Ok.
Wait... I didn't knew that gedit could see some errors like AC_PROG_MKDIR_P 
case! COOL!

So, back to build thing...
./autogen.sh ; ./configure -q ; make -s
[BLAH]
autogen.sh ran successfully.
[BLAH]
configure ran successfully.
[BLAH BLAH]
make ran sucefully.
atlas regenerated.