Merge pull request apache#64 from palantir/rk/merge

Merge upstream

Author: robert3005

.gitignore

@@ -57,6 +57,8 @@ project/plugins/project/build.properties
 project/plugins/src_managed/
 project/plugins/target/
 python/lib/pyspark.zip
+python/deps
+python/pyspark/python
 reports/
 scalastyle-on-compile.generated.xml
 scalastyle-output.xml

NOTICE

@@ -421,9 +421,6 @@ Copyright (c) 2011, Terrence Parr.
 This product includes/uses ASM (http://asm.ow2.org/),
 Copyright (c) 2000-2007 INRIA, France Telecom.
 
-This product includes/uses org.json (http://www.json.org/java/index.html),
-Copyright (c) 2002 JSON.org
-
 This product includes/uses JLine (http://jline.sourceforge.net/),
 Copyright (c) 2002-2006, Marc Prud'hommeaux <[email protected]>.
 

R/CRAN_RELEASE.md

@@ -0,0 +1,91 @@
+# SparkR CRAN Release
+
+To release SparkR as a package to CRAN, we would use the `devtools` package. Please work with the
+`[email protected]` community and R package maintainer on this.
+
+### Release
+
+First, check that the `Version:` field in the `pkg/DESCRIPTION` file is updated. Also, check for stale files not under source control.
+
+Note that while `check-cran.sh` is running `R CMD check`, it is doing so with `--no-manual --no-vignettes`, which skips a few vignettes or PDF checks - therefore it will be preferred to run `R CMD check` on the source package built manually before uploading a release.
+
+To upload a release, we would need to update the `cran-comments.md`. This should generally contain the results from running the `check-cran.sh` script along with comments on status of all `WARNING` (should not be any) or `NOTE`. As a part of `check-cran.sh` and the release process, the vignettes is build - make sure `SPARK_HOME` is set and Spark jars are accessible.
+
+Once everything is in place, run in R under the `SPARK_HOME/R` directory:
+
+```R
+paths <- .libPaths(); .libPaths(c("lib", paths)); Sys.setenv(SPARK_HOME=tools::file_path_as_absolute("..")); devtools::release(); .libPaths(paths)
+```
+
+For more information please refer to http://r-pkgs.had.co.nz/release.html#release-check
+
+### Testing: build package manually
+
+To build package manually such as to inspect the resulting `.tar.gz` file content, we would also use the `devtools` package.
+
+Source package is what get released to CRAN. CRAN would then build platform-specific binary packages from the source package.
+
+#### Build source package
+
+To build source package locally without releasing to CRAN, run in R under the `SPARK_HOME/R` directory:
+
+```R
+paths <- .libPaths(); .libPaths(c("lib", paths)); Sys.setenv(SPARK_HOME=tools::file_path_as_absolute("..")); devtools::build("pkg"); .libPaths(paths)
+```
+
+(http://r-pkgs.had.co.nz/vignettes.html#vignette-workflow-2)
+
+Similarly, the source package is also created by `check-cran.sh` with `R CMD build pkg`.
+
+For example, this should be the content of the source package:
+
+```sh
+DESCRIPTION	R		inst		tests
+NAMESPACE	build		man		vignettes
+
+inst/doc/
+sparkr-vignettes.html
+sparkr-vignettes.Rmd
+sparkr-vignettes.Rman
+
+build/
+vignette.rds
+
+man/
+ *.Rd files...
+
+vignettes/
+sparkr-vignettes.Rmd
+```
+
+#### Test source package
+
+To install, run this:
+
+```sh
+R CMD INSTALL SparkR_2.1.0.tar.gz
+```
+
+With "2.1.0" replaced with the version of SparkR.
+
+This command installs SparkR to the default libPaths. Once that is done, you should be able to start R and run:
+
+```R
+library(SparkR)
+vignette("sparkr-vignettes", package="SparkR")
+```
+
+#### Build binary package
+
+To build binary package locally, run in R under the `SPARK_HOME/R` directory:
+
+```R
+paths <- .libPaths(); .libPaths(c("lib", paths)); Sys.setenv(SPARK_HOME=tools::file_path_as_absolute("..")); devtools::build("pkg", binary = TRUE); .libPaths(paths)
+```
+
+For example, this should be the content of the binary package:
+
+```sh
+DESCRIPTION	Meta		R		html		tests
+INDEX		NAMESPACE	help		profile		worker
+```

R/README.md

@@ -6,7 +6,7 @@ SparkR is an R package that provides a light-weight frontend to use Spark from R
 
 Libraries of sparkR need to be created in `$SPARK_HOME/R/lib`. This can be done by running the script `$SPARK_HOME/R/install-dev.sh`.
 By default the above script uses the system wide installation of R. However, this can be changed to any user installed location of R by setting the environment variable `R_HOME` the full path of the base directory where R is installed, before running install-dev.sh script.
-Example: 
+Example:
 ```bash
 # where /home/username/R is where R is installed and /home/username/R/bin contains the files R and RScript
 export R_HOME=/home/username/R
@@ -46,19 +46,19 @@ Sys.setenv(SPARK_HOME="/Users/username/spark")
 # This line loads SparkR from the installed directory
 .libPaths(c(file.path(Sys.getenv("SPARK_HOME"), "R", "lib"), .libPaths()))
 library(SparkR)
-sc <- sparkR.init(master="local")
+sparkR.session()
 ```
 
 #### Making changes to SparkR
 
 The [instructions](https://cwiki.apache.org/confluence/display/SPARK/Contributing+to+Spark) for making contributions to Spark also apply to SparkR.
 If you only make R file changes (i.e. no Scala changes) then you can just re-install the R package using `R/install-dev.sh` and test your changes.
 Once you have made your changes, please include unit tests for them and run existing unit tests using the `R/run-tests.sh` script as described below.
-    
+
 #### Generating documentation
 
 The SparkR documentation (Rd files and HTML files) are not a part of the source repository. To generate them you can run the script `R/create-docs.sh`. This script uses `devtools` and `knitr` to generate the docs and these packages need to be installed on the machine before using the script. Also, you may need to install these [prerequisites](https://github.com/apache/spark/tree/master/docs#prerequisites). See also, `R/DOCUMENTATION.md`
-    
+
 ### Examples, Unit tests
 
 SparkR comes with several sample programs in the `examples/src/main/r` directory.

R/check-cran.sh

@@ -36,11 +36,27 @@ if [ ! -z "$R_HOME" ]
 fi
 echo "USING R_HOME = $R_HOME"
 
-# Build the latest docs
+# Build the latest docs, but not vignettes, which is built with the package next
 $FWDIR/create-docs.sh
 
-# Build a zip file containing the source package
-"$R_SCRIPT_PATH/"R CMD build $FWDIR/pkg
+# Build source package with vignettes
+SPARK_HOME="$(cd "${FWDIR}"/..; pwd)"
+. "${SPARK_HOME}"/bin/load-spark-env.sh
+if [ -f "${SPARK_HOME}/RELEASE" ]; then
+  SPARK_JARS_DIR="${SPARK_HOME}/jars"
+else
+  SPARK_JARS_DIR="${SPARK_HOME}/assembly/target/scala-$SPARK_SCALA_VERSION/jars"
+fi
+
+if [ -d "$SPARK_JARS_DIR" ]; then
+  # Build a zip file containing the source package with vignettes
+  SPARK_HOME="${SPARK_HOME}" "$R_SCRIPT_PATH/"R CMD build $FWDIR/pkg
+
+  find pkg/vignettes/. -not -name '.' -not -name '*.Rmd' -not -name '*.md' -not -name '*.pdf' -not -name '*.html' -delete
+else
+  echo "Error Spark JARs not found in $SPARK_HOME"
+  exit 1
+fi
 
 # Run check as-cran.
 VERSION=`grep Version $FWDIR/pkg/DESCRIPTION | awk '{print $NF}'`
@@ -54,11 +70,16 @@ fi
 
 if [ -n "$NO_MANUAL" ]
 then
-  CRAN_CHECK_OPTIONS=$CRAN_CHECK_OPTIONS" --no-manual"
+  CRAN_CHECK_OPTIONS=$CRAN_CHECK_OPTIONS" --no-manual --no-vignettes"
 fi
 
 echo "Running CRAN check with $CRAN_CHECK_OPTIONS options"
 
-"$R_SCRIPT_PATH/"R CMD check $CRAN_CHECK_OPTIONS SparkR_"$VERSION".tar.gz
-
+if [ -n "$NO_TESTS" ] && [ -n "$NO_MANUAL" ]
+then
+  "$R_SCRIPT_PATH/"R CMD check $CRAN_CHECK_OPTIONS SparkR_"$VERSION".tar.gz
+else
+  # This will run tests and/or build vignettes, and require SPARK_HOME
+  SPARK_HOME="${SPARK_HOME}" "$R_SCRIPT_PATH/"R CMD check $CRAN_CHECK_OPTIONS SparkR_"$VERSION".tar.gz
+fi
 popd > /dev/null

R/create-docs.sh

@@ -20,7 +20,7 @@
 # Script to create API docs and vignettes for SparkR
 # This requires `devtools`, `knitr` and `rmarkdown` to be installed on the machine.
 
-# After running this script the html docs can be found in 
+# After running this script the html docs can be found in
 # $SPARK_HOME/R/pkg/html
 # The vignettes can be found in
 # $SPARK_HOME/R/pkg/vignettes/sparkr_vignettes.html
@@ -52,21 +52,4 @@ Rscript -e 'libDir <- "../../lib"; library(SparkR, lib.loc=libDir); library(knit
 
 popd
 
-# Find Spark jars.
-if [ -f "${SPARK_HOME}/RELEASE" ]; then
-  SPARK_JARS_DIR="${SPARK_HOME}/jars"
-else
-  SPARK_JARS_DIR="${SPARK_HOME}/assembly/target/scala-$SPARK_SCALA_VERSION/jars"
-fi
-
-# Only create vignettes if Spark JARs exist
-if [ -d "$SPARK_JARS_DIR" ]; then
-  # render creates SparkR vignettes
-  Rscript -e 'library(rmarkdown); paths <- .libPaths(); .libPaths(c("lib", paths)); Sys.setenv(SPARK_HOME=tools::file_path_as_absolute("..")); render("pkg/vignettes/sparkr-vignettes.Rmd"); .libPaths(paths)'
-
-  find pkg/vignettes/. -not -name '.' -not -name '*.Rmd' -not -name '*.md' -not -name '*.pdf' -not -name '*.html' -delete
-else
-  echo "Skipping R vignettes as Spark JARs not found in $SPARK_HOME"
-fi
-
 popd

R/pkg/DESCRIPTION

@@ -1,8 +1,8 @@
 Package: SparkR
 Type: Package
 Title: R Frontend for Apache Spark
-Version: 2.0.0
-Date: 2016-08-27
+Version: 2.1.0
+Date: 2016-11-06
 Authors@R: c(person("Shivaram", "Venkataraman", role = c("aut", "cre"),
                     email = "[email protected]"),
              person("Xiangrui", "Meng", role = "aut",
@@ -18,7 +18,9 @@ Depends:
 Suggests:
     testthat,
     e1071,
-    survival
+    survival,
+    knitr,
+    rmarkdown
 Description: The SparkR package provides an R frontend for Apache Spark.
 License: Apache License (== 2.0)
 Collate:
@@ -48,3 +50,4 @@ Collate:
     'utils.R'
     'window.R'
 RoxygenNote: 5.0.1
+VignetteBuilder: knitr

R/pkg/NAMESPACE

@@ -45,7 +45,8 @@ exportMethods("glm",
               "spark.als",
               "spark.kstest",
               "spark.logit",
-              "spark.randomForest")
+              "spark.randomForest",
+              "spark.gbt")
 
 # Job group lifecycle management methods
 export("setJobGroup",
@@ -353,7 +354,9 @@ export("as.DataFrame",
        "read.ml",
        "print.summary.KSTest",
        "print.summary.RandomForestRegressionModel",
-       "print.summary.RandomForestClassificationModel")
+       "print.summary.RandomForestClassificationModel",
+       "print.summary.GBTRegressionModel",
+       "print.summary.GBTClassificationModel")
 
 export("structField",
        "structField.jobj",
@@ -380,6 +383,8 @@ S3method(print, summary.GeneralizedLinearRegressionModel)
 S3method(print, summary.KSTest)
 S3method(print, summary.RandomForestRegressionModel)
 S3method(print, summary.RandomForestClassificationModel)
+S3method(print, summary.GBTRegressionModel)
+S3method(print, summary.GBTClassificationModel)
 S3method(structField, character)
 S3method(structField, jobj)
 S3method(structType, jobj)

R/pkg/R/DataFrame.R

@@ -788,7 +788,7 @@ setMethod("write.json",
           function(x, path, mode = "error", ...) {
             write <- callJMethod(x@sdf, "write")
             write <- setWriteOptions(write, mode = mode, ...)
-            invisible(callJMethod(write, "json", path))
+            invisible(handledCallJMethod(write, "json", path))
           })
 
 #' Save the contents of SparkDataFrame as an ORC file, preserving the schema.
@@ -819,7 +819,7 @@ setMethod("write.orc",
           function(x, path, mode = "error", ...) {
             write <- callJMethod(x@sdf, "write")
             write <- setWriteOptions(write, mode = mode, ...)
-            invisible(callJMethod(write, "orc", path))
+            invisible(handledCallJMethod(write, "orc", path))
           })
 
 #' Save the contents of SparkDataFrame as a Parquet file, preserving the schema.
@@ -851,7 +851,7 @@ setMethod("write.parquet",
           function(x, path, mode = "error", ...) {
             write <- callJMethod(x@sdf, "write")
             write <- setWriteOptions(write, mode = mode, ...)
-            invisible(callJMethod(write, "parquet", path))
+            invisible(handledCallJMethod(write, "parquet", path))
           })
 
 #' @rdname write.parquet
@@ -895,7 +895,7 @@ setMethod("write.text",
           function(x, path, mode = "error", ...) {
             write <- callJMethod(x@sdf, "write")
             write <- setWriteOptions(write, mode = mode, ...)
-            invisible(callJMethod(write, "text", path))
+            invisible(handledCallJMethod(write, "text", path))
           })
 
 #' Distinct
@@ -936,7 +936,9 @@ setMethod("unique",
 
 #' Sample
 #'
-#' Return a sampled subset of this SparkDataFrame using a random seed.
+#' Return a sampled subset of this SparkDataFrame using a random seed. 
+#' Note: this is not guaranteed to provide exactly the fraction specified
+#' of the total count of of the given SparkDataFrame.
 #'
 #' @param x A SparkDataFrame
 #' @param withReplacement Sampling with replacement or not
@@ -3342,7 +3344,7 @@ setMethod("write.jdbc",
             jprops <- varargsToJProperties(...)
             write <- callJMethod(x@sdf, "write")
             write <- callJMethod(write, "mode", jmode)
-            invisible(callJMethod(write, "jdbc", url, tableName, jprops))
+            invisible(handledCallJMethod(write, "jdbc", url, tableName, jprops))
           })
 
 #' randomSplit

R/pkg/R/SQLContext.R

@@ -350,7 +350,7 @@ read.json.default <- function(path, ...) {
   paths <- as.list(suppressWarnings(normalizePath(path)))
   read <- callJMethod(sparkSession, "read")
   read <- callJMethod(read, "options", options)
-  sdf <- callJMethod(read, "json", paths)
+  sdf <- handledCallJMethod(read, "json", paths)
   dataFrame(sdf)
 }
 
@@ -422,7 +422,7 @@ read.orc <- function(path, ...) {
   path <- suppressWarnings(normalizePath(path))
   read <- callJMethod(sparkSession, "read")
   read <- callJMethod(read, "options", options)
-  sdf <- callJMethod(read, "orc", path)
+  sdf <- handledCallJMethod(read, "orc", path)
   dataFrame(sdf)
 }
 
@@ -444,7 +444,7 @@ read.parquet.default <- function(path, ...) {
   paths <- as.list(suppressWarnings(normalizePath(path)))
   read <- callJMethod(sparkSession, "read")
   read <- callJMethod(read, "options", options)
-  sdf <- callJMethod(read, "parquet", paths)
+  sdf <- handledCallJMethod(read, "parquet", paths)
   dataFrame(sdf)
 }
 
@@ -496,7 +496,7 @@ read.text.default <- function(path, ...) {
   paths <- as.list(suppressWarnings(normalizePath(path)))
   read <- callJMethod(sparkSession, "read")
   read <- callJMethod(read, "options", options)
-  sdf <- callJMethod(read, "text", paths)
+  sdf <- handledCallJMethod(read, "text", paths)
   dataFrame(sdf)
 }
 
@@ -914,12 +914,13 @@ read.jdbc <- function(url, tableName,
     } else {
       numPartitions <- numToInt(numPartitions)
     }
-    sdf <- callJMethod(read, "jdbc", url, tableName, as.character(partitionColumn),
-                       numToInt(lowerBound), numToInt(upperBound), numPartitions, jprops)
+    sdf <- handledCallJMethod(read, "jdbc", url, tableName, as.character(partitionColumn),
+                              numToInt(lowerBound), numToInt(upperBound), numPartitions, jprops)
   } else if (length(predicates) > 0) {
-    sdf <- callJMethod(read, "jdbc", url, tableName, as.list(as.character(predicates)), jprops)
+    sdf <- handledCallJMethod(read, "jdbc", url, tableName, as.list(as.character(predicates)),
+                              jprops)
   } else {
-    sdf <- callJMethod(read, "jdbc", url, tableName, jprops)
+    sdf <- handledCallJMethod(read, "jdbc", url, tableName, jprops)
   }
   dataFrame(sdf)
 }