Zotero locks on launch after automatic update to Zotero 8 (Kubuntu 25.10)

cpsyctc
Zotero has updated itself to version 8 but now locks on launch with the two announcement strips at the top ("You've been upgraded ...", and "Zotero now automatically ...") there. The "My library" strip below the tool bar, and the tool bar, are greyed out but the library visible as is the library tree on the left. However, everything is locked solid: no response to key presses, button clicks or Alt-F4 (which eventually gives me the "unresponsive" message box and the only detail is "Process ID: 3500" which I assume is uniformative really.

Not good as Zotero is a really important program for me which I use repeatedly and daily.

Suggestions please!

Chris
  • adamsmith
    How did you install Zotero?
  • dstillman Zotero Team
    edited 22 days ago
    @cpsyctc: Also, can you provide a screenshot of the whole window, either here or in an email to support@zotero.org with a link to this thread?

    Can you reproduce this in Troubleshooting Mode (Help → "Restart in Troubleshooting Mode…”)?
  • cpsyctc
    Installed from the official tarball at some level of version 7 I would guess.
    If you read what I said you will see that I can't restart in troubleshooting mode that way as the toolbar is greyed out so no "Help -> ".

    Both "zotero" and "Zotero" from the user command line get "command not found", I guess that's logical as I normally launch from the task manager icon.

    So I cd to /opt/zotero/ and then ran ./zotero-bin --safe-mode which gets me this:

    [11125] Sandbox: CanCreateUserNamespace() unshare(CLONE_NEWPID): EPERM
    [Parent 11123, Main Thread] WARNING: g_dbus_connection_unregister_object: assertion 'G_IS_DBUS_CONNECTION (connection)' failed: 'glib warning', file /builds/worker/checkouts/gecko/toolkit/xre/nsSigHandlers.cpp:201

    (firefox-esr:11123): GLib-GIO-CRITICAL **: 15:38:04.982: g_dbus_connection_unregister_object: assertion 'G_IS_DBUS_CONNECTION (connection)' failed
    [Parent 11123, Main Thread] WARNING: nsDBusRemoteServer: Unable to unregister root object from within onNameLost!: 'glib warning', file /builds/worker/checkouts/gecko/toolkit/xre/nsSigHandlers.cpp:201

    ** (firefox-esr:11123): WARNING **: 15:38:04.982: nsDBusRemoteServer: Unable to unregister root object from within onNameLost!

    No usable Zotero launches and ps aux | grep -i zotero only shows that grep process.

    Does that throw any more light on things? Something nasty in the dbus connections? I have slow launching for Vivaldi and Chrome but haven't previously had any problems with Zotero.
  • cpsyctc
    I have sent this next to suppor@zotero with link to this thread:

    Relates to https://forums.zotero.org/discussion/129196/zotero-locks-on-launch-after-automatic-update-to-zotero-8-kubuntu-25-10?new=1

    OK. I launched Zotero from the task manager again (my usual route) and I noticed that the Zotero tool bar was _NOT_ initially greyed out, that only happens after I try to dismiss either of the two message strips.

    First screen shot: tool bar _NOT_ greyed out: Zotero_Screenshot_20260123_154612.png

    But if I click to dismiss the "Zotero now automatically ..." message strip it does grey out and Zotero locks:
    Zotero_Screenshot_20260123_154706.png

    Interestingly, if I refrain from dismissing either strip, Zotero seems to be functional, however if I dismiss either, it locks but with the slight difference that I dismiss the upper message strip with "Done" it is locked but the tool bar is _NOT_ greyed out:
    Screenshot_20260123_155539.png

    So pretty definitely some message handling issue between Zotero and Kubuntu?

    TIA,

    Chris
  • dstillman Zotero Team
    You launch Zotero with ./zotero, not ./zotero-bin, so it's ./zotero -safe-mode to launch in Troubleshooting Mode.

    Can you launch with ./zotero -safe-mode -ZoteroDebugText and, after reproducing the hang, send the output to support@zotero.org?
  • cpsyctc
    Done. I had opened a note (a very short one) last time I had Z open and after crashing it after the last freeze on closing the message strips and following that, it opens (not full screen) with that note open ... and has been there for probably ten minutes now. I have taken a screen grab and I'll wait to hear whether you think I should continue to wait for it to come out of its torpor or kill it and send you the output. Is it automatically saved to a file, hundreds of lines have scrolled past in the terminal?
  • cpsyctc
    Here are the most recent lines in the terminal. Been here for at least ten minutes now, probably longer.

    zotero(4)(+0000001): SELECT itemID FROM items WHERE (itemID NOT IN (SELECT itemID FROM deletedItems UNION SELECT itemID FROM itemNotes WHERE parentItemID IS NOT NULL AND parentItemID IN (SELECT itemID FROM deletedItems) UNION SELECT itemID FROM itemAttachments WHERE parentItemID IS NOT NULL AND parentItemID IN (SELECT itemID FROM deletedItems)UNION SELECT itemID FROM itemAnnotations WHERE parentItemID IN (SELECT itemID FROM deletedItems)UNION SELECT itemID FROM itemAnnotations WHERE parentItemID IN (SELECT itemID FROM itemAttachments WHERE parentItemID IN (SELECT itemID FROM deletedItems)))) AND itemID IN (SELECT itemID FROM items WHERE (libraryID=?)) AND itemID IN (SELECT itemID FROM items WHERE (itemTypeID IN (SELECT itemTypeID FROM itemTypesCombined WHERE typeName=?))) [1, 'note']

    zotero(4)(+0000001): CREATE TEMPORARY TABLE tagDelete AS SELECT tagID FROM tags WHERE tagID NOT IN (SELECT tagID FROM itemTags)

    zotero(3)(+0001569): Cached CSL.Engine instance with {"locale":"en-GB","format":"html","automaticJournalAbbreviations":false} for http://www.zotero.org/styles/chicago-shortened-notes-bibliography

    zotero(3)(+0001539): Cached CSL.Engine instance with {"locale":"en-GB","format":"text","automaticJournalAbbreviations":false} for http://www.zotero.org/styles/chicago-shortened-notes-bibliography

    zotero(3)(+0000001): Preloading 1412e9e2-51e1-42ec-aa35-e036a895534b for Quick Copy

    zotero(3)(+0000000): Getting contents of /home/chris/Zotero/translators/Note Markdown.js



  • dstillman Zotero Team
    You can redirect the output to a file with > log.txt, but if it stopped, you can just copy all the text that's available and send that.
  • cpsyctc
    Just done that for those last lines, very happy to kill it and restart with redirect (I had wondered!)
  • dstillman Zotero Team
    By "all the text that's available" I mean your terminal's entire scrollback buffer — ideally hundreds or thousands of lines. If it's easier to redirect to a file, you can do that.
  • cpsyctc
    Done
  • cpsyctc
    Any progress with this. The issue isn't so reliably a freeze on launch now but it's still freezing at some point within a very short period of launch/use (minutes maximum). That means Z8.0 is unusable for me. Is there a safe way for me to wind back to 7.? which was working fine?
  • cpsyctc
    So no update on this and Zotero remains unusable for me which is about to become a really nasty problem. Is the obvious way forward for me to completely purge Zotero from this system and then to install v7 from https://www.zotero.org/download/client/dl?channel=release&platform=linux-x86_64&version=7.0.32 and pray that that works and that resynchronising my libraries is the only option for me at this point? I would appreciate confirmation as that's a fair bit of work so if there is a better alternative then I really would like to know. TIA, Chris
  • dstillman Zotero Team
    edited 15 days ago
    I'm a bit confused by the output you sent. It shows you starting up and then shutting down Zotero, with no obvious problems. Are you saying it's freezing and coming back? (After how long?) Or does the output you sent not show a freeze?

    The point of sending raw output was to show the output up until the point that it freezes, so we can see the last thing it was doing when it froze.
  • cpsyctc
    Yes, sadly that was a freak. Since then Zotero doesn't function usably for more than seconds. Earlier in the week it launched and saving a web page to it with the connector worked but the minute I clicked on the record in Z it locked up solid. Since then it has locked up pretty immediately after launching and loading my library. Today I tried to save a web page to Z and it failed with a message from the connector that something was locked. I did say that (see "3 days ago"
  • dstillman Zotero Team
    Then we need debug output for any of those other startups through the freeze happening. Debug output from where it’s working fine isn’t useful.
  • cpsyctc
    Fair enough, sorry but, I had thought you would come back to me after I sent that log to say what you wanted next. My bad.

    Things get more confusing to me at least:
    OK. I ran "./zotero -safe-mode -ZoteroDebugText > log.txt"

    Zotero opened not in full screen and was frozen at "loading ..." for over 30 minutes. I then meant to copy the console output which was, and is:

    ./zotero -safe-mode -ZoteroDebugText > log.txt
    [21819] Sandbox: CanCreateUserNamespace() unshare(CLONE_NEWPID): EPERM
    Missing chrome or resource URL: chrome://zotero/skin/16/white/loading.svg

    Stupidly I typed ctrl-c not shift-ctrl-c for the copy and then copied root output of "ps aux | grep -i zotero" in case that was useful. It was:
    ps aux | grep -i zotero
    chris 21814 0.0 0.0 10292 3936 pts/2 S+ 15:19 0:00 /bin/bash ./zotero -safe-mode -ZoteroDebugText
    chris 21817 0.9 3.8 12079360 1154672 pts/2 Sl+ 15:19 0:18 /opt/zotero/zotero-bin -app /opt/zotero/app/application.ini -safe-mode -ZoteroDebugText
    chris 21897 0.0 0.1 230036 42764 pts/2 Sl+ 15:19 0:00 /opt/zotero/zotero-bin -contentproc -parentBuildID 20251201132345 -prefsHandle 0:28258 -prefMapHandle 1:281513 -sandboxReporter 2 -ipcHandle 3 -initialChannelId {28ddf6b1-2b83-412e-ae99-5a9b5ca52132} -parentPid 21817 -appDir /opt/zotero/app 1 socket
    root 23558 0.0 0.0 9472 2652 pts/1 S+ 15:52 0:00 grep --color=auto -i zotero

    (and still is very similar). I went back to Zotero and found that it is now full screen and was running fine on clicking a few records. I came here to write the above and now Zotero is locked again (full screen) and is still another five minutes on.

    I have sent log_20260131.txt to support@zotero.org in case this helps looking at the time stamp on it I think it was created when I hit ctrl-c when to me zotero looked to be locked and not full screen but I suppose it may have been created as zotero apparently awoke transiently from that lock.

    I am willing to do more, e.g. repeat that and send you a log while zotero is definitely locked. However, my writing work is pretty crippled while zotero behaves like this so I do need to find some way to get back to a working copy soon, presumably by the purge and install 7 from Zotero-7.0.32_linux-x86_64.tar.bz2 so I probably need to take that step by Monday some time.
  • dstillman Zotero Team
    You can run 7.0.32 at any time. You don’t need to wait for us or do anything to your data.
  • cpsyctc
    I didn't want to mess up getting to the bottom of this but can I just install 7.0.32 alongside 8.0 say in /opt/zotero7/ and run it manually from the console so I wouldn't have changed anything in 8.0?
  • dstillman Zotero Team
    Yes.
  • cpsyctc
    Great. Thanks for that. Done and I can confirm that 7.0.32 launched manually from /opt/zotero7/ with a lag of a few seconds of a blank screen and then has my libraries there. The console shows:
    Sandbox: seccomp sandbox violation: pid 31475, tid 31475, syscall 28, args 135829141385216 4096 102 266240 4294967295 0.
    Missing chrome or resource URL: chrome://zotero/skin/16/white/loading.svg
    In case that says anything about something wrong with my system.
    But 7.0.32 seems to be continuing to work fine which is a huge relief: many thanks. I am very happy to try to do more with 8 if it's at all helpful.
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