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 #3023 (Resolved): ImageJ does not display images for files with spaces in pathhttps://projects.ecoinformatics.org/ecoinfo/issues/30232007-12-06T17:44:23ZDan Higginshiggins@nceas.ucsb.edu
<p>Several of the workflows in demos/R/ no longer work correctly. The workflow execute but the ImageJ actor does not display an image with the output graph.</p>
<p>It appears that the problem is due to spaces in the path to the output file. (Change the R working directory to a path with no spaces and the images appear.) These workflows used to execute OK - it is suspected that a change in some PT code details may be the cause. (Note that this is not a problem in Beta3, just in the head of CVS.)</p> Bug #3020 (Resolved): Exporting an actor to a kar does not include internal jarshttps://projects.ecoinformatics.org/ecoinfo/issues/30202007-11-29T22:59:34ZDan Higginshiggins@nceas.ucsb.edu
<p>It is now possible to include jars with class files needed by an actor inside a kar file. One can add these kars to the kar/actors/ directory or load them from the File/Import Archive menu. Note that these kar files are currently created by 'hand' and are of use in inserting new actors without rebuilding all of Kepler.</p>
<p>However, if one tries to create a kar from an actor in the work area, the jar information is lost! That seems to be because the kar is built only from the moml of the display which does not know that a kar for the actor already exists! (I think the same problem occurs when Uploading to the Registry.)</p>
<p>The menu action to create a kar should check to see if a kar already exists and modify it as necessary. Or an additional dialog should appear that allow the user to add various resources to the created kar.</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>