documentation available that further explains error messages?

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

documentation available that further explains error messages?

Jeremy Claisse
I'm trying to figure out how to overcome this error message:
 
Error in optim(c(5, -0.5), llfunc.prop.female.age, method = "BFGS") :
  non-finite finite-difference value [2]
 
And particularly would like to know what the "[2]" is pointing towards, I'm
assuming that will help me search out the problem.  Is there any
documentation available that explains the particulars of error messages?
 
Thanks,
Jeremy
 
Jeremy Claisse
Hawaii Cooperative Fishery Research Unit
University of Hawaii
 <mailto:[hidden email]> [hidden email]
 


        [[alternative HTML version deleted]]

_______________________________________________
R-sig-ecology mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Reply | Threaded
Open this post in threaded view
|

Re: documentation available that further explains error messages?

Kingsford Jones
Hi Jeremy,

Since R is open source, the code is usually the best reference when
you can't decipher an error message.  Often the easiest way to see
what is going on is to type traceback() after receiving the error
message -- this will show you the calls that led to the error.

Another very useful tool is to type
debug(name.of.function.to.be.debugged) prior to calling the function
of interest.
The next time you use that function, debug will take you step-by-step
through the function calls while allowing full interactive ability so
you can, e.g. look at the structure of objects as they are created
within the function (using, e.g., the str function).

Another option is to open the function's source file in a text window
and use Find in your text editor to find the error.

Finally, searching for the error message in the help archives can
often be fruitful.  That technique just led me to this:

https://stat.ethz.ch/pipermail/r-help/2006-January/086747.html

which indicates what the '[2]' is referring to.


Kingsford Jones


On Wed, May 7, 2008 at 12:30 PM, Jeremy Claisse <[hidden email]> wrote:

> I'm trying to figure out how to overcome this error message:
>
>  Error in optim(c(5, -0.5), llfunc.prop.female.age, method = "BFGS") :
>   non-finite finite-difference value [2]
>
>  And particularly would like to know what the "[2]" is pointing towards, I'm
>  assuming that will help me search out the problem.  Is there any
>  documentation available that explains the particulars of error messages?
>
>  Thanks,
>  Jeremy
>
>  Jeremy Claisse
>  Hawaii Cooperative Fishery Research Unit
>  University of Hawaii
>   <mailto:[hidden email]> [hidden email]
>
>
>
>         [[alternative HTML version deleted]]
>
>  _______________________________________________
>  R-sig-ecology mailing list
>  [hidden email]
>  https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>

_______________________________________________
R-sig-ecology mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Reply | Threaded
Open this post in threaded view
|

Re: documentation available that further explains error messages?

Ben Bolker-3

   A couple more suggestions:

  Mark Bravington's "debug" package (mvbdebug, available
on CRAN) can be a more powerful debugging tool if you
want to do a more graphical stepping-through your code;

   a cruder but effective technique is to put a cat()
statement into your objective function, e.g.

  objfun <- function(params,...) {
   ## calculate neg log likelihood
   neg.log.likel <- ...
   cat(params[1],params[2],neg.log.likel,"\n")
   neg.log.likel
}

   that way you can see where the function is getting in
trouble.



Kingsford Jones wrote:

> Hi Jeremy,
>
> Since R is open source, the code is usually the best reference when
> you can't decipher an error message.  Often the easiest way to see
> what is going on is to type traceback() after receiving the error
> message -- this will show you the calls that led to the error.
>
> Another very useful tool is to type
> debug(name.of.function.to.be.debugged) prior to calling the function
> of interest.
> The next time you use that function, debug will take you step-by-step
> through the function calls while allowing full interactive ability so
> you can, e.g. look at the structure of objects as they are created
> within the function (using, e.g., the str function).
>
> Another option is to open the function's source file in a text window
> and use Find in your text editor to find the error.
>
> Finally, searching for the error message in the help archives can
> often be fruitful.  That technique just led me to this:
>
> https://stat.ethz.ch/pipermail/r-help/2006-January/086747.html
>
> which indicates what the '[2]' is referring to.
>
>
> Kingsford Jones
>
>
> On Wed, May 7, 2008 at 12:30 PM, Jeremy Claisse <[hidden email]> wrote:
>> I'm trying to figure out how to overcome this error message:
>>
>>  Error in optim(c(5, -0.5), llfunc.prop.female.age, method = "BFGS") :
>>   non-finite finite-difference value [2]
>>
>>  And particularly would like to know what the "[2]" is pointing towards, I'm
>>  assuming that will help me search out the problem.  Is there any
>>  documentation available that explains the particulars of error messages?
>>
>>  Thanks,
>>  Jeremy
>>
>>  Jeremy Claisse
>>  Hawaii Cooperative Fishery Research Unit
>>  University of Hawaii
>>   <mailto:[hidden email]> [hidden email]
>>
>>
>>
>>         [[alternative HTML version deleted]]
>>
>>  _______________________________________________
>>  R-sig-ecology mailing list
>>  [hidden email]
>>  https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>>
>
> _______________________________________________
> R-sig-ecology mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology


_______________________________________________
R-sig-ecology mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

signature.asc (260 bytes) Download Attachment