R SIG Debian - Dec 2010 - R crashes when making graphs

hi,

i am running R with JGR and Deducer under Ubuntu Mint Lucid. since i updated to
R 2.12 i can no longer make graphs - R just crashes.
the full error report was posted to launchpad
(https://bugs.launchpad.net/ubuntu/+source/openjdk-6/+bug/675905) without any
success so far.

anyone with a similar problem or helpful suggestions?

thanks!
kat

I had a similar problem when I initially upgraded to 2.12.. are you 
using Cairo graphics perchance?

-c

On 12/6/2010 1:42 PM, Manderscheid Katharina wrote:
> hi,
>
> i am running R with JGR and Deducer under Ubuntu Mint Lucid. since i
updated to R 2.12 i can no longer make graphs - R just crashes.
> the full error report was posted to launchpad
(https://bugs.launchpad.net/ubuntu/+source/openjdk-6/+bug/675905) without any
success so far.
>
> anyone with a similar problem or helpful suggestions?
>
> thanks!
> kat
> _______________________________________________
> R-SIG-Debian mailing list
> R-SIG-Debian at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-debian

On 12/06/2010 01:42 PM, Manderscheid Katharina wrote:
> hi,
>
> i am running R with JGR and Deducer under Ubuntu Mint Lucid. since i
updated to R 2.12 i can no longer make graphs - R just crashes.
> the full error report was posted to launchpad
(https://bugs.launchpad.net/ubuntu/+source/openjdk-6/+bug/675905) without any
success so far.
>
> anyone with a similar problem or helpful suggestions?
>
> thanks!
> kat
kat,

I think heading over to the Deducer mailing list will be your best bet:

http://www.deducer.org/manual.html

I have played around with Deducer a little bit in Ubuntu, and it is 
still very much in beta. The mailing list has a pretty fast response rate.

The other thing to do is figure out what program is causing the problem. 
  You are using an slightly older version of Ubuntu with JGR and 
Deducer.  I would first check to make sure you can make graphs with just 
JGR.

Michael

-- 
Dr. Michael A. Rutter
School of Science
Penn State Erie, The Behrend College
Station Road
Erie, PA 16563
http://math.bd.psu.edu/faculty/rutter

it does not seem to be a deducer problem but a jgr one. i cannot make graphs in
jgr without deducer, only in the basic console-version of R.

________________________________________
Von: Michael Rutter [mar36 at psu.edu]
Gesendet: Montag, 6. Dezember 2010 20:01
An: Manderscheid Katharina
Cc: r-sig-debian at r-project.org
Betreff: Re: [R-sig-Debian] R crashes when making graphs

On 12/06/2010 01:42 PM, Manderscheid Katharina wrote:
> hi,
>
> i am running R with JGR and Deducer under Ubuntu Mint Lucid. since i
updated to R 2.12 i can no longer make graphs - R just crashes.
> the full error report was posted to launchpad
(https://bugs.launchpad.net/ubuntu/+source/openjdk-6/+bug/675905) without any
success so far.
>
> anyone with a similar problem or helpful suggestions?
>
> thanks!
> kat
kat,

I think heading over to the Deducer mailing list will be your best bet:

http://www.deducer.org/manual.html

I have played around with Deducer a little bit in Ubuntu, and it is
still very much in beta. The mailing list has a pretty fast response rate.

The other thing to do is figure out what program is causing the problem.
  You are using an slightly older version of Ubuntu with JGR and
Deducer.  I would first check to make sure you can make graphs with just
JGR.

Michael

--
Dr. Michael A. Rutter
School of Science
Penn State Erie, The Behrend College
Station Road
Erie, PA 16563
http://math.bd.psu.edu/faculty/rutter

Please reply to the list.

On Mon, Dec 6, 2010 at 10:35 PM, Manderscheid Katharina
<Katharina.Manderscheid at unilu.ch> wrote:
> other attached packages:
> [1] JGR_1.7-3 ? ?iplots_1.1-3 JavaGD_0.5-3 rJava_0.8-7
>
Seems up to date.

> # JRE version: 6.0_20-b20
> # Java VM: OpenJDK Client VM (19.0-b09 mixed mode, sharing linux-x86 )
>
I see you use openjdk. You might want to try the sun java jdk. Regards
Liviu

here is the sessionInfo:
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: i486-pc-linux-gnu (32-bit)

locale:
 [1] LC_CTYPE=de_CH.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=de_CH.UTF-8        LC_COLLATE=de_CH.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=de_CH.UTF-8
 [7] LC_PAPER=de_CH.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_CH.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] JGR_1.7-3    iplots_1.1-3 JavaGD_0.5-3 rJava_0.8-7

loaded via a namespace (and not attached):
[1] tools_2.12.0

and in the terminal the following:
> #
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00000000, pid=19893, tid=3032509296
#
# JRE version: 6.0_20-b20
# Java VM: OpenJDK Client VM (19.0-b09 mixed mode, sharing linux-x86 )
# Derivative: IcedTea6 1.9.2
# Distribution: Ubuntu 10.04.1 LTS, package 6b20-1.9.2-0ubuntu1~10.04.1
# Problematic frame:
# C  0x00000000
#
# An error report file with more information is saved as:
# /root/hs_err_pid19893.log
#
# If you would like to submit a bug report, please include
# instructions how to reproduce the bug and visit:
#   https://bugs.launchpad.net/ubuntu/+source/openjdk-6/
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#
Aborted

dr. katharina manderscheid

soziologisches seminar
universit?t luzern

kasernenplatz 3
6000 luzern 7

tel. ++41 41 228 4657

________________________________________
Von: Liviu Andronic [landronimirc at gmail.com]
Gesendet: Montag, 6. Dezember 2010 21:17
An: Manderscheid Katharina
Cc: mar36 at psu.edu; r-sig-debian at r-project.org
Betreff: Re: [R-sig-Debian] R crashes when making graphs

On Mon, Dec 6, 2010 at 8:15 PM, Manderscheid Katharina
<Katharina.Manderscheid at unilu.ch> wrote:
> it does not seem to be a deducer problem but a jgr one. i cannot make
graphs in jgr without deducer, only in the basic console-version of R.
>
The Deducer devel is one of JGR devels, so you're still better off
trying your luck there. You didn't give us
sessionInfo()

but make sure your have all your software up to date before. Try
old.packages()
update.packages(ask=F)

Regards
Liviu

hi liviu,

i tried java sun, ran a plot and it crashed again.
here the new error report:
> #
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00000000, pid=5729, tid=3012004720
#
# JRE version: 6.0_22-b04
# Java VM: Java HotSpot(TM) Client VM (17.1-b03 mixed mode, sharing linux-x86 )
# Problematic frame:
# C  0x00000000
#
# An error report file with more information is saved as:
# /root/hs_err_pid5729.log
#
# If you would like to submit a bug report, please visit:
#   http://java.sun.com/webapps/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#
Aborted
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: i486-pc-linux-gnu (32-bit)

locale:
 [1] LC_CTYPE=de_CH.UTF-8          LC_NUMERIC=C                 
 [3] LC_TIME=de_CH.UTF-8           LC_COLLATE=de_CH.UTF-8       
 [5] LC_MONETARY=de_CH.UTF-8       LC_MESSAGES=de_CH.UTF-8      
 [7] LC_PAPER=de_CH.UTF-8          LC_NAME=de_CH.UTF-8          
 [9] LC_ADDRESS=de_CH.UTF-8        LC_TELEPHONE=de_CH.UTF-8     
[11] LC_MEASUREMENT=de_CH.UTF-8    LC_IDENTIFICATION=de_CH.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ctv_0.7-0    JGR_1.7-3    iplots_1.1-3 JavaGD_0.5-3 rJava_0.8-7 

loaded via a namespace (and not attached):
[1] tools_2.12.0

any ideas?
thanks!
k.

dr. katharina manderscheid

soziologisches seminar
universit?t luzern

kasernenplatz 3
6000 luzern 7

tel. ++41 41 228 4657

________________________________________
Von: Liviu Andronic [landronimirc at gmail.com]
Gesendet: Montag, 6. Dezember 2010 22:44
An: Manderscheid Katharina
Cc: R-SIG-DEBIAN
Betreff: Re: [R-sig-Debian] R crashes when making graphs

Please reply to the list.

On Mon, Dec 6, 2010 at 10:35 PM, Manderscheid Katharina
<Katharina.Manderscheid at unilu.ch> wrote:
> other attached packages:
> [1] JGR_1.7-3    iplots_1.1-3 JavaGD_0.5-3 rJava_0.8-7
>
Seems up to date.

> # JRE version: 6.0_20-b20
> # Java VM: OpenJDK Client VM (19.0-b09 mixed mode, sharing linux-x86 )
>
I see you use openjdk. You might want to try the sun java jdk. Regards
Liviu

On Tue, Dec 7, 2010 at 9:05 AM, Manderscheid Katharina
<Katharina.Manderscheid at unilu.ch> wrote:
> hi liviu,
>
> i tried java sun, ran a plot and it crashed again.
> here the new error report:
>> #
> # A fatal error has been detected by the Java Runtime Environment:
> #
> # ?SIGSEGV (0xb) at pc=0x00000000, pid=5729, tid=3012004720
> #
> # JRE version: 6.0_22-b04
> # Java VM: Java HotSpot(TM) Client VM (17.1-b03 mixed mode, sharing
linux-x86 )
>
[..]
>any ideas?
>
Yes, <deducer at googlegroups.com> or
stats-rosuda-devel at listserv.uni-augsburg.de . Can you also post the
exact code that you are running, preferably a reproducible example?

Regards
Liviu

>thanks!
> k.
>
> dr. katharina manderscheid
>
> soziologisches seminar
> universit?t luzern
>
> kasernenplatz 3
> 6000 luzern 7
>
> tel. ++41 41 228 4657
>
> ________________________________________
> Von: Liviu Andronic [landronimirc at gmail.com]
> Gesendet: Montag, 6. Dezember 2010 22:44
> An: Manderscheid Katharina
> Cc: R-SIG-DEBIAN
> Betreff: Re: [R-sig-Debian] R crashes when making graphs
>
> Please reply to the list.
>
> On Mon, Dec 6, 2010 at 10:35 PM, Manderscheid Katharina
> <Katharina.Manderscheid at unilu.ch> wrote:
>> other attached packages:
>> [1] JGR_1.7-3 ? ?iplots_1.1-3 JavaGD_0.5-3 rJava_0.8-7
>>
> Seems up to date.
>
>
>> # JRE version: 6.0_20-b20
>> # Java VM: OpenJDK Client VM (19.0-b09 mixed mode, sharing linux-x86 )
>>
> I see you use openjdk. You might want to try the sun java jdk. Regards
> Liviu
>


-- 
Do you know how to read?
http://www.alienetworks.com/srtest.cfm
http://goodies.xfce.org/projects/applications/xfce4-dict#speed-reader
Do you know how to write?
http://garbl.home.comcast.net/~garbl/stylemanual/e.htm#e-mail

here is the example i am using to test if it works.
> data(airquality)
> plot(airquality$Temp)
________________________________________
Von: Liviu Andronic [landronimirc at gmail.com]
Gesendet: Dienstag, 7. Dezember 2010 09:14
An: Manderscheid Katharina
Cc: R-SIG-DEBIAN
Betreff: Re: [R-sig-Debian] R crashes when making graphs

On Tue, Dec 7, 2010 at 9:05 AM, Manderscheid Katharina
<Katharina.Manderscheid at unilu.ch> wrote:
> hi liviu,
>
> i tried java sun, ran a plot and it crashed again.
> here the new error report:
>> #
> # A fatal error has been detected by the Java Runtime Environment:
> #
> #  SIGSEGV (0xb) at pc=0x00000000, pid=5729, tid=3012004720
> #
> # JRE version: 6.0_22-b04
> # Java VM: Java HotSpot(TM) Client VM (17.1-b03 mixed mode, sharing
linux-x86 )
>
[..]
>any ideas?
>
Yes, <deducer at googlegroups.com> or
stats-rosuda-devel at listserv.uni-augsburg.de . Can you also post the
exact code that you are running, preferably a reproducible example?

Regards
Liviu

>thanks!
> k.
>
> dr. katharina manderscheid
>
> soziologisches seminar
> universit?t luzern
>
> kasernenplatz 3
> 6000 luzern 7
>
> tel. ++41 41 228 4657
>
> ________________________________________
> Von: Liviu Andronic [landronimirc at gmail.com]
> Gesendet: Montag, 6. Dezember 2010 22:44
> An: Manderscheid Katharina
> Cc: R-SIG-DEBIAN
> Betreff: Re: [R-sig-Debian] R crashes when making graphs
>
> Please reply to the list.
>
> On Mon, Dec 6, 2010 at 10:35 PM, Manderscheid Katharina
> <Katharina.Manderscheid at unilu.ch> wrote:
>> other attached packages:
>> [1] JGR_1.7-3    iplots_1.1-3 JavaGD_0.5-3 rJava_0.8-7
>>
> Seems up to date.
>
>
>> # JRE version: 6.0_20-b20
>> # Java VM: OpenJDK Client VM (19.0-b09 mixed mode, sharing linux-x86 )
>>
> I see you use openjdk. You might want to try the sun java jdk. Regards
> Liviu
>


--
Do you know how to read?
http://www.alienetworks.com/srtest.cfm
http://goodies.xfce.org/projects/applications/xfce4-dict#speed-reader
Do you know how to write?
http://garbl.home.comcast.net/~garbl/stylemanual/e.htm#e-mail

Lets find out if you have more than one installed first.

Run this in R
> .libPaths()
--> did do:
> .libPaths()
[1] "/home/kat/R/i486-pc-linux-gnu-library/2.12"
[2] "/usr/local/lib/R/site-library"             
[3] "/usr/lib/R/site-library"                   
[4] "/usr/lib/R/library"          

That will show all the places where R looks for things.

Check each one of those locations for JGR or Deducer.  If there's only
one installed, then obviously I'm wrong.

--> i manually deinstalled in all librarys Deducer and JGR with
remove.packages.
--> then i reinstalled JGR with the comands from your earlier mail 
sudo R CMD  javareconf
sudo R
install.packages("JGR", dep=T,
lib="/usr/local/lib/R/site-library")
> JGR()
Starting JGR ...
(You can use /usr/local/lib/R/site-library/JGR/scripts/run to start JGR
directly)
> 
JGR starts, but plotting still makes it crash.
f***
hope, you have any more good ideas?
katharina






--
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas

i fixed it - hurray!
a complete de-installation and removal of all r-files and a nice clean new
installation did the trick. i guess you were right that there were some problems
caused by the various libraries around.
thanks a lot for your support,
katharina


________________________________________
Von: Paul Johnson [pauljohn32 at gmail.com]
Gesendet: Donnerstag, 9. Dezember 2010 20:14
An: Manderscheid Katharina
Betreff: Re: [R-sig-Debian] R crashes when making graphs

Well, I am out of guesses.

Make sure you did remove JGR.  I think remove.packages() might not get
all of them.  In fact, if you have JGR in /usr/lib, I'm certain
remove.packages() will not remove it.  Are you certain there are no
other copies in those other places?

I think you have a problem that is not right for r-sig-debian, because
it is looking like a JGR problem.  There is a list for JGR support,
they are very eager to help.

pj

On Thu, Dec 9, 2010 at 2:45 AM, Manderscheid Katharina
<Katharina.Manderscheid at unilu.ch> wrote:
>
> Lets find out if you have more than one installed first.
>
> Run this in R
>
>> .libPaths()
>
> --> did do:
>> .libPaths()
> [1] "/home/kat/R/i486-pc-linux-gnu-library/2.12"
> [2] "/usr/local/lib/R/site-library"
> [3] "/usr/lib/R/site-library"
> [4] "/usr/lib/R/library"
>
> That will show all the places where R looks for things.
>
> Check each one of those locations for JGR or Deducer.  If there's only
> one installed, then obviously I'm wrong.
>
> --> i manually deinstalled in all librarys Deducer and JGR with
remove.packages.
> --> then i reinstalled JGR with the comands from your earlier mail
> sudo R CMD  javareconf
> sudo R
> install.packages("JGR", dep=T,
lib="/usr/local/lib/R/site-library")
>> JGR()
> Starting JGR ...
> (You can use /usr/local/lib/R/site-library/JGR/scripts/run to start JGR
directly)
>>
> JGR starts, but plotting still makes it crash.
> f***
> hope, you have any more good ideas?
> katharina
>
>
>
>
>
>
> --
> Paul E. Johnson
> Professor, Political Science
> 1541 Lilac Lane, Room 504
> University of Kansas
>


--
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas