[kepler-dev] A very thorny question..

Dan Higgins higgins at nceas.ucsb.edu
Thu Mar 29 14:53:14 PDT 2007

Hi Glen,

    Thank you for your comments. I agree that all the examples in the 
Getting Started Guide should work! I thought they did, at least for the 
Kepler-beta3 installer version on Windows. [I put together the 
installer.] I apparently made a mistake, because I see a problem with 
the BrowserDisplay actor replacement as you mentioned even on a Windows 
box with Beta3. However, the StatisticSummary example does work for me 
on Windows and the Windows installer does include R (not the nightly 
build, however). So it does apparently run for most Windows users (which 
are the majority of our users.) We may well want to include R with Mac 
and Linux versions in the eventual release. [The problem is the size of 
the installation as we keep adding more code; we do consider R to be 
very important and very useful.]

    What OS are you running? I have not seen your "File Error" message 
on the Mac or Linux when R is installed. Can you provide me further 
information on this?

Dan Higgins
NCEAS - UC Santa Barbara


Glen Jarvis wrote:
> I imagine this will not be an easy question to answer. And, I may get  
> different opinions from different people on how to approach the  
> problem. But, before I ask it, let me first take a few minutes to  
> frame the discussion. These questions are technical and are related to  
> infrastructure. I used the nightly build kepler20070325 in this  
> discussion. However, I saw the same problems on Beta3.
> As a new user to Kepler, I've been going through the "Getting Started  
> Guide." I am trying to build an environment for Biologist I work with  
> (and also as a project that I will need to write a classroom paper on)  
> that will be so easy to use it can easily replace BioPerl. After  
> spending a semester's work evaluating Wildfire, Infosense, the Apple  
> Automator, and even the Lego Mindstorms programmable block  
> environment, I found Kepler. It's *exactly* the framework I needed.  
> And, my purpose: To build an environment that is clean to use, has few  
> confusing messages, and a Biologist with little programming would not  
> be intimidated with. From the papers I read here, I know many  
> Biologists use Kepler as is. The Biologists I work with, however feel  
> intimidated by confusing messages and non-intuitive interfaces. They  
> want to get on with the Biology and not bogged down by the tools.
> While going through the "Getting Started Guide," I found it to be well  
> written and easy for me to use. I thought, "Gosh, this is almost not a  
> draft." I have made many notes about small things like parallelism,  
> missed words, etc. But, then, I discovered that the basic problems I  
> had from the beginning were all related to the same core situation.
> The only "real" problem with the Getting Started Guide was that many  
> of the examples didn't work. I thought that would be fixed once Kepler  
> was out of Beta. I now no longer believe this to be the case. I  
> believe the core problem is related to the interoperability between  
> systems and would like to know if several of the examples in the  
> Getting Started Guide could be rewritten to avoid the situation I will  
> explain.
> The first of two examples to show this case is the third demo, "Image  
> Display" example. On my first pass, I was naive and just thought that  
> "nothing happened." On a more recent pass of the guide, I dug into  
> more technical details and saw that when I replaced the ImageJ actor  
> with the Browser Display actor, the following is given to standard out:
>> Reading from the browser - val = false
>> Error invoking browser, cmd=netscape -remote  
>> openURL(file:///...distribution.PNG)
> Now, this makes perfect sense since I don't have netscape installed (I  
> use firefox). But, the more fundamental question is - Do we want to  
> use an example that depends upon a browser that will vary from system  
> to system? This will inevitably fail on some systems no matter how  
> good the Getting Started Guide is written. Ultimately, it's a great  
> demonstration. But, should it be in the first document that  is seen  
> by new users?
> The second of my two examples revolves around section 7.1 Sample  
> Workflow 1 - Simple Statistics.
> Upon the first run, I saw nothing happening again. Now, on a second  
> pass with a more technical mindset, I troubleshot and saw the  
> following displayed on standard out:
>> Problem with creating process in RExpression!
>> Error in _exec()
>> 54 ms. Memory: 142636K Free: 54674K (38%)
> The process couldn't be created because R was not installed on the  
> system. After installing R with default settings, I see the system now  
> work. However, there is an additional message "File Error: Could not  
> open the file." It doesn't stop the demonstration from working, but it  
> adds confusion to the situation. I'm sure I could resolve this as  
> well. But, the same question comes to mind. In an introduction to the  
> software, do we want to use something that involves other programs  
> outside of our normal control? Would we, in the future, include R as  
> part of the install and therefore avoid this issue? How important is  
> it for us to use an R example? Can we give just one example (instead  
> of many examples) that uses R that stresses boldly how it may fail if  
> R is not installed. If an initial user doesn't know what R is, or care  
> to use it, many of the examples will fail.
> In summary, these are the impressions from a new set of eyes. Kepler  
> is impressive as all heck and the framework I want to use for the  
> project that will probably take the next few years of my life. If I  
> learned nothing else in studying my second year of Bioinformatics, it  
> is that if a software looks too confusing, no matter how good it is,  
> my Biologists tell me they shy away from it. I'd like to see the  
> software work so well that it becomes the de facto standard like  
> BioPerl is.
> Warmest Regards,
> Glen
> P.S. Kirsten, I still have about a zillion notes I made on reading the  
> guide (like parallelism, some omitted words, etc.). But, they seem so  
> insignificant compared to the big issues seen in this email.

Dan Higgins                                  higgins at nceas.ucsb.edu
http://www.nceas.ucsb.edu/    Ph: 805-893-5127
National Center for Ecological Analysis and Synthesis (NCEAS) Marine Science Building - Room 3405
Santa Barbara, CA 93195

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