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iqbal-lab-org / gramtools

Genome inference from a population reference graph
MIT License
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pip error when installing on Oxford servers #119

Closed iqbal-lab closed 6 years ago

iqbal-lab commented 6 years ago

What does this install error mean?

/apps/well/python/3.4.3/bin/pip3  install git+https://github.com/iqbal-lab-org/gramtools
Collecting git+https://github.com/iqbal-lab-org/gramtools
  Cloning https://github.com/iqbal-lab-org/gramtools to /tmp/pip-jqommg3u-build
Collecting scipy>=1.0.1 (from gramtools==2.0)
  Using cached https://files.pythonhosted.org/packages/56/b5/1a47572236785278db0c8a1e7bb4040eebb63b78fbb470b6f5efc357ffcf/scipy-1.1.0-cp34-cp34m-manylinux1_x86_64.whl
Requirement already satisfied (use --upgrade to upgrade): numpy>=1.8.2 in /gpfs0/apps/well/python/3.4.3/lib/python3.4/site-packages (from scipy>=1.0.1->gramtools==2.0)
Installing collected packages: scipy, gramtools
  Found existing installation: scipy 0.18.1
    Uninstalling scipy-0.18.1:
Exception:
Traceback (most recent call last):
  File "/apps/well/python/3.4.3/lib/python3.4/shutil.py", line 523, in move
    os.rename(src, real_dst)
OSError: [Errno 18] Invalid cross-device link: '/gpfs0/apps/well/python/3.4.3/lib/python3.4/site-packages/scipy-0.18.1.dist-info/DESCRIPTION.rst' -> '/tmp/pip-w29uxv1n-uninstall/gpfs0/apps/well/python/3.4.3/lib/python3.4/site-packages/scipy-0.18.1.dist-info/DESCRIPTION.rst'
ffranr commented 6 years ago

This command is attempting to uninstall scipy as part of package management. You may not have the correct rights to do so. You should probably ensure that all modifications occur as locally as possible. Virtual environments can be very useful to this effect: 

$ virtualenv gramtools_venv
$ source ./gramtools_venv/bin/activate
$ pip3 install git+https://github.com/iqbal-lab-org/gramtools
iqbal-lab commented 6 years ago

This is not a bug, closing