[R-SIG-Mac] Experiences with macOS Sierra

Bob Rudis bob at rud.is
Fri Sep 23 16:59:34 CEST 2016

I've finally had some time to look at the local build status for some
compiled packages I have locally and also some that are on CRAN after the
Sierra upgrade (and also the 10.12.1 patch which I'm also testing).

This isn't a warning for my own code but from usage of a now deprecated
function in R.framework:

In file included from
warning: 'OSMemoryBarrier' is deprecated: first deprecated in macOS 10.12 -
Use std::atomic_thread_fence() from <atomic> instead
note: 'OSMemoryBarrier' has been explicitly marked deprecated here
void    OSMemoryBarrier( void );

Passing this on just in case this hasn't come up with CRAN macOS checks for
the R Core team.


On Fri, Sep 23, 2016 at 7:18 AM, Prof Brian Ripley <ripley at stats.ox.ac.uk>

> 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
> to
> prefix=/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
>>     _______________________________________________
>>     R-SIG-Mac mailing list
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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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