Merge pull request apache#3 from apache/master

Pulling functionality from apache spark
prabeesh · Jun 22, 2015 · 0be142d · 0be142d
2 parents 106fd8e + a189442
commit 0be142d
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diff --git a/.gitignore b/.gitignore
@@ -66,6 +66,7 @@ scalastyle-output.xml
 R-unit-tests.log
 R/unit-tests.out
 python/lib/pyspark.zip
+lint-r-report.log
 
 # For Hive
 metastore_db/

diff --git a/.rat-excludes b/.rat-excludes
@@ -28,6 +28,7 @@ spark-env.sh
 spark-env.cmd
 spark-env.sh.template
 log4j-defaults.properties
+log4j-defaults-repl.properties
 bootstrap-tooltip.js
 jquery-1.11.1.min.js
 d3.min.js
@@ -80,5 +81,9 @@ local-1425081759269/*
 local-1426533911241/*
 local-1426633911242/*
 local-1430917381534/*
+local-1430917381535_1
+local-1430917381535_2
 DESCRIPTION
 NAMESPACE
+test_support/*
+.lintr
diff --git a/LICENSE b/LICENSE
@@ -836,6 +836,68 @@ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 See the License for the specific language governing permissions and
 limitations under the License.
 
+========================================================================
+For vis.js (core/src/main/resources/org/apache/spark/ui/static/vis.min.js):
+========================================================================
+Copyright (C) 2010-2015 Almende B.V.
+
+Vis.js is dual licensed under both
+
+  * The Apache 2.0 License
+    http://www.apache.org/licenses/LICENSE-2.0
+
+and
+
+  * The MIT License
+    http://opensource.org/licenses/MIT
+
+Vis.js may be distributed under either license.
+
+========================================================================
+For dagre-d3 (core/src/main/resources/org/apache/spark/ui/static/dagre-d3.min.js):
+========================================================================
+Copyright (c) 2013 Chris Pettitt
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+
+========================================================================
+For graphlib-dot (core/src/main/resources/org/apache/spark/ui/static/graphlib-dot.min.js):
+========================================================================
+Copyright (c) 2012-2013 Chris Pettitt
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
 
 ========================================================================
 BSD-style licenses
@@ -845,7 +907,7 @@ The following components are provided under a BSD-style license. See project lin
 
      (BSD 3 Clause) core (com.github.fommil.netlib:core:1.1.2 - https://github.com/fommil/netlib-java/core)
      (BSD 3 Clause) JPMML-Model (org.jpmml:pmml-model:1.1.15 - https://github.com/jpmml/jpmml-model)
-     (BSD 3-clause style license) jblas (org.jblas:jblas:1.2.3 - http://jblas.org/)
+     (BSD 3-clause style license) jblas (org.jblas:jblas:1.2.4 - http://jblas.org/)
      (BSD License) AntLR Parser Generator (antlr:antlr:2.7.7 - http://www.antlr.org/)
      (BSD License) Javolution (javolution:javolution:5.5.1 - http://javolution.org)
      (BSD licence) ANTLR ST4 4.0.4 (org.antlr:ST4:4.0.4 - http://www.stringtemplate.org)
@@ -888,3 +950,4 @@ The following components are provided under the MIT License. See project link fo
      (MIT License) scopt (com.github.scopt:scopt_2.10:3.2.0 - https://github.com/scopt/scopt)
      (The MIT License) Mockito (org.mockito:mockito-all:1.8.5 - http://www.mockito.org)
      (MIT License) jquery (https://jquery.org/license/)
+     (MIT License) AnchorJS (https://github.com/bryanbraun/anchorjs)
diff --git a/R/README.md b/R/README.md
@@ -52,7 +52,7 @@ The SparkR documentation (Rd files and HTML files) are not a part of the source
 SparkR comes with several sample programs in the `examples/src/main/r` directory.
 To run one of them, use `./bin/sparkR <filename> <args>`. For example:
 
-    ./bin/sparkR examples/src/main/r/pi.R local[2]
+    ./bin/sparkR examples/src/main/r/dataframe.R
 
 You can also run the unit-tests for SparkR by running (you need to install the [testthat](http://cran.r-project.org/web/packages/testthat/index.html) package first):
 
@@ -63,5 +63,5 @@ You can also run the unit-tests for SparkR by running (you need to install the [
 The `./bin/spark-submit` and `./bin/sparkR` can also be used to submit jobs to YARN clusters. You will need to set YARN conf dir before doing so. For example on CDH you can run
 ```
 export YARN_CONF_DIR=/etc/hadoop/conf
-./bin/spark-submit --master yarn examples/src/main/r/pi.R 4
+./bin/spark-submit --master yarn examples/src/main/r/dataframe.R
 ```
diff --git a/R/create-docs.sh b/R/create-docs.sh
@@ -23,14 +23,14 @@
 # After running this script the html docs can be found in 
 # $SPARK_HOME/R/pkg/html
 
+set -o pipefail
+set -e
+
 # Figure out where the script is
 export FWDIR="$(cd "`dirname "$0"`"; pwd)"
 pushd $FWDIR
 
-# Generate Rd file
-Rscript -e 'library(devtools); devtools::document(pkg="./pkg", roclets=c("rd"))'
-
-# Install the package
+# Install the package (this will also generate the Rd files)
 ./install-dev.sh
 
 # Now create HTML files

diff --git a/R/install-dev.sh b/R/install-dev.sh
@@ -26,11 +26,20 @@
 # NOTE(shivaram): Right now we use $SPARK_HOME/R/lib to be the installation directory
 # to load the SparkR package on the worker nodes.
 
+set -o pipefail
+set -e
 
 FWDIR="$(cd `dirname $0`; pwd)"
 LIB_DIR="$FWDIR/lib"
 
 mkdir -p $LIB_DIR
 
-# Install R
+pushd $FWDIR
+
+# Generate Rd files if devtools is installed
+Rscript -e ' if("devtools" %in% rownames(installed.packages())) { library(devtools); devtools::document(pkg="./pkg", roclets=c("rd")) }'
+
+# Install SparkR to $LIB_DIR
 R CMD INSTALL --library=$LIB_DIR $FWDIR/pkg/
+
+popd
diff --git a/R/log4j.properties b/R/log4j.properties
@@ -19,7 +19,7 @@
 log4j.rootCategory=INFO, file
 log4j.appender.file=org.apache.log4j.FileAppender
 log4j.appender.file.append=true
-log4j.appender.file.file=R-unit-tests.log
+log4j.appender.file.file=R/target/unit-tests.log
 log4j.appender.file.layout=org.apache.log4j.PatternLayout
 log4j.appender.file.layout.ConversionPattern=%d{yy/MM/dd HH:mm:ss.SSS} %t %p %c{1}: %m%n
 

diff --git a/R/pkg/.lintr b/R/pkg/.lintr
@@ -0,0 +1,2 @@
+linters: with_defaults(line_length_linter(100), camel_case_linter = NULL)
+exclusions: list("inst/profile/general.R" = 1, "inst/profile/shell.R")
diff --git a/R/pkg/NAMESPACE b/R/pkg/NAMESPACE
@@ -1,25 +1,37 @@
 # Imports from base R
 importFrom(methods, setGeneric, setMethod, setOldClass)
-useDynLib(SparkR, stringHashCode)
+
+# Disable native libraries till we figure out how to package it
+# See SPARKR-7839
+#useDynLib(SparkR, stringHashCode)
 
 # S3 methods exported
 export("sparkR.init")
 export("sparkR.stop")
 export("print.jobj")
 
+# Job group lifecycle management methods
+export("setJobGroup",
+       "clearJobGroup",
+       "cancelJobGroup")
+
 exportClasses("DataFrame")
 
-exportMethods("cache",
+exportMethods("arrange",
+              "cache",
               "collect",
               "columns",
               "count",
               "describe",
               "distinct",
+              "dropna",
               "dtypes",
               "except",
               "explain",
+              "fillna",
               "filter",
               "first",
+              "group_by",
               "groupBy",
               "head",
               "insertInto",
@@ -28,12 +40,15 @@ exportMethods("cache",
               "join",
               "limit",
               "orderBy",
+              "mutate",
               "names",
               "persist",
               "printSchema",
               "registerTempTable",
+              "rename",
               "repartition",
-              "sampleDF",
+              "sample",
+              "sample_frac",
               "saveAsParquetFile",
               "saveAsTable",
               "saveDF",
@@ -42,42 +57,68 @@ exportMethods("cache",
               "selectExpr",
               "show",
               "showDF",
-              "sortDF",
+              "summarize",
               "take",
               "unionAll",
               "unpersist",
               "where",
               "withColumn",
-              "withColumnRenamed")
+              "withColumnRenamed",
+              "write.df")
 
 exportClasses("Column")
 
 exportMethods("abs",
+              "acos",
               "alias",
               "approxCountDistinct",
               "asc",
+              "asin",
+              "atan",
+              "atan2",
               "avg",
               "cast",
+              "cbrt",
+              "ceiling",
               "contains",
+              "cos",
+              "cosh",
               "countDistinct",
               "desc",
               "endsWith",
+              "exp",
+              "expm1",
+              "floor",
               "getField",
               "getItem",
+              "hypot",
               "isNotNull",
               "isNull",
               "last",
               "like",
+              "log",
+              "log10",
+              "log1p",
               "lower",
               "max",
               "mean",
               "min",
+              "n",
+              "n_distinct",
+              "rint",
               "rlike",
+              "sign",
+              "sin",
+              "sinh",
               "sqrt",
               "startsWith",
               "substr",
               "sum",
               "sumDistinct",
+              "tan",
+              "tanh",
+              "toDegrees",
+              "toRadians",
               "upper")
 
 exportClasses("GroupedData")
@@ -94,6 +135,7 @@ export("cacheTable",
        "jsonFile",
        "loadDF",
        "parquetFile",
+       "read.df",
        "sql",
        "table",
        "tableNames",