Hi Giselle,
I'm no Mac OS X specialist, but this code 51 means (99 percent sure)
that java 7 is required. Which, if I am not mistaken, can require to
upgrade your system to at least 7.5.3.
You can download the Mac OS installer for java from Oracle archives:
http://www.oracle.com/technetwork/java/javase/downloads/jre7-downloads-1880261.html
Note: also make sure, once java installed, to have the right path for
the 1.7, which could conflict with 1.6 already installed. After
installation, if typing "java --version" in a terminal still gives you
1.6.xx, than, locate the right one and change the JAVA_COMMAND variable
to fit the correct version:
#JAVA_COMMAND=`/usr/libexec/java_home -v 1.6+`/usr/bin/java
JAVA_COMMAND="/Library/Internet
Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/bin/java"
There is certainly facilities under Mac OS to make the new version the
default one, but I don't know how. You will. You've got a Mac ;)
The best thing to do, instead, would probably be to uninstall the old
Java 6, before installing the 7, or even the 8, if the version of your
OS allows you to do so. Avoiding conflicts is always the best approach.
Hope this helps.
Regards
Gauthier
On 06/01/2015 10:00 PM, Giselle Tamayo wrote:
Hi!
I can not run MZmine after the last update (2.14.2-2). Terminal gives the
following response:
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
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Gauthier BOAGLIO
CEFE - UMR 5175
1919 route de Mende
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Fax: +33/0 4 67 61 33 36
email: gauthier.boag...@cefe.cnrs.fr
www:
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http://www.evolepid.org/people.php?name=boaglio
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