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 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
