Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362008-04-30T15:19:49ZEcoinformatics Redmine
Redmine Bug #3253 (Resolved): IzPack Windows Installer should install in a directory with the version numberhttps://projects.ecoinformatics.org/ecoinfo/issues/32532008-04-30T15:19:49ZChristopher Brookscxh@eecs.berkeley.edu
<p>The installer should install in a directory that contains the<br />version number of the release. <br />Under Windows, the default is c:\Program Files\Kepler,<br />it should be c:\Program Files\Kepler\1.0.0.</p>
<p>The reason is so that it is possible to have multiple versions<br />of Kepler without changing the default path. If the user<br />already has an installation of Kepler, then if they overwrite<br />the old version, will "good things" happen?</p>
<p>In a similar fashion, the installer should create separate<br />menus for each version.<br />What we have now is :<br />Start -> All Programs -> Kepler -> Kepler-1.0.0<br />Start -> All Programs -> Kepler -> Kepler Uninstaller<br />Instead, we should have:<br />Start -> All Programs -> Kepler -> Kepler-1.0.0 -> Kepler-1.0.0<br />Start -> All Programs -> Kepler -> Kepler-1.0.0 -> Kepler-1.0.0 Uninstaller</p>
<p>This is just my opinion, feel free to ignore.</p> Bug #3252 (Resolved): Ptolemy ack in installer splash screen has typos and was outdatedhttps://projects.ecoinformatics.org/ecoinfo/issues/32522008-04-30T15:13:44ZChristopher Brookscxh@eecs.berkeley.edu
<p>In the Kepler 1.0.0 IzPack installer splash screen, there is a<br />missing "S" and an extra </p> in the Ptolemy support statement:</p>
<p>Ptolemy receives support in part from the Center for Hybrid and Embedded<br />oftware Systems (CHESS) at UC Berkeley, which receives support from the<br />^ Missing S</p>
<p>Hewlett Packard, Infineon, Microsoft, and Toyota.</p><br /> ^</p>
<p>I updated kepler/README.txt in the devel and release branch with new text. To close this, a new installer would need to be made and<br />the text checked.</p> 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 #3083 (Resolved): Need sample CommandLine workflows for Windowshttps://projects.ecoinformatics.org/ecoinfo/issues/30832008-01-22T19:29:33ZDan Higginshiggins@nceas.ucsb.edu
<p>We need some simple examples of how to use the CommandLine actors especially for Windows systems. These should be in the Demos directory. They should be annotated so that typical non-programmer can understand how to use commandline applications to launch external applications within Kepler.</p>
<p>Dan Higgins - Jan 2008</p> Bug #3052 (Resolved): Installer crashes with EXC_BAD_ACCESShttps://projects.ecoinformatics.org/ecoinfo/issues/30522008-01-04T00:58:38ZDavid Brooksdave@bcs.co.nz
<p>Here's the start of the crash log:</p>
<p>Host Name: djbmac<br />Date/Time: 2008-01-04 13:20:10.617 +1300<br />OS Version: 10.4.11 (Build 8S2167)<br />Report Version: 4</p>
<p>Command: Kepler_beta3_install<br />Path: /Users/dave/Desktop/Kepler_beta3_install.app/Contents/MacOS/Kepler_beta3_install<br />Parent: WindowServer [57]<br />Rosetta: Yes</p>
<p>Version: ??? (5.0)</p>
<p>PID: 9484<br />Thread: Unknown</p>
<p>Exception: EXC_BAD_ACCESS (0x0001)<br />Codes: KERN_PROTECTION_FAILURE (0x0002) at 0x00000000</p>
<p>Thread 0:<br />0 Kepler_beta3_install 0xb80a564f 0xb8000000 + 677455<br />1 Kepler_beta3_install 0xb809fb15 0xb8000000 + 654101<br />2 Kepler_beta3_install 0xb80bd72e 0xb8000000 + 775982<br />3 Kepler_beta3_install 0xb811e403 spin_lock_wrapper + 1985</p>
<p>Thread 1:<br />0 Kepler_beta3_install 0xb822fa6b strchr + 72<br />1 Kepler_beta3_install 0xb81cb487 pthread_cond_wait + 3114<br />2 Kepler_beta3_install 0xb816765e catch_exception_raise_state_identity + 318<br />3 Kepler_beta3_install 0xb8166b9a CallPPCFunctionAtAddressInt + 177124<br />4 Kepler_beta3_install 0xb8166a91 CallPPCFunctionAtAddressInt + 176859<br />5 Kepler_beta3_install 0xb816775c catch_exception_raise_state_identity + 572<br />6 Kepler_beta3_install 0xb8200c00 pthread_create + 1124</p>
<p>Unknown thread crashed with i386 Thread State:<br />eax: 0x00000000 ebx: 0xb80a5628 ecx:0x00000000 edx: 0x00000003<br />edi: 0x00000000 esi: 0x80d03660 ebp:0xb7fff9f8 esp: 0xb7fff9c0<br /> ss: 0x0000001f efl: 0x00010206 eip:0xb80a564f cs: 0x00000017<br /> ds: 0x0000001f es: 0x0000001f fs:0x00000000 gs: 0x00000037</p> Bug #2978 (Resolved): saving to actor library from kepler no longer consistently works and port i...https://projects.ecoinformatics.org/ecoinfo/issues/29782007-10-08T23:40:11ZShawn Bowersbowers@gonzaga.edu
<p>It appears as though some new issues have cropped up w.r.t. the kepler actor library, in particular:</p>
<p>- when actors are added to the library from the canvas, they sometimes do not appear in the library, sometimes require a change in another actor to appear, and sometimes require kepler to be restarted to appear. I haven't nailed down exactly what sequence of events are causing this / needed to make an actor show up.</p>
<p>- input/output port properties are no longer saved when an actor is saved to a library (and dragged back to the canvas). This includes port data types as well as port semantic types. The same holds (i.e., port information is lost) when an actor is built via buildkarlib as well.</p>
<p>- the actor library interface appears to have changed, e.g., calling entityList() returns a null pointer (it seems ...)</p>
<p>The above behavior occurs on a fresh cvs checkout ...</p>
<p>Thanks,<br />-shawn</p> Bug #2319 (Resolved): Ptolemy build problemshttps://projects.ecoinformatics.org/ecoinfo/issues/23192005-12-15T23:18:02ZDan Higginshiggins@nceas.ucsb.edu
<p>Currently kepler uses 'ant ptolemy' to compile PtolemyII source code. Some<br />source code is just ignored (skipped) if it doesn't compile and isn't directly<br />used by Kepler. Often this problem is handled in PT by config/make dynamic<br />configuration of files.<br /> We should make the ant ptolemy build 'smarter' to handle some of the dynamic<br />build problems (e.g Java 3D samples).</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 #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>