updated R dependencies (#1619)

R-package/DESCRIPTION

@@ -23,23 +23,23 @@ URL: https://github.com/Microsoft/LightGBM
 BugReports: https://github.com/Microsoft/LightGBM/issues
 VignetteBuilder: knitr
 Suggests:
+    Ckmeans.1d.dp (>= 3.3.1),
+    DiagrammeR (>= 0.8.1),
+    ggplot2 (>= 1.0.1),
+    igraph (>= 1.0.1),
     knitr,
     rmarkdown,
-    ggplot2 (>= 1.0.1),
-    DiagrammeR (>= 0.8.1),
-    Ckmeans.1d.dp (>= 3.3.1),
-    vcd (>= 1.3),
+    stringi (>= 0.5.2),
     testthat,
-    igraph (>= 1.0.1),
-    stringi (>= 0.5.2)
+    vcd (>= 1.3)
 Depends:
     R (>= 3.0),
     R6 (>= 2.0)
 Imports:
-    graphics,
-    methods,
-    Matrix (>= 1.1-0),
     data.table (>= 1.9.6),
+    graphics,
+    jsonlite (>= 1.0),
     magrittr (>= 1.5),
-    jsonlite (>= 1.0)
+    Matrix (>= 1.1-0),
+    methods
 RoxygenNote: 6.0.1

R-package/NAMESPACE

@@ -38,9 +38,15 @@ export(slice)
 import(methods)
 importFrom(R6,R6Class)
 importFrom(data.table,":=")
+importFrom(data.table,data.table)
+importFrom(data.table,rbindlist)
 importFrom(data.table,set)
 importFrom(graphics,barplot)
 importFrom(graphics,par)
+importFrom(jsonlite,fromJSON)
 importFrom(magrittr,"%>%")
 importFrom(magrittr,"%T>%")
+importFrom(magrittr,extract)
+importFrom(magrittr,inset)
+importFrom(methods,is)
 useDynLib(lib_lightgbm)

R-package/R/lgb.Dataset.R

+
+#' @importFrom methods is
 Dataset <- R6Class(
   classname = "lgb.Dataset",
   cloneable = FALSE,
@@ -120,7 +122,7 @@ Dataset <- R6Class(
 
       # Get feature names
       cnames <- NULL
-      if (is.matrix(private$raw_data) || is(private$raw_data, "dgCMatrix")) {
+      if (is.matrix(private$raw_data) || methods::is(private$raw_data, "dgCMatrix")) {
         cnames <- colnames(private$raw_data)
       }
 
@@ -200,7 +202,7 @@ Dataset <- R6Class(
                              params_str,
                              ref_handle)
 
-        } else if (is(private$raw_data, "dgCMatrix")) {
+        } else if (methods::is(private$raw_data, "dgCMatrix")) {
           if (length(private$raw_data@p) > 2147483647) {
             stop("Cannot support large CSC matrix")
           }
@@ -304,7 +306,7 @@ Dataset <- R6Class(
         c(lgb.call("LGBM_DatasetGetNumData_R", ret = num_row, private$handle),
           lgb.call("LGBM_DatasetGetNumFeature_R", ret = num_col, private$handle))
 
-      } else if (is.matrix(private$raw_data) || is(private$raw_data, "dgCMatrix")) {
+      } else if (is.matrix(private$raw_data) || methods::is(private$raw_data, "dgCMatrix")) {
 
         # Check if dgCMatrix (sparse matrix column compressed)
         dim(private$raw_data)
@@ -329,7 +331,7 @@ Dataset <- R6Class(
         private$colnames <- as.character(base::strsplit(cnames, "\t")[[1]])
         private$colnames
 
-      } else if (is.matrix(private$raw_data) || is(private$raw_data, "dgCMatrix")) {
+      } else if (is.matrix(private$raw_data) || methods::is(private$raw_data, "dgCMatrix")) {
 
         # Check if dgCMatrix (sparse matrix column compressed)
         colnames(private$raw_data)

R-package/R/lgb.Predictor.R

+
+#' @importFrom methods is
 Predictor <- R6Class(
   classname = "lgb.Predictor",
   cloneable = FALSE,
@@ -31,7 +33,7 @@ Predictor <- R6Class(
         handle <- lgb.call("LGBM_BoosterCreateFromModelfile_R", ret = handle, lgb.c_str(modelfile))
         private$need_free_handle <- TRUE
 
-      } else if (is(modelfile, "lgb.Booster.handle")) {
+      } else if (methods::is(modelfile, "lgb.Booster.handle")) {
 
         # Check if model file is a booster handle already
         handle <- modelfile
@@ -131,7 +133,7 @@ Predictor <- R6Class(
                             as.integer(num_iteration),
                             private$params)
 
-        } else if (is(data, "dgCMatrix")) {
+        } else if (methods::is(data, "dgCMatrix")) {
           if (length(data@p) > 2147483647) {
             stop("Cannot support large CSC matrix")
           }

R-package/R/lgb.model.dt.tree.R

@@ -47,7 +47,8 @@
 #' }
 #'
 #' @importFrom magrittr %>%
-#' @importFrom data.table :=
+#' @importFrom data.table := data.table
+#' @importFrom jsonlite fromJSON
 #' @export
 lgb.model.dt.tree <- function(model, num_iteration = NULL) {
 
@@ -77,6 +78,7 @@ lgb.model.dt.tree <- function(model, num_iteration = NULL) {
 
 }
 
+#' @importFrom data.table data.table rbindlist
 single.tree.parse <- function(lgb_tree) {
 
   # Traverse tree function
@@ -161,6 +163,7 @@ single.tree.parse <- function(lgb_tree) {
 
 }
 
+#' @importFrom magrittr %>% extract inset
 Lookup <- function(key, key_lookup, value_lookup, missing = NA) {
 
   # Match key by looked up key