Issue in installing Pm

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Issue in installing Pm

michele basile

Dear Help Octave,

 

I have been trying to install Pmtk3 in Octave but I keep receiving the message below:

 

Iteration   FunEvals     Step Length    Function Val        Opt Cond

         1          2    6.75744e-001    6.42259e+000    3.08556e-001

error: 'lbfgsC' undefined near line 527 column 25

error: called from

    minFunc at line 527 column 23

    logregFit at line 139 column 45

    logregL2FitTest at line 20 column 8

    testPmtk3 at line 61 column 1

>> 

 

Does anyone know what to do in this case?

 

Look Forward

 

Best

 

Michele


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Re: Issue in installing Pm

tmacchant
----- Original Message -----

>From: michele basile 
>To: help-octave
>Date: 2017/3/8, Wed 06:37
>Subject: Issue in installing Pm
>
>
>Dear Help Octave,

>I have been trying to install Pmtk3 in Octave but I keep receiving the message below:

>Iteration   FunEvals     Step Length    Function Val        Opt Cond
>         1          2    6.75744e-001    6.42259e+000    3.08556e-001
>error: 'lbfgsC' undefined near line 527 column 25
>error: called from
>    minFunc at line 527 column 23
>    logregFit at line 139 column 45
>    logregL2FitTest at line 20 column 8
>    testPmtk3 at line 61 column 1
>>>  

>Does anyone know what to do in this case?

>Look Forward

>Best

>Michele


Your question is difficult to answer due to inadequate information.

Clarify the below

1. Octave environments
 platform (windows 10, ubunutu 16.04 etcs)
 version of octave (4.0.0, 4.2.1 etcs)

2. Way of install of Pmtk3

3. octave command or script you tried.

Tatsuro

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Re: Issue in installing Pm

tmacchant
----- Original Message -----

> From: Tatsuro MATSUOKA 
> To: michele basile ; "help-octave
> Cc:
> Date: 2017/3/8, Wed 18:04
> Subject: Re: Issue in installing Pm
>
> ----- Original Message -----
>> From: michele basile 
>> To: help-octave
>> Date: 2017/3/8, Wed 06:37
>> Subject: Issue in installing Pm
>>
>>
>> Dear Help Octave,
>>  
>> I have been trying to install Pmtk3 in Octave but I keep receiving the
> message below:
>>  
>> Iteration   FunEvals     Step Length    Function Val        Opt Cond
>>          1          2    6.75744e-001    6.42259e+000    3.08556e-001
>> error: 'lbfgsC' undefined near line 527 column 25
>> error: called from
>>     minFunc at line 527 column 23
>>     logregFit at line 139 column 45
>>     logregL2FitTest at line 20 column 8
>>     testPmtk3 at line 61 column 1
>>>>   
>>  
>> Does anyone know what to do in this case?
>>  
>> Look Forward
>>  
>> Best
>>  
>> Michele
>
>
> Your question is difficult to answer due to inadequate information.
>
> Clarify the below
>
> 1. Octave environments
>  platform (windows 10, ubunutu 16.04 etcs)
>  version of octave (4.0.0, 4.2.1 etcs)
>
> 2. Way of install of Pmtk3
>
> 3. octave command or script you tried.
>
> Tatsuro
>


Seem to be related to
lbfgsC cannot be found #79 
https://github.com/probml/pmtk3/issues/79



Workaround is described the above

However, lbfgs  seem not to implemented on octave nor matlab.

You seem to have build the below by yourself.
https://jp.mathworks.com/matlabcentral/fileexchange/15061-matlab-interface-for-l-bfgs-b/content/lbfgsb-for-matlab/README.html





Tatsuro

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R: Issue in installing Pm

michele basile
Hi Tatsuro,

Thanks for your prompt reply.

Concerning your questions below you will find my answers;

1) Platform Windows Home Premium


2) & 3) I have used the commands below a suggested by the PMTK3:


Download the latest zip file from github, or clone the repository.

Start Matlab/Octave. Suppose the directory where you unzipped pmtk is called
'C:\pmtk3'. Then type the following (you will need to modify the directory
names if you unzipped these files to a different place).

  cd C:\pmtk3
  initPmtk3
You should see something like this.

  initializing pmtk3
  downloading 38 packages to pmtk3/pmtksupportCopy from
pmtksupport.googlecode.com - this may take a few      minutes
  downloading GGM-GWishart............success
  ...

I have to add that of course the initialization part did not take place

Hope this can help to indentify the issue

Best

Michele




-----Messaggio originale-----
Da: Tatsuro MATSUOKA [mailto:[hidden email]]
Inviato: 08 March 2017 11:00
A: [hidden email]; michele basile; [hidden email]
Oggetto: Re: Issue in installing Pm

----- Original Message -----

> From: Tatsuro MATSUOKA 
> To: michele basile ; "help-octave
> Cc:
> Date: 2017/3/8, Wed 18:04
> Subject: Re: Issue in installing Pm
>
> ----- Original Message -----
>> From: michele basile 
>> To: help-octave
>> Date: 2017/3/8, Wed 06:37
>> Subject: Issue in installing Pm
>>
>>
>> Dear Help Octave,
>>  
>> I have been trying to install Pmtk3 in Octave but I keep receiving the
> message below:
>>  
>> Iteration   FunEvals     Step Length    Function Val        Opt Cond
>>          1          2    6.75744e-001    6.42259e+000    3.08556e-001
>> error: 'lbfgsC' undefined near line 527 column 25
>> error: called from
>>     minFunc at line 527 column 23
>>     logregFit at line 139 column 45
>>     logregL2FitTest at line 20 column 8
>>     testPmtk3 at line 61 column 1
>>>>   
>>  
>> Does anyone know what to do in this case?
>>  
>> Look Forward
>>  
>> Best
>>  
>> Michele
>
>
> Your question is difficult to answer due to inadequate information.
>
> Clarify the below
>
> 1. Octave environments
>  platform (windows 10, ubunutu 16.04 etcs)
>  version of octave (4.0.0, 4.2.1 etcs)
>
> 2. Way of install of Pmtk3
>
> 3. octave command or script you tried.
>
> Tatsuro
>


Seem to be related to
lbfgsC cannot be found #79 
https://github.com/probml/pmtk3/issues/79



Workaround is described the above

However, lbfgs  seem not to implemented on octave nor matlab.

You seem to have build the below by yourself.
https://jp.mathworks.com/matlabcentral/fileexchange/15061-matlab-interface-f
or-l-bfgs-b/content/lbfgsb-for-matlab/README.html





Tatsuro


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Re: R: Issue in installing Pm

tmacchant


>>>
>>>  Dear Help Octave,
>>>   
>>>  I have been trying to install Pmtk3 in Octave but I keep receiving the
>>  message below:
>>>   
>>>  Iteration   FunEvals     Step Length    Function Val        Opt Cond
>>>           1          2    6.75744e-001    6.42259e+000    3.08556e-001
>>>  error: 'lbfgsC' undefined near line 527 column 25
>>>  error: called from
>>>      minFunc at line 527 column 23
>>>      logregFit at line 139 column 45
>>>      logregL2FitTest at line 20 column 8
>>>      testPmtk3 at line 61 column 1
>>>>>    
>>>   
>>>  Does anyone know what to do in this case?
>>>   
>>>  Look Forward
>>>   
>>>  Best
>>>   
>>>  Michele
>>
>>
>>  Your question is difficult to answer due to inadequate information.
>>
>>  Clarify the below
>>
>>  1. Octave environments
>>   platform (windows 10, ubunutu 16.04 etcs)
>>   version of octave (4.0.0, 4.2.1 etcs)
>>
>>  2. Way of install of Pmtk3
>>
>>  3. octave command or script you tried.
>>
>>  Tatsuro
>>
>
>
> Seem to be related to
> lbfgsC cannot be found #79 
> https://github.com/probml/pmtk3/issues/79
>
>
>
> Workaround is described the above
>
> However, lbfgs  seem not to implemented on octave nor matlab.
>
> You seem to have build the below by yourself.
> https://jp.mathworks.com/matlabcentral/fileexchange/15061-matlab-interface-f
> or-l-bfgs-b/content/lbfgsb-for-matlab/README.html
>


Thanks for reply

I tried to trace what you did on octave-4.2.1 64bit on windows 10 home.


>> initPmtk3
initializing pmtk3
error: run initPmtk3Octave instead
error: called from
    initPmtk3 at line 17 column 5


So I run initPmtk3Octave instead.

Then I executed 

>> testPmtk3
Checking initialization..........PASSED
Checking pmtkSupport packages....PASSED
Checking pmtkData................warning: load: 'C:\pmtk3\data\crabs\crabs.mat'
found by searching load path
PASSED
warning: pmtk3 has not yet been made fully octave compliant
Testing selected code............



 Iteration   FunEvals     Step Length    Function Val        Opt Cond
         1          2    6.75744e-001    6.42259e+000    3.08556e-001
error: 'lbfgsC' undefined near line 527 column 25
error: called from
    minFunc at line 527 column 23
    logregFit at line 139 column 45
    logregL2FitTest at line 20 column 8
    testPmtk3 at line 61 column 1

I saw the same error as you described.

As I wrote in second reply, this problem is the same as 

 lbfgsC cannot be found #79 
 https://github.com/probml/pmtk3/issues/79


But the above is mere work around
Correct way is to build lbfgsC.mex from lbfgsC.c in C:\pmtk3\pmtksupportCopy\markSchmidt-9march2011\markSchmidt\minFunc

>> cd C:\pmtk3\pmtksupportCopy\markSchmidt-9march2011\markSchmidt\minFunc
>> mex lbfgsC.c

Confirm lbfgsC.mex is generated in C:\pmtk3\pmtksupportCopy\markSchmidt-9march2011\markSchmidt\minFunc.




And execute testPmtk3 again
>> cd C:\pmtk3

>> testPmtk3
Checking initialization..........PASSED
Checking pmtkSupport packages....PASSED
Checking pmtkData................warning: load: 'C:\pmtk3\data\crabs\crabs.mat' found by
searching load path
PASSED
warning: pmtk3 has not yet been made fully octave compliant
Testing selected code............



 Iteration   FunEvals     Step Length    Function Val        Opt Cond
         1          2    6.75744e-001    6.42259e+000    3.08556e-001
         2          3    1.00000e+000    6.31963e+000    1.27336e-001
         3          5    4.50069e-001    6.31343e+000    3.40558e-002
         4          6    1.00000e+000    6.31267e+000    1.22561e-002
         5          7    1.00000e+000    6.31257e+000    6.20464e-004
         6          8    1.00000e+000    6.31257e+000    1.07863e-005
Directional Derivative below progTol
low =  23.571
high =  28.854
warning: implicit conversion from numeric to char
warning: called from
    randraw>validateParam at line 4120 column 21
    randraw at line 3541 column 26
    newcombDemo at line 33 column 5
    testPmtk3 at line 62 column 1
warning: implicit conversion from numeric to char
warning: called from
    randraw>validateParam at line 4120 column 21
    randraw at line 1177 column 21
    randraw at line 3548 column 32
    newcombDemo at line 33 column 5
    testPmtk3 at line 62 column 1
warning: implicit conversion from numeric to char
warning: called from
    randraw>validateParam at line 4120 column 21
    randraw at line 1672 column 26
    randraw at line 1180 column 30
    randraw at line 3548 column 32
    newcombDemo at line 33 column 5
    testPmtk3 at line 62 column 1
trueModel LL: -172.456
emModel LL: -156.393
warning: function name 'normalize' does not agree with function filename 'C:\pmtk3\matlab
Tools\stats\normalise.m'
warning: called from
    viterbi_path at line 54 column 19
    hmmMap at line 22 column 6
    hmmDiscreteTest at line 38 column 24
    testPmtk3 at line 68 column 2
trueModelViterbiError =  0.57000
trueModelMaxMargError =  0.52000
emModelViterbiError =  0.55000
emModelMaxMargError =  0.55000
warning: load: 'C:\pmtk3\data\knnClassify3c\knnClassify3c.mat' found by searching load pa
th
error: errorbar: data argument 5 must be numeric
error: called from
    __errplot__ at line 40 column 7
    errorbar at line 181 column 10
    knnClassifyDemo at line 141 column 1
    testPmtk3 at line 69 column 1

************************************************************************************

Error 
error: 'lbfgsC' undefined near line 527 column 25


was disappeared but another error is appeared.

errorbar error occur in C:\pmtk3\demos\knnClassifyDemo.m

This seems to come from incompatibility of errorbar function between octave and matlab.

*********************
Change code in C:\pmtk3\demos\knnClassifyDemo.m
from
errorbar(ndx, mu, se, 'ko-','linewidth', 2, 'MarkerSize', 12);

to 

errh=errorbar(ndx, mu, se, 'ko-');
set(errh,'linewidth', 2, 'MarkerSize', 12);

testPmtk3 runs successfully. 



As in the warning, pmtk3 has not yet been made fully octave compliant so that limitation or workaround is required.

Tatsuro

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Re: R: Issue in installing Pm

tmacchant
This thread moved to private mail so that I just write what I have done to run test suite of Pmtk3
on octave for windows.

1. Download Pmtk3 in zip archive and extracted to C:\pmtk3

2. change current directory by "cd C:\pmtk3"

3. run initPmtk3Octave (instead of run initPmtk3 for matlab)

4. confirm many supporting tool folders are installed in C:\pmtk3\pmtksupportCopy folder by "run initPmtk3Octave" .
 (I confirmed C:\pmtk3\pmtksupportCopy\markSchmidt-9march2011\markSchmidt\minFunc is generated one of them.)

5. change current directory by
"cd C:\pmtk3\pmtksupportCopy\markSchmidt-9march2011\markSchmidt\minFunc"

6. generate lbfgsC.mex from lbfgsC.c on octave by executing mex command from octave prompt.
"mex lbfgsC.c"
lbfgsC.mex is mex file complied using C compiler embedded with Octave using mex command.

7.  Modify code in C:\pmtk3\demos\knnClassifyDemo.m
from
errorbar(ndx, mu, se, 'ko-','linewidth', 2, 'MarkerSize', 12);

to
 
errh=errorbar(ndx, mu, se, 'ko-');
set(errh,'linewidth', 2, 'MarkerSize', 12);


(around line 139)

8. change current directory by "cd C:\pmtk3"

9. run  testPmtk3


Tatsuro
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