hi everybody,
today I decided (unwisely, it appears) to install 2.7.0
under MacOS 10.4.7. now, when I run R from the terminal
command line and do something like
plot(1:10)
a X11 graphic window pops up, the 10 points are drawn on an
otherwise blank canvas (no axes, no labels, no ticks etc),
CPU time goes to 100% and stays there and R does not come
back to the prompt ("hangs"). I tried to `ktrace' this but
this produced a one Gig logfile in a few seconds from which
a learned nothing ...
a quick search of the archive did not yield a hit. so
please: what's going on here?
thanks
joerg
PS: I've done this in fullscreen X11 mode using two different
WMs (`dwm', `fluxbox') which otherwise work perfectly.
problem with X11() after install of 2.7.0.
10 messages · Joerg van den Hoff, Simon Urbanek, Jean Thioulouse +1 more
On Apr 30, 2008, at 10:34 AM, Joerg van den Hoff wrote:
hi everybody,
today I decided (unwisely, it appears) to install 2.7.0
under MacOS 10.4.7. now, when I run R from the terminal
command line and do something like
plot(1:10)
a X11 graphic window pops up, the 10 points are drawn on an
otherwise blank canvas (no axes, no labels, no ticks etc),
CPU time goes to 100% and stays there and R does not come
back to the prompt ("hangs"). I tried to `ktrace' this but
this produced a one Gig logfile in a few seconds from which
a learned nothing ...
a quick search of the archive did not yield a hit. so
please: what's going on here?
Ancient system? As a very first step for your own good I'd recommend updating your system which is way out of date (the current version Tiger is 10.4.11). Then if the issue persists, please report your full sessionInfo() and machine used. The above works without problems on both 10.5.2 and 10.4.11 (Mac Pro and iMac). Thanks, Simon
PS: I've done this in fullscreen X11 mode using two different WMs (`dwm', `fluxbox') which otherwise work perfectly.
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On Wed, Apr 30, 2008 at 10:55:38AM -0400, Simon Urbanek wrote:
On Apr 30, 2008, at 10:34 AM, Joerg van den Hoff wrote:
hi everybody,
today I decided (unwisely, it appears) to install 2.7.0
under MacOS 10.4.7. now, when I run R from the terminal
command line and do something like
plot(1:10)
a X11 graphic window pops up, the 10 points are drawn on an
otherwise blank canvas (no axes, no labels, no ticks etc),
CPU time goes to 100% and stays there and R does not come
back to the prompt ("hangs"). I tried to `ktrace' this but
this produced a one Gig logfile in a few seconds from which
a learned nothing ...
a quick search of the archive did not yield a hit. so
please: what's going on here?
thanks a lot for this "real time" response.
Ancient system? As a very first step for your own good I'd recommend
well, no. actually I _have_ 10.4.11 installed (I somehow was sure it's 10.4.7, still. that's probably alzheimer casting his shadow :-)).
updating your system which is way out of date (the current version Tiger is 10.4.11). Then if the issue persists, please report your full sessionInfo() and machine used. The above works without problems on both 10.5.2 and 10.4.11 (Mac Pro and iMac).
10.5.2 is no option for me since I need a working fullscreen X11 mode. I now checked it again both on a dual 2Ghz G5 PPC and a 1.5 GHz power book PPC G4, both running 10.4.11: same problem. actually, R hangs only when really plotting. so I can first open the device with X11() and get back to the R prompt. only when executing the `plot(1:10)' R apparently hangs and everything is as described in my first mail. here comes the session info: R version 2.7.0 (2008-04-22) powerpc-apple-darwin8.10.1 locale: C/de_DE.ISO8859-15/C/C/C/C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] micropet_1.7.0 psflib_1.0 pkc_1.1 fzrutils_1.3 roiutils_1.3 (identical on both machines). any hint/help really appreciated. regards, joerg
Thanks, Simon
At 10:55 AM -0400 4/30/08, Simon Urbanek wrote:
Ancient system? As a very first step for your own good I'd recommend updating your system which is way out of date (the current version Tiger is 10.4.11). Then if the issue persists, please report your full sessionInfo() and machine used. The above works without problems on both 10.5.2 and 10.4.11 (Mac Pro and iMac).
I had the same (?) problem after upgrading to R 2.7.0 on a MacPro with MacOS 10.5.2, using XQuartz 2.2.0.1 instead of Apple X11. I didn't try to dig it as I decided to start using the quartz device (very good job) instead. The x11 device has no problem with tcltk though, and even with tkrplot. Jean
sessionInfo()
R version 2.7.0 (2008-04-22) i386-apple-darwin9.2.2 locale: en_US/en_US/C/C/en_US/en_US attached base packages: [1] stats graphics grDevices utils datasets tcltk methods [8] base other attached packages: [1] ade4TkGUI_0.2-2 ade4_1.4-7
x11() plot(0)
*** caught bus error *** address 0xac, cause 'non-existent physical address' Traceback: 1: axis(side = side, at = at, labels = labels, ...) 2: Axis.default(...) 3: Axis(...) 4: localAxis(xy$x, side = 1, ...) 5: plot.default(0) 6: plot(0) 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: 1 aborting ... Bus error Informations mat?riel : Nom du mod?le : Mac Pro Identifiant du mod?le : MacPro1,1 Nom du processeur : Dual-Core Intel Xeon Vitesse du processeur : 2.66 GHz Nombre de processeurs : 2 Nombre total de c?urs : 4 Cache de niveau 2 (par processeur) : 4 Mo M?moire : 4 Go Vitesse du bus : 1.33 GHz Version de la ROM de d?marrage : MP11.005C.B08 Version SMC : 1.7f10 Num?ro de s?rie : CK7270APUPZ
Jean Thioulouse - Labo Biometrie et Biologie Evolutive, UMR CNRS 5558 Universite Lyon 1, Batiment Mendel, 43 Boulevard du 11 Novembre 1918 69622 Villeurbanne Cedex - France http://pbil.univ-lyon1.fr/JTHome/ Tel : (33) (0)4 72 43 27 56 Fax : (33) (0)4 72 43 13 88
On Wed, Apr 30, 2008 at 05:32:45PM +0200, Jean Thioulouse wrote:
At 10:55 AM -0400 4/30/08, Simon Urbanek wrote:
Ancient system? As a very first step for your own good I'd recommend updating your system which is way out of date (the current version Tiger is 10.4.11). Then if the issue persists, please report your full sessionInfo() and machine used. The above works without problems on both 10.5.2 and 10.4.11 (Mac Pro and iMac).
I had the same (?) problem after upgrading to R 2.7.0 on a MacPro with MacOS 10.5.2, using XQuartz 2.2.0.1 instead of Apple X11. I didn't try to dig it as I decided to start using the quartz device (very good job) instead. The x11 device has no problem with tcltk though, and even with tkrplot. Jean
thanks for this information. so at least there seems to be a reall issue (though I'm still under Tiger wit Apple's X11 and I don't see bus errors ) regards, joerg
sessionInfo()
R version 2.7.0 (2008-04-22) i386-apple-darwin9.2.2 locale: en_US/en_US/C/C/en_US/en_US attached base packages: [1] stats graphics grDevices utils datasets tcltk methods [8] base other attached packages: [1] ade4TkGUI_0.2-2 ade4_1.4-7
x11() plot(0)
*** caught bus error *** address 0xac, cause 'non-existent physical address' Traceback: 1: axis(side = side, at = at, labels = labels, ...) 2: Axis.default(...) 3: Axis(...) 4: localAxis(xy$x, side = 1, ...) 5: plot.default(0) 6: plot(0) 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: 1 aborting ... Bus error Informations mat?riel : Nom du mod?le : Mac Pro Identifiant du mod?le : MacPro1,1 Nom du processeur : Dual-Core Intel Xeon Vitesse du processeur : 2.66 GHz Nombre de processeurs : 2 Nombre total de c?urs : 4 Cache de niveau 2 (par processeur) : 4 Mo M?moire : 4 Go Vitesse du bus : 1.33 GHz Version de la ROM de d?marrage : MP11.005C.B08 Version SMC : 1.7f10 Num?ro de s?rie : CK7270APUPZ -- Jean Thioulouse - Labo Biometrie et Biologie Evolutive, UMR CNRS 5558 Universite Lyon 1, Batiment Mendel, 43 Boulevard du 11 Novembre 1918 69622 Villeurbanne Cedex - France http://pbil.univ-lyon1.fr/JTHome/ Tel : (33) (0)4 72 43 27 56 Fax : (33) (0)4 72 43 13 88
On Apr 30, 2008, at 11:31 AM, Joerg van den Hoff wrote:
On Wed, Apr 30, 2008 at 10:55:38AM -0400, Simon Urbanek wrote:
On Apr 30, 2008, at 10:34 AM, Joerg van den Hoff wrote:
hi everybody,
today I decided (unwisely, it appears) to install 2.7.0
under MacOS 10.4.7. now, when I run R from the terminal
command line and do something like
plot(1:10)
a X11 graphic window pops up, the 10 points are drawn on an
otherwise blank canvas (no axes, no labels, no ticks etc),
CPU time goes to 100% and stays there and R does not come
back to the prompt ("hangs"). I tried to `ktrace' this but
this produced a one Gig logfile in a few seconds from which
a learned nothing ...
a quick search of the archive did not yield a hit. so
please: what's going on here?
thanks a lot for this "real time" response.
Ancient system? As a very first step for your own good I'd recommend
well, no. actually I _have_ 10.4.11 installed (I somehow was sure it's 10.4.7, still. that's probably alzheimer casting his shadow :-)).
updating your system which is way out of date (the current version Tiger is 10.4.11). Then if the issue persists, please report your full sessionInfo() and machine used. The above works without problems on both 10.5.2 and 10.4.11 (Mac Pro and iMac).
10.5.2 is no option for me since I need a working fullscreen X11 mode. I now checked it again both on a dual 2Ghz G5 PPC and a 1.5 GHz power book PPC G4, both running 10.4.11: same problem. actually, R hangs only when really plotting. so I can first open the device with X11() and get back to the R prompt. only when executing the `plot(1:10)' R apparently hangs and everything is as described in my first mail. here comes the session info: R version 2.7.0 (2008-04-22) powerpc-apple-darwin8.10.1
Hmm - I have tried even the PowerPC version now and it works without problems for me. Are you using Apple's X11 or something else? Also do you get the error in the "regular" (non-root) mode? Thanks, Simon
locale: C/de_DE.ISO8859-15/C/C/C/C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] micropet_1.7.0 psflib_1.0 pkc_1.1 fzrutils_1.3 roiutils_1.3 (identical on both machines). any hint/help really appreciated. regards, joerg
Thanks, Simon
On Apr 30, 2008, at 11:42 AM, Joerg van den Hoff wrote:
On Wed, Apr 30, 2008 at 05:32:45PM +0200, Jean Thioulouse wrote:
At 10:55 AM -0400 4/30/08, Simon Urbanek wrote:
Ancient system? As a very first step for your own good I'd recommend updating your system which is way out of date (the current version Tiger is 10.4.11). Then if the issue persists, please report your full sessionInfo() and machine used. The above works without problems on both 10.5.2 and 10.4.11 (Mac Pro and iMac).
I had the same (?) problem after upgrading to R 2.7.0 on a MacPro with MacOS 10.5.2, using XQuartz 2.2.0.1 instead of Apple X11. I didn't try to dig it as I decided to start using the quartz device (very good job) instead. The x11 device has no problem with tcltk though, and even with tkrplot. Jean
thanks for this information. so at least there seems to be a reall issue (though I'm still under Tiger wit Apple's X11 and I don't see bus errors )
Well that above doesn't say anything in that respect - the CRAN binary is meant to work with Apple's X11 only. If you use anything else, you're on your own and possibly have to compile your own version. For example if you have a different version of fontconfig it is enough to crash since fontconfig changed the internal format of the cache. Cheers, Simon
regards, joerg
sessionInfo()
R version 2.7.0 (2008-04-22) i386-apple-darwin9.2.2 locale: en_US/en_US/C/C/en_US/en_US attached base packages: [1] stats graphics grDevices utils datasets tcltk methods [8] base other attached packages: [1] ade4TkGUI_0.2-2 ade4_1.4-7
x11() plot(0)
*** caught bus error *** address 0xac, cause 'non-existent physical address' Traceback: 1: axis(side = side, at = at, labels = labels, ...) 2: Axis.default(...) 3: Axis(...) 4: localAxis(xy$x, side = 1, ...) 5: plot.default(0) 6: plot(0) 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: 1 aborting ... Bus error Informations mat?riel : Nom du mod?le : Mac Pro Identifiant du mod?le : MacPro1,1 Nom du processeur : Dual-Core Intel Xeon Vitesse du processeur : 2.66 GHz Nombre de processeurs : 2 Nombre total de c?urs : 4 Cache de niveau 2 (par processeur) : 4 Mo M?moire : 4 Go Vitesse du bus : 1.33 GHz Version de la ROM de d?marrage : MP11.005C.B08 Version SMC : 1.7f10 Num?ro de s?rie : CK7270APUPZ -- Jean Thioulouse - Labo Biometrie et Biologie Evolutive, UMR CNRS 5558 Universite Lyon 1, Batiment Mendel, 43 Boulevard du 11 Novembre 1918 69622 Villeurbanne Cedex - France http://pbil.univ-lyon1.fr/ JTHome/ Tel : (33) (0)4 72 43 27 56 Fax : (33) (0)4 72 43 13 88
At 11:49 AM -0400 4/30/08, Simon Urbanek wrote:
On Apr 30, 2008, at 11:42 AM, Joerg van den Hoff wrote:
On Wed, Apr 30, 2008 at 05:32:45PM +0200, Jean Thioulouse wrote:
At 10:55 AM -0400 4/30/08, Simon Urbanek wrote:
Ancient system? As a very first step for your own good I'd recommend updating your system which is way out of date (the current version Tiger is 10.4.11). Then if the issue persists, please report your full sessionInfo() and machine used. The above works without problems on both 10.5.2 and 10.4.11 (Mac Pro and iMac).
I had the same (?) problem after upgrading to R 2.7.0 on a MacPro with MacOS 10.5.2, using XQuartz 2.2.0.1 instead of Apple X11. I didn't try to dig it as I decided to start using the quartz device (very good job) instead. The x11 device has no problem with tcltk though, and even with tkrplot. Jean
thanks for this information. so at least there seems to be a reall issue (though I'm still under Tiger wit Apple's X11 and I don't see bus errors )
Well that above doesn't say anything in that respect - the CRAN binary is meant to work with Apple's X11 only. If you use anything else, you're on your own and possibly have to compile your own version. For example if you have a different version of fontconfig it is enough to crash since fontconfig changed the internal format of the cache.
I am not using CRAN binaries. Jean
Jean Thioulouse - Labo Biometrie et Biologie Evolutive, UMR CNRS 5558 Universite Lyon 1, Batiment Mendel, 43 Boulevard du 11 Novembre 1918 69622 Villeurbanne Cedex - France http://pbil.univ-lyon1.fr/JTHome/ Tel : (33) (0)4 72 43 27 56 Fax : (33) (0)4 72 43 13 88
On Apr 30, 2008, at 12:10 PM, Jean Thioulouse wrote:
At 11:49 AM -0400 4/30/08, Simon Urbanek wrote:
On Apr 30, 2008, at 11:42 AM, Joerg van den Hoff wrote:
On Wed, Apr 30, 2008 at 05:32:45PM +0200, Jean Thioulouse wrote:
At 10:55 AM -0400 4/30/08, Simon Urbanek wrote:
Ancient system? As a very first step for your own good I'd recommend updating your system which is way out of date (the current version Tiger is 10.4.11). Then if the issue persists, please report your full sessionInfo() and machine used. The above works without problems on both 10.5.2 and 10.4.11 (Mac Pro and iMac).
I had the same (?) problem after upgrading to R 2.7.0 on a MacPro with MacOS 10.5.2, using XQuartz 2.2.0.1 instead of Apple X11. I didn't try to dig it as I decided to start using the quartz device (very good job) instead. The x11 device has no problem with tcltk though, and even with tkrplot. Jean
thanks for this information. so at least there seems to be a reall issue (though I'm still under Tiger wit Apple's X11 and I don't see bus errors )
Well that above doesn't say anything in that respect - the CRAN binary is meant to work with Apple's X11 only. If you use anything else, you're on your own and possibly have to compile your own version. For example if you have a different version of fontconfig it is enough to crash since fontconfig changed the internal format of the cache.
I am not using CRAN binaries.
Oh, then you really are on your own ;). Can you send me the get the backtrace, please? Cheers, Simon
Jean -- Jean Thioulouse - Labo Biometrie et Biologie Evolutive, UMR CNRS 5558 Universite Lyon 1, Batiment Mendel, 43 Boulevard du 11 Novembre 1918 69622 Villeurbanne Cedex - France http://pbil.univ-lyon1.fr/JTHome/ Tel : (33) (0)4 72 43 27 56 Fax : (33) (0)4 72 43 13 88
FWIW, we have a machine using XQuartz 2.2, and both my own build of R and the original CRAN release of 2.7.0 work with it. (I am not differing from Simon's advice -- that the CRAN release works is a bonus.)
On Wed, 30 Apr 2008, Jean Thioulouse wrote:
At 11:49 AM -0400 4/30/08, Simon Urbanek wrote:
On Apr 30, 2008, at 11:42 AM, Joerg van den Hoff wrote:
On Wed, Apr 30, 2008 at 05:32:45PM +0200, Jean Thioulouse wrote:
At 10:55 AM -0400 4/30/08, Simon Urbanek wrote:
Ancient system? As a very first step for your own good I'd recommend updating your system which is way out of date (the current version Tiger is 10.4.11). Then if the issue persists, please report your full sessionInfo() and machine used. The above works without problems on both 10.5.2 and 10.4.11 (Mac Pro and iMac).
I had the same (?) problem after upgrading to R 2.7.0 on a MacPro with MacOS 10.5.2, using XQuartz 2.2.0.1 instead of Apple X11. I didn't try to dig it as I decided to start using the quartz device (very good job) instead. The x11 device has no problem with tcltk though, and even with tkrplot. Jean
thanks for this information. so at least there seems to be a reall issue (though I'm still under Tiger wit Apple's X11 and I don't see bus errors )
Well that above doesn't say anything in that respect - the CRAN binary is meant to work with Apple's X11 only. If you use anything else, you're on your own and possibly have to compile your own version. For example if you have a different version of fontconfig it is enough to crash since fontconfig changed the internal format of the cache.
I am not using CRAN binaries. Jean -- Jean Thioulouse - Labo Biometrie et Biologie Evolutive, UMR CNRS 5558 Universite Lyon 1, Batiment Mendel, 43 Boulevard du 11 Novembre 1918 69622 Villeurbanne Cedex - France http://pbil.univ-lyon1.fr/JTHome/ Tel : (33) (0)4 72 43 27 56 Fax : (33) (0)4 72 43 13 88
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Brian D. Ripley, ripley at 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, UK Fax: +44 1865 272595