Merge pull request #343 from stan-dev/various_minor_fixes

Minor fixes and version 0.2.0

Author: jgabry

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: cmdstanr
 Title: R Interface to 'CmdStan'
-Version: 0.1.3
-Date: 2020-08-21
+Version: 0.2.0
+Date: 2020-11-12
 Authors@R: 
     c(person(given = "Jonah", family = "Gabry", role = c("aut", "cre"),
            email = "[email protected]"),

NEWS.md

@@ -1,4 +1,4 @@
-# Items for next tagged release
+# cmdstanr 0.2.0
 
 ### Bug fixes
 
@@ -20,10 +20,12 @@ in fitting methods. (#281, #294)
 
 * Fix issue where names of generated files could clash. (#326, #328)
 
-* Fix missing `include_paths` in `$syntax_check()`. (#335)
+* Fix missing `include_paths` in `$syntax_check()`. (#335, @mike-lawrence)
 
 ### New features
 
+* CSV reading is now faster by using `data.table::fread()`. (#318)
+
 * `install_cmdstan()` gains argument `version` for specifying which version of
 CmdStan to install. (#300, #308)
 
@@ -35,7 +37,7 @@ specifying custom chain IDs. (#319)
 
 * Added support for the `sig_figs` argument in CmdStan versions 2.25 and above. (#327)
 
-* CSV reading is now faster by using `data.table::fread()`. (#318)
+* Added checks if the user has the necessary permissions in the RTools and temporary folders. (#343)
 
 # cmdstanr 0.1.3
 

R/install.R

@@ -427,11 +427,16 @@ build_status_ok <- function(process_log, quiet = FALSE) {
 }
 
 install_mingw32_make <- function(quiet = FALSE) {
+  rtools_usr_bin <- file.path(Sys.getenv("RTOOLS40_HOME"), "usr", "bin")
+  if (!checkmate::test_directory(rtools_usr_bin, access = "w")) {
+    warning("No write permissions in the RTools folder. This might prevent installing mingw32-make.",
+            " Consider changing permissions or reinstalling RTools in a different folder.", call. = FALSE)
+  }
   if (!quiet) message("Installing mingw32-make and writing RTools path to ~/.Renviron ...")
   processx::run(
     "pacman",
     args = c("-Syu", "mingw-w64-x86_64-make","--noconfirm"),
-    wd = file.path(Sys.getenv("RTOOLS40_HOME"), "usr", "bin"),
+    wd = rtools_usr_bin,
     error_on_status = TRUE
   )
   write('PATH="${RTOOLS40_HOME}\\usr\\bin;${RTOOLS40_HOME}\\mingw64\\bin;${PATH}"', file = "~/.Renviron", append = TRUE)
@@ -595,6 +600,9 @@ check_cmdstan_toolchain <- function(fix = FALSE, quiet = FALSE) {
     check_unix_make()
     check_unix_cpp_compiler()
   }
+  if (!checkmate::test_directory(dirname(tempdir()), access = "w")) {
+    stop("No write permissions to the temporary folder! Please change the permissions or location of the temporary folder.", call. = FALSE)
+  }
   if (!quiet) {
     message("The CmdStan toolchain is setup properly!")
   }

R/model.R

@@ -201,6 +201,7 @@ CmdStanModel <- R6::R6Class(
       private$stan_file_ <- absolute_path(stan_file)
 
       args <- list(...)
+      check_stanc_options(args$stanc_options)
       private$precompile_cpp_options_ <- args$cpp_options %||% list()
       private$precompile_stanc_options_ <- args$stanc_options %||% list()
       private$precompile_include_paths_ <- args$include_paths
@@ -366,6 +367,7 @@ compile_method <- function(quiet = TRUE,
   if (length(stanc_options) == 0 && !is.null(private$precompile_stanc_options_)) {
     stanc_options <- private$precompile_stanc_options_
   }
+  check_stanc_options(stanc_options)
   if (is.null(include_paths) && !is.null(private$precompile_include_paths_)) {
     include_paths <- private$precompile_include_paths_
   }
@@ -465,19 +467,18 @@ compile_method <- function(quiet = TRUE,
   if (is.null(stanc_options[["name"]])) {
     stanc_options[["name"]] <- model_name
   }
-  stanc_built_options = c()
+  stanc_built_options <- c()
   for (i in seq_len(length(stanc_options))) {
     option_name <- names(stanc_options)[i]
     if (isTRUE(as.logical(stanc_options[[i]]))) {
-      stanc_built_options = c(stanc_built_options, paste0("--", option_name))
+      stanc_built_options <- c(stanc_built_options, paste0("--", option_name))
+    } else if (is.null(option_name) || !nzchar(option_name)) {
+      stanc_built_options <- c(stanc_built_options, paste0("--", stanc_options[[i]]))
     } else {
-      stanc_built_options = c(stanc_built_options, paste0("--", option_name, "=", "'", stanc_options[[i]], "'"))
+      stanc_built_options <- c(stanc_built_options, paste0("--", option_name, "=", "'", stanc_options[[i]], "'"))
     }
   }
   stancflags_val <- paste0("STANCFLAGS += ", stancflags_val, paste0(stanc_built_options, collapse = " "))
-  if (cmdstan_version() < "2.24") {
-    prepare_precompiled(cpp_options, quiet)
-  }
   run_log <- processx::run(
     command = make_cmd(),
     args = c(tmp_exe,

R/utils.R

@@ -208,64 +208,22 @@ cpp_options_to_compile_flags <- function(cpp_options) {
   paste0(cpp_built_options, collapse = " ")
 }
 
-prepare_precompiled <- function(cpp_options = list(), quiet = FALSE) {
-  flags <- NULL
-  if (!is.null(cpp_options$stan_threads)) {
-    flags <- c(flags, "threads")
-  }
-  if (!is.null(cpp_options$stan_mpi)) {
-    flags <- c(flags, "mpi")
-  }
-  if (!is.null(cpp_options$stan_opencl)) {
-    flags <- c(flags, "opencl")
-  }
-  if (is.null(flags)) {
-    flags <- "noflags"
-  } else {
-    flags <- paste0(flags, collapse = "_")
-  }
-  main_path_w_flags <- file.path(cmdstan_path(), "src", "cmdstan", paste0("main_", flags, ".o"))
-  main_path_o <- file.path(cmdstan_path(), "src", "cmdstan", "main.o")
-  model_header_path_w_flags <- file.path(cmdstan_path(), "stan", "src", "stan", "model", paste0("model_header_", flags, ".hpp.gch"))
-  model_header_path_gch <- file.path(cmdstan_path(), "stan", "src", "stan", "model", "model_header.hpp.gch")
-  if (file.exists(model_header_path_gch)) {
-    model_header_gch_used <- TRUE
-  } else {
-    model_header_gch_used <- FALSE
-  }
-  if (!file.exists(main_path_w_flags)) {
-    message(
-      "Compiling the main object file and precompiled headers (may take up to a few minutes). ",
-      "This is only necessary the first time a model is compiled after installation or when ",
-      "threading, MPI or OpenCL are used for the first time."
-    )
-    clean_compile_helper_files()
-    run_log <- processx::run(
-      command = make_cmd(),
-      args = c(cpp_options_to_compile_flags(cpp_options),
-               main_path_o),
-      wd = cmdstan_path(),
-      echo_cmd = !quiet,
-      echo = !quiet,
-      spinner = quiet,
-      stderr_line_callback = function(x,p) { if (!quiet) message(x) },
-      error_on_status = TRUE
-    )
-    file.copy(main_path_o, main_path_w_flags)
-    if (model_header_gch_used) {
-      run_log <- processx::run(
-        command = make_cmd(),
-        args = c(cpp_options_to_compile_flags(cpp_options),
-                 file.path("stan", "src", "stan", "model", "model_header.hpp.gch")),
-        wd = cmdstan_path(),
-        echo_cmd = !quiet,
-        echo = !quiet,
-        spinner = quiet,
-        stderr_line_callback = function(x,p) { if (!quiet) message(x) },
-        error_on_status = TRUE
-      )
-      file.copy(model_header_path_gch, model_header_path_w_flags)
+check_stanc_options <- function(stanc_options) {
+  i <- 1
+  names <- names(stanc_options)
+  for (s in stanc_options){
+    if (!is.null(names[i]) && nzchar(names[i])) {
+      name <- names[i]
+    } else {
+      name <- s
     }
+    if (startsWith(name, "--")) {
+      stop("No leading hyphens allowed in stanc options (", name, "). ",
+           "Use options without leading hyphens, like for example ",
+           "`stanc_options = list('allow-undefined')`",
+           call. = FALSE)
+    }
+    i <- i + 1
   }
 }
 
@@ -288,7 +246,8 @@ num_threads <- function() {
 #' @export
 #' @param num_threads (positive integer) The number of threads to set.
 set_num_threads <- function(num_threads) {
-  stop("Please use the 'threads_per_chain' argument in the $sample() method instead of set_num_threads().")
+  stop("Please use the 'threads_per_chain' argument in the $sample() method instead of set_num_threads().",
+       call. = FALSE)
 }
 
 check_divergences <- function(data_csv) {
@@ -381,3 +340,4 @@ variable_dims <- function(variable_names = NULL) {
   }
   dims
 }
+

README.md

@@ -41,8 +41,8 @@ install.packages("cmdstanr", repos = c("https://mc-stan.org/r-packages/", getOpt
 or you can install the latest development version from GitHub:
 
 ```r
-# install.packages("devtools")
-devtools::install_github("stan-dev/cmdstanr")
+# install.packages("remotes")
+remotes::install_github("stan-dev/cmdstanr")
 ```
 
 ### Contributing