From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp2 ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms0.migadu.com with LMTPS id YL3yDSrc0GBWJAAAgWs5BA (envelope-from ) for ; Mon, 21 Jun 2021 20:36:26 +0200 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp2 with LMTPS id +DetCSrc0GA6bAAAB5/wlQ (envelope-from ) for ; Mon, 21 Jun 2021 18:36:26 +0000 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id 7AE75EF62 for ; Mon, 21 Jun 2021 20:36:25 +0200 (CEST) Received: from localhost ([::1]:51718 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lvOmV-0003l1-DM for larch@yhetil.org; Mon, 21 Jun 2021 14:36:23 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:55418) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lvOgk-0000O6-Ki for help-guix@gnu.org; Mon, 21 Jun 2021 14:30:28 -0400 Received: from minsky.hcoop.net ([104.248.1.95]:35344) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lvOgg-0007uo-Hk for help-guix@gnu.org; Mon, 21 Jun 2021 14:30:26 -0400 Received: from marsh.hcoop.net ([45.55.52.66]) by minsky.hcoop.net with esmtpsa (TLS1.3:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.92) (envelope-from ) id 1lvOgf-0004S9-60 for help-guix@gnu.org; Mon, 21 Jun 2021 14:30:21 -0400 Date: Mon, 21 Jun 2021 14:30:20 -0400 (EDT) From: Jack Hill X-X-Sender: jackhill@marsh.hcoop.net To: help-guix@gnu.org Subject: Corrupt/missing store items Message-ID: User-Agent: Alpine 2.21 (DEB 202 2017-01-01) MIME-Version: 1.0 Received-SPF: pass client-ip=104.248.1.95; envelope-from=jackhill@jackhill.us; helo=minsky.hcoop.net 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 Content-Type: text/plain; format=flowed; charset=UTF-8 Content-Transfer-Encoding: 8BIT X-Content-Filtered-By: Mailman/MimeDel 2.1.23 X-BeenThere: help-guix@gnu.org X-Mailman-Version: 2.1.23 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: help-guix-bounces+larch=yhetil.org@gnu.org Sender: "Help-Guix" X-Migadu-Flow: FLOW_IN ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1624300585; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:mime-version:mime-version: content-type:content-type: content-transfer-encoding:content-transfer-encoding:list-id:list-help: list-unsubscribe:list-subscribe:list-post; bh=SJUUMB9o52eoK+ymvzktIDk1MK0vvrhArQt0AQp7uiI=; b=ZCfTT08Z9z6L4qdE9WwEvdRolgaO/K7ZCGYC+/jv5ekv9PDbTLtBkyIbUN3QPbUkchoVWE rBtybJnBYjeqV/a/3Xk+PwY6RQ4FHTV+obVvgL2AVFjGzy+873L8nGbz1D3O64s28uqm8o I11cIoBTnoFKUOGpE6cxhBBdH3AMRJaOYxnQzEQWCyeNNnJ+/Mvio9v+BHuYyZbWb5EBwT rcuhsjgxSTJWnoX22u63in3qfjdg400shVkLxnSu8pUKYUsg8VK5Vyx8+yvwdjm7zN6D3E Qr6CR1kV4ogoYuIZrhlwBJWglRX+AE620vxzMO7ITtO3TDPMVnKIDwhany/slg== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1624300585; a=rsa-sha256; cv=none; b=nEV38JZ6EZXTIx5RAJTRttzOcdqWO352jvUciUlNgdw4cYRHl0xcyJnEWXG7XBGNyMiDYA 8Fdk8l0rmHbyUNIlKxUSxSN0auTvSHtctCFmaj4TjDrQrtcpmMwqGMZxrvJ6trimwQFRi9 4ZIaXC4YDy+R4W1NyXlK2LwTt8JktxyRnmFJ+6yqUKFSYm2xFpVd+/RbaJq1lwS3ifEYLi 8cEInWG8tMrtJkrKsMeghM1oMUQI0kjkSlmwSkg2aCCUkmKpzb4O19A+XgYRR0tTnoIZjO 7aHJlTPiMGF+FMDUyt3k3p2StQFHbPtPzKq1mdA2mOr8Y75nUGAFn3jvaWhrLg== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=none; spf=pass (aspmx1.migadu.com: domain of help-guix-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=help-guix-bounces@gnu.org X-Migadu-Spam-Score: -1.92 Authentication-Results: aspmx1.migadu.com; dkim=none; dmarc=none; spf=pass (aspmx1.migadu.com: domain of help-guix-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=help-guix-bounces@gnu.org X-Migadu-Queue-Id: 7AE75EF62 X-Spam-Score: -1.92 X-Migadu-Scanner: scn1.migadu.com X-TUID: 3duSBCGdPuWG Hi Guix, I could use some help figuring out what's happened to my store and how to recover. I first noticed the problem when trying to check if a package build reproducably. Unfortunately, I did not capture the output from that, but did capture subsequent commands. It seems as if the metadata has gotten out of sync with the store: jackhill@kalessin ~$ guix gc --verify reading the store... checking path existence... path `/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16' disappeared, but it still has valid referrers! jackhill@kalessin ~$ guix build /gnu/store/zkhymfsbrv0s4y7l778g78k6y65nidxd-gnutls-3.6.16.drv The following graft will be made: /gnu/store/zkhymfsbrv0s4y7l778g78k6y65nidxd-gnutls-3.6.16.drv applying 1 graft for /gnu/store/zkhymfsbrv0s4y7l778g78k6y65nidxd-gnutls-3.6.16.drv ... grafting '/gnu/store/199npi1hcv7zn0r19vl29np6ccshii4p-gnutls-3.6.16-debug' -> '/gnu/store/2vjql2vd6srqxhr0r9xnhclqgc5kxlh1-gnutls-3.6.16-debug'... grafting '/gnu/store/8ixa3p7hwb26warjinffcrvzl064wbcg-gnutls-3.6.16-doc' -> '/gnu/store/ads39f4czri8s1k43qd0qpxi6dr3w0zn-gnutls-3.6.16-doc'... grafting '/gnu/store/akc7l65z459pnifrr6bcm97cjvmpvp9k-gnutls-3.6.16' -> '/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16'... updating '.gnu_debuglink' CRC in '/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16/bin/certtool' updating '.gnu_debuglink' CRC in '/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16/bin/gnutls-cli' updating '.gnu_debuglink' CRC in '/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16/bin/gnutls-cli-debug' updating '.gnu_debuglink' CRC in '/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16/bin/gnutls-serv' updating '.gnu_debuglink' CRC in '/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16/bin/ocsptool' updating '.gnu_debuglink' CRC in '/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16/bin/psktool' updating '.gnu_debuglink' CRC in '/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16/bin/srptool' updating '.gnu_debuglink' CRC in '/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16/lib/guile/3.0/extensions/guile-gnutls-v-2.so.0.0.0' updating '.gnu_debuglink' CRC in '/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16/lib/guile/3.0/site-ccache/gnutls.go' updating '.gnu_debuglink' CRC in '/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16/lib/guile/3.0/site-ccache/gnutls/extra.go' updating '.gnu_debuglink' CRC in '/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16/lib/libgnutls.so.30.28.2' updating '.gnu_debuglink' CRC in '/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16/lib/libgnutlsxx.so.28.1.0' successfully built /gnu/store/zkhymfsbrv0s4y7l778g78k6y65nidxd-gnutls-3.6.16.drv /gnu/store/2vjql2vd6srqxhr0r9xnhclqgc5kxlh1-gnutls-3.6.16-debug /gnu/store/ads39f4czri8s1k43qd0qpxi6dr3w0zn-gnutls-3.6.16-doc /gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16 jackhill@kalessin ~$ guix gc --verify reading the store... checking path existence... path `/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16' disappeared, but it still has valid referrers! jackhill@kalessin ~$ ls -l /gnu/store/^C ^C^C jackhill@kalessin ~$ ls -l /gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16 ls: cannot access '/gnu/store/jlk67v3nddhv0z963wfvahk8fc8gqcz8-gnutls-3.6.16': No such file or directory Then, I ran `guix gc` to collect all the garbage. Trying to rebuild the gnutls derivation results in: jackhill@kalessin ~$ guix build /gnu/store/zkhymfsbrv0s4y7l778g78k6y65nidxd-gnutls-3.6.16.drv 18.6 MB will be downloaded: /gnu/store/2wrp7x9aclqsapm58dz5i654qds8nbb8-guile-2.0.14 /gnu/store/mz5fvdfks10rmwxf29n95bp9bim6wq7g-nettle-3.5.1 /gnu/store/fa6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-2.31 /gnu/store/s3dcqzwqaakv1yx37by9chksdbkgih17-glibc-2.31-static /gnu/store/199npi1hcv7zn0r19vl29np6ccshii4p-gnutls-3.6.16-debug /gnu/store/8ixa3p7hwb26warjinffcrvzl064wbcg-gnutls-3.6.16-doc /gnu/store/akc7l65z459pnifrr6bcm97cjvmpvp9k-gnutls-3.6.16 The following graft will be made: /gnu/store/zkhymfsbrv0s4y7l778g78k6y65nidxd-gnutls-3.6.16.drv substituting /gnu/store/2wrp7x9aclqsapm58dz5i654qds8nbb8-guile-2.0.14... Backtrace: In ice-9/boot-9.scm: 1752:10 19 (with-exception-handler _ _ #:unwind? _ # _) 1752:10 18 (with-exception-handler _ _ #:unwind? _ # _) In guix/scripts/substitute.scm: 771:15 17 (_) In ice-9/exceptions.scm: 406:15 16 (process-substitution # _ "/gnu/store/…" …) In ice-9/boot-9.scm: 1752:10 15 (with-exception-handler _ _ #:unwind? _ # _) In guix/scripts/substitute.scm: 479:9 14 (_) In ice-9/boot-9.scm: 1747:15 13 (with-exception-handler # …) In guix/scripts/substitute.scm: 408:14 12 (_) 382:28 11 (_ #< scheme: https userinfo: #f host: "ci.guix.g…> …) In guix/build/download.scm: 453:4 10 (open-connection-for-uri _ #:timeout _ # _) 251:2 9 (tls-wrap # "ci.guix.gnu.org" # …) 164:15 8 (load-gnutls) In ice-9/boot-9.scm: 3329:6 7 (resolve-interface (gnutls) #:select _ #:hide _ #:prefix …) 1685:16 6 (raise-exception _ #:continuable? _) 1683:16 5 (raise-exception _ #:continuable? _) 1685:16 4 (raise-exception _ #:continuable? _) 1780:13 3 (_ #<&compound-exception components: (#<&error> #<&orig…>) 1685:16 2 (raise-exception _ #:continuable? _) 1683:16 1 (raise-exception _ #:continuable? _) 1685:16 0 (raise-exception _ #:continuable? _) ice-9/boot-9.scm:1685:16: In procedure raise-exception: no code for module (gnutls) substitution of /gnu/store/2wrp7x9aclqsapm58dz5i654qds8nbb8-guile-2.0.14 failed guix build: error: corrupt input while restoring archive from # Both /gnu and /var/guix are on the same btrfs filesystem. I ran a btrfs scrub, and that did not turn up any errors. The other "interesting" thing about this system, is that it once had deduplication turned off, but that has since been turned back on because of bug 47115 [0]. [0] https://issues.guix.gnu.org/47115 Best, Jack