Re: [Rd] Source for bash_completion.d/R?

2011-05-03 Thread Deepayan Sarkar
On Tue, May 3, 2011 at 4:40 AM, Dirk Eddelbuettel e...@debian.org wrote: On 2 May 2011 at 11:32, Sharpie wrote: | Hello, I was just tweaking the R build for the Homebrew package manager and I | thought it would be nice to enable bash completion. I noticed that | Debian-based systems install

Re: [Rd] R CMD check and Suggests Packages

2011-05-03 Thread Martin Maechler
Hervé Pagès hpa...@fhcrc.org on Mon, 02 May 2011 11:55:08 -0700 writes: Hi, On 11-04-28 07:00 PM, Dario Strbenac wrote: Hello, In my description file, I have an example data package in Suggests: that I've deleted from my library to test what the user who

[Rd] Location of Internal Code

2011-05-03 Thread Robin Evans
Hello, This seems like a fairly elementary question, but I couldn't seem to find the answer anywhere online. Where can I find code which is called with .Internal?  Specifically, the R function colSums() calls an internal function with the same name (I presume a C function), and I'd like to see

Re: [Rd] Bug report: R 2.14.0dev Sweave option width does not work

2011-05-03 Thread Alexander Favorov
Thank you! It works. On 01.05.2011 19:17, Duncan Murdoch wrote: On 11-05-01 7:35 AM, Duncan Murdoch wrote: On 30/04/11 7:25 PM, Alexander Favorov wrote: Hi! In R 2.14.0dev (R version 2.14.0 Under development (unstable) (2011-04-29 r55692), Windows release

[Rd] [R] Sweave stops when opening X11 device fails

2011-05-03 Thread Andreas Borg
Hi all, I am posting this again because I got no reply on r-help. Maybe the devel-list is the right place for this kind of question. I've run into the following problem with Sweave: I frequently run Sweave from a xterm console within an X session owned by a different user, i.e. my colleague

Re: [Rd] How to create vignette.pdf for R-2.13.0?

2011-05-03 Thread Uwe Ligges
On 02.05.2011 21:24, cstrato wrote: Dear Prof. Ripley, Thank you for your confirmation and explanation, I understand the reason for cleaning things up to save memory. However, it was very convenient to have this feature in earlier versions of R. It would be really helpful to have an

Re: [Rd] Location of Internal Code

2011-05-03 Thread Uwe Ligges
On 03.05.2011 01:59, Robin Evans wrote: Hello, This seems like a fairly elementary question, but I couldn't seem to find the answer anywhere online. Where can I find code which is called with .Internal? Specifically, the R function colSums() calls an internal function with the same name (I

Re: [Rd] [R] Sweave stops when opening X11 device fails

2011-05-03 Thread peter dalgaard
On May 3, 2011, at 12:35 , Andreas Borg wrote: Hi all, I am posting this again because I got no reply on r-help. Maybe the devel-list is the right place for this kind of question. Actually, not an R problem at all, but try one of these... 1) get rid of the DISPLAY environment variable

[Rd] R CMD build - will reset the timestamps of all files in a package

2011-05-03 Thread Valentin Todorov
Dear developers, I wonder why (R version 2.13.0 and after) the command R CMD build sets the timestamp of all files in the package to the current date/time. This seems not to be mentioned in the list of changes. Is there an option to avoid this? Best regards, Valentin

Re: [Rd] [R] Sweave stops when opening X11 device fails

2011-05-03 Thread Dirk Eddelbuettel
On 3 May 2011 at 13:19, peter dalgaard wrote: | | On May 3, 2011, at 12:35 , Andreas Borg wrote: | | Hi all, | | I am posting this again because I got no reply on r-help. Maybe the devel-list is the right place for this kind of question. | | Actually, not an R problem at all, but try one

Re: [Rd] Reference Classes: Accessing methods via [[...]], bug?

2011-05-03 Thread Geoff Jentry
On Sun, 1 May 2011, Martin Morgan wrote: On 05/01/2011 03:09 PM, John Chambers wrote: It would be interesting to get some experience and opinions on whether this is a good idea or not. It breaks encapsulation, in that the behavior of the class can no longer be inferred from the class definition

Re: [Rd] How to create vignette.pdf for R-2.13.0?

2011-05-03 Thread cstrato
Dear Uwe, This is my development cycle: First, I run R CMD check until there are no more warnings/errors. Since years it was very convenient that R CMD check builds the pdf-files of the vignettes, too, since this allowed me to correct errors in the manual files and the vignette files at the

Re: [Rd] How to create vignette.pdf for R-2.13.0?

2011-05-03 Thread Uwe Ligges
On 03.05.2011 21:14, cstrato wrote: Dear Uwe, This is my development cycle: First, I run R CMD check until there are no more warnings/errors. Since years it was very convenient that R CMD check builds the pdf-files of the vignettes, too, since this allowed me to correct errors in the manual

Re: [Rd] How to create vignette.pdf for R-2.13.0?

2011-05-03 Thread cstrato
Dear Uwe, Thank you, however since I use R CMD INSTALL xps.tar.gz my source code is not polluted. Furthermore, I forgot to mention that finally I upload the source code only to the BioC svn repository. The rest is done by the BioC servers, including building the pdf-files for the vignettes.

Re: [Rd] How to create vignette.pdf for R-2.13.0?

2011-05-03 Thread Simon Urbanek
On May 3, 2011, at 4:48 PM, cstrato cstr...@aon.at wrote: Dear Uwe, Thank you, however since I use R CMD INSTALL xps.tar.gz my source code is not polluted. But then you already used build to create the tar ball so the vignette has been built. So what is your point? Cheers, S

Re: [Rd] How to create vignette.pdf for R-2.13.0?

2011-05-03 Thread cstrato
No, I simply do tar czf xps_1.13.1.tar.gz xps. Best regards Christian On 5/3/11 11:11 PM, Simon Urbanek wrote: On May 3, 2011, at 4:48 PM, cstratocstr...@aon.at wrote: Dear Uwe, Thank you, however since I use R CMD INSTALL xps.tar.gz my source code is not polluted. But then you

Re: [Rd] Reference Classes: Accessing methods via [[...]], bug?

2011-05-03 Thread Hadley Wickham
Part of the motivation for the reference classes was to bring a general OOP view to R.  One can start from some essential concepts of objects and their properties, inheritance and class definition, as have evolved over a very long time. Next, there is a fundamental choice of paradigm between

Re: [Rd] How to create vignette.pdf for R-2.13.0?

2011-05-03 Thread Simon Urbanek
On May 3, 2011, at 5:15 PM, cstrato wrote: No, I simply do tar czf xps_1.13.1.tar.gz xps. Well, that's your problem then, not R's. Source packages are created using R CMD build, not by manual tarring (you can do the latter if you know what you're doing, but then you can't complain about the

[Rd] Wishlist: write R's bin path to the PATH variable and remove the version string in the installation dir under Windows

2011-05-03 Thread Yihui Xie
Hi, I guess this issue must have been brought forward long time ago, but I still hope you can consider under Windows (during installation): 1. put R's bin path in the PATH variable of the system so that we can use the commands R and Rscript more easily; 2. remove the version string like

Re: [Rd] R CMD check and Suggests Packages

2011-05-03 Thread Dario Strbenac
Hello, If Dario really uses R 2.13.0 (or newer), and he gets the above error message for a package that is not required but only suggested, I think we'd need a clear, ideally simple, reproducible example, here. I was able to reproduce it. I made a new package with package.skeleton(), then added

Re: [Rd] Wishlist: write R's bin path to the PATH variable and remove the version string in the installation dir under Windows

2011-05-03 Thread Gabor Grothendieck
On Tue, May 3, 2011 at 7:44 PM, Yihui Xie x...@yihui.name wrote: Hi, I guess this issue must have been brought forward long time ago, but I still hope you can consider under Windows (during installation): 1. put R's bin path in the PATH variable of the system so that we can use the commands

Re: [Rd] Wishlist: write R's bin path to the PATH variable and remove the version string in the installation dir under Windows

2011-05-03 Thread Duncan Murdoch
On 03/05/2011 7:44 PM, Yihui Xie wrote: Hi, I guess this issue must have been brought forward long time ago, but I still hope you can consider under Windows (during installation): 1. put R's bin path in the PATH variable of the system so that we can use the commands R and Rscript more easily;

Re: [Rd] Wishlist: write R's bin path to the PATH variable and remove the version string in the installation dir under Windows

2011-05-03 Thread Yihui Xie
1. Few Windows users use these commands does not imply they are not useful, and I have no idea how many Windows users really use them. How do you run R CMD build when you build R packages under Windows? You don't write C:/Program Files/R/R-2.13.0/bin/i386/R.exe CMD build, do you? I think the

Re: [Rd] Wishlist: write R's bin path to the PATH variable and remove the version string in the installation dir under Windows

2011-05-03 Thread Simon Urbanek
On May 3, 2011, at 11:25 PM, Yihui Xie wrote: 1. Few Windows users use these commands does not imply they are not useful, and I have no idea how many Windows users really use them. How do you run R CMD build when you build R packages under Windows? You don't write C:/Program

Re: [Rd] Wishlist: write R's bin path to the PATH variable and remove the version string in the installation dir under Windows

2011-05-03 Thread Gabor Grothendieck
On Tue, May 3, 2011 at 7:44 PM, Yihui Xie x...@yihui.name wrote: Hi, I guess this issue must have been brought forward long time ago, but I still hope you can consider under Windows (during installation): 1. put R's bin path in the PATH variable of the system so that we can use the commands

Re: [Rd] Wishlist: write R's bin path to the PATH variable and remove the version string in the installation dir under Windows

2011-05-03 Thread Yihui Xie
Thanks! But I'm sorry this is not what I wanted. I just hope we can call R as a command like we do under *nix -- this will make it easier for *other* software packages to find R. BTW, for the cmd package: if we were evil enough, we can directly execute this in R to permanently set the PATH

Re: [Rd] Wishlist: write R's bin path to the PATH variable and remove the version string in the installation dir under Windows

2011-05-03 Thread Thomas Lumley
On Wed, May 4, 2011 at 3:25 PM, Yihui Xie x...@yihui.name wrote: 1. Few Windows users use these commands does not imply they are not useful, and I have no idea how many Windows users really use them. How do you run R CMD build when you build R packages under Windows? You don't write C:/Program

Re: [Rd] Wishlist: write R's bin path to the PATH variable and remove the version string in the installation dir under Windows

2011-05-03 Thread Gabor Grothendieck
On Wed, May 4, 2011 at 1:04 AM, Yihui Xie x...@yihui.name wrote: Thanks! But I'm sorry this is not what I wanted. I just hope we can call R as a command like we do under *nix -- this will make it easier for *other* software packages to find R. You asked for an R program that gives the ability

Re: [Rd] Wishlist: write R's bin path to the PATH variable and remove the version string in the installation dir under Windows

2011-05-03 Thread Wincent
I also prefer to keep the old versions. Sometimes, I have spent time to set up the system with older version and don't want to update to the latest (e.g. the new RGtk2 needs updated GTk2 as well) because the older still works and I don't need the new features. Regards Ronggui On 4 May 2011