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

[Dirk Eddelbuettel]

On 27 April 2017 at 23:41, Charles Plessy wrote:
| Le Thu, Apr 27, 2017 at 07:24:18AM -0500, Dirk Eddelbuettel a écrit :
| > 
| > On 27 April 2017 at 13:58, Johannes Ranke wrote:
| > | Am Donnerstag, 27. April 2017, 06:32:13 schrieb Dirk Eddelbuettel:
| > | > On 27 April 2017 at 12:01, Johannes Ranke wrote:
| > | 
| > | > This may be a use case for r-api-4. Or not as it doesn't break _all_
| > | > packages so I am not sure we should force _all_ packages to be rebuilt.
| > | > 
| > | > Can we not find the ones that use .C and .Fortran ?
| > | 
| > | I do not understand how the use of r-api-x works, but my feeling is that it 
| > | will not allow to differentiate between packages using .C and .Fortan and the 
| > | rest.
| > 
| > Right. And therefore cast too wide a net. 
| > 
| > | I am surprised that I did not see a related bug report in the Debian BTS yet, 
| > | did I overlook something? I only looked for r-base.
| > 
| > They may not know yet. I should write to debian-devel.
| > 
| > Any debian-med or debian-science readers here?
| 
| Yes I am here :)

:)

| I spotted the breakage caused by R 3.4.0 when seeing regression tests
| failing on ci.debian.net.  But I did not report them yet as I am still
| busy with the breakage caused by R 3.3.3 (mostly on Bioconductor packages).
| In the case of R 3.3.3 it was a bit tedious to identify which packages were
| to rebuild because some test failures were only indirect consequences, and
| a pacakge responsible for the failures had its own tests passing because
| their coverage was shallow... Hence for 3.4.0 I would say that in doubt,
| let's rebuild everything.

Could you fill me in about what broke with BioC and what caused it?

I am not (yet?) on board with recommending a point-blank rebuild of all.
 
| If r-base starts to provide r-api-4 instead of r-api-3 then it will not be
| co-installable with the r-cran/bioc/other-* packages until they have been
| rebuilt.
| 
|  - The benefit is that it will prevent people doing partial upgrades
|    from Stable, that would break their packages.

I am not sure I understand why people would want to do partial upgrades.
Debian stable is support. Debian testing is supported.  Hybrid mixes of the
two are risque.

|  - The drawback is the extra work of rebuilding the packages that do not
|    use .C and .Fortran.
| 
| Within the Debian infrastructure, the architecture-dependant packages can be
| easily rebuilt by binNMUs.  The architecture-independant packages are easier to
| rebuild than before, because it is now possible to do source-only uploads.
| Also, it may be worth asking on debian-devel if binNMUs of arch-independant
| packages will become possible (since we now have autobuilders that can handle
| them).

It sure would help.

| For the Debian packages provided on CRAN, I am not familiar on build is
| trigger, so I can not comment on the ease of rebuilding.

I think that is a different topic for which we may want a different
discussion.

Dirk

| Have a nice day,
| 
| -- 
| Charles Plessy
| Debian Med packaging team,
| http://www.debian.org/devel/debian-med
| Tsurumi, Kanagawa, Japan

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