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bug#39885: Bioconductor URI, fallback and time-machine

From: Ricardo Wurmus
Subject: bug#39885: Bioconductor URI, fallback and time-machine
Date: Mon, 23 Mar 2020 22:20:52 +0100
User-agent: mu4e 1.2.0; emacs 26.3

zimoun <address@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/<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.


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