[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.urbanek at 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 <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]]
> >>>
> >>> _______________________________________________
> >>> R-SIG-Mac mailing list
> >>> R-SIG-Mac at r-project.org
> >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >>>
> >>>
> >>
> >> --
> >> 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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> > R-SIG-Mac at r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
>
>

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