[ome-users] Makefile out-of-date with respect to Makefile.PL

[Anh Vu]

These are the errors I get from the new cvs checkout.

Error I get running the test.

Cannot open a connection to Matlab! at
/usr/lib/perl5/5.8.3/CGI/Carp.pm line 314.

content of configuration table.

     19 |                1 | administration_module_id | 26
      1 |                1 | xml_dir                  | /OME/xml
      2 |                1 | db_instance              | 1cooCx
     23 |                  | matlab_exec              | /usr/local/bin/matlab
     24 |                1 | matlab_src_dir           | /home/avu/OME/src/matlab
      9 |                1 | db_version               | 2.16
     25 |                1 | matlab_exec              |
/usr/local/matlab/bin/matlab
     17 |                1 | executor                 |
OME::Analysis::Engine::UnthreadedPerlExecutor
     18 |                1 | super_user               | 1
     26 |                1 | matlab_user              | avu
      3 |                1 | ome_root                 | /OME
      5 |                1 | mac_address              | 00:11:11:3F:3D:11
      6 |                1 | lsid_authority           | batch2112b.ucr.edu
      4 |                1 | import_formats           |
OME::ImportEngine::MetamorphHTDFormat OME::ImportEngine::DVreader
OME::ImportEngine::STKreader OME::ImportEngine::BioradReader
OME::ImportEngine::LSMreader OME::ImportEngine::TIFFreader
OME::ImportEngine::BMPreader OME::ImportEngine::DICOMreader
OME::ImportEngine::XMLreader
      7 |                1 | tmp_dir                  | /var/tmp/OME
      8 |                1 | bin_dir                  | /OME/bin
     10 |                1 | template_dir             | /OME/html/Templates
     11 |                1 | annotation_module_id     | 7
     12 |                1 | original_files_module_id | 1
     13 |                1 | global_import_module_id  | 2
     14 |                1 | dataset_import_module_id | 3
     15 |                1 | image_import_module_id   | 4
     16 |                1 | import_chain_id          | 2

Also, I noticed in "View Chain Results" the time stamps for the listed
exercuted chains are all set to 2004-10-31 14:56:11

Anh

On 8/8/05, T. J. Macura <tm289 at cam.ac.uk> wrote:
> Dear Anh,
> 
> I gave you the wrong SQL command. Sorry, the difficulties lie in the
> fact that I don't have a good way to locally test and mimic your setup.
>   It ought to have been
>         INSERT INTO configuration (name,value, configuration_id) VALUES
> ('matlab_exec', '/usr/local/bin/matlab', 1);
> 
> This is now a mote point because I fixed bug [554] over the weekend.
> Please check-out from CVS, reinstall and try again. Should work. If not
> please do SELECT * FROM configuration and email me the contents.
> 
> Tom
> 
> On Aug 8, 2005, at 12:54 AM, Anh Vu wrote:
> 
> > The command I entered is.
> > INSERT INTO configuration (name,value)
> > VALUES('matlab_exec','/usr/local/bin/matlab');
> >
> > The error I get is a little different from the previous one once I ran
> > the "Matlab Test Chain' execution chain for the datase.
> >
> > couldn't retrieve matlab exec path from configuration at
> > /usr/lib/perl5/site_perl/5.8.3/OME/Analysis/Engine/
> > UnthreadedPerlExecutor.pm
> > line 80
> >
> > I also tried select * from configuration; to confirm that the values
> > are inserted and they are.
> >
> > P.S. I think OME has a lot of potential and uses, so I'm glad to help
> > out in anyway I can.
> >
> > Anh
> >
> > On 8/5/05, T. J. Macura <tm289 at cam.ac.uk> wrote:
> >> Anh,
> >>
> >> Thanks. This behaviour is not normal and exposes a bug based on an
> >> update from 2.4.0:
> >> http://bugs.openmicroscopy.org.uk/show_bug.cgi?id=554
> >>
> >> In the meantime, please type the following SQL command after psql ome
> >> (assuming /usr/bin/matlab is correct path to your MATLAB executable):
> >> INSERT INTO configuration (name, value) VALUES ('matlab_exec',
> >> '/usr/bin/matlab');
> >>
> >> Don't hesitate to write if things don't work as expected for you.
> >>
> >> Tom
> >>
> >> On Aug 5, 2005, at 6:12 PM, Anh Vu wrote:
> >>
> >>> Can't locate object method "matlab_exec" via package
> >>> "OME::Configuration" at
> >>> /usr/lib/perl5/site_perl/5.8.3/OME/Analysis/Handlers/MatlabHandler.pm
> >>> line 1064.
> >>>
> >>> is what I get for one of the images inside a dataset when I run the
> >>> "Matlab Test Chain" from Execute Analysis Chain. Is this normal for
> >>> the current CVS version? BTW, I imported the Matlab Test Chain using
> >>> $ome import MatlabTestChain.ome         from ~/OME/src/xml/OME/Tests
> >>>
> >>> Anh
> >>
> >>
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >
> 
>