Janet Choate-2 wrote:
>
> Thanx for clarification on stating my problem, Charlie.
>
> I am attempting to merge to files, i.e.:
> hi39 = merge(comb[,c("hillID","geo")], hi.h39, by=c("hillID"))
>
> if this is relevant or helps to explain:
> the file 'comb' is 3 columns and 1127 rows
> the file 'hi.h39' is 5 columns and 19758564 rows
>
> i started a new clean R session in which i was able to read those 2 files
> in, but get the following error when i try to merge them:
>
> R(2175) malloc: *** mmap(size=79036416) failed (error code=12)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
> R(2175) malloc: *** mmap(size=79036416) failed (error code=12)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
> R(2175) malloc: *** mmap(size=158068736) failed (error code=12)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
> R(2175) malloc: *** mmap(size=158068736) failed (error code=12)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
> R(2175) malloc: *** mmap(size=158068736) failed (error code=12)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
> Error: cannot allocate vector of size 150.7 Mb
>
> so the final error is "Cannot allocate vector of size 150.7 Mb", as
> suggested when R runs out of memory.
>
> i am running R version 2.9.2, on mac os X 10.5 - leopard.
>
> any suggestion on how to increase R's memory on a mac?
> thanx for any much needed help!
> Janet
>
Ah, so it is indeed a shortage of memory problem. With R 2.9.2, you are
likely running a 32 bit version of R which will be limited to accessing at
most 4 GB of RAM. You may want to try the newest version of R, 2.10.1, as
it includes a 64 bit version that will allow you to access significantly
more memory- provided you have the RAM installed on your system.
I'm not too hot on memory usage calculation, but someone else on this list
may be able to give you a ballpark estimate of how much RAM this merge would
require. If it turns out to be a ridiculous amount, you will need to
consider breaking the merge up into chunks or finding an out-of-core (i.e.
not dependent on RAM for storage) merge tool.
Hope this helps!
-Charlie
-----
Charlie Sharpsteen
Undergraduate-- Environmental Resources Engineering
Humboldt State University
--
View this message in context:
http://n4.nabble.com/memory-error-tp1747357p1747733.html
Sent from the R help mailing list archive at Nabble.com.
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
