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

[Liviu Andronic]

Dear all,
To follow up on my troubles, I encounter the same issues on Ubuntu.
I've installed a fresh copy of Jaunty Jackalope, R 2.8.1, Sun's Java
6, and built JGR from source. On the first run, I get this message:
liviu at ubuntu-liv:~$ JGR
05-Aug-2009 14:51:36 java.util.prefs.FileSystemPreferences$2 run
INFO: Created user preferences directory.

Subsequently, after each start JGR starts using 100% of CPU (which
causes heat and makes the programme unusable) and I also get the same
warning as on Ubuntu.
liviu at ubuntu-liv:~$ JGR
WARNING: org.rosuda.JRI.Mutex was unlocked by other thread than
locked! This may soon lead to a crash...

I'm currently migrating from Gentoo to Debian, and on Gentoo I had no
such issues.

If anyone has any ideas on what might be wrong or how to approach
these issues, please let me know.
Liviu



## On Ubuntu
> sessionInfo()
R version 2.8.1 (2008-12-22)
x86_64-pc-linux-gnu

locale:
LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] JGR_1.6-7    iplots_1.1-3 JavaGD_0.5-2 rJava_0.6-3





On Tue, Aug 4, 2009 at 12:35 PM, 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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