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ucsc-cgp / cgp-deployment

The UCSC Genomics Institute's Computational Genomics Platform (CGP). This repo contains the Docker compose-based deployment process.
https://ucsc-cgp.org
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install_bootstrap: dcc-dashboard-service build chokes on pycparser uninstall #23

Closed natanlao closed 6 years ago

natanlao commented 6 years ago 
$ sudo ./install_bootstrap

...

Building dcc-dashboard-service
Step 1/36 : FROM nginx:1.10
 ---> 0346349a1a64
Step 2/36 : RUN apt-get update
 ---> Using cache
 ---> c1ec722b311a
Step 3/36 : RUN apt-get install -y build-essential libpq-dev libssl-dev libffi-dev python-dev
 ---> Using cache
 ---> 46f0a62e438b
Step 4/36 : RUN apt-get install -y python-pip postgresql
 ---> Using cache
 ---> 8b22005b5974
Step 5/36 : RUN pip install -U pip
 ---> Using cache
 ---> d96b3e2b450f
Step 6/36 : RUN pip install uwsgi
 ---> Using cache
 ---> 8b85d6a96eb3
Step 7/36 : RUN pip install --upgrade cffi
 ---> Using cache
 ---> bf63fc7fbd54
Step 8/36 : RUN apt-get install -y uwsgi-plugin-python
 ---> Using cache
 ---> 11fd3f157f47
Step 9/36 : ADD ./requirements.txt /app/requirements.txt
 ---> Using cache
 ---> 75d0fc236c33
Step 10/36 : RUN pip install -r /app/requirements.txt
 ---> Running in c08fcc04307c

...

cryptography 1.7.2 has requirement setuptools>=11.3, but you'll have setuptools 5.5.1 which is incompatible.
Installing collected packages: SQLAlchemy, MarkupSafe, Mako, python-editor, alembic, appdirs, pytz, funcsigs, tzlocal, six, futures, APScheduler, backports-abc, boto, certifi, pycparser, cffi, click, idna, pyasn1, enum34, ipaddress, cryptography, docutils, urllib3, elasticsearch, python-dateutil, elasticsearch-dsl, itsdangerous, Jinja2, Werkzeug, Flask, Flask-APScheduler, Flask-Cors, Flask-Elasticsearch, pyexcel-io, texttable, pyexcel, pyexcel-webio, Flask-Excel, Flask-SQLAlchemy, Flask-Script, Flask-Migrate, PyMySQL, pg8000, Paginator, inflection, backports.functools-lru-cache, arrow, sqlalchemy-utils, active-alchemy, configparser, mccabe, pyflakes, pycodestyle, flake8, flask-login, jsonlines, jsonobject, lockfile, singledispatch, tornado, python-daemon, luigi, lxml, pyparsing, packaging, psycopg2, pyOpenSSL, py, pytest
  Found existing installation: six 1.8.0
    Uninstalling six-1.8.0:
      Successfully uninstalled six-1.8.0
  Found existing installation: pycparser 2.10
Cannot uninstall 'pycparser'. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall.
ERROR: Service 'dcc-dashboard-service' failed to build: The command '/bin/sh -c pip install -r /app/requirements.txt' returned a non-zero code: 1

┆Issue is synchronized with this JIRA Task ┆Project Name: CGP-Deployment ┆Issue Number: DEP-10

natanlao commented 6 years ago

DataBiosphere/cgp-dashboard-service#71