Re: [Rd] zero variance in part of a glm (PR#11355)

2008-05-04 Thread Peter Dalgaard
[EMAIL PROTECTED] wrote: In this real example (below), all four of the replicates in one treatment combination had zero failures, and this produced a very high standard error in the summary.lm. Why are you reporting trouble with your own understanding as a bug in R? I don't see anything out

Re: [Rd] error with R-patched (2008-05-02 r45591)

2008-05-04 Thread Peter Dalgaard
Prof Brian Ripley wrote: From the NEWS file for R-patchd: BUG FIXES oThe parser sometimes accepted invalid quoted strings in a UTF-8 locale. This is likely to be the issue, but we still don't have a reproducible example (see the posting guide). As Brian probably already kno

[Rd] Change in the Tcl/Tk loading in R 2.7.0 (under Unix/Mac OS X)?

2008-05-04 Thread Philippe Grosjean
Hello, Up to R 2.6.2, I used to start Tcl *without Tk* (I need only Tcl for some part of my work, like a socket server written in Tcl only, for instance) with this code under Mac OS X (particularly on this system, because I don't want to start X11 just to use Tcl code, which is required for T

Re: [Rd] Change in the Tcl/Tk loading in R 2.7.0 (under Unix/Mac OS X)?

2008-05-04 Thread Prof Brian Ripley
First, this does depend on what build of R you use. The 'HAVE_AQUA' define matters, and is only defined on some Mac OS X builds (e.g. not the default one, but the one used for the CRAN binary). Second, there are several possible versions of Tcl/Tk and X11 on MacOS X, and as I suspect one of y

Re: [Rd] Change in the Tcl/Tk loading in R 2.7.0 (under Unix/Mac OS X)?

2008-05-04 Thread Philippe Grosjean
Prof Brian Ripley wrote: First, this does depend on what build of R you use. The 'HAVE_AQUA' define matters, and is only defined on some Mac OS X builds (e.g. not the default one, but the one used for the CRAN binary). Second, there are several possible versions of Tcl/Tk and X11 on MacOS X,

Re: [Rd] R CMD check: small tests suggestion

2008-05-04 Thread hadley wickham
> > It would be nice if R CMD check ran any file in the tests directory > > that has "one of the extensions .R, .S, .q, .r, or .s" - i.e. it > > should match the files processed in the R directory. > > > > Whereas what it is documented in 'Writing R Extensions' is to use .R or > .Rin files. This

[Rd] A patch for extending pdf device to embed popup text and web links

2008-05-04 Thread Tadashi Kadowaki
Dear all, I am sending a patch for R-2.7.0 for extending pdf device to embed pop up text and web links. The patch is available at http://www.okada.jp.org/RWiki/?plugin=attach&pcmd=open&file=R-2.7.0.patch&refer=pdf%20device%20patch You can see what the patch can do through a sample output, which is

Re: [Rd] A patch for extending pdf device to embed popup text and web links

2008-05-04 Thread Tobias Verbeke
Dear Tadashi, Thank you very much for sharing your work. I am sending a patch for R-2.7.0 for extending pdf device to embed pop up text and web links. The patch is available at http://www.okada.jp.org/RWiki/?plugin=attach&pcmd=open&file=R-2.7.0.patch&refer=pdf%20device%20patch You can see what

[Rd] S4 / S3 / Sweave problem

2008-05-04 Thread Paul Gilbert
I'm not sure if this as a bug or something I am doing wrong. It occurs in both 2.7.0 and 2.6.2. require("methods") setClassUnion("OptionalPOSIXct", c("POSIXct", "NULL")) setClass("TSmetax", representation(serIDs="character", ExtractionDate="OptionalPOSIXct" )) setGeneric("TSmetax", d

Re: [Rd] S4 / S3 / Sweave problem

2008-05-04 Thread Prof Brian Ripley
I'm not sure what the issue being asked about here is. The peculiar printing I don't see and may well be a locale issue. (Is this UTF-8 and TeX has not been told so?) The other issue is that when printing an object with attributes, there is no consideration of S4 classes amongst the attribut

[Rd] ~/.Rprofile executed twice by R.app under Mac OS X (PR#11380)

2008-05-04 Thread phgrosjean
All is in the title. My config is: Version: platform = i386-apple-darwin8.10.1 arch = i386 os = darwin8.10.1 system = i386, darwin8.10.1 status = major = 2 minor = 7.0 year = 2008 month = 04 day = 22 svn rev = 45424 language = R version.string = R version 2.7.0 (2008-04-22

[Rd] help with segmentation fault

2008-05-04 Thread Kyeongmi Cheon
Hello all, I'm trying to have C called by R. I wrote C codes that worked perfectly fine with R-2.6.0 in windows system ( using R tools). I had to change to SuSE Linux (this system has 3.2 GHz Intel Xeon processors and 4 GB of RAM), the C codes were compiled okay but when it was called to R-2.6.

Re: [Rd] help with segmentation fault

2008-05-04 Thread Oleg Sklyar
Katie, 99% it's a bug in your C code caused by accessing memory (probably writing to) which was not allocated or freed already or out of boundary. The fact that it worked fine on Windows is likely to be a pure coincidence of different compiler/optimisation settings. However, the main problem

Re: [Rd] help with segmentation fault

2008-05-04 Thread Kasper Daniel Hansen
One thing that may help with debugging (and seeing if you get the same error on windows) is to run your code with R> gctorture(TRUE) R> your.function() That way everything is garbage collected all the time so to speak and this may trigger an error on your windows machine. I agree with O

Re: [Rd] A patch for extending pdf device to embed popup text and web links

2008-05-04 Thread Paul Murrell
Hi Tobias Verbeke wrote: > Dear Tadashi, > > Thank you very much for sharing your work. > >> I am sending a patch for R-2.7.0 for extending pdf device to embed pop >> up text and >> web links. The patch is available at >> http://www.okada.jp.org/RWiki/?plugin=attach&pcmd=open&file=R-2.7.0.patch

Re: [Rd] S4 / S3 / Sweave problem

2008-05-04 Thread Paul Gilbert
Prof Brian Ripley wrote: I'm not sure what the issue being asked about here is. The peculiar printing I don't see and may well be a locale issue. (Is this UTF-8 and TeX has not been told so?) It seems to happen in locales UTF-8, POSIX and C. I have not tried others. The other issue is

[Rd] troubles with R CMD check and examples under Ubuntu gutsy

2008-05-04 Thread Patrick Giraudoux
Dear listers, I was used to package pgirmess under Windows with everything OK, but, for the first time, I had a trial this afternoon on Ubuntu 7.10 gutsy (I have a double boot computer and work more and more under unix) and R 2.7.0. Everything went OK except this: sudo R CMD check pgirmess .

Re: [Rd] troubles with R CMD check and examples under Ubuntu gutsy

2008-05-04 Thread Prof Brian Ripley
It seems likely that the contents of 'pgirmess' under Linux are incomplete. There's a recent version of pgirmess on CRAN, and that works under Linux. I suggest you try that (start with the tarball, perhaps). On Mon, 5 May 2008, Patrick Giraudoux wrote: Dear listers, I was used to package p

Re: [Rd] error with R-patched (2008-05-02 r45591)

2008-05-04 Thread Mark Kimpel
Thanks guys. For the benefit of anyone following up on this in the future, I solved my problem in my offending file with: iconv -f LATIN1 -t UTF-8 methods.output.func.R >> methods.output.func.R Mark On Sun, May 4, 2008 at 4:13 AM, Peter Dalgaard <[EMAIL PROTECTED]> wrote: > Prof Brian Ripley wr

Re: [Rd] error with R-patched (2008-05-02 r45591)

2008-05-04 Thread Peter Dalgaard
Mark Kimpel wrote: Thanks guys. For the benefit of anyone following up on this in the future, I solved my problem in my offending file with: iconv -f LATIN1 -t UTF-8 methods.output.func.R >> methods.output.func.R Mark That line triggers a knee-jerk reflex with me (possibly unfairly since i

Re: [Rd] error with R-patched (2008-05-02 r45591)

2008-05-04 Thread Mark Kimpel
You're correct, bad form on my part. In reality, I did it in two steps as you suggested, just condensed for purposes of a brief communication. mark On Mon, May 5, 2008 at 1:52 AM, Peter Dalgaard <[EMAIL PROTECTED]> wrote: > Mark Kimpel wrote: > > > Thanks guys. For the benefit of anyone following

Re: [Rd] troubles with R CMD check and examples under Ubuntu gutsy

2008-05-04 Thread Patrick Giraudoux
Prof Brian Ripley a écrit : It seems likely that the contents of 'pgirmess' under Linux are incomplete. There's a recent version of pgirmess on CRAN, and that works under Linux. I suggest you try that (start with the tarball, perhaps). Sorry prof Ripley, but this is the same version as the one

Re: [Rd] troubles with R CMD check and examples under Ubuntu gutsy

2008-05-04 Thread Patrick Giraudoux
Berwin A Turlach a écrit : G'day Patrick On Mon, 05 May 2008 07:02:23 +0200 Patrick Giraudoux <[EMAIL PROTECTED]> wrote: I was used to package pgirmess under Windows with everything OK, but, for the first time, I had a trial this afternoon on Ubuntu 7.10 gutsy (I have a double boot compute

Re: [Rd] troubles with R CMD check and examples under Ubuntu gutsy

2008-05-04 Thread Prof Brian Ripley
On Mon, 5 May 2008, Patrick Giraudoux wrote: Prof Brian Ripley a écrit : It seems likely that the contents of 'pgirmess' under Linux are incomplete. There's a recent version of pgirmess on CRAN, and that works under Linux. I suggest you try that (start with the tarball, perhaps). Sorry prof R

Re: [Rd] troubles with R CMD check and examples under Ubuntu gutsy

2008-05-04 Thread Patrick Giraudoux
Berwin A Turlach a écrit : G'day Patrick, On Mon, 05 May 2008 08:15:29 +0200 Patrick Giraudoux <[EMAIL PROTECTED]> wrote: Berwin A Turlach a écrit : But I have compiled R on my boxes myself. How did you install R? >From source or by using the prepackaged Ubuntu deb files?