Zotero broken

Hi,
it seems the dependencies for Zotero are broken - though we might consider Zotero as key for scientific users (see eg Apps for doing Research in Linux - #3 by astraadria4ari ).

zotero on wayland / Linux / Fedora 35 broken - Zotero Forums suggests that Zotero is based currently on Firefox 60esr. But that does not run anymore on Fedora 35.

What to do to make Zotero run again, any ideas here in this wonderful community?

You could consider using the Zotero flatpak.
https://flathub.org/apps/details/org.zotero.Zotero

Thank you!
I already use the flatpak, but it does not run anymore since the upgrade to 35.

I installed it before posting, just to be sure. Obviously I don’t use it. So I don’t know if it really works. At least it runs.
What do you mean with “but it does not run anymore”? That it doesn’t start?

3 Likes

I have the Zotero flatpak on Silverblue 35 and use it virtually everyday–it runs and it works just fine…

Repair the flatpak installation or check permissions? :thinking:

2 Likes

Thank you!

Zotero’s user interface does not become visible. As a process, I can see it, but no interaction is possible. Calling it from the shell does not point to any significant error – that is, it only suggests:

Gtk-Message: 00:25:08.101: Failed to load module "canberra-gtk-module"
Gtk-Message: 00:25:08.101: Failed to load module "pk-gtk-module"
Gtk-Message: 00:25:08.101: Failed to load module "canberra-gtk-module"
Gtk-Message: 00:25:08.101: Failed to load module "pk-gtk-

I reinstalled the flatpak package, no change.

Thank you for the suggestion. Sorry, how do I repair the flatpak installation? how to check permissions?

Just run: sudo flatpak repair It is supposed to detect and resolve any issues:
https://docs.flatpak.org/en/latest/flatpak-command-reference.html#flatpak-repair

Permissions are most easily managed with Flatseal. You will definitely love this app! :wink:
https://flathub.org/apps/details/com.github.tchx84.Flatseal

Thanks for the repair command.
Flatseal indeed looks fine.

Even giving Zotero access to all files does not help.

I downloaded Firefox 60 ESR and it doesn’t run on F35 here either on Wayland or X11. On Wayland, the app window does come up but tabs keep crashing. On X, I can’t even get the window to come up. The errors in the terminal are the same for both:

###!!! [Parent][MessageChannel] Error: (msgtype=0x15007F,name=PBrowser::Msg_Destroy) Channel error: cannot send/recv

[Parent 1741883, Gecko_IOThread] WARNING: pipe error (112): Connection reset by peer: file /builds/worker/workspace/build/src/ipc/chromium/src/chrome/common/ipc_channel_posix.cc, line 353
[Parent 1741883, Gecko_IOThread] WARNING: pipe error (100): Connection reset by peer: file /builds/worker/workspace/build/src/ipc/chromium/src/chrome/common/ipc_channel_posix.cc, line 353
[Parent 1741883, Gecko_IOThread] WARNING: pipe error (88): Connection reset by peer: file /builds/worker/workspace/build/src/ipc/chromium/src/chrome/common/ipc_channel_posix.cc, line 353
[Parent 1741883, Gecko_IOThread] WARNING: pipe error (120): Connection reset by peer: file /builds/worker/workspace/build/src/ipc/chromium/src/chrome/common/ipc_channel_posix.cc, line 353
[Parent 1741883, Gecko_IOThread] WARNING: pipe error (114): Connection reset by peer: file /builds/worker/workspace/build/src/ipc/chromium/src/chrome/common/ipc_channel_posix.cc, line 353

Since it doesn’t work on either, it’s probably not a Wayland/X11 related issue. I’ve looked around a bit but not found what the error may be caused by yet.

1 Like

I don’t think this issue is likely to have to do with Firefox ESR 60. As I said, Zotero works fine on my Fedora 35 installation, and there’s no need for Firefox ESR 60 specifically. I’d like to help; my technical knowledge is very limited, though. :neutral_face:

1 Like

Hrm, yeh, I can confirm that. Just installed zotero from flathub and it works fine (at least it starts up and so on):

 flatpak --user install flathub org.zotero.Zotero

@ingli : could you create a new user and install zotero there to see what happens?

ha, good idea. funny, no, cannot log in as another user on my machine (why is that, different story, just tried - - but have followed Improve login security with challenge-response authentication - Fedora Magazine - which seems to effect not being able to log users in if they do not have a hardware token).

Dear all, I believe you it runs on your machines. Hmm, what to do? remove all flatpaks and subsequently reinstall? But that would be like the “repair”, I guess, so no need to do this.

For the record, installing the flatpak systemwide vs only for the users, does not seem tol make a difference.

Let’s start with comparing system information to see if what’s different in our hardware etc? Here’s what fpaste --sysinfo --pasteonly gives for my system:

$ fpaste --sysinfo --printonly

=== fpaste 0.4.2.0 System Information ===
* OS Release (cat /etc/*-release | uniq):
     Fedora release 35 (Thirty Five)
     NAME="Fedora Linux"
     VERSION="35 (CompNeuro)"
     ID=fedora
     VERSION_ID=35
     VERSION_CODENAME=""
     PLATFORM_ID="platform:f35"
     PRETTY_NAME="Fedora Linux 35 (CompNeuro)"
     ANSI_COLOR="0;38;2;60;110;180"
     LOGO=fedora-logo-icon
     CPE_NAME="cpe:/o:fedoraproject:fedora:35"
     HOME_URL="https://labs.fedoraproject.org"
     DOCUMENTATION_URL="https://neuro.fedoraproject.org"
     SUPPORT_URL="https://ask.fedoraproject.org/"
     BUG_REPORT_URL="https://bugzilla.redhat.com/"
     REDHAT_BUGZILLA_PRODUCT="Fedora"
     REDHAT_BUGZILLA_PRODUCT_VERSION=35
     REDHAT_SUPPORT_PRODUCT="Fedora"
     REDHAT_SUPPORT_PRODUCT_VERSION=35
     PRIVACY_POLICY_URL="https://fedoraproject.org/wiki/Legal:PrivacyPolicy"
     VARIANT="Comp Neuro"
     VARIANT_ID=compneuro
     Fedora release 35 (Thirty Five)
     
* Kernel (uname -r ; cat /proc/cmdline):
     5.14.15-300.fc35.x86_64
     BOOT_IMAGE=(hd0,msdos1)/vmlinuz-5.14.15-300.fc35.x86_64 root=UUID=ca51f7bd-aa8e-417e-87cb-2ee37aa19f69 ro resume=UUID=6c3ad40a-3833-451d-b639-b37ad11900e0 rhgb quiet crashkernel=1G-4G:192M,4G-64G:256M,64G-:512M
     
* Desktop(s) Running (ps -eo comm= | grep -E '(gnome-session|startkde|startactive|xfce.?-session|fluxbox|blackbox|hackedbox|ratpoison|enlightenment|icewm-session|od-session|wmaker|wmx|openbox-lxde|openbox-gnome-session|openbox-kde-session|mwm|e16|fvwm|xmonad|sugar-session|mate-session|lxqt-session|cinnamon|lxdm-session)' ):
     gnome-session-b
     gnome-session-c
     gnome-session-b
     
* Desktop(s) Installed (ls -m /usr/share/xsessions/ | sed 's/\.desktop//g' ):
     gnome, gnome-xorg
     
* SELinux Status (sestatus):
     SELinux status:                 enabled
     SELinuxfs mount:                /sys/fs/selinux
     SELinux root directory:         /etc/selinux
     Loaded policy name:             targeted
     Current mode:                   enforcing
     Mode from config file:          enforcing
     Policy MLS status:              enabled
     Policy deny_unknown status:     allowed
     Memory protection checking:     actual (secure)
     Max kernel policy version:      33
     
* SELinux Errors (without results: "selinuxenabled && journalctl --since yesterday |grep avc: | grep -Eo comm="[^ ]+" | sort |uniq -c |sort -rn"):
     N/A

* CPU Model (grep 'model name' /proc/cpuinfo | awk -F: '{print $2}' | uniq -c |
     sed -re 's/^ +//' ):
     8  Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz
     
* 64-bit Support (grep -q ' lm ' /proc/cpuinfo && echo Yes || echo No):
     Yes
     
* Hardware Virtualization Support (grep -Eq '(vmx|svm)' /proc/cpuinfo && echo Yes || echo No):
     Yes
     
* Load average (uptime):
      18:19:19 up 7 days, 31 min,  2 users,  load average: 0.92, 0.31, 0.33
     
* Memory usage (free -m):
                    total        used        free      shared  buff/cache   available
     Mem:           31710        8802        5906        2910       17002       19542
     Swap:          16000        5197       10803
     
* Top 5 CPU hogs (ps axuScnh | awk '$2!=2893092' | sort -rnk3 | head -5):
         1000    1025 43.9  0.0  23476  9024 ?        Ss   Nov02 4443:52 systemd
         1000 2801772 11.0  0.1 325380 53792 ?        Ss   Nov05 648:53 tmux: server
         1000 2892327  2.9  0.0 225524  7124 pts/16   Ss   18:19   0:00 bash
         1000    5463  2.8  1.0 6016996 351404 ?      Ssl  Nov02 288:20 gnome-shell
         1000 2626948  2.5  7.1 10842744 2324076 ?    Sl   Nov05 151:08 qutebrowser
     
* Top 5 Memory hogs (ps axuScnh | sort -rnk4 | head -5):
         1000 2626948  2.5  7.1 10842744 2324076 ?    Sl   Nov05 151:08 qutebrowser
         1000    5857  0.0  2.0 2237240 657888 ?      Sl   Nov02   2:12 gnome-software
         1000 2627126  0.8  1.7 2155792 565932 ?      Sl   Nov05  52:20 QtWebEngineProc
         1000    5463  2.8  1.0 6016996 351404 ?      Ssl  Nov02 288:20 gnome-shell
         1000 1774786  0.5  0.7 6639148 238160 ?      Sl   Nov08   9:12 QtWebEngineProc
     
* Disk space usage (df -hT):
     Filesystem     Type      Size  Used Avail Use% Mounted on
     devtmpfs       devtmpfs   16G     0   16G   0% /dev
     tmpfs          tmpfs      16G  120M   16G   1% /dev/shm
     tmpfs          tmpfs     6.2G  2.0M  6.2G   1% /run
     /dev/sdb5      ext4       89G   53G   31G  64% /
     /dev/sda1      ext4      222G   56G  156G  27% /mnt/Scratch
     /dev/sdb1      ext4      477M  356M   92M  80% /boot
     /dev/sdb2      ext4      591G  258G  303G  46% /home
     tmpfs          tmpfs      16G  3.0G   13G  20% /tmp
     tmpfs          tmpfs     3.1G  280K  3.1G   1% /run/user/1000
     
* Block devices (without results: "blkid" AND "/sbin/blkid"):
     N/A

* PCI devices (lspci -nn):
     00:00.0 Host bridge [0600]: Intel Corporation 4th Gen Core Processor DRAM Controller [8086:0c00] (rev 06)
     00:01.0 PCI bridge [0604]: Intel Corporation Xeon E3-1200 v3/4th Gen Core Processor PCI Express x16 Controller [8086:0c01] (rev 06)
     00:02.0 VGA compatible controller [0300]: Intel Corporation Xeon E3-1200 v3/4th Gen Core Processor Integrated Graphics Controller [8086:0412] (rev 06)
     00:03.0 Audio device [0403]: Intel Corporation Xeon E3-1200 v3/4th Gen Core Processor HD Audio Controller [8086:0c0c] (rev 06)
     00:14.0 USB controller [0c03]: Intel Corporation 8 Series/C220 Series Chipset Family USB xHCI [8086:8c31] (rev 05)
     00:16.0 Communication controller [0780]: Intel Corporation 8 Series/C220 Series Chipset Family MEI Controller #1 [8086:8c3a] (rev 04)
     00:16.3 Serial controller [0700]: Intel Corporation 8 Series/C220 Series Chipset Family KT Controller [8086:8c3d] (rev 04)
     00:19.0 Ethernet controller [0200]: Intel Corporation Ethernet Connection I217-LM [8086:153a] (rev 05)
     00:1a.0 USB controller [0c03]: Intel Corporation 8 Series/C220 Series Chipset Family USB EHCI #2 [8086:8c2d] (rev 05)
     00:1b.0 Audio device [0403]: Intel Corporation 8 Series/C220 Series Chipset High Definition Audio Controller [8086:8c20] (rev 05)
     00:1d.0 USB controller [0c03]: Intel Corporation 8 Series/C220 Series Chipset Family USB EHCI #1 [8086:8c26] (rev 05)
     00:1f.0 ISA bridge [0601]: Intel Corporation Q87 Express LPC Controller [8086:8c4e] (rev 05)
     00:1f.2 SATA controller [0106]: Intel Corporation 8 Series/C220 Series Chipset Family 6-port SATA Controller 1 [AHCI mode] [8086:8c02] (rev 05)
     00:1f.3 SMBus [0c05]: Intel Corporation 8 Series/C220 Series Chipset Family SMBus Controller [8086:8c22] (rev 05)
     
* USB devices (lsusb):
     Bus 002 Device 002: ID 8087:8000 Intel Corp. Integrated Rate Matching Hub
     Bus 002 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
     Bus 001 Device 002: ID 8087:8008 Intel Corp. Integrated Rate Matching Hub
     Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
     Bus 004 Device 001: ID 1d6b:0003 Linux Foundation 3.0 root hub
     Bus 003 Device 004: ID 1b3f:2247 Generalplus Technology Inc. GENERAL WEBCAM
     Bus 003 Device 003: ID 045e:07a5 Microsoft Corp. Wireless Receiver 1461C
     Bus 003 Device 002: ID 2f68:0082 Hoksi Technology DURGOD Taurus K320
     Bus 003 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
     
* DRM Information (journalctl -k -b | grep -o 'kernel:.*drm.*$' | cut -d ' ' -f 2- ):
     [drm] Initialized i915 1.6.0 20201103 for 0000:00:02.0 on minor 0
     i915 0000:00:02.0: [drm] fb0: i915 frame buffer device
     
* Xorg modules (grep LoadModule /var/log/Xorg.0.log ~/.local/share/xorg/Xorg.0.log | cut -d \" -f 2 | xargs):
     
     
* GL Support (without results: "glxinfo | grep -E "OpenGL version|OpenGL renderer""):
     N/A

* Xorg errors (without results: "grep '^\[.*(EE)' /var/log/Xorg.0.log ~/.local/share/xorg/Xorg.0.log | cut -d ':' -f 2- "):
     N/A

* Kernel buffer tail (dmesg | tail):
     [317432.892471] ata2.00: supports DRM functions and may not be fully accessible
     [317432.947016] ata2.00: configured for UDMA/133
     [317434.084947] ata2.00: Enabling discard_zeroes_data
     [317434.183220] e1000e 0000:00:19.0 eno1: NIC Link is Down
     [317437.866406] ata1: link is slow to respond, please be patient (ready=0)
     [317438.855431] ata1: SATA link up 6.0 Gbps (SStatus 133 SControl 300)
     [317439.373191] ata1.00: configured for UDMA/100
     [317454.012340] e1000e 0000:00:19.0 eno1: NIC Link is Up 100 Mbps Full Duplex, Flow Control: Rx/Tx
     [317454.012344] e1000e 0000:00:19.0 eno1: 10/100 speed: disabling TSO
     [317454.012380] IPv6: ADDRCONF(NETDEV_CHANGE): eno1: link becomes ready
     
* Last few reboots (last -x -n10 reboot runlevel):
     runlevel (to lvl 5)   5.14.15-300.fc35 Tue Nov  2 17:48   still running
     reboot   system boot  5.14.15-300.fc35 Tue Nov  2 17:47   still running
     reboot   system boot  5.14.15-300.fc35 Tue Nov  2 17:47 - 17:47  (00:00)
     runlevel (to lvl 5)   5.14.15-300.fc35 Sun Oct 31 16:26 - 17:46 (2+01:19)
     reboot   system boot  5.14.15-300.fc35 Sun Oct 31 16:26 - 17:46 (2+01:20)
     reboot   system boot  5.14.14-300.fc35 Sun Oct 31 16:24 - 16:26  (00:02)
     runlevel (to lvl 5)   5.14.14-300.fc35 Fri Oct 22 12:07 - 16:23 (9+05:16)
     reboot   system boot  5.14.14-300.fc35 Fri Oct 22 12:06 - 16:23 (9+05:16)
     reboot   system boot  5.14.11-300.fc35 Fri Oct 22 12:04 - 12:06  (00:02)
     runlevel (to lvl 5)   5.14.11-300.fc35 Thu Oct 14 16:42 - 12:03 (7+19:21)
     
     wtmp begins Fri Oct 25 12:31:45 2019
     
* DNF Repositories (dnf repolist):
     repo id                                                            repo name
     copr:copr.fedorainfracloud.org:ankursinha:rubygem-taskjuggler      Copr repo for rubygem-taskjuggler owned by ankursinha
     copr:copr.fedorainfracloud.org:flatcap:neomutt                     Copr repo for neomutt owned by flatcap
     copr:copr.fedorainfracloud.org:group_neurofedora:neurofedora-extra Copr repo for neurofedora-extra owned by @neurofedora
     copr:copr.fedorainfracloud.org:jgoguen:universal-ctags             Copr repo for universal-ctags owned by jgoguen
     docker-ce-stable                                                   Docker CE Stable - x86_64
     fedora                                                             Fedora 35 - x86_64
     fedora-cisco-openh264                                              Fedora 35 openh264 (From Cisco) - x86_64
     fedora-modular                                                     Fedora Modular 35 - x86_64
     rpmfusion-free                                                     RPM Fusion for Fedora 35 - Free
     rpmfusion-free-updates                                             RPM Fusion for Fedora 35 - Free - Updates
     rpmfusion-nonfree                                                  RPM Fusion for Fedora 35 - Nonfree
     rpmfusion-nonfree-updates                                          RPM Fusion for Fedora 35 - Nonfree - Updates
     updates                                                            Fedora 35 - x86_64 - Updates
     updates-modular                                                    Fedora Modular 35 - x86_64 - Updates
     updates-testing                                                    Fedora 35 - x86_64 - Test Updates
     
* DNF Extras (dnf -C list extras):
     Last metadata expiration check: 2:51:49 ago on Tue 09 Nov 2021 15:27:32 GMT.
     Extra Packages
     ICAClient.x86_64                         21.9.0.25-0           @@commandline    
     adobe-release-x86_64.noarch              1.0-1                 @System          
     ctxusb.x86_64                            21.9.0.25-1           @@commandline    
     flash-plugin.x86_64                      32.0.0.465-release    @System          
     google-chrome-stable.x86_64              94.0.4606.61-1        @google-chrome   
     jabref.x86_64                            5.3.60000-1           @@commandline    
     kernel-debuginfo.x86_64                  5.14.7-300.fc35       @fedora-debuginfo
     kernel-debuginfo-common-x86_64.x86_64    5.14.7-300.fc35       @fedora-debuginfo
     minikube.x86_64                          1.23.0-0              @@commandline    
     pyplane.noarch                           2.0.0-1.fc35          @@commandline    
     qtpass.x86_64                            1.3.2-5.fc34          @fedora          
     zoom.x86_64                              5.7.28991.0726-1      @@commandline    
     
* Last 20 packages installed (rpm -qa --nodigest --nosignature --last | head -20):
     pngquant-2.15.1-2.fc35.x86_64                 Wed 03 Nov 2021 20:14:23 GMT
     libappstream-glib-builder-0.7.18-3.fc35.x86_64 Wed 03 Nov 2021 20:14:23 GMT
     maven-openjdk17-3.6.3-12.fc35.noarch          Wed 03 Nov 2021 15:31:48 GMT
     java-latest-openjdk-devel-17.0.1.0.12-1.rolling.fc35.x86_64 Wed 03 Nov 2021 15:31:48 GMT
     python3-PyLEMS-0.5.8-1.fc35.noarch            Tue 02 Nov 2021 17:47:22 GMT
     python3-fsleyes-1.3.0-1.fc35.noarch           Tue 02 Nov 2021 17:47:22 GMT
     simple-scan-40.6-1.fc35.x86_64                Tue 02 Nov 2021 17:47:21 GMT
     python3-regex-2021.10.23-1.fc35.x86_64        Tue 02 Nov 2021 17:47:21 GMT
     python3-pyelectro-0.2.0-1.fc35.noarch         Tue 02 Nov 2021 17:47:21 GMT
     python3-libNeuroML-0.2.58-1.fc35.noarch       Tue 02 Nov 2021 17:47:21 GMT
     vim-X11-8.2.3568-1.fc35.x86_64                Tue 02 Nov 2021 17:47:20 GMT
     vim-minimal-8.2.3568-1.fc35.x86_64            Tue 02 Nov 2021 17:47:20 GMT
     vim-default-editor-8.2.3568-1.fc35.noarch     Tue 02 Nov 2021 17:47:20 GMT
     ucx-1.11.2-1.fc35.x86_64                      Tue 02 Nov 2021 17:47:20 GMT
     pypy-devel-7.3.6-1.fc35.x86_64                Tue 02 Nov 2021 17:47:20 GMT
     gnome-shell-41.0-8.fc35.x86_64                Tue 02 Nov 2021 17:47:20 GMT
     bind-utils-9.16.22-1.fc35.x86_64              Tue 02 Nov 2021 17:47:20 GMT
     bind-license-9.16.22-1.fc35.noarch            Tue 02 Nov 2021 17:47:20 GMT
     bind-libs-9.16.22-1.fc35.x86_64               Tue 02 Nov 2021 17:47:20 GMT
     vim-enhanced-8.2.3568-1.fc35.x86_64           Tue 02 Nov 2021 17:47:19 GMT
     
* EFI boot manager output (without results: "efibootmgr -v"):
     N/A

Ingmar, if you have a strong and unique password and full disk encryption, I can seen little point in increasing complexity of the system by the use of additional authentication methods–it is just unbreakable, but more complexity normally implies more issues. This may be a diffrent story, perhaps not related to your problem with Zotero… Yet, I feel there may be some deeper issues with your system installation. Zotero works fine on bare Silverblue 35 (and seems to work on the standard Workstation as attested by others) and all its dependencies are met by installing the flatpak… If I were you, I’d probably make a fresh installation of Fedora Linux 35 (or Silverblue).

2 Likes

Thank you Piotr! Yeah, it seems I might have to go for a fresh install.

Just as an update in case others stumble upon this issue.
no reinstall yet, but I noted something curious:

When I try to start Zotero, several processes are started

  • bwrap
  • bwrap
  • zotero-bin
  • zotero-bin
  • zotero

When I kill one of the zotero-bin processes, then the UI for Zotero comes up.

Ha, also this was quite wrong. Managed to log in as another user.

I find, the problem with Zotero is the same for that account.