patch CRAN notes about Catch called functions

Author: pachadotdev

catch2-update/02-install.sh

@@ -27,5 +27,3 @@ fi
 echo "Catch2 v2.13.10 installed to inst/include/testthat/vendor/catch.hpp"
 echo ""
 echo "inst/include/testthat/testthat.h now uses catch.hpp instead of catch.h"
-echo "test compilation with: R CMD INSTALL --preclean ."
-echo "run tests with: Rscript -e 'testthat::test_local()'"

catch2-update/03-patch-r-compat.sh

@@ -0,0 +1,79 @@
+#!/bin/sh
+
+# Patch Catch2 to be compatible with R CMD check requirements
+# Fixes warnings about abort, sprintf, and srand
+
+cd ~/Documents/testthat/
+
+CATCH_FILE="inst/include/testthat/vendor/catch.hpp"
+
+if [ ! -f "$CATCH_FILE" ]; then
+  echo "ERROR: $CATCH_FILE not found. Run 02-install.sh first."
+  exit 1
+fi
+
+echo "Creating backup of catch.hpp..."
+cp "$CATCH_FILE" "$CATCH_FILE.backup"
+
+echo "Patching Catch2 for R compatibility..."
+
+# First, add R header includes after the initial header guard
+echo "  - Adding R headers..."
+sed -i '/#define TWOBLUECUBES_SINGLE_INCLUDE_CATCH_HPP_INCLUDED/a\
+#ifdef __cplusplus\
+extern "C" {\
+#endif\
+#include <R_ext/Error.h>\
+#ifdef __cplusplus\
+}\
+#endif' "$CATCH_FILE"
+
+# Fix 1: Replace std::abort() with Rf_error()
+# This uses R's native error mechanism instead of terminating the process
+echo "  - Replacing abort() with Rf_error()..."
+sed -i 's/std::abort();/Rf_error("Fatal error in test framework");/g' "$CATCH_FILE"
+
+# Fix 2: Replace std::sprintf() with std::snprintf() for safety
+# snprintf is safer and avoids R CMD check warnings
+echo "  - Replacing sprintf() with snprintf()..."
+sed -i 's/std::sprintf(buffer, "%.3f", duration);/std::snprintf(buffer, sizeof(buffer), "%.3f", duration);/g' "$CATCH_FILE"
+
+# Fix 3: Comment out std::srand() - R uses its own RNG
+# R packages should use R's RNG via GetRNGstate()/PutRNGstate()
+echo "  - Commenting out srand()..."
+sed -i 's/std::srand(config.rngSeed());/\/\/ std::srand(config.rngSeed()); \/\/ Disabled for R compatibility/g' "$CATCH_FILE"
+
+echo ""
+echo "Verifying patches..."
+echo ""
+
+echo "1. Checking abort() was replaced:"
+if grep -q "std::abort()" "$CATCH_FILE"; then
+  echo "   WARNING: std::abort() still found!"
+else
+  echo "   No abort() calls found"
+fi
+
+echo ""
+echo "2. Checking sprintf() was replaced:"
+if grep -q "std::sprintf(buffer" "$CATCH_FILE"; then
+  echo "   WARNING: std::sprintf() still found!"
+else
+  echo "   No sprintf() calls found"
+fi
+
+echo ""
+echo "3. Checking srand() was commented out:"
+if grep -q "^[[:space:]]*std::srand(config.rngSeed());" "$CATCH_FILE"; then
+  echo "   WARNING: Uncommented std::srand() still found!"
+else
+  echo "   srand() has been disabled"
+fi
+
+echo ""
+echo "Patch complete!"
+echo ""
+echo "To test: R CMD INSTALL --preclean . && R CMD check --as-cran ."
+echo ""
+echo "If you need to restore the original, run:"
+echo "  mv $CATCH_FILE.backup $CATCH_FILE"

catch2-update/03-test.sh catch2-update/04-test.shcatch2-update/03-test.sh renamed to catch2-update/04-test.sh

@@ -74,7 +74,7 @@ if [ $? -eq 0 ]; then
   echo " Package build successful"
   echo ""
   echo "======================================"
-  echo "All tests passed! ✓"
+  echo "All tests passed!"
   echo "======================================"
 else
   echo " Package build failed"

inst/include/testthat/vendor/catch.h

@@ -10,6 +10,13 @@
  */
 #ifndef TWOBLUECUBES_SINGLE_INCLUDE_CATCH_HPP_INCLUDED
 #define TWOBLUECUBES_SINGLE_INCLUDE_CATCH_HPP_INCLUDED
+#ifdef __cplusplus
+extern "C" {
+#endif
+#include <R_ext/Error.h>
+#ifdef __cplusplus
+}
+#endif
 // start catch.hpp
 
 
@@ -9021,7 +9028,7 @@ namespace detail {
             assert( m_type != ResultBase::LogicError );
             assert( m_type != ResultBase::RuntimeError );
             if( m_type != ResultBase::Ok )
-                std::abort();
+                Rf_error("Fatal error in test framework");
         }
 
         std::string m_errorMessage; // Only populated if resultType is an error
@@ -13151,7 +13158,7 @@ namespace Catch {
 
     void seedRng(IConfig const& config) {
         if (config.rngSeed() != 0) {
-            std::srand(config.rngSeed());
+            // std::srand(config.rngSeed()); // Disabled for R compatibility
             rng().seed(config.rngSeed());
         }
     }
@@ -15786,7 +15793,7 @@ namespace Catch {
 #ifdef _MSC_VER
         sprintf_s(buffer, "%.3f", duration);
 #else
-        std::sprintf(buffer, "%.3f", duration);
+        std::snprintf(buffer, sizeof(buffer), "%.3f", duration);
 #endif
         return std::string(buffer);
     }