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cggh / biipy

Docker image for bioinformatics analysis.
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2.4.0 rpy2 issue #38

Open hardingnj opened 7 years ago

hardingnj commented 7 years ago

get_ipython().magic('reload_ext rpy2.ipython')

Generates an error.

/anaconda/envs/science/lib/python3.5/site-packages/rpy2/ipython/rmagic.py in load_ipython_extension(ip) 786 # Initialising rpy2 interferes with readline. Since, at this point, we've 787 # probably just loaded rpy2, we reset the delimiters. See issue gh-2759. --> 788 if ip.has_readline: 789 ip.readline.set_completer_delims(ip.readline_delims)

AttributeError: 'ZMQInteractiveShell' object has no attribute 'has_readline'

alimanfoo commented 7 years ago

FWIW I think both Chris C and I have seen something like this and have been avoiding using rpy2.

On Friday, October 7, 2016, Nick Harding notifications@github.com wrote:

get_ipython().magic('reload_ext rpy2.ipython')

Generates an error.

/anaconda/envs/science/lib/python3.5/site-packages/rpy2/ipython/rmagic.py in load_ipython_extension(ip) 786 # Initialising rpy2 interferes with readline. Since, at this point, we've 787 # probably just loaded rpy2, we reset the delimiters. See issue gh-2759. --> 788 if ip.has_readline: 789 ip.readline.set_completer_delims(ip.readline_delims)

AttributeError: 'ZMQInteractiveShell' object has no attribute 'has_readline'

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Alistair Miles Head of Epidemiological Informatics Centre for Genomics and Global Health http://cggh.org The Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Email: alimanfoo@googlemail.com Web: http://purl.org/net/aliman Twitter: https://twitter.com/alimanfoo Tel: +44 (0)1865 287721

hardingnj commented 7 years ago

Will leave this open for now until we see how updated rpy2 behaves in 2.5.0

alimanfoo commented 7 years ago

Would be nice to find an automated way to check if rpy2 is behaving, it's been the problem child so far. I wonder if there is an easy way to run the rpy2 test suite (assuming it has one) within the travis CI...

On Tue, Jan 31, 2017 at 3:34 PM, Nick Harding notifications@github.com wrote:

Will leave this open for now until we see how updated rpy2 behaves

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/cggh/biipy/issues/38#issuecomment-276396845, or mute the thread https://github.com/notifications/unsubscribe-auth/AAq8QjW6Tj7ptcy6CwYu4CWUcZTDMKmfks5rX1SNgaJpZM4KRLLN .

-- Alistair Miles Head of Epidemiological Informatics Centre for Genomics and Global Health http://cggh.org The Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Email: alimanfoo@googlemail.com Web: http://purl.org/net/aliman Twitter: https://twitter.com/alimanfoo Tel: +44 (0)1865 287721

alimanfoo commented 7 years ago

So I think rpy2 is still broken. I've added a PR to run the rpy2 test suite (#43), let's see if test suite runs OK on travis (fails on my local install)...

On Tuesday, January 31, 2017, Alistair Miles alimanfoo@googlemail.com wrote:

Would be nice to find an automated way to check if rpy2 is behaving, it's been the problem child so far. I wonder if there is an easy way to run the rpy2 test suite (assuming it has one) within the travis CI...

On Tue, Jan 31, 2017 at 3:34 PM, Nick Harding <notifications@github.com javascript:_e(%7B%7D,'cvml','notifications@github.com');> wrote:

Will leave this open for now until we see how updated rpy2 behaves

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/cggh/biipy/issues/38#issuecomment-276396845, or mute the thread https://github.com/notifications/unsubscribe-auth/AAq8QjW6Tj7ptcy6CwYu4CWUcZTDMKmfks5rX1SNgaJpZM4KRLLN .

-- Alistair Miles Head of Epidemiological Informatics Centre for Genomics and Global Health http://cggh.org The Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Email: alimanfoo@googlemail.com javascript:_e(%7B%7D,'cvml','alimanfoo@googlemail.com'); Web: http://purl.org/net/aliman Twitter: https://twitter.com/alimanfoo Tel: +44 (0)1865 287721

-- Alistair Miles Head of Epidemiological Informatics Centre for Genomics and Global Health http://cggh.org The Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Email: alimanfoo@googlemail.com Web: http://purl.org/net/aliman Twitter: https://twitter.com/alimanfoo Tel: +44 (0)1865 287721

alimanfoo commented 7 years ago

This is what I'm getting locally:

(biipy_20170126_py35) aliman@uluru:~$ python -m rpy2.tests
Traceback (most recent call last):
  File "/home/aliman/miniconda3/envs/biipy_20170126_py35/lib/python3.5/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/home/aliman/miniconda3/envs/biipy_20170126_py35/lib/python3.5/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/home/aliman/miniconda3/envs/biipy_20170126_py35/lib/python3.5/site-packages/rpy2/tests.py", line 23, in <module>
    import rpy2.tests_rpy_classic
  File "/home/aliman/miniconda3/envs/biipy_20170126_py35/lib/python3.5/site-packages/rpy2/tests_rpy_classic.py", line 3, in <module>
    import rpy2.rpy_classic as rpy
  File "/home/aliman/miniconda3/envs/biipy_20170126_py35/lib/python3.5/site-packages/rpy2/rpy_classic.py", line 5, in <module>
    import rpy2.rinterface as ri
  File "/home/aliman/miniconda3/envs/biipy_20170126_py35/lib/python3.5/site-packages/rpy2/rinterface/__init__.py", line 92, in <module>
    from rpy2.rinterface._rinterface import (baseenv,
ImportError: libicuuc.so.54: cannot open shared object file: No such file or directory