Bugfix is at https://github.com/snapcore/snapcraft/pull/2240 , but it’s not at newest snap package.
So I removed snap version, and installed snapcraft from source, and it seems to work for me.
Snapcraft source install on Ubuntu 16.04 64bit
# Add to /root/.bashrc:
export PATH="$PATH:/home/user/repos/snapcraft/bin"
# Install dependencies
sudo apt install python3-yaml python3-tabulate python3-pymacaroons python3-progressbar \
python3-requests-unixsocket python3-petname python3-pyelftools xdelta3
# Install snapcraft
cd ~/repos
git clone https://github.com/snapcore/snapcraft.git
cd snapcraft
sudo python3 setup.py install
# Workaround bug https://bugs.launchpad.net/snapcraft/+bug/1656884/comments/1
sudo ln -s /usr/local/lib/python3.5/dist-packages/snapcraft-2.43-py3.5.egg/share/snapcraft/ /usr/share/snapcraft
# Build package
cd ~/repos/myproject
sudo snapcraft