Tomas: thanks! it corrected the problem!
Cheers,
Giselle
Giselle Tamayo
E-mail personal: tamayo.casti...@gmail.com
> On Jun 1, 2015, at 22:27, Tomas Pluskal <plus...@oist.jp> wrote:
>
> 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
>
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