open-discussion
open-discussion > RE: PRoNTo ——specify model
May 14, 2013 12:05 PM | Christophe Phillips
RE: PRoNTo ——specify model
Dear Lin,
the problem you encountered is not new... and due either to some path setup problem or a compilation problem.
As you can see from the error message:
1 : function [svmtrain] in file [D:\MATLAB\R2012a\toolbox\bioinfo\biolearning\svmtrain.m] at line [233]
PRoNTo is accessing the "wrong" svmtrain function, in this case the one from some official Matlab toolbox ("bioinfo" it seems) instead of the one distributed with PRoNTo (which unfortunately has the same name...).
Follow the instructions detailed here
https://www.jiscmail.ac.uk/cgi-bin/webad...
and you should be sorted.
You're also advised to register with the PRoNTo-users mailing list where you may find answers to yours questions (in the archive) and more people to help you otherwise.
See info here: http://www.mlnl.cs.ucl.ac.uk/pronto/prtm...
HTH,
Chris
Originally posted by lin jiang:
the problem you encountered is not new... and due either to some path setup problem or a compilation problem.
As you can see from the error message:
1 : function [svmtrain] in file [D:\MATLAB\R2012a\toolbox\bioinfo\biolearning\svmtrain.m] at line [233]
PRoNTo is accessing the "wrong" svmtrain function, in this case the one from some official Matlab toolbox ("bioinfo" it seems) instead of the one distributed with PRoNTo (which unfortunately has the same name...).
Follow the instructions detailed here
https://www.jiscmail.ac.uk/cgi-bin/webad...
and you should be sorted.
You're also advised to register with the PRoNTo-users mailing list where you may find answers to yours questions (in the archive) and more people to help you otherwise.
See info here: http://www.mlnl.cs.ucl.ac.uk/pronto/prtm...
HTH,
Chris
Originally posted by lin jiang:
Now, I'm using the PRoNTo. And the
SPM8 and Haxbydataset hane been downloaded and installed .The
Matlab path showed follow:
>> which spm
D:\MATLAB\R2012a\toolbox\spm8\spm.m
>> which prt
D:\MATLAB\R2012a\toolbox\pronto\pronto_v1.1_beta\prt.m
But,when I do the example on the PRoNTo manual.At the step
11.1.3:specify model
when I clicked the "specify and run model" MATLAB getting the following:
--------------------------------------------------------
Running model svmFacesHouses
--------------------------------------------------------
Model 'svmFacesHouses' found in PRT.mat.
Model 'svmFacesHouses' found in PRT.mat.
Loading data files.....>>
Feature set 'Haxby' found in PRT.mat.
> running CV fold: 1 of 12 ...
prt_machine: machine did not run sucessfully.
SOLUTION: Please read the message below and attempt to correct the problem, or ask the developpers for assistance by copy-pasting all messages and explaining the exact steps that led to the problem.
These kinds of issues are typically caused by Matlab path problems.
9 : function [@(hObject,eventdata)prt_ui_cv_model('runbutt_Callback',hObject,eventdata,guidata(hObject))] in file [] at line [0]
8 : function [prt_ui_cv_model] in file [D:\MATLAB\R2012a\toolbox\pronto\pronto_v1.1_beta\prt_ui_cv_model.m] at line [50]
7 : function [gui_mainfcn] in file [D:\MATLAB\R2012a\toolbox\matlab\guide\gui_mainfcn.m] at line [96]
6 : function [runbutt_Callback] in file [D:\MATLAB\R2012a\toolbox\pronto\pronto_v1.1_beta\prt_ui_cv_model.m] at line [393]
5 : function [prt_cv_model] in file [D:\MATLAB\R2012a\toolbox\pronto\pronto_v1.1_beta\prt_cv_model.m] at line [82]
4 : function [prt_cv_fold] in file [D:\MATLAB\R2012a\toolbox\pronto\pronto_v1.1_beta\prt_cv_fold.m] at line [65]
3 : function [prt_machine] in file [D:\MATLAB\R2012a\toolbox\pronto\pronto_v1.1_beta\machines\prt_machine.m] at line [206]
2 : function [prt_machine_svm_bin] in file [D:\MATLAB\R2012a\toolbox\pronto\pronto_v1.1_beta\machines\prt_machine_svm_bin.m] at line [100]
1 : function [svmtrain] in file [D:\MATLAB\R2012a\toolbox\bioinfo\biolearning\svmtrain.m] at line [233]
Warning: Prediction method did not return [Error running machine prt_machine_svm_bin:
stats:svmtrain:GroupNotVector Error using svmtrain (line 233)
Y must be a vector or a character array.]
> In prt_cv_fold at 67
In prt_cv_model at 82
In prt_ui_cv_model>runbutt_Callback at 393
In gui_mainfcn at 96
In prt_ui_cv_model at 50
In @(hObject,eventdata)prt_ui_cv_model('runbutt_Callback',hObject,eventdata,guidata(hObject))
Warning: model.type not specified, defaulting to classifier
> In prt_stats at 34
In prt_cv_model at 85
In prt_ui_cv_model>runbutt_Callback at 393
In gui_mainfcn at 96
In prt_ui_cv_model at 50
In @(hObject,eventdata)prt_ui_cv_model('runbutt_Callback',hObject,eventdata,guidata(hObject))
Attempted to access stats.con_mat(0,1); index must be a positive integer or logical.
Error in prt_stats>compute_stats_classifier (line 67)
stats.con_mat(pred_lb,true_lb) = stats.con_mat(pred_lb,true_lb) + 1;
Error in prt_stats (line 42)
stats = compute_stats_classifier(model, tte, ttr);
Error in prt_cv_model (line 85)
stats = prt_stats(model, targets.test, targets.train);
Error in prt_ui_cv_model>runbutt_Callback (line 393)
prt_cv_model(PRT, in);
Error in gui_mainfcn (line 96)
feval(varargin{:});
Error in prt_ui_cv_model (line 50)
gui_mainfcn(gui_State, varargin{:});
Error in @(hObject,eventdata)prt_ui_cv_model('runbutt_Callback',hObject,eventdata,guidata(hObject))
Error while evaluating uicontrol Callback
Is anyone having the same problem ?And anyone who konws please help! Thanks!!
>> which spm
D:\MATLAB\R2012a\toolbox\spm8\spm.m
>> which prt
D:\MATLAB\R2012a\toolbox\pronto\pronto_v1.1_beta\prt.m
But,when I do the example on the PRoNTo manual.At the step
11.1.3:specify model
when I clicked the "specify and run model" MATLAB getting the following:
--------------------------------------------------------
Running model svmFacesHouses
--------------------------------------------------------
Model 'svmFacesHouses' found in PRT.mat.
Model 'svmFacesHouses' found in PRT.mat.
Loading data files.....>>
Feature set 'Haxby' found in PRT.mat.
> running CV fold: 1 of 12 ...
prt_machine: machine did not run sucessfully.
SOLUTION: Please read the message below and attempt to correct the problem, or ask the developpers for assistance by copy-pasting all messages and explaining the exact steps that led to the problem.
These kinds of issues are typically caused by Matlab path problems.
9 : function [@(hObject,eventdata)prt_ui_cv_model('runbutt_Callback',hObject,eventdata,guidata(hObject))] in file [] at line [0]
8 : function [prt_ui_cv_model] in file [D:\MATLAB\R2012a\toolbox\pronto\pronto_v1.1_beta\prt_ui_cv_model.m] at line [50]
7 : function [gui_mainfcn] in file [D:\MATLAB\R2012a\toolbox\matlab\guide\gui_mainfcn.m] at line [96]
6 : function [runbutt_Callback] in file [D:\MATLAB\R2012a\toolbox\pronto\pronto_v1.1_beta\prt_ui_cv_model.m] at line [393]
5 : function [prt_cv_model] in file [D:\MATLAB\R2012a\toolbox\pronto\pronto_v1.1_beta\prt_cv_model.m] at line [82]
4 : function [prt_cv_fold] in file [D:\MATLAB\R2012a\toolbox\pronto\pronto_v1.1_beta\prt_cv_fold.m] at line [65]
3 : function [prt_machine] in file [D:\MATLAB\R2012a\toolbox\pronto\pronto_v1.1_beta\machines\prt_machine.m] at line [206]
2 : function [prt_machine_svm_bin] in file [D:\MATLAB\R2012a\toolbox\pronto\pronto_v1.1_beta\machines\prt_machine_svm_bin.m] at line [100]
1 : function [svmtrain] in file [D:\MATLAB\R2012a\toolbox\bioinfo\biolearning\svmtrain.m] at line [233]
Warning: Prediction method did not return [Error running machine prt_machine_svm_bin:
stats:svmtrain:GroupNotVector Error using svmtrain (line 233)
Y must be a vector or a character array.]
> In prt_cv_fold at 67
In prt_cv_model at 82
In prt_ui_cv_model>runbutt_Callback at 393
In gui_mainfcn at 96
In prt_ui_cv_model at 50
In @(hObject,eventdata)prt_ui_cv_model('runbutt_Callback',hObject,eventdata,guidata(hObject))
Warning: model.type not specified, defaulting to classifier
> In prt_stats at 34
In prt_cv_model at 85
In prt_ui_cv_model>runbutt_Callback at 393
In gui_mainfcn at 96
In prt_ui_cv_model at 50
In @(hObject,eventdata)prt_ui_cv_model('runbutt_Callback',hObject,eventdata,guidata(hObject))
Attempted to access stats.con_mat(0,1); index must be a positive integer or logical.
Error in prt_stats>compute_stats_classifier (line 67)
stats.con_mat(pred_lb,true_lb) = stats.con_mat(pred_lb,true_lb) + 1;
Error in prt_stats (line 42)
stats = compute_stats_classifier(model, tte, ttr);
Error in prt_cv_model (line 85)
stats = prt_stats(model, targets.test, targets.train);
Error in prt_ui_cv_model>runbutt_Callback (line 393)
prt_cv_model(PRT, in);
Error in gui_mainfcn (line 96)
feval(varargin{:});
Error in prt_ui_cv_model (line 50)
gui_mainfcn(gui_State, varargin{:});
Error in @(hObject,eventdata)prt_ui_cv_model('runbutt_Callback',hObject,eventdata,guidata(hObject))
Error while evaluating uicontrol Callback
Is anyone having the same problem ?And anyone who konws please help! Thanks!!
Threaded View
Title | Author | Date |
---|---|---|
lin jiang | May 14, 2013 | |
Christophe Phillips | May 14, 2013 | |