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conda环境使用rpy2时如何指定加载conda安装的R而非系统R

太长不看版

我能否配置rpy2,使其加载conda安装的R而非系统安装的R?

问题描述

我运行rpy2时调用的是系统安装的R,但却会从我的conda R安装路径中检索和加载库,这会引发包括段错误(segfault)在内的诸多副作用。

问题复现

我使用的Ubuntu 18服务器上由管理员预装了R,我想搭配使用conda、Python和rpy2,以便灵活选择各工具的版本。
我处于名为(rnvp)的conda环境中,rpy2识别到了conda安装的4.0.5版本R,但rpy2.robjects库却加载了版本为4.0.3的系统R。
运行rpy2内置的环境检查脚本得到如下输出:

(rnvp) ludhu126@hyperion:~/real-nvp/real-nvp$ python
Python 3.9.6 (default, Aug 18 2021, 19:38:01) 
[GCC 7.5.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import rpy2.robjects as ro
During startup - Warning messages:
1: package ‘methods’ was built under R version 4.0.5 
2: package ‘datasets’ was built under R version 4.0.5 
3: package ‘utils’ was built under R version 4.0.5 
4: package ‘grDevices’ was built under R version 4.0.5 
5: package ‘graphics’ was built under R version 4.0.5 
6: package ‘stats’ was built under R version 4.0.5 
>>> print(ro.r)
<rpy2.robjects.R object at 0x7f8f16ece8b0>
platform: x86_64-pc-linux-gnu
arch: x86_64
os: linux-gnu
system: x86_64, linux-gnu
status: 
major: 4
minor: 0.3
year: 2020
month: 10
day: 10
svn rev: 79318
language: R
version.string: R version 4.0.3 (2020-10-10)
nickname: Bunny-Wunnies Freak Out
>>> import rpy2.situation
>>> for row in rpy2.situation.iter_info():
...     print(row)
... 
rpy2 version:
3.4.5
Python version:
3.9.6 (default, Aug 18 2021, 19:38:01) 
[GCC 7.5.0]
Looking for R's HOME:
    Environment variable R_HOME: /home/ludhu126/miniconda3/envs/rnvp/lib/R
    Calling `R RHOME`: /home/ludhu126/miniconda3/envs/rnvp/lib/R
    Environment variable R_LIBS_USER: None
R's additions to LD_LIBRARY_PATH:

R version:
    In the PATH: R version 4.0.5 (2021-03-31) -- "Shake and Throw"
    Loading R library from rpy2: OK
Additional directories to load R packages from:
None
C extension compilation:
  include:
  ['/home/ludhu126/miniconda3/envs/rnvp/lib/R/include']
  libraries:
  ['R', 'pcre2-8', 'lzma', 'bz2', 'z', 'rt', 'dl', 'm', 'iconv', 'icuuc', 'icui18n']
  library_dirs:
  ['/home/ludhu126/miniconda3/envs/rnvp/lib', '/home/ludhu126/miniconda3/envs/rnvp/lib/R/lib', '/home/ludhu126/miniconda3/envs/rnvp/lib']
  extra_compile_args:
  []
  extra_link_args:
  ['-Wl,--export-dynamic', '-fopenmp', '-Wl,-O2', '-Wl,--sort-common', '-Wl,--as-needed', '-Wl,-z,relro', '-Wl,-z,now', '-Wl,--disable-new-dtags', '-Wl,--gc-sections', '-Wl,-rpath,/home/ludhu126/miniconda3/envs/rnvp/lib', '-Wl,-rpath-link,/home/ludhu126/miniconda3/envs/rnvp/lib']

终端指向的conda R安装版本确实为4.0.5:

(rnvp) ludhu126@hyperion:~/real-nvp/real-nvp$ which R
/home/ludhu126/miniconda3/envs/rnvp/bin/R
(rnvp) ludhu126@hyperion:~/real-nvp/real-nvp$ R --version
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-conda-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
https://www.gnu.org/licenses/.

退出rnvp环境后,默认调用的是位于/usr/lib/R的4.0.3版本系统R:

(rnvp) ludhu126@hyperion:~/real-nvp/real-nvp$ conda activate base
(base) ludhu126@hyperion:~/real-nvp/real-nvp$ which R
/usr/bin/R
(base) ludhu126@hyperion:~/real-nvp/real-nvp$ R --version
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
https://www.gnu.org/licenses/.
核心问题

我能否配置rpy2使其加载conda安装的R?

相近问题参考
  • 有提问诉求为使用本地安装的R而非conda安装的R,且针对Python 2.7版本,与本问题诉求相反
  • 有提问提及rpy2安装失败、lapack动态库绑定失败、R_HOME变量未配置等问题,本问题不存在上述情况
  • 有提问提到PATH变量用于解析R安装路径,但本问题中which R输出显示PATH配置无问题
  • 有提问涉及错误加载R库的问题,本问题中R库可正常从conda路径加载,不存在该问题
  • 有提问给出的解决方案为卸载系统R安装包,本问题提问者无服务器管理员权限无法执行该操作

内容的提问来源于stack exchange,提问作者LudvigH

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最近更新时间:2026.10.06 08:18:00