GNU logs - #54787, boring messages


Message sent to rekado@HIDDEN, bug-guix@HIDDEN:


X-Loop: help-debbugs@HIDDEN
Subject: bug#54787: importer Bioconductor: no tarball, only Git
Resent-From: zimoun <zimon.toutoune@HIDDEN>
Original-Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org>
Resent-CC: rekado@HIDDEN, bug-guix@HIDDEN
Resent-Date: Fri, 08 Apr 2022 11:52:01 +0000
Resent-Message-ID: <handler.54787.B.164941871812430 <at> debbugs.gnu.org>
Resent-Sender: help-debbugs@HIDDEN
X-GNU-PR-Message: report 54787
X-GNU-PR-Package: guix
X-GNU-PR-Keywords: 
To: 54787 <at> debbugs.gnu.org
Cc: Ricardo Wurmus <rekado@HIDDEN>
X-Debbugs-Original-To: Bug Guix <bug-guix@HIDDEN>
X-Debbugs-Original-Xcc: Ricardo Wurmus <rekado@HIDDEN>
Received: via spool by submit <at> debbugs.gnu.org id=B.164941871812430
          (code B ref -1); Fri, 08 Apr 2022 11:52:01 +0000
Received: (at submit) by debbugs.gnu.org; 8 Apr 2022 11:51:58 +0000
Received: from localhost ([127.0.0.1]:34057 helo=debbugs.gnu.org)
	by debbugs.gnu.org with esmtp (Exim 4.84_2)
	(envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>)
	id 1ncn9h-0003EQ-SO
	for submit <at> debbugs.gnu.org; Fri, 08 Apr 2022 07:51:58 -0400
Received: from lists.gnu.org ([209.51.188.17]:47156)
 by debbugs.gnu.org with esmtp (Exim 4.84_2)
 (envelope-from <zimon.toutoune@HIDDEN>) id 1ncn9f-0003EI-GF
 for submit <at> debbugs.gnu.org; Fri, 08 Apr 2022 07:51:55 -0400
Received: from eggs.gnu.org ([2001:470:142:3::10]:37738)
 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 1ncn9f-00027Y-8U
 for bug-guix@HIDDEN; Fri, 08 Apr 2022 07:51:55 -0400
Received: from mail-wr1-x42d.google.com ([2a00:1450:4864:20::42d]:46837)
 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 1ncn9d-0001oP-Kp
 for bug-guix@HIDDEN; Fri, 08 Apr 2022 07:51:54 -0400
Received: by mail-wr1-x42d.google.com with SMTP id v2so1589655wrv.13
 for <bug-guix@HIDDEN>; Fri, 08 Apr 2022 04:51:53 -0700 (PDT)
DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112;
 h=from:to:subject:date:message-id:mime-version;
 bh=CbvDk3xh5EqOZsCZ08RcHjXl3tne+c0vkY/OIMfHsRM=;
 b=N9ta99EiCWyhqkFKftOufAfDDuNYIzAyGLERf7YSotawN2BVvQO6EgkoPKq6hOLnWb
 3n4T/fSBhsQ176NNsBjrQ24wKc4inwEInCQpTwEcbJqDWjBkD1mmVlIRIc20Hp2dY+jq
 Y1qM5f3qDtdDKP+nXzEEie5l1oXTBZCkD1W5X9TJSt50mHLa9enAbT3nJpuYYweBAspO
 Mxg3RgmmXtP89TqLxodnw28b3yDIzjjMBjS8s6RaBJeN0gJgKrUaDSUFLr9dEJZZsP6h
 u9V2DKOLq+p8/1sK8kN4xDAMI0CyokBcpnqzVg//vcmfNQMaLClxDOx8uvLfFuf90Nml
 pE6g==
X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed;
 d=1e100.net; s=20210112;
 h=x-gm-message-state:from:to:subject:date:message-id:mime-version;
 bh=CbvDk3xh5EqOZsCZ08RcHjXl3tne+c0vkY/OIMfHsRM=;
 b=MA4MRJwJYbh8KFej8Cgi9w7bpyztVQViuzJvEJYeKmDIhomk8XAIVxJxHv0iukkJsd
 95LEdyrTXWjophJbdzCSVAzzUX55HxpfSW79J6umeFB6hnSGW/caW6G3KWXAHax/Je4i
 5zwPWnu4gUw9SZSV/7V0+tqNzwwPcu+KtE2Y3ULtx4GV069JNaXETFcBvzql4LZ23KUP
 N9rh3U7UJf8JryrrwOCmO3NAvO00p95MGLxy3uiYGYYUxTK7DYdfvPJiOmxc6Fnir57j
 tdnMbcIIsglZQ/ybQYFPHbryqPTtiIFMjQtko8j0T6/V8KKdsPIv/OiblPU6mm6xXTes
 4XqQ==
X-Gm-Message-State: AOAM531uonMiNKjENoPMARZUDnG050g9jC5leEEDD3UOPHXk41XW2nvt
 FuOU/qEh9H+8PNhln93dYkdIe6zw1hI=
X-Google-Smtp-Source: ABdhPJyQTIuy4tx7Nw5ZYsE4hoDNtqZEy2iokUrBDfMBmt0lttcMVBBDNyfKVaz/dkTk8E5F9YoXEw==
X-Received: by 2002:a5d:47a1:0:b0:204:9f5:e72f with SMTP id
 1-20020a5d47a1000000b0020409f5e72fmr14998405wrb.656.1649418711664; 
 Fri, 08 Apr 2022 04:51:51 -0700 (PDT)
Received: from lili ([88.126.110.68]) by smtp.gmail.com with ESMTPSA id
 o9-20020a056000010900b00206186ac25esm10942822wrx.12.2022.04.08.04.51.51
 for <bug-guix@HIDDEN>
 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256);
 Fri, 08 Apr 2022 04:51:51 -0700 (PDT)
From: zimoun <zimon.toutoune@HIDDEN>
Date: Fri, 08 Apr 2022 13:48:58 +0200
Message-ID: <868rsf23th.fsf@HIDDEN>
MIME-Version: 1.0
Content-Type: text/plain
Received-SPF: pass client-ip=2a00:1450:4864:20::42d;
 envelope-from=zimon.toutoune@HIDDEN; helo=mail-wr1-x42d.google.com
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_HELO_NONE=0.001, SPF_PASS=-0.001,
 T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no
X-Spam_action: no action
X-Spam-Score: -1.3 (-)
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 (--)

Hi,

Consider the package CHETAH, included in Bioconductor release 3.14;

<https://bioconductor.org/packages/release/bioc/html/CHETAH.html>

but then,

--8<---------------cut here---------------start------------->8---
$ guix import cran -a bioconductor CHETAH
guix import: warning: failed to retrieve package information from https://cran.r-project.org/web/packages/CHETAH/DESCRIPTION: 404 (Not Found)
guix import: error: failed to download description for package 'CHETAH'
--8<---------------cut here---------------end--------------->8---

The reason is because there is no source package.  Only the Git source
repo.


Cheers,
simon




Message sent:


Content-Disposition: inline
Content-Transfer-Encoding: quoted-printable
MIME-Version: 1.0
X-Mailer: MIME-tools 5.505 (Entity 5.505)
Content-Type: text/plain; charset=utf-8
X-Loop: help-debbugs@HIDDEN
From: help-debbugs@HIDDEN (GNU bug Tracking System)
To: zimoun <zimon.toutoune@HIDDEN>
Subject: bug#54787: Acknowledgement (importer Bioconductor: no tarball,
 only Git)
Message-ID: <handler.54787.B.164941871812430.ack <at> debbugs.gnu.org>
References: <868rsf23th.fsf@HIDDEN>
X-Gnu-PR-Message: ack 54787
X-Gnu-PR-Package: guix
Reply-To: 54787 <at> debbugs.gnu.org
Date: Fri, 08 Apr 2022 11:52:02 +0000

Thank you for filing a new bug report with debbugs.gnu.org.

This is an automatically generated reply to let you know your message
has been received.

Your message is being forwarded to the package maintainers and other
interested parties for their attention; they will reply in due course.

As you requested using X-Debbugs-CC, your message was also forwarded to
  Ricardo Wurmus <rekado@HIDDEN>
(after having been given a bug report number, if it did not have one).

Your message has been sent to the package maintainer(s):
 bug-guix@HIDDEN

If you wish to submit further information on this problem, please
send it to 54787 <at> debbugs.gnu.org.

Please do not send mail to help-debbugs@HIDDEN unless you wish
to report a problem with the Bug-tracking system.

--=20
54787: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D54787
GNU Bug Tracking System
Contact help-debbugs@HIDDEN with problems


Message sent to bug-guix@HIDDEN:


X-Loop: help-debbugs@HIDDEN
Subject: bug#54787: importer Bioconductor: no tarball, only Git
Resent-From: Ricardo Wurmus <rekado@HIDDEN>
Original-Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org>
Resent-CC: bug-guix@HIDDEN
Resent-Date: Mon, 11 Apr 2022 16:19:01 +0000
Resent-Message-ID: <handler.54787.B54787.164969388314208 <at> debbugs.gnu.org>
Resent-Sender: help-debbugs@HIDDEN
X-GNU-PR-Message: followup 54787
X-GNU-PR-Package: guix
X-GNU-PR-Keywords: 
To: zimoun <zimon.toutoune@HIDDEN>
Cc: 54787 <at> debbugs.gnu.org
X-Debbugs-Original-Cc: debbugs-submit <at> debbugs.gnu.org, 54787 <at> debbugs.gnu.org
Received: via spool by 54787-submit <at> debbugs.gnu.org id=B54787.164969388314208
          (code B ref 54787); Mon, 11 Apr 2022 16:19:01 +0000
Received: (at 54787) by debbugs.gnu.org; 11 Apr 2022 16:18:03 +0000
Received: from localhost ([127.0.0.1]:45429 helo=debbugs.gnu.org)
	by debbugs.gnu.org with esmtp (Exim 4.84_2)
	(envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>)
	id 1ndwjr-0003h5-Ev
	for submit <at> debbugs.gnu.org; Mon, 11 Apr 2022 12:18:03 -0400
Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21097)
 by debbugs.gnu.org with esmtp (Exim 4.84_2)
 (envelope-from <rekado@HIDDEN>)
 id 1ndwjp-0003gb-Bb; Mon, 11 Apr 2022 12:18:01 -0400
ARC-Seal: i=1; a=rsa-sha256; t=1649693878; cv=none; 
 d=zohomail.com; s=zohoarc; 
 b=W6Z1cl3LZmeVLJW1UE4iU2z43oJAWuEko1oKM9ncTVJ/XOFkbSs7XKmtzqTCxFNMEcaPz4TEq6gm+GZNqM4fgJS0+KgZf1GT9vYVyMtk7+HdigaExg0K5fT9wDA9kG5G8QZtwaYnKc1VmlXUTy+It09cWKrmqLuduJnGCBdjp20=
ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com;
 s=zohoarc; t=1649693878;
 h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To;
 bh=xR0naLFgCGIYkHo6MXQyQ54Z/eXmZ1yYyO0I5vPDUp4=; 
 b=NyrBRZCoVKv8cqtdTdyyvlMSuFuOYFhn5QYetDAq+5RhPXB7j4LzGJAumVnj8IpldFrMDW9xBLVltEFrlowc6gPNAItxmV1KksSUe70+vjUnyVcNA2V8DfMN/Aah+kGAVRcDdRmb3OnS7TLRjInrlGsxLKVpG6TLDO/40Vg+x64=
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>
DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1649693878; 
 s=zoho; d=elephly.net; i=rekado@HIDDEN;
 h=References:From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To;
 bh=xR0naLFgCGIYkHo6MXQyQ54Z/eXmZ1yYyO0I5vPDUp4=;
 b=GoRL0n/d1E92B42v/NYEDxSHqW+cWqwoe/GFNxucJqaSMDcPjyi+SYFczaI4Qh0t
 YD4VXQg/l8E76aD64V2lJwixTzvKaE9rLrdUG40BMEX8YWRdfBUZn4RSY5JoYo82655
 xilwDvuGvm6x+VJ/bnctrQzhDQ8VwRokXZjs+MLw=
Received: from localhost (i5E862D75.versanet.de [94.134.45.117]) by
 mx.zohomail.com with SMTPS id 1649693877699188.37067792420635;
 Mon, 11 Apr 2022 09:17:57 -0700 (PDT)
References: <868rsf23th.fsf@HIDDEN>
User-agent: mu4e 1.6.10; emacs 28.0.50
From: Ricardo Wurmus <rekado@HIDDEN>
Date: Mon, 11 Apr 2022 18:15:39 +0200
In-reply-to: <868rsf23th.fsf@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
Message-ID: <874k2zzj9p.fsf@HIDDEN>
MIME-Version: 1.0
Content-Type: text/plain; charset=utf-8
Content-Transfer-Encoding: quoted-printable
X-ZohoMailClient: External
X-Spam-Score: -0.0 (/)
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 (-)


zimoun <zimon.toutoune@HIDDEN> writes:

> $ guix import cran -a bioconductor CHETAH
> guix import: warning: failed to retrieve package information from https:/=
/cran.r-project.org/web/packages/CHETAH/DESCRIPTION: 404 (Not Found)
> guix import: error: failed to download description for package 'CHETAH'
>
> The reason is because there is no source package.  Only the Git source
> repo.

We should finally switch to fetching the sources from Git.  I wonder why
we haven=E2=80=99t done this earlier.

I guess we should do this gradually to avoid mass updates, so perhaps we
should introduce bioconductor-git-reference and switch over packages one
by one.

What do you think?

--=20
Ricardo




Message sent to bug-guix@HIDDEN:


X-Loop: help-debbugs@HIDDEN
Subject: bug#54787: importer Bioconductor: no tarball, only Git
Resent-From: zimoun <zimon.toutoune@HIDDEN>
Original-Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org>
Resent-CC: bug-guix@HIDDEN
Resent-Date: Tue, 12 Apr 2022 16:27:02 +0000
Resent-Message-ID: <handler.54787.B54787.164978076725512 <at> debbugs.gnu.org>
Resent-Sender: help-debbugs@HIDDEN
X-GNU-PR-Message: followup 54787
X-GNU-PR-Package: guix
X-GNU-PR-Keywords: 
To: Ricardo Wurmus <rekado@HIDDEN>
Cc: 54787 <at> debbugs.gnu.org
Received: via spool by 54787-submit <at> debbugs.gnu.org id=B54787.164978076725512
          (code B ref 54787); Tue, 12 Apr 2022 16:27:02 +0000
Received: (at 54787) by debbugs.gnu.org; 12 Apr 2022 16:26:07 +0000
Received: from localhost ([127.0.0.1]:49571 helo=debbugs.gnu.org)
	by debbugs.gnu.org with esmtp (Exim 4.84_2)
	(envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>)
	id 1neJLC-0006dI-M1
	for submit <at> debbugs.gnu.org; Tue, 12 Apr 2022 12:26:07 -0400
Received: from mail-wm1-f50.google.com ([209.85.128.50]:39758)
 by debbugs.gnu.org with esmtp (Exim 4.84_2)
 (envelope-from <zimon.toutoune@HIDDEN>) id 1neJL9-0006bu-3w
 for 54787 <at> debbugs.gnu.org; Tue, 12 Apr 2022 12:26:03 -0400
Received: by mail-wm1-f50.google.com with SMTP id
 ay11-20020a05600c1e0b00b0038eb92fa965so2142212wmb.4
 for <54787 <at> debbugs.gnu.org>; Tue, 12 Apr 2022 09:26:03 -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:content-transfer-encoding;
 bh=cDLiDOHh8hXPCfJhLHR6pFxPiR7C2NJ4EvTJmaDd91A=;
 b=NpTyHHqHfWFi61m7MFe/QHtd6Sbu72QSYzH3p1mt9u1HXcT4l1CSZd2aVC5nfIobBL
 8gmP+ZShy+XjHuwVPMOhzoeh5z0GY5eU8lTjCF/RF9kDdSud8zWAjcnfhSM0j6p1cDn3
 tlp8Ymnnu6kXgnuQStlGWGpEOAEFOW3VE9dwlkWnV4Fj/X+WmYKzZ4gmrBR+zSGKJiD8
 ghRKjt3R/iaZnTyZj/0o9zJDI/gMHHIHsUxL58rFhyKAmHqFfkwLJDIP7mo+WZ4Cc/gf
 R5lfV0AIa6oQVnCP0t2fi+dz1jv0/VS37cFgU12kDPBNyyDY1rZ23FztPZkgWgvZt0vF
 HvIw==
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:content-transfer-encoding;
 bh=cDLiDOHh8hXPCfJhLHR6pFxPiR7C2NJ4EvTJmaDd91A=;
 b=Izps/uLqfAXU/PDIL48j2MCj2oiEedrZKsA1ul+1yIYlJMZKdOn1X4mgi/MBBDjY8n
 0UNkqjgqtT9xfoGkOyNoPhwQwn8trLRM1kcNSVZA7d1qXmkFfVOOj6TZCg94tuzuFqDb
 GSbfPIXWxfq8kh5DPPU/IgXnBmMq5sKxyUpqc1AfiNeoER3phdoR6CaU2sVRQgAC6YFc
 4f8IXwJYtySVJVjVPeAM/TbqDKIpG6NibUqys1KvYOyj8MO+DjkN8Hu2KY5nMfMWdpTr
 tnmgDRzoRyyWTjQAveGTNwrZu4vJ8TRhw8Sid/dEsm+VdQO/uVS74ekvr5Uz+5UM9qtC
 L1Dw==
X-Gm-Message-State: AOAM531Wan6dlG3GbY6G4UKLYAU4THeXyd0+KYzUiDyCTvHYPQz7zle7
 fvTJ6BGVKt921ZfhXPKQxQY/cdg49Ms=
X-Google-Smtp-Source: ABdhPJwHENHncLY3gvww7sb8pB66ThMZmTv2iaiWlLHz6HyV/4vHAM4kbX/JmhODmm0IGM+WmVwtNQ==
X-Received: by 2002:a05:600c:35d5:b0:38e:3bca:716f with SMTP id
 r21-20020a05600c35d500b0038e3bca716fmr4786044wmq.200.1649780757370; 
 Tue, 12 Apr 2022 09:25:57 -0700 (PDT)
Received: from pfiuh07 ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id
 m20-20020a05600c3b1400b0038ebbbb2ad2sm2779779wms.44.2022.04.12.09.25.56
 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256);
 Tue, 12 Apr 2022 09:25:56 -0700 (PDT)
From: zimoun <zimon.toutoune@HIDDEN>
References: <868rsf23th.fsf@HIDDEN> <874k2zzj9p.fsf@HIDDEN>
Date: Tue, 12 Apr 2022 18:25:51 +0200
In-Reply-To: <874k2zzj9p.fsf@HIDDEN> (Ricardo Wurmus's message of "Mon,
 11 Apr 2022 18:15:39 +0200")
Message-ID: <87ilre5kvk.fsf@HIDDEN>
User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/27.2 (gnu/linux)
MIME-Version: 1.0
Content-Type: text/plain; charset=utf-8
Content-Transfer-Encoding: quoted-printable
X-Spam-Score: -0.0 (/)
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 (-)

Hi Ricardo,

On lun., 11 avril 2022 at 18:15, Ricardo Wurmus <rekado@HIDDEN> wrote:
> zimoun <zimon.toutoune@HIDDEN> writes:
>
>> $ guix import cran -a bioconductor CHETAH
>> guix import: warning: failed to retrieve package information from
>> https://cran.r-project.org/web/packages/CHETAH/DESCRIPTION: 404 (Not Fou=
nd)
>> guix import: error: failed to download description for package 'CHETAH'
>>
>> The reason is because there is no source package.  Only the Git source
>> repo.
>
> We should finally switch to fetching the sources from Git.  I wonder why
> we haven=E2=80=99t done this earlier.

Because, maybe, we have just finished the janitor work cleaning the
files cran.scm, bioconductor.scm and bioinformatics.scm. :-)

> I guess we should do this gradually to avoid mass updates, so perhaps we
> should introduce bioconductor-git-reference and switch over packages one
> by one.

First, note that annotations do not have Git repo; at least not always,
e.g.,

<https://bioconductor.org/packages/release/data/annotation/html/GenomeInfoD=
bData.html>

Second, if we go for something like:

--8<---------------cut here---------------start------------->8---
(define* (bioconductor-git-reference name #:optional
                                     (release %bioconductor-version))
  "Return a <git-reference> for the R package archive on Bioconductor for t=
he
RELEASE corresponding to NAME."
  (git-reference
   (url (string-append %bioconductor-git-url name))
   (commit (string-append "RELEASE_" (string-replace-substring
                                      %bioconductor-version "." "_")))))
--8<---------------cut here---------------end--------------->8---

then, it raises the question: import/cran.scm or build-system/r.scm ?
i.e., do we put a module dependency against (guix git-download) for the
r-build-system or not?

TeXLive already has a dependency to svn-download, so why not.

Well, I am also in favor to break the API and move %bioconductor-version
and %bioconductor-url to (guix build-system r).  WDYT?  It would
simplify some things (#36805 and #39885), I guess.


Third, the adjustments of the importer require a large cup of coffee.


Back to CHETAH, note that

   guix import cran -a git htpps://git.bioconductor.org/CHETAH

works but it points to master instead of RELEASE_3_14.  Well, I am not
very familiar with the Bioconductor workflow for their release.


Last, using this in gnu/packages/bioconductor.scm,

--8<---------------cut here---------------start------------->8---
(define-public r-chetah
  (package
    (name "r-chetah")
    (version "1.11.2")
    (source
     (origin
       (method git-fetch)
       (uri (bioconductor-git-reference "CHETAH"))
       (file-name (git-file-name name version))
       (sha256
        (base32 "021v5831zqdy4pirfsb35kbnz8kmz4lxqc4cwi55qgd6r081xlgh"))))
    (properties `((upstream-name . "CHETAH")))
    (build-system r-build-system)
    (propagated-inputs
     (list r-biodist
           r-corrplot
           r-cowplot
           r-dendextend
           r-ggplot2
           r-gplots
           r-pheatmap
           r-plotly
           r-reshape2
           r-s4vectors
           r-shiny
           r-singlecellexperiment
           r-summarizedexperiment))
    (native-inputs (list r-knitr))
    (home-page "https://git.bioconductor.org/packages/CHETAH")
    (synopsis "Fast and accurate scRNA-seq cell type identification")
    (description
     "CHETAH (CHaracterization of cEll Types Aided by Hierarchical classifi=
cation) is
an accurate, selective and fast scRNA-seq classifier.  Classification is gu=
ided
by a reference dataset, preferentially also a scRNA-seq dataset.  By
hierarchical clustering of the reference data, CHETAH creates a classificat=
ion
tree that enables a step-wise, top-to-bottom classification.  Using a novel
stopping rule, CHETAH classifies the input cells to the cell types of the
references and to \"intermediate types\": more general classifications that=
 ended
in an intermediate node of the tree.")
    (license #f)))
--8<---------------cut here---------------end--------------->8---

it just builds with,

    ./pre-inst-env guix build r-chetah



WDYT?


Cheers,
simon




Message sent to bug-guix@HIDDEN:


X-Loop: help-debbugs@HIDDEN
Subject: bug#54787: importer Bioconductor: no tarball, only Git
Resent-From: Ricardo Wurmus <rekado@HIDDEN>
Original-Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org>
Resent-CC: bug-guix@HIDDEN
Resent-Date: Thu, 14 Apr 2022 11:48:02 +0000
Resent-Message-ID: <handler.54787.B54787.16499368551853 <at> debbugs.gnu.org>
Resent-Sender: help-debbugs@HIDDEN
X-GNU-PR-Message: followup 54787
X-GNU-PR-Package: guix
X-GNU-PR-Keywords: 
To: zimoun <zimon.toutoune@HIDDEN>
Cc: 54787 <at> debbugs.gnu.org
Received: via spool by 54787-submit <at> debbugs.gnu.org id=B54787.16499368551853
          (code B ref 54787); Thu, 14 Apr 2022 11:48:02 +0000
Received: (at 54787) by debbugs.gnu.org; 14 Apr 2022 11:47:35 +0000
Received: from localhost ([127.0.0.1]:55500 helo=debbugs.gnu.org)
	by debbugs.gnu.org with esmtp (Exim 4.84_2)
	(envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>)
	id 1nexwk-0000Tn-Vt
	for submit <at> debbugs.gnu.org; Thu, 14 Apr 2022 07:47:35 -0400
Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21080)
 by debbugs.gnu.org with esmtp (Exim 4.84_2)
 (envelope-from <rekado@HIDDEN>) id 1nexwi-0000TU-FL
 for 54787 <at> debbugs.gnu.org; Thu, 14 Apr 2022 07:47:33 -0400
ARC-Seal: i=1; a=rsa-sha256; t=1649936850; cv=none; 
 d=zohomail.com; s=zohoarc; 
 b=kp/M6A6OQ5ZAPnhyn7G0LE8Urbc5oPojfQW8KwhrQB56fYTD2b+1dlY3nv8q9wld8RLiPUo2EmkKLIBQN/9b9ta1bS+eT5F4JSNF2bSjdxsqPOenR6b6WRhJz9pKcWShb41qMAPtdQAkdTeKm3weo1EzwyjIyJDTCVhMOIyY56Y=
ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com;
 s=zohoarc; t=1649936850;
 h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To;
 bh=+rAXGJpxct5Ij19dKkv7N/6onhyaUnz5pjzo8BVMwZw=; 
 b=Vkh1Mw+oGVz/4pKFxslAO7h+T46tl/NppKb0zJGvyhCGVYPOa3igjFEcOlOlFX2kvQ50s03gkxqHJChevWbNHH6lBi4/8P98ENpNGpbBj7YIXJQ5AMotDxL8JrzrF74f7UeE2l9k8ZcXHLCzXYGna4W60SQVTOH40+3NX4wmGEo=
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>
DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1649936850; 
 s=zoho; d=elephly.net; i=rekado@HIDDEN;
 h=References:From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To;
 bh=+rAXGJpxct5Ij19dKkv7N/6onhyaUnz5pjzo8BVMwZw=;
 b=dvL77awij6snInHDr0go9DUfd3Bvr2JytcRqltId0VYRA6Z+Sk7pI+Q5zwwBDx/z
 SSzM7hCTTMD3E7VwzOYMwXxH6SPo8xnfvKf9WOhHSMei2LmUD3DgAxXLS4JdoExNxUD
 pplElK5XypRsd2p4oPCxbwD+jMbwNiSrMKv+zcfA=
Received: from localhost (152-108-142-46.pool.kielnet.net [46.142.108.152]) by
 mx.zohomail.com with SMTPS id 1649936849792691.6268642098051;
 Thu, 14 Apr 2022 04:47:29 -0700 (PDT)
References: <868rsf23th.fsf@HIDDEN> <874k2zzj9p.fsf@HIDDEN>
 <87ilre5kvk.fsf@HIDDEN>
User-agent: mu4e 1.6.10; emacs 28.0.50
From: Ricardo Wurmus <rekado@HIDDEN>
Date: Thu, 14 Apr 2022 13:43:36 +0200
In-reply-to: <87ilre5kvk.fsf@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
Message-ID: <87wnfrvqcw.fsf@HIDDEN>
MIME-Version: 1.0
Content-Type: text/plain; charset=utf-8
Content-Transfer-Encoding: quoted-printable
X-ZohoMailClient: External
X-Spam-Score: -0.0 (/)
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 (-)


zimoun <zimon.toutoune@HIDDEN> writes:

> First, note that annotations do not have Git repo; at least not always,
> e.g.,
>
> <https://bioconductor.org/packages/release/data/annotation/html/GenomeInf=
oDbData.html>

That=E2=80=99s fine.  We just ignore annotation and experiment packages, an=
d use
git only for regular packages.

> Second, if we go for something like:
>
> (define* (bioconductor-git-reference name #:optional
>                                      (release %bioconductor-version))
>   "Return a <git-reference> for the R package archive on Bioconductor for=
 the
> RELEASE corresponding to NAME."
>   (git-reference
>    (url (string-append %bioconductor-git-url name))
>    (commit (string-append "RELEASE_" (string-replace-substring
>                                       %bioconductor-version "." "_")))))
>
>
> then, it raises the question: import/cran.scm or build-system/r.scm ?
> i.e., do we put a module dependency against (guix git-download) for the
> r-build-system or not?
>
> TeXLive already has a dependency to svn-download, so why not.

Yes, I don=E2=80=99t think that=E2=80=99s a problem.

We probably should *not* use RELEASE_3_14 (or whatever) as the commit,
though, because that is a moving target.  We need to resolve to the
actual commit and use its hash.

I wonder how the updater would need to be changed.  It would need to
know about the release branch and look for new commits in that branch
only.

> Well, I am also in favor to break the API and move %bioconductor-version
> and %bioconductor-url to (guix build-system r).  WDYT?  It would
> simplify some things (#36805 and #39885), I guess.

We tried this before and we couldn=E2=80=99t do this because of a circular
reference.

> Back to CHETAH, note that
>
>    guix import cran -a git htpps://git.bioconductor.org/CHETAH
>
> works but it points to master instead of RELEASE_3_14.  Well, I am not
> very familiar with the Bioconductor workflow for their release.

That=E2=80=99s because the importer doesn=E2=80=99t let us specify a differ=
ent branch.
We should add that, but it=E2=80=99s strictly separate from the migration w=
e=E2=80=99re
about to embark on.

> Last, using this in gnu/packages/bioconductor.scm,
>
> (define-public r-chetah
>   (package
>     (name "r-chetah")
>     (version "1.11.2")
>     (source
>      (origin
>        (method git-fetch)
>        (uri (bioconductor-git-reference "CHETAH"))
>        (file-name (git-file-name name version))
>        (sha256
>         (base32 "021v5831zqdy4pirfsb35kbnz8kmz4lxqc4cwi55qgd6r081xlgh"))))
>     (properties `((upstream-name . "CHETAH")))
>     (build-system r-build-system)
>     (propagated-inputs
>      (list r-biodist
>            r-corrplot
>            r-cowplot
>            r-dendextend
>            r-ggplot2
>            r-gplots
>            r-pheatmap
>            r-plotly
>            r-reshape2
>            r-s4vectors
>            r-shiny
>            r-singlecellexperiment
>            r-summarizedexperiment))
>     (native-inputs (list r-knitr))
>     (home-page "https://git.bioconductor.org/packages/CHETAH")
>     (synopsis "Fast and accurate scRNA-seq cell type identification")
>     (description
>      "CHETAH (CHaracterization of cEll Types Aided by Hierarchical classi=
fication) is
> an accurate, selective and fast scRNA-seq classifier.  Classification is =
guided
> by a reference dataset, preferentially also a scRNA-seq dataset.  By
> hierarchical clustering of the reference data, CHETAH creates a classific=
ation
> tree that enables a step-wise, top-to-bottom classification.  Using a nov=
el
> stopping rule, CHETAH classifies the input cells to the cell types of the
> references and to \"intermediate types\": more general classifications th=
at ended
> in an intermediate node of the tree.")
>     (license #f)))
>
> it just builds with,
>
>     ./pre-inst-env guix build r-chetah
>
>
>
> WDYT?

Neat :)

--=20
Ricardo




Message sent to bug-guix@HIDDEN:


X-Loop: help-debbugs@HIDDEN
Subject: bug#54787: importer Bioconductor: no tarball, only Git
Resent-From: zimoun <zimon.toutoune@HIDDEN>
Original-Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org>
Resent-CC: bug-guix@HIDDEN
Resent-Date: Thu, 14 Apr 2022 13:10:01 +0000
Resent-Message-ID: <handler.54787.B54787.16499417949999 <at> debbugs.gnu.org>
Resent-Sender: help-debbugs@HIDDEN
X-GNU-PR-Message: followup 54787
X-GNU-PR-Package: guix
X-GNU-PR-Keywords: 
To: Ricardo Wurmus <rekado@HIDDEN>
Cc: 54787 <at> debbugs.gnu.org
Received: via spool by 54787-submit <at> debbugs.gnu.org id=B54787.16499417949999
          (code B ref 54787); Thu, 14 Apr 2022 13:10:01 +0000
Received: (at 54787) by debbugs.gnu.org; 14 Apr 2022 13:09:54 +0000
Received: from localhost ([127.0.0.1]:55587 helo=debbugs.gnu.org)
	by debbugs.gnu.org with esmtp (Exim 4.84_2)
	(envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>)
	id 1nezEQ-0002bC-D1
	for submit <at> debbugs.gnu.org; Thu, 14 Apr 2022 09:09:54 -0400
Received: from mail-wr1-f45.google.com ([209.85.221.45]:33289)
 by debbugs.gnu.org with esmtp (Exim 4.84_2)
 (envelope-from <zimon.toutoune@HIDDEN>) id 1nezEO-0002aw-Td
 for 54787 <at> debbugs.gnu.org; Thu, 14 Apr 2022 09:09:53 -0400
Received: by mail-wr1-f45.google.com with SMTP id c7so6893446wrd.0
 for <54787 <at> debbugs.gnu.org>; Thu, 14 Apr 2022 06:09:52 -0700 (PDT)
DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112;
 h=from:to:cc:subject:in-reply-to:references:date:message-id
 :mime-version:content-transfer-encoding;
 bh=RjMrVGNhwTkDMIH9KP/SO4HYW5H7AY8ymh+rCZ4hyzs=;
 b=RSZ5fAAajwv1qzu1VpAaCEdyvgP/tUS0nw74YyCSd4r+xEwp6CaJiPCAZ51Se7KHNE
 XjjXXngvhOuimWEyFJKtEBSLW7dOohBM2xK8dPw+RK+mzkxaLEwRuV0Ro6WSrf/K0ido
 P3dvhdCH/b2uhhohd5mFBV7gwc601TtqdWbxOS6CUpG5RikQmXDTDv7+8Brf2m8f5SW5
 HYnKzDaITunn7BC1u1q9P/k2lzuEO7jdBbQHi57uEugS5cg8ZhEazI/Sn0oBsxOcdutt
 6tA8lDBFUK5CtwGbd35KQHqjM/B7I5kqfnlO8WcEUEzO3o/TdmrRUYji6Tpbosp5BPeN
 pUPw==
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:in-reply-to:references:date
 :message-id:mime-version:content-transfer-encoding;
 bh=RjMrVGNhwTkDMIH9KP/SO4HYW5H7AY8ymh+rCZ4hyzs=;
 b=gY6O897Xqj3lLpTO/V1GbmjNrdkqFgW9WJD3qPz9ya2aPK1aD5Jz9s2BxtGkc0R4vu
 jXkUctOHaZg9hGLALvuzZ3dpLc/ZkCU1KwemYd9fqGLEq6SydDAxEIqEQxgYnNrCPciS
 P71hN8fd6kPnWTcX25ByO2zajsWTnbyVG9W4kKy0J5TomTVTeBpUwMkNdnrzJtXiEBy4
 GEaDkzKbiElE+edPYQBOF2seeuUo90rumwmwTJ4Oixh2UHr4CinE7It3P/G+E3Q3wjGQ
 VG7E5CmH3GVKFctzxqGeeTwzJjRyotbaG48/ziClZz1Kv00BOKfG+hrVFiIqZbFyRSgc
 qrxA==
X-Gm-Message-State: AOAM5337RRwGB4rShzAM6ROT0CzLWUZ0NIhGU/BTMvK4QMQuzkNmupls
 rYM2k/8j+kUXmiIn1TfM0dWcpf0QY1k=
X-Google-Smtp-Source: ABdhPJwq5G7ymNd9fUilqvlDrdGqooIo9kK546Ro20miymuxx0qgo4Nn5FUiVM6sGrgWb3MVKEHC4A==
X-Received: by 2002:a5d:53cb:0:b0:207:ab75:3ce7 with SMTP id
 a11-20020a5d53cb000000b00207ab753ce7mr2121740wrw.171.1649941786981; 
 Thu, 14 Apr 2022 06:09:46 -0700 (PDT)
Received: from lili ([2a01:e0a:59b:9120:65d2:2476:f637:db1e])
 by smtp.gmail.com with ESMTPSA id
 s7-20020a5d6a87000000b00207aad420c4sm1730396wru.101.2022.04.14.06.09.45
 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256);
 Thu, 14 Apr 2022 06:09:46 -0700 (PDT)
From: zimoun <zimon.toutoune@HIDDEN>
In-Reply-To: <87wnfrvqcw.fsf@HIDDEN>
References: <868rsf23th.fsf@HIDDEN> <874k2zzj9p.fsf@HIDDEN>
 <87ilre5kvk.fsf@HIDDEN> <87wnfrvqcw.fsf@HIDDEN>
Date: Thu, 14 Apr 2022 14:59:54 +0200
Message-ID: <86k0brzuph.fsf@HIDDEN>
MIME-Version: 1.0
Content-Type: text/plain; charset=utf-8
Content-Transfer-Encoding: quoted-printable
X-Spam-Score: -0.0 (/)
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 (-)

Hi Ricardo,

On Thu, 14 Apr 2022 at 13:43, Ricardo Wurmus <rekado@HIDDEN> wrote:

> We probably should *not* use RELEASE_3_14 (or whatever) as the commit,
> though, because that is a moving target.  We need to resolve to the
> actual commit and use its hash.
>
> I wonder how the updater would need to be changed.  It would need to
> know about the release branch and look for new commits in that branch
> only.

To be honest, I have not checked the Bioconductor documentation about
their Git repo structure.  What I see is:

--8<---------------cut here---------------start------------->8---
$ git clone https://git.bioconductor.org/packages/CHETAH
$ cd CHETAH
$ git branch -av
* master                      5d5f5df [origin/master] Pass serialized S4 in=
stances thru updateObject()
  remotes/origin/HEAD         -> origin/master
  remotes/origin/RELEASE_3_10 063de2d bump x.y.z version to even y prior to=
 creation of RELEASE_3_10 branch
  remotes/origin/RELEASE_3_11 701ca7f bump x.y.z version to even y prior to=
 creation of RELEASE_3_11 branch
  remotes/origin/RELEASE_3_12 cd3dd78 bump x.y.z version to even y prior to=
 creation of RELEASE_3_12 branch
  remotes/origin/RELEASE_3_13 1eacdb8 bump x.y.z version to even y prior to=
 creation of RELEASE_3_13 branch
  remotes/origin/RELEASE_3_14 03295c9 bump x.y.z version to even y prior to=
 creation of RELEASE_3_14 branch
  remotes/origin/RELEASE_3_9  22b53f2 version bump
  remotes/origin/master       5d5f5df Pass serialized S4 instances thru upd=
ateObject()
--8<---------------cut here---------------end--------------->8---


Do we follow =E2=80=99master=E2=80=99?  Is it a mirror of what Bioconductor=
 names their
3.14 release?

My guess was that RELEASE_3_14 mirrors their 3.14 release.


>> Well, I am also in favor to break the API and move %bioconductor-version
>> and %bioconductor-url to (guix build-system r).  WDYT?  It would
>> simplify some things (#36805 and #39885), I guess.
>
> We tried this before and we couldn=E2=80=99t do this because of a circular
> reference.

Well, I have something that works.  So I do not know if this circular
reference is still there.



> That=E2=80=99s because the importer doesn=E2=80=99t let us specify a diff=
erent branch.
> We should add that, but it=E2=80=99s strictly separate from the migration=
 we=E2=80=99re
> about to embark on.

I am not familiar with the updater (guix refresh -u).  My plan is:

 1. Add bioconductor-git-reference
 2. Adapt the bioconductor importer.
 3. Updater?

The question is: do we have to include the migration in the updater?  Or
do we do the migration by custom scripts?


Note that, because we do not support shallow clones, the complete
sources will be a bit bigger; since they contain all the Bioconductor
history of all the packages.


Cheers,
simon





Message sent to bug-guix@HIDDEN:


X-Loop: help-debbugs@HIDDEN
Subject: bug#54787: importer Bioconductor: no tarball, only Git
Resent-From: Ricardo Wurmus <rekado@HIDDEN>
Original-Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org>
Resent-CC: bug-guix@HIDDEN
Resent-Date: Thu, 14 Apr 2022 14:01:02 +0000
Resent-Message-ID: <handler.54787.B54787.164994484219089 <at> debbugs.gnu.org>
Resent-Sender: help-debbugs@HIDDEN
X-GNU-PR-Message: followup 54787
X-GNU-PR-Package: guix
X-GNU-PR-Keywords: 
To: zimoun <zimon.toutoune@HIDDEN>
Cc: 54787 <at> debbugs.gnu.org
Received: via spool by 54787-submit <at> debbugs.gnu.org id=B54787.164994484219089
          (code B ref 54787); Thu, 14 Apr 2022 14:01:02 +0000
Received: (at 54787) by debbugs.gnu.org; 14 Apr 2022 14:00:42 +0000
Received: from localhost ([127.0.0.1]:56827 helo=debbugs.gnu.org)
	by debbugs.gnu.org with esmtp (Exim 4.84_2)
	(envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>)
	id 1nf01Z-0004xJ-Ug
	for submit <at> debbugs.gnu.org; Thu, 14 Apr 2022 10:00:42 -0400
Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21042)
 by debbugs.gnu.org with esmtp (Exim 4.84_2)
 (envelope-from <rekado@HIDDEN>) id 1nf01X-0004td-OY
 for 54787 <at> debbugs.gnu.org; Thu, 14 Apr 2022 10:00:40 -0400
ARC-Seal: i=1; a=rsa-sha256; t=1649944837; cv=none; 
 d=zohomail.com; s=zohoarc; 
 b=Zup6Q8GHoGhn01TtvxAbSrNOmA4lpAXi7WxI7yUyjb2z2xpwqZXsHJSRrzrZgua+9vooxaQLHPHO/ts7y5dv2JmoNHnlG7q4AFPxjhNpDrtT/Y/+OZwP3WG6hVn9uTdBZgeQjABNKJSN1DCUGx6ut1BBgI4w3uFCpA+B6w9rJjE=
ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com;
 s=zohoarc; t=1649944837;
 h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To;
 bh=IKrnNCTW1zF6DinFrcbjog9s9CStBV/9JH9cGr90ePo=; 
 b=Pb9MuTUM0TpKl+DQ+C+L8FugN1WIqFT/i6GlWueFJuoezHJSMNXRnjOJgaSC8Y3sXr7k1KvIb57xo35yBG4hoDPpMNiaSL/Chr/kNWUGts32BI9cD5u/WiKbD+M3ym+Y2CiajwXPBRuGT3UqrLrRWBdxeqp8496/kKJEtymQ3xs=
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>
DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1649944837; 
 s=zoho; d=elephly.net; i=rekado@HIDDEN;
 h=References:From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To;
 bh=IKrnNCTW1zF6DinFrcbjog9s9CStBV/9JH9cGr90ePo=;
 b=FvYlxPhkRBeuImNS0WloUl9jtxla4JnGl8T/Fu6dM/0L8rceObJ1KefPUMC+gaJY
 UwQ1gWosBvGLjRH9ea9AVXYYmqFkOkQKw663B6KBdrUCcm6kCtE6xlTbTgyZibqdUnc
 MF4OVvxtOzRffWGCCIwSKQ2X43HNpfee2DPPwBvA=
Received: from localhost (152-108-142-46.pool.kielnet.net [46.142.108.152]) by
 mx.zohomail.com with SMTPS id 1649944835027771.3960230007689;
 Thu, 14 Apr 2022 07:00:35 -0700 (PDT)
References: <868rsf23th.fsf@HIDDEN> <874k2zzj9p.fsf@HIDDEN>
 <87ilre5kvk.fsf@HIDDEN> <87wnfrvqcw.fsf@HIDDEN>
 <86k0brzuph.fsf@HIDDEN>
User-agent: mu4e 1.6.10; emacs 28.0.50
From: Ricardo Wurmus <rekado@HIDDEN>
Date: Thu, 14 Apr 2022 15:57:25 +0200
In-reply-to: <86k0brzuph.fsf@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
Message-ID: <87k0brvk73.fsf@HIDDEN>
MIME-Version: 1.0
Content-Type: text/plain; charset=utf-8
Content-Transfer-Encoding: quoted-printable
X-ZohoMailClient: External
X-Spam-Score: -0.0 (/)
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 (-)


zimoun <zimon.toutoune@HIDDEN> writes:

> On Thu, 14 Apr 2022 at 13:43, Ricardo Wurmus <rekado@HIDDEN> wrote:
>
>> We probably should *not* use RELEASE_3_14 (or whatever) as the commit,
>> though, because that is a moving target.  We need to resolve to the
>> actual commit and use its hash.
>>
>> I wonder how the updater would need to be changed.  It would need to
>> know about the release branch and look for new commits in that branch
>> only.
>
> To be honest, I have not checked the Bioconductor documentation about
> their Git repo structure.  What I see is:
>
> $ git clone https://git.bioconductor.org/packages/CHETAH
> $ cd CHETAH
> $ git branch -av
> * master                      5d5f5df [origin/master] Pass serialized S4 =
instances thru updateObject()
>   remotes/origin/HEAD         -> origin/master
>   remotes/origin/RELEASE_3_10 063de2d bump x.y.z version to even y prior =
to creation of RELEASE_3_10 branch
>   remotes/origin/RELEASE_3_11 701ca7f bump x.y.z version to even y prior =
to creation of RELEASE_3_11 branch
>   remotes/origin/RELEASE_3_12 cd3dd78 bump x.y.z version to even y prior =
to creation of RELEASE_3_12 branch
>   remotes/origin/RELEASE_3_13 1eacdb8 bump x.y.z version to even y prior =
to creation of RELEASE_3_13 branch
>   remotes/origin/RELEASE_3_14 03295c9 bump x.y.z version to even y prior =
to creation of RELEASE_3_14 branch
>   remotes/origin/RELEASE_3_9  22b53f2 version bump
>   remotes/origin/master       5d5f5df Pass serialized S4 instances thru u=
pdateObject()
>
>
> Do we follow =E2=80=99master=E2=80=99?  Is it a mirror of what Bioconduct=
or names their
> 3.14 release?

We should not follow =E2=80=9Cmaster=E2=80=9D.  That=E2=80=99s the developm=
ent branch.  We
should follow the current release branch.

> My guess was that RELEASE_3_14 mirrors their 3.14 release.

Correct.

>>> Well, I am also in favor to break the API and move %bioconductor-version
>>> and %bioconductor-url to (guix build-system r).  WDYT?  It would
>>> simplify some things (#36805 and #39885), I guess.
>>
>> We tried this before and we couldn=E2=80=99t do this because of a circul=
ar
>> reference.
>
> Well, I have something that works.  So I do not know if this circular
> reference is still there.

If =E2=80=9Cmake as-derivation=E2=80=9D does not fail it is probably okay.

>> That=E2=80=99s because the importer doesn=E2=80=99t let us specify a dif=
ferent branch.
>> We should add that, but it=E2=80=99s strictly separate from the migratio=
n we=E2=80=99re
>> about to embark on.
>
> I am not familiar with the updater (guix refresh -u).  My plan is:
>
>  1. Add bioconductor-git-reference
>  2. Adapt the bioconductor importer.
>  3. Updater?

The updater is closely connected to the importer.  It just needs to be
told how it can find new releases.

> The question is: do we have to include the migration in the updater?  Or
> do we do the migration by custom scripts?

We can do the migration manually.  But if we end up with a broken
updater I won=E2=80=99t be able to update Bioconductor packages in bulk; th=
at
would be a serious problem for future maintenance.

> Note that, because we do not support shallow clones, the complete
> sources will be a bit bigger; since they contain all the Bioconductor
> history of all the packages.

Doesn=E2=80=99t Guile-Git support shallow clones?  In any case, this should=
 not
be an obstacle for us.  Ensuring long-term reproducibility is more
important than space savings.

--=20
Ricardo




Message sent to bug-guix@HIDDEN:


X-Loop: help-debbugs@HIDDEN
Subject: bug#54787: importer Bioconductor: no tarball, only Git
Resent-From: Maxime Devos <maximedevos@HIDDEN>
Original-Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org>
Resent-CC: bug-guix@HIDDEN
Resent-Date: Thu, 14 Apr 2022 14:05:02 +0000
Resent-Message-ID: <handler.54787.B54787.164994509525196 <at> debbugs.gnu.org>
Resent-Sender: help-debbugs@HIDDEN
X-GNU-PR-Message: followup 54787
X-GNU-PR-Package: guix
X-GNU-PR-Keywords: 
To: Ricardo Wurmus <rekado@HIDDEN>, zimoun <zimon.toutoune@HIDDEN>
Cc: 54787 <at> debbugs.gnu.org
Received: via spool by 54787-submit <at> debbugs.gnu.org id=B54787.164994509525196
          (code B ref 54787); Thu, 14 Apr 2022 14:05:02 +0000
Received: (at 54787) by debbugs.gnu.org; 14 Apr 2022 14:04:55 +0000
Received: from localhost ([127.0.0.1]:56845 helo=debbugs.gnu.org)
	by debbugs.gnu.org with esmtp (Exim 4.84_2)
	(envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>)
	id 1nf05e-0006YK-WC
	for submit <at> debbugs.gnu.org; Thu, 14 Apr 2022 10:04:55 -0400
Received: from baptiste.telenet-ops.be ([195.130.132.51]:36350)
 by debbugs.gnu.org with esmtp (Exim 4.84_2)
 (envelope-from <maximedevos@HIDDEN>) id 1nf05d-0006YB-NA
 for 54787 <at> debbugs.gnu.org; Thu, 14 Apr 2022 10:04:54 -0400
Received: from ptr-bvsjgyhxw7psv60dyze.18120a2.ip6.access.telenet.be
 ([IPv6:2a02:1811:8c09:9d00:3c5f:2eff:feb0:ba5a])
 by baptiste.telenet-ops.be with bizsmtp
 id Je4r2700D4UW6Th01e4rrL; Thu, 14 Apr 2022 16:04:52 +0200
Message-ID: <2944d00df0662c6e041e9bf075616dd8e5e37169.camel@HIDDEN>
From: Maxime Devos <maximedevos@HIDDEN>
Date: Thu, 14 Apr 2022 16:04:51 +0200
In-Reply-To: <87wnfrvqcw.fsf@HIDDEN>
References: <868rsf23th.fsf@HIDDEN> <874k2zzj9p.fsf@HIDDEN>
 <87ilre5kvk.fsf@HIDDEN> <87wnfrvqcw.fsf@HIDDEN>
Content-Type: multipart/signed; micalg="pgp-sha512";
 protocol="application/pgp-signature"; boundary="=-XINam8b8N0XQ/IpdToQA"
User-Agent: Evolution 3.38.3-1 
MIME-Version: 1.0
DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=telenet.be; s=r22;
 t=1649945092; bh=2QFnw7I23PcWtmD5/x5TQxPCR3NeJc560amWKfy9RLc=;
 h=Subject:From:To:Cc:Date:In-Reply-To:References;
 b=W05NXOVA6Zu9WSnwW6wj2SvxYSJA+MlCAImSSeRVDkg4v5j5/VBANwbkjeSiedhIG
 v0MIxOrnfaKLDMX/DxXhmw0NltPqPwCMBjMxT4R8OP2Gke0rILM3JmTMVsVQ/CKFl/
 /kbcrzWeFaGE4ZL4odrIVj/d0u3vhOMXe+wvzPmNfDC9yw9F42hZcnFcIKXMe8WhWS
 6WQQ46fJHPN+kk1LDO1ApGDfvDf2Imjqdp1plvm951yA8K/h9ndll9k6bXwAOOB7WM
 rVNzrCseXobQlJQ0Ayf6igB1sdKk6mdWgKOOZEl4whWDNNtfLz3AlyFRkc6kKBJjgK
 tdCUU4c2g/bsQ==
X-Spam-Score: -0.0 (/)
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 (-)


--=-XINam8b8N0XQ/IpdToQA
Content-Type: text/plain; charset="UTF-8"
Content-Transfer-Encoding: quoted-printable

Ricardo Wurmus schreef op do 14-04-2022 om 13:43 [+0200]:
> I wonder how the updater would need to be changed.=C2=A0 It would need to
> know about the release branch and look for new commits in that branch
> only.

Perhaps <https://issues.guix.gnu.org/53144> would be useful?  It adds a
'latest-git-updater' refresher that looks in a branch (or more
generally, any reference, so in principle a tag that is repeatedly
replaced would work as well) for the latest commit.  There are some
unaddressed comments though ...

Greetings,
Maxime.

--=-XINam8b8N0XQ/IpdToQA
Content-Type: application/pgp-signature; name="signature.asc"
Content-Description: This is a digitally signed message part
Content-Transfer-Encoding: 7bit

-----BEGIN PGP SIGNATURE-----

iI0EABYKADUWIQTB8z7iDFKP233XAR9J4+4iGRcl7gUCYlgqAxccbWF4aW1lZGV2
b3NAdGVsZW5ldC5iZQAKCRBJ4+4iGRcl7r53AP9DlogcwqzNVNiIbvZVv8rP8A6e
0/wj7D0y26tFjrQ7dAEAm1ci9dT/ccFlZksZTOMxdHQecUgPo/Tw2SUoPnXXswo=
=zoB3
-----END PGP SIGNATURE-----

--=-XINam8b8N0XQ/IpdToQA--






Last modified: Thu, 14 Apr 2022 14:15:01 UTC

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