Re: [R-SIG-Mac] [External] Re: [External] Re: [External] Please test R 4.0.4 RC
another new session
> setwd('/Users/rmh/Rwd/')
> 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 ''
> Sys.getenv("DISPLAY")
[1] ":0.0"
>
I didn't make any more changes to the Xquartz. I previously had the beta and
replaced it with 2.7.11, so I just continued from there.
From: Duncan Murdoch
Sent: Saturday, February 13, 2021 4:55 PM
To: Richard M. Heiberger; R-SIG-Mac
Subject: Re: [External] Re: [R-SIG-Mac] [External] Re: [External] Please test R
4.0.4 RC
Thanks for your detailed descriptions! I can now reproduce this, and I
have an ugly workaround. I should be able to get a better workaround soon.
To reproduce:
Install the beta. (I did this when it was pushed to me.) It worked
fine for me.
Install the previous version, 2.7.11. Reboot the system.
Now running x11() in R causes the spinning beach ball.
The workaround:
Start R. The DISPLAY environment variable will show the name something like
[1] "/private/tmp/com.apple.launchd.RuLLnvteCn/org.xquartz:0"
This is a socket, not a regular file.
Delete this, and set DISPLAY to ":0.0":
unlink(Sys.getenv("DISPLAY"))
Sys.setenv(DISPLAY=":0.0")
Now x11() is fine.
This is only a workaround. The unlink() is permanent, but setting the
environment variable only lasts for the length of the R session. You'll
need to enter Sys.setenv(DISPLAY=":0.0") again in future sessions, and I
would guess the socket will be recreated the next time you restart the
system (or maybe on login).
Duncan Murdoch
On 13/02/2021 4:21 p.m., Richard M. Heiberger wrote:
> That is next. Again a fresh session.
>
>
>> setwd('/Users/rmh/Rwd/')
>> 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 ''
>>
>
>
> and the R session is still alive.
>
>
> This rasies for me a different question. Why should I want X11()?
>
> When X11 was working it was very slow, and didn't allow paging back through
> previous images.
>
> In favor of X11, I think it uses the display space better. X11() has better
> size and spacing for xlab, ylab, and main than quartz(). But that isn't a
> strong enough
> reason to use it while develkoping a graph. When I want it to look good,
> I go directly to pdf() and get the spacing that I think looks better.
>
>
> From: Duncan Murdoch
> Sent: Saturday, February 13, 2021 4:05 PM
> To: Richard M. Heiberger; R-SIG-Mac
> Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Please test R
> 4.0.4 RC
>
> Have you tried the change to DISPLAY, i.e.
>
> Sys.setenv(DISPLAY=":0.0")
>
> before running X11()?
>
> Duncan Murdoch
>
> On 13/02/2021 3:50 p.m., Richard M. Heiberger 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
>> Sent: Saturday, February 13, 2021 3:33 AM
>> To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger
>> Cc: e...@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 , 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
Re: [R-SIG-Mac] [External] Re: [External] Re: [External] Please test R 4.0.4 RC
Thanks for your detailed descriptions! I can now reproduce this, and I
have an ugly workaround. I should be able to get a better workaround soon.
To reproduce:
Install the beta. (I did this when it was pushed to me.) It worked
fine for me.
Install the previous version, 2.7.11. Reboot the system.
Now running x11() in R causes the spinning beach ball.
The workaround:
Start R. The DISPLAY environment variable will show the name something like
[1] "/private/tmp/com.apple.launchd.RuLLnvteCn/org.xquartz:0"
This is a socket, not a regular file.
Delete this, and set DISPLAY to ":0.0":
unlink(Sys.getenv("DISPLAY"))
Sys.setenv(DISPLAY=":0.0")
Now x11() is fine.
This is only a workaround. The unlink() is permanent, but setting the
environment variable only lasts for the length of the R session. You'll
need to enter Sys.setenv(DISPLAY=":0.0") again in future sessions, and I
would guess the socket will be recreated the next time you restart the
system (or maybe on login).
Duncan Murdoch
On 13/02/2021 4:21 p.m., Richard M. Heiberger wrote:
That is next. Again a fresh session.
setwd('/Users/rmh/Rwd/')
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 ''
and the R session is still alive.
This rasies for me a different question. Why should I want X11()?
When X11 was working it was very slow, and didn't allow paging back through
previous images.
In favor of X11, I think it uses the display space better. X11() has better
size and spacing for xlab, ylab, and main than quartz(). But that isn't a
strong enough
reason to use it while develkoping a graph. When I want it to look good,
I go directly to pdf() and get the spacing that I think looks better.
From: Duncan Murdoch
Sent: Saturday, February 13, 2021 4:05 PM
To: Richard M. Heiberger; R-SIG-Mac
Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Please test R
4.0.4 RC
Have you tried the change to DISPLAY, i.e.
Sys.setenv(DISPLAY=":0.0")
before running X11()?
Duncan Murdoch
On 13/02/2021 3:50 p.m., Richard M. Heiberger 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
Sent: Saturday, February 13, 2021 3:33 AM
To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger
Cc: e...@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 , 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 on behalf of Simon Urbanek
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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Re: [R-SIG-Mac] [External] Re: [External] Re: [External] Please test R 4.0.4 RC
the Xcode Command line tools are missing. Install them and see what happens.
Did you recently upgrade MacOS?
el
—
Sent from Dr Lisse’s iPhone
On 13 Feb 2021, 23:21 +0200, Richard M. Heiberger , wrote:
> That is next. Again a fresh session.
>
>
> > setwd('/Users/rmh/Rwd/')
> > 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 ''
> >
>
>
> and the R session is still alive.
>
>
> This rasies for me a different question. Why should I want X11()?
>
> When X11 was working it was very slow, and didn't allow paging back through
> previous images.
>
> In favor of X11, I think it uses the display space better. X11() has better
> size and spacing for xlab, ylab, and main than quartz(). But that isn't a
> strong enough
> reason to use it while develkoping a graph. When I want it to look good,
> I go directly to pdf() and get the spacing that I think looks better.
>
>
> From: Duncan Murdoch
> Sent: Saturday, February 13, 2021 4:05 PM
> To: Richard M. Heiberger; R-SIG-Mac
> Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Please test R
> 4.0.4 RC
>
> Have you tried the change to DISPLAY, i.e.
>
> Sys.setenv(DISPLAY=":0.0")
>
> before running X11()?
>
> Duncan Murdoch
>
> On 13/02/2021 3:50 p.m., Richard M. Heiberger 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
> > Sent: Saturday, February 13, 2021 3:33 AM
> > To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger
> > Cc: e...@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 , 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 on behalf of Simon
> > Urbanek
> > 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
> >
> > ___
> > R-SIG-Mac mailing list
> > R-SIG-Mac@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
> > ___
> > R-SIG-Mac mailing list
> > R-SIG-Mac@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
> > ___
> > R-SIG-Mac mailing list
> > R-SIG-Mac@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
>
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
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Re: [R-SIG-Mac] [External] Re: [External] Re: [External] Please test R 4.0.4 RC
That is next. Again a fresh session.
> setwd('/Users/rmh/Rwd/')
> 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 ''
>
and the R session is still alive.
This rasies for me a different question. Why should I want X11()?
When X11 was working it was very slow, and didn't allow paging back through
previous images.
In favor of X11, I think it uses the display space better. X11() has better
size and spacing for xlab, ylab, and main than quartz(). But that isn't a
strong enough
reason to use it while develkoping a graph. When I want it to look good,
I go directly to pdf() and get the spacing that I think looks better.
From: Duncan Murdoch
Sent: Saturday, February 13, 2021 4:05 PM
To: Richard M. Heiberger; R-SIG-Mac
Subject: [External] Re: [R-SIG-Mac] [External] Re: [External] Please test R
4.0.4 RC
Have you tried the change to DISPLAY, i.e.
Sys.setenv(DISPLAY=":0.0")
before running X11()?
Duncan Murdoch
On 13/02/2021 3:50 p.m., Richard M. Heiberger 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
> Sent: Saturday, February 13, 2021 3:33 AM
> To: Simon Urbanek; R-SIG-Mac; Richard M. Heiberger
> Cc: e...@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 , 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 on behalf of Simon Urbanek
>
> 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
>
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
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