I recently started building a Lync 2013 Pilot Pool alongside my Lync 2010 deployment. When publishing the topology I got the following errors:

_Publishing in progress
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_Failed adding “AccessWrite” permissions for “RTCComponentUniversalServices”
Failed adding “AccessRead” permissions for “RTCComponentUniversalServices”
Failed adding “AccessWrite” permissions for “RTCHSUniversalServices”
Failed adding “AccessRead” permissions for “RTCHSUniversalServices”
Failed adding “AccessWrite” permissions for “RTCUniversalServerAdmins”
Failed adding “AccessRead” permissions for “RTCUniversalServerAdmins”
_

_Access control list (ACL) might fail on UNIX file shares. Refer to the deployment guide to manually set the ACLs in the file share.
_

When the Publishing wizard is complete you see the error:

_Enabling Topology… Completed with errors
_

When you view the log file you see the following errors for the Lync File Share:

ACLError: Access permissions error.

Error: Failed to save permissions on “\server.domain.localLyncFS$”.

Updated Fix: When running Topology Builder, right click and “Run As Administrator”.  Thanks to Dave in the comments below.

To fix this I had to add the following groups to the Share (Not NTFS) permissions on the Lync File Share. I had to do this even though Everyone had Full Control on the Share Permissions. Topology Builder would fail publishing the topology until I added these groups on.

RTCComponentUniversalServices
RTCHSUniversalServices
RTCUniversalServerAdmins

After changing the Share permissions, the topology published successfully: