Ben,
Yes, R is in my path. Other R examples with plots work fine. In fact, in
00-StatisticalSummary.xml if I add a Display connected to the SummaryStatistics
'output' port, I get a text display with the following R output:
R> setwd('/home/twain/.kepler/')
R> png(filename = 'SummaryStatistics1.png',width = 480, height = 480, pointsize
= 12, bg = 'white')
R> x <- c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10)
R> xmean = mean(x)
R> xstd = sd(x)
R> xvar = var(x)
R>
So, I know R is running, but the Displays for the statistics all fail with the
following errors (repeated 3 times, once for each Display):
Problem sending to output port! java.lang.NullPointerException
java.lang.NullPointerException
at
org.ecoinformatics.seek.R.RExpression.setOutputToken(RExpression.java:906)
at org.ecoinformatics.seek.R.RExpression.getOutput(RExpression.java:791)
at org.ecoinformatics.seek.R.RExpression.fire(RExpression.java:735)
at ptolemy.actor.AtomicActor.iterate(AtomicActor.java:398)
at
ptolemy.actor.sched.StaticSchedulingDirector.fire(StaticSchedulingDirector.java:170)
at ptolemy.actor.CompositeActor.fire(CompositeActor.java:400)
at ptolemy.actor.Manager.iterate(Manager.java:688)
at ptolemy.actor.Manager.execute(Manager.java:332)
at ptolemy.actor.Manager.run(Manager.java:1071)
at ptolemy.actor.Manager$3.run(Manager.java:1112)
If R 2.20.1 works for you, it may be another system config problem, maybe the
64-bit OpenJDK with java 1.6.0?? The specific rpm I'm using is
java-1.6.0-openjdk-1.6.0.0-33.b17.fc11.x86_64.
Anyway, as the example works fine under Kepler-2.0-RC1, I won't worry about it
for now.
Tom
On 03/30/2010 06:51 PM, ben leinfelder wrote:
> Tom,
> While different versions of R do have subtle differences that can cause
> undesired behavior of the RExpression actor, I actually think it's not
> that esoteric of an issue that you're encountering.
> I've tried running the 00-StatisticalSummary.xml workflow with Kepler
> 1.0 and R 2.10.1 in the PATH on my system and it worked just fine.
> Can you verify that R is indeed on your PATH?
> Thanks,
> -ben
>
> On Mar 30, 2010, at 2:22 PM, Matt Jones wrote:
>
>> Hi Tom,
>>
>> Kepler 2.0.0 is being prepared for release, and is going through
>> testing. For that purpose, we are developing a series of release
>> candidates. These will not be supported after 2.0.0 comes out, but any
>> issues you find with them would be valuable to report to kepler-dev to
>> improve the quality of the release. Discussion of the new release
>> occurs on kepler-dev rather than kepler-users.
>>
>> For 1.0.0, the reason that you are probably having trouble is your R
>> version. Kepler 1.0.0 shipped with an earlier version of R (2.6.2),
>> and the R actor was fairly sensitive to the particular version used
>> (because different R versions serialize their output differently). I
>> believe that Ben has upgraded to R 2.10 for the 2.0.0 release series
>> (hopefully he'll confirm), which is why things probably work now for
>> you. This is just a guess on my part, but likely is related to the
>> problem. If you want 1.0.0 to work, install a parallel copy of the old
>> version of R and put it first on your path and I'll bet Kepler 1.0.0's
>> R functionality will work for you again.
>>
>> Matt
>>
>> On Tue, Mar 30, 2010 at 1:05 PM, Tom Wainwright
>> <Thomas.Wainwright at noaa.gov> wrote:
>> Hi,
>>
>> I have been trying to use Kepler 1.0.0 to organize some complicated
>> R-based analyses, and have run into some problems. In particular, the
>> "getting-started" example "00-StatisticalSummary.xml" produces no
>> output, and results in NullPointerException errors in the RExpression
>> class. (It worked last year, but not now--I am currently running
>> Fedora-11 x86_64 Linux, with R version 2.10.1 and java version
>> "1.6.0_17" OpenJDK.)
>>
>> Poking about, I found Kepler-2.0-RC1 on
>> http://dist.kepler-project.org/dist. I downloaded and ran it, and my
>> problem seems to be fixed.
>>
>> I haven't seen any public announcement about availability of the RC.
>> Is this something that is useable at this point? For learning and
>> early development, should I go ahead and use it, assuming bugs will be
>> fixed in the near future?
>>
>> Thanks!
>>
>> --
>> Tom Wainwright
>> NOAA Northwest Fisheries Science Center
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> The contents of this message are mine personally and do not necessarily
>> reflect any position of the Government or the National Oceanic and
>> Atmospheric Administration.
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> _______________________________________________
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>> Kepler-users at kepler-project.org
>> http://mercury.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
>>
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> _______________________________________________
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>
--
Tom Wainwright
NOAA Northwest Fisheries Science Center
Newport, Oregon
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The contents of this message are mine personally and do not necessarily
reflect any position of the Government or the National Oceanic and
Atmospheric Administration.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
