[R] enable R compile

[R] Enable R build for windows and linux

Makefile

@@ -55,7 +55,7 @@ else
 endif
 
 # specify tensor path
-.PHONY: clean all lint clean_all
+.PHONY: clean all lint clean_all rcpplint Rpack Rbuild Rcheck
 
 all: lib/libxgboost.a lib/libxgboost.so xgboost
 
@@ -98,15 +98,50 @@ lib/libxgboost.so: $(ALL_DEP)
 xgboost: $(CLI_OBJ) lib/libxgboost.a $(LIB_DEP)
 	$(CXX) $(CFLAGS) -o $@  $(filter %.o %.a, $^)  $(LDFLAGS)
 
-lint:
+rcpplint:
+	python2 dmlc-core/scripts/lint.py xgboost ${LINT_LANG} R-package/src
+
+lint: rcpplint
 	python2 dmlc-core/scripts/lint.py xgboost ${LINT_LANG} include src
 
 clean:
-	$(RM) -rf build lib bin *~ */*~ */*/*~ */*/*/*~ $(AMALGA_OBJ) xgboost
+	$(RM) -rf build lib bin *~ */*~ */*/*~ */*/*/*~ amalgamation/*.o xgboost
 
 clean_all: clean
 	cd $(DMLC_CORE); make clean; cd -
 	cd $(RABIT); make clean; cd -
 
+# Script to make a clean installable R package.
+Rpack:
+	make clean_all
+	rm -rf xgboost xgboost*.tar.gz
+	cp -r R-package xgboost
+	rm -rf xgboost/src/*.o xgboost/src/*.so xgboost/src/*.dll
+	rm -rf xgboost/src/*/*.o
+	rm -rf xgboost/demo/*.model xgboost/demo/*.buffer xgboost/demo/*.txt
+	rm -rf xgboost/demo/runall.R
+	cp -r src xgboost/src/src
+	cp -r include xgboost/src/include
+	cp -r amalgamation xgboost/src/amalgamation
+	mkdir -p xgboost/src/rabit
+	cp -r rabit/include xgboost/src/rabit/include
+	cp -r rabit/src xgboost/src/rabit/src
+	rm -rf xgboost/src/rabit/src/*.o
+	mkdir -p xgboost/src/dmlc-core
+	cp -r dmlc-core/include xgboost/src/dmlc-core/include
+	cp -r dmlc-core/src xgboost/src/dmlc-core/src
+	cp ./LICENSE xgboost
+	cat R-package/src/Makevars|sed '2s/.*/PKGROOT=./' | sed '3s/.*/ENABLE_STD_THREAD=0/' > xgboost/src/Makevars
+	cp xgboost/src/Makevars xgboost/src/Makevars.win
+
+Rbuild:
+	make Rpack
+	R CMD build --no-build-vignettes xgboost
+	rm -rf xgboost
+
+Rcheck:
+	make Rbuild
+	R CMD check  xgboost*.tar.gz
+
 -include build/*.d
 -include build/*/*.d

R-package/src/Makevars

@@ -1,8 +1,10 @@
 # package root
 PKGROOT=../../
+ENABLE_STD_THREAD=1
 # _*_ mode: Makefile; _*_
-PKG_CPPFLAGS= -DXGBOOST_CUSTOMIZE_MSG_ -DXGBOOST_CUSTOMIZE_PRNG_ -DXGBOOST_STRICT_CXX98_ -DRABIT_CUSTOMIZE_MSG_ -DRABIT_STRICT_CXX98_ -I$(PKGROOT)
+CXX_STD = CXX11
+XGB_RFLAGS = -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=$(ENABLE_STD_THREAD)
+PKG_CPPFLAGS=  -I$(PKGROOT)/include -I$(PKGROOT)/dmlc-core/include -I$(PKGROOT)/rabit/include $(XGB_RFLAGS)
 PKG_CXXFLAGS= $(SHLIB_OPENMP_CFLAGS) $(SHLIB_PTHREAD_FLAGS)
 PKG_LIBS = $(SHLIB_OPENMP_CFLAGS) $(SHLIB_PTHREAD_FLAGS)
-OBJECTS= xgboost_R.o xgboost_assert.o $(PKGROOT)/wrapper/xgboost_wrapper.o $(PKGROOT)/src/io/io.o $(PKGROOT)/src/gbm/gbm.o $(PKGROOT)/src/tree/updater.o $(PKGROOT)/subtree/rabit/src/engine_empty.o $(PKGROOT)/src/io/dmlc_simple.o
+OBJECTS= ./xgboost_R.o $(PKGROOT)/amalgamation/xgboost-all0.o $(PKGROOT)/amalgamation/dmlc-minimum0.o $(PKGROOT)/rabit/src/engine_empty.o
-

R-package/src/Makevars.win

@@ -1,5 +1,6 @@
 # package root
 PKGROOT=./
+ENABLE_STD_THREAD=0
 # _*_ mode: Makefile; _*_
 
 # This file is only used for windows compilation from github
@@ -9,11 +10,16 @@ all: $(SHLIB)
 $(SHLIB): xgblib
 xgblib:
 	cp -r ../../src .
-	cp -r ../../wrapper .
+	cp -r ../../rabit .
-	cp -r ../../subtree .
+	cp -r ../../dmlc-core .
+	cp -r ../../include .
+	cp -r ../../amalgamation .
 
-PKG_CPPFLAGS= -DXGBOOST_CUSTOMIZE_MSG_ -DXGBOOST_CUSTOMIZE_PRNG_ -DXGBOOST_STRICT_CXX98_ -DRABIT_CUSTOMIZE_MSG_ -DRABIT_STRICT_CXX98_ -I$(PKGROOT) -I../..
+CXX_STD = CXX11
+XGB_RFLAGS = -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=$(ENABLE_STD_THREAD)
+PKG_CPPFLAGS=  -I$(PKGROOT)/include -I$(PKGROOT)/dmlc-core/include -I$(PKGROOT)/rabit/include $(XGB_RFLAGS)
 PKG_CXXFLAGS= $(SHLIB_OPENMP_CFLAGS) $(SHLIB_PTHREAD_FLAGS)
 PKG_LIBS = $(SHLIB_OPENMP_CFLAGS) $(SHLIB_PTHREAD_FLAGS)
-OBJECTS= xgboost_R.o xgboost_assert.o $(PKGROOT)/wrapper/xgboost_wrapper.o $(PKGROOT)/src/io/io.o $(PKGROOT)/src/gbm/gbm.o $(PKGROOT)/src/tree/updater.o $(PKGROOT)/subtree/rabit/src/engine_empty.o $(PKGROOT)/src/io/dmlc_simple.o
+OBJECTS=  ./xgboost_R.o $(PKGROOT)/amalgamation/xgboost-all0.o $(PKGROOT)/amalgamation/dmlc-minimum0.o $(PKGROOT)/rabit/src/engine_empty.o
+
 $(OBJECTS) : xgblib

R-package/src/xgboost_R.cc

@@ -0,0 +1,364 @@
+// Copyright (c) 2014 by Contributors
+#include <dmlc/logging.h>
+#include <dmlc/omp.h>
+#include <xgboost/c_api.h>
+#include <vector>
+#include <string>
+#include <utility>
+#include <cstring>
+#include <cstdio>
+#include <sstream>
+#include "./xgboost_R.h"
+
+/*!
+ * \brief macro to annotate begin of api
+ */
+#define R_API_BEGIN()                           \
+  GetRNGstate();                                \
+  try {
+/*!
+ * \brief macro to annotate end of api
+ */
+#define R_API_END()                             \
+  } catch(dmlc::Error& e) {                     \
+    PutRNGstate();                              \
+    error(e.what());                            \
+  }                                             \
+  PutRNGstate();
+
+/*!
+ * \brief macro to check the call.
+ */
+#define CHECK_CALL(x)                           \
+  if ((x) != 0) {                               \
+    error(XGBGetLastError());                   \
+  }
+
+namespace xgboost {
+namespace common {
+bool CheckNAN(double v) {
+  return ISNAN(v);
+}
+double LogGamma(double v) {
+  return lgammafn(v);
+}
+}  // namespace common
+}  // namespace xgboost
+
+using namespace dmlc;
+
+SEXP XGCheckNullPtr_R(SEXP handle) {
+  return ScalarLogical(R_ExternalPtrAddr(handle) == NULL);
+}
+
+void _DMatrixFinalizer(SEXP ext) {
+  R_API_BEGIN();
+  if (R_ExternalPtrAddr(ext) == NULL) return;
+  CHECK_CALL(XGDMatrixFree(R_ExternalPtrAddr(ext)));
+  R_ClearExternalPtr(ext);
+  R_API_END();
+}
+
+SEXP XGDMatrixCreateFromFile_R(SEXP fname, SEXP silent) {
+  SEXP ret;
+  R_API_BEGIN();
+  DMatrixHandle handle;
+  CHECK_CALL(XGDMatrixCreateFromFile(CHAR(asChar(fname)), asInteger(silent), &handle));
+  ret = PROTECT(R_MakeExternalPtr(handle, R_NilValue, R_NilValue));
+  R_RegisterCFinalizerEx(ret, _DMatrixFinalizer, TRUE);
+  UNPROTECT(1);
+  R_API_END();
+  return ret;
+}
+
+SEXP XGDMatrixCreateFromMat_R(SEXP mat,
+                              SEXP missing) {
+  SEXP ret;
+  R_API_BEGIN();
+  SEXP dim = getAttrib(mat, R_DimSymbol);
+  size_t nrow = static_cast<size_t>(INTEGER(dim)[0]);
+  size_t ncol = static_cast<size_t>(INTEGER(dim)[1]);
+  double *din = REAL(mat);
+  std::vector<float> data(nrow * ncol);
+  #pragma omp parallel for schedule(static)
+  for (omp_ulong i = 0; i < nrow; ++i) {
+    for (size_t j = 0; j < ncol; ++j) {
+      data[i * ncol +j] = din[i + nrow * j];
+    }
+  }
+  DMatrixHandle handle;
+  CHECK_CALL(XGDMatrixCreateFromMat(BeginPtr(data), nrow, ncol, asReal(missing), &handle));
+  ret = PROTECT(R_MakeExternalPtr(handle, R_NilValue, R_NilValue));
+  R_RegisterCFinalizerEx(ret, _DMatrixFinalizer, TRUE);
+  UNPROTECT(1);
+  R_API_END();
+  return ret;
+}
+
+SEXP XGDMatrixCreateFromCSC_R(SEXP indptr,
+                              SEXP indices,
+                              SEXP data) {
+  SEXP ret;
+  R_API_BEGIN();
+  const int *p_indptr = INTEGER(indptr);
+  const int *p_indices = INTEGER(indices);
+  const double *p_data = REAL(data);
+  int nindptr = length(indptr);
+  int ndata = length(data);
+  std::vector<bst_ulong> col_ptr_(nindptr);
+  std::vector<unsigned> indices_(ndata);
+  std::vector<float> data_(ndata);
+
+  for (int i = 0; i < nindptr; ++i) {
+    col_ptr_[i] = static_cast<bst_ulong>(p_indptr[i]);
+  }
+  #pragma omp parallel for schedule(static)
+  for (int i = 0; i < ndata; ++i) {
+    indices_[i] = static_cast<unsigned>(p_indices[i]);
+    data_[i] = static_cast<float>(p_data[i]);
+  }
+  DMatrixHandle handle;
+  CHECK_CALL(XGDMatrixCreateFromCSC(BeginPtr(col_ptr_), BeginPtr(indices_),
+                                    BeginPtr(data_), nindptr, ndata,
+                                    &handle));
+  ret = PROTECT(R_MakeExternalPtr(handle, R_NilValue, R_NilValue));
+  R_RegisterCFinalizerEx(ret, _DMatrixFinalizer, TRUE);
+  UNPROTECT(1);
+  R_API_END();
+  return ret;
+}
+
+SEXP XGDMatrixSliceDMatrix_R(SEXP handle, SEXP idxset) {
+  SEXP ret;
+  R_API_BEGIN();
+  int len = length(idxset);
+  std::vector<int> idxvec(len);
+  for (int i = 0; i < len; ++i) {
+    idxvec[i] = INTEGER(idxset)[i] - 1;
+  }
+  DMatrixHandle res;
+  CHECK_CALL(XGDMatrixSliceDMatrix(R_ExternalPtrAddr(handle),
+                                   BeginPtr(idxvec), len,
+                                   &res));
+  ret = PROTECT(R_MakeExternalPtr(res, R_NilValue, R_NilValue));
+  R_RegisterCFinalizerEx(ret, _DMatrixFinalizer, TRUE);
+  UNPROTECT(1);
+  R_API_END();
+  return ret;
+}
+
+void XGDMatrixSaveBinary_R(SEXP handle, SEXP fname, SEXP silent) {
+  R_API_BEGIN();
+  CHECK_CALL(XGDMatrixSaveBinary(R_ExternalPtrAddr(handle),
+                                 CHAR(asChar(fname)),
+                                 asInteger(silent)));
+  R_API_END();
+}
+
+void XGDMatrixSetInfo_R(SEXP handle, SEXP field, SEXP array) {
+  R_API_BEGIN();
+  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]);
+    }
+    CHECK_CALL(XGDMatrixSetGroup(R_ExternalPtrAddr(handle), BeginPtr(vec), len));
+  } else {
+    std::vector<float> vec(len);
+    #pragma omp parallel for schedule(static)
+    for (int i = 0; i < len; ++i) {
+      vec[i] = REAL(array)[i];
+    }
+    CHECK_CALL(XGDMatrixSetFloatInfo(R_ExternalPtrAddr(handle),
+                                   CHAR(asChar(field)),
+                                   BeginPtr(vec), len));
+  }
+  R_API_END();
+}
+
+SEXP XGDMatrixGetInfo_R(SEXP handle, SEXP field) {
+  SEXP ret;
+  R_API_BEGIN();
+  bst_ulong olen;
+  const float *res;
+  CHECK_CALL(XGDMatrixGetFloatInfo(R_ExternalPtrAddr(handle),
+                                   CHAR(asChar(field)),
+                                 &olen,
+                                 &res));
+  ret = PROTECT(allocVector(REALSXP, olen));
+  for (size_t i = 0; i < olen; ++i) {
+    REAL(ret)[i] = res[i];
+  }
+  UNPROTECT(1);
+  R_API_END();
+  return ret;
+}
+
+SEXP XGDMatrixNumRow_R(SEXP handle) {
+  bst_ulong nrow;
+  R_API_BEGIN();
+  CHECK_CALL(XGDMatrixNumRow(R_ExternalPtrAddr(handle), &nrow));
+  R_API_END();
+  return ScalarInteger(static_cast<int>(nrow));
+}
+
+// functions related to booster
+void _BoosterFinalizer(SEXP ext) {
+  if (R_ExternalPtrAddr(ext) == NULL) return;
+  CHECK_CALL(XGBoosterFree(R_ExternalPtrAddr(ext)));
+  R_ClearExternalPtr(ext);
+}
+
+SEXP XGBoosterCreate_R(SEXP dmats) {
+  SEXP ret;
+  R_API_BEGIN();
+  int len = length(dmats);
+  std::vector<void*> dvec;
+  for (int i = 0; i < len; ++i) {
+    dvec.push_back(R_ExternalPtrAddr(VECTOR_ELT(dmats, i)));
+  }
+  BoosterHandle handle;
+  CHECK_CALL(XGBoosterCreate(BeginPtr(dvec), dvec.size(), &handle));
+  ret = PROTECT(R_MakeExternalPtr(handle, R_NilValue, R_NilValue));
+  R_RegisterCFinalizerEx(ret, _BoosterFinalizer, TRUE);
+  UNPROTECT(1);
+  R_API_END();
+  return ret;
+}
+
+void XGBoosterSetParam_R(SEXP handle, SEXP name, SEXP val) {
+  R_API_BEGIN();
+  CHECK_CALL(XGBoosterSetParam(R_ExternalPtrAddr(handle),
+                             CHAR(asChar(name)),
+                             CHAR(asChar(val))));
+  R_API_END();
+}
+
+void XGBoosterUpdateOneIter_R(SEXP handle, SEXP iter, SEXP dtrain) {
+  R_API_BEGIN();
+  CHECK_CALL(XGBoosterUpdateOneIter(R_ExternalPtrAddr(handle),
+                                  asInteger(iter),
+                                  R_ExternalPtrAddr(dtrain)));
+  R_API_END();
+}
+
+void XGBoosterBoostOneIter_R(SEXP handle, SEXP dtrain, SEXP grad, SEXP hess) {
+  R_API_BEGIN();
+  CHECK_EQ(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];
+  }
+  CHECK_CALL(XGBoosterBoostOneIter(R_ExternalPtrAddr(handle),
+                                 R_ExternalPtrAddr(dtrain),
+                                 BeginPtr(tgrad), BeginPtr(thess),
+                                 len));
+  R_API_END();
+}
+
+SEXP XGBoosterEvalOneIter_R(SEXP handle, SEXP iter, SEXP dmats, SEXP evnames) {
+  const char *ret;
+  R_API_BEGIN();
+  CHECK_EQ(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());
+  }
+  CHECK_CALL(XGBoosterEvalOneIter(R_ExternalPtrAddr(handle),
+                                asInteger(iter),
+                                BeginPtr(vec_dmats),
+                                BeginPtr(vec_sptr),
+                                len, &ret));
+  R_API_END();
+  return mkString(ret);
+}
+
+SEXP XGBoosterPredict_R(SEXP handle, SEXP dmat, SEXP option_mask, SEXP ntree_limit) {
+  SEXP ret;
+  R_API_BEGIN();
+  bst_ulong olen;
+  const float *res;
+  CHECK_CALL(XGBoosterPredict(R_ExternalPtrAddr(handle),
+                            R_ExternalPtrAddr(dmat),
+                            asInteger(option_mask),
+                            asInteger(ntree_limit),
+                            &olen, &res));
+  ret = PROTECT(allocVector(REALSXP, olen));
+  for (size_t i = 0; i < olen; ++i) {
+    REAL(ret)[i] = res[i];
+  }
+  UNPROTECT(1);
+  R_API_END();
+  return ret;
+}
+
+void XGBoosterLoadModel_R(SEXP handle, SEXP fname) {
+  R_API_BEGIN();
+  CHECK_CALL(XGBoosterLoadModel(R_ExternalPtrAddr(handle), CHAR(asChar(fname))));
+  R_API_END();
+}
+
+void XGBoosterSaveModel_R(SEXP handle, SEXP fname) {
+  R_API_BEGIN();
+  CHECK_CALL(XGBoosterSaveModel(R_ExternalPtrAddr(handle), CHAR(asChar(fname))));
+  R_API_END();
+}
+
+void XGBoosterLoadModelFromRaw_R(SEXP handle, SEXP raw) {
+  R_API_BEGIN();
+  CHECK_CALL(XGBoosterLoadModelFromBuffer(R_ExternalPtrAddr(handle),
+                                          RAW(raw),
+                                          length(raw)));
+  R_API_END();
+}
+
+SEXP XGBoosterModelToRaw_R(SEXP handle) {
+  SEXP ret;
+  R_API_BEGIN();
+  bst_ulong olen;
+  const char *raw;
+  CHECK_CALL(XGBoosterGetModelRaw(R_ExternalPtrAddr(handle), &olen, &raw));
+  ret = PROTECT(allocVector(RAWSXP, olen));
+  if (olen != 0) {
+    memcpy(RAW(ret), raw, olen);
+  }
+  UNPROTECT(1);
+  R_API_END();
+  return ret;
+}
+
+SEXP XGBoosterDumpModel_R(SEXP handle, SEXP fmap, SEXP with_stats) {
+  SEXP out;
+  R_API_BEGIN();
+  bst_ulong olen;
+  const char **res;
+  CHECK_CALL(XGBoosterDumpModel(R_ExternalPtrAddr(handle),
+                                CHAR(asChar(fmap)),
+                                asInteger(with_stats),
+                                &olen, &res));
+  out = PROTECT(allocVector(STRSXP, olen));
+  for (size_t i = 0; i < olen; ++i) {
+    std::stringstream stream;
+    stream <<  "booster[" << i <<"]\n" << res[i];
+    SET_STRING_ELT(out, i, mkChar(stream.str().c_str()));
+  }
+  UNPROTECT(1);
+  R_API_END();
+  return out;
+}
+

R-package/src/xgboost_R.cpp

@@ -1,344 +0,0 @@
-// Copyright (c) 2014 by Contributors
-#include <vector>
-#include <string>
-#include <utility>
-#include <cstring>
-#include <cstdio>
-#include <sstream>
-#include "wrapper/xgboost_wrapper.h"
-#include "src/utils/utils.h"
-#include "src/utils/omp.h"
-#include "xgboost_R.h"
-
-using namespace std;
-using namespace xgboost;
-
-extern "C" {
-  void XGBoostAssert_R(int exp, const char *fmt, ...);
-  void XGBoostCheck_R(int exp, const char *fmt, ...);
-  int XGBoostSPrintf_R(char *buf, size_t size, const char *fmt, ...);
-}
-
-// implements error handling
-namespace xgboost {
-namespace utils {
-extern "C" {
-  void (*Printf)(const char *fmt, ...) = Rprintf;
-  int (*SPrintf)(char *buf, size_t size, const char *fmt, ...) = XGBoostSPrintf_R;
-  void (*Assert)(int exp, const char *fmt, ...) = XGBoostAssert_R;
-  void (*Check)(int exp, const char *fmt, ...) = XGBoostCheck_R;
-  void (*Error)(const char *fmt, ...) = error;
-}
-bool CheckNAN(double v) {
-  return ISNAN(v);
-}
-double LogGamma(double v) {
-  return lgammafn(v);
-}
-}  // namespace utils
-
-namespace random {
-void Seed(unsigned seed) {
-  //  warning("parameter seed is ignored, please set random seed using set.seed");
-}
-double Uniform(void) {
-  return unif_rand();
-}
-double Normal(void) {
-  return norm_rand();
-}
-}  // namespace random
-}  // namespace xgboost
-
-// call before wrapper starts
-inline void _WrapperBegin(void) {
-  GetRNGstate();
-}
-// call after wrapper starts
-inline void _WrapperEnd(void) {
-  PutRNGstate();
-}
-
-// do nothing, check error
-inline void CheckErr(int ret) {
-}
-
-extern "C" {
-  SEXP XGCheckNullPtr_R(SEXP handle) {
-    return ScalarLogical(R_ExternalPtrAddr(handle) == NULL);
-  }
-  void _DMatrixFinalizer(SEXP ext) {
-    if (R_ExternalPtrAddr(ext) == NULL) return;
-    XGDMatrixFree(R_ExternalPtrAddr(ext));
-    R_ClearExternalPtr(ext);
-  }
-  SEXP XGDMatrixCreateFromFile_R(SEXP fname, SEXP silent) {
-    _WrapperBegin();
-    DMatrixHandle handle;
-    CheckErr(XGDMatrixCreateFromFile(CHAR(asChar(fname)), asInteger(silent), &handle));
-    _WrapperEnd();
-    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) {
-    _WrapperBegin();
-    SEXP dim = getAttrib(mat, R_DimSymbol);
-    size_t nrow = static_cast<size_t>(INTEGER(dim)[0]);
-    size_t ncol = static_cast<size_t>(INTEGER(dim)[1]);
-    double *din = REAL(mat);
-    std::vector<float> data(nrow * ncol);
-    #pragma omp parallel for schedule(static)
-    for (bst_omp_uint i = 0; i < nrow; ++i) {
-      for (size_t j = 0; j < ncol; ++j) {
-        data[i * ncol +j] = din[i + nrow * j];
-      }
-    }
-    DMatrixHandle handle;
-    CheckErr(XGDMatrixCreateFromMat(BeginPtr(data), nrow, ncol, asReal(missing), &handle));
-    _WrapperEnd();
-    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) {
-    _WrapperBegin();
-    const int *p_indptr = INTEGER(indptr);
-    const int *p_indices = INTEGER(indices);
-    const double *p_data = REAL(data);
-    int nindptr = length(indptr);
-    int ndata = length(data);
-    std::vector<bst_ulong> col_ptr_(nindptr);
-    std::vector<unsigned> indices_(ndata);
-    std::vector<float> data_(ndata);
-
-    for (int i = 0; i < nindptr; ++i) {
-      col_ptr_[i] = static_cast<bst_ulong>(p_indptr[i]);
-    }
-    #pragma omp parallel for schedule(static)
-    for (int i = 0; i < ndata; ++i) {
-      indices_[i] = static_cast<unsigned>(p_indices[i]);
-      data_[i] = static_cast<float>(p_data[i]);
-    }
-    DMatrixHandle handle;
-    CheckErr(XGDMatrixCreateFromCSC(BeginPtr(col_ptr_), BeginPtr(indices_),
-                                    BeginPtr(data_), nindptr, ndata,
-                                    &handle));
-    _WrapperEnd();
-    SEXP ret = PROTECT(R_MakeExternalPtr(handle, R_NilValue, R_NilValue));
-    R_RegisterCFinalizerEx(ret, _DMatrixFinalizer, TRUE);
-    UNPROTECT(1);
-    return ret;
-  }
-  SEXP XGDMatrixSliceDMatrix_R(SEXP handle, SEXP idxset) {
-    _WrapperBegin();
-    int len = length(idxset);
-    std::vector<int> idxvec(len);
-    for (int i = 0; i < len; ++i) {
-      idxvec[i] = INTEGER(idxset)[i] - 1;
-    }
-    DMatrixHandle res;
-    CheckErr(XGDMatrixSliceDMatrix(R_ExternalPtrAddr(handle),
-                                   BeginPtr(idxvec), len,
-                                   &res));
-    _WrapperEnd();
-    SEXP ret = PROTECT(R_MakeExternalPtr(res, R_NilValue, R_NilValue));
-    R_RegisterCFinalizerEx(ret, _DMatrixFinalizer, TRUE);
-    UNPROTECT(1);
-    return ret;
-  }
-  void XGDMatrixSaveBinary_R(SEXP handle, SEXP fname, SEXP silent) {
-    _WrapperBegin();
-    CheckErr(XGDMatrixSaveBinary(R_ExternalPtrAddr(handle),
-                                 CHAR(asChar(fname)), asInteger(silent)));
-    _WrapperEnd();
-  }
-  void XGDMatrixSetInfo_R(SEXP handle, SEXP field, SEXP array) {
-    _WrapperBegin();
-    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]);
-      }
-      CheckErr(XGDMatrixSetGroup(R_ExternalPtrAddr(handle), BeginPtr(vec), len));
-    } else {
-      std::vector<float> vec(len);
-      #pragma omp parallel for schedule(static)
-      for (int i = 0; i < len; ++i) {
-        vec[i] = REAL(array)[i];
-      }
-      CheckErr(XGDMatrixSetFloatInfo(R_ExternalPtrAddr(handle),
-                                     CHAR(asChar(field)),
-                                     BeginPtr(vec), len));
-    }
-    _WrapperEnd();
-  }
-  SEXP XGDMatrixGetInfo_R(SEXP handle, SEXP field) {
-    _WrapperBegin();
-    bst_ulong olen;
-    const float *res;
-    CheckErr(XGDMatrixGetFloatInfo(R_ExternalPtrAddr(handle),
-                                   CHAR(asChar(field)),
-                                   &olen,
-                                   &res));
-    _WrapperEnd();
-    SEXP ret = PROTECT(allocVector(REALSXP, olen));
-    for (size_t i = 0; i < olen; ++i) {
-      REAL(ret)[i] = res[i];
-    }
-    UNPROTECT(1);
-    return ret;
-  }
-  SEXP XGDMatrixNumRow_R(SEXP handle) {
-    bst_ulong nrow;
-    CheckErr(XGDMatrixNumRow(R_ExternalPtrAddr(handle), &nrow));
-    return ScalarInteger(static_cast<int>(nrow));
-  }
-  // functions related to booster
-  void _BoosterFinalizer(SEXP ext) {
-    if (R_ExternalPtrAddr(ext) == NULL) return;
-    CheckErr(XGBoosterFree(R_ExternalPtrAddr(ext)));
-    R_ClearExternalPtr(ext);
-  }
-  SEXP XGBoosterCreate_R(SEXP dmats) {
-    _WrapperBegin();
-    int len = length(dmats);
-    std::vector<void*> dvec;
-    for (int i = 0; i < len; ++i) {
-      dvec.push_back(R_ExternalPtrAddr(VECTOR_ELT(dmats, i)));
-    }
-    BoosterHandle handle;
-    CheckErr(XGBoosterCreate(BeginPtr(dvec), dvec.size(), &handle));
-    _WrapperEnd();
-    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) {
-    _WrapperBegin();
-    CheckErr(XGBoosterSetParam(R_ExternalPtrAddr(handle),
-                               CHAR(asChar(name)),
-                               CHAR(asChar(val))));
-    _WrapperEnd();
-  }
-  void XGBoosterUpdateOneIter_R(SEXP handle, SEXP iter, SEXP dtrain) {
-    _WrapperBegin();
-    CheckErr(XGBoosterUpdateOneIter(R_ExternalPtrAddr(handle),
-                                    asInteger(iter),
-                                    R_ExternalPtrAddr(dtrain)));
-    _WrapperEnd();
-  }
-  void XGBoosterBoostOneIter_R(SEXP handle, SEXP dtrain, SEXP grad, SEXP hess) {
-    _WrapperBegin();
-    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];
-    }
-    CheckErr(XGBoosterBoostOneIter(R_ExternalPtrAddr(handle),
-                                   R_ExternalPtrAddr(dtrain),
-                                   BeginPtr(tgrad), BeginPtr(thess),
-                                   len));
-    _WrapperEnd();
-  }
-  SEXP XGBoosterEvalOneIter_R(SEXP handle, SEXP iter, SEXP dmats, SEXP evnames) {
-    _WrapperBegin();
-    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());
-    }
-    const char *ret;
-    CheckErr(XGBoosterEvalOneIter(R_ExternalPtrAddr(handle),
-                                  asInteger(iter),
-                                  BeginPtr(vec_dmats),
-                                  BeginPtr(vec_sptr),
-                                  len, &ret));
-    _WrapperEnd();
-    return mkString(ret);
-  }
-  SEXP XGBoosterPredict_R(SEXP handle, SEXP dmat, SEXP option_mask, SEXP ntree_limit) {
-    _WrapperBegin();
-    bst_ulong olen;
-    const float *res;
-    CheckErr(XGBoosterPredict(R_ExternalPtrAddr(handle),
-                              R_ExternalPtrAddr(dmat),
-                              asInteger(option_mask),
-                              asInteger(ntree_limit),
-                              &olen, &res));
-    _WrapperEnd();
-    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) {
-    _WrapperBegin();
-    CheckErr(XGBoosterLoadModel(R_ExternalPtrAddr(handle), CHAR(asChar(fname))));
-    _WrapperEnd();
-  }
-  void XGBoosterSaveModel_R(SEXP handle, SEXP fname) {
-    _WrapperBegin();
-    CheckErr(XGBoosterSaveModel(R_ExternalPtrAddr(handle), CHAR(asChar(fname))));
-    _WrapperEnd();
-  }
-  void XGBoosterLoadModelFromRaw_R(SEXP handle, SEXP raw) {
-    _WrapperBegin();
-    XGBoosterLoadModelFromBuffer(R_ExternalPtrAddr(handle),
-                                 RAW(raw),
-                                 length(raw));
-    _WrapperEnd();
-  }
-  SEXP XGBoosterModelToRaw_R(SEXP handle) {
-    bst_ulong olen;
-    _WrapperBegin();
-    const char *raw;
-    CheckErr(XGBoosterGetModelRaw(R_ExternalPtrAddr(handle), &olen, &raw));
-    _WrapperEnd();
-    SEXP ret = PROTECT(allocVector(RAWSXP, olen));
-    if (olen != 0) {
-      memcpy(RAW(ret), raw, olen);
-    }
-    UNPROTECT(1);
-    return ret;
-  }
-  SEXP XGBoosterDumpModel_R(SEXP handle, SEXP fmap, SEXP with_stats) {
-    _WrapperBegin();
-    bst_ulong olen;
-    const char **res;
-    CheckErr(XGBoosterDumpModel(R_ExternalPtrAddr(handle),
-                                CHAR(asChar(fmap)),
-                                asInteger(with_stats),
-                                &olen, &res));
-    _WrapperEnd();
-    SEXP out = PROTECT(allocVector(STRSXP, olen));
-    for (size_t i = 0; i < olen; ++i) {
-      stringstream stream;
-      stream <<  "booster[" << i <<"]\n" << res[i];
-      SET_STRING_ELT(out, i, mkChar(stream.str().c_str()));
-    }
-    UNPROTECT(1);
-    return out;
-  }
-}

R-package/src/xgboost_R.h

@@ -4,155 +4,171 @@
  * \author Tianqi Chen
  * \brief R wrapper of xgboost
  */
-#ifndef XGBOOST_WRAPPER_R_H_ // NOLINT(*)
+#ifndef XGBOOST_R_H_ // NOLINT(*)
-#define XGBOOST_WRAPPER_R_H_ // NOLINT(*)
+#define XGBOOST_R_H_ // NOLINT(*)
 
 extern "C" {
 #include <Rinternals.h>
 #include <R_ext/Random.h>
 #include <Rmath.h>
 }
+#include <xgboost/c_api.h>
 
-extern "C" {
+/*!
-  /*!
+ * \brief check whether a handle is NULL
-   * \brief check whether a handle is NULL
+ * \param handle
-   * \param handle
+ * \return whether it is null ptr
-   * \return whether it is null ptr
+ */
+XGB_DLL SEXP XGCheckNullPtr_R(SEXP handle);
+
+/*!
+ * \brief load a data matrix
+ * \param fname name of the content
+ * \param silent whether print messages
+ * \return a loaded data matrix
+ */
+XGB_DLL 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
+ */
+XGB_DLL 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
+ */
+XGB_DLL SEXP XGDMatrixCreateFromCSC_R(SEXP indptr,
+                                      SEXP indices,
+                                      SEXP data);
+
+/*!
+ * \brief create a new dmatrix from sliced content of existing matrix
+ * \param handle instance of data matrix to be sliced
+ * \param idxset index set
+ * \return a sliced new matrix
+ */
+XGB_DLL SEXP XGDMatrixSliceDMatrix_R(SEXP handle, SEXP idxset);
+
+/*!
+ * \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
+ */
+XGB_DLL 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
+ */
+XGB_DLL 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
+ */
+XGB_DLL SEXP XGDMatrixGetInfo_R(SEXP handle, SEXP field);
+
+/*!
+ * \brief return number of rows
+ * \param handle a instance of data matrix
+ */
+XGB_DLL SEXP XGDMatrixNumRow_R(SEXP handle);
+
+/*!
+ * \brief create xgboost learner
+ * \param dmats a list of dmatrix handles that will be cached
+ */
+XGB_DLL SEXP XGBoosterCreate_R(SEXP dmats);
+
+/*!
+ * \brief set parameters
+ * \param handle handle
+ * \param name  parameter name
+ * \param val value of parameter
+ */
+XGB_DLL 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
+ */
+XGB_DLL 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
+ */
+XGB_DLL 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
+ */
+XGB_DLL 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 option_mask output_margin:1 predict_leaf:2
+ * \param ntree_limit limit number of trees used in prediction
+ */
+XGB_DLL SEXP XGBoosterPredict_R(SEXP handle, SEXP dmat, SEXP option_mask, SEXP ntree_limit);
+/*!
+ * \brief load model from existing file
+ * \param handle handle
+ * \param fname file name
+ */
+XGB_DLL void XGBoosterLoadModel_R(SEXP handle, SEXP fname);
+
+/*!
+ * \brief save model into existing file
+ * \param handle handle
+ * \param fname file name
+ */
+XGB_DLL void XGBoosterSaveModel_R(SEXP handle, SEXP fname);
+
+/*!
+ * \brief load model from raw array
+ * \param handle handle
+ */
+XGB_DLL void XGBoosterLoadModelFromRaw_R(SEXP handle, SEXP raw);
+
+/*!
+ * \brief save model into R's raw array
+ * \param handle handle
+ * \return raw array
    */
-  SEXP XGCheckNullPtr_R(SEXP handle);
+XGB_DLL SEXP XGBoosterModelToRaw_R(SEXP handle);
-  /*!
+
-   * \brief load a data matrix
+/*!
-   * \param fname name of the content
+ * \brief dump model into a string
-   * \param silent whether print messages
+ * \param handle handle
-   * \return a loaded data matrix
+ * \param fmap  name to fmap can be empty string
-   */
+ * \param with_stats whether dump statistics of splits
-  SEXP XGDMatrixCreateFromFile_R(SEXP fname, SEXP silent);
+ */
-  /*!
+XGB_DLL SEXP XGBoosterDumpModel_R(SEXP handle, SEXP fmap, SEXP with_stats);
-   * \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 create a new dmatrix from sliced content of existing matrix
-   * \param handle instance of data matrix to be sliced
-   * \param idxset index set
-   * \return a sliced new matrix
-   */
-  SEXP XGDMatrixSliceDMatrix_R(SEXP handle, SEXP idxset);
-  /*!
-   * \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 return number of rows
-   * \param handle a instance of data matrix
-   */
-  SEXP XGDMatrixNumRow_R(SEXP handle);
-  /*!
-   * \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 option_mask output_margin:1 predict_leaf:2
-   * \param ntree_limit limit number of trees used in prediction
-   */
-  SEXP XGBoosterPredict_R(SEXP handle, SEXP dmat, SEXP option_mask, SEXP ntree_limit);
-  /*!
-   * \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 load model from raw array
-   * \param handle handle
-   */
-  void XGBoosterLoadModelFromRaw_R(SEXP handle, SEXP raw);
-  /*!
-   * \brief save model into R's raw array
-   * \param handle handle
-   * \return raw array
-   */
-  SEXP XGBoosterModelToRaw_R(SEXP handle);
-  /*!
-   * \brief dump model into a string
-   * \param handle handle
-   * \param fmap  name to fmap can be empty string
-   * \param with_stats whether dump statistics of splits
-   */
-  SEXP XGBoosterDumpModel_R(SEXP handle, SEXP fmap, SEXP with_stats);
-}
 #endif  // XGBOOST_WRAPPER_R_H_ // NOLINT(*)

R-package/src/xgboost_assert.c

@@ -1,34 +0,0 @@
-// Copyright (c) 2014 by Contributors
-#include <stdio.h>
-#include <stdarg.h>
-#include <Rinternals.h>
-
-// implements error handling
-void XGBoostAssert_R(int exp, const char *fmt, ...) {
-  char buf[1024];
-  if (exp == 0) {
-    va_list args;
-    va_start(args, fmt);
-    vsprintf(buf, fmt, args);
-    va_end(args);
-    error("AssertError:%s\n", buf);
-  }
-}
-void XGBoostCheck_R(int exp, const char *fmt, ...) {
-  char buf[1024];
-  if (exp == 0) {
-    va_list args;
-    va_start(args, fmt);
-    vsprintf(buf, fmt, args);
-    va_end(args);
-    error("%s\n", buf);
-  }
-}
-int XGBoostSPrintf_R(char *buf, size_t size, const char *fmt, ...) {
-  int ret;
-  va_list args;
-  va_start(args, fmt);
-  ret = vsnprintf(buf, size, fmt, args);
-  va_end(args);
-  return ret;
-}

amalgamation/dmlc-minimum0.cc

@@ -0,0 +1,14 @@
+/*!
+ * Copyright 2015 by Contributors.
+ * \brief Mininum DMLC library Amalgamation, used for easy plugin of dmlc lib.
+ *  Normally this is not needed.
+ */
+#include "../dmlc-core/src/io/line_split.cc"
+#include "../dmlc-core/src/io/recordio_split.cc"
+#include "../dmlc-core/src/io/input_split_base.cc"
+#include "../dmlc-core/src/io/local_filesys.cc"
+#include "../dmlc-core/src/data.cc"
+#include "../dmlc-core/src/io.cc"
+#include "../dmlc-core/src/recordio.cc"
+
+

amalgamation/xgboost-all0.cc

@@ -30,8 +30,11 @@
 #include "../src/data/data.cc"
 #include "../src/data/simple_csr_source.cc"
 #include "../src/data/simple_dmatrix.cc"
+
+#if DMLC_ENABLE_STD_THREAD
 #include "../src/data/sparse_page_source.cc"
 #include "../src/data/sparse_page_dmatrix.cc"
+#endif
 
 // tress
 #include "../src/tree/tree_model.cc"

dmlc-core

@@ -1 +1 @@
-Subproject commit c0325077a3ceda08fe04b2aa115e004a3520630a
+Subproject commit ea9b247b6f9965c95aa66f42374d0867c46d9abd

src/c_api/c_api.cc

@@ -107,7 +107,7 @@ int XGDMatrixCreateFromCSR(const bst_ulong* indptr,
   for (bst_ulong i = 0; i < nelem; ++i) {
     mat.row_data_[i] = RowBatch::Entry(indices[i], data[i]);
     mat.info.num_col = std::max(mat.info.num_col,
-                                static_cast<size_t>(indices[i] + 1));
+                                static_cast<uint64_t>(indices[i] + 1));
   }
   mat.info.num_row = nindptr - 1;
   mat.info.num_nonzero = static_cast<uint64_t>(nelem);

src/common/math.h

@@ -103,7 +103,7 @@ inline static bool CmpSecond(const std::pair<float, unsigned> &a,
   return a.second > b.second;
 }
 
-#ifdef XGBOOST_STRICT_R_MODE_
+#if XGBOOST_STRICT_R_MODE
 // check nan
 bool CheckNAN(double v);
 double LogGamma(double v);

src/common/thread_local.h

@@ -6,7 +6,10 @@
 #ifndef XGBOOST_COMMON_THREAD_LOCAL_H_
 #define XGBOOST_COMMON_THREAD_LOCAL_H_
 
+#if DMLC_ENABLE_STD_THREAD
 #include <mutex>
+#endif
+
 #include <memory>
 #include <vector>
 
@@ -63,12 +66,19 @@ class ThreadLocalStore {
    * \param str the string pointer
    */
   void RegisterDelete(T *str) {
+#if DMLC_ENABLE_STD_THREAD
     std::unique_lock<std::mutex> lock(mutex_);
     data_.push_back(str);
     lock.unlock();
+#else
+    data_.push_back(str);
+#endif
   }
+
+#if DMLC_ENABLE_STD_THREAD
   /*! \brief internal mutex */
   std::mutex mutex_;
+#endif
   /*!\brief internal data */
   std::vector<T*> data_;
 };

src/data/data.cc

@@ -8,9 +8,12 @@
 #include "./sparse_batch_page.h"
 #include "./simple_dmatrix.h"
 #include "./simple_csr_source.h"
+#include "../common/io.h"
+
+#if DMLC_ENABLE_STD_THREAD
 #include "./sparse_page_source.h"
 #include "./sparse_page_dmatrix.h"
-#include "../common/io.h"
+#endif
 
 namespace xgboost {
 // implementation of inline functions
@@ -194,11 +197,16 @@ DMatrix* DMatrix::Create(dmlc::Parser<uint32_t>* parser,
     source->CopyFrom(parser);
     return DMatrix::Create(std::move(source), cache_prefix);
   } else {
+#if DMLC_ENABLE_STD_THREAD
     if (!data::SparsePageSource::CacheExist(cache_prefix)) {
       data::SparsePageSource::Create(parser, cache_prefix);
     }
     std::unique_ptr<data::SparsePageSource> source(new data::SparsePageSource(cache_prefix));
     return DMatrix::Create(std::move(source), cache_prefix);
+#else
+    LOG(FATAL) << "External memory is not enabled in mingw";
+    return nullptr;
+#endif
   }
 }
 
@@ -214,7 +222,12 @@ DMatrix* DMatrix::Create(std::unique_ptr<DataSource>&& source,
   if (cache_prefix.length() == 0) {
     return new data::SimpleDMatrix(std::move(source));
   } else {
+#if DMLC_ENABLE_STD_THREAD
     return new data::SparsePageDMatrix(std::move(source), cache_prefix);
+#else
+    LOG(FATAL) << "External memory is not enabled in mingw";
+    return nullptr;
+#endif
   }
 }
 }  // namespace xgboost

src/data/simple_csr_source.cc

@@ -51,7 +51,7 @@ void SimpleCSRSource::CopyFrom(dmlc::Parser<uint32_t>* parser) {
       bst_float fvalue = batch.value == nullptr ? 1.0f : batch.value[i];
       row_data_.push_back(SparseBatch::Entry(index, fvalue));
       this->info.num_col = std::max(this->info.num_col,
-                                    static_cast<size_t>(index + 1));
+                                    static_cast<uint64_t>(index + 1));
     }
     size_t top = row_ptr_.size();
     row_ptr_.resize(top + batch.size);

src/data/sparse_page_dmatrix.h

@@ -4,15 +4,15 @@
  * \brief In-memory version of DMatrix.
  * \author Tianqi Chen
  */
-#ifndef XGBOOST_SPARSE_PAGE_DMATRIX_H_
+#ifndef XGBOOST_DATA_SPARSE_PAGE_DMATRIX_H_
-#define XGBOOST_SPARSE_PAGE_DMATRIX_H_
+#define XGBOOST_DATA_SPARSE_PAGE_DMATRIX_H_
 
 #include <xgboost/base.h>
 #include <xgboost/data.h>
 #include <dmlc/threadediter.h>
 #include <vector>
 #include <algorithm>
-#include <cstring>
+#include <string>
 #include "./sparse_batch_page.h"
 
 namespace xgboost {
@@ -125,4 +125,4 @@ class SparsePageDMatrix : public DMatrix {
 };
 }  // namespace data
 }  // namespace xgboost
-#endif  // XGBOOST_SPARSE_PAGE_DMATRIX_H_
+#endif  // XGBOOST_DATA_SPARSE_PAGE_DMATRIX_H_