Received: (at 36687) by debbugs.gnu.org; 30 Dec 2023 02:26:13 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Fri Dec 29 21:26:12 2023 Received: from localhost ([127.0.0.1]:42730 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1rJP3E-0007T3-Jy for submit <at> debbugs.gnu.org; Fri, 29 Dec 2023 21:26:12 -0500 Received: from mailtransmit05.runbox.com ([2a0c:5a00:149::26]:33760) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <pkill9@HIDDEN>) id 1rJP3C-0007Sh-30 for 36687 <at> debbugs.gnu.org; Fri, 29 Dec 2023 21:26:11 -0500 Received: from mailtransmit02.runbox ([10.9.9.162] helo=aibo.runbox.com) by mailtransmit05.runbox.com with esmtps (TLS1.2) tls TLS_ECDHE_RSA_WITH_AES_128_GCM_SHA256 (Exim 4.93) (envelope-from <pkill9@HIDDEN>) id 1rJP33-005mfc-2R for 36687 <at> debbugs.gnu.org; Sat, 30 Dec 2023 03:26:01 +0100 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=runbox.com; s=selector2; h=Content-Type:MIME-Version:Message-Id:To:Subject:From:Date; bh=J0NewfP7mBf4JgvF0Yu/fK8Srtsr5AyI7ed33PnIqE4=; b=FcJdNncx3r31bmzXAENUl07Kt JBzAeX3K0KlD1PGZ4PfDGBS+q9difxtalx6T/Gaw/TbGHkUxbJ1Pb9mriUWbAzjCPDb8RUD81GqXK huU/9yizslgesvIRXKktfoKMwhehA7Vfh0T9Lu7mfciFUMnEl2GQPC9WEaAkPsUHam3c7gb7Dl7qQ vyrr7gR9Au1HMhKoe4c+SZHExDT1WVBLHMexEERMAjC1/9GZwzGtqUZb840NiGZ9zLqudkArtp74p e30rZqVYStxnVQ2kklYQdzLQphuFliqJIUupg+5yOK4qZuIzO0XKSl2mTR8iT6MDJBMnwPVVjVTwT frxoecZCw==; Received: from [10.9.9.72] (helo=submission01.runbox) by mailtransmit02.runbox with esmtp (Exim 4.86_2) (envelope-from <pkill9@HIDDEN>) id 1rJP32-0002wY-Jv for 36687 <at> debbugs.gnu.org; Sat, 30 Dec 2023 03:26:00 +0100 Received: by submission01.runbox with esmtpsa [Authenticated ID (780724)] (TLS1.2:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.93) id 1rJP2y-007CmA-Dp for 36687 <at> debbugs.gnu.org; Sat, 30 Dec 2023 03:25:56 +0100 Date: Sat, 30 Dec 2023 02:25:49 +0000 From: pkill9 <pkill9@HIDDEN> Subject: guix gc: error: executing SQLite statement: database disk image is malformed To: 36687 <at> debbugs.gnu.org Message-Id: <13KG6S.9JVA2Q8FX3TN@HIDDEN> X-Mailer: geary/44.1 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="=-fadujGU4cQCY/Q00yZIS" X-Spam-Score: -0.5 (/) X-Debbugs-Envelope-To: 36687 X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.5 (-) --=-fadujGU4cQCY/Q00yZIS Content-Type: text/plain; charset=us-ascii; format=flowed Hi, I fixed this issue using sqlite3's built-in recover command: sudo mv /var/guix/db/db.sqlite /var/guix/db/db.sqlite.bak sqlite3 /var/guix/db/db.sqlite.bak ".recover" | sudo sqlite3 /var/guix/db/db.sqlite Solution was found at <https://stackoverflow.com/questions/18259692/how-to-recover-a-corrupt-sqlite3-database/57872238#57872238> --=-fadujGU4cQCY/Q00yZIS Content-Type: text/html; charset=us-ascii <div id="geary-body" dir="auto"><div>Hi, I fixed this issue using sqlite3's built-in recover command:</div><div><br></div><div>sudo mv /var/guix/db/db.sqlite /var/guix/db/db.sqlite.bak</div><div><pre class="lang-sql s-code-block"><code class="hljs language-sql">sqlite3 /var/guix/db/db.sqlite.bak ".recover" <span class="hljs-operator">|</span> sudo sqlite3 /var/guix/db/db.sqlite</code></pre></div><div><br></div><div>Solution was found at <a href="https://stackoverflow.com/questions/18259692/how-to-recover-a-corrupt-sqlite3-database/57872238#57872238">https://stackoverflow.com/questions/18259692/how-to-recover-a-corrupt-sqlite3-database/57872238#57872238</a></div></div> --=-fadujGU4cQCY/Q00yZIS--
bug-guix@HIDDEN
:bug#36687
; Package guix
.
Full text available.Received: (at 36687) by debbugs.gnu.org; 16 Nov 2019 23:30:24 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Sat Nov 16 18:30:24 2019 Received: from localhost ([127.0.0.1]:39882 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1iW7WK-0000hq-EV for submit <at> debbugs.gnu.org; Sat, 16 Nov 2019 18:30:24 -0500 Received: from mail-pg1-f180.google.com ([209.85.215.180]:35690) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <cmmarusich@HIDDEN>) id 1iW7WI-0000hd-Sb for 36687 <at> debbugs.gnu.org; Sat, 16 Nov 2019 18:30:23 -0500 Received: by mail-pg1-f180.google.com with SMTP id k32so1995764pgl.2 for <36687 <at> debbugs.gnu.org>; Sat, 16 Nov 2019 15:30:22 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:references:date:in-reply-to:message-id :user-agent:mime-version; bh=/sqzpIE1JXCB7pTVivOFIuT6u+Eok/yQSZZJvm3SEWs=; b=LLGJddqu/odUioz/jmgdsIANfYRWDprVpNZ6hhjk9YaiqoGhRZ8tQtlHoQJI+Ig0ga gcd+9CUZlSmqWADG2JhK8h6KRFe5p/UlMyX0+bYRY99TOdVrAWPjrsMjBNiZMqQUFKXi XDMRn/F6V7lF7331FfQpHuRt1SsR2pKc2fztxwhH8jIubchqOpwy9Zej8/MZ1ayEDXno auPaiQnVwd1f4INuCUSCUtAa70Sad68e7MqtQGdHh7goe4hmiJSxaevC3FtcYUZHM6ti oUFZC5kroagDDU40arJxROGmmsVsWhg3L3LlkrV0W1DhGZYqInojPijGqaJ1121Y4jX8 P9TQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:references:date:in-reply-to :message-id:user-agent:mime-version; bh=/sqzpIE1JXCB7pTVivOFIuT6u+Eok/yQSZZJvm3SEWs=; b=IjHPzI20NsKER0JZ/UKBK/qrXopzYn4WZu1P0oO8TqKDQ6V6BYV27IstHLnsDtc78N 9aSRGLS9E7AkA5IJhMuB1zFhjy23vUPakL6pCK8Zw2nqRmrrUqw7xEE8yPWTYwYXRm7f vYBZWmYNElkSEbwSBg8Z0jSRM+tBotC8MKzAF6KyOb3HDeaRtkcNfMz/1to2rXE4SF/U HzVdI8W3CParcZ4O6BIvvkFxphoF3EnqRDwd0dOEZu5n5gV8mrjLJAFlx7G4d1reNiT7 LpiSMGMmQOKJOg9pRtjnKgIRW0y0T7SCGOAxnGQn7NL+2yiQZkgRUzBLQTE4FoDNJWPg ddOQ== X-Gm-Message-State: APjAAAXnsnd0UfL/V28scD/0MD9DMztoGnUqNnqMZBHb3uAepaF+fWbl NqQ6n71XOemnYinfjmHMt4Jybprp X-Google-Smtp-Source: APXvYqwNS+p09hvUNeSP33uK8gmgoIysIapqNgowkz8By2volmV5c+h1MNGO6JusSt/YDKfyySrqlg== X-Received: by 2002:a63:4441:: with SMTP id t1mr6854947pgk.179.1573947016368; Sat, 16 Nov 2019 15:30:16 -0800 (PST) Received: from garuda.local ([2607:fb90:f28:6b41:1492:c5bc:21ab:9489]) by smtp.gmail.com with ESMTPSA id n15sm15609864pfq.146.2019.11.16.15.30.14 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sat, 16 Nov 2019 15:30:15 -0800 (PST) From: Chris Marusich <cmmarusich@HIDDEN> X-Google-Original-From: Chris Marusich <marusich@HIDDEN> To: Chris Marusich <cmmarusich@HIDDEN> Subject: Re: bug#36687: guix gc: error: executing SQLite statement: database disk image is malformed References: <87v9w2ctpm.fsf@HIDDEN> <87tvbmgndy.fsf@HIDDEN> <87pnm6egm4.fsf@HIDDEN> Date: Sat, 16 Nov 2019 15:30:09 -0800 In-Reply-To: <87pnm6egm4.fsf@HIDDEN> (Chris Marusich's message of "Thu, 18 Jul 2019 22:30:11 -0700") Message-ID: <8736en762m.fsf@HIDDEN> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux) 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: 36687 Cc: Ricardo Wurmus <rekado@HIDDEN>, 36687 <at> debbugs.gnu.org X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) --=-=-= Content-Type: text/plain Content-Transfer-Encoding: quoted-printable Chris Marusich <cmmarusich@HIDDEN> writes: > I wonder what has brought my installation into this state. I can't > think of a way to fix it since I don't even know what caused it, so I > will probably re-install Guix to work around the issue I re-installed Guix to work around the issue. =2D-=20 Chris --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEy/WXVcvn5+/vGD+x3UCaFdgiRp0FAl3QhoEACgkQ3UCaFdgi Rp3qQw/9FgEj4Vxknpe7nP2ox6eEyNJsrPMk/P1TKrdZl8cHnMq9gOcig93cuApO NEUSLDNZfxEcg7eU6zq31wbsWzAwXh4QBicjRQRd3tnPWGA6LX7zuMuD4iQtrj+1 QrbQmBja5+lVVrXBsL2vmTud3H/um6y2mICeOcvFX3gIZG4yUjYMs8r0tTxuxXiz gV+TdwDjlq0VLkd/6xi9x04BmJ5xl4pmBiaI7oPCJFwjviPX5Tp2GMBXjJJOqewB +wp3YSmOkuiNeFrMlEa0CvKZR6ky91jny5E4iihg915gVRxUMO/weCOVaEJLqxRf EMeOjUPjDgKk/IPtrNSTKXhZscr8JMFqhPAGFnVU7O1fZHeOScLe3Cl+FFLDClwO jEMdLpkAGaoQr+se3mLS7fLo+7AufVggzDvOyq77PZ7msx34zbcPHdu+a8ROW1cB YsVO0JoJffPTf8Ml4ALJRP6rcHE5aOdniPgxCg5juLXZAKEgu0QaqCiKRZsUL7iS clVXn1hEZO38c3XKN0eJ7Aw/e+rHGxTs6wdfE0StGdMYHfIJ3t4ph6PqZQxuJ+Ls hvhwgDOqT0Fg4pM7DooLrgGC+iTSo4nVfV9matcSq5zSWQmK491xI3qf/u0E5/Jl KrE5K8z3IQI+3L1iZ5PLJ1W4QE4xRAguUBm2DZM6A1Jf/03uMec= =OJ5A -----END PGP SIGNATURE----- --=-=-=--
bug-guix@HIDDEN
:bug#36687
; Package guix
.
Full text available.Received: (at 36687) by debbugs.gnu.org; 3 Aug 2019 13:07:56 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Sat Aug 03 09:07:56 2019 Received: from localhost ([127.0.0.1]:58543 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1httlK-0001nH-Oy for submit <at> debbugs.gnu.org; Sat, 03 Aug 2019 09:07:55 -0400 Received: from eggs.gnu.org ([209.51.188.92]:49474) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <mtg@HIDDEN>) id 1httlI-0001n5-A7 for 36687 <at> debbugs.gnu.org; Sat, 03 Aug 2019 09:07:52 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:57090) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from <mtg@HIDDEN>) id 1httl9-0000rV-8G; Sat, 03 Aug 2019 09:07:44 -0400 Received: from localhost ([::1]:54764 helo=mikegerwitz-pc.gerwitz.local) by fencepost.gnu.org with esmtps (TLS1.2:DHE_RSA_AES_128_CBC_SHA1:128) (Exim 4.82) (envelope-from <mtg@HIDDEN>) id 1httl7-0001On-R9; Sat, 03 Aug 2019 09:07:43 -0400 From: Mike Gerwitz <mtg@HIDDEN> To: Chris Marusich <cmmarusich@HIDDEN> Subject: Re: bug#36687: guix gc: error: executing SQLite statement: database disk image is malformed In-Reply-To: <87wofuipfp.fsf@HIDDEN> (Chris Marusich's message of "Sat, 03 Aug 2019 02:11:22 -0700") Date: Sat, 03 Aug 2019 09:06:54 -0400 Message-ID: <87pnlmtn2p.fsf@HIDDEN> References: <87v9w2ctpm.fsf@HIDDEN> <87tvbmgndy.fsf@HIDDEN> <87pnm6egm4.fsf@HIDDEN> <87blxqfo25.fsf@HIDDEN> <87wofuipfp.fsf@HIDDEN> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/27.0.50 (gnu/linux) OpenPGP: id=D6E9B930028A6C38F43B2388FEF635745E6F6D05 MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha512; protocol="application/pgp-signature" X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 36687 Cc: Ricardo Wurmus <rekado@HIDDEN>, 36687 <at> debbugs.gnu.org X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -3.3 (---) --=-=-= Content-Type: text/plain Content-Transfer-Encoding: quoted-printable Sorry I hadn't seen this bug report; it was opened after I researched this issue a couple months ago and I didn't bother checking since. Here's the thread I posted to help-guix: <87lfwbuj27.fsf@HIDDEN>. =2D-=20 Mike Gerwitz Free Software Hacker+Activist | GNU Maintainer & Volunteer GPG: D6E9 B930 028A 6C38 F43B 2388 FEF6 3574 5E6F 6D05 https://mikegerwitz.com --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- Version: GnuPG v2 iQIcBAEBCgAGBQJdRYbuAAoJEIyRe39dxRuiVCsP/RVg5DZR+54/cXRIjxPiR9fl oFTlQdUg3vLrJdG6fdaqGfZ2H0bm0mdFl3PveBLDMX/M1TWc4CoyuGlKxY8z5FOW 1BMIetdHhfxfQZ1Rf5W9An+H9LEmwxXZI5o4oba+n3n0Kz3yj5ujdxAym2ljVPOB curArnHXSaLvcteoyX0tDmeYsCbvp8LN9VkMq2A9KoRFMgIeqABe/i2OfUr7MdUX 3U5nmiM6qikqKJMjkcc9c/jOldIPSdaRcuRUKMygBOGzfjxpmWEAYoTrE7HDNOjH y9ZlFcjOTCA9cYv7yys704RCR7CTFR7DnGUd6QDPnK9WMQq+SGuRFuU9VdI5QYgB yrEbD7xG3r2XnUyRNGpX4yQNMt9K6QNpVHvMYH3f6OgX7V3AWb3uCCGvlgE1jRHX a3E+UIDxAlp8psk9+7Y9sjhK2p0vIN30spTlWaZbZCjFh0DS+QxoWeA68AbiAWFS Cgp7Iqbm/FMyykJDnEAucGGHFq8R0DJ0+ClBW29XCk8umcM1u3h3k06fXbhTema1 F/8NituQn+rgWFZ+ScPA2KWmw6sarfBltfi/i59cFW1pUTTEsApw643FEpMaBiHR hgv1UJ9nyed+U5VEvYegdRNR7Q6B6Mex+PbCHlukO8e3qGYSofYfhPSBSY40zGEc BdqVKUSb2XoI+A+OF2md =UEuU -----END PGP SIGNATURE----- --=-=-=--
bug-guix@HIDDEN
:bug#36687
; Package guix
.
Full text available.Received: (at 36687) by debbugs.gnu.org; 3 Aug 2019 09:11:37 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Sat Aug 03 05:11:37 2019 Received: from localhost ([127.0.0.1]:58284 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1htq4e-0001oQ-Uk for submit <at> debbugs.gnu.org; Sat, 03 Aug 2019 05:11:37 -0400 Received: from mail-pl1-f194.google.com ([209.85.214.194]:44633) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <cmmarusich@HIDDEN>) id 1htq4c-0001oA-8D for 36687 <at> debbugs.gnu.org; Sat, 03 Aug 2019 05:11:34 -0400 Received: by mail-pl1-f194.google.com with SMTP id t14so34524820plr.11 for <36687 <at> debbugs.gnu.org>; Sat, 03 Aug 2019 02:11:34 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:references:date:in-reply-to:message-id :user-agent:mime-version; bh=p903jsLOrD8tpuhJOG3MX4DXgfl6d5Q3BCt/lo728SA=; b=XoEWUlyG7E/JqcygpOwkr+aivenXqEzEAlB37Nf16/GQrKIrjzfCaE5g1xp0vcT1dE Iz56iufxsPKYRb+IcyvsskXJ88PPQ7cjfbdJkJG4q+ecqtHfqgkX9Immq4T1Zwzlu39v KzH5eMEjTejpdb+dYhuuqNhAhmkBd8FI+sgdm/7lNLKsGMh5nG3rmxYYCpNy5TJGlv9Q xkVLNXy/qHxH6ctrnc4i2vx/OQ7MIGy0UdkR7TvaNJeBXbVMpiDvXhtzH1J0Bh4opAca n9WV408TDOSD+dpY3XoM2oHDFfdsO5ApSUgx5Q9CYSXa6B71jBJuxoVDygrMJsRCWFDr imrg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:references:date:in-reply-to :message-id:user-agent:mime-version; bh=p903jsLOrD8tpuhJOG3MX4DXgfl6d5Q3BCt/lo728SA=; b=LUW7PzLMayQp3IUa2fZx2+PnS43BZPR9yla+LCc0UE7GSUZ/ZmIY1CMhT2DZdEP8mB 8EmGUnv7h+AwS2AFP3Ui4XDUqhuNkuVuN5ovBjLO+cBUxHQamIB9mxCk0iHtT0b5aU9H sDaFHol1kU1TnDnoWYWeilBpNvgxhcz8tDvjrd9b6CisZupwQLe4oZU8+j3UvPrfpSfY dG8ak8q9YINH9IkbxLlbz2ZN5MVf0fQXJ623YBQY1DXKZttOjxGnaIgGfvfVsGlp8Mt2 KaPoDaQQf8b2y6MCzkvFG+htPfT/9bUJdQXQVsaDzfzKLtJv8HbtyBRZ5Zq2k/8rIJiv AzMA== X-Gm-Message-State: APjAAAWMBsHktsR1fCfRYMH5ROz1T1m+pKCu/ZO3Cga+lj659T8xQTka tfQQbyt3zi05seOmMPXfnmo= X-Google-Smtp-Source: APXvYqwYMbxqShWWEwqgzTgID8crGzwPL15Do6WT58KcuBgCeZONWbZ4yVa0wDsRdIL7dv47Eym6Ew== X-Received: by 2002:a17:902:e287:: with SMTP id cf7mr134307297plb.32.1564823488048; Sat, 03 Aug 2019 02:11:28 -0700 (PDT) Received: from garuda.local ([2601:601:9d80:25b2::fa8]) by smtp.gmail.com with ESMTPSA id l17sm3535947pgj.44.2019.08.03.02.11.26 (version=TLS1_2 cipher=ECDHE-RSA-CHACHA20-POLY1305 bits=256/256); Sat, 03 Aug 2019 02:11:26 -0700 (PDT) From: Chris Marusich <cmmarusich@HIDDEN> To: Ricardo Wurmus <rekado@HIDDEN> Subject: Re: bug#36687: guix gc: error: executing SQLite statement: database disk image is malformed References: <87v9w2ctpm.fsf@HIDDEN> <87tvbmgndy.fsf@HIDDEN> <87pnm6egm4.fsf@HIDDEN> <87blxqfo25.fsf@HIDDEN> Date: Sat, 03 Aug 2019 02:11:22 -0700 In-Reply-To: <87blxqfo25.fsf@HIDDEN> (Ricardo Wurmus's message of "Fri, 19 Jul 2019 10:04:02 +0200") Message-ID: <87wofuipfp.fsf@HIDDEN> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.1 (gnu/linux) 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: 36687 Cc: Mike Gerwitz <mtg@HIDDEN>, 36687 <at> debbugs.gnu.org X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) --=-=-= Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Ricardo Wurmus <rekado@HIDDEN> writes: > Chris Marusich <cmmarusich@HIDDEN> writes: > >> is there anything we can check to understand why the database >> corruption has occurred? > [=E2=80=A6] >> For the record, I do sometimes abruptly power off my machine, and it >> does rarely abruptly crash (I think I have reported this when it occurs, >> but I can't be sure). > > This can be a cause of corruption. > > Have you manually run fsck on the unmounted disk yet? Yes, I have. The file system containing the database is my root file system, and it is ext4. On my system, Guix runs e2fsck on the root file system automatically on each boot [1]. However, just to be sure, I ran it manually on the unmounted device with the -f option to force a check. It reported the following (I've copied this output by hand): =2D-8<---------------cut here---------------start------------->8--- root@spaceship ~# e2fsck -f /dev/mapper/home e2fsck 1.45.2 (27-May-2019) Pass 1: Checking inodes, blocks, and sizes Inode 290237 extent tree (at level 2) could be narrower. Optimize<y>? yes Inode 291644 extent tree (at level 2) could be narrower. Optimize<y>? yes Inode 446822 extent tree (at level 1) could be narrower. Optimize<y>? yes Inode 3016396 extent tree (at level 2) could be narrower. Optimize<y>? yes Pass 1E: Optimizing extent trees Pass 2: Checking directory structure Problem in HTREE directory inode 12451844: block #21606 has bad min hash Invalid HTREE directory inode 12451844 (/gnu/store/.links). Clear HTree in= dex<y>? yes Pass 3: Checking directory connectivity Pass 3A: Optimizing directories Pass 4: Checking reference counts Pass 5: Checking group summary information root: ***** FILE SYSTEM WAS MODIFIED ***** root: 1761282/14000128 files (0.4% non-contiguous), 50020294/55985664 blocks root@spaceship ~# echo $? 1 =2D-8<---------------cut here---------------end--------------->8--- Unfortunately, when I rebooted and tried "guix gc", the same problem as before occurred. I saw that Mike Gerwitz encountered the same error, so I thought I would try his work-around [2]. Before proceeding, I stopped guix-daemon ("sudo herd stop guix-daemon") and verified that no processes were accessing the database file ("sudo fuser db.sqlite"). Then I made a backup of my entire /var/guix directory. I dumped the database to SQL and recreated it like so: sudo sqlite3 db.sqlite .dump > /tmp/db.sqlite.dump sudo rm db.sqlite sudo sqlite3 db.sqlite < /tmp/db.sqlite.dump This succeeded without errors or warnings, and it reduced the size of the db.sqlite file from 145 MiB to 49 MiB. Although Mike's dump ended with a "ROLLBACK" and needed to be manually modified, mine ended with a "COMMIT" and did not require manual modification. I then started guix-daemon ("sudo herd start guix-daemon") and attempted to run "guix gc -C 1GiB", which succeeded. I followed that up with another "guix gc -C 40GiB", which also succeeded. The sqlite documentation says that this method of dumping and recreating the database is supported [3], so I think it's a valid work-around. However, you never know... Dumping and restoring the database file obviously changed it, so even if the restored database is "equivalent" to the original, it's still conceivable that the difference might cause a problem somehow. After all, obviously it was different enough that guix-daemon stopped failing. But maybe I'm being too pessimistic. In any case, it's notable that guix-daemon claimed the database was corrupt, even though sqlite3 didn't complain about it. Since the size was reduced, I suppose sqlite3 cleaned it up or optimized it somehow. Maybe in doing so, it fixed something that guix-daemon didn't know how to handle? That's just a guess. It's concerning that this "corruption" has occurred for two different people recently. We might want to check the Nix bug reports to see if they've encountered a bug like this. I did a (very) cursory search and found only this possibly similar, but possibly unrelated issue: https://github.com/NixOS/nixpkgs/issues/3958 It may be worth looking harder before diving too deeply into debugging. If you can think of anything I can do to drill into the files or debug this more, please let me know. If the database files do not contain sensitive information, I would also be willing to share them with you for further debugging. Footnotes:=20 [1] https://git.savannah.gnu.org/cgit/guix.git/tree/gnu/build/linux-boot.s= cm?id=3Dafb986e77cd669c2f21953f501f7893237730ca7#n383 [2] https://lists.gnu.org/archive/html/help-guix/2019-08/msg00012.html [3] https://sqlite.org/cli.html#dump =2D-=20 Chris --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEy/WXVcvn5+/vGD+x3UCaFdgiRp0FAl1FT7oACgkQ3UCaFdgi Rp0unA//Q3adnK5tsXdLuLSHDYlhTWv7H+MBYVtuDT+l6AN3TVpPrmLrrXG/0qXN RPww50/TgjDCl+1G99a3ocxBJvUSbnq2IssGylE+Ott06YRG5LTXxZfA9HZg7j2Y skBm6I7YFFN0JCdNJCceobSaSWcl4ZWV+70RudarI6VOnku3PDmMM9Rz2a4+88wF MSPa3piVK6j6KGI/VQZf3ocdOo8s3oQFSf+VBtvVnq5a+53wKLBOL8jVpjJ3jrpi qYO92zvVs04FvTClLPjmWrV4HzSVotg2yf6egfSucLsFg2807YSmkz6mAYkkPIXk Fei9kTRH17bKUGckmIEEhJJpHAYyKSYTEkVhBDOesreHWw4sGTQq+JoRImcAdarQ gmwaCrw8+LadZrT2xRjh68DK7F69wFlOFO1Vc3E9p7oxWJWDi2Wl77uqbGQBZQVp CiaAPM4/MgSPjggP/EtaOH8tUQsiNFmm+1C4FfqFRSs2vo3xdzcUgsq9SxPZz7Na OxhnRT1P7asC57PdnAY/bvaIhuZfHWnBmjS2BxAlGrXS+Wt3vcKwnQJpnvJ3gSFv LZWdf4g7WcnKIXKGpD1U/oZhJu9xqxAfJW8GLpDZkuY6+ULOkKMZaLtuRtamklxK QiQA2EvXuFL86SdB5b2mCBiaW8p5aVoyyYnEXiCIPh852mGQ7tA= =9ur8 -----END PGP SIGNATURE----- --=-=-=--
bug-guix@HIDDEN
:bug#36687
; Package guix
.
Full text available.Received: (at 36687) by debbugs.gnu.org; 19 Jul 2019 08:04:11 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Fri Jul 19 04:04:11 2019 Received: from localhost ([127.0.0.1]:55077 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1hoNsA-0002Oi-Vn for submit <at> debbugs.gnu.org; Fri, 19 Jul 2019 04:04:11 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21276) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <rekado@HIDDEN>) id 1hoNs9-0002Oa-UK for 36687 <at> debbugs.gnu.org; Fri, 19 Jul 2019 04:04:10 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1563523446; cv=none; d=zoho.com; s=zohoarc; b=lQqJiULYkX8rK+Wa2nhws596XM4LUm6q1h4OJKjiXpCxCwhptW4puIO3DyPNN5MrMOIWEetojMhky4ymeTlG+LICUAlKqP4HQE6gPd0gazvAJveoGcavuX4PnEUzWIa6xEgdTvzUeIa7MNU4jHBUR4h7DIiSmNzy/aUEJ86GCew= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zoho.com; s=zohoarc; t=1563523446; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To:ARC-Authentication-Results; bh=MOUJiyZizB80l58sMFaKld07BPDKvJ06Yo6SQBE5mjs=; b=mO93rFOTJ/W97Vr73ujbS/dtBo1kyiCQPH9dfdm2NNDZKVfpJYecC2LF0kHk8SAsDlcx5B+d/4fke2+USczAKiHXaGL5h/Fj1ryPSwSEgLfcgyJ8KNGTRzXk+XE6ObsLlpp1rZuQ4A1IOQeUwKrTTrfIoi+iPJC+EfLyLsbe0us= ARC-Authentication-Results: i=1; mx.zoho.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@HIDDEN; dmarc=pass header.from=<rekado@HIDDEN> header.from=<rekado@HIDDEN> DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1563523446; s=zoho; d=elephly.net; i=rekado@HIDDEN; h=References:From:To:Cc:Subject:In-reply-to:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding; l=443; bh=MOUJiyZizB80l58sMFaKld07BPDKvJ06Yo6SQBE5mjs=; b=RQszz2o3+SjuBEiKp4yZMs2C9PQdz5uPcelfORS8d5+ujBhaWi/YmiAoedxU0qV8 Un/mSbpW9xtSjFXW1KsvAoJLP/40uv/+QjgZOjyW9yonrixwiL7Gz9AnBeZE6GIfIU8 jk48J6SNg0IsPUNLFL5NR9yD9fcgJYaSiZTv0s7c= Received: from localhost (141.80.247.250 [141.80.247.250]) by mx.zohomail.com with SMTPS id 1563523445453552.432106443709; Fri, 19 Jul 2019 01:04:05 -0700 (PDT) References: <87v9w2ctpm.fsf@HIDDEN> <87tvbmgndy.fsf@HIDDEN> <87pnm6egm4.fsf@HIDDEN> User-agent: mu4e 1.2.0; emacs 26.2 From: Ricardo Wurmus <rekado@HIDDEN> To: Chris Marusich <cmmarusich@HIDDEN> Subject: Re: bug#36687: guix gc: error: executing SQLite statement: database disk image is malformed In-reply-to: <87pnm6egm4.fsf@HIDDEN> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Fri, 19 Jul 2019 10:04:02 +0200 Message-ID: <87blxqfo25.fsf@HIDDEN> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 36687 Cc: 36687 <at> debbugs.gnu.org X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) Chris Marusich <cmmarusich@HIDDEN> writes: > is there anything we can check to understand why the database > corruption has occurred? [=E2=80=A6] > For the record, I do sometimes abruptly power off my machine, and it > does rarely abruptly crash (I think I have reported this when it occurs, > but I can't be sure). This can be a cause of corruption. Have you manually run fsck on the unmounted disk yet? --=20 Ricardo
bug-guix@HIDDEN
:bug#36687
; Package guix
.
Full text available.Received: (at 36687) by debbugs.gnu.org; 19 Jul 2019 05:30:24 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Fri Jul 19 01:30:24 2019 Received: from localhost ([127.0.0.1]:54997 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1hoLTM-0007CS-7W for submit <at> debbugs.gnu.org; Fri, 19 Jul 2019 01:30:24 -0400 Received: from mail-pf1-f171.google.com ([209.85.210.171]:37367) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <cmmarusich@HIDDEN>) id 1hoLTL-00078B-05 for 36687 <at> debbugs.gnu.org; Fri, 19 Jul 2019 01:30:23 -0400 Received: by mail-pf1-f171.google.com with SMTP id 19so13653234pfa.4 for <36687 <at> debbugs.gnu.org>; Thu, 18 Jul 2019 22:30:22 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:references:date:in-reply-to:message-id :user-agent:mime-version; bh=LgSNd+KxPVHbbXkBj0rl1m6PUOTjGd1ZJCWkCyrwsgc=; b=kq80Xiq7SiD22rUGfXiaBKwLwuPpSN4b/mG5dU/1aw3I59stAJafk05kcDhEaa/Baa +n0SDxC2kBY77F6/e9Hk7ahHcNHppnK766HAqUIj9g3FnzsS552r9Qdcd/i4/vH0NmvT amyQCo5Ti9Tuc03ALvE6L2o/EXXDbf7R003Qr+xN/RaL3V2GKvI8aCq/mGtL0bQrRzJY pQHQ7C4bsYKvvGlPDwbUL3UncNc2rVEG2FsOiPldhFSWCXR+zv5cfaMWF5NZIf/+gKiZ Kk34sJYHh1EaXtKB66pWK+6X+w3L9Mu0874f3qJwtmAIsW8IkglcY1ReGVb+jcTzJvj7 fsIA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:references:date:in-reply-to :message-id:user-agent:mime-version; bh=LgSNd+KxPVHbbXkBj0rl1m6PUOTjGd1ZJCWkCyrwsgc=; b=C3fxUe0SEdNOTUYWn44bsaV01pH+vVajyQBPxmb92LwzWWQW7+LtbLhWknlMJ1OZ+X Bi93vVb5LYuS6H52zEwP22c6ucspHfPfRaKRPy5uJFIAC058KOHyhsv7CSwVYBz8tf1f VuLCy/6q9VMHeay6YcUSMiidO9jB7ykG+PwFkzLJaIs2JITEFQYDdkzjKpzIte7X2R4q Zj6cRrUt/Q2QmUOb9eBco7ZaZRt8XlMHg7nzfrOaDkr2ChB4UpFBmPrhLHykVeCQndyS MKoCx76SCeC7iAVwWGr1F+8GvP4VpXn4N1JQgIkJgYVgXQrfHFCp9ETEs2C+bH7qrvCY y0eg== X-Gm-Message-State: APjAAAWQvOfzjmq62bM7JShDFlNkYea06CMpY7fdU4q3LdTHrm2UsXsF Y9uJk/5mYE2vnSERrn/ksy4uJZPP X-Google-Smtp-Source: APXvYqzG2PfpbWRHRd2leMnwY8CMAA3Xbmjp9nvFz7yaYF++5SDGmbZIzYk0RqgTZf7E5Q/3QZCxKw== X-Received: by 2002:a63:b919:: with SMTP id z25mr51581687pge.201.1563514216545; Thu, 18 Jul 2019 22:30:16 -0700 (PDT) Received: from garuda.local ([2601:601:9d80:25b2::d12]) by smtp.gmail.com with ESMTPSA id 85sm30129121pfv.130.2019.07.18.22.30.14 (version=TLS1_2 cipher=ECDHE-RSA-CHACHA20-POLY1305 bits=256/256); Thu, 18 Jul 2019 22:30:15 -0700 (PDT) From: Chris Marusich <cmmarusich@HIDDEN> To: Ricardo Wurmus <rekado@HIDDEN> Subject: Re: bug#36687: guix gc: error: executing SQLite statement: database disk image is malformed References: <87v9w2ctpm.fsf@HIDDEN> <87tvbmgndy.fsf@HIDDEN> Date: Thu, 18 Jul 2019 22:30:11 -0700 In-Reply-To: <87tvbmgndy.fsf@HIDDEN> (Ricardo Wurmus's message of "Tue, 16 Jul 2019 14:44:09 +0200") Message-ID: <87pnm6egm4.fsf@HIDDEN> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.1 (gnu/linux) 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: 36687 Cc: 36687 <at> debbugs.gnu.org X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) --=-=-= Content-Type: text/plain Content-Transfer-Encoding: quoted-printable Ricardo Wurmus <rekado@HIDDEN> writes: > Chris Marusich <cmmarusich@HIDDEN> writes: > >> My disk was filling up, so I tried to run "guix gc", but I got an error >> instead: >> >> --8<---------------cut here---------------start------------->8--- >> $ guix gc -C 25GiB >> ... >> deleting `/gnu/store/n0gyzfw77ik35ld9d0d4737w88f11m4b-profile.drv' >> deleting `/gnu/store/fl7w0dlki7c906isiiflf9ka4c49zcmi-ca-certificate-bun= dle.drv' >> deleting `/gnu/store/ipn4xvvb3wrbx4lhzwdyyylvj42vyg6f-xdg-desktop-databa= se.drv' >> guix gc: error: executing SQLite statement: database disk image is malfo= rmed >> --8<---------------cut here---------------end--------------->8--- >> >> What does this mean? > > I think this means that the database has been corrupted. I ran it a second time. It printed more messages, but curiously it errored out after saying that it deleted another xdg-desktop-database.drv: =2D-8<---------------cut here---------------start------------->8--- $ guix gc -C 25GiB ... deleting `/gnu/store/d5z2lazx11qz571mwy59gwlqxidj0h4r-gtk-im-modules.drv' deleting `/gnu/store/gc36aax38fs194ll5s17j8a8l8arm09a-gtk-icon-themes.drv' deleting `/gnu/store/hbxvgm2pc6f6jn2fai30izc7f5kd25qd-gtk-im-modules.drv' deleting `/gnu/store/hrc7yacy4ckmp3zi5pgmzd5ciqzv40ih-xdg-desktop-database.= drv' guix gc: error: executing SQLite statement: database disk image is malformed =2D-8<---------------cut here---------------end--------------->8--- I ran it a third time, and it printed: =2D-8<---------------cut here---------------start------------->8--- $ guix gc -C 25GiB finding garbage collector roots... deleting garbage... deleting `/gnu/store/1dqflkm3029ncacx5vl9r95ldfcfs3m0-pugixml-1.9.drv' guix gc: error: executing SQLite statement: database disk image is malformed =2D-8<---------------cut here---------------end--------------->8--- I ran it a fourth time, and it printed: =2D-8<---------------cut here---------------start------------->8--- $ guix gc -C 25GiB ... deleting `/gnu/store/w0nbsjjb1pj9pi1aim1qcbjq93zss9pn-libwpd-0.10.2.drv' deleting `/gnu/store/ywdgn73h9kdfcvs6cr1nfjqqj245p788-librevenge-0.0.4.drv' deleting `/gnu/store/ryawkapgxirj6yp54zb5vak027xxk2i1-cppunit-1.14.0.drv' deleting `/gnu/store/g2p20iss1r58r4ch2qggzyqn9d5q4kaf-cppunit-1.14.0.tar.gz= .drv' guix gc: error: executing SQLite statement: database disk image is malformed =2D-8<---------------cut here---------------end--------------->8--- I wonder what has brought my installation into this state. I can't think of a way to fix it since I don't even know what caused it, so I will probably re-install Guix to work around the issue, but before I do that, is there anything we can check to understand why the database corruption has occurred? For the record, I do sometimes abruptly power off my machine, and it does rarely abruptly crash (I think I have reported this when it occurs, but I can't be sure). In such cases, when booting, I see messages telling me that the system is recovering the journal from my ext4 file system, and I do not recall ever seeing an error from that process, but who knows what mischief I've been causing to my system over the years. =2D-=20 Chris --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEy/WXVcvn5+/vGD+x3UCaFdgiRp0FAl0xVWMACgkQ3UCaFdgi Rp0MkA//Z97cWkEVwi+5qbpcNNGq886118WNDdIrClciHClxeHRmGE88B3nVaJ68 6nkCk9hdyYj647o3qqz7WVubqQRbMct2G0bz66uKTcebwIaDEW4grWzM85bQgQ8F Bs4PzmobYZ7morhGdgwgA32KhRfuxwkM1the0iasJnAgQ7VNMkCNnsFQkqubOQ41 CmpbZkcJvX1IWYhYjkb2jvExcumV+oZwvEX64oT1EOQYXGj9Qs4whAJkIwY26w8/ wUcYIXxxxQ7q1DDvOgxz0bLA8Hay1vv6WYXZ2gIkgJWGV+md2/CZIuSO1+cpIr4s q67bRd4v/5HtRnsdnynDWYXYFnxj/yBayb/8mzSVXRwWxqQZ5hnL3gagYfl4CvXz HrgiVXyoYkpJjdNjcySw1zQSgHK05dACfPPDDl+mejlbw5QddUmNLHqOiLcF893N VMmwBR1Pt/J7/tV5rNKpYNqa8/5zQ08niB4gAn/70DHfNI7XOshhdGvV41PQwjjw Rwsb31EGddQkDutlBpX+BtnyypC0Yiw4lL3Mse3y8tu9DxDgyXSKlIdzKvcwntKX q3GXJpDLaDcLUKhoaSFePLN0euHoIaQRgpdNjqQ+93Y+rg5JQC59UJcDCAUJ/gxm g3iVvJiS/fLSPKgRhuepWRoCspIkL4J2rk9Er75NGXsFgil6Qig= =evKQ -----END PGP SIGNATURE----- --=-=-=--
bug-guix@HIDDEN
:bug#36687
; Package guix
.
Full text available.Received: (at 36687) by debbugs.gnu.org; 16 Jul 2019 12:44:19 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Tue Jul 16 08:44:18 2019 Received: from localhost ([127.0.0.1]:49681 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1hnMoc-0007cd-KU for submit <at> debbugs.gnu.org; Tue, 16 Jul 2019 08:44:18 -0400 Received: from sender4-of-o53.zoho.com ([136.143.188.53]:21354) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <rekado@HIDDEN>) id 1hnMoa-0007cV-P9 for 36687 <at> debbugs.gnu.org; Tue, 16 Jul 2019 08:44:17 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1563281054; cv=none; d=zoho.com; s=zohoarc; b=fcjXvuOeY1dY2cDy8dGj7Cbb9J4AWJEw2uJzOWoufV5nHf6fMHdT04gM9g9KKIpLtTmSvU4fM6CVC1qeJA9G9+8pOsFO9VeuDF3jGrBt73rst3TnHICiM2+D9xjBPZkf1ATiUsfUJf835bU9dKLvUusO07LGbtaZuxTov7ZtwSM= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zoho.com; s=zohoarc; t=1563281054; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To:ARC-Authentication-Results; bh=QJlc9R6ps0Tk3dBjdVsNovbl6D/zIYmrtX2Xiyhl6p8=; b=Disf2oPNpRkD5fbzJeUwgpvE83FQnML+tAd4PvdkvJDmtYjOUqEXzvWgLlYZUV+1Tpbtgbx4yP/sKKWLbeQP9CTd2iX6I3IFWRm1l6H/aG7dRl/zf0OVamMr1LLuapYvGxlybVBKbSfiT1+yeVM1rtGLhFL41IqPCL9NinSwq6o= ARC-Authentication-Results: i=1; mx.zoho.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@HIDDEN; dmarc=pass header.from=<rekado@HIDDEN> header.from=<rekado@HIDDEN> DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1563281054; s=zoho; d=elephly.net; i=rekado@HIDDEN; h=References:From:To:Cc:Subject:In-reply-to:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding; l=1234; bh=QJlc9R6ps0Tk3dBjdVsNovbl6D/zIYmrtX2Xiyhl6p8=; b=bbR4JphyPT5pdK0VSqzUYAnKXla3aLHf5/tt8TGavYnPR2aHUUuaqXHsBUeMsqEq Q5bOxfd3V9oKipAXxt4leKOSN2rfKJ4p6pzgerUBITij1y7qp6Y4h/776Xp92q5lrI6 oFe0wGLBWIuebSVua/xSwTJUmMI/zSSnIIafSFYQ= Received: from localhost (141.80.247.250 [141.80.247.250]) by mx.zohomail.com with SMTPS id 156328105335313.837258643557561; Tue, 16 Jul 2019 05:44:13 -0700 (PDT) References: <87v9w2ctpm.fsf@HIDDEN> User-agent: mu4e 1.2.0; emacs 26.2 From: Ricardo Wurmus <rekado@HIDDEN> To: cmmarusich@HIDDEN Subject: Re: bug#36687: guix gc: error: executing SQLite statement: database disk image is malformed In-reply-to: <87v9w2ctpm.fsf@HIDDEN> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Tue, 16 Jul 2019 14:44:09 +0200 Message-ID: <87tvbmgndy.fsf@HIDDEN> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 36687 Cc: 36687 <at> debbugs.gnu.org X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) Chris Marusich <cmmarusich@HIDDEN> writes: > My disk was filling up, so I tried to run "guix gc", but I got an error > instead: > > --8<---------------cut here---------------start------------->8--- > $ guix gc -C 25GiB > ... > deleting `/gnu/store/n0gyzfw77ik35ld9d0d4737w88f11m4b-profile.drv' > deleting `/gnu/store/fl7w0dlki7c906isiiflf9ka4c49zcmi-ca-certificate-bund= le.drv' > deleting `/gnu/store/ipn4xvvb3wrbx4lhzwdyyylvj42vyg6f-xdg-desktop-databas= e.drv' > guix gc: error: executing SQLite statement: database disk image is malfor= med > --8<---------------cut here---------------end--------------->8--- > > What does this mean? I think this means that the database has been corrupted. > FYI, I was building one package using my Guix installation via "guix > build --cores=3D1", and another package using a Guix checkout via > "./pre-inst-env guix build --cores", when I decided to run this "guix > gc" command in another shell. I don't know if that matters. I don=E2=80=99t think this is related. > My expectation is that I can run GC even when building software, > thanks to the guix-daemon's safe concurrent garbage collection > algorithm. That=E2=80=99s correct. -- Ricardo
bug-guix@HIDDEN
:bug#36687
; Package guix
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Full text available.Received: (at submit) by debbugs.gnu.org; 16 Jul 2019 07:41:22 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Tue Jul 16 03:41:21 2019 Received: from localhost ([127.0.0.1]:49581 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1hnI5R-0004Vl-Jf for submit <at> debbugs.gnu.org; Tue, 16 Jul 2019 03:41:21 -0400 Received: from lists.gnu.org ([209.51.188.17]:59789) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <cmmarusich@HIDDEN>) id 1hnI5O-0004Va-9D for submit <at> debbugs.gnu.org; Tue, 16 Jul 2019 03:41:18 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:50460) by lists.gnu.org with esmtp (Exim 4.86_2) (envelope-from <cmmarusich@HIDDEN>) id 1hnI5N-0004HN-7E for bug-guix@HIDDEN; Tue, 16 Jul 2019 03:41:18 -0400 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,FREEMAIL_FROM autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from <cmmarusich@HIDDEN>) id 1hnI5M-000569-6V for bug-guix@HIDDEN; Tue, 16 Jul 2019 03:41:17 -0400 Received: from mail-pl1-x629.google.com ([2607:f8b0:4864:20::629]:38117) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from <cmmarusich@HIDDEN>) id 1hnI5L-00054i-Uo for bug-guix@HIDDEN; Tue, 16 Jul 2019 03:41:16 -0400 Received: by mail-pl1-x629.google.com with SMTP id az7so9652366plb.5 for <bug-guix@HIDDEN>; Tue, 16 Jul 2019 00:41:15 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:subject:date:message-id:user-agent:mime-version; bh=/eLetefdfIKgDOgcy6JnIsxFi8S/voZRalapsT4eSMk=; b=UCTyGHWLmJ/EoEc1P1lzqpUFcGWdwJ87IW/4K+WImKwBS3SiBJo/yqyT830Mc8+hlS 0U/a5FvSKpKjmJGA0426t9ZEY3/PC+eZaYFQQmTwg2fpDaq2+1E6ffBSNRJsFMSzB2mJ lZW+UNGf3ACN0Aj+J5dF2Coq4V9L36alOB+bDdSXWp/ahOfwgmoFvEf76WLgJ5Ggy7q3 IjtsSuPPAiW4ZKipyv9JKPB4UDuLcTeV+cfa6xR8puIYlKcnu9vzREdP2wkuNvvWXkCz XQZl71xYBjxr2/KWkIMLyWsY2bBh766MOHXihbxhqns6aQviD10gMQqskJ+atCZPPn1i HBfw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:subject:date:message-id:user-agent :mime-version; bh=/eLetefdfIKgDOgcy6JnIsxFi8S/voZRalapsT4eSMk=; b=mn1XITOdmHU6qK/K/uWdUElK4GPNtVDzdjhWlOOegGkvBvDhBDvpRTSzEZMzaoEurT 7Ub5V7zlmIY9d3Jp/Qgv337LjN24j0niJDXfaWJzfY2VQZDaN6upm2RS68ibMu3EfHUi d/ipq/fIlwbtfsQVkPRFaPqmmEDN4UFKf+OYdLpylPI6oieuf5OtpoCR3u8CjZkdojkp /Qj01JzV82nNzGaPXICpeb+3hJTgE9uFdfmkT/zO8MVWKYdLXEgCmixRXgPmEpf/NACG NEE3nURjhP9mjBBSj6t3A01vQvme4hkTYqfdclVE00jkwZZqtU0/WOpd9jRwU3lpLNbi HcXQ== X-Gm-Message-State: APjAAAWzR6FeM3ie/APAFUDg4iTex9KwxbA1C/rFAkM5fRcY4mihhjoD X8FyJOkaxxm6xCSa61tLBng44nn0 X-Google-Smtp-Source: APXvYqwMzwc/dyr8jx+TBPlQLkmuCOLQlUkYqvJQ7YR1vpKM2CDBsTtSvC46TbSdz1rrpRWkxeziOg== X-Received: by 2002:a17:902:28e9:: with SMTP id f96mr32166656plb.114.1563262872401; Tue, 16 Jul 2019 00:41:12 -0700 (PDT) Received: from garuda.local ([2601:601:9d80:25b2::d12]) by smtp.gmail.com with ESMTPSA id j16sm15488192pjz.31.2019.07.16.00.41.10 for <bug-guix@HIDDEN> (version=TLS1_2 cipher=ECDHE-RSA-CHACHA20-POLY1305 bits=256/256); Tue, 16 Jul 2019 00:41:10 -0700 (PDT) From: Chris Marusich <cmmarusich@HIDDEN> To: bug-guix@HIDDEN Subject: guix gc: error: executing SQLite statement: database disk image is malformed Date: Tue, 16 Jul 2019 00:41:09 -0700 Message-ID: <87v9w2ctpm.fsf@HIDDEN> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.1 (gnu/linux) MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha256; protocol="application/pgp-signature" X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-Received-From: 2607:f8b0:4864:20::629 X-Spam-Score: -1.3 (-) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -2.3 (--) --=-=-= Content-Type: text/plain Content-Transfer-Encoding: quoted-printable Hi, My disk was filling up, so I tried to run "guix gc", but I got an error instead: =2D-8<---------------cut here---------------start------------->8--- $ guix gc -C 25GiB ... deleting `/gnu/store/n0gyzfw77ik35ld9d0d4737w88f11m4b-profile.drv' deleting `/gnu/store/fl7w0dlki7c906isiiflf9ka4c49zcmi-ca-certificate-bundle= .drv' deleting `/gnu/store/ipn4xvvb3wrbx4lhzwdyyylvj42vyg6f-xdg-desktop-database.= drv' guix gc: error: executing SQLite statement: database disk image is malformed =2D-8<---------------cut here---------------end--------------->8--- What does this mean? How concerned should I be? How can I fix it? I looked for existing bug reports, but I didn't find anything. I haven't tried running the command a second time. FYI, I was building one package using my Guix installation via "guix build --cores=3D1", and another package using a Guix checkout via "./pre-inst-env guix build --cores", when I decided to run this "guix gc" command in another shell. I don't know if that matters. My expectation is that I can run GC even when building software, thanks to the guix-daemon's safe concurrent garbage collection algorithm. =2D-=20 Chris --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEy/WXVcvn5+/vGD+x3UCaFdgiRp0FAl0tf5UACgkQ3UCaFdgi Rp21yQ/+Ny2OXro3Hx5LNCQXbHVOZQaOvDBArLnLlBr3i5pGiPmk0HpkdZupSRco Auvp2vsAuAN+i5NefQbky4kczJPo9EfXPskHFv9jMnJeNboMWoLaNBYUVyezeNcr WMbYEnG1sA7VvBl3Tb2oFEUMwCctAEbIbyrqA1K6Pt1MMZxWUjzCM2Wp+jGtsuEd aUzZ9/fWbDiOjiODLBVpQrGGuBp8vNw2eGgbilRIX5cP/s1UGDs9afyuf5gGXVVz aZmeKz4x7aR3pu01qgFqMODzrjnh40Hcem/OJIXiN2vcpOUbXixNdAssSAULR3NY Lh5PzAoiYG3Qg/sjWKRlNLJkM4xDY01vkIczNIq1FasOXiKmyYMszhS9gJBYJz+z OzBrdW9UBrUHNigq3pfARMP3bOddaUUpGag8wjKJAUS8ElWcB1+sNC6anarT0pFr lCtGsoLH1CUaGdZfEoun/a8NDy8bmI+WV4vbk9yrz2p0UWHkzqfqqDDlyndKIspy gEGDHmlh9QxeNgViCA6RNnHUCYUIgg2J7CeJVZTjL3nQQSzUCHMWD6kdVsLf2Kra D75Bw9vMsvol1mz9E6VIbAkQ/zASlLm2p0Pd61RubWPofxale7bj0IsAjse5pyZ9 80jDcmKBDxgenk+IU1wsk8WsVFU2xugzwK80V9axjuILUCwXndk= =amZa -----END PGP SIGNATURE----- --=-=-=--
Chris Marusich <cmmarusich@HIDDEN>
:bug-guix@HIDDEN
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:bug#36687
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