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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!

A. Vislova
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    Possible duplicate of [How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning?](http://stackoverflow.com/questions/25721884/how-should-i-deal-with-package-xxx-is-not-available-for-r-version-x-y-z-wa) – zx8754 Jun 28 '16 at 10:25
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    Not quite the same - my problem has to do with installing R packages specifically for use in the Jupyter Notebook software. – A. Vislova Jun 28 '16 at 20:30

1 Answers1

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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.

A. Vislova
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