[R-pkg-team] Bug#947004: Bug#947001: r-base blocked by r-bioc-{iranges, s4vectors}

[Dirk Eddelbuettel]

On 24 December 2019 at 09:34, Graham Inggs wrote:
| Control: severity -1 serious
| 
| On Mon, 23 Dec 2019 at 22:30, Dirk Eddelbuettel <edd at debian.org> wrote:
| > I would be very surprised if these were not self-inflicted by us. I know CRAN
| > (much) better than BioC, but both of them are doing extensive self-tests (and
| > generally without any arbitrary restrictions, say about timing and versions)
| > we may impose.
| 
| This situation reminds me of #877288, where I believe Debian's
| autopkgtests detected the problem before upstream.

Maybe, maybe not.  Here is the BioC build report for iranges and s4vectors:

  http://bioconductor.org/checkResults/3.10/bioc-LATEST/IRanges/
  http://bioconductor.org/checkResults/3.10/bioc-LATEST/S4Vectors/

"All green".

To me th likeliest cause is one of synchronization: BioC generally "steps" in
full releases dependenting on R releases, that does not map to our rolling
scheme. That is, to me, what happened in #877288 too -- R releases and BioC
releases out of step.  (And I still don't know what the best move would
be as thinks could break with either BioC release or devel...)

| > I tried a quick test on a Debian testing machine I use for (extensive)
| > reverse dependency checks (at the upstream level) but it was incloncusive.
| 
| Hopefully we get an answer from upstream BioConductor soon.

Well as shown above there is not bug they see.  

| > Still a pity that r-base is held back by this.
| 
| This is better than allowing a package that breaks others to migrate
| into testing.

What if the breakage is in fact self-inflicted?

| If there is no progress for some time, Release Team may remove
| r-bioc-iranges and r-bioc-s4vectors from testing to allow r-base to
| migrate, as in any other transition.

I guess we have to wait. I run R via the CRAN-ports-for-Ubuntu or via
unstable-on-testing so I have R 3.6.2 on both but it is not fair to our users
to withhold it.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org