外部函数调用中的 rpy2 自动 NumPy 转换 NA/NaN/Inf

Question

当尝试使用简单数据从 python 调用 BayesTree R 包时，我收到错误 "NA/NaN/Inf in foreign function call"，即使所有数据都是正实数。

源代码

import numpy as np
# R interface for python
import rpy2
# For importing R packages
from rpy2.robjects.packages import importr
# Activate conversion from numpy to R
import rpy2.robjects.numpy2ri
rpy2.robjects.numpy2ri.activate()

train_x_py = np.array([[0.0, 0.0],
                       [0.0, 1.0],
                       [1.0, 1.0]])

# Any 3-length float vector fails for training y
train_y_py = np.array([1.0,2.0,3.0])

test_x_py  = np.array([[0.2, 0.0],
                       [0.2, 0.2],
                       [1.0, 0.2]])

# Create R versions of the training and testing data
train_x = rpy2.robjects.r.matrix(train_x_py, nrow=3, ncol=2)
train_y = rpy2.robjects.vectors.FloatVector(train_y_py)
test_x = rpy2.robjects.r.matrix(test_x_py, nrow=3, ncol=2)

print(train_x)
print(train_y)
print(test_x)

BayesTree = importr('BayesTree')
response = BayesTree.bart(train_x, train_y, test_x,
                          verbose=False, ntree=100)

# The 7th return value is the estimated response
response = response[7]

print(response)

代码输出/错误

     [,1] [,2]
[1,]    0    0
[2,]    0    1
[3,]    1    1

[1] 1 2 3

     [,1] [,2]
[1,]  0.2  0.0
[2,]  0.2  0.2
[3,]  1.0  0.2

Traceback (most recent call last):
  File "broken_rpy2.py", line 32, in <module>
    verbose=False, ntree=100)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/rpy2/robjects/functions.py", line 178, in __call__
    return super(SignatureTranslatedFunction, self).__call__(*args, **kwargs)
  File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/rpy2/robjects/functions.py", line 106, in __call__
    res = super(Function, self).__call__(*new_args, **new_kwargs)
rpy2.rinterface.RRuntimeError: Error in (function (x.train, y.train, x.test = matrix(0, 0, 0), sigest = NA,  : 
  NA/NaN/Inf in foreign function call (arg 7)

它所指的第 32 行的错误是：

response = BayesTree.bart(train_x, train_y, test_x,
                          verbose=False, ntree=100)

系统设置

操作系统： Mac OS X 塞拉利昂 10.12.6

Python 版本: Python3.6.1

R版本： R 3.4.1

Python 包： 点子 9.0.1， rpy2 2.8.6, 麻木 1.13.0

问题

这是我自己的用户错误，还是 rpy2 中的错误？

Answer 1

这是 R 包 "BayesTree" 中的问题。您可以使用以下代码直接在 R 中重现该问题（假设您已经安装了 BayesTree 包）。

train_x = matrix(c(0,0,1,0,1,1),nrow=3,ncol=2)
train_y = as.vector(c(1,2,3))
test_x = matrix(c(.2,.2,1.,.0,.2,.2),nrow=3,ncol=2)
result = bart(train_x,train_y,test_x,verbose=FALSE,ntree=100)

外部函数调用中的 rpy2 自动 NumPy 转换 NA/NaN/Inf

rpy2 automatic NumPy conversion NA/NaN/Inf in foreign function call

numpy

rpy2

python-3.x

源代码

代码输出/错误

问题