NEWS | R Documentation |
R News
CHANGES IN R-devel
SIGNIFICANT USER-VISIBLE CHANGES
.
NEW FEATURES
-
as.integer(rl)
and henceas.raw(rl)
now work for alist
ofraw(1)
elements, as proposed by Michael Chirico's PR#18696. -
graphics'
grid()
gains optional argumentnintLog
. New functions
check_package_urls()
andcheck_package_dois()
in package tools for checking URLs and DOIs in package sources.New
head()
andtail()
methods for class"ts"
time series, proposed by Spencer Graves on R-devel.New
qr.influence()
function, a “bare bones” interface to thelm.influence()
leave-one-out diagnostics computations; wished for in PR#18739.Package
citation()
results auto-generated from the package metadata now also provide package DOIs for CRAN and Bioconductor packages.New function
grepv()
identical togrep()
except with the defaultvalue = TRUE
.-
methods(<pkg>:::<genfun>)
now does report methods when neither the generic nor the methods have been exported. -
pdf()
gains anauthor
argument to set the corresponding metadata field, and logical argumentstimestamp
andproducer
to optionally omit the respective metadata. (Thanks to Edzer Pebesma.) -
grDevices::glyphInfo()
gainsrot
argument to allow per-glyph rotation. (Thanks to Daniel Sabanes Bove.) Package tools now exports functions
CRAN_current_db()
,CRAN_aliases_db()
,CRAN_rdxrefs_db()
,CRAN_archive_db()
, andCRAN_authors_db()
.Package tools now exports functions
R()
andparse_URI_reference()
.Package tools now exports functions
base_aliases_db()
andbase_rdxrefs_db()
.It is now possible to set the background color for row and column names in the data editor on Windows (
Rgui
).-
Rterm
on Windows now accepts input lines of unlimited length. -
file.info()
on Windows now provides file owner name and domain. -
Sys.info()
on Windows now provides current user domain. -
findInterval()
gets new optionscheckSorted
andcheckNA
which allow to skip relatively costly checks; related to PR#16567. -
pnorm(x)
underflows more gracefully. -
get(nam, env)
now signals a classed error,"getMissingError"
, as “subclass” of"missingArgError"
where the latter is used also in similar situations, e.g.,f <- function(x) exp(x); try(f())
. The set operations now avoid the
as.vector()
transformation for same-kind apparently vector-like operands.-
md5sum()
can be used to compute an MD5 hash of a raw vector of bytes by using thebytes=
argument instead offiles=
. The two arguments are mutually exclusive. Added function
sha256sum()
in package tools analogous tomd5sum()
implementing the SHA-256 hashing algorithm.
INSTALLATION on a UNIX-ALIKE
The minimum
autoconf
requirement for a maintainer build has been increased toautoconf
2.72.Building the HTML (and Info) versions of the R manuals now requires
texi2any
from Texinfo 6.1 or later.Failures in building the manuals under ‘doc’ now abort the installation, removing any file which caused the failure.
DEPRECATED AND DEFUNCT
-
is.R()
is defunct. Environment variable _R_DEPRECATED_IS_R_ no longer has any effect. Deprecated (for more than 9 years!) functions
linearizeMlist
,listFromMlist
, andshowMlist
and the"MethodsList"
class for S4 method handling were removed from package methods. Deprecated functionsbalanceMethodsList
,emptyMethodsList
,inheritedSubMethodLists
,insertMethod
,insertMethodInEmptyList
,makeMethodsList
,mergeMethods
,MethodsList
,MethodsListSelect
, andSignatureMethod
were made defunct, as were the"MethodsList"
branches of functionsassignMethodsMetaData
,finalDefaultMethod
, andMethodAddCoerce
.
INSTALLATION
Control of symbol visibility is now supported on macOS (the previous check only worked on ELF platforms).
PACKAGE INSTALLATION
.
C-LEVEL FACILITIES
The non-API and hidden entry points
Rf_setIVector
,Rf_setRVector
andRf_setSVector
have been removed.The internal code for changing the parent of an environment now signals an error if the new parent is not an environment or if the change would create a cycle in the parent chain.
The ‘Writing R Extensions’ Texinfo source now contains very experimental annotations for more clearly identifying the API status of C entry points. These annotations are used to produce indices for API, experimental API, and embedded API entry points in the rendered versions. This is very preliminary and may be dropped if a better approach emerges.
-
SET_TYPEOF
now signals an error unless the old and new types have compatible memory structure and content. Use ofSET_TYPE
in package C code should be avoided and may be deprecated in the near future. It is better to allocate an object of the proper type in the first place. New API function
R_mkClosure
. This checks that its arguments are valid and should be used instead ofallocSExp(CLOSXP
followed bySET_FORMALS
,SET_BODY
, andSET_CLOENV
.New API functions
R_ClosureFormals
,R_ClosureBody
, andR_ClosureEnv
for extracting closure components. The existing functionsR_ClosureExpr
andR_BytecodeExpr
have also been added to the API.New API function
R_ParentEnv
.Some non-API entry points have been added to those reported by
R CMD check
:COMPLEX0
,ddfind
,DDVAL
,ENSURE_NAMEDMAX
,ENVFLAGS
,FRAME
,HASHTAB
,INTERNAL
,IS_ASCII
,IS_UTF8
,LEVELS
,NAMED
,PRSEEN
,RDEBUG
,REAL0
,Rf_findVarInFrame3
,SET_BODY
,SET_CLOENV
,SET_FORMALS
,SET_PRSEEN
,SET_RDEBUG
,STRING_PTR
,SYMVALUE
, andVECTOR_PTR
. Any declarations for these in public header files will be removed in the near future, and they will be hidden where possible.-
‘Writing R Extensions’ has a new section ‘Moving into C API compliance’ to help package authors move away from using non-API endpoints. This section will continue to be updated as work on clarifying and tightening the C API continues.
Some ‘NOTE’s for use of non-API entry points have been upgraded to ‘WARNING’s in preparation for removing declarations and, where possible, hiding these entry points.
The set of LAPACK (double and complex) routines in API headers ‘R_ext/Lapack.h’ and ‘R_ext/Applic.h’ has been extended, mostly to routines actually in use from packages.
Additional non-API entry points added to those reported by
R CMD check
:IS_LONG_VEC
,PRCODE
,PRENV
,PRVALUE
,R_nchar
,Rf_NonNullStringMatch
,R_shallow_duplicate_attr
,Rf_StringBlank
,SET_TYPEOF
,TRUELENGTH
,XLENGTH_EX
, andXTRUELENGTH
.Memory allocation messages now use the (non-standard notation)
"Mb"
,"Gb"
, ..., and"Mbytes"
strings as arguments instead of as part of the (translatable format) string. This is one step for PR#18297; from Henrik Bengtsson.Header ‘R_ext/Constants.h’ (included by ‘R.h’) now includes header ‘float.h’ or ‘cfloat’ for constants such as
DBL_MAX
even if ‘STRICT_R_HEADERS’ is defined.It is intended that ‘STRICT_R_HEADERS’ will become the default prior to release. This will remove the legacy definitions of
PI
,Calloc
,Realloc
andFree
: useM_PI
,R_Calloc
,R_Realloc
orR_Free
instead.The deprecated S-compatibility macros
F77_COM
andF77_COMDECL
have been removed from header ‘R_ext/RS.h’.
UTILITIES
-
R CMD check --as-cran
will compile C++ code with-DR_NO_REMAP
. -
R CMD check --as-cran
notes bad parts in the ‘DESCRIPTION’ file's URL fields. Installation will define
STRICT_R_HEADERS
if environment variable _R_USE_STRICT_R_HEADERS_ is set to a true value: this is done byR CMD check --as-cran
.-
R CMD check
now reports more warnings on long-deprecated/obsolete Fortran features fromgfortran -Wall
. For hints on how to modernize these, see https://fortranwiki.org/fortran/show/Modernizing+Old+Fortran.
BUG FIXES
Auto-generated
citation()
entries no longer include (additional) URLs in the ‘note’ field (PR#18547).-
as.data.frame.list()
gets a new optionnew.names
and now preservesNA
names, thus fixing theformat()
method for data frames, and also bug PR#18745. Relatedly, theformat()
method gets an optioncut.names
. -
stem()
formats correctly also in cases where rounding up, e.g., from 9.96 to 10 needs more digits; thanks to Ella Kaye and Kelly Bodwin, fixing PR#8934 during ‘R Dev Day’ at useR!2024.Additionally,
stem(x)
now works normally also whenlength(x) == 1
. -
tools'
toTitleCase()
now works better, fixing PR#18674, thanks to Shannon Pileggi, Sarah Zeller, Reiko Okamoto, and Hugo Gruson's ‘R Dev Day’ effort. Printing matrices (typically with many rows and or columns) now also omits columns when desirable according to option
max.print
, or argumentmax
, respectively. This is primarily the work of Lorena Abad, Ekaterina Akimova, Hanne Oberman, Abhishek Ulayil, and Lionel Henry at the ‘R Dev Day’, thus fixing PR#15027.-
Sys.setLanguage()
now works in anLC_ALL=C R
session on some platforms, warns about some failures to change the language and gets an option related to these warning messages. Printing
ls.str()
now shows"<missing>"
even when R's language setting is not English.-
xyTable()
now handles and reportsNA
s fixing PR#18654. Thanks to Heather Turner and Zhian Kamvar for report and patch. -
as(*, "raw")
now works as documented, thanks to Mikael Jagan's PR#18795. Informational messages of e.g.,
print(1:1e4, max=1000)
, now correctly mentionmax
in addition togetOption("max.print")
.-
methods' internal
.requirePackage()
now re-enables primitive method dispatch when needed; thanks to Ivan Krylov for demystifying CRAN package check failures on the R*devel mailing lists.
CHANGES IN R 4.4.1 patched
C-LEVEL FACILITIES
The S-compatibility macros
F77_COM
andF77_COMDECL
defined in header ‘R_ext/RS.h’ are deprecated and will be removed shortly. We could find no record of their use.
BUG FIXES
-
Mathlib function
lgammacor(x)
no longer warns about underflow to zero for largex
. Text widths and heights were incorrectly reported by the Quartz device if the drawing context didn't exist yet (typically when drawing off-screen to a window that is yet to appear, see PR#18591).
The Quartz device could segfault in cases where paths with spaces are used in the new glyph drawing API. Thanks to Tomek Gieorgijewski (PR#18758).
CHANGES IN R 4.4.1
C-LEVEL FACILITIES
Functions
R_atof
andR_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
andRf_isBlankString
have been added to those reported byR CMD check
.The new function
Rf_allocLang
is now available. This provides an alternative to the idiom of callingRf_allocList
followed bySET_TYPEOF
.
UTILITIES
-
R CMD check
now reports as warnings whatgfortran
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 functionR_strtod
now require a non-empty digit sequence in a decimal or binary exponent. This aligns with the C/POSIX standard forstrtod
and with?NumericConstants
. -
as.data.frame(m, make.names=NA)
now works correctly for a matrixm
withNA
'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 potentiallyqpois()
,qnbinom()
, no longer sometimes fail accurate inversion (ofpbinom()
, 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 returnscharacter(0)
whench0
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 invalidVignetteBuilder
in ‘DESCRIPTION’ but has no vignettes.
CHANGES IN R 4.4.0
SIGNIFICANT USER-VISIBLE CHANGES
Startup banners,
R --version
,sessionInfo()
andR 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 returnsFALSE
, asNULL
is not an atomic vector. Strict back-compatibility would replaceis.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 forprofile()
and theplot()
andpairs()
methods for class"profile"
have been copied from MASS to stats. (profile.nls()
andplot.profile.nls()
were already instats
.)The
confint()
andprofile
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 newtest =
argument.The
pairs()
method for"profile"
objects has been extended with awhich =
argument to allow plotting only a subset of the parameters.The
"glm"
method foranova()
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 argumenttest
a false logical value.In
setRepositories()
the repositories can be set using their names vianame =
instead of indexind =
.-
methods()
and.S3methods()
gain aall.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, currentlySys.info()["user"]
or LOGNAME. This is a (modified) fulfillment of Will Landau's suggestion in PR#17530.-
tools::testInstalledBasic()
gets new optional argumentsoutDir
andtestSrcdir
, e.g., allowing to use it in abuilddir != 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 torange.default()
, as proposed by Davis Vaughan on R-devel. Otherrange()
-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 argumentuplo = "U" | "L"
allows the upper or lower triangular part to be specified. -
memDecompress(type = "unknown")
recognizes compression in the default ‘zlib’ format as used bymemCompress(type = "gzip")
. -
memCompress()
andmemDecompress()
will use thelibdeflate
library (https://github.com/ebiggers/libdeflate) if installed. This uses the same type of compression fortype = "gzip"
but is 1.5-2x faster than the systemlibz
library on some common platforms: the speed-up may depend on the library version. -
diff()
for objects of class"Date"
,"POSIXct"
, and"POSIXlt"
accepts aunits
argument passed via...
. Dynamic help now does a much better job of rendering package ‘DESCRIPTION’ metadata.
-
Rprof()
gains anevent
argument and support for elapsed (real) time profiling on Unix (PR#18076). -
filled.contour()
gains akey.border
argument. -
tools::update_pkg_po()
gets argumentspot_make
andmo_make
for not re-making the corresponding files, and additionally averbose
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()
andrsmirnov()
in package stats have had argumenttwo.sided
renamed toalternative
, 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 vectorsz
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()
andExec()
to support writing stack-space-efficient recursive functions.Where characters are attempted to be plotted by
pdf()
,postscript()
andxfig()
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 whoseiconv()
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()
andtcrossprod()
are now also primitive and S3 generic, as%*%
had become in R 4.3.0.-
source()
andexample()
have a new optional argumentcatch.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()
andcairo_ps()
default toonefile = TRUE
to closer matchpdf()
andpostscript()
. 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 phrasesif(!is.null(L)) L else R
orif(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 returnedNULL
.-
as.complex("1i")
now returns0 + 1i
instead ofNA
with a warning. -
z <- c(NA, 1i)
now keeps the imaginary partIm(z[1]) == 0
, no longer coercing toNA_complex_
. Similarly,cumsum(z)
correctly sums real and imaginary parts separately, i.e., without “crosstalk” in case ofNA
s. 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 to2^{21} - 1
and so will never need more than 6 digits.) -
NCOL(NULL)
now returns 0 instead of 1, for consistency withcbind()
. 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()
andpostscript()
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 ofall.equal()
get acheck.class
option.-
zapsmall()
gets new optional arguments, functionmFUN
andmin.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 anignore
argument.New generic function
sort_by()
, primarily useful for thedata.frame
method which can be used to sort rows of a data frame by one or more columns.The licence 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.The numeric version creators now stop on invalid non-character version specifications.
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 value1
or2
.-
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 thanlibz
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 toautoconf
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
andCXXSTD
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 usinglld
,clang
/flang-new
andlibc++
.
UTILITIES
-
R CMD check
notes when S4-style exports are used without declaring a strong dependence on package methods. -
tools::checkRd()
(used byR CMD check
) detects more problems with\Sexpr
-based dynamic content, including bad nesting of\Sexpr
s and invalid arguments. -
tools::checkRd()
now reports Rd titles and section names ending in a period; this is ignored byR 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 fromtools::checkRd()
totools::checkRdContents()
. -
R CMD check
now visits ‘inst/NEWS.Rd’ and OS-specific ‘man’ subdirectories when checking Rd files. -
tools::checkDocFiles()
andtools::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 FortranKIND
such asINTEGER(KIND=4)
andREAL(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” thattools::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 hencecheck
) 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 recommendedexportPattern("^[^.]")
, 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 fromdo_missing()
, used to fix PR#18579.-
SEXP
typeS4SXP
has been renamed toOBJSXP
to support experimenting with alternative object systems. TheS4SXP
value can still be used inC
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 asize_t
length but was implemented withint
(and character strings in R are limited to2^{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()
andxfig()
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 thepdf()
andpostscript()
devices – this was a legacy encoding supporting classic macOS up to 2001 and no longer has universallibiconv
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 inR CMD check --as-cran
are formally deprecated now in favour of callingas.data.frame()
oras.data.frame.vector()
. The deprecation “check” now works also whenas.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()
, deprecateabb
andneg.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 withpool.sd = TRUE
. (PR#18594 by Jack Berry). Probability distribution functions
[dpq]<distrib>(x, *)
, but alsobessel[IKJY](x, .)
now consistently preserveattributes(x)
whenlength(x) == 0
, e.g., for a2 \times 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 either17
orNN
forLL
true or false, as proposed by Ivan Krylov on the R-devel mailing list. (This also means it is now an error to specifyna.rm
more than once.)-
as.complex(x)
now returnscomplex(real = x, imaginary = 0)
for all numerical and logicalx
, notably also forNA
orNA_integer_
. Directories are now omitted by
file.copy(, recursive = FALSE)
and infile.append()
(PR#17337).-
gsub()
andsub()
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. Argumentold.coords = TRUE
provides back compatibility. -
palette.colors()
gains aname
argument that defaults toFALSE
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 fromwarningCondition
anderrorCondition
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 byprompt()
. These cases are now noted byR CMD check
. Plain-text help no longer outputs spurious colons in the arguments list (for multi-line
\item
labels in the Rd source).-
kappa()
andrcond()
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()
orpromptData()
now use a dummy title (soR CMD build
works).tools::checkRdContents()
has been updated to detect such template leftovers, including frompromptPackage()
.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 preservessrcref
s 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 fort.test()
andwilcox.test()
now catch whenpaired
is passed, addressing PR#14359; usePair(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()
andrbind()
, the optionaldeparse.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)
anddim(m) <- d
are now correct about sizes, usinglong 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 withgzip
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 forlm()
-models withcharacter
categorical predictor variables rather thanfactor
ones, fixing PR#18635 reported by Jinsong Zhao. -
formals(f) <- formals(f)
now also works for a function w/o arguments and atomic constantbody(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 levelbinom_raw(x, n, ..)
hasx == 0
orx== n
. -
warning()
withoptions(warn = 1)
has improved output for multi-line messages. -
axis.Date()
andaxis.POSIXct()
now respect thepar("lab")
setting for the number ofpretty()
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 whenR CMD check
runs the examples.-
as.data.frame(matrix(*, ncol=0))
now gets validnames()
andcolnames()
; reported by Davis Vaughan on the R-devel list. Internal Mathlib function
stirlerr(n)
is now almost fully (52-bit) accurate for alln >= ~5.9
and more accurate also in the range1 -- 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 internalR_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 tona.action = na.pass
, usingna.rm = FALSE
(added as an argument) when summing overFreq
(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.
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 inpdf()
andpostscript()
: 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 Hervé Pagès for the report PR#18538.
Some invalid
file
arguments topictex()
,postscript()
andxfig()
opened a file called ‘NA’ rather than throw an error. These includedpostscript(NULL)
(which some people expected to work likepdf(NULL)
).Passing
filename = NA
tosvg()
,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 itslength.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, anddrop.terms()
no longer makes up a response, PR#18566, fixing both bugs thanks to Mikael Jagan. -
getS3method("t", "test")
no longer finds thet.test()
function, fixing PR#18627. -
pdf()
andpostscript()
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()
andpostscript()
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 vectorx
, 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 ensuresport
is in proper range, fixing PR#18645. -
pbeta(x, a,b)
is correct now forx
=0 or 1 in the boundary cases wherea
orb
or both are 0, fixing PR#18672 thanks to Michael Fay. -
pmatch(x, table)
for largetable
, also called for data frame row selection,dfrm[nm, ]
, is now interruptible, fixing PR#18656. -
predict(<rank-deficient lm>, newdata=*)
fix computing ofnbasis
, 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.
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 toNULL
such thatgetOption("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 thanNA_character_
). -
trans3d()
gains optionscontinuous
andverbose
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 oficonv()
). -
tiff(type = "quartz")
(the default on macOS) now warns ifcompression
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 generatorRANDOM_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 stringsx
whenL > nchar(x)
, thanks to a report and patch by ‘Architect 95’. -
contrib.url(character())
now returns 0-lengthcharacter()
as documented, which also avoids spurious warnings fromavailable.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 ofparallel
could fail on platforms that do not support an arbitrarily large payload in system functionsread()
/write()
on pipes (seen on macOS where a restriction toINT_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 whenlength(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 atitle
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 intools::encoded_text_to_latex()
. -
tar(*, tar = "internal")
no longer creates out-of-spec tar files in the very rare case of user or group names longer than 32 bytes, fixing PR#17871 with thanks to Ivan Krylov. When using the “internal” timezone datetime code, adding a fraction of a second no longer adds one second, fixing PR#16856 from a patch by Ivan Krylov.
-
tools::checkRd()
no longer produces spurious notes about “unnecessary braces” from multi-line Rd results of\Sexpr
macros.
CHANGES IN R 4.3.1
C-LEVEL FACILITIES
The C-level API version of R's
integrate()
,Rdqags()
in ‘Applic.h’, now returns the correct number of integrand evaluationsneval
, fixing PR#18515 reported and diagnosed by Stephen Wade.The C prototypes for LAPACK calls
dspgv
anddtptrs
in ‘R_ext/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_ext/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 frommethods()
, again marks methods from package base asvisible
.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>)
andtail(..)
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 existingattr(*,"tsp")
but otherwise no longer sets one. -
chol(<not pos.def>, pivot = <T|F>)
now gives a correct error or warning message (depending onpivot
), thanks to Mikael Jagan's (PR#18541).
CHANGES IN R 4.3.0
SIGNIFICANT USER-VISIBLE CHANGES
Calling
&&
or||
with LHS or (if evaluated) RHS of length greater than one is now always an error, with a report of the form'length = 4' in coercion to 'logical(1)'
Environment variable _R_CHECK_LENGTH_1_LOGIC2_ no longer has any effect.
NEW FEATURES
The included BLAS sources have been updated to those shipped with LAPACK version 3.10.1. (This caused some platform-dependent changes to package check output.) And then to the sources from LAPACK version 3.11.0 (with changes only to double complex subroutines).
The included LAPACK sources have been updated to include the four Fortran 90 routines rather than their Fortran 77 predecessors. This may give some different signs in SVDs or eigendecompositions.. (This completes the transition to LAPACK 3.10.x begun in R 4.2.0.)
The LAPACK sources have been updated to version 3.11.0. (No new subroutines have been added, so this almost entirely bug fixes: Those fixes do affect some computations with
NaN
s, including R'sNA
.)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 atoeplitz2()
variant. -
xy.coords()
andxyz.coords()
and consequently, e.g.,plot(x,y, log = "y")
now signal a classed warning about negative values of y (wherelog(.)
isNA
). 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()
andstrsplit()
has been improved, particularly withperl = TRUE
andfixed = TRUE
. Use ofuseBytes = TRUE
for performance reasons should no longer be needed and is discouraged: it may lead to incorrect results.-
apropos()
gains an argumentdot_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, ...)
gainsconf.level
andconf.args
arguments for computing and plotting a confidence band for the treatment function transforming the distribution ofx
into the distribution ofy
(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()
andstrsplit()
, 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 averbose
option. -
type.convert()
and henceread.table()
get new optiontryLogical = 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 beyond10^{27}
instandard = "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"
, thus fulfilling the wish of PR#18421, by Benjamin Feakins. The
as.data.frame.vector()
utility now errors for wrong-lengthrow.names
. It warned for almost six years, with “Will be an error!”.-
sessionInfo()
now also containsLa_version()
and reports codepage and timezone when relevant, in bothprint()
andtoLatex()
methods which also get new optiontzone
for displaying timezone information whenlocale = 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 anoffset
of all0
s. -
solve()
for complex inputs now uses argumenttol
and by default checks for ‘computational singularity’ (as it long has done for numeric inputs). -
predict(<rank-deficient lm>, newdata=*)
now obeys a new argumentrankdeficient
, with new default"warnif"
, warning only if there are non-estimable cases innewdata
. Other options includerankdeficient = "NA"
, predictingNA
for non-estimablenewdata
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 theNVDA
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 offwithWarnings()
andtryCatchWEMs()
. As an experimental feature the placeholder
_
can now also be used in therhs
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 switchgiveErr
to return the numeric error as attribute. Relatedly,stopifnot(all.equal<some>(a, b, ..))
is as “smart” now, asstopifnot(all.equal(....))
has been already, thus allowing customizedall.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 argumentwhat
. A new generic,nameOfClass()
, is called to resolve the class name fromwhat
. 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 forsubset()
now warns about extraneous arguments, typically catching the use of ‘=’ instead of ‘==’ in thesubset
expression.Calling
a:b
when numerica
orb
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 usingweights
; new optionalwarnWbw
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 argumentshow.residuals
can be used to show them if required.The
tapply()
function now accepts a data frame as itsX
argument, and allowsINDEX
to be a formula in that case.by.data.frame()
similarly allowsINDICES
to be a formula.The performance of
df[j] <- value
(including for missingj
) andwrite.table(df)
has been improved for data framesdf
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 genericmatrixOps
. From Tomasz Kalinowski's contribution in PR#18483.New function
array2DF()
to convert arrays to data frames, particularly useful for the list arrays created bytapply()
.
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: componentzone
is always set, and componentgmtoff
is set for times in UTC and usually set on the (almost all) platforms which have C-level support, otherwise isNA
.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>)
andas.POSIXlt(.)
(without specifyingorigin
) now work. So doesas.Date(<numeric>)
. -
as.Date.POSIXct(., tz)
now treats severaltz
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. Complemented by the low-levelunCfillPOSIXlt()
utility.More experimentally, a
"POSIXlt"
object may have an attribute"balanced"
indicating if it is known to be filled or fully balanced.Functions
axis.Date()
andaxis.POSIXct()
are rewritten to gain better default tick locations and better default formats via the correspondingpretty()
methods. 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 to16
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()
andgrid::grid.glyph()
.Rendering of typeset glyphs is only supported so far on the Cairo-based graphics devices and on the
pdf()
andquartz()
devices.The defined behaviour for
"clear"
and"source"
compositing operators (viagrid::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 betweenPOSIXlt
andPOSIXct
around year 2020. Failure (which has been seen on platforms missingtzdata
) is fatal. If
configure
option --with-valgrind-instrumentation is given value1
or2
, option --with-system-valgrind-headers is now the default and ignored (with a warning). It is highly recommended that the system headers are installed alongsidevalgrind
: 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 byconfigure
: 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’ §6.6.1. There is initial support for C++23 as several compilers are now supporting
-std=c++23
or-std=c++2b
or similar. As for C++20, there no additionalconfigure
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 GCC from 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
andR CMD SHLIB
.For further details see “Writing R Extensions” §1.2.5.
(Windows) A ‘src/Makefile.ucrt’ or ‘src/Makefile.win’ file is now included after ‘R_HOME/etcR_ARCH/Makeconf’ and so no longer needs to include that file itself. Installation of a package with such a file now uses a site ‘Makevars’ file in the same way as a package with a ‘src/Makevars.win’ file would.
-
configure
is now passed crucial variables such as CC and CFLAGS in its environment, as many packages were not setting them (as documented in ‘Writing R Extensions’ §1.2).This has most effect where
configure
is used to compile parts of the package – most often bycmake
orlibtool
which obfuscate the actual compile commands used.Also used for
configure.win
andconfigure.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
andSfloat
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++
andclang++
: 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 leftoverbrowser()
statements in the package.The use of
sprintf
andvsprintf
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 bysnprintf
orvsnprintf
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 ofR 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 argumentskip
, which is used byR 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 functionfindMatches()
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 inR CMD check --as-cran
.
BUG FIXES
Hashed
environment
s with sizes less than 5 can now grow. (Reported to R-devel by Duncan Garmonsway.)-
as.character(<Rd>, deparse = TRUE)
failed to re-escape curly braces in LaTeX-like text. (Reported by Hadley Wickham in PR#18324.) -
library()
now passes itslib.loc
argument when requiringDepends
packages; reported (with fix) in PR#18331 by Mikael Jagan. -
R CMD Stangle
: improved message about ‘Output’ files. -
head(x, n)
andtail(x, n)
now signal an error ifn
is not numeric, instead of incidentally “working” sometimes returning all ofx
. Reported and discussed by Colin Fay, in PR#18357. The
"lm"
method forsummary()
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 matches2
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 supportsNULL
elements in the skeleton (PR#15854).-
ordered(levels = *)
(missingx
) now works analogously tofactor(, 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()
andtools::Rd2latex()
no longer split\arguments
and\value
lists at Rd comments. -
tools::Rd2latex()
now correctly handles optional text outside\item
s 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 byoptions()
. Ditto foras.character(<Date>)
. Theas.character()
method gets argumentsdigits
andOutDec
with defaults not depending onoptions()
. Use ofas.character(*, format = .)
now warns. Similarly, the
as.character.hexmode()
and*.octmode()
methods also behave asgood citizen
methods and back compatibility optionkeepStr = TRUE
.The
as.POSIXlt(<POSIXlt>)
andas.POSIXct(<POSIXct>)
default methods now do obey theirtz
argument, also in this case.-
as.POSIXlt(<Date>)
now does apply atz
(time zone) argument, as doesas.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 withoutdata
. Reported in PR#18414. -
time()
now (also) uses thets.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 Andreï V. Kostyrka on R-help. Printing of a
factanal()
result with just one factor andsort = 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()
queriestimedatectl
only ifsystemd
is loaded; addressing a report by Jan Gorecki in PR#17421. The formula method of
cor.test()
had scoping problems whenenvironment(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 invaliddownload.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
orinstall.packages(*)
, now parses each of the ‘<pkg>/R/*.R’ files individually instead of first concatenating and thenparse()
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 André Gillibert's report and patch in PR#18456. -
getInitial(<formula>)
now finds theselfStart
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 matrixm
by adding a class attribute. -
packageDate(pkg)
now only warns once if there is nopkg
. When
ts()
creates a multivariate time series,"mts"
, it also inherits from"array"
now, andis.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 whereabs(f(x)) == Inf
for anx
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()
, orhcl.colors()
works correctly now, thanks to Achim Zeileis' report and patch in PR#18476.Formatting and
print()
ing ofbibentry
objects has dropped the deprecatedcitation.bibtex.max
argument, such that thebibtex
argument's default forprint.bibentry()
depends directly on thecitation.bibtex.max
option, whereas informat.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 setoptions(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 assummary.glm()
.-
bs()
andns()
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).
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 exampleR_GetCCallable
need to be cast to an appropriate type if they have any arguments.-
.Machine
has a new elementsizeof.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 ofNA
in R 4.2.2, e.g., forx <- 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>")
withn > 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 whena
containsNA
orNaN
values. When
UseMethod()
cannot dispatch, it no longer segfaults producing the error message in case of a longclass()
, 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 leavesdevAskNewPage()
unchanged even when it wasFALSE
, thus fixing a 14 years old ‘FIXME’.-
packageDescription()
again catches errors from encoding conversions. This also fixes brokenpackageVersion()
in C locale on systems whereiconv
does not support transliteration.
CHANGES IN R 4.2.2
NEW FEATURES
-
tools::Rdiff(useDiff = TRUE)
checks for the presence of an externaldiff
command and switches touseDiff = FALSE
if none is found. This allowsR 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()
andwriteClipboard()
has been changed to13
(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 whereasgfortran
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 producesNaN
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) whenx
is a"Date"
or"POSIXct"
object, or of another class while fulfillingmode(x) == "numeric"
. This also enablespoly(x, *, raw=TRUE)
for such variables. Reported by Michael Chirico to R-devel. -
write.table()
,write.csv()
andwrite.csv2()
restore their numerical precision (internal equivalent ofdigits = 15
) after an interrupt (PR#18384). One can now read also byte
FF
from a clipboard connection (PR#18385).-
source("")
andsource(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 datesx
, fixing PR#18401 reported by Hannes Mühleisen. 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 toformat()
them correctly.Added methods for
is.finite()
,is.infinite()
andis.nan()
for"POSIXlt"
date-time objects.
BUG FIXES on Windows
Non-ASCII characters are now properly displayed on Windows in windows created using GraphApp via e.g.
winDialogString
thanks to a workaround for an at least surprising Windows behavior with UTF-8 as the system encoding (PR#18382).Find and replace operations work again in the script editor in
Rgui
on Windows.Computation of window size based on requested client size in GraphApp when running in a multi-byte locale on Windows has been fixed (regression in R 4.2.0 for users of systems where R 4.1 used a single-byte locale).
Rgui
again respects the number of console rows and columns given in ‘Rconsole’ file.-
Rterm
support forAlt+xxx
sequences has been fixed to produce the corresponding character (only) once. This fixes pasting text with tilde on Italian keyboard (PR#18391).
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 astools::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 problematictidy
.The 2006 version that ships with macOS is always skipped.
C-LEVEL FACILITIES
The undocumented legacy declarations of
Sint
,Sfloat
,SINT_MAX
andSINT_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()
withmulti = 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-defaultna.last = FALSE
orTRUE
, 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 passtidy
5.8.0.
BUG FIXES on Windows
Writing to a clipboard connection works again, fixing a regression in R 4.2.0 (PR#18332). Re-using a closed clipboard connection no longer issues a spurious warning about an ignored encoding argument.
C function
getlocale
no longer attempts to query an unsupported category from the OS, even when requested at R level, which may cause crashes when R 4.2.0 (which uses UCRT) is embedded (reported by Kevin Ushey).Accent keys now work in GraphApp Unicode windows, which are used by
Rgui
whenever running in a multibyte locale (so also in UTF-8, hence fixing a regression in R 4.2.0 for users of systems where R 4.1 used a single-byte locale).Completion in
Rgui
now works also with non-ASCII characters.-
Rgui
no longer truncates usage information with --help. Text injection from external applications via
SendInput
now works in GraphApp Unicode windows, fixing a regression in R 4.2.0 forRgui
users of systems where R 4.1 used a single-byte locale but R 4.2.0 uses UTF-8.Performance of
txtProgressBar()
inRgui
when running in a multi-byte locale has been improved (fixing a performance regression in R 4.2.0 for users of systems where R 4.1 used a single-byte locale).The script editor in
Rgui
now works also on systems using UTF-8 as the native encoding. Users of the script editor have to convert their scripts with non-ASCII characters to UTF-8 before reading them in R 4.2.1 or newer (on recent Windows where UTF-8 is used). This fixes a regression in R 4.2.0, which prevented some operations with scripts when they contained non-ASCII characters.
CHANGES IN R 4.2.0
SIGNIFICANT USER-VISIBLE CHANGES
The
formula
method ofaggregate()
now matches the generic in naming its first argumentx
(resolving PR#18299 by Thomas Soeiro).This means that calling
aggregate()
with a formula as a named first argument requires nameformula
in earlier versions of R and namex
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()
orwhile()
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 wherelength(x)
differs fromn * 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 anexcept
argument for controlling the exceptions used bysapply()
. 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 defaulthow.many = NULL
rather than just usingmissing(how.many)
.-
grid.pretty()
gains a new optional argumentn = 5
. There is a new function
.pretty()
with optionbounds
as a technical-utility version ofpretty()
. It andpretty()
gain a new argumentf.min
with a better than back-compatible default.Function
grDevices::axisTicks()
and related functions such asgraphics::axis()
work better, notably for the log scale; partly because of thepretty()
improvements, but also because care is taken e.g., whenylim
is finite butdiff(ylim)
is infinite.-
nclass.FD()
gains adigits
option. The R Mathlib internal C function
bd0()
(called indirectly from a dozen probability density and distribution functions such asdpois()
,dbinom()
,dgamma()
,pgamma()
etc) has been complemented by a more sophisticated and (mostly) more accurate C functionebd0()
, currently called only by internaldpois_raw()
improving accuracy for R leveldpois()
and potentially others calling it such asdnbinom()
,dgamma()
orpgamma()
. (Thanks to Morten Welinder's PR#15628.)-
write.ftable()
gainssep = " "
argument as suggested by Thomas Soeiro. The names of the locale categories supported by R's
Sys.getlocale()
andSys.setlocale()
are now provided by variable.LC.categories
in thebase
namespace.The
Date
andPOSIXt
methods forhist()
and thehistogram
method forplot()
now also use the new defaultcol = "lightgray"
in consistency with the corresponding change tohist()
's default for R 4.0.0.-
hist.default()
gains newfuzz
argument, and the histogramplot
method no longer uses fractional axis ticks when displaying counts ("Frequency"
). -
mapply()
and henceMap()
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 ruleas.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 commonmode
.-
substr(ch, start,end) <- new
now e.g., preservesnames(ch)
; ditto forsubstring()
, thanks to a patch from Brodie Gaslam. -
plot(<lm>)
gains aextend.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 viacook.col
andcook.lty
with a different default color and their legend is nicer by default and customizable viacook.legendChanges
. Attempting to subset an object that is not subsettable now signals an error of class
notSubsettableError
. The non-subsettable object is contained in theobject
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()
andgettextf()
get a new optiontrim = 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 aextptr.as.ref
argument for requesting that external pointer objects be compared as reference objects. -
reorder()
gets an argumentdecreasing
which it passes tosort()
for level creation; based on the wish and patch by Thomas Soeiro in PR#18243. -
as.vector()
gains adata.frame
method which returns a simple named list, also clearing a long standing ‘FIXME’ to enableas.vector(<data.frame>, mode="list")
. This breaks code relying onas.vector(<data.frame>)
to return the unchanged data frame. -
legend()
is now vectorized for argumentscex
,x.intersp
, andtext.width
. The latter can now also be specified as a vector (one element for each column of the legend) or asNA
for computing a proper column wise maximum value ofstrwidth(legend)
. The argumenty.intersp
can be specified as a vector with one entry for each row of the legend.legend()
also gains new argumentstitle.cex
andtitle.font
. Thanks to Swetlana Herbrandt. Deparsing no longer remaps attribute names
dim
,dimnames
,levels
,names
andtsp
to historical S-compatible names (whichstructure()
maps back).-
sample()
andsample.int()
have additional sanity checks on theirsize
andn
arguments.all.equal.numeric()
gains a sanity check on itstolerance
argument – callingall.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 =)
andmethods::is(class2 =)
have more robust sanity checks on their arguments.R CMD Rd2pdf
(used byR CMD check
) has a more robust sanity check on the format of\alias{}
commands. -
psigamma(x, deriv)
for negativex
now also works forderiv = 4
and5
; their underlying C leveldpsifn()
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, withy ~ 1
for the one-sample (Kolmogorov) test andy ~ group
for the two-sample (Smirnov) test. Contributed by Torsten Hothorn. The return value from
ks.test()
now has classc("ks.test", "htest")
– packages usingtry()
need to take care to useinherits()
and not==
on the class.New functions
psmirnov()
,qsmirnov()
andrsmirnov()
in package stats implementing the asymptotic and exact distributions of the two-sample Smirnov statistic.-
iconv()
now allowssub = "c99"
to use C99-style escapes for UTF-8 inputs which cannot be converted to encodingto
. In a forward pipe
|>
expression it is now possible to use a named argument with the placeholder_
in therhs
call to specify where thelhs
is to be inserted. The placeholder can only appear once on therhs
.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 isfile.exists()
, which silently returns false.) -
trunc(<Date>, *)
now supportsunits = "months"
or"years"
for consistency with thePOSIXt
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 to15
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 togpar()
accepts a list of gradients and/or patterns and the functionslinearGradient()
,radialGradient()
, andpattern()
have a newgroup
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()
, andgrid.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()
, andgrid.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 functionas.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)}
.
WINDOWS
-
R uses UTF-8 as the native encoding on recent Windows systems (at least Windows 10 version 1903, Windows Server 2022 or Windows Server 1903). As a part of this change, R uses UCRT as the C runtime. UCRT should be installed manually on systems older than Windows 10 or Windows Server 2016 before installing R.
The default personal library on Windows, folder ‘R\win-library\x.y’ where ‘x.y’ stands for R release ‘x.y.z’, is now a subdirectory of Local Application Data directory (usually a hidden directory ‘C:\Users\username\AppData\Local’). Use
shell.exec(.libPaths()[1])
from R to open the personal library in Explorer when it is first in the list (PR#17842).-
R uses a new 64-bit Tcl/Tk bundle. The previous 32-bit/64-bit bundle had a different layout and can no longer be used.
Make files and installer scripts for Windows have been tailored to ‘Rtools42’, the newly recommended 64-bit
gcc
10.3 MinGW-W64 UCRT toolchain.-
‘Rtools42’ by default uses the Windows security features ASLR and DEP; hence CRAN builds of R and packages also do.
-
R now supports files ‘Makevars.ucrt’, ‘Makefile.ucrt’, ‘configure.ucrt’ and ‘cleanup.ucrt’ in packages, which are used in preference to the ‘.win’ variants. This allows keeping the ‘.win’ files around to support older versions of R. This feature will be removed in the future once support for older versions of R would no longer be needed.
-
R.version
gains a new fieldcrt
(only on Windows) to denote the C runtime. The value is"ucrt"
. On Windows,
download.file(method = "auto")
andurl(method = "default")
now follow Unix in using"libcurl"
for all except ‘file://’ URIs.-
‘Rtools42’ includes an unpatched Msys2 build of GNU
tar
. Paths including drive letters can be made to work by adding --force-local to environment variable TAR_OPTIONS. (‘Rtools40’ and earlier included a patched version which defaulted to this option.) Installer builds of R automatically find the ‘Rtools42’ software collection as well as the compiler toolchain. No PATH setting is required from the user.
The default installation directory of R for a user-only installation has been changed to the User Program Files directory (usually a hidden directory ‘C:\Users\username\AppData\Local\Programs’) to follow Windows conventions. Use
shell.exec(R.home())
from R to open the R installation directory in Explorer (PR#17842).-
R now supports installation-time patching of packages. Patches may be installed from a supplied URL or a local directory or disabled. Patches are included into the installed packages for reference. This experimental feature may be removed in the future.
-
libcurl
is now required for building from source. The clipboard connection now works also with text in other than the current native encoding (PR#18267, with Hiroaki Yutani). Text is always pasted to the clipboard in UTF16-LE and the
encoding
argument is ignored.The internal case-changing functions are now used by default on Windows – this circumvents problems (for example with E acute) of the UCRT Windows' runtime.
-
R on Windows now uses the system memory allocator. Doug Lea's allocator was used since R 1.2.0 to mitigate performance limitations seen with system allocators on earlier versions of Windows.
-
memory.limit()
andmemory.size()
are now stubs on Windows (as on Unix-alikes). Applications embedding R on Windows can now use additional callbacks, which have so far only been available only on Unix (PR#18286).
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 anR CMD build
change in R 3.0.0 and affects packages built before R 3.0.2. Such packages should be re-made withR 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’ §6.6.1. (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 §8 for further details. -
R CMD check --use-valgrind
also usesvalgrind
when re-building vignettes as some non-Sweave vignettes unhelpfully comment out all their code whenR 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 byR CMD build
when building the PDF package manual. -
R CMD Rd2pdf
now always runs LaTeX in batch mode, consistent with Texinfo\ge
6.7. The --batch option is ignored. -
R CMD build
andR 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.-
R CMD check
can optionally (but included in --as-cran) validate the HTML produced from the packages ‘.Rd’ files. See https://blog.r-project.org/2022/04/08/enhancements-to-html-documentation/: this needs a fairly recent version of HTML Tidy to be available.
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’ §6 should not be affected.
The macro
USE_RINTERNALS
no longer has any effect when compiling package code. Packages which also useR_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_ext/RS.h’ (included by ‘R.h’). Replace these by calls toRf_error
andRf_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
andR_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 whenSTRICT_R_HEADERS
is defined. -
rmultinom
has been documented in ‘Writing R Extensions’ §6 so is now part of the R API. Similarly,
Rtanpi
, called from R leveltanpi()
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"
fordownload.file()
andurl()
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 bothdownload.file()
andurl()
. (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
informat()
,print.default()
(and hence typicallyprint()
) oroptions()
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 finitex
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)
whenanyNA(x)
is true, now removes weights “in parallel” tox
, fixing PR#18151, reported by Matthias Gondan. Additionally, it gets asubdensity
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 togettext()
; rather translation needs explicitdomain = *
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 argumentchar
, without which no progress can be visible. -
dimnames(table(d))
is more consistent in the case whered
is a list with a single component, thanks to Thomas Soeiro's report to R-devel.Further,
table(d1, d2)
now gives an error whend1
andd2
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 uninstallPriority: base
packages, thanks to a report and suggestions by Colin Fay in PR#18227. -
win.metafile()
now hasxpinch
andypinch
arguments so that the user can override Windows' (potentially wrong) guess at device dimensions. -
x[i]
andx[[i]]
for non-integeri
should now behave in all cases as always documented: the index used is equivalent toas.integer(i)
unless that would overflow wheretrunc(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 withbibentry()
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 logicalcv
argument more safely, fixing a rare bug when printing, and also storesn
. -
smooth.spline(x,y,*)
now computes thecv.crit
statistic correctly, also whenis.unsorted(x)
, fixing PR#18294. The
data.frame
method ofrbind()
now warns when binding not-wholly-recycling vectors, by analogy to the default method (for matrices).-
setAs()
finds the correct class for nameto
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 afactor
f
now keepsnames(f)
, fixing PR#18309. -
qbeta(.001, .9, .009)
and analogousqf()
calls now return a correct value instead ofNaN
or wrongly1
, 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 andprint()
ing of non-finiteDate
andPOSIXt
valuesNaN
and\pm
Inf
no longer show asNA
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\href
s (iftools::Rd2txt_options(showURLs = TRUE)
) and\url
s with percent-encoding and standards-compliant delimiting style (angle brackets and no ‘URL: ’ prefix).\email
is now rendered with a ‘mailto:’ prefix.
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 offile
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 negativestop
values correctly. Reported with a patch in PR#18228 by Brodie Gaslam. Subscripting an array
x
without dimnames by alength(dim(x))
-column character matrix gave "random" non-sense, now an error; reported in PR#18244 by Mikael Jagan.-
...names()
now matchesnames(list(...))
closely, fixing PR#18247. -
all.equal(*, scale = s)
now works as intended whenlength(s) > 1
, partly thanks to Michael Chirico's PR#18272. -
print(x)
for long vectorsx
now also works for named atomic vectors or lists and prints the correct number when reaching thegetOption("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 whenlength(r) > 1
, thanks to Bill Dunlap's PR#18281. Modifying
globalCallingHandlers
insidewithCallingHandlers()
now works or fails correctly, thanks to Henrik Bengtsson's PR#18257.-
hist(<Date>, breaks = "days")
andhist(<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 itsarr.ind
argument is TRUE rather coercing to logical and taking the first element – which gave incorrect results in package code. -
model.weights()
andmodel.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).
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 oflog()
(which should have beenstd::log()
) with anint
argument are reported on Solaris.The undocumented limit of 4095 bytes on messages from the S-compatibility macros
PROBLEM
andMESSAGE
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 ofRf_error
andRf_warning
has long been preferred.
BUG FIXES
-
.mapply(F, dots, .)
no longer segfaults whendots
is not alist
and usesmatch.fun(F)
as always documented; reported by Andrew Simmons in PR#18164. -
hist(<Date>, ...)
andhist(<POSIXt>, ...)
no longer pass arguments forrect()
(such ascol
anddensity
) toaxis()
. (Thanks to Sebastian Meyer's PR#18171.) -
\Sexpr{ch}
now preservesEncoding(ch)
. (Thanks to report and patch by Jeroen Ooms in PR#18152.) Setting the RNG to
"Marsaglia-Multicarry"
e.g., byRNGkind()
, now warns in more places, thanks to André 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 keepsnames(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 somedo.call()
. Thanks to Alexander Kaever's suggestion posted to R-devel. -
qqline(y = <object>)
such asy=I(.)
, now works, see also PR#18190. Non-integer
mgp
par()
settings are now handled correctly inaxis()
andmtext()
, thanks to Mikael Jagan and Duncan Murdoch's report and suggestion in PR#18194.-
formatC(x)
returns length zerocharacter()
now, rather than""
whenx
is of length zero, as documented, thanks to Davis Vaughan's post to R-devel. -
removeSource(fn)
now retains (other)attributes(fn)
.
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 bothdownload.file
andurl
.On Windows,
method = "wininet"
is deprecated for ‘http://’, ‘https://’ and ‘ftp://’ URIs for bothdownload.file
andurl
. (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 iflibcurl
is available, usingmethod = "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 largesize/mu
is correct now in a range of cases (PR#18095); similarly for the(size, prob)
parametrization of the negative binomial. Alsoqpois()
andqbinom()
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 theaxis()
arguments which are passed frombxp()
, and henceboxplot()
. (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, *)
andseq.default(..)
now work better in large range cases wherefrom-to
is infinite where the two boundaries are finite. -
all.equal(x,y)
now returnsTRUE
correctly also when several entries ofabs(x)
andabs(y)
are close to.Machine$double.xmax
, the largest finitenumeric
. -
model.frame()
now clears the object bit when removing theclass
attribute of a value viana.action
(PR#18100). -
charClass()
now works with multi-character strings on Windows (PR#18104, fixed by Bill Dunlap). -
encodeString()
on Solaris now works again in Latin-1 encoding on characters represented differently in UTF-8. Support for surrogate pairs on Solaris has been improved. -
file.show()
on Windows now works with non-ASCII path names representable in the current native encoding (PR#18132). Embedded R on Windows can now find R home directory via the registry even when installed only for the current user (PR#18135).
-
pretty(x)
with finitex
now returns finite values also in the case where the extremex
values are close in size to the maximal representable number.Machine$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, andpretty(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.)
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 asimplify
argument to allow disabling of simplification of results. The
format()
method for class"ftable"
gets a new optionjustify
. (Suggested by Thomas Soeiro.)New
...names()
utility. (Proposed by Neal Fultz in PR#17705.)-
type.convert()
now warns when itsas.is
argument is not specified, as the help file always said it should. In that case, the default is changed toTRUE
in line with its change inread.table()
(related tostringsAsFactors
) 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 isTRUE
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 objectxS4
. Rudimentary support for vi-style tags in
rtags()
andR CMD rtags
has been added. (Based on a patch from Neal Fultz in PR#17214.)-
checkRdContents()
is now exported from tools; it and alsocheckDocFiles()
have a new optionchkInternal
allowing to check Rd files marked with keyword"internal"
as well. The latter can be activated forR CMD check
via environment variable _R_CHECK_RD_INTERNAL_TOO_. New functions
numToBits()
andnumToInts()
extend theraw
conversion utilities to (double precision)numeric
.Functions
URLencode()
andURLdecode()
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 whenreadline
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 removesNULL
arguments before dispatching to methods, thus simplifying the implementation ofc()
methods, but for back compatibility keepsNULL
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 likeparent.frame()
more consistent. (Thanks to Lionel Henry's PR#17907.) -
packBits(bits, type="double")
now works as inverse ofnumToBits()
. (Thanks to Bill Dunlap's proposal in PR#17914.) -
curlGetHeaders()
has two new arguments,timeout
to specify the timeout for that call (overridinggetOption("timeout")
) andTLS
to specify the minimum TLS protocol version to be used forhttps://
URIs (inter alia providing a means to check for sites using deprecated TLS versions 1.0 and 1.1). For
nls()
, an optional constantscaleOffset
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 argumentseps
andcentral
, the latter for taking central divided differences. The latter can be activated fornls()
vianls.control(nDcentral = TRUE)
.-
nls()
now passes thetrace
andcontrol
arguments togetInitial()
, notably for all self-starting models, so these can also be fit in zero-noise situations via ascaleOffset
. For this reason, theinitial
function of aselfStart
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 ofparse(keep.source = TRUE)
. (Report and patch provided by Lionel Henry in PR#17869.) -
textConnection()
gets an optionalname
argument. -
get()
,exists()
, andget0()
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 asfunction(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)
forfunction
s now by default also compares theirenvironment(.)
s, notably via newall.equal
method for classfunction
. Comparison ofnls()
fits, e.g., may now needall.equal(m1, m2, check.environment = FALSE)
. -
.libPaths()
gets a new optioninclude.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 Žakauskas.)
-
names()
now works forDOTSXP
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 onDOTSXP
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 forX11()
. 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 fromSys.getlocale("LC_CTYPE")
).New function
gregexec()
which generalizesregexec()
to find all disjoint matches and 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 asiswprint
).The names of
quantile()
's result no longer depend on the globalgetOption("digits")
, butquantile()
gets a new optional argumentdigits = 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 asGnome
orUnity
; thanks to a patch by Ivan Krylov posted to R-devel.The
split()
method for classdata.frame
now allows thef
argument to be specified as a formula.-
sprintf
now warns on arguments unused by the format string. New palettes
"Rocket"
and"Mako"
forhcl.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 acceptsALT+ +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()
andanyDuplicated()
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 to14
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
. IfTRUE
, the graphics engine will never perform any clipping of output itself.The clipping that the graphics engine does perform (for both
canClip = TRUE
andcanClip = FALSE
) has been improved to avoid producing unnecessary artifacts in clipped output.The grid package now allows
gpar(fill)
to be alinearGradient()
, aradialGradient()
, or apattern()
. Theviewport(clip)
can now also be a grob, which defines a clipping path, and there is a newviewport(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()
orbmp()
device but Cairo is unsupported (sotype = "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 gainlog1mexp()
.
INSTALLATION on a UNIX-ALIKE
-
configure
checks for a programpkgconf
if programpkg-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 inPKG_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
andwcswidth
) 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 notX11(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
andR 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
\ge
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 likeDepends: R (>= 3.4)
PACKAGE INSTALLATION on Windows
-
R CMD INSTALL
andR 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’ §4.5.)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 bogusreturn
statements, which were possibly intended asreturn()
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’ §1.1.6 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()
andchartr()
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. This included treating all control characters as having zero width.
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: useconfigure
option --with-internal-towlower or (on Windows) ‘-DUSE_RI18N_CASE’ in ‘CFLAGS’ when building R. This may be needed to allowtolower()
andtoupper()
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 andpackage.dependencies()
,pkgDepends()
,getDepList()
,installFoundDepends()
, andvignetteDepends()
from package tools are defunct.Defunct functions
checkNEWS()
andreadNEWS()
from package tools andCRAN.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 tochol.default()
,chol2inv()
,solve.default()
andsvd()
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[*]
orddd$x
on aDOTSXP
(dot-dot-dot) objectddd
has been disabled; it worked by accident only and was undocumented.
BUG FIXES
Many more C-level allocations (mainly by
malloc
andstrdup
) 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 anothersavePlot()
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 acceptscall
s for labels such asylab
, the same asplot()
. (Reported by Marius Hofert.) The help page for
xtabs()
now correctly states thataddNA
is settingna.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., inImports:
. (Thanks to the contributors of PR#17179.)-
update.default()
now calls the genericupdate()
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 argumentcheck.tzone = FALSE
as suggested by Sebastian Meyer. -
as.POSIXct()
now populates the"tzone"
attribute from itstz
argument whenx
is a logical vector consisting entirely ofNA
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 improvedaxisTicks()
(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 framesdf
withlogical
columns, notably also of zero rows. (Reported to R-devel by Martin “b706”.) -
unsplit()
had trouble with tibbles due to unsound use ofrep(NA, len)
-indexing, which should useNA_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 whencheck.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 differingDOTSXP
objects, fixing PR#18032. -
str()
now works correctly forDOTSXP
and related exotics, even when these are doomed.Additionally, it no longer fails for
list
s with aclass
and “irregular” method definitions such that e.g.lapply(*)
will necessarily fail, as currently for different igraph objects. Message translation domains, e.g., for errors and warnings, are now correctly determined also when e.g., a base function is called from “top-level” function (i.e., defined in
globalenv()
), thanks to a patch from Joris Goosen fixing PR#17998.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()
andcut.POSIXt()
could produce an empty last interval forbreaks = "months"
orbreaks = "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()
andgsub(pattern, repl, x, *)
now keep attributes ofx
such asnames()
also whenpattern
isNA
(PR#18079). Time differences (
"difftime"
objects) get a replacement and arep()
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
andpvec
no longer accidentally terminate parallel processes started before bymcparallel
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 argumentopen
(PR#15600, PR#18031).
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).
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 differentNA
s 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()
andsignif()
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
haslongdouble.*
elements only ifcapabilities("long.double")
is true, as documented. (Previously they were included if the platform hadlong double
identical todouble
, as ARM does.) -
p.adjust(numeric(), n=0)
now works, fixing PR#18002. -
identical(x,y)
no longer prints "Unknown Type .." fortypeof(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 withdata.frame()
, disregarding names of components ofL
, fixing PR#18034, reported by Kevin Tappe. -
checkRdaFiles(ff)$version
is now correct also whenff
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.
CHANGES IN R 4.0.3
NEW FEATURES
On platforms using
configure
option --with-internal-tzcode, additional values"internal"
and (on macOS only)"macOS"
are accepted for the environment variable TZDIR. (See?TZDIR
.)On macOS,
"macOS"
is used by default if the system timezone database is a newer version than that in the R installation.When
install.packages(type = "source")
fails to find a package in a repository it mentions package versions which are excluded by their R version requirement and links to hints on why a package might not be found.The default value for
options("timeout")
can be set from environment variable R_DEFAULT_INTERNET_TIMEOUT, still defaulting to 60 (seconds) if that is not set or invalid.This may be needed when child R processes are doing downloads, for example during the installation of source packages which download jars or other forms of data.
LINK-TIME OPTIMIZATION on a UNIX-ALIKE
There is now support for parallelized Link-Time Optimization (LTO) with GCC and for ‘thin’ LTO with
clang
via setting the ‘LTO’ macro.There is support for setting a different LTO flag for the Fortran compiler, including to empty when mixing
clang
andgfortran
(as on macOS). See file ‘config.site’.There is a new ‘LTO_LD’ macro to set linker options for LTO compilation, for example to select an alternative linker or to parallelize thin LTO.
DEPRECATED AND DEFUNCT
The
LINPACK
argument tochol.default()
,chol2inv()
,solve.default()
andsvd()
has been defunct since R 3.1.0. Using it now gives a warning which will become an error in R 4.1.0.
BUG FIXES
The code mitigating stack overflow with PCRE regexps on very long strings is enabled for PCRE2 < 10.30 also when JIT is enabled, since stack overflows have been seen in that case.
Fix to correctly show the group labels in
dotchart()
(which where lost in theylab
improvement for R 4.0.0).-
addmargins(*, ..)
now also works whenfn()
is a local function, thanks to bug report and patch PR#17124 from Alex Bertram. -
rank(x)
and hencesort(x)
now work whenx
is an object (as peris.object(x)
) of type"raw"
and provides a valid`[`
method, e.g., forgmp::as.bigz(.)
numbers. -
chisq.test(*, simulate.p.value=TRUE)
andr2dtable()
now work correctly for large table entries (in the millions). Reported by Sebastian Meyer and investigated by more helpers in PR#16184. Low-level socket read/write operations have been fixed to correctly signal communication errors. Previously, such errors could lead to a segfault due to invalid memory access. Reported and debugged by Dmitriy Selivanov in PR#17850.
-
quantile(x, pr)
works more consistently forpr
values slightly outside [0,1], thanks to Suharto Anggono's PR#17891.Further,
quantile(x, prN, names=FALSE)
now works even whenprN
containsNA
s, thanks to Anggono's PR#17892. Ditto for ordered factors orDate
objects whentype = 1
or3
, thanks to PR#17899. Internet access based on libcurl, including
curlGetHeaders()
, was not respecting the"timeout"
option. If this causes unanticipated timeouts, consider increasing the default by setting R_DEFAULT_INTERNET_TIMEOUT.-
as.Date(<char>)
now also works with an initial""
, thanks to Michael Chirico's PR#17909. -
isS3stdGeneric(f)
now detects an S3 generic also when it istrace()
d, thanks to Gabe Becker's PR#17917. -
R_allocLD()
has been fixed to return memory aligned for long double type PR#16534. -
fisher.test()
no longer segfaults when called again after its internal stack has been exceeded PR#17904. Accessing a long vector represented by a compact integer sequence no longer segfaults (reported and debugged by Hugh Parsonage).
-
duplicated()
now works also for strings with multiple encodings inside a single vector PR#17809. -
phyper(11, 15, 0, 12, log.p=TRUE)
no longer givesNaN
; reported as PR#17271 by Alexey Stukalov. Fix incorrect calculation in
logLik.nls()
PR#16100, patch from Sebastian Meyer.A very old bug could cause a segfault in
model.matrix()
when terms involved logical variables. Part of PR#17879.-
model.frame.default()
alloweddata = 1
, leading to involuntary variable capture (rest of PR#17879). -
tar()
no longer skips non-directory files, thanks to a patch by Sebastian Meyer, fixing the remaining part of PR#16716.
CHANGES IN R 4.0.2
UTILITIES
-
R CMD check
skips vignette re-building (with a warning) if the ‘VignetteBuilder’ package(s) are not available.
BUG FIXES
Paths with non-ASCII characters caused problems for package loading on Windows PR#17833.
Using tcltk widgets no longer crashes R on Windows.
-
source(*, echo=TRUE)
no longer fails in some cases with empty lines; reported by Bill Dunlap in PR#17769. -
on.exit()
now correctly matches named arguments, thanks to PR#17815 (including patch) by Brodie Gaslam. -
regexpr(*, perl=TRUE)
no longer returns incorrect positions into text containing characters outside of the Unicode Basic Multilingual Plane on Windows.
CHANGES IN R 4.0.1
NEW FEATURES
-
paste()
andpaste0()
gain a new optional argumentrecycle0
. When set to true, zero-length arguments are recycled leading tocharacter(0)
after thesep
-concatenation, i.e., to the empty string""
ifcollapse
is a string and to the zero-length valuecharacter(0)
whencollapse = NULL
.A package whose code uses this should depend on ‘R (>= 4.0.1)’.
The
summary(<warnings>)
method now maps the counts correctly to the warning messages.
BUG FIXES
-
aov(frml, ...)
now also works where theformula
deparses to more than 500 characters, thanks to a report and patch proposal by Jan Hauffa. Fix a dozen places (code, examples) as
Sys.setlocale()
returns the new rather than the previous setting.Fix for adding two complex grid units via
sum()
. Thanks to Gu Zuguang for the report and Thomas Lin Pedersen for the patch.Fix
parallel::mclapply(..., mc.preschedule=FALSE)
to handle raw vector results correctly. PR#17779Computing the
base
value, i.e., 2, “everywhere”, now usesFLT_RADIX
, as the original ‘machar’ code looped indefinitely on the ppc64 architecture for thelongdouble
case.In R 4.0.0,
sort.list(x)
whenis.object(x)
was true, e.g., forx <- I(letters)
, was accidentally usingmethod = "radix"
. Consequently, e.g.,merge(<data.frame>)
was much slower than previously; reported in PR#17794.-
plot(y ~ x, ylab = quote(y[i]))
now works, as e.g., forxlab
; related to PR#10525. -
parallel::detect.cores(all.tests = TRUE)
tries a matching OS name before the other tests (which were intended only for unknown OSes). Parse data for raw strings is now recorded correctly. Reported by Gabor Csardi.
CHANGES IN R 4.0.0
SIGNIFICANT USER-VISIBLE CHANGES
Packages need to be (re-)installed under this version (4.0.0) of R.
-
matrix
objects now also inherit from class"array"
, so e.g.,class(diag(1))
isc("matrix", "array")
. This invalidates code incorrectly assuming thatclass(matrix_obj))
has length one.S3 methods for class
"array"
are now dispatched formatrix
objects. There is a new syntax for specifying raw character constants similar to the one used in C++:
r"(...)"
with...
any character sequence not containing the sequence ‘)"’. This makes it easier to write strings that contain backslashes or both single and double quotes. For more details see?Quotes
.-
R now uses a ‘stringsAsFactors = FALSE’ default, and hence by default no longer converts strings to factors in calls to
data.frame()
andread.table()
.A large number of packages relied on the previous behaviour and so have needed/will need updating.
The
plot()
S3 generic function is now in package base rather than package graphics, as it is reasonable to have methods that do not use the graphics package. The generic is currently re-exported from the graphics namespace to allow packages importing it from there to continue working, but this may change in future.Packages which define S4 generics for
plot()
should be re-installed and package code using such generics from other packages needs to ensure that they are imported rather than rely on their being looked for on the search path (as in a namespace, the base namespace has precedence over the search path).
REFERENCE COUNTING
Reference counting is now used instead of the
NAMED
mechanism for determining when objects can be safely mutated in base C code. This reduces the need for copying in some cases and should allow further optimizations in the future. It should help make the internal code easier to maintain.This change is expected to have almost no impact on packages using supported coding practices in their C/C++ code.
MIGRATION TO PCRE2
This version of R is built against the PCRE2 library for Perl-like regular expressions, if available. (On non-Windows platforms PCRE1 can optionally be used if PCRE2 is not available at build time.) The version of PCRE in use can be obtained via
extSoftVersion()
: PCRE1 (formerly known as ‘PCRE’) has versions <= 8, PCRE2 versions >= 10.Making PCRE2 available when building R from source is strongly recommended (preferably version 10.30 or later) as PCRE1 is no longer developed: version 8.44 is ‘likely to be the final release’.
PCRE2 reports errors for some regular expressions that were accepted by PCRE1. A hyphen now has to be escaped in a character class to be interpreted as a literal (unless first or last in the class definition). ‘\R’, ‘\B’ and ‘\X’ are no longer allowed in character classes (PCRE1 treated these as literals).
Option
PCRE_study
is no longer used with PCRE2, and is reported asFALSE
when that is in use.
NEW FEATURES
-
assertError()
andassertWarning()
(in package tools) can now check for specific error or warning classes via the new optional second argumentclasses
(which is not back compatible with previous use of an unnamed second argument). -
DF2formula()
, the utility for the data frame method offormula()
, now works without parsing and explicit evaluation, starting from Suharto Anggono's suggestion in PR#17555. -
approxfun()
andapprox()
gain a new argumentna.rm
defaulting to true. If set to false, missingy
values now propagate into the interpolated values. Long vectors are now supported as the
seq
argument of afor()
loop.-
str(x)
gets a newdeparse.lines
option with a default to speed it up whenx
is a largecall
object. The internal traceback object produced when an error is signalled (
.Traceback
), now contains thecall
s rather than thedeparse()
d calls, deferring the deparsing to the user-level functions.traceback()
andtraceback()
. This fulfils the wish of PR#17580, reported including two patch proposals by Brodie Gaslam.-
data.matrix()
now converts character columns to factors and from this to integers. -
package.skeleton()
now explicitly lists all exports in the ‘NAMESPACE’ file. New function
.S3method()
to register S3 methods in R scripts.-
file.path()
has some support for file paths not in the session encoding, e.g. with UTF-8 inputs in a non-UTF-8 locale the output is marked as UTF-8. Most functions with file-path inputs will give an explicit error if a file-path input in a marked encoding cannot be translated (to the native encoding or in some cases on Windows to UTF-8), rather than translate to a different file path using escapes. Some (such as
dir.exists()
,file.exists()
,file.access()
,file.info()
,list.files()
,normalizePath()
andpath.expand()
) treat this like any other non-existent file, often with a warning.There is a new help document accessed by
help("file path encoding")
detailing how file paths with marked encodings are handled.New function
list2DF()
for creating data frames from lists of variables.-
iconv()
has a new optionsub = "Unicode"
to translate UTF-8 input invalid in the ‘to’ encoding using ‘<U+xxxx>’ escapes. There is a new function
infoRDS()
providing information about the serialization format of a serialized object.S3 method lookup now by default skips the elements of the search path between the global and base environments.
Added an argument
add_datalist(*, small.size = 0)
to allow the creation of a ‘data/datalist’ file even when the total size of the data sets is small.The backquote function
bquote()
has a new argumentsplice
to enable splicing a computed list of values into an expression, like,@
in LISP's backquote.The formula interface to
t.test()
andwilcox.test()
has been extended to handle one-sample and paired tests.The
palette()
function has a new default set of colours (which are less saturated and have better accessibility properties). There are also some new built-in palettes, which are listed by the newpalette.pals()
function. These include the old default palette under the name"R3"
. Finally, the newpalette.colors()
function allows a subset of colours to be selected from any of the built-in palettes.-
n2mfrow()
gains an optionasp = 1
to specify the aspect ratio, fulfilling the wish and extending the proposal of Michael Chirico in PR#17648. For
head(x, n)
andtail()
the default and other S3 methods notably for vectorn
, e.g. to get a “corner” of a matrix, has been extended toarray
's of higher dimension thanks to the patch proposal by Gabe Becker in PR#17652. Consequently, optional argumentaddrownums
is deprecated and replaced by the (more general) argumentkeepnums
. An invalid second argumentn
now leads to typically more easily readable error messages.New function
.class2()
provides the full character vector of class names used for S3 method dispatch.Printing
methods(..)
now uses a newformat()
method.-
sort.list(x)
now works for non-atomic objectsx
andmethod = "auto"
(the default) or"radix"
in casesorder(x)
works, typically via axtfrm()
method. Where they are available,
writeBin()
allows long vectors.New function
deparse1()
produces one string, wrappingdeparse()
, to be used typically indeparse1(substitute(*))
, e.g., to fix PR#17671.-
wilcox.test()
enhancements: In the (non-paired) two-sample case,Inf
values are treated as very large for robustness consistency. If exact computations are used, the result now has"exact"
in themethod
element of its return value. New argumentstol.root
anddigits.rank
where the latter may be used for stability to treat very close numbers as ties. -
readBin()
andwriteBin()
now report an error for an invalidendian
value. The affected code needs to be fixed with care as the old undocumented behavior was to swap endianness in such cases. -
sequence()
is now an S3 generic with an internally implemented default method, and gains arguments to generate more complex sequences. Based on code from the S4Vectors Bioconductor package and the advice of Hervé Pagès. -
print()
's default method and many other methods (by calling the default eventually and passing...
) now make use of a new optionalwidth
argument, avoiding the need for the user to set and resetoptions("width")
. -
memDecompress()
supports the RFC 1952 format (e.g. in-memory copies ofgzip
-compressed files) as well as RFC 1950. -
memCompress()
andmemDecompress()
support long raw vectors for types"gzip"
and"zx"
. -
sweep()
andslice.index()
can now use names of dimnames for theirMARGIN
argument (apply
has had this for almost a decade). New function
proportions()
andmarginSums()
. These should replace the unfortunately namedprop.table()
andmargin.table()
. They are drop-in replacements, but also add named-margin functionality. The old function names are retained as aliases for back-compatibility.Functions
rbinom()
,rgeom()
,rhyper()
,rpois()
,rnbinom(),
rsignrank()
andrwilcox()
which have returned integer since R 3.0.0 and henceNA
when the numbers would have been outside the integer range, now return double vectors (without NAs, typically) in these cases.-
matplot(x,y)
(and hencematlines()
andmatpoints()
) now call the corresponding methods ofplot()
andlines()
, e.g, whenx
is a"Date"
or"POSIXct"
object; prompted by Spencer Graves' suggestion. -
stopifnot()
now allows customizing error messages via argument names, thanks to a patch proposal by Neal Fultz in PR#17688. -
unlink()
gains a new argumentexpand
to disable wildcard and tilde expansion. Elements ofx
of value"~"
are now ignored. -
mle()
in thestats4
package has had its interface extended so that arguments to the negative log-likelihood function can be one or more vectors, with similar conventions applying to bounds, start values, and parameter values to be kept fixed. This required a minor extension to class"mle"
, so saved objects from earlier versions may need to be recomputed. The default for
pdf()
is nowuseDingbats = FALSE
.The default fill colour for
hist()
andboxplot()
is nowcol = "lightgray"
.The default order of the levels on the y-axis for
spineplot()
andcdplot()
has been reversed.If the R_ALWAYS_INSTALL_TESTS environment variable is set to a true value,
R CMD INSTALL
behaves as if the --install-tests option is always specified. Thanks to Reinhold Koch for the suggestion.New function
R_user_dir()
in package tools suggests paths appropriate for storing R-related user-specific data, configuration and cache files.-
capabilities()
gains a new logical optionXchk
to avoid warnings about X11-related capabilities. The internal implementation of grid units has changed, but the only visible effects at user-level should be
a slightly different print format for some units (especially unit arithmetic),
faster performance (for unit operations) and
two new functions
unitType()
andunit.psum()
.
Based on code contributed by Thomas Lin Pedersen.
When internal dispatch for
rep.int()
andrep_len()
fails, there is an attempt to dispatch on the equivalent call torep()
.Object
.Machine
now contains newlongdouble.*
entries (when R uses long doubles internally).-
news()
has been enhanced to cover the news on R 3.x and 2.x. For consistency,
N <- NULL; N[[1]] <- val
now turnsN
into alist
also whenval)
has length one. This enablesdimnames(r1)[[1]] <- "R1"
for a 1-row matrixr1
, fixing PR#17719 reported by Serguei Sokol.-
deparse(..)
,dump(..)
, anddput(x, control = "all")
now include control option"digits17"
which typically ensures 1:1 invertibility. New optioncontrol = "exact"
ensures numeric exact invertibility via"hexNumeric"
. When loading data sets via
read.table()
,data()
now uses ‘LC_COLLATE=C’ to ensure locale-independent results for possible string-to-factor conversions.A server socket connection, a new connection type representing a listening server socket, is created via
serverSocket()
and can accept multiple socket connections viasocketAccept()
.New function
socketTimeout()
changes the connection timeout of a socket connection.The time needed to start a homogeneous ‘PSOCK’ cluster on ‘localhost’ with many nodes has been significantly reduced (package parallel).
New
globalCallingHandlers()
function to establish global condition handlers. This allows registering default handlers for specific condition classes. Developed in collaboration with Lionel Henry.New function
tryInvokeRestart()
to invoke a specified restart if one is available and return without signaling an error if no such restart is found. Contributed by Lionel Henry in PR#17598.-
str(x)
now shows the length ofattributes
in some cases for a data framex
. -
Rprof()
gains a new argumentfilter.callframes
to request that intervening call frames due to lazy evaluation or expliciteval()
calls be omitted from the recorded profile data. Contributed by Lionel Henry in PR#17595. The handling of
${FOO-bar}
and${FOO:-bar}
in ‘Renviron’ files now follows POSIX shells (at least on a Unix-alike), so the first treats empty environment variables as set and the second does not. Previously both ignored empty variables. There are several uses of the first form in ‘etc/Renviron’.New
classes
argument forsuppressWarnings()
andsuppressMessages()
to selectively suppress only warnings or messages that inherit from particular classes. Based on patch from Lionel Henry submitted with PR#17619.New function
activeBindingFunction()
retrieves the function of an active binding.New
"cairoFT"
and"pango"
components in the output ofgrSoftVersion()
.New argument
symbolfamily
in cairo-based graphics devices and new functioncairoSymbolFont()
that can be used to provide the value for that argument.
Windows
-
Rterm
now works also when invoked from MSYS2 terminals. Line editing is possible when commandwinpty
is installed. -
normalizePath()
now resolves symbolic links and normalizes case of long names of path elements in case-insensitive folders (PR#17165). -
md5sum()
supports UTF-8 file names with characters that cannot be translated to the native encoding (PR#17633). -
Rterm
gains a new option --workspace to specify the workspace to be restored. This allows equals to be part of the name when opening via Windows file associations (reported by Christian Asseburg). -
Rterm
now acceptsALT+xxx
sequences also with NumLock on. Tilde can be pasted with an Italian keyboard (PR#17679). -
R falls back to copying when junction creation fails during package checking (patch from Duncan Murdoch).
DEPRECATED AND DEFUNCT
Make macro ‘F77_VISIBILITY’ has been removed and replaced by ‘F_VISIBILITY’.
Make macros ‘F77’, ‘FCPIFCPLAGS’ and ‘SHLIB_OPENMP_FCFLAGS’ have been removed and replaced by ‘FC’, ‘FPICFLAGS’ and ‘SHLIB_OPENMP_FFLAGS’ respectively. (Most
make
programs will set ‘F77’ to the value of ‘FC’, which is set for package compilation. But portable code should not rely on this.)The deprecated support for specifying C++98 for package installation has been removed.
-
R CMD config
no longer knows about the unused settings ‘F77’ and ‘FCPIFCPLAGS’, nor ‘CXX98’ and similar. Either PCRE2 or PCRE1 >= 8.32 (Nov 2012) is required: the deprecated provision for 8.20–8.31 has been removed.
Defunct functions
mem.limits()
,.readRDS()
,.saveRDS()
,.find.package()
, and.path.package()
from package base andallGenerics()
,getAccess()
,getAllMethods()
,getClassName()
,getClassPackage()
,getExtends()
,getProperties()
,getPrototype()
,getSubclasses()
,getVirtual()
,mlistMetaName()
,removeMethodsObject()
,seemsS4Object()
,traceOff()
, andtraceOn()
from methods have been removed.
C-LEVEL FACILITIES
-
installChar
is now remapped in ‘Rinternals.h’ toinstallTrChar
, of which it has been a wrapper since R 3.6.0. Neither are part of the API, but packages usinginstallChar
can replace it if they depend on ‘R >= 3.6.2’. Header ‘R_ext/Print.h’ defines ‘R_USE_C99_IN_CXX’ and hence exposes
Rvprintf
andREvprintf
if used with a C++11 (or later) compiler.There are new Fortran subroutines
dblepr1
,realpr1
andintpr1
to print a scalar variable (gfortran
10 enforces the distinction between scalars and length-one arrays). Alsolabelpr
to print just a label.-
R_withCallingErrorHandler
is now available for establishing a calling handler in C code for conditions inheriting from classerror
.
INSTALLATION on a UNIX-ALIKE
User-set ‘DEFS’ (e.g., in ‘config.site’) is now used for compiling packages (including base packages).
There is a new variant option --enable-lto=check for checking consistency of BLAS/LAPACK/LINPACK calls — see ‘Writing R Extensions’.
A C++ compiler default is set only if the C++11 standard is supported: it no longer falls back to C++98.
PCRE2 is used if available. To make use of PCRE1 if PCRE2 is unavailable, configure with option --with-pcre1.
The minimum required version of
libcurl
is now 7.28.0 (Oct 2012).New make target
distcheck
checks-
R can be rebuilt from the tarball created by
make dist
, the build from the tarball passes
make check-all
,the build installs and uninstalls,
the source files are properly cleaned by
make distclean
.
-
UTILITIES
-
R --help
now mentions the option--no-echo
(renamed from--slave
) and its previously undocumented short form-s
. -
R CMD check
now optionally checksconfigure
andcleanup
scripts for non-Bourne-shell code (‘bashisms’). -
R CMD check --as-cran
now runs\donttest
examples (which are run byexample()
) instead of instructing the tester to do so. This can be temporarily circumvented during development by setting environment variable _R_CHECK_DONTTEST_EXAMPLES_ to a false value.
PACKAGE INSTALLATION
There is the beginnings of support for the recently approved C++20 standard, specified analogously to C++14 and C++17. There is currently only limited support for this in compilers, with flags such as -std=c++20 and -std=c++2a. For the time being the
configure
test is of accepting one of these flags and compiling C++17 code.
BUG FIXES
-
formula(x)
withlength(x) > 1
character vectors, is deprecated now. Such use has been rare, and has ‘worked’ as expected in some cases only. In other cases, wrongx
have silently been truncated, not detecting previous errors. Long-standing issue where the X11 device could lose events shortly after startup has been addressed (PR#16702).
The
data.frame
method forrbind()
no longer drops<NA>
levels from factor columns by default (PR#17562).-
available.packages()
and henceinstall.packages()
now pass their...
argument todownload.file()
, fulfilling the wish of PR#17532; subsequently,available.packages()
gets new argumentquiet
, solving PR#17573. -
stopifnot()
gets new argumentexprObject
to allow an R object of classexpression
(or other ‘language’) to work more consistently, thanks to suggestions by Suharto Anggono. -
conformMethod()
now works correctly in cases containing a “&&
logic” bug, reported by Henrik Bengtsson. It now creates methods with"missing"
entries in the signature. Consequently,rematchDefinition()
is amended to use appropriate.local()
calls with named arguments where needed. -
format.default(*, scientific = FALSE)
now corresponds to a practically most extremeoptions(scipen = n)
setting rather than arbitraryn = 100
. -
format(as.symbol("foo"))
now works (returning"foo"
). -
postscript(.., title = *)
now signals an error when the title string contains a character which would produce corrupt PostScript, thanks to PR#17607 by Daisuko Ogawa. Certain
Ops
(notably comparison such as==
) now also work for 0-length data frames, after reports by Hilmar Berger.-
methods(class = class(glm(..)))
now warns more usefully and only once. -
write.dcf()
no longer mangles field names (PR#17589). Primitive replacement functions no longer mutate a referenced first argument when used outside of a complex assignment context.
A better error message for
contour(*, levels = Inf)
.The return value of
contourLines()
is no longerinvisible()
.The Fortran code for calculating the
coefficients
component inlm.influence()
was very inefficient. It has (for now) been replaced with much faster R code (PR#17624).-
cm.colors(n)
etc no longer append the code foralpha = 1
,"FF"
, to all colors. Hence all eight*.colors()
functions andrainbow()
behave consistently and have the same non-explicit default (PR#17659). -
dnorm
had a problematic corner case withsd == -Inf
or negativesd
which was not flagged as an error in all cases. Thanks to Stephen D. Weigand for reporting and Wang Jiefei for analyzing this; similar change has been made indlnorm()
. The optional
iter.smooth
argument ofplot.lm()
, (theplot()
method forlm
andglm
fits) now defaults to0
for allglm
fits. Especially for binary observations with high or low fitted probabilities, this effectively deleted all observations of 1 or 0. Also, the type of residuals used in theglm
case has been switched to"pearson"
since deviance residuals do not in general have approximately zero mean.In
plot.lm
, Cook's distance was computed from unweighted residuals, leading to inconsistencies. Replaced with usual weighted version. (PR#16056)Time-series
ts(*, start, end, frequency)
with fractionalfrequency
are supported more consistently; thanks to a report from Johann Kleinbub and analysis and patch by Duncan Murdoch in PR#17669.In case of errors
mcmapply()
now preserves attributes of returned"try-error"
objects and avoids simplification, overridingSIMPLIFY
toFALSE
. (PR#17653)-
as.difftime()
gets new optionaltz = "UTC"
argument which should fix behaviour during daylight-savings-changeover days, fixing PR#16764, thanks to proposals and analysis by Johannes Ranke and Kirill Müller. -
round()
does a better job of rounding “to nearest” by measuring and “to even”; thanks to a careful algorithm originally prompted by the report from Adam Wheeler and then others, in PR#17668.
round(x, dig)
for negative digits is much more rational now, notably for large|dig|
. Inheritance information on S4 classes is maintained more consistently, particularly in the case of class unions (in part due to PR#17596 and a report from Ezra Tucker).
-
is()
behaves more robustly when its argumentclass2
is aclassRepresentation
object. The warning message when attempting to export an nonexistent class is now more readable; thanks to Thierry Onkelinx for recognizing the problem.
-
choose()
misbehaved in corner cases where it switchedn - k
fork
andn
was only nearly integer (report from Erik Scott Wright). -
mle()
in thestats4
package had problems combining use of box constraints and fixed starting values (in particular, confidence intervals were affected). Operator
?
now has lower precedence than=
to work as documented, so=
behaves like<-
in help expressions (PR#16710).-
smoothEnds(x)
now returnsinteger
type in both cases whenx
isinteger
, thanks to a report and proposal by Bill Dunlap PR#17693. The methods package does a better job of tracking inheritance relationships across packages.
-
norm(diag(c(1, NA)), "2")
now works. -
subset()
had problems with 0-col dataframes (reported by Bill Dunlap, PR#17721). Several cases of integer overflow detected by the ‘undefined behaviour sanitizer’ of
clang
10 have been circumvented. One inrhyper()
may change the generated value for large input values.-
dotchart()
now places the y-axis label (ylab
) much better, not overplotting labels, thanks to a report and suggestion by Alexey Shipunov. A rare C-level array overflow in
chull()
has been worked around.Some invalid specifications of the day-of-the-year (via
%j
, e.g. day 366 in 2017) or week plus day-of-the-week are now detected bystrptime()
. They now returnNA
but give a warning as they may have given random results or corrupted memory in earlier versions of R.-
socketConnection(server = FALSE)
now respects the connection timeout also on Linux. -
socketConnection(server = FALSE)
no longer leaks a connection that is available right away without waiting (e.g. on ‘localhost’). Socket connections are now robust against spurious readability and spurious availability of an incoming connection.
-
blocking = FALSE
is now respected also on the server side of a socket connection, allowing non-blocking read operations. -
anova.glm()
andanova.glmlist()
computed incorrect score (Rao) tests in no-intercept cases. (André Gillibert, PR#17735) -
summaryRprof()
now should work correctly for theRprof(*, memory.profiling=TRUE)
case with small chunk size (and"tseries"
or similar) thanks to a patch proposal by Benjamin Tyner, in PR#15886. -
xgettext()
ignores strings passed tongettext()
, since the latter is handled byxngettext()
. Thanks to Daniele Medri for the report and all the recent work he has done on the Italian translations. -
data(package = "P")
forP
in base and stats no longer reports the data sets from package datasets (which it did for back compatibility for 16 years), fixing PR#17730. -
x[[Inf]]
(returningNULL
) no longer leads to undefined behavior, thanks to a report by Kirill Müller in PR#17756. Further,x[[-Inf]]
andx[[-n]]
now give more helpful error messages. -
Gamma()
family sometimes had trouble storing link name PR#15891
BUG FIXES (Windows)
-
Sys.glob()
now supports all characters from the Unicode Basic Multilingual Plane, no longer corrupting some (less commonly used) characters (PR#17638). -
Rterm
now correctly displays multi-byte-coded characters representable in the current native encoding (at least on Windows 10 they were sometimes omitted, PR#17632). -
scan()
issues with UTF-8 data when running in a DBCS locale have been resolved (PR#16520, PR#16584). -
Rterm
now accepts enhanced/arrow keys also with ConPTY. -
R can now be started via the launcher icon in a user documents directory whose path is not representable in the system encoding.
-
socketConnection(server = FALSE)
now returns instantly also on Windows when connection failure is signalled. Problems with UTF-16 surrogate pairs have been fixed in several functions, including
tolower()
andtoupper()
(PR#17645).
CHANGES in previous versions
Older news can be found in text format in files NEWS.0, NEWS.1, NEWS.2 and NEWS.3 in the ‘doc’ directory. News in HTML format for R versions 3.x and from 2.10.0 to 2.15.3 are available at NEWS.3.html and NEWS.2.html.