using_R.md

Configuration

(Instructions shared by Dr.Emma Johnson)

YOU ONLY NEED TO DO THIS ONCE

Edit your bash alias file to include aliases to more easily load the lab's R library and load R from spack:

echo "alias labr='export R_LIBS_SITE=/ref/dblab/software/r-envs/4.3.0'" >> ~/.bash_aliases
echo "alias runr='eval \`spack load --sh /3ggwaqr`'" >> ~/.bash_aliases # load spec with X=True

Add this line to your ~/.bashrc file if you do not have it already:

[ -f ~/.bash_aliases ] && . ~/.bash_aliases

Source these files or start a new terminal session.

Once you have completed the initial configuration, you're ready to start using R!

AIM 1: Load and use R interactively

## log on to interactive node
srun -J interactive -p interactive --pty /bin/bash

## load R library (using alias)
labr

## load R software (using alias)
runr

## start R
R

## you can make sure it's loaded by checking the libraries using
.libPaths()

AIM 2: Run an R script in a batch job

## load R library (using alias)
labr
## load R software (using alias)
runr

## run R script
Rscript my_script.R

AIM 3: Update or install a package in the lab's library

Making any updates or installs has to be done in an interactive session (plus that makes troubleshooting easier).

## log on to interactive node
srun -J interactive -p interactive --pty /bin/bash

## load R library (using alias)
labr

## load R (using alias)
runr

## start R
R

## set primary library to the lab's library (this will make sure all installs go in here)
.libPaths("/ref/dblab/software/r-envs/4.3.0")

## install package, e.g.:
install.packages("ggdogs")

Troubleshooting Notes:

This section includes notes on any issues we have had installing packages and how they were fixed.

Tidyverse

The error message:

Error: package or namespace load failed for ‘tidyverse’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘xml2’

The problem: xml2 wasn't installed

The solution: install xml2

install.packages("xml2")
library(xml2)

xml2

The error message:

------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libxml-2.0 was not found. Try installing:
 * deb: libxml2-dev (Debian, Ubuntu, etc)
 * rpm: libxml2-devel (Fedora, CentOS, RHEL)
 * csw: libxml2_dev (Solaris)
If libxml-2.0 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libxml-2.0.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘xml2’
* removing ‘/ref/dblab/software/r-envs/dblab_R/4.1.3/xml2’

The problem: libxml software wasn't loaded in the environment

The solution: use spack to load libxml-2.0 IN THE SHELL, then can open R and install xml2 pkg

eval `spack load --sh   libxml2`

Getting external Lapack working (unresolved)

# load spec with external-lapack
#echo "alias runr='eval \`spack load --sh   r+external-lapack\`'" >> ~/.bash_aliases
#echo "alias runr='eval \`spack load --sh /me7fcwi`'" >> ~/.bash_aliases