andzajan/mzmatch.r

mzmatch.r's Issues

Unrecognized option: -d64

This is a nice project, but I encountered a small problem when I installed PeakML.Viewer(). I think this is the problem that the new version of Java no longer has the - d64 option. So what should I do？ Using the older java version or a newer version of the PeakML.Viewer are available?

Not able to run PeakML

Hi,
I tried to follow the mzMatch/PeakML tutorial (http://mzmatch.sourceforge.net/tutorial.mzmatch.r.advanced.php), but I am not able to run PeakML. When I run
PeakML.Viewer()

I get

OS type: x86_64-apple-darwin17.0
arguments 'show.output.on.console', 'minimized' and 'invisible' are for Windows only
2022-01-16 14:09:23.372 java[1857:23423] *** WARNING: Method userSpaceScaleFactor in class NSWindow is deprecated on 10.7 and later. It should not be used in new applications. Use convertRectToBacking: instead.
Exception in thread "main" org.eclipse.swt.SWTError: Not implemented (java.lang.ClassNotFoundException: apple.awt.CEmbeddedFrame)
at org.eclipse.swt.SWT.error(Unknown Source)
at org.eclipse.swt.SWT.error(Unknown Source)
at org.eclipse.swt.awt.SWT_AWT.new_Frame(Unknown Source)
at peakmlviewer.widgets.MoleculePanel.(MoleculePanel.java:68)
at peakmlviewer.view.IdentificationView.(IdentificationView.java:100)
at peakmlviewer.MainWnd.(MainWnd.java:140)
at peakmlviewer.PeakMLViewer.main(PeakMLViewer.java:44)
Caused by: java.lang.ClassNotFoundException: apple.awt.CEmbeddedFrame
at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:641)
at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:188)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:520)
at java.base/java.lang.Class.forName0(Native Method)
at java.base/java.lang.Class.forName(Class.java:467)
... 5 more

I am running MacOS Monterey 12.1, RStudio 1.4.1717 and updated Java to the latest version. I also downloaded and tried to run the PeakML.Viewer.jar file but I get a similar error:

***WARNING: Display must be created on main thread due to Cocoa restrictions.
Exception in thread "main" org.eclipse.swt.SWTException: Invalid thread access
at org.eclipse.swt.SWT.error(Unknown Source)
at org.eclipse.swt.SWT.error(Unknown Source)
at org.eclipse.swt.SWT.error(Unknown Source)
at org.eclipse.swt.widgets.Display.error(Unknown Source)
at org.eclipse.swt.widgets.Display.createDisplay(Unknown Source)
at org.eclipse.swt.widgets.Display.create(Unknown Source)
at org.eclipse.swt.graphics.Device.(Unknown Source)
at org.eclipse.swt.widgets.Display.(Unknown Source)
at org.eclipse.swt.widgets.Display.(Unknown Source)
at peakmlviewer.MainWnd.(MainWnd.java:57)
at peakmlviewer.PeakMLViewer.main(PeakMLViewer.java:44)

I am very much a beginner in R and have no knowledge of Java, so I am not quite sure how to diagnose this. Is this an issue with newer versions of Java or my OS?
Thanks for your help!