On 12/13/2011 03:48 PM, Jeffrey Pollock wrote:
Hello all,
I've been working on a package to do various things related to the
Conway-Maxwell-Poisson distribution and wanted to be able to make fast
random draws from the distribution. My R code was running quite slow so I
decided to give Rcpp a bas
In
> R.version.string
[1] "R Under development (unstable) (2011-12-15 r57901)"
section 1.6.6 of 'Writing R Extensions' says
Note that exporting methods on a generic in the namespace will
also export the generic, and exporting a generic in the
namespace will also export its methods.
and
In
> R.version.string
[1] "R Under development (unstable) (2011-12-15 r57901)"
PkgA promotes 'unique' to a generic and exports that
DESCRIPTION:
Imports: methods
R/f.R:
setGeneric("unique")
NAMESPACE:
export(unique)
and PkgB creates and exports a method on unique
DESCRIPTION
On 12/15/2011 03:40 PM, Martin Morgan wrote:
In
> R.version.string
[1] "R Under development (unstable) (2011-12-15 r57901)"
PkgA promotes 'unique' to a generic and exports that
DESCRIPTION:
Imports: methods
R/f.R:
setGeneric("unique")
NAMESPACE:
export(uniq
On 12/16/2011 02:02 AM, Martin Maechler wrote:
On 12/15/2011 03:40 PM, Martin Morgan wrote:
In
> R.version.string
[1] "R Under development (unstable) (2011-12-15 r57901)"
PkgA promotes 'unique' to a generic and exports that
DESCRIPTION:
Imports: methods
R/
tar of Pkgs A, B, C attached. Martin
On 12/15/2011 03:34 PM, Martin Morgan wrote:
In
> R.version.string
[1] "R Under development (unstable) (2011-12-15 r57901)"
section 1.6.6 of 'Writing R Extensions' says
Note that exporting methods on a generic in the namespa
y if
the generic found in either PkgB's namespace or namespace imports were
imported along with the method. Not sure that I like the idea of calling
setGeneric() -- PkgA could have done something non-standard -- and would
rather an error.
Thans for your attention.
Martin
Comments?
John
O
if the generic function was created from base::unique
by the standard call. That's what would make an automatic
imputation of the generic from importMethods() possible.
On 12/16/11 2:57 PM, Martin Morgan wrote:
On 12/16/2011 12:19 PM, John Chambers wrote:
The subject heading is correct if referrin
On 12/23/2011 11:54 AM, Hadley Wickham wrote:
And one last note: I'm reasonably certain I haven't forgotten to
export an S3 method because I wrote the following script to (crudely)
compare the function definitions in ggplot2 with its namespace:
ns<- parseNamespaceFile("ggplot", "~/Documents/g
On 12/23/2011 02:11 PM, Martin Morgan wrote:
On 12/23/2011 11:54 AM, Hadley Wickham wrote:
And one last note: I'm reasonably certain I haven't forgotten to
export an S3 method because I wrote the following script to (crudely)
compare the function definitions in ggplot2 with its name
On 12/23/2011 02:38 PM, Hadley Wickham wrote:
in scales_add_defaults, where the symbol isn't found in the globalenv()
when nstest is attached and ggplot2 only loaded, but is (via the search
path) when ggplot2 is attached.
and topenv(parent.frame()) is a replacement that gets to .GlobalEnv for
g
This
setOldClass(c("file", "connection"))
.A <- setRefClass("A", fields=list(con="connection"),
methods=list(
finalize = function() {
if (isOpen(con)) close(con)
}))
f <- tempdir()
a <- .A$new(con=file(f, "rb"))
cl
On 01/10/2012 02:54 PM, Simon Urbanek wrote:
On Jan 10, 2012, at 4:12 PM, Jeroen Ooms wrote:
On Tue, Jan 10, 2012 at 6:17 AM, Simon Urbanek
wrote:
Unfortunately R doesn't provide a way for this. Without changes to
unserialization (on the wishlist for a few years now, but not easy to design)
On 02/03/2012 02:49 AM, Titus von der Malsburg wrote:
Dear list!
I have a script that processes a large number of data files. When one
file fails to process correctly, I want the script to write a message
and to continue with the next file. I achieved this with tryCatch:
for (f in files)
On 02/06/2012 04:46 AM, Titus von der Malsburg wrote:
On Sat, Feb 4, 2012 at 4:37 PM, Martin Morgan wrote:
On 02/03/2012 02:49 AM, Titus von der Malsburg wrote:
Hi Titus -- use withCallingHandlers to capture the warning, and
invokeRestart() to continue after handling it.
withCallingHandlers
On 02/06/2012 12:45 PM, Jeroen Ooms wrote:
After upgrading my servers to 2.14, log files were filled warnings
that 'mem.limits' has been deprecated and to use gc instead. After
reading the NEWS for R 2.14.0 and PR#14795 I learned that it is
actually deprecated without replacement.
Hereby I just
the function; the return in the
_PRINT_DEAL_c_eq_0 macro makes it difficult to balance the protection
stack, and R_alloc seems to be a better solution anyway. diff attached.
Martin Morgan
I get something similar with R 2.14.1.
Cheers,
H.
> sessionInfo()
R Under development (unstable) (
On 02/14/2012 08:43 AM, james.fo...@diamond.ac.uk wrote:
Dear R-developers community, I have the following generic:
setGeneric(
name="newsample",
def=function(x,y,z,a,b,c,...){standardGeneric("newsample")}
And I can build several methods for this generic.
Running R CMD check on a package can take quite a lot of time. Checks
seem like they could be run in parallel (separate processes for, e.g.,
codoc, examples, tests, ...). Is there a way to do this? My current
usage is typically
R CMD build
R CMD check pkg_x.y.z.tar.gz
Thanks for any hi
On 02/17/2012 01:42 AM, Prof Brian Ripley wrote:
On 17/02/2012 06:50, Martin Morgan wrote:
Running R CMD check on a package can take quite a lot of time. Checks
seem like they could be run in parallel (separate processes for, e.g.,
codoc, examples, tests, ...). Is there a way to do this? My
On 02/21/2012 08:13 AM, Steve Lianoglou wrote:
Hi all,
This feature was throwing me for a loop for quite some time until I
played with the names of the slots.
Consider exhibit A:
==
setClass("SVM",
representation=representation(
x='numeric',
y='num
pkgA's NAMESPACE has
importFrom(graphics, plot)
exportClasses("A")
exportMethods("plot")
R/foo.R has
setClass("A")
setMethod("plot", "A", function(x, y, ...) {})
During R CMD INSTALL pkgA_1.0.tar.gz we are told
** preparing package for lazy loading
Creating a generic function for 'p
> R.version.string
[1] "R Under development (unstable) (2012-02-26 r58493)"
In the recent addition "It is important if you export S4 methods that
the corresponding generics are available: the requirementa on this are
stricter as from R 2.15.0. You may for example need to import plot from
graph
With
> R.version.string
[1] "R version 2.15.0 alpha (2012-03-14 r58748)"
trying to trace a method using the 'signature' argument fails rather
than enabling the trace:
> trace(initialize, signature="ANY")
Error in matchSignature(signature, fdef, where) :
trying to match a method signature of
On 03/14/2012 05:15 AM, Jon Clayden wrote:
Dear all,
I recognise the reason for strongly discouraging use of printf() and
similar C functions in R packages, but I wonder what people do in
practice about third-party code which may be littered with such calls.
I maintain a package (RNiftyReg) whic
re I still reference stderr /
stdout. But it seems like the meaningful problem (writing to stderr /
stdout, which R might have re-directed) has been addressed (except for
the third branch, in your code above).
Martin
All the best,
Jon
On 15 March 2012 05:04, Martin Morgan wrote:
On 03/14/201
On 04/13/2012 01:40 AM, Uwe Ligges wrote:
You have to export the new generic as well.
that's not correct.
Uwe Ligges
On 12.04.2012 20:41, Roebuck,Paul L wrote:
Late to the show on this release, unfortunately.
One of our production packages no longer builds under R-2.15.0
with the followin
tat.ethz.ch/mailman/**listinfo/r-devel<https://stat.ethz.ch/mailman/listinfo/r-devel>
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On 05/13/2012 12:14 PM, Jeroen Ooms wrote:
On Sun, May 13, 2012 at 10:14 AM, Uwe Ligges
wrote:
I do not see any problem in R. If someone is going to import a Namespace, he
or she has to do that via import directives in the NAMESPACE file. If
someone is going to have a package on the search pa
On 05/13/2012 01:39 PM, Duncan Murdoch wrote:
On 12-05-13 4:06 PM, Martin Morgan wrote:
On 05/13/2012 12:14 PM, Jeroen Ooms wrote:
On Sun, May 13, 2012 at 10:14 AM, Uwe Ligges
wrote:
I do not see any problem in R. If someone is going to import a
Namespace, he
or she has to do that via
On 06/20/2012 07:25 PM, Hadley Wickham wrote:
Hi all,
Any ideas about this? As far as I can tell it should work - and I
don't understand why it's ok when run outside of a package.
from ?groupGeneric under 'Ops' (of which "+" is one)
used. If different methods are found, there is a
On 06/18/2012 01:01 AM, Janko Thyson wrote:
Dear list,
is there a way to declare public and private methods in S4 Reference
Classes? If not, are there plans to add such a feature?
Hi Janko -- your question is a little ambiguous; if it's about a
built-in facility to create public vs. private m
On 06/20/2012 08:06 PM, Hadley Wickham wrote:
from ?groupGeneric under 'Ops' (of which "+" is one)
used. If different methods are found, there is a warning
about 'incompatible methods': in that case or if no method is
found for either argument the internal method i
On 07/02/2012 06:23 PM, Charlie Friedemann wrote:
The error message you are getting makes it rather clear what the problem is.
R is unable to find the function 'hasArg'. As the hasArg function is part
of the package 'methods', a solution would be to put require(methods) at the
beginning of your
On 07/03/2012 09:07 AM, Mauricio Zambrano-Bigiarini wrote:
On 02/07/12 22:51, Martin Morgan wrote:
On 07/02/2012 06:23 PM, Charlie Friedemann wrote:
The error message you are getting makes it rather clear what the
problem is.
R is unable to find the function 'hasArg'. As the hasArg f
cation to avoid
confusion (avoiding 'first time users should do A, return users should
do B').
As a 'normal' user it is safe and appropriate to use biocLite to manage
Bioconductor (and CRAN) packages. One takes a more cautious approach as
'root', but I personally
after this
setClass("A")
setGeneric("bar", function(x, y) standardGeneric("bar"))
setMethod(bar, signature(x="A", y="A"), function(x, y) {})
setMethod(bar, signature(x="A", y="ANY"), function(x, y) {})
the method for signature c("A", "A") contains package information
> str(getMethod(ba
On 08/07/2012 02:43 PM, John Chambers wrote:
Good catch. This should have been fixed in r-devel, revision 60192. If
nothing bad results in other tests, we'll port it to the current patched
version.
Thank you for the fix. Martin
Thanks,
John
On 8/5/12 4:31 PM, Martin Morgan
On 08/10/2012 12:04 PM, peter dalgaard wrote:
Not to spoil your fun, but this is getting a bit off-topic for R-help. If you
wish to continue the debugging process in public, I think you should move to
R-devel.
Also, it sounds like the problem is in the glmulti package, so you might want
to in
Under ?data
package: a character vector giving the package(s) to look in for data
sets, or 'NULL'.
By default, all packages in the search path are used, then
the 'data' subdirectory (if present) of the current working
directory.
which I think is accurate
?mccollect say
'mccollect' returns any results that are available in a list. The
results will have the same order as the specified jobs. If there
are multiple jobs and a job has a name it will be used to name the
result, otherwise its process ID will be used. If none of the
invoking parLapply without a cluster fails to find a previously
registered cluster
> library(parallel)
> setDefaultCluster(makePSOCKcluster(2))
> parLapply(X=1:2, fun=function(...) {})
Error in cut.default(i, breaks) : invalid number of intervals
This is because in parLapply length(cl) is deter
Thank you for the fix, in svn R-devel and 2-15-patched r60447, r60448.
Martin
On 08/21/2012 06:50 AM, Martin Morgan wrote:
invoking parLapply without a cluster fails to find a previously
registered cluster
> library(parallel)
> setDefaultCluster(makePSOCKcluster(2))
> parLapply(X
I think this belongs on R-devel and I'm forwarding there.
Here's a more refined example
library("XLConnect")
load(file="ddr.Rda")
oV <- function(x) {
if (is.leaf(x)) {
return(x)
}
for (j in seq_along(x)) {
b <- oV(x[[j]])
}
x
}
res <-
For an external pointer
> xp
one might expect all.equal to behave as for environments
> e = new.env()
> all.equal(e, e)
[1] TRUE
but it does not
> all.equal(xp, xp)
Error in unclass(target) : cannot unclass an external pointer
A solution is to dispatch to all.equal.language (?) in
src/libr
On 09/11/2012 04:19 PM, Henrik Bengtsson wrote:
Hi,
I'm trying to implement an abort() method that works just like stop()
but does not signal the condition such that try() and tryCatch(...,
condition=...) are, contrary to stop(), effectively non-working with
abort() calls.
In order to achieve t
a safe way for a package to use cbind2?
This came up in the context of complex package dependencies in
Bioconductor, as detailed in this thread (sorry for the html).
https://stat.ethz.ch/pipermail/bioc-devel/2012-September/003617.html
--
Dr. Martin Morgan
Fred Hutchinson Cancer Research Center
option is wholesale deprecation of S4 ... but I won't start
that conversation with either of you ;-)
Jeff
On Fri, Sep 14, 2012 at 3:00 AM, Martin Maechler
wrote:
Martin Morgan
on Wed, 12 Sep 2012 15:23:02 -0700 writes:
> The methods package ?cbind2 includes the instru
we are all novice R
developers am hoping someone on the list can provide some insight.
many thanks for your time,
brian
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R-devel@r-project.org mailing list
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--
Dr. Martin Morgan, PhD
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
__
R-devel@r-project.org mailing list
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Seemed like a good idea at the time, but
> options(max.print = .Machine$integer.max)
> 1:10
[1]
Program received signal SIGSEGV, Segmentation fault.
because of an integer overflow at src/main/printvector.c:176
> sessionInfo()
R Under development (unstable) (2012-09-24 r60800)
Platf
On 09/25/2012 05:26 AM, Martin Maechler wrote:
Seemed like a good idea at the time,
I'm curious. Why is it (setting max.print much too large)
a good idea?
I usually set it considerably smaller (50) than default to conserve
screen real estate, but then occasionally need to see more than my
On 09/28/2012 11:57 AM, David L Lorenz wrote:
I get an error when I try to use \S4method in a usage section in an Rd
file for a function. I tried to duplicate exactly how stats4 documents its
method functions, but I must be missing something. Here is the top part of
the Rd file:
\name{xyPlot-met
On 10/02/2012 05:19 PM, Henrik Bengtsson wrote:
Hi,
I'm looking for a super-duper fast mean/sum binning implementation
available in R, and before implementing z = binnedMeans(x y) in native
code myself, does any one know of an existing function/package for
this? I'm sure it already exists. So,
On 10/3/2012 6:47 AM, Martin Morgan wrote:
On 10/02/2012 05:19 PM, Henrik Bengtsson wrote:
Hi,
I'm looking for a super-duper fast mean/sum binning implementation
available in R, and before implementing z = binnedMeans(x y) in native
code myself, does any one know of an existing fun
> setClass("A", "integer")
> isS4(new("A"))
[1] TRUE
> identical(isS4(new("A")), TRUE)
[1] FALSE
> sessionInfo()
R Under development (unstable) (2012-10-04 r60876)
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-8LC
On 10/04/2012 02:23 PM, Duncan Murdoch wrote:
On 12-10-04 4:57 PM, Martin Morgan wrote:
> setClass("A", "integer")
> isS4(new("A"))
[1] TRUE
> identical(isS4(new("A")), TRUE)
[1] FALSE
> sessionInfo()
R Under development (unstable
On 10/04/2012 04:05 PM, Duncan Murdoch wrote:
On 12-10-04 5:50 PM, Martin Morgan wrote:
On 10/04/2012 02:23 PM, Duncan Murdoch wrote:
On 12-10-04 4:57 PM, Martin Morgan wrote:
> setClass("A", "integer")
> isS4(new("A"))
[1] TRUE
> id
On 10/04/2012 05:56 PM, Martin Morgan wrote:
On 10/04/2012 04:05 PM, Duncan Murdoch wrote:
On 12-10-04 5:50 PM, Martin Morgan wrote:
On 10/04/2012 02:23 PM, Duncan Murdoch wrote:
On 12-10-04 4:57 PM, Martin Morgan wrote:
> setClass("A", "integer")
&g
Initialization of this simple hierarchy
A = setClass("A", representation(x="numeric"))
setClass("B", contains=c("VIRTUAL", "A"))
C = setClass("C", contains="B")
fails (neat that setClass returns generators; I hadn't realized that before!)
> C(A())
Error: evaluation nested too deeply: infi
On 10/21/2012 12:28 PM, Ben Bolker wrote:
Not desperately important, but nice to have and possibly of use to
others, is the ability to suppress specific warnings rather than
suppressing warnings indiscriminately. I often know of a specific
warning that I want to ignore (because I know that's
On 10/22/2012 09:57 AM, luke-tier...@uiowa.edu wrote:
On Sun, 21 Oct 2012, Martin Morgan wrote:
On 10/21/2012 12:28 PM, Ben Bolker wrote:
Not desperately important, but nice to have and possibly of use to
others, is the ability to suppress specific warnings rather than
suppressing
iocGenerics.
Maybe I am missing something obvious here, but imo there is no way to
overwrite parLapply globally for my own class unless the generic is
imported by everyone who wants to make use of the special method.
Florian
--
On 10/23/12 2:20 PM, "Martin Morgan" wrote:
On 10/17/
The attached diff address the following issues in mclapply
mclapply coerces non-lists or objects (S3 or S4) to lists, but a list may not be
an efficient representation and is not required if the object implements length,
[, and [[ methods (lapply must also work on the object, either through coe
S3 and S4 symbols defined, but this seems to be required? A
workaround might extend the check to include getGeneric(genname)@default.
This scenario is reproducible in the attached tarball
tar xzf PkgAB.tar.gz
R CMD INSTALL PkgA
R CMD check PkgB
Martin Morgan
--
Computational Biology / Fre
real example. Martin
Thanks for the catch.
John
On 12/8/12 3:05 PM, Martin Morgan wrote:
PkgA wishes to write a method for 'unique' on S4 class 'A'. ?Methods
indicates that one should
setGeneric("unique")
setClass("A")
unique.A <- function(x,
On 12/14/2012 09:46 AM, Ulrich Bodenhofer wrote:
Hi,
I just figured out that I accidentally posted my message in HTML, so I am
retrying in plain text only. Sorry.
I am currently extending one of our CRAN packages and ran into an unexpected
problem when checking the source package. I got some wa
On 12/17/2012 12:57 AM, Ulrich Bodenhofer wrote:
On 12/15/2012 06:26 AM, Martin Morgan wrote:
In ?setMethod there is this paragraph
It is possible to have some differences between the formal
arguments to a method supplied to 'setMethod' and those of the
generic. Rough
While trying to install a package, I received this error
** preparing package for lazy loading
Error in matchSignature(signature, fdef, where) :
more elements in the method signature (2) than in the generic signature (1)
A more helpful variant is
Error in matchSignature(signature, fdef, wher
With
> R.version.string
[1] "R Under development (unstable) (2013-01-26 r61752)"
'split.default' recycles a short factor for unclassed 'x', but not for an
instance of x that is a class
> split(1:5, 1:2)
$`1`
[1] 1 3 5
$`2`
[1] 2 4
Warning message:
In split.default(1:5, 1:2) :
data length
ction."
You haven't mentioned your DESCRIPTION or NAMEPSACE file, but the right thing to
do is
DESCRIPTION:
Depends: reshape
NAMESPACE:
importFrom(reshape, cast)
R/somefile.R:
setGeneric("cast")
Perhaps your current setGeneric is being performed inside the namespace w
On 02/03/2013 09:36 AM, Martin Morgan wrote:
On 02/02/2013 02:34 PM, Tim Bergsma wrote:
r-devel,
In a development version of the CRAN package metrumrg, I write ...
require(reshape)
setGeneric('cast')
setOldClass(c('keyed','data.frame'))
setMethod('cast
I be doing
if (tools:::.OStype() == "unix") {
importFrom(parallel, mccollect, mcparallel)
}
in my NAMESPACE? I have a recollection that this has come up before, perhaps
even in the parallel package, but I'm not able to find anything.
Thanks,
Martin Morgan
--
Computational Bi
On 02/25/2013 01:28 PM, Hadley Wickham wrote:
To summarize, it appears that the only way to call functions from a
suggested package is by using either 'require' (which will dynamically
attach it) or the double colon method. Is this something that should be
mentioned in R-exts?
Except the double
- dstruct.c (revision 62113)
+++ dstruct.c (working copy)
@@ -59,6 +59,7 @@
if (result == R_NilValue) {
result = allocSExp(type);
SET_PRIMOFFSET(result, offset);
+ SET_VECTOR_ELT(PrimCache, offset, result);
}
else if (TYPEOF(result) != type)
error("reque
In this post
https://stat.ethz.ch/pipermail/bioc-devel/2013-March/004152.html
a package author reports that S4 dispatch fails. I can reproduce this with a
PkgA (attached; 'intervals' is a relatively light-weight CRAN package) that has
DESCRIPTION with
Depends: intervals
Imports: graphics
On 03/15/2013 04:42 AM, Martin Maechler wrote:
Martin Morgan
on Wed, 13 Mar 2013 12:43:59 -0700 writes:
> In this post
> https://stat.ethz.ch/pipermail/bioc-devel/2013-March/004152.html
> a package author reports that S4 dispatch fails. I can reproduce thi
When R is configured with CFLAGS=-O2, clock_gettime is included
$ nm src/main/libR.a | grep clock_gettime
U clock_gettime
whereas when configured with -O0 it is not
$ nm src/main/libR.a | grep clock_gettime
$
Similarly when built as a shared library the linker flags include or
On 04/01/2013 05:37 PM, Henrik Bengtsson wrote:
Hi,
things have indeed changed on how non-Sweave vignettes are built (this
happened around R devel 2013-03-05 r62130). However, it's not clear
to me what changes would be behind your problems, if any.
Build your vignette with the following buildV
For what it's worth, the package loads many DLLs in its NAMESPACE via repeated
calls to useDynLib. antsImageRead is not in the first DLL loaded, and from
NEWS.Rd, the problem comes from
o A foreign function call (.C() etc) in a package without a PACKAGE
argument will only look in
On 04/14/2013 07:11 PM, luke-tier...@uiowa.edu wrote:
There were a couple of bug fixes to somewhat obscure compound
assignment related bugs that required bumping up internal reference
counts. It's possible that one or more of these are responsible. If so
it is unavoidable for now, but it's worth
muffleWarning")
} )
...which are then caught as
withCallingHandlers({
warning(w) # 'curves'; caught
warning("another warning")
}, curves=function(w) invokeRestart("muffleWarning"))
The tricky part is to come
On 04/19/2013 01:16 AM, Prof Brian Ripley wrote:
On 17/04/2013 21:25, Michael Lawrence wrote:
It's tough to reliably reproduce, but I often get stack imbalance warnings
when calling max.col() on non-real/double matrix. The code is conditionally
PROTECTing but not incrementing its nprot counter f
On 04/26/2013 07:50 AM, Adam Seering wrote:
Hi,
I've been playing around with the R source code a little; mostly just
trying to familiarize myself. I have access to some computers on a reservation
system; so I've been reserving a computer, downloading and compiling R, and
going from there.
On 05/02/2013 01:35 PM, Duncan Murdoch wrote:
On 13-05-02 3:05 PM, Terry Therneau wrote:
I have a debugging environment for the survival package, perhaps unique to me,
but I find
it works very well.
To wit, a separate directory with copies of the source code but none of the
package
accuements of
On 05/08/2013 10:25 AM, Simon Urbanek wrote:
On May 7, 2013, at 11:35 PM, Peter Meilstrup wrote:
Encountered an error in scripting, which can be reproduced using Rscript as
follows:
$ Rscript -e "library(httr); handle('http://cran.r-project.org')"
Error in getCurlHandle(cookiefile = cookie_p
axes = axes, asp = asp, ...)
> }
> .local(x, y, ...)
> }
>
>
> Signatures:
> xy
> target "pixmap" "missing"
> defined "pixmap" "ANY"
>
>
>
>
>
>> sessionInfo()
> R version 2.9.0 (2009-04-17)
>
S.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
Martin
--
Martin Morgan
Computational Biology / F
Hi Troy --
Troy Robertson wrote:
> I am new to R programming but have dived into a medium sized modelling
> software development project.
>
> Having come from a Java OO background I have a couple of questions about S4
> objects.
>
>
>
> Is there a way to make S4 slots (and methods) private a
Duncan Murdoch wrote:
> Martin Kober wrote:
>> I have an S4 object extending "function". Is it there a good way to
>> access the object (resp. its slots) from within the function in .Data?
>>
>
> I don't think so. That's not really the way the S4 object system is
> designed to work. If a func
Troy Robertson wrote:
> Hi all,
>
>
>
> Prefix: I am a frustrated Java coder in R.
ah good, if you're frustrated with Java you'll find R very different ;)
>
>
>
> I am coding a medium sized ecosystem modelling program in R. I have changed
> to using S4 objects and it has cost me an order
Hi Kynn --
(gdb) call Rf_PrintValue(x)
'void' is I think the return value of R_PV()
Martin
Kynn Jones wrote:
> Hi, everyone. I'm trying to debug an R-module, written in C, and I'm using
> gdb for this.
>
> How can I print "standard" R objects from within C code?
>
> BTW, I'm familiar with th
Kynn Jones wrote:
> I'm very green with R, so maybe this is not a bug, but it looks like one to
> me. The following program segfaults at the second call to Rf_PrintValue().
> To failure depends on the value of the y-string. E.g., if I change it from
> "coverage" to, say, "COVERAGE", the segfault
nction(.Object,.xData=new.env(parent=emptyenv())) {
> .Object <- callNextMethod(.Object, .xData=.xData)
> return(.Object)
> }
> )
>
> s <- new("Element")
>
>
> Not sure why that changes things though?
&
Stavros Macrakis wrote:
> On Mon, Jun 29, 2009 at 9:19 AM, Martin Morgan <mailto:mtmor...@fhcrc.org>> wrote:
>
> ...I'm not sure that including a connection in a slot is going to be
> a good
> idea, though -- a connection has reference-like semantics,
Fish
> Australian Antarctic Division
> Channel Highway, Kingston 7050
> PH: 03 62323571
> troy.robert...@aad.gov.au
>
>
>> -Original Message-
>> From: Martin Morgan [mailto:mtmor...@fhcrc.org]
>> Sent: Tuesday, 23 June 2009 11:25 PM
>> To: Troy Robertson
>> C
R-devel,
factor(x) can take a long time on large character vectors (more than a
minute in the example below). This is because of a call to sort.list.
> str(x)
chr [1:3436831] "chr5" "chr10" "chr16" "chr3" "chr4" "chr15" ...
> Rprof("/tmp/factor.Rprof")
> invisible(factor(x))
> Rprof()
> summaryR
s with (silently drops) NA. Perhaps the .C could have
NAOK=TRUE? This is useful in apply'ing tabulate to the rows or columns
of a (large) matrix, where the work-around involves introducing some
artificial NA value (and consequently copying the matrix) outside the
range of tabulate's nbin
artly concrete proposals, partly just
> ideas, asking for feedback, from you, experienced
> programmeRs, ...
>
> Martin Maechler, ETH Zurich
>
>
> ---
> *1) as there will always be if the S4 methods
> have been setup properly and *after* the S3 ones.
> This will typica
Yohan Chalabi wrote:
> Dear list,
>
> It seems that a package (pkgB) using another package (pkgA) with S4
> generics formed by taking existing functions (for example 'plot') must
> not import the existing functions ('plot') in its namespace to avoid
> the warning "replacing previous import: plot".
e a work around for this, or I am just doomed to write the same
> validity method for each children class?
I think you're doomed, but checking the number of slots in an instance
seems like a very unusual validity method -- isn't this the job of the
methods package, not your implement
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