[R-SIG-Mac] Experiences with macOS Sierra
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
>> 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
> R-SIG-Mac mailing list
> R-SIG-Mac at r-project.org
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