r-devel-requ...@r-project.org wrote:
Impressive stuff. Nice to see people giving some though to this.
I will explore the packages you mentioned.
Thank you
Saptarshi Guha
On Mon, May 11, 2009 at 12:37 AM, Patrick Aboyoun <paboy...@fhcrc.org> wrote:
Saptarshi,
I know of two alternatives you can use to do fast extraction of consecutive
subsequences of a vector:
1) Fast copy: ?The method you mentioned of creating a memcpy'd vector
2) Pointer management: Creating an externalptr object in R and manage the
start and end of your data
If you are looking for a prototyping environment to try, I recommend using
the IRanges and Biostrings packages from the Bioconductor project. The
IRanges package contains a function called subseq for performing 1) on all
basic vector types (raw, logical, integer, etc.) and Biostrings package
contains a subseq method on an externalptr based class that implements 2.
I was going to lobby R core members quietly about adding something akin to
subseq from IRanges into base R since it is extremely useful for all long
vectors and could replace all a:b calls with a <= b in R code, but this
publicity can't hurt.
The Python development team has been developing something similar for
python 3.0 (Buffer and Memoryview), and they are backporting it to the
latest 2.x releases.
I have just started toying with it, and it seems looking very nice.
There might be good ideas to take from there into a possible R built-in
capability.
L.
Here is an example:
source("http://bioconductor.org/biocLite.R";)
biocLite(c("IRanges", "Biostrings"))
<< download output omitted >>
suppressMessages(library(Biostrings))
x <- rep(charToRaw("a"), 1e7)
y <- BString(rawToChar(x))
suppressMessages(library(Biostrings))
x <- rep(charToRaw("a"), 1e7)
y <- BString(rawToChar(x))
system.time(x[13:1e7])
? user ?system elapsed
?0.304 ? 0.073 ? 0.378
system.time(subseq(x, 13))
? user ?system elapsed
?0.011 ? 0.007 ? 0.019
system.time(subseq(y, 13))
? user ?system elapsed
?0.003 ? 0.000 ? 0.004
identical(x[13:1e7], subseq(x, 13))
[1] TRUE
identical(x[13:1e7], charToRaw(as.character(subseq(y, 13))))
[1] TRUE
sessionInfo()
R version 2.10.0 Under development (unstable) (2009-05-08 r48504)
i386-apple-darwin9.6.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base
other attached packages:
[1] Biostrings_2.13.5 IRanges_1.3.5
loaded via a namespace (and not attached):
[1] Biobase_2.5.2
Quoting Saptarshi Guha <saptarshi.g...@gmail.com>:
Hello,
Suppose in the following code,
PROTECT(sr = R_tryEval( .... ))
sr is a RAWSXP vector. I wish to return another RAWSXP starting at
position 13 onwards (base=0).
I could create another RAWSXP of the correct length and then memcpy
the required bytes and length to this new one.
However is there a more efficient method?
Regards
Saptarshi Guha
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