Can't update python3-libs@3.6.8-13.el7 from ce-base

[arohl (Andrew Rohl)]

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

[mark_nl (Mark Verlinde)]

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

[arohl (Andrew Rohl)]

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    

[mark_nl (Mark Verlinde)]

@arohl

hope is an error message that means something to someone

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.

[mark_nl (Mark Verlinde)]

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

[arohl (Andrew Rohl)]

@mark_nl

yum reinstall http://vault.centos.org/centos/7.7.1908/os/x86_64/Packages/python3-libs-3.6.8-10.el7.x86_64.rpm

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!

[arohl (Andrew Rohl)]

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

[mark_nl (Mark Verlinde)]

@arohl

-??? ? ? ? ? ? wintypes.cpython-36.opt-1.pyc

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

[arohl (Andrew Rohl)]

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…

[mark_nl (Mark Verlinde)]

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?

[arohl (Andrew Rohl)]

@mark_nl

/usr/lib64/python3.6/ctypes/pycache/

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

[mark_nl (Mark Verlinde)]

Glad you are sorted out!

I’ll gues you can mark your own resume above as the solution

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