bch441-work-abc-units/ABC-Install_all_packages.R

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# tocID <- "ABC-Install_all_packages.R"
#
# Purpose: A Bioinformatics Course:
# Installing all packages in this course
#
# Version: 1.0
#
# Date: 2021 10
# Author: Boris Steipe (boris.steipe@utoronto.ca)
#
# Versions:
# 1.0 New code
#
#
# TODO:
#
# ==============================================================================
#TOC> ==========================================================================
#TOC>
#TOC> Section Title Line
#TOC> ----------------------------------------------
#TOC> 1 Packages 33
#TOC> 2 CRAN packages 98
#TOC> 3 Bioconductor packages 127
#TOC> 4 Other package sources 142
#TOC> 5 Updating packages 148
#TOC>
#TOC> ==========================================================================
# = 1 Packages ============================================================
# Much of R's functionality is contributed in packages: bundles of R scripts
# or code in other languages, pre-configured objects, and datasets. Making this
# functionality available is often done by issuing a library(<package-name>)
# command, however this is not the preferred way, since it may override other
# R functions and it makes it harder to understand where the source code of
# a particular function is located. In this course we call the function name
# prefixed with the package name and two colons:
# <package-name>::<function-name>()
# This is the preferred way, since it is explicit.
#
# Regardless of which idiom one uses to call the actual function, the package
# needs to be "installed" first, i.e. the code must have been downloaded
# from CRAN, or using the BiocManager::install() function.
#
# This script contains download commands for all packages that are used in the
# course. You can execute the script line by line (or even source the entire
# script) to make sure all packages can be installed on your computer. Just
# one reminder: if you are ever asked to install from source, the correct
# answer is usually "no" - except if you really know what you are doing and why.
#
# Once packages are installed you can get additional information about
# the contents of a package with the commands:
# library(help=<package-name>) # basic information
# browseVignettes("<package-name>") # available vignettes
# data(package = "<package-name>") # available datasets
#
# ... and you can load data sets with:
# data(<data-set-name>, package = "<package-name>")
#
# All packages here are installed only when they have not been installed
# before, using the following idiom:
#
# if (! requireNamespace("<package-name>", quietly=TRUE)) {
# install.packages("<package-name>")
# }
#
# ... or its BiocManager::install() equivalent:
#
# if (! requireNamespace("<bioconductor-package-name>", quietly=TRUE)) {
# BiocManager::install("<bioconductor-package-name>")
# }
#
# If you want to _force_ a re-installation of the package, simply issue
# the install.packages("<package-name>") command on its own. For compactness
# we wrap the idiom into a function, which can also switch between CRAN
# and BIOconductor sources:
installIfNeeded <- function(package, s = "CRAN") {
# s: "CRAN" or "BIO"
if (s == "CRAN") {
if (! requireNamespace(package, quietly=TRUE)) {
install.packages(package)
}
} else if (s == "BIO") {
if (! requireNamespace("BiocManager", quietly=TRUE)) {
install.packages("BiocManager")
}
if (! requireNamespace(package, quietly=TRUE)) {
BiocManager::install(package)
}
} else {
stop(sprintf("Unknown source \"%s\".", s))
}
}
# = 2 CRAN packages =======================================================
installIfNeeded("ape")
installIfNeeded("BiocManager")
installIfNeeded("bio3d")
installIfNeeded("evd")
installIfNeeded("ggseqlogo")
installIfNeeded("ggtern")
installIfNeeded("hexbin")
installIfNeeded("httr")
installIfNeeded("igraph")
installIfNeeded("jsonlite")
installIfNeeded("magrittr")
installIfNeeded("MASS")
installIfNeeded("microbenchmark")
installIfNeeded("phangorn")
installIfNeeded("plotly")
installIfNeeded("plotrix")
installIfNeeded("profvis")
installIfNeeded("robustbase")
installIfNeeded("RColorBrewer")
installIfNeeded("Rphylip")
installIfNeeded("rvest")
installIfNeeded("seqinr")
installIfNeeded("stringi")
installIfNeeded("taxize")
installIfNeeded("testthat")
installIfNeeded("xml2")
# = 3 Bioconductor packages ===============================================
installIfNeeded("Biobase", s = "BIO")
installIfNeeded("biomaRt", s = "BIO")
installIfNeeded("Biostrings", s = "BIO")
installIfNeeded("DECIPHER", s = "BIO")
installIfNeeded("GEOquery", s = "BIO")
installIfNeeded("GOSim", s = "BIO")
installIfNeeded("limma", s = "BIO")
installIfNeeded("msa", s = "BIO")
installIfNeeded("org.Sc.sgd.db", s = "BIO")
installIfNeeded("prada", s = "BIO")
installIfNeeded("topGO", s = "BIO")
# = 4 Other package sources ===============================================
# Using sources other than CRAN or Bioconductor to download general-purpose
# programs that run on your computer is not generally recommended.
# = 5 Updating packages ===================================================
# From time to time, update CRAN packages with the following command ...
update.packages()
# ... and also update Bioconductor packages as follows:
BiocManager::install()
# [END]