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[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 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-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-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=burningswell-com.20210112.gappssmtp.com header.s=20210112 header.b=tLkJ5EFt; dmarc=none; 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" ARC-Seal: i=1; s=key1; d=yhetil.org; t=1671563892; a=rsa-sha256; cv=none; b=IIdE3nD/xzFSp47S95T93YyRagYyhKsxwK/tSK/ZQWh68WYR+LgTtNAGZ4BhAHV/T1TZvY 0U+eKaA6lWFeVdddKATcckOdRHPFE8xiMJ6zShV4hgaZhk7dbikIPi1vXXaF17L9DT+2/b k/F791IHyolQ3O3h2vKBGMh/Hk1wcvMKEJelYR6DyBU3ClE2WWVGc5RxdlWFmvLdZFhATo djrTj9+dij84zvwZlY0P26K0v5L/6bDgctBAV+fQ++05nCbjMd1gmlGBZ0xHtoL8oAXw7J 0+IJifw0Qr+fZtlvCGgc12SEtRP8ZWzknkE1G7j/fGNaYhN298DePXo8fciP0g== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1671563892; 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=JuU9Fd9Yz0sZyR0MNW/PsaKLqdtC57RTmL+88KPXoUU=; b=Yq4F3pP1QI+Eww2OGC2vBYgwysMql2II/3+JjlBp9/iOkG2Gqi60lxKq9ZL1m9wJXuE32B 0fbhKHbApPBtin8dAg6xAl0z7JsKVdgkAWtqvpkl9Hr71ZKJZcof5xekGx0YHUa9q4q/NW 2jmP+3tsYj/f/z9YvtRpkIQggde0Hkxn17xPW7dH8W4lAhhxWT6/LEP0T/Yi3J06nDiQ2S WhkIuoS/EnKqJrAJrea/laUaHSiR2kaqIu5TEK34jmHUQIkXI1k5D/9tWaYpedYl9YMDlA MQV74Bmw4bY3kXsNgpc3LU4npLy8+dPUzJ+TrVmq+QwDeXNCG9GT2xsNT0Gqdw== Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=burningswell-com.20210112.gappssmtp.com header.s=20210112 header.b=tLkJ5EFt; dmarc=none; 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" X-Migadu-Scanner: scn1.migadu.com X-Migadu-Spam-Score: -4.09 X-Spam-Score: -4.09 X-Migadu-Queue-Id: 6ED911439B X-TUID: CCRe8SazJiFD --==-=-= 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----- --==-=-=--