As it seems that the Teltonika developers never tested their SDK (At least for the RUTX12). I put the final solution here for other users. The problem solved by one week of test and trial:
By default, some packages are broken is the Teltonika SDK. Before building the SDK, these errors should be fixed.
First go to the Teltonika SDK directory:
cd ~/workspace/Teltonika/rutos-ipq40xx-rutx-gpl/
Then, the README file should be created for the packages coova-chili , easycwmp and shellinabox . After making the README file, the source should be reconfigured by autoreconf -i:
coova-chilli package:
$ cd package/teltonika/coova-chilli/src/
$ touch README
$ autoreconf -i
easycwmp package:
$ cd package/teltonika/easycwmp/src/
$ touch README
$ autoreconf -i
shellinabox package
$ cd package/teltonika/shellinabox/src/
$ touch README
$ autoreconf -i
Then make the sdk by calling make -j<n>