Apt Update: Problem unlinking the file ... (30: Read-only file system)

Question

Tried the solutions provided by several other questions on AskUbuntu, but none of them work as described below.

On Ubuntu 16.04.1 LTS, when I run

sudo apt update

we get the following error.

Ign:1 http://security.ubuntu.com/ubuntu xenial-security InRelease
Err:3 http://security.ubuntu.com/ubuntu xenial-security Release
  Could not open file /var/lib/apt/lists/partial/security.ubuntu.com_ubuntu_dists_xenial-security_Release - open (30: Read-only file system) [IP: 2001:67c:1560:8001::11 80]
Hit:2 http://nyc2.mirrors.digitalocean.com/ubuntu xenial InRelease
Err:2 http://nyc2.mirrors.digitalocean.com/ubuntu xenial InReleasetempfiles for splitting up /var/lib/apt/lists/mirrors.digitalocean.com_ubuntu_dists_xenial_InRelease
  Could not execute 'apt-key' to verify signature (is gnupg installed?)
Ign:4 http://nyc2.mirrors.digitalocean.com/ubuntu xenial-updates InRelease
Ign:5 http://nyc2.mirrors.digitalocean.com/ubuntu xenial-backports InRelease
Err:6 http://nyc2.mirrors.digitalocean.com/ubuntu xenial-updates Release
  Could not open file /var/lib/apt/lists/partial/mirrors.digitalocean.com_ubuntu_dists_xenial-updates_Release - open (30: Read-only file system) [IP: 2604:a880:0:1::4 80]
Err:7 http://nyc2.mirrors.digitalocean.com/ubuntu xenial-backports Release
  Could not open file /var/lib/apt/lists/partial/mirrors.digitalocean.com_ubuntu_dists_xenial-backports_Release - open (30: Read-only file system) [IP: 192.241.164.26 80]
Reading package lists... Done
W: chown to _apt:root of directory /var/lib/apt/lists/partial failed - SetupAPTPartialDirectory (30: Read-only file system)
W: chmod 0700 of directory /var/lib/apt/lists/partial failed - SetupAPTPartialDirectory (30: Read-only file system)
W: Not using locking for read only lock file /var/lib/apt/lists/lock
W: Problem unlinking the file /var/lib/apt/lists/partial/.apt-acquire-privs-test.IRU0Ss - IsAccessibleBySandboxUser (30: Read-only file system)
W: Problem unlinking the file /var/lib/apt/lists/partial/.apt-acquire-privs-test.xj8X0s - IsAccessibleBySandboxUser (30: Read-only file system)
W: Problem unlinking the file /var/lib/apt/lists/partial/.apt-acquire-privs-test.3xfW8s - IsAccessibleBySandboxUser (30: Read-only file system)
W: Problem unlinking the file /var/lib/apt/lists/partial/.apt-acquire-privs-test.DxtUgt - IsAccessibleBySandboxUser (30: Read-only file system)
W: Problem unlinking the file /var/lib/apt/lists/partial/security.ubuntu.com_ubuntu_dists_xenial-security_InRelease - PrepareFiles (30: Read-only file system)
W: Problem unlinking the file /var/lib/apt/lists/partial/security.ubuntu.com_ubuntu_dists_xenial-security_Release - PrepareFiles (30: Read-only file system)
E: The repository 'http://security.ubuntu.com/ubuntu xenial-security Release' does not have a Release file.
N: Updating from such a repository can't be done securely, and is therefore disabled by default.
N: See apt-secure(8) manpage for repository creation and user configuration details.
W: Problem unlinking the file /var/lib/apt/lists/partial/mirrors.digitalocean.com_ubuntu_dists_xenial_InRelease - PrepareFiles (30: Read-only file system)
W: chown to _apt:root of file /var/lib/apt/lists/mirrors.digitalocean.com_ubuntu_dists_xenial_InRelease failed - Item::QueueURI (30: Read-only file system)
W: chmod 0600 of file /var/lib/apt/lists/mirrors.digitalocean.com_ubuntu_dists_xenial_InRelease failed - Item::QueueURI (30: Read-only file system)
W: chown to root:root of file /var/lib/apt/lists/mirrors.digitalocean.com_ubuntu_dists_xenial_InRelease failed - 400::URIFailure (30: Read-only file system)
W: chmod 0644 of file /var/lib/apt/lists/mirrors.digitalocean.com_ubuntu_dists_xenial_InRelease failed - 400::URIFailure (30: Read-only file system)
W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: http://nyc2.mirrors.digitalocean.com/ubuntu xenial InRelease: Could not execute 'apt-key' to verify signature (is gnupg installed?)
W: Problem unlinking the file /var/lib/apt/lists/partial/mirrors.digitalocean.com_ubuntu_dists_xenial-updates_InRelease - PrepareFiles (30: Read-only file system)
W: Problem unlinking the file /var/lib/apt/lists/partial/mirrors.digitalocean.com_ubuntu_dists_xenial-backports_InRelease - PrepareFiles (30: Read-only file system)
W: Problem unlinking the file /var/lib/apt/lists/partial/mirrors.digitalocean.com_ubuntu_dists_xenial-updates_Release - PrepareFiles (30: Read-only file system)
E: The repository 'http://mirrors.digitalocean.com/ubuntu xenial-updates Release' does not have a Release file.
N: Updating from such a repository can't be done securely, and is therefore disabled by default.
N: See apt-secure(8) manpage for repository creation and user configuration details.
W: Problem unlinking the file /var/lib/apt/lists/partial/mirrors.digitalocean.com_ubuntu_dists_xenial-backports_Release - PrepareFiles (30: Read-only file system)
E: The repository 'http://mirrors.digitalocean.com/ubuntu xenial-backports Release' does not have a Release file.
N: Updating from such a repository can't be done securely, and is therefore disabled by default.
N: See apt-secure(8) manpage for repository creation and user configuration details.
W: Problem unlinking the file /var/cache/apt/pkgcache.bin - RemoveCaches (30: Read-only file system)
W: Problem unlinking the file /var/cache/apt/srcpkgcache.bin - RemoveCaches (30: Read-only file system)
W: Not using locking for read only lock file /var/lib/dpkg/lock

Attempt 1

~# mount -o remount,rw /
~# reboot

Result: Same error encountered after reboot.

Attempt 2

~# sudo fsck -Af
fsck from util-linux 2.27.1
~#reboot

Result: Same error encountered after reboot.

More Info

~# dmesg | grep "EXT4-fs error"
~# mount -t ext4
/dev/vda1 on / type ext4 (ro,relatime,data=ordered)

What is happening? Any ideas?

Solution

I had the same problem on Ubuntu 18.04.4.

Then, I saw that I can't run anything when terminal on home directory because home directory file system was read-only. I thought that rebooting will solve the problem but my computer stuck at (initramfs) _ section during reboot. My home directory mounted as /dev/sda2 (sudo fdisk -l to see that).

According to this answer I typed:

(initramfs) fsck /dev/sda2

then:

(initramfs) reboot

This solved my problem and I can run apt update and other things.

note: this solution is a temporary solution. I'll let you know if I find a permanent solution.

edit: I've found the solution. The problem occurs if your disk has lots of bad sectors. You have to ignore these bad sectors on the disk.

Comments

[Chai T. Rex]

Mounting should not be followed by a reboot, since the mount goes away after reboot.

[N. Cornet]

Do you always get the error ? If not, please try to specify when this happen (I encounter this issue, but only after waking up from sleep mode, and not so often). And does your mount command outputs smth ? For me it says mount: /: cannot remount /dev/sda7 read-write, is write-protected.