“安装和加载错误”；没有名为‘的包；基因组特征“；通过Python3 rpy2

我试图通过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 )')

我得到了相应的错误：

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’

错误：依赖项“XML”不可用于包“rtracklayer”
*删除“/Users/nalomran/opt/anaconda3/envs/ReQTL/lib/R/library/rtracklayer”
错误：依赖项“XML”不可用于包“biomaRt”
*删除“/Users/nalomran/opt/anaconda3/envs/ReQTL/lib/R/library/biomaRt”
错误：依赖项“rtracklayer”、“biomaRt”不可用于包“GenomicFeatures”
*删除“/Users/nalomran/opt/anaconda3/envs/ReQTL/lib/R/library/GenomicFeatures”
R[写入控制台]：库中错误（特征）：
没有称为“基因组特征”的软件包
R[写入控制台]：1:包“XML”不可用（适用于R版本3.6.3）
R[写入控制台]：包“功能”的安装具有非零退出状态
回溯（最近一次呼叫最后一次）：
文件“annotate_cis_trans.py”，第64行，中
robjects.r（‘库（基因组特征）’）
文件“/Users/nalomran/opt/anaconda3/envs/ReQTL/lib/python3.8/site packages/rpy2/robjects/__init__.py”，第416行，在调用中__
res=自我评估（p）
文件“/Users/nalomran/opt/anaconda3/envs/ReQTL/lib/python3.8/site packages/rpy2/robjects/functions.py”，第197行，在调用中__
返回（超级（SignatureTranslatedFunction，self）
文件“/Users/nalomran/opt/anaconda3/envs/ReQTL/lib/python3.8/site packages/rpy2/robjects/functions.py”，第125行，在调用中__
res=super（函数，自）.\uuuuuuuuu调用（*新参数，**新参数）
文件“/Users/nalomran/opt/anaconda3/envs/ReQTL/lib/python3.8/site packages/rpy2/rinterface_lib/conversion.py”，第44行_
cdata=函数（*args，**kwargs）
文件“/Users/nalomran/opt/anaconda3/envs/ReQTL/lib/python3.8/site packages/rpy2/rinterface.py”，第621行，在调用中__
引发嵌入的.rrontimeerror（\u rinterface.\u geterrmessage（））
rpy2.rinterface_lib.embedded.rrontimeerror:库中出错（基因组特征）：
没有称为“基因组特征”的软件包

我将Python3.8与conda env一起用于rpy2，如何解决此问题

---

提前谢谢。

幸亏我能够通过

rpy2>从python3.8中修复Bioconductor
基因组功能的安装和加载问题。我花了几个小时找到了解决方案，所以我想分享我所做的工作，以便如果谁最终遇到同样的问题，我可以找到我的解决方案t

基本上，在跟踪错误日志时，实际错误似乎指向此特定错误行：

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

在我进行一些研究时，我发现了这个特殊的StackOverflow问题，他们无法将包xml安装到R，并且Genomic Features需要该包，因此我在安装BioManager之前添加了以下行（如果未安装BioManager）：

这个答案来自上述StackOverflow问题的@Jaeyoung Chun

运行修改后的代码（如下所示）后，我能够安装并加载这样一个包，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 )')

您是在为rpy2使用conda env还是docker映像？您好，MiguelTrejo，正在使用conda env。
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 )')