R SIG Debian - Sep 2006 - R 2.4.0 pre-release in unstable may break some packages

Hi all,

Today's apt-get update should bring the first R 2.4.0 snapshot packages. As
with previous releases, I intend to renew the packages every week until the
release of 2.4.0 by R Core that is scheduled for October 3.  That way, R
2.3.1-3 will remain the version in testing.

As you may have seen on the r-devel list, 2.4.0 will require that packages
using S4 classes and the methods package will need to be rebuilt. In other
words, your current unstable installation may break.  If that is a concern
please put r-base-core on hold using e.g.  $ echo "r-cran-base hold" |
dpkg
--set-selections

We will try to establish which r-cran-* et al packages need an update and hope
to get updated Debian packages of those CRAN package -- with a Depends on
"r-base-core (>> 2.3.1)" into the archive.

Cheers, Dirk

-- 
Hell, there are no rules here - we're trying to accomplish something. 
                                                  -- Thomas A. Edison

On 20 September 2006 at 14:53, Dirk Eddelbuettel wrote:
| 
| Hi all,
| 
| Today's apt-get update should bring the first R 2.4.0 snapshot packages.
As
| with previous releases, I intend to renew the packages every week until the
| release of 2.4.0 by R Core that is scheduled for October 3.  That way, R
| 2.3.1-3 will remain the version in testing.
| 
| As you may have seen on the r-devel list, 2.4.0 will require that packages
| using S4 classes and the methods package will need to be rebuilt. In other
| words, your current unstable installation may break.  If that is a concern
| please put r-base-core on hold using e.g.  $ echo "r-cran-base hold"
| dpkg
| --set-selections
| 
| We will try to establish which r-cran-* et al packages need an update and hope
| to get updated Debian packages of those CRAN package -- with a Depends on
| "r-base-core (>> 2.3.1)" into the archive.

I may have overlooked something deeper, but as a first pass, the following
approach (encoded in the script below) worked:
i)   make sure all available packages are installed
ii)  loop over a library() directory and try to install each package therein
iii) rinse and repeat ii)

I uploaded new versions of Matrix, its, latticeExtra, foreign and lme4 and
asked Chris to update eco  --  the rest seems to work. For now, I am ignoring
(as the last line indicates) a few of the older packages in my /usr/local/
tree. 

Cheers, Dirk


#!/bin/sh -e

function installAllAvailable() {
  ## install all available packages (and let apt skip current ones)
  pkgs=`apt-cache search ^r-.* | grep ^r- | grep -v
"r-base\|r-doc\|r-gnome\|r-math\|r-recom" | grep -vi dummy | sort |
cut -f1 -d" "`
  sudo apt-get -t unstable install $pkgs
}

function iterateOver() {
  dirs=`find $1 -maxdepth 1 -mindepth 1 -type d | sort | grep -v $2`
  for f in $dirs
  do
    p=`basename $f`
    echo ""
    echo "Looking at $p"
    echo "stopifnot(require($p, quiet=TRUE)); cat('--- works:
$p\n')"| R --slave
  done
}

## uncomment whatever needs to be run ...

#installAllAvailable
#iterateOver /usr/lib/R/site-library "eco"
#iterateOver /usr/lib/R/library "nothingToIgnore"

## for comparison, my /usr/local tree also tripped up a few
#iterateOver /usr/local/lib/R/site-library
"JGR\|JavaGD\|Ruuid\|Rgraphviz\|VGAM\|VLMC\|graph\|iWidgets\|iplots\|portfolio\|rJava"

echo "Done!"


-- 
Hell, there are no rules here - we're trying to accomplish something. 
                                                  -- Thomas A. Edison