在 conda 虚拟环境中使用为 `R` 安装的软件包的 `rpy2`？

Question

我一直在努力保持我的环境不冗余和干净，所以我创建了一个R 环境并清除了我计算机上所有其他现有的Rs。

那个环境叫做r-conda，它在：

/Users/jespinoz/anaconda/envs/r-conda/bin/R

我意识到我没有安装 rpy2 并通过 conda 安装它想要安装新版本的 R 和所有我不想要的 r-essentials，因为我已经有了完美运行的 R 环境。

我意识到我可以为在 R conda 环境中关联的 Python 安装 rpy2：

source activate r-conda
pip install rpy2
source deactivate

但并非所有路径都排成一行

如何让rpy2 在我的r-conda 环境中识别我所有的R 关联文件和路径？

当我尝试导入包时找不到正确的文件：

os.environ['R_HOME'] = "/Users/jespinoz/anaconda/envs/r-conda/bin/R"
from rpy2.robjects.packages import importr
importr("dynamicTreeCut")

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-29-8b0a88dfe12d> in <module>()
      1 # os.environ['R_HOME'] = '/Users/jespinoz/anaconda/envs/r-conda/bin/'
      2 os.environ['R_HOME'] = "/Users/jespinoz/anaconda/envs/r-conda/bin/R"
----> 3 from rpy2.robjects.packages import importr
      4 importr("dynamicTreeCut")

/Users/jespinoz/anaconda/lib/python3.6/site-packages/rpy2/robjects/__init__.py in <module>()
     14 import itertools
     15 from datetime import datetime
---> 16 import rpy2.rinterface as rinterface
     17 import rpy2.rlike.container as rlc
     18 

/Users/jespinoz/anaconda/lib/python3.6/site-packages/rpy2/rinterface/__init__.py in <module>()
     90 del(os)
     91 
---> 92 from rpy2.rinterface._rinterface import (baseenv,
     93                                          emptyenv,
     94                                          endr,

ImportError: dlopen(/Users/jespinoz/anaconda/lib/python3.6/site-packages/rpy2/rinterface/_rinterface.cpython-36m-darwin.so, 2): Library not loaded: @rpath/R/lib/libR.dylib
  Referenced from: /Users/jespinoz/anaconda/lib/python3.6/site-packages/rpy2/rinterface/_rinterface.cpython-36m-darwin.so
  Reason: image not found

通过将其添加到我的~/.bash_profile 来修复该错误，但生成了一个类似的新错误： 我试了一下，错误改了：

export LD_LIBRARY_PATH="/Users/jespinoz/anaconda/envs/r-conda/lib/R/lib/:$LD_LIBRARY_PATH" 

>>> from rpy2.robjects.packages import importr
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/jespinoz/anaconda/lib/python3.6/site-packages/rpy2/robjects/__init__.py", line 16, in <module>
    import rpy2.rinterface as rinterface
  File "/Users/jespinoz/anaconda/lib/python3.6/site-packages/rpy2/rinterface/__init__.py", line 92, in <module>
    from rpy2.rinterface._rinterface import (baseenv,
ImportError: dlopen(/Users/jespinoz/anaconda/lib/python3.6/site-packages/rpy2/rinterface/_rinterface.cpython-36m-darwin.so, 2): Library not loaded: libicuuc.54.dylib
  Referenced from: /Users/jespinoz/anaconda/lib/python3.6/site-packages/rpy2/rinterface/_rinterface.cpython-36m-darwin.so
  Reason: image not found

所以我尝试了这个，然后得到了同样的错误：

export LD_LIBRARY_PATH="/Users/jespinoz/anaconda/envs/r-conda/lib/R/lib/:/Users/jespinoz/anaconda/pkgs/icu-54.1-0/lib/:$LD_LIBRARY_PATH"

如果我使用conda install rpy2，它想安装Python=3.5.2，即使我的主要 conda 环境的默认版本是Python=3.6。 @asmeurer 建议在我的r-conda 环境中安装rpy2 时指定Python=3.6，但现在它看起来像一个包冲突错误：

(r-conda) jespinozlt-osx:~ jespinoz$ conda install rpy2 python=3.6
Fetching package metadata .............
Solving package specifications: .


UnsatisfiableError: The following specifications were found to be in conflict:
  - python 3.6*
  - r-permute
  - rpy2
Use "conda info <package>" to see the dependencies for each package

Answer 1

你应该 conda install rpy2 而不是 pip 安装它。另外，保持环境激活。你应该 conda install python 和任何你想在同一个 R 环境中使用的 Python 包，这样一切都在一个环境中完成。