Re: Updating to latest Bioconductor release

[Roel Janssen <roel@gnu.org>]

Hi Simon,

On Mon, 2020-11-16 at 13:29 +0100, zimoun wrote:
> Hi Roel,
> 
> On Mon, 16 Nov 2020 at 13:10, Roel Janssen <roel@gnu.org> wrote:
> 
> > Hehe. I'm building all R packages in the "wip-r" branch now to see
> > what's left for me to fix.
> 
> Cool!  I do not know if Ricardo fetched my branch to update ’wip-r’
> because an error about a missing symbol was there and then I
> corrected
> it in my branch.  Anyway.
> 
> BTW, I would like to add the type ’workflow’ in addition to
> ’annotation’
> and ’experiment’.  Because I need:
> 
> <https://bioconductor.org/packages/3.11/workflows/html/cytofWorkflow.html
> >
> 
> Well, I do not know if that should go to ’wip-r’ or directly to
> ’master’.  WDYT?

Well, I see we're getting R packages that fail to build because the
source cannot be downloaded (anymore), due to the outdated Bioconductor
version.  So if we can do an upgrade to 3.12 soon, and add the
'workflow' type later, that'd be my preferred route.

So to achieve that, I think we need to:
1. Update the Bioconductor version to 3.12
2. Update/build the Bioconductor packages that are already in Guix.
3. --> When all build failures have been resolved, push to master?

4. Add the bits for 'workflow' packages.
5. Add workflow packages / adjust the ones we have (do we have any?)
and build/test them.
6. --> Push to master?

WDYT?

Kind regards,
Roel Janssen