Merge pull request #1159 from stan-dev/more-outdated-code

Remove more outdated code for v1.0

Author: jgabry

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

@@ -59,7 +59,7 @@ jobs:
 
       - name: Install cmdstan
         run: |
-          cmdstanr::check_cmdstan_toolchain(fix = TRUE)
+          cmdstanr::check_cmdstan_toolchain()
           cmdstanr::install_cmdstan(cores = 2, wsl = TRUE, overwrite = TRUE)
         shell: Rscript {0}
 

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

@@ -115,7 +115,7 @@ jobs:
 
       - name: Install cmdstan
         run: |
-          cmdstanr::check_cmdstan_toolchain(fix = TRUE)
+          cmdstanr::check_cmdstan_toolchain()
           tarball_url <- Sys.getenv("CMDSTAN_TEST_TARBALL_URL")
           if (nzchar(tarball_url)) {
             cmdstanr::install_cmdstan(

.github/workflows/Test-coverage.yaml

@@ -55,7 +55,7 @@ jobs:
 
       - name: Install cmdstan
         run: |
-          cmdstanr::check_cmdstan_toolchain(fix = TRUE)
+          cmdstanr::check_cmdstan_toolchain()
           cmdstanr::install_cmdstan(cores = 2)
         shell: Rscript {0}
 

NEWS.md

@@ -1,15 +1,20 @@
 # cmdstanr (development version)
 
+* Informative error when exposing functions using names that are reserved 
+keywords (@VisruthSK, #1154)
+* `save_cmdstan_config` and `save_metric` default to `FALSE` but can be 
+set to `TRUE` for an entire R session via new global options. (#1159)
+
 * CmdStanModel objects created using `compile_model_methods = TRUE` that are
 then saved and reloaded no longer error in model fitting methods. Model methods
-are recompiled lazily if needed.
+are recompiled lazily if needed. (#1158)
 
-* CmdStan versions older than 2.35.0 are no longer supported.
-* Minimum R version increased to 4.0.0.
-* Removed legacy Windows toolchain paths for older CmdStan releases.
-* `CMDSTANR_USE_MSYS_TOOLCHAIN` is now deprecated and ignored (with a warning).
+* CmdStan versions older than 2.35.0 are no longer supported. (#1144)
+* Minimum R version increased to 4.0.0. (#1144)
+* Removed legacy Windows toolchain paths for older CmdStan releases. (#1144)
+* `CMDSTANR_USE_MSYS_TOOLCHAIN` is now deprecated and ignored (with a warning). (#1144)
 
-* Removed deprecated items (replacements in parentheses):
+* Removed deprecated items (replacements in parentheses). (#1061)
   - `read_sample_csv()` (`read_cmdstan_csv()`)
   - `write_stan_tempfile()` (`write_stan_file()`)
   - `jacobian_adjustment` argument to `fit$log_prob()` and similar methods (`jacobian` argument)

R/args.R

@@ -692,9 +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$refresh)
   }
@@ -710,9 +707,6 @@ validate_cmdstan_args <- function(self) {
   validate_init(self$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$opencl_ids, len = 2)
   }
   invisible(TRUE)
@@ -830,9 +824,6 @@ validate_optimize_args <- function(self) {
                            choices = c("bfgs", "lbfgs", "newton"))
   checkmate::assert_flag(self$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)
   }
 
@@ -1494,12 +1485,7 @@ 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
-  }
-  checkmate::assert_integerish(seed, lower = lower_seed)
+  checkmate::assert_integerish(seed, lower = 0)
   if (length(seed) > 1 && length(seed) != num_procs) {
     stop("If 'seed' is specified it must be a single integer or one per chain.",
          call. = FALSE)

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"))

R/cpp_opts.R

@@ -52,27 +52,24 @@ parse_exe_info_string <- function(ret_stdout) {
 # old (current) parser
 model_compile_info <- function(exe_file, version) {
   info <- NULL
-  if (version > "2.26.1") {
-
-    ret <- run_info_cli(exe_file)
-    if (ret$status == 0) {
-      info <- list()
-      info_raw <- strsplit(strsplit(ret$stdout, "\n")[[1]], "=")
-      for (key_val in info_raw) {
-        if (length(key_val) > 1) {
-          key_val <- trimws(key_val)
-          val <- key_val[2]
-          if (!is.na(as.logical(val))) {
-            val <- as.logical(val)
-          }
-          info[[toupper(key_val[1])]] <- val
+  ret <- run_info_cli(exe_file)
+  if (ret$status == 0) {
+    info <- list()
+    info_raw <- strsplit(strsplit(ret$stdout, "\n")[[1]], "=")
+    for (key_val in info_raw) {
+      if (length(key_val) > 1) {
+        key_val <- trimws(key_val)
+        val <- key_val[2]
+        if (!is.na(as.logical(val))) {
+          val <- as.logical(val)
         }
+        info[[toupper(key_val[1])]] <- val
       }
-      info[["STAN_VERSION"]] <- paste0(info[["STAN_VERSION_MAJOR"]], ".", info[["STAN_VERSION_MINOR"]], ".", info[["STAN_VERSION_PATCH"]])
-      info[["STAN_VERSION_MAJOR"]] <- NULL
-      info[["STAN_VERSION_MINOR"]] <- NULL
-      info[["STAN_VERSION_PATCH"]] <- NULL
     }
+    info[["STAN_VERSION"]] <- paste0(info[["STAN_VERSION_MAJOR"]], ".", info[["STAN_VERSION_MINOR"]], ".", info[["STAN_VERSION_PATCH"]])
+    info[["STAN_VERSION_MAJOR"]] <- NULL
+    info[["STAN_VERSION_MINOR"]] <- NULL
+    info[["STAN_VERSION_PATCH"]] <- NULL
   }
   info
 }

R/data.R

@@ -20,18 +20,15 @@
 #' The `list` to `array` conversion is intended to make it easier to prepare
 #' the data for certain Stan declarations involving arrays:
 #'
-#' * `vector[J] v[K]` (or equivalently `array[K] vector[J] v ` as of Stan 2.27)
-#' can be constructed in \R as a list with `K` elements where each element a
-#' vector of length `J`
-#' * `matrix[I,J] v[K]` (or equivalently `array[K] matrix[I,J] m ` as of Stan
-#' 2.27 ) can be constructed in \R as a list with `K` elements where each element
-#' an `IxJ` matrix
+#' * `array[K] vector[J] v ` can be constructed in \R as a list with `K`
+#' elements where each element a vector of length `J`
+#' * `array[K] matrix[I,J] m ` can be constructed in \R as a list with `K`
+#' elements where each element an `IxJ` matrix
 #'
 #' These can also be passed in from \R as arrays instead of lists but the list
 #' option is provided for convenience. Unfortunately for arrays with more than
-#' one dimension, e.g., `vector[J] v[K,L]` (or equivalently
-#' `array[K,L] vector[J] v ` as of Stan 2.27) it is not possible to use an \R
-#' list and an array must be used instead. For this example the array in \R
+#' one dimension (e.g. `array[K,L] vector[J] v `) it is not possible to use an
+#' \R list and an array must be used instead. For this example the array in \R
 #' should have dimensions `KxLxJ`.
 #'
 #' @examples
@@ -49,7 +46,7 @@
 #'
 #'
 #' # demonstrating list to array conversion
-#' # suppose x is declared as `vector[3] x[2]` (or equivalently `array[2] vector[3] x`)
+#' # suppose x is declared as `array[2] vector[3] x`
 #' # we can use a list of length 2 where each element is a vector of length 3
 #' data <- list(x = list(1:3, 4:6))
 #' file <- tempfile(fileext = ".json")
@@ -159,14 +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)

R/fit.R

@@ -1205,8 +1205,8 @@ CmdStanFit$set("public", name = "return_codes", value = return_codes)
 #'   profiling data if any profiling data was written to the profile CSV files.
 #'   See [save_profile_files()] to control where the files are saved.
 #'
-#'   Support for profiling Stan programs is available with CmdStan >= 2.26 and
-#'   requires adding profiling statements to the Stan program.
+#'   Profiling requires adding profiling statements to the Stan program. See
+#'   **Examples** for a demonstration.
 #'
 #' @return A list of data frames with profiling data if the profiling CSV files
 #'   were created.

R/install.R

@@ -108,7 +108,7 @@ install_cmdstan <- function(dir = NULL,
     .cmdstanr$WSL <- FALSE
   }
   if (check_toolchain) {
-    check_cmdstan_toolchain(fix = FALSE, quiet = quiet)
+    check_cmdstan_toolchain(quiet = quiet)
   }
   make_local_msg <- NULL
   if (!is.null(cmdstan_version(error_on_NA = FALSE))) {
@@ -336,17 +336,20 @@ 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? The default is `FALSE`.
-#'   This argument is currently ignored and retained for compatibility.
+#' @param fix As of v1.0 this argument is deprecated and ignored and only
+#'   retained for compatibility.
 #'
 check_cmdstan_toolchain <- function(fix = FALSE, quiet = FALSE) {
+  if (isTRUE(fix)) {
+    warning("The 'fix' argument is deprecated and will be removed in a future release.",
+            call. = FALSE)
+  }
   warn_if_ignored_msys_toolchain_env()
   if (os_is_windows()) {
     if (os_is_wsl()) {
       check_wsl_toolchain()
     } else {
-      check_rtools4x_windows_toolchain(fix = fix, quiet = quiet)
+      check_rtools4x_windows_toolchain(quiet = quiet)
     }
   } else {
     check_unix_make()
@@ -593,7 +596,7 @@ check_wsl_toolchain <- function() {
   }
 }
 
-check_rtools4x_windows_toolchain <- function(fix = FALSE, quiet = FALSE) {
+check_rtools4x_windows_toolchain <- function(quiet = FALSE) {
   rtools_path <- rtools4x_home_path()
   rtools_version <- paste0("Rtools", rtools4x_version())
   # If RTOOLS4X_HOME is not set (the env. variable gets set on install)
@@ -697,8 +700,7 @@ 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
+  if (!os_needs_arch) {
     return(NULL)
   }