I started using Eclim a couple days ago, and kept running into Error running command: pyflakes <path to my code>, when my files contained more than one syntax error/warning. After a bit of googling I discovered this bug, which suggests that the version of pyflakes in Debian isn’t compatible with Eclim. Sure enough, removing the the .deb package (apt-get remove pyflakes) and installing it from pip (pip install pyflakes), fixed it.