When we run the moodle cron in the CLI version from moodle 2.6.4+, we get an error message during the backup portion of the cron:
PHP Warning: apc_cache_info(): No APC info available. Perhaps APC is not enabled? Check apc.enabled in your ini file in /moodle/cache/stores/apc/lib.php on line 257
PHP Warning: Invalid argument supplied for foreach() in /moodle/cache/stores/apc/lib.php on line 258

APC is indeed enabled, for both CLI and apache PHP.

I would not worry about this, but I am paranoid about backups.