* unfortunately there seem to be some situations that cause digest differences but
  they are almost impossible to debug on CRAN
* digest::sha1 does attempt to create a 32/64 bit stable hash,
  but even there are differences across package versions

* just contains bits and pieces for development

* UTF-8 for roxygen

* see also 9f3e51d / #393
  which was unfortunately too

* some of these spotted by R CMD check

* closes #402
* depending on filehash >=2.3 ensures that the bug this code was trying to kludge over
  is fixed at source.

* NB the pointsinside function will internally check if suggested Rvcg package is available

* see #411
* skipped on CRAN anyway but coming up elsewher now

* having trouble building Rvcg on trusty

* we weren't relying on the old behaviour beyond this test
* closes #444

* See emails from BDR and Duncam Murdoch Re: CRAN packages requiring webshot2 but not declaring it
* this is because rgl now prefers webshot2 (a non-CRAN package) for snapshots
  and offers no way to override this when using knitr rgl=T

* due to a change in base mappply docs

Warning: Topic 'fileformats': no parameters to inherit with @inheritParams

* I suppose once upon a time registerformat was documented separately

* straight from master branch

* should allow vignettes to be built when pandoc missing
Duncan Murdoch wrote:
I think you need to add "markdown" to the Suggests list to allow the fallback. The message with the Github link is coming from the htmlwidgets package

* includes some html documentation url changes
  e.g. to natverse site

* for some reason webgl=F as a chunk option doesn't seem to have any effect

Seglist updated to the latest igraph version

* nb there seems to be a regression wrt inheritance of docstrings for multiple arguments
  so had to separate bounds vs BoundingBox docs

* as discussed in PR

* see igraph/rigraph#633 (comment)

* missed locally and by winbuilder
* seems like all text must start with a * 

Problems with news in 'NEWS':
  Cannot process chunk/lines:
    It also updates URLs to point to nat's new home organisation on GitHub
    (https://github.com/natverse/).
  Cannot process chunk/lines:
    This release includes some bug fixes and significantly improved online package
  Cannot process chunk/lines:
    This is tagged as a major release because of a change in behaviour that (by
  Cannot process chunk/lines:
    default) suppresses interactive rgl windows when running in batch
    (non-interactive) mode. See ?nat "rgl Package" section for details.
      defaulting to rgl's NULL mode display. This should help run nat in batch mode
      situations including knitr runs, the CRAN build server etc. (#272)
    * Add summary.neuron(list) functions to calculate tree statistics such as number
     of nodes and cable length for neurons/neuronlists (#269)
    * Automate progress bar in nlapply - this will always show in interactive mode
      when there are more than 10 neurons being processed. (#271)
    * Fix bug in c.neuronlist when combining more than 2 neuronlists (#270)
    * Fix bug in read.neuronlistfh on Windows (#268)
    * Fix bug when constructing an ngraph with a single node (#267)
    * Fix bug in `[<-.neuronlist` when assigning a whole data.frame using (#256)
    * Fix bug in bounding box with input = "bounds" (#273)
    * Documentation improvements (especiall package overview - see ?nat)
    * nat will only activate an rgl display in interactive mode, otherwise

citEntry was deprecated ...

* website is down right now
* just cite paper instead

* r-devel now refuses to compare a number with a numeric_version
* reported by CRAN (Kurt Hornik, who also kindly pointed out the precise error)

* Simple Neurite Tracer is no more
* The successor plugin, SNT, uses the same tracse format

* there are many functions deprecated in igraph v2.0.0
* unfortunately, I don't know what is the minimum igraph version for the new function names
  currently we only require igraph (>= 0.7.1)

get.vertex.attribute->vertex_attr
add.edges->add_edges
decompose.graph->decompose
graph.bfs->bfs
graph.dfs->dfs
is.connected->is_connected
is.directed->is_directed
get.vertex.attribute->vertex_attr
shortest.paths->distances
get.shortest.paths->shortest_paths

induced.subgraph -> induced_subgraph
no.clusters -> count_components
clusters -> components
minimum.spanning.tree -> mst
delete.vertices -> delete_vertices
set.vertex.attribute -> set_vertex_attr
get.edgelist -> as_edgelist
delete.edges -> delete_edges

* this still seems to be up in the air but at least some preparatory branches
 for igraph 2.0 use a 0 rather than NaN to signal unreachable nodes
* see #517

* used to be an int, now numeric with igraph 2.0

* cmtk will never be installed there