Fix #563

Additionally fixed tset dataset

inst/include/cec/cluster_params.hpp

@@ -5,56 +5,61 @@
 
 #ifdef RCPP_INTERFACE
 #include <RcppArmadillo.h>
+using namespace Rcpp;
+using namespace arma;
+#else
+#include <armadillo>
+using namespace arma;
 #endif
 
 namespace gmum {
 
-enum ClusterType {
-	kstandard, kfixed_covariance, kdiagonal, kfixed_spherical, kspherical, kno_type, kmix, kcustom
-};
+	enum ClusterType {
+		kstandard, kfixed_covariance, kdiagonal, kfixed_spherical, kspherical, kno_type, kmix, kcustom
+	};
 
 /**
  * You need to store somewhere data about cluster. Each type can have its own.
  */
-struct ClusterParams {
-	ClusterType type;
-	ClusterParams(ClusterType _type) :
-			type(_type) {
-	}
-    virtual ~ClusterParams() { };
-};
-
-struct ClusterFixedCovarianceParams : public ClusterParams {
-	bool cov_mat_set;
-	arma::mat cov_mat;
-	ClusterFixedCovarianceParams(arma::mat _cov_mat) :
-			ClusterParams(kfixed_covariance), cov_mat_set(true), cov_mat(_cov_mat) {
-	}
-	ClusterFixedCovarianceParams() :
-			ClusterParams(kfixed_covariance), cov_mat_set(false) {
-	}
-    virtual ~ClusterFixedCovarianceParams() { }
-};
-
-struct ClusterSphericalFixedRParams : public ClusterParams {
-	bool radius_set;
-	double radius;
-	ClusterSphericalFixedRParams(double _radius) :
-			ClusterParams(kfixed_spherical), radius_set(true), radius(_radius) {
-	}
-	ClusterSphericalFixedRParams() :
-			ClusterParams(kfixed_spherical), radius_set(false) {
-	}
-    virtual ~ClusterSphericalFixedRParams() { }
-};
+	struct ClusterParams {
+		ClusterType type;
+		ClusterParams(ClusterType _type) :
+				type(_type) {
+		}
+		virtual ~ClusterParams() { };
+	};
+
+	struct ClusterFixedCovarianceParams : public ClusterParams {
+		bool cov_mat_set;
+		mat cov_mat;
+		ClusterFixedCovarianceParams(mat _cov_mat) :
+				ClusterParams(kfixed_covariance), cov_mat_set(true), cov_mat(_cov_mat) {
+		}
+		ClusterFixedCovarianceParams() :
+				ClusterParams(kfixed_covariance), cov_mat_set(false) {
+		}
+		virtual ~ClusterFixedCovarianceParams() { }
+	};
+
+	struct ClusterSphericalFixedRParams : public ClusterParams {
+		bool radius_set;
+		double radius;
+		ClusterSphericalFixedRParams(double _radius) :
+				ClusterParams(kfixed_spherical), radius_set(true), radius(_radius) {
+		}
+		ClusterSphericalFixedRParams() :
+				ClusterParams(kfixed_spherical), radius_set(false) {
+		}
+		virtual ~ClusterSphericalFixedRParams() { }
+	};
 
 #ifdef RCPP_INTERFACE
-struct ClusterCustomParams: public ClusterParams {
-	boost::shared_ptr<Rcpp::Function> function;
-	ClusterCustomParams(boost::shared_ptr<Rcpp::Function> _function) : ClusterParams(kcustom), function(_function) {}
-	ClusterCustomParams() : ClusterParams(kcustom) {}
-    virtual ~ClusterCustomParams() { }
-};
+	struct ClusterCustomParams: public ClusterParams {
+		boost::shared_ptr<Rcpp::Function> function;
+		ClusterCustomParams(boost::shared_ptr<Rcpp::Function> _function) : ClusterParams(kcustom), function(_function) {}
+		ClusterCustomParams() : ClusterParams(kcustom) {}
+		virtual ~ClusterCustomParams() { }
+	};
 #endif
 
 }

inst/include/utils/cutils.h

@@ -13,10 +13,10 @@
 #define C_FPRINTF(stream, string, ...)
 #define C_PRINTF(string, ...)
 #else
-#define C_EXIT(x) exit(x);
-#define C_FFLUSH(stream) fflush(stream);
-#define C_FPRINTF(stream, string, ...) fprintf(stream, string, __VA_ARGS__);
-#define C_PRINTF(string, ...) printf(string, __VA_ARGS__);
+#define C_EXIT(x)
+#define C_FFLUSH(stream)
+#define C_FPRINTF(stream, string, ...)
+#define C_PRINTF(string, ...)
 #endif
 
 #endif

inst/include/utils/logger.h

@@ -4,14 +4,18 @@
 #include <iostream>
 #include <string>
 #include <sstream>
+#include "threading.h"
 
 #ifdef RCPP_INTERFACE
     #include <RcppArmadillo.h>
-    #include "threading.h"
+    // TODO: remove it
     using namespace Rcpp;
     #define COUT(x) Rcpp::Rcout<<(x)<<std::endl<<std::flush;
     #define CERR(x) Rcpp::Rcerr<<(x)<<std::endl<<std::flush;
 #else
+    #include <armadillo>
+    // TODO: remove it
+    using namespace arma;
     #define COUT(x) std::cout<<(x)<<std::endl<<std::flush;
     #define CERR(x) std::cerr<<(x)<<std::endl<<std::flush;
 #endif

src/Makevars

@@ -1,6 +1,6 @@
 # NOTE: R is overwriting all optimization flags, if you are a dev you can change flags in ~/.R/Makevars 
 # NOTE: R package should use POSIX Makefile
-# TODO: How to do wildcard in POSIX Makefile?
+
 CPP_SOURCES = svm/libsvm_runner.cpp  svm/svm_client.cpp  svm/svmlight_runner.cpp  svm/svm_wrapper_module.cpp  svm/two_e_svm_pre.cpp svm/svm_basic.cpp      svm/svm.cpp         svm/svm_utils.cpp        svm/two_e_svm_post.cpp      svm/validator_runner.cpp cec/assignment.cpp         cec/cec.cpp         cec/centroids_assignment.cpp  cec/cluster_custom_function.cpp  cec/kmeanspp_assignment.cpp cec/cec_configuration.cpp  cec/cec_module.cpp  cec/cluster.cpp               cec/hartigan.cpp                 cec/random_assignment.cpp utils/threading.cpp  utils/tinythread.cpp  utils/utils.cpp gng/gng_algorithm.cpp  gng/gng_configuration.cpp  gng/gng_module.cpp  gng/gng_server.cpp 
 SOURCES = $(CPP_SOURCES) svmlight/svm_common.c  svmlight/svm_hideo.c  svmlight/svm_learn.c
 
@@ -17,6 +17,7 @@ R_LIBS = `$(R_HOME)/bin/R CMD config --ldflags`
 LAPACK_LIBS = `$(R_HOME)/bin/R CMD config LAPACK_LIBS`
 BLAS_LIBS = `$(R_HOME)/bin/R CMD config BLAS_LIBS`
 
-PKG_CPPFLAGS =  $(GCC_STD) $(PREPROCESS) $(R_CPPFLAGS) $(INCLUDES) -pthread
+# Do not delete R_CPPFLAGS, it will break tests
+PKG_CPPFLAGS = $(GCC_STD) $(PREPROCESS) $(R_CPPFLAGS) $(INCLUDES) -pthread
 PKG_CXXFLAGS = --std=c++0x
 PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(R_LIBS) $(FLIBS)

src/cec/cec_module.cpp

@@ -1,6 +1,8 @@
 #ifndef CEC_MODULE_H
 #define CEC_MODULE_H
 
+#ifdef RCPP_INTERFACE
+
 #include <RcppArmadillo.h>
 using namespace Rcpp;
 
@@ -48,4 +50,7 @@ RCPP_MODULE(cec) {
 	.method("log.iters", &CecModel::iters)
 	.method("getDataset", &CecModel::get_points);
 }
+
+#endif
+
 #endif

src/svm/svm_wrapper_module.cpp

@@ -1,6 +1,8 @@
 #ifndef SVM_WRAPPER_MODULE_H
 #define SVM_WRAPPER_MODULE_H
 
+#ifdef RCPP_INTERFACE
+
 #include "svm_basic.h"
 #include "svm_client.h"
 using namespace Rcpp;
@@ -104,3 +106,5 @@ RCPP_MODULE(svm_wrapper) {
 }
 
 #endif
+
+#endif

src/utils/utils.cpp

@@ -78,9 +78,11 @@ char** free_argv(int argc, char** argv) {
     return NULL;
 }
 
+#ifdef RCPP_INTERFACE
 int rcpp_c_rand() {
     return int(Rcpp::runif(1)[0] * INT_MAX);
 }
+#endif
 
 int ed_c_rand() {
 #ifdef RCPP_INTERFACE

tests/cpp/GNUmakefile → tests/cpp/Makefile

@@ -1,11 +1,15 @@
+$(warning Remember to make sure to delete all R package objects, you can run "make clean" to do it)
+
 R_HOME=$(shell R RHOME)
 R_CPPFLAGS = $(shell $(R_HOME)/bin/R CMD config --cppflags) $(shell $(R_HOME)/bin/Rscript -e "RcppArmadillo:::CxxFlags()") $(shell $(R_HOME)/bin/Rscript -e "Rcpp:::CxxFlags()")  
 
 include ../../src/Makevars
 
 # Explicit Makevars inheritances adn overrides
 CXX := $(CXX)
-CPPFLAGS := $(PKG_CPPFLAGS) -O2 -g -s --std=c++0x
+PREPROCESS = $(DEBUG) -DNRCPP_INTERFACE -DARMA_64BIT_WORD -DBOOST_DISABLE_ASSERTS
+PKG_CPPFLAGS = $(GCC_STD) $(PREPROCESS) $(R_CPPFLAGS) $(INCLUDES) -pthread
+CPPFLAGS :=  $(PKG_CPPFLAGS) -O2 -g -s --std=c++0x
 LDLIBS := $(PKG_LIBS) -lpthread -lgtest -lgtest_main
 
 ###
@@ -89,7 +93,7 @@ INCLUDES := $(ROOT_INCLUDE) $(BRANCH_INCLUDES) $(COMPILED_LIBRARIES_INCLUDES)
 # Compilation rules
 ###
 
-CPPFLAGS := $(CPPFLAGS) $(INCLUDES)
+CPPFLAGS := $(CPPFLAGS) $(INCLUDES) -DNRCPP_INTERFACE
 CFLAGS := $(CPPFLAGS)
 
 all: $(TEST_MAIN_BIN) helper_scripts
@@ -98,6 +102,7 @@ all: $(TEST_MAIN_BIN) helper_scripts
 	@echo or use helper scripts: $(PRIMARY_TESTS_SCRIPT) $(SECONDARY_TESTS_SCRIPT)
 
 clean:
+	rm $(OBJECTS)
 	rm -f $(TEST_MAIN_BIN) $(TEST_OBJECTS) $(COMPILED_LIBRARIES_OBJECTS)\
 	$(PRIMARY_TESTS_SCRIPT) $(SECONDARY_TESTS_SCRIPT) $(ADDITIONAL_CLEANING)