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From 04/05/2008 to 05/04/2008

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

04/16/2008

04:48 PM Bug #3231 (New): 3-way table output (multiway cross tabulation actor?)
3-way tables are a useful extension of 2-way tables, which are a basic tool for exploring relationships in data. R h... Kevin Drury
04:40 PM Bug #3230 (New): Matrix Viewer actor does not accept RExpression matrices
2-way tables are a common way to view relationships between bivariate data. The The RExpression actor is quite good ... Kevin Drury
04:23 PM Bug #3209: ecogrid SearchRegistryAction error when disconnected from network
The short term solution is just removing the error message. Kepler will keep silent if it couldn't connect to the reg... Jing Tao
03:40 PM Bug #3209: ecogrid SearchRegistryAction error when disconnected from network
retarget to 1.1 Chad Berkley
04:21 PM Bug #3228 (New): Kepler need a central place to handle network disconnection
When we start kepler, if there is no network disconnection, kepler should have a decent way to handle it - for exampl... Jing Tao
04:08 PM Bug #2318: Copyrights and licenses of subpackages need to be handled
odc-kepler-0.1.r18530.jar has been removed from 1.0 branch. Daniel Crawl
03:59 PM Bug #3206: ecogrid error message occurs when running disconnected from network
It was fixed base above solution. Jing Tao
03:42 PM Bug #3226 (New): Eval: subplots from RExpression overly condensed
Using nightly build 14 Apr 08 under WinXP. The code below generates a publication-quality graphic when run from the ... Kevin Drury
03:30 PM Bug #3115: Need to check Kepler for memory leaks
My notes are at:
http://ptolemy.eecs.berkeley.edu/ptolemyII/ptIIlatest/ptII/doc/coding/performance.htm
Christopher Brooks
03:24 PM Bug #3225 (Resolved): If R is not present, then error message just says "null"
If I build Kepler using RELEASE-BRANCH-1-0-0 and ptII using rel-7-0-beta-2
from source using:
ant full-clean rebuil...
Christopher Brooks
01:01 PM Bug #3196: Find/Change license on gpl/lgpl code
The four Opendap actor files now have a BSD license. Daniel Crawl

04/15/2008

08:01 PM Bug #3097: incorrect classpath in generated ptexecute.sh and momlexecute.sh
I tried wfexecute, it looks pretty slick, below are some comments.
- The name is a little funny. wtf comes to mind, ...
Christopher Brooks
07:16 PM Bug #3122: Get installer size down
For comparison,
Ptolemy II 7.0.1 Windows Installer: 131Mb
Ptolemy II 7.0.1 Windows zip: 44.7Mb
Ptolemy II 7.0.1 Unix...
Christopher Brooks
07:03 PM Bug #3207: consolidate command line execution actors
I can fold this in to the ptII devel tree asap, but should this ship in 1.0.0
or wait?
Christopher Brooks
04:13 PM Bug #3207: consolidate command line execution actors
I updated the External Execution actor based on the design in comment #2.
If there are no complaints, I will remove ...
Daniel Crawl
07:02 PM Bug #3208: consolidate matlab actors
Perhaps consolidating the Matlab actors should be post 1.0.0? Christopher Brooks
06:59 PM Bug #2531: The link from Kepler intro page to the Ptolemy quick links page is broken
I checked this in Kepler-1.0.0 and the Ptolemy demos all open.
I'm closing this bug.
Christopher Brooks
06:29 PM Bug #3179: Distinguish "download" and "information" attribute values in eml distributlon online url
Tested it against server and it worked. Jing Tao
03:17 PM Bug #3209: ecogrid SearchRegistryAction error when disconnected from network
I'm reopening this since the error window now occurs regardless of any data sources actually being used (either the D... Daniel Crawl
02:51 PM Bug #3130: Add an accelerator (keyboard shortcut) for opening a new blank workflow
Thanks Christopher, works great. Daniel Crawl
02:39 PM Bug #3206: ecogrid error message occurs when running disconnected from network
I followed the procedure and duplicated this error message. However, i didn't see it hurt anything. I took a look at ... Jing Tao
02:34 PM Bug #3223 (New): interactive graphics in R
Hello,
Just fyi, the identify() function does not seem to work when called from the RExpression actor. (I'm using...
Kevin Drury
02:07 PM Bug #3222 (New): save new workflow template
Hello,
This is a suggestion about usability, not a bug. It would be very nice to be able to save a workflow that...
Kevin Drury
01:09 PM Bug #3144: add link in OSX Applications folder
The mac installer now installs like this:
/Applications/Kepler/Kepler(.app) - launcher directory...includes most of ...
Chad Berkley
12:18 PM Bug #3221 (New): offset new windows
New blank workflow windows overlap exactly. It would be nice if each new window was slightly offset from the last. Derik Barseghian
11:35 AM Bug #3202: Remove the workflows directory from the release
I created two clean targets in the build script so that you can either clean the directory for a windows or a mac ins... Chad Berkley

04/14/2008

11:29 PM Bug #3130: Add an accelerator (keyboard shortcut) for opening a new blank workflow
I merged these changes into the ptII tree, but not into
the ptII rel-7-0-beta-2 branch for two reasons:
1) Adding Con...
Christopher Brooks
01:26 PM Bug #3130: Add an accelerator (keyboard shortcut) for opening a new blank workflow
This has been implemented in TableauFrame.java.
However, ClassDefinitionController.java already set meta-n to create...
Daniel Crawl
06:55 PM Bug #2962: Add metadata to data tokens so that it can be used downstream
Turns out there is a strict vector test that does not allow extra attributes on a vector (used in barplot() method). ... ben leinfelder
06:31 PM Bug #3179: Distinguish "download" and "information" attribute values in eml distributlon online url
Modified the Entity and EML2Parser class. The value of attribute "function" in distribution url will be stored. In EM... Jing Tao
03:01 PM Bug #3140: RBNBToKepler2 actor output port generation problem
niagara-dev is back up, contains a few empty channels and a channel with a period in its name, and all is well. Derik Barseghian
02:23 PM Bug #3220: "Save" from TextEditor interferes with workflow save-before-closing prompt
aaron will take a look at this - really dives into the ptolemy code. Some starting places:
ptolemy.actor.gui.Effigy
...
ben leinfelder
12:15 PM Bug #3220 (New): "Save" from TextEditor interferes with workflow save-before-closing prompt
While editing an RExpression script using the built-in TextEditor ("Open Actor"), Kevin Drury found that if he used "... ben leinfelder
01:41 PM Bug #3144: add link in OSX Applications folder
I think the installed version is for users only. Developers who want to write java code should get a development ver... Chad Berkley
01:13 PM Bug #2318: Copyrights and licenses of subpackages need to be handled
IANAL (I am not a lawyer), but what I suggest is that you clearly document
that some portions of Kepler are released ...
Christopher Brooks
11:42 AM Bug #2318: Copyrights and licenses of subpackages need to be handled
I have removed those from the RELEASE-BRANCH-1-0-0, I should have said. They are still in head. Derik Barseghian
11:40 AM Bug #2318: Copyrights and licenses of subpackages need to be handled
I have removed rbnb-3.1b2.jar and RDIPD0Ensemble.jar (and associated code and workflows). Derik Barseghian
10:36 AM Bug #3216: Demo workflows do not run
IPCC_Change_MinTemp.xml, IPCC_Change_Precip.xml, IPCC_Change_Rad,
IPCC_Change_Wind.xml, - Errors upon opening. Path ...
Dan Higgins

04/11/2008

05:43 PM Bug #2318: Copyrights and licenses of subpackages need to be handled
If you need to remove a jar...
If there is a jar on the "bad list" and you cannot get the license fixed. (Say it is ...
David Welker
03:36 PM Bug #2318: Copyrights and licenses of subpackages need to be handled
The problem with jar licenses illustrates one good reason to cleanly partition the Kepler system into a core of essen... Timothy McPhillips
03:03 PM Bug #2318: Copyrights and licenses of subpackages need to be handled
We have some major problems with licensing here. Very major problems.
Sean Riddle and I have examined licenses for o...
David Welker
03:06 PM Bug #3216: Demo workflows do not run
It looks like most, if not all, of the problems reported here are Macintosh (and maybe Linux) specific!
I.e. workflo...
Dan Higgins
03:04 PM Bug #3144: add link in OSX Applications folder
Dan's suggestion that the folder structure in the OS X installation mimic the development version checked out of CVS ... Timothy McPhillips
02:07 PM Bug #3144: add link in OSX Applications folder
I took a look at the installation XML definition, with an eye toward hiding
away much of the complexity. I got it to ...
Sean Riddle
02:12 PM Bug #3219: White space in installation path fails on config file read
added to both the HEAD and the release branch ben leinfelder
11:16 AM Bug #3219: White space in installation path fails on config file read
*** Bug 3215 has been marked as a duplicate of this bug. *** Derik Barseghian
11:10 AM Bug #3219: White space in installation path fails on config file read
I do not have write permissions yet for checking it in. Aaron Aaron
11:06 AM Bug #3219 (Resolved): White space in installation path fails on config file read
When Kepler is installed on windows with white spaces in the installation path an exception is thrown from ConfigXML.... Aaron Aaron
11:16 AM Bug #3215: Spaces in KEPLER path causes build problems
Duplicate of bug 3219.
*** This bug has been marked as a duplicate of bug 3219 ***
Derik Barseghian

04/10/2008

03:34 PM Bug #3122: Get installer size down
windows installer with R: 166 MB
windows installer without R: 93 MB
Chad Berkley
02:57 PM Bug #3122: Get installer size down
added new build targets to pair down the kepler directory for each operating system. so far I have built a Mac insta... Chad Berkley
01:55 PM Bug #2318: Copyrights and licenses of subpackages need to be handled
The licensing on gnu-regexp-1.0.8.jar could be problematic. It is only used in org.ecoinformatics.util.Util.substitut... Sean Riddle
11:45 AM Bug #2318: Copyrights and licenses of subpackages need to be handled
Note that our proposal for handling LGPL jars in Kepler 1.0 is limited to those with version 3 of the LGPL license only. Timothy McPhillips
11:30 AM Bug #2318: Copyrights and licenses of subpackages need to be handled
David Welker is investigating the licenses for all 3rd-party jar files included in Kepler. Not all of them are BSD co... Timothy McPhillips
11:49 AM Bug #3216: Demo workflows do not run
I'm using MacOS 10.5.2, Java 1.5.0_13, with a 2.4 GHz processor and 2 gigs of RAM. Sean Riddle
11:46 AM Bug #3130: Add an accelerator (keyboard shortcut) for opening a new blank workflow
I'll postpone. Looking in Top.java, where I thought this change might go (now I'm not sure), it isn't immediately app... Derik Barseghian
11:23 AM Bug #3196: Find/Change license on gpl/lgpl code
> Jianting Zhang suggests removing GRASS support in cpp/gis/grass from the Kepler
> distribution. Comments?
There a...
Chad Berkley
11:06 AM Bug #3196: Find/Change license on gpl/lgpl code
Source licenses update:
Jianting Zhang suggests removing GRASS support in cpp/gis/grass from the Kepler distribution...
Timothy McPhillips

04/09/2008

03:31 PM Bug #3026: Actor documentation does not appear in older workflows
Done with all but ENM demos. I will wait until they all run before I run the automated document replacement. Sean Riddle
02:28 PM Bug #3216: Demo workflows do not run
IPCC_Change_MinTemp.xml, IPCC_Change_Precip.xml, IPCC_Change_Rad,
IPCC_Change_Wind.xml, - Errors upon opening. ---- ...
Dan Higgins
12:41 PM Bug #3216: Demo workflows do not run
ENM/GARP_SingleSpecies_BestRuleSet-IV.xml - After completing its ten iterations, actually crashes the Kepler environm... Sean Riddle
11:32 AM Bug #3216 (Resolved): Demo workflows do not run
I have run into a couple of demo workflows that don't run while checking the replacement of the embedded documentatio... Sean Riddle
01:12 PM Bug #3195: Check all documentation for 1.0 release
Kirsten has found a bunch of actors that still have no documentation. Here's the current list:
AddPointToSVG (no do...
Chad Berkley
12:23 PM Bug #3182: check for consistent licensing text in all source files
I was given permission by John Harris on 4/9/08 to change the license in the code owned by Numeric Solutions. I chan... Chad Berkley
11:51 AM Bug #3126: add R system installation to the Mac installer
This is now working on multiple computers. I'll send the installer out for others to test. Chad Berkley
10:53 AM Bug #3187: RExpression actor does not share focus
This will not be included in the branch of ptolemy (rel70b2) we are using to build kepler 1.0
Retargeting for after 1...
ben leinfelder
10:14 AM Bug #3211: Need XSLT stylesheet to build actor docs
created stylesheet and build target to build the actor documentation and an index to go with it. Chad Berkley

04/08/2008

05:59 PM Bug #3215 (Resolved): Spaces in KEPLER path causes build problems
Aaron Schultz reports - when trying to build under windows (in eclipse) with spaces in the -DKEPLER variable, Config... Derik Barseghian
10:51 AM Bug #3207: consolidate command line execution actors
Hi Christopher,
Thanks for helping out. The Ptolemy Exec actor is called "External
Execution" in its KAR file, so th...
Daniel Crawl
10:38 AM Bug #3214: R actor does not handle single quotes in character string data
R allows the use of single or double quotes to indicate character strings. The RExpression actor was using single qu... ben leinfelder
10:34 AM Bug #3214 (Resolved): R actor does not handle single quotes in character string data
When string values (in my case they were from a RecordToken emitted by the EML actor) include single quotes (or apost... ben leinfelder
10:31 AM Bug #3213: R expression actor introduces leading/trailing whitespace
Added the "strip.white=TRUE" parameter to calls to the scan() method in the R code we generate when dealing with char... ben leinfelder
10:29 AM Bug #3213 (Resolved): R expression actor introduces leading/trailing whitespace
When a temporary file is used for caching length R commands, leading whitespace is being added. The list values: "OB... ben leinfelder
10:26 AM Bug #3212: EML2 Actor does not reconfigure available columns after initial download
Added calls to the generteLabelListAndTypteListFromColumns() [sic] method whenever the _columns variable was modified. ben leinfelder
10:24 AM Bug #3212 (Resolved): EML2 Actor does not reconfigure available columns after initial download
After the selected entity has been changed for the EML actor, the ports are reconfigured to show the available column... ben leinfelder
10:02 AM Bug #3209: ecogrid SearchRegistryAction error when disconnected from network
added messagehandler error reporting when the services registry is not available.
if, on start up, there is an error ...
ben leinfelder

04/07/2008

09:21 PM Bug #3210: add netCDF support to Kepler
The RExpression actor could also be used to read/write netCDF files using one of several netCDF packages available in... Dan Higgins
04:56 PM Bug #3156: RBNBToKepler actors should only download data for connected ports.
This has been fixed. I will close it when bug 3159 is closed. Derik Barseghian
04:55 PM Bug #3161: progress meter when downloading data with RBNBToKepler actors
I'm using org.ecoinformatics.seek.datasource.DataSourceIcon now, and the icon renders "Busy" when busy.
If this is ...
Derik Barseghian
04:51 PM Bug #3155: RBNBToKepler actors should allow different output formats
This has been added to the new DataTurbine actor.
Bug can be closed when bug 3159 is fixed.
Derik Barseghian
04:49 PM Bug #3140: RBNBToKepler2 actor output port generation problem
I believe these are the answers to my original questions:
1) Does one need to do a Fetch to get channel types?
Yes....
Derik Barseghian
03:39 PM Bug #3126: add R system installation to the Mac installer
This works on my computer, but for some reason not on other computers. not sure why. reopening the bug. Chad Berkley
11:36 AM Bug #3126: add R system installation to the Mac installer
The installer can now include and launch the R installer. I tried figuring out a way to not have to launch the R ins... Chad Berkley
10:46 AM Bug #3126: add R system installation to the Mac installer
I've got this mostly working now. Just adding some finishing touches. Chad Berkley
03:25 PM Bug #3211 (Resolved): Need XSLT stylesheet to build actor docs
Kirsten wants to include the actor documentation in an indexed PDF along with the release. We need to write an XSLT ... Chad Berkley
03:11 PM Bug #3198: test dynamic library installations on all platforms
does not work on ubuntu. need to figure out how to set the LD_LIBRARY_PATH with izpack. Chad Berkley
02:39 PM Bug #3198: test dynamic library installations on all platforms
tested on windows. works. Chad Berkley
02:15 PM Bug #3198: test dynamic library installations on all platforms
tested on osx. works. Chad Berkley
01:48 PM Bug #3209: ecogrid SearchRegistryAction error when disconnected from network
I'd say show an alert when something is trying to use a data source, e.g. the ecogrid actor. Otherwise, ignore it. Daniel Crawl
12:32 PM Bug #3144: add link in OSX Applications folder
I think that Kepler.app should be inside the Kepler folder mainly to keep the installed version looking like the CBS ... Dan Higgins
12:00 PM Bug #3144: add link in OSX Applications folder
Currently, Kepler is installed in /Applications/Kepler. The Kepler.app shortcut shows up in the Kepler folder. This... Chad Berkley
12:04 PM Bug #2872: md5 checksums
I will do this when the final installers are cut. Chad Berkley
12:03 PM Bug #3199: include R 2.6 in the installer
R 2.6.2 is now included in the windows and mac installer. We may want to have a non-R installer for both mac and win... Chad Berkley
09:26 AM Bug #3196: Find/Change license on gpl/lgpl code
IANAL, but my recollection of the LGPL is that you need to make the source code
available, but it is not necessary to...
Christopher Brooks
 

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