GNU bug report logs - #39885
Bioconductor URI, fallback and time-machine

Please note: This is a static page, with minimal formatting, updated once a day.
Click here to see this page with the latest information and nicer formatting.

Package: guix; Reported by: zimoun <zimon.toutoune@HIDDEN>; dated Tue, 3 Mar 2020 16:00:02 UTC; Maintainer for guix is bug-guix@HIDDEN.

Message received at 39885 <at> debbugs.gnu.org:


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.




Information forwarded to bug-guix@HIDDEN:
bug#39885; Package guix. Full text available.

Message received at 39885 <at> debbugs.gnu.org:


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




Information forwarded to bug-guix@HIDDEN:
bug#39885; Package guix. Full text available.

Message received at submit <at> debbugs.gnu.org:


Received: (at submit) by debbugs.gnu.org; 21 May 2020 23:29:24 +0000
From debbugs-submit-bounces <at> debbugs.gnu.org Thu May 21 19:29:24 2020
Received: from localhost ([127.0.0.1]:57557 helo=debbugs.gnu.org)
	by debbugs.gnu.org with esmtp (Exim 4.84_2)
	(envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>)
	id 1jbucu-0002B4-47
	for submit <at> debbugs.gnu.org; Thu, 21 May 2020 19:29:24 -0400
Received: from lists.gnu.org ([209.51.188.17]:52062)
 by debbugs.gnu.org with esmtp (Exim 4.84_2)
 (envelope-from <zimon.toutoune@HIDDEN>) id 1jbucs-0002Ax-Fa
 for submit <at> debbugs.gnu.org; Thu, 21 May 2020 19:29:22 -0400
Received: from eggs.gnu.org ([2001:470:142:3::10]:35370)
 by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256)
 (Exim 4.90_1) (envelope-from <zimon.toutoune@HIDDEN>)
 id 1jbucs-0008Cf-8k
 for bug-guix@HIDDEN; Thu, 21 May 2020 19:29:22 -0400
Received: from mail-qk1-x729.google.com ([2607:f8b0:4864:20::729]:39182)
 by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128)
 (Exim 4.90_1) (envelope-from <zimon.toutoune@HIDDEN>)
 id 1jbucq-000650-Ku
 for bug-guix@HIDDEN; Thu, 21 May 2020 19:29:21 -0400
Received: by mail-qk1-x729.google.com with SMTP id w3so3553176qkb.6
 for <bug-guix@HIDDEN>; Thu, 21 May 2020 16:29:20 -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
 :cc:content-transfer-encoding;
 bh=wtsfHXo0CmcX4LU44eKI+QOxf+klOFvkaIdQR4MG89Y=;
 b=TkPtwSn3rsH1WZt/HhVRgMCxaLH/+w9fCAyoDUXtbQ9AcAdosXSs9byvZfXOiUOUsW
 mItV+gO7r49R6ZRXilGVKc8wv2GHhyjHSRlvNbHlojVz+iHXjpTRcDQGmpAm4yGrd2S3
 Y2M/x7lyt954qJnHqorMuBXtaf1lHdGYd2dT6NtQ+wUEClb5W1jALkRKIJF+OD2HSt9z
 aFJPNcE2/mnstn6edPtlbKWnTgFcU3YZwWsM2GNBIxD2OpDf1n2SnsVJMpVmZ+NxoxYn
 tCUF2ox2FjwOsnQ68Y7j2oE97VBR9Cqyy/q2t6lqDAASfDz+cWPw7SrdueXUXleR7ta+
 IfJQ==
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:cc:content-transfer-encoding;
 bh=wtsfHXo0CmcX4LU44eKI+QOxf+klOFvkaIdQR4MG89Y=;
 b=PVozaQCnWC4dIeryyZy9l6Nw6BkytPhHQPhdGy6tWpGD+z9xVCIxNtfiFAm/vLvjbt
 5Q8GbUUl/FUXk3qLTlQuqnFaFrJUsAJ8feEcRZDqmAAkvEA5HUSrcfJYKkivm2+B8uK2
 Zd02/onxqvHN8VJXKsML5V6pXhWJayT+nNutcHUKAlKPZzhWV29bHET1UndcdijcfG+v
 CvFOexcJLhqafDxbYOD9JmFWB9EPFoLWN6T/atqxja8/MJtga/tGAz9CxE6Qyz6AKgB4
 DVEWN3Dc/9FZtKiak0UGgMtKNoL6ZIJhnuu4J23OtYtRqJOV7IpqZlmbOARfbBWEOcB2
 JhaQ==
X-Gm-Message-State: AOAM531RdEOnpoiTlKeFaA5fBLZ6SRQoxSZSelgY7K5dt/3PHfPyMlaM
 uMlvg56bRU6W3LI7lEspKD7z+NPozKL6BChrQtQ=
X-Google-Smtp-Source: ABdhPJyVbij/NfZ4xxArEkiRnCu1j4sfRcnvxdXI9tBHwSJuVfBVxVo5anyWkQeV4zJ0uH5dRzWNyojUO3jlsIogmeI=
X-Received: by 2002:a05:620a:148a:: with SMTP id
 w10mr719359qkj.201.1590103759532; 
 Thu, 21 May 2020 16:29:19 -0700 (PDT)
MIME-Version: 1.0
References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN>
 <87ftdylqdn.fsf@HIDDEN>
In-Reply-To: <87ftdylqdn.fsf@HIDDEN>
From: zimoun <zimon.toutoune@HIDDEN>
Date: Fri, 22 May 2020 01:29:08 +0200
Message-ID: <CAJ3okZ1Ttjh+iG3qU1a_PcK_m5-64+KLAGKYT7b5Cum7fGgkKA@HIDDEN>
Subject: Re: Bioconductor URI, fallback and time-machine
To: Ricardo Wurmus <rekado@HIDDEN>
Content-Type: text/plain; charset="UTF-8"
Content-Transfer-Encoding: quoted-printable
Received-SPF: pass client-ip=2607:f8b0:4864:20::729;
 envelope-from=zimon.toutoune@HIDDEN; helo=mail-qk1-x729.google.com
X-detected-operating-system: by eggs.gnu.org: No matching host in p0f cache.
 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




Information forwarded to bug-guix@HIDDEN:
bug#39885; Package guix. Full text available.

Message received at submit <at> debbugs.gnu.org:


Received: (at submit) by debbugs.gnu.org; 23 Mar 2020 21:21:07 +0000
From debbugs-submit-bounces <at> debbugs.gnu.org Mon Mar 23 17:21:07 2020
Received: from localhost ([127.0.0.1]:53634 helo=debbugs.gnu.org)
	by debbugs.gnu.org with esmtp (Exim 4.84_2)
	(envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>)
	id 1jGUVO-0007hC-O4
	for submit <at> debbugs.gnu.org; Mon, 23 Mar 2020 17:21:06 -0400
Received: from lists.gnu.org ([209.51.188.17]:52629)
 by debbugs.gnu.org with esmtp (Exim 4.84_2)
 (envelope-from <rekado@HIDDEN>) id 1jGUVN-0007h5-6z
 for submit <at> debbugs.gnu.org; Mon, 23 Mar 2020 17:21:05 -0400
Received: from eggs.gnu.org ([2001:470:142:3::10]:36409)
 by lists.gnu.org with esmtp (Exim 4.90_1)
 (envelope-from <rekado@HIDDEN>) id 1jGUVL-00083V-N9
 for bug-guix@HIDDEN; Mon, 23 Mar 2020 17:21:05 -0400
X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org
X-Spam-Level: 
X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00, RCVD_IN_DNSWL_NONE, 
 URIBL_BLOCKED autolearn=disabled version=3.3.2
Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71)
 (envelope-from <rekado@HIDDEN>) id 1jGUVJ-0004y9-UB
 for bug-guix@HIDDEN; Mon, 23 Mar 2020 17:21:03 -0400
Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21170)
 by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
 (Exim 4.71) (envelope-from <rekado@HIDDEN>) id 1jGUVJ-0004wp-JP
 for bug-guix@HIDDEN; Mon, 23 Mar 2020 17:21:01 -0400
ARC-Seal: i=1; a=rsa-sha256; t=1584998457; cv=none; 
 d=zohomail.com; s=zohoarc; 
 b=guUwXEnS6NkYyOAcv0bVurZAyMgcbR4aB95JSc+/73PrVxu46donkJyNcN9+tS8Z5QnVhQZWuIERZJjjAcWkkUd6S+j3SwCmgxZuZxfhVUjAg7aF+s97gu7PzmWpKXFgBS+p2NeuaWssJ2NHw7v4soQ0Svl1dkDWPAPhYM2nu60=
ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com;
 s=zohoarc; t=1584998457;
 h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To;
 bh=n8NrkkNG/fHNgvYtRKhtjssxxEvyVaopQnSHXvx34dE=; 
 b=I0FjMKLQxMKIq+V1bk4eY1o50Em4iO60eNhmS9XIPF4yvIHIIuGWsmeIdAHzALaUS75exxW2ceOidKP6muIdU7gOHr7N86ZQKICcxRj/9qL9A1VKoEjpa+yzNbjqOirLyh5Um9/ylVF3tyUb/zPop+9mfHwYb0PdRvJ6ci1KfBE=
ARC-Authentication-Results: i=1; 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




Information forwarded to bug-guix@HIDDEN:
bug#39885; Package guix. Full text available.

Message received at submit <at> debbugs.gnu.org:


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
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==
--000000000000aa3660059ff5625d--




Acknowledgement sent to zimoun <zimon.toutoune@HIDDEN>:
New bug report received and forwarded. Copy sent to bug-guix@HIDDEN. Full text available.
Report forwarded to bug-guix@HIDDEN:
bug#39885; Package guix. Full text available.
Please note: This is a static page, with minimal formatting, updated once a day.
Click here to see this page with the latest information and nicer formatting.
Last modified: Sun, 28 Jun 2020 20:30:03 UTC

GNU bug tracking system
Copyright (C) 1999 Darren O. Benham, 1997 nCipher Corporation Ltd, 1994-97 Ian Jackson.