Arch Linux

1. Yaourt is a 3rd party util, use pacman
2. What is "breaks entire upgrade process", any errors?

Yup, sorry for the long paste (Yaourt is calling pacman in this scenario so the have the same response):

:: Proceed with installation? [Y/n]
(1/1) checking keys in keyring [####################################################################] 100%
(1/1) checking package integrity [####################################################################] 100%
(1/1) loading package files [####################################################################] 100%
(1/1) checking for file conflicts [####################################################################] 100%
error: failed to commit transaction (conflicting files)
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/__init__.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/__pycache__/__init__.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/__pycache__/basecommand.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/__pycache__/baseparser.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/__pycache__/build_env.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/__pycache__/cache.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/__pycache__/cmdoptions.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/__pycache__/compat.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/__pycache__/configuration.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/__pycache__/download.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/__pycache__/exceptions.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/__pycache__/index.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/__pycache__/locations.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/__pycache__/pep425tags.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/__pycache__/resolve.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/__pycache__/status_codes.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/__pycache__/wheel.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/basecommand.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/baseparser.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/build_env.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/cache.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/cmdoptions.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/commands/__init__.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/commands/__pycache__/__init__.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/commands/__pycache__/check.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/commands/__pycache__/completion.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/commands/__pycache__/configuration.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/commands/__pycache__/download.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/commands/__pycache__/freeze.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/commands/__pycache__/hash.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/commands/__pycache__/help.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/commands/__pycache__/install.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/commands/__pycache__/list.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/commands/__pycache__/search.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/commands/__pycache__/show.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/commands/__pycache__/uninstall.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/commands/__pycache__/wheel.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/commands/check.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/commands/completion.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/commands/configuration.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/commands/download.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/commands/freeze.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/commands/hash.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/commands/help.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/commands/install.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/commands/list.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/commands/search.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/commands/show.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/commands/uninstall.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/commands/wheel.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/compat.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/configuration.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/download.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/exceptions.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/index.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/locations.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/models/__init__.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/models/__pycache__/__init__.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/models/__pycache__/index.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/models/index.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/operations/__init__.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/operations/__pycache__/__init__.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/operations/__pycache__/check.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/operations/__pycache__/freeze.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/operations/__pycache__/prepare.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/operations/check.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/operations/freeze.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/operations/prepare.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/pep425tags.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/req/__init__.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/req/__pycache__/__init__.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/req/__pycache__/req_file.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/req/__pycache__/req_install.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/req/__pycache__/req_set.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/req/__pycache__/req_uninstall.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/req/req_file.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/req/req_install.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/req/req_set.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/req/req_uninstall.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/resolve.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/status_codes.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/utils/__init__.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/utils/__pycache__/__init__.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/utils/__pycache__/appdirs.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/utils/__pycache__/deprecation.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/utils/__pycache__/encoding.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/utils/__pycache__/filesystem.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/utils/__pycache__/glibc.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/utils/__pycache__/hashes.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/utils/__pycache__/logging.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/utils/__pycache__/misc.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/utils/__pycache__/outdated.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/utils/__pycache__/packaging.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/utils/__pycache__/setuptools_build.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/utils/__pycache__/temp_dir.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/utils/__pycache__/typing.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/utils/__pycache__/ui.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/utils/appdirs.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/utils/deprecation.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/utils/encoding.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/utils/filesystem.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/utils/glibc.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/utils/hashes.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/utils/logging.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/utils/misc.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/utils/outdated.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/utils/packaging.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/utils/setuptools_build.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/utils/temp_dir.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/utils/typing.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/utils/ui.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/vcs/__init__.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/vcs/__pycache__/__init__.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/vcs/__pycache__/bazaar.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/vcs/__pycache__/git.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/vcs/__pycache__/mercurial.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/vcs/__pycache__/subversion.cpython-36.pyc exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/vcs/bazaar.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/vcs/git.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/vcs/mercurial.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/vcs/subversion.py exists in filesystem
python-pip: /usr/lib/python3.6/site-packages/pip/_internal/wheel.py exists in filesystem
Errors occurred, no packages were upgraded.
No database errors have been found!

So you most likely used pip as root to update pip. This is what happens when you go around pacman. See https://wiki.archlinux.org/index.php/Pacman#.22Failed_to_commit_transaction_.28conflicting_files.29.22_error