r-devel@r-project.org discussions for January 2009

14	[Rd] Segfault when mistakenly calling [.data.frame (PR#13487)

Full_Name: Christian Brechbuehler Version: 2.7.2, 2.8.1 OS: linux-gnu Submission from: (NULL) (24.128.51.18) Calling [.data.frame on an object that's not a data frame, specifically 1:10, causes ...

Brechbuehler
Jan 29, 2009 at 3:35 pm
Feb 5, 2009 at 12:17 pm

12	[Rd] particulars of importing/loading libraries

Dear List: Sorry for posting maybe a trivial question, but I have a basic understanding problem. If I have say pack1 and pack2, two R packages, and pack2 depends on and imports pack1 fully (as in the ...

Sklyar, Oleg (London)
Jan 13, 2009 at 4:00 pm
Jan 14, 2009 at 4:49 pm

10	[Rd] x <- 1:2; dim(x) <- 2? A vector or not?

Ran into the follow intermediate case in an external package (w/ recent R v2.8.1 patched and R v2.9.0 devel): Error in x[1, ] : incorrect number of dimensions Is str() treating single-dimension ...

Henrik Bengtsson
Jan 12, 2009 at 8:43 pm
Jan 26, 2009 at 10:56 am

10	[Rd] NY Times article

Sorry if this is spam, but I couldn't see it having popped up on the list yet. http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html?emc=eta1 Anand

Anand Patil
Jan 8, 2009 at 12:53 pm
Jan 11, 2009 at 7:26 pm

9	[Rd] legend() in a multiple figure environment

Dear all, there seems to be a problem with displayed legends when a multiple figure environment is used, see the following example: par(mfrow=c(1,2)) curve(dnorm,col=4,from=-4,to=4) ...

Simone Giannerini
Jan 8, 2009 at 10:31 am
Jan 8, 2009 at 3:59 pm

7	[Rd] Documentation suggestions for vignettes

Dear R-devel, I am putting together a package vignette for the first time (R 2.8.1, OS X) and had some bumps from section 1.4 ("Writing package vignettes") of the "Writing R Extensions" document ...

Perry de Valpine
Jan 14, 2009 at 7:53 pm
Jan 15, 2009 at 7:12 pm

7	[Rd] R as a scripting engine

Those of you tracking R development will have noticed that we are moving towards using R as a scripting engine. (It is often overlooked as such.) Thus far INSTALL, REMOVE, SHLIB and massage-examples ...

Prof Brian Ripley
Jan 11, 2009 at 8:18 pm
Jan 13, 2009 at 6:47 pm

6	[Rd] Package (PR#13475)

Full_Name: Partho Bhowmick Version: 2.8.1 OS: Windows XP Submission from: (NULL) (199.43.48.131) While trying to install package sn (I have tried multiple mirrors), I get the following message trying ...

Partho_bhowmick
Jan 27, 2009 at 3:15 pm
Apr 10, 2009 at 4:42 pm

6	[Rd] Side-effects of require() vs library() on x86_64 aka amd64

RDieHarder fails its regression tests on x86_64 (aka "amd64") at CRAN (using Debian), and I see the same on Ubuntu 8.10 in 64 bit. No issues on 32bit. One odd thing is that the program behaves well ...

Dirk Eddelbuettel
Jan 29, 2009 at 4:26 am
Jan 31, 2009 at 4:15 pm

6	[Rd] Package Matrix does not compile in R-devel_2009-01-10

Dear developers, today I tried to build and install R-devel_2009-01-10 on FreeBSD 8.0-CURRENT (i386) for testing purposes. All went well until compiling the now recommended (integrated) Matrix ...

Rainer Hurling
Jan 11, 2009 at 10:13 pm
Jan 21, 2009 at 10:50 am

6	[Rd] cat cannot write more than 10000 characters? [R 2.8.1]

Hi, during the examination of a Sweave hang-up inside an odfWeave call (OOo XMLs have looong lines) I have discovered that my cat function cannot write more than 10000 characters to a text file ...

Daniel Sabanés Bové
Jan 4, 2009 at 5:54 pm
Jan 11, 2009 at 5:49 pm

6	[Rd] Apparant bug in binomial model in GLM (PR#13434)

Full_Name: S?ren Faurby Version: 2.4.1 and 2.7.2 OS: Submission from: (NULL) (192.38.46.92) There appear to be a bug in the estimation of significance in the binomial model in GLM. This bug ...

Soren Faurby
Jan 6, 2009 at 11:25 am
Jan 7, 2009 at 4:40 pm

5	[Rd] overwriting '<-' and infinite recursions

Hello all, I'm having a problem when overwriting the '<-' function and was told I'd better post it here for help. The reason why I need to overwrite it is complicated and not easy to tell in a few ...

Yi Zhang
Jan 23, 2009 at 8:41 pm
Jan 24, 2009 at 8:54 pm

5	[Rd] Embeding R

Hi, I'm planning to embed R into an application, with the following context: - This application is written in Java (and managed with maven). I plan accessing R using JRI. - This application must be ...

Sylvain Loiseau
Jan 20, 2009 at 3:37 pm
Jan 21, 2009 at 11:18 am

5	[Rd] R-intro

Currently the pdf/dvi versions of R-intro do not build, the tex compilation hangs on page 21 (standard TeXLive, OS X). =============================================================== Jan de Leeuw, ...

Jan de Leeuw
Jan 4, 2009 at 7:20 pm
Jan 5, 2009 at 8:02 am

4	[Rd] Firefox 3 and HTML Search

I finally upgraded to Firefox 3.05 from 2.x, and now I can reproduce a bug a colleague has been complaining about but which I hadn't been able to reproduce before. In Windows, set Firefox as the ...

Duncan Murdoch
Jan 9, 2009 at 4:59 pm
Mar 5, 2009 at 4:03 pm

4	[Rd] Italics in svg output display as bold (PR#13463)

Full_Name: Yan Wong Version: 2.8.1 OS: Mac OS X 10.4 Submission from: (NULL) (78.149.167.246) When printing a plot to and svg file, text intended to be in italics is rendered in bold (svg file viewed ...

Yan
Jan 21, 2009 at 10:00 pm
Feb 10, 2009 at 4:05 pm

4	[Rd] In Rd: \describe \itemize and \item

I rebuilt a test version of my yaImpute package using Uwe Ligges' windows build service. I got this reply: Check result: OK R version 2.9.0 Under development (unstable) (2009-01-27 r47756) Here is ...

Nicholas L Crookston
Jan 29, 2009 at 10:22 pm
Jan 30, 2009 at 8:37 pm

4	[Rd] uninitialised value in R (PR#13476)

Hi, I get an "Conditional jump or move depends on uninitialised value(s)" from valgrind when using 'solve' in combination with some simple C-code. (I did not use other functions of R besides ...

Schlather
Jan 27, 2009 at 3:20 pm
Jan 28, 2009 at 10:54 am

4	[Rd] Defining an iterator

Inspired by Rudolf Biczok's query of Fri, Jan 23, 2009 at 1:25 AM, I tried to implement iteration in a generic way using S4. (Though I am admittedly still struggling with learning S4.) Given this, I ...

Stavros Macrakis
Jan 25, 2009 at 9:09 pm
Jan 26, 2009 at 3:09 am

4	[Rd] irrelevant warning message

Context: R version 2.7.1 (2008-06-23) I don't know when this was upgraded in the department, I just ran into the aberrent behavior today. Problem: Our group BY CHOICE does not change character ...

Terry Therneau
Jan 12, 2009 at 11:12 pm
Jan 13, 2009 at 1:34 pm

4	[Rd] Function to recognise convert dates between gregorian and other calendars (e.g. Persian)?

Dear list, I will shortly have some data that contains numeric dates in the Persian / Jalali calendar format, which I would like to convert to gregorian. At the moment there doesn't seem to be a ...

Amy Mikhail
Jan 7, 2009 at 3:23 pm
Jan 7, 2009 at 7:05 pm

3	[Rd] File and console output does not work in C code

Hello all, I am getting into trouble when trying to do standard I/O from a C function called within R environment. This function is written in a small C library that is loaded whith dyn.load() and ...

Benjamin Leblanc
Jan 28, 2009 at 4:46 pm
Jan 29, 2009 at 11:26 am

3	[Rd] FW: [R] The Quality & Accuracy of R

Dear R Developers, This is my first time subscribing to this list, so let me start out by saying thank you all very much for the incredible contribution you have made to science through your work on ...

Muenchen, Robert A (Bob)
Jan 24, 2009 at 1:13 pm
Jan 27, 2009 at 1:01 am

3	[Rd] loading RBlas.dll

hi everyone, Im implementing a new RBlas dll but just for optimising sake i need to know how and WHERE (which source code) RBlas gets loaded. there is a call to loadlibrary() in dynload.c BUT it ...

Sachin1234
Jan 23, 2009 at 3:17 am
Jan 26, 2009 at 8:10 am

3	[Rd] patch for textspecial and defaultfont in xfig

Hello, The current xfig device lacks the functionality to set the textspecial flag and use the defaultfont in xfig. This is necessary when you want to export to xfig and use interpreted text (e.g., $ ...

Sebastian Fischmeister
Jan 19, 2009 at 5:54 am
Jan 21, 2009 at 10:29 am

3	[Rd] sub and gsub treat \\ incorrectly (PR#13454)

Sub and gsub treat \\ replacement pattern incorrectly I expect sub("a","\\", "a", perl=T) to produce [1] "\" instead it generates [1] "" On the other hand, if I run sub("a","\\\\", "a", perl=T) it ...

Amiransk
Jan 19, 2009 at 6:25 pm
Jan 20, 2009 at 11:30 am

3	[Rd] Missing links on Windows and \link[bar]{foo}; clarification

Dear List, In one of my packages on R-Forge I have a custom panel function for Lattice graphics. In the Rd file for this panel function I want to provide links to some lattice functions (in package ...

Gavin Simpson
Jan 13, 2009 at 9:35 am
Jan 13, 2009 at 12:40 pm

3	[Rd] forcing the use of the c++ linker with c++ and fortran sources

I'm trying to build a package which has both gfortran and c++ code. In my installation of R, the R CMD INSTALL process compiles each c++ and gfortran code with the correct compiler, but performs the ...

Steve Guerrero
Jan 9, 2009 at 9:04 pm
Jan 10, 2009 at 7:49 am

3	[Rd] can't get names of R_env

Hi, I'm quite knew in R, so I might not have the R specific jargon. But here is my problem, I'm trying to access and use variabels given by a function environment, more specifically the rho in ...

Torpedo fisken
Jan 5, 2009 at 10:14 am
Jan 9, 2009 at 9:51 am

3	[Rd] Bug report in foreign library (PR#13425)

here appears to be a bug in the foreign library. The following code used to work, but now generates an error when 'package="SAS"' is specified: ds <- ...

Nhorton
Jan 3, 2009 at 8:15 pm
Jan 4, 2009 at 2:21 pm

2	[Rd] Inherited Methods in r-devel (for package maintainers mainly)

A recently committed revison of R-devel (47740) has introduced a new mechanism for ordering superclasses consistently, with related changes for selecting inherited methods. As part of the process, a ...

John Chambers
Jan 27, 2009 at 2:01 am
Jan 31, 2009 at 11:15 pm

2	[Rd] Methods not loaded in R-Devel vs 2.8.1

Dear list-member, I am currently developing a package with S4 classes. The NAMESPACE and DESCRIPTION is printed below. Within this package I have set a method "residuals" for two classes. In version ...

Pfaff, Bernhard Dr.
Jan 30, 2009 at 11:12 am
Jan 30, 2009 at 11:56 am

2	[Rd] length of POSIXlt object (PR#13482)

The length() of a POSIXlt object is given as 9 regardless of the actual length. For example: function (year=c(2006,2006),month=c(8,8),day=2:5,hour,minuteE) {# convert year, etc., into POSIXlt object ...

Twoutopias
Jan 28, 2009 at 10:15 pm
Jan 30, 2009 at 10:14 am

2	[Rd] Return values from .Call and garbage collection

Hi all, I'm posting this here as it discusses an issue with an external C library. If it would be better in R-Help, then I'll repost. I'm using an external library which I've written, which provides ...

Jon Senior
Jan 27, 2009 at 12:08 pm
Jan 27, 2009 at 5:18 pm

2	[Rd] [R] can't load rJava in R 2.8.1 on Windows XP

Yes, I've moved this to R-devel. If this is an R problem, it's in Sys.setenv: putting a very long string and then starting a shell shows the truncated string, but within the shell it's possible to ...

Duncan Murdoch
Jan 26, 2009 at 12:04 pm
Jan 26, 2009 at 5:25 pm

2	[Rd] Automatic shortening of text to fit into area

Hello, A comment in engine.c states: "/* don't draw anything; this could be made less crude :) */". The following patch makes it less crude: If the device doesn't support clipping and the text ...

Sebastian Fischmeister
Jan 25, 2009 at 4:05 am
Jan 25, 2009 at 10:01 pm

2	[Rd] Possible Bug in file.show (PR#13469)

Dear R-developers, Bug Report: R 2.8.1, i386-pc-mingw32 When I want to display two existing files using the command file.show(c("A.txt", "B.txt")) or file.show("A.txt", "B.txt") the same file ...

Wolfgang Koller
Jan 23, 2009 at 7:45 pm
Jan 24, 2009 at 1:09 pm

2	[Rd] [R] pdf() and pch problems

[Moved to R-Devel] Same problem on Fedora 8 through 10. The snippet Martin shows fixes the problem on those systems also. It would be very useful to have this documented somewhere either as a note in ...

Gavin Simpson
Jan 22, 2009 at 2:41 pm
Jan 22, 2009 at 3:52 pm

2	[Rd] encountering difficulty asking R to manipulate the correct columns in Expression Set class (object 4). (PR#13464)

Full_Name: Guy W. Tillinghast Version: 2.8.0 OS: Windows XP professional Submission from: (NULL) (24.248.24.3) I am encountering difficulty asking R to manipulate the correct columns in Expression ...

Guy Tillinghast
Jan 21, 2009 at 11:00 pm
Jan 22, 2009 at 2:37 pm

2	[Rd] Floating point excepting when cbind()ing a matrix of grobs (or environments) with a 0-column matrix

library(grid) e <- rectGrob() # OR: # e <- environment() a <- matrix(list(e), ncol = 1, nrow = 2) b <- matrix(ncol = 0, nrow = 2) cbind(a, b) cbind(a, b) This reliably crashes R for me. I realise ...

Hadley wickham
Jan 19, 2009 at 3:18 pm
Jan 21, 2009 at 10:31 am

2	[Rd] DierckxSpline segfault

I've just encountered a segfault when using DierckxSpline::percur function. Below is the minimal example which triggers the error: --- library(DierckxSpline) x <- 1:10 y <- rep(0, 10) pspline <- ...

Андрей Парамонов
Jan 17, 2009 at 6:59 pm
Jan 18, 2009 at 6:04 pm

2	[Rd] 2009 Wish list for R

2009 Wish list for R (no particular order): - some way of placing backslashes in literal strings without escaping them. Useful for latex, regular expressions and Windows file paths. This seems to ...

Gabor Grothendieck
Jan 17, 2009 at 1:57 am
Jan 17, 2009 at 12:36 pm

2	[Rd] interrupting R from a GUI

list(...), I am looking for a way to interrupt R from a callback: specifically, to interrupt plotting (typically on a cairoDevice, but would be good if it worked with other devices too). Of course, ...

Felix Andrews
Jan 16, 2009 at 6:07 am
Jan 17, 2009 at 5:55 am

2	[Rd] [Q] R CMD check signals error on code that works from UI

Add the following to example section of a dot-Rd manpage: ## :WHY: The following kills R CMD check but runs fine on console. foos <- c("aaa", "bbb", "ccc") cat(sapply(foos, function(foo) { ...

Paul Roebuck
Jan 15, 2009 at 5:50 pm
Jan 15, 2009 at 6:14 pm

2	[Rd] More intensive checking of R help files

We have been working on handling Rd (R help) files with R rather than Perl scripts. As part of that work, Duncan has written a parser which has revealed many problems in package help files, and we ...

Prof Brian Ripley
Jan 9, 2009 at 9:25 am
Jan 15, 2009 at 10:45 am

2	[Rd] Windows installer text bug (PR#13445)

Full_Name: Rob Cranfill Version: 2.8.1 OS: Windows XP SP2 Submission from: (NULL) (130.76.32.19) Using the Windows installer for 2.8.1, partway through the process there is a dialog that looks ...

Robert E Cranfill
Jan 14, 2009 at 12:30 am
Jan 14, 2009 at 11:34 am

2	[Rd] Problem with compiling shared C/C++ library for loading into R (Linux)

Dear all, I am using the .Call interface to call c++ code from R. For that, I am trying to create a dynamic library (mylib.so) using "R CMD SHLIB" by linking my own c++ code and an external c++ ...

Samsiddhi Bhattacharjee
Jan 10, 2009 at 11:54 pm
Jan 14, 2009 at 8:49 am

2	[Rd] Callbacks seems to get GCed.

Dear list, I am trying to implement a publish-subscribe mechanism in for an embedded R interpreter. But somehow my registered closures seem to get collected by the GC, even though I have protected ...

Bernd Schoeller
Jan 8, 2009 at 2:30 pm
Jan 8, 2009 at 3:22 pm

2	[Rd] Strange error message

I'm testing out some changes to survreg and got the following output, the likes of which I've never seen before: ---------------------------------------------------------------------- R version 2.7.1 ...

Terry Therneau
Jan 6, 2009 at 2:58 pm
Jan 6, 2009 at 3:47 pm

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