Difference between revisions of "Installing R packages on Freebee"
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Revision as of 21:20, 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
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.