r-devel@r-project.org discussions for February 2012

16	[Rd] portable parallel seeds project: request for critiques

I've got another edition of my simulation replication framework. I'm attaching 2 R files and pasting in the readme. I would especially like to know if I'm doing anything that breaks .Random.seed or ...

Paul Johnson
Feb 17, 2012 at 8:57 pm
Mar 2, 2012 at 1:51 pm

13	[Rd] requesting a new SIG mailing list

Dear R developers, Due to the increasing use R in hydrology and other close-related environmental sciences, I would like to ask if it would be possible to create a new Special Interest Group mailing ...

Mauricio Zambrano-Bigiarini
Feb 13, 2012 at 4:30 pm
Feb 16, 2012 at 1:08 pm

10	[Rd] Jazzing up the Task Views index page

A little while ago here we had a short discussion about Task Views - I think ignited by someone saying 'how many times do I have to say "have you read the Optimisation Task View?"?' and I poured some ...

Barry Rowlingson
Feb 21, 2012 at 12:58 pm
Feb 27, 2012 at 6:07 pm

9	[Rd] function remains loaded in the search space after detaching the package

I ran into some very irritating behaviour I don't understand. Let me illustrate with the package gdata() and the function print.object_size() : A single object matching ?print.object_size? was found ...

Joris Meys
Feb 24, 2012 at 10:24 am
Feb 24, 2012 at 4:08 pm

9	[Rd] Using custom R_LIBS with R CMD install

Hi all, Am I using the correct syntax to set a custom R_LIBS when running R CMD INSTALL from the command line? I get: R_LIBS=/Users/hadley/R-dev R CMD INSTALL aL3xa-rapport-08e68ca/ # Desktop ...

Hadley Wickham
Feb 7, 2012 at 6:13 pm
Feb 9, 2012 at 1:32 pm

8	[Rd] Canonical package directory name for JAR files?

We have an R package which needs to include a JAR file. Is there a canonical directory for it?

Roebuck,Paul L
Feb 7, 2012 at 9:34 pm
Feb 9, 2012 at 1:08 am

7	[Rd] executable files R package

I am in the process of creating a package in R which calls pre-compiled C code i.e. '.exe' files in Windows. Since CRAN will not accept packages with binary code files, what are my options to meet ...

Sahir bhatnagar
Feb 13, 2012 at 7:36 pm
Feb 20, 2012 at 6:23 pm

7	[Rd] R CMD SHLIB in Windows XP - No output at all

Hello all, I'm trying hard to make R CMD SHLIB work on Windows XP (32-bit) - please note that I don't have the admin rights on the computer. In terms of setup, I have followed the procedure : = ...

Lorenzo
Feb 14, 2012 at 12:09 am
Feb 16, 2012 at 5:06 am

6	[Rd] include <R.h>

I am trying to add #include <R.h to a .c file in one of my package, so I can call error() without a complaint about implicit defined function. The src/ has a Makefile, to build some exec/ files that ...

Paul Gilbert
Feb 19, 2012 at 7:45 pm
Feb 20, 2012 at 2:46 am

6	[Rd] Task views (was: Re: [R] Schwefel Function Optimization)

... ... Now it could be that people are not trying very hard to solve their own problems, but to be fair it is a pretty gruelling process to find the Task Views. May I suggest that there be a "Task ...

Patrick Burns
Feb 11, 2012 at 5:55 pm
Feb 15, 2012 at 4:30 am

6	[Rd] Creating XML document extremely slow

Hi list, I'm using the package XML to create a simple XML document. Unfortunately constructing the XML tree is extremely slow. My code (see below) adds only about 100 nodes per second on an Intel i5 ...

Titus von der Malsburg
Feb 10, 2012 at 12:18 pm
Feb 10, 2012 at 6:12 pm

5	[Rd] FORTRAN compilation error

I get an error when trying to compile a FORTRAN source file for use in a package that I am developing. The error, reported in 00install.out is below. * installing *source* package 'USGSstats' ... ** ...

David L Lorenz
Feb 8, 2012 at 8:16 pm
Feb 9, 2012 at 3:55 pm

5	[Rd] location of check.Renviron on Windows

Doing package development on a Windows 7 machine, and I want to tell R check not to worry about the "suggested" packages. I realize this can be done using the ~/.R/check.Renviron file, but what ...

Robert M. Flight
Feb 1, 2012 at 7:10 pm
Feb 1, 2012 at 9:44 pm

4	[Rd] Replace back slashes with forward slashes?

Hello, All: What can people tell me about converting back slashes to forward slashes in character strings? Several years ago, Prof. Ripley provided a solution, which I lost and have not been able to ...

Spencer Graves
Feb 29, 2012 at 5:37 pm
Feb 29, 2012 at 6:24 pm

4	[Rd] Identical copy of base function

Hello, Regarding this in R-devel/NEWS/New features : o ?library(pkg)? no longer warns about a conflict with a function from ?package:base? if the function is an identical copy of the base one but ...

Matthew Dowle
Feb 27, 2012 at 9:59 am
Feb 27, 2012 at 3:34 pm

4	[Rd] RFC: Proposal to make NROW() and NCOL() slightly more general

The help has I'm proposing to extend these two convenience functions to also work ``correctly'' for generalized versions of matrices. The current implementation : NROW <- function(x) ...

Martin Maechler
Feb 4, 2012 at 4:38 pm
Feb 9, 2012 at 12:08 am

3	[Rd] Out of date instructions to build R using MKL

Hi! I've been playing with MKL for a few days and I noticed the instructions in the R Installation Administration manual [1] no longer apply. It seems that since version 10.0 (the one used by the ...

Milan Bouchet-Valat
Feb 10, 2012 at 3:15 pm
May 30, 2012 at 10:32 pm

3	[Rd] Unexpected behaviour for RowSideColors in function heatmap

Hello, I have come across some unexpected behaviour of the function heatmap in the stats package. This looks like a bug to me, but I might have misunderstood something. When calling the function in ...

Pär Engström
Feb 28, 2012 at 10:04 am
Mar 12, 2012 at 5:42 pm

3	[Rd] OpenMP and random number generation

Dear all, Now that R has OpenMP facilities, I'm trying to use it for my own package but I'm still wondering if it is safe to use random number generation within a OpenMP block. I looked at the R ...

Mathieu Ribatet
Feb 22, 2012 at 8:23 am
Feb 22, 2012 at 3:29 pm

3	[Rd] text(1:10, col=NA) is not transparent

Maybe I am missing something, but according to the help page to par (section "Color Specification"), which is referred to in the help to text argument col: ?"transparent"? or (integer) ?NA? is ...

Peter Ruckdeschel
Feb 20, 2012 at 11:09 am
Feb 21, 2012 at 12:14 am

3	[Rd] Parallel R CMD check?

Running R CMD check on a package can take quite a lot of time. Checks seem like they could be run in parallel (separate processes for, e.g., codoc, examples, tests, ...). Is there a way to do this? ...

Martin Morgan
Feb 17, 2012 at 6:50 am
Feb 17, 2012 at 7:46 pm

3	[Rd] help.search() in html?

Hi, I have options(help_type="html") in my .Rprofile and when I type ?foo, the man page appears as a new tab in my web browser (which is already running). Fine. However, when I type ??foo, rather ...

Hkawakat
Feb 15, 2012 at 1:03 pm
Feb 15, 2012 at 5:49 pm

3	[Rd] capture.output() is trying to allocate 17179869182.6 Gb on my not so big data.frame

Hi, This is what I get with recent R devel on a 64-bit Ubuntu laptop: Error in print.default(m, ..., quote = quote, right = right) : cannot allocate memory block of size 17179869182.6 Gb I get ...

Hervé Pagès
Feb 8, 2012 at 12:08 am
Feb 9, 2012 at 1:36 am

3	[Rd] Resume processing after warning handler.

Dear list! I have a script that processes a large number of data files. When one file fails to process correctly, I want the script to write a message and to continue with the next file. I achieved ...

Titus von der Malsburg
Feb 3, 2012 at 10:49 am
Feb 6, 2012 at 5:02 pm

3	[Rd] Crash in R using embedded.

Hi, I'm new to R, and am trying to embed R into another application. I'm calling gev.fit() from the ismev package, and it is crashing somewhere inside it. gdb is not catching it, and valgrind is not ...

Dave Pugmire
Feb 1, 2012 at 3:24 pm
Feb 1, 2012 at 6:07 pm

2	[Rd] improved error message when existing implicit S4 generic is not imported?

pkgA's NAMESPACE has importFrom(graphics, plot) exportClasses("A") exportMethods("plot") R/foo.R has setClass("A") setMethod("plot", "A", function(x, y, ...) {}) During R CMD INSTALL pkgA_1.0.tar.gz ...

Martin Morgan
Feb 26, 2012 at 6:39 am
Mar 1, 2012 at 8:28 pm

2	[Rd] Typo in NEWS: -as-cran should be --as-cran

Under 'CHANGES IN R VERSION 2.14.2' in NEWS, there is: "R CMD check has a new option -as-cran to turn on most of the customizations that CRAN uses for its incoming checks." "-as-cran" should be ...

Henrik Bengtsson
Feb 29, 2012 at 2:13 am
Feb 29, 2012 at 5:12 pm

2	[Rd] Why cant my S4 class have a slot named `C`?

Hi all, This feature was throwing me for a loop for quite some time until I played with the names of the slots. Consider exhibit A: ============== setClass("SVM", representation=representation( ...

Steve Lianoglou
Feb 21, 2012 at 4:13 pm
Feb 21, 2012 at 5:25 pm

2	[Rd] read.spss issues

Someone supplied me with a small SPSS datafile that caused a buffer overflow and then a crash when reading it in R. It seems like a pretty serious issue to me. Unfortunately I can't supply the ...

Jeroen Ooms
Feb 15, 2012 at 6:05 am
Feb 15, 2012 at 10:04 pm

2	[Rd] method using several (and different) arguments in turn

Dear R-developers community, I have the following generic: setGeneric( name="newsample", def=function(x,y,z,a,b,c,...){standardGeneric("newsample")} And I can build several methods for this generic ...

James Foadi
Feb 14, 2012 at 4:43 pm
Feb 14, 2012 at 5:57 pm

2	[Rd] Overwrite S3 methond from base package

Dear all, I am developing a package, which bundles my most frequently used functions. One of those is a modified version of droplevels from the base package (basically, it preserves any contrast ...

Thaler,Thorn,LAUSANNE,Applied Mathematics
Feb 13, 2012 at 11:59 am
Feb 14, 2012 at 7:12 am

2	[Rd] [R] Version control (git, mercurial) for R packages

CCd to r-devel as suggested by Peter. Thanks Hadley - I should definitely look closer into the devtools package - there really seem to be some gems in there. One example is this function - sounds ...

Rainer M Krug
Feb 10, 2012 at 8:11 am
Feb 13, 2012 at 8:31 am

2	[Rd] scan() doesn't like '1.#IND'

Hi, Since C++ code compiled with g++ 4.6.3 on Windows (the version included in latest Rtools) now can produce things like '1.#IND' when writing doubles to a file (using the << operator), I wonder ...

Hervé Pagès
Feb 9, 2012 at 1:59 am
Feb 9, 2012 at 4:36 am

2	[Rd] mem.limits deprecated

After upgrading my servers to 2.14, log files were filled warnings that 'mem.limits' has been deprecated and to use gc instead. After reading the NEWS for R 2.14.0 and PR#14795 I learned that it is ...

Jeroen Ooms
Feb 6, 2012 at 8:45 pm
Feb 6, 2012 at 9:57 pm

2	[Rd] Segfault on ".C" registration via R_CMethodDef according to 'Writing R Extensions'.

Dear R List, I encountered a serious problem regarding the registration of ".C" when following the documentation "Writing R Extensions" that leads to a segmentation fault (tested on windows and mac ...

Daniel Adler
Feb 6, 2012 at 1:27 pm
Feb 6, 2012 at 3:42 pm

2	[Rd] Is the link to the R wiki down?

I am getting a 404 page for this: http://wiki.r-project.org/ I was not sure who to write this to - so I am writing it here. Best, Tal ----------------Contact ...

Tal Galili
Feb 3, 2012 at 3:55 pm
Feb 3, 2012 at 5:08 pm

1	[Rd] missing value break my if clause and crash my program

I have a program which is designed to read through a dbf file and carry out certain amount of further calculation if one condition obtained from the newly read line. The condition to determine if the ...

Zisheng xing
Feb 29, 2012 at 12:36 pm
Mar 1, 2012 at 6:52 pm

1	[Rd] prior.weights and weights()

I'm wondering whether anyone has any insight into why the 'simulate' methods for the built-in glm() families (binomial, Poisson, Gamma ...) extract the prior weights using object$prior.weights rather ...

Ben Bolker
Feb 21, 2012 at 9:57 pm
Feb 27, 2012 at 1:10 pm

1	[Rd] Unexpected behavior in factor level ordering

Hello, Everybody: This may not be a "bug", but for me it is an unexpected outcome. A factor variable's levels do not retain their ordering after the levels function is used. I supply an example in ...

Paul Johnson
Feb 25, 2012 at 6:16 pm
Feb 25, 2012 at 6:25 pm

1	[Rd] R devel [and R 2.14.1 patched]: R CMD build now sources ~/.Rprofile

I'd like to follow up on this one. It may be that I have misunderstood something, but on both R devel (2012-02-22 r58452) and R 2.14.1 patched (2012-02-18 r58394) I can't seem to avoid loading ...

Henrik Bengtsson
Feb 23, 2012 at 8:14 am
Feb 24, 2012 at 12:31 am

1	[Rd] Private Variables in R5-Classes possible?

Hi list, is there a way to define some kind of private Variable? I would like to prevent the user from manipulating fields on his own, in order to not destroy data structures. The problem is, that as ...

Claus Jonathan Fritzemeier
Feb 21, 2012 at 11:07 am
Feb 22, 2012 at 7:55 pm

1	[Rd] tempdir() documentation or real bug ?

?tempdir says By default, ?tmpdir? will be the directory given by ?tempdir()?. This will be a subdirectory of the temporary directory found by the following rule. The environment variables ?TMPDIR?, ...

Brian G. Peterson
Feb 21, 2012 at 7:20 pm
Feb 21, 2012 at 7:50 pm

1	[Rd] Controlling simplification in apply()?

Dear list, Fully according to the documented behaviour, I was bitten by apply() simplifying results to vectors or arrays when the lengths of the individual objects returns by FUN are the same (over ...

Gavin Simpson
Feb 20, 2012 at 4:03 pm
Feb 21, 2012 at 7:09 am

1	[Rd] Unstable reproduce for potential issue with CHARSXP creation

I stumbled across one of those intermittent bugs where the code sometimes works and sometimes doesn't. Below is an example run showing a failure where a CHARSXP object was not properly created (by ...

Patrick Aboyoun
Feb 16, 2012 at 10:08 pm
Feb 19, 2012 at 5:21 pm

1	[Rd] building r-devel

I'm sure I'm being an absolute bonehead (again), but can someone suggest what I might be doing wrong? Trying to build latest r-devel on Ubuntu 10.04; as recommended in various places, trying to build ...

Ben Bolker
Feb 17, 2012 at 4:31 pm
Feb 17, 2012 at 7:46 pm

1	[Rd] which R package is used for browsing web pages through coding

i know RCurl pakage to retrieve web content,it has limited use, i want interactive package like (in perl--- Mechanize, In java--- Watij,Prowser,HTMLunit,HTTPunit, in Ruby---- Watir ,etc) this ...

Sagarnikam123
Feb 10, 2012 at 10:54 am
Feb 15, 2012 at 3:59 pm

1	[Rd] Can I use "..." in parallel:::clusterApplyLB?

Hello, Can I do the following? Is parallel:::clusterApplyLB() designed to work like this? The code below is for illustrative purposes only. library(parallel) myFunction<-function(myPar1, myPar2, ...) ...

Slava Razbash
Feb 13, 2012 at 6:51 am
Feb 13, 2012 at 8:54 am

1	[Rd] Options for keeping files when package re-install or update.

Hi! All I want to keep some file which user defined when re-installing or updating package. Is there any way to do? Thanks. --Heewon--

전희원
Feb 8, 2012 at 12:02 am
Feb 8, 2012 at 2:11 pm

0	[Rd] Alternative to .Internal(.dfltStop(msg, call))?

Hi, I'm looking for a way to generate a "full stop" that will not be caught by signal handlers, cf. .Internal(.dfltStop(msg, call)). RATIONALE: In the R.oo package I have throw() which (leaving out ...

Henrik Bengtsson
Feb 29, 2012 at 7:11 pm
Feb 29, 2012 at 7:11 pm

0	[Rd] Fetching email in R (IMAP)

Is there an R package for fetching email from an IMAP mail server? I found the CRAN package sendmailR (for sending mail via SMTP) and the CRAN package Imap (but that is actually Interactive Mapping, ...

Stavros Macrakis
Feb 28, 2012 at 7:43 pm
Feb 28, 2012 at 7:43 pm

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