NethServer Version: 7.8.2003
Cockpit tells me that I have an update, I choose update all, all seems to go well but after the install it still says I have an update. I can choose to update it again but the same thing happens. Reboot and still says I have an update.
Andrew
hi @arohl,
What happens if you run the update after clicking the reload button in the software center?
(right-side under corner in pic below)
If this does not help;
Does a manual update from the (cockpit) terminal give you some clues about what went wrong?
(in terminal) run: yum update
reload didn’t help but yum update failed with what I hope is an error message that means something to someone 
[root@nethserver andrew]# yum update
Loaded plugins: changelog, fastestmirror, nethserver_events
Determining fastest mirrors
* ce-base: mirror.internode.on.net
* ce-extras: mirror.internode.on.net
* ce-sclo-rh: mirror.internode.on.net
* ce-sclo-sclo: mirror.internode.on.net
* ce-updates: mirror.internode.on.net
* epel: mirror.aarnet.edu.au
* nethforge: mirror.nethserver.org
* nethserver-base: mirror.nethserver.org
* nethserver-updates: mirror.nethserver.org
Resolving Dependencies
--> Running transaction check
---> Package python3-libs.x86_64 0:3.6.8-10.el7 will be updated
---> Package python3-libs.x86_64 0:3.6.8-13.el7 will be an update
--> Finished Dependency Resolution
Dependencies Resolved
=================================================================================================================================================================================================
Package Arch Version Repository Size
=================================================================================================================================================================================================
Updating:
python3-libs x86_64 3.6.8-13.el7 ce-base 7.0 M
Transaction Summary
=================================================================================================================================================================================================
Upgrade 1 Package
Total download size: 7.0 M
Is this ok [y/d/N]: y
Downloading packages:
No Presto metadata available for ce-base
python3-libs-3.6.8-13.el7.x86_64.rpm | 7.0 MB 00:00:10
Running transaction check
Running transaction test
Transaction test succeeded
Running transaction
Updating : python3-libs-3.6.8-13.el7.x86_64 1/2
Error unpacking rpm package python3-libs-3.6.8-13.el7.x86_64
error: unpacking of archive failed on file /usr/lib64/python3.6/ctypes/__pycache__/wintypes.cpython-36.opt-1.pyc: cpio: rename
Verifying : python3-libs-3.6.8-13.el7.x86_64 1/2
python3-libs-3.6.8-10.el7.x86_64 was supposed to be removed but is not!
Verifying : python3-libs-3.6.8-10.el7.x86_64 2/2
Failed:
python3-libs.x86_64 0:3.6.8-10.el7 python3-libs.x86_64 0:3.6.8-13.el7
Me too 
It is very unusual, in other words: I can not give a conclusive answer.
I have some clue’s what is happening here: before installing the new package version rpm tries to remove
/usr/lib64/python3.6/ctypes/__pycache__/wintypes.cpython-36.opt-1.pyc
but fails…
Solution on the net suggest a quite intrusive solution: move the offending file out off of the way and run the update. However because I can not reproduce this, i hesitate to give you this advise.
python3-libs-3.6.8-10.el7.x86_64
Is a left over from centos 7.7.1908.
I think it is save to try to reinstall this particular version of the package before updating:
yum reinstall http://vault.centos.org/centos/7.7.1908/os/x86_64/Packages/python3-libs-3.6.8-10.el7.x86_64.rpm
if this succeeds run the update again.
EDIT:
on my updated system the contents of the directory offending file looks like this:
ls -ltr /usr/lib64/python3.6/ctypes/__pycache__/
total 108
-rw-r--r-- 1 root root 5097 Apr 2 15:36 wintypes.cpython-36.opt-2.pyc
-rw-r--r-- 1 root root 6980 Apr 2 15:36 util.cpython-36.opt-2.pyc
-rw-r--r-- 1 root root 13657 Apr 2 15:36 __init__.cpython-36.opt-2.pyc
-rw-r--r-- 1 root root 1580 Apr 2 15:36 _endian.cpython-36.opt-2.pyc
-rw-r--r-- 1 root root 5090 Apr 2 15:37 wintypes.cpython-36.pyc
-rw-r--r-- 1 root root 7221 Apr 2 15:37 util.cpython-36.pyc
-rw-r--r-- 1 root root 15918 Apr 2 15:37 __init__.cpython-36.pyc
-rw-r--r-- 1 root root 1919 Apr 2 15:37 _endian.cpython-36.pyc
-rw-r--r-- 1 root root 5090 Apr 2 15:37 wintypes.cpython-36.opt-1.pyc
-rw-r--r-- 1 root root 7221 Apr 2 15:37 util.cpython-36.opt-1.pyc
-rw-r--r-- 1 root root 15918 Apr 2 15:37 __init__.cpython-36.opt-1.pyc
-rw-r--r-- 1 root root 1919 Apr 2 15:37 _endian.cpython-36.opt-1.pyc
Note the date Apr 2, the older python3-libs-3.6.8-10 is probably dated Aug 7 2019
Same error
yum reinstall http://vault.centos.org/centos/7.7.1908/os/x86_64/Packages/python3-libs-3.6.8-10.el7.x86_64.rpm
Loaded plugins: changelog, fastestmirror, nethserver_events
python3-libs-3.6.8-10.el7.x86_64.rpm | 7.0 MB 00:00:07
Examining /var/tmp/yum-root-45_Y3H/python3-libs-3.6.8-10.el7.x86_64.rpm: python3-libs-3.6.8-10.el7.x86_64
Resolving Dependencies
--> Running transaction check
---> Package python3-libs.x86_64 0:3.6.8-10.el7 will be reinstalled
--> Finished Dependency Resolution
Dependencies Resolved
=================================================================================================================================================================================================
Package Arch Version Repository Size
=================================================================================================================================================================================================
Reinstalling:
python3-libs x86_64 3.6.8-10.el7 /python3-libs-3.6.8-10.el7.x86_64 35 M
Transaction Summary
=================================================================================================================================================================================================
Reinstall 1 Package
Total size: 35 M
Installed size: 35 M
Is this ok [y/d/N]: y
Downloading packages:
Running transaction check
Running transaction test
Transaction test succeeded
Running transaction
Installing : python3-libs-3.6.8-10.el7.x86_64 1/1
Error unpacking rpm package python3-libs-3.6.8-10.el7.x86_64
error: unpacking of archive failed on file /usr/lib64/python3.6/ctypes/__pycache__/wintypes.cpython-36.opt-1.pyc: cpio: rename
Verifying : python3-libs-3.6.8-10.el7.x86_64 1/1
Failed:
python3-libs.x86_64 0:3.6.8-10.el7
Complete!Woah!
[root@nethserver ~]# ls -l /usr/lib64/python3.6/ctypes/__pycache__
ls: cannot access /usr/lib64/python3.6/ctypes/__pycache__/wintypes.cpython-36.opt-1.pyc: Structure needs cleaning
total 196
-rw-r--r-- 1 root root 1919 Aug 8 2019 _endian.cpython-36.opt-1.pyc
-rw-r--r-- 1 root root 1580 Aug 8 2019 _endian.cpython-36.opt-2.pyc
-rw-r--r-- 1 root root 1919 Aug 8 2019 _endian.cpython-36.pyc
-rw-r--r-- 1 root root 15918 Aug 8 2019 __init__.cpython-36.opt-1.pyc
-rw-r--r-- 1 root root 13657 Aug 8 2019 __init__.cpython-36.opt-2.pyc
-rw-r--r-- 1 root root 15918 Aug 8 2019 __init__.cpython-36.pyc
-rw-r--r-- 1 root root 7221 Aug 8 2019 util.cpython-36.opt-1.pyc
-rw-r--r-- 1 root root 6980 Aug 8 2019 util.cpython-36.opt-2.pyc
-rw-r--r-- 1 root root 7221 Aug 8 2019 util.cpython-36.pyc
-?????????? ? ? ? ? ? wintypes.cpython-36.opt-1.pyc
-rw-r--r-- 1 root root 5090 Apr 2 21:37 wintypes.cpython-36.opt-1.pyc;5ec2652d
-rw-r--r-- 1 root root 5090 Apr 2 21:37 wintypes.cpython-36.opt-1.pyc;5ec27f10
-rw-r--r-- 1 root root 5090 Apr 2 21:37 wintypes.cpython-36.opt-1.pyc;5ec27f34
-rw-r--r-- 1 root root 5090 Apr 2 21:37 wintypes.cpython-36.opt-1.pyc;5ec938e7
-rw-r--r-- 1 root root 5090 Apr 2 21:37 wintypes.cpython-36.opt-1.pyc;5ec9398b
-rw-r--r-- 1 root root 5090 Apr 2 21:37 wintypes.cpython-36.opt-1.pyc;5ec9d9c8
-rw-r--r-- 1 root root 5090 Apr 2 21:37 wintypes.cpython-36.opt-1.pyc;5eca8dc0
-rw-r--r-- 1 root root 5090 Apr 2 21:37 wintypes.cpython-36.opt-1.pyc;5eccc0bb
-rw-r--r-- 1 root root 5090 Apr 2 21:37 wintypes.cpython-36.opt-1.pyc;5eccc23f
-rw-r--r-- 1 root root 5090 Apr 2 21:37 wintypes.cpython-36.opt-1.pyc;5eccd1a0
-rw-r--r-- 1 root root 5090 Aug 8 2019 wintypes.cpython-36.opt-1.pyc;5eccdf92
-rw-r--r-- 1 root root 5090 Aug 8 2019 wintypes.cpython-36.opt-1.pyc;5eccdfb7
-rw-r--r--. 1 root root 5097 Aug 8 2019 wintypes.cpython-36.opt-2.pyc
-rw-r--r--. 1 root root 5090 Aug 8 2019 wintypes.cpython-36.pyc
Do you know how I can run a fsck via web interface. I guess option b is to remove the directory as it appears only to be cache files.
Andrew
This file is corrupted! try to move it:
mv /usr/lib64/python3.6/ctypes/pycache/wintypes.cpython-36.opt-1.pyc .
then reinstall the old package , then update
Its really sick 
The file is there but not there - I can’t delete it or move it. I tried deleting the directory surrounding it; it deleted all the files in the directory but not this file. Seems I have to run xfs_repair but the drive has to be unmounted. It a headless server so rebooting via an external USB will be a real pain…
Yes, there is a serious problem with the file system…
AFAIK (and as you mentioned) to check / repair a root file system it has to be unmounted,
however had not have to deal with this since decades.
IIRC there was a boot flag for it, but one can never be sure of the outcome…
EDIT:
Probably a no go, did you try chmod 644 wintypes.cpython-36.opt-1.pyc and chown root:root wintypes.cpython-36.opt-1.pyc ? or even touch wintypes.cpython-36.opt-1.pyc
Maybe someone else has an idea to fix / remove a corrupt file?
I booted into recovery mode and did an xfs repair on a mounted but readonly filesystem. Warned me not to do it but went ahead and all good (there was a bad inode for that file). Update installed fine and all is working now. Many thanks for your help.
Andrew
Glad you are sorted out!
I’ll gues you can mark your own resume above as the solution 