In Ubuntu Mate 18.04, Zotero is broken

edited 18 days ago
Hi
We have 3 computers (2 Ubuntu Mate 18.04.1 and 1 windows 8.1) with Zotero 5.0.59. All computers are running Firefox, the windows pc has ms office 2007 and the Mate computers are running LibreOffice version 6.0.7.3. We have the computers syncing via the wonderful Zotero Sync function and the library's are intact (but I have saved a copy of the library). The Zotero on the windows desktop is working normally but the two Ubuntu computers have developed an issue.

In LibreOffice writer, when I go to “Add/Edit Citation” the “Zotero-Document Preferences” window opens but there are no Styles listed (normally this window is populated with about 8-10 styles). Clicking “Manage Styles” takes me an unpopulated Zotero Preferences>Cite>Styles window and clicking “Get additional Styles” takes me to the “Zotero Style Repository” window where any attempt to install a style results in an error message for the desired style e.g.
An unexpected error occurred while installing "https://www.zotero.org/styles/apa".

I can manually create a new library Item and the Firefox "Save to Zotero" button still works. Also, running Zotero as root works (i.e. the expected styles list appears and one can be selected) however, all of the library data is missing, there is no library data available.

On one of the Mate machines I have tried reinstalling Zotero (with Synaptic Packet Manager) but this didn't change anything.

I am not sure where to go from here (i don't want to make it worse), so any advice/suggestions are welcome.

Regards


  • How are you installing Zotero in the first place? Zotero doesn't provide a package for Ubuntu (or any other distribution), so the first thing to try would be a clean run from the tarball downloaded from zotero.org/download
  • edited 17 days ago
    Thanks for the reply.

    I used the following Ubuntu install process;
    sudo add-apt-repository ppa:smathot/cogscinl
    sudo apt-get update
    sudo apt-get install zotero-standalone
    There is also the instructions at https://www.zotero.org/support/installation

    I reinstalled the Zotero Stand Alone and after a restart the problem still existed.
    I then tried downloading some styles e.g. https://www.zotero.org/styles/apa or http://www.zotero.org/styles/ieee etc, they appear to have downloaded successfully to the Zotero>Styles folder but Zotero wouldn't load them, it gives me the same error message; “An unexpected error occurred while installing...”
    except with a local folder address instead of a URL.

    I found that some styles will load and work as expected, it was when I was trying one of these (Academic Paediatrics) that all the others reappeared in the Style Manager window and now Zotero works as before….
    I tried this process on another Mate computer and it now works as well.

    I have no idea what happened but I will take this as a solution :-)

    Thanks
  • https://github.com/retorquere/zotero-deb works, just tested on Mate (it's also more up to date)
  • Given the error description here, it sounds like this may be some sort of permission (or, less likely, security software) setting on the Zotero data directory. Zotero definitely works on Mate, both using Emiliano's deb and using the unpacked tarball from Zotero directly (the two being basically identical).
  • They binaries will be identical, the only thing the deb does is put the binaries in place and generate menu files.
  • Zotero is working as expected now and thanks for the replies and the link.

    In case others like me (novices) want to try Zotero in Mate or want to remove and reinstall Zotero here is the method I used to remove Zotero;

    sudo apt-get remove zotero-standalone

    This will uninstall the Zotero software but doesn't remove the library's that have been created (in my Ubuntu Mate 18.04 the library(s) are in the Mate Home>Zotero>Storage folder)

    Then reinstall with the following;
    sudo add-apt-repository ppa:smathot/cogscinl
    sudo apt-get update
    sudo apt-get install zotero-standalone
  • Newest version is apt-gettable from https://github.com/retorquere/zotero-deb . I believe ppa:smathot/cogscinl hasn't been updated for a while.
  • My mistake -- it's just been updated
  • Bad news, the issue has returned on one of the MATE computers.
    The PC with the problem is now running Zotero 5.0.60 and the other (functioning correctly) one is still on 5.0.59

    With the exception that the Mate computers have different Zotero versions, everything described in the first post is the same.

    The pressure is off us at the moment so we have a little time to find a cause/solution, any help diagnosing-resolving this problem is appreciated.

    Regards
  • Where did you install 5.0.60 from? PPA or https://github.com/retorquere/zotero-deb?
  • The 5.0.60 install came via an update, i.e. Help>Check for Updates
  • But the version you upgraded from, how was that installed?
  • Ahh sorry,
    The orrigional install on both computers (and subsiquent reinstall) was via;
    sudo add-apt-repository ppa:smathot/cogscinl

  • Can't help you there, I don't manage that repo.

    Can you check who the owner is of /opt/zotero (where I think the PPA installs to)? It should be root but I screwed that up too (now fixed), and when it's root-owned, a "Check for updates" (unless ran by root, but you *really* don't want to do that) should not have the possibility to perform the upgrade.

    Help-Check is great for local (user-performed) installs on Linux (no idea how it works under Windows), but for global (packaged) installs, you really just want to stick with the package upgrades.
  • Using the method outlined in a previous post I uninstalled-reinstalled Zotero, the reinstall reverted Zotero from 5.0.60 to 5.0.59, unfortunately the problem still persisted.

    I then ran ~$ stat /opt/zotero which returned;
    File: /opt/zotero
    Size: 4096 Blocks: 8 IO Block: 4096 directory
    Device: 842h/2114d Inode: 1049136 Links: 12
    Access: (0775/drwxrwxr-x) Uid: ( 501/ UNKNOWN) Gid: ( 501/ UNKNOWN)
    Access: 2019-01-12 10:36:38.387408489 +0100
    Modify: 2018-12-19 03:25:39.000000000 +0100
    Change: 2019-01-12 10:28:59.160767936 +0100

    As best as I can tell… the UID and GID should have an owner-user but are returning UNKNOWN… I also checked the other computer in which Zotero (5.0.59) works, it returned the same output so perhaps UNKNOWN isn't the problem.

    I then ran ls -l on the /opt/zotero and /home/user name/Zotero folders in both computers, they appear to have the same distribution of RWX permissions.

    Finally, on the “problem” computer, I changed the permissions in /home/user name/Zotero to 777 and found that this not only returned access to the downloaded Styles (/home/user name/Zotero/Styles) but also access to the online Style library.

    It looks like 5.0.59 is working but updating to 5.0.60 causes the problem.
    But it is working again, for now… :-)
  • I'd *seriously* advice against setting permissions to 777. 777 can be *sort of* ok if you're very sure only you access this machine, but it's a seriously bad habit to get into.

    You could try uninstalling zotero from that ppa and installing from https://github.com/retorquere/zotero-deb. I think I got the permissions right there and the latest Zotero will be found there no more than a day after Zotero releases a new version.
  • Thanks for the info emilianoeheyns,
    I reset the permissions from 777 to their original after my “test”. Changing the folders permissions to 777 and back again corrected the problem and allowed normal operation.

    I have uninstalled the ppa stand-alone and reinstalled Zotero with the ‘curl’ option (wget didn't work) on the page you linked, we have had 5.0.60 running faultlessly for a few days now.

    Thanks.
  • Cool. The wget version should now work too.
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