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

[Dirk Eddelbuettel]

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:
| > | > so it seems to me this must affect all packages in Debian sid that were
| > | > built before the release of R 3.4.0!
| > | 
| > | or rather before 14 April 2017, which is when R from revision r72510 was
| > | uploaded to sid as pre-release candidate.
| > 
| > Another example with KernSmooth:
| >    > library(KernSmooth)
| > 
| >    KernSmooth 2.23 loaded
| >    Copyright M. P. Wand 1997-2009
| > 
| >    > example(bkde)
| > 
| >    bkde> data(geyser, package="MASS")
| > 
| >    bkde> x <- geyser$duration
| > 
| >    bkde> est <- bkde(x, bandwidth=0.25)
| >    Error in linbin(x, gpoints, truncate) : object 'F_linbin' not found
| > 
| > 
| > Maybe this part of NEWS is what matters:
| > 
| >     * Packages which register native routines for .C or .Fortran need
| >       to be re-installed for this version (unless installed with
| >       R-devel SVN revision r72375 or later).
| 
| Yes, that is what Martin Mächler referred to in the answer to Björan's call 
| for help on r-help.
| 
| > KernSmooth surely has .Fortran. Your spatial example had VR_frset failing,
| > and that too is called by the old .C.
| > 
| > A counter-example is eg my RcppEigen package -- I can load it and run
| > example(fastLm) just fine as that uses .Call rather than .C or .Fortran.
| > 
| > I think you are
| > 
| >  -- correct in that we need rebuilds
| >  -- but only for packages using .C and .Fortran calls to compiled
| 
| Yes.

Here is a quick script snippet. Looks like about 1/3 of my r-cran-* packages
use .C() or .Fortran() and need a rebuild for R 3.4.0 (which some may already
have gotten as some upstream packages got updates):

-----------------------------------------------------------------------------
#!/bin/bash

## source directories are all named foo-1.2.3
dirs=$(find . -maxdepth 1 -type d -name \*-\* | sort)

for d in ${dirs}; do
    if test -d ${d}/src; then
        if grep -q -r \\.Fortran\( ${d}/R; then
            echo ".Fortran in ${d}"
        fi
        if grep -q -r \\.C\( ${d}/R; then
            echo ".C       in ${d}"
        fi
    fi
done
-----------------------------------------------------------------------------
         

| 
| > 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?

Dirk

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