[pkg-bioc] R building question

[David Vernazobres]

On Mon, Oct 01, 2007 at 05:14:34PM -0500, Dirk Eddelbuettel wrote :
> 
> On 30 September 2007 at 20:40, David Vernazobres wrote:
> | Hi Dirk, 
> | 
> | Could you please apply the following patch to your r-base-dev
> | package. 
> | Is it ok to ask you here, or do you prefer a which-list bug against
> | r-base-dev ?
> | 
> | Doing so I would be able to add the following line in debian/rules:
> | extraInstallFlags=--no-latex or what ever option that I may need for
> | building the cran packages.
> 
> Good idea, applied to the package. Along with the overdue change of
> supporting 'R CMD javareconf' if /usr/bin/java is found. According to Simon,
> that is all we need for rJava which I should package for Debian.

Well, I just have a problem, with this solution.
This mean that 
* you need to depend on Java, or if java is installed after R, R will
  still be unconfigure, but on the other hand, I am not sure that a hard
  dependencies in Java is good.

* So what about a meta-pacakge, r-base-java, which is recommend in
  r-base and depend on java,r-base. But in this case, I think that you need to
  have java installed on the computer before r-base-java.
  This sound like a need of using Pre-Depends on java ?

* There is still an issue, what is happening when a new java package is
  installed which modify the alternative of java, javah, javac, ... ?
  Which mean that we need to somehow invoque dpkg-reconfigure
  r-base-java, isn't it ? How the other java related package are dealing
  with that ? 

ok I was blocked here in my reflexion about R and java, this is may be 
a discussion for the debian-dev mailing-list.

> | hopefully as you already started preparing the out coming of R 2.6 
> | (3rd October), it should not take too long, before we could start 
> | using it... 
> | > 
> It was a tad late, but I made a new 2.6.0~20070930 release. Let's test that
> tomorrow so that I could fix things for R 2.6.0 if need be.

Ok, thanks a lot, I will try to play with. 

David