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help about the dist() error message

4 messages · Meng Xue, Thomas Lumley, Douglas Bates

Meng Xue
# 
hello,

I have a problem when call dist() of package mva on a large data
set. The following error message are obtained when I use dist()
on m, a two dimensional data set with the size 100,000. It seems
that the length of vector out of bound, since when I compute
dist on small data set(10,000), it works well. but for large
data set, it   exit with the message "negative length vector are
not allowed" .

Could you please give me an idea about how to solve it? Thanks
in advance.
Meng 
****error message***
Error in vector("double", length) : negative length vectors are
not allowed
In addition: Warning message: 
NAs introduced by coercion
Thomas Lumley
#
On Wed, 16 Apr 2003, Meng Xue wrote:

            

      
      
      
    

        
With 100,000 points there are 50 billion pairwise distances, which would
take at least 400 Gb of memory.  It probably wouldn't even fit on your
disk, let alone in memory.

You need to work out why you want the pairwise distances and decide what
you can do instead.

	-thomas

  
  


  


      

    

    

      
      

        


  

        

      Douglas Bates
    

    

      
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Thomas Lumley <tlumley at u.washington.edu> writes:

            

      
      
      
    

        
You exaggerate.  It's a mere 40 GB, I believe.

            

      
      
      
    

        
[1] 39999600000

            

      
      
      
    

        
[1] 37.25253

  
  


  


      

    

    

      
      

        


  

        

      Thomas Lumley
    

    

      
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On 16 Apr 2003, Douglas Bates wrote:

            

      
      
      
    

        
Ok. I should use R rather than doing mental arithmetic.  There might well
be sufficient virtual memory if Meng's machine is 64-bit and can address
it. :)


	-thomas