Re: [Rd] C macros and Makevars/package building

2005-09-09 Thread Peter Dalgaard
Kasper Daniel Hansen [EMAIL PROTECTED] writes: Hi We are currently embedding a rather large C++ library in R (BioC), and we want some comments on the portability of how we have approach this. First of, we are not really able to do much about the portability of the basic library,

[Rd] nls fails to return correlation matrix (PR#8127)

2005-09-09 Thread Carsten . Urbach
Full_Name: Carsten Urbach Version: 2.1.1 (2005-06-20) OS: Linux Submission from: (NULL) (141.34.5.241) I observed one case where nls failed to return the correlation matrix, while the parameter estimates were computed correctly. In the follwing I include all the commands leading to this

Re: [Rd] nls fails to return correlation matrix (PR#8127)

2005-09-09 Thread Peter Dalgaard
[EMAIL PROTECTED] writes: Full_Name: Carsten Urbach Version: 2.1.1 (2005-06-20) OS: Linux Submission from: (NULL) (141.34.5.241) I observed one case where nls failed to return the correlation matrix, while the parameter estimates were computed correctly. In the follwing I include all

Re: [Rd] [R] Debugging R/Fortran in Windows

2005-09-09 Thread Duncan Murdoch
[Moved from R-help] James Wettenhall wrote: Hi, I'm trying to debug an R interface to a Fortran subroutine from Windows. (Yes, I know I should try Unix/Linux as well, but a quick attempt suggested that the (MinGW g77) Fortran compiler I have installed on my Windows laptop works better on

Re: [Rd] C macros and Makevars/package building

2005-09-09 Thread Kurt Hornik
Kasper Daniel Hansen writes: Hi We are currently embedding a rather large C++ library in R (BioC), and we want some comments on the portability of how we have approach this. First of, we are not really able to do much about the portability of the basic library, which of course is

[Rd] two almost identical packages: best practice

2005-09-09 Thread Robin Hankin
Hi I have written a whole bunch of methods for objects of class octonion. [ an octonion is a single column of an eight-row matrix. Octonions have their own multiplication rules and are a generalization of quaternions, which are columns of a four-row matrix. ] So far I've done about a dozen

Re: [Rd] two almost identical packages: best practice

2005-09-09 Thread Gabor Grothendieck
On 9/9/05, Robin Hankin [EMAIL PROTECTED] wrote: Hi I have written a whole bunch of methods for objects of class octonion. [ an octonion is a single column of an eight-row matrix. Octonions have their own multiplication rules and are a generalization of quaternions, which are columns of

Re: [Rd] Wishlist: write.delim()

2005-09-09 Thread Douglas Grove
On Fri, 9 Sep 2005, Martin Maechler wrote: Douglas == Douglas Grove [EMAIL PROTECTED] on Thu, 8 Sep 2005 15:33:02 -0700 (PDT) writes: Douglas Hi, Douglas It would be great if someone would add write.delim() as an Douglas adjunct to write.table(), just as with write.csv().

[Rd] A question on R memory management in .Fortran() calls under Windows

2005-09-09 Thread Simone Giannerini
Dear R community, I have a question on how R manages memory allocation in .Fortran() calls under Windows. In brief, apparently, it is not possible to allocate large matrices inside a Fortran subroutine unless you pass them as arguments. If you do not act in this way RGUI crashes with a stack

[Rd] Issue tracking in packages [was: Re: [R] change in read.spss, package foreign?]

2005-09-09 Thread Gabor Grothendieck
On 9/9/05, Thomas Lumley [EMAIL PROTECTED] wrote: Many packages have a NEWS or ChangeLog file describing changes. You would typically have to look at the source package to find them, since by Unix tradition they are usually in the top-level directory and so are not included in the binary

Re: [Rd] Issue tracking in packages [was: Re: [R] change in read.spss, package foreign?]

2005-09-09 Thread Thomas Lumley
On Fri, 9 Sep 2005, Gabor Grothendieck wrote: I personally put NEWS, WISHLIST and THANKS files in the 'inst' directory of all my source packages. This has the effect of copying them to the top level of the built version so that they are accessible from R via: I'm not sure that WISHLIST

Re: [Rd] Issue tracking in packages [was: Re: [R] change in read.spss, package foreign?]

2005-09-09 Thread Gabor Grothendieck
On 9/9/05, Thomas Lumley [EMAIL PROTECTED] wrote: On Fri, 9 Sep 2005, Gabor Grothendieck wrote: I personally put NEWS, WISHLIST and THANKS files in the 'inst' directory of all my source packages. This has the effect of copying them to the top level of the built version so that they

Re: [Rd] A question on R memory management in .Fortran() calls under Windows

2005-09-09 Thread Simon Urbanek
Simone, On Sep 9, 2005, at 1:04 PM, Simone Giannerini wrote: Dear R community, I have a question on how R manages memory allocation in .Fortran() calls under Windows. In brief, apparently, it is not possible to allocate large matrices inside a Fortran subroutine I suspect that this is

Re: [Rd] Issue tracking in packages [was: Re: [R] change in read.spss, package foreign?]

2005-09-09 Thread Gabor Grothendieck
On 9/9/05, Thomas Lumley [EMAIL PROTECTED] wrote: On Fri, 9 Sep 2005, Gabor Grothendieck wrote: How about if there were just a standard location and name such as inst/NEWS, inst/WISHLIST, inst/THANKS (which has the advantage that they are automatically made available in the built package

Re: [Rd] two almost identical packages: best practice

2005-09-09 Thread Seth Falcon
On 9 Sep 2005, [EMAIL PROTECTED] wrote: I have written a whole bunch of methods for objects of class octonion. So far I've done about a dozen generic functions such as seq.octonion(), rep.octonion(), [-.octonion(), and so on and so on. Very nearly all of these functions are applicable to

Re: [Rd] Install packages to non-default lib on Windows

2005-09-09 Thread Seth Falcon
On 8 Sep 2005, [EMAIL PROTECTED] wrote: installing inst files installing data files installing man source files installing indices cannot create d:/biocbld/R-devel/doc/html/search/index.txt: permission denied I was also annoyed about this point a couple of times. But what are possible

[Rd] MikTeX will be assumed in R 2.2.0 in Windows

2005-09-09 Thread Duncan Murdoch
I've just committed some changes to allow R to be built and to use MikTeX without needing the Rd.sty files to be installed to localtexmf. Unfortunately, the changes are not compatible with other TeX packages, so if you're not using MikTeX you'll need to edit a couple of the config files (or

Re: [Rd] MikTeX will be assumed in R 2.2.0 in Windows

2005-09-09 Thread Duncan Murdoch
Gabor Grothendieck wrote: Great. What specifically is the change? There are a number of changes to make use of the --include-directory command line option that Miktex supports. It needed to be done in several places because tex is called from makefiles, Perl and shell scripts. Duncan

[Rd] \dontshow

2005-09-09 Thread Gabor Grothendieck
In R 2.2.0 I find that even if I use \dontshow in the examples section of an .Rd file that the code still shows. Has anyone else seen this? Are there any packages that use this facility that I could try in order to check this? I am using R.version.string # XP R version 2.2.0, 2005-09-03

[Rd] Copying libraries from one version of R to another (was Re: MikTeX will be assumed in R 2.2.0 in Windows)

2005-09-09 Thread Gabor Grothendieck
On 9/9/05, Duncan Murdoch [EMAIL PROTECTED] wrote: I've just committed some changes to allow R to be built and to use MikTeX without needing the Rd.sty files to be installed to localtexmf. Unfortunately, the changes are not compatible with other TeX packages, so if you're not using MikTeX

Re: [Rd] \dontshow

2005-09-09 Thread Gabor Grothendieck
On 9/9/05, Gabor Grothendieck [EMAIL PROTECTED] wrote: In R 2.2.0 I find that even if I use \dontshow in the examples section of an .Rd file that the code still shows. Has anyone else seen this? Are there any packages that use this facility that I could try in order to check this? I am