Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362014-08-21T20:27:56ZEcoinformatics Redmine
Redmine Bug #6588 (New): R actor does not have error for missing outputhttps://projects.ecoinformatics.org/ecoinfo/issues/65882014-08-21T20:27:56ZDaniel Crawldanielcrawl@gmail.com
<p>If the R actor has an output port "x", but the script does not assign a value to a variable "x", then the actor should report an error. Currently, the actor successfully runs but does not write a token to the output port.</p> Feature #6575 (New): reference parameters in R actor's scripthttps://projects.ecoinformatics.org/ecoinfo/issues/65752014-07-09T21:40:18ZDaniel Crawldanielcrawl@gmail.com
<p>It would be nice if the script in the R actor could reference parameters that were added to the R actor. Currently the R actor only converts tokens read on input ports to the R script.</p> Bug #5590 (New): RExpression forces pdf if 'automatically show graphics' is checkedhttps://projects.ecoinformatics.org/ecoinfo/issues/55902012-04-26T01:34:05ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Look into this forced format change side-effect which is confusing to a user. If you select e.g. png, and 'auto show..', you get a pdf.</p> Bug #5030 (New): RExpression2 actor will fail if the libs are not foundhttps://projects.ecoinformatics.org/ecoinfo/issues/50302010-05-26T21:20:31ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Creating a new bug from discussion originating in bug#4985, relevant sections posted below:</p>
<p>Jianwu said:<br />I also tried workflows in Kepler-2.0.0-Demos\demos\R\r-2.0.0\demos\JRI<br />directory, the whole Kepler just quit with the following message in the<br />console. It makes sense that the dll doesn't work for 64 bit machine. But just<br />quitting Kepler is too unfriendly.</p>
<pre><code>[null] Cannot find JRI native library!<br /> [null] Please make sure that the JRI native library is in a directory<br />liste<br />d in java.library.path.<br /> [null]<br /> [null] java.lang.UnsatisfiedLinkError: C:\Program<br />Files\Kepler-2.0-RC2\r-2.<br />0.0\lib\jri.dll: Can't load IA 32-bit .dll on a AMD 64-bit platform<br /> [null] at java.lang.ClassLoader$NativeLibrary.load(Native Method)<br /> [null] at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1753)<br /> [null] at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1678)<br /> [null] at java.lang.Runtime.loadLibrary0(Runtime.java:822)<br /> [null] at java.lang.System.loadLibrary(System.java:993)<br /> [null] at org.rosuda.JRI.Rengine.&lt;clinit&gt;(Rengine.java:19)<br /> [null] at<br />org.ecoinformatics.seek.R.RExpression2._initializeRengine(REx<br />pression2.java:569)<br /> [null] at<br />org.ecoinformatics.seek.R.RExpression2._fireUsingJRI(RExpress<br />ion2.java:547)<br /> [null] at<br />org.ecoinformatics.seek.R.RExpression2.fire(RExpression2.java<br />:289)<br /> [null] at ptolemy.actor.AtomicActor.iterate(AtomicActor.java:469)<br /> [null] at<br />ptolemy.actor.sched.StaticSchedulingDirector.fire(StaticSched<br />ulingDirector.java:188)<br /> [null] at ptolemy.actor.CompositeActor.fire(CompositeActor.java:458)<br /> [null] at ptolemy.actor.Manager.iterate(Manager.java:749)<br /> [null] at ptolemy.actor.Manager.execute(Manager.java:351)<br /> [null] at ptolemy.actor.Manager.run(Manager.java:1162)<br /> [null] at ptolemy.actor.Manager$3.run(Manager.java:1215)<br />Exception in thread "main" Java returned: 1<br /> at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:105)<br /> at org.kepler.build.runner.Kepler.main(Kepler.java:78)<br />Caused by: Java returned: 1<br /> at org.apache.tools.ant.taskdefs.Java.execute(Java.java:108)<br /> at org.kepler.build.Run.runSuite(Run.java:298)<br /> at org.kepler.build.Run.run(Run.java:202)<br /> at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:101)<br /> ... 1 more<br />--- Nested Exception ---<br />Java returned: 1<br /> at org.apache.tools.ant.taskdefs.Java.execute(Java.java:108)<br /> at org.kepler.build.Run.runSuite(Run.java:298)<br /> at org.kepler.build.Run.run(Run.java:202)<br /> at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:101)<br /> at org.kepler.build.runner.Kepler.main(Kepler.java:78)</code></pre>
<p>and Ben responded:<br />2. The RExpression2 (JRI-based) actor will fail if the libs are not found. This<br />is probably deep in the JRI.jar library when it cannot load the correct native<br />lib for the platform. We could probably try to detect the 32 v. 64 bitness of<br />the system and prevent the actor from attempting to use JRI if it was on a 64<br />bit machine - otherwise it will be the hard failure (system.exit)</p>
<p>and Jianwu:<br /> Matlab actors also have 32 and 64 bit issue when using JNI libraries to<br />communicate with Matlab. It will pop up an exception message when the JNI lib<br />doesn't work with the system. You can find some information at<br /><a class="external" href="https://kepler-project.org/developers/teams/build/matlab-lib-build-instructions-in-kepler-for-matlab-actor">https://kepler-project.org/developers/teams/build/matlab-lib-build-instructions-in-kepler-for-matlab-actor</a>.<br />It may help this bug.</p> Bug #4881 (New): RExpression outputs [false] for any matrix of booleanshttps://projects.ecoinformatics.org/ecoinfo/issues/48812010-03-12T18:53:40ZOliver Soongsoong@nceas.ucsb.edu
<p>In an RExpression, add an output port "out" and use this R script:</p>
<p>out <- matrix(c(TRUE, FALSE, TRUE, FALSE), 2)</p>
<p>I get [false] as the output token, which seems to be because RExpression.java on line 1108 says:</p>
<p>mt = new BooleanMatrixToken();</p>
<p>instead of:</p>
<p>mt = new BooleanMatrixToken(valS);</p>
<p>or something similar. I'm not actually sure such a constructor exists, but it seems like it should given the other constructors in the lines before.</p> Bug #4880 (New): RExpression cannot output matrix of stringshttps://projects.ecoinformatics.org/ecoinfo/issues/48802010-03-12T18:45:03ZOliver Soongsoong@nceas.ucsb.edu
<p>Create an RExpression with the output port "out" and for the script, use:</p>
<p>out <- matrix(letters, 2)</p>
<p>Looking at the code, it seems as if a matrix of strings was never really considered. Commas in the strings would likely cause problems, and I don't actually know if there's a StringMatrixToken.</p> Bug #4879 (New): RExpression replaces ) in string vectors with } when outputting to a porthttps://projects.ecoinformatics.org/ecoinfo/issues/48792010-03-12T18:37:49ZOliver Soongsoong@nceas.ucsb.edu
<p>In an RExpression, create the output port "out" and in the R script, use:</p>
<p>out <- c("(", ")")</p>
<p>Hooking this to a Display actor, I get {"(", "}"}. This is because RExpression.java line 1139 (I think) has:</p>
<p>temp = temp.replace(')', '}');</p>
<p>which replaces all occurrences of ), even within the string.</p> Bug #4873 (Resolved): Actors in repository library subtree are crammed togetherhttps://projects.ecoinformatics.org/ecoinfo/issues/48732010-03-09T23:53:44ZChad Berkleyberkley@nceas.ucsb.edu
<p>On Windows XP (maybe on other versions of windows) the actor icons are crammed tightly together when you open up Actors-2_0/CoreActors,kar or the other yellow repositories. They should be spaced similarly to the mac.</p> Bug #4629 (Resolved): Undo doesn't roll LSID revisionhttps://projects.ecoinformatics.org/ecoinfo/issues/46292009-12-14T21:48:26ZAaron Aaronaschultz@nceas.ucsb.edu
<p>When undoing changes in a workflow the LSID of the workflow does not get incremented.</p> Bug #4581 (Resolved): Handle multiple revisions of components in the Component Libraryhttps://projects.ecoinformatics.org/ecoinfo/issues/45812009-11-25T05:23:19ZAaron Aaronaschultz@nceas.ucsb.edu
<p>It is possible for many different revisions of an object to contain the same semantic types. The question is how to handle this in the Component Library.</p>
<p>Imagine you have two different KARS<br />one with a component, urn:lsid:someauth:namespace:24:10<br />and the other with a component, urn:lsid:someauth:namespace:24:11<br />both of which have equivalent semantic types.</p>
<p>These two components should show up properly in the Ontology tree in the Component Library but since they would be in the same place there is a collision. For this reason, LSID cannot be used as the identifier in the Component Library. The new Library Index has a unique Library Index ID (LIID) for each item that shows up in the Component Library tree. With this LIID we can associated multiple LSIDs with any given LIID (see LIBRARY_LSIDS table in the sql).</p>
<p>This problem is not limited to LSID revisions. But also objects that have the same name and the same semantic type.</p> Bug #4477 (Resolved): Grey out "undraggables"https://projects.ecoinformatics.org/ecoinfo/issues/44772009-10-16T19:17:34Zben leinfelderleinfelder@nceas.ucsb.edu
<p>In the Components tree we now have non-workflow items (items contained in KARs). These should be marked as different so that it's clear that we are mixing metaphors.</p> Bug #4475 (Resolved): Order context menu items consistentlyhttps://projects.ecoinformatics.org/ecoinfo/issues/44752009-10-16T19:15:36Zben leinfelderleinfelder@nceas.ucsb.edu
<p>There is a mix of options, sure, but options that appear across different context menus (ie "Open") should appear in similar locations on the list.</p> Bug #4380 (Resolved): Removing LocalRepository does not remove actors from Ontologieshttps://projects.ecoinformatics.org/ecoinfo/issues/43802009-09-11T04:28:03ZAaron Aaronaschultz@nceas.ucsb.edu
<p>scenario:<br />place a kar containing a component that has a semantic type in a folder<br />add that folder as a local repository<br />see that the component has shown up in the appropriate ontology<br />now remove that local repository<br />see that the folder is no longer in the library<br />but the component still shows up in the ontology</p> Bug #4174 (Resolved): Actor library not building correctlyhttps://projects.ecoinformatics.org/ecoinfo/issues/41742009-06-19T04:19:15ZAaron Aaronaschultz@nceas.ucsb.edu
<p>Many of the actors are not appearing in the actor library when using the WRP suite. No visible errors are given...</p> Bug #3898 (Resolved): update .kepler instead of removing it between versionshttps://projects.ecoinformatics.org/ecoinfo/issues/38982009-03-17T16:59:32ZChristopher Brookscxh@eecs.berkeley.edu
<p>Thanks to Qiao Huijie for pointing this out.<br />When switching between Kepler-1.0.0 and the Subversion development tree,<br />the ~/.kepler directory must be removed.<br />If it is not removed, then no actors are present in the actor browser pane.</p>
<p>I'm not sure why there is an incompatibility, but the code should detect<br />this incompatibility and prompt the user.</p>
<p>In addition, upon startup, the code should check to see if the actor browser<br />pane is empty and, if it is, prompt the user to delete their ~/.kepler <br />directory</p>
<p>Also, the developer instructions should be updated to mention removing<br />the ~/.kepler directory. I'll update the instructions.</p>