[Rcpp-devel] Attribute does not compile with 'compileAttributes' but with 'sourceCpp'
Dominick Samperi
djsamperi at gmail.com
Fri Nov 1 21:24:32 CET 2013
I assumed incorrectly that getting the pure Octave test working would imply
that
RcppOctave will work. I just checked, and I'm seeing the same memory fault
that you see. As I mentioned in the rcppoctave-users thread even the pure
Octave
test will fail (for the same reason) if it is not terminated properly, and
it appears that
the way the embedded session is terminated in RcppOctave may not be correct
in the Mac OS X environment. Further comments on this will move to
rcppoctave-users
list...
On Fri, Nov 1, 2013 at 3:44 PM, Simon Zehnder <szehnder at uni-bonn.de> 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 <djsamperi at gmail.com> 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 <szehnder at uni-bonn.de>
> 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 <djsamperi at gmail.com> 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 <szehnder at uni-bonn.de>
> 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 <djsamperi at gmail.com>
> 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 <szehnder at uni-bonn.de>
> 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 <djsamperi at gmail.com>
> 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 <
> szehnder at uni-bonn.de> 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 <jj.allaire at gmail.com> 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 <
> szehnder at uni-bonn.de> 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
> > > > > > Rcpp-devel at lists.r-forge.r-project.org
> > > > > >
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
> > > > > >
> > > > >
> > > > > _______________________________________________
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> > > > > Rcpp-devel at lists.r-forge.r-project.org
> > > > >
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
> > > > >
> > > >
> > > >
> > >
> > >
> >
> >
>
>
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