[R] how do I tell configure where to find Java?

[Liaw, Andy]

Thanks to everyone who provided the info.  I tried Martin Morgan's 
suggestion (adding JAVA_HOME=/where/jdk/install/itself) to the 
list of variables defined after `configure', and config.log shows
that the desired Java is found.

The Scyld system is based on RH, but I believe it lags far 
behind FC.  The JDK is from Sun, and didn't come as a RPM.

Best,
Andy

From: Peter Dalgaard
> 
> Logan Lewis <lkderedhat at proxc.net> writes:
> 
> > Andy,
> > 
> > On Tuesday 03 October 2006 3:30 pm, Liaw, Andy wrote:
> > > Before I do that, I would need to remove the gcj stuff 
> that are in 
> > > /usr/bin. If I know how to remove gcj, I'd gladly do 
> that.  However, 
> > > for the particular version of the OS, the entire GCC seems to be 
> > > bundled into one rpm, and I could not remove just the gcj 
> component.  
> > > Neither do I wish to mess with files that are part of 
> some RPMs--- 
> > > in my experience that's invitation for trouble later.
> > 
> > The Red Hat way of dealing with different packages 
> providing the same 
> > binaries is "alternatives".  You will see a bunch of links in 
> > /etc/alternatives, and the command /usr/sbin/alternatives 
> allows you 
> > to switch between options that provide the same binaries.  
> The trouble 
> > is that the Sun JDK package does not interface into this 
> system, and 
> > doesn't show up as an option when you execute 
> /usr/sbin/alternatives --config java.
> 
> Hmm... I actually have it, but how did it get there?
> 
> [pd at titmouse2 R]$ /usr/sbin/alternatives --config java
> 
> There are 2 programs which provide 'java'.
> 
>   Selection    Command
> -----------------------------------------------
>    1           /usr/lib/jvm/jre-1.4.2-gcj/bin/java
> *+ 2           /usr/lib/jvm/jre-1.5.0-sun/bin/java
> 
> Enter to keep the current selection[+], or type selection number:
> failed to create /var/lib/alternatives/java.new: Permission denied
> 
> 
> 
> 
> 
> -- 
>    O__  ---- Peter Dalgaard             Øster Farimagsgade 5, Entr.B
>   c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
>  (*) \(*) -- University of Copenhagen   Denmark          Ph:  
> (+45) 35327918
> ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)                  FAX: 
> (+45) 35327907
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide 
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
> 
> 
> 


------------------------------------------------------------------------------
Notice:  This e-mail message, together with any attachments,...{{dropped}}