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Objects disappearing in my R work space

16 messages · Aldo, R. Michael Weylandt, Uwe Ligges +6 more

Aldo
# 
I am running MCMC chains with a self written MCMC algorithm. When I have
multiple R terminals open while running the Chain, when it finishes it is
not there. when I press ls() it does not show up and when I type the Name it
says the Object is not found. I assume It is unrecoverable... but how do I
stop it from happening in the future?

Thanks

Mike 

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R. Michael Weylandt
# 
Can you say more about how your algorithm is implemented? If it's
wrapped in a function, the result might disappear with the end of the
function's environment. I don't think having multiple R sessions would
be a problem...it's never been for me.

Michael
On Thu, Nov 24, 2011 at 10:50 AM, Aldo <michael.v.clawson at gmail.com> wrote:
Aldo
# 
It works when I do not have multiple windows open, but is not there when I do
have multiple windows open, so I dont think it has to do with the
function.... The function is pretty complicated but I can share more if you
think it will help

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Uwe Ligges
#
On 25.11.2011 05:07, Aldo wrote:
Please read the posting guide! You failed to follow in multiple way, 
most important one so far: quote the thread! We do not know your 
original question nor the answers you got so far. This is the R mailing 
list that is sometimes misused by Nabble user, unfortunately.

Please define "multiple windows".  Do you mean graphics devices, R 
instances, ...?
Actually, the posting guide asks you to provide commented, *minimal*, 
self-contained, reproducible code.

Uwe Ligges
Uwe Ligges
#
On 25.11.2011 05:12, Aldo wrote:
????
So you mean you open a million windows at the same time? In that case we 
really need your definition of "window".
I do not know if any OS / window manager has the capability to open that 
many numbers of windows. But as I said, we need some difintions and 
examples.

Uwe Ligges
Uwe Ligges
#
On 25.11.2011 16:08, Michael Clawson wrote:
Please: "provide commented, minimal, self-contained, reproducible code."

Uwe Ligges
David Winsemius
#
On Nov 25, 2011, at 10:08 AM, Michael Clawson wrote:

            

      
      
      
    

        
It would probably be better to adopt the terminology that the things  
you are calling "windows" are "sessions".

            

      
      
      
    

        
The most common cause of that behavior is failing to assign the output  
of a function to a name. There is an object named ".Last.value" that  
hosld the results of the last returned object even it it doesn't have  
another name.

lapply(1:10,  I)
test <- .Last.value
test
[[1]]
[1] 1

[[2]]
[1] 2
snipped rest of output

But as Uwe said ... without the code, ... and your OS (to answer the  
question about memory)  .... and your sessionInfo() to make sure that  
this is not a GUI-related issue ... we cannot say very much.

            

      
      
      
    

        
David Winsemius, MD
West Hartford, CT

  
  


  


      

    

    

      
      

        
      

    

    

      
      

        


  

        

      Ben Bolker
    

    

      
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Michael Clawson <michael.v.clawson <at> gmail.com> writes:

            

      
      
      
    

        
Reproducible is essential, minimal is strongly recommended.  The more you
can pare down your code, the more likely it is is that someone will actually
take the time to take a look at it and see what's going on.
  Are you using an external program (JAGS, WinBUGS, etc.) or writing to 
external files that might be getting clobbered by other instances when
you have more than one instance running at once?

  
  


  


      

    

    

      
      

        


  

        

      Duncan Murdoch
    

    

      
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On 11-11-25 1:03 PM, Michael Clawson wrote:

            

      
      
      
    

        
I don't understand.  If you can't make your code simple enough to post, 
how do you think we can possibly imagine what you're doing?

Duncan Murdoch

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Rolf Turner
    

    

      
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On 26/11/11 12:19, Duncan Murdoch wrote:

            

      
      
      
    

        
This *has* to be a fortune!!!:

            

      
      
      
    

        
cheers,

         Rolf Turner

  
  


  


      

    

    

      
      

        


  

        

      jim holtman
    

    

      
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One thing is to define "missing" a little better.  For example, as
mentioned previously, are you returning the values from a function
call?  If you, print out an indication that they exist at that point.
If there is further processing happening, put some checks as to their
existance as the code continues.  Can you localize where this is
happening?  If they are "disappearing", then there is something you
are doing in your code to most likely make it happen.  Until there is
something that people can reproduce, there are all types of theories
we can expound on.

If I was looking at the code, I could probably put checks in at
various points to see in what section these things disappeared.  Do
you have some 'try' functions around parts of the code that might not
be reporting some error conditions?  So probably until you can provide
something that we can at least look at, and exactly how you determined
that something disappeared, there is probably not much more we can do
at this point.

On Fri, Nov 25, 2011 at 6:19 PM, Duncan Murdoch

        
<murdoch.duncan at gmail.com> wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        
      

    

    

      
      

        


  

        

      jim holtman
    

    

      
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at least put

print(str(Samples))

right after the function call to make sure it is there, and if you
have more code after that, sprinkle that print statement in the
following code.  You might at least send the code and indicate where
you have tested to see if the object is still there.

So put some of those print statements to help isolate what section of
code the problem is happening in  because just saying it disappears is
not sufficient.  This is elementary debugging of a program.  If your
program is as big and complicated as you say, then you have to start
learning some debugging techniques to help you find where the problem
is.

On Fri, Nov 25, 2011 at 7:48 PM, Michael Clawson

        
<michael.v.clawson at gmail.com> wrote: