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Wed, 21 Feb 2024 13:16:10 -0500 (EST) From: Timothy Sample <samplet@HIDDEN> To: Simon Tournier <zimon.toutoune@HIDDEN> Subject: Re: bug#39885: Bioconductor tarballs are not archived In-Reply-To: <87v86k4cuk.fsf@HIDDEN> (Simon Tournier's message of "Mon, 19 Feb 2024 17:50:59 +0100") References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> <87lesqmmrr.fsf@HIDDEN> <874jgacq4u.fsf_-_@HIDDEN> <8734utba2a.fsf@HIDDEN> <87wmr7kr23.fsf@HIDDEN> <87y1bkwfly.fsf@HIDDEN> <87v86k4cuk.fsf@HIDDEN> Date: Wed, 21 Feb 2024 12:16:08 -0600 Message-ID: <87sf1lwumv.fsf@HIDDEN> User-Agent: Gnus/5.13 (Gnus v5.13) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: -2.6 (--) X-Debbugs-Envelope-To: 39885 Cc: rekado@HIDDEN, Ludovic =?utf-8?Q?Court=C3=A8s?= <ludovic.courtes@HIDDEN>, me@HIDDEN, 39885 <at> debbugs.gnu.org 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: -3.6 (---) Hi Simon, Simon Tournier <zimon.toutoune@HIDDEN> writes: > Just to be sure: we are speaking about Bioconductor only, right? I took =E2=80=9Cthis report=E2=80=9D to be the PoG report not the bug repor= t. My mistake! Sorry for the confusion. -- Tim
bug-guix@HIDDEN:bug#39885; Package guix.
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[194.254.61.44]) by smtp.gmail.com with ESMTPSA id bu19-20020a056000079300b0033d3d9447e3sm5973401wrb.83.2024.02.19.12.41.33 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 19 Feb 2024 12:41:33 -0800 (PST) From: Simon Tournier <zimon.toutoune@HIDDEN> To: Timothy Sample <samplet@HIDDEN> Subject: Re: bug#39885: Bioconductor tarballs are not archived In-Reply-To: <87y1bkwfly.fsf@HIDDEN> References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> <87lesqmmrr.fsf@HIDDEN> <874jgacq4u.fsf_-_@HIDDEN> <8734utba2a.fsf@HIDDEN> <87wmr7kr23.fsf@HIDDEN> <87y1bkwfly.fsf@HIDDEN> Date: Mon, 19 Feb 2024 17:50:59 +0100 Message-ID: <87v86k4cuk.fsf@HIDDEN> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: -0.3 (/) X-Debbugs-Envelope-To: 39885 Cc: rekado@HIDDEN, Ludovic =?utf-8?Q?Court=C3=A8s?= <ludovic.courtes@HIDDEN>, me@HIDDEN, 39885 <at> debbugs.gnu.org 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: -1.3 (-) Hi, On ven., 16 f=C3=A9vr. 2024 at 10:14, Timothy Sample <samplet@HIDDEN> wr= ote: >> Can we consider that this report is now done? Because: >> >> 1. SWH supports ExtID and nar hash lookup. >> >> 2. Missing origins are currently ingested by SWH. >> (via specific sources.json) > > I think that would be jumping the gun a little bit. > > In some sense, the report is only *done* when =E2=80=9Cstored=E2=80=9D hi= ts 100% (or > close to it, with the remainder being stuff we are pretty sure no longer > exists). This won=E2=80=99t happen just because of your second point the= re. Just to be sure: we are speaking about Bioconductor only, right? > When the historical =E2=80=9Csources.json=E2=80=9D is loaded, things will= be much, much, > better, sure. Sources will still be missing, though. Yeah, sources will still be missing but I expect that Bioconductor will be not. The only issue is about =E2=80=9Cannotation=E2=80=9D and maybe =E2= =80=9Cexperiment=E2=80=9D. However, here we are hitting the boundary between code and data: annotation and experiment might be very large and potentially skipped by SWH and they contain few if no code but plain data. We can still discuss what to do here; in this already long thread. :-) Or we can open another thread for this specific case about Bioconductor annotation and experiment. > To me, this is an > invitation to more subtle analysis, like weighing sources by their > =E2=80=9Cimportance=E2=80=9D in the package graph. Then there=E2=80=99s = still shortcomings with > Disarchive that have to be resolved (which is work best guided by > numbers in the report). Yeah. But that seems a large scope than Bioconductor case, no? > Also, it will always be a good idea to verify that things are working. > Ideally this could be simpler (leveraging ExtID lookup) and continuous. Indeed, checking that all Bioconductor sources can be extracted from SWH+Disarchive seems the path forward closing this report. :-) Cheers, simon
bug-guix@HIDDEN:bug#39885; Package guix.
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Fri, 16 Feb 2024 11:14:51 -0500 (EST) From: Timothy Sample <samplet@HIDDEN> To: Simon Tournier <zimon.toutoune@HIDDEN> Subject: Re: bug#39885: Bioconductor tarballs are not archived In-Reply-To: <87wmr7kr23.fsf@HIDDEN> (Simon Tournier's message of "Wed, 14 Feb 2024 16:23:48 +0100") References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> <87lesqmmrr.fsf@HIDDEN> <874jgacq4u.fsf_-_@HIDDEN> <8734utba2a.fsf@HIDDEN> <87wmr7kr23.fsf@HIDDEN> Date: Fri, 16 Feb 2024 10:14:49 -0600 Message-ID: <87y1bkwfly.fsf@HIDDEN> User-Agent: Gnus/5.13 (Gnus v5.13) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: -2.6 (--) X-Debbugs-Envelope-To: 39885 Cc: rekado@HIDDEN, Ludovic =?utf-8?Q?Court=C3=A8s?= <ludovic.courtes@HIDDEN>, me@HIDDEN, 39885 <at> debbugs.gnu.org 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: -3.6 (---) Simon Tournier <zimon.toutoune@HIDDEN> writes: > Cool! > > Can we consider that this report is now done? Because: > > 1. SWH supports ExtID and nar hash lookup. > > 2. Missing origins are currently ingested by SWH. > (via specific sources.json) I think that would be jumping the gun a little bit. In some sense, the report is only *done* when =E2=80=9Cstored=E2=80=9D hits= 100% (or close to it, with the remainder being stuff we are pretty sure no longer exists). This won=E2=80=99t happen just because of your second point there. When the historical =E2=80=9Csources.json=E2=80=9D is loaded, things will b= e much, much, better, sure. Sources will still be missing, though. To me, this is an invitation to more subtle analysis, like weighing sources by their =E2=80=9Cimportance=E2=80=9D in the package graph. Then there=E2=80=99s st= ill shortcomings with Disarchive that have to be resolved (which is work best guided by numbers in the report). Also, it will always be a good idea to verify that things are working. Ideally this could be simpler (leveraging ExtID lookup) and continuous. -- Tim
bug-guix@HIDDEN:bug#39885; Package guix.
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bug-guix@HIDDEN:bug#39885; Package guix.
Full text available.Received: (at 39885) by debbugs.gnu.org; 23 Jan 2024 09:10:46 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Tue Jan 23 04:10:46 2024 Received: from localhost ([127.0.0.1]:42204 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1rSCnt-0001xb-Se for submit <at> debbugs.gnu.org; Tue, 23 Jan 2024 04:10:46 -0500 Received: from mail2-relais-roc.national.inria.fr ([192.134.164.83]:15325) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <ludovic.courtes@HIDDEN>) id 1rSCno-0001xF-LA for 39885 <at> debbugs.gnu.org; Tue, 23 Jan 2024 04:10:44 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=inria.fr; s=dc; h=from:to:cc:subject:in-reply-to:references:date: message-id:mime-version:content-transfer-encoding; bh=7Mjr3o+zqqdUC81bql4HwDt9J79NNwtOji/FvLcSvrM=; b=tMnaOuT6o3Flo/7TP4G3vTsAiCPGq57BjypQE/ZQmfVsqlHFx5caCDQO CDb4AP4vLFGCxQHgbiYuRhxZ/PounJhPZhSBRZydaJeNKl6SCOjlnDxl1 3siiTNOwrU4HnPDW7mkcbjUfnDsEB3zuFeBa9p3neLN5VaOnf+hjEbhhf s=; Authentication-Results: mail2-relais-roc.national.inria.fr; dkim=none (message not signed) header.i=none; spf=SoftFail smtp.mailfrom=ludovic.courtes@HIDDEN; dmarc=fail (p=none dis=none) d=inria.fr X-IronPort-AV: E=Sophos;i="6.05,214,1701126000"; d="scan'208";a="148123271" Received: from unknown (HELO ribbon) ([193.50.110.52]) by mail2-relais-roc.national.inria.fr with ESMTP/TLS/ECDHE-RSA-AES256-GCM-SHA384; 23 Jan 2024 10:10:28 +0100 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= <ludovic.courtes@HIDDEN> To: Timothy Sample <samplet@HIDDEN> Subject: Re: Bioconductor tarballs are not archived In-Reply-To: <8734utba2a.fsf@HIDDEN> (Timothy Sample's message of "Fri, 19 Jan 2024 09:46:21 -0600") References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> <87lesqmmrr.fsf@HIDDEN> <874jgacq4u.fsf_-_@HIDDEN> <8734utba2a.fsf@HIDDEN> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: Quartidi 4 =?utf-8?Q?Pluvi=C3=B4se?= an 232 de la =?utf-8?Q?R=C3=A9volution=2C?= jour du Perce-neige 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: Tue, 23 Jan 2024 10:10:28 +0100 Message-ID: <87cytswh2z.fsf@HIDDEN> User-Agent: Gnus/5.13 (Gnus v5.13) 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: rekado@HIDDEN, 39885 <at> debbugs.gnu.org, me@HIDDEN, zimoun <zimon.toutoune@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 Timothy, Timothy Sample <samplet@HIDDEN> skribis: > Hello, > > Ludovic Court=C3=A8s <ludovic.courtes@HIDDEN> writes: > >> As for past tarballs, #swh-devel comrades say we could send them a list >> of URLs and they=E2=80=99d create =E2=80=9CSave Code Now=E2=80=9D reques= ts on our behalf (we >> cannot do it ourselves since the site doesn=E2=80=99t accept plain tarba= lls.) >> >> Any volunteer to write a script that=E2=80=99d generate a list of Biocon= ductor >> content-addressed URLs (the bordeaux.guix.gnu.org/file ones) for say the >> past couple of years? > > Sorry I=E2=80=99m a little late to this party, but I wrote a similar scri= pt a > while ago. It creates a =E2=80=9Csources.json=E2=80=9D file of all the s= ources that the > PoG database analyzed and found missing in SWH. It only covers what PoG > monitors (which is *almost* everything, but not quite). Excellent! > With some modifications, I used it to generate the attached list of > Bioconductor sources (based off of recent, unpublished PoG data). I=E2= =80=99ve > also attached the modifications in case anyone is curious or wants to > make a similar list. I will publish the PoG database soon (today?), so > maybe wait for that before generating any lists. After discussing it on #swh-devel, I filed this issue: https://gitlab.softwareheritage.org/swh/infra/sysadm-environment/-/issues= /5222 Tim, you were planning to offer a larger list of missing sources extracted from the PoG database, right? Thank you! Ludo=E2=80=99.
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19 Jan 2024 10:46:22 -0500 (EST)
From: Timothy Sample <samplet@HIDDEN>
To: Ludovic =?utf-8?Q?Court=C3=A8s?= <ludovic.courtes@HIDDEN>
Subject: Re: Bioconductor tarballs are not archived
In-Reply-To: <874jgacq4u.fsf_-_@HIDDEN> ("Ludovic =?utf-8?Q?Court=C3=A8s?=
=?utf-8?Q?=22's?= message of "Fri, 22 Dec 2023 14:40:01 +0100")
References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN>
<87lesqmmrr.fsf@HIDDEN> <874jgacq4u.fsf_-_@HIDDEN>
Date: Fri, 19 Jan 2024 09:46:21 -0600
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--=-=-=
Content-Type: text/plain; charset=utf-8
Content-Transfer-Encoding: quoted-printable
Hello,
Ludovic Court=C3=A8s <ludovic.courtes@HIDDEN> writes:
> As for past tarballs, #swh-devel comrades say we could send them a list
> of URLs and they=E2=80=99d create =E2=80=9CSave Code Now=E2=80=9D request=
s on our behalf (we
> cannot do it ourselves since the site doesn=E2=80=99t accept plain tarbal=
ls.)
>
> Any volunteer to write a script that=E2=80=99d generate a list of Biocond=
uctor
> content-addressed URLs (the bordeaux.guix.gnu.org/file ones) for say the
> past couple of years?
Sorry I=E2=80=99m a little late to this party, but I wrote a similar script=
a
while ago. It creates a =E2=80=9Csources.json=E2=80=9D file of all the sou=
rces that the
PoG database analyzed and found missing in SWH. It only covers what PoG
monitors (which is *almost* everything, but not quite).
$ git clone https://git.ngyro.com/preservation-of-guix
$ cd preservation-of-guix
$ wget https://ngyro.com/pog-reports/latest/pog.db
[Wait a long time because my server is sloooow.]
$ guile -L . etc/sources.scm pog.db > missing-sources.json
With some modifications, I used it to generate the attached list of
Bioconductor sources (based off of recent, unpublished PoG data). I=E2=80=
=99ve
also attached the modifications in case anyone is curious or wants to
make a similar list. I will publish the PoG database soon (today?), so
maybe wait for that before generating any lists.
-- Tim
--=-=-=
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--=-=-=
Content-Type: text/x-patch; charset=utf-8
Content-Disposition: inline; filename=bioconductor.patch
Content-Transfer-Encoding: quoted-printable
diff --git a/etc/sources.scm b/etc/sources.scm
index 71d157d..515cf00 100644
--- a/etc/sources.scm
+++ b/etc/sources.scm
@@ -1,5 +1,5 @@
;;; Preservation of Guix
-;;; Copyright =C2=A9 2022 Timothy Sample <samplet@HIDDEN>
+;;; Copyright =C2=A9 2022, 2024 Timothy Sample <samplet@HIDDEN>
;;;
;;; This file is part of Preservation of Guix.
;;;
@@ -61,6 +61,7 @@ FROM fods f
WHERE f.algorithm =3D 'sha256'
AND (fr.reference LIKE '\"%'
OR fr.reference LIKE '(\"%')
+ AND fr.reference LIKE '%bioconductor.org%'
AND NOT fr.is_error
AND f.is_in_swh IS NOT NULL
AND NOT f.is_in_swh")
@@ -85,22 +86,25 @@ Subresource Integrity metadata value."
(define b64 (base64-encode bv))
(string-append "sha256-" b64))
=20
-(define (web-reference-urls reference)
+(define (web-reference-filename reference)
(define uris
(match (call-with-input-string reference read)
((urls ...) (map string->uri urls))
(url (list (string->uri url)))))
- (append-map (lambda (uri)
- (map uri->string
- (maybe-expand-mirrors uri %mirrors)))
- uris))
+ (or (any (lambda (uri)
+ (and (string-suffix? "bioconductor.org" (uri-host uri))
+ (basename (uri-path uri))))
+ uris)
+ (error "Not a 'bioconductor.org' refernce" reference)))
=20
(define (record->url-source rec)
(match-let ((#(digest reference) rec))
- (let ((urls (web-reference-urls reference))
- (integrity (nix-base32-sha256->subresource-integrity digest)))
+ (let* ((filename (web-reference-filename reference))
+ (url (string-append "https://bordeaux.guix.gnu.org/file/"
+ filename "/sha256/" digest))
+ (integrity (nix-base32-sha256->subresource-integrity digest)))
`(("type" . "url")
- ("urls" . ,(list->vector urls))
+ ("urls" . ,(vector url))
("integrity" . ,integrity)))))
=20
(define (lookup-missing-sources db)
--=-=-=--
bug-guix@HIDDEN:bug#39885; Package guix.
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From: Simon Tournier <zimon.toutoune@HIDDEN>
To: Ricardo Wurmus <rekado@HIDDEN>, Ludovic =?utf-8?Q?Court=C3=A8s?=
<ludovic.courtes@HIDDEN>
Subject: Re: bug#39885: Bioconductor URI, fallback and time-machine
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Hi,
On Mon, 08 Jan 2024 at 16:34, Ricardo Wurmus <rekado@HIDDEN> wrote:
> The WIP commit is here:
>
> https://git.savannah.gnu.org/cgit/guix.git/commit/?h=3Dwip-r&id=3De81a75a=
7b28c633a658ceeb0a728255674f56c58
IIRC, the main feedback [1] of this approach is:
- the repositories at https://git.bioconductor.org/package/NAME do =
not
tag package versions. The only method of organization is branches
that are named after *Bioconductor releases* (not package release=
s),
e.g. RELEASE_3_15. We can only determine the package version by
reading its DESCRIPTION file or by looking up the version index f=
or
all Bioconductor packages (we do that already). This means that =
there
could be different commits for the same package version in the sa=
me
release branch =E2=80=94 so we have to include the commit hash an=
d a revision
counter in the version string.
Have you tried the wip commit at scale?
Cheers,
simon
1:bug#39885: Bioconductor URI, fallback and time-machine
Ricardo Wurmus <rekado@HIDDEN>
Wed, 10 Aug 2022 20:25:00 +0200
id:878rnwuemq.fsf@HIDDEN
https://issues.guix.gnu.org/39885
https://issues.guix.gnu.org/msgid/878rnwuemq.fsf@HIDDEN
https://yhetil.org/guix/878rnwuemq.fsf@HIDDEN
bug-guix@HIDDEN:bug#39885; Package guix.
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Subject: Re: bug#39885: Bioconductor tarballs are not archived
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Hi,
On Wed, 10 Jan 2024 at 13:42, Ricardo Wurmus <rekado@HIDDEN> wrote:
> Do we have a list of desired tarballs?
I made one. :-) I will share the manifest once a bit more polish. ;-)
Roughly, until 3.11 -- for earlier, I am still fighting with
time-machine -- and only the versions right before a Bioconductor
upgrade (and sadly not the version after such upgrade that, for many
have disappeared from Bioconductor). If you have them, cool! Well,
for now, I am speaking about all the Bioconductor packages except
annotations for these Guix revisions:
--8<---------------cut here---------------start------------->8---
git log --format="%P %s" --after=2019-04-30 \
| grep -i -E 'bioconductor' | grep -i -E '(update|upgrade)' \
| cut -f1 -d' ' \
| head -8
--8<---------------cut here---------------end--------------->8---
And for instance, I have this kind of sources.json.
--8<---------------cut here---------------start------------->8---
{
"sources": [
{
"type": "url",
"urls": [
"https://bordeaux.guix.gnu.org/file/progeny_1.22.0.tar.gz/sha256/047x6by3xa15gvi3kny5pkqxaq8d2kzcfi55ic5j7a351715l6l7",
"https://ci.guix.gnu.org/file/progeny_1.22.0.tar.gz/sha256/047x6by3xa15gvi3kny5pkqxaq8d2kzcfi55ic5j7a351715l6l7",
"https://bioconductor.org/packages/3.17/bioc/src/contrib/progeny_1.22.0.tar.gz",
"https://tarballs.nixos.org/sha256/047x6by3xa15gvi3kny5pkqxaq8d2kzcfi55ic5j7a351715l6l7"
],
"integrity": "sha256-hxpawgllqCMLi6VEx/4UDWHV8bzF2znifiWoPvwy/RA=",
"outputHashAlgo": "sha256",
"outputHashMode": "flat"
},
{
"type": "url",
"urls": [
"https://bordeaux.guix.gnu.org/file/AWFisher_1.14.0.tar.gz/sha256/1c6rr1z1rhvn8w1kb3nnjlfacfr22vwm1rsa1xqm2hmghs01bq4x",
"https://ci.guix.gnu.org/file/AWFisher_1.14.0.tar.gz/sha256/1c6rr1z1rhvn8w1kb3nnjlfacfr22vwm1rsa1xqm2hmghs01bq4x",
"https://bioconductor.org/packages/3.17/bioc/src/contrib/AWFisher_1.14.0.tar.gz",
"https://tarballs.nixos.org/sha256/1c6rr1z1rhvn8w1kb3nnjlfacfr22vwm1rsa1xqm2hmghs01bq4x"
],
"integrity": "sha256-neAVgIavQlFxD0rnUPkWIjumHJXWjjUDR3bDHH7I2bA=",
"outputHashAlgo": "sha256",
"outputHashMode": "flat"
},
--8<---------------cut here---------------end--------------->8---
Where the URL for ci.guix is incorrect, I guess.
Cheers,
simon
bug-guix@HIDDEN:bug#39885; Package guix.
Full text available.Received: (at 39885) by debbugs.gnu.org; 10 Jan 2024 14:28:01 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Wed Jan 10 09:28:01 2024 Received: from localhost ([127.0.0.1]:39420 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1rNZYn-00018X-1P for submit <at> debbugs.gnu.org; Wed, 10 Jan 2024 09:28:01 -0500 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21068) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <rekado@HIDDEN>) id 1rNZYg-00018G-WE for 39885 <at> debbugs.gnu.org; Wed, 10 Jan 2024 09:28:00 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1704890559; cv=none; d=zohomail.com; s=zohoarc; b=Vw3YVvVg+l8Ww+730VH8LgbkUcL13axymrkoTd0aj8ORpvn1nWw5jr9lNFS6PzlSjY1WdNdPSS1beYkQ3GuSJreePIE1VivjuK+QG4i1M4IIPPJqEwMgtSST4oIts+nLN3Bej+tKQ2m1I2PXZYDw70cEnugSgDLIA7y2ClIZI/4= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1704890559; h=Content-Type:Content-Transfer-Encoding:Cc:Cc:Date:Date:From:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:Subject:To:To:Message-Id:Reply-To; bh=V5l26fbAPpyPZ0PsL7NS82dGJU5DKtbz0VQctoO1LYU=; b=QgtKN3IVxmu+Nz/o/FG+GmBz4Cbv/JIEss+wM7GXP3P33GPdAppRjwqyoTkvb8z3BhgnaoLLddxgGJZCMFakTCXnXNg97FINksfV21T5KVGDhb+koGoD82mfdlCPZsbQHVV4A7yr08mIqri/RpuIj38SQoK48EwnjdTAbxuNaco= 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=1704890559; 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=V5l26fbAPpyPZ0PsL7NS82dGJU5DKtbz0VQctoO1LYU=; b=E8pC404Had4z7WRVZD4SxdjbPY3GbAnC9GMDNLWtk9+upk+hlaz++AE1c9+IDYSK NKafub4FngjCUuat1jtnOWyzjOySJ6dzN9Gw4T58GLSFPhP98SVsM6HoMUdWnvMIMiV wo58aXan8l6DrDaDSWHD7D68AhhrTqDeyyK6EIPc= Received: from localhost (103-108-142-46.pool.kielnet.net [46.142.108.103]) by mx.zohomail.com with SMTPS id 1704890558340799.109935415033; Wed, 10 Jan 2024 04:42:38 -0800 (PST) References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> <87lesqmmrr.fsf@HIDDEN> <874jgacq4u.fsf_-_@HIDDEN> <87le9019aj.fsf@HIDDEN> <878r4z7tr6.fsf@HIDDEN> User-agent: mu4e 1.10.8; emacs 29.1 From: Ricardo Wurmus <rekado@HIDDEN> To: Ludovic =?utf-8?Q?Court=C3=A8s?= <ludovic.courtes@HIDDEN> Subject: Re: bug#39885: Bioconductor tarballs are not archived Date: Wed, 10 Jan 2024 13:41:16 +0100 In-reply-to: <878r4z7tr6.fsf@HIDDEN> Message-ID: <87y1cx5phh.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-Debbugs-Envelope-To: 39885 Cc: Timothy Sample <samplet@HIDDEN>, 39885 <at> debbugs.gnu.org, me@HIDDEN, Simon Tournier <zimon.toutoune@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: -1.0 (-) Ludovic Court=C3=A8s <ludovic.courtes@HIDDEN> writes: > I my previous message, I wrote: > >> As for past tarballs, #swh-devel comrades say we could send them a list >> of URLs and they=E2=80=99d create =E2=80=9CSave Code Now=E2=80=9D reques= ts on our behalf (we >> cannot do it ourselves since the site doesn=E2=80=99t accept plain tarba= lls.) > > Were you able to retrieve some of these? What are the chances of > success? Do we have a list of desired tarballs? I still have an archived /gnu/store from before we moved the shared cluster installation at the MDC to different storage. It might contain old tarballs that we no longer have elsewhere. --=20 Ricardo
bug-guix@HIDDEN:bug#39885; Package guix.
Full text available.Received: (at 39885) by debbugs.gnu.org; 8 Jan 2024 15:35:04 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Mon Jan 08 10:35:04 2024 Received: from localhost ([127.0.0.1]:37315 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1rMrea-0005tv-2o for submit <at> debbugs.gnu.org; Mon, 08 Jan 2024 10:35:04 -0500 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21056) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <rekado@HIDDEN>) id 1rMreX-0005tG-It for 39885 <at> debbugs.gnu.org; Mon, 08 Jan 2024 10:35:03 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1704728092; cv=none; d=zohomail.com; s=zohoarc; b=Prxt9I+dmq2QNZdIBdLR0uQnmMlq0JmY4nodnBRe53vgOpqInX/cufS3Jj/uKufiMaxgm1/9AlR8q9xoqB4fIg63321e4R1wmLALcYZDSDYMDjx/MMHIcibvS/Z/13BT7jFXfCTJ57X5wFD/oJJ6BTVSBESHEG8Sb/z8xXqjFH8= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1704728092; h=Content-Type:Content-Transfer-Encoding:Cc:Cc:Date:Date:From:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:Subject:To:To:Message-Id:Reply-To; bh=EWZGmgCKEqapAwh2T1jMHEAM8KrExu0TV4nSIVceOc4=; b=kHRsXDQo2abFIWQjHqSeUJxg52UHpOCxWmKKgkacUP1ILjbkRf/eQF6az1BODFpMmy+e28/SxCT3kazGmM5+aHJUeL+Jo4/keTeRH902ZtZ4RVwys9Pu7TMv2PXEqD4isCThJKrxU5g6s1wK2gJxBOYbEbIYNvKLt3cVZdM1uL8= 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=1704728092; 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=EWZGmgCKEqapAwh2T1jMHEAM8KrExu0TV4nSIVceOc4=; b=RYj8xoG9GTCHZiPqsudbbDSXlMAztd8pCHsbw10/WUSwpXmayFsMAiXb+XDa5+y2 uLFDXHZNyLp7+R9ezalReWnSDZYbMo3mQYi23Bui28CKi5I9GSq1kxWbdDtbIdSPPYQ 8L3vcfL+iVBKx6A3haej9h9Cm7aKgH3P15K7JUvg= Received: from localhost (37-122-142-46.pool.kielnet.net [46.142.122.37]) by mx.zohomail.com with SMTPS id 17047280897031023.0038184204624; Mon, 8 Jan 2024 07:34:49 -0800 (PST) References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> <87lesqmmrr.fsf@HIDDEN> <87bktmtmol.fsf@HIDDEN> <878rnwuemq.fsf@HIDDEN> <87y1cz6ez3.fsf@HIDDEN> User-agent: mu4e 1.10.8; emacs 29.1 From: Ricardo Wurmus <rekado@HIDDEN> To: Ludovic =?utf-8?Q?Court=C3=A8s?= <ludovic.courtes@HIDDEN> Subject: Re: bug#39885: Bioconductor URI, fallback and time-machine Date: Mon, 08 Jan 2024 16:34:00 +0100 In-reply-to: <87y1cz6ez3.fsf@HIDDEN> Message-ID: <87frz7j0tl.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-Debbugs-Envelope-To: 39885 Cc: Timothy Sample <samplet@HIDDEN>, 39885 <at> debbugs.gnu.org, me@HIDDEN, zimoun <zimon.toutoune@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: -1.0 (-) Ludovic Court=C3=A8s <ludovic.courtes@HIDDEN> writes: >> With all these notes out of the way I=E2=80=99ll prepare a series of pat= ches >> next. > > I don=E2=80=99t think it happened but it=E2=80=99d still be nice. :-) The WIP commit is here: https://git.savannah.gnu.org/cgit/guix.git/commit/?h=3Dwip-r&id=3De81a75a7b= 28c633a658ceeb0a728255674f56c58 --=20 Ricardo
bug-guix@HIDDEN:bug#39885; Package guix.
Full text available.Received: (at 39885) by debbugs.gnu.org; 8 Jan 2024 15:07:45 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Mon Jan 08 10:07:45 2024 Received: from localhost ([127.0.0.1]:37273 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1rMrE8-0008Si-Ii for submit <at> debbugs.gnu.org; Mon, 08 Jan 2024 10:07:45 -0500 Received: from mail2-relais-roc.national.inria.fr ([192.134.164.83]:26486) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <ludovic.courtes@HIDDEN>) id 1rMrE5-0008SS-R8 for 39885 <at> debbugs.gnu.org; Mon, 08 Jan 2024 10:07:43 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=inria.fr; s=dc; h=from:to:cc:subject:in-reply-to:references:date: message-id:mime-version:content-transfer-encoding; bh=DihbBpiXSld5FpoMc0zDxghGaVFzRB3VrPlsPQNiMtE=; b=J00senfIRTGuoTJqo/uonIpMwkrIPsahmj+8uH/s/X4hBfW5hyHC0NAH S8Nq93U/HkW75w9Hk0BEPBYGKC3fRx9h3/fPMCr2bpflk4ji4RvBOPKN1 Glpxmc8bOSJ314ygzCLKVbpGHfSQ5M9lUX0loK29zWiFEZ3t39GSEg5lf A=; Authentication-Results: mail2-relais-roc.national.inria.fr; dkim=none (message not signed) header.i=none; spf=SoftFail smtp.mailfrom=ludovic.courtes@HIDDEN; dmarc=fail (p=none dis=none) d=inria.fr X-IronPort-AV: E=Sophos;i="6.04,180,1695679200"; d="scan'208";a="145443751" Received: from unknown (HELO ribbon) ([193.50.110.52]) by mail2-relais-roc.national.inria.fr with ESMTP/TLS/ECDHE-RSA-AES256-GCM-SHA384; 08 Jan 2024 16:07:30 +0100 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= <ludovic.courtes@HIDDEN> To: Ricardo Wurmus <rekado@HIDDEN> Subject: Re: bug#39885: Bioconductor URI, fallback and time-machine In-Reply-To: <878rnwuemq.fsf@HIDDEN> (Ricardo Wurmus's message of "Wed, 10 Aug 2022 20:25:00 +0200") References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> <87lesqmmrr.fsf@HIDDEN> <87bktmtmol.fsf@HIDDEN> <878rnwuemq.fsf@HIDDEN> Date: Mon, 08 Jan 2024 16:07:28 +0100 Message-ID: <87y1cz6ez3.fsf@HIDDEN> User-Agent: Gnus/5.13 (Gnus v5.13) 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: Timothy Sample <samplet@HIDDEN>, 39885 <at> debbugs.gnu.org, me@HIDDEN, zimoun <zimon.toutoune@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, (Replying to a 1.5-year-old message=E2=80=A6) Ricardo Wurmus <rekado@HIDDEN> skribis: > I have finally taken the time to review this and implement a first draft > of a change to the bioconductor importer and updater. > > There are some limitations: > > - we cannot use the updater to go from =E2=80=9Curl-fetch=E2=80=9D to =E2= =80=9Cgit-fetch=E2=80=9D. > That=E2=80=99s because =E2=80=9Cpackage-update=E2=80=9D in (guix upstre= am) decides whether to > use package-update/url-fetch or package-update/git-fetch based on the > *current* package value=E2=80=99s origin fetch procedure. For the swit= ch we > can hack around this (adding an exception for bioconductor packages), > but there is no pretty way to do this in a generic fashion that could > be committed. > > Perhaps we could operate on the url included in the <upstream-source> > instead of looking at the *current* package value. We=E2=80=99re only > accessing =E2=80=9Cpackage=E2=80=9D once in the url-fetch case, so mayb= e we can work > around this problem. Alternatively, how about writing a custom one-shot tool to change the =E2=80=98source=E2=80=99 field of all the Bioconductor packages to =E2=80= =98git-fetch=E2=80=99? It may be easier than adjusting (guix upstream) to cater to this probably unusual case. > - the repositories at https://git.bioconductor.org/package/NAME do not > tag package versions. The only method of organization is branches > that are named after *Bioconductor releases* (not package releases), > e.g. RELEASE_3_15. We can only determine the package version by > reading its DESCRIPTION file or by looking up the version index for > all Bioconductor packages (we do that already). This means that there > could be different commits for the same package version in the same > release branch =E2=80=94 so we have to include the commit hash and a re= vision > counter in the version string. OK, sounds acceptable. > - the updater doesn=E2=80=99t work on version expressions like (git-versi= on > "1.12" revision commit). It expects to be able to replace literal > strings. Because of that my changes let the importer generate a > string literal such as "1.12-0.cafebab" without a let-bound commit > string. Maybe we can build upon Maxime=E2=80=99s patch at <https://issues.guix.gnu.org/53144#13>? > - =E2=80=9Cexperiment=E2=80=9D or =E2=80=9Cdata=E2=80=9D packages are not= kept in Git. They only exist > as volatile tarballs that will be overwritten. Thankfully, they don=E2= =80=99t > change all that often, so they have a good chance of making it into > our archives. > > - the above exception means that we need to litter the importer and > updater code with extra checks. > > With all these notes out of the way I=E2=80=99ll prepare a series of patc= hes > next. I don=E2=80=99t think it happened but it=E2=80=99d still be nice. :-) Thanks, Ludo=E2=80=99.
bug-guix@HIDDEN:bug#39885; Package guix.
Full text available.Received: (at 39885) by debbugs.gnu.org; 8 Jan 2024 15:03:10 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Mon Jan 08 10:03:10 2024 Received: from localhost ([127.0.0.1]:37261 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1rMr9i-0008Lk-14 for submit <at> debbugs.gnu.org; Mon, 08 Jan 2024 10:03:10 -0500 Received: from mail2-relais-roc.national.inria.fr ([192.134.164.83]:26138) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <ludovic.courtes@HIDDEN>) id 1rMr9f-0008LD-2q for 39885 <at> debbugs.gnu.org; Mon, 08 Jan 2024 10:03:08 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=inria.fr; s=dc; h=from:to:cc:subject:in-reply-to:references:date: message-id:mime-version:content-transfer-encoding; bh=qbj/JfvBSQWwsE/H3sHWuV7ZUqUL+1oVforSbs2mDmA=; b=nwSAYJ/edjmGEkJssYDrD/T/d+CVn5QIT11NZkS6v8gP0+jpAa/A78Ap okPOLV1vfTPHm/POmeahAFFqH6TeFiOawCvxwqM/VZWyLvbwzVceA+vNe RAYWv+aQ9ec+Y6q2i6qjxY2iOVi/iP0Y5a1Va9okrcNeop4wqJHE4WAoN U=; Authentication-Results: mail2-relais-roc.national.inria.fr; dkim=none (message not signed) header.i=none; spf=SoftFail smtp.mailfrom=ludovic.courtes@HIDDEN; dmarc=fail (p=none dis=none) d=inria.fr X-IronPort-AV: E=Sophos;i="6.04,180,1695679200"; d="scan'208";a="145442450" Received: from unknown (HELO ribbon) ([193.50.110.52]) by mail2-relais-roc.national.inria.fr with ESMTP/TLS/ECDHE-RSA-AES256-GCM-SHA384; 08 Jan 2024 16:02:54 +0100 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= <ludovic.courtes@HIDDEN> To: Simon Tournier <zimon.toutoune@HIDDEN> Subject: Re: bug#39885: Bioconductor tarballs are not archived In-Reply-To: <87le9019aj.fsf@HIDDEN> (Simon Tournier's message of "Mon, 08 Jan 2024 10:09:08 +0100") References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> <87lesqmmrr.fsf@HIDDEN> <874jgacq4u.fsf_-_@HIDDEN> <87le9019aj.fsf@HIDDEN> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: Nonidi 19 =?utf-8?Q?Niv=C3=B4se?= an 232 de la =?utf-8?Q?R=C3=A9volution=2C?= jour du Marbre 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: Mon, 08 Jan 2024 16:02:53 +0100 Message-ID: <878r4z7tr6.fsf@HIDDEN> User-Agent: Gnus/5.13 (Gnus v5.13) 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: rekado@HIDDEN, Timothy Sample <samplet@HIDDEN>, 39885 <at> debbugs.gnu.org, 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! Simon Tournier <zimon.toutoune@HIDDEN> skribis: >> I was wondering whether we=E2=80=99re now doing better for Bioconductor >> tarballs. The answer, based on small sample, seems to be =E2=80=9Cnot q= uite=E2=80=9D: [...] > but, now the past reads, > > $ for url in https://bioconductor.org/packages/release/bioc/src/contrib/B= iocNeighbors_1.20.0.tar.gz \ > https://bioconductor.org/packages/3.18/bioc/src/contrib/Bioc= Neighbors_1.20.0.tar.gz ; \ > do guix download $url ;done Thanks for investigating & explaining! I my previous message, I wrote: > As for past tarballs, #swh-devel comrades say we could send them a list > of URLs and they=E2=80=99d create =E2=80=9CSave Code Now=E2=80=9D request= s on our behalf (we > cannot do it ourselves since the site doesn=E2=80=99t accept plain tarbal= ls.) Were you able to retrieve some of these? What are the chances of success? > Hence the discussion we had: switch from url-fetch to git-fetch. > However, after some investigations, it does not seem straightforward: > The main issue being the almost automatic current updater. See for > details [2]. [...] > https://issues.guix.gnu.org/msgid/878rnwuemq.fsf@HIDDEN Indeed, thanks for the link. I agree that long-term moving to =E2=80=98git-fetch=E2=80=99 sounds preferable, but there are quite a few ob= stacles to overcome. Ludo=E2=80=99.
bug-guix@HIDDEN:bug#39885; Package guix.
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From: Simon Tournier <zimon.toutoune@HIDDEN>
To: Ludovic =?utf-8?Q?Court=C3=A8s?= <ludovic.courtes@HIDDEN>
Subject: Re: bug#39885: Bioconductor tarballs are not archived
In-Reply-To: <874jgacq4u.fsf_-_@HIDDEN>
References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN>
<87lesqmmrr.fsf@HIDDEN> <874jgacq4u.fsf_-_@HIDDEN>
Date: Mon, 08 Jan 2024 10:09:08 +0100
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Hi,
On Fri, 22 Dec 2023 at 14:40, Ludovic Court=C3=A8s <ludovic.courtes@HIDDEN=
r> wrote:
>> guix build: error: build of `/gnu/store/q9ggmh5a9bzmnr49p10x1w9sv6pzjarv=
-BiocNeighbors_1.4.1.tar.gz.drv' failed
First thing first, please note that we are speaking about tag 1.4.1 and
not 1.20.0. And this 1.4.1 is gone from =E2=80=9Cour=E2=80=9D infra since=
=E2=80=A6 ?? That=E2=80=99s
one of the things I do not like with Guix: I never know what to expect
from the infra. Anyway, I have my list of TODOs for improving the
annoyances (I and maybe others have :-)); stay tuned. ;-)
Considering the state of =E2=80=9Cour=E2=80=9D infra and how Bioconductor m=
anages the
tarballs, many tarballs are lost forever, sadly. Although the content
is still around, I guess.
> I was wondering whether we=E2=80=99re now doing better for Bioconductor
> tarballs. The answer, based on small sample, seems to be =E2=80=9Cnot qu=
ite=E2=80=9D:
Thanks for diving into this.
> <https://guix.gnu.org/sources.json> has entries like:
>
> --8<---------------cut here---------------start------------->8---
> {
> "type": "url",
> "urls": [
> "https://bioconductor.org/packages/release/bioc/src/contrib/BiocN=
eighbors_1.20.0.tar.gz",
> "https://bioconductor.org/packages/3.18/bioc/src/contrib/BiocNeig=
hbors_1.20.0.tar.gz",
> "https://bordeaux.guix.gnu.org/file/BiocNeighbors_1.20.0.tar.gz/s=
ha256/0a5wg099fgwjbzd6r3mr4l02rcmjqlkdcz1w97qzwx1mir41fmas",
> "https://ci.guix.gnu.org/file/BiocNeighbors_1.20.0.tar.gz/sha256/=
0a5wg099fgwjbzd6r3mr4l02rcmjqlkdcz1w97qzwx1mir41fmas",
> "https://tarballs.nixos.org/sha256/0a5wg099fgwjbzd6r3mr4l02rcmjql=
kdcz1w97qzwx1mir41fmas"
> ],
> "integrity": "sha256-WlUXSI41dP7xSTx81ibFsrIsACW5jmzaX5I/lxJ4vCg=3D=
",
> "outputHashAlgo": "sha256",
> "outputHashMode": "flat"
> },
> --8<---------------cut here---------------end--------------->8---
Please note that Bioconductor 3.18 released BiocNeighbors v1.20.0 but
then updated to v1.20.1 still under Bioconductor 3.18 and Ricardo did
this update with 5673484cbc2ed74c61ae81d623646fa7829fbc32. On a side
note, between the Bioconductor update and the update on our side, there
is a mismatch where the source of r-biocneighbors is unreachable.
Other said, post-update on our side,
--8<---------------cut here---------------start------------->8---
$ zcat sources.json | jq | grep BiocNeighbors | grep bioconductor | sed 's/=
"//g' | sed 's/,//g'
https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeig=
hbors_1.20.1.tar.gz
https://bioconductor.org/packages/3.18/bioc/src/contrib/BiocNeighbo=
rs_1.20.1.tar.gz
$ for url in $(zcat sources.json | jq | grep BiocNeighbors | grep bioconduc=
tor | sed 's/"//g' | sed 's/,//g'); \
do guix download $url ;done
Starting download of /tmp/guix-file.STc9fQ
From https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbo=
rs_1.20.1.tar.gz...
=E2=80=A6_1.20.1.tar.gz 1015KiB =
60.3MiB/s 00:00 =E2=96=95=E2=
=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=
=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=
=E2=96=88=E2=96=8F 100.0%
/gnu/store/nxab1pskh9zcjspczph6jcs5fk79pb7k-BiocNeighbors_1.20.1.tar.gz
0w7hd6w0lmj1jaaq9zd5gwnnpkzcr0byqm5q584wjg4xgvsb981j
Starting download of /tmp/guix-file.aZFRLv
From https://bioconductor.org/packages/3.18/bioc/src/contrib/BiocNeighbors_=
1.20.1.tar.gz...
=E2=80=A6_1.20.1.tar.gz 1015KiB =
63.5MiB/s 00:00 =E2=96=95=E2=
=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=
=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=E2=96=88=
=E2=96=88=E2=96=8F 100.0%
/gnu/store/nxab1pskh9zcjspczph6jcs5fk79pb7k-BiocNeighbors_1.20.1.tar.gz
0w7hd6w0lmj1jaaq9zd5gwnnpkzcr0byqm5q584wjg4xgvsb981j
--8<---------------cut here---------------end--------------->8---
but, now the past reads,
--8<---------------cut here---------------start------------->8---
$ for url in https://bioconductor.org/packages/release/bioc/src/contrib/Bio=
cNeighbors_1.20.0.tar.gz \
https://bioconductor.org/packages/3.18/bioc/src/contrib/BiocNe=
ighbors_1.20.0.tar.gz ; \
do guix download $url ;done
> >=20
Starting download of /tmp/guix-file.MUB3ow
From https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbo=
rs_1.20.0.tar.gz...
download failed "https://bioconductor.org/packages/release/bioc/src/contrib=
/BiocNeighbors_1.20.0.tar.gz" 404 "Not Found"
Starting download of /tmp/guix-file.MUB3ow
From https://web.archive.org/web/20240102105016/https://bioconductor.org/pa=
ckages/release/bioc/src/contrib/BiocNeighbors_1.20.0.tar.gz...
download failed "https://web.archive.org/web/20240102105016/https://biocond=
uctor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.20.0.tar.gz" 40=
4 "NOT FOUND"
Trying to use Disarchive to assemble /tmp/guix-file.MUB3ow...
could not find its Disarchive specification
failed to download "/tmp/guix-file.MUB3ow" from "https://bioconductor.org/p=
ackages/release/bioc/src/contrib/BiocNeighbors_1.20.0.tar.gz"
guix download: error: https://bioconductor.org/packages/release/bioc/src/co=
ntrib/BiocNeighbors_1.20.0.tar.gz: download failed
Starting download of /tmp/guix-file.ZO9N08
From https://bioconductor.org/packages/3.18/bioc/src/contrib/BiocNeighbors_=
1.20.0.tar.gz...
download failed "https://bioconductor.org/packages/3.18/bioc/src/contrib/Bi=
ocNeighbors_1.20.0.tar.gz" 404 "Not Found"
Starting download of /tmp/guix-file.ZO9N08
From https://web.archive.org/web/20240102105018/https://bioconductor.org/pa=
ckages/3.18/bioc/src/contrib/BiocNeighbors_1.20.0.tar.gz...
download failed "https://web.archive.org/web/20240102105018/https://biocond=
uctor.org/packages/3.18/bioc/src/contrib/BiocNeighbors_1.20.0.tar.gz" 404 "=
NOT FOUND"
Trying to use Disarchive to assemble /tmp/guix-file.ZO9N08...
could not find its Disarchive specification
failed to download "/tmp/guix-file.ZO9N08" from "https://bioconductor.org/p=
ackages/3.18/bioc/src/contrib/BiocNeighbors_1.20.0.tar.gz"
guix download: error: https://bioconductor.org/packages/3.18/bioc/src/contr=
ib/BiocNeighbors_1.20.0.tar.gz: download failed
--8<---------------cut here---------------end--------------->8---
As explained in [1], Bioconductor removes v1.20.0 from their URI scheme
and despite the fact Bioconductor v3.18 had released v1.20.0, arf! And
I do not even know if the tarball of v1.20.0 is kept on Bioconductor
infra. Hum?
Hence the discussion we had: switch from url-fetch to git-fetch.
However, after some investigations, it does not seem straightforward:
The main issue being the almost automatic current updater. See for
details [2].
1: bug#39885: Bioconductor URI, fallback and time-machine
zimoun <zimon.toutoune@HIDDEN>
Mon, 18 Jul 2022 18:03:04 +0200
id:87lesqmmrr.fsf@HIDDEN
https://issues.guix.gnu.org/39885
https://issues.guix.gnu.org/msgid/87lesqmmrr.fsf@HIDDEN
https://yhetil.org/guix/87lesqmmrr.fsf@HIDDEN
2: bug#39885: Bioconductor URI, fallback and time-machine
Ricardo Wurmus <rekado@HIDDEN>
Wed, 10 Aug 2022 20:25:00 +0200
id:878rnwuemq.fsf@HIDDEN
https://issues.guix.gnu.org/39885
https://issues.guix.gnu.org/msgid/878rnwuemq.fsf@HIDDEN
https://yhetil.org/guix/878rnwuemq.fsf@HIDDEN
> Any volunteer to write a script that=E2=80=99d generate a list of Biocond=
uctor
> content-addressed URLs (the bordeaux.guix.gnu.org/file ones) for say the
> past couple of years?
I did stuff past week about that. I will report this week what I did.
Cheers,
simon
bug-guix@HIDDEN:bug#39885; Package guix.
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From: Simon Tournier <zimon.toutoune@HIDDEN>
To: Ludovic =?utf-8?Q?Court=C3=A8s?= <ludo@HIDDEN>
Subject: Re: bug#39885: Bioconductor URI, fallback and time-machine
In-Reply-To: <87ttoa7y6p.fsf@HIDDEN>
References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN>
<87lesqmmrr.fsf@HIDDEN> <87ttoa7y6p.fsf@HIDDEN>
Date: Tue, 02 Jan 2024 10:20:27 +0100
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Content preview: Hi Ludo, On Fri, 22 Dec 2023 at 21:57, Ludovic Courtès wrote:
> In hindsight this is not surprising: this is a Dec. 2019 commit and I >
set up <https://ci.guix.gnu.org/jobset/disarchive>, > disarchive.guix.gnu.org,
and related machinery in Sep/Oct 2021. > > Of c [...]
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Content preview: Hi Ludo, On Fri, 22 Dec 2023 at 21:57, Ludovic Courtès wrote:
> In hindsight this is not surprising: this is a Dec. 2019 commit and I >
set up <https://ci.guix.gnu.org/jobset/disarchive>, > disarchive.guix.gnu.org,
and related machinery in Sep/Oct 2021. > > Of c [...]
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manager
Hi Ludo,
On Fri, 22 Dec 2023 at 21:57, Ludovic Court=C3=A8s <ludo@HIDDEN> wrote:
> In hindsight this is not surprising: this is a Dec. 2019 commit and I
> set up <https://ci.guix.gnu.org/jobset/disarchive>,
> disarchive.guix.gnu.org, and related machinery in Sep/Oct 2021.
>
> Of course Timothy set up <https://disarchive.ngyro.com> earlier, but not
> so much=E2=80=94Timothy started work on Disarchive ca. July 2020:
> <https://issues.guix.gnu.org/42162#15>.
>
> (Not that it helps but at least it=E2=80=99s a relief to know that this
> particular problem predates our more serious efforts.)
Yeah! On the other hand, I wish that Guix will be able to build all =E2=80=
=93
or at least most of =E2=80=93 the packages that time-machine is able to rea=
ch =E2=80=93
say Guix v1.0. :-) Let be ambitious. ;-)
Cheers,
simon
bug-guix@HIDDEN:bug#39885; Package guix.
Full text available.
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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
In-Reply-To: <87lesqmmrr.fsf@HIDDEN> (zimoun's message of "Mon, 18 Jul 2022
18:03:04 +0200")
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Date: Fri, 22 Dec 2023 21:57:18 +0100
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zimoun <zimon.toutoune@HIDDEN> skribis:
> $ guix time-machine --commit=3D77e2de365497bf4c8b81cbd78624f78293490485 \
> -- build r-biocneighbors -S
[...]
> Trying to use Disarchive to assemble /gnu/store/zgf7x09kgiqbvj0dmhplxi1xz=
pljxd7k-BiocNeighbors_1.4.1.tar.gz...
> could not find its Disarchive specification
> failed to download "/gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeigh=
bors_1.4.1.tar.gz" from ("https://bioconductor.org/packages/release/bioc/sr=
c/contrib/BiocNeighbors_1.4.1.tar.gz" "https://bioconductor.org/packages/3.=
10/bioc/src/contrib/Archive/BiocNeighbors_1.4.1.tar.gz")
> builder for `/gnu/store/q9ggmh5a9bzmnr49p10x1w9sv6pzjarv-BiocNeighbors_1.=
4.1.tar.gz.drv' failed to produce output path `/gnu/store/zgf7x09kgiqbvj0dm=
hplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz'
In hindsight this is not surprising: this is a Dec. 2019 commit and I
set up <https://ci.guix.gnu.org/jobset/disarchive>,
disarchive.guix.gnu.org, and related machinery in Sep/Oct 2021.
Of course Timothy set up <https://disarchive.ngyro.com> earlier, but not
so much=E2=80=94Timothy started work on Disarchive ca. July 2020:
<https://issues.guix.gnu.org/42162#15>.
(Not that it helps but at least it=E2=80=99s a relief to know that this
particular problem predates our more serious efforts.)
Ludo=E2=80=99.
bug-guix@HIDDEN:bug#39885; Package guix.
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From: =?utf-8?Q?Ludovic_Court=C3=A8s?= <ludovic.courtes@HIDDEN>
To: zimoun <zimon.toutoune@HIDDEN>
Subject: Bioconductor tarballs are not archived
In-Reply-To: <87lesqmmrr.fsf@HIDDEN> (zimoun's message of "Mon, 18 Jul 2022
18:03:04 +0200")
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Date: Fri, 22 Dec 2023 14:40:01 +0100
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Hello!
zimoun <zimon.toutoune@HIDDEN> skribis:
> Since 2020, I provided several examples of breakage with bug#39885 [1].
> Here another one:
>
> $ guix time-machine --commit=3D77e2de365497bf4c8b81cbd78624f78293490485 \
> -- build r-biocneighbors -S
[...]
> Starting download of /gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeig=
hbors_1.4.1.tar.gz
>>From https://web.archive.org/web/20220718175152/https://bioconductor.org/=
packages/release/bioc/src/contrib/BiocNeighbors_1.4.1.tar.gz...
> download failed "https://web.archive.org/web/20220718175152/https://bioco=
nductor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.4.1.tar.gz" 4=
04 "NOT FOUND"
> Trying to use Disarchive to assemble /gnu/store/zgf7x09kgiqbvj0dmhplxi1xz=
pljxd7k-BiocNeighbors_1.4.1.tar.gz...
> could not find its Disarchive specification
> failed to download "/gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeigh=
bors_1.4.1.tar.gz" from ("https://bioconductor.org/packages/release/bioc/sr=
c/contrib/BiocNeighbors_1.4.1.tar.gz" "https://bioconductor.org/packages/3.=
10/bioc/src/contrib/Archive/BiocNeighbors_1.4.1.tar.gz")
> builder for `/gnu/store/q9ggmh5a9bzmnr49p10x1w9sv6pzjarv-BiocNeighbors_1.=
4.1.tar.gz.drv' failed to produce output path `/gnu/store/zgf7x09kgiqbvj0dm=
hplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz'
> build of /gnu/store/q9ggmh5a9bzmnr49p10x1w9sv6pzjarv-BiocNeighbors_1.4.1.=
tar.gz.drv failed
> View build log at '/var/log/guix/drvs/q9/ggmh5a9bzmnr49p10x1w9sv6pzjarv-B=
iocNeighbors_1.4.1.tar.gz.drv.gz'.
> guix build: error: build of `/gnu/store/q9ggmh5a9bzmnr49p10x1w9sv6pzjarv-=
BiocNeighbors_1.4.1.tar.gz.drv' failed
>
> Well, several comments:
>
> 1. Berlin or Bordeaux do not have it as substitutes,
> 2. Diasarchive does not have it,
> 3. Many others neither.
I was wondering whether we=E2=80=99re now doing better for Bioconductor
tarballs. The answer, based on small sample, seems to be =E2=80=9Cnot quit=
e=E2=80=9D:
--8<---------------cut here---------------start------------->8---
$ guix lint -c archival $(guix package -A ^r-bioc | cut -f1)
gnu/packages/bioconductor.scm:19708:12: r-biocbaseutils@HIDDEN: Disarchive e=
ntry refers to non-existent SWH directory '726af85395d163b5a21e52e4df1bf18a=
a0072f6b'
gnu/packages/bioconductor.scm:19752:12: r-bioccheck@HIDDEN: Disarchive entr=
y refers to non-existent SWH directory '12cfedcbc27005a3fb7e01c5c4b727e0116=
f596f'
gnu/packages/bioconductor.scm:16892:5: r-biocfilecache@HIDDEN: Disarchive e=
ntry refers to non-existent SWH directory '6a2d6d909a7cedd56e96f5a98770deea=
aaa8d220'
gnu/packages/bioconductor.scm:4540:12: r-biocgenerics@HIDDEN: Disarchive en=
try refers to non-existent SWH directory '6f19ea14f46dbc75909b77bc08e9023da=
ae6fb9e'
gnu/packages/bioconductor.scm:19785:5: r-biocgraph@HIDDEN: Disarchive entry=
refers to non-existent SWH directory '977ff052b4e6c948af7af0fc14ae61f71427=
cb1a'
gnu/packages/bioconductor.scm:21524:6: r-biocio@HIDDEN: Disarchive entry re=
fers to non-existent SWH directory '29d8fef9a5b386384f20513c612f1e34f611853=
2'
gnu/packages/bioconductor.scm:13090:5: r-biocneighbors@HIDDEN: Disarchive e=
ntry refers to non-existent SWH directory '6d3728b2dee78cceecdeba0318f3e57b=
6013d96f'
gnu/packages/bioconductor.scm:19957:5: r-bioconcotk@HIDDEN: Disarchive entr=
y refers to non-existent SWH directory '251081d4bc3f061ef8e16338eb042ad4c71=
ed02d'
gnu/packages/bioconductor.scm:20003:5: r-biocor@HIDDEN: Disarchive entry re=
fers to non-existent SWH directory '0cc9d3dcde06fb353cdd77f3b538845d16a7772=
0'
gnu/packages/bioconductor.scm:6613:12: r-biocparallel@HIDDEN: Disarchive en=
try refers to non-existent SWH directory '41e09414898f61655bcc99fdd44d69b05=
31c0b2d'
gnu/packages/bioconductor.scm:20030:5: r-biocpkgtools@HIDDEN: Disarchive en=
try refers to non-existent SWH directory '55de8618648ed16797a8effd5b508c652=
a5d7cbe'
gnu/packages/bioconductor.scm:20144:5: r-biocset@HIDDEN: Disarchive entry r=
efers to non-existent SWH directory '1cfa6cac0cb453f2882a35c8f5ae6ddfa713ad=
2d'
gnu/packages/bioconductor.scm:13276:5: r-biocsingular@HIDDEN: Disarchive en=
try refers to non-existent SWH directory '992d3f9d48633fa5d46b9a7640a825054=
e9538aa'
gnu/packages/bioconductor.scm:19806:12: r-biocstyle@HIDDEN: Disarchive entr=
y refers to non-existent SWH directory 'bb17c3bd9ac7c373b24782fcfecdde5fa2f=
0a965'
gnu/packages/bioconductor.scm:22965:5: r-biocthis@HIDDEN: Disarchive entry =
refers to non-existent SWH directory '3d08f77aae1e81ce9ca9bb9ae2adf4d4c7421=
d11'
gnu/packages/bioconductor.scm:4521:5: r-biocversion@HIDDEN: source not arch=
ived on Software Heritage and missing from the Disarchive database
gnu/packages/bioconductor.scm:19830:12: r-biocviews@HIDDEN: Disarchive entr=
y refers to non-existent SWH directory '47e0877ab988469fc09a37505dd769f9626=
cac2e'
gnu/packages/bioconductor.scm:20182:5: r-biocworkflowtools@HIDDEN: Disarchi=
ve entry refers to non-existent SWH directory '393f3472cc27f632caea3488aef9=
3a7675b403ef'
$ guix describe
Generation 285 Dec 17 2023 23:31:56 (current)
guix 6ab2426
repository URL: https://git.savannah.gnu.org/git/guix.git
branch: master
commit: 6ab242609daec00e8bd54f7bff54557c92695724
--8<---------------cut here---------------end--------------->8---
In all cases but one, we=E2=80=99re doing the right thing Disarchive-wise, =
but
our SWH did not archive them.
<https://guix.gnu.org/sources.json> has entries like:
--8<---------------cut here---------------start------------->8---
{
"type": "url",
"urls": [
"https://bioconductor.org/packages/release/bioc/src/contrib/BiocNei=
ghbors_1.20.0.tar.gz",
"https://bioconductor.org/packages/3.18/bioc/src/contrib/BiocNeighb=
ors_1.20.0.tar.gz",
"https://bordeaux.guix.gnu.org/file/BiocNeighbors_1.20.0.tar.gz/sha=
256/0a5wg099fgwjbzd6r3mr4l02rcmjqlkdcz1w97qzwx1mir41fmas",
"https://ci.guix.gnu.org/file/BiocNeighbors_1.20.0.tar.gz/sha256/0a=
5wg099fgwjbzd6r3mr4l02rcmjqlkdcz1w97qzwx1mir41fmas",
"https://tarballs.nixos.org/sha256/0a5wg099fgwjbzd6r3mr4l02rcmjqlkd=
cz1w97qzwx1mir41fmas"
],
"integrity": "sha256-WlUXSI41dP7xSTx81ibFsrIsACW5jmzaX5I/lxJ4vCg=3D",
"outputHashAlgo": "sha256",
"outputHashMode": "flat"
},
--8<---------------cut here---------------end--------------->8---
Note that we have at least one copy on our infra:
--8<---------------cut here---------------start------------->8---
$ wget -qO- "https://bordeaux.guix.gnu.org/file/BiocNeighbors_1.20.0.tar.gz=
/sha256/0a5wg099fgwjbzd6r3mr4l02rcmjqlkdcz1w97qzwx1mir41fmas"|guix hash - =
-f base64
WlUXSI41dP7xSTx81ibFsrIsACW5jmzaX5I/lxJ4vCg=3D
--8<---------------cut here---------------end--------------->8---
<https://ci.guix.gnu.org/file/BiocNeighbors_1.20.0.tar.gz/sha256/0a5wg099fg=
wjbzd6r3mr4l02rcmjqlkdcz1w97qzwx1mir41fmas>
is 404 (but I can see why: for /file, =E2=80=98guix publish=E2=80=99 relies=
on things
being available in the store and we no longer keep them on ci.guix; we
do have a substitute at
<https://ci.guix.gnu.org/nar/6kfpflffl7b4hx6ibb5k879ar8ffcxb7-BiocNeighbors=
_1.20.0.tar.gz>
though; we should fix this).
What about hypothesis (2)? This is what we have:
--8<---------------cut here---------------start------------->8---
$ wget -qO- https://disarchive.guix.gnu.org/sha256//5a5517488e3574fef1493c7=
cd626c5b2b22c0025b98e6cda5f923f971278bc28 |grep swh
(swhid "swh:1:dir:6d3728b2dee78cceecdeba0318f3e57b6=
013d96f"))
--8<---------------cut here---------------end--------------->8---
I checked with folks on #swh-devel and it turns out that =E2=80=9Cthe legacy
nixguix lister that is still used in production did not detect the
fallback URL as a tarball URL=E2=80=9D (the bordeaux.guix.gnu.org URL), but=
this
is fixed in the new lister, which should be in production =E2=80=9Csoon=E2=
=80=9D.
As for past tarballs, #swh-devel comrades say we could send them a list
of URLs and they=E2=80=99d create =E2=80=9CSave Code Now=E2=80=9D requests =
on our behalf (we
cannot do it ourselves since the site doesn=E2=80=99t accept plain tarballs=
.)
Any volunteer to write a script that=E2=80=99d generate a list of Bioconduc=
tor
content-addressed URLs (the bordeaux.guix.gnu.org/file ones) for say the
past couple of years?
Thanks!
Ludo=E2=80=99.
bug-guix@HIDDEN:bug#39885; Package guix.
Full text available.Received: (at 39885) by debbugs.gnu.org; 9 Sep 2022 17:31:09 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Fri Sep 09 13:31:09 2022 Received: from localhost ([127.0.0.1]:35339 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1oWhqP-00058f-E7 for submit <at> debbugs.gnu.org; Fri, 09 Sep 2022 13:31:09 -0400 Received: from mail-wm1-f53.google.com ([209.85.128.53]:52917) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <zimon.toutoune@HIDDEN>) id 1oWhqM-00057e-Kn for 39885 <at> debbugs.gnu.org; Fri, 09 Sep 2022 13:31:08 -0400 Received: by mail-wm1-f53.google.com with SMTP id k17so1959315wmr.2 for <39885 <at> debbugs.gnu.org>; Fri, 09 Sep 2022 10:31:06 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=content-transfer-encoding:mime-version:message-id:date:references :in-reply-to:subject:cc:to:from:from:to:cc:subject:date; bh=30UyClpR35f238PPvnrXeSqi8iXd3D64lce5xlpYj+Y=; b=I05xII/4MKR96B0cm+gxjKr0fDCxNXKsd46Zvu9f56dUTosHprY+7H8708py8qDm/I zOh7/jXdWGGFCiaXlzwbVh9mLzX8DlpuosknTi1tfbeQMFq04cmpfzrKrzRhkUNcRMy2 eCcasLC16wSx5HypyC5Oryp0DH3pbGq4vK5Xr3ETAKGmncdrwH4kVTDDRhUKtO3RkV4f 6ZY/VRSPBIwLwbf5bCSMNwkxTsIR7EhyONXuJvRLYnuRIfQoAlY+VB6dZQKAvUk43N6B lVCDbp5OA191GXPehFgBVhhHyjPUDmO46a4z7eFBP4TNf1D+2hjZvBEM7bPnY5QfLWS4 hWGA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=content-transfer-encoding:mime-version:message-id:date:references :in-reply-to:subject:cc:to:from:x-gm-message-state:from:to:cc :subject:date; bh=30UyClpR35f238PPvnrXeSqi8iXd3D64lce5xlpYj+Y=; b=DZt96w9kMgc3vHqvw6X24Hpg+lZ7CRfJdZoVwjUIu1IaCqKSL2xwtwgtLhP5LNruP9 h11o7InNHm+8elziZ1bAmM6CaD6EI++sLnsiRk6DHrIm2hTNaNkEtKeih4TywB9hmelE 95RxGJWHkBR6XOoIv3tviaBGyHwV1K1ZpEQPpcwjd7HiSQJYAoh3BqzNp2TnRi/V1QDd hxMrdPB23DMf15UjqZ5vpM4B5onsX/TYS93ZnSZwcZS18f0HBlMlOQvNcGGh5OnGtfBc 4+i3fmJWP5sjuVZMkFr44Rh/bcMWKJ5iiboAcL72AqTuyLGwHod3KP+Qy6iA8dhTDvv2 2x2w== X-Gm-Message-State: ACgBeo3etLuc1+GoSXFccdLdXOHZjdtuSkynon3mRkGWnumc49UjzcQn zhgUr9GVaKKi0T7ATPesFFw= X-Google-Smtp-Source: AA6agR55IkmlW6LdxcOfP6NW1WoGRyBFkT2x+4yiNhBeie+YoMTCxlgJicu3MAA18CJp5GU0eJH/Sw== X-Received: by 2002:a05:600c:4ed3:b0:3a6:15c5:297f with SMTP id g19-20020a05600c4ed300b003a615c5297fmr6344306wmq.49.1662744660578; Fri, 09 Sep 2022 10:31:00 -0700 (PDT) Received: from lili (roam-nat-fw-prg-194-254-61-47.net.univ-paris-diderot.fr. [194.254.61.47]) by smtp.gmail.com with ESMTPSA id a3-20020adff7c3000000b00228db6b9406sm1237736wrq.45.2022.09.09.10.30.59 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 09 Sep 2022 10:31:00 -0700 (PDT) From: zimoun <zimon.toutoune@HIDDEN> To: Ricardo Wurmus <rekado@HIDDEN> Subject: Re: bug#39885: Bioconductor URI, fallback and time-machine In-Reply-To: <878rnwuemq.fsf@HIDDEN> References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> <87lesqmmrr.fsf@HIDDEN> <87bktmtmol.fsf@HIDDEN> <878rnwuemq.fsf@HIDDEN> Date: Fri, 09 Sep 2022 19:23:12 +0200 Message-ID: <865yhwpim7.fsf@HIDDEN> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 39885 Cc: Timothy Sample <samplet@HIDDEN>, 39885 <at> debbugs.gnu.org, 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: -1.0 (-) Hi Ricardo, I am late. This message landed when I was traveling for holidays. :-) On Wed, 10 Aug 2022 at 20:25, Ricardo Wurmus <rekado@HIDDEN> wrote: > - we cannot use the updater to go from =E2=80=9Curl-fetch=E2=80=9D to =E2= =80=9Cgit-fetch=E2=80=9D. > That=E2=80=99s because =E2=80=9Cpackage-update=E2=80=9D in (guix upstre= am) decides whether to > use package-update/url-fetch or package-update/git-fetch based on the > *current* package value=E2=80=99s origin fetch procedure. For the swit= ch we > can hack around this (adding an exception for bioconductor packages), > but there is no pretty way to do this in a generic fashion that could > be committed. It appears to me acceptable to have an exception. Or even to do it just once as a big replacement of Bioconductor packages. > - the repositories at https://git.bioconductor.org/package/NAME do not > tag package versions. The only method of organization is branches > that are named after *Bioconductor releases* (not package releases), > e.g. RELEASE_3_15. We can only determine the package version by > reading its DESCRIPTION file or by looking up the version index for > all Bioconductor packages (we do that already). This means that there > could be different commits for the same package version in the same > release branch =E2=80=94 so we have to include the commit hash and a re= vision > counter in the version string. This is the most annoying part. Indeed, when I check out some Bioconductor Git repositories, I am always confused by their Git structure. From my understanding, the tarball you fetch from bioconductor.org has the same content than the commit tagged =E2=80=9CBioconductor release=E2=80= =9D (RELEASE_X_Y). The content of the upstream release can mismatch the content of the Bioconductor tarball release. I do not know how it would be complicated or inaccurate to consider the package version from the Bioconductor index and assign this version to the commit tagged RELEASE_X_Y. This commit would appear in the Guix package definition though. Or maybe we transparently could RELEASE_X_Y to determine this commit. > - the updater doesn=E2=80=99t work on version expressions like (git-versi= on > "1.12" revision commit). It expects to be able to replace literal > strings. Because of that my changes let the importer generate a > string literal such as "1.12-0.cafebab" without a let-bound commit > string. Maxime pointed patch#53144 [1] but I have not looked at it yet. 1: <https://issues.guix.gnu.org/53144#13> > - =E2=80=9Cexperiment=E2=80=9D or =E2=80=9Cdata=E2=80=9D packages are not= kept in Git. They only exist > as volatile tarballs that will be overwritten. Thankfully, they don=E2= =80=99t > change all that often, so they have a good chance of making it into > our archives. That=E2=80=99s an interesting question for Disarchive and Software Heritage. Cheers, simon
bug-guix@HIDDEN:bug#39885; Package guix.
Full text available.Received: (at 39885) by debbugs.gnu.org; 10 Aug 2022 19:48:40 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Wed Aug 10 15:48:40 2022 Received: from localhost ([127.0.0.1]:50818 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1oLrh2-0005hC-Fr for submit <at> debbugs.gnu.org; Wed, 10 Aug 2022 15:48:40 -0400 Received: from xavier.telenet-ops.be ([195.130.132.52]:41934) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <maximedevos@HIDDEN>) id 1oLrh0-0005h4-HR for 39885 <at> debbugs.gnu.org; Wed, 10 Aug 2022 15:48:39 -0400 Received: from [IPV6:2a02:1811:8c09:9d00:5dba:d409:33f7:a16] ([IPv6:2a02:1811:8c09:9d00:5dba:d409:33f7:a16]) by xavier.telenet-ops.be with bizsmtp id 5vod2800320ykKC01vodJG; Wed, 10 Aug 2022 21:48:37 +0200 Message-ID: <0d6b6bae-4ab3-aad5-f03d-f6e369620267@HIDDEN> Date: Wed, 10 Aug 2022 21:48:37 +0200 MIME-Version: 1.0 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:91.0) Gecko/20100101 Thunderbird/91.12.0 Subject: Re: bug#39885: Bioconductor URI, fallback and time-machine Content-Language: en-US From: Maxime Devos <maximedevos@HIDDEN> To: Ricardo Wurmus <rekado@HIDDEN>, zimoun <zimon.toutoune@HIDDEN> References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> <87lesqmmrr.fsf@HIDDEN> <87bktmtmol.fsf@HIDDEN> <878rnwuemq.fsf@HIDDEN> <4041b7dd-df1d-318c-0ca9-efe296203ea9@HIDDEN> In-Reply-To: <4041b7dd-df1d-318c-0ca9-efe296203ea9@HIDDEN> Content-Type: multipart/signed; micalg=pgp-sha256; protocol="application/pgp-signature"; boundary="------------5NR32MArIFNI7RA2FDeUYReA" DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=telenet.be; s=r22; t=1660160917; bh=MHI2K69UpMZnN+Lo+o4vxlI6vPFS6pi1rbsta96jadg=; h=Date:Subject:From:To:Cc:References:In-Reply-To; b=cRjEZpSFnrIZ7ahluPCxvh8lWcmexhaowX7Pl73l2sgEuiFy5LjIonog5qCSkkQxJ yRKZ4x0AXS3T7wJKaQtVHwUSOQfD0C2JQIcUu4Ke0mXDrffrppjg3811HdZ0eyhNTn xDW+2bSVYUWn/q7RxYgkrcbl8y3jius8YOb1g9J1b/KnmErxUJaB3jNQNQbUfDTyE7 e5DcFjh+VUbU+7ZVaPQCE6w0jisQr5/T94+mMzf6XB7Oflia2W6G0JapIU3F97k+pt Du626Wx6syh22DbOe4k0Ru8gXgXhjIRNr+/GyiJAFLRGrQnMMB5YZMsVti/PWnDC6+ HCAXZbjUwQoSQ== X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 39885 Cc: Timothy Sample <samplet@HIDDEN>, 39885 <at> debbugs.gnu.org, 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: -1.7 (-) This is an OpenPGP/MIME signed message (RFC 4880 and 3156) --------------5NR32MArIFNI7RA2FDeUYReA Content-Type: multipart/mixed; boundary="------------j7Ow3tgqmo4iFFRcVqiBw5I0"; protected-headers="v1" From: Maxime Devos <maximedevos@HIDDEN> To: Ricardo Wurmus <rekado@HIDDEN>, zimoun <zimon.toutoune@HIDDEN> Cc: Timothy Sample <samplet@HIDDEN>, 39885 <at> debbugs.gnu.org, me@HIDDEN Message-ID: <0d6b6bae-4ab3-aad5-f03d-f6e369620267@HIDDEN> Subject: Re: bug#39885: Bioconductor URI, fallback and time-machine References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> <87lesqmmrr.fsf@HIDDEN> <87bktmtmol.fsf@HIDDEN> <878rnwuemq.fsf@HIDDEN> <4041b7dd-df1d-318c-0ca9-efe296203ea9@HIDDEN> In-Reply-To: <4041b7dd-df1d-318c-0ca9-efe296203ea9@HIDDEN> --------------j7Ow3tgqmo4iFFRcVqiBw5I0 Content-Type: multipart/mixed; boundary="------------0QRLayFZcg5CTE6HmrKY6GRz" --------------0QRLayFZcg5CTE6HmrKY6GRz Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: base64 DQpPbiAxMC0wOC0yMDIyIDIxOjQ0LCBNYXhpbWUgRGV2b3Mgd3JvdGU6DQo+DQo+IE9uIDEw LTA4LTIwMjIgMjA6MjUsIFJpY2FyZG8gV3VybXVzIHdyb3RlOg0KPj4gLSB0aGUgdXBkYXRl ciBkb2VzbuKAmXQgd29yayBvbiB2ZXJzaW9uIGV4cHJlc3Npb25zIGxpa2UgKGdpdC12ZXJz aW9uDQo+PiDCoMKgICIxLjEyIiByZXZpc2lvbiBjb21taXQpLsKgIEl0IGV4cGVjdHMgdG8g YmUgYWJsZSB0byByZXBsYWNlIGxpdGVyYWwNCj4+IMKgwqAgc3RyaW5ncy7CoCBCZWNhdXNl IG9mIHRoYXQgbXkgY2hhbmdlcyBsZXQgdGhlIGltcG9ydGVyIGdlbmVyYXRlIGENCj4+IMKg wqAgc3RyaW5nIGxpdGVyYWwgc3VjaCBhcyAiMS4xMi0wLmNhZmViYWIiIHdpdGhvdXQgYSBs ZXQtYm91bmQgY29tbWl0DQo+PiDCoMKgIHN0cmluZy4NCj4gSSd2ZSBhIHBhdGNoIHRoYXQg aW1wbGVtZW50cyByZXBsYWNpbmcgKHJldmlzaW9uICJOIikgYnkgKHJldmlzaW9uIA0KPiAi TisxIiksIGFwcGFyZW50bHkgaXQncyBub3QgYXBwbGllZCB5ZXQgYnV0IGxldCBtZSBzZWFy Y2ggZm9yIGl0IC4uLg0KDQpGb3VuZCBpdDoNCg0KPGh0dHBzOi8vaXNzdWVzLmd1aXguZ251 Lm9yZy81MzE0NCMxMz4NCg0KVGhhdCBwYXRjaCBzZXJpZXMgd2FzIHdyaXR0ZW4gd2l0aCBN aW5ldGVzdCAvIENvbnRlbnREQiBhbmQgYSBuZXcgDQonbGF0ZXN0LWdpdCcgdXBkYXRlciBp biBtaW5kLCBidXQgdGhlIENvbnRlbnREQiBhbmQgbGF0ZXN0LWdpdCBiaXRzIA0Kc2hvdWxk IGJlIHNlcGFyYWJsZSB3aXRob3V0IG11Y2ggdHJvdWJsZS4NCg0KR3JlZXRpbmdzLA0KTWF4 aW1lLg0KDQo= --------------0QRLayFZcg5CTE6HmrKY6GRz Content-Type: application/pgp-keys; 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bug-guix@HIDDEN:bug#39885; Package guix.
Full text available.Received: (at 39885) by debbugs.gnu.org; 10 Aug 2022 19:44:54 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Wed Aug 10 15:44:54 2022 Received: from localhost ([127.0.0.1]:50813 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1oLrdN-0005YX-Tv for submit <at> debbugs.gnu.org; Wed, 10 Aug 2022 15:44:54 -0400 Received: from xavier.telenet-ops.be ([195.130.132.52]:37760) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <maximedevos@HIDDEN>) id 1oLrdK-0005YM-10 for 39885 <at> debbugs.gnu.org; Wed, 10 Aug 2022 15:44:52 -0400 Received: from [IPV6:2a02:1811:8c09:9d00:5dba:d409:33f7:a16] ([IPv6:2a02:1811:8c09:9d00:5dba:d409:33f7:a16]) by xavier.telenet-ops.be with bizsmtp id 5vkn2800120ykKC01vknjF; Wed, 10 Aug 2022 21:44:48 +0200 Message-ID: <4041b7dd-df1d-318c-0ca9-efe296203ea9@HIDDEN> Date: Wed, 10 Aug 2022 21:44:46 +0200 MIME-Version: 1.0 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:91.0) Gecko/20100101 Thunderbird/91.12.0 Subject: Re: bug#39885: Bioconductor URI, fallback and time-machine Content-Language: en-US To: Ricardo Wurmus <rekado@HIDDEN>, zimoun <zimon.toutoune@HIDDEN> References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> <87lesqmmrr.fsf@HIDDEN> <87bktmtmol.fsf@HIDDEN> <878rnwuemq.fsf@HIDDEN> From: Maxime Devos <maximedevos@HIDDEN> In-Reply-To: <878rnwuemq.fsf@HIDDEN> Content-Type: multipart/signed; micalg=pgp-sha256; protocol="application/pgp-signature"; boundary="------------kZthixqD0lRwLYSdlfte8yIx" DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=telenet.be; s=r22; t=1660160688; bh=vklUgoy0gA5SxO9KNthNg0AF2SwknnpX1WSSOz/VgZs=; h=Date:Subject:To:Cc:References:From:In-Reply-To; b=jWsyYjZzytptGQsA9UUtc9fqFqOxMr5vdriIDXvMwMbyfSIdVLCpzh32vg6TDWIqj ax4uLOfXrksuDRWQcJEv2FBJirpXEmgYCi88wMGW2z+BC8GaFDUiekDt3JxLtu2GUj WNT2nFUyGC4vhE2SGE7RYI2xYajQw5nHc7xvWQLasQn9FYAJX28XOgO62XFmpbViVu DJmNfVebJkw+O3+eWdqH/kdlcrYNdDnwvsMrE5T46zMKwTBx/lGp1GyrJjWR/40pWy Q5GBgtmpAyN/TArl76c9RONPP8XuU26dtWtMyBCi7xP7yevBtm8Ah+87Ugge2ctsN3 WHZm0KzWCgn6g== X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 39885 Cc: Timothy Sample <samplet@HIDDEN>, 39885 <at> debbugs.gnu.org, 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: -1.7 (-) This is an OpenPGP/MIME signed message (RFC 4880 and 3156) --------------kZthixqD0lRwLYSdlfte8yIx Content-Type: multipart/mixed; boundary="------------T0SWrOg5MZ5FP3FwRTAr0Wlk"; protected-headers="v1" From: Maxime Devos <maximedevos@HIDDEN> To: Ricardo Wurmus <rekado@HIDDEN>, zimoun <zimon.toutoune@HIDDEN> Cc: Timothy Sample <samplet@HIDDEN>, 39885 <at> debbugs.gnu.org, me@HIDDEN Message-ID: <4041b7dd-df1d-318c-0ca9-efe296203ea9@HIDDEN> Subject: Re: bug#39885: Bioconductor URI, fallback and time-machine References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> <87lesqmmrr.fsf@HIDDEN> <87bktmtmol.fsf@HIDDEN> <878rnwuemq.fsf@HIDDEN> In-Reply-To: <878rnwuemq.fsf@HIDDEN> --------------T0SWrOg5MZ5FP3FwRTAr0Wlk Content-Type: multipart/mixed; boundary="------------h5iTW6m3qu3ULcZizGeBfV8X" --------------h5iTW6m3qu3ULcZizGeBfV8X Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: base64 DQpPbiAxMC0wOC0yMDIyIDIwOjI1LCBSaWNhcmRvIFd1cm11cyB3cm90ZToNCj4gLSB0aGUg dXBkYXRlciBkb2VzbuKAmXQgd29yayBvbiB2ZXJzaW9uIGV4cHJlc3Npb25zIGxpa2UgKGdp dC12ZXJzaW9uDQo+ICAgICIxLjEyIiByZXZpc2lvbiBjb21taXQpLiAgSXQgZXhwZWN0cyB0 byBiZSBhYmxlIHRvIHJlcGxhY2UgbGl0ZXJhbA0KPiAgICBzdHJpbmdzLiAgQmVjYXVzZSBv ZiB0aGF0IG15IGNoYW5nZXMgbGV0IHRoZSBpbXBvcnRlciBnZW5lcmF0ZSBhDQo+ICAgIHN0 cmluZyBsaXRlcmFsIHN1Y2ggYXMgIjEuMTItMC5jYWZlYmFiIiB3aXRob3V0IGEgbGV0LWJv dW5kIGNvbW1pdA0KPiAgICBzdHJpbmcuDQpJJ3ZlIGEgcGF0Y2ggdGhhdCBpbXBsZW1lbnRz IHJlcGxhY2luZyAocmV2aXNpb24gIk4iKSBieSAocmV2aXNpb24gDQoiTisxIiksIGFwcGFy ZW50bHkgaXQncyBub3QgYXBwbGllZCB5ZXQgYnV0IGxldCBtZSBzZWFyY2ggZm9yIGl0IC4u Lg0K --------------h5iTW6m3qu3ULcZizGeBfV8X Content-Type: application/pgp-keys; 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bug-guix@HIDDEN:bug#39885; Package guix.
Full text available.Received: (at 39885) by debbugs.gnu.org; 10 Aug 2022 18:39:53 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Wed Aug 10 14:39:53 2022 Received: from localhost ([127.0.0.1]:50758 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1oLqcS-0003vd-Kr for submit <at> debbugs.gnu.org; Wed, 10 Aug 2022 14:39:52 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21186) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <rekado@HIDDEN>) id 1oLqcN-0003vQ-K4 for 39885 <at> debbugs.gnu.org; Wed, 10 Aug 2022 14:39:51 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1660156785; cv=none; d=zohomail.com; s=zohoarc; b=oI1wx+LoiUZ66DqvhGL2gR7QrUtwZDxCHp2+bmVbD8xKmkjNU3ewmG6TVFqaLSaZyOXSVPvEsQJnuEZLVcZa+mLc9Mp+S+9l2+YIxdbEqa6ePZtZx5AVkmNIKwaGY1+QrQYqdEcjvtRWxKQ7yFzdXhq0GyBLLJCP3DL+AdDYuZk= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1660156785; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=TeXmwSVxSxS260Wh7R3Zw5zrphz8e645fb7uLQEv5cQ=; b=P3NVT84apMP/W0OqPCDPmXR5w70V3xyEKXwF41o0WI5mSwVvkY5M4ljgdL6niiEND7zRuA2fsUbBqxB9vx5SWG1FhxuM9/H9jDDT3XJdmmn81exaEMAIA23tD90vmvQVX11O6yLWiORSa8C9WoBhgONcuUcocsOD7h41nk+AYDw= 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=1660156785; 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=TeXmwSVxSxS260Wh7R3Zw5zrphz8e645fb7uLQEv5cQ=; b=H/7bGZSneLGmrCs/7YoQLZqBbwOnKEtUULLVmcXphRcAtynR0MgILbKlx9bhjeB8 HLLFWcb6szztx33LqYih8XCESNZ9SY0MkQhA1bpx5F1wO0yCxr1ozhltBPm8DESSuHH YdC6ATsE2AndG8QJAmF8cuCTeIksSluyELJvh7RY= Received: from localhost (i5E862C5E.versanet.de [94.134.44.94]) by mx.zohomail.com with SMTPS id 1660156784131221.60771061448702; Wed, 10 Aug 2022 11:39:44 -0700 (PDT) References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> <87lesqmmrr.fsf@HIDDEN> <87bktmtmol.fsf@HIDDEN> User-agent: mu4e 1.8.7; emacs 28.1 From: Ricardo Wurmus <rekado@HIDDEN> To: zimoun <zimon.toutoune@HIDDEN> Subject: Re: bug#39885: Bioconductor URI, fallback and time-machine Date: Wed, 10 Aug 2022 20:25:00 +0200 In-reply-to: <87bktmtmol.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: <878rnwuemq.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-Debbugs-Envelope-To: 39885 Cc: Timothy Sample <samplet@HIDDEN>, 39885 <at> debbugs.gnu.org, 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: -1.0 (-) Ricardo Wurmus <rekado@HIDDEN> writes: > zimoun <zimon.toutoune@HIDDEN> writes: > >> At the cost of more bandwidth, we could switch from url-fetch to >> git-fetch. > > Let=E2=80=99s do it! I=E2=80=99m tired of Bioconductor archive shenaniga= ns messing with > package availability. I have finally taken the time to review this and implement a first draft of a change to the bioconductor importer and updater. There are some limitations: - we cannot use the updater to go from =E2=80=9Curl-fetch=E2=80=9D to =E2= =80=9Cgit-fetch=E2=80=9D. That=E2=80=99s because =E2=80=9Cpackage-update=E2=80=9D in (guix upstream= ) decides whether to use package-update/url-fetch or package-update/git-fetch based on the *current* package value=E2=80=99s origin fetch procedure. For the switch= we can hack around this (adding an exception for bioconductor packages), but there is no pretty way to do this in a generic fashion that could be committed. Perhaps we could operate on the url included in the <upstream-source> instead of looking at the *current* package value. We=E2=80=99re only accessing =E2=80=9Cpackage=E2=80=9D once in the url-fetch case, so maybe = we can work around this problem. - the repositories at https://git.bioconductor.org/package/NAME do not tag package versions. The only method of organization is branches that are named after *Bioconductor releases* (not package releases), e.g. RELEASE_3_15. We can only determine the package version by reading its DESCRIPTION file or by looking up the version index for all Bioconductor packages (we do that already). This means that there could be different commits for the same package version in the same release branch =E2=80=94 so we have to include the commit hash and a revi= sion counter in the version string. - the updater doesn=E2=80=99t work on version expressions like (git-version "1.12" revision commit). It expects to be able to replace literal strings. Because of that my changes let the importer generate a string literal such as "1.12-0.cafebab" without a let-bound commit string. - =E2=80=9Cexperiment=E2=80=9D or =E2=80=9Cdata=E2=80=9D packages are not k= ept in Git. They only exist as volatile tarballs that will be overwritten. Thankfully, they don=E2= =80=99t change all that often, so they have a good chance of making it into our archives. - the above exception means that we need to litter the importer and updater code with extra checks. With all these notes out of the way I=E2=80=99ll prepare a series of patches next. --=20 Ricardo
bug-guix@HIDDEN:bug#39885; Package guix.
Full text available.Received: (at 39885) by debbugs.gnu.org; 18 Jul 2022 16:23:17 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Mon Jul 18 12:23:17 2022 Received: from localhost ([127.0.0.1]:51910 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1oDTWe-0001sO-UT for submit <at> debbugs.gnu.org; Mon, 18 Jul 2022 12:23:17 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21149) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <rekado@HIDDEN>) id 1oDTWa-0001sC-Bl for 39885 <at> debbugs.gnu.org; Mon, 18 Jul 2022 12:23:16 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1658161390; cv=none; d=zohomail.com; s=zohoarc; b=L4Za99exrEzRCpsUrDq1WoW9fYTGdH6kXedMrUtz37L6a4YZYtEBorMA/Hp4fttxDcw+iyI+MAteUyUstcsvMfpnFY//hvEYFuhRYAwMVB+Hp0Nn6JR0JPzlKeuwc3C3T7AifHwSUqqj+yYL5P4pF4GaznAKBKJkaSIHEvWiH0k= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1658161390; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=rDwB9hlLn6y3Ll9lcY0vgweAsUrgjRk7+iiUggPqo9o=; b=e7yBCzLYtd5MDvDiSruzw2hwP5ZcUzh5yYdrmMdO2w2bO1GkXuRQo6CPo8oSws2+CYP1/tkkg6upQFU5XceaVfv6Nu19POdzHZEOB6DCvWRzdyHiUa/UWRalcTwqlAX/m0maqW3xjozNDMXnt2rdYzf5N9+zamvtXP6zDXypdNw= 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=1658161390; 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=rDwB9hlLn6y3Ll9lcY0vgweAsUrgjRk7+iiUggPqo9o=; b=UFgA+0poJd9kw6PmWNE96kkLYIWIdv9QpVu5DLh02EzW0uYgSLSpPWBEKbMSj4cA oSytHfOLpwFJ3NHbe+Jc7UJAauGvFtYlp+wfipXmS5t+t6dqxBYETyCxRCUXCbhOvzZ THNyidiDYFTsWxImk8XSng9I3VOBqL0eWeZwuiOM= Received: from localhost (i5E862CB9.versanet.de [94.134.44.185]) by mx.zohomail.com with SMTPS id 1658161389855328.6619222096223; Mon, 18 Jul 2022 09:23:09 -0700 (PDT) References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> <87lesqmmrr.fsf@HIDDEN> User-agent: mu4e 1.6.11; emacs 28.1 From: Ricardo Wurmus <rekado@HIDDEN> To: zimoun <zimon.toutoune@HIDDEN> Subject: Re: bug#39885: Bioconductor URI, fallback and time-machine Date: Mon, 18 Jul 2022 18:21:56 +0200 In-reply-to: <87lesqmmrr.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: <87bktmtmol.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-Debbugs-Envelope-To: 39885 Cc: Timothy Sample <samplet@HIDDEN>, 39885 <at> debbugs.gnu.org, 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: -1.0 (-) zimoun <zimon.toutoune@HIDDEN> writes: > At the cost of more bandwidth, we could switch from url-fetch to > git-fetch. Let=E2=80=99s do it! I=E2=80=99m tired of Bioconductor archive shenanigans= messing with package availability. --=20 Ricardo
bug-guix@HIDDEN:bug#39885; Package guix.
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From: zimoun <zimon.toutoune@HIDDEN>
To: 39885 <at> debbugs.gnu.org
Subject: Re: bug#39885: Bioconductor URI, fallback and time-machine
References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN>
Date: Mon, 18 Jul 2022 18:03:04 +0200
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(zimoun's message of "Tue, 3 Mar 2020 16:59:03 +0100")
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Hi,
Since 2020, I provided several examples of breakage with bug#39885 [1].
Here another one:
--8<---------------cut here---------------start------------->8---
$ guix time-machine --commit=77e2de365497bf4c8b81cbd78624f78293490485 \
-- build r-biocneighbors -S
substitute: updating substitutes from 'https://ci.guix.gnu.org'... 100.0%
substitute: updating substitutes from 'https://bordeaux.guix.gnu.org'... 100.0%
The following derivation will be built:
/gnu/store/q9ggmh5a9bzmnr49p10x1w9sv6pzjarv-BiocNeighbors_1.4.1.tar.gz.drv
building /gnu/store/q9ggmh5a9bzmnr49p10x1w9sv6pzjarv-BiocNeighbors_1.4.1.tar.gz.drv...
Starting download of /gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz
From https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.4.1.tar.gz...
download failed "https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.4.1.tar.gz" 404 "Not Found"
Starting download of /gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz
From https://bioconductor.org/packages/3.10/bioc/src/contrib/Archive/BiocNeighbors_1.4.1.tar.gz...
download failed "https://bioconductor.org/packages/3.10/bioc/src/contrib/Archive/BiocNeighbors_1.4.1.tar.gz" 404 "Not Found"
Starting download of /gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz
From https://ci.guix.gnu.org/file/BiocNeighbors_1.4.1.tar.gz/sha256/05vi1cij37s8wgj92k3l6a3f3dwldj8jvijdp4695zczka6kypdf...
download failed "https://ci.guix.gnu.org/file/BiocNeighbors_1.4.1.tar.gz/sha256/05vi1cij37s8wgj92k3l6a3f3dwldj8jvijdp4695zczka6kypdf" 404 "Not Found"
Starting download of /gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz
From https://tarballs.nixos.org/sha256/05vi1cij37s8wgj92k3l6a3f3dwldj8jvijdp4695zczka6kypdf...
download failed "https://tarballs.nixos.org/sha256/05vi1cij37s8wgj92k3l6a3f3dwldj8jvijdp4695zczka6kypdf" 404 "Not Found"
Starting download of /gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz
From https://archive.softwareheritage.org/api/1/content/sha256:ae5d3f8d9a9ffd920cb94dc62d916c94b7e18632744c91e4e3489f21230b7117/raw/...
download failed "https://archive.softwareheritage.org/api/1/content/sha256:ae5d3f8d9a9ffd920cb94dc62d916c94b7e18632744c91e4e3489f21230b7117/raw/" 404 "Not Found"
Starting download of /gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz
From https://web.archive.org/web/20220718175152/https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.4.1.tar.gz...
download failed "https://web.archive.org/web/20220718175152/https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.4.1.tar.gz" 404 "NOT FOUND"
Trying to use Disarchive to assemble /gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz...
could not find its Disarchive specification
failed to download "/gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz" from ("https://bioconductor.org/packages/release/bioc/src/contrib/BiocNeighbors_1.4.1.tar.gz" "https://bioconductor.org/packages/3.10/bioc/src/contrib/Archive/BiocNeighbors_1.4.1.tar.gz")
builder for `/gnu/store/q9ggmh5a9bzmnr49p10x1w9sv6pzjarv-BiocNeighbors_1.4.1.tar.gz.drv' failed to produce output path `/gnu/store/zgf7x09kgiqbvj0dmhplxi1xzpljxd7k-BiocNeighbors_1.4.1.tar.gz'
build of /gnu/store/q9ggmh5a9bzmnr49p10x1w9sv6pzjarv-BiocNeighbors_1.4.1.tar.gz.drv failed
View build log at '/var/log/guix/drvs/q9/ggmh5a9bzmnr49p10x1w9sv6pzjarv-BiocNeighbors_1.4.1.tar.gz.drv.gz'.
guix build: error: build of `/gnu/store/q9ggmh5a9bzmnr49p10x1w9sv6pzjarv-BiocNeighbors_1.4.1.tar.gz.drv' failed
--8<---------------cut here---------------end--------------->8---
Well, several comments:
1. Berlin or Bordeaux do not have it as substitutes,
2. Diasarchive does not have it,
3. Many others neither.
but the question in the first place is: why is Bioconductor failing?
Because they do ugly things!
Our history reads:
f431d5e299 Sun Dec 15 15:38:51 2019 +0100 guix: Upgrade to Bioconductor 3.10
12e2aa96dc Sun Dec 15 15:38:55 2019 +0100 gnu: r-biocneighbors: Update to 1.4.1.
aece78fe2f Sun Mar 1 23:38:12 2020 +0100 gnu: r-biocneighbors: Update to 1.4.2.
8e518d4802 Sat Jun 13 01:19:38 2020 +0200 guix: Update to Bioconductor 3.11.
which means that Bioconductor removes v1.4.1 from their URI scheme
(even, I do not know if the tarball is still available on their infra)
and despite the fact Bioconductor v3.10 had released v1.4.1, then it is
not stable.
At the cost of more bandwidth, we could switch from url-fetch to
git-fetch. Or we also could examine why Disarchive is failing here.
1: <http://issues.guix.gnu.org/issue/39885>
Cheers,
simon
bug-guix@HIDDEN:bug#39885; Package guix.
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From: zimoun <zimon.toutoune@HIDDEN>
To: 39885 <at> debbugs.gnu.org
Subject: Re: bug#39885: Bioconductor URI, fallback and time-machine
References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN>
Date: Mon, 22 Nov 2021 20:48:05 +0100
In-Reply-To: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN>
(zimoun's message of "Tue, 3 Mar 2020 16:59:03 +0100")
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Hi,
On Tue, 03 Mar 2020 at 16:59, zimoun <zimon.toutoune@HIDDEN> wrote:
> Currently, the URI scheme (see 'bioconductor-uri' in
> guix/build-system/r.scm) is:
>
> https://bioconductor.org/packages/release/data/<type-url-part>/src/contr=
ib/<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/<u=
pstream-name>-<version>.tar.gz
It is still the case and for concrete breakage, see [1]. I will not
detail but each time Guix lags behind Bioconductor new release, it is
broken. For sure, Guix upgrades more or less quickly. Each time
Bioconductor remove a package, it is broken. Well, because a lot
of care about R packages, the forward breakages happen barely. :-) But
backward breakages are not negligible, IMHO.
Well, this URL choice is not The Right Thing and somehow broken by design.
1: <https://issues.guix.gnu.org/39885#7>
> 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).
We are now 1.5 years after. And we did nothing; well we did other
things instead. ;-). Now, I have an strong opinion that option a) is
not doable: I speak using my janitor moves of Bioconductor packages.
Instead, something along the proposed patch below half-fixes the issue
now. We just have to append the releases and let the fallback mechanism
takes care. It reduces the maintenance burden, IMHO.
For sure, it is not perfect but it appears to me a pragmatical fix
waiting something better.
This better is unknown (at least from me :-)). On one hand Disarchive
would improve the situation for tarballs=E2=80=A6 but some work remains (ch=
eck
that SWH ingestion and rebuild is bullet-proof). On the other hand,
Bioconductor uses Git, for instance:
git clone https://git.bioconductor.org/packages/CATALYST
<https://bioconductor.org/packages/release/bioc/html/CATALYST.html>
And Bioconductor uses =E2=80=99origin/RELEASE_3.14=E2=80=99 as Git tag. Ba=
sed on this,
it would avoid the eternal inplace-change fixes.
For instance, the package tximeta [2], recently updated by Ricardo.
Well, from their Bioconductor Git repo,
git clone https://git.bioconductor.org/packages/tximeta
it is not clear that the current version is at 1.12.3. And it is not
clear either if they tagged origin/RELEASE_3_14 at 1.12.0 and did
something ugly to then get 1.12.3. Anyway, switch from url-fetch to
git-fetch is an option. However, it is as option a) and I am not
convinced it is doable with the resource at hand.
2: <https://bioconductor.org/packages/3.14/bioc/html/tximeta.html>
What could a plan to have a bullet-proof =E2=80=9Cguix time-machine=E2=80=
=9D for
Bioconductor?
Cheers,
simon
> From 87e73e02202fe5e342d68f1fb17efdd4425737cd Mon Sep 17 00:00:00 2001
> From: zimoun <zimon.toutoune@HIDDEN>
> Date: Tue, 3 Mar 2020 16:53:39 +0100
> Subject: [PATCH] build-system: r: Use Bioconductor old releases to fallba=
ck.
>
> * guix/build-system/r.scm (bioconductor-uri): Extend the fallback list.
> ---
> guix/build-system/r.scm | 21 ++++++++++++---------
> 1 file changed, 12 insertions(+), 9 deletions(-)
>
> diff --git a/guix/build-system/r.scm b/guix/build-system/r.scm
> index 2d328764b0..8638e1b888 100644
> --- a/guix/build-system/r.scm
> +++ b/guix/build-system/r.scm
> @@ -54,15 +54,18 @@ release corresponding to NAME and VERSION."
> ('annotation "/data/annotation")
> ('experiment "/data/experiment")
> (_ "/bioc"))))
> - (list (string-append "https://bioconductor.org/packages/release"
> - type-url-part
> - "/src/contrib/"
> - name "_" version ".tar.gz")
> - ;; TODO: use %bioconductor-version from (guix import cran)
> - (string-append "https://bioconductor.org/packages/3.10"
> - type-url-part
> - "/src/contrib/Archive/"
> - name "_" version ".tar.gz"))))
> + (append (list (string-append "https://bioconductor.org/packages/rele=
ase"
> + type-url-part
> + "/src/contrib/"
> + name "_" version ".tar.gz"))
> + (map (lambda (release)
> + (string-append "https://bioconductor.org/packages/"
> + release
> + type-url-part
> + "/src/contrib/"
> + name "_" version ".tar.gz"))
> + (list (@@ (guix import cran) %bioconductor-version)
> + "3.9" "3.8" "3.7")))))
>
> (define %r-build-system-modules
> ;; Build-side modules imported by default.
bug-guix@HIDDEN:bug#39885; Package guix.
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From: zimoun <zimon.toutoune@HIDDEN>
To: 39885 <at> debbugs.gnu.org
Subject: Re: bug#39885: Bioconductor URI, fallback and time-machine
References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN>
Date: Thu, 19 Nov 2020 15:22:11 +0100
In-Reply-To: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN>
(zimoun's message of "Tue, 3 Mar 2020 16:59:03 +0100")
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Hi,
Some explanations of the issue are provided here:
<http://issues.guix.gnu.org/issue/39885>
Since we are currently updating to 3.12, maybe it is the occasion to fix
the issue. See option a) below.
On Tue, 03 Mar 2020 at 16:59, zimoun <zimon.toutoune@HIDDEN> wrote:
> Currently, the URI scheme (see 'bioconductor-uri' in
> guix/build-system/r.scm) is:
>
> https://bioconductor.org/packages/release/data/<type-url-part>/src/contr=
ib/<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.
An example of this issue is for example:
--8<---------------cut here---------------start------------->8---
$ guix time-machine --commit=3Daee183e -- import cran -a bioconductor CATAL=
YST -r
Updating channel 'guix' from Git repository at 'https://git.savannah.gnu.or=
g/git/guix.git'...
Starting download of /tmp/guix-file.Nxajqh
From https://bioconductor.org/packages/release/bioc/src/contrib/CATALYST_1.=
12.2.tar.gz...
download failed "https://bioconductor.org/packages/release/bioc/src/contrib=
/CATALYST_1.12.2.tar.gz" 404 "Not Found"
failed to download "/tmp/guix-file.Nxajqh" from "https://bioconductor.org/p=
ackages/release/bioc/src/contrib/CATALYST_1.12.2.tar.gz"
error: failed to retrieve package information from "https://cran.r-project.=
org/web/packages/CATALYST/DESCRIPTION": 404 ("Not Found")
Backtrace:
4 (primitive-load "/home/simon/.cache/guix/inferiors/vznc=E2=80=
=A6")
In guix/ui.scm:
2117:12 3 (run-guix-command _ . _)
In guix/scripts/import.scm:
120:11 2 (guix-import . _)
In srfi/srfi-1.scm:
586:17 1 (map1 (#f))
In guix/import/utils.scm:
258:2 0 (package->definition _)
guix/import/utils.scm:258:2: In procedure package->definition:
Throw to key `match-error' with args `("match" "no matching pattern" #f)'.
--8<---------------cut here---------------end--------------->8---
Aside the ugly backtrace which is tracked by #44115, the main issue is
because Bioconductor updated to 3.12 and Guix is still at 3.11.
Concretely, the issue is that =E2=80=99release=E2=80=99 in the URL:
<https://bioconductor.org/packages/release/bioc/src/contrib/CATALYST_1.12.2=
.tar.gz>
now refers to 3.12 (because Bioconductor update) and Guix still think it
is 3.11 (because Guix has not yet updated; work-in-progress). And
CATALYST in 3.12 is at version 1.14.0 against 1.12.2 for 3.11.
Therefore, the conflict and the error.
It means that while:
(define %bioconductor-version "3.11")
is not updated to 3.12, all the Bioconductor packages are broken; in the
meaning not buildable from source.
> 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, e.g.:
>
> https://bioconductor.org/packages/release/data/<type-url-part>/src/contri=
b/<upstream-name>-<version>.tar.gz
> https://bioconductor.org/packages/3.11/data/<type-url-part>/src/contrib/<=
upstream-name>-<version>.tar.gz
>
> Attached, a quick patch showing the option b).
Then each time we update Bioconductor, we add an URL to the list.
> As discussed on IRC, Tobias seems more inclined with the option a) and
> I am more in favour of option b.
Tobias and Ricardo are in favor for a) (see this thread). Which means a
lot of work IMHO, i.e., add 3.11 as arguments and then 3.12 to all the
Bioconductor packages and fix the importer, IIUC; while b) means do
nothing except merge the proposed patch (possibly re-worked).
Just to note that only the task to group in bioconductor.scm all the
Bioconductor packages scattered here and there is still not done, I
think option a) is not doable by hand =E2=80=93 I do not volunteer! :-) Els=
e,
any suggestion to script the task instead?
Since I am more in favor of b), I am less motivated to fix the a). ;-)
But I am motivated to fix the issue at hand. :-)
Other option c) is to switch all the Bioconductor to git-fetch instead
of url-fetch. I have not checked yet how could be the transition.
> Please also consider #36805 which was never merged or closed.
> http://issues.guix.gnu.org/issue/36805
This patch could help for option a).
WDYT?
All the best,
simon
bug-guix@HIDDEN:bug#39885; Package guix.
Full text available.Received: (at 39885) by debbugs.gnu.org; 29 Jun 2020 20:42:56 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Mon Jun 29 16:42:56 2020 Received: from localhost ([127.0.0.1]:49623 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1jq0cC-0003zQ-4z for submit <at> debbugs.gnu.org; Mon, 29 Jun 2020 16:42:56 -0400 Received: from eggs.gnu.org ([209.51.188.92]:56408) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <ludo@HIDDEN>) id 1jq0c9-0003zC-V3 for 39885 <at> debbugs.gnu.org; Mon, 29 Jun 2020 16:42:54 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:38276) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from <ludo@HIDDEN>) id 1jq0c4-0005yQ-A3; Mon, 29 Jun 2020 16:42:48 -0400 Received: from [2a01:e0a:1d:7270:af76:b9b:ca24:c465] (port=46640 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from <ludo@HIDDEN>) id 1jq0c3-0002JI-PK; Mon, 29 Jun 2020 16:42:48 -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> <87lfk7gd7d.fsf@HIDDEN> <CAJ3okZ36KrALgMq69zdkDsHcfMv09Lk=DPBmzW-4SePZPRAvnA@HIDDEN> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 12 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: Mon, 29 Jun 2020 22:42:46 +0200 In-Reply-To: <CAJ3okZ36KrALgMq69zdkDsHcfMv09Lk=DPBmzW-4SePZPRAvnA@HIDDEN> (zimoun's message of "Mon, 29 Jun 2020 19:36:07 +0200") Message-ID: <87r1txa9ix.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 (---) zimoun <zimon.toutoune@HIDDEN> skribis: > From c1c963a3b86e306a20c14626127e54d21843c22c Mon Sep 17 00:00:00 2001 > From: zimoun <zimon.toutoune@HIDDEN> > Date: Mon, 29 Jun 2020 19:18:20 +0200 > Subject: [PATCH] build-system/r: bioconductor-uri: Fix archive URL. > > * guix/build-system/r.scm (bioconductor-uri): Fix archive URL. Applied, thanks! I let the rest of you discuss the other issues. :-) Ludo=E2=80=99.
bug-guix@HIDDEN:bug#39885; Package guix.
Full text available.Received: (at 39885) by debbugs.gnu.org; 29 Jun 2020 17:36:29 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Mon Jun 29 13:36:29 2020 Received: from localhost ([127.0.0.1]:49368 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1jpxhl-0003L2-AJ for submit <at> debbugs.gnu.org; Mon, 29 Jun 2020 13:36:29 -0400 Received: from mail-qk1-f177.google.com ([209.85.222.177]:33059) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <zimon.toutoune@HIDDEN>) id 1jpxhh-0003Kn-5s for 39885 <at> debbugs.gnu.org; Mon, 29 Jun 2020 13:36:27 -0400 Received: by mail-qk1-f177.google.com with SMTP id j80so16029715qke.0 for <39885 <at> debbugs.gnu.org>; Mon, 29 Jun 2020 10:36:25 -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; bh=8838tFRDuAOB4S8wBy/TixFHHxWd8OOaO/HiJIDDrkg=; b=l6E50j768qJ5/I4b+rsrNZqAqO6dSyw8CUbTb3B1wxo/0xQQdXmZpEDPHjC3aaJD6v EyhNwoYe8WtxafkCshH1LC0F6sCpQMSGEx0qLptgLANCW6eax2yo1d1cCKUFqz6bWWDh V6bz7MR0kysj89z+RJt9sdrJ+W7a8NdIk/FSHNMJnIQKp6qQVATMu7jxVUweZhpB7ANj ilusBtMzS3IZmvIZtrg8DL1zKQlLIBCqFAIqSEhbCL4bWhxI8VHAJgHj0HJbpkym7ZCq I5hRpOfbH+ob2J2ScE1SdXXw2D1Cstb4dQV8H4aRIcSVVaZnFCExKCNXDGXPolO3AXNG 2JZw== 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; bh=8838tFRDuAOB4S8wBy/TixFHHxWd8OOaO/HiJIDDrkg=; b=ajI2qY9j1SAY+zM4NpCf1bZjkBhpVpshYdS/U+OquZZUHfN2DW66g4w4sVIP6EuQYM Uz52H5IcySTJq1l61plDO3XlXhEFMd8F3JWcBbbeaPqG1/94NYr6t5wP2BhfYjoE1/a2 aw43FJmPyDZfrtykZgae11tq8nZrJYi7jcfXyTijOsTIgjo2VQgFul6Li54MNVqG1wUT d8jfakgHX2xpNAYxEXGLUYfoN3uPPDmA3akss6StJOD5Aihrj9rxqVSyGGAkLvJGLJsw hDEB5MbKeInxqMvRaalKV/sFzQQeyx1XJHrI3tvaE5UXvgOcJH55g/c4RcVskvK01um7 2ERQ== X-Gm-Message-State: AOAM532E8mwbEbPUVz1IfHriJcDEA7tXw84b3cwbpa7lV0Zaa+2w1j52 9NTOnrh9Rh1YVKsgbKJ1k6eLE5mJkEqNqxRr5bg= X-Google-Smtp-Source: ABdhPJwuhjPLw0gdCi1UPHOkF1V47K6izRCl3Y77FztVienTNtfLzaknRlDjjpeQK09ldVWbHR+zDbVMBeJqvjBBvY8= X-Received: by 2002:a37:b847:: with SMTP id i68mr15888531qkf.126.1593452179449; Mon, 29 Jun 2020 10:36:19 -0700 (PDT) MIME-Version: 1.0 References: <CAJ3okZ3dFunYgafRH6=9LsLKLf6OrZBpXqUMxZAjEhaiL93ARA@HIDDEN> <CAJ3okZ1Xwd-2WArzNus3xE_KOayDdXPp+ku1SxYBon4Zm0qQQg@HIDDEN> <87lfk7gd7d.fsf@HIDDEN> In-Reply-To: <87lfk7gd7d.fsf@HIDDEN> From: zimoun <zimon.toutoune@HIDDEN> Date: Mon, 29 Jun 2020 19:36:07 +0200 Message-ID: <CAJ3okZ36KrALgMq69zdkDsHcfMv09Lk=DPBmzW-4SePZPRAvnA@HIDDEN> Subject: Re: bug#39885: Bioconductor URI, fallback and time-machine To: =?UTF-8?Q?Ludovic_Court=C3=A8s?= <ludo@HIDDEN> Content-Type: multipart/mixed; boundary="0000000000001f9a8e05a93c7f12" X-Spam-Score: 0.0 (/) 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: -1.0 (-) --0000000000001f9a8e05a93c7f12 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi Ludo, On Sun, 28 Jun 2020 at 22:14, Ludovic Court=C3=A8s <ludo@HIDDEN> wrote: > Could you provide a patch for this? About the url, for sure, see attached. But it does not address the root of the problem. Well, I will try to find a slot and propose something. All the best, simon --0000000000001f9a8e05a93c7f12 Content-Type: text/x-patch; charset="US-ASCII"; name="0001-build-system-r-bioconductor-uri-Fix-archive-URL.patch" Content-Disposition: attachment; filename="0001-build-system-r-bioconductor-uri-Fix-archive-URL.patch" Content-Transfer-Encoding: base64 Content-ID: <f_kc0rske80> X-Attachment-Id: f_kc0rske80 RnJvbSBjMWM5NjNhM2I4NmUzMDZhMjBjMTQ2MjYxMjdlNTRkMjE4NDNjMjJjIE1vbiBTZXAgMTcg MDA6MDA6MDAgMjAwMQpGcm9tOiB6aW1vdW4gPHppbW9uLnRvdXRvdW5lQGdtYWlsLmNvbT4KRGF0 ZTogTW9uLCAyOSBKdW4gMjAyMCAxOToxODoyMCArMDIwMApTdWJqZWN0OiBbUEFUQ0hdIGJ1aWxk LXN5c3RlbS9yOiBiaW9jb25kdWN0b3ItdXJpOiBGaXggYXJjaGl2ZSBVUkwuCgoqIGd1aXgvYnVp bGQtc3lzdGVtL3Iuc2NtIChiaW9jb25kdWN0b3ItdXJpKTogRml4IGFyY2hpdmUgVVJMLgotLS0K IGd1aXgvYnVpbGQtc3lzdGVtL3Iuc2NtIHwgMiArLQogMSBmaWxlIGNoYW5nZWQsIDEgaW5zZXJ0 aW9uKCspLCAxIGRlbGV0aW9uKC0pCgpkaWZmIC0tZ2l0IGEvZ3VpeC9idWlsZC1zeXN0ZW0vci5z Y20gYi9ndWl4L2J1aWxkLXN5c3RlbS9yLnNjbQppbmRleCBjOGVjOWFiZDBkLi41ZWY5ODJkNjZh IDEwMDY0NAotLS0gYS9ndWl4L2J1aWxkLXN5c3RlbS9yLnNjbQorKysgYi9ndWl4L2J1aWxkLXN5 c3RlbS9yLnNjbQpAQCAtNjEsNyArNjEsNyBAQCByZWxlYXNlIGNvcnJlc3BvbmRpbmcgdG8gTkFN RSBhbmQgVkVSU0lPTi4iCiAgICAgICAgICAgOzsgVE9ETzogdXNlICViaW9jb25kdWN0b3ItdmVy c2lvbiBmcm9tIChndWl4IGltcG9ydCBjcmFuKQogICAgICAgICAgIChzdHJpbmctYXBwZW5kICJo dHRwczovL2Jpb2NvbmR1Y3Rvci5vcmcvcGFja2FnZXMvMy4xMSIKICAgICAgICAgICAgICAgICAg ICAgICAgICB0eXBlLXVybC1wYXJ0Ci0gICAgICAgICAgICAgICAgICAgICAgICAgIi9zcmMvY29u dHJpYi9BcmNoaXZlLyIKKyAgICAgICAgICAgICAgICAgICAgICAgICAiL3NyYy9jb250cmliLyIK ICAgICAgICAgICAgICAgICAgICAgICAgICBuYW1lICJfIiB2ZXJzaW9uICIudGFyLmd6IikpKSkK IAogKGRlZmluZSAlci1idWlsZC1zeXN0ZW0tbW9kdWxlcwoKYmFzZS1jb21taXQ6IDZlYmYzMDA5 NTlhNThmZDFlZGE4NzUyMDVjNzVkMjExMzc4NjIyODUKLS0gCjIuMjYuMgoK --0000000000001f9a8e05a93c7f12--
bug-guix@HIDDEN:bug#39885; Package guix.
Full text available.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.
Full text available.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
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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