a.robotham at bris.ac.uk
2007-Dec-05 16:10 UTC
[Rd] os x crash using rpanel and tcltk (PR#10495)
Hello, I've recently discovered a persistent issue with rpanel when running R.app (2.6.1) on Mac OS X 10.4.11. tcltk and rpanel load without any apparent error, and the interactive panels appear to work as expected, however upon closing the panels rpanel has created I get catastrophic errors and R crashes completely. For the most part R manages to crash with dignity and work can be saved, but sometimes it will crash straight out. Below is an example of an entire work session (only base packages loaded) with the crash at the end typical of those encountered:> library(tcltk)Loading Tcl/Tk interface ... done> library(rpanel)Package `rpanel', version 1.0-4 type help(rpanel) for summary information> density.draw <- function(panel) {+ plot(density(panel$x, bw = panel$h)) + panel + }> panel <- rp.control(x = rnorm(50)) > rp.slider(panel, h, 0.5, 5, log = TRUE, action = density.draw)*** caught bus error *** address 0x0, cause 'non-existent physical address' Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace All packages that are required are up to date, and I can find no evidence of similar issues from searching the mailing lists. Any suggestions would be appreciated. Aaron
a.robotham at bris.ac.uk wrote:> Hello, > I've recently discovered a persistent issue with rpanel when running > R.app (2.6.1) on Mac OS X 10.4.11. tcltk and rpanel load without any > apparent error, and the interactive panels appear to work as expected, > however upon closing the panels rpanel has created I get catastrophic > errors and R crashes completely. For the most part R manages to crash > with dignity and work can be saved, but sometimes it will crash > straight out. Below is an example of an entire work session (only base > packages loaded) with the crash at the end typical of those > encountered: > > >> library(tcltk) >> > Loading Tcl/Tk interface ... done > >> library(rpanel) >> > Package `rpanel', version 1.0-4 > type help(rpanel) for summary information > >> density.draw <- function(panel) { >> > + plot(density(panel$x, bw = panel$h)) > + panel > + } > >> panel <- rp.control(x = rnorm(50)) >> rp.slider(panel, h, 0.5, 5, log = TRUE, action = density.draw) >> > > *** caught bus error *** > address 0x0, cause 'non-existent physical address' > > Possible actions: > 1: abort (with core dump, if enabled) > 2: normal R exit > 3: exit R without saving workspace > 4: exit R saving workspace > > All packages that are required are up to date, and I can find no > evidence of similar issues from searching the mailing lists. Any > suggestions would be appreciated. > >Can you run this under gdb? A breakpoint in the error handler and a backtrace could be valuable.> Aaron > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >-- O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
simon.urbanek at r-project.org
2007-Dec-06 21:30 UTC
[Rd] os x crash using rpanel and tcltk (PR#10495)
On Dec 6, 2007, at 9:26 AM, Aaron Robotham wrote:> I know of gdb but I'm not certain how to use it with Mac OS X's =20 > R.app, do you just do something like "gdb open R.app" in the =20 > terminal?. >You can attach it once it's running - just type "attach R" in gdb =20 while R is runningm then "c", then let it crash and then "bt". FWIW: I cannot reproduce the problem and I have tried 3 different =20 machines... (you didn't even tell us what machine type this is ...). Cheers, Simon> Interestingly I don't get this crash when I launch the X11 version of > R through the terminal, so this would suggest the bug in question is > to do with the actual Rgui in R.app. Hopefully this information might > help to narrow down the problem. Any advice for using gdb on R.app > would be appreciated, I couldn't find much in the way of guidance when > searching online. > > thanks > > Aaron > > On 05/12/2007, Peter Dalgaard <p.dalgaard at biostat.ku.dk> wrote: >> a.robotham at bris.ac.uk wrote: >>> Hello, >>> I've recently discovered a persistent issue with rpanel when running >>> R.app (2.6.1) on Mac OS X 10.4.11. tcltk and rpanel load without any >>> apparent error, and the interactive panels appear to work as =20 >>> expected, >>> however upon closing the panels rpanel has created I get =20 >>> catastrophic >>> errors and R crashes completely. For the most part R manages to =20 >>> crash >>> with dignity and work can be saved, but sometimes it will crash >>> straight out. Below is an example of an entire work session (only =20 >>> base >>> packages loaded) with the crash at the end typical of those >>> encountered: >>> >>> >>>> library(tcltk) >>>> >>> Loading Tcl/Tk interface ... done >>> >>>> library(rpanel) >>>> >>> Package `rpanel', version 1.0-4 >>> type help(rpanel) for summary information >>> >>>> density.draw <- function(panel) { >>>> >>> + plot(density(panel$x, bw =3D panel$h)) >>> + panel >>> + } >>> >>>> panel <- rp.control(x =3D rnorm(50)) >>>> rp.slider(panel, h, 0.5, 5, log =3D TRUE, action =3D density.draw) >>>> >>> >>> *** caught bus error *** >>> address 0x0, cause 'non-existent physical address' >>> >>> Possible actions: >>> 1: abort (with core dump, if enabled) >>> 2: normal R exit >>> 3: exit R without saving workspace >>> 4: exit R saving workspace >>> >>> All packages that are required are up to date, and I can find no >>> evidence of similar issues from searching the mailing lists. Any >>> suggestions would be appreciated. >>> >>> >> Can you run this under gdb? A breakpoint in the error handler and a >> backtrace could be valuable. >> >>> Aaron >>> >>> ______________________________________________ >>> R-devel at r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-devel >>> >> >> >> -- >> O__ ---- Peter Dalgaard =D8ster Farimagsgade 5, Entr.B >> c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K >> (*) \(*) -- University of Copenhagen Denmark Ph: (+45) =20 >> 35327918 >> ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) =20 >> 35327907 >> >> >> >> > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > >
a.robotham at bristol.ac.uk
2007-Dec-07 14:35 UTC
[Rd] os x crash using rpanel and tcltk (PR#10495)
Here's the back trace i get after it crashes: Program received signal SIGTRAP, Trace/breakpoint trap. 0x90a61b09 in _objc_error () (gdb) bt #0 0x90a61b09 in _objc_error () #1 0x90a61b40 in __objc_error () #2 0x90a601a0 in _freedHandler () #3 0x93442c64 in -[NSDocument close] () #4 0x00015f0b in -[RQuartz close] () #5 0x00016c93 in RQuartz_Close () #6 0x0039b6dc in removeDevice () #7 0x00015f3f in -[RQuartz windowShouldClose:] () #8 0x934429b2 in -[NSWindow _document:shouldClose:contextInfo:] () #9 0x93442437 in -[NSWindow __close] () #10 0x93382dbc in -[NSApplication sendAction:to:from:] () #11 0x93382d15 in -[NSControl sendAction:to:] () #12 0x93384ec1 in -[NSCell _sendActionFrom:] () #13 0x933976a1 in -[NSCell trackMouse:inRect:ofView:untilMouseUp:] () #14 0x933b5289 in -[NSButtonCell trackMouse:inRect:ofView:untilMouseUp:] () #15 0x933b4b39 in -[NSControl mouseDown:] () #16 0x934422f8 in -[_NSThemeWidget mouseDown:] () #17 0x933723e3 in -[NSWindow sendEvent:] () #18 0x93364384 in -[NSApplication sendEvent:] () #19 0x00005151 in -[RController handleReadConsole:] () #20 0x0000c641 in Re_ReadConsole () #21 0x00015c76 in run_REngineRmainloop () #22 0x0000ec4a in -[REngine runREPL] () #23 0x0000226d in main () Is this what is wanted? Thanks for the gdb advice btw. I'm not sure if it's important, but before it crashed I got lots of warnings similar to the following in gdb when I attached the tcltk package: warning: Could not find object file "/Builds/Rdev-web/QA/Simon/R-build/tiger-ppc/R-2.6-branch/src/extra/blas/blas00.o" - no debug information available for "../../../../../R-2.6-branch/src/extra/blas/blas00.c". Is there an issue with a previous version of R on my machine causing problems? Thanks for the help. Aaron On 07/12/2007, Aaron Robotham <a.robotham at bristol.ac.uk> wrote:> The machine in question is a black MacBook, a pretty standard setup > with the rest of the details as listed in my first post (R 2.6.1 OSX > 10.4.11). I'll give the back trace a try and let you know the result. > > On 06/12/2007, Simon Urbanek <simon.urbanek at r-project.org> wrote: > > > > On Dec 6, 2007, at 9:26 AM, Aaron Robotham wrote: > > > > > I know of gdb but I'm not certain how to use it with Mac OS X's > > > R.app, do you just do something like "gdb open R.app" in the > > > terminal?. > > > > > > > You can attach it once it's running - just type "attach R" in gdb > > while R is runningm then "c", then let it crash and then "bt". > > > > FWIW: I cannot reproduce the problem and I have tried 3 different > > machines... (you didn't even tell us what machine type this is ...). > > > > Cheers, > > Simon > > > > > > > Interestingly I don't get this crash when I launch the X11 version of > > > R through the terminal, so this would suggest the bug in question is > > > to do with the actual Rgui in R.app. Hopefully this information might > > > help to narrow down the problem. Any advice for using gdb on R.app > > > would be appreciated, I couldn't find much in the way of guidance when > > > searching online. > > > > > > thanks > > > > > > Aaron > > > > > > On 05/12/2007, Peter Dalgaard <p.dalgaard at biostat.ku.dk> wrote: > > >> a.robotham at bris.ac.uk wrote: > > >>> Hello, > > >>> I've recently discovered a persistent issue with rpanel when running > > >>> R.app (2.6.1) on Mac OS X 10.4.11. tcltk and rpanel load without any > > >>> apparent error, and the interactive panels appear to work as > > >>> expected, > > >>> however upon closing the panels rpanel has created I get > > >>> catastrophic > > >>> errors and R crashes completely. For the most part R manages to > > >>> crash > > >>> with dignity and work can be saved, but sometimes it will crash > > >>> straight out. Below is an example of an entire work session (only > > >>> base > > >>> packages loaded) with the crash at the end typical of those > > >>> encountered: > > >>> > > >>> > > >>>> library(tcltk) > > >>>> > > >>> Loading Tcl/Tk interface ... done > > >>> > > >>>> library(rpanel) > > >>>> > > >>> Package `rpanel', version 1.0-4 > > >>> type help(rpanel) for summary information > > >>> > > >>>> density.draw <- function(panel) { > > >>>> > > >>> + plot(density(panel$x, bw =3D panel$h)) > > >>> + panel > > >>> + } > > >>> > > >>>> panel <- rp.control(x =3D rnorm(50)) > > >>>> rp.slider(panel, h, 0.5, 5, log =3D TRUE, action =3D density.draw) > > >>>> > > >>> > > >>> *** caught bus error *** > > >>> address 0x0, cause 'non-existent physical address' > > >>> > > >>> Possible actions: > > >>> 1: abort (with core dump, if enabled) > > >>> 2: normal R exit > > >>> 3: exit R without saving workspace > > >>> 4: exit R saving workspace > > >>> > > >>> All packages that are required are up to date, and I can find no > > >>> evidence of similar issues from searching the mailing lists. Any > > >>> suggestions would be appreciated. > > >>> > > >>> > > >> Can you run this under gdb? A breakpoint in the error handler and a > > >> backtrace could be valuable. > > >> > > >>> Aaron > > >>> > > >>> ______________________________________________ > > >>> R-devel at r-project.org mailing list > > >>> https://stat.ethz.ch/mailman/listinfo/r-devel > > >>> > > >> > > >> > > >> -- > > >> O__ ---- Peter Dalgaard =D8ster Farimagsgade 5, Entr.B > > >> c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K > > >> (*) \(*) -- University of Copenhagen Denmark Ph: (+45) > > >> 35327918 > > >> ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) > > >> 35327907 > > >> > > >> > > >> > > >> > > > > > > ______________________________________________ > > > R-devel at r-project.org mailing list > > > https://stat.ethz.ch/mailman/listinfo/r-devel > > > > > > > > > > > > >
---------- Forwarded message ---------- From: Aaron Robotham <a.robotham at bristol.ac.uk> Date: 7 Dec 2007 14:30 Subject: Re: [Rd] os x crash using rpanel and tcltk (PR#10495) To: Simon Urbanek <simon.urbanek at r-project.org> Cc: Peter Dalgaard <p.dalgaard at biostat.ku.dk>, R-bugs at biostat.ku.dk, r-devel at stat.math.ethz.ch Here's the back trace i get after it crashes: Program received signal SIGTRAP, Trace/breakpoint trap. 0x90a61b09 in _objc_error () (gdb) bt #0 0x90a61b09 in _objc_error () #1 0x90a61b40 in __objc_error () #2 0x90a601a0 in _freedHandler () #3 0x93442c64 in -[NSDocument close] () #4 0x00015f0b in -[RQuartz close] () #5 0x00016c93 in RQuartz_Close () #6 0x0039b6dc in removeDevice () #7 0x00015f3f in -[RQuartz windowShouldClose:] () #8 0x934429b2 in -[NSWindow _document:shouldClose:contextInfo:] () #9 0x93442437 in -[NSWindow __close] () #10 0x93382dbc in -[NSApplication sendAction:to:from:] () #11 0x93382d15 in -[NSControl sendAction:to:] () #12 0x93384ec1 in -[NSCell _sendActionFrom:] () #13 0x933976a1 in -[NSCell trackMouse:inRect:ofView:untilMouseUp:] () #14 0x933b5289 in -[NSButtonCell trackMouse:inRect:ofView:untilMouseUp:] () #15 0x933b4b39 in -[NSControl mouseDown:] () #16 0x934422f8 in -[_NSThemeWidget mouseDown:] () #17 0x933723e3 in -[NSWindow sendEvent:] () #18 0x93364384 in -[NSApplication sendEvent:] () #19 0x00005151 in -[RController handleReadConsole:] () #20 0x0000c641 in Re_ReadConsole () #21 0x00015c76 in run_REngineRmainloop () #22 0x0000ec4a in -[REngine runREPL] () #23 0x0000226d in main () Is this what is wanted? Thanks for the gdb advice btw. I'm not sure if it's important, but before it crashed I got lots of warnings similar to the following in gdb when I attached the tcltk package: warning: Could not find object file "/Builds/Rdev-web/QA/Simon/R-build/tiger-ppc/R-2.6-branch/src/extra/blas/blas00.o" - no debug information available for "../../../../../R-2.6-branch/src/extra/blas/blas00.c". Is there an issue with a previous version of R on my machine causing problems? Thanks for the help. Aaron On 07/12/2007, Aaron Robotham <a.robotham at bristol.ac.uk> wrote:> The machine in question is a black MacBook, a pretty standard setup > with the rest of the details as listed in my first post (R 2.6.1 OSX > 10.4.11). I'll give the back trace a try and let you know the result. > > On 06/12/2007, Simon Urbanek <simon.urbanek at r-project.org> wrote: > > > > On Dec 6, 2007, at 9:26 AM, Aaron Robotham wrote: > > > > > I know of gdb but I'm not certain how to use it with Mac OS X's > > > R.app, do you just do something like "gdb open R.app" in the > > > terminal?. > > > > > > > You can attach it once it's running - just type "attach R" in gdb > > while R is runningm then "c", then let it crash and then "bt". > > > > FWIW: I cannot reproduce the problem and I have tried 3 different > > machines... (you didn't even tell us what machine type this is ...). > > > > Cheers, > > Simon > > > > > > > Interestingly I don't get this crash when I launch the X11 version of > > > R through the terminal, so this would suggest the bug in question is > > > to do with the actual Rgui in R.app. Hopefully this information might > > > help to narrow down the problem. Any advice for using gdb on R.app > > > would be appreciated, I couldn't find much in the way of guidance when > > > searching online. > > > > > > thanks > > > > > > Aaron > > > > > > On 05/12/2007, Peter Dalgaard <p.dalgaard at biostat.ku.dk> wrote: > > >> a.robotham at bris.ac.uk wrote: > > >>> Hello, > > >>> I've recently discovered a persistent issue with rpanel when running > > >>> R.app (2.6.1) on Mac OS X 10.4.11. tcltk and rpanel load without any > > >>> apparent error, and the interactive panels appear to work as > > >>> expected, > > >>> however upon closing the panels rpanel has created I get > > >>> catastrophic > > >>> errors and R crashes completely. For the most part R manages to > > >>> crash > > >>> with dignity and work can be saved, but sometimes it will crash > > >>> straight out. Below is an example of an entire work session (only > > >>> base > > >>> packages loaded) with the crash at the end typical of those > > >>> encountered: > > >>> > > >>> > > >>>> library(tcltk) > > >>>> > > >>> Loading Tcl/Tk interface ... done > > >>> > > >>>> library(rpanel) > > >>>> > > >>> Package `rpanel', version 1.0-4 > > >>> type help(rpanel) for summary information > > >>> > > >>>> density.draw <- function(panel) { > > >>>> > > >>> + plot(density(panel$x, bw = panel$h)) > > >>> + panel > > >>> + } > > >>> > > >>>> panel <- rp.control(x = rnorm(50)) > > >>>> rp.slider(panel, h, 0.5, 5, log = TRUE, action = density.draw) > > >>>> > > >>> > > >>> *** caught bus error *** > > >>> address 0x0, cause 'non-existent physical address' > > >>> > > >>> Possible actions: > > >>> 1: abort (with core dump, if enabled) > > >>> 2: normal R exit > > >>> 3: exit R without saving workspace > > >>> 4: exit R saving workspace > > >>> > > >>> All packages that are required are up to date, and I can find no > > >>> evidence of similar issues from searching the mailing lists. Any > > >>> suggestions would be appreciated. > > >>> > > >>> > > >> Can you run this under gdb? A breakpoint in the error handler and a > > >> backtrace could be valuable. > > >> > > >>> Aaron > > >>> > > >>> ______________________________________________ > > >>> R-devel at r-project.org mailing list > > >>> https://stat.ethz.ch/mailman/listinfo/r-devel > > >>> > > >> > > >> > > >> -- > > >> O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B > > >> c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K > > >> (*) \(*) -- University of Copenhagen Denmark Ph: (+45) > > >> 35327918 > > >> ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) > > >> 35327907 > > >> > > >> > > >> > > >> > > > > > > ______________________________________________ > > > R-devel at r-project.org mailing list > > > https://stat.ethz.ch/mailman/listinfo/r-devel > > > > > > > > > > > > >