README.md

In pshannon-bioc/graph: graph: A package to handle graph data structures

graph

The bioc graph class, an experiment for github

Tasks

The essential tasks are to develop simple constructors graphNEL() and graphAM(), to be used in place of new("graphNEL", <...>) or new("graphAM", <...>) for creating graphNEL or graphAM instances.

Unit tests

There are new unit tests that currently fail; graphNEL() and graphAM() should be implemented so these, and other existing and reasonable tests, pass.

inst/unitTests/graphNEL.R:testConstructorFunction()
inst/unitTests/graphAM.R:testConstructorFunction()

In addition, existing tests use new("graphNEL", ...), etc; these should be updated to use the new constructors, and should pass without further change.

Documentation

The graphNEL() and graphAM() constructors should be documented, on the graphNEL-class and graphAM-class man/ pages. Aliases should be added so that

?graphNEL

takes the user to the appropriate location. It is appropriate to document constructors on the same page as the class and its methods; a stub is provided as an example in

man/graphNEL-class.Rd

Deliverables

On completion, the package will pass

R CMD build graph
R CMD check graph_*gz

without warning or errors.

In addition,

grep -r graphNEL graph/* | grep new

will return only entries from the constructor functions themselves; all direct uses of 'new' for constructing graphNEL (and graphAM)

The version number should be bumped so the most-minor digit is 1 more than the most-minor digit in the devel branch at the time of project completion.

pshannon-bioc/graph documentation built on May 26, 2019, 10:32 a.m.