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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
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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.
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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
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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).
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