In short, no. The configure script didn't even finish running.
It looks like /var/tmp was mounted with the 'noexec' option. As a kludge, you can remount it with the 'exec' option, perform the upgrade, and then change it back to 'noexec' once done.
Generally, the safest way is to stick with the default settings provided by the configure script.
Features marked as EXPERIMENTAL should normally not be enabled in a production environment unless you exactly know what you are doing and are aware of possible consequences.
To figure out which configuration options were set execute a phpinfo();. Scroll down to the APC section and check what Locking type tells you. By default it is something like thread / mutex locks and if it doesn't mention the spin locks, they are most likely not enabled.
Note that this is from memory - cannot verify this on a live server at the moment since I prefer eAccelerator over APC.