Ecoinformatics Redmine: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362015-08-12T23:39:08ZEcoinformatics Redmine
Redmine Kepler - Bug #6829 (Closed): ant change-to fails under Windows Server 2012 R2 with Cygwinhttps://projects.ecoinformatics.org/ecoinfo/issues/68292015-08-12T23:39:08ZChristopher Brookscxh@eecs.berkeley.edu
<p>Under Windows Server 2012 R2 with Cygwin, I ran<br /><pre>
mkdir kepler.modules
cd kepler.modules
svn co https://code.kepler-project.org/code/kepler/trunk/modules/build-area
cd build-area
</pre></p>
<p>and then ant change-to failed:</p>
<pre>
$ ant change-to -Dsuite=kepler
Buildfile: C:\Users\cxh\src\kepler.modules\build-area\build.xml
change-to:
[change-to] Copying 1 file to C:\Users\cxh\src\kepler.modules\build-area
[change-to] Retrieving modules....
[change-to]
[change-to] kepler:
[change-to] Downloading (if necessary) kepler...
[change-to] svn co -r head https://code.kepler-project.org/code/kepler/trunk/modules/kepler C:\Users\cxh\src\kep\
ler.modules\kepler
[change-to] svn: E000002: Can't make directory '/cygdrive/c/Users/cxh/src/kepler.modules/build-area/C:\Users\cxh\
\src\kepler.modules\kepler': No such file or directory
[change-to]
BUILD FAILED
C:\Users\cxh\src\kepler.modules\build-area\build.xml:104: ERROR: It appears that the command did not execute pro\
perly and exited with an exit code of: 1
Total time: 1 second
cxh@AMPERE ~/src/kepler.modules/build-area
$
</pre>
<p>I can give out accounts on ampere.eecs.berkele.edu if necessary.</p> Kepler - Bug #6167 (New): Model Context Menu should have the enableBackwardTypeInference choicehttps://projects.ecoinformatics.org/ecoinfo/issues/61672013-10-23T01:07:20ZChristopher Brookscxh@eecs.berkeley.edu
<p>Ptolemy II now supports backward type inference. The way this is enabled is that the top level container has a parameter called "enableBackwardTypeInference" that is set to true or false.</p>
<p>In Ptolemy II's Vergil, this is visible by right clicking on the background of the top level model.</p>
<p>This functionality is not present in the devel tree of Kepler.</p>
<p>The workaround is to drag in a Parameter, name it "enableBackgroundTypeInference" and set the value to true.</p> Kepler - Bug #6165 (Resolved): The names of instances of the Stop actor do not display in Mac OSX.https://projects.ecoinformatics.org/ecoinfo/issues/61652013-10-22T00:48:43ZChristopher Brookscxh@eecs.berkeley.edu
<p>On Kepler-users, Kenneth Jones wrote:</p>
<blockquote>
<p>The names of instances of the Stop actor do not display in Mac OSX. Let me know if you need more info.</p>
</blockquote>
<p>Indeed, dragging in the Stop Actor results in icons without instance names</p> Kepler - Bug #5633 (Resolved): Actor/Attribute Search/Find Facility needs menu choiceshttps://projects.ecoinformatics.org/ecoinfo/issues/56332012-06-22T21:40:21ZChristopher Brookscxh@eecs.berkeley.edu
<p>Edward developed a search facility for models.<br />Under Mac OS X in the Kepler trunk, if the mouse is over the graph canvas,<br />then typing Command-F brings up a search dialog.</p>
<p>This dialog should be added to the Kepler menus.</p> Kepler - Bug #5192 (New): Module Manager reacts badly to dot files in resources/configuration dir...https://projects.ecoinformatics.org/ecoinfo/issues/51922010-09-29T15:16:30ZChristopher Brookscxh@eecs.berkeley.edu
<p>I was trying to follow the 2.1 instructions at<br /><a class="external" href="https://kepler-project.org/developers/teams/build/kepler-2.1-release-roadmap/?searchterm=roadmap">https://kepler-project.org/developers/teams/build/kepler-2.1-release-roadmap/?searchterm=roadmap</a></p>
<p>and edited <br />kepler-2.1/module-manager-2.1/resources/configurations/configuration.xml<br />with Emacs, which created<br />kepler-2.1/module-manager-2.1/resources/configurations/.#configuration.xml</p>
<p>Then ant clean-all run<br />failed:</p>
<p>run:<br /> [run] setting dock icon to -Xdock:icon=/Users/cxh/src/kepler-2.1/common-2.1/resources/icons/kepler-dock-icon.png<br /> [run] Set environment variable: PATH = /Users/cxh/bin:/Users/cxh/ptII/bin:/usr/local/apache-maven/bin:/Users/cxh/bin:/Users/cxh/ptII/bin:/usr/local/apache-maven/bin:/Users/cxh/ptII/vendors/misc/dbxml-2.5.16/install/bin:/Users/cxh/bin:/Users/cxh/ptII/bin:/usr/local/apache-maven/bin:/opt/subversion/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin:/usr/X11/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/texbin:/usr/local/texlive/2007/bin:/usr/local/git/bin:/Users/cxh/ptII/vendors/misc/dbxml-2.5.16/install/bin:/Users/cxh/ptII/vendors/misc/dbxml-2.5.16/install/bin:/Users/cxh/bin:/Users/cxh/ptII/bin:/usr/local/apache-maven/bin:/opt/subversion/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin:/usr/X11/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/texbin:/usr/local/texlive/2007/bin:/usr/texbin:/usr/local/texlive/2007/bin:/Users/cxh/ptII/vendors/misc/dbxml-2.5.16/install/bin:/Users/cxh/src/kepler-2.1/r-2.1/lib:/Users/cxh/src/kepler-2.1/common-2.1/lib/ptolemy/matlab:/Users/cxh/src/kepler-2.1/common-2.1/lib<br /> [run] Set environment variable: R_HOME = /Library/Frameworks/R.framework/Resources<br /> [run] /Users/cxh/src/kepler-2.1<br /> [run] java.io.FileNotFoundException: /Users/cxh/src/kepler-2.1/module-manager-2.1/resources/configurations/.#configuration.xml (No such file or directory)<br /> [run] at java.io.FileInputStream.open(Native Method)<br /> [run] at java.io.FileInputStream.<init>(FileInputStream.java:106)<br /> [run] at org.kepler.configuration.CommonsConfigurationReader.loadConfiguration(CommonsConfigurationReader.java:144)<br /> [run] at org.kepler.configuration.CommonsConfigurationReader.loadConfigurations(CommonsConfigurationReader.java:92)<br /> [run] at org.kepler.configuration.CommonsConfigurationReader.loadConfigurations(CommonsConfigurationReader.java:64)<br /> [run] at org.kepler.configuration.ConfigurationManager.loadConfiguration(ConfigurationManager.java:420)<br /> [run] at org.kepler.configuration.ConfigurationManager.<init>(ConfigurationManager.java:87)<br /> [run] at org.kepler.configuration.ConfigurationManager.getInstance(ConfigurationManager.java:116)<br /> [run] at org.kepler.configuration.ConfigurationManager.getInstance(ConfigurationManager.java:105)<br /> [run] at org.kepler.modulemanager.RepositoryLocations.initReleaseLocation(RepositoryLocations.java:24)<br /> [run] at org.kepler.modulemanager.RepositoryLocations.getReleaseLocation(RepositoryLocations.java:18)<br /> [run] at org.kepler.Kepler.main(Kepler.java:89)<br /> [run] org.kepler.configuration.ConfigurationManagerException: Error loading configuration file: /Users/cxh/src/kepler-2.1/module-manager-2.1/resources/configurations/.#configuration.xml (No such file or directory)<br /> [run] at org.kepler.configuration.CommonsConfigurationReader.loadConfiguration(CommonsConfigurationReader.java:171)<br /> [run] at org.kepler.configuration.CommonsConfigurationReader.loadConfigurations(CommonsConfigurationReader.java:92)<br /> [run] at org.kepler.configuration.CommonsConfigurationReader.loadConfigurations(CommonsConfigurationReader.java:64)<br /> [run] at org.kepler.configuration.ConfigurationManager.loadConfiguration(ConfigurationManager.java:420)<br /> [run] at org.kepler.configuration.ConfigurationManager.<init>(ConfigurationManager.java:87)<br /> [run] at org.kepler.configuration.ConfigurationManager.getInstance(ConfigurationManager.java:116)<br /> [run] at org.kepler.configuration.ConfigurationManager.getInstance(ConfigurationManager.java:105)<br /> [run] at org.kepler.modulemanager.RepositoryLocations.initReleaseLocation(RepositoryLocations.java:24)<br /> [run] at org.kepler.modulemanager.RepositoryLocations.getReleaseLocation(RepositoryLocations.java:18)<br /> [run] at org.kepler.Kepler.main(Kepler.java:89)<br /> [run] org.kepler.configuration.ConfigurationManagerException: Error loading configuration: Error loading configuration file: /Users/cxh/src/kepler-2.1/module-manager-2.1/resources/configurations/.#configuration.xml (No such file or directory)<br /> [run] at org.kepler.configuration.CommonsConfigurationReader.loadConfigurations(CommonsConfigurationReader.java:105)<br /> [run] at org.kepler.configuration.CommonsConfigurationReader.loadConfigurations(CommonsConfigurationReader.java:64)<br /> [run] at org.kepler.configuration.ConfigurationManager.loadConfiguration(ConfigurationManager.java:420)<br /> [run] at org.kepler.configuration.ConfigurationManager.<init>(ConfigurationManager.java:87)<br /> [run] at org.kepler.configuration.ConfigurationManager.getInstance(ConfigurationManager.java:116)<br /> [run] at org.kepler.configuration.ConfigurationManager.getInstance(ConfigurationManager.java:105)<br /> [run] at org.kepler.modulemanager.RepositoryLocations.initReleaseLocation(RepositoryLocations.java:24)<br /> [run] at org.kepler.modulemanager.RepositoryLocations.getReleaseLocation(RepositoryLocations.java:18)<br /> [run] at org.kepler.Kepler.main(Kepler.java:89)<br /> [run] Exception in thread "main" java.lang.RuntimeException: Could not load configuration: Error loading configuration: Error loading configuration file: /Users/cxh/src/kepler-2.1/module-manager-2.1/resources/configurations/.#configuration.xml (No such file or directory)<br /> [run] at org.kepler.configuration.ConfigurationManager.<init>(ConfigurationManager.java:93)<br /> [run] at org.kepler.configuration.ConfigurationManager.getInstance(ConfigurationManager.java:116)<br /> [run] at org.kepler.configuration.ConfigurationManager.getInstance(ConfigurationManager.java:105)<br /> [run] at org.kepler.modulemanager.RepositoryLocations.initReleaseLocation(RepositoryLocations.java:24)<br /> [run] at org.kepler.modulemanager.RepositoryLocations.getReleaseLocation(RepositoryLocations.java:18)<br /> [run] at org.kepler.Kepler.main(Kepler.java:89)</p>
<p>BUILD FAILED<br />/Users/cxh/src/kepler-2.1/build-area/build.xml:36: Java returned: 1</p>
<p>Total time: 2 minutes 52 seconds<br />bash-3.2$ ls ~/src/kepler-2.1/module-manager-2.1/resources/configurations/<br />configuration.xml<br />bash-3.2$ ls -a ~/src/kepler-2.1/module-manager-2.1/resources/configurations/<br />. .. configuration.xml<br />.#configuration.xml .svn<br />bash-3.2$</p> Kepler - Bug #5155 (New): To exclude a file or directory requires updating at least four places, ...https://projects.ecoinformatics.org/ecoinfo/issues/51552010-08-18T22:53:13ZChristopher Brookscxh@eecs.berkeley.edu
<p>jianwu <<a class="email" href="mailto:jianwu@sdsc.edu">jianwu@sdsc.edu</a>> writes:</p>
<blockquote>
<p>If excluding those from building system, please make sure it's also updated for<br />eclipse building. To update it, just modify the PtolemyClasspathStart file at<br />build-area/resources/eclipse.</p>
<p>We probably also need to update corresponding files at<br />build-area/resources/netbeans and build-area/resources/idea.</p>
</blockquote>
<p>I'm mystified as to why a human has to update four locations with<br />the same data. Isn't this why we have computers?<br />I should update one master file, the Netbeans, Eclipse and Idea <br />files should be automatically updated.</p> Kepler - Bug #5081 (New): A system for adding and removing GUI menus.https://projects.ecoinformatics.org/ecoinfo/issues/50812010-07-07T17:25:27ZChristopher Brookscxh@eecs.berkeley.edu
<p>The existing system needs documentation.</p>
<p>Also, refactoring to use RCP would help here</p> Kepler - Bug #5027 (New): Users should be able to build installers for the Kepler-2.0 branchhttps://projects.ecoinformatics.org/ecoinfo/issues/50272010-05-24T17:32:46ZChristopher Brookscxh@eecs.berkeley.edu
<p>Kepler users should be able to build installers so that they may deploy<br />a shrinkwrapped installation to other users. Currently, "ant installer" <br />works in the Kepler devel trunk, but fails in the 2.0 branch.</p>
<p>[installer] Writing installer file to /Users/cxh/src/kepler-2.0/build-area/installer/install.xml<br /> [izpack] ERROR: 'The content of elements must consist of well-formed character data or markup.'<br /> [izpack] ERROR: 'com.sun.org.apache.xml.internal.utils.WrappedRuntimeException: The content of elements must consist of well-formed character data or markup.'<br /> [izpack] javax.xml.transform.TransformerException: javax.xml.transform.TransformerException: com.sun.org.apache.xml.internal.utils.WrappedRuntimeException: The content of elements must consist of well-formed character data or markup.<br /> [izpack] at com.sun.org.apache.xalan.internal.xsltc.trax.TransformerImpl.transform(TransformerImpl.java:673)<br /> [izpack] at com.sun.org.apache.xalan.internal.xsltc.trax.TransformerImpl.transform(TransformerImpl.java:300)<br /> [izpack] at com.izforge.izpack.adaptator.impl.XMLParser.parseLineNrFromInputSource(Unknown Source)</p>
<p>We are not currently exposing the "ant installer" command to users, so<br />this is an RFE, not a bug.</p>
<p>See bug 4994 at<br /><a class="external" href="http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4994">http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4994</a></p> Kepler - Bug #5022 (Resolved): 2.0-RC3 Windows installer creates Kepler 2.0-RC2 start menu choice...https://projects.ecoinformatics.org/ecoinfo/issues/50222010-05-20T19:52:20ZChristopher Brookscxh@eecs.berkeley.edu
<p>With the Kepler-2.0-RC3 Windows installer, the shortcut in Start->All Programs<br />->Kepler is Kepler 2.0-RC2, not Kepler-2.0-RC3.</p>
<p>Also, the icon for "Kepler 2.0-RC2" is missing, I get a default<br />icon, not the Kepler Icon.</p> Kepler - Bug #5020 (Resolved): 2.0-RC3 installer: R Kepler Module is not optionalhttps://projects.ecoinformatics.org/ecoinfo/issues/50202010-05-20T17:28:08ZChristopher Brookscxh@eecs.berkeley.edu
<p>When installing Kepler-2.0-RC3, I'm presented with<br />two choices:<br />Kepler<br />R Kepler Module</p>
<p>Both are required, I can't uncheck "R Kepler Module",<br />so why bother with this window?</p> Kepler - Bug #4996 (Resolved): 2.0-RC2 demos don't workhttps://projects.ecoinformatics.org/ecoinfo/issues/49962010-05-10T04:55:59ZChristopher Brookscxh@eecs.berkeley.eduKepler - Bug #4995 (In Progress): ant installer fails under Linuxhttps://projects.ecoinformatics.org/ecoinfo/issues/49952010-05-10T00:15:32ZChristopher Brookscxh@eecs.berkeley.edu
<p>In a clean Kepler 2.0 tree, "ant installer" fails under linux:</p>
<p>build-macapp:<br /> [echo] jarbunder<br /> [null] Deleting directory /home/cxh/src/kepler-2.0/Kepler.app<br />[jarbundler] Creating application bundle: /home/cxh/src/kepler-2.0/Kepler.app</p>
<p>BUILD FAILED<br />/home/cxh/src/kepler-2.0/build-area/build.xml:339: The following error occurred while executing this line:<br />/home/cxh/src/kepler-2.0/build-area/build.xml:370: The following error occurred while executing this line:<br />/home/cxh/src/kepler-2.0/build-area/build.xml:439: Cannot copy Java Application Stub: java.io.FileNotFoundException: /System/Library/Frameworks/JavaVM.framework/Versions/Current/Resources/MacOS/JavaApplicationStub (No such file or directory)</p>
<p>The problem is that the JavaApplicationStub file is not present under Linux.</p> Kepler - Bug #4994 (Resolved): ant installer fails with "Invalid directory 'dir' ... outreach-2.0...https://projects.ecoinformatics.org/ecoinfo/issues/49942010-05-08T03:14:26ZChristopher Brookscxh@eecs.berkeley.edu
<p>Working from the instructions at<br /><a class="external" href="https://kepler-project.org/developers/teams/build/building-kepler-installers">https://kepler-project.org/developers/teams/build/building-kepler-installers</a><br />and using Kepler-2.0 instead of the devel trunk, I have problems with<br />"ant install" </p>
<pre><code>mkdir kepler-2.0<br /> cd kepler-2.0<br /> svn co <a class="external" href="https://code.kepler-project.org/code/kepler/releases/release-branches/build-area-2.0/">https://code.kepler-project.org/code/kepler/releases/release-branches/build-area-2.0/</a> build-area<br /> cd build-area<br /> ant change-to -Dsuite=kepler-2.0<br /> ant clean-cache<br /> ant eclipse<br /> ant installer</code></pre>
<p>Fails with:<br />--start--<br />[installer] Appending packs from the outreach-2.0 module.<br />[installer] Appending packs from the r-2.0 module.<br />[installer] Appending packs from the ptolemy-8.0 module.<br />[installer] basedirPath: /Users/cxh/src/kepler-2.0<br />[installer] Filtering out non-used OS elements.<br />[installer] Writing installer file to /Users/cxh/src/kepler-2.0/build-area/installer/install.xml</p>
<p>BUILD FAILED<br />/Users/cxh/src/kepler-2.0/build-area/build.xml:337: The following error occurred while executing this line:<br />/Users/cxh/src/kepler-2.0/build-area/build.xml:361: com.izforge.izpack.compiler.CompilerException: installer/install.xml:252: Invalid directory 'dir': /Users/cxh/src/kepler-2.0/outreach-2.0.0/resources<br />--end--</p>
<p>build-area/installer/install.xml is generated by the build process and includes<br />a reference to outreach-2.0.0, which does not exist. outreach-2.0 does<br />exist.</p>
<p>See also<br /><a class="external" href="http://mercury.nceas.ucsb.edu/kepler/pipermail/kepler-users/2010-April/002154.html">http://mercury.nceas.ucsb.edu/kepler/pipermail/kepler-users/2010-April/002154.html</a></p>
<p>A test suite would help with this sort of problem.</p> Kepler - Bug #3903 (New): Use Java logging utilities instead of Apache commons logging facilityhttps://projects.ecoinformatics.org/ecoinfo/issues/39032009-03-18T19:21:30ZChristopher Brookscxh@eecs.berkeley.edu
<p>ersonally, I'd like to switch to the logging utilities that<br />now ship with Java, see<br /><a class="external" href="http://java.sun.com/j2se/1.4.2/docs/guide/util/logging/">http://java.sun.com/j2se/1.4.2/docs/guide/util/logging/</a><br />The advantage is that it would be one less jar file to ship.<br />A quick search finds 144 files that use the apache logging facility.<br />Most of these changes could be handled automatically by a script.</p>
<p>Notes about the logging system can be found at<br /><a class="external" href="https://kepler-project.org/developers/reference/using-commons-logging">https://kepler-project.org/developers/reference/using-commons-logging</a></p> Kepler - Bug #2349 (New): Actors should have preconditions to test for long runshttps://projects.ecoinformatics.org/ecoinfo/issues/23492006-02-07T18:19:21ZChristopher Brookscxh@eecs.berkeley.edu
<p>It would be nice if there was an easy way to for a model to test for<br />trivial problems before getting far down a long run.</p>
<p>One idea would be to have such actors implement an interface that included a<br />method that the director would run.</p>
<p>We should think about why having actors do more testing in preinitialize()<br />will not work here. For example, if we have an FSM model, do all<br />the actors get preinitialize() called right away? What about the Case actor.</p>