With pyflakes-0.7.3:

make -j5 check 
Making check in .
make[1]: Entering directory `/var/tmp/portage/dev-python/pygobject-3.12.2/work/pygobject-3.12.2-python3_3'
for f in gi/__init__.py gi/types.py gi/module.py gi/importer.py gi/pygtkcompat.py gi/docstring.py gi/_constants.py gi/_propertyhelper.py gi/_signalhelper.py gi/_option.py; do \
	[ -e ./$f ] || \
		ln -s /var/tmp/portage/dev-python/pygobject-3.12.2/work/pygobject-3.12.2-python3_3/$f ./$f; \
done
make  check-local
make[2]: Entering directory `/var/tmp/portage/dev-python/pygobject-3.12.2/work/pygobject-3.12.2-python3_3'
for f in gi/__init__.py gi/types.py gi/module.py gi/importer.py gi/pygtkcompat.py gi/docstring.py gi/_constants.py gi/_propertyhelper.py gi/_signalhelper.py gi/_option.py; do \
	[ -e ./$f ] || \
		ln -s /var/tmp/portage/dev-python/pygobject-3.12.2/work/pygobject-3.12.2-python3_3/$f ./$f; \
done
  CHECK  Pyflakes examples gi tests pygtkcompat
examples/properties.py:18: invalid syntax
print "MyObject properties: ", list(MyObject.props)
                             ^
tests/runtests-windows.py:47: invalid syntax
        except Exception, e:
                         ^
gi/_option.py:40: undefined name 'basestring'
gi/_propertyhelper.py:46: undefined name 'basestring'
gi/_propertyhelper.py:47: undefined name 'long'
gi/overrides/GObject.py:259: undefined name 'unicode'
gi/overrides/Gtk.py:35: undefined name 'basestring'
tests/test_properties.py:35: undefined name 'unicode'
tests/test_properties.py:842: undefined name 'long'
tests/test_everything.py:30: undefined name 'unicode'
tests/compathelper.py:66: undefined name 'long'
tests/compathelper.py:67: undefined name 'basestring'
tests/compathelper.py:69: undefined name 'unicode'
tests/test_gi.py:29: undefined name 'unicode'
make[2]: *** [check-local] Error 1
make[2]: Leaving directory `/var/tmp/portage/dev-python/pygobject-3.12.2/work/pygobject-3.12.2-python3_3'
make[1]: *** [check-am] Error 2
make[1]: Leaving directory `/var/tmp/portage/dev-python/pygobject-3.12.2/work/pygobject-3.12.2-python3_3'
make: *** [check-recursive] Error 1