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Difference between revisions of "R"

From Montana Tech High Performance Computing

(Install R Packages)
Line 16: Line 16:
 
:<code style=display:block>Would you like to create a personal library<br>‘~/R/x86_64-pc-linux-gnu-library/3.6’<br>to install packages into? (yes/No/cancel)</code>
 
:<code style=display:block>Would you like to create a personal library<br>‘~/R/x86_64-pc-linux-gnu-library/3.6’<br>to install packages into? (yes/No/cancel)</code>
 
Answer <code>yes</code> again, R will start the installation process.
 
Answer <code>yes</code> again, R will start the installation process.
 +
 +
In addition, you can also install R packages in a different folder other than the default one. For example, to install a package at <code>~/libs/R_libs</code>:
 +
First create the directory:
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:<code style=display:block>mkdir ~/libs/R_libs</code>
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Then inside R:
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:<code style=display:block>> install.packages("ggplot2", lib="~/libs/R_libs")</code>

Revision as of 09:58, 28 May 2020

The R package for statistical computing and graphics is installed on the system. Version 3.6.1 installed with the gnu8 toolchain. To access it:

module load R

Install R Packages

Generally, if you need to use R packages that are not available, you can always install it locally in your account. First start an R session:

module load R
R

Then you can use the install.packages command inside R to install a package. For example,

> install.packages("ggplot2")

Because you don't have a write permission in the /opt directory, where R is installed, R will throw the following warings:

Warning in install.packages("ggplot2") :
'lib = "/opt/ohpc/pub/libs/gnu8/R/3.6.1/lib64/R/library"' is not writable
Would you like to use a personal library instead? (yes/No/cancel)

Answer yes, R will then ask you to create a library folder in your own directory:

Would you like to create a personal library
‘~/R/x86_64-pc-linux-gnu-library/3.6’
to install packages into? (yes/No/cancel)

Answer yes again, R will start the installation process.

In addition, you can also install R packages in a different folder other than the default one. For example, to install a package at ~/libs/R_libs: First create the directory:

mkdir ~/libs/R_libs

Then inside R:

> install.packages("ggplot2", lib="~/libs/R_libs")