the main tool to extend R?
What is our view on the (not so well known) dotCall64 package which is an
interesting alternative for extending R?
Thank you
Best regards,
Morgan
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Hi,
Is there a way to resize a matrix defined as follows:
SEXP a = PROTECT(allocMatrix(INTSXP, 10, 2));
int *pa = INTEGER(a)
To row = 5 and col = 1 or do I have to allocate a second matrix "b" with
pointer *pb and do a "for" loop to transfer the value of a to b?
Thank you
lease let me if you need more informations.
Thank you
Best regards
Morgan
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nk you
Best regards
Morgan
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from the R core team (if you wish) and
suggest an implementation in C.
Thank you
Best regards,
Morgan
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On Fri, 11 Oct 2019 10:45 Duncan Murdoch, wrote:
> On 11/10/2019 6:44 a.m., Morgan Morgan wrote:
> > Hi All,
> >
> > I was looking for a function to find a small matrix inside a larger
> matrix
> > in R similar to the one described in the following link:
>
How do you prove usefulness of a feature?
Do you have an example of a feature that has been added after proving to be
useful in the package space first?
Thank you,
Morgan
On Fri, 11 Oct 2019 13:53 Michael Lawrence,
wrote:
> Thanks for this interesting suggestion, Morgan. While there is
I think you are confusing package and function here. Plus some of the R
Core packages, that you mention, contain functions that should probably be
replaced by functions with better implementation from packages on CRAN.
Best regards
Morgan
On Fri, 11 Oct 2019 15:22 Joris Meys, wrote:
>
>
Your answer makes much more sense to me.
I will probably end up adding the function to a package.
Some processes and decisions on how R is developed seems to be obscure to
me.
Thank you
Morgan
On Fri, 11 Oct 2019 15:30 Avraham Adler, wrote:
> It’s rather difficult. For example, the bas
-matrix
Best
Morgan
On Fri, 11 Oct 2019 23:36 Gabor Grothendieck,
wrote:
> The link you posted used the same inputs as in my example. If that is
> not what you meant maybe
> a different example is needed.
> Regards.
>
> On Fri, Oct 11, 2019 at 2:39 PM Pages, Herve wrote:
&
ments before going to the C call? Do I have to
do it at the R level or can it be done at the C level?
Thank you very much in advance.
Best regards
Morgan
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Thank you for your reply Jiefei.
I think in theory your solution should work. I'll have to give them a try.
On Mon, 4 Nov 2019 23:41 Wang Jiefei, wrote:
> Hi Morgan,
>
> My solutions might not be the best one(I believe it's not), but it should
> work for your que
aggregate(`Petal.Width` ~ addNA(Species), df, sum) # include NA
data.table and dplyr include NA by default.
Python pandas has an aggreagate function inspired by base R aggregate. An
option has been added to include NA.
Thank you
Best regards
Morgan
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Thank you for your time.
Best regards
Morgan
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"kit" package (I am
the author) on CRAN.
I will continue working on the package in my spare time if I see that users
are missing basic functionalities not implemented in base R.
Have a great weekend.
Kind regards
Morgan Jacob
[[alternative HTML versi
For idx= 1, 2, 3, 4 the last line is equal to TRUE. For 5, 6 and many
others the difference is small but still.
Is that expected or is it a bug?
Thank you
Best Regards
Morgan Jacob
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Sorry, posting back to the list.
Thank you all.
Morgan
On Thu, 21 May 2020, 16:33 Henrik Bengtsson,
wrote:
> Hi.
>
> Good point and a good example. Feel free to post to the list. The purpose
> of my reply wasn't to take away Peter's point but to emphasize that
> bas
m the name of the column without having to loop over columns names to
find the index?
Thank you
Best regards
Morgan
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version of the unique and duplicated function. The function
unique is particularly slow for data.frame. So far I got a 100x speedup.
Best regards
Morgan
On Tue, 23 Jun 2020, 21:11 Jim Hester, wrote:
> It looks to me like internally .subset2 uses `get1index()`, but this
> function is decla
Hi All,
I was reading the R extension manual section 5.11 ( Evaluating R expression
from C) and I tried to build a simple call to the sum function. Please see
below.
call_to_sum <- inline::cfunction(
language = "C",
sig = c(x = "SEXP"), body = "
SEXP e = PROTECT(lang2(install(\"sum\"), x));
Thanks Jan and Tomas for the feedback.
Answer from Jan is what I am looking for.
Maybe I am not looking in the right place buy it is not easy to understand
how these LCONS, CONS, SETCDR...etc works.
Thank you
Best regards
Morgan
On Tue, 30 Jun 2020, 12:36 Tomas Kalibera, wrote:
> On 6/30
Sorry Dirk, I don't remember discussing this topic or alternatives with you
at all.
Have a nice day.
On Tue, 30 Jun 2020, 14:42 Morgan Morgan, wrote:
> Thanks Jan and Tomas for the feedback.
> Answer from Jan is what I am looking for.
> Maybe I am not looking in the right place
(free of charge of course!).
Thank you
Best regards
Morgan
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different than positive double...
Please read the pdf link I sent, everything is explained in it.
Thank you
Morgan
On Mon, 15 Mar 2021, 16:52 Avraham Adler, wrote:
> Isn’t the default method now “radix” which is the data.table sort, and
> isn’t that already parallel using openmp where ava
ther improved as I did
not really try hard.
If there is interest in both the implementation and cross community
sharing, please let know
Best regards,
Morgan
On Wed, 17 Mar 2021, 00:37 Radford Neal, wrote:
> Those interested in faster sorting may want to look at the merge sort
>
My apologies to Professor Neal.
Thank you for correcting me.
Best regards
Morgan
On Mon, 22 Mar 2021, 05:05 , wrote:
> I think it is "Professor Neal" :)
>
> I also appreciate the pqR comparisons.
>
> On Wed, Mar 17, 2021 at 09:23:15AM +, Morgan Morgan wrote:
&
] 100%NULL] 0%
I am using R 4.0.4 (Mac) / 4.0.5 (Windows)
Is that a bug or am I doing something wrong?
Thank you
Best regards,
Morgan
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REprintf and R_FlushConsole.
Best regards,
Morgan
On Sat, Apr 17, 2021 at 12:36 AM Simon Urbanek
wrote:
> Sorry, unable to reproduce on macOS, in R console:
>
> > dyn.load("test.so")
> > .Call("printtest",1e4L)
>
>Processing data chunk 1
On Wed, 2 Jun 2021, 22:31 Duncan Murdoch, wrote:
> On 02/06/2021 4:33 p.m., xiaoyan yu wrote:
> > I have a R Script Predict.R:
> > set.seed(42)
> > C <- seq(1:1000)
> > A <- rep(seq(1:200),5)
> > E <- (seq(1:1000) * (0.8 + (0.4*runif(50, 0, 1
> > L <- ifelse(runif(100
don't want to team up? Is it because you don't want? Any
particular reasons? Different philosophies?
Thank you
Kind regards
Morgan
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Thank you all for these explanations.
Kind regards,
Morgan
On 11 Jun 2017 02:47, "Duncan Murdoch" wrote:
> On 10/06/2017 6:09 PM, Duncan Murdoch wrote:
>
>> On 10/06/2017 2:38 PM, Morgan wrote:
>>
>>> Hi,
>>>
>>> I had a question that mi
mit of 16 menus. The limit is reached in
Bioconductor, as packages add vignettes.
R version 2.2.0, 2005-11-21, i386-pc-mingw32
attached base packages:
[1] "methods" "stats" "graphics" "grDevices" "utils" "datasets"
[7] &
A command
R CMD build
that fails, e.g., because of C code compilation errors, leaves a
directory %TMPDIR%/Rinst.xxx containing the file R.css. Although R
CMD INSTALL --build cleans up after itself, build does not. A fix is
below. Also, build.in references Rcmd.exe, which I thought was no
longer
Utils.pm (revision 36565)
+++ share/perl/R/Utils.pm (working copy)
@@ -75,7 +75,7 @@
$pat . $$ . sprintf("%05d", rand(10**5)));
my $n=0;
-while(-f $retval){
+while(-e $retval){
$retval = file_path($R::Vars::TMPDIR,
Here's my slow response; if there were other off-list replies it would
be great to have a summary.
Not exactly sure what you're looking for. You might adopt a parallel
program so that the 'master' node does something like
myprog.c:
MPI_Init(...)
/* parallel computations, e.g., of pi */
>> Duncan Murdoch
I would have expected numeric(0) as the result (numeric(0) is the
result from log(numeric(0)), etc).
Martin (Morgan)
Martin Maechler <[EMAIL PROTECTED]> writes:
>>>>>> "Ben" == Ben Bolker <[EMAIL PROTECTED]>
>
mean x == numeric(0),
n == 0 (0 copies of an empty set), x == ANY n == numeric(0) (an empty
set of ANYthing), x == numeric(0), n == numeric(0) ? For all of these,
x^n evaluates to numeric(0).
Martin (Morgan)
Duncan Murdoch <[EMAIL PROTECTED]> writes:
> On 1/9/2006 12:40 PM, Martin Morg
hat zero is the
>> identity element for addition, and one is the identity element for
>> multiplication.
>> Andy
>> From: Martin Morgan
>>> I guess I have to say yes, I'd exepct
>>> x <- 1:10
>>> sum(x[x>10]) ==> numeric(0)
>
table 'release' branch, once every six months. This means that the
Bioconductor devel branch periodically (as recently and I suspect over
the next several days) contains considerable carnage that propagates to
CRAN devel builds, creating additional work for CRAN maintainers.
Martin Morg
tandard / best practice for merging branches
git checkout master
git merge ... a-pull-request
git push ...
Creating pull requests is a problem for the developer wanting to
contribute to R, not for the R-core developer. As we've seen in this
thread, R-core would not need to feel responsib
On 05/02/2018 03:21 PM, Joris Meys wrote:
Dear all,
I've noticed by trying to download gz files from here :
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM907811
At the bottom one can download GSM907811.CEL.gz . If I download this
manually and try
oligo::read.celfiles("GSM907811.CEL.g
On 05/03/2018 05:48 AM, Joris Meys wrote:
Dear all,
I've been diving a bit deeper into this per request of Tomas Kalibra, and
found the following :
- the lock on the file is only after trying to read it using oligo, so
that's not a R problem in itself. The problem is independent of extrenal
pa
nargs() provides the number of arguments without evaluating them
> f = function(x, ..., y) nargs()
> f()
[1] 0
> f(a=1, b=2)
[1] 2
> f(1, a=1, b=2)
[1] 3
> f(x=1, a=1, b=2)
[1] 3
> f(stop())
[1] 1
On 05/03/2018 11:01 AM, William Dunlap via R-devel wrote:
In R-3.5.0 you can use ...length():
vis builds of Bioconductor packages
https://stat.ethz.ch/pipermail/bioc-devel/2019-January/014506.html
and elsewhere
Martin Morgan
On 1/3/19, 7:05 PM, "R-devel on behalf of Duncan Murdoch"
wrote:
On 03/01/2019 3:37 p.m., Duncan Murdoch wrote:
> I see this too; by bisection, it see
g the version of the API, as advised in the
header file!)
Martin Morgan
On 5/6/20, 2:26 PM, "R-devel on behalf of Duncan Murdoch"
wrote:
On 06/05/2020 1:09 p.m., frede...@ofb.net wrote:
> Dear R Devel,
>
> Since Linux moved away from using a file-system interfac
ages I personally would implement a connection.
(I mistakenly thought this was a more specialized mailing list; I wouldn't have
posted to R-devel on this topic otherwise)
Martin Morgan
On 5/6/20, 4:12 PM, "Gábor Csárdi" wrote:
AFAIK that API is not allowed on CRAN. It triggers
;s DESCRIPTION file:
> Package: Test
> Type: Package
> Title: Testing format
> Version: 1.0
> Date: 2010-06-22
> Author: Dan Murphy
> Maintainer: Dan Murphy
> Depends: methods
> Description: Does format in a package work with S4 format me
", x=5:1)
An object of class "A"
Slot "x":
[1] 5 8 9 8 5
Martin
>
>
> I can't see what's wrong in my method definition. Can anyone help me =
> with this?
>
> J
>
> Dr James Foadi PhD
> Membrane Protein Laboratory (MPL)
> Diamond Lig
>
> Thanks,
> Dominick
>
> [[alternative HTML version deleted]]
>
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--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research
ple-darwin9.8.0
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> Best regards
> Christian
> _._._._._._._._._._._._._._._._._._
> C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a
> V.i.e.n.n.a A.u.s.t.
)
@674e88 09 CHARSXP g0c1 [MARK,gp=0x21] "x"
@728c38 09 CHARSXP g0c1 [MARK,gp=0x21] "y"
Martin
> a table of size 754KB seems still to be pretty large?
>
> Best regards
> Christian
>
>
> On 7/12/10 11:44 PM, Martin Morgan wrote:
>>
>
> What the people who do the CRAN package checks do get unhappy about are
> packages which fail running the R code in their vignettes, since this
> often indicates a problem in the package which is not exercised by the
> examples nor tests. This gives a warning, as you will see in
0, sep="")))
>> system.time(y4 <- x4[keys])
>user system elapsed
> 130.390 0.000 132.316
>
> And it's apparently worse than quadratic in time!
>
> I'm wondering why this subsetting by name is so slow since it
> seems it could be implemented with x4
On 07/15/2010 08:38 AM, Martin Morgan wrote:
> On 07/15/2010 01:12 AM, Hervé Pagès wrote:
>> Hi,
>>
>> I'm subsetting a named vector using character indices.
>> My vector of indices (or keys) is 10x longer than the vector
>> I'm subsetting. All my ke
always work?
> What are the additional rules?
callNextMethod() will cause additional problems; the idea that you'll
grab things from somewhere other than function arguments doesn't seem
like a robust design, even if it's used in some important parts of R.
Martin
>
> Man
On 09/03/2010 04:42 AM, Duncan Murdoch wrote:
> Philippe Grosjean wrote:
>> Hello,
>>
>> It's several days I try to track this bug, and even cannot cook a
>> reproducible example. Yet, it occurs consistently in a long-running
>> task after a variable period of time. Here is an example:
>>
>
> I
If I
f = function() {}
package.skeleton("PkgA", "f", path="/tmp")
and then edit man/PkgA-pacakge.Rd to read in part
\description{
More about what it does (maybe more than one line)
\Sexpr{1}
}
and then
R CMD build PkgA
I end up with
Saving output to ‘/tmp/PkgA/build/PkgA.pdf’ ...
Warning in
On 09/06/2010 10:00 PM, Dario Strbenac wrote:
> Hello,
>
> I've been attempting to make a generic method that dispatches on the first
> argument, which can be either an S3 or an S4 class. This is as far as I've
> gotten. Any suggestions about what to try next ?
>
> library(aroma.affymetrix)
> lib
On 10/06/2010 06:12 PM, Troy Robertson wrote:
> Hi all,
>
> After no replies to my previous message I thought I might show some code to
> demonstrate the change and again seek any explanation for the error now
> thrown by my code after upgrading from 2.10.1 to 2.11.1.
>
> Thanks
> Troy
> --
On 10/08/2010 01:25 PM, Dirk Eddelbuettel wrote:
>
> With several versions of R 2.12.0 I have been seeing this when running
>
> R CMD build Rcpp
>
> from the SVN sources:
>
> [...]
> Transcript written on Rd2.log.
> Saving output to '/home/edd/svn/rcpp/pkg/Rcpp/build/Rcpp.pdf' ...
> W
On 10/12/2010 07:38 AM, lan gao wrote:
> Dear R Developers,
>
> I am developing a package to submit to bioconductor. Right now, a gene-set
> sample data is saved as a data frame. Each row contains a probe set and its
> corresponding gene-set name ( mutiple probe -set may map to a gene-set name)
>
On 10/19/2010 08:33 PM, Dario Strbenac wrote:
> Hello,
>
> I'm looking for a way to extract objects from what gets created when I Sweave
> with driver = weaver(). I found where the .Rdata objects are, but when I load
> one into R, I don't see anything that looks like the objects that were
> cre
On 10/20/2010 04:25 PM, Dominick Samperi wrote:
> Thanks David, but this doesn't work. Under R 2.12.0 the "Loading required
> packages"
> messages appear under R 2.12.0 when I use, for example:
>
> Rscript --vanilla -e "{ invisible(library(cxxPack)); cat(sqrt(2)) }"
?suppressPackageStartupMessage
If I try to build a package with a vignette
R CMD build Biobase
I see
* checking for file 'Biobase/DESCRIPTION' ... OK
* preparing 'Biobase':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* creating vignettes ... OK
* cleaning src
On 10/25/2010 03:21 AM, Prof Brian Ripley wrote:
> Biobase is not self-contained so I cannot easily test it, but as far as
> I know this is now resolved.
Thank you it is. Martin
>
> On Sun, 24 Oct 2010, Martin Morgan wrote:
>
>> If I try to build a package with a vignet
On 10/26/2010 03:53 AM, Robin Hankin wrote:
> Hello.
>
> I am trying to write an S4 method for rbind(). I have a class of objects
> called 'mdm', and I want to be able to rbind() them to one another.
>
> I do not want the method for rbind() to coerce anything to an mdm object.
> I want rbind(x1,x
On 11/12/2010 02:31 PM, Patrick Leyshock wrote:
> Hello,
>
> I've created this class:
>
> setClass("example",
>representation (
> size = "numeric",
> id= "character"
>)
> )
>
> Suppose I create a new instance of this class:
>
>> x <- new("example", 4, "id_value"
alysis: Programming with R chapters
11 & 12,
Gentleman, 2008, R Programming for Bioinformatics chapter 6
might be helpful, but by the time they arrive you might find that you're
most of the way through the material covered...
I guess my opinion is that Rcpp would not be useful for u
On 11/15/2010 04:56 PM, Hadley Wickham wrote:
>> Well, that's what I thought too. But:
>>
>> parents <- function(x) {
>> if (identical(x, emptyenv())) return()
>> c(environmentName(x), parents(parent.env(x)))
>> }
>>> parents(as.environment("package:devtools"))
>> [1] "package:devtools" "package
On 11/22/2010 03:23 AM, evilphil wrote:
>
>
>
> anyone?
Hi evilphil --
Your method signature doesn't have 'missing' for its third argument, and
hence isn't the target of dispatch when the generic is invoked with a
missing argument. I guess you'd figured that out and are really asking
whether i
On 01/24/2011 08:37 AM, Kasper Daniel Hansen wrote:
> Johann,
>
> whether S4 is "better" than S3 is a heated subject. No-one (I think)
> disputes that S4 is in some sense more flexible (for some suitable
> definition of flexible), but it does incur some performance overhead
> (how much is debatab
On 01/26/2011 02:56 PM, wayne.zh...@barclayscapital.com wrote:
> Hi,
>
> I'd like to construct an R list object in C++, fill it with relevant data,
> and pass it to an R function which will return a different list object back.
> I have browsed through all the R manuals, and examples under tests
help too. I'm doing something very simple at the
moment, so I prefer not to bring in Rinside/Rcpp if possible.
Thanks again,
Wayne
-Original Message-
From: Martin Morgan [mailto:mtmor...@fhcrc.org]
Sent: Wednesday, January 26, 2011 10:04 PM
To: Zhang, Wayne: IT (NYK)
Cc: r-devel@r-proj
On 01/27/2011 08:51 PM, Paul Bailey wrote:
> Hi,
>
> I'm trying to make a new S4 object with a slot for a "link-glm" object. R
> doesn't like me have a slot of class "link-glm"
>
>> class(make.link("probit"))
> [1] "link-glm"
Tell the S4 system that you'd like to use this 'old' class
setOldCla
On 02/03/2011 09:29 AM, Paul Gilbert wrote:
> I am trying to extend an S3 method to work with an S4 object as well
> as the S3 objects it works with, but UseMethod does not seem to
> recognize the S4 class and dispatches to the default method. Is this
> to be expected or should I be looking for an
On 02/14/2011 11:54 PM, robin hankin wrote:
> Hello everybody
>
> [R-2.12.1]
>
> I am having difficulty dealing with Oarray objects.
> I have a generic function, call it foo(), and I wish
> to define a method for Oarray objects.
>
> I do not have or want a method for regular arrays [actually,
>
On 03/01/2011 03:19 PM, Benilton Carvalho wrote:
> Hi,
>
> I have a BioC infra-structure package that works fine (I can build,
> check and load it successfully) on revision r53950. The very same
> package fails on r54591 with the error below:
>
> Error in loadNamespace(package, c(which.lib.loc, l
On 03/10/2011 08:21 AM, ONKELINX, Thierry wrote:
> Dear all,
>
> I'm writing a package and I would like to reuse the residuals()
> function. When I use a function which calls the redefined residuals
> (for my custom class) I get an error (see below). It looks like the
> wrong method is used. The s
On 03/11/2011 02:07 AM, Andreas Borg wrote:
> Hi all,
>
> I have a function which makes use of missing() to determine which
> arguments are provided in the call - basically, there are two sets of
> arguments that map to different strategies the function uses to fulfill
> its task. After conversion
On 03/21/2011 07:22 PM, Simon Urbanek wrote:
On Mar 21, 2011, at 9:07 PM, Dan Tenenbaum wrote:
Hello,
I have come across two separate packages that have a Makefile in inst/doc
which use the R_HOME variable.
In both cases, the path to R_HOME gets munged in such a way that commands
that includ
ry, not on base::summary, so without the
Matrix::summary generic your object never sees the summary method for
lme4 objects.
So you need to Import: Matrix and importFrom(Matrix, summary).
Martin Morgan
exportMethods("coef","summary","show","print")
exportCla
R version 2.13.0 alpha (2011-03-27 r55091)
This error occurs when R CMD check'ing a Bioconductor package:
* checking for unstated dependencies in R code ... WARNING
Error in e[keep] : invalid subscript type 'list'
Execution halted
See the information on DESCRIPTION files in the chapter 'Creating
On 04/13/2011 11:34 AM, Dirk Eddelbuettel wrote:
On 13 April 2011 at 13:00, Terry Therneau wrote:
| I have a test directory for the survival suite, and dyn.load has ceased
| to work in it. Below shows the log:
|
| tmt1075% R --vanilla
|
| R version 2.12.2 (2011-02-25)
| Copyright (C) 2011 The R
On 04/15/2011 11:18 AM, Simon Urbanek wrote:
On Apr 14, 2011, at 11:00 PM, Dario Strbenac wrote:
I have a confusing error from R CMD check that I don't get when running the
example manually by hand.
In the \examples section of an Rd file, I create a GRanges object, then I call
a function wi
On 04/19/2011 05:00 PM, Dario Strbenac wrote:
Hello,
I've got a DESCRIPTION file with a the first line:
Package: Repitools
But, when I run R CMD INSTALL Repitools I get:
* installing *source* package Repitools ...
** R
** data
** inst
** preparing package for lazy loading
Warning in FUN(X[[1L
ly?
Martin
I guess I need to use there where argument. But how do I have this call outside
any S4 functions, but without having to load aroma.affymetrix when my package
loads ?
Original message
Date: Tue, 19 Apr 2011 19:23:20 -0700
From: Martin Morgan
Subject: Re: [Rd]
as.factor / as.ordered is not written as a generic. This differs from
as.numeric, as.matrix, and other as.*. The following seems to address
this and does not break make check-all.
FWIW, the patch is against r55563, because with r55564 I see
/home/mtmorgan/src/R-devel/src/main/dounzip.c:75:15:
On 04/20/2011 10:13 AM, William Dunlap wrote:
-Original Message-
From: r-devel-boun...@r-project.org
[mailto:r-devel-boun...@r-project.org] On Behalf Of Martin Morgan
Sent: Wednesday, April 20, 2011 9:56 AM
To: R-devel@r-project.org
Subject: [Rd] Make as.factor an S3 generic?
as.factor
.double.A instead of as.numeric.A) until factor.
Martin
On Wed, 20 Apr 2011, Martin Morgan wrote:
as.factor / as.ordered is not written as a generic. This differs from
as.numeric, as.matrix, and other as.*. The following seems to address
this and does not break make check-all.
FWIW, the pat
ls without installing RepitoolsExamples.
"if (require(RepitoolsExamples))" in an example on a man page is much
preferred to \dontrun{}, as Simon mentions.
Martin Morgan
For more info: this is covered in the "Writing R Extensions," but is
also described here:
http
Several Bioconductor packages were expecting Windows Rzlib.dll to
provide gzopen / gzread / gzseek / gzgets / gzrewind / gzclose. Are
these gone for good, viz., r55624 ?
Martin
--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
On 05/01/2011 03:09 PM, John Chambers wrote:
Yes, as presented on that site it makes a little more sense:
"While experimenting with the new reference classes in R I noticed some
odd behaviour if you use the "[[ ]]" notation for methods
(X[["doSomething"]] instead of X$doSomething). This notation
This change has significant consequences for Windows packages using R's
zlib, including packages providing core Bioconductor functionality. Are
the changes in r55624 meant to be long-term?
Martin
On 04/29/2011 03:13 PM, Martin Morgan wrote:
Several Bioconductor packages were expe
An .Rnw file in the vignettes/ directory might reasonably \usepackage or
\include .sty, .bib, or other (e.g., image) files in the same directory
or a sub-directory. The .Rnw file is copied to inst/doc and hence
installed, but the additional files are not. This means that the
installed .Rnw file
also seems like a poor choice. What other strategies are recommended?
Martin
On 05/06/2011 09:58 AM, Martin Morgan wrote:
This change has significant consequences for Windows packages using R's
zlib, including packages providing core Bioconductor functionality. Are
the changes in r55624 meant
On 05/27/2011 06:13 AM, Janko Thyson wrote:
Dear list,
is it possible that method dispatch checks for superclasses/virtual
classes before checking "ANY"?
I'd like to build a generic initialization method for all my Reference
Class (say "MyDataFrame") objects by having them inherit from class, s
On 05/30/2011 08:54 AM, Janko Thyson wrote:
Dear List,
when I first started to use S4 classes, I used the function
'completeClassDef()' in order to see the super- and subclasses of a
certain class:
Hi Janko -- I think 'complete' is meant as an adverb here; what you
might want is names(getClas
On 06/03/2011 02:03 PM, mcguirebc wrote:
Is there a simple way to assign values to S4 slots from within a function?
Doing this doesn't work:
assign_slot<-function(x){
assign("OBJECT@slot",x,envir=parent.env(environment())
}
assign_slot(x)
All I get from this is a new object with the nam
On 06/04/2011 03:07 AM, soeren.vo...@uzh.ch wrote:
Hello, an S4 class "Foo" is defined with a setter, $. For several reasons, the
setter calls a function, .foo.update(). However, bypassing the argument names of the
setter does not work. Question 1: Why not and how can I fix this? Question 2: Wh
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