[R-package] manage Dataset and Booster handles as R external pointers (fixes #3016) (#4265)

* started converting handles

* more changes

* sort of working for Dataset

* yay all the tests are passing for Dataset handle changes

* working for other handle types

* remove debugging logging

* remove unnecessary spaces

* fix null logic

* more NULL

* updates

* Apply suggestions from code review
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* consolidate steps
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

R-package/R/lgb.Booster.R

@@ -37,7 +37,7 @@ Booster <- R6::R6Class(
 
       # Create parameters and handle
       params <- append(params, list(...))
-      handle <- lgb.null.handle()
+      handle <- NULL
 
       # Attempts to create a handle for the dataset
       try({
@@ -52,11 +52,10 @@ Booster <- R6::R6Class(
           params <- modifyList(params, train_set$get_params())
           params_str <- lgb.params2str(params = params)
           # Store booster handle
-          .Call(
+          handle <- .Call(
             LGBM_BoosterCreate_R
             , train_set_handle
             , params_str
-            , handle
           )
 
           # Create private booster information
@@ -88,10 +87,9 @@ Booster <- R6::R6Class(
           }
 
           # Create booster from model
-          .Call(
+          handle <- .Call(
             LGBM_BoosterCreateFromModelfile_R
             , modelfile
-            , handle
           )
 
         } else if (!is.null(model_str)) {
@@ -102,10 +100,9 @@ Booster <- R6::R6Class(
           }
 
           # Create booster from model
-          .Call(
+          handle <- .Call(
             LGBM_BoosterLoadModelFromString_R
             , model_str
-            , handle
           )
 
         } else {

R-package/R/lgb.Dataset.R

@@ -192,7 +192,6 @@ Dataset <- R6::R6Class(
       if (!is.null(private$reference)) {
         ref_handle <- private$reference$.__enclos_env__$private$get_handle()
       }
-      handle <- lgb.null.handle()
 
       # Not subsetting
       if (is.null(private$used_indices)) {
@@ -200,25 +199,23 @@ Dataset <- R6::R6Class(
         # Are we using a data file?
         if (is.character(private$raw_data)) {
 
-          .Call(
+          handle <- .Call(
             LGBM_DatasetCreateFromFile_R
             , private$raw_data
             , params_str
             , ref_handle
-            , handle
           )
 
         } else if (is.matrix(private$raw_data)) {
 
           # Are we using a matrix?
-          .Call(
+          handle <- .Call(
             LGBM_DatasetCreateFromMat_R
             , private$raw_data
             , nrow(private$raw_data)
             , ncol(private$raw_data)
             , params_str
             , ref_handle
-            , handle
           )
 
         } else if (methods::is(private$raw_data, "dgCMatrix")) {
@@ -226,7 +223,7 @@ Dataset <- R6::R6Class(
             stop("Cannot support large CSC matrix")
           }
           # Are we using a dgCMatrix (sparsed matrix column compressed)
-          .Call(
+          handle <- .Call(
             LGBM_DatasetCreateFromCSC_R
             , private$raw_data@p
             , private$raw_data@i
@@ -236,7 +233,6 @@ Dataset <- R6::R6Class(
             , nrow(private$raw_data)
             , params_str
             , ref_handle
-            , handle
           )
 
         } else {
@@ -257,13 +253,12 @@ Dataset <- R6::R6Class(
         }
 
         # Construct subset
-        .Call(
+        handle <- .Call(
           LGBM_DatasetGetSubset_R
           , ref_handle
           , c(private$used_indices) # Adding c() fixes issue in R v3.5
           , length(private$used_indices)
           , params_str
-          , handle
         )
 
       }

R-package/R/lgb.Predictor.R

@@ -30,17 +30,15 @@ Predictor <- R6::R6Class(
     initialize = function(modelfile, ...) {
       params <- list(...)
       private$params <- lgb.params2str(params = params)
-      # Create new lgb handle
-      handle <- lgb.null.handle()
+      handle <- NULL
 
       # Check if handle is a character
       if (is.character(modelfile)) {
 
         # Create handle on it
-        .Call(
+        handle <- .Call(
           LGBM_BoosterCreateFromModelfile_R
           , modelfile
-          , handle
         )
         private$need_free_handle <- TRUE
 

R-package/R/utils.R

@@ -6,16 +6,13 @@ lgb.is.Dataset <- function(x) {
   return(lgb.check.r6.class(object = x, name = "lgb.Dataset"))
 }
 
-lgb.null.handle <- function() {
-  if (.Machine$sizeof.pointer == 8L) {
-    return(NA_real_)
-  } else {
-    return(NA_integer_)
-  }
-}
-
 lgb.is.null.handle <- function(x) {
-  return(is.null(x) || is.na(x))
+  if (is.null(x)) {
+    return(TRUE)
+  }
+  return(
+    isTRUE(.Call(LGBM_HandleIsNull_R, x))
+  )
 }
 
 # [description] Get the most recent error stored on the C++ side and raise it

R-package/src/R_object_helper.h

-/*!
- * Copyright (c) 2017 Microsoft Corporation. All rights reserved.
- * Licensed under the MIT License. See LICENSE file in the project root for license information.
- *
- * \brief A simple wrapper for accessing data in R object.
- *
- * \note
- * We previously did not want to use R's headers because of license concerns. This is no longer a concern:
- * https://github.com/microsoft/LightGBM/issues/629#issuecomment-474995635
- * For now, this wrapper is LightGBM's interface from R to C.
- * If R changes the way it defines objects, this file will need to be updated as well.
- */
-#ifndef R_OBJECT_HELPER_H_
-#define R_OBJECT_HELPER_H_
-
-#include <cstdint>
-
-#define NAMED_BITS 16
-struct lgbm_sxpinfo {
-  unsigned int type : 5;
-  unsigned int scalar : 1;
-  unsigned int obj : 1;
-  unsigned int alt : 1;
-  unsigned int gp : 16;
-  unsigned int mark : 1;
-  unsigned int debug : 1;
-  unsigned int trace : 1;
-  unsigned int spare : 1;
-  unsigned int gcgen : 1;
-  unsigned int gccls : 3;
-  unsigned int named : NAMED_BITS;
-  unsigned int extra : 32 - NAMED_BITS;
-};
-
-struct lgbm_primsxp {
-  int offset;
-};
-
-struct lgbm_symsxp {
-  struct LGBM_SER *pname;
-  struct LGBM_SER *value;
-  struct LGBM_SER *internal;
-};
-
-struct lgbm_listsxp {
-  struct LGBM_SER *carval;
-  struct LGBM_SER *cdrval;
-  struct LGBM_SER *tagval;
-};
-
-struct lgbm_envsxp {
-  struct LGBM_SER *frame;
-  struct LGBM_SER *enclos;
-  struct LGBM_SER *hashtab;
-};
-
-struct lgbm_closxp {
-  struct LGBM_SER *formals;
-  struct LGBM_SER *body;
-  struct LGBM_SER *env;
-};
-
-struct lgbm_promsxp {
-  struct LGBM_SER *value;
-  struct LGBM_SER *expr;
-  struct LGBM_SER *env;
-};
-
-typedef struct LGBM_SER {
-  struct lgbm_sxpinfo sxpinfo;
-  struct LGBM_SER* attrib;
-  struct LGBM_SER* gengc_next_node, *gengc_prev_node;
-  union {
-    struct lgbm_primsxp primsxp;
-    struct lgbm_symsxp symsxp;
-    struct lgbm_listsxp listsxp;
-    struct lgbm_envsxp envsxp;
-    struct lgbm_closxp closxp;
-    struct lgbm_promsxp promsxp;
-  } u;
-} LGBM_SER, *LGBM_SE;
-
-struct lgbm_vecsxp {
-  R_xlen_t length;
-  R_xlen_t truelength;
-};
-
-typedef struct VECTOR_SER {
-  struct lgbm_sxpinfo sxpinfo;
-  struct LGBM_SER* attrib;
-  struct LGBM_SER* gengc_next_node, *gengc_prev_node;
-  struct lgbm_vecsxp vecsxp;
-} VECTOR_SER, *VECSE;
-
-typedef union { VECTOR_SER s; double align; } SEXPREC_ALIGN;
-
-#define DATAPTR(x)     ((reinterpret_cast<SEXPREC_ALIGN*>(x)) + 1)
-
-#define R_IS_NULL(x)   ((*reinterpret_cast<LGBM_SE>(x)).sxpinfo.type == 0)
-
-// 64bit pointer
-#if INTPTR_MAX == INT64_MAX
-
-  #define R_ADDR(x)  (reinterpret_cast<int64_t*> DATAPTR(x))
-
-  inline void R_SET_PTR(LGBM_SE x, void* ptr) {
-    if (ptr == nullptr) {
-      R_ADDR(x)[0] = (int64_t)(NULL);
-    } else {
-      R_ADDR(x)[0] = (int64_t)(ptr);
-    }
-  }
-
-  inline void* R_GET_PTR(LGBM_SE x) {
-    if (R_IS_NULL(x)) {
-      return nullptr;
-    } else {
-      auto ret = reinterpret_cast<void*>(R_ADDR(x)[0]);
-      if (ret == NULL) {
-        ret = nullptr;
-      }
-      return ret;
-    }
-  }
-
-#else
-
-  #define R_ADDR(x) (reinterpret_cast<int32_t*> DATAPTR(x))
-
-  inline void R_SET_PTR(LGBM_SE x, void* ptr) {
-    if (ptr == nullptr) {
-      R_ADDR(x)[0] = (int32_t)(NULL);
-    } else {
-      R_ADDR(x)[0] = (int32_t)(ptr);
-    }
-  }
-
-  inline void* R_GET_PTR(LGBM_SE x) {
-    if (R_IS_NULL(x)) {
-      return nullptr;
-    } else {
-      auto ret = reinterpret_cast<void*>(R_ADDR(x)[0]);
-      if (ret == NULL) {
-        ret = nullptr;
-      }
-      return ret;
-    }
-  }
-
-#endif  // INTPTR_MAX == INT64_MAX
-
-#endif  // R_OBJECT_HELPER_H_

R-package/src/lightgbm_R.cpp

@@ -50,15 +50,25 @@ SEXP LGBM_GetLastError_R() {
   return out;
 }
 
+SEXP LGBM_HandleIsNull_R(SEXP handle) {
+  return Rf_ScalarLogical(R_ExternalPtrAddr(handle) == NULL);
+}
+
 SEXP LGBM_DatasetCreateFromFile_R(SEXP filename,
   SEXP parameters,
-  LGBM_SE reference,
-  LGBM_SE out) {
+  SEXP reference) {
+  SEXP ret;
   R_API_BEGIN();
   DatasetHandle handle = nullptr;
+  DatasetHandle ref = nullptr;
+  if (!Rf_isNull(reference)) {
+    ref = R_ExternalPtrAddr(reference);
+  }
   CHECK_CALL(LGBM_DatasetCreateFromFile(CHAR(Rf_asChar(filename)), CHAR(Rf_asChar(parameters)),
-    R_GET_PTR(reference), &handle));
-  R_SET_PTR(out, handle);
+    ref, &handle));
+  ret = PROTECT(R_MakeExternalPtr(handle, R_NilValue, R_NilValue));
+  UNPROTECT(1);
+  return ret;
   R_API_END();
 }
 
@@ -69,8 +79,8 @@ SEXP LGBM_DatasetCreateFromCSC_R(SEXP indptr,
   SEXP nelem,
   SEXP num_row,
   SEXP parameters,
-  LGBM_SE reference,
-  LGBM_SE out) {
+  SEXP reference) {
+  SEXP ret;
   R_API_BEGIN();
   const int* p_indptr = INTEGER(indptr);
   const int* p_indices = INTEGER(indices);
@@ -80,10 +90,16 @@ SEXP LGBM_DatasetCreateFromCSC_R(SEXP indptr,
   int64_t ndata = static_cast<int64_t>(Rf_asInteger(nelem));
   int64_t nrow = static_cast<int64_t>(Rf_asInteger(num_row));
   DatasetHandle handle = nullptr;
+  DatasetHandle ref = nullptr;
+  if (!Rf_isNull(reference)) {
+    ref = R_ExternalPtrAddr(reference);
+  }
   CHECK_CALL(LGBM_DatasetCreateFromCSC(p_indptr, C_API_DTYPE_INT32, p_indices,
     p_data, C_API_DTYPE_FLOAT64, nindptr, ndata,
-    nrow, CHAR(Rf_asChar(parameters)), R_GET_PTR(reference), &handle));
-  R_SET_PTR(out, handle);
+    nrow, CHAR(Rf_asChar(parameters)), ref, &handle));
+  ret = PROTECT(R_MakeExternalPtr(handle, R_NilValue, R_NilValue));
+  UNPROTECT(1);
+  return ret;
   R_API_END();
 }
 
@@ -91,24 +107,30 @@ SEXP LGBM_DatasetCreateFromMat_R(SEXP data,
   SEXP num_row,
   SEXP num_col,
   SEXP parameters,
-  LGBM_SE reference,
-  LGBM_SE out) {
+  SEXP reference) {
+  SEXP ret;
   R_API_BEGIN();
   int32_t nrow = static_cast<int32_t>(Rf_asInteger(num_row));
   int32_t ncol = static_cast<int32_t>(Rf_asInteger(num_col));
   double* p_mat = REAL(data);
   DatasetHandle handle = nullptr;
+  DatasetHandle ref = nullptr;
+  if (!Rf_isNull(reference)) {
+    ref = R_ExternalPtrAddr(reference);
+  }
   CHECK_CALL(LGBM_DatasetCreateFromMat(p_mat, C_API_DTYPE_FLOAT64, nrow, ncol, COL_MAJOR,
-    CHAR(Rf_asChar(parameters)), R_GET_PTR(reference), &handle));
-  R_SET_PTR(out, handle);
+    CHAR(Rf_asChar(parameters)), ref, &handle));
+  ret = PROTECT(R_MakeExternalPtr(handle, R_NilValue, R_NilValue));
+  UNPROTECT(1);
+  return ret;
   R_API_END();
 }
 
-SEXP LGBM_DatasetGetSubset_R(LGBM_SE handle,
+SEXP LGBM_DatasetGetSubset_R(SEXP handle,
   SEXP used_row_indices,
   SEXP len_used_row_indices,
-  SEXP parameters,
-  LGBM_SE out) {
+  SEXP parameters) {
+  SEXP ret;
   R_API_BEGIN();
   int len = Rf_asInteger(len_used_row_indices);
   std::vector<int> idxvec(len);
@@ -118,14 +140,16 @@ SEXP LGBM_DatasetGetSubset_R(LGBM_SE handle,
     idxvec[i] = INTEGER(used_row_indices)[i] - 1;
   }
   DatasetHandle res = nullptr;
-  CHECK_CALL(LGBM_DatasetGetSubset(R_GET_PTR(handle),
+  CHECK_CALL(LGBM_DatasetGetSubset(R_ExternalPtrAddr(handle),
     idxvec.data(), len, CHAR(Rf_asChar(parameters)),
     &res));
-  R_SET_PTR(out, res);
+  ret = PROTECT(R_MakeExternalPtr(res, R_NilValue, R_NilValue));
+  UNPROTECT(1);
+  return ret;
   R_API_END();
 }
 
-SEXP LGBM_DatasetSetFeatureNames_R(LGBM_SE handle,
+SEXP LGBM_DatasetSetFeatureNames_R(SEXP handle,
   SEXP feature_names) {
   R_API_BEGIN();
   auto vec_names = Split(CHAR(Rf_asChar(feature_names)), '\t');
@@ -134,16 +158,16 @@ SEXP LGBM_DatasetSetFeatureNames_R(LGBM_SE handle,
   for (int i = 0; i < len; ++i) {
     vec_sptr.push_back(vec_names[i].c_str());
   }
-  CHECK_CALL(LGBM_DatasetSetFeatureNames(R_GET_PTR(handle),
+  CHECK_CALL(LGBM_DatasetSetFeatureNames(R_ExternalPtrAddr(handle),
     vec_sptr.data(), len));
   R_API_END();
 }
 
-SEXP LGBM_DatasetGetFeatureNames_R(LGBM_SE handle) {
+SEXP LGBM_DatasetGetFeatureNames_R(SEXP handle) {
   SEXP feature_names;
   R_API_BEGIN();
   int len = 0;
-  CHECK_CALL(LGBM_DatasetGetNumFeature(R_GET_PTR(handle), &len));
+  CHECK_CALL(LGBM_DatasetGetNumFeature(R_ExternalPtrAddr(handle), &len));
   const size_t reserved_string_size = 256;
   std::vector<std::vector<char>> names(len);
   std::vector<char*> ptr_names(len);
@@ -155,7 +179,7 @@ SEXP LGBM_DatasetGetFeatureNames_R(LGBM_SE handle) {
   size_t required_string_size;
   CHECK_CALL(
     LGBM_DatasetGetFeatureNames(
-      R_GET_PTR(handle),
+      R_ExternalPtrAddr(handle),
       len, &out_len,
       reserved_string_size, &required_string_size,
       ptr_names.data()));
@@ -168,7 +192,7 @@ SEXP LGBM_DatasetGetFeatureNames_R(LGBM_SE handle) {
     }
     CHECK_CALL(
       LGBM_DatasetGetFeatureNames(
-        R_GET_PTR(handle),
+        R_ExternalPtrAddr(handle),
         len,
         &out_len,
         required_string_size,
@@ -185,24 +209,24 @@ SEXP LGBM_DatasetGetFeatureNames_R(LGBM_SE handle) {
   R_API_END();
 }
 
-SEXP LGBM_DatasetSaveBinary_R(LGBM_SE handle,
+SEXP LGBM_DatasetSaveBinary_R(SEXP handle,
   SEXP filename) {
   R_API_BEGIN();
-  CHECK_CALL(LGBM_DatasetSaveBinary(R_GET_PTR(handle),
+  CHECK_CALL(LGBM_DatasetSaveBinary(R_ExternalPtrAddr(handle),
     CHAR(Rf_asChar(filename))));
   R_API_END();
 }
 
-SEXP LGBM_DatasetFree_R(LGBM_SE handle) {
+SEXP LGBM_DatasetFree_R(SEXP handle) {
   R_API_BEGIN();
-  if (R_GET_PTR(handle) != nullptr) {
-    CHECK_CALL(LGBM_DatasetFree(R_GET_PTR(handle)));
-    R_SET_PTR(handle, nullptr);
+  if (R_ExternalPtrAddr(handle)) {
+    CHECK_CALL(LGBM_DatasetFree(R_ExternalPtrAddr(handle)));
+    R_ClearExternalPtr(handle);
   }
   R_API_END();
 }
 
-SEXP LGBM_DatasetSetField_R(LGBM_SE handle,
+SEXP LGBM_DatasetSetField_R(SEXP handle,
   SEXP field_name,
   SEXP field_data,
   SEXP num_element) {
@@ -215,21 +239,21 @@ SEXP LGBM_DatasetSetField_R(LGBM_SE handle,
     for (int i = 0; i < len; ++i) {
       vec[i] = static_cast<int32_t>(INTEGER(field_data)[i]);
     }
-    CHECK_CALL(LGBM_DatasetSetField(R_GET_PTR(handle), name, vec.data(), len, C_API_DTYPE_INT32));
+    CHECK_CALL(LGBM_DatasetSetField(R_ExternalPtrAddr(handle), name, vec.data(), len, C_API_DTYPE_INT32));
   } else if (!strcmp("init_score", name)) {
-    CHECK_CALL(LGBM_DatasetSetField(R_GET_PTR(handle), name, REAL(field_data), len, C_API_DTYPE_FLOAT64));
+    CHECK_CALL(LGBM_DatasetSetField(R_ExternalPtrAddr(handle), name, REAL(field_data), len, C_API_DTYPE_FLOAT64));
   } else {
     std::vector<float> vec(len);
 #pragma omp parallel for schedule(static, 512) if (len >= 1024)
     for (int i = 0; i < len; ++i) {
       vec[i] = static_cast<float>(REAL(field_data)[i]);
     }
-    CHECK_CALL(LGBM_DatasetSetField(R_GET_PTR(handle), name, vec.data(), len, C_API_DTYPE_FLOAT32));
+    CHECK_CALL(LGBM_DatasetSetField(R_ExternalPtrAddr(handle), name, vec.data(), len, C_API_DTYPE_FLOAT32));
   }
   R_API_END();
 }
 
-SEXP LGBM_DatasetGetField_R(LGBM_SE handle,
+SEXP LGBM_DatasetGetField_R(SEXP handle,
   SEXP field_name,
   SEXP field_data) {
   R_API_BEGIN();
@@ -237,7 +261,7 @@ SEXP LGBM_DatasetGetField_R(LGBM_SE handle,
   int out_len = 0;
   int out_type = 0;
   const void* res;
-  CHECK_CALL(LGBM_DatasetGetField(R_GET_PTR(handle), name, &out_len, &res, &out_type));
+  CHECK_CALL(LGBM_DatasetGetField(R_ExternalPtrAddr(handle), name, &out_len, &res, &out_type));
 
   if (!strcmp("group", name) || !strcmp("query", name)) {
     auto p_data = reinterpret_cast<const int32_t*>(res);
@@ -262,7 +286,7 @@ SEXP LGBM_DatasetGetField_R(LGBM_SE handle,
   R_API_END();
 }
 
-SEXP LGBM_DatasetGetFieldSize_R(LGBM_SE handle,
+SEXP LGBM_DatasetGetFieldSize_R(SEXP handle,
   SEXP field_name,
   SEXP out) {
   R_API_BEGIN();
@@ -270,7 +294,7 @@ SEXP LGBM_DatasetGetFieldSize_R(LGBM_SE handle,
   int out_len = 0;
   int out_type = 0;
   const void* res;
-  CHECK_CALL(LGBM_DatasetGetField(R_GET_PTR(handle), name, &out_len, &res, &out_type));
+  CHECK_CALL(LGBM_DatasetGetField(R_ExternalPtrAddr(handle), name, &out_len, &res, &out_type));
   if (!strcmp("group", name) || !strcmp("query", name)) {
     out_len -= 1;
   }
@@ -285,109 +309,115 @@ SEXP LGBM_DatasetUpdateParamChecking_R(SEXP old_params,
   R_API_END();
 }
 
-SEXP LGBM_DatasetGetNumData_R(LGBM_SE handle, SEXP out) {
+SEXP LGBM_DatasetGetNumData_R(SEXP handle, SEXP out) {
   int nrow;
   R_API_BEGIN();
-  CHECK_CALL(LGBM_DatasetGetNumData(R_GET_PTR(handle), &nrow));
+  CHECK_CALL(LGBM_DatasetGetNumData(R_ExternalPtrAddr(handle), &nrow));
   INTEGER(out)[0] = static_cast<int>(nrow);
   R_API_END();
 }
 
-SEXP LGBM_DatasetGetNumFeature_R(LGBM_SE handle,
+SEXP LGBM_DatasetGetNumFeature_R(SEXP handle,
   SEXP out) {
   int nfeature;
   R_API_BEGIN();
-  CHECK_CALL(LGBM_DatasetGetNumFeature(R_GET_PTR(handle), &nfeature));
+  CHECK_CALL(LGBM_DatasetGetNumFeature(R_ExternalPtrAddr(handle), &nfeature));
   INTEGER(out)[0] = static_cast<int>(nfeature);
   R_API_END();
 }
 
 // --- start Booster interfaces
 
-SEXP LGBM_BoosterFree_R(LGBM_SE handle) {
+SEXP LGBM_BoosterFree_R(SEXP handle) {
   R_API_BEGIN();
-  if (R_GET_PTR(handle) != nullptr) {
-    CHECK_CALL(LGBM_BoosterFree(R_GET_PTR(handle)));
-    R_SET_PTR(handle, nullptr);
+  if (R_ExternalPtrAddr(handle)) {
+    CHECK_CALL(LGBM_BoosterFree(R_ExternalPtrAddr(handle)));
+    R_ClearExternalPtr(handle);
   }
   R_API_END();
 }
 
-SEXP LGBM_BoosterCreate_R(LGBM_SE train_data,
-  SEXP parameters,
-  LGBM_SE out) {
+SEXP LGBM_BoosterCreate_R(SEXP train_data,
+  SEXP parameters) {
+  SEXP ret;
   R_API_BEGIN();
   BoosterHandle handle = nullptr;
-  CHECK_CALL(LGBM_BoosterCreate(R_GET_PTR(train_data), CHAR(Rf_asChar(parameters)), &handle));
-  R_SET_PTR(out, handle);
+  CHECK_CALL(LGBM_BoosterCreate(R_ExternalPtrAddr(train_data), CHAR(Rf_asChar(parameters)), &handle));
+  ret = PROTECT(R_MakeExternalPtr(handle, R_NilValue, R_NilValue));
+  UNPROTECT(1);
+  return ret;
   R_API_END();
 }
 
-SEXP LGBM_BoosterCreateFromModelfile_R(SEXP filename,
-  LGBM_SE out) {
+SEXP LGBM_BoosterCreateFromModelfile_R(SEXP filename) {
+  SEXP ret;
   R_API_BEGIN();
   int out_num_iterations = 0;
   BoosterHandle handle = nullptr;
   CHECK_CALL(LGBM_BoosterCreateFromModelfile(CHAR(Rf_asChar(filename)), &out_num_iterations, &handle));
-  R_SET_PTR(out, handle);
+  ret = PROTECT(R_MakeExternalPtr(handle, R_NilValue, R_NilValue));
+  UNPROTECT(1);
+  return ret;
   R_API_END();
 }
 
-SEXP LGBM_BoosterLoadModelFromString_R(SEXP model_str,
-  LGBM_SE out) {
+SEXP LGBM_BoosterLoadModelFromString_R(SEXP model_str) {
+  SEXP ret;
   R_API_BEGIN();
   int out_num_iterations = 0;
   BoosterHandle handle = nullptr;
   CHECK_CALL(LGBM_BoosterLoadModelFromString(CHAR(Rf_asChar(model_str)), &out_num_iterations, &handle));
-  R_SET_PTR(out, handle);
+  ret = PROTECT(R_MakeExternalPtr(handle, R_NilValue, R_NilValue));
+  UNPROTECT(1);
+  return ret;
   R_API_END();
 }
 
-SEXP LGBM_BoosterMerge_R(LGBM_SE handle,
-  LGBM_SE other_handle) {
+SEXP LGBM_BoosterMerge_R(SEXP handle,
+  SEXP other_handle) {
   R_API_BEGIN();
-  CHECK_CALL(LGBM_BoosterMerge(R_GET_PTR(handle), R_GET_PTR(other_handle)));
+  CHECK_CALL(LGBM_BoosterMerge(R_ExternalPtrAddr(handle), R_ExternalPtrAddr(other_handle)));
   R_API_END();
 }
 
-SEXP LGBM_BoosterAddValidData_R(LGBM_SE handle,
-  LGBM_SE valid_data) {
+SEXP LGBM_BoosterAddValidData_R(SEXP handle,
+  SEXP valid_data) {
   R_API_BEGIN();
-  CHECK_CALL(LGBM_BoosterAddValidData(R_GET_PTR(handle), R_GET_PTR(valid_data)));
+  CHECK_CALL(LGBM_BoosterAddValidData(R_ExternalPtrAddr(handle), R_ExternalPtrAddr(valid_data)));
   R_API_END();
 }
 
-SEXP LGBM_BoosterResetTrainingData_R(LGBM_SE handle,
-  LGBM_SE train_data) {
+SEXP LGBM_BoosterResetTrainingData_R(SEXP handle,
+  SEXP train_data) {
   R_API_BEGIN();
-  CHECK_CALL(LGBM_BoosterResetTrainingData(R_GET_PTR(handle), R_GET_PTR(train_data)));
+  CHECK_CALL(LGBM_BoosterResetTrainingData(R_ExternalPtrAddr(handle), R_ExternalPtrAddr(train_data)));
   R_API_END();
 }
 
-SEXP LGBM_BoosterResetParameter_R(LGBM_SE handle,
+SEXP LGBM_BoosterResetParameter_R(SEXP handle,
   SEXP parameters) {
   R_API_BEGIN();
-  CHECK_CALL(LGBM_BoosterResetParameter(R_GET_PTR(handle), CHAR(Rf_asChar(parameters))));
+  CHECK_CALL(LGBM_BoosterResetParameter(R_ExternalPtrAddr(handle), CHAR(Rf_asChar(parameters))));
   R_API_END();
 }
 
-SEXP LGBM_BoosterGetNumClasses_R(LGBM_SE handle,
+SEXP LGBM_BoosterGetNumClasses_R(SEXP handle,
   SEXP out) {
   int num_class;
   R_API_BEGIN();
-  CHECK_CALL(LGBM_BoosterGetNumClasses(R_GET_PTR(handle), &num_class));
+  CHECK_CALL(LGBM_BoosterGetNumClasses(R_ExternalPtrAddr(handle), &num_class));
   INTEGER(out)[0] = static_cast<int>(num_class);
   R_API_END();
 }
 
-SEXP LGBM_BoosterUpdateOneIter_R(LGBM_SE handle) {
+SEXP LGBM_BoosterUpdateOneIter_R(SEXP handle) {
   int is_finished = 0;
   R_API_BEGIN();
-  CHECK_CALL(LGBM_BoosterUpdateOneIter(R_GET_PTR(handle), &is_finished));
+  CHECK_CALL(LGBM_BoosterUpdateOneIter(R_ExternalPtrAddr(handle), &is_finished));
   R_API_END();
 }
 
-SEXP LGBM_BoosterUpdateOneIterCustom_R(LGBM_SE handle,
+SEXP LGBM_BoosterUpdateOneIterCustom_R(SEXP handle,
   SEXP grad,
   SEXP hess,
   SEXP len) {
@@ -400,46 +430,46 @@ SEXP LGBM_BoosterUpdateOneIterCustom_R(LGBM_SE handle,
     tgrad[j] = static_cast<float>(REAL(grad)[j]);
     thess[j] = static_cast<float>(REAL(hess)[j]);
   }
-  CHECK_CALL(LGBM_BoosterUpdateOneIterCustom(R_GET_PTR(handle), tgrad.data(), thess.data(), &is_finished));
+  CHECK_CALL(LGBM_BoosterUpdateOneIterCustom(R_ExternalPtrAddr(handle), tgrad.data(), thess.data(), &is_finished));
   R_API_END();
 }
 
-SEXP LGBM_BoosterRollbackOneIter_R(LGBM_SE handle) {
+SEXP LGBM_BoosterRollbackOneIter_R(SEXP handle) {
   R_API_BEGIN();
-  CHECK_CALL(LGBM_BoosterRollbackOneIter(R_GET_PTR(handle)));
+  CHECK_CALL(LGBM_BoosterRollbackOneIter(R_ExternalPtrAddr(handle)));
   R_API_END();
 }
 
-SEXP LGBM_BoosterGetCurrentIteration_R(LGBM_SE handle,
+SEXP LGBM_BoosterGetCurrentIteration_R(SEXP handle,
   SEXP out) {
   int out_iteration;
   R_API_BEGIN();
-  CHECK_CALL(LGBM_BoosterGetCurrentIteration(R_GET_PTR(handle), &out_iteration));
+  CHECK_CALL(LGBM_BoosterGetCurrentIteration(R_ExternalPtrAddr(handle), &out_iteration));
   INTEGER(out)[0] = static_cast<int>(out_iteration);
   R_API_END();
 }
 
-SEXP LGBM_BoosterGetUpperBoundValue_R(LGBM_SE handle,
+SEXP LGBM_BoosterGetUpperBoundValue_R(SEXP handle,
   SEXP out_result) {
   R_API_BEGIN();
   double* ptr_ret = REAL(out_result);
-  CHECK_CALL(LGBM_BoosterGetUpperBoundValue(R_GET_PTR(handle), ptr_ret));
+  CHECK_CALL(LGBM_BoosterGetUpperBoundValue(R_ExternalPtrAddr(handle), ptr_ret));
   R_API_END();
 }
 
-SEXP LGBM_BoosterGetLowerBoundValue_R(LGBM_SE handle,
+SEXP LGBM_BoosterGetLowerBoundValue_R(SEXP handle,
   SEXP out_result) {
   R_API_BEGIN();
   double* ptr_ret = REAL(out_result);
-  CHECK_CALL(LGBM_BoosterGetLowerBoundValue(R_GET_PTR(handle), ptr_ret));
+  CHECK_CALL(LGBM_BoosterGetLowerBoundValue(R_ExternalPtrAddr(handle), ptr_ret));
   R_API_END();
 }
 
-SEXP LGBM_BoosterGetEvalNames_R(LGBM_SE handle) {
+SEXP LGBM_BoosterGetEvalNames_R(SEXP handle) {
   SEXP eval_names;
   R_API_BEGIN();
   int len;
-  CHECK_CALL(LGBM_BoosterGetEvalCounts(R_GET_PTR(handle), &len));
+  CHECK_CALL(LGBM_BoosterGetEvalCounts(R_ExternalPtrAddr(handle), &len));
 
   const size_t reserved_string_size = 128;
   std::vector<std::vector<char>> names(len);
@@ -453,7 +483,7 @@ SEXP LGBM_BoosterGetEvalNames_R(LGBM_SE handle) {
   size_t required_string_size;
   CHECK_CALL(
     LGBM_BoosterGetEvalNames(
-      R_GET_PTR(handle),
+      R_ExternalPtrAddr(handle),
       len, &out_len,
       reserved_string_size, &required_string_size,
       ptr_names.data()));
@@ -466,7 +496,7 @@ SEXP LGBM_BoosterGetEvalNames_R(LGBM_SE handle) {
     }
     CHECK_CALL(
       LGBM_BoosterGetEvalNames(
-        R_GET_PTR(handle),
+        R_ExternalPtrAddr(handle),
         len,
         &out_len,
         required_string_size,
@@ -483,36 +513,36 @@ SEXP LGBM_BoosterGetEvalNames_R(LGBM_SE handle) {
   R_API_END();
 }
 
-SEXP LGBM_BoosterGetEval_R(LGBM_SE handle,
+SEXP LGBM_BoosterGetEval_R(SEXP handle,
   SEXP data_idx,
   SEXP out_result) {
   R_API_BEGIN();
   int len;
-  CHECK_CALL(LGBM_BoosterGetEvalCounts(R_GET_PTR(handle), &len));
+  CHECK_CALL(LGBM_BoosterGetEvalCounts(R_ExternalPtrAddr(handle), &len));
   double* ptr_ret = REAL(out_result);
   int out_len;
-  CHECK_CALL(LGBM_BoosterGetEval(R_GET_PTR(handle), Rf_asInteger(data_idx), &out_len, ptr_ret));
+  CHECK_CALL(LGBM_BoosterGetEval(R_ExternalPtrAddr(handle), Rf_asInteger(data_idx), &out_len, ptr_ret));
   CHECK_EQ(out_len, len);
   R_API_END();
 }
 
-SEXP LGBM_BoosterGetNumPredict_R(LGBM_SE handle,
+SEXP LGBM_BoosterGetNumPredict_R(SEXP handle,
   SEXP data_idx,
   SEXP out) {
   R_API_BEGIN();
   int64_t len;
-  CHECK_CALL(LGBM_BoosterGetNumPredict(R_GET_PTR(handle), Rf_asInteger(data_idx), &len));
+  CHECK_CALL(LGBM_BoosterGetNumPredict(R_ExternalPtrAddr(handle), Rf_asInteger(data_idx), &len));
   INTEGER(out)[0] = static_cast<int>(len);
   R_API_END();
 }
 
-SEXP LGBM_BoosterGetPredict_R(LGBM_SE handle,
+SEXP LGBM_BoosterGetPredict_R(SEXP handle,
   SEXP data_idx,
   SEXP out_result) {
   R_API_BEGIN();
   double* ptr_ret = REAL(out_result);
   int64_t out_len;
-  CHECK_CALL(LGBM_BoosterGetPredict(R_GET_PTR(handle), Rf_asInteger(data_idx), &out_len, ptr_ret));
+  CHECK_CALL(LGBM_BoosterGetPredict(R_ExternalPtrAddr(handle), Rf_asInteger(data_idx), &out_len, ptr_ret));
   R_API_END();
 }
 
@@ -530,7 +560,7 @@ int GetPredictType(SEXP is_rawscore, SEXP is_leafidx, SEXP is_predcontrib) {
   return pred_type;
 }
 
-SEXP LGBM_BoosterPredictForFile_R(LGBM_SE handle,
+SEXP LGBM_BoosterPredictForFile_R(SEXP handle,
   SEXP data_filename,
   SEXP data_has_header,
   SEXP is_rawscore,
@@ -542,13 +572,13 @@ SEXP LGBM_BoosterPredictForFile_R(LGBM_SE handle,
   SEXP result_filename) {
   R_API_BEGIN();
   int pred_type = GetPredictType(is_rawscore, is_leafidx, is_predcontrib);
-  CHECK_CALL(LGBM_BoosterPredictForFile(R_GET_PTR(handle), CHAR(Rf_asChar(data_filename)),
+  CHECK_CALL(LGBM_BoosterPredictForFile(R_ExternalPtrAddr(handle), CHAR(Rf_asChar(data_filename)),
     Rf_asInteger(data_has_header), pred_type, Rf_asInteger(start_iteration), Rf_asInteger(num_iteration), CHAR(Rf_asChar(parameter)),
     CHAR(Rf_asChar(result_filename))));
   R_API_END();
 }
 
-SEXP LGBM_BoosterCalcNumPredict_R(LGBM_SE handle,
+SEXP LGBM_BoosterCalcNumPredict_R(SEXP handle,
   SEXP num_row,
   SEXP is_rawscore,
   SEXP is_leafidx,
@@ -559,13 +589,13 @@ SEXP LGBM_BoosterCalcNumPredict_R(LGBM_SE handle,
   R_API_BEGIN();
   int pred_type = GetPredictType(is_rawscore, is_leafidx, is_predcontrib);
   int64_t len = 0;
-  CHECK_CALL(LGBM_BoosterCalcNumPredict(R_GET_PTR(handle), Rf_asInteger(num_row),
+  CHECK_CALL(LGBM_BoosterCalcNumPredict(R_ExternalPtrAddr(handle), Rf_asInteger(num_row),
     pred_type, Rf_asInteger(start_iteration), Rf_asInteger(num_iteration), &len));
   INTEGER(out_len)[0] = static_cast<int>(len);
   R_API_END();
 }
 
-SEXP LGBM_BoosterPredictForCSC_R(LGBM_SE handle,
+SEXP LGBM_BoosterPredictForCSC_R(SEXP handle,
   SEXP indptr,
   SEXP indices,
   SEXP data,
@@ -591,14 +621,14 @@ SEXP LGBM_BoosterPredictForCSC_R(LGBM_SE handle,
   int64_t nrow = Rf_asInteger(num_row);
   double* ptr_ret = REAL(out_result);
   int64_t out_len;
-  CHECK_CALL(LGBM_BoosterPredictForCSC(R_GET_PTR(handle),
+  CHECK_CALL(LGBM_BoosterPredictForCSC(R_ExternalPtrAddr(handle),
     p_indptr, C_API_DTYPE_INT32, p_indices,
     p_data, C_API_DTYPE_FLOAT64, nindptr, ndata,
     nrow, pred_type,  Rf_asInteger(start_iteration), Rf_asInteger(num_iteration), CHAR(Rf_asChar(parameter)), &out_len, ptr_ret));
   R_API_END();
 }
 
-SEXP LGBM_BoosterPredictForMat_R(LGBM_SE handle,
+SEXP LGBM_BoosterPredictForMat_R(SEXP handle,
   SEXP data,
   SEXP num_row,
   SEXP num_col,
@@ -618,23 +648,23 @@ SEXP LGBM_BoosterPredictForMat_R(LGBM_SE handle,
   const double* p_mat = REAL(data);
   double* ptr_ret = REAL(out_result);
   int64_t out_len;
-  CHECK_CALL(LGBM_BoosterPredictForMat(R_GET_PTR(handle),
+  CHECK_CALL(LGBM_BoosterPredictForMat(R_ExternalPtrAddr(handle),
     p_mat, C_API_DTYPE_FLOAT64, nrow, ncol, COL_MAJOR,
     pred_type, Rf_asInteger(start_iteration), Rf_asInteger(num_iteration), CHAR(Rf_asChar(parameter)), &out_len, ptr_ret));
 
   R_API_END();
 }
 
-SEXP LGBM_BoosterSaveModel_R(LGBM_SE handle,
+SEXP LGBM_BoosterSaveModel_R(SEXP handle,
   SEXP num_iteration,
   SEXP feature_importance_type,
   SEXP filename) {
   R_API_BEGIN();
-  CHECK_CALL(LGBM_BoosterSaveModel(R_GET_PTR(handle), 0, Rf_asInteger(num_iteration), Rf_asInteger(feature_importance_type), CHAR(Rf_asChar(filename))));
+  CHECK_CALL(LGBM_BoosterSaveModel(R_ExternalPtrAddr(handle), 0, Rf_asInteger(num_iteration), Rf_asInteger(feature_importance_type), CHAR(Rf_asChar(filename))));
   R_API_END();
 }
 
-SEXP LGBM_BoosterSaveModelToString_R(LGBM_SE handle,
+SEXP LGBM_BoosterSaveModelToString_R(SEXP handle,
   SEXP num_iteration,
   SEXP feature_importance_type) {
   SEXP model_str;
@@ -644,11 +674,11 @@ SEXP LGBM_BoosterSaveModelToString_R(LGBM_SE handle,
   int64_t num_iter = Rf_asInteger(num_iteration);
   int64_t importance_type = Rf_asInteger(feature_importance_type);
   std::vector<char> inner_char_buf(buf_len);
-  CHECK_CALL(LGBM_BoosterSaveModelToString(R_GET_PTR(handle), 0, num_iter, importance_type, buf_len, &out_len, inner_char_buf.data()));
+  CHECK_CALL(LGBM_BoosterSaveModelToString(R_ExternalPtrAddr(handle), 0, num_iter, importance_type, buf_len, &out_len, inner_char_buf.data()));
   // if the model string was larger than the initial buffer, allocate a bigger buffer and try again
   if (out_len > buf_len) {
     inner_char_buf.resize(out_len);
-    CHECK_CALL(LGBM_BoosterSaveModelToString(R_GET_PTR(handle), 0, num_iter, importance_type, out_len, &out_len, inner_char_buf.data()));
+    CHECK_CALL(LGBM_BoosterSaveModelToString(R_ExternalPtrAddr(handle), 0, num_iter, importance_type, out_len, &out_len, inner_char_buf.data()));
   }
   model_str = PROTECT(Rf_allocVector(STRSXP, 1));
   SET_STRING_ELT(model_str, 0, Rf_mkChar(inner_char_buf.data()));
@@ -657,7 +687,7 @@ SEXP LGBM_BoosterSaveModelToString_R(LGBM_SE handle,
   R_API_END();
 }
 
-SEXP LGBM_BoosterDumpModel_R(LGBM_SE handle,
+SEXP LGBM_BoosterDumpModel_R(SEXP handle,
   SEXP num_iteration,
   SEXP feature_importance_type) {
   SEXP model_str;
@@ -667,11 +697,11 @@ SEXP LGBM_BoosterDumpModel_R(LGBM_SE handle,
   int64_t num_iter = Rf_asInteger(num_iteration);
   int64_t importance_type = Rf_asInteger(feature_importance_type);
   std::vector<char> inner_char_buf(buf_len);
-  CHECK_CALL(LGBM_BoosterDumpModel(R_GET_PTR(handle), 0, num_iter, importance_type, buf_len, &out_len, inner_char_buf.data()));
+  CHECK_CALL(LGBM_BoosterDumpModel(R_ExternalPtrAddr(handle), 0, num_iter, importance_type, buf_len, &out_len, inner_char_buf.data()));
   // if the model string was larger than the initial buffer, allocate a bigger buffer and try again
   if (out_len > buf_len) {
     inner_char_buf.resize(out_len);
-    CHECK_CALL(LGBM_BoosterDumpModel(R_GET_PTR(handle), 0, num_iter, importance_type, out_len, &out_len, inner_char_buf.data()));
+    CHECK_CALL(LGBM_BoosterDumpModel(R_ExternalPtrAddr(handle), 0, num_iter, importance_type, out_len, &out_len, inner_char_buf.data()));
   }
   model_str = PROTECT(Rf_allocVector(STRSXP, 1));
   SET_STRING_ELT(model_str, 0, Rf_mkChar(inner_char_buf.data()));
@@ -683,10 +713,11 @@ SEXP LGBM_BoosterDumpModel_R(LGBM_SE handle,
 // .Call() calls
 static const R_CallMethodDef CallEntries[] = {
   {"LGBM_GetLastError_R"              , (DL_FUNC) &LGBM_GetLastError_R              , 0},
-  {"LGBM_DatasetCreateFromFile_R"     , (DL_FUNC) &LGBM_DatasetCreateFromFile_R     , 4},
-  {"LGBM_DatasetCreateFromCSC_R"      , (DL_FUNC) &LGBM_DatasetCreateFromCSC_R      , 9},
-  {"LGBM_DatasetCreateFromMat_R"      , (DL_FUNC) &LGBM_DatasetCreateFromMat_R      , 6},
-  {"LGBM_DatasetGetSubset_R"          , (DL_FUNC) &LGBM_DatasetGetSubset_R          , 5},
+  {"LGBM_HandleIsNull_R"              , (DL_FUNC) &LGBM_HandleIsNull_R              , 1},
+  {"LGBM_DatasetCreateFromFile_R"     , (DL_FUNC) &LGBM_DatasetCreateFromFile_R     , 3},
+  {"LGBM_DatasetCreateFromCSC_R"      , (DL_FUNC) &LGBM_DatasetCreateFromCSC_R      , 8},
+  {"LGBM_DatasetCreateFromMat_R"      , (DL_FUNC) &LGBM_DatasetCreateFromMat_R      , 5},
+  {"LGBM_DatasetGetSubset_R"          , (DL_FUNC) &LGBM_DatasetGetSubset_R          , 4},
   {"LGBM_DatasetSetFeatureNames_R"    , (DL_FUNC) &LGBM_DatasetSetFeatureNames_R    , 2},
   {"LGBM_DatasetGetFeatureNames_R"    , (DL_FUNC) &LGBM_DatasetGetFeatureNames_R    , 1},
   {"LGBM_DatasetSaveBinary_R"         , (DL_FUNC) &LGBM_DatasetSaveBinary_R         , 2},
@@ -697,10 +728,10 @@ static const R_CallMethodDef CallEntries[] = {
   {"LGBM_DatasetUpdateParamChecking_R", (DL_FUNC) &LGBM_DatasetUpdateParamChecking_R, 2},
   {"LGBM_DatasetGetNumData_R"         , (DL_FUNC) &LGBM_DatasetGetNumData_R         , 2},
   {"LGBM_DatasetGetNumFeature_R"      , (DL_FUNC) &LGBM_DatasetGetNumFeature_R      , 2},
-  {"LGBM_BoosterCreate_R"             , (DL_FUNC) &LGBM_BoosterCreate_R             , 3},
+  {"LGBM_BoosterCreate_R"             , (DL_FUNC) &LGBM_BoosterCreate_R             , 2},
   {"LGBM_BoosterFree_R"               , (DL_FUNC) &LGBM_BoosterFree_R               , 1},
-  {"LGBM_BoosterCreateFromModelfile_R", (DL_FUNC) &LGBM_BoosterCreateFromModelfile_R, 2},
-  {"LGBM_BoosterLoadModelFromString_R", (DL_FUNC) &LGBM_BoosterLoadModelFromString_R, 2},
+  {"LGBM_BoosterCreateFromModelfile_R", (DL_FUNC) &LGBM_BoosterCreateFromModelfile_R, 1},
+  {"LGBM_BoosterLoadModelFromString_R", (DL_FUNC) &LGBM_BoosterLoadModelFromString_R, 1},
   {"LGBM_BoosterMerge_R"              , (DL_FUNC) &LGBM_BoosterMerge_R              , 2},
   {"LGBM_BoosterAddValidData_R"       , (DL_FUNC) &LGBM_BoosterAddValidData_R       , 2},
   {"LGBM_BoosterResetTrainingData_R"  , (DL_FUNC) &LGBM_BoosterResetTrainingData_R  , 2},

R-package/src/lightgbm_R.h

@@ -11,14 +11,21 @@
 #define R_USE_C99_IN_CXX
 #include <Rinternals.h>
 
-#include "R_object_helper.h"
-
 /*!
 * \brief get string message of the last error
 * \return err_msg string with error information
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_GetLastError_R();
 
+/*!
+* \brief check if an R external pointer (like a Booster or Dataset handle) is a null pointer
+* \param handle handle for a Booster, Dataset, or Predictor
+* \return R logical, TRUE if the handle is a null pointer
+*/
+LIGHTGBM_C_EXPORT SEXP LGBM_HandleIsNull_R(
+  SEXP handle
+);
+
 // --- start Dataset interface
 
 /*!
@@ -26,14 +33,12 @@ LIGHTGBM_C_EXPORT SEXP LGBM_GetLastError_R();
 * \param filename the name of the file
 * \param parameters additional parameters
 * \param reference used to align bin mapper with other Dataset, nullptr means not used
-* \param out created Dataset
-* \return R NULL value
+* \return Dataset handle
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_DatasetCreateFromFile_R(
   SEXP filename,
   SEXP parameters,
-  LGBM_SE reference,
-  LGBM_SE out
+  SEXP reference
 );
 
 /*!
@@ -46,8 +51,7 @@ LIGHTGBM_C_EXPORT SEXP LGBM_DatasetCreateFromFile_R(
 * \param num_row number of rows
 * \param parameters additional parameters
 * \param reference used to align bin mapper with other Dataset, nullptr means not used
-* \param out created Dataset
-* \return R NULL value
+* \return Dataset handle
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_DatasetCreateFromCSC_R(
   SEXP indptr,
@@ -57,8 +61,7 @@ LIGHTGBM_C_EXPORT SEXP LGBM_DatasetCreateFromCSC_R(
   SEXP nelem,
   SEXP num_row,
   SEXP parameters,
-  LGBM_SE reference,
-  LGBM_SE out
+  SEXP reference
 );
 
 /*!
@@ -68,16 +71,14 @@ LIGHTGBM_C_EXPORT SEXP LGBM_DatasetCreateFromCSC_R(
 * \param num_col number columns
 * \param parameters additional parameters
 * \param reference used to align bin mapper with other Dataset, nullptr means not used
-* \param out created Dataset
-* \return R NULL value
+* \return Dataset handle
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_DatasetCreateFromMat_R(
   SEXP data,
   SEXP num_row,
   SEXP num_col,
   SEXP parameters,
-  LGBM_SE reference,
-  LGBM_SE out
+  SEXP reference
 );
 
 /*!
@@ -86,15 +87,13 @@ LIGHTGBM_C_EXPORT SEXP LGBM_DatasetCreateFromMat_R(
 * \param used_row_indices Indices used in subset
 * \param len_used_row_indices length of Indices used in subset
 * \param parameters additional parameters
-* \param out created Dataset
-* \return R NULL value
+* \return Dataset handle
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_DatasetGetSubset_R(
-  LGBM_SE handle,
+  SEXP handle,
   SEXP used_row_indices,
   SEXP len_used_row_indices,
-  SEXP parameters,
-  LGBM_SE out
+  SEXP parameters
 );
 
 /*!
@@ -104,7 +103,7 @@ LIGHTGBM_C_EXPORT SEXP LGBM_DatasetGetSubset_R(
 * \return R character vector of feature names
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_DatasetSetFeatureNames_R(
-  LGBM_SE handle,
+  SEXP handle,
   SEXP feature_names
 );
 
@@ -114,7 +113,7 @@ LIGHTGBM_C_EXPORT SEXP LGBM_DatasetSetFeatureNames_R(
 * \return an R character vector with feature names from the Dataset or NULL if no feature names
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_DatasetGetFeatureNames_R(
-  LGBM_SE handle
+  SEXP handle
 );
 
 /*!
@@ -124,7 +123,7 @@ LIGHTGBM_C_EXPORT SEXP LGBM_DatasetGetFeatureNames_R(
 * \return R NULL value
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_DatasetSaveBinary_R(
-  LGBM_SE handle,
+  SEXP handle,
   SEXP filename
 );
 
@@ -134,7 +133,7 @@ LIGHTGBM_C_EXPORT SEXP LGBM_DatasetSaveBinary_R(
 * \return R NULL value
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_DatasetFree_R(
-  LGBM_SE handle
+  SEXP handle
 );
 
 /*!
@@ -148,7 +147,7 @@ LIGHTGBM_C_EXPORT SEXP LGBM_DatasetFree_R(
 * \return R NULL value
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_DatasetSetField_R(
-  LGBM_SE handle,
+  SEXP handle,
   SEXP field_name,
   SEXP field_data,
   SEXP num_element
@@ -162,7 +161,7 @@ LIGHTGBM_C_EXPORT SEXP LGBM_DatasetSetField_R(
 * \return R NULL value
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_DatasetGetFieldSize_R(
-  LGBM_SE handle,
+  SEXP handle,
   SEXP field_name,
   SEXP out
 );
@@ -175,7 +174,7 @@ LIGHTGBM_C_EXPORT SEXP LGBM_DatasetGetFieldSize_R(
 * \return R NULL value
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_DatasetGetField_R(
-  LGBM_SE handle,
+  SEXP handle,
   SEXP field_name,
   SEXP field_data
 );
@@ -199,7 +198,7 @@ LIGHTGBM_C_EXPORT SEXP LGBM_DatasetUpdateParamChecking_R(
 * \return R NULL value
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_DatasetGetNumData_R(
-  LGBM_SE handle,
+  SEXP handle,
   SEXP out
 );
 
@@ -210,7 +209,7 @@ LIGHTGBM_C_EXPORT SEXP LGBM_DatasetGetNumData_R(
 * \return R NULL value
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_DatasetGetNumFeature_R(
-  LGBM_SE handle,
+  SEXP handle,
   SEXP out
 );
 
@@ -220,13 +219,11 @@ LIGHTGBM_C_EXPORT SEXP LGBM_DatasetGetNumFeature_R(
 * \brief create a new boosting learner
 * \param train_data training Dataset
 * \param parameters format: 'key1=value1 key2=value2'
-* \param out handle of created Booster
-* \return R NULL value
+* \return Booster handle
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_BoosterCreate_R(
-  LGBM_SE train_data,
-  SEXP parameters,
-  LGBM_SE out
+  SEXP train_data,
+  SEXP parameters
 );
 
 /*!
@@ -235,29 +232,25 @@ LIGHTGBM_C_EXPORT SEXP LGBM_BoosterCreate_R(
 * \return R NULL value
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_BoosterFree_R(
-  LGBM_SE handle
+  SEXP handle
 );
 
 /*!
 * \brief load an existing Booster from model file
 * \param filename filename of model
-* \param out handle of created Booster
-* \return R NULL value
+* \return Booster handle
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_BoosterCreateFromModelfile_R(
-  SEXP filename,
-  LGBM_SE out
+  SEXP filename
 );
 
 /*!
 * \brief load an existing Booster from a string
 * \param model_str string containing the model
-* \param out handle of created Booster
-* \return R NULL value
+* \return Booster handle
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_BoosterLoadModelFromString_R(
-  SEXP model_str,
-  LGBM_SE out
+  SEXP model_str
 );
 
 /*!
@@ -267,8 +260,8 @@ LIGHTGBM_C_EXPORT SEXP LGBM_BoosterLoadModelFromString_R(
 * \return R NULL value
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_BoosterMerge_R(
-  LGBM_SE handle,
-  LGBM_SE other_handle
+  SEXP handle,
+  SEXP other_handle
 );
 
 /*!
@@ -278,8 +271,8 @@ LIGHTGBM_C_EXPORT SEXP LGBM_BoosterMerge_R(
 * \return R NULL value
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_BoosterAddValidData_R(
-  LGBM_SE handle,
-  LGBM_SE valid_data
+  SEXP handle,
+  SEXP valid_data
 );
 
 /*!
@@ -289,8 +282,8 @@ LIGHTGBM_C_EXPORT SEXP LGBM_BoosterAddValidData_R(
 * \return R NULL value
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_BoosterResetTrainingData_R(
-  LGBM_SE handle,
-  LGBM_SE train_data
+  SEXP handle,
+  SEXP train_data
 );
 
 /*!
@@ -300,7 +293,7 @@ LIGHTGBM_C_EXPORT SEXP LGBM_BoosterResetTrainingData_R(
 * \return R NULL value
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_BoosterResetParameter_R(
-  LGBM_SE handle,
+  SEXP handle,
   SEXP parameters
 );
 
@@ -311,7 +304,7 @@ LIGHTGBM_C_EXPORT SEXP LGBM_BoosterResetParameter_R(
 * \return R NULL value
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_BoosterGetNumClasses_R(
-  LGBM_SE handle,
+  SEXP handle,
   SEXP out
 );
 
@@ -321,7 +314,7 @@ LIGHTGBM_C_EXPORT SEXP LGBM_BoosterGetNumClasses_R(
 * \return R NULL value
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_BoosterUpdateOneIter_R(
-  LGBM_SE handle
+  SEXP handle
 );
 
 /*!
@@ -334,7 +327,7 @@ LIGHTGBM_C_EXPORT SEXP LGBM_BoosterUpdateOneIter_R(
 * \return R NULL value
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_BoosterUpdateOneIterCustom_R(
-  LGBM_SE handle,
+  SEXP handle,
   SEXP grad,
   SEXP hess,
   SEXP len
@@ -346,7 +339,7 @@ LIGHTGBM_C_EXPORT SEXP LGBM_BoosterUpdateOneIterCustom_R(
 * \return R NULL value
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_BoosterRollbackOneIter_R(
-  LGBM_SE handle
+  SEXP handle
 );
 
 /*!
@@ -356,7 +349,7 @@ LIGHTGBM_C_EXPORT SEXP LGBM_BoosterRollbackOneIter_R(
 * \return R NULL value
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_BoosterGetCurrentIteration_R(
-  LGBM_SE handle,
+  SEXP handle,
   SEXP out
 );
 
@@ -367,7 +360,7 @@ LIGHTGBM_C_EXPORT SEXP LGBM_BoosterGetCurrentIteration_R(
 * \return R NULL value
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_BoosterGetUpperBoundValue_R(
-    LGBM_SE handle,
+    SEXP handle,
     SEXP out_result
 );
 
@@ -378,7 +371,7 @@ LIGHTGBM_C_EXPORT SEXP LGBM_BoosterGetUpperBoundValue_R(
 * \return R NULL value
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_BoosterGetLowerBoundValue_R(
-    LGBM_SE handle,
+    SEXP handle,
     SEXP out_result
 );
 
@@ -388,7 +381,7 @@ LIGHTGBM_C_EXPORT SEXP LGBM_BoosterGetLowerBoundValue_R(
 * \return R character vector with names of eval metrics
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_BoosterGetEvalNames_R(
-  LGBM_SE handle
+  SEXP handle
 );
 
 /*!
@@ -399,7 +392,7 @@ LIGHTGBM_C_EXPORT SEXP LGBM_BoosterGetEvalNames_R(
 * \return R NULL value
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_BoosterGetEval_R(
-  LGBM_SE handle,
+  SEXP handle,
   SEXP data_idx,
   SEXP out_result
 );
@@ -412,7 +405,7 @@ LIGHTGBM_C_EXPORT SEXP LGBM_BoosterGetEval_R(
 * \return R NULL value
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_BoosterGetNumPredict_R(
-  LGBM_SE handle,
+  SEXP handle,
   SEXP data_idx,
   SEXP out
 );
@@ -426,7 +419,7 @@ LIGHTGBM_C_EXPORT SEXP LGBM_BoosterGetNumPredict_R(
 * \return R NULL value
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_BoosterGetPredict_R(
-  LGBM_SE handle,
+  SEXP handle,
   SEXP data_idx,
   SEXP out_result
 );
@@ -448,7 +441,7 @@ LIGHTGBM_C_EXPORT SEXP LGBM_BoosterGetPredict_R(
 * \return R NULL value
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_BoosterPredictForFile_R(
-  LGBM_SE handle,
+  SEXP handle,
   SEXP data_filename,
   SEXP data_has_header,
   SEXP is_rawscore,
@@ -475,7 +468,7 @@ LIGHTGBM_C_EXPORT SEXP LGBM_BoosterPredictForFile_R(
 * \return R NULL value
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_BoosterCalcNumPredict_R(
-  LGBM_SE handle,
+  SEXP handle,
   SEXP num_row,
   SEXP is_rawscore,
   SEXP is_leafidx,
@@ -509,7 +502,7 @@ LIGHTGBM_C_EXPORT SEXP LGBM_BoosterCalcNumPredict_R(
 * \return R NULL value
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_BoosterPredictForCSC_R(
-  LGBM_SE handle,
+  SEXP handle,
   SEXP indptr,
   SEXP indices,
   SEXP data,
@@ -546,7 +539,7 @@ LIGHTGBM_C_EXPORT SEXP LGBM_BoosterPredictForCSC_R(
 * \return R NULL value
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_BoosterPredictForMat_R(
-  LGBM_SE handle,
+  SEXP handle,
   SEXP data,
   SEXP num_row,
   SEXP num_col,
@@ -568,7 +561,7 @@ LIGHTGBM_C_EXPORT SEXP LGBM_BoosterPredictForMat_R(
 * \return R NULL value
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_BoosterSaveModel_R(
-  LGBM_SE handle,
+  SEXP handle,
   SEXP num_iteration,
   SEXP feature_importance_type,
   SEXP filename
@@ -582,7 +575,7 @@ LIGHTGBM_C_EXPORT SEXP LGBM_BoosterSaveModel_R(
 * \return R character vector (length=1) with model string
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_BoosterSaveModelToString_R(
-  LGBM_SE handle,
+  SEXP handle,
   SEXP num_iteration,
   SEXP feature_importance_type
 );
@@ -595,7 +588,7 @@ LIGHTGBM_C_EXPORT SEXP LGBM_BoosterSaveModelToString_R(
 * \return R character vector (length=1) with model JSON
 */
 LIGHTGBM_C_EXPORT SEXP LGBM_BoosterDumpModel_R(
-  LGBM_SE handle,
+  SEXP handle,
   SEXP num_iteration,
   SEXP feature_importance_type
 );

R-package/tests/testthat/test_dataset.R

@@ -73,16 +73,14 @@ test_that("lgb.Dataset: nrow is correct for a very sparse matrix", {
 
 test_that("lgb.Dataset: Dataset should be able to construct from matrix and return non-null handle", {
   rawData <- matrix(runif(1000L), ncol = 10L)
-  handle <- lgb.null.handle()
   ref_handle <- NULL
-  .Call(
+  handle <- .Call(
     LGBM_DatasetCreateFromMat_R
     , rawData
     , nrow(rawData)
     , ncol(rawData)
     , lightgbm:::lgb.params2str(params = list())
     , ref_handle
-    , handle
   )
   expect_false(is.na(handle))
   .Call(LGBM_DatasetFree_R, handle)

build_r.R

@@ -324,7 +324,7 @@ result <- file.copy(
   , overwrite = TRUE
 )
 .handle_result(result)
-for (src_file in c("lightgbm_R.cpp", "lightgbm_R.h", "R_object_helper.h")) {
+for (src_file in c("lightgbm_R.cpp", "lightgbm_R.h")) {
   result <- file.copy(
     from = file.path(TEMP_SOURCE_DIR, src_file)
     , to = file.path(TEMP_SOURCE_DIR, "src", src_file)
@@ -386,11 +386,6 @@ dynlib_line <- grep(
 
 c_api_contents <- readLines(file.path(TEMP_SOURCE_DIR, "src", "lightgbm_R.h"))
 c_api_contents <- c_api_contents[grepl("^LIGHTGBM_C_EXPORT", c_api_contents)]
-c_api_contents <- gsub(
-  pattern = "LIGHTGBM_C_EXPORT LGBM_SE "
-  , replacement = ""
-  , x = c_api_contents
-)
 c_api_contents <- gsub(
   pattern = "LIGHTGBM_C_EXPORT SEXP "
   , replacement = ""