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Posted to reviews@spark.apache.org by felixcheung <gi...@git.apache.org> on 2017/08/22 06:56:32 UTC
[GitHub] spark pull request #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fa...
GitHub user felixcheung opened a pull request:
https://github.com/apache/spark/pull/19018
[SPARK-21801][SPARKR][TEST] unit test randomly fail with randomforest
## What changes were proposed in this pull request?
fix the random seed to eliminate variability
## How was this patch tested?
jenkins, appveyor, lots more jenkins
You can merge this pull request into a Git repository by running:
$ git pull https://github.com/felixcheung/spark rrftest
Alternatively you can review and apply these changes as the patch at:
https://github.com/apache/spark/pull/19018.patch
To close this pull request, make a commit to your master/trunk branch
with (at least) the following in the commit message:
This closes #19018
----
commit 05b3cabaff89396d352ece41d57c7fd9eb2ef917
Author: Felix Cheung <fe...@hotmail.com>
Date: 2017-08-22T06:50:48Z
random seed
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/19018
#19111
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/19018
**[Test build #81188 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/81188/testReport)** for PR 19018 at commit [`ed11d40`](https://github.com/apache/spark/commit/ed11d40c90f32e8d69f5e595f235f7085dec3581).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
https://github.com/apache/spark/pull/19018
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/19018
jenkins, retest this please
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/19018
**[Test build #80998 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/80998/testReport)** for PR 19018 at commit [`05b3cab`](https://github.com/apache/spark/commit/05b3cabaff89396d352ece41d57c7fd9eb2ef917).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/19018
**[Test build #80966 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/80966/testReport)** for PR 19018 at commit [`05b3cab`](https://github.com/apache/spark/commit/05b3cabaff89396d352ece41d57c7fd9eb2ef917).
* This patch **fails due to an unknown error code, -9**.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/19018
jenkins, retest this please
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/19018
**[Test build #81029 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/81029/testReport)** for PR 19018 at commit [`05b3cab`](https://github.com/apache/spark/commit/05b3cabaff89396d352ece41d57c7fd9eb2ef917).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by AmplabJenkins <gi...@git.apache.org>.
Github user AmplabJenkins commented on the issue:
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/19018
**[Test build #81029 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/81029/testReport)** for PR 19018 at commit [`05b3cab`](https://github.com/apache/spark/commit/05b3cabaff89396d352ece41d57c7fd9eb2ef917).
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/19018
merged to master
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/19018
**[Test build #81181 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/81181/testReport)** for PR 19018 at commit [`ed11d40`](https://github.com/apache/spark/commit/ed11d40c90f32e8d69f5e595f235f7085dec3581).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
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https://github.com/apache/spark/pull/19018
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by WeichenXu123 <gi...@git.apache.org>.
Github user WeichenXu123 commented on the issue:
https://github.com/apache/spark/pull/19018
@felixcheung In Jenkins Log I only found Random forest and Decision Tree failed, random forest failed more frequently. thanks!
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/19018
Jenkins, retest this please
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/19018
**[Test build #80970 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/80970/testReport)** for PR 19018 at commit [`05b3cab`](https://github.com/apache/spark/commit/05b3cabaff89396d352ece41d57c7fd9eb2ef917).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/19018
**[Test build #81070 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/81070/testReport)** for PR 19018 at commit [`05b3cab`](https://github.com/apache/spark/commit/05b3cabaff89396d352ece41d57c7fd9eb2ef917).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by AmplabJenkins <gi...@git.apache.org>.
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/19018
but i think in general it's better to make tests more predictable like this
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by AmplabJenkins <gi...@git.apache.org>.
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by WeichenXu123 <gi...@git.apache.org>.
Github user WeichenXu123 commented on the issue:
https://github.com/apache/spark/pull/19018
ping @felixcheung We can make all R tests for trees deterministic (not only random trees). Leave other problems to separate PR. It would be great to fix it soon, Thanks!
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/19018
jenkins, retest this please
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[GitHub] spark pull request #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fa...
Posted by asfgit <gi...@git.apache.org>.
Github user asfgit closed the pull request at:
https://github.com/apache/spark/pull/19018
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
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https://github.com/apache/spark/pull/19018
**[Test build #81181 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/81181/testReport)** for PR 19018 at commit [`ed11d40`](https://github.com/apache/spark/commit/ed11d40c90f32e8d69f5e595f235f7085dec3581).
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by AmplabJenkins <gi...@git.apache.org>.
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/19018
jenkins, retest this pleace
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Posted by SparkQA <gi...@git.apache.org>.
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https://github.com/apache/spark/pull/19018
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by HyukjinKwon <gi...@git.apache.org>.
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https://github.com/apache/spark/pull/19018
retest this please
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by SparkQA <gi...@git.apache.org>.
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https://github.com/apache/spark/pull/19018
**[Test build #81041 has finished](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/81041/testReport)** for PR 19018 at commit [`05b3cab`](https://github.com/apache/spark/commit/05b3cabaff89396d352ece41d57c7fd9eb2ef917).
* This patch passes all tests.
* This patch merges cleanly.
* This patch adds no public classes.
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by SparkQA <gi...@git.apache.org>.
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https://github.com/apache/spark/pull/19018
**[Test build #80970 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/80970/testReport)** for PR 19018 at commit [`05b3cab`](https://github.com/apache/spark/commit/05b3cabaff89396d352ece41d57c7fd9eb2ef917).
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/19018
Can you point me to other failures? How frequently does it occur?
I'm reasonably sure setting the seed should fix the randomness, I can get to other changes within a day, but I want to know how many test runs should tell us if it really fixes the problem
________________________________
From: WeichenXu <no...@github.com>
Sent: Sunday, August 27, 2017 6:53:11 PM
To: apache/spark
Cc: Felix Cheung; Mention
Subject: Re: [apache/spark] [SPARK-21801][SPARKR][TEST] unit test randomly fail with randomforest (#19018)
ping @felixcheung<https://github.com/felixcheung> We can make all R tests for trees deterministic (not only random trees). Leave other problems to separate PR. It would be great to fix it soon, Thanks!
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by WeichenXu123 <gi...@git.apache.org>.
Github user WeichenXu123 commented on the issue:
https://github.com/apache/spark/pull/19018
cc @felixcheung
I encounter RTest failed again even when this seed added.
https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/81350/console
error:
```
Failed -------------------------------------------------------------------------
1. Error: spark.decisionTree (@test_mllib_tree.R#355) --------------------------
java.lang.IllegalArgumentException: requirement failed: The input column stridx_629e10e5fd28 should have at least two distinct values.
at scala.Predef$.require(Predef.scala:224)
at org.apache.spark.ml.feature.OneHotEncoder$$anonfun$5.apply(OneHotEncoder.scala:113)
at org.apache.spark.ml.feature.OneHotEncoder$$anonfun$5.apply(OneHotEncoder.scala:111)
at scala.Option.map(Option.scala:146)
at org.apache.spark.ml.feature.OneHotEncoder.transformSchema(OneHotEncoder.scala:111)
at org.apache.spark.ml.feature.OneHotEncoder.transform(OneHotEncoder.scala:141)
at org.apache.spark.ml.Pipeline$$anonfun$fit$2.apply(Pipeline.scala:161)
at org.apache.spark.ml.Pipeline$$anonfun$fit$2.apply(Pipeline.scala:149)
at scala.collection.Iterator$class.foreach(Iterator.scala:893)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1336)
at scala.collection.IterableViewLike$Transformed$class.foreach(IterableViewLike.scala:44)
at scala.collection.SeqViewLike$AbstractTransformed.foreach(SeqViewLike.scala:37)
at org.apache.spark.ml.Pipeline.fit(Pipeline.scala:149)
at org.apache.spark.ml.feature.RFormula.fit(RFormula.scala:270)
at org.apache.spark.ml.r.DecisionTreeClassifierWrapper$.fit(DecisionTreeClassificationWrapper.scala:84)
at org.apache.spark.ml.r.DecisionTreeClassifierWrapper.fit(DecisionTreeClassificationWrapper.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at org.apache.spark.api.r.RBackendHandler.handleMethodCall(RBackendHandler.scala:167)
at org.apache.spark.api.r.RBackendHandler.channelRead0(RBackendHandler.scala:108)
at org.apache.spark.api.r.RBackendHandler.channelRead0(RBackendHandler.scala:40)
at io.netty.channel.SimpleChannelInboundHandler.channelRead(SimpleChannelInboundHandler.java:105)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343)
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336)
at io.netty.handler.timeout.IdleStateHandler.channelRead(IdleStateHandler.java:287)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343)
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336)
at io.netty.handler.codec.MessageToMessageDecoder.channelRead(MessageToMessageDecoder.java:102)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343)
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336)
at io.netty.handler.codec.ByteToMessageDecoder.fireChannelRead(ByteToMessageDecoder.java:293)
at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:267)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343)
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336)
at io.netty.channel.DefaultChannelPipeline$HeadContext.channelRead(DefaultChannelPipeline.java:1294)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343)
at io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:911)
at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:131)
at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:643)
at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:566)
at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:480)
at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:442)
at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:131)
at io.netty.util.concurrent.DefaultThreadFactory$DefaultRunnableDecorator.run(DefaultThreadFactory.java:144)
at java.lang.Thread.run(Thread.java:745)
1: spark.decisionTree(traindf, clicked ~ ., type = "classification", maxDepth = 5, maxBins = 16,
seed = 46) at /home/jenkins/workspace/SparkPullRequestBuilder/R/pkg/tests/fulltests/test_mllib_tree.R:355
2: spark.decisionTree(traindf, clicked ~ ., type = "classification", maxDepth = 5, maxBins = 16,
seed = 46)
3: .local(data, formula, ...)
4: callJStatic("org.apache.spark.ml.r.DecisionTreeClassifierWrapper", "fit", data@sdf,
formula, as.integer(maxDepth), as.integer(maxBins), impurity, as.integer(minInstancesPerNode),
as.numeric(minInfoGain), as.integer(checkpointInterval), seed, as.integer(maxMemoryInMB),
as.logical(cacheNodeIds), handleInvalid)
5: invokeJava(isStatic = TRUE, className, methodName, ...)
6: handleErrors(returnStatus, conn)
7: stop(readString(conn))
DONE ===========================================================================
Error: Test failures
Execution halted
```
Would you like take a look ?
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/19018
jenkins, retest this please
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by WeichenXu123 <gi...@git.apache.org>.
Github user WeichenXu123 commented on the issue:
https://github.com/apache/spark/pull/19018
@felixcheung This error occur in the OneHotEncoder inside the RFormula I think. Only OneHotEncoder will print this error message after I search the project...
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/19018
ouch. I think this is because
```
# Test unseen labels
data <- data.frame(clicked = base::sample(c(0, 1), 10, replace = TRUE),
someString = base::sample(c("this", "that"), 10, replace = TRUE),
stringsAsFactors = FALSE)
trainidxs <- base::sample(nrow(data), nrow(data) * 0.7)
traindf <- as.DataFrame(data[trainidxs, ])
testdf <- as.DataFrame(rbind(data[-trainidxs, ], c(0, "the other")))
model <- spark.decisionTree(traindf, clicked ~ ., type = "classification",
maxDepth = 5, maxBins = 16, seed = 46)
```
traindf is created from a sampled data.frame. this sampling will be random as well. let me see what I can do.
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/19018
the error specifically is:
`The input column stridx_87ea3065aeb2 should have at least two distinct values.`
I don't think this would be only happening in R - I suppose whenever the string label has only one distinct value, ml's random forest will just give up like this.
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by SparkQA <gi...@git.apache.org>.
Github user SparkQA commented on the issue:
https://github.com/apache/spark/pull/19018
**[Test build #81188 has started](https://amplab.cs.berkeley.edu/jenkins/job/SparkPullRequestBuilder/81188/testReport)** for PR 19018 at commit [`ed11d40`](https://github.com/apache/spark/commit/ed11d40c90f32e8d69f5e595f235f7085dec3581).
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[GitHub] spark issue #19018: [SPARK-21801][SPARKR][TEST] unit test randomly fail with...
Posted by felixcheung <gi...@git.apache.org>.
Github user felixcheung commented on the issue:
https://github.com/apache/spark/pull/19018
I mean Jenkins log of the test run that failed
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