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

[Fox, John]

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/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.
> 
> 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
> >