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nesi / eri-easyconfigs

AgR eRI cluster easybuild easyconfig files
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R Modules #3

Open MattBixley opened 4 months ago

MattBixley commented 4 months ago

Simplification of R Modules.

Build one module for each version of R, eg 4.3.2, 4.3.3, 4.4.0 etc

Base starting point is a simplfied version of R-Geo containing the required system libraries GDAL, proj etc to enable the packages raster, sp, terra to be installed. Addtional libraries to be added by eri-apps-admin and install.packages()

Install

Use Pacman to install and update packages as required, link here gives example function for various install options. Base funstion will install from CRAN and Bioconductor. pacman examples

install.packages("packman")
library(pacman)


p_load(devtools, BiocManager, tidyverse, tidymodels, renv, MASS, Matrix)
p_load(formatR, lambda.r, futile.options, futile.logger, perm, gridBase, registry, bibtex, rmapshaper)
p_load(ggExtra, ggmap, ggspatial, ggplot2movies, ggthemes, ggvis, gt, ggsci, kableExtra, gganimate, palmerpenguins)
p_load(limma, edgeR, vegan, ape, phyloseq, metagenomeSeq, metacoder, metacoderLite, metagenomeFeatures, metagenomeSeq)
p_load(sp, terra, raster, dismo, spData, units, abind, maptools, sf, stars, lwgeom, gstat, DCluster, gdistance, ipdw, spacetime, wk, s2, sftime, spdep, leaflet, mapview, osmdata, rasterVis, rmapshaper, tmap)

p_load(palmerpenguins)
p_load_gh("G-Thomson/Manu") # example Github Install

Fails

DESeq2 failed. Exit, Purge, Reload and install SparseArray, DelayedArray, SummarizedExperiment, DESeq2

BiocManager::install("DESeq2")

MattBixley commented 3 months ago

R/4.4 https://github.com/nesi/eri-easyconfigs/blob/main/r/R-4.4.0-foss2023a.eb