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

2017-11-21 Thread 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 
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 
> 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

2017-11-21 Thread Simon Urbanek 
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  wrote:
> 
> On Tue, Nov 21, 2017 at 3:34 AM, Prof Brian Ripley 
> 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

2017-11-21 Thread Vincent Carey 
On Tue, Nov 21, 2017 at 3:34 AM, Prof Brian Ripley 
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] huge cursor lag, 2017 Macbook Air, latest version of R, not R Studio

2017-11-21 Thread kevin bleakley 
Hi,

I'm running High Sierra on a new "2017" Macbook Air.  I upgraded R from a
previous version (3.2 or 3.3 ?) and now there is a huge lag on the curser
in the R command window itself and in script files. I am not using RStudio.

There is a page on GitHub detailing the same problem currently when using
Rstudio. I have no idea whether this problem is related or not.

Any ideas/comments?

Cheers

Kevin

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

2017-11-21 Thread Prof Brian Ripley 

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.html#macOS-packages

https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Customizing-package-compilation



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.





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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--
Brian D. Ripley,  rip...@stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford

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