R News

CHANGES IN R 3.2.5:

  BUG FIXES:

    • format.POSIXlt() behaved incorrectly in R 3.2.4.  E.g. the output
      of format(as.POSIXlt(paste0(1940:2000,"-01-01"), tz = "CET"),
      usetz = TRUE) ended in two "CEST" time formats.

    • A typo in the Makefile for src/extra/xz prevented builds of
      liblzma.a. (Notice that this will become unbundled in 3.3.0.)

CHANGES IN R 3.2.4:

  NEW FEATURES:

    • install.packages() and related functions now give a more
      informative warning when an attempt is made to install a base
      package.

    • summary(x) now prints with less rounding when x contains infinite
      values. (Request of PR#16620.)

    • provideDimnames() gets an optional unique argument.

    • shQuote() gains type = "cmd2" for quoting in cmd.exe in Windows.
      (Response to PR#16636.)

    • The data.frame method of rbind() gains an optional argument
      stringsAsFactors (instead of only depending on
      getOption("stringsAsFactors")).

    • smooth(x, *) now also works for long vectors.

    • tools::texi2dvi() has a workaround for problems with the texi2dvi
      script supplied by texinfo 6.1.

      It extracts more error messages from the LaTeX logs when in
      emulation mode.

  UTILITIES:

    • R CMD check will leave a log file build_vignettes.log from the
      re-building of vignettes in the .Rcheck directory if there is a
      problem, and always if environment variable
      _R_CHECK_ALWAYS_LOG_VIGNETTE_OUTPUT_ is set to a true value.

  DEPRECATED AND DEFUNCT:

    • Use of SUPPORT_OPENMP from header Rconfig.h is deprecated in
      favour of the standard OpenMP define _OPENMP.

      (This has been the recommendation in the manual for a while now.)

    • The make macro AWK which is long unused by R itself but recorded
      in file etc/Makeconf is deprecated and will be removed in R
      3.3.0.

    • The C header file S.h is no longer documented: its use should be
      replaced by R.h.

  BUG FIXES:

    • kmeans(x, centers = <1-row>) now works. (PR#16623)

    • Vectorize() now checks for clashes in argument names.  (PR#16577)

    • file.copy(overwrite = FALSE) would signal a successful copy when
      none had taken place.  (PR#16576)

    • ngettext() now uses the same default domain as gettext().
      (PR#14605)

    • array(.., dimnames = *) now warns about non-list dimnames and,
      from R 3.3.0, will signal the same error for invalid dimnames as
      matrix() has always done.

    • addmargins() now adds dimnames for the extended margins in all
      cases, as always documented.

    • heatmap() evaluated its add.expr argument in the wrong
      environment.  (PR#16583)

    • require() etc now give the correct entry of lib.loc in the
      warning about an old version of a package masking a newer
      required one.

    • The internal deparser did not add parentheses when necessary,
      e.g. before [] or [[]].  (Reported by Lukas Stadler; additional
      fixes included as well).

    • as.data.frame.vector(*, row.names=*) no longer produces
      ‘corrupted’ data frames from row names of incorrect length, but
      rather warns about them.  This will become an error.

    • url connections with method = "libcurl" are destroyed properly.
      (PR#16681)

    • withCallingHandler() now (again) handles warnings even during S4
      generic's argument evaluation.  (PR#16111)

    • deparse(..., control = "quoteExpressions") incorrectly quoted
      empty expressions.  (PR#16686)

    • format()ting datetime objects ("POSIX[cl]?t") could segfault or
      recycle wrongly.  (PR#16685)

    • plot.ts(<matrix>, las = 1) now does use las.

    • saveRDS(*, compress = "gzip") now works as documented.
      (PR#16653)

    • (Windows only) The Rgui front end did not always initialize the
      console properly, and could cause R to crash.  (PR#16998)

    • dummy.coef.lm() now works in more cases, thanks to a proposal by
      Werner Stahel (PR#16665).  In addition, it now works for
      multivariate linear models ("mlm", manova) thanks to a proposal
      by Daniel Wollschlaeger.

    • The as.hclust() method for "dendrogram"s failed often when there
      were ties in the heights.

    • reorder() and midcache.dendrogram() now are non-recursive and
      hence applicable to somewhat deeply nested dendrograms, thanks to
      a proposal by Suharto Anggono in PR#16424.

    • cor.test() now calculates very small p values more accurately
      (affecting the result only in extreme not statistically relevant
      cases).  (PR#16704)

    • smooth(*, do.ends=TRUE) did not always work correctly in R
      versions between 3.0.0 and 3.2.3.

    • pretty(D) for date-time objects D now also works well if range(D)
      is (much) smaller than a second.  In the case of only one unique
      value in D, the pretty range now is more symmetric around that
      value than previously.

      Similarly, pretty(dt) no longer returns a length 5 vector with
      duplicated entries for Date objects dt which span only a few
      days.

    • The figures in help pages such as ?points were accidentally
      damaged, and did not appear in R 3.2.3.  (PR#16708)

    • available.packages() sometimes deleted the wrong file when
      cleaning up temporary files.  (PR#16712)

    • The X11() device sometimes froze on Red Hat Enterprise Linux 6.
      It now waits for MapNotify events instead of Expose events,
      thanks to Siteshwar Vashisht. (PR#16497)

    • [dpqr]nbinom(*, size=Inf, mu=.) now works as limit case, for
      ‘dpq’ as the Poisson.  (PR#16727)
      pnbinom() no longer loops infinitely in border cases.

    • approxfun(*, method="constant") and hence ecdf() which calls the
      former now correctly “predict” NaN values as NaN.

    • summary.data.frame() now displays NAs in Date columns in all
      cases.  (PR#16709)

CHANGES IN R 3.2.3:

  NEW FEATURES:

    • Some recently-added Windows time zone names have been added to
      the conversion table used to convert these to Olson names.
      (Including those relating to changes for Russia in Oct 2014, as
      in PR#16503.)

    • (Windows) Compatibility information has been added to the
      manifests for Rgui.exe, Rterm.exe and Rscript.exe.  This should
      allow win.version() and Sys.info() to report the actual Windows
      version up to Windows 10.

    • Windows "wininet" FTP first tries EPSV / PASV mode rather than
      only using active mode (reported by Dan Tenenbaum).

    • which.min(x) and which.max(x) may be much faster for logical and
      integer x and now also work for long vectors.

    • The ‘emulation’ part of tools::texi2dvi() has been somewhat
      enhanced, including supporting quiet = TRUE.  It can be selected
      by texi2dvi = "emulation".

      (Windows) MiKTeX removed its texi2dvi.exe command in Sept 2015:
      tools::texi2dvi() tries texify.exe if it is not found.

    • (Windows only) Shortcuts for printing and saving have been added
      to menus in Rgui.exe.  (Request of PR#16572.)

    • loess(..., iterTrace=TRUE) now provides diagnostics for
      robustness iterations, and the print() method for
      summary(<loess>) shows slightly more.

    • The included version of PCRE has been updated to 8.38, a bug-fix
      release.

    • View() now displays nested data frames in a more friendly way.
      (Request with patch in PR#15915.)

  INSTALLATION and INCLUDED SOFTWARE:

    • The included configuration code for libintl has been updated to
      that from gettext version 0.19.5.1 - this should only affect how
      an external library is detected (and the only known instance is
      under OpenBSD).  (Wish of PR#16464.)

    • configure has a new argument --disable-java to disable the checks
      for Java.

    • The configure default for MAIN_LDFLAGS has been changed for the
      FreeBSD, NetBSD and Hurd OSes to one more likely to work with
      compilers other than gcc (FreeBSD 10 defaults to clang).

    • configure now supports the OpenMP flags -fopenmp=libomp (clang)
      and -qopenmp (Intel C).

    • Various macros can be set to override the default behaviour of
      configure when detecting OpenMP: see file config.site.

    • Source installation on Windows has been modified to allow for
      MiKTeX installations without texi2dvi.exe.  See file
      MkRules.dist.

  BUG FIXES:

    • regexpr(pat, x, perl = TRUE) with Python-style named capture did
      not work correctly when x contained NA strings.  (PR#16484)

    • The description of dataset ToothGrowth has been
      improved/corrected.  (PR#15953)

    • model.tables(type = "means") and hence TukeyHSD() now support
      "aov" fits without an intercept term.  (PR#16437)

    • close() now reports the status of a pipe() connection opened with
      an explicit open argument.  (PR#16481)

    • Coercing a list without names to a data frame is faster if the
      elements are very long. (PR#16467)

    • (Unix-only) Under some rare circumstances piping the output from
      Rscript or R -f could result in attempting to close the input
      file twice, possibly crashing the process.  (PR#16500)

    • (Windows) Sys.info() was out of step with win.version() and did
      not report Windows 8.

    • topenv(baseenv()) returns baseenv() again as in R 3.1.0 and
      earlier.  This also fixes compilerJIT(3) when used in .Rprofile.

    • detach()ing the methods package keeps .isMethodsDispatchOn()
      true, as long as the methods namespace is not unloaded.

    • Removed some spurious warnings from configure about the
      preprocessor not finding header files.  (PR#15989)

    • rchisq(*, df=0, ncp=0) now returns 0 instead of NaN, and
      dchisq(*, df=0, ncp=*) also no longer returns NaN in limit cases
      (where the limit is unique).  (PR#16521)

    • pchisq(*, df=0, ncp > 0, log.p=TRUE) no longer underflows (for
      ncp > ~60).

    • nchar(x, "w") returned -1 for characters it did not know about
      (e.g. zero-width spaces): it now assumes 1.  It now knows about
      most zero-width characters and a few more double-width
      characters.

    • Help for which.min() is now more precise about behavior with
      logical arguments.  (PR#16532)

    • The print width of character strings marked as "latin1" or
      "bytes" was in some cases computed incorrectly.

    • abbreviate() did not give names to the return value if minlength
      was zero, unlike when it was positive.

    • (Windows only) dir.create() did not always warn when it failed to
      create a directory.  (PR#16537)

    • When operating in a non-UTF-8 multibyte locale (e.g. an East
      Asian locale on Windows), grep() and related functions did not
      handle UTF-8 strings properly.  (PR#16264)

    • read.dcf() sometimes misread lines longer than 8191 characters.
      (Reported by Hervé Pagès with a patch.)

    • within(df, ..) no longer drops columns whose name start with a
      ".".

    • The built-in HTTP server converted entire Content-Type to
      lowercase including parameters which can cause issues for
      multi-part form boundaries (PR#16541).

    • Modifying slots of S4 objects could fail when the methods package
      was not attached. (PR#16545)

    • splineDesign(*, outer.ok=TRUE) (splines) is better now
      (PR#16549), and interpSpline() now allows sparse=TRUE for speedup
      with non-small sizes.

    • If the expression in the traceback was too long, traceback() did
      not report the source line number.  (Patch by Kirill Müller.)

    • The browser did not truncate the display of the function when
      exiting with options("deparse.max.lines") set.  (PR#16581)

    • When bs(*, Boundary.knots=) had boundary knots inside the data
      range, extrapolation was somewhat off.  (Patch by Trevor Hastie.)

    • var() and hence sd() warn about factor arguments which are
      deprecated now. (PR#16564)

    • loess(*, weights = *) stored wrong weights and hence gave
      slightly wrong predictions for newdata.  (PR#16587)

    • aperm(a, *) now preserves names(dim(a)).

    • poly(x, ..) now works when either raw=TRUE or coef is specified.
      (PR#16597)

    • data(package=*) is more careful in determining the path.

    • prettyNum(*, decimal.mark, big.mark): fixed bug introduced when
      fixing PR#16411.

CHANGES IN R 3.2.2:

  SIGNIFICANT USER-VISIBLE CHANGES:

    • It is now easier to use secure downloads from https:// URLs on
      builds which support them: no longer do non-default options need
      to be selected to do so.  In particular, packages can be
      installed from repositories which offer https:// URLs, and those
      listed by setRepositories() now do so (for some of their
      mirrors).

      Support for https:// URLs is available on Windows, and on other
      platforms if support for libcurl was compiled in and if that
      supports the https protocol (system installations can be expected
      to do).  So https:// support can be expected except on rather old
      OSes (an example being OS X ‘Snow Leopard’, where a non-system
      version of libcurl can be used).

      (Windows only) The default method for accessing URLs _via_
      download.file() and url() has been changed to be "wininet" using
      Windows API calls.  This changes the way proxies need to be set
      and security settings made: there have been some reports of ftp:
      sites being inaccessible under the new default method (but the
      previous methods remain available).

  NEW FEATURES:

    • cmdscale() gets new option list. for increased flexibility when a
      list should be returned.

    • configure now supports texinfo version 6.0, which (unlike the
      change from 4.x to 5.0) is a minor update.  (Wish of PR#16456.)

    • (Non-Windows only) download.file() with default method = "auto"
      now chooses "libcurl" if that is available and a https:// or
      ftps:// URL is used.

    • (Windows only) setInternet2(TRUE) is now the default.  The
      command-line option --internet2 and environment variable
      R_WIN_INTERNET2 are now ignored.

      Thus by default the "internal" method for download.file() and
      url() uses the "wininet" method: to revert to the previous
      default use setInternet2(FALSE).

      This means that https:// URLs can be read by default by
      download.file() (they have been readable by file() and url()
      since R 3.2.0).

      There are implications for how proxies need to be set (see
      ?download.file).

    • chooseCRANmirror() and chooseBioCmirror() now offer HTTPS mirrors
      in preference to HTTP mirrors.  This changes the interpretation
      of their ind arguments: see their help pages.

    • capture.output() gets optional arguments type and split to pass
      to sink(), and hence can be used to capture messages.

  C-LEVEL FACILITIES:

    • Header Rconfig.h now defines HAVE_ALLOCA_H if the platform has
      the alloca.h header (it is needed to define alloca on Solaris and
      AIX, at least: see ‘Writing R Extensions’ for how to use it).

  INSTALLATION and INCLUDED SOFTWARE:

    • The libtool script generated by configure has been modified to
      support FreeBSD >= 10 (PR#16410).

  BUG FIXES:

    • The HTML help page links to demo code failed due to a change in R
      3.2.0.  (PR#16432)

    • If the na.action argument was used in model.frame(), the original
      data could be modified. (PR#16436)

    • getGraphicsEvent() could cause a crash if a graphics window was
      closed while it was in use. (PR#16438)

    • matrix(x, nr, nc, byrow = TRUE) failed if x was an object of type
      "expression".

    • strptime() could overflow the allocated storage on the C stack
      when the timezone had a non-standard format much longer than the
      standard formats. (Part of PR#16328.)

    • options(OutDec = s) now signals a warning (which will become an
      error in the future) when s is not a string with exactly one
      character, as that has been a documented requirement.

    • prettyNum() gains a new option input.d.mark which together with
      other changes, e.g., the default for decimal.mark, fixes some
      format()ting variants with non-default getOption("OutDec") such
      as in PR#16411.

    • download.packages() failed for type equal to either "both" or
      "binary".  (Reported by Dan Tenenbaum.)

    • The dendrogram method of labels() is much more efficient for
      large dendrograms, now using rapply().  (Comment #15 of PR#15215)

    • The "port" algorithm of nls() could give spurious errors.
      (Reported by Radford Neal.)

    • Reference classes that inherited from reference classes in
      another package could invalidate methods of the inherited class.
      Fixing this requires adding the ability for methods to be
      “external”, with the object supplied explicitly as the first
      argument, named .self. See "Inter-Package Superclasses" in the
      documentation.

    • readBin() could fail on the SPARC architecture due to alignment
      issues.  (Reported by Radford Neal.)

    • qt(*, df=Inf, ncp=.) now uses the natural qnorm() limit instead
      of returning NaN. (PR#16475)

    • Auto-printing of S3 and S4 values now searches for print() in the
      base namespace and show() in the methods namespace instead of
      searching the global environment.

    • polym() gains a coefs = NULL argument and returns class "poly"
      just like poly() which gets a new simple=FALSE option.  They now
      lead to correct predict()ions, e.g., on subsets of the original
      data.

    • rhyper(nn, <large>) now works correctly. (PR#16489)

    • ttkimage() did not (and could not) work so was removed. Ditto for
      tkimage.cget() and tkimage.configure(). Added two Ttk widgets and
      missing subcommands for Tk's image command: ttkscale(),
      ttkspinbox(), tkimage.delete(), tkimage.height(),
      tkimage.inuse(), tkimage.type(), tkimage.types(),
      tkimage.width(). (PR#15372, PR#16450)

    • getClass("foo") now also returns a class definition when it is
      found in the cache more than once.

CHANGES IN R 3.2.1:

  NEW FEATURES:

    • utf8ToInt() now checks that its input is valid UTF-8 and returns
      NA if it is not.

    • install.packages() now allows type = "both" with repos = NULL if
      it can infer the type of file.

    • nchar(x, *) and nzchar(x) gain a new argument keepNA which
      governs how the result for NAs in x is determined.  For nzchar()
      in general and nchar() in the R 3.2.x series, the default remains
      FALSE which is fully back compatible.  From R 3.3.0, nchar()'s
      default will change to keepNA = NA and you are advised to
      consider this for code portability.

    • news() more flexibly extracts dates from package NEWS.Rd files.

    • lengths(x) now also works (trivially) for atomic x and hence can
      be used more generally as an efficient replacement of sapply(x,
      length) and similar.

    • The included version of PCRE has been updated to 8.37, a bug-fix
      release.

    • diag() no longer duplicates a matrix when extracting its
      diagonal.

    • as.character.srcref() gains an argument to allow characters
      corresponding to a range of source references to be extracted.

  BUG FIXES:

    • acf() and ccf() now guarantee values strictly in [-1,1] (instead
      of sometimes very slightly outside). PR#15832.

    • as.integer("111111111111") now gives NA (with a warning) as it
      does for the corresponding numeric or negative number coercions.
      Further, as.integer(M + 0.1) now gives M (instead of NA) when M
      is the maximal representable integer.

    • On some platforms nchar(x, "c") and nchar(x, "w") would return
      values (possibly NA) for inputs which were declared to be UTF-8
      but were not, or for invalid strings without a marked encoding in
      a multi-byte locale, rather than give an error.  Additional
      checks have been added to mitigate this.

    • apply(a, M, function(u) c(X = ., Y = .)) again has dimnames
      containing "X" and "Y" (as in R < 3.2.0).

    • (Windows only) In some cases, the --clean option to R CMD INSTALL
      could fail.  (PR#16178)

    • (Windows only) choose.files() would occasionally include
      characters from the result of an earlier call in the result of a
      later one.  (PR#16270)

    • A change in RSiteSearch() in R 3.2.0 caused it to submit invalid
      URLs.  (PR#16329)

    • Rscript and command line R silently ignored incomplete statements
      at the end of a script; now they are reported as parse errors.
      (PR#16350)

    • Parse data for very long strings was not stored.  (PR#16354)

    • plotNode(), the workhorse of the plot method for "dendrogram"s is
      no longer recursive, thanks to Suharto Anggono, and hence also
      works for deeply nested dendrograms.  (PR#15215)

    • The parser could overflow internally when given numbers in
      scientific format with extremely large exponents.  (PR#16358)

    • If the CRAN mirror was not set, install.packages(type = "both")
      and related functions could repeatedly query the user for it.
      (Part of PR#16362)

    • The low-level functions .rowSums() etc. did not check the length
      of their argument, so could segfault. (PR#16367)

    • The quietly argument of library() is now correctly propagated
      from .getRequiredPackages2().

    • Under some circumstances using the internal PCRE when building R
      from source would cause external libs such as -llzma to be
      omitted from the main link.

    • The .Primitive default methods of the logic operators, i.e., !, &
      and |, now give correct error messages when appropriate, e.g.,
      for `&`(TRUE) or `!`().  (PR#16385)

    • cummax(x) now correctly propagates NAs also when x is of type
      integer and begins with an NA.

    • summaryRprof() could fail when the profile contained only two
      records.  (PR#16395)

    • HTML vignettes opened using vignette() did not support links into
      the rest of the HTML help system.  (Links worked properly when
      the vignette was opened using browseVignettes() or from within
      the help system.)

    • arima(*, xreg = .) (for d >= 1) computes estimated variances
      based on a the number of effective observations as in R version
      3.0.1 and earlier.  (PR#16278)

    • slotNames(.) is now correct for "signature" objects (mostly used
      internally in methods).

    • On some systems, the first string comparison after a locale
      change would result in NA.

CHANGES IN R 3.2.0:

  NEW FEATURES:

    • anyNA() gains a recursive argument.

    • When x is missing and names is not false (including the default
      value), Sys.getenv(x, names) returns an object of class "Dlist"
      and hence prints tidily.

    • (Windows.)  shell() no longer consults the environment variable
      SHELL: too many systems have been encountered where it was set
      incorrectly (usually to a path where software was compiled, not
      where it was installed).  R_SHELL, the preferred way to select a
      non-default shell, can be used instead.

    • Some unusual arguments to embedFonts() can now be specified as
      character vectors, and the defaults have been changed
      accordingly.

    • Functions in the Summary group duplicate less.  (PR#15798)

    • (Unix-alikes.) system(cmd, input = ) now uses
      ‘shell-execution-environment’ redirection, which will be more
      natural if cmd is not a single command (but requires a
      POSIX-compliant shell). (Wish of PR#15508)

    • read.fwf() and read.DIF() gain a fileEncoding argument, for
      convenience.

    • Graphics devices can add attributes to their description in
      .Device and .Devices.  Several of those included with R use a
      "filepath" attribute.

    • pmatch() uses hashing in more cases and so is faster at the
      expense of using more memory. (PR#15697)

    • pairs() gains new arguments to select sets of variables to be
      plotted against each other.

    • file.info(, extra_cols = FALSE) allows a minimal set of columns
      to be computed on Unix-alikes: on some systems without
      properly-configured caching this can be significantly faster with
      large file lists.

    • New function dir.exists() in package base to test efficiently
      whether one or more paths exist and are directories.

    • dput() and friends gain new controls hexNumeric and digits17
      which output double and complex quantities as, respectively,
      binary fractions (exactly, see sprintf("%a")) and as decimals
      with up to 17 significant digits.

    • save(), saveRDS() and serialize() now support ascii = NA which
      writes ASCII files using sprintf("%a") for double/complex
      quantities.  This is read-compatible with ascii = TRUE but avoids
      binary->decimal->binary conversions with potential loss of
      precision.  Unfortunately the Windows C runtime's lack of C99
      compliance means that the format cannot be read correctly there
      in R before 3.1.2.

    • The default for formatC(decimal.mark =) has been changed to be
      getOption("OutDec"); this makes it more consistent with format()
      and suitable for use in print methods, e.g. those for classes
      "density", "ecdf", "stepfun" and "summary.lm".

      getOption("OutDec") is now consulted by the print method for
      class "kmeans", by cut(), dendrogram(), plot.ts() and quantile()
      when constructing labels and for the report from legend(trace =
      TRUE).

      (In part, wish of PR#15819.)

    • printNum() and hence format() and formatC() give a warning if
      big.mark and decimal.mark are set to the same value (period and
      comma are not uncommonly used for each, and this is a check that
      conventions have not got mixed).

    • merge() can create a result which uses long vectors on 64-bit
      platforms.

    • dget() gains a new argument keep.source which defaults to FALSE
      for speed (dput() and dget() are most often used for data objects
      where this can make dget() many times faster).

    • Packages may now use a file of common macro definitions in their
      help files, and may import definitions from other packages.

    • A number of macros have been added in the new share/Rd directory
      for use in package overview help pages, and promptPackage() now
      makes use of them.

    • tools::parse_Rd() gains a new permissive argument which converts
      unrecognized macros into text.  This is used by
      utils:::format.bibentry to allow LaTeX markup to be ignored.

    • options(OutDec =) can now specify a multi-byte character, e.g.,
      options(OutDec = "\u00b7") in a UTF-8 locale.

    • is.recursive(x) is no longer true when x is an external pointer,
      a weak reference or byte code; the first enables all.equal(x, x)
      when x <- getClass(.).

    • ls() (aka objects()) and as.list.environment() gain a new
      argument sorted.

    • The "source" attribute (which has not been added to functions by
      R since before R version 2.14.0) is no longer treated as special.

    • Function returnValue() has been added to give on.exit() code
      access to a function's return value for debugging purposes.

    • crossprod(x, y) allows more matrix coercions when x or y are
      vectors, now equalling t(x) %*% y in these cases (also reported
      by Radford Neal).  Similarly, tcrossprod(x,y) and %*% work in
      more cases with vector arguments.

    • Utility function dynGet() useful for detecting cycles, aka
      infinite recursions.

    • The byte-code compiler and interpreter include new instructions
      that allow many scalar subsetting and assignment and scalar
      arithmetic operations to be handled more efficiently. This can
      result in significant performance improvements in scalar
      numerical code.

    • apply(m, 2, identity) is now the same as the matrix m when it has
      _named_ row names.

    • A new function debuggingState() has been added, allowing to
      temporarily turn off debugging.

    • example() gets a new optional argument run.donttest and
      tools::Rd2ex() a corresponding commentDonttest, with a default
      such that example(..) in help examples will run \donttest code
      only if used interactively (a change in behaviour).

    • rbind.data.frame() gains an optional argument make.row.names, for
      potential speedup.

    • New function extSoftVersion() to report on the versions of
      third-party software in use in this session.  Currently reports
      versions of zlib, bzlib, the liblzma from xz, PCRE, ICU, TRE and
      the iconv implementation.

      A similar function grSoftVersion() in package grDevices reports
      on third-party graphics software.

      Function tcltk::tclVersion() reports the Tcl/Tk version.

    • Calling callGeneric() without arguments now works with primitive
      generics to some extent.

    • vapply(x, FUN, FUN.VALUE) is more efficient notably for large
      length(FUN.VALUE); as extension of PR#16061.

    • as.table() now allows tables with one or more dimensions of
      length 0 (such as as.table(integer())).

    • names(x) <- NULL now clears the names of call and ... objects.

    • library() will report a warning when an insufficient dependency
      version is masking a sufficient one later on the library search
      path.

    • A new plot() method for class "raster" has been added.

    • New check_packages_in_dir_changes() function in package tools for
      conveniently analyzing how changing sources impacts the check
      results of their reverse dependencies.

    • Speed-up from Peter Haverty for ls() and
      methods:::.requirePackage() speeding up package loading.
      (PR#16133)

    • New get0() function, combining exists() and get() in one call,
      for efficiency.

    • match.call() gains an envir argument for specifying the
      environment from which to retrieve the ... in the call, if any;
      this environment was wrong (or at least undesirable) when the
      definition argument was a function.

    • topenv() has been made .Internal() for speedup, based on Peter
      Haverty's proposal in PR#16140.

    • getOption() no longer calls options() in the main case.

    • Optional use of libcurl (version 7.28.0 from Oct 2012 or later)
      for Internet access:

        • capabilities("libcurl") reports if this is available.

        • libcurlVersion() reports the version in use, and other
          details of the "libcurl" build including which URL schemes it
          supports.

        • curlGetHeaders() retrieves the headers for http://, https://,
          ftp:// and ftps:// URLs: analysis of these headers can
          provide insights into the `existence' of a URL (it might for
          example be permanently redirected) and is so used in R CMD
          check --as-cran.

        • download.file() has a new optional method "libcurl" which
          will handle more URL schemes, follow redirections, and allows
          simultaneous downloads of multiple URLs.

        • url() has a new method "libcurl" which handles more URL
          schemes and follows redirections.  The default method is
          controlled by a new option url.method, which applies also to
          the opening of URLs _via_ file() (which happens implicitly in
          functions such as read.table.)

        • When file() or url() is invoked with a https:// or ftps://
          URL which the current method cannot handle, it switches to a
          suitable method if one is available.

    • (Windows.) The DLLs internet.dll and internet2.dll have been
      merged.  In this version it is safe to switch (repeatedly)
      between the internal and Windows internet functions within an R
      session.

      The Windows internet functions are still selected by flag
      --internet2 or setInternet2().  This can be overridden for an
      url() connection _via_ its new method argument.

      download.file() has new method "wininet", selected as the default
      by --internet2 or setInternet2().

    • parent.env<- can no longer modify the parent of a locked
      namespace or namespace imports environment.  Contributed by Karl
      Millar.

    • New function isNamespaceLoaded() for readability and speed.

    • names(env) now returns all the object names of an environment
      env, equivalently to ls(env, all.names = TRUE, sorted = FALSE)
      and also to the names of the corresponding list,
      names(as.list(env, all.names = TRUE)).  Note that although
      names() returns a character vector, the names have no particular
      ordering.

    • The memory manager now grows the heap more aggressively. This
      reduces the number of garbage collections, in particular while
      data or code are loaded, at the expense of slightly increasing
      the memory footprint.

    • New function trimws() for removing leading/trailing whitespace.

    • cbind() and rbind() now consider S4 inheritance during S3
      dispatch and also obey deparse.level.

    • cbind() and rbind() will delegate recursively to methods::cbind2
      (methods::rbind2) when at least one argument is an S4 object and
      S3 dispatch fails (due to ambiguity).

    • (Windows.)  download.file(quiet = FALSE) now uses text rather
      than Windows progress bars in non-interactive use.

    • New function hsearch_db() in package utils for building and
      retrieving the help search database used by help.search(), along
      with functions for inspecting the concepts and keywords in the
      help search database.

    • New function .getNamespaceInfo(), a no-check version of
      getNamespaceInfo() mostly for internal speedups.

    • The help search system now takes \keyword entries in Rd files
      which are not standard keywords (as given in KEYWORDS in the R
      documentation directory) as concepts.  For standard keyword
      entries the corresponding descriptions are additionally taken as
      concepts.

    • New lengths() function for getting the lengths of all elements in
      a list.

    • New function toTitleCase() in package tools, tailored to package
      titles.

    • The matrix methods of cbind() and rbind() allow matrices as
      inputs which have 2^31 or more elements.  (For cbind(), wish of
      PR#16198.)

    • The default method of image() has an explicit check for a numeric
      or logical matrix (which was always required).

    • URLencode() will not by default encode further URLs which appear
      to be already encoded.

    • BIC(mod) and BIC(mod, mod2) now give non-NA numbers for arima()
      fitted models, as nobs(mod) now gives the number of “used”
      observations for such models.  This fixes PR#16198, quite
      differently than proposed there.

    • The print() methods for "htest", "pairwise.htest" and
      "power.htest" objects now have a digits argument defaulting to (a
      function of) getOption("digits"), and influencing all printed
      numbers coherently.  Unavoidably, this changes the display of
      such test results in some cases.

    • Code completion for namespaces now recognizes all loaded
      namespaces, rather than only the ones that are also attached.

    • The code completion mechanism can now be replaced by a
      user-specified completer function, for (temporary) situations
      where the usual code completion is inappropriate.

    • unzip() will now warn if it is able to detect truncation when
      unpacking a file of 4GB or more (related to PR#16243).

    • methods() reports S4 in addition to S3 methods; output is
      simplified when the class argument is used.  .S3methods() and
      methods::.S4methods() report S3 and S4 methods separately.

    • Higher order functions such as the apply functions and Reduce()
      now force arguments to the functions they apply in order to
      eliminate undesirable interactions between lazy evaluation and
      variable capture in closures.  This resolves PR#16093.

  INSTALLATION and INCLUDED SOFTWARE:

    • The \donttest sections of R's help files can be tested by
      make check TEST_DONTTEST=TRUE .

    • It is possible to request the use of system valgrind headers
      _via_ configure option --with-system-valgrind-headers: note the
      possible future incompatibility of such headers discussed in the
      'R Installation and Administration' manual. (Wish of PR#16068.)

    • The included version of liblzma has been updated to xz-utils
      5.0.7 (minor bug fixes from 5.0.5).

    • configure options --with-system-zlib, --with-system-bzlib and
      --with-system-pcre are now the default.  For the time being there
      is fallback to the versions included in the R sources if no
      system versions are found or (unlikely) if they are too old.

      Linux users should check that the -devel or -dev versions of
      packages zlib, bzip2/libbz2 and pcre as well as
      xz-devel/liblzma-dev (or similar names) are installed.

    • configure by default looks for the texi2any script from texinfo
      5.1 or later, rather than the makeinfo program.  (makeinfo is a
      link to the Perl script texi2any in texinfo 5.x.)

    • R CMD INSTALL gains an option --built-timestamp=STAMP allowing
      100% reproducible package building, thanks to Dirk Eddelbuettel.

  UTILITIES:

    • There is support for testing the \dontrun and \donttest parts of
      examples in packages.

      tools::testInstalledPackage() accepts new arguments
      commentDontrun = FALSE and commentDonttest = FALSE.

      R CMD check gains options --run-dontrun and --run-donttest.

    • The HTML generated by tools::Rd2HTML() and tools::toHTML()
      methods is now ‘XHTML 1.0 Strict’.

    • The compiler package's utility function setCompilerOptions() now
      returns the old values invisibly. The initial optimization level
      can also be set with the environment variable
      R_COMPILER_OPTIMIZE.

    • R CMD build adds a NeedsCompilation field if one is not already
      present in the DESCRIPTION file.

    • R CMD check gains option --test-dir to specify an alternative set
      of tests to run.

    • R CMD check will now by default continue with testing after many
      types of errors, and will output a summary count of errors at the
      end if any have occurred.

    • R CMD check now checks that the Title and Description fields are
      correctly terminated.

    • R CMD check --as-cran now:

        • checks a README.md file can be processed: this needs pandoc
          installed.

        • checks the existence and accessibility of URLs in the
          DESCRIPTION, CITATION, NEWS.Rd and README.md files and in the
          help files (provided the build has libcurl support).

        • reports non-ASCII characters in R source files when there is
          no package encoding declared in the DESCRIPTION file.

        • reports (apparent) S3 methods exported but not registered.

        • reports overwriting registered S3 methods from
          base/recommended packages.  (Such methods are replaced in the
          affected package for the rest of the session, even if the
          replacing namespace is unloaded.)

        • reports if the Title field does not appear to be in title
          case (see ‘Writing R Extensions’: there may be false
          positives, but note that technical words should be
          single-quoted and will then be accepted).

      Most of these checks can also be selected by environment
      variables: see the ‘R Internals’ manual.

  C-LEVEL FACILITIES:

    • New C API utility logspace_sum(logx[], n).

    • Entry points rbinom_mu, rnbinom_mu and rmultinom are remapped (by
      default) to Rf_rbinom_mu etc.  This requires packages using them
      to be re-installed.

    • .C(DUP = FALSE) and .Fortran(DUP = FALSE) are now ignored, so
      arguments are duplicated if DUP = TRUE would do so.  As their
      help has long said, .Call() is much preferred.

    • New entry point R_allocLD, like R_alloc but guaranteed to have
      sufficient alignment for long double pointers.

    • isPairList() now returns TRUE for DOTSXP.

  WINDOWS BUILD CHANGES:

  A number of changes to the Windows build system are in development.
  The following are currently in place.

    • Installation using external binary distributions of zlib, bzip2,
      liblzma, pcre, libpng, jpeglib and libtiff is now required, and
      the build instructions have been revised.

    • A new make target rsync-extsoft has been added to obtain copies
      of the external libraries from CRAN.

    • Building the manuals now requires texi2any from texinfo 5.1 or
      later.  CRAN binary builds include the manuals, but by default
      builds from source will not, and they will be accessed from CRAN.
      See the comments in src/gnuwin32/MkRules.dist for how to specify
      the location of texi2any.

    • (Windows) Changes have been made to support an experimental
      Windows toolchain based on GCC 4.9.2.  The default toolchain
      continues to be based on GCC 4.6.3, as the new toolchain is not
      yet stable enough.  A change to a new toolchain is expected
      during the R 3.2.x lifetime.

  PACKAGE INSTALLATION:

    • (Windows) The use of macro ZLIB_LIBS in file src/Makevars.win
      (which has not been documented for a long time) now requires an
      external libz.a to be available (it is part of the ‘goodies’ used
      to compile Windows binary packages).  It would be simpler to use
      -lz instead.

    • The default for option pkgType on platforms using binary packages
      is now "both", so source packages will be tried if binary
      versions are not available or not up to date.

      There are options for what install.packages(type = "both")
      (possibly called _via_ update.packages()) will do if compilation
      of a source package is desirable: see ?options (under utils).

      If you intend not to accept updates as source packages, you
      should use update.packages(type = "binary").

  DEPRECATED AND DEFUNCT:

    • download.file(method = "lynx") is defunct.

    • Building R using the included versions of zlib, bzip2, xz and
      PCRE is deprecated: these are frozen (bar essential bug-fixes)
      and will be removed for R 3.3.0.

    • The configure option --with-valgrind-instrumentation=3 has been
      withdrawn, as it did not work with recent valgrind headers: it is
      now treated as level 2.

    • The MethodsList class in package methods had been deprecated in R
      2.11.0 and is defunct now.  Functions using it are defunct if
      they had been deprecated in R 2.11.0, and are deprecated now,
      otherwise.

  BUG FIXES:

    • Fixed two obscure bugs in pairlist subassignment, reported by
      Radford Neal as part of pqR issue 16.

    • Fixes for bugs in handling empty arguments and argument matching
      by name in log().

    • all.equal() gains methods for environments and refClasses.

    • [<- and [[<- gain S4 data.frame methods to avoid corruption of S4
      class information by the S3 methods.

    • callNextMethod() should now work within a .local call when ... is
      absent from formals(.local).

    • dput(pairlist(x)) generates a call to the pairlist constructor
      instead of the list constructor.

    • Fix missing() when arguments are propagated through ... .
      (PR#15707)

    • eigen(m) now defaults to symmetric = TRUE even when the dimnames
      are asymmetric if the matrix is otherwise symmetric.  (PR#16151)

    • Fix issues with forwarding ... through callGeneric() and
      callNextMethod().  (PR#16141)

    • callGeneric() now works after a callNextMethod().

    • Subclass information is kept consistent when replacing an
      ordinary S4 class with an “old class” _via_ the S4Class argument
      to setOldClass(). Thus, for example, a data.frame is valid for a
      list argument in the signature, and a factor is valid for vector
      arguments.

    • In qbeta() the inversion of pbeta() is much more sophisticated.
      This works better in corner cases some of which failed completely
      previously (PR#15755), or were using too many iterations.

    • Auto-printing no longer duplicates objects when printing is
      dispatched to a method.

    • kmeans(x, k) would fail when nrow(x) >= 42949673.  (Comment 6 of
      PR#15364)

    • ‘Abbreviated’ locale-specific day and month names could have been
      truncated in those rare locales where there are the same as the
      full names.

    • An irrelevant warning message from updating subclass information
      was silenced (the namespace would not be writable in this case).

CHANGES IN R 3.1.3:

  NEW FEATURES:

    • The internal method of download.file() can now handle files
      larger than 2GB on 32-bit builds which support such files (tested
      on 32-bit R running on 64-bit Windows).

    • kruskal.test() warns on more types of suspicious input.

    • The as.dendrogram() method for "hclust" objects gains a check
      argument protecting against memory explosion for invalid inputs.

    • capabilities() has a new item long.double which indicates if the
      build uses a long double type which is longer than double.

    • nlm() no longer modifies the callback argument in place (a new
      vector is allocated for each invocation, which mimics the
      implicit duplication that occurred in R < 3.1.0); note that this
      is a change from the previously documented behavior. (PR#15958)

    • icuSetCollate() now accepts locale = "ASCII" which uses the basic
      C function strcmp and so collates strings byte-by-byte in
      numerical order.

    • sessionInfo() tries to report the OS version in use (not just
      that compiled under, and including details of Linux
      distributions).

    • model.frame() (used by lm() and many other modelling functions)
      now warns when it drops contrasts from factors.  (Wish of
      PR#16119)

    • install.packages() and friends now accept the value type =
      "binary" as a synonym for the native binary type on the platform
      (if it has one).

    • Single source or binary files can be supplied for
      install.packages(type = "both") and the appropriate type and
      repos = NULL will be inferred.

    • New function pcre_config() to report on some of the configuration
      options of the version of PCRE in use.  In particular, this
      reports if regular expressions using \p{xx} are supported.

    • (Windows.) download.file(cacheOK = FALSE) is now supported when
      internet2.dll is used.

    • browseURL() has been updated to work with Firefox 36.0 which has
      dropped support for the -remote interface.

  INSTALLATION and INCLUDED SOFTWARE:

    • The included version of PCRE has been updated to 8.36.

    • configure accepts MAKEINFO=texi2any as another way to ensure
      texinfo 5.x is used when both 5.x and 4.x are installed.

  UTILITIES:

    • R CMD check now checks the packages used in \donttest sections of
      the examples are specified in the DESCRIPTION file.  (These are
      needed to run the examples interactively.)

    • R CMD check checks for the undeclared use of GNU extensions in
      Makefiles, and for Makefiles with a missing final linefeed.

      R CMD build will correct line endings in all Makefiles, not just
      those in the src directory.

    • R CMD check notes uses of library() and require() in package
      code: see the section ‘Suggested packages’ of ‘Writing R
      Extensions’ for good practice.

  DEPRECATED AND DEFUNCT:

    • The configure option --with-valgrind-instrumentation=3 is
      deprecated and will be removed in R 3.2.0.

  BUG FIXES:

    • (Windows.) Rscript.exe was missing a manifest specifying the
      modern style for common controls (e.g., the download progress
      bar).

    • If a package had extra documentation files but no vignette, the
      HTML help system produced an empty index page.

    • The parser now gives an error if a null character is included in
      a string using Unicode escapes. (PR#16046)

    • qr.Q() failed on complex arguments due to pre-3.0(!) typo.
      (PR#16054)

    • abs() failed with named arguments when the argument was complex.
      (PR#16047)

    • "noquote" objects may now be used as columns in data frames.
      (PR#15997)

    • Some values with extremely long names were printed incorrectly.
      (PR#15999)

    • Extremely large exponents on zero expressed in scientific
      notation (e.g. 0.0e50000) could give NaN.  (PR#15976)

    • download.file() reported downloaded sizes as 0KB if less than
      1MB, only for R 3.1.2 and only on big-endian platforms.

    • prompt() did not escape percent signs in the automatically
      generated usage section of help files.

    • drop.terms() dropped some of the attributes of the object it was
      working with.  (PR#16029)

    • (Windows.) The command completion in Rgui.exe messed up the
      console.  (PR#15791)

    • (Windows.) The choose.files() command returned a blank string
      when the user asked for a single file but cancelled the request.
      (PR#16074)

    • Math2 S4 group generics failed to correctly dispatch "structure"-
      and "nonStructure"-derived classes.

    • loadNamespace() imposed undocumented restrictions on the
      versionCheck parameter.  (Reported by Geoff Lee.)

    • Rare over-runs detected by AddressSanitizer in substr() and its
      replacement version have been avoided.

      _Inter alia_ that fix gives the documented behaviour for
      substr(x, 1, 2) <- "" (subsequently reported as PR#16214).

    • Loading packages incorrectly defining an S4 generic followed by a
      function of the same name caused an erroneous cyclic namespace
      dependency error.

    • Declared vignette encodings are now always passed to the vignette
      engine.

    • Port Tomas Kalibera's fix from R-devel that restores the
      loadMethod() fast path, effectively doubling the speed of S4
      dispatch.

    • power.t.test() and power.prop.test() now make use of the
      extendInt option of uniroot() and hence work in more extreme
      cases.  (PR#15792)

    • If a package was updated and attached when its namespace was
      already loaded, it could end up with parts from one version and
      parts from the other.  (PR#16120)

    • tools:::.Rdconv() didn't accept --encoding= due to a typo.
      (PR#16121)

    • Unix-alike builds without a suitable makeinfo were documented to
      link the missing HTML manuals to CRAN, but did not.

    • save(*, ascii=TRUE) and load() now correctly deal with NaN's.
      (PR#16137)

    • split.Date() retains fractional representations while avoiding
      incomplete class propagation.

    • R_ext/Lapack.h had not been updated for changes made by LAPACK to
      the argument lists of its (largely internal) functions dlaed2 and
      dlaed3.  (PR#16157)

    • RShowDoc("NEWS", "txt") had not been updated for the layout
      changes of R 3.1.0.

    • The xtfrm() method for class "Surv" has been corrected and its
      description expanded.

    • mode(x) <- y would incorrectly evaluate x before changing its
      mode. (PR#16215)

    • besselJ(1, 2^64) and besselY(..) now signal a warning, returning
      NaN instead of typically segfaulting. (Issue 3 of PR#15554)

    • HTML conversion of \href markup in .Rd files did not remove the
      backslash from \% and so gave an invalid URL.  In a related
      change, the \ escape is now required in such URLs.

CHANGES IN R 3.1.2:

  NEW FEATURES:

    • embedFonts() now defaults to format = "ps2write" for .ps and .eps
      files.  This is available in Ghostscript 9.x (since 2010) whereas
      the previous default, format = "pswrite", was removed in
      Ghostscript 9.10.

    • For consistency with [dpqr]norm(), [dp]lnorm(sdlog = 0) model a
      point mass at exp(mulog) rather than return NaN (for an error).

    • capabilities() now reports if ICU is compiled in for use for
      collation (it is only actually used if a suitable locale is set
      for collation, and never for a C locale).

    • (OS X only.) Package tcltk checks when loaded if it is linked
      against the CRAN X11-based Tcl/Tk and if so that the Tcl/Tk
      component and the X11 libraries are installed.  This allows more
      informative error messages to be given advising the installation
      of the missing component or of XQuartz.

      The X11() device and X11-based versions of the data editor and
      viewer (invoked by edit() and View() for data frames and matrices
      from command-line R) check that the X11 libraries are installed
      and if not advises installing XQuartz.

    • icuSetCollate() allows locale = "default", and locale = "none" to
      use OS services rather than ICU for collation.

      Environment variable R_ICU_LOCALE can be used to set the default
      ICU locale, in case the one derived from the OS locale is
      inappropriate (this is currently necessary on Windows).

    • New function icuGetCollate() to report on the ICU collation
      locale in use (if any).

    • utils::URLencode() was updated to use unreserved and reserved
      characters from RFC 3986 (<URL:
      http://tools.ietf.org/html/rfc3986>) instead of RFC 1738.

    • unique(warnings()) and c(warnings()) are now supported.

    • The Bioconductor ‘version’ used by setRepositories() now defaults
      to 3.0. (It can be set at runtime _via_ environment variable
      R_BIOC_VERSION.)

    • Omegahat is no longer listed as providing Windows binary
      packages, e.g. by setRepositories().  It has no binary packages
      available for R 3.1.x and those for earlier versions were 32-bit
      only.

  INSTALLATION and INCLUDED SOFTWARE:

    • The configure script reports on the more important
      capabilities/options which will not be compiled in.

      More types of external BLAS are recognized by name in that
      report.

    • When building R as a shared library, the -L${R_HOME}/lib${R_ARCH}
      flag is placed earlier in the link commands used during
      installation and when packages are installed: this helps ensure
      that the current build has priority if an R shared library has
      already been installed by e.g. install-libR in a library
      mentioned in LDFLAGS (and not in ‘your system's library
      directory’ as documented). (Wish of PR#15790.)

    • LaTeX package upquote is no longer required for R's use of
      inconsolata.

    • (Windows only) If both 32- and 64-bit versions of R are
      installed, the bin/R.exe and bin/Rscript.exe executables now run
      64-bit R.  (To run 32-bit R, overwrite these files with copies of
      bin/i386/Rfe.exe.)

  UTILITIES:

    • Running R CMD check with _R_CHECK_DEPENDS_ONLY_ true now makes
      the VignetteBuilder packages available even if they are listed in
      Suggests, since they are needed to recognise and process
      non-Sweave vignettes.

    • R CMD check now reports empty importFrom declarations in a
      NAMESPACE file, as these are common errors (writing
      importFrom(Pkg) where import(Pkg) was intended).

    • R CMD check now by default checks code usage directly on the
      package namespace without loading and attaching the package and
      its suggests and enhances.  For good practice with packages in
      the Suggests field, see §1.1.3.1 of ‘Writing R Extensions’.  For
      use of lazy-data objects in the package's own code, see ?data.

  BUG FIXES:

    • dmultinom() did not handle non-finite probabilities correctly.

    • prettyNum(x, zero.print=*) now also works when x contains NAs.

    • A longstanding bug exhibited by nlminb() on Windows was traced to
      a compiler bug in gcc 4.6.3; a workaround has been put in place.
      (PR#15244 and PR#15914).

    • Rendering of \command in HTML versions of help pages has been
      improved: this is particularly evident on the help page for
      INSTALL.

    • as.hexmode(x) and as.octmode(x) now behave correctly for some
      numeric x, e.g., c(NA, 1) or c(1, pi).

    • drop1() failed if the scope argument had no variables to drop.
      (PR#15935)

    • edit() (and hence fix()) failed if an object had a non-character
      attribute named "source" (an attribute that had been used in R
      prior to version 2.14.0).

    • callGeneric() could fail if the generic had ... as a formal
      argument. (PR#15937).

    • Forking in package parallel called C entry point exit in the
      child.  This was unsafe (_exit should have been called), and
      could flush stdin of the main R process (seen most often on
      Solaris).

      As good practice, stdout is now flushed before forking a child.

    • R objects such as list(`a\b` = 1) now print correctly.

    • getAnywhere("C_pbinom") now returns correctly a single object
      (rather than unlisting it).

    • The confint() method for nls() fits failed it these has specified
      parameter limits despite using an algorithm other than "port".
      (PR#15960)

    • Subclassing an S4 class failed if the class required arguments to
      the generator, through its initialize() method.

    • removeSource() did not properly handle expressions containing
      arguments that were supplied as missing, e.g.  x[i,]. (PR#15957)

    • as.environment(list()) now works, and as.list() of such an
      environment is now the same as list().

    • Several tcltk functions failed when run in unusual environments.
      (PR#15970)

    • options(list()) now works (trivially). (PR#15979)

    • merge(<dendrogram>, ..) now works correctly for two `independent'
      dendrograms (PR#15648), and still compatibly via adjust = "auto"
      e.g. for two branches of an existing dendrogram.

    • The plot method for "hclust" objects gets an optional argument
      check; when that is true (the default) it checks more carefully
      for valid input.

    • (Windows only) If a user chose to install 64 bit R but not 32 bit
      R, the bin/R and bin/Rscript executables failed to run.
      (PR#15981)

    • Various possible buffer overruns have been prevented, and missed
      memory protection added. (PR#15990)

    • Rscript no longer passes --args to R when there are no extra
      (“user”) arguments.

    • objects like getClass("refClass")@prototype now print() and str()
      without error.

    • identical() now also looks at the S4 bit.

    • hist(x, breaks) is more robust in adding a small fuzz to few
      breaks when some are very large. (PR#15988)

    • sub() and gsub() did not handle regular expressions like "\s{2,}"
      properly if the text contained NA or non-ASCII elements in a
      UTF-8 locale.  Part of this was due to a bug in the TRE library.
      (PR#16009)

    • RShowDoc("NEWS") now displays the PDF version.

    • Matrices and arrays with last dimension zero did not print at all
      or incompletely.  (PR#16012)

    • plot.histogram() and hence hist() now respect the xaxs, yaxs and
      lab graphics parameters.  (PR#16021)

    • bw.SJ(x) and other bw.*() no longer segfault when x contains
      non-finite values. (PR#16024)

    • R CMD Rd2pdf unintentionally ignored its --os option.

    • The internal method of download.file() was not reporting file
      sizes and progress correctly on files larger than 2GB (inherited
      from libxml2).  This is corrected for 64-bit builds (32-bit
      platforms may not support such files, but where possible will be
      supported in future versions of R).

    • Work around a bug in OS X Yosemite where key environment
      variables may be duplicated causing issues in subprocesses. The
      duplicates are now removed on R startup (via Rprofile).
      (PR#16042)

    • Adjust X11 auto-launch detection in DISPLAY on OS X to recognize
      latest XQuartz.

CHANGES IN R 3.1.1:

  NEW FEATURES:

    • When attach() reports conflicts, it does so compatibly with
      library() by using message().

    • R CMD Sweave no longer cleans any files by default, compatibly
      with versions of R prior to 3.1.0.  There are new options
      --clean, --clean=default and --clean=keepOuts.

    • tools::buildVignette() and tools::buildVignettes() with clean =
      FALSE no longer remove any created files.  buildvignette() gains
      a keep argument for more cleaning customization.

    • The Bioconductor ‘version’ used by setRepositories() can now be
      set by environment variable R_BIOC_VERSION at runtime, not just
      when R is installed.  (It has been stated that Bioconductor will
      switch from ‘version’ 2.14 to ‘version’ 3.0 during the lifetime
      of the R 3.1 series.)

    • Error messages from bugs in embedded Sexpr code in Sweave
      documents now report the source location.

    • type.convert(), read.table() and similar read.*() functions get a
      new numerals argument, specifying how numeric input is converted
      when its conversion to double precision loses accuracy.  The
      default value, "allow.loss" allows accuracy loss, as in R
      versions before 3.1.0.

    • For some compilers, integer addition could overflow without a
      warning.  R's internal code for both integer addition and
      subtraction is more robust now.  (PR#15774)

    • The function determining the default number of knots for
      smooth.spline() is now exported, as .nknots.smspl().

    • dbeta(, a,b), pbeta(), qbeta() and rbeta() are now defined also
      for a = 0, b = 0, or infinite a and b (where they typically
      returned NaN before).

    • Many package authors report that the RStudio graphics device does
      not work correctly with their package's use of dev.new().  The
      new option dev.new(noRStudioGD = TRUE) replaces the RStudio
      override by the default device as selected by R itself, still
      respecting environment variables R_INTERACTIVE_DEVICE and
      R_DEFAULT_DEVICE.

    • readRDS() now returns visibly.

    • Modifying internal logical scalar constants now results in an
      error instead of a warning.

    • install.packages(repos = NULL) now accepts http:// or ftp:// URLs
      of package archives as well as file paths, and will download as
      required.  In most cases repos = NULL can be deduced from the
      extension of the URL.

    • The warning when using partial matching with the $ operator on
      data frames is now only given when
      options("warnPartialMatchDollar") is TRUE.

    • Package help requests like package?foo now try the package foo
      whether loaded or not.

    • General help requests now default to trying all loaded packages,
      not just those on the search path.

    • Added a new function promptImport(), to generate a help page for
      a function that was imported from another package (and presumably
      re-exported, or help would not be needed).

  INSTALLATION and INCLUDED SOFTWARE:

    • configure option --with-internal-tzcode can now be used with
      variable rsharedir.

    • The included version of PCRE has been updated to 8.35.

    • There is a new target make uninstall-libR to remove an installed
      shared/static libR.

      make install-libR now works if a sub-architecture is used,
      although the user will need to specify libdir differently for
      different sub-architectures.

    • There is more extensive advice on which LaTeX packages are
      required to install R or to make package manuals (as done by R
      CMD check) in the ‘Writing R Extensions’ manual.

    • Compilers/linkers were handling the visibility control in
      src/extra/xz inconsistently (and apparently in some cases
      incorrectly), so it has been simplified.  (PR#15327)

    • (Windows) There is updated support for the use of ICU for
      collation: see the ‘R Installation and Administration Manual’.

  BUG FIXES:

    • dbinom(x, n), pbinom(), dpois(), etc, are slightly less
      restrictive in checking if n is integer-valued.  (Wish of
      PR#15734.)

    • pchisq(x, df, ncp, log.p = TRUE) is more accurate and no longer
      underflows for small x and ncp < 80, e.g, for pchisq(1e-5, df =
      100, ncp = 1, log = TRUE).  (Based on PR#15635 and a suggestion
      by Roby Joehanes.)

    • The s (“step into”) command in the debugger would cause R to step
      into expressions evaluated there, not just into functions being
      debugged.  (PR#15770)

    • The C code used by strptime() rejected time-zone offsets of more
      than +1200 (+1245, +1300 and +1400 can occur).  (PR#15768)

    • (Windows only.)  png(type = "cairo", antialias = "gray") was not
      accepted.  (PR#15760)

    • Use of save(..., envir=) with named objects could fail.
      (PR#15758)

    • Sweave() mis-parsed Sexpr expressions that contained backslashes.
      (PR#15779)

    • The return value from options(foo = NULL) was not the previous
      value of the option.  (PR#15781)

    • enc2utf8() and enc2native() did not always mark the encoding of
      the return values when it was known.

    • dnbinom(x, size = <large>, mu, log = TRUE) no longer underflows
      to -Inf for large mu, thanks to a suggestion from Alessandro
      Mammana (MPI MolGen, Berlin).

    • pbeta(x, a, b, log = TRUE) no longer behaves discontinuously (in
      a small x-region) because of denormalized numbers.  Also,
      pbeta(1-1e-12, 1e30, 1.001, log=TRUE) now terminates “in real
      time”.

    • The "CRAN" filter (see available.packages()) no longer removes
      duplicates other than of packages on CRAN, and does not fail if
      there is no CRAN repository in getOption("repos").

    • The device listing from dev2bitmap() and bitmap() was truncated
      to 1000 characters: modern versions of GhostScript on most
      platforms have many more devices.

    • (Windows.)  Commands such as Sys.which() and pipe() which needed
      to find the full path to a command could segfault if the ‘long’
      path name was much longer than the ‘short’ path name (which
      Sys.which() returns), as the behaviour of the Windows API call
      had changed.

    • R CMD build will fail with an error if one of the packages
      specified in the VignetteBuilder field is not installed.
      (Without loading those packages it cannot be ascertained which
      files are intended to be vignettes. This means that the
      VignetteBuilder packages have to be installed for package
      checking too.)  (Wish of PR#15775.)

    • Misguided attempts to use chull() with non-finite points now give
      an error (related to PR#15777).

    • For a formula with exactly 32 variables the 32nd variable was
      aliased to the intercept in some C-level computations of terms,
      so that for example attempting to remove it would remove the
      intercept instead (and leave a corrupt internal structure).
      (PR#15735)

    • anyDuplicated() silently returned wrong values when the first
      duplicate was at an index which was too large to be stored in an
      integer vector (although a lot of RAM and patience would have
      been needed to encounter this).

    • tools::Rd2ex(commentDontrun = FALSE) failed if the block had only
      one line.

    • Hexadecimal constants such as 0x110p-5L which were incorrectly
      qualified by L were parsed incorrectly since R 3.0.0, with a
      slightly garbled warning. (PR#15753)

    • system() returned success on some platforms even if the system
      was unable to launch a process. (PR#15796)

    • (Windows Rgui console.)  Unbuffered output was sometimes not
      output immediately if the prompt was not on the last line of the
      console.

    • The built-in help server did not declare the encoding for the
      DESCRIPTION or other text files to be the package encoding, so
      non-ASCII characters could be displayed incorrectly.

    • R is now trying harder to not cleanup child processes that were
      not spawned by mcparallel() on platforms that provide information
      about the source process of the SIGCHLD signal. This allows 3rd
      party libraries to manage the exit status of children that they
      spawn without R interfering.

    • mcmapply() was only parallelizing if the number of jobs was
      bigger than the number of cores. It now parallelizes if the
      number of jobs is more than one.

    • Auto-printing would re-evaluate its argument when trying to
      dispatch to a print method.  This is now avoided when possible.

    • Unserializing (including load() and readRDS()) could silently
      return incorrect numeric values from ASCII saves if there was a
      read error.

    • getParseData() could return incorrect values for the parents of
      some elements. (Reported by Andrew Redd.)

    • Attempting to use data frames of 2^31 or more rows with merge()
      or to create a merged data frame of that size now gives a clearer
      error message.

    • parse() did not check its file argument was a connection if it
      was not a character string, so e.g. parse(FALSE) attempted to
      read from stdin.

      Nor did dump() and dput().

    • The "help.try.all.packages" option was ignored when the shortcut
      syntax for help was used, e.g. ?foo.

    • A potential segfault in string allocation has been fixed.  (Found
      by Radford Neal.)

    • Potential memory protection errors in sort() and D() have been
      fixed. (Found by Radford Neal.)

    • Fixed a lack of error checking in graphics event functions.
      (Found by Radford Neal; a different patch used here than the one
      in pqR.)

    • numericDeriv() sometimes miscalculated the gradient.  (PR#15849,
      reported originally by Radford Neal)

CHANGES IN R 3.1.0:

  NEW FEATURES:

    • type.convert() (and hence by default read.table()) returns a
      character vector or factor when representing a numeric input as a
      double would lose accuracy.  Similarly for complex inputs.

      If a file contains numeric data with unrepresentable numbers of
      decimal places that are intended to be read as numeric, specify
      colClasses in read.table() to be "numeric".

    • tools::Rdiff(useDiff = FALSE) is closer to the POSIX definition
      of diff -b (as distinct from the description in the man pages of
      most systems).

    • New function anyNA(), a version of any(is.na(.)) which is fast
      for atomic vectors, based on a proposal by Tim Hesterberg. (Wish
      of PR#15239.)

    • arrayInd(*, useNames = TRUE) and, analogously, which(*, arr.ind =
      TRUE) now make use of names(.dimnames) when available.

    • is.unsorted() now also works for raw vectors.

    • The "table" method for as.data.frame() (also useful as
      as.data.frame.table()) now passes sep and base arguments to
      provideDimnames().

    • uniroot() gets new optional arguments, notably extendInt,
      allowing to auto-extend the search interval when needed.  The
      return value has an extra component, init.it.

    • switch(f, ...) now warns when f is a factor, as this typically
      happens accidentally where the useR meant to pass a character
      string, but f is treated as integer (as always documented).

    • The parser has been modified to use less memory.

    • The way the unary operators (+ - !) handle attributes is now more
      consistent.  If there is no coercion, all attributes (including
      class) are copied from the input to the result: otherwise only
      names, dims and dimnames are.

    • colorRamp() and colorRampPalette() now allow non-opaque colours
      and a ramp in opacity via the new argument alpha = TRUE.
      (Suggested by Alberto Krone-Martins, but optionally as there are
      existing uses which expect only RGB values.)

    • grid.show.layout() and grid.show.viewport() get an optional vp.ex
      argument.

    • There is a new function find_gs_cmd() in the tools package to
      locate a GhostScript executable.  (This is an enhanced version of
      a previously internal function there.)

    • object.size() gains a format() method.

    • There is a new family, "ArialMT", for the pdf() and postscript()
      devices.  This will only be rendered correctly on viewers which
      have access to Monotype TrueType fonts (which are sometimes
      requested by journals).

    • The text and PDF news files, including NEWS and NEWS.2, have been
      moved to the doc directory.

    • combn(x, simplify = TRUE) now gives a factor result for factor
      input x (previously user error).  (Related to PR#15442.)

    • Added utils::fileSnapshot() and utils::changedFiles() functions
      to allow snapshots and comparison of directories of files.

    • make.names(names, unique=TRUE) now tries to preserve existing
      names. (Suggestion of PR#15452.)

    • New functions cospi(x), sinpi(x), and tanpi(x), for more accurate
      computation of cos(pi*x), etc, both in R and the C API.  Using
      these gains accuracy in some cases, e.g., inside lgamma() or
      besselI().  (Suggested by Morten Welinder in PR#15529.)

    • print.table(x, zero.print = ".") now also has an effect when x is
      not integer-valued.

    • There is more support to explore the system's idea of time-zone
      names.  Sys.timezone() tries to give the current system setting
      by name (and succeeds at least on Linux, OS X, Solaris and
      Windows), and OlsonNames() lists the names in the system's Olson
      database. Sys.timezone(location = FALSE) gives the previous
      behaviour.

    • Platforms with a 64-bit time_t type are allowed to handle
      conversions between the "POSIXct" and "POSIXlt" classes for
      date-times outside the 32-bit range (before 1902 or after 2037):
      the existing workarounds are used on other platforms.  (Note that
      time-zone information for post-2037 is speculative at best, and
      the OS services are tested for known errors and so not used on OS
      X.)

      Currently time_t is usually long and hence 64-bit on Unix-alike
      64-bit platforms: however in several cases the time-zone database
      is 32-bit.  For R for Windows it is 64-bit (for both
      architectures as from this version).

    • The "save.defaults" option can include a value for
      compression_level.  (Wish of PR#15579.)

    • colSums() and friends now have support for arrays and data-frame
      columns with 2^31 or more elements.

    • as.factor() is faster when f is an unclassed integer vector (for
      example, when called from tapply()).

    • fft() now works with longer inputs, from the 12 million
      previously supported up to 2 billion.  (PR#15593)

    • Complex svd() now uses LAPACK subroutine ZGESDD, the complex
      analogue of the routine used for the real case.

    • Sweave now outputs .tex files in UTF-8 if the input encoding is
      declared to be UTF-8, regardless of the local encoding.  The
      UTF-8 encoding may now be declared using a LaTeX comment
      containing the string %\SweaveUTF8 on a line by itself.

    • file.copy() gains a copy.date argument.

    • Printing of date-times will make use of the time-zone
      abbreviation in use at the time, if known.  For example, for
      Paris pre-1940 this could be LMT, PMT, WET or WEST.  To enable
      this, the "POSIXlt" class has an optional component "zone"
      recording the abbreviation for each element.

      For platforms which support it, there is also a component
      "gmtoff" recording the offset from GMT where known.

    • (On Windows, by default on OS X and optionally elsewhere.)  The
      system C function strftime has been replaced by a more
      comprehensive version with closer conformance to the POSIX 2008
      standard.

    • dnorm(x, log = FALSE) is more accurate (but somewhat slower) for
      |x| > 5; as suggested in PR#15620.

    • Some versions of the tiff() device have further compression
      options.

    • read.table(), readLines() and scan() have a new argument to
      influence the treatment of embedded nuls.

    • Avoid duplicating the right hand side values in complex
      assignments when possible.  This reduces copying of replacement
      values in expressions such as Z$a <- a0 and ans[[i]] <- tmp: some
      package code has relied on there being copies.

      Also, a number of other changes to reduce copying of objects; all
      contributed by or based on suggestions by Michael Lawrence.

    • The fast argument of KalmanLike(), KalmanRun() and
      KalmanForecast() has been replaced by update, which instead of
      updating mod in place, optionally returns the updated model in an
      attribute "mod" of the return value.

    • arima() and makeARIMA() get a new optional argument SSinit,
      allowing the choice of a different *s*tate *s*pace initialization
      which has been observed to be more reliable close to
      non-stationarity: see PR#14682.

    • warning() has a new argument noBreaks., to simplify
      post-processing of output with options(warn = 1).

    • pushBack() gains an argument encoding, to support reading of
      UTF-8 characters using scan(), read.table() and related functions
      in a non-UTF-8 locale.

    • all.equal.list() gets a new argument use.names which by default
      labels differing components by names (if they match) rather than
      by integer index.  Saved R output in packages may need to be
      updated.

    • The methods for all.equal() and attr.all.equal() now have
      argument check.attributes after ... so it cannot be partially nor
      positionally matched (as it has been, unintentionally).

      A side effect is that some previously undetected errors of
      passing empty arguments (no object between commas) to all.equal()
      are detected and reported.

      There are explicit checks that check.attributes is logical,
      tolerance is numeric and scale is NULL or numeric.  This catches
      some unintended positional matching.

      The message for all.equal.numeric() reports a "scaled difference"
      only for scale != 1.

    • all.equal() now has a "POSIXt" method replacing the "POSIXct"
      method.

    • The "Date" and "POSIXt" methods of seq() allows by = "quarter"
      for completeness (by = "3 months" always worked).

    • file.path() removes any trailing separator on Windows, where they
      are invalid (although sometimes accepted).  This is intended to
      enhance the portability of code written by those using POSIX file
      systems (where a trailing / can be used to confine path matching
      to directories).

    • New function agrepl() which like grepl() returns a logical
      vector.

    • fifo() is now supported on Windows. (PR#15600)

    • sort.list(method = "radix") now allows negative integers (wish of
      PR#15644).

    • Some functionality of print.ts() is now available in
      .preformat.ts() for more modularity.

    • mcparallel() gains an option detach = TRUE which allows execution
      of code independently of the current session.  It is based on a
      new estranged = TRUE argument to mcfork() which forks child
      processes such that they become independent of the parent
      process.

    • The pdf() device omits circles and text at extremely small sizes,
      since some viewers were failing on such files.

    • The rightmost break for the "months", "quarters" and "years"
      cases of hist.POSIXlt() has been increased by a day.  (Inter
      alia, fixes PR#15717.)

    • The handling of DF[i,] <- a where i is of length 0 is improved.
      (Inter alia, fixes PR#15718.)

    • hclust() gains a new method "ward.D2" which implements Ward's
      method correctly.  The previous "ward" method is "ward.D" now,
      with the old name still working.  Thanks to research and
      proposals by Pierre Legendre.

    • The sunspot.month dataset has been amended and updated from the
      official source, whereas the sunspots and sunspot.year datasets
      will remain immutable. The documentation and source links have
      been updated correspondingly.

    • The summary() method for "lm" fits warns if the fit is
      essentially perfect, as most of the summary may be computed
      inaccurately (and with platform-dependent values).

      Programmers who use summary() in order to extract just a
      component which will be reliable (e.g., $cov.unscaled) should
      wrap their calls in suppressWarnings().

  INSTALLATION and INCLUDED SOFTWARE:

    • The included version of LAPACK has been updated to 3.5.0.

    • There is some support for parallel testing of an installation, by
      setting TEST_MC_CORES to an integer greater than one to indicate
      the maximum number of cores to be used in parallel. (It is worth
      specifying at least 8 cores if available.)  Most of these require
      a make program (such as GNU make and dmake) which supports the
      $MAKE -j nproc syntax.

      Except on Windows: the tests of standard package examples in make
      check are done in parallel.  This also applies to running
      tools::testInstalledPackages().

      The more time-consuming regression tests are done in parallel.

      The package checks in make check-devel and make check-recommended
      are done in parallel.

    • More of make check will work if recommended packages are not
      installed: but recommended packages remain needed for thorough
      checking of an R build.

    • The version of tzcode included in src/extra/tzone has been
      updated.  (Formerly used only on Windows.)

    • The included (64-bit) time-zone conversion code and Olson
      time-zone database can be used instead of the system version: use
      configure option --with-internal-tzcode.  This is the default on
      Windows and OS X.  (Note that this does not currently work if a
      non-default rsharedir configure variable is used.)

      (It might be necessary to set environment variable TZ on OSes
      where this is not already set, although the system timezone is
      deduced correctly on at least Linux, OS X and Windows.)

      This option also switches to the version of strftime included in
      directory src/extra/tzone.

    • configure now tests for a C++11-compliant compiler by testing
      some basic features.  This by default tries flags for the
      compiler specified by CXX, but an alternative compiler, options
      and standard can be specified by variables CXX1X, CXX1XFLAGS and
      CXX1XSTD (e.g., -std=gnu++11).

    • R can now optionally be compiled to use reference counting
      instead of the NAMED mechanism by defining SWITCH_TO_REFCNT in
      Rinternals.h. This may become the default in the future.

    • There is a new option --use-system-tre to use a suitable system
      tre library: at present this means a version from their git
      repository, after corrections.  (Wish of PR#15660.)

  PACKAGE INSTALLATION:

    • The CRANextra repository is no longer a default repository on
      Windows: all the binary versions of packages from CRAN are now on
      CRAN, although CRANextra contains packages from Omegahat and
      elsewhere used by CRAN packages.

    • Only vignettes sources in directory vignettes are considered to
      be vignettes and hence indexed as such.

    • In the DESCRIPTION file,
      
          License: X11

      is no longer recognized as valid.  Use MIT or BSD_2_clause
      instead, both of which need + file LICENSE.

    • For consistency, entries in .Rinstignore are now matched
      case-insensitively on all platforms.

    • Help for S4 methods with very long signatures now tries harder to
      split the description in the Usage field to no more than 80
      characters per line (some packages had over 120 characters).

    • R CMD INSTALL --build (not Windows) now defaults to the internal
      tar() unless R_INSTALL_TAR is set.

    • There is support for compiling C++11 code in packages on suitable
      platforms: see ‘Writing R Extensions’.

    • Fake installs now install the contents of directory inst: some
      packages use this to install e.g. C++ headers for use by other
      packages that are independent of the package itself.  Option
      --no-inst can be used to get the previous behaviour.

  DEBUGGING:

    • The behaviour of the code browser has been made more consistent,
      in part following the suggestions in PR#14985.

    • Calls to browser() are now consistent with calls to the browser
      triggered by debug(), in that Enter will default to n rather than
      c.

    • A new browser command s has been added, to “step into” function
      calls.

    • A new browser command f has been added, to “finish” the current
      loop or function.

    • Within the browser, the command help will display a short list of
      available commands.

  UTILITIES:

    • Only vignettes sources in directory vignettes are considered to
      be vignettes by R CMD check.  That has been the preferred
      location since R 2.14.0 and is now obligatory.

    • For consistency, R CMD build now matches entries in .Rbuildignore
      and vignettes/.install_extras case-insensitively on all platforms
      (not just on Windows).

    • checkFF() (called by R CMD check by default) can optionally check
      foreign function calls for consistency with the registered type
      and argument count.  This is the default for R CMD check
      --as-cran or can be enabled by setting environment variable
      _R_CHECK_FF_CALLS_ to registration (but is in any case suppressed
      by --install=no).  Because this checks calls in which .NAME is an
      R object and not just a literal character string, some other
      problems are detected for such calls.

      Functions suppressForeignCheck() and dontCheck() have been added
      to allow package authors to suppress false positive reports.

    • R CMD check --as-cran warns about a false value of the
      DESCRIPTION field BuildVignettes for Open Source packages, and
      ignores it.  (An Open Source package needs to have complete
      sources for its vignettes which should be usable on a suitably
      well-equipped system).

    • R CMD check --no-rebuild-vignettes is defunct:
      R CMD check --no-build-vignettes has been preferred since R
      3.0.0.

    • R CMD build --no-vignettes is defunct:
      R CMD build --no-build-vignettes has been preferred since R
      3.0.0.

    • R CMD Sweave and R CMD Stangle now process both Sweave and
      non-Sweave vignettes.  The tools::buildVignette() function has
      been added to do the same tasks from within R.

    • The flags returned by R CMD config --ldflags and (where
      installed) pkg-config --libs libR are now those needed to link a
      front-end against the (shared or static) R library.

    • Sweave.sty has a new option [inconsolata].

    • R CMD check customizations such as _R_CHECK_DEPENDS_ONLY_ make
      available packages only in LinkingTo only for installation, and
      not for loading/runtime tests.

    • tools::checkFF() reports on .C and .Fortran calls with DUP =
      FALSE if argument check_DUP is true.  This is selected by R CMD
      check by default.

    • R CMD check --use-gct can be tuned to garbage-collect less
      frequently using gctorture2() _via_ the setting of environment
      variable _R_CHECK_GCT_N_.

    • Where supported, tools::texi2dvi() limits the number of passes
      tried to 20.

  C-LEVEL FACILITIES:

    • (Windows only) A function R_WaitEvent() has been added (with
      declaration in headerR.h) to block execution until the next event
      is received by R.

    • Remapping in the Rmath.h header can be suppressed by defining
      R_NO_REMAP_RMATH.

    • The remapping of rround() in header Rmath.h has been removed: use
      fround() instead.

    • ftrunc() in header Rmath.h is now a wrapper for the C99 function
      trunc(), which might as well be used in C code: ftrunc() is still
      needed for portable C++ code.

    • The never-documented remapping of prec() to fprec() in header
      Rmath.h has been removed.

    • The included LAPACK subset now contains ZGESDD and ZGELSD.

    • The function LENGTH() now checks that it is only applied to
      vector arguments.  However, in packages length() should be used.
      (In R itself LENGTH() is a macro without the function overhead of
      length().)

    • Calls to SET_VECTOR_ELT() and SET_STRING_ELT() are now checked
      for indices which are in-range: several packages were writing one
      element beyond the allocated length.

    • allocVector3 has been added which allows custom allocators to be
      used for individual vector allocations.

  DEPRECATED AND DEFUNCT:

    • chol(pivot = TRUE, LINPACK = TRUE) is defunct.

      Arguments EISPACK for eigen() and LINPACK for chol(), chol2inv(),
      solve() and svd() are ignored: LAPACK is always used.

    • .find.package() and .path.package() are defunct: only the
      versions without the initial dot introduced in R 2.13.0 have ever
      been in the API.

    • Partial matching when using the $ operator _on data frames_ now
      throws a warning and may become defunct in the future. If partial
      matching is intended, replace foo$bar by foo[["bar", exact =
      FALSE]].

    • The long-deprecated use of \synopsis in the Usage section of .Rd
      files has been removed: such sections are now ignored (with a
      warning).

    • package.skeleton()'s deprecated argument namespace has been
      removed.

    • Many methods are no longer exported by package stats.  They are
      all registered on their generic, which should be called rather
      than calling a method directly.

    • Functions readNEWS() and checkNEWS() in package tools are
      defunct.

    • download.file(method = "lynx") is deprecated.

    • .C(DUP = FALSE) and .Fortran(DUP = FALSE) are now deprecated, and
      may be disabled in future versions of R.  As their help has long
      said, .Call() is much preferred.

      R CMD check notes such usages (by default).

    • The workaround of setting R_OSX_VALGRIND has been removed: it is
      not needed in current valgrind.

  BUG FIXES:

    • Calling lm.wfit() with no non-zero weights gave an array-overrun
      in the Fortran code and a not very sensible answer.  It is now
      special-cased with a simpler answer (no qr component).

    • Error messages involving non-syntactic names (e.g., as produced
      by `\r` when that object does not exist) now encode the control
      characters.  (Reported by Hadley Wickham.)

    • getGraphicsEvent() caused 100% usage of one CPU in Windows.
      (PR#15500)

    • nls() with no start argument may now work inside another function
      (scoping issue).

    • pbeta() and similar work better for very large (billions) ncp.

    • Where time zones have changed abbreviations over the years, the
      software tries to more consistently use the abbreviation
      appropriate to the time or if that is unknown, the current
      abbreviation.  On some platforms where the C function localtime
      changed the tzname variables the reported abbreviation could have
      been that of the last time converted.

    • all.equal(list(1), identity) now works.

    • Bug fix for pushing viewports in grid (reported by JJ Allaire and
      Kevin Ushey).

      NOTE for anyone poking around within the graphics engine display
      list (despite the warnings not to) that this changes what is
      recorded by grid on the graphics engine display list.

    • Extra checks have been added for unit resolution and conversion
      in grid, to catch instances of division-by-zero.  This may
      introduce error messages in existing code and/or produce a
      different result in existing code (but only where a non-finite
      location or dimension may now become zero).

    • Some bugs in TRE have been corrected by updating from the git
      repository.  This allows R to be installed on some platforms for
      which this was a blocker (PR#15087 suggests Linux on ARM and
      HP-UX).

    • ? applied to a call to an S4 generic failed in several cases.
      (PR#15680)

    • The implicit S4 generics for primitives with ... in their
      argument list were incorrect. (PR#15690)

    • Bug fixes to methods::callGeneric(). (PR#15691)

    • The bug fix to aggregrate() in PR#15004 introduced a new bug in
      the case of no grouping variables. (PR#15699)

    • In rare cases printing deeply nested lists overran a buffer by
      one byte and on a few platforms segfaulted. (PR#15679)

    • The dendrogram method of as.dendrogram() was hidden accidentally,
      (PR#15703), and order.dendrogram(d) gave too much for a leaf d.
      (PR#15702)

    • R would try to kill processes on exit that have pids ever used by
      a child process spawned by mcparallel even though the current
      process with that pid was not actually its child.

    • cophenetic() applied to a "dendrogram" object sometimes
      incorrectly returned a "Labels" attribute with dimensions.
      (PR#15706)

    • printCoefmat() called from quite a few print() methods now obeys
      small getOption("width") settings, line wrapping the "signif.
      codes" legend appropriately.  (PR#15708)

    • model.matrix() assumed that the stored dimnames for a matrix was
      NULL or length 2, but length 1 occurred.

    • The clipping region for a device was sometimes used in base
      graphics before it was set.

CHANGES IN R 3.0.3:

  NEW FEATURES:

    • On Windows there is support for making .texi manuals using
      texinfo 5.0 or later: the setting is in file
      src/gnuwin32/MkRules.dist.

      A packaging of the Perl script and modules for texinfo 5.2 has
      been made available at <URL:
      http://www.stats.ox.ac.uk/pub/Rtools/>.

    • write.table() now handles matrices of 2^31 or more elements, for
      those with large amounts of patience and disc space.

    • There is a new function, La_version(), to report the version of
      LAPACK in use.

    • The HTML version of ‘An Introduction to R’ now has links to PNG
      versions of the figures.

    • There is some support to produce manuals in ebook formats. (See
      doc/manual/Makefile.  Suggested by Mauro Cavalcanti.)

    • On a Unix-alike Sys.timezone() returns NA if the environment
      variable TZ is unset, to distinguish it from an empty string
      which on some OSes means the UTC time zone.

    • The backtick may now be escaped in strings, to allow names
      containing them to be constructed, e.g. `\``.  (PR#15621)

    • read.table(), readLines() and scan() now warn when an embedded
      nul is found in the input.  (Related to PR#15625 which was
      puzzled by the behaviour in this unsupported case.)

    • (Windows only.)  file.symlink() works around the undocumented
      restriction of the Windows system call to backslashes.  (Wish of
      PR#15631.)

    • KalmanForecast(fast = FALSE) is now the default, and the help
      contains an example of how fast = TRUE can be used in this
      version.  (The usage will change in 3.1.0.)

    • strptime() now checks the locale only when locale-specific
      formats are used and caches the locale in use: this can halve the
      time taken on OSes with slow system functions (e.g., OS X).

    • strptime() and the format() methods for classes "POSIXct",
      "POSIXlt" and "Date" recognize strings with marked encodings:
      this allows, for example, UTF-8 French month names to be read on
      (French) Windows.

    • iconv(to = "utf8") is now accepted on all platforms (some
      implementations did already, but GNU libiconv did not: however
      converted strings were not marked as being in UTF-8).  The
      official name, "UTF-8" is still preferred.

    • available.packages() is better protected against corrupt metadata
      files.  (A recurring problem with Debian package shogun-r:
      PR#14713.)

    • Finalizers are marked to be run at garbage collection, but run
      only at a somewhat safer later time (when interrupts are
      checked).  This circumvents some problems with finalizers running
      arbitrary code during garbage collection (the known instances
      being running options() and (C-level) path.expand()
      re-entrantly).

  INSTALLATION and INCLUDED SOFTWARE:

    • The included version of PCRE has been updated to 8.34.  This
      fixes bugs and makes the behaviour closer to Perl 5.18.  In
      particular, the concept of ‘space’ includes VT and hence agrees
      with POSIX's.

  PACKAGE INSTALLATION:

    • The new field SysDataCompression in the DESCRIPTION file allows
      user control over the compression used for sysdata.rda objects in
      the lazy-load database.

    • install.packages(dependencies = value) for value = NA (the
      default) or value = TRUE omits packages only in LinkingTo for
      binary package installs.

  C-LEVEL FACILITIES:

    • The long undocumented remapping of rround() to Rf_fround() in
      header Rmath.h is now formally deprecated: use fround() directly.

    • Remapping of prec() and trunc() in the Rmath.h header has been
      disabled in C++ code (it has caused breakage with libc++
      headers).

  BUG FIXES:

    • getParseData() truncated the imaginary part of complex number
      constants.  (Reported by Yihui Xie.)

    • dbeta(x, a, b) with a or b within a factor of 2 of the largest
      representable number could infinite-loop.  (Reported by Ioannis
      Kosmidis.)

    • provideDimnames() failed for arrays with a 0 dimension.
      (PR#15465)

    • rbind() and cbind() did not handle list objects correctly.
      (PR#15468)

    • replayPlot() now checks if it is replaying a plot from the same
      session.

    • rasterImage() and grid.raster() now give error on an empty
      (zero-length) raster.  (Reported by Ben North.)

    • plot.lm() would sometimes scramble the labels in plot type 5.
      (PR#15458 and PR#14837)

    • min() did not handle NA_character_ values properly.  (Reported by
      Magnus Thor Torfason.)

    • (Windows only.)  readRegistry() would duplicate default values
      for keys.  (PR#15455)

    • str(..., strict.width = "cut") did not handle it properly when
      more than one line needed to be cut.  (Reported by Gerrit
      Eichner.)

    • Removing subclass back-references when S4 classes were removed or
      their namespace unloaded had several bugs (e.g., PR#15481).

    • aggregate() could fail when there were too many levels present in
      the by argument.  (PR#15004)

    • namespaceImportFrom() needed to detect primitive functions when
      checking for duplicated imports (reported by Karl Forner).

    • getGraphicsEvent() did not exit when a user closed the graphics
      window.  (PR#15208)

    • Errors in vignettes were not always captured and displayed
      properly.  (PR#15495)

    • contour() could fail when dealing with extremely small z values.
      (PR#15454)

    • Several functions did not handle zero-length vectors properly,
      including browseEnv(), format(), gl(), relist() and
      summary.data.frame().  (E.g., PR#15499)

    • Sweave() did not restore the R output to the console if it was
      interrupted by a user in the middle of evaluating a code chunk.
      (Reported by Michael Sumner.)

    • Fake installs of packages with vignettes work again.

    • Illegal characters in the input caused parse() (and thus
      source()) to segfault.  (PR#15518)

    • The nonsensical use of nmax = 1 in duplicated() or unique() is
      now silently ignored.

    • qcauchy(p, *) is now fully accurate even when p is very close to
      1. (PR#15521)

    • The validmu() and valideta() functions in the standard glm()
      families now also report non-finite values, rather than failing.

    • Saved vignette results (in a .Rout.save file) were not being
      compared to the new ones during R CMD check.

    • Double-clicking outside of the list box (e.g., on the scrollbar)
      of a Tk listbox widget generated by tk_select.list() no longer
      causes the window to close. (PR#15407)

    • Improved handling of edge cases in parallel::splitindices().
      (PR#15552)

    • HTML display of results from help.search() and ?? sometimes
      contained badly constructed links.

    • c() and related functions such as unlist() converted raw vectors
      to invalid logical vectors. (PR#15535)

    • (Windows only) When a call to system2() specified one of stdin,
      stdout or stderr to be a file, but the command was not found
      (e.g., it contained its arguments, or the program was not on the
      PATH), it left the file open and unusable until R terminated.
      (Reported by Mathew McLean.)

    • The bmp() device was not recording res = NA correctly: it is now
      recorded as 72 ppi.

    • Several potential problems with compiler-specific behaviour have
      been identified using the ‘Undefined Behaviour Sanitizer’ in
      conjunction with the clang compiler.

    • hcl() now honours NA inputs (previously they were mapped to
      black).

    • Some translations in base packages were being looked up in the
      main catalog rather than that for the package.

    • As a result of the 3.0.2 change about ‘the last second before the
      epoch’, most conversions which should have given NA returned that
      time.  (The platforms affected include Linux and OS X, but not
      Windows nor Solaris.)

    • rowsum() has more support for matrices and data frames with 2^31
      or more elements. (PR#15587)

    • predict(<lm object>, interval = "confidence", scale =
      <something>) now works.  (PR#15564)

    • The bug fix in 3.0.2 for PR#15411 was too aggressive, and
      sometimes removed spaces that should not have been removed.
      (PR#15583)

    • Running R code in a tcltk callback failed to set the busy flag,
      which will be needed to tell OS X not to ‘App Nap’.

    • The code for date-times before 1902 assumed that the offset from
      GMT in 1902 was a whole number of minutes: that was not true of
      Paris (as recorded on some platforms).

    • Using Sys.setlocale to set LC_NUMERIC to "C" (to restore the sane
      behavior) no longer gives a warning.

    • deparse() now deparses complex vectors in a way that re-parses to
      the original values.  (PR#15534, patch based on code submitted by
      Alex Bertram.)

    • In some extreme cases (more than 10^15) integer inputs to
      dpqrxxx() functions might have been rounded up by one (with a
      warning about being non-integer).  (PR#15624)

    • Plotting symbol pch = 14 had the triangle upside down on some
      devices (typically screen devices). The triangle is supposed to
      be point up.  (Reported by Bill Venables.)

    • getSrcref() did not work on method definitions if
      rematchDefinition() had been used.

    • KalmanForecast(fast = FALSE) reported a (harmless) stack
      imbalance.

    • The count of observations used by KalmanRun() did not take
      missing values into account.

    • In locales where the abbreviated name of one month is a partial
      match for the full name of a later one, the %B format in
      strptime() could fail.  An example was French on OS X, where juin
      is abbreviated to jui and partially matches juillet.  Similarly
      for weekday names.

    • pbeta(x, a, b, log.p = TRUE) sometimes underflowed to zero for
      very small and very differently sized a, b.  (PR#15641)

    • approx() and approxfun() now handle infinite values with the
      "constant" method. (PR#15655)

    • stripchart() again respects reversed limits in xlim and ylim.
      (PR#15664)

CHANGES IN R 3.0.2:

  NEW FEATURES:

    • The NEWS files have been re-organized.

      This file contains news for R >= 3.0.0: news for the 0.x.y, 1.x.y
      and 2.x.y releases is in files NEWS.0, NEWS.1 and NEWS.2.  The
      latter files are now installed when R is installed.  An HTML
      version of news from 2.10.0 to 2.15.3 is available as
      doc/html/NEWS.2.html.

    • sum() for integer arguments now uses an integer accumulator of at
      least 64 bits and so will be more accurate in the very rare case
      that a cumulative sum exceeds 2^53 (necessarily summing more than
      4 million elements).

    • The example() and tools::Rd2ex() functions now have parameters to
      allow them to ignore \dontrun markup in examples.  (Suggested by
      Peter Solymos.)

    • str(x) is considerably faster for very large lists, or factors
      with 100,000 levels, the latter as in PR#15337.

    • col2rgb() now converts factors to character strings not integer
      codes (suggested by Bryan Hanson).

    • tail(warnings()) now works, via the new `[` method.

    • There is now support for the LaTeX style file zi4.sty which has
      in some distributions replaced inconsolata.sty.

    • unlist(x) now typically returns all non-list xs unchanged, not
      just the “vector” ones.  Consequently, format(lst) now also works
      when the list lst has non-vector elements.

    • The tools::getVignetteInfo() function has been added to give
      information about installed vignettes.

    • New assertCondition(), etc. utilities in tools, useful for
      testing.

    • Profiling now records non-inlined calls from byte-compiled code
      to BUILTIN functions.

    • Various functions in stats and elsewhere that use non-standard
      evaluation are now more careful to follow the namespace scoping
      rules.  E.g., stats::lm() can now find stats::model.frame() even
      if stats is not on the search path or if some package defines a
      function of that name.

    • If an invalid/corrupt .Random.seed object is encountered in the
      workspace it is ignored with a warning rather than giving an
      error.  (This allows R itself to rely on a working RNG, e.g. to
      choose a random port.)

    • seq() and seq.int() give more explicit error messages if called
      with invalid (e.g., NaN) inputs.

    • When parse() finds a syntax error, it now makes partial parse
      information available up to the location of the error.  (Request
      of Reijo Sund.)

    • Methods invoked by NextMethod() had a different dynamic parent to
      the generic. This was causing trouble where S3 methods invoked
      via lazy evaluation could lose track of their generic.
      (PR#15267)

    • Code for the negative binomial distribution now treats the case
      size == 0 as a one-point distribution at zero.

    • abbreviate() handles without warning non-ASCII input strings
      which require no abbreviation.

    • read.dcf() no longer has a limit of 8191 bytes per line. (Wish of
      PR#15250.)

    • formatC(x) no longer copies the class of x to the result, to
      avoid misuse creating invalid objects as in PR#15303.  A warning
      is given if a class is discarded.

    • Dataset npk has been copied from MASS to allow more tests to be
      run without recommended packages being installed.

    • The initialization of the regression coefficients for
      non-degenerate differenced models in arima() has been changed and
      in some examples avoids a local maximum.  (PR#15396)

    • termplot() now has an argument transform.x to control the display
      of individual terms in the plot.  (PR#15329)

    • format() now supports digits = 0, to display nsmall decimal
      places.

    • There is a new read-only par() parameter called "page", which
      returns a logical value indicating whether the next plot.new()
      call will start a new page.

    • Processing Sweave and Rd documents to PDF now renders backticks
      and single quotes better in several instances, including in \code
      and \samp expressions.

    • utils::modifyList() gets a new argument keep.null allowing NULL
      components in the replacement to be retained, instead of causing
      corresponding components to be deleted.

    • tools::pkgVignettes() gains argument check; if set to TRUE, it
      will warn when it appears a vignette requests a non-existent
      vignette engine.

  UTILITIES:

    • R CMD check --as-cran checks the line widths in usage and
      examples sections of the package Rd files.

    • R CMD check --as-cran now implies --timings.

    • R CMD check looks for command gfile if a suitable file is not
      found.  (Although file is not from GNU, OpenCSW on Solaris
      installs it as gfile.)

    • R CMD build (with the internal tar) checks the permissions of
      configure and cleanup files and adds execute permission to the
      recorded permissions for these files if needed, with a warning.
      This is useful on OSes and file systems which do not support
      execute permissions (notably, on Windows).

    • R CMD build now weaves and tangles all vignettes, so suggested
      packages are not required during package installation if the
      source tarball was prepared with current R CMD build.

    • checkFF() (used by R CMD check) does a better job of detecting
      calls from other packages, including not reporting those where a
      function has been copied from another namespace (e.g., as a
      default method).  It now reports calls where .NAME is a symbol
      registered in another package.

    • On Unix-alike systems, R CMD INSTALL now installs packages group
      writably whenever the library (lib.loc) is group writable.
      Hence, update.packages() works for other group members (suggested
      originally and from a patch by Dirk Eddelbuettel).

    • R CMD javareconf now supports the use of symbolic links for
      JAVA_HOME on platforms which have realpath.  So it is now
      possible to use
      
      R CMD javareconf JAVA_HOME=/usr/lib/jvm/java-1.7.0

      on a Linux system and record that value rather than the
      frequently-changing full path such as
      /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.25.x86_64.

    • (Windows only.) Rscript -e requires a non-empty argument for
      consistency with Unix versions of R.  (Also Rterm -e and R -e.)

    • R CMD check does more thorough checking of declared packages and
      namespaces.  It reports

        • packages declared in more than one of the Depends, Imports,
          Suggests and Enhances fields of the DESCRIPTION file.

        • namespaces declared in Imports but not imported from, neither
          in the NAMESPACE file nor using the :: nor ::: operators.

        • packages which are used in library() or requires() calls in
          the R code but were already put on the search path _via_
          Depends.

        • packages declared in Depends not imported _via_ the NAMESPACE
          file (except the standard packages).  Objects used from
          Depends packages should be imported to avoid conflicts and to
          allow correct operation when the namespace is loaded but not
          attached.

        • objects imported _via_ ::: calls where :: would do.

        • objects imported by :: which are not exported.

        • objects imported by ::: calls which do not exist.

      See ‘Writing R Extensions’ for good practice.

    • R CMD check optionally checks for non-standard top-level files
      and directories (which are often mistakes): this is enabled for
      --as-cran.

    • LaTeX style file upquote.sty is no longer included (the version
      was several years old): it is no longer used in R.  A much later
      version is commonly included in LaTeX distributions but does not
      play well with the ae fonts which are the default for Sweave
      vignettes.

    • R CMD build makes more use of the build sub-directory of package
      sources, for example to record information about the vignettes.

    • R CMD check analyses ::: calls.

  INSTALLATION and INCLUDED SOFTWARE:

    • The macros used for the texinfo manuals have been changed to work
      better with the incompatible changes made in texinfo 5.x.

    • The minimum version for a system xz library is now 5.0.3 (was
      4.999).  This is in part to avoid 5.0.2, which can compress in
      ways other versions cannot decompress.

    • The included version of PCRE has been updated to 8.33.

    • The included version of zlib has been updated to 1.2.8, a bug-fix
      release.

    • The included version of xz utils's liblzma has been updated to
      5.0.5.

    • Since javareconf (see above) is used when R is installed, a
      stable link for JAVA_HOME can be supplied then.

    • Configuring with --disable-byte-compilation will override the
      DESCRIPTION files of recommended packages, which typically
      require byte-compilation.

    • More of the installation and checking process will work even when
      TMPDIR is set to a path containing spaces, but this is not
      recommended and external software (such as texi2dvi) may fail.

  PACKAGE INSTALLATION:

    • Installation is aborted immediately if a LinkingTo package is not
      installed.

    • R CMD INSTALL has a new option --no-byte-compile which will
      override a ByteCompile field in the package's DESCRIPTION file.

    • License BSD is deprecated: use BSD_3_clause or BSD_2_clause
      instead.

      License X11 is deprecated: use MIT or BSD_2_clause instead.

    • Version requirements for LinkingTo packages are now recognized:
      they are checked at installation.  (Fields with version
      requirements were previously silently ignored.)

    • The limit of 500 S3method entries in a NAMESPACE file has been
      removed.

    • The default ‘version’ of Bioconductor for its packages has been
      changed to the upcoming 2.13, but this can be set by the
      environment variable R_BIOC_VERSION when R is installed.

  C-LEVEL FACILITIES:

    • Rdefines.h has been tweaked so it can be included in C++ code
      after R_ext/Boolean.h (which is included by R.h).

      Note that Rdefines.h is not kept up-to-date, and Rinternals.h is
      preferred for new code.

    • eval and applyClosure are now protected against package code
      supplying an invalid rho.

  DEPRECATED AND DEFUNCT:

    • The unused namespace argument to package.skeleton() is now
      formally deprecated and will be removed in R 3.1.0.

    • plclust() is deprecated: use the plot() method for class "hclust"
      instead.

    • Functions readNEWS() and checkNEWS() in package tools are
      deprecated (and they have not worked with current NEWS files for
      a long time).

  DOCUMENTATION:

    • ‘An Introduction to R’ has a new chapter on using R as a
      scripting language including interacting with the OS.

  BUG FIXES:

    • help.request() could not determine the current version of R on
      CRAN.  (PR#15241)

    • On Windows, file.info() failed on root directories unless the
      path was terminated with an explicit ".".  (PR#15302)

    • The regmatches<-() replacement function mishandled results coming
      from regexpr().  (PR#15311)

    • The help for setClass() and representation() still suggested the
      deprecated argument representation=. (PR#15312)

    • R CMD config failed in an installed build of R 3.0.1 (only) when
      a sub-architecture was used.  (Reported by Berwin Turlach.)

    • On Windows, the installer modified the etc/Rconsole and
      etc/Rprofile.site files even when default options were chosen, so
      the MD5 sums did not refer to the installed versions.  (Reported
      by Tal Galili.)

    • plot(hclust(), cex =) respects cex again (and possibly others
      similarly).  (Reported by Peter Langfelder.)

    • If multiple packages were checked by R CMD check, and one was
      written for a different OS, it would set --no-install for all
      following packages as well as itself.

    • qr.coef() and related functions did not properly coerce real
      vectors to complex when necessary.  (PR#15332)

    • ftable(a) now fixes up empty dimnames such that the result is
      printable.

    • package.skeleton() was not starting its search for function
      objects in the correct place if environment was supplied.
      (Reported by Karl Forner.)

    • Parsing code was changing the length field of vectors and
      confusing the memory manager.  (PR#15345)

    • The Fortran routine ZHER2K in the reference BLAS had a
      comment-out bug in two places.  This caused trouble with eigen()
      for Hermitian matrices.  (PR#15345 and report from Robin Hankin)

    • vignette() and browseVignettes() did not display non-Sweave
      vignettes properly.

    • Two warning/error messages have been corrected: the (optional)
      warning produced by a partial name match with a pairlist, the
      error message from a zero-length argument to the : operator.
      (Found by Radford Neal; PR#15358, PR#15356)

    • svd() returned NULL rather than omitting components as
      documented.  (Found by Radford Neal; PR#15360)

    • mclapply() and mcparallel() with silent = TRUE could break a
      process that uses stdout output unguarded against broken pipes
      (e.g., zip will fail silently). To work around such issues, they
      now replace stdout with a descriptor pointed to /dev/null
      instead. For this purpose, internal closeStdout and closeStderr
      functions have gained the to.null flag.

    • log(), signif() and round() now raise an error if a single named
      argument is not named x.  (PR#15361)

    • deparse() now deparses raw vectors in a form that is
      syntactically correct. (PR#15369)

    • The jpeg driver in Sweave created a JPEG file, but gave it a .png
      extension. (PR#15370)

    • Deparsing of infix operators with named arguments is improved.
      (PR#15350)

    • mget(), seq.int() and numericDeriv() did not duplicate arguments
      properly. (PR#15352, PR#15353, PR#15354)

    • kmeans(algorithm = "Hartigan-Wong") now always stops iterating in
      the QTran stage. (PR#15364).

    • read.dcf() re-allocated incorrectly and so could segfault when
      called on a file with lines of more than 100 bytes.

    • On systems where mktime() does not set errno, the last second
      before the epoch could not be converted from POSIXlt to POSIXct.
      (Reported by Bill Dunlap.)

    • add1.glm() miscalculated F-statistics when df > 1. (Bill Dunlap,
      PR#15386).

    • stem() now discards infinite inputs rather than hanging.
      (PR#15376)

    • The parser now enforces C99 syntax for floating point hexadecimal
      constants (e.g., 0x1.1p0), rather than returning unintended
      values for malformed constants. (PR#15234)

    • model.matrix() now works with very long LHS names (more than 500
      bytes).  (PR#15377)

    • integrate() reverts to the pre-2.12.0 behaviour: from 2.12.0 to
      3.0.1 it sometimes failed to achieve the requested tolerance and
      reported error estimates that were exceeded.  (PR#15219)

    • strptime() now handles %W fields with value 0. (PR#15915)

    • R is now better protected against people trying to interact with
      the console in startup code.  (PR#15325)

    • Subsetting 1D arrays often lost dimnames (PR#15301).

    • Unary + on a logical vector did not coerce to integer, although
      unary - did.

    • na.omit() and na.exclude() added a row to a zero-row data frame.
      (PR#15399)

    • All the (where necessary cut-down) vignettes are installed if R
      was configured with --without-recommended-packages.

    • source() did not display filenames when reporting syntax errors.

    • Syntax error reports misplaced the caret pointing out the bad
      token.

    • (Windows only) Starting R with R (instead of Rterm or Rgui) would
      lose any zero-length strings from the command line arguments.
      (PR#15406)

    • Errors in the encoding specified on the command line via
      --encoding=foo were not handled properly.  (PR#15405)

    • If x is a symbol, is.vector(x, "name") now returns TRUE, since
      "name" and "symbol" should be synonyms.  (Reported by Hervé
      Pagès.)

    • R CMD rtags works on platforms (such as OS X) with a
      XSI-conformant shell command echo. (PR#15231)

    • is.unsorted(NA) returns false as documented (rather than NA).

    • R CMD LINK did not know about sub-architectures.

    • system() and system2() are better protected against users who
      misguidedly have spaces in the temporary directory path.

    • file.show() and edit() are now more likely to work on file paths
      containing spaces.  (Where external utilities are used, not the
      norm on Windows nor in R.app which should previously have
      worked.)

    • Packages using the methods package are more likely to work when
      they import it but it is not attached.  (Several parts of its C
      code were looking for its R functions on the search path rather
      than in its namespace.)

    • lgamma(-x) is no longer NaN for very small x.

    • (Windows) system2() now respects specifying stdout and stderr as
      files if called from Rgui. (PR#15393)

    • Closing an x11() device whilst locator() or identify() is in
      progress no longer hangs R.  (PR#15253)

    • list.dirs(full.names = FALSE) was not implemented.  (PR#15170)

    • format() sometimes added unnecessary spaces.  (PR#15411)

    • all.equal(check.names = FALSE) would ignore the request to ignore
      the names and would check them as attributes.

    • The symbol set by tools::Rd2txt_options(itemBullet=) was not
      respected in some locales. (PR#15435)

    • mcMap() was not exported by package parallel. (PR#15439)

    • plot() for TukeyHSD objects did not balance dev.hold() and
      dev.flush() calls on multi-page plots.  (PR#15449)

CHANGES IN R 3.0.1:

  NEW FEATURES:

    • chooseCRANmirror() and chooseBioCmirror() gain an ind argument
      (like setRepositories()).

    • mcparallel has a new argument mc.interactive which can modify the
      interactive flag in the child process. The new default is FALSE
      which makes child processes non-interactive by default (this
      prevents lock-ups due to children waiting for interactive input).

    • scan() now warns when end-of-file occurs within a quoted string.

    • count.fields() is now consistent with scan() in its handling of
      newlines in quoted strings.  Instead of triggering an error, this
      results in the current line receiving NA as the field count, with
      the next line getting the total count of the two lines.

    • The default method of image() will plot axes of the class of xlim
      and ylim (and hence of x and y if there is a suitable range()
      method).  Based on a suggestion of Michael Sumner.

    • load() now has a verbose argument for debugging support, to print
      the names of objects just before loading them.

    • When loading a serialized object encounters a reference to a
      namespace which cannot be loaded, this is replaced by a reference
      to the global environment, with a warning.

    • pairs() gains a line.main option for title placement.

    • The remaining instances in which serialization to a raw vector
      was limited to 2GB have been unlimited on a 64-bit platform, and
      in most cases serialization to a vector of more than 1GB will be
      substantially faster.

  UTILITIES:

    • R CMD config now make use of personal Makevars files under ~/.R
      and a site file Makevars.site, in the same way as R CMD SHLIB and
      R CMD INSTALL.  This makes the utility more useful in package
      configure scripts.

      On Windows finding the personal files may require the environment
      variable HOME set.

      The old behaviour can be obtained with the new options
      --no-user-files and --no-site-files.

  PACKAGE INSTALLATION:

    • Alternatives to the site and user customization files
      Makevars.site and ~/.R/Makevars can be specified _via_ the
      environment variables R_MAKEVARS_SITE and R_MAKEVARS_USER
      respectively.  These can be used to suppress the use of the
      default files by setting an empty value (where possible) or a
      non-existent path.

  BUG FIXES:

    • sys.source() did not report error locations when keep.source =
      TRUE.

    • as.POSIXct.numeric was coercing origin using the tz argument and
      not "GMT" as documented (PR#14973).

    • The active binding to assign fields in reference classes has been
      cleaned up to reduce dependence on the class' package
      environment, also fixing bug in initializing read-only fields
      (inspired by a report from Hadley Wickham).

    • str(d) no longer gives an error when names(d) contain illegal
      multibyte strings (PR#15247).

    • Profiling of built-in functions with line.profiling= TRUE did not
      record the line from which they were called.

    • citation(pkg) dropped the header and footer specified in the
      CITATION file (PR#15257).

    • Quotes were handled differently when reading the first line and
      reading the rest, so read.table() misread some files that
      contained quote characters (PR#15245).

    • cat() with sep a character vector of length greater than one and
      more than one argument was using separators inconsistently
      (PR#15261).

    • On Windows in R 3.0.0, savePlot() failed because of an incorrect
      check on the argument count.

    • unzip(list = TRUE) returned Names as a factor and not a character
      vector (as documented) for the internal method.  (Noticed by Sean
      O'Riordain.)

    • contourLines() now checks more comprehensively for conformance of
      its x, y and z arguments (it was used incorrectly in package
      R2G2).

    • Saved graphics display lists are R version-specific.  Attempting
      to load workspaces containing them (or some other
      version-specific objects) aborted the load in R 3.0.0 and
      earlier; now it does a partial load and generates a warning
      instead.

    • In R 3.0.0, identify() and locator() did not record information
      correctly, so replaying a graph (e.g., by copying it to another
      device) would fail. (PR#15271)

    • Calling file.copy() or dirname() with the invalid input "" (which
      was being used in packages, despite not being a file path) could
      have caused a segfault.

      dirname("") is now "" rather than "." (unless it segfaulted).

    • supsmu() could read/write outside its input vectors for very
      short inputs (seen in package rms for n = 4).

    • as.dendrogram()'s hclust method uses less memory and hence gets
      considerably faster for large (n ~ 1000) clusterings, thanks to
      Daniel Müllner. (PR#15174)

    • The return value when all workers failed from
      parallel::mclapply(mc.preschedule = TRUE) was a list of strings
      and not of error objects.  (Spotted by Karl Forner and Bernd
      Bischl.)

    • In R 3.0.0, when help() found multiple pages with the same alias,
      the HTML display of all the selections was not produced.
      (PR#15282)

    • splinefun(method="monoH.FC") now produces a function with first
      argument named x and allows deriv=3, as documented. (PR#15273)

    • summaryRprof() would only read the first chunksize lines of an
      Rprof file produced with line.profiling=TRUE. By default, this is
      the first 100 seconds.  (PR#15288)

    • lsfit() produced an incorrect error message when argument x had
      more columns than rows or x had a different number of rows than
      y. (Spotted by Renaud Gaujoux.)

    • Binary operations on equal length vectors copied the class name
      from the second operand when the first had no class name, but did
      not set the object bit. (PR#15299)

    • The trace() method for reference generator objects failed after
      those objects became function definitions.

    • write.table() did not check that factors were constructed
      correctly, and so caused a segment fault when writing bad ones.
      (PR#15300)

    • The internal HTTP server no longer chokes on POST requests
      without body. It will also pass-through other request types for
      custom handlers (with the method stored in Request-Method header)
      instead of failing.

CHANGES IN R 3.0.0:

  SIGNIFICANT USER-VISIBLE CHANGES:

    • Packages need to be (re-)installed under this version (3.0.0) of
      R.

    • There is a subtle change in behaviour for numeric index values
      2^31 and larger.  These never used to be legitimate and so were
      treated as NA, sometimes with a warning.  They are now legal for
      long vectors so there is no longer a warning, and x[2^31] <- y
      will now extend the vector on a 64-bit platform and give an error
      on a 32-bit one.

    • It is now possible for 64-bit builds to allocate amounts of
      memory limited only by the OS.  It may be wise to use OS
      facilities (e.g., ulimit in a bash shell, limit in csh), to set
      limits on overall memory consumption of an R process,
      particularly in a multi-user environment.  A number of packages
      need a limit of at least 4GB of virtual memory to load.

      64-bit Windows builds of R are by default limited in memory usage
      to the amount of RAM installed: this limit can be changed by
      command-line option --max-mem-size or setting environment
      variable R_MAX_MEM_SIZE.

    • Negative numbers for colours are consistently an error:
      previously they were sometimes taken as transparent, sometimes
      mapped into the current palette and sometimes an error.

  NEW FEATURES:

    • identical() has a new argument, ignore.environment, used when
      comparing functions (with default FALSE as before).

    • There is a new option, options(CBoundsCheck=), which controls how
      .C() and .Fortran() pass arguments to compiled code.  If true
      (which can be enabled by setting the environment variable
      R_C_BOUNDS_CHECK to yes), raw, integer, double and complex
      arguments are always copied, and checked for writing off either
      end of the array on return from the compiled code (when a second
      copy is made).  This also checks individual elements of character
      vectors passed to .C().

      This is not intended for routine use, but can be very helpful in
      finding segfaults in package code.

    • In layout(), the limits on the grid size have been raised
      (again).

    • New simple provideDimnames() utility function.

    • Where methods for length() return a double value which is
      representable as an integer (as often happens for package
      Matrix), this is converted to an integer.

    • Matrix indexing of data frames by two-column numeric indices is
      now supported for replacement as well as extraction.

    • setNames() now has a default for its object argument, useful for
      a character result.

    • StructTS() has a revised additive constant in the loglik
      component of the result: the previous definition is returned as
      the loglik0 component.  However, the help page has always warned
      of a lack of comparability of log-likelihoods for non-stationary
      models.  (Suggested by Jouni Helske.)

    • The logic in aggregate.formula() has been revised.  It is now
      possible to use a formula stored in a variable; previously, it
      had to be given explicitly in the function call.

    • install.packages() has a new argument quiet to reduce the amount
      of output shown.

    • Setting an element of the graphics argument lwd to a negative or
      infinite value is now an error.  Lines corresponding to elements
      with values NA or NaN are silently omitted.

      Previously the behaviour was device-dependent.

    • Setting graphical parameters cex, col, lty, lwd and pch in par()
      now requires a length-one argument.  Previously some silently
      took the first element of a longer vector, but not always when
      documented to do so.

    • Sys.which() when used with inputs which would be unsafe in a
      shell (e.g., absolute paths containing spaces) now uses
      appropriate quoting.

    • as.tclObj() has been extended to handle raw vectors.  Previously,
      it only worked in the other direction.  (Contributed by Charlie
      Friedemann, PR#14939.)

    • New functions cite() and citeNatbib() have been added, to allow
      generation of in-text citations from "bibentry" objects.  A
      cite() function may be added to bibstyle() environments.

    • A sort() method has been added for "bibentry" objects.

    • The bibstyle() function now defaults to setting the default
      bibliography style. The getBibstyle() function has been added to
      report the name of the current default style.

    • scatter.smooth() now has an argument lpars to pass arguments to
      lines().

    • pairs() has a new log argument, to allow some or all variables to
      be plotted on logarithmic scale.  (In part, wish of PR#14919.)

    • split() gains a sep argument.

    • termplot() does a better job when given a model with interactions
      (and no longer attempts to plot interaction terms).

    • The parser now incorporates code from Romain Francois' parser
      package, to support more detailed computation on the code, such
      as syntax highlighting, comment-based documentation, etc.
      Functions getParseData() and getParseText() access the data.

    • There is a new function rep_len() analogous to rep.int() for when
      speed is required (and names are not).

    • The undocumented use rep(NULL, length.out = n) for n > 0 (which
      returns NULL) now gives a warning.

    • demo() gains an encoding argument for those packages with
      non-ASCII demos: it defaults to the package encoding where there
      is one.

    • strwrap() converts inputs with a marked encoding to the current
      locale: previously it made some attempt to pass through as bytes
      inputs invalid in the current locale.

    • Specifying both rate and scale to [dpqr]gamma is a warning (if
      they are essentially the same value) or an error.

    • merge() works in more cases where the data frames include
      matrices.  (Wish of PR#14974.)

    • optimize() and uniroot() no longer use a shared parameter object
      across calls.  (nlm(), nlminb() and optim() with numerical
      derivatives still do, as documented.)

    • The all.equal() method for date-times is now documented: times
      are regarded as equal (by default) if they differ by up to 1
      msec.

    • duplicated() and unique() gain a nmax argument which can be used
      to make them much more efficient when it is known that there are
      only a small number of unique entries.  This is done
      automatically for factors.

    • Functions rbinom(), rgeom(), rhyper(), rpois(), rnbinom(),
      rsignrank() and rwilcox() now return integer (not double)
      vectors.  This halves the storage requirements for large
      simulations.

    • sort(), sort.int() and sort.list() now use radix sorting for
      factors of less than 100,000 levels when method is not supplied.
      So does order() if called with a single factor, unless na.last =
      NA.

    • diag() as used to generate a diagonal matrix has been re-written
      in C for speed and less memory usage.  It now forces the result
      to be numeric in the case diag(x) since it is said to have ‘zero
      off-diagonal entries’.

    • backsolve() (and forwardsolve()) are now internal functions, for
      speed and support for large matrices.

    • More matrix algebra functions (e.g., chol() and solve()) accept
      logical matrices (and coerce to numeric).

    • sample.int() has some support for n >= 2^31: see its help for the
      limitations.

      A different algorithm is used for (n, size, replace = FALSE, prob
      = NULL) for n > 1e7 and size <= n/2.  This is much faster and
      uses less memory, but does give different results.

    • approxfun() and splinefun() now return a wrapper to an internal
      function in the stats namespace rather than a .C() or .Call()
      call.  This is more likely to work if the function is saved and
      used in a different session.

    • The functions .C(), .Call(), .External() and .Fortran() now give
      an error (rather than a warning) if called with a named first
      argument.

    • Sweave() by default now reports the locations in the source
      file(s) of each chunk.

    • clearPushBack() is now a documented interface to a long-existing
      internal call.

    • aspell() gains filters for R code, Debian Control Format and
      message catalog files, and support for R level dictionaries.  In
      addition, package utils now provides functions
      aspell_package_R_files() and aspell_package_C_files() for spell
      checking R and C level message strings in packages.

    • bibentry() gains some support for “incomplete” entries with a
      crossref field.

    • gray() and gray.colors() finally allow alpha to be specified.

    • monthplot() gains parameters to control the look of the reference
      lines.  (Suggestion of Ian McLeod.)

    • Added support for new %~% relation (“is distributed as”) in
      plotmath.

    • domain = NA is accepted by gettext() and ngettext(), analogously
      to stop() etc.

    • termplot() gains a new argument plot = FALSE which returns
      information to allow the plots to be modified for use as part of
      other plots, but does not plot them.  (Contributed by Terry
      Therneau, PR#15076.)

    • quartz.save(), formerly an undocumented part of R.app, is now
      available to copy a device to a quartz() device.  dev.copy2pdf()
      optionally does this for PDF output: quartz.save() defaults to
      PNG.

    • The default method of pairs() now allows text.panel = NULL and
      the use of <foo>.panel = NULL is now documented.

    • setRefClass() and getRefClass() now return class generator
      functions, similar to setClass(), but still with the reference
      fields and methods as before (suggestion of Romain Francois).

    • New functions bitwNot(), bitwAnd(), bitwOr() and bitwXor(), using
      the internal interfaces previously used for classes "octmode" and
      "hexmode".

      Also bitwShiftL() and bitwShiftR() for shifting bits in elements
      of integer vectors.

    • New option "deparse.cutoff" to control the deparsing of language
      objects such as calls and formulae when printing.  (Suggested by
      a comment of Sarah Goslee.)

    • colors() gains an argument distinct.

    • New demo(colors) and demo(hclColors), with utility functions.

    • list.files() (aka dir()) gains a new optional argument no.. which
      allows to exclude "." and ".." from listings.

    • Multiple time series are also of class "matrix"; consequently,
      head(), e.g., is more useful.

    • encodeString() preserves UTF-8 marked encodings.  Thus if factor
      levels are marked as UTF-8 an attempt is made to print them in
      UTF-8 in RGui on Windows.

    • readLines() and scan() (and hence read.table()) in a UTF-8 locale
      now discard a UTF-8 byte-order-mark (BOM).  Such BOMs are allowed
      but not recommended by the Unicode Standard: however Microsoft
      applications can produce them and so they are sometimes found on
      websites.

      The encoding name "UTF-8-BOM" for a connection will ensure that a
      UTF-8 BOM is discarded.

    • mapply(FUN, a1, ..) now also works when a1 (or a further such
      argument) needs a length() method (which the documented arguments
      never do).  (Requested by Hervé Pagès; with a patch.)

    • .onDetach() is supported as an alternative to .Last.lib.  Unlike
      .Last.lib, this does not need to be exported from the package's
      namespace.

    • The srcfile argument to parse() may now be a character string, to
      be used in error messages.

    • The format() method for ftable objects gains a method argument,
      propagated to write.ftable() and print(), allowing more compact
      output, notably for LaTeX formatting, thanks to Marius Hofert.

    • The utils::process.events() function has been added to trigger
      immediate event handling.

    • Sys.which() now returns NA (not "") for NA inputs (related to
      PR#15147).

    • The print() method for class "htest" gives fewer trailing spaces
      (wish of PR#15124).

      Also print output from HoltWinters(), nls() and others.

    • loadNamespace() allows a version specification to be given, and
      this is used to check version specifications given in the Imports
      field when a namespace is loaded.

    • setClass() has a new argument, slots, clearer and less ambiguous
      than representation.  It is recommended for future code, but
      should be back-compatible.  At the same time, the allowed slot
      specification is slightly more general.  See the documentation
      for details.

    • mget() now has a default for envir (the frame from which it is
      called), for consistency with get() and assign().

    • close() now returns an integer status where available, invisibly.
      (Wish of PR#15088.)

    • The internal method of tar() can now store paths too long for the
      ustar format, using the (widely supported) GNU extension.  It can
      also store long link names, but these are much less widely
      supported.  There is support for larger files, up to the ustar
      limit of 8GB.

    • Local reference classes have been added to package methods.
      These are a technique for avoiding unneeded copying of large
      components of objects while retaining standard R functional
      behavior.  See ?LocalReferenceClasses.

    • untar() has a new argument restore_times which if false (not the
      default) discards the times in the tarball.  This is useful if
      they are incorrect (some tarballs submitted to CRAN have times in
      a local time zone or many years in the past even though the
      standard required them to be in UTC).

    • replayplot() cannot (and will not attempt to) replay plots
      recorded under R < 3.0.0.  It may crash the R session if an
      attempt is made to replay plots created in a different build of R
      >= 3.0.0.

    • Palette changes get recorded on the display list, so replaying
      plots (including when resizing screen devices and using
      dev.copy()) will work better when the palette is changed during a
      plot.

    • chol(pivot = TRUE) now defaults to LAPACK, not LINPACK.

    • The parse() function has a new parameter keep.source, which
      defaults to options("keep.source").

    • Profiling via Rprof() now optionally records information at the
      statement level, not just the function level.

    • The Rprof() function now quotes function names in in its output
      file on Windows, to be consistent with the quoting in Unix.

    • Profiling via Rprof() now optionally records information about
      time spent in GC.

    • The HTML help page for a package now displays non-vignette
      documentation files in a more accessible format.

    • To support options(stringsAsFactors = FALSE), model.frame(),
      model.matrix() and replications() now automatically convert
      character vectors to factors without a warning.

    • The print method for objects of class "table" now detects tables
      with 0-extents and prints the results as, e.g., < table of extent
      0 x 1 x 2 >. (Wish of PR#15198.)

    • Deparsing involving calls to anonymous functions has been made
      closer to reversible by the addition of extra parentheses.

    • The function utils::packageName() has been added as a lightweight
      version of methods::getPackageName().

    • find.package(lib.loc = NULL) now treats loaded namespaces
      preferentially in the same way as attached packages have been for
      a long time.

    • In Windows, the Change Directory dialog now defaults to the
      current working directory, rather than to the last directory
      chosen in that dialog.

    • available.packages() gains a "license/restricts_use" filter which
      retains only packages for which installation can proceed solely
      based on packages which are guaranteed not to restrict use.

    • New check_packages_in_dir() function in package tools for
      conveniently checking source packages along with their reverse
      dependencies.

    • R's completion mechanism has been improved to handle help
      requests (starting with a question mark).  In particular, help
      prefixes are now supported, as well as quoted help topics.  To
      support this, completion inside quotes are now handled by R by
      default on all platforms.

    • The memory manager now allows the strategy used to balance
      garbage collection and memory growth to be controlled by setting
      the environment variable R_GC_MEM_GROW. See ?Memory for more
      details.

    • (‘For experts only’, as the introductory manual says.)  The use
      of environment variables R_NSIZE and R_VSIZE to control the
      initial (= minimum) garbage collection trigger for number of cons
      cels and size of heap has been restored: they can be overridden
      by the command-line options --min-nsize and --min-vsize; see
      ?Memory.

    • On Windows, the device name for bitmap devices as reported by
      .Device and .Devices no longer includes the file name.  This is
      for consistency with other platforms and was requested by the
      lattice maintainer.

      win.metafile() still uses the file name: the exact form is used
      by package tkrplot.

    • set.seed(NULL) re-initializes .Random.seed as done at the
      beginning of the session if not already set.  (Suggestion of Bill
      Dunlap.)

    • The breaks argument in hist.default() can now be a function that
      returns the breakpoints to be used (previously it could only
      return the suggested number of breakpoints).

    • File share/licenses/licenses.db has some clarifications,
      especially as to which variants of ‘BSD’ and ‘MIT’ is intended
      and how to apply them to packages.  The problematic licence
      ‘Artistic-1.0’ has been removed.

  LONG VECTORS:

  This section applies only to 64-bit platforms.

    • There is support for vectors longer than 2^31 - 1 elements.  This
      applies to raw, logical, integer, double, complex and character
      vectors, as well as lists.  (Elements of character vectors remain
      limited to 2^31 - 1 bytes.)

    • Most operations which can sensibly be done with long vectors
      work: others may return the error ‘long vectors not supported
      yet’.  Most of these are because they explicitly work with
      integer indices (e.g., anyDuplicated() and match()) or because
      other limits (e.g., of character strings or matrix dimensions)
      would be exceeded or the operations would be extremely slow.

    • length() returns a double for long vectors, and lengths can be
      set to 2^31 or more by the replacement function with a double
      value.

    • Most aspects of indexing are available.  Generally double-valued
      indices can be used to access elements beyond 2^31 - 1.

    • There is some support for matrices and arrays with each dimension
      less than 2^31 but total number of elements more than that.  Only
      some aspects of matrix algebra work for such matrices, often
      taking a very long time.  In other cases the underlying Fortran
      code has an unstated restriction (as was found for complex
      svd()).

    • dist() can produce dissimilarity objects for more than 65536 rows
      (but for example hclust() cannot process such objects).

    • serialize() to a raw vector is unlimited in size (except by
      resources).

    • The C-level function R_alloc can now allocate 2^35 or more bytes.

    • agrep() and grep() will return double vectors of indices for long
      vector inputs.

    • Many calls to .C() have been replaced by .Call() to allow long
      vectors to be supported (now or in the future).  Regrettably
      several packages had copied the non-API .C() calls and so failed.

    • .C() and .Fortran() do not accept long vector inputs.  This is a
      precaution as it is very unlikely that existing code will have
      been written to handle long vectors (and the R wrappers often
      assume that length(x) is an integer).

    • Most of the methods for sort() work for long vectors.

      rank(), sort.list() and order() support long vectors (slowly
      except for radix sorting).

    • sample() can do uniform sampling from a long vector.

  PERFORMANCE IMPROVEMENTS:

    • More use has been made of R objects representing registered entry
      points, which is more efficient as the address is provided by the
      loader once only when the package is loaded.

      This has been done for packages base, methods, splines and tcltk:
      it was already in place for the other standard packages.

      Since these entry points are always accessed by the R entry
      points they do not need to be in the load table which can be
      substantially smaller and hence searched faster.  This does mean
      that .C / .Fortran / .Call calls copied from earlier versions of
      R may no longer work - but they were never part of the API.

    • Many .Call() calls in package base have been migrated to
      .Internal() calls.

    • solve() makes fewer copies, especially when b is a vector rather
      than a matrix.

    • eigen() makes fewer copies if the input has dimnames.

    • Most of the linear algebra functions make fewer copies when the
      input(s) are not double (e.g., integer or logical).

    • A foreign function call (.C() etc) in a package without a PACKAGE
      argument will only look in the first DLL specified in the
      NAMESPACE file of the package rather than searching all loaded
      DLLs.  A few packages needed PACKAGE arguments added.

    • The @<- operator is now implemented as a primitive, which should
      reduce some copying of objects when used.  Note that the operator
      object must now be in package base: do not try to import it
      explicitly from package methods.

  PACKAGE INSTALLATION:

    • The transitional support for installing packages without
      namespaces (required since R 2.14.0) has been removed.  R CMD
      build will still add a namespace, but a .First.lib() function
      will need to be converted.

      R CMD INSTALL no longer adds a namespace (so installation will
      fail), and a .First.lib() function in a package will be ignored
      (with an installation warning for now).

      As an exception, packages without a R directory and no NAMESPACE
      file can still be installed.

    • Packages can specify in their DESCRIPTION file a line like
      
           Biarch: yes

      to be installed on Windows with --force-biarch.

    • Package vignettes can now be processed by other engines besides
      Sweave; see ‘Writing R Extensions’ and the tools::vignetteEngine
      help topic for details.

    • The *.R tangled source code for vignettes is now included in
      tarballs when R CMD build is used to produce them.  In R 3.0.0,
      *.R files not in the sources will be produced at install time,
      but eventually this will be dropped.

    • The package type "mac.binary" now looks in a path in the
      repository without any Mac subtype (which used to be universal or
      leopard): it looks in bin/macosx/contrib/3.0 rather than
      bin/macosx/leopard/contrib/2.15).  This is the type used for the
      CRAN binary distribution for OS X as from R 3.0.0.

    • File etc/Makeconf makes more use of the macros $(CC), $(CXX),
      $(F77) and $(FC), so the compiler in use can be changed by
      setting just these (and if necessary the corresponding flags and
      FLIBS) in file ~/.R/Makevars.

      This is convenient for those working with binary distributions of
      R, e.g. on OS X.

  UTILITIES:

    • R CMD check now gives a warning rather than a note if it finds
      calls to abort, assert or exit in compiled code, and has been
      able to find the .o file in which the calls occur.

      Such calls can terminate the R process which loads the package.

    • The location of the build and check environment files can now be
      specified by the environment variables R_BUILD_ENVIRON and
      R_CHECK_ENVIRON, respectively.

    • R CMD Sweave gains a --compact option to control possibly
      reducing the size of the PDF file it creates when --pdf is given.

    • R CMD build now omits Eclipse's .metadata directories, and R CMD
      check warns if it finds them.

    • R CMD check now does some checks on functions defined within
      reference classes, including of .Call() etc calls.

    • R CMD check --as-cran notes assignments to the global
      environment, calls to data() which load into the global
      environment, and calls to attach().

    • R CMD build by default uses the internal method of tar() to
      prepare the tarball.  This is more likely to produce a tarball
      compatible with R CMD INSTALL and R CMD check: an external tar
      program, including options, can be specified _via_ the
      environment variable R_BUILD_TAR.

    • tools::massageExamples() is better protected against packages
      which re-define base functions such as cat() and get() and so can
      cause R CMD check to fail when checking examples.

    • R CMD javareconf has been enhanced to be more similar to the code
      used by configure.

      There is now a test that a JNI program can be compiled (like
      configure did) and only working settings are used.

      It makes use of custom settings from configuration recorded in
      etc/javaconf.

    • The --no-vignettes argument of R CMD build has been renamed to
      the more accurate --no-build-vignettes: its action has always
      been to (re)build vignettes and never omitted them.

      R CMD check accepts --no-build-vignettes as a preferred synonym
      for --no-rebuild-vignettes.

  DEPRECATED AND DEFUNCT:

    • The ENCODING argument to .C() is defunct.  Use iconv() instead.

    • The .Internal(eval.with.vis) non-API function has been removed.

    • Support for the converters for use with .C() has been removed,
      including the oft misused non-API header R_ext/RConverters.h.

    • The previously deprecated uses of array() with a 0-length dim
      argument and tapply() with a 0-length INDEX list are now errors.

    • Translation packages are defunct.

    • Calling rep() or rep.int() on a pairlist or other non-vector
      object is now an error.

    • Several non-API entry points have been transferred to packages
      (e.g., R_zeroin2) or replaced by different non-API entry points
      (e.g., R_tabulate).

    • The ‘internal’ graphics device invoked by
      .Call("R_GD_nullDevice", package = "grDevices") has been removed:
      use pdf(file = NULL) instead.

    • The .Fortran() entry point "dqrls" which has not been used by R
      since version 2.15.1 is no longer available.

    • Functions traceOn() and traceOff() in package methods are now
      defunct.

    • Function CRAN.packages() is finally defunct.

    • Use of col2rgb(0) is defunct: use par("bg") or NA instead.

    • The long-defunct functions Rd_parse(), anovalist.lm(),
      categpry(), clearNames(), gammaCody(), glm.fit.null(),
      lm.fit.null(), lm.wfit.null(), manglePackageNames(),
      mauchley.test(), package.contents(), print.coefmat(),
      reshapeLong(), reshapeWide(), tkclose(), tkcmd(), tkfile.dir(),
      tkfile.tail(), tkopen(), tkputs(), tkread(), trySilent() and
      zip.file.extract() have been removed entirely (but are still
      documented in the help system).

    • The unused dataPath argument to attachNamespace() has been
      removed.

    • grid.prompt() has been removed: use devAskNewPage() instead.

    • The long-deprecated intensities component is no longer returned
      by hist().

    • mean() for data frames and sd() for data frames and matrices are
      defunct.

    • chol(pivot = FALSE, LINPACK = TRUE), ch2inv(LINPACK = TRUE),
      eigen(EISPACK = TRUE), solve(LINPACK = TRUE) and svd(LINPACK =
      TRUE) are defunct: LAPACK will be used, with a warning.

    • The keep.source argument to library() and require() is defunct.
      This option needs to be set at install time.

    • Documentation for real(), as.real() and is.real() has been moved
      to ‘defunct’ and the functions removed.

    • The maxRasters argument of pdf() (unused since R 2.14.0) has been
      removed.

    • The unused fontsmooth argument has been removed from the quartz()
      device.

    • All the (non-API) EISPACK entry points in R have been removed.

    • chol(pivot = TRUE, LINPACK = TRUE) is deprecated.

    • The long-deprecated use of \synopsis in the Usage section of .Rd
      files will be removed in R 3.1.0.

    • .find.package() and .path.package() are deprecated: only the
      public versions without the dot have ever been in the API.

    • In a package's DESCRIPTION file,
      
          License: X11

      is deprecated, since it includes ‘Copyright (C) 1996 X
      Consortium’ which cannot be appropriate for a current R package.
      Use ‘MIT’ or ‘BSD_2_clause’ instead.

  CODE MIGRATION:

    • The C code underlying base graphics has been migrated to the
      graphics package (and hence no longer uses .Internal() calls).

    • Most of the .Internal() calls used in the stats package have been
      migrated to C code in that package.

      This means that a number of .Internal() calls which have been
      used by packages no longer exist, including .Internal(cor)
      .Internal(cov), .Internal(optimhess) and
      .Internal(update.formula).

    • Some .External() calls to the base package (really to the R
      executable or shared library) have been moved to more appropriate
      packages.  Packages should not have been using such calls, but
      some did (mainly those used by integrate()).

  PACKAGE parallel:

    • There is a new function mcaffinity() which allows getting or
      setting the CPU affinity mask for the current R process on
      systems that supports this (currently only Linux has been tested
      successfully).  It has no effect on systems which do not support
      process affinity.  Users are not expected to use this function
      directly (with the exception of fixing libraries that break
      affinity settings like OpenBLAS) - the function is rather
      intended to support affinity control in high-level parallel
      functions.  In the future, R may supplement lack of affinity
      control in the OS by its own bookkeeping via mcaffinity() related
      to processes and threads it spawns.

    • mcparallel() has a new argument mc.affinity which attempts to set
      the affinity of the child process according to the specification
      contained therein.

    • The port used by socket clusters is chosen randomly: this should
      help to avoid clashes observed when two users of a multi-user
      machine try to create a cluster at the same time.  To reproduce
      the previous behaviour set environment variable R_PARALLEL_PORT
      to 10187.

  C-LEVEL FACILITIES:

    • There has been some minor re-organization of the non-API header
      files.  In particular, Rinternals.h no longer includes the
      non-API header R_exts/PrtUtil.h, and that no longer includes
      R_exts/Print.h.

    • Passing NULL to .C() is now an error.

    • .C() and .Fortran() now warn if "single" arguments are used with
      DUP = FALSE, as changes to such arguments are not returned to the
      caller.

    • C entry points R_qsort and R_qsort_I now have start and end as
      size_t to allow them to work with longer vectors on 64-bit
      platforms.  Code using them should be recompiled.

    • A few recently added C entry points were missing the remapping to
      Rf_, notably [dpq]nbinom_mu.

    • Some of the interface pointers formerly available only to R.app
      are now available to front-ends on all Unix-alikes: one has been
      added for the interface to View().

    • PACKAGE = "" is now an error in .C() etc calls: it was always
      contrary to the documentation.

    • Entry point rcont2 has been migrated to package stats and so is
      no longer available.

    • R_SVN_REVISION in Rversion.h is now an integer (rather than a
      string) and hence usable as e.g.  #if R_SVN_REVISION < 70000.

    • The entry points rgb2hsv and hsv2rgb have been migrated to
      package grDevices and so are no longer available.

    • R_GE_version has been increased to 10 and name2col removed (use
      R_GE_str2col instead).  R internal colour codes are now defined
      using the typedef rcolor.

    • The REPROTECT macro now checks that the protect index is valid.

    • Several non-API entry points no longer used by R have been
      removed, including the Fortran entry points chol, chol2inv, cg,
      ch and rg, and the C entry points Brent_fmin, fft_factor and
      fft_work.

    • If a .External call is registered with a number of arguments
      (other than -1), the number of arguments passed is checked for
      each call (as for other foreign function calls).

    • It is now possible to write custom connection implementations
      outside core R using R_ext/Connections.h.  Please note that the
      implementation of connections is still considered internal and
      may change in the future (see the above file for details).

  INTERNATIONALIZATION:

    • The management of translations has been converted to R code: see
      ?tools::update_pkg_po.

    • The translations for the R interpreter and RGui.exe are now part
      of the base package (rather than having sources in directory po
      and being installed to share/locale).  Thus the base package
      supports three translation domains, R-base, R and RGui.

    • The compiled translations which ship with R are all installed to
      the new package translations for easier updating.  The first
      package of that name found on .libPaths() at the start of the R
      session will be used.  (It is possible messages will be used
      before .libPaths() is set up in which case the default
      translations will be used: set environment variable
      R_TRANSLATIONS to point to the location of the intended
      translations package to use this right from the start.)

    • The translations form a separate group in the Windows installer,
      so can be omitted if desired.

    • The markup for many messages has been changed to make them easier
      to translate, incorporating suggestions from Łukasz Daniel.

  INSTALLATION:

    • There is again support for building without using the C ‘long
      double’ type.  This is required by C99, but system
      implementations can be slow or flawed.  Use configure option
      --disable-long-double.

    • make pdf and make install-pdf now make and install the full
      reference index (including all base and recommended packages).

    • The 'reference manual' on the Windows GUI menu and included in
      the installer is now the full reference index, including all base
      and recommended packages.

    • R help pages and manuals have no ISBNs because ISBN rules no
      longer allow constantly changing content to be assigned an ISBN.

    • The Windows installer no longer installs a Start Menu link to the
      static help pages; as most pages are generated dynamically, this
      led to a lot of broken links.

    • Any custom settings for Java configuration are recorded in file
      etc/javaconf for subsequent use by R CMD javareconf.

    • There is now support for makeinfo version 5.0 (which requires a
      slightly different .texi syntax).

    • The minimum versions for --use-system-zlib and --use-system-pcre
      are now tested as 1.2.5 and 8.10 respectively.

    • On Windows, the stack size is reduced to 16MB on 32-bit systems:
      misguided users were launching many threads without controlling
      the stack size.

    • configure no longer looks for file ~/.Rconfig: ~/.R/config has
      long been preferred.

  BUG FIXES:

    • When R CMD build is run in an encoding other than the one
      specified in the package's DESCRIPTION file it tries harder to
      expand the authors@R field in the specified encoding.  (PR#14958)

    • If R CMD INSTALL is required to expand the authors@R field of the
      DESCRIPTION file, it tries harder to do so in the encoding
      specified for the package (rather than using ASCII escapes).

    • Fix in package grid for pushing a viewport into a layout cell,
      where the layout is within a viewport that has zero physical
      width OR where the layout has zero total relative width (likewise
      for height).  The layout column widths (or row heights) in this
      case were being calculated with non-finite values.  (Reported by
      Winston Chang.)

    • solve(A, b) for a vector b gave the answer names from colnames(A)
      for LINPACK = TRUE but not in the default case.

    • La.svd() accepts logical matrices (as documented, and as svd()
      did).

    • legend() now accepts negative pch values, in the same way
      points() long has.

    • Parse errors when installing files now correctly display the name
      of the file containing the bad code.

    • In Windows, tcltk windows were not always properly constructed.
      (PR#15150)

    • The internal functions implementing parse(), tools::parseLatex()
      and tools::parse_Rd() were not reentrant, leading to errors in
      rare circumstances such as a garbage collection triggering a
      recursive call.

    • Field assignments in reference class objects via $<- were not
      being checked because the magic incantation to turn methods on
      for that primitive operator had been inadvertently omitted.

    • setHook(hookname, value, action="replace") set the hook to be the
      value, rather than a list containing the value as documented.
      (PR#15167)

    • If a package used a NEWS.Rd file, the main HTML package index
      page did not link to it.  (Reported by Dirk Eddelbuettel.)

    • The primitive implementation of @<- was not checking the class of
      the replacement.  It now does a check, quicker but less general
      than slot<-. See the help.

    • split(x, f) now recycles classed objects x in the same way as
      vectors.  (Reported by Martin Morgan.)

    • pbeta(.28, 1/2, 2200, lower.tail=FALSE, log.p=TRUE) is no longer
      -Inf; ditto for corresponding pt() and pf() calls, such as pt(45,
      df=5000, lower.tail=FALSE, log.p=TRUE). (PR#15162)

    • The Windows graphics device would crash R if a user attempted to
      load the graphics history from a variable that was not a saved
      history. (PR#15230)

    • The workspace size for the predict() method for loess() could
      exceed the maximum integer size.  (Reported by Hiroyuki
      Kawakatsu.)

    • ftable(x, row.vars, col.vars) now also works when the *.vars
      arguments are (integer or character vectors) of length zero.

    • Calling cat() on a malformed UTF-8 string could cause the Windows
      GUI to lock up. (PR#15227)

    • removeClass(cc) gave "node stack overflow" for some class
      definitions containing "array" or "matrix".

CHANGES in previous versions:

  • Older news can be found in text format in files NEWS.0, NEWS.1 and
    NEWS.2 in the doc directory.  News in HTML format for R versions
    from 2.10.0 to 2.15.3 is in doc/html/NEWS.2.html.

