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fixes for enabling HTML output with .db data packages

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Replaced usage of soon to be defunct class exprSet with ExpressionSet.

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fix to handle .db annotation packages

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Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.

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Standardizing reference to Artistic License 2.0.

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Replaced usage of newly defunct phenoData class and geneName method with AnnotatedDataFrame and featureName respectively.

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Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.

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Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.

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cleaned up documentation and source code

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