[R-SIG-Mac] Problems with R and Big Sur

Spencer Graves @pencer@gr@ve@ @end|ng |rom prod@y@e@com
Wed Dec 2 18:52:25 CET 2020 

	  Sorry:  Typo:  I tried "sudo xcode-select --install" and got the same 
error.  This was in Terminal where "The default interactive shell is now 
zsh."  It's not critical, because "I was able to update Xcode from App 
Store."


	  Thanks for the reply.  sg


On 2020-12-02 11:48, Dr Eberhard W Lisse wrote:
> sudo xcode-select --install
> 
> el
> 
> On 2020-12-02 18:52 , Spencer Graves wrote:
>> $ clang --version
>> Apple clang version 11.0.3 (clang-1103.0.32.59)
>> Target: x86_64-apple-darwin20.1.0
>> Thread model: posix
>> InstalledDir:
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
>>
>>
>>
>>        ** "sudo rm -rf /Library/Developer/CommandLineTools" deleted
>> "CommandLineTools".  Then "sudo xcode-select —install" gave me "invalid
>> argument '—install'".  "sudo xcode-select —install" gave me the same.
>>
>>
>>        ** Fortunately, I was able to update Xcode from App Store.  Now I
>> get:
>>
>>
>> $ clang --version
>> Apple clang version 12.0.0 (clang-1200.0.32.27)
>> Target: x86_64-apple-darwin20.1.0
>> Thread model: posix
>> InstalledDir:
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
>>
>>
>>
>>        If you also have a problem with "sudo xcode-select —install", you
>> might try the App Store.
>>
>>
>>        Thanks, Spencer
>>
>>
>> On 2020-12-02 08:18, Gilberto Camara wrote:
>>> For me, it worked as follows
>>>
>>> sudo rm -rf /Library/Developer/CommandLineTools
>>> sudo xcode-select —install
>>>
>>> Best
>>> Gilberto
>>>
>>>
>>>> On 2 Dec 2020, at 15:15, Spencer Graves <spencer.graves using prodsyse.com>
>>>> wrote:
>>>>
>>>>        What should I do to "make sure to have installed the latest
>>>> version of Apple's development environment, including version 12.0 of
>>>> the compiler"?
>>>>
>>>>
>>>>        Thanks,
>>>>        Spencer Graves
>>>>
>>>>
>>>> On 2020-12-02 07:36, GilbertoCamara wrote:
>>>>> Dear all,
>>>>> I am running R 4.0.3 on BigSur without major performance issues. I
>>>>> am using RStudio instead of the R GUI.
>>>>> I had to build all spatial packages (rgdal, sf, terra and raster)
>>>>> from source using the Apple clang version 12.0.0 compiler. I also
>>>>> had to build GDAL from scratch, since neither the “homebrew” version
>>>>> nor the “kyngchaos” version work well with BigSur.
>>>>> If anyone is building packages from source, please make sure to have
>>>>> installed the latest version of Apple’s development environment,
>>>>> including version 12.0 of the compiler as earlier versions do not
>>>>> work well in BigSur.
>>>>> Best
>>>>> Gilberto
>>>>> ===========================
>>>>> Prof Dr Gilberto Camara
>>>>> Secretariat Director
>>>>> GEO - Group on Earth Observations
>>>>>> On 2 Dec 2020, at 14:15, Bob Rudis <bob using rud.is> wrote:
>>>>>>
>>>>>> After a bit of git and google poking it seems this is happening to
>>>>>> users
>>>>>> of MacVim (https://github.com/macvim-dev/macvim/issues/1114) and a few
>>>>>> other FOSS projects.
>>>>>>
>>>>>> In various GH issues (like that one) the issue claims to be
>>>>>> resolved by
>>>>>> using the latest Xcode & SDK but that’s not likely to be a solution
>>>>>> for R
>>>>>> GUI (which I’m assuming you're using and where this error is coming
>>>>>> up).
>>>>>>
>>>>>> Some of the threads I saw made it seem like it was happening
>>>>>> especially on
>>>>>> Touch Bar-equipped MacBook Pros (but that’s not confirmed).
>>>>>>
>>>>>> When I try R GUI on Big Sur (on the new M1 Mini) — either just plain R
>>>>>> scripts or plotting — I do not see this, nor do I see this on my Intel
>>>>>> MacBook Pro (both are on the latest Big Sur beta and R 4.0.3).
>>>>>>
>>>>>> On Dec 2, 2020 at 7:53:26 AM, Spencer Graves
>>>>>> <spencer.graves using prodsyse.com>
>>>>>> wrote:
>>>>>>
>>>>>>> I didn't get this with R 4.0.3 under macOS Big Sur 11.0.1 with "time
>>>>>>> R CMD build" / check.  I have not tried it under RStudio.
>>>>>>>
>>>>>>>
>>>>>>> sg
>>>>>>>
>>>>>>>
>>>>>>> On 2020-12-02 05:01, Dr Eberhard W Lisse wrote:
>>>>>>>
>>>>>>> I don't get this in 4.0.3 (using the command line version of R) and I
>>>>>>>
>>>>>>> don't get this in RStudio 1.3.1093 either.  I use the homebrew
>>>>>>> versions
>>>>>>>
>>>>>>> without the R GUI even installed.
>>>>>>>
>>>>>>>
>>>>>>> I am sure more detail will be helpful to the developers.
>>>>>>>
>>>>>>>
>>>>>>> el
>>>>>>>
>>>>>>>
>>>>>>> On 02/12/2020 11:09, Maria-Angeles Casares-de-Cal via R-SIG-Mac
>>>>>>> wrote:
>>>>>>>
>>>>>>>> To those in charge of R for Mac OS X:
>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>> I have installed the new Big Sur operating system and now I
>>>>>>>> always get
>>>>>>>
>>>>>>>> a warning similar to:
>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>> 2020-12-02 09:52:00.647 R[703:11786] Warning: Expected min height of
>>>>>>>
>>>>>>>> view: (<NSPopoverTouchBarItemButton: 0x7f9c6bb3df50>) to be less
>>>>>>>> than
>>>>>>>
>>>>>>>> or equal to 30 but got a height of 32.000000.  This error will be
>>>>>>>
>>>>>>>> logged once per view in violation.
>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>> and the computer becomes very slow.
>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>> Can I do something to fix it, or will we have to wait for an R
>>>>>>>> update?
>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>> Thank you very much for your attention.
>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>> Sincerely,
>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>> María-Ángeles Casares-de-Cal
>>>>>>>
>>>>>>> [...]
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> R-SIG-Mac mailing list
>>>>>>> R-SIG-Mac using r-project.org
>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>>>
>>>>>>
>>>>>>      [[alternative HTML version deleted]]
>>>>>>
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