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3 messages · Mark A. Beaumont, Peter Dalgaard

Original
Mark A. Beaumont
#
Douglas Bates wrote:

            

      
      
      
    

        
That is what I figured, which is why I did the make install, as described
in my earlier message,  but to no avail. According to the Makeconf file my
prefix is /usr/local. So now I have the actual R script in /usr/local/bin
and various bits and pieces in /usr/local/man/man1 and the R tree in
/usr/local/lib//R.

        
Peter Dalgaard wrote:

        

            

      
      
      
    

        
I have kept the 0.61.1 directory. Comparing /usr/local/lib/R/library/base/R
in 0.62.1
with the 0.61.1 equivalent, the Rprofile and base files seem pretty much
the same (though not exactly the same, obviously)


source('/usr/local/lib/R/library/base/R/base',echo=T) gives
Error: memory exhausted.

            

      
      
      
    

        
source( '/usr/local/lib/R/library/base/R/Rprofile',echo=T) also gives
Error: memory exhausted.

This is quite good, because Rprofile is short enough to copy  in line by
line.

Everything seems ok until
.Library <- paste(getenv("RHOME"), "library", sep= "/")
Error: memory exhausted

getenv("RHOME") gives "/usr/local/lib/R",  so getenv
does seem to be working.

The problem is with paste:
paste("the cat","sat on the mat")
Error, memory exhausted

            

      
      
      
    

        
There are no .RData and .Rprofile files in the directory I have been using.

For additional information:
gc() gives
Garbage collection ...
123580 cons cells free (61%)
1738k bytes of heap free (89%)

I am very grateful for your help and advice. Do you have any more
suggestions? Do you think there is a simple patch for paste?

All the best,
Mark



Mark A. Beaumont
Institute of Zoology
Zoological Society of London
Regent's Park
London NW1 4RY UK
Tel:  0171 449 6617
Fax: 0171 586 2870
m.beaumont at ucl.ac.uk


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      Mark A. Beaumont
    

    

      
      #
    

  


  

      
Peter Dalgaard wrote:

        

            

      
      
      
    

        
I have replaced the offending paste line in Rprofile with an assignment
to the appropriate string.

I then get the first prompt without a "memory exhausted" error, so it does
look as though this use of paste was causing the initial problem.

            

      
      
      
    

        
it looks fine

            

      
      
      
    

        
This produces

	> debug(paste)
	> paste("the cat","sat on the mat")
	debugging in: paste("the cat", "sat on the mat")
	debug: args <- list(...)
	Browse[1]>
	debug: if (is.null(args)) "" else {
            	for (i in 1:length(args)) args[[i]] <- as.character(args[[i]])
            	.Internal(paste(args, sep, collapse))
	}
	Browse[1]>
	debug: for (i in 1:length(args)) args[[i]] <- as.character(args[[i]])
	Browse[1]>
	Error: memory exhausted

Following on from Albrecht Gephardt's message, I find
1:3 gives "error: memory exhausted", similarly with seq(1,5).

Thus, it would appear that the problem lies somewhere in here. Though why
it should manifest itself in two different ways on our two systems is
rather mysterious. Could there be an obscure long/int problem somewhere?
People tend to forget that they have different lengths on an alpha.

            

      
      
      
    

        
Thats right.


All the best,
Mark

Mark A. Beaumont
Institute of Zoology
Zoological Society of London
Regent's Park
London NW1 4RY UK
Tel:  0171 449 6617
Fax: 0171 586 2870
m.beaumont at ucl.ac.uk


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r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !)  To: r-help-request at stat.math.ethz.ch
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      Peter Dalgaard
    

    

      
      #
    

  


  

      
"Mark A. Beaumont" <M.Beaumont at ucl.ac.uk> writes:

            

      
      
      
    

        
Yes, I'm suspecting something like that very strongly now. Albrecht
seems to have ':' always getting results of length 15 or 17, whereas
yours may be - er - longer... 

Everything seems to be explained by a miscomputation of n in the seq()
C function. If more or less random items are getting in there, it is
not all that strange that you and Albrecht are not getting exactly the
same type of trouble.

The next thing would be to scrutinize the seq  and asReal functions.