First, I didn’t. But for getting some output from the functions in attributes.cpp I later compiled the Rcpp package from source. When I compile with the option “-headerpad_max_install_names” the compileAttributes runs without an error. If I compile without this flag, I get the pointer error. Problems with header padding is a well-known issue on the Mac (https://svn.boost.org/trac/boost/ticket/1927), usually in frameworks. It is used a relative path in the sections of shared objects (sometimes also in dynamic libs). When the library/shared object has to be included in other libraries, the relative path has to be changed to an absolute path. If then there is not enough space in the header of the Mach-O file, it gives you an exception.
But my guess is for the compileAttributes function, that no library binding is done, though it takes library paths as arguments when calling ‘.Call’. My perception has been so far, that this function solely creates the RcppExports.cpp and *.R files without any compilation or linking (this is done later, when we compile the package with the attributes). The depends/linkingto names from the DESCRIPTION file are used for headers in the RcppExports.cpp file I have guessed. The point, that I am seemingly the only one, that encounters this error, points me to my compiler (gcc4.8.2). Could be, that under the hood clang uses already a larger header padding. Btw: When you are on Mac, could you check what “otool -L Rcpp.so” give you? Is the path relative (Rcpp.so) or absolute (has it something like @exectuable_path in front)? Best Simon On 02 Nov 2013, at 01:02, Hadley Wickham <[email protected]> wrote: > 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/ _______________________________________________ Rcpp-devel mailing list [email protected] https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
