Simon,
as promised I attach a simple package that utilises gtkdatabox. It is
Linux only, sorry for that: as it was hacked together in the last two
hours I did not have time for Windows stuff.
Under my Ubuntu I only had to install libgtkdatabox-dev from standard
repos (which would pull libgtk2-de
tion
this is what I probably will have to do, reexport everything.
Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
oskl...@maninvestments.com
-Original Message-
From: Martin Morgan [mailto:mtmor...@fhcrc.org] Sent: 13 January 2009
16:31
To: Sklyar, Oleg (
ED]
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ed an R-SIG-HPC list? Anyone besides me interested?
I'd join.
Dirk
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d I did not find any related errors in my codes. How could this
happen and how can I fix it? Does this have to do with different
systems (linux vs windows) or C/R program?
Thank you in advance.
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Dr Oleg Sklyar * EBI-EMBL, Cambridge CB10 1SD, UK * +44-1223-494466
hanges
to vignette have not been significant and the compilation goes through
fine with 2.6.0.
Or I am missing something and doing something wrong?
Best,
Oleg
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R-devel
validity should return a character in case of errors
2) default initializer usually does the job
3) define constructors as methods to allow different signatures and
conversions from other classes
4) If you derive your class from numeric, rather than add slots,
the performance will be much better
27;s, like in STL vectors etc and then move it to SEXP at the end.
>
> Thanks again,
> Charles
>
> On Wed, Mar 5, 2008 at 11:14 AM, Oleg Sklyar <[EMAIL PROTECTED]> wrote:
>> Rblah in your example is a SEXP structure. Realloc is an interface to C
>> realloc an
;
> PROTECT(Rblah = blah);
>
> UNPROTECT(1);
> return(Rblah);
> }
>
> Any suggestions for someone still new to SEXP memory management?
>
> Thanks,
> Charles
>
> __
would appreciate any help with this matter.
>
> Regards,
> Vadim
>
> [[alternative HTML version deleted]]
>
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s
> [1] -0.5477293 -0.5624539 0.5551133
>
> Another S3 class, basically any object plus a label attribute.
> There are a few methods for this class, otherwise it works
> out of the box.
>
> The third is "lm" - a list with an S3 class. Functions that
> operate on lists work fine without extra methods. And you can
> add extra components without needing to define a new class
> (I've done this in library(resample)).
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More precisely, personally, I use 'print', 'summary' and 'plot' a lot.
>> So for my new class, I define these 3 methods and of course, a get and a
>> set for each slot. What else? Is there some other methods that a R user
>> can reasonably expect?
tion(x="numeric"),
> containt="fatherClass"
>
>
> Is there any difference ? What is the usal way ?
>
> Christophe
>
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<- list(a = 1, b = 2, c = 3)
>
> a$b <- NULL
>
>
> On Feb 13, 2008 9:39 AM, Oleg Sklyar <[EMAIL PROTECTED]> wrote:
>> Hmm, I think the pretty traditional R style does the job...
>>
>> a = list(1,2,3)
>> a[-2]
>>
>> So I real
;> x <- list(a=c(1L,2L), b=matrix(runif(4),2,2), c=LETTERS[1:3])
>> x[2] <- list(NULL)
>>
>> is what I think you are intending.
>>
>> See e.g. the comment in subassign.c
>>
>> /* If "val" is NULL, this is an element deletion */
>
when
assigning a NULL in fact removed the element from the list. Is this an
intended behaviour? If so, does anybody know where is it documented and
what is a good way around?
Thanks for help,
Oleg Sklyar
Here goes an example, the inline C-code does exactly what I would prefer
R were doing, but
a device causes R to crash, e.g.,
>
> pdf("foo%s.pdf")
> win.metafile("foo%s.wmf")
> postscript("foo%s.ps")
>
> ______
> R-devel@r-project.org mailing list
> https://st
> Would you like existing functions such as mean, range, sum,
> colSums, dim, apply, length, and many more to operate on the array of
> numbers? If so use an S3 class.
The above is misleading as 'setClass("NewArray", [additional structures
go in here], contains="array")' will give the NewArray a
t would be connected with the speed of
method dispatch (although I would not argue that there are none).
Regards,
Oleg
Dr Oleg Sklyar | EBI-EMBL, Cambridge CB10 1SD, UK | +44-1223-494466
John Chambers wrote:
> Prof Brian Ripley wrote:
>> On Mon, 7 Jan 2008, Robin Hankin wrote:
>>
Should adding PREFIX/library/XML/libs to PATH before system32 solve the
issue as Windows relies on PATH when searching for libs as well?
Dr Oleg Sklyar | EBI-EMBL, Cambridge CB10 1SD, UK | +44-1223-494466
Martin Morgan wrote:
> The XML package relies on libxml2.dll (e.g., bundled with the C
RGtk2'
>
> I've re-started R again and the same happened. I've also tried downloading
> the
> RGtk2 zip files from the CRAN website and installing from a local zip file
> option which gave the same results. I haven't
> definitely think that there should be a Side Effects section
> in the help files of functions whose whole point is a side
> effect.
>
> Patrick Burns
> [EMAIL PROTECTED]
> +44 (0)20 8525 0696
> http://www.burns-stat.com
> (home of S Poetry and "A Guide for the U
ake sure
> 'names' were removed from lists used to construct objects. As a
> consequence I lose a nice little bit of sapply magic.
>
> > setClass('A', 'list')
> [1] "A"
> > setMethod('[', 'A', function(x, i, j, ...
too).
>
> cheers
> Ben Bolker
>
> -----BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.6 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>
> iD8DBQFHYL1pc5UpGjwzenMRAqErAJ9jj1KgVVSGIf+DtK7Km/+JBaDu2QCaAkl/
> eMi+WCEWK6FPpVMpUbo+RBQ=
> =huvz
> -END PGP SIGNATURE-
>
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package development and SVN I might
> write it up for R-newsletter - there's a couple of other tricks I've had
> to employ...
What exactly?
>
> Barry
>
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SEXP x,y,res;
PROTECT(res = allocVector(VECSXP, 2));
SET_VECTOR_ELT(res, 0, x = allocVector(REALSXP, 20));
SET_VECTOR_ELT(res, 1, y = allocVector(INTSXP, 10));
// code with x,y goes here
UNPROTECT(1);
return res;
On Fri, 2007-11-16 at 15:49 -0500, Charles Danko wrote:
> Hello,
>
> Quick questi
You assume that when you call any of those functions its arguments are
protected (as it is the case when the function is called from within R).
However, I do not see why they would be if you do not do it explicitly.
Therefore, it is very likely that a result of one function, used in turn
in a call
nth 10
> > day03
> > svn rev43063
> > language R
> > version.string R version 2.6.0 (2007-10-03)
> >
> > --
> >
> > __
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
>
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Hi.
I believe it is virtually impossible, maybe even not virtually: if you
manage to do so somehow, please report it as a bug because such things
must be impossible as they break the integrity of R and data.
Forget about changing size in place: it is C and 'realloc' would be
about the only way to
; Hi!
>
> Is there any way to test if R is running on a Mac? I usually use
> value of .Platform$OS.type for windows or unix, but Mac falls in the
> latter group.
>
> Thanks, Gregor
>
> __
> R-devel@r-project.org mailing list
&g
in C++ from R.
> My questions are:
> 1. How should I include libraries (for example, iomanip,
> sstream, iostream)?
> 2. Can I use namespace?
>
> Thanks All :)
> Olga
>
> __
> R-devel@r-project.org mailing list
> http
S=C;LC_TELEPHONE=C;LC_MEASUREMENT=C;LC_IDENTIFICATION=C"
>
> Under kde it works fine.
>
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as*, since no one is forced to use it.
> >
> > It also suggests that your documentation is organized by generic,
> > which might also be a bit unusual -- I typically have an object (e.g.,
> > an Image) and wonder what can be done to it (e.g., write it to
> >
cumentation and
code/documentation mismatches.
Best regards,
Oleg
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a1 = new("A1", array(1:8, rep(2,3)), flag = "test")
> > a2 = new("A2", array(8:1, rep(2,3)), positive = rep(TRUE,8))
> > a1+a2
> , , 1
>
> [,1] [,2]
> [1,]99
> [2,]99
>
> , , 2
>
> [,1] [,2]
> [1
efore using them.
>
> On Mon, 23 Jul 2007, Oleg Sklyar wrote:
>
> > Any idea why CHAR(asChar(STRING_ELT( produces NA whereas
> > CHAR(STRING_ELT( gets a pointer to a string? It's generally expected
> > that STRING_ELT should already be a character,
>
> I
alue;
"
code2 <- "
for (int i = 0; i < LENGTH(x); i++ )
Rprintf(\"%s\\n\", CHAR(asChar(STRING_ELT(x, i;
return R_NilValue;
"
setCMethod(c("p1","p2"), list(sig,sig), list(code1,code2))
#---
07-07-16 14:32:16 +0100 (Mon, 16 Jul 2007) | 1 line
implicitGeneric() and structure class
----
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*,/,-)? If yes, could someone point me to the following two things: what
are the reasons behind and WHAT operators and functions have been
affected -- I will need to redefine all those then. Moreover, it is not
consistent:
> class(a*2)
[1] "Image"
attr(,"package")
[1] "EBIm
uld I do it?
>
> If not, then are there an recommendations for a solution?
> An alternative I can try is to have 2 separate packages,
> 'fame' and 'fame-remote'.
>
> Thanks,
> Rick Jones
>
> __
>
e code
in setCMethod on load, different calling conventions (.C, .Call,
.Fortan) and allows to inline not only C, but also Fortran and
ObjectiveC (needs testing) code, it performs clean up of all temp files
created during compilation etc.
Best,
Oleg
--
Dr Oleg Sklyar * EBI/EMBL, Cambridge CB10 1S
used for compilation allowing for
the use of the correct R version when several are installed
The update has been submitted to CRAN and should appear shortly.
Meanwhile, the package is available from
http://www.ebi.ac.uk/~osklyar/inline
Best,
Oleg
--
Dr Oleg Sklyar * EBI/EMBL, Cambridge CB1
kages:
[1] "stats" "graphics" "grDevices" "utils" "datasets"
"methods"
[7] "base"
other attached packages:
rae230a
"1.16.0"
>
On Jun 11, 2007, at 11:27 PM, Seth Falcon wrote:
> "James
ion, rather than rely on on the R garbage
> collector?
Not that I know about.
Best,
Oleg
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nd to script this, dump the processed chunks as
> Rdata files and later re-read the pieces. That works reliably.
>
> So one think you could try is to dump your data in 'gsl ready' format from R,
> quit R, leave it out of the equation and then see if what happens if you do
> th
cing a list of functions to evaluate them,
> all compiled into one DLL.
Simon Urbanek wrote:
> I really like the idea! Except for the fact that it's forcing the use
> of C++ which adds unnecessary overhead :P I'd like a configurable
> extension [including .m] and the ability
uot; implementation.
Thanks,
Oleg
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> That is actually a (rare) case that can be completely vectorized:
Thanks for the vectorization solution.
> I really like the idea! Except for the fact that it's forcing the use of
> C++ which adds unnecessary overhead :P
I can make it optional. I was just thinking that C++ would be more
general
t;- " rdata[x + y*nx] = data[x + y*nx] * exp(-d2/sigma2);"
code[15] <- " }}"
code[16] <- " UNPROTECT(nprotect);"
code[17] <- " return res;"
library(inline)
funx <- cfunction(signature(a="array", s="numeric", centre=&q
} else
> +prototype <-
> +setDataPart(prototype, getDataPart(pri))
> dataPartDone <- TRUE
> }
> }
&g
: unable to load R code in package 'ggplot'
> Error: package/namespace load failed for 'ggplot'
>
> Can anyone suggest how I could get around this?
>
> Regards,
>
> Hadley
>
> ______
> R-devel@r-projec
> TLB size : 1024 4K pages
> clflush size : 64
> cache_alignment : 64
> address sizes : 40 bits physical, 48 bits virtual
> power management: ts fid vid ttp
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l if anyone could tell me what could be the problem with my
> C function that makes R behave this way?
>
>
>
> Thank you very much in advance, and apologies for this long email.
>
>
>
> Xavier Solé.
>
>
>
>
>
>
> [[alternative HTML version deleted]]
>
>
>
> ---
1] "stats" "graphics" "grDevices" "utils" "datasets" "methods"
[7] "base"
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Dr Oleg Sklyar | EBI-EMBL, Cambridge CB10 1SD, UK | +44-1223-494466
Herve Pages wrote:
> Hi Oleg,
>
> Oleg Sklyar wrote:
>> m
"graphics" "grDevices" "utils" "datasets" "methods"
[7] "base"
>
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Dr Oleg Sklyar | EBI-EMBL, Cambridge CB10 1SD, UK | +44-1223-494466
[EMAIL PROTECTED] wrote:
> Hi,
>
> On my system, I get the following error message
ronment on every single step. Where is the gain?
Oleg
--
Dr Oleg Sklyar | EBI-EMBL, Cambridge CB10 1SD, UK | +44-1223-494466
Byron Ellis wrote:
> Actually, why not use a closure to store previous value(s)?
>
> In the simple case, which depends on x_i and y_{i-1}
>
> gen.it
g
Tamas K Papp wrote:
> On Tue, Jan 30, 2007 at 12:15:29PM +, Oleg Sklyar wrote:
>
>> magnitude using c-functions for "complex" vector indexing operations. If
>> you need instructions, I can send you a very nice "Step-by-step guide
>> for using C/C++ in R&q
on it is easier to use a for loop.
> Also I have seen 'rle' which I think may help me but am not sure as I have
> only just come across it, any ideas?
>
> Many thanks
>
> Tom
>
>
>
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short etc etc.
Here the power of R in freestyle indexing of arrays becomes a pain.
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ole R includes into a unique namespace? It
wouldn't require any modifications in the existing libraries because if
the code is not conflicting, namespace can be omitted.
Does it have sense?
Regards
Oleg Sklyar
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European Bioinformatics Institute
Wellcome Trust Genome Camp
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