r-devel@r-project.org discussions for April 2008

26	[Rd] RFC: What should ?foo do?

Currently ?foo does help("foo"), which looks for a man page with alias foo. If foo happens to be a function call, it will do a bit more, so ?mean(something) will find the mean method for something if ...

Duncan Murdoch
Apr 24, 2008 at 10:45 pm
Apr 30, 2008 at 11:23 am

17	[Rd] R CMD check should check date in description

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? Hadley -- http://had.co.nz/

Hadley wickham
Apr 4, 2008 at 7:05 pm
Apr 5, 2008 at 2:41 pm

14	[Rd] build packages with vignettes in Windows

I've been trying to build a Windows binary of a package of mine without success. It seems that the files under inst/doc throw the script off. I am using the command 'Rcmd INSTALL --build'. ---------- ...

Michael
Apr 29, 2008 at 4:54 pm
May 8, 2008 at 8:33 pm

13	[Rd] graphics::Axis loosing S3/S4 class attributes of 'x' in 2.7.0 RC

Following my previous post on S3 method despatch, I put debug messages in the code of Axis, Axis.default and plot.default in graphics/R/axis.R and graphics/R/plot.R to print the class of x, at and y ...

Sklyar, Oleg (MI London)
Apr 22, 2008 at 11:25 am
Apr 22, 2008 at 6:14 pm

12	[Rd] X11 image problem in R-2.8.0 Under development / R-2.7

I apologize if this is too obscure to reproduce, or some idiosyncratic aspects of my system. If I create a plot, e.g., I get a graphics device as expected. I then click on the 'zoom' box on my X11 ...

Martin Morgan
Apr 3, 2008 at 11:09 pm
Apr 7, 2008 at 6:42 pm

10	[Rd] package building problem under Windows Vista

Dear list members, I've encountered the following problem trying to build a package under Windows Vista (SP1). The problem occurs with both R 2.6.2 and R 2.7.0 RC (from which this output was ...

John Fox
Apr 19, 2008 at 11:52 am
Apr 20, 2008 at 11:07 pm

10	[Rd] HOW TO AVOID LOOPS

Appreciate any suggetions.

Carlos martinez
Apr 12, 2008 at 4:47 pm
Apr 14, 2008 at 11:41 pm

10	[Rd] Windows problem related to using shortPathName for Sweave style file

In the process of updating R to R 2.7 alpha or R 2.7 beta for the BioConductor 2.2 builds on Windows, I have hit a snag because the BioC build system has long path names (e.g ...

Patrick Aboyoun
Apr 9, 2008 at 9:08 pm
Apr 13, 2008 at 9:44 am

10	[Rd] Adding a Matrix Exponentiation Operator

Hi all I recently started to write a matrix exponentiation operator for R (by adding a new operator definition to names.c, and adding the following code to arrays.c). It is not finished yet, but I ...

Rory Winston
Apr 5, 2008 at 1:44 pm
Apr 11, 2008 at 2:33 pm

8	[Rd] R-Forge SVN repositories: R CMD build/check error on Windows machines

Dear R-devel, One of our R-Forge developers pointed out that it is not possible to build packages under Windows using the R-Forge repository structure: a package resides in ./pkg - not in a directory ...

Stefan Theussl
Apr 28, 2008 at 4:22 pm
Apr 29, 2008 at 12:01 pm

8	[Rd] AddComment (gram.y)

AddComment in gram.y would have been an extremely useful feature, but it's been #if-0'd out; is it unimplemented? It should have attached a comment attribute to any SEXP associated with a comment.

Peter Danenberg
Apr 19, 2008 at 5:09 am
Apr 21, 2008 at 10:08 pm

8	[Rd] swig 1.3.35 & R - is the R wrapper still maintained and of interest?

Dear all, I was trying to use the R swig wrapper with R 2.7 and shogun ( http://www.shogun-toolbox.org ) but it fails completely, as in doesn't even compile and even after patching then though ...

Soeren Sonnenburg
Apr 18, 2008 at 10:49 am
Apr 21, 2008 at 12:02 am

8	[Rd] Fortran underscore problem persists on Linux x86/64 (PR#11206)

Full_Name: Thomas Petzoldt Version: R 2.8.0 devel, svn version 45389 OS: Linux x86/64 Ubuntu 7.1 Submission from: (NULL) (217.235.62.12) In contrast to all other tested operating systems a call of ...

Thomas Petzoldt
Apr 19, 2008 at 6:15 pm
Apr 20, 2008 at 4:26 pm

6	[Rd] reproducible segmentation fault caused by textConnection()

Dear all, It seems that textConnection() can trigger a segmentation fault. The following script (using two large loops) makes this bug reproducible: for (i in 1:10000) { ...

Gregoire Pau
Apr 29, 2008 at 1:52 pm
May 1, 2008 at 12:42 pm

6	[Rd] plot(x) in 2.7.0 (with y=NULL) proposed code correction

Hi all: following the previous discussion, it looks like plot(x) with y=NULL still does not work correctly. If one tries for example plot(1:5) it works, but already for plot(runif(100)) it does not ...

Sklyar, Oleg (MI London)
Apr 22, 2008 at 4:34 pm
Apr 23, 2008 at 7:00 am

5	[Rd] R 2.7.0, match() and strings containing \0 - bug?

Hi, A piece of my code that uses readBin() to read a certain file type is behaving strangely with R 2.7.0. This seems to be because of a failure to match() strings after using rawToChar() when the ...

Jon Clayden
Apr 28, 2008 at 10:00 am
Apr 28, 2008 at 10:43 pm

5	[Rd] returning vectors of unknown size from C (with .C)

Dear All, In a package, I am using ".C" to call some C functions. In one case, the number of elements of the return vectors are not known in R before the C call. (Two of the vectors are integers, the ...

Ramon Diaz-Uriarte
Apr 26, 2008 at 12:23 am
Apr 26, 2008 at 8:17 pm

5	[Rd] prod(0, 1:1000) ; 0 * Inf etc

I think most of us would expect prod(0:1000) to return 0, and ... ... it does. However, many of us also expect prod(x1, x2) to be equivalent to prod(c(x1,x2)) the same as we can expect that for ...

Martin Maechler
Apr 21, 2008 at 4:40 pm
Apr 22, 2008 at 8:22 am

5	[Rd] Couldn't (and shouldn't) is.unsorted() be faster?

Hi, Couldn't is.unsorted() bail out immediately here (after comparing the first 2 elements): user system elapsed 0.084 0.040 0.124 user system elapsed 0.772 0.440 1.214 Thanks! H.

Herve Pages
Apr 17, 2008 at 7:04 pm
Apr 19, 2008 at 1:56 am

5	[Rd] clean-up actions after non-local exits

Dear R-devel, Some time ago I started a thread that boiled down to clean-up actions after non-local exits in R, see below. I wonder if there has been any progress on this? R-ext 2.6.1 doesn't say ...

Vadim Organovich
Apr 14, 2008 at 8:33 pm
Apr 15, 2008 at 7:13 pm

5	[Rd] Doing the right amount of copy for large data frames.

Hi there, Problem :: When one tries to change one or some of the columns of a data.frame, R makes a copy of the whole data.frame using the '*tmp*' mechanism (this does not happen for components of a ...

Gopi Goswami
Apr 14, 2008 at 11:47 am
Apr 15, 2008 at 7:03 am

5	[Rd] Overriding axis formatting with custom Axis method, Axis.numeric etc

Dear list: I would like to override the default way R formats plot axes with a custom method(s). Obviously I would prefer to define it as general as possible avoiding writing a custom method for each ...

Sklyar, Oleg (MI London)
Apr 7, 2008 at 11:22 am
Apr 7, 2008 at 1:23 pm

4	[Rd] Bug in R 2.7 for over long lines (crasher+proposed fix!) (PR#11281)

OK, I am just sending it here too as it looks like r-devel at r-project.org is not the right place: ï»¿On Fri, 2008-04-25 at 08:48 +0200, Soeren Sonnenburg wrote: Looking at the code again there ...

Bugreports
Apr 25, 2008 at 7:55 pm
May 13, 2008 at 5:48 am

4	[Rd] help text for xlim

Dear R-developers, A student asked me today of how to specify the limits of the x-axis. I knew that he should use xlim, but I tried to encourage him to have a try himself with the various help ...

Henrik Parn
Apr 29, 2008 at 2:38 pm
May 1, 2008 at 10:42 am

4	[Rd] R-extension in unix system -- help to locate header files

Hi list, To call C, I used to use R-extension in windows but I'm moving to unix system because my PC doesn't have enough memory. My C codes requires to include the following header files: #include ...

Kyeongmi Cheon
Apr 18, 2008 at 4:23 am
Apr 18, 2008 at 5:18 pm

4	[Rd] && and \|\|

Hello there, I got a small problem about logical calculation: we can get a sequene from a+b as below: [1] 4 6 but when the sequences are logical. (I want to get (True,False) && (True, True) == (True, ...

Yuan Jian
Apr 14, 2008 at 6:48 am
Apr 15, 2008 at 1:21 am

4	[Rd] R 2.7 package.skeleton

Hi the devel list I am testing package.skeleton in R 2.7 (download today). I get an error that I do not understand. I guess it is not an error from my code since I have no probleme when I source it ...

Cgenolin
Apr 13, 2008 at 5:56 pm
Apr 13, 2008 at 9:36 pm

4	[Rd] coerce methods and inheritance

Hi, It doesn't seem that the dispatching algo is finding my coerce method under some circumstances. Let's say I have 2 classes, A and AA and that AA is just a direct extension of A with no additional ...

Herve Pages
Apr 9, 2008 at 6:58 pm
Apr 12, 2008 at 11:24 pm

4	[Rd] autocompletion problem

Hi, Let's create the xxx object just to avoid confusion even if it's not necessary for reproducing the problem below: xxx <- 8:3 If I start typing this: max(xxx[ and now try to autocomplete with <TAB ...

Herve Pages
Apr 9, 2008 at 9:35 pm
Apr 10, 2008 at 8:04 pm

4	[Rd] [R] How to improve the "OPTIM" results

<moved to R-devel What would people suggest someone do to improve the optimization capabilities in R? A few ideas are mentioned below. I just got 578 hits from RSiteSearch("optimization", "fun"), and ...

Spencer Graves
Apr 6, 2008 at 3:37 pm
Apr 6, 2008 at 5:29 pm

3	[Rd] r won't start: "r: symbol lookup error: r: undefined symbol: R_Visible" (PR#11265)

Full_Name: Jakob Stoeger Version: 2.7.0 OS: ubuntu 7.10 Submission from: (NULL) (137.248.74.38) Hi! I hope, it is justified to write this email... I'm relatively new to linux, and haven't worked with ...

Jakobstoeger
Apr 24, 2008 at 6:20 pm
Apr 25, 2008 at 10:30 pm

3	[Rd] naive question regarding running parallel C code from R

Hi, I have only the vaguest notions of what parallel programing, but I think I have a situation where it might be of use to me, or at least provide me with the opportunity to learn more about it ...

Tyler
Apr 18, 2008 at 4:03 pm
Apr 19, 2008 at 7:23 pm

3	[Rd] Pb with package::foo(x) <- value

Hi, The parser doesn't seem to like this: somePackage::foo(x) <- value somePackage:::foo(x) <- value where foo() is a replacement function or method defined in package somePackage. For example: Error ...

Herve Pages
Apr 19, 2008 at 2:17 am
Apr 19, 2008 at 1:49 pm

3	[Rd] [rd] sage <--> r integration

I would like to re-emphasize the above points that William makes. Both projects could benefit a lot from working with each other. A fair number of people, including Persi Diaconis and Susan Holmes, ...

Mike Hansen
Apr 17, 2008 at 10:33 am
Apr 18, 2008 at 3:26 pm

3	[Rd] segments() with zero-length arguments (PR#11192)

Uwe Ligges suggested I post this on R-bugs as a wishlist item with a proposed patch. R considers zero-length arguments to segments() to be an error. I would like R to allow this and to return without ...

Rmh
Apr 16, 2008 at 10:30 pm
Apr 17, 2008 at 10:35 am

3	[Rd] matrix

Hello, I have a matrix, I want to change value to 0 when a element in the matrix has less than 10. do you know how to do it without using loops? ---------------------------------

Yuan Jian
Apr 16, 2008 at 11:33 pm
Apr 17, 2008 at 6:24 am

3	[Rd] promptFunctions() to handle multiple names

Hi all, I wanted to set up my first (private) R-package and wondered if there was a function to prompt() for multiple aliases in one Rd-file, e.g. to create something like the normal distribution ...

Daniel Sabanés Bové
Apr 13, 2008 at 2:52 pm
Apr 14, 2008 at 8:59 pm

3	[Rd] Matrix multiplication in a C code

Dear list members, I've got a small question on matrix multiplications in a C code. Because of a really cpu demanding likelihood, I had to use a C code within an R function wrapper. I'm pretty sure ...

Mathieu Ribatet
Apr 6, 2008 at 12:46 pm
Apr 13, 2008 at 10:00 pm

3	[Rd] problem with Rmpi 0.5-5 and openmpi

Dear knowledgeable experts :-), I am trying to get openmpi, Rmpi and SNOW running on a Myrinet/GM cluster. I'm not an IT expert, but I surely could use a working installation of Rmpi and SNOW. I try ...

Peter Pearman
Apr 7, 2008 at 12:52 pm
Apr 12, 2008 at 7:50 am

3	[Rd] suggested minor patch for optim.R

optim ignores misspelled control parameters, so that trying to set (e.g.) "maxint00" in the control argument silently does nothing. The patch below (watch out for line breaks! also posted at ...

Ben Bolker
Apr 4, 2008 at 11:08 pm
Apr 5, 2008 at 4:30 pm

3	[Rd] g++ 4.3 warning: deprecated conversion from string constant to ‘char*’

Hello, I've noticed that with g++ 4.3 I get the following "warning: deprecated conversion from string constant to ?char*?" when I call e.g., Rprintf("Hello world"); or when I try to define a const ...

Andrew Finley
Apr 3, 2008 at 2:48 pm
Apr 3, 2008 at 6:14 pm

2	[Rd] HTML help solveLP(linprog) (PR#11250)

Dear R team! I found in HTML help for function solveLP(linprog) a small mistake. It says in Description "Minimizes c'x, subject to A x = b and x = 0", but tests show that there should be A x <= b ...

Ludek Salom
Apr 23, 2008 at 2:25 pm
Jun 18, 2008 at 2:37 pm

2	[Rd] Quotation marks (PR#11353)

Full_Name: Mitchell Steven Wachtel, MD Version: 2.7.0 RC OS: Vista Submission from: (NULL) (66.230.2.56) Single (') and double (") quotation marks are not being read as quotation marks when commands ...

Mitchell Wachtel
Apr 30, 2008 at 4:20 pm
May 1, 2008 at 2:34 am

2	[Rd] non-digits in svnversion output mess up windows build if USE_SVNVERSION=yes (PR#11339)

Full_Name: Bill Dunlap Version: 2.8.0dev OS: Windows XP Submission from: (NULL) (70.98.76.47) I tried for the first time to build R from source on Windows, where I got the source code via svn. Per ...

Bill
Apr 29, 2008 at 6:30 pm
Apr 29, 2008 at 9:05 pm

2	[Rd] X11 window title setting in X11() Device (PR#11325)

--=-=-Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hi, I think I have found a very little bug in the new version of the X11() device in R 2.7.0, more precisely ...

Julien Barnier
Apr 28, 2008 at 2:40 pm
Apr 29, 2008 at 9:40 am

2	[Rd] R_DEFAULT_DEVICE (PR#11294)

Setting enviroment variable R_DEFAULT_DEVICE causes an error. The patch below fixes this. I guess the same goes for R_INTERACTIVE_DEVICE. --- R-2.7.0/src/library/grDevices/R/zzz.R 2008-04-27 ...

P C J Kleiweg
Apr 27, 2008 at 12:10 pm
Apr 28, 2008 at 8:55 am

2	[Rd] S4 default for coercing

Something has changed in the S4 default for coercing. Am I now suppose to use setAs, or is there something else I should do to make this work: R version 2.7.0 (2008-04-22) ... ...

Paul Gilbert
Apr 23, 2008 at 3:01 pm
Apr 27, 2008 at 5:12 pm

2	[Rd] median methods

Can we please have a ... argument in median() to make it possible to pass arguments to specific methods. Rob J Hyndman Professor of Statistics, Monash University Editor-in-Chief, International ...

Rob Hyndman
Apr 26, 2008 at 12:46 pm
Apr 27, 2008 at 10:15 am

2	[Rd] R-devel Digest, Vol 62, Issue 24

The columns of the model matrix are all orthogonal. So the problem lies with poly(), not with lm(). y = rnorm(15) z <- model.matrix(lm(y ~ poly(x, 12))) x = rep(1:5,3) (Intercept) poly(x, 12)1 ...

John Maindonald
Apr 25, 2008 at 12:05 am
Apr 25, 2008 at 3:26 am

2	[Rd] Seqfault, Address 0, track X11() (PR#11231)

Full_Name: Liqun Xing Version: 2.6.2 OS: Solaris 9 Submission from: (NULL) (76.182.91.82) When first time launch X11(), it was fine. However, when closed the X11 windon by clicking the close button, ...

Liqun Xing
Apr 22, 2008 at 2:15 am
Apr 23, 2008 at 3:15 pm

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