Commit made by the Bioconductor Git-SVN bridge.
Consists of 8 commit(s).

Commit information:

    Commit id: 136c8f3fd6d0ff0c98ded19b8f6adf175343d120
    Commit message:
    VanillaICE::rescale()  -> rescale(). IRanges to imports
    Committed by Rob Scharpf <rscharpf at jhsph.edu>
    Commit date: 2014-03-19T08:02:01-04:00

    Commit id: 3c114c0ae53264d4622b0c338a4870ed40b721b5
    Commit message:
    define .getArm and setSequenceLengths within this package
    Committed by Rob Scharpf <rscharpf at jhsph.edu>
    Commit date: 2014-03-19T11:16:07-04:00

    Commit id: 6f8bb0b202e13c7e7c54699a6e1208651e9e74cd
    Commit message:
    define .checkOrder locally
    Committed by Rob Scharpf <rscharpf at jhsph.edu>
    Commit date: 2014-03-19T11:19:25-04:00

    Commit id: 8575e51f8aa07e2ff52828b721311705c467256f
    Commit message:
    replace assayDataStorageMode with storageMode.  Replace annotatedDataFrameFromMatrix with annotatedDataFrameFrom
    Committed by Rob Scharpf <rscharpf at jhsph.edu>
    Commit date: 2014-03-19T12:00:49-04:00

    Commit id: 94d0e8a73ccafa2866f4a4117dfe8c6f062bf178
    Commit message:
    Got rid of Biobase:::assayDataDims
    Committed by Rob Scharpf <rscharpf at jhsph.edu>
    Commit date: 2014-03-19T12:38:47-04:00

    Commit id: 552c8313364c7ffad2591cd4c2a1a00735d868b6
    Commit message:
    remove assayDataEnvLock.  Remove :::originalNames and :::stackColIndex
    Committed by Rob Scharpf <rscharpf at jhsph.edu>
    Commit date: 2014-03-19T13:00:56-04:00

    Commit id: 5e2fb770ec57e43cab17439d9ed94e41ae27bd70
    Commit message:
    remove computeBayesFactorTrioSet
    Committed by Rob Scharpf <rscharpf at jhsph.edu>
    Commit date: 2014-03-19T15:50:54-04:00

    Commit id: fa195aca92767d5565d6ea396c6d0ba4e252e0b5
    Commit message:
    provide alias for '[' methods (Pedigree, TrioSet, and TrioSetList classes)
    Committed by Rob Scharpf <rscharpf at jhsph.edu>
    Commit date: 2014-03-20T11:26:22-04:00

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git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MinimumDistance@87645 bc3139a8-67e5-0310-9ffc-ced21a209358