Fixes for CRAN + R-4.5.1

.github/workflows/R-CMD-check.yaml

@@ -48,7 +48,7 @@ jobs:
           needs: check
 
       - name: Build CMTK
-        if: ${{matrix.config.os != 'windows-latest'}}
+        if: ${{matrix.config.os == 'macos-latest'}}
         run: sh ./build-cmtk.sh
         env:
           CC: clang

NAMESPACE

@@ -402,8 +402,6 @@ importFrom(igraph,"V<-")
 importFrom(igraph,E)
 importFrom(igraph,V)
 importFrom(igraph,add_edges)
-importFrom(igraph,as.directed)
-importFrom(igraph,as.undirected)
 importFrom(igraph,as_edgelist)
 importFrom(igraph,bfs)
 importFrom(igraph,decompose)

R/alphashape3d.R

@@ -15,7 +15,7 @@
 #'   \code{triang} entry in \bold{Value} section of
 #'   \code{\link[alphashape3d]{ashape3d}} docs for details.)
 #' @return a \code{\link[rgl]{mesh3d}} object which can be plotted and
-#'   manipulated using \code{\link{rgl}} and \code{nat} packages.
+#'   manipulated using \code{rgl} and \code{nat} packages.
 #' @export
 #' 
 #' @name as.mesh3d

R/cmtk-reformat.R

@@ -87,7 +87,7 @@ cmtk.targetvolume.default <- function(target, ...) {
 }
 
 #' Reformat an image with a CMTK registration using the reformatx tool
-#' 
+#'
 #' @details Note that if you are reformatting a mask then you will need to
 #'   change the interpolation to "nn", since interpolating between e.g. mask
 #'   levels 72 and 74 with 73 may have unintended consequences. Presently we
@@ -97,37 +97,38 @@ cmtk.targetvolume.default <- function(target, ...) {
 #' @param registrations One or more CMTK format registrations on disk
 #' @param output The path to the output image (defaults to
 #'   \code{"<targetstem>_<floatingstem>.nrrd"})
-#' @param mask Whether to treat target as a binary mask (only reformatting 
+#' @param mask Whether to treat target as a binary mask (only reformatting
 #'   positive voxels)
-#' @param interpolation What interpolation scheme to use for output image 
+#' @param interpolation What interpolation scheme to use for output image
 #'   (defaults to linear - see details)
 #' @param dryrun Just print command
 #' @param Verbose Whether to show cmtk status messages and be verbose about file
 #'   update checks. Sets command line \code{--verbose} option.
-#' @param MakeLock Whether to use a lock file to allow simple parallelisation 
-#'   (see \code{makelock})
-#' @param OverWrite Whether to OverWrite an existing output file. One of 
-#'   c("no","update","yes"). When OverWrite='update' 
-#'   \code{\link{RunCmdForNewerInput}} is used to determine if the output is 
-#'   older than any of the input files.
-#' @param filesToIgnoreModTimes Input files whose modification time should not 
+#' @param MakeLock Whether to use a lock file to allow simple parallelisation
+#'   (see \code{\link[nat.utils]{makelock}})
+#' @param OverWrite Whether to OverWrite an existing output file. One of
+#'   c("no","update","yes"). When OverWrite='update'
+#'   \code{\link[nat.utils]{RunCmdForNewerInput}} is used to determine if the
+#'   output is older than any of the input files.
+#' @param filesToIgnoreModTimes Input files whose modification time should not
 #'   be checked when determining if new output is required.
-#' @param ... additional arguments passed to CMTK \code{reformatx} after 
+#' @param ... additional arguments passed to CMTK \code{reformatx} after
 #'   processing by \code{\link{cmtk.call}}.
 #' @inheritParams cmtk.targetvolume
 #' @inheritParams xformimage.cmtkreg
 #' @importFrom nat.utils makelock removelock RunCmdForNewerInput
-#' @seealso \code{\link{cmtk.bindir}, \link{cmtk.call}, \link{makelock}, 
-#'   \link{RunCmdForNewerInput}}
+#' @seealso \code{\link{cmtk.bindir}}, \code{\link{cmtk.call}},
+#'   \code{\link[nat.utils]{makelock}},
+#'   \code{\link[nat.utils]{RunCmdForNewerInput}}
 #' @export
-#' @return the path to the output image (whether or not it was re-created afresh)
-#'   or \code{NA_character_} if no output was possible.
+#' @return the path to the output image (whether or not it was re-created
+#'   afresh) or \code{NA_character_} if no output was possible.
 #' @examples
 #' \dontrun{
 #' cmtk.reformatx('myimage.nrrd', target='template.nrrd',
 #'   registrations='template_myimage.list')
-#' 
-#' # get full listing of command line options  
+#'
+#' # get full listing of command line options
 #' system(cmtk.call('reformatx', help=TRUE))
 #' }
 cmtk.reformatx<-function(floating, registrations, output, target, mask=FALSE,

R/graph-nodes.R

@@ -4,10 +4,10 @@
 #'   friends. It is conceived of as slightly lower level and end users would
 #'   normally use the \code{rootpoints} methods.
 #'
-#'   \code{graph.nodes} should work for any \code{\link{igraph}} object
+#'   \code{graph.nodes} should work for any \code{\link[igraph]{igraph}} object
 #'   (including \code{\link{ngraph}} objects, which inherit from \code{igraph}).
 #'   However the graph must be directed in order to return a root point
-#' @param x An \code{\link{ngraph}} or raw \code{\link{igraph}} object
+#' @param x An \code{\link{ngraph}} or raw \code{\link[igraph]{igraph}} object
 #' @param type one of root, end (which includes root) or branch
 #' @param original.ids Use named attribute to return original vertex ids (when
 #'   available). Set to FALSE when this is not desired.

R/im3d.R

@@ -419,7 +419,7 @@ boundingbox.character<-function(x, ...) {
 #'   \code{\link{xyzmatrix}} method is defined including \code{matrix} or
 #'   \code{data.frame} objects describing 3D points as well as specialised
 #'   classes such as \code{\link{neuron}}, \code{\link{neuronlist}}, \code{rgl}
-#'   \code{\link{mesh3d}} objects.
+#'   \code{\link[rgl]{mesh3d}} objects.
 #'
 #' @export
 #' @rdname boundingbox

R/interactive.R

@@ -100,20 +100,26 @@ correct_root <- function(someneuronlist, brain = NULL){
 #' @description Generate a mesh3d model based on points contained in a
 #'   neuronlist or neuron object, or another object that consists of 3D points.
 #'
-#' @param x a neuronlist or neuron object, or another object that consists of 3D points
+#' @param x a neuronlist or neuron object, or another object that consists of 3D
+#'   points
 #' @param substrate whether to make the model based on the 3D location of
-#'   connectors, neuron cable or both. Connectors are pre-synapse locations, 
-#'   e.g. the pre-synapses of a \code{catmaidneuron} from the R package \code{catmaid})
+#'   connectors, neuron cable or both. Connectors are pre-synapse locations,
+#'   e.g. the pre-synapses of a \code{catmaidneuron} from the R package
+#'   \code{catmaid})
 #' @param alpha a single value or vector of values for alpha, fed to
 #'   \code{alphashape3d::ashape3d}. Selection is subsequently interactive.
-#' @param auto.selection logical, whether or not to try and remove points based on interactively
-#'   choosing simple values for clustering.
-#' @details Interactive function that allows a users to select points in 3D space from neuronlist/neuron objects,
-#' or another object that is coercible in 3D points using \code{\link{xyzmatrix}}. Points can first be automatically chosen, by
-#' selecting an integer number of nearest neighbours to find for each point using \code{nabor::\link{knn}}, and then a 
-#' maximum distance at which nodes can be part of a cluster. Next, \code{\link{select_points}} is used to manually pick desired 3D
-#' points. Lastly, \code{alphashape3d::ashape3d} is used to create an alphashape around these points. The user can trial different values for
-#' alpha until they get their desired result.
+#' @param auto.selection logical, whether or not to try and remove points based
+#'   on interactively choosing simple values for clustering.
+#' @details Interactive function that allows a users to select points in 3D
+#'   space from neuronlist/neuron objects, or another object that is coercible
+#'   in 3D points using \code{\link{xyzmatrix}}. Points can first be
+#'   automatically chosen, by selecting an integer number of nearest neighbours
+#'   to find for each point using \code{nabor::\link[nabor]{knn}}, and then a
+#'   maximum distance at which nodes can be part of a cluster. Next,
+#'   \code{\link{select_points}} is used to manually pick desired 3D points.
+#'   Lastly, \code{alphashape3d::ashape3d} is used to create an alphashape
+#'   around these points. The user can trial different values for alpha until
+#'   they get their desired result.
 #' @examples
 #' \dontrun{
 #' # Make a model based off of fly olfactory projection neuron arbours

R/nat-package.R

@@ -24,7 +24,7 @@
 #'
 #'   \code{neuron} objects containing connected trees can be converted to
 #'   \code{\link{ngraph}} objects, a lightweight wrapper around the
-#'   \code{\link{igraph}} library's \code{\link[igraph]{graph}} class that
+#'   \code{\link[igraph]{igraph}} library's \code{\link[igraph]{graph}} class that
 #'   preserves 3D coordinate information. This allows neurons to be manipulated
 #'   based on their graph structure, e.g. by finding all nodes upstream (closer
 #'   to the root) or downstream of a given node. The \code{\link{as.neuron}}
@@ -47,7 +47,7 @@
 #'   \code{\link{plot3d.neuronlist}} and \code{\link{subset.neuronlist}}).
 #'   Interactive 3D selection of neurons in a neuronlist is also possible using
 #'   \code{\link{find.neuron}} (which makes use of \code{rgl}'s
-#'   \code{\link{select3d}} function.
+#'   \code{\link[rgl]{select3d}} function.
 #'
 #'   \code{neuronlist} objects also provide additional functionality to
 #'   streamline arithmetic (e.g. scaling all the points in all neurons see
@@ -165,7 +165,7 @@
 #' @seealso \code{\link{neuron}}, \code{\link{dotprops}},
 #'   \code{\link{neuronlist}}, \code{\link{nlapply}}, \code{\link[nat]{plot3d}},
 #'   \code{\link{xform}}, \code{\link{im3d}}, \code{\link{read.hxsurf}},
-#'   \code{\link{rgl}} which is used for visualisation,
+#'   \code{\link[rgl]{rgl}} which is used for visualisation,
 #'   \code{\link{fileformats}}, \code{\link{read.neurons}}, \code{\link{cmtk}}.
 #' @keywords package
 #' @import rgl graphics grDevices utils

R/ndigest.R

@@ -7,12 +7,12 @@
 #'   machine on which the digest is being computed.
 #' @param x Object for which a normalised digest will be computed.
 #' @param ... Additional arguments passed to methods and then on to 
-#'   \code{\link{digest}}
+#'   \code{\link[digest]{digest}}
 #' @return A character string containing the digest of the supplied object 
-#'   computed by \code{\link{digest}}.
+#'   computed by \code{\link[digest]{digest}}.
 #' @export
 #' @importFrom digest digest
-#' @seealso \code{\link{digest}}
+#' @seealso \code{\link[digest]{digest}}
 ndigest<-function(x, ...) UseMethod('ndigest')
 
 #' @details \code{ndigest.neuronlistfh} only considers the \code{keyfilemap} and

R/neuron-io-amira.R

@@ -1,5 +1,4 @@
 # read neurons in the format produced by Amira skeletonize plugin
-#' @importFrom igraph as.undirected
 read.neuron.hxskel<-function(file, ...){
   ndata=read.amiramesh(file)
   required_fields=c("Coordinates", "NeighbourCount", "Radii", "NeighbourList")
@@ -40,7 +39,7 @@ read.neuron.hxskel<-function(file, ...){
   doubleg=ngraph(el, d$PointNo, directed=TRUE)
   # TODO see if we can make appropriate directed graph rather than converting
   # to undirected.
-  ug=as.undirected(doubleg, mode='collapse')
+  ug=as_undirected_nat(doubleg, mode='collapse')
   if(!inherits(ug,'ngraph')) class(ug)=c("ngraph",class(ug))
   n=as.neuron(ug, vertexData=d, origin=Origin, InputFileName=file, ... )
   n

R/neuron-plot.R

@@ -254,19 +254,20 @@ NULL
 #'   Note that sometimes (parts of) objects seem to disappear after panning and
 #'   zooming. See help for \code{\link{pan3d}}.
 #'
-#'   \code{\link{rgl}} and \code{\link[plotly:plot_ly]{plotly}} have quite
+#'   \code{\link[rgl]{rgl}} and \code{\link[plotly:plot_ly]{plotly}} have quite
 #'   different models for how to handle the active plot. \code{nopen3d} and
 #'   \code{\link{nclear3d}} allow you to treat them more similarly. Use them
-#'   wherever you use the rgl \code{clear3d} and \code{open3d} commands and your
-#'   could she be able to run with both \bold{plotly} or \bold{rgl} as the
+#'   wherever you use the rgl \code{\link[rgl]{clear3d}} and
+#'   \code{\link[rgl]{open3d}} commands and your
+#'   code should be able to run with both \bold{plotly} or \bold{rgl} as the
 #'   \code{plotengine}.
 #'
 #' @param bgcol background colour
 #' @param FOV field of view
 #' @param ... additional options passed to open3d
 #' @return current rgl device
 #' @export
-#' @seealso \code{\link{open3d},\link{pan3d}}, \code{\link{nclear3d}}
+#' @seealso \code{\link[rgl]{open3d}, \link{pan3d}}, \code{\link{nclear3d}}
 nopen3d<- function(bgcol='white', FOV=0, ...){
   res=open3d(mouseMode=c("trackball", "user", "zoom", "pull"), FOV=FOV, ...)
   bg3d(col=bgcol)
@@ -282,7 +283,7 @@ nopen3d<- function(bgcol='white', FOV=0, ...){
 #' @param extramat An optional extra transformation matrix to be applied after
 #'   the one implied by the viewpoint argument.
 #' @param ... additional arguments passed to \code{\link[rgl]{par3d}}
-#' @seealso \code{\link{nopen3d}}, \code{\link{view3d}}
+#' @seealso \code{\link{nopen3d}}, \code{\link[rgl]{view3d}}
 #' @export
 #' @importFrom rgl rotationMatrix scaleMatrix par3d
 #' @examples 
@@ -319,17 +320,17 @@ nview3d <- function(viewpoint=c("frontal", "anterior", "dorsal", "ventral",
 }
 
 #' Some useful extensions / changes to rgl defaults
-#' 
+#'
 #' Set up pan call back for current rgl device
-#' 
+#'
 #' Copied verbatim from ?rgl.setMouseCallbacks for rgl version 0.92.892 Mouse
 #' button 2 is right and button 3 is middle (accessed by Meta/Alt key)
-#' 
-#' Note that sometimes (parts of) objects seem to disappear after panning and 
-#' zooming. The example in \code{\link{rgl.setMouseCallbacks}} from which this
-#' is copied includes a note that "this doesn't play well with rescaling"
+#'
+#' Note that sometimes (parts of) objects seem to disappear after panning and
+#' zooming. The example in \code{\link[rgl]{rgl.setMouseCallbacks}} from which
+#' this is copied includes a note that "this doesn't play well with rescaling"
 #' @param button Integer from 1 to 3 indicating mouse button
-#' @seealso \code{\link{rgl.setMouseCallbacks}}
+#' @seealso \code{\link[rgl]{rgl.setMouseCallbacks}}
 #' @author Duncan Murdoch
 #' @export
 #' @examples
@@ -599,7 +600,7 @@ plot3d.boundingbox <- function(x, col='black',
 
 #' Clear the rgl or plotly 3D scene
 #'
-#' @details \code{\link{rgl}} and \code{\link[plotly:plot_ly]{plotly}} have
+#' @details \code{\link[rgl]{rgl}} and \code{\link[plotly:plot_ly]{plotly}} have
 #'   quite different models for how to handle the active plot. \code{nclear3d}
 #'   and \code{\link{nopen3d}} allow you to treat them more similarly. Use them
 #'   wherever you use the rgl \code{clear3d} and \code{open3d} commands and your
@@ -649,12 +650,11 @@ check_plotengine <- function(plotengine) {
 #' Plot 3d representation of neuron (ngraph) with directed edges
 #'
 #' @param x A \code{\link{ngraph}} object
-#' @param type They type of arrows (lines by default, see \code{\link{arrow3d}}
-#'   for details).
+#' @param type They type of arrows (lines by default, see
+#'   \code{\link[rgl]{arrow3d}} for details).
 #' @param soma radius of soma (or \code{FALSE} to suppress plotting)
-#' @param labels Whether to label nodes/all points with their raw index (not
-#'   id)
-#' @param ... Additional arguments passed to \code{\link{arrow3d}}
+#' @param labels Whether to label nodes/all points with their raw index (not id)
+#' @param ... Additional arguments passed to \code{\link[rgl]{arrow3d}}
 #'
 #' @export
 #'

R/neuron.R

@@ -73,14 +73,16 @@
 #' plot(as.neuron(gstem))
 #' 
 #' # but if you had an undirected graph 
-#' ug=igraph::as.undirected(gstem)
+#' if(utils::packageVersion('igraph')>='2.1.0') {
+#' ug=igraph::as_undirected(gstem)
 #' # you get a warning because there is no explicit origin for the graph
 #' as.neuron(ug)
 #' 
 #' # If you need finer control of the conversion process 
 #' gstem2=as.ngraph(ug, root = 10)
 #' plot(gstem2)
 #' plot(as.neuron(gstem2))
+#' }
 neuron<-function(d, NumPoints=nrow(d), StartPoint, BranchPoints=integer(), EndPoints,
                  SegList, SubTrees=NULL, InputFileName=NULL, NeuronName=NULL, ...,
                  MD5=TRUE){get
@@ -208,7 +210,7 @@ normalise_swc<-function(x, requiredColumns=c('PointNo','Label','X','Y','Z','W','
 #' @export
 #' @importFrom igraph V V<- vcount decompose
 #' @rdname neuron
-#' @seealso \code{\link{dfs}, \link{as.seglist}}
+#' @seealso \code{\link[igraph]{dfs}, \link{as.seglist}}
 as.neuron.ngraph<-function(x, vertexData=NULL, origin=NULL, Verbose=FALSE, ...){
   # translate origin into raw vertex id if necessary 
   if(length(origin)){

R/neuronlist.R

@@ -396,13 +396,14 @@ as.data.frame.neuronlist<-function(x, row.names = names(x), optional = FALSE, ..
 #'   overridden for the current session by setting the value of
 #'   \code{options(nat.progressbar)} (see examples). Values of \code{T} and
 #'   \code{F} are aliases for 'text' and 'none', respectively.
-#'   
+#'
 #' @section Progress bar: There are currently two supported approaches to
 #'   defining progress bars for \code{nlapply}. The default (when
 #'   \code{progress="auto"}) now uses a progress bar built using
-#'   \code{\link{progress_bar}} from the progress package, which can be highly
-#'   customised. The alternative is to use the progress bars distributed
-#'   directly with the \code{plyr} package such as \code{\link{progress_text}}.
+#'   \code{\link[progress]{progress_bar}} from the progress package, which can
+#'   be highly customised. The alternative is to use the progress bars
+#'   distributed directly with the \code{plyr} package such as
+#'   \code{\link[plyr]{progress_text}}.
 #'
 #'   In either case the value of the \code{.progress} argument must be a
 #'   character vector which names a function. According to \code{plyr}'s
@@ -526,7 +527,7 @@ nlapply<-function (X, FUN, ..., subset=NULL, OmitFailures=NA,
 #' @export
 #' @rdname nlapply
 #' @description \code{progress_natprogress} provides a progress bar compatible
-#'   with the \code{progress::\link{progress_bar}}.
+#'   with the \code{progress::\link[progress]{progress_bar}}.
 progress_natprogress <- function(...) {
   pb <- NULL
   list(