Re: Updating to latest Bioconductor release

[Ricardo Wurmus]

Roel Janssen <roel@gnu.org> writes:

> On Thu, 2020-11-19 at 22:13 +0100, Ricardo Wurmus wrote:
>> Hi,
>> 
>> > > > http://logs.guix.gnu.org/guix/2020-11-19.log#182349
>> > 
>> > > Right, so I shouldn't have pushed to "wip-r" in the first place.
>> > 
>> > Well, I think it is a lack of synchronisation between all of 3;
>> > especially with this work around via external GitHub upstream.
>> 
>> Yeah, sorry.  I didn’t realize wip-r was worked on by any one other than
>> simon and myself.  The commits are still there, they just don’t have a
>> named pointer (= branch) to them any longer:
>> 
>> https://git.savannah.gnu.org/cgit/guix.git/log/?id=8ed6a08a998d4abd58eb67c85699f38f87f76d05
>> 
>> If that’s the last commit (or if you have another one that was pushed) I
>> can simply reset the branch pointer to it and then stay out of it :)
>> 
>
> This is the most recent commit I pushed:
> https://git.savannah.gnu.org/cgit/guix.git/log/?id=ea92cec586893748b6de32b930117c598225c38c
>
> It'd be great if you could reset the branch pointer! :)

Done!  I rebased onto master and pushed to r-wip.

> On IRC you noted that the commit messages are wrong.  I interpret that as "my
> commit messages are wrong", which I guess will be those where I updated the
> inputs of packages.  Could you tell me how I need to format the commit 
> messages?
> Then I can perhaps rewrite the most recent history of the wip-r branch to fix 
> my
> commit messages.

Many of the commit messages were incomplete (didn’t mention all changed
inputs) and used the wrong heading “gnu: Update r-foo to 1.2.3.” instead
of the more greppable “gnu: r-foo: Update to 1.2.3.”.

You can save yourself some time in the future by using
./etc/committer.scm; I strongly recommend it for R package upgrades.
(First commit all package additions manually, then run
./etc/committer.scm for all the updates.)

I have manually rewritten the commit messages.

There are some open questions: the changes to r-mutationalpatterns
invalidate the comment

   ;; These two packages are suggested packages

above r-bsgenome-hsapiens-1000genomes-hs37d5 and
r-bsgenome-hsapiens-ucsc-hg19.  Would be good to adjust the comment or
to move it down.

I also saw that r-rsubread fails to build.

-- 
Ricardo