R 2.10.0: Error in gsub/calloc

Gabor,

What about the error message that I got with strapply? ?That seemed to be the
same kind of problem (i.e., integer overflow of index) as with gsub.

Regards,
Richard

On Fri, 6 Nov 2009 08:00:06 -0500, Gabor Grothendieck wrote

Note that strapply without perl = TRUE runs an order of magnitude
faster than with perl = TRUE and takes nearly the same set of regular
expressions anyways since its default is tcl regular expressions.
strsplit should still be fastest where it applies since splitting is
its only purpose.

On Fri, Nov 6, 2009 at 1:43 AM, Richard R. Liu <richard.liu at pueo-
owl.ch> wrote:

Bert,

Thanks for the tip. ?Yes, strsplit works, and works fast! ?For me,
white-space tokenization means splitting at the white spaces, so the "^" and
the outermost square brackets should/can be omitted.

Regards ... from Basel to South San Francisco,
Richard

On Nov 3, 2009, at 22:03 , Bert Gunter wrote:

Try:

tokens <- strsplit(d,"[^[:space:]]+")

This splits each "sentence" in your vector into a vector of groups of
whitespace characters that you can then play with as you described, I
think
(The results is a list of such vectors -- see strsplit()).

## example:

x <- "xx ?xdfg; *&^%kk ? ?"

strsplit(x,"[^[:blank:]]+")

[[1]]
[1] "" ? ? " ?" ? " " ? ?" ? ?"


You might have to use PERL = TRUE and "\\w+" depending on your locale and
what "[:space:]" does there.

If this works, it should be way faster than strapply() and should not have
any memory allocation issues either.

HTH.

Bert Gunter
Genentech Nonclinical Biostatistics



-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
On
Behalf Of Richard R. Liu
Sent: Tuesday, November 03, 2009 11:32 AM
To: Uwe Ligges
Cc: r-help at r-project.org
Subject: Re: [R] R 2.10.0: Error in gsub/calloc

I apologize for not being clear. ?d is a character vector of length
158908. ?Each element in the vector has been designated by sentDetect
(package: openNLP) as a sentence. ?Some of these are really
sentences. ?Others are merely groups of meaningless characters
separated by white space. ?strapply is a function in the package
gosubfn. ?It applies to each element of the first argument the regular
expression (second argument). ?Every match is then sent to the
designated function (third argument, in my case missing, hence the
identity function). ?Thus, with strapply I am simply performing a
white-space tokenization of each sentence. ?I am doing this in the
hope of being able to distinguish true sentences from false ones on
the basis of mean length of token, maximum length of token, or similar.

Richard R. Liu
Dittingerstr. 33
CH-4053 Basel
Switzerland

Tel.: ?+41 61 331 10 47
Email: ?richard.liu at pueo-owl.ch


On Nov 3, 2009, at 18:30 , Uwe Ligges wrote:

richard.liu at pueo-owl.ch wrote:

I'm running R 2.10.0 under Mac OS X 10.5.8; however, I don't think
this
is a Mac-specific problem.
I have a very large (158,908 possible sentences, ca. 58 MB) plain
text
document d which I am
trying to tokenize: ?t <- strapply(d, "\\w+", perl = T). ?I am
encountering the following error:

What is strapply() and what is d?

Uwe Ligges

Error in base::gsub(pattern, rs, x, ...) :
Calloc could not allocate (-1398215180 of 1) memory
This happens regardless of whether I run in 32- or 64-bit mode. ?The
machine has 8 GB of RAM, so
I can hardly believe that RAM is a problem.
Thanks,
Richard

--
Richard R. Liu
Dittingerstr. 33
CH-4053 Basel
Switzerland

Tel.: ?+41 61 331 10 47
Email: ?richard.liu at pueo-owl.ch