Backup up Fedora Problems? Any solution?

Hi all I have been trying to back up my system for awhile(HOME folder) but I keep running into issues.

I first messed up with installing flatpak versions of Pika and Vorta which didn’t work due to root access permissions. I then uninstalled all and installed Vorta, Deja Dup via CLI and still get the same issue.

My most recent attempt of backup via Vorta still shows this error in log

“2025-11-24 04:42:03,585 - vorta.borg.borg_job - WARNING - /home/e/desktop: open: [Errno 13] Permission denied: ‘desktop’”

I have heard of rsync and restic I believe but any really good step by step guide would be greatly appreciated.

EDIT
I have launched vorta via CLI through sudo vorta

Copied HOME DIR pasted it in settings within VORTA .. is this a good method?

Thank you

I use Deja Dup for my backups (I place them on GDrive).

The RPM version from Fedora repositories. I stay away from flatpaks.

Probably it is not a good idea to backup the whole /home directory since it includes many things you don’t need, like the browser cache and alike.

I save only the /documents directory and Thunderbird profile which contains my email. If I needed more I would select the single subdirectories.

I am of a different opinion than @lendenu (while respecting his choice), and am using the Flatpak version of Deja-Dup from Flathub, given that it’s more up to date, is using the more suitable restic backend by default and it has some fixed issues.

Keep in mind that the backup software (obviously) won’t back up files/folders which are not accessible by the user running the backup process.

Besides, since some days ago Gnome Online Accounts and Deja Dup crash on my own PC.

Hey Lorenzo,

Will the RPM package allow to back up the entire home directory( assuming running sudo command)? I can deselect that which isn’t relevant

I do not use cloud storage either just local external ssd

Well if your in session how the hell are you to back up home ?

I.e if your user A backing up user A your saying it cant be done?

Did i miss something?

Dejadup spits out the same error message. So im guessing i have to install that as a rpm package for it to be able to copy /home

He’s saying that if you’re running as user A, you can’t back up files which user A doesn’t have permission to read.

Generally a user should be able to read everything in their own homedir, so this shouldn’t be an issue.

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That shouldn’t be a problem. The same way you can copy or rsync your home directory while in a user session, you should be able to use Deja-Dup. After all, once set up, it usually runs in the background (but can be run manually as well).

My setup is to back up my home directory, and I’m benefitting of the default paths to be excluded. The only additional paths not to be backed up are the Downloads folder and the path to containers.

You didn’t mention what Fedora flavor are you using.

What is the permission set for your Desktop folder?

All I can say is the RPM Deja Dup worked for me until the last backup wednesday.

It runs from my own user session for automated backup once a week and, like I said, I save two directories, /documents and /.thunderbird (note that this is hidden).

I never tried to save /home but now I can’t do anything because it crashes, probably when it tries to connect to GDrive and I don’t know why, I guess some Fedora upgrade.

Pika Flatpaks runs as a user rather than as root, meaning it cannot access files outside the home directory. This is, however, outside the scope of Pika. Pika is simple backup software for user data.

From the Creators:

Pika Backup is designed to save your personal data and does not support complete system recovery. Pika Backup is powered by the well-tested BorgBackup software. For more information and support see the help pages

Pika has worked perfectly for me for about two years. Before that, I used Deja-Dup and always struggled to restore files, so I lost faith in it and switched to Pika.

FYI, this morning upgrade fixed the crash in Gnome Online Accounts and Deja Dup, both work on my system now.

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I am Using Fedora Workstation 43

I’m going try this tonight the RPM Deja Dup.

I tried running it via SUDO VORTA to run as ROOT but couldn’t add a REPO :confused:

I am going to try this tonight. Fingers crossed.
RPM Package DejaDup.

I really don’t understand why they could not have made this so simple in Fedora out of the box …

My suggestion is to start with some single directory inside "/home”, see if it works.

Since it works for me, try “/documents”.

If it works and you can save and recover those directories, you can simply add as many as you need instead of subtract from the whole “/home”.

Speaking of “simple”, it is the story of “linux”. When it works, it is so simple. Unfortunately sometimes it does not work and since there are many ways to achieve the same goal, you get easily lost in the labirinth.

I understand I think i may have found an issue please see attached photo.. In my home folder I have a desktop file thats locked? maybe that was causing the failed backup?
Screenshot From 2025-11-27 00-09-23

I will. Keep you posted:)