Test failures on master with Anaconda

[ellisonbg]

I am seeing a couple of test failures on master as of Monday the 3rd. I am running OS 10.9 with latest Anaconda.

Here is the first:

======================================================================
ERROR: IPython.extensions.tests.test_rmagic.test_push_dataframe
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/bgranger/anaconda/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/Users/bgranger/Documents/Computing/IPython/code/ipython/IPython/testing/decorators.py", line 225, in skipper_func
    return f(*args, **kwargs)
  File "/Users/bgranger/Documents/Computing/IPython/code/ipython/IPython/extensions/tests/test_rmagic.py", line 44, in test_push_dataframe
    ip.run_line_magic('Rpush', 'df')
  File "/Users/bgranger/Documents/Computing/IPython/code/ipython/IPython/core/interactiveshell.py", line 2108, in run_line_magic
    result = fn(*args,**kwargs)
  File "<string>", line 2, in Rpush
  File "/Users/bgranger/Documents/Computing/IPython/code/ipython/IPython/core/magic.py", line 193, in <lambda>
    call = lambda f, *a, **k: f(*a, **k)
  File "/Users/bgranger/Documents/Computing/IPython/code/ipython/IPython/extensions/rmagic.py", line 275, in Rpush
    self.r.assign(input, self.pyconverter(val))
  File "/Users/bgranger/anaconda/lib/python2.7/site-packages/rpy2/robjects/functions.py", line 86, in __call__
    return super(SignatureTranslatedFunction, self).__call__(*args, **kwargs)
  File "/Users/bgranger/anaconda/lib/python2.7/site-packages/rpy2/robjects/functions.py", line 31, in __call__
    new_args = [conversion.py2ri(a) for a in args]
  File "/Users/bgranger/anaconda/lib/python2.7/site-packages/rpy2/robjects/pandas2ri.py", line 28, in pandas2ri
    od[name] = ro.conversion.py2ri(values)
  File "/Users/bgranger/anaconda/lib/python2.7/site-packages/rpy2/robjects/pandas2ri.py", line 51, in pandas2ri
    res = original_conversion(obj)
  File "/Users/bgranger/anaconda/lib/python2.7/site-packages/rpy2/robjects/numpy2ri.py", line 58, in numpy2ri
    res = ro.default_py2ri(o)
  File "/Users/bgranger/anaconda/lib/python2.7/site-packages/rpy2/robjects/__init__.py", line 148, in default_py2ri
    raise(ValueError("Nothing can be done for the type %s at the moment." %(type(o))))
ValueError: Nothing can be done for the type <class 'pandas.core.series.Series'> at the moment.

Here is the second, which is followed by a segfault:

..........F..Qt internal error: qt_menu.nib could not be loaded. The .nib file should be placed in QtGui.framework/Versions/Current/Resources/  or in the resources directory of your application bundle.

And the third:

======================================================================
FAIL: test_list_dirs (IPython.html.services.notebooks.tests.test_notebooks_api.APITest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/bgranger/Documents/Computing/IPython/code/ipython/IPython/html/services/notebooks/tests/test_notebooks_api.py", line 175, in test_list_dirs
    self.assertEqual(dir_names, self.top_level_dirs)  # Excluding hidden dirs
AssertionError: Items in the first set but not the second:
u'unicode\u0301'
u'a\u030a b'
Items in the second set but not the first:
u'unicod\xe9'
u'\xe5 b'
    """Fail immediately, with the given message."""
>>  raise self.failureException("Items in the first set but not the second:\nu'unicode\\u0301'\nu'a\\u030a b'\nItems in the second set but not the first:\nu'unicod\\xe9'\nu'\\xe5 b'")

And the fourth:

======================================================================
ERROR: IPython.core.tests.test_pylabtools.test_figure_to_jpg
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/bgranger/anaconda/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/Users/bgranger/Documents/Computing/IPython/code/ipython/IPython/testing/decorators.py", line 225, in skipper_func
    return f(*args, **kwargs)
  File "/Users/bgranger/Documents/Computing/IPython/code/ipython/IPython/core/tests/test_pylabtools.py", line 67, in test_figure_to_jpg
    jpg = pt.print_figure(fig, 'jpg', quality=50)[:100].lower()
  File "/Users/bgranger/Documents/Computing/IPython/code/ipython/IPython/core/pylabtools.py", line 127, in print_figure
    fig.canvas.print_figure(bytes_io, **kw)
  File "/Users/bgranger/anaconda/lib/python2.7/site-packages/matplotlib/backend_bases.py", line 2220, in print_figure
    **kwargs)
  File "/Users/bgranger/anaconda/lib/python2.7/site-packages/matplotlib/backend_bases.py", line 2018, in print_jpg
    return image.save(filename_or_obj, format='jpeg', **options)
  File "/Users/bgranger/anaconda/lib/python2.7/site-packages/PIL/Image.py", line 1439, in save
    save_handler(self, fp, filename)
  File "/Users/bgranger/anaconda/lib/python2.7/site-packages/PIL/JpegImagePlugin.py", line 471, in _save
    ImageFile._save(im, fp, [("jpeg", (0,0)+im.size, 0, rawmode)])
  File "/Users/bgranger/anaconda/lib/python2.7/site-packages/PIL/ImageFile.py", line 476, in _save
    fh = fp.fileno()
UnsupportedOperation: fileno

[takluyver]

I've also seen the first - I guess rpy2 is broken at the moment.

[takluyver]

Yep, a change in pandas broke rpy2's conversion machinery: https://bitbucket.org/lgautier/rpy2/issue/173/pandasseries-change-breaks-rpy2

[takluyver]

...and updating rpy2 fixed it for me.

[ellisonbg]

Let me try that.

On Mon, Mar 3, 2014 at 2:41 PM, Thomas Kluyver notifications@github.comwrote:

...and updating rpy2 fixed it for me.

Reply to this email directly or view it on GitHubhttps://github.com//issues/5264#issuecomment-36570013
.

Brian E. Granger
Cal Poly State University, San Luis Obispo
bgranger@calpoly.edu and ellisonbg@gmail.com

[minrk]

Why are there any tests for rmagic still in IPython? Shouldn't they be removed, since it is not our module anymore?

[ellisonbg]

I was wondering about that myself. I am +1 on removing these tests.

On Mon, Mar 3, 2014 at 2:53 PM, Min RK notifications@github.com wrote:

Why are there any tests for rmagic still in IPython? Shouldn't they be
removed, since it is not our module anymore?

Reply to this email directly or view it on GitHubhttps://github.com//issues/5264#issuecomment-36571329
.

Brian E. Granger
Cal Poly State University, San Luis Obispo
bgranger@calpoly.edu and ellisonbg@gmail.com

[takluyver]

Well, we haven't removed the module yet - I don't know what state it's in in rpy2. @davclark, can you update us? Is rmagic in a usable state in rpy2, and how long ago was it released?

[ellisonbg]

The notebook_api test is fixed by #5267

[davclark]

while the version in rpy2 has (I think) some fixes that are not in ipython, rpy2 2.4.0 is not yet released. So, until that point, probably best to keep things in IPython. That said, maybe it's time to release 2.4... The main blocker for me is that I still haven't ported the documentation over.

[takluyver]

For rmagic? I thought the only documentation of it was the docstrings, and we just assembled them into a Sphinx page.

[davclark]

Ah - lovely! Indeed, the docs have been copied over in the docstrings. We
just need to set them up so they build properly.

D

On Mon, Mar 3, 2014 at 4:45 PM, Thomas Kluyver notifications@github.comwrote:

For rmagic? I thought the only documentation of it was the docstrings, and
we just assembled them into a Sphinx page.

Reply to this email directly or view it on GitHubhttps://github.com//issues/5264#issuecomment-36579833
.

[takluyver]

So just to be clear: rmagic didn't go into any 2.3.x version of rpy2, so it's not released just yet?