[ome-users] matlab version

[T. J. Macura]

Anh,

Did you do a fresh CVS checkout or just a CVS update?
Please try a fresh CVS checkout. If you have more problems with the  
installer, please send me the complete  
/var/tmp/OME/install/PerlModuleTask.log file.

The error message suggests that you are having conflicts between old  
and new Makefiles:
"Makefile out-of-date with respect to Makefile.PL
Cleaning current config before rebuilding Makefile..."

Tom

My output was :
TESTING MODULE -- su -l tmacur1 -c 'make test '
SUCCESS -- OUTPUT: "Agent pid 13847
  rm -f blib/arch/auto/OME/Matlab/Matlab.bundle
   
LD_RUN_PATH="/Applications/MATLAB701/bin/mac:/Applications/MATLAB701/ 
bin/mac" MACOSX_DEPLOYMENT_TARGET=10.3 cc  -bundle -undefined  
dynamic_lookup -L/usr/local/lib Matlab.o  -o  
blib/arch/auto/OME/Matlab/Matlab.bundle    
-L/Applications/MATLAB701/bin/mac -lmx -leng -lut -lmat -licudata  
-licui18n -licuuc -lustdio -lz -L/usr/local/lib -L/sw/lib
  chmod 755 blib/arch/auto/OME/Matlab/Matlab.bundle
  cp Matlab.bs blib/arch/auto/OME/Matlab/Matlab.bs
  chmod 644 blib/arch/auto/OME/Matlab/Matlab.bs
  PERL_DL_NONLAZY=1 LD_LIBRARY_PATH=/Applications/MATLAB701/bin/mac  
/usr/bin/perl "-Iblib/lib" "-Iblib/arch" test.pl
  Trying to compute 4x8 using MATLAB ...
  Perl: OME::Matlab::Array=SCALAR(0x18560fc)
      Class:  double
      Order:  2
      Dims:   1x1
      Values: (32)
  Test Passed. Perl Matlab API is correctly installed.
"

Tom

On Jul 23, 2005, at 1:57 AM, Anh Vu wrote:

> Hi! I tried the instructions within the email and downloaded the
> newest CVS version and make modification to the ld file, but when i
> tried to install, it gave me an error at the testing stage during
> Matlab perl api configuration. A standard installation without the
> optional perl module setup installed and worked just fine.
>
> This is the error message from within PerlModuleTask.log
> *********************************************************************** 
> **********************************
> ----------------------------
>  Optional Perl Module Setup
> ----------------------------
>
> (All verbose information logged in  
> /var/tmp/OME/install/PerlModuleTask.log)
>
>
> MATLAB Perl API configuration:
>  Install MATLAB Perl API?: no
>    Config MATLAB for dev?: no
>
> Are these values correct ? [y/n]: n
> Install analysis engine interface to MATLAB ? [y/n]: y
> The user which MATLAB should be run under [avu]:
> Path to MATLAB installation [/usr/local/matlab]:
> Path to MATLAB binary [/usr/local/bin/matlab]:
> Configure MATLAB Perl API for developers? [y/n]: y
> Path to OME's matlab src files [/home/avu/OME/src/matlab]:
> "
>
> TESTING MODULE -- su -l avu -c 'make test '
> FAILURE -- OUTPUT: "Makefile out-of-date with respect to Makefile.PL
>  Cleaning current config before rebuilding Makefile...
>  make -f Makefile.old clean > /dev/null 2>&1 || /bin/sh -c true
>  /usr/bin/perl Makefile.PL "avu" "/usr/local/matlab"
>  You must run the makefile as root to pass it a matlab_user at
> MatlabInfo.pl line 58.
>  Matlab Vers:
>  Matlab Arch:
>  Matlab Home:
>  Include:
>  Lib:
>  Lib Path:
>
>  Could not open '../../OME.pm': No such file or directory at
> /usr/lib/perl5/5.8.3/ExtUtils/MM_Unix.pm line 3079.
>  Checking if your kit is complete...
>  Looks good
>  make: *** [Makefile] Error 2
> "
> *********************************************************************** 
> **********************************
>
> Thanks!
> -Anh
>
> On 7/22/05, T. J. Macura <tm289 at cam.ac.uk> wrote:
>> Hi Anh,
>>
>> I looked back to the list archive and saw the message you wrote on Jun
>> 14th.
>> Sorry I didn't get back to you sooner, I was very busy then and didn't
>> have spare time to help users. Your email fell through the cracks.
>>
>> In fact, now I am on vacation (for 7 days) in Wyoming USA enjoying
>> Teton National Forest (near Yellowstone). Hiking, cycling, and
>> white-water rafting.
>> I hope I can make it up to you.
>>
>> Last week I installed OME from CVS on RH Fedora Core 3.  I was able to
>> get the MatlabHandler to work, but only after lots of tweeking.
>> This necessitated some changes to the installer. So please try to get
>> OME from CVS and let me know how it works with importing the Matlab
>> Modules.
>>
>> One thing I had to do (and you probably will have to do as well) is to
>> modify ld.so.conf and run /sbin/ldconfig.
>> Here is the contents of my /etc/ld.so.conf
>> [tmacur1 at ome2 ~]$ cat /etc/ld.so.conf
>> include ld.so.conf.d/*.conf
>> /usr/lib/
>> /usr/local/lib
>> /usr/bin/MATLAB7SP2/bin/glnx86
>> /usr/X11R6/lib
>>
>> You probably need to change the MATLAB line. You see /usr/local/* etc?
>> I added those by hand. Those directories must be put before the MATLAB
>> directory so default system libraries (and not system libraries that
>> come with MATLAB) are used during linking.
>>
>> If you have problems with the Module Import once more, please send me
>> the error messages and I will get back to you promptly.
>>
>> Tom
>>
>>> I'm running OME 2.4.0 on Fedora Core 3 with kernel version 2.6.5. I
>>> also have matlab R14 running on the server. I have written some  
>>> matlab
>>> scripts that perform identification for a given input image and
>>> outputs some statistical data for that image and I am trying to
>>> intergrate those scripts into OME so that I can run the analysis and
>>> store the statistical data into the OME database.
>>>
>>> -Anh
>>>
>>
>>
>> On Jul 21, 2005, at 12:07 PM, Anh Vu wrote:
>>
>>> I also have problem with the matlabhandler trying to get it to work
>>> with OME. Whenever I try to import a matlab module it would fail and
>>> complains about the matlabhandler, so could anyone help me on that?
>>> Any suggestion as to what I should do to get it working? I'm using  
>>> the
>>> very early release of OME version 2.3.0 btw. I have some basic
>>> knowledge in Perl, so I can try to modify the code, but then I can't
>>> narrow down where the problem is.
>>>
>>> Anh
>>>
>>
>>
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