2.4.0 rpy2 issue

[hardingnj]

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]

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
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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]

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

[alimanfoo]

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 ***@***.***> 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 <#38 (comment)>, 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]

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 ***@***.*** ***@***.***');>> 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 > <#38 (comment)>, 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: ***@***.*** ***@***.***');> 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]

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