[Rd] windows() device: plot does not refresh with new drawing after opening and closing a new device

2012-03-14 Thread Michael Sumner
Hello, I see this problem in 2.14.1, a recent dev, and 2.15.0 alpha, but not in an older build. Start the R windows console and run this code: plot(1:10);windows();dev.off();points(10:1) The second set of points does not show up until the window is minimized and restored. If the device is repl

Re: [Rd] Dealing with printf() &c. in third-party library code

2012-03-14 Thread Martin Morgan
On 03/14/2012 05:15 AM, Jon Clayden wrote: Dear all, I recognise the reason for strongly discouraging use of printf() and similar C functions in R packages, but I wonder what people do in practice about third-party code which may be littered with such calls. I maintain a package (RNiftyReg) whic

[Rd] methods::trace fails when signature specified

2012-03-14 Thread Martin Morgan
With > R.version.string [1] "R version 2.15.0 alpha (2012-03-14 r58748)" trying to trace a method using the 'signature' argument fails rather than enabling the trace: > trace(initialize, signature="ANY") Error in matchSignature(signature, fdef, where) : trying to match a method signature of

[Rd] using predict() with poly(x, raw=TRUE)

2012-03-14 Thread John Fox
Dear r-devel list members, I've recently encountered the following problem using predict() with a model that has raw-polynomial terms. (Actually, I encountered the problem using model.frame(), but the source of the error is the same.) The problem is technical and concerns the design of poly(), whi

[Rd] issue with Rd2pdf and \Sexpr in Rd files

2012-03-14 Thread Dan Tenenbaum
Hi, The following command: R CMD Rd2pdf --no-preview --output=./tmp.pdf --title=test genefu-package.Rd run against this file: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/genefu/man/genefu-package.Rd (username: readonly; password: readonly) produces a very verbose error (see below)

[Rd] Dealing with printf() &c. in third-party library code

2012-03-14 Thread Jon Clayden
Dear all, I recognise the reason for strongly discouraging use of printf() and similar C functions in R packages, but I wonder what people do in practice about third-party code which may be littered with such calls. I maintain a package (RNiftyReg) which provides an R interface to a third-party li

[Rd] merge bug fix in R 2.15.0

2012-03-14 Thread Matthew Dowle
Is it intended that the first suffix can no longer be blank? Seems to be caused by a bug fix to merge in R 2.15.0. $Rdevel --vanilla DF1 = data.frame(a=1:3,b=4:6) DF2 = data.frame(a=1:3,b=7:9) merge(DF1,DF2,by="a",suffixes=c("",".1")) Error in merge.data.frame(DF1, DF2, by = "a", suffixes = c("",

Re: [Rd] [ESS] completion in [] (R internal completion fails)

2012-03-14 Thread Vitalie Spinu
Hello, I am forwarding this from ESS mailing list, as it's a failure of internal R completion system: This fails: utils:::.assignLinebuffer('iris[iris$Spec') utils:::.assignEnd(15) utils:::.guessTokenFromLine() utils:::.completeToken() utils:::.retrieveCompletions() ## -> [1] "iris[iris$Spec"

Re: [Rd] Invalid date-times and as.POSIXct problems (remotely related to DST issues)

2012-03-14 Thread Karl Ove Hufthammer
Karl Ove Hufthammer wrote: > I think this should be handled as a bug, but I’m not sure which > platforms and versions it applies to, so I’m writing to this list. No response, so I‘ve filed a bug at https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14845 (with some additional info). -- Karl Ov