From debbugs-submit-bounces@debbugs.gnu.org Fri Jan 14 11:07:02 2022 Received: (at submit) by debbugs.gnu.org; 14 Jan 2022 16:07:03 +0000 Received: from localhost ([127.0.0.1]:37904 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n8P6S-00057J-El for submit@debbugs.gnu.org; Fri, 14 Jan 2022 11:07:02 -0500 Received: from lists.gnu.org ([209.51.188.17]:60654) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n8NYr-0007xP-Ao for submit@debbugs.gnu.org; Fri, 14 Jan 2022 09:28:15 -0500 Received: from eggs.gnu.org ([209.51.188.92]:52900) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1n8NYp-0002jm-Cn for bug-guix@gnu.org; Fri, 14 Jan 2022 09:28:12 -0500 Received: from m1-out-mua-3.websupport.sk ([45.13.137.12]:57778) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1n8NYW-00068b-Vc for bug-guix@gnu.org; Fri, 14 Jan 2022 09:27:55 -0500 Received: from m1-u6-ing.websupport.sk (unknown [10.30.6.2]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) (No client certificate requested) by m1-out-mua-3.websupport.sk (Postfix) with ESMTPS id 4Jb3PF3bStzK3m for ; Fri, 14 Jan 2022 15:20:49 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=felsoci.sk; s=mail; t=1642170049; bh=6JSTRyog3Ai3g06bBjZ6QwNHdFYChWJtU0WlTes5Ih8=; h=To:From:Subject:Date:From; b=l3/eT1MtyarrjO8g1GYPQjmLaud7uKwReuZREEaUyqB9V6LCQ05wDEQ+2nPK0Tvkc kVDyYPlrRuFLjypSSaqEvyGNl8KMUKo+3mhkjMPMUWndQ4XDWFaUt88FZh4mpDxmOL 4ivkiGWUI4v1T5Se6eiEQxuyM07ND3ifecVML198B4IDp3nvjyNMVIVFJP2RV2RYje JvypcrHGMnzKrF/g2vcXl1TUBH7BzTYnOo+kz4IJLJZtMFl3BfE04T/yh1wCuIszOx MofKRhKLta4SUs+LQoC52vWivgs6usNgaDFRPUd7i6MgtDmn169+ZX/YY+oBPl36e4 yTokQZtzRK2tA== Received: from in-2.websupport.sk (pfsense-ha.websupport.sk [37.9.169.236]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) (No client certificate requested) by m1-u6-ing.websupport.sk (Postfix) with ESMTPS id 4Jb3PF2F8HzbCcq for ; Fri, 14 Jan 2022 15:20:49 +0100 (CET) Received: from [10.113.0.135] (unknown [138.199.15.152]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) (No client certificate requested) (Authenticated sender: marek@felsoci.sk) by in-2.websupport.sk (Postfix) with ESMTPSA id 4Jb3PD5MMkz40ZJS for ; Fri, 14 Jan 2022 15:20:48 +0100 (CET) To: bug-guix@gnu.org From: =?UTF-8?B?TWFyZWsgRmVsxaHDtmNp?= Subject: Python unable to find modules within a Singularity container created with guix pack Message-ID: <67e7d225-f824-b691-7125-6b37abef8bb0@felsoci.sk> Date: Fri, 14 Jan 2022 15:20:46 +0100 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0 SeaMonkey/2.53.10.2 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 8bit X-Out-Spamd-Result: default: False [-0.10 / 1000.00]; ARC_NA(0.00)[]; MID_RHS_MATCH_FROM(0.00)[]; FROM_HAS_DN(0.00)[]; TO_MATCH_ENVRCPT_ALL(0.00)[]; MIME_GOOD(-0.10)[text/plain]; FROM_EQ_ENVFROM(0.00)[]; MIME_TRACE(0.00)[0:+]; R_MIXED_CHARSET(0.00)[subject]; ASN(0.00)[asn:60068, ipnet:138.199.14.0/23, country:GB]; RCPT_COUNT_ONE(0.00)[1]; RCVD_COUNT_ZERO(0.00)[0]; TO_DN_NONE(0.00)[] Authentication-Results: in-2.websupport.sk; auth=pass smtp.auth=marek@felsoci.sk smtp.mailfrom=marek@felsoci.sk X-Out-Rspamd-Server: mail-antispam-4 X-Out-Rspamd-Queue-Id: 4Jb3PD5MMkz40ZJS Received-SPF: pass client-ip=45.13.137.12; envelope-from=marek@felsoci.sk; helo=m1-out-mua-3.websupport.sk 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, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.6 (-) X-Debbugs-Envelope-To: submit X-Mailman-Approved-At: Fri, 14 Jan 2022 11:06:59 -0500 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: -2.6 (--) Hello folks, Recently, I have come around this issue. I created a Singularity container using the following `guix pack` command: `guix pack -f squashfs bash coreutils python python-numpy` Then, I run a bash shell within the container: `singularity exec test.gz.squashfs bash` Now, if I want to use numpy, `python3 -m numpy` it gives me the following error and the numpy module IS NOT found: Error in sitecustomize; set PYTHONVERBOSE for traceback: ValueError: '/gnu/store/2dyd6rlcc9m68k3mvkw86k8dygkbg025-profile/bin/../../p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.9/site-packages' is not in list /gnu/store/2dyd6rlcc9m68k3mvkw86k8dygkbg025-profile/bin/python3: No module named numpy However, if I do, `export PYTHONPATH=$GUIX_PYTHONPATH` the numpy module IS found: Error in sitecustomize; set PYTHONVERBOSE for traceback: ValueError: '/gnu/store/2dyd6rlcc9m68k3mvkw86k8dygkbg025-profile/bin/../../p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.9/site-packages' is not in list /gnu/store/2dyd6rlcc9m68k3mvkw86k8dygkbg025-profile/bin/python3: No module named numpy.__main__; 'numpy' is a package and cannot be directly executed Still, the sitecustomize error persists. See the output of `guix describe` below (only the guix channel): Pokolenie 3    14. január 2022 14:33:06    (súčasné)   guix 5c5d9e5     zdroj repozitára: https://git.savannah.gnu.org/git/guix.git     vetva: master     úprava: 5c5d9e5a3208fa51351c6ad8267eba3d96fa2232 Thanks, Marek From debbugs-submit-bounces@debbugs.gnu.org Fri Jan 14 12:45:38 2022 Received: (at 53258) by debbugs.gnu.org; 14 Jan 2022 17:45:38 +0000 Received: from localhost ([127.0.0.1]:38087 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n8Qdt-00085v-Qa for submit@debbugs.gnu.org; Fri, 14 Jan 2022 12:45:38 -0500 Received: from mail2-relais-roc.national.inria.fr ([192.134.164.83]:49480) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n8Qdp-00085a-D2 for 53258@debbugs.gnu.org; Fri, 14 Jan 2022 12:45:37 -0500 X-IronPort-AV: E=Sophos;i="5.88,289,1635199200"; d="scan'208";a="15900436" Received: from 91-160-117-201.subs.proxad.net (HELO ribbon) ([91.160.117.201]) by mail2-relais-roc.national.inria.fr with ESMTP/TLS/ECDHE-RSA-AES256-GCM-SHA384; 14 Jan 2022 18:45:26 +0100 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= To: Marek =?utf-8?B?RmVsxaHDtmNp?= 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> Date: Fri, 14 Jan 2022 18:45:26 +0100 In-Reply-To: <67e7d225-f824-b691-7125-6b37abef8bb0@felsoci.sk> ("Marek =?utf-8?B?RmVsxaHDtmNpIidz?= message of "Fri, 14 Jan 2022 15:20:46 +0100") Message-ID: <87wnj22ouh.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: -2.3 (--) X-Debbugs-Envelope-To: 53258 Cc: 53258@debbugs.gnu.org, 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: -3.3 (---) Hi Marek, Marek Fel=C5=A1=C3=B6ci skribis: > Recently, I have come around this issue. I created a Singularity > container using the following `guix pack` command: > > `guix pack -f squashfs bash coreutils python python-numpy` > > Then, I run a bash shell within the container: > > `singularity exec test.gz.squashfs bash` > > Now, if I want to use numpy, > > `python3 -m numpy` > > it gives me the following error and the numpy module IS NOT found: > > Error in sitecustomize; set PYTHONVERBOSE for traceback: > ValueError: > '/gnu/store/2dyd6rlcc9m68k3mvkw86k8dygkbg025-profile/bin/../../p5fgysbcnn= p8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.9/site-packages'=20 > is not in list > /gnu/store/2dyd6rlcc9m68k3mvkw86k8dygkbg025-profile/bin/python3: No > module named numpy I can kinda reproduce via a relocatable pack (relocatable packs and Singularity packs have in common that they use relative symlinks in their profile, to allow for relocation): guix pack -RR python python-numpy -S /bin=3Dbin -S /etc=3Detc Then I unpack the thing: mkdir /tmp/pack; cd /tmp/pack; tar xf /gnu/store/=E2=80=A6-pack.tar.gz And from there I use the same trick as in =E2=80=98tests/guix-pack-relocatable.sh=E2=80=99 to =E2=80=9Chide=E2=80=9D = /gnu/store: --8<---------------cut here---------------start------------->8--- $ unshare -mrf sh -c 'mount -t tmpfs -o ro none /gnu/store; . /tmp/pack/etc= /profile; echo $GUIX_PYTHONPATH ; /tmp/pack/bin/python3 ' /gnu/store/w5cz9gbqbja99x0636zsg2fzksmfig4n-profile/lib/python3.9/site-pack= ages Python 3.9.6 (default, Jan 1 1970, 00:00:01)=20 [GCC 10.3.0] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import numpy Traceback (most recent call last): File "", line 1, in ModuleNotFoundError: No module named 'numpy' >>> import os >>> os.listdir("/gnu/store/w5cz9gbqbja99x0636zsg2fzksmfig4n-profile/lib/pyt= hon3.9/site-packages") ['setuptools-56.0.0.dist-info', 'distutils-precedence.pth', '_distutils_hac= k', 'setuptools', 'pip-21.1.3.dist-info', 'sitecustomize.py', 'README.txt',= 'pip', 'numpy-1.20.3-py3.9.egg-info', 'numpy', 'pkg_resources', '__pycache= __'] >>> os.listdir("/gnu/store/w5cz9gbqbja99x0636zsg2fzksmfig4n-profile/lib/pyt= hon3.9/site-packages/numpy") ['__init__.pyi', 'doc', 'matlib.py', 'ctypeslib.pyi', 'linalg', 'ctypeslib.= py', 'compat', 'typing', '__init__.pxd', 'lib', 'char.pyi', 'version.py', '= __config__.py', 'core', '_distributor_init.py', 'distutils', 'tests', 'emat= h.pyi', '_pytesttester.py', 'fft', '__init__.cython-30.pxd', 'conftest.py',= '__init__.py', 'py.typed', '_globals.py', 'rec.pyi', 'testing', 'LICENSE.t= xt', 'polynomial', 'f2py', 'matrixlib', 'random', 'ma', 'dual.py', 'setup.p= y', '__pycache__'] --8<---------------cut here---------------end--------------->8--- So in this case =E2=80=98GUIX_PYTHONPATH=E2=80=99 is correctly set, but it = looks as though =E2=80=98sitecustomize.py=E2=80=99 wasn=E2=80=99t loaded. (I don=E2= =80=99t get the =E2=80=9CError in sitecustomize=E2=80=9D message that Marek sees though, weird!) >From Marek=E2=80=99s message, it would seem that somewhere file names are constructed by appending =E2=80=9C..=E2=80=9D. Given Unix=E2=80=99s weird = dot-dot semantics, relative symlinks could be interfering: --8<---------------cut here---------------start------------->8--- $ ls -l /tmp/pack/gnu/store/w5cz9gbqbja99x0636zsg2fzksmfig4n-profile/lib/py= thon3.9/site-packages/ totalo 48 lrwxrwxrwx 1 ludo users 102 Jan 1 1970 _distutils_hack -> ../../../../nid= dlj0qbk5vzk1mdn5im9y4x6l8a2k9-python-3.9.6R/lib/python3.9/site-packages/_di= stutils_hack lrwxrwxrwx 1 ludo users 111 Jan 1 1970 distutils-precedence.pth -> ../../= ../../niddlj0qbk5vzk1mdn5im9y4x6l8a2k9-python-3.9.6R/lib/python3.9/site-pac= kages/distutils-precedence.pth lrwxrwxrwx 1 ludo users 99 Jan 1 1970 numpy -> ../../../../mlccgh05bf8cd= inq0ilpvpdmsspq36pv-python-numpy-1.20.3R/lib/python3.9/site-packages/numpy lrwxrwxrwx 1 ludo users 121 Jan 1 1970 numpy-1.20.3-py3.9.egg-info -> ../= ../../../mlccgh05bf8cdinq0ilpvpdmsspq36pv-python-numpy-1.20.3R/lib/python3.= 9/site-packages/numpy-1.20.3-py3.9.egg-info lrwxrwxrwx 1 ludo users 90 Jan 1 1970 pip -> ../../../../niddlj0qbk5vzk1= mdn5im9y4x6l8a2k9-python-3.9.6R/lib/python3.9/site-packages/pip lrwxrwxrwx 1 ludo users 107 Jan 1 1970 pip-21.1.3.dist-info -> ../../../.= ./niddlj0qbk5vzk1mdn5im9y4x6l8a2k9-python-3.9.6R/lib/python3.9/site-package= s/pip-21.1.3.dist-info lrwxrwxrwx 1 ludo users 100 Jan 1 1970 pkg_resources -> ../../../../niddl= j0qbk5vzk1mdn5im9y4x6l8a2k9-python-3.9.6R/lib/python3.9/site-packages/pkg_r= esources lrwxrwxrwx 1 ludo users 98 Jan 1 1970 __pycache__ -> ../../../../niddlj0= qbk5vzk1mdn5im9y4x6l8a2k9-python-3.9.6R/lib/python3.9/site-packages/__pycac= he__ lrwxrwxrwx 1 ludo users 97 Jan 1 1970 README.txt -> ../../../../niddlj0q= bk5vzk1mdn5im9y4x6l8a2k9-python-3.9.6R/lib/python3.9/site-packages/README.t= xt lrwxrwxrwx 1 ludo users 97 Jan 1 1970 setuptools -> ../../../../niddlj0q= bk5vzk1mdn5im9y4x6l8a2k9-python-3.9.6R/lib/python3.9/site-packages/setuptoo= ls lrwxrwxrwx 1 ludo users 114 Jan 1 1970 setuptools-56.0.0.dist-info -> ../= ../../../niddlj0qbk5vzk1mdn5im9y4x6l8a2k9-python-3.9.6R/lib/python3.9/site-= packages/setuptools-56.0.0.dist-info lrwxrwxrwx 1 ludo users 103 Jan 1 1970 sitecustomize.py -> ../../../../ni= ddlj0qbk5vzk1mdn5im9y4x6l8a2k9-python-3.9.6R/lib/python3.9/site-packages/si= tecustomize.py --8<---------------cut here---------------end--------------->8--- Now look below how dot-dot resolution whereas =E2=80=9Clexical=E2=80=9D dot= -dot resolution dose the right thing: --8<---------------cut here---------------start------------->8--- $ ls -l /tmp/pack/gnu/store/2dyd6rlcc9m68k3mvkw86k8dygkbg025-profile/bin/..= /../p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.9/site-packag= es ls: ne eblas atingi '/tmp/pack/gnu/store/2dyd6rlcc9m68k3mvkw86k8dygkbg025-p= rofile/bin/../../p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/lib/python3.= 9/site-packages': Dosiero a=C5=AD dosierujo ne ekzistas $ ls -l /tmp/pack/gnu/store/p5fgysbcnnp8b1d91mrvjvababmczga0-python-3.9.6/l= ib/python3.9/site-packages totalo 40 dr-xr-xr-x 3 ludo users 4096 Jan 1 1970 _distutils_hack/ -r--r--r-- 1 ludo users 152 Jan 1 1970 distutils-precedence.pth dr-xr-xr-x 5 ludo users 4096 Jan 1 1970 pip/ dr-xr-xr-x 2 ludo users 4096 Jan 1 1970 pip-21.1.3.dist-info/ dr-xr-xr-x 6 ludo users 4096 Jan 1 1970 pkg_resources/ dr-xr-xr-x 2 ludo users 4096 Jan 1 1970 __pycache__/ -r--r--r-- 1 ludo users 119 Jan 1 1970 README.txt dr-xr-xr-x 7 ludo users 4096 Jan 1 1970 setuptools/ dr-xr-xr-x 2 ludo users 4096 Jan 1 1970 setuptools-56.0.0.dist-info/ -r--r--r-- 1 ludo users 2172 Jan 1 1970 sitecustomize.py --8<---------------cut here---------------end--------------->8--- In Python=E2=80=99s =E2=80=98site.py=E2=80=99, the =E2=80=98addsitedir=E2= =80=99 method indirectly calls =E2=80=98os.path.abspath=E2=80=99, not sure if that is at fault. I also see that =E2=80=98sys.path=E2=80=99 is in fact completely bogus, wit= h =E2=80=9Cpack=E2=80=9D missing from every directory name: --8<---------------cut here---------------start------------->8--- $ unshare -mrf sh -c 'mount -t tmpfs -o ro none /gnu/store; . /tmp/pack/et= c/profile; echo $GUIX_PYTHONPATH ; /tmp/pack/bin/python3 ' /gnu/store/w5cz9gbqbja99x0636zsg2fzksmfig4n-profile/lib/python3.9/site-pack= ages Python 3.9.6 (default, Jan 1 1970, 00:00:01)=20 [GCC 10.3.0] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import sys >>> sys.path ['', '/tmp/niddlj0qbk5vzk1mdn5im9y4x6l8a2k9-python-3.9.6R/lib/python39.zip'= , '/tmp/niddlj0qbk5vzk1mdn5im9y4x6l8a2k9-python-3.9.6R/lib/python3.9', '/tm= p/niddlj0qbk5vzk1mdn5im9y4x6l8a2k9-python-3.9.6R/lib/python3.9/lib-dynload'= , '/tmp/niddlj0qbk5vzk1mdn5im9y4x6l8a2k9-python-3.9.6R/lib/python3.9/site-p= ackages'] --8<---------------cut here---------------end--------------->8--- So I think something somewhere is manipulating file names and gets confused. Does that ring a bell, Maxim? Thanks, Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Fri Feb 04 15:51:05 2022 Received: (at 53258) by debbugs.gnu.org; 4 Feb 2022 20:51:05 +0000 Received: from localhost ([127.0.0.1]:32961 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nG5Xs-0002SH-Ou for submit@debbugs.gnu.org; Fri, 04 Feb 2022 15:51:04 -0500 Received: from hera.aquilenet.fr ([185.233.100.1]:42680) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nG5Xq-0002Rm-Mw for 53258@debbugs.gnu.org; Fri, 04 Feb 2022 15:51:03 -0500 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 234E9123; Fri, 4 Feb 2022 21:50:56 +0100 (CET) X-Virus-Scanned: Debian amavisd-new at aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id TLf-0Y_RWRse; Fri, 4 Feb 2022 21:50:55 +0100 (CET) Received: from ribbon (91-160-117-201.subs.proxad.net [91.160.117.201]) by hera.aquilenet.fr (Postfix) with ESMTPSA id B11053D5; Fri, 4 Feb 2022 21:50:54 +0100 (CET) From: =?utf-8?Q?Ludovic_Court=C3=A8s?= To: Marek =?utf-8?B?RmVsxaHDtmNp?= 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> Date: Fri, 04 Feb 2022 21:50:54 +0100 In-Reply-To: <87wnj22ouh.fsf@gnu.org> ("Ludovic =?utf-8?Q?Court=C3=A8s=22'?= =?utf-8?Q?s?= message of "Fri, 14 Jan 2022 18:45:26 +0100") Message-ID: <87v8xumk41.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-Spamd-Bar: + X-Spam-Level: * X-Rspamd-Server: hera Authentication-Results: hera.aquilenet.fr; none X-Rspamd-Queue-Id: 234E9123 X-Spamd-Result: default: False [1.40 / 15.00]; ARC_NA(0.00)[]; RCVD_VIA_SMTP_AUTH(0.00)[]; FREEMAIL_CC(0.00)[debbugs.gnu.org,gmail.com,jpoiret.xyz]; FROM_HAS_DN(0.00)[]; RCPT_COUNT_THREE(0.00)[4]; FREEMAIL_ENVRCPT(0.00)[gmail.com]; TO_MATCH_ENVRCPT_ALL(0.00)[]; TAGGED_RCPT(0.00)[]; MIME_GOOD(-0.10)[text/plain]; TO_DN_SOME(0.00)[]; FROM_EQ_ENVFROM(0.00)[]; MIME_TRACE(0.00)[0:+]; RCVD_COUNT_TWO(0.00)[2]; RCVD_TLS_ALL(0.00)[]; MID_RHS_MATCH_FROM(0.00)[]; SUSPICIOUS_RECIPS(1.50)[] X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 53258 Cc: 53258@debbugs.gnu.org, Josselin Poiret , 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: -0.0 (/) Hello! Ludovic Court=C3=A8s skribis: >>>From Marek=E2=80=99s message, it would seem that somewhere file names are > constructed by appending =E2=80=9C..=E2=80=9D. Given Unix=E2=80=99s weir= d dot-dot semantics, > relative symlinks could be interfering: Some news! Here=E2=80=99s a recap of the IRC discussion earlier today: =E2=80=98sys.prefix=E2=80=99 looks like /tmp/pack2/bin/../../zmv1alp7dzjd6hkc7l6fjz817n2mfzzw-python-3.9.9R. =E2=80=98sys.normpath=E2=80=99 does lexical dot-dot resolution (which is in= correct on POSIX): https://docs.python.org/3.11/library/os.path.html#os.path.normpath Thus, passing the prefix above to =E2=80=98sys.normpath=E2=80=99 leads =E2= =80=9Cpack2=E2=80=9D to be erased. Josselin mentioned =E2=80=9Cpath_hooks=E2=80=9D as a possible solution, tho= ugh I=E2=80=99m not sure what that means; could you explain? :-) Thanks! Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Sat Feb 05 17:28:48 2022 Received: (at 53258) by debbugs.gnu.org; 5 Feb 2022 22:28:48 +0000 Received: from localhost ([127.0.0.1]:35799 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nGTXz-0003Z7-Ov for submit@debbugs.gnu.org; Sat, 05 Feb 2022 17:28:47 -0500 Received: from jpoiret.xyz ([206.189.101.64]:38402) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nGTXu-0003Yv-Gf for 53258@debbugs.gnu.org; Sat, 05 Feb 2022 17:28:46 -0500 Received: from authenticated-user (jpoiret.xyz [206.189.101.64]) by jpoiret.xyz (Postfix) with ESMTPA id 748A8184F6E; Sat, 5 Feb 2022 22:28:40 +0000 (UTC) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=jpoiret.xyz; s=dkim; t=1644100121; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc:mime-version:mime-version:content-type:content-type: in-reply-to:in-reply-to:references:references; bh=QqJDITg38sYKWig2lH6LNzbPeFC6CWtF3JRlkrBqMak=; b=kMWu4iJp2xZkAoIl+f2S0DcK45x8JKiDlwgWRySd7Uwre5xIB17U0SXETsqJqbij22B1u1 wbLYAaitfxoKo2B2CAfEccNiB476FcsxFtgZmdlKBupCbUy7V2ya3zIIp1u26CfjTm1q1O ZMV54VF6S4BV/2LgcwwlfDbulkTh4Gmu80AG8X+L8ytYWlnkqr7z4QYI+XJ5hCI+JbtIda MmNzYiDxRW36N4ojDgXZnHnNWp0ppsEuk8fBnmcwApvwhQt+LGW2F2wJEgN6NlIhv/2OcS 4ZPqs0hzSWGasQMRoSBEEjgcuo7Er0g8d/VreVKjxj0Ydb/JJq0Htxc464OX9g== From: Josselin Poiret To: Ludovic =?utf-8?Q?Court=C3=A8s?= , Marek =?utf-8?B?RmVs?= =?utf-8?B?xaHDtmNp?= Subject: Re: bug#53258: Python unable to find modules within a Singularity container created with guix pack In-Reply-To: <87v8xumk41.fsf@gnu.org> References: <67e7d225-f824-b691-7125-6b37abef8bb0@felsoci.sk> <87wnj22ouh.fsf@gnu.org> <87v8xumk41.fsf@gnu.org> Date: Sat, 05 Feb 2022 23:28:39 +0100 Message-ID: <87v8xt3q3s.fsf@jpoiret.xyz> MIME-Version: 1.0 Content-Type: text/plain Authentication-Results: jpoiret.xyz; auth=pass smtp.auth=jpoiret@jpoiret.xyz smtp.mailfrom=dev@jpoiret.xyz X-Spam-Level: * X-Spamd-Bar: + X-Spam-Score: 2.1 (++) X-Spam-Report: Spam detection software, running on the system "debbugs.gnu.org", has NOT identified this incoming email as spam. The original message has been attached to this so you can view it or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: Hello everyone, 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 - [...] Content analysis details: (2.1 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- -0.0 SPF_HELO_PASS SPF: HELO matches SPF record -0.0 SPF_PASS SPF: sender matches SPF record 1.6 PDS_OTHER_BAD_TLD Untrustworthy TLDs [URI: jpoiret.xyz (xyz)] 0.5 FROM_SUSPICIOUS_NTLD From abused NTLD -0.0 T_SCC_BODY_TEXT_LINE No description available. X-Debbugs-Envelope-To: 53258 Cc: 53258@debbugs.gnu.org, 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: 2.1 (++) X-Spam-Report: Spam detection software, running on the system "debbugs.gnu.org", has NOT identified this incoming email as spam. The original message has been attached to this so you can view it or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: Hello everyone, 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 - [...] Content analysis details: (2.1 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- -0.0 SPF_HELO_PASS SPF: HELO matches SPF record -0.0 SPF_PASS SPF: sender matches SPF record 1.6 PDS_OTHER_BAD_TLD Untrustworthy TLDs [URI: jpoiret.xyz (xyz)] 1.0 BULK_RE_SUSP_NTLD Precedence bulk and RE: from a suspicious TLD 0.5 FROM_SUSPICIOUS_NTLD From abused NTLD -0.0 T_SCC_BODY_TEXT_LINE No description available. -1.0 MAILING_LIST_MULTI Multiple indicators imply a widely-seen list manager Hello everyone, 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=bin -S /etc=etc` 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. Best, -- Josselin Poiret From debbugs-submit-bounces@debbugs.gnu.org Sat Feb 05 17:30:44 2022 Received: (at 53258) by debbugs.gnu.org; 5 Feb 2022 22:30:44 +0000 Received: from localhost ([127.0.0.1]:35812 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nGTZs-0003e1-Ak for submit@debbugs.gnu.org; Sat, 05 Feb 2022 17:30:44 -0500 Received: from jpoiret.xyz ([206.189.101.64]:38802) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nGTZq-0003dt-3j for 53258@debbugs.gnu.org; Sat, 05 Feb 2022 17:30:42 -0500 Received: from authenticated-user (jpoiret.xyz [206.189.101.64]) by jpoiret.xyz (Postfix) with ESMTPA id 473211851F1; Sat, 5 Feb 2022 22:30:40 +0000 (UTC) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=jpoiret.xyz; s=dkim; t=1644100240; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc:mime-version:mime-version:content-type:content-type: in-reply-to:in-reply-to:references:references; bh=MLUZj1Iw5z/m3XqevDFEWa7AF1pdOUHgLagbUNjWF3c=; b=deFI0wVbJDbw2BQoH8UlI7g0yw7M/gyiCtyBwsLZXSCtSBYbDf0JvTAa/ocXsW1G8lASrk IKnXZhVbX7iGRmGDV7Ilae/Napy3gPfjhPrN0Hy74udHRFxDKDrnk25h6CUzNhTodetjga YtFNRsCN5/vM7uhTUtrzADlOmGjQrKz67iFJEv3VHwyJkrikTEo0A8+PkUtTJTca6/sNIK k5X8kGyLfj4dIFNKyDgeheXvAgKeqdwbU2ICYS9u1EdKCafIGL3Ox1+zwzpiN2KW1zbMhd lLXpc93tL00vFWRyjERvZS24etqwjrq1vqfHrCW6tqbK4LBScxu5ZSE9m4dgMA== From: Josselin Poiret To: Ludovic =?utf-8?Q?Court=C3=A8s?= , Marek =?utf-8?B?RmVs?= =?utf-8?B?xaHDtmNp?= Subject: Re: bug#53258: Python unable to find modules within a Singularity container created with guix pack In-Reply-To: <87v8xt3q3s.fsf@jpoiret.xyz> References: <67e7d225-f824-b691-7125-6b37abef8bb0@felsoci.sk> <87wnj22ouh.fsf@gnu.org> <87v8xumk41.fsf@gnu.org> <87v8xt3q3s.fsf@jpoiret.xyz> Date: Sat, 05 Feb 2022 23:30:39 +0100 Message-ID: <87sfsx3q0g.fsf@jpoiret.xyz> MIME-Version: 1.0 Content-Type: text/plain Authentication-Results: jpoiret.xyz; auth=pass smtp.auth=jpoiret@jpoiret.xyz smtp.mailfrom=dev@jpoiret.xyz X-Spam-Level: * X-Spamd-Bar: + X-Spam-Score: 2.1 (++) X-Spam-Report: Spam detection software, running on the system "debbugs.gnu.org", has NOT identified this incoming email as spam. The original message has been attached to this so you can view it or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: Silly me forgetting the link, here it is: [1] https://bugs.python.org/issue46653 Apologies for the noise, -- Josselin Poiret Content analysis details: (2.1 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- -0.0 SPF_HELO_PASS SPF: HELO matches SPF record -0.0 SPF_PASS SPF: sender matches SPF record 1.6 PDS_OTHER_BAD_TLD Untrustworthy TLDs [URI: jpoiret.xyz (xyz)] 0.5 FROM_SUSPICIOUS_NTLD From abused NTLD -0.0 T_SCC_BODY_TEXT_LINE No description available. X-Debbugs-Envelope-To: 53258 Cc: 53258@debbugs.gnu.org, 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: 2.1 (++) X-Spam-Report: Spam detection software, running on the system "debbugs.gnu.org", has NOT identified this incoming email as spam. The original message has been attached to this so you can view it or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: Silly me forgetting the link, here it is: [1] https://bugs.python.org/issue46653 Apologies for the noise, -- Josselin Poiret Content analysis details: (2.1 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- -0.0 SPF_HELO_PASS SPF: HELO matches SPF record -0.0 SPF_PASS SPF: sender matches SPF record 1.6 PDS_OTHER_BAD_TLD Untrustworthy TLDs [URI: jpoiret.xyz (xyz)] 1.0 BULK_RE_SUSP_NTLD Precedence bulk and RE: from a suspicious TLD 0.5 FROM_SUSPICIOUS_NTLD From abused NTLD -0.0 T_SCC_BODY_TEXT_LINE No description available. -1.0 MAILING_LIST_MULTI Multiple indicators imply a widely-seen list manager Silly me forgetting the link, here it is: [1] https://bugs.python.org/issue46653 Apologies for the noise, -- Josselin Poiret 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. From debbugs-submit-bounces@debbugs.gnu.org Thu Feb 02 09:44:42 2023 Received: (at 53258) by debbugs.gnu.org; 2 Feb 2023 14:44:42 +0000 Received: from localhost ([127.0.0.1]:33019 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNapO-0004Ft-H1 for submit@debbugs.gnu.org; Thu, 02 Feb 2023 09:44:42 -0500 Received: from jpoiret.xyz ([206.189.101.64]:38454) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNapN-0004Fm-9q for 53258@debbugs.gnu.org; Thu, 02 Feb 2023 09:44:41 -0500 Received: from authenticated-user (jpoiret.xyz [206.189.101.64]) by jpoiret.xyz (Postfix) with ESMTPA id C043C184F0F; Thu, 2 Feb 2023 14:44:38 +0000 (UTC) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=jpoiret.xyz; s=dkim; t=1675349079; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding: in-reply-to:in-reply-to:references:references; bh=zRmI4SytIA4pIn4ziy8Pc44A99/sZRtK1jvcNrIs254=; b=uHZDVXlptaI4cAAj4XcI+ZHzrSSzhDNyc0c3rq2fwJ1tB1eDLOSTYt/mV23Z5x25U2xmq1 /xHdItrvz9iekYsoGGSm6kXwcA6kzeclH+QG/NQrvEM5xO8cjnmsXrXwtFsO5vLzomA76O 11jyhnwYwInvZ/mqavYHSZFK+HEezICXBC6u2iOmNigDia/RA+rcQAwkE5cj1wIAMMA99/ FFfeMyo1XrN55Oq//rEUeIOXv30X3XOmFnL3eyCk1x1fnCHgXOoq7oS6PGgGWNBEWe3gsy qfARvpL0MBoM24R/T6JbTn8XK6jX+RbbqI2HOHvm5zcBo7o6KUr55sEJNn/E/g== From: Josselin Poiret To: Ludovic =?utf-8?Q?Court=C3=A8s?= Subject: Re: bug#53258: Python unable to find modules within a Singularity container created with guix pack In-Reply-To: <877d9641ab.fsf@gnu.org> References: <67e7d225-f824-b691-7125-6b37abef8bb0@felsoci.sk> <87wnj22ouh.fsf@gnu.org> <87v8xumk41.fsf@gnu.org> <87v8xt3q3s.fsf@jpoiret.xyz> <877d9641ab.fsf@gnu.org> Date: Thu, 02 Feb 2023 15:44:38 +0100 Message-ID: <87v8kkw2i1.fsf@jpoiret.xyz> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Authentication-Results: jpoiret.xyz; auth=pass smtp.auth=jpoiret@jpoiret.xyz smtp.mailfrom=dev@jpoiret.xyz X-Spam-Level: * X-Spamd-Bar: + X-Spam-Score: 0.0 (/) 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: 0.0 (/) Hi Ludo, Ludovic Court=C3=A8s writes: > 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? So, upstream hasn't replied at all to the above proposal. How do we move forward? I have a patch that still applies on Python 3.9.9 that we can put into core-updates. Would that be fine? Best, --=20 Josselin Poiret From debbugs-submit-bounces@debbugs.gnu.org Thu Feb 02 10:40:58 2023 Received: (at 53258) by debbugs.gnu.org; 2 Feb 2023 15:40:58 +0000 Received: from localhost ([127.0.0.1]:35535 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNbhq-0006Ju-0i for submit@debbugs.gnu.org; Thu, 02 Feb 2023 10:40:58 -0500 Received: from mail-yw1-f181.google.com ([209.85.128.181]:37399) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNbho-0006Jh-8A for 53258@debbugs.gnu.org; Thu, 02 Feb 2023 10:40:56 -0500 Received: by mail-yw1-f181.google.com with SMTP id 00721157ae682-523e3a0300eso9213207b3.4 for <53258@debbugs.gnu.org>; Thu, 02 Feb 2023 07:40:56 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=content-transfer-encoding:mime-version:user-agent:message-id :in-reply-to:date:references:subject:cc:to:from:from:to:cc:subject :date:message-id:reply-to; bh=YyYZdqCN2Z6Cx7Pl4+QsrAoLNuG7+iqlKX5I6rZs74U=; b=cgRxowXBQM/5HhJs8CHzmqoncTERfQ76cEBe4fcgPG3CTxGsAmz4Tp5jMQgAoAmo/9 07+D05HlMfrZ+9dZI4reje+TPE/kvOJGnovH9ifA4FF6+9qvLsuW1qib0iQRIBtS7fzy gNzA6ZC3L0UTjOCpnzN3TiLZmotf1zFyNxSy5hxaDeZv0RHYMPzr7Gma0UWCtn0qBzPM P+dlIp8nmAneN+teCUD3YpRHtTlZZ6/Grd8HI+iv6TTypywgyqgYwFExtinQfOqu3f+w zcTrqHeGYNheofY3bgK71A+E6XZU+zciUYqvOR2cN1+q2pPm6NOyPfZrDKzrAgx1CEq2 EKww== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=content-transfer-encoding:mime-version:user-agent:message-id :in-reply-to:date:references:subject:cc:to:from:x-gm-message-state :from:to:cc:subject:date:message-id:reply-to; bh=YyYZdqCN2Z6Cx7Pl4+QsrAoLNuG7+iqlKX5I6rZs74U=; b=KvZ97zpicKSJtcpILREGAhFXCC4SMzbGb1DxIvJyN/QAbtdtne7Bd1Y6fzWBIjHbl3 GltzH5LXVg+Unk0o3XTly+PkUTspg1Xmw86unDHwwx+y/kXfps7XxQ1wUkMFzkhoEMR1 5zv4DIHGkYaNRyxRljI+0Rw0b2Hlr5rB6uTjHX/PaMxe/kMLCEeNK5rsm1/vNQvGhVXS IHkhH6yIANfQx6ClY1N3cpNi7jC3PclPqCAtO2oRIu1H04kBSDxZj826znnQBIFM1OdK /G0rtpHbtFwv8xB4Wb/c6uFxdGZgbkrJ9UgfODjvom+2lh2Zh6VRSnSQoRb6tSQ8tn2W Gb7g== X-Gm-Message-State: AO0yUKU9ntatMV31HorfJiAXVmTGaApHxsgoFNMxaYQLK6l5/r2fsr3d XCXb2uO3S7QTgAI/5DdwvsspbjtozvpMLw== X-Google-Smtp-Source: AK7set8f4V5/Er1/UiYQ010lErSKd2JzD/syXD5jZAjj+khlMlNS1Ak/CeMeheitV/C7z9K1PXFH8Q== X-Received: by 2002:a0d:fb04:0:b0:4fe:eda8:cb25 with SMTP id l4-20020a0dfb04000000b004feeda8cb25mr4151721ywf.6.1675352450518; Thu, 02 Feb 2023 07:40:50 -0800 (PST) Received: from hurd ([2607:fad8:4:3::1000]) by smtp.gmail.com with ESMTPSA id dm35-20020a05620a1d6300b00721299cfffesm7303534qkb.39.2023.02.02.07.40.49 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Thu, 02 Feb 2023 07:40:49 -0800 (PST) From: Maxim Cournoyer 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> <877d9641ab.fsf@gnu.org> <87v8kkw2i1.fsf@jpoiret.xyz> Date: Thu, 02 Feb 2023 10:40:49 -0500 In-Reply-To: <87v8kkw2i1.fsf@jpoiret.xyz> (Josselin Poiret's message of "Thu, 02 Feb 2023 15:44:38 +0100") Message-ID: <87tu04oz26.fsf@gmail.com> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/28.2 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 53258 Cc: 53258@debbugs.gnu.org, Ludovic =?utf-8?Q?Court=C3=A8s?= , Marek =?utf-8?B?RmVs?= =?utf-8?B?xaHDtmNp?= 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: -1.0 (-) Hi Josselin, Josselin Poiret writes: > Hi Ludo, > > Ludovic Court=C3=A8s writes: > >> 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? > > So, upstream hasn't replied at all to the above proposal. How do we move > forward? I have a patch that still applies on Python 3.9.9 that we can > put into core-updates. Would that be fine? I haven't revisited that patch, but if you are confident it wouldn't break anything in the Python world, core-updates would be a fine place, yes. --=20 Thanks, Maxim From debbugs-submit-bounces@debbugs.gnu.org Mon Feb 06 13:20:27 2023 Received: (at 53258) by debbugs.gnu.org; 6 Feb 2023 18:20:28 +0000 Received: from localhost ([127.0.0.1]:49884 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pP66N-00005G-MV for submit@debbugs.gnu.org; Mon, 06 Feb 2023 13:20:27 -0500 Received: from mail-wm1-f43.google.com ([209.85.128.43]:39461) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pP66L-0008W1-LJ for 53258@debbugs.gnu.org; Mon, 06 Feb 2023 13:20:26 -0500 Received: by mail-wm1-f43.google.com with SMTP id hn2-20020a05600ca38200b003dc5cb96d46so11402335wmb.4 for <53258@debbugs.gnu.org>; Mon, 06 Feb 2023 10:20:25 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=content-transfer-encoding:mime-version:message-id:date:references :in-reply-to:subject:cc:to:from:from:to:cc:subject:date:message-id :reply-to; bh=Gi4+LyyUY9ggHil7JioIGSL9XD7xC0+xASNKC8hadMM=; b=jAZ517ibnRwgvmHw4253o9aicVCNjrh0DHYuYeCFkqUbFyb9voP5qCj+6bBnXoRnoZ lUY+NFmnmi2hFlthedjZSCvngRaoa5Ln+Ac++ULCITssfTNh11jnKuKWqclfnDbXdPmf swhqpH3E63sGIkRSI3Xi/eLlWGpqGjOp7bKPcjRheGhS/1/Cc6l/EaphRpRhVrbM8NhU A6fhToWvFnaa5Sn3rHw04JpjG2V9CuxiiERi+wnhXnvwpfTDH/YSjnr2edh73Lr5IlAT hezRVRY88v+nU0440p2dJ+/OAzueWMQjDHPIMzMhltnsg8/923TB8GVZFIoCo1JkaGRy nxTw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=content-transfer-encoding:mime-version:message-id:date:references :in-reply-to:subject:cc:to:from:x-gm-message-state:from:to:cc :subject:date:message-id:reply-to; bh=Gi4+LyyUY9ggHil7JioIGSL9XD7xC0+xASNKC8hadMM=; b=hPgVSyBOIij1CpiLt1VHA1x8oORu5Zuqa7cuuYDEIEPhC3FpQIgcMF4+E5QAYo5E7Z GLMGcDoPQ94iaTS2DIRz7TjD/jKPJu7EVa+8e3ItH8j1YrZI7u3wl0qxIXnlUgSXwqWZ RTPW1zMpUTLpTcmBI99rsKxXpUiFqrvp+VmBWrsVuplKHWFA3HeqTrOkmrXpyWcgQbKO f25aydTUTfdPJuoIZsG6W6GHb8YpjIditTmsL2iaXZc/IZM1gcC0aRmCXXhpmmbKmC2b FvIQTAEE8hdGXLfslEOSogkhnxGFFkWzFDS4jMZbygFVQwdLFJKgrBZabAsiJm1OlyqG lXpg== X-Gm-Message-State: AO0yUKWRVRT6VjexsFWljcVWaDNn5xnRiYzISNtzVLAl6gyYj+GtKTqU 2/78hC3c80Ixn2HlsK9F2ro= X-Google-Smtp-Source: AK7set/DwYqWNavEsrq01hwBDP+mUJ8Z4yzrrUHnRyk3Kv6FKSM3KTQdFemCzrYZEsb1Kgd3Xfbozw== X-Received: by 2002:a05:600c:4f8e:b0:3dc:5032:2895 with SMTP id n14-20020a05600c4f8e00b003dc50322895mr780719wmq.0.1675707620099; Mon, 06 Feb 2023 10:20:20 -0800 (PST) Received: from pfiuh07 ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id o5-20020a5d6845000000b002bdff778d87sm9321173wrw.34.2023.02.06.10.20.19 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 06 Feb 2023 10:20:19 -0800 (PST) From: Simon Tournier To: Maxim Cournoyer , Josselin Poiret Subject: Re: bug#53258: Python unable to find modules within a Singularity container created with guix pack In-Reply-To: <87tu04oz26.fsf@gmail.com> References: <67e7d225-f824-b691-7125-6b37abef8bb0@felsoci.sk> <87wnj22ouh.fsf@gnu.org> <87v8xumk41.fsf@gnu.org> <87v8xt3q3s.fsf@jpoiret.xyz> <877d9641ab.fsf@gnu.org> <87v8kkw2i1.fsf@jpoiret.xyz> <87tu04oz26.fsf@gmail.com> Date: Mon, 06 Feb 2023 18:34:48 +0100 Message-ID: <87sffiiton.fsf@gmail.com> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 53258 Cc: 53258@debbugs.gnu.org, Ludovic =?utf-8?Q?Court=C3=A8s?= , Marek =?utf-8?B?RmVsxaHDtmNp?= 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: -1.0 (-) Hi, On jeu., 02 f=C3=A9vr. 2023 at 10:40, Maxim Cournoyer wrote: >> So, upstream hasn't replied at all to the above proposal. How do we move >> forward? I have a patch that still applies on Python 3.9.9 that we can >> put into core-updates. Would that be fine? > > I haven't revisited that patch, but if you are confident it wouldn't > break anything in the Python world, core-updates would be a fine place, > yes. Maybe for testing this change, you could create one Python interpreter variant containing the patch. Then using =E2=80=99package-with-explicit-py= thon=E2=80=99 package transformation from (guix build-system python) we could build Python packages and check if it correctly fixes and also incrementally check if nothing break. It would avoid a full world rebuild. Cheers, simon From debbugs-submit-bounces@debbugs.gnu.org Thu Jan 04 07:35:45 2024 Received: (at 53258) by debbugs.gnu.org; 4 Jan 2024 12:35:45 +0000 Received: from localhost ([127.0.0.1]:53828 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rLMwr-0004io-5v for submit@debbugs.gnu.org; Thu, 04 Jan 2024 07:35:45 -0500 Received: from out3-smtp.messagingengine.com ([66.111.4.27]:37289) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rLMwo-0004iY-5h for 53258@debbugs.gnu.org; Thu, 04 Jan 2024 07:35:44 -0500 Received: from compute5.internal (compute5.nyi.internal [10.202.2.45]) by mailout.nyi.internal (Postfix) with ESMTP id 34F745C01DD; Thu, 4 Jan 2024 07:35:32 -0500 (EST) Received: from mailfrontend1 ([10.202.2.162]) by compute5.internal (MEProxy); Thu, 04 Jan 2024 07:35:32 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=fastmail.net; h= cc:content-type:content-type:date:date:from:from:in-reply-to :message-id:mime-version:reply-to:subject:subject:to:to; s=fm2; t=1704371732; x=1704458132; bh=PIDcuCQM5Lmp+MWIEUUdnsG5eaRrKy33 WnSyIFUu/MQ=; b=KcMl1l5z8NTJl/NLMu003bp+uMFoiDkdlGqMSmwqqSULys6W mNlxtQh5HhyMYMqgEUKN7qse3pO0iYL2ULlBPz52xgIvvaw3WWCFjSLlIUvIZsCT DZILH4zQ6h5zoSYPZhp4WGRyo+IzoBfQjyXDa98demrHTmYB3/36ZRR6RL1wyspj nHqOr9pBDCsM9f7o3QiEhHtIWzKeM/HDFguIQodVZ/nlbgSmUqbYU/ZwPpaWdWbk vrjy6eWe+zuRlgUfBnQMoP6oe49rpkcUUCqarw7QciJoiPTlE+e7XaMVftXOtjJL leUTLZbILmMP4FotAdvHZdHuVoALv9pPnLvORg== DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d= messagingengine.com; h=cc:content-type:content-type:date:date :feedback-id:feedback-id:from:from:in-reply-to:message-id :mime-version:reply-to:subject:subject:to:to:x-me-proxy :x-me-proxy:x-me-sender:x-me-sender:x-sasl-enc; s=fm2; t= 1704371732; x=1704458132; bh=PIDcuCQM5Lmp+MWIEUUdnsG5eaRrKy33WnS yIFUu/MQ=; b=cThG2cjZ/M6c5n32Gkfxl9DwvpDAA1A9tIC+Y++uOyKu8kOEP6E Eg8HNO8TB1u9QTrNpvKIGMU7RrYEW9vVCB61/A7crNHt6TggKYe6iQqyeS1sCHF7 s0ExKcZ1GW8iQk2DANoXYDxtqYyrzuY8/5p0pSSPosqDHWTF0qvKNVwD+jpr8VrV MTnXiThddEBCRU+rlhJqHUS0OZdEIn1isc2Nfr3XXn1GF6GBA5kztaigfxsfiI2l 9ouU5DtAfAp47VZ0PbMalg9SxscWeOGKQcrZUndLOKajqdeAMwWTfMqLYZkOULqD 1I2sIOUoRpe05aKFrnytIamjE+xc90wWwzg== X-ME-Sender: X-ME-Received: X-ME-Proxy-Cause: gggruggvucftvghtrhhoucdtuddrgedvkedrvdegjedggeduucetufdoteggodetrfdotf fvucfrrhhofhhilhgvmecuhfgrshhtofgrihhlpdfqfgfvpdfurfetoffkrfgpnffqhgen uceurghilhhouhhtmecufedttdenucenucfjughrpefhvffufffkgggtsehttdertddttd dtnecuhfhrohhmpefmohhnrhgrugcujfhinhhsvghnuceokhhonhhrrggurdhhihhnshgv nhesfhgrshhtmhgrihhlrdhnvghtqeenucggtffrrghtthgvrhhnpeevfeevuedtiedtte etgfeghedvudeileekgfehkeehudetveehgeeuteeuveejheenucevlhhushhtvghrufhi iigvpedtnecurfgrrhgrmhepmhgrihhlfhhrohhmpehkohhnrhgrugdrhhhinhhsvghnse hfrghsthhmrghilhdrnhgvth X-ME-Proxy: Feedback-ID: i184641e2:Fastmail Received: by mail.messagingengine.com (Postfix) with ESMTPA; Thu, 4 Jan 2024 07:35:31 -0500 (EST) From: Konrad Hinsen To: 53258@debbugs.gnu.org Subject: Re: Python unable to find modules within a Singularity container created with guix pack Date: Thu, 04 Jan 2024 13:35:28 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 53258 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 everyone, I found this issue while investigating a related one (the error message). It looks like the core problem discussed here has been solved in the meantime: Singularity> python3 -m numpy Error in sitecustomize; set PYTHONVERBOSE for traceback: ValueError: '/gnu/store/kx98dz2vc3gdpjficy4nbd7rscnkvz4s-profile/bin/../../h855kddqbay0pcbwr8a7i8m6ilz67cfn-python-3.10.7/lib/python3.10/site-packages' is not in list /gnu/store/kx98dz2vc3gdpjficy4nbd7rscnkvz4s-profile/bin/python3: No module named numpy.__main__; 'numpy' is a package and cannot be directly executed This error message is to be expected, and NumPy can be imported: Singularity> python3 Error in sitecustomize; set PYTHONVERBOSE for traceback: ValueError: '/gnu/store/kx98dz2vc3gdpjficy4nbd7rscnkvz4s-profile/bin/../../h855kddqbay0pcbwr8a7i8m6ilz67cfn-python-3.10.7/lib/python3.10/site-packages' is not in list Python 3.10.7 (main, Jan 1 1970, 00:00:01) [GCC 11.3.0] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import numpy >>> What remains is the error message, which comes from a bug in Guix' sitecustomize.py. It compares a raw path (sys.prefix) with paths that have been normalized (os.path.normpath). That comparison fails if sys.prefix contains "../", as it does when run from a Singularity container. I will submit a patch for this. Cheers, Konrad From debbugs-submit-bounces@debbugs.gnu.org Thu Jan 04 08:01:23 2024 Received: (at 53258) by debbugs.gnu.org; 4 Jan 2024 13:01:23 +0000 Received: from localhost ([127.0.0.1]:53870 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rLNLe-0001xG-O8 for submit@debbugs.gnu.org; Thu, 04 Jan 2024 08:01:23 -0500 Received: from out3-smtp.messagingengine.com ([66.111.4.27]:43565) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rLNLa-0001pq-Ox for 53258@debbugs.gnu.org; Thu, 04 Jan 2024 08:01:22 -0500 Received: from compute2.internal (compute2.nyi.internal [10.202.2.46]) by mailout.nyi.internal (Postfix) with ESMTP id 3C8985C0120; Thu, 4 Jan 2024 08:01:09 -0500 (EST) Received: from mailfrontend2 ([10.202.2.163]) by compute2.internal (MEProxy); Thu, 04 Jan 2024 08:01:09 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=fastmail.net; h= cc:content-type:content-type:date:date:from:from:in-reply-to :in-reply-to:message-id:mime-version:references:reply-to:subject :subject:to:to; s=fm2; t=1704373269; x=1704459669; bh=QsNa09H8oN aXup2MLnuKgTVpR1w8IVUB9r7/357J3kk=; b=oTdvZ+iZ0MjvbedpyHNC3c+sHo CmOh9lHyHt6Maflz9js76NiCJT4VM+cq0E9DDgxIh5eTEWmBTvp79RPO0ZErYymb pVt4+TK3q7dpGg6TRx8KMzVrPXyiDO2I26xSkVq2rRpIw/7v5GzqRFaTxWqoPqG+ ZabpZl0M0xxemCwhPj34UwCNEoqD9Mg+gfYBEu8ghdlkoXfXZaPHT7GYIpOj9Z/A ZAfYm5T2Pl2dWjuIUhpjhK7Ewx62KhhdyOsKRbNeWFe/wj2EIHRgJs+XpjThkJhO l4MMfCu2RUaM8jXx+8hel4q7LEOkpNl/YN4Nao0jzoY3Vg0aUIrQJrfnnN5g== DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d= messagingengine.com; h=cc:content-type:content-type:date:date :feedback-id:feedback-id:from:from:in-reply-to:in-reply-to :message-id:mime-version:references:reply-to:subject:subject:to :to:x-me-proxy:x-me-proxy:x-me-sender:x-me-sender:x-sasl-enc; s= fm2; t=1704373269; x=1704459669; bh=QsNa09H8oNaXup2MLnuKgTVpR1w8 IVUB9r7/357J3kk=; b=9O82TJY2uxSEfxB1djyg2zPhBw/Tg6XfWNwECsMOdU+N 3tgx5TeSdkjdMJwOgNBbPzfmfZGizb8gEaoqIotaWdPEAA1rwPh6b4JeSqVbq5mO NLa2Rokqcv1Oll0/nYySGBb3sdxcRW9e3byeYZgl/wXfqoz2y7t7GwUfszye8E4u i1zHsiaoHTa8Uxa0qgRcZYb+1OctYDwrTcO9LvhHBKBQ7X4gehFIzBqEtLtPPp+0 uwrxUvO9E+8G7ElU6PWHHU1IaQQUupUaBnsp2jMgZ9vQkCQeWlkX0g6GcGFMV+vf Lc1HSfumT0gByDfUDcD755Iz//dcT3tpKIdodGBD1w== X-ME-Sender: X-ME-Received: X-ME-Proxy-Cause: gggruggvucftvghtrhhoucdtuddrgedvkedrvdegjedggeeiucetufdoteggodetrfdotf fvucfrrhhofhhilhgvmecuhfgrshhtofgrihhlpdfqfgfvpdfurfetoffkrfgpnffqhgen uceurghilhhouhhtmecufedttdenucenucfjughrpefhvffujghffffkgggtsehttdertd dttddtnecuhfhrohhmpefmohhnrhgrugcujfhinhhsvghnuceokhhonhhrrggurdhhihhn shgvnhesfhgrshhtmhgrihhlrdhnvghtqeenucggtffrrghtthgvrhhnpeegleelffduue eigeetudeiffdtleeukeelgeeiieeftddvueegueejvdefjeegheenucffohhmrghinhep ghhnuhdrohhrghenucevlhhushhtvghrufhiiigvpedtnecurfgrrhgrmhepmhgrihhlfh hrohhmpehkohhnrhgrugdrhhhinhhsvghnsehfrghsthhmrghilhdrnhgvth X-ME-Proxy: Feedback-ID: i184641e2:Fastmail Received: by mail.messagingengine.com (Postfix) with ESMTPA; Thu, 4 Jan 2024 08:01:08 -0500 (EST) From: Konrad Hinsen To: 53258@debbugs.gnu.org Subject: Re: Python unable to find modules within a Singularity container created with guix pack In-Reply-To: References: Date: Thu, 04 Jan 2024 14:01:06 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 53258 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 (-) Konrad Hinsen writes: > I will submit a patch for this. Patch at https://issues.guix.gnu.org/68241 Cheers, Konrad From debbugs-submit-bounces@debbugs.gnu.org Fri Jan 05 10:23:51 2024 Received: (at 53258) by debbugs.gnu.org; 5 Jan 2024 15:23:51 +0000 Received: from localhost ([127.0.0.1]:57619 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rLm35-0005fV-Bu for submit@debbugs.gnu.org; Fri, 05 Jan 2024 10:23:51 -0500 Received: from out5-smtp.messagingengine.com ([66.111.4.29]:50083) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rLm32-0005fD-QF for 53258@debbugs.gnu.org; Fri, 05 Jan 2024 10:23:50 -0500 Received: from compute6.internal (compute6.nyi.internal [10.202.2.47]) by mailout.nyi.internal (Postfix) with ESMTP id AA4945C018E; Fri, 5 Jan 2024 10:23:37 -0500 (EST) Received: from mailfrontend2 ([10.202.2.163]) by compute6.internal (MEProxy); Fri, 05 Jan 2024 10:23:37 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=fastmail.net; h= cc:content-type:content-type:date:date:from:from:in-reply-to :in-reply-to:message-id:mime-version:references:reply-to:subject :subject:to:to; 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Fri, 5 Jan 2024 10:23:36 -0500 (EST) From: Konrad Hinsen To: 53258@debbugs.gnu.org Subject: Re: Python unable to find modules within a Singularity container created with guix pack In-Reply-To: References: Date: Fri, 05 Jan 2024 16:23:34 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 53258 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 (-) Konrad Hinsen writes: > Patch at https://issues.guix.gnu.org/68241 If you want to test it without rebuilding tons of packages, here is a version that grafts a patched Python onto the existing ones (as substitutes): https://codeberg.org/khinsen/guix/src/branch/graft-fix-python-sitecustomize Cheers, Konrad From debbugs-submit-bounces@debbugs.gnu.org Sun Jan 21 13:31:34 2024 Received: (at 53258-done) by debbugs.gnu.org; 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[72.10.128.232]) by smtp.gmail.com with ESMTPSA id jr42-20020a05622a802a00b0042545c7beccsm1751187qtb.59.2024.01.21.10.31.19 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sun, 21 Jan 2024 10:31:19 -0800 (PST) From: Maxim Cournoyer To: Konrad Hinsen Subject: Re: bug#53258: Python unable to find modules within a Singularity container created with guix pack In-Reply-To: (Konrad Hinsen's message of "Fri, 05 Jan 2024 16:23:34 +0100") References: Date: Sun, 21 Jan 2024 13:31:18 -0500 Message-ID: <87r0ia8rnt.fsf@gmail.com> User-Agent: Gnus/5.13 (Gnus v5.13) MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 53258-done Cc: 53258-done@debbugs.gnu.org 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: -1.0 (-) Hi Konrad, Konrad Hinsen writes: > Konrad Hinsen writes: > >> Patch at https://issues.guix.gnu.org/68241 > > If you want to test it without rebuilding tons of packages, here is a > version that grafts a patched Python onto the existing ones (as substitutes): > > https://codeberg.org/khinsen/guix/src/branch/graft-fix-python-sitecustomize I've applied your patch to core-updates. I trust that it fixed this issue based on your own testing. Closing; we can always reopen if we find it didn't fix every use cases or create a fresh issue. -- Thanks, Maxim From unknown Sat Jun 14 03:57:51 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Mon, 19 Feb 2024 12:24:17 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator