R devel - Dec 2009 - reshape() makes R run out of memory (PR#14121)

Full_Name: Alexander L. Belikoff
Version: 2.8.1
OS: Ubuntu 9.04 (x86_64)
Submission from: (NULL) (67.244.71.200)


I'm trying to reshape the following data frame:

ID                     DATE1             DATE2      VALUE_TYPE        VALUE
'abcd1233'         2009-11-12        2009-12-23     'TYPE1'     
123.45
...

VALUE_TYPE is a string and is a factor with only 2 values (say TYPE1 and TYPE2).
I need to transform it into the following data frame ("wide"
transpose) based on
common ID and DATEs:

ID                     DATE1             DATE2      VALUE.TYPE1   VALUE.TYPE2
'abcd1233'         2009-11-12       2009-12-23      123.45        NA
...

Using stock reshape() as follows:

    tbl2 <- reshape(tbl, direction = "wide", idvar =
c("ID", "DATE1", "DATE2"),
timevar = "VALUE_TYPE");

On a toy data frame this works fine. On a real one with 4.7 million entries
(although about 70% of VALUEs are NA) it runs out of memory:

    Error: cannot allocate vector of size 4.8 Gb

When the real data frame is loaded the R process takes about 200Mb of virtual
memory. The machine has 4 Gb of RAM.

I've posted a .Rdata file with the data frame in question at
http://belikoff.net/stuff/other/reshape_test.Rdata.gz


P.S. Just checked R 2.10.0 using an Intel PC with 2Gb RAM running Xp Pro (32
bit):
> tbl2 <- reshape(tbl, direction = "wide", idvar =
c("ID", "DATE1", "DATE2"),
timevar = "VALUE_TYPE");
Error: cannot allocate vector of size 53.9 Mb
In addition: Warning messages:
1: In format.POSIXlt(as.POSIXlt(x), ...) :
  Reached total allocation of 1535Mb: see help(memory.size)
2: In format.POSIXlt(as.POSIXlt(x), ...) :
  Reached total allocation of 1535Mb: see help(memory.size)
3: In format.POSIXlt(as.POSIXlt(x), ...) :
  Reached total allocation of 1535Mb: see help(memory.size)
4: In format.POSIXlt(as.POSIXlt(x), ...) :
  Reached total allocation of 1535Mb: see help(memory.size)
5: In format.POSIXlt(as.POSIXlt(x), ...) :
  Reached total allocation of 1535Mb: see help(memory.size)
6: In format.POSIXlt(as.POSIXlt(x), ...) :
  Reached total allocation of 1535Mb: see
help(memory.size)
>

abelikoff at gmail.com wrote:
> Full_Name: Alexander L. Belikoff
> Version: 2.8.1
> OS: Ubuntu 9.04 (x86_64)
> Submission from: (NULL) (67.244.71.200)
> 
> 
> I'm trying to reshape the following data frame:
> 
> ID                     DATE1             DATE2      VALUE_TYPE        VALUE
> 'abcd1233'         2009-11-12        2009-12-23     'TYPE1'
123.45
> ...
> 
> VALUE_TYPE is a string and is a factor with only 2 values (say TYPE1 and
TYPE2).
> I need to transform it into the following data frame ("wide"
transpose) based on
> common ID and DATEs:
> 
> ID                     DATE1             DATE2      VALUE.TYPE1  
VALUE.TYPE2
> 'abcd1233'         2009-11-12       2009-12-23      123.45       
NA
> ...
> 
> Using stock reshape() as follows:
> 
>     tbl2 <- reshape(tbl, direction = "wide", idvar =
c("ID", "DATE1", "DATE2"),
> timevar = "VALUE_TYPE");
> 
> On a toy data frame this works fine. On a real one with 4.7 million entries
> (although about 70% of VALUEs are NA) it runs out of memory:
> 
>     Error: cannot allocate vector of size 4.8 Gb
> 
> When the real data frame is loaded the R process takes about 200Mb of
virtual
> memory. The machine has 4 Gb of RAM.
> 
> I've posted a .Rdata file with the data frame in question at
> http://belikoff.net/stuff/other/reshape_test.Rdata.gz
> 
> 
> P.S. Just checked R 2.10.0 using an Intel PC with 2Gb RAM running Xp Pro
(32
> bit):
> 
>> tbl2 <- reshape(tbl, direction = "wide", idvar =
c("ID", "DATE1", "DATE2")c("ID",
"DATE1", "DATE2"),
> timevar = "VALUE_TYPE");
> Error: cannot allocate vector of size 53.9 Mb
> In addition: Warning messages:
....

Yes. The culprit would seem to be interaction(), as in

 > x <- y <- z <- 1:999
 > i <- interaction(x,y,z, drop=TRUE)
Error: cannot allocate vector of size 3.7 Gb

which is happening due to the occurrence of three idvar variables. This 
works basically as interaction(x,y,z)[,drop=TRUE], i.e. it first creates 
a factor with 999^3 levels, and removes the empty levels afterward.

In the absense of a better interaction(), you might try making your own 
single idvar as do.call("paste",tbl[,c("ID",
"DATE1", "DATE2")]) or so.

-- 
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   c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
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