'Re: [Wekalist] About RPlugin on Weka 3.92'

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List:       wekalist
Subject:    Re: [Wekalist] About RPlugin on Weka 3.92
From:       Eibe Frank <eibe.frank () waikato ! ac ! nz>
Date:       2018-05-18 12:17:34
Message-ID: CADehzLVKh3mje1vy51qnphw1XxHkTuPG22Kq6DWy61xRrs4xZQ () mail ! gmail ! com
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It should be possible to use MLRClassifier in RotationForest, specifying
C5.0 as the learner argument in MLRClassifier.

It is currently not possible to use R preprocessing tools inside WEKA's
FilteredClassifier, unless you use a very circuitous route via
WekaPyScript, which enables implementation of a filter in Python.

However, you can use R preprocessing tools via the RScriptExecutor
component in the KnowledgeFlow. The third WEKA MOOC has information on how
to do this:

https://www.cs.waikato.ac.nz/ml/weka/mooc/advanceddataminingwithweka/

Cheers,
Eibe

On Fri, 18 May 2018 at 10:11 PM, Alim Samat <alim.smt@gmail.com> wrote:

> Dear Eibe,
>
> Thank you very much for your reply, now RPlugin is running perfectly after
> I reinstalled JVM and deleted the manually installed deeplearning4j
> packages.
> And, can we replace the J4.8 adopted in RotationForest with C5.0 available
> for R, and use other dimensional reduction methods that unavailable in weka
> but available in R while constructing DR based classification methods? If
> we can, what will be the solution? thanks.
>
> bests,
>
>
>
> *Alim ·Samat*
>
> Associate Professor,
> Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences,
> No.818, South Beijing  Road,
> Urumqi, Xinjiang, China, 830011.
>
>
>
> On Fri, May 18, 2018 at 11:50 AM, Eibe Frank <eibe.frank@waikato.ac.nz>
> wrote:
>
>> I just installed 64-bit R 3.5.0 on my 64-bit Windows 10 laptop, on which
>> I use 64-bit Oracle Java 9. Going through the installation steps for the
>> RPlugin worked fine, but I had to manually install the XML library for R
>> from the R console to get MLRClassifier to work (in addition to manually
>> installing rJava, of course). Not sure why automatic installation by WEKA
>> failed. Anyway, I didn't have any issues with rJava.
>>
>> I don't run WEKA or R as administrator, so all my R libraries get
>> installed in my user home. Here are my relevant environment variables:
>>
>> R_HOME   C:/Program Files/R/R-3.5.0
>> R_LIBS_USER  C:/Users/eibe/R/win-library/3.5
>> PATH  C:\Program Files\R\R-3.5.0\bin\x64 (only relevant part shown)
>>
>> Your issue is most likely due to the fact that RPlugin cannot find the
>> rJava package for R in your R_LIBS_USER location.
>>
>> Cheers,
>> Eibe
>>
>>
>> On Thu, May 17, 2018 at 10:06 PM, Alim Samat <alim.smt@gmail.com> wrote:
>>
>>> Deaer all,
>>> By following the instruction for RPlugin, setting environment variable
>>> R_HOME to "D:\Program Files\R\R-3.5.0\library" and R_LIBS_USER to
>>> "D:\Program Files\R\R-3.5.0\library", rJava package was installed for R x64
>>> 3.5.0, Weka comes the error of:
>>> Exception in thread "Thread-19" java.lang.UnsatisfiedLinkError:
>>> org.rosuda.JRI.Rengine.rniSetupR([Ljava/lang/String;)I
>>>         org.rosuda.JRI.Rengine.rniSetupR(Native Method)
>>>         org.rosuda.JRI.Rengine.setupR(Rengine.java:170)
>>>         org.rosuda.JRI.Rengine.run(Rengine.java:635)
>>>
>>>         at org.rosuda.JRI.Rengine.rniSetupR(Native Method)
>>>         at org.rosuda.JRI.Rengine.setupR(Rengine.java:170)
>>>         at org.rosuda.JRI.Rengine.run(Rengine.java:635)
>>>
>>> And I don't have much information from http://www.rforge.net/JRI to
>>> solve above issue.
>>>
>>> If any of you have successful usage of RPlugin on Week 3.92 version,
>>> could you enlightened me specific solution? thanks.
>>>
>>> bests,
>>>
>>>
>>> *Alim ·Samat*
>>>
>>> Associate Professor,
>>> Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences,
>>> No.818, South Beijing  Road,
>>> Urumqi, Xinjiang, China, 830011.
>>>
>>>
>>>
>>> _______________________________________________
>>> Wekalist mailing list
>>> Send posts to: Wekalist@list.waikato.ac.nz
>>> List info and subscription status:
>>> https://list.waikato.ac.nz/mailman/listinfo/wekalist
>>> List etiquette:
>>> http://www.cs.waikato.ac.nz/~ml/weka/mailinglist_etiquette.html
>>>
>>>
>>
>> _______________________________________________
>> Wekalist mailing list
>> Send posts to: Wekalist@list.waikato.ac.nz
>> List info and subscription status:
>> https://list.waikato.ac.nz/mailman/listinfo/wekalist
>> List etiquette:
>> http://www.cs.waikato.ac.nz/~ml/weka/mailinglist_etiquette.html
>>
>>
> _______________________________________________
> Wekalist mailing list
> Send posts to: Wekalist@list.waikato.ac.nz
> List info and subscription status:
> https://list.waikato.ac.nz/mailman/listinfo/wekalist
> List etiquette:
> http://www.cs.waikato.ac.nz/~ml/weka/mailinglist_etiquette.html
>

[Attachment #5 (text/html)]

<div><div>It should be possible to use MLRClassifier in RotationForest, specifying \
C5.0 as the learner argument in MLRClassifier.</div></div><div \
dir="auto"><br></div><div dir="auto">It is currently not possible to use R \
preprocessing tools inside WEKA's FilteredClassifier, unless you use a very \
circuitous route via WekaPyScript, which enables implementation of a filter in \
Python.</div><div dir="auto"><br></div><div dir="auto">However, you can use R \
preprocessing tools via the RScriptExecutor component in the KnowledgeFlow. The third \
WEKA MOOC has information on how to do this:</div><div dir="auto"><br></div><div \
dir="auto"><div><a href="https://www.cs.waikato.ac.nz/ml/weka/mooc/advanceddataminingw \
ithweka/">https://www.cs.waikato.ac.nz/ml/weka/mooc/advanceddataminingwithweka/</a></div></div><div \
dir="auto"><br></div><div dir="auto">Cheers,</div><div \
dir="auto">Eibe</div><div><br><div class="gmail_quote"><div>On Fri, 18 May 2018 at \
10:11 PM, Alim Samat &lt;<a \
href="mailto:alim.smt@gmail.com">alim.smt@gmail.com</a>&gt; \
wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 \
.8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="gmail_default" \
style="font-family:georgia,serif">Dear Eibe,</div><div class="gmail_default" \
style="font-family:georgia,serif"><br></div><div class="gmail_default" \
style="font-family:georgia,serif">Thank you very much for your reply, now RPlugin is \
running perfectly after I reinstalled JVM and deleted the manually installed \
deeplearning4j packages.  </div><div class="gmail_default" \
style="font-family:georgia,serif">And, can we replace the J4.8 adopted in \
RotationForest with C5.0 available for R, and use other dimensional reduction methods \
that unavailable in weka but available in R while constructing DR based \
classification methods? If we can, what will be the solution? thanks.</div><div \
class="gmail_default" style="font-family:georgia,serif"><br></div><div \
class="gmail_default" style="font-family:georgia,serif">bests,</div><div \
class="gmail_default" style="font-family:georgia,serif"><br></div><div \
class="gmail_default" style="font-family:georgia,serif"><br></div></div><div \
class="gmail_extra"></div><div class="gmail_extra"><br clear="all"><div><div \
class="m_4131536667302608423gmail_signature" \
data-smartmail="gmail_signature"><div><div><div><div><div><font color="#3333ff" \
face="arial, helvetica, sans-serif" size="4"><b>Alim \
·Samat</b></font><div><div><br></div><div><font color="#3d85c6" face="comic sans ms, \
sans-serif">Associate Professor,</font></div><div><span \
style="color:rgb(0,0,153)"><font face="comic sans ms, sans-serif">Xinjiang Institute \
of Ecology and Geography, Chinese Academy of Sciences,</font></span></div><div><font \
face="comic sans ms, sans-serif"><font color="#000099">No.818,  </font><span \
style="color:rgb(0,0,153);font-size:12.8px">South  </span><span \
style="color:rgb(0,0,153);font-size:12.8px">Beijing   \
Road,</span></font></div><div><font face="comic sans ms, sans-serif"><font \
color="#000099">Urumqi, Xinjiang,  </font><font color="#000099">China, \
830011</font><span style="color:rgb(0,0,153)">.</span></font></div></div><div><span \
style="color:rgb(0,0,153);font-family:arial,helvetica,sans-serif"><span></span><span></span><br><br></span></div></div></div></div></div></div></div></div>
 <br></div><div class="gmail_extra"><div class="gmail_quote">On Fri, May 18, 2018 at \
11:50 AM, Eibe Frank <span>&lt;<a href="mailto:eibe.frank@waikato.ac.nz" \
target="_blank">eibe.frank@waikato.ac.nz</a>&gt;</span> wrote:<br><blockquote \
class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc \
solid;padding-left:1ex"><div><div><div><span \
style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-va \
riant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-inden \
t:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;display:inline;float:none">I \
just installed 64-bit R 3.5.0 on my 64-bit Windows 10 laptop, on which I use 64-bit \
Oracle Java 9. Going through the installation steps for the RPlugin worked fine, but \
I had to  <span style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-styl \
e:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align: \
start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;display:inline;float:none">manually \
</span>

install the XML library for R from the R console to get MLRClassifier to work (in \
addition to manually installing rJava, of course). Not sure why automatic \
installation by WEKA failed. Anyway, I didn't have any issues with rJava.</span><div \
style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-va \
riant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-inden \
t:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br></div><div \
style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-va \
riant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-inden \
t:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">I \
don't run WEKA or R as administrator, so all my R libraries get installed in my user \
home. Here are my relevant environment variables:<br><br></div><div \
style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-va \
riant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-inden \
t:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">R_HOME \
C:/Program Files/R/R-3.5.0<br></div><div \
style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-va \
riant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-inden \
t:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">R_LIBS_USER \
C:/Users/eibe/R/win-library/3.5<br></div><div \
style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-va \
riant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-inden \
t:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">PATH \
C:\Program Files\R\R-3.5.0\bin\x64 (only relevant part \
shown)<br></div><br></div><div>Your issue is most likely due to the fact that RPlugin \
cannot find the rJava package for R in your R_LIBS_USER \
location.<br></div><div><br></div>Cheers,<br></div>Eibe<br><div><div><br></div></div><div \
class="gmail_extra"><br><div class="gmail_quote"><div><div \
class="m_4131536667302608423h5">On Thu, May 17, 2018 at 10:06 PM, Alim Samat \
<span>&lt;<a href="mailto:alim.smt@gmail.com" \
target="_blank">alim.smt@gmail.com</a>&gt;</span> wrote:<br></div></div><blockquote \
class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc \
solid;padding-left:1ex"><div><div class="m_4131536667302608423h5"><div><div \
style="font-family:georgia,serif">Deaer all,</div><div \
style="font-family:georgia,serif">By following the instruction for RPlugin, setting \
environment variable R_HOME to &quot;D:\Program Files\R\R-3.5.0\library&quot; and \
R_LIBS_USER to &quot;D:\Program Files\R\R-3.5.0\library&quot;, rJava package was \
installed for R x64 3.5.0, Weka comes the error of:<br></div><div><div><font \
face="georgia, serif" color="#ff00ff">Exception in thread &quot;Thread-19&quot; \
java.lang.UnsatisfiedLinkError: \
org.rosuda.JRI.Rengine.rniSetupR([Ljava/lang/String;)I</font></div><div><font \
face="georgia, serif" color="#ff00ff">            \
org.rosuda.JRI.Rengine.rniSetupR(Native Method)</font></div><div><font face="georgia, \
serif" color="#ff00ff">            \
org.rosuda.JRI.Rengine.setupR(Rengine.java:170)</font></div><div><font face="georgia, \
serif" color="#ff00ff">            \
org.rosuda.JRI.Rengine.run(Rengine.java:635)</font></div><div><font face="georgia, \
serif" color="#ff00ff"><br></font></div><div><font face="georgia, serif" \
color="#ff00ff">            at org.rosuda.JRI.Rengine.rniSetupR(Native \
Method)</font></div><div><font face="georgia, serif" color="#ff00ff">            at \
org.rosuda.JRI.Rengine.setupR(Rengine.java:170)</font></div><div><font face="georgia, \
serif" color="#ff00ff">            at \
org.rosuda.JRI.Rengine.run(Rengine.java:635)</font></div><div><br></div><div><font \
face="georgia, serif">And I don&#39;t have much information from <a \
href="http://www.rforge.net/JRI" target="_blank">http://www.rforge.net/JRI</a> to \
solve above issue.  </font></div><div><font face="georgia, \
serif"><br></font></div><span style="font-family:georgia,serif">If any of you have \
successful usage of RPlugin on Week 3.92 version, could you enlightened me specific \
solution? thanks.</span></div><div><span \
style="font-family:georgia,serif"><br></span></div><div><span \
style="font-family:georgia,serif">bests,</span></div><div><span \
style="font-family:georgia,serif">    </span></div><div \
style="font-family:georgia,serif"><br></div><div><div \
class="m_4131536667302608423m_-8426301228837585963gmail-m_4662075670001731668gmail_signature"><div><div><div><div><div><font \
face="arial, helvetica, sans-serif" size="4" color="#3333ff"><b>Alim \
·Samat</b></font><div><div><br></div><div><font face="comic sans ms, sans-serif" \
color="#3d85c6">Associate Professor,</font></div><div><span \
style="color:rgb(0,0,153)"><font face="comic sans ms, sans-serif">Xinjiang Institute \
of Ecology and Geography, Chinese Academy of Sciences,</font></span></div><div><font \
face="comic sans ms, sans-serif"><font color="#000099">No.818,  </font><span \
style="color:rgb(0,0,153);font-size:12.8px">South  </span><span \
style="color:rgb(0,0,153);font-size:12.8px">Beijing   \
Road,</span></font></div><div><font face="comic sans ms, sans-serif"><font \
color="#000099">Urumqi, Xinjiang,  </font><font color="#000099">China, \
830011</font><span style="color:rgb(0,0,153)">.</span></font></div></div><div><span \
style="color:rgb(0,0,153);font-family:arial,helvetica,sans-serif"><span></span><span></span><br><br></span></div></div></div></div></div></div></div></div>
 </div>
<br></div></div>_______________________________________________<br>
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 <br></blockquote></div><br></div></div>
<br>_______________________________________________<br>
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 <br></blockquote></div><br></div>
_______________________________________________<br>
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 </blockquote></div></div>

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