R devel - Mar 2017 - Incompatible change in R-devel

As of today's commit r72375 all packages with native-routine 
registration of C or Fortran routines need to be reinstalled in R-devel 
(and that include some of the recommended packages in R itself which 
will not be reinstalled via make dependencies, so we advise a clean 
rebuild of R).

We try to avoid such things, but now is a least bad time (before binary 
packages for pre-3.4.0 are built in earnest, although CRAN Windows ones 
have been available for a while and will be rebuilt now).

Packages aster2 used undocumented/defunct fields and is overdue for 
update: AFIAWK all other CRAN/BioC packages can be reinstalled.

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford

Hi Brian,

On 21 March 2017 at 07:29, Prof Brian Ripley wrote:
| As of today's commit r72375 all packages with native-routine 
| registration of C or Fortran routines need to be reinstalled in R-devel 
| (and that include some of the recommended packages in R itself which 
| will not be reinstalled via make dependencies, so we advise a clean 
| rebuild of R).

I am confused by this.

So in order to test this, I just triggered rebuild of the smaller drd
("daily
r-devel") and r-devel Docker images for R.  

Using drd, I used R 3.3.3 to install digest and anytime (also installing Rcpp
and BH). I then launch the R-devel build freshly created, and reported as 

 root at b00daf469882:/# RD --version
 R Under development (unstable) (2017-03-21 r72380) -- "Unsuffered
Consequences"

yet both digest and anytime loaded fine by R-devel. Despite the fact that
they were installed by R 3.3.3.

As I understand your email, that should not have worked.  So I must be
missing something -- can you help set me straight?

Thanks, Dirk

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

On 21/03/2017 16:38, Dirk Eddelbuettel wrote:
>
> Hi Brian,
>
> On 21 March 2017 at 07:29, Prof Brian Ripley wrote:
> | As of today's commit r72375 all packages with native-routine
> | registration of C or Fortran routines need to be reinstalled in R-devel
> | (and that include some of the recommended packages in R itself which
> | will not be reinstalled via make dependencies, so we advise a clean
> | rebuild of R).
>
> I am confused by this.
>
> So in order to test this, I just triggered rebuild of the smaller drd
("daily
> r-devel") and r-devel Docker images for R.
>
> Using drd, I used R 3.3.3 to install digest and anytime (also installing
Rcpp
> and BH). I then launch the R-devel build freshly created, and reported as
>
>  root at b00daf469882:/# RD --version
>  R Under development (unstable) (2017-03-21 r72380) -- "Unsuffered
Consequences"
>
> yet both digest and anytime loaded fine by R-devel. Despite the fact that
> they were installed by R 3.3.3.
None register C/Fortran routines for .C or .Fortran.

My belief is that packages which register more than one .C or more than 
one .Fortran native routine are affected, but that may not be exhaustive 
(and might depend on the compiler).
> As I understand your email, that should not have worked.  So I must be
> missing something -- can you help set me straight?
All packages should load ... the issue is finding (all of the) 
registered symbols.  Here's an example of what can go wrong, x86_64 Linux;

 > library(mgcv, lib = "/usr/local/lib64/R/library") # R 3.3.3
Loading required package: nlme
This is mgcv 1.8-17. For overview type 'help("mgcv-package")'.
 > mgcv:::in.out
...
     um <- .C(C_in_out, bx = as.double(bnd[, 1]), by = as.double(bnd[,
...
 > mgcv:::C_in_out
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
   object 'C_in_out' not found

(the last message being found in testing a package which called mgcv).

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford