是否可以在Jupyter R笔记本电脑中安装生物导体包装“雨水"? [英] Is it possible to install bioconductor package 'rain' in R Jupyter notebook?
问题描述
我想为R安装生物导体雨套件在Jupyter笔记本中.
I want to install the bioconductor rain package for R in Jupyter notebook.
我无法按照上面链接的网站上给出的说明在Jupyter笔记本中安装此软件包-在R Jupiter笔记本中:
I am not able to install this package in Jupyter notebook following instructions given on the website linked above - in an R Jupiter notebook:
source("https://bioconductor.org/biocLite.R")
biocLite("rain")
我收到以下错误:
Warning message:
In install.packages(pkgs = doing, lib = lib, ...): installation of package ‘gmp’ had non-zero exit statusWarning message:
In install.packages(pkgs = doing, lib = lib, ...): installation of package ‘rain’ had non-zero exit status
我能够在Jupyter中安装其他生物导体包装( DESeq2 )在命令行中使用以下命令:
I was able to install a different bioconductor package in Jupyter (DESeq2) using the following - in command line:
conda install bioconductor-deseq2
但是这种方法不适用于下雨包，因为与deseq2不同，下雨没有在蟒蛇云上.
But this method does not work for the rain package, because, unlike deseq2, rain is not on the anaconda cloud.
是否有可能不在Jupyter的水蟒云上安装生物导体包装(如雨水包装)?如果是的话，怎么办?
Is it possible to install a bioconductor package not on the anaconda cloud (like the rain package) in Jupyter, and, if so, how?
谢谢！
推荐答案
我找到了解决问题的方法.有两种安装IRkernel的方法:1)使用CRAN + Github(说明: http://irkernel.github.io/)和2)作为名为r-irkernel的conda程序包.我使用的后一种方法将安装并运行conda自己的R版本，就可安装的软件包而言，它的功能更为有限.而CRAN + Github方法允许Jupyter将计算机上已安装的R版本与它可以运行的任何软件包一起使用.
I have found a solution to my problem. There are two ways to install IRkernel: 1) using CRAN+Github (instructions: http://irkernel.github.io/) and 2) as a conda package called r-irkernel. The later method, which I had used, installs and runs conda's own version of R, which has more limited functionality in terms of packages that can be installed. Whereas the CRAN+Github method allows Jupyter to use the version of R already installed on your computer with any packages that it can run.
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