[Rcpp-devel] beginner questions on MinGW, Rcpp and inline packages
ravi
rv15i at yahoo.se
Mon Jul 5 18:31:05 CEST 2010
Hi Dirk,
Thanks for your help. Following your suggestion, I tried the following code
library(inline)
example(cfunction)
This executed without any problem. This must mean that I have all the basic tools.
Also followed your suggestion by looking at the tutorial by Rossi on making R packages. Surprisingly, I find there instructions for installing MinGW in addition to Rtools. Have the requirements changed since 2006? Almost sure of this, having just read the reference to Rtools in the R adm and installation manual.
I have tried to follow your presentations (for example, the one for R/Finance 2010). It would be helpful if you made available the code text in a seperate file(s). I could then run the code and follow your presentation.
Thanking you,
Ravi
----- Original Message ----
From: Dirk Eddelbuettel <edd at debian.org>
To: ravi <rv15i at yahoo.se>
Cc: rcpp-devel at lists.r-forge.r-project.org
Sent: Sat, 3 July, 2010 2:39:16
Subject: Re: [Rcpp-devel] beginner questions on MinGW, Rcpp and inline packages
On 2 July 2010 at 14:07, ravi wrote:
| Hi,
| I am fairly familiar with R but a total newcomer to C++. Still, I can see the new possibilities that are opened up by the integration of R with C++. I am excited by the new developments in Rcpp and related packages in recent months. I
| have decided to at least begin by wetting my feet in these topics.
|
| If this is not the forum for the questions that I
| am raising here, please let me know whom I should contact.
|
| Right now, I am on a PC with win XP. I would like to have some help in knowing what tools I need to get started. I have Rtools 2.11 installed. Is it
| sufficient to have this to access the C compilers? I even have a
Yes, it should be. Follow one of the tutorials for R package development on
Windows. Once you have the tools, Rcpp and inline should just work together
(and in isolation too...)
| seperate installation of MinGW. The following commands show the versions of gcc and g++ (and g77 too) :
|
| > system("gcc --version")
| gcc.exe (GCC)
| 4.2.1-sjlj (mingw32-2)
|
| > system("g++ --version")
| G__~1.EXE
| (GCC) 4.2.1-sjlj (mingw32-2)
|
| > system("g77 --version")
| GNU Fortran (GCC) 3.4.5 (mingw special)
| Copyright (C) 2004 Free Software Foundation, Inc.
|
| But I am confused by
| the MingW installation procedure. I tried to install MinGW with the most recent
| version (5.1.6) from SourceForge. But this led to a older version of gcc and g++ (v 3.4.5 if I remember correctly). And it was difficult to
| locate the MSYS installation file. My Norton Internet security program
| warned of security risks with the file that I located. I have now gone
| back to the installation with MinGW 5.1.4 and MSYS 1.0.1.
You do not need a separate MinGW installation, and I do not believe we ever
say you do.
| I
| tried to test my set of tools with the examples in the reference manual
| of the inline package. Except for the fortran bit, I find that I am able to run the commands. I am reproducing here the results from the R
| console. How do I solve the problem that I experience with Fortran code? What am I missing? Are the results OK for the other commands? How can I upgrade to the latest version of Mingw? I find some of the
| documentation on the Mingw site a little too difficult to follow? Can I
| use the mingw files on Rtools (and upgrade to Rtools 2.12)?
|
| I first show the results with
| sessionInfo() and then show the results from running the inline
| examples.
| ########################################
| >
| sessionInfo()
| R version 2.11.0 (2010-04-22)
| i386-pc-mingw32
| locale:
| [1] LC_COLLATE=Swedish_Sweden.1252 LC_CTYPE=Swedish_Sweden.1252
| LC_MONETARY=Swedish_Sweden.1252 LC_NUMERIC=C
| [5]
| LC_TIME=Swedish_Sweden.1252
| attached base packages:
| [1]
| grDevices datasets splines graphics stats tcltk utils
| methods base
| other attached packages:
| [1]
| RcppArmadillo_0.2.3 Rcpp_0.8.2 inline_0.3.5
| svSocket_0.9-48 TinnR_1.0.3 R2HTML_2.0.0
| Hmisc_3.8-0
| [8] survival_2.35-8 rcom_2.2-1
| rscproxy_1.3-1
| loaded via a namespace (and not attached):
| [1] cluster_1.12.3 grid_2.11.0 lattice_0.18-5 svMisc_0.9-57
| tools_2.11.0
| ###########################################
| >
| library(inline)
| Warning message:
| package 'inline' was built under R version 2.11.1
| > x <- as.numeric(1:10)
| > n <-
| as.integer(10)
| > code <- "
| + integer i
| + do 1 i=1, n(1)
| + 1 x(i) = x(i)**3
| + "
| > cubefn <-
| cfunction(signature(n="integer", x="numeric"), code,
| convention=".Fortran")
| ERROR(s) during compilation: source code
| errors or compiler configuration errors!
Something is wrong here... Maybe you did something wrong with the source.
Can you do example(cfunction) ?
| Program source:
| 1:
| 2: SUBROUTINE file678418be ( n, x )
| 3: INTEGER n(*)
| 4: DOUBLE PRECISION x(*)
| 5: integer i
| 6: do 1 i=1, n(1)
| 7: 1 x(i) = x(i)**3
| 8:
| 9: RETURN
| 10: END
| Error in compileCode(f, code, language, verbose) :
| Compilation ERROR,
| function(s)/method(s) not created!
| > cubefn(n, x)$x
| Error:
| could not find function "cubefn"
That is a side effect from the error above.
| > sigSq <-
| signature(n="integer", x="numeric")
| > codeSq <- "
| + for (int i=0; i < *n; i++) {
| + x[i] = x[i]*x[i];
| + }"
| > sigQd
| <- signature(n="integer", x="numeric")
| > codeQd <- "
| +
| squarefn(n, x);
| + squarefn(n, x);
| + "
| > fns <- cfunction( list(squarefn=sigSq, quadfn=sigQd),
| + list(codeSq, codeQd),
| +
| convention=".C")
| > squarefn <- fns[["squarefn"]]
| > quadfn <- fns[["quadfn"]]
| > squarefn(n, x)$x
| [1] 1 4 9 16 25 36 49 64 81 100
| > quadfn(n, x)$x
| [1] 1 16
| 81 256 625 1296 2401 4096 6561 10000
| >
| setCMethod(c("squarefn", "quadfn"), list(sigSq, sigQd),
| +
| list(codeSq, codeQd), convention=".C")
| Warning message:
| In
| getPackageName(environment(fdef)) :
| Created a package name,
| "2010-07-01 16:05:30", when none found
| > squarefn(n, x)$x
| [1] 1 4 9 16 25 36 49 64 81 100
| > quadfn(n, x)$x
| [1] 1 16 81 256 625 1296 2401 4096 6561 10000
| > code
| <- "
| + SEXP res;
| + int nprotect = 0, nx, ny, nz, x, y;
| +
| PROTECT(res = Rf_duplicate(a)); nprotect++;
| + nx =
| INTEGER(GET_DIM(a))[0];
| + ny = INTEGER(GET_DIM(a))[1];
| + nz =
| INTEGER(GET_DIM(a))[2];
| + double sigma2 = REAL(s)[0] * REAL(s)[0], d2 ;
| + double cx = REAL(centre)[0], cy = REAL(centre)[1], *data,
| *rdata;
| + for (int im = 0; im < nz; im++) {
| + data =
| &(REAL(a)[im*nx*ny]); rdata = &(REAL(res)[im*nx*ny]);
| + for
| (x = 0; x < nx; x++)
| + for (y = 0; y < ny; y++) {
| + d2 =
| (x-cx)*(x-cx) + (y-cy)*(y-cy);
| + rdata[x + y*nx] = data[x + y*nx] *
| exp(-d2/sigma2);
| + }
| + }
| + UNPROTECT(nprotect);
| + return
| res;
| + "
| > funx <- cfunction(signature(a="array",
| s="numeric", centre="numeric"), code)
| > x <-
| array(runif(50*50), c(50,50,1))
| > res <- funx(a=x, s=10,
| centre=c(25,15))
| > head(res)
| [1] 9.168592e-05 2.790754e-04
| 6.208501e-05 7.655548e-04 7.868005e-04 3.288564e-04
| > if
| (interactive()) image(res[,,1])
| > setCMethod("funy",
| signature(a="array", s="numeric", centre="numeric"), code, verbose=TRUE)
| Compilation argument:
| C:\PROGRA~1\R\R-211~1.0/bin/R CMD SHLIB file276e6f8.cpp
| g++ -I"C:/PROGRA~1/R/R-211~1.0/include" -O2 -Wall -c
| file276e6f8.cpp -o file276e6f8.o
| g++ -shared -s -static-libgcc -o
| file276e6f8.dll tmp.def file276e6f8.o -LC:/PROGRA~1/R/R-211~1.0/bin -lR
| Program source:
| 1: #include <R.h>
| 2: #include
| <Rdefines.h>
| 3: #include <R_ext/Error.h>
| 4:
|
| 5:
| 6:
| 7:
| 8: extern "C" {
| 9: SEXP funy ( SEXP a, SEXP s, SEXP centre );
| 10: }
| 11:
| 12: SEXP funy ( SEXP a,
| SEXP s, SEXP centre ) {
| 13:
| 14: SEXP res;
| 15: int nprotect = 0, nx, ny, nz, x, y;
| 16: PROTECT(res = Rf_duplicate(a));
| nprotect++;
| 17: nx = INTEGER(GET_DIM(a))[0];
| 18: ny =
| INTEGER(GET_DIM(a))[1];
| 19: nz = INTEGER(GET_DIM(a))[2];
| 20:
| double sigma2 = REAL(s)[0] * REAL(s)[0], d2 ;
| 21: double cx =
| REAL(centre)[0], cy = REAL(centre)[1], *data, *rdata;
| 22: for (int
| im = 0; im < nz; im++) {
| 23: data = &(REAL(a)[im*nx*ny]);
| rdata = &(REAL(res)[im*nx*ny]);
| 24: for (x = 0; x < nx; x++)
| 25: for (y = 0; y < ny; y++) {
| 26: d2 = (x-cx)*(x-cx) +
| (y-cy)*(y-cy);
| 27: rdata[x + y*nx] = data[x + y*nx] *
| exp(-d2/sigma2);
| 28: }
| 29: }
| 30: UNPROTECT(nprotect);
| 31: return res;
| 32:
| 33: warning("your C program does not return
| anything!");
| 34: return R_NilValue;
| 35: }
| The following
| methods are now defined:
| Function: funy (package .GlobalEnv)
| a="array", s="numeric", centre="numeric"
| > res <- funy(x, 10, c(35,35))
| > head(res)
| [1] 1.031789e-11 3.835913e-11 1.042300e-11 1.569789e-10
| 1.970555e-10 1.005979e-10
| > if (interactive()) { x11();
| image(res[,,1]) }
| > fx <- cxxfunction( signature(x = "integer", y = "numeric" ) , '
| + return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) ;
| + ' )
| > fx( 2L, 5 )
| [1] 10
| > if( require( Rcpp ) ){
| + fx <- cxxfunction( signature(x = "integer", y = "numeric" ) , '
| + return wrap( as<int>(x) * as<double>(y) ) ;
| + ', plugin = "Rcpp" )
| + fx( 2L, 5 )
| + }
| Loading required package: Rcpp
| [1] 10
| Warning message:
| package 'Rcpp' was built under R version
| 2.11.1
| > fx(6L,7)
| [1] 42
| > if( require( RcppArmadillo )
| ){
| + fx <- cxxfunction( signature(x = "integer", y = "numeric" ) , '
| + int dim = as<int>( x ) ;
| + arma::mat z =
| as<double>(y) * arma::eye<arma::mat>( dim, dim ) ;
| +
| return wrap( arma::accu(z) ) ;
| + ', plugin = "RcppArmadillo" )
| +
| fx( 2L, 5 )
| + }
| Loading required package: RcppArmadillo
| [1] 10
| Warning message:
| package 'RcppArmadillo' was built under R version 2.11.1
| ###########################################
| I would appreciate any help that I can get.
| Thanking you,
| Ravi
|
| PS : Instead of sending a long stream of text, I attempted to get the
| output in a file with the following commands :
| setwd("M:\\CtoRf\\Rcpp")
| sink("inlineExOut.txt") # send output to inlineExOut.txt
| source("inlineExamples.r",echo=TRUE) #inlineExamples.r is the file with the script
| sink()
|
| This
| gave the following error :
| Error in compileCode(f, code, language,
| verbose) :
| Compilation ERROR, function(s)/method(s) not created!
| Is there any workaround?
*If* you have the tools installed, then
> library(inline)
> example(cfunction)
should just work. Likewise for the Rcpp package and the assorted other
packages like RcppExamples.
But if all this is very new to you, try to start with some basic tutorials
about R package building as e.g. the ones Rossi or Leisch.
--
Regards, Dirk
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