I have downloaded and tried to install JGR - Java GUI for R - Version 1.5. I followed all the instructions (at least in my best resolution) and installed Java latest version. R installation complete fine. Has anyone succeded in installing JGR on SuSE 10.3 ? In the following I hade detailed the failed installation, As root /i did the following: linux-Mimin:/usr/local/bin # ./R R version 2.6.0 (2007-10-03) Copyright (C) 2007 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.> install.packages("JGR",dep=TRUE)--- Please select a CRAN mirror for use in this session --- CRAN mirror 1: Argentina 2: Australia (QLD) 3: Australia (VIC) 4: Austria 5: Belgium 6: Brazil (PR) 7: Brazil (MG) 8: Brazil (RJ) 9: Brazil (SP 1) 10: Brazil (SP 2) 11: Canada (BC) 12: Canada (ON) 13: Chile (Santiago) 14: Croatia 15: Czech Republic 16: Denmark 17: France (Toulouse) 18: France (Lyon) 19: France (Paris) 20: Germany (Bamberg) 21: Germany (Mainz) 22: Germany (Muenchen) 23: India (Kolkata) 24: India 25: Ireland 26: Italy (Ferrara) 27: Italy (Milano) 28: Italy (Padua) 29: Italy (Palermo) 30: Japan (Aizu) 31: Japan (Tokyo) 32: Japan (Tsukuba) 33: Korea 34: Netherlands (Amsterdam 2) 35: Netherlands (Amsterdam) 36: Netherlands (Utrecht) 37: Norway 38: Poland (Lublin) 39: Poland (Wroclaw) 40: Portugal 41: Slovenia (Ljubljana) 42: South Africa 43: Spain (Madrid) 44: Sweden 45: Switzerland (Zuerich) 46: Switzerland (Bern) 47: Taiwan (Taichung) 48: Taiwan (Taipeh) 49: UK (Bristol) 50: UK (London) 51: USA (CA 1) 52: USA (CA 3) 53: USA (CA 2) 54: USA (IA) 55: USA (IL) 56: USA (MI) 57: USA (MO) 58: USA (NC) 59: USA (PA 2) 60: USA (PA) 61: USA (TX) 62: USA (WA) Selection: 20 trying URL 'http://www.centervenus.com/mirrors/CRAN/src/contrib/JGR_1.5-5.tar.gz' Content type 'application/x-gzip' length 370920 bytes (362 Kb) opened URL =================================================downloaded 362 Kb * Installing *source* package 'JGR' ... ** R ** inst ** help >>> Building/Updating help pages for package 'JGR' Formats: text html latex example jgr.addMenu text html latex example jgr.addMenuItem text html latex example jgr.addMenuSeperator text html latex example supplements text html latex ** building package indices ... * DONE (JGR) The downloaded packages are in /tmp/Rtmp8XtRf8/downloaded_packages Updating HTML index of packages in '.Library'> library(JGR)Loading required package: rJava Loading required package: JavaGD Loading required package: iplots R: xcb_xlib.c:52: xcb_xlib_unlock: Assertion `c->xlib.lock' failed. Aborted Thank you in advance -- Maura E.M
This is a known problem with Suse10.3 --- lots of things that use Java
(e.g., Matlab) produce the same error message. I'm currently trying to
fix this upon my machine, but haven't succeeded yet. Josh Triplett
(http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6532373) suggested
the following:
---begin---
I worked with jcristau and christoph4 via IRC on #debian-x, and we
managed to
track down the problem with broken locking in Sun Java 1.5 and 1.6. It only
occurs if Java finds the Xinerama extension, at which point it does
something
broken with locking and triggers the assertion. If Java never finds the
Xinerama extension, it doesn't trigger the assertion for broken locking.
The following workarounds address this problem:
For sun-java5-bin:
sed -i 's/XINERAMA/FAKEEXTN/g'
/usr/lib/jvm/java-1.5.0-sun-1.5.0.11/jre/lib/i386/xawt/libmawt.so
---end---
You need to modify the path for your jre. This seems to have helped
several people. But it didn't work for me.
A sure fix is going back to Suse10.2! :(
Ted.
--
Dr E.A. Catchpole
Visiting Fellow
Univ of New South Wales at ADFA, Canberra, Australia
_ and University of Kent, Canterbury, England
'v' - www.pems.adfa.edu.au/~ecatchpole
/ \ - fax: +61 2 6268 8786
m m - ph: +61 2 6268 8895
Maura E Monville wrote on 11/01/2007 09:43 AM:> I have downloaded and tried to install JGR - Java GUI for R - Version 1.5.
> I followed all the instructions (at least in my best resolution) and
> installed Java latest version.
> R installation complete fine.
> Has anyone succeded in installing JGR on SuSE 10.3 ?
> In the following I hade detailed the failed installation,
>
> As root /i did the following:
> linux-Mimin:/usr/local/bin # ./R
>
> R version 2.6.0 (2007-10-03)
> Copyright (C) 2007 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
> Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
>
>> install.packages("JGR",dep=TRUE)
>>
> --- Please select a CRAN mirror for use in this session ---
> CRAN mirror
>
> 1: Argentina 2: Australia (QLD)
> 3: Australia (VIC) 4: Austria
> 5: Belgium 6: Brazil (PR)
> 7: Brazil (MG) 8: Brazil (RJ)
> 9: Brazil (SP 1) 10: Brazil (SP 2)
> 11: Canada (BC) 12: Canada (ON)
> 13: Chile (Santiago) 14: Croatia
> 15: Czech Republic 16: Denmark
> 17: France (Toulouse) 18: France (Lyon)
> 19: France (Paris) 20: Germany (Bamberg)
> 21: Germany (Mainz) 22: Germany (Muenchen)
> 23: India (Kolkata) 24: India
> 25: Ireland 26: Italy (Ferrara)
> 27: Italy (Milano) 28: Italy (Padua)
> 29: Italy (Palermo) 30: Japan (Aizu)
> 31: Japan (Tokyo) 32: Japan (Tsukuba)
> 33: Korea 34: Netherlands (Amsterdam 2)
> 35: Netherlands (Amsterdam) 36: Netherlands (Utrecht)
> 37: Norway 38: Poland (Lublin)
> 39: Poland (Wroclaw) 40: Portugal
> 41: Slovenia (Ljubljana) 42: South Africa
> 43: Spain (Madrid) 44: Sweden
> 45: Switzerland (Zuerich) 46: Switzerland (Bern)
> 47: Taiwan (Taichung) 48: Taiwan (Taipeh)
> 49: UK (Bristol) 50: UK (London)
> 51: USA (CA 1) 52: USA (CA 3)
> 53: USA (CA 2) 54: USA (IA)
> 55: USA (IL) 56: USA (MI)
> 57: USA (MO) 58: USA (NC)
> 59: USA (PA 2) 60: USA (PA)
> 61: USA (TX) 62: USA (WA)
>
>
> Selection: 20
> trying URL
'http://www.centervenus.com/mirrors/CRAN/src/contrib/JGR_1.5-5.tar.gz'
> Content type 'application/x-gzip' length 370920 bytes (362 Kb)
> opened URL
> =================================================> downloaded 362 Kb
>
> * Installing *source* package 'JGR' ...
> ** R
> ** inst
> ** help
> >>> Building/Updating help pages for package 'JGR'
> Formats: text html latex example
> jgr.addMenu text html latex example
> jgr.addMenuItem text html latex example
> jgr.addMenuSeperator text html latex example
> supplements text html latex
> ** building package indices ...
> * DONE (JGR)
>
> The downloaded packages are in
> /tmp/Rtmp8XtRf8/downloaded_packages
> Updating HTML index of packages in '.Library'
>
>> library(JGR)
>>
> Loading required package: rJava
> Loading required package: JavaGD
> Loading required package: iplots
> R: xcb_xlib.c:52: xcb_xlib_unlock: Assertion `c->xlib.lock' failed.
> Aborted
>
>
> Thank you in advance
>
Maura, The workaround from https://bugzilla.novell.com/show_bug.cgi?id=330991 seems to fix this for most people (but not me): just add export LIBXCB_ALLOW_SLOPPY_LOCK=1 to your ~/.profile file (or to /etc/profile to make it available for all users). Ted. Maura E Monville wrote on 11/03/2007 04:35 AM:> Thank you . > I followed all the path on my installation. I got the following: > mauede at linux-Mimin:/usr/lib/jvm/java-1.6.0.u3-sun-1.6.0.u3/jre/lib/i386> ll > total 636 > -rwxr-xr-x 1 root root 80594 2007-09-25 01:10 libjavaplugin_jni.so > -rwxr-xr-x 1 root root 297535 2007-09-25 01:10 libjavaplugin_nscp_gcc29.so > -rwxr-xr-x 1 root root 257071 2007-09-25 01:10 libjavaplugin_nscp.so > > I do not have "xawt/libmawt.so" as you can see from the above. > I do not know what that is. > I run Linux/SuSE 10.3 > > > > On 10/31/07, ecatchpole <e.catchpole at adfa.edu.au> wrote: > >> This is a known problem with Suse10.3 --- lots of things that use Java >> (e.g., Matlab) produce the same error message. I'm currently trying to >> fix this upon my machine, but haven't succeeded yet. Josh Triplett >> (http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6532373) suggested >> the following: >> >> ---begin--- >> I worked with jcristau and christoph4 via IRC on #debian-x, and we >> managed to >> track down the problem with broken locking in Sun Java 1.5 and 1.6. It >> only >> occurs if Java finds the Xinerama extension, at which point it does >> something >> broken with locking and triggers the assertion. If Java never finds the >> Xinerama extension, it doesn't trigger the assertion for broken locking. >> >> The following workarounds address this problem: >> >> For sun-java5-bin: >> sed -i 's/XINERAMA/FAKEEXTN/g' >> /usr/lib/jvm/java-1.5.0-sun-1.5.0.11/jre/lib/i386/xawt/libmawt.so >> ---end--- >> >> You need to modify the path for your jre. This seems to have helped >> several people. But it didn't work for me. >> >> A sure fix is going back to Suse10.2! :( >> >> Ted. >> >> -- >> Dr E.A. Catchpole >> Visiting Fellow >> Univ of New South Wales at ADFA, Canberra, Australia >> _ and University of Kent, Canterbury, England >> 'v' - www.pems.adfa.edu.au/~ecatchpole<http://www.pems.adfa.edu.au/%7Eecatchpole> >> / \ - fax: +61 2 6268 8786 >> m m - ph: +61 2 6268 8895 >> >> >> >> >> Maura E Monville wrote on 11/01/2007 09:43 AM: >> >>> I have downloaded and tried to install JGR - Java GUI for R - Version >>> >> 1.5. >> >>> I followed all the instructions (at least in my best resolution) and >>> installed Java latest version. >>> R installation complete fine. >>> Has anyone succeded in installing JGR on SuSE 10.3 ? >>> In the following I hade detailed the failed installation, >>> >>> As root /i did the following: >>> linux-Mimin:/usr/local/bin # ./R >>> >>> R version 2.6.0 (2007-10-03) >>> Copyright (C) 2007 The R Foundation for Statistical Computing >>> ISBN 3-900051-07-0 >>> >>> R is free software and comes with ABSOLUTELY NO WARRANTY. >>> You are welcome to redistribute it under certain conditions. >>> Type 'license()' or 'licence()' for distribution details. >>> >>> Natural language support but running in an English locale >>> >>> R is a collaborative project with many contributors. >>> Type 'contributors()' for more information and >>> 'citation()' on how to cite R or R packages in publications. >>> >>> Type 'demo()' for some demos, 'help()' for on-line help, or >>> 'help.start()' for an HTML browser interface to help. >>> Type 'q()' to quit R. >>> >>> >>> >>>> install.packages ("JGR",dep=TRUE) >>>> >>>> >>> --- Please select a CRAN mirror for use in this session --- >>> CRAN mirror >>> >>> 1: Argentina 2: Australia (QLD) >>> 3: Australia (VIC) 4: Austria >>> 5: Belgium 6: Brazil (PR) >>> 7: Brazil (MG) 8: Brazil (RJ) >>> 9: Brazil (SP 1) 10: Brazil (SP 2) >>> 11: Canada (BC) 12: Canada (ON) >>> 13: Chile (Santiago) 14: Croatia >>> 15: Czech Republic 16: Denmark >>> 17: France (Toulouse) 18: France (Lyon) >>> 19: France (Paris) 20: Germany (Bamberg) >>> 21: Germany (Mainz) 22: Germany (Muenchen) >>> 23: India (Kolkata) 24: India >>> 25: Ireland 26: Italy (Ferrara) >>> 27: Italy (Milano) 28: Italy (Padua) >>> 29: Italy (Palermo) 30: Japan (Aizu) >>> 31: Japan (Tokyo) 32: Japan (Tsukuba) >>> 33: Korea 34: Netherlands (Amsterdam 2) >>> 35: Netherlands (Amsterdam) 36: Netherlands (Utrecht) >>> 37: Norway 38: Poland (Lublin) >>> 39: Poland (Wroclaw) 40: Portugal >>> 41: Slovenia (Ljubljana) 42: South Africa >>> 43: Spain (Madrid) 44: Sweden >>> 45: Switzerland (Zuerich) 46: Switzerland (Bern) >>> 47: Taiwan (Taichung) 48: Taiwan (Taipeh) >>> 49: UK (Bristol) 50: UK (London) >>> 51: USA (CA 1) 52: USA (CA 3) >>> 53: USA (CA 2) 54: USA (IA) >>> 55: USA (IL) 56: USA (MI) >>> 57: USA (MO) 58: USA (NC) >>> 59: USA (PA 2) 60: USA (PA) >>> 61: USA (TX) 62: USA (WA) >>> >>> >>> Selection: 20 >>> trying URL ' >>> >> http://www.centervenus.com/mirrors/CRAN/src/contrib/JGR_1.5-5.tar.gz' >> >>> Content type 'application/x-gzip' length 370920 bytes (362 Kb) >>> opened URL >>> =================================================>>> downloaded 362 Kb >>> >>> * Installing *source* package 'JGR' ... >>> ** R >>> ** inst >>> ** help >>> >>> Building/Updating help pages for package 'JGR' >>> Formats: text html latex example >>> jgr.addMenu text html latex example >>> jgr.addMenuItem text html latex example >>> jgr.addMenuSeperator text html latex example >>> supplements text html latex >>> ** building package indices ... >>> * DONE (JGR) >>> >>> The downloaded packages are in >>> /tmp/Rtmp8XtRf8/downloaded_packages >>> Updating HTML index of packages in '.Library' >>> >>> >>>> library(JGR) >>>> >>>> >>> Loading required package: rJava >>> Loading required package: JavaGD >>> Loading required package: iplots >>> R: xcb_xlib.c:52: xcb_xlib_unlock: Assertion `c-> xlib.lock' failed. >>> Aborted >>> >>> >>> Thank you in advance >>> >>> >> >> > > >-- Dr E.A. Catchpole Visiting Fellow Univ of New South Wales at ADFA, Canberra, Australia _ and University of Kent, Canterbury, England 'v' - www.pems.adfa.edu.au/~ecatchpole / \ - fax: +61 2 6268 8786 m m - ph: +61 2 6268 8895