Yes. I also met this issue. It is likely related to recent R versions.
Could you help to submit a JIRA issue? I will take a look at it
> On May 20, 2016, at 11:13, Kai Jiang <jiang...@gmail.com> wrote:
>
> I was trying to build SparkR this week. hmm~ But, I encountered problem with
> SparkR unit testing. That is probably similar as Gayathri encountered with.
> I tried many times with running ./R/run-tests.sh script. It seems like every
> time the test will be failed.
>
> Here are some environments when I was building:
> java 7
> R 3.30 (sudo apt-get install r-base-dev under ubuntu 15.04)
> set SPARK_HOME=/path
>
> R -e 'install.packages("testthat", repos="http://cran.us.r-project.org
> <http://cran.us.r-project.org/>")'
> build with: build/mvn -Pyarn -Phadoop-2.4 -Dhadoop.version=2.4.0
> -Psparkr -DskipTests -T 1C clean package
>
> ./R/install-dev.sh
> ./R/run-tests.sh
>
> Here is the error message I got:
> https://gist.github.com/vectorijk/71f4ff34e3d34a628b8a3013f0ca2aa2
> <https://gist.github.com/vectorijk/71f4ff34e3d34a628b8a3013f0ca2aa2>
>
> I guess this issue related to permission. It seems I used `sudo
> ./R/run-tests.sh` and it worked sometimes. Without permission, maybe we
> couldn't access /tmp directory. However, the SparkR unit testing is brittle.
>
> Could someone give any hints of how to solve this?
>
> Best,
> Kai.
>
> On Thu, May 19, 2016 at 6:59 PM, Sun Rui <sunrise_...@163.com
> <mailto:sunrise_...@163.com>> wrote:
> You must specify -Psparkr when building from source.
>
>> On May 20, 2016, at 08:09, Gayathri Murali <gayathri.m.sof...@gmail.com
>> <mailto:gayathri.m.sof...@gmail.com>> wrote:
>>
>> That helped! Thanks. I am building from source code and I am not sure what
>> caused the issue with SparkR.
>>
>> On Thu, May 19, 2016 at 4:17 PM, Xiangrui Meng <men...@gmail.com
>> <mailto:men...@gmail.com>> wrote:
>> We no longer have `SparkRWrappers` in Spark 2.0. So if you are testing the
>> latest branch-2.0, there could be an issue with your SparkR installation.
>> Did you try `R/install-dev.sh`?
>>
>> On Thu, May 19, 2016 at 11:42 AM Gayathri Murali
>> <gayathri.m.sof...@gmail.com <mailto:gayathri.m.sof...@gmail.com>> wrote:
>> This is on Spark 2.0. I see the following on the unit-tests.log when I run
>> the R/run-tests.sh. This on a single MAC laptop, on the recently rebased
>> master. R version is 3.3.0.
>>
>> 16/05/19 11:28:13.863 Executor task launch worker-1 ERROR Executor:
>> Exception in task 0.0 in stage 5186.0 (TID 10370)
>> 1384595 org.apache.spark.SparkException: R computation failed with
>> 1384596
>> 1384597 Execution halted
>> 1384598
>> 1384599 Execution halted
>> 1384600
>> 1384601 Execution halted
>> 1384602 at org.apache.spark.api.r.RRunner.compute(RRunner.scala:107)
>> 1384603 at org.apache.spark.api.r.BaseRRDD.compute(RRDD.scala:49)
>> 1384604 at
>> org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:318)
>> 1384605 at org.apache.spark.rdd.RDD.iterator(RDD.scala:282)
>> 1384606 at
>> org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:70)
>> 1384607 at org.apache.spark.scheduler.Task.run(Task.scala:85)
>> 1384608 at
>> org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274)
>> 1384609 at
>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>> 1384610 at
>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>> 1384611 at java.lang.Thread.run(Thread.java:745)
>> 1384612 16/05/19 11:28:13.864 Thread-1 INFO ContextHandler: Stopped
>> o.s.j.s.ServletContextHandler@22f76fa8{/jobs/json,null,UNAVAILABLE}
>> 1384613 16/05/19 11:28:13.869 Thread-1 INFO ContextHandler: Stopped
>> o.s.j.s.ServletContextHandler@afe0d9f{/jobs,null,UNAVAILABLE}
>> 1384614 16/05/19 11:28:13.869 Thread-1 INFO SparkUI: Stopped Spark web UI at
>> http://localhost:4040 <http://localhost:4040/>
>> 1384615 16/05/19 11:28:13.871 Executor task launch worker-4 ERROR Executor:
>> Exception in task 1.0 in stage 5186.0 (TID 10371)
>> 1384616 org.apache.spark.SparkException: R computation failed with
>> 1384617
>> 1384618 Execution halted
>> 1384619
>> 1384620 Execution halted
>> 1384621
>> 1384622 Execution halted
>> 1384623 at org.apache.spark.api.r.RRunner.compute(RRunner.scala:107)
>> 1384624 at org.apache.spark.api.r.BaseRRDD.compute(RRDD.scala:49)
>> 1384625 at
>> org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:318)
>> 1384626 at org.apache.spark.rdd.RDD.iterator(RDD.scala:282)
>> 1384627 at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.
>> t org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274)
>> 1384630 at
>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>> 1384631 at
>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>> 1384632 at java.lang.Thread.run(Thread.java:745)
>> 1384633 16/05/19 11:28:13.874 nioEventLoopGroup-2-1 INFO DAGScheduler: Job
>> 5183 failed: collect at null:-1, took 0.211674 s
>> 1384634 16/05/19 11:28:13.875 nioEventLoopGroup-2-1 ERROR RBackendHandler:
>> collect on 26345 failed
>> 1384635 16/05/19 11:28:13.876 Thread-1 INFO DAGScheduler: ResultStage 5186
>> (collect at null:-1) failed in 0.210 s
>> 1384636 16/05/19 11:28:13.877 Thread-1 ERROR LiveListenerBus:
>> SparkListenerBus has already stopped! Dropping event
>> SparkListenerStageCompleted(org.apache.spark.scheduler.StageIn
>> fo@413da307)
>> 1384637 16/05/19 11:28:13.878 Thread-1 ERROR LiveListenerBus:
>> SparkListenerBus has already stopped! Dropping event
>> SparkListenerJobEnd(5183,1463682493877,JobFailed(org.apache.sp
>> ark.SparkException: Job 5183 cancelled because SparkContext was shut down))
>> 1384638 16/05/19 11:28:13.880 dispatcher-event-loop-1 INFO
>> MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
>> 1384639 16/05/19 11:28:13.904 Thread-1 INFO MemoryStore: MemoryStore cleared
>> 1384640 16/05/19 11:28:13.904 Thread-1 INFO BlockManager: BlockManager
>> stopped
>> 1384641 16/05/19 11:28:13.904 Thread-1 INFO BlockManagerMaster:
>> BlockManagerMaster stopped
>> 1384642 16/05/19 11:28:13.905 dispatcher-event-loop-0 INFO
>> OutputCommitCoordinator$OutputCommitCoordinatorEndpoint:
>> OutputCommitCoordinator stopped!
>> 1384643 16/05/19 11:28:13.909 Thread-1 INFO SparkContext: Successfully
>> stopped SparkContext
>> 1384644 16/05/19 11:28:13.910 Thread-1 INFO ShutdownHookManager: Shutdown
>> hook called
>> 1384645 16/05/19 11:28:13.911 Thread-1 INFO ShutdownHookManager: Deleting
>> directory
>> /private/var/folders/xy/qc35m0y55vq83dsqzg066_c40000gn/T/spark-dfafdddc-fd25-4eb4-bb1d-565915
>> 1c8231
>>
>>
>> On Thu, May 19, 2016 at 8:46 AM, Xiangrui Meng <men...@gmail.com
>> <mailto:men...@gmail.com>> wrote:
>> Is it on 1.6.x?
>>
>>
>> On Wed, May 18, 2016, 6:57 PM Sun Rui <sunrise_...@163.com
>> <mailto:sunrise_...@163.com>> wrote:
>> I saw it, but I can’t see the complete error message on it.
>> I mean the part after “error in invokingJava(…)”
>>
>>> On May 19, 2016, at 08:37, Gayathri Murali <gayathri.m.sof...@gmail.com
>>> <mailto:gayathri.m.sof...@gmail.com>> wrote:
>>>
>>> There was a screenshot attached to my original email. If you did not get
>>> it, attaching here again.
>>>
>>> On Wed, May 18, 2016 at 5:27 PM, Sun Rui <sunrise_...@163.com
>>> <mailto:sunrise_...@163.com>> wrote:
>>> It’s wrong behaviour that head(df) outputs no row
>>> Could you send a screenshot displaying whole error message?
>>>> On May 19, 2016, at 08:12, Gayathri Murali <gayathri.m.sof...@gmail.com
>>>> <mailto:gayathri.m.sof...@gmail.com>> wrote:
>>>>
>>>> I am trying to run a basic example on Interactive R shell and run into the
>>>> following error. Also note that head(df) does not display any rows. Can
>>>> someone please help if I am missing something?
>>>>
>>>> <Screen Shot 2016-05-18 at 5.09.29 PM.png>
>>>>
>>>> Thanks
>>>> Gayathri
>>>>
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>>> Screen Shot 2016-05-18 at 5.09.29 PM.png(155K)
>>> 极速下载
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>>> Shot 2016-05-18 at 5.09.29 PM.png>
>>
>>
>>
>
>
