[Rd] package Geneland / Rgui under windows (PR#9964)
Full_Name: Gilles Guillot Version: 2.6.0 OS: windows XP professional Submission from: (NULL) (129.240.88.50) This sequence of command does not work in the R gui 2.6.0: library(Geneland) set.seed(1) data <- simdata(nindiv=200, coord.lim=c(0,1,0,1) , number.nuclei=5 , allele.numbers=rep(10,20), IBD=FALSE, npop=2, give.tess.grid=FALSE) geno <- data$genotypes coord <- t(data$coord.indiv) path.mcmc <- paste(tempdir(),"/",sep="") set.seed(1) mcmcFmodel(coordinates=coord, genotypes=geno, path.mcmc=path.mcmc, rate.max=10, delta.coord=0, npopmin=1, npopinit=5, npopmax=5, nb.nuclei.max=50, nit=500, thinning=1, freq.model="Dirichlet", varnpop=FALSE, spatial=TRUE) the call to mcmcFmodel freezes R The same sequence of command works in the R command line of R 2.6.0 and also in the R GUI of 2.5.1 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Calling C from Fortran
I would like to call C routines from Fortran under linux as suggested in
section 5.6 of
the "Writing R extensions" documentation.
I'm familiar with Fortran but not with C.
I understand the example provided in Fortran:
subroutine testit()
double precision normrnd, x
call rndstart()
x = normrnd()
call dblepr("X was", 5, x, 1)
call rndend()
end
but I don't understand the purpose of this C wrapper:
#include
void F77_SUB(rndstart)(void) { GetRNGstate(); }
void F77_SUB(rndend)(void) { PutRNGstate(); }
double F77_SUB(normrnd)(void) { return norm_rand(); }
neither how I should compile it.
Could anyone explain how I should compile and link
the C and Fortran files above, and call the Fortran subroutine from R.
Thanks,
Gilles
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[Rd] Calling C function from Fortran
Hi all,
the example in the R doc
and the hints from Shusong Jin , Ingmar Visser and Reid Huntsinger
(thanks all three) refer to the case where the function does not have
arguments.
I'm still looking for a proper sequence of commands
to call C functions with arguemnts from R.
Imagine I want to evaluate the gamma function.
I want to use the C function called by R.
(I guess it is the one corresponding to the source code
I found in the directory R-2.1.0/src/nmath/gamma.c
of the source distribution).
The following programs do not work (it returns fancy values)
#include
#include
void F77_SUB(mygammac)(double x, double y) { y = gammafn(x); }
subroutine mygammaf(x,y)
double precision x,y
call mygammac(x,y)
end
called in R through
x <- 3
y <- -999
res <- .Fortran("mygammaf",
as.double(x),
as.double(y))
While changing the C code into
#include
#include
void F77_SUB(mygammac)(double *x, double *y) { *y = gammafn(*x); }
seems to work fine.
But R-2.1.0/src/nmath/gamma.c does not need a pointer ?
What is wrong whit he first set of lines ?
What is the correct way to call the C function in R-2.1.0/src/nmath/gamma.c ?
Thanks in advance
Gilles
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Re: [Rd] Calling C from Fortran
Thanks for your reply.
Am I write if I say that the wrapper shoul be
double F77_SUB(mygammafn)(double *x) { return gammafn(*x); }
instead of
double F77_SUB(mygammafn)(double *x) { return gammafn(x); }
the first does not compile.
wrapper2.c: In function `mygammafn_':
wrapper2.c:6: error: incompatible type for argument 1 of `Rf_gammafn'
The second compiles and works fine.
But still, I find it very strange as the C function gammafn actually called
( as I can see from /R-2.1.0/src/nmath/gamma.c)
is not defined as
double gammafn(double *x)
but as
double gammafn(double x)
Am I missing something ?
Gilles
Le Mercredi 15 Juin 2005 17:06, vous avez écrit :
> I actually deleted a part of my reply, dealing with exactly that. Sorry!
> You need to declare the C wrapper to take a pointer to a double ("double
> *") rather than a double. C passes by value whereas Fortran passes by
> reference; in C you get this effect by passing a pointer to the value
> (which is also a value). So you want
>
> double F77_SUB(mygammafn)(double *x) { return gammafn(x); }
>
> That should work; if not let me know and I'll look more carefully at
> Fortran <-> C conventions.
>
> Reid Huntsinger
>
> -Original Message-
> From: Gilles GUILLOT [mailto:[EMAIL PROTECTED]
> Sent: Wednesday, June 15, 2005 3:50 AM
> To: Huntsinger, Reid
> Subject: Re: [Rd] Calling C from Fortran
>
>
> Thanks Reid!
> And now if I want to call a C function with arguments,
> e.g. to compute the gamma function at x,
> my C wrapper is:
>
> #include
> #include
> void F77_SUB(rndstart)(void) { GetRNGstate(); }
> void F77_SUB(rndend)(void) { PutRNGstate(); }
> double F77_SUB(normrnd)(void) { return norm_rand(); }
> double F77_SUB(mygammafn)(double x) { return gammafn(x); }
>
> And my Fortran is:
> subroutine testit()
> implicit none
> double precision normrnd, x, y, mygammafn
> call rndstart()
> x = dabs(normrnd())
> write(*,*) 'x=',x
> call rndend()
>
> y = mygammafn(x)
> write(*,*) 'y=',y
> end
>
> And it does not work, all calls of testit return the same y value.
> What is incorrect in my files ?
>
>
> Gilles
>
>
>
>
>
> ---
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--
_
Gilles GUILLOT
INRA -Département Mathématiques et Informatique Appliquées
Unité Mixte de Recherche INRA - INAPG - ENGREF
Institut National Agronomique de Paris-Grignon
16, rue Claude Bernard
75231 Paris cedex 5 France
phone 33 1 44 08 18 42
fax 33 1 44 08 16 66
http://www.inapg.fr/ens_rech/mathinfo/personnel/guillot/welcome.html
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[Rd] calling fortran functions CHOL and DPOTRF form Fortran
Hi all,
I'm working out some Fortran code for which
I want to compute the Choleski decomposition of a covariance matrix
in Fortran.
I tried to do it by two methods :
1) Calling the lapack function DPOTRF.
I can see the source code and check that my call is correct,
but it does not compile with:
system("R CMD SHLIB ~/main.f")
dyn.load("~/main.so")
I get:
Error in dyn.load(x, as.logical(local), as.logical(now)) :
unable to load shared library
[...]
undefined symbol: dpotrf_
Could anyone point out how to compile with such a call to lapack?
2) Calling the Fortran function CHOL
The previous combination of R CMD SHLIB and dyn.load
compiles fine but I would like to see the source code of this function
to check if my call is correct. I've not been able to find it in the R source
distribution.
Could anyone point the place of that file?
Thanks in advance,
Gilles
--
_________
Gilles GUILLOT
INRA -Département Mathématiques et Informatique Appliquées
Unité Mixte de Recherche INRA - INAPG - ENGREF
Institut National Agronomique de Paris-Grignon
16, rue Claude Bernard
75231 Paris cedex 5 France
phone 33 1 44 08 18 42
fax 33 1 44 08 16 66
http://www.inapg.fr/ens_rech/mathinfo/personnel/guillot/welcome.html
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[Rd] pb with dyn.load
Hi,
here are a couple of strange things happening with R.2.2.0 compiled
under Mandrake-10.1
At the begining of the story I have segmentation fault
using package RandomFields in conjuction with some Fortran code of mine
loaded with dyn.load.
One of my fortran programs contains a subroutine named fstat
Trying to trace , I simplified the sequence as much as possible
and I end up with the the simple fortran programs and R code atached
which give the result below.
Any explanation about the strange things below and what
I should do to avoid them would help.
Gilles
#
QUESTION 1:
[EMAIL PROTECTED] guillot]$ R
R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.2.0 (2005-10-06 r35749)
ISBN 3-900051-07-0
>system("R CMD SHLIB ~/tmp/test1.f")
g77 -fPIC -g -O2 -c /home/guillot/tmp/test1.f -o /home/guillot/tmp/test1.o
gcc -shared -L/usr/local/lib
-o /home/guillot/tmp/test1.so /home/guillot/tmp/test1.o -lg2c -lm -lgcc_s
> system("R CMD SHLIB ~/tmp/test2.f")
g77 -fPIC -g -O2 -c /home/guillot/tmp/test2.f -o /home/guillot/tmp/test2.o
gcc -shared -L/usr/local/lib
-o /home/guillot/tmp/test2.so /home/guillot/tmp/test2.o -lg2c -lm -lgcc_s
>
> is.loaded("sub")
[1] FALSE
> is.loaded("sub_")
[1] FALSE
>
## OK
> dyn.load("~/tmp/test1.so")
> is.loaded("sub")
[1] FALSE
> is.loaded("sub_")
[1] TRUE
>
## it seems it does not comply with the 'value' section of the help
## of function is.loaded:
## "it needs the
##name you would give to '.C' or '.Fortran' and *not* that remapped
##by 'symbol.C' and 'symbol.For'."
##
## am i missing something ?
> q()
QUESTION 2:
[EMAIL PROTECTED] guillot]$R
R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.2.0 (2005-10-06 r35749)
ISBN 3-900051-07-0
>is.loaded("fstat")
[1] FALSE
> is.loaded("fstat_")
[1] FALSE
> dyn.load("~/tmp/test1.so")
> is.loaded("fstat")
[1] FALSE
> is.loaded("fstat_")
[1] TRUE
## why ?
> dyn.load("~/tmp/test2.so")
> .Fortran(name="fstat",
+ as.integer(999),
+ as.integer(100),
+ as.integer(200))
[[1]]
[1] 1073913012
[[2]]
[1] 0
[[3]]
[1] 200
## pb in memory management ?
system("R CMD SHLIB ~/tmp/test1.f")
system("R CMD SHLIB ~/tmp/test2.f")
is.loaded("sub")
is.loaded("sub_")
dyn.load("~/tmp/test1.so")
is.loaded("sub")
is.loaded("sub_")
q()
R
s.loaded("fstat")
is.loaded("fstat_")
dyn.load("~/tmp/test1.so")
is.loaded("fstat")
is.loaded("fstat_")
dyn.load("~/tmp/test2.so")
.Fortran(name="fstat",
as.integer(999),
as.integer(100),
as.integer(200))
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[Rd] pb with dyn.load - fortran code now attached
Hi,
here are a couple of strange things happening with R.2.2.0 compiled
under Mandrake-10.1
At the begining of the story I have segmentation fault
using package RandomFields in conjuction with some Fortran code of mine
loaded with dyn.load.
One of my fortran programs contains a subroutine named fstat
Trying to trace , I simplified the sequence as much as possible
and I end up with the the simple fortran programs and R code atached
which give the result below.
Any explanation about the strange things below and what
I should do to avoid them would help.
Gilles
#
QUESTION 1:
[EMAIL PROTECTED] guillot]$ R
R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.2.0 (2005-10-06 r35749)
ISBN 3-900051-07-0
>system("R CMD SHLIB ~/tmp/test1.f")
g77 -fPIC -g -O2 -c /home/guillot/tmp/test1.f -o /home/guillot/tmp/test1.o
gcc -shared -L/usr/local/lib
-o /home/guillot/tmp/test1.so /home/guillot/tmp/test1.o -lg2c -lm -lgcc_s
> system("R CMD SHLIB ~/tmp/test2.f")
g77 -fPIC -g -O2 -c /home/guillot/tmp/test2.f -o /home/guillot/tmp/test2.o
gcc -shared -L/usr/local/lib
-o /home/guillot/tmp/test2.so /home/guillot/tmp/test2.o -lg2c -lm -lgcc_s
>
> is.loaded("sub")
[1] FALSE
> is.loaded("sub_")
[1] FALSE
>
## OK
> dyn.load("~/tmp/test1.so")
> is.loaded("sub")
[1] FALSE
> is.loaded("sub_")
[1] TRUE
>
## it seems it does not comply with the 'value' section of the help
## of function is.loaded:
## "it needs the
##name you would give to '.C' or '.Fortran' and *not* that remapped
##by 'symbol.C' and 'symbol.For'."
##
## am i missing something ?
> q()
QUESTION 2:
[EMAIL PROTECTED] guillot]$R
R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.2.0 (2005-10-06 r35749)
ISBN 3-900051-07-0
>is.loaded("fstat")
[1] FALSE
> is.loaded("fstat_")
[1] FALSE
> dyn.load("~/tmp/test1.so")
> is.loaded("fstat")
[1] FALSE
> is.loaded("fstat_")
[1] TRUE
## why ?
> dyn.load("~/tmp/test2.so")
> .Fortran(name="fstat",
+ as.integer(999),
+ as.integer(100),
+ as.integer(200))
[[1]]
[1] 1073913012
[[2]]
[1] 0
[[3]]
[1] 200
## pb in memory management ?
system("R CMD SHLIB ~/tmp/test1.f")
system("R CMD SHLIB ~/tmp/test2.f")
is.loaded("sub")
is.loaded("sub_")
dyn.load("~/tmp/test1.so")
is.loaded("sub")
is.loaded("sub_")
q()
R
s.loaded("fstat")
is.loaded("fstat_")
dyn.load("~/tmp/test1.so")
is.loaded("fstat")
is.loaded("fstat_")
dyn.load("~/tmp/test2.so")
.Fortran(name="fstat",
as.integer(999),
as.integer(100),
as.integer(200))
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Re: [Rd] pb with dyn.load - fortran code now attached
> > is.loaded("supsmu_")
>
> [1] FALSE
>
> > is.loaded("supsmu")
>
> [1] TRUE
>
> That is a Fortran entry point, and it complies with the description
> quoted.
>
> What is.loaded() needs depends on how the symbol would be found
> and so it is not much use.
OK, thanks.
But still
> is.loaded("fstat_")
[1] FALSE
> dyn.load("~/tmp/test1.so")
> is.loaded("fstat_")
[1] TRUE
while test1.so does not contains any reference to fstat.
How does anything like fstat happens to be loaded ?
Gilles
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[Rd] R build under mandriva 10.2
After upgrading from mandrake 10.1 to mandriva 10.2 I can't build shared archive with R 2.2.0 [EMAIL PROTECTED] src]$ R CMD SHLIB main.f sub.f wrapper.c gcc -shared -L/usr/local/lib -o main.so main.o sub.o wrapper.o -lg2c -lm -lgcc_s /usr//bin/ld: cannot find -lg2c collect2: ld returned 1 exit status make: *** [main.so] Erreur 1 I guess the information in http://finzi.psych.upenn.edu/R/Rhelp01/archive/5146.html are not relevant any longer. What is missing ? Gilles __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R binomial RNG stuck at 1 via Fortran call
Hi, I have some trouble with the result of a fortran function calling the R binomial RNG: The C function rbinom is wrapped as in the file attached. My main fortran program starts as call rndstart() and ends as call rndend() I happen to call the binomial RNG within a loop as b = ggrbinom(1.d0,0.5d0) write(*,*) 'b=',b In certain cases, after a few iterations in the loop, b get stuck at 1 Any hint to explain that would help. Gilles -- ÅÅÅ Gilles Guillot INRA - MIA Paris Currently working from Göteborg Stochastic Centre Eklandagatan 86 - Rum1439 Chalmers University of Technology SE 412-96 Göteborg Sweden Phone +46 31 772 3514 / Fax +46 31772 3508 www.inapg.inra.fr/ens_rech/mathinfo/personnel/guillot/welcome.html ÅÅÅ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R binomial RNG stuck at 1 via Fortran call
wrapper now attached -- ÅÅÅ Gilles Guillot INRA - MIA Paris Currently working from Göteborg Stochastic Centre Eklandagatan 86 - Rum1439 Chalmers University of Technology SE 412-96 Göteborg Sweden Phone +46 31 772 3514 / Fax +46 31772 3508 www.inapg.inra.fr/ens_rech/mathinfo/personnel/guillot/welcome.html ÅÅÅ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R binomial RNG stuck at 1 via Fortran call
wrapper now as part as the message,
sorry about previous mail
#include
#include
void F77_SUB(rndstart)(void)
{ GetRNGstate(); }
void F77_SUB(rndend)(void)
{ PutRNGstate(); }
double F77_SUB(ggrnorm)(double *mu, double *sigma)
{ return rnorm(*mu, *sigma); }
double F77_SUB(ggrexp)(double *scale)
{return rexp(*scale);}
double F77_SUB(ggrgam)(double *a, double *scale)
{return rgamma(*a, *scale);}
double F77_SUB(ggrunif)(double *a, double *b)
{return runif(*a, *b);}
double F77_SUB(ggrbinom)(double *n, double *p)
{return rbinom(*n, *p);}
double F77_SUB(ggrpois)(double *lambda)
{return rpois(*lambda);}
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[Rd] RNG stuck via Fortran call
Having not much success with my previous question I try to reformulate it:
I'm simulating a Markow chain in Fortran interfaced with R.
Each loop of my Fortran calls various functions of the R RNG through
the wrapper given below.
In a run of 100 iterations of the Markov kernel,
after 20 iterations, the RNG seems like frozen.
For example, the first call to the RNG in my loop is:
rpostlamb = ggrgam(dble(m),1.d0)
write(*,*) 'rpostlamb=',rpostlamb
after the 20th iteration, it will return the same value
rpostlamb= 1.24634557
for all the following interations.
Is there any suggestion of explanation for this strange fact ?
Thanks in advance
Gilles
R Version 2.2.0 compiled under Mandrake 10.1
#include
#include
/**/
/* random numbers */
/**/
void F77_SUB(rndstart)(void)
{ GetRNGstate(); }
void F77_SUB(rndend)(void)
{ PutRNGstate(); }
double F77_SUB(ggrnorm)(double *mu, double *sigma)
{ return rnorm(*mu, *sigma); }
double F77_SUB(ggrexp)(double *scale)
{return rexp(*scale);}
double F77_SUB(ggrgam)(double *a, double *scale)
{return rgamma(*a, *scale);}
double F77_SUB(ggrunif)(double *a, double *b)
{return runif(*a, *b);}
double F77_SUB(ggrbinom)(double *n, double *p)
{return rbinom(*n, *p);}
double F77_SUB(ggrpois)(double *lambda)
{return rpois(*lambda);}
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[Rd] package Geneland / Rgui under windows
Hi, I experienced a problem with the package Geneland under R 2.6.0 with windows XP professional. The commands below should simulate a dataset, then make an MCMC simulation stored in tempdir(). It works with R 2.5.1 (both GUI and command line) It works with the command line of R 2.6.0 but not with the R GUI of 2.6.0: no output file is created in tempdir() and R remains frozen. I reported it as a bug (PR#9964) but did not get any feed back. Thanks in advance for any help. Gilles set.seed(1) data <- simdata(nindiv=200, coord.lim=c(0,1,0,1) , number.nuclei=5 , allele.numbers=rep(10,20), IBD=FALSE, npop=2, give.tess.grid=FALSE) path.mcmc <- paste(tempdir(),"/",sep="") mcmcFmodel(coordinates= t(data$coord.indiv), genotypes=data$genotypes, path.mcmc=path.mcmc, rate.max=10, delta.coord=0, npopmin=1, npopinit=5, npopmax=5, nb.nuclei.max=50, nit=500, thinning=1, freq.model="Dirichlet", varnpop=FALSE, spatial=TRUE) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] package Geneland / Rgui under windows
I forgot to say that I was the package author. I suspected a bug of R as Geneland worked fine for two years and the problem popped up with the release of R 2.6.0 And I can't see any explanation. So, any clue would help. gilles > Gilles GUILLOT wrote: >> Hi, >> I experienced a problem with the package Geneland under R 2.6.0 >> with windows XP professional. >> >> The commands below should simulate a dataset, >> then make an MCMC simulation stored in tempdir(). >> >> It works with R 2.5.1 (both GUI and command line) >> It works with the command line of R 2.6.0 >> but not with the R GUI of 2.6.0: no output file is created in tempdir() >> and R remains frozen. >> I reported it as a bug >> (PR#9964) but did not get any feed back. > > I think the general rule-of-thumb is to contact the package author for > problems with individual packages. Many package authors read this list, > but there are probably some that do not. Sometimes problems with > individual packages are actually bugs in R, but I would say that this is > not usually the case. However, the package author is probably the best > person to make this judgment. > > Sean > _ Gilles GUILLOT INRA MIA Paris - FRANCE Now working from Matematisk Statistik Chalmers University of Technology, S-412 96 Göteborg, SWEDEN Rum: 3079 tel: +46 31 772 5338, Email: [EMAIL PROTECTED] http://www.inapg.inra.fr/ens_rech/mathinfo/personnel/guillot/welcome.html __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
