Thank you Tomas.
Best regards,
Pino
El 04/12/2012, a las 3:13a.m., Tomas Pluskal <plus...@oist.jp> escribió:
> 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>
> 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> 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
>>>>
>>>>
>>>>
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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
>>
>>
>>
>> ------------------------------------------------------------------------------
>> 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
>
> ===============================================
> 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
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