Update in Ubuntu

claudiuscluever · February 10, 2020

I tried to update Zotero to 5.0.82. I unpacked the tar.bz in home/Zotero.

(Because it wouldn't let me update from Zotero, saying it didn't have the necessary rights. The Zotero folder in /opt is owned by a user called "501".)

When I run Zotero from home/Zotero in the terminal, everything works fine. (The exception being that it doesn't use the Zotero icon but the generic grey gear.)

But when I try to pull it up from the OS (i.e. the dash) it always gives me the old version from opt/zotero, saying the Database needs 5.0.82:

>>Die Zotero Datenbank benötigt Zotero 5.0.82 oder höher.

>>Aktuelle Version: 5.0.45

>>Bitte upgraden Sie auf die neueste Version von zotero.org.

What do I do? Please help.

bmx2019 · February 13, 2020

If you do a

locate zotero.desktop

you will get a zotero at /opt//zotero.desktop

Just delete this entire folder by user called 501.

>>> What do I do? Please help.

This is not an issue with zotero but there is OLD zotero in your computer. Ask your admin to delete the zotero inside the /opt folder.

Can you type in a terminal

ls -l /opt/

claudiuscluever · February 14, 2020

Thanks for your answer!

>> This is not an issue with zotero but there is OLD zotero in your computer.

With all respect and gratitude: Sure it is. I updated Zotero following the instructions I found on the homepage and wound up with two versions of Zotero interfering with each other The issue with Zotero is that there isn't a seamless update process - at least none that is working on my machine.

>> Just delete this entire folder by user called 501.

How do I do that? I don't have the access rights. I would start nautilus with sudo, but I read that that generally is a bad idea.

>> Ask your admin to delete the zotero inside the /opt folder.

That's me, this is my computer.

>> Can you type in a terminal ls -l /opt/

ls -l /opt/
insgesamt 12
drwxr-xr-x 4 root root 4096 Dez 16 2018 net.downloadhelper.coapp
drwxr-xr-x 6 root root 4096 Dez 15 2018 wine-stable
drwxrwxr-x 12 501 501 4096 Apr 16 2018 zotero

dstillman · February 14, 2020

I updated Zotero following the instructions I found on the homepage and wound up with two versions of Zotero interfering with each other

No, this would be a misunderstanding on your part. All we offer is a standard Linux tarball (with a script to update the icon for a bundled Ubuntu desktop file that you can symlink into place). You can extract it and run it and, if you don't change the file permissions, it will update itself automatically — that's the update process. If you have multiple copies on your system, you simply installed it multiple times. And if the files are owned by another user account, that's something you did.

I unpacked the tar.bz in home/Zotero.

If you really mean ~/Zotero, that's incorrect (and /home/Zotero would also be wrong). ~/Zotero is the Zotero data directory, and other files don't belong there. You can put the application files anywhere else, but they shouldn't be in there.

If you're having trouble with this, I'd suggest deleting both sets of application files (but not your Zotero data) as well as the launcher icon and then switching to a packaged version of Zotero created by a Zotero community member. (There's a good chance we'll officially take over distribution of those packages in the future.)

emilianoeheyns · February 15, 2020

To make that easier I've created a script that builds only zotero and uploads the repo to a S3 bucket (which is what Zotero uses for its downloads as far as I can tell). It can be ran from a cronjob (travis offers once-per-day cronjobs) and should be set and forget after some config in the ini file and the S3 creds.

claudiuscluever · February 18, 2020

>>You can extract it and run it and, if you don't change the file permissions, it will update itself automatically — that's the update process.

I understand that, but it didn't. It wouldn't update saying it didn't have the necessary rights.

>>If you have multiple copies on your system, you simply installed it multiple times.

Yes, because I then tried to update it "manually" by downloading the new tarball and extracting it somewhere. I thought it would make sense to put it in home/[user]/Zotero, but i now learned that that was wrong. Allright.

>>And if the files are owned by another user account, that's something you did.

Interesting. I doubt it honestly, but I am inclined to believe you. Any idea how I did that and why the user is called "501"? I have no idea how to set that up or change it. Originally I downloaded the tarball at one point and ran those setup scripts from some Zotero folder, I think.

>>If you're having trouble with this, I'd suggest deleting both sets of application files (but not your Zotero data) as well as the launcher icon and then switching to a packaged version of Zotero created by a Zotero community member.

Good, I'll do that. How do I delete the files in opt/zotero? It will not let me delete them because they are still owned by the user account 501 - whoever that is.

Thank you all for your advice and patience! I really have no idea why it didn't update like normal.

dstillman · February 18, 2020

I understand that, but it didn't. It wouldn't update saying it didn't have the necessary rights.

If it says that, you did something to change the permissions. A program can't change the permissions of its own files to be owned by another user without superuser privileges.

Any idea how I did that and why the user is called "501"?

Generally speaking, if a user id is displayed, the files either came from another computer or were created by a user account that has since been deleted (and therefore doesn't appear in /etc/passwd).

This is getting into generic Linux stuff, so this isn't really the best forum for it. Ideally your file manager would prompt you to delete files you need root privileges to modify, but I don't know if Nautilus will do that. You can also run sudo rm -rf /opt/zotero, but if you do that incorrectly you'll wipe out your entire disk, so I'd strongly discourage you from doing that without understanding exactly what you're doing.