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From 04/17/2008 to 05/16/2008

05/16/2008

08:02 PM Bug #3300: CompositeActor does not support multiport
You need to explicitly set the width of the input link inside the composite.
See below.
I've opened a RFE in Ptolem...
Christopher Brooks
04:06 PM Bug #3300 (Resolved): CompositeActor does not support multiport
You can create a CompositeActor with input and output ports that are set as Multiports, but only the first value on t... ben leinfelder

05/13/2008

12:13 PM Bug #3292: ENM/GDAL_h1K_NS workflow giving an exception
Ah, I see comment #2 on bug 3291 now (general disclaimer in demos/Readme.txt for all workflows).
I will bump this to ...
Derik Barseghian
11:33 AM Bug #3292: ENM/GDAL_h1K_NS workflow giving an exception

SEEK/garpModel_ImageJ, also gives a similar "Can't load IA 32-bit..." problem on ubuntu 8.04.
ENM/GARP_Multispecies...
Derik Barseghian
12:10 PM Bug #3291: IPCC_ChangeNightlyBuildTest got an exception
I have this problem too, on mac 10.5.2 and ubuntu 8.04. Derik Barseghian
11:43 AM Bug #3295 (New): Python/Ptolemnizer welcome text does not display
A minor annoyance, but the SampleDelay actor's "Welcome to the..." text is not displaying in the InteractiveShell as ... Derik Barseghian

05/12/2008

06:04 PM Bug #3292 (New): ENM/GDAL_h1K_NS workflow giving an exception
I upgraded to ubuntu 8.04 today, and now the GDAL_h1K_NS workflow is giving an exception (i'm using java 1.5.0_13).
...
Derik Barseghian
12:33 PM Bug #3290: DarwinCore_test workflow takes forever to downloading data
I put a general disclaimer in the demos directory so that this will not delay the release. Chad Berkley
12:33 PM Bug #3291: IPCC_ChangeNightlyBuildTest got an exception
I put a general disclaimer in the demos directory so that this will not delay the release. Chad Berkley
12:31 PM Bug #2872: md5 checksums
done. Chad Berkley
12:31 PM Bug #3122: Get installer size down
Installer sizes are as follows:
-rw-r--r-- 1 berkley berkley 104866787 2008-05-12 11:04 kepler-linux-1.0.0.jar
-rw-...
Chad Berkley
09:41 AM Bug #3266: ENM/GARP_MultipleSpecies-V.xml problems
Matt and I have decided to go ahead an release these workflows with the
following annotation attached:
ATTENTION ENM...
Chad Berkley

05/09/2008

02:58 PM Bug #3290: DarwinCore_test workflow takes forever to downloading data
change to 1.0.0 Jing Tao
01:48 PM Bug #3290 (New): DarwinCore_test workflow takes forever to downloading data
DarwindCore actor in demos/ENM/DarwindCore_test.xml work-flow takes forever to downloading data (more than two hours)... Jing Tao
02:58 PM Bug #3291: IPCC_ChangeNightlyBuildTest got an exception
Change to 1.0.0 Jing Tao
02:57 PM Bug #3291 (New): IPCC_ChangeNightlyBuildTest got an exception
Running work-flow, demos/ENM/IPCC_Change_NightlyBuildTest.xml, got an exception. The supposed result is "true", but t... Jing Tao
11:33 AM Bug #3282: v3 installer intro says Kepler-1.0.0 1.0.0
looks good in win/mac v4 installer Aaron Aaron
10:44 AM Bug #3282: v3 installer intro says Kepler-1.0.0 1.0.0
It has gone in mac v4 installer. Jing Tao
11:23 AM Bug #3252: Ptolemy ack in installer splash screen has typos and was outdated
Looks good in win and mac v4 installers Aaron Aaron
10:49 AM Bug #3252: Ptolemy ack in installer splash screen has typos and was outdated
It looks good now in mac v4 installer. Jing Tao
11:17 AM Bug #3269: authentication system throws NPE
It worked fine in mac v4 installer. Jing Tao
11:16 AM Bug #3271: Random Errors with data authentication system
In mac v4 installer, it seemed fine. Jing Tao
11:07 AM Bug #3270: disable DIGIR Data Source by default
works in mac v4 installer. Jing Tao

05/08/2008

05:40 PM Bug #3122: Get installer size down
the files in lib/jar/base-jars/apache/xalan.jar (~1 MB) are included in lib/jar/jwsdp/xalan.jar (~7 MB) and could lik... Aaron Aaron
11:28 AM Bug #3122: Get installer size down
I notice that standalone-compiler.jar (~4 mb) is still in the installer version. Not sure if this is needed after iz... Aaron Aaron
03:28 PM Bug #3266: ENM/GARP_MultipleSpecies-V.xml problems
Chad - As the creator of this workflow, I should have great insights into what is wrong - but I don't!
I would guess ...
Dan Higgins
01:35 PM Bug #3266: ENM/GARP_MultipleSpecies-V.xml problems
This complex workflow depends on a lot of external dependencies. If any one of them fail, the workflow fails. I've ... Chad Berkley
01:38 PM Bug #3269: authentication system throws NPE
Looks ok here, we'll see what happens in the next installer... Aaron Aaron
09:25 AM Bug #3269: authentication system throws NPE
Was able to see the errors on my local workspace version (thank goodness). I've added synchronized to the Ecogridser... ben leinfelder
10:27 AM Bug #3253: IzPack Windows Installer should install in a directory with the version number
i rechecked this and it is doing what it is supposed to do. Chad Berkley
10:26 AM Bug #3248: .sh files should be removed for windows installer
added a line to the install.xml and build.xml files to make sure the .sh Chad Berkley
09:02 AM Bug #3283: Welcome splash screen shows up when starting windows kepler
It doesn't show up if you have a .ptolemyII directory with a PtolemyPreferences.xml file in it. If you remove that d... Chad Berkley

05/07/2008

09:59 PM Bug #3267: ENM/GARP_SingleSpecies_BestRuleSet-IV.xml problems
this may again be that i didn't succeed with the expat and scew instructions, but after trying those instructions thi... Derik Barseghian
04:52 PM Bug #3267: ENM/GARP_SingleSpecies_BestRuleSet-IV.xml problems
GARP_SingleSpecies_BestRuleSet-IV.xml runs on windows v3 installer and Mac os X v3 installer.
garpModel_ImageJ.xml ru...
Aaron Aaron
09:56 PM Bug #3266: ENM/GARP_MultipleSpecies-V.xml problems
jing and ben - did you get ubuntu crashes after following the expat and scew instructions?
chad - i followed those bu...
Derik Barseghian
04:33 PM Bug #3266: ENM/GARP_MultipleSpecies-V.xml problems
In windows v3 installer, runs for several minutes, generates several maps and then gives
ptolemy.kernel.util.Illegal...
Aaron Aaron
03:39 PM Bug #3266: ENM/GARP_MultipleSpecies-V.xml problems
In ubuntu, it crashed keper twice:
****done with main garp algorithm*****
DONE Calling RunGarpAlgorithm in CPP Code.
...
Jing Tao
03:33 PM Bug #3266: ENM/GARP_MultipleSpecies-V.xml problems
running this workflow on my linux box (ubuntu 7.10) crashes Kepler with no error shown nor logged to the log file. ben leinfelder
06:42 PM Bug #3269: authentication system throws NPE
Works on win v3 installer.
On mac when I did the search a second time, after restarting kepler, it hangs for a long ...
Aaron Aaron
03:40 PM Bug #3269: authentication system throws NPE
works on ubuntu (v3 installer) ben leinfelder
06:01 PM Bug #3268: Python/PythonFileLineCounter.xml workflow problem
works on win and mac (v3 installer). Aaron Aaron
03:36 PM Bug #3268: Python/PythonFileLineCounter.xml workflow problem
works on osx and ubuntu (v3 installer) ben leinfelder
04:19 PM Bug #3264: workflow ENM/ASC2RAWTest gives an exception under ubuntu
runs on windows and OSX (v3 installer) Aaron Aaron
03:33 PM Bug #3264: workflow ENM/ASC2RAWTest gives an exception under ubuntu
Tried v3 in ubuntu, mac and windows. It works. Jing Tao
02:52 PM Bug #3264: workflow ENM/ASC2RAWTest gives an exception under ubuntu
runs successfully (multiple times) on both OSX and Linux (v3 installer) ben leinfelder
04:09 PM Bug #3261: ApplicationFramework/CredentialRetrieve workflow has problems
verified, file has been removed from windows and mac v3 installer Aaron Aaron
04:01 PM Bug #3256: path problems on Mac with CommandLine demo workflows
looks good in Mac and win (v3 installer) Aaron Aaron
03:29 PM Bug #3256: path problems on Mac with CommandLine demo workflows
both work flows worked in Mac Jing Tao
02:41 PM Bug #3256: path problems on Mac with CommandLine demo workflows
ran both demos in OSX - worked great (v3 installer). ben leinfelder
03:46 PM Bug #3254: Annotations for some Ptolemy demos are not wrapped
The SDF Expression annotation looks good. I ran through all the SDF demos. SynthesizedVoice.xml cannot find the file... Aaron Aaron
03:40 PM Bug #3270: disable DIGIR Data Source by default
works on OSX and ubuntu (v3 installer) ben leinfelder
03:27 PM Bug #3253: IzPack Windows Installer should install in a directory with the version number
C:\Program Files\Kepler-1.0.0 in windows v3 installer. Looks good. Aaron Aaron
03:04 PM Bug #3253: IzPack Windows Installer should install in a directory with the version number
I got the same result as ben in mac and linux.
In windows, i got c:\Porgram Files\Kepler-1.0.0.
but in the menu, we ...
Jing Tao
02:33 PM Bug #3253: IzPack Windows Installer should install in a directory with the version number
i get /Applications/Kepler-1.0.0 in OSX
and /home/leinfelder/Kepler-1.0.0 in linux
as defaults with the v3 installer ...
ben leinfelder
03:26 PM Bug #3283 (Resolved): Welcome splash screen shows up when starting windows kepler
In mac and linux, the Welcome splash screen doesn't show up when user starts kepler. However, in windows version, I d... Jing Tao
03:12 PM Bug #3248: .sh files should be removed for windows installer
we ended up creating a kepler-console.bat file which launches kepler with a console window. we also updated kepler.e... Chad Berkley
03:00 PM Bug #3248: .sh files should be removed for windows installer
kpeler.sh is in kepler-1.0.0 dir. But i don't have an cgwin, I didn't run it. Jing Tao
02:53 PM Bug #3248: .sh files should be removed for windows installer
(v3 installer)
running ./kepler.sh in cygwin on win xp doesn't work for me.
Verified keplerexecute.sh is gone.
kepler...
Aaron Aaron
02:54 PM Bug #3252: Ptolemy ack in installer splash screen has typos and was outdated
this didn't get checked into the branch. it's in there now. Chad Berkley
02:47 PM Bug #3252: Ptolemy ack in installer splash screen has typos and was outdated
It is still a issue in windows,mac and linux installer. Jing Tao
02:30 PM Bug #3252: Ptolemy ack in installer splash screen has typos and was outdated
this is still a problem in the linux and OSX v3 installers ben leinfelder
02:51 PM Bug #3282: v3 installer intro says Kepler-1.0.0 1.0.0
ok, i just fixed this. Chad Berkley
02:30 PM Bug #3282 (Resolved): v3 installer intro says Kepler-1.0.0 1.0.0
v3 installer intro says:
Welcome to the installation of Kepler-1.0.0 1.0.0!
Daniel Crawl
02:41 PM Bug #3247: Documentation intro screen typo
looks good in windows (v3 installer) Aaron Aaron
02:26 PM Bug #3247: Documentation intro screen typo
verified in OSX, linux (v3 installer)-BRL ben leinfelder
02:38 PM Bug #3246: Typo in Documentation Screen
Looks good in windows Aaron Aaron
02:32 PM Bug #3246: Typo in Documentation Screen
Fixed in mac and linux Jing Tao
02:28 PM Bug #3246: Typo in Documentation Screen
checked in linux and OSX. i also re-read the entire doc-index page and checked all of the links. everything seems ok. Chad Berkley
02:25 PM Bug #3246: Typo in Documentation Screen
verified in OSX, linux (v3 installer)-BRL ben leinfelder

05/06/2008

03:51 PM Bug #3278: Search result count is inflated when using both KNB sources ([un]authenticated)
I'm going to push this to 1.1. Since the auth query is off by default, it will rarely be seen and it's purely a cosm... Chad Berkley
02:48 PM Bug #3278 (New): Search result count is inflated when using both KNB sources ([un]authenticated)
The results get merged and duplicates are not shown in the result list, but the count does not match the results show... ben leinfelder
02:45 PM Bug #3271: Random Errors with data authentication system
closing this bug - not seeing crazy authentication errors nor race conditions when using the authenticated query.
wil...
ben leinfelder
10:07 AM Bug #3271: Random Errors with data authentication system
changed the ldap authentication gui to get away from static method calls (in favor of singleton getInstance calls tha... ben leinfelder
02:42 PM Bug #3277 (Resolved): Create reusable jython-based SelectionDialog actor to collect runtime parameters
Dan (Higgins) did a prototype of this use of the PythonScript actor to create Swing interfaces for displaying drop do... ben leinfelder
02:02 PM Bug #3276: MatlabExpression not finding ptmatlab.dylib
fixed bug in ptII code that was causing this. Chad Berkley
02:00 PM Bug #3266: ENM/GARP_MultipleSpecies-V.xml problems
added a note in the workflow and in the README about scew and expat on linux. Chad Berkley
01:59 PM Bug #3267: ENM/GARP_SingleSpecies_BestRuleSet-IV.xml problems
I added a note in the README and in the workflow itself about scew and expat for linux. Chad Berkley
11:29 AM Bug #3267: ENM/GARP_SingleSpecies_BestRuleSet-IV.xml problems
I was finally able to reproduce the crash on ubuntu by installing a fresh version of ubuntu in a VM and running keple... Chad Berkley
10:10 AM Bug #3273: Improve authentication dialogue so that the reason for authentication is clear
Now that some of the threading issues are being hammered out, this should be easier to work with.
Adding a message ar...
ben leinfelder
10:04 AM Bug #3269: authentication system throws NPE
actually found that this bug still existed as an artifact of multiple login dialogues appearing when concurrent threa... ben leinfelder

05/05/2008

05:19 PM Bug #3274: IPCC_Base_Layers.xml work-flow gets out of memeory error
At end of January 2008, the src/org/ecoinformatics/ecogrid/queryservice/QueryServiceGetToStreamClient.java class some... Jing Tao
01:01 PM Bug #3274: IPCC_Base_Layers.xml work-flow gets out of memeory error
5M is a typo :) Jing Tao
12:47 PM Bug #3274: IPCC_Base_Layers.xml work-flow gets out of memeory error
heap size was 512M, not 5M; so I hope that is a typo in comment #1
Dan Higgins
12:35 PM Bug #3274: IPCC_Base_Layers.xml work-flow gets out of memeory error
Previously this workflow worked OK (during training in Jan 2008) so heap space usage would appear to be a 'new' probl... Dan Higgins
12:18 PM Bug #3274 (Resolved): IPCC_Base_Layers.xml work-flow gets out of memeory error
When this work-flow tried to download 10 big data files, it can finish part of downloading - maybe 6 and the rest 4 w... Jing Tao
03:23 PM Bug #3275: EML200DataSource interface
HIstorical Note: The EML 2 Dataset actor was added to the tree mainly for use in displaying local file based data pac... Dan Higgins
01:15 PM Bug #3275 (New): EML200DataSource interface
1)When you drag an EML 2 Dataset actor to canvas and Configure Actor, you're presented with different parameters than... Derik Barseghian
03:15 PM Bug #3276 (Resolved): MatlabExpression not finding ptmatlab.dylib
MatlabExpression actor is not finding ptmatlab.dylib on the mac, after setting DYLD_LIBRARY_PATH=/Applications/MATLAB... Derik Barseghian
03:12 PM Bug #3266: ENM/GARP_MultipleSpecies-V.xml problems
got this to work on windows and mostly on linux. it wasn't working due to the setting of the .kepler directory as th... Chad Berkley
02:03 PM Bug #3266: ENM/GARP_MultipleSpecies-V.xml problems
workflow completes successfully on OSX Chad Berkley
01:50 PM Bug #3266: ENM/GARP_MultipleSpecies-V.xml problems
this workflow crashes on windows almost immediately after beginning execution. on ubuntu, it doesn't crash until alm... Chad Berkley
12:35 PM Bug #3269: authentication system throws NPE
this now works in the cvs branch and in a new installer i just created. closing this bug. Chad Berkley
10:03 AM Bug #3273 (Resolved): Improve authentication dialogue so that the reason for authentication is clear
As it exists currently, the LDAP authentication mechanism is reused for a number of authentication scenarios. It is ... ben leinfelder
09:50 AM Bug #2960: Change RExpression actor to use meaningful graphic file output names
During the follow up meeting, we decided to use the following approach for the R expression file output:
For each run...
ben leinfelder

05/04/2008

11:32 AM Bug #3269: authentication system throws NPE
i can recreate this error in the installer version of kepler, but not in my local development version (using release ... ben leinfelder
10:45 AM Bug #3271: Random Errors with data authentication system
I am able to start an authenticated query, hit cancel when prompted for login (once for each document type being sear... ben leinfelder
10:38 AM Bug #3270: disable DIGIR Data Source by default
i've committed changes to the release branch that allow the selection status of the services to be preserved when the... ben leinfelder

05/02/2008

04:04 PM Bug #3270: disable DIGIR Data Source by default
ben - awhile ago i had things such that when you clicked on the data tab it would then invoke the update, graying out... Derik Barseghian
03:17 PM Bug #3270: disable DIGIR Data Source by default
also, I don't know that there is a benefit for waiting 30 seconds before executing the services list refresh thread. ... ben leinfelder
03:16 PM Bug #3270: disable DIGIR Data Source by default
keep in mind that there is a 30 second delay after kepler starts up at which point the service list is automatically ... ben leinfelder
03:10 PM Bug #3270: disable DIGIR Data Source by default
Chad, i think we can reproduce the reset selection issue (at least in ubuntu).
1. Diselect digir in source window an...
Jing Tao
03:01 PM Bug #3270: disable DIGIR Data Source by default
There seem to be some major issues with the threading in this functionality. The check box for digir is getting rese... Chad Berkley
02:48 PM Bug #3270: disable DIGIR Data Source by default
this may not as straightforward as you might think since the services are retrieved from the registry every time kepl... ben leinfelder
02:21 PM Bug #3270 (Resolved): disable DIGIR Data Source by default
chatting on irc, chad jing and i think we should disable DIGIR in the Services List panel by default, since it's stil... Derik Barseghian
03:46 PM Bug #3269: authentication system throws NPE
The login anonymously is needed for the kepler component repository. It's there so that people don't have to have a ... Chad Berkley
03:23 PM Bug #3269: authentication system throws NPE
is there a reason we have the "login anonymously" button?
i believe it is an artifact of functionality that is no lon...
ben leinfelder
02:05 PM Bug #3269 (Resolved): authentication system throws NPE
after a fresh install, go to the data tab. remove the digir selection, search for 'datos'. click the 'login anonymo... Chad Berkley
03:07 PM Bug #3271: Random Errors with data authentication system
The cancel button does not cancel after the 2nd authentication. You may have one successful search, but if you resta... Chad Berkley
03:03 PM Bug #3271 (Resolved): Random Errors with data authentication system
There are many random errors occurring with the data search/authentication system. This is a tracking bug for these ... Chad Berkley
01:14 PM Bug #3268: Python/PythonFileLineCounter.xml workflow problem
Changed it to use itself instead of build.xml. Derik Barseghian
01:11 PM Bug #3268: Python/PythonFileLineCounter.xml workflow problem
Pick any text file that is in the release. The workflow just counts lines. I had assumed that build.xml would be there Dan Higgins
12:23 PM Bug #3268: Python/PythonFileLineCounter.xml workflow problem
This should be changed. nothing should depend on build.xml in the installed version of kepler. Chad Berkley
12:14 PM Bug #3268 (Resolved): Python/PythonFileLineCounter.xml workflow problem
This workflow wants to operate on file build.xml, but build.xml is not in the release. Derik Barseghian
12:14 PM Bug #3266: ENM/GARP_MultipleSpecies-V.xml problems
fixed the mac problem by adding a plugins symlink to the working dir. Chad Berkley
11:02 AM Bug #3266 (In Progress): ENM/GARP_MultipleSpecies-V.xml problems
ENM/GARP_MultipleSpecies-V.xml crashes Ubuntu Kepler.
On mac execution completes but just gives ImageJ "Unrecognize...
Derik Barseghian
12:08 PM Bug #3267: ENM/GARP_SingleSpecies_BestRuleSet-IV.xml problems
Fixed the problem on the mac by creating a symlink to the plugins directory. Chad Berkley
11:38 AM Bug #3267: ENM/GARP_SingleSpecies_BestRuleSet-IV.xml problems
The Mac error 'ImageJ "Unrecognized comand: ASC
TextReader" also occurs on the GARP Model ImageJ workflow. It looks l...
Dan Higgins
11:32 AM Bug #3267: ENM/GARP_SingleSpecies_BestRuleSet-IV.xml problems
It crashed my kepler in ubuntu too. Jing Tao
11:25 AM Bug #3267: ENM/GARP_SingleSpecies_BestRuleSet-IV.xml problems
I just ran this on ubuntu and had no problems. Is there a way to make the error occur? Chad Berkley
11:14 AM Bug #3267 (Resolved): ENM/GARP_SingleSpecies_BestRuleSet-IV.xml problems
ENM/GARP_SingleSpecies_BestRuleSet-IV.xml crashes Ubuntu Kepler.
On mac execution completes but gives ImageJ "Unreco...
Derik Barseghian
11:20 AM Bug #3250: windows exe opens dos box
kepler.exe has been changed back to a gui application and kepler-console.bat
added. (We chose .bat instead of .exe s...
Daniel Crawl
10:41 AM Bug #3265 (New): ascToRaw needs more error handling
There are several try/catch statements in AscToRaw.java that either have nothing in the catch statement or just a sin... Chad Berkley
10:40 AM Bug #3264: workflow ENM/ASC2RAWTest gives an exception under ubuntu
fixed. the directory listing actor was pulling in all the files in the lib/testdata/garp directory instead of just t... Chad Berkley
10:30 AM Bug #3264: workflow ENM/ASC2RAWTest gives an exception under ubuntu
This looks like a problem with AscToRaw.getHeaderInformation(). The error handling for missing header information is... Chad Berkley
10:03 AM Bug #3264: workflow ENM/ASC2RAWTest gives an exception under ubuntu
I also see the error on 2nd run problem on the Mac. So ignore comment #2
If one deletes the *.raw files created the ...
Dan Higgins
09:55 AM Bug #3264: workflow ENM/ASC2RAWTest gives an exception under ubuntu
I just tried in mac too. The first time, the workflow worked. However, it failed when i clicked the run button at the... Jing Tao
09:34 AM Bug #3264: workflow ENM/ASC2RAWTest gives an exception under ubuntu
Dan, did you try run twice? Sometimes, the first time worked, but the second time failed. Jing Tao
09:11 AM Bug #3264: workflow ENM/ASC2RAWTest gives an exception under ubuntu
This workflow seems to run fine on a Mac. This suggests that the problem is not with the workflow (ie a platform spec... Dan Higgins
10:07 AM Bug #3261: ApplicationFramework/CredentialRetrieve workflow has problems
I removed this workflow since no one commented. Chad Berkley

05/01/2008

06:39 PM Bug #3254: Annotations for some Ptolemy demos are not wrapped
The annotations in the Ptolemy demos are fixed.
I hacked up a filter that did most of the heavy lifting.
The Ptolemy ...
Christopher Brooks
01:10 PM Bug #3254: Annotations for some Ptolemy demos are not wrapped
I'm still at it . . .
The filter has problems. I should have this done sometime today.
Christopher Brooks
12:08 PM Bug #3254: Annotations for some Ptolemy demos are not wrapped
christopher, is this now fixed? If so, can I close this bug? Chad Berkley
10:49 AM Bug #3254: Annotations for some Ptolemy demos are not wrapped
Ok, I have a filter than can fix this problem.
Unless I hear otherwise, I'm going to update the appropriate demos
in ...
Christopher Brooks
03:34 PM Bug #3264: workflow ENM/ASC2RAWTest gives an exception under ubuntu
added that this blocks 3245 Derik Barseghian
03:33 PM Bug #3264 (Resolved): workflow ENM/ASC2RAWTest gives an exception under ubuntu
This workflow needs to be removed or fixed for release
Running under Ubuntu gives an exception that starts with: "...
Derik Barseghian
03:21 PM Bug #2318: Copyrights and licenses of subpackages need to be handled
The file licenses.txt now includes the text of all of the non-BSD licenses that apply to libraries included in the re... Timothy McPhillips
01:57 PM Bug #3261: ApplicationFramework/CredentialRetrieve workflow has problems
I've seen that change of UI look and feel before on linux. I'm not sure what causes it.
I think we can remove thi...
Chad Berkley
01:49 PM Bug #3261 (Resolved): ApplicationFramework/CredentialRetrieve workflow has problems
I think this needs to be fixed or removed for release.
To reproduce (on Ubuntu running Kepler from Chad's latest i...
Derik Barseghian
11:39 AM Bug #3253: IzPack Windows Installer should install in a directory with the version number
BTW -
Ptolemy II does the Ptolemy/ptII7.0.1 trick, take a look
in ptII/adm/gen-7.0 of the rel-7-0-beta-2 tree
Basic...
Christopher Brooks
11:15 AM Bug #3253: IzPack Windows Installer should install in a directory with the version number
I changed the installer to default to Kepler-1.0.0. I can't find a way to specify ../Kepler/1.0 or ../Kepler/Kepler-... Chad Berkley
11:17 AM Bug #3250: windows exe opens dos box
maybe as a compromise, we could have kepler.exe and kepler-console.exe. The first would not open the dos box, the la... Chad Berkley
09:23 AM Bug #3196: Find/Change license on gpl/lgpl code
Did all tasks in comment 13. Also removed libgishull.so. I think this bug is now finished. I'm closing it. Chad Berkley

04/30/2008

11:54 PM Bug #3255: Diva ConcurrentModificationException
I've checked in a fix to ptolemy.kernel.util.Attribute.
Basically, if incrementWorkspaceVersion is false, then get w...
Christopher Brooks
07:36 PM Bug #3255: Diva ConcurrentModificationException
I think I've narrowed down the problem and hope to have a solution tonight
or tomorrow. I posted my notes to the ptd...
Christopher Brooks
12:33 PM Bug #3255: Diva ConcurrentModificationException
I saw it with the Kepler 1.0.0 kepler.exe
I can't repeat it. I was trying
ptolemy/actor/lib/hoc/demo/ApplyFFT/Apply...
Christopher Brooks
12:16 PM Bug #3255: Diva ConcurrentModificationException
You're seeing this when you run the installer or a specific workflow? Chad Berkley
09:18 AM Bug #3255 (Resolved): Diva ConcurrentModificationException
I'm seeing the following stack trace in the DOS window when
I run the Kepler-1.0.0 installer on a Windows 2003 Serve...
Christopher Brooks
05:51 PM Bug #3196: Find/Change license on gpl/lgpl code
The following source files have been deleted:
cpp/gis/grass/GISHull/hull.cpp
org/nmiworkflow/GlobusJob.java
org/nmiw...
Timothy McPhillips
05:37 PM Bug #2318: Copyrights and licenses of subpackages need to be handled
We need to add to the distribution a file including all of the non-BSD licenses that apply to libraries included in t... Timothy McPhillips
03:26 PM Bug #3250: windows exe opens dos box
Reopening this an an enhancement (Forgot to leave it open last time). Christopher Brooks
03:16 PM Bug #3250: windows exe opens dos box
I'm removing the block on 3245 for this bug, but leaving
it open. I'm also changing this to an enhancment.
Feel free...
Christopher Brooks
02:01 PM Bug #3250: windows exe opens dos box
The configuration was changed from gui to console so that stdout would appear.
I'm not sure sending it to a log file ...
Daniel Crawl
12:20 PM Bug #3250: windows exe opens dos box
Kepler.exe is created using Launch4j.
Docs are at http://launch4j.sourceforge.net/docs.html#Configuration_file
Ptolem...
Christopher Brooks
11:55 AM Bug #3250: windows exe opens dos box
I don't see how to easily do this, so I'm going to leave it as is. Chad Berkley
02:21 PM Bug #3257: Typos in html docs and demos.
Checked in fixed typos to release branch. Aaron Aaron
02:07 PM Bug #3257 (Resolved): Typos in html docs and demos.
A couple of typos in the documentation and demos. Aaron Aaron
01:24 PM Bug #3254: Annotations for some Ptolemy demos are not wrapped
This is an 'old' problem that, as I remember, had to do with the exact way the annotation was created. We had to go b... Dan Higgins
12:31 PM Bug #3254: Annotations for some Ptolemy demos are not wrapped
These models are in Ptolemy.
I don't know if this should hold up the release.
To replicate, start Kepler 1.0.0 from t...
Christopher Brooks
12:13 PM Bug #3254: Annotations for some Ptolemy demos are not wrapped
which file is this in? Chad Berkley
09:11 AM Bug #3254 (Resolved): Annotations for some Ptolemy demos are not wrapped
The annotation for the SDF Expression demo is not wrapped,
it runs off the right side of the screen.
However, the...
Christopher Brooks
12:17 PM Bug #3248: .sh files should be removed for windows installer
kepler.sh will stay. closing this bug. Chad Berkley
11:15 AM Bug #3248: .sh files should be removed for windows installer
The kepler.exe from the 4/29 kepler-1.0.0 windows installer works for me.
However, I really think that we need to in...
Christopher Brooks
11:08 AM Bug #3248: .sh files should be removed for windows installer
It would be nice if kepler.exe were the only executable on Windows.
Christopher: does this work for you on cygwin?
Daniel Crawl
10:57 AM Bug #3248: .sh files should be removed for windows installer
ok, I'll leave them. I've asked dan crawl if he's going to create a keplerexecute.bat file. right now, the only bat... Chad Berkley
07:32 AM Bug #3248: .sh files should be removed for windows installer
I think the .sh files should stay under Windows
as I use cygwin. I don't think the .bat files
will work under cygwin.
Christopher Brooks
11:53 AM Bug #3256: path problems on Mac with CommandLine demo workflows
fixed with method from comment 2. Chad Berkley
11:32 AM Bug #3256: path problems on Mac with CommandLine demo workflows
Solution is to create a symbolic link in the Kepler.app/Kepler directory back to the /Applications/Kepler/demos direc... Chad Berkley
10:58 AM Bug #3256: path problems on Mac with CommandLine demo workflows
The demos/getting-started/03_ImageDisplay.xml example also fails on the Mac
It looks like moving the demos dir up on...
Dan Higgins
10:52 AM Bug #3256 (Resolved): path problems on Mac with CommandLine demo workflows
On 1.0 release installer check, the CommandLine_1 and CommandLine_2 demo workflows (in demos/getting-started dir) fai... Dan Higgins
10:30 AM Bug #3252: Ptolemy ack in installer splash screen has typos and was outdated
I'm going to go ahead and close this bug since it's fixed in cvs. I'll go back and check all of the 3245 blockers wh... Chad Berkley
08:13 AM Bug #3252 (Resolved): Ptolemy ack in installer splash screen has typos and was outdated
In the Kepler 1.0.0 IzPack installer splash screen, there is a
missing "S" and an extra </p> in the Ptolemy support ...
Christopher Brooks
10:28 AM Bug #3247: Documentation intro screen typo
fixed. Chad Berkley
10:26 AM Bug #3246: Typo in Documentation Screen
fixed. Chad Berkley
08:19 AM Bug #3253 (Resolved): IzPack Windows Installer should install in a directory with the version number
The installer should install in a directory that contains the
version number of the release.
Under Windows, the d...
Christopher Brooks
08:05 AM Bug #3251 (Resolved): Installer Splash Screen should be an HTML Widget
Is there anyway to use an HTML widget for the Installation Screen here?
The Ptolemy IzPack Installer uses an HTML wi...
Christopher Brooks

04/29/2008

05:15 PM Bug #3250 (Resolved): windows exe opens dos box
try to make the kepler.exe file not open a dos box with windows. Chad Berkley
05:11 PM Bug #3248 (Resolved): .sh files should be removed for windows installer
remove the kepler.sh and keplerexecute.sh files in the windows installer. Chad Berkley
05:02 PM Bug #3247: Documentation intro screen typo
This is also the "about" screen. Chad Berkley
05:01 PM Bug #3247: Documentation intro screen typo
Date is also wrong. Chad Berkley
04:59 PM Bug #3247 (Resolved): Documentation intro screen typo
Still says "Release Candidate" Chad Berkley
04:56 PM Bug #3246 (Resolved): Typo in Documentation Screen
Giude to Ecological Niche Modeling should be *Guide* to ... Chad Berkley
12:30 PM Bug #3245 (Resolved): Release 1.0 installer tracking bug
Current issues:
1) IzPack is extremely slow when an installer is built for multiple OSs. I've alerted the IzPack t...
Chad Berkley

04/28/2008

02:10 PM Bug #3195: Check all documentation for 1.0 release
I have now reviewed all documentation. Kirstin is making changes and will have the pdf files for the release hopeful... Chad Berkley

04/25/2008

01:40 PM Bug #2318: Copyrights and licenses of subpackages need to be handled
Here's a list of the files I removed. the ones with a "--" are had a secondary compile time dependency on the jar (i... Chad Berkley
12:12 PM Bug #2318: Copyrights and licenses of subpackages need to be handled
Here are other file that will have to be removed if these jars are deleted. This list does not include the actors th... Chad Berkley
11:02 AM Bug #3198: test dynamic library installations on all platforms
this now works on all platforms. will retest with real installers before the release. Chad Berkley
09:59 AM Bug #3195: Check all documentation for 1.0 release
I've incorporated Chad's User Manual and GSG feedback and created new PDF files of the docs for the 1.0.0 release. Al... Kirsten Menger-Anderson

04/24/2008

11:50 PM Bug #3233: finalize ptolemy matlab actor for 1.0 release
I'm closing the Matlab bug because I opened bug# 3242
"dlls should not go in c:/Windows/System32"
Christopher Brooks
03:04 PM Bug #3233: finalize ptolemy matlab actor for 1.0 release
cplibs.bat/sh is run by the installer. If it doesn't run, the libraries for the gdal stuff don't work. I'm open to ... Chad Berkley
02:50 PM Bug #3233: finalize ptolemy matlab actor for 1.0 release
Sorry, I forgot to add -kb. I added it to the linux and mac versions.
The current ptmatlab.dll works for me, both in...
Daniel Crawl
12:43 PM Bug #3233: finalize ptolemy matlab actor for 1.0 release
I fixed the cvs -kb problem of ptmatlab.dll in the devel head and release branch. Christopher Brooks
12:23 PM Bug #3233: finalize ptolemy matlab actor for 1.0 release
This is the cygcheck -s output from my machine. Christopher Brooks
12:22 PM Bug #3233: finalize ptolemy matlab actor for 1.0 release
I'm not sure what's up with c:/Windows/System32/ptmatlab.dll.
The file I have is
$ ls -l c:/Windows/System32/ptmatlab...
Christopher Brooks
12:11 PM Bug #3233: finalize ptolemy matlab actor for 1.0 release
I updated the repository so that ptmatlab.dll is executable. I'm moving Christopher's other suggestions for permissi... Chad Berkley
11:48 PM Bug #3242 (Resolved): dlls should not go in c:/Windows/System32
In bug# 3233, I noticed that dlls were showing up in c:/Windows/System32.
Chad wrote:
> cplibs.bat/sh is run by the...
Christopher Brooks
06:30 PM Bug #2318: Copyrights and licenses of subpackages need to be handled
We can delete the following jar files:
doublePolygon.jar
NimrodService.jar
griddlesActorLib.jar
ncsu.jar
edu.sdsc.gl...
Timothy McPhillips
03:01 PM Bug #3216: Demo workflows do not run
I've sent the list of non-working demos to everyone. It's best to discard them as they are not critical except for a ... Ilkay Altintas
12:40 PM Bug #3234: IJMacro does not work in several demo workflows
Works for me now on a clean checkout. Not sure what was up. Sean Riddle
11:55 AM Bug #3234: IJMacro does not work in several demo workflows
Sean, can you please clarify whether this is still a bug. If it isn't, please close it. If you are having related i... Chad Berkley
12:12 PM Bug #3240 (Resolved): Fix permissions on kepler CVS files.
Christopher suggests we redo all of the permissions for kepler:
I suggest fixing the permissions for the java and ...
Chad Berkley
11:50 AM Bug #3237: Search actor in remote repository doesn't work
Following the above plan, we fixed the issue. Ben, chand and i tested it and it worked. Now kepler can search the rem... Jing Tao
11:45 AM Bug #3195: Check all documentation for 1.0 release
finished reviewing the GSG. I checked my changes into CVS with track changes on. Chad Berkley
09:25 AM Bug #3238 (Resolved): Refactor NMI build
The NMI build needs to be refactored in several ways after the release. Here's the list of things I think needs to b... Chad Berkley

04/23/2008

05:37 PM Bug #3196: Find/Change license on gpl/lgpl code
The header files in the following folders under src/cpp need to have license text inserted into them:
backprop
garp
...
David Welker
09:54 AM Bug #3196: Find/Change license on gpl/lgpl code
The following source files still have GPL licenses:
- cpp/gis/grass/GISHull/hull.cpp
- org/geon/GridOverlay.java
- o...
Timothy McPhillips
04:00 PM Bug #3233: finalize ptolemy matlab actor for 1.0 release
FYI, I had no problems with ptmatlab.dll on cygwin.
Was your c:\windows\system32\ptmatlab.dll was the same version f...
Daniel Crawl
03:37 PM Bug #3233: finalize ptolemy matlab actor for 1.0 release
I replaced the kepler/lib/ptmatlab.dll with the $PTII/lib/ptmatlab.dll_msvc
because the previous ptmatlab.dll gave me...
Christopher Brooks
03:47 PM Bug #2990: file|open dialog should open in workflows directory
I'm reopening this bug because if the user uses the kepler.sh script
then having File->Open open kepler/demos is odd....
Christopher Brooks
12:52 PM Bug #3097: incorrect classpath in generated ptexecute.sh and momlexecute.sh
I updated kepler.exe for windows and removed kepler.bat.
The remaining tasks are enhancements for a later release.
Daniel Crawl
12:24 PM Bug #3207: consolidate command line execution actors
Ok, I folded these changes into ptII rel-7-0-beta-2.
I spent some time working with the file redirection operators by...
Christopher Brooks
12:23 PM Bug #3207: consolidate command line execution actors
This model writes a random number to a file using the Exec actor, but
the file is not created before the attempt to r...
Christopher Brooks
11:02 AM Bug #3108: ENM GARP Baseline 3-Actor GARP - Browser Display demo fails with NameDuplication: convertTo?
A workflow in the workflows/ folder doesn't affect Kepler 1.0, since we're not releasing it, just demos/ Sean Riddle
10:02 AM Bug #3182: check for consistent licensing text in all source files
Most of the remaining issues are listed under bug #2318 now (as well as bug #3196).
*** This bug has been marked as ...
Timothy McPhillips
10:02 AM Bug #2318: Copyrights and licenses of subpackages need to be handled
*** Bug 3182 has been marked as a duplicate of this bug. *** Timothy McPhillips
08:24 AM Bug #3237: Search actor in remote repository doesn't work
Targeting this at 1.0.0 to fix a critical problem. Matt Jones

04/22/2008

10:06 PM Bug #3237 (Resolved): Search actor in remote repository doesn't work
The reason of the search not work is that kepler sets "entity" as
namespace when it searches actors. In query.xsd an...
Jing Tao
05:46 PM Bug #3026: Actor documentation does not appear in older workflows
All updated workflows have been committed. Sean Riddle
05:30 PM Bug #3115: Need to check Kepler for memory leaks
I did not detect significant memory leaks. From a cost-benefit perspective, there is little advantage to push to find... Sean Riddle
05:10 PM Bug #3207: consolidate command line execution actors
Ok, I'll update ptII rel-7-0-beta-2 tomorrow (Wed).
I'm taking this bug pending the update.
Christopher Brooks
02:14 PM Bug #3207: consolidate command line execution actors
By prepending sh or cmd, the command can use file redirection operators.
I tested this actor on several platforms, a...
Daniel Crawl
05:07 PM Bug #3233: finalize ptolemy matlab actor for 1.0 release
I'm just back from running a workshop yesterday.
I can patch these on Wed, 4/23, so I'm taking this bug. I'll reassi...
Christopher Brooks
04:50 PM Bug #3195: Check all documentation for 1.0 release

page 280: The page ends with "can be found here:" but the path after the colon
is not a link.
page 303: include a U...
Chad Berkley

04/21/2008

04:34 PM Bug #3195: Check all documentation for 1.0 release

page 170: heading of table is widowed
page 181: kepler earthgrid
page 181: table header widowed
page 183: in the ...
Chad Berkley
11:45 AM Bug #3195: Check all documentation for 1.0 release
need to update http://www.kepler-project.org/Wiki.jsp?page=Documentation Chad Berkley
02:05 PM Bug #3097: incorrect classpath in generated ptexecute.sh and momlexecute.sh
I moved the wfexecute functionality into kepler.sh and kepler.bat.
Remaining tasks:
1. kepler.bat functionality sho...
Daniel Crawl
01:01 PM Bug #2318: Copyrights and licenses of subpackages need to be handled
Okay, it looks like I was looking at compile-time dependencies instead of the full list. That negates the problems wi... Sean Riddle
11:49 AM Bug #2318: Copyrights and licenses of subpackages need to be handled
We need to include extra JARs per these license restrictions: http://java.sun.com/webservices/docs/1.5/ReleaseNotes.h... Sean Riddle
11:38 AM Bug #3234: IJMacro does not work in several demo workflows
Seems to be a problem with my checkout. IJMacro works fine now. I am still getting hangs whenever I need to use a Dar... Sean Riddle
10:09 AM Bug #3236 (Resolved): remove strict requirements for PTII and KEPLER env variables
From an email from matt on kepler-dev:
I agree, it would be better if we could build without requiring that
JAVA...
Chad Berkley

04/20/2008

03:52 PM Bug #3233: finalize ptolemy matlab actor for 1.0 release
Once the patches in comments #1 and #2 have been applied, this bug can be closed. Daniel Crawl
03:47 PM Bug #3233: finalize ptolemy matlab actor for 1.0 release
UtilityFunctions.loadLibrary() fails to find the jni library on Linux. Please apply the attached patch. Daniel Crawl
03:43 PM Bug #3233: finalize ptolemy matlab actor for 1.0 release
I updated the KAR file to use TextStyle for the expression parameter, but the KAR parser ignores it. (If I add the sa... Daniel Crawl

04/18/2008

04:10 PM Bug #3207: consolidate command line execution actors
I did the merge.
I added a parameter called "prependPlatformDependentShellCommand",
which, if set to true, will prepe...
Christopher Brooks
08:58 AM Bug #3207: consolidate command line execution actors
I'm part way through the merge, and had two questions.
1) The new version of the actor always uses adds prepends cmd...
Christopher Brooks
03:59 PM Bug #3195: Check all documentation for 1.0 release

page 115: figure 5.17 looks kinda bad. the pull out box needs to be redone.
page 122: reference to the "kepler ear...
Chad Berkley
07:52 AM Bug #3195: Check all documentation for 1.0 release
Chad wrote:
> page 13: Kepler 1.0 is based on the Jan 31 ...
> It's based on Ptolemy 7 beta 2
Kepler 1.0 is based o...
Christopher Brooks
12:07 PM Bug #3234: IJMacro does not work in several demo workflows
Using a new check out of the 1.0 RELEASE version of Kepler, I see no problems with the IJMacro actor on a MacbookPro,... Dan Higgins
09:01 AM Bug #3234: IJMacro does not work in several demo workflows
Is this in the head of CVS or the 1.0 release branch?
I cannot check on a Mac at the moment, but the message looks l...
Dan Higgins
12:38 AM Bug #3234 (Resolved): IJMacro does not work in several demo workflows
Running on an installed version of Kepler on OS X.5, in several ENM workflows that try to use IJMacro to display an i... Sean Riddle
10:35 AM Bug #3235 (New): Add an Edit, Select All menu item and respective accelerator
Many (most?) programs have a Select All feature. This would allow, for example, a Kepler Mac user to "apple A" and th... Derik Barseghian

04/17/2008

08:35 PM Bug #2318: Copyrights and licenses of subpackages need to be handled
Good News. I have finished examining all of the remaining runtime jars, and I have found only one major problem.
The...
David Welker
05:28 PM Bug #3209: ecogrid SearchRegistryAction error when disconnected from network
Remove the error message panel and decrease debug level from error to warn in src/org/ecoinformatics/seek/ecogrid/Sea... Jing Tao
05:01 PM Bug #3195: Check all documentation for 1.0 release
page 13: Kepler 1.0 is based on the Jan 31 ...
It's based on Ptolemy 7 beta 2
page 13: cheminformatics
is that the ...
Chad Berkley
04:44 PM Bug #3233 (Resolved): finalize ptolemy matlab actor for 1.0 release
For 1.0 release, we decided to use the Ptolemy matlab actor. The following needs to be done:
- use TextArea for ex...
Daniel Crawl
01:13 PM Bug #3207: consolidate command line execution actors
I'll take this bug and fold the Exec actor changes into the ptII release
branch.
Christopher Brooks
12:57 PM Bug #3207: consolidate command line execution actors
I committed my remaining updates to Exec.java. Once it has been folded into ptII CVS, this bug can be closed. Daniel Crawl
10:57 AM Bug #3225: If R is not present, then error message just says "null"
Added a better error message. Also pointed the user to section 8.2.2 of the user manual that explains how to install... Chad Berkley
09:38 AM Bug #3208: consolidate matlab actors
retarget to 1.1 Chad Berkley
09:32 AM Bug #3230: Matrix Viewer actor does not accept RExpression matrices
The RExpression matrix was created solely to pass a matrix to another RExpression actor. It is NOT a Kepler/Ptolemy m... Dan Higgins
09:25 AM Bug #3226: Eval: subplots from RExpression overly condensed
Differences in graphs created by R depend on the graphics device (i.e. png file, pdf file, or R plotting window and t... Dan Higgins
 

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