From bb5aeca97ba05dc0a0c54173e5640d408723ac38 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 13 Apr 2026 19:11:04 +0000
Subject: [PATCH 1/7] Bump Vampire/setup-wsl from 6 to 7

Bumps [Vampire/setup-wsl](https://github.com/vampire/setup-wsl) from 6 to 7.
- [Release notes](https://github.com/vampire/setup-wsl/releases)
- [Commits](https://github.com/vampire/setup-wsl/compare/v6...v7)

---
updated-dependencies:
- dependency-name: Vampire/setup-wsl
  dependency-version: '7'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/R-CMD-check-wsl.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/R-CMD-check-wsl.yaml b/.github/workflows/R-CMD-check-wsl.yaml
index 2d6475c3..7e77a422 100644
--- a/.github/workflows/R-CMD-check-wsl.yaml
+++ b/.github/workflows/R-CMD-check-wsl.yaml
@@ -44,7 +44,7 @@ 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

From 33f435ca716fc5a65c22872ceeedc4864847eed4 Mon Sep 17 00:00:00 2001
From: jgabry <jgabry@gmail.com>
Date: Mon, 13 Apr 2026 20:21:06 -0600
Subject: [PATCH 2/7] try fixing WSL CI

---
 .github/workflows/R-CMD-check-wsl.yaml | 7 ++++++-
 .github/workflows/R-CMD-check.yaml     | 2 +-
 .github/workflows/Test-coverage.yaml   | 2 +-
 3 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/R-CMD-check-wsl.yaml b/.github/workflows/R-CMD-check-wsl.yaml
index 7e77a422..a753680b 100644
--- a/.github/workflows/R-CMD-check-wsl.yaml
+++ b/.github/workflows/R-CMD-check-wsl.yaml
@@ -32,7 +32,7 @@ jobs:
     steps:
       - name: cmdstan env vars
         run: |
-          echo "CMDSTAN_PATH=${HOME}/.cmdstan" >> $GITHUB_ENV
+          echo "CMDSTAN=${HOME}/.cmdstan" >> $GITHUB_ENV
         shell: bash
 
       - uses: actions/checkout@v6
@@ -61,6 +61,11 @@ jobs:
         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
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index be322ea4..a0df178b 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -55,7 +55,7 @@ jobs:
     steps:
       - name: cmdstan env vars
         run: |
-          echo "CMDSTAN_PATH=${HOME}/.cmdstan" >> $GITHUB_ENV
+          echo "CMDSTAN=${HOME}/.cmdstan" >> $GITHUB_ENV
         shell: bash
 
       - uses: actions/checkout@v6
diff --git a/.github/workflows/Test-coverage.yaml b/.github/workflows/Test-coverage.yaml
index 5598d53b..65a2b4e4 100644
--- a/.github/workflows/Test-coverage.yaml
+++ b/.github/workflows/Test-coverage.yaml
@@ -34,7 +34,7 @@ jobs:
     steps:
       - name: cmdstan env vars
         run: |
-          echo "CMDSTAN_PATH=${HOME}/.cmdstan" >> $GITHUB_ENV
+          echo "CMDSTAN=${HOME}/.cmdstan" >> $GITHUB_ENV
         shell: bash
 
       - uses: n1hility/cancel-previous-runs@v3

From 6d7187cc694154993b098fa4054ae4d2b6480f35 Mon Sep 17 00:00:00 2001
From: jgabry <jgabry@gmail.com>
Date: Tue, 14 Apr 2026 08:20:45 -0600
Subject: [PATCH 3/7] Remove unnecessary cmdstan env vars step in all workflows

---
 .github/workflows/R-CMD-check-wsl.yaml | 5 -----
 .github/workflows/R-CMD-check.yaml     | 5 -----
 .github/workflows/Test-coverage.yaml   | 5 -----
 3 files changed, 15 deletions(-)

diff --git a/.github/workflows/R-CMD-check-wsl.yaml b/.github/workflows/R-CMD-check-wsl.yaml
index a753680b..6b564d1d 100644
--- a/.github/workflows/R-CMD-check-wsl.yaml
+++ b/.github/workflows/R-CMD-check-wsl.yaml
@@ -30,11 +30,6 @@ jobs:
       CMDSTANR_OPENCL_TESTS: true
 
     steps:
-      - name: cmdstan env vars
-        run: |
-          echo "CMDSTAN=${HOME}/.cmdstan" >> $GITHUB_ENV
-        shell: bash
-
       - uses: actions/checkout@v6
 
       - uses: r-lib/actions/setup-r@v2
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index a0df178b..85293dab 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.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=${HOME}/.cmdstan" >> $GITHUB_ENV
-        shell: bash
-
       - uses: actions/checkout@v6
 
       - uses: r-lib/actions/setup-r@v2
diff --git a/.github/workflows/Test-coverage.yaml b/.github/workflows/Test-coverage.yaml
index 65a2b4e4..166ad66c 100644
--- a/.github/workflows/Test-coverage.yaml
+++ b/.github/workflows/Test-coverage.yaml
@@ -32,11 +32,6 @@ jobs:
       NOT_CRAN: true
 
     steps:
-      - name: cmdstan env vars
-        run: |
-          echo "CMDSTAN=${HOME}/.cmdstan" >> $GITHUB_ENV
-        shell: bash
-
       - uses: n1hility/cancel-previous-runs@v3
         with:
           token: ${{ secrets.GITHUB_TOKEN }}

From 11d90f355525743addcf2fd745d4ac021b3f5f16 Mon Sep 17 00:00:00 2001
From: Visruth Srimath Kandali <public@visruth.com>
Date: Tue, 14 Apr 2026 09:55:38 -0700
Subject: [PATCH 4/7] Update R-CMD-check-wsl.yaml

Trying what copilot suggested--user perms changed with v7
---
 .github/workflows/R-CMD-check-wsl.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/R-CMD-check-wsl.yaml b/.github/workflows/R-CMD-check-wsl.yaml
index 6b564d1d..699958a9 100644
--- a/.github/workflows/R-CMD-check-wsl.yaml
+++ b/.github/workflows/R-CMD-check-wsl.yaml
@@ -50,6 +50,7 @@ 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

From c7621839938bd81ad8d4376cff84c0e2abe9911e Mon Sep 17 00:00:00 2001
From: jgabry <jgabry@gmail.com>
Date: Tue, 14 Apr 2026 12:31:51 -0600
Subject: [PATCH 5/7] Honor CMDSTAN in set_cmdstan_path()

---
 R/path.R                   | 108 +++++++++++++++++++++++++------------
 R/zzz.R                    |  41 +-------------
 man/set_cmdstan_path.Rd    |   3 +-
 tests/testthat/test-path.R |  27 +++++++++-
 4 files changed, 102 insertions(+), 77 deletions(-)

diff --git a/R/path.R b/R/path.R
index 3e4fecc1..a8af3565 100644
--- a/R/path.R
+++ b/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)
@@ -50,9 +64,7 @@ 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
@@ -60,7 +72,7 @@ set_cmdstan_path <- function(path = NULL) {
     .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)
     }
@@ -195,7 +251,7 @@ 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) {
@@ -242,6 +298,7 @@ read_cmdstan_version <- function(path) {
   sub("CMDSTAN_VERSION := ", "", version_line)
 }
 
+
 #' Returns whether the supplied installation is a release candidate
 #' @noRd
 #' @param path Path to installation.
@@ -253,12 +310,6 @@ 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 +326,3 @@ 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
-}
diff --git a/R/zzz.R b/R/zzz.R
index 68d59245..bea367db 100644
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -35,46 +35,7 @@ startup_messages <- function() {
 }
 
 cmdstanr_initialize <- function() {
-  # First check for environment variable CMDSTAN, but if not found
-  # then see if default
-  path <- Sys.getenv("CMDSTAN")
-  if (isTRUE(nzchar(path))) { # CMDSTAN environment variable found
-    if (dir.exists(path)) {
-      path <- absolute_path(path)
-      suppressWarnings(suppressMessages(set_cmdstan_path(path)))
-      if (is.null(cmdstan_version(error_on_NA = FALSE))) {
-        path <- cmdstan_default_path(dir = path)
-        if (is.null(path)) {
-          warning(
-            "No CmdStan installation found in the path specified ",
-            "by the environment variable 'CMDSTAN'.",
-            call. = FALSE
-          )
-          .cmdstanr$PATH <- NULL
-          .cmdstanr$VERSION <- NULL
-          .cmdstanr$WSL <- FALSE
-        } else {
-          set_cmdstan_path(path)
-        }
-      }
-    } else {
-      warning(
-        "Can't find directory specified by environment variable 'CMDSTAN'. ",
-        "Path not set.",
-        call. = FALSE
-      )
-      .cmdstanr$PATH <- NULL
-      .cmdstanr$VERSION <- NULL
-      .cmdstanr$WSL <- FALSE
-    }
-
-  } else { # environment variable not found
-    path <- cmdstan_default_path()
-    if (!is.null(path)) {
-      suppressMessages(set_cmdstan_path(path))
-    }
-  }
-
+  suppressMessages(set_cmdstan_path())
   .cmdstanr$TEMP_DIR <- tempdir(check = TRUE)
   invisible(TRUE)
 }
diff --git a/man/set_cmdstan_path.Rd b/man/set_cmdstan_path.Rd
index b803cdd8..fe77e09c 100644
--- a/man/set_cmdstan_path.Rd
+++ b/man/set_cmdstan_path.Rd
@@ -14,7 +14,8 @@ cmdstan_version(error_on_NA = TRUE)
 }
 \arguments{
 \item{path}{(string) The full file path to the CmdStan installation. If
-\code{NULL} (the default) then the path is set to the default path used by
+\code{NULL} (the default) then the path is set using the \code{"CMDSTAN"}
+environment variable when available, otherwise the default path used by
 \code{\link[=install_cmdstan]{install_cmdstan()}} if it exists.}
 
 \item{error_on_NA}{(logical) Should an error be thrown if CmdStan is not
diff --git a/tests/testthat/test-path.R b/tests/testthat/test-path.R
index 5bc25819..d2c7d9d7 100644
--- a/tests/testthat/test-path.R
+++ b/tests/testthat/test-path.R
@@ -45,6 +45,31 @@ test_that("Setting path from env var is detected", {
   expect_false(is.null(.cmdstanr$VERSION))
 })
 
+test_that("set_cmdstan_path() uses CMDSTAN env var when path is omitted", {
+  unset_cmdstan_path()
+  withr::local_envvar(c(CMDSTAN = PATH))
+  expect_message(
+    set_cmdstan_path(),
+    paste("CmdStan path set to:", PATH),
+    fixed = TRUE
+  )
+  expect_equal(cmdstan_path(), PATH)
+})
+
+test_that("set_cmdstan_path() clears cached state when no path is detected", {
+  .cmdstanr$PATH <- PATH
+  .cmdstanr$VERSION <- VERSION
+  .cmdstanr$WSL <- TRUE
+  local_mocked_bindings(
+    resolve_cmdstan_path_from_env = function() NULL,
+    cmdstan_default_path = function(dir = NULL) NULL
+  )
+  expect_silent(set_cmdstan_path())
+  expect_null(.cmdstanr$PATH)
+  expect_null(.cmdstanr$VERSION)
+  expect_false(isTRUE(.cmdstanr$WSL))
+})
+
 test_that("Unsupported CmdStan path from env var is rejected", {
   unset_cmdstan_path()
   .cmdstanr$WSL <- TRUE
@@ -73,7 +98,7 @@ test_that("Existing CMDSTAN env path with no install resets cached state", {
   withr::local_envvar(c(CMDSTAN = empty_parent))
   expect_warning(
     cmdstanr_initialize(),
-    "No CmdStan installation found in the path specified by the environment variable 'CMDSTAN'.",
+    "CmdStan path not set. No CmdStan installation found in the path specified by the environment variable 'CMDSTAN'.",
     fixed = TRUE
   )
   expect_null(.cmdstanr$PATH)

From f5c8c2425688613a4979c02b8743ac3bbd203bde Mon Sep 17 00:00:00 2001
From: jgabry <jgabry@gmail.com>
Date: Tue, 14 Apr 2026 12:32:19 -0600
Subject: [PATCH 6/7] update Rd files

---
 man/cmdstan_default_install_path.Rd |  2 +-
 man/cmdstan_default_path.Rd         |  6 +-----
 man/cmdstanr-package.Rd             | 21 +++++++++++----------
 3 files changed, 13 insertions(+), 16 deletions(-)

diff --git a/man/cmdstan_default_install_path.Rd b/man/cmdstan_default_install_path.Rd
index b5ebd9b7..5faaa03e 100644
--- a/man/cmdstan_default_install_path.Rd
+++ b/man/cmdstan_default_install_path.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/path.R
 \name{cmdstan_default_install_path}
 \alias{cmdstan_default_install_path}
-\title{cmdstan_default_install_path}
+\title{Path to where  \code{\link[=install_cmdstan]{install_cmdstan()}} with default settings installs CmdStan.}
 \usage{
 cmdstan_default_install_path(wsl = FALSE)
 }
diff --git a/man/cmdstan_default_path.Rd b/man/cmdstan_default_path.Rd
index 2d4ffe9b..c4b8f3fb 100644
--- a/man/cmdstan_default_path.Rd
+++ b/man/cmdstan_default_path.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/path.R
 \name{cmdstan_default_path}
 \alias{cmdstan_default_path}
-\title{cmdstan_default_path}
+\title{Path to the installation of CmdStan with the most recent release version}
 \usage{
 cmdstan_default_path(dir = NULL)
 }
@@ -14,10 +14,6 @@ Path to the CmdStan installation with the most recent release
 version, or \code{NULL} if no installation found.
 }
 \description{
-Returns the path to the installation of CmdStan with the most recent release
-version.
-}
-\details{
 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.
 Otherwise, the most recent release is chosen, regardless of whether it is
diff --git a/man/cmdstanr-package.Rd b/man/cmdstanr-package.Rd
index e6479f57..be303bac 100644
--- a/man/cmdstanr-package.Rd
+++ b/man/cmdstanr-package.Rd
@@ -34,22 +34,22 @@ algorithms, and writing results to output files.
 \subsection{Advantages of RStan}{
 \itemize{
 \item Allows other developers to distribute R packages with \emph{pre-compiled}
-Stan programs (like \strong{rstanarm}) on CRAN. (Note: As of 2023, this
-can mostly be achieved with CmdStanR as well. See \href{https://mc-stan.org/cmdstanr/articles/cmdstanr-internals.html#developing-using-cmdstanr}{Developing using CmdStanR}.)
-\item Avoids use of R6 classes, which may result in more familiar syntax
-for many R users.
+Stan programs (like \strong{rstanarm}) on CRAN. (Note: As of 2023, this can
+mostly be achieved with CmdStanR as well. See \href{https://mc-stan.org/cmdstanr/articles/cmdstanr-internals.html#developing-using-cmdstanr}{Developing using CmdStanR}.)
+\item Avoids use of R6 classes, which may result in more familiar syntax for
+many R users.
 \item CRAN binaries available for Mac and Windows.
 }
 }
 
 \subsection{Advantages of CmdStanR}{
 \itemize{
-\item Compatible with latest versions of Stan. Keeping up with Stan
-releases is complicated for RStan, often requiring non-trivial
-changes to the \strong{rstan} package and new CRAN releases of both
-\strong{rstan} and \strong{StanHeaders}. With CmdStanR the latest improvements
-in Stan will be available from R immediately after updating CmdStan
-using \code{cmdstanr::install_cmdstan()}.
+\item Compatible with latest versions of Stan. Keeping up with Stan releases
+is complicated for RStan, often requiring non-trivial changes to the
+\strong{rstan} package and new CRAN releases of both \strong{rstan} and
+\strong{StanHeaders}. With CmdStanR the latest improvements in Stan will be
+available from R immediately after updating CmdStan using
+\code{cmdstanr::install_cmdstan()}.
 \item Running Stan via external processes results in fewer unexpected
 crashes, especially in RStudio.
 \item Less memory overhead.
@@ -229,6 +229,7 @@ Other contributors:
   \item Martin Modrák [contributor]
   \item Ven Popov [contributor]
   \item Visruth Srimath Kandali [contributor]
+  \item Aki Vehtari [contributor]
 }
 
 }

From 5b9717f7dcbb81d7ad3eaa04e6f17bdf8e50779e Mon Sep 17 00:00:00 2001
From: jgabry <jgabry@gmail.com>
Date: Tue, 14 Apr 2026 16:22:25 -0600
Subject: [PATCH 7/7] Avoid fragile file checks on WSL CmdStan paths

---
 R/install.R                 | 12 +++++++++---
 R/path.R                    | 15 +++++----------
 tests/testthat/test-path.R  | 12 ++++++++++++
 tests/testthat/test-utils.R |  8 ++++++++
 4 files changed, 34 insertions(+), 13 deletions(-)

diff --git a/R/install.R b/R/install.R
index 2aa5453c..ee91fd1c 100644
--- a/R/install.R
+++ b/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
diff --git a/R/path.R b/R/path.R
index a8af3565..6df8e65b 100644
--- a/R/path.R
+++ b/R/path.R
@@ -253,14 +253,6 @@ cmdstan_default_path <- function(dir = NULL) {
 
 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)
@@ -282,7 +274,11 @@ latest_cmdstan_installed <- function(installs_path) {
 #' @return Version number as a string.
 read_cmdstan_version <- function(path) {
   makefile_path <- file.path(path, "makefile")
-  if (!file.exists(makefile_path)) {
+  makefile <- tryCatch(
+    suppressWarnings(readLines(makefile_path, warn = FALSE)),
+    error = function(e) NULL
+  )
+  if (is.null(makefile)) {
     warning(
       "Can't find CmdStan makefile to detect version number. ",
       "Path may not point to valid installation.",
@@ -290,7 +286,6 @@ read_cmdstan_version <- function(path) {
     )
     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)
diff --git a/tests/testthat/test-path.R b/tests/testthat/test-path.R
index d2c7d9d7..aff71d08 100644
--- a/tests/testthat/test-path.R
+++ b/tests/testthat/test-path.R
@@ -203,6 +203,18 @@ test_that("cmdstan_default_path() returns NULL for empty custom install director
   expect_null(cmdstan_default_path(dir = installs))
 })
 
+test_that("cmdstan_default_path() ignores unversioned cmdstan directory", {
+  installs <- withr::local_tempdir(pattern = "cmdstan-legacy-installs")
+  dir.create(file.path(installs, "cmdstan"), recursive = TRUE, showWarnings = FALSE)
+  dir.create(file.path(installs, "cmdstan-2.36.0"), recursive = TRUE, showWarnings = FALSE)
+
+  expect_equal(
+    cmdstan_default_path(dir = installs),
+    file.path(installs, "cmdstan-2.36.0")
+  )
+  expect_true(dir.exists(file.path(installs, "cmdstan")))
+})
+
 test_that("CmdStan version helpers handle invalid inputs", {
   expect_identical(cmdstan_min_version(), "2.35.0")
   expect_false(is_supported_cmdstan_version(NULL))
diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
index b27628c5..2aaf0aba 100644
--- a/tests/testthat/test-utils.R
+++ b/tests/testthat/test-utils.R
@@ -196,6 +196,14 @@ test_that("cmdstan_make_local() works", {
   cmdstan_make_local(cpp_options = as.list(exisiting_make_local), append = FALSE)
 })
 
+test_that("cmdstan_make_local() preserves empty make/local behavior", {
+  dir <- withr::local_tempdir()
+  dir.create(file.path(dir, "make"), recursive = TRUE, showWarnings = FALSE)
+  file.create(file.path(dir, "make", "local"))
+
+  expect_identical(cmdstan_make_local(dir = dir), "")
+})
+
 test_that("matching_variables() works", {
   ret <- matching_variables(c("beta"),  c("alpha", "beta[1]", "beta[2]", "beta[3]"))
   expect_equal(