{"action":"created","issue":{"url":"https://api.github.com/repos/mzmine/mzmine2/issues/94","labels_url":"https://api.github.com/repos/mzmine/mzmine2/issues/94/labels{/name}","comments_url":"https://api.github.com/repos/mzmine/mzmine2/issues/94/comments","events_url":"https://api.github.com/repos/mzmine/mzmine2/issues/94/events","html_url":"https://github.com/mzmine/mzmine2/issues/94","id":102569402,"number":94,"title":"Java error when i try to import Waters raw files","user":{"login":"amrsalem","id":3181706,"avatar_url":"https://avatars.githubusercontent.com/u/3181706?v=3","gravatar_id":"","url":"https://api.github.com/users/amrsalem","html_url":"https://github.com/amrsalem","followers_url":"https://api.github.com/users/amrsalem/followers","following_url":"https://api.github.com/users/amrsalem/following{/other_user}","gists_url":"https://api.github.com/users/amrsalem/gists{/gist_id}","starred_url":"https://api.github.com/users/amrsalem/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/amrsalem/subscriptions","organizations_url":"https://api.github.com/users/amrsalem/orgs","repos_url":"https://api.github.com/users/amrsalem/repos","events_url":"https://api.github.com/users/amrsalem/events{/privacy}","received_events_url":"https://api.github.com/users/amrsalem/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":{"login":"tomas-pluskal","id":1796692,"avatar_url":"https://avatars.githubusercontent.com/u/1796692?v=3","gravatar_id":"","url":"https://api.github.com/users/tomas-pluskal","html_url":"https://github.com/tomas-pluskal","followers_url":"https://api.github.com/users/tomas-pluskal/followers","following_url":"https://api.github.com/users/tomas-pluskal/following{/other_user}","gists_url":"https://api.github.com/users/tomas-pluskal/gists{/gist_id}","starred_url":"https://api.github.com/users/tomas-pluskal/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tomas-pluskal/subscriptions","organizations_url":"https://api.github.com/users/tomas-pluskal/orgs","repos_url":"https://api.github.com/users/tomas-pluskal/repos","events_url":"https://api.github.com/users/tomas-pluskal/events{/privacy}","received_events_url":"https://api.github.com/users/tomas-pluskal/received_events","type":"User","site_admin":false},"milestone":null,"comments":3,"created_at":"2015-08-22T21:49:18Z","updated_at":"2016-01-14T17:35:32Z","closed_at":"2015-08-23T20:36:42Z","body":"I tried with mzML and the import works but when I try to use the Water raw file it gives me an error.  I am using the new version of mzmine 2.15 but I also tried this on 2.14.2 and it still doesn't work.  I tried this on a PC and it imported the waters raw file fine but I want to use my mac because it has much more power.  Any help is highly appreciated. Below is the information you requested.  \r\n\r\nI am using 64bit OSX 10.9.5\r\n\r\n java -version\r\njava version \"1.8.0_60\"\r\nJava(TM) SE Runtime Environment (build 1.8.0_60-b27)\r\nJava HotSpot(TM) 64-Bit Server VM (build 25.60-b23, mixed mode)\r\n R --version\r\nR version 3.1.3 (2015-03-09) -- \"Smooth Sidewalk\"\r\nCopyright (C) 2015 The R Foundation for Statistical Computing\r\nPlatform: x86_64-apple-darwin13.4.0 (64-bit)\r\n\r\n\r\n\r\nthe console log:\r\nChecking physical memory size...\r\nFound 8192 MB memory\r\nJava heap size set to 6144 MB\r\njava version \"1.8.0_60\"\r\nJava(TM) SE Runtime Environment (build 1.8.0_60-b27)\r\nJava HotSpot(TM) 64-Bit Server VM (build 25.60-b23, mixed mode)\r\n\r\n[17:47:49|INFO|MZmineCore]: Starting MZmine 2.15\r\n[17:47:49|FINE|TmpFileCleanup]: Checking for old temporary files...\r\n[17:47:49|FINE|MZmineCore]: Loading core classes..\r\n[17:47:49|FINE|MZmineCore]: Initializing core classes..\r\n[17:47:49|FINE|MZmineCore]: Loading modules\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.projectmethods.projectload.ProjectLoadModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.projectmethods.projectsave.ProjectSaveModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.projectmethods.projectsave.ProjectSaveAsModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.projectmethods.projectclose.ProjectCloseModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.batchmode.BatchModeModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethods.rawdataimport.RawDataImportModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethods.peakpicking.massdetection.MassDetectionModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.masslistmethods.shoulderpeaksfilter.ShoulderPeaksFilterModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.masslistmethods.chromatogrambuilder.ChromatogramBuilderModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethods.peakpicking.gridmass.GridMassModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethods.peakpicking.manual.ManualPeakPickerModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethods.peakpicking.msms.MsMsPeakPickerModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethods.filtering.scanfilters.ScanFiltersModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethods.filtering.cropper.CropFilterModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethods.filtering.baselinecorrection.BaselineCorrectionModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethods.filtering.alignscans.AlignScansModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethods.filtering.scansmoothing.ScanSmoothingModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethods.orderdatafiles.OrderDataFilesModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.orderpeaklists.OrderPeakListsModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.alignment.join.JoinAlignerModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.alignment.ransac.RansacAlignerModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.io.csvexport.CSVExportModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.io.metaboanalystexport.MetaboAnalystExportModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.io.mztabexport.MzTabExportModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.io.sqlexport.SQLExportModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.io.xmlexport.XMLExportModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.io.casmiimport.CasmiImportModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.io.mztabimport.MzTabImportModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.io.xmlimport.XMLImportModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.gapfilling.peakfinder.PeakFinderModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.gapfilling.samerange.SameRangeGapFillerModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.isotopes.deisotoper.IsotopeGrouperModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.isotopes.isotopeprediction.IsotopePatternCalculator\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.peakpicking.smoothing.SmoothingModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.peakpicking.deconvolution.DeconvolutionModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.peakpicking.shapemodeler.ShapeModelerModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.peakpicking.peakextender.PeakExtenderModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.rawdatamethods.peakpicking.targetedpeakdetection.TargetedPeakDetectionModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.filtering.duplicatefilter.DuplicateFilterModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.filtering.rowsfilter.RowsFilterModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.normalization.rtnormalizer.RTNormalizerModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.normalization.linear.LinearNormalizerModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.normalization.standardcompound.StandardCompoundNormalizerModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.dataanalysis.rtmzplots.cvplot.CVPlotModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.dataanalysis.rtmzplots.logratioplot.LogratioPlotModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.dataanalysis.projectionplots.PCAPlotModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.dataanalysis.projectionplots.CDAPlotModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.dataanalysis.projectionplots.SammonsPlotModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.dataanalysis.clustering.ClusteringModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.dataanalysis.heatmaps.HeatMapModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.identification.customdbsearch.CustomDBSearchModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.identification.formulaprediction.FormulaPredictionModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.identification.fragmentsearch.FragmentSearchModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.identification.adductsearch.AdductSearchModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.identification.complexsearch.ComplexSearchModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.identification.onlinedbsearch.OnlineDBSearchModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.identification.glycerophospholipidsearch.GPLipidSearchModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.identification.camera.CameraSearchModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.identification.nist.NistMsSearchModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.peaklistmethods.identification.formulapredictionpeaklist.FormulaPredictionPeakListModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization.tic.TICVisualizerModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization.spectra.SpectraVisualizerModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization.ida.IDAVisualizerModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization.twod.TwoDVisualizerModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization.threed.ThreeDVisualizerModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization.neutralloss.NeutralLossVisualizerModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization.peaklisttable.PeakListTableModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization.peaklisttable.export.IsotopePatternExportModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization.peaklisttable.export.MSMSExportModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization.scatterplot.ScatterPlotVisualizerModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization.histogram.HistogramVisualizerModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization.infovisualizer.InfoVisualizerModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.visualization.intensityplot.IntensityPlotModule\r\n[17:47:49|FINEST|MZmineCore]: Loading module net.sf.mzmine.modules.tools.mzrangecalculator.MzRangeCalculatorModule\r\n[17:47:50|FINE|MZmineCore]: Initializing GUI\r\n[17:47:51|FINEST|MZmineConfigurationImpl]: Loading desktop configuration\r\n[17:47:51|FINEST|MZmineConfigurationImpl]: Loading modules configuration\r\n[17:47:51|INFO|MZmineConfigurationImpl]: Loaded configuration from file conf/config.xml\r\n[17:47:51|INFO|MZmineCore]: Showing main window\r\n[17:47:55|FINEST|MainMenu]: Setting parameters for module Raw data import\r\n[17:47:57|FINEST|MainMenu]: Starting module Raw data import with parameters Raw data file names: [/Users/aali/Desktop/Lipid Experiments Mac/150815 Sample Prep & LC Trial 1/Mass Spec/Blank1.raw]\r\n[17:47:57|FINEST|RawDataImportModule]: File /Users/aali/Desktop/Lipid Experiments Mac/150815 Sample Prep & LC Trial 1/Mass Spec/Blank1.raw type detected as WATERS_RAW\r\n[17:47:57|FINEST|TaskQueue]: Adding task \"Opening file /Users/aali/Desktop/Lipid Experiments Mac/150815 Sample Prep & LC Trial 1/Mass Spec/Blank1.raw\" to the task controller queue\r\n[17:47:57|INFO|WorkerThread]: Starting processing of task Opening file /Users/aali/Desktop/Lipid Experiments Mac/150815 Sample Prep & LC Trial 1/Mass Spec/Blank1.raw\r\n[17:47:57|INFO|NativeFileReadTask]: Opening file /Users/aali/Desktop/Lipid Experiments Mac/150815 Sample Prep & LC Trial 1/Mass Spec/Blank1.raw\r\njava.io.IOException: Cannot run program \"wine\": error=2, No such file or directory\r\n\tat java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)\r\n\tat java.lang.Runtime.exec(Runtime.java:620)\r\n\tat java.lang.Runtime.exec(Runtime.java:485)\r\n\tat net.sf.mzmine.modules.rawdatamethods.rawdataimport.fileformats.NativeFileReadTask.run(NativeFileReadTask.java:131)\r\n\tat net.sf.mzmine.taskcontrol.impl.WorkerThread.run(WorkerThread.java:61)\r\nCaused by: java.io.IOException: error=2, No such file or directory\r\n\tat java.lang.UNIXProcess.forkAndExec(Native Method)\r\n\tat java.lang.UNIXProcess.<init>(UNIXProcess.java:248)\r\n\tat java.lang.ProcessImpl.start(ProcessImpl.java:134)\r\n\tat java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)\r\n\t... 4 more\r\n[17:47:57|SEVERE|WorkerThread]: Error of task Opening file /Users/aali/Desktop/Lipid Experiments Mac/150815 Sample Prep & LC Trial 1/Mass Spec/Blank1.raw: java.io.IOException: Cannot run program \"wine\": error=2, No such file or directory (ProcessBuilder.java:1048)\r\n\r\n\r\n\r\n\r\n\r\n![java error 1](https://cloud.githubusercontent.com/assets/3181706/9425992/5a7048c2-48f5-11e5-84cc-14954dd24ecf.jpg)\r\n"},"comment":{"url":"https://api.github.com/repos/mzmine/mzmine2/issues/comments/171717261","html_url":"https://github.com/mzmine/mzmine2/issues/94#issuecomment-171717261","issue_url":"https://api.github.com/repos/mzmine/mzmine2/issues/94","id":171717261,"user":{"login":"MrDarkHorse","id":9271182,"avatar_url":"https://avatars.githubusercontent.com/u/9271182?v=3","gravatar_id":"","url":"https://api.github.com/users/MrDarkHorse","html_url":"https://github.com/MrDarkHorse","followers_url":"https://api.github.com/users/MrDarkHorse/followers","following_url":"https://api.github.com/users/MrDarkHorse/following{/other_user}","gists_url":"https://api.github.com/users/MrDarkHorse/gists{/gist_id}","starred_url":"https://api.github.com/users/MrDarkHorse/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MrDarkHorse/subscriptions","organizations_url":"https://api.github.com/users/MrDarkHorse/orgs","repos_url":"https://api.github.com/users/MrDarkHorse/repos","events_url":"https://api.github.com/users/MrDarkHorse/events{/privacy}","received_events_url":"https://api.github.com/users/MrDarkHorse/received_events","type":"User","site_admin":false},"created_at":"2016-01-14T17:35:32Z","updated_at":"2016-01-14T17:35:32Z","body":"Running into this same issue.  Why would it even be looking for wine if that's not an option.  Isn't the point of wine to run Windows stuff in a UNIX environment?"}}