Zotero is either "not responding" or giving very long "Beach Ball" delay

Hogenson
I have recently run into problems loading data to Zotero. It either crashes altogether, and requires that I force quit, or I get a MAC beach ball on every item of data entry--in other words very long delays between entering the title of a pdf, the author, etc. I have just upgraded my memory, which was nearly full, but that does not seem to have changed anything. I drag and drop a file and Zotero crashes. I am not having any other noticeable system or application problems with this computer, so it seems to be something with Zotero.
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  • adamsmith
    Check your database integrity from the advanced tab of the Zotero preferences.

    How many items total (incl. notes and attachments) are in your Zotero library? https://www.zotero.org/support/kb/item_count

    If you wait a while and click continue if possible, does Zotero "recover"?
  • Hogenson
    Thank you for getting back to me so quickly. I ran the database integrity and it says there are no errors in the system. I do have a very large library with 4233 items, and I still have many books to load. Is that possibly the cause of the problem
  • aurimas
    edited May 15, 2014
    4233 total items is a reasonable size database. It should not be causing these issues. Can you provide a Debug ID for an action that causes Zotero to freeze up? https://www.zotero.org/support/debug_output

    Edit: regarding the crashes, do you mean that Zotero quits on its own out dies it display an error?
  • adamsmith
    and if Zotero never recovers from the freeze, we'll need real time debug output
    https://www.zotero.org/support/debug_output#real-time_debug_output
  • Hogenson
    OK, so I did a drag and drop of a pdf and first got the Beach Ball, then the system went dead on me--I had first followed the instructions to open the debug output. Force Quit showed the Zotero was not responding. Went through the appropriate steps and got the debug ID--below--and then the system came back to life.

    Here is the ID:

    D1145608529
  • aurimas
    edited May 15, 2014
    Force Quit showed the Zotero was not responding. Went through the appropriate steps and got the debug ID--below--and then the system came back to life.
    So did you close Zotero? If so, the Debug ID is not going to be useful. If not, then I'm not sure how you got the Debug ID while it was still frozen.
  • dstillman
    There's a ton of debug output in here, but I don't actually have any idea what it is. So we'll need the answer to aurimas's question, but also, if this is actually the output for the drag, how many items are you trying to drag, and what are your Quick Copy settings in the Export pane of the Zotero preferences? Specifically, what's the output setting, and did you change "Disable Quick Copy when dragging more than x items" setting (which defaults to 50, for good reason).
  • dstillman
    Oh, you say above this was a drag of a single PDF, but I don't see any way that that's possible — there's all sorts of translator output in here and other stuff that wouldn't be there for a single item drag.

    Also, if you have any other Zotero-related extensions installed, be sure you've tried disabling them.
  • Hogenson
    Sorry for the delay in getting back to you--had to deal with some other matters. So I found a single normal journal article that was not in Zotero yet and did a drag and drop. I had already followed the instructions for getting the debug code and when Zotero stopped on me I got that code. I looked at the Force Quit drop down to see what was registered there, but I did not close Zotero. Once I had the code Zotero was, though no action of mine, running again. Again checked the Force Quit drop down, and it now showed Zotero as active.

    In order to finish a project I have had to load some other information--chapters in books--that is done manually. What I have encountered there is, for example, I put in the title, get a beach ball that probably runs for 30 seconds, then enter the next line of data, beach ball again, and so on. Takes about 5 minutes to enter a single book item, assuming the whole system does't crash.
  • dstillman
    edited May 15, 2014
    for example, I put in the title, get a beach ball that probably runs for 30 seconds
    OK, I'm still not really understanding what the debug output above is for, but how about a Debug ID just for this? Stop the output and submit it as soon as it comes back from the first freeze.

    Again, make sure you've disabled any other extensions you've installed into Zotero.
  • aurimas
    I put in the title, get a beach ball that probably runs for 30 seconds, then enter the next line of data, beach ball again, and so on.
    Could you produce a debug ID for this instead?
  • Hogenson
    Back again. So, I do not have any extensions--that I am aware of at least--so proceeded to set up the debug protocol and then started to manually load another chapter from a book. Entered the title of the chapter, got a beach ball, went to the debut output and sent it to you. The debug ID code is:

    D507220465

    I then finished inputting the information on the book chapter. Beach balls all the way down.
  • Hogenson
    Just did some times. After making an entry, say title of chapter, there is a five second delay before the beach ball appears, and then the beach ball runs for 20 seconds.
  • dstillman
    Sorry, but you're not doing this correctly. That debug output doesn't have anything related to editing an item — it's output for totally unrelated things like checking the PDF tools versions in the preferences and loading web pages in Safari.

    Please re-read the Debug ID instructions. You need to start the debug output, immediately perform the relevant action (editing an item title), and then immediately submit the output, with nothing else in between.
  • Hogenson
    Ok. I closed Zotero, reopened it, enabled debug, pressed the new item button, and a beach ball appeared even before the input area came up. I had set my screen so I could see the debug screen and as soon as the send to Zotero button illuminated I sent it to you. In other words immediately after the first beach ball appeared. The ID code is:

    D581030289

    Best I can do at this point.
  • dstillman
    Can you provide a Report ID as well?
  • Hogenson
    Sorry, I am trying to do everything to describe what is happening. I went though the steps outlined in the Debug protocol after you told me I was doing it wrong. I sent you another debug ID two hours ago, and and hour after that you want me to provide a Report ID. To repeat the last Report:

    D581030289

    I have a good sense of how tricky it can be to deal with complex software, but I either need you to tell me what to do with this system, which I greatly appreciate for many of it's functions, or just tell me you do not know what is happening. Something has gone terribly wrong with Zotero on my machine. I cannot work with it under these conditions, and I have very pressing commitments for a series of lectures in Moscow. If you have more detailed instructions on what I should do to help you fix things please send them along, but in the mean time I need to get some system working. Don't just tell me to repeat what I have now done several times.
  • aurimas
    Debug ID (what you provide above and I'm sure is very useful) is not the same as a Report ID (see Dan's link). The reason he's asking for a Report ID is, I suspect, to check what add-ons/plugins you may have installed (possibly unknowingly). This information is not included in a Debug ID. If that's accurate, I'm guessing that there is indeed something very strange going on with your system that we have not seen before.
  • Hogenson
    OK, now you are making sense. You want me to do something different. Let me get back to you.
  • Hogenson
    So, on the New York Times web page this is what comes up from the Zotero errors query

    Report Errors
    Zotero Connector has not experienced any errors since it was first started.

    So what are the next steps?
  • dstillman
    We need a Report ID from Zotero, not from the Safari connector.
  • Hogenson
    Tell me what part of these instructions I did not follow. It says right click on a web page. I did that and I got exactly what the instructions suggested I would get. Tell me what to do next (for simplicity I deleted the chrome instructions).

    Zotero Connectors (Chrome and Safari)

    If you're experiencing a problem, before restarting the browser, open Zotero preferences:


    Safari: right-click anywhere on a webpage and select “Zotero Preferences…”
    If there are no reportable errors, the Report Errors section will contain the message “Zotero Connector has not experienced any errors since it was first started.”

    If a potential Zotero error has occurred, a text box containing all error will be displayed along with a “Report Errors” button in the Report Errors section. Clicking the button will submit the error report to Zotero servers and will display a popup with a Report ID. Please post the Report ID to the forums. You may not be able to select text inside the popup dialog, but you may still be able to copy the complete contents of the popup using Ctrl-C (or Cmd-C on Mac).

    Not all issues result in a reportable error, and not all errors that are displayed will necessarily be related to Zotero, but this is the first thing to try when encountering a problem.

    If you are unable to provide a Report ID, be sure to include your Zotero Standalone version, Zotero Connector version, Chrome or Safari version, and operating system in your forum post.
  • aurimas
    Top of the page
    Firefox and Zotero Standalone

    If you're experiencing a problem, before restarting Firefox, check the Actions menu (gear icon) in the Zotero toolbar for the status of the “Report Errors…” menu option.

    If a potential Zotero error has occurred, “Report Errors…” will appear in black; otherwise, it will appear in gray and will not be selectable. If it is active, you can first use the error reporting wizard to submit an error report and then post the Report ID you received (not the contents of the report) to the forums. We don't read error reports sent via Report Errors unless there's a forum post pointing to them, since they're generally not helpful without context and/or follow-up.

    Not all problems will show up in the wizard, and not all errors that show up in the wizard will necessarily be related to Zotero, but this is the first thing to try when encountering a problem.

    If you are unable to provide a Report ID, be sure to include your Zotero version, Firefox version (if applicable), and operating system in your forum post.
    The issues we've been discussing are all occurring in Zotero Standalone. There's no reason to report errors from Safari (is that where the Debug IDs are from?)
  • aurimas
    I can see where you may have been confused (since the paragraph mentions Firefox and not Zotero Standalone in the beginning). I adjusted the instructions accordingly.
  • Hogenson
    But I am using safari. Let me get back to you after looking at the actual web site.
  • aurimas
    You're only using Safari to import items into Zotero Standalone. All the editing and library managing you are doing is done inside Zotero Standalone (which is a separate application, independent of Safari). This may be a helpful read https://www.zotero.org/support/installation
  • Hogenson
    OK guys, its getting late at this end of the conversation, which has now gone on for 13 hours. I have a difficult day tomorrow, so I will leave it to you to figure out what is going on in my machine. Keep me posted. If you cannot give me some sense of what to do I fear that there are other options. I do appreciate your sticking with the problem, but please realize that I have been trying to to stick with the problem as well. I will pick up email and posts to this discussion site tomorrow around 6:30 Central Daylight Time. If you have any thoughts let me know.
  • adamsmith
    Dan will want the error report ID from Zotero Standalone (following the instructions quoted in full by Aurimas) before he can say more.

    You can decide whether you want to invest that time or not.
  • dstillman
    edited May 16, 2014
    The Report ID from Standalone (not Safari, which has nothing to do with manual item editing) was supposed to save us all time — it's literally a 15-second process that would definitively answer the question of whether you have other extensions installed. But I'm just going to say that, yes, you installed AutoZotBib or a similar third-party extension, and it's generating a BibTeX file of your entire Zotero library every time you make a change:
    (3)(+0000000): Translate: Got value [...] for %a

    (3)(+0000000): Translate: Got value books for %t

    (3)(+0000000): DATE: retrieved with algorithms: {"order":"y","year":1986}

    (3)(+0000000): Translate: Got value 1986 for %y
    This is BibTeX generation output, and there's tons of it, and as far as I know there's no other way that would be triggered when you edit an item unless you installed something that's doing that.

    So go to Tools -> Add-ons -> Extensions and uninstall AutoZotBib or whatever it was you installed, and this should go away.
  • Hogenson
    Dear Zotero folks--
    First, sorry for getting testy yesterday. I was getting tired and very frustrated. Shouting, even in writing, is not my usual style. Anyway, with the mention of going to the Tools drop down I did find the extensions--three in addition to the MAC adaptation extension. I disabled those three and I think things are indeed now working properly. If anything else comes up I will contact you. In the mean time thank you for your help. I know this was frustrating for you as well.
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