Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362010-03-02T15:41:15ZEcoinformatics Redmine
Redmine Bug #4859 (In Progress): GDALTranslate does not work on Windows 7 (64bit)https://projects.ecoinformatics.org/ecoinfo/issues/48592010-03-02T15:41:15ZTom Parrisparris@isciences.com
<p>GDALJniGlue fails to intialize on Windows 64bit operating systems.</p>
<p>ptolemy.kernel.util.IllegalActionException: in .GDAL_Translate_test_oak.manager<br />Because:<br />Could not initialize class org.ecoinformatics.seek.gis.gdal.GDALJniGlue<br />at ptolemy.actor.Manager.execute(Manager.java:472)<br />at ptolemy.actor.Manager.run(Manager.java:1119)<br />at ptolemy.actor.Manager$3.run(Manager.java:1160)<br />Caused by: java.lang.NoClassDefFoundError: Could not initialize class org.ecoinformatics.seek.gis.gdal.GDALJniGlue<br />at org.ecoinformatics.seek.gis.gdal.GDALTranslateActor.fire(GDALTranslateActor.java:207)<br />at ptolemy.actor.AtomicActor.iterate(AtomicActor.java:469)<br />at ptolemy.actor.sched.StaticSchedulingDirector.fire(StaticSchedulingDirector.java:188)<br />at ptolemy.actor.CompositeActor.fire(CompositeActor.java:458)<br />at ptolemy.actor.Manager.iterate(Manager.java:714)<br />at ptolemy.actor.Manager.execute(Manager.java:349)<br />... 2 more<br />Caused by: java.lang.NoClassDefFoundError: Could not initialize class org.ecoinformatics.seek.gis.gdal.GDALJniGlue<br />at org.ecoinformatics.seek.gis.gdal.GDALTranslateActor.fire(GDALTranslateActor.java:207)<br />at ptolemy.actor.AtomicActor.iterate(AtomicActor.java:469)<br />at ptolemy.actor.sched.StaticSchedulingDirector.fire(StaticSchedulingDirector.java:188)<br />at ptolemy.actor.CompositeActor.fire(CompositeActor.java:458)<br />at ptolemy.actor.Manager.iterate(Manager.java:714)<br />at ptolemy.actor.Manager.execute(Manager.java:349)<br />at ptolemy.actor.Manager.run(Manager.java:1119)<br />at ptolemy.actor.Manager$3.run(Manager.java:1160)</p> Bug #4827 (New): RExpression does not handle matrix tokens correctly.https://projects.ecoinformatics.org/ecoinfo/issues/48272010-02-23T20:38:25ZTom Parrisparris@isciences.com
<p>I've attached a simple workflow that demonstrates a bug in the way the RExpression actor translates Kepler/Ptolemy matrices to R matrices. There seems to be a problem in the autmatically generated "matrix" statement in R that is likely due to confusing row and column counts.</p>
<p>A simple 2 row x 5 column constant matrix ([1, 2, 3, 4, 5; 101, 102, 103, 104, 105]) is passed to Rexpression on the min port. The R script simply displays the matrix and passes it along to the mout port.</p>
<p>There are three displays.</p>
<p>1. min displays the matrix before it enters the RExpression actor. It is fine.</p>
<p>2. mout displays the matrix after it leaves the RExpression actor. It too is fine (indicating that the translation problem inverts itself when baorcasting to the output port).</p>
<p>3. The problem is in the Routput display.</p>
<blockquote>
<p>min</p>
</blockquote>
[,1] [,2] [,3] [,4] [,5]<br />[1,] 1 3 5 102 104<br />[2,] 2 4 101 103 105
<p>Note how the matrix is scrambled. The automatically generated R script line that reads:</p>
<pre><code>`min` <- matrix(c(1, 2, 3, 4, 5, 101, 102, 103, 104, 105), nrow=2,ncol=5)</code></pre>
<p>should read</p>
<pre><code>`min` <- matrix(c(1, 101, 2, 102, 3, 103, 4, 104, 5, 105), nrow=2,ncol=5)</code></pre> Bug #4826 (Resolved): intermittent exceptions displaying matrix tokenshttps://projects.ecoinformatics.org/ecoinfo/issues/48262010-02-23T18:22:46ZTom Parrisparris@isciences.com
<p>I experience intermittent exceptions displaying matrix tokens in a simple workflow. The problems are more frequent when using the runtime window, but I can generate the exceptions either way.</p>
<p>The offending workflow is attached to this message.</p>
<p>Sample of problem while repeatedely pressing the "run workflow " button (normal presentation window).<br /> [run] 16 ms. Memory: 58332K Free: 18864K (32%)<br /> [run] 15 ms. Memory: 58332K Free: 17878K (31%)<br /> [run] 16 ms. Memory: 58332K Free: 17001K (29%)<br /> [run] 16 ms. Memory: 58332K Free: 16048K (28%)<br /> [run] 16 ms. Memory: 58332K Free: 18800K (32%)<br /> [run] 16 ms. Memory: 58332K Free: 17876K (31%)<br /> [run] Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: 3 >= 2<br /> [run] at java.util.Vector.elementAt(Vector.java:427)<br /> [run] at javax.swing.table.DefaultTableColumnModel.getColumn(DefaultTableColumnModel.java:277)<br /> [run] at javax.swing.plaf.basic.BasicTableUI.paintCells(BasicTableUI.java:1967)<br /> [run] at javax.swing.plaf.basic.BasicTableUI.paint(BasicTableUI.java:1767)<br /> [run] at javax.swing.plaf.ComponentUI.update(ComponentUI.java:143)<br /> [run] at javax.swing.JComponent.paintComponent(JComponent.java:751)<br /> [run] at javax.swing.JComponent.paint(JComponent.java:1017)<br /> [run] at javax.swing.JComponent.paintToOffscreen(JComponent.java:5112)<br /> [run] at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1475)<br /> [run] at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1406)<br /> [run] at javax.swing.RepaintManager.paint(RepaintManager.java:1220)<br /> [run] at javax.swing.JComponent._paintImmediately(JComponent.java:5060)<br /> [run] at javax.swing.JComponent.paintImmediately(JComponent.java:4870)<br /> [run] at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:803)<br /> [run] at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:714)<br /> [run] at javax.swing.RepaintManager.seqPaintDirtyRegions(RepaintManager.java:694)<br /> [run] at javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(SystemEventQueueUtilities.java:125)<br /> [run] at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)<br /> [run] at java.awt.EventQueue.dispatchEvent(EventQueue.java:597)<br /> [run] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)<br /> [run] at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)<br /> [run] at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)<br /> [run] at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)</p>
<p>Sample of problem while repeatedly pressing the "go" button in the "run time window"</p>
<p>[run] 15 ms. Memory: 58332K Free: 15914K (27%)<br />[run] 16 ms. Memory: 58332K Free: 11679K (20%)<br />[run] 0 ms. Memory: 58332K Free: 10640K (18%)<br />[run] Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: 2 >= 2<br />[run] at java.util.Vector.elementAt(Vector.java:427)<br />[run] at javax.swing.table.DefaultTableColumnModel.getColumn(DefaultTableColumnModel.java:277)<br />[run] 16 ms. Memory: 58332K Free: 13221K (23%)<br />[run] at javax.swing.plaf.basic.BasicTableUI.paintGrid(BasicTableUI.java:1928)<br />[run] at javax.swing.plaf.basic.BasicTableUI.paint(BasicTableUI.java:1764)<br />[run] at javax.swing.plaf.ComponentUI.update(ComponentUI.java:143)<br />[run] at javax.swing.JComponent.paintComponent(JComponent.java:751)<br />[run] at javax.swing.JComponent.paint(JComponent.java:1017)<br />[run] at javax.swing.JComponent.paintToOffscreen(JComponent.java:5112)<br />[run] at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1475)<br />[run] at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1406)<br />[run] at javax.swing.RepaintManager.paint(RepaintManager.java:1220)<br />[run] at javax.swing.JComponent._paintImmediately(JComponent.java:5060)<br />[run] at javax.swing.JComponent.paintImmediately(JComponent.java:4870)<br />[run] at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:803)<br />[run] at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:714)<br />[run] at javax.swing.RepaintManager.seqPaintDirtyRegions(RepaintManager.java:694)<br />[run] at javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(SystemEventQueueUtilities.java:125)<br />[run] at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)<br />[run] at java.awt.EventQueue.dispatchEvent(EventQueue.java:597)<br />[run] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)<br />[run] at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)<br />[run] at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)<br />[run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)<br />[run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)<br />[run] at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)</p>