Re: [Bioc-devel] Data Package Size Issues (.idat and .rda)

2013-11-07 Thread Kasper Daniel Hansen
To give some background: it is true that the RGsetEx object (in data/RGsetEx.rda) is a 1-1 correspondence with the raw data files in inst/extdata, so one could consider it redundant. However, having the IDAT files are convenient for testing parsing, and also for other tools who want to have 450k

Re: [Bioc-devel] Data Package Size Issues (.idat and .rda)

2013-11-07 Thread Nicolas De Jay
Thanks for the prompt answer. The data set I am packaging closely resembles that of minfiData except that there are 52 samples; the IDAT files together are some 800MB whereas the Rda file is closer to 150MB. It is worth noting that my experiment data package will be submitted to Bioconductor

Re: [Rd] cat with backspace and newline characters

2013-11-07 Thread Jari Oksanen
On 07/11/2013, at 09:35 AM, Renaud Gaujoux wrote: I agree that the handling of \b is not that strange, once one agrees on what \b actually means, i.e. go back one character and not delete previous character. The fact that R GUI on Mac and Windows interprets/renders it differently shows that

Re: [Rd] cat with backspace and newline characters

2013-11-07 Thread Barry Rowlingson
On Thu, Nov 7, 2013 at 8:28 AM, Jari Oksanen jari.oksa...@oulu.fi wrote: On 07/11/2013, at 09:35 AM, Renaud Gaujoux wrote: I agree that the handling of \b is not that strange, once one agrees on what \b actually means, i.e. go back one character and not delete previous character. It means,

Re: [Rd] cat with backspace and newline characters

2013-11-07 Thread peter dalgaard
On 07 Nov 2013, at 10:13 , Barry Rowlingson b.rowling...@lancaster.ac.uk wrote: On Thu, Nov 7, 2013 at 8:28 AM, Jari Oksanen jari.oksa...@oulu.fi wrote: On 07/11/2013, at 09:35 AM, Renaud Gaujoux wrote: I agree that the handling of \b is not that strange, once one agrees on what \b

Re: [Rd] Dynamic list creation (SEXP in C) returns error unimplemented type (29) in 'duplicate'

2013-11-07 Thread George Vega Yon
Hi! I didn't wanted to do this but I think that this is the easiest way for you to understand my problem (thanks again for all the comments that you have made). Here is a copy of the function that I'm working on. This may be tedious to analyze, so I understand if you don't feel keen to give it a

Re: [Rd] Dynamic list creation (SEXP in C) returns error unimplemented type (29) in 'duplicate'

2013-11-07 Thread Romain Francois
Hello, Any particular reason you're not using Rcpp? You would have access to nice abstraction instead of these MACROS all over the place. The cost of these abstractions is close to 0. Looping around and SET_LENGTH is going to be quite expensive. I would urge you to accumulate data in data

Re: [Rd] Dynamic list creation (SEXP in C) returns error unimplemented type (29) in 'duplicate'

2013-11-07 Thread George Vega Yon
Romain, Thanks for your quick response. I've already received that suggestion, but, besides of haven't ever used C++, I wanted to understand first what am I doing wrong. Still, would you give me a small example, in R C++, of: - Creating a generic vector L1 of size N - Creating a data.frame D

Re: [Rd] Dynamic list creation (SEXP in C) returns error unimplemented type (29) in 'duplicate'

2013-11-07 Thread Romain Francois
Le 07/11/2013 14:30, George Vega Yon a écrit : Romain, Thanks for your quick response. I've already received that suggestion, but, besides of haven't ever used C++, I wanted to understand first what am I doing wrong. For that type of code, it is actually quite simpler to learn c++ than it is

Re: [Rd] Dynamic list creation (SEXP in C) returns error unimplemented type (29) in 'duplicate'

2013-11-07 Thread Romain Francois
Le 07/11/2013 14:43, Romain Francois a écrit : Le 07/11/2013 14:30, George Vega Yon a écrit : Romain, Thanks for your quick response. I've already received that suggestion, but, besides of haven't ever used C++, I wanted to understand first what am I doing wrong. For that type of code, it is

Re: [Rd] cat with backspace and newline characters

2013-11-07 Thread Prof J C Nash (U30A)
Over the years, this has been useful to me (not just in R) for many nonlinear optimization tasks. The alternatives often clutter the screen. On 13-11-06 06:00 AM, r-devel-requ...@r-project.org wrote: People do sometimes use this pattern for displaying progress (e.g. iteration counts).

Re: [Rd] Dynamic list creation (SEXP in C) returns error unimplemented type (29) in 'duplicate'

2013-11-07 Thread George Vega Yon
Thank you very much! Just what I needed. Too bad I never got to understand what was wrong with my original code... Thanks again! George Vega Yon +56 9 7 647 2552 http://ggvega.cl 2013/11/7 Romain Francois rom...@r-enthusiasts.com: Le 07/11/2013 14:43, Romain Francois a écrit : Le

[Rd] R interface to C API Rf_logspace_{add,sub}?

2013-11-07 Thread William Dunlap
Is there an R-language interface to the R API C-language functions Rf_logspace_add() and Rf_logspace_sub()? I don't see one but I may not looking under the right name. Various packages have functions which do that same sort of thing (log(exp(x)+exp(y)) and log(exp(x)-exp(y)) without