Hi Ben, I wonder if the RProgress could be triggering something. It does some thread manipulation if I recall. If the code does not evoke any warnings from valgrind, that is the place I would look next. You could also ask your reporters to run R in a debugger while triggering the fault.
THK http://www.keittlab.org/ On Wed, Nov 1, 2017 at 10:47 AM, Benjamin Blonder < benjamin.blon...@ouce.ox.ac.uk> wrote: > I am writing with a very puzzling crash issue I have been unable to > resolve myself. It concerns my hypervolume R package, which uses Rcpp to > call some custom functions to build and evaluate a k-d tree data structure. > Everything has been working fine for several versions of the package, and > the package passes the CRAN tests. > > The complication is on Windows. On a Windows 7/8/10 install, calling > functions via Rstudio, the package runs just fine. When using Windows > Rgui/Rscript, if antivirus software (e.g. Sophos or McAfee) is NOT > installed, the package also runs just fine. However on Windows with > antivirus and the Rgui/Rscript program, the package repeatably crashes the > entire program. > > A minimally reproducible example is below: > > library(hypervolume) > data(iris) > hv = hypervolume_svm(iris[,1:2]) > > On a debug trace, the problem occurs when hypervolume_svm() eventually > internally calls kdtree_ball_query_multiple(), which is just a wrapper > for an Rcpp call to a C++ function (in the package's src/convert.cpp): > > SEXP kdtree_ball_query_multiple(SEXP tr, SEXP ptlist, SEXP nr, SEXP nc, > SEXP r, SEXP verb) > > { > > XPtr<KDTree> tree = as<XPtr<KDTree> >(tr); > > int nrow = as<int>(nr); > > int ncol = as<int>(nc); > > NumericVector data(ptlist); > > double radius = as<double>(r); > > bool verbose = as<int>(verb); > > > > vector<vector< double > > dataMatrix > > = convertMatrixToVector(data.begin(), nrow, ncol); > > > > vector<int> finalCounts; > > > > if (ncol != tree->ndims()) > > { > > throw(length_error("Points not same dimensionality as data in kdtree")); > > > } > > > > RProgress::RProgress pb("[:bar]", nrow); > > if (verbose==1) > > { > > Rcpp::Rcout << "Ball query... \n"; > > pb.tick(0); > > } > > > > for (int i=0; i<nrow; i++) > > { > > > > vector<int> thisIndices; > > vector<double> thisDistances; > > > > vector<double> thisPoint = dataMatrix[i]; > > tree->ball_query(thisPoint, radius, thisIndices, thisDistances); > > > > // store the number of points within the ball for each point > > finalCounts.push_back(thisIndices.size()); > > > > if (i%10==0 && verbose==1) > > { > > pb.update(1.0*(i+1)/nrow); > > } > > > > } > > > > if (verbose==1) > > { > > Rcpp::Rcout << "\ndone.\n"; > > } > > > > pb.update(1); > > > > return(wrap(finalCounts)); > > } > > As noted above, that same code works just fine on other platforms and has > worked well on Windows in other package versions too, with or without > antivirus. > > Does anyone have any ideas for what is going on, or how to fix it? Are > there any other reports of antivirus programs causing this kind of crash, > or of Rcpp issues between Rstudio and Rgui or Rscript? > > The problem is hard for me to debug as I only get user error reports and > have limited access to Windows machines with antivirus software - my test > environment has been Windows 7, no antivirus, in VirtualBox. > > Code for the package is up at https://github.com/bblonder/hypervolume. > > Thank you for your time! > > Best wishes, > Benjamin Blonder > > -- > Benjamin Blonder > Environmental Change Institute > School of Geography and the Environment > University of Oxford > > Website: http://www.benjaminblonder.org > Photo-blog (Natural Curiosities): http://bblonder.wordpress.com/ > Google Scholar: http://scholar.google.com/citations?user=l3FNoE8AAAAJ > University of Arizona Sky School: https://skyschool.arizona.edu/ > > _______________________________________________ > Rcpp-devel mailing list > Rcpp-devel@lists.r-forge.r-project.org > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel >
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