44 lines
1.6 KiB
R
44 lines
1.6 KiB
R
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#!/usr/bin/env Rscript
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# Installer pak (lui-même en binaire si possible)
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install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))
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pak::pkg_install("cli")
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# Détection automatique du système et installation de tous les paquets en binaire
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pak::pkg_install(c(
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"IRkernel",
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"tidyverse",
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"vegan",
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"ade4",
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"BiocManager",
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"remotes",
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"igraph",
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"Rdpack"
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))
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# ------------------------------------------------------------
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# Paquets Bioconductor (toujours via BiocManager)
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# ------------------------------------------------------------
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pak::pkg_install("bioc::biomformat")
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# ------------------------------------------------------------
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# Paquets depuis GitHub / dépôts git
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# ------------------------------------------------------------
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pak::pkg_install("metabaRfactory/metabaR")
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pak::pkg_install("git::https://forge.metabarcoding.org/obitools/ROBIUtils.git")
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pak::pkg_install("git::https://forge.metabarcoding.org/obitools/ROBITaxonomy.git")
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pak::pkg_install("git::https://forge.metabarcoding.org/obitools/ROBITools.git")
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pak::pkg_install("git::https://forge.metabarcoding.org/MetabarcodingSchool/biodiversity-metrics.git")
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# ------------------------------------------------------------
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# Installation du noyau Jupyter pour IRkernel
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# ------------------------------------------------------------
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# Si on est root -> installation système, sinon -> user
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if (Sys.info()["user"] == "root") {
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IRkernel::installspec(user = FALSE)
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} else {
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IRkernel::installspec(user = TRUE)
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}
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cat("\n✅ Tous les paquets R ont été installés avec succès.\n")
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