remove BH dependency

Cyclops.Rproj

@@ -1,7 +1,7 @@
 Version: 1.0
 
-RestoreWorkspace: Default
-SaveWorkspace: Default
+RestoreWorkspace: No
+SaveWorkspace: No
 AlwaysSaveHistory: Default
 
 EnableCodeIndexing: Yes

DESCRIPTION

@@ -41,7 +41,6 @@ Imports:
     survival,
     bit64
 LinkingTo: Rcpp,
-    BH (>= 1.51.0),
     RcppEigen (>= 0.3.2)
 Suggests:
     testthat,

src/cyclops/CcdInterface.cpp

@@ -29,7 +29,7 @@
 #include "CyclicCoordinateDescent.h"
 #include "ModelData.h"
 
-#include "boost/iterator/counting_iterator.hpp"
+//#include "boost/iterator/counting_iterator.hpp"
 #include "Thread.h"
 
 // #include "io/InputReader.h"
@@ -370,9 +370,9 @@ double CcdInterface::profileModel(CyclicCoordinateDescent *ccd, AbstractModelDat
                       }
                     );
     } else {
-        auto scheduler = TaskScheduler<boost::counting_iterator<int> >(
-            boost::make_counting_iterator(0),
-            boost::make_counting_iterator(static_cast<int>(bounds.size())),
+        auto scheduler = TaskScheduler<IncrementableIterator<size_t>>(
+            IncrementableIterator<size_t>(0), // boost::make_counting_iterator(0),
+            IncrementableIterator<size_t>(bounds.size()), //boost::make_counting_iterator(static_cast<int>(bounds.size())),
             nThreads);
 
         auto oneTask = [&getBound, &scheduler, &ccdPool, &bounds](unsigned long task) {
@@ -583,8 +583,10 @@ double CcdInterface::evaluateProfileModel(CyclicCoordinateDescent *ccd, Abstract
             values[i] = evaluate(points[i], ccd);
         }
     } else {
-        auto scheduler = TaskScheduler<boost::counting_iterator<int>>(
-            boost::make_counting_iterator(0), boost::make_counting_iterator(static_cast<int>(points.size())), nThreads);
+        auto scheduler = TaskScheduler<IncrementableIterator<size_t>>(
+            IncrementableIterator<size_t>(0), //boost::make_counting_iterator(0),
+            IncrementableIterator<size_t>(points.size()), //boost::make_counting_iterator(static_cast<int>(points.size())),
+            nThreads);
 
         auto oneTask = [&evaluate, &scheduler, &ccdPool, &points, &values](unsigned long task) {
             values[task] = evaluate(points[task], ccdPool[scheduler.getThreadIndex(task)]);

src/cyclops/CyclicCoordinateDescent.cpp

@@ -209,12 +209,12 @@ void CyclicCoordinateDescent::init(bool offset) {
 
 	// initialize starting betas to default value 0.0
 	startingBeta.resize(J, static_cast<double>(0.0));
-	
+
 // 	hXBeta.resize(K, static_cast<double>(0.0));
 // 	hXBetaSave.resize(K, static_cast<double>(0.0));
 
 	fixBeta.resize(J, false);
-	
+
 	hWeights.resize(0);
     cWeights.resize(0); // ESK: For censor weights
 
@@ -695,7 +695,7 @@ void CyclicCoordinateDescent::kktSwindle(const ModeFindingArguments& arguments)
 	int swindleIterationCount = 1;
 
 //	int initialActiveSize = activeSet.size();
-	int perPassSize = arguments.swindleMultipler;
+	// int perPassSize = arguments.swindleMultipler;
 
 	while (!done) {
 
@@ -823,7 +823,7 @@ void CyclicCoordinateDescent::kktSwindle(const ModeFindingArguments& arguments)
 			}
 		}
 		++swindleIterationCount;
-		perPassSize *= 2;
+		// perPassSize *= 2;
 
 		logger->yield();			// This is not re-entrant safe
 	}

src/cyclops/Iterators.h

@@ -1,7 +1,8 @@
 #ifndef ITERATORS_H
 #define ITERATORS_H
 
-#include <boost/tuple/tuple.hpp>
+//#include <boost/tuple/tuple.hpp>
+#include <tuple>
 
 #include "CompressedDataMatrix.h"
 
@@ -14,6 +15,40 @@ namespace bsccs {
  * single run-time determined iterator
  */
 
+template <typename T>
+class IncrementableIterator : public std::iterator<std::input_iterator_tag, T> {
+public:
+    IncrementableIterator(T value) : value(value) { }
+
+    IncrementableIterator& operator++() {
+        ++value;
+        return *this;
+    }
+
+    T operator*() const { return value; }
+
+    bool operator==(const IncrementableIterator& rhs) const {
+        return value == rhs.value;
+    }
+
+    bool operator!=(const IncrementableIterator& rhs) const {
+        return !(*this == rhs);
+    }
+
+    template <typename V>
+    IncrementableIterator operator+(V n) const {
+        IncrementableIterator copy = *this;
+        copy.value += n;
+        return copy;
+    }
+
+    bool operator<(const IncrementableIterator& rhs) const {
+        return value < rhs.value;
+    }
+
+private:
+    T value;
+};
 
 struct IndicatorTag {};
 struct SparseTag {};
@@ -31,7 +66,7 @@ class IndicatorIterator {
 	typedef IndicatorTag tag;
 	typedef int Index;
 	typedef Scalar ValueType;
-	typedef boost::tuples::tuple<Index> XTuple;
+	typedef std::tuple<Index> XTuple;
 
 	const static std::string name;
 
@@ -123,7 +158,8 @@ class SparseIterator {
 	typedef SparseTag tag;
 	typedef int Index;
 	typedef Scalar ValueType;
-	typedef boost::tuples::tuple<Index, Scalar> XTuple;
+//	typedef boost::tuples::tuple<Index, Scalar> XTuple;
+	typedef std::tuple<Index, Scalar> XTuple;
 
 	const static std::string name;
 
@@ -300,7 +336,8 @@ class DenseIterator {
 	typedef DenseTag tag;
 	typedef int Index;
 	typedef Scalar ValueType;
-	typedef boost::tuples::tuple<Index, Scalar> XTuple;
+// 	typedef boost::tuples::tuple<Index, Scalar> XTuple;
+	typedef std::tuple<Index, Scalar> XTuple;
 
 	const static std::string name;
 
@@ -392,7 +429,8 @@ class InterceptIterator {
 	typedef InterceptTag tag; // TODO Fix!!!
 	typedef int Index;
 	typedef Scalar ValueType;
-	typedef boost::tuples::tuple<Index> XTuple;
+// 	typedef boost::tuples::tuple<Index> XTuple;
+	typedef std::tuple<Index> XTuple;
 
 	const static std::string name;
 

src/cyclops/ModelData.cpp

@@ -17,8 +17,8 @@
 #include <list>
 #include <functional>
 
-#include <boost/iterator/permutation_iterator.hpp>
-#include <boost/iterator/transform_iterator.hpp>
+// #include <boost/iterator/permutation_iterator.hpp>
+// #include <boost/iterator/transform_iterator.hpp>
 
 #include "ModelData.h"
 

src/cyclops/drivers/AbstractCrossValidationDriver.cpp

@@ -8,7 +8,7 @@
 #include <numeric>
 #include <cmath>
 
-#include "boost/iterator/counting_iterator.hpp"
+// #include "boost/iterator/counting_iterator.hpp"
 
 #include "Types.h"
 #include "Thread.h"
@@ -146,10 +146,15 @@ double AbstractCrossValidationDriver::doCrossValidationStep(
 	auto& weightsExclude = this->weightsExclude;
 	auto& logger = this->logger;
 
-	auto scheduler = TaskScheduler<decltype(boost::make_counting_iterator(0))>(
-		boost::make_counting_iterator(0),
-		boost::make_counting_iterator(arguments.foldToCompute),
-		nThreads);
+	// auto scheduler = TaskScheduler<decltype(boost::make_counting_iterator(0))>(
+	// 	boost::make_counting_iterator(0),
+	// 	boost::make_counting_iterator(arguments.foldToCompute),
+	// 	nThreads);
+
+	auto scheduler = TaskScheduler<IncrementableIterator<size_t>>(
+	    IncrementableIterator<size_t>(0),
+	    IncrementableIterator<size_t>(arguments.foldToCompute),
+	    nThreads);
 
 	auto oneTask =
 		[step, coldStart, nThreads, &ccdPool, &selectorPool,

src/cyclops/drivers/AutoSearchCrossValidationDriver.cpp

@@ -21,7 +21,7 @@
 #include "AbstractSelector.h"
 #include "../utils/HParSearch.h"
 
-#include "boost/iterator/counting_iterator.hpp"
+// #include "boost/iterator/counting_iterator.hpp"
 
 namespace bsccs {
 
@@ -115,7 +115,7 @@ MaxPoint AutoSearchCrossValidationDriver::doCrossValidationLoop(
 	            // Newly re-located code
 	            double pointEstimate = doCrossValidationStep(ccd, selector, allArguments, step,
                                                           nThreads, ccdPool, selectorPool,
-                                                          predLogLikelihood);             
+                                                          predLogLikelihood);
 
 	            double stdDevEstimate = computeStDev(predLogLikelihood, pointEstimate);
 

src/cyclops/engine/ModelSpecifics.h

@@ -1696,7 +1696,7 @@ struct TupleXGetterNew {
 
     template <class TupleType>
     inline ReturnType operator()(TupleType& tuple) const {
-        return boost::get<index>(tuple);
+        return std::get<index>(tuple);
     }
 };
 
@@ -1728,7 +1728,7 @@ struct TestNumeratorKernel {
     template <class NumeratorType, class TupleType>
     NumeratorType operator()(const NumeratorType lhs, const TupleType tuple) {
 
-        const auto expXBeta = boost::get<0>(tuple);
+        const auto expXBeta = std::get<0>(tuple);
         const auto x = getX(tuple); //boost::get<1>(tuple);
 
         return {
@@ -1752,8 +1752,8 @@ struct TestGradientKernel {
 
     template <class GradientType, class NumeratorType, class TupleType>
     GradientType operator()(const GradientType lhs, const NumeratorType numerator, const TupleType tuple) {
-        const auto denominator = boost::get<0>(tuple);
-        const auto weight = boost::get<1>(tuple);
+        const auto denominator = std::get<0>(tuple);
+        const auto weight = std::get<1>(tuple);
 
         return BaseModel::template incrementGradientAndHessian<IteratorType,
                                                                WeightType>(

src/cyclops/engine/ModelSpecifics.hpp

@@ -19,7 +19,7 @@
 
 #include "Recursions.hpp"
 #include "ParallelLoops.h"
-#include "Ranges.h"
+// #include "Ranges.h"
 
 #ifdef USE_RCPP_PARALLEL
 #include <tbb/combinable.h>

src/cyclops/engine/ParallelLoops.h

@@ -5,7 +5,7 @@
 #include <vector>
 #include <numeric>
 #include <thread>
-#include <boost/iterator/counting_iterator.hpp>
+// #include <boost/iterator/counting_iterator.hpp>
 
 // #define USE_RCPP_PARALLEL
 #undef USE_RCPP_PARALLEL