Re: [R] fisher.test FEXACT error 7

[Ken Edwards]

Thanks Sundar,
That changes the behaviour of R, but only in so far as it waits longer 
before giving the same error:

fisher.test(testDataTwoColumns, workspace = 2e8)
Error in fisher.test(testDataTwoColumns, workspace = 2e+08) :
       FEXACT error 7.
LDSTP is too small for this problem.
Try increasing the size of the workspace.
...There also seems to be an upper limit of how big the workspace can be...
> fisher.test(testDataTwoColumns, workspace = 2e9)
Error in fisher.test(testDataTwoColumns, workspace = 2e+09) :
       negative length vectors are not allowed
> fisher.test(testDataTwoColumns, workspace = 2e10)
Error in fisher.test(testDataTwoColumns, workspace = 2e+10) :
       NAs in foreign function call (arg 10)
In addition: Warning message:
NAs introduced by coercion
A further question - do you (or anyone else) think that this is a 
problem with the physical capabilities of the box that I'm running on, 
or is it likely to be an upper limit with the amount of data that the 
algorithm can handle? 

Many thanks,
Ken
Sundar Dorai-Raj wrote:

Ken Edwards wrote:
Hello,
I have an error message that doesn't seem to make sense in that 
having read the R documentation I was under the impression that R was 
able to grab as much memory as it needed, and has been able to do so 
for some time, so the advice given below about increasing the size of 
the workspace is redundant.
If I'm right, does anyone have a solution to the problem of the size 
of LDSTP?  Or is this really a message about the limit of data size 
that the function can handle?

I have tried the function using test data containing a similar number 
of (randomly generated) data points, and it worked then. There are 
258 data points in two columns (i.e. 2 * 134), if that helps.

Any advice would be very much appreciated,
Many thanks,
Ken Edwards.
R script below:
fisher.test(testData)
Error in fisher.test(testData) :
       FEXACT error 7.
LDSTP is too small for this problem.
Try increasing the size of the workspace.
Maybe you should try increasing the workspace:
fisher.test(testData, workspace = 2e6)
--sundar

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