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From 05/03/2008 to 06/01/2008

05/30/2008

01:34 PM Bug #3349: RExpression getUniqueFileName functionality is broken
Fixed.
- added overloaded getUniqueFileName method that also takes portname as an argument.
- using this method, my...
Derik Barseghian
12:20 PM Bug #3349 (Resolved): RExpression getUniqueFileName functionality is broken
My fix to bug #3324 has broken getUniqueFileName functionality, so e.g. if you have two actors with the same name (e.... Derik Barseghian

05/29/2008

03:56 PM Bug #3324: RExpression actor doesn't output properly with >1 dataframe output port
Sorry -- fix was checked in may 27, not yesterday. Derik Barseghian
03:54 PM Bug #3324: RExpression actor doesn't output properly with >1 dataframe output port
Closing, I checked in a fix yesterday. Port name is now prefixed to filename when data is serialized to disk for data... Derik Barseghian
02:25 PM Bug #3339 (Resolved): directory param Browse button for External Execution actor doesn't work properly
The 'Browse' button for the directory parameter for this actor doesn't allow you to select a directory -- only a file... Derik Barseghian
11:01 AM Bug #3333 (New): "configure actor" dialog box changes after "documentation->display"
With a workflow loaded into Virgil, right click on an actor and select "Configure Actor". Note the contents of that d... Paul Allen

05/28/2008

08:56 PM Bug #3332: RExpression_Matrix_IO_Test workflow gives an error
I should note I'm seeing that error on stdout, not in the gui.
I have the same version of R as you on both Ubuntu an...
Derik Barseghian

05/27/2008

04:59 PM Bug #3332: RExpression_Matrix_IO_Test workflow gives an error
what version of R are you running?
I've got:
R version 2.6.2 (2008-02-08)
Copyright (C) 2008 The R Foundation for St...
ben leinfelder
04:54 PM Bug #3332 (Resolved): RExpression_Matrix_IO_Test workflow gives an error
RExpression_Matrix_IO_Test workflow gives this error. This bug slipped into Kepler release too.
java.lang.NumberFo...
Derik Barseghian
11:53 AM Bug #3324 (Resolved): RExpression actor doesn't output properly with >1 dataframe output port
If you configure the R actor to have more than 1 dataframe output port, only the last dataframe used is output throug... Derik Barseghian

05/22/2008

01:23 PM Bug #3312 (Resolved): DataTurbine (formerly RBNBToKepler) actor - error with empty server
DataTurbine actor gives an error when trying to connect to a server that is running but contains no data channels. It... Derik Barseghian

05/17/2008

08:02 PM Bug #3300: CompositeActor does not support multiport
You need to explicitly set the width of the input link inside the composite.
See below.
I've opened a RFE in Ptolem...
Christopher Brooks

05/16/2008

04:06 PM Bug #3300 (Resolved): CompositeActor does not support multiport
You can create a CompositeActor with input and output ports that are set as Multiports, but only the first value on t... ben leinfelder

05/13/2008

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

SEEK/garpModel_ImageJ, also gives a similar "Can't load IA 32-bit..." problem on ubuntu 8.04.
ENM/GARP_Multispecies...
Derik Barseghian
06:04 PM Bug #3292 (New): ENM/GDAL_h1K_NS workflow giving an exception
I upgraded to ubuntu 8.04 today, and now the GDAL_h1K_NS workflow is giving an exception (i'm using java 1.5.0_13).
...
Derik Barseghian
12:10 PM Bug #3291: IPCC_ChangeNightlyBuildTest got an exception
I have this problem too, on mac 10.5.2 and ubuntu 8.04. Derik Barseghian
11:43 AM Bug #3295 (New): Python/Ptolemnizer welcome text does not display
A minor annoyance, but the SampleDelay actor's "Welcome to the..." text is not displaying in the InteractiveShell as ... Derik Barseghian

05/12/2008

12:33 PM Bug #3290: DarwinCore_test workflow takes forever to downloading data
I put a general disclaimer in the demos directory so that this will not delay the release. Chad Berkley
12:33 PM Bug #3291: IPCC_ChangeNightlyBuildTest got an exception
I put a general disclaimer in the demos directory so that this will not delay the release. Chad Berkley
12:31 PM Bug #2872: md5 checksums
done. Chad Berkley
12:31 PM Bug #3122: Get installer size down
Installer sizes are as follows:
-rw-r--r-- 1 berkley berkley 104866787 2008-05-12 11:04 kepler-linux-1.0.0.jar
-rw-...
Chad Berkley
09:41 AM Bug #3266: ENM/GARP_MultipleSpecies-V.xml problems
Matt and I have decided to go ahead an release these workflows with the
following annotation attached:
ATTENTION ENM...
Chad Berkley

05/09/2008

02:58 PM Bug #3290: DarwinCore_test workflow takes forever to downloading data
change to 1.0.0 Jing Tao
01:48 PM Bug #3290 (New): DarwinCore_test workflow takes forever to downloading data
DarwindCore actor in demos/ENM/DarwindCore_test.xml work-flow takes forever to downloading data (more than two hours)... Jing Tao
02:58 PM Bug #3291: IPCC_ChangeNightlyBuildTest got an exception
Change to 1.0.0 Jing Tao
02:57 PM Bug #3291 (New): IPCC_ChangeNightlyBuildTest got an exception
Running work-flow, demos/ENM/IPCC_Change_NightlyBuildTest.xml, got an exception. The supposed result is "true", but t... Jing Tao
11:33 AM Bug #3282: v3 installer intro says Kepler-1.0.0 1.0.0
looks good in win/mac v4 installer Aaron Aaron
10:44 AM Bug #3282: v3 installer intro says Kepler-1.0.0 1.0.0
It has gone in mac v4 installer. Jing Tao
11:23 AM Bug #3252: Ptolemy ack in installer splash screen has typos and was outdated
Looks good in win and mac v4 installers Aaron Aaron
10:49 AM Bug #3252: Ptolemy ack in installer splash screen has typos and was outdated
It looks good now in mac v4 installer. Jing Tao
11:17 AM Bug #3269: authentication system throws NPE
It worked fine in mac v4 installer. Jing Tao
11:16 AM Bug #3271: Random Errors with data authentication system
In mac v4 installer, it seemed fine. Jing Tao
11:07 AM Bug #3270: disable DIGIR Data Source by default
works in mac v4 installer. Jing Tao
05:40 PM Bug #3122: Get installer size down
the files in lib/jar/base-jars/apache/xalan.jar (~1 MB) are included in lib/jar/jwsdp/xalan.jar (~7 MB) and could lik... Aaron Aaron

05/08/2008

03:28 PM Bug #3266: ENM/GARP_MultipleSpecies-V.xml problems
Chad - As the creator of this workflow, I should have great insights into what is wrong - but I don't!
I would guess ...
Dan Higgins
01:35 PM Bug #3266: ENM/GARP_MultipleSpecies-V.xml problems
This complex workflow depends on a lot of external dependencies. If any one of them fail, the workflow fails. I've ... Chad Berkley
09:56 PM Bug #3266: ENM/GARP_MultipleSpecies-V.xml problems
jing and ben - did you get ubuntu crashes after following the expat and scew instructions?
chad - i followed those bu...
Derik Barseghian
01:38 PM Bug #3269: authentication system throws NPE
Looks ok here, we'll see what happens in the next installer... Aaron Aaron
09:25 AM Bug #3269: authentication system throws NPE
Was able to see the errors on my local workspace version (thank goodness). I've added synchronized to the Ecogridser... ben leinfelder
06:42 PM Bug #3269: authentication system throws NPE
Works on win v3 installer.
On mac when I did the search a second time, after restarting kepler, it hangs for a long ...
Aaron Aaron
11:28 AM Bug #3122: Get installer size down
I notice that standalone-compiler.jar (~4 mb) is still in the installer version. Not sure if this is needed after iz... Aaron Aaron
10:27 AM Bug #3253: IzPack Windows Installer should install in a directory with the version number
i rechecked this and it is doing what it is supposed to do. Chad Berkley
10:26 AM Bug #3248: .sh files should be removed for windows installer
added a line to the install.xml and build.xml files to make sure the .sh Chad Berkley
09:02 AM Bug #3283: Welcome splash screen shows up when starting windows kepler
It doesn't show up if you have a .ptolemyII directory with a PtolemyPreferences.xml file in it. If you remove that d... Chad Berkley
09:59 PM Bug #3267: ENM/GARP_SingleSpecies_BestRuleSet-IV.xml problems
this may again be that i didn't succeed with the expat and scew instructions, but after trying those instructions thi... Derik Barseghian
06:01 PM Bug #3268: Python/PythonFileLineCounter.xml workflow problem
works on win and mac (v3 installer). Aaron Aaron

05/07/2008

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

05/06/2008

03:51 PM Bug #3278: Search result count is inflated when using both KNB sources ([un]authenticated)
I'm going to push this to 1.1. Since the auth query is off by default, it will rarely be seen and it's purely a cosm... Chad Berkley
02:48 PM Bug #3278 (New): Search result count is inflated when using both KNB sources ([un]authenticated)
The results get merged and duplicates are not shown in the result list, but the count does not match the results show... ben leinfelder
02:45 PM Bug #3271: Random Errors with data authentication system
closing this bug - not seeing crazy authentication errors nor race conditions when using the authenticated query.
wil...
ben leinfelder
10:07 AM Bug #3271: Random Errors with data authentication system
changed the ldap authentication gui to get away from static method calls (in favor of singleton getInstance calls tha... ben leinfelder
02:42 PM Bug #3277 (Resolved): Create reusable jython-based SelectionDialog actor to collect runtime parameters
Dan (Higgins) did a prototype of this use of the PythonScript actor to create Swing interfaces for displaying drop do... ben leinfelder
02:02 PM Bug #3276: MatlabExpression not finding ptmatlab.dylib
fixed bug in ptII code that was causing this. Chad Berkley
02:00 PM Bug #3266: ENM/GARP_MultipleSpecies-V.xml problems
added a note in the workflow and in the README about scew and expat on linux. Chad Berkley
01:59 PM Bug #3267: ENM/GARP_SingleSpecies_BestRuleSet-IV.xml problems
I added a note in the README and in the workflow itself about scew and expat for linux. Chad Berkley
11:29 AM Bug #3267: ENM/GARP_SingleSpecies_BestRuleSet-IV.xml problems
I was finally able to reproduce the crash on ubuntu by installing a fresh version of ubuntu in a VM and running keple... Chad Berkley
10:10 AM Bug #3273: Improve authentication dialogue so that the reason for authentication is clear
Now that some of the threading issues are being hammered out, this should be easier to work with.
Adding a message ar...
ben leinfelder
10:04 AM Bug #3269: authentication system throws NPE
actually found that this bug still existed as an artifact of multiple login dialogues appearing when concurrent threa... ben leinfelder
05:19 PM Bug #3274: IPCC_Base_Layers.xml work-flow gets out of memeory error
At end of January 2008, the src/org/ecoinformatics/ecogrid/queryservice/QueryServiceGetToStreamClient.java class some... Jing Tao

05/05/2008

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

05/04/2008

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

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