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| Name: R-survival | Distribution: openSUSE Tumbleweed |
| Version: 3.6.4 | Vendor: openSUSE |
| Release: 50.1 | Build date: Fri Jun 14 10:20:44 2024 |
| Group: Unspecified | Build host: reproducible |
| Size: 8395214 | Source RPM: R-base-4.4.1-50.1.src.rpm |
| Packager: http://bugs.opensuse.org | |
| Url: http://www.r-project.org/ | |
| Summary: Package provides recommended R-survival | |
This packages provides R-survival, one of the recommended packages.
GPL-2.0-only OR GPL-3.0-only
* Fri Jun 14 2024 Detlef Steuer <detlef.steuer@gmx.de>
- CHANGES IN R 4.4.1:
C-LEVEL FACILITIES:
* Functions R_atof and R_strtod declared in header R_ext/Utils.h
are now documented in 'Writing R Extensions' and so formally part
of the API.
* The non-API entry points Rf_setSVector, Rf_StringFalse,
Rf_StringTrue and Rf_isBlankString have been added to those
reported by R CMD check.
* The new function Rf_allocLang is now available. This provides an
alternative to the idiom of calling Rf_allocList followed by
SET_TYPEOF.
UTILITIES:
* R CMD check now reports as warnings what gfortran calls 'Fortran
2018 deleted features', all of which have long been marked as
'obsolescent' and some of which were deleted in Fortran 2008 or
earlier. Fortran compilers are no longer required to support
these.
BUG FIXES:
* as.numeric(), scan(), type.convert() and other places which use
the internal C function R_strtod now require a _non-empty_ digit
sequence in a decimal or binary exponent. This aligns with the
C/POSIX standard for strtod and with ?NumericConstants.
* as.data.frame(m, make.names=NA) now works correctly for a matrix
m with NA's in row names.
* The error message from <POSIXlt>[["hour"]] and similar now
mentions *[[, "hour"]], as wished for in PR#17409 and proposed by
Michael Chirico.
* qbinom() and potentially qpois(), qnbinom(), no longer sometimes
fail accurate inversion (of pbinom(), etc), thanks to Christopher
Chang's report and patch in PR#18711.
* The internal help server on Windows can again serve requests sent
in quick succession, fixing a regression in R 4.4.0.
* debugcall(<S3Generic>()) now also works when a corresponding
S4-generic version is in the methods cache (PR#18143).
* Package tools' toTitleCase(ch0) now returns character(0) when ch0
is of zero length; fixing PR#18724, reported by David Hugh Jones.
* R CMD check is no longer broken (without a check result and no
explanation in 00check.log) for a package which declares an
invalid VignetteBuilder in DESCRIPTION but has no vignettes.
* Wed Apr 24 2024 Detlef Steuer <detlef.steuer@gmx.de>
- 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
logical value.
* In setRepositories() the repositories can be set using their
names via name = instead of index ind =.
* methods() and .S3methods() gain a all.names option for the (rare)
case where functions starting with a . should be included.
* Serializations can now be interrupted (e.g., by Ctrl-C on a
Unix-alike) if they take too long, e.g., from save.image(),
thanks to suggestions by Ivan Krylov and others on R-devel.
* New startup option --max-connections to set the maximum number of
simultaneous connections for the session. Defaults to 128 as
before: allowed values up to 4096 (but resource limits may in
practice restrict to smaller values).
* R on Windows (since Windows 10 2004) now uses the new Segment
Heap allocator. This may improve performance of some
memory-intensive applications.
* When R packages are built, typically by R CMD build <pkg>, the
new --user=<build_user> option overrides the (internally
determined) user name, currently Sys.info()["user"] or LOGNAME.
This is a (modified) fulfillment of Will Landau's suggestion in
PR#17530.
* tools::testInstalledBasic() gets new optional arguments outDir
and testSrcdir, e.g., allowing to use it in a <builddir> !=
<srcdir> setup, and in standard "binary" Windows installation
* if* a source tests/ folder is present.
* range(<DT_with_Inf>, finite = TRUE) now work for objects of class
"Date", "POSIXct", and "POSIXlt" with infinite entries,
analogously to range.default(), as proposed by Davis Vaughan on
R-devel. Other range()-methods can make use of new function
.rangeNum().
* New .internalGenerics object complementing .S3PrimitiveGenerics,
for documentation and low-level book-keeping.
* grid() now invisibly returns the x- and y- coordinates at which
the grid-lines were drawn.
* norm(., type) now also works for complex matrices.
* kappa(., exact = TRUE, norm = *) now works for all norms and also
for complex matrices. In symmetric / triangular cases, the new
argument uplo = "U" | "L" allows the upper or lower triangular
part to be specified.
* memDecompress(type = "unknown") recognizes compression in the
default 'zlib' format as used by memCompress(type = "gzip").
* memCompress() and memDecompress() will use the libdeflate library
(<https://github.com/ebiggers/libdeflate>) if installed. This
uses the same type of compression for type = "gzip" but is 1.5-2x
faster than the system libz library on some common platforms: the
speed-up may depend on the library version.
* diff() for objects of class "Date", "POSIXct", and "POSIXlt"
accepts a units argument passed via ....
* Dynamic help now does a much better job of rendering package
DESCRIPTION metadata.
* Rprof() gains an event argument and support for elapsed (real)
time profiling on Unix (PR#18076).
* filled.contour() gains a key.border argument.
* tools::update_pkg_po() gets arguments pot_make and mo_make for
_not_ re-making the corresponding files, and additionally a
verbose argument.
* Hexadecimal string colour specifications are now accepted in
short form, so, for example, we can use "#123", which is
equivalent to "#112233".
Thanks to MikeFC for the original idea and Ella Kaye, Malcolm
Barrett, George Stagg, and Hanne Oberman for the patch.
* Plain-text help shows \var markup by angle brackets.
* The new experimental primitive function declare() is intended to
eventually allow information about R code to be communicated to
the interpreter, compiler, and code analysis tools. The syntax
for declarations is still being developed.
* Functions psmirnov(), qsmirnov() and rsmirnov() in package stats
have had argument two.sided renamed to alternative, to take into
account that the permutation distributions of the one-sided
statistics can be different in the case of ties. Consequence of
PR#18582.
* sort() is now an implicit S4 generic in methods.
* Formatting and printing, format(z), print(z), of complex vectors
z no longer zap relatively small real or imaginary parts to zero,
fixing PR#16752. This is an API change, as it was documented
previously to round real and imaginary parts together on purpose,
producing nicer looking output. As mentioned, e.g. in the PR,
this change is compatible with many other "R-like" programming
environments.
We have simplified the internal code and now basically format the
real and imaginary parts independently of each other.
* New experimental functions Tailcall() and Exec() to support
writing stack-space-efficient recursive functions.
* Where characters are attempted to be plotted by pdf(),
postscript() and xfig() which are not in the selected 8-bit
character set (most often Latin-1) and the R session is using a
UTF-8 locale, the warning messages will show the UTF-8 character
rather than its bytes and one dot will be substituted per
character rather than per byte. (Platforms whose iconv() does
transliteration silently plot the transliteration.)
In a UTF-8 locale some transliterations are now done with a
warning (e.g., dashes and Unicode minus to hyphen, ligatures are
expanded, permille (‰) is replaced by o/oo), although the OS may
have got there first. These are warnings as they will continue
to be replaced by dots in earlier versions of R.
* The matrix multiplication functions crossprod() and tcrossprod()
are now also primitive and S3 generic, as %*% had become in R
4.3.0.
* source() and example() have a new optional argument catch.aborts
which allows continued evaluation of the R code after an error.
* The non-Quartz tiff() devices allow additional types of
compression if supported by the platform's libtiff library.
* The list of base and recommended package names is now provided by
tools::standard_package_names().
* cairo_pdf() and cairo_ps() default to onefile = TRUE to closer
match pdf() and postscript().
* New option catch.script.errors provides a documented way to catch
errors and then continue in non-interactive use.
* L %||% R newly in base is an expressive idiom for the phrases
if(!is.null(L)) L else R or if(is.null(L)) R else L.
* The return value from warnings() now always inherits from
"warnings" as documented, now also in the case of no warnings
where it previously returned NULL.
* as.complex("1i") now returns 0 + 1i instead of NA with a warning.
* z <- c(NA, 1i) now keeps the imaginary part Im(z[1]) == 0, no
longer coercing to NA_complex_. Similarly, cumsum(z) correctly
sums real and imaginary parts separately, i.e., without
"crosstalk" in case of NAs.
* On Alpine Linux iconv() now maps "latin2", "latin-2", "latin9"
and "latin-9" to encoding names the OS knows about
(case-insensitively).
* iconv(sub = "Unicode") now always zero-pads to four (hex) digits,
rather than to 4 or 8. (This seems to have become the convention
once Unicode restricted the number of Unicode points to 2^21 - 1
and so will never need more than 6 digits.)
* NCOL(NULL) now returns 0 instead of 1, for consistency with
cbind().
* The information for the Euro glyph missing from the Adobe .afm
files for the Courier, Helvetica and Times families has been
copied from their URW equivalents - this will improve vertical
centring in the pdf() and postscript() devices.
* The included BLAS sources have been updated to those shipped with
LAPACK version 3.12.0. The changes are almost entirely cosmetic.
* The included LAPACK sources have been updated to version 3.12.0
and some further double-complex routines added.
* There are new font families for the 2014--5 URW 2.0 fonts (see
?pdf) which are included in recent versions of Ghostscript.
These have font widths for most Greek glyphs and a few others
which were missing from the original versions (whose font
families remain available for reproducibility, although
Ghostscript-based viewers will render using the 2.0 versions).
* Improve the large-n efficiency of as.matrix(<dist>), thanks an R
contributors effort, notably by Tim Taylor and Heather Turner,
see PR#18660.
* The default and numeric methods of all.equal() get a check.class
option.
* zapsmall() gets new optional arguments, function mFUN and min.d,
for extra flexibility; fulfills a wish in PR#18199. Also, it is
now an implicit S4 generic in package methods.
* The Rd filter for aspell() gains an ignore argument.
* New generic function sort_by(), primarily useful for the
data.frame method which can be used to sort rows of a data frame
by one or more columns.
* The icence headers for the RPC code in src/extra/xdr have been
updated to use the GPL-compatible licence published by Oracle
America in 2010.
* New function pkg2HTML() in tools to create single-page HTML
reference manuals for R packages.
* The byte code evaluator now uses less C stack space for recursive
calls to byte-compiled functions. It also makes more of an effort
to avoid allocations for scalar return values.
* New completion option backtick (disabled by default) allows
non-syntactic completions to be wrapped in backquotes. This is
currently only useful for Jupyter notebooks via the IRkernel
package, and may cause problems for other backends.
INSTALLATION:
* The parser has been updated to work with bison 3.8.2, which is
now used for the pre-generated parsers in gram.c, file.c, and
gramRd.c. A few parser error messages have changed, which may
affect code that relies on exact messages.
INSTALLATION on a UNIX-ALIKE:
* System valgrind headers are now required to use configure option
- -with-valgrind-instrumentation with value 1 or 2.
* configure will warn if it encounters a 32-bit build, as that is
nowadays almost untested.
* Environment variable R_SYSTEM_ABI is no longer used and so no
longer recorded in etc/Renviron (it was not on Windows and was
only ever used when preparing package tools).
* If the libdeflate library and headers are available, libdeflate
rather than libz is used to (de)compress R objects in lazy-load
databases. Typically tasks spend up to 5% of their time on such
operations, although creating lazy-data databases is one of the
exceptions.
This can be suppressed if the library is available by the
configure option --without-libdeflate-compression.
* configure option --enable-lto=check has not worked reliably since
2019 and has been removed.
* The minimum autoconf requirement for a maintainer build has been
increased to autoconf 2.71.
It is intended to increase this to 2.72 for R 4.5.0: the
distributed configure file was generated using 2.72.
* The minimum version requirement for an external LAPACK has been
reduced to 3.9.0.
* No default C++ compiler is set if no C++17 compiler is detected:
there is no longer an automatic fallback to C++14 or C++11.
Compilers from the last five years should have sufficient
support: for others macros CXX and CXXSTD can be set in file
config.site to provide a fallback if needed.
The Objective-C++ compiler now by default uses the standard
selected by R for C++ (currently C++17) rather than the default
standard for the C++ compiler (which on macOS is still C++98).
INSTALLATION on macOS:
* A new configure option --with-newAccelerate makes use of Apple's
'new' BLAS / LAPACK interfaces in their Accelerate framework.
Those interfaces are only available in macOS 13.3 or later, and
building requires SDK 13.3 or later (from the Command Line Tools
or Xcode 14.3 or later).
By default the option uses new Accelerate for BLAS calls: to also
use it for LAPACK use option --with-newAccelerate=lapack. The
later interfaces provide LAPACK 3.9.1 rather than 3.2.1: 3.9.1 is
from 2021-04 and does not include the improved algorithms
introduced in LAPACK 3.10.0 (including for BLAS calls).
INSTALLATION on WINDOWS:
* The makefiles and installer scripts for Windows have been
tailored to Rtools44, an update of the Rtools43 toolchain. It is
based on GCC 13 and newer versions of MinGW-W64, binutils and
libraries (targeting 64-bit Intel CPUs). R-devel can no longer
be built using Rtools43 without changes.
* Rtools44 has experimental support for 64-bit ARM (aarch64) CPUs
_via_ the LLVM 17 toolchain using lld, clang/flang-new and
libc++.
UTILITIES:
* R CMD check notes when S4-style exports are used without
declaring a strong dependence on package methods.
* tools::checkRd() (used by R CMD check) detects more problems with
\Sexpr-based dynamic content, including bad nesting of \Sexprs
and invalid arguments.
* tools::checkRd() now reports Rd titles and section names ending
in a period; this is ignored by R CMD check unless environment
variable _R_CHECK_RD_CHECKRD_MINLEVEL_ is set to -5 or smaller.
* R CMD check now notes Rd files without an \alias, as long
documented in 'Writing R Extensions' §1.3.1. The check for a
missing \description has been moved from tools::checkRd() to
tools::checkRdContents().
* R CMD check now visits inst/NEWS.Rd and OS-specific man
subdirectories when checking Rd files.
* tools::checkDocFiles() and tools::checkRdContents() now also
check internal Rd files by default, but "specially" (ignoring
missing documentation of arguments).
* R CMD Rdiff gets option --useEx.
* R CMD check now warns on non-portable uses of Fortran KIND such
as INTEGER(KIND=4) and REAL(KIND=8).
To see the failing lines set environment variable
_R_CHECK_FORTRAN_KIND_DETAILS_ to a true value.
* When checking Rd files, R CMD check now notes some of the "lost
braces" that tools::checkRd() finds. Typical problems are Rd
macros missing the initial backslash (e.g., code{...}), in-text
set notation (e.g., {1, 2}, where the braces need escaping), and
\itemize lists with \describe-style entries of the form
\item{label}{description}.
* R CMD INSTALL (and hence check) will compile C++ code with
- DR_NO_REMAP if environment variable _R_CXX_USE_NO_REMAP_ is set
to a true value. It is planned that this will in future become
the default for compiling C++.
* The new built-in Rd macro \dontdiff{} can be used to mark example
code whose output should be ignored when comparing check output
to reference output (tests/Examples/<pkg>-Ex.Rout.save). The
\dontdiff tag, like \donttest, is _not_ shown on the rendered
help page, so provides a clean alternative to ##
IGNORE_RDIFF_(BEGIN|END) comments.
* R CMD build when there is no NAMESPACE, now uses the recommended
exportPattern("^[^.]"), instead of exporting everything.
* R CMD check now warns about non-ASCII characters in the NAMESPACE
file (in addition to R files). Such packages are not portable and
may fail to install on some platforms.
C-LEVEL FACILITIES:
* Headers R_ext/Applic.h and R-ext/Linpack.h used to include
R_ext/BLAS.h although this was undocumented and unneeded by their
documented entry points. They no longer do so.
* New function R_missing(), factored out from do_missing(), used to
fix PR#18579.
* SEXP type S4SXP has been renamed to OBJSXP to support
experimenting with alternative object systems. The S4SXP value
can still be used in C code but is now deprecated. Based on
contributions from the R Consortium's Object-Oriented Programming
Working Group.
* New function pow1p(x,y) for accurate (1+x)^y.
* mkCharLenCE was incorrectly documented to take a size_t length
but was implemented with int (and character strings in R are
limited to 2^31 - 1 bytes).
DEPRECATED AND DEFUNCT:
* data() no longer handles zipped data from long-defunct (since R
2.13.0) --use-zip-data installations.
* The legacy graphics devices pictex() and xfig() are now
deprecated. They do not support recent graphics enhancements and
their font handling is rudimentary. The intention is to retain
them for historical interest as long as they remain somewhat
functional.
* Support for encoding = "MacRoman" has been removed from the pdf()
and postscript() devices - this was a legacy encoding supporting
classic macOS up to 2001 and no longer has universal libiconv
support.
* is.R() is deprecated as no other S dialect is known to be in use
(and this could only identify historical dialects, not future
ones).
Further information on calls can be obtained by setting the
environment variable _R_DEPRECATED_IS_R_ to error which turns the
deprecation warning into an error and so by default gives a
traceback. (This is done by R CMD check --as-cran.)
* UseMethod() no longer forwards local variables assigned in the
generic function into method call environments before evaluating
the method body. This makes method calls behave more like
standard function calls and makes method code easier to analyze
correctly.
* The twelve as.data.frame.<class>() methods which were deprecated
only via _R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_ and in R CMD
check --as-cran are formally deprecated now in favour of calling
as.data.frame() or as.data.frame.vector(). The deprecation
"check" now works also when as.data.frame() is S4 generic thanks
to Ivan Krylov.
* The default method for the directional comparison operators <, >,
<=, and >= now signals an error when one of the operands is a
language object, i.e. a symbol or a call.
* For terms.formula(), deprecate abb and neg.out arguments
_formally_ in addition to just documenting it.
BUG FIXES:
* The methods package is more robust to not being attached to the
search path. More work needs to be done.
* pairwise.t.test() misbehaved when subgroups had 0 DF for
variance, even with pool.sd = TRUE. (PR#18594 by Jack Berry).
* Probability distribution functions [dpq]<distrib>(x, *), but also
bessel[IKJY](x, .) now consistently preserve attributes(x) when
length(x) == 0, e.g., for a 2 x 0 matrix, thanks to Karolis
Koncevičius' report PR#18509.
* Group "Summary" computations such as sum(1:3, 4, na.rm = 5, NA,
7, na.rm = LL) now give an error instead of either 17 or NN for
LL true or false, as proposed by Ivan Krylov on the R-devel
mailing list. (This also means it is now an error to specify
na.rm more than once.)
* as.complex(x) now returns complex(real = x, imaginary = 0) for
_all_ numerical and logical x, notably also for NA or
NA_integer_.
* Directories are now omitted by file.copy(, recursive = FALSE) and
in file.append() (PR#17337).
* gsub() and sub() are now more robust to integer overflow when
reporting errors caused by too large input strings (PR#18346).
* Top-level handlers are now more robust to attempts to remove a
handler whilst handlers are running (PR#18508).
* The handling of Alt+F4 in dialogs created on Windows using
GraphApp has been fixed (PR#13870).
* density() more consistently computes grid values for the
FFT-based convolution, following Robert Schlicht's analysis and
proposal in PR#18337, correcting density values typically by a
factor of about 0.999. Argument old.coords = TRUE provides back
compatibility.
* palette.colors() gains a name argument that defaults to FALSE
controlling whether the vector of colours that is returned has
names (where possible). PR#18529.
* tools::xgettext() no longer extracts the (non-translatable) class
names from warningCondition and errorCondition calls.
* S3method(<gen>, <class>, <func>) in the NAMESPACE file now works
(again) when <func> is visible from the namespace, e.g.,
imported, or in base.
* getParseData(f) now also works for a function defined in the
first of several <pkg>/R/*.R source files, thanks to Kirill
Müller's report and Duncan Murdoch's patch in PR#16756.
* Rd \Sexpr macros with nested #ifdef conditionals were not
processed.
* A non-blocking connection with non-default encoding (such as a
socket) now correctly returns from readLines() after new data has
arrived also when its EOF had been reached previously. Thanks to
Peter Meilstrup's report on R-devel and Ivan Krylov's report and
patch proposal in PR#18555.
* tools::checkRdContents() failed to detect empty argument
descriptions when they spanned multiple lines, including those
generated by prompt(). These cases are now noted by R CMD check.
* Plain-text help no longer outputs spurious colons in the
arguments list (for multi-line \item labels in the Rd source).
* kappa() and rcond() work correctly in more cases; kappa(., norm =
"2") now warns that it computes the 1-norm with (default) exact =
FALSE; prompted by Mikael Jagan's quite comprehensive PR#18543.
* Rd skeletons generated by prompt() or promptData() now use a
dummy title (so R CMD build works). tools::checkRdContents() has
been updated to detect such template leftovers, including from
promptPackage().
* When S4 method dispatch fails because no method was found, the
error message now includes the signature argument names; thanks
to Michael Chirico's proposal on the R-devel list.
* withAutoprint({ .. }) now preserves srcrefs previously lost,
thanks to Andrew Simmons' report plus fix in PR#18572.
* transform.data.frame() no longer adjusts names; in particular,
untransformed variables are kept as-is, including those with
syntactically invalid names (PR#17890).
* The keep.source option for Rd \Sexpr blocks is no longer ignored.
* The formula methods for t.test() and wilcox.test() now catch when
paired is passed, addressing PR#14359; use Pair(x1, x2) ~ 1 for a
paired test.
* The level reported in the browser prompt was often too large. It
now shows the number of browser contexts on the stack.
* For cbind() and rbind(), the optional deparse.level argument is
now properly passed to methods, thanks to Mikael Jagan's PR#18579
and comments there.
* Some error and warning messages for large ('long vector')
matrix(v, nr, nc) and dim(m) <- d are now correct about sizes,
using long long formatting, fixing PR#18612 (and more) reported
by Mikael Jagan.
* readChar(useBytes = TRUE) now terminates strings even when the
underlying connection uses extra spaces in the input buffer.
This fixes problems with extra garbage seen with gzip
connections, PR#18605.
* Named capture in PCRE regular expressions now works also with
more than 127 named groups (PR#18588).
* Datetime functions are now robust against long jumps when dealing
with internal time zone changes. This avoids confusing warnings
about an invalid time zone, previously triggered by turning
warnings into errors or handling them via tryCatch (PR#17966,
PR#17780).
* Datetime functions now restore even an empty TZ environment
variable after internal time zone changes (PR#17724). This makes
results of datetime functions with this (typically unintentional)
setting more predictable.
* drop.terms(*) now drops response as by default, keep.response =
FALSE, fixing PR#18564 thanks to Mikael Jagan.
* dummy.coef(.) now also works for lm()-models with character
categorical predictor variables rather than factor ones, fixing
PR#18635 reported by Jinsong Zhao.
* formals(f) <- formals(f) now also works for a function w/o
arguments and atomic _constant_ body(f).
* Correct as.function(<invalid list>, .)'s error message.
* removeSource() is yet more thorough in finding and removing
"srcref" and the other source references from parsed R language
chunks, fixing PR#18638 thanks to Andrew Simmons.
* dgeom() is more accurate now, notably when its result is very
small, fixing PR#18642 thanks to the proposal of Morten Welinder,
also improving other instances where C level binom_raw(x, n, ..)
has x == 0 or x== n.
* warning() with options(warn = 1) has improved output for
multi-line messages.
* axis.Date() and axis.POSIXct() now respect the par("lab") setting
for the number of pretty() intervals.
* Comparisons for language objects (which are based on deparsing)
are now more careful about using accurate deparsed results
(PR#18676).
* Plain-text help (Rd2txt) now correctly preserves blank lines
following single-line \dontrun code.
* <POSIXlt>[*] no longer sets wrong "balanced" attribute, fixing
PR#18681 thanks to Mikael Jagan.
* str(<classed-call>) now deparses the call as expected, fixing
PR#18684, reported by Dave Slager.
* In Rd examples, code following the closing brace of a \dontrun,
\dontshow or \donttest tag on the same line is no longer skipped
when R CMD check runs the examples.
* as.data.frame(matrix(*, ncol=0)) now gets valid names() and
colnames(); reported by Davis Vaughan on the R-devel list.
* Internal Mathlib function stirlerr(n) is now almost fully
(52-bit) accurate for all n >= ~5.9 and more accurate also in the
range 1 -- 5.9. This entails small ("after 12th decimal")
changes in density functions, e.g., dgamma() in _some_ regions of
their support. The fix was partly prompted by Morten Welinder's
PR#18640.
* Numbers like 9876543.2 are now considered non-integer by Mathlib
internal R_nonint(), amending original fix of PR#15734.
* Rd comment lines no longer cause broken paragraphs in the
rendered PDF and plain-text help. In code blocks, pure comment
lines (starting with %) no longer produce an empty line.
* xtabs(Freq ~ .) now consistently defaults to na.action = na.pass,
using na.rm = FALSE (added as an argument) when summing over Freq
(PR#17770).
* tools::testInstalledPackage() is no longer silent about failures
from running examples or tests and its return code no longer
ignores failures from checking vignettes.
* Thu Feb 29 2024 Detlef Steuer <detlef.steuer@gmx.de>
- 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,
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.
* Fri Nov 03 2023 Detlef Steuer <detlef.steuer@gmx.de>
- 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.
* Fri Jun 16 2023 Detlef Steuer <detlef.steuer@gmx.de>
- 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).
* Fri Apr 21 2023 Detlef Steuer <detlef.steuer@gmx.de>
- 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,
log = "y") now signal a _classed_ warning 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 0s.
* 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' SS6.6.1.
* 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 _via_ options --use-C17 and so
on of R CMD INSTALL and R CMD SHLIB.
For further details see "Writing R Extensions" SS1.2.5.
* (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' SS1.2).
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 _via_ KaTeX 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 environments 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
_classed_ error. 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 Fuss 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"i 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 _does_ require 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'e 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 _and_
stricter.
* 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 _outside_
the 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).
* Mon Apr 10 2023 Detlef Steuer <detlef.steuer@gmx.de>
- add patch to build with libcurl >= 8
* Wed Mar 15 2023 Detlef Steuer <detlef.steuer@gmx.de>
- 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
deprecated ATS which is no longer supported in the macOS 13 SDK
(PR#18426). This also addresses an issue where the currently
used font in the Quartz device context was not correctly
retained.
* (Windows) Math symbols in text drawing functions are again
rendered correctly (PR#18440). This fixes a regression in R
4.2.1 caused by a fix in PR#18382 which uncovered an issue in
GraphApp due to which the symbol charset was not used with TT
Symbol font face.
* (Windows) Installing a package with a src/Makefile.{win,ucrt}
file includes ~/.R/Makevars.win64 in the search for user
makevars, as documented in "R Installation and Administration"
and done for packages with a src/Makevars.{win,ucrt} file.
* format(<POSIXlt_w/_unbalanced_sec>, "....%OS<n>") with n > 0 no
longer accidentally uses the unbalanced seconds, thanks to
Suharto Anggono's report (including patch) in PR#18448.
* solve.default(a, b) works around issues with some versions of
LAPACK when a contains NA or NaN values.
* When UseMethod() cannot dispatch, it no longer segfaults
producing the error message in case of a long class(), thanks to
Joris Vankerschaver's report (including patch) in PR#18447.
* When example(foo, ..) produces graphics on an interactive device
it needs to open itself, it now leaves devAskNewPage() unchanged
even when it was FALSE, thus fixing a 14 years old '<FIXME>'.
* packageDescription() again catches errors from encoding
conversions. This also fixes broken packageVersion() in C locale
on systems where iconv does not support transliteration.
* Mon Oct 31 2022 Detlef Steuer <detlef.steuer@gmx.de>
- 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:
* Rscript -e would fail if stdin were closed (Reported by Henrik
Bengtsson.)
* qt(*, log.p=TRUE) in outer tails no longer produces NaN in its
final steps, thus fixing PR#18360.
* tools::Rd2latex() now escapes hashes and ampersands when writing
URLs, fixing LaTeX errors with such URLs in \tabular.
* When isGeneric(f, fdef=*) is used with mismatching names, the
warning is better understandable; reported (with fix) in PR#18370
by Gabe Becker.
* poly(x, n) now works again (and is now documented) when x is a
"Date" or "POSIXct" object, or of another class while fulfilling
mode(x) == "numeric". This also enables poly(x, *, raw=TRUE) for
such variables. Reported by Michael Chirico to R-devel.
* write.table(), write.csv() and write.csv2() restore their
numerical precision (internal equivalent of digits = 15) after an
interrupt (PR#18384).
* One can now read also byte FF from a clipboard connection
(PR#18385).
* source("") and source(character()) now give more helpful error
messages.
* R CMD check --as-cran set _R_CHECK_TIMINGS_ too late to have the
intended effect.
* as.POSIXlt(x) now also works with very large dates x, fixing
PR#18401 reported by Hannes M"uhleisen.
* Files can now be extracted even from very large zip archives
(PR#18390, thanks to Martin Jakt).
* Non-finite objects of class "POSIXlt" are now correctly coerced
to classes "Date" and "POSIXct"; following up on the extension to
format() them correctly.
* Added methods for is.finite(), is.infinite() and is.nan() for
"POSIXlt" date-time objects.
* Thu Jun 23 2022 Detlef Steuer <detlef.steuer@gmx.de>
- 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.
* tar(., files=*) now produces correctly the warning about invalid
uid or gid of files, fixing PR#18344, reported by Martin Morgan.
* tk_choose.files() with multi = FALSE misbehaved on paths
containing spaces (PR#18334) (regression introduced in R 4.0.0).
* sort(x, partial = ind, *) now works correctly notably for the
non-default na.last = FALSE or TRUE, fixing PR#18335 reported by
James Edwards.
* Environment variable _R_CHECK_XREFS_REPOSITORIES_ is only used
for checking .Rd cross-references in R CMD check (as documented)
and not for other uses looking for a CRAN mirror.
* The search for a CRAN mirror when checking packages now uses
getOption("repos") if that specifies a CRAN mirror, even when it
does not also specify all three Bioconductor repositories (as was
previously required).
* The HTML code generated by tools::Rd2HTML() has been improved to
pass tidy 5.8.0.
* Fri Apr 22 2022 Detlef Steuer <detlef.steuer@gmx.de>
- 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.
* Function file_test() in package utils gains tests for symlinks,
readability and writability.
* capabilities("libxml") is now false.
The description of capabilities("http/ftp") now reflects that it
refers to the default method, no longer the internal one.
* simplify2array() gains an except argument for controlling the
exceptions used by sapply().
* Environment variables R_LIBS_USER and R_LIBS_SITE are both now
set to the R system default if unset or empty, and can be set to
NULL to indicate an empty list of user or site library
directories.
* The warning for axis()(-like) calls in cases of relatively small
ranges (typically in log-scale situations) is slightly improved
_and_ suppressed from explicit calls to .axisPars() as has always
been the intention.
* The contrasts setter function `contrasts<-` gains an explicit
default how.many = NULL rather than just using missing(how.many).
* grid.pretty() gains a new optional argument n = 5.
* There is a new function .pretty() with option bounds as a
technical-utility version of pretty(). It and pretty() gain a
new argument f.min with a better than back-compatible default.
* Function grDevices::axisTicks() and related functions such as
graphics::axis() work better, notably for the log scale; partly
because of the pretty() improvements, but also because care is
taken e.g., when ylim is finite but diff(ylim) is infinite.
* nclass.FD() gains a digits option.
* The R Mathlib internal C function bd0() (called indirectly from a
dozen probability density and distribution functions such as
dpois(), dbinom(), dgamma(), pgamma() _etc_) has been
complemented by a more sophisticated and (mostly) more accurate C
function ebd0(), currently called only by internal dpois_raw()
improving accuracy for R level dpois() and potentially others
calling it such as dnbinom(), dgamma() or pgamma(). (Thanks to
Morten Welinder's PR#15628.)
* write.ftable() gains sep = " " argument as suggested by Thomas
Soeiro.
* The names of the locale categories supported by R's
Sys.getlocale() and Sys.setlocale() are now provided by variable
.LC.categories in the base namespace.
* The Date and POSIXt methods for hist() and the histogram method
for plot() now also use the new default col = "lightgray" in
consistency with the corresponding change to hist()'s default for
R 4.0.0.
* hist.default() gains new fuzz argument, and the histogram plot
method no longer uses fractional axis ticks when displaying
counts ("Frequency").
* mapply() and hence Map() now also obey the "max-or-0-if-any"
recycling rule, such that, e.g., Map(`+`, 1:3, 1[0]) is valid
now.
* as.character(<obj>) for "hexmode" or "octmode" objects now
fulfils the important basic rule as.character(x)[j] ===
as.character(x[j]).
* The set utility functions, notably intersect() have been tweaked
to be more consistent and symmetric in their two set arguments,
also preserving a common mode.
* substr(ch, start,end) <- new now e.g., preserves names(ch); ditto
for substring(), thanks to a patch from Brodie Gaslam.
* plot(<lm>) gains a extend.ylim.f argument, in partial response to
PR#15285; further PR#17784 is fixed thanks to several
contributors and a patch by Elin Waring. The Cook's dist
contours get customizable via cook.col and cook.lty with a
different default color and their legend is nicer by default and
customizable via cook.legendChanges.
* Attempting to subset an object that is not subsettable now
signals an error of class notSubsettableError. The
non-subsettable object is contained in the object field of the
error condition.
* Subscript-out-of-bounds errors are now signaled as errors of
class subscriptOutOfBoundsError.
* Stack-overflow errors are now signaled as errors inheriting from
class stackOverflowError. See ?stackOverflowError for more
details.
* New partly experimental Sys.setLanguage() utility, solving the
main problem of PR#18055.
* gettext() and gettextf() get a new option trim = TRUE which when
set to false allows translations for strings such as "Execution
halted\n" typical for C code.
* An experimental implementation of hash tables is now available.
See ?hashtab for more details.
* identical() gains a extptr.as.ref argument for requesting that
external pointer objects be compared as reference objects.
* reorder() gets an argument decreasing which it passes to sort()
for level creation; based on the wish and patch by Thomas Soeiro
in PR#18243.
* as.vector() gains a data.frame method which returns a simple
named list, also clearing a long standing 'FIXME' to enable
as.vector(<data.frame>, mode="list"). This breaks code relying
on as.vector(<data.frame>) to return the unchanged data frame.
* legend() is now vectorized for arguments cex, x.intersp, and
text.width. The latter can now also be specified as a vector
(one element for each column of the legend) or as NA for
computing a proper column wise maximum value of strwidth(legend).
The argument y.intersp can be specified as a vector with one
entry for each row of the legend.
legend() also gains new arguments title.cex and title.font.
Thanks to Swetlana Herbrandt.
* Deparsing no longer remaps attribute names dim, dimnames, levels,
names and tsp to historical S-compatible names (which structure()
maps back).
* sample() and sample.int() have additional sanity checks on their
size and n arguments.
all.equal.numeric() gains a sanity check on its tolerance
argument - calling all.equal(a, b, c) for three numeric vectors
is a surprisingly common error.
mean(na.rm =), rank(na.last =), barplot(legend.text =),
boxplot(), contour(drawlabels =), polygon(border =) and
methods::is(class2 =) have more robust sanity checks on their
arguments.
R CMD Rd2pdf (used by R CMD check) has a more robust sanity check
on the format of \alias{} commands.
* psigamma(x, deriv) for negative x now also works for deriv = 4
and 5; their underlying C level dpsifn() is documented in
'Writing R Extensions'.
* The HTML help system now uses HTML5 (wish of PR#18149).
* ks.test() now provides exact p-values also with ties and MC
p-values in the two-sample (Smirnov) case. By Torsten Hothorn.
* ks.test() gains a formula interface, with y ~ 1 for the
one-sample (Kolmogorov) test and y ~ group for the two-sample
(Smirnov) test. Contributed by Torsten Hothorn.
* The return value from ks.test() now has class c("ks.test",
"htest") - packages using try() need to take care to use
inherits() and not == on the class.
* New functions psmirnov(), qsmirnov() and rsmirnov() in package
stats implementing the asymptotic and exact distributions of the
two-sample Smirnov statistic.
* iconv() now allows sub = "c99" to use C99-style escapes for UTF-8
inputs which cannot be converted to encoding to.
* In a forward pipe |> expression it is now possible to use a named
argument with the placeholder _ in the rhs call to specify where
the lhs is to be inserted. The placeholder can only appear once
on the rhs.
* The included LAPACK sources have been updated to version 3.10.0,
except for the four Fortran 77 routines which 3.10.0 has
re-implemented in Fortran 90 (where the older versions have been
retained as the R build process does not support Fortran 90).
* path.expand() and most other uses of tilde expansion now warn if
a path would be too long if expanded. (An exception is
file.exists(), which silently returns false.)
* trunc(<Date>, *) now supports units = "months" or "years" for
consistency with the POSIXt method, thanks to Dirk Eddelbuettel's
proposal in PR#18099.
* list2DF() now checks that its arguments are of the same length,
rather than use recycling.
* The HTML help system has several new features: LaTeX-like math
can be typeset using either KaTeX or MathJax, usage and example
code is highlighted using Prism, and for dynamic help the output
of examples and demos can be shown within the browser if the
knitr package is installed. These features can be disabled by
setting the environment variable _R_HELP_ENABLE_ENHANCED_HTML_ to
a false value.
GRAPHICS:
* The graphics engine version, R_GE_version, has been bumped to 15
and so packages that provide graphics devices should be
reinstalled.
* The grid package now allows the user to specify a "vector" of
pattern fills. The fill argument to gpar() accepts a list of
gradients and/or patterns and the functions linearGradient(),
radialGradient(), and pattern() have a new group argument.
Points grobs (data symbols) can now also have a pattern fill.
The grobCoords() function now returns a more informative and
complex result.
* The grid package has new functions for drawing isolated groups:
grid.group(), grid.define(), and grid.use(). These functions add
compositing operators and affine transformations to R's graphics
capabilities.
The grid package also has new functions for stroking and filling
paths: grid.stroke(), grid.fill(), and grid.fillStroke().
A new function as.path() allows the user to specify the fill rule
for a path that is to be used for clipping, stroking, or filling;
available options are "winding" and "evenodd". A new function
as.mask() allows the user to specify the type of a mask;
available options are "alpha" and "luminance".
These new features are only supported so far (at most) on the
Cairo-based graphics devices and on the pdf() device.
* dev.capabilities() reports on device support for the new
features.
* par() now warns about unnamed non-character arguments to prevent
misuse such as {usr <- par("usr"); par(usr)}.
INSTALLATION:
* Facilities for accessing ftp:// sites are no longer tested
(except _pro tem_ for curlGetHeaders()) as modern browsers have
removed support.
* R can now be built with DEFS = -DSTRICT_R_HEADERS .
PACKAGE INSTALLATION:
* R CMD INSTALL no longer tangles vignettes. This completes an R
CMD build change in R 3.0.0 and affects packages built before R
3.0.2. Such packages should be re-made with R CMD build to have
the tangled R code of vignettes shipped with the tarball.
* USE_FC_LEN_T will become the default: this uses the correct
prototypes for Fortran BLAS/LAPACK routines called from C/C++,
and requires adjustment of most such calls - see 'Writing R
Extensions' SS6.6.2. (This has been supported since R 3.6.2.)
* Package installation speed for packages installed with
keep.source has been improved. This resolve the issue reported by
Ofek Shilon in PR#18236.
UTILITIES:
* R CMD check can optionally report files/directories left behind
in home, /tmp (even though TMPDIR is set) and other directories.
See the "R Internals" manual for details.
* R CMD check now reports byte-compilation errors during
installation. These are not usually fatal but may result in
parts of the package not being byte-compiled.
* _R_CHECK_DEPENDS_ONLY_ can be applied selectively to examples,
tests and/or vignettes in R CMD check: see the "R Internals"
manual.
* _R_CHECK_SRC_MINUS_W_IMPLICIT_ now defaults to true: recent
versions of Apple clang on macOS have made implicit function
declarations in C into a compilation error.
* R CMD check --as-cran makes use of the environment variable
AUTORECONF. See the "R Internals" manual SS8 for further details.
* R CMD check --use-valgrind also uses valgrind when re-building
vignettes as some non-Sweave vignettes unhelpfully comment out
all their code when R CMD check runs vignettes.
* Errors in re-building vignettes (unless there are LaTeX errors)
are reported by R CMD check as ERROR rather than WARNING when
running vignettes has been skipped (as it frequently is in CRAN
checks and by --as-cran).
* R CMD Rd2pdf gains a --quiet option that is used by R CMD build
when building the PDF package manual.
* R CMD Rd2pdf now always runs LaTeX in batch mode, consistent with
Texinfo >= 6.7. The --batch option is ignored.
* R CMD build and R CMD check now include the Rd file name and line
numbers in the error message of an \Sexpr evaluation failure.
* For packages using the \doi Rd macro (now an install-time \Sexpr)
but no other dynamic Rd content, R CMD build now produces a
smaller tarball and is considerably faster - skipping temporary
package installation.
C-LEVEL FACILITIES:
* The non-API header R_ext/R-ftp-http.h is no longer provided, as
the entry points it covered are now all defunct.
* A number of non-API declarations and macro definitions have been
moved from the installed header Rinternals.h to the internal
header Defn.h. Packages that only use entry points and
definitions documented to be part of the API as specified in
'Writing R Extensions' SS6 should not be affected.
* The macro USE_RINTERNALS no longer has any effect when compiling
package code. Packages which also use R_NO_REMAP will need to
ensure that the remapped names are used for calls to API
functions that were formerly also made available as macros.
* The deprecated legacy S-compatibility macros PROBLEM, MESSAGE,
ERROR, WARN, WARNING, RECOVER, ... are no longer defined in
R_exts/RS.h (included by R.h). Replace these by calls to
Rf_error and Rf_warning (defined in header R_ext/Error.h included
by R.h).
Header R_ext/RS.h no longer includes R_ext/Error.h.
* Header R_ext/Constants.h (included by R.h) when included from C++
now includes the C++ header cfloat rather than the C header
float.h (now possible as C++11 is required).
* The legacy S-compatibility macros DOUBLE_* in R_ext/Constants.h
(included by R.h) are deprecated.
* The deprecated S-compatibility macros SINGLE_* in
R_ext/Constants.h (included by R.h) have been removed.
* R_Calloc, R_Free and R_Realloc are preferred to their unprefixed
forms and error messages now use the prefix. These forms were
introduced in R 3.4.0 and are available even when
STRICT_R_HEADERS is defined.
* rmultinom has been documented in 'Writing R Extensions' SS6 so is
now part of the R API.
* Similarly, Rtanpi, called from R level tanpi() is now part of the
R API.
* The long-deprecated, undocumented and non-API entry point call_R
is no longer declared in R_ext/RS.h (included by R.h).
* The header S.h which has been unsupported since Jan 2016 has been
removed. Use R.h instead.
DEPRECATED AND DEFUNCT:
* The (non-default and deprecated) method = "internal" for
download.file() and url() no longer supports http:// nor ftp://
URIs. (It is used only for file:// URIs.)
On Windows, download.file(method = "wininet") no longer supports
ftp:// URIs. (It is no longer the default method, which is
"libcurl" and does.)
On Windows, the deprecated method = "wininet" now gives a warning
for http:// and https:// URIs for both download.file() and url().
(It is no longer the default method.)
* On Windows, the command-line option --max-mem-size and
environment variable R_MAX_MEM_SIZE are defunct. The memory
allocation limit was important for 32-bit builds, but these are
no longer supported.
* default.stringsAsFactors() is now formally deprecated, where that
was only mentioned on its regular help page, previously. So it
now gives a warning if called.
* unix.time() is defunct now; it had been deprecated since R 3.4.0.
BUG FIXES:
* Setting digits = 0 in format(), print.default() (and hence
typically print()) or options() is again invalid. Its behaviour
was platform-dependent, and it is unclear what "zero significant
digits" should mean (PR#18098).
* Messages from C code in the cairo section of package grDevices
are now also offered for translation, thanks to Michael Chirico's
PR#18123.
* mean(x) with finite x now is finite also without "long.double"
capability.
* R CMD Rd2pdf no longer leaves an empty build directory behind
when it aborts due to an already existing output file. (Thanks
to Sebastian Meyer's PR#18141.)
* density(x, weights = w, na.rm = TRUE) when anyNA(x) is true, now
removes weights "in parallel" to x, fixing PR#18151, reported by
Matthias Gondan. Additionally, it gets a subdensity option.
* Conversion of \Sexpr[]{<expR>} to LaTeX or HTML no longer
produces long blocks of empty lines when <expR> itself contains
several lines all producing empty output. Thanks to a report and
patch by Ivan Krylov posted to R-devel.
* R CMD build no longer fails if a package vignette uses child
documents and inst/doc exists. (Thanks to Sebastian Meyer's
PR#18156.)
* When an R documentation ('help' source) file man/foo.Rd in a
package has \donttest{..} examples with a syntax error, it is now
signalled as ERROR and with correct line numbers relating to the
* -Ex.R file, thanks to Duncan Murdoch and Sebastian Meyer's
reports and patch proposals in PR#17501.
* Improved determination of the correct translation domain in
non-base packages, addressing the combination of PR#18092 and
PR#17998 (#c6) with reports and _augmented_ patch #2904 by
Suharto Anggono.
Note that "R-base" is no longer the default domain e.g., for
top-level calls to gettext(); rather translation needs explicit
domain = * specification in such cases.
* identical(attrib.as.set=FALSE) now works correctly with data
frames with default row names (Thanks to Charlie Gao's PR#18179).
* txtProgressBar() now enforces a non-zero width for argument char,
without which no progress can be visible.
* dimnames(table(d)) is more consistent in the case where d is a
list with a single component, thanks to Thomas Soeiro's report to
R-devel.
Further, table(d1, d2) now gives an error when d1 and d2 are data
frames as suggested by Thomas in PR#18224.
* Fix for drawing semi-transparent lines and fills on the native
Windows graphics device (PR#18219 and PR#16694). Thanks to Nick
Ray for helpful diagnosis on Bugzilla.
* The deparser now wraps sub-expressions such as if(A) .. with
parentheses when needed; thanks to Duncan Murdoch's PR#18232 and
Lionel Henry's patches there.
* remove.packages() no longer tries to uninstall Priority: base
packages, thanks to a report and suggestions by Colin Fay in
PR#18227.
* win.metafile() now has xpinch and ypinch arguments so that the
user can override Windows' (potentially wrong) guess at device
dimensions.
* x[i] and x[[i]] for non-integer i should now behave in all cases
as always documented: the index used is equivalent to
as.integer(i) unless that would overflow where trunc(i) is used
instead; thanks to Suharto Anggono's report and patch proposals
in PR#17977.
* asOneSidedFormula() now associates the resulting formula with the
global environment rather than the evaluation environment created
for the call.
* <bibentry>$name now matches the field name case-insensitively,
consistent with bibentry() creation and the replacement method.
* cbind() failed to detect some length mismatches with a mixture of
time-series and non-time-series inputs.
* The default LaTeX style file Sweave.sty used by the RweaveLatex
driver no longer loads the obsolete ae package; thanks to a
report by Thomas Soeiro in PR#18271. Furthermore, it now skips
\usepackage[T1]{fontenc} for engines other than pdfTeX (if
detected) or if the new [nofontenc] option is used.
* smooth.spline() now stores its logical cv argument more safely,
fixing a rare bug when printing, and also stores n.
* smooth.spline(x,y,*) now computes the cv.crit statistic
correctly, also when is.unsorted(x), fixing PR#18294.
* The data.frame method of rbind() now warns when binding
not-wholly-recycling vectors, by analogy to the default method
(for matrices).
* setAs() finds the correct class for name to when multiple
packages define a class with that name. Thanks to Gabor Csardi
for the report.
* Fix for detaching a package when two classes of the same name are
present in method signatures for the same generic. Thanks to
Gabor Csardi for the report.
* match.arg("", c("", "a", "B")) gives a better error message, in
part from PR#17959, thanks to Elin Waring.
* R CMD Sweave --clean no longer removes pre-existing files or
subdirectories (PR#18242).
* The quartz() device no longer splits polylines into subpaths.
That has caused narrowly-spaced lines with many points to always
look solid even when dashed line type was used due to dash phase
restarts.
* Deparsing constructs such as quote(1 + `!`(2) + 3) works again as
before R 3.5.0, thanks to the report and patch in PR#18284 by
Suharto Anggono.
* as.list(f) for a factor f now keeps names(f), fixing PR#18309.
* qbeta(.001, .9, .009) and analogous qf() calls now return a
correct value instead of NaN or wrongly 1, all with a warning;
thanks to the report by Ludger Goeminne in PR#18302.
* plot.lm() failed to produce the plot of residuals vs. factor
levels (i.e., which=5 when leverages are constant) for models
with character predictors (PR#17840).
* interaction.plot(..., xtick = TRUE) misplaced the x-axis line
(PR#18305).
* Not strictly fixing a bug, format()ing and print()ing of
non-finite Date and POSIXt values NaN and +/-Inf no longer show
as NA but the respective string, e.g., Inf, for consistency with
numeric vector's behaviour, fulfilling the wish of PR#18308.
* R CMD check no longer runs test scripts generated from
corresponding .Rin files twice and now signals an ERROR if
processing an .Rin script fails.
* tools::Rd2txt() used for plain-text help pages now renders \hrefs
(if tools::Rd2txt_options(showURLs = TRUE)) and \urls with
percent-encoding and standards-compliant delimiting style (angle
brackets and no URL: prefix). \email is now rendered with a
mailto: prefix.
* Fri Mar 11 2022 Detlef Steuer <detlef.steuer@gmx.de>
- 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.
* all.equal(<selfStart>, *) no longer signals a deprecation
warning.
* reformulate(*, response=r) gives a helpful error message now when
length(r) > 1, thanks to Bill Dunlap's PR#18281.
* Modifying globalCallingHandlers inside withCallingHandlers() now
works or fails correctly, thanks to Henrik Bengtsson's PR#18257.
* hist(<Date>, breaks = "days") and hist(<POSIXt>, breaks = "secs")
no longer fail for inputs of length 1.
* qbeta(.001, .9, .009) and similar cases now converge correctly
thanks to Ben Bolker's report in PR#17746.
* window(x, start, end) no longer wrongly signals "'start' cannot
be after 'end'", fixing PR#17527 and PR#18291.
* data() now checks that its (rarely used) list argument is a
character vector - a couple of packages passed other types and
gave incorrect results.
* which() now checks its arr.ind argument is TRUE rather coercing
to logical and taking the first element - which gave incorrect
results in package code.
* model.weights() and model.offset() more carefully extract their
model components, thanks to Ben Bolker and Tim Taylor's R-devel
post.
* list.files(recursive = TRUE) now shows all broken symlinks
(previously, some of them may have been omitted, PR#18296).
* Mon Nov 01 2021 Detlef Steuer <detlef.steuer@gmx.de>
- CHANGES IN R 4.1.2:
C-LEVEL FACILITIES:
* The workaround in headers R.h and Rmath.h (using namespace std;)
for the Oracle Developer Studio compiler is no longer needed now
C++11 is required so has been removed. A couple more usages of
log() (which should have been std::log()) with an int argument
are reported on Solaris.
* The undocumented limit of 4095 bytes on messages from the
S-compatibility macros PROBLEM and MESSAGE is now documented and
longer messages will be silently truncated rather than
potentially causing segfaults.
* If the R_NO_SEGV_HANDLER environment variable is non-empty, the
signal handler for SEGV/ILL/BUS signals (which offers recovery
user interface) is not set. This allows more reliable debugging
of crashes that involve the console.
DEPRECATED AND DEFUNCT:
* The legacy S-compatibility macros PROBLEM, MESSAGE, ERROR, WARN,
WARNING, RECOVER, ... are deprecated and will be hidden in R
4.2.0. R's native interface of Rf_error and Rf_warning has long
been preferred.
BUG FIXES:
* .mapply(F, dots, .) no longer segfaults when dots is not a list
and uses match.fun(F) as always documented; reported by Andrew
Simmons in PR#18164.
* hist(<Date>, ...) and hist(<POSIXt>, ...) no longer pass
arguments for rect() (such as col and density) to axis().
(Thanks to Sebastian Meyer's PR#18171.)
* \Sexpr{ch} now preserves Encoding(ch). (Thanks to report and
patch by Jeroen Ooms in PR#18152.)
* Setting the RNG to "Marsaglia-Multicarry" e.g., by RNGkind(), now
warns in more places, thanks to Andr'e Gillibert's report and
patch in PR#18168.
* gray(numeric(), alpha=1/2) no longer segfaults, fixing PR#18183,
reported by Till Krenz.
* Fixed dnbinom(x, size=<very_small>, .., log=TRUE) regression,
reported by Martin Morgan.
* as.Date.POSIXlt(x) now keeps names(x), thanks to Davis Vaughan's
report and patch in PR#18188.
* model.response() now strips an "AsIs" class typically, thanks to
Duncan Murdoch's report and other discussants in PR#18190.
* try() is considerably faster in case of an error and long call,
as e.g., from some do.call(). Thanks to Alexander Kaever's
suggestion posted to R-devel.
* qqline(y = <object>) such as y=I(.), now works, see also
PR#18190.
* Non-integer mgp par() settings are now handled correctly in
axis() and mtext(), thanks to Mikael Jagan and Duncan Murdoch's
report and suggestion in PR#18194.
* formatC(x) returns length zero character() now, rather than ""
when x is of length zero, as documented, thanks to Davis
Vaughan's post to R-devel.
* removeSource(fn) now retains (other) attributes(fn).
* Mon Oct 25 2021 Detlef Steuer <detlef.steuer@gmx.de>
- repaired https://bugzilla.suse.com/show_bug.cgi?id=1191380
(rpmacros now go to rpmmacrodir)
- minor clean-ups in spec file
* Tue Aug 10 2021 Detlef Steuer <detlef.steuer@gmx.de>
- CHANGES IN R 4.1.1:
NEW FEATURES:
* require(pkg, quietly = TRUE) is quieter and in particular does
not warn if the package is not found.
DEPRECATED AND DEFUNCT:
* Use of ftp:// URIs should be regarded as deprecated, with
on-going support confined to method = "libcurl" and not routinely
tested. (Nowadays no major browser supports them.)
* The non-default method = "internal" is deprecated for http:// and
ftp:// URIs for both download.file and url.
* On Windows, method = "wininet" is deprecated for http://,
https:// and ftp:// URIs for both download.file and url. (A
warning is only given for ftp://.)
For ftp:// URIs the default method is now "libcurl" if available
(which it is on CRAN builds).
method = "wininet" remains the default for http:// and https://
URIs but if libcurl is available, using method = "libcurl" is
preferred.
INSTALLATION:
* make check now works also without a LaTeX installation. (Thanks
to Sebastian Meyer's PR#18103.)
BUG FIXES:
* make check-devel works again in an R build configured with
- -without-recommended-packages.
* qnbinom(p, size, mu) for large size/mu is correct now in a range
of cases (PR#18095); similarly for the (size, prob)
parametrization of the negative binomial. Also qpois() and
qbinom() are better and or faster for extreme cases. The
underlying C code has been modularized and is common to all four
cases of discrete distributions.
* gap.axis is now part of the axis() arguments which are passed
from bxp(), and hence boxplot(). (Thanks to Martin Smith's
report and suggestions in PR#18109.)
* .First and .Last can again be set from the site profile.
* seq.int(from, to, *) and seq.default(..) now work better in large
range cases where from-to is infinite where the two boundaries
are finite.
* all.equal(x,y) now returns TRUE correctly also when several
entries of abs(x) and abs(y) are close to .Machine$double.xmax,
the largest finite numeric.
* model.frame() now clears the object bit when removing the class
attribute of a value via na.action (PR#18100).
* charClass() now works with multi-character strings on Windows
(PR#18104, fixed by Bill Dunlap).
* encodeString() on Solaris now works again in Latin-1 encoding on
characters represented differently in UTF-8. Support for
surrogate pairs on Solaris has been improved.
* file.show() on Windows now works with non-ASCII path names
representable in the current native encoding (PR#18132).
* Embedded R on Windows can now find R home directory via the
registry even when installed only for the current user
(PR#18135).
* pretty(x) with finite x now returns finite values also in the
case where the extreme x values are close in size to the maximal
representable number .Machine$double.xmax.
Also, it's been tweaked for very small ranges and when a boundary
is close (or equal) to zero; e.g., pretty(c(0,1e-317)) no longer
has negative numbers, currently still warning about a very small
range, and pretty(2^-(1024 - 2^-1/(c(24,10)))) is more accurate.
* The error message for not finding vignette files when weaving has
correct file sizes now. (Thanks to Sebastian Meyer's PR#18154.)
* dnbinom(20, <large>, 1) now correctly gives 0, and similar cases
are more accurate with underflow precaution. (Reported by Francisco Vera Alcivar in PR#18072.)
* Fri Jun 04 2021 Detlef Steuer <detlef.steuer@gmx.de>
- The line %{__install} -m 755 -d %{_infodir}
no longer works in TW or Factory.
But without that line it works everywhere. So this instruction
was commented out of the spec file.
* Tue May 18 2021 Detlef Steuer <detlef.steuer@gmx.de>
- CHANGES IN R 4.1.0:
FUTURE DIRECTIONS:
* It is planned that the 4.1.x series will be the last to support
32-bit Windows, with production of binary packages for that
series continuing until early 2023.
SIGNIFICANT USER-VISIBLE CHANGES:
* Data set esoph in package datasets now provides the correct
numbers of controls; previously it had the numbers of cases added
to these. (Reported by Alexander Fowler in PR#17964.)
NEW FEATURES:
* www.omegahat.net is no longer one of the repositories known by
default to setRepositories(). (Nowadays it only provides source
packages and is often unavailable.)
* Function package_dependencies() (in package tools) can now use
different dependency types for direct and recursive dependencies.
* The checking of the size of tarball in R CMD check --as-cran
<pkg> may be tweaked via the new environment variable
_R_CHECK_CRAN_INCOMING_TARBALL_THRESHOLD_, as suggested in
PR#17777 by Jan Gorecki.
* Using c() to combine a factor with other factors now gives a
factor, an ordered factor when combining ordered factors with
identical levels.
* apply() gains a simplify argument to allow disabling of
simplification of results.
* The format() method for class "ftable" gets a new option justify.
(Suggested by Thomas Soeiro.)
* New ...names() utility. (Proposed by Neal Fultz in PR#17705.)
* type.convert() now warns when its as.is argument is not
specified, as the help file always said it _should_. In that
case, the default is changed to TRUE in line with its change in
read.table() (related to stringsAsFactor) in R 4.0.0.
* When printing list arrays, classed objects are now shown _via_
their format() value if this is a short enough character string,
or by giving the first elements of their class vector and their
length.
* capabilities() gets new entry "Rprof" which is TRUE when R has
been configured with the equivalent of --enable-R-profiling (as
it is by default). (Related to Michael Orlitzky's report
PR#17836.)
* str(xS4) now also shows extraneous attributes of an S4 object
xS4.
* Rudimentary support for vi-style tags in rtags() and R CMD rtags
has been added. (Based on a patch from Neal Fultz in PR#17214.)
* checkRdContents() is now exported from tools; it and also
checkDocFiles() have a new option chkInternal allowing to check
Rd files marked with keyword "internal" as well. The latter can
be activated for R CMD check via environment variable
_R_CHECK_RD_INTERNAL_TOO_.
* New functions numToBits() and numToInts() extend the raw
conversion utilities to (double precision) numeric.
* Functions URLencode() and URLdecode() in package utils now work
on vectors of URIs. (Based on patch from Bob Rudis submitted
with PR#17873.)
* path.expand() can expand ~user on most Unix-alikes even when
readline is not in use. It tries harder to expand ~, for example
should environment variable HOME be unset.
* For HTML help (both dynamic and static), Rd file links to help
pages in external packages are now treated as references to
topics rather than file names, and fall back to a file link only
if the topic is not found in the target package. The earlier rule
which prioritized file names over topics can be restored by
setting the environment variable _R_HELP_LINKS_TO_TOPICS_ to a
false value.
* c() now removes NULL arguments before dispatching to methods,
thus simplifying the implementation of c() methods, _but_ for
back compatibility keeps NULL when it is the first argument.
(From a report and patch proposal by Lionel Henry in PR#17900.)
* Vectorize()'s result function's environment no longer keeps
unneeded objects.
* Function ...elt() now propagates visibility consistently with
..n. (Thanks to Lionel Henry's PR#17905.)
* capture.output() no longer uses non-standard evaluation to
evaluate its arguments. This makes evaluation of functions like
parent.frame() more consistent. (Thanks to Lionel Henry's
PR#17907.)
* packBits(bits, type="double") now works as inverse of
numToBits(). (Thanks to Bill Dunlap's proposal in PR#17914.)
* curlGetHeaders() has two new arguments, timeout to specify the
timeout for that call (overriding getOption("timeout")) and TLS
to specify the minimum TLS protocol version to be used for
https:// URIs (_inter alia_ providing a means to check for sites
using deprecated TLS versions 1.0 and 1.1).
* For nls(), an optional constant scaleOffset may be added to the
denominator of the relative offset convergence test for cases
where the fit of a model is expected to be exact, thanks to a
proposal by John Nash. nls(*, trace=TRUE) now also shows the
convergence criterion.
* Numeric differentiation _via_ numericDeriv() gets new optional
arguments eps and central, the latter for taking central divided
differences. The latter can be activated for nls() via
nls.control(nDcentral = TRUE).
* nls() now passes the trace and control arguments to getInitial(),
notably for all self-starting models, so these can also be fit in
zero-noise situations via a scaleOffset. For this reason, the
initial function of a selfStart model must now have ... in its
argument list.
* bquote(splice = TRUE) can now splice expression vectors with
attributes: this makes it possible to splice the result of
parse(keep.source = TRUE). (Report and patch provided by Lionel
Henry in PR#17869.)
* textConnection() gets an optional name argument.
* get(), exists(), and get0() now signal an error if the first
argument has length greater than 1. Previously additional
elements were silently ignored. (Suggested by Antoine Fabri on
R-devel.)
* R now provides a shorthand notation for creating functions, e.g.
\(x) x + 1 is parsed as function(x) x + 1.
* R now provides a simple native forward pipe syntax |>. The
simple form of the forward pipe inserts the left-hand side as the
first argument in the right-hand side call. The pipe
implementation as a syntax transformation was motivated by
suggestions from Jim Hester and Lionel Henry.
* all.equal(f, g) for functions now by default also compares their
environment(.)s, notably via new all.equal method for class
function. Comparison of nls() fits, e.g., may now need
all.equal(m1, m2, check.environment = FALSE).
* .libPaths() gets a new option include.site, allowing to _not_
include the site library. (Thanks to Dario Strbenac's suggestion
and Gabe Becker's PR#18016.)
* Lithuanian translations are now available. (Thanks to Rimantas
Zakauskas.)
* names() now works for DOTSXP objects. On the other hand, in
R-lang, the R language manual, we now warn against relying on the
structure or even existence of such dot-dot-dot objects.
* all.equal() no longer gives an error on DOTSXP objects.
* capabilities("cairo") now applies only to the file-based devices
as it is now possible (if very unusual) to build R with Cairo
support for those but not for X11().
* There is optional support for tracing the progress of
loadNamespace() - see its help.
* (Not Windows.) l10n_info() reports an additional element, the
name of the encoding as reported by the OS (which may differ from
the encoding part (if any) of the result from
Sys.getlocale("LC_CTYPE").
* New function gregexec() which generalizes regexec() to find _all_
disjoint matches and well as all substrings corresponding to
parenthesized subexpressions of the given regular expression.
(Contributed by Brodie Gaslam.)
* New function charClass() in package utils to query the
wide-character classification functions in use (such as
iswprint).
* The names of quantile()'s result no longer depend on the global
getOption("digits"), but quantile() gets a new optional argument
digits = 7 instead.
* grep(), sub(), regexp and variants work considerably faster for
long factors with few levels. (Thanks to Michael Chirico's
PR#18063.)
* Provide grouping of x11() graphics windows within a window
manager such as Gnome or Unity; thanks to a patch by Ivan Krylov
posted to R-devel.
* The split() method for class data.frame now allows the f argument
to be specified as a formula.
* sprintf now warns on arguments unused by the format string.
* New palettes "Rocket" and "Mako" for hcl.colors() (approximating
palettes of the same name from the 'viridisLite' package).
Contributed by Achim Zeileis.
* The base environment and its namespace are now locked (so one can
no longer add bindings to these or remove from these).
* Rterm handling of multi-byte characters has been improved,
allowing use of such characters when supported by the current
locale.
* Rterm now accepts ALT+ +xxxxxxxx sequences to enter Unicode
characters as hex digits.
* Environment variable LC_ALL on Windows now takes precedence over
LC_CTYPE and variables for other supported categories, matching
the POSIX behaviour.
* duplicated() and anyDuplicated() are now optimized for integer
and real vectors that are known to be sorted via the ALTREP
framework. Contributed by Gabriel Becker via PR#17993.
GRAPHICS:
* The graphics engine version, R_GE_version, has been bumped to 14
and so packages that provide graphics devices should be
reinstalled.
* Graphics devices should now specify deviceVersion to indicate
what version of the graphics engine they support.
* Graphics devices can now specify deviceClip. If TRUE, the
graphics engine will never perform any clipping of output itself.
The clipping that the graphics engine does perform (for both
canClip = TRUE and canClip = FALSE) has been improved to avoid
producing unnecessary artifacts in clipped output.
* The grid package now allows gpar(fill) to be a linearGradient(),
a radialGradient(), or a pattern(). The viewport(clip) can now
also be a grob, which defines a clipping path, and there is a new
viewport(mask) that can also be a grob, which defines a mask.
These new features are only supported so far on the Cairo-based
graphics devices and on the pdf() device.
* (Not Windows.) A warning is given when a Cairo-based type is
specified for a png(), jpeg(), tiff() or bmp() device but Cairo
is unsupported (so type = "Xlib" is tried instead).
* grSoftVersion() now reports the versions of FreeType and
FontConfig if they are used directly (not _via_ Pango), as is
most commonly done on macOS.
C-LEVEL FACILITIES:
* The _standalone_ libRmath math library and R's C API now provide
log1pexp() again as documented, and gain log1mexp().
INSTALLATION on a UNIX-ALIKE:
* configure checks for a program pkgconf if program pkg-config is
not found. These are now only looked for on the path (like
almost all other programs) so if needed specify a full path to
the command in PKG_CONFIG, for example in file config.site.
* C99 function iswblank is required - it was last seen missing ca
2003 so the workaround has been removed.
* There are new configure options --with-internal-iswxxxxx,
- -with-internal-towlower and --with-internal-wcwidth which allows
the system functions for wide-character classification,
case-switching and width (wcwidth and wcswidth) to be replaced by
internal ones. The first has long been used on macOS, AIX (and
Windows) but this enables it to be unselected there and selected
for other platforms (it is the new default on Solaris). The
second is new in this version of R and is selected by default on
macOS and Solaris. The third has long been the default and
remains so as it contains customizations for East Asian
languages.
System versions of these functions are often minimally
implemented (sometimes only for ASCII characters) and may not
cover the full range of Unicode points: for example Solaris (and
Windows) only cover the Basic Multilingual Plane.
* Cairo installations without X11 are more likely to be detected by
configure, when the file-based Cairo graphics devices will be
available but not X11(type = "cairo").
* There is a new configure option --with-static-cairo which is the
default on macOS. This should be used when only static cairo
(and where relevant, Pango) libraries are available.
* Cairo-based graphics devices on platforms without Pango but with
FreeType/FontConfig will make use of the latter for font
selection.
LINK-TIME OPTIMIZATION on a UNIX-ALIKE:
* Configuring with flag --enable-lto=R now also uses LTO when
installing the recommended packages.
* R CMD INSTALL and R CMD SHLIB have a new flag --use-LTO to use
LTO when compiling code, for use with R configured with
- -enable-lto=R. For R configured with --enable-lto, they have
the new flag --no-use-LTO.
Packages can opt in or out of LTO compilation _via_ a UseLTO
field in the DESCRIPTION file. (As usual this can be overridden
by the command-line flags.)
BUILDING R on Windows:
* for GCC >= 8, FC_LEN_T is defined in config.h and hence character
lengths are passed from C to Fortran in _inter alia_ BLAS and
LAPACK calls.
* There is a new text file src/gnuwin32/README.compilation, which
outlines how C/Fortran code compilation is organized and
documents new features:
* R can be built with Link-Time Optimization with a suitable
compiler - doing so with GCC 9.2 showed several
inconsistencies which have been corrected.
* There is support for cross-compiling the C and Fortran code
in R and standard packages on suitable (Linux) platforms.
This is mainly intended to allow developers to test later
versions of compilers - for example using GCC 9.2 or 10.x has
detected issues that GCC 8.3 in Rtools40 does not.
* There is experimental support for cross-building R packages
with C, C++ and/or Fortran code.
* The R installer can now be optionally built to support a single
architecture (only 64-bit or only 32-bit).
PACKAGE INSTALLATION:
* The default C++ standard has been changed to C++14 where
available (which it is on all currently checked platforms): if
not (as before) C++11 is used if available otherwise C++ is not
supported.
Packages which specify C++11 will still be installed using C++11.
C++14 compilers may give deprecation warnings, most often for
std::random_shuffle (deprecated in C++14 and removed in C++17).
Either specify C++11 (see 'Writing R Extensions') or modernize
the code and if needed specify C++14. The latter has been
supported since R 3.4.0 so the package's DESCRIPTION would need
to include something like
Depends: R (>= 3.4)
PACKAGE INSTALLATION on Windows:
* R CMD INSTALL and R CMD SHLIB make use of their flag --use-LTO
when the LTO_OPT make macro is set in file etc/${R_ARCH}/Makeconf
or in a personal/site Makevars file. (For details see 'Writing R
Extensions' SS4.5.)
This provides a valuable check on code consistency. It does work
with GCC 8.3 as in Rtools40, but that does not detect everything
the CRAN checks with current GCC do.
PACKAGE INSTALLATION on macOS:
* The default personal library directory on builds with
- -enable-aqua (including CRAN builds) now differs by CPU type,
one of
~/Library/R/x86_64/x.y/library
~/Library/R/arm64/x.y/library
This uses the CPU type R (and hence the packages) were built for,
so when a x86_64 build of R is run under Rosetta emulation on an
arm64 Mac, the first is used.
UTILITIES:
* R CMD check can now scan package functions for bogus return
statements, which were possibly intended as return() calls (wish
of PR#17180, patch by Sebastian Meyer). This check can be
activated via the new environment variable
_R_CHECK_BOGUS_RETURN_, true for --as-cran.
* R CMD build omits tarballs and binaries of previous builds from
the top-level package directory. (PR#17828, patch by Sebastian
Meyer.)
* R CMD check now runs sanity checks on the use of LazyData, for
example that a data directory is present and that
LazyDataCompression is not specified without LazyData and has a
documented value. For packages with large LazyData databases
without specifying LazyDataCompression, there is a reference to
the code given in 'Writing R Extensions' SS1.1.6 to test the
choice of compression (as in all the CRAN packages tested a
non-default method was preferred).
* R CMD build removes LazyData and LazyDataCompression fields from
the DESCRIPTION file of packages without a data directory.
ENCODING-RELATED CHANGES:
* The parser now treats \Unnnnnnnn escapes larger than the upper
limit for Unicode points (\U10FFFF) as an error as they cannot be
represented by valid UTF-8.
Where such escapes are used for outputting non-printable
(including unassigned) characters, 6 hex digits are used (rather
than 8 with leading zeros). For clarity, braces are used, for
example \U{0effff}.
* The parser now looks for non-ASCII spaces on Solaris (as
previously on most other OSes).
* There are warnings (including from the parser) on the use of
unpaired surrogate Unicode points such as \uD834. (These cannot
be converted to valid UTF-8.)
* Functions nchar(), tolower(), toupper() and chartr() and those
using regular expressions have more support for inputs with a
marked Latin-1 encoding.
* The character-classification functions used (by default) to
replace the system iswxxxxx functions on Windows, macOS and AIX
have been updated to Unicode 13.0.0.
The character-width tables have been updated to include new
assignments in Unicode 13.0.0.
* The code for evaluating default (extended) regular expressions
now uses the same character-classification functions as the rest
of R (previously they differed on Windows, macOS and AIX).
* There is a build-time option to replace the system's
wide-character wctrans C function by tables shipped with R: use
configure option --with-internal-towlower or (on Windows)
- DUSE_RI18N_CASE in CFLAGS when building R. This may be needed
to allow tolower() and toupper() to work with Unicode characters
beyond the Basic Multilingual Plane where not supported by system
functions (e.g. on Solaris where it is the new default).
* R is more careful when truncating UTF-8 and other multi-byte
strings that are too long to be printed, passed to the system or
libraries or placed into an internal buffer. Truncation will no
longer produce incomplete multibyte characters.
DEPRECATED AND DEFUNCT:
* Function plclust() from the package stats and
package.dependencies(), pkgDepends(), getDepList(),
installFoundDepends(), and vignetteDepends() from package tools
are defunct.
* Defunct functions checkNEWS() and readNEWS() from package tools
and CRAN.packages() from utils have been removed.
* R CMD config CXXCPP is defunct (it was deprecated in R 3.6.2).
* parallel::detectCores() drops support for Irix (retired in 2013).
* The LINPACK argument to chol.default(), chol2inv(),
solve.default() and svd() has been defunct since R 3.1.0. It was
silently ignored up to R 4.0.3 but now gives an error.
* Subsetting/indexing, such as ddd[*] or ddd$x on a DOTSXP
(dot-dot-dot) object ddd has been disabled; it worked by accident
only and was undocumented.
BUG FIXES:
* Many more C-level allocations (mainly by malloc and strdup) are
checked for success with suitable alternative actions.
* Bug fix for replayPlot(); this was turning off graphics engine
display list recording if a recorded plot was replayed in the
same session. The impact of the bug became visible if resize the
device after replay OR if attempted another savePlot() after
replay (empty display list means empty screen on resize or empty
saved plot).
* R CMD check etc now warn when a package exports non-existing S4
classes or methods, also in case of no "methods" presence.
(Reported by Alex Bertram; reproducible example and patch by
Sebastian Meyer in PR#16662.)
* boxplot() now also accepts calls for labels such as ylab, the
same as plot(). (Reported by Marius Hofert.)
* The help page for xtabs() now correctly states that addNA is
setting na.action = na.pass among others. (Reported as PR#17770
by Thomas Soeiro.)
* The R CMD check <pkg> gives a longer and more comprehensible
message when DESCRIPTION misses dependencies, e.g., in Imports:.
(Thanks to the contributors of PR#17179.)
* update.default() now calls the generic update() on the formula to
work correctly for models with extended formulas. (As reported
and suggested by Neal Fultz in PR#17865.)
* The horizontal position of leaves in a dendrogram is now correct
also with center = FALSE. (PR#14938, patch from Sebastian
Meyer.)
* all.equal.POSIXt() no longer warns about and subsequently ignores
inconsistent "tzone" attributes, but describes the difference in
its return value (PR#17277). This check can be disabled _via_
the new argument check.tzone = FALSE as suggested by Sebastian
Meyer.
* as.POSIXct() now populates the "tzone" attribute from its tz
argument when x is a logical vector consisting entirely of NA
values.
* x[[2^31]] <- v now works. (Thanks to the report and patch by
Suharto Anggono in PR#17330.)
* In log-scale graphics, axis() ticks and label positions are now
computed more carefully and symmetrically in their range,
typically providing _more_ ticks, fulfilling wishes in PR#17936.
The change really corresponds to an improved axisTicks() (package
grDevices), potentially influencing grid and lattice, for
example.
* qnorm(<very large negative>, log.p=TRUE) is now correct to at
least five digits where it was catastrophically wrong,
previously.
* sum(df) and similar "Summary"- and "Math"-group member functions
now work for data frames df with logical columns, notably also of
zero rows. (Reported to R-devel by Martin "b706".)
* unsplit() had trouble with tibbles due to unsound use of rep(NA,
len)-indexing, which should use NA_integer_ (Reported to R-devel
by Mario Annau.)
* pnorm(x, log.p = TRUE) underflows to -Inf slightly later.
* show(<hidden S4 generic>) prints better and without quotes for
non-hidden S4 generics.
* read.table() and relatives treated an "NA" column name as missing
when check.names = FALSE PR#18007.
* Parsing strings containing UTF-16 surrogate pairs such as
"\uD834\uDD1E" works better on some (uncommon) platforms.
sprintf("%X", utf8ToInt("\uD834\uDD1E")) should now give "1D11E"
on all platforms.
* identical(x,y) is no longer true for differing DOTSXP objects,
fixing PR#18032.
* str() now works correctly for DOTSXP and related exotics, even
when these are doomed.
Additionally, it no longer fails for lists with a class and
"irregular" method definitions such that e.g. lapply(*) will
necessarily fail, as currently for different igraph objects.
* Too long lines in environment files (e.g. Renviron) no longer
crash R. This limit has been increased to 100,000 bytes.
(PR#18001.)
* There is a further workaround for FreeType giving incorrect
italic font faces with cairo-based graphics devices on macOS.
* add_datalist(*, force = TRUE) (from package tools) now actually
updates an existing data/datalist file for new content. (Thanks
to a report and patch by Sebastian Meyer in PR#18048.)
* cut.Date() and cut.POSIXt() could produce an empty last interval
for breaks = "months" or breaks = "years". (Reported as PR#18053
by Christopher Carbone.)
* Detection of the encoding of 'regular' macOS locales such as
en_US (which is UTF-8) had been broken by a macOS change:
fortunately these are now rarely used with en_US.UTF-8 being
preferred.
* sub() and gsub(pattern, repl, x, *) now keep attributes of x such
as names() also when pattern is NA (PR#18079).
* Time differences ("difftime" objects) get a replacement and a
rep() method to keep "units" consistent. (Thanks to a report and
patch by Nicolas Bennett in PR#18066.)
* The \RdOpts macro, setting defaults for \Sexpr options in an Rd
file, had been ineffective since R 2.12.0: it now works again.
(Thanks to a report and patch by Sebastian Meyer in PR#18073.)
* mclapply and pvec no longer accidentally terminate parallel
processes started before by mcparallel or related calls in
package parallel (PR#18078).
* grep and other functions for evaluating (extended) regular
expressions handle in Unicode also strings not explicitly flagged
UTF-8, but flagged native when running in UTF-8 locale.
* Fixed a crash in fifo implementation on Windows (PR#18031).
* Binary mode in fifo on Windows is now properly detected from
argument open (PR#15600, PR#18031).
* Tue May 18 2021 Detlef Steuer <detlef.steuer@gmx.de>
- improved spec file according to comments of dimstar in
https://build.opensuse.org/request/show/892685
* Thu May 06 2021 Detlef Steuer <detlef.steuer@gmx.de>
- To get in sync with d:l:R:autoCRAN the Matrix package's split
in -devel was reversed.
* Wed Mar 31 2021 Detlef Steuer <detlef.steuer@gmx.de>
- CHANGES IN R 4.0.5:
BUG FIXES:
* The change to the internal table in R 4.0.4 for iswprint has been
reverted: it contained some errors in printability of 'East
Asian' characters.
* For packages using LazyData, R CMD build ignored the
- -resave-data option and the BuildResaveData field of the
DESCRIPTION file (in R versions 4.0.0 to 4.0.4).
* Mon Feb 15 2021 Detlef Steuer <detlef.steuer@gmx.de>
- CHANGES IN R 4.0.4:
NEW FEATURES:
* File share/texmf/tex/latex/jss.cls has been updated to work with
LaTeX versions since Oct 2020.
* Unicode character width tables (as used by nchar(, type = "w"))
have been updated to Unicode 12.1 by Brodie Gaslam (PR#17781),
including many emoji.
* The internal table for iswprint (used on Windows, macOS and AIX)
has been updated to include many recent Unicode characters.
INSTALLATION on a UNIX-ALIKE:
* If an external BLAS is specified by --with-blas=foo or _via_
environment variable BLAS_LIBS is not found, this is now a
configuration error. The previous behaviour was not clear from
the documentation: it was to continue the search as if
- -with-blas=yes was specified.
BUG FIXES:
* all.equal(x,y) now "sees" the two different NAs in factors,
thanks to Bill Dunlap and others in PR#17897.
* (~ NULL)[1] and similar formula subsetting now works, thanks to a
report and patch by Henrik Bengtsson in PR#17935. Additionally,
subsetting leaving an empty formula now works too, thanks to
suggestions by Suharto Anggono.
* .traceback(n) keeps source references again, as before R 4.0.0,
fixing a regression; introduced by the PR#17580, reported
including two patch proposals by Brodie Gaslam.
* unlist(plst, recursive=FALSE) no longer drops content for
pairlists with list components, thanks to the report and patch by
Suharto Anggono in PR#17950.
* iconvlist() now also works on MUSL based (Linux) systems, from a
report and patch suggestion by Wesley Chan in PR#17970.
* round() and signif() no longer tolerate wrong argument names,
notably in 1-argument calls; reported by Shane Mueller on R-devel
(mailing list); later reported as PR#17976.
* .Machine has longdouble.* elements only if
capabilities("long.double") is true, as documented. (Previously
they were included if the platform had long double identical to
double, as ARM does.)
* p.adjust(numeric(), n=0) now works, fixing PR#18002.
* identical(x,y) no longer prints "Unknown Type .." for typeof(x)
== "..." objects.
* Fix (auto-)print()ing of named complex vectors, see PR#17868 and
PR#18019.
* all.equal(<language>, <...>) now works, fixing PR#18029.
* as.data.frame.list(L, row.names=NULL) now behaves in line with
data.frame(), disregarding names of components of L, fixing
PR#18034, reported by Kevin Tappe.
* checkRdaFiles(ff)$version is now correct also when ff contains
files of different versions, thanks to a report and patch from
Sebastian Meyer in PR#18041.
* macOS: Quartz device live drawing could fail (no plot is shown)
if the system changes the drawing context after view update
(often the case since macOS Big Sur). System log may show
"CGContextDelegateCreateForContext: invalid context" error.
/usr/lib/R/library/survival /usr/lib/R/library/survival/CITATION /usr/lib/R/library/survival/COPYRIGHTS /usr/lib/R/library/survival/DESCRIPTION /usr/lib/R/library/survival/INDEX /usr/lib/R/library/survival/Meta /usr/lib/R/library/survival/Meta/Rd.rds /usr/lib/R/library/survival/Meta/data.rds /usr/lib/R/library/survival/Meta/features.rds /usr/lib/R/library/survival/Meta/hsearch.rds /usr/lib/R/library/survival/Meta/links.rds /usr/lib/R/library/survival/Meta/nsInfo.rds /usr/lib/R/library/survival/Meta/package.rds /usr/lib/R/library/survival/Meta/vignette.rds /usr/lib/R/library/survival/NAMESPACE /usr/lib/R/library/survival/NEWS.Rd /usr/lib/R/library/survival/R /usr/lib/R/library/survival/R/survival /usr/lib/R/library/survival/R/survival.rdb /usr/lib/R/library/survival/R/survival.rdx /usr/lib/R/library/survival/data /usr/lib/R/library/survival/data/Rdata.rdb /usr/lib/R/library/survival/data/Rdata.rds /usr/lib/R/library/survival/data/Rdata.rdx /usr/lib/R/library/survival/doc /usr/lib/R/library/survival/doc/adjcurve.R /usr/lib/R/library/survival/doc/adjcurve.Rnw /usr/lib/R/library/survival/doc/adjcurve.pdf /usr/lib/R/library/survival/doc/approximate.R /usr/lib/R/library/survival/doc/approximate.Rnw /usr/lib/R/library/survival/doc/approximate.pdf /usr/lib/R/library/survival/doc/compete.R /usr/lib/R/library/survival/doc/compete.Rnw /usr/lib/R/library/survival/doc/compete.pdf /usr/lib/R/library/survival/doc/concordance.R /usr/lib/R/library/survival/doc/concordance.Rnw /usr/lib/R/library/survival/doc/concordance.pdf /usr/lib/R/library/survival/doc/index.html /usr/lib/R/library/survival/doc/matrix.R /usr/lib/R/library/survival/doc/matrix.Rnw /usr/lib/R/library/survival/doc/matrix.pdf /usr/lib/R/library/survival/doc/methods.R /usr/lib/R/library/survival/doc/methods.Rnw /usr/lib/R/library/survival/doc/methods.pdf /usr/lib/R/library/survival/doc/multi.Rnw /usr/lib/R/library/survival/doc/multi.pdf /usr/lib/R/library/survival/doc/other.Rnw /usr/lib/R/library/survival/doc/other.pdf /usr/lib/R/library/survival/doc/population.R /usr/lib/R/library/survival/doc/population.Rnw /usr/lib/R/library/survival/doc/population.pdf /usr/lib/R/library/survival/doc/redistribute.R /usr/lib/R/library/survival/doc/redistribute.Rnw /usr/lib/R/library/survival/doc/redistribute.pdf /usr/lib/R/library/survival/doc/splines.R /usr/lib/R/library/survival/doc/splines.Rnw /usr/lib/R/library/survival/doc/splines.pdf /usr/lib/R/library/survival/doc/survival.R /usr/lib/R/library/survival/doc/survival.Rnw /usr/lib/R/library/survival/doc/survival.pdf /usr/lib/R/library/survival/doc/tiedtimes.R /usr/lib/R/library/survival/doc/tiedtimes.Rnw /usr/lib/R/library/survival/doc/tiedtimes.pdf /usr/lib/R/library/survival/doc/timedep.R /usr/lib/R/library/survival/doc/timedep.Rnw /usr/lib/R/library/survival/doc/timedep.pdf /usr/lib/R/library/survival/doc/validate.R /usr/lib/R/library/survival/doc/validate.Rnw /usr/lib/R/library/survival/doc/validate.pdf /usr/lib/R/library/survival/help /usr/lib/R/library/survival/help/AnIndex /usr/lib/R/library/survival/help/aliases.rds /usr/lib/R/library/survival/help/figures /usr/lib/R/library/survival/help/figures/logo.png /usr/lib/R/library/survival/help/paths.rds /usr/lib/R/library/survival/help/survival.rdb /usr/lib/R/library/survival/help/survival.rdx /usr/lib/R/library/survival/html /usr/lib/R/library/survival/html/00Index.html /usr/lib/R/library/survival/html/R.css /usr/lib/R/library/survival/libs /usr/lib/R/library/survival/libs/survival.so
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Fabrice Bellet, Fri Oct 4 01:02:02 2024