is local. Then the duplicated
version has only one reference and the primitive replacement doesn't
copy it.
...
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Martin Morgan
Computational Biology / Fred
for
this issue. Thanks in advance for your time.
Best regards,
Thibaut Jombart.
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
.
Any guidance would be appreciated. Thank you
Dan Murphy
[[alternative HTML version deleted]]
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Martin Morgan
Computational Biology / Fred Hutchinson
Laboratory (MPL)
Diamond Light Source Ltd
Diamond House
Harewell Science and Innovation Campus
Chilton, Didcot
Oxfordshire OX11 0DE
Email: james.fo...@diamond.ac.uk
Alt Email: j.fo...@imperial.ac.uk
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100
[[alternative HTML version deleted]]
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
__
R
?
Best regards
Christian
On 7/12/10 11:44 PM, Martin Morgan wrote:
On 07/12/2010 01:45 PM, cstrato wrote:
Dear all,
With great interest I followed the discussion:
https://stat.ethz.ch/pipermail/r-devel/2010-July/057901.html
since I have currently a similar problem:
In a new R session
tests. This gives a warning, as you will see in quite a
few CRAN package checks.
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research
wondering why this subsetting by name is so slow since it
seems it could be implemented with x4[match(keys, names(x4))],
which is very fast: only 0.012s!
This is with R-2.11.0 and R-2.12.0.
Thanks,
H.
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100
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 keys are distinct and only 10% of them
are valid (i.e. match
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 would look
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)
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' ...
Warning in
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 10/20/2010 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)) }
?suppressPackageStartupMessages
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 vignette
R CMD build Biobase
I
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
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)
This creates an S4
covered...
I guess my opinion is that Rcpp would not be useful for understanding
R's C layer, whatever its merits for 'getting the job done'.
Martin
Thank you,
Patrick
On Fri, Nov 12, 2010 at 4:36 PM, Martin Morgan mtmor...@fhcrc.org
mailto:mtmor...@fhcrc.org wrote:
On 11/12/2010
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:methods Autoloads
On 11/22/2010 03:23 AM, evilphil wrote:
BUMP
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
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 debatable) and
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
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-project.org
Subject: Re: [Rd] Dealing with R
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
setOldClass(link-glm)
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,
I want
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,
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
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 to
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
to Import: Matrix and importFrom(Matrix, summary).
Martin Morgan
exportMethods(coef,summary,show,print)
exportClasses(mer,summary.mer)
S3method(coeftab,default)
The package passes the routine parts of R CMD check. The following
test shows that, with lme4 loaded, coef(summary([object of class
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
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
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
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
On 04/19/2011 08:00 PM, Dario Strbenac wrote:
Ah, I think it's happening because I have
setOldClass(AffymetrixCelSet) in my package.
if AffymetrixCelSet is from aroma.affymetrix, then the line above results in
setOldClass(AffymetrixCelSet)
Error in x[length(x):1L] : object of type 'closure'
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
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 patch is against r55563
)) 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://stackoverflow.com/questions/1454211/what-does-not-run-mean-in-r-help-pages
HTH,
-steve
--
Steve
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 expecting
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
it
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, say
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
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 name
On 06/04/2011 03:07 AM, soeren.vo...@uzh.ch wrote:
Hello, an S4 class Foo is defined with a setter, $. For several reasons, the
setter calls a function, .foo.update(). However, bypassing the argument names of the
setter does not work. Question 1: Why not and how can I fix this? Question 2:
On 06/09/2011 10:11 AM, John Chambers wrote:
Good catch.
Here's the problem. To save space and time, reference methods are not
all copied to every object in the class. Instead, the methods are copied
in when first accessed. Methods are functions which use the object as
their environment. So
On 06/10/2011 04:04 PM, Kornelius Rohmeyer wrote:
I'm sorry for sending a wrongly formated mail before. This is the missing text:
Dear all,
for a CRAN-package that depends on another Bioconductor-package I find
two things annoying and would like to know whether there are some
workarounds:
1)
On 06/10/2011 05:46 PM, Kornelius Rohmeyer wrote:
Dear Martin,
thanks for your response.
The superclass graphBase is introduced in graph 1.30. In my
understanding the problem is that our package gMCP is build on CRAN
for R 2.12 with the package graph in version 1.30. Unfortunately
biocLite
On 07/04/2011 05:08 AM, Prof Brian Ripley wrote:
There was an R-core meeting the week before last, and various planned
changes will appear in R-devel over the next few weeks.
These are changes planned for R 2.14.0 scheduled for Oct 31. As we are
sick of people referring to R-devel as '2.14' or
It would be convenient if, under R-devel r56422, packages that require
re-installation because they do not have a NAMESPACE were marked as
old.packages, so their lack of functionality can be discovered more easily.
snow %in% row.names(old.packages())
[1] FALSE
library(snow)
Error in
With this set-up
options(warn = 1)
tf - tempfile()
finalizer - function(obj) {
message(finalizer)
close(obj$f)
}
this code works
ev - new.env()
ev$f - file(tf, w)
reg.finalizer(ev, finalizer)
rm(ev)
gc()
whereas this (reversing the order of file() and reg.finalizer())
ev - new.env()
On 08/23/2011 03:02 PM, Janko Thyson wrote:
Dear list,
I was wondering how to best implement some sort of a plugin paradigm
using R methods and the dispatcher:
Say we have a function/method ('foo') that does something useful, but
that should be open for extension in ONE specific area by OTHERS
On 08/26/2011 04:44 AM, Gavin Simpson wrote:
Dear List,
This may be related to this email thread initiated by Ben Bolker last
month: https://stat.ethz.ch/pipermail/r-devel/2011-July/061630.html
In answering this Question on StackOverflow
http://stackoverflow.com/q/7195628/429846 I noticed that
On 08/29/2011 05:36 PM, Simon Urbanek wrote:
On Aug 29, 2011, at 7:48 PM, Alireza Mahani wrote:
I am trying to parallelize part of a C function that is called from
R (via .C) using OpenMP's parallel for pragma. I get mixed
results: some runs finish with no problem, but some lead to R
crashing
On 09/23/2011 01:46 PM, Hervé Pagès wrote:
Hi,
cbind() doesn't seem to like raw vectors:
df - cbind(a=integer(4000), b=raw(4000))
df
*** glibc detected *** /home/hpages/R-2.13.1/bin/exec/R: malloc():
memory corruption: 0x02d73ca0 ***
For what it's worth, under valgrind
R -d
On windows under current R-devel (r57066), R CMD INSTALL, for instance,
invokes gcc with -I$(R_HOME)/include prior to any user-defined include
paths. This means that a package cannot specify an alternative zlib.h,
as a (reduced) version of this is in $(R_HOME)/include.
One way around this is
Allocating many small objects triggers numerous garbage collections as R
grows its memory, seriously degrading performance. The specific use case
is in creating a STRSXP of several 1,000,000's of elements of 60-100
characters each; a simplified illustration understating the effects
(because
language characteristics).
Martin
Thanks for sharing your insight and time,
gopi.
http://gopi-goswami.net/
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Martin Morgan
Computational Biology / Fred Hutchinson
] tools_2.10.0
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M2 B169
Phone: (206) 667-2793
__
R-devel@r-project.org mailing list
https
A little more precisely, unlink fails when the file being unlinked is
a broken symbolic link (as in the example below). This is because
R_FileExists checks stat() == 0, and stat fails (returns -1) when
trying to resolve the broken link. Perhaps lstat() is more
appropriate?
Martin
Martin Morgan
.
Martin
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M2 B169
Phone: (206) 667-2793
__
R-devel@r-project.org mailing list
https
missing?
Thanks,
Whit
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location
Stavros Macrakis wrote:
On Tue, Mar 31, 2009 at 12:41 PM, Martin Morgan mtmor...@fhcrc.org
mailto:mtmor...@fhcrc.org wrote:
I don't konw about preferred, but one method is
pkgVars - local({
x - NULL
list(getX=function() x, setX=function(value) x - value
expect
environment: bdplot
from environment().
How can I get to write to .FOO via bar()?
Thank you very much
Philip.
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Martin Morgan
Computational Biology / Fred
://www.fss.uu.nl/soc/bojanowski
http://www.ifispan.waw.pl/socnierowno
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave
;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 / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024
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 and hence
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 function needs
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 of
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 the
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 does
(parent=emptyenv())) {
.Object - callNextMethod(.Object, .xData=.xData)
return(.Object)
}
)
s - new(Element)
Not sure why that changes things though?
Troy
-Original Message-
From: Martin Morgan [mailto:mtmor...@fhcrc.org]
Sent: Monday
Stavros Macrakis wrote:
On Mon, Jun 29, 2009 at 9:19 AM, Martin Morgan mtmor...@fhcrc.org
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, so you can
end
of having to hide
them in .xData
Troy
Troy Robertson
Database and Computing Support Provider
Southern Ocean Ecosystems, ERM/Fish
Australian Antarctic Division
Channel Highway, Kingston 7050
PH: 03 62323571
troy.robert...@aad.gov.au
-Original Message-
From: Martin Morgan
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()
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 argument.
Martin
--
Martin Morgan
Computational Biology / Fred
@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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.
package, not your implementation of particular classes?
Martin
Many thanks,
Vitalie.
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
Vitalie S. wrote:
On Tue, 18 Aug 2009 15:42:48 +0200, Martin Morgan mtmor...@fhcrc.org
wrote:
Vitalie S. vitosm...@rambler.ru writes:
Dear Developers,
In current implementation of validity method, objects are first
coerced to superclass (slots are striped). Thus, it is not possible
Hi Christos --
Christos Hatzis wrote:
Hello,
After running R CMD check on my package I received the following error on
package dependencies:
* using log directory 'C:/z-zBackup/Nuvera Bio on
Iatros01/Development/RPackages/nvNormalize/nvNormalize.Rcheck'
* using R version 2.9.1
Thanks. I think I got the hang of it. I will try it out and post any
more queries I have regarding handling data types onto the mailing list.
Regards
Abhijit Bera
On Tue, Aug 25, 2009 at 7:15 PM, Martin Morgan mtmor...@fhcrc.org
mailto:mtmor...@fhcrc.org wrote
for
b.initialize is used (not starting with k), everything is fine.
Other workarounds:
- in setMethod write kl = .Object instead of simply .Object
yes, this avoids mixing matching by name and by position.
Martin Morgan
- this does not happen if the contents of b.initialize are directly
moved
. Please update your package
and provide sessionInfo again' might well serve to address the user's
original problem, but it would have been better to spot the outdated
package by looking at the version number produced by sessionInfo().
Martin Morgan
Best,
Fritz
pleyd...@supagro.inra.fr wrote:
Writing R Extensions says
{quotes}
If you have a crash which gives a core dump you can use something like
gdb /path/to/R/bin/exec/R core.12345
to examine the core dump. If core dumps are disabled...
{unquotes}
sadly it doesn't go on to say how to
pleyd...@supagro.inra.fr wrote:
not really answering your question, but I find it more useful to
R -d gdb
or
R -d gdb -f test.R
where test.R reproduces the bug in some minimal code. A variant is
R -d valgrind -f test.R
if the memory problem is not easy to spot.
Thanks for your
Hi Christos --
Christos Hatzis wrote:
I am developing a package that imports some functions from another package.
The imported package (qcc) does not have a namespace and this is causing
problems with loading of my package, which has a namespace. Is there a
workaround to allow loading the
list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
__
R-devel
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman
-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
Thanks.
Ross Boylan
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold
success using library.dynam in .onLoad?
Thanks in advacne
Martin
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
1 - 100 of 1367 matches
Mail list logo
