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The errors are related to GPT size mismatch and file system errors.

[Thu May 12 10:58:25 2022] GPT:Primary header thinks Alt. header is not at the end of the disk.
[Thu May 12 10:58:25 2022] GPT:239649 != 245759
[Thu May 12 10:58:25 2022] GPT:Alternate GPT header not at the end of the disk.
[Thu May 12 10:58:25 2022] GPT:239649 != 245759
[Thu May 12 10:58:25 2022] GPT: Use GNU Parted to correct GPT errors.

When I try to install a package, I get this error:

2022/05/12 12:14:34 install Plex Media Server 1.18.5.2309-f5213a238 Begin preinst
2022/05/12 12:14:34 install Plex Media Server 1.18.5.2309-f5213a238 End preinst ret=[0]
2022/05/12 12:14:34 install Plex Media Server 1.18.5.2309-f5213a238 Begin /bin/rm -rf /volume1/@appstore/Plex Media Server
2022/05/12 12:14:35 install Plex Media Server 1.18.5.2309-f5213a238 End /bin/rm -rf /volume1/@appstore/Plex Media Server ret=[1]
2022/05/12 12:14:35 install Plex Media Server 1.18.5.2309-f5213a238 Begin /bin/rm -rf /volume1/@tmp/pkginstall
2022/05/12 12:14:35 install Plex Media Server 1.18.5.2309-f5213a238 End /bin/rm -rf /volume1/@tmp/pkginstall ret=[0]
2022/05/12 12:14:35 install Plex Media Server 1.18.5.2309-f5213a238 failed

Attempting to manually delete the folder referenced gives this error:

rm: cannot remove ‘Plex Media Server/Resources/Graphics/dvr/device-hdhomerun-connect-duo-560.png’: Structure needs cleaning
rm: cannot remove ‘Plex Media Server/Resources/Graphics/dvr/dvr-watchnow-icon.png’: Structure needs cleaning
rm: cannot remove ‘Plex Media Server/Resources/Graphics/dvr/dvr-sports-icon.png’: Structure needs cleaning
rm: cannot remove ‘Plex Media Server/Resources/Graphics/dvr/dvr-news-icon.png’: Structure needs cleaning
rm: cannot remove ‘Plex Media Server/Resources/Graphics/dvr/dvr-schedule-icon.png’: Structure needs cleaning
rm: cannot remove ‘Plex Media Server/Resources/Graphics/dvr/device-hdhomerun-dual-560.png’: Structure needs cleaning
rm: cannot remove ‘Plex Media Server/Resources/Graphics/tag-geo-256.png’: Structure needs cleaning

I'm trying to do a file system repair (ie e2fsck) but running into some issues.

Identified the drive:

Model: ATA ST4000DM004-2CV1 (scsi)
Disk /dev/hda: 4001GB
Sector size (logical/physical): 512B/512B
Partition Table: gpt
Disk Flags:

Number Start End Size File system Name Flags
1 1049kB 2551MB 2550MB ext4 raid
2 2551MB 4699MB 2147MB linux-swap(v1) raid
5 4840MB 4001GB 3996GB raid

@plexmediaserver:/opt/sbin$ sudo e2fsck /dev/hda
e2fsck 1.42.6 (21-Sep-2012)
/dev/hda is in use.
e2fsck: Cannot continue, aborting.

PLEXMEDIASERVER:/opt/sbin$ df -Th
Filesystem Type Size Used Avail Use% Mounted on
/dev/md0 ext4 2.3G 999M 1.2G 46% /
none devtmpfs 2.9G 0 2.9G 0% /dev
/tmp tmpfs 2.9G 1.7M 2.9G 1% /tmp
/run tmpfs 2.9G 3.6M 2.9G 1% /run
/dev/shm tmpfs 2.9G 4.0K 2.9G 1% /dev/shm
none tmpfs 4.0K 0 4.0K 0% /sys/fs/cgroup
cgmfs tmpfs 100K 0 100K 0% /run/cgmanager/fs
/dev/vg1000/lv ext4 3.6T 3.3T 338G 91% /volume1

@plexmediaserver:/opt/sbin$ sudo umount /dev/vg1000/lv
Password:
umount: /volume1/@docker: target is busy
(In some cases useful info about processes that
use the device is found by lsof(8) or fuser(1).)

@plexmediaserver:/opt/sbin$ sudo e2fsck /dev/vg1000/lv
e2fsck 1.42.6 (21-Sep-2012)
/dev/vg1000/lv is mounted.
e2fsck: Cannot continue, aborting.

@plexmediaserver:/opt/sbin$ /opt/sbin/lsof | grep volume1
sh 13429 williamcaput cwd DIR 252,0 4096 202448897 /volume1/@optware/sbin
lsof 20901 williamcaput cwd DIR 252,0 4096 202448897 /volume1/@optware/sbin
lsof 20901 williamcaput txt REG 252,0 130960 202378565 /volume1/@optware/sbin/lsof
lsof 20901 williamcaput mem REG 252,0 10747920 202376113 /volume1/@optware/lib/locale/locale-archive
lsof 20901 williamcaput mem REG 252,0 1681104 202375219 /volume1/@optware/lib/libc-2.25.so
lsof 20901 williamcaput mem REG 252,0 149128 202375232 /volume1/@optware/lib/ld-2.25.so
grep 20902 williamcaput cwd DIR 252,0 4096 202448897 /volume1/@optware/sbin
lsof 20904 williamcaput cwd DIR 252,0 4096 202448897 /volume1/@optware/sbin
lsof 20904 williamcaput txt REG 252,0 130960 202378565 /volume1/@optware/sbin/lsof
lsof 20904 williamcaput mem REG 252,0 10747920 202376113 /volume1/@optware/lib/locale/locale-archive
lsof 20904 williamcaput mem REG 252,0 1681104 202375219 /volume1/@optware/lib/libc-2.25.so
lsof 20904 williamcaput mem REG 252,0 149128 202375232 /volume1/@optware/lib/ld-2.25.so

Can you assist from here?