preferences not stored

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preferences not stored

hovlanddag
Hi! I am having trouble with the preferences disappearing between
sessions. I am using a fresh download of Protege-5.1 from today, with no
plugins or extensions, and whenever I restart Protege, any changes I
have dont to preferences are removed. They remain in effect during the
protege session, but when I exit and restart they are gone. I am running
on a ubuntu/linux machine, and I have tried deleting the .protege and
.Protege folders to no effect.

Regards,

Dag Hovland




_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

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Re: preferences not stored

Tania Tudorache

Please post the console output and the logs in ~/.protege/logs. There may be some error messages related to storing the preferences. Protege stores some of the preferences in binary format, and we know of other users with Ubuntu who got errors because of that.


Protege uses the Java preferences, and on Linux they are stored in: ~/.java/.userPrefs


You can try clearing the preferences, here are the instructions:

http://protegewiki.stanford.edu/wiki/ClearingP4Preferences


Tania




From: protege-user <[hidden email]> on behalf of Dag Hovland <[hidden email]>
Sent: Tuesday, March 14, 2017 3:47:26 AM
To: [hidden email]
Subject: [protege-user] preferences not stored
 
Hi! I am having trouble with the preferences disappearing between
sessions. I am using a fresh download of Protege-5.1 from today, with no
plugins or extensions, and whenever I restart Protege, any changes I
have dont to preferences are removed. They remain in effect during the
protege session, but when I exit and restart they are gone. I am running
on a ubuntu/linux machine, and I have tried deleting the .protege and
.Protege folders to no effect.

Regards,

Dag Hovland




_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
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Re: preferences not stored

Tania Tudorache
There is also an easier way to reset the preferences: Go to the File -> Preferences menu, and click on the "Reset preferences.." button at the bottom of the Preferences panel.

Tania

From: protege-user <[hidden email]> on behalf of Tania Tudorache <[hidden email]>
Sent: Tuesday, March 14, 2017 10:16:01 AM
To: [hidden email]
Subject: Re: [protege-user] preferences not stored
 

Please post the console output and the logs in ~/.protege/logs. There may be some error messages related to storing the preferences. Protege stores some of the preferences in binary format, and we know of other users with Ubuntu who got errors because of that.


Protege uses the Java preferences, and on Linux they are stored in: ~/.java/.userPrefs


You can try clearing the preferences, here are the instructions:

http://protegewiki.stanford.edu/wiki/ClearingP4Preferences


Tania




From: protege-user <[hidden email]> on behalf of Dag Hovland <[hidden email]>
Sent: Tuesday, March 14, 2017 3:47:26 AM
To: [hidden email]
Subject: [protege-user] preferences not stored
 
Hi! I am having trouble with the preferences disappearing between
sessions. I am using a fresh download of Protege-5.1 from today, with no
plugins or extensions, and whenever I restart Protege, any changes I
have dont to preferences are removed. They remain in effect during the
protege session, but when I exit and restart they are gone. I am running
on a ubuntu/linux machine, and I have tried deleting the .protege and
.Protege folders to no effect.

Regards,

Dag Hovland




_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
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Re: preferences not stored

hovlanddag
Hi!

Thanks for the tips. I tried all the different ways of deleting all
preferences, and they do not help. I paste the console output from a
Protege session below, where I only open protege, reset preferences,
and then exit. .protege/logs is attached. I think the relevant error is
this:

An error occurred whilst saving the list of recent items 
java.util.pref
s.BackingStoreException:
/home/dag/.java/.userPrefs/_!&!!`g">!&@![@"(!%`!|w"@!&)![@"'!%`!`g"&!%4
!@w"&!&:=/_!%k!^g"'!%`!`g"&!%4!@w"&!&8!`!"]!%`![g"^!&8!`w"&!&@=/_!'8!cg
"n!#4!c!"y!'8!d!"l!'c!~@!u!'`!~!"p!(@!bw"y!#4!bw"3!'w!.g"t!'8!~!"l!'w!.
g"p!'4!~g"l!()!~@"u!':!~@!u!&)!~@"h!(:!bw"u!'`!cg"@!()!~@"m!'`!cg"l!'4!
}w"l!(:= create failed.

I don't know why it tries to create the preferences with such a strange folder name?

Regards,

Dag Hovland


Console log:

dag@dagsjobblaptop:~/Nedlastingar/Protege-5.1.0$ ./run.sh 
CompilerOracle: exclude javax/swing/text/GlyphView.getBreakSpot
***********************************************************************
********* 
**                                  Protege                            
       ** 
***********************************************************************
********* 
 
----------------- Initialising and Starting the OSGi Framework --------
--------- 
FrameworkFactory Class: org.apache.felix.framework.FrameworkFactory 
 
The OSGi framework has been initialised 
------------------------------- Starting Bundles ----------------------
--------- 
Starting bundle org.protege.common 
Starting bundle org.eclipse.equinox.common 
Starting bundle org.eclipse.equinox.supplement 
Starting bundle org.eclipse.equinox.registry 
Starting bundle org.protege.editor.core.application 
Starting bundle jul.to.slf4j 
Starting bundle ch.qos.logback.core 
Starting bundle org.eclipse.equinox.registry 
Starting bundle org.apache.servicemix.bundles.aopalliance 
Starting bundle com.google.inject 
Starting bundle org.semanticweb.owl.owlapi 
Starting bundle org.apache.servicemix.bundles.javax-inject 
Starting bundle org.jsr-305 
Starting bundle log4j.over.slf4j 
Starting bundle org.protege.common 
Starting bundle ch.qos.logback.classic 
Not starting bundle com.google.inject.multibindings explicitly because
it is a fragment bundle. 
Starting bundle slf4j.api 
Not starting bundle com.google.inject.assistedinject explicitly because
it is a fragment bundle. 
Starting bundle org.eclipse.equinox.common 
Starting bundle org.apache.commons.io 
Starting bundle org.protege.editor.core.application 
Starting bundle org.protege.editor.owl 
Starting bundle org.eclipse.equinox.supplement 
Starting bundle com.google.guava 
Starting bundle org.protege.ontograf 
Starting bundle org.coode.dlquery 
Starting bundle org.coode.owlviz 
Starting bundle swrltab-plugin 
Starting bundle org.coode.browser 
Starting bundle uk.ac.manchester.cs.owl.explanation 
Starting bundle org.protege.owl.rdf 
Starting bundle existentialquery 
Starting bundle cellfie 
Starting bundle org.protege.editor.owl.rdf 
Starting bundle code-generation 
Starting bundle org.semanticweb.hermit 
The OSGi framework has been started 
 
------------------------------------ Protege --------------------------
--------- 
Protege Desktop 
Version 5.1.0, Build  
 
 
----------------------------------- Platform --------------------------
--------- 
Java: JVM 1.8.0_40-b26  Memory: 466M 
Language: nb, Country: NO 
Framework: Apache Software Foundation (1.7)  
OS: linux (4.4.0-66-generic) 
Processor: x86-64
 
 
------------------------------------ Plugins --------------------------
--------- 
Plugin: OntoGraf (2.0.3) 
Plugin: DL Query (4.0.1) 
Plugin: OWLViz (5.0.3) 
Plugin: SWRLTab Protege 5.0+ Plugin (1.0.3) 
Plugin: Browser View (OWLDoc) (3.0.3) 
Plugin: Explanation Workbench (3.0.0) 
Plugin: OWLAPI RDF Library (2.0.2) 
Plugin: Existential Query (2.0.0) 
Plugin: Cellfie Protege 5.0+ Plugin (2.1.0) 
Plugin: Protege SPARQL Plugin (2.0.1) 
Plugin: OWL Code Generation Plug-in (2.0.0) 
Plugin: HermiT (1.3.8.413) 
 
Creating and setting up empty (default) editor kit 
OWL API Version: 4.2.6.20160910-2108 
Cannot generate ontology catalog for ontology at http://www.semanticweb
.org/dag/ontologies/2017/2/untitled-ontology-2 
------------------------------- Auto-update Check -------------------
----------- 
Auto-update last performed: Thu Jan 01 01:00:00 CET 1970 
Auto-update has not been performed today.  Running it. 
 
### Excluding compile: javax.swing.text.GlyphView::getBreakSpot
------------------------------ Running Auto-update --------------------
--------- 
 
--- Searching for plugins --- 
Checking https://raw.githubusercontent.com/protegeproject/autoupdate/ma
ster/update-info/5.0.0/plugins.repository 
    Processing https://raw.githubusercontent.com/protegeproject/autoupd
ate/master/update-info/5.0.0/plugins.repository as a plugin registry 
        Cannot open remote plugin registry at raw.githubusercontent.com
(Unknown Host) 
 
---------------------------- Disposing of Workspace -----------------
----------- 
Saved tab state for 'Active Ontology' tab 
Saved tab state for 'Entities' tab 
Saved tab state for 'DL Query' tab 
Saved tab state for 'Individuals by class' tab 
Saved workspace 
Disposed of 'Active Ontology' tab 
Disposed of 'Entities' tab 
Disposed of 'DL Query' tab 
Disposed of 'Individuals by class' tab 
Disposed of workspace 
 
An error occurred whilst saving the list of recent items 
java.util.prefs.BackingStoreException:
/home/dag/.java/.userPrefs/_!&!!`g">!&@![@"(!%`!|w"@!&)![@"'!%`!`g"&!%4
!@w"&!&:=/_!%k!^g"'!%`!`g"&!%4!@w"&!&8!`!"]!%`![g"^!&8!`w"&!&@=/_!'8!cg
"n!#4!c!"y!'8!d!"l!'c!~@!u!'`!~!"p!(@!bw"y!#4!bw"3!'w!.g"t!'8!~!"l!'w!.
g"p!'4!~g"l!()!~@"u!':!~@!u!&)!~@"h!(:!bw"u!'`!cg"@!()!~@"m!'`!cg"l!'4!
}w"l!(:= create failed.
        at
java.util.prefs.FileSystemPreferences$7.run(FileSystemPreferences.java:
619) ~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences$7.run(FileSystemPreferences.java:
615) ~[na:1.8.0_40]
        at java.security.AccessController.doPrivileged(Native Method)
~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences.writeBackCache(FileSystemPreferen
ces.java:614) ~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences.syncSpiPrivileged(FileSystemPrefe
rences.java:801) ~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences.access$2300(FileSystemPreferences
.java:50) ~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences$12.run(FileSystemPreferences.java
:771) ~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences$12.run(FileSystemPreferences.java
:769) ~[na:1.8.0_40]
        at java.security.AccessController.doPrivileged(Native Method)
~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences.syncSpi(FileSystemPreferences.jav
a:768) ~[na:1.8.0_40]
        at
java.util.prefs.AbstractPreferences.sync2(AbstractPreferences.java:1338
) ~[na:1.8.0_40]
        at
java.util.prefs.AbstractPreferences.sync2(AbstractPreferences.java:1343
) ~[na:1.8.0_40]
        at
java.util.prefs.AbstractPreferences.sync2(AbstractPreferences.java:1343
) ~[na:1.8.0_40]
        at
java.util.prefs.AbstractPreferences.sync2(AbstractPreferences.java:1343
) ~[na:1.8.0_40]
        at
java.util.prefs.AbstractPreferences.sync(AbstractPreferences.java:1329)
~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences.sync(FileSystemPreferences.java:7
47) ~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences.flush(FileSystemPreferences.java:
824) ~[na:1.8.0_40]
        at
org.protege.editor.core.editorkit.RecentEditorKitManager.save(RecentEdi
torKitManager.java:123) ~[protege-editor-core.jar:na]
        at
org.protege.editor.core.ProtegeApplication.stop(ProtegeApplication.java
:121) [protege-editor-core.jar:na]
        at
org.apache.felix.framework.util.SecureAction.stopActivator(SecureAction
.java:667) [org.apache.felix.main.jar:na]
        at org.apache.felix.framework.Felix.stopBundle(Felix.java:2538)
[org.apache.felix.main.jar:na]
        at
org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1317)
[org.apache.felix.main.jar:na]
        at
org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLe
velImpl.java:304) [org.apache.felix.main.jar:na]
        at java.lang.Thread.run(Thread.java:745) [na:1.8.0_40]
----------------------- Shutting down Protege ----------------------- 
Cleaning up temporary directories 
dag@dagsjobblaptop:~/Nedlastingar/Protege-5.1.0$ 

ti., 14.03.2017 kl. 17.27 +0000, skrev Tania Tudorache:

> There is also an easier way to reset the preferences: Go to the File
> -> Preferences menu, and click on the "Reset preferences.." button at
> the bottom of the Preferences panel.
>
> Tania
> From: protege-user <[hidden email]> on
> behalf of Tania Tudorache <[hidden email]>
> Sent: Tuesday, March 14, 2017 10:16:01 AM
> To: [hidden email]
> Subject: Re: [protege-user] preferences not stored
>  
> Please post the console output and the logs in ~/.protege/logs. There
> may be some error messages related to storing the preferences.
> Protege stores some of the preferences in binary format, and we know
> of other users with Ubuntu who got errors because of that.
>
> Protege uses the Java preferences, and on Linux they are stored
> in: ~/.java/.userPrefs
>
> You can try clearing the preferences, here are the instructions:
> http://protegewiki.stanford.edu/wiki/ClearingP4Preferences
>
> Tania
>
>
> From: protege-user <[hidden email]> on
> behalf of Dag Hovland <[hidden email]>
> Sent: Tuesday, March 14, 2017 3:47:26 AM
> To: [hidden email]
> Subject: [protege-user] preferences not stored
>  
> Hi! I am having trouble with the preferences disappearing between 
> sessions. I am using a fresh download of Protege-5.1 from today, with
> no 
> plugins or extensions, and whenever I restart Protege, any changes I 
> have dont to preferences are removed. They remain in effect during
> the 
> protege session, but when I exit and restart they are gone. I am
> running 
> on a ubuntu/linux machine, and I have tried deleting the .protege
> and 
> .Protege folders to no effect.
>
> Regards,
>
> Dag Hovland
>
>
>
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

protege.log (17K) Download Attachment
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Re: preferences not stored

Tania Tudorache

Hi Dag,


Thank you for providing the console and the logs. 


We had this problem reported before on Ubuntu. I have reopened the issue:

https://github.com/protegeproject/protege/issues/248


The report was related to flushing the preferences, but it is likely the long name that prevents their storing, too.


Can you check out the links in the comments of the issue, see if they are relevant for you?


Tania



From: protege-user <[hidden email]> on behalf of Dag Hovland <[hidden email]>
Sent: Wednesday, March 15, 2017 1:12:16 AM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] preferences not stored
 
Hi!

Thanks for the tips. I tried all the different ways of deleting all
preferences, and they do not help. I paste the console output from a
Protege session below, where I only open protege, reset preferences,
and then exit. .protege/logs is attached. I think the relevant error is
this:

An error occurred whilst saving the list of recent items 
java.util.pref
s.BackingStoreException:
/home/dag/.java/.userPrefs/_!&!!`g">!&@![@"(!%`!|w"@!&)![@"'!%`!`g"&!%4
!@w"&!&:=/_!%k!^g"'!%`!`g"&!%4!@w"&!&8!`!"]!%`![g"^!&8!`w"&!&@=/_!'8!cg
"n!#4!c!"y!'8!d!"l!'c!~@!u!'`!~!"p!(@!bw"y!#4!bw"3!'w!.g"t!'8!~!"l!'w!.
g"p!'4!~g"l!()!~@"u!':!~@!u!&)!~@"h!(:!bw"u!'`!cg"@!()!~@"m!'`!cg"l!'4!
}w"l!(:= create failed.

I don't know why it tries to create the preferences with such a strange folder name?

Regards,

Dag Hovland


Console log:

dag@dagsjobblaptop:~/Nedlastingar/Protege-5.1.0$ ./run.sh 
CompilerOracle: exclude javax/swing/text/GlyphView.getBreakSpot
***********************************************************************
********* 
**                                  Protege                            
       ** 
***********************************************************************
********* 
 
----------------- Initialising and Starting the OSGi Framework --------
--------- 
FrameworkFactory Class: org.apache.felix.framework.FrameworkFactory 
 
The OSGi framework has been initialised 
------------------------------- Starting Bundles ----------------------
--------- 
Starting bundle org.protege.common 
Starting bundle org.eclipse.equinox.common 
Starting bundle org.eclipse.equinox.supplement 
Starting bundle org.eclipse.equinox.registry 
Starting bundle org.protege.editor.core.application 
Starting bundle jul.to.slf4j 
Starting bundle ch.qos.logback.core 
Starting bundle org.eclipse.equinox.registry 
Starting bundle org.apache.servicemix.bundles.aopalliance 
Starting bundle com.google.inject 
Starting bundle org.semanticweb.owl.owlapi 
Starting bundle org.apache.servicemix.bundles.javax-inject 
Starting bundle org.jsr-305 
Starting bundle log4j.over.slf4j 
Starting bundle org.protege.common 
Starting bundle ch.qos.logback.classic 
Not starting bundle com.google.inject.multibindings explicitly because
it is a fragment bundle. 
Starting bundle slf4j.api 
Not starting bundle com.google.inject.assistedinject explicitly because
it is a fragment bundle. 
Starting bundle org.eclipse.equinox.common 
Starting bundle org.apache.commons.io 
Starting bundle org.protege.editor.core.application 
Starting bundle org.protege.editor.owl 
Starting bundle org.eclipse.equinox.supplement 
Starting bundle com.google.guava 
Starting bundle org.protege.ontograf 
Starting bundle org.coode.dlquery 
Starting bundle org.coode.owlviz 
Starting bundle swrltab-plugin 
Starting bundle org.coode.browser 
Starting bundle uk.ac.manchester.cs.owl.explanation 
Starting bundle org.protege.owl.rdf 
Starting bundle existentialquery 
Starting bundle cellfie 
Starting bundle org.protege.editor.owl.rdf 
Starting bundle code-generation 
Starting bundle org.semanticweb.hermit 
The OSGi framework has been started 
 
------------------------------------ Protege --------------------------
--------- 
Protege Desktop 
Version 5.1.0, Build  
 
 
----------------------------------- Platform --------------------------
--------- 
Java: JVM 1.8.0_40-b26  Memory: 466M 
Language: nb, Country: NO 
Framework: Apache Software Foundation (1.7)  
OS: linux (4.4.0-66-generic) 
Processor: x86-64
 
 
------------------------------------ Plugins --------------------------
--------- 
Plugin: OntoGraf (2.0.3) 
Plugin: DL Query (4.0.1) 
Plugin: OWLViz (5.0.3) 
Plugin: SWRLTab Protege 5.0+ Plugin (1.0.3) 
Plugin: Browser View (OWLDoc) (3.0.3) 
Plugin: Explanation Workbench (3.0.0) 
Plugin: OWLAPI RDF Library (2.0.2) 
Plugin: Existential Query (2.0.0) 
Plugin: Cellfie Protege 5.0+ Plugin (2.1.0) 
Plugin: Protege SPARQL Plugin (2.0.1) 
Plugin: OWL Code Generation Plug-in (2.0.0) 
Plugin: HermiT (1.3.8.413) 
 
Creating and setting up empty (default) editor kit 
OWL API Version: 4.2.6.20160910-2108 
Cannot generate ontology catalog for ontology at http://www.semanticweb
.org/dag/ontologies/2017/2/untitled-ontology-2 
------------------------------- Auto-update Check -------------------
----------- 
Auto-update last performed: Thu Jan 01 01:00:00 CET 1970 
Auto-update has not been performed today.  Running it. 
 
### Excluding compile: javax.swing.text.GlyphView::getBreakSpot
------------------------------ Running Auto-update --------------------
--------- 
 
--- Searching for plugins --- 
Checking https://raw.githubusercontent.com/protegeproject/autoupdate/ma
ster/update-info/5.0.0/plugins.repository 
    Processing https://raw.githubusercontent.com/protegeproject/autoupd
ate/master/update-info/5.0.0/plugins.repository as a plugin registry 
        Cannot open remote plugin registry at raw.githubusercontent.com
(Unknown Host) 
 
---------------------------- Disposing of Workspace -----------------
----------- 
Saved tab state for 'Active Ontology' tab 
Saved tab state for 'Entities' tab 
Saved tab state for 'DL Query' tab 
Saved tab state for 'Individuals by class' tab 
Saved workspace 
Disposed of 'Active Ontology' tab 
Disposed of 'Entities' tab 
Disposed of 'DL Query' tab 
Disposed of 'Individuals by class' tab 
Disposed of workspace 
 
An error occurred whilst saving the list of recent items 
java.util.prefs.BackingStoreException:
/home/dag/.java/.userPrefs/_!&!!`g">!&@![@"(!%`!|w"@!&)![@"'!%`!`g"&!%4
!@w"&!&:=/_!%k!^g"'!%`!`g"&!%4!@w"&!&8!`!"]!%`![g"^!&8!`w"&!&@=/_!'8!cg
"n!#4!c!"y!'8!d!"l!'c!~@!u!'`!~!"p!(@!bw"y!#4!bw"3!'w!.g"t!'8!~!"l!'w!.
g"p!'4!~g"l!()!~@"u!':!~@!u!&)!~@"h!(:!bw"u!'`!cg"@!()!~@"m!'`!cg"l!'4!
}w"l!(:= create failed.
        at
java.util.prefs.FileSystemPreferences$7.run(FileSystemPreferences.java:
619) ~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences$7.run(FileSystemPreferences.java:
615) ~[na:1.8.0_40]
        at java.security.AccessController.doPrivileged(Native Method)
~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences.writeBackCache(FileSystemPreferen
ces.java:614) ~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences.syncSpiPrivileged(FileSystemPrefe
rences.java:801) ~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences.access$2300(FileSystemPreferences
.java:50) ~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences$12.run(FileSystemPreferences.java
:771) ~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences$12.run(FileSystemPreferences.java
:769) ~[na:1.8.0_40]
        at java.security.AccessController.doPrivileged(Native Method)
~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences.syncSpi(FileSystemPreferences.jav
a:768) ~[na:1.8.0_40]
        at
java.util.prefs.AbstractPreferences.sync2(AbstractPreferences.java:1338
) ~[na:1.8.0_40]
        at
java.util.prefs.AbstractPreferences.sync2(AbstractPreferences.java:1343
) ~[na:1.8.0_40]
        at
java.util.prefs.AbstractPreferences.sync2(AbstractPreferences.java:1343
) ~[na:1.8.0_40]
        at
java.util.prefs.AbstractPreferences.sync2(AbstractPreferences.java:1343
) ~[na:1.8.0_40]
        at
java.util.prefs.AbstractPreferences.sync(AbstractPreferences.java:1329)
~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences.sync(FileSystemPreferences.java:7
47) ~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences.flush(FileSystemPreferences.java:
824) ~[na:1.8.0_40]
        at
org.protege.editor.core.editorkit.RecentEditorKitManager.save(RecentEdi
torKitManager.java:123) ~[protege-editor-core.jar:na]
        at
org.protege.editor.core.ProtegeApplication.stop(ProtegeApplication.java
:121) [protege-editor-core.jar:na]
        at
org.apache.felix.framework.util.SecureAction.stopActivator(SecureAction
.java:667) [org.apache.felix.main.jar:na]
        at org.apache.felix.framework.Felix.stopBundle(Felix.java:2538)
[org.apache.felix.main.jar:na]
        at
org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1317)
[org.apache.felix.main.jar:na]
        at
org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLe
velImpl.java:304) [org.apache.felix.main.jar:na]
        at java.lang.Thread.run(Thread.java:745) [na:1.8.0_40]
----------------------- Shutting down Protege ----------------------- 
Cleaning up temporary directories 
dag@dagsjobblaptop:~/Nedlastingar/Protege-5.1.0$ 

ti., 14.03.2017 kl. 17.27 +0000, skrev Tania Tudorache:
> There is also an easier way to reset the preferences: Go to the File
> -> Preferences menu, and click on the "Reset preferences.." button at
> the bottom of the Preferences panel.
>
> Tania
> From: protege-user <[hidden email]> on
> behalf of Tania Tudorache <[hidden email]>
> Sent: Tuesday, March 14, 2017 10:16:01 AM
> To: [hidden email]
> Subject: Re: [protege-user] preferences not stored
>  
> Please post the console output and the logs in ~/.protege/logs. There
> may be some error messages related to storing the preferences.
> Protege stores some of the preferences in binary format, and we know
> of other users with Ubuntu who got errors because of that.
>
> Protege uses the Java preferences, and on Linux they are stored
> in: ~/.java/.userPrefs
>
> You can try clearing the preferences, here are the instructions:
> http://protegewiki.stanford.edu/wiki/ClearingP4Preferences
>
> Tania
>
>
> From: protege-user <[hidden email]> on
> behalf of Dag Hovland <[hidden email]>
> Sent: Tuesday, March 14, 2017 3:47:26 AM
> To: [hidden email]
> Subject: [protege-user] preferences not stored
>  
> Hi! I am having trouble with the preferences disappearing between 
> sessions. I am using a fresh download of Protege-5.1 from today, with
> no 
> plugins or extensions, and whenever I restart Protege, any changes I 
> have dont to preferences are removed. They remain in effect during
> the 
> protege session, but when I exit and restart they are gone. I am
> running 
> on a ubuntu/linux machine, and I have tried deleting the .protege
> and 
> .Protege folders to no effect.
>
> Regards,
>
> Dag Hovland
>
>
>
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
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Re: preferences not stored

hovlanddag

Hi Tania. Thanks for the links. I do indeed have the same encrypted file system setup as one of the previous reporters. One of the links mentions that a proabably cause is a violation of the 143 characters maximum length of filenames in this setup. Could this still be the case?


Regards,


Dag Hovland


Den 18. mars 2017 00:09, skrev Tania Tudorache:

Hi Dag,


Thank you for providing the console and the logs. 


We had this problem reported before on Ubuntu. I have reopened the issue:

https://github.com/protegeproject/protege/issues/248


The report was related to flushing the preferences, but it is likely the long name that prevents their storing, too.


Can you check out the links in the comments of the issue, see if they are relevant for you?


Tania



From: protege-user [hidden email] on behalf of Dag Hovland [hidden email]
Sent: Wednesday, March 15, 2017 1:12:16 AM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] preferences not stored
 
Hi!

Thanks for the tips. I tried all the different ways of deleting all
preferences, and they do not help. I paste the console output from a
Protege session below, where I only open protege, reset preferences,
and then exit. .protege/logs is attached. I think the relevant error is
this:

An error occurred whilst saving the list of recent items 
java.util.pref
s.BackingStoreException:
/home/dag/.java/.userPrefs/_!&!!`g">!&@![@"(!%`!|w"@!&)![@"'!%`!`g"&!%4
!@w"&!&:=/_!%k!^g"'!%`!`g"&!%4!@w"&!&8!`!"]!%`![g"^!&8!`w"&!&@=/_!'8!cg
"n!#4!c!"y!'8!d!"l!'c!~@!u!'`!~!"p!(@!bw"y!#4!bw"3!'w!.g"t!'8!~!"l!'w!.
g"p!'4!~g"l!()!~@"u!':!~@!u!&)!~@"h!(:!bw"u!'`!cg"@!()!~@"m!'`!cg"l!'4!
}w"l!(:= create failed.

I don't know why it tries to create the preferences with such a strange folder name?

Regards,

Dag Hovland


Console log:

[hidden email] ./run.sh 
CompilerOracle: exclude javax/swing/text/GlyphView.getBreakSpot
***********************************************************************
********* 
**                                  Protege                            
       ** 
***********************************************************************
********* 
 
----------------- Initialising and Starting the OSGi Framework --------
--------- 
FrameworkFactory Class: org.apache.felix.framework.FrameworkFactory 
 
The OSGi framework has been initialised 
------------------------------- Starting Bundles ----------------------
--------- 
Starting bundle org.protege.common 
Starting bundle org.eclipse.equinox.common 
Starting bundle org.eclipse.equinox.supplement 
Starting bundle org.eclipse.equinox.registry 
Starting bundle org.protege.editor.core.application 
Starting bundle jul.to.slf4j 
Starting bundle ch.qos.logback.core 
Starting bundle org.eclipse.equinox.registry 
Starting bundle org.apache.servicemix.bundles.aopalliance 
Starting bundle com.google.inject 
Starting bundle org.semanticweb.owl.owlapi 
Starting bundle org.apache.servicemix.bundles.javax-inject 
Starting bundle org.jsr-305 
Starting bundle log4j.over.slf4j 
Starting bundle org.protege.common 
Starting bundle ch.qos.logback.classic 
Not starting bundle com.google.inject.multibindings explicitly because
it is a fragment bundle. 
Starting bundle slf4j.api 
Not starting bundle com.google.inject.assistedinject explicitly because
it is a fragment bundle. 
Starting bundle org.eclipse.equinox.common 
Starting bundle org.apache.commons.io 
Starting bundle org.protege.editor.core.application 
Starting bundle org.protege.editor.owl 
Starting bundle org.eclipse.equinox.supplement 
Starting bundle com.google.guava 
Starting bundle org.protege.ontograf 
Starting bundle org.coode.dlquery 
Starting bundle org.coode.owlviz 
Starting bundle swrltab-plugin 
Starting bundle org.coode.browser 
Starting bundle uk.ac.manchester.cs.owl.explanation 
Starting bundle org.protege.owl.rdf 
Starting bundle existentialquery 
Starting bundle cellfie 
Starting bundle org.protege.editor.owl.rdf 
Starting bundle code-generation 
Starting bundle org.semanticweb.hermit 
The OSGi framework has been started 
 
------------------------------------ Protege --------------------------
--------- 
Protege Desktop 
Version 5.1.0, Build  
 
 
----------------------------------- Platform --------------------------
--------- 
Java: JVM 1.8.0_40-b26  Memory: 466M 
Language: nb, Country: NO 
Framework: Apache Software Foundation (1.7)  
OS: linux (4.4.0-66-generic) 
Processor: x86-64
 
 
------------------------------------ Plugins --------------------------
--------- 
Plugin: OntoGraf (2.0.3) 
Plugin: DL Query (4.0.1) 
Plugin: OWLViz (5.0.3) 
Plugin: SWRLTab Protege 5.0+ Plugin (1.0.3) 
Plugin: Browser View (OWLDoc) (3.0.3) 
Plugin: Explanation Workbench (3.0.0) 
Plugin: OWLAPI RDF Library (2.0.2) 
Plugin: Existential Query (2.0.0) 
Plugin: Cellfie Protege 5.0+ Plugin (2.1.0) 
Plugin: Protege SPARQL Plugin (2.0.1) 
Plugin: OWL Code Generation Plug-in (2.0.0) 
Plugin: HermiT (1.3.8.413) 
 
Creating and setting up empty (default) editor kit 
OWL API Version: 4.2.6.20160910-2108 
Cannot generate ontology catalog for ontology at http://www.semanticweb
.org/dag/ontologies/2017/2/untitled-ontology-2 
------------------------------- Auto-update Check -------------------
----------- 
Auto-update last performed: Thu Jan 01 01:00:00 CET 1970 
Auto-update has not been performed today.  Running it. 
 
### Excluding compile: javax.swing.text.GlyphView::getBreakSpot
------------------------------ Running Auto-update --------------------
--------- 
 
--- Searching for plugins --- 
Checking https://raw.githubusercontent.com/protegeproject/autoupdate/ma
ster/update-info/5.0.0/plugins.repository 
    Processing https://raw.githubusercontent.com/protegeproject/autoupd
ate/master/update-info/5.0.0/plugins.repository as a plugin registry 
        Cannot open remote plugin registry at raw.githubusercontent.com
(Unknown Host) 
 
---------------------------- Disposing of Workspace -----------------
----------- 
Saved tab state for 'Active Ontology' tab 
Saved tab state for 'Entities' tab 
Saved tab state for 'DL Query' tab 
Saved tab state for 'Individuals by class' tab 
Saved workspace 
Disposed of 'Active Ontology' tab 
Disposed of 'Entities' tab 
Disposed of 'DL Query' tab 
Disposed of 'Individuals by class' tab 
Disposed of workspace 
 
An error occurred whilst saving the list of recent items 
java.util.prefs.BackingStoreException:
/home/dag/.java/.userPrefs/_!&!!`g">!&@![@"(!%`!|w"@!&)![@"'!%`!`g"&!%4
!@w"&!&:=/_!%k!^g"'!%`!`g"&!%4!@w"&!&8!`!"]!%`![g"^!&8!`w"&!&@=/_!'8!cg
"n!#4!c!"y!'8!d!"l!'c!~@!u!'`!~!"p!(@!bw"y!#4!bw"3!'w!.g"t!'8!~!"l!'w!.
g"p!'4!~g"l!()!~@"u!':!~@!u!&)!~@"h!(:!bw"u!'`!cg"@!()!~@"m!'`!cg"l!'4!
}w"l!(:= create failed.
        at
java.util.prefs.FileSystemPreferences$7.run(FileSystemPreferences.java:
619) ~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences$7.run(FileSystemPreferences.java:
615) ~[na:1.8.0_40]
        at java.security.AccessController.doPrivileged(Native Method)
~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences.writeBackCache(FileSystemPreferen
ces.java:614) ~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences.syncSpiPrivileged(FileSystemPrefe
rences.java:801) ~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences.access$2300(FileSystemPreferences
.java:50) ~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences$12.run(FileSystemPreferences.java
:771) ~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences$12.run(FileSystemPreferences.java
:769) ~[na:1.8.0_40]
        at java.security.AccessController.doPrivileged(Native Method)
~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences.syncSpi(FileSystemPreferences.jav
a:768) ~[na:1.8.0_40]
        at
java.util.prefs.AbstractPreferences.sync2(AbstractPreferences.java:1338
) ~[na:1.8.0_40]
        at
java.util.prefs.AbstractPreferences.sync2(AbstractPreferences.java:1343
) ~[na:1.8.0_40]
        at
java.util.prefs.AbstractPreferences.sync2(AbstractPreferences.java:1343
) ~[na:1.8.0_40]
        at
java.util.prefs.AbstractPreferences.sync2(AbstractPreferences.java:1343
) ~[na:1.8.0_40]
        at
java.util.prefs.AbstractPreferences.sync(AbstractPreferences.java:1329)
~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences.sync(FileSystemPreferences.java:7
47) ~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences.flush(FileSystemPreferences.java:
824) ~[na:1.8.0_40]
        at
org.protege.editor.core.editorkit.RecentEditorKitManager.save(RecentEdi
torKitManager.java:123) ~[protege-editor-core.jar:na]
        at
org.protege.editor.core.ProtegeApplication.stop(ProtegeApplication.java
:121) [protege-editor-core.jar:na]
        at
org.apache.felix.framework.util.SecureAction.stopActivator(SecureAction
.java:667) [org.apache.felix.main.jar:na]
        at org.apache.felix.framework.Felix.stopBundle(Felix.java:2538)
[org.apache.felix.main.jar:na]
        at
org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1317)
[org.apache.felix.main.jar:na]
        at
org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLe
velImpl.java:304) [org.apache.felix.main.jar:na]
        at java.lang.Thread.run(Thread.java:745) [na:1.8.0_40]
----------------------- Shutting down Protege ----------------------- 
Cleaning up temporary directories 
[hidden email] 

ti., 14.03.2017 kl. 17.27 +0000, skrev Tania Tudorache:
> There is also an easier way to reset the preferences: Go to the File
> -> Preferences menu, and click on the "Reset preferences.." button at
> the bottom of the Preferences panel.
>
> Tania
> From: protege-user [hidden email] on
> behalf of Tania Tudorache [hidden email]
> Sent: Tuesday, March 14, 2017 10:16:01 AM
> To: [hidden email]
> Subject: Re: [protege-user] preferences not stored
>  
> Please post the console output and the logs in ~/.protege/logs. There
> may be some error messages related to storing the preferences.
> Protege stores some of the preferences in binary format, and we know
> of other users with Ubuntu who got errors because of that.
>
> Protege uses the Java preferences, and on Linux they are stored
> in: ~/.java/.userPrefs
>
> You can try clearing the preferences, here are the instructions:
> http://protegewiki.stanford.edu/wiki/ClearingP4Preferences
>
> Tania
>
>
> From: protege-user [hidden email] on
> behalf of Dag Hovland [hidden email]
> Sent: Tuesday, March 14, 2017 3:47:26 AM
> To: [hidden email]
> Subject: [protege-user] preferences not stored
>  
> Hi! I am having trouble with the preferences disappearing between 
> sessions. I am using a fresh download of Protege-5.1 from today, with
> no 
> plugins or extensions, and whenever I restart Protege, any changes I 
> have dont to preferences are removed. They remain in effect during
> the 
> protege session, but when I exit and restart they are gone. I am
> running 
> on a ubuntu/linux machine, and I have tried deleting the .protege
> and 
> .Protege folders to no effect.
>
> Regards,
>
> Dag Hovland
>
>
>
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

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Re: preferences not stored

Tania Tudorache

Yes, it is probably the same 143 character length file name issue. I am afraid there is no good solution for it, though, expect not using the double-encryption.


Tania


From: protege-user <[hidden email]> on behalf of Dag Hovland <[hidden email]>
Sent: Monday, March 20, 2017 1:38:46 AM
To: [hidden email]
Subject: Re: [protege-user] preferences not stored
 

Hi Tania. Thanks for the links. I do indeed have the same encrypted file system setup as one of the previous reporters. One of the links mentions that a proabably cause is a violation of the 143 characters maximum length of filenames in this setup. Could this still be the case?


Regards,


Dag Hovland


Den 18. mars 2017 00:09, skrev Tania Tudorache:

Hi Dag,


Thank you for providing the console and the logs. 


We had this problem reported before on Ubuntu. I have reopened the issue:

https://github.com/protegeproject/protege/issues/248


The report was related to flushing the preferences, but it is likely the long name that prevents their storing, too.


Can you check out the links in the comments of the issue, see if they are relevant for you?


Tania



From: protege-user [hidden email] on behalf of Dag Hovland [hidden email]
Sent: Wednesday, March 15, 2017 1:12:16 AM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] preferences not stored
 
Hi!

Thanks for the tips. I tried all the different ways of deleting all
preferences, and they do not help. I paste the console output from a
Protege session below, where I only open protege, reset preferences,
and then exit. .protege/logs is attached. I think the relevant error is
this:

An error occurred whilst saving the list of recent items 
java.util.pref
s.BackingStoreException:
/home/dag/.java/.userPrefs/_!&!!`g">!&@![@"(!%`!|w"@!&)![@"'!%`!`g"&!%4
!@w"&!&:=/_!%k!^g"'!%`!`g"&!%4!@w"&!&8!`!"]!%`![g"^!&8!`w"&!&@=/_!'8!cg
"n!#4!c!"y!'8!d!"l!'c!~@!u!'`!~!"p!(@!bw"y!#4!bw"3!'w!.g"t!'8!~!"l!'w!.
g"p!'4!~g"l!()!~@"u!':!~@!u!&)!~@"h!(:!bw"u!'`!cg"@!()!~@"m!'`!cg"l!'4!
}w"l!(:= create failed.

I don't know why it tries to create the preferences with such a strange folder name?

Regards,

Dag Hovland


Console log:

[hidden email] ./run.sh 
CompilerOracle: exclude javax/swing/text/GlyphView.getBreakSpot
***********************************************************************
********* 
**                                  Protege                            
       ** 
***********************************************************************
********* 
 
----------------- Initialising and Starting the OSGi Framework --------
--------- 
FrameworkFactory Class: org.apache.felix.framework.FrameworkFactory 
 
The OSGi framework has been initialised 
------------------------------- Starting Bundles ----------------------
--------- 
Starting bundle org.protege.common 
Starting bundle org.eclipse.equinox.common 
Starting bundle org.eclipse.equinox.supplement 
Starting bundle org.eclipse.equinox.registry 
Starting bundle org.protege.editor.core.application 
Starting bundle jul.to.slf4j 
Starting bundle ch.qos.logback.core 
Starting bundle org.eclipse.equinox.registry 
Starting bundle org.apache.servicemix.bundles.aopalliance 
Starting bundle com.google.inject 
Starting bundle org.semanticweb.owl.owlapi 
Starting bundle org.apache.servicemix.bundles.javax-inject 
Starting bundle org.jsr-305 
Starting bundle log4j.over.slf4j 
Starting bundle org.protege.common 
Starting bundle ch.qos.logback.classic 
Not starting bundle com.google.inject.multibindings explicitly because
it is a fragment bundle. 
Starting bundle slf4j.api 
Not starting bundle com.google.inject.assistedinject explicitly because
it is a fragment bundle. 
Starting bundle org.eclipse.equinox.common 
Starting bundle org.apache.commons.io 
Starting bundle org.protege.editor.core.application 
Starting bundle org.protege.editor.owl 
Starting bundle org.eclipse.equinox.supplement 
Starting bundle com.google.guava 
Starting bundle org.protege.ontograf 
Starting bundle org.coode.dlquery 
Starting bundle org.coode.owlviz 
Starting bundle swrltab-plugin 
Starting bundle org.coode.browser 
Starting bundle uk.ac.manchester.cs.owl.explanation 
Starting bundle org.protege.owl.rdf 
Starting bundle existentialquery 
Starting bundle cellfie 
Starting bundle org.protege.editor.owl.rdf 
Starting bundle code-generation 
Starting bundle org.semanticweb.hermit 
The OSGi framework has been started 
 
------------------------------------ Protege --------------------------
--------- 
Protege Desktop 
Version 5.1.0, Build  
 
 
----------------------------------- Platform --------------------------
--------- 
Java: JVM 1.8.0_40-b26  Memory: 466M 
Language: nb, Country: NO 
Framework: Apache Software Foundation (1.7)  
OS: linux (4.4.0-66-generic) 
Processor: x86-64
 
 
------------------------------------ Plugins --------------------------
--------- 
Plugin: OntoGraf (2.0.3) 
Plugin: DL Query (4.0.1) 
Plugin: OWLViz (5.0.3) 
Plugin: SWRLTab Protege 5.0+ Plugin (1.0.3) 
Plugin: Browser View (OWLDoc) (3.0.3) 
Plugin: Explanation Workbench (3.0.0) 
Plugin: OWLAPI RDF Library (2.0.2) 
Plugin: Existential Query (2.0.0) 
Plugin: Cellfie Protege 5.0+ Plugin (2.1.0) 
Plugin: Protege SPARQL Plugin (2.0.1) 
Plugin: OWL Code Generation Plug-in (2.0.0) 
Plugin: HermiT (1.3.8.413) 
 
Creating and setting up empty (default) editor kit 
OWL API Version: 4.2.6.20160910-2108 
Cannot generate ontology catalog for ontology at http://www.semanticweb
.org/dag/ontologies/2017/2/untitled-ontology-2 
------------------------------- Auto-update Check -------------------
----------- 
Auto-update last performed: Thu Jan 01 01:00:00 CET 1970 
Auto-update has not been performed today.  Running it. 
 
### Excluding compile: javax.swing.text.GlyphView::getBreakSpot
------------------------------ Running Auto-update --------------------
--------- 
 
--- Searching for plugins --- 
Checking https://raw.githubusercontent.com/protegeproject/autoupdate/ma
ster/update-info/5.0.0/plugins.repository 
    Processing https://raw.githubusercontent.com/protegeproject/autoupd
ate/master/update-info/5.0.0/plugins.repository as a plugin registry 
        Cannot open remote plugin registry at raw.githubusercontent.com
(Unknown Host) 
 
---------------------------- Disposing of Workspace -----------------
----------- 
Saved tab state for 'Active Ontology' tab 
Saved tab state for 'Entities' tab 
Saved tab state for 'DL Query' tab 
Saved tab state for 'Individuals by class' tab 
Saved workspace 
Disposed of 'Active Ontology' tab 
Disposed of 'Entities' tab 
Disposed of 'DL Query' tab 
Disposed of 'Individuals by class' tab 
Disposed of workspace 
 
An error occurred whilst saving the list of recent items 
java.util.prefs.BackingStoreException:
/home/dag/.java/.userPrefs/_!&!!`g">!&@![@"(!%`!|w"@!&)![@"'!%`!`g"&!%4
!@w"&!&:=/_!%k!^g"'!%`!`g"&!%4!@w"&!&8!`!"]!%`![g"^!&8!`w"&!&@=/_!'8!cg
"n!#4!c!"y!'8!d!"l!'c!~@!u!'`!~!"p!(@!bw"y!#4!bw"3!'w!.g"t!'8!~!"l!'w!.
g"p!'4!~g"l!()!~@"u!':!~@!u!&)!~@"h!(:!bw"u!'`!cg"@!()!~@"m!'`!cg"l!'4!
}w"l!(:= create failed.
        at
java.util.prefs.FileSystemPreferences$7.run(FileSystemPreferences.java:
619) ~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences$7.run(FileSystemPreferences.java:
615) ~[na:1.8.0_40]
        at java.security.AccessController.doPrivileged(Native Method)
~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences.writeBackCache(FileSystemPreferen
ces.java:614) ~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences.syncSpiPrivileged(FileSystemPrefe
rences.java:801) ~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences.access$2300(FileSystemPreferences
.java:50) ~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences$12.run(FileSystemPreferences.java
:771) ~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences$12.run(FileSystemPreferences.java
:769) ~[na:1.8.0_40]
        at java.security.AccessController.doPrivileged(Native Method)
~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences.syncSpi(FileSystemPreferences.jav
a:768) ~[na:1.8.0_40]
        at
java.util.prefs.AbstractPreferences.sync2(AbstractPreferences.java:1338
) ~[na:1.8.0_40]
        at
java.util.prefs.AbstractPreferences.sync2(AbstractPreferences.java:1343
) ~[na:1.8.0_40]
        at
java.util.prefs.AbstractPreferences.sync2(AbstractPreferences.java:1343
) ~[na:1.8.0_40]
        at
java.util.prefs.AbstractPreferences.sync2(AbstractPreferences.java:1343
) ~[na:1.8.0_40]
        at
java.util.prefs.AbstractPreferences.sync(AbstractPreferences.java:1329)
~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences.sync(FileSystemPreferences.java:7
47) ~[na:1.8.0_40]
        at
java.util.prefs.FileSystemPreferences.flush(FileSystemPreferences.java:
824) ~[na:1.8.0_40]
        at
org.protege.editor.core.editorkit.RecentEditorKitManager.save(RecentEdi
torKitManager.java:123) ~[protege-editor-core.jar:na]
        at
org.protege.editor.core.ProtegeApplication.stop(ProtegeApplication.java
:121) [protege-editor-core.jar:na]
        at
org.apache.felix.framework.util.SecureAction.stopActivator(SecureAction
.java:667) [org.apache.felix.main.jar:na]
        at org.apache.felix.framework.Felix.stopBundle(Felix.java:2538)
[org.apache.felix.main.jar:na]
        at
org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1317)
[org.apache.felix.main.jar:na]
        at
org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLe
velImpl.java:304) [org.apache.felix.main.jar:na]
        at java.lang.Thread.run(Thread.java:745) [na:1.8.0_40]
----------------------- Shutting down Protege ----------------------- 
Cleaning up temporary directories 
[hidden email] 

ti., 14.03.2017 kl. 17.27 +0000, skrev Tania Tudorache:
> There is also an easier way to reset the preferences: Go to the File
> -> Preferences menu, and click on the "Reset preferences.." button at
> the bottom of the Preferences panel.
>
> Tania
> From: protege-user [hidden email] on
> behalf of Tania Tudorache [hidden email]
> Sent: Tuesday, March 14, 2017 10:16:01 AM
> To: [hidden email]
> Subject: Re: [protege-user] preferences not stored
>  
> Please post the console output and the logs in ~/.protege/logs. There
> may be some error messages related to storing the preferences.
> Protege stores some of the preferences in binary format, and we know
> of other users with Ubuntu who got errors because of that.
>
> Protege uses the Java preferences, and on Linux they are stored
> in: ~/.java/.userPrefs
>
> You can try clearing the preferences, here are the instructions:
> http://protegewiki.stanford.edu/wiki/ClearingP4Preferences
>
> Tania
>
>
> From: protege-user [hidden email] on
> behalf of Dag Hovland [hidden email]
> Sent: Tuesday, March 14, 2017 3:47:26 AM
> To: [hidden email]
> Subject: [protege-user] preferences not stored
>  
> Hi! I am having trouble with the preferences disappearing between 
> sessions. I am using a fresh download of Protege-5.1 from today, with
> no 
> plugins or extensions, and whenever I restart Protege, any changes I 
> have dont to preferences are removed. They remain in effect during
> the 
> protege session, but when I exit and restart they are gone. I am
> running 
> on a ubuntu/linux machine, and I have tried deleting the .protege
> and 
> .Protege folders to no effect.
>
> Regards,
>
> Dag Hovland
>
>
>
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