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

[Liviu Andronic]

Oh, and this is the java-related ./configure information rJava gives me:
checking Java support in R... present:
interpreter : '/usr/bin/java'
archiver    : '/usr/bin/jar'
compiler    : '/usr/bin/javac'
header prep.: '/usr/bin/javah'
cpp flags   : '-I/usr/lib/jvm/java-6-sun-1.6.0.14/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.14/jre/../include/linux'
java libs   : '-L/usr/lib/jvm/java-6-sun-1.6.0.14/jre/lib/amd64/server
-L/usr/lib/jvm/java-6-sun-1.6.0.14/jre/lib/amd64
-L/usr/lib/jvm/java-6-sun-1.6.0.14/jre/../lib/amd64 -L
-L/usr/java/packages/lib/amd64 -L/lib -L/usr/lib -ljvm'
checking whether JNI programs can be compiled... yes
checking JNI data types... ok
checking whether JRI should be compiled (autodetect)... yes
checking whether debugging output should be enabled... no
checking whether memory profiling is desired... no
checking whether threads support is requested... no
checking whether callbacks support is requested... no
checking whether JNI cache support is requested... no
checking whether JRI is requested... yes


Liviu

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