R SIG Debian - Apr 2018 - R 3.5.0 binaries for Debian and Ubuntu

On 04/29/2018 09:30 AM, Jeroen Ooms wrote:
> On Sat, Apr 28, 2018 at 10:00 PM, Michael Rutter <marutter at
gmail.com> wrote:
>> These have not been mirrored to CRAN as I want to have the other r-cran
>> packages built against R 3.5 before adding to CRAN.  Worried about
breaking
>> working systems currently on R 3.4.4.
> 
> Thanks, Michael. I did some simple tests, upgrading existing r-base
> installations to R 3.5. on Xenial and Bionic, and initially apt did
> the correct thing of removing the incompatible r-cran-xyz packages.
> 
> However then I tried installing the (knowingly incompatible)
> r-cran-rcpp from c2d4u and apt didn't stop me. Do the r-cran-xyz
> packages from c2d4u not have the same r-api-nn dependency
> restrictions?
Since c2d4u is (for the most part) automatic, it only grabs depends from 
the CRAN web page.  Therefore, there is no r-api-nn dependency for 
packages built from c2d4u source packages.  How that effects things is 
unclear.  As Dirk just posted, it was an executive decision that we made 
(or possibly ignored).

However, sometimes I need to borrow a package from Debian (when someone 
else has built it on Launchpad before I did), and those will have the 
r-api-nn dependency.  There are also the universe packages.

 From my end, this is a mess.  Rebuilding the universe packages for 3.5 
is a slow process (crazy dependencies).  Plan is to build everything 
against 3.5, but it will take some time.

Michael

To clarify:

- We have known since last summer when ALTREP was merged in r-devel that you
  CANNOT mix and match BINARY BUILDS between R 3.5.0 and prior versions. And
  R 3.5.0 is very clear about this in the NEWS file (albeit many lines down,
  and in somewhat vague language):

  C-LEVEL FACILITIES:

    [...]

    * The object header layout has been changed to support merging the
      ALTREP branch. This requires re-installing packages that use
      compiled code.

- To repeat: You *must* reinstall every binary package.

- This means eg that the vast and superbly useful collection in Michael's
  c2d4u repo continues to work with R 3.4.* (for which it was built) but will
  not work with the new R 3.5.*.  Do not mix and match.

- Debian is even more adamant about this, and fellow maintainers made me add
  a binary tag to every package: r-api-3.4 for the old ones, r-api-3.5 for
  the new ones. Hence the need for a COMPLETE rebuild, which is filed, but
  has not yet started. You can monitor it here as previously mentioned:
    https://release.debian.org/transitions/html/r-base-3.5.html

- This is the same for the 'official' Ubuntu packages from the distro as
they
  are built the same way. See eg https://packages.ubuntu.com/artful/r-cran-rcpp

- Our contributed Ubuntu repos have NOT enforced the tag so they allow you to
  co-install.  But per the above things will still break. So they will also
  get a complete rebuild.

- For Ubuntu, Michael has started a new repo:
    https://launchpad.net/~marutter/+archive/ubuntu/rrutter3.5/+packages
  I added a small one of mine too:
    https://launchpad.net/~edd/+archive/ubuntu/r-3.5
  and with that (and by reducing installed r-cran-packages down to a minimum)
  was able to install R 3.5.* packages on my 17.10 laptop. But let me repeat
  that for clarity: I involved removing r-api-3.4 packages and reinstalling
  in /usr/local

- For Debian, I started a similar 'minimal' R 3.5.0 repo here
    https://github.com/eddelbuettel/drr35
  which allowed me eg to update the 'base' Rocker image for R 3.5.0
    https://github.com/rocker-org/rocker/blob/master/r-base/Dockerfile
    https://hub.docker.com/r/rocker/r-base/
  and I will send the usual PR to the offical library for the r-base image
  mirroring this.

- Travis remains an issue if and when you mix with preinstalled packages. We
  probably want to wait there.

- Michael uses the excellent Ubuntu PPA infrastructure, but uploads are
  in fact manual. Please be patient.


This was just a quick braindump to put some facts out there while the noise
level keeps escalating on Twitter.  It is not efficient for me to try to
follow each conversation there.  If we could, let's please keep the meat of
the discussion HERE and feel free to distribute some common knowledge
established over whichever social media strategy you feel you must use.

Thanks,  Dirk

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

Hi,
> - For Debian, I started a similar 'minimal' R 3.5.0 repo here
>     https://github.com/eddelbuettel/drr35
>   which allowed me eg to update the 'base' Rocker image for R 3.5.0
>     https://github.com/rocker-org/rocker/blob/master/r-base/Dockerfile
>     https://hub.docker.com/r/rocker/r-base/
>   and I will send the usual PR to the offical library for the r-base image
>   mirroring this.
I would like to add that R 3.5.0 is available for Debian stable and oldstable 
in repositories stretch-cran35/ and jessie-cran35/ on CRAN:

https://cran.r-project.org/bin/linux/debian/

Johannes