diff --git a/.gitignore b/.gitignore
index 2620533dc..f7d420946 100644
--- a/.gitignore
+++ b/.gitignore
@@ -36,3 +36,7 @@ Debug
 *test*
 .Rhistory
 *.dll
+*i386
+*x64
+*dump
+*save
diff --git a/R-package/inst/examples/model.dump b/R-package/inst/examples/model.dump
deleted file mode 100644
index ddeb6546d..000000000
--- a/R-package/inst/examples/model.dump
+++ /dev/null
@@ -1,72 +0,0 @@
-booster[0]:
-0:[f28<1.00001] yes=1,no=2,missing=2
-	1:[f108<1.00001] yes=3,no=4,missing=4
-		3:leaf=1.85965
-		4:leaf=-1.94071
-	2:[f55<1.00001] yes=5,no=6,missing=6
-		5:leaf=-1.70044
-		6:leaf=1.71218
-booster[1]:
-0:[f59<1.00001] yes=1,no=2,missing=2
-	1:leaf=-6.23624
-	2:[f28<1.00001] yes=3,no=4,missing=4
-		3:leaf=-0.96853
-		4:leaf=0.784718
-booster[2]:
-0:[f101<1.00001] yes=1,no=2,missing=2
-	1:[f110<1.00001] yes=3,no=4,missing=4
-		3:leaf=-9.42142
-		4:leaf=-0.791407
-	2:[f66<1.00001] yes=5,no=6,missing=6
-		5:leaf=5.77229
-		6:leaf=0.658725
-booster[3]:
-0:[f26<1.00001] yes=1,no=2,missing=2
-	1:leaf=1.07748
-	2:[f38<1.00001] yes=3,no=4,missing=4
-		3:leaf=-0.877906
-		4:leaf=0.614153
-booster[4]:
-0:[f108<1.00001] yes=1,no=2,missing=2
-	1:leaf=2.92191
-	2:[f35<1.00001] yes=3,no=4,missing=4
-		3:leaf=0.152607
-		4:leaf=-1.26934
-booster[5]:
-0:[f22<1.00001] yes=1,no=2,missing=2
-	1:[f35<1.00001] yes=3,no=4,missing=4
-		3:leaf=-1.02315
-		4:leaf=-3.02414
-	2:[f23<1.00001] yes=5,no=6,missing=6
-		5:leaf=-1.53846
-		6:leaf=0.431742
-booster[6]:
-0:[f28<1.00001] yes=1,no=2,missing=2
-	1:[f108<1.00001] yes=3,no=4,missing=4
-		3:leaf=0.836115
-		4:leaf=-0.912605
-	2:[f23<1.00001] yes=5,no=6,missing=6
-		5:leaf=-1.1971
-		6:leaf=0.777142
-booster[7]:
-0:[f38<1.00001] yes=1,no=2,missing=2
-	1:[f26<1.00001] yes=3,no=4,missing=4
-		3:leaf=0.890623
-		4:leaf=-0.908312
-	2:[f111<1.00001] yes=5,no=6,missing=6
-		5:leaf=1.43619
-		6:leaf=-0.0180106
-booster[8]:
-0:[f22<1.00001] yes=1,no=2,missing=2
-	1:leaf=-1.01502
-	2:[f101<1.00001] yes=3,no=4,missing=4
-		3:leaf=0.568838
-		4:leaf=-0.515293
-booster[9]:
-0:[f114<1.00001] yes=1,no=2,missing=2
-	1:[f60<1.00001] yes=3,no=4,missing=4
-		3:leaf=-0.609475
-		4:leaf=3.63443
-	2:[f28<1.00001] yes=5,no=6,missing=6
-		5:leaf=-0.734556
-		6:leaf=0.217203
diff --git a/R-package/src-i386/Makevars b/R-package/src-i386/Makevars
deleted file mode 100644
index 10b2661d0..000000000
--- a/R-package/src-i386/Makevars
+++ /dev/null
@@ -1,28 +0,0 @@
-# _*_ mode: Makefile; _*_
-export CC  = gcc
-export CXX = g++
-
-# expose these flags to R CMD SHLIB
-PKG_CPPFLAGS = -O3 -Wno-unknown-pragmas  -DXGBOOST_CUSTOMIZE_ERROR_  -fPIC  $(SHLIB_OPENMP_CFLAGS)
-PKG_LIBS = $(SHLIB_OPENMP_CFLAGS)
-
-ifeq ($(no_omp),1)
-	PKG_CPPFLAGS += -DDISABLE_OPENMP 
-endif
-
-CXXOBJ= xgboost_wrapper.o xgboost_io.o
-OBJECTS= xgboost_R.o $(CXXOBJ)
-
-.PHONY: all clean
-all: $(SHLIB)
-$(SHLIB): $(OBJECTS)
-
-xgboost_wrapper.o: ../../wrapper/xgboost_wrapper.cpp
-xgboost_io.o: ../../src/io/io.cpp
-
-$(CXXOBJ) : 
-	$(CXX) -c $(PKG_CPPFLAGS) -o $@ $(firstword $(filter %.cpp %.c, $^) )
-
-clean:
-	rm -rf *.so *.o *~ *.dll
-
diff --git a/R-package/src-i386/Makevars.win b/R-package/src-i386/Makevars.win
deleted file mode 100644
index 5d2261230..000000000
--- a/R-package/src-i386/Makevars.win
+++ /dev/null
@@ -1,32 +0,0 @@
-# _*_ mode: Makefile; _*_
-export CC  = gcc
-export CXX = g++
-
-# expose these flags to R CMD SHLIB
-PKG_CPPFLAGS = -O3 -Wno-unknown-pragmas  -DXGBOOST_CUSTOMIZE_ERROR_ -fopenmp -fPIC  $(SHLIB_OPENMP_CFLAGS)
-PKG_LIBS = $(SHLIB_OPENMP_CFLAGS)
-
-# add flag to build native code even in cross compiler
-ifeq "$(WIN)" "64"
-	PKG_CPPFLAGS += -m64
-endif
-
-ifeq ($(no_omp),1)
-	PKG_CPPFLAGS += -DDISABLE_OPENMP 
-endif
-
-CXXOBJ= xgboost_wrapper.o xgboost_io.o
-OBJECTS= xgboost_R.o $(CXXOBJ)
-
-.PHONY: all clean
-all: $(SHLIB)
-$(SHLIB): $(OBJECTS)
-
-xgboost_wrapper.o: ../../wrapper/xgboost_wrapper.cpp
-xgboost_io.o: ../../src/io/io.cpp
-
-$(CXXOBJ) : 
-	$(CXX) -c $(PKG_CPPFLAGS) -o $@ $(firstword $(filter %.cpp %.c, $^) )
-
-clean:
-	rm -rf *.so *.o *~ *.dll
diff --git a/R-package/src-i386/xgboost_R.cpp b/R-package/src-i386/xgboost_R.cpp
deleted file mode 100644
index 1ca232509..000000000
--- a/R-package/src-i386/xgboost_R.cpp
+++ /dev/null
@@ -1,221 +0,0 @@
-#include <vector>
-#include <string>
-#include <utility>
-#include <cstring>
-#include "xgboost_R.h"
-#include "../../wrapper/xgboost_wrapper.h"
-#include "../../src/utils/utils.h"
-#include "../../src/utils/omp.h"
-#include "../../src/utils/matrix_csr.h"
-
-using namespace xgboost;
-// implements error handling
-namespace xgboost {
-namespace utils {
-void HandleAssertError(const char *msg) {
-  error("%s", msg);
-}
-void HandleCheckError(const char *msg) {
-  error("%s", msg);
-}
-}  // namespace utils
-}  // namespace xgboost
-
-extern "C" {
-  void _DMatrixFinalizer(SEXP ext) {    
-    if (R_ExternalPtrAddr(ext) == NULL) return;
-    XGDMatrixFree(R_ExternalPtrAddr(ext));
-    R_ClearExternalPtr(ext);
-  }
-  SEXP XGDMatrixCreateFromFile_R(SEXP fname, SEXP silent) {
-    void *handle = XGDMatrixCreateFromFile(CHAR(asChar(fname)), asInteger(silent));
-    SEXP ret = PROTECT(R_MakeExternalPtr(handle, R_NilValue, R_NilValue));
-    R_RegisterCFinalizerEx(ret, _DMatrixFinalizer, TRUE);
-    UNPROTECT(1);
-    return ret;
-  }
-  SEXP XGDMatrixCreateFromMat_R(SEXP mat, 
-                                SEXP missing) {
-    SEXP dim = getAttrib(mat, R_DimSymbol);
-    int nrow = INTEGER(dim)[0];
-    int ncol = INTEGER(dim)[1];    
-    double *din = REAL(mat);
-    std::vector<float> data(nrow * ncol);
-    #pragma omp parallel for schedule(static)
-    for (int i = 0; i < nrow; ++i) {
-      for (int j = 0; j < ncol; ++j) {
-        data[i * ncol +j] = din[i + nrow * j];
-      }
-    }
-    void *handle = XGDMatrixCreateFromMat(&data[0], nrow, ncol, asReal(missing));
-    SEXP ret = PROTECT(R_MakeExternalPtr(handle, R_NilValue, R_NilValue));
-    R_RegisterCFinalizerEx(ret, _DMatrixFinalizer, TRUE);
-    UNPROTECT(1);
-    return ret;    
-  }
-  SEXP XGDMatrixCreateFromCSC_R(SEXP indptr,
-                                SEXP indices,
-                                SEXP data) {
-    const int *col_ptr = INTEGER(indptr);
-    const int *row_index = INTEGER(indices);
-    const double *col_data = REAL(data);
-    int ncol = length(indptr) - 1;
-    int ndata = length(data);
-    // transform into CSR format
-    std::vector<bst_ulong> row_ptr;
-    std::vector< std::pair<unsigned, float> > csr_data;
-    utils::SparseCSRMBuilder<std::pair<unsigned,float>, false, bst_ulong> builder(row_ptr, csr_data);
-    builder.InitBudget();
-    for (int i = 0; i < ncol; ++i) {
-      for (int j = col_ptr[i]; j < col_ptr[i+1]; ++j) {
-        builder.AddBudget(row_index[j]);
-      }
-    }
-    builder.InitStorage();
-    for (int i = 0; i < ncol; ++i) {
-      for (int j = col_ptr[i]; j < col_ptr[i+1]; ++j) {
-        builder.PushElem(row_index[j], std::make_pair(i, col_data[j]));
-      }
-    }
-    utils::Assert(csr_data.size() == static_cast<size_t>(ndata), "BUG CreateFromCSC");
-    std::vector<float> row_data(ndata);
-    std::vector<unsigned> col_index(ndata);
-    #pragma omp parallel for schedule(static)
-    for (int i = 0; i < ndata; ++i) {
-      col_index[i] = csr_data[i].first;
-      row_data[i] = csr_data[i].second;      
-    }
-    void *handle = XGDMatrixCreateFromCSR(&row_ptr[0], &col_index[0], &row_data[0], row_ptr.size(), ndata );
-    SEXP ret = PROTECT(R_MakeExternalPtr(handle, R_NilValue, R_NilValue));
-    R_RegisterCFinalizerEx(ret, _DMatrixFinalizer, TRUE);
-    UNPROTECT(1);
-    return ret;
-  }
-  void XGDMatrixSaveBinary_R(SEXP handle, SEXP fname, SEXP silent) {
-    XGDMatrixSaveBinary(R_ExternalPtrAddr(handle),
-                        CHAR(asChar(fname)), asInteger(silent));
-  }
-  void XGDMatrixSetInfo_R(SEXP handle, SEXP field, SEXP array) {
-    int len = length(array);
-    const char *name = CHAR(asChar(field));
-    if (!strcmp("group", name)) {
-      std::vector<unsigned> vec(len);
-      #pragma omp parallel for schedule(static)      
-      for (int i = 0; i < len; ++i) {
-        vec[i] = static_cast<unsigned>(INTEGER(array)[i]);
-      }
-      XGDMatrixSetGroup(R_ExternalPtrAddr(handle), &vec[0], len);
-      return;
-    }
-    {
-      std::vector<float> vec(len);
-      #pragma omp parallel for schedule(static)
-      for (int i = 0; i < len; ++i) {
-        vec[i] = REAL(array)[i];
-      }
-      XGDMatrixSetFloatInfo(R_ExternalPtrAddr(handle), 
-                            CHAR(asChar(field)),
-                            &vec[0], len);
-    }
-  }
-  SEXP XGDMatrixGetInfo_R(SEXP handle, SEXP field) {
-    bst_ulong olen;
-    const float *res = XGDMatrixGetFloatInfo(R_ExternalPtrAddr(handle),
-                                             CHAR(asChar(field)), &olen);
-    SEXP ret = PROTECT(allocVector(REALSXP, olen));
-    for (size_t i = 0; i < olen; ++i) {
-      REAL(ret)[i] = res[i];
-    }
-    UNPROTECT(1);
-    return ret;
-  }
-  // functions related to booster
-  void _BoosterFinalizer(SEXP ext) {    
-    if (R_ExternalPtrAddr(ext) == NULL) return;
-    XGBoosterFree(R_ExternalPtrAddr(ext));
-    R_ClearExternalPtr(ext);
-  }
-  SEXP XGBoosterCreate_R(SEXP dmats) {
-    int len = length(dmats);
-    std::vector<void*> dvec;
-    for (int i = 0; i < len; ++i){
-      dvec.push_back(R_ExternalPtrAddr(VECTOR_ELT(dmats, i)));
-    }
-    void *handle = XGBoosterCreate(&dvec[0], dvec.size());
-    SEXP ret = PROTECT(R_MakeExternalPtr(handle, R_NilValue, R_NilValue));
-    R_RegisterCFinalizerEx(ret, _BoosterFinalizer, TRUE);
-    UNPROTECT(1);
-    return ret;
-  }
-  void XGBoosterSetParam_R(SEXP handle, SEXP name, SEXP val) {
-    XGBoosterSetParam(R_ExternalPtrAddr(handle),
-                      CHAR(asChar(name)),
-                      CHAR(asChar(val)));
-  }
-  void XGBoosterUpdateOneIter_R(SEXP handle, SEXP iter, SEXP dtrain) {
-    XGBoosterUpdateOneIter(R_ExternalPtrAddr(handle),
-                           asInteger(iter),
-                           R_ExternalPtrAddr(dtrain));
-  }
-  void XGBoosterBoostOneIter_R(SEXP handle, SEXP dtrain, SEXP grad, SEXP hess) {
-    utils::Check(length(grad) == length(hess), "gradient and hess must have same length");
-    int len = length(grad);
-    std::vector<float> tgrad(len), thess(len);
-    #pragma omp parallel for schedule(static)
-    for (int j = 0; j < len; ++j) {
-      tgrad[j] = REAL(grad)[j];
-      thess[j] = REAL(hess)[j];
-    }
-    XGBoosterBoostOneIter(R_ExternalPtrAddr(handle),
-                          R_ExternalPtrAddr(dtrain),
-                          &tgrad[0], &thess[0], len);
-  }
-  SEXP XGBoosterEvalOneIter_R(SEXP handle, SEXP iter, SEXP dmats, SEXP evnames) {
-    utils::Check(length(dmats) == length(evnames), "dmats and evnams must have same length");
-    int len = length(dmats);
-    std::vector<void*> vec_dmats;
-    std::vector<std::string> vec_names;
-    std::vector<const char*> vec_sptr;
-    for (int i = 0; i < len; ++i) {
-      vec_dmats.push_back(R_ExternalPtrAddr(VECTOR_ELT(dmats, i)));
-      vec_names.push_back(std::string(CHAR(asChar(VECTOR_ELT(evnames, i)))));
-    }
-    for (int i = 0; i < len; ++i) {
-      vec_sptr.push_back(vec_names[i].c_str());
-    }
-    return mkString(XGBoosterEvalOneIter(R_ExternalPtrAddr(handle),
-                                         asInteger(iter),
-                                         &vec_dmats[0], &vec_sptr[0], len));
-  }
-  SEXP XGBoosterPredict_R(SEXP handle, SEXP dmat, SEXP output_margin) {
-    bst_ulong olen;
-    const float *res = XGBoosterPredict(R_ExternalPtrAddr(handle),
-                                        R_ExternalPtrAddr(dmat),
-                                        asInteger(output_margin),
-                                        &olen);
-    SEXP ret = PROTECT(allocVector(REALSXP, olen));
-    for (size_t i = 0; i < olen; ++i) {
-      REAL(ret)[i] = res[i];
-    }
-    UNPROTECT(1);
-    return ret;
-  }
-  void XGBoosterLoadModel_R(SEXP handle, SEXP fname) {
-    XGBoosterLoadModel(R_ExternalPtrAddr(handle), CHAR(asChar(fname)));
-  }
-  void XGBoosterSaveModel_R(SEXP handle, SEXP fname) {
-    XGBoosterSaveModel(R_ExternalPtrAddr(handle), CHAR(asChar(fname)));
-  }
-  void XGBoosterDumpModel_R(SEXP handle, SEXP fname, SEXP fmap) {
-    bst_ulong olen;
-    const char **res = XGBoosterDumpModel(R_ExternalPtrAddr(handle),
-                                          CHAR(asChar(fmap)),
-                                          &olen);
-    FILE *fo = utils::FopenCheck(CHAR(asChar(fname)), "w");
-    for (size_t i = 0; i < olen; ++i) {
-      fprintf(fo, "booster[%u]:\n", static_cast<unsigned>(i));
-      fprintf(fo, "%s", res[i]);
-    }
-    fclose(fo);
-  }
-}
diff --git a/R-package/src-i386/xgboost_R.h b/R-package/src-i386/xgboost_R.h
deleted file mode 100644
index 8e8b2728b..000000000
--- a/R-package/src-i386/xgboost_R.h
+++ /dev/null
@@ -1,124 +0,0 @@
-#ifndef XGBOOST_WRAPPER_R_H_
-#define XGBOOST_WRAPPER_R_H_
-/*!
- * \file xgboost_wrapper_R.h
- * \author Tianqi Chen
- * \brief R wrapper of xgboost
- */
-extern "C" {
-#include <Rinternals.h>
-}
-
-extern "C" {
-  /*!
-   * \brief load a data matrix 
-   * \param fname name of the content
-   * \param silent whether print messages
-   * \return a loaded data matrix
-   */
-  SEXP XGDMatrixCreateFromFile_R(SEXP fname, SEXP silent);
-  /*!
-   * \brief create matrix content from dense matrix
-   * This assumes the matrix is stored in column major format
-   * \param data R Matrix object
-   * \param missing which value to represent missing value
-   * \return created dmatrix
-   */
-  SEXP XGDMatrixCreateFromMat_R(SEXP mat, 
-                                SEXP missing);
-  /*! 
-   * \brief create a matrix content from CSC format
-   * \param indptr pointer to column headers
-   * \param indices row indices
-   * \param data content of the data
-   * \return created dmatrix
-   */
-  SEXP XGDMatrixCreateFromCSC_R(SEXP indptr,
-                                SEXP indices,
-                                SEXP data);
-  /*!
-   * \brief load a data matrix into binary file
-   * \param handle a instance of data matrix
-   * \param fname file name
-   * \param silent print statistics when saving
-   */
-  void XGDMatrixSaveBinary_R(SEXP handle, SEXP fname, SEXP silent);
-  /*!
-   * \brief set information to dmatrix
-   * \param handle a instance of data matrix
-   * \param field field name, can be label, weight
-   * \param array pointer to float vector
-   */
-  void XGDMatrixSetInfo_R(SEXP handle, SEXP field, SEXP array);
-  /*!
-   * \brief get info vector from matrix
-   * \param handle a instance of data matrix
-   * \param field field name
-   * \return info vector
-   */  
-  SEXP XGDMatrixGetInfo_R(SEXP handle, SEXP field);
-  /*! 
-   * \brief create xgboost learner 
-   * \param dmats a list of dmatrix handles that will be cached
-   */  
-  SEXP XGBoosterCreate_R(SEXP dmats);
-  /*! 
-   * \brief set parameters 
-   * \param handle handle
-   * \param name  parameter name
-   * \param val value of parameter
-   */
-  void XGBoosterSetParam_R(SEXP handle, SEXP name, SEXP val);
-  /*! 
-   * \brief update the model in one round using dtrain
-   * \param handle handle
-   * \param iter current iteration rounds
-   * \param dtrain training data
-   */
-  void XGBoosterUpdateOneIter_R(SEXP ext, SEXP iter, SEXP dtrain);
-  /*!
-   * \brief update the model, by directly specify gradient and second order gradient,
-   *        this can be used to replace UpdateOneIter, to support customized loss function
-   * \param handle handle
-   * \param dtrain training data
-   * \param grad gradient statistics
-   * \param hess second order gradient statistics
-   */
-  void XGBoosterBoostOneIter_R(SEXP handle, SEXP dtrain, SEXP grad, SEXP hess);
-  /*!
-   * \brief get evaluation statistics for xgboost
-   * \param handle handle
-   * \param iter current iteration rounds
-   * \param dmats list of handles to dmatrices
-   * \param evname name of evaluation
-   * \return the string containing evaluation stati
-   */
-  SEXP XGBoosterEvalOneIter_R(SEXP handle, SEXP iter, SEXP dmats, SEXP evnames);
-  /*!
-   * \brief make prediction based on dmat
-   * \param handle handle
-   * \param dmat data matrix
-   * \param output_margin whether only output raw margin value
-   */
-  SEXP XGBoosterPredict_R(SEXP handle, SEXP dmat, SEXP output_margin);
-  /*!
-   * \brief load model from existing file
-   * \param handle handle
-   * \param fname file name
-   */
-  void XGBoosterLoadModel_R(SEXP handle, SEXP fname);
-  /*!
-   * \brief save model into existing file
-   * \param handle handle
-   * \param fname file name
-   */    
-  void XGBoosterSaveModel_R(SEXP handle, SEXP fname);
-  /*!
-   * \brief dump model into text file 
-   * \param handle handle
-   * \param fname file name of model that can be dumped into
-   * \param fmap  name to fmap can be empty string
-   */
-  void XGBoosterDumpModel_R(SEXP handle, SEXP fname, SEXP fmap);
-};
-#endif  // XGBOOST_WRAPPER_R_H_
diff --git a/R-package/src-x64/Makevars b/R-package/src-x64/Makevars
deleted file mode 100644
index 10b2661d0..000000000
--- a/R-package/src-x64/Makevars
+++ /dev/null
@@ -1,28 +0,0 @@
-# _*_ mode: Makefile; _*_
-export CC  = gcc
-export CXX = g++
-
-# expose these flags to R CMD SHLIB
-PKG_CPPFLAGS = -O3 -Wno-unknown-pragmas  -DXGBOOST_CUSTOMIZE_ERROR_  -fPIC  $(SHLIB_OPENMP_CFLAGS)
-PKG_LIBS = $(SHLIB_OPENMP_CFLAGS)
-
-ifeq ($(no_omp),1)
-	PKG_CPPFLAGS += -DDISABLE_OPENMP 
-endif
-
-CXXOBJ= xgboost_wrapper.o xgboost_io.o
-OBJECTS= xgboost_R.o $(CXXOBJ)
-
-.PHONY: all clean
-all: $(SHLIB)
-$(SHLIB): $(OBJECTS)
-
-xgboost_wrapper.o: ../../wrapper/xgboost_wrapper.cpp
-xgboost_io.o: ../../src/io/io.cpp
-
-$(CXXOBJ) : 
-	$(CXX) -c $(PKG_CPPFLAGS) -o $@ $(firstword $(filter %.cpp %.c, $^) )
-
-clean:
-	rm -rf *.so *.o *~ *.dll
-
diff --git a/R-package/src-x64/Makevars.win b/R-package/src-x64/Makevars.win
deleted file mode 100644
index 5d2261230..000000000
--- a/R-package/src-x64/Makevars.win
+++ /dev/null
@@ -1,32 +0,0 @@
-# _*_ mode: Makefile; _*_
-export CC  = gcc
-export CXX = g++
-
-# expose these flags to R CMD SHLIB
-PKG_CPPFLAGS = -O3 -Wno-unknown-pragmas  -DXGBOOST_CUSTOMIZE_ERROR_ -fopenmp -fPIC  $(SHLIB_OPENMP_CFLAGS)
-PKG_LIBS = $(SHLIB_OPENMP_CFLAGS)
-
-# add flag to build native code even in cross compiler
-ifeq "$(WIN)" "64"
-	PKG_CPPFLAGS += -m64
-endif
-
-ifeq ($(no_omp),1)
-	PKG_CPPFLAGS += -DDISABLE_OPENMP 
-endif
-
-CXXOBJ= xgboost_wrapper.o xgboost_io.o
-OBJECTS= xgboost_R.o $(CXXOBJ)
-
-.PHONY: all clean
-all: $(SHLIB)
-$(SHLIB): $(OBJECTS)
-
-xgboost_wrapper.o: ../../wrapper/xgboost_wrapper.cpp
-xgboost_io.o: ../../src/io/io.cpp
-
-$(CXXOBJ) : 
-	$(CXX) -c $(PKG_CPPFLAGS) -o $@ $(firstword $(filter %.cpp %.c, $^) )
-
-clean:
-	rm -rf *.so *.o *~ *.dll
diff --git a/R-package/src-x64/xgboost_R.cpp b/R-package/src-x64/xgboost_R.cpp
deleted file mode 100644
index 1ca232509..000000000
--- a/R-package/src-x64/xgboost_R.cpp
+++ /dev/null
@@ -1,221 +0,0 @@
-#include <vector>
-#include <string>
-#include <utility>
-#include <cstring>
-#include "xgboost_R.h"
-#include "../../wrapper/xgboost_wrapper.h"
-#include "../../src/utils/utils.h"
-#include "../../src/utils/omp.h"
-#include "../../src/utils/matrix_csr.h"
-
-using namespace xgboost;
-// implements error handling
-namespace xgboost {
-namespace utils {
-void HandleAssertError(const char *msg) {
-  error("%s", msg);
-}
-void HandleCheckError(const char *msg) {
-  error("%s", msg);
-}
-}  // namespace utils
-}  // namespace xgboost
-
-extern "C" {
-  void _DMatrixFinalizer(SEXP ext) {    
-    if (R_ExternalPtrAddr(ext) == NULL) return;
-    XGDMatrixFree(R_ExternalPtrAddr(ext));
-    R_ClearExternalPtr(ext);
-  }
-  SEXP XGDMatrixCreateFromFile_R(SEXP fname, SEXP silent) {
-    void *handle = XGDMatrixCreateFromFile(CHAR(asChar(fname)), asInteger(silent));
-    SEXP ret = PROTECT(R_MakeExternalPtr(handle, R_NilValue, R_NilValue));
-    R_RegisterCFinalizerEx(ret, _DMatrixFinalizer, TRUE);
-    UNPROTECT(1);
-    return ret;
-  }
-  SEXP XGDMatrixCreateFromMat_R(SEXP mat, 
-                                SEXP missing) {
-    SEXP dim = getAttrib(mat, R_DimSymbol);
-    int nrow = INTEGER(dim)[0];
-    int ncol = INTEGER(dim)[1];    
-    double *din = REAL(mat);
-    std::vector<float> data(nrow * ncol);
-    #pragma omp parallel for schedule(static)
-    for (int i = 0; i < nrow; ++i) {
-      for (int j = 0; j < ncol; ++j) {
-        data[i * ncol +j] = din[i + nrow * j];
-      }
-    }
-    void *handle = XGDMatrixCreateFromMat(&data[0], nrow, ncol, asReal(missing));
-    SEXP ret = PROTECT(R_MakeExternalPtr(handle, R_NilValue, R_NilValue));
-    R_RegisterCFinalizerEx(ret, _DMatrixFinalizer, TRUE);
-    UNPROTECT(1);
-    return ret;    
-  }
-  SEXP XGDMatrixCreateFromCSC_R(SEXP indptr,
-                                SEXP indices,
-                                SEXP data) {
-    const int *col_ptr = INTEGER(indptr);
-    const int *row_index = INTEGER(indices);
-    const double *col_data = REAL(data);
-    int ncol = length(indptr) - 1;
-    int ndata = length(data);
-    // transform into CSR format
-    std::vector<bst_ulong> row_ptr;
-    std::vector< std::pair<unsigned, float> > csr_data;
-    utils::SparseCSRMBuilder<std::pair<unsigned,float>, false, bst_ulong> builder(row_ptr, csr_data);
-    builder.InitBudget();
-    for (int i = 0; i < ncol; ++i) {
-      for (int j = col_ptr[i]; j < col_ptr[i+1]; ++j) {
-        builder.AddBudget(row_index[j]);
-      }
-    }
-    builder.InitStorage();
-    for (int i = 0; i < ncol; ++i) {
-      for (int j = col_ptr[i]; j < col_ptr[i+1]; ++j) {
-        builder.PushElem(row_index[j], std::make_pair(i, col_data[j]));
-      }
-    }
-    utils::Assert(csr_data.size() == static_cast<size_t>(ndata), "BUG CreateFromCSC");
-    std::vector<float> row_data(ndata);
-    std::vector<unsigned> col_index(ndata);
-    #pragma omp parallel for schedule(static)
-    for (int i = 0; i < ndata; ++i) {
-      col_index[i] = csr_data[i].first;
-      row_data[i] = csr_data[i].second;      
-    }
-    void *handle = XGDMatrixCreateFromCSR(&row_ptr[0], &col_index[0], &row_data[0], row_ptr.size(), ndata );
-    SEXP ret = PROTECT(R_MakeExternalPtr(handle, R_NilValue, R_NilValue));
-    R_RegisterCFinalizerEx(ret, _DMatrixFinalizer, TRUE);
-    UNPROTECT(1);
-    return ret;
-  }
-  void XGDMatrixSaveBinary_R(SEXP handle, SEXP fname, SEXP silent) {
-    XGDMatrixSaveBinary(R_ExternalPtrAddr(handle),
-                        CHAR(asChar(fname)), asInteger(silent));
-  }
-  void XGDMatrixSetInfo_R(SEXP handle, SEXP field, SEXP array) {
-    int len = length(array);
-    const char *name = CHAR(asChar(field));
-    if (!strcmp("group", name)) {
-      std::vector<unsigned> vec(len);
-      #pragma omp parallel for schedule(static)      
-      for (int i = 0; i < len; ++i) {
-        vec[i] = static_cast<unsigned>(INTEGER(array)[i]);
-      }
-      XGDMatrixSetGroup(R_ExternalPtrAddr(handle), &vec[0], len);
-      return;
-    }
-    {
-      std::vector<float> vec(len);
-      #pragma omp parallel for schedule(static)
-      for (int i = 0; i < len; ++i) {
-        vec[i] = REAL(array)[i];
-      }
-      XGDMatrixSetFloatInfo(R_ExternalPtrAddr(handle), 
-                            CHAR(asChar(field)),
-                            &vec[0], len);
-    }
-  }
-  SEXP XGDMatrixGetInfo_R(SEXP handle, SEXP field) {
-    bst_ulong olen;
-    const float *res = XGDMatrixGetFloatInfo(R_ExternalPtrAddr(handle),
-                                             CHAR(asChar(field)), &olen);
-    SEXP ret = PROTECT(allocVector(REALSXP, olen));
-    for (size_t i = 0; i < olen; ++i) {
-      REAL(ret)[i] = res[i];
-    }
-    UNPROTECT(1);
-    return ret;
-  }
-  // functions related to booster
-  void _BoosterFinalizer(SEXP ext) {    
-    if (R_ExternalPtrAddr(ext) == NULL) return;
-    XGBoosterFree(R_ExternalPtrAddr(ext));
-    R_ClearExternalPtr(ext);
-  }
-  SEXP XGBoosterCreate_R(SEXP dmats) {
-    int len = length(dmats);
-    std::vector<void*> dvec;
-    for (int i = 0; i < len; ++i){
-      dvec.push_back(R_ExternalPtrAddr(VECTOR_ELT(dmats, i)));
-    }
-    void *handle = XGBoosterCreate(&dvec[0], dvec.size());
-    SEXP ret = PROTECT(R_MakeExternalPtr(handle, R_NilValue, R_NilValue));
-    R_RegisterCFinalizerEx(ret, _BoosterFinalizer, TRUE);
-    UNPROTECT(1);
-    return ret;
-  }
-  void XGBoosterSetParam_R(SEXP handle, SEXP name, SEXP val) {
-    XGBoosterSetParam(R_ExternalPtrAddr(handle),
-                      CHAR(asChar(name)),
-                      CHAR(asChar(val)));
-  }
-  void XGBoosterUpdateOneIter_R(SEXP handle, SEXP iter, SEXP dtrain) {
-    XGBoosterUpdateOneIter(R_ExternalPtrAddr(handle),
-                           asInteger(iter),
-                           R_ExternalPtrAddr(dtrain));
-  }
-  void XGBoosterBoostOneIter_R(SEXP handle, SEXP dtrain, SEXP grad, SEXP hess) {
-    utils::Check(length(grad) == length(hess), "gradient and hess must have same length");
-    int len = length(grad);
-    std::vector<float> tgrad(len), thess(len);
-    #pragma omp parallel for schedule(static)
-    for (int j = 0; j < len; ++j) {
-      tgrad[j] = REAL(grad)[j];
-      thess[j] = REAL(hess)[j];
-    }
-    XGBoosterBoostOneIter(R_ExternalPtrAddr(handle),
-                          R_ExternalPtrAddr(dtrain),
-                          &tgrad[0], &thess[0], len);
-  }
-  SEXP XGBoosterEvalOneIter_R(SEXP handle, SEXP iter, SEXP dmats, SEXP evnames) {
-    utils::Check(length(dmats) == length(evnames), "dmats and evnams must have same length");
-    int len = length(dmats);
-    std::vector<void*> vec_dmats;
-    std::vector<std::string> vec_names;
-    std::vector<const char*> vec_sptr;
-    for (int i = 0; i < len; ++i) {
-      vec_dmats.push_back(R_ExternalPtrAddr(VECTOR_ELT(dmats, i)));
-      vec_names.push_back(std::string(CHAR(asChar(VECTOR_ELT(evnames, i)))));
-    }
-    for (int i = 0; i < len; ++i) {
-      vec_sptr.push_back(vec_names[i].c_str());
-    }
-    return mkString(XGBoosterEvalOneIter(R_ExternalPtrAddr(handle),
-                                         asInteger(iter),
-                                         &vec_dmats[0], &vec_sptr[0], len));
-  }
-  SEXP XGBoosterPredict_R(SEXP handle, SEXP dmat, SEXP output_margin) {
-    bst_ulong olen;
-    const float *res = XGBoosterPredict(R_ExternalPtrAddr(handle),
-                                        R_ExternalPtrAddr(dmat),
-                                        asInteger(output_margin),
-                                        &olen);
-    SEXP ret = PROTECT(allocVector(REALSXP, olen));
-    for (size_t i = 0; i < olen; ++i) {
-      REAL(ret)[i] = res[i];
-    }
-    UNPROTECT(1);
-    return ret;
-  }
-  void XGBoosterLoadModel_R(SEXP handle, SEXP fname) {
-    XGBoosterLoadModel(R_ExternalPtrAddr(handle), CHAR(asChar(fname)));
-  }
-  void XGBoosterSaveModel_R(SEXP handle, SEXP fname) {
-    XGBoosterSaveModel(R_ExternalPtrAddr(handle), CHAR(asChar(fname)));
-  }
-  void XGBoosterDumpModel_R(SEXP handle, SEXP fname, SEXP fmap) {
-    bst_ulong olen;
-    const char **res = XGBoosterDumpModel(R_ExternalPtrAddr(handle),
-                                          CHAR(asChar(fmap)),
-                                          &olen);
-    FILE *fo = utils::FopenCheck(CHAR(asChar(fname)), "w");
-    for (size_t i = 0; i < olen; ++i) {
-      fprintf(fo, "booster[%u]:\n", static_cast<unsigned>(i));
-      fprintf(fo, "%s", res[i]);
-    }
-    fclose(fo);
-  }
-}
diff --git a/R-package/src-x64/xgboost_R.h b/R-package/src-x64/xgboost_R.h
deleted file mode 100644
index 8e8b2728b..000000000
--- a/R-package/src-x64/xgboost_R.h
+++ /dev/null
@@ -1,124 +0,0 @@
-#ifndef XGBOOST_WRAPPER_R_H_
-#define XGBOOST_WRAPPER_R_H_
-/*!
- * \file xgboost_wrapper_R.h
- * \author Tianqi Chen
- * \brief R wrapper of xgboost
- */
-extern "C" {
-#include <Rinternals.h>
-}
-
-extern "C" {
-  /*!
-   * \brief load a data matrix 
-   * \param fname name of the content
-   * \param silent whether print messages
-   * \return a loaded data matrix
-   */
-  SEXP XGDMatrixCreateFromFile_R(SEXP fname, SEXP silent);
-  /*!
-   * \brief create matrix content from dense matrix
-   * This assumes the matrix is stored in column major format
-   * \param data R Matrix object
-   * \param missing which value to represent missing value
-   * \return created dmatrix
-   */
-  SEXP XGDMatrixCreateFromMat_R(SEXP mat, 
-                                SEXP missing);
-  /*! 
-   * \brief create a matrix content from CSC format
-   * \param indptr pointer to column headers
-   * \param indices row indices
-   * \param data content of the data
-   * \return created dmatrix
-   */
-  SEXP XGDMatrixCreateFromCSC_R(SEXP indptr,
-                                SEXP indices,
-                                SEXP data);
-  /*!
-   * \brief load a data matrix into binary file
-   * \param handle a instance of data matrix
-   * \param fname file name
-   * \param silent print statistics when saving
-   */
-  void XGDMatrixSaveBinary_R(SEXP handle, SEXP fname, SEXP silent);
-  /*!
-   * \brief set information to dmatrix
-   * \param handle a instance of data matrix
-   * \param field field name, can be label, weight
-   * \param array pointer to float vector
-   */
-  void XGDMatrixSetInfo_R(SEXP handle, SEXP field, SEXP array);
-  /*!
-   * \brief get info vector from matrix
-   * \param handle a instance of data matrix
-   * \param field field name
-   * \return info vector
-   */  
-  SEXP XGDMatrixGetInfo_R(SEXP handle, SEXP field);
-  /*! 
-   * \brief create xgboost learner 
-   * \param dmats a list of dmatrix handles that will be cached
-   */  
-  SEXP XGBoosterCreate_R(SEXP dmats);
-  /*! 
-   * \brief set parameters 
-   * \param handle handle
-   * \param name  parameter name
-   * \param val value of parameter
-   */
-  void XGBoosterSetParam_R(SEXP handle, SEXP name, SEXP val);
-  /*! 
-   * \brief update the model in one round using dtrain
-   * \param handle handle
-   * \param iter current iteration rounds
-   * \param dtrain training data
-   */
-  void XGBoosterUpdateOneIter_R(SEXP ext, SEXP iter, SEXP dtrain);
-  /*!
-   * \brief update the model, by directly specify gradient and second order gradient,
-   *        this can be used to replace UpdateOneIter, to support customized loss function
-   * \param handle handle
-   * \param dtrain training data
-   * \param grad gradient statistics
-   * \param hess second order gradient statistics
-   */
-  void XGBoosterBoostOneIter_R(SEXP handle, SEXP dtrain, SEXP grad, SEXP hess);
-  /*!
-   * \brief get evaluation statistics for xgboost
-   * \param handle handle
-   * \param iter current iteration rounds
-   * \param dmats list of handles to dmatrices
-   * \param evname name of evaluation
-   * \return the string containing evaluation stati
-   */
-  SEXP XGBoosterEvalOneIter_R(SEXP handle, SEXP iter, SEXP dmats, SEXP evnames);
-  /*!
-   * \brief make prediction based on dmat
-   * \param handle handle
-   * \param dmat data matrix
-   * \param output_margin whether only output raw margin value
-   */
-  SEXP XGBoosterPredict_R(SEXP handle, SEXP dmat, SEXP output_margin);
-  /*!
-   * \brief load model from existing file
-   * \param handle handle
-   * \param fname file name
-   */
-  void XGBoosterLoadModel_R(SEXP handle, SEXP fname);
-  /*!
-   * \brief save model into existing file
-   * \param handle handle
-   * \param fname file name
-   */    
-  void XGBoosterSaveModel_R(SEXP handle, SEXP fname);
-  /*!
-   * \brief dump model into text file 
-   * \param handle handle
-   * \param fname file name of model that can be dumped into
-   * \param fmap  name to fmap can be empty string
-   */
-  void XGBoosterDumpModel_R(SEXP handle, SEXP fname, SEXP fmap);
-};
-#endif  // XGBOOST_WRAPPER_R_H_