Difference between revisions of "Installing R packages on Freebee"

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<code>install.packages("ggplot2")</code>
 
<code>install.packages("ggplot2")</code>
  
After it hast finished you can test the installation by <code>typing library(package_name</code>)
+
After it has finished you can test the installation by <code>typing library(package_name</code>)
  
 
If everything worked fine you can type:
 
If everything worked fine you can type:

Revision as of 20:17, 3 December 2018

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

Then just paste and run all these lines. It will take a long time (probably at least 30 min):

install.packages("pheatmap")

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.