Did you install Rcpp from source? That's what I had to do to solve a similar problem.
Hadley On Friday, November 1, 2013, Simon Zehnder wrote: > Same thing actually on my side: I had a hardware crash lately with 10.8 > and made fresh install after formatting my harddrive NSA-style :) > > Afterwards I compiled R 3.0.1 and from macports the gcc48 port as well as > gettext. Then, Mavericks came and I updated - nothing worked anymore: I > reinstalled gcc48 port and deleted R 3.0.1. Then I installed gcc4.8.2 from > http://hpc.sourceforge.net, Xcode Command line tools for Mavericks and > XQuartz 4.7.2. I work with environment modules, where I can load a certain > compiler with its needed environment variables. With gcc 4.8.2 I installed > R-3.0.2 and then the packages. Always have to type “module load > compilers/gcc-4.8.2 before starting R, but that doesn’t bother me … I still > can use openMP to its great extent :) > > My problem is linked to the install_name_tool and the way on Mac OS paths > are set and replaced in dynamic libraries … this could of course be caused > by “older tools” like the llvm-gcc4.2 “laying” around…. though locate does > not find them…. > > > > On 01 Nov 2013, at 20:33, Dominick Samperi <[email protected]> wrote: > > > My original attempt to update to Mavericks failed (unrelated hardware > issue), and this > > may have actually worked in my favor. It forced me to install Mac OS X > 10.8 from > > scratch, a "clean" install, that I later upgraded to Mavericks. If you > upgraded from > > an existing configuration you may have old tools (like llvm-g++-4.2) > laying around > > that could cause problems. > > > > > > On Fri, Nov 1, 2013 at 3:02 PM, Simon Zehnder <[email protected]> > wrote: > > I read through all the thread answers and my variables in the Makeconf > are the same alsso I installed the Xcode Command Line Tools for Mavericks. > Are there any other apps and libs that have been to be updated? (I do not > use brew). What remains is the following: > > > > Compiling Rcpp give the pointer exception (when calling > compileAttributes), also encountered in the thread you referred to. > > > > Compiling Rcpp and adding the flag “-headerpad_max_install_names” lets > the compileAttributes function do its work without any exception. My next > guess is: possibly the gettext library… > > > > Best > > > > Simon > > > > On 01 Nov 2013, at 19:20, Dominick Samperi <[email protected]> wrote: > > > > > In your original post you mention the "pointer being freed was not > allocated" error message. I have just tracked this down in another context > (Octave > > > under Mac OS X). In my case the error occurs on the dlopen() call for > > > an R package shared library. The fix was to make sure all apps and libs > > > are updated after moving to Mavericks. See the thread in > rcppoctave-users > > > list for a blow-by-blow description. > > > > > > > > > On Fri, Nov 1, 2013 at 1:11 PM, Simon Zehnder <[email protected]> > wrote: > > > You are right, working with apple and C++ is often a mess. Up to now, > llvm does not yet support openmp. It is coming but I do not see it fully > implemented before next summer. If I want to use openmp I have thus to rely > on the gcc which brings a lot of problems with it and from what I read on > the R-lists most of the Mac Users suffer. I guess that this time a > reinstall of R was unavoidable for most of us. I thought about using the > xcrun —find gcc/g++ etc. to get what is needed in a Makevars but this does > not give anything so far. > > > > > > > > > On 01 Nov 2013, at 17:50, Dominick Samperi <[email protected]> > wrote: > > > > > > > With Apple moving from gcc/g++ to LLVM/clang++ I guess it makes sense > > > > for R/Rcpp to use the LLVM/clang++ tool chain eventuallly, but I > don't know > > > > if there are plans to do this. Otherwise, the R community would need > to > > > > support "MACtools" following the model provided by "Rtools" under > Windows... > > > > > > > > > > > > On Fri, Nov 1, 2013 at 12:12 PM, Simon Zehnder <[email protected]> > wrote: > > > > Hi Dominick, > > > > > > > > I did install files from brew but instead used the gcc from > http://hpc.sourceforge.net > > > > > > > > > > > > On 01 Nov 2013, at 16:55, Dominick Samperi <[email protected]> > wrote: > > > > > > > > > If you depend on tools installed using brew, you might want to try > > > > > removing those that were installed before the Mavericks update, > > > > > using: > > > > > rm -rf /usr/local/Cellar > > > > > brew prune > > > > > brew doctor > > > > > brew install <what-you-need> > > > > > > > > > > > > > > > On Fri, Nov 1, 2013 at 11:19 AM, Simon Zehnder < > [email protected]> wrote: > > > > > Point landing J.J.! > > > > > > > > > > I already compiled a new R when Mavericks came out with a newly > installed a gcc-4.8.2, that I can load via environment modules. I also > installed th -- Chief Scientist, RStudio http://had.co.nz/
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