Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362008-05-07T22:26:35ZEcoinformatics Redmine
Redmine Bug #3283 (Resolved): Welcome splash screen shows up when starting windows keplerhttps://projects.ecoinformatics.org/ecoinfo/issues/32832008-05-07T22:26:35ZJing Taotao@nceas.ucsb.edu
<p>In mac and linux, the Welcome splash screen doesn't show up when user starts kepler. However, in windows version, I did see this screen during the startup when i double clicked either kepler.exe file or kepler-console.bat file.</p> Bug #3282 (Resolved): v3 installer intro says Kepler-1.0.0 1.0.0https://projects.ecoinformatics.org/ecoinfo/issues/32822008-05-07T21:30:55ZDaniel Crawldanielcrawl@gmail.com
<p>v3 installer intro says:</p>
<p>Welcome to the installation of Kepler-1.0.0 1.0.0!</p> Bug #3276 (Resolved): MatlabExpression not finding ptmatlab.dylibhttps://projects.ecoinformatics.org/ecoinfo/issues/32762008-05-05T22:15:30ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>MatlabExpression actor is not finding ptmatlab.dylib on the mac, after setting DYLD_LIBRARY_PATH=/Applications/MATLAB_R2007b/bin/maci and launching kepler with ./kepler.sh or sh kepler.sh from term or xterm.</p> Bug #3274 (Resolved): IPCC_Base_Layers.xml work-flow gets out of memeory errorhttps://projects.ecoinformatics.org/ecoinfo/issues/32742008-05-05T19:18:22ZJing Taotao@nceas.ucsb.edu
<p>When this work-flow tried to download 10 big data files, it can finish part of downloading - maybe 6 and the rest 4 will keep busy. From log message, we can find something like:<br />Exception in thread "Data ecogrid://knb/IPCC.200735416582829.1" java.lang.OutOfMemoryError: Java heap space<br />Exception in thread "Data ecogrid://knb/IPCC.200735416192871.1" java.lang.OutOfMemoryError: Java heap space<br />Exception in thread "Data ecogrid://knb/IPCC.200735417143125.1" java.lang.OutOfMemoryError: Java heap space<br />Exception in thread "Data ecogrid://knb/IPCC.200735416271261.1" java.lang.OutOfMemoryError: Java heap space</p>
<p>When I increase the heap size of Kepler to 1.2G (current value is 5M), the downloading can be done without any problem.</p>
<p>I went to through the downloading code again, it seems to me we use input and out stream, so not sure why it uses so many memory.</p>
<p>If it is possible we can remove this work-flow from this release?</p> Bug #3270 (Resolved): disable DIGIR Data Source by defaulthttps://projects.ecoinformatics.org/ecoinfo/issues/32702008-05-02T21:21:33ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>chatting on irc, chad jing and i think we should disable DIGIR in the Services List panel by default, since it's still severely slowing down search.</p> Bug #3267 (Resolved): ENM/GARP_SingleSpecies_BestRuleSet-IV.xml problemshttps://projects.ecoinformatics.org/ecoinfo/issues/32672008-05-02T18:14:46ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>ENM/GARP_SingleSpecies_BestRuleSet-IV.xml crashes Ubuntu Kepler.<br />On mac execution completes but gives ImageJ "Unrecognized comand: ASC TextReader" messages.</p> Bug #3264 (Resolved): workflow ENM/ASC2RAWTest gives an exception under ubuntuhttps://projects.ecoinformatics.org/ecoinfo/issues/32642008-05-01T22:33:36ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>This workflow needs to be removed or fixed for release</p>
<p>Running under Ubuntu gives an exception that starts with: "For input string: [very long string of squares with some other characters at the end]"</p>
<p>If you display stack trace, it's a java.lang.NumberFormatException. The problem is likely in AscToRaw.java</p> Bug #3261 (Resolved): ApplicationFramework/CredentialRetrieve workflow has problemshttps://projects.ecoinformatics.org/ecoinfo/issues/32612008-05-01T20:49:34ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>I think this needs to be fixed or removed for release.</p>
<p>To reproduce (on Ubuntu running Kepler from Chad's latest installer at least):<br />1)Open ApplicationFramework/CredentialRetrieve.xml. <br />2)Run. <br />3)Click cancel on the login dialog box.</p>
<p>Problems:<br />1) workflow continues to execute without stopping<br />2) If you try to open any other Kepler workflows, the Kepler Open dialog box appearance has changed; it now looks like the CredentialRetrieve password dialog box.</p> Bug #3257 (Resolved): Typos in html docs and demos.https://projects.ecoinformatics.org/ecoinfo/issues/32572008-04-30T21:07:35ZAaron Aaronaschultz@nceas.ucsb.edu
<p>A couple of typos in the documentation and demos.</p> Bug #3256 (Resolved): path problems on Mac with CommandLine demo workflowshttps://projects.ecoinformatics.org/ecoinfo/issues/32562008-04-30T17:52:49ZDan Higginshiggins@nceas.ucsb.edu
<p>On 1.0 release installer check, the CommandLine_1 and CommandLine_2 demo workflows (in demos/getting-started dir) fail with a path problem on the Mac.</p>
<p>This is apparently due to moving the demos directory.</p> 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 #3250 (Resolved): windows exe opens dos boxhttps://projects.ecoinformatics.org/ecoinfo/issues/32502008-04-30T00:15:31ZChad Berkleyberkley@nceas.ucsb.edu
<p>try to make the kepler.exe file not open a dos box with windows.</p> Bug #3198 (Resolved): test dynamic library installations on all platformshttps://projects.ecoinformatics.org/ecoinfo/issues/31982008-04-02T15:49:15ZChad Berkleyberkley@nceas.ucsb.edu
<p>Make sure that the dylibs work on windows, osx and linux and that they get put in the correct place by the installer.</p> Bug #2872 (Resolved): md5 checksumshttps://projects.ecoinformatics.org/ecoinfo/issues/28722007-06-11T23:16:45ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>We should add md5 checksums to our releases.</p> Bug #2318 (Resolved): Copyrights and licenses of subpackages need to be handledhttps://projects.ecoinformatics.org/ecoinfo/issues/23182005-12-14T02:41:42ZChristopher Brookscxh@eecs.berkeley.edu
<p>Just so we don't forget, I'm submitting the copyright issue as a bug.</p>
<p>As a proposed feature, I modified the Kepler configuration.xml and<br />added copyright.htm so that Kepler can take advantage of the Ptolemy<br />II about: facility that helps handle copyright issues.</p>
<p>The problem is that packages such as Ptolemy and Kepler include<br />copyrighted software from various sources. Each package has<br />a different copyright that usually must be displayed somewhere<br />in the release.</p>
<p>I hacked up the about:copyright facilty to help handle this. The<br />current implementation is not perfect, but it helps.</p>
<p>Here's how it works.</p>
<p>If a URL starts with "about:", then code in ptolemy.actor.gui<br />specially interprets it.</p>
<p>"about:copyright" creates a page that includes links to some base<br />copyrights, such as the Ptolemy copyright and the Aelfred copyright.<br />It also looks for particular actors and if those actors are found, it<br />includes a link to the appropriate copyright. One issue here is<br />that searching for the actors can take time, the user might notice a lag.</p>
<p>If the configuration includes a property called _applicationCopyrights<br />then that the value of that parameter is assumed to be an array of<br />records of the form
{{actor="dot.separated.actor.class.name", copyright="relative/url/to/copyright.\<br />htm"}...}</p>
<p>So, if the util.ImageJActor actor is present, then going to about:copyright<br />will include a link to the javadoc and also to imagej-copyright.htm<br />imagej-copyright.htm does not currently exist, but usually this file<br />would include the ImageJ jar file copyright.</p>
<p>One issue as that the link to the javadoc defaults to pointing to the<br />Ptolemy website if the documentation cannot be found. We could add<br />yet another parameter that would send this traffic to the Kepler website.<br />I'll do this later.</p>
<p>So, to try this out, update your Kepler tree, run "ant run-dev" <br />and then at the bottom of the intro.htm, follow the<br />"This software is protected by this license." link.</p>
<p>On the Kepler copyright page, follow the link at the bottom:<br />"Kepler is based on Ptolemy II" <br />This will bring you to the about:copyright page.</p>
<p>On other cool feature is at the bottom of the Kepler copyright page<br />is "Other information about this configuration"</p>
<p>This brings up a page that includes a link (about:configuration) to<br />expand the configuration, which is a good way to quickly test for<br />missing classes. For Kepler, this will not expand to include all the<br />actors the way it does under Ptolemy, but it still has value.</p>
<p>There are also links to expand all the .xml files listed in a file.<br />For example, "about:demos#ptolemy/configs/kepler/intro.htm" <br />will expand all the workflows listed on the Kepler splash page.<br />One can then run all the demos.</p>
<p>Also, "about:links#ptolemy/configs/kepler/intro.htm" will open<br />up all the .htm, .pdf and .xml links on the splash page, which<br />is a good way to check documentation.</p>
<p>In both cases, the expansion is only one level deep, but I use it<br />all the time to check releases.</p>
<p>I don't think this is a perfect solution but it can be used to<br />help address the copyright problem. Further refinement would help.<br />What would need to be done is that for each actor that uses a third<br />party jar file we would need to create a web page that includes<br />the copyright. This takes quite a bit of work, but helps ensure<br />that the copyright is actually shipped with the release.</p>
<p>If this utility is not of interest, then feel free to remove<br />the link at the bottom of copyright.htm.</p>