Re: [Rd] Reference Classes: shortcut like 'isS4' for Ref Classes?

2011-06-06 Thread John Chambers
As it says on the help page ?ReferenceClasses: All reference classes inherit from the class "envRefClass" So, is(x, "envRefClass") And, less well documented but less typing: is(x, "refClass") also works. On 6/6/11 9:48 AM, Janko Thyson wrote: Dear list, is there a shortcut-function to c

Re: [Rd] Overloading S4 methods

2011-06-06 Thread John Chambers
This is a bug, medium-subtle, but also raises an interesting software design point. The Bug: Nothing specific about "ANY" and "missing", but the issue is whether the method was inherited (the "ANY" case) or defined directly (the "missing" case). Generic functions keep a cached table of disp

Re: [Rd] Possible bug in termplot function (stats package) ?

2011-06-06 Thread Thomas Lumley
On Tue, Jun 7, 2011 at 7:30 AM, Joris Meys wrote: > On Mon, Jun 6, 2011 at 9:15 PM, peter dalgaard wrote: >> >> I'd say that the burden of proof is really on your side, but how hard can it >> be: >> >>> x <- 1:10 >>> y <- rnorm(10) >>> m <- lm(y~x) >>> m$call >> lm(formula = y ~ x) >>> m$call$da

Re: [Rd] Possible bug in termplot function (stats package) ?

2011-06-06 Thread Joris Meys
On Mon, Jun 6, 2011 at 9:15 PM, peter dalgaard wrote: > > I'd say that the burden of proof is really on your side, but how hard can it > be: > >> x <- 1:10 >> y <- rnorm(10) >> m <- lm(y~x) >> m$call > lm(formula = y ~ x) >> m$call$data > NULL > I see... indeed, thx for the answer and sorry for m

Re: [Rd] Possible bug in termplot function (stats package) ?

2011-06-06 Thread peter dalgaard
On Jun 6, 2011, at 20:38 , Joris Meys wrote: > On Mon, Jun 6, 2011 at 6:29 PM, peter dalgaard wrote: >> >> On Jun 6, 2011, at 17:15 , Joris Meys wrote: >> > **snip** >>> If nothing is found, an error is returned. If >>> anything is found, data won't be NULL, so line 20, when reached, will >>>

Re: [Rd] Possible bug in termplot function (stats package) ?

2011-06-06 Thread Joris Meys
On Mon, Jun 6, 2011 at 6:29 PM, peter dalgaard wrote: > > On Jun 6, 2011, at 17:15 , Joris Meys wrote: > **snip** >> If nothing is found, an error is returned. If >> anything is found, data won't be NULL, so line 20, when reached, will >> always return FALSE. Can it be that lines 18 and 19 should

Re: [Rd] Log file of building vignette in RCMD check

2011-06-06 Thread Prof Brian Ripley
On Mon, 6 Jun 2011, Uwe Ligges wrote: On 06.06.2011 15:30, Stefan McKinnon Høj-Edwards wrote: Hello, I am trying to run "RCMD check" on a package. It performs OK, with the exception of a single warning: * checking package vignettes in 'inst/doc' ... WARNING Package vignette(s) without corr

[Rd] Reference Classes: shortcut like 'isS4' for Ref Classes?

2011-06-06 Thread Janko Thyson
Dear list, is there a shortcut-function to check whether a class is a Reference Class or not? There's something like this for S4 classes ('isS4(object)'), but I couldn't find anything regarding Ref Classes. Currently, I'm doing it this way, which is a bit clumsy: A <- setRefClass("A", fields

Re: [Rd] Bug or feature: using "ANY" as a generic field class

2011-06-06 Thread Janko Thyson
Wow, that was fast! Thanks a lot! Regards, Janko On 06.06.2011 18:29, John Chambers wrote: > Should now behave as expected in r-devel and 2.13 patched, as of SVN > 56045, June 4. (noted in the NEWS file.) > > > On 6/6/11 6:27 AM, Janko Thyson wrote: >> Thanks a lot for your reply and I'm sorry

[Rd] Fwd: Error in svg() : cairo-based devices are not supported on this build

2011-06-06 Thread Karl Forner
Check what configure is saying when you build R and config.log. You may be > simply missing something like pango-dev - Cairo doesn't use pango while R > does - but it is usually optional (it works on my Mac without pango) so > there may be more to it - config.log will tell you. > I managed to comp

Re: [Rd] Possible bug in termplot function (stats package) ?

2011-06-06 Thread peter dalgaard
On Jun 6, 2011, at 17:15 , Joris Meys wrote: > Hi all, > > I noticed some very odd behaviour in the termplot function of the > stats package due to the following lines : > > 18.if (is.null(data)) > 19. data <- eval(model$call$data, envir) > > This one will look in the global environm

Re: [Rd] Bug or feature: using "ANY" as a generic field class (was: '[R] Is there a (virtual) class that all R objects inherit from?)

2011-06-06 Thread John Chambers
Should now behave as expected in r-devel and 2.13 patched, as of SVN 56045, June 4. (noted in the NEWS file.) On 6/6/11 6:27 AM, Janko Thyson wrote: Thanks a lot for your reply and I'm sorry if I didn't make it quite clear what I expected, but you got it right: I'd simply like to see the sam

Re: [Rd] Log file of building vignette in RCMD check

2011-06-06 Thread Uwe Ligges
On 06.06.2011 15:30, Stefan McKinnon Høj-Edwards wrote: Hello, I am trying to run "RCMD check" on a package. It performs OK, with the exception of a single warning: * checking package vignettes in 'inst/doc' ... WARNING Package vignette(s) without corresponding PDF: AnnotationFuncsUsergui

Re: [Rd] read.csv and FileEncoding in Windows version of R 2.13.0

2011-06-06 Thread Alexander Peterhansl
Hello Duncan, thank you very much for your reply. The file is attached. Again, the issue is that opening this UTF-8 encoded file under R 2.13.0 yields an error, but opening it under R 2.12.2 works without any issues. The command I used to open the file is: read.csv("test.csv",fileEncoding="UTF

[Rd] Log file of building vignette in RCMD check

2011-06-06 Thread Stefan McKinnon Høj-Edwards
Hello, I am trying to run "RCMD check" on a package. It performs OK, with the exception of a single warning: * checking package vignettes in 'inst/doc' ... WARNING Package vignette(s) without corresponding PDF: AnnotationFuncsUserguide.Rnw As I understand the problem, the vignette is not buil

[Rd] Possible bug in termplot function (stats package) ?

2011-06-06 Thread Joris Meys
Hi all, I noticed some very odd behaviour in the termplot function of the stats package due to the following lines : 18.if (is.null(data)) 19. data <- eval(model$call$data, envir) This one will look in the global environment, and renders the two lines after this 20. if (is.null(data

Re: [Rd] C-Side: Applying a function (given as param) to data (given as param)

2011-06-06 Thread Simon Urbanek
On Jun 5, 2011, at 12:22 PM, oliver wrote: > On Sat, Jun 04, 2011 at 07:51:08AM -0400, Duncan Murdoch wrote: >> On 11-06-03 4:19 PM, oliver wrote: >>> On Fri, Jun 03, 2011 at 11:14:39AM -0500, Douglas Bates wrote: On Fri, Jun 3, 2011 at 5:17 AM, oliver wrote: > Hello, > > I'm i

Re: [Rd] Bug or feature: using "ANY" as a generic field class (was: '[R] Is there a (virtual) class that all R objects inherit from?)

2011-06-06 Thread Janko Thyson
Thanks a lot for your reply and I'm sorry if I didn't make it quite clear what I expected, but you got it right: I'd simply like to see the same behavior for Reference Classes as for S4 classes when extending classes with "ANY" fields as featured in the example below. > setClass("A", represe

Re: [Rd] Interfacing a C++ class

2011-06-06 Thread Romain Francois
Le 04/06/11 16:31, soeren.vo...@uzh.ch a écrit : Hello Apologies for cross-posting, the discussion should (if) go to R-devel, but I also want to reach the rcpp-devel people. My C++ class FOO is a module available through Rcpp, and it works fine and is -- so far -- bug free. With trying to fu

Re: [Rd] Overloading S4 methods

2011-06-06 Thread Iago Mosqueira
On Wed, Jun 1, 2011 at 6:04 PM, Martin Morgan wrote: > On 06/01/2011 04:39 AM, Iago Mosqueira wrote: >> >> Dear all, >> >> I am experiencing some problems with S4 method overloading. I have >> defined a generic for graphics:plot, using >> >> setGeneric("plot", useAsDefault = plot) >> >> and with >

Re: [Rd] tag \href not recognised in rd doc

2011-06-06 Thread Duncan Murdoch
On 11-06-06 12:41 AM, Patrick Giraudoux wrote: Le 05/06/2011 22:30, Duncan Murdoch a écrit : I don't get any error when I insert that code into a .Rd file in R 2.13.0 patched. The NEWS file says this was fixed in 2.12.2 patched. What version are you using? Duncan Murdoch Currently R version