The paragraph mentions that it is talking about Linux. Further down in the article it digs in to the speed problems on Windows, and links to a quick run down of the speed comparisons¹.
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Just saw it, if I'm interpreting the numbers there - it's even worse (as expected on Windows/NTFS), even from cache. Still though I love ninja, and just recently used it for generating .proto files to 4 different languages.
Also love bazel (after using 2-3 years blaze), but for the use case above it would've been a real "killer" :)