packaging biom for FreeBSD

Question

I'm working on packaging biom (2.1.5) for FreeBSD.

Based on the documentation, I initially had it depending on pynumpy and h5py, but digging I think it should also depend on:

py27-click-6.6
py27-future-0.14.3
py27-pyqi-0.2.0
py27-scipy-0.16.1.

Now I'm at the point where running biom gives the errors below. Do you have suggestions for debugging? I'm not a python developer, so please be gentle.

Traceback (most recent call last):
  File "/usr/local/bin/biom", line 9, in <module>
    load_entry_point('biom-format==2.1.5', 'console_scripts', 'biom')()
  File "/usr/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 547, in load_entry_point
    return get_distribution(dist).load_entry_point(group, name)
  File "/usr/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2720, in load_entry_point
    return ep.load()
  File "/usr/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2380, in load
    return self.resolve()
  File "/usr/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2386, in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "/usr/local/lib/python2.7/site-packages/biom/__init__.py", line 51, in <module>
    from .table import Table
  File "/usr/local/lib/python2.7/site-packages/biom/table.py", line 188, in <module>
    from future.utils import string_types
ImportError: cannot import name string_types

score 1 · Accepted Answer · answered May 26 '16 at 05:48

In future 0.14.3, there is no string_types in future.utils. (Although it is mentioned in the documentation). Look at the 0.14.x branch of the github repo for future.

At the time of writing the current version of the future module is 0.15.2. So that port needs to be updated before biom will work. I'd suggest to contact the maintainer of that port.

packaging biom for FreeBSD

1 Answers1