[R] error loading huge .RData

Liaw, Andy andy_liaw at merck.com
Wed Apr 24 14:17:06 CEST 2002


I appreciate your comments, and practice everything that you preach.
However, that workspace image contains only 2~3 R objects: the input and
output of a single R command.  I knew there could be problems, so I've
stripped it down to the bare minimum.  Yes, I also kept the commands in a
script.  That single command (in case you want to know: a random forest run
with 4000 rows and nearly 7000 variables) took over 3 days to run.  There's
not a whole lot I can do here when the data is so large.


> -----Original Message-----
> From: Patrick Connolly [mailto:P.Connolly at hortresearch.co.nz]
> Sent: Tuesday, April 23, 2002 7:18 PM
> To: andy_liaw at merck.com
> Subject: Re: [R] error loading huge .RData
> According to Liaw, Andy:
> |> 
> |> Dear R-help,
> |> 
> |> I've run into a problem loading .RData:  I was running a 
> large computation,
> |> which supposedly produce a large R object.  At the end of 
> the session, I did
> |> a save.image() and then quit.  The .RData has size 
> 613,249,399 bytes.  Now I
> |> can't get R to load this .RData file.  Whenever I tried, I 
> get "Error:
> |> vector memory exhausted (limit reached)".  I tried adding
> |> "--min-vsize=1000M", but that didn't help.  I also tried R 
>  --vanilla and
> |> then attach(".RData"), same error.
> |> 
> |> From what I can see, the file is not corrupted.  How can I 
> get R to load it?
> What would you look for to see if it's corrupted?  That's a big file
> to find it in.
> I've never used a .RData file greater than 100 Mb, so my experience is
> not directly comparable, but I feel uneasy having too much in one
> file.  It's a safer practice to make sure you keep a file of the
> commands you used to create your R objects so that it's easy (even if
> not quick) to reproduce them.  It's also good to keep not too many
> objects in one Data file.  I had only one occasion when I had a
> corrupt .RData file, but it was easy to recover.  The bigger the file,
> the more opportunity for corruption to happen.  How many objects would
> there have been in your .RData file?
> Might not be much help for now, but it might help in the future.
> best
> -- 
> *************************************************************
>    ___      Patrick Connolly
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