Zotero is already running, but is not responding

folquet

Hi all,

so, months after the Firefox upgrade that put the old extension out of business, I am still struggling to get the standalone client up and running.

I initially reported my difficulties in this thread: https://forums.zotero.org/discussion/67593, as my symptoms appeared to match those described by the OP. After some rather disordinate fiddling, the "Your Zotero profile cannot be loaded" message stopped popping up, but that did not get me any closer to a solution.

Here is how things stand now. I am running Ubuntu 14.04.1. Just downloaded a fresh tarball from zotero.org. Unzipped it.

mu@Pr0teus:~/Zotero_linux-x86_64$ sudo chown -R mu:mu ~/.cache

mu@Pr0teus:~/Zotero_linux-x86_64$ sh zotero

(zotero:11907): GLib-GObject-CRITICAL **: g_object_ref: assertion 'object->ref_count > 0' failed

(zotero:11907): GLib-GObject-CRITICAL **: g_object_unref: assertion 'object->ref_count > 0' failed

(zotero:11907): GLib-GObject-CRITICAL **: g_object_ref: assertion 'object->ref_count > 0' failed

(zotero:11907): GLib-GObject-CRITICAL **: g_object_unref: assertion 'object->ref_count > 0' failed

Outside the terminal, the error message "Zotero is already running, but is not responding. To open a new window, you must first close the existing Zotero process, or restart your system" pops up.

I tried running the program as root. Here is what I get:

mu@Pr0teus:~/Zotero_linux-x86_64$ sudo sh zotero
[sudo] password for mu:

(zotero:11961): GLib-GObject-CRITICAL **: g_object_ref: assertion 'object->ref_count > 0' failed

(zotero:11961): GLib-GObject-CRITICAL **: g_object_unref: assertion 'object->ref_count > 0' failed

(zotero:11961): GLib-GObject-CRITICAL **: g_object_ref: assertion 'object->ref_count > 0' failed

(zotero:11961): GLib-GObject-CRITICAL **: g_object_unref: assertion 'object->ref_count > 0' failed
Home directory not accessible: Permission denied
ERROR: cannot run unopkg as root without --shared or --bundled option.
ERROR: cannot run unopkg as root without --shared or --bundled option.
ii libreoffice-writer 1:6.0.2~rc1-0ubuntu0.14.04.1~lo3 amd64 office productivity suite -- word processor
ii libreoffice-java-common 1:6.0.2~rc1-0ubuntu0.14.04.1~lo3 all office productivity suite -- arch-independent Java support files
Home directory not accessible: Permission denied
Home directory not accessible: Permission denied
Home directory not accessible: Permission denied

(zotero:11961): GLib-GObject-CRITICAL **: g_object_ref: assertion 'object->ref_count > 0' failed

(zotero:11961): GLib-GObject-CRITICAL **: g_object_unref: assertion 'object->ref_count > 0' failed

(zotero:11961): GLib-GObject-CRITICAL **: g_object_ref: assertion 'object->ref_count > 0' failed

(zotero:11961): GLib-GObject-CRITICAL **: g_object_unref: assertion 'object->ref_count > 0' failed

After this, surprisingly, the program actually starts and appears to function normally. I get the warning message about running it as root, but my library loads fine and everything is there.

The bit that confuses me is that "Home directory not accessible: Permission denied". How is that possible, when I am launching the programme as root? Plus, if it is not accessible, why does my library then appear?

If you can spare a minute and some thought, I could use some help. And of course, apologies if the solution is already out there: I scanned the fora but couldn't find anything resolutive on the matter.

dstillman

I'm sure this isn't the answer you want, but best I can suggest is to update to a more recent Ubuntu. 14.04 is obviously quite old, and even if it's not yet EOL from Canonical, we haven't tested Zotero on 14.04 in years. It works fine on stock installations of newer versions.

But don't run Zotero as root, regardless. If you get an error, fix the permissions.

folquet

thanks, dstillman. I have been trying to fix the permissions - and actually tried some of your suggestions from that other thread. I thought I was getting somewhere, but that latest error message threw me off entirely.

And yes, I thought of upgrading Ubuntu as my next move. I have been putting off the upgrade for ages, but I really need Zotero back, so I might just have to bite the bullet.

I'll keep trying to troubleshoot the permission issue (?) until the weekend. If I make any progress, I'll report back. Otherwise, I'll go ahead and upgrade the OS on Saturday.

Meanwhile, if anybody has any other ideas, I'm all ears.

folquet

Hello folks.
I just wanted to leave a note of how things went in the end, in case someone else encounters a similar issue.

I finally got around updating Ubuntu to the latest version. Full of hope, I then proceeded to try and launch Zotero. No luck. Exactly the same issue: running the executable as user returned the "Zotero is already running" message, running it as root worked fine, but well, that was not what I wanted.

I didn't give up, however. Instead, I set out to fix the permissions. I used chmod to get a list of what folders in /home were currently as root only.

It turned out that all Firefox and Zotero-related folders were (and only those). I am not sure how that happened - probably a mistake on my part during the installation process. So I changed the permissions for all of those folders, and THEN, finally, Zotero was able to launch with just user privileges.

Note: I had done this exact same thing before, so this does not explain why it had not worked before, but I thought it worth to leave a trace anyway.