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OpenChrom / openchrom

Visualization and Analysis of mass spectrometric and chromatographic data.
https://www.openchrom.net
Eclipse Public License 1.0
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MicrobeMS .pkf Tests #93

Closed eselmeister closed 3 years ago

eselmeister commented 3 years ago

The MicrobeMS fail. When running it locally, the following error log is generated:

java.lang.NoSuchMethodError: java.nio.ByteBuffer.limit(I)Ljava/nio/ByteBuffer;
    at us.hebi.matlab.mat.types.Sources$ByteBufferSource.readBytesAsStream(Sources.java:280)
    at us.hebi.matlab.mat.types.AbstractSource.readInflated(AbstractSource.java:177)
    at us.hebi.matlab.mat.format.Mat5Reader.readEntry(Mat5Reader.java:270)
    at us.hebi.matlab.mat.format.Mat5Reader.readMatContent(Mat5Reader.java:228)
    at us.hebi.matlab.mat.format.Mat5Reader.readMat(Mat5Reader.java:194)
    at us.hebi.matlab.mat.format.Mat5.readFromFile(Mat5.java:53)
    at net.openchrom.msd.converter.supplier.pkf.converter.io.PkfReader.read(PkfReader.java:47)
    at net.openchrom.msd.converter.supplier.pkf.converter.DatabaseImportConverter.convert(DatabaseImportConverter.java:40)
    at net.openchrom.msd.converter.supplier.pkf.converter.MassSpectrumImportConverter_Ecoli_ITest.setUp(MassSpectrumImportConverter_Ecoli_ITest.java:36)
    at junit.framework.TestCase.runBare(TestCase.java:139)
    at junit.framework.TestResult$1.protect(TestResult.java:122)
    at junit.framework.TestResult.runProtected(TestResult.java:142)
    at junit.framework.TestResult.run(TestResult.java:125)
    at junit.framework.TestCase.run(TestCase.java:129)
    at junit.framework.TestSuite.runTest(TestSuite.java:252)
    at junit.framework.TestSuite.run(TestSuite.java:247)
    at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:86)
    at org.eclipse.jdt.internal.junit4.runner.JUnit4TestReference.run(JUnit4TestReference.java:86)
    at org.eclipse.jdt.internal.junit.runner.TestExecution.run(TestExecution.java:38)
    at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:538)
    at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:760)
    at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.run(RemoteTestRunner.java:460)
    at org.eclipse.pde.internal.junit.runtime.RemotePluginTestRunner.main(RemotePluginTestRunner.java:229)
    at org.eclipse.pde.internal.junit.runtime.PlatformUITestHarness.lambda$0(PlatformUITestHarness.java:43)
    at org.eclipse.swt.widgets.RunnableLock.run(RunnableLock.java:37)
    at org.eclipse.swt.widgets.Synchronizer.runAsyncMessages(Synchronizer.java:182)
    at org.eclipse.swt.widgets.Display.runAsyncMessages(Display.java:4915)
    at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:4521)
    at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine$5.run(PartRenderingEngine.java:1170)
    at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:336)
    at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine.run(PartRenderingEngine.java:1059)
    at org.eclipse.e4.ui.internal.workbench.E4Workbench.createAndRunUI(E4Workbench.java:153)
    at org.eclipse.ui.internal.Workbench.lambda$3(Workbench.java:667)
    at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:336)
    at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:597)
    at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:148)
    at org.eclipse.ui.internal.ide.application.IDEApplication.start(IDEApplication.java:152)
    at org.eclipse.pde.internal.junit.runtime.NonUIThreadTestApplication.runApp(NonUIThreadTestApplication.java:52)
    at org.eclipse.pde.internal.junit.runtime.UITestApplication.runApp(UITestApplication.java:43)
    at org.eclipse.pde.internal.junit.runtime.NonUIThreadTestApplication.start(NonUIThreadTestApplication.java:46)
    at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
    at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
    at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
    at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:388)
    at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:243)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:656)
    at org.eclipse.equinox.launcher.Main.basicRun(Main.java:592)
    at org.eclipse.equinox.launcher.Main.run(Main.java:1498)
    at org.eclipse.equinox.launcher.Main.main(Main.java:1471

The CI also produces errors:

Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.092 s <<< FAILURE! - in net.openchrom.msd.converter.supplier.pkf.converter.MassSpectrumImportConverter_Ecoli_ITest

eselmeister commented 3 years ago

See: https://github.com/OpenChrom/openchrom/pull/92

Mailaender commented 3 years ago

Sorry for the hassle, but I can't reproduce the problem locally:

image

Mailaender commented 3 years ago 
eclipse.buildId=unknown
java.version=11.0.8
java.vendor=N/A
BootLoader constants: OS=linux, ARCH=x86_64, WS=gtk, NL=de_DE
Framework arguments:  -version 3 -port 33075 -testLoaderClass org.eclipse.jdt.internal.junit4.runner.JUnit4TestLoader -loaderpluginname org.eclipse.jdt.junit4.runtime -classNames net.openchrom.msd.converter.supplier.pkf.AllTests -application org.eclipse.pde.junit.runtime.coretestapplication -testpluginname net.openchrom.msd.converter.supplier.pkf
Command-line arguments:  -os linux -ws gtk -arch x86_64 -consoleLog -version 3 -port 33075 -testLoaderClass org.eclipse.jdt.internal.junit4.runner.JUnit4TestLoader -loaderpluginname org.eclipse.jdt.junit4.runtime -classNames net.openchrom.msd.converter.supplier.pkf.AllTests -application org.eclipse.pde.junit.runtime.coretestapplication -data /home/matthias/Entwicklung/Eclipse/openchrom-workspace/../junit-workspace -dev file:/home/matthias/Entwicklung/Eclipse/openchrom-workspace/.metadata/.plugins/org.eclipse.pde.core/pde-junit/dev.properties -os linux -ws gtk -arch x86_64 -consoleLog -testpluginname net.openchrom.msd.converter.supplier.pkf

I use Java 11 but https://github.com/HebiRobotics/MFL requires Java version 1.6 (only the tests require version 7 and 8) so that does not seem to be the problem.

laeubi commented 3 years ago

This can happen if MFL is compiled with a more recent JDK (e.g. Java 9+) even if the class-file-compatibility might be 1.6 ...

See for example https://github.com/eclipse/jetty.project/issues/3244 and stuart-marks comment for a solution.

Mailaender commented 3 years ago

Ah, yes the MFL was self compiled by me using OpenJDK 11.

eselmeister commented 3 years ago

@Matthias Is it possible for you to compile the library using Java 8?

Am 22.10.20 um 16:13 schrieb Matthias Mailänder:

Ah, yes the MFL was self compiled by me using OpenJDK 11.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/OpenChrom/openchrom/issues/93#issuecomment-714523247, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAFHUT2PV6YCH2XBV6SIHW3SMA4YHANCNFSM4SVXGZ7Q.

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OpenChrom - the open source alternative for chromatography / mass spectrometry
Dr. Philip Wenig » Founder » philip.wenig@openchrom.net » http://www.openchrom.net
Mailaender commented 3 years ago

Yes, @openSUSE has a wide variety of Java packages including 1.8.0 which I now downgraded to.

eselmeister commented 3 years ago

Perfect. I'll check the PR. I would like to upgrade to the latest Eclipse release and the latest Java version better sooner than later. Currently, JavaFX is used, which needs to be removed first. There is also an issue with GTK3 and SWT, which also needs to be solved first. So I assume, an upgrade can be scheduled for Q2/2021.

Am 22.10.20 um 19:30 schrieb Matthias Mailänder:

Yes, @openSUSE https://github.com/openSUSE has a wide variety of Java packages including 1.8.0 which I now downgraded to.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/OpenChrom/openchrom/issues/93#issuecomment-714646007, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAFHUT5EU5VIWV7XHWDPLDDSMBT3TANCNFSM4SVXGZ7Q.

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OpenChrom - the open source alternative for chromatography / mass spectrometry
Dr. Philip Wenig » Founder » philip.wenig@openchrom.net » http://www.openchrom.net