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.
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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")
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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
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bug-guix@HIDDEN:bug#36687; Package guix.
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bug-guix@HIDDEN:bug#36687; Package guix.
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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.
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.
Full text available.bug-guix@HIDDEN:bug#36687; Package guix.
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