Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-04-08 Thread peter dalgaard
(Resending with fewer recipients...) On Apr 8, 2011, at 07:09 , Hin-Tak Leung wrote: --- On Fri, 8/4/11, peter dalgaard pda...@gmail.com wrote: On Apr 7, 2011, at 23:57 , Hin-Tak Leung wrote: Oh, I am tracking both R and Matrix via git-svn and retrieves all revisions to all branches

Re: [Rd] super basic questions about S4 classes

2011-04-08 Thread Andreas Borg
Hi Andre, 1. Keep in mind that a S4 method belongs to a specific generic function, not to a specific object or class. There is none such thing as a class member function in the S4 system. As an example for illustration, consider the following class definitions in Java: class myClassA { int

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-04-08 Thread Prof Brian Ripley
On Fri, 8 Apr 2011, peter dalgaard wrote: (Resending with fewer recipients...) On Apr 8, 2011, at 07:09 , Hin-Tak Leung wrote: --- On Fri, 8/4/11, peter dalgaard pda...@gmail.com wrote: On Apr 7, 2011, at 23:57 , Hin-Tak Leung wrote: Oh, I am tracking both R and Matrix via git-svn and

[Rd] Invalid connection after closing?

2011-04-08 Thread Joris Meys
Dear all, I do not completely understand following behaviour : con - file(test.txt) isOpen(con) [1] FALSE open(con) isOpen(con) [1] TRUE close(con) isOpen(con) Error in isOpen(con) : invalid connection str(con) Classes 'file', 'connection' atomic [1:1] 3 ..- attr(*,

[Rd] duplicates() function

2011-04-08 Thread Duncan Murdoch
I need a function which is similar to duplicated(), but instead of returning TRUE/FALSE, returns indices of which element was duplicated. That is, x - c(9,7,9,3,7) duplicated(x) [1] FALSE FALSE TRUE FALSE TRUE duplicates(x) [1] NA NA 1 NA 2 (so that I know that element 3 is a

Re: [Rd] duplicates() function

2011-04-08 Thread Joshua Ulrich
How about: y - rep(NA,length(x)) y[duplicated(x)] - match(x[duplicated(x)] ,x) -- Joshua Ulrich  |  FOSS Trading: www.fosstrading.com On Fri, Apr 8, 2011 at 9:59 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: I need a function which is similar to duplicated(), but instead of returning

Re: [Rd] Invalid connection after closing?

2011-04-08 Thread Duncan Murdoch
On 08/04/2011 10:56 AM, Joris Meys wrote: Dear all, I do not completely understand following behaviour : con- file(test.txt) isOpen(con) [1] FALSE open(con) isOpen(con) [1] TRUE close(con) isOpen(con) Error in isOpen(con) : invalid connection str(con) Classes 'file', 'connection'

Re: [Rd] duplicates() function

2011-04-08 Thread Hadley Wickham
On Fri, Apr 8, 2011 at 9:59 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: I need a function which is similar to duplicated(), but instead of returning TRUE/FALSE, returns indices of which element was duplicated.  That is, x - c(9,7,9,3,7) duplicated(x) [1] FALSE FALSE  TRUE FALSE TRUE

Re: [Rd] Invalid connection after closing?

2011-04-08 Thread Joris Meys
Thx for the information. I read it, but I wasn't sure what was going on inside. Is there a way to close a connection without destroying it? Guess not, but you never know... Cheers Joris On Fri, Apr 8, 2011 at 5:09 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 08/04/2011 10:56 AM, Joris

Re: [Rd] duplicates() function

2011-04-08 Thread Kasper Daniel Hansen
On Fri, Apr 8, 2011 at 11:08 AM, Joshua Ulrich josh.m.ulr...@gmail.com wrote: How about: y - rep(NA,length(x)) y[duplicated(x)] - match(x[duplicated(x)] ,x) I use Joshua's trick all the time. But it might still be nice with a C implementation. While we are discussing duplication, I would

Re: [Rd] How to debug reference classes?

2011-04-08 Thread A Zege
Thank you very much, gentlemen. It seems reference classes will make my life much easier. I won't pretend that i fully understand the wizardry with environments that you do, but it works :). Namely the steps to mtrace a class method by doing what John and Mark outlined xx$edit-xx$edit

Re: [Rd] duplicates() function

2011-04-08 Thread Joshua Ulrich
On Fri, Apr 8, 2011 at 10:15 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 08/04/2011 11:08 AM, Joshua Ulrich wrote: How about: y- rep(NA,length(x)) y[duplicated(x)]- match(x[duplicated(x)] ,x) That's a nice solution for vectors.  Unfortunately for me, I have a matrix (which

Re: [Rd] duplicates() function

2011-04-08 Thread William Dunlap
-Original Message- From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] On Behalf Of Duncan Murdoch Sent: Friday, April 08, 2011 8:16 AM To: Joshua Ulrich Cc: R-devel@r-project.org Subject: Re: [Rd] duplicates() function On 08/04/2011 11:08 AM, Joshua

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-04-08 Thread Hin-Tak Leung
--- On Fri, 8/4/11, peter dalgaard pda...@gmail.com wrote: On Apr 7, 2011, at 23:57 , Hin-Tak Leung wrote: Oh, I am tracking both R and Matrix via git-svn and retrieves all revisions to all branches daily (or at least, regularly). I.e. R svn head.  2.13.0 only forked off recently and

Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

2011-04-08 Thread peter dalgaard
On Apr 7, 2011, at 23:57 , Hin-Tak Leung wrote: Oh, I am tracking both R and Matrix via git-svn and retrieves all revisions to all branches daily (or at least, regularly). I.e. R svn head. 2.13.0 only forked off recently and most of the trunk-2.13.0rc differences are so far mostly

Re: [Rd] question about assignment warnings for replacement methods

2011-04-08 Thread Hervé Pagès
Hi Duncan, Marc, On 11-04-05 11:15 AM, Duncan Murdoch wrote: On 05/04/2011 1:51 PM, Marc Carlson wrote: Hi, I have seen several packages that with the most recent version of R are giving a warning like this: Assignments in \usage in documentation object 'marginalData-methods':

Re: [Rd] question about assignment warnings for replacement methods

2011-04-08 Thread Simon Urbanek
On Apr 8, 2011, at 2:55 PM, Hervé Pagès wrote: Hi Duncan, Marc, On 11-04-05 11:15 AM, Duncan Murdoch wrote: On 05/04/2011 1:51 PM, Marc Carlson wrote: Hi, I have seen several packages that with the most recent version of R are giving a warning like this: Assignments in \usage in

[Rd] Consistency of messages from R CMD {check,build,install}

2011-04-08 Thread Michael Friendly
A minor gripe/request: Could all R CMD package tools not at the very least be consistent in indicating when they are done, as in * DONE (packagename) or at least * DONE R CMD build leaves one hanging, not knowing whether it has completed or it is time to get another coffee. * checking for

[Rd] Compression of largish expression array files in the DAAGbio/inst/doc directory?

2011-04-08 Thread John Maindonald
The inst/doc directory of the DAAG package has 6 files coral551.spot, ... that are around 0.85 MB each. It would be useful to be able to zip then, but that as matters stand interferes with the use of the Sweave file that uses them to demonstrate input of expression array data that is in the spot