From unknown Sun Aug 10 16:43:02 2025 X-Loop: help-debbugs@gnu.org Subject: bug#42434: Shell can't find basic system tools after massive garbage collection Resent-From: Alexandru-Sergiu Marton Original-Sender: "Debbugs-submit" Resent-CC: bug-guix@gnu.org Resent-Date: Sun, 19 Jul 2020 20:10:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 42434 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: 42434@debbugs.gnu.org X-Debbugs-Original-To: bug-guix@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.159518936115643 (code B ref -1); Sun, 19 Jul 2020 20:10:02 +0000 Received: (at submit) by debbugs.gnu.org; 19 Jul 2020 20:09:21 +0000 Received: from localhost ([127.0.0.1]:33112 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jxFce-00044F-QL for submit@debbugs.gnu.org; Sun, 19 Jul 2020 16:09:20 -0400 Received: from lists.gnu.org ([209.51.188.17]:53542) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jxFcd-000447-J9 for submit@debbugs.gnu.org; Sun, 19 Jul 2020 16:09:20 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:40588) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1jxFcd-0002Zh-Ec for bug-guix@gnu.org; Sun, 19 Jul 2020 16:09:19 -0400 Received: from mout01.posteo.de ([185.67.36.65]:54651) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1jxFca-0002wv-Tw for bug-guix@gnu.org; Sun, 19 Jul 2020 16:09:18 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id C0C8416005C for ; Sun, 19 Jul 2020 22:09:11 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.ro; s=2017; t=1595189351; bh=MKr6gR4TEIMUh5lZPgGy2S8AaxWHxpYS4Pa64y93LdI=; h=From:To:Subject:Date:From; b=K93dYlgbzzelrD2mf5VisfbIpgKz1s0shRyDifXZOwOezBPlzDqBJXlUFivqMnuNh BK6CaOA+bLm0ljXiAxZz4i9sLHypR9ySDQsw6yVEEMtfirHG/EAHFWSkI0RP8K0tBQ q22XR7Jd/ZJA/18XFOwB6zNNQJ+DmpvtVuuMDYt4VeV2sQv6DHKuNa+8TIwUNvfp+S 2oaR3BOqZcb/jaQ2qC+IQd8RNDp6l7ouFQGpPx0XiywJBsKZnsKq99dkenIAKFPfVU mPMNKWGyXbeB7qenpdB1tLxEaxg+ktS/B56DyL9lw3iNKwLMqN1MvqNejMmygfi04F KaagCe9FJs1sg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4B8wtH1HV5z6tmB for ; Sun, 19 Jul 2020 22:09:10 +0200 (CEST) From: Alexandru-Sergiu Marton Date: Sun, 19 Jul 2020 23:09:09 +0300 Message-ID: <87eep7jmhm.fsf@posteo.ro> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain Received-SPF: pass client-ip=185.67.36.65; envelope-from=brown121407@posteo.ro; helo=mout01.posteo.de X-detected-operating-system: by eggs.gnu.org: First seen = 2020/07/19 16:09:12 X-ACL-Warn: Detected OS = Linux 3.11 and newer X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, RCVD_IN_MSPIKE_H4=-0.01, RCVD_IN_MSPIKE_WL=-0.01, SPF_HELO_NONE=0.001, SPF_PASS=-0.001, URIBL_BLOCKED=0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.3 (-) 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: -2.3 (--) Hi, I run Guix System on my laptop and I wanted to free some space so I ran all the cleaning stuff I could think of: --8<---------------cut here---------------start------------->8--- guix package --delete-generations guix gc --delete-generations sudo guix system delete-generations --8<---------------cut here---------------end--------------->8--- After running them all, I had troubles using some of the most basic tools, like ls or rm. Other programs seemed fine (make, gcc, guix) as I could compile my builds of dwm and st. After I ran `guix system reconfigure` and I made sure my profile contains all the software I need at the latest version by running `guix package -m` on my manifest, everything went back to normal -- I could use ls and rm again. Sadly, I didn't gather more information as I didn't experiment much with the broken system because I freaked out and tried to fix it as fast as possible. I don't know what to make of this. Brett Gilio suggested it may have been a bad symlink job. Cheers, Sergiu From unknown Sun Aug 10 16:43:02 2025 X-Loop: help-debbugs@gnu.org Subject: bug#42434: Shell can't find basic system tools after massive garbage collection Resent-From: Brett Gilio Original-Sender: "Debbugs-submit" Resent-CC: bug-guix@gnu.org Resent-Date: Fri, 24 Jul 2020 23:03:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 42434 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: Alexandru-Sergiu Marton Cc: 42434@debbugs.gnu.org Received: via spool by 42434-submit@debbugs.gnu.org id=B42434.15956317505908 (code B ref 42434); Fri, 24 Jul 2020 23:03:01 +0000 Received: (at 42434) by debbugs.gnu.org; 24 Jul 2020 23:02:30 +0000 Received: from localhost ([127.0.0.1]:48931 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jz6hy-0001XE-IH for submit@debbugs.gnu.org; Fri, 24 Jul 2020 19:02:30 -0400 Received: from eggs.gnu.org ([209.51.188.92]:53440) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jz6hw-0001X2-LB for 42434@debbugs.gnu.org; Fri, 24 Jul 2020 19:02:29 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:34922) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1jz6hq-0005wK-2I; Fri, 24 Jul 2020 19:02:22 -0400 Received: from [2605:6000:1a0d:48fb::e9] (port=59238 helo=lenovo-t430) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1jz6hp-00038c-Cl; Fri, 24 Jul 2020 19:02:21 -0400 From: Brett Gilio References: <87eep7jmhm.fsf@posteo.ro> Date: Fri, 24 Jul 2020 18:02:32 -0500 In-Reply-To: <87eep7jmhm.fsf@posteo.ro> (Alexandru-Sergiu Marton's message of "Sun, 19 Jul 2020 23:09:09 +0300") Message-ID: <87wo2sectz.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: -2.3 (--) 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 (---) Alexandru-Sergiu Marton writes: > Hi, > > I run Guix System on my laptop and I wanted to free some space so I ran > all the cleaning stuff I could think of: > > guix package --delete-generations > guix gc --delete-generations > sudo guix system delete-generations > > After running them all, I had troubles using some of the most basic > tools, like ls or rm. Other programs seemed fine (make, gcc, guix) as I > could compile my builds of dwm and st. > > After I ran `guix system reconfigure` and I made sure my profile > contains all the software I need at the latest version by running `guix > package -m` on my manifest, everything went back to normal -- I could > use ls and rm again. > > Sadly, I didn't gather more information as I didn't experiment much with > the broken system because I freaked out and tried to fix it as fast as > possible. > > I don't know what to make of this. Brett Gilio suggested it may have > been a bad symlink job. > > Cheers, > Sergiu I haven't investigated this myself, but on more thought it may also have to do with some outdated environment variables. Did you happen to reboot your computer or restart your X/Wayland session anytime after deleting the old generations and running the garbage collector? Brett Gilio From unknown Sun Aug 10 16:43:02 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: Alexandru-Sergiu Marton Subject: bug#42434: closed (Re: bug#42434: Shell can't find basic system tools after massive garbage collection) Message-ID: References: <877duh9ymd.fsf@posteo.ro> <87eep7jmhm.fsf@posteo.ro> X-Gnu-PR-Message: they-closed 42434 X-Gnu-PR-Package: guix Reply-To: 42434@debbugs.gnu.org Date: Sun, 02 Aug 2020 06:39:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1596350342-5242-1" This is a multi-part message in MIME format... ------------=_1596350342-5242-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #42434: Shell can't find basic system tools after massive garbage collection which was filed against the guix package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 42434@debbugs.gnu.org. --=20 42434: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D42434 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1596350342-5242-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 42434-done) by debbugs.gnu.org; 2 Aug 2020 06:38:12 +0000 Received: from localhost ([127.0.0.1]:41512 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1k27dM-0001LR-LN for submit@debbugs.gnu.org; Sun, 02 Aug 2020 02:38:12 -0400 Received: from mout01.posteo.de ([185.67.36.65]:49809) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1k27dJ-0001L8-8v for 42434-done@debbugs.gnu.org; Sun, 02 Aug 2020 02:38:11 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id B0A7616005F for <42434-done@debbugs.gnu.org>; Sun, 2 Aug 2020 08:38:02 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.ro; s=2017; t=1596350282; bh=cvdtDrr1hM7xoAzs7kIFAOQrRaFUry3llp+zwvYdze8=; h=From:To:Cc:Subject:Date:From; b=qtgKoUizOAXebgW8gd4lf7+HND4D9Gk4FORWZXd/UBZNP/bgBnZn4NCroWqHcM9CM WACF4Ssr08cx43EEqb/xbhAe9nEOc3m6ghpo/m8l2OrV+h71aLXb8S3977lpgW4da9 o1R2msRbI7qQzR1qYsFCJ/MOleGEenyDbVfJ/Ejuh4AqJdw7Rqtzdotof8z2mFf2u+ z3xgAdfKn+siLy3QT+RZLiRz8fTyxpcAs9UFof0xPHJvTkM/le0HG1As8tM3QY9o/G dDJ9gzxA+LLsuj32cLlOoai3LPrmUw+W1BDUHcn0zDTZQ7C+V1GqRnR2R9c8VePAIT nN5CwqSQ0Z7vg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4BKBCt0Qlgz9rxX; Sun, 2 Aug 2020 08:38:01 +0200 (CEST) From: Alexandru-Sergiu Marton To: Brett Gilio Subject: Re: bug#42434: Shell can't find basic system tools after massive garbage collection References: <87eep7jmhm.fsf@posteo.ro> <87wo2sectz.fsf@gnu.org> Date: Sun, 02 Aug 2020 12:38:02 +0300 In-Reply-To: <87wo2sectz.fsf@gnu.org> (Brett Gilio's message of "Fri, 24 Jul 2020 18:02:32 -0500") Message-ID: <877duh9ymd.fsf@posteo.ro> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 42434-done Cc: 42434-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: -3.3 (---) Hi, Brett Gilio writes: > I haven't investigated this myself, but on more thought it may also have > to do with some outdated environment variables. Did you happen to reboot > your computer or restart your X/Wayland session anytime after deleting > the old generations and running the garbage collector? > > Brett Gilio I ran those commands again on two of my machines that run Guix System and the problem no longer exists. Closing. Cheers, Sergiu ------------=_1596350342-5242-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 19 Jul 2020 20:09:21 +0000 Received: from localhost ([127.0.0.1]:33112 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jxFce-00044F-QL for submit@debbugs.gnu.org; Sun, 19 Jul 2020 16:09:20 -0400 Received: from lists.gnu.org ([209.51.188.17]:53542) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jxFcd-000447-J9 for submit@debbugs.gnu.org; Sun, 19 Jul 2020 16:09:20 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:40588) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1jxFcd-0002Zh-Ec for bug-guix@gnu.org; Sun, 19 Jul 2020 16:09:19 -0400 Received: from mout01.posteo.de ([185.67.36.65]:54651) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1jxFca-0002wv-Tw for bug-guix@gnu.org; Sun, 19 Jul 2020 16:09:18 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id C0C8416005C for ; Sun, 19 Jul 2020 22:09:11 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.ro; s=2017; t=1595189351; bh=MKr6gR4TEIMUh5lZPgGy2S8AaxWHxpYS4Pa64y93LdI=; h=From:To:Subject:Date:From; b=K93dYlgbzzelrD2mf5VisfbIpgKz1s0shRyDifXZOwOezBPlzDqBJXlUFivqMnuNh BK6CaOA+bLm0ljXiAxZz4i9sLHypR9ySDQsw6yVEEMtfirHG/EAHFWSkI0RP8K0tBQ q22XR7Jd/ZJA/18XFOwB6zNNQJ+DmpvtVuuMDYt4VeV2sQv6DHKuNa+8TIwUNvfp+S 2oaR3BOqZcb/jaQ2qC+IQd8RNDp6l7ouFQGpPx0XiywJBsKZnsKq99dkenIAKFPfVU mPMNKWGyXbeB7qenpdB1tLxEaxg+ktS/B56DyL9lw3iNKwLMqN1MvqNejMmygfi04F KaagCe9FJs1sg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4B8wtH1HV5z6tmB for ; Sun, 19 Jul 2020 22:09:10 +0200 (CEST) From: Alexandru-Sergiu Marton To: bug-guix@gnu.org Subject: Shell can't find basic system tools after massive garbage collection Date: Sun, 19 Jul 2020 23:09:09 +0300 Message-ID: <87eep7jmhm.fsf@posteo.ro> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain Received-SPF: pass client-ip=185.67.36.65; envelope-from=brown121407@posteo.ro; helo=mout01.posteo.de X-detected-operating-system: by eggs.gnu.org: First seen = 2020/07/19 16:09:12 X-ACL-Warn: Detected OS = Linux 3.11 and newer X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, RCVD_IN_MSPIKE_H4=-0.01, RCVD_IN_MSPIKE_WL=-0.01, SPF_HELO_NONE=0.001, SPF_PASS=-0.001, URIBL_BLOCKED=0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.3 (-) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit@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: -2.3 (--) Hi, I run Guix System on my laptop and I wanted to free some space so I ran all the cleaning stuff I could think of: --8<---------------cut here---------------start------------->8--- guix package --delete-generations guix gc --delete-generations sudo guix system delete-generations --8<---------------cut here---------------end--------------->8--- After running them all, I had troubles using some of the most basic tools, like ls or rm. Other programs seemed fine (make, gcc, guix) as I could compile my builds of dwm and st. After I ran `guix system reconfigure` and I made sure my profile contains all the software I need at the latest version by running `guix package -m` on my manifest, everything went back to normal -- I could use ls and rm again. Sadly, I didn't gather more information as I didn't experiment much with the broken system because I freaked out and tried to fix it as fast as possible. I don't know what to make of this. Brett Gilio suggested it may have been a bad symlink job. Cheers, Sergiu ------------=_1596350342-5242-1--