Hi Tomas,
I hope this is what you're looking for.
Regards,Padma
On Wednesday, 1 April 2015 10:49 AM, Tomas Pluskal <plus...@oist.jp> wrote:
Hi,
You attached the output of the script execution.
I am asking for the contents of the script.
Please attach the startMZmine_Windows.bat file.
Tomas
> On Apr 1, 2015, at 14:06, padma ramakrishnan <padma...@yahoo.co.in> wrote:
>
> Hi Tomas,
>
> Thank you for your reply. I've attached the MZmine start script as requested.
>
> Regards,
> Padma
>
>
>
> On Tuesday, 31 March 2015 7:30 PM, Tomas Pluskal <plus...@oist.jp> wrote:
>
>
> Hi Padma,
>
> Please attach the complete startMZmine script.
> Your R_LIBS_USER setting looks suspicious.
>
> Tomas
>
>
> > On Mar 31, 2015, at 8:58 PM, padma ramakrishnan <padma...@yahoo.co.in>
> > wrote:
> >
> > Hi,
> >
> > We are working with untargeted metabolomics data sets and are eager to try
> > out MZmine for our analyses. However we are stuck at the raw data
> > filtering step (baseline correction). A screenshot of the error is
> > attached.
> >
> > Some of the details you may require are as follows.
> >
> > 1) MZmine 2.13.1
> > Java version "1.8.0_25"
> > R 3.1.0
> >
> > 2)Java Heap Size set to 1024MB
> >
> > 3)We are having a problem running "baseline correction". We tried
> > configuring these in the R script, but we keep getting a message that
> > these are incompatible with our version of R. Installing an older version
> > of R also did not seem to help.
> >
> > Details of R in the command line are also attached.
> >
> > 4) We are using the 64bit version of R.
> >
> > Please advice on what we need to do to overcome this.
> >
> > Thank you.
> >
> > With regards,
> > Padma Ramakrishnan
> > C-CAMP, Bangalore.
>
> >
> >
> > <R command line.docx><mzmine
> > error.pptx>------------------------------------------------------------------------------
> > Dive into the World of Parallel Programming The Go Parallel Website,
> > sponsored
> > by Intel and developed in partnership with Slashdot Media, is your hub for
> > all
> > things parallel software development, from weekly thought leadership blogs
> > to
> > news, videos, case studies, tutorials and more. Take a look and join the
> > conversation now.
> > http://goparallel.sourceforge.net/_______________________________________________
> > Mzmine-devel mailing list
> > Mzmine-devel@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/mzmine-devel
>
> ===============================================
> 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
>
>
>
> <mzminestartscript.docx>
===============================================
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
Checking physical memory size...
Found 32710 MB memory, 64-bit system
Java heap size set to 1024 MB
'#set' is not recognized as an internal or external command,
operable program or batch file.
java version "1.8.0_25"
Java(TM) SE Runtime Environment (build 1.8.0_25-b18)
Java HotSpot(TM) Client VM (build 25.25-b02, mixed mode)
[13:15:19|INFO|MZmineCore]: Starting MZmine 2.13.1
[13:15:19|FINE|TmpFileCleanup]: Checking for old temporary files...
[13:15:19|FINE|MZmineCore]: Loading core classes..
[13:15:19|FINE|MZmineCore]: Initializing core classes..
[13:15:19|FINE|MZmineCore]: Loading modules
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.projectmethod
s.projectload.ProjectLoadModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.projectmethod
s.projectsave.ProjectSaveModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.projectmethod
s.projectsave.ProjectSaveAsModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.projectmethod
s.projectclose.ProjectCloseModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.batchmode.Bat
chModeModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethod
s.rawdataimport.RawDataImportModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethod
s.peakpicking.massdetection.MassDetectionModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.masslistmetho
ds.shoulderpeaksfilter.ShoulderPeaksFilterModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.masslistmetho
ds.chromatogrambuilder.ChromatogramBuilderModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethod
s.peakpicking.gridmass.GridMassModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethod
s.peakpicking.manual.ManualPeakPickerModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethod
s.peakpicking.msms.MsMsPeakPickerModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethod
s.filtering.scanfilters.ScanFiltersModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethod
s.filtering.datasetfilters.DataSetFiltersModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethod
s.filtering.baselinecorrection.BaselineCorrectionModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethod
s.filtering.alignscans.AlignScansModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethod
s.filtering.scansmoothing.ScanSmoothingModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethod
s.orderdatafiles.OrderDataFilesModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.orderpeaklists.OrderPeakListsModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.alignment.join.JoinAlignerModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.alignment.ransac.RansacAlignerModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.io.csvexport.CSVExportModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.io.metaboanalystexport.MetaboAnalystExportModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.io.mztabexport.MzTabExportModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.io.sqlexport.SQLExportModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.io.xmlexport.XMLExportModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.io.casmiimport.CasmiImportModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.io.mztabimport.MzTabImportModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.io.xmlimport.XMLImportModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.gapfilling.peakfinder.PeakFinderModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.gapfilling.samerange.SameRangeGapFillerModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.isotopes.deisotoper.IsotopeGrouperModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.isotopes.isotopeprediction.IsotopePatternCalculator
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.peakpicking.smoothing.SmoothingModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.peakpicking.deconvolution.DeconvolutionModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.peakpicking.shapemodeler.ShapeModelerModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.peakpicking.peakextender.PeakExtenderModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethod
s.peakpicking.targetedpeakdetection.TargetedPeakDetectionModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.filtering.duplicatefilter.DuplicateFilterModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.filtering.rowsfilter.RowsFilterModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.normalization.rtnormalizer.RTNormalizerModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.normalization.linear.LinearNormalizerModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.normalization.standardcompound.StandardCompoundNormalizerModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.dataanalysis.rtmzplots.cvplot.CVPlotModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.dataanalysis.rtmzplots.logratioplot.LogratioPlotModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.dataanalysis.projectionplots.PCAPlotModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.dataanalysis.projectionplots.CDAPlotModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.dataanalysis.projectionplots.SammonsPlotModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.dataanalysis.clustering.ClusteringModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.dataanalysis.heatmaps.HeatMapModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.identification.custom.CustomDBSearchModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.identification.formulaprediction.FormulaPredictionModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.identification.fragmentsearch.FragmentSearchModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.identification.adductsearch.AdductSearchModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.identification.complexsearch.ComplexSearchModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.identification.dbsearch.OnlineDBSearchModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.identification.glycerophospholipidsearch.GPLipidSearchModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.identification.camera.CameraSearchModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.identification.nist.NistMsSearchModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmetho
ds.identification.formulapredictionpeaklist.FormulaPredictionPeakListModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization
.tic.TICVisualizerModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization
.spectra.SpectraVisualizerModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization
.twod.TwoDVisualizerModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization
.threed.ThreeDVisualizerModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization
.neutralloss.NeutralLossVisualizerModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization
.peaklist.PeakListTableModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization
.peaklist.export.IsotopePatternExportModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization
.peaklist.export.MSMSExportModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization
.scatterplot.ScatterPlotVisualizerModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization
.histogram.HistogramVisualizerModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization
.infovisualizer.InfoVisualizerModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization
.intensityplot.IntensityPlotModule
[13:15:19|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.tools.mzrange
calculator.MzRangeCalculatorModule
[13:15:19|FINE|MZmineCore]: Initializing GUI
[13:15:19|FINEST|MZmineConfigurationImpl]: Loading desktop configuration
[13:15:19|FINEST|MZmineConfigurationImpl]: Loading modules configuration
[13:15:19|INFO|MZmineConfigurationImpl]: Loaded configuration from file conf\con
fig.xml
[13:15:19|INFO|MZmineCore]: Showing main window
------------------------------------------------------------------------------
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
_______________________________________________
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Mzmine-devel@lists.sourceforge.net
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