freezes on macOS High Sierra #3236

iTao8 · 2017-09-27T05:17:43Z

Open a library
double click an entry to open the entry editor
freezes

When the entry editor is opened, then move the down arrow to move the entry to the next one, and then freezes

JabRef 4.0-dev--snapshot--2017-09-26--master--35c447bd8
Mac OS X 10.13 x86_64
Java 1.8.0_144

This problem appears on the version snapshot--2017-09-26 and the current one

chochreiner · 2017-09-29T10:10:55Z

I can confirm this bug on High Sierra (10.13), which was not there on Sierra (10.12).
This bug only affects the entry editor, but not the about window (which is also a javafx component).
There are no hints in the log files/console output and updating to the java8u152(beta) did not change anything.
Is there any high resolution specific stuff in the entry editor (especially fonts)? @tobiasdiez

tobiasdiez · 2017-09-29T13:12:08Z

There is no real difference between the entry editor and other javafx implementations (like the groups interface or the search bar). The entry editor however accesses the file system, maybe the problem lies there. Can you please create a thread dump and/or use a debugger to investigate this problem further? Thanks!

chochreiner · 2017-09-29T14:25:04Z

There seems to be an issue with the related articles tab.
When I am within the university network, the performance is okish, but otherwise it is not acceptable.

@iTao8 could you please try to disable the "related articles" tab in the preferences (Entry editor -> "Show 'Related Articles' tab"

iTao8 · 2017-09-29T17:47:36Z

@chochreiner The "related articles" tab is always disabled.

chochreiner · 2017-09-29T17:56:59Z

@tobiasdiez are there any other requests to scientific portals like ieee, acm, ... which could result in a timeout outside of university networks/when the user has no permission to access these services

matthiasgeiger · 2017-09-29T20:47:38Z

Potentially #3227?

manfredlift · 2017-10-04T19:18:20Z

For anyone on macOS Sierra, I had the same issue on 4.0.0 and following the workaround in #3227 fixed it.

tobiasdiez · 2017-10-05T02:33:40Z

@manfredlift (or somebody else using macOS): you you please add the workaround in the installation notes so that new users find the information more easily. Thanks!

dvbowen · 2017-10-12T17:45:34Z

With version 4.0 (on macOS Sierra 10.12.6) I'm getting the freeze after the following steps:

"Press the add article button" ;
Paste a reference into the "biblatex source" pane after copying from Chrome;
Jabref hangs after either a) highlighting a piece of text in the "biblatex source" pane with the cursor, or b) simply selecting the "General" pane.

Appending my host name to localhost in /etc/hosts (and then rebooting) has no effect. This is a machine connected to a university network however. Haven't tried 4.0 at home yet.

Problem seems to be consistently reproducible. :(

adcox · 2017-10-13T13:47:50Z

I am running into the same error. I downloaded JabRef-4.0.jar from the repo and ran it from the terminal to capture the output. When I first open the program, the output is

09:42:25.693 [AWT-EventQueue-0] INFO  org.jabref.logic.importer.OpenDatabase - Opening: PaperDatabase_JabRef.bib
Oct 13, 2017 9:42:26 AM com.sun.javafx.css.StyleConverterImpl getInstance
SEVERE: StyleConverterImpl : converter Class is null for : com.sun.javafx.scene.layout.region.CornerRadiiConverter
Oct 13, 2017 9:42:26 AM com.sun.javafx.css.StyleConverterImpl readBinary
SEVERE: could not deserialize com.sun.javafx.scene.layout.region.CornerRadiiConverter
could not deserialize com.sun.javafx.scene.layout.region.CornerRadiiConverter
File: grouptree.fxml not found, attempting with camel case
Oct 13, 2017 9:42:27 AM javafx.fxml.FXMLLoader$ValueElement processValue
WARNING: Loading FXML document with JavaFX API of version 8.0.112 by JavaFX runtime of version 8.0.45
File: grouptree.css not found, attempting with camel case

Then, when I click on the add entry button and select "Article", an exception is thrown:

WARNING: Loading FXML document with JavaFX API of version 8.0.112 by JavaFX runtime of version 8.0.45
09:44:06.321 [AWT-EventQueue-0] ERROR org.jabref.FallbackExceptionHandler - Uncaught exception occurred in Thread[AWT-EventQueue-0,6,main]
java.lang.NullPointerException: null
	at javafx.embed.swing.JFXPanel$HostContainer.lambda$setEmbeddedScene$53(JFXPanel.java:929) ~[jfxrt.jar:?]
	at javafx.embed.swing.JFXPanel$HostContainer$$Lambda$873/1399918834.run(Unknown Source) ~[?:?]
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) ~[?:1.8.0_45]
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) ~[?:1.8.0_45]
	at java.awt.EventQueue.access$500(EventQueue.java:97) ~[?:1.8.0_45]
	at java.awt.EventQueue$3.run(EventQueue.java:709) ~[?:1.8.0_45]
	at java.awt.EventQueue$3.run(EventQueue.java:703) ~[?:1.8.0_45]
	at java.security.AccessController.doPrivileged(Native Method) ~[?:1.8.0_45]
	at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75) ~[?:1.8.0_45]
	at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:86) ~[?:1.8.0_45]
	at java.awt.EventQueue$4.run(EventQueue.java:731) ~[?:1.8.0_45]
	at java.awt.EventQueue$4.run(EventQueue.java:729) ~[?:1.8.0_45]
	at java.security.AccessController.doPrivileged(Native Method) ~[?:1.8.0_45]
	at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75) ~[?:1.8.0_45]
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) ~[?:1.8.0_45]
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [?:1.8.0_45]
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [?:1.8.0_45]
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [?:1.8.0_45]
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [?:1.8.0_45]
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [?:1.8.0_45]
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [?:1.8.0_45]

I will note that the program doesn't hang when I'm running it in this mode, although it does hang when I run the bundled application version installed by the dmg.

lenhard · 2017-10-13T14:36:22Z

I have now added a note regarding the host mapping solution for the freezes into the installation help. Hopefully, this helps some users to fix their setup instead of reporting an issue here.

@adcox The log says that you have an older JavaFX runtime installed. This might be the reason why some classes cannot be instantiated and trigger a NullPointerException later. Please make sure you have an up-to-date version of JavaFX on your system.

bdcaf · 2017-10-16T10:05:20Z

Regarding the hostname - can you confirm what hostname outputs agrees to your hosts file?
If not you can in addition try to manually set it: https://superuser.com/questions/49891/how-can-i-stop-mac-os-x-overriding-my-hostname-when-i-receive-a-dhcp-request-on#50104

dvbowen · 2017-10-16T18:12:25Z

Yep, % hostname gives the correct hostname, as set in /etc/hosts.

dvbowen · 2017-10-16T18:20:32Z

Oh... and what version of Java should I be using? In the Settings panel, it tells me I have v9, build 9+181. I'm not sure I even know what "javaFX" is I'm afraid 😀

LinusDietz · 2017-10-16T20:43:45Z

@dvbowen you need to use java 8. http://blog.jabref.org/#october-04-2017-–-jabref-4-0

dvbowen · 2017-10-16T22:27:07Z

@lynyus thanks! May have fixed this. For others....

deleted Java 9
installed Java 8u144
installed JDK 8u144
removed /Applications/JabRef.app/
reinstalled JabRef v4
rebooted

I've actually gotten as far as adding a new entry without JabRef 4 hanging, so, fingers-crossed....

gsk1692 · 2017-10-18T15:02:06Z

Did u get it working?
Actually I am on Java 8 and I still have this problem. Am I missing anything?

EDIT: Actually, I found that the freeze is temporary. It shows that its loading and stays frozen for around 5 minutes and then start working. But this happens every time I try to add a new publication.

dvbowen · 2017-10-18T20:14:55Z

Yeah, I wrote too soon. I get further than I did to start with, but I now regularly freeze on the "open file" command in the "General" pane. This is very funny, because earlier versions of JabRef had a button that simply let me link to a pdf file (in a local dropbox folder) that had the same name as the Bibtexkey. That option seems to have disappeared (somewhere new in "Options" perhaps? Can't see it).

Need to downgrade my version of Jabref. Hope the older versions are still kicking around....

serialc · 2017-11-17T22:43:27Z

Hi,

I have the same issue. Double clicking on a record or selecting the next record when the TableEntry is open causes a ~30 second hang.

JabRef 4.1-dev--snapshot--2017-11-13--master--c1d425a31
Mac OS X 10.13.1 x86_64 
Java 1.8.0_152

I resolved the issue by following the links above. I thought I would make it explicit here for others as it took me a little while to get it right.

I found my hostname by typing 'hostname' in terminal (Mine is called carbon.local). At first I thought the hostname specified in System Preferences -> Sharing -> Computer Name (Carbon) was the full hostname. It isn't.

In my /etc/hosts file I replaced the line:
127.0.0.1 localhost
with:
127.0.0.1 localhost carbon.local
That's it - bliss has instantly returned to JabRef. No need to restart JabRef.

Here is the portion of the dump (kill -3 ps#) that caused the hang:

"JavaFX Application Thread" #12 prio=5 os_prio=31 tid=0x00007fed9e97c000 nid=0x307 runnable [0x00007ffee1c16000]
   java.lang.Thread.State: RUNNABLE
	at java.net.Inet6AddressImpl.lookupAllHostAddr(Native Method)
	at java.net.InetAddress$2.lookupAllHostAddr(InetAddress.java:928)
	at java.net.InetAddress.getAddressesFromNameService(InetAddress.java:1323)
	at java.net.InetAddress.getLocalHost(InetAddress.java:1500)
	- locked <0x0000000740014330> (a java.lang.Object)
	at org.jabref.preferences.JabRefPreferences.getUser(JabRefPreferences.java:938)
	at org.jabref.preferences.JabRefPreferences.getFileDirectoryPreferences(JabRefPreferences.java:1382)
	at org.jabref.gui.fieldeditors.FieldEditors.getForField(FieldEditors.java:35)
	at org.jabref.gui.entryeditor.FieldsEditorTab.setupPanel(FieldsEditorTab.java:75)
	at org.jabref.gui.entryeditor.FieldsEditorTab.bindToEntry(FieldsEditorTab.java:220)
	at org.jabref.gui.entryeditor.EntryEditorTab.notifyAboutFocus(EntryEditorTab.java:35)
	at org.jabref.gui.entryeditor.EntryEditor.lambda$setEntry$3(EntryEditor.java:211)
	at org.jabref.gui.entryeditor.EntryEditor$$Lambda$770/690621272.run(Unknown Source)
	at com.sun.javafx.application.PlatformImpl.lambda$null$172(PlatformImpl.java:295)
	at com.sun.javafx.application.PlatformImpl$$Lambda$49/1611113609.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at com.sun.javafx.application.PlatformImpl.lambda$runLater$173(PlatformImpl.java:294)
	at com.sun.javafx.application.PlatformImpl$$Lambda$48/1567581361.run(Unknown Source)
	at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:95)

koppor · 2018-07-09T07:20:34Z

Refs #3995.

Siedlerchr · 2018-10-27T18:55:38Z

Closing this issue due to inactivity 💤
Please reopen the issue with additional information if the problem persists.

stefan-kolb added the os: macOS label Sep 27, 2017

This was referenced Oct 13, 2017

Freeze when New Entry clicked | Mac OS Sierra #3296

Closed

MacOS Sierra - Crash while copy a code to '{}BibTex - sourcecode' #3290

Closed

lenhard mentioned this issue Oct 13, 2017

Jabref not opening window after fresh installation on macOS High Sierra #3298

Closed

tobiasdiez mentioned this issue Oct 29, 2017

BibTex editor cannot open #3371

Closed

tobiasdiez added the bug Confirmed bugs or reports that are very likely to be bugs label Oct 29, 2017

koppor mentioned this issue Dec 30, 2017

JR still hangs in High Sierra Mac #3589

Closed

Siedlerchr closed this as completed Oct 27, 2018

CharlesVilliers mentioned this issue Nov 21, 2018

Still freezes on macOS High Sierra #3995

Closed

champagnealexandre mentioned this issue Jan 3, 2019

Impossible to get JabRef running on MacOS Mojave 10.14.2 #4563

Closed

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freezes on macOS High Sierra #3236

freezes on macOS High Sierra #3236

iTao8 commented Sep 27, 2017

chochreiner commented Sep 29, 2017

tobiasdiez commented Sep 29, 2017

chochreiner commented Sep 29, 2017

iTao8 commented Sep 29, 2017

chochreiner commented Sep 29, 2017

matthiasgeiger commented Sep 29, 2017

manfredlift commented Oct 4, 2017

tobiasdiez commented Oct 5, 2017

dvbowen commented Oct 12, 2017

adcox commented Oct 13, 2017

lenhard commented Oct 13, 2017

bdcaf commented Oct 16, 2017

dvbowen commented Oct 16, 2017

dvbowen commented Oct 16, 2017

LinusDietz commented Oct 16, 2017

dvbowen commented Oct 16, 2017

gsk1692 commented Oct 18, 2017 •

edited

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dvbowen commented Oct 18, 2017

serialc commented Nov 17, 2017

koppor commented Jul 9, 2018

Siedlerchr commented Oct 27, 2018

freezes on macOS High Sierra #3236

freezes on macOS High Sierra #3236

Comments

iTao8 commented Sep 27, 2017

chochreiner commented Sep 29, 2017

tobiasdiez commented Sep 29, 2017

chochreiner commented Sep 29, 2017

iTao8 commented Sep 29, 2017

chochreiner commented Sep 29, 2017

matthiasgeiger commented Sep 29, 2017

manfredlift commented Oct 4, 2017

tobiasdiez commented Oct 5, 2017

dvbowen commented Oct 12, 2017

adcox commented Oct 13, 2017

lenhard commented Oct 13, 2017

bdcaf commented Oct 16, 2017

dvbowen commented Oct 16, 2017

dvbowen commented Oct 16, 2017

LinusDietz commented Oct 16, 2017

dvbowen commented Oct 16, 2017

gsk1692 commented Oct 18, 2017 • edited Loading

dvbowen commented Oct 18, 2017

serialc commented Nov 17, 2017

koppor commented Jul 9, 2018

Siedlerchr commented Oct 27, 2018

gsk1692 commented Oct 18, 2017 •

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