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python - GenomicFeatures 安装和加载错误“通过 Python3 rpy2 没有名为‘GenomicFeatures’的包”

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’

我正在使用 Python3.8 和 conda env for rpy2，我该如何解决这个问题？

先感谢您。

标签： pythonrrpy2

解决方案

值得庆幸的是，我能够解决我GenomicFeatures在 python3.8 中通过安装和加载 Bioconductor 时遇到的问题rpy2 。我花了几个小时才找到该解决方案，所以我想分享我所做的解决方案，以便最终得到谁同样的问题可以找到它。

基本上，在跟踪错误日志时，实际错误似乎指向这个特定的错误行：

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

当我进行一些研究时，我发现了这个特定的 StackOverflow 问题无法将包 XML 安装到 R，他们无法将包 xml 安装到 R 并且 GenomicFeatures 需要该包，因此我在安装 BiocManager 之前添加了以下行（以防 BiocManager 不是安装）：

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

这个答案取自上述 StackOverflow 问题的@Jaeyoung Chun。

运行修改后的代码（见下文）后，我能够安装和加载这样的包，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 )')

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