Cleanup more deprecations

stan-dev · May 18, 2024 · 1e886a0 · 1e886a0
1 parent de8ff1e
commit 1e886a0
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Showing 11 changed files with 56 additions and 312 deletions.
diff --git a/.github/workflows/R-CMD-check-wsl.yaml b/.github/workflows/R-CMD-check-wsl.yaml
@@ -2,15 +2,12 @@
 # Github Actions workflow to check CmdStanR
 # yamllint disable rule:line-length
 
-name: Unit tests - WSL Backend
+name: v1.0 Branch Unit tests - WSL Backend
 
 'on':
   push:
     branches:
-      - master
-  pull_request:
-    branches:
-      - master
+      - v1.0
 
 jobs:
   WSL-R-CMD-check:
@@ -61,7 +58,7 @@ jobs:
       - name: Install cmdstan
         run: |
           cmdstanr::check_cmdstan_toolchain(fix = TRUE)
-          cmdstanr::install_cmdstan(cores = 2, wsl = TRUE, overwrite = TRUE)
+          cmdstanr::install_cmdstan(cores = 2, wsl = TRUE, overwrite = TRUE, version = "2.35.0-rc2")
         shell: Rscript {0}
 
       - name: Session info

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -2,15 +2,12 @@
 # Github Actions workflow to check CmdStanR
 # yamllint disable rule:line-length
 
-name: Unit tests
+name: v1.0 Branch Unit tests
 
 'on':
   push:
     branches:
-      - master
-  pull_request:
-    branches:
-      - master
+      - v1.0
 
 jobs:
   R-CMD-check:
@@ -63,7 +60,7 @@ jobs:
       - name: Install cmdstan
         run: |
           cmdstanr::check_cmdstan_toolchain(fix = TRUE)
-          cmdstanr::install_cmdstan(cores = 2)
+          cmdstanr::install_cmdstan(cores = 2, version = "2.35.0-rc2")
         shell: Rscript {0}
 
       - name: Session info

diff --git a/R/args.R b/R/args.R
@@ -68,14 +68,8 @@ CmdStanArgs <- R6::R6Class(
         self$output_dir <- ifelse(is.null(output_dir),
                                   file.path(wsl_dir_prefix(), wsl_tempdir()),
                                   wsl_safe_path(output_dir))
-      } else if (getRversion() < "3.5.0") {
-        self$output_dir <- output_dir %||% tempdir()
       } else {
-        if (getRversion() < "3.5.0") {
-          self$output_dir <- output_dir %||% tempdir()
-        } else {
-          self$output_dir <- output_dir %||% tempdir(check = TRUE)
-        }
+        self$output_dir <- output_dir %||% tempdir(check = TRUE)
       }
       self$output_dir <- repair_path(self$output_dir)
       self$output_basename <- output_basename
@@ -698,9 +692,6 @@ validate_cmdstan_args <- function(self) {
   checkmate::assert_integerish(self$refresh, lower = 0, null.ok = TRUE)
   checkmate::assert_integerish(self$sig_figs, lower = 1, upper = 18, null.ok = TRUE)
   checkmate::assert_integerish(self$save_cmdstan_config, lower = 0, upper = 1, len = 1, null.ok = TRUE)
-  if (!is.null(self$sig_figs) && cmdstan_version() < "2.25") {
-    warning("The 'sig_figs' argument is only supported with cmdstan 2.25+ and will be ignored!", call. = FALSE)
-  }
   if (!is.null(self$refresh)) {
     self$refresh <- as.integer(self$refresh)
   }
@@ -716,9 +707,6 @@ validate_cmdstan_args <- function(self) {
   validate_init(self$init, num_inits)
   validate_seed(self$seed, num_procs)
   if (!is.null(self$opencl_ids)) {
-    if (cmdstan_version() < "2.26") {
-      stop("Runtime selection of OpenCL devices is only supported with CmdStan version 2.26 or newer.", call. = FALSE)
-    }
     checkmate::assert_vector(self$opencl_ids, len = 2)
   }
   invisible(TRUE)
@@ -836,9 +824,6 @@ validate_optimize_args <- function(self) {
                            choices = c("bfgs", "lbfgs", "newton"))
   checkmate::assert_flag(self$jacobian, null.ok = TRUE)
   if (!is.null(self$jacobian)) {
-    if (cmdstan_version() < "2.32") {
-      warning("The 'jacobian' argument is only supported with cmdstan 2.32+ and will be ignored!", call. = FALSE)
-    }
     self$jacobian <- as.integer(self$jacobian)
   }
 
@@ -1476,11 +1461,7 @@ validate_seed <- function(seed, num_procs) {
   if (is.null(seed)) {
     return(invisible(TRUE))
   }
-  if (cmdstan_version() < "2.26") {
-    lower_seed <- 1
-  } else {
-    lower_seed <- 0
-  }
+  lower_seed <- 1
   checkmate::assert_integerish(seed, lower = lower_seed)
   if (length(seed) > 1 && length(seed) != num_procs) {
     stop("If 'seed' is specified it must be a single integer or one per chain.",

diff --git a/R/cmdstanr-package.R b/R/cmdstanr-package.R
@@ -35,4 +35,4 @@
 #'
 "_PACKAGE"
 
-if (getRversion() >= "2.15.1")  utils::globalVariables(c("self", "private", "super"))
+utils::globalVariables(c("self", "private", "super"))
diff --git a/R/data.R b/R/data.R
@@ -156,14 +156,6 @@ process_data <- function(data, model_variables = NULL) {
   } else if (is.character(data)) {
     path <- absolute_path(data)
   } else if (is.list(data) && !is.data.frame(data)) {
-    if (cmdstan_version() < "2.22" && any_zero_dims(data)) {
-      stop(
-        "Data includes 0-dimensional data structures. To use this data please ",
-        "either update your CmdStan installation with install_cmdstan() ",
-        "or specify data as a file created by rstan::stan_rdump().",
-        call. = FALSE
-      )
-    }
     if (!is.null(model_variables)) {
       data_variables <- model_variables$data
       is_data_supplied <- names(data_variables) %in%  names(data)

diff --git a/R/example.R b/R/example.R
@@ -185,16 +185,3 @@ write_stan_file <- function(code,
   }
   file
 }
-
-
-#' Write Stan code to a temporary file
-#'
-#' This function is deprecated. Please use [write_stan_file()] instead.
-#' @keywords internal
-#' @export
-#' @inheritParams write_stan_file
-write_stan_tempfile <- function(code, dir = tempdir()) {
-  warning("write_stan_tempfile() is deprecated. Please use write_stan_file() instead.",
-          call. = FALSE)
-  write_stan_file(code, dir)
-}
diff --git a/R/install.R b/R/install.R
@@ -136,7 +136,6 @@ install_cmdstan <- function(dir = NULL,
       warning("version and release_url shouldn't both be specified!",
               "\nrelease_url will be ignored.", call. = FALSE)
     }
-
     release_url <- paste0("https://github.com/stan-dev/cmdstan/releases/download/v",
                           version, "/cmdstan-", version, cmdstan_arch_suffix(version), ".tar.gz")
   }
@@ -151,6 +150,10 @@ install_cmdstan <- function(dir = NULL,
     tar_name <- utils::tail(split_url[[1]], n = 1)
     tar_name <- gsub("-linux-(.*).tar.gz", ".tar.gz", tar_name)
     cmdstan_ver <- substr(tar_name, 0, nchar(tar_name) - 7)
+    if (cmdstan_ver < "2.35.0") {
+      warning("CmdStanR 1.0 and later only officially support CmdStan >= 2.35",
+              call. = FALSE)
+    }
     tar_gz_file <- paste0(cmdstan_ver, ".tar.gz")
     dir_cmdstan <- file.path(dir, cmdstan_ver)
     dest_file <- file.path(dir, tar_gz_file)
@@ -224,15 +227,6 @@ install_cmdstan <- function(dir = NULL,
     )
   }
 
-  # Building fails on Apple silicon with < v2.31 due to a makefiles setting
-  # for stanc3, so manually implement the patch if needed from:
-  # https://github.com/stan-dev/cmdstan/pull/1127
-  stanc_makefile <- readLines(file.path(dir_cmdstan, "make", "stanc"))
-  stanc_makefile <- gsub("\\bxattr -d com.apple.quarantine bin/stanc",
-                          "-xattr -d com.apple.quarantine bin/stanc",
-                          stanc_makefile)
-  writeLines(stanc_makefile, con = file.path(dir_cmdstan, "make", "stanc"))
-
   # Suppress noisy warnings from Boost
   cmdstan_make_local(
     dir = dir_cmdstan,
@@ -321,12 +315,8 @@ cmdstan_make_local <- function(dir = cmdstan_path(),
 
 #' @rdname install_cmdstan
 #' @export
-#' @param fix For `check_cmdstan_toolchain()`, should CmdStanR attempt to fix
-#'   any detected toolchain problems? Currently this option is only available on
-#'   Windows. The default is `FALSE`, in which case problems are only reported
-#'   along with suggested fixes.
 #'
-check_cmdstan_toolchain <- function(fix = FALSE, quiet = FALSE) {
+check_cmdstan_toolchain <- function(quiet = FALSE) {
   if (os_is_windows()) {
     if (os_is_wsl()) {
       check_wsl_toolchain()
@@ -645,11 +635,6 @@ check_unix_cpp_compiler <- function() {
 
 cmdstan_arch_suffix <- function(version = NULL) {
   os_needs_arch <- os_is_linux() || os_is_wsl()
-  if ((!is.null(version) && version < "2.26") || !os_needs_arch) {
-    # pre-CmdStan 2.26, only the x86 tarball was provided
-    return(NULL)
-  }
-
   arch <- NULL
   if (os_is_wsl()) {
     arch <- wsl_compatible_run(command = "uname", args = "-m")$stdout
@@ -719,9 +704,6 @@ rtools4x_home_path <- function() {
 
 rtools_home_path <- function() {
   path <- NULL
-  if (R.version$major == "3") {
-    path <- Sys.getenv("RTOOLS_HOME")
-  }
   if (R.version$major == "4") {
     path <- rtools4x_home_path()
   }