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[Mark A. Beaumont]

Douglas Bates wrote:

>From 0.62 onward you should not have to create a symbolic link in
>/usr/local/bin.  It should be that you can run
> cd $RSOURCE
> ./configure --prefix=/usr/local
> make install
>and you will end up with the R script installed in /usr/local/bin and
>all the files needed to run R in /usr/local/lib/R.
>
>Can you tell what the prefix is set to after you run ./configure?
>
>BTW, the reason for these changes is to bring R more closely in line
>with the coding standards for GNU.  It is very helpful to be able to
>have the sources in one directory but make the installation in another
>directory, especially in a multi-architecture environment.

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:

>Some thing is clearly going wrong during the reading of the init code.
>The question is "where?". It *is* a bit of a design problem in R that
>that isn't readily seen.
>
>It could be in the reading of $RHOME/library/base/R/base which you
>might want to check looks reasonable. You could also try to run
>(from the top level of the R source tree) something like
>
>R> source('library/base/R/base',echo=T)

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.




>
>which should rerun the init code, but with echoing turned on, so that
>if it stops prematurely, you'll know why.
>
>It is somewhat unlikely that the base file should be the culprit,
>though, because it only defines a bunch of functions without actually
>executing anything except "<-".
>
>Perhaps something in the system Rprofile is doing you in. Again, try
>sourcing it with echo on. In particular, might there be a problem with
>getenv() on your system?

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

>
>Just to be sure, also check for stray .RData and .Rprofile files. If
>the former exists and is too large, that would explain it all by
>itself...

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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