Re: [R] the use of the .C function
On Sat, 13 Oct 2007, Bernardo Lagos Alvarez wrote:
> Hi all,
>
> here others doubts, when load and running the function
>
> void gdot(double *x,double *y,int *n,double *output){
> int i;
> *output=0;
> for (i=0;i<*n;i++){
> *output+=x[i]*y[i];
> }
> }
>
>
> as following
>
> /examplesC$ R CMD SHLIB xby.c
> gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -fpic -g
> -O2 -c xby.c
> -o xby.o
> gcc -std=gnu99 -shared -o xby.so xby.o -L/usr/lib/R/lib -lR
>
> /examplesC$ R
>> x<-c(1,4,6,2)
>> y<-c(3,2.4,1,9)
>> dyn.load("xby.so")
>> product<-.C("gdot",myx=as.double(x),myy=as.double(y),myn=as.integer(NROW(x)),myoutput=numeric())
> *** caught segfault ***
> address (nil), cause 'memory not mapped'
>
> Traceback:
> 1: .C("gdot", myx = as.double(x), myy = as.double(y), myn =
> as.integer(NROW(x)),
> myoutput = numeric())
>
> Possible actions:
> 1: abort (with core dump)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection:
> Selection:
> Selection:
>
>
> Can anybody answerme that happening with this Traceback?
Yes. It detects that your routine has caused a segfault.
You need to be very careful in constructing .C() calls. A _little_ mistake
there will cause loads of problems.
As section 5.2 of Writing R Extensions says
"Note that we take care to coerce all the arguments to the correct R
storage mode before calling .C; mistakes in matching the types can lead to
wrong results or hard-to-catch errors."
Also, if you get the length of one or more arguments wrong this will cause
problems.
Try to dissect your R code little by little. I suggest
you do this
product.call.args <-
list( "gdot",
myx=as.double(x),
myy=as.double(y),
myn=as.integer(NROW(x)),
myoutput=numeric() )
Can you see your mistake yet?
If not now do
print( product.call.args )
If you still cannot see your mistake look hard at 'myoutput' and the C
code.
How much storage was allocated to 'output' ??
How much does it need ??
HTH
Chuck
>
>
> Thanking you in advance,
> Bernardo Lagos A.
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
Charles C. Berry(858) 534-2098
Dept of Family/Preventive Medicine
E mailto:[EMAIL PROTECTED] UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] the use of the .C function
Let me also comment that you are trying to interface to a function ported
to C++ from the Cephes library, which is in C. You have not explained why
you are trying to interface to the function (is this an exercise, or do
you suspect a problem with digamma()?), but if you just want access to it
as implemented in Cephes, you may as well use the original C:
http://www.netlib.org/cephes/
On Sun, 14 Oct 2007, Duncan Temple Lang wrote:
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
>
>
> The code is C++ and so is compiled
> using the C++ compiler, not the C compiler.
> This is because the name of the file is .cpp
> (and you include iostream.h, but don't seem to make any use of it.)
> As a result, the names of the routines are "mangled"
> and so psi is not the actual name of the compiled routine,
> but something more like _Z3psid which encodes the
> types of the parameters in the name (to allow overloaded routines).
>
> To avoid the mangling, use
>
> #ifdef __cplusplus
> extern "C"
> #endif
> double psi(double)
>
> Alternatively, you can use the registration mechanism to
> associate a name with a routine directly for R. See
> "Writing R Extensions" which would be a good thing to read
> as trying to get this sort of thing working by trial and
> error can be both very time consuming, and also very confusing
> to the point that you "unlearn" things.
>
> After that you will still need to make some changes
> to use the routine with the .C() interface.
> That expects inputs as pointers, i.e. the double
> should be a double * and you fetch the value from
> that. And a routine called by .C() should return nothing
> directly, but provide the results in space provided
> by the inputs
>
> So
> void R_psi(double *x)
> {
>*x = psi(*x);
> }
>
> and make certain R_psi is not mangled.
>
>
> Also, you might want to upgrade to the latest version of R.
>
> Bernardo Lagos Alvarez wrote:
> > Dear All,
> > could someone please shed some light on the use of the .C or .Fortran
> > function:
> >
> >
> > I am trying load and running on R the following function
> >
> > // psi.cpp -- psi function for real arguments.
> >
> > // Algorithms and coefficient values from "Computation of Special
> >
> > // Functions", Zhang and Jin, John Wiley and Sons, 1996.
> >
> > //
> >
> > // (C) 2003, C. Bond. All rights reserved.
> >
> > //
> >
> > // Returns psi function for real argument 'x'.
> >
> > // NOTE: Returns 1e308 for argument 0 or a negative integer.
> >
> > //
> >
> > #include // or ?
> >
> > #include
> >
> > #define el 0.5772156649015329
> >
> >
> >
> > double psi(double x)
> >
> > {
> >
> > double s,ps,xa,x2;
> >
> > int n,k;
> >
> > static double a[] = {
> >
> > -0.8e-01,
> >
> > 0.8e-02,
> >
> > -0.39682539682539683e-02,
> >
> > 0.41667e-02,
> >
> > -0.75757575757575758e-02,
> >
> > 0.21092796092796093e-01,
> >
> > -0.8e-01,
> >
> > 0.4432598039215686};
> >
> >
> >
> > xa = fabs(x);
> >
> > s = 0.0;
> >
> > if ((x == (int)x) && (x <= 0.0)) {
> >
> > ps = 1e308;
> >
> > return ps;
> >
> > }
> >
> > if (xa == (int)xa) {
> >
> > n = xa;
> >
> > for (k=1;k >
> > s += 1.0/k;
> >
> > }
> >
> > ps = s-el;
> >
> > }
> >
> > else if ((xa+0.5) == ((int)(xa+0.5))) {
> >
> > n = xa-0.5;
> >
> > for (k=1;k<=n;k++) {
> >
> > s += 1.0/(2.0*k-1.0);
> >
> > }
> >
> > ps = 2.0*s-el-1.386294361119891;
> >
> > }
> >
> > else {
> >
> > if (xa < 10.0) {
> >
> > n = 10-(int)xa;
> >
> > for (k=0;k >
> > s += 1.0/(xa+k);
> >
> > }
> >
> > xa += n;
> >
> > }
> >
> > x2 = 1.0/(xa*xa);
> >
> > ps = log(xa)-0.5/xa+x2*(((a[7]*x2+a[6])*x2+a[5])*x2+
> >
> > a[4])*x2+a[3])*x2+a[2])*x2+a[1])*x2+a[0]);
> >
> > ps -= s;
> >
> > }
> >
> > if (x < 0.0)
> >
> > ps = ps - M_PI*cos(M_PI*x)/sin(M_PI*x)-1.0/x;
> >
> > return ps;
> >
> > }
> >
> >
> > However, when applicated the codes
> >> digamma(-0.9)
> > [1] -9.312644 OK!
> >
> > But when
> >> dyn.load("psi.so")
> >> out<-.C("psi", as.double(-0.9))
> > Erro en .C("psi", as.double(-0.9)) : C symbol name "psi" not in load table
> >
> >> out
> > Error: objeto "out" no encontrado
> >
> > More information on OS:
> >> version
> >_
> > platform i486-pc-linux-gnu
> > arch i486
> > os linux-gnu
> > system i486, linux-gnu
> > status
> > major 2
> > minor 4.1
> > year 2006
> > month 12
> > day18
> > svn rev40228
> > language R
> > version.string R version 2.4.1 (2006-12-18)
> >
> >
> >
> > Many thanks for any insight or comments.
> >
> > Bernardo Lagos A.
> >
> > _
Re: [R] the use of the .C function
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
The code is C++ and so is compiled
using the C++ compiler, not the C compiler.
This is because the name of the file is .cpp
(and you include iostream.h, but don't seem to make any use of it.)
As a result, the names of the routines are "mangled"
and so psi is not the actual name of the compiled routine,
but something more like _Z3psid which encodes the
types of the parameters in the name (to allow overloaded routines).
To avoid the mangling, use
#ifdef __cplusplus
extern "C"
#endif
double psi(double)
Alternatively, you can use the registration mechanism to
associate a name with a routine directly for R. See
"Writing R Extensions" which would be a good thing to read
as trying to get this sort of thing working by trial and
error can be both very time consuming, and also very confusing
to the point that you "unlearn" things.
After that you will still need to make some changes
to use the routine with the .C() interface.
That expects inputs as pointers, i.e. the double
should be a double * and you fetch the value from
that. And a routine called by .C() should return nothing
directly, but provide the results in space provided
by the inputs
So
void R_psi(double *x)
{
*x = psi(*x);
}
and make certain R_psi is not mangled.
Also, you might want to upgrade to the latest version of R.
Bernardo Lagos Alvarez wrote:
> Dear All,
> could someone please shed some light on the use of the .C or .Fortran
> function:
>
>
> I am trying load and running on R the following function
>
> // psi.cpp -- psi function for real arguments.
>
> // Algorithms and coefficient values from "Computation of Special
>
> // Functions", Zhang and Jin, John Wiley and Sons, 1996.
>
> //
>
> // (C) 2003, C. Bond. All rights reserved.
>
> //
>
> // Returns psi function for real argument 'x'.
>
> // NOTE: Returns 1e308 for argument 0 or a negative integer.
>
> //
>
> #include // or ?
>
> #include
>
> #define el 0.5772156649015329
>
>
>
> double psi(double x)
>
> {
>
> double s,ps,xa,x2;
>
> int n,k;
>
> static double a[] = {
>
> -0.8e-01,
>
> 0.8e-02,
>
> -0.39682539682539683e-02,
>
> 0.41667e-02,
>
> -0.75757575757575758e-02,
>
> 0.21092796092796093e-01,
>
> -0.8e-01,
>
> 0.4432598039215686};
>
>
>
> xa = fabs(x);
>
> s = 0.0;
>
> if ((x == (int)x) && (x <= 0.0)) {
>
> ps = 1e308;
>
> return ps;
>
> }
>
> if (xa == (int)xa) {
>
> n = xa;
>
> for (k=1;k
> s += 1.0/k;
>
> }
>
> ps = s-el;
>
> }
>
> else if ((xa+0.5) == ((int)(xa+0.5))) {
>
> n = xa-0.5;
>
> for (k=1;k<=n;k++) {
>
> s += 1.0/(2.0*k-1.0);
>
> }
>
> ps = 2.0*s-el-1.386294361119891;
>
> }
>
> else {
>
> if (xa < 10.0) {
>
> n = 10-(int)xa;
>
> for (k=0;k
> s += 1.0/(xa+k);
>
> }
>
> xa += n;
>
> }
>
> x2 = 1.0/(xa*xa);
>
> ps = log(xa)-0.5/xa+x2*(((a[7]*x2+a[6])*x2+a[5])*x2+
>
> a[4])*x2+a[3])*x2+a[2])*x2+a[1])*x2+a[0]);
>
> ps -= s;
>
> }
>
> if (x < 0.0)
>
> ps = ps - M_PI*cos(M_PI*x)/sin(M_PI*x)-1.0/x;
>
> return ps;
>
> }
>
>
> However, when applicated the codes
>> digamma(-0.9)
> [1] -9.312644 OK!
>
> But when
>> dyn.load("psi.so")
>> out<-.C("psi", as.double(-0.9))
> Erro en .C("psi", as.double(-0.9)) : C symbol name "psi" not in load table
>
>> out
> Error: objeto "out" no encontrado
>
> More information on OS:
>> version
>_
> platform i486-pc-linux-gnu
> arch i486
> os linux-gnu
> system i486, linux-gnu
> status
> major 2
> minor 4.1
> year 2006
> month 12
> day18
> svn rev40228
> language R
> version.string R version 2.4.1 (2006-12-18)
>
>
>
> Many thanks for any insight or comments.
>
> Bernardo Lagos A.
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
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R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] the use of the .C function
Hi all,
here others doubts, when load and running the function
void gdot(double *x,double *y,int *n,double *output){
int i;
*output=0;
for (i=0;i<*n;i++){
*output+=x[i]*y[i];
}
}
as following
/examplesC$ R CMD SHLIB xby.c
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2
-c xby.c
-o xby.o
gcc -std=gnu99 -shared -o xby.so xby.o -L/usr/lib/R/lib -lR
/examplesC$ R
>x<-c(1,4,6,2)
>y<-c(3,2.4,1,9)
> dyn.load("xby.so")
>product<-.C("gdot",myx=as.double(x),myy=as.double(y),myn=as.integer(NROW(x)),myoutput=numeric())
*** caught segfault ***
address (nil), cause 'memory not mapped'
Traceback:
1: .C("gdot", myx = as.double(x), myy = as.double(y), myn =
as.integer(NROW(x)),
myoutput = numeric())
Possible actions:
1: abort (with core dump)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:
Selection:
Selection:
Can anybody answerme that happening with this Traceback?
Thanking you in advance,
Bernardo Lagos A.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] the use of the .C function
Dear All,
could someone please shed some light on the use of the .C or .Fortran function:
I am trying load and running on R the following function
// psi.cpp -- psi function for real arguments.
// Algorithms and coefficient values from "Computation of Special
// Functions", Zhang and Jin, John Wiley and Sons, 1996.
//
// (C) 2003, C. Bond. All rights reserved.
//
// Returns psi function for real argument 'x'.
// NOTE: Returns 1e308 for argument 0 or a negative integer.
//
#include // or ?
#include
#define el 0.5772156649015329
double psi(double x)
{
double s,ps,xa,x2;
int n,k;
static double a[] = {
-0.8e-01,
0.8e-02,
-0.39682539682539683e-02,
0.41667e-02,
-0.75757575757575758e-02,
0.21092796092796093e-01,
-0.8e-01,
0.4432598039215686};
xa = fabs(x);
s = 0.0;
if ((x == (int)x) && (x <= 0.0)) {
ps = 1e308;
return ps;
}
if (xa == (int)xa) {
n = xa;
for (k=1;kdigamma(-0.9)
[1] -9.312644 OK!
But when
> dyn.load("psi.so")
> out<-.C("psi", as.double(-0.9))
Erro en .C("psi", as.double(-0.9)) : C symbol name "psi" not in load table
> out
Error: objeto "out" no encontrado
More information on OS:
> version
_
platform i486-pc-linux-gnu
arch i486
os linux-gnu
system i486, linux-gnu
status
major 2
minor 4.1
year 2006
month 12
day18
svn rev40228
language R
version.string R version 2.4.1 (2006-12-18)
Many thanks for any insight or comments.
Bernardo Lagos A.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
