See below.
> Lots of software sources are configured with GNU autotools, which is why
> a lot of third party software will only compile with GNU make. In the
> case of dealii, not only are its sources configured with autotools, but
> I looked at their docs and at http://www.dealii.org/developer/index.html
> you can plainly see that they "use GNU make, version 3.78 or later".
> I'm not sure where the confusion is ... but it seems like you think you
>   have to invoke GNU make under the moniker 'make'. But you don't, it's
> just a Linux convention to have GNU make installed as 'make'.

 The root of confusion is not in FreeBSD :) but in my thinking.
I totally forgot about the existence of BSD make untill it came
back to me:
 During installation of ATLAS some shell script or C program calls
'make' by the name "make", and I totally forgot it can be not the 'make'
I called the build process with.
After I was explained about it (by ATLAS people), everything went just fine.

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