bump version, replace donttest with dontrun in examples

CHANGES

@@ -2,10 +2,11 @@ freesurferformats Changes
 =========================
 
 
-Version 0.1.16.dev (WIP)
+Version 0.1.17
 -------------------------
 - Introduce 'default_label_name' parameter to read.fs.annot, better doc string for the same function.
 - Add function fs.surface.to.tmesh3d to transform an fs.surface mesh datastructure into an RGL tmesh datastructure. This method does not require rgl.
+- Replace all 'donttest' in examples with 'dontrun' so CRAN does not run them.
 
 
 

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: freesurferformats
 Type: Package
 Title: Read and Write 'FreeSurfer' Neuroimaging File Formats
-Version: 0.1.16.1
+Version: 0.1.17
 Authors@R: person("Tim", "Schäfer", role = c("aut", "cre"), email = "[email protected]", comment = c(ORCID = "0000-0002-3683-8070"))
 Maintainer: Tim Schäfer <[email protected]>
 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.

R/write_fs_annot.R

@@ -53,7 +53,7 @@ write.fs.colortable <- function(filepath, colortable) {
 #' @param fs.annot instance of class `fs.annot`. If passed, this takes precedence over all other parameters and they should all be NULL (with the exception of `filepath`).
 #'
 #' @examples
-#' \donttest{
+#' \dontrun{
 #'    # Load annotation
 #'    annot_file = system.file("extdata", "lh.aparc.annot.gz",
 #'                                package = "freesurferformats",
@@ -187,7 +187,7 @@ write.fs.annot <- function(filepath, num_vertices=NULL, colortable=NULL, labels_
 #' @param annot fs.annot instance, an annotation.
 #'
 #' @examples
-#' \donttest{
+#' \dontrun{
 #'    # Load annotation
 #'    annot_file = system.file("extdata", "lh.aparc.annot.gz",
 #'                                package = "freesurferformats",

R/write_fs_label.R

@@ -18,7 +18,7 @@
 #' @family label functions
 #'
 #' @examples
-#' \donttest{
+#' \dontrun{
 #'     # Write a simple label containing only vertex indices:
 #'     label_vertices = c(1,2,3,4,5,1000,2000,2323,34,34545,42);
 #'     write.fs.label(tempfile(fileext=".label"), label_vertices);

R/write_fs_surface.R

@@ -18,7 +18,7 @@
 #'
 #'
 #' @examples
-#' \donttest{
+#' \dontrun{
 #'     # Read a surface from a file:
 #'     surface_file = system.file("extdata", "lh.tinysurface",
 #'      package = "freesurferformats", mustWork = TRUE);
@@ -142,7 +142,7 @@ check.verts.faces <- function(vertex_coords, faces) {
 #' @family mesh functions
 #'
 #' @examples
-#' \donttest{
+#' \dontrun{
 #'     # Read a surface from a file:
 #'     surface_file = system.file("extdata", "lh.tinysurface",
 #'      package = "freesurferformats", mustWork = TRUE);
@@ -194,7 +194,7 @@ write.fs.surface.asc <- function(filepath, vertex_coords, faces) {
 #' @family mesh functions
 #'
 #' @examples
-#' \donttest{
+#' \dontrun{
 #'     # Read a surface from a file:
 #'     surface_file = system.file("extdata", "lh.tinysurface",
 #'      package = "freesurferformats", mustWork = TRUE);
@@ -255,7 +255,7 @@ write.fs.surface.vtk <- function(filepath, vertex_coords, faces) {
 #' @note Do not confuse the Wavefront object file format (.obj) with the OFF format (.off), they are not identical.
 #'
 #' @examples
-#' \donttest{
+#' \dontrun{
 #'     # Read a surface from a file:
 #'     surface_file = system.file("extdata", "lh.tinysurface",
 #'      package = "freesurferformats", mustWork = TRUE);
@@ -323,7 +323,7 @@ write.fs.surface.obj <- function(filepath, vertex_coords, faces, vertex_colors=N
 #' @family mesh export functions
 #'
 #' @examples
-#' \donttest{
+#' \dontrun{
 #'     # Read a surface from a file:
 #'     surface_file = system.file("extdata", "lh.tinysurface",
 #'      package = "freesurferformats", mustWork = TRUE);
@@ -358,7 +358,7 @@ write.fs.surface.off <- function(filepath, vertex_coords, faces) {
 #' @family mesh export functions
 #'
 #' @examples
-#' \donttest{
+#' \dontrun{
 #'     # Read a surface from a file:
 #'     surface_file = system.file("extdata", "lh.tinysurface",
 #'      package = "freesurferformats", mustWork = TRUE);
@@ -416,7 +416,7 @@ write.fs.surface.off.ply2 <- function(filepath, vertex_coords, faces, format) {
 #' @family mesh export functions
 #'
 #' @examples
-#' \donttest{
+#' \dontrun{
 #'     # Read a surface from a file:
 #'     surface_file = system.file("extdata", "lh.tinysurface",
 #'      package = "freesurferformats", mustWork = TRUE);
@@ -451,7 +451,7 @@ write.fs.surface.ply2 <- function(filepath, vertex_coords, faces) {
 #' @family mesh export functions
 #'
 #' @examples
-#' \donttest{
+#' \dontrun{
 #'     # Read a surface from a file:
 #'     surface_file = system.file("extdata", "lh.tinysurface",
 #'      package = "freesurferformats", mustWork = TRUE);
@@ -550,7 +550,7 @@ ply.header.lines <- function(num_verts, num_faces, use_vertex_colors) {
 #' @family gifti writers
 #'
 #' @examples
-#' \donttest{
+#' \dontrun{
 #'     # Read a surface from a file:
 #'     surface_file = system.file("extdata", "lh.tinysurface",
 #'      package = "freesurferformats", mustWork = TRUE);
@@ -584,7 +584,7 @@ write.fs.surface.gii <- function(filepath, vertex_coords, faces) {
 #' @family mesh functions
 #'
 #' @examples
-#' \donttest{
+#' \dontrun{
 #'     # Read a surface from a file:
 #'     surface_file = system.file("extdata", "lh.tinysurface",
 #'      package = "freesurferformats", mustWork = TRUE);
@@ -695,7 +695,7 @@ fixed.format.lines <- function(vdata, format_string, max_entries_per_line=NULL)
 #' @family mesh functions
 #'
 #' @examples
-#' \donttest{
+#' \dontrun{
 #'     # Read a surface from a file:
 #'     surface_file = system.file("extdata", "lh.tinysurface",
 #'      package = "freesurferformats", mustWork = TRUE);