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the bioc graph class, an experiment for github
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DESCRIPTION
NAMESPACE
README.md
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README.md

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.

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