Hi Tim, Thanks for the idea. I removed all the RProgress calls from the C++ code underlying the package, and there are no more crashed on Windows with antivirus software. Mysterious as to the details, but a good enough solution for me for now. Thanks!
Ben On Wed, Nov 1, 2017 at 4:37 PM, Tim Keitt <tke...@utexas.edu> wrote: > 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 >> > > -- 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/
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