From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp11.migadu.com ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms5.migadu.com with LMTPS id eIJWLMOG1WLzOQEAbAwnHQ (envelope-from ) for ; Mon, 18 Jul 2022 18:13:55 +0200 Received: from aspmx1.migadu.com ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp11.migadu.com with LMTPS id 6MhjLMOG1WLugAEA9RJhRA (envelope-from ) for ; Mon, 18 Jul 2022 18:13:55 +0200 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 499F53D056 for ; Mon, 18 Jul 2022 18:13:55 +0200 (CEST) Received: from localhost ([::1]:45694 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1oDTNa-0005Wq-En for larch@yhetil.org; Mon, 18 Jul 2022 12:13:54 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:56324) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oDTMl-00056h-Kq for bug-guix@gnu.org; Mon, 18 Jul 2022 12:13:05 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:54137) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1oDTMk-0007m2-BN for bug-guix@gnu.org; Mon, 18 Jul 2022 12:13:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1oDTMj-0001ZV-Un for bug-guix@gnu.org; Mon, 18 Jul 2022 12:13:01 -0400 X-Loop: help-debbugs@gnu.org Subject: bug#39885: Bioconductor URI, fallback and time-machine Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: bug-guix@gnu.org Resent-Date: Mon, 18 Jul 2022 16:13:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 39885 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: 39885@debbugs.gnu.org Cc: rekado@elephly.net, Timothy Sample , me@tobias.gr Received: via spool by 39885-submit@debbugs.gnu.org id=B39885.16581607656008 (code B ref 39885); Mon, 18 Jul 2022 16:13:01 +0000 Received: (at 39885) by debbugs.gnu.org; 18 Jul 2022 16:12:45 +0000 Received: from localhost ([127.0.0.1]:51894 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oDTMS-0001Yp-Cb for submit@debbugs.gnu.org; Mon, 18 Jul 2022 12:12:45 -0400 Received: from mail-wm1-f42.google.com ([209.85.128.42]:50987) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oDTMM-0001YP-QD for 39885@debbugs.gnu.org; Mon, 18 Jul 2022 12:12:42 -0400 Received: by mail-wm1-f42.google.com with SMTP id p4so7448465wms.0 for <39885@debbugs.gnu.org>; Mon, 18 Jul 2022 09:12:38 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:references:date:in-reply-to:message-id :user-agent:mime-version; bh=AuK1ryknu/XtQ8RJ8C0uu7LjTXG4NvbJ/Xh3Xyf/vsw=; b=W3DWwl2utCyZkSJD06BO8DOo1avOcez4/eIjm/daaCSNnSrqwukwtvOjU7LWHuPOlH 2xIAdlKF5nwK8o+/aw5GG0Am/2VWAJQv0Amhi1Ka+jQsSJAO0m8Jzq5+6CXGbq/wSwoD tYwTBscLMNMBxM9Gdzu7EtqJqchmoIKdHFPRN63HeZfCuIDukklwM/9/ZQj5i0ffbJoq fQ+r9EqYKGPf/mZFjDpR3oCRfDTgul5//Ym/EN7wEyVvVVK0WpmU3GgMs1ZPzzAtftJp VKcHk1LuSXqYPojKIS/ROhq5MeKdZc6zUf1pqNrAmNf5Tlf0NiCQ5sJohnfQWpqfkMFl YR+w== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:references:date:in-reply-to :message-id:user-agent:mime-version; bh=AuK1ryknu/XtQ8RJ8C0uu7LjTXG4NvbJ/Xh3Xyf/vsw=; b=1OgTRO2OxWydK+Z5nXLihYd6Uv2Tzh5u2Cx+jSMtrd3egqzaodml8o4bkcJSTrgmYn btTHJZ5Mjkpga03FaUPv6FPWsRwNoKH4PIVuZBWe6Xl6Orma0EJM3pED54fADy1FdHBc jJcxcz/xvWuh8Q8yhdhPVwXUMA5fG0a3nlxw/ZXnZP6zgKxFO09DokCavQh/3yfJP5lC 9YmcXmcNM07j7C+2E4I/GMlJE7Rh10syyV15983+kpOTzl0hqSOMPPzVR3m2gi0u8FoI uDvPTdOUC+bjhsAJgpMKkSXBzM5WFJaqjFZDrtyfYNBE/RvYvvRJ7RWLgXmls/xwRWF7 Uy1A== X-Gm-Message-State: AJIora9D8UxrFbV+B29chR2tdjwAskjnpIPOUmDWZsXJ89XmYentWzx/ lyqaFuH6bXFpy4r0/ZkQknU= X-Google-Smtp-Source: AGRyM1uOJjjXO0uunPEsCnu3YkeXoX2zVzJLVma6SnviSyServPB3EewB4iUbffIxLGzDurMwM+a1g== X-Received: by 2002:a05:600c:3506:b0:3a2:feb0:9f8e with SMTP id h6-20020a05600c350600b003a2feb09f8emr24044199wmq.42.1658160751899; Mon, 18 Jul 2022 09:12:31 -0700 (PDT) Received: from pfiuh07 ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id j16-20020a5d4530000000b0021d6d9c0bd9sm11011383wra.82.2022.07.18.09.12.31 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 18 Jul 2022 09:12:31 -0700 (PDT) From: zimoun References: Date: Mon, 18 Jul 2022 18:03:04 +0200 In-Reply-To: (zimoun's message of "Tue, 3 Mar 2020 16:59:03 +0100") Message-ID: <87lesqmmrr.fsf@gmail.com> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/27.2 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: bug-guix@gnu.org List-Id: Bug reports for GNU Guix List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: bug-guix-bounces+larch=yhetil.org@gnu.org Sender: "bug-Guix" X-Migadu-Flow: FLOW_IN X-Migadu-To: larch@yhetil.org X-Migadu-Country: US ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1658160835; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-type:content-type:resent-cc:resent-from:resent-sender: resent-message-id:in-reply-to:in-reply-to:references:references: list-id:list-help:list-unsubscribe:list-subscribe:list-post: dkim-signature; bh=AuK1ryknu/XtQ8RJ8C0uu7LjTXG4NvbJ/Xh3Xyf/vsw=; b=hyDsvB2oBNfbe3vPp06xF1nX49izmPvjcK2sgwXdMEn9QAz0FPdanjYJrGDtpeXsf5vrsF 74/d8wv1Jsub3PfE8p25ACOUQ6EXB4I5aSVWl6sa3Rj1u3QWZHmBdNrptbRMAmC1b6JQ3M wP+pQh5+Em8FIQkBy/q/O3mu4Bmx/WEIgTW7DGkIGwoWrgor4pW8FuthVJg5CUCxckdAeA dcmkEoVRdbho6yj8e15mMod85SCFGoL+f9+X5LMhvN/fB5wu4LcTKRSkU2zuJ2tOlh3lND ubim3KxYABzjE+hUNlmRuF284JrjtbHGdIS0TwSOV/KRsZTiDdxx1mNFjaxMbg== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1658160835; a=rsa-sha256; cv=none; b=IV8GIy2y3qX2MQnVxqeNRLJcr6LSWcPg7MVW0IZXg2RyElrwrCG1xmxWXzVgMQgSy5feqw v6YE5amHuXk5EGQGhwHa4rlsB3CpZhSiMZy/RRX9deg5nuntrolo5XFkZeqM4Hf9DUY2Qs WgxyM5aC9NKFPejrSZ5a0dERNepl2lufkkPuupFGguEE/9RC8asxTx3UcvbMpuXoAQjgVb cSPzuiyQ2gBIIp2cf0zjmwk2f2yPzQ4eCNg6dXe+3Rak45lVm1XNY+mKVAS0hTnVCHSPxk 8Nyuv6YcCeM39Nc1w4x/AEmVpocfuN+YGregUp5JKtEo5CRAzlITPyiTLEG9rA== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=W3DWwl2u; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of "bug-guix-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="bug-guix-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: 5.46 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=W3DWwl2u; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of "bug-guix-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="bug-guix-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: 499F53D056 X-Spam-Score: 5.46 X-Migadu-Scanner: scn0.migadu.com X-TUID: lA1zgCUCcRCL Hi, Since 2020, I provided several examples of breakage with bug#39885 [1]. Here another one: --8<---------------cut here---------------start------------->8--- $ guix time-machine --commit=77e2de365497bf4c8b81cbd78624f78293490485 \ -- build r-biocneighbors -S substitute: updating substitutes from 'https://ci.guix.gnu.org'... 100.0% substitute: updating substitutes from 'https://bordeaux.guix.gnu.org'... 100.0% The following derivation will be built: /gnu/store/q9ggmh5a9bzmnr49p10x1w9sv6pzjarv-BiocNeighbors_1.4.1.tar.gz.drv building /gnu/store/q9ggmh5a9bzmnr49p10x1w9sv6pzjarv-BiocNeighbors_1.4.1.tar.gz.drv... Starting download of /gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz >From https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.4.1.tar.gz... download failed "https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.4.1.tar.gz" 404 "Not Found" Starting download of /gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz >From https://bioconductor.org/packages/3.10/bioc/src/contrib/Archive/BiocNeighbors_1.4.1.tar.gz... download failed "https://bioconductor.org/packages/3.10/bioc/src/contrib/Archive/BiocNeighbors_1.4.1.tar.gz" 404 "Not Found" Starting download of /gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz >From https://ci.guix.gnu.org/file/BiocNeighbors_1.4.1.tar.gz/sha256/05vi1cij37s8wgj92k3l6a3f3dwldj8jvijdp4695zczka6kypdf... download failed "https://ci.guix.gnu.org/file/BiocNeighbors_1.4.1.tar.gz/sha256/05vi1cij37s8wgj92k3l6a3f3dwldj8jvijdp4695zczka6kypdf" 404 "Not Found" Starting download of /gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz >From https://tarballs.nixos.org/sha256/05vi1cij37s8wgj92k3l6a3f3dwldj8jvijdp4695zczka6kypdf... download failed "https://tarballs.nixos.org/sha256/05vi1cij37s8wgj92k3l6a3f3dwldj8jvijdp4695zczka6kypdf" 404 "Not Found" Starting download of /gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz >From https://archive.softwareheritage.org/api/1/content/sha256:ae5d3f8d9a9ffd920cb94dc62d916c94b7e18632744c91e4e3489f21230b7117/raw/... download failed "https://archive.softwareheritage.org/api/1/content/sha256:ae5d3f8d9a9ffd920cb94dc62d916c94b7e18632744c91e4e3489f21230b7117/raw/" 404 "Not Found" Starting download of /gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz >From https://web.archive.org/web/20220718175152/https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.4.1.tar.gz... download failed "https://web.archive.org/web/20220718175152/https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.4.1.tar.gz" 404 "NOT FOUND" Trying to use Disarchive to assemble /gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz... could not find its Disarchive specification failed to download "/gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz" from ("https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.4.1.tar.gz" "https://bioconductor.org/packages/3.10/bioc/src/contrib/Archive/BiocNeighbors_1.4.1.tar.gz") builder for `/gnu/store/q9ggmh5a9bzmnr49p10x1w9sv6pzjarv-BiocNeighbors_1.4.1.tar.gz.drv' failed to produce output path `/gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz' build of /gnu/store/q9ggmh5a9bzmnr49p10x1w9sv6pzjarv-BiocNeighbors_1.4.1.tar.gz.drv failed View build log at '/var/log/guix/drvs/q9/ggmh5a9bzmnr49p10x1w9sv6pzjarv-BiocNeighbors_1.4.1.tar.gz.drv.gz'. guix build: error: build of `/gnu/store/q9ggmh5a9bzmnr49p10x1w9sv6pzjarv-BiocNeighbors_1.4.1.tar.gz.drv' failed --8<---------------cut here---------------end--------------->8--- Well, several comments: 1. Berlin or Bordeaux do not have it as substitutes, 2. Diasarchive does not have it, 3. Many others neither. but the question in the first place is: why is Bioconductor failing? Because they do ugly things! Our history reads: f431d5e299 Sun Dec 15 15:38:51 2019 +0100 guix: Upgrade to Bioconductor 3.10 12e2aa96dc Sun Dec 15 15:38:55 2019 +0100 gnu: r-biocneighbors: Update to 1.4.1. aece78fe2f Sun Mar 1 23:38:12 2020 +0100 gnu: r-biocneighbors: Update to 1.4.2. 8e518d4802 Sat Jun 13 01:19:38 2020 +0200 guix: Update to Bioconductor 3.11. which means that Bioconductor removes v1.4.1 from their URI scheme (even, I do not know if the tarball is still available on their infra) and despite the fact Bioconductor v3.10 had released v1.4.1, then it is not stable. At the cost of more bandwidth, we could switch from url-fetch to git-fetch. Or we also could examine why Disarchive is failing here. 1: Cheers, simon