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> 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 ------------------------------------------------------------------------------ Keep yourself connected to Go Parallel: TUNE You got it built. Now make it sing. Tune shows you how. http://goparallel.sourceforge.net _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel
