Zotero 7 Beta: Every now and then the right-click menu stops working

sojusnik

Every now and then the right-click menu stops working throughout the whole desktop app. When trying to open it, then the right-click menu appears for a fraction of a second, before vanishing again. Some goes for the drop-down menu of the menu bar at the top (where File, Edit etc. is)

There seems to be no event that triggers this strange behaviour. The only solution is to restart the app.

What's the best way to debug this?

Happens on Zotero 7.0.0-beta.38+b79e0b3d7 (64-bit) on Ubuntu 23.04.

danielborek

I use Zotero Beta on Ubuntu 23.04 with Gnome/Xorg without issues. To troubleshoot your problem, more details might be useful (apart of the logs for the devs):

- Display server (Wayland/Xorg)? Wayland can cause unexpected behavior (at least it was like that a few years ago).
- Desktop environment and version?
- Any add-ons/plugins installed? Disable temporarily to check for conflicts.
- Does the problem occur in other Zotero profiles? Try a fresh profile to isolate issue,

sojusnik

Using Gnome 44.3 on Ubuntu 23.04 with with Xorg (X11).

No add-ons or plugins installed.

Created a fresh profile with Zotero 7 Beta and using it only for some days. Didn't use previous versions, so can't say if this issue also appeared there.

Since I can't use the menu after this bug appears, I'm providing an error report immediately after I restarted Zotero, with the following ID: 270500684

sojusnik

Just observed the following: If only the main window of the desktop app is open, working regularly, and then Gnome is reloaded (by using alt+f2, then writing r and pressing enter), Zotero isn't responding any more, the main window turns black and is flickering. Only closing the app by ctrl+q helps.

After closing with ctrl+q in this situation, a zotero entry appears in Gnome's system monitor (type zotero and you should see it), that takes 0 memory and CPU, but can't be terminated or killed. So if you do the above-mentioned procedure (reloading Gnome and quitting Zotero) several times, you should see several of those entries in Gnome's system monitor.

This happens only when solely the main window is open (without another one, like the pdf reader) and the window must be focused when reloading Gnome. Else, reloading Gnome won't affect Zotero at all.

Can you reproduce that?

danielborek

no, it doesnt hangs after the gnome restart

danielborek

can you run the Zotero stable (from deb) without error? should it be possible to install both version alongside; another idea to check, when you start Zotero from command line, does it leave any error in the terminal? did you install fresh ubuntu or update from earlier version? i am just guessing, but it might be gnome related, can you install other desktop or check on Wayland if the behaviour is the same?

sojusnik

> can you run the Zotero stable (from deb) without error? should it be possible to install both version alongside;

Where can I find this deb file? The Ubuntu repo doesn't offer such a file, nor is the Zotero homepage.

> another idea to check, when you start Zotero from command line, does it leave any error in the terminal?

Indeed! When typing "pathtozotero/Zotero/zotero" in the terminal, I get the following when the program is starting:

ATTENTION: default value of option mesa_glthread overridden by environment.
ATTENTION: default value of option mesa_glthread overridden by environment.
ATTENTION: default value of option mesa_glthread overridden by environment.
ATTENTION: default value of option mesa_glthread overridden by environment.

> did you install fresh ubuntu or update from earlier version?

Fresh Ubuntu installation with fresh Zotero installation (app source + config + data folder).

> i am just guessing, but it might be gnome related, can you install other desktop or check on Wayland if the behaviour is the same?

Installing another desktop is too cumbersome. Since in a Wayland session you can't reload Gnome with ALT+F2 with "r", it's not possible to reproduce this behaviour, but the terminal gives the same error, but this time it has only 3 lines:

ATTENTION: default value of option mesa_glthread overridden by environment.
ATTENTION: default value of option mesa_glthread overridden by environment.
ATTENTION: default value of option mesa_glthread overridden by environment.

mjthoraval

Where can I find this deb file?

You need to follow the Installation Help link in the Download page.
There is a section "Debian/Ubuntu-based Distros" on that page, linking to the zotero-deb solution maintained by retorquere.

mjthoraval

If only the main window of the desktop app is open, working regularly, and then Gnome is reloaded (by using alt+f2, then writing r and pressing enter), Zotero isn't responding any more, the main window turns black and is flickering. Only closing the app by ctrl+q helps.

For me, reloading Gnome simply crashes Zotero completely: it is unresponsive at first and then completely disappears. It also disappears from the Gnome's system monitor.
It produces an Ubuntu crash report. But the report shows that it is actually Gnome that has crashed:

DistroRelease: Ubuntu 23.04
ExecutablePath: /usr/bin/gnome-shell
ExecutableTimestamp: 1688737270
Package: gnome-shell 44.3-0ubuntu1
PackageArchitecture: amd64
ProcCmdline: /usr/bin/gnome-shell

Tested with 7.0.0-beta.39+ecba25be0 (64-bit) on Ubuntu 23.04
Zotero 6.0.27 also does the same.

mjthoraval

Every now and then the right-click menu stops working throughout the whole desktop app. When trying to open it, then the right-click menu appears for a fraction of a second, before vanishing again. Some goes for the drop-down menu of the menu bar at the top (where File, Edit etc. is)

I cannot reproduce the original problem reported in this thread though.

sojusnik

> There is a section "Debian/Ubuntu-based Distros" on that page, linking to the zotero-deb solution maintained by retorquere.

Thanks!

Installing Zotero 6 was a mess! Used this deb file: https://mirror.mwt.me/zotero/deb/zotero_6.0.27_amd64.deb taken from: https://github.com/retorquere/zotero-deb

Had to completely remove Zotero 7 Beta with all folders, because on my system I couldn't get both versions running at the same time.

So when starting Zotero 6.0.27 from the terminal, I get only:

(zotero:218556): Gtk-WARNING **: 21:36:48.799: Theme parsing error: :1:34: Expected ')' in color definition

(zotero:218556): Gtk-WARNING **: 21:36:48.799: Theme parsing error: :1:76: Expected ')' in color definition

And refreshing Gnome (alt+f2 then r) while the main window of Zotero 6 is opened does nothing to the app, so everything works fine in version 6.

Also tried Zotero 7 Beta with a completely new installation, fresh from the start, and I have the same terminal output:

ATTENTION: default value of option mesa_glthread overridden by environment.
ATTENTION: default value of option mesa_glthread overridden by environment.
ATTENTION: default value of option mesa_glthread overridden by environment.
ATTENTION: default value of option mesa_glthread overridden by environment.

And Zotero still freezes when refreshing Gnome while the main Zotero window is active.

> I cannot reproduce the original problem reported in this thread though.

Since it only happens occasionally, one or two times a day, I can't pinpoint what is triggering it.

apswartz

I am using 6.0.27 on Fedora Linux 38 (Workstation Edition). I am having the same problem with the menus. They will suddenly stop working. Sometimes it may flash quickly. The only thing I am able to do is to stop and restart Zotero to fix it.

Kernel 6.4.14

Hardware...
HP Slim Desktop 290
16G memory
AMD A-6-9225 Radeon R4, 5 Compute Cores
AMD Radeon R4 Graphics

mjthoraval

@sojusnik:

Installing Zotero 6 was a mess!

Following the installation instructions provided on the front page of the GitHub repository, you only need to type 3 command lines.

Had to completely remove Zotero 7 Beta with all folders

And the uninstall instruction are here.

because on my system I couldn't get both versions running at the same time

See Beta packages:

This repo also has the nightly beta's, installable as the zotero-beta and jurism-beta packages. You can install these alongside the regular packages.

apswartz

I'm just wondering. Does anybody know what toolkit is used for the Linux version and do other applications using it have similar problems?

sojusnik

@apswartz

I also have an AMD graphic card:

AMD Ryzen 5 3400G with AMD Radeon Vega 11 Graphics

Maybe that's the reason, because "mesa_glthread" from the error messages hints at an issue with the graphic card?

apswartz

@sojusnik good question.

Surely there are others having this issue crop up. In my case it involves all menus, not just the right-click menus.

msl3v

I would like to confirm this behavior. My details:
Fedora 38 / GNOME 44.4 / X11 / Linux 6.4.12 / Intel i7 / NVIDIA

Tried the stable version 6.0 and the beta version 7.0. Same behavior for both.

It only seems to happen after I drag a pdf into the Zotero window to add it to my library. I don't get any error messages (running the zotero executable from the commandline) and there are no error messages logged in the system.

If I restart Zotero, it works fine. But again, as soon as I drag something across the window and add it to the library, I can't access any menus. Neither the dropdowns, nor the right-click menus.

msl3v

addendum: interestingly when the issue starts with Zotero, it also starts happening in my mail client (Thunderbird). I can't reproduce it through Thunderbird alone. I have to trigger it in Zotero 1st.