[Rcpp-devel] Compiling RcppArmadillo through R CMD SHLIB onWindows XP
Savitsky, Terrance
savitsky at rand.org
Tue Dec 14 19:12:09 CET 2010
Thanks. Does it work with this code employing RcppArmadillo?
#include <RcppArmadillo.h>
using namespace Rcpp;
extern "C" SEXP foo(){
arma::mat x(2,2);
NumericMatrix res = wrap (x + x);
return res;
}
Are you able to compile and link via R CMD SHLIB with this code snippet? That something works via inline, but not R CMD SHLIB, leaves me concerned I will be unable to employ code composed under RcppArmadillo to build a package. I have been able to successively compile and build RcppArmadillo code in my Windows XP installation through inline. What I'm not able to do is the same through R CMD SHLIB. With Romain's help, the Rcpp/RcppArmadillo dependencies are resolved, but not the simple snprintf error. I don't think there's an issue with my installation of the Rtools toolchain as I've reviewed it a number of times (including environment variable settings). Including additional headers or namespace declarations is not solving this problem. I'm wondering if there is not a Windows issue driving it and whether the root cause is something other than making additional includes on my end.
Thanks.
-----Original Message-----
From: Dirk Eddelbuettel [mailto:edd at debian.org]
Sent: Tuesday, December 14, 2010 8:52 AM
To: Savitsky, Terrance
Cc: Dirk Eddelbuettel; rcpp-devel at r-forge.wu-wien.ac.at
Subject: RE: [Rcpp-devel] Compiling RcppArmadillo through R CMD SHLIB onWindows XP
On 14 December 2010 at 08:31, Savitsky, Terrance wrote:
| This header is not in the helpful examples, nor in the simple 'bla.cpp' Romain crafted that employed RcppArmadillo. Is the requirement for me to add this header related to the Windows version of Rcpp or is it universal and obvious to a C++ developer?
a) Well it just works over here:
R> src <- 'char buffer[128];
+ snprintf(buffer, 127, "Hello, %s\\n", "world");
+ return(Rcpp::wrap(std::string(buffer)));'
R> foo <- cxxfunction(, src, plugin="Rcpp")
R> foo()
[1] "Hello, world\n"
R>
b) My version of Rtools (ie g++ on Windows) has cstdio (as the C++ version of
stdio.h) and defines snprintf.
Hope this helps, Dirk
| Thanks. Terrance
|
| -----Original Message-----
| From: Dirk Eddelbuettel [mailto:edd at debian.org]
| Sent: Tuesday, December 14, 2010 7:56 AM
| To: Savitsky, Terrance
| Cc: rcpp-devel at r-forge.wu-wien.ac.at
| Subject: Re: [Rcpp-devel] Compiling RcppArmadillo through R CMD SHLIB onWindows XP
|
|
| On 13 December 2010 at 12:23, Savitsky, Terrance wrote:
| | Hello Romain, Thank you for your expertise. I will use the documentation to make a package. At this point, however, I want to see every method I've tried work, however, so that I understand any and all differences I might expect for developing with Rcpp/RcppArmadillo under Windows XP. So I followed the process (using Verbose=TRUE under an inline invocation) with the bla.cpp you included for me to obtain PKG_LIBS and CLINK-CPPFLAGS values. When I return to my cygwin bash shell session and attempt to compile and link bla.cpp, it does now seem to properly source my #include<RcppArmadillo.h>. statement. I do, however, receive the following error: 'snprintf' is not a member of 'std'. So I guess I'm missing a header linked to std::snprintf. The only thing that comes to mind is that I have somehow corrupted my installation of Rcpp. I would appreciate any insight you would offer.
|
| snprintf is defined in the cstdio header.
|
| Dirk
|
| |
| | Thanks, Terrance Savitsky
| |
| | -----Original Message-----
| | From: Romain Francois [mailto:romain at r-enthusiasts.com]
| | Sent: Sunday, December 12, 2010 3:58 AM
| | To: Savitsky, Terrance
| | Cc: rcpp-devel at r-forge.wu-wien.ac.at
| | Subject: Re: [Rcpp-devel] Compiling RcppArmadillo through R CMD SHLIB on Windows XP
| |
| | Le 12/12/10 04:03, Savitsky, Terrance a écrit :
| | > Hello,
| | >
| | > I employ a variant of the following lines in a cygwin bash session in
| | > Windows XP to compile my .cpp file.
| | >
| | > $ export PKG_LIBS=`Rscript.exe -e "RcppArmadillo:::LdFlags()"`
| | >
| | > $ export PKG_CXXFLAGS=`Rscript.exe -e "RcppArmadillo:::CxxFlags()"`
| | >
| | > $ R CMD SHLIB fastLm.cpp
| | >
| | > I receive the following compile error:
| | >
| | > G++ -I"C:/PROGRA~1/R/R-212~1.0/include" Rscript.exe -e
| | > "RcppArmadillo:::CxxxFlags()" -O2 - Wall -pedantic - c fastLm.cpp - o
| | > fastLm.o
| | >
| | > G++:Rscript.exe: No such file or directory
| | >
| | > fastLm.cpp:1:27: error: RcppArmadillo.h: No such file or directory
| | >
| | > fastLm.cpp:2: error: 'SEXP' does not have name a type
| | >
| | > I've included the R bin directory containing Rscript.exe to the PATH
| | > environment statement. Should one use a different syntax for windows to
| | > capture RcppArmadillo dependencies? (Fyi, I am able to build using
| | > inline, though my code is 600 lines and I will have multiple versions,
| | > so using the old approach may provide the most modular de-bugging
| | > approach vs. re-installing a package as I add files).
| | >
| | > Thanks, Terrance Savitsky
| |
| | Hello,
| |
| | I would strongly advise you to make it a package, especially if you deal
| | with multiple files, etc ...
| |
| | One thing you might want to consider is to use the verbose argument of
| | cxxfunction, so that inline shows you how it runs the show.
| |
| | For example:
| |
| | require(RcppArmadillo)
| | require(inline)
| |
| | f <- cxxfunction( , '
| | arma::mat x(2,2) ;
| | NumericMatrix res = wrap( x + x ) ;
| | return res ;
| | ', plugin = "RcppArmadillo", verbose = TRUE )
| |
| | When you run this, you'll see what inline does with the PKG_LIBS, etc ...:
| |
| | For example, it shows me this on OSX:
| |
| | romain at naxos ~/svn/rcpp/pkg $ Rscript bla.R
| | Le chargement a nécessité le package : RcppArmadillo
| | Le chargement a nécessité le package : Rcpp
| | Le chargement a nécessité le package : methods
| | Le chargement a nécessité le package : inline
| | >> setting environment variables:
| | PKG_LIBS =
| | /Library/Frameworks/R.framework/Versions/2.12/Resources/library/Rcpp/lib/x86_64/libRcpp.a
| | $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
| |
| | >> LinkingTo : RcppArmadillo, Rcpp
| | CLINK_CPPFLAGS =
| | -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/RcppArmadillo/include"
| | -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Rcpp/include"
| |
| |
| | >> Program source :
| |
| | 1 :
| | 2 : // includes from the plugin
| | 3 : #include <RcppArmadillo.h>
| | 4 : #include <Rcpp.h>
| | 5 :
| | 6 :
| | 7 : #ifndef BEGIN_RCPP
| | 8 : #define BEGIN_RCPP
| | 9 : #endif
| | 10 :
| | 11 : #ifndef END_RCPP
| | 12 : #define END_RCPP
| | 13 : #endif
| | 14 :
| | 15 : using namespace Rcpp;
| | 16 :
| | 17 :
| | 18 : // user includes
| | 19 :
| | 20 :
| | 21 : // declarations
| | 22 : extern "C" {
| | 23 : SEXP file313a14a1( ) ;
| | 24 : }
| | 25 :
| | 26 : // definition
| | 27 :
| | 28 : SEXP file313a14a1( ){
| | 29 : BEGIN_RCPP
| | 30 :
| | 31 : arma::mat x(2,2) ;
| | 32 : NumericMatrix res = wrap( x + x ) ;
| | 33 : return res ;
| | 34 :
| | 35 : END_RCPP
| | 36 : }
| | 37 :
| | 38 :
| | Compilation argument:
| | /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB
| | file313a14a1.cpp 2> file313a14a1.cpp.err.txt
| | g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include
| | -I/Library/Frameworks/R.framework/Resources/include/x86_64
| | -I/usr/local/include
| | -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/RcppArmadillo/include"
| | -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Rcpp/include"
| | -fPIC -g -O3 -Wall -pipe -c file313a14a1.cpp -o file313a14a1.o
| | g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined
| | dynamic_lookup -single_module -multiply_defined suppress
| | -L/usr/local/lib -o file313a14a1.so file313a14a1.o
| | /Library/Frameworks/R.framework/Versions/2.12/Resources/library/Rcpp/lib/x86_64/libRcpp.a
| | -L/Library/Frameworks/R.framework/Resources/lib/x86_64 -lRlapack
| | -L/Library/Frameworks/R.framework/Resources/lib/x86_64 -lRblas
| | -lgfortran -F/Library/Frameworks/R.framework/.. -framework R
| | -Wl,-framework -Wl,CoreFoundation
| |
| | Then you can just hardcode PKG_LIBS and CLINK_CPPFLAGS (or use
| | PKG_CPPFLAGS if you prefer).
| |
| |
| |
| | Another tip with inline is that you can read the code from a file, e.g :
| |
| | f <- cxxfunction( ,
| | paste( readLines("bla.cpp"), collapse = "\n") ,
| | plugin = "RcppArmadillo", verbose = TRUE )
| |
| | This way you can import multiple files, etc ... while keeping the C++
| | code out of the R code. I would still however very strongly recommend
| | you to make a package. It is well documented, easy and it will save you
| | some time.
| |
| | Romain
| |
| | --
| | Romain Francois
| | Professional R Enthusiast
| | +33(0) 6 28 91 30 30
| | http://romainfrancois.blog.free.fr
| | |- http://bit.ly/fT2rZM : highlight 0.2-5
| | |- http://bit.ly/gpCSpH : Evolution of Rcpp code size
| | `- http://bit.ly/hovakS : RcppGSL initial release
| |
| |
| |
| | __________________________________________________________________________
| |
| | This email message is for the sole use of the intended recipient(s) and
| | may contain confidential information. Any unauthorized review, use,
| | disclosure or distribution is prohibited. If you are not the intended
| | recipient, please contact the sender by reply email and destroy all copies
| | of the original message.
| |
| | _______________________________________________
| | 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
|
| --
| Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
--
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
More information about the Rcpp-devel
mailing list