R Portable Changelog

What's new in R Portable 4.2.0

• SIGNIFICANT USER-VISIBLE CHANGES:
• The formula method of aggregate() now matches the generic in naming its first argument x (resolving PR#18299 by Thomas Soeiro).
• This means that calling aggregate() with a formula as a named first argument requires name formula in earlier versions of R and name x now, so portable code should not name the argument (code in many packages did).
• Calling && or || with either argument of length greater than one now gives a warning (which it is intended will become an error).
• Calling if() or while() with a condition of length greater than one gives an error rather than a warning. Consequently, environment variable R_CHECK_LENGTH_1_CONDITION no longer has any effect.
• Windows users should consult the WINDOWS section below for some profound changes including
• Support for 32-bit builds has been dropped.
• UTF-8 locales are used where available.
• The default locations for the R installation and personal library folder have been changed.
• Thanks to Tomas Kalibera for months of work on the Windows port for this release.
• NEW FEATURES:
• matrix(x, n, m) now warns in more cases where length(x) differs from n * m, as suggested by Abby Spurdle and Wolfgang Huber in Feb 2021 on the R-devel mailing list.
• This warning can be turned into an error by setting environment variable R_CHECK_MATRIX_DATA to TRUE: R CMD check --as-cran does so unless it is already set.
• Function file_test() in package utils gains tests for symlinks, readability and writability.
• capabilities("libxml") is now false.
• The description of capabilities("http/ftp") now reflects that it refers to the default method, no longer the internal one.
• simplify2array() gains an except argument for controlling the exceptions used by sapply().
• Environment variables R_LIBS_USER and R_LIBS_SITE are both now set to the R system default if unset or empty, and can be set to NULL to indicate an empty list of user or site library directories.
• The warning for axis()(-like) calls in cases of relatively small ranges (typically in log-scale situations) is slightly improved and suppressed from explicit calls to .axisPars() as has always been the intention.
• The contrasts setter function contrasts<- gains an explicit default how.many = NULL rather than just using missing(how.many).
• grid.pretty() gains a new optional argument n = 5.
• There is a new function .pretty() with option bounds as a technical-utility version of pretty(). It and pretty() gain a new argument f.min with a better than back-compatible default.
• Function grDevices::axisTicks() and related functions such as graphics::axis() work better, notably for the log scale; partly because of the pretty() improvements, but also because care is taken e.g., when ylim is finite but diff(ylim) is infinite.
• nclass.FD() gains a digits option.
• The R Mathlib internal C function bd0() (called indirectly from a dozen probability density and distribution functions such as dpois(), dbinom(), dgamma(), pgamma() etc) has been complemented by a more sophisticated and (mostly) more accurate C function ebd0(), currently called only by internal dpois_raw() improving accuracy for R level dpois() and potentially others calling it such as dnbinom(), dgamma() or pgamma(). (Thanks to Morten Welinder's PR#15628.)
• write.ftable() gains sep = " " argument as suggested by Thomas Soeiro.
• The names of the locale categories supported by R's Sys.getlocale() and Sys.setlocale() are now provided by variable .LC.categories in the base namespace.
• The Date and POSIXt methods for hist() and the histogram method for plot() now also use the new default col = "lightgray" in consistency with the corresponding change to hist()'s default for R 4.0.0.
• hist.default() gains new fuzz argument, and the histogram plot method no longer uses fractional axis ticks when displaying counts ("Frequency").
• mapply() and hence Map() now also obey the "max-or-0-if-any" recycling rule, such that, e.g., Map(+, 1:3, 1[0]) is valid now.
• as.character(<obj>) for "hexmode" or "octmode" objects now fulfils the important basic rule as.character(x)[j] === as.character(x[j]).
• The set utility functions, notably intersect() have been tweaked to be more consistent and symmetric in their two set arguments, also preserving a common mode.
• substr(ch, start,end) <- new now e.g., preserves names(ch); ditto for substring(), thanks to a patch from Brodie Gaslam.
• plot(<lm>) gains a extend.ylim.f argument, in partial response to PR#15285; further PR#17784 is fixed thanks to several contributors and a patch by Elin Waring. The Cook's dist contours get customizable via cook.col and cook.lty with a different default color and their legend is nicer by default and customizable via cook.legendChanges.
• Attempting to subset an object that is not subsettable now signals an error of class notSubsettableError. The non-subsettable object is contained in the object field of the error condition.
• Subscript-out-of-bounds errors are now signaled as errors of class subscriptOutOfBoundsError.
• Stack-overflow errors are now signaled as errors inheriting from class stackOverflowError. See ?stackOverflowError for more details.
• New partly experimental Sys.setLanguage() utility, solving the main problem of PR#18055.
• gettext() and gettextf() get a new option trim = TRUE which when set to false allows translations for strings such as "Execution haltedn" typical for C code.
• An experimental implementation of hash tables is now available. See ?hashtab for more details.
• identical() gains a extptr.as.ref argument for requesting that external pointer objects be compared as reference objects.
• reorder() gets an argument decreasing which it passes to sort() for level creation; based on the wish and patch by Thomas Soeiro in PR#18243.
• as.vector() gains a data.frame method which returns a simple named list, also clearing a long standing 'FIXME' to enable as.vector(<data.frame>, mode="list"). This breaks code relying on as.vector(<data.frame>) to return the unchanged data frame.
• legend() is now vectorized for arguments cex, x.intersp, and text.width. The latter can now also be specified as a vector (one element for each column of the legend) or as NA for computing a proper column wise maximum value of strwidth(legend). The argument y.intersp can be specified as a vector with one entry for each row of the legend.
• legend() also gains new arguments title.cex and title.font. Thanks to Swetlana Herbrandt.
• Deparsing no longer remaps attribute names dim, dimnames, levels, names and tsp to historical S-compatible names (which structure() maps back).
• sample() and sample.int() have additional sanity checks on their size and n arguments.
• all.equal.numeric() gains a sanity check on its tolerance argument - calling all.equal(a, b, c) for three numeric vectors is a surprisingly common error.
• mean(na.rm =), rank(na.last =), barplot(legend.text =), boxplot(), contour(drawlabels =), polygon(border =) and methods::is(class2 =) have more robust sanity checks on their arguments.
• R CMD Rd2pdf (used by R CMD check) has a more robust sanity check on the format of alias{} commands.
• psigamma(x, deriv) for negative x now also works for deriv = 4 and 5; their underlying C level dpsifn() is documented in 'Writing R Extensions'.
• The HTML help system now uses HTML5 (wish of PR#18149).
• ks.test() now provides exact p-values also with ties and MC p-values in the two-sample (Smirnov) case. By Torsten Hothorn.
• ks.test() gains a formula interface, with y ~ 1 for the one-sample (Kolmogorov) test and y ~ group for the two-sample (Smirnov) test. Contributed by Torsten Hothorn.
• The return value from ks.test() now has class c("ks.test", "htest") - packages using try() need to take care to use inherits() and not == on the class.
• New functions psmirnov(), qsmirnov() and rsmirnov() in package stats implementing the asymptotic and exact distributions of the two-sample Smirnov statistic.
• iconv() now allows sub = "c99" to use C99-style escapes for UTF-8 inputs which cannot be converted to encoding to.
• In a forward pipe |> expression it is now possible to use a named argument with the placeholder _ in the rhs call to specify where the lhs is to be inserted. The placeholder can only appear once on the rhs.
• The included LAPACK sources have been updated to version 3.10.0, except for the four Fortran 77 routines which 3.10.0 has re-implemented in Fortran 90 (where the older versions have been retained as the R build process does not support Fortran 90).
• path.expand() and most other uses of tilde expansion now warn if a path would be too long if expanded. (An exception is file.exists(), which silently returns false.)
• trunc(<Date>, *) now supports units = "months" or "years" for consistency with the POSIXt method, thanks to Dirk Eddelbuettel's proposal in PR#18099.
• list2DF() now checks that its arguments are of the same length, rather than use recycling.
• The HTML help system has several new features: LaTeX-like math can be typeset using either KaTeX or MathJax, usage and example code is highlighted using Prism, and for dynamic help the output of examples and demos can be shown within the browser if the knitr package is installed. These features can be disabled by setting the environment variable R_HELP_ENABLE_ENHANCED_HTML to a false value.
• GRAPHICS:
• The graphics engine version, R_GE_version, has been bumped to 15 and so packages that provide graphics devices should be reinstalled.
• The grid package now allows the user to specify a "vector" of pattern fills. The fill argument to gpar() accepts a list of gradients and/or patterns and the functions linearGradient(), radialGradient(), and pattern() have a new group argument.
• Points grobs (data symbols) can now also have a pattern fill.
• The grobCoords() function now returns a more informative and complex result.
• The grid package has new functions for drawing isolated groups: grid.group(), grid.define(), and grid.use(). These functions add compositing operators and affine transformations to R's graphics capabilities.
• The grid package also has new functions for stroking and filling paths: grid.stroke(), grid.fill(), and grid.fillStroke().
• A new function as.path() allows the user to specify the fill rule for a path that is to be used for clipping, stroking, or filling; available options are "winding" and "evenodd". A new function as.mask() allows the user to specify the type of a mask; available options are "alpha" and "luminance".
• These new features are only supported so far (at most) on the Cairo-based graphics devices and on the pdf() device.
• dev.capabilities() reports on device support for the new features.
• par() now warns about unnamed non-character arguments to prevent misuse such as {usr <- par("usr"); par(usr)}.
• 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 Rwin-libraryx.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:UsersusernameAppDataLocal). 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:UsersusernameAppDataLocalPrograms) 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' SS6.6.2. (This has been supported since R 3.6.2.)
• Package installation speed for packages installed with keep.source has been improved. This resolve the issue reported by Ofek Shilon in PR#18236.
• UTILITIES:
• R CMD check can optionally report files/directories left behind in home, /tmp (even though TMPDIR is set) and other directories. See the "R Internals" manual for details.
• R CMD check now reports byte-compilation errors during installation. These are not usually fatal but may result in parts of the package not being byte-compiled.
• R_CHECK_DEPENDS_ONLY can be applied selectively to examples, tests and/or vignettes in R CMD check: see the "R Internals" manual.
• R_CHECK_SRC_MINUS_W_IMPLICIT now defaults to true: recent versions of Apple clang on macOS have made implicit function declarations in C into a compilation error.
• R CMD check --as-cran makes use of the environment variable AUTORECONF. See the "R Internals" manual SS8 for further details.
• R CMD check --use-valgrind also uses valgrind when re-building vignettes as some non-Sweave vignettes unhelpfully comment out all their code when R CMD check runs vignettes.
• Errors in re-building vignettes (unless there are LaTeX errors) are reported by R CMD check as ERROR rather than WARNING when running vignettes has been skipped (as it frequently is in CRAN checks and by --as-cran).
• R CMD Rd2pdf gains a --quiet option that is used by R CMD build when building the PDF package manual.
• R CMD Rd2pdf now always runs LaTeX in batch mode, consistent with Texinfo >= 6.7. The --batch option is ignored.
• R CMD build and R CMD check now include the Rd file name and line numbers in the error message of an Sexpr evaluation failure.
• For packages using the doi Rd macro (now an install-time Sexpr) but no other dynamic Rd content, R CMD build now produces a smaller tarball and is considerably faster - skipping temporary package installation.
• C-LEVEL FACILITIES:
• The non-API header R_ext/R-ftp-http.h is no longer provided, as the entry points it covered are now all defunct.
• A number of non-API declarations and macro definitions have been moved from the installed header Rinternals.h to the internal header Defn.h. Packages that only use entry points and definitions documented to be part of the API as specified in 'Writing R Extensions' SS6 should not be affected.
• The macro USE_RINTERNALS no longer has any effect when compiling package code. Packages which also use R_NO_REMAP will need to ensure that the remapped names are used for calls to API functions that were formerly also made available as macros.
• The deprecated legacy S-compatibility macros PROBLEM, MESSAGE, ERROR, WARN, WARNING, RECOVER, ... are no longer defined in R_exts/RS.h (included by R.h). Replace these by calls to Rf_error and Rf_warning (defined in header R_ext/Error.h included by R.h). Header R_ext/RS.h no longer includes R_ext/Error.h.
• Header R_ext/Constants.h (included by R.h) when included from C++ now includes the C++ header cfloat rather than the C header float.h (now possible as C++11 is required).
• The legacy S-compatibility macros DOUBLE_* in R_ext/Constants.h (included by R.h) are deprecated.
• The deprecated S-compatibility macros SINGLE_* in R_ext/Constants.h (included by R.h) have been removed.
• R_Calloc, R_Free and R_Realloc are preferred to their unprefixed forms and error messages now use the prefix. These forms were introduced in R 3.4.0 and are available even when STRICT_R_HEADERS is defined.
• rmultinom has been documented in 'Writing R Extensions' SS6 so is now part of the R API.
• Similarly, Rtanpi, called from R level tanpi() is now part of the R API.
• The long-deprecated, undocumented and non-API entry point call_R is no longer declared in R_ext/RS.h (included by R.h).
• The header S.h which has been unsupported since Jan 2016 has been removed. Use R.h instead.
• DEPRECATED AND DEFUNCT:
• The (non-default and deprecated) method = "internal" for download.file() and url() no longer supports http:// nor ftp:// URIs. (It is used only for file:// URIs.) On Windows, download.file(method = "wininet") no longer supports ftp:// URIs. (It is no longer the default method, which is "libcurl" and does.) On Windows, the deprecated method = "wininet" now gives a warning for http:// and https:// URIs for both download.file() and url(). (It is no longer the default method.)
• On Windows, the command-line option --max-mem-size and environment variable R_MAX_MEM_SIZE are defunct. The memory allocation limit was important for 32-bit builds, but these are no longer supported.
• default.stringsAsFactors() is now formally deprecated, where that was only mentioned on its regular help page, previously. So it now gives a warning if called.
• unix.time() is defunct now; it had been deprecated since R 3.4.0.
• BUG FIXES:
• Setting digits = 0 in format(), print.default() (and hence typically print()) or options() is again invalid. Its behaviour was platform-dependent, and it is unclear what "zero significant digits" should mean (PR#18098).
• Messages from C code in the cairo section of package grDevices are now also offered for translation, thanks to Michael Chirico's PR#18123.
• mean(x) with finite x now is finite also without "long.double" capability.
• R CMD Rd2pdf no longer leaves an empty build directory behind when it aborts due to an already existing output file. (Thanks to Sebastian Meyer's PR#18141.)
• density(x, weights = w, na.rm = TRUE) when anyNA(x) is true, now removes weights "in parallel" to x, fixing PR#18151, reported by Matthias Gondan. Additionally, it gets a subdensity option.
• Conversion of Sexpr[]{<expR>} to LaTeX or HTML no longer produces long blocks of empty lines when <expR> itself contains several lines all producing empty output. Thanks to a report and patch by Ivan Krylov posted to R-devel.
• R CMD build no longer fails if a package vignette uses child documents and inst/doc exists. (Thanks to Sebastian Meyer's PR#18156.)
• When an R documentation ('help' source) file man/foo.Rd in a package has donttest{..} examples with a syntax error, it is now signalled as ERROR and with correct line numbers relating to the *-Ex.R file, thanks to Duncan Murdoch and Sebastian Meyer's reports and patch proposals in PR#17501.
• Improved determination of the correct translation domain in non-base packages, addressing the combination of PR#18092 and PR#17998 (#c6) with reports and augmented patch #2904 by Suharto Anggono.
• Note that "R-base" is no longer the default domain e.g., for top-level calls to gettext(); rather translation needs explicit domain = * specification in such cases.
• identical(attrib.as.set=FALSE) now works correctly with data frames with default row names (Thanks to Charlie Gao's PR#18179).
• txtProgressBar() now enforces a non-zero width for argument char, without which no progress can be visible.
• dimnames(table(d)) is more consistent in the case where d is a list with a single component, thanks to Thomas Soeiro's report to R-devel.
• Further, table(d1, d2) now gives an error when d1 and d2 are data frames as suggested by Thomas in PR#18224.
• Fix for drawing semi-transparent lines and fills on the native Windows graphics device (PR#18219 and PR#16694). Thanks to Nick Ray for helpful diagnosis on Bugzilla.
• The deparser now wraps sub-expressions such as if(A) .. with parentheses when needed; thanks to Duncan Murdoch's PR#18232 and Lionel Henry's patches there.
• remove.packages() no longer tries to uninstall Priority: base packages, thanks to a report and suggestions by Colin Fay in PR#18227.
• win.metafile() now has xpinch and ypinch arguments so that the user can override Windows' (potentially wrong) guess at device dimensions.
• x[i] and x[[i]] for non-integer i should now behave in all cases as always documented: the index used is equivalent to as.integer(i) unless that would overflow where trunc(i) is used instead; thanks to Suharto Anggono's report and patch proposals in PR#17977.
• asOneSidedFormula() now associates the resulting formula with the global environment rather than the evaluation environment created for the call.
• <bibentry>$name now matches the field name case-insensitively, consistent with bibentry() creation and the replacement method.
• cbind() failed to detect some length mismatches with a mixture of time-series and non-time-series inputs.
• The default LaTeX style file Sweave.sty used by the RweaveLatex driver no longer loads the obsolete ae package; thanks to a report by Thomas Soeiro in PR#18271. Furthermore, it now skips usepackage[T1]{fontenc} for engines other than pdfTeX (if detected) or if the new [nofontenc] option is used.
• smooth.spline() now stores its logical cv argument more safely, fixing a rare bug when printing, and also stores n.
• smooth.spline(x,y,*) now computes the cv.crit statistic correctly, also when is.unsorted(x), fixing PR#18294.
• The data.frame method of rbind() now warns when binding not-wholly-recycling vectors, by analogy to the default method (for matrices).
• setAs() finds the correct class for name to when multiple packages define a class with that name. Thanks to Gabor Csardi for the report.
• Fix for detaching a package when two classes of the same name are present in method signatures for the same generic. Thanks to Gabor Csardi for the report.
• match.arg("", c("", "a", "B")) gives a better error message, in part from PR#17959, thanks to Elin Waring.
• R CMD Sweave --clean no longer removes pre-existing files or subdirectories (PR#18242).
• The quartz() device no longer splits polylines into subpaths. That has caused narrowly-spaced lines with many points to always look solid even when dashed line type was used due to dash phase restarts.
• Deparsing constructs such as quote(1 + !(2) + 3) works again as before R 3.5.0, thanks to the report and patch in PR#18284 by Suharto Anggono.
• as.list(f) for a factor f now keeps names(f), fixing PR#18309.
• qbeta(.001, .9, .009) and analogous qf() calls now return a correct value instead of NaN or wrongly 1, all with a warning; thanks to the report by Ludger Goeminne in PR#18302.
• plot.lm() failed to produce the plot of residuals vs. factor levels (i.e., which=5 when leverages are constant) for models with character predictors (PR#17840).
• interaction.plot(..., xtick = TRUE) misplaced the x-axis line (PR#18305).
• Not strictly fixing a bug, format()ing and print()ing of non-finite Date and POSIXt values NaN and +/-Inf no longer show as NA but the respective string, e.g., Inf, for consistency with numeric vector's behaviour, fulfilling the wish of PR#18308.
• R CMD check no longer runs test scripts generated from corresponding .Rin files twice and now signals an ERROR if processing an .Rin script fails.
• tools::Rd2txt() used for plain-text help pages now renders hrefs (if tools::Rd2txt_options(showURLs = TRUE)) and urls with percent-encoding and standards-compliant delimiting style (angle brackets and no URL: prefix). email is now rendered with a mailto: prefix.