Thanks for the work on this, especially the comment on xml2.  I had noticed
problems with xml2 while compiling Emacs 25.1 using the new Xcode on El
Capitan, but I have not had time to track it down.

Best,
Kasper

On Thu, Sep 22, 2016 at 2:39 AM, Prof Brian Ripley <rip...@stats.ox.ac.uk>
wrote:

> So far I have encountered few problems.  R.app runs but I do not normally
> use it so my tests were minimal.
>
> My observations are about installing packages from source.
>
> - It seems Apple has been tidying up, and I had ca 20GB more free space
> after upgrading (which is worthwhile on my MBA with a 128GB SSD).  It seems
> that includes removing some headers, including those for openssl (used by
> packages PKI and RSclient - package opensssl uses its own). This is but the
> latest instance in a long-term trend, e.g. iodbc, pcre and liblzma have
> libraries but no headers.
>
> - Finally the POSIX 2008 function clock_gettime is supported (and will be
> used by R): but package scrypt calls it incorrectly.
>
> Xcode 8 is available for EL Capitan but I would caution against using it
> there (despite it being pushed as an update from the AppStore).  AFAICS
> (and googling will find other reports) it defaults to the macOS 10.12 SDK
> and that declares functions such as clock_gettime not available in El
> Capitan.  (I believe that R checks thoroughly enough not to be caught by
> this.)
>
> There is a further problem with Xcode 8, also seen on Sierra.  Packages
> using xml2-config (such as XML) fail to install.  Apple modified
> xml2-config to look on the SDK path, which means packages using it attempt
> to link to .tbd files rather than .dylibs.  Which should be OK but the
> supplied .tbd attempt to link to libraries removed in Sierra and so linking
> fails. (This is not a problem with the version 8 of the Command Line Tools,
> only available for Sierra.)
>
> --
> Brian D. Ripley,                  rip...@stats.ox.ac.uk
> Emeritus Professor of Applied Statistics, University of Oxford
>
> _______________________________________________
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