fix CRAN ASAN-UBSAN warnings

rpkg/NEWS.md

@@ -1,3 +1,9 @@
+# redatam 2.0.3
+
+* Fixes memory management issues suggested by Ivan Krylov regarding the C++ to R
+  list casting.
+* Uses 2 threads during R CMD check
+
 # redatam 2.0.1
 
 * Fixes memory leaks warned by CRAN on clang-ASAN and gcc-UBSAN.

rpkg/configure

@@ -27,7 +27,7 @@ LDFLAGS="-stdlib=libc++"
 
 # False positive error in ASAN
 # see https://github.com/microsoft/DirectXShaderCompiler/issues/created_by/5971)
-export ASAN_OPTIONS=detect_container_overflow=0
+# export ASAN_OPTIONS=alloc_dealloc_mismatch=0
 
 # Write to Makevars using sed to replace placeholders
 sed -e "s|@cflags@|$PKG_CFLAGS|" \

rpkg/cran-comments.md

@@ -1,5 +1,26 @@
 ## R CMD check results
 
-0 errors | 0 warnings | 1 note
+0 errors | 0 warnings | 2 note
 
-* This was tested with all available R-Hub images.
+❯ checking CRAN incoming feasibility ... [5s/15s] NOTE
+  Maintainer: ‘Mauricio Vargas Sepulveda <m.sepulveda@mail.utoronto.ca>’
+
+  New submission
+
+  Package was archived on CRAN
+
+  CRAN repository db overrides:
+    X-CRAN-Comment: Archived on 2024-11-06 for repeated policy violation.
+
+    Repeatedy spamming a team member's personal email address in HTML.
+
+❯ checking compilation flags used ... NOTE
+  Compilation used the following non-portable flag(s):
+    ‘-Wp,-D_FORTIFY_SOURCE=3’
+
+Fixes: 
+
+* This was tested with all available R-Hub images including the Clang ASAN image.
+* Fixes UBSan issues (https://win-builder.r-project.org/incoming_pretest/redatam_2.0.3_20241107_154750/specialChecks/clang-san/summary.txt)
+* Fixes the empty string issue (https://www.stats.ox.ac.uk/pub/bdr/memtests/clang-ASAN/redatam/00check.log)
+* Uses 2 threads during R CMD check

rpkg/src/redatamlib/exporters/RListExporter.cpp

@@ -1,9 +1,10 @@
+#include "RListExporter.hpp"
+
 #include <algorithm>  // For std::replace
 #include <sstream>
 
 #include "Entity.hpp"
 #include "ParentIDCalculator.hpp"
-#include "RListExporter.hpp"
 
 namespace RedatamLib {
 using std::endl;
@@ -12,7 +13,7 @@ using std::ostringstream;
 // just to mimic the original CSVExporter
 ListExporter::ListExporter(const std::string &outputDirectory)
     : m_path(outputDirectory) {
-  if ('/' != m_path.back()) {
+  if (!m_path.empty() && '/' != m_path.back()) {
     m_path.append("/");
   }
 }

rpkg/src/redatamlib/readers/FuzzyVariableParser.cpp

@@ -18,8 +18,17 @@ FuzzyVariableParser::FuzzyVariableParser(ByteArrayReader reader,
 void FuzzyVariableParser::ParseAllVariables(vector<Entity> &entities) {
   vector<pair<size_t, size_t>> searchBounds = GetSearchBounds(entities);
 
-  size_t numThreads = std::thread::hardware_concurrency();
-  numThreads = std::min(entities.size(), numThreads);
+  // R-devel suggestion: Default to using all available hardware concurrency
+  size_t maxThreads = std::thread::hardware_concurrency();
+
+  // Then check for _R_CHECK_LIMIT_CORES_ environment variable
+  const char *checkLimitCoresEnv = std::getenv("_R_CHECK_LIMIT_CORES_");
+  if (checkLimitCoresEnv != nullptr &&
+      std::string(checkLimitCoresEnv) == "TRUE") {
+    maxThreads = 2;
+  }
+
+  size_t numThreads = std::min(entities.size(), maxThreads);
 
   size_t chunkSize = entities.size() / numThreads;
 
@@ -42,6 +51,10 @@ vector<pair<size_t, size_t>>
 FuzzyVariableParser::GetSearchBounds(vector<Entity> entities) {
   vector<pair<size_t, size_t>> ret;
 
+  if (entities.empty()) {
+    return ret;
+  }
+
   for (size_t i = 0; i < entities.size() - 1; ++i) {
     ret.push_back(
         {entities[i].GetBounds().second, entities[i + 1].GetBounds().first});