From unknown Fri Jun 20 19:51:43 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#52139 <52139@debbugs.gnu.org> To: bug#52139 <52139@debbugs.gnu.org> Subject: Status: jupyter trying to modify /gnu/store Reply-To: bug#52139 <52139@debbugs.gnu.org> Date: Sat, 21 Jun 2025 02:51:43 +0000 retitle 52139 jupyter trying to modify /gnu/store reassign 52139 guix submitter 52139 Alexander Asteroth severity 52139 normal thanks From debbugs-submit-bounces@debbugs.gnu.org Sat Nov 27 05:20:23 2021 Received: (at submit) by debbugs.gnu.org; 27 Nov 2021 10:20:23 +0000 Received: from localhost ([127.0.0.1]:33012 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mquob-0004wT-Kf for submit@debbugs.gnu.org; Sat, 27 Nov 2021 05:20:23 -0500 Received: from lists.gnu.org ([209.51.188.17]:51992) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mquoZ-0004wK-VF for submit@debbugs.gnu.org; Sat, 27 Nov 2021 05:20:16 -0500 Received: from eggs.gnu.org ([209.51.188.92]:48320) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mquoZ-0007Wy-QG for bug-guix@gnu.org; Sat, 27 Nov 2021 05:20:15 -0500 Received: from sv-2s11.infcs.de ([194.95.66.48]:38512 helo=ux-2s-mailproxy.inf.h-brs.de) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mquoU-00066Q-89 for bug-guix@gnu.org; Sat, 27 Nov 2021 05:20:14 -0500 Received: from condor.h-brs.de (p5797302f.dip0.t-ipconnect.de [87.151.48.47]) (authenticated bits=0) by ux-2s-mailproxy.inf.h-brs.de (8.15.2/8.15.2/Debian-8ska0) with ESMTPSA id 1ARAK3sQ032124 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT) for ; Sat, 27 Nov 2021 11:20:03 +0100 User-agent: mu4e 1.6.10; emacs 27.2 From: Alexander Asteroth To: bug-guix@gnu.org Subject: jupyter trying to modify /gnu/store Date: Sat, 27 Nov 2021 11:14:07 +0100 Message-ID: <87pmqlq4s1.fsf@h-brs.de> MIME-Version: 1.0 Content-Type: text/plain X-Auth: by SMTP AUTH @ ux-2s11 X-MIMEDefang-Info-ge: Gescannt in Inf@FH-BRS, Regeln s. MiniFAQ E-Mail/Mailscanner X-Spam-Status: No, Sender is auth'ed X-Scanned-By: MIMEDefang @ FB02 @ H-BRS Received-SPF: pass client-ip=194.95.66.48; envelope-from=alexander.asteroth@h-brs.de; helo=ux-2s-mailproxy.inf.h-brs.de X-Spam_score_int: -18 X-Spam_score: -1.9 X-Spam_bar: - X-Spam_report: (-1.9 / 5.0 requ) BAYES_00=-1.9, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.4 (-) X-Debbugs-Envelope-To: submit 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: -0.1 (/) Dear all, yesterday I added jupyter to my profile and it worked perfectly fine. Overnight I shut down the computer and rebooted today. Now jupyter refuses to start with the messages below. It seems that jupyter-notebook tries to create directories (or modifiy them) in the location it is installed wich is mounted ro. I have no idea why this didn't happen yesterday but it seems that there is some misconfiguration somewhere... Cheers, Alex PS: same effect with jupyterlab from the guix-science channel. ------------------------------- ~$ jupyter-notebook Traceback (most recent call last): File "/gnu/store/1v8dgchnis87a4p3g9i3j1ayv0dfr4ds-python-notebook-6.3.0/bin/.jupyter-notebook-real", line 11, in load_entry_point('notebook==6.3.0', 'console_scripts', 'jupyter-notebook')() File "/gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/application.py", line 254, in launch_instance return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs) File "/gnu/store/i037rnmqzwcc7nrgcswzb8dcckfrngzp-python-traitlets-4.3.3/lib/python3.8/site-packages/traitlets/config/application.py", line 663, in launch_instance app.initialize(argv) File "/gnu/store/f7y0fd230nc6l2qwq58g7q26rlkwjkf3-python-decorator-5.0.9/lib/python3.8/site-packages/decorator.py", line 232, in fun return caller(func, *(extras + args), **kw) File "/gnu/store/i037rnmqzwcc7nrgcswzb8dcckfrngzp-python-traitlets-4.3.3/lib/python3.8/site-packages/traitlets/config/application.py", line 87, in catch_config_error return method(app, *args, **kwargs) File "/gnu/store/1v8dgchnis87a4p3g9i3j1ayv0dfr4ds-python-notebook-6.3.0/lib/python3.8/site-packages/notebook/notebookapp.py", line 2122, in initialize super().initialize(argv) File "/gnu/store/f7y0fd230nc6l2qwq58g7q26rlkwjkf3-python-decorator-5.0.9/lib/python3.8/site-packages/decorator.py", line 232, in fun return caller(func, *(extras + args), **kw) File "/gnu/store/i037rnmqzwcc7nrgcswzb8dcckfrngzp-python-traitlets-4.3.3/lib/python3.8/site-packages/traitlets/config/application.py", line 87, in catch_config_error return method(app, *args, **kwargs) File "/gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/application.py", line 229, in initialize self.migrate_config() File "/gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/application.py", line 155, in migrate_config migrate() File "/gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/migrate.py", line 244, in migrate ensure_dir_exists(env['jupyter_config']) File "/gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/utils/__init__.py", line 11, in ensure_dir_exists os.makedirs(path, mode=mode) File "/gnu/store/sd2ic7bpv8fx3imy1j8xcjclx71sv6q0-python-3.8.2/lib/python3.8/os.py", line 213, in makedirs makedirs(head, exist_ok=exist_ok) File "/gnu/store/sd2ic7bpv8fx3imy1j8xcjclx71sv6q0-python-3.8.2/lib/python3.8/os.py", line 213, in makedirs makedirs(head, exist_ok=exist_ok) File "/gnu/store/sd2ic7bpv8fx3imy1j8xcjclx71sv6q0-python-3.8.2/lib/python3.8/os.py", line 213, in makedirs makedirs(head, exist_ok=exist_ok) [Previous line repeated 7 more times] File "/gnu/store/sd2ic7bpv8fx3imy1j8xcjclx71sv6q0-python-3.8.2/lib/python3.8/os.py", line 223, in makedirs mkdir(name, mode) OSError: [Errno 30] Read-only file system: '/home/[user]/.guix-profile/etc/jupyter:' From debbugs-submit-bounces@debbugs.gnu.org Sat Nov 27 11:33:12 2021 Received: (at submit) by debbugs.gnu.org; 27 Nov 2021 16:33:12 +0000 Received: from localhost ([127.0.0.1]:34469 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mr0dO-0000fo-Rf for submit@debbugs.gnu.org; Sat, 27 Nov 2021 11:33:12 -0500 Received: from lists.gnu.org ([209.51.188.17]:55718) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mr0dK-0000fe-W4 for submit@debbugs.gnu.org; Sat, 27 Nov 2021 11:33:03 -0500 Received: from eggs.gnu.org ([209.51.188.92]:50816) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mr0dK-0006sG-RI for bug-guix@gnu.org; Sat, 27 Nov 2021 11:33:02 -0500 Received: from sv-2s11.infcs.de ([194.95.66.48]:43026 helo=ux-2s-mailproxy.inf.h-brs.de) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mr0dJ-00051o-46 for bug-guix@gnu.org; Sat, 27 Nov 2021 11:33:02 -0500 Received: from gyps.h-brs.de (p5797302f.dip0.t-ipconnect.de [87.151.48.47]) (authenticated bits=0) by ux-2s-mailproxy.inf.h-brs.de (8.15.2/8.15.2/Debian-8ska0) with ESMTPSA id 1ARGWbrW006709 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT); Sat, 27 Nov 2021 17:32:52 +0100 References: <87pmqlq4s1.fsf@h-brs.de> User-agent: mu4e 1.7.4; emacs 27.2 From: Alexander Asteroth Subject: Re: bug#52139: jupyter trying to modify /gnu/store Date: Sat, 27 Nov 2021 17:31:59 +0100 In-reply-to: <87pmqlq4s1.fsf@h-brs.de> Message-ID: <871r318spu.fsf@h-brs.de> MIME-Version: 1.0 Content-Type: text/plain X-Auth: by SMTP AUTH @ ux-2s11 X-MIMEDefang-Info-ge: Gescannt in Inf@FH-BRS, Regeln s. MiniFAQ E-Mail/Mailscanner X-Spam-Status: No, Sender is auth'ed X-Scanned-By: MIMEDefang @ FB02 @ H-BRS Received-SPF: pass client-ip=194.95.66.48; envelope-from=alexander.asteroth@h-brs.de; helo=ux-2s-mailproxy.inf.h-brs.de X-Spam_score_int: -8 X-Spam_score: -0.9 X-Spam_bar: / X-Spam_report: (-0.9 / 5.0 requ) BAYES_00=-1.9, MISSING_HEADERS=1.021, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=no autolearn_force=no X-Spam_action: no action X-Spam-Score: -0.2 (/) X-Debbugs-Envelope-To: submit Cc: bug-guix@gnu.org, 52139@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: 1.1 (+) 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: I found the cause: in ~/.guix-profile/etc/profile environment variables are set for jupyter: > export JUPYTER_PATH="${GUIX_PROFILE:-/gnu/store/ichrcarq2k4lhdmm2izc3f1xjbziz49v-profile}/share/jupyter${JUPYTER_PATH:+:}$JUPYTER_PATH" > export JUPYTER_CONFIG_DIR="${GUIX_PROFILE:-/gnu/store/ichrca [...] Content analysis details: (1.1 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- -0.0 RCVD_IN_MSPIKE_H2 RBL: Average reputation (+2) [209.51.188.17 listed in wl.mailspike.net] 0.9 SPF_FAIL SPF: sender does not match SPF record (fail) [SPF failed: Please see http://www.openspf.org/Why?s=mfrom;id=alexander.asteroth%40h-brs.de;ip=209.51.188.17;r=debbugs.gnu.org] 1.2 MISSING_HEADERS Missing To: header -0.0 SPF_HELO_PASS SPF: HELO matches SPF record -1.0 MAILING_LIST_MULTI Multiple indicators imply a widely-seen list manager I found the cause: in ~/.guix-profile/etc/profile environment variables are set for jupyter: > export JUPYTER_PATH="${GUIX_PROFILE:-/gnu/store/ichrcarq2k4lhdmm2izc3f1xjbziz49v-profile}/share/jupyter${JUPYTER_PATH:+:}$JUPYTER_PATH" > export JUPYTER_CONFIG_DIR="${GUIX_PROFILE:-/gnu/store/ichrcarq2k4lhdmm2izc3f1xjbziz49v-profile}/etc/jupyter${JUPYTER_CONFIG_DIR:+:}$JUPYTER_CONFIG_DIR" The jupyter config path causes the problem, since jupyter tries to write into it (and it is located in a read only filesystem). Unsetting the environment variable solves the issue. Cheers, Alex On Sat, Nov 27 2021, 11:14:07, Alexander Asteroth wrote: > Dear all, > > yesterday I added jupyter to my profile and it worked perfectly > fine. Overnight I shut down the computer and rebooted today. > Now jupyter refuses to start with the messages below. It seems that > jupyter-notebook tries to create directories (or modifiy them) in the location it > is installed wich is mounted ro. I have no idea why this didn't happen > yesterday but it seems that there is some misconfiguration somewhere... > > Cheers, > Alex > > PS: same effect with jupyterlab from the guix-science channel. > > ------------------------------- > ~$ jupyter-notebook > Traceback (most recent call last): > File "/gnu/store/1v8dgchnis87a4p3g9i3j1ayv0dfr4ds-python-notebook-6.3.0/bin/.jupyter-notebook-real", line 11, in > load_entry_point('notebook==6.3.0', 'console_scripts', 'jupyter-notebook')() > File "/gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/application.py", line 254, in launch_instance > return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs) > File "/gnu/store/i037rnmqzwcc7nrgcswzb8dcckfrngzp-python-traitlets-4.3.3/lib/python3.8/site-packages/traitlets/config/application.py", line 663, in launch_instance > app.initialize(argv) > File "/gnu/store/f7y0fd230nc6l2qwq58g7q26rlkwjkf3-python-decorator-5.0.9/lib/python3.8/site-packages/decorator.py", line 232, in fun > return caller(func, *(extras + args), **kw) > File "/gnu/store/i037rnmqzwcc7nrgcswzb8dcckfrngzp-python-traitlets-4.3.3/lib/python3.8/site-packages/traitlets/config/application.py", line 87, in catch_config_error > return method(app, *args, **kwargs) > File "/gnu/store/1v8dgchnis87a4p3g9i3j1ayv0dfr4ds-python-notebook-6.3.0/lib/python3.8/site-packages/notebook/notebookapp.py", line 2122, in initialize > super().initialize(argv) > File "/gnu/store/f7y0fd230nc6l2qwq58g7q26rlkwjkf3-python-decorator-5.0.9/lib/python3.8/site-packages/decorator.py", line 232, in fun > return caller(func, *(extras + args), **kw) > File "/gnu/store/i037rnmqzwcc7nrgcswzb8dcckfrngzp-python-traitlets-4.3.3/lib/python3.8/site-packages/traitlets/config/application.py", line 87, in catch_config_error > return method(app, *args, **kwargs) > File "/gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/application.py", line 229, in initialize > self.migrate_config() > File "/gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/application.py", line 155, in migrate_config > migrate() > File "/gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/migrate.py", line 244, in migrate > ensure_dir_exists(env['jupyter_config']) > File "/gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/utils/__init__.py", line 11, in ensure_dir_exists > os.makedirs(path, mode=mode) > File "/gnu/store/sd2ic7bpv8fx3imy1j8xcjclx71sv6q0-python-3.8.2/lib/python3.8/os.py", line 213, in makedirs > makedirs(head, exist_ok=exist_ok) > File "/gnu/store/sd2ic7bpv8fx3imy1j8xcjclx71sv6q0-python-3.8.2/lib/python3.8/os.py", line 213, in makedirs > makedirs(head, exist_ok=exist_ok) > File "/gnu/store/sd2ic7bpv8fx3imy1j8xcjclx71sv6q0-python-3.8.2/lib/python3.8/os.py", line 213, in makedirs > makedirs(head, exist_ok=exist_ok) > [Previous line repeated 7 more times] > File "/gnu/store/sd2ic7bpv8fx3imy1j8xcjclx71sv6q0-python-3.8.2/lib/python3.8/os.py", line 223, in makedirs > mkdir(name, mode) > OSError: [Errno 30] Read-only file system: '/home/[user]/.guix-profile/etc/jupyter:' From debbugs-submit-bounces@debbugs.gnu.org Sat Nov 27 20:08:45 2021 Received: (at 52139) by debbugs.gnu.org; 28 Nov 2021 01:08:45 +0000 Received: from localhost ([127.0.0.1]:34748 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mr8gP-0006Wa-ET for submit@debbugs.gnu.org; Sat, 27 Nov 2021 20:08:45 -0500 Received: from mx1.dismail.de ([78.46.223.134]:46188) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mr8gO-0006WO-4p for 52139@debbugs.gnu.org; Sat, 27 Nov 2021 20:08:44 -0500 Received: from mx1.dismail.de (localhost [127.0.0.1]) by mx1.dismail.de (OpenSMTPD) with ESMTP id 3b6d8789 for <52139@debbugs.gnu.org>; Sun, 28 Nov 2021 02:08:37 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed; d=dismail.de; h=date :message-id:from:to:references:mime-version:content-type :content-transfer-encoding; s=20190914; bh=zpsJkYk9Md+8MG4mT/5ov Z0FUOXc9l93sY/kSmYUb8s=; b=jLAh/+fKQpx2kYa0bAJC+Z/PAHtwcmoXGEVBU kaJx+X72IL6F3JbOwaed9K0hgDWW8eajM6kLqQhYp9C6kUt9CogFR/UzJnlt0aYK P90BBXsMTTZNE3X+m6f6ZYo7uDx+W0JcPPQdHcCQuFom3qkd/AWcQEptGDyBbXsL QD9J6JNXQLUhQykxembzPO4AEohQQEtxRZJvyjfJEYY8u1CSJVKGuFDRvi5X3QEe 2758Aw1JHjjKKzm5MV60OyHNKi7Mjyw4JojiqRhG2FMkOvI5qAYS2NV3Zv51qm8k 3KEIYKtq94CM6sUasoGnPPEmIgUMiyM//Wg7sHnGeejzV4hpg== Received: from smtp2.dismail.de ( [10.240.26.12]) by mx1.dismail.de (OpenSMTPD) with ESMTP id 4fff4f9b for <52139@debbugs.gnu.org>; Sun, 28 Nov 2021 02:08:37 +0100 (CET) Received: from smtp2.dismail.de (localhost [127.0.0.1]) by smtp2.dismail.de (OpenSMTPD) with ESMTP id 8c31c519 for <52139@debbugs.gnu.org>; Sun, 28 Nov 2021 02:08:37 +0100 (CET) Received: by dismail.de (OpenSMTPD) with ESMTPSA id 4d4ce19e (TLSv1.3:AEAD-AES256-GCM-SHA384:256:NO) for <52139@debbugs.gnu.org>; Sun, 28 Nov 2021 02:08:36 +0100 (CET) Date: Sat, 27 Nov 2021 20:08:35 -0500 Message-ID: <20211127200835.GB7916@gac.attlocal.net> From: jgart To: 52139@debbugs.gnu.org References: MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-Spam-Score: 1.3 (+) 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: Hi Alex, Would you like to submit a patch to remove those environment variables from being set in the jupyter package? Content analysis details: (1.3 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- -0.7 RCVD_IN_DNSWL_LOW RBL: Sender listed at https://www.dnswl.org/, low trust [78.46.223.134 listed in list.dnswl.org] -0.0 SPF_PASS SPF: sender matches SPF record 0.0 SPF_HELO_NONE SPF: HELO does not publish an SPF Record 1.8 MISSING_SUBJECT Missing Subject: header 0.2 NO_SUBJECT Extra score for no subject X-Debbugs-Envelope-To: 52139 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: 0.3 (/) Hi Alex, Would you like to submit a patch to remove those environment variables from being set in the jupyter package? From debbugs-submit-bounces@debbugs.gnu.org Sun Nov 28 04:55:53 2021 Received: (at 52139) by debbugs.gnu.org; 28 Nov 2021 09:55:53 +0000 Received: from localhost ([127.0.0.1]:34974 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mrGuV-0003CW-9G for submit@debbugs.gnu.org; Sun, 28 Nov 2021 04:55:53 -0500 Received: from sv-2s11.infcs.de ([194.95.66.48]:39342 helo=ux-2s-mailproxy.inf.h-brs.de) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mrGuJ-0003C2-D9 for 52139@debbugs.gnu.org; Sun, 28 Nov 2021 04:55:50 -0500 Received: from gyps.h-brs.de (p5797302f.dip0.t-ipconnect.de [87.151.48.47]) (authenticated bits=0) by ux-2s-mailproxy.inf.h-brs.de (8.15.2/8.15.2/Debian-8ska0) with ESMTPSA id 1AS9tVbG023848 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT); Sun, 28 Nov 2021 10:55:31 +0100 References: User-agent: mu4e 1.7.4; emacs 27.2 From: Alexander Asteroth To: 52139@debbugs.gnu.org Subject: Re: bug-Guix Digest, Vol 109, Issue 119 Date: Sun, 28 Nov 2021 10:51:53 +0100 In-reply-to: Message-ID: <87sfvg7gfr.fsf@h-brs.de> MIME-Version: 1.0 Content-Type: text/plain X-Auth: by SMTP AUTH @ ux-2s11 X-MIMEDefang-Info-ge: Gescannt in Inf@FH-BRS, Regeln s. MiniFAQ E-Mail/Mailscanner X-Spam-Status: No, Sender is auth'ed X-Scanned-By: MIMEDefang @ FB02 @ H-BRS X-Spam-Score: 0.4 (/) X-Debbugs-Envelope-To: 52139 Cc: bug-guix@gnu.org, jgart@dismail.de 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 (-) I'd like to but feel still too much of a newbie currently. If someone would point me to the right steps to take, I'd do so - and in future I will be able to help and contribute (and not just report errors). Cheers, Alex PS: BTW I didn't receive this message directly only found it in the bug-guix digest. Shouldn't I receive replies to the bug i filed? On Sun, Nov 28 2021, 02:41:05, bug-guix-request@gnu.org wrote: > ------------------------------ > > Message: 2 > Date: Sat, 27 Nov 2021 20:08:35 -0500 > From: jgart > To: 52139@debbugs.gnu.org > Subject: bug#52139: (no subject) > Message-ID: <20211127200835.GB7916@gac.attlocal.net> > Content-Type: text/plain; charset=utf-8 > > > Hi Alex, > > Would you like to submit a patch to remove those environment variables from being set in the jupyter package? > > From debbugs-submit-bounces@debbugs.gnu.org Wed Dec 08 12:23:13 2021 Received: (at control) by debbugs.gnu.org; 8 Dec 2021 17:23:13 +0000 Received: from localhost ([127.0.0.1]:41273 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mv0ev-0005I0-KN for submit@debbugs.gnu.org; Wed, 08 Dec 2021 12:23:13 -0500 Received: from hera.aquilenet.fr ([185.233.100.1]:33698) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mv0et-0005Hk-VH for control@debbugs.gnu.org; Wed, 08 Dec 2021 12:23:12 -0500 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 8DE46331 for ; Wed, 8 Dec 2021 18:23:04 +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 IwGG6-790kmA for ; Wed, 8 Dec 2021 18:23:04 +0100 (CET) Received: from ribbon (91-160-117-201.subs.proxad.net [91.160.117.201]) by hera.aquilenet.fr (Postfix) with ESMTPSA id F1304239 for ; Wed, 8 Dec 2021 18:23:03 +0100 (CET) Date: Wed, 08 Dec 2021 18:23:03 +0100 Message-Id: <87o85rggeg.fsf@gnu.org> To: control@debbugs.gnu.org From: =?utf-8?Q?Ludovic_Court=C3=A8s?= Subject: control message for bug #52139 MIME-version: 1.0 Content-type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Spamd-Bar: / Authentication-Results: hera.aquilenet.fr; none X-Rspamd-Server: hera X-Rspamd-Queue-Id: 8DE46331 X-Spamd-Result: default: False [0.61 / 15.00]; ARC_NA(0.00)[]; RCVD_VIA_SMTP_AUTH(0.00)[]; FROM_HAS_DN(0.00)[]; TO_MATCH_ENVRCPT_ALL(0.00)[]; MIME_GOOD(-0.10)[text/plain]; TO_DN_NONE(0.00)[]; PREVIOUSLY_DELIVERED(0.00)[control@debbugs.gnu.org]; RCPT_COUNT_ONE(0.00)[1]; FROM_EQ_ENVFROM(0.00)[]; MIME_TRACE(0.00)[0:+]; R_MIXED_CHARSET(0.71)[subject]; RCVD_COUNT_TWO(0.00)[2]; RCVD_TLS_ALL(0.00)[]; MID_RHS_MATCH_FROM(0.00)[] X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: control 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 (/) merge 52139 52159 quit From debbugs-submit-bounces@debbugs.gnu.org Fri Dec 10 08:28:12 2021 Received: (at 52139) by debbugs.gnu.org; 10 Dec 2021 13:28:12 +0000 Received: from localhost ([127.0.0.1]:45894 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mvfwX-0005Vg-B0 for submit@debbugs.gnu.org; Fri, 10 Dec 2021 08:28:12 -0500 Received: from eggs.gnu.org ([209.51.188.92]:58662) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mvfwN-0005V2-Qh for 52139@debbugs.gnu.org; Fri, 10 Dec 2021 08:28:07 -0500 Received: from [2001:470:142:3::e] (port=47126 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 1mvfwG-0003uC-VF; Fri, 10 Dec 2021 08:27:52 -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=x5wTGW2Qz0B5+HIadfRCkJdTvVSNnQLBEi7Zs4T6rgs=; b=qOcm90v/fm2IVwAQmh9B aIwmLXrl0wijMPVRbu2oJB+nT7tdgS37EsKfk3IlBo5LSPTvEXHDZNlkZDkVlH65JldyNQ1rrCLxd MzV7RJ4qnZ18GUiELkp+ME9sMas88BH1sNMm/XAQohRoXSe/5NQHK7zvbEbStQWrYMZO8aUT258FN zsWsuZBdEdhQ06U93iyJC4ryvkseKd9qsOJDjViD7wVAL0K3Zjt/Zly5EgxB679Bx0bkv2J0DDPYR pPzDGh30az3Pb53SfqGLJ4UDxFNm1eOv2Jca1qJ05q9hkUol9Bu+/P8CiFqt8IKM6+gYQbbmRGCaH PFbmX9udTI+eKA==; Received: from 91-160-117-201.subs.proxad.net ([91.160.117.201]:59479 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mvfwG-0000nZ-Ah; Fri, 10 Dec 2021 08:27:52 -0500 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= To: Alexander Asteroth Subject: Re: bug#52139: jupyter trying to modify /gnu/store References: <87pmqlq4s1.fsf@h-brs.de> <871r318spu.fsf@h-brs.de> Date: Fri, 10 Dec 2021 14:27:49 +0100 In-Reply-To: <871r318spu.fsf@h-brs.de> (Alexander Asteroth's message of "Sat, 27 Nov 2021 17:31:59 +0100") Message-ID: <87pmq4a8tm.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: 0.0 (/) X-Debbugs-Envelope-To: 52139 Cc: Lars-Dominik Braun , 52139@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: -3.3 (---) Hi Alexander, Alexander Asteroth skribis: > I found the cause: > > in ~/.guix-profile/etc/profile environment variables are set for jupyter: > >> export JUPYTER_PATH=3D"${GUIX_PROFILE:-/gnu/store/ichrcarq2k4lhdmm2izc3f= 1xjbziz49v-profile}/share/jupyter${JUPYTER_PATH:+:}$JUPYTER_PATH" >> export JUPYTER_CONFIG_DIR=3D"${GUIX_PROFILE:-/gnu/store/ichrcarq2k4lhdmm= 2izc3f1xjbziz49v-profile}/etc/jupyter${JUPYTER_CONFIG_DIR:+:}$JUPYTER_CONFI= G_DIR" > > The jupyter config path causes the problem, since jupyter tries to write > into it (and it is located in a read only filesystem). Unsetting the > environment variable solves the issue. I can=E2=80=99t reproduce it with: --8<---------------cut here---------------start------------->8--- $ guix describe Generacio 196 Dec 06 2021 11:23:08 (nuna) guix 9478a25 repository URL: https://git.savannah.gnu.org/git/guix.git branch: master commit: 9478a252509a93f3e7f486cbc549631185ba071d $ guix shell jupyter -CN --no-cwd -- jupyter notebook --8<---------------cut here---------------end--------------->8--- Perhaps that=E2=80=99s because I didn=E2=80=99t trigger actions that would = cause Jupyter to attempt to write to $JUPYTER_CONFIG_DIR? The JUPYTER_CONFIG_DIR search path was added to =E2=80=98python-jupyter-cor= e=E2=80=99 in commit 1683e9d9677d54f695a54fc44ed309287989fc34. Lars, what are you thoughts? Thanks, Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Fri Dec 10 08:29:53 2021 Received: (at control) by debbugs.gnu.org; 10 Dec 2021 13:29:53 +0000 Received: from localhost ([127.0.0.1]:45899 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mvfyD-0005YZ-Mo for submit@debbugs.gnu.org; Fri, 10 Dec 2021 08:29:53 -0500 Received: from eggs.gnu.org ([209.51.188.92]:59512) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mvfyC-0005YK-Jc for control@debbugs.gnu.org; Fri, 10 Dec 2021 08:29:52 -0500 Received: from [2001:470:142:3::e] (port=47296 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 1mvfy7-0005Gv-Cf for control@debbugs.gnu.org; Fri, 10 Dec 2021 08:29:47 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=gnu.org; s=fencepost-gnu-org; h=MIME-version:Subject:From:To:Date:in-reply-to: references; bh=MsvhAPwHkpnkrSkEjks3D3cNe3vWw7KdHM5Y8H8p3TY=; b=hxxCXxnsWSs4RU 01QRsOZdM3CGmCyb6ZamezABRH6pT1qb3DGVTKsvmAN6VNfSbBUcI+ITJ8Kp65cGuB+t8eUOcQ4yL 5W7XRPlvzR1V54fb3/q879TADXVEU48akp1BLH61MKAD6xd33hpiZoeG7kQTUcQYuvY1dgeP6JRCu 6/dIepE9fbfXHVJwdId9G0Drt0zxxR1d5mtdW6sJ2snZ+I/W3oRu6ViB/XL6UlDT1IqkZ0I+lTVjj 5YnKcz82Yu1k3/ZFEfJJLcpINq6XAgyZdH7w6xct73qkKoOdksilvYsPZqUZgSRhcXaifg/cPCHqK 7S4EMcgPqq/O4j8aUyqw==; Received: from 91-160-117-201.subs.proxad.net ([91.160.117.201]:53154 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mvfy5-0000wQ-E3 for control@debbugs.gnu.org; Fri, 10 Dec 2021 08:29:47 -0500 Date: Fri, 10 Dec 2021 14:29:43 +0100 Message-Id: <87o85oa8qg.fsf@gnu.org> To: control@debbugs.gnu.org From: =?utf-8?Q?Ludovic_Court=C3=A8s?= Subject: control message for bug #52139 MIME-version: 1.0 Content-type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: control 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 (---) merge 52139 52159 quit From debbugs-submit-bounces@debbugs.gnu.org Fri Dec 10 09:02:17 2021 Received: (at 52139) by debbugs.gnu.org; 10 Dec 2021 14:02:17 +0000 Received: from localhost ([127.0.0.1]:45958 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mvgTZ-0000Il-Gx for submit@debbugs.gnu.org; Fri, 10 Dec 2021 09:02:17 -0500 Received: from sv-2s11.infcs.de ([194.95.66.48]:53286 helo=ux-2s-mailproxy.inf.h-brs.de) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mvgTW-0000IU-Nl for 52139@debbugs.gnu.org; Fri, 10 Dec 2021 09:02:16 -0500 Received: from condor.h-brs.de (p5797302f.dip0.t-ipconnect.de [87.151.48.47]) (authenticated bits=0) by ux-2s-mailproxy.inf.h-brs.de (8.15.2/8.15.2/Debian-8ska0) with ESMTPSA id 1BAE1jO5004037 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT); Fri, 10 Dec 2021 15:01:45 +0100 References: <87pmqlq4s1.fsf@h-brs.de> <871r318spu.fsf@h-brs.de> <87pmq4a8tm.fsf@gnu.org> User-agent: mu4e 1.6.10; emacs 27.2 From: Alexander Asteroth To: Ludovic =?utf-8?Q?Court=C3=A8s?= Subject: Re: bug#52139: jupyter trying to modify /gnu/store Date: Fri, 10 Dec 2021 14:59:44 +0100 In-reply-to: <87pmq4a8tm.fsf@gnu.org> Message-ID: <875yrwftj3.fsf@h-brs.de> MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha256; protocol="application/pgp-signature" X-Auth: by SMTP AUTH @ ux-2s11 X-MIMEDefang-Info-ge: Gescannt in Inf@FH-BRS, Regeln s. MiniFAQ E-Mail/Mailscanner X-Spam-Status: No, Sender is auth'ed X-Scanned-By: MIMEDefang @ FB02 @ H-BRS X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 52139 Cc: Lars-Dominik Braun , 52139@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 (-) --=-=-= Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hi Ludovic, On Fri, Dec 10 2021, 14:27:49, Ludovic Court=C3=A8s wrote: > Hi Alexander, > > Alexander Asteroth skribis: > >> I found the cause: >> >> in ~/.guix-profile/etc/profile environment variables are set for jupyter: >> >>> export JUPYTER_PATH=3D"${GUIX_PROFILE:-/gnu/store/ichrcarq2k4lhdmm2izc3= f1xjbziz49v-profile}/share/jupyter${JUPYTER_PATH:+:}$JUPYTER_PATH" >>> export JUPYTER_CONFIG_DIR=3D"${GUIX_PROFILE:-/gnu/store/ichrcarq2k4lhdm= m2izc3f1xjbziz49v-profile}/etc/jupyter${JUPYTER_CONFIG_DIR:+:}$JUPYTER_CONF= IG_DIR" >> >> The jupyter config path causes the problem, since jupyter tries to write >> into it (and it is located in a read only filesystem). Unsetting the >> environment variable solves the issue. > > I can=E2=80=99t reproduce it with: > > $ guix describe > Generacio 196 Dec 06 2021 11:23:08 (nuna) > guix 9478a25 > repository URL: https://git.savannah.gnu.org/git/guix.git > branch: master > commit: 9478a252509a93f3e7f486cbc549631185ba071d > $ guix shell jupyter -CN --no-cwd -- jupyter notebook > > Perhaps that=E2=80=99s because I didn=E2=80=99t trigger actions that woul= d cause Jupyter > to attempt to write to $JUPYTER_CONFIG_DIR? Yes. I happes for also only if I used jupyter once. At the second attempt the error occured. The problem is easily solved by setting the config dir to (e.g.) ~/.config/jupyter. Cheers, Alex > > The JUPYTER_CONFIG_DIR search path was added to =E2=80=98python-jupyter-c= ore=E2=80=99 in > commit 1683e9d9677d54f695a54fc44ed309287989fc34. Lars, what are you > thoughts? > > Thanks, > Ludo=E2=80=99. --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQFQBAEBCAA6FiEEXU8UwBfdlxG/YNXXLg/GxGpHPCwFAmGzXcAcHGFsZXhhbmRl ci5hc3Rlcm90aEBoLWJycy5kZQAKCRAuD8bEakc8LKHoB/0WujJfuhObFpB8jEFc gZ9X6hyu4mkh/hHxUPTwneVF/oNryEft7Ho4FpAEiuHkTFulGav4Q1v762+nRkjI 1BWKhBX2csjV4k+GFpTdHlfR9Gj4GIes+B6TozQtpQc7K1pn0+eExH0sM8a7Z682 IqhuG9gzqnnXd6HBZMkp4XF/ntwmpJI0WPoKX/k9W8iH2hO1l8PkRS1bA2qGOoty x7FgD0WXBgRLnF2ENcVgKP3hm1g+RLa0I+yTP8gnXBt9/etwwg5FQFV/6NdOUebJ D23AdXDFG8VIKI5UDBEI8d8DkE//qNFdDXZeCLdOEffJ5unUOhYxk4owyAuBu2bA JrSl =M/rq -----END PGP SIGNATURE----- --=-=-=-- From debbugs-submit-bounces@debbugs.gnu.org Sat Dec 11 04:36:59 2021 Received: (at 52139) by debbugs.gnu.org; 11 Dec 2021 09:36:59 +0000 Received: from localhost ([127.0.0.1]:48534 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mvyoM-0005Za-RO for submit@debbugs.gnu.org; Sat, 11 Dec 2021 04:36:59 -0500 Received: from mout-p-102.mailbox.org ([80.241.56.152]:39864) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mvyoK-0005ZN-PA for 52139@debbugs.gnu.org; Sat, 11 Dec 2021 04:36:58 -0500 Received: from smtp1.mailbox.org (smtp1.mailbox.org [IPv6:2001:67c:2050:105:465:1:1:0]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange ECDHE (P-384) server-signature RSA-PSS (4096 bits) server-digest SHA256) (No client certificate requested) by mout-p-102.mailbox.org (Postfix) with ESMTPS id 4JB2jG438SzQjgG; Sat, 11 Dec 2021 10:36:50 +0100 (CET) X-Virus-Scanned: amavisd-new at heinlein-support.de DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=6xq.net; s=MBO0001; t=1639215408; 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=vHEPte4yVXljgcbAeZ5JHWtOOnwoNijy/U56M1jfTqc=; b=yqBAn7PLPb2QT+AhkPBe5hbiE3ZE1Nz+3Ibr0XMZJ3ou8eg82X1XhhJ9mFJ60fvdXnrN3X m6ALowAI5e4SzUrbsTHbF8+H5xueY7i7d7pyLq7UMMt99alsn3NB5dxscVI0rt0ZzVxZ/Z xecLAG874bVibsCrL4YgMMS0tSFwOXQF4LQjo6428snQ63uxyeR9GxKUL2zvJ1CICrhZnY VFARPyzwg8tzm6o8DpW2RmFH1hdGXaCzNTBJF1lWxpMl7xwMVaoY0RP2XHvXSJu7gwhYv+ E//6Y+VBfEEBn2RXrR1DM56PQJyHHAVaAozXUUzHtLYxObxjjPJ84WrJ/pmWLg== Date: Sat, 11 Dec 2021 10:36:45 +0100 From: Lars-Dominik Braun To: Ludovic =?iso-8859-1?Q?Court=E8s?= Subject: Re: bug#52139: jupyter trying to modify /gnu/store Message-ID: References: <87pmqlq4s1.fsf@h-brs.de> <871r318spu.fsf@h-brs.de> <87pmq4a8tm.fsf@gnu.org> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: 8bit In-Reply-To: <87pmq4a8tm.fsf@gnu.org> X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 52139 Cc: Alexander Asteroth , 52139@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: -1.7 (-) Hi, > I can’t reproduce it with: […] I cannot reproduce it either and this migration should not happen™, because the phase 'disable-migration should disable it. (See /gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib/python3.8/site-packages/jupyter_core/application.py:145). Alexander: Does this file exists for you too? guix shell python-notebook -- sh -c "stat \$JUPYTER_CONFIG_DIR/migrated" > The JUPYTER_CONFIG_DIR search path was added to ‘python-jupyter-core’ in > commit 1683e9d9677d54f695a54fc44ed309287989fc34. Lars, what are you > thoughts? Please *do not* remove this environment variable. It is required, because packages like jupyterlab drop a config file into this directory. Without it the jupyterlab extension will not be loaded by default and a simple `guix shell python-jupyterlab -- jupyter lab` will not work. Cheers, Lars From debbugs-submit-bounces@debbugs.gnu.org Sat Dec 11 07:48:20 2021 Received: (at 52139) by debbugs.gnu.org; 11 Dec 2021 12:48:20 +0000 Received: from localhost ([127.0.0.1]:48719 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mw1nY-00045M-7l for submit@debbugs.gnu.org; Sat, 11 Dec 2021 07:48:20 -0500 Received: from sv-2s11.infcs.de ([194.95.66.48]:43474 helo=ux-2s-mailproxy.inf.h-brs.de) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mw1nT-000452-7h for 52139@debbugs.gnu.org; Sat, 11 Dec 2021 07:48:18 -0500 Received: from condor.h-brs.de (p5797302f.dip0.t-ipconnect.de [87.151.48.47]) (authenticated bits=0) by ux-2s-mailproxy.inf.h-brs.de (8.15.2/8.15.2/Debian-8ska0) with ESMTPSA id 1BBCm0X4030894 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT); Sat, 11 Dec 2021 13:48:00 +0100 References: <87pmqlq4s1.fsf@h-brs.de> <871r318spu.fsf@h-brs.de> <87pmq4a8tm.fsf@gnu.org> User-agent: mu4e 1.6.10; emacs 27.2 From: Alexander Asteroth To: Lars-Dominik Braun Subject: Re: bug#52139: jupyter trying to modify /gnu/store Date: Sat, 11 Dec 2021 13:46:50 +0100 In-reply-to: Message-ID: <877dcbpatg.fsf@h-brs.de> MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha256; protocol="application/pgp-signature" X-Auth: by SMTP AUTH @ ux-2s11 X-MIMEDefang-Info-ge: Gescannt in Inf@FH-BRS, Regeln s. MiniFAQ E-Mail/Mailscanner X-Spam-Status: No, Sender is auth'ed X-Scanned-By: MIMEDefang @ FB02 @ H-BRS X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 52139 Cc: Ludovic =?utf-8?Q?Court=C3=A8s?= , 52139@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 (-) --=-=-= Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Nope: > stat: cannot statx '/gnu/store/djb0y6kn86ijbvkx93q48q484krp1kbb-profile/e= tc/jupyter:/home/aster/.config/jupyter/migrated': No such file or directory Cheers, Alex On Sat, Dec 11 2021, 10:36:45, Lars-Dominik Braun wrote: > Hi, > >> I can=E2=80=99t reproduce it with: [=E2=80=A6] > I cannot reproduce it either and this migration should not happen=E2=84= =A2, > because the phase 'disable-migration should disable it. (See > /gnu/store/8ncan0ipzb240h23fwfspdhrzkzdw277-python-jupyter-core-4.7.1/lib= /python3.8/site-packages/jupyter_core/application.py:145). > > Alexander: Does this file exists for you too? > > guix shell python-notebook -- sh -c "stat \$JUPYTER_CONFIG_DIR/migrat= ed" > >> The JUPYTER_CONFIG_DIR search path was added to =E2=80=98python-jupyter-= core=E2=80=99 in >> commit 1683e9d9677d54f695a54fc44ed309287989fc34. Lars, what are you >> thoughts? > Please *do not* remove this environment variable. It is required, because > packages like jupyterlab drop a config file into this directory. Without > it the jupyterlab extension will not be loaded by default and a simple > `guix shell python-jupyterlab -- jupyter lab` will not work. > > Cheers, > Lars --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQFQBAEBCAA6FiEEXU8UwBfdlxG/YNXXLg/GxGpHPCwFAmG0nfscHGFsZXhhbmRl ci5hc3Rlcm90aEBoLWJycy5kZQAKCRAuD8bEakc8LHOLCACMILTTc+zpm999BDhe J+4PiVLbrSnZd1wHHlxUFgJ5v6O5yprtQBu9eK+c7AJXGMIHaYI29u9OGjROhzkP ylxbjap9154EkaTjQQ89p8nI0HW4ulAW+LGCMDeHfeAcTnXDDPy7V6xRkTm7+jNs q0Pu55zxjXDlbN7jH6S4knhULe2rcxcvsFL9ar9GzTsNtL2c9ANn8Kr3nfLCFEj/ NdGx1bgSwhhm+WjqV3vX8vdfb2TMV9EYoLNGBOalvDUJsMpxupbBoL7X1CaPSSNo ZMmyEimxGkgxI85mFsSji19UkXrW1ZB4jQfBkqHzXGLuE306zLblbLjngzD48V2y CCam =FGaA -----END PGP SIGNATURE----- --=-=-=-- From debbugs-submit-bounces@debbugs.gnu.org Sun Dec 12 16:41:34 2021 Received: (at 52139) by debbugs.gnu.org; 12 Dec 2021 21:41:34 +0000 Received: from localhost ([127.0.0.1]:53354 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mwWb8-0004O9-2k for submit@debbugs.gnu.org; Sun, 12 Dec 2021 16:41:34 -0500 Received: from eggs.gnu.org ([209.51.188.92]:56906) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mwWb5-0004Nw-GJ for 52139@debbugs.gnu.org; Sun, 12 Dec 2021 16:41:32 -0500 Received: from [2001:470:142:3::e] (port=40658 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 1mwWaz-0002TW-CK; Sun, 12 Dec 2021 16:41:25 -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=o0Ccey9iE9hBhRhhJWtuiKhVFOzJZtg3CFwTCUG8JFM=; b=joNpVnwn8Y/B/8002zVI VsT5EnjvPEXO+a9SntEyWQaLsbXGHr82eNGiniZRWtiLw4wpbKLf/X7xfo/yUEsnjnYK+dNN3Cwig UJShJCrQtn9ksHrJ2RQ0wHDDy9IAO/1FeTRFAIGK6WuKx3KZlpn0i0RfEZU/FaxuS535BqodcGqQ4 G300AC/3LdNJ62uDuABPb6DGcW1Gtax0+K3sdYstOUaYxiU6uIZYSLYFWcmRNOdTjRNKxOiX4ISLI qqsw+31MYqJuBHSNYIjPKTFPAHUax5gU/rN8QDItTJ245uQq3G/YbcGbeVjJGDGTNkiLr2vZZf4rN W8Qw50NoKQt2Fw==; Received: from 91-160-117-201.subs.proxad.net ([91.160.117.201]:62947 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mwWay-0004ub-Pp; Sun, 12 Dec 2021 16:41:25 -0500 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= To: Lars-Dominik Braun Subject: Re: bug#52139: jupyter trying to modify /gnu/store References: <87pmqlq4s1.fsf@h-brs.de> <871r318spu.fsf@h-brs.de> <87pmq4a8tm.fsf@gnu.org> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 22 Frimaire an 230 de la =?utf-8?Q?R=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: Sun, 12 Dec 2021 22:41:21 +0100 In-Reply-To: (Lars-Dominik Braun's message of "Sat, 11 Dec 2021 10:36:45 +0100") Message-ID: <87k0g94i2m.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/27.2 (gnu/linux) MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 52139 Cc: Alexander Asteroth , 52139@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: -3.3 (---) --=-=-= Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hi Lars, Lars-Dominik Braun skribis: >> The JUPYTER_CONFIG_DIR search path was added to =E2=80=98python-jupyter-= core=E2=80=99 in >> commit 1683e9d9677d54f695a54fc44ed309287989fc34. Lars, what are you >> thoughts? > Please *do not* remove this environment variable. It is required, because > packages like jupyterlab drop a config file into this directory. But precisely: as Alexander wrote, when JUPYTER_CONFIG_DIR points to the store, jupyterlab cannot drop a config file there. Or am I missing something? BTW, if JUPYTER_CONFIG_DIR is meant to contain a directory name, as opposed to a colon-separated search path, we should make this change: --=-=-= Content-Type: text/x-patch Content-Disposition: inline diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b3a350aca4..57f66e18f1 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -8479,6 +8479,7 @@ (define-public python-jupyter-core (native-search-paths (list (search-path-specification (variable "JUPYTER_CONFIG_DIR") + (separator #f) ;single entry (files '("etc/jupyter"))) (search-path-specification (variable "JUPYTER_PATH") --=-=-= Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable WDYT? Thanks, Ludo=E2=80=99. --=-=-=-- From debbugs-submit-bounces@debbugs.gnu.org Mon Dec 13 03:20:53 2021 Received: (at 52139) by debbugs.gnu.org; 13 Dec 2021 08:20:53 +0000 Received: from localhost ([127.0.0.1]:53986 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mwgZp-0006H4-Aa for submit@debbugs.gnu.org; Mon, 13 Dec 2021 03:20:53 -0500 Received: from mout-p-202.mailbox.org ([80.241.56.172]:33174) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mwgZl-0006Gq-SQ for 52139@debbugs.gnu.org; Mon, 13 Dec 2021 03:20:51 -0500 Received: from smtp102.mailbox.org (smtp102.mailbox.org [IPv6:2001:67c:2050:105:465:1:3:0]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange ECDHE (P-384) server-signature RSA-PSS (4096 bits) server-digest SHA256) (No client certificate requested) by mout-p-202.mailbox.org (Postfix) with ESMTPS id 4JCDwX0PH0zQjmQ; Mon, 13 Dec 2021 09:20:44 +0100 (CET) X-Virus-Scanned: amavisd-new at heinlein-support.de DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=6xq.net; s=MBO0001; t=1639383641; 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=BGqZEbW+Sq7Jjn2B5XjaPLn5KNy0ZOhpzoXyStas3b8=; b=xecPWk9dGO6Y9qCg6DbFhWQGrWDBEYUu5qQ5KdCPeZTwLunfGHykoAj+k7wlLJc+qFmkK0 IKvXVhtXkIb5MJqq+pdRkV+6L3OGV54Mvwj8mX+hCfvBTQQbUDMg2gqCXkZOJgN0NkcaOK P2XS6iWl/8CHguRIVCbA4ucVDyDT/sGwl9cpLq030ulEZqNRGD1WomHo4/NCAzr+huzKYH XmOe/0QFgIvpiyp+MhH1nMqDbX/KBZLFEiFlX3/WkJL38oY91SjpIkpzeOsOQEWjPiccoo ZClL8D3wY1JRz0gMPw6ad5ozxh2Q7752nUzpgBaRYtdO/JGAmVxtZnVvliycNg== Date: Mon, 13 Dec 2021 09:20:37 +0100 From: Lars-Dominik Braun To: Ludovic =?iso-8859-1?Q?Court=E8s?= Subject: Re: bug#52139: jupyter trying to modify /gnu/store Message-ID: References: <87pmqlq4s1.fsf@h-brs.de> <871r318spu.fsf@h-brs.de> <87pmq4a8tm.fsf@gnu.org> <87k0g94i2m.fsf@gnu.org> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="m0rvPhIORydFLqs8" Content-Disposition: inline Content-Transfer-Encoding: 8bit In-Reply-To: <87k0g94i2m.fsf@gnu.org> X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 52139 Cc: Alexander Asteroth , 52139@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: -1.7 (-) --m0rvPhIORydFLqs8 Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: 8bit Hi Ludo, > But precisely: as Alexander wrote, when JUPYTER_CONFIG_DIR points to the > store, jupyterlab cannot drop a config file there. Or am I missing > something? sorry, my message was unclear here. The config file is written at build time. > BTW, if JUPYTER_CONFIG_DIR is meant to contain a directory name, as > opposed to a colon-separated search path, we should make this change: Looking at the documentation[1] again this is correct, but I feel we should use JUPYTER_CONFIG_PATH instead, because it supports colon-delimited entries, see attached patch. However that does not get rid of error messages like these, when trying to use Settings→JupyterLab Theme for example: [W 08:10:14.476 LabApp] 500 PUT /lab/api/workspaces/lab?1639383014500 (127.0.0.1): [Errno 30] Read-only file system: '/gnu/store/8q7wdpdddfqh46plbbsa3rwci5092n5y-profile/etc/jupyter/lab' So it seems that JUPYTER_CONFIG_PATH overrides the default JUPYTER_CONFIG_DIR, when the latter is not set. Or maybe guix-science’s jupyterlab is simply too old – not sure right now. Cheers, Lars [1] https://jupyter.readthedocs.io/en/latest/use/jupyter-directories.html --m0rvPhIORydFLqs8 Content-Type: text/x-diff; charset=us-ascii Content-Disposition: attachment; filename="jupyter-core-config-path.patch" diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index db2ab8e5f0..450d17208f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -8478,7 +8478,7 @@ (define-public python-jupyter-core ;; search paths. (native-search-paths (list (search-path-specification - (variable "JUPYTER_CONFIG_DIR") + (variable "JUPYTER_CONFIG_PATH") (files '("etc/jupyter"))) (search-path-specification (variable "JUPYTER_PATH") @@ -12145,8 +12145,6 @@ (define-public python-nbconvert (when tests? ;; Some tests invoke the installed nbconvert binary. (add-installed-pythonpath inputs outputs) - ;; Tries to write to this path. - (unsetenv "JUPYTER_CONFIG_DIR") ;; Tests depend on templates installed to output. (setenv "JUPYTER_PATH" (string-append @@ -12254,6 +12252,8 @@ (define-public python-notebook ;; Some tests do not expect all files to be installed in the ;; same directory, but JUPYTER_PATH contains multiple entries. (unsetenv "JUPYTER_PATH") + ;; Interferes with tests that check paths. + (unsetenv "JUPYTER_CONFIG_PATH") ;; Some tests need HOME (setenv "HOME" "/tmp") (with-directory-excursion "/tmp" --m0rvPhIORydFLqs8-- From debbugs-submit-bounces@debbugs.gnu.org Tue Dec 14 10:07:09 2021 Received: (at 52139) by debbugs.gnu.org; 14 Dec 2021 15:07:09 +0000 Received: from localhost ([127.0.0.1]:59296 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mx9OW-00059D-Rs for submit@debbugs.gnu.org; Tue, 14 Dec 2021 10:07:09 -0500 Received: from eggs.gnu.org ([209.51.188.92]:48484) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mx9OV-00058s-LD for 52139@debbugs.gnu.org; Tue, 14 Dec 2021 10:07:08 -0500 Received: from [2001:470:142:3::e] (port=42044 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 1mx9OP-0002BA-Ay; Tue, 14 Dec 2021 10:07:01 -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=Kz4s9hFK6lralcSazYq43yU2gTf14+Yavnc4rBtxy/A=; b=ejqFl/Vm95U/ELpGLzOS hS7Y58p58/M2YF9rLrkfDwqpE04/reEpU8a4uqxjbha8YQTbW6FSIBbxsTCwp4I4oV/uWUfaZl1WI 2+RD+arulqGcF3tAb3Q5eAyhLEIl6IsKx9KKahTqlKblEjh9fsqJiX+RbjNRPAmcCWHoqq+j3TtjG c6Wd62sPYyo2uOGpDQRFEC+7kypQBBK9uTbVKceJ3JvPyRqL9IvA2PWeFLV97tJQEHzrNASiN7Qt5 2dswDC4eNRXfxU8sXqQuz/blWtJsaqfS1oC6GDIwEAudbV1YG8Kzxaa8eUeYZf8MvGWb8d59X+Cye XNERbaTT2cmkpQ==; Received: from 91-160-117-201.subs.proxad.net ([91.160.117.201]:62299 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mx9OP-00071s-9m; Tue, 14 Dec 2021 10:07:01 -0500 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= To: Lars-Dominik Braun Subject: Re: bug#52139: jupyter trying to modify /gnu/store References: <87pmqlq4s1.fsf@h-brs.de> <871r318spu.fsf@h-brs.de> <87pmq4a8tm.fsf@gnu.org> <87k0g94i2m.fsf@gnu.org> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 24 Frimaire an 230 de la =?utf-8?Q?R=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: Tue, 14 Dec 2021 16:06:58 +0100 In-Reply-To: (Lars-Dominik Braun's message of "Mon, 13 Dec 2021 09:20:37 +0100") Message-ID: <87v8zrz0ml.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: 52139 Cc: Alexander Asteroth , 52139@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: -3.3 (---) Hi Lars, Lars-Dominik Braun skribis: >> But precisely: as Alexander wrote, when JUPYTER_CONFIG_DIR points to the >> store, jupyterlab cannot drop a config file there. Or am I missing >> something? > sorry, my message was unclear here. The config file is written at > build time. Oh I see. >> BTW, if JUPYTER_CONFIG_DIR is meant to contain a directory name, as >> opposed to a colon-separated search path, we should make this change: > Looking at the documentation[1] again this is correct, but I feel we > should use JUPYTER_CONFIG_PATH instead, because it supports > colon-delimited entries, see attached patch. However that does not get > rid of error messages like these, when trying to use Settings=E2=86=92Jup= yterLab > Theme for example: > > [W 08:10:14.476 LabApp] 500 PUT /lab/api/workspaces/lab?1639383014500 (12= 7.0.0.1): [Errno 30] Read-only file system: '/gnu/store/8q7wdpdddfqh46plbbs= a3rwci5092n5y-profile/etc/jupyter/lab' > > So it seems that JUPYTER_CONFIG_PATH overrides the default > JUPYTER_CONFIG_DIR, when the latter is not set. Or maybe guix-science=E2= =80=99s > jupyterlab is simply too old =E2=80=93 not sure right now. OK. > +++ b/gnu/packages/python-xyz.scm > @@ -8478,7 +8478,7 @@ (define-public python-jupyter-core > ;; search paths. > (native-search-paths > (list (search-path-specification > - (variable "JUPYTER_CONFIG_DIR") > + (variable "JUPYTER_CONFIG_PATH") > (files '("etc/jupyter"))) > (search-path-specification > (variable "JUPYTER_PATH") > @@ -12145,8 +12145,6 @@ (define-public python-nbconvert > (when tests? > ;; Some tests invoke the installed nbconvert binary. > (add-installed-pythonpath inputs outputs) > - ;; Tries to write to this path. > - (unsetenv "JUPYTER_CONFIG_DIR") > ;; Tests depend on templates installed to output. > (setenv "JUPYTER_PATH" > (string-append > @@ -12254,6 +12252,8 @@ (define-public python-notebook > ;; Some tests do not expect all files to be installed in = the > ;; same directory, but JUPYTER_PATH contains multiple ent= ries. > (unsetenv "JUPYTER_PATH") > + ;; Interferes with tests that check paths. > + (unsetenv "JUPYTER_CONFIG_PATH") > ;; Some tests need HOME > (setenv "HOME" "/tmp") > (with-directory-excursion "/tmp" If that works for you, go for it. Thanks, Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Thu Dec 16 04:16:28 2021 Received: (at 52139) by debbugs.gnu.org; 16 Dec 2021 09:16:28 +0000 Received: from localhost ([127.0.0.1]:34595 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mxmsG-00066S-6t for submit@debbugs.gnu.org; Thu, 16 Dec 2021 04:16:28 -0500 Received: from mout-p-201.mailbox.org ([80.241.56.171]:27494) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mxmsE-00066C-Ga for 52139@debbugs.gnu.org; Thu, 16 Dec 2021 04:16:27 -0500 Received: from smtp2.mailbox.org (smtp2.mailbox.org [80.241.60.241]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange ECDHE (P-384) server-signature RSA-PSS (4096 bits) server-digest SHA256) (No client certificate requested) by mout-p-201.mailbox.org (Postfix) with ESMTPS id 4JF61J2swszQlWq; Thu, 16 Dec 2021 10:16:20 +0100 (CET) X-Virus-Scanned: amavisd-new at heinlein-support.de DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=6xq.net; s=MBO0001; t=1639646177; 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=6T4OCvZoQc+WT/6cTEVoPiCfArOmlaLqYTQPpPQr0Bk=; b=rkFALKvSHSesXSy1gA2fYGAe3mcvVJ9GXFAolMgnVA9tZoWI2WBtjJbgnYsoAB45s0/+3U LHA9BrMukD0o6+nwSW9yr2GQLldy0iERsQ1LFqqmKLk7Jkv9ZNJLdQtMd2DhjGKWbR0UVx Z6fl+vP2Rh8VsxnkWxMcSw09U6biPp3GRLB+EtdgQX3U1F7Jsq/vSLGlQdAOpRZczLRdA0 cSUp05/oy6dENDKtuV92pVPsUjiqbGpXdZ+55Du6snC52aZFT0/2see3jj4gpR6AQLcDr3 eCNnz1AQQQXlf6+uyOgppsjxqW8uEMV+qGvwfT6baptAkPv2eOxFKIL/mQAitA== Date: Thu, 16 Dec 2021 10:16:14 +0100 From: Lars-Dominik Braun To: Ludovic =?iso-8859-1?Q?Court=E8s?= Subject: Re: bug#52139: jupyter trying to modify /gnu/store Message-ID: References: <87pmqlq4s1.fsf@h-brs.de> <871r318spu.fsf@h-brs.de> <87pmq4a8tm.fsf@gnu.org> <87k0g94i2m.fsf@gnu.org> <87v8zrz0ml.fsf@gnu.org> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: 8bit In-Reply-To: <87v8zrz0ml.fsf@gnu.org> X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 52139 Cc: Alexander Asteroth , 52139@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: -1.7 (-) Hi, > If that works for you, go for it. merged as c63b55d1283d9a4bfc5ecaf1cab01cd98a467b69. I’ll investigate why jupyterlab is trying to write to /gnu/store when trying to save settings. Cheers, Lars From debbugs-submit-bounces@debbugs.gnu.org Tue Dec 21 08:48:19 2021 Received: (at 52139-done) by debbugs.gnu.org; 21 Dec 2021 13:48:19 +0000 Received: from localhost ([127.0.0.1]:52750 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mzfV5-0004cF-Kb for submit@debbugs.gnu.org; Tue, 21 Dec 2021 08:48:19 -0500 Received: from mout-p-102.mailbox.org ([80.241.56.152]:41324) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mzfV2-0004bx-OA for 52139-done@debbugs.gnu.org; Tue, 21 Dec 2021 08:48:18 -0500 Received: from smtp102.mailbox.org (smtp102.mailbox.org [IPv6:2001:67c:2050:105:465:1:3:0]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange ECDHE (P-384) server-signature RSA-PSS (4096 bits) server-digest SHA256) (No client certificate requested) by mout-p-102.mailbox.org (Postfix) with ESMTPS id 4JJHpf0qVPzQkwr; Tue, 21 Dec 2021 14:48:10 +0100 (CET) X-Virus-Scanned: amavisd-new at heinlein-support.de DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=6xq.net; s=MBO0001; t=1640094488; 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=K3DfgAYk6PdZ4ZC80tRjY6aQEklpZKF69rCNQGL692g=; b=ufdiLufB+CEb5LIocxnG6dtG2GbUMZAQll4CDf2GtjI3OxOhMEVAu7oVvBHduvsHdQlyfF PjE7rdjW72Pt071wLJyRZhywCBUPVcTB9hfyOEDYuxT0l9MaJj/tPzVUd/vJS6cTP26OpI nyWE9qUv6Obi1gSOlMFSNKkLceO8jw5X/Crb4lTGa5FuZhO75BepYfJWj1tDx7hOVZUQ95 PlPdzgzHK1m1G3gDpksXutChFIJMwxEBjjRs1uJ85m7Dj91x1gJVP4PXCw/qDx0Y3LNPfX xBBuXgODA9yfIHUngBnNv21nvyRi0ocVal85+iijy76AxVb97JWMZ8nUm0GB0A== Date: Tue, 21 Dec 2021 14:48:04 +0100 From: Lars-Dominik Braun To: Alexander Asteroth Subject: Re: bug#52139: jupyter trying to modify /gnu/store Message-ID: References: <87pmqlq4s1.fsf@h-brs.de> <871r318spu.fsf@h-brs.de> <87pmq4a8tm.fsf@gnu.org> <8735mzpaep.fsf@h-brs.de> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: 8bit In-Reply-To: <8735mzpaep.fsf@h-brs.de> X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 52139-done Cc: 52139-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: -1.7 (-) Hi Alexander, > [W 13:52:18.502 LabApp] 500 PUT /lab/api/workspaces/lab?1639227138494 (127.0.0.1): [Errno 30] Read-only file system: '[user]/.guix-profile/etc/jupyter/lab' I’ve fixed this via https://github.com/guix-science/guix-science/commit/ca5d2b79cc730f6d52f93f4e7347102b620ed988 Cheers, Lars From unknown Fri Jun 20 19:51:43 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Wed, 19 Jan 2022 12:24:06 +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