Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362008-02-05T21:50:17ZEcoinformatics Redmine
Redmine Bug #3133 (Resolved): R is not added to the pathhttps://projects.ecoinformatics.org/ecoinfo/issues/31332008-02-05T21:50:17ZChad Berkleyberkley@nceas.ucsb.edu
<p>The errors cxh got with R seem to be coming from the fact that R is installed, but not put into the path on windows. I'm trying to figure out how to do that with IzPack right now.</p> Bug #2850 (Resolved): Better Error message for missing 'R'https://projects.ecoinformatics.org/ecoinfo/issues/28502007-05-22T21:02:22ZDan Higginshiggins@nceas.ucsb.edu
<p>If a workflow containing an RExpression actor is executed and R cannot be started from the command line (missing or not in PATH), a cryptic error message like 'The pipe has been ended appears'. Need to catch this error and provide a more meaningful error message (or check for R installation in some other way).</p> Bug #2809 (Resolved): Browser Display actor fails for Mac/Linuxhttps://projects.ecoinformatics.org/ecoinfo/issues/28092007-04-03T17:40:07ZDan Higginshiggins@nceas.ucsb.edu
<p>Browser Display actor does not detect MacOSX and always uses Netscape for Linux systems. Need to detect the default browser and use that.</p>
<p>see <a class="external" href="http://www.centerkey.com/java/browser/">http://www.centerkey.com/java/browser/</a> <br />for java code that detects default browser and works across multiple OSs</p> Bug #2779 (Resolved): ASC_To_Raw actor has bug in setting output directoryhttps://projects.ecoinformatics.org/ecoinfo/issues/27792007-02-21T22:17:18ZDan Higginshiggins@nceas.ucsb.edu
<p>Actor works OK if the outputRawFileName parameter is left blank (raw files are created in the same directory as the asc files). However, if set to a directory, all but first of the *.raw files are still added to the dir *.asc files are in!</p> Bug #2461 (Resolved): Add MetadataSource actor to treehttps://projects.ecoinformatics.org/ecoinfo/issues/24612006-06-15T21:49:54ZDan Higginshiggins@nceas.ucsb.edu
<p>The MetadataSource actor has been around since June 2005 but apparently was never added to the actor tree when kar system was created. It is used in the 'EcogridWriterTest.xml' workflow in $KEPLER/workflows/test/ to provide metadata to the EcogridWriter. It needs to be added to the actor tree and perhaps extended to allow metadata input on ports (in additon to the parameter input) for use in saving GARP best rulesets.</p> Bug #2304 (Resolved): RExpression accepts only limited input size.https://projects.ecoinformatics.org/ecoinfo/issues/23042005-11-30T23:13:50ZLareo Lareodieter.zucht@freenet.de
<p>The R expression actor accepts only a very limited size of input. For example,<br />a vector x <- 1:20000 with 20000 elements cannot be in the input.<br />It was mentioned that it is planed to implement a TCP/IP binding to the R platform.<br />Maybe this binding does not have such limitation.</p>
<p>The bug is severe for the bioinformatics/microarray community. Here, dataframes<br />and tables of very large dimensions are handled.</p> Bug #2243 (Resolved): bug in inverse distance interpolation in Grid Rescaling actorhttps://projects.ecoinformatics.org/ecoinfo/issues/22432005-11-04T17:22:58ZDan Higginshiggins@nceas.ucsb.edu
<p>An attempt to smooth the IDW interpolation near NO_DATA edges of a grid has<br />resulted in errors in interpolation (that are clearly visible as a 'waffle' type<br />background in images).</p>
<p>Reason for this bug is currenly unclear. Needs to be fixed for use in ENM workflow.</p> Bug #2224 (Resolved): Annotation actor not working correctly from KAR filehttps://projects.ecoinformatics.org/ecoinfo/issues/22242005-10-10T22:03:18ZDan Higginshiggins@nceas.ucsb.edu
<p>With the new .kar files for building the actor tree, the Annotation actor gives<br />a simple rectangle with dragged to the graph area rather than an editable text<br />box. Apparently, something is wrong with the configuration.</p> Bug #2044 (Resolved): R actor for means and error by grouphttps://projects.ecoinformatics.org/ecoinfo/issues/20442005-03-11T23:37:40ZMatt Jonesjones@nceas.ucsb.edu
<p>This bug is to create an actor that wraps an R script (using the generic R actor<br />described in bug <a class="issue tracker-1 status-3 priority-5 priority-highest closed" title="Bug: need R actor (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/1342">#1342</a>) for calculating the mean, standard deviation, and<br />standard error of a numeric variable that is passed into the script. Optionally<br />the stats should be calculated using a grouping variable (by group), with one<br />mean/std/se for each group.</p>
<p>There are two inputs:<br /> 1) dataValue (type double)<br /> 2) group (type string)</p>
<p>The actor will accululate all data passed in as a series of {dataValue, group}<br />tuples and pass this along to R to calculate the mean, stdev, and stderr by<br />group. If group is not present then the tuples will be {dataValue}. When the R<br />script is finished, a matrix of {group, mean, stdev, stderr} will be passed back<br />to the R actor and then emitted on the output port. So for N tokens that come<br />in on the input port the actor will output on 1 token on the output port after<br />all input data has been received (this is a grouping operation).</p> Bug #1579 (Resolved): need sub-sampling actorhttps://projects.ecoinformatics.org/ecoinfo/issues/15792004-05-25T16:36:07ZMatt Jonesjones@nceas.ucsb.edu
<p>We need an actor that can perform various sub-sampling functions such as<br />jackknife and bootstrapping operations. Most ecologists use R and similar<br />systems for this type of work. We specifically need to do some<br />spatially-explicit sub-sampling for the GARP pipeline. In addition, we could<br />probably create a sub-sampling actor as a composite actor that uses the ptolemy<br />signal processing actors.</p> Bug #1557 (Resolved): problems with paths with 'spaces'https://projects.ecoinformatics.org/ecoinfo/issues/15572004-05-06T19:43:29ZDan Higginshiggins@nceas.ucsb.edu
<p>There are sometimes problems when the kepler directory is in a path that has<br />'spaces' like "Program Files". Should figure out the cause and fix</p> Bug #1342 (Resolved): need R actorhttps://projects.ecoinformatics.org/ecoinfo/issues/13422004-02-10T16:56:48ZChad Berkleyberkley@nceas.ucsb.edu
<p>create an actor to execute R jobs via kepler. Later, establish a GridService<br />that can handle this for us.</p> Bug #1338 (Resolved): find GIS system for inclusion in keplerhttps://projects.ecoinformatics.org/ecoinfo/issues/13382004-02-09T19:14:52ZChad Berkleyberkley@nceas.ucsb.edu
<p>need to look at the various proposed solutions for GIS integration into Kepler.<br /> The possibilities that I've heard so far are GDAL and GRASS. It has also been<br />mentioned that the more basic GIS functionality could probably be implemented in<br />java or with a ptolemy pipeline using existing actors.</p> Bug #1334 (Resolved): need installer for keplerhttps://projects.ecoinformatics.org/ecoinfo/issues/13342004-02-09T16:53:43ZChad Berkleyberkley@nceas.ucsb.edu
<p>We need a user friendly installer for Kepler. We could possibly use<br />installanywhere or a similar commercial product to produce the installer. it<br />would be nice if the creation of the installer is automated into the ant build<br />process so that it's easy to create releases. This needs to be done by the SEEK<br />meeting in EDI May 8.</p> Bug #1332 (Resolved): GARP improvements and further implemenationhttps://projects.ecoinformatics.org/ecoinfo/issues/13322004-02-09T16:30:40ZChad Berkleyberkley@nceas.ucsb.edu
<p>The GARP pipeline needs to be extended to include the entire workflow from start<br />to finish. This has been prototyped but not implemented. also need to modify<br />the garp actors so that the inputs and outputs are more intuitive and use<br />streams instead of filenames.</p>
<p>expose garp params<br />(look at desktop garp)<br />------------------<br />runs<br />convergence limit<br />max iterations</p>
<p>--develop xml schema for the internal garp data rep. (cellset and ruleset xml files)<br />--get dave's and ricardo's garp code integrated with the kepler garp code (use a<br />single repository)<br />--standardize IO file format</p>