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 #5894 (Closed): Clone problems in NamedObjIdhttps://projects.ecoinformatics.org/ecoinfo/issues/58942013-03-19T19:07:23ZChristopher Brookscxh@eecs.berkeley.edu
<p>Checking the configuration results in messages about clone problems in NamedObjId:</p>
<p>The valueListeners java.util.Vector field<br /> in the clone of "org.kepler.moml.NamedObjId" <br /> does not point to an object distinct from the master. <br /> This may cause problems with actor oriented classes.<br /> The clone(Workspace) method should have a line like:<br /> newObject.valueListeners = (Vector)newObject<br /> /* Get the object method or null? <strong>/ valueListeners;<br />The _id org.kepler.objectmanager.lsid.KeplerLSID field<br /> in the clone of "org.kepler.moml.NamedObjId" <br /> does not point to an object distinct from the master. <br /> This may cause problems with actor oriented classes.<br /> The clone(Workspace) method should have a line like:<br /> newObject._id = (KeplerLSID)newObject<br /> /</strong> Get the object method or null? */ _id;</p>
<p>To replicate:<br />1) Start Kepler<br />2) Click on the Documentation link<br />3) Click on "Background information about Ptolemy" <br />4) Click on the Copyright link<br />5) Click on the Copyright link at the bottom (Other copyrights ...)<br />6) Click on "other" information about this configuration at the bottom<br />7) Click on "about:configuration"</p>
<p>The text above will appear.</p>
<p>The issue with cloning could be causing problems with actor oriented classes.</p>
<p>This class should have a clone(Workspace) method added.</p> Kepler - Bug #5893 (Closed): During installation, Kepler takes a long time to start up under Windowshttps://projects.ecoinformatics.org/ecoinfo/issues/58932013-03-19T14:51:33ZChristopher Brookscxh@eecs.berkeley.edu
<p>With Kepler-2.4RC3 under Windows2008R2 64-bit, the user is asked if they want to start up Kepler. I chose "yes" and nothing happened, so I completed the installation.</p>
<p>Then, I started up Kepler from the menu and it took a long time (over a minute?) to start up.</p>
<p>Then, it seemed like there were two Kepler instances?</p>
<p>It seems like Kepler took a long time to start, which is why when Kepler was starting during the installation, it seemed like nothing was happening.</p> Kepler - Bug #5892 (Resolved): After running various demos like HelloWorld, the user is prompted ...https://projects.ecoinformatics.org/ecoinfo/issues/58922013-03-19T14:47:26ZChristopher Brookscxh@eecs.berkeley.edu
<p>In the 2.4RC3 Windows installer, after I run various demos, when I close the demo, the "Save changes to KAR" dialog pops up.</p>
<p>Probably the Kar files need to be updated in the svn repository.</p>
<p>HelloWorld, SimpleAddition and others are affected.</p> Kepler - Bug #5659 (Closed): Kepler CaseGraphFrame and CaseGraphTableau have duplicated Ptolemy c...https://projects.ecoinformatics.org/ecoinfo/issues/56592012-08-06T23:45:27ZChristopher Brookscxh@eecs.berkeley.edu
<p>./gui/src/org/kepler/gui/frame/CaseGraphFrame.java<br />FIXME: Refactor!<br /> Duplicate of ptolemy/src/ptolemy/vergil/modal/CaseGraphFrame.java<br /> The Kepler version extends the Kepler-specific MultiCompositeGraphFrame which extends KeplerGraphFrame</p>
<ol>
<li><br />./gui/src/org/kepler/gui/frame/CaseGraphTableau.java<br />FIXME: Refactor!<br /> Probably like CaseGraphFrame above.</li>
</ol> Kepler - Bug #5650 (Resolved): actors LidarWorkflowExecute and load WorkflowExecute have duplicat...https://projects.ecoinformatics.org/ecoinfo/issues/56502012-08-06T23:27:32ZChristopher Brookscxh@eecs.berkeley.edu
<p>Duplicates detected with CPD. See</p>
<p><a class="external" href="http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4926#c1">http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4926#c1</a></p>
<p>actors/src/org/geon/LidarWorkflowExecute.java line 260<br />loader/src/org/geon/WorkflowExecute.java line 118
# lines : 387 duplicated</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 #5453 (Resolved): ant javadoc -Dfull=true failshttps://projects.ecoinformatics.org/ecoinfo/issues/54532011-08-05T15:08:21ZChristopher Brookscxh@eecs.berkeley.edu
<p>Running "ant" says</p>
<blockquote>
<p>javadoc Create javadoc for all the modules in modules.txt. Use -Dfull=true if you want to link your documentation to documentation of Kepler and Ptolemy too.</p>
</blockquote>
<p>However, ant javadoc <del>Dfull=true fails.<br />--start-</del></p>
<p>bash-3.2$ ant javadoc -Dfull=true<br />Buildfile: /Users/cxh/src/kepler/build-area/build.xml</p>
<p>javadoc:</p>
<p>BUILD FAILED<br />/Users/cxh/src/kepler/build-area/build.xml:204: src '/Users/cxh/src/kepler/null/lib/jar/kepler-r7920.jar' doesn't exist.</p>
<p>Total time: 0 seconds</p>
<p>--end--</p>
<p>ant javadoc -Dfull=true should be part of the nightly test suite.</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 #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 #4974 (Resolved): ant run and ant force-ptolemy fail to compile an updated filehttps://projects.ecoinformatics.org/ecoinfo/issues/49742010-05-04T01:01:36ZChristopher Brookscxh@eecs.berkeley.edu
<p>In the devel tree, if I update a Ptolemy java file, then "ant run" <br />and "ant force-ptolemy" fail to compile the file.</p>
<p>I have to use "ant compile"</p>
<p>I think I reported this earlier, but I could not find a bug for it.</p>
<p>bash-3.2$ touch ../ptolemy/src/ptolemy/actor/parameters/ParameterPort.java <br />bash-3.2$ ant run<br />Buildfile: build.xml</p>
<p>compile:<br /> [compile] Compiling configuration-manager...<br /> [compile] Compiling module-manager...<br /> [compile] Compiling core...<br /> [compile] Compiling event-state...<br /> [compile] Compiling util...<br /> [compile] Compiling component-library...<br /> [compile] Compiling sms...<br /> [compile] Compiling data-handling...<br /> [compile] Compiling ssh...<br /> [compile] Compiling io...<br /> [compile] Compiling job...<br /> [compile] Compiling repository...<br /> [compile] Compiling authentication...<br /> [compile] Compiling gui...<br /> [compile] Compiling module-manager-gui...<br /> [compile] Compiling authentication-gui...<br /> [compile] Compiling ecogrid...<br /> [compile] Compiling dataturbine...<br /> [compile] Compiling opendap...<br /> [compile] Compiling actors...<br /> [compile] Compiling loader...<br /> [compile] Compiling r...<br /> [compile] Compiling apple-extensions...</p>
<p>run:<br /> [run] setting dock icon to -Xdock:icon=/Users/cxh/src/kepler/common/resources/icons/kepler-dock-icon.png<br /> [run] Set environment variable: PATH = /System/Library/Frameworks/JavaVM.framework/Versions/1.6/Commands:/Users/cxh/bin:/Users/cxh/ptII/bin:/usr/local/apache-maven/bin:/opt/subversion/bin:/System/Library/Frameworks/JavaVM.framework/Versions/1.5/Commands:/opt/local/bin:/opt/local/sbin:/Users/cxh/bin:/Users/cxh/ptII/bin:/usr/local/apache-maven/bin:/opt/subversion/bin:/System/Library/Frameworks/JavaVM.framework/Versions/1.5/Commands:/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:/Users/cxh/bin:/Users/cxh/ptII/bin:/usr/local/apache-maven/bin:/opt/subversion/bin:/System/Library/Frameworks/JavaVM.framework/Versions/1.5/Commands:/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/src/kepler/kepler/lib:/Users/cxh/src/kepler/outreach/lib:/Users/cxh/src/kepler/apple-extensions/lib:/Users/cxh/src/kepler/r/lib:/Users/cxh/src/kepler/loader/lib:/Users/cxh/src/kepler/actors/lib:/Users/cxh/src/kepler/directors/lib:/Users/cxh/src/kepler/opendap/lib:/Users/cxh/src/kepler/dataturbine/lib:/Users/cxh/src/kepler/ecogrid/lib:/Users/cxh/src/kepler/authentication-gui/lib:/Users/cxh/src/kepler/module-manager-gui/lib:/Users/cxh/src/kepler/gui/lib:/Users/cxh/src/kepler/authentication/lib:/Users/cxh/src/kepler/repository/lib:/Users/cxh/src/kepler/job/lib:/Users/cxh/src/kepler/io/lib:/Users/cxh/src/kepler/ssh/lib:/Users/cxh/src/kepler/data-handling/lib:/Users/cxh/src/kepler/sms/lib:/Users/cxh/src/kepler/component-library/lib:/Users/cxh/src/kepler/util/lib:/Users/cxh/src/kepler/event-state/lib:/Users/cxh/src/kepler/core/lib:/Users/cxh/src/kepler/common/lib:/Users/cxh/src/kepler/module-manager/lib:/Users/cxh/src/kepler/configuration-manager/lib:/Users/cxh/src/kepler/kepler-tasks/lib:/Users/cxh/src/kepler/ptolemy/lib<br /> [run] Set environment variable: R_HOME = /Library/Frameworks/R.framework/Resources<br /> [run] /Users/cxh/src/kepler<br /> [run] Found OS Extension file: /Users/cxh/src/kepler/apple-extensions/module-info/osextension.txt<br /> [run] loading OS extensions for OS Mac OS X with class org.kepler.osx.KeplerOSXExtension<br /> [run] Building Kars...<br /> C-c C-c</p>
<p>BUILD FAILED<br />/Users/cxh/src/kepler/build-area/build.xml:35: Java returned: 130</p>
<p>Total time: 10 seconds<br />bash-3.2$ ant force-ptolemy<br />Buildfile: build.xml</p>
<p>force-ptolemy:</p>
<p>BUILD SUCCESSFUL<br />Total time: 0 seconds<br />bash-3.2$ ant compile<br />Buildfile: build.xml</p>
<p>compile:<br /> [compile] Compiling ptolemy...<br /> [compile] Compiling 1 source file to /Users/cxh/src/kepler/ptolemy/target/classes<br /> [compile] Compiling configuration-manager...<br /> [compile] Compiling module-manager...<br /> [compile] Compiling core...<br /> [compile] Compiling event-state...<br /> [compile] Compiling util...<br /> [compile] Compiling component-library...<br /> [compile] Compiling sms...<br /> [compile] Compiling data-handling...<br /> [compile] Compiling ssh...<br /> [compile] Compiling io...<br /> [compile] Compiling job...<br /> [compile] Compiling repository...<br /> [compile] Compiling authentication...<br /> [compile] Compiling gui...<br /> [compile] Compiling module-manager-gui...<br /> [compile] Compiling authentication-gui...<br /> [compile] Compiling ecogrid...<br /> [compile] Compiling dataturbine...<br /> [compile] Compiling opendap...<br /> [compile] Compiling actors...<br /> [compile] Compiling loader...<br /> [compile] Compiling r...<br /> [compile] Compiling apple-extensions...</p>
<p>BUILD SUCCESSFUL<br />Total time: 11 seconds<br />bash-3.2$</p> Kepler - Bug #4913 (Resolved): ant change-to -Dsuite=kepler-2.0 checks out ptolemy from the head ...https://projects.ecoinformatics.org/ecoinfo/issues/49132010-03-30T02:38:26ZChristopher Brookscxh@eecs.berkeley.edu
<p>How do I check out the 2.0 branch?</p>
<p>svn co <a class="external" href="https://code.kepler-project.org/code/kepler/branches/releases/release-branches/build-area-2.0">https://code.kepler-project.org/code/kepler/branches/releases/release-branches/build-area-2.0</a> build-area<br />cd build-area<br />ant change-to -Dsuite=kepler-2.0</p>
<p>Checks out the ptII head, not the rel-8-0-beta-2 branch</p>
<p>svn co svn+ssh://source.eecs.berkeley.edu/chess/ptII/branches/rel-8-0-beta-2 ptolemy-8.0</p>
<p>This is critical because it means that anyone who is working on the <br />Kepler 2.0 branch is working from the Ptolemy head, not the 8.0 release.<br />The primary issue is that the Ptolemy head is larger than the 8.0 release.<br />Over time, a second issue will be that the Ptolemy head will evolve.</p>
<p>The way to check is to look at CURRENT_VERSION in VersionAttribute.jar:<br />bash-3.2$ grep CURRENT_VERSION kepler-2.0/ptolemy-8.0/src/ptolemy/kernel/attributes/VersionAttribute.java<br /> Iterator versionTuples = CURRENT_VERSION.iterator();
* if (VersionAttribute.CURRENT_VERSION.isLessThan(assumedVersion)) {
* if (VersionAttribute.CURRENT_VERSION.compareTo(<br /> public static final VersionAttribute CURRENT_VERSION;<br /> CURRENT_VERSION = new VersionAttribute("8.1.devel");<br /> "Failed to create CURRENT_VERSION: "</p>
<p>The above is the current ptII svn head.<br />Another way is to look at intro.htm:</p>
<p>bash-3.2$ grep Version kepler-2.0/ptolemy-8.0/src/ptolemy/configs/full/intro.htm <br />Ptolemy II Version 8.1.devel</p>
<p>If we had a build system test suite (bug <a class="issue tracker-1 status-1 priority-5 priority-highest" title="Bug: Add a test suite for the build system (New)" href="https://projects.ecoinformatics.org/ecoinfo/issues/4260">#4260</a>), then we could test for<br />this sort of problem.</p> Kepler - Bug #3254 (Resolved): Annotations for some Ptolemy demos are not wrappedhttps://projects.ecoinformatics.org/ecoinfo/issues/32542008-04-30T16:11:33ZChristopher Brookscxh@eecs.berkeley.edu
<p>The annotation for the SDF Expression demo is not wrapped,<br />it runs off the right side of the screen.</p>
<p>However, the annotation for the LMS Adaptive demo does properly wrap.</p>
<p>A quick look at the xml shows that the SDF Expression:</p>
<p><property name="annotation1" class="ptolemy.kernel.util.Attribute"><br /> <property name="_location" class="ptolemy.kernel.util.Location" value="140.0, 5.0"><br /> </property><br /> <property name="_iconDescription" class="ptolemy.kernel.util.SingletonConfigurableAttribute"><br /> <configure><br /> <svg><br /> <text x="20" style="font-size:14; font-family:sanserif; fill:blue" y="20">This model repeatedly evaluates an expression, a function of two ramp<br />signals, slow and fast. Try right clicking on the expr actor, select<br />"Configure" and change it to "cos(slow)*cos(fast)" and then run<br />the demo with View->Run Window->Go. Other interesting alternatives<br />include:<br /> "cos(fast*cos(slow))" <br /> "0.2*slow + cos(fast)"</text><br /> </svg><br /> </configure><br /> </property><br /> <property name="_hideName" class="ptolemy.kernel.util.SingletonAttribute"><br /> </property><br /> </property></p>
<p>The LMS Adaptive demo has:</p>
<p><property name="Annotation" class="ptolemy.vergil.kernel.attributes.TextAttribute"><br /> <property name="text" class="ptolemy.kernel.util.StringAttribute" value="This model illustrates an LMS (least mean square) adaptive filter that learns the response of a fixed FIR (finite impulse response) filter by observing the input and noisy output of the filter."><br /> </property><br /> <property name="_location" class="ptolemy.kernel.util.Location" value="[15.0, 265.0]"><br /> </property><br /> </property></p>
<p>Note that LMS Adaptive uses a TextAttribute and it uses<br /> instead of newlines (the above example text is probably wrapped).</p>
<p>The solution here is to filter the demos and change the older style<br />annotation to the newer style.</p>