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

Timothy Redmond tredmond at stanford.edu
Mon Apr 2 16:37:09 PDT 2007


I might be able to give a workaround and would like to know how it goes.


> 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... ]


This error tells me something about what must be going wrong here.   
It is not a Java error.  This means that it is either a problem with  
the Protege Installer - the application did not install correctly -  
or a problem with the apple JVM.  I am suspecting that because the  
errors start with "Protege(" it is a problem with the installer.

I am wondering if you could try starting Protege with the  
run_protege.applescript.  (Go to the Protege application directory,  
double click on the applescript and click run).   My guess is that  
maybe your problems will go away.

I just tried starting Protege with the applescript on my Mac and I  
did have to make a small edit before it ran.  My application  
directory was not in the standard place (/Applications/Protege_3.2.1)  
and I had to change that bit in the applescript before it would run.

If this is the case then I can start figuring out why the Protege  
installation was bad.  Also your version of java is JVM 1.5.0_02-56  
but the version of java on my mac is 1.5.0_07.  Seems like you aren't  
using the latest???

-Timothy



On Apr 2, 2007, at 11:07 AM, Jeroen Lapre' wrote:

> 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.
>
>
>
>
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> faq.html#01a.03
>
>
>
> -- 
> -jeroen lapre
> www.distant-galaxy.com
> making science compelling
>
> _______________________________________________
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> 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
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
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> Instructions for unsubscribing: http://protege.stanford.edu/doc/ 
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