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From 03/27/2008 to 04/25/2008

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

04/04/2008

05:41 PM Bug #3196: Find/Change license on gpl/lgpl code
Apache-licensed code is generally redistributable in both source and binary forms (it is similar to BSD), although it... Matt Jones
05:31 PM Bug #3196: Find/Change license on gpl/lgpl code
Ok, we're looking more deeply into LGPL. Thanks, Christopher. I think we'll at least need to include the source code... Timothy McPhillips
03:04 PM Bug #3196: Find/Change license on gpl/lgpl code
I also thought that LGPL'd code should be acceptable.
But what about the Apache Licence, Kepler has a whole bunch o...
Dan Higgins
02:54 PM Bug #3196: Find/Change license on gpl/lgpl code
I might be confused, but I thought that LGPL code was ok to include
because it is non-viral
http://ptolemy.eecs.berke...
Christopher Brooks
02:39 PM Bug #3196: Find/Change license on gpl/lgpl code
The jar file lib/jar/cipres/jacorb.jar needs to be removed and dependencies on it satisfied some other way. The Jaco... Timothy McPhillips
05:01 PM Bug #2965: Ability to easily concatenate identical data structures (EMLDatasource)
I've worked with kevin to implement this in some of his workflows.
I've also packaged a custom R actor called "UnionA...
ben leinfelder
02:44 PM Bug #3154: Documentation missing for DarwinCoreDataSource
added documentation to the actor moml and also added method for pulling the documentation from the actor library for ... ben leinfelder
10:06 AM Bug #3209: ecogrid SearchRegistryAction error when disconnected from network
sounds like some error catching is in order. should there be an alert using MessageHandler (attack of the pop up win... ben leinfelder
10:00 AM Bug #3209 (Resolved): ecogrid SearchRegistryAction error when disconnected from network
About 30 seconds after starting kepler with no network connection, a long error
message is displayed, starting with:...
Daniel Crawl
10:05 AM Bug #3210 (New): add netCDF support to Kepler
Many scientific data sets are represented in netcdf format (http://www.unidata.ucar.edu/software/netcdf/). Kepler sh... Matt Jones
09:17 AM Bug #3208: consolidate matlab actors
I can help on this one.
Combining the two actors seems reasonable to me.
In addition, the expression language has a ...
Christopher Brooks
09:10 AM Bug #3208 (New): consolidate matlab actors
MatlabExpression and PtMatlabExpression both execute expressions
in matlab. They should be combined such that if the...
Daniel Crawl
09:12 AM Bug #3207: consolidate command line execution actors
The Ptolemy Exec actor also has duplicate functionality.
I looked at CommandLineExec and it looked like it
really nee...
Christopher Brooks
09:03 AM Bug #3207 (Resolved): consolidate command line execution actors
Command Line Exec and External Execution have different interfaces
but perform the same basic functionality. They sh...
Daniel Crawl

04/03/2008

04:30 PM Bug #3206 (Resolved): ecogrid error message occurs when running disconnected from network
[java] ERROR (org.ecoinformatics.seek.datasource.EcogridDataCacheItem:cleanUpCache:373) Couldn't close the output str... Daniel Crawl
01:51 PM Bug #3201: Remove all links to FSM from the GUI
It looks like this works. I'll close this, but if anyone has any objections to the way this works or thinks it break... Chad Berkley
01:46 PM Bug #3200: create a 1.0.0 branch in cvs
The branch is there. See kepler-dev email for checkin instructions. Chad Berkley
01:12 PM Bug #3167: Customize documentation fails when ports added
This seems to work for me. I might have fixed it and forgotten to close this bug. reopen this bug if it fails to wo... Chad Berkley
01:08 PM Bug #3138: remove the distributed options menu item for 1.0 release
both have now been removed from the release branch. Chad Berkley
09:24 AM Bug #3205 (New): gdalTranslate actor crashes on bad format and won't work with all gdal formats
Niels Hoffman reports that the gdalTranslate actor will not work with all of the current formats supported by gdal_tr... Chad Berkley
08:00 AM Bug #3203: Add dateType
See also https://chess.eecs.berkeley.edu/bugzilla/show_bug.cgi?id=141
"Plotter should be better about displaying times"
Christopher Brooks
06:44 AM Bug #2571: position of new elements on screen
One way to do this would be to translate the coordinates
relative to the location of the mouse.
Christopher Brooks
06:41 AM Bug #3110: Can't access actors via http
I can't replicate my own bug (Can't access actors via http),
so I'm closing this.
Christopher Brooks

04/02/2008

04:32 PM Bug #3162: ptExecuteConfig.xml depends on removed basicKeplerLibrary.xml
basicKeplerLibrary is not necessary to run ptexecute and has been removed from
ptExecuteConfig.xml.
Daniel Crawl
04:15 PM Bug #3097: incorrect classpath in generated ptexecute.sh and momlexecute.sh
I added a new target to the build file: 'ant build_wfexecute_sh' creates
wfexecute.sh, which accepts -gui/-nogui and ...
Daniel Crawl
09:13 AM Bug #3097: incorrect classpath in generated ptexecute.sh and momlexecute.sh
On the 1.0 release conference call, we discussed creating one shell script to replace all of the current ones. There... Chad Berkley
03:11 PM Bug #2509: FSM & Modal Model Menu selections do not work
I hadn't realized about the State button being on the toolbar. So it seems that we can successfully create an FSM. S... Matt Jones
02:47 PM Bug #2509: FSM & Modal Model Menu selections do not work
In Ptolemy, a State does appear in the left hand palette.
This state is not present in Kepler.
However, in both Ptol...
Christopher Brooks
02:28 PM Bug #2509: FSM & Modal Model Menu selections do not work
Actually, the problem was not with the menu item itself -- the problem is that when you create an FSM model, the acto... Matt Jones
02:17 PM Bug #2509: FSM & Modal Model Menu selections do not work
File | New Workflow | FSM Model
and
File | New Workflow | Modal Model
both work for me.
I'm marking this as fixed, ...
Christopher Brooks
08:59 AM Bug #2509: FSM & Modal Model Menu selections do not work
moving to post 1.0 Chad Berkley
02:19 PM Bug #3201: Remove all links to FSM from the GUI
Ok, I've fixed bug #3022 and bug #2509.
bug #3204 is a RFE for FSM examples to be added to Kepler
Unless someone ind...
Christopher Brooks
09:38 AM Bug #3201: Remove all links to FSM from the GUI
Mainly the reason is that we don't have time to re-integrate it and figure out all of the dependencies that we've bro... Chad Berkley
09:31 AM Bug #3201: Remove all links to FSM from the GUI
I feel that Kepler should ship with FSM.
What's the reasoning behind not shipping FSM?
There is this bug:
FSM State ...
Christopher Brooks
09:00 AM Bug #3201 (Resolved): Remove all links to FSM from the GUI
We are postponing re-adding the FSM items to kepler to post-1.0. All GUI items related to FSM should be removed from... Chad Berkley
02:15 PM Bug #3204 (New): Kepler should have FSM examples
Finite State Machines are very powerful, there should
be a Kepler-specific scientific workflow that
illustrates FSMs.
Christopher Brooks
11:31 AM Bug #3022: FSM State cannot be opened from context menu
The issue here is that in Ptolemy, the transition menu choices
are "Look Inside", not "Open Actor".
See bug #2110 f...
Christopher Brooks
08:58 AM Bug #3022: FSM State cannot be opened from context menu
moving to post 1.0. Chad Berkley
11:13 AM Bug #3203 (Resolved): Add dateType
Add a date type to Kepler; being able to pass date tokens between a variety of actors would be nice. My original moti... Derik Barseghian
10:50 AM Bug #3196: Find/Change license on gpl/lgpl code
Here are the GPL'd and LGPL'd sources Sean Riddle found in the
Kepler source tree (with known authors/copyright hold...
Timothy McPhillips
08:45 AM Bug #3196 (Resolved): Find/Change license on gpl/lgpl code
We need to find any code and/or libraries that currently are using gpl or lgpl as the license and negotiate with the ... Chad Berkley
10:30 AM Bug #2531: The link from Kepler intro page to the Ptolemy quick links page is broken
This bug is ready to be closed.
It should be checked in the release branch and then closed.
Christopher Brooks
10:16 AM Bug #2531: The link from Kepler intro page to the Ptolemy quick links page is broken
This bug could be assigned to me.
I just added CCodeGenerator to this list of classes to be
excluded in:
kepler/conf...
Christopher Brooks
08:51 AM Bug #2531: The link from Kepler intro page to the Ptolemy quick links page is broken
Ilkay will take this on. We basically need to make sure that any ptII demos that are actually linked to the kepler d... Chad Berkley
09:27 AM Bug #3172: windows mouse wheel doesn't scroll canvas
This is fixed in the ptII devel branch. See:
https://chess.eecs.berkeley.edu/bugzilla/show_bug.cgi?id=73
I believe ...
Christopher Brooks
09:13 AM Bug #3172: windows mouse wheel doesn't scroll canvas
This should be fixed with the other ui bugs that are outstanding. pushing this to 1.1. Chad Berkley
09:10 AM Bug #3149: cannot add arbitrary jars when exporting archive
postponing to 1.1.0 There are numerous items that need to be worked out with this bug. How the user interacts with ... Chad Berkley
09:09 AM Bug #3130: Add an accelerator (keyboard shortcut) for opening a new blank workflow
If this bug is easily fixable, do it. If not, postpone it. Chad Berkley
09:08 AM Bug #3115: Need to check Kepler for memory leaks
We should run each of the demo workflows with a memory usage analyzer to make sure that no major leaks are found with... Chad Berkley
09:06 AM Bug #3108: ENM GARP Baseline 3-Actor GARP - Browser Display demo fails with NameDuplication: convertTo?
We should not be linking to any workflows that do not work. All html links need to be checked and if any broken work... Chad Berkley
09:04 AM Bug #3126: add R system installation to the Mac installer
*** Bug 3101 has been marked as a duplicate of this bug. *** Chad Berkley
08:48 AM Bug #3126: add R system installation to the Mac installer
We should also try to get this to work with the NMI build. Chad Berkley
09:04 AM Bug #3101: Inclusion of R executable for Mac and Linux ?
duplicate bug of 3126
*** This bug has been marked as a duplicate of bug 3126 ***
Chad Berkley
09:03 AM Bug #3074: Code library installation issues
postponing this development until after 1.0. We just don't have the time to get this done. This will be something k... Chad Berkley
09:02 AM Bug #3202 (Resolved): Remove the workflows directory from the release
Many of the workflows in this directory are broken, and although they are useful as examples, we do not want to inclu... Chad Berkley
08:57 AM Bug #3144: add link in OSX Applications folder
also need to clean up the installer for osx. make sure no windows specific files are included. Sean also agreed to ... Chad Berkley
08:54 AM Bug #3200 (Resolved): create a 1.0.0 branch in cvs
We need a branch for 1.0 targeted development so that normal dev can go on in the head. Any items that need to be in... Chad Berkley
08:52 AM Bug #3122: Get installer size down
Try to locate all extraneous items and remove them from the installer. Chad Berkley
08:50 AM Bug #3199 (Resolved): include R 2.6 in the installer
We are currently including 2.4 in the windows installer. we'd like to upgrade that to 2.6 and also see if we can get... Chad Berkley
08:49 AM Bug #3198 (Resolved): test dynamic library installations on all platforms
Make sure that the dylibs work on windows, osx and linux and that they get put in the correct place by the installer. Chad Berkley
08:41 AM Bug #3195 (Resolved): Check all documentation for 1.0 release
All of the documentation needs to be checked for accuracy and completeness before the 1.0 release, which is currently... Chad Berkley

04/01/2008

06:22 PM Bug #3124: Automatically refresh ecogrid sources (endpoints) once per Kepler
data sources are now refreshed by a new thread that is scheduled to execute 30 seconds (configurable in config.xml) a... ben leinfelder
02:49 PM Bug #3124: Automatically refresh ecogrid sources (endpoints) once per Kepler
from 1.0.0 release meeting:
-at startup, queue a thread for refreshing the endpoints after a small delay (~minute)
ben leinfelder
03:39 PM Bug #3179: Distinguish "download" and "information" attribute values in eml distributlon online url
Here are solutions after the 04/01/2008 telephone conference:
1. Modify the query to exclude the eml packages which o...
Jing Tao
03:02 PM Bug #3192: behavior of documentation actor
I may have found the reason for the loss of my documentation after the first view in Windows XP. When I right-click ... Kevin Drury
03:01 PM Bug #3154: Documentation missing for DarwinCoreDataSource
-solicit information from Dave V. and Jing to flesh out documentation in the actor library
-include actor documentati...
ben leinfelder
10:11 AM Bug #3147: Get rid of Swing componets in Ecogrid data access classes
As ben said, this bug was fixed. Jing Tao

03/31/2008

11:58 PM Bug #3194 (New): add actors to support Sun Grid
Chirs Zhu <chris.zhu@sun.com> and others at Sun have contributed actors that allow Kepler to be used as a client for ... Matt Jones
04:38 PM Bug #3192 (New): behavior of documentation actor
Hello. The documentation actor will be an important component of workflows that outlive individual analyst's involve... Kevin Drury
03:00 PM Bug #3103: Building actor documentation from within Kepler fails
This is now fixed. The documentation can be edited with the Customize function. Chad Berkley
01:36 PM Bug #3187: RExpression actor does not share focus
I think you have it inverted. the frame _won't_ be null in our Kepler case for the R actor. The code block should b... ben leinfelder
01:16 PM Bug #3187: RExpression actor does not share focus
Ok, I put the setTitle inside the if block, so this might now work.
What we have is:
if (frame == null) {
...
Christopher Brooks
11:14 AM Bug #3187: RExpression actor does not share focus
It's less than ideal to have a bunch of open text editor windows all named "Unnamed".
But I think we can handle it fo...
ben leinfelder
12:43 PM Bug #3152: Use EcoGridServicesController with EcoGridWriter actor
retargeting for after 1.0 - not a high priority. ben leinfelder
12:38 PM Bug #3147: Get rid of Swing componets in Ecogrid data access classes
I believe this is fixed. There was spot in the EML actor that was using Swing directly, but I replaced that with Mes... ben leinfelder
12:18 PM Bug #3138: remove the distributed options menu item for 1.0 release
We should also remove the DCA actor from the tree to be sure it isn't used, and check the documentation to be sure we... Matt Jones
11:24 AM Bug #3184: right-click context menu in RExpression actor
the best solution for adding a feature like code commenting would be to use an external editor.
there's apparently a ...
ben leinfelder
11:17 AM Bug #3185: Ctrl-z does not "undo" in RExpression actor
This has been added in the ptolemy base classes now. ben leinfelder
11:16 AM Bug #3186: commit RExpression code changes, but leave actor open
Rather than just double clicking on the actor, if you "Open" the actor, the expression editing window will appear. c... ben leinfelder
11:15 AM Bug #3191: Merge TextEditor changes with ptII source
closing this bug - I'm happy with the undo/redo. (thanks, cxh) ben leinfelder

03/29/2008

08:53 PM Bug #3191: Merge TextEditor changes with ptII source
Ok, I updated Query, UndoListener and TextEditor in the ptII tree and
removed these files from kepler/src/exp/ptolemy...
Christopher Brooks
08:46 PM Bug #3187: RExpression actor does not share focus
The change to TextEditorTableau is marked below
if (frame == null) {
frame = new TextEditor(title...
Christopher Brooks

03/28/2008

02:48 PM Bug #3191 (Resolved): Merge TextEditor changes with ptII source
These changes from src/exp in Kepler should be included in the ptII tree:
src/exp/ptolemy/gui
Query.java
UndoL...
ben leinfelder

03/27/2008

04:54 PM Bug #3187: RExpression actor does not share focus
Until a change is included in ptII code (specifically ptolemy.actor.gui.TextEditorTableau), only one RExpresison text... ben leinfelder
03:26 PM Bug #3187: RExpression actor does not share focus
By using the ptolemy.actor.gui.TextEditor when "Open Actor" is invoked on the RExpression we can support having multi... ben leinfelder
03:28 PM Bug #3185: Ctrl-z does not "undo" in RExpression actor
from kepler-dev email that i sent:
---
After looking at this again, I realized it could be made even more
generic b...
ben leinfelder
10:19 AM Bug #3185: Ctrl-z does not "undo" in RExpression actor
Locally, I have implemented an UndoableEditListener for the JTextArea that is used in ptolemy.gui.Query along with so... ben leinfelder
03:09 PM Bug #3186: commit RExpression code changes, but leave actor open
Proposed implementation (working locally for me):
By using the ptolemy.actor.gui.TextEditor when "Open Actor" is invo...
ben leinfelder
 

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