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.
> >>>
> >>>
> >>> --
> >>> 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, UK Fax: +44 1865 272595
> >>>
> >>> _______________________________________________
> >>> R-SIG-Mac mailing list
> >>> R-SIG-Mac@r-project.org
> >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >>
> >
> >
> > --
> > 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, UK Fax: +44 1865 272595
>
> --
> 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
>
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
--
Jonathan A. Greenberg, PhD
Assistant Professor
Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
Department of Geography and Geographic Information Science
University of Illinois at Urbana-Champaign
259 Computing Applications Building, MC-150
605 East Springfield Avenue
Champaign, IL 61820-6371
Phone: 217-300-1924
http://www.geog.illinois.edu/~jgrn/
AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007
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