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