[R] *** caught segfault *** address 0x18, cause 'memory not mapped'
Hello R Community,
I've been run the following codes. However, I've been getting an
unusual segfault
that I'm unable to trace its origin. Please give me a light to
decipher the "caught segfault"
Thanks for you attention.
Bernardo.
> options(STERM='iESS', editor='emacsclient')
> rm(list = ls())
> > source("fgenIGLD.R")#RNG of IGLD(mu,b,sigma)
> > source("fsYUTH.R") #the fucntions Y,U,Tbbarran and H necessary to
> > calcualte the hat{b}
> > source("fMLEPFP.R") #the maximun likelihood profile estimation of
> > IGLD(mu,sigma)
> > source("f04P.R")#it to compute the mle, jacknife and bootstrap
> > source("fprofileloglik06.R") #the log-likelihood profile of IGLD(mu,sigma)
> > source("fmgfIGLD.R")#read the fmgfIGLD.R file defining the fmgfIGLD
> > function. It is useful for the prox.
> > source("f02.R")#here the function kappas.and.deriv(n,
> > source("fsimbiasIGLDP.R")#it to compute de bias of jacknife and
> > bootstrap
> > source("f01P.R") #in this is "fmainsimbiasP"
> > ptm<-proc.time()
> sink("out22031001.txt")
> > fmainsimbiasP(1,100)
proc.time()-ptm
*** caught segfault ***
address 0x18, cause 'memory not mapped'
Traceback:
1: nlm(f = fprof_deriv, x = x, p = parHInt, b = parFIX, hessian = T,
iterlim = 2000, check.analyticals = F, stepmax = 10)
2: doTryCatch(return(expr), name, parentenv, handler)
3: tryCatchOne(expr, names, parentenv, handlers[[1]])
4: tryCatchList(expr, classes, parentenv, handlers)
5: tryCatch(expr, error = function(e) {call <- conditionCall(e)
if (!is.null(call)) {if (identical(call[[1]],
quote(doTryCatch))) call <- sys.call(-4)dcall <-
deparse(call)[1]prefix <- paste("Error in", dcall, ": ")
LONG <- 75msg <- conditionMessage(e)sm <-
strsplit(msg, "\n")[[1]]if (14 + nchar(dcall, type = "w") +
nchar(sm[1], type = "w") > LONG) prefix <-
paste(prefix, "\n ", sep = "")}else prefix <- "Error : "
msg <- paste(prefix, conditionMessage(e), "\n", sep = "")
.Internal(seterrmessage(msg[1]))if (!silent &&
identical(getOption("show.error.messages"), TRUE)) {
cat(msg, file = stderr()).Internal(printDeferredWarnings())
}invisible(structure(msg, class = "try-error"))})
6: try(nlm(f = fprof_deriv, x = x, p = parHInt, b = parFIX, hessian =
T, iterlim = 2000, check.analyticals = F, stepmax = 10), silent =
T)
7: fMLEPFP(datanpboot, FALSE)
8: fboot.jack.mleP(data, B)
9: fsimbiasIGLDP(N[i], parH[, j], R, B)
10: fmainsimbiasP(1, 100)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: Selection: Selection: 2
Save workspace image? [y/n/c]: n
Process R:2 finished at Thu Mar 25 08:06:26 2010
>sessionInfo()
R version 2.7.2 beta (2008-08-16 r46368)
i486-pc-linux-gnu
locale:
LC_CTYPE=es_CL.UTF-8;LC_NUMERIC=C;LC_TIME=es_CL.UTF-8;LC_COLLATE=es_CL.UTF-8;LC_MONETARY=C;LC_MESSAGES=es_CL.UTF-8;LC_PAPER=es_CL.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=es_CL.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
> version
_
platform i486-pc-linux-gnu
arch i486
os linux-gnu
system i486, linux-gnu
status beta
major 2
minor 7.2
year 2008
month 08
day16
svn rev46368
language R
version.string R version 2.7.2 beta (2008-08-16 r46368)
__
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Re: [R] postscript, greek lellters
The problem is of the .dvi. It was arranged,using the solution of Baptiste.
Bernardo.
2010/1/9 bernardo lagos alvarez :
> Thank you, Dennis and Baptisite
>
> By including the. eps in my . tex and the compilation of the .tex,
> this does not generate the symbol of the greek letter.
>
> Bernardo.
>
> 2010/1/9 baptiste auguie :
>> Hi,
>>
>> Something like this maybe,
>>
>> plot.new()
>>
>> lab = expression(bar(T)*"("*-x*" ; "*alpha*")"-G*"("*x*" ; "*alpha*" ,
>> "*J*")")
>>
>> text(0.5,0.5,lab)
>>
>> ?plotmath
>>
>> HTH,
>>
>> baptiste
>>
>> 2010/1/8 bernardo lagos alvarez :
>>> Dear useRs,
>>>
>>> How can I, writting the correct greek letter using postscrip or pdf
>>> function.
>>>
>>> In my figures appears only the first letter (a of alpha, n of nu)
>>> when include the graphs in my .tex doxument. I am using
>>>
>>> title( expression(bar(T)(paste(-x,";",alpha))-G(paste(x,";",alpha,",",J
>>> title( expression(bar(T)(paste(-x,";"~alpha))-G(paste(x,";"~alpha,",",J
>>> title( expression(bar(T)(paste(-x,";"*alpha))-G(paste(x,";"*alpha,",",J,
>>> not work.
>>>
>>>>sessionInfo()
>>> R version 2.9.0 (2009-04-17)
>>> i386-pc-mingw32
>>>
>>> locale:
>>> LC_COLLATE=Spanish_Spain.1252;LC_CTYPE=Spanish_Spain.1252;LC_MONETARY=Spanish_Spain.1252;LC_NUMERIC=C;LC_TIME=Spanish_Spain.1252
>>>
>>> attached base packages:
>>> [1] stats graphics grDevices utils datasets methods base
>>>
>>>
>>> Thanks for your help,
>>>
>>> Bernardo.
>>>
>>> __
>>> 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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] postscript, greek lellters
Thank you, Dennis and Baptisite
By including the. eps in my . tex and the compilation of the .tex,
this does not generate the symbol of the greek letter.
Bernardo.
2010/1/9 baptiste auguie :
> Hi,
>
> Something like this maybe,
>
> plot.new()
>
> lab = expression(bar(T)*"("*-x*" ; "*alpha*")"-G*"("*x*" ; "*alpha*" ,
> "*J*")")
>
> text(0.5,0.5,lab)
>
> ?plotmath
>
> HTH,
>
> baptiste
>
> 2010/1/8 bernardo lagos alvarez :
>> Dear useRs,
>>
>> How can I, writting the correct greek letter using postscrip or pdf function.
>>
>> In my figures appears only the first letter (a of alpha, n of nu)
>> when include the graphs in my .tex doxument. I am using
>>
>> title( expression(bar(T)(paste(-x,";",alpha))-G(paste(x,";",alpha,",",J
>> title( expression(bar(T)(paste(-x,";"~alpha))-G(paste(x,";"~alpha,",",J
>> title( expression(bar(T)(paste(-x,";"*alpha))-G(paste(x,";"*alpha,",",J,
>> not work.
>>
>>>sessionInfo()
>> R version 2.9.0 (2009-04-17)
>> i386-pc-mingw32
>>
>> locale:
>> LC_COLLATE=Spanish_Spain.1252;LC_CTYPE=Spanish_Spain.1252;LC_MONETARY=Spanish_Spain.1252;LC_NUMERIC=C;LC_TIME=Spanish_Spain.1252
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>>
>> Thanks for your help,
>>
>> Bernardo.
>>
>> __
>> 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-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] postscript, greek lellters
Dear useRs, How can I, writting the correct greek letter using postscrip or pdf function. In my figures appears only the first letter (a of alpha, n of nu) when include the graphs in my .tex doxument. I am using title( expression(bar(T)(paste(-x,";",alpha))-G(paste(x,";",alpha,",",J title( expression(bar(T)(paste(-x,";"~alpha))-G(paste(x,";"~alpha,",",J title( expression(bar(T)(paste(-x,";"*alpha))-G(paste(x,";"*alpha,",",J, not work. >sessionInfo() R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=Spanish_Spain.1252;LC_CTYPE=Spanish_Spain.1252;LC_MONETARY=Spanish_Spain.1252;LC_NUMERIC=C;LC_TIME=Spanish_Spain.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base Thanks for your help, Bernardo. __ 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] please, a help or information
Hi users R list
I have been running some codes for some simulations. Such intensive
use runif, nlm and simpleError("...") functions no more. But still
remain the error that has been greatly discussed in the list of users
of R, the problem !crashes RGui.¡
"R for Windows GUI front-end has encountered a problem and needs to close. We
are sorry for the inconvenience."
here are the details of the crash:
AppName: rgui.exe AppVer: 2.81.47281.0 ModName: r.dll
ModVer: 2.81.47281.0 Offset: 000c1939
Anybody know a version of R, that is not making such errors?
I am waiting for your assistance as soon as possible.
Thanks you by your atention.
Here datails of windows and an installed R:
---
Nombre de host:TOSHIBA-USER
Nombre del sistema operativo: Microsoft Windows XP Professional
Versi¢n del sistema operativo: 5.1.2600 Service Pack 3
Compilaci¢n 2600
Fabricante del sistema operativo: Microsoft Corporation
Configuraci¢n del sistema operativo: Estaci¢n de trabajo independiente
Tipo de compilaci¢n del sistema operativo: Multiprocessor Free
Propiedad de: Bernardo
Organizaci¢n registrada:
Id. del producto: 76460-OEM-0011903-00111
Fecha de instalaci¢n original: 25/09/2006, 08:06:26 p.m.
Tiempo de actividad del sistema: 0 d¡as, 0 horas, 58
minutos, 26 segundos
Fabricante del sistema:TOSHIBA
Modelo el sistema: TECRA A7
Tipo de sistema: X86-based PC
Procesador(es):1 Procesadores instalados.
[01]: x86 Family 6 Model 14
Stepping 8 GenuineIntel ~1829 Mhz
Versi¢n del BIOS: TOSINV - 604
Directorio de Windows: C:\WINDOWS
Directorio de sistema: C:\WINDOWS\system32
Dispositivo de inicio: \Device\HarddiskVolume1
Configuraci¢n regional del sistema:0c0a
Idioma:040A
Zona horaria: N/D
Cantidad total de memoria f¡sica: 1,022 MB
Memoria f¡sica disponible: 396 MB
Memoria virtual: tama¤o m ximo:2,048 MB
Memoria virtual: disponible: 2,006 MB
-
release of R
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 8.1
year 2008
month 12
day22
svn rev47281
language R
version.string R version 2.8.1 (2008-12-22)
--
Bernardo.
University of Concepción.
Chile.
__
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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] arima function fix the coefficients
Dear all, How can I fix the all coefficients of ar and ma, except for the sigma? Hoping this helps, Bernardo __ 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] indexed expression
Hello expeRts,
I need generate symbolize the autocovariances matrix of a Gaussian
ARMA(1,1), for derivate it and evaluate.
I try this codes, but whitout sucess
vacv<-NULL
vacv[1]<-1-2*phi*theta-theta^2
vacv[2]<-(1-phi*theta)*(phi-theta)
vacv[3:n]<-acv[2]*(phi^(1:(n-2)))
facv<-list()
for(i in 1:2)
facv[[i]]<-deriv(y~vacv[i],c("phi","theta"),function(phi,theta){})
Erro en deriv.formula(y ~ vacv[i], c("phi", "theta"), function(phi, theta) { :
Función '`[`' no está en la tabla de derivadas
dfg<-for(n in 1:2) as.formula(sprintf("y~(1 - phi * theta) * (phi -
theta)*phi^ %d",n))
dfg
y ~ (1 - phi * theta) * (phi - theta) * phi^2
deriv(dfg[[1]],phi)
Erro en deriv.default(expr, namevec, function.arg, tag, hessian) :
nombres de variable inválidos
Give me a help, please.
Bernardo.
__
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[R] Error en nlm(logdgenexpn, p = c(vmomest[[1]], vmomest[[2]]), x = x.genexp, : valor no finito provisto por 'nlm'
Dear useRs,
I am analysing the behaviour of MLE for the two parameters of a kind
of exponential distribution, leaving as initial values the estimators
moments produced by the variation coefficient.
I do using simulations, giving them an accountant, r. But running my
codes remains a problem with the nlm function. To review details
wearing
On one of the lines put status
cond04<-is.finite(mle.nlm$minimum)
{
.
An Introduction to the Interactive Debugging Tools in R, Roger D.
Peng, UCLA Department of Statistics, August 28, 2002
The error message is delivered:
Error en nlm(logdgenexpn, p = c(vmomest[[1]], vmomest[[2]]), x = x.genexp, :
valor no finito provisto por 'nlm'
Además: Hubo 50 o más avisos (use warnings() para ver los primeros 50)
One possibility is to re-generate the data set that produces such
error, but not know how to do it.
Someone knows how to keep in an object the parameters of the
generator which produces such shows.
l can send codes for details.
Thank you for your attention.
Bernardo.
University of Concepción
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] messages from mle function
Dears useRs,
I am using the mle function but this gives me the follow erros that I
don't understand. Perhaps there is someone that can help me.
thank you for you atention.
Bernardo.
> erizo <- read.csv("Datos_Stokes_1.csv", header = TRUE)
> head(erizo)
EDAD TALLA
10 7.7
21 14.5
31 16.9
41 13.2
51 24.4
61 22.5
> TAN <- function(edad,f,c,a,d) (1/sqrt(f))*log(abs(2*f*(edad-c)+
> 2*sqrt((f^2)*((edad-c)^2)+f*a)))+d
> loglike = function(f,c,a,d) {
+ edad <- erizo$EDAD
+ LT<- erizo$TALLA
+ N <- length(edad)
+ sigma <- sum((LT - TAN(edad,f,c,a,d))^2) / N
+ logl <- (N/2)*log(sigma) + (sum((LT - TAN(edad,f,c,a,d))^2) / (2*sigma))
+ }
> ini.pars <- list(f=5.91e-05,c=-0.41732,a=0.009661,d=846.7179)
> library(stats4)
> erizo.mle <- mle(start= ini.pars, minuslogl = loglike, method="Nelder-Mead",
> control = list(maxit=1500, trace=TRUE))
Nelder-Mead direct search function minimizer
function value for initial parameters = 1159.477620
Scaled convergence tolerance is 1.72776e-05
Stepsize computed as 84.671790
BUILD 5 3165.307359 1159.477620
.
.
.
HI-REDUCTION 303 1158.377359 1158.377314
LO-REDUCTION 305 1158.377339 1158.377303
LO-REDUCTION 307 1158.377321 1158.377303
Exiting from Nelder Mead minimizer
309 function evaluations used
Error en optim(start, f, method = method, hessian = TRUE, ...) :
non-finite finite-difference value [1]
Además: Hubo 50 o más avisos (use warnings() para ver los primeros 50)
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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] matrix to gal object
useR's I need transform the matrix wdat [,1] [,2] [,3] [,4] [,5] [,6] [1,]010110 [2,]100110 [3,]000011 [4,]110010 [5,]111100 [6,]001000 to gal object. How I do with spdep? Thanks in advance for the help. Bernardo. University of Concepció. __ 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] rgdal for R.2.4.0?
Hi, Know anyone where to find the package rgdal for R.2.4.0? I would appreciate advice very much. Best wishes, Bernardo Lagos Department of Statistics University of Concepción __ 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
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.
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[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.
__
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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] psi using .C with R
Hi All, Anybody know as run the function psi on http://www.alglib.net/translator/dl/specialfunctions.psi.csharp.zip or http://www.alglib.net/translator/dl/specialfunctions.psi.cpp.zip using .C or .Fortran ? Thank for your attention. Bernardo. __ 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] .C("myHadamaProduct", xx, yy, nr, nc, out=as.double(rep(0.0, n)))
Konw anybody as run the function psi on
>>
>>
>> http://www.alglib.net/translator/dl/specialfunctions.psi.csharp.zip
>>
>> or
>>
>> http://www.alglib.net/translator/dl/specialfunctions.psi.cpp.zip
>>
>> using .C with R.
>> ?
>>
>> Thank for your attention.
>>
>> Bernardo.
>>
>>
>>> If anybody has an idea what is causing these problems I would be very
>>> much appreciate your help.
>>>
>>> I am running the exampls on
>>>
>>> http://www.stat.ubc.ca/~webmaste/howto/statsoftware/splusR.html#callFortran
>>>
>>> But
>>>
>>> res<-.C("myHadamaProduct", xx, yy, nr, nc, out=as.double(rep(0.0, n)))
>>> Erro en as.double(rep(0, n)) : objeto "n" no encontrado
>>>
>>>
>>> n=2 or n=5?
>>>
>>> Tanks verymuch.
>>>
>>> Bernardo.
__
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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] .C("myHadamaProduct", xx, yy, nr, nc, out=as.double(rep(0.0, n)))
>
> Konw anybody as run the function psi on
>
>
> http://www.alglib.net/translator/dl/specialfunctions.psi.csharp.zip
>
> or
>
> http://www.alglib.net/translator/dl/specialfunctions.psi.cpp.zip
>
> using .C with R.
> ?
>
> Thank for your attention.
>
> Bernardo.
>
>
>> If anybody has an idea what is causing these problems I would be very
>> much appreciate your help.
>>
>> I am running the exampls on
>>
>> http://www.stat.ubc.ca/~webmaste/howto/statsoftware/splusR.html#callFortran
>>
>> But
>>
>> res<-.C("myHadamaProduct", xx, yy, nr, nc, out=as.double(rep(0.0, n)))
>> Erro en as.double(rep(0, n)) : objeto "n" no encontrado
>>
>>
>> n=2 or n=5?
>>
>> Tanks verymuch.
>>
>> Bernardo.
>>
>
>
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