mjhjmtu

I am trying to expand the size of one of the virtual machines I use. For that reason, I need to install the pvcreate command to be able of creating a physical volume.

When I try to install it, I get the following errors:

Notes:

Reading the output and looking for some information and other questions like this one, I understand I need to update the operating system, but I can't manage do it.

Errors that I have encountered:

1) "dpkg was interrupted, you must manually run 'sudo dpkg --configure -a' to correct the problem." (solved)

2) Read-only file system

3) "Unexpected inconsistency. Run fsck manually." (solved by running the command 'fsck -M /dev/sda1'; '/dev/sda1' is where my root is mounted on)

Things that I have tried:

1) https://askubuntu.com/questions/909719/dpkg-unrecoverable-fatal-error-aborting-files-list-file-for-package-linux-ge

Note: Before upgrading I have marked as hold some packages related to mariadb to avoid some conflicts due to unmet dependencies when upgrading.

Output:

rafa@ubuntu:~$ sudo apt update
Hit:1 http://tedeco.fi.upm.es/mirror/mariadb/repo/10.0/ubuntu xenial 
InRelease
Hit:2 http://ppa.launchpad.net/webupd8team/java/ubuntu xenial InRelease
Get:3 http://security.ubuntu.com/ubuntu xenial-security InRelease [107 kB] 
Hit:4 http://us.archive.ubuntu.com/ubuntu xenial InRelease 
Ign:5 http://mirror.jmu.edu/pub/mariadb/repo/5.5/ubuntu trusty InRelease 
Get:6 http://us.archive.ubuntu.com/ubuntu xenial-updates InRelease [109 
kB] 
Err:7 http://mirror.jmu.edu/pub/mariadb/repo/5.5/ubuntu trusty Release 
404 Not Found
Get:8 http://us.archive.ubuntu.com/ubuntu xenial-backports InRelease [107 
kB] 
Get:9 http://security.ubuntu.com/ubuntu xenial-security/main amd64 DEP-11 
Metadata [67.7 kB]
Get:10 http://security.ubuntu.com/ubuntu xenial-security/main DEP-11 64x64 
Icons [72.3 kB]
Get:11 http://security.ubuntu.com/ubuntu xenial-security/universe amd64 
DEP- 
11 Metadata [108 kB]
Get:12 http://security.ubuntu.com/ubuntu xenial-security/universe DEP-11 
64x64 Icons [150 kB] 
Get:13 http://us.archive.ubuntu.com/ubuntu xenial-updates/main amd64 DEP- 
11 Metadata [320 kB] 
Get:14 http://us.archive.ubuntu.com/ubuntu xenial-updates/main DEP-11 
64x64 Icons [231 kB] 
Get:15 http://us.archive.ubuntu.com/ubuntu xenial-updates/universe amd64 
DEP-11 Metadata [247 kB]
Get:16 http://us.archive.ubuntu.com/ubuntu xenial-updates/universe DEP-11 
64x64 Icons [333 kB]
Get:17 http://us.archive.ubuntu.com/ubuntu xenial-updates/multiverse amd64 
DEP-11 Metadata [5,960 B]
Get:18 http://us.archive.ubuntu.com/ubuntu xenial-updates/multiverse DEP- 
11 64x64 Icons [14.3 kB]
Get:19 http://us.archive.ubuntu.com/ubuntu xenial-backports/main amd64 
DEP-11 Metadata [3,328 B]
Get:20 http://us.archive.ubuntu.com/ubuntu xenial-backports/universe amd64 
DEP-11 Metadata [5,104 B]
Reading package lists... Done 
E: The repository 'http://mirror.jmu.edu/pub/mariadb/repo/5.5/ubuntu 
trusty 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.
rafa@ubuntu:~$ sudo apt-mark hold mariadb*

mariadb-common set on hold.
mariadb-client-10.0 set on hold.
mariadb-server set on hold.
mariadb-client set on hold.
mariadb-client-core-10.0 set on hold.
mariadb-server-10.0 set on hold.
mariadb-plugin-connect set on hold.
mariadb-galera-server-10.0 set on hold.
mariadb-connect-engine-10.0 set on hold.
mariadb-plugin-mroonga set on hold.
mariadb-plugin-oqgraph set on hold.
mariadb-oqgraph-engine-10.0 set on hold.
mariadb-plugin-spider set on hold.
mariadb-plugin-tokudb set on hold.
mariadb-server-core-10.0 set on hold.
mariadb-galera-server set on hold.
mariadb-test set on hold.
mariadb-test-data set on hold.
mariadb-test-10.0 set on hold.
mariadb-galera-test set on hold.
mariadb-galera-test-10.0 set on hold.
mariadb-client-10.0-dbgsym set on hold.
mariadb-client-core-10.0-dbgsym set on hold.
mariadb-connect-engine-10.0-dbgsym set on hold.
mariadb-galera-server-10.0-dbgsym set on hold.
mariadb-galera-test-10.0-dbgsym set on hold.
mariadb-oqgraph-engine-10.0-dbgsym set on hold.
mariadb-server-10.0-dbgsym set on hold.
mariadb-server-core-10.0-dbgsym set on hold.
mariadb-test-10.0-dbgsym set on hold.

rafa@ubuntu:~$ sudo apt upgrade
Reading package lists... Done
Building dependency tree 
Reading state information... Done
Calculating upgrade... Done
The following package was automatically installed and is no longer 
required:
libllvm4.0
Use 'sudo apt autoremove' to remove it.
The following NEW packages will be installed:
 libdrm-common libllvm6.0 libqmi-glib5
The following packages have been kept back:
 mariadb-client-10.0 mariadb-client-core-10.0 mariadb-common mariadb- 
 server mariadb-server-10.0 mariadb-server-core-10.0
The following packages will be upgraded:
 amd64-microcode apparmor appstream apt apt-transport-https apt-utils 
 avahi-autoipd avahi-daemon avahi-utils base-files bind9-host binutils 
 bsdutils console-setup console-setup-linux
 desktop-file-utils dnsutils dpkg fonts-opensymbol friendly-recovery 
 fwupd fwupdate fwupdate-signed ghostscript ghostscript-x gir1.2- 
 gdkpixbuf-2.0 gir1.2-packagekitglib-1.0
 gnome-accessibility-themes gnome-software gnome-software-common gnome- 
 themes-standard gnome-themes-standard-data grub-common grub-pc grub-pc- 
 bin grub2-common gtk2-engines-pixbuf gvfs
 gvfs-backends gvfs-bin gvfs-common gvfs-daemons gvfs-fuse gvfs-libs 
 hdparm hicolor-icon-theme ifupdown initramfs-tools initramfs-tools-bin 
 initramfs-tools-core iproute2 isc-dhcp-client
 isc-dhcp-common keyboard-configuration klibc-utils libapparmor-perl 
 libapparmor1 libappstream-glib8 libappstream3 libapt-inst2.0 libapt- 
 pkg5.0 libaudit-common libaudit1 libavahi-client3
 libavahi-common-data libavahi-common3 libavahi-core7 libavahi-glib1 
 libbind9-140 libblkid1 libcryptsetup4 libdfu1 libdns-export162 libdns162 
 libdrm-amdgpu1 libdrm-intel1 libdrm-nouveau2
 libdrm-radeon1 libdrm2 libegl1-mesa libfdisk1 libfwup0 libfwupd1 libgbm1 
 libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgl1-mesa-dri libgl1-mesa- 
 glx libglapi-mesa libglib2.0-0
 libglib2.0-bin libglib2.0-data libgnutls-openssl27 libgnutls30 libgs9 
 libgs9-common libgtk2.0-0 libgtk2.0-bin libgtk2.0-common libisc- 
 export160 libisc160 libisccc140 libisccfg140 libklibc
 liblcms2-2 liblcms2-utils libldap-2.4-2 liblwres141 libmbim-glib4 
 libmbim-proxy libmm-glib0 libmount1 libnm-glib-vpn1 libnm-glib4 libnm- 
 gtk-common libnm-gtk0 libnm-util2 libnm0
 libnma-common libnma0 libopencv-core2.4v5 libopencv-imgproc2.4v5 
 libpackagekit-glib2-16 libpam-modules libpam-modules-bin libpam-runtime 
 libpam-systemd libpam0g libparted2 libpci3
 libplymouth4 libpulse-mainloop-glib0 libpulse0 libpulsedsp libpython- 
 stdlib libpython2.7 libpython2.7-minimal libpython2.7-stdlib libqmi- 
 proxy libreoffice-base-core libreoffice-calc
 libreoffice-common libreoffice-core libreoffice-gtk libreoffice-math 
 libreoffice-style-elementary libreoffice-style-galaxy libreoffice-writer 
 libseccomp2 libslang2 libsmartcols1
 libsmbclient libsnapd-glib1 libsnmp-base libsnmp30 libsystemd0 libudev1 
 libunity-protocol-private0 libunity-scopes-json-def-desktop libunity9 
 libuuid1 libva1 libwayland-egl1-mesa
 libxatracker2 linux-firmware linux-libc-dev logrotate lshw mesa-vdpau- 
 drivers modemmanager mount mysql-common network-manager network-manager- 
 gnome oracle-java8-installer
 oracle-java8-set-default parted pciutils plymouth plymouth-label 
 plymouth-theme-ubuntu-text pulseaudio pulseaudio-module-x11 pulseaudio- 
 utils python python-apt-common python-minimal
 python2.7 python2.7-minimal python3-apt python3-uno python3-update- 
 manager python3-urllib3 resolvconf rfkill samba-libs shared-mime-info 
 snapd snapd-login-service squashfs-tools systemd
 systemd-sysv ubuntu-core-launcher ubuntu-minimal ubuntu-mono ubuntu- 
 standard udev unattended-upgrades uno-libs3 update-manager update- 
 manager-core update-notifier update-notifier-common
 ure util-linux uuid-runtime va-driver-all wireless-regdb x11-common xdg- 
 user-dirs xorg xserver-common xserver-xorg-core-hwe-16.04 xserver-xorg- 
 legacy-hwe-16.04
 xserver-xorg-video-amdgpu-hwe-16.04 xserver-xorg-video-ati-hwe-16.04 
 xserver-xorg-video-intel-hwe-16.04 xserver-xorg-video-nouveau-hwe-16.04 
 xserver-xorg-video-radeon-hwe-16.04
 230 upgraded, 3 newly installed, 0 to remove and 6 not upgraded.
 Need to get 213 MB/223 MB of archives.
 After this operation, 123 MB of additional disk space will be used.
 Do you want to continue? [Y/n] Y

 ...
 (All the Get requests)
 ...

 Fetched 213 MB in 8min 44s (406 kB/s) 
 Extracting templates from packages: 100%
 Preconfiguring packages ...
 setting xserver-xorg-legacy/xwrapper/allowed_users from configuration 
 file
 dpkg: unrecoverable fatal error, aborting:
 unable to open files list file for package 'linux-headers-generic-hwe- 
 16.04': Structure needs cleaning
 touch: cannot touch '/var/lib/update-notifier/dpkg-run-stamp': Read-only 
 file system
 E: Sub-process /usr/bin/dpkg returned an error code (2)
 W: Problem unlinking the file /var/cache/apt/pkgcache.bin - 
 pkgDPkgPM::Go (30: Read-only file system)

The most important part is the last:

 dpkg: unrecoverable fatal error, aborting:
 unable to open files list file for package 'linux-headers-generic-hwe- 
 16.04': Structure needs cleaning
 touch: cannot touch '/var/lib/update-notifier/dpkg-run-stamp': Read-only 
 file system
 E: Sub-process /usr/bin/dpkg returned an error code (2)
 W: Problem unlinking the file /var/cache/apt/pkgcache.bin - 
 pkgDPkgPM::Go (30: Read-only file system)

2) Reboot

3) Install the package linux-headers-4.15.0-34-generic

4) Install the package linux-headers-generic-hwe-16.04

5) Install the package linux-modules-4.15.0-generic

6) Reinstall those packages using the command 'sudo apt/apt-get install --reinstall package_name'

7) I have checked that anything I try to do with the apt/apt-get command, I can't uninstall some package without getting the error 'Read only file system'.

Example: To remove the snapd package:

(reportingApp) rafa@ubuntu:~/Documents/projects/reporting/reporting_project$ 
sudo apt-get autoremove --purge snapd
Reading package lists... Done
Building dependency tree 
Reading state information... Done
The following packages will be REMOVED:
 snapd* ubuntu-core-launcher*
0 upgraded, 0 newly installed, 2 to remove and 234 not upgraded.
After this operation, 57.9 MB disk space will be freed.
Do you want to continue? [Y/n] Y
dpkg: unrecoverable fatal error, aborting:
 unable to open files list file for package 'linux-headers-generic-hwe- 
16.04': Structure needs cleaning
touch: cannot touch '/var/lib/update-notifier/dpkg-run-stamp': Read-only file 
system
E: Sub-process /usr/bin/dpkg returned an error code (2)
W: Problem unlinking the file /var/cache/apt/pkgcache.bin - pkgDPkgPM::Go 
(30: Read-only file system)

How can I solve this error?