[R-SIG-Mac] [External] Re: [External] Please test R 4.0.4 RC

Sun Feb 14 00:13:17 CET 2021

Well, my original report didn't give full information because R locked up too early.

>From here I am following instructions and reporting back:

R version 4.0.4 RC (2021-02-12 r79998) -- "Lost Library Book"
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Platform: x86_64-apple-darwin17.0 (64-bit)

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> setwd('/Users/rmh/Rwd/')
> system("Applications/Xquartz")
sh: Applications/Xquartz: No such file or directory
Warning message:
In system("Applications/Xquartz") : error in running command
> system("/Applications/Xquartz")
sh: /Applications/Xquartz: No such file or directory
Warning message:
In system("/Applications/Xquartz") : error in running command
> system("/Applications/Utilities/Xquartz")
sh: /Applications/Utilities/Xquartz: No such file or directory
Warning message:
In system("/Applications/Utilities/Xquartz") : error in running command
> system("/Applications/Utilities/Xquartz.app")
sh: /Applications/Utilities/Xquartz.app: is a directory
> system("/Applications/Utilities/Xquartz.app/Contents/MacOS/X11")
> X11()
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize,  :
  unable to start device X11
In addition: Warning messages:
1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) :
  running command ''otool' -L '/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1
2: In X11() : unable to open connection to X11 display ''
> system("/Applications/Utilities/Xquartz.app/Contents/MacOS/X11")
> ## from the Cmd-Tab I opened Xquartz, and from its Applications I opened xterm, and then ran an ls in xterm. it works.
> X11()
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize,  :
  unable to start device X11
In addition: Warning messages:
1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) :
  running command ''otool' -L '/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1
2: In X11() : unable to open connection to X11 display ''
> Sys.getenv("DISPLAY")
[1] "/private/tmp/com.apple.launchd.l0xAmiv83n/org.xquartz:0"
> unlink(Sys.getenv("DISPLAY"))
>    Sys.setenv(DISPLAY=":0.0")
> X11()
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize,  :
  unable to start device X11
In addition: Warning messages:
1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) :
  running command ''otool' -L '/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1
2: In X11() : unable to open connection to X11 display ''
>

________________________________________
From: Simon Urbanek <simon.urbanek using R-project.org>
Sent: Saturday, February 13, 2021 5:35 PM
To: Richard M. Heiberger
Cc: Dr Eberhard W Lisse; R-SIG-Mac
Subject: Re: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC

Richard,

thanks - finally a more complete output to go on. This is exactly the reminder why it is so important to post the _full_output - the actual facts were completely missing from your previous report.

Firstly, the xcrun output is just a warning which indicates that R can't find out whether you have XQuartz installed or not. It also shows that your Xcode/command line tools are broken. That in itself is not a problem as long as you don't intend to compile packages - but probably you should look into it.

But more importantly your XQuartz doesn't work - or at least is not running at the time you are trying to run X11() in R. Make sure you start XQuartz first (from Applications -> Utilities) and it works. If in doubt, you can wipe it (it lives in /opt/X11) and re-install.

Either way, neither seems to be an R issue per se.

Cheers,
Simon

`
> On Feb 14, 2021, at 11:00 AM, Richard M. Heiberger <rmh using temple.edu> wrote:
>
> another fresh R session
>
>> X11(":0")
> xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
> Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize,  :
>  unable to start device X11
> In addition: Warning messages:
> 1: In system2("otool", c("-L", shQuote(DSO)), stdout = TRUE) :
>  running command ''otool' -L '/Library/Frameworks/R.framework/Resources/modules/R_X11.so'' had status 1
> 2: In X11(":0") : unable to open connection to X11 display ':0'
>>
>
> ________________________________________
> From: Simon Urbanek <simon.urbanek using R-project.org>
> Sent: Saturday, February 13, 2021 4:54 PM
> To: Richard M. Heiberger
> Cc: Dr Eberhard W Lisse; R-SIG-Mac
> Subject: Re: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC
>
> As mentioned earlier, the issue is likely that your X11-auto-launch is not working. You can start X11 (=XQuartz) yourself and set DISPLAY=:0 as you would on any unix system or start X11 with X11(":0")
> [personally, I hate that auto-launch "feature" since it tries to start XQuartz even if you don't want it].
>
> Cheers,
> Simon
>
>
>> On Feb 14, 2021, at 9:50 AM, Richard M. Heiberger <rmh using temple.edu> wrote:
>>
>> I tried this.  It made no difference.  Both before and after running
>> sudo xcode-select —install
>> I ran (in both cases, in a brand new *R* sessio n)
>>
>>> X11()
>> xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
>>
>>
>> My prior was that the xcode call was irrelevant is that X11() using XQuart 8.0.3beta
>> worked with intel R_4.0.3 on the Mac M1.
>>
>> ________________________________________
>> From: Dr Eberhard W Lisse <el using lisse.na>
>> Sent: Saturday, February 13, 2021 3:33 AM
>> To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger
>> Cc: el using lisse.NA
>> Subject: [External] Re: [R-SIG-Mac] [External] Please test R 4.0.4 RC
>>
>> that has nothing to do with Xquartz but means you need to install the Command line tools
>>
>> sudo xcode-select —install
>>
>> —
>> Sent from Dr Lisse’s iPhone
>> On 13 Feb 2021, 06:13 +0200, Richard M. Heiberger <rmh using temple.edu>, wrote:
>> Using the intel R_4.0.4RC on the Mac M1.
>>
>> Based on your recommendation I reinstalled XQuartz 2.7.11 instead of the 8.0.3beta.
>> X11() now does not work at all.
>>
>> X11()
>> xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
>> C-c C-c C-c C-c
>>
>> Force-Killing XQuartz from the Activity Monitor doesn't help.
>> I have to Force-kill the R process.
>>
>> ________________________________________
>> From: R-SIG-Mac <r-sig-mac-bounces using r-project.org> on behalf of Simon Urbanek <simon.urbanek using R-project.org>
>> Sent: Friday, February 12, 2021 6:50 PM
>> To: R-SIG-Mac
>> Subject: [External] [R-SIG-Mac] Please test R 4.0.4 RC
>>
>> Dear macOS useRs,
>>
>> please test the latest R 4.0.4 RC builds from
>>
>> https://mac.r-project.org/
>>
>> especially if you are running macOS Big Sur. The known issues introduced by Big Sur have been fixed, but I cannot replicate nor test the spurious touchbar warning.
>>
>> Also a reminder to *not* install XQuartz betas even if XQuartz ask you to - they are betas for a reason (=unstable) and break things.
>>
>> Cheers,
>> Simon
>>
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>