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[SPARK-6807] [SparkR] Merge recent SparkR-pkg changes - #5436

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davies wants to merge 35 commits into
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davies:R3
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[SPARK-6807] [SparkR] Merge recent SparkR-pkg changes#5436
davies wants to merge 35 commits into
apache:masterfrom
davies:R3

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@davies

@daviesdavies commented Apr 9, 2015

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This PR pulls in recent changes in SparkR-pkg, including

cartesian, intersection, sampleByKey, subtract, subtractByKey, except, and some API for StructType and StructField.

@SparkQA

SparkQA commented Apr 9, 2015

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Test build #29928 has finished for PR 5436 at commit a5d8fc6.

  • This patch fails Scala style tests.
  • This patch merges cleanly.
  • This patch adds no public classes.
  • This patch removes the following dependencies:
    • RoaringBitmap-0.4.5.jar
    • activation-1.1.jar
    • akka-actor_2.10-2.3.4-spark.jar
    • akka-remote_2.10-2.3.4-spark.jar
    • akka-slf4j_2.10-2.3.4-spark.jar
    • aopalliance-1.0.jar
    • arpack_combined_all-0.1.jar
    • avro-1.7.7.jar
    • breeze-macros_2.10-0.11.2.jar
    • breeze_2.10-0.11.2.jar
    • chill-java-0.5.0.jar
    • chill_2.10-0.5.0.jar
    • commons-beanutils-1.7.0.jar
    • commons-beanutils-core-1.8.0.jar
    • commons-cli-1.2.jar
    • commons-codec-1.10.jar
    • commons-collections-3.2.1.jar
    • commons-compress-1.4.1.jar
    • commons-configuration-1.6.jar
    • commons-digester-1.8.jar
    • commons-httpclient-3.1.jar
    • commons-io-2.1.jar
    • commons-lang-2.5.jar
    • commons-lang3-3.3.2.jar
    • commons-math-2.1.jar
    • commons-math3-3.1.1.jar
    • commons-net-2.2.jar
    • compress-lzf-1.0.0.jar
    • config-1.2.1.jar
    • core-1.1.2.jar
    • curator-client-2.4.0.jar
    • curator-framework-2.4.0.jar
    • curator-recipes-2.4.0.jar
    • gmbal-api-only-3.0.0-b023.jar
    • grizzly-framework-2.1.2.jar
    • grizzly-http-2.1.2.jar
    • grizzly-http-server-2.1.2.jar
    • grizzly-http-servlet-2.1.2.jar
    • grizzly-rcm-2.1.2.jar
    • groovy-all-2.3.7.jar
    • guava-14.0.1.jar
    • guice-3.0.jar
    • hadoop-annotations-2.2.0.jar
    • hadoop-auth-2.2.0.jar
    • hadoop-client-2.2.0.jar
    • hadoop-common-2.2.0.jar
    • hadoop-hdfs-2.2.0.jar
    • hadoop-mapreduce-client-app-2.2.0.jar
    • hadoop-mapreduce-client-common-2.2.0.jar
    • hadoop-mapreduce-client-core-2.2.0.jar
    • hadoop-mapreduce-client-jobclient-2.2.0.jar
    • hadoop-mapreduce-client-shuffle-2.2.0.jar
    • hadoop-yarn-api-2.2.0.jar
    • hadoop-yarn-client-2.2.0.jar
    • hadoop-yarn-common-2.2.0.jar
    • hadoop-yarn-server-common-2.2.0.jar
    • ivy-2.4.0.jar
    • jackson-annotations-2.4.0.jar
    • jackson-core-2.4.4.jar
    • jackson-core-asl-1.8.8.jar
    • jackson-databind-2.4.4.jar
    • jackson-jaxrs-1.8.8.jar
    • jackson-mapper-asl-1.8.8.jar
    • jackson-module-scala_2.10-2.4.4.jar
    • jackson-xc-1.8.8.jar
    • jansi-1.4.jar
    • javax.inject-1.jar
    • javax.servlet-3.0.0.v201112011016.jar
    • javax.servlet-3.1.jar
    • javax.servlet-api-3.0.1.jar
    • jaxb-api-2.2.2.jar
    • jaxb-impl-2.2.3-1.jar
    • jcl-over-slf4j-1.7.10.jar
    • jersey-client-1.9.jar
    • jersey-core-1.9.jar
    • jersey-grizzly2-1.9.jar
    • jersey-guice-1.9.jar
    • jersey-json-1.9.jar
    • jersey-server-1.9.jar
    • jersey-test-framework-core-1.9.jar
    • jersey-test-framework-grizzly2-1.9.jar
    • jets3t-0.7.1.jar
    • jettison-1.1.jar
    • jetty-util-6.1.26.jar
    • jline-0.9.94.jar
    • jline-2.10.4.jar
    • jodd-core-3.6.3.jar
    • json4s-ast_2.10-3.2.10.jar
    • json4s-core_2.10-3.2.10.jar
    • json4s-jackson_2.10-3.2.10.jar
    • jsr305-1.3.9.jar
    • jtransforms-2.4.0.jar
    • jul-to-slf4j-1.7.10.jar
    • kryo-2.21.jar
    • log4j-1.2.17.jar
    • lz4-1.2.0.jar
    • management-api-3.0.0-b012.jar
    • mesos-0.21.0-shaded-protobuf.jar
    • metrics-core-3.1.0.jar
    • metrics-graphite-3.1.0.jar
    • metrics-json-3.1.0.jar
    • metrics-jvm-3.1.0.jar
    • minlog-1.2.jar
    • netty-3.8.0.Final.jar
    • netty-all-4.0.23.Final.jar
    • objenesis-1.2.jar
    • opencsv-2.3.jar
    • oro-2.0.8.jar
    • paranamer-2.6.jar
    • parquet-column-1.6.0rc3.jar
    • parquet-common-1.6.0rc3.jar
    • parquet-encoding-1.6.0rc3.jar
    • parquet-format-2.2.0-rc1.jar
    • parquet-generator-1.6.0rc3.jar
    • parquet-hadoop-1.6.0rc3.jar
    • parquet-jackson-1.6.0rc3.jar
    • protobuf-java-2.4.1.jar
    • protobuf-java-2.5.0-spark.jar
    • py4j-0.8.2.1.jar
    • pyrolite-2.0.1.jar
    • quasiquotes_2.10-2.0.1.jar
    • reflectasm-1.07-shaded.jar
    • scala-compiler-2.10.4.jar
    • scala-library-2.10.4.jar
    • scala-reflect-2.10.4.jar
    • scalap-2.10.4.jar
    • scalatest_2.10-2.2.1.jar
    • slf4j-api-1.7.10.jar
    • slf4j-log4j12-1.7.10.jar
    • snappy-java-1.1.1.6.jar
    • spark-bagel_2.10-1.4.0-SNAPSHOT.jar
    • spark-catalyst_2.10-1.4.0-SNAPSHOT.jar
    • spark-core_2.10-1.4.0-SNAPSHOT.jar
    • spark-graphx_2.10-1.4.0-SNAPSHOT.jar
    • spark-launcher_2.10-1.4.0-SNAPSHOT.jar
    • spark-mllib_2.10-1.4.0-SNAPSHOT.jar
    • spark-network-common_2.10-1.4.0-SNAPSHOT.jar
    • spark-network-shuffle_2.10-1.4.0-SNAPSHOT.jar
    • spark-repl_2.10-1.4.0-SNAPSHOT.jar
    • spark-sql_2.10-1.4.0-SNAPSHOT.jar
    • spark-streaming_2.10-1.4.0-SNAPSHOT.jar
    • spire-macros_2.10-0.7.4.jar
    • spire_2.10-0.7.4.jar
    • stax-api-1.0.1.jar
    • stream-2.7.0.jar
    • tachyon-0.5.0.jar
    • tachyon-client-0.5.0.jar
    • uncommons-maths-1.2.2a.jar
    • unused-1.0.0.jar
    • xmlenc-0.52.jar
    • xz-1.0.jar
    • zookeeper-3.4.5.jar

@daviesdavies changed the title [WIP] Merge recent SparkR-pkg changes[WIP] [SPARK-6807] [SparkR] Merge recent SparkR-pkg changesApr 9, 2015
@shivaramshivaram mentioned this pull request Apr 9, 2015
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@shivaram

shivaram commented Apr 9, 2015

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@davies could you reopen this PR or try to create it from a fresh branch ? Even though the diff looks fine, this has 250 commits or so and will mess up the commit message.

This was referenced Apr 9, 2015
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@davies

davies commented Apr 9, 2015

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@shivaram Should we combine these commit into a single huge commit? We will lose the history anyway, I think it's fine.

@shivaram

shivaram commented Apr 9, 2015

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Hmm does it work if you cherry-pick these new commits from sparkr-sql branch to a new spark branch ? If we are doing the one big commit lets add the SparkR PR numbers or JIRA links in the description.

@davies

davies commented Apr 9, 2015

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I think that the cherry-pick may not work, because we change the directory. I will try to collect all the commit messages into the description.

@shivaramshivaram mentioned this pull request Apr 11, 2015
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cafreemanand others added 20 commits April 14, 2015 13:05
cafreemanDavies Liu
Define functions for schema and fields
0e2a94f
Instead of using a list[list[list[]]], use specific constructors for schema and field objects.
cafreemanDavies Liu
Documentation
7dd81b7
@shivaramDavies Liu
Merge pull requestapache#233from redbaron/fail-early-on-missing-dep
8b76e81
Fail worker early if dependency is missing
cafreemanDavies Liu
new line at EOF
cd66603
@concretevitaminDavies Liu
Merge pull requestapache#242from hqzizania/stats
136a07e
[SPARKR-92] Phase 2: implement sum(rdd)
@concretevitaminDavies Liu
Merge pull requestapache#243from hqzizania/master
b317aa7
[SPARKR-199] Change takeOrdered, top to fetch one partition at a time
@shivaramDavies Liu
Merge pull requestapache#208from lythesia/master
c9497a3
[SPARKR-188] Add profiling of R execution on worker side
Conflicts:
pkg/inst/worker/worker.R
@shivaramDavies Liu
Merge pull requestapache#238from sun-rui/SPARKR-154_4
ba54e34
[SPARKR-154] Phase 3: implement intersection().
@concretevitaminDavies Liu
Merge pull requestapache#234from hqzizania/assist
20b97a6
[SPARKR-163] Support sampleByKey()
Conflicts:
pkg/R/pairRDD.R
@concretevitaminDavies Liu
Merge pull requestapache#244from sun-rui/SPARKR-154_5
40338a4
[SPARKR-154] Phase 4: implement subtract() and subtractByKey().
cafreemanDavies Liu
refactor schema functions
be5d5c1
Refactored `structType` and `structField` so that they can be used to create schemas from R for use with `createDataFrame`.
Moved everything to `schema.R`
Added new methods to `SQLUtils.scala` for handling `StructType` and `StructField` on the JVM side
cafreemanDavies Liu
Update createDataFrame and toDF
836c4bf
Refactored to use the new `structType` and `structField` functions.
cafreemanDavies Liu
new version of CreateDF
1a3b63d
New version uses takes a `StructType` from R and creates a DataFrame.
Commented out the `tojson` version since we don't currently use it.
cafreemanDavies Liu
Update NAMESPACE and tests
275deb4
Updated `NAMESPACE`, `DESCRIPTION`, and unit tests for new schema functions.
Deleted `SQLTypes.R` since everything has been moved to `schema.R`.
cafreemanDavies Liu
Fixed duplicate export
f3ba785
cafreemanDavies Liu
Update subtract to work with generics.R
ed66c81
@shivaramDavies Liu
Merge pull requestapache#246from hlin09/fixCombineByKey
7e8caa3
Fixes combineByKey
Sun RuiDavies Liu
[SPARKR-244] Fix test failure after integration of subtract() and sub…
07d0dbc
…tractByKey() for RDD.
@shivaramDavies Liu
Move except into sorted position
40199eb
Davies Liu
fix style
9387402
@SparkQA

SparkQA commented Apr 14, 2015

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Test build #30275 has finished for PR 5436 at commit 4f5ac09.

  • This patch fails RAT tests.
  • This patch merges cleanly.
  • This patch adds no public classes.
  • This patch does not change any dependencies.

@daviesdavies changed the title [WIP] [SPARK-6807] [SparkR] Merge recent SparkR-pkg changes[SPARK-6807] [SparkR] Merge recent SparkR-pkg changesApr 14, 2015
@shivaram

shivaram commented Apr 14, 2015

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@davies We need to add license to schema.R

@SparkQA

SparkQA commented Apr 14, 2015

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Test build #672 has started for PR 5436 at commit 168b7fe.

@SparkQA

SparkQA commented Apr 14, 2015

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Test build #30276 has finished for PR 5436 at commit b1fe460.

  • This patch passes all tests.
  • This patch merges cleanly.
  • This patch adds no public classes.
  • This patch adds the following new dependencies:
    • RoaringBitmap-0.4.5.jar
    • activation-1.1.jar
    • akka-actor_2.10-2.3.4-spark.jar
    • akka-remote_2.10-2.3.4-spark.jar
    • akka-slf4j_2.10-2.3.4-spark.jar
    • aopalliance-1.0.jar
    • arpack_combined_all-0.1.jar
    • avro-1.7.7.jar
    • breeze-macros_2.10-0.11.2.jar
    • breeze_2.10-0.11.2.jar
    • chill-java-0.5.0.jar
    • chill_2.10-0.5.0.jar
    • commons-beanutils-1.7.0.jar
    • commons-beanutils-core-1.8.0.jar
    • commons-cli-1.2.jar
    • commons-codec-1.10.jar
    • commons-collections-3.2.1.jar
    • commons-compress-1.4.1.jar
    • commons-configuration-1.6.jar
    • commons-digester-1.8.jar
    • commons-httpclient-3.1.jar
    • commons-io-2.1.jar
    • commons-lang-2.5.jar
    • commons-lang3-3.3.2.jar
    • commons-math-2.1.jar
    • commons-math3-3.4.1.jar
    • commons-net-2.2.jar
    • compress-lzf-1.0.0.jar
    • config-1.2.1.jar
    • core-1.1.2.jar
    • curator-client-2.4.0.jar
    • curator-framework-2.4.0.jar
    • curator-recipes-2.4.0.jar
    • gmbal-api-only-3.0.0-b023.jar
    • grizzly-framework-2.1.2.jar
    • grizzly-http-2.1.2.jar
    • grizzly-http-server-2.1.2.jar
    • grizzly-http-servlet-2.1.2.jar
    • grizzly-rcm-2.1.2.jar
    • groovy-all-2.3.7.jar
    • guava-14.0.1.jar
    • guice-3.0.jar
    • hadoop-annotations-2.2.0.jar
    • hadoop-auth-2.2.0.jar
    • hadoop-client-2.2.0.jar
    • hadoop-common-2.2.0.jar
    • hadoop-hdfs-2.2.0.jar
    • hadoop-mapreduce-client-app-2.2.0.jar
    • hadoop-mapreduce-client-common-2.2.0.jar
    • hadoop-mapreduce-client-core-2.2.0.jar
    • hadoop-mapreduce-client-jobclient-2.2.0.jar
    • hadoop-mapreduce-client-shuffle-2.2.0.jar
    • hadoop-yarn-api-2.2.0.jar
    • hadoop-yarn-client-2.2.0.jar
    • hadoop-yarn-common-2.2.0.jar
    • hadoop-yarn-server-common-2.2.0.jar
    • ivy-2.4.0.jar
    • jackson-annotations-2.4.0.jar
    • jackson-core-2.4.4.jar
    • jackson-core-asl-1.8.8.jar
    • jackson-databind-2.4.4.jar
    • jackson-jaxrs-1.8.8.jar
    • jackson-mapper-asl-1.8.8.jar
    • jackson-module-scala_2.10-2.4.4.jar
    • jackson-xc-1.8.8.jar
    • jansi-1.4.jar
    • javax.inject-1.jar
    • javax.servlet-3.0.0.v201112011016.jar
    • javax.servlet-3.1.jar
    • javax.servlet-api-3.0.1.jar
    • jaxb-api-2.2.2.jar
    • jaxb-impl-2.2.3-1.jar
    • jcl-over-slf4j-1.7.10.jar
    • jersey-client-1.9.jar
    • jersey-core-1.9.jar
    • jersey-grizzly2-1.9.jar
    • jersey-guice-1.9.jar
    • jersey-json-1.9.jar
    • jersey-server-1.9.jar
    • jersey-test-framework-core-1.9.jar
    • jersey-test-framework-grizzly2-1.9.jar
    • jets3t-0.7.1.jar
    • jettison-1.1.jar
    • jetty-util-6.1.26.jar
    • jline-0.9.94.jar
    • jline-2.10.4.jar
    • jodd-core-3.6.3.jar
    • json4s-ast_2.10-3.2.10.jar
    • json4s-core_2.10-3.2.10.jar
    • json4s-jackson_2.10-3.2.10.jar
    • jsr305-1.3.9.jar
    • jtransforms-2.4.0.jar
    • jul-to-slf4j-1.7.10.jar
    • kryo-2.21.jar
    • log4j-1.2.17.jar
    • lz4-1.2.0.jar
    • management-api-3.0.0-b012.jar
    • mesos-0.21.0-shaded-protobuf.jar
    • metrics-core-3.1.0.jar
    • metrics-graphite-3.1.0.jar
    • metrics-json-3.1.0.jar
    • metrics-jvm-3.1.0.jar
    • minlog-1.2.jar
    • netty-3.8.0.Final.jar
    • netty-all-4.0.23.Final.jar
    • objenesis-1.2.jar
    • opencsv-2.3.jar
    • oro-2.0.8.jar
    • paranamer-2.6.jar
    • parquet-column-1.6.0rc3.jar
    • parquet-common-1.6.0rc3.jar
    • parquet-encoding-1.6.0rc3.jar
    • parquet-format-2.2.0-rc1.jar
    • parquet-generator-1.6.0rc3.jar
    • parquet-hadoop-1.6.0rc3.jar
    • parquet-jackson-1.6.0rc3.jar
    • protobuf-java-2.4.1.jar
    • protobuf-java-2.5.0-spark.jar
    • py4j-0.8.2.1.jar
    • pyrolite-2.0.1.jar
    • quasiquotes_2.10-2.0.1.jar
    • reflectasm-1.07-shaded.jar
    • scala-compiler-2.10.4.jar
    • scala-library-2.10.4.jar
    • scala-reflect-2.10.4.jar
    • scalap-2.10.4.jar
    • scalatest_2.10-2.2.1.jar
    • slf4j-api-1.7.10.jar
    • slf4j-log4j12-1.7.10.jar
    • snappy-java-1.1.1.7.jar
    • spark-bagel_2.10-1.4.0-SNAPSHOT.jar
    • spark-catalyst_2.10-1.4.0-SNAPSHOT.jar
    • spark-core_2.10-1.4.0-SNAPSHOT.jar
    • spark-graphx_2.10-1.4.0-SNAPSHOT.jar
    • spark-launcher_2.10-1.4.0-SNAPSHOT.jar
    • spark-mllib_2.10-1.4.0-SNAPSHOT.jar
    • spark-network-common_2.10-1.4.0-SNAPSHOT.jar
    • spark-network-shuffle_2.10-1.4.0-SNAPSHOT.jar
    • spark-repl_2.10-1.4.0-SNAPSHOT.jar
    • spark-sql_2.10-1.4.0-SNAPSHOT.jar
    • spark-streaming_2.10-1.4.0-SNAPSHOT.jar
    • spire-macros_2.10-0.7.4.jar
    • spire_2.10-0.7.4.jar
    • stax-api-1.0.1.jar
    • stream-2.7.0.jar
    • tachyon-0.5.0.jar
    • tachyon-client-0.5.0.jar
    • uncommons-maths-1.2.2a.jar
    • unused-1.0.0.jar
    • xmlenc-0.52.jar
    • xz-1.0.jar
    • zookeeper-3.4.5.jar

@SparkQA

SparkQA commented Apr 14, 2015

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Test build #30277 has finished for PR 5436 at commit 168b7fe.

  • This patch passes all tests.
  • This patch merges cleanly.
  • This patch adds no public classes.
  • This patch removes the following dependencies:
    • RoaringBitmap-0.4.5.jar
    • activation-1.1.jar
    • akka-actor_2.10-2.3.4-spark.jar
    • akka-remote_2.10-2.3.4-spark.jar
    • akka-slf4j_2.10-2.3.4-spark.jar
    • aopalliance-1.0.jar
    • arpack_combined_all-0.1.jar
    • avro-1.7.7.jar
    • breeze-macros_2.10-0.11.2.jar
    • breeze_2.10-0.11.2.jar
    • chill-java-0.5.0.jar
    • chill_2.10-0.5.0.jar
    • commons-beanutils-1.7.0.jar
    • commons-beanutils-core-1.8.0.jar
    • commons-cli-1.2.jar
    • commons-codec-1.10.jar
    • commons-collections-3.2.1.jar
    • commons-compress-1.4.1.jar
    • commons-configuration-1.6.jar
    • commons-digester-1.8.jar
    • commons-httpclient-3.1.jar
    • commons-io-2.1.jar
    • commons-lang-2.5.jar
    • commons-lang3-3.3.2.jar
    • commons-math-2.1.jar
    • commons-math3-3.4.1.jar
    • commons-net-2.2.jar
    • compress-lzf-1.0.0.jar
    • config-1.2.1.jar
    • core-1.1.2.jar
    • curator-client-2.4.0.jar
    • curator-framework-2.4.0.jar
    • curator-recipes-2.4.0.jar
    • gmbal-api-only-3.0.0-b023.jar
    • grizzly-framework-2.1.2.jar
    • grizzly-http-2.1.2.jar
    • grizzly-http-server-2.1.2.jar
    • grizzly-http-servlet-2.1.2.jar
    • grizzly-rcm-2.1.2.jar
    • groovy-all-2.3.7.jar
    • guava-14.0.1.jar
    • guice-3.0.jar
    • hadoop-annotations-2.2.0.jar
    • hadoop-auth-2.2.0.jar
    • hadoop-client-2.2.0.jar
    • hadoop-common-2.2.0.jar
    • hadoop-hdfs-2.2.0.jar
    • hadoop-mapreduce-client-app-2.2.0.jar
    • hadoop-mapreduce-client-common-2.2.0.jar
    • hadoop-mapreduce-client-core-2.2.0.jar
    • hadoop-mapreduce-client-jobclient-2.2.0.jar
    • hadoop-mapreduce-client-shuffle-2.2.0.jar
    • hadoop-yarn-api-2.2.0.jar
    • hadoop-yarn-client-2.2.0.jar
    • hadoop-yarn-common-2.2.0.jar
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    • spark-graphx_2.10-1.4.0-SNAPSHOT.jar
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    • spire-macros_2.10-0.7.4.jar
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    • zookeeper-3.4.5.jar

@davies

davies commented Apr 15, 2015

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@shivaram this PR is ready to review

shivaram
shivaram reviewed Apr 15, 2015
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Comment threadsql/core/src/main/scala/org/apache/spark/sql/api/r/SQLUtils.scala

@shivaramshivaramApr 15, 2015

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minor style nit: no space between fields and : here

@shivaram

shivaram commented Apr 15, 2015

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Thanks @davies -- This is looking pretty good to me. I had a minor style comment.

cc @cafreeman@sun-rui (who authored some of the original changes)

@SparkQA

SparkQA commented Apr 16, 2015

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Test build #30435 timed out for PR 5436 at commit c2b09be after a configured wait of 120m.

@SparkQA

SparkQA commented Apr 17, 2015

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Test build #687 has started for PR 5436 at commit c2b09be.

@shivaram

shivaram commented Apr 17, 2015

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Jenkins, retest this please

@SparkQA

SparkQA commented Apr 17, 2015

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Test build #30465 has finished for PR 5436 at commit c2b09be.

  • This patch passes all tests.
  • This patch merges cleanly.
  • This patch adds no public classes.
  • This patch does not change any dependencies.

@shivaram

shivaram commented Apr 17, 2015

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LGTM. Merging this

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4 participants

@davies@SparkQA@shivaram@concretevitamin