I suggest that you cc Martin Maechler on this discussion. I happen to be
on the Bioc-devel list but I'm not sure if he is. Although both of us are
still listed as maintainers of the Matrix package, he is, and has been for
several years, the de facto maintainer.
On Wed, Nov 1, 2017 at 4:15 PM
Is there a difference in the copying behavior of
x@little - other
and
x@little[] - other
I was using the second form in (yet another!) modification of the internal
representation of mixed-effects models in the lme4 package in the hopes
that it would not trigger copying of the entire object.
My purpose in mentioning the Julia language (julialang.org) here is
not to start a flame war. I find it to be a very interesting
development and others who read this list may want to read about it
too.
It is still very much early days for this language - about the same
stage as R was in 1995 or
On Thu, Mar 1, 2012 at 11:20 AM, Jeffrey Ryan jeffrey.r...@lemnica.com wrote:
Doug,
Agreed on the interesting point - looks like it has some real promise.
I think the spike in interest could be attributable to Mike
Loukides's tweet on Feb 20. (editor at O'Reilly)
On Wed, Jan 11, 2012 at 11:49 AM, Simon Urbanek
simon.urba...@r-project.org wrote:
On Jan 11, 2012, at 12:08 PM, Taylor Arnold wrote:
R-devel,
I have noticed that making a copy of an object in R prior to using
.Call on the original object can
cause the C code to alter not only the object
On Thu, Dec 29, 2011 at 8:05 AM, Yves Deville deville.y...@alpestat.com wrote:
Dear R-devel members,
I am looking for a fast Cholesky update/downdate. The matrix A being
symmetric positive definite (n, n) and factorized as
A = L %*% t(L), the goal is to factor the new matrix A +- C %*% t(C)
On Dec 6, 2011 8:30 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote:
On 05/12/2011 1:22 PM, Paul Viefers wrote:
Dear all,
running the example by D. Eddebuettel (
http://dirk.eddelbuettel.com/blog/2011/04/23/) I get an error message.
Specifically, the R code I was taking from the above
On Nov 11, 2011 6:13 PM, Bryan W. Lewis ble...@illposed.net wrote:
Dear R-devel readers:
I am really stuck trying resolving an issue with the use of the
Matrix in one of my packages, irlba, with R-2.14.0. When I use
crossprod with at least one sparse argument in the packaged code I
receive
On Thu, Jul 14, 2011 at 10:21 AM, Alireza Mahani
alireza.s.mah...@gmail.com wrote:
(I am using a LINUX machine)
Jeff,
In creating reproducible results, I 'partially' answered my question. I have
attached two scripts, 'mvMultiply.r' and 'mvMultiply.cc'. Please copy both
files into your
the pointer first, then the
dimensions. For the first _Rout.txt file this part of the code is not
used.
On Tue, Jul 19, 2011 at 10:00 AM, Douglas Bates ba...@stat.wisc.edu wrote:
On Thu, Jul 14, 2011 at 10:21 AM, Alireza Mahani
alireza.s.mah...@gmail.com wrote:
(I am using a LINUX machine
Questions like this would get a faster response on the Rcpp-devel list, to
which I am copying this reply.
On Jun 21, 2011 6:35 AM, oyvfos oyv...@yahoo.no wrote:
Hi, I get an error using RcppGSL: fatal error: gsl/gsl_vector.h:No such
file
or directory. What is the best way to install these files
On Fri, Jun 3, 2011 at 5:17 AM, oliver oli...@first.in-berlin.de wrote:
Hello,
I'm implementing a package (C-extension),
where one function gets data and a function
that needs to be applied to the data.
I want to apply the function to (parts of)
the data on the C-side.
1) how do I apply
On Tue, Mar 29, 2011 at 2:17 PM, Douglas Bates ba...@stat.wisc.edu wrote:
On Tue, Mar 29, 2011 at 5:34 AM, Hin-Tak Leung
ht...@users.sourceforge.net wrote:
Martin Maechler wrote:
Douglas Bates ba...@stat.wisc.edu
on Mon, 28 Mar 2011 09:24:39 -0500 writes:
Can you provide the output
On Sun, Feb 20, 2011 at 4:39 PM, Jason Rudy jcr...@gmail.com wrote:
I've never used C++ before, so for this project I think I will stick
with just using the BLAS and LAPACK routines directly. Another issue
is that I will need to do some sparse matrix computations, for which I
am planning to
It is more effective to send such inquiries to the Rcpp-devel mailing
list which I am cc'ing on this reply.
On Thu, Jan 20, 2011 at 3:05 PM, mtck1982 xiaoch@gmail.com wrote:
Hi All,
I am new to this area and use Rcpp to call C++ from R and try to build the
package under Windows 7. I use
On Fri, Dec 3, 2010 at 11:01 AM, Ravi Varadhan rvarad...@jhmi.edu wrote:
Dear Duncan,
What constitutes a convincing argument for making significant changes?
Taking the example of optimization algorithms (say, for smooth objective
functions), how does one make a convincing argument that a
Reply redirected to the R-devel list.
On Tue, Nov 16, 2010 at 1:02 PM, Prof. John C Nash nas...@uottawa.ca wrote:
Ravi Varadhan and I have been looking at UCMINF to try to identify why it
gives occasional
(but not reproducible) errors, seemingly on Windows only. There is some
suspicion that
On Tue, Nov 16, 2010 at 2:35 PM, Prof. John C Nash nas...@uottawa.ca wrote:
I normally see digest once per day, but got msg from Doug Bates so responding
with context.
UCMINF is a package on CRAN that implements a variable metric minimizer.
A pedant might point out that the package is called
On Thu, Oct 28, 2010 at 1:44 PM, Dominick Samperi djsamp...@gmail.com wrote:
See comments on Rcpp below.
On Thu, Oct 28, 2010 at 11:28 AM, William Dunlap wdun...@tibco.com wrote:
-Original Message-
From: r-devel-boun...@r-project.org
[mailto:r-devel-boun...@r-project.org] On
On Fri, Oct 22, 2010 at 4:30 AM, Nick Sabbe nick.sa...@ugent.be wrote:
Hello all.
I'm developing a package for R holding a Gibbs sampler, which tends to have
better performance when written in C than in R.
During each iteration in the Gibbs sampler, I need the inverse of a
symmetric matrix.
On Sun, Jun 13, 2010 at 8:28 AM, Uwe Ligges
lig...@statistik.tu-dortmund.de wrote:
On 13.06.2010 01:09, Dr. David Kirkby wrote:
On 06/12/10 05:27 PM, Douglas Bates wrote:
On Sat, Jun 12, 2010 at 8:37 AM, Dr. David Kirkby
david.kir...@onetel.net wrote:
R 2.10.1 is used in the Sage maths
There is a Debian/Ubuntu specific list, r-sig-deb...@r-project.org,
which I am cc:'ing on this reply, that is a better location for this
discussion.
It appears that you may be going about things the hard way. There are
Ubuntu packages for atlas and for R that can handle all of this for
you.
On Mon, Apr 12, 2010 at 10:27 PM, shotwelm shotw...@musc.edu wrote:
r-devel list,
I have recently written an R package that solves a linear least squares
problem, and computes the multivariate normal density function.
For both of those applications you can use a Cholesky decomposition of
the
I think a simpler solution, which I have implemented in lme4 but not
yet released is to have
importFrom(nlme, ranef, fixef)
in the NAMESPACE file of packages that implement methods for those
generics (and, of course, add nlme to the Imports: specification in
the DESCRIPTION file). As nlme is a
Did you run
$RHOME/src/tools/rsync-recommended
to obtain the most recent versions of the recommended packages before
trying to compile them?
On Fri, Mar 5, 2010 at 3:01 PM, Alex Bryant abry...@i-review.com wrote:
Hi folks, I'm having a problem with installing R on Solaris. Has anyone
seen
On Mon, Jan 11, 2010 at 10:34 AM, Ben Bolker bol...@ufl.edu wrote:
who wants to write rgl code to do these?
http://tinyurl.com/yzojfn2
http://tinyurl.com/ylrz2p8
:-)
I think that on this one we should follow Nancy Reagan's advice and
Just say no.
I wonder if they have read Tufte's
On Sun, Nov 8, 2009 at 2:26 PM, Doran, Harold hdo...@air.org wrote:
I've defined the following for objects of a class called jml
summary.jml - function(object, ...){
tab - cbind(Estimate = coef(object),
StdError = object$se,
Infit =
On Fri, Oct 23, 2009 at 7:27 PM, Douglas Bates ba...@stat.wisc.edu wrote:
On Fri, Oct 23, 2009 at 9:23 AM, Douglas Bates ba...@stat.wisc.edu
wrote:
On Fri, Oct 23, 2009 at 8:39 AM, Abhijit Bera abhib...@gmail.com
wrote:
Hi
I'm having slight confusion.
Indeed.
I plan to grow
On Fri, Oct 23, 2009 at 8:39 AM, Abhijit Bera abhib...@gmail.com wrote:
Hi
I'm having slight confusion.
Indeed.
I plan to grow/realloc a matrix depending on the data available in a C
program.
Here is what I'm tried to do:
Data=allocMatrix(REALSXP,3,4);
SEXP Data;
Those lines should be
On Fri, Oct 23, 2009 at 9:23 AM, Douglas Bates ba...@stat.wisc.edu wrote:
On Fri, Oct 23, 2009 at 8:39 AM, Abhijit Bera abhib...@gmail.com wrote:
Hi
I'm having slight confusion.
Indeed.
I plan to grow/realloc a matrix depending on the data available in a C
program.
Here is what I'm
On Mon, Oct 12, 2009 at 6:41 AM, Romain Francois
romain.franc...@dbmail.com wrote:
On 10/12/2009 02:05 AM, m...@stat.ubc.ca wrote:
Full_Name: Mike Danilov
Version: 2.9.0
OS: Fedora Core 9
Submission from: (NULL) (142.103.121.198)
When checking for the symmetry of a matrix, function
On Thu, Sep 24, 2009 at 2:09 PM, Vinh Nguyen vqngu...@uci.edu wrote:
On Thu, Sep 24, 2009 at 11:49 AM, Simon Urbanek
simon.urba...@r-project.org wrote:
As Doug pointed out you don't want to be using .C(). As for matrix
manipulations - they are usually done directly on the objects which are
On Wed, Sep 23, 2009 at 2:39 AM, Vinh Nguyen vqngu...@uci.edu wrote:
dear list,
since matrix manipulations is often of interest in statistical
computations, i'd like to get a working example of using Lapack for
regression. However, i run into an error.
My matrix-lapack-example.c file:
On Fri, Sep 11, 2009 at 1:48 PM, rudjer rkoen...@uiuc.edu wrote:
Comrades,
When talk turns to the purity of the revolution, and purge of packages then
the guillotine can't be far behind. We all remember Lenin berating the
renegade Kautsky for his pragmatism, and we know where that led...
On Thu, Sep 3, 2009 at 10:02 AM, Martin
Maechlermaech...@stat.math.ethz.ch wrote:
MM == Martin Maechler maech...@stat.math.ethz.ch
on Thu, 3 Sep 2009 16:14:24 +0200 writes:
HW == Hadley Wickham had...@rice.edu
on Thu, 3 Sep 2009 08:16:27 -0500 writes:
HW Just noticed these two
On Mon, Aug 17, 2009 at 9:23 AM, Jeffrey J. Hallmanjhall...@frb.gov wrote:
One hassle I could do without is the necessity of writing C wrapper functions
like this:
void fameInit(int *status){
cfmini(status);
return;
}
when I want to call a library function (cfmini, in this case) that
On Sat, Aug 8, 2009 at 1:31 PM, Gavin Simpsongavin.simp...@ucl.ac.uk wrote:
Dear List,
I am writing a formula method for a function in a package I maintain. I
want the method to return a data.frame that potentially only contains
some of the variables in 'data', as specified by the formula.
On Fri, Jun 26, 2009 at 2:43 PM, Paul Johnsonpauljoh...@gmail.com wrote:
Hello, again.
I'm interested to learn how programmers develop test C/C++ code with
R packages in Linux. I've been reading R source and the manual on
Writing R Extensions but there are just a couple of details I can't
There have been several messages on R-devel mentioning the interior
point optimization software Ipopt, https://projects.coin-op/Ipopt/.
This C++ library is released under a license called the Common Public
License.
I have two questions that readers of R-devel may be able to answer.
1) Would
On Sun, Feb 22, 2009 at 7:44 AM, Christophe Dutang duta...@gmail.com wrote:
Dear all,
I have just found a 'good' tutorial R for datamining. I think it should be
on the contributed docs.
http://cran.r-project.org/other-docs.html
Here is the link
On Sun, Feb 22, 2009 at 3:05 PM, Douglas Bates ba...@stat.wisc.edu wrote:
There have been several messages on R-devel mentioning the interior
point optimization software Ipopt, https://projects.coin-op/Ipopt/.
This C++ library is released under a license called the Common Public
License.
I
On Fri, Jan 23, 2009 at 1:25 AM, Biczok Rudolf
r.bic...@dkfz-heidelberg.de wrote:
Hi all,
I'm working with the S4-Class system and I have a little problem with
Implementing iteration functionality in my S4 class but it don't work:
setClass(foo,representation(bar=list))
x -
This question is only related to R-devel in that I need to work out
how to reach R-forge.R-project.org to update and commit files of R
packages for which I am a developer.
My desktop computer at work runs Ubuntu 8.04. Because this is not a
supported operating system this computer is behind a
On Fri, Apr 4, 2008 at 2:26 PM, Kurt Hornik [EMAIL PROTECTED] wrote:
hadley wickham writes:
I'm always forgetting to update the date in DESCRIPTION. Would it be
possible to add a warning to R CMD check if it's old?
I recently thought about this. I see several issues.
* How can we
In the R Programming Style thread on R-help Ronald Rau gave a list
of aphorisms from Elements of Programming Style by Kernighan and
Plauger. These include
10.0 times 0.1 is hardly ever 1.0
I think that should be included in FAQ 7.31
__
On Jan 7, 2008 1:34 PM, John Chambers [EMAIL PROTECTED] wrote:
Prof Brian Ripley wrote:
On Mon, 7 Jan 2008, Robin Hankin wrote:
I am writing a package and need to decide whether to use S3 or S4.
I have a single class, multipol; this needs methods for [ and [-
and I also need a print
On 10/18/07, Ben Bolker [EMAIL PROTECTED] wrote:
Tom Short-2 wrote:
See this link for more on creating/converting to HTML:
http://biostat.mc.vanderbilt.edu/twiki/bin/view/Main/SweaveConvert
For using ESS with mixed HTML/R files, see this:
My university provides me with a powerful course management system for
the courses that I teach. Among other things I can create a wiki for
the course, which is very convenient for cross-linking different bits
of the course.
Naturally I use R extensively in my teaching and I want to incorporate
On 8/1/07, Marc Schwartz [EMAIL PROTECTED] wrote:
On Wed, 2007-08-01 at 11:13 -0500, Douglas Bates wrote:
Has anyone installed Linux on a Sony Playstation 3 and compiled R for it?
Doug,
I don't have any personal experience with both Linux and R on the PS3,
but do know folks who have run
P.S. A site with instructions for installing Ubuntu on the PS3 is
psubuntu.com or google PS3 Ubuntu to get the community pages
documentation.
It is a good idea to have an Ethernet connection so that once you
install from the CD you can upgrade the packages. The kernel on the
installation CD
On 8/3/07, Paul Gilbert [EMAIL PROTECTED] wrote:
Doug
Does it still play DVDs?
(My wife keeps telling me that academics have to do all their serious
work in the summer.)
The way that you install Linux on a PS3 it becomes a dual-boot
machine. You have to reboot to the original operating
Has anyone installed Linux on a Sony Playstation 3 and compiled R for it?
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Some time ago Deepayan and I created a package called MEMSS for the
data sets from the nlme package as data frames but not groupedData
objects. Because of advances that Deepayan has made in lattice
graphics many of the specialized plotting methods for the groupedData
objects are no longer
Martin and I will soon release a new version of the Matrix package
with a modified API. This will affect the authors of any packages
that use calls to the C function R_GetCCallable to directly access C
functions in the DLL or shared object object in the libs directory of
the Matrix package. (If
I would appreciate some pointers on how to set up a doxygen
configuration file for C source code. In particular I would like to
be able to generate a call graph. I tend to write a lot of short
utility functions and, by the time the final design reveals itself, it
is quite possible that some of
Version 3 of the GNU Public License (GPL) has been released. A ZDNet
article about it can be found at
http://news.zdnet.com/2100-3513_22-6194139.html?part=rsstag=feedsubj=zdnn
__
R-devel@r-project.org mailing list
On 6/6/07, Aniko Szabo [EMAIL PROTECTED] wrote:
Thanks to everybody who responded to my question.
asInteger(coerceVector(x,INTSXP)) indeed does what I need. I guess there
is a lot I don't understand about type coercion, as I would not have
expected it to work.
It is better to use
I did read your second message about the problem symptoms disappearing
but I thought that I might make a couple of suggestions about your
code anyway.
There are a number of helper functions declared in Rinternals.h such
as ScalarReal, which is equivalent to your mkans. (Also
ScalarInteger,
On 3/20/07, Ernest Turro [EMAIL PROTECTED] wrote:
On 20 Mar 2007, at 07:53, Martin Maechler wrote:
Wolfi == Wolfgang Huber [EMAIL PROTECTED]
on Mon, 19 Mar 2007 15:38:00 + writes:
the problem with results=hide is that it suppresses everything. I
just
need Sweave to suppress
On 11/29/06, Tamas K Papp [EMAIL PROTECTED] wrote:
I have a sparse Matrix (kronecker product of spline design matrices),
and I need to multiply each row by a number to get another matrix. If
the matrix is A and the numbers are stored in a vector k, with plain
vanilla matrices I would do
On 31 Oct 2006 12:05:21 +0100, Peter Dalgaard [EMAIL PROTECTED] wrote:
[move to r-devel, put maintainer in loop]
Patrick Connolly [EMAIL PROTECTED] writes:
On Mon, 30-Oct-2006 at 04:44PM -0500, Duncan Murdoch wrote:
| Try R CMD printenv R_HOME and you'll find which R home directory it
On 06 Nov 2006 15:41:11 +0100, Peter Dalgaard [EMAIL PROTECTED] wrote:
Douglas Bates [EMAIL PROTECTED] writes:
On 31 Oct 2006 12:05:21 +0100, Peter Dalgaard [EMAIL PROTECTED] wrote:
[move to r-devel, put maintainer in loop]
Patrick Connolly [EMAIL PROTECTED] writes:
On Mon
I am encountering segfaults when checking the lme4 package on an
Athlon64 system if I use the acml blas. R was built as a 64-bit
application using the GCC 4.0.3 compiler suite including gfortran.
The version of acml is 3.5.0 gfortran64.
I do not encounter the segfaults when I compile R with R's
On 10/14/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote:
Full_Name: Din Chen
Version: 2.4.0
OS: Windows XP
Submission from: (NULL) (66.17.122.18)
I just updated the R.2.4.0. and got the error message for random effect
modelling, which was working on R.2.3.1.
library(lme4)
mmod -
We are very pleased that an R project has been selected as one of the GNU
projects for the Google Summer of Code 2006 (http://code.google.com/soc/).
Miguel Angel R. Manese, an M.S. Statistics student at the University of
the Philippines, will be working with Douglas Bates and Brian Ripley
The documentation for gsummary describes the argument FUN as
FUN: an optional summary function or a list of summary functions
to be applied to each variable in the frame. The function or
functions are applied only to variables in 'object' that vary
within the
with you if I forward this message to Simon Urbanek? I am
having similar difficulties in the timing with R on a dual-core Intel
MacBook.
On Fri, 3 Mar 2006, Prof Brian Ripley wrote:
On Fri, 3 Mar 2006, Douglas Bates wrote:
I have been timing a particular model fit using lmer on several
I have been timing a particular model fit using lmer on several
different computers and came up with a peculiar result - the model fit
is considerably slower on a dual-core Athlon 64 using Goto's
multithreaded BLAS than on a single-core processor.
Here is the timing on a single-core Athlon 64
and R than it was running 32 bit
Linux and R. All the programs are bigger. (Some, like the clock applet,
are a lot bigger for no obvious reason.) The difference is enough to
put my meager 1GB machine into swapping much more, with the result that
it is a lot slower.
Paul
Douglas Bates wrote
On 7/19/05, Paul Roebuck [EMAIL PROTECTED] wrote:
Had been looking into Luke Tierney's R_AllocatePtr() and
was left with a question about exactly when does R reclaim
heap memory. Implication of 'simpleref.nw' is that one can
allocate C data on the R heap, and as long as pointer object
is
I have noticed spurious message of the form
environment: namespace:base
when developing code for the Matrix package and testing under R-devel.
These messages are not present when testing under R-2.1.1
I have not reported this because I didn't know if it was caused by my
code in the Matrix
On 7/12/05, Duncan Temple Lang [EMAIL PROTECTED] wrote:
Hi Doug.
I noticed this also after the recent change to the
code to handle missing PACKAGE arguments for
.C/.Call/.Fortran routines.
There is a line in the dotcode.c (1510) that
has a call to Rf_PrintValue(env) and that is
what
On 6/19/05, Rob Lopaka Lee [EMAIL PROTECTED] wrote:
I'm interfacing to C code that uses 1-based indexing on arrays -- it
ignores the zeroth element. Thus, input vectors from R must be moved up
one, and output arrays must be moved down one.
What is the best way to deal with this using R
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