yuri@FreeBSD

I tried ```-flto=thin``` but the errors were same.

For example, ```-ffat-lto-objects``` isn't needed or supported in clang.

Based on the linked clang example only ```-flto=thin``` should be added to both compile and link flags.

I don't think anything is broken. LTO succeeded for me every time I tried it. You just need to use correct flags in case of clang, as described in the...

> But when you try you always specify thin lto, no? Yes. It boils down to ```-flto=thin```.

I also happen to work on a large cmake-based project with a lot of static libraries. I've turned on LTO and it has built like a charm.

The problem must be in custom options encoded in GNU makefiles.

I am not sure if there is a standard way. You can do ```--enable-docs/--disable-docs``` and ```--enable-examples/--disable-examples```.

> On the py3Dmol, the environment must be failing import nglview [...] So it should be listed in ```setup.py``` as a test dependency?

> We embed Qt version 6.1.2 in our source code so try to use qwt6-qt5-6.1.6_1. You should also fix configure to not accept external Qwt5.