drop C++11 features which seem very difficult to make work with OpenM…

…P in a way acceptable to CRAN.

DESCRIPTION

@@ -8,7 +8,7 @@ Description: Calculate comorbidities, Charlson scores, perform fast and accurate
     hospital billing databases to comorbidities. ICD-9 to comorbidity mappings
     from Quan (Deyo and Elixhauser versions), Elixhauser and AHRQ included.
 Version: 1.1
-Date: 2015-03-08
+Date: 2015-03-14
 Authors@R: person(given = "Jack O.", family = "Wasey",
     role = c("aut", "cre", "cph"),
     email = c("jack@jackwasey.com"))

cran-comments.md

@@ -1,5 +1,5 @@
 ## Resubmission
-* removed tr1/unordered_map include, replaced with Makevars C++11 flags per Writing R Extensions 1.2.4, and tested for C++11 before choice of std::unordered_map or std::map depending on availability.
+* now I better understand 1.2.1.1 of Writing R Extensions (specifically that adding the C++11 flag constitutes using a C++11 compiler), and given my current inability to write a configure script, this resubmission drops all C++11 code and flags.
 
 ## Test environments
 * Ubuntu 14.10 R 3.1.3, clang and gcc

src/Makevars

@@ -1,7 +1,8 @@
-CXX_STD = CXX11
+# CXX_STD = CXX11
+# PKG_CXXFLAGS += $(CXX1XSTD) # on hold until CRAN will accept this (or I figured out how to write a configure script to generate this Makefile)
 
 PKG_CPPFLAGS = -I.
-PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) $(CXX1XSTD)
+PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
 PKG_CFLAGS = $(SHLIB_OPENMP_CFLAGS)
 PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS)
 

src/Makevars.win

@@ -1,8 +1,7 @@
-CXX_STD = CXX11
+# CXX_STD = CXX11
+# $(CXX1XSTD)
 
 PKG_CPPFLAGS = -I.
-PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) $(CXX1XSTD) -mtune=native
-PKG_CFLAGS = $(SHLIB_OPENMP_CFLAGS) -mtune=native
+PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
+PKG_CFLAGS = $(SHLIB_OPENMP_CFLAGS)
 PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS)
-
-#CXX_STD = CXX11 # note that this trashes my choice of compiler reverting to g++ instead of clang

src/comorbidSetup.cpp

@@ -34,9 +34,9 @@ void buildVisitCodesVec(const SEXP& icd9df, const std::string& visitId,
 	const int approx_cmb_per_visit = 15; // just an estimate
 	int vlen = Rf_length(icds); // or vsexp
 
-#if defined(ICD9_DEBUG) && defined(_GLIBCXX_UNORDERED_MAP)
-	Rcout << "unordered_map is available\n";
-#endif
+//#if defined(ICD9_DEBUG) && defined(ICD9_UNORDERED_MAP)
+//	Rcout << "unordered_map is available\n";
+//#endif
 	VisLk vis_lookup;
 
 	vcdb.resize(vlen); // over-estimate and allocate all at once (alternative is to reserve)
@@ -64,7 +64,7 @@ void buildVisitCodesVec(const SEXP& icd9df, const std::string& visitId,
 		if (lastVisitId != vi) {
 			// assume new visitId unless aggregating
 			vcdb_new_idx = vcdb_max_idx + 1;
-			if (aggregate) { // only use unordered_map if aggregating
+			if (aggregate) { // only use map if aggregating
 				VisLk::iterator found = vis_lookup.find(vi); // TODO make const?
 				if (found != vis_lookup.end()) {
 					vcdb[found->second].push_back(n);

src/local.h

@@ -34,7 +34,6 @@ extern "C" {
 #define ICD9_OPENMP
 #endif
 
-// enable linux performance counting
 #ifdef ICD9_VALGRIND
 #include <valgrind/callgrind.h>
 #endif
@@ -44,17 +43,18 @@ typedef std::vector<Str> VecStr;
 
 typedef std::vector<int> VecInt;
 typedef std::vector<char> ComorbidOut; // TODO: someday benchmark int vs char (or possibly Boost bitset)
-// vector<bool> dangerous with multiple threads, and note that char doesn't cast to bool with Rcpp
+// vector<bool> dangerous with multiple threads, and note that char doesn't cast to bool (directly) with Rcpp, yet.
 
 typedef std::vector<VecStr> VecVecStr;
 typedef std::vector<VecInt> VecVecInt;
 typedef VecVecInt::size_type VecVecIntSz;
-#ifdef _GLIBCXX_UNORDERED_MAP
-#include <unordered_map>
-typedef std::unordered_map<std::string, VecInt::size_type> VisLk;
-#else
+//#if defined(_GLIBCXX_UNORDERED_MAP) && defined(__GXX_EXPERIMENTAL_CXX0X__)
+//#define ICD9_UNORDERED_MAP
+//#include <unordered_map>
+//typedef std::unordered_map<std::string, VecInt::size_type> VisLk;
+//#else
 typedef std::map<std::string, VecInt::size_type> VisLk;
-#endif
+//#endif
 
 void buildMap(const Rcpp::List& icd9Mapping, VecVecInt& map);
 void buildVisitCodesVec(const SEXP& icd9df, const std::string& visitId,