[R-sig-Debian] R-3.4.0 and recommended packages

[Johannes Ranke]

Am Dienstag, 25. April 2017, 11:21:31 schrieb Dirk Eddelbuettel:
> On 25 April 2017 at 16:11, Johannes Ranke wrote:
> | This looks similar to what I got this morning when I tested my
> | (unreleased)
> | backport of R 3.4.0 to Debian jessie. My test was
> | 
> | library(MASS)
> | example(rlm)
> | 
> | and there was an object that was not found. I am on a train on the way to
> | a
> | meeting right now, so I can not look into it at the moment. Maybe a side
> | effect of the new registration requirements for compiled objects?
> 
> I doubt that as it works for me under R 3.4.0 on a current-ish Ubuntu 16.10
> box.

This is because the version of MASS in sid (r-cran-mass) was released on 21 
April

https://packages.qa.debian.org/r/r-cran-mass.html

which is the same day when r-base was released for R 3.4.0, so MASS was 
obviously built against the current version.

I just tried r-cran-spatial on a **fresh Debian sid chroot**, and get

> library(spatial)
> example(surf.gls)

srf.gl> library(MASS)  # for eqscplot

srf.gl> data(topo, package="MASS")

srf.gl> topo.kr <- surf.gls(2, expcov, topo, d=0.7)
Error in surf.gls(2, expcov, topo, d = 0.7) : object 'VR_frset' not found

so it seems to me this must affect all packages in Debian sid that were built 
before the release of R 3.4.0!

And in fact, nlme, is affected as well:

> library(nlme)
> example(nlme)

nlme> fm1 <- nlme(height ~ SSasymp(age, Asym, R0, lrc),
nlme+             data = Loblolly,
nlme+             fixed = Asym + R0 + lrc ~ 1,
nlme+             random = Asym ~ 1,
nlme+             start = c(Asym = 103, R0 = -8.5, lrc = -3.3))
Error in pdFactor.pdLogChol(X[[i]], ...) : object 'logChol_pd' not found

So before I start spamming the Debian BTS, what would be the right way to deal 
with this? Do we need r-api-x here?

Cheers,

Johannes

P.S.: Sorry of the other post, I pressed send before typing and even before 
thinking ...