如何将 R conda env 连接到 jupyter notebook [英] How to connect R conda env to jupyter notebook

问题描述

我正在使用以下代码创建 conda 环境

I am creating conda environment using following code

 conda create --prefix r_venv_conda r=3.3  r-essentials  r-base --y

然后我通过跟随

 conda activate r_venv_conda/

然后我尝试运行 Jupyter Notebook(通过运行 jupyter notebook 来运行 jupyter 希望能连接 R env.但是，我收到以下错误

Then I tried to run Jupyter Notebook (by running jupyter notebook to run jupyter hoping that will connect R env. However, I am getting following error

Traceback (most recent call last):
  File "/home/Documents/project/r_venv_conda/bin/jupyter-notebook", line 7, in <module>
    from notebook.notebookapp import main
  File "/home/Documents/project/r_venv_conda/lib/python3.6/site-packages/notebook/__init__.py", line 25, in <module>
    from .nbextensions import install_nbextension
  File "/home/Documents/project/r_venv_conda/lib/python3.6/site-packages/notebook/nbextensions.py", line 26, in <module>
    from .config_manager import BaseJSONConfigManager
  File "/home/Documents/project/r_venv_conda/lib/python3.6/site-packages/notebook/config_manager.py", line 14, in <module>
    from traitlets.config import LoggingConfigurable
  File "/home/Documents/project/r_venv_conda/lib/python3.6/site-packages/traitlets/config/__init__.py", line 6, in <module>
    from .application import *
  File "/home/Documents/project/r_venv_conda/lib/python3.6/site-packages/traitlets/config/application.py", line 38, in <module>
    import api.helper.background.config_related
ModuleNotFoundError: No module named 'api'

我该如何解决这个问题?

How can I fix this issue?

推荐答案

Jupyter 不会自动识别 Conda 环境，无论是否激活.

Jupyter does not automatically recognize Conda environments, activated or not.

首先，对于作为内核运行的环境，它需要安装适当的内核包.在这种情况下，就是r-irkernel，所以你需要运行

First, for an environment to run as a kernel, it needs to have the appropriate kernel package installed. In this case, that is r-irkernel, so you need to run

conda install -n r_venv_conda r-irkernel

对于 Python 内核，它是 ipykernel.

For Python kernels, it's ipykernel.

其次，内核需要注册到 Jupyter.如果您通过 Conda 安装了 Jupyter(比如在 Anaconda base 环境中)，那么我建议使用 nb_conda_kernels 包，它可以自动发现内核就绪的 Conda-envs.这必须安装在安装了 jupyter 的环境中(你只需要一个！)，例如，如果这是 base，那么

Second, kernels need to be registered with Jupyter. If you have Jupyter installed via Conda (say in an Anaconda base env), then I recommend using the nb_conda_kernels package, which enables auto-discovery of kernel-ready Conda-envs. This must be installed in the env that has jupyter installed (you only need one!), for example, if this is base, then

conda install -n base nb_conda_kernels

请阅读文档了解详情.

如果您使用的是系统级安装的 Jupyter(即不是由 Conda 安装的)，那么您需要手动注册您的内核.

If you are using a system-level installation of Jupyter (i.e., not installed by Conda), then you need to manually register your kernel.

conda activate r_venv_conda
Rscript -e 'IRkernel::installspec(name="ir33", displayname="R 3.3")'

您可以在其中为 name 和 displayname 设置自己的值.查看 IRkernel 了解详情.

where you can set your own values for name and displayname. See IRkernel for details.

如果使用安装了 Conda 的 Jupyter，它只需要安装在单个环境中.这是在运行 jupyter notebook 之前应该激活的环境.运行后，您可以选择要使用的内核.

If using a Conda-installed Jupyter, again, it only needs to be installed in a single env. This is the env that should be activated before running jupyter notebook. Once running, then you select the kernel you wish to use.

这篇关于如何将 R conda env 连接到 jupyter notebook的文章就介绍到这了，希望我们推荐的答案对大家有所帮助，也希望大家多多支持IT屋！