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 the Xcode Command Line Tools for Mavericks. > > > > > > > > I now reinstalled Rcpp with the gcc-4.8.2 and threw away all object > and shared-object files in my /src/ folder of my package. The problem > remains. Is there something special I can look for in my Makeconf file? > What is so different about ‘compileAttributes’ in contrast to ‘sourceCpp’ > or a usual package compilation via R CMD INSTALL? Does compileAttributes > uses some additional flags and/or libraries? > > > > > > > > Best > > > > Simon > > > > > > > > > > > > > > > > On 01 Nov 2013, at 15:56, JJ Allaire <[email protected]> wrote: > > > > > > > > > Are you by any chance on OS X Mavericks? I had one other user > report this specific error on Mavericks and it seemed to be related to the > use of different compilers (and thus different heaps) within the same > compilation (there is exposure to this with the changes made by Apple to > the toolchain in Mavericks). > > > > > > > > > > J.J. > > > > > > > > > > > > > > > On Fri, Nov 1, 2013 at 10:01 AM, Simon Zehnder < > [email protected]> wrote: > > > > > Dear Rcpp::Users and Rcpp::Devels, > > > > > > > > > > I get a weird exception when I try to compile an attribute in one > of my packages: > > > > > > > > > > compileAttributes("/Users/simonzehnder/git/mmstruct/mmstruct/") > > > > > R(6256,0x7fff79ad9310) malloc: *** error for object > 0x7fff7ac48330: pointer being freed was not allocated > > > > > *** set a breakpoint in malloc_error_break to debug > > > > > Abort trap: 6 > > > > > > > > > > If I instead use the sourceCpp function all works fine: > > > > > > > > > > > sourceCpp("/Users/simonzehnder/git/mmstruct/mmstruct/src/testing.cpp”) > > > > > testfunction_cc(c(0,0,0), list(trades = rnorm(10), T = 360)) > > > > > [1] 0.000000e+00 3.509927e-05 1.169976e-05 > > > > > > > > > > The function in my file is actually pretty simple (and its the > only one): > > > > > > > > > > #include<Rcpp.h> > > > > > > > > > > // [[Rcpp::export]] > > > > > > > > > > Rcpp::NumericVector testfunction_cc(Rcpp::NumericVector par, > > > > > Rcpp::List list) > > > > > { > > > > > const unsigned int K = par.size(); > > > > > Rcpp::NumericVector trades = list["trades"]; > > > > > const unsigned int T = list["T"]; > > > > > double tmp = mean(trades)/T; > > > > > std::vector<double> startp(K); > > > > > startp[0] = 0.0; > > > > > startp[1] = tmp * 0.75/2; > > > > > startp[2] = tmp * 0.25/2; > > > > > > > > > > return Rcpp::wrap(startp); > > > > > } > > > > > > > > > > At this moment I am a little perplexed. Where should I search for > a possible error? What are things to try out? > > > > > > > > > > Best > > > > > > > > > > Simon > > > > > > > > > > _______________________________________________ > > > > > Rcpp-devel mailing list > > > > > [email protected] > > > > > > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel > > > > > > > > > > > > > _______________________________________________ > > > > Rcpp-devel mailing list > > > > [email protected] > > > > > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel > > > > > > > > > > > > > > > >
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