[Rcpp-devel] basic usage help

Dear Rcpp list,

It's time for me to finally try out Rcpp

since I have to do some
computing for my research.  Some questions (please be kind as I'm only
a beginner C programmer using .C() and not smart enough to understand .
Call()):

1.  I plan to use objects like
Rcpp::NumericMatrix orig(matrix);
to store.  To confirm, storing to orig directly stores into the
original R object matrix right?
orig(i,j) = some double;

2.  int n = orig.rows();
Where can I find documentation on all the functions associated with
the class?  I'd like to know all the available functions plus
information about it (for example, the above returns an int).

3.  Is there a class for multidimensional arrays?  I'm thinking of
array() in R.  I use something like
S2[i + (*nObs)*j + (*nObs)*(*nParam)*k] = ...;
for all vectors, matrices, and arrays in C, and this is a pain as it
is a souce of a lot of my errors.

4.  My original code is using nlm() in R to fit my model. However, I
think it is best to do the Newton-Raphson directly in C/C++.  Can some
how evaluate matrix multiplication using "%*%" in R directly in my C++
code (using the Rcpp::NumericMatrix class)?

5.  How do I return a list in R that consists of a value, vector, and
matrix?  The three can be allocated in C++ or allocated prior to
entering C++ and passed on in .Call()?

6.  How do I compile the .cpp file on the
command line?  I got the following based on Dirk's HPC talk but
getting errors on my mac os x:

$ PKG_CPPFLAGS='r -e'Rcpp:::CxxFlags\(\)'' PKG_LIBS='r
-e'Rcpp:::LdFlags\(\)'' R CMD SHLIB rcpp.cpp
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/x86_64 r
-eRcpp:::CxxFlags() -I/usr/local/include    -fPIC  -g -O2 -c rcpp.cpp
-o rcpp.o
/bin/sh: -c: line 0: syntax error near unexpected token `('
/bin/sh: -c: line 0: `g++ -arch x86_64
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/x86_64 r
-eRcpp:::CxxFlags() -I/usr/local/include    -fPIC  -g -O2 -c rcpp.cpp
-o rcpp.o'
make: *** [rcpp.o] Error 2

If I get these things going then I'd be happy to release the code as
an example on using Rcpp to do maximization/model fitting.

Thanks.
Vinh

Le 26/05/10 18:55, Vinh Nguyen a ?crit :

Dear Rcpp list,

It's time for me to finally try out Rcpp

Great. You won't regret it ;-)

since I have to do some
computing for my research. ?Some questions (please be kind as I'm only
a beginner C programmer using .C() and not smart enough to understand .
Call()):

This is where Rcpp comes in. It will make you forget that .Call looks silly
and complicated. .C seems easier, but that is an illusion.

1. ?I plan to use objects like
Rcpp::NumericMatrix orig(matrix);
to store. ?To confirm, storing to orig directly stores into the
original R object matrix right?
orig(i,j) = some double;

Yes. Rcpp classes of the new api (e.g. Rcpp::NumericMatrix) act as a
wrapper. They change the way you look at the R object, but not the object
itself.

However, if you pass a SEXP that really is an integer matrix, Rcpp will cast
it to a numeric matrix. see the thread :
http://permalink.gmane.org/gmane.comp.lang.r.rcpp/369 for how that might
byte you if you are not aware of it.

2. ?int n = orig.rows();
Where can I find documentation on all the functions associated with
the class? ?I'd like to know all the available functions plus
information about it (for example, the above returns an int).

Dirk maintains a this http://dirk.eddelbuettel.com/code/rcpp/html/index.html
generated by doxygen. Some people like it.

The issue with classes like NumericMatrix is that they are generated from a
template and this makes it difficult for things like doxygen to produce
something nice. (some people don't like it)

One approximate way is to grep around the unit tests. We do have quite a
good coverage and we try to stress each functionality of Rcpp.

Otherwise the source code.

3. ?Is there a class for multidimensional arrays? ?I'm thinking of
array() in R. ?I use something like
S2[i + (*nObs)*j + (*nObs)*(*nParam)*k] = ...;
for all vectors, matrices, and arrays in C, and this is a pain as it
is a souce of a lot of my errors.

Not currently. Not that it is difficult to achieve, but it has to raise up
on our list of priorities.

4. ?My original code is using nlm() in R to fit my model. However, I
think it is best to do the Newton-Raphson directly in C/C++. ?Can some
how evaluate matrix multiplication using "%*%" in R directly in my C++
code (using the Rcpp::NumericMatrix class)?

we don't currently have operators on Rcpp types. maybe some day.

we however developped the RcppArmadillo package, which gives you the full
power of armadillo (http://arma.sourceforge.net/) plus the convenience of
Rcpp, at a small cost (see examples in RcppArmadillo)

5. ?How do I return a list in R that consists of a value, vector, and
matrix? ?The three can be allocated in C++ or allocated prior to
entering C++ and passed on in .Call()?

Something like this:


using namespace Rcpp ; // for _

IntegerVector z(5) ;
NumericMatrix foo( 3, 4 );
return List::create(
? ? ? ?_["x"] = 2,
? ? ? ?_["z"] = z,
? ? ? ?_["foo"] = foo ) ;


You don't need to (but you can if you want) allocate things before. I told
you .C was only easier by illusion ;-)

In fact, with Rcpp you don't have to care too much about allocation, etc ...
and you can concentrate on the problem you are trying to solve rather than
fighting with the R API.

6. ?How do I compile the .cpp file on the
command line? ?I got the following based on Dirk's HPC talk but
getting errors on my mac os x:

The easiest way by far is to make a package and follow the guidelines of our
last release notes. See the section "Using Rcpp in other packages" here
http://romainfrancois.blog.free.fr/index.php?post/2010/05/17/Rcpp-0.8.0


The next easy way is to build on the smartness of the inline package. With
verbose = TRUE, it will show you how to run the show:

fx <- cppfunction( , "return R_NilValue ;", verbose = TRUE )

$ PKG_CPPFLAGS='r -e'Rcpp:::CxxFlags\(\)'' PKG_LIBS='r
-e'Rcpp:::LdFlags\(\)'' R CMD SHLIB rcpp.cpp
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/x86_64 r
-eRcpp:::CxxFlags() -I/usr/local/include ? ?-fPIC ?-g -O2 -c rcpp.cpp
-o rcpp.o
/bin/sh: -c: line 0: syntax error near unexpected token `('
/bin/sh: -c: line 0: `g++ -arch x86_64
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/x86_64 r
-eRcpp:::CxxFlags() -I/usr/local/include ? ?-fPIC ?-g -O2 -c rcpp.cpp
-o rcpp.o'
make: *** [rcpp.o] Error 2

If I get these things going then I'd be happy to release the code as
an example on using Rcpp to do maximization/model fitting.

We look forward to it.

Thanks.
Vinh

--
Romain Francois
Professional R Enthusiast
+33(0) 6 28 91 30 30
http://romainfrancois.blog.free.fr
|- http://bit.ly/cork4b : highlight 0.1-8
|- http://bit.ly/bklUXt : RcppArmadillo 0.2.1
`- http://bit.ly/936ck2 : Rcpp 0.8.0

6. ?How do I compile the .cpp file on the
command line? ?I got the following based on Dirk's HPC talk but
getting errors on my mac os x:

The easiest way by far is to make a package and follow the guidelines of our
last release notes. See the section "Using Rcpp in other packages" here
http://romainfrancois.blog.free.fr/index.php?post/2010/05/17/Rcpp-0.8.0


The next easy way is to build on the smartness of the inline package. With
verbose = TRUE, it will show you how to run the show:

fx <- cppfunction( , "return R_NilValue ;", verbose = TRUE )

dyn.load("PH_CIC_Rcpp.so")

Also, I didn't include BLAS or LAPACK linking -- still don't know how
to get the compilation flags easily.   I read the skeleton stuff but I
don't understand (sorry).

On 2010-05-26, at 4:08 PM, Vinh Nguyen wrote:

Also, I didn't include BLAS or LAPACK linking -- still don't know how
to get the compilation flags easily. ? I read the skeleton stuff but I
don't understand (sorry).

Just put in your package's 'src' directory the Makevars file that's generated by RcppArmadillo's package.skeleton function. This is what it looks like on my machine:

PKG_LIBS = $(shell $(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()" ) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

How do you compile the code, by the way? It sounds like you do it by hand. Why not let R do it? With the above Makevars and the correct 'Depends' line in your package description (again, see the skeleton), you won't have to muck about with compiler switches and lookup paths, and everything should 'just work'.

Davor

On Wed, May 26, 2010 at 6:31 PM, Davor Cubranic<cubranic at stat.ubc.ca>  wrote:

On 2010-05-26, at 4:08 PM, Vinh Nguyen wrote:

Also, I didn't include BLAS or LAPACK linking -- still don't know how
to get the compilation flags easily.   I read the skeleton stuff but I
don't understand (sorry).

Just put in your package's 'src' directory the Makevars file that's generated by RcppArmadillo's package.skeleton function. This is what it looks like on my machine:

PKG_LIBS = $(shell $(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()" ) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

How do you compile the code, by the way? It sounds like you do it by hand. Why not let R do it? With the above Makevars and the correct 'Depends' line in your package description (again, see the skeleton), you won't have to muck about with compiler switches and lookup paths, and everything should 'just work'.

Davor

Yes, I'm doing it by hand since I'm still coding.  I compile after
some progress to make sure everything is OK.

Let's say I place the my code in in /src.  Do I HAVE to turn this into
a package in order to compile?  Or is there a way to compile from
here.  Sorry I'm new at this approach.

Thanks.

Vinh

You don't have to, but it makes your life easier. Now that we use LinkingTo:
Rcpp, RcppArmadillo it makes our Makevars smaller and more robust. R figures
out on its own where to find Rcpp and RcppArmadillo include paths.

If you don't want to use what R and Rcpp provides for you, you can emulate
this by using this Makevars :

PKG_LIBS = $(shell $(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()" )
$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
PKG_CXXFLAGS = $(shell $(R_HOME)/bin/Rscript -e "Rcpp:::CxxFlags()" )
$(shell Rscript -e "cat( '-I', system.file('include', package =
'RcppArmadillo'), sep = '' )" )


The PKG_LIBS line is the same that the one that gets generated ?by
RcppArmadillo.package.skeleton.

The PKG_CXXFLAGS line pulls in the include path of Rcpp and RcppArmadillo.

Just save this as a "Makevars" in the directory where your cpp files are,
and run:

R CMD SHLIB *cpp -o mylib.so


I will add a RcppArmadillo:::CxxFlags() for consistency between Rcpp and
RcppArmadillo.

Romain

On Wed, May 26, 2010 at 11:33 PM, Romain Francois
<romain at r-enthusiasts.com> wrote:

You don't have to, but it makes your life easier. Now that we use LinkingTo:
Rcpp, RcppArmadillo it makes our Makevars smaller and more robust. R figures
out on its own where to find Rcpp and RcppArmadillo include paths.

If you don't want to use what R and Rcpp provides for you, you can emulate
this by using this Makevars :

PKG_LIBS = $(shell $(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()" )
$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
PKG_CXXFLAGS = $(shell $(R_HOME)/bin/Rscript -e "Rcpp:::CxxFlags()" )
$(shell Rscript -e "cat( '-I', system.file('include', package =
'RcppArmadillo'), sep = '' )" )


The PKG_LIBS line is the same that the one that gets generated ?by
RcppArmadillo.package.skeleton.

The PKG_CXXFLAGS line pulls in the include path of Rcpp and RcppArmadillo.

Just save this as a "Makevars" in the directory where your cpp files are,
and run:

R CMD SHLIB *cpp -o mylib.so


I will add a RcppArmadillo:::CxxFlags() for consistency between Rcpp and
RcppArmadillo.

Romain

Thanks Romain. ?This is what I'm used to while working with compiled code for R.