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Hotz, T.

2003-May-08 13:04 UTC

R crashes with package SJava; was [R] Memory leakage?

Dear all,

Maybe this has something to do with R crashing?
When my R version crashes, there is Rgui.exe still
running in the background (i.e. W2K's task manager
recognises it only as a process, which apparently 
is using almost 100% of the CPU).

I can reproduce that by "using" the SJava package 
(from Brian Ripley's homepage, as suggested on 
http://www.omegahat.org/RSJava/). When loading the 
package, and running the ttest example, my Rgui.exe 
crashes, and I end up with the process Rgui.exe 
still alive using the CPU extensively. The same 
happens on my stand-alone machine at home (with the 
same OS and R versions but newest Sun JDK).

Any comments greatly appreciated.

Best wishes

Thomas

P.S. At the end an error message appears, but I'm not 
able to sink it. I could run it in a terminal - but 
are there other possibilities?

--- R code pasted into Rgui

rm(list=ls())
# see below for ouput,
# used sink to get probale error messages
# (doesn't work; can one "sink" error messages?)
sink("k:/SJavaFault.rout")
version
# load SJava
library(SJava)
library(help=SJava)
.JavaInit()
# try SJava
.Java("Math","PI")
# load example
source("d:/R/rw1062/library/SJava/examples/ttest.R")
x<-rnorm(10)
y<-rnorm(10,1)
# test example, crashes after specifying x and y in the dialog and pressing
"Submit"
dialog.t.test()
# Rgui.exe still running as a process, but not an application (according to task
manager)


--- Output of sink and library(help=...)

         _              
platform i386-pc-mingw32
arch     i386           
os       mingw32        
system   i386, mingw32  
status                  
major    1              
minor    6.2            
year     2003           
month    01             
day      10             
language R              
using JAVA_HOME = Y:/Java Development Kit/Java2sdk1.4/jre 

[...]
Package: SJava
Version: 0.65
Date: 2002/07/17
Title: The Omegahat interface for R and Java.
Author: Duncan Temple Lang <duncan at research.bell-labs.com>, John
        Chambers <jmc at research.bell-labs.com>
Depends: R (>= 1.1.0)
Maintainer: Duncan Temple Lang <duncan at research.bell-labs.com>
Description: An interface from R to Java to create and call Java
        objects and methods.
License: GPL version 2 or newer. http://www.gnu.org/copyleft/gpl.html
URL: http://www.omegahat.org/RSJava, http://www.omegahat.org
        http://www.omegahat.org/bugs
Built: R 1.6.2; Win32; Thu Feb 27 19:18:38 GMTST 2003
[...]

[1] 3.141593
$id
[1] "1"

$value
$value$actionPerformed
function(ev) {
   cmd <- ev$getActionCommand()
   if(cmd == "Reset")
     reset()
   else {
     print(compute())
   }

  NULL
 }
<environment: 013B8AC4>


$className
character(0)

$targetClasses
character(0)

attr(,"class")
[1] "AnonymousRReference"

---

Thomas Hotz
Research Associate in Medical Statistics
University of Leicester
United Kingdom

Department of Epidemiology and Public Health
22-28 Princess Road West
Leicester
LE1 6TP
Tel +44 116 252-5410
Fax +44 116 252-5423

Division of Medicine for the Elderly
Department of Medicine
The Glenfield Hospital
Leicester
LE3 9QP
Tel +44 116 256-3643
Fax +44 116 232-2976


-----Original Message-----
From: Duncan Murdoch [mailto:dmurdoch at pair.com]
Sent: 03 May 2003 23:59
To: tshi at itsa.ucsf.edu
Cc: r-help at stat.math.ethz.ch
Subject: Re: [R] Memory leakage?


On Sat, 03 May 2003 20:33:49 +0000, you wrote:
>I haven't tried re-installing windows yet, because it seems to be a big
task
>for me and also I kind of doubt that the problem is due to my own 
>computer(s), because the same problem happens to 3 different computers: one 
>Dell desktop in school runing Win2K and R 1.6.1, my Dell laptop runing Win 
>XP Professional Edition and R 1.7.0 and my new Dell desktop at home (just 
>bought less than a month and only a few basic softwares were installed) 
>runing Win XP Home Edition and R1.7.0.  (may be they're all from Dell
:-))
>I'm still looking for the pattern of when this happens, but so far, it
seems
>to be random.
I don't think it's a Windows problem.  I've seen it occasionally,
but
not reproducibly.  If you can figure out some sequence of operations
that reliably produces it, please let me know.

Duncan Murdoch

______________________________________________
R-help at stat.math.ethz.ch mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help

Christian Schulz

2003-May-08 13:45 UTC

head link

R crashes with package SJava; was [R] Memory leakage?

Hmm,

this steps run without problems on my locale win2k.
Perhaps you make the same mistake like me in the past
and have no file named .Renviron  with entry

JAVA_HOME = c:/YourPath/j2re1.4.1_02

and saved in \rw1070 ?
>> library(sjava)
using JAVA_HOME = c:/Programme/Java/j2re1.4.1_02>>.JavaInit()
>>source("C:/Chris/dm/rw1070/library/SJava/examples/calc.R")
>>calc()[[1]]
$id
[1] "1"

$value
$value$actionPerformed
function(ev) {
   txt <- ev$getActionCommand()
   back <- 0
   if(txt == "=") {
     txt <- input$getText()
     val <- as.character(eval(parse(text=txt)))
     input$setText(val)
     jcombo$getModel()$insertElementAt(txt, as.integer(0))
     return(NULL)
   } else if(!is.na(match(txt, unaryOps))) {
     if(txt == "()")
       txt <- ""
     val <- paste(txt, "()",sep="")
     back <- -1
   } else if(txt == "Clear") {
      input$setText("")
      return(NULL)
   } else {
     val <- txt
   }

    doc <- input$getDocument()
    doc$insertString(input$getCaretPosition(), val, NULL)
    if(back < 0) {
      input$setCaretPosition(as.integer(input$getCaretPosition() + back))
    }
 }
<environment: 0194B3CC>


$className
character(0)

$targetClasses
character(0)

attr(,"class")
[1] "AnonymousRReference"

$input
$key
[1] "67"

$className
[1] "javax.swing.plaf.metal.MetalComboBoxEditor$1"

attr(,"class")
[1] "AnonymousOmegahatReference"
>>calc()


----- Original Message -----
From: "Hotz, T." <th50 at leicester.ac.uk>
To: <r-help at stat.math.ethz.ch>
Cc: "Duncan Murdoch" <dmurdoch at pair.com>; <tshi at
itsa.ucsf.edu>
Sent: Thursday, May 08, 2003 3:04 PM
Subject: R crashes with package SJava; was [R] Memory leakage?

> Dear all,
>
> Maybe this has something to do with R crashing?
> When my R version crashes, there is Rgui.exe still
> running in the background (i.e. W2K's task manager
> recognises it only as a process, which apparently
> is using almost 100% of the CPU).
>
> I can reproduce that by "using" the SJava package
> (from Brian Ripley's homepage, as suggested on
> http://www.omegahat.org/RSJava/). When loading the
> package, and running the ttest example, my Rgui.exe
> crashes, and I end up with the process Rgui.exe
> still alive using the CPU extensively. The same
> happens on my stand-alone machine at home (with the
> same OS and R versions but newest Sun JDK).
>
> Any comments greatly appreciated.
>
> Best wishes
>
> Thomas
>
> P.S. At the end an error message appears, but I'm not
> able to sink it. I could run it in a terminal - but
> are there other possibilities?
>
> --- R code pasted into Rgui
>
> rm(list=ls())
> # see below for ouput,
> # used sink to get probale error messages
> # (doesn't work; can one "sink" error messages?)
> sink("k:/SJavaFault.rout")
> version
> # load SJava
> library(SJava)
> library(help=SJava)
> .JavaInit()
> # try SJava
> .Java("Math","PI")
> # load example
> source("d:/R/rw1062/library/SJava/examples/ttest.R")
> x<-rnorm(10)
> y<-rnorm(10,1)
> # test example, crashes after specifying x and y in the dialog and
pressing "Submit"> dialog.t.test()
> # Rgui.exe still running as a process, but not an application (according
to task manager)>
>
> --- Output of sink and library(help=...)
>
>          _
> platform i386-pc-mingw32
> arch     i386
> os       mingw32
> system   i386, mingw32
> status
> major    1
> minor    6.2
> year     2003
> month    01
> day      10
> language R
> using JAVA_HOME = Y:/Java Development Kit/Java2sdk1.4/jre
>
> [...]
> Package: SJava
> Version: 0.65
> Date: 2002/07/17
> Title: The Omegahat interface for R and Java.
> Author: Duncan Temple Lang <duncan at research.bell-labs.com>, John
>         Chambers <jmc at research.bell-labs.com>
> Depends: R (>= 1.1.0)
> Maintainer: Duncan Temple Lang <duncan at research.bell-labs.com>
> Description: An interface from R to Java to create and call Java
>         objects and methods.
> License: GPL version 2 or newer. http://www.gnu.org/copyleft/gpl.html
> URL: http://www.omegahat.org/RSJava, http://www.omegahat.org
>         http://www.omegahat.org/bugs
> Built: R 1.6.2; Win32; Thu Feb 27 19:18:38 GMTST 2003
> [...]
>
> [1] 3.141593
> $id
> [1] "1"
>
> $value
> $value$actionPerformed
> function(ev) {
>    cmd <- ev$getActionCommand()
>    if(cmd == "Reset")
>      reset()
>    else {
>      print(compute())
>    }
>
>   NULL
>  }
> <environment: 013B8AC4>
>
>
> $className
> character(0)
>
> $targetClasses
> character(0)
>
> attr(,"class")
> [1] "AnonymousRReference"
>
> ---
>
> Thomas Hotz
> Research Associate in Medical Statistics
> University of Leicester
> United Kingdom
>
> Department of Epidemiology and Public Health
> 22-28 Princess Road West
> Leicester
> LE1 6TP
> Tel +44 116 252-5410
> Fax +44 116 252-5423
>
> Division of Medicine for the Elderly
> Department of Medicine
> The Glenfield Hospital
> Leicester
> LE3 9QP
> Tel +44 116 256-3643
> Fax +44 116 232-2976
>
>
> -----Original Message-----
> From: Duncan Murdoch [mailto:dmurdoch at pair.com]
> Sent: 03 May 2003 23:59
> To: tshi at itsa.ucsf.edu
> Cc: r-help at stat.math.ethz.ch
> Subject: Re: [R] Memory leakage?
>
>
> On Sat, 03 May 2003 20:33:49 +0000, you wrote:
>
> >I haven't tried re-installing windows yet, because it seems to be a
big
task> >for me and also I kind of doubt that the problem is due to my own
> >computer(s), because the same problem happens to 3 different computers:
one> >Dell desktop in school runing Win2K and R 1.6.1, my Dell laptop runing
Win> >XP Professional Edition and R 1.7.0 and my new Dell desktop at home
(just
> >bought less than a month and only a few basic softwares were installed)
> >runing Win XP Home Edition and R1.7.0.  (may be they're all from
Dell
:-))> >I'm still looking for the pattern of when this happens, but so far,
it
seems> >to be random.
>
> I don't think it's a Windows problem.  I've seen it
occasionally, but
> not reproducibly.  If you can figure out some sequence of operations
> that reliably produces it, please let me know.
>
> Duncan Murdoch
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-help
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-help

Hotz, T.

2003-May-08 13:59 UTC

head link

R crashes with package SJava; was [R] Memory leakage?

As is visible from the output, I set JAVA_HOME properly 
in my .Renviron file. Otherwise I couldn't even call .Java(). 
However, I use R 1.6.2, maybe that's the problem (although the
SJava version I use was built for R 1.6.2). Example calc() 
doesn't cause R to crash, but gives me the following warning
when called twice:

Warning message: 
`restart' is deprecated.
Use `try' instead.
See ?Deprecated. 

Moreover, I don't really understand the example: where am I
supposed to get the result of the calculation? I don't see it
in the Java Dialog, and can't spot it in the return value 
either.

Regards

Thomas

-----Original Message-----
From: Christian Schulz [mailto:ozric at web.de]
Sent: 08 May 2003 14:46
To: Hotz, T.; r-help at stat.math.ethz.ch
Subject: Re: R crashes with package SJava; was [R] Memory leakage?


Hmm,

this steps run without problems on my locale win2k.
Perhaps you make the same mistake like me in the past
and have no file named .Renviron  with entry

JAVA_HOME = c:/YourPath/j2re1.4.1_02

and saved in \rw1070 ?
>> library(sjava)
using JAVA_HOME = c:/Programme/Java/j2re1.4.1_02>>.JavaInit()
>>source("C:/Chris/dm/rw1070/library/SJava/examples/calc.R")
>>calc()[[1]]
$id
[1] "1"

$value
$value$actionPerformed
function(ev) {
   txt <- ev$getActionCommand()
   back <- 0
   if(txt == "=") {
     txt <- input$getText()
     val <- as.character(eval(parse(text=txt)))
     input$setText(val)
     jcombo$getModel()$insertElementAt(txt, as.integer(0))
     return(NULL)
   } else if(!is.na(match(txt, unaryOps))) {
     if(txt == "()")
       txt <- ""
     val <- paste(txt, "()",sep="")
     back <- -1
   } else if(txt == "Clear") {
      input$setText("")
      return(NULL)
   } else {
     val <- txt
   }

    doc <- input$getDocument()
    doc$insertString(input$getCaretPosition(), val, NULL)
    if(back < 0) {
      input$setCaretPosition(as.integer(input$getCaretPosition() + back))
    }
 }
<environment: 0194B3CC>


$className
character(0)

$targetClasses
character(0)

attr(,"class")
[1] "AnonymousRReference"

$input
$key
[1] "67"

$className
[1] "javax.swing.plaf.metal.MetalComboBoxEditor$1"

attr(,"class")
[1] "AnonymousOmegahatReference"
>>calc()


----- Original Message -----
From: "Hotz, T." <th50 at leicester.ac.uk>
To: <r-help at stat.math.ethz.ch>
Cc: "Duncan Murdoch" <dmurdoch at pair.com>; <tshi at
itsa.ucsf.edu>
Sent: Thursday, May 08, 2003 3:04 PM
Subject: R crashes with package SJava; was [R] Memory leakage?

> Dear all,
>
> Maybe this has something to do with R crashing?
> When my R version crashes, there is Rgui.exe still
> running in the background (i.e. W2K's task manager
> recognises it only as a process, which apparently
> is using almost 100% of the CPU).
>
> I can reproduce that by "using" the SJava package
> (from Brian Ripley's homepage, as suggested on
> http://www.omegahat.org/RSJava/). When loading the
> package, and running the ttest example, my Rgui.exe
> crashes, and I end up with the process Rgui.exe
> still alive using the CPU extensively. The same
> happens on my stand-alone machine at home (with the
> same OS and R versions but newest Sun JDK).
>
> Any comments greatly appreciated.
>
> Best wishes
>
> Thomas
>
> P.S. At the end an error message appears, but I'm not
> able to sink it. I could run it in a terminal - but
> are there other possibilities?
>
> --- R code pasted into Rgui
>
> rm(list=ls())
> # see below for ouput,
> # used sink to get probale error messages
> # (doesn't work; can one "sink" error messages?)
> sink("k:/SJavaFault.rout")
> version
> # load SJava
> library(SJava)
> library(help=SJava)
> .JavaInit()
> # try SJava
> .Java("Math","PI")
> # load example
> source("d:/R/rw1062/library/SJava/examples/ttest.R")
> x<-rnorm(10)
> y<-rnorm(10,1)
> # test example, crashes after specifying x and y in the dialog and
pressing "Submit"> dialog.t.test()
> # Rgui.exe still running as a process, but not an application (according
to task manager)>
>
> --- Output of sink and library(help=...)
>
>          _
> platform i386-pc-mingw32
> arch     i386
> os       mingw32
> system   i386, mingw32
> status
> major    1
> minor    6.2
> year     2003
> month    01
> day      10
> language R
> using JAVA_HOME = Y:/Java Development Kit/Java2sdk1.4/jre
>
> [...]
> Package: SJava
> Version: 0.65
> Date: 2002/07/17
> Title: The Omegahat interface for R and Java.
> Author: Duncan Temple Lang <duncan at research.bell-labs.com>, John
>         Chambers <jmc at research.bell-labs.com>
> Depends: R (>= 1.1.0)
> Maintainer: Duncan Temple Lang <duncan at research.bell-labs.com>
> Description: An interface from R to Java to create and call Java
>         objects and methods.
> License: GPL version 2 or newer. http://www.gnu.org/copyleft/gpl.html
> URL: http://www.omegahat.org/RSJava, http://www.omegahat.org
>         http://www.omegahat.org/bugs
> Built: R 1.6.2; Win32; Thu Feb 27 19:18:38 GMTST 2003
> [...]
>
> [1] 3.141593
> $id
> [1] "1"
>
> $value
> $value$actionPerformed
> function(ev) {
>    cmd <- ev$getActionCommand()
>    if(cmd == "Reset")
>      reset()
>    else {
>      print(compute())
>    }
>
>   NULL
>  }
> <environment: 013B8AC4>
>
>
> $className
> character(0)
>
> $targetClasses
> character(0)
>
> attr(,"class")
> [1] "AnonymousRReference"
>
> ---
>
> Thomas Hotz
> Research Associate in Medical Statistics
> University of Leicester
> United Kingdom
>
> Department of Epidemiology and Public Health
> 22-28 Princess Road West
> Leicester
> LE1 6TP
> Tel +44 116 252-5410
> Fax +44 116 252-5423
>
> Division of Medicine for the Elderly
> Department of Medicine
> The Glenfield Hospital
> Leicester
> LE3 9QP
> Tel +44 116 256-3643
> Fax +44 116 232-2976
>
>
> -----Original Message-----
> From: Duncan Murdoch [mailto:dmurdoch at pair.com]
> Sent: 03 May 2003 23:59
> To: tshi at itsa.ucsf.edu
> Cc: r-help at stat.math.ethz.ch
> Subject: Re: [R] Memory leakage?
>
>
> On Sat, 03 May 2003 20:33:49 +0000, you wrote:
>
> >I haven't tried re-installing windows yet, because it seems to be a
big
task> >for me and also I kind of doubt that the problem is due to my own
> >computer(s), because the same problem happens to 3 different computers:
one> >Dell desktop in school runing Win2K and R 1.6.1, my Dell laptop runing
Win> >XP Professional Edition and R 1.7.0 and my new Dell desktop at home
(just
> >bought less than a month and only a few basic softwares were installed)
> >runing Win XP Home Edition and R1.7.0.  (may be they're all from
Dell
:-))> >I'm still looking for the pattern of when this happens, but so far,
it
seems> >to be random.
>
> I don't think it's a Windows problem.  I've seen it
occasionally, but
> not reproducibly.  If you can figure out some sequence of operations
> that reliably produces it, please let me know.
>
> Duncan Murdoch
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-help
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-help

Tao Shi

2003-May-09 19:48 UTC

head link

R crashes with package SJava; was [R] Memory leakage?

I observe this even when I exit R naturally by close the R windows or type 
q().  I'm still searching for the patterns.............  One thing for sure 
(may be kind of obvious to you guys) is that this only happens when the CPU 
is already runing at 100% before I exit R.

...Tao

---------------------------------------------------------------------
Dear all,

Maybe this has something to do with R crashing?
When my R version crashes, there is Rgui.exe still
running in the background (i.e. W2K's task manager
recognises it only as a process, which apparently
is using almost 100% of the CPU).

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