All checksums have been double-checked against existing RMD160 and
SHA512 hashes
Could not be committed due to merge conflict:
devel/py-traitlets/distinfo
The following distfiles were unfetchable (note: some may be only fetched
conditionally):
./devel/pvs/distinfo pvs-3.2-solaris.tgz
./devel/eclipse/distinfo eclipse-sourceBuild-srcIncluded-3.0.1.zip
CHANGES IN bit VERSION 4.0.4
USER VISIBLE CHANGES
o copy() and reverse() have been renamed to
copy_vector() and reverse_vector() to avoid
naming conflict with data.table
CHANGES IN bit VERSION 4.0.3
BUG FIXES
o temporarily removed link to clone.ff
to satisfy CRAN checks
CHANGES IN bit VERSION 4.0.2
USER VISIBLE CHANGES
o Vignettes nolonger execute ff code
for ff-version prior 4.0.0
BUG FIXES
o NA could crash bit_extract_unsorted
o now DESCRIPTION URL points to github
CHANGES IN bit VERSION 4.0.1
USER VISIBLE CHANGES
o bbatch now checks input N >= 0, B > 0
and returns batchsize b in 1..N
BUG FIXES
o NA could crash bit_extract_unsorted
CHANGES IN bit VERSION 4.0.0
NEW FEATURES
o new superclass ?booltype now allows proper method
dispatch even for two user defined booleans, e.g. (bit | bitwhich)
o new ordinal 'booltypes' nobool < logical < bit < bitwhich < which < ri
and diagnostic functions booltype() and is.booltype()
o bitwhich now has methods for [[ [ [[<- and [<-
o new functions 'c', '==', '!=', '|', '&', 'xor' for .booltype
o new function bitwhich_representation() to inspect the bitwhich
representation without the cost of unclass()
o new method 'is' for .which, .ri, .hi (and .booltype)
o new coercion generic as.booltype with .default method
o new coercion method as.logical.which
o new generic as.ri with methods for .ri and .default (lossy)
o new methods rep, rev, as.character and str for .bit and .bitwhich
o new methods all, any, min, max, range, sum, summary for .booltype, .which
o new method anyNA for all booltypes
o new dummy method 'is.na' for .bit, .bitwhich
o new function in.bitwhich much faster than %in%
o new integer sorting function bitsort() using bit_sort() or bit_sort_unique()
which can be by an order of magnitude faster than radix sorts
or falling back to one of countsort(), quicksort2(), quicksort3()
o new symmetric set function symdiff
o new functions copy(), reverse() for copying and reversing integer vectors
o new helper functions range_na(), range_nanozero(), range_sortna()
join multiple tasks in one go
o new fast unary functions for integers: bit_unique, bit_duplicated,
bit_anyDuplicated, bit_sumDuplicated
o new fast binary functions for integers: bit_in, bit_intersect, bit_union,
bit_setequal, bit_symdiff, bit_setdiff, bit_rangediff
o new fast unary functions for sorted integers: merge_rev,
merge_unique, merge_duplicated, merge_anyDuplicated, merge_sumDuplicated,
merge_first, merge_last,
o new fast binary functions for sorted integers:
merge_firstin, merge_firstnotin, merge_lastin, merge_lastnotin,
merge_match, merge_in, merge_notin,
merge_union, merge_intersect, merge_setdiff, merge_symdiff,
merge_setequal
o new even faster binary functions when the first argument is a range of integers:
merge_rangein, merge_rangenotin, merge_rangesect, merge_rangediff
o new function firstNA substantially faster than which.max(is.na(x))
o new function getsetattr() does setattr() but returns the old attr()
o new function get_length() directly returns LENGTH(SEXP)
circumventing all method dispatch for length()
o new methods rlepack.integer, rleunpack.rlepack anyDuplicated.rlepack
USER VISIBLE CHANGES
o license has been extendend from GPL-2 to GPL-2 | GPL-3
o S3methods are no longer exported in NAMESPACE
(except for .booltype)
o class bitwhich
- now is a fully functional alternative to bit vectors
- has argument order changed to (maxindex, x, poslength)
- its internal representation of bitwhich(0) has been changed
from FALSE to logical() and from unsorted to sorted integers
o class 'which' now carries an attribute 'maxindex' if available
o as.which() and bitwhich() now filter zeroes and store data unique(sort(x))
o as.which() now has methods for .which, .logical, .integer and .numeric
instead of .default.
o bit() and bitwhich() now behave more like logical(), without
arguments they return objects of length zero
o as.bit, as.bitwhich and as.which now have methods for class NULL
such that for example as.bit(c()) will return bit(0)
(wish of Martijn Schuemle)
o binary operators now allow for different lengths
and recycle instead of throwing an error
o xor.default now keeps the original definition of xor() and uses
a new method xor.logical to speed-up logicals
o the generics poslength and maxindex have been moved from package ff
with methods now for .default, .logical, .bit, .bitwhich, .which, .ri
o old method chunk.default has been renamed to chunks and now returns with names
(for backward compatibility chunk() with named arguments behaves as before)
o new method chunk.default calls chunks() along the length(x)
using typeof(x) or vmode(x), this replaces chunk.bit from package ff
o clone.default now uses R's C-function duplicate()
and clone.list has been removed
o intisasc() and intisdesc() have a new argument
na.method=c("none","break","skip") to specify tie handling
TESTING and DOCUMENTATION
o there are much more regression tests now
o testing uses package testthat
o documentation uses package roxygen2 now
o new vignettes bit-demo, bit-usage and bit-performance
BUG FIXES
o assignment functions '[<-.bit' now behave like '[<-.logical' when it
comes to NAs or ZEROs in subscripts
o length<-.bit no longer tries to access memory before it is allocated
o as.bit.bitwhich now handles non-positive bitwhich correctly
o declare as static many functions/variables in bit.c. (Thanks to Brian Ripley)
The canonical form [1] of an R package Makefile includes the
following:
- The first stanza includes R_PKGNAME, R_PKGVER, PKGREVISION (as
needed), and CATEGORIES.
- HOMEPAGE is not present but defined in math/R/Makefile.extension to
refer to the CRAN web page describing the package. Other relevant
web pages are often linked from there via the URL field.
This updates all current R packages to this form, which will make
regular updates _much_ easier, especially using pkgtools/R2pkg.
[1] http://mail-index.netbsd.org/tech-pkg/2019/08/02/msg021711.html
Each R package should include ../../math/R/Makefile.extension, which also
defines MASTER_SITES. Consequently, it is redundant for the individual
packages to do the same. Package-specific definitions also prevent
redefining MASTER_SITES in a single common place.
Upstream changes:
CHANGES IN bit VERSION 1.1-14
BUG FIXES
o bit[i] and bit[i]<-v now check for non-positive integers
which prevents a segfault when bit[NA] or bit[NA]<-v
CHANGES IN bit VERSION 1.1-13
USER VISIBLE CHANGES
o logical NA is now mapped to bit FALSE as in ff booleans
o extractor function '[.bit' with positive numeric subscripts
(integer, double, bitwhich) now behaves like '[.logical' and returns
NA for out-of-bound requests and no element for 0
o extractor function '[[.bit' with positive numeric (integer, double,
bitwhich) subscripts now behaves like '[[.logical' and throws an error
for out-of-bound requests
o extractor function '[.bit' with range index subscripts (ri)
subscripts now behaves like '[[.bit' and throws an error
for out-of-bound requests
o assignment functions '[<-.bit' and '[[<-.bit' with positive numeric
(integer, double, bitwhich) subscripts now behave like '[<-.logical' and
'[[<-.logical' and silently increase vector length if necessary
o assignment function '[<-.bit' with range index subscripts (ri) now
behaves like '[[<-.bit' and silently increases vector length if necessary
o rlepack() is now a generic with a method for class 'integer'
o rleunpack() is now a generic with a method for class 'rlepack'
o unique.rlepack() now gives correct results for unordered sequences
o anyDuplicated.rlepack() now returns the position of the first
duplicate and gives correct results for unordered sequences
TUNING
o The package can now compiled with 64bit words instead of 32bit words,
since we only measured a minor speedup, we left 32bit as the default.
BUG FIXES
o extractor and assignment functions now check for legal (positive)
subscript bounds, hence illegally large subscripts or zero no longer
cause memory violations
bitmapped vectors of booleans (no NAs), coercion from and to logicals,
integers and integer subscripts; fast boolean operators and fast
summary statistics. With 'bit' vectors you can store true binary
booleans {FALSE,TRUE} at the expense of 1 bit only, on a 32 bit
architecture this means factor 32 less RAM and ~ factor 32 more speed
on boolean operations. Due to overhead of R calls, actual speed gain
depends on the size of the vector: expect gains for vectors of size >
10000 elements. Even for one-time boolean operations it can pay-off to
convert to bit, the pay-off is obvious, when such components are used
more than once. Reading from and writing to bit is approximately as
fast as accessing standard logicals - mostly due to R's time for
memory allocation. The package allows to work with pre-allocated
memory for return values by calling .Call() directly: when evaluating
the speed of C-access with pre-allocated vector memory, coping from
bit to logical requires only 70% of the time for copying from logical
to logical; and copying from logical to bit comes at a performance
penalty of 150%. the package now contains further classes for
representing logical selections: 'bitwhich' for very skewed selections
and 'ri' for selecting ranges of values for chunked processing. All
three index classes can be used for subsetting 'ff' objects (ff-2.1-0
and higher).
