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

[Fox, John]

Dear José

> -----Original Message-----
> From: "José G. Conde" [mailto:jose.conde1 at upr.edu]
> Sent: October 19, 2015 11:55 AM
> To: Fox, John <jfox at mcmaster.ca>; Duncan Murdoch
> <murdoch.duncan at gmail.com>; r-sig-mac at r-project.org
> Subject: Re: rgl crashes R.app in El Capitan
> 
> Hello all.
> 
> For your information, I just updated Xquartz to version 2.7.8, and the
> problem persists.

I think that you may have misunderstood the source of the problem, which isn't in XQuartz but in the rgl package when R.app is run under El Capitan. Duncan will remove aglrgl.so from the rgl package to fix the problem, and you may do so in the interim, as he explained.

Best,
 John

> 
> Thanks.
> 
> 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 4:22 PM, Fox, John <jfox at mcmaster.ca> wrote:
> >
> > Hi Duncan,
> >
> > Thanks again for taking care of this.
> >
> > John
> >
> >> -----Original Message-----
> >> From: Duncan Murdoch [mailto:murdoch.duncan at gmail.com]
> >> Sent: Thursday, October 15, 2015 2:46 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 15/10/2015 2:21 PM, Fox, John 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/l
> >> ibs
> >>>> /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.
> >>
> >> Yes, I'll be dropping aglrgl.so.  rgl can run without any display
> >> (using options(rgl.useNULL = TRUE) and writing WebGL or some other
> >> kinds of output to a file), so I'm not sure whether a warning will be
> >> needed; I'll have to think about use cases.
> >>
> >> Duncan Murdoch
> >>
> >>>
> >>> 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
> >>>
> >