Problem to update to Zotero 5 on Linux Mint

edu carrillo

Hello! I have linux mint and been trying to update Zotero to the 5.0 version. For some reason, the system says I don't have sufficient permissions and requires a manual update. Concretely, the warning of zotero says: "A recommended update is available, but you do not have permission to install it. To update automatically, modify the Zotero program directory through your user account to have write permission"

Has anyone else experienced similar problems? I have been unsuccessful to find this program directory the warning mentions. Thank you so much for any help you can give me!

emilianoeheyns

You may have installed Zotero as root. The built-in Zotero updater only works if the user running Zotero is allowed to write to the installation directory.

edu carrillo

Hi! Thank you for your answer. Is there a way I can check for this? I have all the admin permissions of the computer, since it's mine. Sorry if I don't quite understand some terms since I am not a technical person

emilianoeheyns

Even if you have admin access ("root") you will likely not (should absolutely not) be running as root regularly.

You can see who installed Zotero using ls -lhd <directory where the "zotero" binary lives>.

edu carrillo

Thank you for this. I pasted the line but it says "syntax error near the unexpected 'newline' element"

emilianoeheyns

Just retype it manually. I don't know what the forum adds.

dstillman

(I think edu carrillo literally copied the line as is instead of substituting the path to the Zotero application directory.)

edu carrillo

Yes indeeed! Sorry about that. How would I know the path to the Zotero application?

dstillman

It's wherever you put the files.

edu carrillo

Would this be the route? /home/edu/.zotero
That is the path I follow to my zotero file, but I never put anything there, I always charged my files with the browser extension.
I have put this in the terminal: ls -lhd but the same problem appears

emilianoeheyns

How do you usually start zotero?

edu carrillo

I normally just open the programme from my desktop and then I also have the extension on firefox to save the files I might need

edu carrillo

Ive been reading other querys similar to mine and its all about finding where the programe directory is, just as you have indicated. I am just not sure on how to get this information

emilianoeheyns

which zotero

edu carrillo

5.0.60

emilianoeheyns

If you type which zotero on the command line it should give you a full path to the binary.

edu carrillo

Thanks, I type it in the terminal and this is what I got /usr/bin/zotero

emilianoeheyns

That's likely a symlink. What does file /usr/bin/zotero say?

edu carrillo

It says /usr/bin/zotero: Bourne-Again shell script, ASCII text executable

emilianoeheyns

Inside that file you'll find the actual path of the zotero binary. But this was almost certainly installed as root. I would recommend against running zotero as root (which would allow zotero to upgrade itself), but to either re-do the installation that got you in the current state using the latest Zotero download, or to remove the current zotero and go with the Deb packages instead. Note that even though the debs deliver (and upgrade) the official zotero binaries, the Deb packages are volunteer-provided by yours truly, they are *not* maintained by the zotero crew.

edu carrillo

Ok, thank you for this.

In relation to "re-do the installation that got you in the current state using the latest Zotero download" I have tried to do that but was unsuccessful on this (going to the website and download the last version). I don't know if this was due to the fact that I didnt uninstall the version I currently have. Is this what you are referring to?

In relation to the second point, the deb packages one, would that mean to do it through the Synaptic package manager?

So sorry for this questions I am really learning to use Linux on my own thats why all the questions. This version that I had was one my old office installed on my computer so I was never involved in installing it in the first place.

emilianoeheyns

Don't worry about it. If you can put the contents of /usr/bin/zotero on https://pastebin.com/ I can probably tell you how to uninstall Zotero from your system.

Not that I'm not necessarily advocating for installing the debs rather than doing it manually from the Zotero tarball, but you'd be getting the exact same binaries, and management of upgrades would be through the package manager that's familiar to you. Initial install will require a few shell commands.

edu carrillo

Thanks for your help, I just really need the best way of the system to update itself because that pop-up really annoys me and I want to make sure that I have the last version of the system.
Step 1 then I paste /usr/bin/zotero into this link: https://pastebin.com/ is that correct?

edu carrillo

Also, once its installed it should all work the same no? I will be able to work with zotero on libreoffice and google drive etc and save papers and news with the firefox and chrome extension?

emilianoeheyns

What is the best way will vary from person to person -- I'm not saying the debs are the best way, but they will help you keep Zotero up to date with the GUI tooling you're likely to be familiar with, with no command-line work beyond initial setup.

Yes, step 1 is paste /usr/bin/zotero into this link: https://pastebin.com/, and then report back the new link you got.

Once the installation of the debs is done, Zotero is exactly the same as had you installed it by hand. Its location in the filesystem will be different, and the internal update mechanism is disabled, because upgrades will be handled by your package manager, not Zotero itself. Other than that, it is 100% the same, and you can take a checksum of the binaries to verify this. You are getting the exact same Zotero, just with upgrades handled by your package manager.

edu carrillo

Thanks, I pasted but received the same link

/usr/bin/zotero

emilianoeheyns

Sorry: you need to paste the contents of /usr/bin/zotero into pastebin. If you then click "Create New Paste", your browser will be redirected from https://pastebin.com/ to something like https://pastebin.com/zebuLLHH, where you'll see the contents you just pasted again. If you post the URL to which you were redirected here, we can see the contents too, and we may be able to tell where Zotero lives on your system.

edu carrillo

what do you mean by contents?

edu carrillo

This is the link I believe https://pastebin.com/RKVNF3Jc

emilianoeheyns

That is the path to the file. You need to open that file using a text editor and edit the contents of that file. I honestly don't know how to explain the concept of file contents. What you're posting here is the file *name*. I need the actual text that's *in* the file. Like the text of a Word file rather than the filename (but please don't use Word to open the file - any text editor will do)