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According to James in this post:
https://lists.centos.org/pipermail/centos/2016-March/158173.html
(snippet)
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The generated makefile has a '(sleep 3; cp Makefile.dist Makefile) &' in
it for the distclean target.
The Makefile.dist is the bare empty one.
Note how this backgrounds ? There is no wait after this ...
So three seconds after the make distclean target is hit *bam* the full
Makefile with the install target gets overwritten by the bare one.
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This is a race condition in the mtr .spec file. Reassigning.
As an experiment, I changed to '(sleep 30; cp Makefile.dist Makefile) &' and rebuilt successfully. My build machine is on pretty slow storage (6x 3TB 7200rpm in software RAID level 6 hosting multiple VMs), so I think James hit the nail on the head here.