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(SOLVED) Can't upgrade to 6.2.3, Plugins not showing up but working.

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Another day I mistakenly deleted /config/plugins directory. I tried to recreate it. Now I can't upgrade and having weird issues. When I stop my array it keeps telling me that registration key is missing (trust me its there and it doesn't report any problems when array is started). Then, i see no plugins in web gui and yet they are working (got dynamiux temp app, which is working but doesn't show up in gui). More weird issues, here is the message on my main dashboard:

 

 

Warning: parse_ini_file(/boot/config/docker.cfg): failed to open stream: No such file or directory in /usr/local/emhttp/plugins/dynamix.docker.manager/include/DockerClient.php on line 38 Warning: parse_ini_file(/boot/config/domain.cfg): failed to open stream: No such file or directory in /usr/local/emhttp/plugins/dynamix.vm.manager/classes/libvirt_helpers.php on line 441

 

 

Here is the message I get when I try to upgrade:

 

 

plugin: updating: unRAIDServer.plg

plugin: downloading: https://s3.amazonaws.com/dnld.lime-technology.com/stable/unRAIDServer-6.2.4-x86_64.zip ... done

plugin: downloading: https://s3.amazonaws.com/dnld.lime-technology.com/stable/unRAIDServer-6.2.4-x86_64.md5 ... done

Archive: /tmp/unRAIDServer.zip

inflating: /tmp/unRAIDServer/bzimage

inflating: /tmp/unRAIDServer/bzroot

inflating: /tmp/unRAIDServer/bzroot-gui

inflating: /tmp/unRAIDServer/changes.txt

creating: /tmp/unRAIDServer/config/

inflating: /tmp/unRAIDServer/config/ident.cfg

inflating: /tmp/unRAIDServer/config/network.cfg

extracting: /tmp/unRAIDServer/config/go

creating: /tmp/unRAIDServer/config/plugins/

creating: /tmp/unRAIDServer/config/plugins/dockerMan/

extracting: /tmp/unRAIDServer/config/plugins/dockerMan/template-repos

extracting: /tmp/unRAIDServer/config/docker.cfg

extracting: /tmp/unRAIDServer/config/domain.cfg

inflating: /tmp/unRAIDServer/license.txt

inflating: /tmp/unRAIDServer/make_bootable.bat

inflating: /tmp/unRAIDServer/make_bootable_linux

inflating: /tmp/unRAIDServer/make_bootable_mac

inflating: /tmp/unRAIDServer/memtest

creating: /tmp/unRAIDServer/syslinux/

inflating: /tmp/unRAIDServer/syslinux/ldlinux.c32

inflating: /tmp/unRAIDServer/syslinux/libcom32.c32

inflating: /tmp/unRAIDServer/syslinux/libutil.c32

inflating: /tmp/unRAIDServer/syslinux/make_bootable_mac.sh

inflating: /tmp/unRAIDServer/syslinux/mboot.c32

inflating: /tmp/unRAIDServer/syslinux/mbr.bin

inflating: /tmp/unRAIDServer/syslinux/menu.c32

inflating: /tmp/unRAIDServer/syslinux/syslinux

inflating: /tmp/unRAIDServer/syslinux/syslinux.cfg

inflating: /tmp/unRAIDServer/syslinux/syslinux.cfg-

inflating: /tmp/unRAIDServer/syslinux/syslinux.exe

inflating: /tmp/unRAIDServer/syslinux/make_bootable_linux.sh

inflating: /tmp/unRAIDServer/syslinux/syslinux_linux

flash write error 0, maybe corrupted?

plugin: run failed: /bin/bash retval: 1

 

 

Here is the messages that show up in lsystem ogs:

 

 

Nov 10 17:38:20 DUAL root: Warning: file_put_contents(/boot/config/domain.cfg): failed to open stream: No such file or directory in /usr/local/emhttp/plugins/dynamix.vm.manager/scripts/libvirtconfig.php on line 39

Nov 10 17:38:20 DUAL kernel: FAT-fs (sde1): FAT read failed (blocknr 2788)

Nov 10 17:38:20 DUAL kernel: ------------[ cut here ]------------

Nov 10 17:38:20 DUAL kernel: WARNING: CPU: 3 PID: 4433 at fs/fs-writeback.c:2112 __mark_inode_dirty+0x1d2/0x1e3()

Nov 10 17:38:20 DUAL kernel: bdi-block not registered

Nov 10 17:38:20 DUAL kernel: Modules linked in: xt_CHECKSUM iptable_mangle ipt_REJECT nf_reject_ipv4 ebtable_filter ebtables vhost_net tun vhost macvtap macvlan ipt_MASQUERADE nf_nat_masquerade_ipv4 iptable_nat nf_conntrack_ipv4 nf_nat_ipv4 iptable_filter ip_tables nf_nat md_mod bonding hid_logitech_hidpp hid_logitech_dj nvme i2c_i801 mxm_wmi x86_pkg_temp_thermal i2c_core coretemp e1000e kvm_intel ptp kvm ahci pps_core libahci wmi

Nov 10 17:38:20 DUAL kernel: CPU: 3 PID: 4433 Comm: php Not tainted 4.4.30-unRAID #1

Nov 10 17:38:20 DUAL kernel: Hardware name: System manufacturer System Product Name/SABERTOOTH Z170 S, BIOS 1902 06/27/2016

Nov 10 17:38:20 DUAL kernel: 0000000000000000 ffff88086d297ba0 ffffffff8136b117 ffff88086d297be8

Nov 10 17:38:20 DUAL kernel: 0000000000000840 ffff88086d297bd8 ffffffff8104a49a ffffffff8112a26f

Nov 10 17:38:20 DUAL kernel: ffff880858738340 ffff8808692c5cd8 0000000000000000 ffff8808587383c0

Nov 10 17:38:20 DUAL kernel: Call Trace:

 

 

Nov 10 17:46:19 DUAL root: Warning: file_put_contents(/boot/config/domain.cfg): failed to open stream: No such file or directory in /usr/local/emhttp/plugins/dynamix.vm.manager/scripts/libvirtconfig.php on line 39

Nov 10 17:46:20 DUAL root:

Nov 10 17:46:20 DUAL root: Warning: file_put_contents(/boot/config/docker.cfg): failed to open stream: No such file or directory in /usr/local/emhttp/plugins/dynamix.docker.manager/scripts/dockerconfig.php on line 35

Nov 10 17:46:20 DUAL root:

Nov 10 17:46:20 DUAL root: Warning: file_put_contents(/boot/config/domain.cfg): failed to open stream: No such file or directory in /usr/local/emhttp/plugins/dynamix.vm.manager/scripts/libvirtconfig.php on line 39

 

 

From what I understand, some system files are missing or corrupt. I am trying to google my way out of this right now. If anybody can point me in a right direction it would be much appreciated. Thanks.

 

EDIT: Turns up the reason I was getting those errors is because I plugged in USB into another port on the motherboard and that port was getting passed through to a VM. I never configured that USB controller to be passed through at all so that's quite weird...

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Did you reboot since accidentally deleting your plugins directory? A reboot would probably have been best so you could just reinstall them correctly. They might have been working because they were already loaded in memory, but you may have messed something up by trying to put them back on the flash yourself instead of just rebooting and reinstalling them.

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You need to first fix the corrupted file system on the unRAID boot flash disk.  Take it to a Windows machine and run Check disk or scandisk, or take it to a Mac and run whatever the comparable tool is.  Make sure it's safely ejected.

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