remove magick links completely, the new version generates warnings on…

… my R 3.6 installation under MacOS. sigh.

R/brainview_magick.R

@@ -14,7 +14,7 @@
 #'
 #' @param grid_like logical, whether to arrange the images in a grid-like fashion. If FALSE, they will all be merged horizontally.
 #'
-#' @param border_geometry string, a geometry string passed to \code{\link{image_border}} to define the borders to add to each image tile. The default value adds 5 pixels, both horizontally and vertically.
+#' @param border_geometry string, a geometry string passed to \code{magick::image_border} to define the borders to add to each image tile. The default value adds 5 pixels, both horizontally and vertically.
 #'
 #' @param background_color string, a valid ImageMagick color string such as "white" or "#000080". The color to use when extending images (e.g., when creating the border).
 #'
@@ -88,9 +88,9 @@ arrange.brainview.images <- function(brainview_images, output_img, colorbar_img=
 #'
 #' @description Create a tight layout view of coloredmeshes from several angles. Creates separate `sd_<angle>` images, then crops and finally merges them into a single output image with image magick. The `coloredmeshes` to pass to this function are usually obtained by running any `vis*` function (like \code{\link[fsbrain]{vis.subject.morph.native}}, \code{\link[fsbrain]{vis.subject.morph.standard}}, \code{\link[fsbrain]{vis.subject.label}}, \code{\link[fsbrain]{vis.subject.annot}}, and others). That means you can use this function to visualize all kinds of data, e.g., morphometry data in native and standard space, labels, and brain atlases.
 #
-#' @param coloredmeshes, list of coloredmesh. A coloredmesh is a named list as returned by the `coloredmesh.from*` functions (like \code{\link[fsbrain]{coloredmesh.from.morph.native}}). It has the entries 'mesh' of type tmesh3d, a 'col', which is a color specification for such a mesh. The `vis*` functions (like \code{\link[fsbrain]{vis.subject.morph.native}}) all return a list of coloredmeshes.
+#' @param coloredmeshes, list of coloredmesh. A coloredmesh is a named list as returned by the `coloredmesh.from*` functions (like \code{\link{coloredmesh.from.morph.native}}). It has the entries 'mesh' of type tmesh3d, a 'col', which is a color specification for such a mesh. The `vis*` functions (like \code{\link[fsbrain]{vis.subject.morph.native}}) all return a list of coloredmeshes.
 #'
-#' @param view_angles list of strings. See \code{\link[fsbrain]{get.view.angle.names}} for all valid strings.
+#' @param view_angles list of strings. See \code{\link{get.view.angle.names}} for all valid strings.
 #'
 #' @param rgloptions option list passed to \code{\link{par3d}}. Example: \code{rgloptions = list("windowRect"=c(50,50,1000,1000))}.
 #'

R/cbar_magick.R

@@ -10,7 +10,7 @@
 #'
 #' @param output_img path to output image, including the file extension.
 #'
-#' @param offset offset string passed to \code{\link{image_composite}}. Allows you to shift the location of the colorbar in the final image.
+#' @param offset offset string passed to \code{magick::image_composite}. Allows you to shift the location of the colorbar in the final image.
 #'
 #' @param extend_brainview_img_height_by integer value in pixels, the size of the lower border to add to the brainview_img. Increase this if the lower part of the colorbar is off the image canvas.
 #'
@@ -185,7 +185,7 @@ combine.colorbar.with.brainview.image.vertical <- function(brainview_img, colorb
 #'
 #' @param output_animation path to output image in gif format, must include the '.gif' file extension
 #'
-#' @param offset offset string passed to \code{\link{image_composite}}. Allows you to shift the location of the colorbar in the final image.
+#' @param offset offset string passed to \code{magick::image_composite}. Allows you to shift the location of the colorbar in the final image.
 #'
 #' @param extend_brainview_img_height_by integer value in pixels, the size of the lower border to add to the brainview_img. Use this if the lower part of the colorbar is off the image canvas.
 #'

R/vis_volume.R

@@ -278,11 +278,11 @@ vol.planes <- function(plane=NULL) {
 #'
 #' @description Create an image from each slice along the axis, then stack those into an ImageMagick image stack.
 #'
-#' @param volume a 3D image volume. Can be numeric, or something that can be read directly by \code{\link{image_read}} in 2D matrices (slices along the axis), e.g., a 3D array of color strings. If a 2D matrix is passed, the resulting stack will contain a single image.
+#' @param volume a 3D image volume. Can be numeric, or something that can be read directly by \code{magick::image_read} in 2D matrices (slices along the axis), e.g., a 3D array of color strings. If a 2D matrix is passed, the resulting stack will contain a single image.
 #'
 #' @param axis positive integer in range 1L..3L or an axis name, the axis to use.
 #'
-#' @param intensity_scale integer, value by which to scale the intensities in the volume to the range `[0, 1]`. Only used for numeric volumes. Set to NULL for data that can be read directly by \code{\link{image_read}}, and to 1 for intensity data that requires no scaling. Defaults to 255, which is suitable for 8 bit image data.
+#' @param intensity_scale integer, value by which to scale the intensities in the volume to the range `[0, 1]`. Only used for numeric volumes. Set to NULL for data that can be read directly by \code{magick::image_read}, and to 1 for intensity data that requires no scaling. Defaults to 255, which is suitable for 8 bit image data.
 #'
 #' @return a vectorized ImageMagick image, containing one subimage per slice. This can be interpreted as an animation or whatever.
 #'
@@ -358,7 +358,7 @@ vol.overlay.colors.from.activation <- function(volume, colormap_fn=squash::blueo
 #'
 #' @param per_col positive integer, the number of subimages per column in the output image. If `NULL`, automatically computed from the number of slices and the `per_row` parameter.
 #'
-#' @param border_geometry string, a geometry string passed to \code{\link{image_border}} to define the borders to add to each image tile. The default value adds 5 pixels, both horizontally and vertically.
+#' @param border_geometry string, a geometry string passed to \code{magick::image_border} to define the borders to add to each image tile. The default value adds 5 pixels, both horizontally and vertically.
 #'
 #' @param background_color string, a valid ImageMagick color string such as "white" or "#000080". The color to use when extending images (e.g., when creating the border). Defaults to black.
 #'