RWeka setup

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RWeka setup

Patrick Connolly
I installed weka in /usr/local/weka-3-8-1/weka.jar and when I installed RWeka, it has
another weka.jar in the R package library.  I assume the latter is
used when I try this (in R):

> WPM("refresh-cache")
Refresh in progress. Please wait...
Unable to download repository zip archve (connect timed out) - trying legacy routine...
java.net.SocketTimeoutException: connect timed out

My guess is that the CLASSPATH isn't specified.  Without setting an
environment variable, where do I specify the class path option?

TIA

Patrick Connolly
Biometrician

www.plantandfood.co.nz
The New Zealand Institute for Plant & Food Research Limited



The contents of this e-mail are confidential and may be subject to legal privilege.
 If you are not the intended recipient you must not use, disseminate, distribute or
 reproduce all or any part of this e-mail or attachments.  If you have received this
 e-mail in error, please notify the sender and delete all material pertaining to this
 e-mail.  Any opinion or views expressed in this e-mail are those of the individual
 sender and may not represent those of The New Zealand Institute for Plant and
 Food Research Limited.

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Re: RWeka setup

Eibe Frank-2
Administrator
The WEKA package manager needs web access to connect to the SourceForge site. You probably don't have direct access and instead need to go through a proxy server. Oracle's JVM reads the _JAVA_OPTIONS environment variable and you can provide proxy settings via that variable, as explained here:

  https://weka.wikispaces.com/Weka+package+manager+does+not+start

However, WEKA may not be able to pop up the GUI for entering the proxy credentials, so you may have to add those as part of the environment variable as well, using http.proxyUser and http.proxyPassword, as explained here:

  https://weka.wikispaces.com/How+do+I+use+the+package+manager%3F#GUI%20package%20manager-Using%20a%20HTTP%20proxy

Cheers,
Eibe

> On 24 Apr 2017, at 16:33, Patrick Connolly <[hidden email]> wrote:
>
> I installed weka in /usr/local/weka-3-8-1/weka.jar and when I installed RWeka, it has
> another weka.jar in the R package library.  I assume the latter is
> used when I try this (in R):
>
>> WPM("refresh-cache")
> Refresh in progress. Please wait...
> Unable to download repository zip archve (connect timed out) - trying legacy routine...
> java.net.SocketTimeoutException: connect timed out
>
> My guess is that the CLASSPATH isn't specified.  Without setting an
> environment variable, where do I specify the class path option?
>
> TIA
>
> Patrick Connolly
> Biometrician
>
> www.plantandfood.co.nz
> The New Zealand Institute for Plant & Food Research Limited
>
>
>
> The contents of this e-mail are confidential and may be subject to legal privilege.
> If you are not the intended recipient you must not use, disseminate, distribute or
> reproduce all or any part of this e-mail or attachments.  If you have received this
> e-mail in error, please notify the sender and delete all material pertaining to this
> e-mail.  Any opinion or views expressed in this e-mail are those of the individual
> sender and may not represent those of The New Zealand Institute for Plant and
> Food Research Limited.
>
> _______________________________________________
> Wekalist mailing list
> Send posts to: [hidden email]
> 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

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Re: RWeka setup

Patrick Connolly
I followed the directions at
https://weka.wikispaces.com/Weka+package+manager+does+not+start :
Now when I start RWeka, I get

> require(RWeka)
Loading required package: RWeka
Picked up _JAVA_OPTIONS: -Dhttp.proxyHost=http://proxy.pfr.co.nz -Dhttp.proxyPort=8080

which indicates to me that I have the syntax correct, but I then get

> WPM("refresh-cache")
Refresh in progress. Please wait...
Unable to download repository zip archve (http://proxy.pfr.co.nz) - trying legacy routine...


... that is unless I install the repo manually in
~/wekafiles/repCache.  In that case, there's no message but
~/wekafiles/repCache is deleted.

The proxy does not require authentication, so something else is amiss.

If I try
> WPM("list-packages", "installed")

R crashes.

Am I on a hiding to nowhere trying to use RWeka without a JAVACLASS
environment variable?


Patrick Connolly
Biometrician

Postal Address: Plant & Food Research
Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
Physical Address: Plant & Food Research
120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand

> -----Original Message-----
> From: [hidden email] [mailto:wekalist-
> [hidden email]] On Behalf Of Eibe Frank
> Sent: Monday, 24 April 2017 10:56 p.m.
> To: Weka machine learning workbench list.
> Subject: Re: [Wekalist] RWeka setup
>
> The WEKA package manager needs web access to connect to the SourceForge
> site. You probably don't have direct access and instead need to go through a
> proxy server. Oracle's JVM reads the _JAVA_OPTIONS environment variable and
> you can provide proxy settings via that variable, as explained here:
>
>   https://weka.wikispaces.com/Weka+package+manager+does+not+start
>
> However, WEKA may not be able to pop up the GUI for entering the proxy
> credentials, so you may have to add those as part of the environment variable as
> well, using http.proxyUser and http.proxyPassword, as explained here:
>
>
> https://weka.wikispaces.com/How+do+I+use+the+package+manager%3F#GUI
> %20package%20manager-Using%20a%20HTTP%20proxy
>
> Cheers,
> Eibe
>
> > On 24 Apr 2017, at 16:33, Patrick Connolly
> <[hidden email]> wrote:
> >
> > I installed weka in /usr/local/weka-3-8-1/weka.jar and when I installed
> RWeka, it has
> > another weka.jar in the R package library.  I assume the latter is
> > used when I try this (in R):
> >
> >> WPM("refresh-cache")
> > Refresh in progress. Please wait...
> > Unable to download repository zip archve (connect timed out) - trying legacy
> routine...
> > java.net.SocketTimeoutException: connect timed out
> >
> > My guess is that the CLASSPATH isn't specified.  Without setting an
> > environment variable, where do I specify the class path option?
> >
> > TIA
> >
> > Patrick Connolly
> > Biometrician
> >
> > www.plantandfood.co.nz
> > The New Zealand Institute for Plant & Food Research Limited
> >
> >
> >
> > The contents of this e-mail are confidential and may be subject to legal
> privilege.
> > If you are not the intended recipient you must not use, disseminate, distribute
> or
> > reproduce all or any part of this e-mail or attachments.  If you have received
> this
> > e-mail in error, please notify the sender and delete all material pertaining to
> this
> > e-mail.  Any opinion or views expressed in this e-mail are those of the
> individual
> > sender and may not represent those of The New Zealand Institute for Plant
> and
> > Food Research Limited.
> >
> > _______________________________________________
> > Wekalist mailing list
> > Send posts to: [hidden email]
> > 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: [hidden email]
> 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
The contents of this e-mail are confidential and may be subject to legal privilege.
 If you are not the intended recipient you must not use, disseminate, distribute or
 reproduce all or any part of this e-mail or attachments.  If you have received this
 e-mail in error, please notify the sender and delete all material pertaining to this
 e-mail.  Any opinion or views expressed in this e-mail are those of the individual
 sender and may not represent those of The New Zealand Institute for Plant and
 Food Research Limited.

_______________________________________________
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Send posts to: [hidden email]
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Re: RWeka setup

Mark Hall
Hmm. I'm not sure what is going wrong here. However, you should be able to establish a repository cache by manually installing in ~/wekafiles/repCache (as you did), but not executing WPM("refresh-cache"). You can then install any packages that you're interested in manually (being careful to get the versions compatible with 3.8.1) by downloading via your browser from:

http://weka.sourceforge.net/packageMetaData/

Cheers,
Mark.

On 26/04/17, 3:02 PM, "Patrick Connolly" <[hidden email] on behalf of [hidden email]> wrote:

    I followed the directions at
    https://weka.wikispaces.com/Weka+package+manager+does+not+start :
    Now when I start RWeka, I get
   
    > require(RWeka)
    Loading required package: RWeka
    Picked up _JAVA_OPTIONS: -Dhttp.proxyHost=http://proxy.pfr.co.nz -Dhttp.proxyPort=8080
   
    which indicates to me that I have the syntax correct, but I then get
   
    > WPM("refresh-cache")
    Refresh in progress. Please wait...
    Unable to download repository zip archve (http://proxy.pfr.co.nz) - trying legacy routine...
   
   
    ... that is unless I install the repo manually in
    ~/wekafiles/repCache.  In that case, there's no message but
    ~/wekafiles/repCache is deleted.
   
    The proxy does not require authentication, so something else is amiss.
   
    If I try
    > WPM("list-packages", "installed")
   
    R crashes.
   
    Am I on a hiding to nowhere trying to use RWeka without a JAVACLASS
    environment variable?
   
   
    Patrick Connolly
    Biometrician
   
    Postal Address: Plant & Food Research
    Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
    Physical Address: Plant & Food Research
    120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
    > -----Original Message-----
    > From: [hidden email] [mailto:wekalist-
    > [hidden email]] On Behalf Of Eibe Frank
    > Sent: Monday, 24 April 2017 10:56 p.m.
    > To: Weka machine learning workbench list.
    > Subject: Re: [Wekalist] RWeka setup
    >
    > The WEKA package manager needs web access to connect to the SourceForge
    > site. You probably don't have direct access and instead need to go through a
    > proxy server. Oracle's JVM reads the _JAVA_OPTIONS environment variable and
    > you can provide proxy settings via that variable, as explained here:
    >
    >   https://weka.wikispaces.com/Weka+package+manager+does+not+start
    >
    > However, WEKA may not be able to pop up the GUI for entering the proxy
    > credentials, so you may have to add those as part of the environment variable as
    > well, using http.proxyUser and http.proxyPassword, as explained here:
    >
    >
    > https://weka.wikispaces.com/How+do+I+use+the+package+manager%3F#GUI
    > %20package%20manager-Using%20a%20HTTP%20proxy
    >
    > Cheers,
    > Eibe
    >
    > > On 24 Apr 2017, at 16:33, Patrick Connolly
    > <[hidden email]> wrote:
    > >
    > > I installed weka in /usr/local/weka-3-8-1/weka.jar and when I installed
    > RWeka, it has
    > > another weka.jar in the R package library.  I assume the latter is
    > > used when I try this (in R):
    > >
    > >> WPM("refresh-cache")
    > > Refresh in progress. Please wait...
    > > Unable to download repository zip archve (connect timed out) - trying legacy
    > routine...
    > > java.net.SocketTimeoutException: connect timed out
    > >
    > > My guess is that the CLASSPATH isn't specified.  Without setting an
    > > environment variable, where do I specify the class path option?
    > >
    > > TIA
    > >
    > > Patrick Connolly
    > > Biometrician
    > >
    > > www.plantandfood.co.nz
    > > The New Zealand Institute for Plant & Food Research Limited
    > >
    > >
    > >
    > > The contents of this e-mail are confidential and may be subject to legal
    > privilege.
    > > If you are not the intended recipient you must not use, disseminate, distribute
    > or
    > > reproduce all or any part of this e-mail or attachments.  If you have received
    > this
    > > e-mail in error, please notify the sender and delete all material pertaining to
    > this
    > > e-mail.  Any opinion or views expressed in this e-mail are those of the
    > individual
    > > sender and may not represent those of The New Zealand Institute for Plant
    > and
    > > Food Research Limited.
    > >
    > > _______________________________________________
    > > Wekalist mailing list
    > > Send posts to: [hidden email]
    > > 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: [hidden email]
    > 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
    The contents of this e-mail are confidential and may be subject to legal privilege.
     If you are not the intended recipient you must not use, disseminate, distribute or
     reproduce all or any part of this e-mail or attachments.  If you have received this
     e-mail in error, please notify the sender and delete all material pertaining to this
     e-mail.  Any opinion or views expressed in this e-mail are those of the individual
     sender and may not represent those of The New Zealand Institute for Plant and
     Food Research Limited.
   
    _______________________________________________
    Wekalist mailing list
    Send posts to: [hidden email]
    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
   


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Re: RWeka setup

Eibe Frank-2
Administrator
In reply to this post by Patrick Connolly
Are you sure you have the proxy details right?

$ ping proxy.pfr.co.nz
ping: cannot resolve proxy.pfr.co.nz: Unknown host

Cheers,
Eibe

> On 26/04/2017, at 3:02 PM, Patrick Connolly <[hidden email]> wrote:
>
> I followed the directions at
> https://weka.wikispaces.com/Weka+package+manager+does+not+start :
> Now when I start RWeka, I get
>
>> require(RWeka)
> Loading required package: RWeka
> Picked up _JAVA_OPTIONS: -Dhttp.proxyHost=http://proxy.pfr.co.nz -Dhttp.proxyPort=8080
>
> which indicates to me that I have the syntax correct, but I then get
>
>> WPM("refresh-cache")
> Refresh in progress. Please wait...
> Unable to download repository zip archve (http://proxy.pfr.co.nz) - trying legacy routine...
>
>
> ... that is unless I install the repo manually in
> ~/wekafiles/repCache.  In that case, there's no message but
> ~/wekafiles/repCache is deleted.
>
> The proxy does not require authentication, so something else is amiss.
>
> If I try
>> WPM("list-packages", "installed")
>
> R crashes.
>
> Am I on a hiding to nowhere trying to use RWeka without a JAVACLASS
> environment variable?
>
>
> Patrick Connolly
> Biometrician
>
> Postal Address: Plant & Food Research
> Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
> Physical Address: Plant & Food Research
> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
>> -----Original Message-----
>> From: [hidden email] [mailto:wekalist-
>> [hidden email]] On Behalf Of Eibe Frank
>> Sent: Monday, 24 April 2017 10:56 p.m.
>> To: Weka machine learning workbench list.
>> Subject: Re: [Wekalist] RWeka setup
>>
>> The WEKA package manager needs web access to connect to the SourceForge
>> site. You probably don't have direct access and instead need to go through a
>> proxy server. Oracle's JVM reads the _JAVA_OPTIONS environment variable and
>> you can provide proxy settings via that variable, as explained here:
>>
>>  https://weka.wikispaces.com/Weka+package+manager+does+not+start
>>
>> However, WEKA may not be able to pop up the GUI for entering the proxy
>> credentials, so you may have to add those as part of the environment variable as
>> well, using http.proxyUser and http.proxyPassword, as explained here:
>>
>>
>> https://weka.wikispaces.com/How+do+I+use+the+package+manager%3F#GUI
>> %20package%20manager-Using%20a%20HTTP%20proxy
>>
>> Cheers,
>> Eibe
>>
>>> On 24 Apr 2017, at 16:33, Patrick Connolly
>> <[hidden email]> wrote:
>>>
>>> I installed weka in /usr/local/weka-3-8-1/weka.jar and when I installed
>> RWeka, it has
>>> another weka.jar in the R package library.  I assume the latter is
>>> used when I try this (in R):
>>>
>>>> WPM("refresh-cache")
>>> Refresh in progress. Please wait...
>>> Unable to download repository zip archve (connect timed out) - trying legacy
>> routine...
>>> java.net.SocketTimeoutException: connect timed out
>>>
>>> My guess is that the CLASSPATH isn't specified.  Without setting an
>>> environment variable, where do I specify the class path option?
>>>
>>> TIA
>>>
>>> Patrick Connolly
>>> Biometrician
>>>
>>> www.plantandfood.co.nz
>>> The New Zealand Institute for Plant & Food Research Limited
>>>
>>>
>>>
>>> The contents of this e-mail are confidential and may be subject to legal
>> privilege.
>>> If you are not the intended recipient you must not use, disseminate, distribute
>> or
>>> reproduce all or any part of this e-mail or attachments.  If you have received
>> this
>>> e-mail in error, please notify the sender and delete all material pertaining to
>> this
>>> e-mail.  Any opinion or views expressed in this e-mail are those of the
>> individual
>>> sender and may not represent those of The New Zealand Institute for Plant
>> and
>>> Food Research Limited.
>>>
>>> _______________________________________________
>>> Wekalist mailing list
>>> Send posts to: [hidden email]
>>> 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: [hidden email]
>> 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
> The contents of this e-mail are confidential and may be subject to legal privilege.
> If you are not the intended recipient you must not use, disseminate, distribute or
> reproduce all or any part of this e-mail or attachments.  If you have received this
> e-mail in error, please notify the sender and delete all material pertaining to this
> e-mail.  Any opinion or views expressed in this e-mail are those of the individual
> sender and may not represent those of The New Zealand Institute for Plant and
> Food Research Limited.
>
> _______________________________________________
> Wekalist mailing list
> Send posts to: [hidden email]
> 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

_______________________________________________
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Send posts to: [hidden email]
List info and subscription status: https://list.waikato.ac.nz/mailman/listinfo/wekalist
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Re: RWeka setup

Patrick Connolly
In reply to this post by Mark Hall
I  took it to indicate RWeka was no set up properly.  Is it just WPM that has a bug?

Other examples in  the vignette work - so far at least.

Patrick Connolly
Biometrician

T: +64 9 925 7079
F: +64 9 925 7001
E: [hidden email]
www.plantandfood.co.nz
The New Zealand Institute for Plant & Food Research Limited


> -----Original Message-----
> From: [hidden email] [mailto:wekalist-
> [hidden email]] On Behalf Of Mark Hall
> Sent: Wednesday, 26 April 2017 3:21 p.m.
> To: Weka machine learning workbench list.
> Subject: Re: [Wekalist] RWeka setup
>
> Hmm. I'm not sure what is going wrong here. However, you should be able to
> establish a repository cache by manually installing in ~/wekafiles/repCache (as
> you did), but not executing WPM("refresh-cache"). You can then install any
> packages that you're interested in manually (being careful to get the versions
> compatible with 3.8.1) by downloading via your browser from:
>
> http://weka.sourceforge.net/packageMetaData/
>
> Cheers,
> Mark.
>
> On 26/04/17, 3:02 PM, "Patrick Connolly" <[hidden email]
> on behalf of [hidden email]> wrote:
>
>     I followed the directions at
>     https://weka.wikispaces.com/Weka+package+manager+does+not+start :
>     Now when I start RWeka, I get
>
>     > require(RWeka)
>     Loading required package: RWeka
>     Picked up _JAVA_OPTIONS: -Dhttp.proxyHost=http://proxy.pfr.co.nz -
> Dhttp.proxyPort=8080
>
>     which indicates to me that I have the syntax correct, but I then get
>
>     > WPM("refresh-cache")
>     Refresh in progress. Please wait...
>     Unable to download repository zip archve (http://proxy.pfr.co.nz) - trying
> legacy routine...
>
>
>     ... that is unless I install the repo manually in
>     ~/wekafiles/repCache.  In that case, there's no message but
>     ~/wekafiles/repCache is deleted.
>
>     The proxy does not require authentication, so something else is amiss.
>
>     If I try
>     > WPM("list-packages", "installed")
>
>     R crashes.
>
>     Am I on a hiding to nowhere trying to use RWeka without a JAVACLASS
>     environment variable?
>
>
>     Patrick Connolly
>     Biometrician
>
>     Postal Address: Plant & Food Research
>     Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
>     Physical Address: Plant & Food Research
>     120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
>     > -----Original Message-----
>     > From: [hidden email] [mailto:wekalist-
>     > [hidden email]] On Behalf Of Eibe Frank
>     > Sent: Monday, 24 April 2017 10:56 p.m.
>     > To: Weka machine learning workbench list.
>     > Subject: Re: [Wekalist] RWeka setup
>     >
>     > The WEKA package manager needs web access to connect to the
> SourceForge
>     > site. You probably don't have direct access and instead need to go through a
>     > proxy server. Oracle's JVM reads the _JAVA_OPTIONS environment variable
> and
>     > you can provide proxy settings via that variable, as explained here:
>     >
>     >   https://weka.wikispaces.com/Weka+package+manager+does+not+start
>     >
>     > However, WEKA may not be able to pop up the GUI for entering the proxy
>     > credentials, so you may have to add those as part of the environment
> variable as
>     > well, using http.proxyUser and http.proxyPassword, as explained here:
>     >
>     >
>     >
> https://weka.wikispaces.com/How+do+I+use+the+package+manager%3F#GUI
>     > %20package%20manager-Using%20a%20HTTP%20proxy
>     >
>     > Cheers,
>     > Eibe
>     >
>     > > On 24 Apr 2017, at 16:33, Patrick Connolly
>     > <[hidden email]> wrote:
>     > >
>     > > I installed weka in /usr/local/weka-3-8-1/weka.jar and when I installed
>     > RWeka, it has
>     > > another weka.jar in the R package library.  I assume the latter is
>     > > used when I try this (in R):
>     > >
>     > >> WPM("refresh-cache")
>     > > Refresh in progress. Please wait...
>     > > Unable to download repository zip archve (connect timed out) - trying
> legacy
>     > routine...
>     > > java.net.SocketTimeoutException: connect timed out
>     > >
>     > > My guess is that the CLASSPATH isn't specified.  Without setting an
>     > > environment variable, where do I specify the class path option?
>     > >
>     > > TIA
>     > >
>     > > Patrick Connolly
>     > > Biometrician
>     > >
>     > > www.plantandfood.co.nz
>     > > The New Zealand Institute for Plant & Food Research Limited
>     > >
>     > >
>     > >
>     > > The contents of this e-mail are confidential and may be subject to legal
>     > privilege.
>     > > If you are not the intended recipient you must not use, disseminate,
> distribute
>     > or
>     > > reproduce all or any part of this e-mail or attachments.  If you have
> received
>     > this
>     > > e-mail in error, please notify the sender and delete all material pertaining
> to
>     > this
>     > > e-mail.  Any opinion or views expressed in this e-mail are those of the
>     > individual
>     > > sender and may not represent those of The New Zealand Institute for Plant
>     > and
>     > > Food Research Limited.
>     > >
>     > > _______________________________________________
>     > > Wekalist mailing list
>     > > Send posts to: [hidden email]
>     > > 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: [hidden email]
>     > List info and subscription status:
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>     > List etiquette:
>     > http://www.cs.waikato.ac.nz/~ml/weka/mailinglist_etiquette.html
>     The contents of this e-mail are confidential and may be subject to legal
> privilege.
>      If you are not the intended recipient you must not use, disseminate, distribute
> or
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> this
>      e-mail in error, please notify the sender and delete all material pertaining to
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>      e-mail.  Any opinion or views expressed in this e-mail are those of the
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> and
>      Food Research Limited.
>
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>
>
> _______________________________________________
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The contents of this e-mail are confidential and may be subject to legal privilege.
 If you are not the intended recipient you must not use, disseminate, distribute or
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Re: RWeka setup

Patrick Connolly
In reply to this post by Eibe Frank-2
It works for installing R packages - though the syntax for setting the environment variable is different.

> ping proxy.pfr.co.nz
PING aklwsa31.pfr.co.nz (172.16.81.6) 56(84) bytes of data.
64 bytes from 172.16.81.6: icmp_seq=1 ttl=61 time=0.983 ms
64 bytes from 172.16.81.6: icmp_seq=2 ttl=61 time=1.64 ms

Patrick Connolly
Biometrician

T: +64 9 925 7079
F: +64 9 925 7001
E: [hidden email]
www.plantandfood.co.nz
The New Zealand Institute for Plant & Food Research Limited


> -----Original Message-----
> From: [hidden email] [mailto:wekalist-
> [hidden email]] On Behalf Of Eibe Frank
> Sent: Wednesday, 26 April 2017 3:54 p.m.
> To: Weka machine learning workbench list.
> Subject: Re: [Wekalist] RWeka setup
>
> Are you sure you have the proxy details right?
>
> $ ping proxy.pfr.co.nz
> ping: cannot resolve proxy.pfr.co.nz: Unknown host
>
> Cheers,
> Eibe
>
> > On 26/04/2017, at 3:02 PM, Patrick Connolly
> <[hidden email]> wrote:
> >
> > I followed the directions at
> > https://weka.wikispaces.com/Weka+package+manager+does+not+start :
> > Now when I start RWeka, I get
> >
> >> require(RWeka)
> > Loading required package: RWeka
> > Picked up _JAVA_OPTIONS: -Dhttp.proxyHost=http://proxy.pfr.co.nz
> > -Dhttp.proxyPort=8080
> >
> > which indicates to me that I have the syntax correct, but I then get
> >
> >> WPM("refresh-cache")
> > Refresh in progress. Please wait...
> > Unable to download repository zip archve (http://proxy.pfr.co.nz) - trying
> legacy routine...
> >
> >
> > ... that is unless I install the repo manually in
> > ~/wekafiles/repCache.  In that case, there's no message but
> > ~/wekafiles/repCache is deleted.
> >
> > The proxy does not require authentication, so something else is amiss.
> >
> > If I try
> >> WPM("list-packages", "installed")
> >
> > R crashes.
> >
> > Am I on a hiding to nowhere trying to use RWeka without a JAVACLASS
> > environment variable?
> >
> >
> > Patrick Connolly
> > Biometrician
> >
> > Postal Address: Plant & Food Research
> > Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
> > Physical Address: Plant & Food Research
> > 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
> >> -----Original Message-----
> >> From: [hidden email] [mailto:wekalist-
> >> [hidden email]] On Behalf Of Eibe Frank
> >> Sent: Monday, 24 April 2017 10:56 p.m.
> >> To: Weka machine learning workbench list.
> >> Subject: Re: [Wekalist] RWeka setup
> >>
> >> The WEKA package manager needs web access to connect to the
> >> SourceForge site. You probably don't have direct access and instead
> >> need to go through a proxy server. Oracle's JVM reads the
> >> _JAVA_OPTIONS environment variable and you can provide proxy settings via
> that variable, as explained here:
> >>
> >>  https://weka.wikispaces.com/Weka+package+manager+does+not+start
> >>
> >> However, WEKA may not be able to pop up the GUI for entering the
> >> proxy credentials, so you may have to add those as part of the
> >> environment variable as well, using http.proxyUser and http.proxyPassword,
> as explained here:
> >>
> >>
> >>
> https://weka.wikispaces.com/How+do+I+use+the+package+manager%3F#GUI
> >> %20package%20manager-Using%20a%20HTTP%20proxy
> >>
> >> Cheers,
> >> Eibe
> >>
> >>> On 24 Apr 2017, at 16:33, Patrick Connolly
> >> <[hidden email]> wrote:
> >>>
> >>> I installed weka in /usr/local/weka-3-8-1/weka.jar and when I
> >>> installed
> >> RWeka, it has
> >>> another weka.jar in the R package library.  I assume the latter is
> >>> used when I try this (in R):
> >>>
> >>>> WPM("refresh-cache")
> >>> Refresh in progress. Please wait...
> >>> Unable to download repository zip archve (connect timed out) -
> >>> trying legacy
> >> routine...
> >>> java.net.SocketTimeoutException: connect timed out
> >>>
> >>> My guess is that the CLASSPATH isn't specified.  Without setting an
> >>> environment variable, where do I specify the class path option?
> >>>
> >>> TIA
> >>>
> >>> Patrick Connolly
> >>> Biometrician
> >>>
> >>> www.plantandfood.co.nz
> >>> The New Zealand Institute for Plant & Food Research Limited
> >>>
> >>>
> >>>
> >>> The contents of this e-mail are confidential and may be subject to
> >>> legal
> >> privilege.
> >>> If you are not the intended recipient you must not use, disseminate,
> >>> distribute
> >> or
> >>> reproduce all or any part of this e-mail or attachments.  If you
> >>> have received
> >> this
> >>> e-mail in error, please notify the sender and delete all material
> >>> pertaining to
> >> this
> >>> e-mail.  Any opinion or views expressed in this e-mail are those of
> >>> the
> >> individual
> >>> sender and may not represent those of The New Zealand Institute for
> >>> Plant
> >> and
> >>> Food Research Limited.
> >>>
> >>> _______________________________________________
> >>> Wekalist mailing list
> >>> Send posts to: [hidden email] 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: [hidden email] 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
> > The contents of this e-mail are confidential and may be subject to legal
> privilege.
> > If you are not the intended recipient you must not use, disseminate,
> > distribute or reproduce all or any part of this e-mail or attachments.
> > If you have received this e-mail in error, please notify the sender
> > and delete all material pertaining to this e-mail.  Any opinion or
> > views expressed in this e-mail are those of the individual sender and
> > may not represent those of The New Zealand Institute for Plant and Food
> Research Limited.
> >
> > _______________________________________________
> > Wekalist mailing list
> > Send posts to: [hidden email] 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: [hidden email] 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
The contents of this e-mail are confidential and may be subject to legal privilege.
 If you are not the intended recipient you must not use, disseminate, distribute or
 reproduce all or any part of this e-mail or attachments.  If you have received this
 e-mail in error, please notify the sender and delete all material pertaining to this
 e-mail.  Any opinion or views expressed in this e-mail are those of the individual
 sender and may not represent those of The New Zealand Institute for Plant and
 Food Research Limited.

_______________________________________________
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Send posts to: [hidden email]
List info and subscription status: https://list.waikato.ac.nz/mailman/listinfo/wekalist
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Re: RWeka setup

Eibe Frank-2
Administrator
OK, it seems that your proxy server is not on the public net then.

The output for WPM("refresh-cache") should look like this:

WPM("refresh-cache")
Refresh in progress. Please wait...
[DefaultPackageManager] downloaded 1913 KB

This works fine for me, both at home (no proxy) and at work (behind a proxy).

The "Unable to download..." message you are getting means that WEKA cannot connect to the SourceForge site. Can you actually browse to that site in your browser? Perhaps your institution has blocked access to that site? Anyway, I would get in touch with your system administrators. They might be able to help.

Cheers,
Eibe

> On 26 Apr 2017, at 16:31, Patrick Connolly <[hidden email]> wrote:
>
> It works for installing R packages - though the syntax for setting the environment variable is different.
>
>> ping proxy.pfr.co.nz
> PING aklwsa31.pfr.co.nz (172.16.81.6) 56(84) bytes of data.
> 64 bytes from 172.16.81.6: icmp_seq=1 ttl=61 time=0.983 ms
> 64 bytes from 172.16.81.6: icmp_seq=2 ttl=61 time=1.64 ms
>
> Patrick Connolly
> Biometrician
>
> T: +64 9 925 7079
> F: +64 9 925 7001
> E: [hidden email]
> www.plantandfood.co.nz
> The New Zealand Institute for Plant & Food Research Limited
>
>
>> -----Original Message-----
>> From: [hidden email] [mailto:wekalist-
>> [hidden email]] On Behalf Of Eibe Frank
>> Sent: Wednesday, 26 April 2017 3:54 p.m.
>> To: Weka machine learning workbench list.
>> Subject: Re: [Wekalist] RWeka setup
>>
>> Are you sure you have the proxy details right?
>>
>> $ ping proxy.pfr.co.nz
>> ping: cannot resolve proxy.pfr.co.nz: Unknown host
>>
>> Cheers,
>> Eibe
>>
>>> On 26/04/2017, at 3:02 PM, Patrick Connolly
>> <[hidden email]> wrote:
>>>
>>> I followed the directions at
>>> https://weka.wikispaces.com/Weka+package+manager+does+not+start :
>>> Now when I start RWeka, I get
>>>
>>>> require(RWeka)
>>> Loading required package: RWeka
>>> Picked up _JAVA_OPTIONS: -Dhttp.proxyHost=http://proxy.pfr.co.nz
>>> -Dhttp.proxyPort=8080
>>>
>>> which indicates to me that I have the syntax correct, but I then get
>>>
>>>> WPM("refresh-cache")
>>> Refresh in progress. Please wait...
>>> Unable to download repository zip archve (http://proxy.pfr.co.nz) - trying
>> legacy routine...
>>>
>>>
>>> ... that is unless I install the repo manually in
>>> ~/wekafiles/repCache.  In that case, there's no message but
>>> ~/wekafiles/repCache is deleted.
>>>
>>> The proxy does not require authentication, so something else is amiss.
>>>
>>> If I try
>>>> WPM("list-packages", "installed")
>>>
>>> R crashes.
>>>
>>> Am I on a hiding to nowhere trying to use RWeka without a JAVACLASS
>>> environment variable?
>>>
>>>
>>> Patrick Connolly
>>> Biometrician
>>>
>>> Postal Address: Plant & Food Research
>>> Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
>>> Physical Address: Plant & Food Research
>>> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
>>>> -----Original Message-----
>>>> From: [hidden email] [mailto:wekalist-
>>>> [hidden email]] On Behalf Of Eibe Frank
>>>> Sent: Monday, 24 April 2017 10:56 p.m.
>>>> To: Weka machine learning workbench list.
>>>> Subject: Re: [Wekalist] RWeka setup
>>>>
>>>> The WEKA package manager needs web access to connect to the
>>>> SourceForge site. You probably don't have direct access and instead
>>>> need to go through a proxy server. Oracle's JVM reads the
>>>> _JAVA_OPTIONS environment variable and you can provide proxy settings via
>> that variable, as explained here:
>>>>
>>>> https://weka.wikispaces.com/Weka+package+manager+does+not+start
>>>>
>>>> However, WEKA may not be able to pop up the GUI for entering the
>>>> proxy credentials, so you may have to add those as part of the
>>>> environment variable as well, using http.proxyUser and http.proxyPassword,
>> as explained here:
>>>>
>>>>
>>>>
>> https://weka.wikispaces.com/How+do+I+use+the+package+manager%3F#GUI
>>>> %20package%20manager-Using%20a%20HTTP%20proxy
>>>>
>>>> Cheers,
>>>> Eibe
>>>>
>>>>> On 24 Apr 2017, at 16:33, Patrick Connolly
>>>> <[hidden email]> wrote:
>>>>>
>>>>> I installed weka in /usr/local/weka-3-8-1/weka.jar and when I
>>>>> installed
>>>> RWeka, it has
>>>>> another weka.jar in the R package library.  I assume the latter is
>>>>> used when I try this (in R):
>>>>>
>>>>>> WPM("refresh-cache")
>>>>> Refresh in progress. Please wait...
>>>>> Unable to download repository zip archve (connect timed out) -
>>>>> trying legacy
>>>> routine...
>>>>> java.net.SocketTimeoutException: connect timed out
>>>>>
>>>>> My guess is that the CLASSPATH isn't specified.  Without setting an
>>>>> environment variable, where do I specify the class path option?
>>>>>
>>>>> TIA
>>>>>
>>>>> Patrick Connolly
>>>>> Biometrician
>>>>>
>>>>> www.plantandfood.co.nz
>>>>> The New Zealand Institute for Plant & Food Research Limited
>>>>>
>>>>>
>>>>>
>>>>> The contents of this e-mail are confidential and may be subject to
>>>>> legal
>>>> privilege.
>>>>> If you are not the intended recipient you must not use, disseminate,
>>>>> distribute
>>>> or
>>>>> reproduce all or any part of this e-mail or attachments.  If you
>>>>> have received
>>>> this
>>>>> e-mail in error, please notify the sender and delete all material
>>>>> pertaining to
>>>> this
>>>>> e-mail.  Any opinion or views expressed in this e-mail are those of
>>>>> the
>>>> individual
>>>>> sender and may not represent those of The New Zealand Institute for
>>>>> Plant
>>>> and
>>>>> Food Research Limited.
>>>>>
>>>>> _______________________________________________
>>>>> Wekalist mailing list
>>>>> Send posts to: [hidden email] 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: [hidden email] 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
>>> The contents of this e-mail are confidential and may be subject to legal
>> privilege.
>>> If you are not the intended recipient you must not use, disseminate,
>>> distribute or reproduce all or any part of this e-mail or attachments.
>>> If you have received this e-mail in error, please notify the sender
>>> and delete all material pertaining to this e-mail.  Any opinion or
>>> views expressed in this e-mail are those of the individual sender and
>>> may not represent those of The New Zealand Institute for Plant and Food
>> Research Limited.
>>>
>>> _______________________________________________
>>> Wekalist mailing list
>>> Send posts to: [hidden email] 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: [hidden email] 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
> The contents of this e-mail are confidential and may be subject to legal privilege.
> If you are not the intended recipient you must not use, disseminate, distribute or
> reproduce all or any part of this e-mail or attachments.  If you have received this
> e-mail in error, please notify the sender and delete all material pertaining to this
> e-mail.  Any opinion or views expressed in this e-mail are those of the individual
> sender and may not represent those of The New Zealand Institute for Plant and
> Food Research Limited.
>
> _______________________________________________
> Wekalist mailing list
> Send posts to: [hidden email]
> 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

_______________________________________________
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Send posts to: [hidden email]
List info and subscription status: https://list.waikato.ac.nz/mailman/listinfo/wekalist
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Re: RWeka setup

Patrick Connolly
THE proxy server needs to be accessible  from this side only, I would have thought.  It works for everything else..

I can manually download the repository  but the cache is erased if I try to refresh it with the WPM() function.

How  does the proxy system know which weka.jar is in use?  I have a suspicion the 2 are being confused.  For that matter, am I correct in assuming weka needs to be installed to use RWeka?




Patrick Connolly
Biometrician


Postal Address: Plant & Food Research
Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
Physical Address: Plant & Food Research
120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand

> -----Original Message-----
> From: [hidden email] [mailto:wekalist-
> [hidden email]] On Behalf Of Eibe Frank
> Sent: Wednesday, 26 April 2017 8:49 p.m.
> To: Weka machine learning workbench list.
> Subject: Re: [Wekalist] RWeka setup
>
> OK, it seems that your proxy server is not on the public net then.
>
> The output for WPM("refresh-cache") should look like this:
>
> WPM("refresh-cache")
> Refresh in progress. Please wait...
> [DefaultPackageManager] downloaded 1913 KB
>
> This works fine for me, both at home (no proxy) and at work (behind a proxy).
>
> The "Unable to download..." message you are getting means that WEKA cannot
> connect to the SourceForge site. Can you actually browse to that site in your
> browser? Perhaps your institution has blocked access to that site? Anyway, I
> would get in touch with your system administrators. They might be able to help.
>
> Cheers,
> Eibe
>
> > On 26 Apr 2017, at 16:31, Patrick Connolly
> <[hidden email]> wrote:
> >
> > It works for installing R packages - though the syntax for setting the
> environment variable is different.
> >
> >> ping proxy.pfr.co.nz
> > PING aklwsa31.pfr.co.nz (172.16.81.6) 56(84) bytes of data.
> > 64 bytes from 172.16.81.6: icmp_seq=1 ttl=61 time=0.983 ms
> > 64 bytes from 172.16.81.6: icmp_seq=2 ttl=61 time=1.64 ms
> >
> > Patrick Connolly
> > Biometrician
> >
> > T: +64 9 925 7079
> > F: +64 9 925 7001
> > E: [hidden email]
> > www.plantandfood.co.nz
> > The New Zealand Institute for Plant & Food Research Limited
> >
> >
> >> -----Original Message-----
> >> From: [hidden email] [mailto:wekalist-
> >> [hidden email]] On Behalf Of Eibe Frank
> >> Sent: Wednesday, 26 April 2017 3:54 p.m.
> >> To: Weka machine learning workbench list.
> >> Subject: Re: [Wekalist] RWeka setup
> >>
> >> Are you sure you have the proxy details right?
> >>
> >> $ ping proxy.pfr.co.nz
> >> ping: cannot resolve proxy.pfr.co.nz: Unknown host
> >>
> >> Cheers,
> >> Eibe
> >>
> >>> On 26/04/2017, at 3:02 PM, Patrick Connolly
> >> <[hidden email]> wrote:
> >>>
> >>> I followed the directions at
> >>> https://weka.wikispaces.com/Weka+package+manager+does+not+start :
> >>> Now when I start RWeka, I get
> >>>
> >>>> require(RWeka)
> >>> Loading required package: RWeka
> >>> Picked up _JAVA_OPTIONS: -Dhttp.proxyHost=http://proxy.pfr.co.nz
> >>> -Dhttp.proxyPort=8080
> >>>
> >>> which indicates to me that I have the syntax correct, but I then get
> >>>
> >>>> WPM("refresh-cache")
> >>> Refresh in progress. Please wait...
> >>> Unable to download repository zip archve (http://proxy.pfr.co.nz) -
> >>> trying
> >> legacy routine...
> >>>
> >>>
> >>> ... that is unless I install the repo manually in
> >>> ~/wekafiles/repCache.  In that case, there's no message but
> >>> ~/wekafiles/repCache is deleted.
> >>>
> >>> The proxy does not require authentication, so something else is amiss.
> >>>
> >>> If I try
> >>>> WPM("list-packages", "installed")
> >>>
> >>> R crashes.
> >>>
> >>> Am I on a hiding to nowhere trying to use RWeka without a JAVACLASS
> >>> environment variable?
> >>>
> >>>
> >>> Patrick Connolly
> >>> Biometrician
> >>>
> >>> Postal Address: Plant & Food Research Private Bag 92169, Auckland
> >>> Mail Centre, Auckland 1142, New Zealand Physical Address: Plant &
> >>> Food Research
> >>> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
> >>>> -----Original Message-----
> >>>> From: [hidden email] [mailto:wekalist-
> >>>> [hidden email]] On Behalf Of Eibe Frank
> >>>> Sent: Monday, 24 April 2017 10:56 p.m.
> >>>> To: Weka machine learning workbench list.
> >>>> Subject: Re: [Wekalist] RWeka setup
> >>>>
> >>>> The WEKA package manager needs web access to connect to the
> >>>> SourceForge site. You probably don't have direct access and instead
> >>>> need to go through a proxy server. Oracle's JVM reads the
> >>>> _JAVA_OPTIONS environment variable and you can provide proxy
> >>>> settings via
> >> that variable, as explained here:
> >>>>
> >>>> https://weka.wikispaces.com/Weka+package+manager+does+not+start
> >>>>
> >>>> However, WEKA may not be able to pop up the GUI for entering the
> >>>> proxy credentials, so you may have to add those as part of the
> >>>> environment variable as well, using http.proxyUser and
> >>>> http.proxyPassword,
> >> as explained here:
> >>>>
> >>>>
> >>>>
> >>
> https://weka.wikispaces.com/How+do+I+use+the+package+manager%3F#GUI
> >>>> %20package%20manager-Using%20a%20HTTP%20proxy
> >>>>
> >>>> Cheers,
> >>>> Eibe
> >>>>
> >>>>> On 24 Apr 2017, at 16:33, Patrick Connolly
> >>>> <[hidden email]> wrote:
> >>>>>
> >>>>> I installed weka in /usr/local/weka-3-8-1/weka.jar and when I
> >>>>> installed
> >>>> RWeka, it has
> >>>>> another weka.jar in the R package library.  I assume the latter is
> >>>>> used when I try this (in R):
> >>>>>
> >>>>>> WPM("refresh-cache")
> >>>>> Refresh in progress. Please wait...
> >>>>> Unable to download repository zip archve (connect timed out) -
> >>>>> trying legacy
> >>>> routine...
> >>>>> java.net.SocketTimeoutException: connect timed out
> >>>>>
> >>>>> My guess is that the CLASSPATH isn't specified.  Without setting
> >>>>> an environment variable, where do I specify the class path option?
> >>>>>
> >>>>> TIA
> >>>>>
> >>>>> Patrick Connolly
> >>>>> Biometrician
> >>>>>
> >>>>> www.plantandfood.co.nz
> >>>>> The New Zealand Institute for Plant & Food Research Limited
> >>>>>
> >>>>>
> >>>>>
> >>>>> The contents of this e-mail are confidential and may be subject to
> >>>>> legal
> >>>> privilege.
> >>>>> If you are not the intended recipient you must not use,
> >>>>> disseminate, distribute
> >>>> or
> >>>>> reproduce all or any part of this e-mail or attachments.  If you
> >>>>> have received
> >>>> this
> >>>>> e-mail in error, please notify the sender and delete all material
> >>>>> pertaining to
> >>>> this
> >>>>> e-mail.  Any opinion or views expressed in this e-mail are those
> >>>>> of the
> >>>> individual
> >>>>> sender and may not represent those of The New Zealand Institute
> >>>>> for Plant
> >>>> and
> >>>>> Food Research Limited.
> >>>>>
> >>>>> _______________________________________________
> >>>>> Wekalist mailing list
> >>>>> Send posts to: [hidden email] 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: [hidden email] 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
> >>> The contents of this e-mail are confidential and may be subject to
> >>> legal
> >> privilege.
> >>> If you are not the intended recipient you must not use, disseminate,
> >>> distribute or reproduce all or any part of this e-mail or attachments.
> >>> If you have received this e-mail in error, please notify the sender
> >>> and delete all material pertaining to this e-mail.  Any opinion or
> >>> views expressed in this e-mail are those of the individual sender
> >>> and may not represent those of The New Zealand Institute for Plant
> >>> and Food
> >> Research Limited.
> >>>
> >>> _______________________________________________
> >>> Wekalist mailing list
> >>> Send posts to: [hidden email] 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: [hidden email] 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
> > The contents of this e-mail are confidential and may be subject to legal
> privilege.
> > If you are not the intended recipient you must not use, disseminate,
> > distribute or reproduce all or any part of this e-mail or attachments.
> > If you have received this e-mail in error, please notify the sender
> > and delete all material pertaining to this e-mail.  Any opinion or
> > views expressed in this e-mail are those of the individual sender and
> > may not represent those of The New Zealand Institute for Plant and Food
> Research Limited.
> >
> > _______________________________________________
> > Wekalist mailing list
> > Send posts to: [hidden email] 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: [hidden email] 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
The contents of this e-mail are confidential and may be subject to legal privilege.
 If you are not the intended recipient you must not use, disseminate, distribute or
 reproduce all or any part of this e-mail or attachments.  If you have received this
 e-mail in error, please notify the sender and delete all material pertaining to this
 e-mail.  Any opinion or views expressed in this e-mail are those of the individual
 sender and may not represent those of The New Zealand Institute for Plant and
 Food Research Limited.

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Re: RWeka setup

Eibe Frank-2
Administrator
No, you don’t need to install WEKA separately. As you said, RWeka comes with its own weka.jar.

You can even start the WEKA GUIs from that .jar by using

  java -jar RWekajars/java/weka.jar

The WEKA package manager can be accessed through the Tools menu in the WEKA GUI Chooser that pops up when your run this.

Cheers,
Eibe

> On 27/04/2017, at 1:41 PM, Patrick Connolly <[hidden email]> wrote:
>
> THE proxy server needs to be accessible  from this side only, I would have thought.  It works for everything else..
>
> I can manually download the repository  but the cache is erased if I try to refresh it with the WPM() function.
>
> How  does the proxy system know which weka.jar is in use?  I have a suspicion the 2 are being confused.  For that matter, am I correct in assuming weka needs to be installed to use RWeka?
>
>
>
>
> Patrick Connolly
> Biometrician
>
>
> Postal Address: Plant & Food Research
> Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
> Physical Address: Plant & Food Research
> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
>> -----Original Message-----
>> From: [hidden email] [mailto:wekalist-
>> [hidden email]] On Behalf Of Eibe Frank
>> Sent: Wednesday, 26 April 2017 8:49 p.m.
>> To: Weka machine learning workbench list.
>> Subject: Re: [Wekalist] RWeka setup
>>
>> OK, it seems that your proxy server is not on the public net then.
>>
>> The output for WPM("refresh-cache") should look like this:
>>
>> WPM("refresh-cache")
>> Refresh in progress. Please wait...
>> [DefaultPackageManager] downloaded 1913 KB
>>
>> This works fine for me, both at home (no proxy) and at work (behind a proxy).
>>
>> The "Unable to download..." message you are getting means that WEKA cannot
>> connect to the SourceForge site. Can you actually browse to that site in your
>> browser? Perhaps your institution has blocked access to that site? Anyway, I
>> would get in touch with your system administrators. They might be able to help.
>>
>> Cheers,
>> Eibe
>>
>>> On 26 Apr 2017, at 16:31, Patrick Connolly
>> <[hidden email]> wrote:
>>>
>>> It works for installing R packages - though the syntax for setting the
>> environment variable is different.
>>>
>>>> ping proxy.pfr.co.nz
>>> PING aklwsa31.pfr.co.nz (172.16.81.6) 56(84) bytes of data.
>>> 64 bytes from 172.16.81.6: icmp_seq=1 ttl=61 time=0.983 ms
>>> 64 bytes from 172.16.81.6: icmp_seq=2 ttl=61 time=1.64 ms
>>>
>>> Patrick Connolly
>>> Biometrician
>>>
>>> T: +64 9 925 7079
>>> F: +64 9 925 7001
>>> E: [hidden email]
>>> www.plantandfood.co.nz
>>> The New Zealand Institute for Plant & Food Research Limited
>>>
>>>
>>>> -----Original Message-----
>>>> From: [hidden email] [mailto:wekalist-
>>>> [hidden email]] On Behalf Of Eibe Frank
>>>> Sent: Wednesday, 26 April 2017 3:54 p.m.
>>>> To: Weka machine learning workbench list.
>>>> Subject: Re: [Wekalist] RWeka setup
>>>>
>>>> Are you sure you have the proxy details right?
>>>>
>>>> $ ping proxy.pfr.co.nz
>>>> ping: cannot resolve proxy.pfr.co.nz: Unknown host
>>>>
>>>> Cheers,
>>>> Eibe
>>>>
>>>>> On 26/04/2017, at 3:02 PM, Patrick Connolly
>>>> <[hidden email]> wrote:
>>>>>
>>>>> I followed the directions at
>>>>> https://weka.wikispaces.com/Weka+package+manager+does+not+start :
>>>>> Now when I start RWeka, I get
>>>>>
>>>>>> require(RWeka)
>>>>> Loading required package: RWeka
>>>>> Picked up _JAVA_OPTIONS: -Dhttp.proxyHost=http://proxy.pfr.co.nz
>>>>> -Dhttp.proxyPort=8080
>>>>>
>>>>> which indicates to me that I have the syntax correct, but I then get
>>>>>
>>>>>> WPM("refresh-cache")
>>>>> Refresh in progress. Please wait...
>>>>> Unable to download repository zip archve (http://proxy.pfr.co.nz) -
>>>>> trying
>>>> legacy routine...
>>>>>
>>>>>
>>>>> ... that is unless I install the repo manually in
>>>>> ~/wekafiles/repCache.  In that case, there's no message but
>>>>> ~/wekafiles/repCache is deleted.
>>>>>
>>>>> The proxy does not require authentication, so something else is amiss.
>>>>>
>>>>> If I try
>>>>>> WPM("list-packages", "installed")
>>>>>
>>>>> R crashes.
>>>>>
>>>>> Am I on a hiding to nowhere trying to use RWeka without a JAVACLASS
>>>>> environment variable?
>>>>>
>>>>>
>>>>> Patrick Connolly
>>>>> Biometrician
>>>>>
>>>>> Postal Address: Plant & Food Research Private Bag 92169, Auckland
>>>>> Mail Centre, Auckland 1142, New Zealand Physical Address: Plant &
>>>>> Food Research
>>>>> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
>>>>>> -----Original Message-----
>>>>>> From: [hidden email] [mailto:wekalist-
>>>>>> [hidden email]] On Behalf Of Eibe Frank
>>>>>> Sent: Monday, 24 April 2017 10:56 p.m.
>>>>>> To: Weka machine learning workbench list.
>>>>>> Subject: Re: [Wekalist] RWeka setup
>>>>>>
>>>>>> The WEKA package manager needs web access to connect to the
>>>>>> SourceForge site. You probably don't have direct access and instead
>>>>>> need to go through a proxy server. Oracle's JVM reads the
>>>>>> _JAVA_OPTIONS environment variable and you can provide proxy
>>>>>> settings via
>>>> that variable, as explained here:
>>>>>>
>>>>>> https://weka.wikispaces.com/Weka+package+manager+does+not+start
>>>>>>
>>>>>> However, WEKA may not be able to pop up the GUI for entering the
>>>>>> proxy credentials, so you may have to add those as part of the
>>>>>> environment variable as well, using http.proxyUser and
>>>>>> http.proxyPassword,
>>>> as explained here:
>>>>>>
>>>>>>
>>>>>>
>>>>
>> https://weka.wikispaces.com/How+do+I+use+the+package+manager%3F#GUI
>>>>>> %20package%20manager-Using%20a%20HTTP%20proxy
>>>>>>
>>>>>> Cheers,
>>>>>> Eibe
>>>>>>
>>>>>>> On 24 Apr 2017, at 16:33, Patrick Connolly
>>>>>> <[hidden email]> wrote:
>>>>>>>
>>>>>>> I installed weka in /usr/local/weka-3-8-1/weka.jar and when I
>>>>>>> installed
>>>>>> RWeka, it has
>>>>>>> another weka.jar in the R package library.  I assume the latter is
>>>>>>> used when I try this (in R):
>>>>>>>
>>>>>>>> WPM("refresh-cache")
>>>>>>> Refresh in progress. Please wait...
>>>>>>> Unable to download repository zip archve (connect timed out) -
>>>>>>> trying legacy
>>>>>> routine...
>>>>>>> java.net.SocketTimeoutException: connect timed out
>>>>>>>
>>>>>>> My guess is that the CLASSPATH isn't specified.  Without setting
>>>>>>> an environment variable, where do I specify the class path option?
>>>>>>>
>>>>>>> TIA
>>>>>>>
>>>>>>> Patrick Connolly
>>>>>>> Biometrician
>>>>>>>
>>>>>>> www.plantandfood.co.nz
>>>>>>> The New Zealand Institute for Plant & Food Research Limited
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> The contents of this e-mail are confidential and may be subject to
>>>>>>> legal
>>>>>> privilege.
>>>>>>> If you are not the intended recipient you must not use,
>>>>>>> disseminate, distribute
>>>>>> or
>>>>>>> reproduce all or any part of this e-mail or attachments.  If you
>>>>>>> have received
>>>>>> this
>>>>>>> e-mail in error, please notify the sender and delete all material
>>>>>>> pertaining to
>>>>>> this
>>>>>>> e-mail.  Any opinion or views expressed in this e-mail are those
>>>>>>> of the
>>>>>> individual
>>>>>>> sender and may not represent those of The New Zealand Institute
>>>>>>> for Plant
>>>>>> and
>>>>>>> Food Research Limited.
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Wekalist mailing list
>>>>>>> Send posts to: [hidden email] 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: [hidden email] 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
>>>>> The contents of this e-mail are confidential and may be subject to
>>>>> legal
>>>> privilege.
>>>>> If you are not the intended recipient you must not use, disseminate,
>>>>> distribute or reproduce all or any part of this e-mail or attachments.
>>>>> If you have received this e-mail in error, please notify the sender
>>>>> and delete all material pertaining to this e-mail.  Any opinion or
>>>>> views expressed in this e-mail are those of the individual sender
>>>>> and may not represent those of The New Zealand Institute for Plant
>>>>> and Food
>>>> Research Limited.
>>>>>
>>>>> _______________________________________________
>>>>> Wekalist mailing list
>>>>> Send posts to: [hidden email] 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: [hidden email] 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
>>> The contents of this e-mail are confidential and may be subject to legal
>> privilege.
>>> If you are not the intended recipient you must not use, disseminate,
>>> distribute or reproduce all or any part of this e-mail or attachments.
>>> If you have received this e-mail in error, please notify the sender
>>> and delete all material pertaining to this e-mail.  Any opinion or
>>> views expressed in this e-mail are those of the individual sender and
>>> may not represent those of The New Zealand Institute for Plant and Food
>> Research Limited.
>>>
>>> _______________________________________________
>>> Wekalist mailing list
>>> Send posts to: [hidden email] 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: [hidden email] 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
> The contents of this e-mail are confidential and may be subject to legal privilege.
> If you are not the intended recipient you must not use, disseminate, distribute or
> reproduce all or any part of this e-mail or attachments.  If you have received this
> e-mail in error, please notify the sender and delete all material pertaining to this
> e-mail.  Any opinion or views expressed in this e-mail are those of the individual
> sender and may not represent those of The New Zealand Institute for Plant and
> Food Research Limited.
>
> _______________________________________________
> Wekalist mailing list
> Send posts to: [hidden email]
> 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

_______________________________________________
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Send posts to: [hidden email]
List info and subscription status: https://list.waikato.ac.nz/mailman/listinfo/wekalist
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Re: RWeka setup

Patrick Connolly
G'day Eibe

Thanks for clearing that one up.  Does that indicate that RWeka has everything a WEKA installation has?

None of our IT folk know anything about Java.  Their only suggestion was that something at the sourceforge end was requiring user authentication, since  it is accessible by browser.  That idea seems odd to me because the browser settings don't require it.

My guess is that it's my _JAVA_OPTIONS.

> Picked up _JAVA_OPTIONS: -Dhttp.proxyHost=http://proxy.pfr.co.nz -Dhttp.proxyPort=8080
Caching repository metadata, please wait...
Refresh in progress. Please wait...
Unable to download repository zip archve (http://proxy.pfr.co.nz)

The fact that the error message doesn't mention the port number could mean my syntax is incorrect.

Ideas welcome.




Patrick Connolly
Biometrician

Postal Address: Plant & Food Research
Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
Physical Address: Plant & Food Research
120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand

> -----Original Message-----
> From: [hidden email] [mailto:wekalist-
> [hidden email]] On Behalf Of Eibe Frank
> Sent: Thursday, 27 April 2017 2:12 p.m.
> To: Weka machine learning workbench list.
> Subject: Re: [Wekalist] RWeka setup
>
> No, you don’t need to install WEKA separately. As you said, RWeka comes with
> its own weka.jar.
>
> You can even start the WEKA GUIs from that .jar by using
>
>   java -jar RWekajars/java/weka.jar
>
> The WEKA package manager can be accessed through the Tools menu in the
> WEKA GUI Chooser that pops up when your run this.
>
> Cheers,
> Eibe
>
> > On 27/04/2017, at 1:41 PM, Patrick Connolly
> <[hidden email]> wrote:
> >
> > THE proxy server needs to be accessible  from this side only, I would have
> thought.  It works for everything else..
> >
> > I can manually download the repository  but the cache is erased if I try to
> refresh it with the WPM() function.
> >
> > How  does the proxy system know which weka.jar is in use?  I have a suspicion
> the 2 are being confused.  For that matter, am I correct in assuming weka needs
> to be installed to use RWeka?
> >
> >
> >
> >
> > Patrick Connolly
> > Biometrician
> >
> >
> > Postal Address: Plant & Food Research
> > Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
> > Physical Address: Plant & Food Research
> > 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
> >> -----Original Message-----
> >> From: [hidden email] [mailto:wekalist-
> >> [hidden email]] On Behalf Of Eibe Frank
> >> Sent: Wednesday, 26 April 2017 8:49 p.m.
> >> To: Weka machine learning workbench list.
> >> Subject: Re: [Wekalist] RWeka setup
> >>
> >> OK, it seems that your proxy server is not on the public net then.
> >>
> >> The output for WPM("refresh-cache") should look like this:
> >>
> >> WPM("refresh-cache")
> >> Refresh in progress. Please wait...
> >> [DefaultPackageManager] downloaded 1913 KB
> >>
> >> This works fine for me, both at home (no proxy) and at work (behind a proxy).
> >>
> >> The "Unable to download..." message you are getting means that WEKA
> >> cannot connect to the SourceForge site. Can you actually browse to
> >> that site in your browser? Perhaps your institution has blocked
> >> access to that site? Anyway, I would get in touch with your system
> administrators. They might be able to help.
> >>
> >> Cheers,
> >> Eibe
> >>
> >>> On 26 Apr 2017, at 16:31, Patrick Connolly
> >> <[hidden email]> wrote:
> >>>
> >>> It works for installing R packages - though the syntax for setting
> >>> the
> >> environment variable is different.
> >>>
> >>>> ping proxy.pfr.co.nz
> >>> PING aklwsa31.pfr.co.nz (172.16.81.6) 56(84) bytes of data.
> >>> 64 bytes from 172.16.81.6: icmp_seq=1 ttl=61 time=0.983 ms
> >>> 64 bytes from 172.16.81.6: icmp_seq=2 ttl=61 time=1.64 ms
> >>>
> >>> Patrick Connolly
> >>> Biometrician
> >>>
> >>> T: +64 9 925 7079
> >>> F: +64 9 925 7001
> >>> E: [hidden email]
> >>> www.plantandfood.co.nz
> >>> The New Zealand Institute for Plant & Food Research Limited
> >>>
> >>>
> >>>> -----Original Message-----
> >>>> From: [hidden email] [mailto:wekalist-
> >>>> [hidden email]] On Behalf Of Eibe Frank
> >>>> Sent: Wednesday, 26 April 2017 3:54 p.m.
> >>>> To: Weka machine learning workbench list.
> >>>> Subject: Re: [Wekalist] RWeka setup
> >>>>
> >>>> Are you sure you have the proxy details right?
> >>>>
> >>>> $ ping proxy.pfr.co.nz
> >>>> ping: cannot resolve proxy.pfr.co.nz: Unknown host
> >>>>
> >>>> Cheers,
> >>>> Eibe
> >>>>
> >>>>> On 26/04/2017, at 3:02 PM, Patrick Connolly
> >>>> <[hidden email]> wrote:
> >>>>>
> >>>>> I followed the directions at
> >>>>> https://weka.wikispaces.com/Weka+package+manager+does+not+start :
> >>>>> Now when I start RWeka, I get
> >>>>>
> >>>>>> require(RWeka)
> >>>>> Loading required package: RWeka
> >>>>> Picked up _JAVA_OPTIONS: -Dhttp.proxyHost=http://proxy.pfr.co.nz
> >>>>> -Dhttp.proxyPort=8080
> >>>>>
> >>>>> which indicates to me that I have the syntax correct, but I then
> >>>>> get
> >>>>>
> >>>>>> WPM("refresh-cache")
> >>>>> Refresh in progress. Please wait...
> >>>>> Unable to download repository zip archve (http://proxy.pfr.co.nz)
> >>>>> - trying
> >>>> legacy routine...
> >>>>>
> >>>>>
> >>>>> ... that is unless I install the repo manually in
> >>>>> ~/wekafiles/repCache.  In that case, there's no message but
> >>>>> ~/wekafiles/repCache is deleted.
> >>>>>
> >>>>> The proxy does not require authentication, so something else is amiss.
> >>>>>
> >>>>> If I try
> >>>>>> WPM("list-packages", "installed")
> >>>>>
> >>>>> R crashes.
> >>>>>
> >>>>> Am I on a hiding to nowhere trying to use RWeka without a
> >>>>> JAVACLASS environment variable?
> >>>>>
> >>>>>
> >>>>> Patrick Connolly
> >>>>> Biometrician
> >>>>>
> >>>>> Postal Address: Plant & Food Research Private Bag 92169, Auckland
> >>>>> Mail Centre, Auckland 1142, New Zealand Physical Address: Plant &
> >>>>> Food Research
> >>>>> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
> >>>>>> -----Original Message-----
> >>>>>> From: [hidden email] [mailto:wekalist-
> >>>>>> [hidden email]] On Behalf Of Eibe Frank
> >>>>>> Sent: Monday, 24 April 2017 10:56 p.m.
> >>>>>> To: Weka machine learning workbench list.
> >>>>>> Subject: Re: [Wekalist] RWeka setup
> >>>>>>
> >>>>>> The WEKA package manager needs web access to connect to the
> >>>>>> SourceForge site. You probably don't have direct access and
> >>>>>> instead need to go through a proxy server. Oracle's JVM reads the
> >>>>>> _JAVA_OPTIONS environment variable and you can provide proxy
> >>>>>> settings via
> >>>> that variable, as explained here:
> >>>>>>
> >>>>>> https://weka.wikispaces.com/Weka+package+manager+does+not+start
> >>>>>>
> >>>>>> However, WEKA may not be able to pop up the GUI for entering the
> >>>>>> proxy credentials, so you may have to add those as part of the
> >>>>>> environment variable as well, using http.proxyUser and
> >>>>>> http.proxyPassword,
> >>>> as explained here:
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>
> >>
> https://weka.wikispaces.com/How+do+I+use+the+package+manager%3F#GUI
> >>>>>> %20package%20manager-Using%20a%20HTTP%20proxy
> >>>>>>
> >>>>>> Cheers,
> >>>>>> Eibe
> >>>>>>
> >>>>>>> On 24 Apr 2017, at 16:33, Patrick Connolly
> >>>>>> <[hidden email]> wrote:
> >>>>>>>
> >>>>>>> I installed weka in /usr/local/weka-3-8-1/weka.jar and when I
> >>>>>>> installed
> >>>>>> RWeka, it has
> >>>>>>> another weka.jar in the R package library.  I assume the latter
> >>>>>>> is used when I try this (in R):
> >>>>>>>
> >>>>>>>> WPM("refresh-cache")
> >>>>>>> Refresh in progress. Please wait...
> >>>>>>> Unable to download repository zip archve (connect timed out) -
> >>>>>>> trying legacy
> >>>>>> routine...
> >>>>>>> java.net.SocketTimeoutException: connect timed out
> >>>>>>>
> >>>>>>> My guess is that the CLASSPATH isn't specified.  Without setting
> >>>>>>> an environment variable, where do I specify the class path option?
> >>>>>>>
> >>>>>>> TIA
> >>>>>>>
> >>>>>>> Patrick Connolly
> >>>>>>> Biometrician
> >>>>>>>
> >>>>>>> www.plantandfood.co.nz
> >>>>>>> The New Zealand Institute for Plant & Food Research Limited
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> The contents of this e-mail are confidential and may be subject
> >>>>>>> to legal
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Re: RWeka setup

Eibe Frank-2
Administrator
Can you start the WEKA GUIs and then run the package manager GUI? Under “Tools” menu in the “GUIChooser” that pops up when you execute the .jar file (see my command below).

Cheers,
Eibe

> On 1/05/2017, at 2:59 PM, Patrick Connolly <[hidden email]> wrote:
>
> G'day Eibe
>
> Thanks for clearing that one up.  Does that indicate that RWeka has everything a WEKA installation has?
>
> None of our IT folk know anything about Java.  Their only suggestion was that something at the sourceforge end was requiring user authentication, since  it is accessible by browser.  That idea seems odd to me because the browser settings don't require it.
>
> My guess is that it's my _JAVA_OPTIONS.
>
>> Picked up _JAVA_OPTIONS: -Dhttp.proxyHost=http://proxy.pfr.co.nz -Dhttp.proxyPort=8080
> Caching repository metadata, please wait...
> Refresh in progress. Please wait...
> Unable to download repository zip archve (http://proxy.pfr.co.nz)
>
> The fact that the error message doesn't mention the port number could mean my syntax is incorrect.
>
> Ideas welcome.
>
>
>
>
> Patrick Connolly
> Biometrician
>
> Postal Address: Plant & Food Research
> Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
> Physical Address: Plant & Food Research
> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
>> -----Original Message-----
>> From: [hidden email] [mailto:wekalist-
>> [hidden email]] On Behalf Of Eibe Frank
>> Sent: Thursday, 27 April 2017 2:12 p.m.
>> To: Weka machine learning workbench list.
>> Subject: Re: [Wekalist] RWeka setup
>>
>> No, you don’t need to install WEKA separately. As you said, RWeka comes with
>> its own weka.jar.
>>
>> You can even start the WEKA GUIs from that .jar by using
>>
>>  java -jar RWekajars/java/weka.jar
>>
>> The WEKA package manager can be accessed through the Tools menu in the
>> WEKA GUI Chooser that pops up when your run this.
>>
>> Cheers,
>> Eibe
>>
>>> On 27/04/2017, at 1:41 PM, Patrick Connolly
>> <[hidden email]> wrote:
>>>
>>> THE proxy server needs to be accessible  from this side only, I would have
>> thought.  It works for everything else..
>>>
>>> I can manually download the repository  but the cache is erased if I try to
>> refresh it with the WPM() function.
>>>
>>> How  does the proxy system know which weka.jar is in use?  I have a suspicion
>> the 2 are being confused.  For that matter, am I correct in assuming weka needs
>> to be installed to use RWeka?
>>>
>>>
>>>
>>>
>>> Patrick Connolly
>>> Biometrician
>>>
>>>
>>> Postal Address: Plant & Food Research
>>> Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
>>> Physical Address: Plant & Food Research
>>> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
>>>> -----Original Message-----
>>>> From: [hidden email] [mailto:wekalist-
>>>> [hidden email]] On Behalf Of Eibe Frank
>>>> Sent: Wednesday, 26 April 2017 8:49 p.m.
>>>> To: Weka machine learning workbench list.
>>>> Subject: Re: [Wekalist] RWeka setup
>>>>
>>>> OK, it seems that your proxy server is not on the public net then.
>>>>
>>>> The output for WPM("refresh-cache") should look like this:
>>>>
>>>> WPM("refresh-cache")
>>>> Refresh in progress. Please wait...
>>>> [DefaultPackageManager] downloaded 1913 KB
>>>>
>>>> This works fine for me, both at home (no proxy) and at work (behind a proxy).
>>>>
>>>> The "Unable to download..." message you are getting means that WEKA
>>>> cannot connect to the SourceForge site. Can you actually browse to
>>>> that site in your browser? Perhaps your institution has blocked
>>>> access to that site? Anyway, I would get in touch with your system
>> administrators. They might be able to help.
>>>>
>>>> Cheers,
>>>> Eibe
>>>>
>>>>> On 26 Apr 2017, at 16:31, Patrick Connolly
>>>> <[hidden email]> wrote:
>>>>>
>>>>> It works for installing R packages - though the syntax for setting
>>>>> the
>>>> environment variable is different.
>>>>>
>>>>>> ping proxy.pfr.co.nz
>>>>> PING aklwsa31.pfr.co.nz (172.16.81.6) 56(84) bytes of data.
>>>>> 64 bytes from 172.16.81.6: icmp_seq=1 ttl=61 time=0.983 ms
>>>>> 64 bytes from 172.16.81.6: icmp_seq=2 ttl=61 time=1.64 ms
>>>>>
>>>>> Patrick Connolly
>>>>> Biometrician
>>>>>
>>>>> T: +64 9 925 7079
>>>>> F: +64 9 925 7001
>>>>> E: [hidden email]
>>>>> www.plantandfood.co.nz
>>>>> The New Zealand Institute for Plant & Food Research Limited
>>>>>
>>>>>
>>>>>> -----Original Message-----
>>>>>> From: [hidden email] [mailto:wekalist-
>>>>>> [hidden email]] On Behalf Of Eibe Frank
>>>>>> Sent: Wednesday, 26 April 2017 3:54 p.m.
>>>>>> To: Weka machine learning workbench list.
>>>>>> Subject: Re: [Wekalist] RWeka setup
>>>>>>
>>>>>> Are you sure you have the proxy details right?
>>>>>>
>>>>>> $ ping proxy.pfr.co.nz
>>>>>> ping: cannot resolve proxy.pfr.co.nz: Unknown host
>>>>>>
>>>>>> Cheers,
>>>>>> Eibe
>>>>>>
>>>>>>> On 26/04/2017, at 3:02 PM, Patrick Connolly
>>>>>> <[hidden email]> wrote:
>>>>>>>
>>>>>>> I followed the directions at
>>>>>>> https://weka.wikispaces.com/Weka+package+manager+does+not+start :
>>>>>>> Now when I start RWeka, I get
>>>>>>>
>>>>>>>> require(RWeka)
>>>>>>> Loading required package: RWeka
>>>>>>> Picked up _JAVA_OPTIONS: -Dhttp.proxyHost=http://proxy.pfr.co.nz
>>>>>>> -Dhttp.proxyPort=8080
>>>>>>>
>>>>>>> which indicates to me that I have the syntax correct, but I then
>>>>>>> get
>>>>>>>
>>>>>>>> WPM("refresh-cache")
>>>>>>> Refresh in progress. Please wait...
>>>>>>> Unable to download repository zip archve (http://proxy.pfr.co.nz)
>>>>>>> - trying
>>>>>> legacy routine...
>>>>>>>
>>>>>>>
>>>>>>> ... that is unless I install the repo manually in
>>>>>>> ~/wekafiles/repCache.  In that case, there's no message but
>>>>>>> ~/wekafiles/repCache is deleted.
>>>>>>>
>>>>>>> The proxy does not require authentication, so something else is amiss.
>>>>>>>
>>>>>>> If I try
>>>>>>>> WPM("list-packages", "installed")
>>>>>>>
>>>>>>> R crashes.
>>>>>>>
>>>>>>> Am I on a hiding to nowhere trying to use RWeka without a
>>>>>>> JAVACLASS environment variable?
>>>>>>>
>>>>>>>
>>>>>>> Patrick Connolly
>>>>>>> Biometrician
>>>>>>>
>>>>>>> Postal Address: Plant & Food Research Private Bag 92169, Auckland
>>>>>>> Mail Centre, Auckland 1142, New Zealand Physical Address: Plant &
>>>>>>> Food Research
>>>>>>> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
>>>>>>>> -----Original Message-----
>>>>>>>> From: [hidden email] [mailto:wekalist-
>>>>>>>> [hidden email]] On Behalf Of Eibe Frank
>>>>>>>> Sent: Monday, 24 April 2017 10:56 p.m.
>>>>>>>> To: Weka machine learning workbench list.
>>>>>>>> Subject: Re: [Wekalist] RWeka setup
>>>>>>>>
>>>>>>>> The WEKA package manager needs web access to connect to the
>>>>>>>> SourceForge site. You probably don't have direct access and
>>>>>>>> instead need to go through a proxy server. Oracle's JVM reads the
>>>>>>>> _JAVA_OPTIONS environment variable and you can provide proxy
>>>>>>>> settings via
>>>>>> that variable, as explained here:
>>>>>>>>
>>>>>>>> https://weka.wikispaces.com/Weka+package+manager+does+not+start
>>>>>>>>
>>>>>>>> However, WEKA may not be able to pop up the GUI for entering the
>>>>>>>> proxy credentials, so you may have to add those as part of the
>>>>>>>> environment variable as well, using http.proxyUser and
>>>>>>>> http.proxyPassword,
>>>>>> as explained here:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>
>>>>
>> https://weka.wikispaces.com/How+do+I+use+the+package+manager%3F#GUI
>>>>>>>> %20package%20manager-Using%20a%20HTTP%20proxy
>>>>>>>>
>>>>>>>> Cheers,
>>>>>>>> Eibe
>>>>>>>>
>>>>>>>>> On 24 Apr 2017, at 16:33, Patrick Connolly
>>>>>>>> <[hidden email]> wrote:
>>>>>>>>>
>>>>>>>>> I installed weka in /usr/local/weka-3-8-1/weka.jar and when I
>>>>>>>>> installed
>>>>>>>> RWeka, it has
>>>>>>>>> another weka.jar in the R package library.  I assume the latter
>>>>>>>>> is used when I try this (in R):
>>>>>>>>>
>>>>>>>>>> WPM("refresh-cache")
>>>>>>>>> Refresh in progress. Please wait...
>>>>>>>>> Unable to download repository zip archve (connect timed out) -
>>>>>>>>> trying legacy
>>>>>>>> routine...
>>>>>>>>> java.net.SocketTimeoutException: connect timed out
>>>>>>>>>
>>>>>>>>> My guess is that the CLASSPATH isn't specified.  Without setting
>>>>>>>>> an environment variable, where do I specify the class path option?
>>>>>>>>>
>>>>>>>>> TIA
>>>>>>>>>
>>>>>>>>> Patrick Connolly
>>>>>>>>> Biometrician
>>>>>>>>>
>>>>>>>>> www.plantandfood.co.nz
>>>>>>>>> The New Zealand Institute for Plant & Food Research Limited
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> The contents of this e-mail are confidential and may be subject
>>>>>>>>> to legal
>>>>>>>> privilege.
>>>>>>>>> If you are not the intended recipient you must not use,
>>>>>>>>> disseminate, distribute
>>>>>>>> or
>>>>>>>>> reproduce all or any part of this e-mail or attachments.  If you
>>>>>>>>> have received
>>>>>>>> this
>>>>>>>>> e-mail in error, please notify the sender and delete all
>>>>>>>>> material pertaining to
>>>>>>>> this
>>>>>>>>> e-mail.  Any opinion or views expressed in this e-mail are those
>>>>>>>>> of the
>>>>>>>> individual
>>>>>>>>> sender and may not represent those of The New Zealand Institute
>>>>>>>>> for Plant
>>>>>>>> and
>>>>>>>>> Food Research Limited.
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Wekalist mailing list
>>>>>>>>> Send posts to: [hidden email] 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: [hidden email] 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
>>>>>>> The contents of this e-mail are confidential and may be subject to
>>>>>>> legal
>>>>>> privilege.
>>>>>>> If you are not the intended recipient you must not use,
>>>>>>> disseminate, distribute or reproduce all or any part of this e-mail or
>> attachments.
>>>>>>> If you have received this e-mail in error, please notify the
>>>>>>> sender and delete all material pertaining to this e-mail.  Any
>>>>>>> opinion or views expressed in this e-mail are those of the
>>>>>>> individual sender and may not represent those of The New Zealand
>>>>>>> Institute for Plant and Food
>>>>>> Research Limited.
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Wekalist mailing list
>>>>>>> Send posts to: [hidden email] 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: [hidden email] 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
>>>>> The contents of this e-mail are confidential and may be subject to
>>>>> legal
>>>> privilege.
>>>>> If you are not the intended recipient you must not use, disseminate,
>>>>> distribute or reproduce all or any part of this e-mail or attachments.
>>>>> If you have received this e-mail in error, please notify the sender
>>>>> and delete all material pertaining to this e-mail.  Any opinion or
>>>>> views expressed in this e-mail are those of the individual sender
>>>>> and may not represent those of The New Zealand Institute for Plant
>>>>> and Food
>>>> Research Limited.
>>>>>
>>>>> _______________________________________________
>>>>> Wekalist mailing list
>>>>> Send posts to: [hidden email] 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: [hidden email] 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
>>> The contents of this e-mail are confidential and may be subject to legal
>> privilege.
>>> If you are not the intended recipient you must not use, disseminate,
>>> distribute or reproduce all or any part of this e-mail or attachments.
>>> If you have received this e-mail in error, please notify the sender
>>> and delete all material pertaining to this e-mail.  Any opinion or
>>> views expressed in this e-mail are those of the individual sender and
>>> may not represent those of The New Zealand Institute for Plant and Food
>> Research Limited.
>>>
>>> _______________________________________________
>>> Wekalist mailing list
>>> Send posts to: [hidden email] 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
>>
>> _______________________________________________
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>> Send posts to: [hidden email] List info and subscription status:
>> https://list.waikato.ac.nz/mailman/listinfo/wekalist
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>
> The contents of this e-mail are confidential and may be subject to legal privilege.
> If you are not the intended recipient you must not use, disseminate, distribute or
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> e-mail.  Any opinion or views expressed in this e-mail are those of the individual
> sender and may not represent those of The New Zealand Institute for Plant and
> Food Research Limited.
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Re: RWeka setup

Patrick Connolly
Yes,  it starts but then I get

Unable to download repository zip archve (http://proxy.pfr.co.nz) - trying legacy routine...
java.net.UnknownHostException: http://proxy.pfr.co.nz

... which indicates to me that it's trying to do what WPM() tried to do -- same typo.  Then I get a longish list beginning:

       java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:178)
        java.net.Socket.connect(Socket.java:576)
        sun.net.NetworkClient.doConnect(NetworkClient.java:175)
        sun.net.www.http.HttpClient.openServer(HttpClient.java:432)

That's before trying the  GUI package manager, the result of which produces the same (similar, at least) list again.



Patrick Connolly
Biometrician

T: +64 9 925 7079
F: +64 9 925 7001
E: [hidden email]
www.plantandfood.co.nz
The New Zealand Institute for Plant & Food Research Limited

Postal Address: Plant & Food Research
Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
Physical Address: Plant & Food Research
120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand

> -----Original Message-----
> From: [hidden email] [mailto:wekalist-
> [hidden email]] On Behalf Of Eibe Frank
> Sent: Monday, 1 May 2017 3:06 p.m.
> To: Weka machine learning workbench list.
> Subject: Re: [Wekalist] RWeka setup
>
> Can you start the WEKA GUIs and then run the package manager GUI? Under
> “Tools” menu in the “GUIChooser” that pops up when you execute the .jar file
> (see my command below).
>
> Cheers,
> Eibe
>
> > On 1/05/2017, at 2:59 PM, Patrick Connolly
> <[hidden email]> wrote:
> >
> > G'day Eibe
> >
> > Thanks for clearing that one up.  Does that indicate that RWeka has everything
> a WEKA installation has?
> >
> > None of our IT folk know anything about Java.  Their only suggestion was that
> something at the sourceforge end was requiring user authentication, since  it is
> accessible by browser.  That idea seems odd to me because the browser settings
> don't require it.
> >
> > My guess is that it's my _JAVA_OPTIONS.
> >
> >> Picked up _JAVA_OPTIONS: -Dhttp.proxyHost=http://proxy.pfr.co.nz
> >> -Dhttp.proxyPort=8080
> > Caching repository metadata, please wait...
> > Refresh in progress. Please wait...
> > Unable to download repository zip archve (http://proxy.pfr.co.nz)
> >
> > The fact that the error message doesn't mention the port number could mean
> my syntax is incorrect.
> >
> > Ideas welcome.
> >
> >
> >
> >
> > Patrick Connolly
> > Biometrician
> >
> > Postal Address: Plant & Food Research
> > Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
> > Physical Address: Plant & Food Research
> > 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
> >> -----Original Message-----
> >> From: [hidden email] [mailto:wekalist-
> >> [hidden email]] On Behalf Of Eibe Frank
> >> Sent: Thursday, 27 April 2017 2:12 p.m.
> >> To: Weka machine learning workbench list.
> >> Subject: Re: [Wekalist] RWeka setup
> >>
> >> No, you don’t need to install WEKA separately. As you said, RWeka
> >> comes with its own weka.jar.
> >>
> >> You can even start the WEKA GUIs from that .jar by using
> >>
> >>  java -jar RWekajars/java/weka.jar
> >>
> >> The WEKA package manager can be accessed through the Tools menu in
> >> the WEKA GUI Chooser that pops up when your run this.
> >>
> >> Cheers,
> >> Eibe
> >>
> >>> On 27/04/2017, at 1:41 PM, Patrick Connolly
> >> <[hidden email]> wrote:
> >>>
> >>> THE proxy server needs to be accessible  from this side only, I
> >>> would have
> >> thought.  It works for everything else..
> >>>
> >>> I can manually download the repository  but the cache is erased if I
> >>> try to
> >> refresh it with the WPM() function.
> >>>
> >>> How  does the proxy system know which weka.jar is in use?  I have a
> >>> suspicion
> >> the 2 are being confused.  For that matter, am I correct in assuming
> >> weka needs to be installed to use RWeka?
> >>>
> >>>
> >>>
> >>>
> >>> Patrick Connolly
> >>> Biometrician
> >>>
> >>>
> >>> Postal Address: Plant & Food Research Private Bag 92169, Auckland
> >>> Mail Centre, Auckland 1142, New Zealand Physical Address: Plant &
> >>> Food Research
> >>> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
> >>>> -----Original Message-----
> >>>> From: [hidden email] [mailto:wekalist-
> >>>> [hidden email]] On Behalf Of Eibe Frank
> >>>> Sent: Wednesday, 26 April 2017 8:49 p.m.
> >>>> To: Weka machine learning workbench list.
> >>>> Subject: Re: [Wekalist] RWeka setup
> >>>>
> >>>> OK, it seems that your proxy server is not on the public net then.
> >>>>
> >>>> The output for WPM("refresh-cache") should look like this:
> >>>>
> >>>> WPM("refresh-cache")
> >>>> Refresh in progress. Please wait...
> >>>> [DefaultPackageManager] downloaded 1913 KB
> >>>>
> >>>> This works fine for me, both at home (no proxy) and at work (behind a
> proxy).
> >>>>
> >>>> The "Unable to download..." message you are getting means that WEKA
> >>>> cannot connect to the SourceForge site. Can you actually browse to
> >>>> that site in your browser? Perhaps your institution has blocked
> >>>> access to that site? Anyway, I would get in touch with your system
> >> administrators. They might be able to help.
> >>>>
> >>>> Cheers,
> >>>> Eibe
> >>>>
> >>>>> On 26 Apr 2017, at 16:31, Patrick Connolly
> >>>> <[hidden email]> wrote:
> >>>>>
> >>>>> It works for installing R packages - though the syntax for setting
> >>>>> the
> >>>> environment variable is different.
> >>>>>
> >>>>>> ping proxy.pfr.co.nz
> >>>>> PING aklwsa31.pfr.co.nz (172.16.81.6) 56(84) bytes of data.
> >>>>> 64 bytes from 172.16.81.6: icmp_seq=1 ttl=61 time=0.983 ms
> >>>>> 64 bytes from 172.16.81.6: icmp_seq=2 ttl=61 time=1.64 ms
> >>>>>
> >>>>> Patrick Connolly
> >>>>> Biometrician
> >>>>>
> >>>>> T: +64 9 925 7079
> >>>>> F: +64 9 925 7001
> >>>>> E: [hidden email]
> >>>>> www.plantandfood.co.nz
> >>>>> The New Zealand Institute for Plant & Food Research Limited
> >>>>>
> >>>>>
> >>>>>> -----Original Message-----
> >>>>>> From: [hidden email] [mailto:wekalist-
> >>>>>> [hidden email]] On Behalf Of Eibe Frank
> >>>>>> Sent: Wednesday, 26 April 2017 3:54 p.m.
> >>>>>> To: Weka machine learning workbench list.
> >>>>>> Subject: Re: [Wekalist] RWeka setup
> >>>>>>
> >>>>>> Are you sure you have the proxy details right?
> >>>>>>
> >>>>>> $ ping proxy.pfr.co.nz
> >>>>>> ping: cannot resolve proxy.pfr.co.nz: Unknown host
> >>>>>>
> >>>>>> Cheers,
> >>>>>> Eibe
> >>>>>>
> >>>>>>> On 26/04/2017, at 3:02 PM, Patrick Connolly
> >>>>>> <[hidden email]> wrote:
> >>>>>>>
> >>>>>>> I followed the directions at
> >>>>>>>
> https://weka.wikispaces.com/Weka+package+manager+does+not+start :
> >>>>>>> Now when I start RWeka, I get
> >>>>>>>
> >>>>>>>> require(RWeka)
> >>>>>>> Loading required package: RWeka
> >>>>>>> Picked up _JAVA_OPTIONS: -Dhttp.proxyHost=http://proxy.pfr.co.nz
> >>>>>>> -Dhttp.proxyPort=8080
> >>>>>>>
> >>>>>>> which indicates to me that I have the syntax correct, but I then
> >>>>>>> get
> >>>>>>>
> >>>>>>>> WPM("refresh-cache")
> >>>>>>> Refresh in progress. Please wait...
> >>>>>>> Unable to download repository zip archve
> >>>>>>> (http://proxy.pfr.co.nz)
> >>>>>>> - trying
> >>>>>> legacy routine...
> >>>>>>>
> >>>>>>>
> >>>>>>> ... that is unless I install the repo manually in
> >>>>>>> ~/wekafiles/repCache.  In that case, there's no message but
> >>>>>>> ~/wekafiles/repCache is deleted.
> >>>>>>>
> >>>>>>> The proxy does not require authentication, so something else is amiss.
> >>>>>>>
> >>>>>>> If I try
> >>>>>>>> WPM("list-packages", "installed")
> >>>>>>>
> >>>>>>> R crashes.
> >>>>>>>
> >>>>>>> Am I on a hiding to nowhere trying to use RWeka without a
> >>>>>>> JAVACLASS environment variable?
> >>>>>>>
> >>>>>>>
> >>>>>>> Patrick Connolly
> >>>>>>> Biometrician
> >>>>>>>
> >>>>>>> Postal Address: Plant & Food Research Private Bag 92169,
> >>>>>>> Auckland Mail Centre, Auckland 1142, New Zealand Physical
> >>>>>>> Address: Plant & Food Research
> >>>>>>> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
> >>>>>>>> -----Original Message-----
> >>>>>>>> From: [hidden email] [mailto:wekalist-
> >>>>>>>> [hidden email]] On Behalf Of Eibe Frank
> >>>>>>>> Sent: Monday, 24 April 2017 10:56 p.m.
> >>>>>>>> To: Weka machine learning workbench list.
> >>>>>>>> Subject: Re: [Wekalist] RWeka setup
> >>>>>>>>
> >>>>>>>> The WEKA package manager needs web access to connect to the
> >>>>>>>> SourceForge site. You probably don't have direct access and
> >>>>>>>> instead need to go through a proxy server. Oracle's JVM reads
> >>>>>>>> the _JAVA_OPTIONS environment variable and you can provide
> >>>>>>>> proxy settings via
> >>>>>> that variable, as explained here:
> >>>>>>>>
> >>>>>>>>
> https://weka.wikispaces.com/Weka+package+manager+does+not+start
> >>>>>>>>
> >>>>>>>> However, WEKA may not be able to pop up the GUI for entering
> >>>>>>>> the proxy credentials, so you may have to add those as part of
> >>>>>>>> the environment variable as well, using http.proxyUser and
> >>>>>>>> http.proxyPassword,
> >>>>>> as explained here:
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>
> >>>>
> >>
> https://weka.wikispaces.com/How+do+I+use+the+package+manager%3F#GUI
> >>>>>>>> %20package%20manager-Using%20a%20HTTP%20proxy
> >>>>>>>>
> >>>>>>>> Cheers,
> >>>>>>>> Eibe
> >>>>>>>>
> >>>>>>>>> On 24 Apr 2017, at 16:33, Patrick Connolly
> >>>>>>>> <[hidden email]> wrote:
> >>>>>>>>>
> >>>>>>>>> I installed weka in /usr/local/weka-3-8-1/weka.jar and when I
> >>>>>>>>> installed
> >>>>>>>> RWeka, it has
> >>>>>>>>> another weka.jar in the R package library.  I assume the
> >>>>>>>>> latter is used when I try this (in R):
> >>>>>>>>>
> >>>>>>>>>> WPM("refresh-cache")
> >>>>>>>>> Refresh in progress. Please wait...
> >>>>>>>>> Unable to download repository zip archve (connect timed out) -
> >>>>>>>>> trying legacy
> >>>>>>>> routine...
> >>>>>>>>> java.net.SocketTimeoutException: connect timed out
> >>>>>>>>>
> >>>>>>>>> My guess is that the CLASSPATH isn't specified.  Without
> >>>>>>>>> setting an environment variable, where do I specify the class path
> option?
> >>>>>>>>>
> >>>>>>>>> TIA
> >>>>>>>>>
> >>>>>>>>> Patrick Connolly
> >>>>>>>>> Biometrician
> >>>>>>>>>
> >>>>>>>>> www.plantandfood.co.nz
> >>>>>>>>> The New Zealand Institute for Plant & Food Research Limited
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> The contents of this e-mail are confidential and may be
> >>>>>>>>> subject to legal
> >>>>>>>> privilege.
> >>>>>>>>> If you are not the intended recipient you must not use,
> >>>>>>>>> disseminate, distribute
> >>>>>>>> or
> >>>>>>>>> reproduce all or any part of this e-mail or attachments.  If
> >>>>>>>>> you have received
> >>>>>>>> this
> >>>>>>>>> e-mail in error, please notify the sender and delete all
> >>>>>>>>> material pertaining to
> >>>>>>>> this
> >>>>>>>>> e-mail.  Any opinion or views expressed in this e-mail are
> >>>>>>>>> those of the
> >>>>>>>> individual
> >>>>>>>>> sender and may not represent those of The New Zealand
> >>>>>>>>> Institute for Plant
> >>>>>>>> and
> >>>>>>>>> Food Research Limited.
> >>>>>>>>>
> >>>>>>>>> _______________________________________________
> >>>>>>>>> Wekalist mailing list
> >>>>>>>>> Send posts to: [hidden email] 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: [hidden email] 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
> >>>>>>> The contents of this e-mail are confidential and may be subject
> >>>>>>> to legal
> >>>>>> privilege.
> >>>>>>> If you are not the intended recipient you must not use,
> >>>>>>> disseminate, distribute or reproduce all or any part of this
> >>>>>>> e-mail or
> >> attachments.
> >>>>>>> If you have received this e-mail in error, please notify the
> >>>>>>> sender and delete all material pertaining to this e-mail.  Any
> >>>>>>> opinion or views expressed in this e-mail are those of the
> >>>>>>> individual sender and may not represent those of The New Zealand
> >>>>>>> Institute for Plant and Food
> >>>>>> Research Limited.
> >>>>>>>
> >>>>>>> _______________________________________________
> >>>>>>> Wekalist mailing list
> >>>>>>> Send posts to: [hidden email] 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: [hidden email] 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
> >>>>> The contents of this e-mail are confidential and may be subject to
> >>>>> legal
> >>>> privilege.
> >>>>> If you are not the intended recipient you must not use,
> >>>>> disseminate, distribute or reproduce all or any part of this e-mail or
> attachments.
> >>>>> If you have received this e-mail in error, please notify the
> >>>>> sender and delete all material pertaining to this e-mail.  Any
> >>>>> opinion or views expressed in this e-mail are those of the
> >>>>> individual sender and may not represent those of The New Zealand
> >>>>> Institute for Plant and Food
> >>>> Research Limited.
> >>>>>
> >>>>> _______________________________________________
> >>>>> Wekalist mailing list
> >>>>> Send posts to: [hidden email] 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: [hidden email] 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
> >>> The contents of this e-mail are confidential and may be subject to
> >>> legal
> >> privilege.
> >>> If you are not the intended recipient you must not use, disseminate,
> >>> distribute or reproduce all or any part of this e-mail or attachments.
> >>> If you have received this e-mail in error, please notify the sender
> >>> and delete all material pertaining to this e-mail.  Any opinion or
> >>> views expressed in this e-mail are those of the individual sender
> >>> and may not represent those of The New Zealand Institute for Plant
> >>> and Food
> >> Research Limited.
> >>>
> >>> _______________________________________________
> >>> Wekalist mailing list
> >>> Send posts to: [hidden email] 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: [hidden email] 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
> >
> > The contents of this e-mail are confidential and may be subject to legal
> privilege.
> > If you are not the intended recipient you must not use, disseminate,
> > distribute or reproduce all or any part of this e-mail or attachments.
> > If you have received this e-mail in error, please notify the sender
> > and delete all material pertaining to this e-mail.  Any opinion or
> > views expressed in this e-mail are those of the individual sender and
> > may not represent those of The New Zealand Institute for Plant and Food
> Research Limited.
> > _______________________________________________
> > Wekalist mailing list
> > Send posts to: [hidden email] 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
>
> _______________________________________________
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> Send posts to: [hidden email] 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

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 If you are not the intended recipient you must not use, disseminate, distribute or
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Re: RWeka setup

Eibe Frank-2
Administrator
Try deleting "http://“ from the _JAVA_OPTIONS string.

Cheers,
Eibe

> On 1/05/2017, at 4:18 PM, Patrick Connolly <[hidden email]> wrote:
>
> Yes,  it starts but then I get
>
> Unable to download repository zip archve (http://proxy.pfr.co.nz) - trying legacy routine...
> java.net.UnknownHostException: http://proxy.pfr.co.nz
>
> ... which indicates to me that it's trying to do what WPM() tried to do -- same typo.  Then I get a longish list beginning:
>
>       java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:178)
>        java.net.Socket.connect(Socket.java:576)
>        sun.net.NetworkClient.doConnect(NetworkClient.java:175)
>        sun.net.www.http.HttpClient.openServer(HttpClient.java:432)
>
> That's before trying the  GUI package manager, the result of which produces the same (similar, at least) list again.
>
>
>
> Patrick Connolly
> Biometrician
>
> T: +64 9 925 7079
> F: +64 9 925 7001
> E: [hidden email]
> www.plantandfood.co.nz
> The New Zealand Institute for Plant & Food Research Limited
>
> Postal Address: Plant & Food Research
> Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
> Physical Address: Plant & Food Research
> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
>
>> -----Original Message-----
>> From: [hidden email] [mailto:wekalist-
>> [hidden email]] On Behalf Of Eibe Frank
>> Sent: Monday, 1 May 2017 3:06 p.m.
>> To: Weka machine learning workbench list.
>> Subject: Re: [Wekalist] RWeka setup
>>
>> Can you start the WEKA GUIs and then run the package manager GUI? Under
>> “Tools” menu in the “GUIChooser” that pops up when you execute the .jar file
>> (see my command below).
>>
>> Cheers,
>> Eibe
>>
>>> On 1/05/2017, at 2:59 PM, Patrick Connolly
>> <[hidden email]> wrote:
>>>
>>> G'day Eibe
>>>
>>> Thanks for clearing that one up.  Does that indicate that RWeka has everything
>> a WEKA installation has?
>>>
>>> None of our IT folk know anything about Java.  Their only suggestion was that
>> something at the sourceforge end was requiring user authentication, since  it is
>> accessible by browser.  That idea seems odd to me because the browser settings
>> don't require it.
>>>
>>> My guess is that it's my _JAVA_OPTIONS.
>>>
>>>> Picked up _JAVA_OPTIONS: -Dhttp.proxyHost=http://proxy.pfr.co.nz
>>>> -Dhttp.proxyPort=8080
>>> Caching repository metadata, please wait...
>>> Refresh in progress. Please wait...
>>> Unable to download repository zip archve (http://proxy.pfr.co.nz)
>>>
>>> The fact that the error message doesn't mention the port number could mean
>> my syntax is incorrect.
>>>
>>> Ideas welcome.
>>>
>>>
>>>
>>>
>>> Patrick Connolly
>>> Biometrician
>>>
>>> Postal Address: Plant & Food Research
>>> Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
>>> Physical Address: Plant & Food Research
>>> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
>>>> -----Original Message-----
>>>> From: [hidden email] [mailto:wekalist-
>>>> [hidden email]] On Behalf Of Eibe Frank
>>>> Sent: Thursday, 27 April 2017 2:12 p.m.
>>>> To: Weka machine learning workbench list.
>>>> Subject: Re: [Wekalist] RWeka setup
>>>>
>>>> No, you don’t need to install WEKA separately. As you said, RWeka
>>>> comes with its own weka.jar.
>>>>
>>>> You can even start the WEKA GUIs from that .jar by using
>>>>
>>>> java -jar RWekajars/java/weka.jar
>>>>
>>>> The WEKA package manager can be accessed through the Tools menu in
>>>> the WEKA GUI Chooser that pops up when your run this.
>>>>
>>>> Cheers,
>>>> Eibe
>>>>
>>>>> On 27/04/2017, at 1:41 PM, Patrick Connolly
>>>> <[hidden email]> wrote:
>>>>>
>>>>> THE proxy server needs to be accessible  from this side only, I
>>>>> would have
>>>> thought.  It works for everything else..
>>>>>
>>>>> I can manually download the repository  but the cache is erased if I
>>>>> try to
>>>> refresh it with the WPM() function.
>>>>>
>>>>> How  does the proxy system know which weka.jar is in use?  I have a
>>>>> suspicion
>>>> the 2 are being confused.  For that matter, am I correct in assuming
>>>> weka needs to be installed to use RWeka?
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Patrick Connolly
>>>>> Biometrician
>>>>>
>>>>>
>>>>> Postal Address: Plant & Food Research Private Bag 92169, Auckland
>>>>> Mail Centre, Auckland 1142, New Zealand Physical Address: Plant &
>>>>> Food Research
>>>>> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
>>>>>> -----Original Message-----
>>>>>> From: [hidden email] [mailto:wekalist-
>>>>>> [hidden email]] On Behalf Of Eibe Frank
>>>>>> Sent: Wednesday, 26 April 2017 8:49 p.m.
>>>>>> To: Weka machine learning workbench list.
>>>>>> Subject: Re: [Wekalist] RWeka setup
>>>>>>
>>>>>> OK, it seems that your proxy server is not on the public net then.
>>>>>>
>>>>>> The output for WPM("refresh-cache") should look like this:
>>>>>>
>>>>>> WPM("refresh-cache")
>>>>>> Refresh in progress. Please wait...
>>>>>> [DefaultPackageManager] downloaded 1913 KB
>>>>>>
>>>>>> This works fine for me, both at home (no proxy) and at work (behind a
>> proxy).
>>>>>>
>>>>>> The "Unable to download..." message you are getting means that WEKA
>>>>>> cannot connect to the SourceForge site. Can you actually browse to
>>>>>> that site in your browser? Perhaps your institution has blocked
>>>>>> access to that site? Anyway, I would get in touch with your system
>>>> administrators. They might be able to help.
>>>>>>
>>>>>> Cheers,
>>>>>> Eibe
>>>>>>
>>>>>>> On 26 Apr 2017, at 16:31, Patrick Connolly
>>>>>> <[hidden email]> wrote:
>>>>>>>
>>>>>>> It works for installing R packages - though the syntax for setting
>>>>>>> the
>>>>>> environment variable is different.
>>>>>>>
>>>>>>>> ping proxy.pfr.co.nz
>>>>>>> PING aklwsa31.pfr.co.nz (172.16.81.6) 56(84) bytes of data.
>>>>>>> 64 bytes from 172.16.81.6: icmp_seq=1 ttl=61 time=0.983 ms
>>>>>>> 64 bytes from 172.16.81.6: icmp_seq=2 ttl=61 time=1.64 ms
>>>>>>>
>>>>>>> Patrick Connolly
>>>>>>> Biometrician
>>>>>>>
>>>>>>> T: +64 9 925 7079
>>>>>>> F: +64 9 925 7001
>>>>>>> E: [hidden email]
>>>>>>> www.plantandfood.co.nz
>>>>>>> The New Zealand Institute for Plant & Food Research Limited
>>>>>>>
>>>>>>>
>>>>>>>> -----Original Message-----
>>>>>>>> From: [hidden email] [mailto:wekalist-
>>>>>>>> [hidden email]] On Behalf Of Eibe Frank
>>>>>>>> Sent: Wednesday, 26 April 2017 3:54 p.m.
>>>>>>>> To: Weka machine learning workbench list.
>>>>>>>> Subject: Re: [Wekalist] RWeka setup
>>>>>>>>
>>>>>>>> Are you sure you have the proxy details right?
>>>>>>>>
>>>>>>>> $ ping proxy.pfr.co.nz
>>>>>>>> ping: cannot resolve proxy.pfr.co.nz: Unknown host
>>>>>>>>
>>>>>>>> Cheers,
>>>>>>>> Eibe
>>>>>>>>
>>>>>>>>> On 26/04/2017, at 3:02 PM, Patrick Connolly
>>>>>>>> <[hidden email]> wrote:
>>>>>>>>>
>>>>>>>>> I followed the directions at
>>>>>>>>>
>> https://weka.wikispaces.com/Weka+package+manager+does+not+start :
>>>>>>>>> Now when I start RWeka, I get
>>>>>>>>>
>>>>>>>>>> require(RWeka)
>>>>>>>>> Loading required package: RWeka
>>>>>>>>> Picked up _JAVA_OPTIONS: -Dhttp.proxyHost=http://proxy.pfr.co.nz
>>>>>>>>> -Dhttp.proxyPort=8080
>>>>>>>>>
>>>>>>>>> which indicates to me that I have the syntax correct, but I then
>>>>>>>>> get
>>>>>>>>>
>>>>>>>>>> WPM("refresh-cache")
>>>>>>>>> Refresh in progress. Please wait...
>>>>>>>>> Unable to download repository zip archve
>>>>>>>>> (http://proxy.pfr.co.nz)
>>>>>>>>> - trying
>>>>>>>> legacy routine...
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ... that is unless I install the repo manually in
>>>>>>>>> ~/wekafiles/repCache.  In that case, there's no message but
>>>>>>>>> ~/wekafiles/repCache is deleted.
>>>>>>>>>
>>>>>>>>> The proxy does not require authentication, so something else is amiss.
>>>>>>>>>
>>>>>>>>> If I try
>>>>>>>>>> WPM("list-packages", "installed")
>>>>>>>>>
>>>>>>>>> R crashes.
>>>>>>>>>
>>>>>>>>> Am I on a hiding to nowhere trying to use RWeka without a
>>>>>>>>> JAVACLASS environment variable?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Patrick Connolly
>>>>>>>>> Biometrician
>>>>>>>>>
>>>>>>>>> Postal Address: Plant & Food Research Private Bag 92169,
>>>>>>>>> Auckland Mail Centre, Auckland 1142, New Zealand Physical
>>>>>>>>> Address: Plant & Food Research
>>>>>>>>> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
>>>>>>>>>> -----Original Message-----
>>>>>>>>>> From: [hidden email] [mailto:wekalist-
>>>>>>>>>> [hidden email]] On Behalf Of Eibe Frank
>>>>>>>>>> Sent: Monday, 24 April 2017 10:56 p.m.
>>>>>>>>>> To: Weka machine learning workbench list.
>>>>>>>>>> Subject: Re: [Wekalist] RWeka setup
>>>>>>>>>>
>>>>>>>>>> The WEKA package manager needs web access to connect to the
>>>>>>>>>> SourceForge site. You probably don't have direct access and
>>>>>>>>>> instead need to go through a proxy server. Oracle's JVM reads
>>>>>>>>>> the _JAVA_OPTIONS environment variable and you can provide
>>>>>>>>>> proxy settings via
>>>>>>>> that variable, as explained here:
>>>>>>>>>>
>>>>>>>>>>
>> https://weka.wikispaces.com/Weka+package+manager+does+not+start
>>>>>>>>>>
>>>>>>>>>> However, WEKA may not be able to pop up the GUI for entering
>>>>>>>>>> the proxy credentials, so you may have to add those as part of
>>>>>>>>>> the environment variable as well, using http.proxyUser and
>>>>>>>>>> http.proxyPassword,
>>>>>>>> as explained here:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>>>>>>
>>>>
>> https://weka.wikispaces.com/How+do+I+use+the+package+manager%3F#GUI
>>>>>>>>>> %20package%20manager-Using%20a%20HTTP%20proxy
>>>>>>>>>>
>>>>>>>>>> Cheers,
>>>>>>>>>> Eibe
>>>>>>>>>>
>>>>>>>>>>> On 24 Apr 2017, at 16:33, Patrick Connolly
>>>>>>>>>> <[hidden email]> wrote:
>>>>>>>>>>>
>>>>>>>>>>> I installed weka in /usr/local/weka-3-8-1/weka.jar and when I
>>>>>>>>>>> installed
>>>>>>>>>> RWeka, it has
>>>>>>>>>>> another weka.jar in the R package library.  I assume the
>>>>>>>>>>> latter is used when I try this (in R):
>>>>>>>>>>>
>>>>>>>>>>>> WPM("refresh-cache")
>>>>>>>>>>> Refresh in progress. Please wait...
>>>>>>>>>>> Unable to download repository zip archve (connect timed out) -
>>>>>>>>>>> trying legacy
>>>>>>>>>> routine...
>>>>>>>>>>> java.net.SocketTimeoutException: connect timed out
>>>>>>>>>>>
>>>>>>>>>>> My guess is that the CLASSPATH isn't specified.  Without
>>>>>>>>>>> setting an environment variable, where do I specify the class path
>> option?
>>>>>>>>>>>
>>>>>>>>>>> TIA
>>>>>>>>>>>
>>>>>>>>>>> Patrick Connolly
>>>>>>>>>>> Biometrician
>>>>>>>>>>>
>>>>>>>>>>> www.plantandfood.co.nz
>>>>>>>>>>> The New Zealand Institute for Plant & Food Research Limited
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> The contents of this e-mail are confidential and may be
>>>>>>>>>>> subject to legal
>>>>>>>>>> privilege.
>>>>>>>>>>> If you are not the intended recipient you must not use,
>>>>>>>>>>> disseminate, distribute
>>>>>>>>>> or
>>>>>>>>>>> reproduce all or any part of this e-mail or attachments.  If
>>>>>>>>>>> you have received
>>>>>>>>>> this
>>>>>>>>>>> e-mail in error, please notify the sender and delete all
>>>>>>>>>>> material pertaining to
>>>>>>>>>> this
>>>>>>>>>>> e-mail.  Any opinion or views expressed in this e-mail are
>>>>>>>>>>> those of the
>>>>>>>>>> individual
>>>>>>>>>>> sender and may not represent those of The New Zealand
>>>>>>>>>>> Institute for Plant
>>>>>>>>>> and
>>>>>>>>>>> Food Research Limited.
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Wekalist mailing list
>>>>>>>>>>> Send posts to: [hidden email] 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: [hidden email] 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
>>>>>>>>> The contents of this e-mail are confidential and may be subject
>>>>>>>>> to legal
>>>>>>>> privilege.
>>>>>>>>> If you are not the intended recipient you must not use,
>>>>>>>>> disseminate, distribute or reproduce all or any part of this
>>>>>>>>> e-mail or
>>>> attachments.
>>>>>>>>> If you have received this e-mail in error, please notify the
>>>>>>>>> sender and delete all material pertaining to this e-mail.  Any
>>>>>>>>> opinion or views expressed in this e-mail are those of the
>>>>>>>>> individual sender and may not represent those of The New Zealand
>>>>>>>>> Institute for Plant and Food
>>>>>>>> Research Limited.
>>>>>>>>>
>>>>>>>>> _______________________________________________
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Re: RWeka setup

Patrick Connolly
Thanks Eibe.

That got over the proxy issue and the Package Management gui looks like it's working. I'd never have thought of deleting the 'http://' part.

> WPM("refresh-cache")
Refresh in progress. Please wait...
[DefaultPackageManager] downloaded 1917 KB

That looks promising,  however, when I try the next thing:

> WPM("list-packages", "installed")

 *** caught segfault ***
address 0x78, cause 'memory not mapped'

Traceback:
 1: .Call(RJavaCheckExceptions, silent)
 2: .jcheck()
 3: .jcall("java/lang/System", "V", "setOut", out)
 4: WPM("list-packages", "installed")

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

Is that because I don't have a JAVACLASS environment variable?
I  installed a package using the GUI, hypothesising that there might be a zero length issue, but I still got the same result.

Patrick Connolly
Biometrician

Postal Address: Plant & Food Research
Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
Physical Address: Plant & Food Research
120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand

> -----Original Message-----
> From: [hidden email] [mailto:wekalist-
> [hidden email]] On Behalf Of Eibe Frank
> Sent: Monday, 1 May 2017 5:03 p.m.
> To: Weka machine learning workbench list.
> Subject: Re: [Wekalist] RWeka setup
>
> Try deleting "http://“ from the _JAVA_OPTIONS string.
>
> Cheers,
> Eibe
>
> > On 1/05/2017, at 4:18 PM, Patrick Connolly
> <[hidden email]> wrote:
> >
> > Yes,  it starts but then I get
> >
> > Unable to download repository zip archve (http://proxy.pfr.co.nz) - trying
> legacy routine...
> > java.net.UnknownHostException: http://proxy.pfr.co.nz
> >
> > ... which indicates to me that it's trying to do what WPM() tried to do -- same
> typo.  Then I get a longish list beginning:
> >
> >
> java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:178)
> >        java.net.Socket.connect(Socket.java:576)
> >        sun.net.NetworkClient.doConnect(NetworkClient.java:175)
> >        sun.net.www.http.HttpClient.openServer(HttpClient.java:432)
> >
> > That's before trying the  GUI package manager, the result of which produces
> the same (similar, at least) list again.
> >
> >
> >
> > Patrick Connolly
> > Biometrician
> >
> > T: +64 9 925 7079
> > F: +64 9 925 7001
> > E: [hidden email]
> > www.plantandfood.co.nz
> > The New Zealand Institute for Plant & Food Research Limited
> >
> > Postal Address: Plant & Food Research
> > Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
> > Physical Address: Plant & Food Research
> > 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
> >
> >> -----Original Message-----
> >> From: [hidden email] [mailto:wekalist-
> >> [hidden email]] On Behalf Of Eibe Frank
> >> Sent: Monday, 1 May 2017 3:06 p.m.
> >> To: Weka machine learning workbench list.
> >> Subject: Re: [Wekalist] RWeka setup
> >>
> >> Can you start the WEKA GUIs and then run the package manager GUI?
> >> Under “Tools” menu in the “GUIChooser” that pops up when you execute
> >> the .jar file (see my command below).
> >>
> >> Cheers,
> >> Eibe
> >>
> >>> On 1/05/2017, at 2:59 PM, Patrick Connolly
> >> <[hidden email]> wrote:
> >>>
> >>> G'day Eibe
> >>>
> >>> Thanks for clearing that one up.  Does that indicate that RWeka has
> >>> everything
> >> a WEKA installation has?
> >>>
> >>> None of our IT folk know anything about Java.  Their only suggestion
> >>> was that
> >> something at the sourceforge end was requiring user authentication,
> >> since  it is accessible by browser.  That idea seems odd to me
> >> because the browser settings don't require it.
> >>>
> >>> My guess is that it's my _JAVA_OPTIONS.
> >>>
> >>>> Picked up _JAVA_OPTIONS: -Dhttp.proxyHost=http://proxy.pfr.co.nz
> >>>> -Dhttp.proxyPort=8080
> >>> Caching repository metadata, please wait...
> >>> Refresh in progress. Please wait...
> >>> Unable to download repository zip archve (http://proxy.pfr.co.nz)
> >>>
> >>> The fact that the error message doesn't mention the port number
> >>> could mean
> >> my syntax is incorrect.
> >>>
> >>> Ideas welcome.
> >>>
> >>>
> >>>
> >>>
> >>> Patrick Connolly
> >>> Biometrician
> >>>
> >>> Postal Address: Plant & Food Research Private Bag 92169, Auckland
> >>> Mail Centre, Auckland 1142, New Zealand Physical Address: Plant &
> >>> Food Research
> >>> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
> >>>> -----Original Message-----
> >>>> From: [hidden email] [mailto:wekalist-
> >>>> [hidden email]] On Behalf Of Eibe Frank
> >>>> Sent: Thursday, 27 April 2017 2:12 p.m.
> >>>> To: Weka machine learning workbench list.
> >>>> Subject: Re: [Wekalist] RWeka setup
> >>>>
> >>>> No, you don’t need to install WEKA separately. As you said, RWeka
> >>>> comes with its own weka.jar.
> >>>>
> >>>> You can even start the WEKA GUIs from that .jar by using
> >>>>
> >>>> java -jar RWekajars/java/weka.jar
> >>>>
> >>>> The WEKA package manager can be accessed through the Tools menu in
> >>>> the WEKA GUI Chooser that pops up when your run this.
> >>>>
> >>>> Cheers,
> >>>> Eibe
> >>>>
> >>>>> On 27/04/2017, at 1:41 PM, Patrick Connolly
> >>>> <[hidden email]> wrote:
> >>>>>
> >>>>> THE proxy server needs to be accessible  from this side only, I
> >>>>> would have
> >>>> thought.  It works for everything else..
> >>>>>
> >>>>> I can manually download the repository  but the cache is erased if
> >>>>> I try to
> >>>> refresh it with the WPM() function.
> >>>>>
> >>>>> How  does the proxy system know which weka.jar is in use?  I have
> >>>>> a suspicion
> >>>> the 2 are being confused.  For that matter, am I correct in
> >>>> assuming weka needs to be installed to use RWeka?
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> Patrick Connolly
> >>>>> Biometrician
> >>>>>
> >>>>>
> >>>>> Postal Address: Plant & Food Research Private Bag 92169, Auckland
> >>>>> Mail Centre, Auckland 1142, New Zealand Physical Address: Plant &
> >>>>> Food Research
> >>>>> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
> >>>>>> -----Original Message-----
> >>>>>> From: [hidden email] [mailto:wekalist-
> >>>>>> [hidden email]] On Behalf Of Eibe Frank
> >>>>>> Sent: Wednesday, 26 April 2017 8:49 p.m.
> >>>>>> To: Weka machine learning workbench list.
> >>>>>> Subject: Re: [Wekalist] RWeka setup
> >>>>>>
> >>>>>> OK, it seems that your proxy server is not on the public net then.
> >>>>>>
> >>>>>> The output for WPM("refresh-cache") should look like this:
> >>>>>>
> >>>>>> WPM("refresh-cache")
> >>>>>> Refresh in progress. Please wait...
> >>>>>> [DefaultPackageManager] downloaded 1913 KB
> >>>>>>
> >>>>>> This works fine for me, both at home (no proxy) and at work
> >>>>>> (behind a
> >> proxy).
> >>>>>>
> >>>>>> The "Unable to download..." message you are getting means that
> >>>>>> WEKA cannot connect to the SourceForge site. Can you actually
> >>>>>> browse to that site in your browser? Perhaps your institution has
> >>>>>> blocked access to that site? Anyway, I would get in touch with
> >>>>>> your system
> >>>> administrators. They might be able to help.
> >>>>>>
> >>>>>> Cheers,
> >>>>>> Eibe
> >>>>>>
> >>>>>>> On 26 Apr 2017, at 16:31, Patrick Connolly
> >>>>>> <[hidden email]> wrote:
> >>>>>>>
> >>>>>>> It works for installing R packages - though the syntax for
> >>>>>>> setting the
> >>>>>> environment variable is different.
> >>>>>>>
> >>>>>>>> ping proxy.pfr.co.nz
> >>>>>>> PING aklwsa31.pfr.co.nz (172.16.81.6) 56(84) bytes of data.
> >>>>>>> 64 bytes from 172.16.81.6: icmp_seq=1 ttl=61 time=0.983 ms
> >>>>>>> 64 bytes from 172.16.81.6: icmp_seq=2 ttl=61 time=1.64 ms
> >>>>>>>
> >>>>>>> Patrick Connolly
> >>>>>>> Biometrician
> >>>>>>>
> >>>>>>> T: +64 9 925 7079
> >>>>>>> F: +64 9 925 7001
> >>>>>>> E: [hidden email]
> >>>>>>> www.plantandfood.co.nz
> >>>>>>> The New Zealand Institute for Plant & Food Research Limited
> >>>>>>>
> >>>>>>>
> >>>>>>>> -----Original Message-----
> >>>>>>>> From: [hidden email] [mailto:wekalist-
> >>>>>>>> [hidden email]] On Behalf Of Eibe Frank
> >>>>>>>> Sent: Wednesday, 26 April 2017 3:54 p.m.
> >>>>>>>> To: Weka machine learning workbench list.
> >>>>>>>> Subject: Re: [Wekalist] RWeka setup
> >>>>>>>>
> >>>>>>>> Are you sure you have the proxy details right?
> >>>>>>>>
> >>>>>>>> $ ping proxy.pfr.co.nz
> >>>>>>>> ping: cannot resolve proxy.pfr.co.nz: Unknown host
> >>>>>>>>
> >>>>>>>> Cheers,
> >>>>>>>> Eibe
> >>>>>>>>
> >>>>>>>>> On 26/04/2017, at 3:02 PM, Patrick Connolly
> >>>>>>>> <[hidden email]> wrote:
> >>>>>>>>>
> >>>>>>>>> I followed the directions at
> >>>>>>>>>
> >> https://weka.wikispaces.com/Weka+package+manager+does+not+start :
> >>>>>>>>> Now when I start RWeka, I get
> >>>>>>>>>
> >>>>>>>>>> require(RWeka)
> >>>>>>>>> Loading required package: RWeka Picked up _JAVA_OPTIONS:
> >>>>>>>>> -Dhttp.proxyHost=http://proxy.pfr.co.nz
> >>>>>>>>> -Dhttp.proxyPort=8080
> >>>>>>>>>
> >>>>>>>>> which indicates to me that I have the syntax correct, but I
> >>>>>>>>> then get
> >>>>>>>>>
> >>>>>>>>>> WPM("refresh-cache")
> >>>>>>>>> Refresh in progress. Please wait...
> >>>>>>>>> Unable to download repository zip archve
> >>>>>>>>> (http://proxy.pfr.co.nz)
> >>>>>>>>> - trying
> >>>>>>>> legacy routine...
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> ... that is unless I install the repo manually in
> >>>>>>>>> ~/wekafiles/repCache.  In that case, there's no message but
> >>>>>>>>> ~/wekafiles/repCache is deleted.
> >>>>>>>>>
> >>>>>>>>> The proxy does not require authentication, so something else is
> amiss.
> >>>>>>>>>
> >>>>>>>>> If I try
> >>>>>>>>>> WPM("list-packages", "installed")
> >>>>>>>>>
> >>>>>>>>> R crashes.
> >>>>>>>>>
> >>>>>>>>> Am I on a hiding to nowhere trying to use RWeka without a
> >>>>>>>>> JAVACLASS environment variable?
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> Patrick Connolly
> >>>>>>>>> Biometrician
> >>>>>>>>>
> >>>>>>>>> Postal Address: Plant & Food Research Private Bag 92169,
> >>>>>>>>> Auckland Mail Centre, Auckland 1142, New Zealand Physical
> >>>>>>>>> Address: Plant & Food Research
> >>>>>>>>> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
> >>>>>>>>>> -----Original Message-----
> >>>>>>>>>> From: [hidden email] [mailto:wekalist-
> >>>>>>>>>> [hidden email]] On Behalf Of Eibe Frank
> >>>>>>>>>> Sent: Monday, 24 April 2017 10:56 p.m.
> >>>>>>>>>> To: Weka machine learning workbench list.
> >>>>>>>>>> Subject: Re: [Wekalist] RWeka setup
> >>>>>>>>>>
> >>>>>>>>>> The WEKA package manager needs web access to connect to the
> >>>>>>>>>> SourceForge site. You probably don't have direct access and
> >>>>>>>>>> instead need to go through a proxy server. Oracle's JVM reads
> >>>>>>>>>> the _JAVA_OPTIONS environment variable and you can provide
> >>>>>>>>>> proxy settings via
> >>>>>>>> that variable, as explained here:
> >>>>>>>>>>
> >>>>>>>>>>
> >> https://weka.wikispaces.com/Weka+package+manager+does+not+start
> >>>>>>>>>>
> >>>>>>>>>> However, WEKA may not be able to pop up the GUI for entering
> >>>>>>>>>> the proxy credentials, so you may have to add those as part
> >>>>>>>>>> of the environment variable as well, using http.proxyUser and
> >>>>>>>>>> http.proxyPassword,
> >>>>>>>> as explained here:
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>
> >>>>>>
> >>>>
> >>
> https://weka.wikispaces.com/How+do+I+use+the+package+manager%3F#GUI
> >>>>>>>>>> %20package%20manager-Using%20a%20HTTP%20proxy
> >>>>>>>>>>
> >>>>>>>>>> Cheers,
> >>>>>>>>>> Eibe
> >>>>>>>>>>
> >>>>>>>>>>> On 24 Apr 2017, at 16:33, Patrick Connolly
> >>>>>>>>>> <[hidden email]> wrote:
> >>>>>>>>>>>
> >>>>>>>>>>> I installed weka in /usr/local/weka-3-8-1/weka.jar and when
> >>>>>>>>>>> I installed
> >>>>>>>>>> RWeka, it has
> >>>>>>>>>>> another weka.jar in the R package library.  I assume the
> >>>>>>>>>>> latter is used when I try this (in R):
> >>>>>>>>>>>
> >>>>>>>>>>>> WPM("refresh-cache")
> >>>>>>>>>>> Refresh in progress. Please wait...
> >>>>>>>>>>> Unable to download repository zip archve (connect timed out)
> >>>>>>>>>>> - trying legacy
> >>>>>>>>>> routine...
> >>>>>>>>>>> java.net.SocketTimeoutException: connect timed out
> >>>>>>>>>>>
> >>>>>>>>>>> My guess is that the CLASSPATH isn't specified.  Without
> >>>>>>>>>>> setting an environment variable, where do I specify the
> >>>>>>>>>>> class path
> >> option?
> >>>>>>>>>>>
> >>>>>>>>>>> TIA
> >>>>>>>>>>>
> >>>>>>>>>>> Patrick Connolly
> >>>>>>>>>>> Biometrician
> >>>>>>>>>>>
> >>>>>>>>>>> www.plantandfood.co.nz
> >>>>>>>>>>> The New Zealand Institute for Plant & Food Research Limited
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>> The contents of this e-mail are confidential and may be
> >>>>>>>>>>> subject to legal
> >>>>>>>>>> privilege.
> >>>>>>>>>>> If you are not the intended recipient you must not use,
> >>>>>>>>>>> disseminate, distribute
> >>>>>>>>>> or
> >>>>>>>>>>> reproduce all or any part of this e-mail or attachments.  If
> >>>>>>>>>>> you have received
> >>>>>>>>>> this
> >>>>>>>>>>> e-mail in error, please notify the sender and delete all
> >>>>>>>>>>> material pertaining to
> >>>>>>>>>> this
> >>>>>>>>>>> e-mail.  Any opinion or views expressed in this e-mail are
> >>>>>>>>>>> those of the
> >>>>>>>>>> individual
> >>>>>>>>>>> sender and may not represent those of The New Zealand
> >>>>>>>>>>> Institute for Plant
> >>>>>>>>>> and
> >>>>>>>>>>> Food Research Limited.
> >>>>>>>>>>>
> >>>>>>>>>>> _______________________________________________
> >>>>>>>>>>> Wekalist mailing list
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> >>>>>>>>
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> >>>>>> Research Limited.
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> >>>> Research Limited.
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> >>> and Food
> >> Research Limited.
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Re: RWeka setup

Eibe Frank-2
Administrator
Hmm, that should work. It looks like Java is working and is able to find WEKA, otherwise the first command wouldn’t work.

Perhaps try removing the wekafiles folder, which is located in your user home. This will delete any packages you may have downloaded previously and any other WEKA-specific configuration options.

Cheers,
Eibe

> On 2/05/2017, at 10:03 AM, Patrick Connolly <[hidden email]> wrote:
>
> Thanks Eibe.
>
> That got over the proxy issue and the Package Management gui looks like it's working. I'd never have thought of deleting the 'http://' part.
>
>> WPM("refresh-cache")
> Refresh in progress. Please wait...
> [DefaultPackageManager] downloaded 1917 KB
>
> That looks promising,  however, when I try the next thing:
>
>> WPM("list-packages", "installed")
>
> *** caught segfault ***
> address 0x78, cause 'memory not mapped'
>
> Traceback:
> 1: .Call(RJavaCheckExceptions, silent)
> 2: .jcheck()
> 3: .jcall("java/lang/System", "V", "setOut", out)
> 4: WPM("list-packages", "installed")
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
>
> Is that because I don't have a JAVACLASS environment variable?
> I  installed a package using the GUI, hypothesising that there might be a zero length issue, but I still got the same result.
>
> Patrick Connolly
> Biometrician
>
> Postal Address: Plant & Food Research
> Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
> Physical Address: Plant & Food Research
> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
>
>> -----Original Message-----
>> From: [hidden email] [mailto:wekalist-
>> [hidden email]] On Behalf Of Eibe Frank
>> Sent: Monday, 1 May 2017 5:03 p.m.
>> To: Weka machine learning workbench list.
>> Subject: Re: [Wekalist] RWeka setup
>>
>> Try deleting "http://“ from the _JAVA_OPTIONS string.
>>
>> Cheers,
>> Eibe
>>
>>> On 1/05/2017, at 4:18 PM, Patrick Connolly
>> <[hidden email]> wrote:
>>>
>>> Yes,  it starts but then I get
>>>
>>> Unable to download repository zip archve (http://proxy.pfr.co.nz) - trying
>> legacy routine...
>>> java.net.UnknownHostException: http://proxy.pfr.co.nz
>>>
>>> ... which indicates to me that it's trying to do what WPM() tried to do -- same
>> typo.  Then I get a longish list beginning:
>>>
>>>
>> java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:178)
>>>       java.net.Socket.connect(Socket.java:576)
>>>       sun.net.NetworkClient.doConnect(NetworkClient.java:175)
>>>       sun.net.www.http.HttpClient.openServer(HttpClient.java:432)
>>>
>>> That's before trying the  GUI package manager, the result of which produces
>> the same (similar, at least) list again.
>>>
>>>
>>>
>>> Patrick Connolly
>>> Biometrician
>>>
>>> T: +64 9 925 7079
>>> F: +64 9 925 7001
>>> E: [hidden email]
>>> www.plantandfood.co.nz
>>> The New Zealand Institute for Plant & Food Research Limited
>>>
>>> Postal Address: Plant & Food Research
>>> Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
>>> Physical Address: Plant & Food Research
>>> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
>>>
>>>> -----Original Message-----
>>>> From: [hidden email] [mailto:wekalist-
>>>> [hidden email]] On Behalf Of Eibe Frank
>>>> Sent: Monday, 1 May 2017 3:06 p.m.
>>>> To: Weka machine learning workbench list.
>>>> Subject: Re: [Wekalist] RWeka setup
>>>>
>>>> Can you start the WEKA GUIs and then run the package manager GUI?
>>>> Under “Tools” menu in the “GUIChooser” that pops up when you execute
>>>> the .jar file (see my command below).
>>>>
>>>> Cheers,
>>>> Eibe
>>>>
>>>>> On 1/05/2017, at 2:59 PM, Patrick Connolly
>>>> <[hidden email]> wrote:
>>>>>
>>>>> G'day Eibe
>>>>>
>>>>> Thanks for clearing that one up.  Does that indicate that RWeka has
>>>>> everything
>>>> a WEKA installation has?
>>>>>
>>>>> None of our IT folk know anything about Java.  Their only suggestion
>>>>> was that
>>>> something at the sourceforge end was requiring user authentication,
>>>> since  it is accessible by browser.  That idea seems odd to me
>>>> because the browser settings don't require it.
>>>>>
>>>>> My guess is that it's my _JAVA_OPTIONS.
>>>>>
>>>>>> Picked up _JAVA_OPTIONS: -Dhttp.proxyHost=http://proxy.pfr.co.nz
>>>>>> -Dhttp.proxyPort=8080
>>>>> Caching repository metadata, please wait...
>>>>> Refresh in progress. Please wait...
>>>>> Unable to download repository zip archve (http://proxy.pfr.co.nz)
>>>>>
>>>>> The fact that the error message doesn't mention the port number
>>>>> could mean
>>>> my syntax is incorrect.
>>>>>
>>>>> Ideas welcome.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Patrick Connolly
>>>>> Biometrician
>>>>>
>>>>> Postal Address: Plant & Food Research Private Bag 92169, Auckland
>>>>> Mail Centre, Auckland 1142, New Zealand Physical Address: Plant &
>>>>> Food Research
>>>>> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
>>>>>> -----Original Message-----
>>>>>> From: [hidden email] [mailto:wekalist-
>>>>>> [hidden email]] On Behalf Of Eibe Frank
>>>>>> Sent: Thursday, 27 April 2017 2:12 p.m.
>>>>>> To: Weka machine learning workbench list.
>>>>>> Subject: Re: [Wekalist] RWeka setup
>>>>>>
>>>>>> No, you don’t need to install WEKA separately. As you said, RWeka
>>>>>> comes with its own weka.jar.
>>>>>>
>>>>>> You can even start the WEKA GUIs from that .jar by using
>>>>>>
>>>>>> java -jar RWekajars/java/weka.jar
>>>>>>
>>>>>> The WEKA package manager can be accessed through the Tools menu in
>>>>>> the WEKA GUI Chooser that pops up when your run this.
>>>>>>
>>>>>> Cheers,
>>>>>> Eibe
>>>>>>
>>>>>>> On 27/04/2017, at 1:41 PM, Patrick Connolly
>>>>>> <[hidden email]> wrote:
>>>>>>>
>>>>>>> THE proxy server needs to be accessible  from this side only, I
>>>>>>> would have
>>>>>> thought.  It works for everything else..
>>>>>>>
>>>>>>> I can manually download the repository  but the cache is erased if
>>>>>>> I try to
>>>>>> refresh it with the WPM() function.
>>>>>>>
>>>>>>> How  does the proxy system know which weka.jar is in use?  I have
>>>>>>> a suspicion
>>>>>> the 2 are being confused.  For that matter, am I correct in
>>>>>> assuming weka needs to be installed to use RWeka?
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Patrick Connolly
>>>>>>> Biometrician
>>>>>>>
>>>>>>>
>>>>>>> Postal Address: Plant & Food Research Private Bag 92169, Auckland
>>>>>>> Mail Centre, Auckland 1142, New Zealand Physical Address: Plant &
>>>>>>> Food Research
>>>>>>> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
>>>>>>>> -----Original Message-----
>>>>>>>> From: [hidden email] [mailto:wekalist-
>>>>>>>> [hidden email]] On Behalf Of Eibe Frank
>>>>>>>> Sent: Wednesday, 26 April 2017 8:49 p.m.
>>>>>>>> To: Weka machine learning workbench list.
>>>>>>>> Subject: Re: [Wekalist] RWeka setup
>>>>>>>>
>>>>>>>> OK, it seems that your proxy server is not on the public net then.
>>>>>>>>
>>>>>>>> The output for WPM("refresh-cache") should look like this:
>>>>>>>>
>>>>>>>> WPM("refresh-cache")
>>>>>>>> Refresh in progress. Please wait...
>>>>>>>> [DefaultPackageManager] downloaded 1913 KB
>>>>>>>>
>>>>>>>> This works fine for me, both at home (no proxy) and at work
>>>>>>>> (behind a
>>>> proxy).
>>>>>>>>
>>>>>>>> The "Unable to download..." message you are getting means that
>>>>>>>> WEKA cannot connect to the SourceForge site. Can you actually
>>>>>>>> browse to that site in your browser? Perhaps your institution has
>>>>>>>> blocked access to that site? Anyway, I would get in touch with
>>>>>>>> your system
>>>>>> administrators. They might be able to help.
>>>>>>>>
>>>>>>>> Cheers,
>>>>>>>> Eibe
>>>>>>>>
>>>>>>>>> On 26 Apr 2017, at 16:31, Patrick Connolly
>>>>>>>> <[hidden email]> wrote:
>>>>>>>>>
>>>>>>>>> It works for installing R packages - though the syntax for
>>>>>>>>> setting the
>>>>>>>> environment variable is different.
>>>>>>>>>
>>>>>>>>>> ping proxy.pfr.co.nz
>>>>>>>>> PING aklwsa31.pfr.co.nz (172.16.81.6) 56(84) bytes of data.
>>>>>>>>> 64 bytes from 172.16.81.6: icmp_seq=1 ttl=61 time=0.983 ms
>>>>>>>>> 64 bytes from 172.16.81.6: icmp_seq=2 ttl=61 time=1.64 ms
>>>>>>>>>
>>>>>>>>> Patrick Connolly
>>>>>>>>> Biometrician
>>>>>>>>>
>>>>>>>>> T: +64 9 925 7079
>>>>>>>>> F: +64 9 925 7001
>>>>>>>>> E: [hidden email]
>>>>>>>>> www.plantandfood.co.nz
>>>>>>>>> The New Zealand Institute for Plant & Food Research Limited
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> -----Original Message-----
>>>>>>>>>> From: [hidden email] [mailto:wekalist-
>>>>>>>>>> [hidden email]] On Behalf Of Eibe Frank
>>>>>>>>>> Sent: Wednesday, 26 April 2017 3:54 p.m.
>>>>>>>>>> To: Weka machine learning workbench list.
>>>>>>>>>> Subject: Re: [Wekalist] RWeka setup
>>>>>>>>>>
>>>>>>>>>> Are you sure you have the proxy details right?
>>>>>>>>>>
>>>>>>>>>> $ ping proxy.pfr.co.nz
>>>>>>>>>> ping: cannot resolve proxy.pfr.co.nz: Unknown host
>>>>>>>>>>
>>>>>>>>>> Cheers,
>>>>>>>>>> Eibe
>>>>>>>>>>
>>>>>>>>>>> On 26/04/2017, at 3:02 PM, Patrick Connolly
>>>>>>>>>> <[hidden email]> wrote:
>>>>>>>>>>>
>>>>>>>>>>> I followed the directions at
>>>>>>>>>>>
>>>> https://weka.wikispaces.com/Weka+package+manager+does+not+start :
>>>>>>>>>>> Now when I start RWeka, I get
>>>>>>>>>>>
>>>>>>>>>>>> require(RWeka)
>>>>>>>>>>> Loading required package: RWeka Picked up _JAVA_OPTIONS:
>>>>>>>>>>> -Dhttp.proxyHost=http://proxy.pfr.co.nz
>>>>>>>>>>> -Dhttp.proxyPort=8080
>>>>>>>>>>>
>>>>>>>>>>> which indicates to me that I have the syntax correct, but I
>>>>>>>>>>> then get
>>>>>>>>>>>
>>>>>>>>>>>> WPM("refresh-cache")
>>>>>>>>>>> Refresh in progress. Please wait...
>>>>>>>>>>> Unable to download repository zip archve
>>>>>>>>>>> (http://proxy.pfr.co.nz)
>>>>>>>>>>> - trying
>>>>>>>>>> legacy routine...
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> ... that is unless I install the repo manually in
>>>>>>>>>>> ~/wekafiles/repCache.  In that case, there's no message but
>>>>>>>>>>> ~/wekafiles/repCache is deleted.
>>>>>>>>>>>
>>>>>>>>>>> The proxy does not require authentication, so something else is
>> amiss.
>>>>>>>>>>>
>>>>>>>>>>> If I try
>>>>>>>>>>>> WPM("list-packages", "installed")
>>>>>>>>>>>
>>>>>>>>>>> R crashes.
>>>>>>>>>>>
>>>>>>>>>>> Am I on a hiding to nowhere trying to use RWeka without a
>>>>>>>>>>> JAVACLASS environment variable?
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Patrick Connolly
>>>>>>>>>>> Biometrician
>>>>>>>>>>>
>>>>>>>>>>> Postal Address: Plant & Food Research Private Bag 92169,
>>>>>>>>>>> Auckland Mail Centre, Auckland 1142, New Zealand Physical
>>>>>>>>>>> Address: Plant & Food Research
>>>>>>>>>>> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
>>>>>>>>>>>> -----Original Message-----
>>>>>>>>>>>> From: [hidden email] [mailto:wekalist-
>>>>>>>>>>>> [hidden email]] On Behalf Of Eibe Frank
>>>>>>>>>>>> Sent: Monday, 24 April 2017 10:56 p.m.
>>>>>>>>>>>> To: Weka machine learning workbench list.
>>>>>>>>>>>> Subject: Re: [Wekalist] RWeka setup
>>>>>>>>>>>>
>>>>>>>>>>>> The WEKA package manager needs web access to connect to the
>>>>>>>>>>>> SourceForge site. You probably don't have direct access and
>>>>>>>>>>>> instead need to go through a proxy server. Oracle's JVM reads
>>>>>>>>>>>> the _JAVA_OPTIONS environment variable and you can provide
>>>>>>>>>>>> proxy settings via
>>>>>>>>>> that variable, as explained here:
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>> https://weka.wikispaces.com/Weka+package+manager+does+not+start
>>>>>>>>>>>>
>>>>>>>>>>>> However, WEKA may not be able to pop up the GUI for entering
>>>>>>>>>>>> the proxy credentials, so you may have to add those as part
>>>>>>>>>>>> of the environment variable as well, using http.proxyUser and
>>>>>>>>>>>> http.proxyPassword,
>>>>>>>>>> as explained here:
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>>>>>>
>>>>
>> https://weka.wikispaces.com/How+do+I+use+the+package+manager%3F#GUI
>>>>>>>>>>>> %20package%20manager-Using%20a%20HTTP%20proxy
>>>>>>>>>>>>
>>>>>>>>>>>> Cheers,
>>>>>>>>>>>> Eibe
>>>>>>>>>>>>
>>>>>>>>>>>>> On 24 Apr 2017, at 16:33, Patrick Connolly
>>>>>>>>>>>> <[hidden email]> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>> I installed weka in /usr/local/weka-3-8-1/weka.jar and when
>>>>>>>>>>>>> I installed
>>>>>>>>>>>> RWeka, it has
>>>>>>>>>>>>> another weka.jar in the R package library.  I assume the
>>>>>>>>>>>>> latter is used when I try this (in R):
>>>>>>>>>>>>>
>>>>>>>>>>>>>> WPM("refresh-cache")
>>>>>>>>>>>>> Refresh in progress. Please wait...
>>>>>>>>>>>>> Unable to download repository zip archve (connect timed out)
>>>>>>>>>>>>> - trying legacy
>>>>>>>>>>>> routine...
>>>>>>>>>>>>> java.net.SocketTimeoutException: connect timed out
>>>>>>>>>>>>>
>>>>>>>>>>>>> My guess is that the CLASSPATH isn't specified.  Without
>>>>>>>>>>>>> setting an environment variable, where do I specify the
>>>>>>>>>>>>> class path
>>>> option?
>>>>>>>>>>>>>
>>>>>>>>>>>>> TIA
>>>>>>>>>>>>>
>>>>>>>>>>>>> Patrick Connolly
>>>>>>>>>>>>> Biometrician
>>>>>>>>>>>>>
>>>>>>>>>>>>> www.plantandfood.co.nz
>>>>>>>>>>>>> The New Zealand Institute for Plant & Food Research Limited
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> The contents of this e-mail are confidential and may be
>>>>>>>>>>>>> subject to legal
>>>>>>>>>>>> privilege.
>>>>>>>>>>>>> If you are not the intended recipient you must not use,
>>>>>>>>>>>>> disseminate, distribute
>>>>>>>>>>>> or
>>>>>>>>>>>>> reproduce all or any part of this e-mail or attachments.  If
>>>>>>>>>>>>> you have received
>>>>>>>>>>>> this
>>>>>>>>>>>>> e-mail in error, please notify the sender and delete all
>>>>>>>>>>>>> material pertaining to
>>>>>>>>>>>> this
>>>>>>>>>>>>> e-mail.  Any opinion or views expressed in this e-mail are
>>>>>>>>>>>>> those of the
>>>>>>>>>>>> individual
>>>>>>>>>>>>> sender and may not represent those of The New Zealand
>>>>>>>>>>>>> Institute for Plant
>>>>>>>>>>>> and
>>>>>>>>>>>>> Food Research Limited.
>>>>>>>>>>>>>
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> Wekalist mailing list
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>>>>>>>>>>>>> subscription status:
>>>>>>>>>>>> https://list.waikato.ac.nz/mailman/listinfo/wekalist
>>>>>>>>>>>>> List etiquette:
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>>>>>>>>>>>> ml
>>>>>>>>>>>>
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> Wekalist mailing list
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>>>>>>>>>>>> subscription
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>>>>>>>>>>>> ml
>>>>>>>>>>> The contents of this e-mail are confidential and may be
>>>>>>>>>>> subject to legal
>>>>>>>>>> privilege.
>>>>>>>>>>> If you are not the intended recipient you must not use,
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>>>>>>>>>>> If you have received this e-mail in error, please notify the
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>>>>>>>>>>> individual sender and may not represent those of The New
>>>>>>>>>>> Zealand Institute for Plant and Food
>>>>>>>>>> Research Limited.
>>>>>>>>>>>
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>>>>>>>>>>> Wekalist mailing list
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>>>>>>>>>>> l
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
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>>>>>>>>> The contents of this e-mail are confidential and may be subject
>>>>>>>>> to legal
>>>>>>>> privilege.
>>>>>>>>> If you are not the intended recipient you must not use,
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>>>>>>>>> opinion or views expressed in this e-mail are those of the
>>>>>>>>> individual sender and may not represent those of The New Zealand
>>>>>>>>> Institute for Plant and Food
>>>>>>>> Research Limited.
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Wekalist mailing list
>>>>>>>>> Send posts to: [hidden email] List info and
>>>>>>>>> subscription
>>>>>>>>> status: https://list.waikato.ac.nz/mailman/listinfo/wekalist
>>>>>>>>> List etiquette:
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>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Wekalist mailing list
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>>>>>>> The contents of this e-mail are confidential and may be subject to
>>>>>>> legal
>>>>>> privilege.
>>>>>>> If you are not the intended recipient you must not use,
>>>>>>> disseminate, distribute or reproduce all or any part of this e-mail or
>> attachments.
>>>>>>> If you have received this e-mail in error, please notify the
>>>>>>> sender and delete all material pertaining to this e-mail.  Any
>>>>>>> opinion or views expressed in this e-mail are those of the
>>>>>>> individual sender and may not represent those of The New Zealand
>>>>>>> Institute for Plant and Food
>>>>>> Research Limited.
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Wekalist mailing list
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>>>>>>
>>>>>> _______________________________________________
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>>>>>
>>>>> The contents of this e-mail are confidential and may be subject to
>>>>> legal
>>>> privilege.
>>>>> If you are not the intended recipient you must not use, disseminate,
>>>>> distribute or reproduce all or any part of this e-mail or attachments.
>>>>> If you have received this e-mail in error, please notify the sender
>>>>> and delete all material pertaining to this e-mail.  Any opinion or
>>>>> views expressed in this e-mail are those of the individual sender
>>>>> and may not represent those of The New Zealand Institute for Plant
>>>>> and Food
>>>> Research Limited.
>>>>> _______________________________________________
>>>>> Wekalist mailing list
>>>>> Send posts to: [hidden email] List info and
>>>>> subscription
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>>>>> List etiquette:
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>>>>
>>>> _______________________________________________
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>>>
>>> The contents of this e-mail are confidential and may be subject to legal
>> privilege.
>>> If you are not the intended recipient you must not use, disseminate,
>>> distribute or reproduce all or any part of this e-mail or attachments.
>>> If you have received this e-mail in error, please notify the sender
>>> and delete all material pertaining to this e-mail.  Any opinion or
>>> views expressed in this e-mail are those of the individual sender and
>>> may not represent those of The New Zealand Institute for Plant and Food
>> Research Limited.
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>
> The contents of this e-mail are confidential and may be subject to legal privilege.
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Re: RWeka setup

Patrick Connolly
G'day  Eibe,


I've tried deleting ~/wekafiles/ before loading RWeka.
In accordance with the WPM() helpfile, I recreated an empty wekafiles directory.
Upon loading RWeka, empty repCache, native & packages directories are  created into it.
When WPM("refresh-cache") is run, about 200 directories are added to repCache which I guess is as intended.

Then nothing else works.


Patrick Connolly
Biometrician

Postal Address: Plant & Food Research
Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
Physical Address: Plant & Food Research
120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand

> -----Original Message-----
> From: [hidden email] [mailto:wekalist-
> [hidden email]] On Behalf Of Eibe Frank
> Sent: Tuesday, 2 May 2017 11:24 a.m.
> To: Weka machine learning workbench list.
> Subject: Re: [Wekalist] RWeka setup
>
> Hmm, that should work. It looks like Java is working and is able to find WEKA,
> otherwise the first command wouldn’t work.
>
> Perhaps try removing the wekafiles folder, which is located in your user home.
> This will delete any packages you may have downloaded previously and any
> other WEKA-specific configuration options.
>
> Cheers,
> Eibe
>
> > On 2/05/2017, at 10:03 AM, Patrick Connolly
> <[hidden email]> wrote:
> >
> > Thanks Eibe.
> >
> > That got over the proxy issue and the Package Management gui looks like it's
> working. I'd never have thought of deleting the 'http://' part.
> >
> >> WPM("refresh-cache")
> > Refresh in progress. Please wait...
> > [DefaultPackageManager] downloaded 1917 KB
> >
> > That looks promising,  however, when I try the next thing:
> >
> >> WPM("list-packages", "installed")
> >
> > *** caught segfault ***
> > address 0x78, cause 'memory not mapped'
> >
> > Traceback:
> > 1: .Call(RJavaCheckExceptions, silent)
> > 2: .jcheck()
> > 3: .jcall("java/lang/System", "V", "setOut", out)
> > 4: WPM("list-packages", "installed")
> >
> > Possible actions:
> > 1: abort (with core dump, if enabled)
> > 2: normal R exit
> > 3: exit R without saving workspace
> > 4: exit R saving workspace
> >
> > Is that because I don't have a JAVACLASS environment variable?
> > I  installed a package using the GUI, hypothesising that there might be a zero
> length issue, but I still got the same result.
> >
> > Patrick Connolly
> > Biometrician
> >
> > Postal Address: Plant & Food Research
> > Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
> > Physical Address: Plant & Food Research
> > 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
> >
> >> -----Original Message-----
> >> From: [hidden email] [mailto:wekalist-
> >> [hidden email]] On Behalf Of Eibe Frank
> >> Sent: Monday, 1 May 2017 5:03 p.m.
> >> To: Weka machine learning workbench list.
> >> Subject: Re: [Wekalist] RWeka setup
> >>
> >> Try deleting "http://“ from the _JAVA_OPTIONS string.
> >>
> >> Cheers,
> >> Eibe
> >>
> >>> On 1/05/2017, at 4:18 PM, Patrick Connolly
> >> <[hidden email]> wrote:
> >>>
> >>> Yes,  it starts but then I get
> >>>
> >>> Unable to download repository zip archve (http://proxy.pfr.co.nz) - trying
> >> legacy routine...
> >>> java.net.UnknownHostException: http://proxy.pfr.co.nz
> >>>
> >>> ... which indicates to me that it's trying to do what WPM() tried to do --
> same
> >> typo.  Then I get a longish list beginning:
> >>>
> >>>
> >> java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:178)
> >>>       java.net.Socket.connect(Socket.java:576)
> >>>       sun.net.NetworkClient.doConnect(NetworkClient.java:175)
> >>>       sun.net.www.http.HttpClient.openServer(HttpClient.java:432)
> >>>
> >>> That's before trying the  GUI package manager, the result of which produces
> >> the same (similar, at least) list again.
> >>>
> >>>
> >>>
> >>> Patrick Connolly
> >>> Biometrician
> >>>
> >>> T: +64 9 925 7079
> >>> F: +64 9 925 7001
> >>> E: [hidden email]
> >>> www.plantandfood.co.nz
> >>> The New Zealand Institute for Plant & Food Research Limited
> >>>
> >>> Postal Address: Plant & Food Research
> >>> Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
> >>> Physical Address: Plant & Food Research
> >>> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
> >>>
> >>>> -----Original Message-----
> >>>> From: [hidden email] [mailto:wekalist-
> >>>> [hidden email]] On Behalf Of Eibe Frank
> >>>> Sent: Monday, 1 May 2017 3:06 p.m.
> >>>> To: Weka machine learning workbench list.
> >>>> Subject: Re: [Wekalist] RWeka setup
> >>>>
> >>>> Can you start the WEKA GUIs and then run the package manager GUI?
> >>>> Under “Tools” menu in the “GUIChooser” that pops up when you execute
> >>>> the .jar file (see my command below).
> >>>>
> >>>> Cheers,
> >>>> Eibe
> >>>>
> >>>>> On 1/05/2017, at 2:59 PM, Patrick Connolly
> >>>> <[hidden email]> wrote:
> >>>>>
> >>>>> G'day Eibe
> >>>>>
> >>>>> Thanks for clearing that one up.  Does that indicate that RWeka has
> >>>>> everything
> >>>> a WEKA installation has?
> >>>>>
> >>>>> None of our IT folk know anything about Java.  Their only suggestion
> >>>>> was that
> >>>> something at the sourceforge end was requiring user authentication,
> >>>> since  it is accessible by browser.  That idea seems odd to me
> >>>> because the browser settings don't require it.
> >>>>>
> >>>>> My guess is that it's my _JAVA_OPTIONS.
> >>>>>
> >>>>>> Picked up _JAVA_OPTIONS: -Dhttp.proxyHost=http://proxy.pfr.co.nz
> >>>>>> -Dhttp.proxyPort=8080
> >>>>> Caching repository metadata, please wait...
> >>>>> Refresh in progress. Please wait...
> >>>>> Unable to download repository zip archve (http://proxy.pfr.co.nz)
> >>>>>
> >>>>> The fact that the error message doesn't mention the port number
> >>>>> could mean
> >>>> my syntax is incorrect.
> >>>>>
> >>>>> Ideas welcome.
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> Patrick Connolly
> >>>>> Biometrician
> >>>>>
> >>>>> Postal Address: Plant & Food Research Private Bag 92169, Auckland
> >>>>> Mail Centre, Auckland 1142, New Zealand Physical Address: Plant &
> >>>>> Food Research
> >>>>> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
> >>>>>> -----Original Message-----
> >>>>>> From: [hidden email] [mailto:wekalist-
> >>>>>> [hidden email]] On Behalf Of Eibe Frank
> >>>>>> Sent: Thursday, 27 April 2017 2:12 p.m.
> >>>>>> To: Weka machine learning workbench list.
> >>>>>> Subject: Re: [Wekalist] RWeka setup
> >>>>>>
> >>>>>> No, you don’t need to install WEKA separately. As you said, RWeka
> >>>>>> comes with its own weka.jar.
> >>>>>>
> >>>>>> You can even start the WEKA GUIs from that .jar by using
> >>>>>>
> >>>>>> java -jar RWekajars/java/weka.jar
> >>>>>>
> >>>>>> The WEKA package manager can be accessed through the Tools menu in
> >>>>>> the WEKA GUI Chooser that pops up when your run this.
> >>>>>>
> >>>>>> Cheers,
> >>>>>> Eibe
> >>>>>>
> >>>>>>> On 27/04/2017, at 1:41 PM, Patrick Connolly
> >>>>>> <[hidden email]> wrote:
> >>>>>>>
> >>>>>>> THE proxy server needs to be accessible  from this side only, I
> >>>>>>> would have
> >>>>>> thought.  It works for everything else..
> >>>>>>>
> >>>>>>> I can manually download the repository  but the cache is erased if
> >>>>>>> I try to
> >>>>>> refresh it with the WPM() function.
> >>>>>>>
> >>>>>>> How  does the proxy system know which weka.jar is in use?  I have
> >>>>>>> a suspicion
> >>>>>> the 2 are being confused.  For that matter, am I correct in
> >>>>>> assuming weka needs to be installed to use RWeka?
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> Patrick Connolly
> >>>>>>> Biometrician
> >>>>>>>
> >>>>>>>
> >>>>>>> Postal Address: Plant & Food Research Private Bag 92169, Auckland
> >>>>>>> Mail Centre, Auckland 1142, New Zealand Physical Address: Plant &
> >>>>>>> Food Research
> >>>>>>> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
> >>>>>>>> -----Original Message-----
> >>>>>>>> From: [hidden email] [mailto:wekalist-
> >>>>>>>> [hidden email]] On Behalf Of Eibe Frank
> >>>>>>>> Sent: Wednesday, 26 April 2017 8:49 p.m.
> >>>>>>>> To: Weka machine learning workbench list.
> >>>>>>>> Subject: Re: [Wekalist] RWeka setup
> >>>>>>>>
> >>>>>>>> OK, it seems that your proxy server is not on the public net then.
> >>>>>>>>
> >>>>>>>> The output for WPM("refresh-cache") should look like this:
> >>>>>>>>
> >>>>>>>> WPM("refresh-cache")
> >>>>>>>> Refresh in progress. Please wait...
> >>>>>>>> [DefaultPackageManager] downloaded 1913 KB
> >>>>>>>>
> >>>>>>>> This works fine for me, both at home (no proxy) and at work
> >>>>>>>> (behind a
> >>>> proxy).
> >>>>>>>>
> >>>>>>>> The "Unable to download..." message you are getting means that
> >>>>>>>> WEKA cannot connect to the SourceForge site. Can you actually
> >>>>>>>> browse to that site in your browser? Perhaps your institution has
> >>>>>>>> blocked access to that site? Anyway, I would get in touch with
> >>>>>>>> your system
> >>>>>> administrators. They might be able to help.
> >>>>>>>>
> >>>>>>>> Cheers,
> >>>>>>>> Eibe
> >>>>>>>>
> >>>>>>>>> On 26 Apr 2017, at 16:31, Patrick Connolly
> >>>>>>>> <[hidden email]> wrote:
> >>>>>>>>>
> >>>>>>>>> It works for installing R packages - though the syntax for
> >>>>>>>>> setting the
> >>>>>>>> environment variable is different.
> >>>>>>>>>
> >>>>>>>>>> ping proxy.pfr.co.nz
> >>>>>>>>> PING aklwsa31.pfr.co.nz (172.16.81.6) 56(84) bytes of data.
> >>>>>>>>> 64 bytes from 172.16.81.6: icmp_seq=1 ttl=61 time=0.983 ms
> >>>>>>>>> 64 bytes from 172.16.81.6: icmp_seq=2 ttl=61 time=1.64 ms
> >>>>>>>>>
> >>>>>>>>> Patrick Connolly
> >>>>>>>>> Biometrician
> >>>>>>>>>
> >>>>>>>>> T: +64 9 925 7079
> >>>>>>>>> F: +64 9 925 7001
> >>>>>>>>> E: [hidden email]
> >>>>>>>>> www.plantandfood.co.nz
> >>>>>>>>> The New Zealand Institute for Plant & Food Research Limited
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>> -----Original Message-----
> >>>>>>>>>> From: [hidden email] [mailto:wekalist-
> >>>>>>>>>> [hidden email]] On Behalf Of Eibe Frank
> >>>>>>>>>> Sent: Wednesday, 26 April 2017 3:54 p.m.
> >>>>>>>>>> To: Weka machine learning workbench list.
> >>>>>>>>>> Subject: Re: [Wekalist] RWeka setup
> >>>>>>>>>>
> >>>>>>>>>> Are you sure you have the proxy details right?
> >>>>>>>>>>
> >>>>>>>>>> $ ping proxy.pfr.co.nz
> >>>>>>>>>> ping: cannot resolve proxy.pfr.co.nz: Unknown host
> >>>>>>>>>>
> >>>>>>>>>> Cheers,
> >>>>>>>>>> Eibe
> >>>>>>>>>>
> >>>>>>>>>>> On 26/04/2017, at 3:02 PM, Patrick Connolly
> >>>>>>>>>> <[hidden email]> wrote:
> >>>>>>>>>>>
> >>>>>>>>>>> I followed the directions at
> >>>>>>>>>>>
> >>>> https://weka.wikispaces.com/Weka+package+manager+does+not+start :
> >>>>>>>>>>> Now when I start RWeka, I get
> >>>>>>>>>>>
> >>>>>>>>>>>> require(RWeka)
> >>>>>>>>>>> Loading required package: RWeka Picked up _JAVA_OPTIONS:
> >>>>>>>>>>> -Dhttp.proxyHost=http://proxy.pfr.co.nz
> >>>>>>>>>>> -Dhttp.proxyPort=8080
> >>>>>>>>>>>
> >>>>>>>>>>> which indicates to me that I have the syntax correct, but I
> >>>>>>>>>>> then get
> >>>>>>>>>>>
> >>>>>>>>>>>> WPM("refresh-cache")
> >>>>>>>>>>> Refresh in progress. Please wait...
> >>>>>>>>>>> Unable to download repository zip archve
> >>>>>>>>>>> (http://proxy.pfr.co.nz)
> >>>>>>>>>>> - trying
> >>>>>>>>>> legacy routine...
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>> ... that is unless I install the repo manually in
> >>>>>>>>>>> ~/wekafiles/repCache.  In that case, there's no message but
> >>>>>>>>>>> ~/wekafiles/repCache is deleted.
> >>>>>>>>>>>
> >>>>>>>>>>> The proxy does not require authentication, so something else is
> >> amiss.
> >>>>>>>>>>>
> >>>>>>>>>>> If I try
> >>>>>>>>>>>> WPM("list-packages", "installed")
> >>>>>>>>>>>
> >>>>>>>>>>> R crashes.
> >>>>>>>>>>>
> >>>>>>>>>>> Am I on a hiding to nowhere trying to use RWeka without a
> >>>>>>>>>>> JAVACLASS environment variable?
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>> Patrick Connolly
> >>>>>>>>>>> Biometrician
> >>>>>>>>>>>
> >>>>>>>>>>> Postal Address: Plant & Food Research Private Bag 92169,
> >>>>>>>>>>> Auckland Mail Centre, Auckland 1142, New Zealand Physical
> >>>>>>>>>>> Address: Plant & Food Research
> >>>>>>>>>>> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
> >>>>>>>>>>>> -----Original Message-----
> >>>>>>>>>>>> From: [hidden email] [mailto:wekalist-
> >>>>>>>>>>>> [hidden email]] On Behalf Of Eibe Frank
> >>>>>>>>>>>> Sent: Monday, 24 April 2017 10:56 p.m.
> >>>>>>>>>>>> To: Weka machine learning workbench list.
> >>>>>>>>>>>> Subject: Re: [Wekalist] RWeka setup
> >>>>>>>>>>>>
> >>>>>>>>>>>> The WEKA package manager needs web access to connect to the
> >>>>>>>>>>>> SourceForge site. You probably don't have direct access and
> >>>>>>>>>>>> instead need to go through a proxy server. Oracle's JVM reads
> >>>>>>>>>>>> the _JAVA_OPTIONS environment variable and you can provide
> >>>>>>>>>>>> proxy settings via
> >>>>>>>>>> that variable, as explained here:
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>> https://weka.wikispaces.com/Weka+package+manager+does+not+start
> >>>>>>>>>>>>
> >>>>>>>>>>>> However, WEKA may not be able to pop up the GUI for entering
> >>>>>>>>>>>> the proxy credentials, so you may have to add those as part
> >>>>>>>>>>>> of the environment variable as well, using http.proxyUser and
> >>>>>>>>>>>> http.proxyPassword,
> >>>>>>>>>> as explained here:
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>
> >>>>>>
> >>>>
> >>
> https://weka.wikispaces.com/How+do+I+use+the+package+manager%3F#GUI
> >>>>>>>>>>>> %20package%20manager-Using%20a%20HTTP%20proxy
> >>>>>>>>>>>>
> >>>>>>>>>>>> Cheers,
> >>>>>>>>>>>> Eibe
> >>>>>>>>>>>>
> >>>>>>>>>>>>> On 24 Apr 2017, at 16:33, Patrick Connolly
> >>>>>>>>>>>> <[hidden email]> wrote:
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> I installed weka in /usr/local/weka-3-8-1/weka.jar and when
> >>>>>>>>>>>>> I installed
> >>>>>>>>>>>> RWeka, it has
> >>>>>>>>>>>>> another weka.jar in the R package library.  I assume the
> >>>>>>>>>>>>> latter is used when I try this (in R):
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>> WPM("refresh-cache")
> >>>>>>>>>>>>> Refresh in progress. Please wait...
> >>>>>>>>>>>>> Unable to download repository zip archve (connect timed out)
> >>>>>>>>>>>>> - trying legacy
> >>>>>>>>>>>> routine...
> >>>>>>>>>>>>> java.net.SocketTimeoutException: connect timed out
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> My guess is that the CLASSPATH isn't specified.  Without
> >>>>>>>>>>>>> setting an environment variable, where do I specify the
> >>>>>>>>>>>>> class path
> >>>> option?
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> TIA
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Patrick Connolly
> >>>>>>>>>>>>> Biometrician
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> www.plantandfood.co.nz
> >>>>>>>>>>>>> The New Zealand Institute for Plant & Food Research Limited
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> The contents of this e-mail are confidential and may be
> >>>>>>>>>>>>> subject to legal
> >>>>>>>>>>>> privilege.
> >>>>>>>>>>>>> If you are not the intended recipient you must not use,
> >>>>>>>>>>>>> disseminate, distribute
> >>>>>>>>>>>> or
> >>>>>>>>>>>>> reproduce all or any part of this e-mail or attachments.  If
> >>>>>>>>>>>>> you have received
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> >>>>>>>>>>>>> e-mail in error, please notify the sender and delete all
> >>>>>>>>>>>>> material pertaining to
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> >>>>>>>>>>>>> e-mail.  Any opinion or views expressed in this e-mail are
> >>>>>>>>>>>>> those of the
> >>>>>>>>>>>> individual
> >>>>>>>>>>>>> sender and may not represent those of The New Zealand
> >>>>>>>>>>>>> Institute for Plant
> >>>>>>>>>>>> and
> >>>>>>>>>>>>> Food Research Limited.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> _______________________________________________
> >>>>>>>>>>>>> Wekalist mailing list
> >>>>>>>>>>>>> Send posts to: [hidden email] List info and
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> >>>>>>>>>>>> https://list.waikato.ac.nz/mailman/listinfo/wekalist
> >>>>>>>>>>>>> List etiquette:
> >>>>>>>>>>>> http://www.cs.waikato.ac.nz/~ml/weka/mailinglist_etiquette.ht
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> >>>>>>>>>>>>
> >>>>>>>>>>>> _______________________________________________
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> >>>>>>>>>>> If you are not the intended recipient you must not use,
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> >>>>>>>>>>> If you have received this e-mail in error, please notify the
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> >>>>>>>>>> Research Limited.
> >>>>>>>>>>>
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> >>>>>>>>>>> List etiquette:
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> >>>>>>>>>>
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> >>>>>>>>> individual sender and may not represent those of The New Zealand
> >>>>>>>>> Institute for Plant and Food
> >>>>>>>> Research Limited.
> >>>>>>>>>
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> >>>>>>>>> Send posts to: [hidden email] List info and
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> >>>>>>>>> List etiquette:
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> >>>>>>> If you are not the intended recipient you must not use,
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> >>>>>>> individual sender and may not represent those of The New Zealand
> >>>>>>> Institute for Plant and Food
> >>>>>> Research Limited.
> >>>>>>>
> >>>>>>> _______________________________________________
> >>>>>>> Wekalist mailing list
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> >>>>> and may not represent those of The New Zealand Institute for Plant
> >>>>> and Food
> >>>> Research Limited.
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> >> Research Limited.
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Re: RWeka setup

Eibe Frank-2
Administrator
Which versions of R, Java, and the RWeka packages are you using? Also, which operating system? Maybe we can replicate your setup.

Cheers,
Eibe

> On 2/05/2017, at 2:50 PM, Patrick Connolly <[hidden email]> wrote:
>
> G'day  Eibe,
>
>
> I've tried deleting ~/wekafiles/ before loading RWeka.
> In accordance with the WPM() helpfile, I recreated an empty wekafiles directory.
> Upon loading RWeka, empty repCache, native & packages directories are  created into it.
> When WPM("refresh-cache") is run, about 200 directories are added to repCache which I guess is as intended.
>
> Then nothing else works.
>
>
> Patrick Connolly
> Biometrician
>
> Postal Address: Plant & Food Research
> Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
> Physical Address: Plant & Food Research
> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
>
>> -----Original Message-----
>> From: [hidden email] [mailto:wekalist-
>> [hidden email]] On Behalf Of Eibe Frank
>> Sent: Tuesday, 2 May 2017 11:24 a.m.
>> To: Weka machine learning workbench list.
>> Subject: Re: [Wekalist] RWeka setup
>>
>> Hmm, that should work. It looks like Java is working and is able to find WEKA,
>> otherwise the first command wouldn’t work.
>>
>> Perhaps try removing the wekafiles folder, which is located in your user home.
>> This will delete any packages you may have downloaded previously and any
>> other WEKA-specific configuration options.
>>
>> Cheers,
>> Eibe
>>
>>> On 2/05/2017, at 10:03 AM, Patrick Connolly
>> <[hidden email]> wrote:
>>>
>>> Thanks Eibe.
>>>
>>> That got over the proxy issue and the Package Management gui looks like it's
>> working. I'd never have thought of deleting the 'http://' part.
>>>
>>>> WPM("refresh-cache")
>>> Refresh in progress. Please wait...
>>> [DefaultPackageManager] downloaded 1917 KB
>>>
>>> That looks promising,  however, when I try the next thing:
>>>
>>>> WPM("list-packages", "installed")
>>>
>>> *** caught segfault ***
>>> address 0x78, cause 'memory not mapped'
>>>
>>> Traceback:
>>> 1: .Call(RJavaCheckExceptions, silent)
>>> 2: .jcheck()
>>> 3: .jcall("java/lang/System", "V", "setOut", out)
>>> 4: WPM("list-packages", "installed")
>>>
>>> Possible actions:
>>> 1: abort (with core dump, if enabled)
>>> 2: normal R exit
>>> 3: exit R without saving workspace
>>> 4: exit R saving workspace
>>>
>>> Is that because I don't have a JAVACLASS environment variable?
>>> I  installed a package using the GUI, hypothesising that there might be a zero
>> length issue, but I still got the same result.
>>>
>>> Patrick Connolly
>>> Biometrician
>>>
>>> Postal Address: Plant & Food Research
>>> Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
>>> Physical Address: Plant & Food Research
>>> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
>>>
>>>> -----Original Message-----
>>>> From: [hidden email] [mailto:wekalist-
>>>> [hidden email]] On Behalf Of Eibe Frank
>>>> Sent: Monday, 1 May 2017 5:03 p.m.
>>>> To: Weka machine learning workbench list.
>>>> Subject: Re: [Wekalist] RWeka setup
>>>>
>>>> Try deleting "http://“ from the _JAVA_OPTIONS string.
>>>>
>>>> Cheers,
>>>> Eibe
>>>>
>>>>> On 1/05/2017, at 4:18 PM, Patrick Connolly
>>>> <[hidden email]> wrote:
>>>>>
>>>>> Yes,  it starts but then I get
>>>>>
>>>>> Unable to download repository zip archve (http://proxy.pfr.co.nz) - trying
>>>> legacy routine...
>>>>> java.net.UnknownHostException: http://proxy.pfr.co.nz
>>>>>
>>>>> ... which indicates to me that it's trying to do what WPM() tried to do --
>> same
>>>> typo.  Then I get a longish list beginning:
>>>>>
>>>>>
>>>> java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:178)
>>>>>      java.net.Socket.connect(Socket.java:576)
>>>>>      sun.net.NetworkClient.doConnect(NetworkClient.java:175)
>>>>>      sun.net.www.http.HttpClient.openServer(HttpClient.java:432)
>>>>>
>>>>> That's before trying the  GUI package manager, the result of which produces
>>>> the same (similar, at least) list again.
>>>>>
>>>>>
>>>>>
>>>>> Patrick Connolly
>>>>> Biometrician
>>>>>
>>>>> T: +64 9 925 7079
>>>>> F: +64 9 925 7001
>>>>> E: [hidden email]
>>>>> www.plantandfood.co.nz
>>>>> The New Zealand Institute for Plant & Food Research Limited
>>>>>
>>>>> Postal Address: Plant & Food Research
>>>>> Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
>>>>> Physical Address: Plant & Food Research
>>>>> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
>>>>>
>>>>>> -----Original Message-----
>>>>>> From: [hidden email] [mailto:wekalist-
>>>>>> [hidden email]] On Behalf Of Eibe Frank
>>>>>> Sent: Monday, 1 May 2017 3:06 p.m.
>>>>>> To: Weka machine learning workbench list.
>>>>>> Subject: Re: [Wekalist] RWeka setup
>>>>>>
>>>>>> Can you start the WEKA GUIs and then run the package manager GUI?
>>>>>> Under “Tools” menu in the “GUIChooser” that pops up when you execute
>>>>>> the .jar file (see my command below).
>>>>>>
>>>>>> Cheers,
>>>>>> Eibe
>>>>>>
>>>>>>> On 1/05/2017, at 2:59 PM, Patrick Connolly
>>>>>> <[hidden email]> wrote:
>>>>>>>
>>>>>>> G'day Eibe
>>>>>>>
>>>>>>> Thanks for clearing that one up.  Does that indicate that RWeka has
>>>>>>> everything
>>>>>> a WEKA installation has?
>>>>>>>
>>>>>>> None of our IT folk know anything about Java.  Their only suggestion
>>>>>>> was that
>>>>>> something at the sourceforge end was requiring user authentication,
>>>>>> since  it is accessible by browser.  That idea seems odd to me
>>>>>> because the browser settings don't require it.
>>>>>>>
>>>>>>> My guess is that it's my _JAVA_OPTIONS.
>>>>>>>
>>>>>>>> Picked up _JAVA_OPTIONS: -Dhttp.proxyHost=http://proxy.pfr.co.nz
>>>>>>>> -Dhttp.proxyPort=8080
>>>>>>> Caching repository metadata, please wait...
>>>>>>> Refresh in progress. Please wait...
>>>>>>> Unable to download repository zip archve (http://proxy.pfr.co.nz)
>>>>>>>
>>>>>>> The fact that the error message doesn't mention the port number
>>>>>>> could mean
>>>>>> my syntax is incorrect.
>>>>>>>
>>>>>>> Ideas welcome.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Patrick Connolly
>>>>>>> Biometrician
>>>>>>>
>>>>>>> Postal Address: Plant & Food Research Private Bag 92169, Auckland
>>>>>>> Mail Centre, Auckland 1142, New Zealand Physical Address: Plant &
>>>>>>> Food Research
>>>>>>> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
>>>>>>>> -----Original Message-----
>>>>>>>> From: [hidden email] [mailto:wekalist-
>>>>>>>> [hidden email]] On Behalf Of Eibe Frank
>>>>>>>> Sent: Thursday, 27 April 2017 2:12 p.m.
>>>>>>>> To: Weka machine learning workbench list.
>>>>>>>> Subject: Re: [Wekalist] RWeka setup
>>>>>>>>
>>>>>>>> No, you don’t need to install WEKA separately. As you said, RWeka
>>>>>>>> comes with its own weka.jar.
>>>>>>>>
>>>>>>>> You can even start the WEKA GUIs from that .jar by using
>>>>>>>>
>>>>>>>> java -jar RWekajars/java/weka.jar
>>>>>>>>
>>>>>>>> The WEKA package manager can be accessed through the Tools menu in
>>>>>>>> the WEKA GUI Chooser that pops up when your run this.
>>>>>>>>
>>>>>>>> Cheers,
>>>>>>>> Eibe
>>>>>>>>
>>>>>>>>> On 27/04/2017, at 1:41 PM, Patrick Connolly
>>>>>>>> <[hidden email]> wrote:
>>>>>>>>>
>>>>>>>>> THE proxy server needs to be accessible  from this side only, I
>>>>>>>>> would have
>>>>>>>> thought.  It works for everything else..
>>>>>>>>>
>>>>>>>>> I can manually download the repository  but the cache is erased if
>>>>>>>>> I try to
>>>>>>>> refresh it with the WPM() function.
>>>>>>>>>
>>>>>>>>> How  does the proxy system know which weka.jar is in use?  I have
>>>>>>>>> a suspicion
>>>>>>>> the 2 are being confused.  For that matter, am I correct in
>>>>>>>> assuming weka needs to be installed to use RWeka?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Patrick Connolly
>>>>>>>>> Biometrician
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Postal Address: Plant & Food Research Private Bag 92169, Auckland
>>>>>>>>> Mail Centre, Auckland 1142, New Zealand Physical Address: Plant &
>>>>>>>>> Food Research
>>>>>>>>> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
>>>>>>>>>> -----Original Message-----
>>>>>>>>>> From: [hidden email] [mailto:wekalist-
>>>>>>>>>> [hidden email]] On Behalf Of Eibe Frank
>>>>>>>>>> Sent: Wednesday, 26 April 2017 8:49 p.m.
>>>>>>>>>> To: Weka machine learning workbench list.
>>>>>>>>>> Subject: Re: [Wekalist] RWeka setup
>>>>>>>>>>
>>>>>>>>>> OK, it seems that your proxy server is not on the public net then.
>>>>>>>>>>
>>>>>>>>>> The output for WPM("refresh-cache") should look like this:
>>>>>>>>>>
>>>>>>>>>> WPM("refresh-cache")
>>>>>>>>>> Refresh in progress. Please wait...
>>>>>>>>>> [DefaultPackageManager] downloaded 1913 KB
>>>>>>>>>>
>>>>>>>>>> This works fine for me, both at home (no proxy) and at work
>>>>>>>>>> (behind a
>>>>>> proxy).
>>>>>>>>>>
>>>>>>>>>> The "Unable to download..." message you are getting means that
>>>>>>>>>> WEKA cannot connect to the SourceForge site. Can you actually
>>>>>>>>>> browse to that site in your browser? Perhaps your institution has
>>>>>>>>>> blocked access to that site? Anyway, I would get in touch with
>>>>>>>>>> your system
>>>>>>>> administrators. They might be able to help.
>>>>>>>>>>
>>>>>>>>>> Cheers,
>>>>>>>>>> Eibe
>>>>>>>>>>
>>>>>>>>>>> On 26 Apr 2017, at 16:31, Patrick Connolly
>>>>>>>>>> <[hidden email]> wrote:
>>>>>>>>>>>
>>>>>>>>>>> It works for installing R packages - though the syntax for
>>>>>>>>>>> setting the
>>>>>>>>>> environment variable is different.
>>>>>>>>>>>
>>>>>>>>>>>> ping proxy.pfr.co.nz
>>>>>>>>>>> PING aklwsa31.pfr.co.nz (172.16.81.6) 56(84) bytes of data.
>>>>>>>>>>> 64 bytes from 172.16.81.6: icmp_seq=1 ttl=61 time=0.983 ms
>>>>>>>>>>> 64 bytes from 172.16.81.6: icmp_seq=2 ttl=61 time=1.64 ms
>>>>>>>>>>>
>>>>>>>>>>> Patrick Connolly
>>>>>>>>>>> Biometrician
>>>>>>>>>>>
>>>>>>>>>>> T: +64 9 925 7079
>>>>>>>>>>> F: +64 9 925 7001
>>>>>>>>>>> E: [hidden email]
>>>>>>>>>>> www.plantandfood.co.nz
>>>>>>>>>>> The New Zealand Institute for Plant & Food Research Limited
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> -----Original Message-----
>>>>>>>>>>>> From: [hidden email] [mailto:wekalist-
>>>>>>>>>>>> [hidden email]] On Behalf Of Eibe Frank
>>>>>>>>>>>> Sent: Wednesday, 26 April 2017 3:54 p.m.
>>>>>>>>>>>> To: Weka machine learning workbench list.
>>>>>>>>>>>> Subject: Re: [Wekalist] RWeka setup
>>>>>>>>>>>>
>>>>>>>>>>>> Are you sure you have the proxy details right?
>>>>>>>>>>>>
>>>>>>>>>>>> $ ping proxy.pfr.co.nz
>>>>>>>>>>>> ping: cannot resolve proxy.pfr.co.nz: Unknown host
>>>>>>>>>>>>
>>>>>>>>>>>> Cheers,
>>>>>>>>>>>> Eibe
>>>>>>>>>>>>
>>>>>>>>>>>>> On 26/04/2017, at 3:02 PM, Patrick Connolly
>>>>>>>>>>>> <[hidden email]> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>> I followed the directions at
>>>>>>>>>>>>>
>>>>>> https://weka.wikispaces.com/Weka+package+manager+does+not+start :
>>>>>>>>>>>>> Now when I start RWeka, I get
>>>>>>>>>>>>>
>>>>>>>>>>>>>> require(RWeka)
>>>>>>>>>>>>> Loading required package: RWeka Picked up _JAVA_OPTIONS:
>>>>>>>>>>>>> -Dhttp.proxyHost=http://proxy.pfr.co.nz
>>>>>>>>>>>>> -Dhttp.proxyPort=8080
>>>>>>>>>>>>>
>>>>>>>>>>>>> which indicates to me that I have the syntax correct, but I
>>>>>>>>>>>>> then get
>>>>>>>>>>>>>
>>>>>>>>>>>>>> WPM("refresh-cache")
>>>>>>>>>>>>> Refresh in progress. Please wait...
>>>>>>>>>>>>> Unable to download repository zip archve
>>>>>>>>>>>>> (http://proxy.pfr.co.nz)
>>>>>>>>>>>>> - trying
>>>>>>>>>>>> legacy routine...
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> ... that is unless I install the repo manually in
>>>>>>>>>>>>> ~/wekafiles/repCache.  In that case, there's no message but
>>>>>>>>>>>>> ~/wekafiles/repCache is deleted.
>>>>>>>>>>>>>
>>>>>>>>>>>>> The proxy does not require authentication, so something else is
>>>> amiss.
>>>>>>>>>>>>>
>>>>>>>>>>>>> If I try
>>>>>>>>>>>>>> WPM("list-packages", "installed")
>>>>>>>>>>>>>
>>>>>>>>>>>>> R crashes.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Am I on a hiding to nowhere trying to use RWeka without a
>>>>>>>>>>>>> JAVACLASS environment variable?
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Patrick Connolly
>>>>>>>>>>>>> Biometrician
>>>>>>>>>>>>>
>>>>>>>>>>>>> Postal Address: Plant & Food Research Private Bag 92169,
>>>>>>>>>>>>> Auckland Mail Centre, Auckland 1142, New Zealand Physical
>>>>>>>>>>>>> Address: Plant & Food Research
>>>>>>>>>>>>> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
>>>>>>>>>>>>>> -----Original Message-----
>>>>>>>>>>>>>> From: [hidden email] [mailto:wekalist-
>>>>>>>>>>>>>> [hidden email]] On Behalf Of Eibe Frank
>>>>>>>>>>>>>> Sent: Monday, 24 April 2017 10:56 p.m.
>>>>>>>>>>>>>> To: Weka machine learning workbench list.
>>>>>>>>>>>>>> Subject: Re: [Wekalist] RWeka setup
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> The WEKA package manager needs web access to connect to the
>>>>>>>>>>>>>> SourceForge site. You probably don't have direct access and
>>>>>>>>>>>>>> instead need to go through a proxy server. Oracle's JVM reads
>>>>>>>>>>>>>> the _JAVA_OPTIONS environment variable and you can provide
>>>>>>>>>>>>>> proxy settings via
>>>>>>>>>>>> that variable, as explained here:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>> https://weka.wikispaces.com/Weka+package+manager+does+not+start
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> However, WEKA may not be able to pop up the GUI for entering
>>>>>>>>>>>>>> the proxy credentials, so you may have to add those as part
>>>>>>>>>>>>>> of the environment variable as well, using http.proxyUser and
>>>>>>>>>>>>>> http.proxyPassword,
>>>>>>>>>>>> as explained here:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>>>>>>
>>>>
>> https://weka.wikispaces.com/How+do+I+use+the+package+manager%3F#GUI
>>>>>>>>>>>>>> %20package%20manager-Using%20a%20HTTP%20proxy
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>>> Eibe
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On 24 Apr 2017, at 16:33, Patrick Connolly
>>>>>>>>>>>>>> <[hidden email]> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> I installed weka in /usr/local/weka-3-8-1/weka.jar and when
>>>>>>>>>>>>>>> I installed
>>>>>>>>>>>>>> RWeka, it has
>>>>>>>>>>>>>>> another weka.jar in the R package library.  I assume the
>>>>>>>>>>>>>>> latter is used when I try this (in R):
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> WPM("refresh-cache")
>>>>>>>>>>>>>>> Refresh in progress. Please wait...
>>>>>>>>>>>>>>> Unable to download repository zip archve (connect timed out)
>>>>>>>>>>>>>>> - trying legacy
>>>>>>>>>>>>>> routine...
>>>>>>>>>>>>>>> java.net.SocketTimeoutException: connect timed out
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> My guess is that the CLASSPATH isn't specified.  Without
>>>>>>>>>>>>>>> setting an environment variable, where do I specify the
>>>>>>>>>>>>>>> class path
>>>>>> option?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> TIA
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Patrick Connolly
>>>>>>>>>>>>>>> Biometrician
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> www.plantandfood.co.nz
>>>>>>>>>>>>>>> The New Zealand Institute for Plant & Food Research Limited
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> The contents of this e-mail are confidential and may be
>>>>>>>>>>>>>>> subject to legal
>>>>>>>>>>>>>> privilege.
>>>>>>>>>>>>>>> If you are not the intended recipient you must not use,
>>>>>>>>>>>>>>> disseminate, distribute
>>>>>>>>>>>>>> or
>>>>>>>>>>>>>>> reproduce all or any part of this e-mail or attachments.  If
>>>>>>>>>>>>>>> you have received
>>>>>>>>>>>>>> this
>>>>>>>>>>>>>>> e-mail in error, please notify the sender and delete all
>>>>>>>>>>>>>>> material pertaining to
>>>>>>>>>>>>>> this
>>>>>>>>>>>>>>> e-mail.  Any opinion or views expressed in this e-mail are
>>>>>>>>>>>>>>> those of the
>>>>>>>>>>>>>> individual
>>>>>>>>>>>>>>> sender and may not represent those of The New Zealand
>>>>>>>>>>>>>>> Institute for Plant
>>>>>>>>>>>>>> and
>>>>>>>>>>>>>>> Food Research Limited.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>> Wekalist mailing list
>>>>>>>>>>>>>>> Send posts to: [hidden email] 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.ht
>>>>>>>>>>>>>> ml
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>> Wekalist mailing list
>>>>>>>>>>>>>> Send posts to: [hidden email] 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.ht
>>>>>>>>>>>>>> ml
>>>>>>>>>>>>> The contents of this e-mail are confidential and may be
>>>>>>>>>>>>> subject to legal
>>>>>>>>>>>> privilege.
>>>>>>>>>>>>> If you are not the intended recipient you must not use,
>>>>>>>>>>>>> disseminate, distribute or reproduce all or any part of this
>>>>>>>>>>>>> e-mail or
>>>>>>>> attachments.
>>>>>>>>>>>>> If you have received this e-mail in error, please notify the
>>>>>>>>>>>>> sender and delete all material pertaining to this e-mail.  Any
>>>>>>>>>>>>> opinion or views expressed in this e-mail are those of the
>>>>>>>>>>>>> individual sender and may not represent those of The New
>>>>>>>>>>>>> Zealand Institute for Plant and Food
>>>>>>>>>>>> Research Limited.
>>>>>>>>>>>>>
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> Wekalist mailing list
>>>>>>>>>>>>> Send posts to: [hidden email] 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.htm
>>>>>>>>>>>>> l
>>>>>>>>>>>>
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> Wekalist mailing list
>>>>>>>>>>>> Send posts to: [hidden email] 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
>>>>>>>>>>> The contents of this e-mail are confidential and may be subject
>>>>>>>>>>> to legal
>>>>>>>>>> privilege.
>>>>>>>>>>> If you are not the intended recipient you must not use,
>>>>>>>>>>> disseminate, distribute or reproduce all or any part of this
>>>>>>>>>>> e-mail or
>>>>>> attachments.
>>>>>>>>>>> If you have received this e-mail in error, please notify the
>>>>>>>>>>> sender and delete all material pertaining to this e-mail.  Any
>>>>>>>>>>> opinion or views expressed in this e-mail are those of the
>>>>>>>>>>> individual sender and may not represent those of The New Zealand
>>>>>>>>>>> Institute for Plant and Food
>>>>>>>>>> Research Limited.
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Wekalist mailing list
>>>>>>>>>>> Send posts to: [hidden email] 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: [hidden email] 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
>>>>>>>>> The contents of this e-mail are confidential and may be subject to
>>>>>>>>> legal
>>>>>>>> privilege.
>>>>>>>>> If you are not the intended recipient you must not use,
>>>>>>>>> disseminate, distribute or reproduce all or any part of this e-mail or
>>>> attachments.
>>>>>>>>> If you have received this e-mail in error, please notify the
>>>>>>>>> sender and delete all material pertaining to this e-mail.  Any
>>>>>>>>> opinion or views expressed in this e-mail are those of the
>>>>>>>>> individual sender and may not represent those of The New Zealand
>>>>>>>>> Institute for Plant and Food
>>>>>>>> Research Limited.
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Wekalist mailing list
>>>>>>>>> Send posts to: [hidden email] 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: [hidden email] 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
>>>>>>>
>>>>>>> The contents of this e-mail are confidential and may be subject to
>>>>>>> legal
>>>>>> privilege.
>>>>>>> If you are not the intended recipient you must not use, disseminate,
>>>>>>> distribute or reproduce all or any part of this e-mail or attachments.
>>>>>>> If you have received this e-mail in error, please notify the sender
>>>>>>> and delete all material pertaining to this e-mail.  Any opinion or
>>>>>>> views expressed in this e-mail are those of the individual sender
>>>>>>> and may not represent those of The New Zealand Institute for Plant
>>>>>>> and Food
>>>>>> Research Limited.
>>>>>>> _______________________________________________
>>>>>>> Wekalist mailing list
>>>>>>> Send posts to: [hidden email] 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: [hidden email] 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
>>>>>
>>>>> The contents of this e-mail are confidential and may be subject to legal
>>>> privilege.
>>>>> If you are not the intended recipient you must not use, disseminate,
>>>>> distribute or reproduce all or any part of this e-mail or attachments.
>>>>> If you have received this e-mail in error, please notify the sender
>>>>> and delete all material pertaining to this e-mail.  Any opinion or
>>>>> views expressed in this e-mail are those of the individual sender and
>>>>> may not represent those of The New Zealand Institute for Plant and Food
>>>> Research Limited.
>>>>> _______________________________________________
>>>>> Wekalist mailing list
>>>>> Send posts to: [hidden email] 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: [hidden email] 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
>>>
>>> The contents of this e-mail are confidential and may be subject to legal
>> privilege.
>>> If you are not the intended recipient you must not use, disseminate, distribute
>> or
>>> reproduce all or any part of this e-mail or attachments.  If you have received
>> this
>>> e-mail in error, please notify the sender and delete all material pertaining to
>> this
>>> e-mail.  Any opinion or views expressed in this e-mail are those of the
>> individual
>>> sender and may not represent those of The New Zealand Institute for Plant
>> and
>>> Food Research Limited.
>>> _______________________________________________
>>> Wekalist mailing list
>>> Send posts to: [hidden email]
>>> 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: [hidden email]
>> 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
>
> The contents of this e-mail are confidential and may be subject to legal privilege.
> If you are not the intended recipient you must not use, disseminate, distribute or
> reproduce all or any part of this e-mail or attachments.  If you have received this
> e-mail in error, please notify the sender and delete all material pertaining to this
> e-mail.  Any opinion or views expressed in this e-mail are those of the individual
> sender and may not represent those of The New Zealand Institute for Plant and
> Food Research Limited.
> _______________________________________________
> Wekalist mailing list
> Send posts to: [hidden email]
> 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

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Re: RWeka setup

Patrick Connolly
> version
               _
platform       x86_64-pc-linux-gnu
arch           x86_64
os             linux-gnu
system         x86_64, linux-gnu
status
major          3
minor          3.3
year           2017
month          03
day            06
svn rev        72310
language       R
version.string R version 3.3.3 (2017-03-06)
nickname       Another Canoe
>
> library(help = "RWeka")

                Information on package ‘RWeka’

Description:

Package:              RWeka
Version:              0.4-33

I'm not familiar enough with Java to know how to find its version, but
it will be whatever an up to date Linux Mint 17.2 has.


Patrick Connolly
Biometrician

Postal Address: Plant & Food Research
Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
Physical Address: Plant & Food Research
120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand

> -----Original Message-----
> From: [hidden email] [mailto:wekalist-
> [hidden email]] On Behalf Of Eibe Frank
> Sent: Tuesday, 2 May 2017 3:42 p.m.
> To: Weka machine learning workbench list.
> Subject: Re: [Wekalist] RWeka setup
>
> Which versions of R, Java, and the RWeka packages are you using? Also, which
> operating system? Maybe we can replicate your setup.
>
> Cheers,
> Eibe
>
> > On 2/05/2017, at 2:50 PM, Patrick Connolly
> <[hidden email]> wrote:
> >
> > G'day  Eibe,
> >
> >
> > I've tried deleting ~/wekafiles/ before loading RWeka.
> > In accordance with the WPM() helpfile, I recreated an empty wekafiles
> directory.
> > Upon loading RWeka, empty repCache, native & packages directories are
> created into it.
> > When WPM("refresh-cache") is run, about 200 directories are added to
> repCache which I guess is as intended.
> >
> > Then nothing else works.
> >
> >
> > Patrick Connolly
> > Biometrician
> >
> > Postal Address: Plant & Food Research
> > Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
> > Physical Address: Plant & Food Research
> > 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
> >
> >> -----Original Message-----
> >> From: [hidden email] [mailto:wekalist-
> >> [hidden email]] On Behalf Of Eibe Frank
> >> Sent: Tuesday, 2 May 2017 11:24 a.m.
> >> To: Weka machine learning workbench list.
> >> Subject: Re: [Wekalist] RWeka setup
> >>
> >> Hmm, that should work. It looks like Java is working and is able to
> >> find WEKA, otherwise the first command wouldn’t work.
> >>
> >> Perhaps try removing the wekafiles folder, which is located in your user
> home.
> >> This will delete any packages you may have downloaded previously and
> >> any other WEKA-specific configuration options.
> >>
> >> Cheers,
> >> Eibe
> >>
> >>> On 2/05/2017, at 10:03 AM, Patrick Connolly
> >> <[hidden email]> wrote:
> >>>
> >>> Thanks Eibe.
> >>>
> >>> That got over the proxy issue and the Package Management gui looks
> >>> like it's
> >> working. I'd never have thought of deleting the 'http://' part.
> >>>
> >>>> WPM("refresh-cache")
> >>> Refresh in progress. Please wait...
> >>> [DefaultPackageManager] downloaded 1917 KB
> >>>
> >>> That looks promising,  however, when I try the next thing:
> >>>
> >>>> WPM("list-packages", "installed")
> >>>
> >>> *** caught segfault ***
> >>> address 0x78, cause 'memory not mapped'
> >>>
> >>> Traceback:
> >>> 1: .Call(RJavaCheckExceptions, silent)
> >>> 2: .jcheck()
> >>> 3: .jcall("java/lang/System", "V", "setOut", out)
> >>> 4: WPM("list-packages", "installed")
> >>>
> >>> Possible actions:
> >>> 1: abort (with core dump, if enabled)
> >>> 2: normal R exit
> >>> 3: exit R without saving workspace
> >>> 4: exit R saving workspace
> >>>
> >>> Is that because I don't have a JAVACLASS environment variable?
> >>> I  installed a package using the GUI, hypothesising that there might
> >>> be a zero
> >> length issue, but I still got the same result.
> >>>
> >>> Patrick Connolly
> >>> Biometrician
> >>>
> >>> Postal Address: Plant & Food Research Private Bag 92169, Auckland
> >>> Mail Centre, Auckland 1142, New Zealand Physical Address: Plant &
> >>> Food Research
> >>> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
> >>>
> >>>> -----Original Message-----
> >>>> From: [hidden email] [mailto:wekalist-
> >>>> [hidden email]] On Behalf Of Eibe Frank
> >>>> Sent: Monday, 1 May 2017 5:03 p.m.
> >>>> To: Weka machine learning workbench list.
> >>>> Subject: Re: [Wekalist] RWeka setup
> >>>>
> >>>> Try deleting "http://“ from the _JAVA_OPTIONS string.
> >>>>
> >>>> Cheers,
> >>>> Eibe
> >>>>
> >>>>> On 1/05/2017, at 4:18 PM, Patrick Connolly
> >>>> <[hidden email]> wrote:
> >>>>>
> >>>>> Yes,  it starts but then I get
> >>>>>
> >>>>> Unable to download repository zip archve (http://proxy.pfr.co.nz)
> >>>>> - trying
> >>>> legacy routine...
> >>>>> java.net.UnknownHostException: http://proxy.pfr.co.nz
> >>>>>
> >>>>> ... which indicates to me that it's trying to do what WPM() tried
> >>>>> to do --
> >> same
> >>>> typo.  Then I get a longish list beginning:
> >>>>>
> >>>>>
> >>>> java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.ja
> >>>> va:178)
> >>>>>      java.net.Socket.connect(Socket.java:576)
> >>>>>      sun.net.NetworkClient.doConnect(NetworkClient.java:175)
> >>>>>      sun.net.www.http.HttpClient.openServer(HttpClient.java:432)
> >>>>>
> >>>>> That's before trying the  GUI package manager, the result of which
> >>>>> produces
> >>>> the same (similar, at least) list again.
> >>>>>
> >>>>>
> >>>>>
> >>>>> Patrick Connolly
> >>>>> Biometrician
> >>>>>
> >>>>> T: +64 9 925 7079
> >>>>> F: +64 9 925 7001
> >>>>> E: [hidden email]
> >>>>> www.plantandfood.co.nz
> >>>>> The New Zealand Institute for Plant & Food Research Limited
> >>>>>
> >>>>> Postal Address: Plant & Food Research Private Bag 92169, Auckland
> >>>>> Mail Centre, Auckland 1142, New Zealand Physical Address: Plant &
> >>>>> Food Research
> >>>>> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
> >>>>>
> >>>>>> -----Original Message-----
> >>>>>> From: [hidden email] [mailto:wekalist-
> >>>>>> [hidden email]] On Behalf Of Eibe Frank
> >>>>>> Sent: Monday, 1 May 2017 3:06 p.m.
> >>>>>> To: Weka machine learning workbench list.
> >>>>>> Subject: Re: [Wekalist] RWeka setup
> >>>>>>
> >>>>>> Can you start the WEKA GUIs and then run the package manager GUI?
> >>>>>> Under “Tools” menu in the “GUIChooser” that pops up when you
> >>>>>> execute the .jar file (see my command below).
> >>>>>>
> >>>>>> Cheers,
> >>>>>> Eibe
> >>>>>>
> >>>>>>> On 1/05/2017, at 2:59 PM, Patrick Connolly
> >>>>>> <[hidden email]> wrote:
> >>>>>>>
> >>>>>>> G'day Eibe
> >>>>>>>
> >>>>>>> Thanks for clearing that one up.  Does that indicate that RWeka
> >>>>>>> has everything
> >>>>>> a WEKA installation has?
> >>>>>>>
> >>>>>>> None of our IT folk know anything about Java.  Their only
> >>>>>>> suggestion was that
> >>>>>> something at the sourceforge end was requiring user
> >>>>>> authentication, since  it is accessible by browser.  That idea
> >>>>>> seems odd to me because the browser settings don't require it.
> >>>>>>>
> >>>>>>> My guess is that it's my _JAVA_OPTIONS.
> >>>>>>>
> >>>>>>>> Picked up _JAVA_OPTIONS:
> >>>>>>>> -Dhttp.proxyHost=http://proxy.pfr.co.nz
> >>>>>>>> -Dhttp.proxyPort=8080
> >>>>>>> Caching repository metadata, please wait...
> >>>>>>> Refresh in progress. Please wait...
> >>>>>>> Unable to download repository zip archve
> >>>>>>> (http://proxy.pfr.co.nz)
> >>>>>>>
> >>>>>>> The fact that the error message doesn't mention the port number
> >>>>>>> could mean
> >>>>>> my syntax is incorrect.
> >>>>>>>
> >>>>>>> Ideas welcome.
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> Patrick Connolly
> >>>>>>> Biometrician
> >>>>>>>
> >>>>>>> Postal Address: Plant & Food Research Private Bag 92169,
> >>>>>>> Auckland Mail Centre, Auckland 1142, New Zealand Physical
> >>>>>>> Address: Plant & Food Research
> >>>>>>> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
> >>>>>>>> -----Original Message-----
> >>>>>>>> From: [hidden email] [mailto:wekalist-
> >>>>>>>> [hidden email]] On Behalf Of Eibe Frank
> >>>>>>>> Sent: Thursday, 27 April 2017 2:12 p.m.
> >>>>>>>> To: Weka machine learning workbench list.
> >>>>>>>> Subject: Re: [Wekalist] RWeka setup
> >>>>>>>>
> >>>>>>>> No, you don’t need to install WEKA separately. As you said,
> >>>>>>>> RWeka comes with its own weka.jar.
> >>>>>>>>
> >>>>>>>> You can even start the WEKA GUIs from that .jar by using
> >>>>>>>>
> >>>>>>>> java -jar RWekajars/java/weka.jar
> >>>>>>>>
> >>>>>>>> The WEKA package manager can be accessed through the Tools menu
> >>>>>>>> in the WEKA GUI Chooser that pops up when your run this.
> >>>>>>>>
> >>>>>>>> Cheers,
> >>>>>>>> Eibe
> >>>>>>>>
> >>>>>>>>> On 27/04/2017, at 1:41 PM, Patrick Connolly
> >>>>>>>> <[hidden email]> wrote:
> >>>>>>>>>
> >>>>>>>>> THE proxy server needs to be accessible  from this side only,
> >>>>>>>>> I would have
> >>>>>>>> thought.  It works for everything else..
> >>>>>>>>>
> >>>>>>>>> I can manually download the repository  but the cache is
> >>>>>>>>> erased if I try to
> >>>>>>>> refresh it with the WPM() function.
> >>>>>>>>>
> >>>>>>>>> How  does the proxy system know which weka.jar is in use?  I
> >>>>>>>>> have a suspicion
> >>>>>>>> the 2 are being confused.  For that matter, am I correct in
> >>>>>>>> assuming weka needs to be installed to use RWeka?
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> Patrick Connolly
> >>>>>>>>> Biometrician
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> Postal Address: Plant & Food Research Private Bag 92169,
> >>>>>>>>> Auckland Mail Centre, Auckland 1142, New Zealand Physical
> >>>>>>>>> Address: Plant & Food Research
> >>>>>>>>> 120 Mt Albert Road, Sandringham, Auckland 1025, New Zealand
> >>>>>>>>>> -----Original Message-----
> >>>>>>>>>> From: [hidden email] [mailto:wekalist-
> >>>>>>>>>> [hidden email]] On Behalf Of Eibe Frank
> >>>>>>>>>> Sent: Wednesday, 26 April 2017 8:49 p.m.
> >>>>>>>>>> To: Weka machine learning workbench list.
> >>>>>>>>>> Subject: Re: [Wekalist] RWeka setup
> >>>>>>>>>>
> >>>>>>>>>> OK, it seems that your proxy server is not on the public net then.
> >>>>>>>>>>
> >>>>>>>>>> The output for WPM("refresh-cache") should look like this:
> >>>>>>>>>>
> >>>>>>>>>> WPM("refresh-cache")
> >>>>>>>>>> Refresh in progress. Please wait...
> >>>>>>>>>> [DefaultPackageManager] downloaded 1913 KB
> >>>>>>>>>>
> >>>>>>>>>> This works fine for me, both at home (no proxy) and at work
> >>>>>>>>>> (behind a
> >>>>>> proxy).
> >>>>>>>>>>
> >>>>>>>>>> The "Unable to download..." message you are getting means
> >>>>>>>>>> that WEKA cannot connect to the SourceForge site. Can you
> >>>>>>>>>> actually browse to that site in your browser? Perhaps your
> >>>>>>>>>> institution has blocked access to that site? Anyway, I would
> >>>>>>>>>> get in touch with your system
> >>>>>>>> administrators. They might be able to help.
> >>>>>>>>>>
> >>>>>>>>>> Cheers,
> >>>>>>>>>> Eibe
> >>>>>>>>>>
> >>>>>>>>>>> On 26 Apr 2017, at 16:31, Patrick Connolly
> >>>>>>>>>> <[hidden email]> wrote:
> >>>>>>>>>>>
> >>>>>>>>>>> It works for installing R packages - though the syntax for
> >>>>>>>>>>> setting the
> >>>>>>>>>> environment variable is different.
> >>>>>>>>>>>
> >>>>>>>>>>>> ping proxy.pfr.co.nz
> >>>>>>>>>>> PING aklwsa31.pfr.co.nz (172.16.81.6) 56(84) bytes of data.
> >>>>>>>>>>> 64 bytes from 172.16.81.6: icmp_seq=1 ttl=61 time=0.983 ms
> >>>>>>>>>>> 64 bytes from 172.16.81.6: icmp_seq=2 ttl=61 time=1.64 ms
> >>>>>>>>>>>
> >>>>>>>>>>> Patrick Connolly
> >>>>>>>>>>> Biometrician
> >>>>>>>>>>>
> >>>>>>>>>>> T: +64 9 925 7079
> >>>>>>>>>>> F: +64 9 925 7001
> >>>>>>>>>>> E: [hidden email]
> >>>>>>>>>>> www.plantandfood.co.nz
> >>>>>>>>>>> The New Zealand Institute for Plant & Food Research Limited
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>> -----Original Message-----
> >>>>>>>>>>>> From: [hidden email] [mailto:wekalist-
> >>>>>>>>>>>> [hidden email]] On Behalf Of Eibe Frank
> >>>>>>>>>>>> Sent: Wednesday, 26 April 2017 3:54 p.m.
> >>>>>>>>>>>> To: Weka machine learning workbench list.
> >>>>>>>>>>>> Subject: Re: [Wekalist] RWeka setup
> >>>>>>>>>>>>
> >>>>>>>>>>>> Are you sure you have the proxy details right?
> >>>>>>>>>>>>
> >>>>>>>>>>>> $ ping proxy.pfr.co.nz
> >>>>>>>>>>>> ping: cannot resolve proxy.pfr.co.nz: Unknown host
> >>>>>>>>>>>>
> >>>>>>>>>>>> Cheers,
> >>>>>>>>>>>> Eibe
> >>>>>>>>>>>>
> >>>>>>>>>>>>> On 26/04/2017, at 3:02 PM, Patrick Connolly
> >>>>>>>>>>>> <[hidden email]> wrote:
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> I followed the directions at
> >>>>>>>>>>>>>
> >>>>>> https://weka.wikispaces.com/Weka+package+manager+does+not+start
> :
> >>>>>>>>>>>>> Now when I start RWeka, I get
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>> require(RWeka)
> >>>>>>>>>>>>> Loading required package: RWeka Picked up _JAVA_OPTIONS:
> >>>>>>>>>>>>> -Dhttp.proxyHost=http://proxy.pfr.co.nz
> >>>>>>>>>>>>> -Dhttp.proxyPort=8080
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> which indicates to me that I have the syntax correct, but
> >>>>>>>>>>>>> I then get
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>> WPM("refresh-cache")
> >>>>>>>>>>>>> Refresh in progress. Please wait...
> >>>>>>>>>>>>> Unable to download repository zip archve
> >>>>>>>>>>>>> (http://proxy.pfr.co.nz)
> >>>>>>>>>>>>> - trying
> >>>>>>>>>>>> legacy routine...
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> ... that is unless I install the repo manually in
> >>>>>>>>>>>>> ~/wekafiles/repCache.  In that case, there's no message
> >>>>>>>>>>>>> but ~/wekafiles/repCache is deleted.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> The proxy does not require authentication, so something
> >>>>>>>>>>>>> else is
> >>>> amiss.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> If I try
> >>>>>>>>>>>>>> WPM("list-packages", "installed")
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> R crashes.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Am I on a hiding to nowhere trying to use RWeka without a
> >>>>>>>>>>>>> JAVACLASS environment variable?
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Patrick Connolly
> >>>>>>>>>>>>> Biometrician
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Postal Address: Plant & Food Research Private Bag 92169,
> >>>>>>>>>>>>> Auckland Mail Centre, Auckland 1142, New Zealand Physical
> >>>>>>>>>>>>> Address: Plant & Food Research
> >>>>>>>>>>>>> 120 Mt Albert Road, Sandringham, Auckland 1025, New
> >>>>>>>>>>>>> Zealand
> >>>>>>>>>>>>>> -----Original Message-----
> >>>>>>>>>>>>>> From: [hidden email]
> >>>>>>>>>>>>>> [mailto:wekalist- [hidden email]] On Behalf
> >>>>>>>>>>>>>> Of Eibe Frank
> >>>>>>>>>>>>>> Sent: Monday, 24 April 2017 10:56 p.m.
> >>>>>>>>>>>>>> To: Weka machine learning workbench list.
> >>>>>>>>>>>>>> Subject: Re: [Wekalist] RWeka setup
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> The WEKA package manager needs web access to connect to
> >>>>>>>>>>>>>> the SourceForge site. You probably don't have direct
> >>>>>>>>>>>>>> access and instead need to go through a proxy server.
> >>>>>>>>>>>>>> Oracle's JVM reads the _JAVA_OPTIONS environment variable
> >>>>>>>>>>>>>> and you can provide proxy settings via
> >>>>>>>>>>>> that variable, as explained here:
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>
> >>>>>> https://weka.wikispaces.com/Weka+package+manager+does+not+start
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> However, WEKA may not be able to pop up the GUI for
> >>>>>>>>>>>>>> entering the proxy credentials, so you may have to add
> >>>>>>>>>>>>>> those as part of the environment variable as well, using
> >>>>>>>>>>>>>> http.proxyUser and http.proxyPassword,
> >>>>>>>>>>>> as explained here:
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>
> >>>>>>
> >>>>
> >>
> https://weka.wikispaces.com/How+do+I+use+the+package+manager%3F#GUI
> >>>>>>>>>>>>>> %20package%20manager-Using%20a%20HTTP%20proxy
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> Cheers,
> >>>>>>>>>>>>>> Eibe
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> On 24 Apr 2017, at 16:33, Patrick Connolly
> >>>>>>>>>>>>>> <[hidden email]> wrote:
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> I installed weka in /usr/local/weka-3-8-1/weka.jar and
> >>>>>>>>>>>>>>> when I installed
> >>>>>>>>>>>>>> RWeka, it has
> >>>>>>>>>>>>>>> another weka.jar in the R package library.  I assume the
> >>>>>>>>>>>>>>> latter is used when I try this (in R):
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>> WPM("refresh-cache")
> >>>>>>>>>>>>>>> Refresh in progress. Please wait...
> >>>>>>>>>>>>>>> Unable to download repository zip archve (connect timed
> >>>>>>>>>>>>>>> out)
> >>>>>>>>>>>>>>> - trying legacy
> >>>>>>>>>>>>>> routine...
> >>>>>>>>>>>>>>> java.net.SocketTimeoutException: connect timed out
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> My guess is that the CLASSPATH isn't specified.  Without
> >>>>>>>>>>>>>>> setting an environment variable, where do I specify the
> >>>>>>>>>>>>>>> class path
> >>>>>> option?
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> TIA
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> Patrick Connolly
> >>>>>>>>>>>>>>> Biometrician
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> www.plantandfood.co.nz
> >>>>>>>>>>>>>>> The New Zealand Institute for Plant & Food Research
> >>>>>>>>>>>>>>> Limited
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> The contents of this e-mail are confidential and may be
> >>>>>>>>>>>>>>> subject to legal
> >>>>>>>>>>>>>> privilege.
> >>>>>>>>>>>>>>> If you are not the intended recipient you must not use,
> >>>>>>>>>>>>>>> disseminate, distribute
> >>>>>>>>>>>>>> or
> >>>>>>>>>>>>>>> reproduce all or any part of this e-mail or attachments.
> >>>>>>>>>>>>>>> If you have received
> >>>>>>>>>>>>>> this
> >>>>>>>>>>>>>>> e-mail in error, please notify the sender and delete all
> >>>>>>>>>>>>>>> material pertaining to
> >>>>>>>>>>>>>> this
> >>>>>>>>>>>>>>> e-mail.  Any opinion or views expressed in this e-mail
> >>>>>>>>>>>>>>> are those of the
> >>>>>>>>>>>>>> individual
> >>>>>>>>>>>>>>> sender and may not represent those of The New Zealand
> >>>>>>>>>>>>>>> Institute for Plant
> >>>>>>>>>>>>>> and
> >>>>>>>>>>>>>>> Food Research Limited.
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> _______________________________________________
> >>>>>>>>>>>>>>> Wekalist mailing list
> >>>>>>>>>>>>>>> Send posts to: [hidden email] List info and
> >>>>>>>>>>>>>>> subscription status:
> >>>>>>>>>>>>>> https://list.waikato.ac.nz/mailman/listinfo/wekalist
> >>>>>>>>>>>>>>> List etiquette:
> >>>>>>>>>>>>>> http://www.cs.waikato.ac.nz/~ml/weka/mailinglist_etiquett
> >>>>>>>>>>>>>> e.ht
> >>>>>>>>>>>>>> ml
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> _______________________________________________
> >>>>>>>>>>>>>> Wekalist mailing list
> >>>>>>>>>>>>>> Send posts to: [hidden email] List info and
> >>>>>>>>>>>>>> subscription
> >>>>>>>>>>>>>> status:
> >>>>>>>>>>>>>> https://list.waikato.ac.nz/mailman/listinfo/wekalist
> >>>>>>>>>>>>>> List etiquette:
> >>>>>>>>>>>>>> http://www.cs.waikato.ac.nz/~ml/weka/mailinglist_etiquett
> >>>>>>>>>>>>>> e.ht
> >>>>>>>>>>>>>> ml
> >>>>>>>>>>>>> The contents of this e-mail are confidential and may be
> >>>>>>>>>>>>> subject to legal
> >>>>>>>>>>>> privilege.
> >>>>>>>>>>>>> If you are not the intended recipient you must not use,
> >>>>>>>>>>>>> disseminate, distribute or reproduce all or any part of
> >>>>>>>>>>>>> this e-mail or
> >>>>>>>> attachments.
> >>>>>>>>>>>>> If you have received this e-mail in error, please notify
> >>>>>>>>>>>>> the sender and delete all material pertaining to this
> >>>>>>>>>>>>> e-mail.  Any opinion or views expressed in this e-mail are
> >>>>>>>>>>>>> those of the individual sender and may not represent those
> >>>>>>>>>>>>> of The New Zealand Institute for Plant and Food
> >>>>>>>>>>>> Research Limited.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> _______________________________________________
> >>>>>>>>>>>>> Wekalist mailing list
> >>>>>>>>>>>>> Send posts to: [hidden email] 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.htm
> >>>>>>>>>>>>> l
> >>>>>>>>>>>>
> >>>>>>>>>>>> _______________________________________________
> >>>>>>>>>>>> Wekalist mailing list
> >>>>>>>>>>>> Send posts to: [hidden email] 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
> >>>>>>>>>>> The contents of this e-mail are confidential and may be
> >>>>>>>>>>> subject to legal
> >>>>>>>>>> privilege.
> >>>>>>>>>>> If you are not the intended recipient you must not use,
> >>>>>>>>>>> disseminate, distribute or reproduce all or any part of this
> >>>>>>>>>>> e-mail or
> >>>>>> attachments.
> >>>>>>>>>>> If you have received this e-mail in error, please notify the
> >>>>>>>>>>> sender and delete all material pertaining to this e-mail.
> >>>>>>>>>>> Any opinion or views expressed in this e-mail are those of
> >>>>>>>>>>> the individual sender and may not represent those of The New
> >>>>>>>>>>> Zealand Institute for Plant and Food
> >>>>>>>>>> Research Limited.
> >>>>>>>>>>>
> >>>>>>>>>>> _______________________________________________
> >>>>>>>>>>> Wekalist mailing list
> >>>>>>>>>>> Send posts to: [hidden email] 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.h
> >>>>>>>>>>> tml
> >>>>>>>>>>
> >>>>>>>>>> _______________________________________________
> >>>>>>>>>> Wekalist mailing list
> >>>>>>>>>> Send posts to: [hidden email] 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.ht
> >>>>>>>>>> ml
> >>>>>>>>> The contents of this e-mail are confidential and may be
> >>>>>>>>> subject to legal
> >>>>>>>> privilege.
> >>>>>>>>> If you are not the intended recipient you must not use,
> >>>>>>>>> disseminate, distribute or reproduce all or any part of this
> >>>>>>>>> e-mail or
> >>>> attachments.
> >>>>>>>>> If you have received this e-mail in error, please notify the
> >>>>>>>>> sender and delete all material pertaining to this e-mail.  Any
> >>>>>>>>> opinion or views expressed in this e-mail are those of the
> >>>>>>>>> individual sender and may not represent those of The New
> >>>>>>>>> Zealand Institute for Plant and Food
> >>>>>>>> Research Limited.
> >>>>>>>>>
> >>>>>>>>> _______________________________________________
> >>>>>>>>> Wekalist mailing list
> >>>>>>>>> Send posts to: [hidden email] 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.htm
> >>>>>>>>> l
> >>>>>>>>
> >>>>>>>> _______________________________________________
> >>>>>>>> Wekalist mailing list
> >>>>>>>> Send posts to: [hidden email] 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
> >>>>>>>
> >>>>>>> The contents of this e-mail are confidential and may be subject
> >>>>>>> to legal
> >>>>>> privilege.
> >>>>>>> If you are not the intended recipient you must not use,
> >>>>>>> disseminate, distribute or reproduce all or any part of this e-mail or
> attachments.
> >>>>>>> If you have received this e-mail in error, please notify the
> >>>>>>> sender and delete all material pertaining to this e-mail.  Any
> >>>>>>> opinion or views expressed in this e-mail are those of the
> >>>>>>> individual sender and may not represent those of The New Zealand
> >>>>>>> Institute for Plant and Food
> >>>>>> Research Limited.
> >>>>>>> _______________________________________________
> >>>>>>> Wekalist mailing list
> >>>>>>> Send posts to: [hidden email] 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: [hidden email] 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
> >>>>>
> >>>>> The contents of this e-mail are confidential and may be subject to
> >>>>> legal
> >>>> privilege.
> >>>>> If you are not the intended recipient you must not use,
> >>>>> disseminate, distribute or reproduce all or any part of this e-mail or
> attachments.
> >>>>> If you have received this e-mail in error, please notify the
> >>>>> sender and delete all material pertaining to this e-mail.  Any
> >>>>> opinion or views expressed in this e-mail are those of the
> >>>>> individual sender and may not represent those of The New Zealand
> >>>>> Institute for Plant and Food
> >>>> Research Limited.
> >>>>> _______________________________________________
> >>>>> Wekalist mailing list
> >>>>> Send posts to: [hidden email] 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: [hidden email] 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
> >>>
> >>> The contents of this e-mail are confidential and may be subject to
> >>> legal
> >> privilege.
> >>> If you are not the intended recipient you must not use, disseminate,
> >>> distribute
> >> or
> >>> reproduce all or any part of this e-mail or attachments.  If you
> >>> have received
> >> this
> >>> e-mail in error, please notify the sender and delete all material
> >>> pertaining to
> >> this
> >>> e-mail.  Any opinion or views expressed in this e-mail are those of
> >>> the
> >> individual
> >>> sender and may not represent those of The New Zealand Institute for
> >>> Plant
> >> and
> >>> Food Research Limited.
> >>> _______________________________________________
> >>> Wekalist mailing list
> >>> Send posts to: [hidden email] 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: [hidden email] 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
> >
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Re: RWeka setup

Peter Reutemann
> I'm not familiar enough with Java to know how to find its version, but
> it will be whatever an up to date Linux Mint 17.2 has.

Just run: java -version

Being Linux Mint, you will most likely run a version of OpenJDK. For
Weka, you should use an Oracle one.

Cheers, Peter
--
Peter Reutemann
Dept. of Computer Science
University of Waikato, NZ
+64 (7) 858-5174
http://www.cms.waikato.ac.nz/~fracpete/
http://www.data-mining.co.nz/
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