Error installing Bottleneck 1.2.0 from behind proxy

[gfairchild]

I just ran into an error where some unit tests are failing after upgrading from 1.1.0 to 1.2.0. This is on a work-hosted GitLab instance that's behind a proxy. Here's my virtual environment:

amqp==1.4.9
anyjson==0.3.3
autopep8==1.2.4
billiard==3.5.0.1
Bottleneck==1.2.0
celery==3.1.24
colormath==2.1.1
decorator==4.0.10
Django==1.9.11
django-celery==3.1.17
django-debug-toolbar==1.5
django-extensions==1.7.4
django-filter==0.15.3
django-nested-admin==3.0.12
django-widget-tweaks==1.4.1
djangorestframework==3.5.2
factory-boy==2.7.0
fake-factory==0.7.2
isodate==0.5.4
isort==4.2.5
kombu==3.0.35
Markdown==2.6.7
networkx==1.11
numexpr==2.6.1
numpy==1.11.2
pandas==0.19.0
pep8==1.7.0
psycopg2==2.6.2
py==1.4.31
pyflakes==1.3.0
pyHarmonySearch==1.3.3
pylibmc==1.5.1
pyshp==1.2.10
pytest==3.0.3
pytest-django==3.0.0
python-dateutil==2.5.3
python-monkey-business==1.0.0
pytz==2016.7
requests==2.11.1
scipy==0.18.1
six==1.10.0
spectra==0.0.7
sqlparse==0.2.2
vine==1.1.3
whitenoise==3.2.2
xlrd==1.0.0

Here's the output of my CI output attempting to install 1.2.0:

...
...
...
$ python3 -m venv env
$ source env/bin/activate
$ pip --proxy $HTTP_PROXY install --upgrade pip
Collecting pip
  Downloading pip-8.1.2-py2.py3-none-any.whl (1.2MB)
Installing collected packages: pip
  Found existing installation: pip 8.1.1
    Uninstalling pip-8.1.1:
      Successfully uninstalled pip-8.1.1
Successfully installed pip-8.1.2
$ pip --proxy $HTTP_PROXY install -r requirements.txt
Collecting amqp==1.4.9 (from -r requirements.txt (line 1))
  Downloading amqp-1.4.9-py2.py3-none-any.whl (51kB)
Collecting anyjson==0.3.3 (from -r requirements.txt (line 2))
  Downloading anyjson-0.3.3.tar.gz
Collecting autopep8==1.2.4 (from -r requirements.txt (line 3))
  Downloading autopep8-1.2.4-py2.py3-none-any.whl (41kB)
Collecting billiard==3.5.0.1 (from -r requirements.txt (line 4))
  Downloading billiard-3.5.0.1.tar.gz (156kB)
Collecting Bottleneck==1.2.0 (from -r requirements.txt (line 5))
  Downloading Bottleneck-1.2.0.tar.gz (92kB)
    Complete output from command python setup.py egg_info:
    Download error on https://pypi.python.org/simple/numpy/: [Errno 101] Network is unreachable -- Some packages may not be found!
    Couldn't find index page for 'numpy' (maybe misspelled?)
    Download error on https://pypi.python.org/simple/: [Errno 101] Network is unreachable -- Some packages may not be found!
    No local packages or download links found for numpy
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-build-2vzimtgq/Bottleneck/setup.py", line 109, in <module>
        setup(**metadata)
      File "/usr/local/lib/python3.4/distutils/core.py", line 108, in setup
        _setup_distribution = dist = klass(attrs)
      File "/builds/bsv/swap/env/lib/python3.4/site-packages/setuptools/dist.py", line 269, in __init__
        self.fetch_build_eggs(attrs['setup_requires'])
      File "/builds/bsv/swap/env/lib/python3.4/site-packages/setuptools/dist.py", line 313, in fetch_build_eggs
        replace_conflicting=True,
      File "/builds/bsv/swap/env/lib/python3.4/site-packages/pkg_resources/__init__.py", line 826, in resolve
        dist = best[req.key] = env.best_match(req, ws, installer)
      File "/builds/bsv/swap/env/lib/python3.4/site-packages/pkg_resources/__init__.py", line 1092, in best_match
        return self.obtain(req, installer)
      File "/builds/bsv/swap/env/lib/python3.4/site-packages/pkg_resources/__init__.py", line 1104, in obtain
        return installer(requirement)
      File "/builds/bsv/swap/env/lib/python3.4/site-packages/setuptools/dist.py", line 380, in fetch_build_egg
        return cmd.easy_install(req)
      File "/builds/bsv/swap/env/lib/python3.4/site-packages/setuptools/command/easy_install.py", line 634, in easy_install
        raise DistutilsError(msg)
    distutils.errors.DistutilsError: Could not find suitable distribution for Requirement.parse('numpy')
    
    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-2vzimtgq/Bottleneck/
ERROR: Build failed: exit code 1

And if I use 1.1.0, it succeeds:

...
...
...
$ python3 -m venv env
$ source env/bin/activate
$ pip --proxy $HTTP_PROXY install --upgrade pip
Collecting pip
  Downloading pip-8.1.2-py2.py3-none-any.whl (1.2MB)
Installing collected packages: pip
  Found existing installation: pip 8.1.1
    Uninstalling pip-8.1.1:
      Successfully uninstalled pip-8.1.1
Successfully installed pip-8.1.2
$ pip --proxy $HTTP_PROXY install -r requirements.txt
Collecting amqp==1.4.9 (from -r requirements.txt (line 1))
  Downloading amqp-1.4.9-py2.py3-none-any.whl (51kB)
Collecting anyjson==0.3.3 (from -r requirements.txt (line 2))
  Downloading anyjson-0.3.3.tar.gz
Collecting autopep8==1.2.4 (from -r requirements.txt (line 3))
  Downloading autopep8-1.2.4-py2.py3-none-any.whl (41kB)
Collecting billiard==3.5.0.1 (from -r requirements.txt (line 4))
  Downloading billiard-3.5.0.1.tar.gz (156kB)
Collecting Bottleneck==1.1.0 (from -r requirements.txt (line 5))
  Downloading Bottleneck-1.1.0.tar.gz (436kB)
Collecting celery==3.1.24 (from -r requirements.txt (line 6))
  Downloading celery-3.1.24-py2.py3-none-any.whl (526kB)
Collecting colormath==2.1.1 (from -r requirements.txt (line 7))
  Downloading colormath-2.1.1.tar.gz
Collecting decorator==4.0.10 (from -r requirements.txt (line 8))
  Downloading decorator-4.0.10-py2.py3-none-any.whl
Collecting Django==1.9.11 (from -r requirements.txt (line 9))
  Downloading Django-1.9.11-py2.py3-none-any.whl (6.6MB)
Collecting django-celery==3.1.17 (from -r requirements.txt (line 10))
  Downloading django-celery-3.1.17.tar.gz (79kB)
Collecting django-debug-toolbar==1.5 (from -r requirements.txt (line 11))
  Downloading django_debug_toolbar-1.5-py2.py3-none-any.whl (204kB)
Collecting django-extensions==1.7.4 (from -r requirements.txt (line 12))
  Downloading django_extensions-1.7.4-py2.py3-none-any.whl (200kB)
Collecting django-filter==0.15.3 (from -r requirements.txt (line 13))
  Downloading django_filter-0.15.3-py2.py3-none-any.whl (48kB)
Collecting django-nested-admin==3.0.12 (from -r requirements.txt (line 14))
  Downloading django_nested_admin-3.0.12-py2.py3-none-any.whl (235kB)
Collecting django-widget-tweaks==1.4.1 (from -r requirements.txt (line 15))
  Downloading django_widget_tweaks-1.4.1-py2.py3-none-any.whl
Collecting djangorestframework==3.5.2 (from -r requirements.txt (line 16))
  Downloading djangorestframework-3.5.2-py2.py3-none-any.whl (709kB)
Collecting factory-boy==2.7.0 (from -r requirements.txt (line 17))
  Downloading factory_boy-2.7.0-py2.py3-none-any.whl
Collecting fake-factory==0.7.2 (from -r requirements.txt (line 18))
  Downloading fake_factory-0.7.2-py2.py3-none-any.whl (530kB)
Collecting isodate==0.5.4 (from -r requirements.txt (line 19))
  Downloading isodate-0.5.4.tar.gz
Collecting isort==4.2.5 (from -r requirements.txt (line 20))
  Downloading isort-4.2.5-py2.py3-none-any.whl (40kB)
Collecting kombu==3.0.35 (from -r requirements.txt (line 21))
  Downloading kombu-3.0.35-py2.py3-none-any.whl (240kB)
Collecting Markdown==2.6.7 (from -r requirements.txt (line 22))
  Downloading Markdown-2.6.7.zip (413kB)
Collecting networkx==1.11 (from -r requirements.txt (line 23))
  Downloading networkx-1.11-py2.py3-none-any.whl (1.3MB)
Collecting numexpr==2.6.1 (from -r requirements.txt (line 24))
  Downloading numexpr-2.6.1-cp34-cp34m-manylinux1_x86_64.whl (387kB)
Collecting numpy==1.11.2 (from -r requirements.txt (line 25))
  Downloading numpy-1.11.2-cp34-cp34m-manylinux1_x86_64.whl (15.6MB)
Collecting pandas==0.19.0 (from -r requirements.txt (line 26))
  Downloading pandas-0.19.0-cp34-cp34m-manylinux1_x86_64.whl (17.6MB)
Collecting pep8==1.7.0 (from -r requirements.txt (line 27))
  Downloading pep8-1.7.0-py2.py3-none-any.whl (41kB)
Collecting psycopg2==2.6.2 (from -r requirements.txt (line 28))
  Downloading psycopg2-2.6.2.tar.gz (376kB)
Collecting py==1.4.31 (from -r requirements.txt (line 29))
  Downloading py-1.4.31-py2.py3-none-any.whl (81kB)
Collecting pyflakes==1.3.0 (from -r requirements.txt (line 30))
  Downloading pyflakes-1.3.0-py2.py3-none-any.whl (222kB)
Collecting pyHarmonySearch==1.3.3 (from -r requirements.txt (line 31))
  Downloading pyHarmonySearch-1.3.3.tar.gz
Collecting pylibmc==1.5.1 (from -r requirements.txt (line 32))
  Downloading pylibmc-1.5.1.tar.gz (59kB)
Collecting pyshp==1.2.10 (from -r requirements.txt (line 33))
  Downloading pyshp-1.2.10.tar.gz (176kB)
Collecting pytest==3.0.3 (from -r requirements.txt (line 34))
  Downloading pytest-3.0.3-py2.py3-none-any.whl (169kB)
Collecting pytest-django==3.0.0 (from -r requirements.txt (line 35))
  Downloading pytest_django-3.0.0-py2.py3-none-any.whl
Collecting python-dateutil==2.5.3 (from -r requirements.txt (line 36))
  Downloading python_dateutil-2.5.3-py2.py3-none-any.whl (201kB)
Collecting python-monkey-business==1.0.0 (from -r requirements.txt (line 37))
  Downloading python_monkey_business-1.0.0-py2.py3-none-any.whl
Collecting pytz==2016.7 (from -r requirements.txt (line 38))
  Downloading pytz-2016.7-py2.py3-none-any.whl (480kB)
Collecting requests==2.11.1 (from -r requirements.txt (line 39))
  Downloading requests-2.11.1-py2.py3-none-any.whl (514kB)
Collecting scipy==0.18.1 (from -r requirements.txt (line 40))
  Downloading scipy-0.18.1-cp34-cp34m-manylinux1_x86_64.whl (40.2MB)
Collecting six==1.10.0 (from -r requirements.txt (line 41))
  Downloading six-1.10.0-py2.py3-none-any.whl
Collecting spectra==0.0.7 (from -r requirements.txt (line 42))
  Downloading spectra-0.0.7.tar.gz
Collecting sqlparse==0.2.2 (from -r requirements.txt (line 43))
  Downloading sqlparse-0.2.2-py2.py3-none-any.whl
Collecting vine==1.1.3 (from -r requirements.txt (line 44))
  Downloading vine-1.1.3-py2.py3-none-any.whl
Collecting whitenoise==3.2.2 (from -r requirements.txt (line 45))
  Downloading whitenoise-3.2.2-py2.py3-none-any.whl
Collecting xlrd==1.0.0 (from -r requirements.txt (line 46))
  Downloading xlrd-1.0.0-py3-none-any.whl (143kB)
Installing collected packages: amqp, anyjson, pep8, autopep8, billiard, numpy, Bottleneck, kombu, pytz, celery, decorator, networkx, colormath, Django, django-celery, sqlparse, django-debug-toolbar, six, django-extensions, django-filter, python-monkey-business, django-nested-admin, django-widget-tweaks, djangorestframework, python-dateutil, fake-factory, factory-boy, isodate, isort, Markdown, numexpr, pandas, psycopg2, py, pyflakes, pyHarmonySearch, pylibmc, pyshp, pytest, pytest-django, requests, scipy, spectra, vine, whitenoise, xlrd
  Running setup.py install for anyjson: started
    Running setup.py install for anyjson: finished with status 'done'
  Running setup.py install for billiard: started
    Running setup.py install for billiard: finished with status 'done'
  Running setup.py install for Bottleneck: started
    Running setup.py install for Bottleneck: finished with status 'done'
  Running setup.py install for colormath: started
    Running setup.py install for colormath: finished with status 'done'
  Running setup.py install for django-celery: started
    Running setup.py install for django-celery: finished with status 'done'
  Running setup.py install for isodate: started
    Running setup.py install for isodate: finished with status 'done'
  Running setup.py install for Markdown: started
    Running setup.py install for Markdown: finished with status 'done'
  Running setup.py install for psycopg2: started
    Running setup.py install for psycopg2: finished with status 'done'
  Running setup.py install for pyHarmonySearch: started
    Running setup.py install for pyHarmonySearch: finished with status 'done'
  Running setup.py install for pylibmc: started
    Running setup.py install for pylibmc: finished with status 'done'
  Running setup.py install for pyshp: started
    Running setup.py install for pyshp: finished with status 'done'
  Running setup.py install for spectra: started
    Running setup.py install for spectra: finished with status 'done'
Successfully installed Bottleneck-1.1.0 Django-1.9.11 Markdown-2.6.7 amqp-1.4.9 anyjson-0.3.3 autopep8-1.2.4 billiard-3.5.0.1 celery-3.1.24 colormath-2.1.1 decorator-4.0.10 django-celery-3.1.17 django-debug-toolbar-1.5 django-extensions-1.7.4 django-filter-0.15.3 django-nested-admin-3.0.12 django-widget-tweaks-1.4.1 djangorestframework-3.5.2 factory-boy-2.7.0 fake-factory-0.7.2 isodate-0.5.4 isort-4.2.5 kombu-3.0.35 networkx-1.11 numexpr-2.6.1 numpy-1.11.2 pandas-0.19.0 pep8-1.7.0 psycopg2-2.6.2 py-1.4.31 pyHarmonySearch-1.3.3 pyflakes-1.3.0 pylibmc-1.5.1 pyshp-1.2.10 pytest-3.0.3 pytest-django-3.0.0 python-dateutil-2.5.3 python-monkey-business-1.0.0 pytz-2016.7 requests-2.11.1 scipy-0.18.1 six-1.10.0 spectra-0.0.7 sqlparse-0.2.2 vine-1.1.3 whitenoise-3.2.2 xlrd-1.0.0
$ printf "[pytest]\nDJANGO_SETTINGS_MODULE = settings_ci\n" > pytest.ini
$ cd webapp/
$ ./manage_ci.py migrate
Operations to perform:
  Apply all migrations: admin, sites, swap, contenttypes, authtoken, djcelery, auth, sessions
Running migrations:
  Rendering model states... DONE
  Applying contenttypes.0001_initial... OK
  Applying auth.0001_initial... OK
  Applying admin.0001_initial... OK
...
...
...

It seems to be related to the way the NumPy requirement is handled in 1.2.0.

[kwgoodman]

A small change to how numpy is handled was made after the 1.2.0 release. Could you test with the current master branch?

[gfairchild]

Here's my updated requirements.txt:

amqp==1.4.9
anyjson==0.3.3
autopep8==1.2.4
billiard==3.5.0.1
-e git+https://github.com/kwgoodman/bottleneck.git#egg=Bottleneck
celery==3.1.24
colormath==2.1.1
decorator==4.0.10
Django==1.9.11
django-celery==3.1.17
django-debug-toolbar==1.5
django-extensions==1.7.4
django-filter==0.15.3
django-nested-admin==3.0.12
django-widget-tweaks==1.4.1
djangorestframework==3.5.2
factory-boy==2.7.0
fake-factory==0.7.2
isodate==0.5.4
isort==4.2.5
kombu==3.0.35
Markdown==2.6.7
networkx==1.11
numexpr==2.6.1
numpy==1.11.2
pandas==0.19.0
pep8==1.7.0
psycopg2==2.6.2
py==1.4.31
pyflakes==1.3.0
pyHarmonySearch==1.3.3
pylibmc==1.5.1
pyshp==1.2.10
pytest==3.0.3
pytest-django==3.0.0
python-dateutil==2.5.3
python-monkey-business==1.0.0
pytz==2016.7
requests==2.11.1
scipy==0.18.1
six==1.10.0
spectra==0.0.7
sqlparse==0.2.2
vine==1.1.3
whitenoise==3.2.2
xlrd==1.0.0

And here's the updated build log:

$ python3 -m venv env
$ source env/bin/activate
$ pip --proxy $HTTP_PROXY install --upgrade pip
Collecting pip
  Downloading pip-8.1.2-py2.py3-none-any.whl (1.2MB)
Installing collected packages: pip
  Found existing installation: pip 8.1.1
    Uninstalling pip-8.1.1:
      Successfully uninstalled pip-8.1.1
Successfully installed pip-8.1.2
$ pip --proxy $HTTP_PROXY install -r requirements.txt
Collecting amqp==1.4.9 (from -r requirements.txt (line 1))
  Downloading amqp-1.4.9-py2.py3-none-any.whl (51kB)
Collecting anyjson==0.3.3 (from -r requirements.txt (line 2))
  Downloading anyjson-0.3.3.tar.gz
Collecting autopep8==1.2.4 (from -r requirements.txt (line 3))
  Downloading autopep8-1.2.4-py2.py3-none-any.whl (41kB)
Collecting billiard==3.5.0.1 (from -r requirements.txt (line 4))
  Downloading billiard-3.5.0.1.tar.gz (156kB)
Obtaining Bottleneck from git+https://github.com/kwgoodman/bottleneck.git#egg=Bottleneck (from -r requirements.txt (line 5))
  Cloning https://github.com/kwgoodman/bottleneck.git to ./env/src/bottleneck
fatal: unable to access 'https://github.com/kwgoodman/bottleneck.git/': Failed to connect to github.com port 443: Connection refused
Command "git clone -q https://github.com/kwgoodman/bottleneck.git /builds/bsv/swap/env/src/bottleneck" failed with error code 128 in None
ERROR: Build failed: exit code 1

Pip doesn't seem to be properly using the proxy when cloning a git HTTPS repo. Not sure how I make it do that. I'll keep playing with it.

[gfairchild]

Hm, just stumbled onto this issue, which has been open since 2011. That doesn't bode well....

[kwgoodman]

How about changing the order of your requirements file? Would it help to put numpy before bottleneck? That might prevent bottleneck from trying to install numpy.

[gfairchild]

In the short term, that would probably work. We have some automated scripts that spit out pip freeze > requirements.txt, and the order there is generally alphabetical.

[gfairchild]

I'd like to reopen this issue. I finally spent the time to move NumPy to the top of the requirements file. Here's my current requirements file:

numpy==1.12.1
amqp==2.1.4
anyjson==0.3.3
appdirs==1.4.3
autopep8==1.3.1
billiard==3.5.0.2
Bottleneck==1.2.0
celery==4.0.2
colormath==2.1.1
coreapi==2.3.0
coreschema==0.0.4
decorator==4.0.11
Django==1.11
django-celery-results==1.0.1
django-crispy-forms==1.6.1
django-debug-toolbar==1.7
django-extensions==1.7.8
django-filter==1.0.2
django-guardian==1.4.8
django-nested-admin==3.0.17
django-widget-tweaks==1.4.1
djangorestframework==3.6.2
factory-boy==2.8.1
Faker==0.7.11
isodate==0.5.4
isort==4.2.5
itypes==1.1.0
Jinja2==2.9.6
kombu==4.0.2
Markdown==2.6.8
MarkupSafe==1.0
networkx==1.11
numexpr==2.6.2
packaging==16.8
pandas==0.19.2
pep8==1.7.0
psycopg2==2.7.1
py==1.4.33
pycodestyle==2.3.1
pyflakes==1.5.0
pyHarmonySearch==1.3.3
pylibmc==1.5.2
pyparsing==2.2.0
pyshp==1.2.10
pytest==3.0.7
pytest-django==3.1.2
pytest-mock==1.6.0
python-dateutil==2.6.0
python-monkey-business==1.0.0
pytz==2017.2
requests==2.13.0
scipy==0.19.0
six==1.10.0
spectra==0.0.7
sqlparse==0.2.3
uritemplate==3.0.0
vine==1.1.3
whitenoise==3.3.0
xlrd==1.0.0

Here's the error that CI is throwing:

$ python3 -m venv env
$ source env/bin/activate
$ pip --proxy $HTTP_PROXY install --upgrade pip
Requirement already up-to-date: pip in ./env/lib/python3.4/site-packages
$ pip --proxy $HTTP_PROXY install -r requirements.txt
Collecting numpy==1.12.1 (from -r requirements.txt (line 1))
  Downloading numpy-1.12.1-cp34-cp34m-manylinux1_x86_64.whl (16.8MB)
Collecting amqp==2.1.4 (from -r requirements.txt (line 2))
  Downloading amqp-2.1.4-py2.py3-none-any.whl (49kB)
Collecting anyjson==0.3.3 (from -r requirements.txt (line 3))
  Downloading anyjson-0.3.3.tar.gz
Collecting appdirs==1.4.3 (from -r requirements.txt (line 4))
  Downloading appdirs-1.4.3-py2.py3-none-any.whl
Collecting autopep8==1.3.1 (from -r requirements.txt (line 5))
  Downloading autopep8-1.3.1.tar.gz (107kB)
Collecting billiard==3.5.0.2 (from -r requirements.txt (line 6))
  Downloading billiard-3.5.0.2-py3-none-any.whl (102kB)
Collecting Bottleneck==1.2.0 (from -r requirements.txt (line 7))
  Downloading Bottleneck-1.2.0.tar.gz (92kB)
    Complete output from command python setup.py egg_info:
    Download error on https://pypi.python.org/simple/numpy/: [Errno 99] Cannot assign requested address -- Some packages may not be found!
    Couldn't find index page for 'numpy' (maybe misspelled?)
    Download error on https://pypi.python.org/simple/: [Errno 99] Cannot assign requested address -- Some packages may not be found!
    No local packages or working download links found for numpy
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-build-8i3udupq/Bottleneck/setup.py", line 109, in <module>
        setup(**metadata)
      File "/usr/local/lib/python3.4/distutils/core.py", line 108, in setup
        _setup_distribution = dist = klass(attrs)
      File "/builds/bsv/swap/env/lib/python3.4/site-packages/setuptools/dist.py", line 315, in __init__
        self.fetch_build_eggs(attrs['setup_requires'])
      File "/builds/bsv/swap/env/lib/python3.4/site-packages/setuptools/dist.py", line 361, in fetch_build_eggs
        replace_conflicting=True,
      File "/builds/bsv/swap/env/lib/python3.4/site-packages/pkg_resources/__init__.py", line 850, in resolve
        dist = best[req.key] = env.best_match(req, ws, installer)
      File "/builds/bsv/swap/env/lib/python3.4/site-packages/pkg_resources/__init__.py", line 1122, in best_match
        return self.obtain(req, installer)
      File "/builds/bsv/swap/env/lib/python3.4/site-packages/pkg_resources/__init__.py", line 1134, in obtain
        return installer(requirement)
      File "/builds/bsv/swap/env/lib/python3.4/site-packages/setuptools/dist.py", line 429, in fetch_build_egg
        return cmd.easy_install(req)
      File "/builds/bsv/swap/env/lib/python3.4/site-packages/setuptools/command/easy_install.py", line 659, in easy_install
        raise DistutilsError(msg)
    distutils.errors.DistutilsError: Could not find suitable distribution for Requirement.parse('numpy')
    
    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-8i3udupq/Bottleneck/
ERROR: Job failed: exit code 1

So even though NumPy is listed before Bottleneck, this doesn't fix the error. Downgrading Bottleneck to 1.1.0 fixes the problem.

[kwgoodman]

Sorry, I don't know why bottleneck doesn't see the numpy you installed.

Your log says:

Collecting numpy==1.12.1 (from -r requirements.txt (line 1))
  Downloading numpy-1.12.1-cp34-cp34m-manylinux1_x86_64.whl (16.8MB)

But it doesn't say anything about installing numpy. Does it get installed (and is available system wide) before bottleneck in downloaded?

[gfairchild]

Excellent question. What is looks like is that running pip install -r requirements.txt causes pip to download all packages before installing them. Something in Bottleneck is causing pip to check for NumPy as soon as Bottleneck is downloaded before pip gets to the install phase for NumPy.