Roel Janssen <roel@gnu.org> writes:

>> I’d be happy if you could take care of the mass update.  I should note
>> that sometimes new inputs are required.  To find them I usually run the
>> update in a separate branch where I’ve applied changes to import anew
>> and compare with the existing package expression when updating.  It’s on
>> my list to clean this all up and submit my changes for review.  It’s
>> ugly but it works pretty well.  If you’re interested I could send you a
>> patch.
>
> How do you test which inputs are required?  I built all the bioconductor
> packages and fixed their builds by adding inputs wherever that was
> needed.  This does not take care of inputs that are no longer needed (if
> any..).  Any way I can test that in a convenient way?

Attached is my rough patch set.  Apply this and run the update with
“guix refresh -t bioconductor,cran -u”.  It will tell you to “consider”
removing or adding inputs.  Some of the suggestions are wrong, but it
really means well :)

It’s terrible code in some places.  Don’t look too closely.