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";)'
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
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> wrote:
> You must specify -Psparkr when building from source.
>
> On May 20, 2016, at 08:09, Gayathri Murali <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> 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> 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
>>> 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> wrote:
>>>
>>>> Is it on 1.6.x?
>>>>
>>>> On Wed, May 18, 2016, 6:57 PM Sun Rui <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> 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> 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> 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
>>>>>>
>>>>>> [image: 提示图标] 邮件带有附件预览链接，若您转发或回复此邮件时不希望对方预览附件，建议您手动删除链接。
>>>>>> 共有 *1* 个附件
>>>>>> Screen Shot 2016-05-18 at 5.09.29 PM.png(155K)极速下载
>>>>>> <http://preview.mail.163.com/xdownload?filename=Screen+Shot+2016-05-18+at+5.09.29+PM.png&mid=xtbB0QpumlUL%2BmgE3wAAs4&part=3&sign=de2b9113bb74f7c3ed7f83a1243fb575&time=1463616821&uid=sunrise_win%40163.com>
>>>>>> 在线预览
>>>>>> <http://preview.mail.163.com/preview?mid=xtbB0QpumlUL%2BmgE3wAAs4&part=3&sign=de2b9113bb74f7c3ed7f83a1243fb575&time=1463616821&uid=sunrise_win%40163.com>
>>>>>>
>>>>>>
>>>>>>
>>>>> [image: 提示图标] 邮件带有附件预览链接，若您转发或回复此邮件时不希望对方预览附件，建议您手动删除链接。
>>>>> 共有 *1* 个附件
>>>>> Screen Shot 2016-05-18 at 5.09.29 PM.png(155K)极速下载
>>>>> <http://preview.mail.163.com/xdownload?filename=Screen+Shot+2016-05-18+at+5.09.29+PM.png&mid=1tbiPhRumlXlgWp0SwAAs6&part=3&sign=e0cf0eb619175e79cfa81bad7c1d26c9&time=1463622289&uid=sunrise_win%40163.com>
>>>>> 在线预览
>>>>> <http://preview.mail.163.com/preview?mid=1tbiPhRumlXlgWp0SwAAs6&part=3&sign=e0cf0eb619175e79cfa81bad7c1d26c9&time=1463622289&uid=sunrise_win%40163.com>
>>>>> <Screen Shot 2016-05-18 at 5.09.29 PM.png>
>>>>>
>>>>>
>>>>>
>>>
>
>
