Could someone with the preference problems try the latest nightly build for R.app to see if the patch helps?

Thanks,
Rob J. Goedman
goedman@icloud.com



On Nov 8, 2013, at 6:58 AM, Robert J Goedman <goedman@icloud.com> wrote:

> Hi,
> 
> Thanks for the feedback/updates. The flashing of the color chooser has been there for a long time but I don't think that is causing this problem.
> 
> I can trigger the problem in Xcode and it shows clearly where it crashes. Its attempting to darken an icon image, pixel by pixel, but the image has no data if (on our systems at least) the 'Set Color' is not used as the path to get there.
> 
> From what I've seen, it happens on a range of systems - below my sessionInfo(). The work around is simple and I think innocuous enough that I think I can commit. But it not very satisfactory not to get to the bottom of this and to understand why only some of us encounter this problem.
> 
> Rob J. Goedman
> goedman@icloud.com
> 
> 
> 
> [R.app GUI 1.62 (6588) x86_64-apple-darwin13.0.0]
> 
> [Workspace restored from /Users/rob/Projects/.RData]
> [History restored from /Users/rob/Projects/.Rapp.history]
> 
> 2013-11-08 06:42:18.669 R[65942:707] No data in destData (darkenedImageWithColor.m)
>> sessionInfo()
> R Under development (unstable) (2013-10-30 r64123)
> Platform: x86_64-apple-darwin13.0.0/x86_64 (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     
> 
> loaded via a namespace (and not attached):
> [1] coda_0.16-1     grid_3.1.0      inline_0.3.13   lattice_0.20-25 Rcpp_0.10.6     rjags_3-11      rstan_2.0.1    
> [8] stats4_3.1.0   
>> 
> 
> 
> On Nov 8, 2013, at 3:00 AM, peter dalgaard <pdalgd@gmail.com> wrote:
> 
>> I was just about to tell you guys that have the problem to try running R.app with gdb attached to the process. Then I realized that gdb has gone in Mavericks to be replaced by lldb, which I don't have much of a clue about how to operate....
>> 
>> However, at least the first few steps seem to be similar to using gdb:
>> 
>> Get the process ID for R.app using
>> 
>> Peters-iMac:~ pd$ ps aux | grep R.app
>> pd              28620   0.1  0.5  3877356  21724   ??  S     1Nov13   0:43.29 /Applications/R.app/Contents/MacOS/R
>> pd              74190   0.0  0.0  2432784    596 s005  S+   11:45AM   0:00.01 grep R.app
>> 
>> Then attach to it using
>> 
>> Peters-iMac:~ pd$ lldb -p 28620
>> 
>> give your password to allow the debugger to control the process, then, when lldb fires up, tell it to resume the process
>> 
>> (lldb) continue
>> Process 28620 resuming
>> 
>> Next, you should try doing whatever it takes to reproduce the crash, figure out how to get a traceback, and report back to the list.
>> 
>> -pd
>> 
>> On 07 Nov 2013, at 10:19 , Rainer M Krug <Rainer@krugs.de> wrote:
>> 
>>> I have to confirm both, the crash and the flashing of the colour wheel.
>>> 
>>> 
>>>> sessionInfo()
>>> R version 3.0.2 (2013-09-25)
>>> 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
>>>> version
>>>             _
>>> platform       x86_64-apple-darwin10.8.0
>>> arch           x86_64
>>> os             darwin10.8.0
>>> system         x86_64, darwin10.8.0
>>> status
>>> major          3
>>> minor          0.2
>>> year           2013
>>> month          09
>>> day            25
>>> svn rev        63987
>>> language       R
>>> version.string R version 3.0.2 (2013-09-25)
>>> nickname       Frisbee Sailing
>>>> 
>>> 
>>> Cheers,
>>> 
>>> Rainer
>>> 
>>> 
>>> 
>>> On 11/07/13, 02:17 , John Magnotti wrote:
>>>> I removed my current R.app and installed the one at:
>>>> http://r.research.att.com/#GUI
>>>> R-3.0-branch-snowleopard-signed.pkg
>>>> 
>>>> but I still get an immediate crash when I 1) open the preferences
>>>> window and 2) click any of the icons in the main "Show All" screen
>>>> (but not the tabs)
>>>> 
>>>> I also noticed that switching away from either the Color or the Syntax
>>>> tab briefly flashes (open then close) the color wheel selection dialog
>>>> 
>>>>> sessionInfo()
>>>> R version 3.0.2 Patched (2013-11-04 r64155)
>>>> 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
>>>> 
>>>> 
>>>> Is there any other specific information that would help?
>>>> 
>>>> Thanks,
>>>> 
>>>> John
>>>> 
>>>> On Wed, Nov 6, 2013 at 10:12 AM, Brandon Hurr <bhive01@gmail.com> wrote:
>>>>> Robert,
>>>>> 
>>>>> I never could reproduce what Brian, John or Ranier were seeing with my
>>>>> install (downloaded from http://r.research.att.com/ .
>>>>> 
>>>>> Perhaps they could chime back in and give you more details.
>>>>> 
>>>>> I'm now running Mavericks and still cannot replicate.
>>>>> R version 3.0.2 (2013-09-25)
>>>>> 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
>>>>> 
>>>>> Brandon
>>>>> 
>>>>> 
>>>>> On Wed, Nov 6, 2013 at 12:13 AM, Robert J Goedman <goedman@icloud.com>wrote:
>>>>> 
>>>>>> Brandon,
>>>>>> 
>>>>>> Do you still see this problem?
>>>>>> 
>>>>>> Are you using Simon's build?
>>>>>> 
>>>>>> Regards,
>>>>>> Rob J. Goedman
>>>>>> goedman@icloud.com
>>>>>> 
>>>>>> 
>>>>>> On Jan 2, 2013, at 3:28 AM, Prof Brian Ripley <ripley@stats.ox.ac.uk>
>>>>>> wrote:
>>>>>> 
>>>>>> On 01/01/2013 17:48, Robert J Goedman wrote:
>>>>>> 
>>>>>> Thanks for taking a look. I'll dig a bit further after getting back home
>>>>>> tomorrow. It only happens through 'Apple-,' and is then not limited to
>>>>>> just the Startup preferences (contrary to what I thought earlier).
>>>>>> 
>>>>>> 
>>>>>> There is a bug report, PR#15017, related to this that we also have not
>>>>>> been able to reproduce.
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> Rob J. Goedman
>>>>>> goedman@icloud.com <mailto:goedman@icloud.com <goedman@icloud.com>>
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> On Jan 1, 2013, at 10:01 AM, Prof Brian Ripley <ripley@stats.ox.ac.uk
>>>>>> <mailto:ripley@stats.ox.ac.uk <ripley@stats.ox.ac.uk>>> wrote:
>>>>>> 
>>>>>> Sorry, cannot reproduce (with Simon's build or mine, on Lion).
>>>>>> 
>>>>>> Brian
>>>>>> 
>>>>>> On 31/12/2012 19:37, Robert J Goedman wrote:
>>>>>> 
>>>>>> Simon & Brian,
>>>>>> 
>>>>>> Surely this is not high on your minds today, but I did notice an
>>>>>> issue with R.app.
>>>>>> 
>>>>>> Using below versions of R-3.0 and the Lion64 version of R.app I
>>>>>> noticed that by immediately invoking the Startup preferences. e.g. by
>>>>>> Command/Apple-, R.app will segfault:
>>>>>> 
>>>>>> *** caught segfault ***
>>>>>> address 0x10121d000, cause 'memory not mapped'
>>>>>> ...
>>>>>> 
>>>>>> Above route seems to always create the crash. I've seen a few other
>>>>>> occurrences, always with the Startup preferences screen not being
>>>>>> mapped, but less reproducible. Same behavior in Simon's build as in
>>>>>> my own build of R.app.
>>>>>> 
>>>>>> A reasonable work around is to get there through the Set Colors icon.
>>>>>> I'm on OSX8.3 preview 3 and using Xcode 4.6 dp4. And using the CRAN
>>>>>> version of R, did not yet build R myself as outlined in the Install file.
>>>>>> 
>>>>>> Happy New Year, regards,
>>>>>> Rob J. Goedman
>>>>>> goedman@icloud.com <mailto:goedman@icloud.com <goedman@icloud.com>>
>>>>>> 
>>>>>> 
>>>>>> ------------ my own build----------------------------
>>>>>> 
>>>>>> R Under development (unstable) (2012-12-30 r61489) -- "Unsuffered
>>>>>> Consequences"
>>>>>> Copyright (C) 2012 The R Foundation for Statistical Computing
>>>>>> ISBN 3-900051-07-0
>>>>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>>>>> 
>>>>>> 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.
>>>>>> 
>>>>>> [R.app GUI 1.53 (6418) x86_64-apple-darwin9.8.0]
>>>>>> 
>>>>>> [Workspace restored from /Users/rob/Projects/.RData]
>>>>>> [History restored from /Users/rob/Projects/.Rapp.history]
>>>>>> 
>>>>>> sessionInfo()
>>>>>> 
>>>>>> R Under development (unstable) (2012-12-30 r61489)
>>>>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (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
>>>>>> 
>>>>>> 
>>>>>> -------------R.app from
>>>>>> Simon---------------------------------------------
>>>>>> 
>>>>>> R Under development (unstable) (2012-12-30 r61489) -- "Unsuffered
>>>>>> Consequences"
>>>>>> Copyright (C) 2012 The R Foundation for Statistical Computing
>>>>>> ISBN 3-900051-07-0
>>>>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>>>>> 
>>>>>> 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.
>>>>>> 
>>>>>> [R.app GUI 1.53 (6418) x86_64-apple-darwin9.8.0]
>>>>>> 
>>>>>> [Workspace restored from /Users/rob/Projects/.RData]
>>>>>> [History restored from /Users/rob/Projects/.Rapp.history]
>>>>>> 
>>>>>> sessionInfo()
>>>>>> 
>>>>>> R Under development (unstable) (2012-12-30 r61489)
>>>>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (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
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> --
>>>>>> Brian D. Ripley, ripley@stats.ox.ac.uk <mailto:ripley@stats.ox.ac.uk<ripley@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
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> --
>>>>>> Brian D. Ripley,                  ripley@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
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> On Oct 2, 2013, at 6:09 AM, Brandon Hurr <bhive01@gmail.com> wrote:
>>>>>> 
>>>>>> I cannot reproduce on my mac mini (2011). OS X 10.8.5.
>>>>>> 
>>>>>> R version 3.0.2 (2013-09-25)
>>>>>> 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
>>>>>> 
>>>>>> 
>>>>>> On Wed, Oct 2, 2013 at 2:03 PM, John Magnotti <john.magnotti@gmail.com
>>>>>>> wrote:
>>>>>> 
>>>>>> Going to the preferences screen in R.app (Command + , or
>>>>>> R->preferences) and selecting any of the icons causes R to crash with
>>>>>> a segfault. If I click any the tabs at the top of the preferences
>>>>>> window R doesn't crash, but if I go back to the  "show all" tab and
>>>>>> choose an option it causes an immediate failure.
>>>>>> 
>>>>>> I'm running OS X 10.8.5, sessionInfo pasted below
>>>>>> 
>>>>>> Thoughts?
>>>>>> 
>>>>>> John
>>>>>> 
>>>>>> 
>>>>>> sessionInfo()
>>>>>> 
>>>>>> R version 3.0.2 (2013-09-25)
>>>>>> 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
>>>>>> 
>>>>>> _______________________________________________
>>>>>> R-SIG-Mac mailing list
>>>>>> R-SIG-Mac@r-project.org
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>> 
>>>>>> 
>>>>>> [[alternative HTML version deleted]]
>>>>>> 
>>>>>> 
>>>>>> _______________________________________________
>>>>>> R-SIG-Mac mailing list
>>>>>> R-SIG-Mac@r-project.org
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>> 
>>>>>> 
>>>>>> 
>>>>> 
>>>>>      [[alternative HTML version deleted]]
>>>>> 
>>>>> _______________________________________________
>>>>> R-SIG-Mac mailing list
>>>>> R-SIG-Mac@r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>> 
>>> 
>>> -- 
>>> Rainer M. Krug
>>> 
>>> email: RMKrug<at>gmail<dot>com
>>> 
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac@r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
>> -- 
>> Peter Dalgaard, Professor
>> Center for Statistics, Copenhagen Business School
>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>> Phone: (+45)38153501
>> Email: pd.mes@cbs.dk  Priv: PDalgd@gmail.com
>> 
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 
> 
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