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

From: Peter Dalgaard <p.dalgaard_at_biostat.ku.dk>
Date: Tue 03 Oct 2006 - 20:10:05 GMT

"Liaw, Andy" <andy_liaw@merck.com> writes:

> 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.
>
> Best,
> Andy

Odd, I've done nothing in particular on FC5 and I got

[pd@titmouse2 BUILD]$ grep -i java Makeconf JAVA = /usr/bin/java
JAVA_HOME = /usr/lib/jvm/java-1.5.0-sun-1.5.0.06/jre JAVA_LD_LIBRARY_PATH =
$(JAVA_HOME)/lib/i386/client:$(JAVA_HOME)/lib/i386:$(JAVA_HOME)/../lib/i386:/usr/local/lib JAVA_LIBS = -L$(JAVA_HOME)/lib/i386/client -L$(JAVA_HOME)/lib/i386 -L$(JAVA_HOME)/../lib/i386 -L/usr/local/lib -ljvm JAVAC = /usr/bin/javac

I suspect the installation of java was according to

http://www.fedorafaq.org/#java

and some of this has installed links from /usr/bin/javac to /usr/lib/jvm/java-1.5.0-sun/bin/javac (via /etc/alternatives/javac)

Otherwise, there's always the option of actually reading the configure script... I notice that it starts off looking for JAVA_HOME.  

> From: mike waters
> >
> > I'm not familiar with gcj, but my initial reaction would be a
> > ln -s for the relevant compiler executable from /usr/java
> > into /usr/bin.
> >
> > -----Original Message-----
> > From: r-help-bounces@stat.math.ethz.ch
> > [mailto:r-help-bounces@stat.math.ethz.ch] On Behalf Of Liaw, Andy
> > Sent: 03 October 2006 19:40
> > To: r-help
> > Subject: [R] how do I tell configure where to find Java?
> >
> > Dear R-help,
> >
> > I'm trying to build R-2.4.0 on our Opteron-based Scyld
> > cluster. The system has gcj (the GNU Java compiler, part of
> > GCC) stuff in /usr/bin. When I installed jdk 1.5.08, the
> > install script placed it in /usr/java (I didn't have a
> > choice, as the script didn't offer that option). Now when I
> > run configure in R-2.4.0, it finds gcj, which is not what I
> > want to use. Is there a way to tell configure where to look
> > for Java? I tried configure --help but didn't see anything
> > related to Java.
> >
> > Best,
> > Andy
> >
> > Andy Liaw, PhD
> > Biometrics Research PO Box 2000 RY33-300
> > Merck Research Labs Rahway, NJ 07065
> > andy_liaw(a)merck.com 732-594-0820
> >
> >
> >
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> >
> >
>
>
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-- 
   O__  ---- Peter Dalgaard             ุster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard@biostat.ku.dk)                  FAX: (+45) 35327907

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Received on Wed Oct 04 06:12:36 2006

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