Revisions of R-base
Detlef Steuer (dsteuer)
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- CHANGES IN R 4.4.0:
SIGNIFICANT USER-VISIBLE CHANGES:
* Startup banners, R --version, sessionInfo() and R CMD check no
longer report (64-bit) as part of the platform as this is almost
universal - the increasingly rare 32-bit platforms will still
report (32-bit).
On Windows, ditto for window titles.
* is.atomic(NULL) now returns FALSE, as NULL is not an atomic
vector. Strict back-compatibility would replace is.atomic(foo)
by (is.null(foo) || is.atomic(foo)) but should happen only
sparingly.
NEW FEATURES:
* The confint() methods for "glm" and "nls" objects have been
copied to the stats package. Previously, they were stubs which
called versions in package MASS. The MASS namespace is no longer
loaded if you invoke (say) confint(glmfit). Further, the "glm"
method for profile() and the plot() and pairs() methods for class
"profile" have been copied from MASS to stats. (profile.nls()
and plot.profile.nls() were already in stats.)
* The confint() and profile methods for "glm" objects have gained a
possibility to do profiling based on the Rao Score statistic in
addition to the default Likelihood Ratio. This is controlled by a
new test = argument.
* The pairs() method for "profile" objects has been extended with a
which = argument to allow plotting only a subset of the
parameters.
* The "glm" method for anova() computes test statistics and
p-values by default, using a chi-squared test or an F test
depending on whether the dispersion is fixed or free. Test
statistics can be suppressed by giving argument test a false
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- 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'e Pag`es 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,
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- 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:
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- 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
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Detlef Steuer (dsteuer)
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(revision 132)
- 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 NaNs, including R's
NA.)
* The parser now signals _classed_ errors, 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,
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(revision 129)
- CHANGES IN R 4.2.3:
C-LEVEL FACILITIES:
* The definition of DL_FUNC in R_ext/Rdynload.h has been changed to
be fully C-compliant. This means that functions loaded _via_ for
example R_GetCCallable need to be cast to an appropriate type if
they have any arguments.
* .Machine has a new element sizeof.time_t to identify old systems
with a 32-bit type and hence a limited range of date-times (and
limited support for dates millions of years from present).
PACKAGE INSTALLATION:
* (Windows) The default C++ standard had accidentally been left at
C++11 when it was changed to C++14 on Unix.
BUG FIXES:
* As "POSIXlt" objects may be "partially filled" and their list
components meant to be recycled, length() now is the length of
the longest component.
* as.POSIXlt.Date() could underflow for dates in the far past (more
than half a million years BCE).
* as.Date.POSIXlt(x) would return "1970-01-01" instead of NA in R
4.2.2, e.g., for
x <- as.POSIXlt(c("2019-01-30","2001-1-1"))
x$mon <- c(0L, NA); as.Date(x)
* R CMD check failed to apply enabled _R_CHECK_SUGGESTS_ONLY_ to
examples and vignettes (regression in R 4.2.0).
* R CMD check did not re-build vignettes in separate processes by
default (regression in R 4.2.0).
* Running examples from HTML documentation now restores previous
knitr settings and options (PR#18420).
* Quartz: fonts are now located using Core Graphics API instead of
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Detlef Steuer (dsteuer)
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Detlef Steuer (dsteuer)
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Detlef Steuer (dsteuer)
committed
(revision 127)
- CHANGES IN R 4.2.2:
NEW FEATURES:
* tools::Rdiff(useDiff = TRUE) checks for the presence of an
external diff command and switches to useDiff = FALSE if none is
found. This allows R CMD Rdiff to always work.
* On Windows, environment variable R_LIBCURL_SSL_REVOKE_BEST_EFFORT
can be used to switch to only 'best-effort' SSL certificate
revocation checks with the default "libcurl" download method.
This reduces security, but may be needed for downloads to work
with MITM proxies (PR#18379).
* (macOS) The run-time check for libraries from XQuartz for X11 and
Tcl/Tk no longer uses otool from the Apple Developer Tools
(PR#18400).
* The LaTeX style for producing the PDF manuals, Rd.sty, now loads
the standard amsmath, amsfonts and amssymb packages for greater
coverage of math commands in the Rd \eqn and \deqn macros. The
\mathscr LaTeX command is also provided (via the mathrsfs
package, if available, or the amsfonts bundle otherwise),
fulfilling the wish of PR#18398.
* (Windows) The default format of readClipboard() and
writeClipboard() has been changed to 13 (CF_UNICODETEXT).
INSTALLATION on a UNIX-ALIKE:
* The PDF manuals (if built) can be compacted by the new target
make compact-pdf (at the top level or in directory doc/manual).
* There is now configure support for LLVM clang 15 on Linux, which
defaults to position-independent (PIE) executables whereas
gfortran does not.
* Many small changes to ease compilation (and suppress warnings)
with LLVM clang 15.
BUG FIXES:
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Detlef Steuer (dsteuer)
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(revision 125)
- CHANGES IN R 4.2.1:
NEW FEATURES:
* New function utils::findCRANmirror() to find out if a CRAN mirror
has been selected, otherwise fallback to the main site. This
behaves in the same way as tools::CRAN_package_db() and is
intended for packages wishing to access CRAN for purposes other
than installing packages.
The need for this was shown by a day when the main CRAN website
was offline and a dozen or so packages which had its URL
hardcoded failed their checks.
INSTALLATION on a UNIX-ALIKE:
* The libraries searched for by --with-blas (without a value) now
include BLIS (after OpenBLAS but before ATLAS). And on macOS,
the Accelerate framework (after ATLAS). (This is patterned after
the AX_BLAS macro from the Autoconf Archive.)
* The included LAPACK sources have been updated to 3.10.1.
UTILITIES:
* The (full path to) the command tidy to be used for HTML
validation can be set by environment variable R_TIDYCMD.
* Setting environment variable _R_CHECK_RD_VALIDATE_RD2HTML_ to a
false value will override R CMD check --as-cran and turn off HTML
validation. This provides a way to circumvent a problematic
tidy.
The 2006 version that ships with macOS is always skipped.
C-LEVEL FACILITIES:
* The undocumented legacy declarations of Sint, Sfloat, SINT_MAX
and SINT_MIN in header R.h are deprecated.
BUG FIXES:
* fisher.test(d) no longer segfaults for "large" d; fixing PR#18336
by preventing/detecting an integer overflow reliably.
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Detlef Steuer (dsteuer)
(revision 124)
Detlef Steuer (dsteuer)
(revision 124)
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Detlef Steuer (dsteuer)
committed
(revision 123)
- CHANGES IN R 4.2.0:
SIGNIFICANT USER-VISIBLE CHANGES:
* The formula method of aggregate() now matches the generic in
naming its first argument x (resolving PR#18299 by Thomas
Soeiro).
This means that calling aggregate() with a formula as a named
first argument requires name formula in earlier versions of R and
name x now, so portable code should not name the argument (code
in many packages did).
* Calling && or || with either argument of length greater than one
now gives a warning (which it is intended will become an error).
* Calling if() or while() with a condition of length greater than
one gives an error rather than a warning. Consequently,
environment variable _R_CHECK_LENGTH_1_CONDITION_ no longer has
any effect.
* Windows users should consult the WINDOWS section below for some
profound changes including
* Support for 32-bit builds has been dropped.
* UTF-8 locales are used where available.
* The default locations for the R installation and personal
library folder have been changed.
Thanks to Tomas Kalibera for months of work on the Windows port
for this release.
NEW FEATURES:
* matrix(x, n, m) now warns in more cases where length(x) differs
from n * m, as suggested by Abby Spurdle and Wolfgang Huber in
Feb 2021 on the R-devel mailing list.
This warning can be turned into an error by setting environment
variable _R_CHECK_MATRIX_DATA_ to TRUE: R CMD check --as-cran
does so unless it is already set.
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Detlef Steuer (dsteuer)
(revision 122)
Detlef Steuer (dsteuer)
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Detlef Steuer (dsteuer)
committed
(revision 121)
- CHANGES IN R 4.1.3:
NEW FEATURES:
* The default version of Bioconductor has been changed to 3.14.
(This is used by setRepositories and the menus in GUIs.)
UTILITIES:
* R CMD check --as-cran has a workaround for a bug in versions of
file up to at least 5.41 which mis-identify DBF files last
changed in 2022 as executables.
C-LEVEL FACILITIES:
* The legacy S-compatibility macros SINGLE_* in R_ext/Constants.h
(included by R.h) are deprecated and will be removed in R 4.2.0.
BUG FIXES:
* Initialization of self-starting nls() models with initialization
functions following the pre-R-4.1.0 API (without the ...
argument) works again for now, with a deprecation warning.
* Fixed quoting of ~autodetect~ in Java setting defaults to avoid
inadvertent user lookup due to leading ~, reported in PR#18231 by
Harold Gutch.
* substr(., start, stop) <- v now treats _negative_ stop values
correctly. Reported with a patch in PR#18228 by Brodie Gaslam.
* Subscripting an array x without dimnames by a
length(dim(x))-column character matrix gave "random" non-sense,
now an error; reported in PR#18244 by Mikael Jagan.
* ...names() now matches names(list(...)) closely, fixing PR#18247.
* all.equal(*, scale = s) now works as intended when length(s) > 1,
partly thanks to Michael Chirico's PR#18272.
* print(x) for long vectors x now also works for named atomic
vectors or lists and prints the correct number when reaching the
getOption("max.print") limit; partly thanks to a report and
proposal by Hugh Parsonage to the R-devel list.
Displaying revisions 1 - 20 of 140
