I left a Gentoo Prefix build running overnight and it completed with no problems. This was on a MacPro5,1 (2.8 GHz Quad-Core Intel Xeon) with 2 vCPUs assigned to the VM, and without VMware Tools installed.
I tried another run this morning with 1 vCPU and with Tools installed, but it failed "early" because www.python.org/ftp/... is temporarily unavailable, it appears. The VM kept running as normal: bootstrap-prefix.sh claimed it found the whole situation most inconvenient, and its ego was apparently crushed. It most apologetically gave up. I love this script.
I'll try again later... Maybe we will be able to expand our sample size a little more and spot a pattern.
Of course, you're not obliged to continue trying to reproduce the problem... If you are happy to just keep using your functional VM as-is, go ahead. But maybe you are as curious as I am to figure out what happened and make sure it doesn't happen again...
Thanks for your patience!
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Darius