1.8 (not for merge) #481
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1.8 (not for merge) #481
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* 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
* 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
* 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
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