Wordpress upgrade not working

Wordpress installer upgrades haven’t worked since the change to wp-cli. Running wp-cli 1.4.1. Executing from the command line works great. Installing from the Virtualmin interface works great. However, upgrading gives me the following:

Upgrading WordPress to version 4.9.1 .. Configuring webserver PHP settings .. .. already done. Downloading http://scripts.virtualmin.com:80/wordpress-4.9.1.zip (9.92 MB) .. Received 1024 bytes (0 %) Received 1017 kB (10 %) Received 1.99 MB (20 %) Received 2.98 MB (30 %) Received 3.97 MB (40 %) Received 4.96 MB (50 %) Received 5.96 MB (60 %) Received 6.95 MB (70 %) Received 7.94 MB (80 %) Received 8.93 MB (90 %) Received 9.92 MB (100 %) .. download complete. wp core upgrade failed : .. done Looking at the system logs, I'm seeing: sh: core: command not found

It’s supposed to be running “wp core upgrade --version=4.9.1”. But that error message leads me to believe it’s leaving off the “wp” from the command.

Looking in wordpress.pl in the scripts directory, for “!upgrade”, the script sets my $wp and then executes it. However, when upgrading, the script does NOT set my $wp, it simply goes straight to executing it. From troubleshooting, it would seem that $wp is not initialized during an upgrade procedure(the else condition) and is null.