Bug 686540

Summary:	sys-apps/portage-2.3.66-r1: OSError: [Errno 117] Structure needs cleaning: b'/usr/src/linux-4.19.5-gentoo/tools/perf/pmu-events/arch/x86/westmereep-sp/memory.json'
Product:	Portage Development	Reporter:	Andrey Grozin <grozin>
Component:	Core - Interface (emerge)	Assignee:	Portage team <dev-portage>
Status:	CONFIRMED ---
Severity:	normal
Priority:	Normal
Version:	unspecified
Hardware:	All
OS:	Linux
Whiteboard:
Package list:		Runtime testing required:	---

Description Andrey Grozin gentoo-dev

2019-05-22 11:35:07 UTC

bilbo ~ # emerge -avc =sys-kernel/gentoo-sources-4.19.5

Calculating dependencies... done!
>>> Calculating removal order...

>>> These are the packages that would be unmerged:

 sys-kernel/gentoo-sources
    selected: 4.19.5 
   protected: none 
     omitted: 4.20.0 5.1.3 

All selected packages: =sys-kernel/gentoo-sources-4.19.5

>>> 'Selected' packages are slated for removal.
>>> 'Protected' and 'omitted' packages will not be removed.

Would you like to unmerge these packages? [Yes/No] 
>>> Waiting 5 seconds before starting...
>>> (Control-C to abort)...
>>> Unmerging in: 5 4 3 2 1
>>> Unmerging (1 of 1) sys-kernel/gentoo-sources-4.19.5...
Traceback (most recent call last):
  File "/usr/lib/python-exec/python3.6/emerge", line 53, in <module>
    retval = emerge_main()
  File "/usr/lib64/python3.6/site-packages/_emerge/main.py", line 1289, in emerge_main
    return run_action(emerge_config)
  File "/usr/lib64/python3.6/site-packages/_emerge/actions.py", line 3230, in run_action
    emerge_config.args, spinner)
  File "/usr/lib64/python3.6/site-packages/_emerge/actions.py", line 2224, in action_uninstall
    scheduler=sched_iface)
  File "/usr/lib64/python3.6/site-packages/_emerge/actions.py", line 693, in action_depclean
    scheduler=scheduler)
  File "/usr/lib64/python3.6/site-packages/_emerge/unmerge.py", line 582, in unmerge
    scheduler=scheduler)
  File "/usr/lib64/python3.6/site-packages/portage/dbapi/vartree.py", line 5406, in unmerge
    retval = mylink.unmerge(ldpath_mtimes=ldpath_mtimes)
  File "/usr/lib64/python3.6/site-packages/portage/dbapi/vartree.py", line 1677, in wrapper
    return f(self, *args, **kwargs)
  File "/usr/lib64/python3.6/site-packages/portage/dbapi/vartree.py", line 2038, in unmerge
    retval = self._security_check([self] + others_in_slot)
  File "/usr/lib64/python3.6/site-packages/portage/dbapi/vartree.py", line 3625, in _security_check
    s = os.lstat(path)
  File "/usr/lib64/python3.6/site-packages/portage/__init__.py", line 246, in __call__
    rval = self._func(*wrapped_args, **wrapped_kwargs)
OSError: [Errno 117] Structure needs cleaning: b'/usr/src/linux-4.19.5-gentoo/tools/perf/pmu-events/arch/x86/westmereep-sp/memory.json'
bilbo ~ #

Comment 1 Zac Medico gentoo-dev

2019-05-22 16:55:51 UTC

It looks like you need to run fsck. It's not really safe to ignore this error (see bug 81097), though the fs.protected_hardlinks sysctl improves the situation. We can handle the error more cleanly, by suppressing the traceback and advising the user to run fsck.