[Rd] GNU make heads-up

2010-11-16 Thread Dominick Samperi
As most GNU Makefiles (or Makevars) tend to use '=' insead of ':=', I thought it might be helpful to point out that there is an important difference in the meaning. When a variable is defined like this: PKG_CPPFLAGS=whatever the RHS (whatever) is evaluated every time PKG_CPPFLAGS is used, and this

Re: [Rd] unloading compiled code.

2010-11-16 Thread Charles C. Berry
On Tue, 16 Nov 2010, Andrew Redd wrote: so should I use reg.finalizer or overwrite .Last()? .Last Error: object '.Last' not found You create your own .Last - there is nothing to overwrite. Chuck If I use reg.finalizer, what should be the environment that I specify? The straight for

Re: [Rd] DBLEPR?

2010-11-16 Thread Prof Brian Ripley
On Tue, 16 Nov 2010, Douglas Bates wrote: On Tue, Nov 16, 2010 at 2:35 PM, Prof. John C Nash wrote: I normally see digest once per day, but got msg from Doug Bates so responding with context. UCMINF is a package on CRAN that implements a variable metric minimizer. A pedant might point ou

Re: [Rd] DBLEPR?

2010-11-16 Thread Prof. John C Nash
My reaction is leaning heavily towards "Virtuoso!" as opposed to "Show Off!". Thanks very much. JN On 11/16/2010 05:39 PM, Douglas Bates wrote: > Try this. > > On Tue, Nov 16, 2010 at 4:06 PM, Prof. John C Nash wrote: >> We've tried to contact Stig since July. Possibly he changed emails. >> >

Re: [Rd] DBLEPR?

2010-11-16 Thread Prof. John C Nash
We've tried to contact Stig since July. Possibly he changed emails. My thought was to use Rprintf as suggested and was looking into doing that to see if our optimx problems would go away. Will keep it as open issue while we give a bit more time for response, and welcome input from others. JN

Re: [Rd] DBLEPR?

2010-11-16 Thread Douglas Bates
On Tue, Nov 16, 2010 at 2:35 PM, Prof. John C Nash wrote: > I normally see digest once per day, but got msg from Doug Bates so responding > with context. > UCMINF is a package on CRAN that implements a variable metric minimizer. A pedant might point out that the package is called "ucminf". > I

[Rd] Plotting an agnes tree with images instead of labels?

2010-11-16 Thread darfunkel
Hi, I'd like to plot a tree with images of molecular structures instead of labels (words). I think this is possible because someone who worked in my office before I arrived did this. However I'm not sure if this person made the image manually or plotted it only with R. Thanks in advance for your

Re: [Rd] unloading compiled code.

2010-11-16 Thread Andrew Redd
so should I use reg.finalizer or overwrite .Last()? If I use reg.finalizer, what should be the environment that I specify? The straight forward solution would be to have a hook .onExit that a package could specify to make sure that the code was unloaded before the program terminates, that way I

Re: [Rd] SEXPs and slots

2010-11-16 Thread Simon Urbanek
On Nov 16, 2010, at 8:52 PM, Patrick Leyshock wrote: > Revisiting the output below: > > 1. Am I correct in thinking that the @XXX items are addresses? yes > 2. What are the meanings of the gXcX items? you should not worry about those - they are internal flags related to the garbage co

Re: [Rd] DBLEPR?

2010-11-16 Thread Prof. John C Nash
I normally see digest once per day, but got msg from Doug Bates so responding with context. UCMINF is a package on CRAN that implements a variable metric minimizer. It does quite well on unconstrained problems. Stig Mortensen packaged the Fortran version for R, but is not at moment responding t

Re: [Rd] SEXPs and slots

2010-11-16 Thread Patrick Leyshock
Revisiting the output below: 1. Am I correct in thinking that the @XXX items are addresses? 2. What are the meanings of the gXcX items? 3. Does one ever see NAM[0]? Thanks, Patrick > .Internal(inspect(eg)) > @df70e48 25 S4SXP g0c0 [OBJ,NAM(2),gp=0x10,ATT] > ATTRIB: > @df70ef0 02 LISTSXP

Re: [Rd] [R] DBLEPR?

2010-11-16 Thread Douglas Bates
Reply redirected to the R-devel list. On Tue, Nov 16, 2010 at 1:02 PM, Prof. John C Nash wrote: > Ravi Varadhan and I have been looking at UCMINF to try to identify why it > gives occasional > (but not reproducible) errors, seemingly on Windows only. There is some > suspicion that its > use of

Re: [Rd] unloading compiled code.

2010-11-16 Thread Charles C. Berry
On Tue, 16 Nov 2010, Andrew Redd wrote: Just found in the documentation for getHook that packages are not unloaded on quit. How should I force a package to unload on quit? See ?q HTH, Chuck -Andrew On Tue, Nov 16, 2010 at 10:25 AM, Andrew Redd wrote: Are packages unloaded on

Re: [Rd] unloading compiled code.

2010-11-16 Thread Andrew Redd
Just found in the documentation for getHook that packages are not unloaded on quit. How should I force a package to unload on quit? -Andrew On Tue, Nov 16, 2010 at 10:25 AM, Andrew Redd wrote: > Are packages unloaded on quit so that the .Last.lib or .onUnload are > called for packages? > > -And

Re: [Rd] unloading compiled code.

2010-11-16 Thread Andrew Redd
Are packages unloaded on quit so that the .Last.lib or .onUnload are called for packages? -Andrew On Fri, Nov 12, 2010 at 3:52 PM, Andrew Redd wrote: > Perhaps you could help me make some sense of this.  Here is a printout > of my sessions. > --- > toys$R -q >> library(test2) >> gpualloctest() >

[Rd] trivial typo in system.Rd

2010-11-16 Thread Ben Bolker
Index: system.Rd === --- system.Rd (revision 53611) +++ system.Rd (working copy) @@ -181,7 +181,7 @@ \item The most important difference is that on a Unix-alike \code{system} launches a shell which then runs \code{command

Re: [Rd] Trying to understand the search path and namespaces

2010-11-16 Thread Berwin A Turlach
G'day Hadley, On Tue, 16 Nov 2010 07:35:09 -0600 Hadley Wickham wrote: > > Well, as the part of "Writing R Extensions" that Martin quoted > > states, the normal search path is part of the search path used by > > packages with name spaces.  So if you attach another package via > > library(), the

Re: [Rd] Trying to understand the search path and namespaces

2010-11-16 Thread Hadley Wickham
>> Ah, my mistake was assuming that the package namespace and environment >> were the same thing. >> >> Interestingly the namespace is dynamic: > > Not sure what you mean with this.  Section 1.6 of "Writing R > Extensions" explicitly states: > >        Name spaces are @emph{sealed} once they are lo

[Rd] Vignette Questions

2010-11-16 Thread Claudia Beleites
Dear List, I recently stumbled over the possibility and need to specifiy % \VignetteDepends{} in my vignettes. I did not know about this, and I notice that it is not mentioned in the R-extensions manual section "Writing package vignettes". I have some questions with regards to that: - would i

Re: [Rd] Bug in read.table?

2010-11-16 Thread peter dalgaard
On Nov 16, 2010, at 02:59 , Ben Bolker wrote: > Ben Bolker gmail.com> writes: > >> >> Ben Bolker gmail.com> writes: >> >>> >>> >> >> Can simplify this still farther: >> >> a b'c >> d e'f >> g h'i > > This example file leads to duplicate lines. > Arguably it should have behavior analo

Re: [Rd] SEXP and slots

2010-11-16 Thread Romain Francois
Le 15/11/10 21:15, Romain Francois a écrit : Hello, Since people have whisperred about Rcpp, I'd like to play too. On 11/15/2010 07:45 AM, Patrick Leyshock wrote: Very helpful, thank you. A couple other questions, please: 1. I've got a function written in C, named "my_c_function". In my R

Re: [Rd] Package with multiple shared libraries

2010-11-16 Thread Andreas Borg
Thanks for your reply. Actually my problem is not how to install the libraries in the sense of copying them to the right place, but how to build more than one .so or .dll file. Anyway, I did read the code and found that absence of a Makefile, a single library is built from all source files in d

Re: [Rd] Trying to understand the search path and namespaces

2010-11-16 Thread Berwin A Turlach
G'day Hadley, On Mon, 15 Nov 2010 19:45:30 -0600 Hadley Wickham wrote: > > 1.6 of Writing R Extensions says > > > > Note that adding a name space to a package changes the search > > strategy. The package name space comes first in the search, then > > the imports, then the base name space and the