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

[Liviu Andronic]

(follow-up)
After managing to get around some strange ./configure errors, I
managed to build JGR and it's java-dependencies (including rJava) from
source, but I still run into trouble. The warning is the same, and so
is the CPU consumption:
liviu at debian-liv:~$ JGR
WARNING: org.rosuda.JRI.Mutex was unlocked by other thread than
locked! This may soon lead to a crash...

Liviu



On 8/4/09, Liviu Andronic <landronimirc at gmail.com> wrote:
> 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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