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
* 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
* many conflicts after cherry picking from master to 1.8
* also remove unnecessary executable permissions
* workaround for new behaviour in R 4.5.1 associated with this change wch/r-source@7bc89c8
* we want to exclude swc.txt files since they are neither swc nor nml
* as.directed, as.undirected, graph * decided to wrap them so we don't have to fast forward igraph dependency to >=2.1.0 from >=1.0 * had to remove the explicit function imports (because we don't know which to import) * note that I also had to make an example conditional based on the installed version for the same reasons * see also igraph/rigraph#1513 * also fix some 1.8 conflicts when cherry-picking
* even private ones where the generic is not exported and will not be visible to outside users * some conflicts against 1.8 had to be resolved
* conflicts inc rda -> rds * had to remake rds I assume because format of summary output different in 1.8
* inc latest winbuilder result
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