Style via {styler}

Author: b-rodrigues

R/available_r.R

@@ -22,8 +22,13 @@ available_df <- function() {
 available_r <- function() {
   r_versions <- unique(available_df()$`R.version`)
   c(
-    "bleeding-edge", "frozen-edge", "r-devel", "bioc-devel",
-    "r-devel-bioc-devel", "latest-upstream", r_versions
+    "bleeding-edge",
+    "frozen-edge",
+    "r-devel",
+    "bioc-devel",
+    "r-devel-bioc-devel",
+    "latest-upstream",
+    r_versions
   )
 }
 

R/ga_cachix.R

@@ -48,7 +48,6 @@ ga_cachix <- function(cache_name, path_default) {
     message("GitHub Actions workflow file saved to: ", path)
   }
 
-
   # The sed command for Darwin is of the form "sed -i '' s/foo/bar"
   # while on Linux it's "sed -i s/foo/bar"
   darwin_specific_quotes <- if (Sys.info()["sysname"] == "Darwin") {
@@ -59,15 +58,23 @@ ga_cachix <- function(cache_name, path_default) {
 
   system(
     paste0(
-      "sed -i ", darwin_specific_quotes, "'s/CACHE_NAME/", cache_name, "/g' ",
+      "sed -i ",
+      darwin_specific_quotes,
+      "'s/CACHE_NAME/",
+      cache_name,
+      "/g' ",
       paste0(path, "/cachix_dev_env.yaml")
     )
   )
 
   system(
     paste0(
-      "sed -i ", darwin_specific_quotes, "'s/PATH_TO_DEFAULT_NIX/",
-      path_default, "/g' ", file.path(path, "cachix_dev_env.yaml")
+      "sed -i ",
+      darwin_specific_quotes,
+      "'s/PATH_TO_DEFAULT_NIX/",
+      path_default,
+      "/g' ",
+      file.path(path, "cachix_dev_env.yaml")
     )
   )
 

R/get_latest.R

@@ -17,14 +17,18 @@ get_latest <- function(r_version) {
   if (nchar(r_version) == 40) {
     return(r_version)
   } else if (
-    !(r_version %in% c(
-      "bioc-devel",
-      "r-devel-bioc-devel",
-      "r-devel",
-      "frozen-edge",
-      "bleeding-edge",
-      "latest-upstream"
-    )) && all(r_version > Filter(function(x) ("latest-upstream" != x), available_r()))
+    !(r_version %in%
+      c(
+        "bioc-devel",
+        "r-devel-bioc-devel",
+        "r-devel",
+        "frozen-edge",
+        "bleeding-edge",
+        "latest-upstream"
+      )) &&
+      all(
+        r_version > Filter(function(x) ("latest-upstream" != x), available_r())
+      )
   ) {
     stop(
       "The provided R version is too recent,\nand not yet included in `nixpkgs`.\n",
@@ -36,10 +40,15 @@ get_latest <- function(r_version) {
       "'bleeding-edge' and 'frozen-edge'."
     )
   } else if (
-    !(r_version %in% c(
-      "r-devel-bioc-devel", "r-devel", "bioc-devel",
-      "bleeding-edge", "frozen-edge", available_r()
-    ))
+    !(r_version %in%
+      c(
+        "r-devel-bioc-devel",
+        "r-devel",
+        "bioc-devel",
+        "bleeding-edge",
+        "frozen-edge",
+        available_r()
+      ))
   ) {
     stop(
       "The provided R version is too recent,\nand not yet included in `nixpkgs`.\n",
@@ -74,7 +83,8 @@ get_right_commit <- function(r_version) {
     api_url <- "https://api.github.com/repos/rstats-on-nix/nixpkgs/commits?sha=r-daily"
   } else if (
     r_version %in% Filter(function(x) `!=`(x, "latest-upstream"), available_r())
-  ) { # all but latest-upstream
+  ) {
+    # all but latest-upstream
     # If a user provides an R version, use most recent date for that version
     return(get_date_from_version(r_version))
   } else {
@@ -101,17 +111,18 @@ get_right_commit <- function(r_version) {
 #' Fetch if available and stop with propagating the curl error. Also show URL
 #' for context
 #' @noRd
-try_get_request <- function(url,
-                            handle,
-                            extra_diagnostics = NULL) {
+try_get_request <- function(url, handle, extra_diagnostics = NULL) {
   tryCatch(
     {
       req <- curl::curl_fetch_memory(url, handle)
     },
     error = function(e) {
-      stop("Request `curl::curl_fetch_memory(",
-        paste0("url = ", "'", url, "'", ")` "), "failed:\n ",
-        e$message[1], extra_diagnostics,
+      stop(
+        "Request `curl::curl_fetch_memory(",
+        paste0("url = ", "'", url, "'", ")` "),
+        "failed:\n ",
+        e$message[1],
+        extra_diagnostics,
         call. = FALSE
       )
     }

R/make_launcher.R

@@ -22,14 +22,19 @@
 make_launcher <- function(editor, project_path) {
   editor <- trimws(editor)
 
-  stopifnot("'editor' argument must be a single word" = grepl("^[A-Za-z]+$", editor))
+  stopifnot(
+    "'editor' argument must be a single word" = grepl("^[A-Za-z]+$", editor)
+  )
 
   if (isFALSE(dir.exists(project_path))) {
     dir.create(path = project_path, recursive = TRUE)
     project_path <- normalizePath(path = project_path)
   }
 
-  script_text <- sprintf("#!/usr/bin/env nix-shell\n#!nix-shell default.nix -i bash\n%s", editor)
+  script_text <- sprintf(
+    "#!/usr/bin/env nix-shell\n#!nix-shell default.nix -i bash\n%s",
+    editor
+  )
   script_path <- file.path(project_path, paste0("start-", editor, ".sh"))
   writeLines(script_text, script_path)
 

R/make_nixpkgs_url.R

@@ -19,15 +19,21 @@ make_nixpkgs_url <- function(r_ver = NULL, date = NULL) {
 
     list(
       "url" = paste0(
-        "https://github.com/", github_repo, "archive/", latest_commit, ".tar.gz"
+        "https://github.com/",
+        github_repo,
+        "archive/",
+        latest_commit,
+        ".tar.gz"
       ),
       "latest_commit" = latest_commit,
       "r_ver" = r_ver
     )
   } else {
     list(
       "url" = paste0(
-        "https://github.com/rstats-on-nix/nixpkgs/archive/", date, ".tar.gz"
+        "https://github.com/rstats-on-nix/nixpkgs/archive/",
+        date,
+        ".tar.gz"
       ),
       "latest_commit" = date,
       "r_ver" = get_version_from_date(date)

R/nix_build_helpers.R

@@ -62,12 +62,15 @@ fix_ld_library_path <- function() {
 
 #'
 #' @noRd
-poll_sys_proc_blocking <- function(cmd, proc,
-                                   what = c("nix-build", "expr", "nix-hash"),
-                                   message_type =
-                                     c("simple", "quiet", "verbose")) {
+poll_sys_proc_blocking <- function(
+  cmd,
+  proc,
+  what = c("nix-build", "expr", "nix-hash"),
+  message_type = c("simple", "quiet", "verbose")
+) {
   what <- match.arg(what, choices = c("nix-build", "expr", "nix-hash"))
-  message_type <- match.arg(message_type,
+  message_type <- match.arg(
+    message_type,
     choices = c("simple", "quiet", "verbose")
   )
   is_quiet <- message_type == "quiet"
@@ -97,13 +100,15 @@ poll_sys_proc_blocking <- function(cmd, proc,
 #' with an error code. The waiting is implemented to not create race conditions
 #'
 #' @noRd
-poll_sys_proc_nonblocking <- function(cmd,
-                                      proc,
-                                      what = c("nix-build", "expr", "nix-hash"),
-                                      message_type =
-                                        c("simple", "quiet", "verbose")) {
+poll_sys_proc_nonblocking <- function(
+  cmd,
+  proc,
+  what = c("nix-build", "expr", "nix-hash"),
+  message_type = c("simple", "quiet", "verbose")
+) {
   what <- match.arg(what, choices = c("nix-build", "expr", "nix-hash"))
-  message_type <- match.arg(message_type,
+  message_type <- match.arg(
+    message_type,
     choices = c("simple", "quiet", "verbose")
   )
   is_quiet <- message_type == "quiet"
@@ -119,7 +124,8 @@ poll_sys_proc_nonblocking <- function(cmd,
     tools::pskill(pid = proc)
     stop(
       "`nix_build()` likely interrupted by SIGINT (ctrl+c)\n",
-      "Stop process with PID ", proc
+      "Stop process with PID ",
+      proc
     )
   }
 
@@ -151,7 +157,8 @@ nix_build_installed <- function() {
 nix_build_exit_msg <- function(x) {
   x_char <- as.character(x)
 
-  err_msg <- switch(x_char,
+  err_msg <- switch(
+    x_char,
     "100" = "generic build failure (100).",
     "101" = "build timeout (101).",
     "102" = "hash mismatch (102).",

R/renv_helpers.R

@@ -40,7 +40,9 @@ read_renv_lock <- function(renv_lock_path = "renv.lock") {
 #' renv_remote_pkgs(read_renv_lock()$Packages)
 #' }
 renv_remote_pkgs <- function(
-    renv_lock_remote_pkgs, host = NULL) {
+  renv_lock_remote_pkgs,
+  host = NULL
+) {
   # , "bitbucket", "git", "local", "svn", "url", "version", "cran", "bioc"
   supported_pkg_hosts <- c("api.github.com", "gitlab.com")
   if (!(is.null(host) || (host %in% supported_pkg_hosts))) {
@@ -61,37 +63,50 @@ renv_remote_pkgs <- function(
         host <- renv_lock_pkg_info$RemoteHost
       } else {
         stop(
-          renv_lock_pkg_info$Package, " has unsupported remote host: ",
-          renv_lock_pkg_info$RemoteHost, "\nSupported hosts are: ",
+          renv_lock_pkg_info$Package,
+          " has unsupported remote host: ",
+          renv_lock_pkg_info$RemoteHost,
+          "\nSupported hosts are: ",
           paste0(supported_pkg_hosts, collapse = ", ")
         )
       }
     } else {
       if (host != renv_lock_pkg_info$RemoteHost) {
         stop(
-          "Remote host (", renv_lock_pkg_info$RemoteHost, ") of ", renv_lock_pkg_info$Package,
-          " does not match the provided host (", host, ")"
+          "Remote host (",
+          renv_lock_pkg_info$RemoteHost,
+          ") of ",
+          renv_lock_pkg_info$Package,
+          " does not match the provided host (",
+          host,
+          ")"
         )
       }
     }
 
     pkg_info <- vector(mode = "list", length = 3)
     names(pkg_info) <- c("package_name", "repo_url", "commit")
-    switch(host,
+    switch(
+      host,
       "api.github.com" = {
         pkg_info[[1]] <- renv_lock_pkg_info$Package
         pkg_info[[2]] <- paste0(
           # RemoteHost is listed as api.github.com for some reason
-          "https://github.com/", renv_lock_pkg_info$RemoteUser, "/",
+          "https://github.com/",
+          renv_lock_pkg_info$RemoteUser,
+          "/",
           renv_lock_pkg_info$RemoteRepo
         )
         pkg_info[[3]] <- renv_lock_pkg_info$RemoteSha
       },
       "gitlab.com" = {
         pkg_info[[1]] <- renv_lock_pkg_info$Package
         pkg_info[[2]] <- paste0(
-          "https://", renv_lock_pkg_info$RemoteHost, "/",
-          renv_lock_pkg_info$RemoteUser, "/",
+          "https://",
+          renv_lock_pkg_info$RemoteHost,
+          "/",
+          renv_lock_pkg_info$RemoteUser,
+          "/",
           renv_lock_pkg_info$RemoteRepo
         )
         pkg_info[[3]] <- renv_lock_pkg_info$RemoteSha
@@ -159,12 +174,13 @@ renv_remote_pkgs <- function(
 #' }
 #'
 renv2nix <- function(
-    renv_lock_path = "renv.lock",
-    project_path,
-    return_rix_call = FALSE,
-    method = c("fast", "accurate"),
-    override_r_ver = NULL,
-    ...) {
+  renv_lock_path = "renv.lock",
+  project_path,
+  return_rix_call = FALSE,
+  method = c("fast", "accurate"),
+  override_r_ver = NULL,
+  ...
+) {
   method <- match.arg(method, c("fast", "accurate"))
   renv_lock <- read_renv_lock(renv_lock_path = renv_lock_path)
   if (method == "fast") {
@@ -175,13 +191,18 @@ renv2nix <- function(
     for (i in seq_along(renv_lock$Packages)) {
       if (renv_lock$Packages[[i]]$Source %in% c("Repository", "Bioconductor")) {
         repo_pkgs[[renv_lock_pkg_names[i]]] <- renv_lock$Packages[[i]]
-      } else if (renv_lock$Packages[[i]]$RemoteHost %in% c("api.github.com", "gitlab.com")) {
+      } else if (
+        renv_lock$Packages[[i]]$RemoteHost %in%
+          c("api.github.com", "gitlab.com")
+      ) {
         remote_pkgs[[renv_lock_pkg_names[i]]] <- renv_lock$Packages[[i]]
       } else {
         # unsupported_pkgs[[renv_lock_pkg_names[i]]] <- renv_lock$Packages[[i]]
         warning(
-          renv_lock$Packages[[i]]$Package, " has the unsupported remote host ",
-          renv_lock$Packages[[i]]$RemoteHost, " and will not be included in the Nix expression.",
+          renv_lock$Packages[[i]]$Package,
+          " has the unsupported remote host ",
+          renv_lock$Packages[[i]]$RemoteHost,
+          " and will not be included in the Nix expression.",
           "\n Consider manually specifying the git remote or a local package install."
         )
       }