bearloga · October 8, 2020 12:46 · Oct 6, 2020 · Oct 6, 2020 · Oct 6, 2020 · Nov 4, 2016
diff --git a/upgrade_packages.R b/upgrade_packages.R
@@ -26,13 +26,14 @@ if (! "remotes" %in% installed.packages()[, "Package"]) {
 
 # First, we locate the various personal R libraries the user has:
 if (Sys.info()["sysname"] == "Linux") {
-  pkg_paths <- dir(paste0("~/R/", R.version$platform, "-library"), full.names = TRUE)
+  pkg_paths <- dir(paste0(Sys.getenv("HOME"), "/R/", R.version$platform, "-library"), full.names = TRUE)
 } else if (Sys.info()["sysname"] == "Darwin") {
   pkg_paths <- file.path(dir("~/Library/R", full.names = TRUE), "library")
 }
 
 # Pick the latest one that is not the current R version's library:
-pkg_path <- tail(setdiff(pkg_paths, .libPaths()), 1)
+pkg_paths <- pkg_paths[!vapply(pkg_paths, function(path) { any(grepl(path, .libPaths(), fixed = TRUE)) }, FALSE)]
+pkg_path <- tail(pkg_paths, 1)
 if (length(pkg_path) == 0) {
   stop("Nothing to do.")
 } else {
@@ -59,6 +60,9 @@ pkgs_info <- do.call(rbind, lapply(installed_pkgs, function(installed_pkg) {
   if (any(grepl("Repository: CRAN", pkg_description))) {
     # message('"', installed_pkg, '" was installed from CRAN.')
     pkg_source <- "cran"; pkg_url <- NA
+  } else if (any(grepl("Additional_repositories", pkg_description))) {
+    # e.g. {cmdstanr} & {posterior} installed from https://mc-stan.org/r-packages/ (drat)
+    pkg_source <- "other"; pkg_url <- extract_param(pkg_description, "Additional_repositories")
   } 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")
@@ -94,6 +98,10 @@ 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 = ", "))
   remotes::install_git(pkgs_info$url[pkgs_info$source == "git"])
 }
+if (sum(pkgs_info$source == "other") > 0) {
+  message("The following ", sum(pkgs_info$source == "other"), " packages will be re-installed from other repos: ", paste(pkgs_info$package[pkgs_info$source == "other"], collapse = ", "))
+  install.packages(pkgs_info$package[pkgs_info$source == "other"], repos = c(CRAN = "https://cran.rstudio.com", pkgs_info$url[pkgs_info$source == "other"]))
+}
 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 = ", "))
 }
diff --git a/upgrade_packages.R b/upgrade_packages.R
@@ -16,7 +16,7 @@ if (!dir.exists(Sys.getenv("R_LIBS_USER"))) {
   message("Personal library found.")
 }
 
-message("Installing devtools for re-installing from GitHub, etc....")
+message("Installing {remotes} for re-installing from GitHub, etc....")
 install.packages("remotes", repos = c(CRAN = "https://cran.rstudio.com"))
 # ^ also ensures that we have a personal library for this version of R
 

diff --git a/upgrade_packages.R b/upgrade_packages.R
@@ -17,11 +17,11 @@ if (!dir.exists(Sys.getenv("R_LIBS_USER"))) {
 }
 
 message("Installing devtools for re-installing from GitHub, etc....")
-install.packages("devtools", repos = "https://cran.rstudio.com/")
+install.packages("remotes", repos = c(CRAN = "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!")
+if (! "remotes" %in% installed.packages()[, "Package"]) {
+  stop("{remotes} is/was not installed!")
 }
 
 # First, we locate the various personal R libraries the user has:
@@ -84,15 +84,15 @@ pkgs_info <- do.call(rbind, lapply(installed_pkgs, function(installed_pkg) {
  # 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/")
+  install.packages(pkgs_info$package[pkgs_info$source == "cran"], repos = c(CRAN = "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"])
+  remotes::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"])
+  remotes::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 = ", "))

diff --git a/upgrade_packages.R b/upgrade_packages.R
@@ -26,7 +26,7 @@ if (! "devtools" %in% installed.packages()[, "Package"]) {
 
 # First, we locate the various personal R libraries the user has:
 if (Sys.info()["sysname"] == "Linux") {
-  pkg_paths <- dir("~/R/x86_64-pc-linux-gnu-library", full.names = TRUE)
+  pkg_paths <- dir(paste0("~/R/", R.version$platform, "-library"), full.names = TRUE)
 } else if (Sys.info()["sysname"] == "Darwin") {
   pkg_paths <- file.path(dir("~/Library/R", full.names = TRUE), "library")
 }

diff --git a/upgrade_packages.R b/upgrade_packages.R
@@ -1,6 +1,11 @@
-message("Setting proxies...")
-Sys.setenv("http_proxy" = "http://webproxy.eqiad.wmnet:8080")
-Sys.setenv("https_proxy" = "http://webproxy.eqiad.wmnet:8080")
+# WMF only:
+if (file.exists("/etc/wikimedia-cluster")) {
+  message('Detected that this script is being run on a WMF machine ("', Sys.info()["nodename"], '"). Setting proxies...')
+  Sys.setenv("http_proxy" = "http://webproxy.eqiad.wmnet:8080")
+  Sys.setenv("https_proxy" = "http://webproxy.eqiad.wmnet:8080")
+}
+
+# General use:
 message("Checking for a personal library...")
 if (!dir.exists(Sys.getenv("R_LIBS_USER"))) {
   warning("Personal library not found, creating one...")
@@ -10,6 +15,7 @@ if (!dir.exists(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
@@ -24,13 +30,15 @@ if (Sys.info()["sysname"] == "Linux") {
 } else if (Sys.info()["sysname"] == "Darwin") {
   pkg_paths <- file.path(dir("~/Library/R", full.names = TRUE), "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) {
@@ -72,6 +80,7 @@ pkgs_info <- do.call(rbind, lapply(installed_pkgs, function(installed_pkg) {
     stringsAsFactors = FALSE
   ))
 }))
+
  # Re-install packages:
 if (sum(pkgs_info$source == "cran") > 0) {
   message("Re-installing ", sum(pkgs_info$source == "cran"), " R packages from CRAN...")

diff --git a/upgrade_packages.R b/upgrade_packages.R
@@ -0,0 +1,90 @@
+message("Setting proxies...")
+Sys.setenv("http_proxy" = "http://webproxy.eqiad.wmnet:8080")
+Sys.setenv("https_proxy" = "http://webproxy.eqiad.wmnet:8080")
+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("~/R/x86_64-pc-linux-gnu-library", full.names = TRUE)
+} else if (Sys.info()["sysname"] == "Darwin") {
+  pkg_paths <- file.path(dir("~/Library/R", full.names = TRUE), "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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