Support:Bugs and solutions

How this system works

1. If a user encounters an error, he may read the 'Known bugs and solutions' section below to find if this error has been reported and solved. If not, the users report this bug in the 'Report new bugs' section.
2. As this page is being 'watched' by COMKAT developers, any changes to this page will trigger the wiki to send us an e-mail notifying us of the new bug report.
3. Then we will look at the bug report, provide an answer and solution and reply to the user who reported it via e-mail.
4. Once this bug is resolved, we will move the report from the 'Report new bugs' section to the 'Previous bugs and solutions' section.

NOTE: This page will not contain the bug reports for the previous releases of COMKAT if this bug has been resolved in the new version.

How to submit a bug report

1. Search to see if this bug has been reported previously. Use the wiki search functions at the top of this page.
2. Get the following information of your system:
   1. Operating system (and whether it's a 64-bit system with the MATLAB command 'computer')
   2. MATLAB version (use commands 'ver' and 'mexext' in MATLAB)
   3. COMKAT version
3. Copy the following text.

Bug reported by [Your name]. [Your e-mail] 

OS: [Your operating system. Please also indicate if it is 32 or 64 bit.]

MATLAB: [Your MATLAB version. Type 'ver' in MATLAB command window to get this information.]

COMKAT: [Your COMKAT Release]

Bug description: [You bug description]

Attachment(optional):

Additional contact information (optional):

Then click 'Edit' near the bottom of this page. Paste the text into the edit box under '== New bugs waiting for response =='. Edit the pasted text according to the bug you found. When finished click 'Save page'. You may also include attachments such as .mat or .m files.

Go to Support:Detailed tutorial on bug report for a more detailed step-by-step instruction with pictures.

New bugs waiting for response

Bug reported by Christophe Nioche christophe.nioche@gmail.com

OS: Linux version 2.6.25.14-69.fc8, Fedora 8

MATLAB: MATLAB Version 7.5.0.338 (R2007b)

COMKAT: COMKAT R3

Bug description: When launching the estimate process "Blood flow model" I obtain the following error message :

Warning: Rank deficient, rank = 0,  tol = NaN.
> In lmwls at 290
  In compartmentModel.fit at 134
  In main_GUI>fitCompartment_Callback at 2437
  In gui_mainfcn at 96
  In main_GUI at 50
??? Error using ==> svd
Input to SVD must not contain NaN or Inf.

Known bugs and solutions

Download and installation

1. When I clicked the link to COMKAT download, the download did not start and I got a 'HTTP 403 Forbidden' error message.
   Solution:The COMKAT server requires you to register and log in before you download the COMKAT files.
2. The fitting function in the example fdgcmd.m returns this error

   fdgcmd('INVERSE') plotOption = 1 ??? Input argument "cm" is undefined. Error in ==> fitfunc at 54 parmToChange = get(cm, 'SensitivityName'); Error in ==> optim\private\snls at 423 [newfvec,newA] = feval(funfcn{3},xargin{:},varargin{:}); Error in ==> optim\private\lsqncommon at 220 [x,FVAL,LAMBDA,JACOB,EXITFLAG,OUTPUT,msg]=... Error in ==> lsqcurvefit at 174 [x,Resnorm,FVAL,EXITFLAG,OUTPUT,LAMBDA,JACOB] = ... Error in ==> compartmentModel.fit at 145 [newParmVal,resnorm,residual,exitFlag,output,lambda,jacobian] = lsqcurvefit('fitfunc', initParmVal, [], data, lb, ub, ... Error in ==> fdgcmd at 208 pfit = fit(cm, pinit, lb, ub);

   
   Solution:This error arises because the newer MATLAB function "lsqcurvefit" has a different argument passing. In MATLAB version earlier than R2006, the lsqcommon passes an extra argument which is empty. That is why there is an "unused" argement in the fitfunc.m. However, this is fixed in R2006a and later so now the cm is passed as "unused". If you are using MATLAB 2006a or later, to solve this problem as a workaround, edit the "fitfunc.m" and insert the following lines in line 38: if nargin<3 cm=unused; end
3. I use two computers, one xp sp1 with MATLAB v7 sp1, the other is sp2. The estimated value from both computers are different. I have checked many times that I use the same data. Would it be possible to happen?
   Solution:The default optimizer of COMKAT is lsqcurvefit. As it is a function of the MATLAB optimization toolbox, in different versions of MATLAB the fitting results may differ. So the fitted values could be slightly different under different service packs. However, the optimizer "LMWLS" is a function of COMKAT so it will not change in different MATLAB versions. So if you use this optimizer you will get the identical parameter estimates regardless the MATLAB version.
4. I just downloaded and attempted to install the latest version of COMKAT. When attempting to validate the first calculation, I get the following error message:

   ??? Undefined command/function 'pxEval'.

   
   Solution:This error was generated because MATLAB 7 does not recognize the 'mexwin32' extension. We have fixed this issue by updating the COMKAT_R3.zip file. Please download and re-install it again. Or you may manually fix this by searching for all '.mexwin32' files and change their extension to '.dll'.

COMKAT command line functions

1. When I tried to set a certain property of COMKAT compartment model, why wasn't the property changed?
   Solution:A common mistake is that you used a command without assigning the correct output like:

   set(cm,'ParameterName',pnames);

   But the correct usage is:

   cm=set(cm,'ParameterName',pnames);

2. Under the 64-bit Windows system, when doing curve fitting I get the following error message:

   Invalid MEX-file

   Solution:This problem is caused by the fact that, when you install 64-bit MATLAB, it does not automatically install the Visual C re-distributable for you. But for 32-bit MATLAB it does. Since we compile our mex files using Visual Studio 2008, you will have to install the Visual Studio 2008 re-distributable in order to run the mex files.
   Please go to Microsoft website: http://www.microsoft.com/downloads/details.aspx?familyid=bd2a6171-e2d6-4230-b809-9a8d7548c1b6&displaylang=en to download and install the re-distributables. If the link is broken, google Microsoft Visual C++ 2008 Redistributable Package x64.

COMKAT GUI

1. Main_GUI -> Model drawer -> I cannot find the "Return to GUI" button when using the Model drawer.
   Solution:You have to implement every step including "check model compatibility" and "Return to GUI" will be enabled.
2. Bug description: Using "inputest" tool. When launching the estimate process with "Use one sample" I obtain the following error message :
   

cvodesGenmod5: Error. Function fengInput does not exist???
??? Error using ==> fmincon at 517
FMINCON cannot continue because user supplied objective function failed with the following error:
Error using ==> cvodesGenmod5
cvodesGenmod5: Error.  Problem in evalInput.  Error status=1

Solution:You

COMKAT Image Tool

1. I get the following error when I try to create and name a new VOI:

??? Undefined function or variable 'name'. 
Error in ==> VOI.VOI at 16
out.name = name;  % what user calls the region

Solution:This is identified as a COMKAT bug. It will be fixed in the next release. For the workaround, edit line 16 of COMKATROOT/@VOI/VOI.m and make it:

out.name = varargin{1};

Misc

1. When launching the validation process "Glucose Minimal Model", I obtain the following error message:

   Kinetic function kinGMM is missing.

   
   Solution:Please add the folder 'examples' under COMKAT root folder into your MATLAB path. This bug will be fixed in a recent COMKAT revision.
2. When running under deployed mode, uitable generates errors for missing functions 'arrayviewfunc'
   Solution:Refer to MATLAB website http://www.mathworks.cn/support/bugreports/details.html?rp=449936 for solution. This bug has been fixed in MATLAB R2008b and later. This bug does not appear under MATLAB.
3. Delete this later...