pathfindR 3.0.0

Major Changes

• Re-implemented the active subnetwork search (GR/SA/GA) in R and C++ (via
  Rcpp), removing the Java dependency. For GR and SA, results are numerically
  identical to the legacy JAR given the same seed and inputs.
• Renamed the exported function active_snw_search() to
  get_active_subnetworks() (its signature has also changed).
• Renamed the exported function filterActiveSnws() to
  filter_active_subnetworks().
• Renamed the utility function fetch_gene_set() to fetch_gene_sets().

Minor Changes and Bug Fixes

• Removed the package start-up message.
• Split term_gene_graph() into create_term_gene_graph() and
  create_term_gene_plot(): create_term_gene_graph() builds the igraph
  structure, while create_term_gene_plot() visualizes the graph from the
  information available in that igraph object.