Installing R packages on Freebee

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If you for some reason can't install the necessary packages on your local computer you can try to use R on Freebee.

Log on to freebee as normal and type:

module load R/3.5.0

To start R type:

R

Try to install a package by typing:

install.packages("pheatmap")

Say Yes to using a local library (don't remember exactly the message).

After it has finished try library(pheatmap). If everything worked fine you can install the rest of the packages. Just paste and run all these lines. It will take a long time (probably at least 30 min):

install.packages("repmis")

install.packages("reshape2")

install.packages("gplots")

install.packages("RColorBrewer")

install.packages("ggplot2")

After it has finished you can test the installation by typing library(package_name)

If everything worked fine you can type:

source("https://bioconductor.org/biocLite.R")

biocLite("DESeq2")

This will also take probably 30 minutes.

You might get a message after installing DESEq2 saying:

installation path not writeable, unable to update packages: coda, doParallel,iterators, lme4, mvtnorm, nloptr, Rcpp, RcppEigen, Rmpi, snow, foreign, lattice, MASS, Matrix, mgcv, survival

This might not be a problem. Try:

library(DESeq2) and if it loads without problems you should be fine.

type quit() to exit R. You don't have to save workspace.

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