[Rcpp-devel] RcppArmadillo error
Hi Romain, I tried the commands you gave and I get the following error: RcppArmadilloEg.cpp: In function ?SEXPREC* fastLm(SEXPREC*, SEXPREC*)?: RcppArmadilloEg.cpp:19: error: ?create? is not a member of ?Rcpp::List? make: *** [RcppArmadilloEg.o] Error 1 is there some kind of update I need to make? almost there! abhisek On Tue, Mar 30, 2010 at 3:12 PM, Romain Francois
<romain at r-enthusiasts.com>wrote:
Le 30/03/10 15:36, Douglas Bates a ?crit : On Tue, Mar 30, 2010 at 1:15 AM, Romain Francois
<romain at r-enthusiasts.com> wrote:
Hi,
If you want to compile the code that is here
http://dirk.eddelbuettel.com/code/rcpp.armadillo.html directly from R CMD SHLIB, you can do this:
romain at naxos /tmp $ export PKG_CXXFLAGS=`Rscript -e
"RcppArmadillo:::CxxFlags()"` romain at naxos /tmp $ export PKG_LIBS=`Rscript -e "RcppArmadillo:::LdFlags()"` romain at naxos /tmp $ R CMD SHLIB armaex.cpp
The way that RcppArmadillo:::LdFlags() is currently defined there is a
possibility of getting different Lapack and BLAS libraries when using
R or calls to RcppArmadillo. R uses the libraries defined by the
macros LAPACK_LIBS, BLAS_LIBS and FLIBS in the file
file.path(R.home("etc"), "Makeconf") # evaluate this in R
It is not certain that those will be the same as the libraries used by
Armadillo. If they are not shared objects you run the risk of getting
two copies of Lapack, etc. and possibly different BLAS, leading to
different performance characteristics and perhaps different results.
Hmmm. Interesting. I did not think of that problem. On my machine, I have : Rscript -e "RcppArmadillo:::LdFlags()" /Library/Frameworks/R.framework/Resources/library/Rcpp/lib/x86_64/libRcpp.a -L/usr/lib -larmadillo so linking against Rcpp "user" library and armadillo... but when I manually set PKG_LIBS to just Rcpp user library, it still works, so we actually do not need to link against armadillo library. armadillo itself does not __need__ to get compiled into a library because it is all templates. 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 |> |> |> |> -- |> |> Registration is open for the 2nd International conference R / Finance |> 2010 |> |> See http://www.RinFinance.com for details, and see you in Chicago in |> |> April! |> |> |> |> -- |> Registration is open for the 2nd International conference R / Finance |> 2010 |> See http://www.RinFinance.com for details, and see you in Chicago in |> April! |> -- Registration is open for the 2nd International conference R / Finance 2010 See http://www.RinFinance.com for details, and see you in Chicago in April!
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-- Romain Francois Professional R Enthusiast +33(0) 6 28 91 30 30 http://romainfrancois.blog.free.fr |- http://tr.im/OIXN : raster images and RImageJ |- http://tr.im/OcQe : Rcpp 0.7.7 `- http://tr.im/O1wO : highlight 0.1-5
_______________________________________________ Rcpp-devel mailing list Rcpp-devel at lists.r-forge.r-project.org https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
-- Romain Francois Professional R Enthusiast +33(0) 6 28 91 30 30 http://romainfrancois.blog.free.fr |- http://tr.im/OIXN : raster images and RImageJ |- http://tr.im/OcQe : Rcpp 0.7.7 `- http://tr.im/O1wO : highlight 0.1-5
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