Hi Giselle,
MZmine requires Java version 1.7 or later. Although you said you installed Java
8, your "java -version" command reports version 1.6.0_65.
There may be multiple version of Java runtime installed in your system. Mac OS
sometimes gets confused with that.
I recommend to install the latest JDK (not JRE) from java.oracle.com. That
usually solves this problem.
Best,
Tomas
> On Jun 2, 2015, at 05:00, Giselle Tamayo <tamayo.casti...@gmail.com> wrote:
>
> Hi!
>
> I can not run MZmine after the last update (2.14.2-2). Terminal gives the
> following response:
> <Screen Shot 2015-06-01 at 13.55.55.png>
>
>
> I have updated Java SE runtime (jre-8u45-macosx-x64.dmg), R several times;
> even downloaded Xcode and Xquarts…. but nothing. I guess the problem is with
> Java, but I can not locate it. The last MZmine version I ran was 2.12, with
> any problems.
>
> It follows the information you usually request. Thanks for your help!
>
> 1) version of MZmine 2.14-2.2
> 2) OS X Yosemite, 64 bits 10.10.3
> 3) Java version: “1.6.0.65”
> 4) R version: 3.2.0 (64 bit version)
> 5) please find in the attachment the report for R commands.
>
>
> 6) Parameters in the startMZmine_MacOSX.command:
>
> #!/bin/sh
>
> # The HEAP_SIZE variable defines the Java heap size in MB.
> # That is the total amount of memory available to MZmine 2.
> # By default we set this to the half of the physical memory
> # size, but feel free to adjust according to your needs.
>
> echo "Checking physical memory size..."
> TOTAL_MEMORY=`sysctl hw.memsize | awk '{ print int($2 / 1024^2) }'`
> echo "Found $TOTAL_MEMORY MB memory"
>
> HEAP_SIZE=`expr $TOTAL_MEMORY / 2`
> echo Java heap size set to $HEAP_SIZE MB
>
> # The TMP_FILE_DIRECTORY parameter defines the location where temporary
> # files (parsed raw data) will be placed. Default is /tmp.
> TMP_FILE_DIRECTORY=/tmp
>
> # Set R environment variables.
> export R_HOME=/Library/Frameworks/R.framework/Versions/Current/Resources/
>
> # The directory holding the JRI shared library (libjri.jnilib).
> JRI_LIB_PATH=${R_HOME}/library/rJava/jri
>
> # It is usually not necessary to modify the JAVA_COMMAND parameter, but
> # if you like to run a specific Java Virtual Machine, you may set the
> # path to the java command of that JVM.
> # JAVA_COMMAND=`/usr/libexec/java_home -v 1.6+`/bin/java
> JAVA_COMMAND=java
>
> # It is not necessary to modify the following section
> JAVA_PARAMETERS="-showversion -classpath lib/\* -Djava.ext.dirs=
> -XX:+UseParallelGC -Xdock:name='MZmine 2' -Xdock:icon=icons/MZmineIcon.png
> -Djava.io.tmpdir=$TMP_FILE_DIRECTORY -Dapple.laf.useScreenMenuBar=true
> -Xms${HEAP_SIZE}m -Xmx${HEAP_SIZE}m -Djava.library.path=${JRI_LIB_PATH}"
> MAIN_CLASS=net.sf.mzmine.main.MZmineCore
>
> # Make sure we are in the correct directory
> SCRIPTDIR=`dirname "$0"`
> cd "$SCRIPTDIR"
>
> # This command starts the Java Virtual Machine
> echo "$JAVA_PARAMETERS" $MAIN_CLASS "$@" | xargs $JAVA_COMMAND
>
>
> Giselle Tamayo
>
> E-mail personal: tamayo.casti...@gmail.com
>
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> Mzmine-devel mailing list
> Mzmine-devel@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/mzmine-devel
> <R Console.pdf>
===============================================
Tomas Pluskal
G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University
1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
WWW: https://groups.oist.jp/g0
TEL: +81-98-966-8684
Fax: +81-98-966-2890
------------------------------------------------------------------------------
_______________________________________________
Mzmine-devel mailing list
Mzmine-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mzmine-devel
