I assume you're using something later than Trusty. This isn't a problem in Trusty as gfortran is still at 4.8.

Assuming a downgrade isn't a real solution, I'll just show you how Trusty has things laid out. You might want to check it's similar in whatever you're running to make sure my conclusions are sound:

$ dpkg -S $(which gfortran) $(which gfortran-4.8)

gfortran: /usr/bin/gfortran

gfortran-4.8: /usr/bin/gfortran-4.8



$ file /usr/bin/gfortran

/usr/bin/gfortran: symbolic link to `gfortran-4.8'

So basically here, the gfortran command is just redirecting to /usr/bin/gfortran-4.8. I expect in your version it's redirecting to /usr/bin/gfortran-4.9.

We can override packaged path binaries without touching them. I suggest (and this may undermine things that use gfortran so be careful) we create a new symlink in /usr/local/bin (note the local). When you call gfortran, the system will find the /usr/local/bin/gfortran version first. Note that anything calling /usr/bin/gfortran explicitly will still get the 4.9 version.

Anyway, creating the symlink is easy:

sudo ln -s /usr/bin/gfortran-4.8 /usr/local/bin/gfortran

This has the pleasant side-effect that you can leave your packages in place, fulfilling whatever dependencies you might need to fulfil. And upgrades to the gfortran package won't nuke our changes.