Installing R packages on Freebee
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:
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 it 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.