subject:"\[R\-SIG\-Mac\] Updating to Mavericks"

Re: [R-SIG-Mac] Updating to Mavericks

2013-11-01 Thread peter dalgaard

On 31 Oct 2013, at 23:19 , Prof Brian Ripley rip...@stats.ox.ac.uk wrote:

On 31/10/2013 14:57, peter dalgaard wrote:
Thanks Brian.

One more item: If building from SVN, you may need to run svn upgrade in
the source directory (at top level).

I suppose that's a consequence of upgrading Xcode rather than Mavericks per
se, but might as well mention it here.

Yes. A quick poll of systems I have access to has svn 1.6.x on 10.7, 1.7.x
on 10.8 and 10.9. As AFAICS it is part of Xcode, it depends on the version
you had installed and I believe those machines were all fully updated.

At any rate, svn up tells you what to do, the only slight confusion is that
make claims that your source directory is not an svn checkout until you have
upgraded it.

One further issue is that gnutar seems to have gone AWOL. We have, in the CRAN
binary,

/Library/Frameworks/R.framework/Resources/etc/Renviron:TAR=${TAR-'/usr/bin/gnutar'}

so this affects R CMD INSTALL --build. I suppose people might discover this
when a teaching package has gotten archived at CRAN. (A colleague bumped into
it with languageR.) Looks like the obvious workaround does work around it:

TAR=/usr/bin/tar R CMD etc.

Do we have any authoritative advice as to what should go into config.site?
Mine seems to work unchanged, but I'm not sure I have a clue about what they
are doing anymore.

I have

% cat config.site
CC=clang -mtune=native
OBJC=$CC
F77=gfortran-4.2 -arch x86_64 -mtune=native
FC=$F77
CXX=clang++ -mtune=native
CFLAGS=-g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion

Those are rather picky C flags, of course: intended to pick up issues with
long vectors.

gcc/g++ are not the same as clang/clang++, although the only differences I
have detected are what they report themselves as. As I don't know if there
are any material differences I chose to use clang explicitly. Similarly
calling gfortran-4.2 explicitly to avoid any other versions (and I would even
consider using /usr/local/bin/gfortran-4.2).

-pd

On 30 Oct 2013, at 15:38 , Prof Brian Ripley rip...@stats.ox.ac.uk wrote:

This is an attempt to collect together various pieces of advice.

If you update to Mavericks and want to compile packages (or run some) with
the CRAN binary R, you will need to

- Update R to 3.0.2 or later if you use R.app.

- Re-install XQuartz. The Mavericks update re-populates /usr/X11 with
links which tell you to install XQuartz (even if it is currently installed).

- Re-install the Apple Java 6 runtime if you use rJava. Try any of the
rJava examples and you will be prompted for an install.

- Install Xcode 5.0.1 if you had not previously done so.

- Re-install the Xcode command-line tools. Xcode for Mavericks has moved
most things inside Xcode (specifically under
/Applications/Xcode.app/Contents/Developer) and the command-line tools
previously installed seemed almost to work, but not entirely.

xcode-select --install

seems to be the recommended way to do so under Mavericks.

If you previously had them installed, the Xcode 4.6.3 compilers (such as
llvm-g++-4.2) should still work. Otherwise you could select clang as your
compiler: see
http://cran.r-project.org/doc/manuals/r-release/R-admin.html#OS-X-packages
. There are also compilers called 'gcc' and 'g++' in Xcode 5.0.1: these are
clang-based but are not quite the same as clang/clang++. Although g++
reports

% g++ --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr
--with-gxx-include-dir=/usr/include/c++/4.2.1

it looks at the libcxx headers at
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/
. And the packages which do not compile under clang++ do not compile
under g++ .

Packages using a C++ interface may need re-compiling if you use clang++ (or
g++) as your C++ compiler. The external software at
http://r.research.att.com/libs/ which I know does is gdal and zeromq. It
would be prudent to compile Rcpp with the same compiler as a Rcpp-using
package, although not always necessary.

--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595

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Center for

Re: [R-SIG-Mac] Updating to Mavericks

2013-11-01 Thread Jonathan Greenberg

This is a small somewhat related note we ran into last week: RStudio had
some issues with Mavericks as well (for this of you using this IDE). There
was a post about it:
http://support.rstudio.org/help/kb/advanced/using-rstudio-with-mac-os-x-109-mavericksand,
at the time of this posting, requires you update to their preview
version.

--j

On Fri, Nov 1, 2013 at 5:17 AM, peter dalgaard pda...@gmail.com wrote:

On 31 Oct 2013, at 23:19 , Prof Brian Ripley rip...@stats.ox.ac.uk
wrote:

On 31/10/2013 14:57, peter dalgaard wrote:
Thanks Brian.

One more item: If building from SVN, you may need to run svn upgrade
in the source directory (at top level).

I suppose that's a consequence of upgrading Xcode rather than Mavericks
per se, but might as well mention it here.

Yes. A quick poll of systems I have access to has svn 1.6.x on 10.7,
1.7.x on 10.8 and 10.9. As AFAICS it is part of Xcode, it depends on the
version you had installed and I believe those machines were all fully
updated.

At any rate, svn up tells you what to do, the only slight confusion is
that make claims that your source directory is not an svn checkout until
you have upgraded it.

One further issue is that gnutar seems to have gone AWOL. We have, in the
CRAN binary,

/Library/Frameworks/R.framework/Resources/etc/Renviron:TAR=${TAR-'/usr/bin/gnutar'}

so this affects R CMD INSTALL --build. I suppose people might discover
this when a teaching package has gotten archived at CRAN. (A colleague
bumped into it with languageR.) Looks like the obvious workaround does work
around it:

TAR=/usr/bin/tar R CMD etc.

Do we have any authoritative advice as to what should go into
config.site? Mine seems to work unchanged, but I'm not sure I have a clue
about what they are doing anymore.

I have

% cat config.site
CC=clang -mtune=native
OBJC=$CC
F77=gfortran-4.2 -arch x86_64 -mtune=native
FC=$F77
CXX=clang++ -mtune=native
CFLAGS=-g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion

Those are rather picky C flags, of course: intended to pick up issues
with long vectors.

gcc/g++ are not the same as clang/clang++, although the only differences
I have detected are what they report themselves as. As I don't know if
there are any material differences I chose to use clang explicitly.
Similarly calling gfortran-4.2 explicitly to avoid any other versions (and
I would even consider using /usr/local/bin/gfortran-4.2).

-pd

On 30 Oct 2013, at 15:38 , Prof Brian Ripley rip...@stats.ox.ac.uk
wrote:

This is an attempt to collect together various pieces of advice.

If you update to Mavericks and want to compile packages (or run some)
with the CRAN binary R, you will need to

- Update R to 3.0.2 or later if you use R.app.

- Re-install XQuartz. The Mavericks update re-populates /usr/X11 with
links which tell you to install XQuartz (even if it is currently installed).

- Re-install the Apple Java 6 runtime if you use rJava. Try any of
the rJava examples and you will be prompted for an install.

- Install Xcode 5.0.1 if you had not previously done so.

- Re-install the Xcode command-line tools. Xcode for Mavericks has
moved most things inside Xcode (specifically under
/Applications/Xcode.app/Contents/Developer) and the command-line tools
previously installed seemed almost to work, but not entirely.

xcode-select --install

seems to be the recommended way to do so under Mavericks.

If you previously had them installed, the Xcode 4.6.3 compilers (such
as llvm-g++-4.2) should still work. Otherwise you could select clang as
your compiler: see
http://cran.r-project.org/doc/manuals/r-release/R-admin.html#OS-X-packages.
There are also compilers called 'gcc' and 'g++' in Xcode 5.0.1: these are
clang-based but are not quite the same as clang/clang++. Although g++
reports

% g++ --version
Configured with:
--prefix=/Applications/Xcode.app/Contents/Developer/usr
--with-gxx-include-dir=/usr/include/c++/4.2.1

it looks at the libcxx headers at

/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/
. And the packages which do not compile under clang++ do not compile under
g++ .

Packages using a C++ interface may need re-compiling if you use
clang++ (or g++) as your C++ compiler. The external software at
http://r.research.att.com/libs/ which I know does is gdal and zeromq. It
would be prudent to compile Rcpp with the same compiler as a Rcpp-using
package, although not always necessary.

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Re: [R-SIG-Mac] Updating to Mavericks

2013-10-31 Thread peter dalgaard

Thanks Brian.

One more item: If building from SVN, you may need to run svn upgrade in the
source directory (at top level).

I suppose that's a consequence of upgrading Xcode rather than Mavericks per se,
but might as well mention it here.

Do we have any authoritative advice as to what should go into config.site? Mine
seems to work unchanged, but I'm not sure I have a clue about what they are
doing anymore.

-pd

On 30 Oct 2013, at 15:38 , Prof Brian Ripley rip...@stats.ox.ac.uk wrote:

This is an attempt to collect together various pieces of advice.

If you update to Mavericks and want to compile packages (or run some) with
the CRAN binary R, you will need to

- Update R to 3.0.2 or later if you use R.app.

- Re-install XQuartz. The Mavericks update re-populates /usr/X11 with links
which tell you to install XQuartz (even if it is currently installed).

- Re-install the Apple Java 6 runtime if you use rJava. Try any of the rJava
examples and you will be prompted for an install.

- Install Xcode 5.0.1 if you had not previously done so.

xcode-select --install

seems to be the recommended way to do so under Mavericks.

If you previously had them installed, the Xcode 4.6.3 compilers (such as
llvm-g++-4.2) should still work. Otherwise you could select clang as your
compiler: see
http://cran.r-project.org/doc/manuals/r-release/R-admin.html#OS-X-packages .
There are also compilers called 'gcc' and 'g++' in Xcode 5.0.1: these are
clang-based but are not quite the same as clang/clang++. Although g++ reports

% g++ --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr
--with-gxx-include-dir=/usr/include/c++/4.2.1

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--
Peter Dalgaard, Professor
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd@cbs.dk Priv: pda...@gmail.com

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Re: [R-SIG-Mac] Updating to Mavericks

2013-10-31 Thread Prof Brian Ripley

On 31/10/2013 14:57, peter dalgaard wrote:

Thanks Brian.

One more item: If building from SVN, you may need to run svn upgrade in the
source directory (at top level).

I suppose that's a consequence of upgrading Xcode rather than Mavericks per se,
but might as well mention it here.

Yes. A quick poll of systems I have access to has svn 1.6.x on 10.7,
1.7.x on 10.8 and 10.9. As AFAICS it is part of Xcode, it depends on
the version you had installed and I believe those machines were all
fully updated.

Do we have any authoritative advice as to what should go into config.site? Mine
seems to work unchanged, but I'm not sure I have a clue about what they are
doing anymore.

I have

% cat config.site
CC=clang -mtune=native
OBJC=$CC
F77=gfortran-4.2 -arch x86_64 -mtune=native
FC=$F77
CXX=clang++ -mtune=native
CFLAGS=-g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion

Those are rather picky C flags, of course: intended to pick up issues
with long vectors.

gcc/g++ are not the same as clang/clang++, although the only differences
I have detected are what they report themselves as. As I don't know if
there are any material differences I chose to use clang explicitly.
Similarly calling gfortran-4.2 explicitly to avoid any other versions
(and I would even consider using /usr/local/bin/gfortran-4.2).

-pd

On 30 Oct 2013, at 15:38 , Prof Brian Ripley rip...@stats.ox.ac.uk wrote:

This is an attempt to collect together various pieces of advice.

If you update to Mavericks and want to compile packages (or run some) with the
CRAN binary R, you will need to

- Update R to 3.0.2 or later if you use R.app.

- Re-install XQuartz. The Mavericks update re-populates /usr/X11 with links
which tell you to install XQuartz (even if it is currently installed).

- Re-install the Apple Java 6 runtime if you use rJava. Try any of the rJava
examples and you will be prompted for an install.

- Install Xcode 5.0.1 if you had not previously done so.

- Re-install the Xcode command-line tools. Xcode for Mavericks has moved most
things inside Xcode (specifically under
/Applications/Xcode.app/Contents/Developer) and the command-line tools
previously installed seemed almost to work, but not entirely.

xcode-select --install

seems to be the recommended way to do so under Mavericks.

If you previously had them installed, the Xcode 4.6.3 compilers (such as
llvm-g++-4.2) should still work. Otherwise you could select clang as your
compiler: see
http://cran.r-project.org/doc/manuals/r-release/R-admin.html#OS-X-packages .
There are also compilers called 'gcc' and 'g++' in Xcode 5.0.1: these are
clang-based but are not quite the same as clang/clang++. Although g++ reports

% g++ --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr
--with-gxx-include-dir=/usr/include/c++/4.2.1

Packages using a C++ interface may need re-compiling if you use clang++ (or
g++) as your C++ compiler. The external software at
http://r.research.att.com/libs/ which I know does is gdal and zeromq. It would
be prudent to compile Rcpp with the same compiler as a Rcpp-using package,
although not always necessary.

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[R-SIG-Mac] Updating to Mavericks

2013-10-30 Thread Prof Brian Ripley

This is an attempt to collect together various pieces of advice.

If you update to Mavericks and want to compile packages (or run some)
with the CRAN binary R, you will need to

- Update R to 3.0.2 or later if you use R.app.

- Re-install XQuartz. The Mavericks update re-populates /usr/X11 with
links which tell you to install XQuartz (even if it is currently installed).

- Re-install the Apple Java 6 runtime if you use rJava. Try any of the
rJava examples and you will be prompted for an install.

- Install Xcode 5.0.1 if you had not previously done so.

- Re-install the Xcode command-line tools. Xcode for Mavericks has
moved most things inside Xcode (specifically under
/Applications/Xcode.app/Contents/Developer) and the command-line tools
previously installed seemed almost to work, but not entirely.

xcode-select --install

seems to be the recommended way to do so under Mavericks.

If you previously had them installed, the Xcode 4.6.3 compilers (such as
llvm-g++-4.2) should still work. Otherwise you could select clang as
your compiler: see
http://cran.r-project.org/doc/manuals/r-release/R-admin.html#OS-X-packages
. There are also compilers called 'gcc' and 'g++' in Xcode 5.0.1: these
are clang-based but are not quite the same as clang/clang++. Although
g++ reports

% g++ --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr
--with-gxx-include-dir=/usr/include/c++/4.2.1

Packages using a C++ interface may need re-compiling if you use clang++
(or g++) as your C++ compiler. The external software at
http://r.research.att.com/libs/ which I know does is gdal and zeromq. It
would be prudent to compile Rcpp with the same compiler as a Rcpp-using
package, although not always necessary.

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Re: [R-SIG-Mac] Updating to Mavericks

2013-10-24 Thread Simon Urbanek

On Oct 24, 2013, at 6:16 PM, Kevin Ushey wrote:

 With XCode 5.0, clang is now the default compiler toolchain supplied,
 and llvm-gcc-4.2 is no longer available.
 
 FWIW, I and many others have had a lot of success compiling packages
 with the version of clang supplied with XCode. The only requirement
 (at this point) is that you set your own ~/.R/Makevars settings, as
 discussed in the SO posts -- in particular, you need
 
CC=clang
CXX=clang++
 
 You may need to reinstall packages from source that your packages link
 to (e.g., Rcpp) and compile them with the new set of compilers for
 them to play nicely together, but in general this should work.
 However, hopefully others can give advice on the 'recommended'
 compiler toolchain now for R and Mavericks.
 

The recommended toolchain as far as CRAN binaries are concerned remains the 
same since the binaries did not change. I cannot currently check on my 10.9 
machine so I'll have to confirm it later, but there are several options - you 
can install Apple's original llvm-gcc package or use our gcc build (which 
includes gfortran). Depending on the route you take, you can also simply 
symlink the compiler to lvm-g*-4.2 instead of modifying Makevars.

If you want to start from scratch (i.e. compile R and packages from sources), 
then you can use clang, it's known to work (modulo a few packages that are not 
up to date).

Cheers,
Simon


 -Kevin
 
 On Thu, Oct 24, 2013 at 3:00 PM, David Winsemius dwinsem...@comcast.net 
 wrote:
 From comments made on the thread regarding the segfault in the R.app GUI 
 following the error from TRUE - FALSE, I'm inferring that at least three 
 people ( Prof. Ripley, S. Urbanek, and T. Bates) have installed R 3.0.2 on 
 Mavericks.  I have R version 3.0.2 (2013-09-25) -- Frisbee Sailing with 
 R.app GUI 1.60 (6475) and XCode Version 3.2.6 in OSX 10.7.5 and have 
 installed the Command Line Tools, so at the moment I'm  generally succeeding 
 when compiling from source. (I see I am rather behind the current GUI 
 version although that was not my intention when I updated to 3.0.2.)  Are 
 there any specific steps one needs to take (or avoid taking) in order to 
 preserve access to (or gain updated access to) tools for compiling packages 
 from source?
 
 (I've seen people posting problems on SO where the error after updating to 
 Mavericks was a missing copy of llvm-gcc-4.2.)
 
 --
 David Winsemius
 Alameda, CA, USA
 
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Re: [R-SIG-Mac] Updating to Mavericks

Re: [R-SIG-Mac] Updating to Mavericks

Re: [R-SIG-Mac] Updating to Mavericks

Re: [R-SIG-Mac] Updating to Mavericks

[R-SIG-Mac] Updating to Mavericks

Re: [R-SIG-Mac] Updating to Mavericks

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