From 4bc50de1a7cd247f149931b0702330f59c702c50 Mon Sep 17 00:00:00 2001
From: dipterix <dipterix.wang@gmail.com>
Date: Tue, 18 Jul 2023 11:12:11 -0400
Subject: [PATCH 1/2] moved rmarkdown to Suggests and installs it interactively
 when missing

---
 DESCRIPTION |  6 +++---
 R/helpers.R | 42 ++++++++++++++++++++++++++++++++++++++++--
 2 files changed, 43 insertions(+), 5 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 00e1244..9b957f1 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: freesurferformats
 Type: Package
 Title: Read and Write 'FreeSurfer' Neuroimaging File Formats
-Version: 0.1.17
+Version: 0.1.17.9000
 Authors@R: person("Tim", "Schäfer", role = c("aut", "cre"), email = "ts+code@rcmd.org", comment = c(ORCID = "0000-0002-3683-8070"))
 Maintainer: Tim Schäfer <ts+code@rcmd.org>
 Description: Provides functions to read and write neuroimaging data in various file formats, with a focus on 'FreeSurfer' <http://freesurfer.net/> formats. This includes, but is not limited to, the following file formats: 1) MGH/MGZ format files, which can contain multi-dimensional images or other data. Typically they contain time-series of three-dimensional brain scans acquired by magnetic resonance imaging (MRI). They can also contain vertex-wise measures of surface morphometry data. The MGH format is named after the Massachusetts General Hospital, and the MGZ format is a compressed version of the same format. 2) 'FreeSurfer' morphometry data files in binary 'curv' format. These contain vertex-wise surface measures, i.e., one scalar value for each vertex of a brain surface mesh. These are typically values like the cortical thickness or brain surface area at each vertex. 3) Annotation file format. This contains a brain surface parcellation derived from a cortical atlas. 4) Surface file format. Contains a brain surface mesh, given by a list of vertices and a list of faces.
@@ -11,10 +11,10 @@ URL: https://github.com/dfsp-spirit/freesurferformats
 BugReports: https://github.com/dfsp-spirit/freesurferformats/issues
 Imports:
     pkgfilecache (>= 0.1.1),
-    xml2,
-    rmarkdown
+    xml2
 Suggests:
     knitr,
+    rmarkdown,
     testthat (>= 2.1.0),
     oro.nifti (>= 0.9),
     gifti (>= 0.7.5),
diff --git a/R/helpers.R b/R/helpers.R
index 13ba923..09d9d35 100644
--- a/R/helpers.R
+++ b/R/helpers.R
@@ -83,11 +83,49 @@ fs.surface.to.tmesh3d <- function(surface) {
 #'
 #' @return logical, whether Pandoc is available.
 #'
-#' @importFrom rmarkdown pandoc_available
-#'
 #' @keywords internal
 has_pandoc <- function() {
+  assert_package("rmarkdown")
   return(rmarkdown::pandoc_available());
 }
 
 
+assert_package <- function(pkg) {
+
+  package_installed <- vapply(pkg, function(p) {
+    return( system.file(package = p) != "" )
+  }, FALSE)
+  if( all(package_installed) ) { return(invisible()) }
+  pkg <- pkg[!package_installed]
+
+  # the package is missing
+  cnd <- structure(list(message = sprintf("Package(s) %s missing. Please install first.", paste(sQuote(pkg), collapse = ", ")), call = NULL),
+                   class = c("package_not_found_error", "simpleError", "error", "condition"))
+
+  # check if rlang has been installed, usually yes if people installs any rlib/posit packages
+  rlang_is_missing <- system.file(package = "rlang") == ""
+  pak_is_missing <- system.file(package = "pak") == ""
+
+  # if not interactive or rlang&pak are missing, per CRAN policy, stop
+  if(!interactive() || (rlang_is_missing && pak_is_missing)) {
+    stop(cnd)
+  }
+
+  if( !rlang_is_missing ) {
+    rlang <- asNamespace("rlang")
+    rlang$check_installed(pkg)
+    return(invisible())
+  }
+
+  # using pak
+  message(sprintf("Package(s) %s missing, install?", paste(sQuote(pkg), collapse = ", ")))
+  if (utils::menu(c("Yes", "No")) != 1) {
+    invokeRestart("abort", cnd)
+  }
+  pak <- asNamespace("pak")
+  pak$pkg_install(pkg, ask = FALSE)
+
+  return(invisible())
+
+}
+

From 56c3abd9a1ba67379af1abab26a8e0daa87ba573 Mon Sep 17 00:00:00 2001
From: dipterix <dipterix.wang@gmail.com>
Date: Tue, 18 Jul 2023 11:21:32 -0400
Subject: [PATCH 2/2] Updated NAMESPACE and added utils to Imports

---
 DESCRIPTION | 3 ++-
 NAMESPACE   | 1 -
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 9b957f1..4b0474f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -10,6 +10,7 @@ Encoding: UTF-8
 URL: https://github.com/dfsp-spirit/freesurferformats
 BugReports: https://github.com/dfsp-spirit/freesurferformats/issues
 Imports:
+    utils,
     pkgfilecache (>= 0.1.1),
     xml2
 Suggests:
@@ -20,4 +21,4 @@ Suggests:
     gifti (>= 0.7.5),
     cifti (>= 0.4.5)
 VignetteBuilder: knitr
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
diff --git a/NAMESPACE b/NAMESPACE
index 498aada..d402e0b 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -162,7 +162,6 @@ importFrom(pkgfilecache,erase_file_cache)
 importFrom(pkgfilecache,get_filepath)
 importFrom(pkgfilecache,get_pkg_info)
 importFrom(pkgfilecache,list_available)
-importFrom(rmarkdown,pandoc_available)
 importFrom(stats,dist)
 importFrom(stats,na.omit)
 importFrom(utils,read.table)