如何设置自定义 R 安装以在 Jupyter 中使用 rpy2？

Question

我有一个 conda 环境，我通过运行将其作为内核提供给我的 Jupyter 实例： python -m ipykernel install --user --name my-env-name --display-name "Python (my-env-name)"

在这个环境中，我想在 Jupyter 中使用 R，利用rpy2's%load_ext rpy2.ipython命令来启用%%R魔法。但是，rpy2使用的是我的全局 R，而不是安装在我的 conda 环境中的 R。我通过以下方式检查了我的 R 家：

%%R
R.home()

（我还可以检查情况%run -m rpy2.situation在Jupyter笔记本（源），然而，这似乎被打破rpy2版本之间的某个地方3.1.0和3.2.1......至少对我来说，被扔UnboundLocalError: local variable 'rpy2' referenced before assignment在3.1.0和它工作3.2.1）。

如何让我的 Jupyter 笔记本从我的 conda 环境加载 R 安装？

Answer 1

有两种方法可以解决这个问题，一种是本地的（针对单个 Jupyter 笔记本），另一种是全局的（针对内核本身）。两者都与设置R_HOME环境变量有关。

本地（来源）：在调用%load_ext rpy2.ipythonJupyter notebook之前，运行：

import os
os.environ['R_HOME'] = '/home/your/anaconda3/envs/myenv/lib/R' #path to your R installation

全局：通过以下方式找到您的内核目录：jupyter kernelspec list并编辑文件kernel.json. 通过添加更新 JSON: "env": {"R_HOME":"/home/your/anaconda3/envs/my-env-name/lib/R"}，然后重新启动内核（您可能还必须重新启动 Jupyter）。

更新（搞砸了LD_LIBRARY_PATH）

最近，我rpy2在使用以下命令设置新环境后再次尝试在 jupyter 中运行conda：

conda config --add channels conda-forge
conda config --set channel_priority strict
conda create -n myenv python=3.7
conda activate myenv
conda install r-essentials pandas rpy2

这次我在尝试%load_ext rpy2.ipython(Jupyter) 或简单地import rpy2.robjects(任何脚本)时遇到了以下问题：

>>> import rpy2.robjects                                            
Warning message:                                                    
package ‘methods’ was built under R version 3.6.3     
Error: package or namespace load failed for ‘stats’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/your/anaconda3/envs/myenv/lib/R/library/stats/libs/stats.so':                  
  /home/your/anaconda3/envs/myenv/lib/R/library/stats/libs/stats.so: undefined symbol: MARK_NOT_MUTABLE
During startup - Warning messages:                                                                                          
1: package ‘datasets’ was built under R version 3.6.3      
2: package ‘utils’ was built under R version 3.6.3                                                                     
3: package ‘grDevices’ was built under R version 3.6.3  
4: package ‘graphics’ was built under R version 3.6.3                                                                       
5: package ‘stats’ was built under R version 3.6.3          
6: package ‘stats’ in options("defaultPackages") was not found                                                       
R[write to console]: Error: package or namespace load failed for ‘tools’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/your/anaconda3/envs/myenv/lib/R/library/tools/libs/tools.so':
  /home/your/anaconda3/envs/myenv/lib/R/library/tools/libs/tools.so: undefined symbol: R_NewPreciousMSet

R[write to console]: Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/home/your/anaconda3/envs/myenv/lib/R/library/tools/libs/tools.so':
  /home/your/anaconda3/envs/myenv/lib/R/library/tools/libs/tools.so: undefined symbol: R_NewPreciousMSet

R[write to console]: In addition:                                      
R[write to console]: Warning message:                        

R[write to console]: package ‘tools’ was built under R version 3.6.3

Traceback (most recent call last):                          
  File "<stdin>", line 1, in <module>                    
  File "/home/your/anaconda3/envs/myenv/lib/python3.7/site-packages/rpy2/robjects/__init__.py", line 20, in <module>
    import rpy2.robjects.functions                                           
  File "/home/your/anaconda3/envs/myenv/lib/python3.7/site-packages/rpy2/robjects/functions.py", line 12, in <module>
    from rpy2.robjects import help                                   
  File "/home/your/anaconda3/envs/myenv/lib/python3.7/site-packages/rpy2/robjects/help.py", line 43, in <module>
    tools_ns = _get_namespace(StrSexpVector(('tools',)))          
  File "/home/your/anaconda3/envs/myenv/lib/python3.7/site-packages/rpy2/rinterface_lib/conversion.py", line 44, in _
    cdata = function(*args, **kwargs)                                     
  File "/home/your/anaconda3/envs/myenv/lib/python3.7/site-packages/rpy2/rinterface.py", line 621, in __call__
    raise embedded.RRuntimeError(_rinterface._geterrmessage())                            
rpy2.rinterface_lib.embedded.RRuntimeError: Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/home/your/anaconda3/envs/myenv/lib/R/library/tools/libs/tools.so':
  /home/your/anaconda3/envs/myenv/lib/R/library/tools/libs/tools.so: undefined symbol: R_NewPreciousMSet

问题似乎是一个搞砸了的 R “情况”（通过%run -m rpy2.situationJupyter 或仅python -m rpy2.situation在命令行上检查），它R's additions to LD_LIBRARY_PATH:指向和旧的、全局安装的 R 版本。

我不得不手动取消设置LD_LIBRARY_PATH来解决这个问题。该路径可以类似地设置/取消设置R_HOME。

PS：我在我的自定义（来自源代码）R 安装中找到R_HOME并LD_LIBRARY_PATH设置了它.bashrc。这显然混淆了 Jupyter 内核。不聪明 ;）

PPS：rpy2.situation仍然告诉我有一个Warning: The environment variable R_HOME differs from the default R in the PATH.：

Looking for R's HOME:
    Environment variable R_HOME: /home/your/anaconda3/envs/myenv/lib/R
    Calling `R RHOME`: /home/your/anaconda3/envs/jupyter-env/lib/R
    Environment variable R_LIBS_USER: None
    Warning: The environment variable R_HOME differs from the default R in the PATH.

这让我担心，R实际上默认为 Jupyter 安装安装了 R。因此，如果有人对此发表评论，我将不胜感激。