I would however strongly recommend you to have this in a package.
Romain
Le 26/03/10 19:00, Abhisek a ?crit :
Hi Dirk,
I was referring to this page:
http://dirk.eddelbuettel.com/code/rcpp.armadillo.html
i was trying to run the code there.
here is my understanding so far (im new to linux and c++ so i apologize
for seeming rather slow!):
1. The Rcpp package helps C++ and R recognize each others stuff (like
variables).
2. The RcppArmadillo package extends this functionality to objects used
in armadillo (such as matrices and vectors e.g. colvec).
3. In FastLM, armadillo is being included but not RcppArmadillo. but
that is ok because there is a loop in there which converts an vector as
defined in armadillo to one which Rcpp recognizes. And it is this
vector which which gets passed back to R through the Rcpp interface.
also, it uses cfunction which is different from what im doing here as i
think you mentioned earlier (it worked by the way!)
what i tried to do was as follows:
a) to run the code as in the link above and include Rcpp and
RcppArmadillo and I was getting the errors as described in my initial post.
b) then i tried the same code but only including Rcpp and armadillo.
if my reasoning above is correct, part (b) should not run as Rcpp would
not recognize stuff like arma::colvec. but, i get the exact same error
as above!
so that suggests, that while compiling the code, the compiler is not
even getting to the point in procedure b when it should encounters an
type it doesnt recognize. which means that somehow, armadillo is giving
problems. but that is as far as i can understand. either that or my
understanding is way off.
appreciate your patience and help!
abhisek
On Fri, Mar 26, 2010 at 4:20 PM, Dirk Eddelbuettel<edd at debian.org
<mailto:edd at debian.org>> wrote:
On 26 March 2010 at 15:32, Abhisek wrote:
| Hi Dirk,
|
| Just so that I understand. I copied the code in the RcppArmadillo
section
| on your website and pasted and saved it.
What code? What page?
| Are you saying I should change
| #include<RcppArmadillo> to #include<Rcpp> and #include<armadillo> ?
No that is not what I said. I said
You can't just look at FastLM() and think your code will run
like it.
RcppArmadillo __does not export its classes__. It is an
implementation
reference -- it gives you guidance as to how to implement C++
packages of
your own against other libraries.
If you "just" want to use Armadillo and have Rcpp help you, look
at the
installed example 'FastLM' in the Rcpp package. In other words
ignore
RcppArmadillo for now.
So look at /usr/local/lib/Rcpp/examples/FastLM/ and the files there.
Run
fastLMviaArmadillo.r
and look at it. That should work.
You can also look at the _entire RcppArmadillo package_ and see how the
pieces fit together, including src/Makevars.
But don't just take semi-random shortcuts and expect that to work. If we
could make it any simpler, we would. There is a reason RcppArmadilli is
package and not just a file.
Dirk
| best,
| abhisek
|
| On Fri, Mar 26, 2010 at 1:40 PM, Dirk Eddelbuettel<edd at debian.org
<mailto:edd at debian.org>> wrote:
|
|>
|> Hi Abhisek,
|>
|> On 26 March 2010 at 12:28, Abhisek wrote:
|> | I downloaded the stuff just last friday so it should be the latest
|> version
|> | of Rcpp as well as Armadillo. I used install.packages() for
Rcpp and
|> | RcppArmadillo. Armadillo is 0.9.4. Im using xubuntu karmic
koala.
|>
|> Ok, that is all good. And if RcppArmadillo installed you have
proper
|> libraries, Armadillo included.
|>
|> I think part of your problem is a misunderstanding of an issue
we may not
|> have made particularly clear: You can't just look at FastLM()
and think
|> your code will run like it. RcppArmadillo __does not export its
classes__.
|> It is an implementation reference -- it gives you guidance as to
how to
|> implement C++ packages of your own against other libraries.
|>
|> If you "just" want to use Armadillo and have Rcpp help you, look
at the
|> installed example 'FastLM' in the Rcpp package. In other words
ignore
|> RcppArmadillo for now.
|>
|> The example (in 0.7.10) uses an idiom we no longer like and I am
about to
|> change that for an upcoming 0.7.11 release, but it should works
as is and
|> just use inline -- so no messing with makefile etc.
|>
|> Try that and see how it goes and keep us posted.
|>
|> Cheers, Dirk
|>
|>
|> | i also had some problem using Armadillo which I posted on the
Armadillo
|> | discussion board. Conrad got back to me. Here is the discussion:
|> | https://sourceforge.net/apps/phpbb/arma/viewtopic.php?f=1&t=4
<https://sourceforge.net/apps/phpbb/arma/viewtopic.php?f=1&t=4>
|> |
|> | so it may be that armadillo is the problem but im really not sure.
|> |
|> | Many thanks
|> | Abhisek
|> |
|> | On Fri, Mar 26, 2010 at 12:17 PM, Dirk Eddelbuettel
<edd at debian.org<mailto:edd at debian.org>>
|> wrote:
|> |
|> |>
|> |> (resending, this time to list I omitted last time, sorry.
--Dirk)
|> |>
|> |> On 26 March 2010 at 11:10, Abhisek wrote:
|> |> | Hi,
|> |> |
|> |> | Ive been trying to make RcppArmadillo work using the
example file
|> |> (fastLM).
|> |> | I copied and pasted the code and saved it as
RcppArmadilloEg.cpp (not
|> to
|> |> use
|> |> | fastLM but to figure out how to work RcppArmadillo). Then
i tried
|> using
|> |> the
|> |> | command R CMD SHLIB RcppArmadilloEg.cpp but an error came
up saying
|> that
|> |> | RcppArmadillo.h not found.
|> |> |
|> |> | So i tried doing a symbolic link from /usr/local/include
to the
|> directory
|> |> | where RcppArmadillo.h and RcppArmadilloDefines.h is
stored. I also
|> did a
|> |> | symbolic link analogously for RcppArmadillo.so. When i
ran R CMD
|> SHLIB
|> |> | again I got the following error:
|> |> |
|> |> | abhisek at shieks:~/Desktop/Personal/Test$ R CMD SHLIB
|> RcppArmadilloEg.cpp
|> |> | g++ -I/usr/share/R/include
|> |> | -I/home/abhisek/R/i486-pc-linux-gnu-library/2.10/Rcpp/lib
-fpic -g
|> -O2
|> |> -c
|> |> | RcppArmadilloEg.cpp -o RcppArmadilloEg.o
|> |>
|> |> So far so good: one -I for R as usual, one for Rcpp.
|> |>
|> |> | In file included from
|> |> |
|>
/home/abhisek/R/i486-pc-linux-gnu-library/2.10/Rcpp/lib/RcppCommon.h:215,
|> |> | from
|> |> |
/home/abhisek/R/i486-pc-linux-gnu-library/2.10/Rcpp/lib/Rcpp.h:28,
|> |> | from RcppArmadilloEg.cpp:1:
|> |> |
|> |>
|>
/home/abhisek/R/i486-pc-linux-gnu-library/2.10/Rcpp/lib/Rcpp/internal/wrap.h:
|> |> | In function ?SEXPREC*
|> |> Rcpp::internal::wrap_dispatch_unknown_iterable(const
|> |> | T&, Rcpp::traits::false_type) [with T = arma::Col<double>]?:
|> |> |
|> |>
|>
/home/abhisek/R/i486-pc-linux-gnu-library/2.10/Rcpp/lib/Rcpp/internal/wrap.h:491:
|> |> | instantiated from ?SEXPREC*
|> Rcpp::internal::wrap_dispatch_unknown(const
|> |> T&,
|> |> | Rcpp::traits::false_type) [with T = arma::Col<double>]?
|> |> |
|> |>
|>
/home/abhisek/R/i486-pc-linux-gnu-library/2.10/Rcpp/lib/Rcpp/internal/wrap.h:509:
|> |> | instantiated from ?SEXPREC*
|> |> | Rcpp::internal::wrap_dispatch_unknown_importable(const T&,
|> |> | Rcpp::traits::false_type) [with T = arma::Col<double>]?
|> |> |
|> |>
|>
/home/abhisek/R/i486-pc-linux-gnu-library/2.10/Rcpp/lib/Rcpp/internal/wrap.h:526:
|> |> | instantiated from ?SEXPREC*
Rcpp::internal::wrap_dispatch(const T&,
|> |> | Rcpp::traits::wrap_type_unknown_tag) [with T =
arma::Col<double>]?
|> |> |
|> |>
|>
/home/abhisek/R/i486-pc-linux-gnu-library/2.10/Rcpp/lib/Rcpp/internal/wrap.h:541:
|> |> | instantiated from ?SEXPREC* Rcpp::wrap(const T&) [with T =
|> |> | arma::Col<double>]?
|> |> |
|>
/home/abhisek/R/i486-pc-linux-gnu-library/2.10/Rcpp/lib/Rcpp/Named.h:54:
|> |> | instantiated from ?Rcpp::Named::Named(const std::string&,
const T&)
|> [with
|> |> T
|> |> | = arma::colvec]?
|> |> | RcppArmadilloEg.cpp:19: instantiated from here
|> |> |
|> |>
|>
/home/abhisek/R/i486-pc-linux-gnu-library/2.10/Rcpp/lib/Rcpp/internal/wrap.h:394:
|> |> | error: cannot convert ?const arma::Col<double>? to
?SEXPREC*? in
|> |> | initialization
|> |> | make: *** [RcppArmadilloEg.o] Error 1
|> |> |
|> |> |
|> |> | could someone provide some advice?
|> |>
|> |> Which Rcpp version do you have installed?
|> |>
|> |> Which Armadillo version do you have installed?
|> |>
|> |> I have not tried the free-floating direct compile you try
here. Maybe
|> the
|> |> defines for RcppArmadillo that we use are missing here --
hard to say.
|> |>
|> |> Could you try to create your own little package but copying the
|> |> RcppArmadillo
|> |> files, changes DESCRIPTION to what you do and changes the
FastLM code
|> in
|> |> C++
|> |> and R?
|> |>
|> |> Dirk
|> |>