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

[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 <stvjc at channing.harvard.edu> wrote:
> 
> On Tue, Nov 21, 2017 at 3:34 AM, Prof Brian Ripley <ripley at 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]]
>>> 
>>> _______________________________________________
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>>> 
>>> 
>> 
>> --
>> Brian D. Ripley,                  ripley at stats.ox.ac.uk
>> Emeritus Professor of Applied Statistics, University of Oxford
>> 
> 
> 	[[alternative HTML version deleted]]
> 
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