Re: [R] segfault caused by `icfit` in `interval` package
Please try with the R-2.12.0 ReleaseCandidate and thwe most recent
version of the package (please report its version number!).
If it still fails, it may be a good idea to contact the package
maintainer of interval first.
Uwe Ligges
On 10.10.2010 17:33, Yuliya Matveyeva wrote:
Dear R community,
I am using the R package `interval` in order to perform some modelling
tests of the
NPMLE convergence in the case of censoring. So all I am doing is drawing a
sample
from exponential distribution, making it a censored sample and computing the
NPMLE of
its distribution function. But when run on Linux Calculate 10.4 the program
keeps
crashing and reporting a segmentation fault
after the call to the `icfit` function when the sample size gets to 70.
When run on Windows 7 it seems to be fine.
That is why I am totally confused and have decided to ask for help.
I have attached the code I am running which results in a segmentation fault
if run on Linux Calculate.
It has the seed set to the value which leads to this error. But it is
important to note
that if the parameters used in the program and the seed are changed it
doesn't
necessarily crash.
Here is the description of my R version and OS:
sessionInfo()
R version 2.10.1 (2009-12-14)
i686-pc-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
After calling `icfit` the program quits with the following output
(I have replaced the output concerning the arguments passed to
initcomputeMLE by
arguments passed to initcomputeMLE so that the description of the
output wouldn't be too long):
*** caught segfault ***
address 0xc, cause 'memory not mapped'
Traceback:
1: .Call(ComputeMLEForR, R, B, max.inner, max.outer, tol)
2: computeMLE(R, B, max.inner = max.inner, max.outer = max.outer, tol =
tol)
3: initcomputeMLE( arguments passed to initcomputeMLE)
4: do.call(initfit, args = list(L = L, R = R, Lin = Lin, Rin = Rin, A =
A))
5: doTryCatch(return(expr), name, parentenv, handler)
6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
7: tryCatchList(expr, classes, parentenv, handlers)
8: tryCatch(expr, error = function(e) {call- conditionCall(e)if
(!is.null(call)) {if (identical(call[[1L]],
quote(doTryCatch))) call- sys.call(-4L)dcall-
deparse(call)[1L]prefix- paste(Error in, dcall, : )
LONG- 75Lmsg- conditionMessage(e)sm- strsplit(msg,
\n)[[1L]]w- 14L + nchar(dcall, type = w) + nchar(sm[1L], type
= w)if (is.na(w)) w- 14L + nchar(dcall, type = b)
+ nchar(sm[1L], type = b)if (w LONG)
prefix- paste(prefix, \n , sep = )}else prefix- Error :
msg- paste(prefix, conditionMessage(e), \n, sep = )
.Internal(seterrmessage(msg[1L]))if (!silent
identical(getOption(show.error.messages), TRUE)) {cat(msg,
file = stderr()).Internal(printDeferredWarnings())}
invisible(structure(msg, class = try-error))})
9: try(do.call(initfit, args = list(L = L, R = R, Lin = Lin, Rin = Rin,
A = A)))
10: icfit.default(L = left, R = right)
11: icfit(L = left, R = right)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
I would greatly appreciate any help provided.
Sincerely yours,
Yuliya Matveyeva.
__
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.
Re: [R] segfault caused by `icfit` in `interval` package
On the main site I have only found
R-2.11.1.tar.gzhttp://cran.gis-lab.info/src/base/R-2/R-2.11.1.tar.gzto
be the latest release (the latest stable release as far as I
understand
it). But unfortunately it doesn't pass the `make check` on my system (that
is probably the reason why the `emerge` command keeps telling me that my R
version is up-to-date). May be I should post a separate message about this
fact, but I am guessing I shouldn't because making a new release suitable
for all OS's is probably just a matter of time.
But before I write to the package maintainer directly could you please tell
if there might be a non-package-specific reason for a segfault in my case ?
Sincerely yours,
Yuliya Matveyeva.
2010/10/10 Uwe Ligges lig...@statistik.tu-dortmund.de
Please try with the R-2.12.0 ReleaseCandidate and thwe most recent version
of the package (please report its version number!).
If it still fails, it may be a good idea to contact the package maintainer
of interval first.
Uwe Ligges
On 10.10.2010 17:33, Yuliya Matveyeva wrote:
Dear R community,
I am using the R package `interval` in order to perform some modelling
tests of the
NPMLE convergence in the case of censoring. So all I am doing is drawing a
sample
from exponential distribution, making it a censored sample and computing
the
NPMLE of
its distribution function. But when run on Linux Calculate 10.4 the
program
keeps
crashing and reporting a segmentation fault
after the call to the `icfit` function when the sample size gets to 70.
When run on Windows 7 it seems to be fine.
That is why I am totally confused and have decided to ask for help.
I have attached the code I am running which results in a segmentation
fault
if run on Linux Calculate.
It has the seed set to the value which leads to this error. But it is
important to note
that if the parameters used in the program and the seed are changed it
doesn't
necessarily crash.
Here is the description of my R version and OS:
sessionInfo()
R version 2.10.1 (2009-12-14)
i686-pc-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
After calling `icfit` the program quits with the following output
(I have replaced the output concerning the arguments passed to
initcomputeMLE by
arguments passed to initcomputeMLE so that the description of
the
output wouldn't be too long):
*** caught segfault ***
address 0xc, cause 'memory not mapped'
Traceback:
1: .Call(ComputeMLEForR, R, B, max.inner, max.outer, tol)
2: computeMLE(R, B, max.inner = max.inner, max.outer = max.outer, tol
=
tol)
3: initcomputeMLE( arguments passed to initcomputeMLE)
4: do.call(initfit, args = list(L = L, R = R, Lin = Lin, Rin = Rin, A
=
A))
5: doTryCatch(return(expr), name, parentenv, handler)
6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
7: tryCatchList(expr, classes, parentenv, handlers)
8: tryCatch(expr, error = function(e) {call- conditionCall(e)if
(!is.null(call)) {if (identical(call[[1L]],
quote(doTryCatch))) call- sys.call(-4L)dcall-
deparse(call)[1L]prefix- paste(Error in, dcall, : )
LONG- 75Lmsg- conditionMessage(e)sm- strsplit(msg,
\n)[[1L]]w- 14L + nchar(dcall, type = w) + nchar(sm[1L], type
= w)if (is.na(w)) w- 14L + nchar(dcall, type =
b)
+ nchar(sm[1L], type = b)if (w LONG)
prefix- paste(prefix, \n , sep = )}else prefix- Error :
msg- paste(prefix, conditionMessage(e), \n, sep = )
.Internal(seterrmessage(msg[1L]))if (!silent
identical(getOption(show.error.messages), TRUE)) {
cat(msg,
file = stderr()).Internal(printDeferredWarnings())}
invisible(structure(msg, class = try-error))})
9: try(do.call(initfit, args = list(L = L, R = R, Lin = Lin, Rin = Rin,
A = A)))
10: icfit.default(L = left, R = right)
11: icfit(L = left, R = right)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
I would greatly appreciate any help provided.
Sincerely yours,
Yuliya Matveyeva.
__
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.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE
Re: [R] segfault caused by `icfit` in `interval` package
The package version is Version: 1.0-1.0 as reported by the
packageDescription(interval).
2010/10/10 Uwe Ligges lig...@statistik.tu-dortmund.de
Please try with the R-2.12.0 ReleaseCandidate and thwe most recent version
of the package (please report its version number!).
If it still fails, it may be a good idea to contact the package maintainer
of interval first.
Uwe Ligges
On 10.10.2010 17:33, Yuliya Matveyeva wrote:
Dear R community,
I am using the R package `interval` in order to perform some modelling
tests of the
NPMLE convergence in the case of censoring. So all I am doing is drawing a
sample
from exponential distribution, making it a censored sample and computing
the
NPMLE of
its distribution function. But when run on Linux Calculate 10.4 the
program
keeps
crashing and reporting a segmentation fault
after the call to the `icfit` function when the sample size gets to 70.
When run on Windows 7 it seems to be fine.
That is why I am totally confused and have decided to ask for help.
I have attached the code I am running which results in a segmentation
fault
if run on Linux Calculate.
It has the seed set to the value which leads to this error. But it is
important to note
that if the parameters used in the program and the seed are changed it
doesn't
necessarily crash.
Here is the description of my R version and OS:
sessionInfo()
R version 2.10.1 (2009-12-14)
i686-pc-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
After calling `icfit` the program quits with the following output
(I have replaced the output concerning the arguments passed to
initcomputeMLE by
arguments passed to initcomputeMLE so that the description of
the
output wouldn't be too long):
*** caught segfault ***
address 0xc, cause 'memory not mapped'
Traceback:
1: .Call(ComputeMLEForR, R, B, max.inner, max.outer, tol)
2: computeMLE(R, B, max.inner = max.inner, max.outer = max.outer, tol
=
tol)
3: initcomputeMLE( arguments passed to initcomputeMLE)
4: do.call(initfit, args = list(L = L, R = R, Lin = Lin, Rin = Rin, A
=
A))
5: doTryCatch(return(expr), name, parentenv, handler)
6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
7: tryCatchList(expr, classes, parentenv, handlers)
8: tryCatch(expr, error = function(e) {call- conditionCall(e)if
(!is.null(call)) {if (identical(call[[1L]],
quote(doTryCatch))) call- sys.call(-4L)dcall-
deparse(call)[1L]prefix- paste(Error in, dcall, : )
LONG- 75Lmsg- conditionMessage(e)sm- strsplit(msg,
\n)[[1L]]w- 14L + nchar(dcall, type = w) + nchar(sm[1L], type
= w)if (is.na(w)) w- 14L + nchar(dcall, type =
b)
+ nchar(sm[1L], type = b)if (w LONG)
prefix- paste(prefix, \n , sep = )}else prefix- Error :
msg- paste(prefix, conditionMessage(e), \n, sep = )
.Internal(seterrmessage(msg[1L]))if (!silent
identical(getOption(show.error.messages), TRUE)) {
cat(msg,
file = stderr()).Internal(printDeferredWarnings())}
invisible(structure(msg, class = try-error))})
9: try(do.call(initfit, args = list(L = L, R = R, Lin = Lin, Rin = Rin,
A = A)))
10: icfit.default(L = left, R = right)
11: icfit(L = left, R = right)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
I would greatly appreciate any help provided.
Sincerely yours,
Yuliya Matveyeva.
__
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.
[[alternative HTML version deleted]]
__
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.
Re: [R] segfault caused by `icfit` in `interval` package
On 10.10.2010 19:10, Yuliya Matveyeva wrote:
On the main site I have only found
R-2.11.1.tar.gzhttp://cran.gis-lab.info/src/base/R-2/R-2.11.1.tar.gzto
be the latest release (the latest stable release as far as I
understand
it). But unfortunately it doesn't pass the `make check` on my system (that
is probably the reason why the `emerge` command keeps telling me that my R
version is up-to-date). May be I should post a separate message about this
fact, but I am guessing I shouldn't because making a new release suitable
for all OS's is probably just a matter of time.
But before I write to the package maintainer directly could you please tell
if there might be a non-package-specific reason for a segfault in my case ?
Probably it is the package, but we would need a reproducible example to
check it.
Uwe Ligges
Sincerely yours,
Yuliya Matveyeva.
2010/10/10 Uwe Liggeslig...@statistik.tu-dortmund.de
Please try with the R-2.12.0 ReleaseCandidate and thwe most recent version
of the package (please report its version number!).
If it still fails, it may be a good idea to contact the package maintainer
of interval first.
Uwe Ligges
On 10.10.2010 17:33, Yuliya Matveyeva wrote:
Dear R community,
I am using the R package `interval` in order to perform some modelling
tests of the
NPMLE convergence in the case of censoring. So all I am doing is drawing a
sample
from exponential distribution, making it a censored sample and computing
the
NPMLE of
its distribution function. But when run on Linux Calculate 10.4 the
program
keeps
crashing and reporting a segmentation fault
after the call to the `icfit` function when the sample size gets to 70.
When run on Windows 7 it seems to be fine.
That is why I am totally confused and have decided to ask for help.
I have attached the code I am running which results in a segmentation
fault
if run on Linux Calculate.
It has the seed set to the value which leads to this error. But it is
important to note
that if the parameters used in the program and the seed are changed it
doesn't
necessarily crash.
Here is the description of my R version and OS:
sessionInfo()
R version 2.10.1 (2009-12-14)
i686-pc-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
After calling `icfit` the program quits with the following output
(I have replaced the output concerning the arguments passed to
initcomputeMLE by
arguments passed to initcomputeMLE so that the description of
the
output wouldn't be too long):
*** caught segfault ***
address 0xc, cause 'memory not mapped'
Traceback:
1: .Call(ComputeMLEForR, R, B, max.inner, max.outer, tol)
2: computeMLE(R, B, max.inner = max.inner, max.outer = max.outer, tol
=
tol)
3: initcomputeMLE( arguments passed to initcomputeMLE)
4: do.call(initfit, args = list(L = L, R = R, Lin = Lin, Rin = Rin, A
=
A))
5: doTryCatch(return(expr), name, parentenv, handler)
6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
7: tryCatchList(expr, classes, parentenv, handlers)
8: tryCatch(expr, error = function(e) {call- conditionCall(e)if
(!is.null(call)) {if (identical(call[[1L]],
quote(doTryCatch))) call- sys.call(-4L)dcall-
deparse(call)[1L]prefix- paste(Error in, dcall, : )
LONG- 75Lmsg- conditionMessage(e)sm- strsplit(msg,
\n)[[1L]]w- 14L + nchar(dcall, type = w) + nchar(sm[1L], type
= w)if (is.na(w)) w- 14L + nchar(dcall, type =
b)
+ nchar(sm[1L], type = b)if (w LONG)
prefix- paste(prefix, \n , sep = )}else prefix- Error :
msg- paste(prefix, conditionMessage(e), \n, sep = )
.Internal(seterrmessage(msg[1L]))if (!silent
identical(getOption(show.error.messages), TRUE)) {
cat(msg,
file = stderr()).Internal(printDeferredWarnings())}
invisible(structure(msg, class = try-error))})
9: try(do.call(initfit, args = list(L = L, R = R, Lin = Lin, Rin = Rin,
A = A)))
10: icfit.default(L = left, R = right)
11: icfit(L = left, R = right)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
I would greatly appreciate any help provided.
Sincerely yours,
Yuliya Matveyeva.
__
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.
[[alternative HTML version deleted]]
__
