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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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 at stat.math.ethz.ch
[mailto:r-help-bounces at 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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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On 3 October 2006 at 14:40, Liaw, Andy wrote:
| 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.
What if you re-order PATH so that /usr/java comes first?
Dirk
--
Hell, there are no rules here - we're trying to accomplish something.
-- Thomas A. Edison
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 ?ster 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}}