Rmagics and Rpy2 broken on Windows 10. All computational results go out to Windows Console not Jupyter output cells. The RWinOut hack no longer works.
As soon as I use RWinout, I get a fatal error that requires me to restart Jupyter NB server, it kills the Jupyter Notebook Python kernel.
I have tried installing in 3 different conda environments, using conda alone, Anaconda Navigator, or pip. It always comes back to same code error after all packages are installed. There are a few people offering step-by-step manual procedures for installing R, then rpy2, then special supporting packages, then Jupyter, etc. That is too tedious for regular data scientists and analysts.
Rpy2 needs to be rewritten to support Windows 10.
I want this to work, because Python-R NBs with Plotly-Dash, Jupyter NB extensions like Qgrid, and others make nice combinations for richly interactive data science applications, without having to run additional servers like RShiny or others.
I can load rpy2 and use its functions and objects, but not R cell magics.
#Here's my version information:
R version: ('3', '6.0', '', 76424) Rpy2 veresion: 2.9.4 Python version 3.7.4: jupyter core : 4.5.0 jupyter-notebook : 6.0.1 qtconsole : 4.5.5 ipython : 7.8.0 ipykernel : 5.1.2 jupyter client : 5.3.3 jupyter lab : 1.1.4 nbconvert : 5.6.0 ipywidgets : 7.5.1 nbformat : 4.4.0 traitlets : 4.3.3 7.8.0 Everything was installed in this environment using Anaconda Navigator, or conda from the command console, unless pip install was required for something that didn't have a conda package.
Conda is the strongly preferred package manager for anything to do with the Jupyter ecosystem, because it is designed to be language-agnostic.
#The R inline magics produce output into the Jupyter Output Cell, but R cell magics put the results out to the Windows Console that I used to start the Jupyter Notebook.
As soon as I run RWinOut, the errors below show up and the kernel dies.
I also get the following messages in the Windows Console:
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.8.0 (2020-02-14 07:10:20 UTC) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.23.0 successfully loaded. See ?R.oo for help.
Attaching package: 'R.oo'
The following object is masked from 'package:R.methodsS3':
throw
The following objects are masked from 'package:methods':
getClasses, getMethods
The following objects are masked from 'package:base':
attach, detach, load, save
R.utils v2.9.2 successfully loaded. See ?R.utils for help.
Attaching package: 'R.utils'
The following object is masked from 'package:utils':
timestamp
The following objects are masked from 'package:base':
cat, commandArgs, getOption, inherits, isOpen, nullfile, parse,
warnings
The strange thing is that inline R magics work okay, but NOT Cell magics.
When I run RWinOut as follows:
!curl -O "https://raw.githubusercontent.com/vitorcurtis/RWinOut/master/RWinOut.py"
%reload_ext RWinOut
I get a long string of errors (below). It also kills the Python kernel for the Jupyter NB.
The rpy2.ipython extension is already loaded. To reload it, use: %reload_ext rpy2.ipython
ValueError Traceback (most recent call last)
<ipython-input-25-49c9701f263c> in <module>
----> 1 get_ipython().run_line_magic('reload_ext', 'RWinOut')
C:\ProgramData\Anaconda3\lib\site-packages\IPython\core\interactiveshell.py in run_line_magic(self, magic_name, line, _stack_depth)
2312 kwargs['local_ns'] = sys._getframe(stack_depth).f_locals
2313 with self.builtin_trap:
-> 2314 result = fn(*args, **kwargs)
2315 return result
2316
<C:\ProgramData\Anaconda3\lib\site-packages\decorator.py:decorator-gen-67> in reload_ext(self, module_str)
C:\ProgramData\Anaconda3\lib\site-packages\IPython\core\magic.py in <lambda>(f, *a, **k)
185 # but it's overkill for just that one bit of state.
186 def magic_deco(arg):
--> 187 call = lambda f, *a, **k: f(*a, **k)
188
189 if callable(arg):
C:\ProgramData\Anaconda3\lib\site-packages\IPython\core\magics\extension.py in reload_ext(self, module_str)
61 if not module_str:
62 raise UsageError('Missing module name.')
---> 63 self.shell.extension_manager.reload_extension(module_str)
C:\ProgramData\Anaconda3\lib\site-packages\IPython\core\extensions.py in reload_extension(self, module_str)
128 self.loaded.add(module_str)
129 else:
--> 130 self.load_extension(module_str)
131
132 def _call_load_ipython_extension(self, mod):
C:\ProgramData\Anaconda3\lib\site-packages\IPython\core\extensions.py in load_extension(self, module_str)
85 dir=compress_user(self.ipython_extension_dir)))
86 mod = sys.modules[module_str]
---> 87 if self._call_load_ipython_extension(mod):
88 self.loaded.add(module_str)
89 else:
C:\ProgramData\Anaconda3\lib\site-packages\IPython\core\extensions.py in _call_load_ipython_extension(self, mod)
132 def _call_load_ipython_extension(self, mod):
133 if hasattr(mod, 'load_ipython_extension'):
--> 134 mod.load_ipython_extension(self.shell)
135 return True
136
c:\Users\rlysakow\Desktop\00-PayEquity-WIP\RWinOut.py in load_ipython_extension(ip)
39 # loading magic and libraries
40 ip.run_line_magic('load_ext', 'rpy2.ipython')
---> 41 ip.run_line_magic('R', 'library(R.utils)')
42 ip.run_line_magic('config', 'Application.verbose_crash=True')
43
C:\ProgramData\Anaconda3\lib\site-packages\IPython\core\interactiveshell.py in run_line_magic(self, magic_name, line, _stack_depth)
2312 kwargs['local_ns'] = sys._getframe(stack_depth).f_locals
2313 with self.builtin_trap:
-> 2314 result = fn(*args, **kwargs)
2315 return result
2316
<C:\ProgramData\Anaconda3\lib\site-packages\decorator.py:decorator-gen-133> in R(self, line, cell, local_ns)
C:\ProgramData\Anaconda3\lib\site-packages\IPython\core\magic.py in <lambda>(f, *a, **k)
185 # but it's overkill for just that one bit of state.
186 def magic_deco(arg):
--> 187 call = lambda f, *a, **k: f(*a, **k)
188
189 if callable(arg):
C:\ProgramData\Anaconda3\lib\site-packages\rpy2\ipython\rmagic.py in R(self, line, cell, local_ns)
755 if result is not ri.NULL:
756 with localconverter(converter) as cv:
--> 757 res = cv.ri2py(result)
758 return res
759
C:\ProgramData\Anaconda3\lib\functools.py in wrapper(*args, **kw)
838 '1 positional argument')
839
--> 840 return dispatch(args[0].__class__)(*args, **kw)
841
842 funcname = getattr(func, '__name__', 'singledispatch function')
C:\ProgramData\Anaconda3\lib\site-packages\rpy2\robjects\pandas2ri.py in ri2py_vector(obj)
137 @ri2py.register(SexpVector)
138 def ri2py_vector(obj):
--> 139 res = numpy2ri.ri2py(obj)
140 return res
141
C:\ProgramData\Anaconda3\lib\functools.py in wrapper(*args, **kw)
838 '1 positional argument')
839
--> 840 return dispatch(args[0].__class__)(*args, **kw)
841
842 funcname = getattr(func, '__name__', 'singledispatch function')
C:\ProgramData\Anaconda3\lib\site-packages\rpy2\robjects\numpy2ri.py in ri2py_sexp(obj)
157 def ri2py_sexp(obj):
158 if (obj.typeof in _vectortypes) and (obj.typeof != VECSXP):
--> 159 res = numpy.asarray(obj)
160 else:
161 res = ro.default_converter.ri2py(obj)
C:\ProgramData\Anaconda3\lib\site-packages\numpy\core\numeric.py in asarray(a, dtype, order)
536
537 """
--> 538 return array(a, dtype, copy=False, order=order)
539
540
ValueError: Buffer for this type not yet supported.
I could not find any hacks or procedures to eliminate this last error.
I don't have time or skill right now to hack ipython extensions to get rpy2 to work.
Anyone have similar experiences with rpy2 ? How did you solve the problems?
