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Save sv99/756558f7a971b1075c4007e62d8052e8 to your computer and use it in GitHub Desktop.
The script can be used to re-install packages after upgrading R (on Linux or Mac), since libraries cannot be reused between different minor versions (e.g. when upgrading 3.2.3 to 3.3.2). It detects when a package was installed from CRAN vs GitHub/Git and re-installs it using the appropriate func. Usage: `Rscript upgrade_packages.R`
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# General use: | |
message("Checking for a personal library...") | |
if (!dir.exists(Sys.getenv("R_LIBS_USER"))) { | |
warning("Personal library not found, creating one...") | |
dir.create(Sys.getenv("R_LIBS_USER"), recursive = TRUE) | |
message("Registering newly created personal library...") | |
.libPaths(Sys.getenv("R_LIBS_USER")) | |
} else { | |
message("Personal library found.") | |
} | |
message("Installing devtools for re-installing from GitHub, etc....") | |
install.packages("devtools", repos = "https://cran.rstudio.com/") | |
# ^ also ensures that we have a personal library for this version of R | |
if (! "devtools" %in% installed.packages()[, "Package"]) { | |
stop("devtools is/was not installed!") | |
} | |
# First, we locate the various personal R libraries the user has: | |
if (Sys.info()["sysname"] == "Linux") { | |
pkg_paths <- dir(paste0("~/R/", R.version$platform, "-library"), full.names = TRUE) | |
} else if (Sys.info()["sysname"] == "Darwin") { | |
# site installer | |
# pkg_paths <- file.path(dir("~/Library/R", full.names = TRUE), "library") | |
# for brew install homebrew/science/r | |
pkg_paths <- file.path(dir("/usr/local/lib/R", full.names = TRUE), "site-library") | |
} | |
# Pick the latest one that is not the current R version's library: | |
pkg_path <- tail(setdiff(pkg_paths, .libPaths()), 1) | |
if (length(pkg_path) == 0) { | |
stop("Nothing to do.") | |
} else { | |
message("Found library from previous R installation: ", pkg_path) | |
} | |
# List of installed packages in the user's personal library: | |
installed_pkgs <- dir(pkg_path) | |
if (length(installed_pkgs) == 0) { | |
stop("Did not find any packages from previous R installation.") | |
} | |
message("Found ", length(installed_pkgs), " packages from previous R installation.") | |
# A helper function for extracting a parameter | |
# from an installed package's DESCRIPTION file | |
extract_param <- function(DESCRIPTION, param) { | |
return(sub(paste0(param, ": "), "", DESCRIPTION[grepl(param, DESCRIPTION)], fixed = TRUE)) | |
} | |
message("Extracting metadata about packages from previous R installation...") | |
pkgs_info <- do.call(rbind, lapply(installed_pkgs, function(installed_pkg) { | |
# message('Checking how "', installed_pkg, '" was installed...') | |
pkg_description <- readLines(file.path(find.package(installed_pkg, lib.loc = pkg_path), "DESCRIPTION")) | |
if (any(grepl("Repository: CRAN", pkg_description))) { | |
# message('"', installed_pkg, '" was installed from CRAN.') | |
pkg_source <- "cran"; pkg_url <- NA | |
} else if (any(grepl("RemoteType", pkg_description))) { | |
# message('"', installed_pkg, '" was installed from a remote source like GitHub.') | |
pkg_source <- extract_param(pkg_description, "RemoteType") | |
if (pkg_source == "github") { | |
pkg_url <- paste(extract_param(pkg_description, "GithubUsername"), extract_param(pkg_description, "GithubRepo"), sep = "/") | |
} else if (pkg_source == "git") { | |
pkg_url <- extract_param(pkg_description, "RemoteUrl") | |
} else { | |
pkg_source <- "other remote"; pkg_url <- NA | |
} | |
} else { | |
# message('"', installed_pkg, '" was installed from a local source.') | |
pkg_source <- "local"; pkg_url <- NA | |
} | |
return(data.frame( | |
package = installed_pkg, | |
source = pkg_source, | |
url = pkg_url, | |
stringsAsFactors = FALSE | |
)) | |
})) | |
# Re-install packages: | |
if (sum(pkgs_info$source == "cran") > 0) { | |
message("Re-installing ", sum(pkgs_info$source == "cran"), " R packages from CRAN...") | |
install.packages(pkgs_info$package[pkgs_info$source == "cran"], repos = "https://cran.rstudio.com/") | |
} | |
if (sum(pkgs_info$source == "github") > 0) { | |
message("The following ", sum(pkgs_info$source == "github"), " packages will be re-installed from GitHub: ", paste(pkgs_info$package[pkgs_info$source == "github"], collapse = ", ")) | |
devtools::install_github(pkgs_info$url[pkgs_info$source == "github"]) | |
} | |
if (sum(pkgs_info$source == "git") > 0) { | |
message("The following ", sum(pkgs_info$source == "git"), " packages will be re-installed from Git repos: ", paste(pkgs_info$package[pkgs_info$source == "git"], collapse = ", ")) | |
devtools::install_git(pkgs_info$url[pkgs_info$source == "git"]) | |
} | |
if (sum(pkgs_info$source %in% c("other remote", "local")) > 0) { | |
message("The following ", sum(pkgs_info$source %in% c("other remote", "local")), " packages will need to be manually re-installed (sorry): ", paste(pkgs_info$package[pkgs_info$source %in% c("other remote", "local")], collapse = ", ")) | |
} |
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