R devel - Aug 2011 - read.table segfaults

> fil2s <- read.table("../Data/fil2_s.txt", header = FALSE, sep
= "\t")
Program received signal SIGSEGV, Segmentation fault.
0x000000000041c2e1 in RunGenCollect (size_needed=8192000) at memory.c:1514
1514	    PROCESS_NODES();
(gdb)

 > sessionInfo()
R version 2.13.1 Patched (2011-08-25 r56798)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base
 >

The text file 'fil2_s.txt' is Huge, around 11 million records and 17
variables, but ...?



-- 
G?ran Brostr?m

It does look like you've got a memory issue. perhaps using 
  as.is=TRUE, and/or stringsAsFactors=FALSE will help as optional arguments
to read.table

if you don't specify these sorts of things, R can have to look through the
file and figure out which columns are characters/factors etc and so the
larger files cause more of a headache for R I'm guess. Hopefully someone
else can comment further on this? I'd true toggling TRUE/FALSE for as.is and
stringsAsFactors.

   do you have other objects loaded in memory as well? this file by itself
might not be the problem - but it's a cumulative issue. 
   have you checked the file structure in any other manner?
   how large (Mb/kb) is the file that you're trying to read?
   if you just read in parts of the file, is it okay?
      read.table(filename,header=FALSE,sep="\t",nrows=100)
      read.table(filename,header=FALSE,sep="\t",skip=20000,nrows=100)



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Another one:

The 'death.RData' was created about a year ago, but ...? Same info as
below.

G?ran
> load("../Data/death.RData")
> summary(death)
 *** caught segfault ***
address 0x40000e04959, cause 'memory not mapped'

Traceback:
 1: match(x, levels)
 2: factor(a, levels = ll[!(ll %in% exclude)], exclude = if (useNA =  
"no") NA)
 3: table(object)
 4: summary.factor(X[[6L]], ...)
 5: FUN(X[[6L]], ...)
 6: lapply(as.list(object), summary, maxsum = maxsum, digits = 12,     ...)
 7: summary.data.frame(death)
 8: summary(death)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:


2011/8/26 G?ran Brostr?m <goran.brostrom at
gmail.com>:
> ?> fil2s <- read.table("../Data/fil2_s.txt", header =
FALSE, sep = "\t")
>
> Program received signal SIGSEGV, Segmentation fault.
> 0x000000000041c2e1 in RunGenCollect (size_needed=8192000) at memory.c:1514
> 1514 ? ? ? ?PROCESS_NODES();
> (gdb)
>
> ?> sessionInfo()
> R version 2.13.1 Patched (2011-08-25 r56798)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> ?[1] LC_CTYPE=en_US.UTF-8 ? ? ? LC_NUMERIC=C
> ?[3] LC_TIME=en_US.UTF-8 ? ? ? ?LC_COLLATE=en_US.UTF-8
> ?[5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=en_US.UTF-8
> ?[7] LC_PAPER=en_US.UTF-8 ? ? ? LC_NAME=C
> ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base
> ?>
>
> The text file 'fil2_s.txt' is Huge, around 11 million records and
17
> variables, but ...?
>
>
>
> --
> G?ran Brostr?m
>


-- 
G?ran Brostr?m