gettext guess is nonsense… On 01 Nov 2013, at 20:02, 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 >>>> >>> >>> >> >> > _______________________________________________ Rcpp-devel mailing list [email protected] https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
