIIyZBSfaRfumQVJkyIP8mbIH2u13fO/Zc2lSUhpKGWiV2Q86pP jIQml/x9kzvbQ== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4Nc3Qw3vH9z6tm4; Tue, 20 Dec 2022 18:26:48 +0100 (CET) References: <86mt7rp4c5.fsf@burningswell.com> From: Guillaume Le Vaillant To: Roman Scherer Subject: Re: [bug#60039] Update GDAL and NetCDF and include lz4 and openjpeg support Date: Tue, 20 Dec 2022 17:07:01 +0000 In-reply-to: <86mt7rp4c5.fsf@burningswell.com> Message-ID: <87y1r2c7fs.fsf@kitej> MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha512; protocol="application/pgp-signature" X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 60039 Cc: 60039@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) --=-=-= Content-Type: text/plain Roman Scherer skribis: > Hello Guix, > > this patch series updates the GDAL, Netcdf and libtiff packages. It also > adds support for lz4 and openjpeg to GDAL. > > Could you please review it? > > Thanks, Roman. > > [2. text/x-diff; 0001-gnu-gdal-Update-to-3.6.0.patch]... Hi, Instead of this patch 1, I pushed the patch from issue 60159 that updates gdal to 3.6.1. > [3. text/x-diff; 0002-gnu-gdal-Add-support-for-lz4-and-openjpeg.patch]... Patch 2 pushed as 3c6f7b53cea7ea5dc8176fec02271bc3770d7fc1. > [4. text/x-diff; 0003-gnu-libtiff-Update-to-4.4.0.patch]... As libtiff as over 9000 dependents, it has to be updated on the core-updates branch instead of master (see [1]). However, libtiff is already at version 4.4.0 on core-updates, so patch 3 is not necessary and libtiff 4.4.0 will end up in master when core-updates gets merged. [1] https://guix.gnu.org/manual/devel/en/guix.html#Submitting-Patches > [5. text/x-diff; 0004-gnu-netcdf-Update-to-4.9.0.patch]... When adding or removing a patch file to "gnu/packages/patches/...", the 'dist_patch_DATA' variable in "gnu/packages/local.mk" has to be updated to track the necessary patch files. Moreover, as this patch fixes only one line, it is also possible to add a custom phase with a '(substitute* ...)' form in the 'arguments' field instead of adding a patch file. Could you send an updated patch 4? Thanks. Also, many tests are disabled in 'configure-flags'. Are they not working at all? --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iIUEAREKAC0WIQTLxZxm7Ce5cXlAaz5r6CCK3yH+PwUCY6HwVw8cZ2x2QHBvc3Rl by5uZXQACgkQa+ggit8h/j+eEgEAnRnWrynaCdDPjFw7aET6jl5dVeqPjCGtf5tq Lipx+lIA/j8ctWlNBVHHT1D0N+qMZoghnZBDI5lZfP9eqJSgGaiO =c4N/ -----END PGP SIGNATURE----- --=-=-=-- From debbugs-submit-bounces@debbugs.gnu.org Tue Dec 20 14:17:25 2022 Received: (at 60039) by debbugs.gnu.org; 20 Dec 2022 19:17:25 +0000 Received: from localhost ([127.0.0.1]:46702 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p7i7B-00075G-8Y for submit@debbugs.gnu.org; Tue, 20 Dec 2022 14:17:25 -0500 Received: from mail-ed1-f50.google.com ([209.85.208.50]:35487) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p7i78-00075A-Dt for 60039@debbugs.gnu.org; Tue, 20 Dec 2022 14:17:23 -0500 Received: by mail-ed1-f50.google.com with SMTP id i15so18963742edf.2 for <60039@debbugs.gnu.org>; Tue, 20 Dec 2022 11:17:22 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=burningswell-com.20210112.gappssmtp.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=JuU9Fd9Yz0sZyR0MNW/PsaKLqdtC57RTmL+88KPXoUU=; b=tLkJ5EFt2KD35TJXQ4avWLYLNyplN/xWSLwfXJJ3/q0DRf1+3Hl5m+UDpdR8jP3Fyp 1AxOpespKZHC98xJHtb96g5+RHacNvPq0fHacPenblOwMdhNj5XG/tWDgnToMoHdvJ3c 762ncNM/yP7Mxc68CSAqBaPSs6mZtQSvPB6uMTgPEuI2lq7tGIHcB1+b4MayKtIJ2r6H 8t82TdaxOSKJM1dJ8l6YJR1QbtZnSrE8+BAl8MmHGgDcdY/YHmew1Ibu71pfjvYyMRy9 fWqEy5APGN4KqEfIfI7sl01d0O3+WVB8PEGA2nV4BjeSpWmqWRnBMzIyBsGpyBF2BEmh ULDg== 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=JuU9Fd9Yz0sZyR0MNW/PsaKLqdtC57RTmL+88KPXoUU=; b=XWQUOW8GoTb3dIRLHitq5Wbwn7qc2/EAW3ga0J6vq/EeI9aFe9aNQujvWA/ONn6AfK 97Ca40n+FFl1zC1E65fnSKtkAHDqz6WkorTCzM14bCsHuv9bjZAWt2nZDV3n7eFV9LJ9 yGG/kXZo8On2Jq9B2GjMBgSLc0m79PsN6qng0PAVwfCD3x5F43LWVfIODFj26zPuY1Ta E5lDNmS8XnlaauxaoO32FxXa72PaFXyYmmIdc9069NLWqWcoOcjBVh9wT3nkAKxlpjGt RJL2JceGAnYFw4UJJtgid4xzgGqx3WtjR+2nyKFF4JMlsL4ZsSlJ+iuknMhTlMFSbajG 0dyw== X-Gm-Message-State: AFqh2kqgzF+rVtgQnhKT4TwhQVf/HI+LUjY1Vs/wsgoxq99LjDhfeuYu VWVpIgVc4yQXeZCbNEabeM0EYbn5+v0b8bAITiE= X-Google-Smtp-Source: AMrXdXs2a+nGyR5MRVt00IFSi1F0CRdxO6bw+8l/uLh/pbzozlbQ2SLadSwx+8A1V5PrfjpfVwrKYQ== X-Received: by 2002:aa7:d146:0:b0:46f:7453:a99d with SMTP id r6-20020aa7d146000000b0046f7453a99dmr2599327edo.6.1671563835955; Tue, 20 Dec 2022 11:17:15 -0800 (PST) Received: from precision (tmo-119-245.customers.d1-online.com. [80.187.119.245]) by smtp.gmail.com with ESMTPSA id ee8-20020a056402290800b0046fb9492961sm6032136edb.25.2022.12.20.11.17.14 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 20 Dec 2022 11:17:15 -0800 (PST) References: <86mt7rp4c5.fsf@burningswell.com> <87y1r2c7fs.fsf@kitej> User-agent: mu4e 1.8.11; emacs 29.0.50 From: Roman Scherer To: Guillaume Le Vaillant Subject: Re: [bug#60039] Update GDAL and NetCDF and include lz4 and openjpeg support Date: Tue, 20 Dec 2022 20:10:23 +0100 In-reply-to: <87y1r2c7fs.fsf@kitej> Message-ID: <86v8m5nava.fsf@burningswell.com> MIME-Version: 1.0 Content-Type: multipart/signed; boundary="==-=-="; micalg=pgp-sha256; protocol="application/pgp-signature" X-Spam-Score: 1.8 (+) X-Spam-Report: Spam detection software, running on the system "debbugs.gnu.org", has NOT identified this incoming email as spam. The original message has been attached to this so you can view it or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: Hi Guillaume, here's the updated patch for Netcdf. I checked the tests again, I believe I left some of them off by accident after trying a couple of things. So, I enabled some of them again. They pass. However, I l [...] Content analysis details: (1.8 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- -0.0 RCVD_IN_DNSWL_NONE RBL: Sender listed at https://www.dnswl.org/, no trust [209.85.208.50 listed in list.dnswl.org] 0.0 SPF_HELO_NONE SPF: HELO does not publish an SPF Record 0.0 SPF_NONE SPF: sender does not publish an SPF Record -0.0 RCVD_IN_MSPIKE_H2 RBL: Average reputation (+2) [209.85.208.50 listed in wl.mailspike.net] 1.8 URI_DOTEDU Has .edu URI X-Debbugs-Envelope-To: 60039 Cc: 60039@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) --==-=-= Content-Type: multipart/mixed; boundary="=-=-=" --=-=-= Content-Type: text/plain Hi Guillaume, here's the updated patch for Netcdf. I checked the tests again, I believe I left some of them off by accident after trying a couple of things. So, I enabled some of them again. They pass. However, I left the remote and large file tests still turned off. I believe the remote tests we do not want anyway on Guix CICD system. Is that correct? And the large file tests seem to take ages. Can we ignore them, because they are super annoying? Thanks for the review. Wdyt? Roman. --=-=-= Content-Type: text/x-diff Content-Disposition: attachment; filename=0005-gnu-netcdf-Update-to-4.9.0.patch Content-Transfer-Encoding: quoted-printable From=20eb2a03112532f6c1482ebaf1634cf3ac67303507 Mon Sep 17 00:00:00 2001 From: r0man Date: Tue, 20 Dec 2022 20:06:57 +0100 Subject: [PATCH] gnu: netcdf: Update to 4.9.0. * gnu/packages/maths.scm (netcdf): Update to 4.9.0. =2D-- gnu/packages/maths.scm | 50 +++++++++++++++++++++++++++++++----------- 1 file changed, 37 insertions(+), 13 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 050450e12c..a5de0f4016 100644 =2D-- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1852,16 +1852,16 @@ (define-public itpp (define-public netcdf (package (name "netcdf") =2D (version "4.7.4") + (version "4.9.0") (source (origin (method url-fetch) (uri (string-append =2D "https://www.unidata.ucar.edu/downloads/netcdf/ftp/" =2D "netcdf-c-" version ".tar.gz")) + "https://downloads.unidata.ucar.edu/netcdf-c/" version + "/netcdf-c-" version ".tar.gz")) (sha256 (base32 =2D "1a2fpp15a2rl1m50gcvvzd9y6bavl6vjf9zzf63sz5gdmq06yiqf")) + "0j8b814mjdqvqanzmrxpq8hn33n22cdzb3gf9vhya24wnwi615ac")) (modules '((guix build utils))) (snippet ;; Make sure this variable is defined only once. Failing to do so @@ -1870,19 +1870,40 @@ (define-public netcdf '(substitute* "ncdump/ocprint.c" (("^int ocdebug") "static int ocdebug"))) (patches (search-patches "netcdf-date-time.patch")))) =2D (build-system gnu-build-system) + (build-system cmake-build-system) (native-inputs =2D (list m4 doxygen graphviz)) + (list m4 doxygen graphviz unzip)) (inputs `(("hdf4" ,hdf4-alt) =2D ("hdf5" ,hdf5) + ("hdf5" ,hdf5-1.12) ("curl" ,curl) ("zlib" ,zlib) =2D ("libjpeg" ,libjpeg-turbo))) + ("libjpeg" ,libjpeg-turbo) + ("libxml2" ,libxml2))) (arguments =2D `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-h= df4") =2D =2D #:phases (modify-phases %standard-phases + `(#:configure-flags + '("-DENABLE_BYTERANGE=3DON" + "-DENABLE_CDF5=3DON" + "-DENABLE_DAP_LONG_TESTS=3DON" + "-DENABLE_DAP_REMOTE_TESTS=3DOFF" + "-DENABLE_EXAMPLE_TESTS=3DON" + "-DENABLE_EXTRA_TESTS=3DON" + "-DENABLE_FILTER_TESTING=3DON" + "-DENABLE_LARGE_FILE_TESTS=3DOFF" + "-DENABLE_UNIT_TESTS=3DON" + "-DSOURCE_DATE_EPOCH=3D0") + #:phases + (modify-phases %standard-phases + (add-before 'configure 'fix-cmake-typo + (lambda _ + ;; Fix a typo in CMakeLists.txt + (substitute* "CMakeLists.txt" + (("SET\\(netCDF_LIB_VERSION 19\\}\\)") + "SET(netCDF_LIB_VERSION 19)")) + #t)) + (add-before 'configure 'disable-nc-byterange-test + (lambda _ + (invoke "sed" "-i" "/test_byterange/d" "nc_test/CMakeLists.tx= t"))) (add-before 'configure 'fix-source-date (lambda _ ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build @@ -1902,8 +1923,11 @@ (define-public netcdf (substitute* "libnetcdf.settings" (("(/gnu/store/)([0-9A-Za-z]*)" all prefix hash) (string-append prefix (string-take hash 10) "..."))) =2D #t))) =2D + #t)) + (add-before 'check 'fix-test-rcmerge + (lambda _ + ;; Set HOME, to fix the test-rcmerge. + (setenv "HOME" "/tmp")))) #:parallel-tests? #f)) ;various race conditions (home-page "https://www.unidata.ucar.edu/software/netcdf/") (synopsis "Library for scientific data") =2D-=20 2.38.1 --=-=-= Content-Type: text/plain Guillaume Le Vaillant writes: > [[PGP Signed Part:Undecided]] > Roman Scherer skribis: > >> Hello Guix, >> >> this patch series updates the GDAL, Netcdf and libtiff packages. It also >> adds support for lz4 and openjpeg to GDAL. >> >> Could you please review it? >> >> Thanks, Roman. >> >> [2. text/x-diff; 0001-gnu-gdal-Update-to-3.6.0.patch]... > > Hi, > > Instead of this patch 1, I pushed the patch from issue 60159 that updates > gdal to 3.6.1. > > >> [3. text/x-diff; 0002-gnu-gdal-Add-support-for-lz4-and-openjpeg.patch]... > > Patch 2 pushed as 3c6f7b53cea7ea5dc8176fec02271bc3770d7fc1. > > >> [4. text/x-diff; 0003-gnu-libtiff-Update-to-4.4.0.patch]... > > As libtiff as over 9000 dependents, it has to be updated on the > core-updates branch instead of master (see [1]). However, libtiff is > already at version 4.4.0 on core-updates, so patch 3 is not necessary > and libtiff 4.4.0 will end up in master when core-updates gets merged. > > [1] https://guix.gnu.org/manual/devel/en/guix.html#Submitting-Patches > > >> [5. text/x-diff; 0004-gnu-netcdf-Update-to-4.9.0.patch]... > > When adding or removing a patch file to "gnu/packages/patches/...", the > 'dist_patch_DATA' variable in "gnu/packages/local.mk" has to be updated > to track the necessary patch files. > Moreover, as this patch fixes only one line, it is also possible to add > a custom phase with a '(substitute* ...)' form in the 'arguments' field > instead of adding a patch file. > Could you send an updated patch 4? > Thanks. > > Also, many tests are disabled in 'configure-flags'. Are they not working > at all? > > [[End of PGP Signed Part]] --=-=-=-- --==-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQFTBAEBCAA9FiEE0iajOdjfRIFd3gygPdpSUn0qwZkFAmOiCjkfHHJvbWFuLnNj aGVyZXJAYnVybmluZ3N3ZWxsLmNvbQAKCRA92lJSfSrBmYjLB/4qodk1WwmQzT7P 6vLCOuqByoRUBfk0oY/2K3gK6DdP7OSgEOLQjeLnEzIKomAMehkxDgL/5RXkw3zj KsmOS43qeEKqHB6mkpwCfWkV5VcPZJUqLbMeU9EwYG8q5AWAxnieEbW7nKu6p2wU dqR+8ikZZEbwUlArpm2cxACVV1taTt+JRA4THMu4K6kEZgwT8xLN8kLzID1SJ+6X qnuf0IU8W2oBiSTE/geZ3T25f3n3/u8xLV4mbKYjIrUCHhLE/Zqy8v3jxIzUt5eo LiTBai2F9rgES4Q0Tekoe5XcMXb8qX/m32KHflS9vFMVyvI3w7GnaXR/LtBgK5mu HqIivc11 =IbSy -----END PGP SIGNATURE----- --==-=-=-- From debbugs-submit-bounces@debbugs.gnu.org Thu Dec 22 06:01:03 2022 Received: (at 60039) by debbugs.gnu.org; 22 Dec 2022 11:01:03 +0000 Received: from localhost ([127.0.0.1]:57684 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p8JJv-00064G-GH for submit@debbugs.gnu.org; Thu, 22 Dec 2022 06:01:03 -0500 Received: from mout02.posteo.de ([185.67.36.66]:55659) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p8JJt-00063d-98 for 60039@debbugs.gnu.org; Thu, 22 Dec 2022 06:01:02 -0500 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id F25B4240106 for <60039@debbugs.gnu.org>; Thu, 22 Dec 2022 12:00:54 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1671706855; bh=7HfMhQ8ikxKsSyE+aIm9aXl0F6s064w0kSdtdOHQZWs=; h=From:To:Cc:Subject:Date:From; b=QX3/0REYO3UgNf6Noq1Tyme2UQXU/S+K4plmTU+sq6GGQw3oovvj2M48HG27BmECT l7aYyPAwStQVK3AwF4Sxfw/deOqT3mKFRM8NNNk9xM5YeE3BMJgVWtIiLpuaXSQ8bm znNSouiYOozN9kEZf5lK3n+1GlUf+jOCd2V7cKZyIbZge3sXGM2hcG9LzJpZ4W9Lvi tHZkHlPRU6nx0ZHa2y6c1s66Mdf4IFCchKr5cMeyfR93aKV4amyHI7S60aUXHj+kf5 cfBeBAZV04QVHZ1Ml/35IUpz9QbVuwYdsJE19ZjBeXJ/eaRyCb1X8s0z9ryLtaF5my x++WfGfE2j35Q== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4Nd6mk0C3Lz9rxY; Thu, 22 Dec 2022 12:00:52 +0100 (CET) References: <86mt7rp4c5.fsf@burningswell.com> <87y1r2c7fs.fsf@kitej> <86v8m5nava.fsf@burningswell.com> From: Guillaume Le Vaillant To: Roman Scherer Subject: Re: [bug#60039] Update GDAL and NetCDF and include lz4 and openjpeg support Date: Thu, 22 Dec 2022 10:41:15 +0000 In-reply-to: <86v8m5nava.fsf@burningswell.com> Message-ID: <87fsd74s9n.fsf@kitej> MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha512; protocol="application/pgp-signature" X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 60039 Cc: 60039@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) --=-=-= Content-Type: text/plain Roman Scherer skribis: > Hi Guillaume, > > here's the updated patch for Netcdf. I checked the tests again, I > believe I left some of them off by accident after trying a couple of > things. So, I enabled some of them again. They pass. However, I left the > remote and large file tests still turned off. > > I believe the remote tests we do not want anyway on Guix CICD > system. Is that correct? And the large file tests seem to take ages. Can > we ignore them, because they are super annoying? > > Thanks for the review. > > Wdyt? > > Roman. > > [2. text/x-diff; 0005-gnu-netcdf-Update-to-4.9.0.patch]... Hi, The build environment doesn't have network access, so indeed remote tests have to be disabled. The netcdf-parallel-openmpi package fails to build with the updated netcdf. I think it's because the package definition for netcdf-parallel-openmpi inherits from the package definition for netcdf, so it has to be updated to take into consideration the build-system change of netcdf. There are also some dependents that fail to build (cdo, python-h5netcdf, python-meshio, qgis). I saw some error messages about conflicting versions of hdf5, probably because in your patch netcdf uses hdf5-1.12 and the dependents also have hdf5 (v1.10) in their dependency graph in some way. Maybe this could be fixed by using hdf5 instead of hdf5-1.12 for netcdf... Could take a look? --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iIUEAREKAC0WIQTLxZxm7Ce5cXlAaz5r6CCK3yH+PwUCY6Q45A8cZ2x2QHBvc3Rl by5uZXQACgkQa+ggit8h/j/bggD/ZcSYIudDix6ZMNvpHSTM1AI6yjWdnUPg9HDT Q/K80HkA/2YipY38XcgxCwG3fNlggHVe8Wr5AJZWWGLwbpboE9GH =lA2G -----END PGP SIGNATURE----- --=-=-=-- From debbugs-submit-bounces@debbugs.gnu.org Thu Dec 22 14:20:36 2022 Received: (at 60039) by debbugs.gnu.org; 22 Dec 2022 19:20:36 +0000 Received: from localhost ([127.0.0.1]:36228 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p8R7L-0004hF-HN for submit@debbugs.gnu.org; Thu, 22 Dec 2022 14:20:36 -0500 Received: from mail-ed1-f47.google.com ([209.85.208.47]:33284) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p8R7J-0004h4-6Z for 60039@debbugs.gnu.org; Thu, 22 Dec 2022 14:20:34 -0500 Received: by mail-ed1-f47.google.com with SMTP id d20so4344264edn.0 for <60039@debbugs.gnu.org>; Thu, 22 Dec 2022 11:20:33 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=burningswell-com.20210112.gappssmtp.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=VQ6nEJiHvB0Uz9R/HwXL9ZVJHZMCkzpvrFi90zIH/kw=; b=WH/vHMt0HPFI3xsT3kbILb9P8yHB9/XI3mX0XHOUoQ2Q4ZtPGZVnd+fVCsRPEiNUOJ d5jV1XTrCxupvEiCRezunyyqV2a4a3pIqERHiN34nkyVLnoD9IpxrFL2KI2AVmXwd8vu oW6ncOgf+A6CvG832aRehj9Mr1lhaUxN4o7pJ9fLXNpe8Cuv5X94q2EP/lsj3zClw0a9 5wjfm0jBtruuSMGUcjzjCpmsaGOcAJLIidbOyc58LU2wIHzOTyilZYzZ5Bo3eJ+6ePI4 T99NHFpc8EzyzUOhHSxCmpZo0X1p+/ZQJ58L0YJm/WRIMKr44OzTwLpB6fytQ5Lyhgeq sUxA== 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=VQ6nEJiHvB0Uz9R/HwXL9ZVJHZMCkzpvrFi90zIH/kw=; b=cWtjPMZpu0hEDKN6zHks7Jpo2SGARvesU5IvWKywl55PvMR0WVOehqtlcbgwlBObNJ 8ELZKHfksaRwD6QDbc0IrdPuU86o1Slo/5yyfg+G08MZOBci0OA3ihy5Kc5zx3BWy+5j KaUWNKaZGqeBrITlN8DlT1fW7doxrJGzceFXKTtwIE0QlpHqmp0VIV+h4BJqurBAe0So RjPoLxfehPRh+iF6CmA43ZCtOLKs1M7FjAHbpkA8lmdKt7FpppRxHcJbP89J+fIvvQOa XFdRb+q/YHn5yg3kH7fTssZBsCXufF0ARzm1+MhdeBVGkPFqLGI8sD23wBp8lNxeTtmC UVNw== X-Gm-Message-State: AFqh2koaEXs0Je7OzwOBtkOrIzBvNFZZud/aS5yeFEdFSheLzVCtZTdY A3MBYt/f42ToWndzoojRyF/NcdIkXFDSq3h5+C0= X-Google-Smtp-Source: AMrXdXv3FbwMmnNGvhTNcAWPqejk/RcuygN4bnJxpT7ySjEPlrVK3CtDvKV+jcMBalHDcRAky2z5Mg== X-Received: by 2002:aa7:ce11:0:b0:464:5ec3:c46 with SMTP id d17-20020aa7ce11000000b004645ec30c46mr6018163edv.16.1671736825894; Thu, 22 Dec 2022 11:20:25 -0800 (PST) Received: from precision (tmo-117-170.customers.d1-online.com. [80.187.117.170]) by smtp.gmail.com with ESMTPSA id m9-20020a1709062ac900b007c0d41736c0sm551593eje.39.2022.12.22.11.20.24 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Thu, 22 Dec 2022 11:20:25 -0800 (PST) References: <86mt7rp4c5.fsf@burningswell.com> <87y1r2c7fs.fsf@kitej> <86v8m5nava.fsf@burningswell.com> <87fsd74s9n.fsf@kitej> User-agent: mu4e 1.8.11; emacs 29.0.50 From: Roman Scherer To: Guillaume Le Vaillant Subject: Re: [bug#60039] Update GDAL and NetCDF and include lz4 and openjpeg support Date: Thu, 22 Dec 2022 20:07:43 +0100 In-reply-to: <87fsd74s9n.fsf@kitej> Message-ID: <86zgbfqm88.fsf@burningswell.com> MIME-Version: 1.0 Content-Type: multipart/signed; boundary="==-=-="; micalg=pgp-sha256; protocol="application/pgp-signature" X-Spam-Score: 0.7 (/) X-Debbugs-Envelope-To: 60039 Cc: 60039@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) --==-=-= Content-Type: multipart/mixed; boundary="=-=-=" --=-=-= Content-Type: text/plain Hi Guillaume, sorry about that. Here is another patch. The failed dependencies you mentioned are working now. Another reason why netcdf-parallel-openmpi failed was that I changed the build system previously to cmake. I went back to use the original gnu build system. I changed it to cmake initially because I saw that in Arch Linux's PKGBUILD and I remember having had some problems initially. I guess it was related to the tests I now patched. While at the topic. Do we prefer any build system over the other in general in Guix, like cmake vs gnu. Does one have more features than the other (I heard something about cross compilation)? And another question. How did you find the failing dependencies in the first place? Did you build all the dependencies of the netcdf packages with --sources=all? Thanks for the help. Roman --=-=-= Content-Type: text/x-diff Content-Disposition: attachment; filename=0006-gnu-netcdf-Update-to-4.9.0.patch Content-Transfer-Encoding: quoted-printable From=20a5ad4273294d0d92eec1eeab2173f12bfe36b74b Mon Sep 17 00:00:00 2001 From: r0man Date: Thu, 22 Dec 2022 19:41:14 +0100 Subject: [PATCH] gnu: netcdf: Update to 4.9.0. * gnu/packages/maths.scm (netcdf): Update to 4.9.0. =2D-- gnu/packages/maths.scm | 33 ++++++++++++++++++++------------- 1 file changed, 20 insertions(+), 13 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 050450e12c..0d1c65636b 100644 =2D-- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1852,16 +1852,16 @@ (define-public itpp (define-public netcdf (package (name "netcdf") =2D (version "4.7.4") + (version "4.9.0") (source (origin (method url-fetch) (uri (string-append =2D "https://www.unidata.ucar.edu/downloads/netcdf/ftp/" =2D "netcdf-c-" version ".tar.gz")) + "https://downloads.unidata.ucar.edu/netcdf-c/" version + "/netcdf-c-" version ".tar.gz")) (sha256 (base32 =2D "1a2fpp15a2rl1m50gcvvzd9y6bavl6vjf9zzf63sz5gdmq06yiqf")) + "0j8b814mjdqvqanzmrxpq8hn33n22cdzb3gf9vhya24wnwi615ac")) (modules '((guix build utils))) (snippet ;; Make sure this variable is defined only once. Failing to do so @@ -1874,13 +1874,18 @@ (define-public netcdf (native-inputs (list m4 doxygen graphviz)) (inputs =2D `(("hdf4" ,hdf4-alt) + `(("curl" ,curl) + ("hdf4" ,hdf4-alt) ("hdf5" ,hdf5) =2D ("curl" ,curl) =2D ("zlib" ,zlib) =2D ("libjpeg" ,libjpeg-turbo))) + ("libjpeg" ,libjpeg-turbo) + ("libxml2" ,libxml2) + ("unzip" ,unzip) + ("zlib" ,zlib))) (arguments =2D `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-h= df4") + `(#:configure-flags '("--enable-doxygen" + "--enable-dot" + "--enable-hdf4" + "--disable-dap-remote-tests") =20 #:phases (modify-phases %standard-phases (add-before 'configure 'fix-source-date @@ -1891,8 +1896,7 @@ (define-public netcdf ;; package not reproducible. (substitute* "./configure" (("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"") =2D "date --date=3D'@0'")) =2D #t)) + "date --date=3D'@0'")))) (add-after 'configure 'patch-settings (lambda _ ;; libnetcdf.settings contains the full filename of the compi= lers @@ -1901,8 +1905,11 @@ (define-public netcdf ;; store items. (substitute* "libnetcdf.settings" (("(/gnu/store/)([0-9A-Za-z]*)" all prefix hash) =2D (string-append prefix (string-take hash 10) "..."))) =2D #t))) + (string-append prefix (string-take hash 10) "..."))))) + (add-before 'check 'fix-test-rcmerge + (lambda _ + ;; Set HOME, to fix the test-rcmerge test. + (setenv "HOME" "/tmp")))) =20 #:parallel-tests? #f)) ;various race conditions (home-page "https://www.unidata.ucar.edu/software/netcdf/") =2D-=20 2.38.1 --=-=-= Content-Type: text/plain Guillaume Le Vaillant writes: > [[PGP Signed Part:Undecided]] > Roman Scherer skribis: > >> Hi Guillaume, >> >> here's the updated patch for Netcdf. I checked the tests again, I >> believe I left some of them off by accident after trying a couple of >> things. So, I enabled some of them again. They pass. However, I left the >> remote and large file tests still turned off. >> >> I believe the remote tests we do not want anyway on Guix CICD >> system. Is that correct? And the large file tests seem to take ages. Can >> we ignore them, because they are super annoying? >> >> Thanks for the review. >> >> Wdyt? >> >> Roman. >> >> [2. text/x-diff; 0005-gnu-netcdf-Update-to-4.9.0.patch]... > > Hi, > > The build environment doesn't have network access, so indeed remote > tests have to be disabled. > > The netcdf-parallel-openmpi package fails to build with the updated > netcdf. I think it's because the package definition for > netcdf-parallel-openmpi inherits from the package definition for netcdf, > so it has to be updated to take into consideration the build-system > change of netcdf. > > There are also some dependents that fail to build (cdo, python-h5netcdf, > python-meshio, qgis). I saw some error messages about conflicting > versions of hdf5, probably because in your patch netcdf uses hdf5-1.12 > and the dependents also have hdf5 (v1.10) in their dependency graph in > some way. Maybe this could be fixed by using hdf5 instead of hdf5-1.12 > for netcdf... > > Could take a look? > > [[End of PGP Signed Part]] --=-=-=-- --==-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQFTBAEBCAA9FiEE0iajOdjfRIFd3gygPdpSUn0qwZkFAmOkrfcfHHJvbWFuLnNj aGVyZXJAYnVybmluZ3N3ZWxsLmNvbQAKCRA92lJSfSrBmdyzCADFGryBgD7LJDbT son0j+ihzrmv5ozGDAoCCVAMYNVusmKzvd/WFuWQYTE1Cz/BBm0CtKT6QaWCNTs7 CJgXRnmFDluCR9KOyEIy3iHNmWHoHT7gmCG4zaYRhtBldHd9rTKLMarjhCrCYdtl /iVLaxEZ1sh4A1nQd+1WPfxdiADFzo7Nh5B1szcdl837zXhNu/u8Og3TIht1SpIw 3OE7OT1tdyI1dLguBMKdi5nWAL0ENHCRVw/L0UFC2a9TQvyHdiJDedFhiU+K0H+u G/7QFwTrvYhXPPZZWwxA0phw+bji/Hz/QhD5oRpJ/H1R82OppBglXpvmT7VehgoF wo2WBRKm =2Qzb -----END PGP SIGNATURE----- --==-=-=-- From debbugs-submit-bounces@debbugs.gnu.org Fri Dec 23 06:11:19 2022 Received: (at 60039-done) by debbugs.gnu.org; 23 Dec 2022 11:11:19 +0000 Received: from localhost ([127.0.0.1]:36934 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p8fxP-0000I4-5C for submit@debbugs.gnu.org; Fri, 23 Dec 2022 06:11:19 -0500 Received: from mout02.posteo.de ([185.67.36.66]:37469) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p8fxM-0000Hy-89 for 60039-done@debbugs.gnu.org; Fri, 23 Dec 2022 06:11:17 -0500 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 527EA240103 for <60039-done@debbugs.gnu.org>; Fri, 23 Dec 2022 12:11:07 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1671793870; bh=frd+pzmbS4phhjl20BzAMhk/G1e797F0r1RuGxq3lz8=; h=From:To:Cc:Subject:Date:From; b=YCrRRP3La+rpkdmahQXP4uvFT5hoPH6YvLNkzURmnk5IffwxV8iVTKNTHKGg+DGfY Fskj1BnzVTCAcogNJxyLM9lMFnqBFFkNZSLfriTA9Fnxh07jFEuB6ebI5gizXSFD/h jd1XH1QlXBPGMKNI80GyBIaqt67e3BQaMZyYeJMEapHlKvWIB/REWlxPR/SYyYRhug 8CA9M1nyBzVBJDHEq0/Ses6gdSh3hDMzmmzBfLPQgJy6QASL8/rl3jTXZTUM1O9wMC b4G6hsGuF8gIe0DNb8+ZBLkIer3Fr02zGSUPSeNBjZwDuwVQmn3Of6mETEJSmro8LP jA1A74c7OCWYw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4Ndky30z4Zz6tmq; Fri, 23 Dec 2022 12:11:04 +0100 (CET) References: <86mt7rp4c5.fsf@burningswell.com> <87y1r2c7fs.fsf@kitej> <86v8m5nava.fsf@burningswell.com> <87fsd74s9n.fsf@kitej> <86zgbfqm88.fsf@burningswell.com> From: Guillaume Le Vaillant To: Roman Scherer Subject: Re: [bug#60039] Update GDAL and NetCDF and include lz4 and openjpeg support Date: Fri, 23 Dec 2022 10:58:44 +0000 In-reply-to: <86zgbfqm88.fsf@burningswell.com> Message-ID: <87wn6iv0hk.fsf@kitej> MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha512; protocol="application/pgp-signature" X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 60039-done Cc: 60039-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) --=-=-= Content-Type: text/plain Roman Scherer skribis: > Hi Guillaume, > > sorry about that. Here is another patch. The failed dependencies you > mentioned are working now. Another reason why netcdf-parallel-openmpi > failed was that I changed the build system previously to cmake. I went > back to use the original gnu build system. I changed it to cmake > initially because I saw that in Arch Linux's PKGBUILD and I remember > having had some problems initially. I guess it was related to the tests > I now patched. > > While at the topic. Do we prefer any build system over the other in > general in Guix, like cmake vs gnu. Does one have more features than the > other (I heard something about cross compilation)? Usually the best build system is the one that upstream developers use. If several equivalent build systems can be used, it depends what works best or what is easier in Guix... > And another question. How did you find the failing dependencies in the > first place? Did you build all the dependencies of the netcdf packages > with --sources=all? You can find the dependents of a package with: --8<---------------cut here---------------start------------->8--- ./pre-inst-env guix refresh -l --8<---------------cut here---------------end--------------->8--- So you can rebuild all the dependents of a package with something like: --8<---------------cut here---------------start------------->8--- ./pre-inst-env guix build $(./pre-inst-env guix refresh -l | cut -d ':' -f 2) --8<---------------cut here---------------end--------------->8--- Patch pushed as 66188398c446bdf9ce044fa539536e9b54c28c60 with a complete commit message. Thanks. --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iIUEAREKAC0WIQTLxZxm7Ce5cXlAaz5r6CCK3yH+PwUCY6WMxw8cZ2x2QHBvc3Rl by5uZXQACgkQa+ggit8h/j+DYAD/ZhD+UcJ7VysznHdz1PO7yTaT0BHeUPz9imOy 01GPdH4A/0+CRxLZT7XWi7xkeFvzInh74LmGqH3J8WA0iuPnVrEg =DtYN -----END PGP SIGNATURE----- --=-=-=-- From debbugs-submit-bounces@debbugs.gnu.org Fri Dec 23 06:13:55 2022 Received: (at 60039-done) by debbugs.gnu.org; 23 Dec 2022 11:13:55 +0000 Received: from localhost ([127.0.0.1]:36942 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p8fzu-0000K3-NS for submit@debbugs.gnu.org; Fri, 23 Dec 2022 06:13:55 -0500 Received: from mail-ed1-f54.google.com ([209.85.208.54]:36838) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p8fzr-0000Jw-E8 for 60039-done@debbugs.gnu.org; Fri, 23 Dec 2022 06:13:53 -0500 Received: by mail-ed1-f54.google.com with SMTP id m21so6693972edc.3 for <60039-done@debbugs.gnu.org>; Fri, 23 Dec 2022 03:13:51 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=burningswell-com.20210112.gappssmtp.com; s=20210112; h=cc:to:subject:message-id:date:from:in-reply-to:references :mime-version:from:to:cc:subject:date:message-id:reply-to; bh=kbNHuBNhTJji6NT2Cfsdv19Q2IWOSwFUD+OyIhiebNg=; b=MdcSgCrFMELaPr+UA9LDDBTExdL3QDw4wm1IoEIyNXVS/JvyJdem+LT+RjEJXHB19K DR/Krp2ia/cOXZLq8V4qBbP/7kKlBGNzkxzI3LlxHyjhklfk31Np+x916OlHSBSx+RUc 40vsrxf975d4exoV84DsdyFY+8QVMiH1eemQ307npRnEe44/GKcQFExqlZUQ61kt71LM KDw7AXLeBYYOf15jZKPRkHEsoUlmMfrayo9MYR44Go7H8jaukWx1+KVBJimfi70GMaCR pWtLNJIneSeThxDETJcaYwvnsh7JPMy7Los4C+dWYdux64K4audrLz1imARlw6QI4nBv JGuw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=cc:to:subject:message-id:date:from:in-reply-to:references :mime-version:x-gm-message-state:from:to:cc:subject:date:message-id :reply-to; bh=kbNHuBNhTJji6NT2Cfsdv19Q2IWOSwFUD+OyIhiebNg=; b=OmC5EQ8O8jFJVd1BXIOuQSYqgwgU3C/lRoMUD99Is9XJyzBYBACYAHAowG4b2DVH2n nW+WTTxF/JzWlDwq5AhHA5KYIZdsduGEUq2Fu6oTamTf0RrHnEBj3Rn+EE69MCwCK0fh rlR7UQl7in99OYIZlalFXlNseHEx7Ns3hlEup9klN+KYZ6FP5+oYJOiwc/uzRZuh7VHu xjCsu5KcpUhneu1Q0Bj2tl15w8bmeeWvqqk2scPduQ0UXfcYblL90MCTwcY3RR8tXmn4 iQViXQb8zxDAqa4eP6zWAlpoO1qMQeQJPNNxO6u5j9oecQbdtwQG+iH8TH7bM8jjOffV DyHw== X-Gm-Message-State: AFqh2kqcXlAP8EUO//87u7zMewuA+RhOxheXkGpsIUS4v5SqMoft6nZB EGqf9xPbKG6EOV87BtzuxwP46j1ztpWmlMnZN60D+g== X-Google-Smtp-Source: AMrXdXvgQwv2Vc9DQxn1gLpE+L4NP8EaUy4jZhJbnUAIJ6rD9Ri8el6rbPhKH85OhAktM2dhyGdSo1XSxWDokLwvgxM= X-Received: by 2002:a05:6402:642:b0:46b:4156:76d2 with SMTP id u2-20020a056402064200b0046b415676d2mr910019edx.224.1671794025455; Fri, 23 Dec 2022 03:13:45 -0800 (PST) MIME-Version: 1.0 References: <86mt7rp4c5.fsf@burningswell.com> <87y1r2c7fs.fsf@kitej> <86v8m5nava.fsf@burningswell.com> <87fsd74s9n.fsf@kitej> <86zgbfqm88.fsf@burningswell.com> <87wn6iv0hk.fsf@kitej> In-Reply-To: <87wn6iv0hk.fsf@kitej> From: Roman Scherer Date: Fri, 23 Dec 2022 12:13:33 +0100 Message-ID: Subject: Re: [bug#60039] Update GDAL and NetCDF and include lz4 and openjpeg support To: Guillaume Le Vaillant Content-Type: multipart/alternative; boundary="000000000000067a1e05f07ce1a2" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 60039-done Cc: 60039-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) --000000000000067a1e05f07ce1a2 Content-Type: text/plain; charset="UTF-8" Thank you! On Fri, Dec 23, 2022, 12:11 Guillaume Le Vaillant wrote: > Roman Scherer skribis: > > > Hi Guillaume, > > > > sorry about that. Here is another patch. The failed dependencies you > > mentioned are working now. Another reason why netcdf-parallel-openmpi > > failed was that I changed the build system previously to cmake. I went > > back to use the original gnu build system. I changed it to cmake > > initially because I saw that in Arch Linux's PKGBUILD and I remember > > having had some problems initially. I guess it was related to the tests > > I now patched. > > > > While at the topic. Do we prefer any build system over the other in > > general in Guix, like cmake vs gnu. Does one have more features than the > > other (I heard something about cross compilation)? > > Usually the best build system is the one that upstream developers use. > If several equivalent build systems can be used, it depends what works > best or what is easier in Guix... > > > > And another question. How did you find the failing dependencies in the > > first place? Did you build all the dependencies of the netcdf packages > > with --sources=all? > > You can find the dependents of a package with: > > --8<---------------cut here---------------start------------->8--- > ./pre-inst-env guix refresh -l > --8<---------------cut here---------------end--------------->8--- > > So you can rebuild all the dependents of a package with something like: > > --8<---------------cut here---------------start------------->8--- > ./pre-inst-env guix build $(./pre-inst-env guix refresh -l > | cut -d ':' -f 2) > --8<---------------cut here---------------end--------------->8--- > > > Patch pushed as 66188398c446bdf9ce044fa539536e9b54c28c60 with a complete > commit message. > Thanks. > --000000000000067a1e05f07ce1a2 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Thank you!

On Fri, Dec 23, 2022, 12:11 Guillaume Le Vail= lant <glv@posteo.net> wrote:
Roman Scherer <roman.s= cherer@burningswell.com> skribis:

> Hi Guillaume,
>
> sorry about that. Here is another patch. The failed dependencies you > mentioned are working now. Another reason why netcdf-parallel-openmpi<= br> > failed was that I changed the build system previously to cmake. I went=
> back to use the original gnu build system. I changed it to cmake
> initially because I saw that in Arch Linux's PKGBUILD and I rememb= er
> having had some problems initially. I guess it was related to the test= s
> I now patched.
>
> While at the topic. Do we prefer any build system over the other in > general in Guix, like cmake vs gnu. Does one have more features than t= he
> other (I heard something about cross compilation)?

Usually the best build system is the one that upstream developers use.
If several equivalent build systems can be used, it depends what works
best or what is easier in Guix...


> And another question. How did you find the failing dependencies in the=
> first place? Did you build all the dependencies of the netcdf packages=
> with --sources=3Dall?

You can find the dependents of a package with:

--8<---------------cut here---------------start------------->8---
./pre-inst-env guix refresh -l <package-name>
--8<---------------cut here---------------end--------------->8---

So you can rebuild all the dependents of a package with something like:

--8<---------------cut here---------------start------------->8---
./pre-inst-env guix build $(./pre-inst-env guix refresh -l <package-name= > | cut -d ':' -f 2)
--8<---------------cut here---------------end--------------->8---


Patch pushed as 66188398c446bdf9ce044fa539536e9b54c28c60 with a complete commit message.
Thanks.
--000000000000067a1e05f07ce1a2-- From unknown Sat Sep 20 13:00:05 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Fri, 20 Jan 2023 12:24:04 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator