Re: [Rd] combining large list of data.frames

2012-04-24 Thread Cole Beck
Thanks Patrick, this is a nice solution. Regarding a patch I'm inclined to believe you're correct, though it is certainly something to consider. Cheers, Cole On 04/20/2012 07:55 PM, Patrick Aboyoun wrote: Cole, Bioconductor's high throughput sequencing infrastructure package IRanges contains

Re: [Rd] url, readLines, source behind a proxy

2012-04-24 Thread Renaud Gaujoux
On 23/04/2012 17:39, Prof Brian Ripley wrote: On 18/04/2012 16:04, Joshua Ulrich wrote: Hi Renaud, On Wed, Apr 18, 2012 at 12:22 AM, Renaud Gaujoux ren...@mancala.cbio.uct.ac.za wrote: Hi Henrik, snip Could anybody behind a proxy check if the issue can be reproduced? My proxy is in fact

[Rd] nobs.glm

2012-04-24 Thread Wincent
Hi all, The nobs method of (MASS:::polr class) takes into account of weight, but nobs method of glm does not. I wonder what is the rationale of such design behind nobs.glm. Thanks in advance. Best Regards. library(MASS) house.plr - polr(Sat ~ Infl + Type + Cont, weights = Freq, data =

Re: [Rd] nobs.glm

2012-04-24 Thread Prof Brian Ripley
On 24/04/2012 14:36, Wincent wrote: Hi all, The nobs method of (MASS:::polr class) takes into account of weight, but nobs method of glm does not. I wonder what is the rationale of such design behind nobs.glm. Thanks in advance. Best Regards. library(MASS) house.plr- polr(Sat ~ Infl + Type +

[Rd] Specifying a function as not being and S3 Class function

2012-04-24 Thread Matt Pocernich
I am compiling a library with legacy code which has functions named with periods in the names - but are not S3 class functions.For example for example, summary.agriculture is not an extension of the summary function for and 'agriculture. class object - it is just poorly named. Is it

[Rd] Where to store and how to load support data ?

2012-04-24 Thread Charles Plessy
Dear R developers, I am writing a R module, which contains a function that needs support data (a table with two columns). I wonder how to make sure the data is available to the function, without making the function reload the data each time it is executed. Is it what the lazy mechanism takes

Re: [Rd] url, readLines, source behind a proxy

2012-04-24 Thread Henrik Bengtsson
Looking at the source code (src/library/tools/R/check.R and src/library/tools/R/QC.R), I found that... WORKAROUND: You can trick 'R CMD check' to quickly skip the check_package_CRAN_incoming test by providing it with invalid URLs to repositories by setting system environment

[Rd] Using other peoples packages from within C-based R-extension

2012-04-24 Thread oliver
Hello, what if I want to write a package mixed R/C-extension and want to use code that is provided by other peoples packages? How for example can I use one of the provided wavelet packages from within my C-based R-extension? Somehow I would need to load the other packages and have access to the

Re: [Rd] Using other peoples packages from within C-based R-extension

2012-04-24 Thread Duncan Murdoch
On 24/04/2012 12:31 PM, oliver wrote: Hello, what if I want to write a package mixed R/C-extension and want to use code that is provided by other peoples packages? How for example can I use one of the provided wavelet packages from within my C-based R-extension? Somehow I would need to load

[Rd] Creating model frame from R formula inside compiled code

2012-04-24 Thread Alireza Mahani
I am developing a custom regression package, which accepts a formula object as way of setting up the model matrix and response variable from a data frame. For large data sets, I expect that going through R memory might be too slow, so I'm thinking about reading the data directly into C (e.g. from

Re: [Rd] Specifying a function as not being and S3 Class function

2012-04-24 Thread S Ellison
Is it possible to keep from triggering the following warning when I check the package? summary: function(object, ...) summary.agriculture: function(x, analyte.names, results.col, analyte.col, by, det.col, [clip] Part of the solution is to add ... to the legacy function; that is

Re: [Rd] Using other peoples packages from within C-based R-extension

2012-04-24 Thread Dirk Eddelbuettel
On 24 April 2012 at 12:39, Duncan Murdoch wrote: | On 24/04/2012 12:31 PM, oliver wrote: | Hello, | | what if I want to write a package mixed R/C-extension | and want to use code that is provided by other peoples packages? | | How for example can I use one of the provided wavelet packages |

[Rd] Write unix format files on windows and vice versa

2012-04-24 Thread Andrew Redd
I go back and forth between windows and linux, and find myself running into problem with line endings. Is there a way to control the line ending conversion when writing files, such as write and cat? More explicitly I want to be able to write files with LF line endings rather than CRLF line

Re: [Rd] Write unix format files on windows and vice versa

2012-04-24 Thread Duncan Murdoch
On 24/04/2012 1:23 PM, Andrew Redd wrote: I go back and forth between windows and linux, and find myself running into problem with line endings. Is there a way to control the line ending conversion when writing files, such as write and cat? More explicitly I want to be able to write files with

Re: [Rd] Write unix format files on windows and vice versa

2012-04-24 Thread Ted Harding
On 24-Apr-2012 17:23:00 Andrew Redd wrote: I go back and forth between windows and linux, and find myself running into problem with line endings. Is there a way to control the line ending conversion when writing files, such as write and cat? More explicitly I want to be able to write files

Re: [Rd] Using other peoples packages from within C-based R-extension

2012-04-24 Thread Jeffrey Ryan
This link may be of help as well... https://stat.ethz.ch/pipermail/r-devel/2008-November/051262.html HTH Jeff On 4/24/12 12:35 PM, oliver oli...@first.in-berlin.de wrote: Hello, OK, thanks for the information... On Tue, Apr 24, 2012 at 12:02:33PM -0500, Dirk Eddelbuettel wrote: On 24