GenomicFeatures 安裝和加載錯誤“沒有名為‘GenomicFeatures’的包，通過 Python3 rpy2

Question

我正在嘗試通過 python rpy2 使用 Bioconductor GenomicFeatures 對象和方法，因此當我執行以下代碼時：

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 )')

我得到相應的錯誤：

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，我該如何解決這個問題？

先感謝您。

Answer 1

謝天謝地，我能夠解決我在通過rpy2從 python3.8 中安裝和加載 Bioconductor GenomicFeatures時遇到的rpy2 。我花了幾個小時來解決這個問題，所以我想分享我所做的解決方案，如果誰結束遇到同樣的問題就可以找到了。

基本上，在跟蹤錯誤日志時，實際錯誤似乎指向此特定錯誤行：

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

當我做了一些研究時，我發現這個特殊的 StackOverflow 問題無法將包 XML 安裝到 R ，他們無法將包 xml 安裝到 R 並且 GenomicFeatures 需要該包，所以我在安裝 BiocManager 之前添加以下行（如果 BiocManager 不是安裝）：

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

這個答案來自上述 StackOverflow 問題的@Jaeyoung Chun。

運行修改后的代碼（見下文）后，我能夠安裝和加載這樣的包，沒有任何錯誤或問題：

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 )')