[pkg-bioc] R building question

[Dirk Eddelbuettel]

On 2 October 2007 at 10:12, David Vernazobres wrote:
| 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.

Yes. You're being entirely off-topic here. I think you also misunderstand the
question. 1) is nto an issue, this really only affect the buildd during
builds. I am not sure what 2) what achieve, or why it would be needed.
Regarding 3), Simon assures me that jars work across Java compilers. I trust
him on this as he _really_ knows his stuff.  Unless I overlooked something,
this change in r-cran.mk should be unnoticeable in all cases but Java
packahes, which were basically unbuildable before.
 
| > | 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. 

Soudns good.

Dirk, off to an early run

-- 
Three out of two people have difficulties with fractions.