diff --git a/R-package/NAMESPACE b/R-package/NAMESPACE
index a6a0f1799..fab1546a2 100644
--- a/R-package/NAMESPACE
+++ b/R-package/NAMESPACE
@@ -1,4 +1,4 @@
-# Generated by roxygen2 (4.0.1): do not edit by hand
+# Generated by roxygen2 (4.1.0): do not edit by hand
 
 export(getinfo)
 export(setinfo)
diff --git a/R-package/man/agaricus.test.Rd b/R-package/man/agaricus.test.Rd
index c050d3ecd..556425379 100644
--- a/R-package/man/agaricus.test.Rd
+++ b/R-package/man/agaricus.test.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/xgboost.R
 \docType{data}
 \name{agaricus.test}
 \alias{agaricus.test}
diff --git a/R-package/man/agaricus.train.Rd b/R-package/man/agaricus.train.Rd
index 02571cf54..879b3d5df 100644
--- a/R-package/man/agaricus.train.Rd
+++ b/R-package/man/agaricus.train.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/xgboost.R
 \docType{data}
 \name{agaricus.train}
 \alias{agaricus.train}
diff --git a/R-package/man/getinfo.Rd b/R-package/man/getinfo.Rd
index 23e3adc84..37e0ad0be 100644
--- a/R-package/man/getinfo.Rd
+++ b/R-package/man/getinfo.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/getinfo.xgb.DMatrix.R
 \docType{methods}
 \name{getinfo}
 \alias{getinfo}
@@ -12,9 +13,9 @@ getinfo(object, ...)
 \arguments{
 \item{object}{Object of class "xgb.DMatrix"}
 
-\item{name}{the name of the field to get}
-
 \item{...}{other parameters}
+
+\item{name}{the name of the field to get}
 }
 \description{
 Get information of an xgb.DMatrix object
diff --git a/R-package/man/predict-xgb.Booster-method.Rd b/R-package/man/predict-xgb.Booster-method.Rd
index 204a8167f..17d0e5a62 100644
--- a/R-package/man/predict-xgb.Booster-method.Rd
+++ b/R-package/man/predict-xgb.Booster-method.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/predict.xgb.Booster.R
 \docType{methods}
 \name{predict,xgb.Booster-method}
 \alias{predict,xgb.Booster-method}
diff --git a/R-package/man/setinfo.Rd b/R-package/man/setinfo.Rd
index 7ea992110..4ed262b46 100644
--- a/R-package/man/setinfo.Rd
+++ b/R-package/man/setinfo.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/setinfo.xgb.DMatrix.R
 \docType{methods}
 \name{setinfo}
 \alias{setinfo}
@@ -12,11 +13,11 @@ setinfo(object, ...)
 \arguments{
 \item{object}{Object of class "xgb.DMatrix"}
 
+\item{...}{other parameters}
+
 \item{name}{the name of the field to get}
 
 \item{info}{the specific field of information to set}
-
-\item{...}{other parameters}
 }
 \description{
 Set information of an xgb.DMatrix object
diff --git a/R-package/man/slice.Rd b/R-package/man/slice.Rd
index a749aa8ff..a7812e886 100644
--- a/R-package/man/slice.Rd
+++ b/R-package/man/slice.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/slice.xgb.DMatrix.R
 \docType{methods}
 \name{slice}
 \alias{slice}
@@ -13,9 +14,9 @@ slice(object, ...)
 \arguments{
 \item{object}{Object of class "xgb.DMatrix"}
 
-\item{idxset}{a integer vector of indices of rows needed}
-
 \item{...}{other parameters}
+
+\item{idxset}{a integer vector of indices of rows needed}
 }
 \description{
 Get a new DMatrix containing the specified rows of
diff --git a/R-package/man/xgb.DMatrix.Rd b/R-package/man/xgb.DMatrix.Rd
index 31efde687..ea644a291 100644
--- a/R-package/man/xgb.DMatrix.Rd
+++ b/R-package/man/xgb.DMatrix.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/xgb.DMatrix.R
 \name{xgb.DMatrix}
 \alias{xgb.DMatrix}
 \title{Contruct xgb.DMatrix object}
diff --git a/R-package/man/xgb.DMatrix.save.Rd b/R-package/man/xgb.DMatrix.save.Rd
index 803de912b..6bbc277b3 100644
--- a/R-package/man/xgb.DMatrix.save.Rd
+++ b/R-package/man/xgb.DMatrix.save.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/xgb.DMatrix.save.R
 \name{xgb.DMatrix.save}
 \alias{xgb.DMatrix.save}
 \title{Save xgb.DMatrix object to binary file}
diff --git a/R-package/man/xgb.cv.Rd b/R-package/man/xgb.cv.Rd
index 149ec392f..75b31cee1 100644
--- a/R-package/man/xgb.cv.Rd
+++ b/R-package/man/xgb.cv.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/xgb.cv.R
 \name{xgb.cv}
 \alias{xgb.cv}
 \title{Cross Validation}
diff --git a/R-package/man/xgb.dump.Rd b/R-package/man/xgb.dump.Rd
index d1968217b..7958a72e8 100644
--- a/R-package/man/xgb.dump.Rd
+++ b/R-package/man/xgb.dump.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/xgb.dump.R
 \name{xgb.dump}
 \alias{xgb.dump}
 \title{Save xgboost model to text file}
diff --git a/R-package/man/xgb.importance.Rd b/R-package/man/xgb.importance.Rd
index 1588639b4..1b2946729 100644
--- a/R-package/man/xgb.importance.Rd
+++ b/R-package/man/xgb.importance.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/xgb.importance.R
 \name{xgb.importance}
 \alias{xgb.importance}
 \title{Show importance of features in a model}
diff --git a/R-package/man/xgb.load.Rd b/R-package/man/xgb.load.Rd
index d2c5d94b6..433b38c79 100644
--- a/R-package/man/xgb.load.Rd
+++ b/R-package/man/xgb.load.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/xgb.load.R
 \name{xgb.load}
 \alias{xgb.load}
 \title{Load xgboost model from binary file}
diff --git a/R-package/man/xgb.model.dt.tree.Rd b/R-package/man/xgb.model.dt.tree.Rd
index 3ac938a9b..069e7ad77 100644
--- a/R-package/man/xgb.model.dt.tree.Rd
+++ b/R-package/man/xgb.model.dt.tree.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/xgb.model.dt.tree.R
 \name{xgb.model.dt.tree}
 \alias{xgb.model.dt.tree}
 \title{Convert tree model dump to data.table}
diff --git a/R-package/man/xgb.plot.tree.Rd b/R-package/man/xgb.plot.tree.Rd
index dc95dfec0..8aec827ec 100644
--- a/R-package/man/xgb.plot.tree.Rd
+++ b/R-package/man/xgb.plot.tree.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/xgb.plot.tree.R
 \name{xgb.plot.tree}
 \alias{xgb.plot.tree}
 \title{Plot a boosted tree model}
diff --git a/R-package/man/xgb.save.Rd b/R-package/man/xgb.save.Rd
index 0ccdf13da..ded444446 100644
--- a/R-package/man/xgb.save.Rd
+++ b/R-package/man/xgb.save.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/xgb.save.R
 \name{xgb.save}
 \alias{xgb.save}
 \title{Save xgboost model to binary file}
diff --git a/R-package/man/xgb.train.Rd b/R-package/man/xgb.train.Rd
index a05e2eeb9..58ef94135 100644
--- a/R-package/man/xgb.train.Rd
+++ b/R-package/man/xgb.train.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/xgb.train.R
 \name{xgb.train}
 \alias{xgb.train}
 \title{eXtreme Gradient Boosting Training}
diff --git a/R-package/man/xgboost.Rd b/R-package/man/xgboost.Rd
index 035eec9e7..39364c64e 100644
--- a/R-package/man/xgboost.Rd
+++ b/R-package/man/xgboost.Rd
@@ -1,4 +1,5 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.1.0): do not edit by hand
+% Please edit documentation in R/xgboost.R
 \name{xgboost}
 \alias{xgboost}
 \title{eXtreme Gradient Boosting (Tree) library}
@@ -13,6 +14,9 @@ xgboost(data = NULL, label = NULL, missing = NULL, params = list(),
 \item{label}{the response variable. User should not set this field,
 if data is local data file or  \code{xgb.DMatrix}.}
 
+\item{missing}{Missing is only used when input is dense matrix, pick a float
+value that represents missing value. Sometime a data use 0 or other extreme value to represents missing values.}
+
 \item{params}{the list of parameters. Commonly used ones are:
 \itemize{
   \item \code{objective} objective function, common ones are
@@ -34,9 +38,6 @@ if data is local data file or  \code{xgb.DMatrix}.}
 information of performance. If 2, xgboost will print information of both
 performance and construction progress information}
 
-\item{missing}{Missing is only used when input is dense matrix, pick a float
-value that represents missing value. Sometime a data use 0 or other extreme value to represents missing values.}
-
 \item{...}{other parameters to pass to \code{params}.}
 }
 \description{