TODO

- Consider making the 'nodes' slot vector_OR_Vector (instead of Vector) for
  consistency with the Factor class defined in the S4Vectors package.

- droplevels() should work on Factor objects (implement this in S4Vectors).

- Consider making fromNode(x) and toNode(x) return a Factor. E.g.

    Factor(levels=nodes(x), index=from(x))

  instead of extractROWS(nodes(x), from(x)).

- Implement dropNodes(). Are we happy with the name? Or should it be
  deleteNodes() or removeNodes() instead?
  Then maybe reintroduce dropNodes() but now it would drop unused nodes
  like droplevels() does on a factor.

- Fix subsetting of DGraphNodes objects (must drop edges that are indicent to
  dropped nodes).

- Implement

    makeDGraphFromPackageDependencies(pkgs=NULL,
                  repos=BiocManager::repositories(),
                  which=c("Depends", "Imports", "LinkingTo"),
                  type=c("source", "mac.binary", "win.binary"))

  By default, i.e. if no arguments are specified, it builds the graph for
  all Bioconductor source packages.
  Nodes are packages and they should be annotated with the repository that
  they are coming from in addition to other things like package version,
  maintainer, etc... See 'fields' arg of available.packages() and
  tools::write_PACKAGES().
  Edges should be annotated with a factor which has the levels specified
  thru the 'which' argument. This is analog to the "relation" metadata
  column on the DGraph returned by makeDGraphFromGO().

- Implement c() method for DGraph objects with the following semantic:
  on DGraph objects 'x' and 'y', c(x, y) merges the nodes (like it does
  with the levels of Factor objects) and concatenates the edges.
  See bindROWS() method for Factor objects.

  No need to support c() on DGraphNodes objects at the moment (not clear what
  it should do). Maybe implement a dummy method for these objects that just
  raises an error with a useful error message.

  Mixing DGraph objects with DGraphNodes objects should not be allowed.

- Add capability to import an OBO file (e.g. from the Gene Ontology or
  Sequence Ontology) as a DGraph object.

- Add "package level" man page (?graph4).