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ipython - 如何解决解析错误？使用 rpy2 时

问题描述

测试一些非常简单的 rpy2 示例代码，但使用 ggplot 在最后一个单元格中经常遇到一些错误消息。运行其他一些 R 代码或库似乎可以工作，所以我不知道为什么我一直看到这条消息。在 Google Colab 上测试了代码并且也可以工作。也许是 rpy2 设置或 ipython 问题？

%load_ext rpy2.ipython
import pandas as pd
import numpy as np
df = pd.DataFrame({
    'cups_of_coffee': [0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
    'productivity': [2, 5, 6, 8, 9, 8, 0, 1, 0, -1]
})
df.transpose()

%%R -i df
head(df)

%%R -i df
library(ggplot2)
ggplot(df, aes(x=reorder(cups_of_coffee,productivity), y=productivity)) + geom_col() + coord_flip()

这是错误消息：

RParsingError: Parsing status not OK - PARSING_STATUS.PARSE_ERROR
---------------------------------------------------------------------------
RParsingError                             Traceback (most recent call last)
<ipython-input-6-dcdd226012b5> in <module>
----> 1 get_ipython().run_cell_magic('R', '-w 800 --type=cairo', '\r\ncat("Running an R code cell.\\n")\r\n\r\nlibrary(ggplot2)\r\n\r\np <- ggplot(dataf) +\r\n     aes(x=longd,\r\n         y=latd,\r\n         color=population_total,\r\n         size=area_total_km2) +\r\n     geom_point(alpha=0.5) +\r\n     scale_x_continuous(\'Longitude\') +\r\n     scale_y_continuous(\'Latitude\') +\r\n     scale_size(range=c(1, 18)) +\r\n     ggtitle(\'California Cities: Area and Population\') +\r\n     theme_light(base_size=16)\r\nprint(p)\n')

C:\Software\anaconda\envs\work\lib\site-packages\IPython\core\interactiveshell.py in run_cell_magic(self, magic_name, line, cell)
   2397             with self.builtin_trap:
   2398                 args = (magic_arg_s, cell)
-> 2399                 result = fn(*args, **kwargs)
   2400             return result
   2401 

<decorator-gen-122> in R(self, line, cell, local_ns)

C:\Software\anaconda\envs\work\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:\Software\anaconda\envs\work\lib\site-packages\rpy2\ipython\rmagic.py in R(self, line, cell, local_ns)
    761                     return_output = False
    762             else:
--> 763                 text_result, result, visible = self.eval(code)
    764                 text_output += text_result
    765                 if visible:

C:\Software\anaconda\envs\work\lib\site-packages\rpy2\ipython\rmagic.py in eval(self, code)
    266             try:
    267                 # Need the newline in case the last line in code is a comment.
--> 268                 value, visible = ro.r("withVisible({%s\n})" % code)
    269             except (ri.embedded.RRuntimeError, ValueError) as exception:
    270                 # Otherwise next return seems to have copy of error.

C:\Software\anaconda\envs\work\lib\site-packages\rpy2\robjects\__init__.py in __call__(self, string)
    435 
    436     def __call__(self, string):
--> 437         p = rinterface.parse(string)
    438         res = self.eval(p)
    439         return conversion.rpy2py(res)

C:\Software\anaconda\envs\work\lib\site-packages\rpy2\rinterface_lib\conversion.py in _(*args, **kwargs)
     43 def _cdata_res_to_rinterface(function):
     44     def _(*args, **kwargs):
---> 45         cdata = function(*args, **kwargs)
     46         # TODO: test cdata is of the expected CType
     47         return _cdata_to_rinterface(cdata)

C:\Software\anaconda\envs\work\lib\site-packages\rpy2\rinterface.py in parse(text, num)
    101     robj = StrSexpVector([text])
    102     with memorymanagement.rmemory() as rmemory:
--> 103         res = _rinterface._parse(robj.__sexp__._cdata, num, rmemory)
    104     return res
    105 

C:\Software\anaconda\envs\work\lib\site-packages\rpy2\rinterface_lib\_rinterface_capi.py in _parse(cdata, num, rmemory)
    650     # PARSE_EOF
    651     if status[0] != openrlib.rlib.PARSE_OK:
--> 652         raise RParsingError('Parsing status not OK',
    653                             status=PARSING_STATUS(status[0]))
    654     return res

RParsingError: Parsing status not OK - PARSING_STATUS.PARSE_ERROR

标签： ipythonjupyter-labrpy2

解决方案

解决方法是这样的：

get_ipython().run_cell_magic(
"R",
"-i df",
'''
library(ggplot2)
ggplot(df, aes(x=reorder(cups_of_coffee,productivity), y=productivity)) +
geom_col() +
coord_flip()
'''
)

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