[R-SIG-Mac] rgl crashes after one successful draw on R.app

Bryan Hanson hanson at depauw.edu
Thu May 30 14:06:46 CEST 2013


Yes, sorry.  I just confirmed (for myself) that showSomething() works just fine from command line R where it uses XQuartz ( 2.7.4) and fails from R.app.  Bryan

On May 30, 2013, at 4:05 AM, Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote:

> On 30/05/2013 02:27, Bryan Hanson wrote:
>> Unfortunately, I already have XQuartz 2.7.4 and it gives the problem I reported. :-(  Bryan
> 
> But as I said way back in this thread, there are two different rgl devices and this trhead has conflated two problems, on in each.
> 
> Roger was using the X11-based version, and that seemed to be an Xquartz issue.
> 
> You are using the AGL-based version in R.app, which does not use X11 AFAIK.
> 
>> On May 29, 2013, at 7:16 PM, Robert J Goedman <goedman at icloud.com> wrote:
>> 
>>> Great, like with Rcmdr, example(rgl) seems to work well.
>>> 
>>> Repeatedly just 'example(plot3d)' and each time removing all rgl windows, will lead to the same problem Bryan mentioned this morning.
>>> 
>>> Rob J. Goedman
>>> goedman at icloud.com
>>> 
>>> 
>>> 
>>> 
>>> On May 29, 2013, at 3:57 PM, Roger Koenker <rkoenker at illinois.edu> wrote:
>>> 
>>>> Rob,
>>>> 
>>>> Well, that was easy....  I upgraded to XQuartz 2.7.4  and now can run example(rgl)
>>>> and also close the windows that are created. ;-).  Many thanks!
>>>> 
>>>> Roger
>>>> 
>>>> url:    www.econ.uiuc.edu/~roger            Roger Koenker
>>>> email    rkoenker at uiuc.edu            Department of Economics
>>>> vox:     217-333-4558                University of Illinois
>>>> fax:       217-244-6678                Urbana, IL 61801
>>>> 
>>>> On May 29, 2013, at 5:41 PM, Robert J Goedman wrote:
>>>> 
>>>>> Roger,
>>>>> 
>>>>> Not sure if that would fix it, but my system is the patched R.3.0.1, using XQuartz 2.7.4 and a slightly newer version of rgl (rgl_0.93.940).
>>>>> 
>>>>> Rob J. Goedman
>>>>> goedman at icloud.com
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> On May 29, 2013, at 3:19 PM, Roger Koenker <rkoenker at illinois.edu> wrote:
>>>>> 
>>>>>> no,  I never get a window....  I get an immediate segfault as soon as
>>>>>> rgl.open() is called.
>>>>>> 
>>>>>> 
>>>>>> url:    www.econ.uiuc.edu/~roger            Roger Koenker
>>>>>> email    rkoenker at uiuc.edu            Department of Economics
>>>>>> vox:     217-333-4558                University of Illinois
>>>>>> fax:       217-244-6678                Urbana, IL 61801
>>>>>> 
>>>>>> On May 29, 2013, at 5:17 PM, Robert J Goedman wrote:
>>>>>> 
>>>>>>> Roger,
>>>>>>> 
>>>>>>> Do you ever see an rgl window pop-up? Just wondering if this is the same issue.
>>>>>>> 
>>>>>>> Rob J. Goedman
>>>>>>> goedman at icloud.com
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> On May 29, 2013, at 2:49 PM, Roger Koenker <rkoenker at illinois.edu> wrote:
>>>>>>> 
>>>>>>>> I doubt that this is helpful, but I get:
>>>>>>>> 
>>>>>>>>> rgl.open()
>>>>>>>> Reading symbols for shared libraries . done
>>>>>>>> 
>>>>>>>> Program received signal EXC_BAD_ACCESS, Could not access memory.
>>>>>>>> Reason: KERN_INVALID_ADDRESS at address: 0x00000000000000e8
>>>>>>>> 0x0000000102e31a90 in gui::X11GUIFactory::createWindowImpl (this=0x1006871d0,
>>>>>>>> window=0x7fff5fbfd330) at x11gui.cpp:612
>>>>>>>> 612  ::Window xparent = RootWindow(xdisplay, DefaultScreen(xdisplay));
>>>>>>>> (gdb) Quit
>>>>>>>> 
>>>>>>>> url:    www.econ.uiuc.edu/~roger            Roger Koenker
>>>>>>>> email    rkoenker at uiuc.edu            Department of Economics
>>>>>>>> vox:     217-333-4558                University of Illinois
>>>>>>>> fax:       217-244-6678                Urbana, IL 61801
>>>>>>>> 
>>>>>>>> On May 29, 2013, at 4:37 PM, Duncan Murdoch wrote:
>>>>>>>> 
>>>>>>>>> On 13-05-29 11:19 AM, Bryan Hanson wrote:
>>>>>>>>>> [originally on R-help, reposted here as the most relevent place]
>>>>>>>>>> 
>>>>>>>>>> NOTE: problem is with R.app, looks OK on command line R
>>>>>>>>>> 
>>>>>>>>>> This is really odd, and probably 100% local to me, but I'm at a loss as to a next step.
>>>>>>>>>> 
>>>>>>>>>> After narrowing things down, here's how to reproduce:
>>>>>>>>> 
>>>>>>>>> I don't see it, but it looks to me like it may be a timing problem.  I'm
>>>>>>>>> guessing the destruction of the old window triggers events in the wrong
>>>>>>>>> order and leaves rgl in an unstable state.  Unfortunately, without being
>>>>>>>>> able to reproduce this, it looks really hard to track down.  Can anyone
>>>>>>>>> reproduce it while running in gdb or some other debugger?
>>>>>>>>> 
>>>>>>>>> Duncan Murdoch
>>>>>>>>> 
>>>>>>>>>> 
>>>>>>>>>> library("rgl")
>>>>>>>>>> showSomething <- function() {
>>>>>>>>>> open3d()
>>>>>>>>>> points3d(rnorm(10),rnorm(10),rnorm(10))
>>>>>>>>>> axes3d()
>>>>>>>>>> title3d('main','sub','xlab','ylab','zlab')
>>>>>>>>>> }
>>>>>>>>>> showSomething() # works as expected.
>>>>>>>>>> # Close the current rgl window
>>>>>>>>>> showSomething() # crashes R with the following report:
>>>>>>>>>> 
>>>>>>>>>> *** caught segfault ***
>>>>>>>>>> address 0x0, cause 'unknown'
>>>>>>>>>> 
>>>>>>>>>> Traceback:
>>>>>>>>>> 1: .C(rgl_dev_open, success = FALSE)
>>>>>>>>>> 2: rgl.open()
>>>>>>>>>> 3: open3d()
>>>>>>>>>> 4: showSomething()
>>>>>>>>>> 
>>>>>>>>>> This will probably work fine for any of you, it's so simple and fundamental.  If I don't close the open rgl windows, it doesn't crash, and I can execute the function over and over successfully.  And the same thing happens if I just do the commands inside the function individually.  SessionInfo() below.
>>>>>>>>>> 
>>>>>>>>>> Perhaps something is corrupt with my X11 window system?  Thanks, Bryan
>>>>>>>>>> 
>>>>>>>>>> R version 3.0.1 (2013-05-16)
>>>>>>>>>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>>>>>>>>> 
>>>>>>>>>> locale:
>>>>>>>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>>>>>>>> 
>>>>>>>>>> attached base packages:
>>>>>>>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>>>>>>> 
>>>>>>>>>> other attached packages:
>>>>>>>>>> [1] rgl_0.93.940 sos_1.3-5    brew_1.0-6
>>>>>>>>>> _______________________________________________
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>>>>>>>>>> 
>>>>>>>>> 
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> 
> 
> -- 
> 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



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