rgl crashes R.app in El Capitan

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/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