[R-SIG-Mac] Experiences with macOS Sierra

Prof Brian Ripley ripley at stats.ox.ac.uk
Fri Sep 23 13:18:29 CEST 2016

On 22/09/2016 14:01, Kasper Daniel Hansen wrote:
> 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.

I had found a workaround for Xcode 8 on El Capitan: copy 
/usr/bin/xml2-config to somewhere earlier on your path (~/bin in my 
case) and edit line 3 from

prefix=$(xcrun -show-sdk-path)/usr



> Best,
> Kasper
> On Thu, Sep 22, 2016 at 2:39 AM, Prof Brian Ripley
> <ripley at stats.ox.ac.uk <mailto:ripley at 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,                  ripley at stats.ox.ac.uk
>     <mailto:ripley at stats.ox.ac.uk>
>     Emeritus Professor of Applied Statistics, University of Oxford
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Brian D. Ripley,                  ripley at stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford

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