version 0.2.0

DESCRIPTION

@@ -6,16 +6,12 @@ Description: Similar to 'rstantools' for 'rstan',
   The models compile once during installation,
   the executables live inside the file systems of their respective packages,
   and users have the full power and convenience of
-  'cmdstanr' without any additional compilation.
-  This approach saves time, allows R package developers
-  to migrate from 'rstan' to the more modern
-  'cmdstanr', and fits well with centrally maintained
-  R installations where users have trouble installing
-  their own packages, diagnosing compilation errors,
-  and setting environment variables.
+  'cmdstanr' without any additional compilation after package installation.
+  This approach saves time and helps R package developers
+  migrate from 'rstan' to the more modern 'cmdstanr'.
   Packages 'rstantools', 'cmdstanr', 'stannis', and
   'stanapi' are similar Stan clients with different objectives.
-Version: 0.0.2
+Version: 0.2.0
 License: MIT + file LICENSE
 URL: https://wlandau.github.io/instantiate/,
         https://github.com/wlandau/instantiate
@@ -25,29 +21,26 @@ Authors@R: c(
     given = c("William", "Michael"),
     family = "Landau",
     role = c("aut", "cre"),
-    email = "will.landau@gmail.com",
+    email = "will.landau.oss@gmail.com",
     comment = c(ORCID = "0000-0003-1878-3253")
   ),
   person(
     family = "Eli Lilly and Company",
     role = c("cph", "fnd")
   ))
 Depends: R (>= 4.0.0)
-Imports: fs, pkglite, rlang, utils
-Suggests: cmdstanr, knitr (>= 1.30), markdown (>= 1.1), rmarkdown (>=
-        2.4), testthat (>= 3.0.0), withr
-Additional_repositories: https://mc-stan.org/r-packages/
-SystemRequirements: CmdStan
-        (https://mc-stan.org/users/interfaces/cmdstan)
+Imports: fs, rlang, utils
+Suggests: knitr (>= 1.30), markdown (>= 1.1), rmarkdown (>= 2.4),
+        testthat (>= 3.0.0), withr
 Encoding: UTF-8
 Language: en-US
 Config/testthat/edition: 3
 RoxygenNote: 7.2.3
 NeedsCompilation: yes
-Packaged: 2023-08-08 19:24:05 UTC; C240390
+Packaged: 2024-01-09 15:40:24 UTC; C240390
 Author: William Michael Landau [aut, cre]
     (<https://orcid.org/0000-0003-1878-3253>),
   Eli Lilly and Company [cph, fnd]
-Maintainer: William Michael Landau <will.landau@gmail.com>
+Maintainer: William Michael Landau <will.landau.oss@gmail.com>
 Repository: CRAN
-Date/Publication: 2023-08-11 07:40:02 UTC
+Date/Publication: 2024-01-09 22:33:21 UTC

MD5

@@ -1,52 +1,62 @@
-fa20e0a4cfdf477151eaca4737b16213 *DESCRIPTION
+6b436f30d1503fe3f4bf5a01cc0a7acc *DESCRIPTION
 251996587bac8db01533ad7011f0c4f5 *LICENSE
-78beea0ac35e1ea45cbc06342c68a831 *NAMESPACE
-c918c770d1fcf17efabb500963f28d4a *NEWS.md
-4096c17c1368aaf04299111dba9a96d1 *R/stan_cmdstan_exists.R
-bdd22a615487885750afa9e366537017 *R/stan_cmdstan_path.R
-b35a2c9af71f3e548714f2bbff69ff13 *R/stan_cmdstan_version.R
-d9c83f68c35851356f82216be6508538 *R/stan_package.R
+500edf9a014381847bf9312201ba9bbb *NAMESPACE
+6ac387c4e85d9cc5f9088f1d61d69660 *NEWS.md
+2bef7698ac8415315bc135a49e578fd7 *R/stan_cmdstan_exists.R
+fbbc28ba2a7f1db7e2cbfdd60ded45ea *R/stan_cmdstan_path.R
+41567ca03c5d51725a8df8671a85df29 *R/stan_cmdstan_version.R
+f1089690180d58f2274a2c019b7eefde *R/stan_package.R
 5e5c02177f5a1f2dbddda85f123e2bd5 *R/stan_package_clean.R
-b4a3777898ff660f516e6e1d112ef2ea *R/stan_package_compile.R
-f65c030d2a92ccc776fafdf691332f1e *R/stan_package_configure.R
-86296963e35b066d4237039fd1d3bbbb *R/stan_package_create.R
-23b72f28c1b926390bc70c29833de8cc *R/stan_package_model.R
-00b795b242ac66d2a70425dbe8e712df *R/stan_package_model_files.R
-8d1c9c73efaf366b5d6bdfc37cc4b150 *R/utils_assert.R
-a5d1fcd86602dd91bbc3de47e172e2f2 *R/utils_cmdstan.R
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+8febf351efa09a0ee3afe6ea49e7a333 *R/utils_assert.R
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 c26a302f5f40a8420c2ea010a4826796 *R/utils_logic.R
 8c719b65887d307d9652cc33c8a624bc *R/utils_os.R
-7ed33c5af77cea2896552b8aa69f1294 *cleanup
-105248ba9946c1c8a8fe16b1e732800c *cleanup.win
-da3517530af446547973dd5067ca8cad *configure
-772af69d3c9d95879dcee8632f57047a *configure.win
+00d80b44380400a761ef43354611cdf2 *cleanup
+246c183dd8d2b2fdf321c4d26136f7e2 *cleanup.win
+c9e3f54962da09c419801231e6d93af6 *configure
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 2f9b7e68130c000bb936834add088476 *inst/WORDLIST
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+ad95a0ead03f3750c14185d1208ea057 *inst/example/DESCRIPTION
+637acb3d8af3a4f654eaccfdeb0bbba1 *inst/example/NAMESPACE
+b30634283cd20ed38b6245815bb00dd1 *inst/example/NOTICE
+4341f75ee5eb85b991fe201e35ba2f18 *inst/example/R/model.R
+5067a3c1eb447626b85d2372ab34e59f *inst/example/R/package.R
+dd674e027f8a360bd2cde6ac98fad66f *inst/example/github/workflows/check.yaml
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 b0b3186edbae1cc801617efbe9f7b858 *man/stan_package_create.Rd
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 d8735c47ab789feba7740aa2469b2389 *tests/testthat.R
 8c06a6808db95a4bed985c5fa4599739 *tests/testthat/helper-utils.R
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 7be7c6e16e4e7334ffd21d4a8b04ab6e *tests/testthat/test-stan_on_windows.R
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 340ef4d3f71daa1d795a4c0039dae92c *tests/testthat/test-utils_assert.R
 4e122d6b839621356a7fba073014c2d7 *tests/testthat/test-utils_logic.R

NAMESPACE

@@ -10,7 +10,6 @@ export(stan_package_create)
 export(stan_package_model)
 export(stan_package_model_files)
 importFrom(fs,dir_copy)
-importFrom(pkglite,unpack)
 importFrom(rlang,abort)
 importFrom(rlang,check_installed)
 importFrom(rlang,inform)

NEWS.md

@@ -1,3 +1,24 @@
+# instantiate 0.2.0
+
+* Remove "internal" installation (#16).
+* In the documentation, remove claims that `instantiate` is a good fit for centralized multi-user R environments (c.f. https://github.com/stan-dev/cmdstan/issues/1175).
+* Check subdirectories of the fixed CmdStan installation path.
+
+# instantiate 0.1.0
+
+* Use `install.libs.R` for both CmdStan in `instantiate` and Stan model compilation in packages (#1, #9, #12).
+* Stan models should now be in `src/stan/` instead of `inst/stan/` (#12). `inst/stan/` should still work for the next few versions, but it is now deprecated. When a modeling package is installed, its `install.libs.R` moves `src/stan/` to `bin/stan/` and then compiles models inside `bin/stan/`.
+* Disable staged installation for `instantiate` itself to help the hard-coded paths in CmdStan work as expected in "internal" installation.
+
+# instantiate 0.0.4
+
+* Relax `cmdstanr` requirement (now minimum version 0.5.2).
+
+# instantiate 0.0.3
+
+* Generate a modified tarball of the package which always installs CmdStan internally, regardless of environment variables (#8). The appropriate version of this tarball will be attached to forthcoming releases on GitHub.
+* Bug fixes for internal CmdStan installation.
+
 # instantiate 0.0.2
 
 * Address CRAN comments from the submission of version 0.0.1.

R/stan_cmdstan_exists.R

@@ -1,14 +1,20 @@
-#' @title Check if `instantiate` can find CmdStan.
+#' @title Check if `instantiate` can find CmdStanR and CmdStan.
 #' @export
 #' @family cmdstan
-#' @description Check if `instantiate` can find CmdStan.
+#' @description Check if `instantiate` can find CmdStanR and CmdStan.
 #' @inheritParams stan_cmdstan_path
-#' @return `TRUE` if `instantiate` can find CmdStan, `FALSE` otherwise.
+#' @return `TRUE` if `instantiate` can find the CmdStanR R package and the
+#'   CmdStan command line tool. Returns `FALSE` otherwise.
 #' @examples
 #' stan_cmdstan_exists()
 stan_cmdstan_exists <- function(
-  cmdstan_install = Sys.getenv("CMDSTAN_INSTALL")
+  cmdstan_install = Sys.getenv("CMDSTAN_INSTALL", unset = "")
 ) {
+  # nocov start
+  if (!rlang::is_installed("cmdstanr")) {
+    return(FALSE) # Not possible to cover in regular unit tests.
+  }
+  # nocov end
   path <- stan_cmdstan_path(cmdstan_install = cmdstan_install)
   cmdstan_valid(path)
 }

R/stan_cmdstan_path.R

@@ -6,49 +6,48 @@
 #' @return Character of length 1, directory path to CmdStan. The path
 #'   may or may not exist. Returns the empty string `""` if the path
 #'   cannot be determined.
-#' @param cmdstan_install Character of length 1, how CmdStan was installed. The
-#'   installation method determines how `instantiate` looks up CmdStan.
-#'   Set the default value with the `CMDSTAN_INSTALL` environment variable.
+#' @param cmdstan_install Character of length 1, how to look for an installed
+#'   copy of CmdStan. See <https://wlandau.github.io/instantiate/> for details.
 #'   Choices:
-#'   1. `"internal"`: Use the copy of CmdStan installed internally inside the
-#'     `instantiate` package file system. Before using this option,
-#'     CmdStan must be installed in the package file system. To do this,
-#'     set the `CMDSTAN_INSTALL` environment variable to `"internal"` before
-#'     installing `instantiate`.
-#'   2. `"fixed"`: Use the copy of CmdStan that was located at the value
-#'     contained in `Sys.getenv("CMDSTAN")` at the time `instantiate`
-#'     was installed. In this case, the path to CmdStan is not inside
-#'     `instantiate` itself, but it is fixed at installation time
-#'     and does not depend on the current value of
-#'     `Sys.getenv("CMDSTAN")` at runtime.
-#'   3. `"cmdstanr"`: Let the `cmdstanr::cmdstan_path()` decide where
-#'     to look for CmdStan. The `cmdstanr` package must be installed. If it
-#'     is not installed, the function returns the empty string `""`.
-#'   4. `""` (default): Try all 3 options in the order above to find a valid
-#'     installed copy of CmdStan.
+#'   1. `""` (default): look at the original value that the `CMDSTAN_INSTALL`
+#'     environment variable contained when `instantiate` at the time
+#'     when it was installed.
+#'     If it was `"implicit"` or `"fixed"`, then choose
+#'     the corresponding option below. Otherwise, default to `"implicit"`.
+#'   2. `"implicit"`: Let the `cmdstanr::cmdstan_path()` decide where
+#'     to look for CmdStan. As explained in the `cmdstanr` documentation,
+#'     the output of `cmdstanr::cmdstan_path()` depends
+#'     on the current value of the `CMDSTAN` environment variable.
+#'     The `cmdstanr` package must be installed. If it
+#'     is not installed, then `stan_cmdstan_path()`
+#'     returns the empty string `""`.
+#'   3. `"fixed"`: Use the path to CmdStan that was originally
+#'     contained in `Sys.getenv("CMDSTAN")` at the time when `instantiate`
+#'     was installed.
 #' @examples
 #' stan_cmdstan_path()
 stan_cmdstan_path <- function(
-  cmdstan_install = Sys.getenv("CMDSTAN_INSTALL")
+  cmdstan_install = Sys.getenv("CMDSTAN_INSTALL", unset = "")
 ) {
-  # It is not feasible to test all these cases in a single test coverage run.
-  # Covered in several GitHub Actions workflows.
   # nocov start
-  install <- stan_cmdstan_install(cmdstan_install)
-  if (identical(install, "internal") || identical(install, "")) {
-    parent <- system.file("cmdstan", package = "instantiate", mustWork = FALSE)
-    out <- file.path(parent, list.files(parent)) %||% ""
-  }
-  if (identical(install, "fixed") || path_next(install, out)) {
-    out <- .Call(c_cmdstan_path)
-  }
-  if (identical(install, "cmdstanr") || path_next(install, out)) {
-    out <- cmdstanr_path()
+  if (!rlang::is_installed("cmdstanr")) {
+    return("") # Not possible to cover in regular unit tests.
   }
   # nocov end
-  out
-}
-
-path_next <- function(install, out) {
-  identical(install, "") && !any(dir.exists(out))
+  install <- if_any(
+    identical(cmdstan_install, ""),
+    .Call(c_cmdstan_path_install, PACKAGE = "instantiate"),
+    cmdstan_install
+  )
+  stan_assert_install(install)
+  path <- if_any(
+    identical(install, "fixed"),
+    .Call(c_cmdstan_path_fixed, PACKAGE = "instantiate"),
+    cmdstanr_path()
+  )
+  if_any(
+    cmdstan_valid(path),
+    path,
+    cmdstanr("cmdstan_default_path")(dir = path)
+  ) %|||% ""
 }

R/stan_cmdstan_version.R

@@ -7,21 +7,22 @@
 #'   package uses. If CmdStan is not found, then the return value depends
 #'   on the `error_on_NA` argument.
 #' @inheritParams stan_cmdstan_path
-#' @inheritParams cmdstanr::cmdstan_version
+#' @param error_on_NA Logical of length 1, whether an error should be thrown
+#'   if CmdStan is not found.
 #' @examples
 #' if (stan_cmdstan_exists()) {
 #'   message(stan_cmdstan_version())
 #' }
 stan_cmdstan_version <- function(
-  cmdstan_install = Sys.getenv("CMDSTAN_INSTALL"),
+  cmdstan_install = Sys.getenv("CMDSTAN_INSTALL", unset = ""),
   error_on_NA = TRUE
 ) {
   stan_assert_cmdstanr()
   path_old <- cmdstanr_path()
   if (cmdstan_valid(path_old)) {
-    on.exit(suppressMessages(cmdstanr::set_cmdstan_path(path = path_old)))
+    on.exit(suppressMessages(cmdstanr("set_cmdstan_path")(path = path_old)))
   }
   path_new <- stan_cmdstan_path(cmdstan_install = cmdstan_install)
-  suppressMessages(cmdstanr::set_cmdstan_path(path = path_new))
-  cmdstanr::cmdstan_version(error_on_NA = error_on_NA)
+  suppressMessages(cmdstanr("set_cmdstan_path")(path = path_new))
+  cmdstanr("cmdstan_version")(error_on_NA = error_on_NA)
 }

R/stan_package.R

@@ -11,16 +11,12 @@
 #'   the executables live inside the file systems of their
 #'   respective packages, and users have the full power
 #'   and convenience of [`CmdStanR`](https://mc-stan.org/cmdstanr/)
-#'   without any additional compilation. This approach saves time,
-#'   allows R package developers to migrate from
-#'   [`rstan`](https://mc-stan.org/rstan/)
-#'   to the more modern [`CmdStanR`](https://mc-stan.org/cmdstanr/),
-#'   and fits well with centrally maintained R installations
-#'   where users may have trouble installing their own packages,
-#'   diagnosing compilation errors, and setting environment variables.
+#'   without any additional compilation after package installation.
+#'   This approach saves time and helps R package developers
+#'   migrate from [`rstan`](https://mc-stan.org/rstan/)
+#'   to the more modern [`CmdStanR`](https://mc-stan.org/cmdstanr/).
 #' @useDynLib instantiate, .registration = TRUE
 #' @importFrom fs dir_copy
-#' @importFrom pkglite unpack
 #' @importFrom rlang abort check_installed inform is_installed warn
 #' @importFrom utils capture.output globalVariables install.packages
 NULL