Ecoinformatics Redmine: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362010-09-29T15:16:30ZEcoinformatics Redmine
Redmine 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 #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 #4887 (New): If a module is added to a configuration, the error message should inclu...https://projects.ecoinformatics.org/ecoinfo/issues/48872010-03-17T22:15:04ZChristopher Brookscxh@eecs.berkeley.edu
<p>Apparently, the dataturbine module was added to the kepler trunk.</p>
<p>After doing<br />ant update<br />ant run</p>
<p>I got:<br />run:<br /> [run] Error: The following modules are missing: <br /> [run] dataturbine</p>
<p>The fix is to do <br />ant change-to -Dsuite=kepler<br />ant run</p>
<p>It would be nice if the error message would tell the user to do an<br />ant change-to</p>
<p>Even better, it would be nice if the system would get the module.</p> Kepler - Bug #4056 (New): create developer documentation for svn configuration.https://projects.ecoinformatics.org/ecoinfo/issues/40562009-05-06T01:00:34ZChristopher Brookscxh@eecs.berkeley.edu
<p>When svn checks in files, it checks them in using a binary mode.<br />This is a problem when files are checked in using windows and checked<br />out under Linux or Mac OS X. Usually, things just work, but<br />not always. When they don't work, the failure is mysterious because<br />the file looks the same, but has the wrong end of line characters.</p>
<p>In addition, svn needs to be configured to properly set the svn keywords<br />such as Id and Version.</p>
<p>For details, see "Keyword Substition and end of line issues" <br /><a class="external" href="http://chess.eecs.berkeley.edu/ptexternal/wiki/Main/Subversion#toc22">http://chess.eecs.berkeley.edu/ptexternal/wiki/Main/Subversion#toc22</a><br />and</p>
<p><a class="external" href="http://chess.eecs.berkeley.edu/ptexternal/nightly/doc/coding/eclipse.htm#Subversive">http://chess.eecs.berkeley.edu/ptexternal/nightly/doc/coding/eclipse.htm#Subversive</a></p>
<p>One quick way to check is:</p>
<p>find . -name "*.java" | grep -v .svn > /tmp/kj<br />cat /tmp/kj | xargs ptolemy/adm/bin/svnpropcheck</p>
<p>another way is:<br />cat /tmp/kj | xargs ptolemy/util/testsuite/controlm</p>
<p>which yields:<br />./core/src/org/kepler/sms/NamedOntClass.java has controlms<br />./core/src/org/kepler/sms/NamedOntModel.java has controlms<br />./core/src/org/kepler/sms/NamedOntProperty.java has controlms<br />./core/src/org/kepler/sms/OntologyCatalog.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/ActuatorOutputDevice.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/SensorInputDevice.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/targets/luminary/GPOutputDeviceA.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/pret/actor/lib/gui/TimedPlotter.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Acceleration.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Const.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/CurrentTime.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Expression.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/logic/Comparator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/MultiplyDivide.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Scale.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Source.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/data/expr/ASTPtLeafNode.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/data/expr/ASTPtProductNode.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/domains/continuous/lib/DiscreteClock.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/domains/continuous/lib/Integrator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Lattice.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Position.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Speed.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Time.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Top.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Unitless.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Unknown.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/continuous/lib/EventSource.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/continuous/lib/Integrator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/modal/kernel/FSMActor.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/PropertyConstraintModalFSMHelper.java has controlms<br />./ptolemy/ptolemy/domains/gro/JavaDia.java has controlms<br />./ptolemy/ptolemy/domains/gro/JavaRenderer.java has controlms<br />./ptolemy/ptolemy/domains/gro/kernel/GRODirector.java has controlms<br />./ptolemy/ptolemy/domains/gro/kernel/GROScheduler.java has controlms<br />./ptolemy/ptolemy/domains/ptides/lib/targets/luminary/GPOutputDevice.java has controlms<br />./ptolemy/ptolemy/domains/ptides/lib/targets/luminary/GPOutputDeviceA.java has controlms<br />./util/src/org/camera/service/AverageGenomeSizeParserV2.java has controlms<br />./util/src/org/camera/service/CAMERARESTService.java has controlms<br />./util/src/org/camera/service/CAMERAURLProcessor.java has controlms<br />./util/src/org/camera/service/IdSizeMapForSeqFile.java has controlms<br />./util/src/org/camera/service/NameValuePair.java has controlms<br />./util/src/org/camera/service/ServiceUtils.java has controlms<br />./util/src/org/kepler/ssh/SftpExec.java has controlms<br />./util/src/org/sdm/spa/actors/transport/BbcpCopier.java has controlms<br />./util/src/org/sdm/spa/actors/transport/FileCopier.java has controlms<br />./util/src/org/sdm/spa/actors/transport/FileCopierFactory.java has controlms<br />./util/src/org/sdm/spa/actors/transport/GenericFileCopier.java has controlms<br />./util/src/org/sdm/spa/actors/transport/LocalFileCopier.java has controlms<br />./util/src/org/sdm/spa/actors/transport/ScpCopier.java has controlms<br />./util/src/org/sdm/spa/actors/transport/SftpCopier.java has controlms<br />./util/src/org/sdm/spa/actors/transport/SrmliteCopier.java has controlms<br />./util/src/org/sdm/spa/actors/transport/vo/ConnectionDetails.java has controlms<br />./util/tests/src/org/sdm/spa/actors/transport/GenericFileCopierTest.java has controlms<br />./util/tests/src/org/sdm/spa/actors/transport/RunGenericFileCopierTests.java has controlms</p>
<p>./core/src/org/kepler/sms/NamedOntClass.java has controlms<br />./core/src/org/kepler/sms/NamedOntModel.java has controlms<br />./core/src/org/kepler/sms/NamedOntProperty.java has controlms<br />./core/src/org/kepler/sms/OntologyCatalog.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/ActuatorOutputDevice.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/SensorInputDevice.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/targets/luminary/GPOutputDeviceA.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/pret/actor/lib/gui/TimedPlotter.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Acceleration.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Const.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/CurrentTime.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Expression.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/logic/Comparator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/MultiplyDivide.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Scale.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Source.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/data/expr/ASTPtLeafNode.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/data/expr/ASTPtProductNode.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/domains/continuous/lib/DiscreteClock.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/domains/continuous/lib/Integrator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Lattice.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Position.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Speed.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Time.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Top.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Unitless.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Unknown.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/continuous/lib/EventSource.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/continuous/lib/Integrator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/modal/kernel/FSMActor.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/PropertyConstraintModalFSMHelper.java has controlms<br />./ptolemy/ptolemy/domains/gro/JavaDia.java has controlms<br />./ptolemy/ptolemy/domains/gro/JavaRenderer.java has controlms<br />./ptolemy/ptolemy/domains/gro/kernel/GRODirector.java has controlms<br />./ptolemy/ptolemy/domains/gro/kernel/GROScheduler.java has controlms<br />./ptolemy/ptolemy/domains/ptides/lib/targets/luminary/GPOutputDevice.java has controlms<br />./ptolemy/ptolemy/domains/ptides/lib/targets/luminary/GPOutputDeviceA.java has controlms<br />./core/src/org/kepler/sms/NamedOntClass.java has controlms<br />./core/src/org/kepler/sms/NamedOntModel.java has controlms<br />./core/src/org/kepler/sms/NamedOntProperty.java has controlms<br />./core/src/org/kepler/sms/OntologyCatalog.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/ActuatorOutputDevice.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/SensorInputDevice.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/targets/luminary/GPOutputDeviceA.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/pret/actor/lib/gui/TimedPlotter.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Acceleration.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Const.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/CurrentTime.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Expression.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/logic/Comparator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/MultiplyDivide.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Scale.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Source.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/data/expr/ASTPtLeafNode.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/data/expr/ASTPtProductNode.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/domains/continuous/lib/DiscreteClock.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/domains/continuous/lib/Integrator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Lattice.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Position.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Speed.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Time.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Top.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Unitless.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Unknown.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/continuous/lib/EventSource.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/continuous/lib/Integrator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/modal/kernel/FSMActor.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/PropertyConstraintModalFSMHelper.java has controlms<br />./ptolemy/ptolemy/domains/gro/JavaDia.java has controlms<br />./ptolemy/ptolemy/domains/gro/JavaRenderer.java has controlms<br />./ptolemy/ptolemy/domains/gro/kernel/GRODirector.java has controlms<br />./ptolemy/ptolemy/domains/gro/kernel/GROScheduler.java has controlms<br />./ptolemy/ptolemy/domains/ptides/lib/targets/luminary/GPOutputDevice.java has controlms<br />./ptolemy/ptolemy/domains/ptides/lib/targets/luminary/GPOutputDeviceA.java has controlms<br />./core/src/org/kepler/sms/NamedOntClass.java has controlms<br />./core/src/org/kepler/sms/NamedOntModel.java has controlms<br />./core/src/org/kepler/sms/NamedOntProperty.java has controlms<br />./core/src/org/kepler/sms/OntologyCatalog.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/ActuatorOutputDevice.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/SensorInputDevice.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/luminary/domains/ptides/lib/targets/luminary/GPOutputDeviceA.java has controlms<br />./ptolemy/ptolemy/codegen/c/targets/pret/actor/lib/gui/TimedPlotter.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Acceleration.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Const.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/CurrentTime.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Expression.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/logic/Comparator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/MultiplyDivide.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Scale.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/actor/lib/Source.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/data/expr/ASTPtLeafNode.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/data/expr/ASTPtProductNode.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/domains/continuous/lib/DiscreteClock.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/domains/continuous/lib/Integrator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Lattice.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Position.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Speed.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Time.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Top.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Unitless.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/dimensionSystem/Unknown.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/continuous/lib/EventSource.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/continuous/lib/Integrator.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/logicalAND/domains/modal/kernel/FSMActor.java has controlms<br />./ptolemy/ptolemy/data/properties/lattice/PropertyConstraintModalFSMHelper.java has controlms<br />./ptolemy/ptolemy/domains/gro/JavaDia.java has controlms<br />./ptolemy/ptolemy/domains/gro/JavaRenderer.java has controlms<br />./ptolemy/ptolemy/domains/gro/kernel/GRODirector.java has controlms<br />./ptolemy/ptolemy/domains/gro/kernel/GROScheduler.java has controlms<br />./ptolemy/ptolemy/domains/ptides/lib/targets/luminary/GPOutputDevice.java has controlms<br />./ptolemy/ptolemy/domains/ptides/lib/targets/luminary/GPOutputDeviceA.java has controlms</p>
<p>I also checked the .xml files, and<br />common/etc/bundle_build.xml has control-ms<br />To fix these, run:</p>
<p>svn propset svn:eol-style native filename</p>
<p>To set the keywords on an alredy checked in file, run:</p>
<p>svn propset svn:keywords "Author Date Id Revision" filename</p>
<p>Then run:</p>
<p>svn commit</p>
<p>to commit the change.</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 #3898 (Resolved): update .kepler instead of removing it between versionshttps://projects.ecoinformatics.org/ecoinfo/issues/38982009-03-17T16:59:32ZChristopher Brookscxh@eecs.berkeley.edu
<p>Thanks to Qiao Huijie for pointing this out.<br />When switching between Kepler-1.0.0 and the Subversion development tree,<br />the ~/.kepler directory must be removed.<br />If it is not removed, then no actors are present in the actor browser pane.</p>
<p>I'm not sure why there is an incompatibility, but the code should detect<br />this incompatibility and prompt the user.</p>
<p>In addition, upon startup, the code should check to see if the actor browser<br />pane is empty and, if it is, prompt the user to delete their ~/.kepler <br />directory</p>
<p>Also, the developer instructions should be updated to mention removing<br />the ~/.kepler directory. I'll update the instructions.</p> Kepler - Bug #3225 (Resolved): If R is not present, then error message just says "null"https://projects.ecoinformatics.org/ecoinfo/issues/32252008-04-16T22:24:21ZChristopher Brookscxh@eecs.berkeley.edu
<p>If I build Kepler using RELEASE-BRANCH-1-0-0 and ptII using rel-7-0-beta-2<br />from source using:<br />ant full-clean rebuild<br />and then run the Statistical Summary demo that uses R, I get:</p>
<p>java.lang.NullPointerException<br /> at org.ecoinformatics.seek.R.RExpression.fire(RExpression.java:698)<br /> at ptolemy.actor.AtomicActor.iterate(AtomicActor.java:398)<br /> at ptolemy.actor.sched.StaticSchedulingDirector.fire(StaticSchedulingDirector.java:170)<br /> at ptolemy.actor.CompositeActor.fire(CompositeActor.java:400)<br /> at ptolemy.actor.Manager.iterate(Manager.java:688)<br /> at ptolemy.actor.Manager.execute(Manager.java:332)<br /> at ptolemy.actor.Manager.run(Manager.java:1071)<br /> at ptolemy.actor.Manager$3.run(Manager.java:1112)</p> Kepler - Bug #3204 (New): Kepler should have FSM exampleshttps://projects.ecoinformatics.org/ecoinfo/issues/32042008-04-02T21:15:37ZChristopher Brookscxh@eecs.berkeley.edu
<p>Finite State Machines are very powerful, there should<br />be a Kepler-specific scientific workflow that <br />illustrates FSMs.</p> Kepler - Bug #3110 (Resolved): Can't access actors via httphttps://projects.ecoinformatics.org/ecoinfo/issues/31102008-01-30T00:14:16ZChristopher Brookscxh@eecs.berkeley.edu
<p>ptolemy.kernel.util.IllegalActionException: Cannot find class: Waveform<br />Because:<br />-- ptolemy.eecs.berkeley.edu<br />-- XML file not found relative to classpath.<br />-- C:\cxh\src\kepler\http://ptolemy.eecs.berkeley.edu/xml/models/Waveform.xml<br />ptolemy.eecs.berkeley.edu<br /> in file:/C:/cxh/ptII/build/classes/ptolemy/moml/demo/Networked/Networked.xml at line 153 and column 118<br /> at ptolemy.moml.MoMLParser._createEntity(MoMLParser.java:3701)<br /> at ptolemy.moml.MoMLParser.startElement(MoMLParser.java:2379)<br /> at com.microstar.xml.XmlParser.parseElement(XmlParser.java:921)<br /> at com.microstar.xml.XmlParser.parseContent(XmlParser.java:1104)<br /> at com.microstar.xml.XmlParser.parseElement(XmlParser.java:924)<br /> at com.microstar.xml.XmlParser.parseDocument(XmlParser.java:481)<br /> at com.microstar.xml.XmlParser.doParse(XmlParser.java:159)<br /> at com.microstar.xml.XmlParser.parse(XmlParser.java:132)<br /> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1334)<br /> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1292)<br /> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1265)<br /> at ptolemy.actor.gui.PtolemyEffigy$Factory.createEffigy(PtolemyEffigy.java:412)<br /> at ptolemy.actor.gui.EffigyFactory.createEffigy(EffigyFactory.java:209)<br /> at ptolemy.actor.gui.Configuration.openModel(Configuration.java:595)<br /> at ptolemy.actor.gui.Configuration.openModel(Configuration.java:555)<br /> at ptolemy.actor.gui.HTMLViewer.hyperlinkUpdate(HTMLViewer.java:264)<br /> at javax.swing.JEditorPane.fireHyperlinkUpdate(JEditorPane.java:320)<br /> at javax.swing.text.html.HTMLEditorKit$LinkController.activateLink(HTMLEditorKit.java:827)<br /> at javax.swing.text.html.HTMLEditorKit$LinkController.mouseClicked(HTMLEditorKit.java:637)<br /> at java.awt.AWTEventMulticaster.mouseClicked(AWTEventMulticaster.java:212)<br /> at java.awt.Component.processMouseEvent(Component.java:5504)<br /> at javax.swing.JComponent.processMouseEvent(JComponent.java:3135)<br /> at java.awt.Component.processEvent(Component.java:5266)<br /> at java.awt.Container.processEvent(Container.java:1966)<br /> at java.awt.Component.dispatchEventImpl(Component.java:3968)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2024)<br /> at java.awt.Component.dispatchEvent(Component.java:3803)<br /> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4212)<br /> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3901)<br /> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3822)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2010)<br /> at java.awt.Window.dispatchEventImpl(Window.java:1778)<br /> at java.awt.Component.dispatchEvent(Component.java:3803)<br /> at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)<br /> at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:242)<br /> at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:163)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:157)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:149)<br /> at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)<br />Caused by: com.microstar.xml.XmlException: -- ptolemy.eecs.berkeley.edu<br />-- XML file not found relative to classpath.<br />-- C:\cxh\src\kepler\http://ptolemy.eecs.berkeley.edu/xml/models/Waveform.xml<br />ptolemy.eecs.berkeley.edu<br /> in file:/C:/cxh/ptII/build/classes/ptolemy/moml/demo/Networked/Networked.xml at line 153 and column 118<br /> at ptolemy.moml.MoMLParser.fileNameToURL(MoMLParser.java:1145)<br /> at ptolemy.moml.MoMLParser._findOrParse(MoMLParser.java:4417)<br /> at ptolemy.moml.MoMLParser._attemptToFindMoMLClass(MoMLParser.java:3498)<br /> at ptolemy.moml.MoMLParser._createEntity(MoMLParser.java:3696)<br /> ... 38 more<br />Caused by: com.microstar.xml.XmlException: -- ptolemy.eecs.berkeley.edu<br />-- XML file not found relative to classpath.<br />-- C:\cxh\src\kepler\http://ptolemy.eecs.berkeley.edu/xml/models/Waveform.xml<br />ptolemy.eecs.berkeley.edu<br /> in file:/C:/cxh/ptII/build/classes/ptolemy/moml/demo/Networked/Networked.xml at line 153 and column 118<br /> at ptolemy.moml.MoMLParser.fileNameToURL(MoMLParser.java:1145)<br /> at ptolemy.moml.MoMLParser._findOrParse(MoMLParser.java:4417)<br /> at ptolemy.moml.MoMLParser._attemptToFindMoMLClass(MoMLParser.java:3498)<br /> at ptolemy.moml.MoMLParser._createEntity(MoMLParser.java:3696)<br /> at ptolemy.moml.MoMLParser.startElement(MoMLParser.java:2379)<br /> at com.microstar.xml.XmlParser.parseElement(XmlParser.java:921)<br /> at com.microstar.xml.XmlParser.parseContent(XmlParser.java:1104)<br /> at com.microstar.xml.XmlParser.parseElement(XmlParser.java:924)<br /> at com.microstar.xml.XmlParser.parseDocument(XmlParser.java:481)<br /> at com.microstar.xml.XmlParser.doParse(XmlParser.java:159)<br /> at com.microstar.xml.XmlParser.parse(XmlParser.java:132)<br /> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1334)<br /> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1292)<br /> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1265)<br /> at ptolemy.actor.gui.PtolemyEffigy$Factory.createEffigy(PtolemyEffigy.java:412)<br /> at ptolemy.actor.gui.EffigyFactory.createEffigy(EffigyFactory.java:209)<br /> at ptolemy.actor.gui.Configuration.openModel(Configuration.java:595)<br /> at ptolemy.actor.gui.Configuration.openModel(Configuration.java:555)<br /> at ptolemy.actor.gui.HTMLViewer.hyperlinkUpdate(HTMLViewer.java:264)<br /> at javax.swing.JEditorPane.fireHyperlinkUpdate(JEditorPane.java:320)<br /> at javax.swing.text.html.HTMLEditorKit$LinkController.activateLink(HTMLEditorKit.java:827)<br /> at javax.swing.text.html.HTMLEditorKit$LinkController.mouseClicked(HTMLEditorKit.java:637)<br /> at java.awt.AWTEventMulticaster.mouseClicked(AWTEventMulticaster.java:212)<br /> at java.awt.Component.processMouseEvent(Component.java:5504)<br /> at javax.swing.JComponent.processMouseEvent(JComponent.java:3135)<br /> at java.awt.Component.processEvent(Component.java:5266)<br /> at java.awt.Container.processEvent(Container.java:1966)<br /> at java.awt.Component.dispatchEventImpl(Component.java:3968)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2024)<br /> at java.awt.Component.dispatchEvent(Component.java:3803)<br /> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4212)<br /> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3901)<br /> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3822)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2010)<br /> at java.awt.Window.dispatchEventImpl(Window.java:1778)<br /> at java.awt.Component.dispatchEvent(Component.java:3803)<br /> at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)<br /> at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:242)<br /> at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:163)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:157)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:149)<br /> at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)</p> Kepler - Bug #3107 (Resolved): http links don't work: Unsupported file type or connection not sup...https://projects.ecoinformatics.org/ecoinfo/issues/31072008-01-29T05:39:54ZChristopher Brookscxh@eecs.berkeley.edu
<p>Under Java 1.5.0 and Windows XP, if I try to click on a http: link<br />in an html window, I get:</p>
<pre><code>Unsupported file type or connection not supported: <br /> <a class="external" href="http://ptolemy.eecs.berkeley.edu#in_browser">http://ptolemy.eecs.berkeley.edu#in_browser</a></code></pre>
<p>The #in_brower is a hack in the Ptolemy HTML code that says to open<br />the link in the external browser (IE, Firefox etc.)</p>
<p>This error message comes from Configuration.java <br />I believe the problem is that<br /><property name="Web Browser" <br /> class="ptolemy.actor.gui.BrowserTableau$Factory"/><br />in ptolemy/configs/extendedEffigyFactory.xml is not handling the link.</p> Kepler - Bug #3105 (Resolved): Getting Started link on Welcome Page should lead to demoshttps://projects.ecoinformatics.org/ecoinfo/issues/31052008-01-29T00:19:50ZChristopher Brookscxh@eecs.berkeley.edu
<p>This might be old news, but I'll report it anyway.</p>
<p>When I start up Kepler, the "Welcome" window has a link "Getting Started",<br />which leads to kepler/configs/kepler/introScientists-beta1.htm</p>
<p>introScientists-beta1.htm should have a link to <br />kepler/src/configs/ptolemy/configs/kepler/introScientists.htm<br />or else perhaps the Welcome Window should link directly to introScientists.htm<br />It is important that the demos be easily visble to new users.</p> Kepler - Bug #3103 (Resolved): Building actor documentation from within Kepler failshttps://projects.ecoinformatics.org/ecoinfo/issues/31032008-01-25T00:49:48ZChristopher Brookscxh@eecs.berkeley.edu
<p>If the actor documentation does not exist, then when I select<br />Documentation -> Display, a window comes up that allows me to build<br />the documentation. The build continues along for awhile and then fails with.<br />BUILD FAILED<br />c:\cxh\src\kepler\build.xml:1232: The following error occurred while executing this line:<br />c:\cxh\src\kepler\build.xml:1280: The following error occurred while executing this line:<br />c:\cxh\src\kepler\build.xml:1289: Javadoc failed: java.io.IOException: CreateProcess: "c:\program files\java\jdk1.5.0_11\bin\javadoc.exe" -d c:\cxh\src\kepler-docs\dev\documentationFramework\generatedJavadocs -J-DKEPLER=c:\cxh\src\kepler -classpath c:\cxh\ptII -sourcepath c:\cxh\ptII -doclet doc.doclets.PtDoclet -docletpath c:\cxh\ptII\lib\kepler.jar;c:\cxh\src\kepler;c:\cxh\src\kepler\configs;c:\cxh\src\kepler\lib;c:\cxh\src\kepler\lib\images;c:\cxh\src\kepler\build\kepler-configs.jar;c:\cxh\src\kepler\build\kepler-icons.jar;c:\cxh\ptII\lib\diva.jar;c:\cxh\ptII\lib\jython.jar;c:\cxh\ptII\build\ptolemy-doc.jar;c:\cxh\ptII\build\classes;c:\cxh\ptII\build\src;c:\cxh\ptII\ptolemy\distributed\jini\jar\tools.jar;c:\cxh\ptII\ptolemy\distributed\jini\jar\jini-core.jar;c:\cxh\ptII\ptolemy\distributed\jini\jar\sun-util.jar;c:\cxh\ptII\ptolemy\distributed\jini\jar\reggie.jar;c:\cxh\ptII\ptolemy\distributed\jini\jar\jsk-policy.jar;c:\cxh\ptII\ptolemy\distributed\jini\jar\jsk-platform.jar;c:\cxh\ptII\ptolemy\distributed\jini\jar\start.jar;c:\cxh\ptII\ptolemy\distributed\jini\jar\reggie-dl.jâ€</p>