Re: [Rd] Small changes to big objects (1)

2013-01-07 Thread Douglas Bates
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.

Re: [Rd] Julia

2012-03-01 Thread Douglas Bates
On Thu, Mar 1, 2012 at 11:20 AM, Jeffrey Ryan 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) > > https://twitter.com/#!/mikeloukides/status/1

[Rd] Julia

2012-03-01 Thread Douglas Bates
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 1

Re: [Rd] Copying objects prior to .Call

2012-01-11 Thread Douglas Bates
On Wed, Jan 11, 2012 at 11:49 AM, Simon Urbanek 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 passed to it but

Re: [Rd] Cholesky update/downdate

2011-12-29 Thread Douglas Bates
On Thu, Dec 29, 2011 at 8:05 AM, Yves Deville 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) where > C is (n, r). F

Re: [Rd] RcppArmadillo compilation error: R CMD SHLIB returns status 1

2011-12-07 Thread Douglas Bates
On Dec 6, 2011 8:30 AM, "Duncan Murdoch" 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 example is >> >>

Re: [Rd] Use of Matrix within packages in R-2.14.0

2011-11-11 Thread Douglas Bates
On Nov 11, 2011 6:13 PM, "Bryan W. Lewis" 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 the error

Re: [Rd] Performance of .C and .Call functions vs. native R code

2011-07-19 Thread Douglas Bates
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 wrote: > On Thu, Jul 14, 2011 at 10:21 AM, Alireza Mahani > wrote: >> (I am using a LINUX machine) >> >> Jeff, >&g

Re: [Rd] Performance of .C and .Call functions vs. native R code

2011-07-19 Thread Douglas Bates
On Thu, Jul 14, 2011 at 10:21 AM, Alireza Mahani 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 chosen directory, then ru

Re: [Rd] Error using RcppGSL

2011-06-21 Thread Douglas Bates
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" 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 as they seem

Re: [Rd] C-Side: Applying a function (given as param) to data (given as param)

2011-06-03 Thread Douglas Bates
On Fri, Jun 3, 2011 at 5:17 AM, oliver 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 a function (give

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-03-30 Thread Douglas Bates
On Tue, Mar 29, 2011 at 2:17 PM, Douglas Bates wrote: > On Tue, Mar 29, 2011 at 5:34 AM, Hin-Tak Leung > wrote: >> Martin Maechler wrote: >>>>>>>> >>>>>>>> Douglas Bates >>>>>>>>    on Mon, 28 Mar

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-03-29 Thread Douglas Bates
On Tue, Mar 29, 2011 at 5:34 AM, Hin-Tak Leung wrote: > Martin Maechler wrote: >>>>>>> >>>>>>> Douglas Bates >>>>>>>    on Mon, 28 Mar 2011 09:24:39 -0500 writes: >> >>    > Can you provide the output from

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-03-28 Thread Douglas Bates
Can you provide the output from sessionInfo() so we can know the platform? Also, did you configure R with --enable-strict-barrier or set the C compilation flag -DTESTING_WRITE_BARRIER? I think that run-time error message can only be thrown under those circumstances (not that it isn't an error,

Re: [Rd] Problem using F77_CALL(dgemm) in a package

2011-02-22 Thread Douglas Bates
On Sun, Feb 20, 2011 at 4:39 PM, Jason Rudy 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 use CSPARSE, a

Re: [Rd] Calling C++ from R

2011-01-21 Thread Douglas Bates
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 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 Rtools and R 2.1

Re: [Rd] Competing with one's own work

2010-12-03 Thread Douglas Bates
On Fri, Dec 3, 2010 at 11:01 AM, Ravi Varadhan 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 particular class >

Re: [Rd] DBLEPR?

2010-11-16 Thread Douglas Bates
On Tue, Nov 16, 2010 at 2:35 PM, Prof. John C Nash 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 "ucminf". > I

Re: [Rd] [R] DBLEPR?

2010-11-16 Thread Douglas Bates
Reply redirected to the R-devel list. On Tue, Nov 16, 2010 at 1:02 PM, Prof. John C Nash 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 its > use of

Re: [Rd] [Rcpp-devel] must .Call C functions return SEXP?

2010-10-28 Thread Douglas Bates
On Thu, Oct 28, 2010 at 1:44 PM, Dominick Samperi wrote: > See comments on Rcpp below. > > On Thu, Oct 28, 2010 at 11:28 AM, William Dunlap wrote: >> >> > -Original Message- >> > From: r-devel-boun...@r-project.org >> > [mailto:r-devel-boun...@r-project.org] On Behalf Of Andrew Piskorski

Re: [Rd] Linking to lapack

2010-10-22 Thread Douglas Bates
On Fri, Oct 22, 2010 at 4:30 AM, Nick Sabbe 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. You may want t

[Rd] Failure to load the recommended package Matrix (Was: [R] Can one get a list of recommended packages?)

2010-06-13 Thread Douglas Bates
On Sun, Jun 13, 2010 at 8:28 AM, Uwe Ligges 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 >>> wrote: >>>> >>

Re: [Rd] Compiling R with ATLAS

2010-05-14 Thread Douglas Bates
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. Take

Re: [Rd] Lapack, determinant, multivariate normal density, solution to linear system, C language

2010-04-19 Thread Douglas Bates
On Mon, Apr 12, 2010 at 10:27 PM, shotwelm 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 symmetric matr

Re: [Rd] Defining a method in two packages

2010-03-10 Thread Douglas Bates
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 r

Re: [Rd] unable to compile Recommended packages

2010-03-09 Thread Douglas Bates
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 wrote: > Hi folks,  I'm having a problem with installing  R on Solaris.  Has anyone > seen a similar issue?  

Re: [Rd] snark of the day: new "features" (??) in Mathematica 7

2010-01-11 Thread Douglas Bates
On Mon, Jan 11, 2010 at 10:34 AM, Ben Bolker 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 descriptions o

Re: [Rd] Summary methods

2009-11-10 Thread Douglas Bates
On Sun, Nov 8, 2009 at 2:26 PM, Doran, Harold wrote: > I've defined the following for objects of a class called jml > > summary.jml <- function(object, ...){ >        tab <- cbind(Estimate = coef(object), >                        StdError = object$se, >                        Infit = object$Infit,

Re: [Rd] Confusion regarding allocating Matrices.

2009-10-24 Thread Douglas Bates
t; > I am aware that R matrices are stored in column major order. > > Thanks for the tip on using float *dat= REAL(Data); > > Regards > > Abhijit Bera > > > > On Fri, Oct 23, 2009 at 7:27 PM, Douglas Bates wrote: >> >> On Fri, Oct 23, 2009 at 9:23 AM, Douglas Bates

Re: [Rd] Confusion regarding allocating Matrices.

2009-10-23 Thread Douglas Bates
On Fri, Oct 23, 2009 at 9:23 AM, Douglas Bates wrote: > On Fri, Oct 23, 2009 at 8:39 AM, Abhijit Bera wrote: >> Hi >> >> I'm having slight confusion. > > Indeed. > >> I plan to grow/realloc a matrix depending on the data available in a C >> progra

Re: [Rd] Confusion regarding allocating Matrices.

2009-10-23 Thread Douglas Bates
On Fri, Oct 23, 2009 at 8:39 AM, Abhijit Bera 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 in the oth

Re: [Rd] unexpected behaviour of isSymmetric() (PR#14000)

2009-10-12 Thread Douglas Bates
On Mon, Oct 12, 2009 at 6:41 AM, Romain Francois 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 isSymmetric.matr

Re: [Rd] R + C + Lapack toy regression example

2009-09-25 Thread Douglas Bates
On Thu, Sep 24, 2009 at 2:09 PM, Vinh Nguyen wrote: > On Thu, Sep 24, 2009 at 11:49 AM, Simon Urbanek > 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 >> vectors stored in column-major order.

Re: [Rd] R + C + Lapack toy regression example

2009-09-24 Thread Douglas Bates
On Wed, Sep 23, 2009 at 2:39 AM, Vinh Nguyen 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: > #include >

Re: [Rd] Non-GPL packages for R

2009-09-12 Thread Douglas Bates
On Fri, Sep 11, 2009 at 1:48 PM, rudjer 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... > > So let

Re: [Rd] clearNames and unname

2009-09-03 Thread Douglas Bates
On Thu, Sep 3, 2009 at 10:02 AM, Martin Maechler wrote: >> "MM" == Martin Maechler >>     on Thu, 3 Sep 2009 16:14:24 +0200 writes: > >> "HW" == Hadley Wickham >>     on Thu, 3 Sep 2009 08:16:27 -0500 writes: > >    HW> Just noticed these two functions (clearNames is stats and unn

Re: [Rd] Calling C functions with value parameters

2009-08-18 Thread Douglas Bates
On Mon, Aug 17, 2009 at 9:23 AM, Jeffrey J. Hallman 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 takes an >

Re: [Rd] Problem using model.frame with argument subset in own function

2009-08-09 Thread Douglas Bates
On Sat, Aug 8, 2009 at 1:31 PM, Gavin Simpson 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. The usual way to call

Re: [Rd] beginner's guide to C++ programming with R packages?

2009-06-29 Thread Douglas Bates
On Fri, Jun 26, 2009 at 2:43 PM, Paul Johnson 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 > understand.  I

Re: [Rd] nlminb - Port library codes

2009-05-04 Thread Douglas Bates
You could always look in the SVN logs but I'll save you the trouble. I did the initial installation of the nlminb function. On Fri, May 1, 2009 at 12:52 PM, John C Nash wrote: > Having looked at documentation and codes, I'm still looking to find out who > did the installation of the Port librarie

Re: [Rd] [SoC09-Info] An IPopt interface for R

2009-02-22 Thread Douglas Bates
On Sun, Feb 22, 2009 at 3:05 PM, Douglas Bates 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. &g

Re: [Rd] R tutorial

2009-02-22 Thread Douglas Bates
On Sun, Feb 22, 2009 at 7:44 AM, Christophe Dutang 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 > http://www.liaad.up.pt/~ltorgo/DataMiningWithR/ > What d

[Rd] [SoC09-Info] An IPopt interface for R

2009-02-22 Thread Douglas Bates
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 creat

Re: [Rd] "for" loop wiht S4 Objects

2009-01-23 Thread Douglas Bates
On Fri, Jan 23, 2009 at 1:25 AM, Biczok Rudolf 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 <- new("foo",bar=list(1,2,3)) >>for

[Rd] Reaching R-forge - tunnel ssh through ssh?

2008-09-12 Thread Douglas Bates
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 fire

Re: [Rd] R CMD check should check date in description

2008-04-04 Thread Douglas Bates
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. >

Re: [Rd] 0.45<0.45 = TRUE (PR#10744)

2008-02-14 Thread Douglas Bates
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 __ R-devel@r-p

Re: [Rd] S3 vs S4 for a simple package

2008-01-07 Thread Douglas Bates
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 "[<-" >

[Rd] The XO laptop from the One Laptop Per Child (OLPC) program

2007-12-17 Thread Douglas Bates
There was recently a question on the R-help list about the eee pc. I had a related question about the XO laptop from OLPC (laptop.org). Has anyone looked at the development environment sufficiently to determine if it would be possible to create an executable image for R? The laptop itself only su

Re: [Rd] Sweave/ESS-like tools for HTML

2007-10-19 Thread Douglas Bates
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: > > https://stat.ethz.ch/pipermail/ess-

[Rd] Sweave/ESS-like tools for HTML

2007-10-16 Thread Douglas Bates
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 R

Re: [Rd] Compiling R for the Sony Playstation 3?

2007-08-03 Thread Douglas Bates
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 operatin

Re: [Rd] Compiling R for the Sony Playstation 3?

2007-08-03 Thread Douglas Bates
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 ima

Re: [Rd] Compiling R for the Sony Playstation 3?

2007-08-03 Thread Douglas Bates
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

[Rd] Compiling R for the Sony Playstation 3?

2007-08-01 Thread Douglas Bates
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

Re: [Rd] Changes in the MEMSS package (data sets from Pinheiro and Bates, 2000, without the groupedData classes)

2007-07-24 Thread Douglas Bates
e data set then you probably want exactly that version and haven't accidently overridden the other). The bottom line is that unless you have been in the habit of attaching the MEMSS package or getting data sets from it as above then you won't notice any difference. > On 7/24/07, Dou

[Rd] Changes in the MEMSS package (data sets from Pinheiro and Bates, 2000, without the groupedData classes)

2007-07-24 Thread Douglas Bates
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 needed.

[Rd] [OT] help in setting up a doxygen configuration file

2007-07-03 Thread Douglas Bates
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 th

[Rd] Forthcoming change in the API of the Matrix package

2007-07-03 Thread Douglas Bates
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 y

[Rd] GPL 3 has been released

2007-06-30 Thread Douglas Bates
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=rss&tag=feed&subj=zdnn __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinf

Re: [Rd] missing IntegerFromString()

2007-06-07 Thread Douglas Bates
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 asInte

Re: [Rd] Developer work cycle

2007-03-29 Thread Douglas Bates
On 3/26/07, "José Luis Aznarte M." <[EMAIL PROTECTED]> wrote: > Hi! I've been browsing through the last months' archive and I can't > find an answer to my question, so here it is (let's hope it's not too > obvious): > I'm working on extensions of an R library, and I would be very > surprise

Re: [Rd] [R] Use of 'defineVar' and 'install' in .Call

2007-03-28 Thread Douglas Bates
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, Scalar

Re: [Rd] Carriage returns and Sweave output

2007-03-20 Thread Douglas Bates
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 > >>>

Re: [Rd] Matrix*vector: coercing sparse to dense matrix for arithmetic

2006-11-29 Thread Douglas Bates
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

Re: [Rd] lme4 install, was Re: [R] Which executable is associated with R CMD INSTALL?

2006-11-06 Thread Douglas Bates
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 maintain

Re: [Rd] lme4 install, was Re: [R] Which executable is associated with R CMD INSTALL?

2006-11-06 Thread Douglas Bates
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

Re: [Rd] error in lme4 for R 2.4.0 (PR#9297)

2006-10-16 Thread Douglas Bates
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) > mmo

[Rd] x86_64, acml-3.5.0-gfortran64 and lme4

2006-10-16 Thread Douglas Bates
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 b

Re: [Rd] alpha, portable use

2006-09-25 Thread Douglas Bates
On 9/25/06, Paul Gilbert <[EMAIL PROTECTED]> wrote: > I am still confused about this (and it is still happening with R-beta). > Writing R Extensions suggests I need a Makefile or Makevars in my > package, but that has not been the case previously. Is there now a > requirement that all packages ne

[Rd] R Project accepted for the Google Summer of Code

2006-05-25 Thread Douglas Bates
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 on a

Re: [Rd] gsummary function (nlme library) (PR#8782)

2006-04-20 Thread Douglas Bates
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 gr

Re: [Rd] Peculiar timing result

2006-03-13 Thread Douglas Bates
imings. It happens that this message ended up in my R-help folder and I only got around to reading that folder today. Is it ok 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,

Re: [Rd] Peculiar timing result

2006-03-03 Thread Douglas Bates
the result that > it is a lot slower. > > Paul > > Douglas Bates wrote: > > >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 usi

[Rd] Peculiar timing result

2006-03-03 Thread Douglas Bates
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 3000

Re: [Rd] Master's project to coerce linux nvidia drivers to run generalised linear models

2006-01-24 Thread Douglas Bates
On 1/23/06, Gabor Grothendieck <[EMAIL PROTECTED]> wrote: > I wonder if it would make more sense to get a relatively > low level package to run on it so that all packages that > used that low level package would benefit. The Matrix > package and the functions runmean and sum.exact in > package caT

Re: [Rd] Questions about calls and formulas

2005-08-22 Thread Douglas Bates
On 8/22/05, Erich Neuwirth <[EMAIL PROTECTED]> wrote: > I am trying to adapt boxplot.formula (in graphics) to accept an > additional parameter, weights. > I already managed to adapt boxplot.default to do this. > > boxplot.formula prepares the data for a call to boxplot.default and to > achieve tha

[Rd] An lgrind definition for the S language

2005-08-22 Thread Douglas Bates
I seem to recall discussion of an language definition file for S for use with the lgrind utility but I can't find any trace of it in an R Site Search. The lgrind utility takes a file of code in a particular programming language and prepares it for "pretty printing" in LaTeX. In my version the ava

Re: [Rd] include C functions from nmath in my own C functions

2005-08-11 Thread Douglas Bates
On 8/11/05, yyan liu <[EMAIL PROTECTED]> wrote: > Hi: > I followed the README in src/nmath/standalone/ > to make the use the command "make shared" to make the > libRmath.so file. I also add the directories containg > libRmath.so to LD_LIBRARY_PATH by using command > "export > D_LIBRARY_PATH

[Rd] Reading a repeated fixed format

2005-08-10 Thread Douglas Bates
The Harwell-Boeing format for exchanging matrices is one of those lovely legacy formats that is based on fixed-format Fortran specifications and 80 character records. (Those of you who don't know why they would be 80 characters instead of, say, 60 or 100 can ask one of us old-timers some day and

Re: [Rd] R_AllocatePtr

2005-07-19 Thread Douglas Bates
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 > i

Re: [Rd] extracting and manipulating components from nlme and gnls objects

2005-07-19 Thread Douglas Bates
On 7/19/05, Nicholas Lewin-Koh <[EMAIL PROTECTED]> wrote: > Hello, > I am writing a set of functions to do prediction and calibration > intervals > for at least the subset of selfstarting models if not some more general > ones. > > I need to be able to extract the varFunction from a fit object > a

Re: [Rd] Spurious output like in R-devel

2005-07-12 Thread Douglas Bates
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 i

[Rd] Spurious output like in R-devel

2005-07-12 Thread Douglas Bates
I have noticed spurious message of the form 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 package or some other code. Today

Re: [Rd] calling fortran functions CHOL and DPOTRF form Fortran

2005-07-05 Thread Douglas Bates
On 7/5/05, Gilles GUILLOT <[EMAIL PROTECTED]> wrote: > Hi all, > > I'm working out some Fortran code for which > I want to compute the Choleski decomposition of a covariance matrix > in Fortran. > > I tried to do it by two methods : > > 1) Calling the lapack function DPOTRF. > I can see the sour

Re: [Rd] How difficult is it to wrap a large C++ library with R?

2005-07-04 Thread Douglas Bates
On 7/4/05, Bo Peng <[EMAIL PROTECTED]> wrote: > > > * Wrap C++ class hierarchy. Virtual functions need to be supported. > > > (SWIG can generate Python shadow classes that behave almost exactly > > > like the underlying C++ classes) > > > > This is hard to do in R, because the R object model is qui

[Rd] Running ./tools/rsync-recommended through a proxy

2005-06-28 Thread Douglas Bates
My computers at my office will no longer be able to connect directly to web sites etc. I will be going through a proxy server. The particular server is running squid on port 3128. I have managed to configure web browsers, ssh, apt, svn and a whole lot of other tools to use the proxy server but I

Re: [Rd] Lapack calls from fortran

2005-06-22 Thread Douglas Bates
On 6/22/05, Paul Gilbert <[EMAIL PROTECTED]> wrote: > I am trying to call the lapack routine dgesv in the R distribution from > the fortran code for a package, but when I dyn.load("dse1.so") I get an > error about undefined symbol: dgesv_ > > I thought the proper incantation was > > MAKEFLAG="FLI

Re: [Rd] 1-based arrays and copying vectors

2005-06-19 Thread Douglas Bates
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