[Rd] Updated Windows toolchain

2011-11-28 Thread Prof Brian Ripley
An updated toolchain is now being used for Windows' builds of R-devel: details are in the R-admin manual and at http://www.murdoch-sutherland.com/Rtools/ and http://www.stats.ox.ac.uk/pub/Rtools/ Both 32- and 64-bit parts of the toolchain use v2.0.1 of the Mingw-w64 project's runtime and a beta

Re: [Rd] Holding back on source code

2011-11-28 Thread Sachinthaka Abeywardana
I was referring specifically to gputools package: http://cran.r-project.org/web/packages/gputools/index.html which has some of Nvidias CuBLAS implemented. What I want to do is release the code and implement the package, and not get in trouble considering I was with CSIRO when I did it. I guess fro

Re: [Rd] Holding back on source code

2011-11-28 Thread Dominick Samperi
On Mon, Nov 28, 2011 at 2:17 AM, Prof Brian Ripley wrote: > On 27/11/2011 23:07, Sachinthaka Abeywardana wrote: >> >> Hi All, >> >> A few years back when I was a CSIRO (an Australian research centre) intern >> I developed a BLAS package for R that uses the GPU. I believe that there >> is >> someth

Re: [Rd] Bug in Sys.which()?

2011-11-28 Thread Dan Tenenbaum
On Mon, Nov 28, 2011 at 2:34 PM, Duncan Murdoch wrote: > On 11-11-28 5:20 PM, Dan Tenenbaum wrote: >> >> At a Windows command prompt: >> C:\>which ls >> /cygdrive/c/Rtools215/bin/ls >> >> C:\>which perl >> /cygdrive/c/perl/bin/perl >> >> In R: >>> >>> Sys.which(c("ls", "perl")) >> >>              

Re: [Rd] Bug in Sys.which()?

2011-11-28 Thread Duncan Murdoch
On 11-11-28 5:20 PM, Dan Tenenbaum wrote: At a Windows command prompt: C:\>which ls /cygdrive/c/Rtools215/bin/ls C:\>which perl /cygdrive/c/perl/bin/perl In R: Sys.which(c("ls", "perl")) lsperl "c:\\RTOOLS~3\\bin\\ls.exe"

Re: [Rd] R CMD ?

2011-11-28 Thread Duncan Murdoch
On 11-11-28 3:19 PM, Hadley Wickham wrote: That does seem to mix up namespaces quite a bit. That was just a proposal - equally R CMD mypackage::mycommand could just run mypackage::mycommand() but then passing argument might get a bit confusing. But what does it get you that "Rscript -e" d

[Rd] Bug in Sys.which()?

2011-11-28 Thread Dan Tenenbaum
At a Windows command prompt: C:\>which ls /cygdrive/c/Rtools215/bin/ls C:\>which perl /cygdrive/c/perl/bin/perl In R: > Sys.which(c("ls", "perl")) lsperl "c:\\RTOOLS~3\\bin\\ls.exe" "" Is this expected behavior? > session

[Rd] extend validObject to validate any object (shallow and deep validation)

2011-11-28 Thread Hervé Pagès
Hi, It would be nice if there was a tool for checking the validity of any object. validObject() is of course the natural candidate for this but right now it doesn't work on S3 objects: df <- data.frame(aa=1:4, bb=letters[4:1]) attributes(df)$row.names <- c("A", "B", "C", "A") 'df' is an inv

Re: [Rd] R CMD ?

2011-11-28 Thread Henrik Bengtsson
On Mon, Nov 28, 2011 at 12:19 PM, Hadley Wickham wrote: >> That does seem to mix up namespaces quite a bit. > > That was just a proposal - equally > > R CMD mypackage::mycommand > > could just run > > mypackage::mycommand() > > but then passing argument might get a bit confusing. > >> But what doe

Re: [Rd] R CMD ?

2011-11-28 Thread Hadley Wickham
> The shell command >  R CMD something > currently acts as though it puts R_HOME/bin on the front > of PATH, looks for an executable file called 'something' > in PATH, and then executes it.  The executable may call R > or it may not. > > I think that running an R script file is sufficiently differe

Re: [Rd] R CMD ?

2011-11-28 Thread William Dunlap
The shell command R CMD something currently acts as though it puts R_HOME/bin on the front of PATH, looks for an executable file called 'something' in PATH, and then executes it. The executable may call R or it may not. I think that running an R script file is sufficiently different from runnin

Re: [Rd] R CMD ?

2011-11-28 Thread Hadley Wickham
> That does seem to mix up namespaces quite a bit. That was just a proposal - equally R CMD mypackage::mycommand could just run mypackage::mycommand() but then passing argument might get a bit confusing. > But what does it get you > that "Rscript -e" doesn't already give you?  You can set up

Re: [Rd] R CMD ?

2011-11-28 Thread Duncan Murdoch
On 28/11/2011 2:48 PM, Hadley Wickham wrote: It'd be cool if R CMD was user extensible through packages, so that (e.g.) R CMD mypackage::mycommand would do something like: path<- system.file("cmd", paste(command, ".r"), package = package) if (!file.exists(path)) { stop("Command ", command,

Re: [Rd] R CMD ?

2011-11-28 Thread Duncan Murdoch
On 28/11/2011 2:16 PM, Henrik Bengtsson wrote: Hi, is it possible to add a custom script such that it is called via R CMD ? Is R CMD searching for it elsewhere than R_HOME/bin/? I'm looking for an non-admin alternative, so copying the script to R_HOME/bin/ will not do (in case the user don't h

Re: [Rd] R CMD ?

2011-11-28 Thread Yihui Xie
I strongly support this proposal. This will be a fantastic feature! Regards, Yihui -- Yihui Xie Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA On Mon, Nov 28, 2011 at 1:48 PM, Hadley Wickham wrote: > It'd be cool if R CM

Re: [Rd] R CMD ?

2011-11-28 Thread Hadley Wickham
It'd be cool if R CMD was user extensible through packages, so that (e.g.) R CMD mypackage::mycommand would do something like: path <- system.file("cmd", paste(command, ".r"), package = package) if (!file.exists(path)) { stop("Command ", command, " in ", package, " does not exist") } else {

[Rd] R CMD ?

2011-11-28 Thread Henrik Bengtsson
Hi, is it possible to add a custom script such that it is called via R CMD ? Is R CMD searching for it elsewhere than R_HOME/bin/? I'm looking for an non-admin alternative, so copying the script to R_HOME/bin/ will not do (in case the user don't have enough permission to write there). /Henrik

Re: [Rd] Avoid package in build process when not supported on OS

2011-11-28 Thread Rau, Roland
Dear Henrik, dear all, thank you very much! What you recommended works, see here: :-D = The files will be removed after roughly 72 hours. Installation time in seconds: 9 Check time in seconds: 22 Check result: OK R version 2.14.0 (2011-10-31) = And also thank you for pointing o

Re: [Rd] Avoid package in build process when not supported on OS

2011-11-28 Thread Henrik Bengtsson
Move doMC from Requests: to Suggests: and load it in the code when needed, e.g. library("doMC"). BTW, make sure you are aware of the new 'parallel' package that comes with R v2.14.0. /H On Mon, Nov 28, 2011 at 7:39 AM, Rau, Roland wrote: > Dear all, > > I am currently working on a package which

[Rd] Avoid package in build process when not supported on OS

2011-11-28 Thread Rau, Roland
Dear all, I am currently working on a package which involves some simulation where no current simulation run depends on a previous simulation run. That is why I decided to parallelize the computation using the doMC package (which exists only for unix-like OS). I can create a package without any

Re: [Rd] 32 vs 64 bit difference?

2011-11-28 Thread Terry Therneau
Thank you both for the nice explanation. I added "digits=4" to my print statements to shorten the display. Mixed effects Cox models can have difficult numerical issues, as it turns out; I've added this to my collection of things to watch for. Terry Therneau On Sat, 2011-11-26 at 11:37 +