From debbugs-submit-bounces@debbugs.gnu.org Mon Mar 07 03:25:50 2022 Received: (at 53258) by debbugs.gnu.org; 7 Mar 2022 08:25:50 +0000 Received: from localhost ([127.0.0.1]:52470 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nR8gb-00059M-LW for submit@debbugs.gnu.org; Mon, 07 Mar 2022 03:25:50 -0500 Received: from eggs.gnu.org ([209.51.188.92]:41260) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nR8gZ-000599-Og for 53258@debbugs.gnu.org; Mon, 07 Mar 2022 03:25:44 -0500 Received: from [2001:470:142:3::e] (port=38728 helo=fencepost.gnu.org) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nR8gU-00058Y-0z; Mon, 07 Mar 2022 03:25:38 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=gnu.org; s=fencepost-gnu-org; h=MIME-Version:In-Reply-To:Date:References:Subject:To: From; bh=ytMAkJqp2VwUFG6iL/8WdXFFoX28Kqbz0VcpoPzQOiI=; b=VLvOSuAzQTcSoWSZGXqd 1woHMinZQgVwS4XCT8nUEVeLfVafS7kDICmQDmtmuOqJCNSamQvzGCNu9b8GMZGYwPHcLaZhKfwBT K4Mlx7FMo+/WkY9q4eRm6pPMq4jNn4nWGCoJMAAX96RkZFmmkEYlJhm2fvi0bDa0ItuVvI7SgPHAT k0LF/6aqlWTzYPwn5ZFkD4T/bZhpzNnrUuNPXAAHGiPoVFaBqp07p3+KGVtl19BJTZZTINaAvWNnZ g5zoEFK1TivtxNysxNOiO8kZcnabqH32F7q7O66aIKxddQuviN5oPqr79mWxoybFqzGnjNFePXB2n ++ZM34UNOpz/RQ==; Received: from 91-160-117-201.subs.proxad.net ([91.160.117.201]:55294 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nR8gQ-00022v-RH; Mon, 07 Mar 2022 03:25:37 -0500 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= To: Josselin Poiret Subject: Re: bug#53258: Python unable to find modules within a Singularity container created with guix pack References: <67e7d225-f824-b691-7125-6b37abef8bb0@felsoci.sk> <87wnj22ouh.fsf@gnu.org> <87v8xumk41.fsf@gnu.org> <87v8xt3q3s.fsf@jpoiret.xyz> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 17 =?utf-8?Q?Vent=C3=B4se?= an 230 de la =?utf-8?Q?R?= =?utf-8?Q?=C3=A9volution?= X-PGP-Key-ID: 0x090B11993D9AEBB5 X-PGP-Key: http://www.fdn.fr/~lcourtes/ludovic.asc X-PGP-Fingerprint: 3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5 X-OS: x86_64-pc-linux-gnu Date: Mon, 07 Mar 2022 09:25:32 +0100 In-Reply-To: <87v8xt3q3s.fsf@jpoiret.xyz> (Josselin Poiret's message of "Sat, 05 Feb 2022 23:28:39 +0100") Message-ID: <877d9641ab.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/27.2 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 53258 Cc: 53258@debbugs.gnu.org, Marek =?utf-8?B?RmVsxaHDtmNp?= , Maxim Cournoyer X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.7 (-) Hi Josselin, Josselin Poiret skribis: > After the IRC investigation, it turned out the use of abspath in > Lib/site.py was in fact the culprit. Replacing all its uses with > realpath and doing `./pre-inst-env guix pack -RR python python-numpy -S > /bin=3Dbin -S /etc=3Detc` did in fact resolve the issue! > > I've raised the issue upstream at [1]. The fix itself is pretty simple, > but it's theoretically a breaking change, so we'll see how Python > maintainers want to move forward with it. We could backport this fix > for the next core-updates cycle, whether or not it gets accepted > upstream, and we will also need to modify sitecustomize.py as well to > call os.path.realpath on python_site. > [1] https://bugs.python.org/issue46653 Thanks for the investigation and for reporting it upstream! Is there a workaround we could apply locally, ideally one that does not lead to a world rebuild? Ludo=E2=80=99.