R News Changes in R 4.6.1: New Features: • The LaTeX class jss bundled in share/texmf/tex/latex/jss.cls has been updated to work with hyperref version 7.01q (2026/04/24). • Plain-text (and legacy HTML) conversion for a simple Rd \eqn{} now handles \geq, \leq, \neq and \ne in addition to \ge and \le (PR#19070). Bug Fixes: • abbreviate() now works better, using iswlower() and *upper() to treat “wide” characters, thanks to Kevin's PR#19058. • cut(1:11, {}) now signals an error for the invalid breaks, fixing PR#19057, thanks to Kevin Ushey. • all() signals an error now, as some similar coercions; previously, the coercion of the symbol resulted in NULL internally, raised a warning, and could access illegal memory; thanks to Kevin Ushey's PR#19054. • stl() now checks its 3 x 3 tuning parameters on the R level; stl(*, s.window = 0) now “works” instead dumping core, stl(*, s.window = 1) “works” correctly, too. Also, the summary() method mentions the robustness weights only if any robustness iterations happened. Further, stl() is now based on C code, translated from previous Fortran, triggered by a flang 22 compiler optimization bug (-O2). • The border case zapsmall(x, digits=Inf) where x contains an Inf entry no longer returns all NaN but rather x. The improved help page now has more non-default examples. • wilcox.test(x, exact=FALSE, correct = k)'s p-value computation got a missing dnorm(z) factor, and so did the 2-sample case, in addition to more fixes. • The data part of getGenerics() listed package names for generic functions defined in more than one package. Now it lists generic function names, as intended. Thanks to Michael Chirico for report and patch proposal (PR#19080). • Overly long dyn.load() error messages (C level dlerror()), should no longer corrupt its state, thanks to Ivan Krylov's PR#19029 report and patch. • as.matrix() again produces a _numeric_ matrix, and the c() and subassignment methods for POSIXlt objects work correctly more often, e.g., without a "tzone" attribute, back porting a few of the PR#18989 fixes from R-devel, both thanks to Suharto Anggono. • In methods, as() now correctly coerces S4 objects to S4 superclasses extending old-style classes, instead of returning only the S3 part. Changes in R 4.6.0: Significant User-Visible Changes: • The R citation now provides a DOI (10.32614/R.manuals): please update your bibliographies accordingly. • The default C++ standard has been changed to C++20 where available (which it is on all known platforms from 2021 on): if not C++17 is used if available otherwise C++ is not supported (as before). (GCC 16 has also switched to C++20 as its default.) Packages can request C++17 if essential. • The Sweave driver Rtangle no longer puts empty lines at the end of tangled scripts. New Features: • The default AIC and BIC methods now check whether the methods namespace is loaded rather than stats4. They still use stats4::logLik (and stats4::nobs), but packages no longer need to load stats4 explicitly. • confint.default() now also works on S4 objects, as long as suitable coef() and vcov() methods exist. • binomial(identity) and quasibinomial(identity) now work without having to quote the argument. • str() now shows more via format() for external pointers. • terms(, specials = *) now treats non-syntactic specials more gracefully, thanks to Mikael Jagan's PR#18568. • help.start() gets a lib.loc option and its default for make.packages.html() is enhanced to allow, e.g., fast access to .Library when that contains only base and recommended packages. • In *.Rd help files, the \linkS4class macro now also works for links to other packages via \linkS4class[]{}, much nicer than the “workaround” \link[:-class]{} necessary in earlier versions of R. Packages with the new syntax need to formally depend on R >= 4.6.0. • tools::analyze_license() now also computes SPDX license identifiers, thanks to Thierry Onkelinx and LLuís Revilla. • read.dcf() now recognizes lines starting with # as comment lines. By Dirk Eddelbuettel, Laurent Gatto and Hugo Gruson. • tcltk::tclVersion() now only optionally includes the ‘patch level’, as Tcl full versions can be of the form 8.7a5 or 9.0b1 without three clear components. • untar(tar = "internal") supports extras = "-P" to use unchanged the recorded file paths (as many external tar programs do). • extSoftVersion()[["zstd"]] now reports the version of the zstd compression library if available, thanks to Trevor Davis' patch proposal in PR#18914. • New logical option() quiet, defaulting to false, set to TRUE by R's command-line option --quiet (and similar), now can be switched during an R session. Prompted by Dirk Eddelbuettel's proposal in PR#18913. • Credentials for basic HTTP authentication with download method "libcurl" can now be provided in a netrc file. The path to the file can be specified in options("netrc"). • tools::deparseLatex() gains a math argument, now used by the default bibstyle to format bibentry() fields with $...$ syntax via Rd \eqn markup. • gzcon() can now decompress a concatenation of compressed streams PR#18887. • Bibliographic citations and references in Rd files can now be auto-generated from bibentries in bibliographic databases in R or BibTeX formats. See RShowDoc("R-exts#Bibliographic-citations-and-references") for more information. • Arguments to loadNamespace() which will be ignored because the namespace is already loaded are now noted. • chkDots()' optional argument allowed has been implemented thanks to Trevor Davis' proposal in PR#18936. • New function messageCondition() to create structured "message" objects analogous to warningCondition() and errorCondition() (PR#18940, by Trevor Davis). • wilcox.test() can now perform exact (conditional) inference in case of ties. Based on contributions by Torsten Hothorn. • wilcox.test() can now optionally compute improved asymptotic p-values by including up to 3 correction terms of the Edgeworth series for the normal approximation. • barplot(.., orderH = *) for stacked bar plots allows to sort the stacks each according to size. • New argument panel.first for hist() (via plot.histogram()), barplot(), bxp(), and hence implicitly boxplot(). All except the former also gain a new panel.last. Suggested by Marieke Stolte and Julian Welz. • plot.default() gets a new switch lim2 to indicate that the default xlim and ylim range computations only use _jointly_ finite x- and y-values; indirectly suggested in PR#7986 by Jincai Jiang. • Rman.css, the stylesheet for the texi2any-generated HTML versions of the R manuals, was improved following joint efforts at the ‘R Dev Days’ of useR! 2024 and RSECon25. • New system Rd macro \manual{}{} to refer to a specific section _etc_ (possibly empty, for Top) of one of the R manuals (e.g., R-exts). • list.files() now has optional argument fixed to allow literal pattern matching. Suggested and implemented by Duncan Murdoch in PR#18925. • substring(txt, i1, i2), substr(..) and their replacement versions now accept i2 = NULL to mean “to the end_of_string”, thus fulfilling Kevin Ushey (and others') suggestions in PR#18851. • The default method for pretty() gets a new switch bounds for completeness, corresponding to .pretty(). Also, it now catches typos such as eps.corrected = 2, noted in PR#18521 by Mikko Korpela. • Plain-text help now renders Rd \describe lists using line breaks after item labels. Set tools::Rd2txt_options(descStyle=NULL) to get the old behaviour with a simple space; a "colon" variant is also available. • x %notin% table newly in base is an idiom for !(x %in% table) and provided almost entirely for convenience and code readability, from an R-devel suggestion, after many years of private definitions mostly hidden in packages, including in R's tools package. • The default method of sequence() gets a new option recycle to swap between current (not fully recycling) and future behaviour where all three of (nvec, from, by) are jointly recycled. • ftable()s default method and the as.table() method for "ftable"s get a perm argument with back compatible default. The as.table() method also gets a named.dim = FALSE switch, no longer creating a named dim() by default. • match.arg() gets a new option several.ok = "all", fulfilling the wish of Jim Hester in PR#16659. • provideDimnames() gets new switch use.names, as proposed including patch by Mikael Jagan, in PR#18975. • The default summary() is more informative for character vectors, optionally resorting to the factor method via the new argument character.method = "factor", e.g., when summarizing a data frame (PR#16750). It also provides more useful summaries for complex vectors, with polar determining if polar or cartesian coordinates are more relevant; mostly based on a proposal by Mikael Jagan. • Error messages from failed Rd \Sexpr code now include the call from the original condition (if available). Warning messages now include Rd source locations. • When the environment variable R_WARN_BOUNDS_OPT is set to "yes", options(warn = val) will check if val is inside -1:2; this may happen unconditionally in the future. • weighted.residuals() now returns weighted working residuals for "glm" objects. It used to return deviance residuals, but these do not give the one-step approximated dfbeta values, as pointed out by Ravi Varadhan. influence.glm() has been amended so that it now returns an object with both a "wt.res" and a "dev.res" element. • Several influence measures for "glm" objects have been updated to use Pearson residuals rather than deviance residuals (the latter are not unbiased) and to not use leave-one-out estimates of dispersion in models with fixed dispersion. Thanks to Ravi Varadhan for discussions and testing of these updates. • R now supports custom binary types which are of the form ".binary." where is lower-case name (letters only) of the system and is the name of the build (alphanumeric and dashes). The corresponding paths returned by contrib.url (which govern the repository layout) with the above type= have the form bin///contrib/ where is the R version without patch level. This is a generalisation of the binary types previously supported on macOS. In addition, binary packages can have the extensions .tar.bz2, .tar.xz, .tar.zst and .tar.zstd with the corresponding compression support. • The value of .Platform$pkgType which defines the native binary type for the current build of R can be overridden with R_PLATFORM_PKGTYPE environment variable (previously this was only set by the macOS builds of R). This should be typically only done by the author of a binary R distribution to define the type of binaries supported by that build of R. • If R uses custom binary type in its .Platform$pkgType then R CMD INSTALL --build will produce __R_-.tar.xz binary files. Please note that future versions may use .zstd compression by default so package tooling should support any of the above mentioned extensions. • New facilities have been introduced for package integrity verification and package signing. The optional file SHA256 in a package contains SHA-256 hashes, lengths and paths of files provided in the package allowing for more reliable integrity verification (relative to MD5). This file is now generated by default in R CMD INSTALL --build and optionally via R CMD build --sha256. A package can be signed by creating a detached GnuPG signature file SHA256.sig signing the entirety of the SHA256 file. Upon installation, the signature is verified using GnuPG, thus ensuring the integrity of the SHA256 file and by induction all files in the package. Both source and binary packages can be signed. Currently, this only applies to tar-based packages, and the command-line GnuPG gpg tool (or equivalent tool named in the GPG environment variable) has to be available for signing and verification to work. R CMD INSTALL --sign can be used to sign binary packages, including its use with --build. System-wide GnuPG keyrings for the R installation can be placed in /etc/keyrings as files with .gpg extensions and will be checked first before consulting user's GnuPG keyring (if present). • Experimentally, several math library (math.h) functions, such as exp(.), log1p(), sin(), atanh(), when called from R, are now ensured to give fully accurate results in a small neighbourhood of special values, such as exp(0) == 1, log1p(0) == 0, etc. This makes R slightly less platform dependent for these functions, notably on platforms with less accurate system math libraries, see also . • Function free1way() implementing semiparametrically efficient inference procedures (likelihood- and permutation-based) in distribution-free stratified K-sample one-way layouts was added to the stats package. Approximate (via power.free1way.test()) and simulation-based (utilising rfree1way() for random number generation) power-assessment and sample-size planning as well as model diagnostics (available from a plot method and probability-probability plots in ppplot()) complement the functionality. Provided by Torsten Hothorn. • plot.data.frame() now supports a formula argument. • New Rd macro \linkS4methods{}, e.g., for easier linking to method docs in other packages, proposed and coded by Mikael Jagan in PR#18998. • Class "difftime" is now also among the S4 "OldClasses". • New function bitstring() as a user-friendly wrapper around intToBits(), etc. • plot.lm() now omits the smoother in the residuals vs leverage plot. This never made much sense, but if you really want it, you can force the old behaviour by setting panel.raw=panel.smooth. • hatvalues() now has a method for nls (nonlinear model) results, prompted by the proposal of Patrice Kiener and Heather Turner in PR#18897. • The Sweave driver RweaveLatex now allows the value of logical and numerical chunk options (only) to be the name of an object defined in earlier, evaluated code chunks. This is useful to pass computed values to options. For options set this way for weaving purposes, the Rtangle driver rather uses their default values, with a warning. By Vincent Goulet. • The Sweave driver RweaveLatex gains an option to include unparsable R code or arbitrary text in code chunks. Chunks marked as ignore.on.weave = TRUE are completely ignored on weaving, i.e., not even parsed. The chunks however remain written out verbatim on tangling. Similarly, the driver Rtangle gains an option to control the extraction of code chunks. Chunks marked as ignore.on.tangle=TRUE are processed as usual on weaving, but left out of the tangled scripts (or thrown away when split=TRUE). The drivers also support the shorter aliases weave for !ignore.on.weave, and tangle for !ignore.on.tangle. A further option ignore, available for both drivers, sets ignore.on.weave and ignore.on.tangle at once. By Vincent Goulet. • The Sweave driver Rtangle now provides an option chunk.sep to control the separator between code chunks in tangled scripts (with an unchanged default of \n\n). Using check.sep=FALSE omits the separator (between two chunks when used as a chunk option). By Vincent Goulet. • The Sweave driver Rtangle now provides an option extension to specify the extension, without the leading dot, for the file name of a tangled code chunk when splitting is selected (the option has no effect with split=FALSE). If TRUE, the default extension of Rtangle (usually .R) is used; if FALSE, no extension is added to the file name. By Vincent Goulet. • New function SweaveGetSourceName in package utils to obtain the name of the file being woven by an Sweave process launched from the command line. By Vincent Goulet. Graphics: • The graphics engine version, R_GE_version, has been bumped to 17 and so packages that provide graphics devices should be reinstalled. The glyphFont() function gains a variations argument, which allows variable font axes to be specified, e.g., c(wght = 100). Only the quartz() device and Cairo-based graphics devices (but not cairo_pdf()) support variable font axes so far. Installation on a Unix-Alike: • configure appends bsdtar to the list of command names it tries when finding a default for TAR. • Failures in building the documentation for the base packages, including from parsing their Rd files, are no longer ignored by make docs. • Building the R manuals now requires Texinfo 6.8 or later. • A new LIBR_LDFLAGS defaulting to LDFLAGS allows more flexibility, e.g., for distributions such as Gentoo, Debian or Ubuntu, fixing PR#18992; additionally a make failure to create libR.pc should no longer be ignored, fixing PR#18993; both thanks to Benjamin Drung. Checking an Installation: • There is a new directory tests/C++Standards which contains small packages which can be test-installed to check support for various C++ standards. This is principally for use on Windows as on a Unix-alike this partially duplicates tests done by configure - although it can also be used to test the behaviour of R CMD INSTALL on unsupported standards. Package Installation: • Specifying C++11 or C++14 in src/Makevars has long given a note: in 99% of CRAN packages the specification was unnecessary as the default C++17 sufficed (in a few cases with a deprecation warning from some compilers). Support for these standards has been removed: the default C++ standard will be used. R CMD config variables CXX11, CXX14 and their associated CXXxxFLAGS, CXXxxPICFLAGS CXXxxSTD, SHLIBCXXxxLD and SHLIBCXXxxLDFLAGS variables are no longer supported and reported as ‘defunct’. • When installing binary packages the time stamp in the "Built" field is considered even if the package version is identical to allow binary package repositories to update binaries without the need to increase the package version. • The "Built" column returned by installed.packages() and old.packages() now contains the full value of the "Built" entry from the (installed) DESCRIPTION file. Previously, only the R version from the "Built" entry was returned. • If the timestamp passed as --built-timestamp to R CMD INSTALL is in RFC-2822 form (with time-zone offset) it will be converted to ISO UTC form to conform to the format used by R for purposes described above. (PR#19037, thanks to Dirk Eddelbuettel) C-Level Facilities: • New functions GEcreateDD() and GEfreeDD() for allocating (and initialising) DevDesc structures. Can be used by external graphics devices. Satisfies PR#18292. • New function R_eval_with_gd() designed to “lock” a graphics device during call to eval() within device drawing routines. External _on-screen_ graphics devices should consider using this function to avoid crashes from the device being closed by the user (e.g., a mouse click) during drawing. • Declarations for non-API functions LOGICAL0, INTEGER0, REAL0, COMPLEX0, and RAW0 have been removed from installed header files. • Non-API entry points Rf_acopy_string and Rf_lazy_duplicate have been added to those reported by R CMD check. • Packages using the non-API functions ATTRIB and SET_ATTRIB will now receive check NOTEs. See ‘Writing R Extensions’ for alternatives to use. • R CMD check NOTEs on the use of these non-API entry points have been upgraded to WARNINGs in preparation for removing declarations and, where possible, hiding these entry points: R_nchar, R_tryWrap, Rf_GetOption, R_lsInternal, BODY, FORMALS, CLOENV, SET_TYPEOF, STRING_PTR, R_duplicate_attr, getConnection, R_data_class, STRING_PTR, SET_OBJECT, ATTRIB, SET_ATTRIB, Rf_findVarInFrame3. • The deprecated macros CHARACTER_DATA and CHARACTER_POINTER now return const pointers since using writable pointers in packages is not safe. • New function DATAPTR_RW() for use in implementing ALTREP Dataptr methods. This function should not be used in any other contexts. • New function R_class() as the C equivalent of class() in R. • New function Rf_isScalarString. • The R_ObjectTable type definitions formerly in R_ext/Callbacks.h are now available in the new header file R_ext/ObjectTable.h. This new header file should be used in packages instead of R_ext/Callbacks.h. • Task callback support declared in R_ext/Callbacks.h has been enabled again. It was disabled for R 4.5.0. • The non-API header file R_ext/PrtUtil.h is no longer copied to the installed include directory. • New function R_mapAttrib for iterating over the attributes of an object. • New functions R_altrep_class_name and R_altrep_class_package for retrieving the class name symbol and package name symbol of an ALTREP object. These should be used instead of ALTREP_CLASS. • New function R_getAttributes returns the same result as the R function attributes. New functions R_getAttribCount, R_getAttribNames, R_hasAttrib, R_nrow, and R_ncol. • The function Rf_isFrame has been removed; use Rf_isDataFrame instead. • The function VECTOR_PTR has been removed. The non-API function DATAPTR is no longer declared in an installed header file. • These entry points are now marked as hidden and no longer have declarations in installed header files: ENVFLAGS, EXTPTR_PROT, FRAME, ENCLOS, EXTPTR_PTR, EXTPTR_TAG, HASHTAB, IS_S4_OBJECT, LEVELS, NAMED, OBJECT, R_shallow_duplicate_attr, Rf_isValidString, Rf_lazy_duplicate, Rf_NonNullStringMatch, SETLENGTH, SETLEVELS, SET_BODY, SET_CLOENV, SET_ENCLOS, SET_FORMALS, SET_ENVFLAGS, SET_FRAME, SET_GROWABLE_BIT, SET_HASHTAB, SET_NAMED, SET_S4_OBJECT, SET_TRUELENGTH, STDVEC_DATAPTR, TRUELENGTH, UNSET_S4_OBJECT, XTRUELENGTH. • New experimental API for working with variable bindings in environments. The function R_GetBindingType identifies the binding type without forcing a delayed or active binding. New bindings care created by R_MakeDelayedBinding, R_MakeForcedBinding and R_MakeMissingBinding. Delayed and forced bindings can be inspected with R_ForcedBindingExpression, R_DelayedBindingExpression, and R_DelayedBindingEnvironment. Bindings for ... in function call environments can be examined with R_findDotsEnv, R_DotsExist, R_DotsLength, R_DotsNames, R_DotsElt, R_GetDotType, R_DotDelayedExpression, R_DotDelayedEnvironment, and R_DotForcedExpression. Contributed by Lionel Henry, Davis Vaughan, and Charlie Gao in PR#18928. • New function R_envSymbols returns a vector of the symbols for which an environment contains bindings (PR#18928). • R CMD check NOTEs on the use of the non-API entry points PRCODE, SET_PRCODE, PRENV, SET_PRENV, PRVALUE, SET_PRVALUE, R_PromiseExpr, and Rf_allocSExp have been upgraded to WARNINGs in preparation for removing declarations and, where possible, hiding these entry points. • New functions R_getVar and R_getVarEx. In most cases these can be used instead of the non-API functions Rf_findVar and Rf_findVarInFrame. Other cases can be handled by the new API for working with variable bindings. • Packages using any non-API variables will now receive check NOTEs. • New function R_getRegisteredNamespace finds and returns the namespace environment registered for a name, or R_NilValue if none is found. Utilities: • R CMD check now reports further clang warnings including -Wkeyword-macro. This is most commonly seen for the C23 keywords bool, true and false, but is also seen for nullptr (C23 and C++11). Masking these by macros _may_ generate correct code (but not always) and always results in confusing-to-read code. • The cascaded stylesheet R.css now adds less vertical white space when rendering Rd files' \itemize, \enumerate, and \describe list \items to HTML. Where R is used via extensive IDEs such as RStudio, their maintainers may need to adapt R.css files accordingly. • R CMD check when passed a tarball looks at its contents and so no longer derives the package name from the tarball name (which can now be arbitrary). • Package README.md files are now installed and featured in HTML help. • package.skeleton() now invisibly returns the path of the created directory, similar to prompt() et al., and allows creating blank skeletons without any R objects. Deprecated and Defunct: • structure(NULL, = ) is now defunct. • Three tk*.slaves() functions were deprecated in favor of tk*.child() which do need Tcl/Tk version 8.6 or higher. Bug Fixes: • chol(x, pivot=TRUE) now zeroes the trailing submatrix when the algorithm stops early. Following the help page instructions on how to reconstruct the matrix in positive semidefinite cases gave incorrect results if the rank was 2 or more less than the dimension (PR#15853). • Profiling "mle" objects (stats4 package) could fail because profile MLE used starting value from full MLE. Now starts from profile MLE from previous step. • Setting attributes on primitive functions is now an error; previously it modified without copying (as noticed by Henrik Bengtsson on the R-devel mailing list). Relatedly, changing the environment() of a primitive function does no longer happen and gives a warning (to become an error, later). • Dataset LifeCycleSavings had a misspelled row name: "Guatamala" was corrected to "Guatemala". • The Pair(x,y) construction in the formula interface to paired tests did not work with the subset argument, due to the absence of a [.Pair method, which has now been added (PR#18898). • Subsetting "table" objects keeps S3 classes more consistently, fixing PR#18845. • When browser() is active or when otherwise debugging, R code such as if(TRUE) no longer triggers a new browser level, fixing PR#18885 (differently than the fix for PR#15770), with thanks to Ivan Krylov. • text() now truncates labels to maximum length of x and y (if it is longer), fixing PR#7084. Thanks to Heather Turner, Ella Kaye, and Philippe Grosjean. • %in% set is again as fast as it was before R 4.3.0, _via_ a new S3 method mtfrm.Date. %in% and vice versa are now documented to work in concordance with == and as an exception to the typical match() behaviour which relies on “univariate” mtfrm() alone. • It is now possible to convert _to_ "snpc" units via, e.g., grid::convertWidth(), fixing PR#18915. Thanks to Trevor Davis. • The precip dataset had typos in the names "Bismarck" and "Pittsburgh" (PR#18895). • tools::checkReplaceFuns() now deals better with replacement methods _not_ available as regular functions in the namespace. • length(xpr) <- n now also works for expression vectors, the same as for lists, i.e., padding with NULL entries if the length is increased. Thanks to Mikael Jagan's PR#18917. • [i] <- NA now only sets the _real_ part to NA, consistently with the as.complex(NA) behaviour since R 4.4.0; thanks to Mikael Jagan's PR#18918. • format() calling format.default() now calls generic format() on each list element (rather than format.default()). • tools::Rd2HTML() detects paragraphs in more cases of \Sexpr-generated Rd code, fixing a regression in R 3.6.0 originally reported by Georgi Boshnakov and later also in PR#18470. An inactive #ifdef block no longer breaks the paragraph. • Parsing a multi-line string from Rd \Sexpr code no longer doubles the newlines. • requireNamespace(.., versionCheck = *) now shows an error and returns FALSE when the package version check is not fulfilled, thanks to Iris Simmons and Trevor Davis's PR#18255. Additionally, the versionCheck argument is checked and when invalid, an error is signalled to avoid subsequent confusing error messages. • requireNamespace() now throws an error even if the name space is already loaded if it is called with an unmatched argument such as quitely = TRUE or quiet = TRUE (argument quietly cannot be abbreviated as it follows ...). • rep() signals more specific error messages, notably when using both times and each optional arguments. Fixes PR#18926, thanks to Ella Kaye and collaborators at useR! 2025's ‘R Dev Day’. • jitter(x, amount, factor) becomes more robust for non-finite x or also negative amount, factor. help(jitter) is easier to read, fixing PR#17279, thanks to its contributors. • Plain-text help (Rd2txt) lacked markup for \cited titles, which are now wrapped in single quotes. • Default column labels are now correctly aligned when printing a matrix with right alignment (PR#18943, thanks to Mikael Jagan). • poly(fct, n) signals an error again, for a non-ordered factor fct, thanks to Roland Fuss' notice on R-devel. • terms(, simplify=TRUE) now works correctly also in the cases where the formula has more than one term with NAs such as f(u, b=NA) or g(NA), finally fixing PR#15275 thanks to Mikael Jagan's patch. • The help page example(matplot) now correctly labels Sepal vs Petal dimensions in its first iris data plot, thanks to Jeff Dick's post on R-devel. • diff(m, lag, dif) for matrix m now still returns matrices, also when lag * dif > nrow(m) (PR#18972, thanks to Mikael Jagan and Suharto Anggono). diff() remains matrix, even when it has length zero. • Values returned by active binding functions are now marked as not mutable to prevent unintended mutation in complex assignment operations. • The default method of sequence() now allows to fully recycle all three of (nvec, from, by) as always documented; with thanks to Mikael Jagan's report and patch in PR#18304. Its behaviour remains back compatible for now, but can be switched to future behaviour via environment variable R_sequence_recycle, or explicit recycle = TRUE. • Subassignment, x[ind] <- val, to 1-dimensional arrays no longer “drops” them to simple vectors when ind is a name, fixing PR#18973, reported by Thomas Soeiro. • The implicitGeneric definition for toeplitz() produced a default method that failed when toeplitz(x, r) was called with more than the first argument. Simple fix from Mikael Jagan. • The error message for array(dim = c()) now uses "'dim'", thanks to Hugo Gruson. • Some legal but strange nested complex assignments are handled a bit more robustly in interpreted code. • cacheMetaData() does not to mangle primitive generics. • The S4 method norm(, type = ) for the implicit generic norm() now uses type = "O" as has been the intention for more than ten years, fixing PR#18979 thanks to Mikael Jagan. • On Windows terminals Ctrl-C now breaks out of waiting for keyboard input, fixing PR#18982. • The default summary() and its factor method now label missing values NAs rather than NA's, fixing a decades-old grammatical faux pas inherited from S (PR#16348 and PR#18948). • Asymmetric toeplitz(x, r) is type consistent now, even when r of length 0 or 1 is not used directly. Fixes PR#18996, thanks to Mikael Jagan's patch and test. • format(r) now keeps names(r) also for raw objects r. • rep.int() and rep_len() again drop names also for factors, fixing a regression in R 4.0.0. (Thanks to a report by Rui Barradas and PR#18999 by Suharto Anggono.) • str(x) with a list-like x of a class having an str() S3 method using NextMethod(), now no longer outputs "List of <...>" in the default method, thanks to Ian Farm's report and fix proposal in PR#19001. • as.POSIXlt(ch), as.Date(ch) etc now also work correctly when ch contains "Inf", via strptime(.), fixing PR#19006. • c(, ..) now fully preserves sub-second accuracy, fulfilling a part of Suharto Anggono's wishlist PR#18989. • When subassigning "POSIXlt", e.g., [i] <- v, v is now converted to the time zone of dat, before being assigned, see PR#18919. • The "tzone" attribute of "POSIXlt" objects should no longer depend on earlier calls, fixing PR#19005 thanks to Ivan Krylov, a patch by Suharto Anggono and reports of “Non-deterministic POSIXlt tzone in Europe/London ..” on R-devel. • In intervals with very low density cdplot() was unreliable, returning probabilities that are greater than one or NaN (PR#19011). Fix from Christoph Dalitz and Achim Zeileis. • R CMD build now installs packages providing their own vignette engine (PR#18191). Patch by Paul Smith. • ar.burg(), ar.yw() and ar.ols() deal better with non finite AIC values thanks to Simone Giannerini's remarks on R-devel. • Parsing deeply nested expressions no longer should segfault in certain circumstances, fixing five different checks on context stack size, thanks to Kevin Ushey's report and Michael Chirico's patch in PR#18994. • The internal cwilcox function used in computations for the Wilcoxon distribution is now based on an implementation of a formula by Andreas Löffler provided by Andreas Löffler, Aidan Lakshman, and Ivan Krylov, substantially reducing the memory complexity of the original implementation (PR#18655). • When Ops group methods for matrix-"ts" return a zero-extent matrix, its type is correct now. E.g., + now returns type "double", see also PR#18972. • intToUtf8() now returns NA and no longer accesses invalid memory, thanks to Kevin Ushey's report with patch in PR#19052. • When file.choose() is terminated with an EOF, it now signals an error rather than returning garbage, thanks to Kevin Ushey's report and patch in PR#19053, Changes in R 4.5.3: Utilities: • tools/fetch-recommended can be used instead of tools/rsync-recommended to fetch recommended packages into R sources using curl on systems without rsync or behind firewalls. Package Installation: • C++ standard specifications (CXX_STD = in src/Makevars* and in the SystemRequirements field of the DESCRIPTION file) are now checked more thoroughly. Invalid values are still ignored but now give a warning, as do contradictory specifications. • (Preliminary) support for C++26 has been extended to Windows. • A non-zero exit status from cleanup, cleanup.win or cleanup.ucrt, if requested via options --clean or --preclean, is now reported with a warning. Bug Fixes: • all.equal(obj, simple, check.class=FALSE) now is true, also when simple is a bare atomic vector and obj has a simple class, fixing the first part of PR#18971 thanks to Jan Gorecki. • str(x, give.attr=FALSE) no longer shows attributes when x is a zero length "Date" or "POSIXt" object. • Tweaks to binning for bw.SJ() and bw.ucv() in the very rare case of data which have an extremely small range compared to their absolute values, e.g., x <- 6e9 + 6:9. • Formatting book-type bibentry objects now converts LaTeX accents also in the publisher and series fields. • model.frame(~1, list(), na.action=na.pass) and similar “border-line” uses no longer produce invalid data frames, fixing PR#18977, reported with patch by Mikael Jagan. • length() <- v is more careful about balancing, notably when v is not integer, thanks to Suharto Anggono's remarks on the mailing list R-devel. • approx(, , na.rm = FALSE) now should always call the ties() function, fixing PR#17604 reported by Bill Dunlap. • besselJ(1, 1e-15) and similar now give correct results, thanks to Leo Mada and other “R-help”ers. • vignette(::) is now a documented usage variant and confines vignette retrieval to the specified package. • pretty(ch) again correctly works with ch a character vector of numbers. • persp() labels the three axes correctly also when C level atan2pi() is available, fixing PR#19007 by Klaus Schliep. • Large (tall) subscripts in plotmath expressions are now positioned correctly. They were being positioned too high. • Ops group (Arith, Compare, ...) methods for matrix-"ts" now do return (zero length) matrices even when the two series do not overlap; a very partial fix of PR#18972, which is to be fully addressed later. Changes in R 4.5.2: Utilities: • R CMD check now handles archives with extension .tar or .tar.zstd (where zstd compression is supported by the R build). Bug Fixes: • t.test(c(1:3, Inf)) and similar no longer produce an error but return a (still not so useful) "htest" result, fixing PR#18901, thanks to Jesse Alderliesten. • attr(., "tsp") <- val now uses getOption("ts.eps") instead of hardwired 1e-5; consequently, ts(.., ts.eps=*) now passes ts.eps to the "tsp" setting C code; both fixing a long-standing ‘FIXME’. • insertSource() now ignores the internal .packageName object, avoiding a superfluous message. • In static HTML help, links to vignette files from the default doc/index.html page now also work for packages not installed in the default .Library, thanks to a report by Patrice Kiener. • fixInNamespace("") failed to update the S3 methods table when the generic was not on the search path. • In plain-text help (Rd2txt), an initial newline from an Rd inline \eqn no longer breaks the paragraph. • hist(*, log = "x") now works without a warning, thanks to Martin Smith's PR#18921. • Subassigning "POSIXlt", i.e., [i] <- val and [[i]] <- val now rebalance as they should; thanks mostly to Mikael Jagan's PR#18919. • [*] (re-)setting "balanced", fixing PR#18681 comment #7, thanks to Mikael Jagan. • All four of {col,row}{Sums,Means}(Z, na.rm=TRUE) now correctly work with complex Z where is.na(Re(Z)) differs from is.na(Im(Z)), fixing PR#18942, unearthed by Dirk Eddelbuettel. • Fix for glyph rendering on the quartz() device when there is other (“normal”) text drawn on the device. The problem was that the text transformation matrix was not reset so glyphs would be rendered incorrectly (often completely outside the device, i.e., not visible). • Functions install.packages() and download.packages() again consult option download.file.method when the download method is unspecified. • Tanguy Barthelemy and colleagues at the ‘R Dev Day’ following Rencontres R in May 2025 extended the help page of lm(), fixing PR#18058. As suggested by Thomas Soeiro, such notes were also added to the glm(), poly() and splines::bs() and ns() pages. • lbeta(1i, 1) now signals an error, as lbeta() is not implemented for complex, fixing PR#18946 from Ben Bolker and Kasper Kristensen. • The Cairo-based SVG device uses pt as the default document unit also with Cairo >= 1.17.8 (PR#18912). • pretty(*, eps.correct = 2) has been fixed, e.g., to avoid over 1 million length result for pretty(c(0, 1e-322), eps.correct = 2). • When "POSIXlt" date-time objects are NA-padded from subsetting or increasing length in the `[` or `length<-` methods, the "balanced" attribute is set to NA, now; noted in PR#18681, thanks to Mikael Jagan. Changes in R 4.5.1: New Features: • The internal method of unzip() now follows unzip 6.00 in how it handles extracted file paths which contain "../". With thanks to Ivan Krylov. Installation: • Standalone nmath can be built with early-2025 versions of clang-based compilers such as LLVM clang 20, Apple clang 17 and Intel icx 2025.0. • Tcl/Tk 9 can be used to build package tcltk: this has become the default in some Linux distributions. Bug Fixes: • Java detection in javareconf could not detect libjvm.* in the zero variant of the JDK (PR#18884). All valid variants as of JDK 24u are now supported. • factanal(.., rotation=*) now correctly updates rotmat, fixing PR#18886. • dnbinom(, , ..) now is 0 correctly, instead of NaN or Inf sometimes. • dbinom(, n=Inf, ..) is 0 now correctly, instead of NaN which also fixes many dnbinom() cases, notably those mentioned in PR#16727 comment #5. • Fixing C level “binomial deviance” bd0() for extreme arguments (preventing under-/overflow) solves more PR#16727 cases and also prevents some full accuracy loss in such cases for dbinom(), dnbinom(), and via dbinom_raw() potentially dgeom(), dhyper(), dbeta(), and df(). • signif(1.**e308, digits) no longer truncates unnecessarily (but still to prevent overflow to Inf), fixing PR#18889. • prettyNum(*, zero.print={>=1-char}, replace.zero=TRUE) now works as documented, thanks to Marttila Mikko and Ivan Krylov's messages on R-devel. • pbeta(x, a,b, ..) for very large a,b no longer returns NaN but the correct values (0 or 1, or their logs for log.p = TRUE). This improves Mathlib's C level bratio() and hence also pnbinom(), etc.. Changes in R 4.5.0: New Features: • as.integer(rl) and hence as.raw(rl) now work for a list of raw(1) elements, as proposed by Michael Chirico's PR#18696. • graphics' grid() gains optional argument nintLog. • New functions check_package_urls() and check_package_dois() in package tools for checking URLs and DOIs in package sources. • New head() and tail() methods for class "ts" time series, proposed by Spencer Graves on R-devel. • New qr.influence() function, a “bare bones” interface to the lm.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 to grep() except for the default value = TRUE. • methods(:::) now does report methods when neither the generic nor the methods have been exported. • pdf() gains an author argument to set the corresponding metadata field, and logical arguments timestamp and producer to optionally omit the respective metadata. (Thanks to Edzer Pebesma.) • grDevices::glyphInfo() gains a rot 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(), and CRAN_authors_db(). • Package tools now exports functions R() and parse_URI_reference(). • Package tools now exports functions base_aliases_db() and base_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 arguments checkSorted and checkNA which allow skipping 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 the bytes= argument instead of files=. The two arguments are mutually exclusive. • Added function sha256sum() in package tools analogous to md5sum() implementing the SHA-256 hashing algorithm. • The xtfrm() method for class "AsIs" is now considerably faster thanks to a patch provided by Ivan Krylov. • The merge() method for data frames will no longer convert row names used for indexing using I(), which will lead to faster execution in cases where sort = TRUE and all.x and/or all.y are set to TRUE. • The methods package internal function .requirePackage() now calls requireNamespace(p) instead of require(p), hence no longer adding packages to the search() path in cases methods or class definitions are needed. Consequently, previous workflows relying on the old behaviour will have to be amended by adding corresponding library(p) calls. • More R-level messages use a common format containing "character string" for more consistency and less translation work. • available.packages() and install.packages() get an optional switch cache_user_dir, somewhat experimentally. • The sunspot.month data have been updated to Oct 2024; because of recalibration also historical numbers are changed, and we keep the previous data as sunspot.m2014 for reproducibility. • The quartz() device now supports alpha masks. Thanks to George Stagg, Gwynn Gebeyhu, Heather Turner, and Tomek Gieorgijewski. • The print() method for date-time objects (POSIX.t) gets an optional digits argument for _fractional_ seconds, passed to improved format.POSIXlt(); consequently, print(, digits = n) allows to print fractions of seconds. • install.packages() and download.packages() download packages simultaneously using libcurl, significantly reducing download times when installing or downloading multiple packages. • Status reporting in download.file() has been extended to report the outcome for individual files in simultaneous downloads. • The Rd \link macro now allows markup in the link text when the topic is given by the optional argument, e.g., \link[=gamma]{\eqn{\Gamma(x)}}. • If La_library() is empty, sessionInfo() still reports La_version() when available. • seq.int(from, to, by, ....) when |by| = 1 now behaves as if by was omitted, and hence returns from:to, possibly integer. • seq.Date(from, to, by, ....) and seq.POSIXt(..) now also work when from is missing and sufficient further arguments are provided, thanks to Michael Chirico's report, patch proposal in PR#17672 and ‘R Dev Day’ contributions. The Date method also works for seq(from, to), when by is missing and now defaults to "1 days". It is now documented (and tested) that the by string may be _abbreviated_ in both seq methods. Both methods return or keep internal type "integer" more consistently now. Also, as.POSIXct({}) is internally integer. • duplicated(), unique(), and anyDuplicated() now also work for class expression vectors. • New function use() to use packages in R scripts with full control over what gets added to the search path. (Actually already available since R 4.4.0.) • New connection type zstdfile for files compressed by zstd if R was built with such support. file() and gzfile() can automagically read such files. • memCompress() and memDecompress() have options to use zstd compression if R was built with support for it. • There is some support for zstd compression of tarballs in tar() and untar(). (This depends on OS support of libzstd or by tar.) • print(summary()) gets new optional argument zdigits to allow more flexible and consistent (double) rounding. The current default zdigits = 4L is somewhat experimental. Specifying both digits = *, zdigits = * allows behaviour independent of the global digits option. • The format() method for "difftime" objects gets a new back compatible option with.units. • A summary() method for "difftime" objects which prints nicely, similar to those for "Date" and "POSIXct". • unique()'s default method now also deals with "difftime" objects. • optimize(f, *) when f(x) is not finite says more about the value in its warning message. It no longer replaces -Inf by the largest _positive_ finite number. • The documentation of gamma() and is.numeric() is more specific, thanks to the contributors of PR#18677. • New dataset gait thanks to Heather Turner and Ella Kaye, used in examples. • New datasets penguins and penguins_raw thanks to Ella Kaye, Heather Turner, and Kristen Gorman. • isSymmetric() gains a new option trans = "C"; when set to non-default, it tests for “simple” symmetry of complex matrices. • model.frame() produces more informative error messages in some cases when variables in the formula are not found, thanks to Ben Bolker's PR#18860. • selectMethod(f, ..) now keeps the function name if the function belongs to a group generic and the method is for the generic. BLAS and LAPACK: • The bundled BLAS and LAPACK sources have been updated to those shipped as part of January 2025's LAPACK 3.12.1. • It is intended that this will be the last update to BLAS and LAPACK in the R sources. Those building R from source are encouraged to use external BLAS and LAPACK and this will be required in future. • This update was mainly bug fixes but contained a barely documented major change. The set of BLAS routines had been unchanged since 1988, so throughout R's history. This update introduced new BLAS routines dgemmtr and zgemmtr which are now used by LAPACK routines. This means that BLAS implementations are no longer interchangeable. • To work around this, R can be configured with option --with-2025blas which arranges for the 2025 BLAS additions to be compiled into libRlapack (the internal LAPACK, not built if an external LAPACK is used). This option allows the continuation of the practice of swapping the BLAS in use by symlinking lib/libRblas.*. It has the disadvantage of using the reference BLAS version of the 2025 routines whereas an enhanced BLAS might have an optimized version (OpenBLAS does as from version 0.3.29). • Windows builds currently use the internal LAPACK and by default the internal BLAS: notes on how to swap the latter _via_ Rblas.dll are in file src/extra/blas/Makefile.win. Installation on a Unix-Alike: • A C23 compiler (if available) is now selected by default for compilation of R and packages. R builds can opt out _via_ the configure flag --without-C23, unless the specified or default (usually gcc) compiler defaults to C23: gcc 15 does. A C23 compiler is known to be selected with gcc 13-15, LLVM clang 18-20 (and 15 should), Apple clang 15-17 and Intel 2024.2-2025.0 (and 2022.2 should). Current binary distributions on macOS use Apple clang 14 and so do not use C23. • The minimum autoconf requirement for a maintainer build has been increased to autoconf 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. • Control of symbol visibility is now supported on macOS (the previous check only worked on ELF platforms). • There is now support for installing the debug symbols for recommended packages on macOS: see REC_INSTALL_OPT in file config.site. • configure is now able to find an external libintl on macOS (the code from an older GNU gettext distribution failed to try linking with the macOS Core Foundation framework). Installation on Windows: • Both building R and installing packages use the C compiler in C23 mode. • R on Windows by default uses pkg-config for linking against external libraries. This makes it easier to test R and packages with alternative toolchains (such as from Msys2, e.g., testing with LLVM and possibly with sanitizers). It also allows more significant Rtools updates within a single R minor release. • The installer scripts for Windows have been tailored to Rtools45, an update of the Rtools44 toolchain. It is based on GCC 14. The experimental support for 64-bit ARM (aarch64) CPUs is based on LLVM 19. R-devel and R 4.5.x are no longer maintained to be buildable using Rtools44 and it is advised to switch to Rtools45. 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, and showMlist and the "MethodsList" class for S4 method handling were removed from package methods. Deprecated functions balanceMethodsList, emptyMethodsList, inheritedSubMethodLists, insertMethod, insertMethodInEmptyList, makeMethodsList, mergeMethods, MethodsList, MethodsListSelect, and SignatureMethod were made defunct, as were the "MethodsList" branches of functions assignMethodsMetaData, finalDefaultMethod, and MethodAddCoerce. • getMethods(*, table = TRUE) is deprecated. • Building with the bundled (and old) version of libintl is deprecated and now gives a configure warning. This should be selected only if neither the OS's libc (as on GNU Linux) nor an external libintl library provide suitable functions. Instead install libintl from a recent version of GNU gettext (available for macOS) or use configure option --disable-nls. The ability to use the bundled version may be removed as soon as R 4.5.1. • The deprecated xfig() graphics device has been removed. Package Installation: • Packages are now installed using C23 where supported by the OS and R build. Packages using R's compiler settings can ask *not* to use C23 _via_ including USE_C17 in SystemRequirements or can be installed by R CMD INSTALL --use-C17. (Some packages ignore these settings in their configure script or when compiling in sub-directories of src, as will those using a src/Makefile.) • Source installs now report the package version in the log. • There is preliminary support for C++26 with GCC >= 14, Apple clang++ >= 16 and LLVM clang++ >= 17. C-Level Facilities: • The non-API and hidden entry points Rf_setIVector, Rf_setRVector and Rf_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. • SET_TYPEOF now signals an error unless the old and new types have compatible memory structure and content. Use of SET_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 desired type in the first place. • The set of LAPACK (double and complex) routines declared in the headers R_ext/Lapack.h and R_ext/Applic.h has been extended, mostly to routines actually in use by packages. • Memory allocation messages now use the (non-SI 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 always includes header float.h or cfloat for constants such as DBL_MAX. • Strict R headers are now the default. This removes the legacy definitions of PI, Calloc, Realloc and Free: use M_PI, R_Calloc, R_Realloc or R_Free instead. • The deprecated and seemingly never-used S-compatibility macros F77_COM and F77_COMDECL have been removed from header R_ext/RS.h. • The enum Rboolean defined in header R_ext/Boolean.h now has a fixed underlying type of int on platforms whose C compiler supports this. This is a C23 feature (taken from C++11) and also supported in all C standards by some versions of clang (from LLVM and Apple) and (with a warning when using -pedantic) by GCC when in C17 mode. A fair amount of code has assumed this: it may be changed to a smaller type in future. In particular, as standard compilers do not check the validity of assignment to an enum, it has been possible to assign NA_INTEGER to an Rboolean variable, coerce it to int and recover the value. If there were a platform which used an underlying type of a different size this would be an ABI-breaking change (but we are unaware of any such platform). • Header R_ext/Boolean.h now ensures that a bool type is available either as a keyword (C23 and C++) or by including the C99 header stdbool.h. This is being used internally in R to replace Rboolean by bool. • There are new functions asRboolean and asBool, variants of asLogical more suited to converting logical arguments to Rboolean or to bool. They require a length-one input and throw an error if that evaluates to NA. • Header R_exts/Error.h now ensures that Rf_error and similar are given a noreturn attribute when used from C++ under all compilers. • Header R_exts/Utils.h no longer contains a declaration for F77_SUB(interv). This is intended to be called from Fortran and was wrongly declared: LOGICAL in Fortran corresponds to int * not Rboolean *. • Defining R_INCLUDE_BOOLEAN_H to 0 before including headers R.h or Rinternals.h (or any other header which includes R_ext/Boolean.h) stops the inclusion of header R_ext/Boolean.h which `defines' constants TRUE, FALSE, true, false and the type bool which some package maintainers wish to avoid. Note that the last three are keywords in C23 and C++11 so cannot be avoided entirely. However, with commonly-used compilers they can be masked by a macro of the same name, often with a warning. C-Level API: • 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. Also for Fortran-callable entry points which are part of the API. • ‘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. • New API function R_mkClosure. This checks that its arguments are valid and should be used instead of allocSExp(CLOSXP followed by SET_FORMALS, SET_BODY, and SET_CLOENV. • New API functions R_ClosureFormals, R_ClosureBody, and R_ClosureEnv for extracting closure components. The existing functions R_ClosureExpr and R_BytecodeExpr have also been added to the API. • New API function R_ParentEnv corresponding to R's parent.env(). • Further 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, and VECTOR_PTR. Any declarations for these in public header files will be removed in the near future, and they will be hidden where possible. • Some R CMD check NOTEs on the use of non-API entry points have been upgraded to WARNINGs in preparation for removing declarations and, where possible, hiding these entry points. • Additional non-API entry points have been 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, and XTRUELENGTH. • Enable defining R_NO_REMAP_RMATH and calling Rf_*() as has been documented in ‘Writing R Extensions’ for a while, fixing PR#18800 thanks to Mikael Jagan and Suharto Anggono. • R_GetCurrentSrcref(skip) now skips calls rather than srcrefs, consistent with counting items in the traceback() display. If skip == NA_INTEGER, it searches for the first srcref, starting at the current evaluation state and proceeding through the call stack; otherwise, it returns the srcref of the requested entry from the call stack. Utilities: • R CMD INSTALL (and hence check) now compile C++ code with -DR_NO_REMAP. ‘Writing R Extensions’ has been revised to describe the remapped entry points, for with the Rf_ prefix remains optional when used from C code (but is recommended for new C code). • R CMD check --as-cran notes bad parts in the DESCRIPTION file's URL fields. • R CMD check now reports more warnings on long-deprecated/obsolete Fortran features reported by gfortran -Wall. For hints on how to modernize these, see . • Since almost all supported R versions now use UTF-8, R CMD check no longer by default reports on marked UTF-8 or Latin-1 strings in character data. Set environment variable _R_CHECK_PACKAGE_DATASETS_SUPPRESS_NOTES_ to a false value for the previous behaviour. • tools::checkDocFiles() notes more cases of usage documentation without corresponding \alias. • R CMD check with a true value for environment variable _R_CHECK_BASHISMS_ checks more thoroughly, including for bash scripts and bashisms in components of autoconf-generated configure scripts. • R CMD check gains option --run-demo to check demo scripts analogously to tests. This includes a check for undeclared package dependencies: it can also be enabled separately by setting the environment variable _R_CHECK_PACKAGES_USED_IN_DEMO_ to a true value (as done by R CMD check --as-cran). • R CMD build now supports --compression=zstd on platforms with sufficient support for zstd. • tools::texi2pdf(..., texinputs=) now _pre_pends the specified to TEXINPUTS. When building R itself (doc/NEWS.pdf and base vignettes) or package manuals using R CMD Rd2pdf, it is ensured that this R's Rd.sty takes precedence over any other (incompatible) versions in default “texmf trees”. • tools::Rd2latex() no longer outputs an \inputencoding{utf8} line by default; such a declaration is obsolete since LaTeX 2018-04-01. Bug Fixes: • update_pkg_po() now copies .mo files to the translation package even if a DESCRIPTION file exists, thanks to Michael Chirico fixing PR#18694. • Auto-generated citation() entries no longer include (additional) URLs in the note field (PR#18547). • as.data.frame.list() gets a new option new.names and now preserves NA names, thus fixing the format() method for data frames, and also bug PR#18745. Relatedly, the format() method gets an option cut.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 when length(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 argument max, 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 warns about _some_ failures to change the language. • Printing ls.str() now shows "" even when R's language setting is not English. • xyTable() now handles and reports NAs 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 mention max in addition to getOption("max.print"). • rowSums(A, dims = dd), colMeans(..), etc, give a more helpful error message when dd is not of length one, thanks to Michael Chirico's PR#18811. • seq.Date() no longer explicitly coerces results from integer to double, analogously with seq.default(), seq.int() and seq.POSIXt(), resolving a _modified_ PR#18782. • axisTicks(usr, ...) documentation clarification for log = TRUE, fixing bug PR#18821 thanks to Duncan Murdoch. • debug() and debugonce(fun) now also accept a string fun when it names an S4 generic, fixing PR#18822 thanks to Mikael Jagan. • debugonce(, signature=*) now works correctly when “called twice”, fixing PR#18824 thanks to Mikael Jagan. • format(dtime, digits=* / format=*) is more consistent when the POSIXt date-time object dtime has fractional (non integer) seconds. Fixes PR#17350, thanks to new contributions by LatinR's ‘R Dev Day’ participants, Heather Turner and Dirk Eddelbuettel; also fixes more cases, notably when format contains %OS. • options(scipen = NULL) and other invalid values now signal an error instead of invalidating ops relying on a finite integer value. Values outside the range -9 .. 9999 are now warned about and set to a boundary or to the default 0, e.g., in case of an NA. This also fixes PR#16322. • cbind() could segfault with NULL inputs. (Seen when R was built with gcc-14, LTO and C99 inlining semantics.) • Fix segfault on quartz() from grid.glyph() call with glyphInfo() that describes non-existent font (PR#18784). Thanks to Tomek Gieorgijewski. • format() etc, using decimal.mark = s, by default getting s <- getOption("OutDec"), signals a warning (to become an error in the future) when s is not a string with exactly one character. • When s <- getOption("OutDec") is not a string of one character, a warning is signalled now whenever it is used in internal C code, notably when calling the default methods of format(). • pwilcox() and qwilcox() now check for user interrupt less frequently. • summary() (which prints directly) finally gets the same digits default as the formatting printing of default summary() method results, and it is documented explicitly. • options(show.error.locations = TRUE) once again shows the most recent known location when an error is reported. Setting its value to "bottom" is no longer supported. Numerical values are converted to logical. • C API function R_GetCurrentSrcref(skip) now returns srcref entries correctly. (Note that there is also a change to the interpretation of skip; see the C-Level API entry above.) • tools::Rd2latex() now removes leading and trailing spaces from \alias entries as documented, fixing indexing and linking hiccups in some PDF manuals. • R CMD Rd2pdf can now render the package manual from a --latex installation also when the help contains figures. • The argument of as.environment() is now named x, not object, as was always documented and shown when printing it; thanks to Gael Millot's PR#18849. • When R CMD check aims at getting the time+date from a world clock, it is more robust against unexpected non-error results, thanks to Michael Chirico's PR#18852. • The tools::parseLatex() parser made several parsing errors (PR#18855). • Error messages produced by tools::parseLatex() are now more readable (PR#18855). • R CMD build excludes more file patterns when it tars the directory, fixing both PR#18432 and PR#18434, for vim and GNU Global emacs users, thanks to Dirk Eddelbuettel's patch. • quantile()'s default method gets an option fuzz to protect against floating point inaccuracy before rounding, thus fixing PR#15811 and, en passant, PR#17683. • Printing arrays now also omits columns, rows and slices when desirable according to option max.print, or argument max, respectively, addressing most of the remaining part of PR#15027, thanks to Sherry Zhang's patch. • drop.terms(y ~ w, 1) and similar now work, thanks to Benjamin Sommer's report in PR#18861 and collaboration with Heather Turner improving reformulate(). • Many arguments which should be length-1 logical are checked more thoroughly. The most commonly seen errors are in unlink(, recursive), tempdir() and the na.rm arguments of max(), min(), sum(), .... grep(), strsplit() and similar took non-TRUE/FALSE values of their logical arguments as FALSE, but these were almost always mismatches to unnamed arguments and are now reported as NA. • vignette("reshape") is now also available on Windows. • trace(coerce, ..) now works correctly, fixing PR#18823 thanks to Mikael Jagan. • R CMD check now also reports bad symbols in package shared objects linked in from local static libraries (PR#18789). • factanal() now works correctly also, e.g., for GPArotation, oblimin() rotations, fixing PR#18417, thanks to Coen Bernaards and others. • Setting attributes on primitive functions is deprecated now and already an error in the development version of R. Changing the environment of a primitive does no longer happen and signals a warning. Changes in R 4.4.3: Installation: • R can be installed using C23 (for example with -std=gnu23 or -std=gnu2x) with recent compilers including gcc 12-14, Apple clang 15-16, LLVM clang 17-20 and Intel icx 2024.2. It can be installed with the upcoming (at the time of writing) gcc 15, which defaults to C23. C-Level Facilities: • The functions R_strtod and R_atof now allow hexadecimal constants without an exponent, for compatibility with their C99 versions (PR#18805). Utilities: • R CMD build and R CMD check now allow reference output for demo scripts (demo/.Rout.save files) to be shipped with the package, as proposed by Torsten Hothorn in PR#18816. Bug Fixes: • kappa(A, exact=TRUE) for singular A returns Inf more generally, fixing PR#18817 reported by Mikael Jagan. • Fixed URLs of the sun spots (sunspot.month etc) data sets and mention future changes due to recalibration. • The parser now accepts hexadecimal constants with a decimal point without an exponent (taken as p0) as documented in ?NumericConstants (PR#18819). • rbind() now works correctly when inputs include a raw vector and a logical, integer or double vector - previously the inclusion of the latter was garbled. • smooth.spline() checks validity of its arguments df.offset and penalty: it could segfault if they were NULL. • isGeneric(, fdef=*, getName=TRUE) now also returns the name instead of just TRUE, fixing PR#18829 reported by Mikael Jagan. • isGeneric(fdef = print) now works, fixing PR#18369 thanks to Mikael Jagan. • sort(x, method = "qsort") made illegal accesses when x has length 0. • dir.create() is protected against being passed an empty string as its path argument. • Silent integer overflow could occur in the ‘exact’ computations for fisher.test() for unrealistic inputs: this is now an error. • Some invalid C-level memory accesses are avoided for loglin(, margin = NULL). loglin(, param = TRUE) no longer gives an error in corner cases such as a one-dimensional input. • dev.capabilities() $ events now reports "Idle" if the device provides it, fixing PR#18836, thanks to Trevor Davis. • arima(.., seasonal = ) correctly errors now, ditto for arima0(), thanks to Norbert Kuder's report on the R-devel list. • binomial()$linkinv(eta) and .. $mu.eta(eta) now also work for "logit" link when is.integer(eta). • as.roman(x) now should work platform independently, also for, e.g., x = "IIIII" (= V) and x = "IIIIII" (= VI). • R CMD Rd2pdf works again on an installed package directory containing LaTeX help (from option --latex), thanks to a report by Peter Ruckdeschel. Changes in R 4.4.2: C-Level Facilities: • The S-compatibility macros F77_COM and F77_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 large x. • 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). • On macOS in R CRAN builds, it is again possible to read little-endian UTF-16 text with a BOM from a connection using encoding="UTF-16". Users building R from source should avoid using the system libiconv in macOS 14.1 and later. • 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 list. Changes in R 4.4.1: C-Level Facilities: • Functions R_atof and R_strtod declared in header R_ext/Utils.h are now documented in ‘Writing R Extensions’ and so formally part of the API. • The non-API entry points Rf_setSVector, Rf_StringFalse, Rf_StringTrue and Rf_isBlankString have been added to those reported by R CMD check. • The new function Rf_allocLang is now available. This provides an alternative to the idiom of calling Rf_allocList followed by SET_TYPEOF. Utilities: • R CMD check now reports as warnings what gfortran calls ‘Fortran 2018 deleted features’, all of which have long been marked as ‘obsolescent’ and some of which were deleted in Fortran 2008 or earlier. Fortran compilers are no longer required to support these. Bug Fixes: • as.numeric(), scan(), type.convert() and other places which use the internal C function R_strtod now require a _non-empty_ digit sequence in a decimal or binary exponent. This aligns with the C/POSIX standard for strtod and with ?NumericConstants. • as.data.frame(m, make.names=NA) now works correctly for a matrix m with NA's in row names. • The error message from [["hour"]] and similar now mentions *[[, "hour"]], as wished for in PR#17409 and proposed by Michael Chirico. • qbinom() and potentially qpois(), qnbinom(), no longer sometimes fail accurate inversion (of pbinom(), etc), thanks to Christopher Chang's report and patch in PR#18711. • The internal help server on Windows can again serve requests sent in quick succession, fixing a regression in R 4.4.0. • debugcall(()) now also works when a corresponding S4-generic version is in the methods cache (PR#18143). • Package tools' toTitleCase(ch0) now returns character(0) when ch0 is of zero length; fixing PR#18724, reported by David Hugh Jones. • R CMD check is no longer broken (without a check result and no explanation in 00check.log) for a package which declares an invalid VignetteBuilder in DESCRIPTION but has no vignettes. Changes in R 4.4.0: Significant User-Visible Changes: • Startup banners, R --version, sessionInfo() and R CMD check no longer report (64-bit) as part of the platform as this is almost universal - the increasingly rare 32-bit platforms will still report (32-bit). On Windows, ditto for window titles. • is.atomic(NULL) now returns FALSE, as NULL is not an atomic vector. Strict back-compatibility would replace is.atomic(foo) by (is.null(foo) || is.atomic(foo)) but should happen only sparingly. New Features: • The confint() methods for "glm" and "nls" objects have been copied to the stats package. Previously, they were stubs which called versions in package MASS. The MASS namespace is no longer loaded if you invoke (say) confint(glmfit). Further, the "glm" method for profile() and the plot() and pairs() methods for class "profile" have been copied from MASS to stats. (profile.nls() and plot.profile.nls() were already in stats.) • The confint() and profile methods for "glm" objects have gained a possibility to do profiling based on the Rao Score statistic in addition to the default Likelihood Ratio. This is controlled by a new test = argument. • The pairs() method for "profile" objects has been extended with a which = argument to allow plotting only a subset of the parameters. • The "glm" method for anova() computes test statistics and p-values by default, using a chi-squared test or an F test depending on whether the dispersion is fixed or free. Test statistics can be suppressed by giving argument test a false logical value. • In setRepositories() the repositories can be set using their names via name = instead of index ind =. • methods() and .S3methods() gain a all.names option for the (rare) case where functions starting with a . should be included. • Serializations can now be interrupted (e.g., by Ctrl-C on a Unix-alike) if they take too long, e.g., from save.image(), thanks to suggestions by Ivan Krylov and others on R-devel. • New startup option --max-connections to set the maximum number of simultaneous connections for the session. Defaults to 128 as before: allowed values up to 4096 (but resource limits may in practice restrict to smaller values). • R on Windows (since Windows 10 2004) now uses the new Segment Heap allocator. This may improve performance of some memory-intensive applications. • When R packages are built, typically by R CMD build , the new --user= option overrides the (internally determined) user name, currently Sys.info()["user"] or LOGNAME. This is a (modified) fulfillment of Will Landau's suggestion in PR#17530. • tools::testInstalledBasic() gets new optional arguments outDir and testSrcdir, e.g., allowing to use it in a != setup, and in standard “binary” Windows installation *if* a source tests/ folder is present. • range(, finite = TRUE) now work for objects of class "Date", "POSIXct", and "POSIXlt" with infinite entries, analogously to range.default(), as proposed by Davis Vaughan on R-devel. Other range()-methods can make use of new function .rangeNum(). • New .internalGenerics object complementing .S3PrimitiveGenerics, for documentation and low-level book-keeping. • grid() now invisibly returns the x- and y- coordinates at which the grid-lines were drawn. • norm(., type) now also works for complex matrices. • kappa(., exact = TRUE, norm = *) now works for all norms and also for complex matrices. In symmetric / triangular cases, the new argument uplo = "U" | "L" allows the upper or lower triangular part to be specified. • memDecompress(type = "unknown") recognizes compression in the default ‘zlib’ format as used by memCompress(type = "gzip"). • memCompress() and memDecompress() will use the libdeflate library () if installed. This uses the same type of compression for type = "gzip" but is 1.5-2x faster than the system libz library on some common platforms: the speed-up may depend on the library version. • diff() for objects of class "Date", "POSIXct", and "POSIXlt" accepts a units argument passed via .... • Dynamic help now does a much better job of rendering package DESCRIPTION metadata. • Rprof() gains an event argument and support for elapsed (real) time profiling on Unix (PR#18076). • filled.contour() gains a key.border argument. • tools::update_pkg_po() gets arguments pot_make and mo_make for _not_ re-making the corresponding files, and additionally a verbose argument. • Hexadecimal string colour specifications are now accepted in short form, so, for example, we can use "#123", which is equivalent to "#112233". Thanks to MikeFC for the original idea and Ella Kaye, Malcolm Barrett, George Stagg, and Hanne Oberman for the patch. • Plain-text help shows \var markup by angle brackets. • The new experimental primitive function declare() is intended to eventually allow information about R code to be communicated to the interpreter, compiler, and code analysis tools. The syntax for declarations is still being developed. • Functions psmirnov(), qsmirnov() and rsmirnov() in package stats have had argument two.sided renamed to alternative, to take into account that the permutation distributions of the one-sided statistics can be different in the case of ties. Consequence of PR#18582. • sort() is now an implicit S4 generic in methods. • Formatting and printing, format(z), print(z), of complex vectors z no longer zap relatively small real or imaginary parts to zero, fixing PR#16752. This is an API change, as it was documented previously to round real and imaginary parts together on purpose, producing nicer looking output. As mentioned, e.g. in the PR, this change is compatible with many other “R-like” programming environments. We have simplified the internal code and now basically format the real and imaginary parts independently of each other. • New experimental functions Tailcall() and Exec() to support writing stack-space-efficient recursive functions. • Where characters are attempted to be plotted by pdf(), postscript() and xfig() which are not in the selected 8-bit character set (most often Latin-1) and the R session is using a UTF-8 locale, the warning messages will show the UTF-8 character rather than its bytes and one dot will be substituted per character rather than per byte. (Platforms whose iconv() does transliteration silently plot the transliteration.) In a UTF-8 locale some transliterations are now done with a warning (e.g., dashes and Unicode minus to hyphen, ligatures are expanded, permille (‰) is replaced by o/oo), although the OS may have got there first. These are warnings as they will continue to be replaced by dots in earlier versions of R. • The matrix multiplication functions crossprod() and tcrossprod() are now also primitive and S3 generic, as %*% had become in R 4.3.0. • source() and example() have a new optional argument catch.aborts which allows continued evaluation of the R code after an error. • The non-Quartz tiff() devices allow additional types of compression if supported by the platform's libtiff library. • The list of base and recommended package names is now provided by tools::standard_package_names(). • cairo_pdf() and cairo_ps() default to onefile = TRUE to closer match pdf() and postscript(). • New option catch.script.errors provides a documented way to catch errors and then continue in non-interactive use. • L %||% R newly in base is an expressive idiom for the phrases if(!is.null(L)) L else R or if(is.null(L)) R else L. • The return value from warnings() now always inherits from "warnings" as documented, now also in the case of no warnings where it previously returned NULL. • as.complex("1i") now returns 0 + 1i instead of NA with a warning. • z <- c(NA, 1i) now keeps the imaginary part Im(z[1]) == 0, no longer coercing to NA_complex_. Similarly, cumsum(z) correctly sums real and imaginary parts separately, i.e., without “crosstalk” in case of NAs. • On Alpine Linux iconv() now maps "latin2", "latin-2", "latin9" and "latin-9" to encoding names the OS knows about (case-insensitively). • iconv(sub = "Unicode") now always zero-pads to four (hex) digits, rather than to 4 or 8. (This seems to have become the convention once Unicode restricted the number of Unicode points to 2^21 - 1 and so will never need more than 6 digits.) • NCOL(NULL) now returns 0 instead of 1, for consistency with cbind(). • The information for the Euro glyph missing from the Adobe .afm files for the Courier, Helvetica and Times families has been copied from their URW equivalents - this will improve vertical centring in the pdf() and postscript() devices. • The included BLAS sources have been updated to those shipped with LAPACK version 3.12.0. The changes are almost entirely cosmetic. • The included LAPACK sources have been updated to version 3.12.0 and some further double-complex routines added. • There are new font families for the 2014-5 URW 2.0 fonts (see ?pdf) which are included in recent versions of Ghostscript. These have font widths for most Greek glyphs and a few others which were missing from the original versions (whose font families remain available for reproducibility, although Ghostscript-based viewers will render using the 2.0 versions). • Improve the large-n efficiency of as.matrix(), thanks an R contributors effort, notably by Tim Taylor and Heather Turner, see PR#18660. • The default and numeric methods of all.equal() get a check.class option. • zapsmall() gets new optional arguments, function mFUN and min.d, for extra flexibility; fulfills a wish in PR#18199. Also, it is now an implicit S4 generic in package methods. • The Rd filter for aspell() gains an ignore argument. • New generic function sort_by(), primarily useful for the data.frame method which can be used to sort rows of a data frame by one or more columns. • The 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 value 1 or 2. • configure will warn if it encounters a 32-bit build, as that is nowadays almost untested. • Environment variable R_SYSTEM_ABI is no longer used and so no longer recorded in etc/Renviron (it was not on Windows and was only ever used when preparing package tools). • If the libdeflate library and headers are available, libdeflate rather than libz is used to (de)compress R objects in lazy-load databases. Typically tasks spend up to 5% of their time on such operations, although creating lazy-data databases is one of the exceptions. This can be suppressed if the library is available by the configure option --without-libdeflate-compression. • configure option --enable-lto=check has not worked reliably since 2019 and has been removed. • The minimum autoconf requirement for a maintainer build has been increased to autoconf 2.71. It is intended to increase this to 2.72 for R 4.5.0: the distributed configure file was generated using 2.72. • The minimum version requirement for an external LAPACK has been reduced to 3.9.0. • No default C++ compiler is set if no C++17 compiler is detected: there is no longer an automatic fallback to C++14 or C++11. Compilers from the last five years should have sufficient support: for others macros CXX and CXXSTD can be set in file config.site to provide a fallback if needed. The Objective-C++ compiler now by default uses the standard selected by R for C++ (currently C++17) rather than the default standard for the C++ compiler (which on macOS is still C++98). Installation on macOS: • A new configure option --with-newAccelerate makes use of Apple's ‘new’ BLAS / LAPACK interfaces in their Accelerate framework. Those interfaces are only available in macOS 13.3 or later, and building requires SDK 13.3 or later (from the Command Line Tools or Xcode 14.3 or later). By default the option uses new Accelerate for BLAS calls: to also use it for LAPACK use option --with-newAccelerate=lapack. The later interfaces provide LAPACK 3.9.1 rather than 3.2.1: 3.9.1 is from 2021-04 and does not include the improved algorithms introduced in LAPACK 3.10.0 (including for BLAS calls). Installation on Windows: • The makefiles and installer scripts for Windows have been tailored to Rtools44, an update of the Rtools43 toolchain. It is based on GCC 13 and newer versions of MinGW-W64, binutils and libraries (targeting 64-bit Intel CPUs). R-devel can no longer be built using Rtools43 without changes. • Rtools44 has experimental support for 64-bit ARM (aarch64) CPUs _via_ the LLVM 17 toolchain using lld, clang/flang-new and libc++. Utilities: • R CMD check notes when S4-style exports are used without declaring a strong dependence on package methods. • tools::checkRd() (used by R CMD check) detects more problems with \Sexpr-based dynamic content, including bad nesting of \Sexprs and invalid arguments. • tools::checkRd() now reports Rd titles and section names ending in a period; this is ignored by R CMD check unless environment variable _R_CHECK_RD_CHECKRD_MINLEVEL_ is set to -5 or smaller. • R CMD check now notes Rd files without an \alias, as long documented in ‘Writing R Extensions’ §1.3.1. The check for a missing \description has been moved from tools::checkRd() to tools::checkRdContents(). • R CMD check now visits inst/NEWS.Rd and OS-specific man subdirectories when checking Rd files. • tools::checkDocFiles() and tools::checkRdContents() now also check internal Rd files by default, but “specially” (ignoring missing documentation of arguments). • R CMD Rdiff gets option --useEx. • R CMD check now warns on non-portable uses of Fortran KIND such as INTEGER(KIND=4) and REAL(KIND=8). To see the failing lines set environment variable _R_CHECK_FORTRAN_KIND_DETAILS_ to a true value. • When checking Rd files, R CMD check now notes some of the “lost braces” that tools::checkRd() finds. Typical problems are Rd macros missing the initial backslash (e.g., code{...}), in-text set notation (e.g., {1, 2}, where the braces need escaping), and \itemize lists with \describe-style entries of the form \item{label}{description}. • R CMD INSTALL (and hence check) will compile C++ code with -DR_NO_REMAP if environment variable _R_CXX_USE_NO_REMAP_ is set to a true value. It is planned that this will in future become the default for compiling C++. • The new built-in Rd macro \dontdiff{} can be used to mark example code whose output should be ignored when comparing check output to reference output (tests/Examples/-Ex.Rout.save). The \dontdiff tag, like \donttest, is _not_ shown on the rendered help page, so provides a clean alternative to ## IGNORE_RDIFF_(BEGIN|END) comments. • R CMD build when there is no NAMESPACE, now uses the recommended exportPattern("^[^.]"), instead of exporting everything. • R CMD check now warns about non-ASCII characters in the NAMESPACE file (in addition to R files). Such packages are not portable and may fail to install on some platforms. C-Level Facilities: • Headers R_ext/Applic.h and R-ext/Linpack.h used to include R_ext/BLAS.h although this was undocumented and unneeded by their documented entry points. They no longer do so. • New function R_missing(), factored out from do_missing(), used to fix PR#18579. • SEXP type S4SXP has been renamed to OBJSXP to support experimenting with alternative object systems. The S4SXP value can still be used in C code but is now deprecated. Based on contributions from the R Consortium's Object-Oriented Programming Working Group. • New function pow1p(x,y) for accurate (1+x)^y. • mkCharLenCE was incorrectly documented to take a size_t length but was implemented with int (and character strings in R are limited to 2^31 - 1 bytes). Deprecated and Defunct: • data() no longer handles zipped data from long-defunct (since R 2.13.0) --use-zip-data installations. • The legacy graphics devices pictex() and xfig() are now deprecated. They do not support recent graphics enhancements and their font handling is rudimentary. The intention is to retain them for historical interest as long as they remain somewhat functional. • Support for encoding = "MacRoman" has been removed from the pdf() and postscript() devices - this was a legacy encoding supporting classic macOS up to 2001 and no longer has universal libiconv support. • is.R() is deprecated as no other S dialect is known to be in use (and this could only identify historical dialects, not future ones). Further information on calls can be obtained by setting the environment variable _R_DEPRECATED_IS_R_ to error which turns the deprecation warning into an error and so by default gives a traceback. (This is done by R CMD check --as-cran.) • UseMethod() no longer forwards local variables assigned in the generic function into method call environments before evaluating the method body. This makes method calls behave more like standard function calls and makes method code easier to analyze correctly. • The twelve as.data.frame.() methods which were deprecated only via _R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_ and in R CMD check --as-cran are formally deprecated now in favour of calling as.data.frame() or as.data.frame.vector(). The deprecation “check” now works also when as.data.frame() is S4 generic thanks to Ivan Krylov. • The default method for the directional comparison operators <, >, <=, and >= now signals an error when one of the operands is a language object, i.e. a symbol or a call. • For terms.formula(), deprecate abb and neg.out arguments _formally_ in addition to just documenting it. Bug Fixes: • The methods package is more robust to not being attached to the search path. More work needs to be done. • pairwise.t.test() misbehaved when subgroups had 0 DF for variance, even with pool.sd = TRUE. (PR#18594 by Jack Berry.) • Probability distribution functions [dpq](x, *), but also bessel[IKJY](x, .) now consistently preserve attributes(x) when length(x) == 0, e.g., for a 2 x 0 matrix, thanks to Karolis Koncevičius' report PR#18509. • Group “Summary” computations such as sum(1:3, 4, na.rm = 5, NA, 7, na.rm = LL) now give an error instead of either 17 or NN for LL true or false, as proposed by Ivan Krylov on the R-devel mailing list. (This also means it is now an error to specify na.rm more than once.) • as.complex(x) now returns complex(real = x, imaginary = 0) for _all_ numerical and logical x, notably also for NA or NA_integer_. • Directories are now omitted by file.copy(, recursive = FALSE) and in file.append() (PR#17337). • gsub() and sub() are now more robust to integer overflow when reporting errors caused by too large input strings (PR#18346). • Top-level handlers are now more robust to attempts to remove a handler whilst handlers are running (PR#18508). • The handling of Alt+F4 in dialogs created on Windows using GraphApp has been fixed (PR#13870). • density() more consistently computes grid values for the FFT-based convolution, following Robert Schlicht's analysis and proposal in PR#18337, correcting density values typically by a factor of about 0.999. Argument old.coords = TRUE provides back compatibility. • palette.colors() gains a name argument that defaults to FALSE controlling whether the vector of colours that is returned has names (where possible). PR#18529. • tools::xgettext() no longer extracts the (non-translatable) class names from warningCondition and errorCondition calls. • S3method(, , ) in the NAMESPACE file now works (again) when 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 /R/*.R source files, thanks to Kirill Müller's report and Duncan Murdoch's patch in PR#16756. • Rd \Sexpr macros with nested #ifdef conditionals were not processed. • A non-blocking connection with non-default encoding (such as a socket) now correctly returns from readLines() after new data has arrived also when its EOF had been reached previously. Thanks to Peter Meilstrup's report on R-devel and Ivan Krylov's report and patch proposal in PR#18555. • tools::checkRdContents() failed to detect empty argument descriptions when they spanned multiple lines, including those generated by prompt(). These cases are now noted by R CMD check. • Plain-text help no longer outputs spurious colons in the arguments list (for multi-line \item labels in the Rd source). • kappa() and rcond() work correctly in more cases; kappa(., norm = "2") now warns that it computes the 1-norm with (default) exact = FALSE; prompted by Mikael Jagan's quite comprehensive PR#18543. • Rd skeletons generated by prompt() or promptData() now use a dummy title (so R CMD build works). tools::checkRdContents() has been updated to detect such template leftovers, including from promptPackage(). • When S4 method dispatch fails because no method was found, the error message now includes the signature argument names; thanks to Michael Chirico's proposal on the R-devel list. • withAutoprint({ .. }) now preserves srcrefs previously lost, thanks to Andrew Simmons' report plus fix in PR#18572. • transform.data.frame() no longer adjusts names; in particular, untransformed variables are kept as-is, including those with syntactically invalid names (PR#17890). • The keep.source option for Rd \Sexpr blocks is no longer ignored. • The formula methods for t.test() and wilcox.test() now catch when paired is passed, addressing PR#14359; use Pair(x1, x2) ~ 1 for a paired test. • The level reported in the browser prompt was often too large. It now shows the number of browser contexts on the stack. • For cbind() and rbind(), the optional deparse.level argument is now properly passed to methods, thanks to Mikael Jagan's PR#18579 and comments there. • Some error and warning messages for large (‘long vector’) matrix(v, nr, nc) and dim(m) <- d are now correct about sizes, using long long formatting, fixing PR#18612 (and more) reported by Mikael Jagan. • readChar(useBytes = TRUE) now terminates strings even when the underlying connection uses extra spaces in the input buffer. This fixes problems with extra garbage seen with gzip connections, PR#18605. • Named capture in PCRE regular expressions now works also with more than 127 named groups (PR#18588). • Datetime functions are now robust against long jumps when dealing with internal time zone changes. This avoids confusing warnings about an invalid time zone, previously triggered by turning warnings into errors or handling them via tryCatch (PR#17966, PR#17780). • Datetime functions now restore even an empty TZ environment variable after internal time zone changes (PR#17724). This makes results of datetime functions with this (typically unintentional) setting more predictable. • drop.terms(*) now drops response as by default, keep.response = FALSE, fixing PR#18564 thanks to Mikael Jagan. • dummy.coef(.) now also works for lm()-models with character categorical predictor variables rather than factor ones, fixing PR#18635 reported by Jinsong Zhao. • formals(f) <- formals(f) now also works for a function w/o arguments and atomic _constant_ body(f). • Correct as.function(, .)'s error message. • removeSource() is yet more thorough in finding and removing "srcref" and the other source references from parsed R language chunks, fixing PR#18638 thanks to Andrew Simmons. • dgeom() is more accurate now, notably when its result is very small, fixing PR#18642 thanks to the proposal of Morten Welinder, also improving other instances where C level binom_raw(x, n, ..) has x == 0 or x== n. • warning() with options(warn = 1) has improved output for multi-line messages. • axis.Date() and axis.POSIXct() now respect the par("lab") setting for the number of pretty() intervals. • Comparisons for language objects (which are based on deparsing) are now more careful about using accurate deparsed results (PR#18676). • Plain-text help (Rd2txt) now correctly preserves blank lines following single-line \dontrun code. • [*] no longer sets wrong "balanced" attribute, fixing PR#18681 thanks to Mikael Jagan. • str() now deparses the call as expected, fixing PR#18684, reported by Dave Slager. • In Rd examples, code following the closing brace of a \dontrun, \dontshow or \donttest tag on the same line is no longer skipped when R CMD check runs the examples. • as.data.frame(matrix(*, ncol=0)) now gets valid names() and colnames(); reported by Davis Vaughan on the R-devel list. • Internal Mathlib function stirlerr(n) is now almost fully (52-bit) accurate for all n >= ~5.9 and more accurate also in the range 1 -- 5.9. This entails small (“after 12th decimal”) changes in density functions, e.g., dgamma() in _some_ regions of their support. The fix was partly prompted by Morten Welinder's PR#18640. • Numbers like 9876543.2 are now considered non-integer by Mathlib internal R_nonint(), amending original fix of PR#15734. • Rd comment lines no longer cause broken paragraphs in the rendered PDF and plain-text help. In code blocks, pure comment lines (starting with %) no longer produce an empty line. • xtabs(Freq ~ .) now consistently defaults to na.action = na.pass, using na.rm = FALSE (added as an argument) when summing over Freq (PR#17770). • tools::testInstalledPackage() is no longer silent about failures from running examples or tests and its return code no longer ignores failures from checking vignettes. Changes in R 4.3.3: New Features: • iconv() now fixes up variant encoding names such as "utf8" case-insensitively. Deprecated and Defunct: • The legacy encoding = "MacRoman" is deprecated in pdf() and postscript(): support was incomplete in earlier versions of R. Bug Fixes: • Arguments are now properly forwarded to methods on S4 generics with ... in the middle of their formal arguments. This was broken for the case when a method introduced an argument but did not include ... in its own formals. Thanks to Hervé Pagès for the report PR#18538. • Some invalid file arguments to pictex(), postscript() and xfig() opened a file called NA rather than throw an error. These included postscript(NULL) (which some people expected to work like pdf(NULL)). • Passing filename = NA to svg(), cairo_pdf(), cairo_ps() or the Cairo-based bitmap devices opened a file called NA: it now throws an error. • quartz(file = NA) opened a file called NA, including when used as a Quartz-based bitmap device. It now gives an error. • rank() now works, fixing PR#18617, thanks to Ilia Kats. • seq.int() did not adequately check its length.out argument. • match(, .) is correct again for differing time zones, ditto for "POSIXlt", fixing PR#18618 reported by Bastian Klein. • drop.terms(*, dropx = <0-length>) now works, fixing PR#18563 as proposed by Mikael Jagan. • drop.terms(*) keeps + offset(.) terms when it should, PR#18565, and drop.terms() no longer makes up a response, PR#18566, fixing both bugs thanks to Mikael Jagan. • getS3method("t", "test") no longer finds the t.test() function, fixing PR#18627. • pdf() and postscript() support for the documented Adobe encodings "Greek" and "Cyrilllic" was missing (although the corresponding Windows' codepages could be used). • Computations of glyph metric information for pdf() and postscript() did not take into account that transliteration could replace one character by two or more (only seen on macOS 14) and typically warned that the information was not known. • rank(x) no longer overflows during integer addition, when computing rank average for largish but not-yet long vector x, fixing PR#18630, thanks to Ilia Kats. • list.files() on Windows now returns also files with names longer that 260 bytes (the Windows limit is 260 characters). Previously, some file names particularly with ‘East Asian’ characters were omitted. • cov2cor(<0 x 0>) now works, fixing PR#18423 thanks to Mikael Jagan and Elin Waring. • cov2cor() and similar now give one warning instead of two, with better wording, fixing PR#18424 thanks to Mikael Jagan. • tools:: startDynamicHelp() now ensures port is in proper range, fixing PR#18645. • pbeta(x, a,b) is correct now for x=0 or 1 in the boundary cases where a or b or both are 0, fixing PR#18672 thanks to Michael Fay. • pmatch(x, table) for large table, also called for data frame row selection, dfrm[nm, ], is now interruptible, fixing PR#18656. • predict(, newdata=*) fix computing of nbasis, see Russ Lenth's comment 29 in PR#16158. • Added a work-around for a bug in macOS 14.3.1 and higher which prevents R plots in the Quartz Cocoa device from updating on screen. Changes in R 4.3.2: New Features: • The default initialization of the "repos" option from the repositories file at startup can be skipped by setting environment variable R_REPOSITORIES to NULL such that getOption("repos") is empty if not set elsewhere. • qr.X() is now an implicit S4 generic in methods. • iconv(to = "ASCII//TRANSLIT") is emulated using substitution on platforms which do not support it (notably Alpine Linux). This should give a human-readable conversion in ASCII on all platforms (rather than NA_character_). • trans3d() gains options continuous and verbose addressing the problem of possible “wrap around” when projecting too long curves, as reported by Achim Zeileis in PR#18537. • tools::showNonASCII() has been rewritten to work better on macOS 14 (which has a changed implementation of iconv()). • tiff(type = "quartz") (the default on macOS) now warns if compression is specified: it continues to be ignored. Installation on a Unix-Alike: • There is some support for building with Intel's LLVM-based compilers on x86_64 Linux, such as (C) icx, (C++) ipcx and (Fortran) ifx from oneAPI 2023.x.y. • There is support for using LLVM's flang-new as the Fortran compiler from LLVM 16.0.x (preferably 17.0.0 or later). Utilities: • R CMD check reports the use of the Fortran 90 random number generator RANDOM_NUMBER() and the subroutines to initialize it. ‘Writing R Extensions’ has example code to use R's RNGs from Fortran. Bug Fixes: • substr(x, n, L) <- cc now works (more) correctly for multibyte UTF-8 strings x when L > nchar(x), thanks to a report and patch by ‘Architect 95’. • contrib.url(character()) now returns 0-length character() as documented, which also avoids spurious warnings from available.packages() et al. in the edge case of an empty vector of repository URLs. • readChar(., 4e8) no longer fails, thanks to Kodi Arfer's report (PR#18557). • lapply(, as.data.frame) no longer warns falsely for some base vector components. • Communication between parent and child processes in the multicore part of parallel could fail on platforms that do not support an arbitrarily large payload in system functions read()/write() on pipes (seen on macOS where a restriction to INT_MAX bytes is documented, without doing a partial read unlike Linux). The payload is now split into 1Gb chunks to avoid that problem. (PR#18571) • qqplot(x,y, conf.level=.) gives better confidence bounds when length(x) != length(y), thanks to Alexander Ploner's report and patch proposal (PR#18557). • norm(<0-length>, "2") now gives zero instead of an error, as all the other norm types, thanks to Mikael Jagan's PR#18542. • Build-stage Rd macros \packageAuthor and \packageMaintainer now process Authors@R, fixing NA results when the package DESCRIPTION omits Author and Maintainer fields. • Formatting and printing complex numbers could give things like 0.1683-0i because of rounding error: -0i is now replaced by +0i. • postscript() refused to accept a title comment containing the letter “W” (PR#18599). • isoreg(c(1,Inf)) signals an error instead of segfaulting, fixing PR#18603. • tiff(type = "Xlib") was only outputting the last page of multi-page plots. • tools::latexToUtf8() again knows about \~{n} and other letters with tilde, fixing a regression in R 4.3.0, and about \^{i} as an alternative to \^{\i} (similarly with other accents). Furthermore, LaTeX codes for accented I letters are now correctly converted, also fixing related mistakes in tools::encoded_text_to_latex(). • tar(*, tar = "internal") no longer creates out-of-spec tar files in the very rare case of user or group names longer than 32 bytes, fixing PR#17871 with thanks to Ivan Krylov. • When using the “internal” timezone datetime code, adding a fraction of a second no longer adds one second, fixing PR#16856 from a patch by Ivan Krylov. • tools::checkRd() no longer produces spurious notes about “unnecessary braces” from multi-line Rd results of \Sexpr macros. Changes in R 4.3.1: C-Level Facilities: • The C-level API version of R's integrate(), Rdqags() in Applic.h, now returns the correct number of integrand evaluations neval, fixing PR#18515 reported and diagnosed by Stephen Wade. • The C prototypes for LAPACK calls dspgv and dtptrs in R_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 // for PR18534fixed #ifdef PR18534fixed # define usePR18534fix 1 #endif #include in your C/C++ code (PR#18534). Installation: • Many of the checks of esoteric Internet operations and those using unreliable external sites have been moved to a new target that is not run by default and primarily intended for the core developers. To run them use cd tests; make test-Internet-dev Bug Fixes: • .S3methods(), typically called from methods(), again marks methods from package base as visible. Also, the visibility of non-base methods is again determined by the method's presence in search(). • tools::Rdiff() is now more robust against invalid strings, fixing installation tests on Windows without Rtools installed (PR#18530). • Fix (new) bug in hcl.colors(2, *), by Achim Zeileis (PR#18523). • head(., ) and tail(..) now produce more useful "Error in ...." error messages, fixing PR#18362. • Package code syntax on Windows is checked in UTF-8 when UTF-8 is the native encoding. • na.contiguous(x) now also returns the first run, when it is at the beginning and there is a later one of the same length; reported to R-devel, including a fix, by Georgi Boshnakov. Further, by default, it modifies only an existing attr(*,"tsp") but otherwise no longer sets one. • chol(, pivot = ) now gives a correct error or warning message (depending on pivot), thanks to Mikael Jagan's (PR#18541). Changes in R 4.3.0: Significant User-Visible Changes: • Calling && or || with LHS or (if evaluated) RHS of length greater than one is now always an error, with a report of the form 'length = 4' in coercion to 'logical(1)' Environment variable _R_CHECK_LENGTH_1_LOGIC2_ no longer has any effect. New Features: • The included BLAS sources have been updated to those shipped with LAPACK version 3.10.1. (This caused some platform-dependent changes to package check output.) And then to the sources from LAPACK version 3.11.0 (with changes only to double complex subroutines). • The included LAPACK sources have been updated to include the four Fortran 90 routines rather than their Fortran 77 predecessors. This may give some different signs in SVDs or eigendecompositions.. (This completes the transition to LAPACK 3.10.x begun in R 4.2.0.) • The LAPACK sources have been updated to version 3.11.0. (No new subroutines have been added, so this almost entirely bug fixes: Those fixes do affect some computations with NaNs, including R's NA.) • The parser now signals _classed_ errors, notably in case of the pipe operator |>. The error object and message now give line and column numbers, mostly as proposed and provided by Duncan Murdoch in PR#18328. • toeplitz() is now generalized for asymmetric cases, with a toeplitz2() variant. • xy.coords() and xyz.coords() and consequently, e.g., plot(x,y, log = "y") now signal a _classed_ warning about negative values of y (where log(.) is NA). Such a warning can be specifically suppressed or caught otherwise. • Regular expression functions now check more thoroughly whether their inputs are valid strings (in their encoding, e.g. in UTF-8). • The performance of grep(), sub(), gsub() and strsplit() has been improved, particularly with perl = TRUE and fixed = TRUE. Use of useBytes = TRUE for performance reasons should no longer be needed and is discouraged: it may lead to incorrect results. • apropos() gains an argument dot_internals which is used by the completion (help(rcompgen)) engine to also see base internals such as .POSIXct(). • Support in tools::Rdiff() for comparing uncompressed PDF files is further reduced - see its help page. • qqplot(x, y, ...) gains conf.level and conf.args arguments for computing and plotting a confidence band for the treatment function transforming the distribution of x into the distribution of y (Switzer, 1976, _Biometrika_). Contributed by Torsten Hothorn. • Performance of package_dependencies() has been improved for cases when the number of dependencies is large. • Strings newly created by gsub(), sub() and strsplit(), when any of the inputs is marked as "bytes", are also marked as "bytes". This reduces the risk of creating invalid strings and accidental substitution of bytes deemed invalid. • Support for readLines(encoding = "bytes") has been added to allow processing special text files byte-by-byte, without creating invalid strings. • iconv(from = "") now takes into account any declared encoding of the input elements and uses it in preference to the native encoding. This reduces the risk of accidental creation of invalid strings, particularly when different elements of the input have different encoding (including "bytes"). • Package repositories in getOption("repos") are now initialized from the repositories file when utils is loaded (if not already set, e.g., in .Rprofile). (From a report and patch proposal by Gabriel Becker in PR#18405.) • compactPDF() gets a verbose option. • type.convert() and hence read.table() get new option tryLogical = TRUE with back compatible default. When set to false, converts "F" or "T" columns to character. • Added new unit prefixes "R" and "Q" for abbreviating (unrealistically large) sizes beyond 10^{27} in standard = "SI", thanks to Henrik Bengtsson's PR#18435. • as.data.frame()'s default method now also works fine with atomic objects inheriting from classes such as "roman", "octmode" and "hexmode", thus fulfilling the wish of PR#18421, by Benjamin Feakins. • The as.data.frame.vector() utility now errors for wrong-length row.names. It warned for almost six years, with “Will be an error!”. • sessionInfo() now also contains La_version() and reports codepage and timezone when relevant, in both print() and toLatex() methods which also get new option tzone for displaying timezone information when locale = FALSE. • New function R_compiled_by() reports the C and Fortran compilers used to build R, if known. • predict(, newdata = *) no longer unnecessarily creates an offset of all 0s. • solve() for complex inputs now uses argument tol and by default checks for ‘computational singularity’ (as it long has done for numeric inputs). • predict(, newdata=*) now obeys a new argument rankdeficient, with new default "warnif", warning only if there are non-estimable cases in newdata. Other options include rankdeficient = "NA", predicting NA for non-estimable newdata cases. This addresses PR#15072 by Russ Lenth and is based on his original proposal and discussions in PR#16158 also by David Firth and Elin Waring. Still somewhat experimental. • Rgui console implementation now works better with the NVDA screen reader when the full blinking cursor is selected. The underlying improvements in cursor handling may help also other screen readers on Windows. • The drop-field control in GraphApp can now be left with the TAB key and all controls can be navigated in the reverse order using the Shift+TAB key, improving accessibility of the Rgui configuration editor. • qnorm(, log.p=TRUE) is now fully accurate (instead of to “only” minimally five digits). • demo(error.catching) now also shows off withWarnings() and tryCatchWEMs(). • As an experimental feature the placeholder _ can now also be used in the rhs of a forward pipe |> expression as the first argument in an extraction call, such as _$coef. More generally, it can be used as the head of a chain of extractions, such as _$coef[[2]]. • Spaces in the environment variable used to choose the R session's temporary directory (TMPDIR, TMP and TEMP are tried in turn) are now fatal. (On Windows the ‘short path’ version of the path is tried and used if that does not contain a space.) • all.equal.numeric() gets a new optional switch giveErr to return the numeric error as attribute. Relatedly, stopifnot(all.equal(a, b, ..)) is as “smart” now, as stopifnot(all.equal(....)) has been already, thus allowing customized all.equal() 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 for more information. • ‘Object not found’ and ‘Missing argument’ errors now give a more accurate error context. Patch provided by Lionel Henry in PR#18241. • The @ operator is now an S3 generic. Based on contributions by Tomasz Kalinowski in PR#18482. • New generic chooseOpsMethod() provides a mechanism for objects to resolve cases where two suitable methods are found for an Ops Group Generic. This supports experimenting with alternative object systems. Based on contributions by Tomasz Kalinowski in PR#18484. • inherits(x, what) now accepts values other than a simple character vector for argument what. A new generic, nameOfClass(), is called to resolve the class name from what. This supports experimenting with alternative object systems. Based on contributions by Tomasz Kalinowski in PR#18485. • Detection of BLAS/LAPACK in use (sessionInfo()) with FlexiBLAS now reports the current backend. • The "data.frame" method for subset() now warns about extraneous arguments, typically catching the use of = instead of == in the subset expression. • Calling a:b when numeric a or b is longer than one may now be made into an error by setting environment variable _R_CHECK_LENGTH_COLON_ to a true value, along the proposal in PR#18419 by Henrik Bengtsson. • density(x, weights = *) now warns if automatic bandwidth selection happens without using weights; new optional warnWbw may suppress the warning. Prompted by Christoph Dalitz' PR#18490 and its discussants. • rm(list = *) is faster and more readable thanks to Kevin Ushey's PR#18492. • The plot.lm() function no longer produces a normal Q-Q plot for GLMs. Instead it plots a half-normal Q-Q plot of the absolute value of the standardized deviance residuals. • The print() method for class "summary.glm" no longer shows summary statistics for the deviance residuals by default. Its optional argument show.residuals can be used to show them if required. • The tapply() function now accepts a data frame as its X argument, and allows INDEX to be a formula in that case. by.data.frame() similarly allows INDICES to be a formula. • The performance of df[j] <- value (including for missing j) and write.table(df) has been improved for data frames df with a large number of columns. (Thanks to Gabriel Becker's PR#18500, PR#18503 and discussants, prompted by a report from Toby Dylan Hocking on the R-devel mailing list.) • The matrix multiply operator %*% is now an S3 generic, belonging to new group generic matrixOps. From Tomasz Kalinowski's contribution in PR#18483. • New function array2DF() to convert arrays to data frames, particularly useful for the list arrays created by tapply(). Dates and Times: • On platforms where (non-UTC) datetimes before 1902 (or before 1900 as with system functions on recent macOS) are guessed by extrapolating time zones from 1902-2037, there is a warning at the first use of extrapolation in a session. (As all time zones post 2037 are extrapolation, we do not warn on those.) • (Platforms using --with-internal-tzone, including Windows and by default macOS). How years are printed in dates or date-times can be controlled by environment variable R_PAD_YEARS_BY_ZERO. The default remains to pad to 4 digits by zeroes, but setting value no gives no padding (as used by default by glibc). • strftime() tries harder to determine the offset for the "%z" format, and succeeds on the mainstream R platforms. • strftime() has a limit of 2048 bytes on the string produced - attempting to exceed this is an error. (Previously it silently truncated at 255 bytes.) • sessionInfo() records (and by default prints) the system time zone as part of the locale information. Also, the source (system/internal) of the date-time conversion and printing functions. • Objects of class "POSIXlt" created in this version of R always have 11 components: component zone is always set, and component gmtoff is set for times in UTC and usually set on the (almost all) platforms which have C-level support, otherwise is NA. • There are comprehensive validity checks on the structure of objects of class "POSIXlt" when converting (including formatting and printing). (This avoids mis-conversions of hand-crafted objects.) • There is some support for using the native date-time routines on macOS: this is only viable on recent versions (e.g. 12.6 and 13) and does get wrong some historical changes (before 1900, during WWII). Use of --with-internal-tzone remains the default. • as.POSIXct() and as.POSIXlt(.) (without specifying origin) now work. So does as.Date(). • as.Date.POSIXct(., tz) now treats several tz values, notably "GMT" as equivalent to "UTC", proposed and improved by Michael Chirico and Joshua Ulrich in PR#17674. • Experimental balancePOSIXlt() utility allows using “ragged” and or out-of-range "POSIXlt" objects more correctly, e.g., in subsetting and subassignments. Such objects are now documented. Complemented by the low-level unCfillPOSIXlt() 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() and axis.POSIXct() are rewritten to gain better default tick locations and better default formats via the corresponding pretty() 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 to 16 and so packages that provide graphics devices should be reinstalled. • The grDevices and grid packages have new functions for rendering typeset glyphs, primarily: grDevices::glyphInfo() and grid::grid.glyph(). Rendering of typeset glyphs is only supported so far on the Cairo-based graphics devices and on the pdf() and quartz() devices. • The defined behaviour for "clear" and "source" compositing operators (via grid::grid.group()) has been changed (to align better with simple interpretation of original Porter-Duff definitions). • Support for gradients, patterns, clipping paths, masks, groups, compositing operators, and affine transformations has been added to the quartz() device. Installation on a Unix-Alike: • A system installation of generic LAPACK 3.10.0 or later will be preferred to the version in the R sources. configure option --with-lapack=no (equivalently --without-lapack) forces compilation of the internal LAPACK sources. If --with-lapack is not specified, a system liblapack is looked for and used if it reports version 3.10.0 or later and does not contain BLAS routines. Packages using LAPACK will need to be reinstalled if this changes to using an external library. • On aarch64 Linux platforms using GCC, configure now defaults to -fPIC (instead of -fpic), as desired in PR#18326. • configure now checks conversion of datetimes between POSIXlt and POSIXct around year 2020. Failure (which has been seen on platforms missing tzdata) is fatal. • If configure option --with-valgrind-instrumentation is given value 1 or 2, option --with-system-valgrind-headers is now the default and ignored (with a warning). It is highly recommended that the system headers are installed alongside valgrind: they are part of its packaging on some Linux distributions and packaged separately (e.g. in the valgrind-devel RPM) on others. configure will give a warning if they are not found. The system headers will be required in a future release of R to build with valgrind instrumentation. • libcurl 8.x is now accepted by configure: despite a change in major version number it changes neither API nor ABI. Installation on Windows: • The makefiles and installer scripts for Windows have been tailored to Rtools43, an update of the Rtools42 toolchain. It is based on GCC 12 and newer versions of MinGW-W64, binutils and libraries. At this time R-devel can still be built using Rtools42 without changes, but when R-devel is installed via the installer, it will by default look for Rtools43. • Old make targets rsync-extsoft and 32-bit ones that are no longer needed have been removed. • Default builds (including for packages) no longer select C99. Thus the C standard used is the default for the compiler, which for the toolchain in Rtools43 is C17. (This is consistent with Unix builds.) Package Installation: • The default C++ standard has been changed to C++17 where available (which it is on all currently checked platforms): if not C++14 or C++11 is used if available otherwise C++ is not supported. • USE_FC_LEN_T is the default: this uses the correct (compiler-dependent) prototypes for Fortran BLAS/LAPACK routines called from C/C++, and requires adjustment of many such calls - see ‘Writing R Extensions’ §6.6.1. • There is initial support for C++23 as several compilers are now supporting -std=c++23 or -std=c++2b or similar. As for C++20, there no additional configure checks for C++23 features beyond a check that the compiler reports a __cplusplus value greater than that in the C++20 standard. C++ feature tests should be used. • There is support for a package to indicate the version of the C standard which should be used to compile it, and for the installing user to specify this. In most cases R defaults to the C compiler's default standard which is C17 (a `bug-fix' of C11) - earlier versions of R or compilers may have defaulted to C99. Current options are: USE_C17 Use a standard that is at most C17. The intention is to allow legacy packages to still be installed when later C standards become the default, including packages using new keywords as identifiers or with K&R-style function declarations. This will use C17 if available, falling back to C11. USE_C90 Use the C90 (aka C89) standard. (As that standard did not require compilers to identify that version, all we can verify is that the compiler does not claim to be using a later standard. It may accept C99 features - for example clang accepts // to make comments.) USE_C99 Use the C99 standard. This should be rarely needed - it avoids the few new features of C11/C17 which can be useful if a package assumes them if C17 is specified and they are not implemented. USE_C23 Use C23 (or in future, later). Compiler/library support for C23 is still being implemented, but LLVM clang from 15.0.0 and 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 and R 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 /etc/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 by cmake or libtool which obfuscate the actual compile commands used. Also used for configure.win and configure.ucrt on Windows. FORTRAN Flags: • The flag -fno-optimize-sibling-calls is no longer forced for gfortran 7 and later. It should no longer be needed now using ‘hidden’ character-length arguments when calling BLAS/LAPACK routines from C/C++ is the default even for packages. (Unless perhaps packages call Fortran code from C/C++ without using R's headers and without allowing for these arguments.) C-Level Facilities: • The deprecated S-compatibility macros DOUBLE_* in R_ext/Constants.h (included by R.h) have been removed. • The deprecated legacy typedefs of Sint and Sfloat in header R.h are no longer defined, and that header no longer includes header limits.h from C nor climits from C++. • New macro CAD5R() is provided in Rinternals.h and used in a few places in the R sources. • ALTREP now supports VECSXP vectors. Contributed by Gabor Csardi in PR#17620. • The Rcomplex definition (in header R_ext/Complex.h) has been extended to prevent possible mis-compilation when interfacing with Fortran (PR#18430). The new definition causes compiler warnings with static initializers such as {1, 2}, which can be changed to {.r=1, .i=2}. Using the new definition from C++ depends on compiler extensions supporting C features that have not been incorporated into the C++ standards but are available in g++ and clang++: this may result in C++ compiler warnings but these have been worked around for recent versions of common compilers (GCC, Apple/LLVM clang, Intel). It is intended to change the inclusion of header R_ext/Complex.h by other R headers, so C/C++ code files which make use of Rcomplex should include that header explicitly. Utilities: • R CMD check does more checking of package .Rd files, warning about invalid email addresses and (some) invalid URIs and noting empty \item labels in description lists. • R CMD check now also reports problems when reading package news in md (file NEWS.md) and (optionally) plain text (file NEWS) formats. • _R_CHECK_TIMINGS_ defaults to a value from the environment even for R CMD check --as-cran; this allows for exceptionally fast or slow platforms. It now applies to checking PDF and HTML versions of the manuals, and ‘checking CRAN incoming feasibility’. • R CMD check can optionally (but included in --as-cran) check whether HTML math rendering _via_ KaTeX works for the package .Rd files. • Non-interactive debugger invocations can be trapped by setting the environment variable _R_CHECK_BROWSER_NONINTERACTIVE_ to a true value. This is enabled by R CMD check --as-cran to detect the use of leftover browser() statements in the package. • The use of sprintf and vsprintf from C/C++ has been deprecated in macOS 13 and is a known security risk. R CMD check now reports (on all platforms) if their use is found in compiled code: replace by snprintf or vsnprintf respectively. [*NB:* whether such calls get compiled into the package is platform-dependent.] • Where recorded at installation, R CMD check reports the C and Fortran compilers used to build R. It reports the OS in use (if known, as given by osVersion) as well as that R was built for. It notes if a C++ standard was specified which is older than the current default: many packages have used C++11 to mean ‘not C++98’ - as C++11 is the minimum supported since R 4.0.0, that specification can probably be removed. • R CMD INSTALL reports the compilers (and on macOS, the SDK) used, and this is copied to the output of R CMD check. Where a C++ standard is specified, it is reported. • R CMD check's ‘checking compilation flags in Makevars’ has been relaxed to accept the use of flags such as -std=f2008 in PKG_FFLAGS. • tools::buildVignettes() has a new argument skip, which is used by R CMD check to skip (and note) vignettes with unavailable \VignetteDepends (PR#18318). • New generic .AtNames() added to enable class-specific completions after @. The formerly internal function findMatches() is now exported, mainly for use in methods for .DollarNames() and .AtNames(). Deprecated and Defunct: • default.stringsAsFactors() is defunct. • Calling as.data.frame.() directly (for 12 atomic classes) is going to be formally deprecated, currently activated by setting the environment variable _R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_ to non-empty, which also happens in R CMD check --as-cran. Bug Fixes: • Hashed environments with sizes less than 5 can now grow. (Reported to R-devel by Duncan Garmonsway.) • as.character(, deparse = TRUE) failed to re-escape curly braces in LaTeX-like text. (Reported by Hadley Wickham in PR#18324.) • library() now passes its lib.loc argument when requiring Depends packages; reported (with fix) in PR#18331 by Mikael Jagan. • R CMD Stangle: improved message about ‘Output’ files. • head(x, n) and tail(x, n) now signal an error if n is not numeric, instead of incidentally “working” sometimes returning all of x. Reported and discussed by Colin Fay, in PR#18357. • The "lm" method for summary() now gives the correct F-statistic when the model contains an offset. Reported in PR#18008. • C() and `contrasts<-`() now preserve factor level names when given a function object (as opposed a function name which did preserve names). Reported in PR#17616. • c(a = 1, 2)[[]] no longer matches 2 but rather signals a _classed_ error. Reported and analysed by Davis Vaughan in PR#18367, a duplicate of PR#18004, by Jan Meis et al. For consistency, NULL[[]] is also erroneous now. x[[]] <- v gives an error of the same class "MissingSubscriptError". • The relist() function of utils now supports NULL elements in the skeleton (PR#15854). • ordered(levels = *) (missing x) now works analogously to factor(, ordered=TRUE); reported (with fix) by Achim Zeileis in PR#18389. • User-defined Rd macro definitions can now span multiple lines, thanks to a patch from Duncan Murdoch. Previously, the Rd parser silently ignored everything after the first line. • Plain-text help (tools::Rd2txt()) now preserves an initial blank line for text following description list items. • tools::Rd2HTML() and tools::Rd2latex() no longer split \arguments and \value lists at Rd comments. • tools::Rd2latex() now correctly handles optional text outside \items of argument lists as well as bracketed text at the beginning of sections, e.g., \value{[NULL]}. • as.character() now behaves more in line with the methods for atomic vectors such as numbers, and is no longer influenced by options(). Ditto for as.character(). The as.character() method gets arguments digits and OutDec with defaults _not_ depending on options(). Use of as.character(*, format = .) now warns. • Similarly, the as.character.hexmode() and *.octmode() methods also behave as good citizen methods and back compatibility option keepStr = TRUE. • The as.POSIXlt() and as.POSIXct() default methods now do obey their tz argument, also in this case. • as.POSIXlt() now does apply a tz (time zone) argument, as does as.POSIXct(); partly suggested by Roland Fuß on the R-devel mailing list. • as.Date.POSIXlt(x) now also works when the list components are of unequal length, aka “partially filled” or “ragged”. • expand.model.frame() looked up variables in the wrong environment when applied to models fitted without data. Reported in PR#18414. • time() now (also) uses the ts.eps = getOption("ts.eps") argument and thus by default rounds values very close to the start (or end) of a year. Based on a proposal by Andreï V. Kostyrka on R-help. • Printing of a factanal() result with just one factor and sort = TRUE now works regularly, fixing PR#17863 by Timothy Bates, thanks to the ‘R Contributors’ working group. • Printing 0-length objects of class "factor", "roman", "hexmode", "octmode", "person", "bibentry", or "citation" now prints something better, one of which fixes PR#18422, reported by Benjamin Feakins. • Sys.timezone() queries timedatectl only if systemd is loaded; addressing a report by Jan Gorecki in PR#17421. • The formula method of cor.test() had scoping problems when environment(formula) was not the calling environment; reported with a patch proposal by Mao Kobayashi in PR#18439. • attach() of an environment with active bindings now preserves the active bindings. Reported by Kevin Ushey in PR#18425. • BLAS detection now works also with system-provided libraries not available as regular files. This fixes detection of the Accelerate framework on macOS since Big Sur. Reported by David Novgorodsky. • download.file() gives a helpful error message in case of an invalid download.file.method option, thanks to Colin Fay's report in PR#18455. • Sporadic crashes of Rterm when using completion have been fixed. • Rprof() is now more reliable. A livelock in thread initialization with too short sampling interval has been fixed on macOS. A deadlock in using the C runtime has been fixed on Windows. A potential deadlock has been prevented on Unix. • Cursor placement in Rgui now works even after a fixed-width font is selected. • Mandatory options (options()) are now set on startup so that saving and restoring them always works (PR#18372). • Package installation, R CMD INSTALL or install.packages(*), now parses each of the /R/*.R files individually instead of first concatenating and then parse()ing the large resulting file. This allows parser or syntax errors to be diagnosed with correct file names and line numbers, thanks to Simon Dedman's report and Bill Dunlap's patch in PR#17859. This _does_ require syntactically self contained R source files now, fixing another inadvertent bug. • predict.lm() now finds the offset in the correct environment, thanks to André Gillibert's report and patch in PR#18456. • getInitial() now finds the selfStart model in the correct environment. (Reported by Ivan Krylov in PR#18368.) • Fix for possible segfault when using recently-added graphics features, such as gradients, clipping paths, masks, and groups with pdf(file=NULL). • class(m) <- class(m) no longer changes a matrix m by adding a class _attribute_. • packageDate(pkg) now only warns once if there is no pkg. • When ts() creates a multivariate time series, "mts", it also inherits from "array" now, and is.mts() is documented _and_ stricter. • Rd2txt() now preserves line breaks of \verb Rd content and from duplicated \cr. The former also fixes the rendering of verbatim output from Rd \Sexpr in plain-text help. • uniroot(f, interval) should no longer wrongly converge _outside_ the interval in some cases where abs(f(x)) == Inf for an x at the interval boundary, thanks to posts by Ben Bolker and Serguei Sokol on R-devel. • Vectorized alpha handling in palette functions such as in gray(), rainbow(), or hcl.colors() works correctly now, thanks to Achim Zeileis' report and patch in PR#18476. • Formatting and print()ing of bibentry objects has dropped the deprecated citation.bibtex.max argument, such that the bibtex argument's default for print.bibentry() depends directly on the citation.bibtex.max option, whereas in format.bibentry() the option no longer applies. • Attempting to use a character string naming a foreign function entry point in a foreign function call in a package will now signal an error if the packages has called R_forceSymbols to specify that symbols must be used. • An error in table() could permanently set options(warn=2) promoting all subsequent warnings to errors. • The sigma() function gave misleading results for binary GLMs. A new method for objects of class "glm" returns the square root of the estimate of the dispersion parameter using the same calculation as summary.glm(). • bs() and ns() in the (typical) case of automatic knot construction, when some of the supposedly inner knots coincide with boundary knots, now moves them inside (with a warning), building on PR#18442 by Ben Bolker. • R CMD on Windows now skips the site profile with --no-site-file and --vanilla even when R_PROFILE is set (PR#18512, from Kevin Ushey). Changes in R 4.2.3: C-Level Facilities: • The definition of DL_FUNC in R_ext/Rdynload.h has been changed to be fully C-compliant. This means that functions loaded _via_ for example R_GetCCallable need to be cast to an appropriate type if they have any arguments. • .Machine has a new element sizeof.time_t to identify old systems with a 32-bit type and hence a limited range of date-times (and limited support for dates millions of years from present). Package Installation: • (Windows) The default C++ standard had accidentally been left at C++11 when it was changed to C++14 on Unix. Bug Fixes: • As "POSIXlt" objects may be “partially filled” and their list components meant to be recycled, length() now is the length of the longest component. • as.POSIXlt.Date() could underflow for dates in the far past (more than half a million years BCE). • as.Date.POSIXlt(x) would return "1970-01-01" instead of NA in R 4.2.2, e.g., for x <- as.POSIXlt(c("2019-01-30","2001-1-1")) x$mon <- c(0L, NA); as.Date(x) • R CMD check failed to apply enabled _R_CHECK_SUGGESTS_ONLY_ to examples and vignettes (regression in R 4.2.0). • R CMD check did not re-build vignettes in separate processes by default (regression in R 4.2.0). • Running examples from HTML documentation now restores previous knitr settings and options (PR#18420). • Quartz: fonts are now located using Core Graphics API instead of deprecated ATS which is no longer supported in the macOS 13 SDK (PR#18426). This also addresses an issue where the currently used font in the Quartz device context was not correctly retained. • (Windows) Math symbols in text drawing functions are again rendered correctly (PR#18440). This fixes a regression in R 4.2.1 caused by a fix in PR#18382 which uncovered an issue in GraphApp due to which the symbol charset was not used with TT Symbol font face. • (Windows) Installing a package with a src/Makefile.{win,ucrt} file includes ~/.R/Makevars.win64 in the search for user makevars, as documented in “R Installation and Administration” and done for packages with a src/Makevars.{win,ucrt} file. • format(, "....%OS") with n > 0 no longer accidentally uses the unbalanced seconds, thanks to Suharto Anggono's report (including patch) in PR#18448. • solve.default(a, b) works around issues with some versions of LAPACK when a contains NA or NaN values. • When UseMethod() cannot dispatch, it no longer segfaults producing the error message in case of a long class(), thanks to Joris Vankerschaver's report (including patch) in PR#18447. • When example(foo, ..) produces graphics on an interactive device it needs to open itself, it now leaves devAskNewPage() unchanged even when it was FALSE, thus fixing a 14 years old ‘FIXME’. • packageDescription() again catches errors from encoding conversions. This also fixes broken packageVersion() in C locale on systems where iconv does not support transliteration. Changes in R 4.2.2: New Features: • tools::Rdiff(useDiff = TRUE) checks for the presence of an external diff command and switches to useDiff = FALSE if none is found. This allows R CMD Rdiff to always work. • On Windows, environment variable R_LIBCURL_SSL_REVOKE_BEST_EFFORT can be used to switch to only ‘best-effort’ SSL certificate revocation checks with the default "libcurl" download method. This reduces security, but may be needed for downloads to work with MITM proxies (PR#18379). • (macOS) The run-time check for libraries from XQuartz for X11 and Tcl/Tk no longer uses otool from the Apple Developer Tools (PR#18400). • The LaTeX style for producing the PDF manuals, Rd.sty, now loads the standard amsmath, amsfonts and amssymb packages for greater coverage of math commands in the Rd \eqn and \deqn macros. The \mathscr LaTeX command is also provided (via the mathrsfs package, if available, or the amsfonts bundle otherwise), fulfilling the wish of PR#18398. • (Windows) The default format of readClipboard() and writeClipboard() has been changed to 13 (CF_UNICODETEXT). Installation on a Unix-Alike: • The PDF manuals (if built) can be compacted by the new target make compact-pdf (at the top level or in directory doc/manual). • There is now configure support for LLVM clang 15 on Linux, which defaults to position-independent (PIE) executables whereas gfortran does not. • Many small changes to ease compilation (and suppress warnings) with LLVM clang 15. Bug Fixes: • Rscript -e would fail if stdin were closed (Reported by Henrik Bengtsson.) • qt(*, log.p=TRUE) in outer tails no longer produces NaN in its final steps, thus fixing PR#18360. • tools::Rd2latex() now escapes hashes and ampersands when writing URLs, fixing LaTeX errors with such URLs in \tabular. • When isGeneric(f, fdef=*) is used with mismatching names, the warning is better understandable; reported (with fix) in PR#18370 by Gabe Becker. • poly(x, n) now works again (and is now documented) when x is a "Date" or "POSIXct" object, or of another class while fulfilling mode(x) == "numeric". This also enables poly(x, *, raw=TRUE) for such variables. Reported by Michael Chirico to R-devel. • write.table(), write.csv() and write.csv2() restore their numerical precision (internal equivalent of digits = 15) after an interrupt (PR#18384). • One can now read also byte FF from a clipboard connection (PR#18385). • source("") and source(character()) now give more helpful error messages. • R CMD check --as-cran set _R_CHECK_TIMINGS_ too late to have the intended effect. • as.POSIXlt(x) now also works with very large dates x, fixing PR#18401 reported by Hannes 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 to format() them correctly. • Added methods for is.finite(), is.infinite() and is.nan() for "POSIXlt" date-time objects. Bug Fixes (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 for Alt+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 as tools::CRAN_package_db() and is intended for packages wishing to access CRAN for purposes other than installing packages. The need for this was shown by a day when the main CRAN website was offline and a dozen or so packages which had its URL hardcoded failed their checks. Installation on a Unix-Alike: • The libraries searched for by --with-blas (without a value) now include BLIS (after OpenBLAS but before ATLAS). And on macOS, the Accelerate framework (after ATLAS). (This is patterned after the AX_BLAS macro from the Autoconf Archive.) • The included LAPACK sources have been updated to 3.10.1. Utilities: • The (full path to) the command tidy to be used for HTML validation can be set by environment variable R_TIDYCMD. • Setting environment variable _R_CHECK_RD_VALIDATE_RD2HTML_ to a false value will override R CMD check --as-cran and turn off HTML validation. This provides a way to circumvent a problematic tidy. The 2006 version that ships with macOS is always skipped. C-Level Facilities: • The undocumented legacy declarations of Sint, Sfloat, SINT_MAX and SINT_MIN in header R.h are deprecated. Bug Fixes: • fisher.test(d) no longer segfaults for “large” d; fixing PR#18336 by preventing/detecting an integer overflow reliably. • tar(., files=*) now produces correctly the warning about invalid UID or GID of files, fixing PR#18344, reported by Martin Morgan. • tk_choose.files() with multi = FALSE misbehaved on paths containing spaces (PR#18334) (regression introduced in R 4.0.0). • sort(x, partial = ind, *) now works correctly notably for the non-default na.last = FALSE or TRUE, fixing PR#18335 reported by James Edwards. • Environment variable _R_CHECK_XREFS_REPOSITORIES_ is only used for checking .Rd cross-references in R CMD check (as documented) and not for other uses looking for a CRAN mirror. • The search for a CRAN mirror when checking packages now uses getOption("repos") if that specifies a CRAN mirror, even when it does not also specify all three Bioconductor repositories (as was previously required). • The HTML code generated by tools::Rd2HTML() has been improved to pass tidy 5.8.0. Bug Fixes (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 for Rgui users of systems where R 4.1 used a single-byte locale but R 4.2.0 uses UTF-8. • Performance of txtProgressBar() in Rgui 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 of aggregate() now matches the generic in naming its first argument x (resolving PR#18299 by Thomas Soeiro). This means that calling aggregate() with a formula as a named first argument requires name formula in earlier versions of R and name x now, so portable code should not name the argument (code in many packages did). • Calling && or || with either argument of length greater than one now gives a warning (which it is intended will become an error). • Calling if() or while() with a condition of length greater than one gives an error rather than a warning. Consequently, environment variable _R_CHECK_LENGTH_1_CONDITION_ no longer has any effect. • Windows users should consult the Windows section below for some profound changes including • Support for 32-bit builds has been dropped. • UTF-8 locales are used where available. • The default locations for the R installation and personal library folder have been changed. Thanks to Tomas Kalibera for months of work on the Windows port for this release. New Features: • matrix(x, n, m) now warns in more cases where length(x) differs from n * m, as suggested by Abby Spurdle and Wolfgang Huber in Feb 2021 on the R-devel mailing list. This warning can be turned into an error by setting environment variable _R_CHECK_MATRIX_DATA_ to TRUE: R CMD check --as-cran does so unless it is already set. • Function file_test() in package utils gains tests for symlinks, readability and writability. • capabilities("libxml") is now false. The description of capabilities("http/ftp") now reflects that it refers to the default method, no longer the internal one. • simplify2array() gains an except argument for controlling the exceptions used by sapply(). • Environment variables R_LIBS_USER and R_LIBS_SITE are both now set to the R system default if unset or empty, and can be set to NULL to indicate an empty list of user or site library directories. • The warning for axis()(-like) calls in cases of relatively small ranges (typically in log-scale situations) is slightly improved _and_ suppressed from explicit calls to .axisPars() as has always been the intention. • The contrasts setter function `contrasts<-` gains an explicit default how.many = NULL rather than just using missing(how.many). • grid.pretty() gains a new optional argument n = 5. • There is a new function .pretty() with option bounds as a technical-utility version of pretty(). It and pretty() gain a new argument f.min with a better than back-compatible default. • Function grDevices::axisTicks() and related functions such as graphics::axis() work better, notably for the log scale; partly because of the pretty() improvements, but also because care is taken e.g., when ylim is finite but diff(ylim) is infinite. • nclass.FD() gains a digits option. • The R Mathlib internal C function bd0() (called indirectly from a dozen probability density and distribution functions such as dpois(), dbinom(), dgamma(), pgamma() _etc_) has been complemented by a more sophisticated and (mostly) more accurate C function ebd0(), currently called only by internal dpois_raw() improving accuracy for R level dpois() and potentially others calling it such as dnbinom(), dgamma() or pgamma(). (Thanks to Morten Welinder's PR#15628.) • write.ftable() gains sep = " " argument as suggested by Thomas Soeiro. • The names of the locale categories supported by R's Sys.getlocale() and Sys.setlocale() are now provided by variable .LC.categories in the base namespace. • The Date and POSIXt methods for hist() and the histogram method for plot() now also use the new default col = "lightgray" in consistency with the corresponding change to hist()'s default for R 4.0.0. • hist.default() gains new fuzz argument, and the histogram plot method no longer uses fractional axis ticks when displaying counts ("Frequency"). • mapply() and hence Map() now also obey the “max-or-0-if-any” recycling rule, such that, e.g., Map(`+`, 1:3, 1[0]) is valid now. • as.character() for "hexmode" or "octmode" objects now fulfils the important basic rule as.character(x)[j] === as.character(x[j]). • The set utility functions, notably intersect() have been tweaked to be more consistent and symmetric in their two set arguments, also preserving a common mode. • substr(ch, start,end) <- new now e.g., preserves names(ch); ditto for substring(), thanks to a patch from Brodie Gaslam. • plot() gains a extend.ylim.f argument, in partial response to PR#15285; further PR#17784 is fixed thanks to several contributors and a patch by Elin Waring. The Cook's dist contours get customizable via cook.col and cook.lty with a different default color and their legend is nicer by default and customizable via cook.legendChanges. • Attempting to subset an object that is not subsettable now signals an error of class notSubsettableError. The non-subsettable object is contained in the object field of the error condition. • Subscript-out-of-bounds errors are now signaled as errors of class subscriptOutOfBoundsError. • Stack-overflow errors are now signaled as errors inheriting from class stackOverflowError. See ?stackOverflowError for more details. • New partly experimental Sys.setLanguage() utility, solving the main problem of PR#18055. • gettext() and gettextf() get a new option trim = TRUE which when set to false allows translations for strings such as "Execution halted\n" typical for C code. • An experimental implementation of hash tables is now available. See ?hashtab for more details. • identical() gains a extptr.as.ref argument for requesting that external pointer objects be compared as reference objects. • reorder() gets an argument decreasing which it passes to sort() for level creation; based on the wish and patch by Thomas Soeiro in PR#18243. • as.vector() gains a data.frame method which returns a simple named list, also clearing a long-standing ‘FIXME’ to enable as.vector(, mode="list"). This breaks code relying on as.vector() to return the unchanged data frame. • legend() is now vectorized for arguments cex, x.intersp, and text.width. The latter can now also be specified as a vector (one element for each column of the legend) or as NA for computing a proper column wise maximum value of strwidth(legend). The argument y.intersp can be specified as a vector with one entry for each row of the legend. legend() also gains new arguments title.cex and title.font. Thanks to Swetlana Herbrandt. • Deparsing no longer remaps attribute names dim, dimnames, levels, names and tsp to historical S-compatible names (which structure() maps back). • sample() and sample.int() have additional sanity checks on their size and n arguments. all.equal.numeric() gains a sanity check on its tolerance argument - calling all.equal(a, b, c) for three numeric vectors is a surprisingly common error. mean(na.rm =), rank(na.last =), barplot(legend.text =), boxplot(), contour(drawlabels =), polygon(border =) and methods::is(class2 =) have more robust sanity checks on their arguments. R CMD Rd2pdf (used by R CMD check) has a more robust sanity check on the format of \alias{} commands. • psigamma(x, deriv) for negative x now also works for deriv = 4 and 5; their underlying C level dpsifn() is documented in ‘Writing R Extensions’. • The HTML help system now uses HTML5 (wish of PR#18149). • ks.test() now provides exact p-values also with ties and MC p-values in the two-sample (Smirnov) case. By Torsten Hothorn. • ks.test() gains a formula interface, with y ~ 1 for the one-sample (Kolmogorov) test and y ~ group for the two-sample (Smirnov) test. Contributed by Torsten Hothorn. • The return value from ks.test() now has class c("ks.test", "htest") - packages using try() need to take care to use inherits() and not == on the class. • New functions psmirnov(), qsmirnov() and rsmirnov() in package stats implementing the asymptotic and exact distributions of the two-sample Smirnov statistic. • iconv() now allows sub = "c99" to use C99-style escapes for UTF-8 inputs which cannot be converted to encoding to. • In a forward pipe |> expression it is now possible to use a named argument with the placeholder _ in the rhs call to specify where the lhs is to be inserted. The placeholder can only appear once on the rhs. • The included LAPACK sources have been updated to version 3.10.0, except for the four Fortran 77 routines which 3.10.0 has re-implemented in Fortran 90 (where the older versions have been retained as the R build process does not support Fortran 90). • path.expand() and most other uses of tilde expansion now warn if a path would be too long if expanded. (An exception is file.exists(), which silently returns false.) • trunc(, *) now supports units = "months" or "years" for consistency with the POSIXt method, thanks to Dirk Eddelbuettel's proposal in PR#18099. • list2DF() now checks that its arguments are of the same length, rather than use recycling. • The HTML help system has several new features: LaTeX-like math can be typeset using either KaTeX or MathJax, usage and example code is highlighted using Prism, and for dynamic help the output of examples and demos can be shown within the browser if the knitr package is installed. These features can be disabled by setting the environment variable _R_HELP_ENABLE_ENHANCED_HTML_ to a false value. Graphics: • The graphics engine version, R_GE_version, has been bumped to 15 and so packages that provide graphics devices should be reinstalled. • The grid package now allows the user to specify a “vector” of pattern fills. The fill argument to gpar() accepts a list of gradients and/or patterns and the functions linearGradient(), radialGradient(), and pattern() have a new group argument. Points grobs (data symbols) can now also have a pattern fill. The grobCoords() function now returns a more informative and complex result. • The grid package has new functions for drawing isolated groups: grid.group(), grid.define(), and grid.use(). These functions add compositing operators and affine transformations to R's graphics capabilities. The grid package also has new functions for stroking and filling paths: grid.stroke(), grid.fill(), and grid.fillStroke(). A new function as.path() allows the user to specify the fill rule for a path that is to be used for clipping, stroking, or filling; available options are "winding" and "evenodd". A new function as.mask() allows the user to specify the type of a mask; available options are "alpha" and "luminance". These new features are only supported so far (at most) on the Cairo-based graphics devices and on the pdf() device. • dev.capabilities() reports on device support for the new features. • par() now warns about unnamed non-character arguments to prevent misuse such as {usr <- par("usr"); par(usr)}. 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 field crt (only on Windows) to denote the C runtime. The value is "ucrt". • On Windows, download.file(method = "auto") and url(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() and memory.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 an R CMD build change in R 3.0.0 and affects packages built before R 3.0.2. Such packages should be re-made with R CMD build to have the tangled R code of vignettes shipped with the tarball. • USE_FC_LEN_T will become the default: this uses the correct prototypes for Fortran BLAS/LAPACK routines called from C/C++, and requires adjustment of most such calls - see ‘Writing R Extensions’ §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 uses valgrind when re-building vignettes as some non-Sweave vignettes unhelpfully comment out all their code when R CMD check runs vignettes. • Errors in re-building vignettes (unless there are LaTeX errors) are reported by R CMD check as ERROR rather than WARNING when running vignettes has been skipped (as it frequently is in CRAN checks and by --as-cran). • R CMD Rd2pdf gains a --quiet option that is used by R CMD build when building the PDF package manual. • R CMD Rd2pdf now always runs LaTeX in batch mode, consistent with Texinfo >= 6.7. The --batch option is ignored. • R CMD build and R CMD check now include the Rd file name and line numbers in the error message of an \Sexpr evaluation failure. • For packages using the \doi Rd macro (now an install-time \Sexpr) but no other dynamic Rd content, R CMD build now produces a smaller tarball and is considerably faster - skipping temporary package installation. • R CMD check can optionally (but included in --as-cran) validate the HTML produced from the packages .Rd files. See : 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 use R_NO_REMAP will need to ensure that the remapped names are used for calls to API functions that were formerly also made available as macros. • The deprecated legacy S-compatibility macros PROBLEM, MESSAGE, ERROR, WARN, WARNING, RECOVER, ... are no longer defined in R_ext/RS.h (included by R.h). Replace these by calls to Rf_error and Rf_warning (defined in header R_ext/Error.h included by R.h). Header R_ext/RS.h no longer includes R_ext/Error.h. • Header R_ext/Constants.h (included by R.h) when included from C++ now includes the C++ header cfloat rather than the C header float.h (now possible as C++11 is required). • The legacy S-compatibility macros DOUBLE_* in R_ext/Constants.h (included by R.h) are deprecated. • The deprecated S-compatibility macros SINGLE_* in R_ext/Constants.h (included by R.h) have been removed. • R_Calloc, R_Free and R_Realloc are preferred to their unprefixed forms and error messages now use the prefix. These forms were introduced in R 3.4.0 and are available even when STRICT_R_HEADERS is defined. • rmultinom has been documented in ‘Writing R Extensions’ §6 so is now part of the R API. • Similarly, Rtanpi, called from R level tanpi() is now part of the R API. • The long-deprecated, undocumented and non-API entry point call_R is no longer declared in R_ext/RS.h (included by R.h). • The header S.h which has been unsupported since Jan 2016 has been removed. Use R.h instead. Deprecated and Defunct: • The (non-default and deprecated) method = "internal" for download.file() and url() no longer supports http:// nor ftp:// URIs. (It is used only for file:// URIs.) On Windows, download.file(method = "wininet") no longer supports ftp:// URIs. (It is no longer the default method, which is "libcurl" and does.) On Windows, the deprecated method = "wininet" now gives a warning for http:// and https:// URIs for both download.file() and url(). (It is no longer the default method.) • On Windows, the command-line option --max-mem-size and environment variable R_MAX_MEM_SIZE are defunct. The memory allocation limit was important for 32-bit builds, but these are no longer supported. • default.stringsAsFactors() is now formally deprecated, where that was only mentioned on its regular help page, previously. So it now gives a warning if called. • unix.time() is defunct now; it had been deprecated since R 3.4.0. Bug Fixes: • Setting digits = 0 in format(), print.default() (and hence typically print()) or options() is again invalid. Its behaviour was platform-dependent, and it is unclear what “zero significant digits” should mean (PR#18098). • Messages from C code in the cairo section of package grDevices are now also offered for translation, thanks to Michael Chirico's PR#18123. • mean(x) with finite x now is finite also without "long.double" capability. • R CMD Rd2pdf no longer leaves an empty build directory behind when it aborts due to an already existing output file. (Thanks to Sebastian Meyer's PR#18141.) • density(x, weights = w, na.rm = TRUE) when anyNA(x) is true, now removes weights “in parallel” to x, fixing PR#18151, reported by Matthias Gondan. Additionally, it gets a subdensity option. • Conversion of \Sexpr[]{} to LaTeX or HTML no longer produces long blocks of empty lines when itself contains several lines all producing empty output. Thanks to a report and patch by Ivan Krylov posted to R-devel. • R CMD build no longer fails if a package vignette uses child documents and inst/doc exists. (Thanks to Sebastian Meyer's PR#18156.) • When an R documentation (‘help’ source) file man/foo.Rd in a package has \donttest{..} examples with a syntax error, it is now signalled as ERROR and with correct line numbers relating to the *-Ex.R file, thanks to Duncan Murdoch and Sebastian Meyer's reports and patch proposals in PR#17501. • Improved determination of the correct translation domain in non-base packages, addressing the combination of PR#18092 and PR#17998 (#c6) with reports and _augmented_ patch #2904 by Suharto Anggono. Note that "R-base" is no longer the default domain e.g., for top-level calls to gettext(); rather translation needs explicit domain = * specification in such cases. • identical(attrib.as.set=FALSE) now works correctly with data frames with default row names. (Thanks to Charlie Gao's PR#18179.) • txtProgressBar() now enforces a non-zero width for argument char, without which no progress can be visible. • dimnames(table(d)) is more consistent in the case where d is a list with a single component, thanks to Thomas Soeiro's report to R-devel. Further, table(d1, d2) now gives an error when d1 and d2 are data frames as suggested by Thomas in PR#18224. • Fix for drawing semi-transparent lines and fills on the native Windows graphics device (PR#18219 and PR#16694). Thanks to Nick Ray for helpful diagnosis on Bugzilla. • The deparser now wraps sub-expressions such as if(A) .. with parentheses when needed; thanks to Duncan Murdoch's PR#18232 and Lionel Henry's patches there. • remove.packages() no longer tries to uninstall Priority: base packages, thanks to a report and suggestions by Colin Fay in PR#18227. • win.metafile() now has xpinch and ypinch arguments so that the user can override Windows' (potentially wrong) guess at device dimensions. • x[i] and x[[i]] for non-integer i should now behave in all cases as always documented: the index used is equivalent to as.integer(i) unless that would overflow where trunc(i) is used instead; thanks to Suharto Anggono's report and patch proposals in PR#17977. • asOneSidedFormula() now associates the resulting formula with the global environment rather than the evaluation environment created for the call. • $name now matches the field name case-insensitively, consistent with bibentry() creation and the replacement method. • cbind() failed to detect some length mismatches with a mixture of time-series and non-time-series inputs. • The default LaTeX style file Sweave.sty used by the RweaveLatex driver no longer loads the obsolete ae package; thanks to a report by Thomas Soeiro in PR#18271. Furthermore, it now skips \usepackage[T1]{fontenc} for engines other than pdfTeX (if detected) or if the new [nofontenc] option is used. • smooth.spline() now stores its logical cv argument more safely, fixing a rare bug when printing, and also stores n. • smooth.spline(x,y,*) now computes the cv.crit statistic correctly, also when is.unsorted(x), fixing PR#18294. • The data.frame method of rbind() now warns when binding not-wholly-recycling vectors, by analogy to the default method (for matrices). • setAs() finds the correct class for name to when multiple packages define a class with that name. Thanks to Gabor Csardi for the report. • Fix for detaching a package when two classes of the same name are present in method signatures for the same generic. Thanks to Gabor Csardi for the report. • match.arg("", c("", "a", "B")) gives a better error message, in part from PR#17959, thanks to Elin Waring. • R CMD Sweave --clean no longer removes pre-existing files or subdirectories (PR#18242). • The quartz() device no longer splits polylines into subpaths. That has caused narrowly-spaced lines with many points to always look solid even when dashed line type was used due to dash phase restarts. • Deparsing constructs such as quote(1 + `!`(2) + 3) works again as before R 3.5.0, thanks to the report and patch in PR#18284 by Suharto Anggono. • as.list(f) for a factor f now keeps names(f), fixing PR#18309. • qbeta(.001, .9, .009) and analogous qf() calls now return a correct value instead of NaN or wrongly 1, all with a warning; thanks to the report by Ludger Goeminne in PR#18302. • plot.lm() failed to produce the plot of residuals vs. factor levels (i.e., which=5 when leverages are constant) for models with character predictors (PR#17840). • interaction.plot(..., xtick = TRUE) misplaced the x-axis line (PR#18305). • Not strictly fixing a bug, format()ing and print()ing of non-finite Date and POSIXt values NaN and +/-Inf no longer show as NA but the respective string, e.g., Inf, for consistency with numeric vector's behaviour, fulfilling the wish of PR#18308. • R CMD check no longer runs test scripts generated from corresponding .Rin files twice and now signals an ERROR if processing an .Rin script fails. • tools::Rd2txt() used for plain-text help pages now renders \hrefs (if tools::Rd2txt_options(showURLs = TRUE)) and \urls with percent-encoding and standards-compliant delimiting style (angle brackets and no URL: prefix). \email is now rendered with a mailto: prefix. Changes in R 4.1.3: New Features: • The default version of Bioconductor has been changed to 3.14. (This is used by setRepositories and the menus in GUIs.) Utilities: • R CMD check --as-cran has a workaround for a bug in versions of file up to at least 5.41 which mis-identify DBF files last changed in 2022 as executables. C-Level Facilities: • The legacy S-compatibility macros SINGLE_* in R_ext/Constants.h (included by R.h) are deprecated and will be removed in R 4.2.0. Bug Fixes: • Initialization of self-starting nls() models with initialization functions following the pre-R-4.1.0 API (without the ... argument) works again for now, with a deprecation warning. • Fixed quoting of ~autodetect~ in Java setting defaults to avoid inadvertent user lookup due to leading ~, reported in PR#18231 by Harold Gutch. • substr(., start, stop) <- v now treats _negative_ stop values correctly. Reported with a patch in PR#18228 by Brodie Gaslam. • Subscripting an array x without dimnames by a length(dim(x))-column character matrix gave "random" non-sense, now an error; reported in PR#18244 by Mikael Jagan. • ...names() now matches names(list(...)) closely, fixing PR#18247. • all.equal(*, scale = s) now works as intended when length(s) > 1, partly thanks to Michael Chirico's PR#18272. • print(x) for long vectors x now also works for named atomic vectors or lists and prints the correct number when reaching the getOption("max.print") limit; partly thanks to a report and proposal by Hugh Parsonage to the R-devel list. • all.equal(, *) no longer signals a deprecation warning. • reformulate(*, response=r) gives a helpful error message now when length(r) > 1, thanks to Bill Dunlap's PR#18281. • Modifying globalCallingHandlers inside withCallingHandlers() now works or fails correctly, thanks to Henrik Bengtsson's PR#18257. • hist(, breaks = "days") and hist(, breaks = "secs") no longer fail for inputs of length 1. • qbeta(.001, .9, .009) and similar cases now converge correctly thanks to Ben Bolker's report in PR#17746. • window(x, start, end) no longer wrongly signals “'start' cannot be after 'end'”, fixing PR#17527 and PR#18291. • data() now checks that its (rarely used) list argument is a character vector - a couple of packages passed other types and gave incorrect results. • which() now checks its arr.ind argument is TRUE rather coercing to logical and taking the first element - which gave incorrect results in package code. • model.weights() and model.offset() more carefully extract their model components, thanks to Ben Bolker and Tim Taylor's R-devel post. • list.files(recursive = TRUE) now shows all broken symlinks (previously, some of them may have been omitted, PR#18296). Changes in R 4.1.2: C-Level Facilities: • The workaround in headers R.h and Rmath.h (using namespace std;) for the Oracle Developer Studio compiler is no longer needed now C++11 is required so has been removed. A couple more usages of log() (which should have been std::log()) with an int argument are reported on Solaris. • The undocumented limit of 4095 bytes on messages from the S-compatibility macros PROBLEM and MESSAGE is now documented and longer messages will be silently truncated rather than potentially causing segfaults. • If the R_NO_SEGV_HANDLER environment variable is non-empty, the signal handler for SEGV/ILL/BUS signals (which offers recovery user interface) is not set. This allows more reliable debugging of crashes that involve the console. Deprecated and Defunct: • The legacy S-compatibility macros PROBLEM, MESSAGE, ERROR, WARN, WARNING, RECOVER, ... are deprecated and will be hidden in R 4.2.0. R's native interface of Rf_error and Rf_warning has long been preferred. Bug Fixes: • .mapply(F, dots, .) no longer segfaults when dots is not a list and uses match.fun(F) as always documented; reported by Andrew Simmons in PR#18164. • hist(, ...) and hist(, ...) no longer pass arguments for rect() (such as col and density) to axis(). (Thanks to Sebastian Meyer's PR#18171.) • \Sexpr{ch} now preserves Encoding(ch). (Thanks to report and patch by Jeroen Ooms in PR#18152.) • Setting the RNG to "Marsaglia-Multicarry" e.g., by RNGkind(), now warns in more places, thanks to 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=, .., log=TRUE) regression, reported by Martin Morgan. • as.Date.POSIXlt(x) now keeps names(x), thanks to Davis Vaughan's report and patch in PR#18188. • model.response() now strips an "AsIs" class typically, thanks to Duncan Murdoch's report and other discussants in PR#18190. • try() is considerably faster in case of an error and long call, as e.g., from some do.call(). Thanks to Alexander Kaever's suggestion posted to R-devel. • qqline(y =