Firefox freezing with LyZ and LyX [Ubuntu 12.04]

petteri_t
I don't know if someone else has the problem but noticed recently without manually changing anything that Firefox started to crash when I tried to cite a Zotero entry in a LyX document (http://www.lyx.org/) with the LyZ plugin's (https://addons.mozilla.org/en-us/firefox/addon/lyz) "Cite in LyX"-command. So previously everything was running perfectly.

I assume that some update messed things up, and I only updated what Ubuntu 12.04 recommended for me so there shouldn't be much of exotic added recently. I thought of it being a problem of Firefox 16 and downgraded to version 15 without any help (http://ubuntuforums.org/showthread.php?p=12289738).

Any ideas where the problem could be?

Firefox 16.0.2
LyX 2.0.4
LyZ 2.1.4

Thanks
P
  • aurimas
    This _might_ be related to a recent BibTeX update (though i don't think it should). Try disabling translator updates under Preferences and manually downgrading the translator to the version here https://raw.github.com/zotero/translators/e5dd4c75630ecd0602821537cd4fdfaa84d8d5cd/BibTeX.js

    Let us know if you need more detailed instructions.
  • petteri_t
    Thanks for the suggestion aurimas,

    I unchecked the automatic updates and then downgraded the BibTeX.js in the "translators" folders but the operation did not affect the crashing. Firefox still jams with no error message. LyX doesn't crash but just doesn't get the citation inserted from Zotero/Firefox
  • dstillman Zotero Team
    Assuming you're talking about a freeze, not a crash, following real-time debug output here might be helpful here to see if it's actually doing something (e.g., in an infinite loop) and, if not, where it stopped.
  • petteri_t
    Hi Dan,

    Those are the debug lines on the terminal after selecting the entry that I wanted to cite in LyX.

    Does it give you any ideas or do you need earlier debug lines as well?

    -----

    zotero(3): Viewing item in pane 0

    zotero(3): Refreshing item box

    zotero(5): SELECT IA.itemID FROM itemAttachments IA NATURAL JOIN items I LEFT JOIN itemData ID ON (IA.itemID=ID.itemID AND fieldID=1) LEFT JOIN itemDataValues IDV ON (ID.valueID=IDV.valueID) WHERE sourceItemID=? AND linkMode NOT IN (?) AND IA.itemID NOT IN (SELECT itemID FROM deletedItems) ORDER BY mimeType='application/pdf' DESC, value=? DESC, dateAdded ASC

    zotero(5): Binding parameter 1 of type int: 8192

    zotero(5): Binding parameter 2 of type int: 3

    zotero(5): Binding parameter 3 of type string: "http://www.ncbi.nlm.nih.gov/pubmed/20448693"

    zotero(3): No arguments provided to Items.get()

    zotero(5): SELECT IA.itemID FROM itemAttachments IA NATURAL JOIN items I LEFT JOIN itemData ID ON (IA.itemID=ID.itemID AND fieldID=1) LEFT JOIN itemDataValues IDV ON (ID.valueID=IDV.valueID) WHERE sourceItemID=? AND linkMode NOT IN (?) AND IA.itemID NOT IN (SELECT itemID FROM deletedItems) ORDER BY mimeType='application/pdf' DESC, value=? DESC, dateAdded ASC

    zotero(5): Binding parameter 1 of type int: 8192

    zotero(5): Binding parameter 2 of type int: 3

    zotero(5): Binding parameter 3 of type string: "http://www.ncbi.nlm.nih.gov/pubmed/20448693"

    zotero(3): No arguments provided to Items.get()

    zotero(5): SELECT IA.itemID FROM itemAttachments IA NATURAL JOIN items I LEFT JOIN itemData ID ON (IA.itemID=ID.itemID AND fieldID=1) LEFT JOIN itemDataValues IDV ON (ID.valueID=IDV.valueID) WHERE sourceItemID=? AND linkMode NOT IN (?) AND IA.itemID NOT IN (SELECT itemID FROM deletedItems) ORDER BY mimeType='application/pdf' DESC, value=? DESC, dateAdded ASC

    zotero(5): Binding parameter 1 of type int: 8192

    zotero(5): Binding parameter 2 of type int: 3

    zotero(5): Binding parameter 3 of type string: "http://www.ncbi.nlm.nih.gov/pubmed/20448693"

    zotero(3): No arguments provided to Items.get()

    zotero(5): SELECT IA.itemID FROM itemAttachments IA NATURAL JOIN items I LEFT JOIN itemData ID ON (IA.itemID=ID.itemID AND fieldID=1) LEFT JOIN itemDataValues IDV ON (ID.valueID=IDV.valueID) WHERE sourceItemID=? AND linkMode NOT IN (?) AND IA.itemID NOT IN (SELECT itemID FROM deletedItems) ORDER BY mimeType='application/pdf' DESC, value=? DESC, dateAdded ASC

    zotero(5): Binding parameter 1 of type int: 8192

    zotero(5): Binding parameter 2 of type int: 3

    zotero(5): Binding parameter 3 of type string: "http://www.ncbi.nlm.nih.gov/pubmed/20448693"

    zotero(3): No arguments provided to Items.get()

    zotero(5): SELECT IA.itemID FROM itemAttachments IA NATURAL JOIN items I LEFT JOIN itemData ID ON (IA.itemID=ID.itemID AND fieldID=1) LEFT JOIN itemDataValues IDV ON (ID.valueID=IDV.valueID) WHERE sourceItemID=? AND linkMode NOT IN (?) AND IA.itemID NOT IN (SELECT itemID FROM deletedItems) ORDER BY mimeType='application/pdf' DESC, value=? DESC, dateAdded ASC

    zotero(5): Binding parameter 1 of type int: 8192

    zotero(5): Binding parameter 2 of type int: 3

    zotero(5): Binding parameter 3 of type string: "http://www.ncbi.nlm.nih.gov/pubmed/20448693"

    zotero(3): No arguments provided to Items.get()
  • dstillman Zotero Team
    edited November 4, 2012
    That's the end of the output when it freezes? Does anything show up in the Error Console? You can show the error console by adding -jsconsole to the command line.
  • petteri_t
    edited November 4, 2012
    Yes that is the end of it.. So repeats the same 5 times apparently (at least when counting the times trying to insert the URL)

    --



    zotero(5): CREATE INDEX tmpSearchResults_5Tl69IIu_itemID ON tmpSearchResults_5Tl69IIu(itemID)

    zotero(5): Committing transaction

    zotero(3): Resetting Notifier event queue

    zotero(5): SELECT DISTINCT tagID, name, type FROM itemTags NATURAL JOIN tags WHERE itemID IN (SELECT itemID FROM tmpSearchResults_5Tl69IIu)

    zotero(3): Reloading all tags

    zotero(5): SELECT ROWID FROM tags

    zotero(5): SELECT * FROM tags WHERE 1

    zotero(4): Registering observer for [collection-item,item-tag,tag] in notifier with hash 9c'

    zotero(3): Refreshing tags selector

    zotero(5): SELECT tagID, name FROM tags WHERE libraryID IS NULL AND type IN (0,1)

    zotero(3): Set tree in 37480 ms

    zotero(3): Viewing item in pane 0

    zotero(3): Refreshing item box

    zotero(5): SELECT itemTypeID AS id, typeName AS name, custom FROM itemTypesCombined

    zotero(5): SELECT fieldID, value FROM itemData NATURAL JOIN itemDataValues WHERE itemID=?

    zotero(5): Binding parameter 1 of type int: 7562

    zotero(5): SELECT creatorTypeID AS id, creatorType AS name FROM itemTypeCreatorTypes NATURAL JOIN creatorTypes WHERE itemTypeID=? ORDER BY primaryField=1 DESC, name

    zotero(5): Binding parameter 1 of type int: 4

    zotero(5): SELECT creatorTypeID AS id, creatorType AS name FROM creatorTypes

    zotero(5): SELECT creatorID, creatorTypeID, orderIndex FROM itemCreators WHERE itemID=? ORDER BY orderIndex

    zotero(5): Binding parameter 1 of type int: 7562

    zotero(5): SELECT COUNT(*) FROM creators WHERE creatorID=?

    zotero(5): Binding parameter 1 of type int: 12303

    zotero(5): SELECT COUNT(*) FROM creators WHERE creatorID=?

    zotero(5): Binding parameter 1 of type int: 12304

    zotero(5): SELECT COUNT(*) FROM creators WHERE creatorID=?

    zotero(5): Binding parameter 1 of type int: 12305

    zotero(3): Loading data for creator 12303 in Zotero.Creator.load()

    zotero(5): SELECT C.*, CD.* FROM creators C NATURAL JOIN creatorData CD WHERE creatorID=?

    zotero(5): Binding parameter 1 of type int: 12303

    zotero(3): Loading data for creator 12304 in Zotero.Creator.load()

    zotero(5): SELECT C.*, CD.* FROM creators C NATURAL JOIN creatorData CD WHERE creatorID=?

    zotero(5): Binding parameter 1 of type int: 12304

    zotero(3): Loading data for creator 12305 in Zotero.Creator.load()

    zotero(5): SELECT C.*, CD.* FROM creators C NATURAL JOIN creatorData CD WHERE creatorID=?

    zotero(5): Binding parameter 1 of type int: 12305

    zotero(5): SELECT IA.itemID FROM itemAttachments IA NATURAL JOIN items I LEFT JOIN itemData ID ON (IA.itemID=ID.itemID AND fieldID=1) LEFT JOIN itemDataValues IDV ON (ID.valueID=IDV.valueID) WHERE sourceItemID=? AND linkMode NOT IN (?) AND IA.itemID NOT IN (SELECT itemID FROM deletedItems) ORDER BY mimeType='application/pdf' DESC, value=? DESC, dateAdded ASC

    zotero(5): Binding parameter 1 of type int: 7562

    zotero(5): Binding parameter 2 of type int: 3

    zotero(5): Binding parameter 3 of type string: "http://dx.doi.org/10.3389/neuro.02.031.2009"

    zotero(5): SELECT mimeType FROM itemAttachments WHERE itemID=?

    zotero(5): Binding parameter 1 of type int: 7563

    zotero(5): SELECT linkMode FROM itemAttachments WHERE itemID=?

    zotero(5): Binding parameter 1 of type int: 7563

    zotero(5): SELECT IA.itemID FROM itemAttachments IA NATURAL JOIN items I LEFT JOIN itemData ID ON (IA.itemID=ID.itemID AND fieldID=1) LEFT JOIN itemDataValues IDV ON (ID.valueID=IDV.valueID) WHERE sourceItemID=? AND linkMode NOT IN (?) AND IA.itemID NOT IN (SELECT itemID FROM deletedItems) ORDER BY mimeType='application/pdf' DESC, value=? DESC, dateAdded ASC

    zotero(5): Binding parameter 1 of type int: 7562

    zotero(5): Binding parameter 2 of type int: 3

    zotero(5): Binding parameter 3 of type string: "http://dx.doi.org/10.3389/neuro.02.031.2009"

    zotero(5): SELECT IA.itemID FROM itemAttachments IA NATURAL JOIN items I LEFT JOIN itemData ID ON (IA.itemID=ID.itemID AND fieldID=1) LEFT JOIN itemDataValues IDV ON (ID.valueID=IDV.valueID) WHERE sourceItemID=? AND linkMode NOT IN (?) AND IA.itemID NOT IN (SELECT itemID FROM deletedItems) ORDER BY mimeType='application/pdf' DESC, value=? DESC, dateAdded ASC

    zotero(5): Binding parameter 1 of type int: 7562

    zotero(5): Binding parameter 2 of type int: 3

    zotero(5): Binding parameter 3 of type string: "http://dx.doi.org/10.3389/neuro.02.031.2009"

    zotero(5): SELECT IA.itemID FROM itemAttachments IA NATURAL JOIN items I LEFT JOIN itemData ID ON (IA.itemID=ID.itemID AND fieldID=1) LEFT JOIN itemDataValues IDV ON (ID.valueID=IDV.valueID) WHERE sourceItemID=? AND linkMode NOT IN (?) AND IA.itemID NOT IN (SELECT itemID FROM deletedItems) ORDER BY mimeType='application/pdf' DESC, value=? DESC, dateAdded ASC

    zotero(5): Binding parameter 1 of type int: 7562

    zotero(5): Binding parameter 2 of type int: 3

    zotero(5): Binding parameter 3 of type string: "http://dx.doi.org/10.3389/neuro.02.031.2009"

    zotero(5): SELECT path FROM itemAttachments WHERE itemID=?

    zotero(5): Binding parameter 1 of type int: 7563

    zotero(2): Attachment file '/home/petteri/Dropbox/Zotero/storage/ZSRPWPEV/Adamantidis et al. - 2010 - Optogenetic deconstruction of sleep–wake circuitry.pdf' not found

    zotero(5): SELECT IA.itemID FROM itemAttachments IA NATURAL JOIN items I LEFT JOIN itemData ID ON (IA.itemID=ID.itemID AND fieldID=1) LEFT JOIN itemDataValues IDV ON (ID.valueID=IDV.valueID) WHERE sourceItemID=? AND linkMode NOT IN (?) AND IA.itemID NOT IN (SELECT itemID FROM deletedItems) ORDER BY mimeType='application/pdf' DESC, value=? DESC, dateAdded ASC

    zotero(5): Binding parameter 1 of type int: 7562

    zotero(5): Binding parameter 2 of type int: 3

    zotero(5): Binding parameter 3 of type string: "http://dx.doi.org/10.3389/neuro.02.031.2009"
  • dstillman Zotero Team
    And the Error Console? For what it's worth, this doesn't look like a problem with Zotero. It's not actually doing anything at the end of that output.
  • dstillman Zotero Team
    edited November 4, 2012
    Well, except "Set tree in 37480 ms" is very odd—that's 37 seconds to render the items list. Is Zotero actually freezing permanently, or just temporarily and then recovering?
  • petteri_t
    I think the 37 480 ms could be just due to the size of my database which is rather huge (5664 items) and it is slow on my laptop anyway to add tags and new entries in general. So yes, Zotero typically freezes Firefox when enabling it but I thought that was kinda normal.
  • dstillman Zotero Team
    You still haven't answered about the Error Console.
  • petteri_t
    And how do you actually log something from error console? from instructions there: http://www.zotero.org/support/reporting_bugs

    In the Tools - Web Developer - Error Console "Errors", there is only that:

    Timestamp: 11/04/2012 10:54:50 PM
    Error: The character encoding of the plain text document was not declared. The document will render with garbled text in some browser configurations if the document contains characters from outside the US-ASCII range. The character encoding of the file needs to be declared in the transfer protocol or file needs to use a byte order mark as an encoding signature.
    Source File: zotero://debug/
    Line: 0
  • dstillman Zotero Team
    The idea is to see if anything shows up there when Firefox freezes.

    You wouldn't be able to copy anything if Firefox is frozen, so I assume the above (which isn't relevant anyway) isn't from after the freeze.
  • petteri_t
    Yes I tried to open the Error Console and cite and observe what is there when Firefox freezes but it did not work as I could not see what was on the window
  • dstillman Zotero Team
    I don't really know what that means. Keep the window open and visible, and then trigger the freeze.
  • petteri_t
    I mean that I triggered the freeze but I don't see any new lines coming to the Error Console and if I then switch some other app and click Firefox on the task bar I cannot see any content of Firefox
  • dstillman Zotero Team
    edited November 4, 2012
    OK. I think you'll have to take this up with the creator of LyZ. I don't know anything about how LyZ integrates with Zotero, and unless you can reproduce this problem in Zotero itself somehow, there's no sign of a problem here on Zotero's side.
  • mobam
    Although this thread is very old, i just had exactly the same problem (at least the same symptoms): FF freezes after clicking "Cite it LyX".

    I tried that for 4-5 times – always the same problem. Then, i restarted LyX and everything was ok again. (Just in case someone else gets the problem)

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