Re: [Rd] [R] Use of .Fortran
On Sat, 19 Jun 2010, David Scott wrote:
I have no experience with incorporating Fortran code and am probably doing
something pretty stupid.
Surely you saw in the posting guide that R-help is not the place for
questions about C, C++, Fortran code? Diverting to R-devel.
I want to use the following Fortran subroutine (not written by me) in the
Well, it is not Fortran 77 but Fortran 95, and so needs to be given a
.f95 extension to be sure to work.
file SSFcoef.f
subroutine SSFcoef(nmax,nu,A,nrowA,ncolA)
implicit double precision(a-h,o-z)
implicit integer (i-n)
integer l,i,nmax
double precision nu,A(0:nmax,0:nmax)
A(0,0) = 1D0
do l=1,nmax
do i=1,l-1
A(l,i) = (-nu+i+l-1D0)*A(l-1,i)+A(l-1,i-1)
end do
A(l,0) = (-nu+l-1D0)*A(l-1,0)
A(l,l) = 1D0
end do
return
end
I created a dll (this is windows) using R CMD SHLIB SSFcoef.f
Then my R code is:
### Load the compiled shared library in.
dyn.load(SSFcoef.dll)
### Write a function that calls the Fortran subroutine
SSFcoef - function(nmax, nu){
.Fortran(SSFcoef,
as.integer(nmax),
as.integer(nu)
)$A
}
That does not match. nrowA and ncolA are unused, so you need
SSFcoef - function(nmax, nu){
.Fortran(SSFcoef,
as.integer(nmax),
as.integer(nu),
A = matrix(0, nmax+1, nmax+1),
0L, 0L)$A
}
SSFcoef(10,2)
which when run gives
SSFcoef(10,2)
NULL
I am pretty sure the problem is that I am not dealing with the matrix A
properly. I also tried this on linux and got a segfault.
Can anyone supply the appropriate modification to my call (and possibly to
the subroutine) to make this work?
David Scott
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The University of Auckland, PB 92019
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Email: d.sc...@auckland.ac.nz, Fax: +64 9 373 7018
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Re: [Rd] CHM help does not find help docs in package stats
On 17.06.2010 09:19, Thaler,Thorn,LAUSANNE,Applied Mathematics wrote: Indeed, the R version is 2.9.2. But the package was built on the very same system. Besides, another package built with the same version of R but on another machine does not show this nasty behavior. Upgrading, however, could pose more problems as it solves, since even if I could upgrade locally, it would be a mess to assure that all colleagues upgrade as well. Anyways, even if the chm format is not supported any more by current versions of R, it should work with older ones, right? So, what can I do additionally to get to the bottom of this problem? During the last years, Mircosoft patched parts of the chm system by disallowing different features by default. It may see some result of these patches. Anyway, hard to say what is going on without seeing your binary package, your system setup, the libraries where you have installed you package and the otehrs, knowing if these are network paths or local storage, . Uwe Ligges Thanks + BR, Thorn -Original Message- From: Uwe Ligges [mailto:lig...@statistik.tu-dortmund.de] Sent: samedi 12 juin 2010 18:21 To: Thaler,Thorn,LAUSANNE,Applied Mathematics Cc: r-devel@r-project.org Subject: Re: [Rd] CHM help does not find help docs in package stats Which version of R is this? CHM help is R 2.10.0. All versions thereafter do not support compiled html help anymore. Please upgrade your version of R and try one of the currently supported help formats. Best wishes, Uwe Ligges On 11.06.2010 12:06, Thaler, Thorn, LAUSANNE, Applied Mathematics wrote: Hi all, currently I'm working on an R package bundling some frequently used functions. When I load my package and type ?one_of_my_functions I get the particular help file. If I try to get help on another function, which is part of package stats (prcomp say), I get This program cannot display the webpage. A help on ?mean does, however, work as it opens a new window showing the help on mean. There is another peculiarity, if it happens that I requested a help file for a function in the package stats before I used the help on one of my functions, everything works out fine. Does anybody know how I can get rid of this annoying behavior? It has to have something to do with my particular package, since everything works as expected with another package of mine. I override one of the functions of stats (biplot.default), which is, however, not exported and resides within my namespace. Could that be the reason? Any help highly appreciated. Thanks + BR, Thorn __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] C Interface
Greetings,
I am trying to call simple C-code from R.
I am on Windows XP with RTools installed.
The C-function is
#include R.h
#include Rinternals.h
#include Rmath.h
#include Rdefines.h
// prevent name mangling
extern C {
SEXP __cdecl test(SEXP s){
SEXP result;
PROTECT(result = NEW_NUMERIC(1));
double* ptr=NUMERIC_POINTER(result);
double t = *REAL(s);
double u = t-floor(t)-0.5;
if(u0) *ptr=-1+4*u; else *ptr=-1-4*u;
Rprintf(The value is %f, *ptr);
UNPROTECT(1);
return result;
}
};
It is compiled with
R CMD SHLIB OrthoFunctions.c
with flag
MAKEFLAGS=CC=g++
However when I call this code from R with
test - function(t){
.Call(test,t)
}
dyn.load(./OrthoFunctions.dll)
test(0)
dyn.unload(./OrthoFunctions.dll)
then R crashes.
If I compile with the default flags (no extern C, no __cdecl) I get an
error message about an undefined reference to __gxx_personality_v0:
C:\...R CMD SHLIB OrthoFunctions.c
C:/Programme/R/R-2.10.1/etc/Makeconf:151: warning: overriding commands for
target `.c.o'
C:/Programme/R/R-2.10.1/etc/Makeconf:142: warning: ignoring old commands for
target `.c.o'
C:/Programme/R/R-2.10.1/etc/Makeconf:159: warning: overriding commands for
target `.c.d'
C:/Programme/R/R-2.10.1/etc/Makeconf:144: warning: ignoring old commands for
target `.c.d'
C:/Programme/R/R-2.10.1/etc/Makeconf:169: warning: overriding commands for
target `.m.o'
C:/Programme/R/R-2.10.1/etc/Makeconf:162: warning: ignoring old commands for
target `.m.o'
g++ -IC:/Programme/R/R-2.10.1/include-O2 -Wall -c
OrthoFunctions.c -o OrthoFunctions.o
gcc -shared -s -o OrthoFunctions.dll tmp.def OrthoFunctions.o
-LC:/Programme/R/R-2.10.1/bin -lR
OrthoFunctions.o:OrthoFunctions.c:(.eh_frame+0x11): undefined reference to
`__gxx_personality_v0'
collect2: ld returned 1 exit status
I have a vague idea of the issue of calling conventions and was hoping that
the __cdecl
specifier would force the appropriate convention.
I also have Cygwin installed as part of the Python(x,y) distribution but I
am assuming that
R CMD SHLIB source.c
calls the right compiler.
What could the problem be?
Many thanks,
Michael
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[Rd] nchar( NA )
Hello, Is this expected ? nchar( c( , NA ) ) [1] 0 2 Should not the second one be NA ? Romain -- Romain Francois Professional R Enthusiast +33(0) 6 28 91 30 30 http://romainfrancois.blog.free.fr |- http://bit.ly/98Uf7u : Rcpp 0.8.1 |- http://bit.ly/c6YnCi : graph gallery collage `- http://bit.ly/bZ7ltC : inline 0.3.5 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] nchar( NA )
Hi Romain, Did you read the help for nchar? Value: For ‘nchar’, an integer vector giving the sizes of each element, currently always ‘2’ for missing values (for ‘NA’). It may be unexpected behavior, but it's *well-documented* unexpected behavior. Sarah On Fri, Jun 18, 2010 at 4:52 PM, Romain Francois rom...@r-enthusiasts.com wrote: Hello, Is this expected ? nchar( c( , NA ) ) [1] 0 2 Should not the second one be NA ? Romain -- Sarah Goslee http://www.functionaldiversity.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] nchar( NA )
The help page says: For nchar, an integer vector giving the sizes of each element, currently always 2 for missing values (for NA). On Fri, Jun 18, 2010 at 5:52 PM, Romain Francois rom...@r-enthusiasts.comwrote: Hello, Is this expected ? nchar( c( , NA ) ) [1] 0 2 Should not the second one be NA ? Romain -- Romain Francois Professional R Enthusiast +33(0) 6 28 91 30 30 http://romainfrancois.blog.free.fr |- http://bit.ly/98Uf7u : Rcpp 0.8.1 |- http://bit.ly/c6YnCi : graph gallery collage `- http://bit.ly/bZ7ltC : inline 0.3.5 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] nchar( NA )
Le 18/06/10 22:58, Sarah Goslee a écrit : Hi Romain, Did you read the help for nchar? Value: For ‘nchar’, an integer vector giving the sizes of each element, currently always ‘2’ for missing values (for ‘NA’). It may be unexpected behavior, but it's *well-documented* unexpected behavior. Oops. My scan of the help page was too quick. I did not see it. Sorry for the noise. Sarah On Fri, Jun 18, 2010 at 4:52 PM, Romain Francois rom...@r-enthusiasts.com wrote: Hello, Is this expected ? nchar( c( , NA ) ) [1] 0 2 Should not the second one be NA ? Romain -- Romain Francois Professional R Enthusiast +33(0) 6 28 91 30 30 http://romainfrancois.blog.free.fr |- http://bit.ly/98Uf7u : Rcpp 0.8.1 |- http://bit.ly/c6YnCi : graph gallery collage `- http://bit.ly/bZ7ltC : inline 0.3.5 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] C Interface
On Jun 18, 2010, at 10:23 AM, michael meyer mjhme...@googlemail.com wrote:
Greetings,
I am trying to call simple C-code from R.
I am on Windows XP with RTools installed.
The C-function is
#include R.h
#include Rinternals.h
#include Rmath.h
#include Rdefines.h
// prevent name mangling
extern C {
SEXP __cdecl test(SEXP s){
SEXP result;
PROTECT(result = NEW_NUMERIC(1));
double* ptr=NUMERIC_POINTER(result);
double t = *REAL(s);
double u = t-floor(t)-0.5;
if(u0) *ptr=-1+4*u; else *ptr=-1-4*u;
Rprintf(The value is %f, *ptr);
UNPROTECT(1);
return result;
}
};
It is compiled with
R CMD SHLIB OrthoFunctions.c
with flag
MAKEFLAGS=CC=g++
That is entirely wrong - g++ is not a C compiler.
Cheers,
Simon
However when I call this code from R with
test - function(t){
.Call(test,t)
}
dyn.load(./OrthoFunctions.dll)
test(0)
dyn.unload(./OrthoFunctions.dll)
then R crashes.
If I compile with the default flags (no extern C, no __cdecl) I get an
error message about an undefined reference to __gxx_personality_v0:
C:\...R CMD SHLIB OrthoFunctions.c
C:/Programme/R/R-2.10.1/etc/Makeconf:151: warning: overriding commands for
target `.c.o'
C:/Programme/R/R-2.10.1/etc/Makeconf:142: warning: ignoring old commands for
target `.c.o'
C:/Programme/R/R-2.10.1/etc/Makeconf:159: warning: overriding commands for
target `.c.d'
C:/Programme/R/R-2.10.1/etc/Makeconf:144: warning: ignoring old commands for
target `.c.d'
C:/Programme/R/R-2.10.1/etc/Makeconf:169: warning: overriding commands for
target `.m.o'
C:/Programme/R/R-2.10.1/etc/Makeconf:162: warning: ignoring old commands for
target `.m.o'
g++ -IC:/Programme/R/R-2.10.1/include-O2 -Wall -c
OrthoFunctions.c -o OrthoFunctions.o
gcc -shared -s -o OrthoFunctions.dll tmp.def OrthoFunctions.o
-LC:/Programme/R/R-2.10.1/bin -lR
OrthoFunctions.o:OrthoFunctions.c:(.eh_frame+0x11): undefined reference to
`__gxx_personality_v0'
collect2: ld returned 1 exit status
I have a vague idea of the issue of calling conventions and was hoping that
the __cdecl
specifier would force the appropriate convention.
I also have Cygwin installed as part of the Python(x,y) distribution but I
am assuming that
R CMD SHLIB source.c
calls the right compiler.
What could the problem be?
Many thanks,
Michael
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Re: [Rd] nchar( NA )
Value: For ‘nchar’, an integer vector giving the sizes of each element, currently always ‘2’ for missing values (for ‘NA’). It may be unexpected behavior, but it's *well-documented* unexpected behavior. Oh, that must make it ok then. For a more sensible take: library(stringr) str_length(c(, NA)) [1] 0 NA Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] C Interface
Michael, You are getting confused in compiler minutia when you could be concentrating on your code. The inline package can help here. Consider the snippet below which loads inline, defines your function body sans headers etc and then uses the magic of inline to compile, link and load your function: --- library(inline) code - ' SEXP result; PROTECT(result = NEW_NUMERIC(1)); double* ptr=NUMERIC_POINTER(result); double t = *REAL(s); double u = t-floor(t)-0.5; if(u0) *ptr=-1+4*u; else *ptr=-1-4*u; Rprintf(The value is %f\\n, *ptr); UNPROTECT(1); return result; ' fun - cfunction(signature(s=numeric), code) fun(0.0001) --- Pasted in my R session I get: library(inline) code - ' + SEXP result; + PROTECT(result = NEW_NUMERIC(1)); + double* ptr=NUMERIC_POINTER(result); + double t = *REAL(s); + double u = t-floor(t)-0.5; + if(u0) *ptr=-1+4*u; else *ptr=-1-4*u; + Rprintf(The value is %f\\n, *ptr); + UNPROTECT(1); + return result; + ' fun - cfunction(signature(s=numeric), code) fun(0.0001) The value is 0.999600 [1] 0.9996 (I added a newline which, given that the code is character string, needed to be escaped.) If you like inline, you may like it even more in conjunction with Rcpp as the program becomes shorter and simpler thanks to as() and wrap(): code - ' + double t = asdouble(s); + double u = t-floor(t)-0.5; + if (u0) t=-1+4*u; else t=-1-4*u; + std::cout The value is t std::endl; + return wrap(t); + ' fun - cxxfunction(signature(s=numeric), code, plugin=Rcpp) fun(0.0001) The value is 0.9996 [1] 0.9996 Rcpp has a few vignettes that help getting started. The rcpp-devel list can help with questions. -- Regards, Dirk __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
