
CHANGES IN VERSION 1.17.1 [2020-11-27]
-----------------------------------

BUG FIXES

    o Fix 'apply()' signatures for R 4.1

CHANGES IN VERSION 1.15.1 [2020-9-3]
-----------------------------------

BUG FIXES

    o Remove '...' from 'which()'

CHANGES IN VERSION 1.13.10 [2020-4-20]
-----------------------------------

NEW FEATURES

    o Added 's_nnzero()' stream-stat for non-zero entries
    o Added 'push()' and 'pull()' generics for future use

CHANGES IN VERSION 1.13.9 [2020-4-18]
-----------------------------------

BUG FIXES

    o Minor updates to 'chunk_apply()' internals

CHANGES IN VERSION 1.13.8 [2020-3-13]
-----------------------------------

BUG FIXES

    o Fixed bugs due to logical condition length > 1

CHANGES IN VERSION 1.13.7 [2020-3-11]
-----------------------------------

BUG FIXES

    o Fixed to internal function 'linearInd()'

CHANGES IN VERSION 1.13.6 [2020-3-3]
-----------------------------------

BUG FIXES

    o Fixed bug caused by change in R 4.0 so that
        class of matrix is now c("matrix", "array")

CHANGES IN VERSION 1.13.5 [2020-3-2]
-----------------------------------

NEW FEATURES

    o Support for 'view="chunk"' when specifying 'pattern'

CHANGES IN VERSION 1.13.4 [2020-2-26]
-----------------------------------

NEW FEATURES

    o Added 'pattern' argument to 'chunk_mapply()'

CHANGES IN VERSION 1.13.3 [2020-2-9]
-----------------------------------

NEW FEATURES

    o Implemented 'outfile' argument for writing results
        to a file for 'chunk_apply()' and 'chunk_mapply()'

CHANGES IN VERSION 1.13.2 [2020-2-9]
-----------------------------------

NEW FEATURES

    o Added 'pattern' argument to 'chunk_apply()'

CHANGES IN VERSION 1.13.1 [2019-10-30]
-----------------------------------

NEW FEATURES

    o Added 'chunk_mapply()'

CHANGES IN VERSION 1.11.7 [2019-10-25]
-----------------------------------

BUG FIXES

    o Fixed errors in 'rowStats()' and 'colStats()' when
        calculating group statistics over minor dimensions

CHANGES IN VERSION 1.11.6 [2019-10-23]
-----------------------------------

NEW FEATURES

    o Added 'locmax()' function for finding local maxima
    o Added 'binvec()' function for binning vectors

CHANGES IN VERSION 1.11.5 [2019-10-13]
-----------------------------------

NEW FEATURES

    o Exposed 'chunk_apply()' for applying functions
        over parallelized chunks of vectors and matrices

CHANGES IN VERSION 1.11.4 [2019-10-13]
-----------------------------------

NEW FEATURES

    o Added 'rowStats()' and 'colStats()' methods for
        chunk-applying grouped summary statistics over
        the rows and columns of matrices

SIGNIFICANT USER-VISIBLE CHANGES

    o Family of 'apply()' and 'lapply()' methods now
        attempt to respect the object's 'chunksize()'
    o Added getOption('matter.default.chunksize') for
        setting default chunksize for matter objects

CHANGES IN VERSION 1.11.3 [2019-10-9]
-----------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Faster subsetting of matter-backed ALTREP objects
    o Updated 'bsearch()' to return the closest match when tol > 0
    o Added getOption('matter.dump.dir') to control where
        temporary files are stored for matter objects

CHANGES IN VERSION 1.11.2 [2019-7-24]
-----------------------------------

NEW FEATURES

    o Coercing to native R types now returns an ALTREP
        representation for most 'matter' objects
    o Use 'as.altrep()' method to coerce an existing
        'matter' object to ALTREP or to coerce native R types
        to 'matter'-backed out-of-memory ALTREP objects
    o ALTREP coercion can be controlled by new options:
        getOption('matter.coerce.altrep')
        getOption('matter.coerce.altrep.list')
        getOption('matter.wrap.altrep')
    o See ?`matter-options` for details

SIGNIFICANT USER-VISIBLE CHANGES

    o The 'show()' method for 'matter' objects now
        prints a preview of the data head
    o Printing of data can be controlled with new options
        getOption('matter.show.head') and
        getOption('matter.show.head.n')

CHANGES IN VERSION 1.11.1 [2019-5-7]
-----------------------------------

NEW FEATURES

    o Added 'stream_stat' class for streaming statistics
        with functions s_mean(), s_var(), s_sd(), etc.

CHANGES IN VERSION 1.9.11 [2019-4-19]
-----------------------------------

BUG FIXES

    o Fixed documentation link to 'base::lapply'

CHANGES IN VERSION 1.9.10 [2018-12-22]
-----------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Vectors can be used as 'virtual_mat' rows/columns now

CHANGES IN VERSION 1.9.9 [2018-12-22]
-----------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Constructor for 'drle' now allows forcing delta = 0
    o Updated display descriptions in 'show' methods
    o Check for NULL dimensions when subsetting
        'virtual_mat' and 'sparse_mat' classes

CHANGES IN VERSION 1.9.8 [2018-12-18]
-----------------------------------

BUG FIXES

    o Check for NULL dimensions in 'matter_arr' subsetting

CHANGES IN VERSION 1.9.7 [2018-12-18]
-----------------------------------

BUG FIXES

    o Fixed bug in atoms() where 'index_offset' and 'index_extent'
        would overflow when creating long 'matter_vec' objects

CHANGES IN VERSION 1.9.6 [2018-12-14]
-----------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Subsetting matter matrices, arrays, and data frames
        now checks for the correct number of dimensions
    o Linear indexing support for 'matter_mat' and 'matter_arr'

BUG FIXES

    o Class checks now use R_check_slot_etc() in C so subclasses
        of 'matter' objects should inherit correct behavior
    o Fixed other indexing issues in subsetting + assignment

CHANGES IN VERSION 1.9.5 [2018-12-14]
-----------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Updated documentation with `matter-datatypes`,
        size of data types are now explicitly defined
    o Changed 'filemode' slot to be a factor with
        levels c('r', 'w', 'rw') instead of a string
    o Data access now uses C++ fstream instead of C

BUG FIXES

    o On Windows, accessing data elements in large files
        with byte offets larger than MAX_INT now works
    o On Windows, data modes of 'long' and 'ulong' are
        now correctly 64-bit integer types
    o Assignment of negative values now checked for 'ulong'

CHANGES IN VERSION 1.9.4 [2018-12-8]
-----------------------------------

NEW FEATURES

    o Added %% and %/% delayed operations from Arith group
    o Added & and | delayed operations from Logic group
    o All Ops group generics now supported as delayed operations
    o Added 'lapply' and 'sapply' functions for 'matter_list'
    o Support for BiocParallel in 'apply', 'lapply', and 'sapply'

BUG FIXES

    o Fix floating point exception error when dividing by
        integer 0L in delayed division operations

CHANGES IN VERSION 1.9.3 [2018-12-8]
-----------------------------------

NEW FEATURES

    o Added matrix multiplication for 'sparse_mat' matrices
    o Added matrix multiplication for 'virtual_mat' matrices

CHANGES IN VERSION 1.9.2 [2018-11-12]
-----------------------------------

BUG FIXES

    o Renamed internal class 'bytes' to 'num_bytes' due to Rcpp

CHANGES IN VERSION 1.9.1 [2018-11-12]
-----------------------------------

BUG FIXES

    o Removed BiocGenerics 'lengths' from NAMESPACE

CHANGES IN VERSION 1.8.2 [2018-12-13]
-----------------------------------

BUG FIXES

    o Fixed large file offset bug on Windows (again)

CHANGES IN VERSION 1.8.1 [2018-12-11]
-----------------------------------

BUG FIXES

    o Fixed bug causing large files to read incorrectly on Windows

CHANGES IN VERSION 1.7.6 [2018-7-24]
-----------------------------------

NEW FEATURES

    o Added 'apply' methods for 'sparse_mat' and 'virtual_mat'
    o Added 'vm_used' function to exported internal utilities
    o Can infer length of 'matter_vec' from paths when missing
    o Can coerce 'matter_list' to 'matter_matc' or 'matter_matr'
        if all elements of the list are the same length

SIGNIFICANT USER-VISIBLE CHANGES

    o Initializing a matter object with data to an existing file
        no longer results in a warning if 'filemode' is supplied

BUG FIXES

    o Fixed bug where subsetting 'sparse_mat' objects
        would pull 'matter_list' key-value pairs into memory
    o Subsetting 'sparse_mat' objects with out-of-bounds
        subscripts when 'drop=NULL' is now an error

CHANGES IN VERSION 1.7.5 [2018-7-23]
-----------------------------------

NEW FEATURES

    o Added 'as.matrix' methods for 'sparse_mat' and 'virtual_mat'

CHANGES IN VERSION 1.7.4 [2018-7-23]
-----------------------------------

NEW FEATURES

    o Added coercion from 'matter_mat' to 'matter_list'

CHANGES IN VERSION 1.7.3 [2018-7-23]
-----------------------------------

NEW FEATURES

    o Added 'rep_vt' class for virtual replicated vectors

CHANGES IN VERSION 1.7.2 [2018-7-22]
-----------------------------------

NEW FEATURES

    o Updated installation instructions for BiocManager
    o Setting 'sparse_mat' keys also updated nrows/ncols

BUG FIXES

    o Fixed mem() to reflect R >= 3.5 gc() function

CHANGES IN VERSION 1.7.1 [2018-5-18]
-----------------------------------

BUG FIXES

    o Fixed file.exists() bug when length(paths) > 1

CHANGES IN VERSION 1.5.4 [2017-12-2]
-----------------------------------

NEW FEATURES

    o Added 'struct' convenience function for on-disk
        C-style structs (wrapper for 'matter_list')

CHANGES IN VERSION 1.5.3 [2017-12-1]
-----------------------------------

NEW FEATURES

    o Added remainder of Summary group, including 'range',
        'min', 'max', 'prod', 'any', and 'all' methods
    o Added options(matter.cast.warning=FALSE) for
        turning off C type coercion warnings
    o Exported low-level utilities 'sizeof', 'make_datamode',
        'convert_datamode', and 'widest_datamode'
    o Added 'combiner' generic function and method for
        setting/getting the 'combiner' for 'sparse_mat'
    o Added 'min' and 'max' combiner functions for
        'sparse_mat' matrices with tolerance > 0
    o Added 'biglm' method for 'matter_df' data frames

BUG FIXES

    o Fixed bug when coercing 'matter_list' to 'matter_vec'

CHANGES IN VERSION 1.5.2 [2017-11-12]
-----------------------------------

NEW FEATURES

    o All 'matter' subclasses now support endomorphic
        subsetting via 'drop=NULL' wherever appropriate
    o Setting the 'dim' slot via 'dim<-' now switches
        the class between 'matter_vec' and 'matter_arr'
    o Added 'virtual_mat' class for virtual matrices

SIGNIFICANT USER-VISIBLE CHANGES

    o Use 'drop=NULL' from now on instead of 'drop=NA'
        to do endomorphic subsetting of matter matrices
    o Added 'matter_vt' virtual class for matter objects
        which may exist both on-disk and in-memory
    o Added 'matter_tbl' virtual class for data tables

BUG FIXES

    o Fixed read/write bug when subsetting across atoms

CHANGES IN VERSION 1.5.1 [2017-11-1]
-----------------------------------

NEW FEATURES

    o Added 'sparse_mat' class for sparse matrics (potentially
        on-disk) with subclasses 'sparse_matc' for CSC matrices
        and 'sparse_matr' for CSR matrices
    o Added 'bsearch' function for fast binary searches
    o Added 'uuid' function for generating UUIDs as both 'raw' and
        and 'character' vectors
    o Added a 'checksum' method for doing sha1 and md5 checksums
        of all files associated with a 'matter' object

CHANGES IN VERSION 1.3.8 [2017-10-26]
-----------------------------------

NEW FEATURES

    o Added 'matter_fc' class for on-disk factors

SIGNIFICANT USER-VISIBLE CHANGES

    o Added character encodings to 'matter_str' on-disk strings

BUG FIXES

    o Fixed bug in 'matter_df' when subsetting by columns
    o Fixed bug when coercing 'data.frame's to 'matter_df'

CHANGES IN VERSION 1.3.7 [2017-10-25]
-----------------------------------

BUG FIXES

    o Fixed bug where default 'matter_df' chunksize was tiny
    o Changed 'datamode' for 'matter_df' from 'list' to 'virtual'

CHANGES IN VERSION 1.3.6 [2017-10-20]
-----------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Lists (ragged arrays) may now be heterogenous (elements
        must still be vectors)
    o More memory-efficient initialization of data on disk
        when length(data) is 1
    o Files are now created by default in constructors if
        they do not already exist
    o When coercing with 'as.matter', names and/or dimnames
        are now retained


CHANGES IN VERSION 1.3.5 [2017-10-18]
-----------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Improved length/dim defaults when data is given to constructors

BUG FIXES

    o Trying to write to a read-only dataset now fails gracefully
    o Fixed integer overflow when subsetting via subsetMatterMatrix

CHANGES IN VERSION 1.3.4 [2017-8-8]
-----------------------------------

BUG FIXES

    o Fixed bug where NAs did not propogate correctly for integers
    o It is now an error when 'matter()' cannot infer data structure


CHANGES IN VERSION 1.3.3 [2017-5-20]
-----------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Added new vignettes with benchmarks and examples on real data

BUG FIXES

    o Fixed bug in delayed arithmetic operations with vectors


CHANGES IN VERSION 1.3.2 [2017-5-15]
-----------------------------------

NEW FEATURES

    o Added class 'matter_list' for homogenous lists (ragged arrays)
    o Added class 'matter_str' for on-disk strings
    o Added class 'matter_df' for on-disk data frames
    o Added 'as.matter' for function coercing to matter objects

CHANGES IN VERSION 1.3.1 [2017-4-27]
-----------------------------------

NEW FEATURES

    o Updated base matter classes (matter_vec, matter_mat, matter_arr)
        to support 'Arith' and 'Compare' group generics

CHANGES IN VERSION 1.1.3 [2017-3-15]
---------------------------------

NEW FEATURES

    o Added class 'drle' for delta-run-length encoding vectors
    o Added '+', '-', '*', '/', '^', 'exp', 'log', 'log2', and 'log10'
        as possible delayed operations to on-disk atoms

SIGNIFICANT USER-VISIBLE CHANGES

    o Slots of 'atoms' class now use delta-run-length encoding
    o Reduced metadata size by changing 'atoms' class to use
        groups rather then relying on a 'list' of 'atoms'
    o The 'scale' method for 'matter_mat' now matches 'scale.default'
        more correctly when 'center = FALSE' and 'scale = TRUE'

CHANGES IN VERSION 1.1.2 [2017-3-12]
---------------------------------

NEW FEATURES

    o Added support for char, uchar, ushort, uint, and ulong datamodes
    o Added support for raw (Rbyte) matter objects

SIGNIFICANT USER-VISIBLE CHANGES

    o S4 methods for matrix-specific summary statistics are
        now only defined on matter_mat and its subclasses

BUG FIXES

    o Dramatically improved speed of matrix multiplication 

CHANGES IN VERSION 1.1.1 [2016-11-29]
---------------------------------

NEW FEATURES

    o Added 'crossprod' (t(x) %*% y) and 'tcrossprod' (x %*% t(y)) methods
    o Added 'atomdata' accessor method, for which 'adata' is now an alias

BUG FIXES

    o Added S3 versions of some S4 methods to fix scoping issues
    o Removed Cardinal package from Suggests to avoid circular dependency
    o Reduced memory consumption in bigglm-matter method

CHANGES IN VERSION 0.99.11 [2016-10-11]
---------------------------------

BUG FIXES

    o Updated documentation details.

CHANGES IN VERSION 0.99.10 [2016-10-11]
---------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Updated vignettes with installation instructions, faster build time
    o Added 'adata' method for accessing 'matter' class @data slot

CHANGES IN VERSION 0.99.9 [2016-10-5]
---------------------------------

NEW FEATURES

    o Added delayed scaling and centering via 'scale' method
    o Added 'prcomp' method for principal components analysis

SIGNIFICANT USER-VISIBLE CHANGES

    o Renamed 'colSd' -> 'colSds', 'colVar' -> 'colVars', etc.
    o Renamed 'filepaths' -> 'paths' and 'file_id' -> 'source_id'
    o Moved 'irlba' from Suggests to Imports to support new 'prcomp' method
    o Updated vignette to use new 'prcomp' method in the PCA example

BUG FIXES

    o Fixed bug when combining 'matter' objects with multiple data sources

CHANGES IN VERSION 0.99.8 [2016-10-3]
---------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o In S4 class 'atoms', slot 'file_id' is now type 'integer' to save space
    o In S4 class 'atoms', slot 'datamode' is now type 'integer' to save space
    o More comprehensive error messages in constructors for S4 classes

CHANGES IN VERSION 0.99.7 [2016-10-1]
---------------------------------

BUG FIXES

    o Try to fix namespace std::isnan scoping issues on Windows

CHANGES IN VERSION 0.99.6 [2016-10-1]
---------------------------------

BUG FIXES

    o Fixed handling of NA, NaN, Inf, and -Inf during C type coercion
    o Improved handling of NA, NaN, Inf, and -Inf in summary stats
    o Fixed handling of NAs in matrix multiplication for integers

CHANGES IN VERSION 0.99.5 [2016-9-27]
---------------------------------

BUG FIXES

    o Fixed .Call native routine registration for C++ methods
    o Added "C_" prefix for C++ methods called through .Call

CHANGES IN VERSION 0.99.4 [2016-9-27]
---------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Added .Call native routine registration for C++ methods

CHANGES IN VERSION 0.99.3 [2016-9-27]
---------------------------------

BUG FIXES

    o Import generics from S4Vectors for 'colMeans', 'colSums',
        'rowMeans', and 'rowSums'
    o Cleaned up method signatures and class unions

CHANGES IN VERSION 0.99.2 [2016-9-26]
---------------------------------

BUG FIXES

    o Cleaned up double assignments in C++ code

CHANGES IN VERSION 0.99.1 [2016-9-26]
---------------------------------

BUG FIXES

    o Version bump for Bioconductor build system

CHANGES IN VERSION 0.99.0 [2016-9-26]
---------------------------------

BUG FIXES

    o Updated PCA example in vignette (irlba now requires 'mult'
        argument to be non-missing for non-C execution)
    o Added irlba unit test

CHANGES IN VERSION 0.6 [2016-9-25]
---------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Updated maintainer and author email address

BUG FIXES

    o Fixed bug in rowVar for matter_matc

CHANGES IN VERSION 0.5 [2016-9-25]
---------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Updated documentation with examples and added unit tests

BUG FIXES

    o Fixed matrix multiplication on mixed data types (int x double)

CHANGES IN VERSION 0.4 [2016-8-3]
---------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Added support for class-preserving subsetting of 'matter'
         matrices with 'drop=NA' argument for Cardinal compatibility.
    o Added new 'show' method for 'matter' vectors and matrices showing
        their size in in-memory and size on disk.

CHANGES IN VERSION 0.3 [2016-8-2]
---------------------------------

NEW FEATURES

    o Added C++ class 'MatterAccessor' for iterating through.
    	a buffered version of a 'matter' vector or matrix
    o Added summary statistics including 'sum', 'mean', 'var',
    	'sd', 'colSums', 'colMeans', 'colVar', 'colSd',
    	'rowSums', 'rowMeans', 'rowVar', and 'rowSd'.
    o Added support for 'apply' method for 'matter' matrices
    o Added support for 'bigglm' linear regression.
    o Added basic matrix multiplication for 'matter' matrices
    	with an in-memory R matrix or vector.

CHANGES IN VERSION 0.2 [2016-7-28]
---------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Overhauled backend to use C++ classes 'Matter' and 'Atoms',
        to maximizes use of sequential reads versus random reads.

CHANGES IN VERSION 0.1 [2016-2-17]
---------------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o First rough implementation of matter including the
        classes 'atoms' and 'matter', and subclasses 'matter_vec',
        'matter_matc', 'matter_matr', with a C backend.
