Hi Tomas,
I just downloaded from Oracle last month. However, it appears that I have
downloaded the wrong version because I have OpenJDK and you have Java(TM) SE.
Could this be the reason. I will try and let you know. Thanks for your help.
Best regards,
Pino
El 20/11/2012, a las 2:31a.m., Tomas Pluskal <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>
> 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(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
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Monitor your physical, virtual and cloud infrastructure from a single
>> web console. Get in-depth insight into apps, servers, databases, vmware,
>> SAP, cloud infrastructure, etc. Download 30-day Free Trial.
>> Pricing starts from $795 for 25 servers or applications!
>> http://p.sf.net/sfu/zoho_dev2dev_nov
>> _______________________________________________
>> Mzmine-devel mailing list
>> Mzmine-devel@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/mzmine-devel
>
> ===============================================
> 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
------------------------------------------------------------------------------
Monitor your physical, virtual and cloud infrastructure from a single
web console. Get in-depth insight into apps, servers, databases, vmware,
SAP, cloud infrastructure, etc. Download 30-day Free Trial.
Pricing starts from $795 for 25 servers or applications!
http://p.sf.net/sfu/zoho_dev2dev_nov
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