Hi,
I think it doesn't matter if you use java version 1.6 or 1.7 - you won't see
any difference with MZmine.
If you do want to use 1.7, there are two ways. One is to edit the startMZmine
script and change the JAVA_COMMAND variable, the other is to change the
preferred JDK in the Mac OS Java preferences (go to System Preferences -> Java
-> Java -> View...).
Best regards,
Tomas
On Dec 1, 2012, at 3:53 AM, Manuel M. Sánchez del Pino
<mspin...@gmail.com<mailto:mspin...@gmail.com>> wrote:
Hi Tomas,
I tried to uninstall all Java versions on my mac. However, version 1.6 was not
removed. Nevertheless, MZmine did work on this version. I downloaded version
1.7 but MZmine is still using version 6. When I type Java -version on
Terminal the output shows:
java version "1.6.0_37"
Java(TM) SE Runtime Environment (build 1.6.0_37-b06-434-11M3909)
Java HotSpot(TM) 64-Bit Server VM (build 20.12-b01-434, mixed mode)
However, if I type /Library/Internet\
Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/bin/java -version, the output
reads:
java version "1.7.0_09"
Java(TM) SE Runtime Environment (build 1.7.0_09-b05)
Java HotSpot(TM) 64-Bit Server VM (build 23.5-b02, mixed mode)
Should it be better that MZmine could use Java 1.7? How can I do it? Thanks.
Best regards,
Pino
El 20/11/2012, a las 2:31a.m., Tomas Pluskal
<plus...@oist.jp<mailto:plus...@oist.jp>> escribió:
Hi Manuel,
Not sure about the cause of the problem, but try updating your Java
distribution.
I am also running on Mac OS X 10.8.2 and I can start MZmine without problems.
My java version reports as:
java version "1.7.0_07"
Java(TM) SE Runtime Environment (build 1.7.0_07-b10)
Java HotSpot(TM) 64-Bit Server VM (build 23.3-b01, mixed mode)
Apparently, your java build is over 1 year old (build 1.7.0-b147-20111031), so
it might help if you upgrade it.
Cheers,
Tomas
On Nov 20, 2012, at 2:11 AM, Manuel M. Sánchez del Pino
<mspin...@gmail.com<mailto:mspin...@gmail.com>> wrote:
Hi,
I have been using MZmine2 on a Mac without any problems until the last Java
update from Apple. After this update, MZmine2 quits before opening. It
happens the same with a few other Java-based software. It appears that it has
something to do while launching the the GUI because I get the following
messages in the terminal window:
cuatri:~ Pino$
/Applications/CIENCIA/MZmine2/MZmine-2.10/startMZmine_MacOSX.command ; exit;
openjdk version "1.7.0-b147"
OpenJDK Runtime Environment (build 1.7.0-b147-20111031)
OpenJDK 64-Bit Server VM (build 21.0-b17, mixed mode)
[18:08:50|INFO|MZmineCore]: Starting MZmine 2.10
[18:08:50|FINE|TmpFileCleanup]: Checking for old temporary files...
[18:08:50|FINE|MZmineCore]: Loading core classes..
[18:08:50|FINE|MZmineCore]: Initializing core classes..
[18:08:51|FINE|MZmineCore]: Loading modules
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.projectmethods.projectload.ProjectLoadModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.projectmethods.projectsave.ProjectSaveModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.projectmethods.projectsave.ProjectSaveAsModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.projectmethods.projectclose.ProjectCloseModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.batchmode.BatchModeModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.rawdatamethods.rawdataimport.RawDataImportModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.rawdatamethods.peakpicking.massdetection.MassDetectionModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.masslistmethods.shoulderpeaksfilter.ShoulderPeaksFilterModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.masslistmethods.chromatogrambuilder.ChromatogramBuilderModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.rawdatamethods.peakpicking.manual.ManualPeakPickerModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.rawdatamethods.peakpicking.msms.MsMsPeakPickerModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.rawdatamethods.filtering.scanfilters.ScanFiltersModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.rawdatamethods.filtering.datasetfilters.DataSetFiltersModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.rawdatamethods.filtering.baselinecorrection.BaselineCorrectionModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.alignment.join.JoinAlignerModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.alignment.ransac.RansacAlignerModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.io.csvexport.CSVExportModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.io.xmlexport.XMLExportModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.io.xmlimport.XMLImportModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.io.sqlexport.SQLExportModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.gapfilling.peakfinder.PeakFinderModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.gapfilling.samerange.SameRangeGapFillerModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.isotopes.deisotoper.IsotopeGrouperModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.isotopes.isotopeprediction.IsotopePatternCalculator
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.peakpicking.smoothing.SmoothingModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.DeconvolutionModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.peakpicking.shapemodeler.ShapeModelerModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.peakpicking.peakextender.PeakExtenderModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.rawdatamethods.targetedpeakdetection.TargetedPeakDetectionModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.filtering.duplicatefilter.DuplicateFilterModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.filtering.rowsfilter.RowsFilterModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.normalization.rtnormalizer.RTNormalizerModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.normalization.linear.LinearNormalizerModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.normalization.standardcompound.StandardCompoundNormalizerModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.dataanalysis.rtmzplots.cvplot.CVPlotModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.dataanalysis.rtmzplots.logratioplot.LogratioPlotModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.dataanalysis.projectionplots.PCAPlotModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.dataanalysis.projectionplots.CDAPlotModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.dataanalysis.projectionplots.SammonsPlotModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.dataanalysis.clustering.ClusteringModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.dataanalysis.heatmaps.HeatMapModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.identification.custom.CustomDBSearchModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.identification.formulaprediction.FormulaPredictionModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.identification.fragmentsearch.FragmentSearchModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.identification.adductsearch.AdductSearchModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.identification.complexsearch.ComplexSearchModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.identification.dbsearch.OnlineDBSearchModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.identification.glycerophospholipidsearch.GPLipidSearchModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.identification.camera.CameraSearchModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.peaklistmethods.identification.nist.NistMsSearchModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.visualization.tic.TICVisualizerModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.visualization.spectra.SpectraVisualizerModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.visualization.twod.TwoDVisualizerModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.visualization.threed.ThreeDVisualizerModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.visualization.neutralloss.NeutralLossVisualizerModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.visualization.peaklist.PeakListTableModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.visualization.peaklist.export.IsotopePatternExportModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.visualization.peaklist.export.MSMSExportModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.visualization.scatterplot.ScatterPlotVisualizerModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.visualization.histogram.HistogramVisualizerModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.visualization.infovisualizer.InfoVisualizerModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.visualization.intensityplot.IntensityPlotModule
[18:08:51|FINEST|MZmineCore]: Loading module
net.sf.mzmine.modules.tools.mzrangecalculator.MzRangeCalculatorModule
[18:08:51|FINE|MZmineCore]: Initializing GUI
[18:08:51|SEVERE|MZmineCore]: Could not initialize
GUI(java.lang.reflect.invocationtargetexcept...@java.awt.EventQueue.invokeAndWait<mailto:java.lang.reflect.invocationtargetexcept...@java.awt.EventQueue.invokeAndWait>(EventQueue.java:1242))
logout
I am using a MacBook Pro (2,4 GHz Intel Core 2 Duo) running under OS X 10.8.2
(12C60). The Java version is included in the terminal output. I did not
change anything from the default settings in the startMZmine script. Thanks a
lot for your help.
Best regards,
Pino
Manuel Sánchez del Pino
Depto de Bioquímica y Biología Molecular
Facultad de Ciencias Biológicas
Universidad de Valencia
Dr. Moliner, 50
46100 Burjassot (Valencia)
Tel. 34-96-3543464
Fax 34-96-3544635
e-mail: sande...@uv.es<mailto:sande...@uv.es>
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Tomáš 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
Manuel Sánchez del Pino
Depto de Bioquímica y Biología Molecular
Facultad de Ciencias Biológicas
Universidad de Valencia
Dr. Moliner, 50
46100 Burjassot (Valencia)
Tel. 34-96-3543464
Fax 34-96-3544635
e-mail: sande...@uv.es<mailto:sande...@uv.es>
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Tomáš 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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