From crunch at 3c58.net  Tue Sep 17 01:12:04 2013
From: crunch at 3c58.net (crunch)
Date: Mon, 16 Sep 2013 16:12:04 -0700 (PDT)
Subject: [Rd] JDK not registered
In-Reply-To: <1379206267713-4676149.post@n4.nabble.com>
References: <1379206267713-4676149.post@n4.nabble.com>
Message-ID: <1379373124502-4676286.post@n4.nabble.com>

Given:
$JAVA_HOME=~/jdk1.7.0_40
$R_SHELL=/bin/sh
$PATH=$R_HOME/bin:$JAVA_HOME/bin:...

which jar --> ~/jdk1.7.0_40/bin/jar
which javac --> ~/jdk1.7.0_40/bin/javac
which javah --> ~/jdk1.7.0_40/bin/javah
which java --> '', even though there is one in $JAVA_HOME/bin
whereis java -->
java: /bin/java /usr/bin/java /sbin/java /usr/sbin/java /lib/java
/usr/lib/java /usr/local/bin/java /usr/share/java
   obviously missing the 1.7.0_40 version in $JAVA_HOME/bin as well as the
1.5 version in /usr/bin

If I push into the Rserve package directory and run ./configure, I get:
...
checking Java support in R... present:
interpreter : ''
archiver    : ''
compiler    : ''
header prep.: ''
cpp flags   : ''
java libs   : ''
configure: error: Java Development Kit (JDK) is missing or not registered.

Of course that may be because I have not yet successfully completed a make
of R

if I run R CMD javareconf -e
I get:
Java interpreter : /home1/optimal1/jdk1.7.0_40/jre/bin/java           (why
not the one in the jdk/bin?)
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.
Error occurred during initialization of VM
Could not reserve enough space for object heap

*** Java interpreter doesn't work properly.

I have found that $JAVA_HOME/bin/java (and the one in the jre/bin directory)
each complain 
Error occurred during initialization of VM
Could not reserve enough space for object heap
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.

but, if I define:
alias java='$JAVA_HOME/bin/java -Xmx668m -XX:MaxPermSize=128m'
I can run java in SSH, though R CMD javareconf -e
still fails to initialize the VM.

What can I do to get javareconf to run java with those memory limits?




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[Rd] JDK not registered
crunch