Re: 0.9.0 - R tutorial - no such kernel named ir

Wed, 01 Jul 2020 09:31:22 -0700 

All:

   So it turns out that the IRKernel is not available for
R 3.6 (actually one of its dependencies)
** testing if installed package keeps a record of temporary installation path 
* DONE (IRdisplay)
Making 'packages.html' ... done
ERROR: dependency ‘pbdZMQ’ is not available for package ‘IRkernel’
* removing ‘/usr/lib64/R/library/IRkernel’

I can not downgrade R because that is inherited by the environment.

So I went back to a straight %r interpreter.
Which takes me back to the original issue I had with Zeppelin 0.8.2 .
When I run the googlevis tests I get no errors and not output.
When I run the plot tests I get:
Error in value[[3L]](cond): could not open file 'figure/unnamed-chunk-1-1.png' 
Need to find where zeppelin thinks the directory is located.


On 7/1/2020 9:56 AM, Jeff Zhang wrote:
If you are using %r.ir <http://r.ir>, then you need to install irkernel https://github.com/IRkernel/IRkernel <https://github.com/IRkernel/IRkernel>
here's full doc about R interpreter in Zeppelin http://zeppelin.apache.org/docs/0.9.0-preview1/interpreter/r.html <http://zeppelin.apache.org/docs/0.9.0-preview1/interpreter/r.html>
David Boyd <db...@incadencecorp.com <mailto:db...@incadencecorp.com>> 于2020年7月1日周三 下午7:45写道： 

    Sorry to be such a pain but I am under a tight deadline to get
    this operational.
    In running the r tutorial I get this message that says there is no
    such kernel named ir

    I can run the same paragraph with a straight %r interpreter just
    fine.

    Where would this get set up?


    org.apache.zeppelin.interpreter.InterpreterException:
    org.apache.zeppelin.interpreter.InterpreterException: Fail to
    open JupyterKernelInterpreter: java.io.IOException: Fail to
    launch Jupyter Kernel as the python process is failed.
    starting...E0701 11:28:38.350657744 25080
    socket_utils_common_posix.cc:222] check for SO_REUSEPORT:
    {"created":"@1593602918.350637104","description":"SO_REUSEPORT
    unavailable on compiling
    
system","file":"src/core/lib/iomgr/socket_utils_common_posix.cc","file_line":190}
    starting...E0701 11:28:38.350657744 25080
    socket_utils_common_posix.cc:222] check for SO_REUSEPORT:
    {"created":"@1593602918.350637104","description":"SO_REUSEPORT
    unavailable on compiling
    
system","file":"src/core/lib/iomgr/socket_utils_common_posix.cc","file_line":190}
    Traceback (most recent call last): File
    "/tmp/zeppelin_jupyter_kernel_ir3856431290391083629/kernel_server.py",
    line 186, in <module> serve(sys.argv[1], sys.argv[2]) File
    "/tmp/zeppelin_jupyter_kernel_ir3856431290391083629/kernel_server.py",
    line 172, in serve kernel.start() File
    "/tmp/zeppelin_jupyter_kernel_ir3856431290391083629/kernel_server.py",
    line 50, in start self._km, self._kc =
    jupyter_client.manager.start_new_kernel(kernel_name=self._kernel_name)
    File
    
"/data01/zeppelin/miniconda/envs/py37/lib/python3.8/site-packages/jupyter_client/manager.py",
    line 745, in start_new_kernel km.start_kernel(**kwargs) File
    
"/data01/zeppelin/miniconda/envs/py37/lib/python3.8/site-packages/jupyter_client/manager.py",
    line 301, in start_kernel kernel_cmd, kw =
    self.pre_start_kernel(**kw) File
    
"/data01/zeppelin/miniconda/envs/py37/lib/python3.8/site-packages/jupyter_client/manager.py",
    line 254, in pre_start_kernel kernel_cmd =
    self.format_kernel_cmd(extra_arguments=extra_arguments) File
    
"/data01/zeppelin/miniconda/envs/py37/lib/python3.8/site-packages/jupyter_client/manager.py",
    line 178, in format_kernel_cmd cmd = self.kernel_spec.argv +
    extra_arguments File
    
"/data01/zeppelin/miniconda/envs/py37/lib/python3.8/site-packages/jupyter_client/manager.py",
    line 84, in kernel_spec self._kernel_spec =
    self.kernel_spec_manager.get_kernel_spec(self.kernel_name) File
    
"/data01/zeppelin/miniconda/envs/py37/lib/python3.8/site-packages/jupyter_client/kernelspec.py",line
    235, in get_kernel_spec raise NoSuchKernel(kernel_name)
    jupyter_client.kernelspec.NoSuchKernel: No such kernel named ir
    at
    
org.apache.zeppelin.jupyter.JupyterKernelInterpreter.launchJupyterKernel(JupyterKernelInterpreter.java:207)
    at
    
org.apache.zeppelin.jupyter.JupyterKernelInterpreter.open(JupyterKernelInterpreter.java:129)
    at
    org.apache.zeppelin.r.IRInterpreter.open(IRInterpreter.java:90)
    at
    
org.apache.zeppelin.interpreter.LazyOpenInterpreter.open(LazyOpenInterpreter.java:70)
    at
    
org.apache.zeppelin.interpreter.remote.RemoteInterpreterServer$InterpretJob.jobRun(RemoteInterpreterServer.java:760)
    at
    
org.apache.zeppelin.interpreter.remote.RemoteInterpreterServer$InterpretJob.jobRun(RemoteInterpreterServer.java:668)at
    org.apache.zeppelin.scheduler.Job.run(Job.java:172) at
    
org.apache.zeppelin.scheduler.AbstractScheduler.runJob(AbstractScheduler.java:130)
    at
    
org.apache.zeppelin.scheduler.FIFOScheduler.lambda$runJobInScheduler$0(FIFOScheduler.java:39)at
    
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at
    
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748) at
    
org.apache.zeppelin.interpreter.LazyOpenInterpreter.open(LazyOpenInterpreter.java:76)at
    
org.apache.zeppelin.interpreter.remote.RemoteInterpreterServer$InterpretJob.jobRun(RemoteInterpreterServer.java:760)
    at
    
org.apache.zeppelin.interpreter.remote.RemoteInterpreterServer$InterpretJob.jobRun(RemoteInterpreterServer.java:668)at
    org.apache.zeppelin.scheduler.Job.run(Job.java:172) at
    
org.apache.zeppelin.scheduler.AbstractScheduler.runJob(AbstractScheduler.java:130)
    at
    
org.apache.zeppelin.scheduler.FIFOScheduler.lambda$runJobInScheduler$0(FIFOScheduler.java:39)at
    
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at
    
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748) Caused by:
    org.apache.zeppelin.interpreter.InterpreterException: Fail to
    open JupyterKernelInterpreter: java.io.IOException: Fail to
    launch Jupyter Kernel as the python process is failed.
    starting...E0701 11:28:38.350657744 25080
    socket_utils_common_posix.cc:222] check for SO_REUSEPORT:
    {"created":"@1593602918.350637104","description":"SO_REUSEPORT
    unavailable on compiling
    
system","file":"src/core/lib/iomgr/socket_utils_common_posix.cc","file_line":190}
    starting...E0701 11:28:38.350657744 25080
    socket_utils_common_posix.cc:222] check for SO_REUSEPORT:
    {"created":"@1593602918.350637104","description":"SO_REUSEPORT
    unavailable on compiling
    
system","file":"src/core/lib/iomgr/socket_utils_common_posix.cc","file_line":190}
    Traceback (most recent call last): File
    "/tmp/zeppelin_jupyter_kernel_ir3856431290391083629/kernel_server.py",
    line 186, in <module> serve(sys.argv[1], sys.argv[2]) File
    "/tmp/zeppelin_jupyter_kernel_ir3856431290391083629/kernel_server.py",
    line 172, in serve kernel.start() File
    "/tmp/zeppelin_jupyter_kernel_ir3856431290391083629/kernel_server.py",
    line 50, in start self._km, self._kc =
    jupyter_client.manager.start_new_kernel(kernel_name=self._kernel_name)
    File
    
"/data01/zeppelin/miniconda/envs/py37/lib/python3.8/site-packages/jupyter_client/manager.py",
    line 745, in start_new_kernel km.start_kernel(**kwargs) File
    
"/data01/zeppelin/miniconda/envs/py37/lib/python3.8/site-packages/jupyter_client/manager.py",
    line 301, in start_kernel kernel_cmd, kw =
    self.pre_start_kernel(**kw) File
    
"/data01/zeppelin/miniconda/envs/py37/lib/python3.8/site-packages/jupyter_client/manager.py",
    line 254, in pre_start_kernel kernel_cmd =
    self.format_kernel_cmd(extra_arguments=extra_arguments) File
    
"/data01/zeppelin/miniconda/envs/py37/lib/python3.8/site-packages/jupyter_client/manager.py",
    line 178, in format_kernel_cmd cmd = self.kernel_spec.argv +
    extra_arguments File
    
"/data01/zeppelin/miniconda/envs/py37/lib/python3.8/site-packages/jupyter_client/manager.py",
    line 84, in kernel_spec self._kernel_spec =
    self.kernel_spec_manager.get_kernel_spec(self.kernel_name) File
    
"/data01/zeppelin/miniconda/envs/py37/lib/python3.8/site-packages/jupyter_client/kernelspec.py",
    line 235, in get_kernel_spec raise NoSuchKernel(kernel_name)
    jupyter_client.kernelspec.NoSuchKernel: No such kernel named ir
    at
    
org.apache.zeppelin.jupyter.JupyterKernelInterpreter.launchJupyterKernel(JupyterKernelInterpreter.java:207)at
    
org.apache.zeppelin.jupyter.JupyterKernelInterpreter.open(JupyterKernelInterpreter.java:129)
    at
    org.apache.zeppelin.r.IRInterpreter.open(IRInterpreter.java:90)
    at
    
org.apache.zeppelin.interpreter.LazyOpenInterpreter.open(LazyOpenInterpreter.java:70)
    at
    
org.apache.zeppelin.interpreter.remote.RemoteInterpreterServer$InterpretJob.jobRun(RemoteInterpreterServer.java:760)
    at
    
org.apache.zeppelin.interpreter.remote.RemoteInterpreterServer$InterpretJob.jobRun(RemoteInterpreterServer.java:668)at
    org.apache.zeppelin.scheduler.Job.run(Job.java:172) at
    
org.apache.zeppelin.scheduler.AbstractScheduler.runJob(AbstractScheduler.java:130)
    at
    
org.apache.zeppelin.scheduler.FIFOScheduler.lambda$runJobInScheduler$0(FIFOScheduler.java:39)at
    
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at
    
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748) at
    
org.apache.zeppelin.jupyter.JupyterKernelInterpreter.open(JupyterKernelInterpreter.java:132)
    at
    org.apache.zeppelin.r.IRInterpreter.open(IRInterpreter.java:90)
    at
    
org.apache.zeppelin.interpreter.LazyOpenInterpreter.open(LazyOpenInterpreter.java:70)
    ... 8 more Caused by: java.io.IOException: Fail to launch Jupyter
    Kernel as the python process is failed. starting...E0701
    11:28:38.350657744 25080 socket_utils_common_posix.cc:222] check
    for SO_REUSEPORT:
    {"created":"@1593602918.350637104","description":"SO_REUSEPORT
    unavailable on compiling
    
system","file":"src/core/lib/iomgr/socket_utils_common_posix.cc","file_line":190}
    starting...E0701 11:28:38.350657744 25080
    socket_utils_common_posix.cc:222] check for SO_REUSEPORT:
    {"created":"@1593602918.350637104","description":"SO_REUSEPORT
    unavailable on compiling
    
system","file":"src/core/lib/iomgr/socket_utils_common_posix.cc","file_line":190}
    Traceback (most recent call last): File
    "/tmp/zeppelin_jupyter_kernel_ir3856431290391083629/kernel_server.py",
    line 186, in <module> serve(sys.argv[1], sys.argv[2]) File
    "/tmp/zeppelin_jupyter_kernel_ir3856431290391083629/kernel_server.py",
    line 172, in serve kernel.start() File
    "/tmp/zeppelin_jupyter_kernel_ir3856431290391083629/kernel_server.py",
    line 50, in start self._km, self._kc =
    jupyter_client.manager.start_new_kernel(kernel_name=self._kernel_name)
    File
    
"/data01/zeppelin/miniconda/envs/py37/lib/python3.8/site-packages/jupyter_client/manager.py",
    line 745, in start_new_kernel km.start_kernel(**kwargs) File
    
"/data01/zeppelin/miniconda/envs/py37/lib/python3.8/site-packages/jupyter_client/manager.py",
    line 301, in start_kernel kernel_cmd, kw =
    self.pre_start_kernel(**kw) File
    
"/data01/zeppelin/miniconda/envs/py37/lib/python3.8/site-packages/jupyter_client/manager.py",
    line 254, in pre_start_kernel kernel_cmd =
    self.format_kernel_cmd(extra_arguments=extra_arguments) File
    
"/data01/zeppelin/miniconda/envs/py37/lib/python3.8/site-packages/jupyter_client/manager.py",
    line 178, in format_kernel_cmd cmd = self.kernel_spec.argv +
    extra_arguments File
    
"/data01/zeppelin/miniconda/envs/py37/lib/python3.8/site-packages/jupyter_client/manager.py",
    line 84, in kernel_spec self._kernel_spec =
    self.kernel_spec_manager.get_kernel_spec(self.kernel_name) File
    
"/data01/zeppelin/miniconda/envs/py37/lib/python3.8/site-packages/jupyter_client/kernelspec.py",line
    235, in get_kernel_spec raise NoSuchKernel(kernel_name)
    jupyter_client.kernelspec.NoSuchKernel: No such kernel named ir
    at
    
org.apache.zeppelin.jupyter.JupyterKernelInterpreter.launchJupyterKernel(JupyterKernelInterpreter.java:207)
    at
    
org.apache.zeppelin.jupyter.JupyterKernelInterpreter.open(JupyterKernelInterpreter.java:129)
    ... 10 more
-- =========mailto:db...@incadencecorp.com <mailto:db...@incadencecorp.com> ============ 
    David W. Boyd
    VP,  Data Solutions
    10432 Balls Ford, Suite 240
    Manassas, VA 20109
    office:   +1-703-552-2862
    cell:     +1-703-402-7908
    ==============http://www.incadencecorp.com/  
<http://www.incadencecorp.com/>  ============
    ISO/IEC JTC1 SC42/WG2, editor ISO/IEC 20546, ISO/IEC 20547-1
    Chair INCITS TG Big Data
    Co-chair NIST Big Data Public Working Group Reference Architecture
    First Robotic Mentor - FRC, FTC -www.iliterobotics.org  
<http://www.iliterobotics.org>
    Board Member- USSTEM Foundation -www.usstem.org  <http://www.usstem.org>

    The information contained in this message may be privileged
    and/or confidential and protected from disclosure.
    If the reader of this message is not the intended recipient
    or an employee or agent responsible for delivering this message
    to the intended recipient, you are hereby notified that any
    dissemination, distribution or copying of this communication
    is strictly prohibited.  If you have received this communication
    in error, please notify the sender immediately by replying to
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--
Best Regards

Jeff Zhang


--
========= mailto:db...@incadencecorp.com ============
David W. Boyd
VP,  Data Solutions
10432 Balls Ford, Suite 240
Manassas, VA 20109
office:   +1-703-552-2862
cell:     +1-703-402-7908
============== http://www.incadencecorp.com/ ============
ISO/IEC JTC1 SC42/WG2, editor ISO/IEC 20546, ISO/IEC 20547-1
Chair INCITS TG Big Data
Co-chair NIST Big Data Public Working Group Reference Architecture
First Robotic Mentor - FRC, FTC - www.iliterobotics.org
Board Member- USSTEM Foundation - www.usstem.org

The information contained in this message may be privileged
and/or confidential and protected from disclosure.
If the reader of this message is not the intended recipient
or an employee or agent responsible for delivering this message
to the intended recipient, you are hereby notified that any
dissemination, distribution or copying of this communication
is strictly prohibited.  If you have received this communication
in error, please notify the sender immediately by replying to
this message and deleting the material from any computer.

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