[Bioc-devel] New package : CausalR

2015-05-18 Thread Glyn Bradley
Hi All, We're pleased to announce the release of our package 'CausalR', which provides functions for causal reasoning (causal network analysis). The idea is to explain sets of observed endpoints by reasoning through causal interaction networks, so for example this type of analysis can be used

[Rd] \alias{} -- rather \concept{} for conceptual links to help pages

2015-05-18 Thread Martin Maechler
From R-help, subject Variable number of loops I've opened a new thread, moving from R-help to R-devel .. Jim Lemon drjimle...@gmail.com on Sun, 17 May 2015 09:19:06 +1000 writes: Hi all, Given the number of help requests that involve permutations/combinations, and the less than

Re: [Bioc-devel] Overloading subset operator for an S4 object with more than two dimensions

2015-05-18 Thread Christian Arnold
Thanks for your input, highly appreciated! I can see that the semantics of [ are violated, so I agree that overwriting the subset method is probably a better way to go. Essentially, the object stores several, individual-specific count matrices from RNA-Seq experiments in an potentially

Re: [Bioc-devel] Overloading subset operator for an S4 object with more than two dimensions

2015-05-18 Thread Martin Morgan
On 05/18/2015 06:06 AM, Christian Arnold wrote: Thanks for your input, highly appreciated! I can see that the semantics of [ are violated, so I agree that overwriting the subset method is probably a better way to go. Essentially, the object stores several, individual-specific count matrices

[Rd] How best to get around shadowing of executables by system()'s prepending of directories to Windows' PATH?

2015-05-18 Thread Josh O'Brien
My question: On Windows, R's system() command prepends several directories to those in the Windows Path variable. From ?system The search path for 'command' may be system-dependent: it will include the R 'bin' directory, the working directory and the Windows system directories

Re: [Rd] How best to get around shadowing of executables by system()'s prepending of directories to Windows' PATH?

2015-05-18 Thread Yihui Xie
+1 I have exactly the same problem. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Mon, May 18, 2015 at 12:29 PM, Josh O'Brien joshmobr...@gmail.com wrote: My question: On Windows, R's system() command prepends several directories to those in the Windows Path

[Rd] A bug in plot.dendrogram - can't plot lty with character color

2015-05-18 Thread Tal Galili
The problem: === Once a dendrogram has a branch with both a line type AND a color (which is a character color), the plot.dendrogram function will not plot and return an error. I say this is a bug because (I believe), we would like a dendrogram to be able to use character colors, while

Re: [Rd] \alias{} -- rather \concept{} for conceptual links to help pages

2015-05-18 Thread Hervé Pagès
Hi Martin, On 05/18/2015 05:14 AM, Martin Maechler wrote: From R-help, subject Variable number of loops I've opened a new thread, moving from R-help to R-devel .. Jim Lemon drjimle...@gmail.com on Sun, 17 May 2015 09:19:06 +1000 writes: Hi all, Given the number of help requests

Re: [Rd] How best to get around shadowing of executables by system()'s prepending of directories to Windows' PATH?

2015-05-18 Thread Henrik Bengtsson
You probably already know, but you can at least work around it as: Sys.which2 - function(cmd) { stopifnot(length(cmd) == 1) if (.Platform$OS.type == windows) { suppressWarnings({ pathname - shell(sprintf(where %s 2 NUL, cmd), intern=TRUE)[1] }) if (!is.na(pathname))