Is it possible to install bioconductor package 

问题:

I want to install the bioconductor rain package for R in Jupyter notebook.

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") 

I get the following error:

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

I was able to install a different bioconductor package in Jupyter (DESeq2) using the following - in command line:

conda install bioconductor-deseq2

But this method does not work for the rain package, because, unlike deseq2, rain is not on the anaconda cloud.

Is it possible to install a bioconductor package not on the anaconda cloud (like the rain package) in Jupyter, and, if so, how?

Thank you!

回答1:

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.