Bump Vampire/setup-wsl from 6 to 7

.github/workflows/R-CMD-check-wsl.yaml

@@ -30,11 +30,6 @@ jobs:
       CMDSTANR_OPENCL_TESTS: true
 
     steps:
-      - name: cmdstan env vars
-        run: |
-          echo "CMDSTAN_PATH=${HOME}/.cmdstan" >> $GITHUB_ENV
-        shell: bash
-
       - uses: actions/checkout@v6
 
       - uses: r-lib/actions/setup-r@v2
@@ -44,7 +39,7 @@ jobs:
         with:
           extra-packages: any::rcmdcheck, local::.
 
-      - uses: Vampire/setup-wsl@v6
+      - uses: Vampire/setup-wsl@v7
         with:
             distribution: Ubuntu-22.04
             wsl-version: 2
@@ -55,12 +50,18 @@ jobs:
         run: |
           sudo apt-get update
           sudo apt-get install -y build-essential libopenmpi-dev ocl-icd-opencl-dev pocl-opencl-icd
+          sudo chmod 755 /root
         shell: wsl-bash {0}
 
       - name: Install cmdstan
         run: |
           cmdstanr::check_cmdstan_toolchain()
           cmdstanr::install_cmdstan(cores = 2, wsl = TRUE, overwrite = TRUE)
+          cat(
+            paste0("CMDSTAN=", cmdstanr::cmdstan_path(), "\n"),
+            file = Sys.getenv("GITHUB_ENV"),
+            append = TRUE
+          )
         shell: Rscript {0}
 
       - name: Session info

.github/workflows/R-CMD-check.yaml

@@ -53,11 +53,6 @@ jobs:
       PKG_SYSREQS_DB_UPDATE_TIMEOUT: 30s
 
     steps:
-      - name: cmdstan env vars
-        run: |
-          echo "CMDSTAN_PATH=${HOME}/.cmdstan" >> $GITHUB_ENV
-        shell: bash
-
       - uses: actions/checkout@v6
 
       - uses: r-lib/actions/setup-r@v2

.github/workflows/Test-coverage.yaml

@@ -32,11 +32,6 @@ jobs:
       NOT_CRAN: true
 
     steps:
-      - name: cmdstan env vars
-        run: |
-          echo "CMDSTAN_PATH=${HOME}/.cmdstan" >> $GITHUB_ENV
-        shell: bash
-
       - uses: n1hility/cancel-previous-runs@v3
         with:
           token: ${{ secrets.GITHUB_TOKEN }}

R/install.R

@@ -327,11 +327,17 @@ cmdstan_make_local <- function(dir = cmdstan_path(),
     }
     write(built_flags, file = make_local_path, append = append)
   }
-  if (file.exists(make_local_path)) {
-    return(trimws(strsplit(trimws(readChar(make_local_path, file.info(make_local_path)$size)), "\n")[[1]]))
-  } else {
+  make_local_contents <- tryCatch(
+    suppressWarnings(readLines(make_local_path, warn = FALSE)),
+    error = function(e) NULL
+  )
+  if (is.null(make_local_contents)) {
     return(NULL)
   }
+  if (length(make_local_contents) == 0) {
+    return("")
+  }
+  trimws(strsplit(trimws(paste(make_local_contents, collapse = "\n")), "\n", fixed = TRUE)[[1]])
 }
 
 #' @rdname install_cmdstan

R/path.R

@@ -9,7 +9,8 @@
 #' @export
 #'
 #' @param path (string) The full file path to the CmdStan installation. If
-#'   `NULL` (the default) then the path is set to the default path used by
+#'   `NULL` (the default) then the path is set using the `"CMDSTAN"`
+#'   environment variable when available, otherwise the default path used by
 #'   [install_cmdstan()] if it exists.
 #' @return A string. Either the file path to the CmdStan installation or the
 #'   CmdStan version number.
@@ -39,7 +40,20 @@
 #'
 set_cmdstan_path <- function(path = NULL) {
   if (is.null(path)) {
-    path <- cmdstan_default_path()
+    env_path <- resolve_cmdstan_path_from_env()
+    if (isTRUE(is.na(env_path))) {
+      unset_cmdstan_path()
+      return(invisible(NULL))
+    }
+    if (!is.null(env_path)) {
+      path <- env_path
+    } else {
+      path <- cmdstan_default_path()
+      if (is.null(path)) {
+        unset_cmdstan_path()
+        return(invisible(NULL))
+      }
+    }
   }
   if (dir.exists(path)) {
     path <- absolute_path(path)
@@ -50,17 +64,15 @@ set_cmdstan_path <- function(path = NULL) {
         "cmdstanr now requires CmdStan v", cmdstan_min_version(), " or newer.",
         call. = FALSE
       )
-      .cmdstanr$PATH <- NULL
-      .cmdstanr$VERSION <- NULL
-      .cmdstanr$WSL <- FALSE
+      unset_cmdstan_path()
       return(invisible(path))
     }
     .cmdstanr$PATH <- path
     .cmdstanr$VERSION <- version
     .cmdstanr$WSL <- grepl("//wsl$", path, fixed = TRUE)
     message("CmdStan path set to: ", path)
   } else {
-    warning("Path not set. Can't find directory: ", path, call. = FALSE)
+    warning("CmdStan path not set. Can't find directory: ", path, call. = FALSE)
   }
   invisible(path)
 }
@@ -102,6 +114,12 @@ cmdstan_version <- function(error_on_NA = TRUE) {
 .cmdstanr$TEMP_DIR <- NULL
 .cmdstanr$WSL <- FALSE
 
+unset_cmdstan_path <- function() {
+  .cmdstanr$PATH <- NULL
+  .cmdstanr$VERSION <- NULL
+  .cmdstanr$WSL <- FALSE
+}
+
 # path to temp directory
 cmdstan_tempdir <- function() {
   .cmdstanr$TEMP_DIR
@@ -128,8 +146,36 @@ is_supported_cmdstan_version <- function(version) {
   isTRUE(cmp >= 0)
 }
 
-#' cmdstan_default_install_path
-#'
+resolve_cmdstan_path_from_env <- function() {
+  path <- Sys.getenv("CMDSTAN")
+  if (!nzchar(path)) {
+    return(NULL)
+  }
+  if (!dir.exists(path)) {
+    warning(
+      "CmdStan path not set. Can't find directory specified by environment ",
+      "variable 'CMDSTAN'.",
+      call. = FALSE
+    )
+    return(NA_character_)
+  }
+  path <- absolute_path(path)
+  version <- suppressWarnings(read_cmdstan_version(path))
+  if (!is.null(version)) {
+    return(path)
+  }
+  path <- cmdstan_default_path(dir = path)
+  if (is.null(path)) {
+    warning(
+      "CmdStan path not set. No CmdStan installation found in the path ",
+      "specified by the environment variable 'CMDSTAN'.",
+      call. = FALSE
+    )
+    return(NA_character_)
+  }
+  path
+}
+
 #' Path to where  [install_cmdstan()] with default settings installs CmdStan.
 #'
 #' @keywords internal
@@ -140,14 +186,24 @@ cmdstan_default_install_path <- function(wsl = FALSE) {
   if (wsl) {
     file.path(paste0(wsl_dir_prefix(wsl = TRUE), wsl_home_dir()), ".cmdstan")
   } else {
-    file.path(.home_path(), ".cmdstan")
+    file.path(home_path(), ".cmdstan")
   }
 }
 
-#' cmdstan_default_path
-#'
-#' Returns the path to the installation of CmdStan with the most recent release
-#' version.
+home_path <- function() {
+  home <- Sys.getenv("HOME")
+  if (os_is_windows()) {
+    userprofile <- Sys.getenv("USERPROFILE")
+    h_drivepath <- file.path(Sys.getenv("HOMEDRIVE"), Sys.getenv("HOMEPATH"))
+    win_home <- ifelse(userprofile == "", h_drivepath, userprofile)
+    if (win_home != "") {
+      home <- win_home
+    }
+  }
+  home
+}
+
+#' Path to the installation of CmdStan with the most recent release version
 #'
 #' For Windows systems with WSL CmdStan installs, if there are side-by-side WSL
 #' and native installs with the same version then the WSL is preferred.
@@ -180,9 +236,9 @@ cmdstan_default_path <- function(dir = NULL) {
   }
   if (dir.exists(installs_path) || wsl_path_exists) {
     latest_cmdstan <- ifelse(dir.exists(installs_path),
-                             .latest_cmdstan_installed(installs_path), "")
+                             latest_cmdstan_installed(installs_path), "")
     latest_wsl_cmdstan <- ifelse(wsl_path_exists,
-                                 .latest_cmdstan_installed(wsl_installs_path), "")
+                                 latest_cmdstan_installed(wsl_installs_path), "")
     if (!nzchar(latest_cmdstan) && !nzchar(latest_wsl_cmdstan)) {
       return(NULL)
     }
@@ -195,16 +251,8 @@ cmdstan_default_path <- function(dir = NULL) {
   NULL
 }
 
-.latest_cmdstan_installed <- function(installs_path) {
+latest_cmdstan_installed <- function(installs_path) {
   cmdstan_installs <- list.dirs(path = installs_path, recursive = FALSE, full.names = FALSE)
-  # if installed in cmdstan folder with no version move to cmdstan-version folder
-  if ("cmdstan" %in% cmdstan_installs) {
-    ver <- read_cmdstan_version(file.path(installs_path, "cmdstan"))
-    old_path <- file.path(installs_path, "cmdstan")
-    new_path <- file.path(installs_path, paste0("cmdstan-", ver))
-    file.rename(old_path, new_path)
-    cmdstan_installs <- list.dirs(path = installs_path, recursive = FALSE, full.names = FALSE)
-  }
   latest_cmdstan <- ""
   if (length(cmdstan_installs) > 0) {
     cmdstan_installs <- grep("^cmdstan-", cmdstan_installs, value = TRUE)
@@ -219,29 +267,109 @@ cmdstan_default_path <- function(dir = NULL) {
   latest_cmdstan
 }
 
+is_wsl_unc_path <- function(path) {
+  is.character(path) &&
+    length(path) == 1 &&
+    !is.na(path) &&
+    startsWith(repair_path(path), "//wsl$/")
+}
+
+# Extract the distro name from a WSL UNC path like //wsl$/Ubuntu-22.04/...
+wsl_unc_distro_name <- function(path) {
+  sub("^//wsl\\$/([^/]+).*$", "\\1", repair_path(path))
+}
+
+# Convert a WSL UNC path to the corresponding Linux path within the distro.
+wsl_unc_path_to_linux <- function(path) {
+  sub("^//wsl\\$/[^/]+", "", repair_path(path))
+}
+
+cmdstan_version_from_path <- function(path) {
+  path <- repair_path(path)
+  match <- regmatches(
+    path,
+    regexpr("cmdstan-[0-9]+\\.[0-9]+\\.[0-9]+(?:-rc[0-9]+)?$", path)
+  )
+  if (!length(match) || is.na(match) || !nzchar(match)) {
+    return(NULL)
+  }
+  sub("^cmdstan-", "", match)
+}
+
+read_lines_direct <- function(path) {
+  tryCatch(
+    suppressWarnings(readLines(path, warn = FALSE)),
+    error = function(e) NULL
+  )
+}
+
+# Fall back to reading through `wsl` when Windows R can't read a WSL UNC path.
+read_lines_via_wsl <- function(path) {
+  wsl_args <- list(
+    c("cat", wsl_unc_path_to_linux(path)),
+    c("-d", wsl_unc_distro_name(path), "cat", wsl_unc_path_to_linux(path))
+  )
+  file_contents <- NULL
+  for (args in wsl_args) {
+    file_contents <- processx::run(
+      command = "wsl",
+      args = args,
+      error_on_status = FALSE
+    )
+    if (file_contents$status == 0) {
+      break
+    }
+  }
+  if (is.null(file_contents) || file_contents$status != 0) {
+    return(NULL)
+  }
+  if (!nzchar(file_contents$stdout)) {
+    return(character(0))
+  }
+  con <- textConnection(file_contents$stdout)
+  on.exit(close(con), add = TRUE)
+  readLines(con, warn = FALSE)
+}
+
+# Preserve existing direct reads and only use the WSL fallback when needed.
+read_lines_with_wsl_fallback <- function(path) {
+  file_contents <- read_lines_direct(path)
+  if (!is.null(file_contents) || !is_wsl_unc_path(path)) {
+    return(file_contents)
+  }
+  read_lines_via_wsl(path)
+}
+
 
 #' Find the version of CmdStan from makefile
 #' @noRd
 #' @param path Path to installation.
 #' @return Version number as a string.
 read_cmdstan_version <- function(path) {
   makefile_path <- file.path(path, "makefile")
-  if (!file.exists(makefile_path)) {
+  makefile <- read_lines_with_wsl_fallback(makefile_path)
+  if (is.null(makefile)) {
+    if (is_wsl_unc_path(path)) {
+      version_from_path <- cmdstan_version_from_path(path)
+      if (!is.null(version_from_path)) {
+        return(version_from_path)
+      }
+    }
     warning(
       "Can't find CmdStan makefile to detect version number. ",
       "Path may not point to valid installation.",
       call. = FALSE
     )
     return(NULL)
   }
-  makefile <- readLines(makefile_path)
   version_line <- grep("^CMDSTAN_VERSION :=", makefile, value = TRUE)
   if (length(version_line) == 0) {
     stop("CmdStan makefile is missing a version number.", call. = FALSE)
   }
   sub("CMDSTAN_VERSION := ", "", version_line)
 }
 
+
 #' Returns whether the supplied installation is a release candidate
 #' @noRd
 #' @param path Path to installation.
@@ -253,12 +381,6 @@ is_release_candidate <- function(path) {
   grepl(pattern = "-rc[0-9]*$", x = path)
 }
 
-# unset the path (only used in tests)
-unset_cmdstan_path <- function() {
-  .cmdstanr$PATH <- NULL
-  .cmdstanr$VERSION <- NULL
-  .cmdstanr$WSL <- FALSE
-}
 
 # fake a cmdstan version (only used in tests)
 fake_cmdstan_version <- function(version, mod = NULL) {
@@ -275,16 +397,3 @@ fake_cmdstan_version <- function(version, mod = NULL) {
 reset_cmdstan_version <- function(mod = NULL) {
   fake_cmdstan_version(read_cmdstan_version(cmdstan_path()), mod = mod)
 }
-
-.home_path <- function() {
-  home <- Sys.getenv("HOME")
-  if (os_is_windows()) {
-    userprofile <- Sys.getenv("USERPROFILE")
-    h_drivepath <- file.path(Sys.getenv("HOMEDRIVE"), Sys.getenv("HOMEPATH"))
-    win_home <- ifelse(userprofile == "", h_drivepath, userprofile)
-    if (win_home != "") {
-      home <- win_home
-    }
-  }
-  home
-}