"directory not empty", "no such file or directory" errors on upgrade

Gary Aitken freebsd at dreamchaser.org
Fri Mar 13 13:05:55 UTC 2020

On 3/12/20 4:57 PM, Polytropon wrote:
> On Thu, 12 Mar 2020 13:03:27 -0600, Gary Aitken wrote:
>> Upgrading from 11.2-RELEASE to 11.3-RELEASE
>> The final invoke of freebsd-update install completed with the following
>> messages:
>> ///usr/src/sys/pc98/include/acpica_machdep.h  no such file or directory
>> rmdir: ///usr/src/contrib/ofed/usr.lib        directory not empty
>> rmdir: ///usr/src/contrib/ofed/usr.bin        directory not empty
>> rmdir: ///usr/src/contrib/llvm/tools/lldb/source/Plugins/InstrumentationRuntime/ThreadSanitizer   directory not empty
>> rmdir: ///usr/src/contrib/llvm/tools/lldb/source/Plugins/InstrumentationRuntime/AddressSanitizer  directory not empty
>> The upgraded system has no
>>     /usr/src/sys/pc98/  directory
>> The files in
>>     /usr/src/contrib/ofed/usr.lib
>>     /usr/src/contrib/ofed/usr.bin
>>     /usr/src/contrib/llvm/tools/lldb/source/Plugins/InstrumentationRuntime/ThreadSanitizer
>>     /usr/src/contrib/llvm/tools/lldb/source/Plugins/InstrumentationRuntime/AddressSanitizer
>> appear to be old versions left over from the original 11.2 install
>> Hints on the proper way to fix this?
> When I read such messages, the first thing that comes to mind
> is filesystem inconsistency. Reboot into single-user mode and
> run a forced (!) fsck on all file systems, maybe repeat it if
> needed.

fsck reported all clean.

> You probably don't have
> 	background_fsck="NO"
> in your /etc/rc.conf which in my opinion should be the default
> setting (instead of YES). See "man 8 fsck" for further options
> that might be needed.

Thanks for the reminder; I used to have it set but on this rebuilt-
after-a-crash system lost it.

> Things like "directory not empty" can also be due to files that
> haven't been removed. This is possible if the schg (immutable)
> flag has been set for a file; use "chflags noschg <file>"; see
> "man 1 chflags" for details.
> First step: Always rule out the obvious. ;-)

The remaining question is:
Are those directories supposed to be repopulated
with more recent versions?  Or should they simply be removed?
If they need to be repopulated, how does one repopulate them?


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