Difference between revisions of "Installing R packages on Freebee"

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(Created page with "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...")
 
Line 3: Line 3:
 
Log on to freebee as normal and type:
 
Log on to freebee as normal and type:
  
module load R/3.5.0
+
<code>module load R/3.5.0</code>
  
 
To start R type:
 
To start R type:
  
R
+
<code>R</code>
  
 
Then just paste and run all these lines. It will take a long time (probably at least 30 min):
 
Then just paste and run all these lines. It will take a long time (probably at least 30 min):
  
install.packages("pheatmap")
+
<code>install.packages("pheatmap")</code>
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)
+
<code>install.packages("repmis")</code>
 +
 
 +
<code>install.packages("reshape2")</code>
 +
 
 +
<code>install.packages("gplots")</code>
 +
 
 +
<code>install.packages("RColorBrewer")</code>
 +
 
 +
<code>install.packages("ggplot2")</code>
 +
 
 +
After it hast 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:
source("https://bioconductor.org/biocLite.R")
+
 
biocLite("DESeq2")
+
<code>source("https://bioconductor.org/biocLite.R")</code>
 +
 
 +
<code>biocLite("DESeq2")</code>
  
 
This will also take probably 30 minutes.
 
This will also take probably 30 minutes.
  
 
You might get a message after installing DESEq2 saying:
 
You might get a message after installing DESEq2 saying:
installation path not writeable, unable to update packages: coda, doParallel,
+
installation path not writeable, unable to update packages: coda, doParallel,iterators, lme4, mvtnorm, nloptr, Rcpp, RcppEigen, Rmpi, snow, foreign, lattice, MASS, Matrix, mgcv, survival
  iterators, lme4, mvtnorm, nloptr, Rcpp, RcppEigen, Rmpi, snow, foreign,
 
  lattice, MASS, Matrix, mgcv, survival
 
 
 
 
This might not be a problem. Try:
 
This might not be a problem. Try:
library(DESeq2) and if it loads without problems you should be fine.
+
 
 +
<code>library(DESeq2)</code> and if it loads without problems you should be fine.
  
 
type quit() to exit R. You don't have to save workspace.
 
type quit() to exit R. You don't have to save workspace.

Revision as of 20:16, 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 hast 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.