Re: [Rd] rcmdr gui not running (PR#13831)

2009-07-15 Thread Peter Dalgaard
francois.gr...@dbmail.com wrote: Full_Name: greff francois Version: 2.8.1 OS: ubuntu 9.04 Submission from: (NULL) (89.227.27.2) into r , the command library(Rcmdr) works well : the r commander GUI is opened , with menu in french ( well !) . But it isn't possible to have a response to any

[Rd] Protection stack overflow

2009-07-15 Thread hpages
Hi, gctorture(TRUE) setGeneric(foo, function(x, y) standardGeneric(foo)) [1] foo setMethod(foo, c(ANY, ANY), + function(x, y) cat(calling foo,ANY,ANY method\n) + ) Error: protect(): protection stack overflow Sorry this is something I already reported one week ago here

[Rd] A question on the serialization of a list vector

2009-07-15 Thread Saptarshi Guha
Hello, I've (by somewhat understanding serialize.c) understood how a vector of type numeric/char/raw/logical are serialized, assuming they have no attributes (e.g no attributes(x)=NULL). I assumed for lists, the content of the list is written first and then the names attribute. However nested

[Rd] Dynamic help pages

2009-07-15 Thread Duncan Murdoch
I've just committed code that allows R to be built with support for dynamic help pages using \Sexpr in Rd files. Define USE_NEW_HELP and the R function tools:::.convertRdfiles will be used instead of the Perl RdConv script, supporting \Sexpr and using the new R converters. Currently only

[Rd] Fwd: DLLs

2009-07-15 Thread robin cowan
Thanks for your help with this problem about dynamic linked libraries. I thought I had it solved, but apparently not. Below is a small piece of Pascal code that I compile into a library. When I load the library using dyn.load R becomes very unstable. The Mac GUI crashes in all kinds of

[Rd] rJava fails compilation on R-2.9.1 but not R-2.7.1 on Debian Lenny

2009-07-15 Thread Mark Kimpel
I have been futzing around for days tying to get rJava to install on my freshly build Debian Lenny installation. I have R-2.9.1 installed from source in my R_HOME directory and R-2.7.1 installed via apt-get install r-recommended. I was tried many different things, but by accident started up

Re: [Rd] rJava fails compilation on R-2.9.1 but not R-2.7.1 on Debian Lenny

2009-07-15 Thread Mark Kimpel
Sorry, My sentence that starts The file was truncated and should say The file jni.h is present and on my PATH, see output below mkimpel-debian-xps /usr/lib/jvm/java-6-sun/include: ls classfile_constants.h jawt.h jdwpTransport.h jni.h jvmti.h linux mkimpel-debian-xps

Re: [Rd] rJava fails compilation on R-2.9.1 but not R-2.7.1 on Debian Lenny

2009-07-15 Thread Joshua Ulrich
Hi Mark, The first thing that jumps out to me is that 2.7.1 compiles JRI, while 2.9.1 does not (for some reason, autodetect decides not to compile). HTH, Josh -- http://www.fosstrading.com On Wed, Jul 15, 2009 at 1:46 PM, Mark Kimpelmwkim...@gmail.com wrote: I have been futzing around for

Re: [Rd] Dynamic help pages

2009-07-15 Thread Duncan Murdoch
On 7/15/2009 9:47 AM, Duncan Murdoch wrote: I've just committed code that allows R to be built with support for dynamic help pages using \Sexpr in Rd files. Define USE_NEW_HELP and the R function tools:::.convertRdfiles will be used instead of the Perl RdConv script, supporting \Sexpr and

Re: [Rd] rJava fails compilation on R-2.9.1 but not R-2.7.1 on Debian Lenny

2009-07-15 Thread Dirk Eddelbuettel
Mark, Again, sudo apt-get install r-cran-rjava does what you want. We do provide these binaries for a reason. Namely, that it can be hard to tame the system requirements. So why don't you just install the binaries we provide? Dirk -- Three out of two people have difficulties with

Re: [Rd] bug in texi2dvi? (PR#13833)

2009-07-15 Thread Duncan Murdoch
On 15/07/2009 6:00 AM, pa...@idsia.ch wrote: I am trying to call texi2dvi on a very simple tex-file (see below) and it fails with a memory access error. I originally tried to call it on another, meaningful tex file with the same error occuring. I am attaching a screenshot. Thank you very

[Rd] Resizing a named vector crashes R with gctorture(TRUE)

2009-07-15 Thread Hervé Pagès
Hi, x - c(a=10, b=20) length(x) - 1 x a 10 But with gctorture turned on, I get: gctorture(TRUE) x - c(a=10, b=20) length(x) - 1 x a a ??? x - c(a=10, b=20) length(x) - 3 *** caught segfault *** address (nil), cause 'unknown' Possible

Re: [Rd] Resizing a named vector crashes R with gctorture(TRUE) (PR#13837)

2009-07-15 Thread murdoch
On 15/07/2009 8:08 PM, Hervé Pagès wrote: Hi, x - c(a=10, b=20) length(x) - 1 x a 10 But with gctorture turned on, I get: gctorture(TRUE) x - c(a=10, b=20) length(x) - 1 x a a ??? x - c(a=10, b=20) length(x) - 3

Re: [Rd] Resizing a named vector crashes R with gctorture(TRUE) (PR#13837)

2009-07-15 Thread Hervé Pagès
murd...@stats.uwo.ca wrote: On 15/07/2009 8:30 PM, murd...@stats.uwo.ca wrote: On 15/07/2009 8:08 PM, Hervé Pagès wrote: Hi, x - c(a=10, b=20) length(x) - 1 x a 10 But with gctorture turned on, I get: gctorture(TRUE) x - c(a=10, b=20) length(x) - 1 x

Re: [Rd] Resizing a named vector crashes R with gctorture(TRUE) (PR#13837)

2009-07-15 Thread murdoch
On 15/07/2009 8:30 PM, murd...@stats.uwo.ca wrote: On 15/07/2009 8:08 PM, Hervé Pagès wrote: Hi, x - c(a=10, b=20) length(x) - 1 x a 10 But with gctorture turned on, I get: gctorture(TRUE) x - c(a=10, b=20) length(x) - 1 x a a ???

Re: [Rd] rJava fails compilation on R-2.9.1 but not R-2.7.1 on Debian Lenny

2009-07-15 Thread Mark Kimpel
Well, guess what, rJava also compiles on R-devel (soon to be R-2.10.0). I'll stick with that for my purposes. Thanks for your suggestion. Mark Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of

[Rd] Handling masked methods

2009-07-15 Thread Gad Abraham
Hi, Say I have two packages, test1 and test2, that both define the generic method train (identical definition), and each has a specific train method for a different S4 object (foo and bar, resp.) I want to be able to call train(foo, x, y) and train(bar, x, y), which doesn't work since test2

Re: [Rd] Resizing a named vector crashes R with gctorture(TRUE) (PR#13837)

2009-07-15 Thread Hervé Pagès
I have to confess that I'm a little bit puzzled by how the PROTECT/UNPROTECT mechanism is used in the C code of R. Duncan, you say the problem you just fixed was an easy one. I looked at the C code too and was able to recognize a pattern that is indeed easy to identify as problematic: an

Re: [Rd] Handling masked methods

2009-07-15 Thread Duncan Murdoch
Gad Abraham wrote: Hi, Say I have two packages, test1 and test2, that both define the generic method train (identical definition), and each has a specific train method for a different S4 object (foo and bar, resp.) I want to be able to call train(foo, x, y) and train(bar, x, y), which

[Rd] question about try and errors

2009-07-15 Thread Kasper Daniel Hansen
I am using try. I have found that sometimes errors are not caught by try. For example, I got the following error message from code that was wrapped in try. After the error, my R CMD BATCH aborted. Error in assign(.target, met...@target, envir = envir) : no function to return from, jumping