[R] R Crashes with .C
Hi everyone,
I'm a beginner in R and I'm trying to load a .dll file, named dll.dll, that's
written in C, into R. It seems to work, now I want to use the functions that
are stored in the .dll file and I encounter problems.
I've searched for a solution or other method in manuals, here and on google.
Would be very thankful if I could get a suggestion of what to use or any idea!
My code:
setwd("C:/Users/MyUser/R")
dyn.load("dll.dll")
is.loaded("DLL_FUNK")
# For some reason True with capital letters, not in lower case
output <- .C("DLL_FUNK", in9 = as.integer(7))
#output # R Crashes before I can write this.
# R Crashes
# In outdata.txt: "in-value= 139375128"
The function should return a number, 1955. But I can't seem to get to that
value. What am I doing wrong?
Update with code (Fortran runned as C), this is the code in dll.dll:
subroutine dll_funk(in9)
implicit none
!+++
!*** Declarations: variables, functions
!+++
integer(4) :: in9
!integer :: in9
! Definitions of variables in the external function calls
!!dec$ attributes c,alias :'dll_funk' :: dll_funk
!dec$ attributes dllexport:: dll_funk
!dec$ attributes value:: in9
open(194,file='outdata.txt')
write(194,*) 'in-value=', in9
! in9 = 1955
close(194)
end subroutine
!end function
So now when it runs, R crashes but before it writes to my file (outdata.txt)
but it't not my number, maybe some kind of address...
Another question, do you recommend me to run the code with .C and from C run
the Fortran code or is it better to run it with .Fortran with only Fortran
code? It seems like .Fortran have problem handling strings, or that's what I
understood from: Interface func .C and
.Fortran
Thanks for your time!
Best regards,
David
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[R] R crashes upon changing directories, loading files, etc.
Hello, I am experiencing an issue, repeatedly, which began today. Example code: load(file.choose()) ##sometimes it crashes here/ endless spinner/ other times I can get through. or: i go up to options at the top to set wd, or select ‘file’ - ‘open’ and it will do the same thing. I found a page where people were indicating they had this issue, but there was no one responding with a fix. see below: bugs.r-project.org/bugzilla/show_bug.cgi?id=14240 I am running : R version 3.1.3 (2015-03-09) -- Smooth Sidewalk Platform: x86_64-apple-darwin13.4.0 (64-bit) On OS X 10.10 Any help/ direction is appreciated. ~Nicole [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] R crashes upon changing directories, loading files, etc.
It seems this is not R but R.app (the separate project providing an OS X console: see the 'R Installation and Administration' manual). If so, the only appropriate list is R-sig-Mac (see the posting guide). On 06/04/2015 19:14, Nicole Ford wrote: Hello, I am experiencing an issue, repeatedly, which began today. Example code: load(file.choose()) ##sometimes it crashes here/ endless spinner/ other times I can get through. or: i go up to options at the top to set wd, or select ‘file’ - ‘open’ and it will do the same thing. I found a page where people were indicating they had this issue, but there was no one responding with a fix. see below: bugs.r-project.org/bugzilla/show_bug.cgi?id=14240 Which is about Windows in 2010, and does have a response. I am running : R version 3.1.3 (2015-03-09) -- Smooth Sidewalk Platform: x86_64-apple-darwin13.4.0 (64-bit) On OS X 10.10 Any help/ direction is appreciated. ~Nicole [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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. -- Brian D. Ripley, rip...@stats.ox.ac.uk Emeritus Professor of Applied Statistics, University of Oxford 1 South Parks Road, Oxford OX1 3TG, UK __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] R crashes upon changing directories, loading files, etc.
On 06 Apr 2015, at 22:17 , Prof Brian Ripley rip...@stats.ox.ac.uk wrote: Nicole Ford wrote: [snip] I found a page where people were indicating they had this issue, but there was no one responding with a fix. see below: bugs.r-project.org/bugzilla/show_bug.cgi?id=14240 Which is about Windows in 2010, and does have a response. It might be noted, though, that this is not the first report from someone having this sort of issue on Yosemite. See e.g. Christopher Swan's note from April 4 on R-sig-Mac. (This sort of issue tends to be slow to fix. We need to have a developer who can reproduce the issue _and_ is capable of debugging Mac GUI code.) -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] R crashes upon changing directories, loading files, etc.
Yes, it definitely is the GUI as it works just fine when I load data using a file path. I can work around it, thankfully, but it would be great if this issue could be fixed. I suspected Yosemite as it's given me multiple problems since install. Thanks for the input. Hopefully someone with that skill set might see this and the other thread you mentioned. ~Nicole Sent from my iPhone On Apr 6, 2015, at 5:26 PM, peter dalgaard pda...@gmail.com wrote: On 06 Apr 2015, at 22:17 , Prof Brian Ripley rip...@stats.ox.ac.uk wrote: Nicole Ford wrote: [snip] I found a page where people were indicating they had this issue, but there was no one responding with a fix. see below: bugs.r-project.org/bugzilla/show_bug.cgi?id=14240 Which is about Windows in 2010, and does have a response. It might be noted, though, that this is not the first report from someone having this sort of issue on Yosemite. See e.g. Christopher Swan's note from April 4 on R-sig-Mac. (This sort of issue tends to be slow to fix. We need to have a developer who can reproduce the issue _and_ is capable of debugging Mac GUI code.) -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] R crashes when I run rgeos::gDistance
Adrian Torchiana adrian.torchiana at gmail.com writes: Hi, This is my first post to R-help. I'm having trouble getting rgeos to work. R-help is arguably too general to help, please ask questions of this kind on R-sig-geo. Info on the server and packages I'm using: ... $ *rpm -qa | grep geos* geos-devel-3.4.2-1.rhel6.x86_64 geos-3.4.2-1.rhel6.x86_64 How did you install rgeos (from source)? Are other versions of GEOS present not installed as RPMs? ... $ *R -q* *library(rgeos)* rgeos version: 0.3-8, (SVN revision 460) GEOS runtime version: 3.4.2-CAPI-1.8.2 r3921 Polygon checking: TRUE *example(gDistance)* gDstnc pt1 = readWKT(POINT(0.5 0.5)) gDstnc pt2 = readWKT(POINT(2 2)) gDstnc p1 = readWKT(POLYGON((0 0,1 0,1 1,0 1,0 0))) gDstnc p2 = readWKT(POLYGON((2 0,3 1,4 0,2 0))) gDstnc gDistance(pt1,pt2) R: GeometryComponentFilter.cpp:34: virtual void geos::geom::GeometryComponentFilter::filter_ro(const geos::geom::Geometry*): Assertion `0' failed. Aborted (core dumped) rgeos is tested regularly and frequently, so the issue here is on your platform, I'm afraid. I'd like to be able to use the gDistance function. What should I do to fix this? The simplest way is to install GEOS from source, because you avoid relying on upstream packaging. This will however interfere with other software that may depend on your existing GEOS. Please let me know if any additional information would be helpful. Thank you for your time, Adrian [[alternative HTML version deleted]] Please do not post HTML. Roger __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] R crashes when I run rgeos::gDistance
Hi, This is my first post to R-help. I'm having trouble getting rgeos to work. Info on the server and packages I'm using: $ *uname -a* Linux some-server.somewhere.com 2.6.32-431.11.2.el6.x86_64 #1 SMP Tue Mar 25 19:59:55 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux $ *R --version* R version 3.0.2 (2013-09-25) -- Frisbee Sailing Copyright (C) 2013 The R Foundation for Statistical Computing Platform: x86_64-redhat-linux-gnu (64-bit) $ *lsb_release -a* LSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch Distributor ID: CentOS Description: CentOS release 6.5 (Final) Release: 6.5 Codename: Final $ *rpm -qa | grep geos* geos-devel-3.4.2-1.rhel6.x86_64 geos-3.4.2-1.rhel6.x86_64 $ *rpm -qa | grep gdal* gdal-1.9.2-6.rhel6.x86_64 gdal-libs-1.9.2-6.rhel6.x86_64 gdal-devel-1.9.2-6.rhel6.x86_64 gdal-java-1.9.2-6.rhel6.x86_64 $ *R -q* *library(rgeos)* rgeos version: 0.3-8, (SVN revision 460) GEOS runtime version: 3.4.2-CAPI-1.8.2 r3921 Polygon checking: TRUE *example(gDistance)* gDstnc pt1 = readWKT(POINT(0.5 0.5)) gDstnc pt2 = readWKT(POINT(2 2)) gDstnc p1 = readWKT(POLYGON((0 0,1 0,1 1,0 1,0 0))) gDstnc p2 = readWKT(POLYGON((2 0,3 1,4 0,2 0))) gDstnc gDistance(pt1,pt2) R: GeometryComponentFilter.cpp:34: virtual void geos::geom::GeometryComponentFilter::filter_ro(const geos::geom::Geometry*): Assertion `0' failed. Aborted (core dumped) I'd like to be able to use the gDistance function. What should I do to fix this? Please let me know if any additional information would be helpful. Thank you for your time, Adrian [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] R crashes with Error in UseMethod(depth) when resizing ggplot windows
Hello everyone, Quite frequently I encounter crashes when resizing ggplot windows. The error message is always as follows: Error in UseMethod(depth) : no applicable method for 'depth' applied to an object of class NULL Process R exited abnormally with code 255 at Tue Feb 24 21:51:18 2015 The error seems to occur rather unpredictably when I do several resizings, e.g. moving a plot window from one monitor to another using Windows+Arrow Key several times. It only seems to happen when plotting rather large data frames. I was about to file this as a ggplot2 issue, but then I realized that I can't reproduce it using RStudio - normally, I use emacs/ESS (on Windows 7). So maybe this is a bug related to the plot engine...? The problem is that I can't even do a traceback(), since R is crashed. How should I proceed? Are there any other options to retrieve valuable debug information? Kind regards, Eike __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] R crashes with Error in UseMethod(depth) when resizing ggplot windows
On 24/02/2015 4:13 PM, Eike Petersen wrote: Hello everyone, Quite frequently I encounter crashes when resizing ggplot windows. The error message is always as follows: Error in UseMethod(depth) : no applicable method for 'depth' applied to an object of class NULL Process R exited abnormally with code 255 at Tue Feb 24 21:51:18 2015 The error seems to occur rather unpredictably when I do several resizings, e.g. moving a plot window from one monitor to another using Windows+Arrow Key several times. It only seems to happen when plotting rather large data frames. I was about to file this as a ggplot2 issue, but then I realized that I can't reproduce it using RStudio - normally, I use emacs/ESS (on Windows 7). So maybe this is a bug related to the plot engine...? The problem is that I can't even do a traceback(), since R is crashed. How should I proceed? Are there any other options to retrieve valuable debug information? It's not easy, but you can run R under a debugger, and it will show you the location of the crash. As far as I know only gdb supports debugging R on Windows (there's a copy in the Rtools collection), but perhaps that will change now that Microsoft has purchased Revolution Analytics. Duncan Murdoch __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] R crashes with memory errors on a 256GB machine (and system shoes only 60GB usage)
Le vendredi 03 janvier 2014 à 22:40 +0200, Xebar Saram a écrit : Hi again and thank you all for the answers i need to add that im a relatively R neewb so i apologize in advance i started R with the --vanilla option and ran gc() this is the output i get: gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 182236 9.8 407500 21.8 35 18.7 Vcells 277896 2.2 786432 6.0 785897 6.0 also this is the memory.profile() memory.profile() NULL symbolpairlist closure environment promise 15611 866952277 3144175 language special builtinchar logical integer 21636 44 63763614574 11089 double complex character ... anylist 782 1 20934 0 08023 expressionbytecode externalptr weakref raw S4 162711272 364 365 831 im running on linux (arch linux) and 'free' shows this: zeltak@zuni ~ ↳ free -h total used free sharedbuffers cached Mem: 251G99G 152G66G 249M84G -/+ buffers/cache:14G 237G Swap: 0B 0B 0B im not running any parrallel stuff at all milan: how does one know if the memory is fragmented? AFAIK you cannot. One thing you can do is compare the report from gc() to was the Linux top command says about the actual memory used by the R process (see the RES column, hit '' three times to sort on it). But are you saying that with the situation you describe above (i.e. 152G of free RAM), you get errors about memory allocation? Regards thank you all again i really appreciate the help best Z On Thu, Jan 2, 2014 at 10:35 PM, Ben Bolker bbol...@gmail.com wrote: Xebar Saram zeltakc at gmail.com writes: Hi All, I have a terrible issue i cant seem to debug which is halting my work completely. I have R 3.02 installed on a linux machine (arch linux-latest) which I built specifically for running high memory use models. the system is a 16 core, 256 GB RAM machine. it worked well at the start but in the recent days i keep getting errors and crashes regarding memory use, such as cannot create vector size of XXX, not enough memory etc when looking at top (linux system monitor) i see i barley scrape the 60 GB of ram (out of 256GB) i really don't know how to debug this and my whole work is halted due to this so any help would be greatly appreciated I'm very sympathetic, but it will be almost impossible to debug this sort of a problem remotely, without a reproducible example. The only guess that I can make, if you *really* are running *exactly* the same code as you previously ran successfully, is that you might have some very large objects hidden away in a saved workspace in a .RData file that's being loaded automatically ... I would check whether gc(), memory.profile(), etc. give sensible results in a clean R session (R --vanilla). Ben Bolker __ 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. __ 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] R crashes with memory errors on a 256GB machine (and system shoes only 60GB usage)
Hi again and thank you all for the answers i need to add that im a relatively R neewb so i apologize in advance i started R with the --vanilla option and ran gc() this is the output i get: gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 182236 9.8 407500 21.8 35 18.7 Vcells 277896 2.2 786432 6.0 785897 6.0 also this is the memory.profile() memory.profile() NULL symbolpairlist closure environment promise 15611 866952277 3144175 language special builtinchar logical integer 21636 44 63763614574 11089 double complex character ... anylist 782 1 20934 0 08023 expressionbytecode externalptr weakref raw S4 162711272 364 365 831 im running on linux (arch linux) and 'free' shows this: zeltak@zuni ~ â³ free -h total used free sharedbuffers cached Mem: 251G99G 152G66G 249M84G -/+ buffers/cache:14G 237G Swap: 0B 0B 0B im not running any parrallel stuff at all milan: how does one know if the memory is fragmented? thank you all again i really appreciate the help best Z On Thu, Jan 2, 2014 at 10:35 PM, Ben Bolker bbol...@gmail.com wrote: Xebar Saram zeltakc at gmail.com writes: Hi All, I have a terrible issue i cant seem to debug which is halting my work completely. I have R 3.02 installed on a linux machine (arch linux-latest) which I built specifically for running high memory use models. the system is a 16 core, 256 GB RAM machine. it worked well at the start but in the recent days i keep getting errors and crashes regarding memory use, such as cannot create vector size of XXX, not enough memory etc when looking at top (linux system monitor) i see i barley scrape the 60 GB of ram (out of 256GB) i really don't know how to debug this and my whole work is halted due to this so any help would be greatly appreciated I'm very sympathetic, but it will be almost impossible to debug this sort of a problem remotely, without a reproducible example. The only guess that I can make, if you *really* are running *exactly* the same code as you previously ran successfully, is that you might have some very large objects hidden away in a saved workspace in a .RData file that's being loaded automatically ... I would check whether gc(), memory.profile(), etc. give sensible results in a clean R session (R --vanilla). Ben Bolker __ 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] R crashes with memory errors on a 256GB machine (and system shoes only 60GB usage)
It would help to know the sizes of the objects that have in your
workspace and also provide the 10 prior lines of your script at the
point of the error so that we can see what you are trying to do. The
following commands will list out the sizes of the objects:
cbind(sapply(ls(), function(x){
object.size(get(x))
}))
copy and paste it into the command line when the error occurs.
Jim Holtman
Data Munger Guru
What is the problem that you are trying to solve?
Tell me what you want to do, not how you want to do it.
On Fri, Jan 3, 2014 at 3:40 PM, Xebar Saram zelt...@gmail.com wrote:
Hi again and thank you all for the answers
i need to add that im a relatively R neewb so i apologize in advance
i started R with the --vanilla option and ran gc()
this is the output i get:
gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 182236 9.8 407500 21.8 35 18.7
Vcells 277896 2.2 786432 6.0 785897 6.0
also this is the memory.profile()
memory.profile()
NULL symbolpairlist closure environment promise
15611 866952277 3144175
language special builtinchar logical integer
21636 44 63763614574 11089
double complex character ... anylist
782 1 20934 0 08023
expressionbytecode externalptr weakref raw S4
162711272 364 365 831
im running on linux (arch linux) and 'free' shows this:
zeltak@zuni ~ ↳ free -h
total used free sharedbuffers cached
Mem: 251G99G 152G66G 249M84G
-/+ buffers/cache:14G 237G
Swap: 0B 0B 0B
im not running any parrallel stuff at all
milan: how does one know if the memory is fragmented?
thank you all again i really appreciate the help
best
Z
On Thu, Jan 2, 2014 at 10:35 PM, Ben Bolker bbol...@gmail.com wrote:
Xebar Saram zeltakc at gmail.com writes:
Hi All,
I have a terrible issue i cant seem to debug which is halting my work
completely. I have R 3.02 installed on a linux machine (arch
linux-latest)
which I built specifically for running high memory use models. the system
is a 16 core, 256 GB RAM machine. it worked well at the start but in the
recent days i keep getting errors and crashes regarding memory use, such
as
cannot create vector size of XXX, not enough memory etc
when looking at top (linux system monitor) i see i barley scrape the 60
GB
of ram (out of 256GB)
i really don't know how to debug this and my whole work is halted due to
this so any help would be greatly appreciated
I'm very sympathetic, but it will be almost impossible to debug
this sort of a problem remotely, without a reproducible example.
The only guess that I can make, if you *really* are running *exactly*
the same code as you previously ran successfully, is that you might
have some very large objects hidden away in a saved workspace in a
.RData file that's being loaded automatically ...
I would check whether gc(), memory.profile(), etc. give sensible results
in a clean R session (R --vanilla).
Ben Bolker
__
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.
__
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] R crashes with memory errors on a 256GB machine (and system shoes only 60GB usage)
Xebar Saram zeltakc at gmail.com writes: Hi All, I have a terrible issue i cant seem to debug which is halting my work completely. I have R 3.02 installed on a linux machine (arch linux-latest) which I built specifically for running high memory use models. the system is a 16 core, 256 GB RAM machine. it worked well at the start but in the recent days i keep getting errors and crashes regarding memory use, such as cannot create vector size of XXX, not enough memory etc when looking at top (linux system monitor) i see i barley scrape the 60 GB of ram (out of 256GB) i really don't know how to debug this and my whole work is halted due to this so any help would be greatly appreciated I'm very sympathetic, but it will be almost impossible to debug this sort of a problem remotely, without a reproducible example. The only guess that I can make, if you *really* are running *exactly* the same code as you previously ran successfully, is that you might have some very large objects hidden away in a saved workspace in a .RData file that's being loaded automatically ... I would check whether gc(), memory.profile(), etc. give sensible results in a clean R session (R --vanilla). Ben Bolker __ 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] R crashes with memory errors on a 256GB machine (and system shoes only 60GB usage)
Describing the problem would help a lot more. For example, if you were using some of the parallel processing options in R, this can make extra copies of objects and drive memory usage up very quickly. Max On Thu, Jan 2, 2014 at 3:35 PM, Ben Bolker bbol...@gmail.com wrote: Xebar Saram zeltakc at gmail.com writes: Hi All, I have a terrible issue i cant seem to debug which is halting my work completely. I have R 3.02 installed on a linux machine (arch linux-latest) which I built specifically for running high memory use models. the system is a 16 core, 256 GB RAM machine. it worked well at the start but in the recent days i keep getting errors and crashes regarding memory use, such as cannot create vector size of XXX, not enough memory etc when looking at top (linux system monitor) i see i barley scrape the 60 GB of ram (out of 256GB) i really don't know how to debug this and my whole work is halted due to this so any help would be greatly appreciated I'm very sympathetic, but it will be almost impossible to debug this sort of a problem remotely, without a reproducible example. The only guess that I can make, if you *really* are running *exactly* the same code as you previously ran successfully, is that you might have some very large objects hidden away in a saved workspace in a .RData file that's being loaded automatically ... I would check whether gc(), memory.profile(), etc. give sensible results in a clean R session (R --vanilla). Ben Bolker __ 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. -- Max [[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] R crashes with memory errors on a 256GB machine (and system shoes only 60GB usage)
Le jeudi 02 janvier 2014 à 09:07 +0200, Xebar Saram a écrit : Hi All, I have a terrible issue i cant seem to debug which is halting my work completely. I have R 3.02 installed on a linux machine (arch linux-latest) which I built specifically for running high memory use models. the system is a 16 core, 256 GB RAM machine. it worked well at the start but in the recent days i keep getting errors and crashes regarding memory use, such as cannot create vector size of XXX, not enough memory etc when looking at top (linux system monitor) i see i barley scrape the 60 GB of ram (out of 256GB) i really don't know how to debug this and my whole work is halted due to this so any help would be greatly appreciated One important thing to note is that while the memory use may appear to be low, if the memory is fragmented, R may not be able to allocate a *contiguous* memory area for a big vector (you didn't tell us how big it was). In that case, AFAIK the only solution is to restart R (saving the session or objects you want to keep). Regards __ 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] R crashes with memory errors on a 256GB machine (and system shoes only 60GB usage)
Hi All, I have a terrible issue i cant seem to debug which is halting my work completely. I have R 3.02 installed on a linux machine (arch linux-latest) which I built specifically for running high memory use models. the system is a 16 core, 256 GB RAM machine. it worked well at the start but in the recent days i keep getting errors and crashes regarding memory use, such as cannot create vector size of XXX, not enough memory etc when looking at top (linux system monitor) i see i barley scrape the 60 GB of ram (out of 256GB) i really don't know how to debug this and my whole work is halted due to this so any help would be greatly appreciated Best wishes Z [[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.
[R] R crashes with kud-kernelUD(data, h=LSCV) script
Hi, I am looking to perform a kernel density analysis in R, following the script that a friend of mine is using successfully. However, unlike for her, when I enter kud-kernelUD(data, h=LSCV), R crashes and closes every time. This does not happen when I perform a different kernel analysis (kud-kernelUD(data)).. I have tried to un-install and re-install R, but it still crashes.. The script I am using is as follows: library(adehabitatHR) library(maptools) data-read.csv(sa 4 trips 13F.csv) xy = data[c(X, Y)] id-data[,c(ID)] coordinates(data) = c(X, Y) class(data) kud-kernelUD(data) # this works fine kud-kernelUD(data, h=LSCV) # this causes R to crash Any suggestions would be greatly appreciated. Many thanks for your time, Kind regards, -Amanda- [[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] R crashes with kud-kernelUD(data, h=LSCV) script
Hi Amanda, I can't reproduce this without your data set. Would it be possible for you to give us dput(head(data, 20)) if you need further help? Also, if you could supply the output of sessionInfo()? That's often helpful for anything that crashes [that term means many things to different people so if you could be more specific that'd be great as well] Finally, you may with to get in touch with the maintainer of the adehabitatHR package directly. You can get contact info by typing maintainer(adehabitatHR) at your prompt. Best, Michael On Thu, Jun 21, 2012 at 6:25 AM, Amanda Kuepfer amandakuep...@yahoo.com wrote: Hi, I am looking to perform a kernel density analysis in R, following the script that a friend of mine is using successfully. However, unlike for her, when I enter kud-kernelUD(data, h=LSCV), R crashes and closes every time. This does not happen when I perform a different kernel analysis (kud-kernelUD(data)).. I have tried to un-install and re-install R, but it still crashes.. The script I am using is as follows: library(adehabitatHR) library(maptools) data-read.csv(sa 4 trips 13F.csv) xy = data[c(X, Y)] id-data[,c(ID)] coordinates(data) = c(X, Y) class(data) kud-kernelUD(data) # this works fine kud-kernelUD(data, h=LSCV) # this causes R to crash Any suggestions would be greatly appreciated. Many thanks for your time, Kind regards, -Amanda- [[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. __ 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] R crashes with kud-kernelUD(data, h=LSCV) script
On 2012-06-21 04:25, Amanda Kuepfer wrote:
Hi,
I am looking to perform a kernel density analysis in R, following the script that a friend of mine is
using successfully. However, unlike for her, when I enterkud-kernelUD(data,
h=LSCV), R crashes and closes every time. This does not happen when I perform a different
kernel analysis (kud-kernelUD(data))..
I have tried to un-install and re-install R, but it still crashes..
The script I am using is as follows:
library(adehabitatHR)
library(maptools)
data-read.csv(sa 4 trips 13F.csv)
xy = data[c(X, Y)]
id-data[,c(ID)]
coordinates(data) = c(X, Y)
class(data)
kud-kernelUD(data) # this works fine
kud-kernelUD(data, h=LSCV) # this causes R to crash
In both cases, shouldn't that be 'xy' instead of 'data'?
Presumably, your data.frame 'data' (bad name) contains
at least one more column ('ID'). Or why did you define
'xy' and then not use it?
Peter Ehlers
Any suggestions would be greatly appreciated.
Many thanks for your time,
Kind regards,
-Amanda-
[[alternative HTML version deleted]]
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Re: [R] R crashes due to stats.dll
Dnia 2012-03-18 01:15, Ted Stankowich pisze: Hello! I've been running a looped AIC analysis using several modules including ape, nlme, and MuMIn, and during one particularly long analysis, R (ver 2.14.12) crashes several minutes into the routine with the simple message R for windows GUI front-end has stopped working. I'm using a brand new laptop with Windows 7, i7 processor, 8GB RAM. I've tried it on both the 64 bit and 32 bit versions of R. Using the 64 bit version, the analysis makes it through a few iterations before it crashes (maybe about 20-25 min into the test). ... Does anyone have any idea what might be going wrong here? I assume you're using MuMIn::dredge. If so, most likely the model fitting function with some combination of parameters causes the crash. You can use 'trace = TRUE' argument for 'dredge' to find out which model is it. To see the output after the crash, use either R in console (not RGUI) or divert the output to a file with 'sink'. kamil __ 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] R crashes due to stats.dll
Hello! I've been running a looped AIC analysis using several modules including ape, nlme, and MuMIn, and during one particularly long analysis, R (ver 2.14.12) crashes several minutes into the routine with the simple message R for windows GUI front-end has stopped working. I'm using a brand new laptop with Windows 7, i7 processor, 8GB RAM. I've tried it on both the 64 bit and 32 bit versions of R. Using the 64 bit version, the analysis makes it through a few iterations before it crashes (maybe about 20-25 min into the test). The event viewer provides this information every time it crashes: Faulting application name: Rgui.exe, version: 2.142.58522.0, time stamp: 0x4f4e7196 Faulting module name: stats.dll, version: 2.142.58522.0, time stamp: 0x4f4e72c0 Exception code: 0xc005 Does anyone have any idea what might be going wrong here? Thanks in advance! __ 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] R crashes due to stats.dll
On 18.03.2012 01:15, Ted Stankowich wrote: Hello! I've been running a looped AIC analysis using several modules including ape, nlme, and MuMIn, and during one particularly long analysis, R (ver 2.14.12) crashes several minutes into the routine with the simple message R for windows GUI front-end has stopped working. I'm using a brand new laptop with Windows 7, i7 processor, 8GB RAM. I've tried it on both the 64 bit and 32 bit versions of R. Using the 64 bit version, the analysis makes it through a few iterations before it crashes (maybe about 20-25 min into the test). The event viewer provides this information every time it crashes: Faulting application name: Rgui.exe, version: 2.142.58522.0, time stamp: 0x4f4e7196 Faulting module name: stats.dll, version: 2.142.58522.0, time stamp: 0x4f4e72c0 Exception code: 0xc005 Does anyone have any idea what might be going wrong here? Not unless you specify a minimal reproducible example that causes the crash, preferrably without using contribted packages. Otherwise the reason for the crash may be caused by them. Uwe Ligges Thanks in advance! __ 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] R crashes due to stats.dll
On 12-03-17 8:15 PM, Ted Stankowich wrote: Hello! I've been running a looped AIC analysis using several modules including ape, nlme, and MuMIn, and during one particularly long analysis, R (ver 2.14.12) crashes several minutes into the routine with the simple message R for windows GUI front-end has stopped working. I'm using a brand new laptop with Windows 7, i7 processor, 8GB RAM. I've tried it on both the 64 bit and 32 bit versions of R. Using the 64 bit version, the analysis makes it through a few iterations before it crashes (maybe about 20-25 min into the test). The event viewer provides this information every time it crashes: Faulting application name: Rgui.exe, version: 2.142.58522.0, time stamp: 0x4f4e7196 Faulting module name: stats.dll, version: 2.142.58522.0, time stamp: 0x4f4e72c0 Exception code: 0xc005 Does anyone have any idea what might be going wrong here? Most likely some function is writing to memory it doesn't own. This might be a bug in the stats package, but I would guess it is much more likely to be a bug in one of the other packages you used, and stats is crashing when it comes across the damage. Debugging this sort of thing is quite hard in Windows: you need to build R with debugging information and run it under a compatible version of a debugger (e.g. gdb). I'd recommend trying the code on a Linux or MacOS system, where you will still need to make sure the debugger is installed, but you tend to get more informative messages from it. Duncan Murdoch __ 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] R crashes when communicating with JAGS
There is a thread on this topic already:
http://finzi.psych.upenn.edu/Rhelp10/2010-August/250934.html
I'm rather mystified by a similar problem and wondering whether I've
overlooked something obvious. I'm running with latest versions of R and
all packages, and latest version of JAGS running under Windows 7.
Here's the problem. I have some source code. It's given below - standard
stuff - seeds example from BUGS volume 1. I'm using R2WinBUGS only to
create the model file, and R2jags as a front end to JAGS. I have the
same problem whether or not I use R2jags.
1. If I start RGUI and source the code from a source file. R crashes
when it tries to execute jags().
Problem Event Name: APPCRASH
Application Name: Rgui.exe
Application Version: 2.131.56322.0
Application Timestamp:4e171fac
Fault Module Name:StackHash_486a
Fault Module Version: 6.1.7601.17514
Fault Module Timestamp: 4ce7ba58
Exception Code: c374
Exception Offset: 000ce653
OS Version: 6.1.7601.2.1.0.768.3
Locale ID:2057
Additional Information 1: 486a
Additional Information 2: 486a33f7a181da7ba2feae88b7ee12b6
Additional Information 3: 9e02
Additional Information 4: 9e02b3fab8ac2ab41c0e936dfef5c6d4
2. If I start RGUI and cut and paste the code from a source file.
Everything works fine.
3. If, after (2) I source the code - and other examples from source
files - everything works fine.
This seems to indicate that there is some kind of initialization which
needs to happen before JAGS will work; that this initialization is
carried out when typing commands into the console, but not carried out
when sourcing identical commands from a source file.
I have tried delaying issuing the jags command when sourcing (using
readline()) in case the issue was with readiness of the bugs model being
written to file; but the crash still happens with any such delay.
I'd be most grateful for tips to circumvent this behaviour.
Cheers,
David
Here's the test code:
#---
require(R2WinBUGS)
require(rjags)
require(R2jags)
## write model file:
print(list.modules())
write.model(con=blah.bug,model=function() {
for( i in 1 : N ) {
r[i] ~ dbin(p[i],n[i])
b[i] ~ dnorm(0.0,tau)
logit(p[i]) - alpha0 + alpha1 * x1[i] + alpha2 * x2[i] +
alpha12 * x1[i] * x2[i] + b[i]
}
alpha0 ~ dnorm(0.0,1.0E-6)
alpha1 ~ dnorm(0.0,1.0E-6)
alpha2 ~ dnorm(0.0,1.0E-6)
alpha12 ~ dnorm(0.0,1.0E-6)
tau ~ dgamma(0.001,0.001)
sigma - 1 / sqrt(tau)
})
g-jags(model.file='blah.bug',
data = list(r = c(10, 23, 23, 26, 17, 5, 53, 55, 32, 46,
10, 8, 10, 8, 23, 0, 3, 22, 15, 32, 3),
n = c(39, 62, 81, 51, 39, 6, 74, 72, 51, 79, 13, 16, 30, 28, 45,
4, 12, 41, 30, 51, 7),
x1 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1),
x2 = c(0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 1, 1,
1, 1),
N = 21),
parameters=c('alpha0', 'alpha1','alpha2','alpha12','tau'),
inits=list(alpha0 = 0, alpha1 = 0, alpha2 = 0, alpha12 =
0, tau = 1) ,
n.iter=1)
#---
--
Dr David Wooff,
Director, Statistics and Mathematics Consultancy Unit,
Senior Lecturer in Statistics, University of Durham.
Department of Mathematical Sciences, Science Laboratories,
South Road, Durham, DH1 3LE, UK. email: d.a.wo...@dur.ac.uk
Tel. 0191 334 3121, Fax 0191 334 3051.
Web: http://maths.dur.ac.uk/stats/people/daw/daw.html
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] R crashes when communicating with JAGS
Works for me with JAGS 3.1.0.
Uwe Ligges
On 11.08.2011 14:09, David Wooff wrote:
There is a thread on this topic already:
http://finzi.psych.upenn.edu/Rhelp10/2010-August/250934.html
I'm rather mystified by a similar problem and wondering whether I've
overlooked something obvious. I'm running with latest versions of R and
all packages, and latest version of JAGS running under Windows 7.
Here's the problem. I have some source code. It's given below - standard
stuff - seeds example from BUGS volume 1. I'm using R2WinBUGS only to
create the model file, and R2jags as a front end to JAGS. I have the
same problem whether or not I use R2jags.
1. If I start RGUI and source the code from a source file. R crashes
when it tries to execute jags().
Problem Event Name: APPCRASH
Application Name: Rgui.exe
Application Version: 2.131.56322.0
Application Timestamp: 4e171fac
Fault Module Name: StackHash_486a
Fault Module Version: 6.1.7601.17514
Fault Module Timestamp: 4ce7ba58
Exception Code: c374
Exception Offset: 000ce653
OS Version: 6.1.7601.2.1.0.768.3
Locale ID: 2057
Additional Information 1: 486a
Additional Information 2: 486a33f7a181da7ba2feae88b7ee12b6
Additional Information 3: 9e02
Additional Information 4: 9e02b3fab8ac2ab41c0e936dfef5c6d4
2. If I start RGUI and cut and paste the code from a source file.
Everything works fine.
3. If, after (2) I source the code - and other examples from source
files - everything works fine.
This seems to indicate that there is some kind of initialization which
needs to happen before JAGS will work; that this initialization is
carried out when typing commands into the console, but not carried out
when sourcing identical commands from a source file.
I have tried delaying issuing the jags command when sourcing (using
readline()) in case the issue was with readiness of the bugs model being
written to file; but the crash still happens with any such delay.
I'd be most grateful for tips to circumvent this behaviour.
Cheers,
David
Here's the test code:
#---
require(R2WinBUGS)
require(rjags)
require(R2jags)
## write model file:
print(list.modules())
write.model(con=blah.bug,model=function() {
for( i in 1 : N ) {
r[i] ~ dbin(p[i],n[i])
b[i] ~ dnorm(0.0,tau)
logit(p[i]) - alpha0 + alpha1 * x1[i] + alpha2 * x2[i] +
alpha12 * x1[i] * x2[i] + b[i]
}
alpha0 ~ dnorm(0.0,1.0E-6)
alpha1 ~ dnorm(0.0,1.0E-6)
alpha2 ~ dnorm(0.0,1.0E-6)
alpha12 ~ dnorm(0.0,1.0E-6)
tau ~ dgamma(0.001,0.001)
sigma - 1 / sqrt(tau)
})
g-jags(model.file='blah.bug',
data = list(r = c(10, 23, 23, 26, 17, 5, 53, 55, 32, 46, 10, 8, 10, 8,
23, 0, 3, 22, 15, 32, 3),
n = c(39, 62, 81, 51, 39, 6, 74, 72, 51, 79, 13, 16, 30, 28, 45, 4, 12,
41, 30, 51, 7),
x1 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1),
x2 = c(0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1),
N = 21),
parameters=c('alpha0', 'alpha1','alpha2','alpha12','tau'),
inits=list(alpha0 = 0, alpha1 = 0, alpha2 = 0, alpha12 = 0, tau = 1) ,
n.iter=1)
#---
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[R] R crashes with 'nlme' and corStruct
Hello, I would like to fit correlation structures with nlme, but R crashes. My data is similar to the growth of orange trees example from Pinheiro and Bates (2000), but data are not equally spaced in time, as the last observation is taken after 6 days ( and not 2 as the others). This is the code I'm using: library(nlme) DO-c(0.107,0.118,0.271,0.431,0.597,0.909,1.259,1.688,2.301, 0.107,0.150,0.200,0.325,0.425,0.641,0.860,1.329,1.780, 0.101,0.159,0.204,0.484,0.663,1.019,1.335,1.880,1.927) mtime-rep(c(seq(1,15,2),21),3) Subject-rep(1:3,each=9) dataset-data.frame(DO=DO, mtime=mtime, Subject=Subject) Joy - groupedData( DO ~ mtime | Subject, data = dataset) m0-nlsList( DO ~ SSlogis(mtime, asym, xmid, scal), data = Joy) m1.nlme-nlme(m0) m3.nlme-update(m1.nlme,random=(asym~1), weights = varPower() ) m4.nlme - update( m3.nlme, corr = corExp(form = ~ mtime) ) # R crashes m5.nlme - update( m3.nlme, corr = corRatio(form = ~ mtime) ) # R crashes m6.nlme - update( m3.nlme, corr = corSpher(form = ~ mtime) ) # R crashes m7.nlme - update( m3.nlme, corr = corLin(form = ~ mtime) ) # R crashes m8.nlme - update( m3.nlme, corr = corGaus(form = ~ mtime) ) # R crashes *sessionInfo():* R version 2.13.0 (2011-04-13) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 LC_MONETARY=French_France.1252 LC_NUMERIC=C LC_TIME=French_France.1252 attached base packages: [1] grDevices datasets splines graphics stats tcltk utils methods base other attached packages: [1] nlme_3.1-100svSocket_0.9-51 TinnR_1.0.3 R2HTML_2.2 Hmisc_3.8-3 survival_2.36-5 loaded via a namespace (and not attached): [1] cluster_1.14.0 drc_2.1-4 grid_2.13.0 lattice_0.19-23 svMisc_0.9-61 tools_2.13.0 Thank you for your help, Andreea Borla [[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] R Crashes when using large matrices (Ubuntu 11.04)
On Fri, 3 Jun 2011, Matias Salibian-Barrera wrote: Hello, This simple SVD calculation (commands are copied immediately below) crashes on my Ubuntu machine (R 2.13.0). However it works fine on my Windows 7 machine, so I suspect there's a problem with (my?) Ubuntu and / or R. Can anybody else reproduce it (with Ubuntu 11.04)? Thanks in advance. From the traceback, the error appears to be in LAPACK or BLAS. There is no evidence here that 'R crashes' rather than one of those crashed R. You don't tell us whether you compiled R yourself or used someone else's pre-compiled distribution -- if the latter, ask on r-sig-debian as this is most likely a problem with the distribution, since Debian/Ubuntu builds normally replace R's LAPACK/BLAS with that from the OS. It works correctly on a vanilla R build on i686 Fedora 14. p - 500 n - 300 set.seed(1234) x - matrix(rnorm(n*p), n, p) sih - var(x) b - svd(sih) produces: *** caught illegal operation *** address 0x42b8c9, cause 'illegal operand' Traceback: 1: .Call(La_svd, jobu, jobv, x, double(min(n, p)), u, v, dgsedd, PACKAGE = base) 2: La.svd(x, nu, nv) 3: svd(sih) I'm using Ubuntu 11.04 and version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major 2 minor 13.0 year 2011 month 04 day 13 svn rev 55427 language R version.string R version 2.13.0 (2011-04-13) Thanks, Matias __ 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. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595__ 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] R Crashes when using large matrices (Ubuntu 11.04)
On Ubuntu 10.04 it ran fine, albeit in a machine with lots of memory, it seems to work fine. Here's the output: rm(list=ls()) gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 131881 7.1 35 18.7 35 18.7 Vcells 128838 1.0 786432 6.0 559631 4.3 p - 500 n - 300 set.seed(1234) x - matrix(rnorm(n*p), n, p) sih - var(x) b - svd(sih) gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 133536 7.2 35 18.7 35 18.7 Vcells 1030006 7.92644909 20.2 2536523 19.4 sessionInfo() R version 2.13.0 (2011-04-13) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8LC_COLLATE=en_US.utf8 [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 [7] LC_PAPER=en_US.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base Maybe another 11.04 glitch. JN On 06/04/2011 06:00 AM, r-help-requ...@r-project.org wrote: Message: 93 Date: Fri, 3 Jun 2011 18:55:06 -0700 (PDT) From: Matias Salibian-Barrera msalib...@yahoo.ca To: R-help@r-project.org R-help@r-project.org Subject: [R] R Crashes when using large matrices (Ubuntu 11.04) Message-ID: 75655.88533...@web161614.mail.bf1.yahoo.com Content-Type: text/plain; charset=iso-8859-1 This simple SVD calculation (commands are copied immediately below) crashes on my Ubuntu machine (R 2.13.0). However it works fine on my Windows 7 machine, so I suspect there's a problem with (my?) Ubuntu and / or R. Can anybody else reproduce it (with Ubuntu 11.04)? Thanks in advance. p - 500 n - 300 set.seed(1234) x - matrix(rnorm(n*p), n, p) sih - var(x) b - svd(sih) __ 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] R Crashes when using large matrices (Ubuntu 11.04)
On Fri, Jun 3, 2011 at 7:03 PM, Matias Salibian-Barrera msalib...@yahoo.ca wrote: Hello, This simple SVD calculation (commands are copied immediately below) crashes on my Ubuntu machine (R 2.13.0). However it works fine on my Windows 7 machine, so I suspect there's a problem with (my?) Ubuntu and / or R. Can anybody else reproduce it (with Ubuntu 11.04)? Thanks in advance. Works fine for me with Ubuntu 11.04 (amd_64) and the pre-compiled R-2.13.0 $ wajig list r-base-core ii r-base-core2.13.0-2natty0 GNU R core of statistical computation and graphics system n - 300 set.seed(1234) x - matrix(rnorm(n*p), n, p) sih - var(x) b - svd(sih) str(b) List of 3 $ d: num [1:500] 5.04 4.94 4.92 4.83 4.82 ... $ u: num [1:500, 1:500] -0.03663 0.05414 0.00182 -0.02847 -0.00117 ... $ v: num [1:500, 1:500] -0.03663 0.05414 0.00182 -0.02847 -0.00117 ... sessionInfo() R version 2.13.0 (2011-04-13) Platform: x86_64-pc-linux-gnu (64-bit) 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 __ 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] R Crashes when using large matrices (Ubuntu 11.04)
Hello, This simple SVD calculation (commands are copied immediately below) crashes on my Ubuntu machine (R 2.13.0). However it works fine on my Windows 7 machine, so I suspect there's a problem with (my?) Ubuntu and / or R. Can anybody else reproduce it (with Ubuntu 11.04)? Thanks in advance. p - 500 n - 300 set.seed(1234) x - matrix(rnorm(n*p), n, p) sih - var(x) b - svd(sih) produces: *** caught illegal operation *** address 0x42b8c9, cause 'illegal operand' Traceback: 1: .Call(La_svd, jobu, jobv, x, double(min(n, p)), u, v, dgsedd, PACKAGE = base) 2: La.svd(x, nu, nv) 3: svd(sih) I'm using Ubuntu 11.04 and version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major 2 minor 13.0 year 2011 month 04 day 13 svn rev 55427 language R version.string R version 2.13.0 (2011-04-13) Thanks, Matias __ 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] R Crashes when using large matrices (Ubuntu 11.04)
Sorry for re-posting, but the original one ended up inside a previous and unrelated thread. -- Matias - Hello, This simple SVD calculation (commands are copied immediately below) crashes on my Ubuntu machine (R 2.13.0). However it works fine on my Windows 7 machine, so I suspect there's a problem with (my?) Ubuntu and / or R. Can anybody else reproduce it (with Ubuntu 11.04)? Thanks in advance. p - 500 n - 300 set.seed(1234) x - matrix(rnorm(n*p), n, p) sih - var(x) b - svd(sih) produces: *** caught illegal operation *** address 0x42b8c9, cause 'illegal operand' Traceback: 1: .Call(La_svd, jobu, jobv, x, double(min(n, p)), u, v, dgsedd, PACKAGE = base) 2: La.svd(x, nu, nv) 3: svd(sih) I'm using Ubuntu 11.04 and version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major 2 minor 13.0 year 2011 month 04 day 13 svn rev 55427 language R version.string R version 2.13.0 (2011-04-13) Thanks, Matias __ 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] R crashes when loading rgl package before minqa package
Hi!
I have been using R for two years, but since last week I have a problem with
rgl, using R 2.12 on Ubuntu 10.04.
In fact, when I load rgl with library(), before any other command, I have
the following error message.
Could anybody help me?
Thanks in advance,
#
+ library(rgl)
*** caught segfault ***
address 0x4, cause 'memory not mapped'
Traceback:
1: .Call(rgl_init, initValue)
2: rgl.init(initValue)
3: fun(...)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(fun(...), error = identity)
8: runHook(.onLoad, package, env, package.lib, package)
9: loadNamespace(package, c(which.lib.loc, lib.loc), keep.source =
keep.source)
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: 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))})
14: try({ns - loadNamespace(package, c(which.lib.loc, lib.loc),
keep.source = keep.source)dataPath - file.path(which.lib.loc, package,
data)env - attachNamespace(ns, pos = pos, dataPath = dataPath,
deps)})
15: library(rgl)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
--- interrupted ---
##
---
Andrea Boneschi
Politecnico di Milano
--
View this message in context:
http://r.789695.n4.nabble.com/R-crashes-when-loading-rgl-package-before-minqa-package-tp2719252p3005193.html
Sent from the R help mailing list archive at Nabble.com.
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Re: [R] R crashes when loading rgl package before minqa package
Gaspard Lequeux Gaspard.Lequeux at biomath.ugent.be writes:
Calling newuoa (from the minqa package) makes R crash when
the package rgl
is loaded first. This however only on certain selected data.
The data used for testing (saved to 'bugs.R'):
xvals =
c(1,2,4,5,7,8,9,10,11,12,14,15,16,18,19,21,22,23,24,25,26,
27,28,29,30,31,32,33,34,35,36)
yvals =
c(857.7597,975.8624,978.2655,979.3034,965.5919,983.8946,992.2512,
992.1178,979.5379,974.4269,968.4113,991.5210,977.3361,985.7800,
975.5220,974.6880,973.8102,980.7295,982.0034,984.7993,978.4948,
970.4351,969.0718,983.7892,976.3637,980.7833,987.1665,976.6000,
975.1332,971.0757,989.4693)
initpar = c(-5.1471384, -3861.8905839, 979.2616002, 0.2572355, 27.5705764)
optimft - function(x) {
yft = x[2] + (x[3] - x[2])/((1 + exp(x[1] * (log(xvals) -
log(x[4]^x[5])
return(sum((yvals - yft)^2))
}
Sequence of commands needed to make the bug appear:
Start R
source('bugs.R')
library(minqa)
library(rgl)
newuoa(initpar, optimft)
= OK
Start R
source('bugs.R')
library(rgl)
library(minqa)
newuoa(initpar, optimft)
= Crash: segfault: address 0x18, cause 'memory not mapped'
I found the bug using the package qpcR, where rgl is loaded when loading
qpcR while minqa is only loaded later, when needed.
Running on Debian squeeze 64 bit.
R version: R version 2.11.1 (2010-05-31) x86_64-pc-linux-gnu
rgl version: 0.91
minqa version: 1.1.9
Rcpp version: 0.8.6 (loaded by minqa)
Kind regards,
Gaspard Lequeux
Duplicated on Ubuntu 10.04
sessionInfo()
R version 2.11.1 (2010-05-31)
i486-pc-linux-gnu
locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_CA.UTF-8LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=en_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] minqa_1.1.9 Rcpp_0.8.6 rgl_0.91.787
Running valgrind:
bol...@ubuntu-10:~/R/misc$ R -d valgrind --vanilla
==26985== Memcheck, a memory error detector
==26985== Copyright (C) 2002-2009, and GNU GPL'd, by Julian Seward et al.
==26985== Using Valgrind-3.6.0.SVN-Debian and LibVEX; rerun with -h for
copyright info
==26985== Command: /usr/lib/R/bin/exec/R --vanilla
==26985==
R version 2.11.1 (2010-05-31)
[snip startup info]
xvals =
c(1,2,4,5,7,8,9,10,11,12,14,15,16,18,19,21,22,23,
24,25,26,27,28,29,30,31,32,33,34,35,36)
yvals =
c(857.7597,975.8624,978.2655,979.3034,965.5919,
983.8946,992.2512,992.1178,979.5379,974.4269,968.4113,
991.5210,977.3361,985.7800,975.5220,974.6880,973.8102,
980.7295,982.0034,984.7993,978.4948,970.4351,969.0718,
983.7892,976.3637,980.7833,987.1665,976.6000,975.1332,
971.0757,989.4693)
initpar = c(-5.1471384, -3861.8905839, 979.2616002, 0.2572355, 27.5705764)
optimft - function(x) {
+yft = x[2] + (x[3] - x[2])/((1 + exp(x[1] * (log(xvals) -
log(x[4]^x[5])
+return(sum((yvals - yft)^2))
+ }
library(rgl)
library(minqa)
Loading required package: Rcpp
newuoa(initpar, optimft)
==26985== Invalid read of size 4
==26985==at 0x6763C17: __cxa_allocate_exception (in
/usr/lib/libstdc++.so.6.0.13)
==26985==by 0x6EC026E: calfun_ (minqa.cpp:30)
==26985==by 0x6EC4F56: newuob_ (newuob.f:323)
==26985==by 0x6EC4ADA: newuoa_ (newuoa.f:68)
==26985==by 0x6EC2350: newuoa_cpp__rcpp__wrapper__(Rcpp::Vector14,
Rcpp::Environment, SEXPREC*) (minqa.cpp:120)
==26985==by 0x6EC27D1: newuoa_cpp (minqa.cpp:110)
==26985==by 0x40BB170: ??? (in /usr/lib/R/lib/libR.so)
==26985==by 0x40F20C1: Rf_eval (in /usr/lib/R/lib/libR.so)
==26985==by 0x40F42BF: ??? (in /usr/lib/R/lib/libR.so)
==26985==by 0x40F1E37: Rf_eval (in /usr/lib/R/lib/libR.so)
==26985==by 0x40F5C6F: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
==26985==by 0x40F1CDC: Rf_eval (in /usr/lib/R/lib/libR.so)
==26985== Address 0xc is not stack'd, malloc'd or (recently) free'd
==26985==
*** caught segfault ***
address 0xc, cause 'memory not mapped'
Traceback:
1: .Call(newuoa_cpp, par, ctrl, fn1)
2: newuoa(initpar, optimft)
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:
I strongly suspect that the problem is with minqa, and
that loading rgl is just a way to make the problem surface.
I may take a look at minqa , but you may want to send an e-mail
to the maintainer [ maintainer(minqa) ] as well ...
Ben Bolker
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Re: [R] R crashes when loading rgl package before minqa package
I get this on Windows (it does not crash):
library(minqa)
library(rgl)
newuoa(initpar, optimft)
Error in newuoa(initpar, optimft) :
non-finite x values not allowed in calfun
In addition: Warning message:
In log(x[4]) : NaNs produced
This tells me that you should be constraining your parameter x[4] (may be even
x[5]) to be non-negative:
Here is what I get with `bobyqa':
bobyqa(initpar, optimft, lower=c(-Inf, -Inf, -Inf, 0, 0))
parameter estimates: -5.311767080681, -3861.89005072333, 979.239647766226,
0.268156271922112, 27.6418856936228
objective: 1457.20987728737
number of function evaluations: 78
Ravi.
Ravi Varadhan, Ph.D.
Assistant Professor,
Division of Geriatric Medicine and Gerontology
School of Medicine
Johns Hopkins University
Ph. (410) 502-2619
email: rvarad...@jhmi.edu
- Original Message -
From: Gaspard Lequeux gaspard.lequ...@biomath.ugent.be
Date: Wednesday, September 29, 2010 11:40 am
Subject: [R] R crashes when loading rgl package before minqa package
To: r-help@r-project.org
Hej,
Calling newuoa (from the minqa package) makes R crash when the
package rgl is loaded first. This however only on certain selected data.
The data used for testing (saved to 'bugs.R'):
xvals =
c(1,2,4,5,7,8,9,10,11,12,14,15,16,18,19,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36)
yvals =
c(857.7597,975.8624,978.2655,979.3034,965.5919,983.8946,992.2512,992.1178,979.5379,974.4269,968.4113,991.5210,977.3361,985.7800,975.5220,974.6880,973.8102,980.7295,982.0034,984.7993,978.4948,970.4351,969.0718,983.7892,976.3637,980.7833,987.1665,976.6000,975.1332,971.0757,989.4693)
initpar = c(-5.1471384, -3861.8905839, 979.2616002, 0.2572355, 27.5705764)
optimft - function(x) {
yft = x[2] + (x[3] - x[2])/((1 + exp(x[1] * (log(xvals) -
log(x[4]^x[5])
return(sum((yvals - yft)^2))
}
Sequence of commands needed to make the bug appear:
Start R
source('bugs.R')
library(minqa)
library(rgl)
newuoa(initpar, optimft)
= OK
Start R
source('bugs.R')
library(rgl)
library(minqa)
newuoa(initpar, optimft)
= Crash: segfault: address 0x18, cause 'memory not mapped'
I found the bug using the package qpcR, where rgl is loaded when
loading qpcR while minqa is only loaded later, when needed.
Running on Debian squeeze 64 bit.
R version: R version 2.11.1 (2010-05-31) x86_64-pc-linux-gnu
rgl version: 0.91
minqa version: 1.1.9
Rcpp version: 0.8.6 (loaded by minqa)
Kind regards,
Gaspard Lequeux
__
R-help@r-project.org mailing list
PLEASE do read the posting guide
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] R crashes when loading rgl package before minqa package
You data is not good enough for the model that you are trying to fit (or
conversely, the model is not appropriate for the data).
Some of the parameters in your model will not be estimable because there is no
information in the data.
See the following:
xvals =
c(1,2,4,5,7,8,9,10,11,12,14,15,16,18,19,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36)
yvals =
c(857.7597,975.8624,978.2655,979.3034,965.5919,983.8946,992.2512,992.1178,979.5379,974.4269,968.4113,991.5210,977.3361,985.7800,975.5220,974.6880,973.8102,980.7295,982.0034,984.7993,978.4948,970.4351,969.0718,983.7892,976.3637,980.7833,987.1665,976.6000,975.1332,971.0757,989.4693)
initpar = c(-5.1471384, -3861.8905839, 979.2616002, 0.2572355, 27.5705764)
fn - function(x) {
yft = x[2] + (x[3] - x[2])/((1 + exp(x[1] * (log(xvals) - log(x[4]^x[5])
return(yft)
}
plot(xvals, yvals, type=p)
lines(xvals, fn(initpar))
Hope this helps,
Ravi.
Ravi Varadhan, Ph.D.
Assistant Professor,
Division of Geriatric Medicine and Gerontology
School of Medicine
Johns Hopkins University
Ph. (410) 502-2619
email: rvarad...@jhmi.edu
- Original Message -
From: Ravi Varadhan rvarad...@jhmi.edu
Date: Thursday, September 30, 2010 10:15 am
Subject: Re: [R] R crashes when loading rgl package before minqa package
To: Gaspard Lequeux gaspard.lequ...@biomath.ugent.be
Cc: r-help@r-project.org
I get this on Windows (it does not crash):
library(minqa)
library(rgl)
newuoa(initpar, optimft)
Error in newuoa(initpar, optimft) :
non-finite x values not allowed in calfun
In addition: Warning message:
In log(x[4]) : NaNs produced
This tells me that you should be constraining your parameter x[4]
(may be even x[5]) to be non-negative:
Here is what I get with `bobyqa':
bobyqa(initpar, optimft, lower=c(-Inf, -Inf, -Inf, 0, 0))
parameter estimates: -5.311767080681, -3861.89005072333,
979.239647766226, 0.268156271922112, 27.6418856936228
objective: 1457.20987728737
number of function evaluations: 78
Ravi.
Ravi Varadhan, Ph.D.
Assistant Professor,
Division of Geriatric Medicine and Gerontology
School of Medicine
Johns Hopkins University
Ph. (410) 502-2619
email: rvarad...@jhmi.edu
- Original Message -
From: Gaspard Lequeux gaspard.lequ...@biomath.ugent.be
Date: Wednesday, September 29, 2010 11:40 am
Subject: [R] R crashes when loading rgl package before minqa package
To: r-help@r-project.org
Hej,
Calling newuoa (from the minqa package) makes R crash when the
package rgl is loaded first. This however only on certain selected
data.
The data used for testing (saved to 'bugs.R'):
xvals =
c(1,2,4,5,7,8,9,10,11,12,14,15,16,18,19,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36)
yvals =
c(857.7597,975.8624,978.2655,979.3034,965.5919,983.8946,992.2512,992.1178,979.5379,974.4269,968.4113,991.5210,977.3361,985.7800,975.5220,974.6880,973.8102,980.7295,982.0034,984.7993,978.4948,970.4351,969.0718,983.7892,976.3637,980.7833,987.1665,976.6000,975.1332,971.0757,989.4693)
initpar = c(-5.1471384, -3861.8905839, 979.2616002, 0.2572355, 27.5705764)
optimft - function(x) {
yft = x[2] + (x[3] - x[2])/((1 + exp(x[1] * (log(xvals) -
log(x[4]^x[5])
return(sum((yvals - yft)^2))
}
Sequence of commands needed to make the bug appear:
Start R
source('bugs.R')
library(minqa)
library(rgl)
newuoa(initpar, optimft)
= OK
Start R
source('bugs.R')
library(rgl)
library(minqa)
newuoa(initpar, optimft)
= Crash: segfault: address 0x18, cause 'memory not mapped'
I found the bug using the package qpcR, where rgl is loaded when
loading qpcR while minqa is only loaded later, when needed.
Running on Debian squeeze 64 bit.
R version: R version 2.11.1 (2010-05-31) x86_64-pc-linux-gnu
rgl version: 0.91
minqa version: 1.1.9
Rcpp version: 0.8.6 (loaded by minqa)
Kind regards,
Gaspard Lequeux
__
R-help@r-project.org mailing list
PLEASE do read the posting guide
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
PLEASE do read the posting guide
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] R crashes when loading rgl package before minqa package
Hej,
On Thu, 30 Sep 2010, Ravi Varadhan wrote:
I get this on Windows (it does not crash):
library(minqa)
library(rgl)
newuoa(initpar, optimft)
Error in newuoa(initpar, optimft) :
non-finite x values not allowed in calfun
In addition: Warning message:
In log(x[4]) : NaNs produced
Does it crash when you load first rgl and then only minqa? Like this:
library(rgl)
library(minqa)
newuoa(initpar, optimft)
/Gaspard
This tells me that you should be constraining your parameter x[4] (may be even
x[5]) to be non-negative:
Here is what I get with `bobyqa':
bobyqa(initpar, optimft, lower=c(-Inf, -Inf, -Inf, 0, 0))
parameter estimates: -5.311767080681, -3861.89005072333, 979.239647766226,
0.268156271922112, 27.6418856936228
objective: 1457.20987728737
number of function evaluations: 78
Ravi.
Ravi Varadhan, Ph.D.
Assistant Professor,
Division of Geriatric Medicine and Gerontology
School of Medicine
Johns Hopkins University
Ph. (410) 502-2619
email: rvarad...@jhmi.edu
- Original Message -
From: Gaspard Lequeux gaspard.lequ...@biomath.ugent.be
Date: Wednesday, September 29, 2010 11:40 am
Subject: [R] R crashes when loading rgl package before minqa package
To: r-help@r-project.org
Hej,
Calling newuoa (from the minqa package) makes R crash when the
package rgl is loaded first. This however only on certain selected data.
The data used for testing (saved to 'bugs.R'):
xvals =
c(1,2,4,5,7,8,9,10,11,12,14,15,16,18,19,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36)
yvals =
c(857.7597,975.8624,978.2655,979.3034,965.5919,983.8946,992.2512,992.1178,979.5379,974.4269,968.4113,991.5210,977.3361,985.7800,975.5220,974.6880,973.8102,980.7295,982.0034,984.7993,978.4948,970.4351,969.0718,983.7892,976.3637,980.7833,987.1665,976.6000,975.1332,971.0757,989.4693)
initpar = c(-5.1471384, -3861.8905839, 979.2616002, 0.2572355, 27.5705764)
optimft - function(x) {
yft = x[2] + (x[3] - x[2])/((1 + exp(x[1] * (log(xvals) - log(x[4]^x[5])
return(sum((yvals - yft)^2))
}
Sequence of commands needed to make the bug appear:
Start R
source('bugs.R')
library(minqa)
library(rgl)
newuoa(initpar, optimft)
= OK
Start R
source('bugs.R')
library(rgl)
library(minqa)
newuoa(initpar, optimft)
= Crash: segfault: address 0x18, cause 'memory not mapped'
I found the bug using the package qpcR, where rgl is loaded when
loading qpcR while minqa is only loaded later, when needed.
Running on Debian squeeze 64 bit.
R version: R version 2.11.1 (2010-05-31) x86_64-pc-linux-gnu
rgl version: 0.91
minqa version: 1.1.9
Rcpp version: 0.8.6 (loaded by minqa)
Kind regards,
Gaspard Lequeux
__
R-help@r-project.org mailing list
PLEASE do read the posting guide
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] R crashes when loading rgl package before minqa package
Hej,
On Thu, 30 Sep 2010, Ravi Varadhan wrote:
You data is not good enough for the model that you are trying to fit (or
conversely, the model is not appropriate for the data).
Yes. I agree. However, this should not cause R to crash. (Around 100.000
models are fitted, and it is not possible to look at the data by hand
first. Bogus results are filtered out afterwards.)
/Gaspard
Some of the parameters in your model will not be estimable because there is no
information in the data.
See the following:
xvals =
c(1,2,4,5,7,8,9,10,11,12,14,15,16,18,19,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36)
yvals =
c(857.7597,975.8624,978.2655,979.3034,965.5919,983.8946,992.2512,992.1178,979.5379,974.4269,968.4113,991.5210,977.3361,985.7800,975.5220,974.6880,973.8102,980.7295,982.0034,984.7993,978.4948,970.4351,969.0718,983.7892,976.3637,980.7833,987.1665,976.6000,975.1332,971.0757,989.4693)
initpar = c(-5.1471384, -3861.8905839, 979.2616002, 0.2572355, 27.5705764)
fn - function(x) {
yft = x[2] + (x[3] - x[2])/((1 + exp(x[1] * (log(xvals) - log(x[4]^x[5])
return(yft)
}
plot(xvals, yvals, type=p)
lines(xvals, fn(initpar))
Hope this helps,
Ravi.
Ravi Varadhan, Ph.D.
Assistant Professor,
Division of Geriatric Medicine and Gerontology
School of Medicine
Johns Hopkins University
Ph. (410) 502-2619
email: rvarad...@jhmi.edu
- Original Message -
From: Ravi Varadhan rvarad...@jhmi.edu
Date: Thursday, September 30, 2010 10:15 am
Subject: Re: [R] R crashes when loading rgl package before minqa package
To: Gaspard Lequeux gaspard.lequ...@biomath.ugent.be
Cc: r-help@r-project.org
I get this on Windows (it does not crash):
library(minqa)
library(rgl)
newuoa(initpar, optimft)
Error in newuoa(initpar, optimft) :
non-finite x values not allowed in calfun
In addition: Warning message:
In log(x[4]) : NaNs produced
This tells me that you should be constraining your parameter x[4]
(may be even x[5]) to be non-negative:
Here is what I get with `bobyqa':
bobyqa(initpar, optimft, lower=c(-Inf, -Inf, -Inf, 0, 0))
parameter estimates: -5.311767080681, -3861.89005072333,
979.239647766226, 0.268156271922112, 27.6418856936228
objective: 1457.20987728737
number of function evaluations: 78
Ravi.
Ravi Varadhan, Ph.D.
Assistant Professor,
Division of Geriatric Medicine and Gerontology
School of Medicine
Johns Hopkins University
Ph. (410) 502-2619
email: rvarad...@jhmi.edu
- Original Message -
From: Gaspard Lequeux gaspard.lequ...@biomath.ugent.be
Date: Wednesday, September 29, 2010 11:40 am
Subject: [R] R crashes when loading rgl package before minqa package
To: r-help@r-project.org
Hej,
Calling newuoa (from the minqa package) makes R crash when the
package rgl is loaded first. This however only on certain selected
data.
The data used for testing (saved to 'bugs.R'):
xvals =
c(1,2,4,5,7,8,9,10,11,12,14,15,16,18,19,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36)
yvals =
c(857.7597,975.8624,978.2655,979.3034,965.5919,983.8946,992.2512,992.1178,979.5379,974.4269,968.4113,991.5210,977.3361,985.7800,975.5220,974.6880,973.8102,980.7295,982.0034,984.7993,978.4948,970.4351,969.0718,983.7892,976.3637,980.7833,987.1665,976.6000,975.1332,971.0757,989.4693)
initpar = c(-5.1471384, -3861.8905839, 979.2616002, 0.2572355, 27.5705764)
optimft - function(x) {
yft = x[2] + (x[3] - x[2])/((1 + exp(x[1] * (log(xvals) -
log(x[4]^x[5])
return(sum((yvals - yft)^2))
}
Sequence of commands needed to make the bug appear:
Start R
source('bugs.R')
library(minqa)
library(rgl)
newuoa(initpar, optimft)
= OK
Start R
source('bugs.R')
library(rgl)
library(minqa)
newuoa(initpar, optimft)
= Crash: segfault: address 0x18, cause 'memory not mapped'
I found the bug using the package qpcR, where rgl is loaded when
loading qpcR while minqa is only loaded later, when needed.
Running on Debian squeeze 64 bit.
R version: R version 2.11.1 (2010-05-31) x86_64-pc-linux-gnu
rgl version: 0.91
minqa version: 1.1.9
Rcpp version: 0.8.6 (loaded by minqa)
Kind regards,
Gaspard Lequeux
__
R-help@r-project.org mailing list
PLEASE do read the posting guide
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
PLEASE do read the posting guide
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] R crashes when loading rgl package before minqa package
No. It still does not crash in Windows.
library(rgl)
library(minqa)
Loading required package: Rcpp
newuoa(initpar, optimft)
Error in newuoa(initpar, optimft) :
non-finite x values not allowed in calfun
In addition: Warning message:
In log(x[4]) : NaNs produced
Ravi.
Ravi Varadhan, Ph.D.
Assistant Professor,
Division of Geriatric Medicine and Gerontology
School of Medicine
Johns Hopkins University
Ph. (410) 502-2619
email: rvarad...@jhmi.edu
- Original Message -
From: Gaspard Lequeux gaspard.lequ...@biomath.ugent.be
Date: Thursday, September 30, 2010 11:43 am
Subject: Re: [R] R crashes when loading rgl package before minqa package
To: r-help@r-project.org
Hej,
On Thu, 30 Sep 2010, Ravi Varadhan wrote:
I get this on Windows (it does not crash):
library(minqa)
library(rgl)
newuoa(initpar, optimft)
Error in newuoa(initpar, optimft) :
non-finite x values not allowed in calfun
In addition: Warning message:
In log(x[4]) : NaNs produced
Does it crash when you load first rgl and then only minqa? Like this:
library(rgl)
library(minqa)
newuoa(initpar, optimft)
/Gaspard
This tells me that you should be constraining your parameter x[4]
(may be even x[5]) to be non-negative:
Here is what I get with `bobyqa':
bobyqa(initpar, optimft, lower=c(-Inf, -Inf, -Inf, 0, 0))
parameter estimates: -5.311767080681, -3861.89005072333,
979.239647766226, 0.268156271922112, 27.6418856936228
objective: 1457.20987728737
number of function evaluations: 78
Ravi.
Ravi Varadhan, Ph.D.
Assistant Professor,
Division of Geriatric Medicine and Gerontology
School of Medicine
Johns Hopkins University
Ph. (410) 502-2619
email: rvarad...@jhmi.edu
- Original Message -
From: Gaspard Lequeux gaspard.lequ...@biomath.ugent.be
Date: Wednesday, September 29, 2010 11:40 am
Subject: [R] R crashes when loading rgl package before minqa package
To: r-help@r-project.org
Hej,
Calling newuoa (from the minqa package) makes R crash when the
package rgl is loaded first. This however only on certain selected
data.
The data used for testing (saved to 'bugs.R'):
xvals =
c(1,2,4,5,7,8,9,10,11,12,14,15,16,18,19,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36)
yvals =
c(857.7597,975.8624,978.2655,979.3034,965.5919,983.8946,992.2512,992.1178,979.5379,974.4269,968.4113,991.5210,977.3361,985.7800,975.5220,974.6880,973.8102,980.7295,982.0034,984.7993,978.4948,970.4351,969.0718,983.7892,976.3637,980.7833,987.1665,976.6000,975.1332,971.0757,989.4693)
initpar = c(-5.1471384, -3861.8905839, 979.2616002, 0.2572355, 27.5705764)
optimft - function(x) {
yft = x[2] + (x[3] - x[2])/((1 + exp(x[1] * (log(xvals) -
log(x[4]^x[5])
return(sum((yvals - yft)^2))
}
Sequence of commands needed to make the bug appear:
Start R
source('bugs.R')
library(minqa)
library(rgl)
newuoa(initpar, optimft)
= OK
Start R
source('bugs.R')
library(rgl)
library(minqa)
newuoa(initpar, optimft)
= Crash: segfault: address 0x18, cause 'memory not mapped'
I found the bug using the package qpcR, where rgl is loaded when
loading qpcR while minqa is only loaded later, when needed.
Running on Debian squeeze 64 bit.
R version: R version 2.11.1 (2010-05-31) x86_64-pc-linux-gnu
rgl version: 0.91
minqa version: 1.1.9
Rcpp version: 0.8.6 (loaded by minqa)
Kind regards,
Gaspard Lequeux
__
R-help@r-project.org mailing list
PLEASE do read the posting guide
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
PLEASE do read the posting guide
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] R crashes when loading rgl package before minqa package
I also cannot reproduce the crash.
sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-unknown-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
other attached packages:
[1] minqa_1.1.9 Rcpp_0.8.6 rgl_0.91
On Thu, 30 Sep 2010, Ravi Varadhan wrote:
No. It still does not crash in Windows.
library(rgl)
library(minqa)
Loading required package: Rcpp
newuoa(initpar, optimft)
Error in newuoa(initpar, optimft) :
non-finite x values not allowed in calfun
In addition: Warning message:
In log(x[4]) : NaNs produced
Ravi.
Ravi Varadhan, Ph.D.
Assistant Professor,
Division of Geriatric Medicine and Gerontology
School of Medicine
Johns Hopkins University
Ph. (410) 502-2619
email: rvarad...@jhmi.edu
- Original Message -
From: Gaspard Lequeux gaspard.lequ...@biomath.ugent.be
Date: Thursday, September 30, 2010 11:43 am
Subject: Re: [R] R crashes when loading rgl package before minqa package
To: r-help@r-project.org
Hej,
On Thu, 30 Sep 2010, Ravi Varadhan wrote:
I get this on Windows (it does not crash):
library(minqa)
library(rgl)
newuoa(initpar, optimft)
Error in newuoa(initpar, optimft) :
non-finite x values not allowed in calfun
In addition: Warning message:
In log(x[4]) : NaNs produced
Does it crash when you load first rgl and then only minqa? Like this:
library(rgl)
library(minqa)
newuoa(initpar, optimft)
/Gaspard
This tells me that you should be constraining your parameter x[4]
(may be even x[5]) to be non-negative:
Here is what I get with `bobyqa':
bobyqa(initpar, optimft, lower=c(-Inf, -Inf, -Inf, 0, 0))
parameter estimates: -5.311767080681, -3861.89005072333,
979.239647766226, 0.268156271922112, 27.6418856936228
objective: 1457.20987728737
number of function evaluations: 78
Ravi.
Ravi Varadhan, Ph.D.
Assistant Professor,
Division of Geriatric Medicine and Gerontology
School of Medicine
Johns Hopkins University
Ph. (410) 502-2619
email: rvarad...@jhmi.edu
- Original Message -
From: Gaspard Lequeux gaspard.lequ...@biomath.ugent.be
Date: Wednesday, September 29, 2010 11:40 am
Subject: [R] R crashes when loading rgl package before minqa package
To: r-help@r-project.org
Hej,
Calling newuoa (from the minqa package) makes R crash when the
package rgl is loaded first. This however only on certain selected
data.
The data used for testing (saved to 'bugs.R'):
xvals =
c(1,2,4,5,7,8,9,10,11,12,14,15,16,18,19,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36)
yvals =
c(857.7597,975.8624,978.2655,979.3034,965.5919,983.8946,992.2512,992.1178,979.5379,974.4269,968.4113,991.5210,977.3361,985.7800,975.5220,974.6880,973.8102,980.7295,982.0034,984.7993,978.4948,970.4351,969.0718,983.7892,976.3637,980.7833,987.1665,976.6000,975.1332,971.0757,989.4693)
initpar = c(-5.1471384, -3861.8905839, 979.2616002, 0.2572355, 27.5705764)
optimft - function(x) {
yft = x[2] + (x[3] - x[2])/((1 + exp(x[1] * (log(xvals) -
log(x[4]^x[5])
return(sum((yvals - yft)^2))
}
Sequence of commands needed to make the bug appear:
Start R
source('bugs.R')
library(minqa)
library(rgl)
newuoa(initpar, optimft)
= OK
Start R
source('bugs.R')
library(rgl)
library(minqa)
newuoa(initpar, optimft)
= Crash: segfault: address 0x18, cause 'memory not mapped'
I found the bug using the package qpcR, where rgl is loaded when
loading qpcR while minqa is only loaded later, when needed.
Running on Debian squeeze 64 bit.
R version: R version 2.11.1 (2010-05-31) x86_64-pc-linux-gnu
rgl version: 0.91
minqa version: 1.1.9
Rcpp version: 0.8.6 (loaded by minqa)
Kind regards,
Gaspard Lequeux
__
R-help@r-project.org mailing list
PLEASE do read the posting guide
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
PLEASE do read the posting guide
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-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
[R] R crashes when loading rgl package before minqa package
Hej,
Calling newuoa (from the minqa package) makes R crash when the package rgl
is loaded first. This however only on certain selected data.
The data used for testing (saved to 'bugs.R'):
xvals =
c(1,2,4,5,7,8,9,10,11,12,14,15,16,18,19,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36)
yvals =
c(857.7597,975.8624,978.2655,979.3034,965.5919,983.8946,992.2512,992.1178,979.5379,974.4269,968.4113,991.5210,977.3361,985.7800,975.5220,974.6880,973.8102,980.7295,982.0034,984.7993,978.4948,970.4351,969.0718,983.7892,976.3637,980.7833,987.1665,976.6000,975.1332,971.0757,989.4693)
initpar = c(-5.1471384, -3861.8905839, 979.2616002, 0.2572355, 27.5705764)
optimft - function(x) {
yft = x[2] + (x[3] - x[2])/((1 + exp(x[1] * (log(xvals) - log(x[4]^x[5])
return(sum((yvals - yft)^2))
}
Sequence of commands needed to make the bug appear:
Start R
source('bugs.R')
library(minqa)
library(rgl)
newuoa(initpar, optimft)
= OK
Start R
source('bugs.R')
library(rgl)
library(minqa)
newuoa(initpar, optimft)
= Crash: segfault: address 0x18, cause 'memory not mapped'
I found the bug using the package qpcR, where rgl is loaded when loading
qpcR while minqa is only loaded later, when needed.
Running on Debian squeeze 64 bit.
R version: R version 2.11.1 (2010-05-31) x86_64-pc-linux-gnu
rgl version: 0.91
minqa version: 1.1.9
Rcpp version: 0.8.6 (loaded by minqa)
Kind regards,
Gaspard Lequeux
__
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] R crashes when communicating with JAGS
Thanks for your answer, Ben. Indeed I tried to use the newest R
version, but just to be sure I tried it again just now, with the same
result, i.e. R crashes. Unfortunately I cannot even look at the system
configurations as this is a university computer and they (stupidly)
don't give us administrator rights on our machines. I'll have to
discuss this with our IT once I'm back home.
But one thing you mentioned I didn't really realize before is
interesting, which is that I don't get any messages from Jags before
the crash. Indeed looking at the Jags-window it doesn't do anything.
What you see on your computer is exactly what I would like to see, but
it doesn't even start compiling. So it might be a problem with Jags. I
just tried to use another version of Jags (the older 2.0 version).
However, now I cannot load the library of rjags any more and I don't
understand why. Is there another package I need to install when using
an older version of Jags? Thanks again, Florian
On Tue, Aug 31, 2010 at 12:38 AM, Ben Bolker bbol...@gmail.com wrote:
Florian Weiler fweiler08 at johnshopkins.it writes:
First I create some data:
N - 1000
x - rnorm(N, 0, 5)
Then I specify a model in JAGS, storing it in the directory with the
extension .bug:
model {
for (i in 1:N) {
x[i] ~ dnorm(mu, tau) ## the model
}
mu ~ dnorm(0, .0001) ## uninformative priors
tau - pow(sigma, -2)
sigma ~ dunif(0, 100)
}
Then I call the rjags library and finally I try to run the jags model:
library('rjags')
jags - jags.model('example.bug',
data = list('x' = x,
'N' = N))
This is where its always crashing, i.e. I don't get an error message,
but R simply stops working and I have to close and reopen the program.
I don't even start drawing samples from the model, it just crashes the
moment I try to call on JAGS.
[snip]
My problem is that every
single time I want to call JAGS from R the latter crashes (i.e. it
turns pale and the Windows tells me R has stopped working.
Strangely, if there is a mistake in my jags code, this will be
reported without a crash. Only when the code is right and the model
should start to run, R stops working. I already tried to use different
version of R (currently R 2.10.1 and JAGS-2.1.0-1),but to no avail. A
couple of days ago I even upgraded from Vista to Windows 7, hoping
this would sort our the problem, but its still exactly the same. Could
anyone think of a possible solution for this problem?
I worked on other computers using Windows without encountering the
described problem. However, I am quite new to using JAGS, so I might
just be missing the obvious.
This sort of thing is unfortunately really hard to debug remotely.
Is it feasible to upgrade to the latest release of R (2.11.1), JAGS, and
rjags, just to rule that out as a possibility? You said you had
used other Windows machines where it worked -- do they have
similar configurations? Can you try to look for differences in the
configurations? Do you get any messages at all from JAGS before
the program stops (I get
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph Size: 1009
|++| 100%
: does any of this appear before R crashes)?
__
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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] R crashes when communicating with JAGS
Florian Weiler wrote:
Thanks for your answer, Ben. Indeed I tried to use the newest R
version, but just to be sure I tried it again just now, with the same
result, i.e. R crashes. Unfortunately I cannot even look at the system
configurations as this is a university computer and they (stupidly)
don't give us administrator rights on our machines. I'll have to
discuss this with our IT once I'm back home.
But one thing you mentioned I didn't really realize before is
interesting, which is that I don't get any messages from Jags before
the crash. Indeed looking at the Jags-window it doesn't do anything.
What you see on your computer is exactly what I would like to see, but
it doesn't even start compiling. So it might be a problem with Jags. I
just tried to use another version of Jags (the older 2.0 version).
However, now I cannot load the library of rjags any more and I don't
understand why. Is there another package I need to install when using
an older version of Jags? Thanks again, Florian
I believe you might have to install an older version of rjags
http://cran.r-project.org/src/contrib/Archive/rjags/ --
I've had problems in the other direction (trying to use new JAGS with
older rjags) and think there may be some
dependencies there. However, trying to use an older JAGS seems a bit
desperate to me. I would probably
start by trying to run JAGS from a Windows shell (see the JAGS manual
for examples), so that you can decide
whether rjags is part of the problem, or whether it's a pure JAGS issue.
On Tue, Aug 31, 2010 at 12:38 AM, Ben Bolker bbol...@gmail.com wrote:
Florian Weiler fweiler08 at johnshopkins.it writes:
First I create some data:
N - 1000
x - rnorm(N, 0, 5)
Then I specify a model in JAGS, storing it in the directory with the
extension .bug:
model {
for (i in 1:N) {
x[i] ~ dnorm(mu, tau) ## the model
}
mu ~ dnorm(0, .0001) ## uninformative priors
tau - pow(sigma, -2)
sigma ~ dunif(0, 100)
}
Then I call the rjags library and finally I try to run the jags model:
library('rjags')
jags - jags.model('example.bug',
data = list('x' = x,
'N' = N))
This is where its always crashing, i.e. I don't get an error message,
but R simply stops working and I have to close and reopen the program.
I don't even start drawing samples from the model, it just crashes the
moment I try to call on JAGS.
[snip]
My problem is that every
single time I want to call JAGS from R the latter crashes (i.e. it
turns pale and the Windows tells me R has stopped working.
Strangely, if there is a mistake in my jags code, this will be
reported without a crash. Only when the code is right and the model
should start to run, R stops working. I already tried to use different
version of R (currently R 2.10.1 and JAGS-2.1.0-1),but to no avail. A
couple of days ago I even upgraded from Vista to Windows 7, hoping
this would sort our the problem, but its still exactly the same. Could
anyone think of a possible solution for this problem?
I worked on other computers using Windows without encountering the
described problem. However, I am quite new to using JAGS, so I might
just be missing the obvious.
This sort of thing is unfortunately really hard to debug remotely.
Is it feasible to upgrade to the latest release of R (2.11.1), JAGS, and
rjags, just to rule that out as a possibility? You said you had
used other Windows machines where it worked -- do they have
similar configurations? Can you try to look for differences in the
configurations? Do you get any messages at all from JAGS before
the program stops (I get
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph Size: 1009
|++| 100%
: does any of this appear before R crashes)?
__
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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.
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and provide commented, minimal, self-contained, reproducible code.
[R] R crashes when communicating with JAGS
Dear all, I have a question regarding using JAGS and R. My problem is that every single time I want to call JAGS from R the latter crashes (i.e. it turns pale and the Windows tells me R has stopped working. Strangely, if there is a mistake in my jags code, this will be reported without a crash. Only when the code is right and the model should start to run, R stops working. I already tried to use different version of R (currently R 2.10.1 and JAGS-2.1.0-1),but to no avail. A couple of days ago I even upgraded from Vista to Windows 7, hoping this would sort our the problem, but its still exactly the same. Could anyone think of a possible solution for this problem? I worked on other computers using Windows without encountering the described problem. However, I am quite new to using JAGS, so I might just be missing the obvious. Thanks for your help and precious time, Florian __ 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] R crashes when communicating with JAGS
Hi again,
I was asked to provide some code. Well, in my case it doesn't really
matter which example I use, so I just write down a very basic and
canned example:
First I create some data:
N - 1000
x - rnorm(N, 0, 5)
Then I specify a model in JAGS, storing it in the directory with the
extension .bug:
model {
for (i in 1:N) {
x[i] ~ dnorm(mu, tau) ## the model
}
mu ~ dnorm(0, .0001) ## uninformative priors
tau - pow(sigma, -2)
sigma ~ dunif(0, 100)
}
Then I call the rjags library and finally I try to run the jags model:
library('rjags')
jags - jags.model('example.bug',
data = list('x' = x,
'N' = N))
This is where its always crashing, i.e. I don't get an error message,
but R simply stops working and I have to close and reopen the program.
I don't even start drawing samples from the model, it just crashes the
moment I try to call on JAGS.
Sorry for not providing the example right away,
Florian
On Mon, Aug 30, 2010 at 9:17 AM, Florian Weiler
fweile...@johnshopkins.it wrote:
Dear all,
I have a question regarding using JAGS and R. My problem is that every
single time I want to call JAGS from R the latter crashes (i.e. it
turns pale and the Windows tells me R has stopped working.
Strangely, if there is a mistake in my jags code, this will be
reported without a crash. Only when the code is right and the model
should start to run, R stops working. I already tried to use different
version of R (currently R 2.10.1 and JAGS-2.1.0-1),but to no avail. A
couple of days ago I even upgraded from Vista to Windows 7, hoping
this would sort our the problem, but its still exactly the same. Could
anyone think of a possible solution for this problem?
I worked on other computers using Windows without encountering the
described problem. However, I am quite new to using JAGS, so I might
just be missing the obvious.
Thanks for your help and precious time,
Florian
__
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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] R crashes when communicating with JAGS
Florian Weiler fweiler08 at johnshopkins.it writes:
First I create some data:
N - 1000
x - rnorm(N, 0, 5)
Then I specify a model in JAGS, storing it in the directory with the
extension .bug:
model {
for (i in 1:N) {
x[i] ~ dnorm(mu, tau) ## the model
}
mu ~ dnorm(0, .0001) ## uninformative priors
tau - pow(sigma, -2)
sigma ~ dunif(0, 100)
}
Then I call the rjags library and finally I try to run the jags model:
library('rjags')
jags - jags.model('example.bug',
data = list('x' = x,
'N' = N))
This is where its always crashing, i.e. I don't get an error message,
but R simply stops working and I have to close and reopen the program.
I don't even start drawing samples from the model, it just crashes the
moment I try to call on JAGS.
[snip]
My problem is that every
single time I want to call JAGS from R the latter crashes (i.e. it
turns pale and the Windows tells me R has stopped working.
Strangely, if there is a mistake in my jags code, this will be
reported without a crash. Only when the code is right and the model
should start to run, R stops working. I already tried to use different
version of R (currently R 2.10.1 and JAGS-2.1.0-1),but to no avail. A
couple of days ago I even upgraded from Vista to Windows 7, hoping
this would sort our the problem, but its still exactly the same. Could
anyone think of a possible solution for this problem?
I worked on other computers using Windows without encountering the
described problem. However, I am quite new to using JAGS, so I might
just be missing the obvious.
This sort of thing is unfortunately really hard to debug remotely.
Is it feasible to upgrade to the latest release of R (2.11.1), JAGS, and
rjags, just to rule that out as a possibility? You said you had
used other Windows machines where it worked -- do they have
similar configurations? Can you try to look for differences in the
configurations? Do you get any messages at all from JAGS before
the program stops (I get
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph Size: 1009
|++| 100%
: does any of this appear before R crashes)?
__
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] R crashes with large vectors
Good afternoon, I have been experiencing a lot of crashes working with large vectors in R. Specifically, I am using XTS of length of minimum 120k elements. My problem is that I cannot display the vector (otherwise R crashes), I cannot plot it either (otherwise R crashes). That could be solved by reducing the amount of points. However, I have been performing some statistical opreations on is and even sd(myXTS) crashes R. By crashes, I mean shuts down without any warning whatsoever. I use R 2.11.1 (64). Has anyone had the same kind of problem? Can we solve this? Best, -- Jeremie [[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] R crashes with large vectors
Hi Jeremie, Maybe you can take a look at the bigmemory package. If you have multi core or have access to clusters, you may want to use any parallel computing strategy. For plotting of large data, if you are using basic R graphics, first try to use line instead of using 'point', if this still doesn't working, you may want to try an alternative way by using qtinterface (R-forge project), install qtbase and qtpaint, they are still under development, but painting in QT interface is a lot faster for large data set. Best Tengfei On Fri, Jul 9, 2010 at 2:42 AM, Jeremie Smaga jere...@4ecap.com wrote: Good afternoon, I have been experiencing a lot of crashes working with large vectors in R. Specifically, I am using XTS of length of minimum 120k elements. My problem is that I cannot display the vector (otherwise R crashes), I cannot plot it either (otherwise R crashes). That could be solved by reducing the amount of points. However, I have been performing some statistical opreations on is and even sd(myXTS) crashes R. By crashes, I mean shuts down without any warning whatsoever. I use R 2.11.1 (64). Has anyone had the same kind of problem? Can we solve this? Best, -- Jeremie [[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. -- Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274 Homepage: www.tengfei.name [[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] R crashes with large vectors
Jeremie Smaga jeremie at 4ecap.com writes: Good afternoon, I have been experiencing a lot of crashes working with large vectors in R. Specifically, I am using XTS of length of minimum 120k elements. My problem is that I cannot display the vector (otherwise R crashes), I cannot plot it either (otherwise R crashes). That could be solved by reducing the amount of points. However, I have been performing some statistical opreations on is and even sd(myXTS) crashes R. By crashes, I mean shuts down without any warning whatsoever. I use R 2.11.1 (64). Has anyone had the same kind of problem? Can we solve this? You need to provide a reproducible example, or as nearly reproducible as possible. You need to provide more information about your system (Windows?) -- the results of sessionInfo() would help. For example, I have no problem taking the standard deviation of a million-element vector: set.seed(1001) sd(runif(1e6)) [1] 0.2884210 sessionInfo() R version 2.11.1 (2010-05-31) i486-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 what happens on your system? sd( __ 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] R crashes
Windows XP 32 bit machine. allocated 2gb as memory for R 2.9.2 data will be 20mb and was running calculations on the data . but the r crashes with out any warning or so. -- View this message in context: http://old.nabble.com/R-crashes-tp26110355p26124740.html Sent from the R help mailing list archive at Nabble.com. __ 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] R crashes
On 10/30/2009 05:17 AM, premmad wrote: Windows XP 32 bit machine. allocated 2gb as memory for R 2.9.2 can you try again whatever you do with 2.10.0 data will be 20mb and was running calculations on the data . but the r crashes with out any warning or so. That is a bit better, but nowhere near something that can help us help you. You are going to need a few more sessions for this therapy to be useful, we cannot read your computer's mind, just interpret what you tell us. I don't want to jump ahead, but can you tell us the childhood of your crashes, etc ... 20mb is not huge Romain -- Romain Francois Professional R Enthusiast +33(0) 6 28 91 30 30 http://romainfrancois.blog.free.fr |- http://tr.im/BcPw : celebrating R commit #5 |- http://tr.im/ztCu : RGG #158:161: examples of package IDPmisc `- http://tr.im/yw8E : New R package : sos __ 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] R crashes
premmad wrote: Windows XP 32 bit machine. allocated 2gb as memory for R 2.9.2 data will be 20mb and was running calculations on the data . but the r crashes with out any warning or so. Ahh, well 20 MB is not huge data for R, so there should be no problem with processing it. The pertinent questions now are: * What does your data look like? A small representational sample will suffice, preferably something that can be copied out of an email and pasted into R. * What operations are you running when R crashes? In your first post you mentioned R crashes frequently-- does this happen with many different data sets, but the same operations? If you could provide us the data and functions that are being executed just prior to the crash, then we may be able to help. But without a reproducible example to test on our own machines, as suggested by the posting guide for this mailing list, there is really nothing we can do to help with your problem. -Charlie - Charlie Sharpsteen Undergraduate Environmental Resources Engineering Humboldt State University -- View this message in context: http://old.nabble.com/R-crashes-tp26110355p26132909.html Sent from the R help mailing list archive at Nabble.com. __ 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] R crashes
My R crashes frequently when run with huge data. -- View this message in context: http://www.nabble.com/R-crashes-tp26110355p26110355.html Sent from the R help mailing list archive at Nabble.com. __ 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] R crashes
And PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. --- On Thu, 10/29/09, premmad mtechp...@gmail.com wrote: From: premmad mtechp...@gmail.com Subject: [R] R crashes To: r-help@r-project.org Received: Thursday, October 29, 2009, 6:13 AM My R crashes frequently when run with huge data. -- View this message in context: http://www.nabble.com/R-crashes-tp26110355p26110355.html Sent from the R help mailing list archive at Nabble.com. __ 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. __ Ask a question on any topic and get answers from real people. Go to Yahoo! Answers and share what you know at http://ca.answers.yahoo.com __ 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] R crashes
On 29/10/2009, at 11:13 PM, premmad wrote:
My R crashes frequently when run with huge data.
Isn't that ***fascinating***!!!
cheers,
Rolf Turner
##
Attention:\ This e-mail message is privileged and confid...{{dropped:9}}
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] R crashes
premmad wrote: My R crashes frequently when run with huge data. I'm afraid this is nowhere near enough information for anyone on this list to provide any sort of meaningful insight. At the very least we need to know: * What operating system are you using? * Specifically, for large data set questions-- are you running a 32 or 64 bit operating system and how much RAM do you have? * What version of R are you running? * What does your data set look like and where does it come from? * How big is the data set? * How are you trying to read the data in? You don't need to provide the complete data set-- just a representational sample that someone interested in your problem could replicate into something of the appropriate size. This is very critical as it is very possible that the problem is arising from feeding R corrupted data rather than R simply choking because the data set is too big. Without this information, the best you can hope for from this mailing list is silence or a flippant response. -Charlie - Charlie Sharpsteen Undergraduate Environmental Resources Engineering Humboldt State University -- View this message in context: http://www.nabble.com/R-crashes-tp26110355p26123323.html Sent from the R help mailing list archive at Nabble.com. __ 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] R crashes when packages 'impute' and 'GeneMeta' are used together.
Dear all, it seems that my original diagnosis (using impute together with GeneMeta) was not correct. Something else is causing the crash (R-console stops working). I will return for questions (probably at the Bioconductor mailing list) after I have investigated the problem further. Thank you all and I apologize for the inappropriate use of your time. - Original Message - From: Duncan Murdoch murd...@stats.uwo.ca To: Vassilis Golfinopoulos vassilis.golfinopou...@gmail.com Cc: r-help@r-project.org Sent: Monday, September 21, 2009 5:13 PM Subject: Re: [R] R crashes when packages 'impute' and 'GeneMeta' are used together. On 9/21/2009 9:18 AM, Vassilis Golfinopoulos wrote: Well, the title says all for this one. It seems to crash the R-console, so it happens whether I use the R-gui or R-console directly or Emacs with ESS. Not for me. (But as Hadley said, you didn't explain what you needed to do to trigger the crash, so I may not have done it. All I did was library(GeneMeta) library(impute) GeneMeta is a Bioconductor package, so you might want to talk about this on the Bioconductor mailing list, where you'll find more people who use it. But you should try it in a current release of R (2.9.2 is current), and report on the version numbers of the packages. Duncan Murdoch I have R 2.9.0 on Windows Vista. Thanks, Vassilis __ 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] R crashes when packages 'impute' and 'GeneMeta' are used together.
Well, the title says all for this one. It seems to crash the R-console, so it happens whether I use the R-gui or R-console directly or Emacs with ESS. I have R 2.9.0 on Windows Vista. Thanks, Vassilis __ 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] R crashes when packages 'impute' and 'GeneMeta' are used together.
Well, the title says all for this one. Not really. What do you mean by crash? What do you mean by used together? Hadley -- http://had.co.nz/ __ 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] R crashes when packages 'impute' and 'GeneMeta' are used together.
On 9/21/2009 9:18 AM, Vassilis Golfinopoulos wrote: Well, the title says all for this one. It seems to crash the R-console, so it happens whether I use the R-gui or R-console directly or Emacs with ESS. Not for me. (But as Hadley said, you didn't explain what you needed to do to trigger the crash, so I may not have done it. All I did was library(GeneMeta) library(impute) GeneMeta is a Bioconductor package, so you might want to talk about this on the Bioconductor mailing list, where you'll find more people who use it. But you should try it in a current release of R (2.9.2 is current), and report on the version numbers of the packages. Duncan Murdoch I have R 2.9.0 on Windows Vista. Thanks, Vassilis __ 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] R crashes while appending to a created table from SQL Server
Folks,
The code below reliably crashes an R 2.8.1 session on XP when connected to
an SQL Server 2005 database. The problem arises when appending data using
sqlSave() with rownames=FALSE to a table that had been previously created
with rownames=TRUE. Certainly it's daft to do this as a regular
procedure, but it would be useful for R to catch the error in a more
graceful manner.
require(RODBC)
lakes - odbcConnect('Lakes',uid='cseelige')
ss - data.frame('a'='1234','b'='5678', c=9012, stringsAsFactors=FALSE)
sqlDrop(lakes, 'foofooB')
sqlSave(lakes, ss, 'foofooB', append=TRUE)
sqlSave(lakes, ss, 'foofooB', append=TRUE)
sqlSave(lakes, ss, 'foofooB', append=TRUE, rownames=FALSE)
# That last sqlSave() produces an error, which seems to indicate that
# the table is forever munged even though you sqlDrop() it:
# Error in sqlSave(lakes, ss, foofooB, append = TRUE, rownames =
FALSE) :
# unable to append to table ?foofooB?
sqlDrop(lakes, 'foofooB')
sqlSave(lakes, ss, 'foofooB', append=TRUE)
sqlSave(lakes, ss, 'foofooB', append=TRUE, rownames=FALSE)
# That last line causes the crash.
--
Curt Seeliger, Data Ranger
Raytheon Information Services - Contractor to ORD
seeliger.c...@epa.gov
541/754-4638
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[R] R crashes when using the RODBC Package
Hi,
Ive written some code that fetches data from an Access Database (2003),
processes the data, then saves the modified data back into a table in the
Access database.
It works if I only pass through the code once, but if I put a loop around
the code so that I fetch data from a different source table, and then save
it again to a different destination table, the code crashes. It is either
the final sqlQuery or sqlSave queries. I have no idea why it is crashing.
As an aside, I also have trouble with the odbcCloseAll() command R tends
to crash with that, also.
Im running this on Windows XP, Access 2003, R version 2.7.2
Any insights would be greatly appreciated! The condensed version of the
code is below.
# import the libraries
library(RODBC)
# Close any existing connections
odbcCloseAll()
# Connect to database
channel - odbcConnect(database, uid=, pwd=)
for ( i in 1:2 ) {
# 1. Weekly 2. Monthly
if (i == 1) {
bWeekly - TRUE
} else {
bWeekly - FALSE
}
# Get Prices
if ( bWeekly ) {
tblName - qryDataWeekly_Crosstab
} else {
tblName - qryDataMonthly_Crosstab
}
prices - sqlFetch(channel, tblName, colnames = FALSE, rownames
= TRUE)
# Get Weightings
sql - SELECT BbSecurity, Weighting FROM qryWeightingsUse
sWeights - sqlQuery(channel, sql)
# Copy Data to Database
if ( bWeekly ) {
tblName - tblIndexWeekly
} else {
tblName - tblIndexMonthly
}
sqlQuery(channel, paste(DELETE * FROM , tblName))
sqlSave(channel, indexDf, tablename = tblName, append=TRUE,
rownames=FALSE)
}
odbcClose(channel)
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[R] Call a Fortran subroutine with R: R crashes
Hello,
I am trying to call a FORTRAN subroutine within R and something really
strange happens:
I have a dll-library, that I load with dyn.load('mpbvv.dll'). I have checked
the [Ordinal/Name Pointer] Table for the function within the library that I
want to call - it is there (objdump - p mpbvv.dll).
Then, I have written an R-wrapper to call the FORTRAN subroutine, which
works fine. SInce I have 200 points, at which I have to evaluate the
function, I have to call it 200 times. It works about 100 times just fine
and then R crashes. The values for which the function is evaluated are
almost the same, there no sudden big differences.
The only thing that is probably not really ok is that is.loaded('mpbvv.dll')
returns FALSE. But if I call getLoadedDLLs(), the library is loaded
getLoadedDLLs()
Filename
base base
methods C:/Programme/R/R-2.7.1/library/methods/libs/methods.dll
grDevices C:/Programme/R/R-2.7.1/library/grDevices/libs/grDevices.dll
stats C:/Programme/R/R-2.7.1/library/stats/libs/stats.dll
mpbvvE:/Zoe/DA/mpbvv.dll
Dynamic.Lookup
base FALSE
methodsFALSE
grDevices FALSE
stats FALSE
mpbvv TRUE
I am loading four more libraries:
library('actuar')
library('bbmle')
library('polynom')
library('NORMT3')
Could this be a problem?
I don't have any idea why R crashes. Do you?
Thanks a lot for your advice in advance!
Cheers,
Zoe
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Call a Fortran subroutine with R: R crashes
Zornitsa Luleva wrote:
Hello,
I am trying to call a FORTRAN subroutine within R and something really
strange happens:
I have a dll-library, that I load with dyn.load('mpbvv.dll'). I have checked
the [Ordinal/Name Pointer] Table for the function within the library that I
want to call - it is there (objdump - p mpbvv.dll).
Then, I have written an R-wrapper to call the FORTRAN subroutine, which
works fine. SInce I have 200 points, at which I have to evaluate the
function, I have to call it 200 times. It works about 100 times just fine
and then R crashes. The values for which the function is evaluated are
almost the same, there no sudden big differences.
The only thing that is probably not really ok is that is.loaded('mpbvv.dll')
returns FALSE. But if I call getLoadedDLLs(), the library is loaded
getLoadedDLLs()
Filename
base base
methods C:/Programme/R/R-2.7.1/library/methods/libs/methods.dll
grDevices C:/Programme/R/R-2.7.1/library/grDevices/libs/grDevices.dll
stats C:/Programme/R/R-2.7.1/library/stats/libs/stats.dll
mpbvvE:/Zoe/DA/mpbvv.dll
Dynamic.Lookup
base FALSE
methodsFALSE
grDevices FALSE
stats FALSE
mpbvv TRUE
I am loading four more libraries:
library('actuar')
library('bbmle')
library('polynom')
library('NORMT3')
Could this be a problem?
I don't have any idea why R crashes. Do you?
The most common case is that people's argument lists to .Fortran do not
match up with the expected types and dimensions of the subroutine. This
may (e.g.) cause you to write past the end of an array, leading to
memory corruption that will not be discovered until it trips up the
memory management some time later. Turning gctorture() on may provoke
the error to occur sooner and become easier to pinpoint.
Thanks a lot for your advice in advance!
--
O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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Re: [R] Call a Fortran subroutine with R: R crashes
On Mon, 18 Aug 2008, Zornitsa Luleva wrote:
Hello,
I am trying to call a FORTRAN subroutine within R and something really
strange happens:
Did you read the posting guide? It suggests the R-devel list for
questions about 'C, C++ etc', and Fortran is part of the 'etc'.
I have a dll-library, that I load with dyn.load('mpbvv.dll'). I have checked
the [Ordinal/Name Pointer] Table for the function within the library that I
want to call - it is there (objdump - p mpbvv.dll).
Then, I have written an R-wrapper to call the FORTRAN subroutine, which
works fine. SInce I have 200 points, at which I have to evaluate the
function, I have to call it 200 times. It works about 100 times just fine
and then R crashes. The values for which the function is evaluated are
almost the same, there no sudden big differences.
The only thing that is probably not really ok is that is.loaded('mpbvv.dll')
returns FALSE.
Correctly: please do read the help before posting: ?is.loaded has
symbol: a character string giving a symbol name.
not, note, a DLL name.
But if I call getLoadedDLLs(), the library is loaded
getLoadedDLLs()
Filename
base base
methods C:/Programme/R/R-2.7.1/library/methods/libs/methods.dll
grDevices C:/Programme/R/R-2.7.1/library/grDevices/libs/grDevices.dll
stats C:/Programme/R/R-2.7.1/library/stats/libs/stats.dll
mpbvvE:/Zoe/DA/mpbvv.dll
Dynamic.Lookup
base FALSE
methodsFALSE
grDevices FALSE
stats FALSE
mpbvv TRUE
I am loading four more libraries:
library('actuar')
library('bbmle')
library('polynom')
library('NORMT3')
Could this be a problem?
I don't have any idea why R crashes. Do you?
Most likely an error in your code. Perhaps a mismatch (in type, in
length) between what you pass .Fortran and what your code expects?
Without the reproducible example the posting guide asks for we can only
guess.
Thanks a lot for your advice in advance!
Cheers,
Zoe
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and provide commented, minimal, self-contained, reproducible code.
PLEASE do.
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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[R] R crashes in Leopard
Hi, I have upgraded to Leopard and I just installed 2.6.1. I opened R and then I opened package installer and clicked get List. After about five seconds R stopped responding. and Leopard reported that R had stopped responding and wanted to sent a report to Apple. What do I need to do get a list of packages so I can download and install them? Thanks, Keith Jones __ 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] R crashes using quantreg censored estimation (method fcen)
Dear List, my R session crashes if I repeatedly run the summary function on a quantreg object generated using the censored estimation method or if I set the number of bootstrap repititions reasonably high. Are there any known incompabilities between quantreg and Windows Vista AMD64? The error is reproducable using R 2.6.1 and R 2.5.1. sessionInfo() R version 2.6.1 (2007-11-26) i386-pc-mingw32 locale: LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] quantreg_4.10 SparseM_0.74 Thanks, Malte -Ursprüngliche Nachricht- Von: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Im Auftrag von Jared O'Connell Gesendet: Donnerstag, 29. November 2007 08:57 An: [EMAIL PROTECTED] Cc: [EMAIL PROTECTED] Betreff: Re: [R] Recommended textbooks for R? This page may be helpful :) http://www.r-project.org/doc/bib/R-books.html Modern Applied Statistics with S is quite broad and very good. On Nov 28, 2007 4:38 PM, Max [EMAIL PROTECTED] wrote: Hi everyone! I've recently begun to learn R for my job as the IT department suffers from lack of funding for new software. I was talking to the guy in charge of Requisitions and have found out the budget for books is in great shape. So, I'm curious what books people know of that have R examples and are good for: 1.) Uni and Multivariate Time Series Analysis/Forecasting 2.) GLMs (at this point it looks like I'll be focusing on nominal and ordinal regression models) 3.) Survival Models 4.) Multiple Regression Any suggestions would be awesome. :) thanks, -Max __ 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-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] R crashes using quantreg censored estimation (method fcen)
On Thu, 2007-11-29 at 09:09 +0100, Malte Brockmann wrote: Dear List, my R session crashes if I repeatedly run the summary function on a quantreg object generated using the censored estimation method or if I set the number of bootstrap repititions reasonably high. Are there any known incompabilities between quantreg and Windows Vista AMD64? The error is reproducable using R 2.6.1 and R 2.5.1. Err, what does this have to do with Jared's reply to Max's posting about suitable textbooks and R? Please don't jump on a thread to ask your own question. Start your own thread. If you want people to help you with your problem, you are probably going to have to give a reproducible example - my R session crashes is way below what is requested in the posting guide. Even the statements about what you did are not enough - people need to be able to reproduce your problem on their machines. Read the posting guide (URL in the footer of this email) and resend a message to the list - a new one mind, so you start a new thread. And make sure you include a reproducible example. If you can't send your data, try it with one of the data sets that come with quantreg and if it fails with that also, use that data set in your example. You should also consider contacting the maintainer of quantreg. HTH G sessionInfo() R version 2.6.1 (2007-11-26) i386-pc-mingw32 locale: LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] quantreg_4.10 SparseM_0.74 Thanks, Malte -Ursprüngliche Nachricht- Von: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Im Auftrag von Jared O'Connell Gesendet: Donnerstag, 29. November 2007 08:57 An: [EMAIL PROTECTED] Cc: [EMAIL PROTECTED] Betreff: Re: [R] Recommended textbooks for R? This page may be helpful :) http://www.r-project.org/doc/bib/R-books.html Modern Applied Statistics with S is quite broad and very good. On Nov 28, 2007 4:38 PM, Max [EMAIL PROTECTED] wrote: Hi everyone! I've recently begun to learn R for my job as the IT department suffers from lack of funding for new software. I was talking to the guy in charge of Requisitions and have found out the budget for books is in great shape. So, I'm curious what books people know of that have R examples and are good for: 1.) Uni and Multivariate Time Series Analysis/Forecasting 2.) GLMs (at this point it looks like I'll be focusing on nominal and ordinal regression models) 3.) Survival Models 4.) Multiple Regression Any suggestions would be awesome. :) thanks, -Max __ 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-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. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ 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] R crashes using quantreg censored estimation (method fcen)
Thanks for your advice, Gavin. I hope to comply with the posting guide this time. With crashing I meant that the R-session is simply terminated without an error message (Vista, R2.6.1 and R2.5.1 with precompiled packages, sessionInfo see below). I could reproduce the error on a linux machine (R2.5.1-1 for which I have compiled the packages on my own). On the linux machine I at least get the following error message: *** caught segfault *** address (nil), cause 'unknown' Traceback: 1: .Fortran(xys, as.integer(m), as.integer(n), as.integer(p), as.integer(R), as.integer(m + 5), as.integer(p + 2), as.double(x), as.double(y), as.double(tau), as.double(tol), flag = integer(R), coef = double(p * R), resid = double(m), integer(m), double((m + 5) * (p + 2)), double(m), as.integer(1), sol = double((p + 2)), dsol = double(m), lsol = as.integer(0), xx = double(m * p), yy = double(m), as.integer(s), PACKAGE = quantreg) 2: boot.rq.xy(x, y, s, tau) 3: boot.rq(x[s, ], y[s], tau, ...) 4: summary.fcrq(model.powell, R = r) 5: summary(model.powell, R = 1e+06) I used the following command to generate the model: model.powell - rq(y ~ x1 + x2 + x3 + x4 + x5 + x6 + x7 + x8 + x9, method=fcen, data=data_test) summary(model.powell, R=100) I used 100 replications to make sure that the error is triggered I uploaded the data to www.esbf.de/quantreg/data_test.RData -Ursprüngliche Nachricht- Von: Gavin Simpson [mailto:[EMAIL PROTECTED] Gesendet: Donnerstag, 29. November 2007 11:45 An: Malte Brockmann Cc: [EMAIL PROTECTED] Betreff: Re: [R] R crashes using quantreg censored estimation (method fcen) On Thu, 2007-11-29 at 09:09 +0100, Malte Brockmann wrote: Dear List, my R session crashes if I repeatedly run the summary function on a quantreg object generated using the censored estimation method or if I set the number of bootstrap repititions reasonably high. Are there any known incompabilities between quantreg and Windows Vista AMD64? The error is reproducable using R 2.6.1 and R 2.5.1. Err, what does this have to do with Jared's reply to Max's posting about suitable textbooks and R? Please don't jump on a thread to ask your own question. Start your own thread. If you want people to help you with your problem, you are probably going to have to give a reproducible example - my R session crashes is way below what is requested in the posting guide. Even the statements about what you did are not enough - people need to be able to reproduce your problem on their machines. Read the posting guide (URL in the footer of this email) and resend a message to the list - a new one mind, so you start a new thread. And make sure you include a reproducible example. If you can't send your data, try it with one of the data sets that come with quantreg and if it fails with that also, use that data set in your example. You should also consider contacting the maintainer of quantreg. HTH G sessionInfo() R version 2.6.1 (2007-11-26) i386-pc-mingw32 locale: LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] quantreg_4.10 SparseM_0.74 Thanks, Malte __ 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. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ 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] R crashes using quantreg censored estimation (method fcen)
1. As the posting guide advises, queries about packages should be sent in the first instance to the package author/maintainer before posting to the list. 2. As the posting guide also advises, a _minimal_ reproducible example is desirable not one that claims that somewhere in the middle of 1,000,000 bootstrap replications something goes wrong. I'll try to take a look at this with valgrind, but I can't promise any immediate resolution. url:www.econ.uiuc.edu/~rogerRoger Koenker email[EMAIL PROTECTED]Department of Economics vox: 217-333-4558University of Illinois fax: 217-244-6678Champaign, IL 61820 On Nov 29, 2007, at 6:32 AM, Malte Brockmann wrote: Thanks for your advice, Gavin. I hope to comply with the posting guide this time. With crashing I meant that the R-session is simply terminated without an error message (Vista, R2.6.1 and R2.5.1 with precompiled packages, sessionInfo see below). I could reproduce the error on a linux machine (R2.5.1-1 for which I have compiled the packages on my own). On the linux machine I at least get the following error message: *** caught segfault *** address (nil), cause 'unknown' Traceback: 1: .Fortran(xys, as.integer(m), as.integer(n), as.integer (p), as.integer(R), as.integer(m + 5), as.integer(p + 2), as.double(x), as.double(y), as.double(tau), as.double(tol), flag = integer(R), coef = double(p * R), resid = double(m), integer(m), double((m + 5) * (p + 2)), double(m), as.integer (1), sol = double((p + 2)), dsol = double(m), lsol = as.integer(0), xx = double(m * p), yy = double(m), as.integer(s), PACKAGE = quantreg) 2: boot.rq.xy(x, y, s, tau) 3: boot.rq(x[s, ], y[s], tau, ...) 4: summary.fcrq(model.powell, R = r) 5: summary(model.powell, R = 1e+06) I used the following command to generate the model: model.powell - rq(y ~ x1 + x2 + x3 + x4 + x5 + x6 + x7 + x8 + x9, method=fcen, data=data_test) summary(model.powell, R=100) I used 100 replications to make sure that the error is triggered I uploaded the data to www.esbf.de/quantreg/data_test.RData -Ursprüngliche Nachricht- Von: Gavin Simpson [mailto:[EMAIL PROTECTED] Gesendet: Donnerstag, 29. November 2007 11:45 An: Malte Brockmann Cc: [EMAIL PROTECTED] Betreff: Re: [R] R crashes using quantreg censored estimation (method fcen) On Thu, 2007-11-29 at 09:09 +0100, Malte Brockmann wrote: Dear List, my R session crashes if I repeatedly run the summary function on a quantreg object generated using the censored estimation method or if I set the number of bootstrap repititions reasonably high. Are there any known incompabilities between quantreg and Windows Vista AMD64? The error is reproducable using R 2.6.1 and R 2.5.1. Err, what does this have to do with Jared's reply to Max's posting about suitable textbooks and R? Please don't jump on a thread to ask your own question. Start your own thread. If you want people to help you with your problem, you are probably going to have to give a reproducible example - my R session crashes is way below what is requested in the posting guide. Even the statements about what you did are not enough - people need to be able to reproduce your problem on their machines. Read the posting guide (URL in the footer of this email) and resend a message to the list - a new one mind, so you start a new thread. And make sure you include a reproducible example. If you can't send your data, try it with one of the data sets that come with quantreg and if it fails with that also, use that data set in your example. You should also consider contacting the maintainer of quantreg. HTH G sessionInfo() R version 2.6.1 (2007-11-26) i386-pc-mingw32 locale: LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany. 1252;LC_MONETARY=German_Germany. 1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] quantreg_4.10 SparseM_0.74 Thanks, Malte __ 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. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e
[R] R Crashes on certain calls of Adapt
I'm having trouble with adapt. I'm trying to use it in a Bayesian setting,
to integrate the posterior distribution, and to find posterior means. I
tried using the following script, and things went ok:
data = rnorm(100,0.2,1.1)
data = c(data,rnorm(10,3,1))
data = data[abs(data)2*sd(data)]
prior = function(x){
dgamma(x[2],shape=2,scale=1)*dnorm(x[1],0,.5)
}
liklihood = function(x,val){
prod(dnorm(val,m=x[1],sd=sqrt(.5/x[2])))#/(pnorm(2,x[1],x[2])-pnorm(-2,x[1],x[2]))^length(val)
}
unsc.post = function(x,val){
prior(x)*liklihood(x,val)
}
cons = adapt(2,c(-5,0),c(5,10),f=unsc.post,min=1e+04,max=5e+05,val=data)
However, if I try to add a skewness parameter using sn as follows, I get an
error.
data = rnorm(20,0.2,1.1)
data = c(data,rnorm(1,3,1))
data = data[abs(data)2*sd(data)]
prior = function(x){
dgamma(x[2],shape=2,scale=1)*dnorm(x[1],0,.5)*dnorm(x[3],0,.1)
}
liklihood = function(x,val){
prod(dsn(val,loc=x[1],sc=sqrt(.5/x[2]),sh=x[3]))
}
unsc.post = function(x,val){
prior(x)*liklihood(x,val)
}
cons = adapt(2,c(-5,0,-.5),c(5,10,.5),f=unsc.post,max=5e+05,val=data)
This produces the error:
*** caught segfault ***
address 0x7eaa8580, cause 'memory not mapped'
Traceback:
1: .C(cadapt, as.integer(ndim), as.double(lower), as.double(upper),
minpts = as.integer(minpts), maxpts = as.integer(maxpts), ff, rho =
environment(), as.double(eps), relerr = double(1), lenwrk =
as.integer(lenwrk),
value = double(1), ifail = integer(1), PACKAGE = adapt)
2: adapt(2, c(-5, 0, -0.5), c(5, 10, 0.5), f = unsc.post, max = 5e+05,
val = data)
On a perhaps related note, if I increase the length of data to 1000+10 in
the original example, I get a garbage answer and:
Warning message:
Ifail=2, lenwrk was too small. -- fix adapt() !
Check the returned relerr! in: adapt(2, c(-5, 0), c(5, 10), f = unsc.post,
min = 1, max = 5e+05.
And If I uncomment the line there with data size 100+10, adapt takes forever
and gives me an error saying maxpts is too low (I don't think this is
related to the previous problem, but I thought I'd provide the information
in case it is useful).
Any help would be greatly appreciated.
Thanks,
Omkar Muralidharan
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