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Re: Bioconductor + R-base transition: next steps and status update

Hi Dirk,

On 9/19/21 8:16 PM, Dirk Eddelbuettel wrote:
> | => Updating a few left-over CRAN packages can help r-base transition move ahead - like knitr, unitizer etc.
> |    But since they are relatively important packages, we need to account for breakages with these too.
> Several of these transition blockages for r-base-core appear to be from
> packages that are behind upstream. Looking at
> https://qa.debian.org/excuses.php?package=r-base

That confirms my suspicion!

> [...]
> parsetools 0.1.3 is no longer on CRAN as of 2020-01-24

I happened to see this removal a couple of days back. For _now_, I am thinking of filing
a release critical bug, to kick this one out of testing.
That could help migration move forward.
Do you have any better suggestions there?

> [...]
> vegan 2.5.7 is current

I'm not too sure why this one does not work. On a quick look, _seems_ like some float-precision
errors. I'm tempted to disable that one and upload.
Any other ideas welcome.

That said, I took a look at the rest of the list, very helpful, and thanks! However, those packages updates
couple with reverse-dependencies is a too much for me to manage alone. It'd be awesome if you could help.
Also, @Andreas, @Dylan, @Steffen, can you take care of some of them?

> (and R Core decided not to call for a formal ABI breakage which I concur with on
> balance but we _could_ of course gone all in here requiring everything to be
> rebuilt; I too think that would have been overkill)


> For tikzDevice we know R 4.0.0 imposed a rebuild for graphics devices so a simple rebuild may do.

The CI logs are pretty much suggestive of that as well: "Error: Graphics API version mismatch"
I just uploaded a new revision let's see if this solves the problem.

> PS FYI A month ago, I actually received an email from an R Core member and
> CRAN co-founder who was wondering why the new r-base migrate would not
> migrate.  I can only say that the matter is not under my control.

Hopefully, we are not too far from migrations.


Nilesh Patra

Debian Developer, Uploading
  ⢿⡄⠘⠷⠚⠋   nilesh@debian.org / nileshpatra.info / tchncs.de

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