Hi,
it seems the dependencies for Zotero are broken - though we might consider Zotero as key for scientific users (see eg mkrawiec/i3desktop ).
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.
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?
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? 
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! 
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.
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. 
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://discussion.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).
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
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.
reinstalled Fedora - Zotero works. Thanks everybody, also for the kind direct message interactions!