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

Previous Next

Full log

Message #8 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: zimoun <zimon.toutoune <at> gmail.com>
Cc: Tobias Geerinckx-Rice <me <at> tobias.gr>, bug-guix <at> gnu.org
Subject: Re: Bioconductor URI, fallback and time-machine
Date: Mon, 23 Mar 2020 22:20:52 +0100

zimoun <zimon.toutoune <at> gmail.com> 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/<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.

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’s not necessarily clear when a package tarball
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.

-- 
Ricardo

Previous Next

GNU bug tracking system
Copyright (C) 1999 Darren O. Benham, 1997,2003 nCipher Corporation Ltd, 1994-97 Ian Jackson.