(ven) b-an01 [~/pfs/NeuroNER-master]$ pip install cffi
Collecting cffi
  Using cached https://files.pythonhosted.org/packages/59/cc/0e1635b4951021ef35f5c92b32c865ae605fac2a19d724fb6ff99d745c81/cffi-1.11.5-cp35-cp35m-manylinux1_x86_64.whl
Collecting pycparser (from cffi)
tensorflow 1.7.0 has requirement numpy>=1.13.3, but you'll have numpy 1.11.1 which is incompatible.
tensorboard 1.7.0 has requirement numpy>=1.12.0, but you'll have numpy 1.11.1 which is incompatible.
Installing collected packages: pycparser, cffi
Successfully installed cffi-1.11.5 pycparser-2.18
(ven) b-an01 [~/pfs/NeuroNER-master]$ pip install networkx
Collecting networkx
Collecting decorator>=4.1.0 (from networkx)
  Using cached https://files.pythonhosted.org/packages/bc/bb/a24838832ba35baf52f32ab1a49b906b5f82fb7c76b2f6a7e35e140bac30/decorator-4.3.0-py2.py3-none-any.whl
tensorboard 1.7.0 has requirement numpy>=1.12.0, but you'll have numpy 1.11.1 which is incompatible.
tensorflow 1.7.0 has requirement numpy>=1.13.3, but you'll have numpy 1.11.1 which is incompatible.
Installing collected packages: decorator, networkx
  Found existing installation: decorator 4.0.10
    Not uninstalling decorator at /pfs/software/eb/amd64_ubuntu1604_bdw/software/MPI/GCC-CUDA/6.4.0-2.28-9.0.176/OpenMPI/2.1.1/Python/3.5.2/lib/python3.5/site-packages/decorator-4.0.10-py3.5.egg, outside environment /pfs/nobackup/home/d/dansjo/NeuroNER-master/ven
    Can't uninstall 'decorator'. No files were found to uninstall.
Successfully installed decorator-4.3.0 networkx-2.1
(ven) b-an01 [~/pfs/NeuroNER-master]$ pip install pycorenlp
Collecting pycorenlp
Collecting requests (from pycorenlp)
  Using cached https://files.pythonhosted.org/packages/49/df/50aa1999ab9bde74656c2919d9c0c085fd2b3775fd3eca826012bef76d8c/requests-2.18.4-py2.py3-none-any.whl
Collecting certifi>=2017.4.17 (from requests->pycorenlp)
  Using cached https://files.pythonhosted.org/packages/7c/e6/92ad559b7192d846975fc916b65f667c7b8c3a32bea7372340bfe9a15fa5/certifi-2018.4.16-py2.py3-none-any.whl
Collecting chardet<3.1.0,>=3.0.2 (from requests->pycorenlp)
  Using cached https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl
Requirement already satisfied: idna<2.7,>=2.5 in /pfs/software/eb/amd64_ubuntu1604_bdw/software/MPI/GCC-CUDA/6.4.0-2.28-9.0.176/OpenMPI/2.1.1/Python/3.5.2/lib/python3.5/site-packages/idna-2.6-py3.5.egg (from requests->pycorenlp) (2.6)
Collecting urllib3<1.23,>=1.21.1 (from requests->pycorenlp)
  Using cached https://files.pythonhosted.org/packages/63/cb/6965947c13a94236f6d4b8223e21beb4d576dc72e8130bd7880f600839b8/urllib3-1.22-py2.py3-none-any.whl
tensorboard 1.7.0 has requirement numpy>=1.12.0, but you'll have numpy 1.11.1 which is incompatible.
tensorflow 1.7.0 has requirement numpy>=1.13.3, but you'll have numpy 1.11.1 which is incompatible.
Installing collected packages: certifi, chardet, urllib3, requests, pycorenlp
Successfully installed certifi-2018.4.16 chardet-3.0.4 pycorenlp-0.3.0 requests-2.18.4 urllib3-1.22
(ven) b-an01 [~/pfs/NeuroNER-master]$ pip install spacy
Collecting spacy
Collecting thinc<6.11.0,>=6.10.1 (from spacy)
Collecting cymem<1.32,>=1.30 (from spacy)
  Using cached https://files.pythonhosted.org/packages/b6/43/39372a0bc24d336dc88b87262c30f09d0a2c759f32a2965f90fb56da46f1/cymem-1.31.2-cp35-cp35m-manylinux1_x86_64.whl
Requirement already satisfied: numpy>=1.7 in /pfs/software/eb/amd64_ubuntu1604_bdw/software/MPI/GCC-CUDA/6.4.0-2.28-9.0.176/OpenMPI/2.1.1/Python/3.5.2/lib/python3.5/site-packages/numpy-1.11.1-py3.5-linux-x86_64.egg (from spacy) (1.11.1)
Collecting regex==2017.4.5 (from spacy)
Collecting pathlib (from spacy)
Collecting murmurhash<0.29,>=0.28 (from spacy)
Collecting plac<1.0.0,>=0.9.6 (from spacy)
  Using cached https://files.pythonhosted.org/packages/9e/9b/62c60d2f5bc135d2aa1d8c8a86aaf84edb719a59c7f11a4316259e61a298/plac-0.9.6-py2.py3-none-any.whl
Collecting ujson>=1.35 (from spacy)
Collecting dill<0.3,>=0.2 (from spacy)
Collecting preshed<2.0.0,>=1.0.0 (from spacy)
Collecting msgpack-python (from thinc<6.11.0,>=6.10.1->spacy)
Collecting wrapt (from thinc<6.11.0,>=6.10.1->spacy)
Collecting tqdm<5.0.0,>=4.10.0 (from thinc<6.11.0,>=6.10.1->spacy)
  Using cached https://files.pythonhosted.org/packages/78/bc/de067ab2d700b91717dc5459d86a1877e2df31abfb90ab01a5a5a5ce30b4/tqdm-4.23.0-py2.py3-none-any.whl
Collecting cytoolz<0.9,>=0.8 (from thinc<6.11.0,>=6.10.1->spacy)
Requirement already satisfied: six<2.0.0,>=1.10.0 in /pfs/software/eb/amd64_ubuntu1604_bdw/software/MPI/GCC-CUDA/6.4.0-2.28-9.0.176/OpenMPI/2.1.1/Python/3.5.2/lib/python3.5/site-packages/six-1.10.0-py3.5.egg (from thinc<6.11.0,>=6.10.1->spacy) (1.10.0)
Collecting msgpack-numpy==0.4.1 (from thinc<6.11.0,>=6.10.1->spacy)
  Using cached https://files.pythonhosted.org/packages/2e/43/393e30e2768b0357541ac95891f96b80ccc4d517e0dd2fa3042fc8926538/msgpack_numpy-0.4.1-py2.py3-none-any.whl
Requirement already satisfied: termcolor in /pfs/software/eb/amd64_ubuntu1604_bdw/software/MPI/GCC-CUDA/6.4.0-2.28-9.0.176/OpenMPI/2.1.1/TensorFlow/1.7.0-Python-3.5.2/lib/python3.5/site-packages (from thinc<6.11.0,>=6.10.1->spacy) (1.1.0)
Collecting toolz>=0.8.0 (from cytoolz<0.9,>=0.8->thinc<6.11.0,>=6.10.1->spacy)
tensorflow 1.7.0 has requirement numpy>=1.13.3, but you'll have numpy 1.11.1 which is incompatible.
tensorboard 1.7.0 has requirement numpy>=1.12.0, but you'll have numpy 1.11.1 which is incompatible.
Installing collected packages: cymem, msgpack-python, wrapt, tqdm, toolz, cytoolz, msgpack-numpy, murmurhash, plac, pathlib, dill, preshed, thinc, regex, ujson, spacy
Successfully installed cymem-1.31.2 cytoolz-0.8.2 dill-0.2.7.1 msgpack-numpy-0.4.1 msgpack-python-0.5.6 murmurhash-0.28.0 pathlib-1.0.1 plac-0.9.6 preshed-1.0.0 regex-2017.4.5 spacy-2.0.11 thinc-6.10.2 toolz-0.9.0 tqdm-4.23.0 ujson-1.35 wrapt-1.10.11