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[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 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-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-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1671736886; 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=VQ6nEJiHvB0Uz9R/HwXL9ZVJHZMCkzpvrFi90zIH/kw=; b=Rm3X6jMyFlcfcKpsFkF4WM0EzloavGAnU33cQ3M/UrkgjjM6rRM0wLFJ+SLz7wL328W7uo CsdhDAlUJ//1vn19eMZa4TDtdk+6x/AikYKCLj4F3iak/hx6ymXCA91EYWP6r5nBob8wS+ C85ZL8IXj8ROY2FaRh9UNUOOdCVVb5XLmSUwuuDaiP1Xnb8dF2+4EU9JFNu2r/iiwMCq+S 7v5/39Dr4s/3C11qZKgNpp7wOxoXH+X2sUA3ZAGUCPFuAu9/0tgWv4iqolleTidKoekLA5 admGipXVxs+Cd24tHvn0Mr37A5h1151HT5aveqVzzzd1ZzgfYfEGD/Dw0tZHWw== 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="WH/vHMt0"; 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"; dmarc=none ARC-Seal: i=1; s=key1; d=yhetil.org; t=1671736886; a=rsa-sha256; cv=none; b=STTrs8Pw3LG5X0oIGmVPP4gDyGg9x1O9kgtsvQCiDdUAytBm8EEllKSBiJ3myYdKiXcvcs 8qk3D4MA6U3DIWIlnBlIuKrHQll+WhZlFMdP4sLhxK3G82yLpuhoTjCqotDNXDzGZe2ASG DRpq2pOLLA7VXPBTrLB/CT9jzpMtLojmtDBlPdLA5YjOFNMTSZnxT8YfkiHJ51YswG0Rfn 2PW+0K/nH92YCUbdCix8AiFgXfWhcoIwSYCkf4f2EFBdnH0ceusniadIBs+OW87oARs1Zk WQW+f5hLB+VbpnMZ36l6RxnW18ZjST8Iim2rl1rSIVT7QqSgCmCwTpf3Yc064g== X-Spam-Score: -1.10 X-Migadu-Queue-Id: 5DC772B423 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=burningswell-com.20210112.gappssmtp.com header.s=20210112 header.b="WH/vHMt0"; 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"; dmarc=none X-Migadu-Scanner: scn1.migadu.com X-Migadu-Spam-Score: -1.10 X-TUID: 9qAxVmQ/TIfV --==-=-= 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----- --==-=-=--