Received: (at 39885) by debbugs.gnu.org; 28 Jun 2020 20:14:41 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Sun Jun 28 16:14:41 2020 Received: from localhost ([127.0.0.1]:47019 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1jpdhI-0004we-N7 for submit <at> debbugs.gnu.org; Sun, 28 Jun 2020 16:14:40 -0400 Received: from eggs.gnu.org ([209.51.188.92]:55892) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <ludo@HIDDEN>) id 1jpdhG-0004wM-6i for 39885 <at> debbugs.gnu.org; Sun, 28 Jun 2020 16:14:40 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:47195) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from <ludo@HIDDEN>) id 1jpdhA-0003Bu-Q6; Sun, 28 Jun 2020 16:14:32 -0400 Received: from [2a01:e0a:1d:7270:af76:b9b:ca24:c465] (port=42162 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from <ludo@HIDDEN>) id 1jpdhA-0007fh-FL; Sun, 28 Jun 2020 16:14:32 -0400 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= <ludo@HIDDEN> To: zimoun <zimon.toutoune@HIDDEN> Subject: Re: bug#39885: Bioconductor URI, fallback and time-machine References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> <CAJ3okZ1Xwd-2WArzNus3xE_KOayDdXPp+ku1SxYBon4Zm0qQQg@HIDDEN> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 11 Messidor an 228 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, 28 Jun 2020 22:14:30 +0200 In-Reply-To: <CAJ3okZ1Xwd-2WArzNus3xE_KOayDdXPp+ku1SxYBon4Zm0qQQg@HIDDEN> (zimoun's message of "Wed, 24 Jun 2020 13:07:13 +0200") Message-ID: <87lfk7gd7d.fsf@HIDDEN> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (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: 39885 Cc: Ricardo Wurmus <rekado@HIDDEN>, 39885 <at> debbugs.gnu.org, Tobias Geerinckx-Rice <me@HIDDEN> X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -3.3 (---) Hi, zimoun <zimon.toutoune@HIDDEN> skribis: > b) The fallback URI in guix/build-system/r.scm(bioconductor-uri) > added by commit c586f427b4831b9b492e5b900b2226e898b8fcfa is not > correct, if I do not misread: > > "https://bioconductor.org/packages/3.10/bioc/src/contrib/Archive/GenomeGr= aphs_1.46.0.tar.gz" > 404 "Not Found" > > The correct seems to be (without Archive): > > https://bioconductor.org/packages/3.10/bioc/src/contrib/GenomeGraphs_1.46= .0.tar.gz Could you provide a patch for this? Thanks, Ludo=E2=80=99.
bug-guix@HIDDEN:bug#39885; Package guix.
Full text available.Received: (at 39885) by debbugs.gnu.org; 24 Jun 2020 11:07:33 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Wed Jun 24 07:07:33 2020 Received: from localhost ([127.0.0.1]:37848 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1jo3Fd-0003gC-6N for submit <at> debbugs.gnu.org; Wed, 24 Jun 2020 07:07:33 -0400 Received: from mail-qt1-f193.google.com ([209.85.160.193]:35378) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <zimon.toutoune@HIDDEN>) id 1jo3Fb-0003fz-0X for 39885 <at> debbugs.gnu.org; Wed, 24 Jun 2020 07:07:31 -0400 Received: by mail-qt1-f193.google.com with SMTP id z1so1326167qtn.2 for <39885 <at> debbugs.gnu.org>; Wed, 24 Jun 2020 04:07:31 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:references:in-reply-to:from:date:message-id:subject:to; bh=Slqk+sBtPl9fPNSnQ7j0tNwurqWmGEnBR3I9Lv5v1vM=; b=XxlfNeoXbbaXVZetzoBj80Gb1GDFstyV/vFmnJBblZ1eTVXw5T+a/+LwZ6Ju7D56+d n+X79YtjVv0aHkuVC/vGZb+adyIxgUnX315ypUL0bwSXrpNXpzP/wyoJYG7uWX8ZA0bn DPb3ho9tgzU1ox4HwX2DsoaMcfHANNXjnrEi+W9FYV3ac0ayiicVCA3GVRvoffB1cmo5 rv6vi8AZAJlIB0i8E8KfouMXStsuGSQBM9X+tzGGVFcUzCQC+WJGftd37NeUROYcZa+I wUAU6gtyZBsp2WRN51h8rPxrUiFzELoczNyGH70hztZOe9n3cDmoju2AspO687WtWpf6 wWHA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to; bh=Slqk+sBtPl9fPNSnQ7j0tNwurqWmGEnBR3I9Lv5v1vM=; b=ZAjknGAD0ag0SwS1U3gIF3DVeNZmbuQeG9cgIgIZqUEAwWnXxM2sFlb5hAV8z9b1BY Ax4g2uvOSKWWECsfvRweGsEP0kVp9A6D7DhbGtmBmGPDbgkfj2FczgevQ2iOpo5eP75q gwvTWmk78/hpKDoDCQ3ViIoLS1mW4XUy/HJDhhDbVfl80MHC2r9Ob9eyZL/m5wL9CdLh aiL96djCb059JBNvAPusGIR7AhsJR5HpBdeUdFuNVmd/3vx8DLuAF8x/o4i//cQbhRxz /Kn6iYVd0uRoHUXKlEWyJAq8wo3y1r+jvI8+clOZP+KmRehWGiPdEYyL2dy2+xZIUKXL 9MzA== X-Gm-Message-State: AOAM533m/hOsTr8/JR+rxoFejYJQkE3Xamb7n73gWnu9fRfGd/eTLMax GlXSx40AJU2XJXcA0V5a05h4/6YOqkxZbtJcsbiWYxxDH60= X-Google-Smtp-Source: ABdhPJyO6Hbb2ZLpgJN9lzKdOjCKbD5bMue1OUOHRlZUKA4tDb5A8ZTSAWzh5eV7KAtEB/AkpJd3EGaIHITsBrIX7C8= X-Received: by 2002:aed:3608:: with SMTP id e8mr26717302qtb.186.1592996844836; Wed, 24 Jun 2020 04:07:24 -0700 (PDT) MIME-Version: 1.0 References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> In-Reply-To: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> From: zimoun <zimon.toutoune@HIDDEN> Date: Wed, 24 Jun 2020 13:07:13 +0200 Message-ID: <CAJ3okZ1Xwd-2WArzNus3xE_KOayDdXPp+ku1SxYBon4Zm0qQQg@HIDDEN> Subject: Re: bug#39885: Bioconductor URI, fallback and time-machine To: 39885 <at> debbugs.gnu.org, Tobias Geerinckx-Rice <me@HIDDEN>, Ricardo Wurmus <rekado@HIDDEN> Content-Type: text/plain; charset="UTF-8" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 39885 X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) Dear, The time-machine is broken for some BioConductor packages.. For an example, consider the package "r-genomegraphs" which has been removed from the BioConductor in 3.11 release. (Well, now the issue is mitigated because ci.guix.gnu.org serves a lot of upstream substitutes but ci.guix.gnu.org could be down. Other said, we should use the upstream resources where they are available.) Concretely, there are 2 issues: a) What to do for the removed packages? For 3.11, the list is there [1]. Do we keep them in gnu/packages/bioconductor.scm but then 'bioconductor-uri' needs some tweaks? Or do we transfer them to the channel guix-past (for example)? b) The fallback URI in guix/build-system/r.scm(bioconductor-uri) added by commit c586f427b4831b9b492e5b900b2226e898b8fcfa is not correct, if I do not misread: --8<---------------cut here---------------start------------->8--- "https://bioconductor.org/packages/3.10/bioc/src/contrib/Archive/GenomeGraphs_1.46.0.tar.gz" 404 "Not Found" --8<---------------cut here---------------end--------------->8--- The correct seems to be (without Archive): https://bioconductor.org/packages/3.10/bioc/src/contrib/GenomeGraphs_1.46.0.tar.gz All the best, simon 1: https://bioconductor.org/news/bioc_3_11_release/#deprecated-and-defunct-packages
bug-guix@HIDDEN:bug#39885; Package guix.
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That's all we know. X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_NONE=-0.0001, SPF_PASS=-0.001, URIBL_BLOCKED=0.001 autolearn=_AUTOLEARN X-Spam_action: no action X-Spam-Score: -1.3 (-) X-Debbugs-Envelope-To: submit Cc: Tobias Geerinckx-Rice <me@HIDDEN>, bug-guix@HIDDEN X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -2.3 (--) Dear Ricardo, On Mon, 23 Mar 2020 at 22:21, Ricardo Wurmus <rekado@HIDDEN> wrote: > > a) Add the Bioconductor release (known at packaging time) to all the > > packages; provide as argument to 'bioconductor-uri'. > > b) Add more URLs to fallback. > > > > As discussed on IRC, Tobias seems more inclined with the option a) and > > I am more in favour of option b. > > I think option a) is more explicit, which is probably what we generally > want to future-proof the time-machine. Fallbacks are okay in the case > of the CRAN URL where it=E2=80=99s not necessarily clear when a package t= arball > moves from the release location to the archive. > > In the case of Bioconductor URLs it seems that we can afford to be a bit > more accurate. We are going for option a) which means rename all the URLs, right? Because it is a lot, I suggest to first address the bug#36805, i.e., provide as an argument the BioConductor version to 'bioconductor-uri' and applies this policy to all the new packages or any update of them. Moreover, I have suggested to reorganise bioconductor.scm, bioinformatics.scm, cran.scm, etc. and I have not dedicated enough time to this boring task. But because I am working remotely (semi-lockdown), I plan to work on it next week and so this change of URLs could be part of the big reorganisation. What do you think? [1] http://issues.guix.gnu.org/issue/36805 All the best, simon
bug-guix@HIDDEN:bug#39885; Package guix.
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mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@HIDDEN; dmarc=pass header.from=<rekado@HIDDEN> header.from=<rekado@HIDDEN> DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1584998457; s=zoho; d=elephly.net; i=rekado@HIDDEN; h=References:From:To:Cc:Subject:In-reply-to:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding; bh=n8NrkkNG/fHNgvYtRKhtjssxxEvyVaopQnSHXvx34dE=; b=i3vn69XpykUi2P7y54xdslnk30VEVJWPXhVHG6fCKtbzbtMJUEVas20Ut1H5JOC+ B+0OBWmmxGEqyiFAcQFtv1BiMSfpwHX6a33niCmGHxXUGEmXPdkAHezD3ALXvDj9Qax T00Ix/Bsx0HzwAi2t0dIfnmB7A0jjsL+YyxoCCsM= Received: from localhost (p54AD4C06.dip0.t-ipconnect.de [84.173.76.6]) by mx.zohomail.com with SMTPS id 158499845592892.48841001393998; Mon, 23 Mar 2020 14:20:55 -0700 (PDT) References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> User-agent: mu4e 1.2.0; emacs 26.3 From: Ricardo Wurmus <rekado@HIDDEN> To: zimoun <zimon.toutoune@HIDDEN> Subject: Re: Bioconductor URI, fallback and time-machine In-reply-to: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Mon, 23 Mar 2020 22:20:52 +0100 Message-ID: <87ftdylqdn.fsf@HIDDEN> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] [fuzzy] X-Received-From: 136.143.188.51 X-Spam-Score: 0.3 (/) X-Debbugs-Envelope-To: submit Cc: Tobias Geerinckx-Rice <me@HIDDEN>, bug-guix@HIDDEN X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -0.7 (/) zimoun <zimon.toutoune@HIDDEN> writes: > 1. when Bioconductor updates their release, some package versions are > updated too, and so, the upstream return 404. > 2. for this reason 1., the "guix time-machine" is broken for all the > Bioconductor packages, at least if Berlin or SWH does not have a > substitute; which is not expected for 'annotation' packages. > > However, the Bioconductor archive still serves the old release, i.e., > > https://bioconductor.org/packages/3.x/data/<type-url-part>/src/contrib/<u= pstream-name>-<version>.tar.gz > > > The ways to fix the both issues are: > > a) Add the Bioconductor release (known at packaging time) to all the > packages; provide as argument to 'bioconductor-uri'. > b) Add more URLs to fallback. > > As discussed on IRC, Tobias seems more inclined with the option a) and > I am more in favour of option b. I think option a) is more explicit, which is probably what we generally want to future-proof the time-machine. Fallbacks are okay in the case of the CRAN URL where it=E2=80=99s not necessarily clear when a package tar= ball moves from the release location to the archive. In the case of Bioconductor URLs it seems that we can afford to be a bit more accurate. --=20 Ricardo
bug-guix@HIDDEN:bug#39885; Package guix.
Full text available.Received: (at submit) by debbugs.gnu.org; 3 Mar 2020 15:59:21 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Tue Mar 03 10:59:21 2020 Received: from localhost ([127.0.0.1]:39878 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1j99x2-0000FJ-UH for submit <at> debbugs.gnu.org; Tue, 03 Mar 2020 10:59:21 -0500 Received: from lists.gnu.org ([209.51.188.17]:55483) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <zimon.toutoune@HIDDEN>) id 1j99x0-0000FA-VN for submit <at> debbugs.gnu.org; Tue, 03 Mar 2020 10:59:19 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:51176) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from <zimon.toutoune@HIDDEN>) id 1j99wz-00031a-KH for bug-guix@HIDDEN; Tue, 03 Mar 2020 10:59:18 -0500 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=BAYES_50,FREEMAIL_FROM, URIBL_BLOCKED autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from <zimon.toutoune@HIDDEN>) id 1j99wy-0004eG-3x for bug-guix@HIDDEN; Tue, 03 Mar 2020 10:59:17 -0500 Received: from mail-qv1-xf30.google.com ([2607:f8b0:4864:20::f30]:34213) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from <zimon.toutoune@HIDDEN>) id 1j99wx-0004ds-T3 for bug-guix@HIDDEN; Tue, 03 Mar 2020 10:59:16 -0500 Received: by mail-qv1-xf30.google.com with SMTP id o18so1906342qvf.1 for <bug-guix@HIDDEN>; Tue, 03 Mar 2020 07:59:15 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:from:date:message-id:subject:to; bh=iBVlumUQoU0iu5kIlGcsDSeMtZQUgC9C48NqR/D85OY=; b=SWVrpEqfF2aB1utVLia3sZ+B44JDgBOpz39r9J5wrkMBha/bLLMxXlcR3x2Y1lYhKK yeg0iad4+lJi7raN/al0pW1JSfLOyCaEBci7MEmDuQ2HiTnPz8YW5KbmKK5YcgqU1zkM P5ukzP3VGHDu1CIM5RGDkgSZ4ysWCWusQoVedwuyz6II4JadCAKSDf4akG2DP4p22/UT 2Z0h/1MQoUw8iyA+1z239MEU6Q8Z16wQ5mhdHebozHWcvnfmJoo+LDNH6i4yw7ofG2g0 ODILzSRer0d66rsHB2VrS3yklpAezeoS92faLN35Zq575aTaHThXK+T0jx+KA1Kshu9j qbxg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=iBVlumUQoU0iu5kIlGcsDSeMtZQUgC9C48NqR/D85OY=; b=nR8T9DK32NJT7FoD/agU4nq+g4feTvJztCmwt+uZGwMngbZaQzrwWr8Ij7MkXzhVGN 7sB7xYN3ldhf0VVtpbD19PfgYV24Ojr+sYQ/5VEoCZO6ISo8lpG88TF2Y0/oOXqv6IAf YAx2d+bfaFb0tjpAmP/BmoHjWmG0cLmWDPgx6k5HnetbV3yWmsaSwmIxV0hYTnp1VT7E ypFbR/ke+r8vvPNP8GxD0Ix2ZUGEvP3jQ1eBQiVW5yLjiuMRDPxkn2fnfdDRXGco2xQ6 GY0TYD6iM8z7KZPs7fltlOLooecBrwNnoCbBYioyTY/WHFIWtRztmCMem68OPaA7Z/6i gOow== X-Gm-Message-State: ANhLgQ2Z7ZnUW3yatQ0Tkv56PEfjkuc2/hdBj5bW2EbaUta7wyeiyIuj GpFeO5sjy/ecFeYJnWKnh9veXy/PSbn9/tZb+LvB5nqo X-Google-Smtp-Source: ADFU+vt4BmdA4UtrRMxkWt0vSOTQASTnc+TDTD+akngrfOIJ2NwFCm/TJPZSPWq9VDv77/05YSJvy2fThlOxOaV1Y7Q= X-Received: by 2002:ad4:4674:: with SMTP id z20mr4612454qvv.6.1583251154670; Tue, 03 Mar 2020 07:59:14 -0800 (PST) MIME-Version: 1.0 From: zimoun <zimon.toutoune@HIDDEN> Date: Tue, 3 Mar 2020 16:59:03 +0100 Message-ID: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> Subject: Bioconductor URI, fallback and time-machine To: bug-guix@HIDDEN, Tobias Geerinckx-Rice <me@HIDDEN>, Ricardo Wurmus <rekado@HIDDEN> Content-Type: multipart/mixed; boundary="000000000000aa3660059ff5625d" X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-Received-From: 2607:f8b0:4864:20::f30 X-Spam-Score: 0.3 (/) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -0.7 (/) --000000000000aa3660059ff5625d Content-Type: text/plain; charset="UTF-8" Dear, Currently, the URI scheme (see 'bioconductor-uri' in guix/build-system/r.scm) is: https://bioconductor.org/packages/release/data/<type-url-part>/src/contrib/<upstream-name>-<version>.tar.gz which leads to 2 issues: 1. when Bioconductor updates their release, some package versions are updated too, and so, the upstream return 404. 2. for this reason 1., the "guix time-machine" is broken for all the Bioconductor packages, at least if Berlin or SWH does not have a substitute; which is not expected for 'annotation' packages. However, the Bioconductor archive still serves the old release, i.e., https://bioconductor.org/packages/3.x/data/<type-url-part>/src/contrib/<upstream-name>-<version>.tar.gz The ways to fix the both issues are: a) Add the Bioconductor release (known at packaging time) to all the packages; provide as argument to 'bioconductor-uri'. b) Add more URLs to fallback. As discussed on IRC, Tobias seems more inclined with the option a) and I am more in favour of option b. Attached, a quick patch showing the option b). Please also consider #36805 which was never merged or closed. http://issues.guix.gnu.org/issue/36805 All the best, simon --000000000000aa3660059ff5625d Content-Type: text/x-patch; charset="US-ASCII"; name="0001-build-system-r-Use-Bioconductor-old-releases-to-fall.patch" Content-Disposition: attachment; filename="0001-build-system-r-Use-Bioconductor-old-releases-to-fall.patch" Content-Transfer-Encoding: base64 Content-ID: <f_k7c2u5mz0> X-Attachment-Id: f_k7c2u5mz0 RnJvbSA4N2U3M2UwMjIwMmZlNWUzNDJkNjhmMWZiMTdlZmRkNDQyNTczN2NkIE1vbiBTZXAgMTcg MDA6MDA6MDAgMjAwMQpGcm9tOiB6aW1vdW4gPHppbW9uLnRvdXRvdW5lQGdtYWlsLmNvbT4KRGF0 ZTogVHVlLCAzIE1hciAyMDIwIDE2OjUzOjM5ICswMTAwClN1YmplY3Q6IFtQQVRDSF0gYnVpbGQt c3lzdGVtOiByOiBVc2UgQmlvY29uZHVjdG9yIG9sZCByZWxlYXNlcyB0byBmYWxsYmFjay4KCiog Z3VpeC9idWlsZC1zeXN0ZW0vci5zY20gKGJpb2NvbmR1Y3Rvci11cmkpOiBFeHRlbmQgdGhlIGZh bGxiYWNrIGxpc3QuCi0tLQogZ3VpeC9idWlsZC1zeXN0ZW0vci5zY20gfCAyMSArKysrKysrKysr KystLS0tLS0tLS0KIDEgZmlsZSBjaGFuZ2VkLCAxMiBpbnNlcnRpb25zKCspLCA5IGRlbGV0aW9u cygtKQoKZGlmZiAtLWdpdCBhL2d1aXgvYnVpbGQtc3lzdGVtL3Iuc2NtIGIvZ3VpeC9idWlsZC1z eXN0ZW0vci5zY20KaW5kZXggMmQzMjg3NjRiMC4uODYzOGUxYjg4OCAxMDA2NDQKLS0tIGEvZ3Vp eC9idWlsZC1zeXN0ZW0vci5zY20KKysrIGIvZ3VpeC9idWlsZC1zeXN0ZW0vci5zY20KQEAgLTU0 LDE1ICs1NCwxOCBAQCByZWxlYXNlIGNvcnJlc3BvbmRpbmcgdG8gTkFNRSBhbmQgVkVSU0lPTi4i CiAgICAgICAgICAgICAgICAgICAgICAgICAgKCdhbm5vdGF0aW9uICIvZGF0YS9hbm5vdGF0aW9u IikKICAgICAgICAgICAgICAgICAgICAgICAgICAoJ2V4cGVyaW1lbnQgIi9kYXRhL2V4cGVyaW1l bnQiKQogICAgICAgICAgICAgICAgICAgICAgICAgIChfICIvYmlvYyIpKSkpCi0gICAgKGxpc3Qg KHN0cmluZy1hcHBlbmQgImh0dHBzOi8vYmlvY29uZHVjdG9yLm9yZy9wYWNrYWdlcy9yZWxlYXNl IgotICAgICAgICAgICAgICAgICAgICAgICAgIHR5cGUtdXJsLXBhcnQKLSAgICAgICAgICAgICAg ICAgICAgICAgICAiL3NyYy9jb250cmliLyIKLSAgICAgICAgICAgICAgICAgICAgICAgICBuYW1l ICJfIiB2ZXJzaW9uICIudGFyLmd6IikKLSAgICAgICAgICA7OyBUT0RPOiB1c2UgJWJpb2NvbmR1 Y3Rvci12ZXJzaW9uIGZyb20gKGd1aXggaW1wb3J0IGNyYW4pCi0gICAgICAgICAgKHN0cmluZy1h cHBlbmQgImh0dHBzOi8vYmlvY29uZHVjdG9yLm9yZy9wYWNrYWdlcy8zLjEwIgotICAgICAgICAg ICAgICAgICAgICAgICAgIHR5cGUtdXJsLXBhcnQKLSAgICAgICAgICAgICAgICAgICAgICAgICAi L3NyYy9jb250cmliL0FyY2hpdmUvIgotICAgICAgICAgICAgICAgICAgICAgICAgIG5hbWUgIl8i IHZlcnNpb24gIi50YXIuZ3oiKSkpKQorICAgIChhcHBlbmQgKGxpc3QgKHN0cmluZy1hcHBlbmQg Imh0dHBzOi8vYmlvY29uZHVjdG9yLm9yZy9wYWNrYWdlcy9yZWxlYXNlIgorICAgICAgICAgICAg ICAgICAgICAgICAgICAgICAgICAgdHlwZS11cmwtcGFydAorICAgICAgICAgICAgICAgICAgICAg ICAgICAgICAgICAgIi9zcmMvY29udHJpYi8iCisgICAgICAgICAgICAgICAgICAgICAgICAgICAg ICAgICBuYW1lICJfIiB2ZXJzaW9uICIudGFyLmd6IikpCisgICAgICAgICAgICAobWFwIChsYW1i ZGEgKHJlbGVhc2UpCisgICAgICAgICAgICAgICAgICAgKHN0cmluZy1hcHBlbmQgImh0dHBzOi8v YmlvY29uZHVjdG9yLm9yZy9wYWNrYWdlcy8iCisgICAgICAgICAgICAgICAgICAgICAgICAgICAg ICAgICAgcmVsZWFzZQorICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgIHR5cGUtdXJs LXBhcnQKKyAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAiL3NyYy9jb250cmliLyIK KyAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICBuYW1lICJfIiB2ZXJzaW9uICIudGFy Lmd6IikpCisgICAgICAgICAgICAgICAgIChsaXN0IChAQCAoZ3VpeCBpbXBvcnQgY3JhbikgJWJp b2NvbmR1Y3Rvci12ZXJzaW9uKQorICAgICAgICAgICAgICAgICAgICAgICAiMy45IiAiMy44IiAi My43IikpKSkpCiAKIChkZWZpbmUgJXItYnVpbGQtc3lzdGVtLW1vZHVsZXMKICAgOzsgQnVpbGQt c2lkZSBtb2R1bGVzIGltcG9ydGVkIGJ5IGRlZmF1bHQuCi0tIAoyLjI1LjAKCg== --000000000000aa3660059ff5625d--
zimoun <zimon.toutoune@HIDDEN>:bug-guix@HIDDEN.
Full text available.bug-guix@HIDDEN:bug#39885; Package guix.
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