[Rcpp-devel] Step-by-Step Plan to Code Writing and Testing withRcpp, RcppGSL or RcppArmadillo

Fri Dec 10 04:48:58 CET 2010

Hi again,  Thanks for your very helpful suggestions; you're right - I
need to just concentrate on Rcpp.  To that end, I followed the process
in the appendix of the R extensions manual, including your point point
to seek out and install Rtools from Murdoch-Sutherland.  I then tried a
simple inline example without any library reference it built and
executed fine.  When I attempted to compile the inline example that
includes the GSL library, it wasn't able to find any GSL header file
locations to make the build.  In particular, I received the following
error message:

fatal error: gsl/gsl_rng.h: No such file or directory

When running firstExample() from RccpInlineWithLibsExamples.r.   Since
I'm able to build, link, execute with Rcpp when not using the GSL
library, I know this problem may not be appropriate for this forum, but
I'm hoping you may have some insight.  My installation of GSL comes via
cygwin and I've added the appropriate links (to C:\cygwin\bin and
C:\cygwin\usr) in the PATH environment variable, as well as creating two
additional environment variables, GSL_INC and GSL_LIB with the
appropriate path locations for the GSL include and library files.  Yet,
nothing seems to work.  So I'd be very thankful if you have any ideas on
what I might next try.

-----Original Message-----
From: Dirk Eddelbuettel [mailto:edd at debian.org] 
Sent: Wednesday, December 08, 2010 8:42 PM
To: Savitsky, Terrance
Cc: Dirk Eddelbuettel; rcpp-devel at r-forge.wu-wien.ac.at
Subject: RE: [Rcpp-devel] Step-by-Step Plan to Code Writing and Testing
withRcpp, RcppGSL or RcppArmadillo

On 8 December 2010 at 20:05, Savitsky, Terrance wrote:
| Hello Dirk,  I sincerely apologize for how I started the dialogue.
May
| I have a do-over? 

Sure.

| I am an inexperienced developer.  So I'm looking
| forward to using Rcpp to improve my productivity and output quality
with
| writing C++ for R implementation.   I will re-read the documents and
| presentations you've publicly posted.
| 
| My interest in examples is focused towards imitation before
innovation.

We actually think along the same lines. What you dismissed earlier as
"marketing" is, seen from another angle, a fairly large set of working
examples. So let's focus on those.

For now, forget RcppArmadillo, RcppGSL, ... and concentrate on just
Rcpp.
There are numerous examples in the package itself -- see the examples/
subdirectory.  Let's get those to work first.

| I'll seek out archived examples for this, which will hopefully focus
my
| start-up efforts.  I do, however, have a couple of f/u questions:
| 
| To your point, "How could there not be debugging support with gdb if
g++
| is used?"  - Does R CMD use the g++ compiler?  Since my code is quite

Yes. It is essentially the only C++ compiler R uses by default. 

| long, I just want to find a way to efficiently debug.  I can't compile
| my Rcpp C++ code (with wrappers around R SEXP objects) outside of R,
so

Why? We do it all the time with Makefiles. See the examples/ mentioned
above.

| I'm looking for how to compile with debugging support in R.  I
typically
| write C code and compile and run (via cygwin gcc in Windows) with gdb.

Have you ever written any C/C++ code for R?  Do you know Cygwin is not
supported?

When I say 'Rtools' do you have a Pavlovian reflex to the
Murdock-Sutherland
site?  You better do ...  See 'Writing R Extensions' for starters.

In a nutshell you need a set of compilers etc just for R. Luckily these
have
been setup.

| It's not obvious to me how this process would work when writing Rcpp
C++
| code for compilation and implementation in R.
| 
| What IDE do Windows users typically choose for their Rcpp C++ code
| writing?  Is it any different from the IDE they would use for non-Rcpp
| standalone C/C++ code not interfaced with R?  

Well personally speaking I use the same IDE on all platforms: Emacs.
Within
the Rcpp Core team, some of us work on OS X and some work on Linux.  But
it
should not matter: R and R add-ons like Rcpp work on Windows, OS X and
Linux.
Use whichever platform you find easiest.  Personally, I like Ubuntu and
Debian a lot.

Dirk

| 
| Terrance Savitsky
| 
| 
| 
| On 8 December 2010 at 17:44, Savitsky, Terrance wrote:
| | I?m having difficulty to find ?How-to? documentation;  the papers
and
| | presentations (including the RcppExamples package) are exciting, but
| focus on
| | marketing use, 
| 
| Nice way to start a dialogue with us by telling us we're idiots. Keep
| going.
| 
| | rather than providing instructions.   I?d appreciate any help to
| | get started to:
| |
| | 1.       Code C++ using the Rcpp, RcppGSL and RcppArmadillo
libraries.
| 
| 
| I don't know how many example we posted on blogs, this list and in
| presentations. Exactly which did not work?
| 
| 	
|  
| | a.       May I link my IDE (netbeans) to the lib.a files and use the
| | appropriate .h files for composing C++ code for compilation in R? 
| 
| Don't know, don't care.  Ex-ant this is for __R__ where the command is
| 'R CMD ...'
| and/or Makefiles.
| 
| If you need netbeans, you get to figure out netbeans. Exiciting to be
| trailblazer, eh?
| 
| | b.      Do RcppGSL and RcppArmadillo contain the Rcpp classes or
| should the
| | header files from both be included (e.g. #include Rcpp.h, #include
| | RcppArmadillo.h)
| 
| Have you looked at the examples. They work, and they provide the
anwwer.
|  
| | c.       The matrix and vector classes, including views, Rcpp
| implementation of
| | the C library GSL employs new C++ capabilities and different syntax
| (e.g.
| | extraction of pointers from matrix or vector view objects).  Is
there
| detailed
| | documentation with examples for these class implementations.  The
| differences
| | from GSL disable using that documentation.
| 
| I have no idea what you are trying to say here. You are mixing two
core
| APIs
| (Views in Rcpp only exist in the classic API) and two 'glued-on'
| libraries
| one of which is C --- so there are bound to differences.
| 
| | d.      Should RcppExport be used in place of ?extern C? in C++
under
| Rcpp
| | whenever we wish to input R data types such as matrix, vector and
list
| (due to
| | need to call .Call)?
| 
| Look at the definiton and decide for yourself. Using the define has
the
| advantage that should we ever change it ...
| 
| | 2.       Compile and debug code using Inline or other preferred
| alternatives.
| | 
| | a.       The illustrations in presentations seem to copy and paste
the
| entire
| | code from C++ in single quotes with an assignment to a variable
| subsequently
| | used with inline in R.  My code (a Bayesian MCMC implementation)
will
| be on the
| | order of 600 lines long with about 10 input variables.  Is there a
| better way
| | to use inline?
| 
| Up to you. Inline is for experimentation. We had a MCMC example on the
| list
| following Whit's question. Did you look at it?
| 
| | b.      Is there any help on code debugging?  (e.g. some equivalent
of
| ?gdb?).
| 
| How could there not be debugging support with gdb if g++ is used?
|  
| | 3.       Writing a package.
| 
| Seen the Vignette?
|  
| | a.       What is the ?LinkingTo? declaration ? what purpose does it
| serve and
| | where is it used? 
| | 
| | b.      Same for Makevars and Makevars.win?
| 
| See 'Writing R Extensions' 
| 
| Dirk
| 
| 
| | Thanks, Terrance Savitsky
| | 
| |  
| | 
| | 
| |
|
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| -- 
| Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com

-- 
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com

__________________________________________________________________________

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