[Rcpp-devel] RcppArmadillo error

Abhisek shieks at gmail.com
Wed Mar 31 12:24:42 CEST 2010


Hi all,

thanks very much for all this advice!  ill be trying this out soon and
hopefully it works.

again, thanks for writing these amazing packages!

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 écrit :
>
>  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 écrit :
>>>
>>>> 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
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>>>
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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
>
>
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