Re: parcellfun test issue on Mac OS 10.8, was Re: problems installing openmpi_ext

[Ben Abbott]

On Sep 11, 2013, at 10:36 AM, c. wrote:

> 
> On 11 Sep 2013, at 15:43, Ben Abbott <address@hidden> wrote:
> 
>> On Sep 11, 2013, at 9:17 AM, Francis Poulin wrote:
>> 
>>>> Alex,
>>>> 
>>>> Sorry for the late response.  I'm able to run the parcellfun_example using 
>>>> 3.6.4 from Macports.  My variants are +atlas+docs+fltk+gcc47+x11.
>>>> 
>>>>    
>>>> https://trac.macports.org/browser/trunk/dports/math/octave-devel/Portfile
>>>> 
>>>> Perhaps duplicating the configure options used by macports will clear 
>>>> things up for you?
>>>> 
>>>> Ben
>>> 
>>> Hello,
>>> 
>>> With my current macports installation of octave-devel, octave-general, 
>>> octave-bim, after I load the packages and try running parcellfun_example I 
>>> get that it cannot find one of the bim functions.
>>> 
>>> octave:5> pkg list
>>> 
>>> Package Name  | Version | Installation directory
>>> --------------+---------+-----------------------
>>>       bim *|   0.1.1 | /opt/local/share/octave/packages/bim-0.1.1
>>>       fpl *|   0.1.6 | /opt/local/share/octave/packages/fpl-0.1.6
>>>       general *|   1.3.2 | /opt/local/share/octave/packages/general-1.3.2
>>>       msh *|   0.1.1 | /opt/local/share/octave/packages/msh-0.1.1
>>>      splines *|   1.0.7 | /opt/local/share/octave/packages/splines-1.0.7
>>> 
>>> octave:6> parcellfun_example
>>> error: 'bim1a_laplacian' undefined near line 40 column 7
>>> error: called from:
>>> error:   /Users/fpoulin/parcellfun_example.m at line 40, column 5
>>> 
>>> 
>>> I can try the other options that Ben suggested but since those don't 
>>> involve bim I wouldn't think they would make a world of difference but 
>>> could give it a try.
>>> 
>>> Cheers, Francis
>> 
>> opps.  I responded to the wrong thread.  I'm seeing this same error.  The 
>> parcellfun_example script must be modified to use the version of the bim 
>> package provided by macports.  Mostly that means changing the names.
> 
> not only the names, unfortunately ... some functions have also exchanged the 
> order of inputs parameters. 
> that is a very old version of bim about 5 y.o. :(

Ok.  That is easily fixed. First from a bash shell ...

        sudo port uninstall octave-bim

Then from macports octave-devel

pkg install -forge bim
pkg load bim
parcellfun_example
Elapsed time is 11.1524 seconds.
parcellfun: child process 35648 created
parcellfun: child process 35649 created
parcellfun: 200/200 jobs done
parcellfun: waiting for child process 35648 to close
parcellfun: waiting for child process 35649 to close
Elapsed time is 5.37539 seconds.

Ben