OK, now I got it. Thanks all for your patience.
José José G. Conde Professor, School of Medicine Director, CentIT2 UPR Medical Sciences Campus Tel (787) 763-9401 Fax (787) 758-5206 Email: jose.con...@upr.edu URL: http://rcmi.rcm.upr.edu > On Oct 19, 2015, at 12:23 PM, Fox, John <j...@mcmaster.ca> wrote: > > Dear José > >> -----Original Message----- >> From: "José G. Conde" [mailto:jose.con...@upr.edu] >> Sent: October 19, 2015 11:55 AM >> To: Fox, John <j...@mcmaster.ca>; Duncan Murdoch >> <murdoch.dun...@gmail.com>; r-sig-mac@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.con...@upr.edu >> >> URL: http://rcmi.rcm.upr.edu >> >>> On Oct 15, 2015, at 4:22 PM, Fox, John <j...@mcmaster.ca> wrote: >>> >>> Hi Duncan, >>> >>> Thanks again for taking care of this. >>> >>> John >>> >>>> -----Original Message----- >>>> From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com] >>>> Sent: Thursday, October 15, 2015 2:46 PM >>>> To: Fox, John; r-sig-mac@r-project.org >>>> Cc: jose.con...@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.dun...@gmail.com] >>>>>> Sent: Thursday, October 15, 2015 12:29 PM >>>>>> To: Fox, John; r-sig-mac@r-project.org >>>>>> Cc: jose.con...@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.dun...@gmail.com] >>>>>>>> Sent: Tuesday, October 13, 2015 3:34 PM >>>>>>>> To: Fox, John; r-sig-mac@r-project.org >>>>>>>> Cc: jose.con...@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 >>>>> >>> > _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
