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

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Message #92 received at 39885 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: Timothy Sample <samplet <at> ngyro.com>
Cc: rekado <at> elephly.net,
 Ludovic Courtès <ludovic.courtes <at> inria.fr>, me <at> tobias.gr,
 39885 <at> debbugs.gnu.org
Subject: Re: bug#39885: Bioconductor tarballs are not archived
Date: Mon, 19 Feb 2024 17:50:59 +0100

Hi,

On ven., 16 févr. 2024 at 10:14, Timothy Sample <samplet <at> ngyro.com> wrote:

>> 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 “stored” hits 100% (or
> close to it, with the remainder being stuff we are pretty sure no longer
> exists).  This won’t happen just because of your second point there.

Just to be sure: we are speaking about Bioconductor only, right?


> When the historical “sources.json” 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 “annotation” and maybe “experiment”.
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
> “importance” in the package graph.  Then there’s 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

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