Ecoinformatics Redmine

03/12/2010

11:01 AM Kepler Bug #4872: listen to director throws error

Oh, and it doesn't seem to cause any serious problems. Oliver Soong

11:00 AM Kepler Bug #4872: listen to director throws error

I'm also seeing something like this when I run, sometimes. I get:
java.lang.reflect.InvocationTargetException
... Oliver Soong

10:53 AM Kepler Bug #4881 (New): RExpression outputs [false] for any matrix of booleans

In an RExpression, add an output port "out" and use this R script:
out <- matrix(c(TRUE, FALSE, TRUE, FALSE), 2)
... Oliver Soong

10:45 AM Kepler Bug #4880 (New): RExpression cannot output matrix of strings

Create an RExpression with the output port "out" and for the script, use:
out <- matrix(letters, 2)
Looking at... Oliver Soong

10:37 AM Kepler Bug #4879 (New): RExpression replaces ) in string vectors with } when outputting to a port

In an RExpression, create the output port "out" and in the R script, use:
out <- c("(", ")")
Hooking this to a... Oliver Soong

03/05/2010

02:14 PM Kepler Bug #4872 (Resolved): listen to director throws error

Add an SDF Director and the Tools->Listen to Director. An error pops up on the console:
Error creating action fo... Oliver Soong

03/04/2010

02:23 PM Kepler Bug #4870 (New): searching for packages with the same name from multiple sources sometimes loses results

I have packages soong.4.14 and soong.28.5 on DEV and soong.4.15 and soong.28.9 on KNB. They all have the same title.... Oliver Soong

11:04 AM Kepler Bug #4869 (In Progress): changes made to workflows during dialogs before committing (Edit Parameters/Cancel)

When I make changes to an actor through the dialog, it seems like the changes are made to the workflow immediately, b... Oliver Soong

02/25/2010

03:45 PM Kepler Bug #4846: error opening kar from local repository

I also noticed that, after restarting Kepler, the KAR and local repository *are* listed in the components pane, but t... Oliver Soong

03:38 PM Kepler Bug #4846: error opening kar from local repository

I just noticed, but I'm getting 2 of these errors every time I save to the local repository:
ERROR (org.kepler.obje... Oliver Soong

02:50 PM Kepler Bug #4846 (Resolved): error opening kar from local repository

This is with wrp at r23202. I deleted .kepler and KeplerData. I create a trivial workflow (default SDF and RExpress... Oliver Soong

01:28 PM Kepler Bug #4801: out of memory

There's another way to trigger a memory leak. I'm not sure if these are 2 different leaks or 2 symptoms of the same ... Oliver Soong

02/24/2010

01:11 PM Kepler Bug #4832: python actor outputting to disconnected composite output throws error

I take back the part about it affecting the 2.0 branch. I can't keep my windows straight. It is affecting wrp. Oliver Soong

01:09 PM Kepler Bug #4832: python actor outputting to disconnected composite output throws error

This seems to affect the 2.0 Kepler branch. Oliver Soong

01:07 PM Kepler Bug #4832 (Resolved): python actor outputting to disconnected composite output throws error

I have a composite actor with an output port. Inside, I have an Expression passing a token to the default python act... Oliver Soong

02/22/2010

03:06 PM Kepler Bug #4820: Out of memory Error: Error creating alternateGetMoml!

How big is the KeplerData folder (specifically, KeplerData/modules/provenance), and if you try this again, do you get... Oliver Soong

02/18/2010

05:18 PM Kepler Bug #4812 (New): local repository KAR [right click]->Delete fails when file does not exist

Save a KAR to a local repository, then delete the file outside Kepler, then from the components tree right click the ... Oliver Soong

03:48 PM Kepler Bug #4804: copy/paste relation changes width from Auto to 1

I'm not 100% sure this is the same bug, but if I delete the actors and relation, then undo the change, the relation w... Oliver Soong

01:40 PM Kepler Bug #4810 (New): [right click]->Save Archive (KAR) on composite actor borks port attributes

Open the example MOML and save the composite actor as a KAR file. If you extract the MOML from the KAR, you'll see e... Oliver Soong

12:51 PM Kepler Bug #4809: Kepler storing authenticated search results

I'm not sure the search is being performed on the server. All I know is I'm not being asked to authenticate again. Oliver Soong

12:18 PM Kepler Bug #4809 (New): Kepler storing authenticated search results

From a clean cache, start Kepler and search using authenticated sources. Authenticate and Kepler will return search ... Oliver Soong

12:02 PM Kepler Bug #4808 (Resolved): ant clean-cache fails, NoClassDefFoundError, org/apache/commons/logging/LogFactory

Chris first reported this by e-mail, but I'm still seeing it. Aaron, svn says you put these lines in.
java.lang.N... Oliver Soong

11:49 AM Kepler Bug #4807 (Resolved): GetMetadata does nothing

Search for any data, right click on a search result, and select the only option, "GetMetadata". This does not seem t... Oliver Soong

02/17/2010

04:11 PM Kepler Bug #4806 (New): add output port to Throw Exception

In some of my workflows, I have an actor that checks that certain components are installed and working before trying ... Oliver Soong

03:52 PM Kepler Bug #4805 (Resolved): searching for data gives an NPE

I searched for Kruger on both KNB and DEV using both authenticated and unauthenticated searches. I authenticated as ... Oliver Soong

03:26 PM Kepler Bug #4804 (Resolved): copy/paste relation changes width from Auto to 1

Drag 2 actors to the canvas and join them with a relation. Copy the actors and relation and immediately paste it. T... Oliver Soong

02:57 PM Kepler Bug #4801: out of memory

After getting the out of memory error, I generated a heap histogram, restarted Kepler, and generated another heap his... Oliver Soong

02:13 PM Kepler Bug #4801 (In Progress): out of memory

ERROR: RecordingException: Unable to query data table: out of memory
I opened tpc01, ran it, closed it, opened tpc... Oliver Soong

12:26 PM Kepler Bug #4789: multiport input to composite actor seems to only pass first token

Inside the composite, the relation between the multiport and the RExpression has width 1. I'm not sure how or why it... Oliver Soong

11:26 AM Kepler Bug #4789: multiport input to composite actor seems to only pass first token

If I listen to the multiport input on the RExpression inside the composite, I see one token on a single channel. If ... Oliver Soong

10:03 AM Kepler Bug #4764: ProvenanceRecorder.changeExecuted slow after workflow run

I finally remembered that I can look directly at the provenance db while Kepler's running. I just deleted all the ru... Oliver Soong

02/12/2010

06:01 PM Kepler Bug #4764: ProvenanceRecorder.changeExecuted slow after workflow run

I think it's too big to attach, so I've put it here:
http://www.nceas.ucsb.edu/~soong/kepler/provenance%20HSQLDB%20... Oliver Soong

04:28 PM Kepler Bug #4764: ProvenanceRecorder.changeExecuted slow after workflow run

So I wiped my .kepler and KeplerData, started Kepler (to initialize these folders), and things ran "fast" (1-3 sec pe... Oliver Soong

04:04 PM Kepler Bug #4764: ProvenanceRecorder.changeExecuted slow after workflow run

Forgot to answer the question. Sort of. I can reproduce the 3000+ function calls, but they seem to resolve faster, ... Oliver Soong

03:41 PM Kepler Bug #4764: ProvenanceRecorder.changeExecuted slow after workflow run

That's correct and expected. recordContainerContents is initiated from changeExecuted, and it's recordContainerConte... Oliver Soong

08:54 AM Kepler Bug #4764: ProvenanceRecorder.changeExecuted slow after workflow run

It's in the Kruger SVN:
https://code.ecoinformatics.org/code/kruger/trunk/workflows/tpc09-plant-dynamics/tpc09-plant... Oliver Soong

05:29 PM Kepler Bug #4795: RExpression & cache cleaning

Zactly. Oliver Soong

05:14 PM Kepler Bug #4795: RExpression & cache cleaning

We could do away with the .sav files. Ben, try this in R:
str <- paste("_data.frame_:", rawToChar(serialize(iris, ... Oliver Soong

04:15 PM Kepler Bug #4795 (New): RExpression & cache cleaning

My .kepler cache bloats pretty quickly because of RExpression's temporary files. Can we have RExpression clear it's ... Oliver Soong

02/11/2010

09:51 PM Kepler Bug #4764: ProvenanceRecorder.changeExecuted slow after workflow run

The function recordContainerContents is the cause of the slow behavior. It is called from _recordWorkflowContents wh... Oliver Soong

07:21 PM Kepler Bug #4764: ProvenanceRecorder.changeExecuted slow after workflow run

I've tracked this down to the ProvenanceRecorder listener on the workflow NamedObj. After running tpc09, I change th... Oliver Soong

12:12 PM Kepler Bug #4764: ProvenanceRecorder.changeExecuted slow after workflow run

I profiled Kepler comparing an execution and an execution followed by a parameter change. First, I loaded tpc09 into... Oliver Soong

11:01 AM Kepler Bug #4789 (Resolved): multiport input to composite actor seems to only pass first token

See attached workflow. The problem is not likely to sit with RExpression itself, as I can move the RExpression actor... Oliver Soong