GenomicFeatures安装和加载错误“通过Python3 rpy2没有名为'GenomicFeatures的软件包”

编程问答 2022-08-13

问题描述

我正在尝试通过python rpy2使用Bioconductor GenomicFeatures对象和方法，因此当我执行以下代码时：

import rpy2.robjects as robjects

robjects.r('install.packages("XML",'
        'repos="http://cran.r-project.org")')
robjects.r('install.packages("BiocManager",'
       'repos="http://cran.r-project.org")')
robjects.r('BiocManager::install("GenomicFeatures ")')

robjects.r('library(GenomicFeatures )')

我得到相应的错误：

ERROR: dependency ‘XML’ is not available for package ‘rtracklayer’ 
* removing ‘/Users/nalomran/opt/anaconda3/envs/ReQTL/lib/R/library/rtracklayer’
ERROR: dependency ‘XML’ is not available for package ‘biomart’
* removing ‘/Users/nalomran/opt/anaconda3/envs/ReQTL/lib/R/library/biomart’
ERROR: dependencies ‘rtracklayer’,‘biomart’ are not available for package ‘GenomicFeatures’
* removing ‘/Users/nalomran/opt/anaconda3/envs/ReQTL/lib/R/library/GenomicFeatures’
R[write to console]: Error in library(GenomicFeatures) : 
 there is no package called ‘GenomicFeatures’
R[write to console]: 1: package ‘XML’ is not available (for R version 3.6.3) 
R[write to console]:  installation of package ‘GenomicFeatures’ had non-zero exit status

Traceback (most recent call last):
File "annotate_cis_trans.py",line 64,in <module>
robjects.r('library(GenomicFeatures)')
File "/Users/nalomran/opt/anaconda3/envs/ReQTL/lib/python3.8/site-packages/rpy2/robjects/__init__.py",line 416,in __call__
res = self.eval(p)
File "/Users/nalomran/opt/anaconda3/envs/ReQTL/lib/python3.8/site-packages/rpy2/robjects/functions.py",line 197,in __call__
return (super(SignatureTranslatedFunction,self)
File "/Users/nalomran/opt/anaconda3/envs/ReQTL/lib/python3.8/site-packages/rpy2/robjects/functions.py",line 125,in __call__
res = super(Function,self).__call__(*new_args,**new_kwargs)
File "/Users/nalomran/opt/anaconda3/envs/ReQTL/lib/python3.8/site-packages/rpy2/rinterface_lib/conversion.py",line 44,in _
cdata = function(*args,**kwargs)
File "/Users/nalomran/opt/anaconda3/envs/ReQTL/lib/python3.8/site-packages/rpy2/rinterface.py",line 621,in __call__
raise embedded.RRuntimeError(_rinterface._geterrmessage())
rpy2.rinterface_lib.embedded.RRuntimeError: Error in         library(GenomicFeatures) : 
there is no package called ‘GenomicFeatures’

我正在将python3.8与conda env一起用于rpy2，如何解决此问题？

谢谢。

解决方法

非常感谢，我能够通过GenomicFeatures在python3.8中解决安装和加载Bioconductor rpy2 所遇到的问题。我花了几个小时才能找到该解决方案，所以我想分享一下我所做的解决方案，以便最终遇到相同问题的人也可以找到它。

基本上，在跟踪错误日志时，似乎实际错误指向此特定错误行：

R[write to console]: 1: package ‘XML’ is not available (for R version 3.6.3)

在进行一些研究时，我发现了这个特定的StackOverflow问题Cannot install package XML to R，他们无法将软件包xml安装到R，而GenomicFeatures需要该软件包，因此我在安装BiocManager之前添加了以下内容（以防BiocManager未安装）：

robjects.r('install.packages("XML",repos = "http://www.omegahat.net/R")')

此答案来自上述StackOverflow问题的@Jaeyoung Chun。

运行修改后的代码（在下面找到）后，我能够安装和加载这样的软件包，而没有任何错误或问题：

import rpy2.robjects as robjects

robjects.r('install.packages("XML",repos = "http://www.omegahat.net/R")')
robjects.r('install.packages("BiocManager",'
   'repos="http://cran.r-project.org")')
robjects.r('BiocManager::install("GenomicFeatures ")')

robjects.r('library(GenomicFeatures )')
pythonrrrpy2