CHANGES IN VERSION 0.14.0
-------------------------
NEW FEATURES
o Support 'type(x) <- new_type' to change the type of a DelayedArray
object.
o 1D-style single bracket subsetting of DelayedArray objects now supports
subsetting by a numeric matrix with one column per dimension.
SIGNIFICANT USER-VISIBLE CHANGES
o No more parallel evaluation by default, that is, getAutoBPPARAM() now
returns NULL on a fresh session instead of one of the parallelization
backends defined in BiocParallel. It is now the responsibility of the
user to set the parallelization backend (with setAutoBPPARAM()) if they
wish things like matrix multiplication, rowsum() or rowSums() use
parallel evaluation again.
Also BiocParallel has been moved from Depends to Suggests.
o Replace arrayInd2() and linearInd() with Lindex2Mindex() and
Mindex2Lindex(). The new functions are implemented in C for better
performances and they properly handle L-index values greater than
INT_MAX (2^31 - 1) in the input and output.
o 2x speedup to coercion from DelayedArray to SparseArraySeed or dgCMatrix.
DEPRECATED AND DEFUNCT
o arrayInd2() and linearInd() are now deprecated in favor of
Lindex2Mindex() and Mindex2Lindex().
BUG FIXES
o Fix handling of linear indices >= 2^31 in 1D-style single bracket
subsetting of DelayedArray objects.
o rowsum() & colsum() methods for DelayedArray objects now respect factor
level ordering (issue #59).
o Coercion from DelayedMatrix to dgCMatrix now propagates the dimnames.
o No more quotes around the NA values of a DelayedArray of type "character".
o Better error message when Ops methods for DelayedArray objects reject
their operands.
CHANGES IN VERSION 0.12.0
-------------------------
NEW FEATURES
o Add isPristine()
o Delayed subassignment now accepts a right value with dimensions that are
not strictly the same as the dimensions of the selection as long as the
"effective dimensions" are the same
o Small improvement to delayed dimnames setter: atomic vectors or factors
in the supplied 'dimnames' list are now accepted and passed thru
as.character()
SIGNIFICANT USER-VISIBLE CHANGES
o Improve show() method for DelayedArray objects (see commit 54540856)
BUG FIXES
o Setting and getting the dimnames of a DelayedArray object or derivative
now preserves the names on the dimnames
o Some fixes related to DelayedArray objects with list array seeds (see
commit 6c94eac7)
CHANGES IN VERSION 0.10.0
-------------------------
NEW FEATURES
o Many improvements to matrix multiplication (%*%) of DelayedMatrix
objects by Aaron Lun. Also add limited support for (t)crossprod methods.
o Add rowsum() and colsum() methods for DelayedMatrix objects.
These methods are block-processed operations.
o Many improvements to the RleArray() contructor (see messages for
commits 582234a7 and 0a36ee01 for more info).
o Add seedApply()
o Add multGrids() utility (still a work-in-progress, not documented yet)
CHANGES IN VERSION 0.8.0
------------------------
NEW FEATURES
o Add get/setAutoBlockSize(), getAutoBlockLength(),
get/setAutoBlockShape() and get/setAutoGridMaker().
o Add rowGrid() and colGrid(), in addition to blockGrid().
o Add get/setAutoBPPARAM() to control the automatic 'BPPARAM' used by
blockApply().
o Reduce memory usage when realizing a sparse DelayedArray to disk
On-disk realization of a DelayedArray object that is reported to be sparse
(by is_sparse()) to a "sparsity-optimized" backend (i.e. to a backend with
a memory efficient write_sparse_block() like the TENxMatrix backend imple-
mented in the HDF5Array package) now preserves sparse representation of
the data all the way. More precisely, each block of data is now kept in
a sparse form during the 3 steps that it goes thru: read from seed,
realize in memory, and write to disk.
o showtree() now displays whether a tree node or leaf is considered sparse
or not.
o Enhance "aperm" method and dim() setter for DelayedArray objects. In
addition to allowing dropping "ineffective dimensions" (i.e. dimensions
equal to 1) from a DelayedArray object, aperm() and the dim() setter now
allow adding "ineffective dimensions" to it.
o Enhance subassignment to a DelayedArray object.
So far subassignment to a DelayedArray object only supported the **linear
form** (i.e. x[i] <- value) with strong restrictions (the subscript 'i'
must be a logical DelayedArray of the same dimensions as 'x', and 'value'
must be an ordinary vector of length 1).
In addition to this linear form, subassignment to a DelayedArray object
now supports the **multi-dimensional form** (e.g. x[3:1, , 6] <- 0). In
this form, one subscript per dimension is supplied, and each subscript
can be missing or be anything that multi-dimensional subassignment to
an ordinary array supports. The replacement value (a.k.a. the right
value) can be an array-like object (e.g. ordinary array, dgCMatrix object,
DelayedArray object, etc...) or an ordinary vector of length 1. Like the
linear form, the multi-dimensional form is also implemented as a delayed
operation.
o Re-implement internal helper simple_abind() in C and support long arrays.
simple_abind() is the workhorse behind realization of arbind() and
acbind() operations on DelayedArray objects.
o Add "table" and (restricted) "unique" methods for DelayedArray objects,
both block-processed.
o range() (block-processed) now supports the 'finite' argument on a
DelayedArray object.
o %*% (block-processed) now works between a DelayedMatrix object and an
ordinary vector.
o Improve support for DelayedArray of type "list".
o Add TENxMatrix to list of supported realization backends.
o Add backend-agnostic RealizationSink() constructor.
o Add linearInd() utility for turning array indices into linear indices.
Note that linearInd() performs the reverse transformation of
base::arrayInd().
o Add low-level utilities mapToGrid() and mapToRef() for mapping reference
array positions to grid positions and vice-versa.
o Add downsample() for reducing the "resolution" of an ArrayGrid object.
o Add maxlength() generic and methods for ArrayGrid objects.
SIGNIFICANT USER-VISIBLE CHANGES
o Multi-dimensional subsetting is no more delayed when drop=TRUE and the
result has only one dimension. In this case the result now is returned
as an **ordinary** vector (atomic or list). This is the only case of
multi-dimensional single bracket subsetting that is not delayed.
o Rename defaultGrid() -> blockGrid(). The 'max.block.length' argument
is replaced with the 'block.length' argument. 2 new arguments are
added: 'chunk.grid' and 'block.shape'.
o Major improvements to the block processing mechanism.
All block-processed operations (except realization by block) now support
blocks of **arbitrary** geometry instead of column-oriented blocks only.
'blockGrid(x)', which is called by the block-processed operations to get
the grid of blocks to use on 'x', has the following new features:
1) It's "chunk aware". This means that, when the chunk grid is known (i.e.
when 'chunkGrid(x)' is not NULL), 'blockGrid(x)' defines blocks that
are "compatible" with the chunks i.e. that any chunk is fully contained
in a block. In other words, blocks are chosen so that chunks don't
cross their boundaries.
2) When the chunk grid is unknown (i.e. when 'chunkGrid(x)' is NULL),
blocks are "isotropic", that is, they're as close as possible to an
hypercube instead of being "column-oriented" (column-oriented blocks,
also known as "linear blocks", are elongated along the 1st dimension,
then along the 2nd dimension, etc...)
3) The returned grid has the lowest "resolution" compatible with
'getAutoBlockSize()', that is, the blocks are made as big as possible
as long as their size in memory doesn't exceed 'getAutoBlockSize()'.
Note that this is not a new feature. What is new though is that an
exception now is made when the chunk grid is known and some chunks
are >= 'getAutoBlockSize()', in which case 'blockGrid(x)' returns a
grid that is the same as the chunk grid.
These new features are supposed to make the returned grid "optimal" for
block processing. (Some benchmarks still need to be done to
confirm/quantify this.)
o The automatic block size now is set to 100 Mb (instead of 4.5 Mb
previously) at package startup. Use setAutoBlockSize() to change the
automatic block size.
o No more 'BPREDO' argument to blockApply().
o Replace block_APPLY_and_COMBINE() with blockReduce().
BUG FIXES
o No-op operations on a DelayedArray derivative really act like no-ops.
Operating on a DelayedArray derivative (e.g. RleArray, HDF5Array or
GDSArray) will now return an objet of the original class if the result
is "pristine" (i.e. if it doesn't carry delayed operations) instead of
degrading the object to a DelayedArray instance. This applies for example
to 't(t(x))' or 'dimnames(x) <- dimnames(x)' etc...