From unknown Fri Jun 20 07:21:38 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#39204 <39204@debbugs.gnu.org> To: bug#39204 <39204@debbugs.gnu.org> Subject: Status: r-rgdal: Reading of vector GIS data causes segfault Reply-To: bug#39204 <39204@debbugs.gnu.org> Date: Fri, 20 Jun 2025 14:21:38 +0000 retitle 39204 r-rgdal: Reading of vector GIS data causes segfault reassign 39204 guix submitter 39204 Wiktor =C5=BBelazny severity 39204 normal thanks From debbugs-submit-bounces@debbugs.gnu.org Mon Jan 20 10:43:15 2020 Received: (at submit) by debbugs.gnu.org; 20 Jan 2020 15:43:15 +0000 Received: from localhost ([127.0.0.1]:45843 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1itZCs-0007wt-VP for submit@debbugs.gnu.org; Mon, 20 Jan 2020 10:43:15 -0500 Received: from lists.gnu.org ([209.51.188.17]:55074) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1itZCq-0007wl-UY for submit@debbugs.gnu.org; Mon, 20 Jan 2020 10:43:13 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:52022) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1itZCp-00043B-SI for bug-guix@gnu.org; Mon, 20 Jan 2020 10:43:12 -0500 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=BAYES_50 autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1itZCo-00056E-R8 for bug-guix@gnu.org; Mon, 20 Jan 2020 10:43:11 -0500 Received: from freeshell.de ([2a01:360:106::2]:43938) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1itZCo-00054C-LP for bug-guix@gnu.org; Mon, 20 Jan 2020 10:43:10 -0500 Date: Mon, 20 Jan 2020 16:43:02 +0100 From: Wiktor =?utf-8?Q?=C5=BBelazny?= To: bug-guix@gnu.org Subject: r-rgdal: Reading of vector GIS data causes segfault Message-ID: <20200120154302.ijni47ou4fk4wd77@wzguix> Mail-Followup-To: bug-guix@gnu.org X-PGP-Key: https://freeshell.de/~wz/pubkey.asc X-PGP-Fingerprint: BDC9 74CD D9C9 BA7D 761A 573D C735 A8C6 AB60 79D5 Content-Type: multipart/signed; micalg=pgp-sha512; protocol="application/pgp-signature"; boundary="3ntvqlmlmobptpmk" Content-Disposition: inline X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-Received-From: 2a01:360:106::2 X-Spam-Score: -1.4 (-) 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: -2.4 (--) --3ntvqlmlmobptpmk Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Hi list, The same behaviour on two machines. To reproduce: guix environment --container --ad-hoc r r-rgdal Rscript -e 'library(rgdal); dsn <- system.file("vectors", package =3D "rgda= l")[1]; ogrInfo(dsn=3Ddsn, layer=3D"cities")' Loading required package: sp rgdal: version: 1.4-8, (SVN revision 845) Geospatial Data Abstraction Library extensions to R successfully loaded Loaded GDAL runtime: GDAL 3.0.2, released 2019/10/28 Path to GDAL shared files: GDAL binary built with GEOS: TRUE Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493] Path to PROJ.4 shared files: (autodetected) Linking to sp version: 1.3-2 *** caught segfault *** address 0x30, cause 'memory not mapped' Traceback: 1: ogrFIDs(dsn =3D dsn, layer =3D layer) 2: ogrInfo(dsn =3D dsn, layer =3D "cities") An irrecoverable exception occurred. R is aborting now ... sh: rm: command not found Segmentation fault Opening with QGIS, which also depends on GDAL (it uses PROJ.6 instead of PROJ.4, though), works. 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The issue is that the error is not catched at build time. It is not expected. This package should fail and not say "successfully built". Well, this needs more investigation. --8<---------------cut here---------------start------------->8--- $ guix build r-rgdal --check --no-grafts -K [...] phase `install' succeeded after 19.0 seconds starting phase `check' Testing examples for package =E2=80=98rgdal=E2=80=99 /gnu/store/dnb6fzp5295fcda66dnjk2y51mcva20f-r-minimal-3.6.2/lib/R/bin/BATCH= : line 60: 598 Segmentation fault ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1 [...] successfully built /gnu/store/7spmagnk5fycwxsigdypwkmk4kazbw7a-r-rgdal-1.4-= 8.drv note: keeping build directory `/tmp/guix-build-r-rgdal-1.4-8.drv-0' /gnu/store/dgkyzlasbqsxcsfk3n3bgmhrpg447f55-r-rgdal-1.4-8 --8<---------------cut here---------------end--------------->8--- Good catch! :-) All the best, simon -- $ guix describe Generation 68 Jan 16 2020 15:57:09 (current) guix d14e474 repository URL: https://git.savannah.gnu.org/git/guix.git branch: master commit: d14e4745b36a835c6babd5b5f5562e12294cd9cf From debbugs-submit-bounces@debbugs.gnu.org Thu Feb 20 05:35:34 2020 Received: (at 39204) by debbugs.gnu.org; 20 Feb 2020 10:35:34 +0000 Received: from localhost ([127.0.0.1]:43897 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j4jB7-0008Uu-Nb for submit@debbugs.gnu.org; Thu, 20 Feb 2020 05:35:33 -0500 Received: from mail-qt1-f170.google.com ([209.85.160.170]:33737) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j4jB2-0008UP-OU for 39204@debbugs.gnu.org; Thu, 20 Feb 2020 05:35:32 -0500 Received: by mail-qt1-f170.google.com with SMTP id d5so2506684qto.0 for <39204@debbugs.gnu.org>; Thu, 20 Feb 2020 02:35:28 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc:content-transfer-encoding; bh=BDKmhC2VJAgSq/JlXwza2CCUmfy1P93FB/vIoXuc0OA=; b=Z0WzVHVjg+8YoIz6JIngjbtAWaDD376LYDN4bCWbVO8dc4pIHJmD19aSecr7RitNjs d7t4E4WH04EL12AGbF0OdwiURrRkgMY5i3YQCdpC/bGGUC00EMcsjyN1rgxysrsabS9j CUR4zXaoOJaVtH0x9PEfiYRrozpDbPdR6RG9xOyCKyVnB7Sg4TQpsPwbPzyfFn/N805Z +ZvV1gFudeEnGsyzCE4tI8CfNTiOGJly0JiDfrx3bilBAChz8m8d+7QDMLe8lJVReiBB zi1It7kEaXFeBT4oIbgRVqHf5S4VqUUoAQfGS4vZl2yrVSyuTrKduOpA3NoJbQ2mxdU9 MwcA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc:content-transfer-encoding; bh=BDKmhC2VJAgSq/JlXwza2CCUmfy1P93FB/vIoXuc0OA=; b=MYYdk0qXNyUsghSlQ7+DNjrFbj48Q7kO3+NthSo78Y/wGAlxUgCurbOlP/BSB7LKlQ agk7dBRYzr3x3kYqXmUJ1O5x3r4VIBBnVzBKiwL0SsfJO+da7dhEHQ76Y21hj1iv149R JUObexe9/KnOJoAlMmFnaRwgYVzo4iQkhiD+S5EZrOyJ/aKBqalB+qd1v+DfFAU+/9CB mqtEIJ8UrksVbn/OuNsOIg8EjkHH0yog42v5UEAd8LGLwjZEoN1Ia8IUGuwTgp5+Mi0t mjKM4Z1+ftpR2G5e6Adgl2dcYiQqO9/0W2Du5ozvWb96qnQYYeKi2rcgNURP7/a9q54h n1Cg== X-Gm-Message-State: APjAAAVUTept4nRFBI7ZorD9il2w+GhvPz0hT8QKIvmbuBIg7qPuiQH6 W4QK3rgtaegcvvzFobQtFaodo+QnLsvUKhkRQKM= X-Google-Smtp-Source: APXvYqzfquvyVM58WeKR7cXSL1mEQhWFO3Dbo1s7pUjKMP8OnD+5htGfyDxtF579ZXyb/C84OISPHfaS6Wmpch6En6M= X-Received: by 2002:aed:2050:: with SMTP id 74mr25720722qta.217.1582194923106; Thu, 20 Feb 2020 02:35:23 -0800 (PST) MIME-Version: 1.0 References: <20200120154302.ijni47ou4fk4wd77@wzguix> In-Reply-To: From: zimoun Date: Thu, 20 Feb 2020 11:35:12 +0100 Message-ID: Subject: Re: bug#39204: r-rgdal: Reading of vector GIS data causes segfault To: wz@freeshell.de, Arun Isaac Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 39204 Cc: 39204@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 (-) Hi Arun, There is 2 issues in this bug report: 1. the `check' phase is failing but the build ends with "success". 2. a regression of r-rgdal introduced by your commit f9d328833fc1f5d0fb76b61b12d1a3cb013932e6 About the point 1., here is what happens: > --8<---------------cut here---------------start------------->8--- > $ guix build r-rgdal --check --no-grafts -K > [...] > phase `install' succeeded after 19.0 seconds > starting phase `check' > Testing examples for package =E2=80=98rgdal=E2=80=99 > /gnu/store/dnb6fzp5295fcda66dnjk2y51mcva20f-r-minimal-3.6.2/lib/R/bin/BAT= CH: > line 60: 598 Segmentation fault ${R_HOME}/bin/R -f ${in} > ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1 > [...] > successfully built /gnu/store/7spmagnk5fycwxsigdypwkmk4kazbw7a-r-rgdal-1.= 4-8.drv > note: keeping build directory `/tmp/guix-build-r-rgdal-1.4-8.drv-0' > /gnu/store/dgkyzlasbqsxcsfk3n3bgmhrpg447f55-r-rgdal-1.4-8 > --8<---------------cut here---------------end--------------->8--- Therefore, more investigations are required to see why the upstream test suite does not report correctly the failure. However, the Segmentation Fault is the point 2. and introduced by the commi= t: --8<---------------cut here---------------start------------->8--- commit f9d328833fc1f5d0fb76b61b12d1a3cb013932e6 Author: Arun Isaac Date: Thu Dec 5 01:47:47 2019 +0530 gnu: libgeotiff: Update to 1.5.1. * gnu/packages/patches/libgeotiff-adapt-test-script-for-proj-6.2.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/geo.scm (libgeotiff): Update to 1.5.1. [inputs]: Replace proj.4 with proj. [sources]: Add libgeotiff-adapt-test-script-for-proj-6.2.patch to patches. gnu/local.mk | 1 + gnu/packages/geo.scm | 17 +++--- ...libgeotiff-adapt-test-script-for-proj-6.2.patch | 63 ++++++++++++++++++= ++++ 3 files changed, 72 insertions(+), 9 deletions(-) create mode 100644 gnu/packages/patches/libgeotiff-adapt-test-script-for-proj-6.2.patch --8<---------------cut here---------------end--------------->8--- I have bisected this way: git bisect start git bisect bad ba7ead2b507d94397481be014d6ac0c41c7ddbfa git bisect good 28d940961cfa1ae6dc574053aec8d03095677df8 # ba7ead2b507d94397481be014d6ac0c41c7ddbfa =3D> bad # 28d940961cfa1ae6dc574053aec8d03095677df8 =3D> good # fe0686864dc57ecdda7ecbb318d2618ac46169ae =3D> bad # 85c945aa97d89fdc17ec5d64c3ffa7f99ba1184b =3D> good # 885424bf7f6e0bc0ad5dd9353690aa82d17dd8b8 =3D> bad # 6f5d849a83c44ffb39c3a976aea10b7b31c24063 =3D> good # ce5b71f98ce39c92637876120f44868ec7ad391f =3D> good # 96211e3f33d1f1c35fd6377db1d8a4c6ec1a9c22 =3D> bad # 6cde07379f2a049b8c7f0eca90959f6c170c4102 =3D> bad # 87a028100c665814c3b5d622701abc6d77144faf =3D> good # 00d81f9866726f85241f08e444ba3932fcb38842 =3D> good # e72557c08f4f2fdd545106a9f4f0fc0bc9496249 =3D> bad # 3500d7addc2f9b2067ffd239383eb0e546be4f43 =3D> good # f9d328833fc1f5d0fb76b61b12d1a3cb013932e6 =3D> bad Please could you confirm? If 'libgeotiff' is really the culprit, then we can try to fix it. All the best, simon From debbugs-submit-bounces@debbugs.gnu.org Thu Feb 20 12:11:11 2020 Received: (at 39204) by debbugs.gnu.org; 20 Feb 2020 17:11:11 +0000 Received: from localhost ([127.0.0.1]:45786 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j4pLz-0007Wh-6b for submit@debbugs.gnu.org; Thu, 20 Feb 2020 12:11:11 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]:33918) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j4pLv-0007WW-Uj for 39204@debbugs.gnu.org; Thu, 20 Feb 2020 12:11:10 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=systemreboot.net; s=default; h=Content-Type:MIME-Version:Message-ID:Date: References:In-Reply-To:Subject:Cc:To:From:Sender:Reply-To: Content-Transfer-Encoding:Content-ID:Content-Description:Resent-Date: Resent-From:Resent-Sender:Resent-To:Resent-Cc:Resent-Message-ID:List-Id: List-Help:List-Unsubscribe:List-Subscribe:List-Post:List-Owner:List-Archive; bh=pesjl4FbtNnQVvAHk1GgOCO3YaZmGoV5UPNdCGurTT8=; b=WA5lGef/kb7MadC02GdOKbIUg /Sjqu3aYwS7MClgu+wUr6JwI66lBiO1Xz1PA7cGrmcjQKTxgT++EGdNdHd1V2xRwzFLE4pVcc1jy8 T27x0YLohmR+gIcAl8GYa2+0s2WiKgJqpJRsTy3XGORpmu4JoX+t1/o8a7xNaNqk+KBx0=; Received: from [192.168.2.1] (helo=steel) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_AES_256_GCM_SHA384 (Exim 4.93) (envelope-from ) id 1j4pLf-000rnf-Me; Thu, 20 Feb 2020 22:40:51 +0530 From: Arun Isaac To: zimoun , wz@freeshell.de Subject: Re: bug#39204: r-rgdal: Reading of vector GIS data causes segfault In-Reply-To: References: <20200120154302.ijni47ou4fk4wd77@wzguix> Date: Thu, 20 Feb 2020 22:40:41 +0530 Message-ID: MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha256; protocol="application/pgp-signature" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 39204 Cc: 39204@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: text/plain > There is 2 issues in this bug report: > > 1. the `check' phase is failing but the build ends with "success". I haven't investigated why this is happening. > 2. a regression of r-rgdal introduced by your commit > f9d328833fc1f5d0fb76b61b12d1a3cb013932e6 Replacing proj.4 with proj in the r-rgdal package seems to fix this regression. Can you confirm? Thanks! --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQEzBAEBCAAdFiEEf3MDQ/Lwnzx3v3nTLiXui2GAK7MFAl5OvZEACgkQLiXui2GA K7OrzggAoTmIMCBwJ5YLCQ7xwwsSevUL9F/VGlxl20FvqBFbBB56Xf+hbkovxlfF Up7AlLYqt/7ngAx8hzc7LXwyvti4fqoEzNuN3XCTWc9RVGtG8j+UmlgDjQ26Yb16 8Z8KQPifcoYwFVr5CT86BI+jntRnkk2Fz3WyJKCkgAPakDptznp4D4ZjoyuBbhDk /A9LUnQWBhf4GCId5pO2PvDlgSzXjFUUqp2Lunhe54ye8ptgGubSP85DQgMnIZdK r8uQeXuzqOgvnzmohuQYqGo36IZNH/2wCu4hjEQp/jz9eQvLl/1c87kr2EXPp01x gLQUvCE84hXPtIOEKylmhRObwH+9nQ== =Boyx -----END PGP SIGNATURE----- --=-=-=-- From debbugs-submit-bounces@debbugs.gnu.org Fri Feb 21 06:19:34 2020 Received: (at 39204) by debbugs.gnu.org; 21 Feb 2020 11:19:34 +0000 Received: from localhost ([127.0.0.1]:46453 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j56LF-0001EE-6h for submit@debbugs.gnu.org; Fri, 21 Feb 2020 06:19:34 -0500 Received: from mail-qt1-f176.google.com ([209.85.160.176]:46934) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j56L9-0001Dz-WD for 39204@debbugs.gnu.org; Fri, 21 Feb 2020 06:19:30 -0500 Received: by mail-qt1-f176.google.com with SMTP id i14so958464qtv.13 for <39204@debbugs.gnu.org>; Fri, 21 Feb 2020 03:19:27 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc; bh=SS/Z5BZe2tKUmPYabpY9DmglpO8uTxduCyoxD5T7cg0=; b=Tz5jiicVxfWpSVzlOH5buxQwQCTovgVWs65uD+544+ZvML0UWTHBup9FjuA/IxGwa3 aBXKmW6xS+lU4GOz9ME1FWQPZIVBjdCFtXQzuNMo5UgoUz97JYJgTZwaAjHkHyDeOQcm 2vICYkNsN2TddTA+LkJq2QndREA3j4bmAenYq6BDR6LEmcrtwiIMxAxfvcswFFsxr7W3 PiPsnUhVMOt1RNRdM4BAbq7y2fA+w8hoKMwOXbcvqa1pjkRgWiu2fJoJ/63Gob5dZOah KhGnAK/aSRtefxkhaKXJ/3hwENLFMXn/vUbcEKT5NbLCTWIJ2ptszXLdyNGSPCDW7zNL T30A== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=SS/Z5BZe2tKUmPYabpY9DmglpO8uTxduCyoxD5T7cg0=; b=JTsfE0AnEtKk2P33vx72R5MsMFw5UT1d6tY8qGX6SERGxSJQwZBAp0Au4+VRaNsJ4d tVghSQottjJKupGy49yiVLtIlrBgtaCaWFLHUVEnx4o6cSkZkGgg7Xnn9yuzx3ndpEIs YhA8uspeoxRIEc8lIs9nJnopiN1lrW4gZSADQVJN9JX0IfklFnuiAQozVapr+yKe+dDl 6ht6DdZFPhgQjSILWQReBBhQQ1ZDF2m0PST85Dn+tz3xL8a8whekFpv60qKZpunZdd++ Yr42fs8sAHC8Tpj2EWZvCY38D1/EtiZZ+QWMnvRRuHmgeT9mvC1NTmIQw0ANgYfBxj7H JQ0A== X-Gm-Message-State: APjAAAWZbPkmP7sU+vZqHKpl5Oq85GH7aYPEvkudnf4yoYsX+QumvYgf BIHHL7La0yWht2EUpgYsxapXX19E9PTdAXIyPK+1KLY2 X-Google-Smtp-Source: APXvYqwMzBmR9zjQAP29g8jRXeUleLQTQ1Y7Nm+LQS/2KcYh6KXqRw2qZ2eJ8pHi1u1G9PcEqZGbOUXSrLQcTmaOSmI= X-Received: by 2002:ac8:319c:: with SMTP id h28mr31810773qte.186.1582283962450; Fri, 21 Feb 2020 03:19:22 -0800 (PST) MIME-Version: 1.0 References: <20200120154302.ijni47ou4fk4wd77@wzguix> In-Reply-To: From: zimoun Date: Fri, 21 Feb 2020 12:19:11 +0100 Message-ID: Subject: Re: bug#39204: r-rgdal: Reading of vector GIS data causes segfault To: Arun Isaac Content-Type: text/plain; charset="UTF-8" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 39204 Cc: wz@freeshell.de, 39204@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 (-) Hi Arun, On Thu, 20 Feb 2020 at 18:11, Arun Isaac wrote: > > 2. a regression of r-rgdal introduced by your commit > > f9d328833fc1f5d0fb76b61b12d1a3cb013932e6 > > Replacing proj.4 with proj in the r-rgdal package seems to fix this > regression. Can you confirm? Maybe, but it is not what the user expects. Upstream explicitly mentions proj.4, see [1]. [1] https://cloud.r-project.org/web/packages/rgdal/index.html which is reflected by: --8<---------------cut here---------------start------------->8--- $ guix show r-rgdal name: r-rgdal version: 1.4-8 outputs: out systems: x86_64-linux i686-linux dependencies: gdal@3.0.2 pkg-config@0.29.2 proj.4@4.9.3 r-sp@1.3-2 zlib@1.2.11 location: gnu/packages/cran.scm:15897:2 homepage: http://rgdal.r-forge.r-project.org license: GPL 2+ synopsis: Bindings for the Geospatial Data Abstraction Library description: This package provides bindings to the Geospatial Data + Abstraction Library (GDAL) and access to projection/transformation + operations from the PROJ.4 library. --8<---------------cut here---------------end--------------->8--- The question is: why proj instead of proj.4 in libgeotiff? The bug [1] cannot be solved using proj.4, why? [2] https://github.com/OSGeo/libgeotiff/issues/22 All the best, simon From debbugs-submit-bounces@debbugs.gnu.org Fri Feb 21 07:13:03 2020 Received: (at 39204) by debbugs.gnu.org; 21 Feb 2020 12:13:03 +0000 Received: from localhost ([127.0.0.1]:46500 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j57B1-0002k8-27 for submit@debbugs.gnu.org; Fri, 21 Feb 2020 07:13:03 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]:37286) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j57Ax-0002jd-20 for 39204@debbugs.gnu.org; Fri, 21 Feb 2020 07:13:01 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=systemreboot.net; s=default; h=Content-Type:MIME-Version:Message-ID:Date: References:In-Reply-To:Subject:Cc:To:From:Sender:Reply-To: Content-Transfer-Encoding:Content-ID:Content-Description:Resent-Date: Resent-From:Resent-Sender:Resent-To:Resent-Cc:Resent-Message-ID:List-Id: List-Help:List-Unsubscribe:List-Subscribe:List-Post:List-Owner:List-Archive; bh=Nwwe8G0HOG9pcp6uG3bNa68vu3rYl+xO2DoTaKQfIcQ=; b=IPe9KaGqCawUfKCMNJHHu1Fu3 jbIkIMdb4tGJfMxBE+UXzeo+ktdXj0JMulqDgx5CrYlFnH84FklKMiJFMvZ1klcevagU2pnlCO4NV 6wjN/iswJS0TXUmfHM/r3gKLkeMYgrYqnUbMRNsjyeg21Is1jvzTi8wEwbq7FXGMq0BrY=; Received: from [192.168.2.1] (helo=steel) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_AES_256_GCM_SHA384 (Exim 4.93) (envelope-from ) id 1j57Ah-000vt8-Hf; Fri, 21 Feb 2020 17:42:43 +0530 From: Arun Isaac To: zimoun Subject: Re: bug#39204: r-rgdal: Reading of vector GIS data causes segfault In-Reply-To: References: <20200120154302.ijni47ou4fk4wd77@wzguix> Date: Fri, 21 Feb 2020 17:42:37 +0530 Message-ID: MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha256; protocol="application/pgp-signature" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 39204 Cc: wz@freeshell.de, 39204@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: text/plain >> > 2. a regression of r-rgdal introduced by your commit >> > f9d328833fc1f5d0fb76b61b12d1a3cb013932e6 >> >> Replacing proj.4 with proj in the r-rgdal package seems to fix this >> regression. Can you confirm? > > Maybe, but it is not what the user expects. Upstream explicitly > mentions proj.4, see [1]. > [1] https://cloud.r-project.org/web/packages/rgdal/index.html No, upstream says that both proj (aka proj6) and proj.4 are supported. Quoting [1], "From 'rgdal' 1.4.1, provision is made for 'PROJ6' accommodation, ..." > The question is: why proj instead of proj.4 in libgeotiff? > The bug [1] cannot be solved using proj.4, why? proj and proj.4 are different versions of the same software, with proj being the newer version. See https://proj.org/faq.html#what-happend-to-proj-4 . I say we completely deprecate our proj.4 package and replace all occurrences of proj.4 with proj. WDYT? --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQEzBAEBCAAdFiEEf3MDQ/Lwnzx3v3nTLiXui2GAK7MFAl5PyTUACgkQLiXui2GA K7M6Swf+IRNnns7KYcuE27dTy7B5qwFygUGq0zZQhgbcBHvw5NZGdSWN6cOlJtRb LNwzsjtnN6ggeiqXnZW64WKMKubqdBPJjcuJpBY2YUIQeO1wJLl8ug+7S5+aS9Qk CpJ1/iMAe50Ws0/q3j3bg094yRm/gWHVJWmG7DNmHp3NbNjPC2JRd+GzeLd9BPGA LIlWWW0XHvIZXBBiiLWtHK/Z68o0sDMaCl9Ba4bMrmWJdtdhS7Oz0m1RdMxYt0Y0 +Xc8CFOgHC7HbRonUtnth4OL8dCCmw+8PgQkLaQEPcIXqOOIKHFmOKdHLiVMnSZ9 +twOq4wF4x5wYfSXaT8CvhbWlvsGng== =lem5 -----END PGP SIGNATURE----- --=-=-=-- From debbugs-submit-bounces@debbugs.gnu.org Fri Feb 21 07:31:18 2020 Received: (at 39204) by debbugs.gnu.org; 21 Feb 2020 12:31:18 +0000 Received: from localhost ([127.0.0.1]:46509 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j57Sf-0004EM-RN for submit@debbugs.gnu.org; Fri, 21 Feb 2020 07:31:18 -0500 Received: from mail-qt1-f178.google.com ([209.85.160.178]:41853) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j57Sd-000493-N1 for 39204@debbugs.gnu.org; Fri, 21 Feb 2020 07:31:16 -0500 Received: by mail-qt1-f178.google.com with SMTP id l21so1098402qtr.8 for <39204@debbugs.gnu.org>; Fri, 21 Feb 2020 04:31:15 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc; bh=rtRKYK7mRIkg/uQhFYtowKH64GJivZAdmky+tQCeaBA=; b=aWowb75PPp8lADt0Z3N1iPrWJpcyyCgMXAmeIyJt0G2VCiN+AAx+fU1buRL+uk9Hwy FgmUA7K2bcP1MALUgoYQJygdmixeI9hwQz/OWVgVXVa60fZBPLQbt8Wcyy6nfj97lIBu HzwtFgwWIr41n4jDaUgT1F3kfHy/SezSN3iA/sJIs+4romvtnUk/TXRxXV8v3Co2ZK0u OEZyK4ZswjIL2EJ97S646AncGl29KWU6gn+67vtctwxCShmD6GW6099AcHmyLw0fX6er GO4dlU6aV0CjA++vXJoxcNqcdsXCJROrCGLooHGOuQgX0VKFxa2n5OMdD47vSs1xBhvY EJQw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=rtRKYK7mRIkg/uQhFYtowKH64GJivZAdmky+tQCeaBA=; b=kKilTJ9JaO9AC+q+xj1LJdEHpigCoWgkxlYuiSctaOkgEIAikBkbS5SJyKkDJjlDej s3LRxGVZWMExktZV3KhfyjWXI9LHG9iE+gIRIRsDLJy4QCSC2JxtOF76nB1yyHq38chM hxtzvJk7OmK8sgS7mdhYdqp/prBWQ3ZcVQpcGADapDSz1CUadT5gkNCz6oBr4VpKVqyd yL65p4TwsGEf4bLo6JJm40DoeUzTmKsnApg1LHN5cvwc9gE6VFhB6PX/OmDprl3JQ5vt xOv0Gy7CrbAg2rhEJ4mrxNTaHxfDTYUEPbdDBinmULzweQrGgqRTD5PJoE2GQap1Um2w z17Q== X-Gm-Message-State: APjAAAUmuXF6Qod0NWo6hyv6tvNkFCSKA7e7W7vtMiZU3TF5tXE0GM3C NgjOdwzTF9ALiE8nl6oV9iwU1Nl7cTHZPZIRw08ngZjD X-Google-Smtp-Source: APXvYqwLqHh6iYVTrbRO9Dywii0c4BbvfzgVKsokAgfd9HDFoH9TyMrBoQxAnfvo21cIhqPP/Hzucm30GhTj32LV1Eo= X-Received: by 2002:ac8:550a:: with SMTP id j10mr32138478qtq.354.1582288270057; Fri, 21 Feb 2020 04:31:10 -0800 (PST) MIME-Version: 1.0 References: <20200120154302.ijni47ou4fk4wd77@wzguix> In-Reply-To: From: zimoun Date: Fri, 21 Feb 2020 13:30:59 +0100 Message-ID: Subject: Re: bug#39204: r-rgdal: Reading of vector GIS data causes segfault To: Arun Isaac Content-Type: text/plain; charset="UTF-8" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 39204 Cc: wz@freeshell.de, 39204@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 (-) On Fri, 21 Feb 2020 at 13:13, Arun Isaac wrote: > >> > 2. a regression of r-rgdal introduced by your commit > >> > f9d328833fc1f5d0fb76b61b12d1a3cb013932e6 > >> > >> Replacing proj.4 with proj in the r-rgdal package seems to fix this > >> regression. Can you confirm? > > > > Maybe, but it is not what the user expects. Upstream explicitly > > mentions proj.4, see [1]. > > > [1] https://cloud.r-project.org/web/packages/rgdal/index.html > > No, upstream says that both proj (aka proj6) and proj.4 are > supported. Quoting [1], > > "From 'rgdal' 1.4.1, provision is made for 'PROJ6' accommodation, ..." I agree, but I was referring to "access to projection/transformation operations from the 'PROJ.4' library." or "Windows and Mac Intel OS X binaries (including 'GDAL', 'PROJ.4' and 'Expat') are provided on 'CRAN'." Well, your comment below says my remark here is irrelevant. :-) > > The question is: why proj instead of proj.4 in libgeotiff? > > The bug [1] cannot be solved using proj.4, why? > > proj and proj.4 are different versions of the same software, with proj > being the newer version. See > https://proj.org/faq.html#what-happend-to-proj-4 . I say we completely > deprecate our proj.4 package and replace all occurrences of proj.4 with > proj. Thank you for the pointer, I was not aware. Well, I agree. Let replace all the dependencies of proj.4 by proj and deprecate our proj.4 package. --8<---------------cut here---------------start------------->8--- $ guix graph -t reverse-package proj.4 \ | grep label | cut -d'=' -f2 | cut -d',' -f1 "proj.4@4.9.3" "r-sf@0.8-0" "r-spdep@1.1-3" "r-monocle3@0.1.2" "r-cicero-monocle3@1.3.2-1.fa2fb65" "r-adegenet@2.1.2" "r-rmetasim@3.1.7" "r-hierfstat@0.04-22" "r-pegas@0.12" "r-rgdal@1.4-8" "libosmium@2.14.2" "osm2pgsql@0.96.0" "mapnik@3.0.18" "python2-mapnik@3.0.16" "xygrib@1.2.6.1" "spatialite-gui@1.7.1" "libspatialite@4.3.0a" "libgaiagraphics@0.5" --8<---------------cut here---------------end--------------->8--- Thanks, simon From debbugs-submit-bounces@debbugs.gnu.org Fri Feb 21 13:53:42 2020 Received: (at 39204) by debbugs.gnu.org; 21 Feb 2020 18:53:42 +0000 Received: from localhost ([127.0.0.1]:48127 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5DQj-0008Qx-Oc for submit@debbugs.gnu.org; Fri, 21 Feb 2020 13:53:42 -0500 Received: from mail-qk1-f170.google.com ([209.85.222.170]:43945) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5DQh-0008Qh-3Z for 39204@debbugs.gnu.org; Fri, 21 Feb 2020 13:53:39 -0500 Received: by mail-qk1-f170.google.com with SMTP id p7so2763526qkh.10 for <39204@debbugs.gnu.org>; Fri, 21 Feb 2020 10:53:39 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc:content-transfer-encoding; bh=EaW/aFaSDwzfAxAyXOfKyatS+DuV0+qNa+4RsGv4Y8o=; b=Uf4L0QdTawOdhP3smhhR43Wv+Vk51jiOnTc6zyF2GFzOxcEEjDGBrjBvW7enTWBwSg XtjNvY0V67VlgO/nfTXl2FSHL8PBxVMptwLExWhuahlLVcdWc8P/Q0rLFu0vvFdFuY0m LhGFHVO/B476zoFp6c8GRXUIiKwEcxrOvYXonvplYuvwn4nTo8GI8RfKZeG7o5vrZhrM dK1ht9jPBg81zZUEFK9Y1TOYbQfibp1PngCAmd1c6gGwAnwSc3I/tmc9vboAenjMFhHm pNYZCCWlWKRr54uXNojFaD1h4jUK9X+JbaU3JJL6B6OV/Pz98xD89QckjH/wrHfpZp9s xWaA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc:content-transfer-encoding; bh=EaW/aFaSDwzfAxAyXOfKyatS+DuV0+qNa+4RsGv4Y8o=; b=Z17/TgQLKuX/rZetMQwDllo017eIIQeSXu+ukiMHRpM2mNN54gFQqyU0o2/PlDAYSA oymQ6LBQaUQyRjHqesk7xeg70glRVTdJyQ86XXK3X+gcjqwIIMQF14wjaD+uNx3KgY4+ a3+grJNxFu8ainSyZXmY5U52hKa26mN0fwL5ffV/+5kDxyROxZtK8SNsAmV4JjBeQDuO 7eqglfdtFmCDDZ5jYKxUdO9BpBkSDHsd3eJt8liA+kx2ZxFTZ+NuaI/ZPb6hn5YYMzSZ sj5cOqcsVLY6bBgMgxqfmNLx0Qh6+BiT3d5DHsP4mJRkkmTiW9kW4ovurotOYByg2Nhl /NsQ== X-Gm-Message-State: APjAAAUwoWGbl9jRzneuS1Q6luWRtWU+ywpjn67hXKrpOHPW46SMBUHL 6y+y8PVqgvAm9/5EZl4nbmqTKT3c3ZD+MMrlgcWCHBlI X-Google-Smtp-Source: APXvYqyVs0VryXYfM4K23NCN+S8vMYfSmyypVU05p9vUld2fDy9D4a1s8Ta83W1oTkg3LH+kR8xkhHoccyRTa50ethU= X-Received: by 2002:a37:a496:: with SMTP id n144mr13110787qke.126.1582311213405; Fri, 21 Feb 2020 10:53:33 -0800 (PST) MIME-Version: 1.0 References: <20200120154302.ijni47ou4fk4wd77@wzguix> In-Reply-To: From: zimoun Date: Fri, 21 Feb 2020 19:53:22 +0100 Message-ID: Subject: Re: bug#39204: r-rgdal: Reading of vector GIS data causes segfault To: Arun Isaac Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 39204 Cc: wz@freeshell.de, 39204@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 (-) Hi Arun, On Thu, 20 Feb 2020 at 18:11, Arun Isaac wrote= : > > 2. a regression of r-rgdal introduced by your commit > > f9d328833fc1f5d0fb76b61b12d1a3cb013932e6 > > Replacing proj.4 with proj in the r-rgdal package seems to fix this > regression. Can you confirm? You mean: guix build --with-input=3Dproj.4=3Dproj r-rgdal then it compiles a lot... and I do not understand why gdal is recompiled. Anyway! So after some CPU burning, I get: --8<---------------cut here---------------start------------->8--- Testing examples for package =E2=80=98rgdal=E2=80=99 Running specific tests for package =E2=80=98rgdal=E2=80=99 Running =E2=80=98srs_rendering.R=E2=80=99 comparing =E2=80=98srs_rendering.Rout=E2=80=99 to =E2=80=98srs_rendering.= Rout.save=E2=80=99 ... 5c5 < [1] "Rel. 6.2.0, September 1st, 2019, [PJ_VERSION: 620]" --- > [1] "Rel. 6.0.0, March 1st, 2019, [PJ_VERSION: 600]" 7c7 < [1] "GDAL 3.0.2, released 2019/10/28" --- > [1] "GDAL 2.4.0, released 2018/12/14" 11c11 < scot_BNG --- > = = trin_inca_pl03 12c12 < "+proj=3Dtmerc +lat_0=3D49 +lon_0=3D-2 +k=3D0.9996012717 +x_0=3D400000 +y_0=3D-100000 +ellps=3Dairy +units=3Dm +no_defs" --- > = = NA 13c13 < trin_inca_pl03 --- > = kiritimat= i_primary_roads 14c14 < NA --- > = "+proj=3Dutm +zone=3D4 +datum=3DWGS8= 4 +units=3Dm +no_defs " 16c16 < "+proj=3Dlonglat +datum=3DWGS84 +no_defs" --- < kiritimati_primary_roads --- > = = scot_BNG 18c18 < "+proj=3Dutm +zone=3D4 +datum=3DWGS84 +units=3Dm +no_defs" --- > "+proj=3Dtmerc +lat_0=3D49 +lon_0=3D-2 +k=3D0.9996012717 +x_0=3D400000 +y= _0=3D-100000 +ellps=3Dairy +towgs84=3D446.448,-125.157,542.06,0.15,0.247,0.= 842,-20.489 +units=3Dm +no_defs " 22c22 < [1] "+proj=3Dlonglat +a=3D6378137.01 +rf=3D298.257223563 +towgs84=3D0,0,0,0,0,0,0 +no_defs" --- > [1] "+proj=3Dlonglat +ellps=3DWGS84 +towgs84=3D0,0,0,0,0,0,0 +no_defs " 24c24 < [1] "+proj=3Dutm +zone=3D23 +south +ellps=3Daust_SA +towgs84=3D-57,1,-41,0,0,0,0 +units=3Dm +no_defs" --- > [1] "+proj=3Dutm +zone=3D23 +south +ellps=3Daust_SA +towgs84=3D-57,1,-41,= 0,0,0,0 +units=3Dm +no_defs " 26c26 < [1] "+proj=3Dlonglat +datum=3DWGS84 +no_defs" --- > [1] "+proj=3Dlonglat +datum=3DWGS84 +no_defs " 28c28 < [1] "+proj=3Dlcc +lat_1=3D46.8 +lat_0=3D46.8 +lon_0=3D0 +k_0=3D0.999877420000019 +x_0=3D600000 +y_0=3D2200000.00000032 +ellps=3Dclrk80ign +pm=3Dparis +towgs84=3D-168,-60,320,0,0,0,0 +units=3Dm +no_defs" --- > [1] "+proj=3Dlcc +lat_1=3D46.8 +lat_0=3D46.8 +lon_0=3D0 +k_0=3D0.99987742= 00000193 +x_0=3D600000 +y_0=3D2200000.000000325 +a=3D6378249.2 +b=3D6356515= .000000472 +towgs84=3D-168,-60,320,0,0,0,0 +pm=3Dparis +units=3Dm +no_defs = " 40c40 < file: SP27GTIF.TIF , SRS: +proj=3Dtmerc +lat_0=3D36.6666666666667 +lon_0=3D-88.3333333333333 +k=3D0.999975 +x_0=3D152400.30480061 +y_0=3D0 +ellps=3Dclrk66 +towgs84=3D-8,160,176,0,0,0,0 +units=3Dus-ft +no_defs --- > file: SP27GTIF.TIF , SRS: +proj=3Dtmerc +lat_0=3D36.66666666666666 +lon= _0=3D-88.33333333333333 +k=3D0.9999749999999999 +x_0=3D152400.3048006096 +y= _0=3D0 +datum=3DNAD27 +units=3Dus-ft +no_defs 41c41 < file: cea.tif , SRS: +proj=3Dcea +lat_ts=3D33.75 +lon_0=3D-117.333333333333 +x_0=3D0 +y_0=3D0 +datum=3DNAD27 +units=3Dm +no_= defs --- > file: cea.tif , SRS: +proj=3Dcea +lon_0=3D-117.333333333333 +lat_ts=3D3= 3.75 +x_0=3D0 +y_0=3D0 +datum=3DNAD27 +units=3Dm +no_defs 42c42 < file: erdas_spnad83.tif , SRS: +proj=3Dtmerc +lat_0=3D30 +lon_0=3D-82.1666666666667 +k=3D0.9999 +x_0=3D200000 +y_0=3D0 +ellps=3DGRS8= 0 +towgs84=3D0,0,0,0,0,0,0 +units=3Dus-ft +no_defs --- > file: erdas_spnad83.tif , SRS: +proj=3Dtmerc +lat_0=3D30 +lon_0=3D-82.1= 6666666666667 +k=3D0.9999 +x_0=3D200000 +y_0=3D0 +ellps=3DGRS80 +towgs84=3D= 0,0,0,0,0,0,0 +units=3Dus-ft +no_defs 43c43 < file: scaleoffset.vrt , SRS: +proj=3Dutm +zone=3D18 +ellps=3DWGS84 +towgs84=3D0,0,0,0,0,0,0 +units=3Dm +no_defs --- > file: scaleoffset.vrt , SRS: +proj=3Dutm +zone=3D18 +datum=3DWGS84 +uni= ts=3Dm +no_defs Running =E2=80=98test_proj.R=E2=80=99 comparing =E2=80=98test_proj.Rout=E2=80=99 to =E2=80=98test_proj.Rout.sav= e=E2=80=99 ... OK Running =E2=80=98tests.R=E2=80=99 comparing =E2=80=98tests.Rout=E2=80=99 to =E2=80=98tests.Rout.save=E2=80= =99 ... OK Running =E2=80=98tripup.R=E2=80=99 comparing =E2=80=98tripup.Rout=E2=80=99 to =E2=80=98tripup.Rout.save=E2= =80=99 ... 266c266 < coords FALSE --- > coords TRUE 267c267 < holes FALSE --- > holes TRUE 273c273 < coords FALSE --- > coords TRUE 274c274 < holes FALSE --- > holes TRUE Running vignettes for package =E2=80=98rgdal=E2=80=99 Running =E2=80=98OGR_shape_encoding.Rnw=E2=80=99 phase `check' succeeded after 18.7 seconds --8<---------------cut here---------------end--------------->8--- Therefore, I do not confirm, I guess. All the best, simon From debbugs-submit-bounces@debbugs.gnu.org Fri Feb 21 13:54:40 2020 Received: (at 39204) by debbugs.gnu.org; 21 Feb 2020 18:54:40 +0000 Received: from localhost ([127.0.0.1]:48131 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5DRg-0008Sb-76 for submit@debbugs.gnu.org; Fri, 21 Feb 2020 13:54:40 -0500 Received: from mail-qv1-f48.google.com ([209.85.219.48]:45626) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5DRe-0008SN-Vk for 39204@debbugs.gnu.org; Fri, 21 Feb 2020 13:54:39 -0500 Received: by mail-qv1-f48.google.com with SMTP id l14so1418350qvu.12 for <39204@debbugs.gnu.org>; Fri, 21 Feb 2020 10:54:38 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc; bh=nFHVlZVLYyFCnsKo0gLkU7/wOxXj+aEVXKDCX0gcgL0=; b=oSm5myi3rMkSkNRe0F1L+sxtAp4u7FLSCi1uIJOhSnFitJxi33pyk99IV3wJCrTW6P kGGtfI0YK9glDRi8GJwtYn8/l482bC4joCWHmNwndG4qn+1K356pNXyTFM7GZNBVTnX5 6EgZMCGAmE3i04XqdUj7c+4ZAyoryeursSkTtBEAWBr+NK48l84LtU2kACdKO/w9+C9/ t8p3tSpgA4JiVZQ+taqk2hmApCghwacaGAyil+pZZa7XNANknImrwMruXH6blX6qc2fn klk+CsVdNbWxp8oBcsHWXr9hbOZA/JKvxH/HXvQmkpUcM8M2UQZcFcVC7H2snZ5XD6ML M8pw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=nFHVlZVLYyFCnsKo0gLkU7/wOxXj+aEVXKDCX0gcgL0=; b=aG/lOQcFHeYhSP3gryOexX0LweIQhhlsbkR21QIaB0lPn6i1sEVrmUBsAAtR2XyOQC Msav03Dy7+sImH9vhgrsYvFxKCk/InYxJ2Oi6LcLKFQJPpx37Sq51o3gC/VtSCm6JAaC lLo9mm5AugQdIqySxHmwSxLsaMP6hQ2/72ua7rpJrsaCo09F+4mFbxLexELeoDRc3Nqv A2UC3spyVvVMirBSbFWUfLLw9vKEMdUIOqBsT6IqPtEp3foXJkLXszr3OSFy4+aYAJx3 jBSWkL5spqb7a1miVRPX1lV0EHIhRmYMBVm1XWBBxZdIPsdB6/dd/wQzbKWMvhFHmhL3 3ZzQ== X-Gm-Message-State: APjAAAXogFMYssnjRvHoemX9GuB4a7Dtb7Y25Yoz1ij55H26/3KzhHGn 3ywHZbVqw8E/nJy7SVzBAHM0drd0rwt9uTFpnzis5LxD X-Google-Smtp-Source: APXvYqxqlYFuRrCKibiLxN5cxZLO+fijUbfFOH50i/tvhXscyAwiQlWcw1i4d4cC+QLwCl2VR1CRXqMnT9e3+DoTAxc= X-Received: by 2002:ad4:46ce:: with SMTP id g14mr32160930qvw.67.1582311273411; Fri, 21 Feb 2020 10:54:33 -0800 (PST) MIME-Version: 1.0 References: <20200120154302.ijni47ou4fk4wd77@wzguix> In-Reply-To: From: zimoun Date: Fri, 21 Feb 2020 19:54:22 +0100 Message-ID: Subject: Re: bug#39204: r-rgdal: Reading of vector GIS data causes segfault To: Arun Isaac Content-Type: text/plain; charset="UTF-8" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 39204 Cc: wz@freeshell.de, 39204@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 (-) Hi Arun, On Fri, 21 Feb 2020 at 13:13, Arun Isaac wrote: > proj and proj.4 are different versions of the same software, with proj > being the newer version. See > https://proj.org/faq.html#what-happend-to-proj-4 . I say we completely > deprecate our proj.4 package and replace all occurrences of proj.4 with > proj. For other packages than r-rgdal depending on proj.4: - ok with proj instead of proj.4: osm2pgsql, xygrib and libgaiagraphics. - not ok: libspatialite and libosmium And some packages do not build at all with the default (proj.4): mapnik and spatialite-gui. Well, it is more than on my machine. ;-) http://data.guix.gnu.org/revision/e40d6c4c7a74fca3572991c55706a787b19d4d90/package/mapnik/3.0.18 http://data.guix.gnu.org/revision/e40d6c4c7a74fca3572991c55706a787b19d4d90/package/spatialite-gui/1.7.1 All the best, simon From debbugs-submit-bounces@debbugs.gnu.org Fri Feb 21 16:36:17 2020 Received: (at 39204) by debbugs.gnu.org; 21 Feb 2020 21:36:17 +0000 Received: from localhost ([127.0.0.1]:48264 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5Fy5-00069t-8q for submit@debbugs.gnu.org; Fri, 21 Feb 2020 16:36:17 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]:39178) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5Fy0-00069h-IB for 39204@debbugs.gnu.org; Fri, 21 Feb 2020 16:36:15 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=systemreboot.net; s=default; h=Content-Type:MIME-Version:Message-ID:Date: References:In-Reply-To:Subject:Cc:To:From:Sender:Reply-To: Content-Transfer-Encoding:Content-ID:Content-Description:Resent-Date: Resent-From:Resent-Sender:Resent-To:Resent-Cc:Resent-Message-ID:List-Id: List-Help:List-Unsubscribe:List-Subscribe:List-Post:List-Owner:List-Archive; bh=mMSOhMrd1sho7yiXuxmr9yCQ9O0qEr2PzcVjJq3esnA=; b=L3yYxvUqpwfzl184WASaKanHE Jt7iR1xCPl6HWDnyG7ewIpsoHgVoxuKv7me6AnK8CFKsKcQeg3lrKpqEEjtz5nAE3kpwh+zlCMPMG O826dixUQYzBnMsMKLfjez0JpOIFAsUtqVEOLvpbsH3TvWlbhzLGOwd+Uzr7XwFWzUC5Y=; Received: from [192.168.2.1] (helo=steel) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_AES_256_GCM_SHA384 (Exim 4.93) (envelope-from ) id 1j5Fxk-000yJG-45; Sat, 22 Feb 2020 03:05:56 +0530 From: Arun Isaac To: zimoun Subject: Re: bug#39204: r-rgdal: Reading of vector GIS data causes segfault In-Reply-To: References: <20200120154302.ijni47ou4fk4wd77@wzguix> Date: Sat, 22 Feb 2020 03:05:41 +0530 Message-ID: MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha256; protocol="application/pgp-signature" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 39204 Cc: wz@freeshell.de, 39204@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: text/plain > For other packages than r-rgdal depending on proj.4: > - ok with proj instead of proj.4: osm2pgsql, xygrib and libgaiagraphics. > - not ok: libspatialite and libosmium Indeed, all packages don't yet support proj. We'll have to keep proj.4 around until their upstreams adds support for proj. > And some packages do not build at all with the default (proj.4): > mapnik and spatialite-gui. Well, it is more than on my machine. ;-) These will have to be fixed too. Do open separate bug reports for those. Please provide patches if possible. Thanks! --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQEzBAEBCAAdFiEEf3MDQ/Lwnzx3v3nTLiXui2GAK7MFAl5QTS4ACgkQLiXui2GA K7PHvQf7B7ZSu2z0OG6Tql3hnxVXlHy8wCRl1w5UfxWjDmlVA1wWFeew5QlSYq9p Qvytrs/F9GJfQDWJ7gneKfd29IeP41wQU3r+ilGJMXxKdhUC2Dq4zH+rxQCfzaCj tKkLjxo/JMb27Fjaple44gqkYj9aq2HMElBAGy/8seaxb6MzZmSuTycBir7prRln SeTUnh2y/mimQRR66roWqd8jm68KpAgA3j3GJsEsks5+Qqost2y5t/MP4/20ZLEI HZWF0ZpHWHqdH8wqmzwp2kJjQBMlW/qyVI2a9y6SBKg7fHEDa3mT5/8od1xKGGN+ RmyIt8Fyux+ql9gL0v/dO0kF894OTg== =uBIP -----END PGP SIGNATURE----- --=-=-=-- From debbugs-submit-bounces@debbugs.gnu.org Fri Feb 21 16:40:43 2020 Received: (at 39204) by debbugs.gnu.org; 21 Feb 2020 21:40:43 +0000 Received: from localhost ([127.0.0.1]:48269 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5G2M-0006GN-PR for submit@debbugs.gnu.org; Fri, 21 Feb 2020 16:40:43 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]:39192) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5G2J-0006GD-Pu for 39204@debbugs.gnu.org; Fri, 21 Feb 2020 16:40:40 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=systemreboot.net; s=default; h=Content-Type:MIME-Version:Message-ID:Date: References:In-Reply-To:Subject:Cc:To:From:Sender:Reply-To: Content-Transfer-Encoding:Content-ID:Content-Description:Resent-Date: Resent-From:Resent-Sender:Resent-To:Resent-Cc:Resent-Message-ID:List-Id: List-Help:List-Unsubscribe:List-Subscribe:List-Post:List-Owner:List-Archive; bh=LOn/Cd+BcUzWotXcDF8mrhMUYslZ8HeYgmvPhSIHzDI=; b=VWpzbHk9VVIGDIqh2k72vHaku JrBBFEeIU8ibFWWbhTQvCgBY6xACK9l37QiTQjMla7X9BR9L6yCF4gitW7OqhNNyAK694qLUbQy5e iunY804WhaLDvvVwgmhz6yfc3DLWsx8m3W1IihyG0GSgXOKssQGbAJHzE/p1am+YNzEJs=; Received: from [192.168.2.1] (helo=steel) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_AES_256_GCM_SHA384 (Exim 4.93) (envelope-from ) id 1j5G24-000yKJ-NL; Sat, 22 Feb 2020 03:10:25 +0530 From: Arun Isaac To: zimoun Subject: Re: bug#39204: r-rgdal: Reading of vector GIS data causes segfault In-Reply-To: References: <20200120154302.ijni47ou4fk4wd77@wzguix> Date: Sat, 22 Feb 2020 03:10:24 +0530 Message-ID: MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha256; protocol="application/pgp-signature" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 39204 Cc: wz@freeshell.de, 39204@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: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable > You mean: > > guix build --with-input=3Dproj.4=3Dproj r-rgdal > > then it compiles a lot... and I do not understand why gdal is > recompiled. Anyway! Your command recursively replaces proj.4 with proj. So, some dependency of gdal might have been modified resulting in a rebuild of gdal. > So after some CPU burning, I get: > > --8<---------------cut here---------------start------------->8--- > Testing examples for package =E2=80=98rgdal=E2=80=99 > Running specific tests for package =E2=80=98rgdal=E2=80=99 > Running =E2=80=98srs_rendering.R=E2=80=99 > comparing =E2=80=98srs_rendering.Rout=E2=80=99 to =E2=80=98srs_renderin= g.Rout.save=E2=80=99 ... > 5c5 > < [1] "Rel. 6.2.0, September 1st, 2019, [PJ_VERSION: 620]" > --- >> [1] "Rel. 6.0.0, March 1st, 2019, [PJ_VERSION: 600]" > 7c7 > < [1] "GDAL 3.0.2, released 2019/10/28" > --- >> [1] "GDAL 2.4.0, released 2018/12/14" > 11c11 > < > scot_BNG > --- >> = = trin_inca_pl03 > 12c12 > < "+proj=3Dtmerc +lat_0=3D49 +lon_0=3D-2 +k=3D0.9996012717 +x_0=3D400000 > +y_0=3D-100000 +ellps=3Dairy +units=3Dm +no_defs" > --- >> = = NA > 13c13 > < > trin_inca_pl03 > --- >> = kiritima= ti_primary_roads > 14c14 > < > NA > --- >> = "+proj=3Dutm +zone=3D4 +datum=3DWGS= 84 +units=3Dm +no_defs " > 16c16 > < > "+proj=3Dlonglat +datum=3DWGS84 +no_defs" > --- > < > kiritimati_primary_roads > --- >> = = scot_BNG > 18c18 > < "+proj=3Dutm > +zone=3D4 +datum=3DWGS84 +units=3Dm +no_defs" > --- >> "+proj=3Dtmerc +lat_0=3D49 +lon_0=3D-2 +k=3D0.9996012717 +x_0=3D400000 += y_0=3D-100000 +ellps=3Dairy +towgs84=3D446.448,-125.157,542.06,0.15,0.247,0= .842,-20.489 +units=3Dm +no_defs " > 22c22 > < [1] "+proj=3Dlonglat +a=3D6378137.01 +rf=3D298.257223563 > +towgs84=3D0,0,0,0,0,0,0 +no_defs" > --- >> [1] "+proj=3Dlonglat +ellps=3DWGS84 +towgs84=3D0,0,0,0,0,0,0 +no_defs " > 24c24 > < [1] "+proj=3Dutm +zone=3D23 +south +ellps=3Daust_SA > +towgs84=3D-57,1,-41,0,0,0,0 +units=3Dm +no_defs" > --- >> [1] "+proj=3Dutm +zone=3D23 +south +ellps=3Daust_SA +towgs84=3D-57,1,-41= ,0,0,0,0 +units=3Dm +no_defs " > 26c26 > < [1] "+proj=3Dlonglat +datum=3DWGS84 +no_defs" > --- >> [1] "+proj=3Dlonglat +datum=3DWGS84 +no_defs " > 28c28 > < [1] "+proj=3Dlcc +lat_1=3D46.8 +lat_0=3D46.8 +lon_0=3D0 > +k_0=3D0.999877420000019 +x_0=3D600000 +y_0=3D2200000.00000032 > +ellps=3Dclrk80ign +pm=3Dparis +towgs84=3D-168,-60,320,0,0,0,0 +units=3Dm > +no_defs" > --- >> [1] "+proj=3Dlcc +lat_1=3D46.8 +lat_0=3D46.8 +lon_0=3D0 +k_0=3D0.9998774= 200000193 +x_0=3D600000 +y_0=3D2200000.000000325 +a=3D6378249.2 +b=3D635651= 5.000000472 +towgs84=3D-168,-60,320,0,0,0,0 +pm=3Dparis +units=3Dm +no_defs= " > 40c40 > < file: SP27GTIF.TIF , SRS: +proj=3Dtmerc +lat_0=3D36.6666666666667 > +lon_0=3D-88.3333333333333 +k=3D0.999975 +x_0=3D152400.30480061 +y_0=3D0 > +ellps=3Dclrk66 +towgs84=3D-8,160,176,0,0,0,0 +units=3Dus-ft +no_defs > --- >> file: SP27GTIF.TIF , SRS: +proj=3Dtmerc +lat_0=3D36.66666666666666 +lo= n_0=3D-88.33333333333333 +k=3D0.9999749999999999 +x_0=3D152400.3048006096 += y_0=3D0 +datum=3DNAD27 +units=3Dus-ft +no_defs > 41c41 > < file: cea.tif , SRS: +proj=3Dcea +lat_ts=3D33.75 > +lon_0=3D-117.333333333333 +x_0=3D0 +y_0=3D0 +datum=3DNAD27 +units=3Dm +n= o_defs > --- >> file: cea.tif , SRS: +proj=3Dcea +lon_0=3D-117.333333333333 +lat_ts=3D= 33.75 +x_0=3D0 +y_0=3D0 +datum=3DNAD27 +units=3Dm +no_defs > 42c42 > < file: erdas_spnad83.tif , SRS: +proj=3Dtmerc +lat_0=3D30 > +lon_0=3D-82.1666666666667 +k=3D0.9999 +x_0=3D200000 +y_0=3D0 +ellps=3DGR= S80 > +towgs84=3D0,0,0,0,0,0,0 +units=3Dus-ft +no_defs > --- >> file: erdas_spnad83.tif , SRS: +proj=3Dtmerc +lat_0=3D30 +lon_0=3D-82.= 16666666666667 +k=3D0.9999 +x_0=3D200000 +y_0=3D0 +ellps=3DGRS80 +towgs84= =3D0,0,0,0,0,0,0 +units=3Dus-ft +no_defs > 43c43 > < file: scaleoffset.vrt , SRS: +proj=3Dutm +zone=3D18 +ellps=3DWGS84 > +towgs84=3D0,0,0,0,0,0,0 +units=3Dm +no_defs > --- >> file: scaleoffset.vrt , SRS: +proj=3Dutm +zone=3D18 +datum=3DWGS84 +un= its=3Dm +no_defs > Running =E2=80=98test_proj.R=E2=80=99 > comparing =E2=80=98test_proj.Rout=E2=80=99 to =E2=80=98test_proj.Rout.s= ave=E2=80=99 ... OK > Running =E2=80=98tests.R=E2=80=99 > comparing =E2=80=98tests.Rout=E2=80=99 to =E2=80=98tests.Rout.save=E2= =80=99 ... OK > Running =E2=80=98tripup.R=E2=80=99 > comparing =E2=80=98tripup.Rout=E2=80=99 to =E2=80=98tripup.Rout.save=E2= =80=99 ... > 266c266 > < coords FALSE > --- >> coords TRUE > 267c267 > < holes FALSE > --- >> holes TRUE > 273c273 > < coords FALSE > --- >> coords TRUE > 274c274 > < holes FALSE > --- >> holes TRUE > Running vignettes for package =E2=80=98rgdal=E2=80=99 > Running =E2=80=98OGR_shape_encoding.Rnw=E2=80=99 > phase `check' succeeded after 18.7 seconds > --8<---------------cut here---------------end--------------->8--- > > > Therefore, I do not confirm, I guess. I don't understand. With proj instead of proj.4, it does work, doesn't it? There are no errors and the check phase succeeds. --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQEzBAEBCAAdFiEEf3MDQ/Lwnzx3v3nTLiXui2GAK7MFAl5QTkgACgkQLiXui2GA K7Nq9wf/XCMkD6XG1IPh/hx9pT37xyLyeAe6PAZb0nXuyhEPNKlY2bI+DHqmli9K m5fDS6QRHi7Z3sLkp3mJ/XyH9fsO1g0q5eHUtVbQijAkod2GSrCMeb6/Ui1eFFfR lBgvCC9OnmIIp6P9WomzQSxBpL8nCBCauaNioYX1Eo319QluArsYn2W6eWy7S5Jz vMq/at5waRdFzIRx5M1t7iekmI5lukwCM4cR2sWOU/Xyeq2ze5aoG0At/YMhD0mV YyiJ/Pd0oV+IgUA8s7oUfydkjZq0DGyGwYi4rz3BSFN9+z5B8QVKivJgX5Das//b 8cEBhGUZcXE/4PUSw8aFeQgebfi0BA== =vayy -----END PGP SIGNATURE----- --=-=-=-- From debbugs-submit-bounces@debbugs.gnu.org Fri Feb 21 17:14:45 2020 Received: (at 39204) by debbugs.gnu.org; 21 Feb 2020 22:14:45 +0000 Received: from localhost ([127.0.0.1]:48305 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5GZI-000782-R9 for submit@debbugs.gnu.org; Fri, 21 Feb 2020 17:14:44 -0500 Received: from mail-qk1-f176.google.com ([209.85.222.176]:33806) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5GZG-00077o-DC for 39204@debbugs.gnu.org; Fri, 21 Feb 2020 17:14:43 -0500 Received: by mail-qk1-f176.google.com with SMTP id c20so3371665qkm.1 for <39204@debbugs.gnu.org>; Fri, 21 Feb 2020 14:14:42 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc; bh=lwnM8hZZ3gTb0UFEOF3tRhZ6fW0DMUv0qg73TMXEQ2g=; b=C6VGWwFPlPokuDXX5VcFD5EAyrNRWgCG47hvmjslZn3/OYd+Vm3ncJuP+l9Ln2mjTf u3jHbgEy8iE+O5dwPHHqhG5JJ0xBVZYYYhoxoFwLJEd3jVKXQv068zUVh/96uFYzkndf rUhDcHCahlaPuPDBLBYntFgELCdGOKeAgIpX2P7f35Nhw/jLabfWDv4kxaHvv7GCg3Zh MNJ+WM7RPvpHn3XEkmq2+7tNTlgCGEXFWixyDpp2K2PIO45H8pqY7/ZWbx1hyfsGEaeg 1sIC8MGeNBe1gPkhBX+ZOR3M6xveh/Ig0n7CWjidzoEADd6xUClUSzDCK/5raP2mOSGT 5unA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=lwnM8hZZ3gTb0UFEOF3tRhZ6fW0DMUv0qg73TMXEQ2g=; b=tU7i/UickhmPt/Ke3eTGYQJ49JxF7yZxR4Vp/NPO2WTBxsc93mEjSX/DhQfJUT/F4+ VFKRzrace9aTVgm6pIdKmgxGvGvHbATls6CkbCSNQBGJd+ncbRgDZkvryFQ/99EAkjcZ 84+yfbOFd/GYuz1Ez6yzdUyQjAeOWbTJLwbl5KGzavEmp7diu7FXWt5HgTd+RbI08qec uaAgiZIkp0ljrA7AXJADuSCtcTFr8tv2MS8k7aQrHnxAuQiHBAvEeOnN6NFSkT5cIRiO iHUnlFQOVBxhVFXyFTlU6vSqFNfXZTt9fim36ps85T0c5et+Ibln937oxnjRj95e4X2O Ta/Q== X-Gm-Message-State: APjAAAUGNxom9ksHmoYYuQWt3trPmnVe3Zjtz6N5Ep8C8rRtRxcxFWUU ftF6wDAn7o53HCXcLDRXMXMtmQReKIw8v07a71uk6A== X-Google-Smtp-Source: APXvYqxrEPFuJ13O6d+zO1VBljMVmZmKmoCVI3pYstT73DPo+350fFYw1qrXVwCOvBY57+/z/3ZI3HeWMDz+5YxL+TA= X-Received: by 2002:a05:620a:1092:: with SMTP id g18mr4159646qkk.80.1582323276816; Fri, 21 Feb 2020 14:14:36 -0800 (PST) MIME-Version: 1.0 References: <20200120154302.ijni47ou4fk4wd77@wzguix> In-Reply-To: From: zimoun Date: Fri, 21 Feb 2020 23:14:25 +0100 Message-ID: Subject: Re: bug#39204: r-rgdal: Reading of vector GIS data causes segfault To: Arun Isaac Content-Type: text/plain; charset="UTF-8" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 39204 Cc: wz@freeshell.de, 39204@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 (-) On Fri, 21 Feb 2020 at 22:36, Arun Isaac wrote: > > For other packages than r-rgdal depending on proj.4: > > - ok with proj instead of proj.4: osm2pgsql, xygrib and libgaiagraphics. > > - not ok: libspatialite and libosmium > > Indeed, all packages don't yet support proj. We'll have to keep proj.4 > around until their upstreams adds support for proj. So it is difficult to deprecate proj.4, IMHO. > > And some packages do not build at all with the default (proj.4): > > mapnik and spatialite-gui. Well, it is more than on my machine. ;-) > > These will have to be fixed too. Do open separate bug reports for > those. Please provide patches if possible. I will do. Thanks, simon From debbugs-submit-bounces@debbugs.gnu.org Fri Feb 21 17:20:06 2020 Received: (at 39204) by debbugs.gnu.org; 21 Feb 2020 22:20:06 +0000 Received: from localhost ([127.0.0.1]:48309 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5GeU-0007Gy-EC for submit@debbugs.gnu.org; Fri, 21 Feb 2020 17:20:06 -0500 Received: from mail-qk1-f172.google.com ([209.85.222.172]:37907) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5GeS-0007GP-8h for 39204@debbugs.gnu.org; Fri, 21 Feb 2020 17:20:05 -0500 Received: by mail-qk1-f172.google.com with SMTP id z19so3358067qkj.5 for <39204@debbugs.gnu.org>; Fri, 21 Feb 2020 14:20:04 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc; bh=6GzWeBw4/EAvhKmGXJBbduBgY/cAj85A8hZQudZJaIE=; b=Cp5noFevFvvFCu3H/jM1V6Ua6L9oBd2zUStrEpDFUCYAhNB5OqLhZr1pfXfPfXnpfm jAPoU2WDe8RfahXuDFV4HxHjb8/k2Y1VFzENMHn86ezaXgKmUVTwQB24aKm3kBfWH2Bx tXOvgkpAfMONYELnXD7WyAdng3DCNfMMg/qdjP9DmEtUtunueXn+Y4QUUzWCzqLiDeRb jOYkFxClVQpVhD8Edh2IZT2D/Sw/gsXCPJ0zGfvwESCSo7nEGTaRbRzA2aOp0U33u20k 69zLX2RIY00Rf4J47Jpj19Wim6heuK2PM6aUrvmmRBRLw0jJ34jM2sQGhoy9FuIz3RSC 8Gmg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=6GzWeBw4/EAvhKmGXJBbduBgY/cAj85A8hZQudZJaIE=; b=qRb175C2vq1Lb4yt8LQo49LdDTHnQdvMgIF6iXyZVTUjEaGFt1O+jXttYH0O/06Apj fapGSmLIDQ/3dE3lGuwlbLuuGPsHbi+IZ60RigF6j/6GGwlzm5L79/3jig7OzsNMbIR2 XR1qz1vm5ToDkjE4Ufj+rosFBT6DyYTHnOV3sIGo6zOMGo03cGqCYa+mfpUuQJ5ZN4F6 bbDSqMBAZ8BFN3cv0+eBq+qBhPIBZQg1lTLza+aqfD5my5CmAkmoTmSKND3wgPMj+pcL oUdoXQ9vAWCcVCfJK6moUH/elMOBdCVrJRrWpRLiLeC5fruIC6OUPJ9yjdNjVKPJFDDD rY1Q== X-Gm-Message-State: APjAAAVJqT4vt7NKHztOJ+Hx218ucWxffGskjO/a2NPZEUeQ52WH3pt6 I49beYoaN/OeI94Qj0wNMKCchdT1+1Gd9EZFzRw= X-Google-Smtp-Source: APXvYqxeHuLAxm8W0DwOqi7p7ELva0DquXEMWXMfZq51FBxCd98ohAzSQLFkwDNi/aIQgh6VS/3QW0rEjeukxsk9Qsg= X-Received: by 2002:a37:a496:: with SMTP id n144mr13925409qke.126.1582323598867; Fri, 21 Feb 2020 14:19:58 -0800 (PST) MIME-Version: 1.0 References: <20200120154302.ijni47ou4fk4wd77@wzguix> In-Reply-To: From: zimoun Date: Fri, 21 Feb 2020 23:19:47 +0100 Message-ID: Subject: Re: bug#39204: r-rgdal: Reading of vector GIS data causes segfault To: Arun Isaac Content-Type: text/plain; charset="UTF-8" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 39204 Cc: wz@freeshell.de, 39204@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 (-) On Fri, 21 Feb 2020 at 22:40, Arun Isaac wrote: > > You mean: > > > > guix build --with-input=proj.4=proj r-rgdal > > > > then it compiles a lot... and I do not understand why gdal is > > recompiled. Anyway! > > Your command recursively replaces proj.4 with proj. So, some dependency > of gdal might have been modified resulting in a rebuild of gdal. Yes, but gdal already depends on proj and not proj.4. Then I examined the graph and did not find the offending package. That's why I do not understand why gdal is recompiled. I mean, let find the intersection between "guix graph gdal" and "guix graph -t reverse-package proj.4", and I do not understand because I find it empty. > > Therefore, I do not confirm, I guess. > > I don't understand. With proj instead of proj.4, it does work, doesn't > it? There are no errors and the check phase succeeds. I have try to replace proj.4 by proj in the inputs field and I get the same error. Well, it does not work for me. Maybe I am doing a mistake. Cheers, simon From debbugs-submit-bounces@debbugs.gnu.org Sat Feb 22 14:42:43 2020 Received: (at 39204) by debbugs.gnu.org; 22 Feb 2020 19:42:44 +0000 Received: from localhost ([127.0.0.1]:50015 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5afj-0007Ec-OJ for submit@debbugs.gnu.org; Sat, 22 Feb 2020 14:42:43 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]:43424) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5afg-0007EQ-Um for 39204@debbugs.gnu.org; Sat, 22 Feb 2020 14:42:43 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=systemreboot.net; s=default; h=Content-Type:MIME-Version:Message-ID:Date: References:In-Reply-To:Subject:Cc:To:From:Sender:Reply-To: Content-Transfer-Encoding:Content-ID:Content-Description:Resent-Date: Resent-From:Resent-Sender:Resent-To:Resent-Cc:Resent-Message-ID:List-Id: List-Help:List-Unsubscribe:List-Subscribe:List-Post:List-Owner:List-Archive; bh=iVzilHyPSorcXClpq2lqAAlph0yRTtRPRE8nPv4f+s0=; b=o4jQ43YU1odJ9sRlPE5HDMaC7 St2wd1mibhhvnEPC2PerddoQlrTAZuVP3h6xj1JOGsXTCkcNNw7S+7YxwNNuR6a4fu0EyOcqOnIRG zhW5trVzItaMIBvC+0AHelu7xw1/aBWL2On+Q0jQagM2V4DeN9huBM7cjaaomZE2sRWis=; Received: from [192.168.2.1] (helo=steel) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_AES_256_GCM_SHA384 (Exim 4.93) (envelope-from ) id 1j5afQ-0013pb-Bs; Sun, 23 Feb 2020 01:12:24 +0530 From: Arun Isaac To: zimoun Subject: Re: bug#39204: r-rgdal: Reading of vector GIS data causes segfault In-Reply-To: References: <20200120154302.ijni47ou4fk4wd77@wzguix> Date: Sun, 23 Feb 2020 01:12:17 +0530 Message-ID: MIME-Version: 1.0 Content-Type: multipart/signed; boundary="==-=-="; micalg=pgp-sha256; protocol="application/pgp-signature" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 39204 Cc: wz@freeshell.de, 39204@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 Let's try to debug the problem you are facing. After applying the attached patch, please provide the complete outputs of the following commands. If the output is too long, feel free to send it as an email attachment. $ ./pre-inst-env guix build r-gdal $ ./pre-inst-env guix environment --container --ad-hoc r r-rgdal -- Rscript -e 'library(rgdal); dsn <- system.file("vectors", package = "rgdal")[1]; ogrInfo(dsn=dsn, layer="cities")' Thank you for your patience! Cheers! :-) --=-=-= Content-Type: text/x-patch; charset=utf-8 Content-Disposition: inline; filename=0001-gnu-r-rgdal-Replace-proj.4-with-proj.patch Content-Transfer-Encoding: quoted-printable From=207b2430788c2d168bd2a8a848e488a0e03140057b Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Sun, 23 Feb 2020 00:46:32 +0530 Subject: [PATCH] gnu: r-rgdal: Replace proj.4 with proj. * gnu/packages/cran.scm (r-rgdal)[inputs]: Replace proj.4 with proj. =2D-- gnu/packages/cran.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b731ddc29e..05759459af 100644 =2D-- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18,6 +18,7 @@ ;;; Copyright =C2=A9 2018, 2019 Brett Gilio ;;; Copyright =C2=A9 2019 Nicol=C3=B2 Balzarotti ;;; Copyright =C2=A9 2019 Wiktor =C5=BBelazny +;;; Copyright =C2=A9 2020 Arun Isaac ;;; ;;; This file is part of GNU Guix. ;;; @@ -15907,7 +15908,7 @@ effect size.") (build-system r-build-system) (inputs `(("gdal" ,gdal) =2D ("proj.4" ,proj.4) + ("proj" ,proj) ("zlib" ,zlib))) (propagated-inputs `(("r-sp" ,r-sp))) =2D-=20 2.23.0 --=-=-=-- --==-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQEzBAEBCAAdFiEEf3MDQ/Lwnzx3v3nTLiXui2GAK7MFAl5RhBkACgkQLiXui2GA K7NckggAwRAvTsNloPg7aj35kib5+2LVDE1pgSLfB0FbeAuWULJ4mFi1KJWefiuU lj9HzLbdwSmpxGkUYkbnOKogVM6R/1t7//wkemO64w1ZrHcpvmMYXaoz6OEx2wos l+2grsBVhZIRPXMKfhXtQQf2mZ0rEIbJmFtYPmD50sqUsraU1OfQSkPJxsOGni90 8iLvQuLHMENxpue3cqXfw87sA44PuxY4vVJoIgb90gOKugIVyFpoznDJSrfxsAp6 T8CkI7QDT4IASXrVGMoKSfZfrMK05ubWu+RcQgEYtZBAf7UlcfCq7ntN7V8VBJqw 1sb79KyhVGvRIQmrfTfJ99HZiKYbDQ== =DcAf -----END PGP SIGNATURE----- --==-=-=-- From debbugs-submit-bounces@debbugs.gnu.org Mon Feb 24 06:33:31 2020 Received: (at 39204) by debbugs.gnu.org; 24 Feb 2020 11:33:31 +0000 Received: from localhost ([127.0.0.1]:52951 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j6BzO-00035D-UQ for submit@debbugs.gnu.org; Mon, 24 Feb 2020 06:33:31 -0500 Received: from mail-qk1-f172.google.com ([209.85.222.172]:46000) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j6BzM-00034w-8W for 39204@debbugs.gnu.org; Mon, 24 Feb 2020 06:33:28 -0500 Received: by mail-qk1-f172.google.com with SMTP id a2so8340212qko.12 for <39204@debbugs.gnu.org>; Mon, 24 Feb 2020 03:33:28 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc; bh=xC6+fE/oUVcVreP7yFstDtwg7bVK7XCHPHBUKSmHAu4=; b=JrqH/FzKp81oE24zK+7QEEom5LT0M+rmwm2DcPF+HblUWbQpWjjt8R6voTNAvw4fYB +gBnlF0X4RcPSkdoHmk+leXAWD+sySObodYDn/JcWSdqm/eMs1RM8gvNHu5tzDob8J4M uFv6j2OPcpgxBVL6MnXNX1djH6RLNllyRFnJJjacCMyqorb2CpSoNMid6GsHhgnY1Gwp +4LMRY/EcyK3XZGgDlJpH9ckIgZ9WYHcgMBRZm0ammMUqQlQsxLfPEEw+qXUh6JU3rDL H0rrZGBCgdVm8BvXtcaLwkUvb6bdUC5AJ5bnJ7RKS+d7WATRfI0GvssvYJXXBhJp3Pgf AWxw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=xC6+fE/oUVcVreP7yFstDtwg7bVK7XCHPHBUKSmHAu4=; b=d54RZKMEztAWxDeH3DJPa2tdIje2OMvoFsNaIyvXVGxJasY8GJXrezvmwAj6fMv3+I JOLcZ/Mes1OHRc4ugqd9iAs9mmUnMGLB4dnfr1QRgs1jf0TBRlVhsD1/Yf2FN+k0TJbe 0aJyFjt1aX1e0kx2v5NNUZQda8VATszO4WNNfokSEIX8v4DH9OLxPmnjGmoi5c4pjZPP oqAxJhCHPCVtNlgI8T2LklFJBR+/On9PR7jTygdlT1WEXdA53hvxS9l9+vCtIHHz+N3A zRXKxgEwX/L6wCNbqrVLtmsECuCOAPaXyvSfQikjrnYLM75ogJo1JKF6tJOsXLF9lvpn SpxQ== X-Gm-Message-State: APjAAAWRaAu8M9E3hLBSCnIE/5AJ2l1tySQmy30SE08Pt3RLANGXtiCi 0V46JJxHTFmNDk0nWNq/btZHAmUObKTUIBeIpNUWBrMe X-Google-Smtp-Source: APXvYqz4pX2xBEgsZ+iMRQhlG+nfR15iVx+kK/lF1hZVwipoGW4M3mO3u+wlPJJMHThaWUEAZNeCJGjuXUNciMW120U= X-Received: by 2002:ae9:ef4c:: with SMTP id d73mr2410737qkg.201.1582544002570; Mon, 24 Feb 2020 03:33:22 -0800 (PST) MIME-Version: 1.0 References: <20200120154302.ijni47ou4fk4wd77@wzguix> In-Reply-To: From: zimoun Date: Mon, 24 Feb 2020 12:33:11 +0100 Message-ID: Subject: Re: bug#39204: r-rgdal: Reading of vector GIS data causes segfault To: Arun Isaac Content-Type: text/plain; charset="UTF-8" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 39204 Cc: wz@freeshell.de, 39204@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 (-) Hi Arun, First, your patch does not apply. Because it should be line 21 and not 18 for the addition of your Copyright. On Sat, 22 Feb 2020 at 20:42, Arun Isaac wrote: > $ ./pre-inst-env guix build r-rgdal I get the same message than I previously sent: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=39204#26 > $ ./pre-inst-env guix environment --container --ad-hoc r r-rgdal -- Rscript -e 'library(rgdal); dsn <- system.file("vectors", package = "rgdal")[1]; ogrInfo(dsn=dsn, layer="cities")' --8<---------------cut here---------------start------------->8--- Loading required package: sp rgdal: version: 1.4-8, (SVN revision 845) Geospatial Data Abstraction Library extensions to R successfully loaded Loaded GDAL runtime: GDAL 3.0.2, released 2019/10/28 Path to GDAL shared files: GDAL binary built with GEOS: TRUE Loaded PROJ.4 runtime: Rel. 6.2.0, September 1st, 2019, [PJ_VERSION: 620] Path to PROJ.4 shared files: (autodetected) Linking to sp version: 1.4-0 Source: "/gnu/store/m4rd975j3979zqqqfwg3b7s070i3n3h3-r-rgdal-1.4-8/site-library/rgdal/vectors", layer: "cities" Driver: ESRI Shapefile; number of rows: 606 Feature type: wkbPoint with 2 dimensions Extent: (-165.27 -53.15) - (177.1302 78.2) CRS: +proj=longlat +datum=WGS84 +no_defs LDID: 0 Number of fields: 4 name type length typeName 1 NAME 4 40 String 2 COUNTRY 4 12 String 3 POPULATION 12 11 Integer64 4 CAPITAL 4 1 String --8<---------------cut here---------------end--------------->8--- But as we have talked before, there is an issue about the upstream test suite of the package (point 1. of [1]). So I am investigating... [1] https://debbugs.gnu.org/cgi/bugreport.cgi?bug=39204#26 All the best, simon From debbugs-submit-bounces@debbugs.gnu.org Mon Feb 24 14:10:05 2020 Received: (at 39204) by debbugs.gnu.org; 24 Feb 2020 19:10:05 +0000 Received: from localhost ([127.0.0.1]:54111 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j6J7F-0006uR-IY for submit@debbugs.gnu.org; Mon, 24 Feb 2020 14:10:05 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]:51846) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j6J7A-0006tu-MM for 39204@debbugs.gnu.org; Mon, 24 Feb 2020 14:10:02 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=systemreboot.net; s=default; h=Content-Type:MIME-Version:Message-ID:Date: References:In-Reply-To:Subject:Cc:To:From:Sender:Reply-To: Content-Transfer-Encoding:Content-ID:Content-Description:Resent-Date: Resent-From:Resent-Sender:Resent-To:Resent-Cc:Resent-Message-ID:List-Id: List-Help:List-Unsubscribe:List-Subscribe:List-Post:List-Owner:List-Archive; bh=OpsvLVbJDNVdFAb2C/JeLWKOKGLHkhI4eqo4u3BhRxo=; b=n7GyWITzQqmvV7XevNOeQ8n18 jzM5dT5WaFCakp+nr6KY++r2X+VuV4SPc7Z5rGIDiAIm59LlIdsnjGwUMtrT9ZNujNgUodBBkX/Eb 4fTM+sGPrW8SjqdfRduMgs4U/UczyBRP4LZLcFbUomLnXbt56NYK9UhkyPmbo5cauELxI=; Received: from [192.168.2.1] (helo=steel) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_AES_256_GCM_SHA384 (Exim 4.93) (envelope-from ) id 1j6J6u-001HQU-MQ; Tue, 25 Feb 2020 00:39:44 +0530 From: Arun Isaac To: zimoun Subject: Re: bug#39204: r-rgdal: Reading of vector GIS data causes segfault In-Reply-To: References: <20200120154302.ijni47ou4fk4wd77@wzguix> Date: Tue, 25 Feb 2020 00:39:43 +0530 Message-ID: MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha256; protocol="application/pgp-signature" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 39204 Cc: wz@freeshell.de, 39204@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: text/plain > First, your patch does not apply. Because it should be line 21 and not > 18 for the addition of your Copyright. Sorry, I should have rebased with master. > But as we have talked before, there is an issue about the upstream > test suite of the package (point 1. of [1]). So I am investigating... Ah, I understand our miscommunication now. You have been talking about point 1 (bug in upstream test suite) and I've been talking about point 2 (segmentation fault when loading vector data). Yes, replacing proj.4 with proj only addresses point 2, not point 1. --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQEzBAEBCAAdFiEEf3MDQ/Lwnzx3v3nTLiXui2GAK7MFAl5UH3gACgkQLiXui2GA K7PisQf/TNxSvKEj8+ev8lDtnHxI881Ug58mAzxGbySng18zVCJxD5PBpDukLY0f KrW9TZqfgsbwVZx5k3p49KztZgjxiGUjybkCbSIkeG++Hr//RLLnPsa56sGZ6SNp s4g1oTfccKbfLPWb4/+edteaVL4foOvgCA41nsrsMcRAIVLdqJ++BLkWqmb/zkns CWbzwt/avAlVrl5EABZGlDOvwyrnO2SIq4PnR2HMldcSw/gRsMrK3PqP2ngQWPzS Cb8l2K36nf6LRBjZbK+CutXEKCUCgTJvSDbLkKIm9VIkaC5qLPMoQ8coUw/rWV8Z W07byUDgGrT+j/YWZ0ntB00RPKm0ew== =IkTu -----END PGP SIGNATURE----- --=-=-=-- From debbugs-submit-bounces@debbugs.gnu.org Tue Feb 25 10:49:52 2020 Received: (at 39204) by debbugs.gnu.org; 25 Feb 2020 15:49:52 +0000 Received: from localhost ([127.0.0.1]:56010 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j6cT2-00055q-0H for submit@debbugs.gnu.org; Tue, 25 Feb 2020 10:49:52 -0500 Received: from mail-qt1-f179.google.com ([209.85.160.179]:36306) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j6cT1-00055c-2h for 39204@debbugs.gnu.org; Tue, 25 Feb 2020 10:49:51 -0500 Received: by mail-qt1-f179.google.com with SMTP id t13so9359411qto.3 for <39204@debbugs.gnu.org>; Tue, 25 Feb 2020 07:49:50 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc; bh=1XIkg0XGx9s5EVo52VMjCbHE7B2PRgfPS7rXPdwTpSs=; b=tw/qPEUyDuVKKGGvA4CBxrxtPYUZMOT06TX143JL82Xlxobc6yNApgGmX/XjPVwF8S /hSow89xMbmBYBnmtX07uu5jP1fhxa/wd5W26RrRWkpTIl1MtaHbXL+9DDSwlUq0OIUV ADjU0yaumJ/w8t9X+/aLXza3BvanItem6FWmywtYdpxd+W+OGudvL60iLR7I1e/sD3lO 8cRNMinzLf1VwECRngLXSvI9ojPOCRSLmpCCVZI9hPsbL/VyO5Q4lIVy/xYzIWD4oyNE +tKtCMTx9sHuAXT1mjKQbMBQBTJsein6+ZdSbW3+WHT8a0I9GnEHOuVPGp6Yd6QBY9fJ IIwA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=1XIkg0XGx9s5EVo52VMjCbHE7B2PRgfPS7rXPdwTpSs=; b=tHOhPHiUemvdxL7b+p06OXbJ2oKJmpU0pY+5xEk4OG75MpMo4ngq/lKFrIB9ecKgW8 iMuJqYBag5u0uq4CcSBZfYbKDo1HBvynXDhWiB0ATTH6vf+BLjXrhmLvNUSXIFqvBT31 Fc5IdWkj5WZHz5jexRvhhOzYPJRphJzjbKPL5d6V5JGvMGoRLe0QLHNXbzjJx9RVtmFT YkzMdNyZMI/vzxTvBU3+AWM5uAQ5u3jrvF2HrjvMxf72nt5NLRM9fNgg9as4gYUwnkcr iEdsxkM/zGX64oPdaqE7tVij8X6q8G6ZHX9meWfe62o/G2nbjRdQLy1cyXV2k+ainXMi FszQ== X-Gm-Message-State: APjAAAXBHlYy23Ix2QQZZVzna42uQYzn75SAFKWzdGu4ZO2FkvAuQM9c +qrgtI5//kVO39Cb5RJmtQgBcutlTFELkGmoggQM0jr5 X-Google-Smtp-Source: APXvYqwUDk4RFJ70lGCoOmF5tBkC6ab39hoIIC3vlnnkDip4od6Az38VSYtalj004DTAV/JJHMm0SjhTMyjtCpBGCvk= X-Received: by 2002:aed:2050:: with SMTP id 74mr53807425qta.217.1582645785490; Tue, 25 Feb 2020 07:49:45 -0800 (PST) MIME-Version: 1.0 References: <20200120154302.ijni47ou4fk4wd77@wzguix> In-Reply-To: From: zimoun Date: Tue, 25 Feb 2020 16:49:34 +0100 Message-ID: Subject: Re: bug#39204: r-rgdal: Reading of vector GIS data causes segfault To: Arun Isaac Content-Type: text/plain; charset="UTF-8" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 39204 Cc: wz@freeshell.de, 39204@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 (-) Hi Arun, On Mon, 24 Feb 2020 at 20:10, Arun Isaac wrote: > > But as we have talked before, there is an issue about the upstream > > test suite of the package (point 1. of [1]). So I am investigating... > > Ah, I understand our miscommunication now. You have been talking about > point 1 (bug in upstream test suite) and I've been talking about point 2 > (segmentation fault when loading vector data). Yes, replacing proj.4 > with proj only addresses point 2, not point 1. It is not segfaulting anymore, I agree. But is it enough to know that everything is ok and the package is not broken? I am mean looking at the output of the 'check' phase (see [1]), it displays a diff and I am not confident if it is good or not. That's why I did not confirm that changing from proj.4 to proj works. Maybe I mispelled "error" in my previous answer and the correct words seem "I get an lengthy message and I do not know if it is ok." :-) [1] https://debbugs.gnu.org/cgi/bugreport.cgi?bug=39204#26 Cheers, simon From debbugs-submit-bounces@debbugs.gnu.org Mon Oct 12 06:22:40 2020 Received: (at 39204-done) by debbugs.gnu.org; 12 Oct 2020 10:22:40 +0000 Received: from localhost ([127.0.0.1]:41774 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kRuyW-0001fQ-2J for submit@debbugs.gnu.org; Mon, 12 Oct 2020 06:22:40 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:38970) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kRuyS-0001fF-H2 for 39204-done@debbugs.gnu.org; Mon, 12 Oct 2020 06:22:38 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=systemreboot.net; s=default; h=Content-Type:MIME-Version:Message-ID:Date: References:In-Reply-To:Subject:Cc:To:From:Sender:Reply-To: Content-Transfer-Encoding:Content-ID:Content-Description:Resent-Date: Resent-From:Resent-Sender:Resent-To:Resent-Cc:Resent-Message-ID:List-Id: List-Help:List-Unsubscribe:List-Subscribe:List-Post:List-Owner:List-Archive; bh=CM6bjK5ZL7k65xRMKfMEEjcB9jtGxRkiVPE5GZMstKA=; b=GJmCUPBjLlc8Q/7LVNvU6RYIs TyH+IUW4kt4n8EQ1fLG08JlaJwxVMa9GAqb7td4GF9v4LsLOKUC3mNG/UeWK1iCOlKdBtiZ9WfbN7 zzycIOuDpqXokOPgT3DBtD8iHxryxbMJ59jGXwynF2HdfRLBNAKnZnMuSwtKKEWkI/7CFjIVV8N6a ELoaJRCMLna+YXrZCB1RyF2ve//Iks81RU8dVnPclL6rwd3SPeMV0h3fQTHjwDU8eAcqT53ubfqEw vArkcmKO4l/TYjhfuABTp5o3WHueRgMF1MFij64t4OImQEq02CCbKmcI88j7L3x4jpolck0alzWtx 9Y29ivHQQ==; Received: from [192.168.2.1] (helo=steel) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_AES_256_GCM_SHA384 (Exim 4.94) (envelope-from ) id 1kRuwJ-000ts5-Sd; Mon, 12 Oct 2020 15:50:23 +0530 From: Arun Isaac To: zimoun Subject: Re: bug#39204: r-rgdal: Reading of vector GIS data causes segfault In-Reply-To: References: <20200120154302.ijni47ou4fk4wd77@wzguix> Date: Mon, 12 Oct 2020 15:52:30 +0530 Message-ID: <875z7f217d.fsf@systemreboot.net> MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 39204-done Cc: wz@freeshell.de, 39204-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 (-) Hi, I pushed to master, my commit replacing proj.4 with proj. This fixes the segfault issue. I also updated the package. If the issue with the check phase still persists, please open a separate issue. Cheers! From debbugs-submit-bounces@debbugs.gnu.org Mon Oct 12 12:23:27 2020 Received: (at 39204-done) by debbugs.gnu.org; 12 Oct 2020 16:23:27 +0000 Received: from localhost ([127.0.0.1]:43764 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kS0bf-00034U-BZ for submit@debbugs.gnu.org; Mon, 12 Oct 2020 12:23:27 -0400 Received: from freeshell.de ([94.247.40.156]:44574 ident=postfix) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kS0bd-00034M-HO for 39204-done@debbugs.gnu.org; Mon, 12 Oct 2020 12:23:26 -0400 Received: from localhost (cst-prg-95-87.cust.vodafone.cz [46.135.95.87]) (Authenticated sender: wz) by freeshell.de (Postfix) with ESMTPSA id 4434535CE002; Mon, 12 Oct 2020 18:23:23 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freeshell.de; s=mail; t=1602519804; bh=VtfVHqRFXgNEcAUuXqIvNsZH/wAgdenlY98ZvkwJqPM=; h=Date:From:To:Cc:Subject:References:In-Reply-To:From; b=T7L+2thrfF1mxy7CBUHT0vB/Vg1C/GSZH0YKy+kzEqMjSPsK+m5I1Pn1wdtEan3O2 xMopJAiuF1Rm0AEFlKHsV+EOvUcxik35HhYGoeWLQbTTMj0xriHlWv4MLoZVStQQH8 tbOwK1upMN4XwY8t9Ssg5jeJkiiX6G5p8oTSIRqs= Date: Mon, 12 Oct 2020 18:23:18 +0200 From: Wiktor =?utf-8?Q?=C5=BBelazny?= To: 39204-done@debbugs.gnu.org Subject: Re: bug#39204: r-rgdal: Reading of vector GIS data causes segfault Message-ID: <20201012162318.ejguit3m3nr6lgmf@wzguix> Mail-Followup-To: 39204-done@debbugs.gnu.org, Arun Isaac , zimoun X-PGP-Key: https://freeshell.de/~wz/pubkey.asc X-PGP-Fingerprint: BDC9 74CD D9C9 BA7D 761A 573D C735 A8C6 AB60 79D5 References: <875z7f217d.fsf@systemreboot.net> MIME-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha512; protocol="application/pgp-signature"; boundary="dg5c5hlyfgzdpwnp" Content-Disposition: inline In-Reply-To: <875z7f217d.fsf@systemreboot.net> X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 39204-done Cc: Arun Isaac , zimoun 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 (-) --dg5c5hlyfgzdpwnp Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable On Mon, Oct 12, 2020 at 03:52:30PM +0530, Arun Isaac wrote: > I pushed to master, my commit replacing proj.4 with proj. Hi Arun, Believe it or not, but on Friday I tried the same thing. First, replacing proj with proj.4 in GDAL, which declined to compile, demanding version 6, then replacing proj.4 with proj in r-rgdal. It kept spitting the error during the check phase, but I was time-machined some months into the past. Maybe with current Guix version the issue does not occur. I will check it out this or the next week. Thank you for your work on this issue. W=C5=BB --dg5c5hlyfgzdpwnp Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQKTBAABCgB9FiEEvcl0zdnJun12Glc9xzWoxqtgedUFAl+EgvZfFIAAAAAALgAo aXNzdWVyLWZwckBub3RhdGlvbnMub3BlbnBncC5maWZ0aGhvcnNlbWFuLm5ldEJE Qzk3NENERDlDOUJBN0Q3NjFBNTczREM3MzVBOEM2QUI2MDc5RDUACgkQxzWoxqtg edUc2w/+NCq1vbqoOlUIc/J/tBiaRXjIQE/2rGC4I1/IFEnAtTeoWkERSeuUizYn rW255wpyyWHWmkJQJdYIhVMgjVgEbosrfFcHl77Grn5hs0ftxTyI/S6h7bAzgKhL d96B5osdsoJOhHVl5VMRR+NRXff+Uub+ZAtbtq18gQQ1pspGuPrrTZ5mVSWN2IBK bBNVk/MgQiTsOSteybjQXZIBLED91s/KcrVhIkwV0kF/PMk6CICZbC98HSZZvvBT DYjuGZgDpqMxQendVnNhAzy3Tx1XKIHo20MgMKqxNo3Si4V3/m1E/cdzI5QLjg8h oZwNYqlt+hbH/GxJ8bSP6BnZ2jUMtrfWBNY+6jrlOrHBc55919qnajX/RQmlRW7P ZLWjxE5p4Go0pVLiwesxMKJag2qclt9BvKAqwtGBuJkJGPF705ohuNNa42mKM5IL 4DlsPxmpFqposJk2Qn45cO7pMljQDDxzpuZ+pafuq0CuM1QmzrBq8cRa56y6WRgx 1cpGzEoaayzTaUFMTS7Z7mvZ/wLXRUOwJ4CyFwM+v1InjUYu1/OUJojUfGIXbxPS mCaj/Z7lnyOAlSwoxWmMZPvDpG2KQD3L11tD4FhcYjm0TR4sviJTtmThDF21eS0l 4QHjHah/+nekMu7lvM2on1uEre0qG11zgMDp7Q6oNwr/+ZBGS/g= =B6n4 -----END PGP SIGNATURE----- --dg5c5hlyfgzdpwnp-- From debbugs-submit-bounces@debbugs.gnu.org Tue Oct 13 00:21:41 2020 Received: (at 39204-done) by debbugs.gnu.org; 13 Oct 2020 04:21:41 +0000 Received: from localhost ([127.0.0.1]:44841 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kSBoj-0002Rx-AR for submit@debbugs.gnu.org; Tue, 13 Oct 2020 00:21:41 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:42470) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kSBof-0002Rj-GY for 39204-done@debbugs.gnu.org; Tue, 13 Oct 2020 00:21:39 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=systemreboot.net; s=default; h=Content-Type:MIME-Version:Message-ID:Date: References:In-Reply-To:Subject:Cc:To:From:Sender:Reply-To: Content-Transfer-Encoding:Content-ID:Content-Description:Resent-Date: Resent-From:Resent-Sender:Resent-To:Resent-Cc:Resent-Message-ID:List-Id: List-Help:List-Unsubscribe:List-Subscribe:List-Post:List-Owner:List-Archive; bh=tvUg1VZU7t1/HFcepJJqmTobb6ynyO/sSlB7G7dmqxM=; b=bnUFRs97RZqObSdRnSpSykyu4 pPwkEKmFTGzG63h1OumADdxoGPsrP/AgsYRl5vI5T0xP0JeW3UgJh/9MN9OK/CyPjtJt2wUPqc+aq tpEuUEYGLuS0Ft2BTw+rKa2JdgC5xlshWCkq2RaBo9/Mqund6ima9oP/uhMDJL1rY1/giV4a/FuVM qT27Gmst6HNB40kb9P37yZ9jZJBlSiL/9Tg5I/gMKpfIA55eONXDwDjLeCiU4WELMl3nvgjW5RsTI pa6ti5y41QHg7Tcr8PmkHrLzCwFD+PT0nyfZgw5NX/aGUZLuiB+Lbyl5a0K89XHDtB/zwDw1eWHxK pdlMg2WCQ==; Received: from [192.168.2.1] (helo=steel) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_AES_256_GCM_SHA384 (Exim 4.94) (envelope-from ) id 1kSBmV-000vTC-3n; Tue, 13 Oct 2020 09:49:23 +0530 From: Arun Isaac To: Wiktor =?utf-8?Q?=C5=BBelazny?= , 39204-done@debbugs.gnu.org Subject: Re: bug#39204: r-rgdal: Reading of vector GIS data causes segfault In-Reply-To: <20201012162318.ejguit3m3nr6lgmf@wzguix> References: <875z7f217d.fsf@systemreboot.net> <20201012162318.ejguit3m3nr6lgmf@wzguix> Date: Tue, 13 Oct 2020 09:51:26 +0530 Message-ID: <87k0vurc1l.fsf@systemreboot.net> MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha256; protocol="application/pgp-signature" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 39204-done Cc: zimoun 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: text/plain > It kept spitting the error during the check phase, but I was > time-machined some months into the past. Maybe with current Guix version > the issue does not occur. I will check it out this or the next week. Sure, check it out and let me know. > Thank you for your work on this issue. My pleasure! :-) --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQFPBAEBCAA5FiEEf3MDQ/Lwnzx3v3nTLiXui2GAK7MFAl+FK0YbHGFydW5pc2Fh Y0BzeXN0ZW1yZWJvb3QubmV0AAoJEC4l7othgCuzjCQH/RMryN1OSDnB4x1N4+JK seFxpmr7I3XHfFyywSMij5tyA2qtfK604LOs+mTLVx6Isy7luQnb4g6ljOtBRjux u1pcZ+AF9AgVqziDnx/VRDi+1gUUc17yJa2FefjZDibP+NaoL+jDBxVQZbe2WB97 ElrwEllZ0gTI1KDwSGsMP5JPfjQxtbm+3Lf38fb9l7jQank2II54YrWp4V1Rxnpq Tj1SISRqDzop7TsJ4o/AcQw+D5UM9jxSNclNEhGzZeCM4f2EbHudXhn3dajomxnV 1/R5wzvvaxvgpyiu7eG6yjRx8BY8zx78NTNIfxx27qnlppJrMMBgXb7uRQLVU8/f pF0= =UFQb -----END PGP SIGNATURE----- --=-=-=-- From unknown Fri Jun 20 07:21:38 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Tue, 10 Nov 2020 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