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(this page)| 2024-04-28 16:26:43 by Makoto Fujiwara | Files touched by this commit (3) |
Log message:
(math/R) Updated 4.3.2 to 4.3.3
CHANGES IN R 4.3.3:
NEW FEATURES:
* 'iconv()' now fixes up variant encoding names such as
'"utf8"' case-insensitively.
DEPRECATED AND DEFUNCT:
* The legacy 'encoding = "MacRoman"' is deprecated in 'pdf()'
and 'postscript()': support was incomplete in earlier
versions of R.
BUG FIXES:
* Arguments are now properly forwarded to methods on S4
generics with ... in the middle of their formal arguments.
This was broken for the case when a method introduced an
argument but did not include ... in its own formals. Thanks
to Herv<c3><a9> Pag<c3><a8>s for the report \
PR#18538.
* Some invalid 'file' arguments to 'pictex()', 'postscript()'
and 'xfig()' opened a file called 'NA' rather than throw an
error. These included 'postscript(NULL)' (which some people
expected to work like 'pdf(NULL)').
* Passing 'filename = NA' to 'svg()', 'cairo_pdf()',
'cairo_ps()' or the Cairo-based bitmap devices opened a file
called 'NA': it now throws an error.
* 'quartz(file = NA)' opened a file called 'NA', including
when used as a Quartz-based bitmap device. It now gives an
error.
* 'rank(<long vector>)' now works, fixing PR#18617, thanks to
Ilia Kats.
* 'seq.int()' did not adequately check its 'length.out'
argument.
* 'match(<POSIXct>, .)' is correct again for differing time
zones, ditto for '"POSIXlt"', fixing PR#18618 reported by
Bastian Klein.
* 'drop.terms(*, dropx = <0-length>)' now works, fixing
PR#18563 as proposed by Mikael Jagan.
* 'drop.terms(*)' keeps ' + offset(.)' terms when it should,
PR#18565, and 'drop.terms()' no longer makes up a response,
PR#18566, fixing both bugs thanks to Mikael Jagan.
* 'getS3method("t", "test")' no longer finds the \
't.test()'
function, fixing PR#18627.
* 'pdf()' and 'postscript()' support for the documented Adobe
encodings '"Greek"' and '"Cyrilllic"' was missing \
(although
the corresponding Windows' codepages could be used).
* Computations of glyph metric information for 'pdf()' and
'postscript()' did not take into account that
transliteration could replace one character by two or more
(only seen on macOS 14) and typically warned that the
information was not known.
* 'rank(x)' no longer overflows during integer addition, when
computing rank average for largish but not-yet long vector
'x', fixing PR#18630, thanks to Ilia Kats.
* 'list.files()' on Windows now returns also files with names
longer that 260 bytes (the Windows limit is 260 characters).
Previously, some file names particularly with 'East Asian'
characters were omitted.
* 'cov2cor(<0 x 0>)' now works, fixing PR#18423 thanks to
Mikael Jagan and Elin Waring.
* 'cov2cor(<negative diagonal>)' and similar now give one
warning instead of two, with better wording, fixing PR#18424
thanks to Mikael Jagan.
* 'tools'':: startDynamicHelp()' now ensures 'port' is in
proper range, fixing PR#18645.
* 'pbeta(x, a,b)' is correct now for 'x'=0 or 1 in the
boundary cases where 'a' or 'b' or both are 0, fixing
PR#18672 thanks to Michael Fay.
* 'pmatch(x, table)' for large 'table', also called for data
frame row selection, 'dfrm[nm, ]', is now interruptible,
fixing PR#18656.
* 'predict(<rank-deficient lm>, newdata=*)' fix computing of
'nbasis', see Russ Lenth's comment 29 in PR#16158.
* Added a work-around for a bug in macOS 14.3.1 and higher
which prevents R plots in the Quartz Cocoa device from
updating on screen.
|
| 2024-04-07 09:35:33 by Thomas Klausner | Files touched by this commit (1138) |
Log message: *: bump for cairo buildlink3.mk change lzo was made an option |
| 2024-03-05 17:12:33 by Jonathan Perkin | Files touched by this commit (2) |
Log message: R: Fix building extensions with C++. |
| 2024-02-15 08:48:50 by Mark Davies | Files touched by this commit (3) |
Log message: R: fix dealing with conflict with NetBSD function strtoi() Just rename the C level function strtoi() to not conflict with the NetBSD function. Don't also change the name of the R level funstion. |
| 2024-01-09 00:15:39 by Makoto Fujiwara | Files touched by this commit (2) |
Log message: (math/R) correction on patch-m4.R again |
| 2024-01-09 00:13:03 by Makoto Fujiwara | Files touched by this commit (2) |
Log message: (math/R) correction on patch-configure.ac.again |
| 2024-01-09 00:03:50 by Makoto Fujiwara | Files touched by this commit (3) |
Log message: (math/R) Correction on patches |
2024-01-08 08:18:26 by Makoto Fujiwara | Files touched by this commit (4) |  |
Log message:
(math/R) Updated 4.2.3 to 4.3.2 with remedy for strtoi
- pkgsrc side change
strtoi function conflicted with NetBSD function. but it was
referenced in the same file. Now it is referenced at various places.
So it is renamed into strtoiR (All the strings for now) by SUBST,
thus including do_strtoi.
(patches/patch-src_main_character.c is dropped)
- upstream info
CHANGES IN R 4.3.2:
NEW FEATURES:
* The default initialization of the '"repos"' option from the
'repositories' file at startup can be skipped by setting
environment variable 'R_REPOSITORIES' to 'NULL' such that
'getOption("repos")' is empty if not set elsewhere.
* 'qr.X()' is now an implicit S4 generic in 'methods'.
* 'iconv(to = "ASCII//TRANSLIT")' is emulated using
substitution on platforms which do not support it (notably
Alpine Linux). This should give a human-readable conversion
in ASCII on all platforms (rather than 'NA_character_').
* 'trans3d()' gains options 'continuous' and 'verbose'
addressing the problem of possible "wrap around" when
projecting too long curves, as reported by Achim Zeileis in
PR#18537.
* 'tools::showNonASCII()' has been rewritten to work better on
macOS 14 (which has a changed implementation of 'iconv()').
* 'tiff(type = "quartz")' (the default on macOS) now warns if
'compression' is specified: it continues to be ignored.
INSTALLATION on a UNIX-ALIKE:
* There is some support for building with Intel's LLVM-based
compilers on 'x86_64' Linux, such as (C) 'icx', (C++) 'ipcx'
and (Fortran) 'ifx' from oneAPI 2023.x.y.
* There is support for using LLVM's 'flang-new' as the Fortran
compiler from LLVM 16.0.x (preferably 17.0.0 or later).
UTILITIES:
* 'R CMD check' reports the use of the Fortran 90 random
number generator 'RANDOM_NUMBER()' and the subroutines to
initialize it.
'Writing R Extensions' has example code to use R's RNGs from
Fortran.
BUG FIXES:
* 'substr(x, n, L) <- cc' now works (more) correctly for
multibyte UTF-8 strings 'x' when 'L > nchar(x)', thanks to a
report and patch by 'Architect 95'.
* 'contrib.url(character())' now returns 0-length
'character()' as documented, which also avoids spurious
warnings from 'available.packages()' et al. in the edge case
of an empty vector of repository URLs.
* 'readChar(., 4e8)' no longer fails, thanks to Kodi Arfer's
report (PR#18557).
* 'lapply(<list>, as.data.frame)' no longer warns falsely for
some base vector components.
* Communication between parent and child processes in the
'multicore' part of 'parallel' could fail on platforms that
do not support an arbitrarily large payload in system
functions 'read()'/'write()' on pipes (seen on macOS where a
restriction to 'INT_MAX' bytes is documented, without doing
a partial read unlike Linux). The payload is now split into
1Gb chunks to avoid that problem. (PR#18571)
* 'qqplot(x,y, conf.level=.)' gives better confidence bounds
when 'length(x) != length(y)', thanks to Alexander Ploner's
report and patch proposal (PR#18557).
* 'norm(<0-length>, "2")' now gives zero instead of an \
error,
as all the other norm types, thanks to Mikael Jagan's
PR#18542.
* Build-stage Rd macros \packageAuthor and \packageMaintainer
now process 'Authors@R', fixing 'NA' results when the
package 'DESCRIPTION' omits 'Author' and 'Maintainer'
fields.
* Formatting and printing complex numbers could give things
like '0.1683-0i' because of rounding error: '-0i' is now
replaced by '+0i'.
* 'postscript()' refused to accept a 'title' comment
containing the letter "W" (PR#18599).
* 'isoreg(c(1,Inf))' signals an error instead of segfaulting,
fixing PR#18603.
* 'tiff(type = "Xlib")' was only outputting the last page of
multi-page plots.
* 'tools::latexToUtf8()' again knows about '\~{n}' and other
letters with tilde, fixing a regression in R 4.3.0, and
about '\^{i}' as an alternative to '\^{\i}' (similarly with
other accents). Furthermore, LaTeX codes for accented I
letters are now correctly converted, also fixing related
mistakes in 'tools::encoded_text_to_latex()'.
* 'tar(*, tar = "internal")' no longer creates out-of-spec tar
files in the very rare case of user or group names longer
than 32 bytes, fixing PR#17871 with thanks to Ivan Krylov.
* When using the "internal" timezone datetime code, adding a
fraction of a second no longer adds one second, fixing
PR#16856 from a patch by Ivan Krylov.
* 'tools::checkRd()' no longer produces spurious notes about
"unnecessary braces" from multi-line Rd results of \Sexpr
macros.
CHANGES IN R 4.3.1:
C-LEVEL FACILITIES:
* The C-level API version of R's 'integrate()', 'Rdqags()' in
'Applic.h', now returns the correct number of integrand
evaluations 'neval', fixing PR#18515 reported and diagnosed
by Stephen Wade.
* The C prototypes for LAPACK calls 'dspgv' and 'dtptrs' in
'R_exts/Lapack.h' had one too many and one too few character
length arguments - but this has not caused any known issues.
To get the corrected prototypes, include
#include <Rconfig.h> // for PR18534fixed
#ifdef PR18534fixed
# define usePR18534fix 1
#endif
#include <R_exts/Lapack.h>
in your C/C++ code (PR#18534).
INSTALLATION:
* Many of the checks of esoteric Internet operations and those
using unreliable external sites have been moved to a new
target that is not run by default and primarily intended for
the core developers. To run them use
cd tests; make test-Internet-dev
BUG FIXES:
* '.S3methods()', typically called from 'methods()', again
marks methods from package 'base' as 'visible'.
Also, the visibility of non-'base' methods is again
determined by the method's presence in 'search()'.
* 'tools::Rdiff()' is now more robust against invalid strings,
fixing installation tests on Windows without Rtools
installed (PR#18530).
* Fix (new) bug in 'hcl.colors(2, *)', by Achim Zeileis
(PR#18523).
* 'head(., <illegal>)' and 'tail(..)' now produce more useful
'"Error in ...."' error messages, fixing PR#18362.
* Package code syntax on Windows is checked in UTF-8 when
UTF-8 is the native encoding.
* 'na.contiguous(x)' now also returns the first run, when it
is at the beginning and there is a later one of the same
length; reported to R-devel, including a fix, by Georgi
Boshnakov. Further, by default, it modifies only an
existing 'attr(*,"tsp")' but otherwise no longer sets one.
* 'chol(<not pos.def>, pivot = <T|F>)' now gives a correct
error or warning message (depending on 'pivot'), thanks to
Mikael Jagan's (PR#18541).
CHANGES IN R 4.3.0:
SIGNIFICANT USER-VISIBLE CHANGES:
* Calling '&&' or '||' with LHS or (if evaluated) RHS of
length greater than one is now always an error, with a
report of the form
'length = 4' in coercion to 'logical(1)'
Environment variable '_R_CHECK_LENGTH_1_LOGIC2_' no longer
has any effect.
NEW FEATURES:
* The included BLAS sources have been updated to those shipped
with LAPACK version 3.10.1. (This caused some
platform-dependent changes to package check output.) And
then to the sources from LAPACK version 3.11.0 (with changes
only to double complex subroutines).
* The included LAPACK sources have been updated to include the
four Fortran 90 routines rather than their Fortran 77
predecessors. This may give some different signs in SVDs or
eigendecompositions.. (This completes the transition to
LAPACK 3.10.x begun in R 4.2.0.)
* The LAPACK sources have been updated to version 3.11.0. (No
new subroutines have been added, so this almost entirely bug
fixes: Those fixes do affect some computations with 'NaN's,
including R's 'NA'.)
* The parser now signals _classederrors, notably in case of
the pipe operator '|>'. The error object and message now
give line and column numbers, mostly as proposed and
provided by Duncan Murdoch in PR#18328.
* 'toeplitz()' is now generalized for asymmetric cases, with a
'toeplitz2()' variant.
* 'xy.coords()' and 'xyz.coords()' and consequently, e.g.,
'plot(x,y, log = "y")' now signal a _classedwarning about
negative values of y (where 'log(.)' is 'NA'). Such a
warning can be specifically suppressed or caught otherwise.
* Regular expression functions now check more thoroughly
whether their inputs are valid strings (in their encoding,
e.g. in UTF-8).
* The performance of 'grep()', 'sub()', 'gsub()' and
'strsplit()' has been improved, particularly with 'perl =
TRUE' and 'fixed = TRUE'. Use of 'useBytes = TRUE' for
performance reasons should no longer be needed and is
discouraged: it may lead to incorrect results.
* 'apropos()' gains an argument 'dot_internals' which is used
by the completion ('help(rcompgen)') engine to also see
'base' internals such as '.POSIXct()'.
* Support in 'tools::Rdiff()' for comparing uncompressed PDF
files is further reduced - see its help page.
* 'qqplot(x, y, ...)' gains 'conf.level' and 'conf.args'
arguments for computing and plotting a confidence band for
the treatment function transforming the distribution of 'x'
into the distribution of 'y ' (Switzer, 1976, _Biometrika_).
Contributed by Torsten Hothorn.
* Performance of 'package_dependencies()' has been improved
for cases when the number of dependencies is large.
* Strings newly created by 'gsub()', 'sub()' and 'strsplit()',
when any of the inputs is marked as '"bytes"', are also
marked as '"bytes"'. This reduces the risk of creating
invalid strings and accidental substitution of bytes deemed
invalid.
* Support for 'readLines(encoding = "bytes")' has been added
to allow processing special text files byte-by-byte, without
creating invalid strings.
* 'iconv(from = "")' now takes into account any declared
encoding of the input elements and uses it in preference to
the native encoding. This reduces the risk of accidental
creation of invalid strings, particularly when different
elements of the input have different encoding (including
'"bytes"').
* Package repositories in 'getOption("repos")' are now
initialized from the 'repositories' file when 'utils' is
loaded (if not already set, e.g., in '.Rprofile'). (From a
report and patch proposal by Gabriel Becker in PR#18405.)
* 'compactPDF()' gets a 'verbose' option.
* 'type.convert()' and hence 'read.table()' get new option
'tryLogical = TRUE' with back compatible default. When set
to false, converts '"F"' or '"T"' columns to \
character.
* Added new unit prefixes '"R"' and '"Q"' for \
abbreviating
(unrealistically large) sizes beyond 10^{27} in 'standard =
"SI"', thanks to Henrik Bengtsson's PR#18435.
* 'as.data.frame()''s default method now also works fine with
atomic objects inheriting from classes such as '"roman"',
'"octmode"' and '"hexmode"', such fulfilling the \
wish of
PR#18421, by Benjamin Feakins.
* The 'as.data.frame.vector()' utility now errors for
wrong-length 'row.names'. It warned for almost six years,
with "Will be an error!".
* 'sessionInfo()' now also contains 'La_version()' and reports
codepage and timezone when relevant, in both 'print()' and
'toLatex()' methods which also get new option 'tzone' for
displaying timezone information when 'locale = FALSE'.
* New function 'R_compiled_by()' reports the C and Fortran
compilers used to build R, if known.
* 'predict(<lm>, newdata = *)' no longer unnecessarily creates
an 'offset' of all '0's.
* 'solve()' for complex inputs now uses argument 'tol' and by
default checks for 'computational singularity' (as it long
has done for numeric inputs).
* 'predict(<rank-deficient lm>, newdata=*)' now obeys a new
argument 'rankdeficient', with new default '"warnif"',
warning only if there are non-estimable cases in 'newdata'.
Other options include 'rankdeficient = "NA"', predicting
'NA' for non-estimable 'newdata' cases. This addresses
PR#15072 by Russ Lenth and is based on his original proposal
and discussions in PR#16158 also by David Firth and Elin
Waring. Still somewhat experimental.
* 'Rgui' console implementation now works better with the
'NVDA' screen reader when the full blinking cursor is
selected. The underlying improvements in cursor handling
may help also other screen readers on Windows.
* The drop-field control in GraphApp can now be left with the
TAB key and all controls can be navigated in the reverse
order using the Shift+TAB key, improving accessibility of
the 'Rgui' configuration editor.
* 'qnorm(<very large negative>, log.p=TRUE)' is now fully
accurate (instead of to "only" minimally five digits).
* 'demo(error.catching)' now also shows off 'withWarnings()'
and 'tryCatchWEMs()'.
* As an experimental feature the placeholder '_' can now also
be used in the 'rhs' of a forward pipe '|>' expression as
the first argument in an extraction call, such as '_$coef'.
More generally, it can be used as the head of a chain of
extractions, such as '_$coef[[2]]'.
* Spaces in the environment variable used to choose the R
session's temporary directory ('TMPDIR', 'TMP' and 'TEMP'
are tried in turn) are now fatal. (On Windows the 'short
path' version of the path is tried and used if that does not
contain a space.)
* 'all.equal.numeric()' gets a new optional switch 'giveErr'
to return the numeric error as attribute. Relatedly,
'stopifnot(all.equal<some>(a, b, ..))' is as "smart" \
now, as
'stopifnot(all.equal(....))' has been already, thus allowing
customized 'all.equal<Some>()' wrappers.
* R on Windows is now able to work with path names longer than
260 characters when these are enabled in the system
(requires at least Windows 10 version 1607). Packages
should be updated to work with long paths as well, instead
of assuming 'PATH_MAX' to be the maximum length. Custom
front-ends and applications embedding R need to update their
manifests if they wish to allow this feature. See
<https://blog.r-project.org/2023/03/07/path-length-limit-on-windows>
for more information.
* 'Object not found' and 'Missing argument' errors now give a
more accurate error context. Patch provided by Lionel Henry
in PR#18241.
* The '@' operator is now an S3 generic. Based on
contributions by Tomasz Kalinowski in PR#18482.
* New generic 'chooseOpsMethod()' provides a mechanism for
objects to resolve cases where two suitable methods are
found for an Ops Group Generic. This supports experimenting
with alternative object systems. Based on contributions by
Tomasz Kalinowski in PR#18484.
* 'inherits(x, what)' now accepts values other than a simple
character vector for argument 'what'. A new generic,
'nameOfClass()', is called to resolve the class name from
'what'. This supports experimenting with alternative object
systems. Based on contributions by Tomasz Kalinowski in
PR#18485.
* Detection of BLAS/LAPACK in use ('sessionInfo()') with
FlexiBLAS now reports the current backend.
* The '"data.frame"' method for 'subset()' now warns about
extraneous arguments, typically catching the use of '='
instead of '==' in the 'subset' expression.
* Calling 'a:b' when numeric 'a' or 'b' is longer than one may
now be made into an error by setting environment variable
'_R_CHECK_LENGTH_COLON_' to a true value, along the proposal
in PR#18419 by Henrik Bengtsson.
* 'density(x, weights = *)' now warns if automatic bandwidth
selection happens without using 'weights'; new optional
'warnWbw' may suppress the warning. Prompted by Christoph
Dalitz' PR#18490 and its discussants.
* 'rm(list = *)' is faster and more readable thanks to Kevin
Ushey's PR#18492.
* The 'plot.lm()' function no longer produces a normal Q-Q
plot for GLMs. Instead it plots a half-normal Q-Q plot of
the absolute value of the standardized deviance residuals.
* The 'print()' method for class '"summary.glm"' no longer
shows summary statistics for the deviance residuals by
default. Its optional argument 'show.residuals' can be used
to show them if required.
* The 'tapply()' function now accepts a data frame as its 'X'
argument, and allows 'INDEX' to be a formula in that case.
'by.data.frame()' similarly allows 'INDICES' to be a
formula.
* The performance of 'df[j] <- value' (including for missing
'j') and 'write.table(df)' has been improved for data frames
'df' with a large number of columns. (Thanks to Gabriel
Becker's PR#18500, PR#18503 and discussants, prompted by a
report from Toby Dylan Hocking on the R-devel mailing list.)
* The matrix multiply operator '%*%' is now an S3 generic,
belonging to new group generic 'matrixOps'. From Tomasz
Kalinowski's contribution in PR#18483.
* New function 'array2DF()' to convert arrays to data frames,
particularly useful for the list arrays created by
'tapply()'.
DATES and TIMES:
* On platforms where (non-UTC) datetimes before 1902 (or
before 1900 as with system functions on recent macOS) are
guessed by extrapolating time zones from 1902-2037, there is
a warning at the first use of extrapolation in a session.
(As all time zones post 2037 are extrapolation, we do not
warn on those.)
* (Platforms using '--with-internal-tzone', including Windows
and by default macOS). How years are printed in dates or
date-times can be controlled by environment variable
'R_PAD_YEARS_BY_ZERO'. The default remains to pad to 4
digits by zeroes, but setting value 'no' gives no padding
(as used by default by 'glibc').
* 'strftime()' tries harder to determine the offset for the
'"%z"' format, and succeeds on the mainstream R platforms.
* 'strftime()' has a limit of 2048 bytes on the string
produced - attempting to exceed this is an error.
(Previously it silently truncated at 255 bytes.)
* 'sessionInfo()' records (and by default prints) the system
time zone as part of the locale information. Also, the
source (system/internal) of the date-time conversion and
printing functions.
* Objects of class '"POSIXlt"' created in this version of R
always have 11 components: component 'zone' is always set,
and component 'gmtoff' is set for times in UTC and usually
set on the (almost all) platforms which have C-level
support, otherwise is 'NA'.
* There are comprehensive validity checks on the structure of
objects of class '"POSIXlt"' when converting (including
formatting and printing). (This avoids mis-conversions of
hand-crafted objects.)
* There is some support for using the native date-time
routines on macOS: this is only viable on recent versions
(e.g. 12.6 and 13) and does get wrong some historical
changes (before 1900, during WWII). Use of
'--with-internal-tzone' remains the default.
* 'as.POSIXct(<numeric>)' and 'as.POSIXlt(.)' (without
specifying 'origin') now work. So does
'as.Date(<numeric>)'.
* 'as.Date.POSIXct(., tz)' now treats several 'tz' values,
notably '"GMT"' as equivalent to '"UTC"', proposed and
improved by Michael Chirico and Joshua Ulrich in PR#17674.
* Experimental 'balancePOSIXlt()' utility allows using
"ragged" and or out-of-range '"POSIXlt"' objects more
correctly, e.g., in subsetting and subassignments. Such
objects are now documented.
More experimentally, a '"POSIXlt"' object may have an
attribute '"balanced"' indicating if it is known to be
filled or fully balanced.
* Functions 'axis.Date()' and 'axis.POSIXct()' are rewritten
to gain better default tick locations and better default
formats by using 'prettyDate()'. Thanks to Swetlana
Herbrandt.
* The mapping of Windows' names for time zones to IANA's
'Olson' names has been updated. When ICU is available (it
is by default), it is used to get a mapping for the current
region set in Windows. This can be overridden by setting
environment variable 'TZ' to the desired Olson name - see
'OlsonNames()' for those currently available.
GRAPHICS:
* The graphics engine version, 'R_GE_version', has been bumped
to '16' and so packages that provide graphics devices should
be reinstalled.
* The 'grDevices' and 'grid' packages have new functions for
rendering typeset glyphs, primarily:
'grDevices::glyphInfo()' and 'grid::grid.glyph()'.
Rendering of typeset glyphs is only supported so far on the
Cairo-based graphics devices and on the 'pdf()' and
'quartz()' devices.
* The defined behaviour for '"clear"' and '"source"'
compositing operators (via 'grid::grid.group()') has been
changed (to align better with simple interpretation of
original Porter-Duff definitions).
* Support for gradients, patterns, clipping paths, masks,
groups, compositing operators, and affine transformations
has been added to the 'quartz()' device.
INSTALLATION on a UNIX-ALIKE:
* A system installation of generic LAPACK 3.10.0 or later will
be preferred to the version in the R sources.
'configure' option '--with-lapack=no' (equivalently
'--without-lapack') forces compilation of the internal
LAPACK sources.
If '--with-lapack' is not specified, a system 'liblapack' is
looked for and used if it reports version 3.10.0 or later
and does not contain BLAS routines.
Packages using LAPACK will need to be reinstalled if this
changes to using an external library.
* On 'aarch64' Linux platforms using GCC, 'configure' now
defaults to '-fPIC' (instead of '-fpic'), as desired in
PR#18326.
* 'configure' now checks conversion of datetimes between
'POSIXlt' and 'POSIXct' around year 2020. Failure (which
has been seen on platforms missing 'tzdata') is fatal.
* If 'configure' option '--with-valgrind-instrumentation' is
given value '1' or '2', option
'--with-system-valgrind-headers' is now the default and
ignored (with a warning). It is highly recommended that the
system headers are installed alongside 'valgrind': they are
part of its packaging on some Linux distributions and
packaged separately (e.g. in the 'valgrind-devel' RPM) on
others. 'configure' will give a warning if they are not
found.
The system headers will be required in a future release of R
to build with 'valgrind' instrumentation.
* 'libcurl' 8.x is now accepted by 'configure': despite a
change in major version number it changes neither API nor
ABI.
INSTALLATION on WINDOWS:
* The makefiles and installer scripts for Windows have been
tailored to 'Rtools43', an update of the 'Rtools42'
toolchain. It is based on 'gcc' 12 and newer versions of
MinGW-W64, binutils and libraries. At this time R-devel can
still be built using Rtools42 without changes, but when
R-devel is installed via the installer, it will by default
look for Rtools43.
* Old make targets 'rsync-extsoft' and 32-bit ones that are no
longer needed have been removed.
* Default builds (including for packages) no longer select
C99. Thus the C standard used is the default for the
compiler, which for the toolchain in 'Rtools43' is C17.
(This is consistent with Unix builds.)
PACKAGE INSTALLATION:
* The default C++ standard has been changed to C++17 where
available (which it is on all currently checked platforms):
if not C++14 or C++11 is used if available otherwise C++ is
not supported.
* 'USE_FC_LEN_T' is the default: this uses the correct
(compiler-dependent) prototypes for Fortran BLAS/LAPACK
routines called from C/C++, and requires adjustment of many
such calls - see 'Writing R Extensions' <c2><a7>6.6.1.
* There is initial support for C++23 as several compilers are
now supporting '-std=c++23' or '-std=c++2b' or similar. As
for C++20, there no additional 'configure' checks for C++23
features beyond a check that the compiler reports a
'__cplusplus' value greater than that in the C++20 standard.
C++ feature tests should be used.
* There is support for a package to indicate the version of
the C standard which should be used to compile it, and for
the installing user to specify this. In most cases R
defaults to the C compiler's default standard which is C17
(a `bug-fix' of C11) - earlier versions of R or compilers
may have defaulted to C99.
Current options are:
USE_C17 Use a standard that is at most C17. The intention
is to allow legacy packages to still be installed when
later C standards become the default, including packages
using new keywords as identifiers or with K&R-style
function declarations. This will use C17 if available,
falling back to C11.
USE_C90 Use the C90 (aka C89) standard. (As that standard
did not require compilers to identify that version, all
we can verify is that the compiler does not claim to be
using a later standard. It may accept C99 features -
for example 'clang' accepts // to make comments.)
USE_C99 Use the C99 standard. This should be rarely needed -
it avoids the few new features of C11/C17 which can be
useful if a package assumes them if C17 is specified and
they are not implemented.
USE_C23 Use C23 (or in future, later). Compiler/library
support for C23 is still being implemented, but LLVM
clang from 15.0.0 and the upcoming GCC 13 have quite
extensive support.
These can be specified as part of the 'SystemRequirements'
field in the package's 'DESCRIPTION' file or _viaoptions
'--use-C17' and so on of 'R CMD INSTALL' and 'R CMD SHLIB'.
For further details see "Writing R Extensions" \
<c2><a7>1.2.5.
* (Windows) A 'src/Makefile.ucrt' or 'src/Makefile.win' file
is now included after 'R_HOME/etcR_ARCH/Makeconf' and so no
longer needs to include that file itself. Installation of a
package with such a file now uses a site 'Makevars' file in
the same way as a package with a 'src/Makevars.win' file
would.
* 'configure' is now passed crucial variables such as 'CC' and
'CFLAGS' in its environment, as many packages were not
setting them (as documented in 'Writing R Extensions' \
<c2><a7>1.2).
This has most effect where 'configure' is used to compile
parts of the package - most often by 'cmake' or 'libtool'
which obfuscate the actual compile commands used.
Also used for 'configure.win' and 'configure.ucrt' on
Windows.
FORTRAN FLAGS:
* The flag '-fno-optimize-sibling-calls' is no longer forced
for 'gfortran' 7 and later. It should no longer be needed
now using 'hidden' character-length arguments when calling
BLAS/LAPACK routines from C/C++ is the default even for
packages. (Unless perhaps packages call Fortran code from
C/C++ without using R's headers and without allowing for
these arguments.)
C-LEVEL FACILITIES:
* The deprecated S-compatibility macros 'DOUBLE_*' in
'R_ext/Constants.h' (included by 'R.h') have been removed.
* The deprecated legacy typedefs of 'Sint' and 'Sfloat' in
header 'R.h' are no longer defined, and that header no
longer includes header 'limits.h' from C nor 'climits' from
C++.
* New macro 'CAD5R()' is provided in 'Rinternals.h' and used
in a few places in the R sources.
* ALTREP now supports 'VECSXP' vectors. Contributed by Gabor
Csardi in PR#17620.
* The 'Rcomplex' definition (in header 'R_ext/Complex.h') has
been extended to prevent possible mis-compilation when
interfacing with Fortran (PR#18430). The new definition
causes compiler warnings with static initializers such as
'{1, 2}', which can be changed to '{.r=1, .i=2}'.
Using the new definition from C++ depends on compiler
extensions supporting C features that have not been
incorporated into the C++ standards but are available in
'g++' and 'clang++': this may result in C++ compiler
warnings but these have been worked around for recent
versions of common compilers (GCC, Apple/LLVM clang, Intel).
It is intended to change the inclusion of header
'R_ext/Complex.h' by other R headers, so C/C++ code files
which make use of 'Rcomplex' should include that header
explicitly.
UTILITIES:
* 'R CMD check' does more checking of package '.Rd' files,
warning about invalid email addresses and (some) invalid
URIs and noting empty '\item' labels in description lists.
* 'R CMD check' now also reports problems when reading package
news in md (file 'NEWS.md') and (optionally) plain text
(file 'NEWS') formats.
* '_R_CHECK_TIMINGS_' defaults to a value from the environment
even for 'R CMD check --as-cran'; this allows for
exceptionally fast or slow platforms.
It now applies to checking PDF and HTML versions of the
manuals, and 'checking CRAN incoming feasibility'.
* 'R CMD check' can optionally (but included in '--as-cran')
check whether HTML math rendering _viaKaTeX works for the
package '.Rd' files.
* Non-interactive debugger invocations can be trapped by
setting the environment variable
'_R_CHECK_BROWSER_NONINTERACTIVE_' to a true value. This is
enabled by 'R CMD check --as-cran' to detect the use of
leftover 'browser()' statements in the package.
* The use of 'sprintf' and 'vsprintf' from C/C++ has been
deprecated in macOS 13 and is a known security risk. 'R CMD
check' now reports (on all platforms) if their use is found
in compiled code: replace by 'snprintf' or 'vsnprintf'
respectively. [*NB:* whether such calls get compiled into
the package is platform-dependent.]
* Where recorded at installation, 'R CMD check' reports the C
and Fortran compilers used to build R.
It reports the OS in use (if known, as given by 'osVersion')
as well as that R was built for.
It notes if a C++ standard was specified which is older than
the current default: many packages have used C++11 to mean
'not C++98' - as C++11 is the minimum supported since R
4.0.0, that specification can probably be removed.
* 'R CMD INSTALL' reports the compilers (and on macOS, the
SDK) used, and this is copied to the output of 'R CMD
check'.
Where a C++ standard is specified, it is reported.
* 'R CMD check''s 'checking compilation flags in Makevars' has
been relaxed to accept the use of flags such as '-std=f2008'
in 'PKG_FFLAGS'.
* 'tools::buildVignettes()' has a new argument 'skip', which
is used by 'R CMD check' to skip (and note) vignettes with
unavailable '\VignetteDepends' (PR#18318).
* New generic '.AtNames()' added to enable class-specific
completions after '@'. The formerly internal function
'findMatches()' is now exported, mainly for use in methods
for '.DollarNames()' and '.AtNames()'.
DEPRECATED AND DEFUNCT:
* 'default.stringsAsFactors()' is defunct.
* Calling 'as.data.frame.<class>()' directly (for 12 atomic
classes) is going to be formally deprecated, currently
activated by setting the environment variable
'_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_' to non-empty,
which also happens in 'R CMD check --as-cran'.
BUG FIXES:
* Hashed 'environment's with sizes less than 5 can now grow.
(Reported to R-devel by Duncan Garmonsway.)
* 'as.character(<Rd>, deparse = TRUE)' failed to re-escape
curly braces in LaTeX-like text. (Reported by Hadley
Wickham in PR#18324.)
* 'library()' now passes its 'lib.loc' argument when requiring
'Depends' packages; reported (with fix) in PR#18331 by
Mikael Jagan.
* 'R CMD Stangle': improved message about 'Output' files.
* 'head(x, n)' and 'tail(x, n)' now signal an error if 'n' is
not numeric, instead of incidentally "working" sometimes
returning all of 'x'. Reported and discussed by Colin Fay,
in PR#18357.
* The '"lm"' method for 'summary()' now gives the correct
F-statistic when the model contains an offset. Reported in
PR#18008.
* 'C()' and '`contrasts<-`()' now preserve factor level names
when given a function object (as opposed a function name
which did preserve names). Reported in PR#17616.
* 'c(a = 1, 2)[[]]' no longer matches '2' but rather signals a
_classederror. Reported and analysed by Davis Vaughan in
PR#18367, a duplicate of PR#18004, by Jan Meis et al. For
consistency, 'NULL[[]]' is also erroneous now. 'x[[]] <- v'
gives an error of the same class '"MissingSubscriptError"'.
* The 'relist()' function of 'utils' now supports 'NULL'
elements in the skeleton (PR#15854).
* 'ordered(levels = *)' (missing 'x') now works analogously to
'factor(, ordered=TRUE)'; reported (with fix) by Achim
Zeileis in PR#18389.
* User-defined Rd macro definitions can now span multiple
lines, thanks to a patch from Duncan Murdoch. Previously,
the Rd parser silently ignored everything after the first
line.
* Plain-text help ('tools::Rd2txt()') now preserves an initial
blank line for text following description list items.
* 'tools::Rd2HTML()' and 'tools::Rd2latex()' no longer split
\arguments and \value lists at Rd comments.
* 'tools::Rd2latex()' now correctly handles optional text
outside \items of argument lists as well as bracketed text
at the beginning of sections, e.g., \value{[NULL]}.
* 'as.character(<POSIXt>)' now behaves more in line with the
methods for atomic vectors such as numbers, and is no longer
influenced by 'options()'. Ditto for
'as.character(<Date>)'. The 'as.character()' method gets
arguments 'digits' and 'OutDec' with defaults _not_
depending on 'options()'. Use of 'as.character(*, format =
.)' now warns.
* Similarly, the 'as.character.hexmode()' and '*.octmode()'
methods also behave as 'good citizen' methods and back
compatibility option 'keepStr = TRUE'.
* The 'as.POSIXlt(<POSIXlt>)' and 'as.POSIXct(<POSIXct>)'
default methods now do obey their 'tz' argument, also in
this case.
* 'as.POSIXlt(<Date>)' now does apply a 'tz' (time zone)
argument, as does 'as.POSIXct()'; partly suggested by Roland
Fu<c3><9f> on the R-devel mailing list.
* 'as.Date.POSIXlt(x)' now also works when the list components
are of unequal length, aka "partially filled" or \
"ragged".
* 'expand.model.frame()' looked up variables in the wrong
environment when applied to models fitted without 'data'.
Reported in PR#18414.
* 'time()' now (also) uses the 'ts.eps = getOption("ts.eps")'
argument and thus by default rounds values very close to the
start (or end) of a year. Based on a proposal by \
Andre<c3><af> V.
Kostyrka on R-help.
* Printing of a 'factanal()' result with just one factor and
'sort = TRUE' now works regularly, fixing PR#17863 by
Timothy Bates, thanks to the 'R Contributors' working group.
* Printing 0-length objects of class '"factor"', \
'"roman"',
'"hexmode"', '"octmode"', '"person"', \
'"bibentry"', or
'"citation"' now prints something better, one of which fixes
PR#18422, reported by Benjamin Feakins.
* 'Sys.timezone()' queries 'timedatectl' only if 'systemd' is
loaded; addressing a report by Jan Gorecki in PR#17421.
* The formula method of 'cor.test()' had scoping problems when
'environment(formula)' was not the calling environment;
reported with a patch proposal by Mao Kobayashi in PR#18439.
* 'attach()' of an environment with active bindings now
preserves the active bindings. Reported by Kevin Ushey in
PR#18425.
* BLAS detection now works also with system-provided libraries
not available as regular files. This fixes detection of the
Accelerate framework on macOS since Big Sur. Reported by
David Novgorodsky.
* 'download.file()' gives a helpful error message in case of
an invalid 'download.file.method' option, thanks to Colin
Fay's report in PR#18455.
* Sporadic crashes of 'Rterm' when using completion have been
fixed.
* 'Rprof()' is now more reliable. A livelock in thread
initialization with too short sampling interval has been
fixed on macOS. A deadlock in using the C runtime has been
fixed on Windows. A potential deadlock has been prevented
on Unix.
* Cursor placement in 'Rgui' now works even after a
fixed-width font is selected.
* Mandatory options ('options()') are now set on startup so
that saving and restoring them always works (PR#18372).
* Package installation, 'R CMD INSTALL' or
'install.packages(*)', now parses each of the '<pkg>/R/*.R'
files individually instead of first concatenating and then
'parse()'ing the large resulting file. This allows parser
or syntax errors to be diagnosed with correct file names and
line numbers, thanks to Simon Dedman's report and Bill
Dunlap's patch in PR#17859.
This _doesrequire syntactically self contained R source
files now, fixing another inadvertent bug.
* 'predict.lm(<model with offset>)' now finds the offset in
the correct environment, thanks to Andr<c3><a9> \
Gillibert's report
and patch in PR#18456.
* 'getInitial(<formula>)' now finds the 'selfStart' model in
the correct environment. (Reported by Ivan Krylov in
PR#18368.)
* Fix for possible segfault when using recently-added graphics
features, such as gradients, clipping paths, masks, and
groups with 'pdf(file=NULL)'.
* 'class(m) <- class(m)' no longer changes a matrix 'm' by
adding a class _attribute_.
* 'packageDate(pkg)' now only warns once if there is no 'pkg'.
* When 'ts()' creates a multivariate time series, '"mts"', it
also inherits from '"array"' now, and 'is.mts()' is
documented _andstricter.
* 'Rd2txt()' now preserves line breaks of \verb Rd content and
from duplicated \cr. The former also fixes the rendering of
verbatim output from Rd \Sexpr in plain-text help.
* 'uniroot(f, interval)' should no longer wrongly converge
_outsidethe interval in some cases where 'abs(f(x)) ==
Inf' for an 'x' at the interval boundary, thanks to posts by
Ben Bolker and Serguei Sokol on R-devel.
* Vectorized alpha handling in palette functions such as in
'gray()', 'rainbow()', or 'hcl.colors()' works correctly
now, thanks to Achim Zeileis' report and patch in PR#18476.
* Formatting and 'print()'ing of 'bibentry' objects has
dropped the deprecated 'citation.bibtex.max' argument, such
that the 'bibtex' argument's default for 'print.bibentry()'
depends directly on the 'citation.bibtex.max' option,
whereas in 'format.bibentry()' the option no longer applies.
* Attempting to use a character string naming a foreign
function entry point in a foreign function call in a package
will now signal an error if the packages has called
'R_forceSymbols' to specify that symbols must be used.
* An error in 'table()' could permanently set
'options(warn=2)' promoting all subsequent warnings to
errors.
* The 'sigma()' function gave misleading results for binary
GLMs. A new method for objects of class '"glm"' returns the
square root of the estimate of the dispersion parameter
using the same calculation as 'summary.glm()'.
* 'bs()' and 'ns()' in the (typical) case of automatic knot
construction, when some of the supposedly inner knots
coincide with boundary knots, now moves them inside (with a
warning), building on PR#18442 by Ben Bolker.
* 'R CMD' on Windows now skips the site profile with
'--no-site-file' and '--vanilla' even when 'R_PROFILE' is
set (PR#18512, from Kevin Ushey).
|
| 2023-12-24 16:17:38 by Thomas Klausner | Files touched by this commit (1) |
Log message: R: remove empty line from PLIST |
| 2023-12-24 15:59:32 by Jason Bacon | Files touched by this commit (1) |
Log message: math/R: Unbreak on Darwin Add missing timezones to PLIST.Darwin |
New packages: