Re: [R-SIG-Mac] Experiences with macOS Sierra

[Kasper Daniel Hansen]

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 
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
>
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>

[[alternative HTML version deleted]]

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

Re: [R-SIG-Mac] Experiences with macOS Sierra

[Marc Schwartz]

> On Sep 22, 2016, at 1:39 AM, Prof Brian Ripley  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


Thanks Prof. Ripley.

Just to add another voice, I have not had any issues with R under Sierra.

I did a clean install of R 3.3.1, after completely deleting the prior 
installation. I then re-installed XQuartz and installed a fairly substantial 
number of CRAN packages, which includes RODBC installed from source.

I do not typically use the default R GUI, but use ESS. In the latter case, I am 
now using Emacs 25.1 and the only issue that I have had so far, is that 
vertically scrolling a large file using either the built-in TrackPad on my 
MacBook Pro or my external TrackPad, results in overly sensitive scrolling. I 
barely need to move my fingers on the TrackPad and the file buffer scrolls a 
very large amount rapidly. I tried this using Emacs 24.5 and the behavior is 
the same, so this is not unique to Emacs 25.1 and seems to be a change under 
Sierra. 

A Google search, so far, does not reveal any reports on this and I do not have 
this behavior in any other apps. I have made some temporary changes to my 
.emacs file relative to scrolling, which helps to slow scrolling, but it is not 
ideal yet. There are no settings pertaining to the TrackPad in System 
Preferences that appear to be relevant.

I will keep playing around with this and perhaps post to the Emacs support 
list, as it is not clear if there is a bug in Sierra causing this, or there is 
a need for a change in Emacs itself or .emacs settings relative to scrolling to 
modify this behavior. There are posts on the Emacs list where folks were using 
Sierra betas, but no mention of this behavior as far as I can see.

Regards,

Marc Schwartz

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

Re: [R-SIG-Mac] Experiences with macOS Sierra

[Bob Rudis]

The detailed update is very much appreciated Prof Ripley.

Many thanks!

-Bob

On Thu, Sep 22, 2016 at 2:39 AM, Prof Brian Ripley 
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
>
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>

[[alternative HTML version deleted]]

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

Re: [R-SIG-Mac] MacOS Sierra

[Bob Rudis]

Hey Roy,

Aye. If you look at recent R-SIG-Mac messages, I gave a report on this
yesterday.

No issues with 3.2, 3.3.1 or R-devel on 10.12 (so far).

-Bob

On Tue, Sep 20, 2016 at 2:59 PM, rmendelss gmail 
wrote:

> Hi All:
>
> Just wanted to double-check, before I even think about an upgrade, if the
> present version of R works with the new release of MacOS Sierra.
>
> Thanks for any information.
>
> -Roy
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>

[[alternative HTML version deleted]]

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

[R-SIG-Mac] MacOS Sierra

[rmendelss gmail]

Hi All:

Just wanted to double-check, before I even think about an upgrade, if the 
present version of R works with the new release of MacOS Sierra.

Thanks for any information.

-Roy
___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

[R-SIG-Mac] Experiences with macOS Sierra

[Prof Brian Ripley]

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

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac