Received: (at 36706) by debbugs.gnu.org; 21 Jul 2019 23:37:14 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Sun Jul 21 19:37:14 2019 Received: from localhost ([127.0.0.1]:59688 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1hpLOE-0000b5-56 for submit <at> debbugs.gnu.org; Sun, 21 Jul 2019 19:37:14 -0400 Received: from mail-pf1-f181.google.com ([209.85.210.181]:33121) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <cmmarusich@HIDDEN>) id 1hpLOD-0000at-4K for 36706 <at> debbugs.gnu.org; Sun, 21 Jul 2019 19:37:13 -0400 Received: by mail-pf1-f181.google.com with SMTP id g2so16466347pfq.0 for <36706 <at> debbugs.gnu.org>; Sun, 21 Jul 2019 16:37:13 -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=RcsbBrMIFNaK0i411i5wBQGPTHQpdS6NtkTsgeYvNWA=; b=qGP1r1QNM5Asn+gR95sGGvde4T0pb4czSxC6fuTNEg3L4BxIGcBiBPq/0B3tpi9qpc CULVfSxA11XjHfDY7Rvb+E4/ncKt87obGPc/blbkaQaU+/XCv+kLHjn9S1VVVi7tMUex scHm8Pt2BPCFe+OSv7CQzW7YSCIhPU9GJsH+afDypJ1qCt/kjesmCU8v9Y7PzfG5LHHl Xss4CDDXl42u02lygOJlQTsP/yy91RhcsQLmS5ccBvHrDVyznk7v253whVQG618j6zvZ LL/+R1+NnwjPomLw6vwH6WRocrFQB3CrFsCuq6f/3CYHiqm/MiNjmB9aZPyaRlr9eikr KBAg== 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=RcsbBrMIFNaK0i411i5wBQGPTHQpdS6NtkTsgeYvNWA=; b=H46o/ybS+0iEKjKjEGMhlGHReP2ExeFw0+raYLad5tWHeG2m0auTzkrAihWy6VLSFW y3HlRjMGk4nF9JNSDXXj3JYR4Ltgu2I/dl9avzRLnT7cMV8NHGbDji60pFNVIBC7gR0g 0IgAyZVz3pjLj/ycG77Vx2YxYS/KGxqodJDfZwQWqb8BYdRgoIdocdqflg+7UY9OxxrF p/6V282YAKTLwOrjJWQ1OvRTE+LG624C3gIpgoB4WOBWvVM35KDoHj6g3wzzfw8/HyOb Y1j1vJ3gTiIOYJa6OYSDLGAn7ghXZgov/72p9eckQhpRFK0mRv9Iy/hBAD5DOZBp8DQS q6CQ== X-Gm-Message-State: APjAAAUjsh05l/sPMkG5B3V18I5VmL+WiHLH29Eng4GK79azCU6lI5aC Gov5NwI0bK6rJDIg60THedKfTEqV X-Google-Smtp-Source: APXvYqwFM8GbCrpj1SYydxoeBiwxXG4y6CjOSDsKsXeFUZ8Sc+FrQYqXzTWWjC7EV/DDmbyTVWg02g== X-Received: by 2002:a65:6552:: with SMTP id a18mr58915486pgw.208.1563752226659; Sun, 21 Jul 2019 16:37:06 -0700 (PDT) Received: from garuda.local ([2601:601:9d80:25b2::d12]) by smtp.gmail.com with ESMTPSA id 65sm37729218pff.148.2019.07.21.16.37.04 (version=TLS1_2 cipher=ECDHE-RSA-CHACHA20-POLY1305 bits=256/256); Sun, 21 Jul 2019 16:37:05 -0700 (PDT) From: Chris Marusich <cmmarusich@HIDDEN> To: Ingo Ruhnke <grumbel@HIDDEN> Subject: Re: bug#36706: "guix gc --verify" fails with "FOREIGN KEY constraint failed" References: <CAHz1FYjJv-dKKZPmjbrcWNgOUOW-pf0iPmWjwLw49crsQw_y-Q@HIDDEN> <874l3kh1kz.fsf@HIDDEN> <CAHz1FYgYYMaq1krLMYtLekU5+0muGi0QER7r3AvzwmHB_xuE3A@HIDDEN> Date: Sun, 21 Jul 2019 16:37:01 -0700 In-Reply-To: <CAHz1FYgYYMaq1krLMYtLekU5+0muGi0QER7r3AvzwmHB_xuE3A@HIDDEN> (Ingo Ruhnke's message of "Wed, 17 Jul 2019 23:26:24 +0200") Message-ID: <87muh7ufhe.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: 36706 Cc: 36706 <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 Ingo Ruhnke <grumbel@HIDDEN> writes: > On Wed, Jul 17, 2019 at 10:02 PM Ricardo Wurmus <rekado@HIDDEN> wrot= e: > >> This is bad and you cannot recover from it. The store should *never* be >> edited manually as it will become inconsistent with the database (which >> I assume you have not edited). >> > > I recovered it just fine with a quick&dirty: > > $ sqlite3 /var/guix/db.sqlite > delete from Refs where reference in (select id from ValidPaths where path > glob "*libreof*"); > delete from Refs where referrer in (select id from ValidPaths where path > glob "*libreof*"); > delete from DerivationOutputs where path glob "*libreof*"; > delete from ValidPaths where path glob "*libreof*"; > > Which I assume is what `guix gc --verify=3Drepair` was trying to do, but = it's > not cleaning up Refs table and thus failing at the FOREIGN KEY constraint. > > $ sqlite3 /var/guix/db/db.sqlite > [...] > sqlite> .schema > [...] > CREATE TABLE Refs ( > referrer integer not null, > reference integer not null, > primary key (referrer, reference), > foreign key (referrer) references ValidPaths(id) on delete cascade, > foreign key (reference) references ValidPaths(id) on delete restrict > <-------- this one here > ); That might work, or it might not. Since manual manipulation of the store and the database is not supported, and your Guix installation might now be in an unknown, invalid state. At the very least, you should probably run "guix gc --verify=3Dcontents,repair". The safest (but admittedly heavy-handed) thing to do is to reinstall Guix completely. The guix-daemon is carefully designed to maintain several critical invariants regarding the state of the store and its database. If by manually modifying the store or the database you have accidentally invalidated one of those invariants (or if you have made a change that is not detected now but which later on might invalidate one of those invariants), there is no guarantee you can easily recover. =2D-=20 Chris --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEy/WXVcvn5+/vGD+x3UCaFdgiRp0FAl009x0ACgkQ3UCaFdgi Rp1FNw//XVzyhnCw8flWgsSgkNRu5tjqPR3sCOdV7oucSpt9pF/lKGGUUEJNOtsr 2bnEBU/tQd+0l1RSSduVH1L9GpyQOAYohwK0zvUo2jlf193XZX3lQ11L41AJm3Wm N5x4kAL8Fp/NaN/iBpWT2YEAEMORMfZmPGfv72V/nEdoVC+E9KtIPahdkczftBFP OC+O6/eVTyc3nzl3aUCIiQTppvHu21ricksnLdN1NdgaSu/kKVIPpaiflmBR3ARN mDmaAo1J0cV81m4M86lfJtrp9saZMaj64/jHPmqBAWf+DORfmYnrUKxcMnF0Quke +hoS7KUmJQKIN7MF07fbFGkRPKa6EFvAjZ1Q1ae4D9Akzfd8HgWxon+IBqlFlK30 NOUOHkA/5fZ0nls6RI83oCjAcssetCrlQU6fX9zKIzZs92MW0UWH84Ftgi5WF21z +GK3jOr/HBnNgWLARW/GXcqgyB9zMKilBfwQST1jRyZve+JV9I5Jj+iMHrEvW5Yg dqm3lb83rDOj0pNFkKvxG7DmqVJb3dyVnNf8aUFPhYjyyxhrQShGI732o5l+po9c ZN49R6cB53o1ph5B1Vbw6ZSCPY0SochUe38Cl2iHiqCjZ1yhzPE2fNfJVA3jjHQg 6eClT6k8d5IJ3ypqZboFBFOwK6cRhq2D1vBsyTJpmB6eMrcLcaw= =GeWq -----END PGP SIGNATURE----- --=-=-=--
bug-guix@HIDDEN:bug#36706; Package guix.
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From: Ingo Ruhnke <grumbel@HIDDEN>
Date: Wed, 17 Jul 2019 23:26:24 +0200
Message-ID: <CAHz1FYgYYMaq1krLMYtLekU5+0muGi0QER7r3AvzwmHB_xuE3A@HIDDEN>
Subject: Re: bug#36706: "guix gc --verify" fails with "FOREIGN KEY constraint
failed"
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On Wed, Jul 17, 2019 at 10:02 PM Ricardo Wurmus <rekado@HIDDEN> wrote:
> This is bad and you cannot recover from it. The store should *never* be
> edited manually as it will become inconsistent with the database (which
> I assume you have not edited).
>
I recovered it just fine with a quick&dirty:
$ sqlite3 /var/guix/db.sqlite
delete from Refs where reference in (select id from ValidPaths where path
glob "*libreof*");
delete from Refs where referrer in (select id from ValidPaths where path
glob "*libreof*");
delete from DerivationOutputs where path glob "*libreof*";
delete from ValidPaths where path glob "*libreof*";
Which I assume is what `guix gc --verify=repair` was trying to do, but it's
not cleaning up Refs table and thus failing at the FOREIGN KEY constraint.
$ sqlite3 /var/guix/db/db.sqlite
[...]
sqlite> .schema
[...]
CREATE TABLE Refs (
referrer integer not null,
reference integer not null,
primary key (referrer, reference),
foreign key (referrer) references ValidPaths(id) on delete cascade,
foreign key (reference) references ValidPaths(id) on delete restrict
<-------- this one here
);
--000000000000dc5b4f058de72556
Content-Type: text/html; charset="UTF-8"
Content-Transfer-Encoding: quoted-printable
<div dir=3D"ltr"><div dir=3D"ltr">On Wed, Jul 17, 2019 at 10:02 PM Ricardo =
Wurmus <<a href=3D"mailto:rekado@HIDDEN">rekado@HIDDEN</a>>=
wrote:<br></div><div class=3D"gmail_quote"><blockquote class=3D"gmail_quot=
e" style=3D"margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204)=
;padding-left:1ex">This is bad and you cannot recover from it.=C2=A0 The st=
ore should *never* be<br>
edited manually as it will become inconsistent with the database (which<br>
I assume you have not edited).<br></blockquote><div><br></div><div>I recove=
red it just fine with a quick&dirty:</div><div><br></div><div>$ sqlite3=
/var/guix/db.sqlite<br></div><div>delete from Refs where reference in (sel=
ect id from ValidPaths where path glob "*libreof*");<br>delete fr=
om Refs where referrer in (select id from ValidPaths where path glob "=
*libreof*");<br>delete from DerivationOutputs where path glob "*l=
ibreof*";<br>delete from ValidPaths where path glob "*libreof*&qu=
ot;;<br></div><div><br></div><div>Which I assume is what `guix gc --verify=
=3Drepair` was trying to do, but it's not cleaning up Refs table and th=
us failing at the FOREIGN KEY constraint.</div><div><br></div><div>$ sqlite=
3 /var/guix/db/db.sqlite<br></div><div>[...]</div><div>sqlite> .schema<b=
r></div><div>[...]</div><div>CREATE TABLE Refs (<br>=C2=A0 =C2=A0 referrer =
=C2=A0integer not null,<br>=C2=A0 =C2=A0 reference integer not null,<br>=C2=
=A0 =C2=A0 primary key (referrer, reference),<br>=C2=A0 =C2=A0 foreign key =
(referrer) references ValidPaths(id) on delete cascade,<br>=C2=A0 =C2=A0 fo=
reign key (reference) references ValidPaths(id) on delete restrict <----=
---- this one here<br>);<br></div><div><br></div></div></div>
--000000000000dc5b4f058de72556--
bug-guix@HIDDEN:bug#36706; Package guix.
Full text available.Received: (at 36706) by debbugs.gnu.org; 17 Jul 2019 20:02:19 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Wed Jul 17 16:02:19 2019 Received: from localhost ([127.0.0.1]:53071 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1hnq83-0006GK-9u for submit <at> debbugs.gnu.org; Wed, 17 Jul 2019 16:02:19 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21294) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <rekado@HIDDEN>) id 1hnq7y-0006G6-6b for 36706 <at> debbugs.gnu.org; Wed, 17 Jul 2019 16:02:17 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1563393730; cv=none; d=zoho.com; s=zohoarc; b=npMfkkcZsZzOVZ5iOSUbXdEJ4JR5GjaFX2Pd/WcbG1flmawro1TqPPiZfszzC4qbhqt3KWx6EN68HBzzVzHU+Qr/L3hHXXSnSNavCNKJWkjzPB3BhDMOj4IO8FOEAU28xX6UzywT/MyMVjx/mFi43YMkp3Byvr5zr90uemD1lrM= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zoho.com; s=zohoarc; t=1563393730; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To:ARC-Authentication-Results; bh=OL7m0IO8ArLl+dsViBg0OFIcNrZHsPvXBdOrq/cjp08=; b=k40yz5DmGtsQUI+uP3vxMpBHgWghsK2DH/JmgSPCxPgolneBTlPOZM0p1zBF2tywJdpGQ5Tw6TUC9AJRCypzu0CWLNI1QwuOS6G9gx9lilZJzqTy6w5fSMwFU2FSZOL2I8pMenpbrXhYfOrlFuNH3HW6Va8g7IMygXdxnwfEdM4= 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=1563393730; 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=495; bh=OL7m0IO8ArLl+dsViBg0OFIcNrZHsPvXBdOrq/cjp08=; b=TOGMt1EUBi+UO3cEB7ro7bOnTBEjei2b2MTO3DSej9aSZ/YpEtqTABb0Ug/4vS9+ H1gCH3zv5WBIUkW57/kfuSGSmW0gMMFM3mpQ/xc93TPXThwRxnhO5qPobIncxUatbgd 2kHE52eqmxw98eFfHcFTUdOCogjkD9I11aPY01U4= Received: from localhost (p54AD4F55.dip0.t-ipconnect.de [84.173.79.85]) by mx.zohomail.com with SMTPS id 1563393728174421.7534142944313; Wed, 17 Jul 2019 13:02:08 -0700 (PDT) References: <CAHz1FYjJv-dKKZPmjbrcWNgOUOW-pf0iPmWjwLw49crsQw_y-Q@HIDDEN> User-agent: mu4e 1.2.0; emacs 26.2 From: Ricardo Wurmus <rekado@HIDDEN> To: grumbel@HIDDEN Subject: Re: bug#36706: "guix gc --verify" fails with "FOREIGN KEY constraint failed" In-reply-to: <CAHz1FYjJv-dKKZPmjbrcWNgOUOW-pf0iPmWjwLw49crsQw_y-Q@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: Wed, 17 Jul 2019 22:02:04 +0200 Message-ID: <874l3kh1kz.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: 36706 Cc: 36706 <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 (-) Ingo Ruhnke <grumbel@HIDDEN> writes: > I am using guix on Ubuntu 19.04, due to some unrelated BTRFS problems I > needed to free some space and did a quick: > > $ rm -rv /gnu/store/*libreoff* This is bad and you cannot recover from it. The store should *never* be edited manually as it will become inconsistent with the database (which I assume you have not edited). You should use =E2=80=9Cguix gc=E2=80=9D instead to remove unused items fro= m the store. --=20 Ricardo
bug-guix@HIDDEN:bug#36706; Package guix.
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From: Ingo Ruhnke <grumbel@HIDDEN>
Date: Wed, 17 Jul 2019 19:12:02 +0200
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Subject: "guix gc --verify" fails with "FOREIGN KEY constraint failed"
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I am using guix on Ubuntu 19.04, due to some unrelated BTRFS problems I
needed to free some space and did a quick:
$ rm -rv /gnu/store/*libreoff*
This expectedly confuses guix a little and leads to error messages such as
this which make it impossible to reinstall any packages:
$ guix install libreoffice
guix install: warning: Consider running 'guix pull' followed by
'guix package -u' to get up-to-date packages and security updates.
guix install: error: opening file
`/gnu/store/kmyp9i01aci0azxwcll41kmn347616q7-libreoffice-orcus.patch.drv':
No such file or directory
However trying to clean up the issue with "guix gc --verify" unexpectedly
fails as well, this time with a failed SQLite constraint, this seems like a
bug:
$ guix gc --verify
reading the store...
checking path existence...
path
`/gnu/store/96ry03xc73c67xs7aj2pnird7icnk578-libreoffice-6.1.5.2.drv'
disappeared, but it still has valid referrers!
path
`/gnu/store/a1hnx6vgwlnqf4fshfln9ljnp9d8y9pl-libreoffice-6.1.5.2.drv'
disappeared, removing from database...
guix gc: error: executing SQLite statement: FOREIGN KEY constraint
failed
$ guix --version
guix (GNU Guix) 84d7784afe00dfc23c7feeb7ede6bce73406760b
--0000000000002451ae058de39851
Content-Type: text/html; charset="UTF-8"
Content-Transfer-Encoding: quoted-printable
<div dir=3D"ltr"><div>I am using guix on Ubuntu 19.04, due to some unrelate=
d BTRFS problems I needed to free some space and did a quick:</div><div><br=
></div><div>=C2=A0 =C2=A0 $ rm -rv /gnu/store/*libreoff*<br></div><div><br>=
</div><div>This expectedly confuses guix a little and leads to error messag=
es such as this which make it impossible to reinstall any packages:</div><d=
iv><br></div><div>=C2=A0 =C2=A0 $ guix install libreoffice<br>=C2=A0 =C2=A0=
=C2=A0guix install: warning: Consider running 'guix pull' followed =
by<br>=C2=A0 =C2=A0=C2=A0'guix package -u' to get up-to-date packag=
es and security updates.<br>=C2=A0 =C2=A0=C2=A0<br>=C2=A0 =C2=A0=C2=A0guix =
install: error: opening file `/gnu/store/kmyp9i01aci0azxwcll41kmn347616q7-l=
ibreoffice-orcus.patch.drv': No such file or directory<br></div><div><b=
r></div><div>However trying to clean up the issue with "guix gc --veri=
fy" unexpectedly fails as well, this time with a failed SQLite constra=
int, this seems like a bug:</div><div><br></div>=C2=A0 =C2=A0=C2=A0$ guix g=
c --verify<br>=C2=A0 =C2=A0=C2=A0reading the store...<br>=C2=A0 =C2=A0=C2=
=A0checking path existence...<br>=C2=A0 =C2=A0=C2=A0path `/gnu/store/96ry03=
xc73c67xs7aj2pnird7icnk578-libreoffice-6.1.5.2.drv' disappeared, but it=
still has valid referrers!<br>=C2=A0 =C2=A0=C2=A0path `/gnu/store/a1hnx6vg=
wlnqf4fshfln9ljnp9d8y9pl-libreoffice-6.1.5.2.drv' disappeared, removing=
from database...<br>=C2=A0 =C2=A0=C2=A0guix gc: error: executing SQLite st=
atement: FOREIGN KEY constraint failed<div><br></div><div>=C2=A0 =C2=A0 $ g=
uix --version<br>=C2=A0 =C2=A0=C2=A0guix (GNU Guix) 84d7784afe00dfc23c7feeb=
7ede6bce73406760b<br></div></div>
--0000000000002451ae058de39851--
Ingo Ruhnke <grumbel@HIDDEN>:bug-guix@HIDDEN.
Full text available.bug-guix@HIDDEN:bug#36706; Package guix.
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