Hi Jose,
this is probably a problem that the ROOT version used in FairSoft does not work with gcc6.
There is always a problem to use older ROOT version with the bleeding edge versions of gcc. If you must use gcc6 you should try the latest root version. To do so you have to change the ROOT version in the file scripts/package_versions.sh
export ROOTVERSION=v6-06-02
should be
export ROOTVERSION=v6-08-02
or
export ROOTVERSION=v6-06-08
Be aware that these versions have not been tested with FairRoot.
Ciao
Florian