CODEWITHSUNDEEP
pythonrrpy2
user5739619
user5739619

Reputation: 1838

rpy2 Conflict when converting R symbols in the package to Python symbols

I simply tried the following:

import rpy2
import rpy2.robjects as RObjects
from rpy2.robjects.packages import importr

princurve = importr('princurve', robject_translations = {"plot_principal_curve": "plot.principal.curve"})
princurve = importr('princurve', robject_translations = {"points_principal_curve": "points.principal.curve"})

and got this error

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Users\me\AppData\Local\Continuum\anaconda3\lib\site-packages\rpy2\robjects\packages.py", line 498, in importr
    symbol_resolve=symbol_resolve)
  File "C:\Users\me\AppData\Local\Continuum\anaconda3\lib\site-packages\rpy2\robjects\packages.py", line 202, in __init__
    self.__fill_rpy2r__(on_conflict=on_conflict)
  File "C:\Users\me\AppData\Local\Continuum\anaconda3\lib\site-packages\rpy2\robjects\packages.py", line 328, in __fill_rpy2r__
    .__fill_rpy2r__(on_conflict=on_conflict))
  File "C:\Users\me\AppData\Local\Continuum\anaconda3\lib\site-packages\rpy2\robjects\packages.py", line 238, in __fill_rpy2r__
    exception)
  File "C:\Users\me\AppData\Local\Continuum\anaconda3\lib\site-packages\rpy2\robjects\packages_utils.py", line 120, in _fix_map_symbols
    raise exception(msg)
rpy2.robjects.packages.LibraryError: Conflict when converting R symbols in the package "princurve" to Python symbols:
-lines_principal_curve -> lines.principal.curve, lines.principal_curve
- plot_principal_curve -> plot.principal.curve, plot.principal_curve
- points_principal_curve -> points.principal.curve, points.principal_curve
To turn this exception into a simple warning use the parameter `on_conflict="warn"`

can anyone help?

Upvotes: 1

Views: 284

Answers (1)

krassowski
krassowski

Reputation: 15379

You were almost there! In robject_translations you need to provide R name -> Python name mapping, but your dictionary seemed to be the other way around. You also need to have all the mappings in a single dictionary. To make it super clear, you can resolve the conflicts like this:

princurve_example_1 = importr(
    "princurve",
    robject_translations={
        "plot.principal.curve": "plot_dot_principal_dot_curve", 
        "lines.principal.curve": "lines_dot_principal_dot_curve", 
        "points.principal.curve": "points_dot_principal_dot_curve",
        # optional (if omitted, you will get them under plot_principal_curve, etc.):
        "plot.principal_curve": "plot_dot_principal_curve",
        "lines.principal_curve": "lines_dot_principal_curve",
        "points.principal_curve": "points_dot_principal_curve"
    }
)
# then, after creating the curve and storing it in curve variable:
princurve_example_1.plot_dot_principal_dot_curve(curve)
# or
princurve_example_1.plot_dot_principal_curve(curve)

However, after consulting the pincurve documentation I see that the principal.curve is deprecated and you should use principal_curve instead (good to see more R packages finally moving to the convention of using underscores in function and variable names when possible!); therefore you can just do:

princurve = importr(
    "princurve",
    robject_translations={
        "plot.principal.curve": "plot_principal_curve_deprecated", 
        "lines.principal.curve": "lines_principal_curve_deprecated", 
        "points.principal.curve": "points_principal_curve_deprecated",
    }
)
# auto-generated from "plot.principal_curve"
princurve.plot_principal_curve(curve)
# manually mapped from "plot.principal.curve"
princurve.plot_principal_curve_deprecated(curve)

Upvotes: 2

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