CHANGES IN VERSION 2.0.1 [2022-11-15]
-----------------------------------
BUG FIXES
o Fixed combining for matter vectors and lists
o Fixed slow 'matter_mat()' constructor for large # of atoms
o Fixed bug with BPPARAM not passed in 'rowStats()'/'colStats()'
CHANGES IN VERSION 1.99.2 [2022-10-31]
-----------------------------------
BUG FIXES
o Fix 'chunkApply()' behavior for when nchunks == 1
o Fix 'atoms' failure when 'source' is a compressed 'drle'
o Properly ignore missing groups in 'rowsweep()' and 'colsweep()'
CHANGES IN VERSION 1.99.1 [2022-10-30]
-----------------------------------
BUG FIXES
o Minor bug fixes to 'matter_list' and 'struct()' behavior
o Minor bug fix to endomorphic subsetting of sparse matrices
o Minor bug fix to 'binvec()' behavior at vector endpoints
CHANGES IN VERSION 1.99.0 [2022-10-23]
-----------------------------------
NEW FEATURES
o Complete re-implementation of sparse array code in C++
o Complete re-implementation of matter object C++ backends
o New 'sparse_arr' class with 'sparse_mat' and 'sparse_vec'
o New 'matter_arr' class with 'matter_mat' and 'matter_vec'
o New 'asearch()' function for approximate search with interpolation
o New 'chunkApply()' function replacing 'chunk_apply()', etc.
o New 'colsweep()' and 'rowsweep()' functions w/ group parameter
o New 'colscale()' and 'rowscale()' functions w/ group parameter
o New 'drle_fct' class for delta-run-length encoded factors
o New interpolation options for 'sparse_arr' objects
o Simplified deferred arithmetic operations interface
SIGNIFICANT USER-VISIBLE CHANGES
o New simplified constructors for most matter objects
o Updated S4 internals for most matter objects
o Updated S4 internals for sparse array objects
o Deprecated some rarely-used functions and classes
o Deprecated some S4 generic conflicts with core BioC packages
BUG FIXES
o Fix to 'stream_var' and 'stream_sd' behavior when n=0 or n=1
CHANGES IN VERSION 1.19.1 [2021-10-20]
-----------------------------------
BUG FIXES
o Fix error in 'cbind()' on two 'matter_vec' objects
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.