[R-SIG-Mac] rgl crashes R.app in El Capitan

[Jose G Conde Santiago]

Hello all.

Upgraded to R 3.2.3 “Wooden Christmas” and installed rgl 0.95.1441 on my iMac. The problem was fixed.

Thank you all.

José 

José G. Conde, MD, MPH
Catedrático, Escuela de Medicina
Director, CentIT2
Recinto de Ciencias Médicas, UPR

Tel  (787) 763-9401  Fax (787) 758-5206

Correo electrónico: jose.conde1 at upr.edu

URL: http://rcmi.rcm.upr.edu

> On Oct 15, 2015, at 2:21 PM, Fox, John <jfox at mcmaster.ca> wrote:
> 
> Hi Duncan,
> 
> Thanks for looking into this. Please see below:
> 
>> -----Original Message-----
>> From: Duncan Murdoch [mailto:murdoch.duncan at gmail.com]
>> Sent: Thursday, October 15, 2015 12:29 PM
>> To: Fox, John; r-sig-mac at r-project.org
>> Cc: jose.conde1 at upr.edu
>> Subject: Re: rgl crashes R.app in El Capitan
>> 
>> One of my students has El Capitan, so I got to see this.  It appears
>> it's the old aglrgl.so problem.  I should just give up on native
>> support, since I don't really know how to debug it.
>> 
>> The "simple" fix is to delete the aglrgl.so file.  This means R.app will
>> use the X11 driver, the same as the terminal version or RStudio would
>> use.  Some users will have problems with this:
>> 
>> - It means they need Xquartz installed.
>> - You need admin privileges to delete aglrgl.so, and you need to know
>> how to find it.  To find it, in R you can run
>> 
>> system.file("libs/aglrgl.so", package="rgl")
>> 
>> in R; I see
>> 
>> "/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rgl/libs
>> /aglrgl.so"
>> 
>> but others may see it elsewhere.  I don't know if there is a way to
>> delete it from R; I'd expect
>> 
>> unlink(system.file("libs/aglrgl.so", package="rgl"))
>> 
>> to fail because of permission problems, but I'm not sure of that.
> 
> Actually, that works for me and fixes the problem.
> 
>> 
>> I'm not going to attempt to describe Xquartz installation, but Google
>> should be able to help.
> 
> Jose encountered this problem using the Rcmdr package, which already requires XQuartz due to Tcl/Tk, but more generally the car package doesn't need XQuartz. XQuartz installation is simple in any event.
> 
> One thing is unclear to me, however. Will you simply remove aglrgl.so from the next version of rgl? If so, you should be able to test for the presence of XQuartz and print a warning message in its absence.
> 
> Best,
> John
> 
>> 
>> Duncan Murdoch
>> 
>> 
>> 
>> On 13/10/2015 4:05 PM, Fox, John wrote:
>>> Dear Duncan,
>>> 
>>>> -----Original Message-----
>>>> From: Duncan Murdoch [mailto:murdoch.duncan at gmail.com]
>>>> Sent: Tuesday, October 13, 2015 3:34 PM
>>>> To: Fox, John; r-sig-mac at r-project.org
>>>> Cc: jose.conde1 at upr.edu
>>>> Subject: Re: rgl crashes R.app in El Capitan
>>>> 
>>>> On 13/10/2015 3:03 PM, Fox, John wrote:
>>>>> Dear r-sig-mac list members,
>>>>> 
>>>>> I can reliably crash R.app in R 3.2.2 under El Capitan with
>>>>> 
>>>>>  library(rgl)
>>>>>  demo("rgl")  # a few returns
>>>>> 
>>>>> My session info:
>>>>> 
>>>>>> sessionInfo()
>>>>> R version 3.2.2 (2015-08-14)
>>>>> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>>>>> Running under: OS X 10.11 (El Capitan)
>>>>> 
>>>>> locale:
>>>>> [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
>>>>> 
>>>>> attached base packages:
>>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>> 
>>>>> other attached packages:
>>>>> [1] rgl_0.95.1367
>>>>> 
>>>>> I see this problem only in R.app, not when R is run in a terminal or
>>>> in RStudio.
>>>>> 
>>>>> This problem was original brought to my attention by Jose Conde (to
>>>> whom I'm cc'ing this message), who encountered the problem using the
>>>> scatter3d() function in the car package via the Rcmdr, but the
>> problem
>>>> isn't unique to either scatter3d() or the Rcmdr. In the case of
>>>> scatter3d() the command
>>>>> 
>>>>>    scatter3d(prestige ~ income + education, data=Prestige)
>>>>> 
>>>>> which draws a regression surface, reliably crashes R.app, but
>>>>> 
>>>>>    scatter3d(prestige ~ income + education, data=Prestige,
>>>> surface=FALSE)
>>>>> 
>>>>> which plots only points (as spheres) doesn't.
>>>>> 
>>>>> I hope that this provides enough clues to diagnose the problem.
>>>>> 
>>>>> 
>>>> 
>>>> I don't have El Capitan, I'm still running under OS X 10.9.5
>>>> (Mavericks), and it doesn't crash.
>>> 
>>> That was my experience as well -- I didn't experience this problem
>> under either Mavericks or Yosemite. BTW, I reinstalled R 3.2.2 and
>> XQuartz after upgrading to El Capitan. I usually upgrade fairly early to
>> see whether there are any problems.
>>> 
>>>> 
>>>> Since you're using the latest rgl, you must have built it yourself --
>>>> CRAN doesn't distribute binaries for it (at least for Mavericks).
>> Did
>>>> you get any errors or warnings during compilation?
>>> 
>>> Right again. I ran update.packages() to make sure that the error
>> wasn't fixed and compiled packages that didn't yet have Mac binaries.
>> AFAICS, there were no errors in compiling the rgl package.
>>> 
>>> BTW, my apologies for posting my message twice -- my mailer complained
>> about the address in the first message and I thought it wasn't sent.
>>> 
>>> Thanks for looking into this,
>>> John
>>> 
>>>> 
>>>> Duncan Murdoch
>