From e4fe08923f02081a5b62d61b10078268a9be3065 Mon Sep 17 00:00:00 2001
From: Craig Gower-Page <craig.gower-page@roche.com>
Date: Mon, 25 Mar 2024 15:09:21 +0000
Subject: [PATCH] Add helpful instructions to direct user if cmdstanr is not
 installed (#292)

---
 DESCRIPTION                    |  4 ++--
 R/JointModelSamples.R          |  2 +-
 R/utilities.R                  |  4 ++++
 R/zzz.R                        | 35 ++++++++++++++++++++++++++++++++++
 man/JointModelSamples-class.Rd |  2 +-
 5 files changed, 43 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 85300e44..f5e90721 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -34,7 +34,6 @@ Imports:
     checkmate,
     dplyr,
     stringr,
-    cmdstanr,
     ggplot2,
     ggplot2.utils,
     statmod,
@@ -46,7 +45,8 @@ Imports:
     digest,
     posterior,
     stats
-Suggests: 
+Suggests:
+    cmdstanr,
     bayesplot,
     knitr,
     rmarkdown,
diff --git a/R/JointModelSamples.R b/R/JointModelSamples.R
index e119535d..fef72be2 100644
--- a/R/JointModelSamples.R
+++ b/R/JointModelSamples.R
@@ -12,7 +12,7 @@ setOldClass("CmdStanMCMC")
 #'
 #' @slot model ([`JointModel`])\cr the model that the samples were drawn from.
 #' @slot data ([`DataJoint`])\cr the data that the model was fitted on.
-#' @slot results ([`CmdStanMCMC`])\cr the STAN samples.
+#' @slot results ([`cmdstanr::CmdStanMCMC`])\cr the STAN samples.
 #'
 #' @aliases JointModelSamples
 #' @export
diff --git a/R/utilities.R b/R/utilities.R
index f3ae0de2..ad7ad291 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -328,3 +328,7 @@ decompose_patients <- function(patients, all_pts) {
         indexes = patients_index
     )
 }
+
+is_cmdstanr_available <- function() {
+    requireNamespace("cmdstanr", quietly = TRUE)
+}
diff --git a/R/zzz.R b/R/zzz.R
index dd419b1a..6711b308 100644
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -3,6 +3,41 @@
     set_options()
 }
 
+.onAttach <- function(libname, pkgname) {
+    if (!is_cmdstanr_available()) {
+        packageStartupMessage(
+            "jmpost uses cmdstanr for compiling and sampling from models, but it does not seem to be installed.\n",
+            "To install:\n",
+            "install.packages(\"cmdstanr\", repos = c(\"https://mc-stan.org/r-packages/\", getOption(\"repos\")))"
+        )
+    } else if (is.null(cmdstanr::cmdstan_version(error_on_NA = FALSE))) {
+        possible_paths <- unique(c(
+            cmdstanr::cmdstan_default_install_path(),
+            Sys.getenv("CMDSTAN"),
+            Sys.getenv("CMDSTAN_PATH"),
+            "/root/.cmdstan",
+            "~/.cmdstan"
+        ))
+        possible_paths <- possible_paths[dir.exists(possible_paths)]
+
+        if (length(possible_paths)) {
+            for (try_path in possible_paths) {
+                new_path <- tryCatch(
+                    suppressMessages(cmdstanr::set_cmdstan_path(try_path)),
+                    warning = function(w) NULL,
+                    error = function(e) NULL
+                )
+            }
+            if (!is.null(new_path)) {
+                packageStartupMessage("CmdStan path set to: ", new_path)
+            }
+        } else {
+            packageStartupMessage("jmpost could not identify CmdStan path. Please use cmdstanr::set_cmdstan_path()")
+        }
+    }
+    return(invisible(NULL))
+}
+
 
 # This only exists to silence the false positive R CMD CHECK warning about
 # importing but not using the posterior package. posterior is a dependency
diff --git a/man/JointModelSamples-class.Rd b/man/JointModelSamples-class.Rd
index b0086ba4..8d1678a7 100644
--- a/man/JointModelSamples-class.Rd
+++ b/man/JointModelSamples-class.Rd
@@ -16,6 +16,6 @@ Contains samples from a \code{\link{JointModel}}.
 
 \item{\code{data}}{(\code{\link{DataJoint}})\cr the data that the model was fitted on.}
 
-\item{\code{results}}{(\code{\link{CmdStanMCMC}})\cr the STAN samples.}
+\item{\code{results}}{(\code{\link[cmdstanr:CmdStanMCMC]{cmdstanr::CmdStanMCMC}})\cr the STAN samples.}
 }}