J.J., I went now on the cluster Linux Scientific and used there compileAttributes (also with gcc-4.8.2). There were no problems.
On my Mac I figured out, where exactly in the compileAttributes function in attributes.cpp the error happens: On line 2794 with generators.writeBegin() And further in the for loop at 1926 in iteration 3, which I believe calls writeFunctions of the CppExportsIncludeGenerator. I then started at the constructor for this class at line 1578 and used an Rprintf(“”) to give me the includeDir_ path string. When I then tried to compile Rcpp from the shell I got a weird error during linking: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool: changing install names or rpaths can't be redone for: libRcpp.dylib (for architecture x86_64) because larger updated load commands do not fit (the program must be relinked, and you may need to use -headerpad or -headerpad_max_install_names) I recompiled Rcpp, including in the MAKEFLAGS=“CXXFLAGS=-headerpad_max_install_names” (described here: http://www.manpages.info/macosx/ld.1.html) and it worked fine. Running afterwards compileAttributes in R did not throw any error. I got the includeDir_: mypackage/inst/include/. RcppExports.cpp contains now the function I coded. I do not know yet, why adding space to the header padding make things work now. Best Simon On 01 Nov 2013, at 17:01, JJ Allaire <[email protected]> wrote: > Simon, > > The other use was also using gcc-4.8.1 so it's got something to do with that > (I don't have a local install of gcc-4.8.1 so can't repo offhand). If you are > running compileAttributes inside RStudio it will run in a separate process. > If not then I don't know of any significant difference between calling > sourceCpp and compileAttributes. > > J.J. > > > 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
