CHANGES IN VERSION 0.12.0
-------------------------

NEW FEATURES

    o Add n-ary "merge" method for Vector objects.

    o "extractROWS" methods for atomic vectors and DataFrame objects now
      support NAs in the subscript. As a consequence a DataFrame can now
      be subsetted by row with a subscript that contains NAs. However that
      will only succeed if all the columns in the DataFrame can also be
      subsetted with a subscript that contains NAs (e.g. it would fail at
      the moment if some columns are Rle's but we have plans to make this
      work in the future).

    o Add "union", "intersect", "setdiff", and "setequal" methods for Vector
      objects.

    o Add coercion from data.table to DataFrame.

    o Add t() S3 methods for Hits and HitsList.

    o Add "c" method for Pairs objects.

    o Add rbind/cbind methods for List, returning a list matrix.

    o aggregate() now supports named aggregator expressions when 'FUN' is
      missing.

SIGNIFICANT USER-VISIBLE CHANGES

    o "c" method for Rle objects handles factor data more gracefully.

    o "eval" method for FilterRules objects now excludes NA results, like
      subset(), instead of failing on NAs.

    o Drop "as.env" method for List objects so that as.env() behaves more like
      as.data.frame() on these objects.

    o Speed up "replaceROWS" method for Vector objects when 'x' has names.

    o Optimize selfmatch for factors.

DOCUMENTATION IMPROVEMENTS

    o Add S4QuickOverview vignette.

DEPRECATED AND DEFUNCT

    o elementLengths() and compare() are now defunct (were deprecated in
      BioC 3.3).

    o Remove "ifelse" methods for Rle objects (were defunct in BioC 3.3),

BUG FIXES

    o Fix bug in showAsCell(x) when 'x' is an AsIs object.

    o DataFrame() avoids NULL names when there are no columns.

    o DataFrame with NULL colnames are now considered invalid.


CHANGES IN VERSION 0.10.0
-------------------------

NEW FEATURES

    o Add SelfHits class, a subclass of Hits for representing objects where the
      left and right nodes are identical.

    o Add utilities isSelfHit() and isRedundantHit() to operate on SelfHits
      objects.

    o Add new Pairs class that couples two parallel vectors.

    o head() and tail() now work on a DataTable object and behave like on an
      ordinary matrix.

    o Add as.matrix.Vector().

    o Add "append" methods for Rle/vector (they promote to Rle).

SIGNIFICANT USER-VISIBLE CHANGES

    o Many changes to the Hits class:
      - Replace the old Hits class (where the hits had to be sorted by query)
        with the SortedByQueryHits class.
      - A new Hits class where the hits can be in any order is re-introduced as
        the parent of the SortedByQueryHits class.
      - The Hits() constructor gets the new 'sort.by.query' argument that is
        FALSE by default. When 'sort.by.query' is set to TRUE, the constructor
        returns a SortedByQueryHits instance instead of a Hits instance.
      - Bidirectional coercion is supported between Hits and SortedByQueryHits.
        When going from Hits to SortedByQueryHits, the hits are sorted by query.
      - Add "c" method for Hits objects.
      - Rename Hits slots:
          queryHits -> from
          subjectHits -> to
          queryLength -> nLnode (nb of left nodes)
          subjectLength -> nRnode (nb of right nodes)
      - Add updateObject() method to update serialized Hits objects from old
        (queryHits/subjectHits) to new (from/to) internal representation.
      - The "show" method for Hits objects now labels columns with from/to by
        default and switches to queryHits/subjectHits labels only when the
        object is a SortedByQueryHits object.
      - New accessors are provided that match the new slot names: from(), to(),
        nLnode(), nRnode(). The old accessors (queryHits(), subjectHits(),
        queryLength(), and subjectLength()) are just aliases for the new
        accessors. Also countQueryHits() and countSubjectHits() are now aliases
        for new countLnodeHits() and countRnodeHits().

    o Transposition of Hits objects now propagates the metadata columns.

    o Rename elementLengths() -> elementNROWS() (the old name was clearly a
      misnomer). For backward compatibility the old name still works but is
      deprecated (now it's just an "alias" for elementNROWS()).

    o Rename compare() -> pcompare(). For backward compatibility the old name
      still works but is just an "alias" for pcompare() and is deprecated.

    o Some refactoring of the Rle() generic and methods:
      - Remove ellipsis from the argument list of the generic.
      - Dispatch on 'values' only.
      - The 'values' and 'lengths' arguments now have explicit default values
        logical(0) and integer(0) respectively.
      - Methods have no more 'check' argument but new low-level (non-exported)
        constructor new_Rle() does and is what should now be used by code that
        needs this feature.

    o Optimize subsetting of an Rle object by an Rle subscript: the subscript
      is no longer decoded (i.e. expanded into an ordinary vector). This
      reduces memory usage and makes the subsetting much faster e.g. it can be
      100x times faster or more if the subscript has many (e.g. thousands) of
      long runs.

    o Modify "replaceROWS" methods so that the replaced elements in 'x' get
      their metadata columns from 'value'. See this thread on bioc-devel:
        https://stat.ethz.ch/pipermail/bioc-devel/2015-November/008319.html

    o Remove ellipsis from the argument list of the "head" and "tail" methods
      for Vector objects.

    o pc() (parallel combine) now returns a List object only if one of the
      supplied objects is a List object, otherwise it returns an ordinary list.

    o The "as.data.frame" method for Vector objects now forwards the
      'row.names' argument.

    o Export the "parallelSlotNames" methods.

DEPRECATED AND DEFUNCT

    o Deprecate elementLengths() in favor of elementNROWS(). New name reflects
      TRUE semantic.

    o Deprecate compare() in favor of pcompare().

    o After being deprecated in BioC 3.2, the "ifelse" methods for Rle objects
      are now defunct.

    o Remove "aggregate" method for vector objects which was an undocumented
      bad idea from the start.

BUG FIXES

    o Fix 2 long-standing bugs in "as.data.frame" method for List objects:
      - must always return an ordinary data.frame (was returning a DataFrame
        when 'use.outer.mcols' was TRUE),
      - when 'x' has names and 'group_name.as.factor' is TRUE, the levels of
        the returned group_name col must be identical to 'unique(names(x))'
        (names of empty list elements in 'x' was not showing up in
        'levels(group_name)').

    o Fix and improve the elementMetadata/mcols setter method for Vector
      objects so that the specific methods for GenomicRanges, GAlignments,
      and GAlignmentPairs objects are not needed anymore and were removed.
      Note that this change also fixes setting the elementMetadata/mcols of a
      SummarizedExperiment object with NULL or an ordinary data frame, which
      was broken until now.

    o Fix bug in match,ANY,Rle method when supplied 'nomatch' is not NA.

    o Fix findMatches() for Rle table.

    o Fix show,DataTable-method to display all rows if <= nhead + ntail + 1


CHANGES IN VERSION 0.4.0
------------------------

NEW FEATURES

    o Add isSorted() and isStrictlySorted() generics, plus some methods.

    o Add low-level wmsg() helper for formatting error/warning messages.

    o Add pc() function for parallel c() of list-like objects.

    o Add coerce,Vector,DataFrame; just adds any mcols as columns on top of the
      coerce,ANY,DataFrame behavior.

    o [[ on a List object now accepts a numeric- or character-Rle of length 1.

    o Add "droplevels" methods for Rle, List, and DataFrame objects.

    o Add table,DataTable and transform,DataTable methods.

    o Add prototype of a better all.equals() for S4 objects.

SIGNIFICANT USER-VISIBLE CHANGES

    o Move Annotated, DataTable, Vector, Hits, Rle, List, SimpleList, and
      DataFrame classes from the IRanges package.

    o Move isConstant(), classNameForDisplay(), and low-level argument
      checking helpers isSingleNumber(), isSingleString(), etc... from the
      IRanges package.

    o Add as.data.frame,List method and remove other inconsistent and not
      needed anymore "as.data.frame" methods for List subclasses.

    o Remove useless and thus probably never used aggregate,DataTable method
      that followed the time-series API.

    o coerce,ANY,List method now propagates the names.

BUG FIXES

    o Fix bug in coercion from list to SimpleList when the list contains
      matrices and arrays.

    o Fix subset() on a zero column DataFrame.

    o Fix rendering of Date/time classes as DataFrame columns.


