Re: [R] how do I tell configure where to find Java? [Broadcast]
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
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: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] 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 ResearchPO Box 2000 RY33-300
Merck Research LabsRahway, NJ 07065
andy_liaw(a)merck.com 732-594-0820
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Re: [R] how do I tell configure where to find Java? [Broadcast]
Liaw, Andy [EMAIL PROTECTED] 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
[EMAIL PROTECTED] 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: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] 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 ResearchPO Box 2000 RY33-300
Merck Research LabsRahway, NJ 07065
andy_liaw(a)merck.com 732-594-0820
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R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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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
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] how do I tell configure where to find Java? [Broadcast]
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. I'm fairly confident you can manually add the JDK as an option (somebody out there must've written it up). This would probably be the most correct way of doing it within the context of RH's utilities. You can probably also just remove gcj's links (I haven't tested this, so be careful) and make sure that the Sun Java binaries are in your path. For my home system, I just set my path to have the /usr/java/... path come first. Logan __ R-help@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.
Re: [R] how do I tell configure where to find Java? [Broadcast]
For a jre you could create a file called /etc/profile.d/java.sh containing
the following (JAVA_HOME path will need to point to the correct directory
for your particular Java version):
#!/bin/sh
JAVA_HOME=/usr/java/jre1.5.0_08
export JAVA_HOME
JAVA_BIN=$JAVA_HOME/bin
CLASSPATH=$CLASSPATH:$JAVA_HOME:$JAVA_HOME/lib
PATH=$JAVA_BIN:$PATH
export JAVA_BIN CLASSPATH PATH
-Original Message-
From: Liaw, Andy [mailto:[EMAIL PROTECTED]
Sent: 03 October 2006 20:31
To: mike waters
Cc: 'r-help'
Subject: RE: [R] how do I tell configure where to find Java? [Broadcast]
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
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: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] 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 ResearchPO Box 2000 RY33-300
Merck Research LabsRahway, NJ 07065
andy_liaw(a)merck.com 732-594-0820
--
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attachments,...{{dropped}}
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R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
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__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] how do I tell configure where to find Java? [Broadcast]
Logan Lewis [EMAIL PROTECTED] 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? [EMAIL PROTECTED] R]$ /usr/sbin/alternatives --config java There are 2 programs which provide 'java'. SelectionCommand --- 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 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@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.
