[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
> 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
> R-SIG-Mac mailing list
> R-SIG-Mac at r-project.org <mailto:R-SIG-Mac at r-project.org>
Brian D. Ripley, ripley at stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
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