[R-sig-Debian] 100% CPU when running (cran2deb) JGR on Debian

[Liviu Andronic]

Dear all,
I installed the amd64 cran2deb [1] JGR binaries on a fresh Debian
testing, and JGR is missbehaving. When JGR starts up, one core of the
CPU goes to 100% and stays there, even though I am keeping it idle and
not performing any operation.

I tried JGR with both sun-java6-jdk and openjdk-6-jdk,
debian-liv:/home/liviu# update-alternatives --config java
There are 4 choices for the alternative java (providing /usr/bin/java).

  Selection    Path                                      Priority   Status
------------------------------------------------------------
  0            /usr/lib/jvm/java-6-openjdk/jre/bin/java   1061      auto mode
  1            /usr/bin/gij-4.3                           43        manual mode
  2            /usr/lib/jvm/java-6-openjdk/jre/bin/java   1061      manual mode
* 3            /usr/lib/jvm/java-6-sun/jre/bin/java       63        manual mode
  4            /usr/lib/jvm/java-gcj/jre/bin/java         1043      manual mode

options 3 and 0, to no avail. After changing the java alternative, I
also executed
debian-liv:/home/liviu# R CMD javareconf
Java interpreter : /usr/bin/java
Java version     : 1.6.0_14
Java home path   : /usr/lib/jvm/java-1.5.0-gcj-4.3-1.5.0.0/jre
Java compiler    : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
Java library path: /usr/lib/../lib/gcj-4.3-90:/usr/lib/jni
JNI linker flags : -L/usr/lib/../lib/gcj-4.3-90 -L/usr/lib/jni -ljvm
JNI cpp flags    :

Updating Java configuration in /etc/R
Done.

Starting JGR via require(JGR) or the stand-alone script
(/usr/local/lib/R/site-library/JGR/scripts/run) makes no difference.
Neither running as user or as root. JGR will start and immediately
begin using 100% of one CPU core.

One thing that it complains of is:
liviu at debian-liv:~$ /usr/local/lib/R/site-library/JGR/scripts/run
WARNING: org.rosuda.JRI.Mutex was unlocked by other thread than
locked! This may soon lead to a crash...

Could anyone suggest a way to work around this issue? Thank you,
Liviu

[1] http://www.mail-archive.com/debian-science@lists.debian.org/msg03306.html





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