[R] Error: cannot allocate vector of size...

Tue Nov 10 18:10:14 CET 2009

On Tue, 10 Nov 2009, maiya wrote:

>
> OK, it's the simple math that's confusing me :)
>
> So you're saying 2.4GB, while windows sees the data as 700KB. Why is that
> different?

Your data are stored on disk as a text file (in CSV format, in fact), not as numbers. This can take up less space.

> And lets say I could potentially live with e.g. 1/3 of the cases - that
> would make it .8GB, which should be fine? But then my question is if there
> is any way to sample the rows in read.table? Or what would be the best way
> of importing a random third of my cases?

A better solution is probably to read a subset of the columns at a time.  The easiest way to do this is probably to read the data into a SQLite database with the 'sqldf' package, but another solution is to use the colClasses= argument to read.table() and specify "NULL" for the classes of the columns you don't want to read. There are other ways as well.

It might even be faster to do the cross-tabulations in a database and read the resulting summaries into R to compute any statistics you need.

> Thanks!
>
> M.
>
>
>
> jholtman wrote:
>> 
>> A little simple math.  You have 3M rows with 100 items on each row.
>> If read in this would be 300M items.  If numeric, 8 bytes/item, this
>> is 2.4GB.  Given that you are probably using a 32 bit version of R,
>> you are probably out of luck.  A rule of thumb is that your largest
>> object should consume at most 25% of your memory since you will
>> probably be making copies as part of your processing.
>> 
>> Given that, is you want to read in 100 variables at a time, I would
>> say your limit would be about 500K rows to be reasonable.  So you have
>> a choice; read in fewer rolls, read in all 3M rows but at 20 columns
>> per read, put the data in a database and extract what you need.
>> Unless you go to a 64-bit version of R you will probably not be able
>> to have the whole file in memory at one time.
>> 
>> On Tue, Nov 10, 2009 at 7:10 AM, maiya <maja.zaloznik at gmail.com> wrote:
>>>
>>> I'm trying to import a table into R the file is about 700MB. Here's my
>>> first
>>> try:
>>>
>>>> DD<-read.table("01uklicsam-20070301.dat",header=TRUE)
>>>
>>> Error: cannot allocate vector of size 15.6 Mb
>>> In addition: Warning messages:
>>> 1: In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,
>>>  :
>>>  Reached total allocation of 1535Mb: see help(memory.size)
>>> 2: In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,
>>>  :
>>>  Reached total allocation of 1535Mb: see help(memory.size)
>>> 3: In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,
>>>  :
>>>  Reached total allocation of 1535Mb: see help(memory.size)
>>> 4: In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,
>>>  :
>>>  Reached total allocation of 1535Mb: see help(memory.size)
>>>
>>> Then I tried
>>>
>>>> memory.limit(size=4095)
>>>  and got
>>>
>>>> DD<-read.table("01uklicsam-20070301.dat",header=TRUE)
>>> Error: cannot allocate vector of size 11.3 Mb
>>>
>>> but no additional errors. Then optimistically to clear up the workspace:
>>>
>>>> rm()
>>>> DD<-read.table("01uklicsam-20070301.dat",header=TRUE)
>>> Error: cannot allocate vector of size 15.6 Mb
>>>
>>> Can anyone help? I'm confused by the values even: 15.6Mb, 1535Mb, 11.3Mb?
>>> I'm working on WinXP with 2 GB of RAM. Help says the maximum obtainable
>>> memory is usually 2Gb. Surely they mean GB?
>>>
>>> The file I'm importing has about 3 million cases with 100 variables that
>>> I
>>> want to crosstabulate each with each. Is this completely unrealistic?
>>>
>>> Thanks!
>>>
>>> Maja
>>> --
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>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list
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>>>
>> 
>> 
>> 
>> -- 
>> Jim Holtman
>> Cincinnati, OH
>> +1 513 646 9390
>> 
>> What is the problem that you are trying to solve?
>> 
>> ______________________________________________
>> R-help at 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.
>> 
>> 
>
> -- 
> View this message in context: http://old.nabble.com/Error%3A-cannot-allocate-vector-of-size...-tp26282348p26283467.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at 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.

Thomas Lumley			Assoc. Professor, Biostatistics
tlumley at u.washington.edu	University of Washington, Seattle