GNU bug report logs - #49439
grafts cause “guix environment” to get killed with OOM

Please note: This is a static page, with minimal formatting, updated once a day.
Click here to see this page with the latest information and nicer formatting.

Package: guix; Severity: important; Reported by: Ricardo Wurmus <rekado@HIDDEN>; dated Tue, 6 Jul 2021 14:39:01 UTC; Maintainer for guix is bug-guix@HIDDEN.
Severity set to 'important' from 'normal' Request was from Ludovic Courtès <ludo@HIDDEN> to control <at> debbugs.gnu.org. Full text available.

Message received at submit <at> debbugs.gnu.org:


Received: (at submit) by debbugs.gnu.org; 6 Jul 2021 14:38:42 +0000
From debbugs-submit-bounces <at> debbugs.gnu.org Tue Jul 06 10:38:42 2021
Received: from localhost ([127.0.0.1]:49619 helo=debbugs.gnu.org)
	by debbugs.gnu.org with esmtp (Exim 4.84_2)
	(envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>)
	id 1m0mDi-0004Gy-Gz
	for submit <at> debbugs.gnu.org; Tue, 06 Jul 2021 10:38:42 -0400
Received: from lists.gnu.org ([209.51.188.17]:44896)
 by debbugs.gnu.org with esmtp (Exim 4.84_2)
 (envelope-from <rekado@HIDDEN>) id 1m0mDg-0004Gr-TT
 for submit <at> debbugs.gnu.org; Tue, 06 Jul 2021 10:38:41 -0400
Received: from eggs.gnu.org ([2001:470:142:3::10]:56622)
 by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256)
 (Exim 4.90_1) (envelope-from <rekado@HIDDEN>)
 id 1m0mDg-0007fq-By
 for bug-guix@HIDDEN; Tue, 06 Jul 2021 10:38:40 -0400
Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21136)
 by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256)
 (Exim 4.90_1) (envelope-from <rekado@HIDDEN>)
 id 1m0mDe-0006LY-3n
 for bug-guix@HIDDEN; Tue, 06 Jul 2021 10:38:40 -0400
ARC-Seal: i=1; a=rsa-sha256; t=1625582312; cv=none; 
 d=zohomail.com; s=zohoarc; 
 b=OeoBW/yCYuTXVauEeK5hmsnFBu/CDhKwTf9BlwTb0AZMDxEcz4z7Vuf9i5dV6IJ4K2bQ0RDkvW5A8pmUi2xfaXdPSkvPPpdnj4o/E0YBScveWxH/FY+BTL2iiuwPB+uN7z9ajjjlENpsc9bLWWov6syXJFDlio1CBNOVeClhC3E=
ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com;
 s=zohoarc; t=1625582312;
 h=Content-Type:Content-Transfer-Encoding:Date:From:MIME-Version:Message-ID:Subject:To;
 bh=RWkcaAO2A/t3ODtW8jyTvEYx+mr7fT6VTDKsiptxKDM=; 
 b=LC6SyQWv7+rCVcJ5A/JMoO3seTT7z5xBsqMe3qS5KxYqWJyr1tbrCZw7xTBQ1YzPN57Er+aXn9MKV8KsJCYwAjmP8UVUmhuQzqq5A7Ko7TVnqJPFk7F45HE6FRRMCnpozTUqlZ3PJhHI4VXjAN74HMvo3gImIAS80OIKPZY+gnQ=
ARC-Authentication-Results: i=1; mx.zohomail.com;
 dkim=pass  header.i=elephly.net;
 spf=pass  smtp.mailfrom=rekado@HIDDEN;
 dmarc=pass header.from=<rekado@HIDDEN>
DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1625582312; 
 s=zoho; d=elephly.net; i=rekado@HIDDEN;
 h=From:To:Subject:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding;
 bh=RWkcaAO2A/t3ODtW8jyTvEYx+mr7fT6VTDKsiptxKDM=;
 b=DNjLXRgRj/puvvIUs2/OpW2CFCuBdQyVEkY1uZmV0qkxqEekuAXpa4dsJ8s9bIMX
 CAaphRzaSbsbWtchKKMBrqxh0CsQopMtkrmYmzNXLc7JOmQ7E8pJWNPiBJ1K2EyyWqO
 h1Pc1kT7FBmlelsMzw+EbeG9emFmC7sdjryXLIs0=
Received: from localhost (p54ad4c3a.dip0.t-ipconnect.de [84.173.76.58]) by
 mx.zohomail.com with SMTPS id 1625582311274952.9963472206382;
 Tue, 6 Jul 2021 07:38:31 -0700 (PDT)
User-agent: mu4e 1.4.15; emacs 27.2
From: Ricardo Wurmus <rekado@HIDDEN>
To: bug-guix@HIDDEN
Subject: grafts cause =?utf-8?Q?=E2=80=9Cguix_environment=E2=80=9D?= to get
 killed with OOM
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, 06 Jul 2021 16:38:28 +0200
Message-ID: <87sg0rse1n.fsf@HIDDEN>
MIME-Version: 1.0
Content-Type: text/plain; charset=utf-8; format=flowed
Content-Transfer-Encoding: quoted-printable
X-ZohoMailClient: External
Received-SPF: pass client-ip=136.143.188.51; envelope-from=rekado@HIDDEN;
 helo=sender4-of-o51.zoho.com
X-Spam_score_int: -20
X-Spam_score: -2.1
X-Spam_bar: --
X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1,
 DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1,
 RCVD_IN_DNSWL_NONE=-0.0001, RCVD_IN_MSPIKE_H4=0.001, RCVD_IN_MSPIKE_WL=0.001,
 SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no
X-Spam_action: no action
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 (--)

With a recent version of Guix, =E2=80=9Cguix environment=E2=80=9D will not=
=20
terminate on its own, keeps the CPU busy, and gets killed when the=20
system eventually runs out of memory.

$ guix describe -f channels

--8<---------------cut here---------------start------------->8---
(list (channel
        (name 'guix)
        (url "/home/rekado/dev/gx/branches/master")
        (commit
          "685cfdec94e5e48c4ad28de53466a28dfc258edb")))
--8<---------------cut here---------------end--------------->8---


$ guix environment pigx-scrnaseq
[wait until it gets killed]

The problem disappears when grafts are disabled:

$ guix environment --no-grafts pigx-scrnaseq
$ [env] yay!

--=20
Ricardo




Acknowledgement sent to Ricardo Wurmus <rekado@HIDDEN>:
New bug report received and forwarded. Copy sent to bug-guix@HIDDEN. Full text available.
Report forwarded to bug-guix@HIDDEN:
bug#49439; Package guix. Full text available.
Please note: This is a static page, with minimal formatting, updated once a day.
Click here to see this page with the latest information and nicer formatting.
Last modified: Fri, 9 Jul 2021 09:45:01 UTC

GNU bug tracking system
Copyright (C) 1999 Darren O. Benham, 1997 nCipher Corporation Ltd, 1994-97 Ian Jackson.