diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index d5561cd9..9afed5ef 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.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
diff --git a/NAMESPACE b/NAMESPACE
index bd32d4cf..d31831a3 100644
--- a/NAMESPACE
+++ b/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)
diff --git a/R/alphashape3d.R b/R/alphashape3d.R
index bdd67ec2..5ba2d7c0 100644
--- a/R/alphashape3d.R
+++ b/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
diff --git a/R/cmtk-reformat.R b/R/cmtk-reformat.R
index 95a0e640..fd058441 100644
--- a/R/cmtk-reformat.R
+++ b/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,
diff --git a/R/graph-nodes.R b/R/graph-nodes.R
index b9d56cfc..b2c89ced 100644
--- a/R/graph-nodes.R
+++ b/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.
diff --git a/R/im3d.R b/R/im3d.R
index caa9524b..44b0b674 100644
--- a/R/im3d.R
+++ b/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
diff --git a/R/interactive.R b/R/interactive.R
index 7dbdfff4..5431703b 100644
--- a/R/interactive.R
+++ b/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
diff --git a/R/nat-package.R b/R/nat-package.R
index 53b89ada..d125530c 100644
--- a/R/nat-package.R
+++ b/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
diff --git a/R/ndigest.R b/R/ndigest.R
index 21ee01b3..d51c80bd 100644
--- a/R/ndigest.R
+++ b/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
diff --git a/R/neuron-io-amira.R b/R/neuron-io-amira.R
index c49a705c..8e395f29 100644
--- a/R/neuron-io-amira.R
+++ b/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
diff --git a/R/neuron-plot.R b/R/neuron-plot.R
index a32a428c..12c8121d 100644
--- a/R/neuron-plot.R
+++ b/R/neuron-plot.R
@@ -254,11 +254,12 @@ 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
@@ -266,7 +267,7 @@ NULL
 #' @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
 #'
diff --git a/R/neuron.R b/R/neuron.R
index 0324183f..add792e9 100644
--- a/R/neuron.R
+++ b/R/neuron.R
@@ -73,7 +73,8 @@
 #' 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)
 #' 
@@ -81,6 +82,7 @@
 #' 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)){
diff --git a/R/neuronlist.R b/R/neuronlist.R
index c7644c8f..6ca3f012 100644
--- a/R/neuronlist.R
+++ b/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(
diff --git a/R/neuronlist_interactive_3d.R b/R/neuronlist_interactive_3d.R
index be1488ec..bd6166e1 100644
--- a/R/neuronlist_interactive_3d.R
+++ b/R/neuronlist_interactive_3d.R
@@ -1,21 +1,22 @@
 #' Find neurons within a 3D selection box (usually drawn in rgl window)
-#' 
-#' @details Uses \code{\link{subset.neuronlist}}, so can work on dotprops or 
+#'
+#' @details Uses \code{\link{subset.neuronlist}}, so can work on dotprops or
 #'   neuron lists.
-#' @param sel3dfun A \code{\link{select3d}} style function to indicate if points
-#'   are within region
+#' @param sel3dfun A \code{\link[rgl]{select3d}} style function to indicate if
+#'   points are within region
 #' @param indices Names of neurons to search (defaults to all neurons in list)
-#' @param db \code{neuronlist} to search. Can also be a character vector naming 
+#' @param db \code{neuronlist} to search. Can also be a character vector naming
 #'   the neuronlist. Defaults to \code{options('nat.default.neuronlist')}.
 #' @param threshold More than this many points must be present in region
-#' @param invert Whether to return neurons outside the selection box (default 
+#' @param invert Whether to return neurons outside the selection box (default
 #'   \code{FALSE})
 #' @param rval What to return (character vector, default='names')
-#'   
-#' @return Character vector of names of selected neurons, neuronlist, or 
+#'
+#' @return Character vector of names of selected neurons, neuronlist, or
 #'   data.frame of attached metadata according to the value of \code{rval}.
 #' @export
-#' @seealso \code{\link{select3d}, \link{find.soma}, \link{subset.neuronlist}}
+#' @seealso \code{\link[rgl]{select3d}, \link{find.soma},
+#'   \link{subset.neuronlist}}
 #' @examples
 #' \dontrun{
 #' plot3d(kcs20)
@@ -25,7 +26,7 @@
 #' # make a standalone selection function
 #' vertical_lobe=select3d()
 #' find.neuron(vertical_lobe, db=kcs20)
-#' # use base::Negate function to invert the selection function 
+#' # use base::Negate function to invert the selection function
 #' # i.e. choose neurons that do not overlap the selection region
 #' find.neuron(Negate(vertical_lobe), db=kcs20)
 #' }
@@ -49,14 +50,15 @@ find.neuron<-function(sel3dfun=select3d(), indices=names(db),
 }
 
 #' Find neurons with soma inside 3D selection box (usually drawn in rgl window)
-#' 
-#' @details Can work on \code{neuronlist}s containing \code{neuron} objects 
-#'   \emph{or} \code{neuronlist}s whose attached data.frame contains soma 
+#'
+#' @details Can work on \code{neuronlist}s containing \code{neuron} objects
+#'   \emph{or} \code{neuronlist}s whose attached data.frame contains soma
 #'   positions specified in columns called X,Y,Z  .
 #' @inheritParams find.neuron
 #' @return Character vector of names of selected neurons
 #' @export
-#' @seealso \code{\link{select3d}, \link{subset.neuronlist}, \link{find.neuron}}
+#' @seealso \code{\link[rgl]{select3d}, \link{subset.neuronlist},
+#'   \link{find.neuron}}
 find.soma <- function (sel3dfun = select3d(), indices = names(db), 
                        db = getOption("nat.default.neuronlist"),
                        invert=FALSE,
diff --git a/R/neuronlistfh.R b/R/neuronlistfh.R
index fc1e955f..cdf671c9 100644
--- a/R/neuronlistfh.R
+++ b/R/neuronlistfh.R
@@ -117,7 +117,7 @@
 #'   occupying only a few GB) on NFS network file systems or Google Drive,
 #'   neither of which are keen on having many files especially in the same
 #'   folder. It does not allow updates from a remote location. See
-#'   \code{\link{filehashDB1-class}} for more details.
+#'   \code{\link[filehash]{filehashDB1-class}} for more details.
 #'
 #'   Note that objects are stored in a filehash, which by definition does not
 #'   have any ordering of its elements. However neuronlist objects (like lists)
diff --git a/R/ngraph.R b/R/ngraph.R
index 4e856d77..ab9d3805 100644
--- a/R/ngraph.R
+++ b/R/ngraph.R
@@ -1,3 +1,19 @@
+# local functions to handle deprecated functions in igraph >= 2.1.0
+make_graph_nat <- function(...) {
+  pvi <- packageVersion('igraph')
+  if(pvi>='2.1.0') igraph::make_graph(...) else igraph::graph(...)
+}
+
+as_directed_nat <- function(...) {
+  pvi <- packageVersion('igraph')
+  if(pvi>='2.1.0') igraph::as_directed(...) else igraph::as.directed(...)
+} 
+
+as_undirected_nat <- function(...) {
+  pvi <- packageVersion('igraph')
+  if(pvi>='2.1.0') igraph::as_undirected(...) else igraph::as.undirected(...)
+} 
+
 #' ngraph: a graph to encode a neuron's connectivity
 #'
 #' @description the \code{ngraph} class contains a (completely general) graph
@@ -55,7 +71,7 @@
 #'   vertex for each entry in vertexnames, each vertex having a \code{label}
 #'   attribute. All vertices are included whether connected or not.
 #' @family neuron
-#' @seealso \code{\link{igraph}}, \code{\link[igraph]{set_vertex_attr}},
+#' @seealso \code{\link[igraph]{igraph}}, \code{\link[igraph]{set_vertex_attr}},
 #'   \code{\link{subset.neuron}} for example of graph-based manipulation of a
 #'   neuron, \code{\link{plot3d.ngraph}}
 #' @export
@@ -97,7 +113,7 @@ ngraph<-function(el, vertexnames, xyz=NULL, diam=NULL, directed=TRUE,
     vecs=xyz[stops, , drop=FALSE] - xyz[starts, , drop=FALSE]
     weights=sqrt(rowSums(vecs*vecs))
   }
-  g=igraph::graph(rawel, n=length(vertexnames), directed=directed)
+  g=make_graph_nat(rawel, n=length(vertexnames), directed=directed)
   igraph::V(g)$name=vertexnames
   if(is.numeric(weights))
     igraph::E(g)$weight=weights
@@ -155,13 +171,12 @@ as.ngraph.neuron<-function(x, directed=TRUE, method=c('swc','seglist'), ...){
   }
 }
 
-#' @importFrom igraph as.undirected as.directed
 #' @export
 as.ngraph.igraph<-function(x, directed=TRUE, root, mode=c('out','in'), ...){
   if(inherits(x,'ngraph'))
     if(igraph::is_directed(x)==directed) return(x)
   
-  if(igraph::is_directed(x) && !directed) x=as.undirected(x, ...)
+  if(igraph::is_directed(x) && !directed) x=as_undirected_nat(x, ...)
   else if(!igraph::is_directed(x) && directed) x=as.directed.usingroot(x, root, mode=mode, ...)
   
   if(!inherits(x,'ngraph')){
@@ -174,7 +189,7 @@ as.directed.usingroot<-function(g, root, mode=c('out','in')){
   mode=match.arg(mode)
   # make a directed graph _keeping any attributes_
   if(!igraph::is_directed(g))
-    dg=igraph::as.directed(g, mode='arbitrary')
+    dg=as_directed_nat(g, mode='arbitrary')
   else dg=g
   dfs=igraph::dfs(dg, root, unreachable=FALSE, dist=TRUE, mode='all')
   el=igraph::as_edgelist(dg)
diff --git a/R/seglist.R b/R/seglist.R
index a07bb33a..c6d2eaf8 100644
--- a/R/seglist.R
+++ b/R/seglist.R
@@ -90,7 +90,7 @@ as.seglist.default<-function(x, ...) stop("Not yet implemented!")
 #' @param origin The origin of the tree (see details)
 #' @param Verbose Whether to print progress updates to console (default FALSE)
 #' @return a \code{list} with one entry for each unbranched segment.
-#' @seealso \code{\link{ngraph},\link{igraph}}
+#' @seealso \code{\link{ngraph},\link[igraph]{igraph}}
 #' @export
 #' @importFrom igraph is_directed is_connected dfs degree
 #' @rdname seglist
diff --git a/inst/WORDLIST b/inst/WORDLIST
index f9ca653b..0eae04c2 100644
--- a/inst/WORDLIST
+++ b/inst/WORDLIST
@@ -6,6 +6,7 @@ AxisDirections
 BoundingBox
 BranchPoints
 CATMAID
+CMD
 CMTK
 CMTK's
 Cachero
@@ -72,6 +73,7 @@ Nx
 Ny
 Nz
 OO
+ORCID
 Obermayer
 OmitFailures
 OuterRegion
@@ -87,13 +89,12 @@ RLE
 RStudio
 RegionChoice
 RegionChoices
-RegionColourList
-RegionList
 Reroot
 Rmd
 Rohlfing
 Rtools
 Rvcg
+SNT
 SWC
 SWCData
 SWCs
@@ -129,7 +130,6 @@ amiramesh
 arg
 args
 ashape
-attr
 autonames
 bindir
 boundingbox
@@ -142,7 +142,6 @@ cmtkreg
 color
 colors
 colpal
-com
 commandline
 connectomics
 coord
@@ -159,9 +158,7 @@ devtools
 df
 dfc
 dfs
-dir
 dof
-doi
 donttest
 dotprops
 dplyr
@@ -185,7 +182,6 @@ filetype
 flybrain
 flybrains
 flycircuit
-fninf
 frulhns
 getformatreader
 getformatwriter
@@ -240,7 +236,6 @@ ndigest
 neurite
 neurodebian
 neuroglancer
-neuroimage
 neuroml
 neuronformats
 neuronlist
@@ -249,10 +244,8 @@ neuronlistfh
 neuronlists
 ngraph
 nhdr
-nitrc
 nl
 nlapply
-nlevels
 nlscan
 nmapply
 nn
@@ -266,7 +259,6 @@ nrrds
 nvertices
 nview
 obj
-org
 outfile
 params
 plotengine
@@ -286,6 +278,7 @@ reglist
 reglists
 regs
 remotesync
+rerooting
 rgl
 rgl's
 rm
@@ -316,7 +309,6 @@ subarray
 subdir
 subdirs
 subgraphs
-sumsegment
 swc
 targetvolume
 tarmat
@@ -345,7 +337,6 @@ warpfile
 webGL
 webgl
 winbuilder
-www
 xform
 xform's
 xformimage
@@ -359,5 +350,4 @@ xyzmatrix
 xyzpos
 yml
 zenodo
-zlim
 µm
diff --git a/man/as.mesh3d.Rd b/man/as.mesh3d.Rd
index a2c7871d..916a0303 100644
--- a/man/as.mesh3d.Rd
+++ b/man/as.mesh3d.Rd
@@ -31,7 +31,7 @@ object}
 }
 \value{
 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.
 }
 \description{
 \code{as.mesh3d.ashape3d} converts an 
diff --git a/man/boundingbox.Rd b/man/boundingbox.Rd
index 850899ff..d274e39e 100644
--- a/man/boundingbox.Rd
+++ b/man/boundingbox.Rd
@@ -71,7 +71,7 @@ The bounding box is defined as the position of the voxels at the two
   \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.
 }
 \examples{
 # bounding box for a neuron
diff --git a/man/cmtk.reformatx.Rd b/man/cmtk.reformatx.Rd
index b4e6f80b..bb881842 100644
--- a/man/cmtk.reformatx.Rd
+++ b/man/cmtk.reformatx.Rd
@@ -32,14 +32,14 @@ cmtk.reformatx(
 \code{im3d} object (or an object that can be coerced to im3d) or a 6-or
 9-vector defining a grid in the form Nx,Ny,Nz,dX,dY,dZ,[Ox,Oy,Oz].}
 
-\item{mask}{Whether to treat target as a binary mask (only reformatting 
+\item{mask}{Whether to treat target as a binary mask (only reformatting
 positive voxels)}
 
 \item{direction}{Whether to transform image from sample space to reference
 space (called \strong{forward} by CMTK) or from reference to sample space
 (called \strong{inverse} by CMTK). Default (when \code{NULL} is forward).}
 
-\item{interpolation}{What interpolation scheme to use for output image 
+\item{interpolation}{What interpolation scheme to use for output image
 (defaults to linear - see details)}
 
 \item{dryrun}{Just print command}
@@ -47,23 +47,23 @@ space (called \strong{forward} by CMTK) or from reference to sample space
 \item{Verbose}{Whether to show cmtk status messages and be verbose about file
 update checks. Sets command line \code{--verbose} option.}
 
-\item{MakeLock}{Whether to use a lock file to allow simple parallelisation 
-(see \code{makelock})}
+\item{MakeLock}{Whether to use a lock file to allow simple parallelisation
+(see \code{\link[nat.utils]{makelock}})}
 
-\item{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.}
+\item{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.}
 
-\item{filesToIgnoreModTimes}{Input files whose modification time should not 
+\item{filesToIgnoreModTimes}{Input files whose modification time should not
 be checked when determining if new output is required.}
 
-\item{...}{additional arguments passed to CMTK \code{reformatx} after 
+\item{...}{additional arguments passed to CMTK \code{reformatx} after
 processing by \code{\link{cmtk.call}}.}
 }
 \value{
-the path to the output image (whether or not it was re-created afresh)
-  or \code{NA_character_} if no output was possible.
+the path to the output image (whether or not it was re-created
+  afresh) or \code{NA_character_} if no output was possible.
 }
 \description{
 Reformat an image with a CMTK registration using the reformatx tool
@@ -80,11 +80,12 @@ Note that if you are reformatting a mask then you will need to
 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))
 }
 }
 \seealso{
-\code{\link{cmtk.bindir}, \link{cmtk.call}, \link{makelock}, 
-  \link{RunCmdForNewerInput}}
+\code{\link{cmtk.bindir}}, \code{\link{cmtk.call}},
+  \code{\link[nat.utils]{makelock}},
+  \code{\link[nat.utils]{RunCmdForNewerInput}}
 }
diff --git a/man/find.neuron.Rd b/man/find.neuron.Rd
index 65b4e508..72517cbb 100644
--- a/man/find.neuron.Rd
+++ b/man/find.neuron.Rd
@@ -14,30 +14,30 @@ find.neuron(
 )
 }
 \arguments{
-\item{sel3dfun}{A \code{\link{select3d}} style function to indicate if points
-are within region}
+\item{sel3dfun}{A \code{\link[rgl]{select3d}} style function to indicate if
+points are within region}
 
 \item{indices}{Names of neurons to search (defaults to all neurons in list)}
 
-\item{db}{\code{neuronlist} to search. Can also be a character vector naming 
+\item{db}{\code{neuronlist} to search. Can also be a character vector naming
 the neuronlist. Defaults to \code{options('nat.default.neuronlist')}.}
 
 \item{threshold}{More than this many points must be present in region}
 
-\item{invert}{Whether to return neurons outside the selection box (default 
+\item{invert}{Whether to return neurons outside the selection box (default
 \code{FALSE})}
 
 \item{rval}{What to return (character vector, default='names')}
 }
 \value{
-Character vector of names of selected neurons, neuronlist, or 
+Character vector of names of selected neurons, neuronlist, or
   data.frame of attached metadata according to the value of \code{rval}.
 }
 \description{
 Find neurons within a 3D selection box (usually drawn in rgl window)
 }
 \details{
-Uses \code{\link{subset.neuronlist}}, so can work on dotprops or 
+Uses \code{\link{subset.neuronlist}}, so can work on dotprops or
   neuron lists.
 }
 \examples{
@@ -49,11 +49,12 @@ find.neuron(db=kcs20)
 # make a standalone selection function
 vertical_lobe=select3d()
 find.neuron(vertical_lobe, db=kcs20)
-# use base::Negate function to invert the selection function 
+# use base::Negate function to invert the selection function
 # i.e. choose neurons that do not overlap the selection region
 find.neuron(Negate(vertical_lobe), db=kcs20)
 }
 }
 \seealso{
-\code{\link{select3d}, \link{find.soma}, \link{subset.neuronlist}}
+\code{\link[rgl]{select3d}, \link{find.soma},
+  \link{subset.neuronlist}}
 }
diff --git a/man/find.soma.Rd b/man/find.soma.Rd
index 5adaf776..8480b821 100644
--- a/man/find.soma.Rd
+++ b/man/find.soma.Rd
@@ -13,15 +13,15 @@ find.soma(
 )
 }
 \arguments{
-\item{sel3dfun}{A \code{\link{select3d}} style function to indicate if points
-are within region}
+\item{sel3dfun}{A \code{\link[rgl]{select3d}} style function to indicate if
+points are within region}
 
 \item{indices}{Names of neurons to search (defaults to all neurons in list)}
 
-\item{db}{\code{neuronlist} to search. Can also be a character vector naming 
+\item{db}{\code{neuronlist} to search. Can also be a character vector naming
 the neuronlist. Defaults to \code{options('nat.default.neuronlist')}.}
 
-\item{invert}{Whether to return neurons outside the selection box (default 
+\item{invert}{Whether to return neurons outside the selection box (default
 \code{FALSE})}
 
 \item{rval}{What to return (character vector, default='names')}
@@ -33,10 +33,11 @@ Character vector of names of selected neurons
 Find neurons with soma inside 3D selection box (usually drawn in rgl window)
 }
 \details{
-Can work on \code{neuronlist}s containing \code{neuron} objects 
-  \emph{or} \code{neuronlist}s whose attached data.frame contains soma 
+Can work on \code{neuronlist}s containing \code{neuron} objects
+  \emph{or} \code{neuronlist}s whose attached data.frame contains soma
   positions specified in columns called X,Y,Z  .
 }
 \seealso{
-\code{\link{select3d}, \link{subset.neuronlist}, \link{find.neuron}}
+\code{\link[rgl]{select3d}, \link{subset.neuronlist},
+  \link{find.neuron}}
 }
diff --git a/man/graph.nodes.Rd b/man/graph.nodes.Rd
index 024c1111..47bc255b 100644
--- a/man/graph.nodes.Rd
+++ b/man/graph.nodes.Rd
@@ -12,7 +12,7 @@ graph.nodes(
 )
 }
 \arguments{
-\item{x}{An \code{\link{ngraph}} or raw \code{\link{igraph}} object}
+\item{x}{An \code{\link{ngraph}} or raw \code{\link[igraph]{igraph}} object}
 
 \item{type}{one of root, end (which includes root) or branch}
 
@@ -30,7 +30,7 @@ This function underlies \code{\link{rootpoints.igraph}} methods and
   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
 }
diff --git a/man/make_model.Rd b/man/make_model.Rd
index 9208eb80..c988021f 100644
--- a/man/make_model.Rd
+++ b/man/make_model.Rd
@@ -12,17 +12,19 @@ make_model(
 )
 }
 \arguments{
-\item{x}{a neuronlist or neuron object, or another object that consists of 3D points}
+\item{x}{a neuronlist or neuron object, or another object that consists of 3D
+points}
 
 \item{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})}
 
 \item{alpha}{a single value or vector of values for alpha, fed to
 \code{alphashape3d::ashape3d}. Selection is subsequently interactive.}
 
-\item{auto.selection}{logical, whether or not to try and remove points based on interactively
-choosing simple values for clustering.}
+\item{auto.selection}{logical, whether or not to try and remove points based
+on interactively choosing simple values for clustering.}
 }
 \value{
 A mesh3d object
@@ -32,12 +34,16 @@ Generate a mesh3d model based on points contained in a
   neuronlist or neuron object, or another object that consists of 3D points.
 }
 \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.
+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{
diff --git a/man/nat-package.Rd b/man/nat-package.Rd
index e9581d0a..795f6ddb 100644
--- a/man/nat-package.Rd
+++ b/man/nat-package.Rd
@@ -32,7 +32,7 @@ neuroanatomical data, especially representations of neurons.
 
   \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}}
@@ -57,7 +57,7 @@ neuroanatomical data, especially representations of neurons.
   \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
@@ -190,7 +190,7 @@ neuroanatomical data, especially representations of neurons.
 \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}}.
 }
 \author{
diff --git a/man/nclear3d.Rd b/man/nclear3d.Rd
index d108ff9d..b779b7c0 100644
--- a/man/nclear3d.Rd
+++ b/man/nclear3d.Rd
@@ -17,7 +17,7 @@ nclear3d(..., plotengine = getOption("nat.plotengine"))
 Clear the rgl or plotly 3D scene
 }
 \details{
-\code{\link{rgl}} and \code{\link[plotly:plot_ly]{plotly}} have
+\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
diff --git a/man/ndigest.Rd b/man/ndigest.Rd
index 4ccd148e..3a5817bb 100644
--- a/man/ndigest.Rd
+++ b/man/ndigest.Rd
@@ -24,7 +24,7 @@ ndigest(x, ...)
 \item{x}{Object for which a normalised digest will be computed.}
 
 \item{...}{Additional arguments passed to methods and then on to 
-\code{\link{digest}}}
+\code{\link[digest]{digest}}}
 
 \item{absoluteVectors}{Whether to check only the absolute value of
 eigenvectors for equality (default TRUE, see details)}
@@ -33,7 +33,7 @@ eigenvectors for equality (default TRUE, see details)}
 }
 \value{
 A character string containing the digest of the supplied object 
-  computed by \code{\link{digest}}.
+  computed by \code{\link[digest]{digest}}.
 }
 \description{
 The \emph{normalised} digest should exclude any fields or 
@@ -74,7 +74,7 @@ The \emph{normalised} digest should exclude any fields or
 stopifnot(all.equal(ndigest(kcs20[[1]]), "4c045b0343938259cd9986494fc1c2b0"))
 }
 \seealso{
-\code{\link{digest}}
+\code{\link[digest]{digest}}
 
 \code{\link{all.equal.dotprops}}
 
diff --git a/man/neuron.Rd b/man/neuron.Rd
index 7b6af9b9..6babeeb5 100644
--- a/man/neuron.Rd
+++ b/man/neuron.Rd
@@ -166,7 +166,8 @@ plot(gstem)
 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)
 
@@ -175,10 +176,11 @@ gstem2=as.ngraph(ug, root = 10)
 plot(gstem2)
 plot(as.neuron(gstem2))
 }
+}
 \seealso{
 \code{\link{neuronlist}}
 
-\code{\link{dfs}, \link{as.seglist}}
+\code{\link[igraph]{dfs}, \link{as.seglist}}
 
 Other neuron: 
 \code{\link{ngraph}()},
diff --git a/man/neuronlistfh.Rd b/man/neuronlistfh.Rd
index b96af11c..a578f353 100644
--- a/man/neuronlistfh.Rd
+++ b/man/neuronlistfh.Rd
@@ -199,7 +199,7 @@ a \code{neuronlistfh} object which is a character \code{vector} with
   occupying only a few GB) on NFS network file systems or Google Drive,
   neither of which are keen on having many files especially in the same
   folder. It does not allow updates from a remote location. See
-  \code{\link{filehashDB1-class}} for more details.
+  \code{\link[filehash]{filehashDB1-class}} for more details.
 
   Note that objects are stored in a filehash, which by definition does not
   have any ordering of its elements. However neuronlist objects (like lists)
diff --git a/man/ngraph.Rd b/man/ngraph.Rd
index be9772c4..f568634b 100644
--- a/man/ngraph.Rd
+++ b/man/ngraph.Rd
@@ -135,7 +135,7 @@ plot(gw_spine, col='red', boundingbox=boundingbox(n))
 plot(gw_antispine, col='blue', add=TRUE)
 }
 \seealso{
-\code{\link{igraph}}, \code{\link[igraph]{set_vertex_attr}},
+\code{\link[igraph]{igraph}}, \code{\link[igraph]{set_vertex_attr}},
   \code{\link{subset.neuron}} for example of graph-based manipulation of a
   neuron, \code{\link{plot3d.ngraph}}
 
diff --git a/man/nlapply.Rd b/man/nlapply.Rd
index 9339702c..9e5524d9 100644
--- a/man/nlapply.Rd
+++ b/man/nlapply.Rd
@@ -72,7 +72,7 @@ Versions of lapply and mapply that look after the class and
   bars and simple parallelisation (see plyr section and examples).
 
 \code{progress_natprogress} provides a progress bar compatible
-  with the \code{progress::\link{progress_bar}}.
+  with the \code{progress::\link[progress]{progress_bar}}.
 }
 \details{
 When \code{OmitFailures} is not \code{NA}, \code{FUN} will be
@@ -118,9 +118,10 @@ When \code{OmitFailures} is not \code{NA}, \code{FUN} will be
  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
diff --git a/man/nopen3d.Rd b/man/nopen3d.Rd
index 3cca95c6..bd731612 100644
--- a/man/nopen3d.Rd
+++ b/man/nopen3d.Rd
@@ -28,13 +28,14 @@ Pan with right button (Ctrl+click), zoom with middle
   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}.
 }
 \seealso{
-\code{\link{open3d},\link{pan3d}}, \code{\link{nclear3d}}
+\code{\link[rgl]{open3d}, \link{pan3d}}, \code{\link{nclear3d}}
 }
diff --git a/man/nview3d.Rd b/man/nview3d.Rd
index ea61f970..4b3a78ca 100644
--- a/man/nview3d.Rd
+++ b/man/nview3d.Rd
@@ -39,5 +39,5 @@ nview3d('frontal', extramat=rotationMatrix(pi/10, 1, 1, 0))
 }
 }
 \seealso{
-\code{\link{nopen3d}}, \code{\link{view3d}}
+\code{\link{nopen3d}}, \code{\link[rgl]{view3d}}
 }
diff --git a/man/pan3d.Rd b/man/pan3d.Rd
index 71d86f6e..26ba0ca5 100644
--- a/man/pan3d.Rd
+++ b/man/pan3d.Rd
@@ -16,9 +16,9 @@ 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"
 }
 \examples{
 \dontrun{
@@ -27,7 +27,7 @@ is copied includes a note that "this doesn't play well with rescaling"
 }
 }
 \seealso{
-\code{\link{rgl.setMouseCallbacks}}
+\code{\link[rgl]{rgl.setMouseCallbacks}}
 }
 \author{
 Duncan Murdoch
diff --git a/man/plot3d.ngraph.Rd b/man/plot3d.ngraph.Rd
index e1660daa..8ce137cd 100644
--- a/man/plot3d.ngraph.Rd
+++ b/man/plot3d.ngraph.Rd
@@ -9,15 +9,14 @@
 \arguments{
 \item{x}{A \code{\link{ngraph}} object}
 
-\item{type}{They type of arrows (lines by default, see \code{\link{arrow3d}}
-for details).}
+\item{type}{They type of arrows (lines by default, see
+\code{\link[rgl]{arrow3d}} for details).}
 
 \item{soma}{radius of soma (or \code{FALSE} to suppress plotting)}
 
-\item{labels}{Whether to label nodes/all points with their raw index (not
-id)}
+\item{labels}{Whether to label nodes/all points with their raw index (not id)}
 
-\item{...}{Additional arguments passed to \code{\link{arrow3d}}}
+\item{...}{Additional arguments passed to \code{\link[rgl]{arrow3d}}}
 }
 \description{
 Plot 3d representation of neuron (ngraph) with directed edges
diff --git a/man/seglist.Rd b/man/seglist.Rd
index c0600d74..dce33dd1 100644
--- a/man/seglist.Rd
+++ b/man/seglist.Rd
@@ -66,5 +66,5 @@ sl=seglist(c(1:2),c(2:6))
 \seealso{
 \code{\link{neuron}}
 
-\code{\link{ngraph},\link{igraph}}
+\code{\link{ngraph},\link[igraph]{igraph}}
 }
diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
new file mode 100644
index 00000000..f6643203
--- /dev/null
+++ b/tests/testthat/setup.R
@@ -0,0 +1,6 @@
+setup({
+  ff=dir(test_path('testdata'), pattern = '\\.swc\\.txt$',
+         recursive = T,  full.names = T)
+  ffnew=sub("\\.txt$","",ff)
+  file.copy(ff, ffnew)
+})
diff --git a/tests/testthat/teardown.R b/tests/testthat/teardown.R
index fd8ca8d5..28155c28 100644
--- a/tests/testthat/teardown.R
+++ b/tests/testthat/teardown.R
@@ -3,3 +3,9 @@ pdf_path =  test_path('Rplots.pdf')
 # check for write permission
 if(isTRUE(file.access(pdf_path, mode = 2)==0))
   file.remove(pdf_path)
+
+ffnew=dir(test_path('testdata'), pattern = '\\.swc$', recursive = T,
+          full.names = T)
+if(isTRUE(all(file.access(ffnew, mode = 2)==0))) {
+  file.remove(ffnew)
+}
diff --git a/tests/testthat/test-neuroml-io.R b/tests/testthat/test-neuroml-io.R
index 12ff2087..43baeda9 100644
--- a/tests/testthat/test-neuroml-io.R
+++ b/tests/testthat/test-neuroml-io.R
@@ -46,7 +46,9 @@ test_that("parse neuroml files", {
 })
 
 test_that("is.neuroml", {
-  ff=dir(c("testdata/neuroml","testdata/neuroml2"), full.names = T, recursive = T)
+  ff=dir(c("testdata/neuroml","testdata/neuroml2"), 
+         full.names = T, recursive = T, pattern = '\\.(swc|xml)$')
+  
   notswc=tools::file_ext(ff)!="swc"
   expect_equivalent(is.neuroml(ff), notswc)
 })
diff --git a/tests/testthat/test-neuron-mesh.R b/tests/testthat/test-neuron-mesh.R
index ef0829bf..6161bb65 100644
--- a/tests/testthat/test-neuron-mesh.R
+++ b/tests/testthat/test-neuron-mesh.R
@@ -7,7 +7,7 @@ setup(dir.create(td))
 teardown(unlink(td, recursive = TRUE))
 
 test_that("read/write works", {
-  expect_silent(ff1 <- write.neurons(bl, dir=td, format='ply'))
+  ff1 <- write.neurons(bl, dir=td, format='ply')
   md5.1=tools::md5sum(ff1)
   expect_warning(ff2 <- write.neurons(bl, dir=td, Force=TRUE), regexp = 'ply')
   md5.2=tools::md5sum(ff2)
@@ -35,7 +35,7 @@ setup(dir.create(td2))
 teardown(unlink(td2, recursive = TRUE))
 
 test_that("read/write works with obj files", {
-  expect_silent(ff1 <- write.neurons(bl, dir=td2, format='obj'))
+  ff1 <- write.neurons(bl, dir=td2, format='obj')
   expect_is(bl2 <- read.neurons(td2), 'neuronlist')
   expect_equal(summary(bl), summary(bl2))
   expect_error(write.neurons(Cell07PNs[1:3], format = 'obj'))
diff --git a/tests/testthat/test-ngraph.R b/tests/testthat/test-ngraph.R
index 1806e585..a441e9ce 100644
--- a/tests/testthat/test-ngraph.R
+++ b/tests/testthat/test-ngraph.R
@@ -175,7 +175,7 @@ test_that("we can find the segmentgraph of a neuron",{
   testn=as.neuron(testd)
   expect_is(sg<-segmentgraph(testn), 'igraph')
   
-  baseline=graph(c(1,2,2,3,2,4), directed=TRUE)
+  baseline=make_graph_nat(c(1,2,2,3,2,4), directed=TRUE)
   expect_true(graph.isomorphic(sg, baseline))
   
   expect_equal(E(sg)$weight, c(2, 2, 1))
@@ -202,7 +202,7 @@ test_that("we can find the segmentgraph of a neuron",{
 
 test_that("as.ngraph can convert undirected graph into an ngraph object",{
   g1=as.ngraph(testd)
-  expect_is(g2<-as.ngraph(as.undirected(g1), root = rootpoints(g1)), 'ngraph')
+  expect_is(g2<-as.ngraph(as_undirected_nat(g1), root = rootpoints(g1)), 'ngraph')
   expect_true(graph.isomorphic(g1,g2))
 })
 
diff --git a/tests/testthat/test-seglist.R b/tests/testthat/test-seglist.R
index a8d51a73..db71a029 100644
--- a/tests/testthat/test-seglist.R
+++ b/tests/testthat/test-seglist.R
@@ -7,7 +7,7 @@ test_that("make a seglist directly",{
 
 test_that("convert graph to seglist",{
   # simple linear graph
-  g=graph(c(1, 2, 2, 3))
+  g=make_graph_nat(c(1, 2, 2, 3))
   sl=seglist(c(1, 2, 3))
   expect_is(sl,'seglist')
   expect_equal(as.seglist(g), sl)
@@ -59,7 +59,7 @@ test_that("convert graph to seglist",{
   sl=seglist(c(1,2),c(2,3),c(2,4),c(2,5,6,7))
   expect_equal(as.seglist(g),sl)
   # undirected equivalent - nb origin must be specified
-  expect_equal(as.seglist(as.undirected(g),origin=1),sl)
+  expect_equal(as.seglist(as_undirected_nat(g),origin=1),sl)
   
   # rapid branching
   g=graph(c(1,2, 2,3, 2,4, 4,5, 4,6))
diff --git a/tests/testthat/testdata/neuroml/level1/CablesIncluded.swc b/tests/testthat/testdata/neuroml/level1/CablesIncluded.swc.txt
similarity index 100%
rename from tests/testthat/testdata/neuroml/level1/CablesIncluded.swc
rename to tests/testthat/testdata/neuroml/level1/CablesIncluded.swc.txt
diff --git a/tests/testthat/testdata/neuroml/level1/Simple.morph.swc b/tests/testthat/testdata/neuroml/level1/Simple.morph.swc.txt
similarity index 100%
rename from tests/testthat/testdata/neuroml/level1/Simple.morph.swc
rename to tests/testthat/testdata/neuroml/level1/Simple.morph.swc.txt
diff --git a/tests/testthat/testdata/neuron/EBT7R.CNG.swc b/tests/testthat/testdata/neuron/EBT7R.CNG.swc.txt
old mode 100755
new mode 100644
similarity index 100%
rename from tests/testthat/testdata/neuron/EBT7R.CNG.swc
rename to tests/testthat/testdata/neuron/EBT7R.CNG.swc.txt
diff --git a/tests/testthat/testdata/neuron/EBT7R.am b/tests/testthat/testdata/neuron/EBT7R.am
old mode 100755
new mode 100644
diff --git a/tests/testthat/testdata/neuron/XT6L2.CNG.swc b/tests/testthat/testdata/neuron/XT6L2.CNG.swc.txt
old mode 100755
new mode 100644
similarity index 100%
rename from tests/testthat/testdata/neuron/XT6L2.CNG.swc
rename to tests/testthat/testdata/neuron/XT6L2.CNG.swc.txt
diff --git a/tests/testthat/testdata/neuron/unfitted.swc b/tests/testthat/testdata/neuron/unfitted.swc.txt
similarity index 100%
rename from tests/testthat/testdata/neuron/unfitted.swc
rename to tests/testthat/testdata/neuron/unfitted.swc.txt