[R-SIG-Mac] tcltk on M1 mac?

[Vincent Carey]

I can't seem to get tcltk running with R on M1 machine.  Homebrew tcltk
seems to have wrong architecture; attempt to build from source does not
help.  Any hints appreciated.


R version 4.1.0 RC (2021-05-10 r80283) -- "Camp Pontanezen"

Copyright (C) 2021 The R Foundation for Statistical Computing

Platform: aarch64-apple-darwin20 (64-bit)


> library(tcltk)

*Error: package or namespace load failed for 'tcltk':*

* .onLoad failed in loadNamespace() for 'tcltk', details:*

*  call: dyn.load(file, DLLpath = DLLpath, ...)*

*  error: unable to load shared object
'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/tcltk/libs/tcltk.so':*

*
dlopen(/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/tcltk/libs/tcltk.so,
10): Library not loaded: /Library/Frameworks/Tcl.framework/Versions/8.6/Tcl*

*  Referenced from:
/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/tcltk/libs/tcltk.so*

*  Reason: image not found*

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Re: [R-SIG-Mac] incompatible lldb on mojave?

[Vincent Carey]

Thanks, I am upgrading a machine to catalina and will get back to you.

On Sun, May 3, 2020 at 8:01 AM Bob Rudis  wrote:

> Can you provide a bit more info on the setup?
>
> I ask b/c: (more below the snippet)
>
> $ R -d lldb
> (lldb) target create
> "/Library/Frameworks/R.framework/Resources/bin/exec/R"
> Current executable set to
> '/Library/Frameworks/R.framework/Resources/bin/exec/R' (x86_64).
> (lldb) run
> Process 3834 launched:
> '/Library/Frameworks/R.framework/Resources/bin/exec/R' (x86_64)
>
> R version 4.0.0 RC (2020-04-21 r78267) -- "Arbor Day"
> 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.
>
> > str(mtcars)
> 'data.frame':   32 obs. of  11 variables:
>  $ mpg : num  21 21 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 ...
>  $ cyl : num  6 6 4 6 8 6 8 4 4 6 ...
>  $ disp: num  160 160 108 258 360 ...
>  $ hp  : num  110 110 93 110 175 105 245 62 95 123 ...
>  $ drat: num  3.9 3.9 3.85 3.08 3.15 2.76 3.21 3.69 3.92 3.92 ...
>  $ wt  : num  2.62 2.88 2.32 3.21 3.44 ...
>  $ qsec: num  16.5 17 18.6 19.4 17 ...
>  $ vs  : num  0 0 1 1 0 1 0 1 1 1 ...
>  $ am  : num  1 1 1 0 0 0 0 0 0 0 ...
>  $ gear: num  4 4 4 3 3 3 3 4 4 4 ...
>  $ carb: num  4 4 1 1 2 1 4 2 2 4 ...
> >
>
> I have full Xcode installed and updated to latest (I'm on developer betas).
>
> $ lldb --version
> lldb-1103.0.17
> Apple Swift version 5.2 (swiftlang-1103.0.22 clang-1103.0.22)
>
> I'm also on a more restrictive OS (Catalina).
>
> Of note: macOS prompted me for permission to use lldb.
>
> -boB
>
> On Sat, May 2, 2020 at 11:26 PM Simon Urbanek
>  wrote:
> >
> > Vince,
> >
> > Apple no longer allows debugging of distributed apps - see R for Mac FAQ
> 10.17:
> >
> http://mac.r-project.org/bin/macosx/RMacOSX-FAQ.html#I-cannot-attach-debugger-to-R
> >
> > Another (not recommended) work-around is to disable SIP.
> >
> > Cheers,
> > Simon
> >
> >
> >
> > > On 3/05/2020, at 10:42 AM, Vincent Carey 
> wrote:
> > >
> > > I'd like to make use of material in
> > >
> > > https://kevinushey.github.io/blog/2015/04/13/debugging-with-lldb/
> > >
> > > But with R 4.0 I get
> > >
> > > %vjcair> R -d lldb
> > >
> > > (lldb) target create
> "/Library/Frameworks/R.framework/Resources/bin/exec/R"
> > >
> > > Current executable set to
> > > '/Library/Frameworks/R.framework/Resources/bin/exec/R' (x86_64).
> > >
> > > (lldb) run
> > >
> > > error: process exited with status -1 (Error 1)
> > >
> > > (lldb) quit
> > >
> > > %vjcair> which lldb
> > >
> > > /usr/bin/lldb
> > >
> > > %vjcair> lldb --version
> > >
> > > lldb-1100.0.30.12
> > >
> > > Apple Swift version 5.1.3 (swiftlang-1100.0.282.1 clang-1100.0.33.15)
> > >
> > >
> > > with gdb, there is a little more info -- and a peculiar warning that
> > > mentions /Volumes/Builds/Simon/R4/h ...
> > >
> > >
> > > %vjcair> R -d gdb
> > >
> > > GNU gdb (GDB) 8.1
> > >
> > > Copyright (C) 2018 Free Software Foundation, Inc.
> > >
> > > License GPLv3+: GNU GPL version 3 or later <
> http://gnu.org/licenses/gpl.html
> > >>
> > >
> > > This is free software: you are free to change and redistribute it.
> > >
> > > There is NO WARRANTY, to the extent permitted by law.  Type "show
> copying"
> > >
> > > and "show warranty" for details.
> > >
> > > This GDB was configured as "x86_64-apple-darwin16.7.0".
> > >
> > > Type "show configuration" for configuration details.
> > >
> > > For bug reporting instru

[R-SIG-Mac] incompatible lldb on mojave?

[Vincent Carey]

I'd like to make use of material in

https://kevinushey.github.io/blog/2015/04/13/debugging-with-lldb/

But with R 4.0 I get

%vjcair> R -d lldb

(lldb) target create "/Library/Frameworks/R.framework/Resources/bin/exec/R"

Current executable set to
'/Library/Frameworks/R.framework/Resources/bin/exec/R' (x86_64).

(lldb) run

error: process exited with status -1 (Error 1)

(lldb) quit

%vjcair> which lldb

/usr/bin/lldb

%vjcair> lldb --version

lldb-1100.0.30.12

Apple Swift version 5.1.3 (swiftlang-1100.0.282.1 clang-1100.0.33.15)


with gdb, there is a little more info -- and a peculiar warning that
mentions /Volumes/Builds/Simon/R4/h ...


%vjcair> R -d gdb

GNU gdb (GDB) 8.1

Copyright (C) 2018 Free Software Foundation, Inc.

License GPLv3+: GNU GPL version 3 or later 

This is free software: you are free to change and redistribute it.

There is NO WARRANTY, to the extent permitted by law.  Type "show copying"

and "show warranty" for details.

This GDB was configured as "x86_64-apple-darwin16.7.0".

Type "show configuration" for configuration details.

For bug reporting instructions, please see:

.

Find the GDB manual and other documentation resources online at:

.

For help, type "help".

Type "apropos word" to search for commands related to "word"...

Reading symbols from /Library/Frameworks/R.framework/Resources/bin/exec/R...

warning:
`/Volumes/Builds/Simon/R4/high-sierra-x86_64/R-4.0-branch/src/main/Rmain.o':
can't open to read symbols: No such file or directory.

(no debugging symbols found)...done.

(gdb) run

Starting program:
/Library/Frameworks/R.framework/Versions/4.0/Resources/bin/exec/R

Unable to find Mach task port for process-id 59032: (os/kern) failure (0x5).

 (please check gdb is codesigned - see taskgated(8))

> sessionInfo()

R version 4.0.0 Patched (2020-04-27 r78309)

Platform: x86_64-apple-darwin17.0 (64-bit)

Running under: macOS Mojave 10.14.6


Matrix products: default

BLAS:
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib

LAPACK:
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

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[R-SIG-Mac] availability of binary for 3.5/patched?

[Vincent Carey]

I don't see this at r.research.att.com

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Re: [R-SIG-Mac] trying to compile packages from source, but lacking /opt/local/bin/gcc-mp-5

[Vincent Carey]

Of course -- there were forgotten settings in $HOME/.R/Makevars -- I should
have inferred that it was a private matter.  Apologies.

On Tue, Nov 21, 2017 at 9:05 AM, Simon Urbanek <simon.urba...@r-project.org>
wrote:

> Vince,
>
> I'm pretty sure you are using custom settings, because the binary uses
> clang:
>
> $ R CMD config CC
> clang
> $ grep -r /opt/local/bin/ /Library/Frameworks/R.framework/
> $
>
> We don't have /opt/local on the build machine so it must be something
> configured in your system.
> Please make sure you don't use custom package managers on you PATH since
> you'd be picking up non-CRAN R.
>
> Cheers,
> Simon
>
>
>
> > On Nov 21, 2017, at 8:26 AM, Vincent Carey <st...@channing.harvard.edu>
> wrote:
> >
> > On Tue, Nov 21, 2017 at 3:34 AM, Prof Brian Ripley <
> rip...@stats.ox.ac.uk>
> > wrote:
> >
> >> On 21/11/2017 04:03, Vincent Carey wrote:
> >>
> >>> %vjcair> R CMD config CC
> >>>
> >>> /opt/local/bin/gcc-mp-5
> >>>
> >>>
> >>> I don't seem to be able to override this using environment variable CC.
> >>> And
> >>>
> >>
> >> When all else fails, read the manual (but, see the posting guide, before
> >> posting here)!  This is covered in, e.g.,
> >>
> >> https://cran.r-project.org/doc/manuals/r-release/R-admin.htm
> >> l#macOS-packages
> >>
> >> https://cran.r-project.org/doc/manuals/r-release/R-admin.htm
> >> l#Customizing-package-compilation
> >>
> >>
> > Yes, section 6.3.3. gives the solution.
> >
> >
> >>
> >>> I cannot see how to install gcc-mp-5.  This version of R was obtained
> from
> >>>
> >>> r.research.att.com, R-3.4-branch-el-capitan.pkg.
> >>>
> >>>
> >>> I would have expected clang to be the c compiler for this build.  I
> will
> >>>
> >>
> >> It was for the released version of 3.4.2.  Problems with off-CRAN builds
> >> are best addressed to the builder, here Simon Urbanek.  But that is a
> >> month-old snapshot build ... I don't understand why you did not simply
> >> update it, and I see 'clang' in the current snapshot.
> >>
> >
> > Without alternate settings in the platform-specific Makevars, the most
> > recent binary gives the value of "R CMD config CC" noted in the original
> > posting.
> >
> > Thank you for your assistance.
> >
> >
> >>
> >>
> >>
> >>> appreciate any suggestions.  As it stands, any installation from source
> >>> requiring
> >>>
> >>> compilation throws errors like
> >>>
> >>> /bin/sh: /opt/local/bin/g++-mp-5: No such file or directory
> >>>
> >>>
> >>> R version 3.4.2 Patched (2017-10-20 r73567) -- "Short Summer"
> >>>
> >>> Copyright (C) 2017 The R Foundation for Statistical Computing
> >>>
> >>> Platform: x86_64-apple-darwin15.6.0 (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.
> >>>
> >>>
> >>> sessionInfo()
> >>>>
> >>>
> >>> R version 3.4.2 Patched (2017-10-20 r73567)
> >>>
> >>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> >>>
> >>> Running under: macOS Sierra 10.12.6
> >>>
> >>>
> >>> Matrix products: default
> >>>
> >>> BLAS:
> >>> /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/
> >>> libRblas.0.dylib
> >>>
> >>> LAPACK: /Library/Frameworks/R.framework/Versions/3.4
> >>>
> >>>[[alternative HTML version deleted]]
> >>>
> >>> ___
> >>> R-SIG-Mac mailing list
> >>> R-SIG-Mac@r-project.org
> >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >>>
> >>>
> >>
> >> --
> >> Brian D. Ripley,  rip...@stats.ox.ac.uk
> >> Emeritus Professor of Applied Statistics, University of Oxford
> >>
> >
> >   [[alternative HTML version deleted]]
> >
> > ___
> > 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] trying to compile packages from source, but lacking /opt/local/bin/gcc-mp-5

[Vincent Carey]

On Tue, Nov 21, 2017 at 3:34 AM, Prof Brian Ripley <rip...@stats.ox.ac.uk>
wrote:

> On 21/11/2017 04:03, Vincent Carey wrote:
>
>> %vjcair> R CMD config CC
>>
>> /opt/local/bin/gcc-mp-5
>>
>>
>> I don't seem to be able to override this using environment variable CC.
>> And
>>
>
> When all else fails, read the manual (but, see the posting guide, before
> posting here)!  This is covered in, e.g.,
>
> https://cran.r-project.org/doc/manuals/r-release/R-admin.htm
> l#macOS-packages
>
> https://cran.r-project.org/doc/manuals/r-release/R-admin.htm
> l#Customizing-package-compilation
>
>
Yes, section 6.3.3. gives the solution.


>
>> I cannot see how to install gcc-mp-5.  This version of R was obtained from
>>
>> r.research.att.com, R-3.4-branch-el-capitan.pkg.
>>
>>
>> I would have expected clang to be the c compiler for this build.  I will
>>
>
> It was for the released version of 3.4.2.  Problems with off-CRAN builds
> are best addressed to the builder, here Simon Urbanek.  But that is a
> month-old snapshot build ... I don't understand why you did not simply
> update it, and I see 'clang' in the current snapshot.
>

Without alternate settings in the platform-specific Makevars, the most
recent binary gives the value of "R CMD config CC" noted in the original
posting.

Thank you for your assistance.


>
>
>
>> appreciate any suggestions.  As it stands, any installation from source
>> requiring
>>
>> compilation throws errors like
>>
>> /bin/sh: /opt/local/bin/g++-mp-5: No such file or directory
>>
>>
>> R version 3.4.2 Patched (2017-10-20 r73567) -- "Short Summer"
>>
>> Copyright (C) 2017 The R Foundation for Statistical Computing
>>
>> Platform: x86_64-apple-darwin15.6.0 (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.
>>
>>
>> sessionInfo()
>>>
>>
>> R version 3.4.2 Patched (2017-10-20 r73567)
>>
>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>>
>> Running under: macOS Sierra 10.12.6
>>
>>
>> Matrix products: default
>>
>> BLAS:
>> /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/
>> libRblas.0.dylib
>>
>> LAPACK: /Library/Frameworks/R.framework/Versions/3.4
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> R-SIG-Mac mailing list
>> R-SIG-Mac@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>>
>
> --
> Brian D. Ripley,  rip...@stats.ox.ac.uk
> Emeritus Professor of Applied Statistics, University of Oxford
>

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[R-SIG-Mac] trying to compile packages from source, but lacking /opt/local/bin/gcc-mp-5

[Vincent Carey]

%vjcair> R CMD config CC

/opt/local/bin/gcc-mp-5


I don't seem to be able to override this using environment variable CC.  And

I cannot see how to install gcc-mp-5.  This version of R was obtained from

r.research.att.com, R-3.4-branch-el-capitan.pkg.


I would have expected clang to be the c compiler for this build.  I will

appreciate any suggestions.  As it stands, any installation from source
requiring

compilation throws errors like

/bin/sh: /opt/local/bin/g++-mp-5: No such file or directory


R version 3.4.2 Patched (2017-10-20 r73567) -- "Short Summer"

Copyright (C) 2017 The R Foundation for Statistical Computing

Platform: x86_64-apple-darwin15.6.0 (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.


> sessionInfo()

R version 3.4.2 Patched (2017-10-20 r73567)

Platform: x86_64-apple-darwin15.6.0 (64-bit)

Running under: macOS Sierra 10.12.6


Matrix products: default

BLAS:
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib

LAPACK: /Library/Frameworks/R.framework/Versions/3.4

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Re: [R-SIG-Mac] 2.14.0 alpha hangs after fg after ctrl-Z

[Vincent Carey]

On Sat, Oct 15, 2011 at 6:00 AM,  r-sig-mac-requ...@r-project.org wrote:
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 Today's Topics:

   1.  2.14.0 alpha hangs after fg after ctrl-Z (Vincent Carey)


 --

 Message: 1
 Date: Fri, 14 Oct 2011 06:45:27 -0400
 From: Vincent Carey st...@channing.harvard.edu
 To: r-sig-mac@r-project.org
 Subject: [R-SIG-Mac] 2.14.0 alpha hangs after fg after ctrl-Z
 Message-ID:
        caant7+u04r1a0j8gbbjwovu9gqdnrnxnbk00qkiny6glec5...@mail.gmail.com
 Content-Type: text/plain; charset=ISO-8859-1

 i am running R version 2.14.0 alpha (2011-10-03 r57154) in an X11
 terminal.  i build from source.
 i often use ctrl-Z to pause the session and return to it via fg.  i
 find that R hangs upon fg -- it does not
 respond to ctrl-C and ctrl-\ takes some time to give a shell back.
 Problem is not present in my
 linux build of r57208.

Could this be a consequence of the intention of the build on MacOSX to
be run through
the GUI?  I did not see any configure switches that would lead to an
alternative build that would
allow job control through the shell.


 sessionInfo()
 R version 2.14.0 alpha (2011-10-03 r57154)
 Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit)

 locale:
 [1] 
 en_US.US-ASCII/en_US.US-ASCII/en_US.US-ASCII/C/en_US.US-ASCII/en_US.US-ASCII

 attached base packages:
 [1] stats     graphics  grDevices datasets  utils     tools     methods
 [8] base

 other attached packages:
 [1] BiocInstaller_1.1.28 weaver_1.19.2        codetools_0.2-8
 [4] digest_0.5.1



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[R-SIG-Mac] 2.14.0 alpha hangs after fg after ctrl-Z

[Vincent Carey]

i am running R version 2.14.0 alpha (2011-10-03 r57154) in an X11
terminal.  i build from source.
i often use ctrl-Z to pause the session and return to it via fg.  i
find that R hangs upon fg -- it does not
respond to ctrl-C and ctrl-\ takes some time to give a shell back.
Problem is not present in my
linux build of r57208.

 sessionInfo()
R version 2.14.0 alpha (2011-10-03 r57154)
Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit)

locale:
[1] en_US.US-ASCII/en_US.US-ASCII/en_US.US-ASCII/C/en_US.US-ASCII/en_US.US-ASCII

attached base packages:
[1] stats graphics  grDevices datasets  utils tools methods
[8] base

other attached packages:
[1] BiocInstaller_1.1.28 weaver_1.19.2codetools_0.2-8
[4] digest_0.5.1

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[R-SIG-Mac] last successful build of R-devel?

[Vincent Carey]

is there a location where the last successful build of R-devel binary for
macosx can be retrieved?  the build for jul 11 is noted as failed at
r.research.att.com

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