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[protege-discussion] protege 3.2.1 Mac OS X crashes during Java Code Gen

Jeroen Lapre' jeroen-lapre at distant-galaxy.com
Mon Apr 2 11:07:39 PDT 2007


I upgraded to the latest version of Mac OS 10.4.9, and the latest available
version of java 1.5.
This appeared to fix the problem I was having with the java code export
plugins.
However, now graphviz no longer works with protege in OWLViz, when before it
did.
Sigh.

On 3/30/07, Jeroen Lapre' <jeroen-lapre at distant-galaxy.com> wrote:
>
> Ok,
> I created a very simple test case:
> An OWL ontology with classes Thing1 & Thing2 as disjoint subclasses of the
> root Thing class.
> When I try to export to Code->Generate EMF Java Interfaces, I get the
> following errors in the Console.
>
> Any ideas?
> thanks
> -jeroen
>
> CONFIG: Protege 3.2.1 Build 365, JVM 1.5.0_02-56, memory=99M, Mac OS X,
> encoding=UTF-8, language=en, country=US
> CONFIG: Loaded plugin edu.stanford.smi.protegex.owl - OWL Plugin
> CONFIG: Loaded plugin ca.uvic.cs.chisel.jambalaya - Jambalaya
> CONFIG: Loaded plugin dfki.protege.ontoviz
> CONFIG: Loaded plugin edu.stanford.smi.protege.script - Script Plugin
> CONFIG: Loaded plugin edu.stanford.smi.protegex.standard_extensions -
> Graph Widget, Table Widget
> CONFIG: Loaded plugin edu.stanford.smi.protege.stringsearch - String
> Search Tab
> CONFIG: Loaded plugin edu.stanford.smi.protegex.rdf_backend - RDF Backend
> CONFIG: Loaded plugin edu.stanford.smi.protegex.changes - Changes tab
> CONFIG: Loaded plugin edu.stanford.smi.protegex.pal_tabs - PAL Tabs
> CONFIG: Loaded plugin edu.stanford.smi.protegex.ezpal - EZPal Tab
> CONFIG: Loaded plugin edu.stanford.smi.protegex.facets_tab
> CONFIG: Loaded plugin edu.stanford.smi.protegex.instance_tree
> CONFIG: Loaded plugin edu.stanford.smi.protegex.prompt - PROMPT Tab
> CONFIG: Loaded plugin edu.stanford.smi.protegex.psm - PSM Librarian
> CONFIG: Loaded plugin edu.stanford.smi.protegex.umls_tab - UMLS Tab
> CONFIG: Loaded plugin edu.stanford.smi.protegex.wordnet - WordNet Tab
> CONFIG: Loaded plugin edu.stanford.smi.protegex.xml_tab - XML Tab
> CONFIG: Loaded plugin edu.washington.datagenie
> CONFIG: Loaded plugin org.algernon - Algernon
> CONFIG: Loaded plugin se.liu.ida.JessTab - JessTab Plugin
> CONFIG: Loaded plugin uk.ac.iam.soton.akt.tgviztab - TGVizTab
> CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.debugger
> CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.manchesterowlsyntaxeditor
> CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.owldoc
> CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.owlindividualstab
> CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.owlunittest
> CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.owlviz
> CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.protege.wizard - Basic
> Wizards
> CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.protege.wizard.owl - OWL
> Wizards
>
> Jambalaya version 2.5.0, Build: 3, 2006/11/06 14:02
> CHISEL Group, University of Victoria, chisel-support at cs.uvic.ca
>
> Protege Wizards v1.0 beta build 14
> Loaded OWL wizards library
> INFO: setting dialog type to : 1
> ... saving successful.
> Protege(192,0x1c6e800) malloc: *** error for object 0x17d351d0: incorrect
> checksum for freed object - object was probably modified after being freed,
> break at szone_error to debug
> Protege(192,0x1c6e800) malloc: *** set a breakpoint in szone_error to
> debug
> Protege(192,0x1c6e800) malloc: *** error for object 0x17d355f0: incorrect
> checksum for freed object - object was probably modified after being freed,
> break at szone_error to debug
> Protege(192,0x1c6e800) malloc: *** set a breakpoint in szone_error to
> debug
> Protege(192,0x1c6e800) malloc: ***  Deallocation of a pointer not
> malloced: 0x33002e; This could be a double free(), or free() called with the
> middle of an allocated block; Try setting environment variable MallocHelp to
> see tools to help debug
> # [ timer expired, abort... ]
>
> On 3/30/07, Jeroen Lapre' <jeroen-lapre at distant-galaxy.com > wrote:
> >
> > Thomas,
> > thanks for your suggestions, I'll give that a try and will post the
> > results.
> > -jeroen
> >
> > On 3/30/07, Thomas Russ < tar at isi.edu> wrote:
> > >
> > >
> > > On Mar 30, 2007, at 11:11 AM, Jeroen Lapre' wrote:
> > >
> > > > Protege 3.2.1 Mac OS X crashes during Java Code Gen.
> > > > Tested linux equivalent and it works fine on linux version.
> > > >
> > > > Any one else experiencing java code gen export crashes?
> > >
> > > Do you know why it is crashing on the Mac?
> > >
> > > If you open the Console application
> > > (normally found in Applications:Utilities)
> > > you should be able to see a trace of what
> > > Protege writes to the output, which will include
> > > information relating to errors encountered.
> > >
> > > If the problem is running out of memory, you may need to
> > > increase the maximum memory size for Protege.  I find that
> > > I usually need to do this on my Mac, to accommodate some of
> > > the ontologies I work on.
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > protege-discussion mailing list
> > > protege-discussion at lists.stanford.edu
> > > https://mailman.stanford.edu/mailman/listinfo/protege-discussion
> > >
> > > Instructions for unsubscribing:
> > > http://protege.stanford.edu/doc/faq.html#01a.03
> > >
> >
> >
> >
> > --
> > -jeroen lapre
> > www.distant-galaxy.com
> > making science compelling
> >
> > _______________________________________________
> > protege-discussion mailing list
> > protege-discussion at lists.stanford.edu
> > https://mailman.stanford.edu/mailman/listinfo/protege-discussion
> >
> > Instructions for unsubscribing:
> > http://protege.stanford.edu/doc/faq.html#01a.03
> >
> >
>
>
> --
> -jeroen lapre
> www.distant-galaxy.com
> making science compelling
>



-- 
-jeroen lapre
www.distant-galaxy.com
making science compelling
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