error on test.sh run

[Fiona Whelan]

I followed the instructions for installation on ubuntu in the README.txt and received the following error when I tried to run test.sh:

Traceback (most recent call last):
  File "/usr/local/bin/lsa_compute", line 9, in <module>
    load_entry_point('lsa==1.0.0', 'console_scripts', 'lsa_compute')()
  File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 351, in load_entry_point
    return get_distribution(dist).load_entry_point(group, name)
  File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 2363, in load_entry_point
    return ep.load()
  File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 2088, in load
    entry = __import__(self.module_name, globals(),globals(), ['__name__'])
  File "/usr/local/lib/python2.7/dist-packages/lsa-1.0.0-py2.7-linux-x86_64.egg/lsa/lsa_compute.py", line 38, in <module>
    import lsalib
  File "/usr/local/lib/python2.7/dist-packages/lsa-1.0.0-py2.7-linux-x86_64.egg/lsa/lsalib.py", line 64, in <module>
    r('''setwd("%s")''' % os.environ.get('PWD'))
  File "/usr/local/lib/python2.7/dist-packages/rpy2/robjects/__init__.py", line 269, in __call__
    res = self.eval(p)
  File "/usr/local/lib/python2.7/dist-packages/rpy2/robjects/functions.py", line 170, in __call__
    return super(SignatureTranslatedFunction, self).__call__(*args, **kwargs)
  File "/usr/local/lib/python2.7/dist-packages/rpy2/robjects/functions.py", line 96, in __call__
    new_args = [conversion.py2ri(a) for a in args]
  File "/usr/local/lib/python2.7/dist-packages/rpy2/robjects/numpy2ri.py", line 46, in numpy2ri
    if not o.dtype.isnative:
AttributeError: 'rpy2.rinterface.SexpVector' object has no attribute 'dtype'

This error repeats ~10 times. Additionally, I run the INSTALL.ubuntu.sh script that I found in the main directory, but also received the same errors with test.sh. I'm running x86_64 GNU/Linux.

Additionally,

$ pip show rpy2
---
Name: rpy2
Version: 2.7.8
Location: /usr/local/lib/python2.7/dist-packages
Requires: six, singledispatch

Thanks for your help!

[Han Gao]

I have the same issue.

[Charlie Xia]

I think this has got fixed in recent versions. rpy2 dependencies haven been removed. Have you both tried v_1.0.2 found here? https://bitbucket.org/charade/elsa/downloads

[Charlie Xia]

This has been fixed.

[Fiona Whelan]

Yes, I tried the most recent version, v_1.0.2.

This issue is not resolved..

[Charlie Xia]

Can you completely remove the elsa package directory under site-packages, in your case: "/usr/local/lib/python2.7/dist-packages/lsa*" and rpy2 if you don't need it otherwise.

And reinstall everything

[Charlie Xia]

I mean just reinstall the elsa-1.0.2 . you don't need the rpy2 anymore.

[Fiona Whelan]

That seems to have done it; test.sh is running now, looks like it will finish without error.

Thanks for your help!

[Charlie Xia]

you are welcome