[R-SIG-Mac] [External] Re: more rgl problems
John Fox
j|ox @end|ng |rom mcm@@ter@c@
Sat Feb 20 18:38:11 CET 2021
Dear Rich,
I see R-4.0.4.pkg (not RC) at <https://cran.r-project.org/bin/macosx/>.
Perhaps refresh the page in your browser?
Best,
John
John Fox, Professor Emeritus
McMaster University
Hamilton, Ontario, Canada
web: https://socialsciences.mcmaster.ca/jfox/
On 2021-02-20 10:45 a.m., Richard M. Heiberger wrote:
> I am running it now on 4.0.4RC.
>
> The cran page
> https://cran.r-project.org
> offers download of 4.0.3 for mac, even though 4.0.4 is available on windows.
>
> ________________________________________
> From: Duncan Murdoch <murdoch.duncan using gmail.com>
> Sent: Saturday, February 20, 2021 9:41 AM
> To: Richard M. Heiberger; r-sig-mac using r-project.org
> Subject: Re: [External] Re: more rgl problems
>
> If you are set up to install from source, could you try this?
>
> devtools::install_github("dmurdoch/rgl using quartzbug", type="source")
>
> If you only have some of the requirements (e.g. no devel versions of
> packages) you might find you only get a partial build with no X11
> display; that won't really test the workaround. In that case I'll try
> to build a binary for your R version.
>
> Duncan Murdoch
>
> On 18/02/2021 6:07 p.m., Richard M. Heiberger wrote:
>> This is from my MacBook Air mid-2012 running Catalina 10.15.7
>> with Xquartz 2.7.11
>> I never placed the beta on this machine.
>> I also see from a fresh R session
>>
>> plot(1:10, col=7)
>> library(rgl)
>> open3d()
>>
>> is fine, whereas this:
>>
>> library(rgl)
>> plot(1:10, col=7)
>> open3d()
>> segfaults
>>
>> R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
>> Copyright (C) 2020 The R Foundation for Statistical Computing
>> Platform: x86_64-apple-darwin17.0 (64-bit)
>>
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under certain conditions.
>> Type 'license()' or 'licence()' for distribution details.
>>
>> Natural language support but running in an English locale
>>
>> R is a collaborative project with many contributors.
>> Type 'contributors()' for more information and
>> 'citation()' on how to cite R or R packages in publications.
>>
>> Type 'demo()' for some demos, 'help()' for on-line help, or
>> 'help.start()' for an HTML browser interface to help.
>> Type 'q()' to quit R.
>>
>>> setwd('/Users/rmh/Rwd/')
>>> library(rgl)
>> plot(1:10, col=7)
>> open3d()
>> library(rgl)
>>> plot(1:10, col=7)
>>> open3d()
>>
>> error: xp_attach_gl_context returned: 2
>>
>> *** caught segfault ***
>> address 0x18, cause 'memory not mapped'
>>
>> Traceback:
>> 1: rgl.open(useNULL)
>> 2: open3d()
>>
>> Possible actions:
>> 1: abort (with core dump, if enabled)
>> 2: normal R exit
>> 3: exit R without saving workspace
>> 4: exit R saving workspace
>> Selection: 2
>> Warning message:
>> In rgl.open(useNULL) : RGL: ERROR: can't bind glx context to window
>>
>> Process R finished at Thu Feb 18 17:57:37 2021
>>
>>
>> ________________________________________
>> From: Duncan Murdoch <murdoch.duncan using gmail.com>
>> Sent: Thursday, February 18, 2021 3:20 PM
>> To: Richard M. Heiberger; r-sig-mac using r-project.org
>> Subject: [External] Re: more rgl problems
>>
>> I've made some progress on this, but I don't know how to fix it properly.
>>
>> What's happening is that rgl is trying to open the new window that
>> open3d() asks for. It gets most of the way through that operation, then
>> calls glXMakeCurrent, which associates the OpenGL context with that
>> window. That call fails, but without generating any of the documented
>> errors: it just fails, triggering an X11 error handler with error code
>> 0 (which typically means no error).
>>
>> In the released versions of rgl, that failure leads to a segfault,
>> because I wasn't doing enough error checking. I've fixed the segfault,
>> but I'm still getting the error (in fact I'm getting it a lot more than
>> I used to; not sure if it's my debugging code causing that), and after I
>> get the error reported on screen, the new rgl window opens but doesn't
>> work to display anything.
>>
>> I think it's probably something wrong in the rgl initialization code;
>> running this:
>>
>> plot(1:10, col=7)
>> library(rgl)
>> open3d()
>>
>> is fine, whereas this:
>>
>> library(rgl)
>> plot(1:10, col=7)
>> open3d()
>>
>> is always failing for me. Or possibly this is an Xquartz bug, maybe a
>> leftover from when I installed the beta.
>>
>> I'd guess what's happening is that calling quartz() invalidates part of
>> the initialization done by rgl.init(), but I don't know what part yet.
>> I do want to call rgl.init() when loading rgl, because it might fail,
>> and then I can drop back to the off-screen drawing. It's too late to do
>> that later.
>>
>> A workaround that works for me is for the .onload() function in rgl to
>> execute
>>
>> dev.new()
>> dev.off()
>>
>> before calling rgl.init(). It is less irritating than you might guess,
>> because the window doesn't have time to appear before being destroyed,
>> but I still don't like it. I'll try it out a bit, and then push it to
>> Github for others to test.
>>
>> Duncan Murdoch
>>
>>
>> On 18/02/2021 6:28 a.m., Duncan Murdoch wrote:
>>> I can reproduce this on a Catalina machine, working in R from the terminal.
>>>
>>> This definitely looks similar to the problem that
>>> rgl::setGraphicsDelay() was designed to solve, but even adding a 10
>>> second delay doesn't help. I get a slightly different message than you:
>>>
>>> > open3d()
>>> error: xp_attach_gl_context returned: 2
>>>
>>> *** caught segfault ***
>>> address 0x18, cause 'memory not mapped'
>>>
>>> but that might just be a different way of reporting the same underlying
>>> issue.
>>>
>>> It's clearly some kind of interaction between the Quartz device and rgl.
>>> I'll see if I can track it down.
>>>
>>> Duncan Murdoch
>>>
>>> On 17/02/2021 7:36 p.m., Richard M. Heiberger wrote:
>>>> This is repeatable when the lines are all pasted in at once.
>>>> The example works if I allow some time delay between lines.
>>>>
>>>> This is might be a relative of the one from a few months ago.
>>>> But this message is about invalid permissions.
>>>> =====
>>>>
>>>> R version 4.0.4 RC (2021-02-12 r79998) -- "Lost Library Book"
>>>> Copyright (C) 2021 The R Foundation for Statistical Computing
>>>> Platform: x86_64-apple-darwin17.0 (64-bit)
>>>>
>>>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>>>> You are welcome to redistribute it under certain conditions.
>>>> Type 'license()' or 'licence()' for distribution details.
>>>>
>>>> Natural language support but running in an English locale
>>>>
>>>> R is a collaborative project with many contributors.
>>>> Type 'contributors()' for more information and
>>>> 'citation()' on how to cite R or R packages in publications.
>>>>
>>>> Type 'demo()' for some demos, 'help()' for on-line help, or
>>>> 'help.start()' for an HTML browser interface to help.
>>>> Type 'q()' to quit R.
>>>>
>>>>> setwd('/Users/rmh/Rwd/')
>>>>> library(rgl)
>>>>> x <- matrix(1:3, 1,3)
>>>>> plot(1:10, col=7)
>>>>> open3d()
>>>> error: xp_attach_gl_context returned: 2
>>>>
>>>> *** caught segfault ***
>>>> address 0x18, cause 'invalid permissions'
>>>>
>>>> Traceback:
>>>> 1: rgl.open(useNULL)
>>>> 2: open3d()
>>>>
>>>> Possible actions:
>>>> 1: abort (with core dump, if enabled)
>>>> 2: normal R exit
>>>> 3: exit R without saving workspace
>>>> 4: exit R saving workspace
>>>> Selection:
>>>>
>>>>
>>>> ====
>>>> MacBookAir with the M1 chip using the regular intel version of R from CRAN.
>>>> Big Sur 11.2.1.
>>>> The plot(1:10), col=7) ## went by default to the quartz() device.
>>>>
>>>>
>>>> I repeated this about 5 times in ESS, and then once in Terminal.
>>>>
>>>> Let me know if you need more information.
>>>>
>>>
>>
>
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