R News

CHANGES IN R VERSION 2.12.2:

  SIGNIFICANT USER-VISIBLE CHANGES:

    • Complex arithmetic (notably z^n for complex z and integer n) gave
      incorrect results since R 2.10.0 on platforms without C99 complex
      support.  This and some lesser issues in trignometric functions
      have been corrected.

      Such platforms were rare (we know of Cygwin and FreeBSD).
      However, because of new compiler optimizations in the way complex
      arguments are handled, the same code was selected on x86_64 Linux
      with gcc 4.5.x at the default -O2 optimization (but not at -O).

    • There is a workaround for crashes seen with several packages on
      systems using zlib 1.2.5: see the INSTALLATION section.

  NEW FEATURES:

    • PCRE has been updated to 8.12 (two bug-fix releases since 8.10).

    • rep(), seq(), seq.int() and seq_len() report more often when the
      first element is taken of an argument of incorrect length.

    • The Cocoa back-end for the quartz() graphics device on Mac OS X
      provides a way to disable event loop processing temporarily
      (useful, e.g., for forked instances of R).

    • kernel()'s default for m was not appropriate if coef was a set of
      coefficients.  (Reported by Pierre Chausse.)

    • bug.report() has been updated for the current R bug tracker,
      which does not accept emailed submissions.

    • R CMD check now checks for the correct use of $(LAPACK_LIBS) (as
      well as $(BLAS_LIBS)), since several CRAN recent submissions have
      ignored ‘Writing R Extensions’.

  INSTALLATION:

    • The zlib sources in the distribution are now built with all
      symbols remapped: this is intended to avoid problems seen with
      packages such as XML and rggobi which link to zlib.so.1 on
      systems using zlib 1.2.5.

    • The default for FFLAGS and FCFLAGS with gfortran on x86_64 Linux
      has been changed back to -g -O2: however, setting -g -O may still
      be needed for gfortran 4.3.x.

  PACKAGE INSTALLATION:

    • A LazyDataCompression field in the DESCRIPTION file will be used
      to set the value for the --data-compress option of R CMD INSTALL.

    • Files R/sysdata.rda of more than 1Mb are now stored in the
      lazyload daabase using xz compression: this for example halves
      the installed size of package Imap.

    • R CMD INSTALL now ensures that directories installed from inst
      have search permission for everyone.

      It no longer installs files inst/doc/Rplots.ps and
      inst/doc/Rplots.pdf.  These are almost certainly left-overs from
      Sweave runs, and are often large.

  DEPRECATED & DEFUNCT:

    • The ‘experimental’ alternative specification of a name space via
      .Export() etc is now deprecated.

    • zip.file.extract() is now deprecated.

    • Zip-ing data sets in packages (and hence R CMD INSTALL
      --use-zip-data and the ZipData: yes field in a DESCRIPTION file)
      is deprecated: using efficiently compressed .rda images and
      lazy-loading of data has superseded it.

  BUG FIXES:

    • identical() could in rare cases generate a warning about
      non-pairlist attributes on CHARSXPs.  As these are used for
      internal purposes, the attribute check should be skipped.
      (Reported by Niels Richard Hansen).

    • If the filename extension (usually .Rnw) was not included in a
      call to Sweave(), source references would not work properly and
      the keep.source option failed.  (PR#14459)

    • format.data.frame() now keeps zero character column names.

    • pretty(x) no longer raises an error when x contains solely
      non-finite values. (PR#14468)

    • The plot.TukeyHSD() function now uses a line width of 0.5 for its
      reference lines rather than lwd = 0 (which caused problems for
      some PDF and PostScript viewers).

    • The big.mark argument to prettyNum(), format(), etc. was inserted
      reversed if it was more than one character long.

    • R CMD check failed to check the filenames under man for Windows'
      reserved names.

    • The "Date" and "POSIXt" methods for seq() could overshoot when to
      was supplied and by was specified in months or years.

    • The internal method of untar() now restores hard links as file
      copies rather than symbolic links (which did not work for
      cross-directory links).

    • unzip() did not handle zip files which contained filepaths with
      two or more leading directories which were not in the zipfile and
      did not already exist.  (It is unclear if such zipfiles are valid
      and the third-party C code used did not support them, but
      PR#14462 created one.)

    • combn(n, m) now behaves more regularly for the border case m = 0.
      (PR#14473)

    • The rendering of numbers in plotmath expressions (e.g.
      expression(10^2)) used the current settings for conversion to
      strings rather than setting the defaults, and so could be
      affected by what has been done before.  (PR#14477)

    • The methods of napredict() and naresid() for na.action =
      na.exclude fits did not work correctly in the very rare event
      that every case had been omitted in the fit.  (Reported by Simon
      Wood.)

    • weighted.residuals(drop0=TRUE) returned a vector when the
      residuals were a matrix (e.g. those of class "mlm").  (Reported
      by Bill Dunlap.)

    • Package HTML index files <pkg>/html/00Index.html were generated
      with a stylesheet reference that was not correct for static
      browsing in libraries.

    • ccf(na.action = na.pass) was not implemented.

    • The parser accepted some incorrect numeric constants, e.g. 20x2.
      (Reported by Olaf Mersmann.)

    • format(*, zero.print) did not always replace the full zero parts.

    • Fixes for subsetting or subassignment of "raster" objects when
      not both i and j are specified.

    • R CMD INSTALL was not always respecting the ZipData: yes field of
      a DESCRIPTION file (although this is frequently incorrectly
      specified for packages with no data or which specify lazy-loading
      of data).

      R CMD INSTALL --use-zip-data was incorrectly implemented as
      --use-zipdata since R 2.9.0.

    • source(file, echo=TRUE) could fail if the file contained #line
      directives.  It now recovers more gracefully, but may still
      display the wrong line if the directive gives incorrect
      information.

    • atan(1i) returned NaN+Infi (rather than 0+Infi) on platforms
      without C99 complex support.

    • library() failed to cache S4 metadata (unlike loadNamespace())
      causing failures in S4-using packages without a namespace (e.g.
      those using reference classes).

    • The function qlogis(lp, log.p=TRUE) no longer prematurely
      overflows to Inf when exp(lp) is close to 1.

    • Updating S4 methods for a group generic function requires
      resetting the methods tables for the members of the group (patch
      contributed by Martin Morgan).

    • In some circumstances (including for package XML), R CMD INSTALL
      installed version-control directories from source packages.

    • Added PROTECT calls to some constructed expressions used in C
      level eval calls.

    • utils:::create.post() (used by bug.report() and help.request())
      failed to quote arguments to the mailer, and so often failed.

    • bug.report() was naive about how to extract maintainer email
      addresses from package descriptions, so would often try mailing
      to incorrect addresses.

    • debugger() could fail to read the environment of a call to a
      function with a ... argument.  (Reported by Charlie Roosen.)

    • prettyNum(c(1i, NA), drop0=TRUE) or str(NA_complex_) now work
      correctly.

CHANGES IN R VERSION 2.12.1:

  NEW FEATURES:

    • The DVI/PDF reference manual now includes the help pages for all
      the standard packages: splines, stats4 and tcltk were previously
      omitted (intentionally).

    • <URL: http://www.rforge.net> has been added to the default set of
      repositories known to setRepositories().

    • xz-utils has been updated to version 5.0.0.

    • reshape() now makes use of sep when forming names during
      reshaping to wide format.  (PR#14435)

    • legend() allows the length of lines to be set by the end user
      _via_ the new argument seg.len.

    • New S4 reference class utility methods copy(), field(),
      getRefClass() and getClass() have been added to package methods.

    • When a character value is used for the EXPR argument in switch(),
      a warning is given if more than one unnamed alternative value is
      given.  This will become an error in R 2.13.0.

    • StructTS(type = "BSM") now allows series with just two seasons.
      (Reported by Birgit Erni.)

  INSTALLATION:

    • The PDF reference manual is now built as PDF version 1.5 with
      object compression, which on platforms for which this is not the
      default (notably MiKTeX) halves its size.

    • Variable FCLIBS can be set during configuration, for any
      additional library flags needed when linking a shared object with
      the Fortran 9x compiler.  (Needed with Solaris Studio 12.2.)

  BUG FIXES:

    • seq.int() no longer sometimes evaluates arguments twice.
      (PR#14388)

    • The data.frame method of format() failed if a column name was
      longer than 256 bytes (the maximum length allowed for an R name).

    • predict(<lm object>, type ="terms", ...) failed if both terms and
      interval were specified.  (Reported by Bill Dunlap.)

      Also, if se.fit = TRUE the standard errors were reported for all
      terms, not just those selected by a non-null terms.

    • The TRE regular expressions engine could terminate R rather than
      give an error when given certain invalid regular expressions.
      (PR#14398)

    • cmdscale(eig = TRUE) was documented to return n-1 eigenvalues but
      in fact only returned k.  It now returns all n eigenvalues.

      cmdscale(add = TRUE) failed to centre the return configuration
      and sometimes lost the labels on the points.  Its return value
      was described wrongly (it is always a list and contains component
      ac).

    • promptClass() in package methods now works for reference classes
      and gives a suitably specialized skeleton of documentation.

      Also, callSuper() now works via the methods() invocation as well
      as for initially specified methods.

    • download.file() could leave the destination file open if the URL
      was not able to be opened.  (PR#14414)

    • Assignment of an environment to functions or as an attribute to
      other objects now works for S4 subclasses of "environment".

    • Use of [[<- for S4 subclasses of "environment" generated an
      infinite recursion from the method.  The method has been replaced
      by internal code.

    • In a reference class S4 method, callSuper() now works in
      initialize() methods when there is no explicit superclass method.

    • ! dropped attributes such as names and dimensions from a
      length-zero argument.  (PR#14424)

    • When list2env() created an environment it was missing a PROTECT
      call and so was vulnerable to garbage collection.

    • Sweave() with keep.source=TRUE dropped comments at the start and
      end of code chunks.  It could also fail when \SweaveInput was
      combined with named chunks.

    • The Fortran code used by nls(algorithm = "port") could
      infinite-loop when compiled with high optimization on a modern
      version of gcc, and SAFE_FFLAGS is now used to make this less
      likely.  (PR#14427, seen with 32-bit Windows using gcc 4.5.0 used
      from R 2.12.0.)

    • sapply() with default simplify = TRUE and mapply() with default
      SIMPLIFY = TRUE wrongly simplified language-like results, as,
      e.g., in mapply(1:2, c(3,7), FUN = function(i,j) call(':',i,j)).

    • Backreferences to undefined patterns in [g]sub(pcre = TRUE) could
      cause a segfault.  (PR#14431)

    • The format() (and hence the print()) method for class "Date"
      rounded fractional dates towards zero: it now always rounds them
      down.

    • Reference S4 class creation could generate ambiguous inheritance
      patterns under very special circumstances.

    • [[<- turned S4 subclasses of "environment" into plain
      environments.

    • Long titles for help pages were truncated in package indices and
      a few other places.

    • Additional utilities now work correctly with S4 subclasses of
      "environment" (rm, locking tools and active bindings).

    • spec.ar() now also work for the "ols" method.  (Reported by
      Hans-Ruedi Kuensch.)

    • The initialization of objects from S4 subclasses of "environment"
      now allocates a new environment object.

    • R CMD check has more protection against (probably erroneous)
      example or test output which is invalid in the current locale.

    • qr.X() with column names and pivoting now also pivots the column
      names.  (PR#14438)

    • unit.pmax() and unit.pmin() in package grid gave incorrect
      results when all inputs were of length 1.  (PR#14443)

    • The parser for NAMESPACE files ignored misspelled directives,
      rather than signalling an error.  For 2.12.x a warning will be
      issued, but this will be correctly reported as an error in later
      releases. (Reported by Charles Berry.)

    • Fix for subsetting of "raster" objects when only one of i or j is
      specified.

    • grid.raster() in package grid did not accept "nativeRaster"
      objects (like rasterImage() does).

    • Rendering raster images in PDF output was resetting the clipping
      region.

    • Rendering of raster images on Cairo X11 device was wrong,
      particularly when a small image was being scaled up using
      interpolation.

      With Cairo < 1.6, will be better than before, though still a
      little clunky.  With Cairo >= 1.6, should be sweet as.

    • Several bugs fixed in read.DIF(): single column inputs caused
      errors, cells marked as "character" could be converted to other
      types, and (in Windows) copying from the clipboard failed.

CHANGES IN R VERSION 2.12.0:

  NEW FEATURES:

    • Reading a package's CITATION file now defaults to ASCII rather
      than Latin-1: a package with a non-ASCII CITATION file should
      declare an encoding in its DESCRIPTION file and use that encoding
      for the CITATION file.

    • difftime() now defaults to the "tzone" attribute of "POSIXlt"
      objects rather than to the current timezone as set by the default
      for the tz argument.  (Wish of PR#14182.)

    • pretty() is now generic, with new methods for "Date" and "POSIXt"
      classes (based on code contributed by Felix Andrews).

    • unique() and match() are now faster on character vectors where
      all elements are in the global CHARSXP cache and have unmarked
      encoding (ASCII).  Thanks to Matthew Dowle for suggesting
      improvements to the way the hash code is generated in unique.c.

    • The enquote() utility, in use internally, is exported now.

    • .C() and .Fortran() now map non-zero return values (other than
      NA_LOGICAL) for logical vectors to TRUE: it has been an implicit
      assumption that they are treated as true.

    • The print() methods for "glm" and "lm" objects now insert
      linebreaks in long calls in the same way that the print() methods
      for "summary.[g]lm" objects have long done.  This does change the
      layout of the examples for a number of packages, e.g. MASS.
      (PR#14250)

    • constrOptim() can now be used with method "SANN".  (PR#14245)

      It gains an argument hessian to be passed to optim(), which
      allows all the ... arguments to be intended for f() and grad().
      (PR#14071)

    • curve() now allows expr to be an object of mode "expression" as
      well as "call" and "function".

    • The "POSIX[cl]t" methods for Axis() have been replaced by a
      single method for "POSIXt".

      There are no longer separate plot() methods for "POSIX[cl]t" and
      "Date": the default method has been able to handle those classes
      for a long time.  This _inter alia_ allows a single date-time
      object to be supplied, the wish of PR#14016.

      The methods had a different default ("") for xlab.

    • Classes "POSIXct", "POSIXlt" and "difftime" have generators
      .POSIXct(), .POSIXlt() and .difftime().  Package authors are
      advised to make use of them (they are available from R 2.11.0) to
      proof against planned future changes to the classes.

      The ordering of the classes has been changed, so "POSIXt" is now
      the second class.  See the document ‘Updating packages for
      changes in R 2.12.x’ on <URL: http://developer.r-project.org> for
      the consequences for a handful of CRAN packages.

    • The "POSIXct" method of as.Date() allows a timezone to be
      specified (but still defaults to UTC).

    • New list2env() utility function as an inverse of
      as.list(<environment>) and for fast multi-assign() to existing
      environment.  as.environment() is now generic and uses list2env()
      as list method.

    • There are several small changes to output which ‘zap’ small
      numbers, e.g. in printing quantiles of residuals in summaries
      from "lm" and "glm" fits, and in test statistics in
      print.anova().

    • Special names such as "dim", "names", etc, are now allowed as
      slot names of S4 classes, with "class" the only remaining
      exception.

    • File .Renviron can have architecture-specific versions such as
      .Renviron.i386 on systems with sub-architectures.

    • installed.packages() has a new argument subarch to filter on
      sub-architecture.

    • The summary() method for packageStatus() now has a separate
      print() method.

    • The default summary() method returns an object inheriting from
      class "summaryDefault" which has a separate print() method that
      calls zapsmall() for numeric/complex values.

    • The startup message now includes the platform and if used,
      sub-architecture: this is useful where different
      (sub-)architectures run on the same OS.

    • The getGraphicsEvent() mechanism now allows multiple windows to
      return graphics events, through the new functions
      setGraphicsEventHandlers(), setGraphicsEventEnv(), and
      getGraphicsEventEnv().  (Currently implemented in the windows()
      and X11() devices.)

    • tools::texi2dvi() gains an index argument, mainly for use by R
      CMD Rd2pdf.

      It avoids the use of texindy by texinfo's texi2dvi >= 1.157,
      since that does not emulate 'makeindex' well enough to avoid
      problems with special characters (such as (, {, !) in indices.

    • The ability of readLines() and scan() to re-encode inputs to
      marked UTF-8 strings on Windows since R 2.7.0 is extended to
      non-UTF-8 locales on other OSes.

    • scan() gains a fileEncoding argument to match read.table().

    • points() and lines() gain "table" methods to match plot().  (Wish
      of PR#10472.)

    • Sys.chmod() allows argument mode to be a vector, recycled along
      paths.

    • There are |, & and xor() methods for classes "octmode" and
      "hexmode", which work bitwise.

    • Environment variables R_DVIPSCMD, R_LATEXCMD, R_MAKEINDEXCMD,
      R_PDFLATEXCMD are no longer used nor set in an R session.  (With
      the move to tools::texi2dvi(), the conventional environment
      variables LATEX, MAKEINDEX and PDFLATEX will be used.
      options("dvipscmd") defaults to the value of DVIPS, then to
      "dvips".)

    • New function isatty() to see if terminal connections are
      redirected.

    • summaryRprof() returns the sampling interval in component
      sample.interval and only returns in by.self data for functions
      with non-zero self times.

    • print(x) and str(x) now indicate if an empty list x is named.

    • install.packages() and remove.packages() with lib unspecified and
      multiple libraries in .libPaths() inform the user of the library
      location used with a message rather than a warning.

    • There is limited support for multiple compressed streams on a
      file: all of [bgx]zfile() allow streams to be appended to an
      existing file, but bzfile() reads only the first stream.

    • Function person() in package utils now uses a given/family scheme
      in preference to first/middle/last, is vectorized to handle an
      arbitrary number of persons, and gains a role argument to specify
      person roles using a controlled vocabulary (the MARC relator
      terms).

    • Package utils adds a new "bibentry" class for representing and
      manipulating bibliographic information in enhanced BibTeX style,
      unifying and enhancing the previously existing mechanisms.

    • A bibstyle() function has been added to the tools package with
      default JSS style for rendering "bibentry" objects, and a
      mechanism for registering other rendering styles.

    • Several aspects of the display of text help are now customizable
      using the new Rd2txt_options() function.
      options("help_text_width") is no longer used.

    • Added \href tag to the Rd format, to allow hyperlinks to URLs
      without displaying the full URL.

    • Added \newcommand and \renewcommand tags to the Rd format, to
      allow user-defined macros.

    • New toRd() generic in the tools package to convert objects to
      fragments of Rd code, and added "fragment" argument to Rd2txt(),
      Rd2HTML(), and Rd2latex() to support it.

    • Directory R_HOME/share/texmf now follows the TDS conventions, so
      can be set as a texmf tree (‘root directory’ in MiKTeX parlance).

    • S3 generic functions now use correct S4 inheritance when
      dispatching on an S4 object.  See ?Methods, section on “Methods
      for S3 Generic Functions” for recommendations and details.

    • format.pval() gains a ... argument to pass arguments such as
      nsmall to format().  (Wish of PR#9574)

    • legend() supports title.adj.  (Wish of PR#13415)

    • Added support for subsetting "raster" objects, plus assigning to
      a subset, conversion to a matrix (of colour strings), and
      comparisons (== and !=).

    • Added a new parseLatex() function (and related functions
      deparseLatex() and latexToUtf8()) to support conversion of
      bibliographic entries for display in R.

    • Text rendering of \itemize in help uses a Unicode bullet in UTF-8
      and most single-byte Windows locales.

    • Added support for polygons with holes to the graphics engine.
      This is implemented for the pdf(), postscript(),
      x11(type="cairo"), windows(), and quartz() devices (and
      associated raster formats), but not for x11(type="Xlib") or
      xfig() or pictex().  The user-level interface is the polypath()
      function in graphics and grid.path() in grid.

    • File NEWS is now generated at installation with a slightly
      different format: it will be in UTF-8 on platforms using UTF-8,
      and otherwise in ASCII.  There is also a PDF version, NEWS.pdf,
      installed at the top-level of the R distribution.

    • kmeans(x, 1) now works.  Further, kmeans now returns between and
      total sum of squares.

    • arrayInd() and which() gain an argument useNames.  For arrayInd,
      the default is now false, for speed reasons.

    • As is done for closures, the default print method for the formula
      class now displays the associated environment if it is not the
      global environment.

    • A new facility has been added for inserting code into a package
      without re-installing it, to facilitate testing changes which can
      be selectively added and backed out.  See ?insertSource.

    • New function readRenviron to (re-)read files in the format of
      ~/.Renviron and Renviron.site.

    • require() will now return FALSE (and not fail) if loading the
      package or one of its dependencies fails.

    • aperm() now allows argument perm to be a character vector when
      the array has named dimnames (as the results of table() calls
      do).  Similarly, array() allows MARGIN to be a character vector.
      (Based on suggestions of Michael Lachmann.)

    • Package utils now exports and documents functions
      aspell_package_Rd_files() and aspell_package_vignettes() for
      spell checking package Rd files and vignettes using Aspell,
      Ispell or Hunspell.

    • Package news can now be given in Rd format, and news() prefers
      these inst/NEWS.Rd files to old-style plain text NEWS or
      inst/NEWS files.

    • New simple function packageVersion().

    • The PCRE library has been updated to version 8.10.

    • The standard Unix-alike terminal interface declares its name to
      readline as 'R', so that can be used for conditional sections in
      ~/.inputrc files.

    • ‘Writing R Extensions’ now stresses that the standard sections in
      .Rd files (other than \alias, \keyword and \note) are intended to
      be unique, and the conversion tools now drop duplicates with a
      warning.

      The .Rd conversion tools also warn about an unrecognized type in
      a \docType section.

    • ecdf() objects now have a quantile() method.

    • format() methods for date-time objects now attempt to make use of
      a "tzone" attribute with "%Z" and "%z" formats, but it is not
      always possible.  (Wish of PR#14358.)

    • tools::texi2dvi(file, clean = TRUE) now works in more cases (e.g.
      where emulation is used and when file is not in the current
      directory).

    • New function droplevels() to remove unused factor levels.

    • system(command, intern = TRUE) now gives an error on a Unix-alike
      (as well as on Windows) if command cannot be run.  It reports a
      non-success exit status from running command as a warning.

      On a Unix-alike an attempt is made to return the actual exit
      status of the command in system(intern = FALSE): previously this
      had been system-dependent but on POSIX-compliant systems the
      value return was 256 times the status.

    • system() has a new argument ignore.stdout which can be used to
      (portably) ignore standard output.

    • system(intern = TRUE) and pipe() connections are guaranteed to be
      available on all builds of R.

    • Sys.which() has been altered to return "" if the command is not
      found (even on Solaris).

    • A facility for defining reference-based S4 classes (in the OOP
      style of Java, C++, etc.) has been added experimentally to
      package methods; see ?ReferenceClasses.

    • The predict method for "loess" fits gains an na.action argument
      which defaults to na.pass rather than the previous default of
      na.omit.

      Predictions from "loess" fits are now named from the row names of
      newdata.

    • Parsing errors detected during Sweave() processing will now be
      reported referencing their original location in the source file.

    • New adjustcolor() utility, e.g., for simple translucent color
      schemes.

    • qr() now has a trivial lm method with a simple (fast) validity
      check.

    • An experimental new programming model has been added to package
      methods for reference (OOP-style) classes and methods.  See
      ?ReferenceClasses.

    • bzip2 has been updated to version 1.0.6 (bug-fix release).
      --with-system-bzlib now requires at least version 1.0.6.

    • R now provides jss.cls and jss.bst (the class and bib style file
      for the Journal of Statistical Software) as well as RJournal.bib
      and Rnews.bib, and R CMD ensures that the .bst and .bib files are
      found by BibTeX.

    • Functions using the TAR environment variable no longer quote the
      value when making system calls.  This allows values such as tar
      --force-local, but does require additional quotes in, e.g., TAR =
      "'/path with spaces/mytar'".

  DEPRECATED & DEFUNCT:

    • Supplying the parser with a character string containing both
      octal/hex and Unicode escapes is now an error.

    • File extension .C for C++ code files in packages is now defunct.

    • R CMD check no longer supports configuration files containing
      Perl configuration variables: use the environment variables
      documented in ‘R Internals’ instead.

    • The save argument of require() now defaults to FALSE and save =
      TRUE is now deprecated.  (This facility is very rarely actually
      used, and was superseded by the Depends field of the DESCRIPTION
      file long ago.)

    • R CMD check --no-latex is deprecated in favour of --no-manual.

    • R CMD Sd2Rd is formally deprecated and will be removed in R
      2.13.0.

  PACKAGE INSTALLATION:

    • install.packages() has a new argument libs_only to optionally
      pass --libs-only to R CMD INSTALL and works analogously for
      Windows binary installs (to add support for 64- or 32-bit
      Windows).

    • When sub-architectures are in use, the installed architectures
      are recorded in the Archs field of the DESCRIPTION file.  There
      is a new default filter, "subarch", in available.packages() to
      make use of this.

      Code is compiled in a copy of the src directory when a package is
      installed for more than one sub-architecture: this avoid problems
      with cleaning the sources between building sub-architectures.

    • R CMD INSTALL --libs-only no longer overrides the setting of
      locking, so a previous version of the package will be restored
      unless --no-lock is specified.

  UTILITIES:

    • R CMD Rprof|build|check are now based on R rather than Perl
      scripts.  The only remaining Perl scripts are the deprecated R
      CMD Sd2Rd and install-info.pl (used only if install-info is not
      found) as well as some maintainer-mode-only scripts.

      *NB:* because these have been completely rewritten, users should
      not expect undocumented details of previous implementations to
      have been duplicated.

      R CMD no longer manipulates the environment variables PERL5LIB
      and PERLLIB.

    • R CMD check has a new argument --extra-arch to confine tests to
      those needed to check an additional sub-architecture.

      Its check for “Subdirectory 'inst' contains no files” is more
      thorough: it looks for files, and warns if there are only empty
      directories.

      Environment variables such as R_LIBS and those used for
      customization can be set for the duration of checking _via_ a
      file ~/.R/check.Renviron (in the format used by .Renviron, and
      with sub-architecture specific versions such as
      ~/.R/check.Renviron.i386 taking precedence).

      There are new options --multiarch to check the package under all
      of the installed sub-architectures and --no-multiarch to confine
      checking to the sub-architecture under which check is invoked.
      If neither option is supplied, a test is done of installed
      sub-architectures and all those which can be run on the current
      OS are used.

      Unless multiple sub-architectures are selected, the install done
      by check for testing purposes is only of the current
      sub-architecture (_via_ R CMD INSTALL --no-multiarch).

      It will skip the check for non-ascii characters in code or data
      if the environment variables _R_CHECK_ASCII_CODE_ or
      _R_CHECK_ASCII_DATA_ are respectively set to FALSE.  (Suggestion
      of Vince Carey.)

    • R CMD build no longer creates an INDEX file (R CMD INSTALL does
      so), and --force removes (rather than overwrites) an existing
      INDEX file.

      It supports a file ~/.R/build.Renviron analogously to check.

      It now runs build-time \Sexpr expressions in help files.

    • R CMD Rd2dvi makes use of tools::texi2dvi() to process the
      package manual.  It is now implemented entirely in R (rather than
      partially as a shell script).

    • R CMD Rprof now uses utils::summaryRprof() rather than Perl.  It
      has new arguments to select one of the tables and to limit the
      number of entries printed.

    • R CMD Sweave now runs R with --vanilla so the environment setting
      of R_LIBS will always be used.

  C-LEVEL FACILITIES:

    • lang5() and lang6() (in addition to pre-existing lang[1-4]())
      convenience functions for easier construction of eval() calls.
      If you have your own definition, do wrap it inside #ifndef lang5
      .... #endif to keep it working with old and new R.

    • Header R.h now includes only the C headers it itself needs, hence
      no longer includes errno.h.  (This helps avoid problems when it
      is included from C++ source files.)

    • Headers Rinternals.h and R_ext/Print.h include the C++ versions
      of stdio.h and stdarg.h respectively if included from a C++
      source file.

  INSTALLATION:

    • A C99 compiler is now required, and more C99 language features
      will be used in the R sources.

    • Tcl/Tk >= 8.4 is now required (increased from 8.3).

    • System functions access, chdir and getcwd are now essential to
      configure R.  (In practice they have been required for some
      time.)

    • make check compares the output of the examples from several of
      the base packages to reference output rather than the previous
      output (if any).  Expect some differences due to differences in
      floating-point computations between platforms.

    • File NEWS is no longer in the sources, but generated as part of
      the installation.  The primary source for changes is now
      doc/NEWS.Rd.

    • The popen system call is now required to build R.  This ensures
      the availability of system(intern = TRUE), pipe() connections and
      printing from postscript().

    • The pkg-config file libR.pc now also works when R is installed
      using a sub-architecture.

    • R has always required a BLAS that conforms to IE60559 arithmetic,
      but after discovery of more real-world problems caused by a BLAS
      that did not, this is tested more thoroughly in this version.

  BUG FIXES:

    • Calls to selectMethod() by default no longer cache inherited
      methods.  This could previously corrupt methods used by as().

    • The densities of non-central chi-squared are now more accurate in
      some cases in the extreme tails, e.g. dchisq(2000, 2, 1000), as a
      series expansion was truncated too early.  (PR#14105)

    • pt() is more accurate in the left tail for ncp large, e.g.
      pt(-1000, 3, 200).  (PR#14069)

    • The default C function (R_binary) for binary ops now sets the S4
      bit in the result if either argument is an S4 object.  (PR#13209)

    • source(echo=TRUE) failed to echo comments that followed the last
      statement in a file.

    • S4 classes that contained one of "matrix", "array" or "ts" and
      also another class now accept superclass objects in new().  Also
      fixes failure to call validObject() for these classes.

    • Conditional inheritance defined by argument test in
      methods::setIs() will no longer be used in S4 method selection
      (caching these methods could give incorrect results).  See
      ?setIs.

    • The signature of an implicit generic is now used by setGeneric()
      when that does not use a definition nor explicitly set a
      signature.

    • A bug in callNextMethod() for some examples with "..." in the
      arguments has been fixed.  See file
      src/library/methods/tests/nextWithDots.R in the sources.

    • match(x, table) (and hence %in%) now treat "POSIXlt" consistently
      with, e.g., "POSIXct".

    • Built-in code dealing with environments (get(), assign(),
      parent.env(), is.environment() and others) now behave
      consistently to recognize S4 subclasses; is.name() also
      recognizes subclasses.

    • The abs.tol control parameter to nlminb() now defaults to 0.0 to
      avoid false declarations of convergence in objective functions
      that may go negative.

    • The standard Unix-alike termination dialog to ask whether to save
      the workspace takes a EOF response as n to avoid problems with a
      damaged terminal connection.  (PR#14332)

    • Added warn.unused argument to hist.default() to allow suppression
      of spurious warnings about graphical parameters used with
      plot=FALSE.  (PR#14341)

    • predict.lm(), summary.lm(), and indeed lm() itself had issues
      with residual DF in zero-weighted cases (the latter two only in
      connection with empty models). (Thanks to Bill Dunlap for
      spotting the predict() case.)

    • aperm() treated resize = NA as resize = TRUE.

    • constrOptim() now has an improved convergence criterion, notably
      for cases where the minimum was (very close to) zero; further,
      other tweaks inspired from code proposals by Ravi Varadhan.

    • Rendering of S3 and S4 methods in man pages has been corrected
      and made consistent across output formats.

    • Simple markup is now allowed in \title sections in .Rd files.

    • The behaviour of as.logical() on factors (to use the levels) was
      lost in R 2.6.0 and has been restored.

    • prompt() did not backquote some default arguments in the \usage
      section.  (Reported by Claudia Beleites.)

    • writeBin() disallows attempts to write 2GB or more in a single
      call. (PR#14362)

    • new() and getClass() will now work if Class is a subclass of
      "classRepresentation" and should also be faster in typical calls.

    • The summary() method for data frames makes a better job of names
      containing characters invalid in the current locale.

    • [[ sub-assignment for factors could create an invalid factor
      (reported by Bill Dunlap).

    • Negate(f) would not evaluate argument f until first use of
      returned function (reported by Olaf Mersmann).

    • quietly=FALSE is now also an optional argument of library(), and
      consequently, quietly is now propagated also for loading
      dependent packages, e.g., in require(*, quietly=TRUE).

    • If the loop variable in a for loop was deleted, it would be
      recreated as a global variable.  (Reported by Radford Neal; the
      fix includes his optimizations as well.)

    • Task callbacks could report the wrong expression when the task
      involved parsing new code. (PR#14368)

    • getNamespaceVersion() failed; this was an accidental change in
      2.11.0. (PR#14374)

    • identical() returned FALSE for external pointer objects even when
      the pointer addresses were the same.

    • L$a@x[] <- val did not duplicate in a case it should have.

    • tempfile() now always gives a random file name (even if the
      directory is specified) when called directly after startup and
      before the R RNG had been used.  (PR#14381)

    • quantile(type=6) behaved inconsistently.  (PR#14383)

    • backSpline(.) behaved incorrectly when the knot sequence was
      decreasing.  (PR#14386)

    • The reference BLAS included in R was assuming that 0*x and x*0
      were always zero (whereas they could be NA or NaN in IEC 60559
      arithmetic).  This was seen in results from tcrossprod, and for
      example that log(0) %*% 0 gave 0.

    • The calculation of whether text was completely outside the device
      region (in which case, you draw nothing) was wrong for screen
      devices (which have [0, 0] at top-left).  The symptom was (long)
      text disappearing when resizing a screen window (to make it
      smaller).  (PR#14391)

    • model.frame(drop.unused.levels = TRUE) did not take into account
      NA values of factors when deciding to drop levels. (PR#14393)

    • library.dynam.unload required an absolute path for libpath.
      (PR#14385)

      Both library() and loadNamespace() now record absolute paths for
      use by searchpaths() and getNamespaceInfo(ns, "path").

    • The self-starting model NLSstClosestX failed if some deviation
      was exactly zero.  (PR#14384)

    • X11(type = "cairo") (and other devices such as png using
      cairographics) and which use Pango font selection now work around
      a bug in Pango when very small fonts (those with sizes between 0
      and 1 in Pango's internal units) are requested.  (PR#14369)

    • Added workaround for the font problem with X11(type = "cairo")
      and similar on Mac OS X whereby italic and bold styles were
      interchanged.  (PR#13463 amongst many other reports.)

    • source(chdir = TRUE) failed to reset the working directory if it
      could not be determined - that is now an error.

    • Fix for crash of example(rasterImage) on x11(type="Xlib").

    • Force Quartz to bring the on-screen display up-to-date
      immediately before the snapshot is taken by grid.cap() in the
      Cocoa implementation. (PR#14260)

    • model.frame had an unstated 500 byte limit on variable names.
      (Example reported by Terry Therneau.)

    • The 256-byte limit on names is now documented.

    • Subassignment by [, [[ or $ on an expression object with value
      NULL coerced the object to a list.

CHANGES IN R VERSION 2.11.1 patched:

  NEW FEATURES:

    • install.packages() has a new optional argument INSTALL_opts which
      can be used to pass options to R CMD INSTALL for source-package
      installs.

    • R CMD check now runs the package-specific tests with LANGUAGE=en
      to facilitate comparison to .Rout.save files.

    • sessionInfo() gives more detailed platform information, including
      32/64-bit and the sub-architecture if one is used.

  DEPRECATED & DEFUNCT:

    • The use of Perl configuration variables for R CMD check (as
      previously documented in ‘Writing R Extensions’) is deprecated
      and will be removed in R 2.12.0.  Use the environment variables
      documented in ‘R Internals’ instead.

  BUG FIXES:

    • R CMD Rd2dvi failed if run from a path containing space(s).  This
      also affected R CMD check, which calls Rd2dvi.

    • stripchart() could fail with an empty factor level.  (PR#14317)

    • Text help rendering of \tabular{} has been improved: under some
      circumstances leading blank columns were not rendered.

    • strsplit(x, fixed=TRUE) marked UTF-8 strings with the local
      encoding when no splits were found.

    • weighted.mean(NA, na.rm=TRUE) and similar now returns NaN again,
      as it did prior to R 2.10.0.

    • R CMD had a typo in its detection of whether the environment
      variable TEXINPUTS was set (reported by Martin Morgan).

    • The command-line parser could mistake --file=size... for one of
      the options for setting limits for Ncells or Vcells.

    • The internal strptime() could corrupt its copy of the timezone
      which would then lead to spurious warnings. (PR#14338)

    • dir.create(recursive = TRUE) could fail if one of the components
      existed but was a directory on a read-only file system.  (Seen on
      Solaris, where the error code returned is not even listed as
      possible on the man page.)

    • The postscript() and pdf() devices will now allow lwd values less
      than 1 (they used to force such values to be 1).

    • Fixed font face for CID fonts in pdf() graphics output.
      (PR#14326)

    • GERaster() now checks for width or height of zero and does
      nothing in those cases; previously the behaviour was undefined,
      probably device-specific, and possibly dangerous.

    • wilcox.test(x, y, conf.int = TRUE) failed with an unhelpful
      message if x and y were constant vectors, and similarly in the
      one-sample case.  (PR#14329)

    • Improperly calling Recall() from outside a function could cause a
      segfault.  (Reported by Robert McGehee.)

    • \Sexpr[result=rd] in an Rd file added a spurious newline, which
      was displayed as extra whitespace when rendered.

    • require(save = TRUE) recorded the names of packages it failed to
      load.

    • packageStatus() could return a data frame with duplicate row
      names which could then not be printed.

    • txtProgressBar(style = 2) did not work correctly.

      txtProgressBar(style = 3) did not display until a non-minimum
      value was set.

    • contour() did not display dashed line types properly when contour
      lines were labelled. (Reported by David B. Thompson.)

    • tools::undoc() again detects undocumented data objects.  Of
      course, this also affects R CMD check.

    • ksmooth(x,NULL) no longer segfaults.

    • approxfun(), approx(), splinefun() and spline() could be confused
      by x values that were different but so close as to print
      identically.  (PR#14377)

CHANGES IN R VERSION 2.11.1:

  NEW FEATURES:

    • R CMD INSTALL checks if dependent packages are available early on
      in the installation of source packages, thereby giving clearer
      error messages.

    • R CMD INSTALL --build now names the file in the format used for
      Mac OS X binary files on that platform.

    • BIC() in package stats4 now also works with multiple fitted
      models, analogously to AIC().

  DEPRECATED & DEFUNCT:

    • Use of file extension .C for C++ code in packages is now
      deprecated: it has caused problems for some makes on
      case-insensitive file systems (although it currently works with
      the recommended toolkits).

  INSTALLATION:

    • Command gnutar is preferred to tar when configure sets TAR.  This
      is needed on Mac OS 10.6, where the default tar, bsdtar 2.6.2,
      has been reported to produce archives with illegal extensions to
      tar (according to the POSIX standard).

  BUG FIXES:

    • The C function mkCharLenCE now no longer reads past len bytes
      (unlikely to be a problem except in user code).  (PR#14246)

    • On systems without any default LD_LIBRARY_PATH (not even
      /usr/local/lib), [DY]LIB_LIBRARY_PATH is now set without a
      trailing colon.  (PR#13637)

    • More efficient implementation of utf8ToInt() on long multi-byte
      strings with many multi-byte characters.  (PR#14262)

    • aggregate.ts() gave platform-dependent results due to rounding
      error for ndeltat != 1.

    • package.skeleton() sometimes failed to fix filenames for .R or
      .Rd files to start with an alphanumeric.  (PR#14253)

      It also failed when only an S4 class without any methods was
      defined.  (PR#14280)

    • splinefun(method = "monoH.FC") was not quite monotone in rare
      cases.  (PR#14215)

    • Rhttpd no longer crashes due to SIGPIPE when the client closes
      the connection prematurely.  (PR#14266)

    • format.POSIXlt() could cause a stack overflow and crash when used
      on very long vectors.  (PR#14267)

    • Rd2latex() incorrectly escaped special characters in \usage
      sections.

    • mcnemar.test() could alter the levels (dropping unused levels) if
      passed x and y as factors (reported by Greg Snow).

    • Rd2pdf sometimes needed a further pdflatex pass to get
      hyperlinked pages correct.

    • interaction() produced malformed results when levels were
      duplicated, causing segfaults in split().

    • cut(d, breaks = <n>) now also works for "Date" or "POSIXt"
      argument d.  (PR#14288)

    • memDecompress() could decompress incompletely rare xz-compressed
      input due to incorrect documentation of xz utils.  (Report and
      patch from Olaf Mersmann.)

    • The S4 initialize() methods for "matrix", "array", and "ts" have
      been fixed to call validObject().  (PR#14284)

    • R CMD INSTALL now behaves the same way with or without
      --no-multiarch on platforms with only one installed architecture.
      (It used to clean the src directory without --no-multiarch.)

    • [<-.data.frame was not quite careful enough in assigning (and
      potentially deleting) columns right-to-left.  (PR#14263)

    • rbeta(n, a, b) no longer occasionally returns NaN for a >> 1 > b.
      (PR#14291)

    • pnorm(x, log.p = TRUE) could return NaN not -Inf for x near
      (minus for lower.tail=TRUE) the largest representable number.

    • Compressed data files *.(txt|tab|csv).(gz|bz2|xz) were not
      recognized for the list of data topics and hence for packages
      using LazyData.  (PR#14273)

    • textConnection() did an unnecessary translation on strings in a
      foreign encoding (e.g. UTF-8 strings on Windows) and so was
      slower than it could have been on very long input strings.
      (PR#14286)

    • tools::Rd2txt() did not render poorly written Rd files
      consistently with other renderers.

      It computed widths of strings that would be print()ed with
      escapes incorrectly, for example in the computation of column
      width for \tabular.

    • na.action() did not extract the na.action component as
      documented.

    • do.call()ing NextMethod in erronous ways no longer segfaults.
      (PR#13487)

CHANGES IN R VERSION 2.11.0:

  SIGNIFICANT USER-VISIBLE CHANGES:

    • Packages must have been installed under R >= 2.10.0, as the
      current help system is the only one now supported.

    • A port to 64-bit Windows is now available as well as binary
      package repositiories: see the ‘R Administration and Installation
      Manual’.

    • Argument matching for primitive functions is now done in the same
      way as for interpreted functions except for the deliberate
      exceptions

      
      
               call switch .C .Fortran .Call .External
             

      all of which use positional matching for their first argument,
      and also some internal-use-only primitives.

    • The default device for command-line R at the console on Mac OS X
      is now quartz() and not X11().

  NEW FEATURES:

    • The open modes for connections are now interpreted more
      consistently.  open = "r" is now equivalent to open = "rt" for
      all connections.  The default open = "" now means "rt" for all
      connections except the compressed-file connections gzfile(),
      bzfile() and xzfile() for which it means "rb".

    • R CMD INSTALL now uses the internal untar() function in package
      utils: this ensures that all platforms can install bzip2- and
      xz-compressed tarballs.  In case this causes problems (as it has
      on some Windows file systems when run from Cygwin tools) it can
      be overridden by the environment variable R_INSTALL_TAR: setting
      this to a modern external tar program will speed up unpacking of
      large (tens of Mb or more) tarballs.

    • help(try.all.packages = TRUE) is much faster (although the time
      taken by the OS to find all the packages the first time it is
      used can dominate the time).

    • R CMD check has a new option --timings to record per-example
      timings in file <pkg>.Rcheck/<pkg>-Ex.timings.

    • The TRE library has been updated to version 0.8.0 (minor
      bugfixes).

    • grep[l], [g]sub and [g]regexpr now work in bytes in an 8-bit
      locales if there is no marked UTF-8 input string: this will be
      somewhat faster, and for [g]sub() give the result in the native
      encoding rather than in UTF-8 (which returns to the behaviour
      prior to R 2.10.0).

    • A new argument skipCalls has been added to browser() so that it
      can report the original context when called by other debugging
      functions.

    • More validity checking of UTF-8 and MBCS strings is done by
      agrep() and the regular-expression matching functions.

    • The undocumented restriction on gregexpr() to length(text) > 0
      has been removed.

    • Package tcltk now sends strings to Tcl in UTF-8: this means that
      strings with a marked UTF-8 encoding are supported in non-UTF-8
      locales.

    • The graphics engine now supports rendering of raster (bitmap)
      images, though not all graphics devices can provide (full)
      support.  Packages providing graphics devices (e.g., Cairo,
      RSvgDevice, cairoDevice) will need to be reinstalled.

      There is also support in the graphics engine for capturing raster
      images from graphics devices (again not supported on all graphics
      devices).

    • R CMD check now also checks if the package and namespace can be
      unloaded: this provides a check of the .Last.lib() and
      .onUnload() hook functions (unless --install=fake).

    • prop.table(x) now accepts a one-dimensional table for x.

    • A new function vapply() has been added, based on a suggestion
      from Bill Dunlap.  It requires that a template for the function
      value be specified, and uses it to determine the output type and
      to check for consistency in the function values.

    • The main HTML help page now links to a reformatted copy of this
      NEWS file.  (Suggested by Henrik Bengtsson.)  Package index files
      link to the package DESCRIPTION and NEWS files and a list of
      demos when using dynamic help.

    • The [ method for class "AsIs" allows the next method to change
      the underlying class.  (Wish of Jens Oehlschlägel.)

    • write.csv[2] no longer allow argument append to be changed: as
      ever, direct calls to write.table() give more flexibility as well
      as more room for error.

    • The index page for HTML help for a package now collapses multiple
      signatures for S4 methods into a single entry.

    • The use of .required by require() and detach() has been replaced
      by .Depends which is set from the Depends field of a package
      (even in packages with name spaces).  By default detach()
      prevents such dependencies from being detached: this can be
      overridden by the argument force.

    • bquote() has been extended to work on function definitions.
      (Wish of PR#14031).

    • detach() when applied to an object other than a package returns
      the environment that has been detached, to parallel attach().

    • readline() in non-interactive use returns "" and does not attempt
      to read from the ‘terminal’.

    • New function file_ext() in package tools.

    • xtfrm() is now primitive and internally generic, as this allows
      S4 methods to be set on it without name-space scoping issues.

      There are now "AsIs" and "difftime" methods, and the default
      method uses unclass(x) if is.numeric(x) is true (which will be
      faster but relies on is.numeric() having been set correctly for
      the class).

    • is.numeric(x) is now false for a "difftime" object
      (multiplication and division make no sense for such objects).

    • The default method of weighted.mean(x, w) coerces w to be numeric
      (aka double); previously only integer weights were coerced.  Zero
      weights are handled specially so an infinite value with zero
      weight does not force an NaN result.

      There is now a "difftime" method.

    • bug.report() now has arguments package and lib.loc to generate
      bug reports about packages.  When this is used, it looks for a
      BugReports field in the package DESCRIPTION file, which will be
      assumed to be a URL at which to submit the report, and otherwise
      generates an email to the package maintainer.  (Suggested by
      Barry Rowlingson.)

    • quantile() now has a method for the date-time class "POSIXt", and
      types 1 and 3 (which never interpolate) work for Dates and
      ordered factors.

    • length(<POSIXlt>) now returns the length of the corresponding
      abstract timedate-vector rather than always 9 (the length of the
      underlying list structure).  (Wish of PR#14073 and PR#10507.)

    • The readline completion backend no longer sorts possible
      completions alphabetically (e.g., function argument names) if R
      was built with readline >= 6.

    • select.list() gains a graphics argument to allow Windows/Mac
      users to choose the text interface.  This changes the behaviour
      of new.packages(ask=TRUE) to be like update.packages(ask=TRUE) on
      those platforms in using a text menu: use ask="graphics" for a
      graphical menu.

    • New function chooseBioCmirror() to set the "BioC_mirror" option.

    • The R grammar now prevents using the argument name in signatures
      of S4 methods for $ and $<-, since they will always be called
      with a character string value for name.  The implicit S4 generic
      functions have been changed to reflect this: packages which
      included name in the signature of their methods need to be
      updated and re-installed.

    • The handling of the method argument of glm() has been refined
      following suggestions by Ioannis Kosmidis and Heather Turner.

    • str() gains a new argument list.len with default 99, limiting the
      number of list() items (per level), thanks to suggestions from
      David Winsenius.

    • Having formal arguments of an S4 method in a different order from
      the generic is now an error (the warning having been ignored by
      some package maintainers for a long time).

    • New functions enc2native() and enc2utf8() convert character
      vectors with possibly marked encodings to the current locale and
      UTF-8 respectively.

    • Unrecognized escapes and embedded nuls in character strings are
      now an error, not just a warning.  Thus option "warnEscapes" is
      no longer needed.  rawToChar() now removes trailing nuls
      silently, but other embedded nuls become errors.

    • Informational messages about masked objects displayed when a
      package is attached are now more compact, using strwrap() instead
      of one object per line.

    • print.rle() gains argument prefix.

    • download.file() gains a "curl" method, mainly for use on
      platforms which have curl but not wget, but also for some
      hard-to-access URLs.

    • In Rd, \eqn and \deqn will render in HTML (and convert to text)
      upper- and lower-case Greek letters (entered as \alpha ...),
      \ldots, ..., \ge and \le.

    • utf8ToInt() and intToUtf8() now map NA inputs to NA outputs.

    • file() has a new argument raw which may help if it is used with
      something other than a regular file, e.g. a character device.

    • New function strtoi(), a wrapper for the C function strtol.

    • as.octmode() and as.hexmode() now allow inputs of length other
      than one.

      The format() and print() methods for "octmode" now preserve names
      and dimensions (as those for "hexmode" did).

      The format() methods for classes "octmode" and "hexmode" gain a
      width argument.

    • seq.int() returns an integer result in some further cases where
      seq() does, e.g. seq.int(1L, 9L, by = 2L).

    • Added \subsection{}{} macro to Rd syntax, for subsections within
      sections.

    • n-dimensional arrays with dimension names can now be indexed by
      an n-column character matrix.  The indices are matched against
      the dimension names.  NA indices are propagated to the result.
      Unmatched values and "" are not allowed and result in an error.

    • interaction(drop=TRUE) uses less memory (related to PR#14121).

    • summary() methods have been added to the "srcref" and "srcfile"
      classes, and various encoding issues have been cleaned up.

    • If option "checkPackageLicense" is set to TRUE (not currently the
      default), users will be asked to agree to non-known-to-be-FOSS
      package licences at first use.

    • Checking setAs(a, b) methods only gives a message instead of a
      warning, when one of a or b is unknown.

    • New function norm() to compute a matrix norm.  norm() and also
      backsolve() and sample() have implicit S4 generics.

    • Files Renviron.site and Rprofile.site can have
      architecture-specific versions on systems with sub-architectures.

    • R CMD check now (by default) also checks Rd files for
      auto-generated content in need of editing, and missing argument
      descriptions.

    • aggregate() gains a formula method thanks to a contribution by
      Arni Magnusson.  The data frame method now allows summary
      functions to return arbitrarily many values.

    • path.expand() now propagates NA values rather than converting
      them to "NA".

    • file.show() now disallows NA values for file names, headers, and
      pager.

    • The ‘fuzz’ used by seq() and seq.int() has been reduced from 1e-7
      to 1e-10, which should be ample for the double-precision
      calculations used in R.  It ensures that the fuzz never comes
      into play with sequences of integers (wish of PR#14169).

    • The default value of RSiteSearch(restrict=) has been changed to
      include vignettes but to exclude R-help.  The R-help archives
      available have been split, with a new option of "Rhelp10" for
      those from 2010.

    • New function rasterImage() in the graphics package for drawing
      raster images.

    • stats:::extractAIC.coxph() now omits aliased terms when computing
      the degrees of freedom (suggestion of Terry Therneau).

    • cor() and cov() now test for misuse with non-numeric arguments,
      such as the non-bug report PR#14207.

    • pchisq(ncp =, log.p = TRUE) is more accurate for probabilities
      near one.  E.g. pchisq(80, 4, ncp=1, log.p=TRUE).  (Maybe what
      was meant in PR#14216.)

    • maintainer() has been added, to give convenient access to the
      name of the maintainer of a package (contributed by David Scott).

    • sample() and sample.int() allow zero items to be sampled from a
      zero-length input.  sample.int() gains a default value size=n to
      be more similar to sample().

    • switch() returned NULL on error (not previously documented on the
      help page): it now does so invisibly, analogously to
      if-without-else.

      It is now primitive: this means that argument EXPR is always
      matched to the first argument and there is no danger of partial
      matching to later named arguments.

    • Primitive functions UseMethod(), attr(), attr<-(), on.exit(),
      retracemem() and substitute() now use standard argument matching
      (rather than positional matching).  This means that all
      multi-argument primitives which are not internal now use standard
      argument matching except where positional matching is desirable
      (as for switch(), call(), .C() ...).

    • All the one-argument primitives now check that any name supplied
      for their first argument is a partial match to the argument name
      as documented on the help page: this also applies to replacement
      functions of two arguments.

    • base::which() uses a new .Internal function when arr.ind is FALSE
      resulting in a 10x speedup.  Thanks to Patrick Aboyoun for
      implementation suggestions.

    • Help conversion to text now uses the first part of \enc{}{}
      markup if it is representable in the current output encoding.  On
      the other hand, conversion to LaTeX with the default
      outputEncoding = "ASCII" uses the second part.

    • A new class "listOfMethods" has been introduced to represent the
      methods in a methods table, to replace the deprecated class
      "MethodsList".

    • any() and all() return early if possible.  This may speed up
      operations on long vectors.

    • strptime() now accepts "%z" (for the offset from UTC in the
      RFC822 format of +/-hhmm).

    • The PCRE library has been updated to version 8.02, a bug-fix
      release which also updates tables to Unicode 5.02.

    • Functions which may use a graphical select.list() (including
      menu() and install.packages()) now check on a Unix-alike that Tk
      can be started (and not just capabilities("tcltk") &&
      capabilities("X11")).

    • The parser no longer marks strings containing octal or hex
      escapes as being in UTF-8 when entered in a UTF-8 locale.

    • On platforms with cairo but not Pango (notably Mac OS X) the
      initial default X11() type is set to "Xlib": this avoids several
      problems with font selection when done by cairo rather than Pango
      (at least on Mac OS X).

    • New function arrayInd() such that which(x, arr.ind = TRUE) for an
      array 'x' is now equivalent to arrayInd(which(x), dim(x),
      dimnames(x)).

  DEPRECATED & DEFUNCT:

    • Bundles of packages are defunct.

    • stats::clearNames() is defunct: use unname().

    • Basic regular expressions are defunct, and strsplit(), grep(),
      grepl(), sub(), gsub(), regexpr() and gregexpr() no longer have
      an extended argument.

    • methods::trySilent() is defunct.

    • index.search() (which was deprecated in 2.10.0) is no longer
      exported and has a different argument list.

    • Use of multiple arguments to return() is now defunct.

    • The use of UseMethod() with more than two arguments is now
      defunct.

    • In the methods package, the "MethodsList" metadata objects which
      had been superseded by hash tables (environments) since R 2.8.0
      are being phased out.  Objects of this class are no longer
      assigned or used as metadata by the package.

      getMethods() is now deprecated, with its internal use replaced by
      findMethods() and other changes.  Creating objects from the
      "MethodsList" class is also deprecated.

    • Parsing strings containing both octal/hex and Unicode escapes now
      gives a warning and will become an error in R 2.12.0.

  INSTALLATION:

    • UTF-8 is now used for the reference manual and package manuals.
      This requires LaTeX ‘2005/12/01’ or later.

    • configure looks for a POSIX compliant tr, Solaris's /usr/ucb/tr
      having been found to cause Rdiff to malfunction.

    • configure is now generated with autoconf 2.65, which works better
      on recent systems and on Mac OS X.

  PACKAGE INSTALLATION:

    • Characters in R source which are not translatable to the current
      locale are now handled more tolerantly: these will be converted
      to hex codes with a warning.  Such characters are only really
      portable if they appear in comments.

    • R CMD INSTALL now tests that the installed package can be loaded
      (and backs out the installation if it cannot): this can be
      suppressed by --no-test-load.  This avoids installing/updating a
      package that cannot be used: common causes of failures to load
      are missing/incompatible external software and missing/broken
      dependent packages.

    • Package installation on Windows for a package with a src
      directory now checks if a DLL is created unless there is a
      src/Makefile.win file: this helps catch broken installations
      where the toolchain has not reported problems in building the
      DLL.  (Note: this can be any DLL, not just one named
      <pkg-name>.dll.)

  BUG FIXES:

    • Using with(), eval() etc with a list with some unnamed elements
      now works.  (PR#14035)

    • The "quick" dispatch of S4 methods for primitive functions was
      not happening, forcing a search each time.  (Dispatch for
      closures was not affected.)  A side effect is that default values
      for arguments in a method that do not have defaults in the
      generic will now be ignored.

    • Trying to dispatch S4 methods for primitives during the search
      for inherited methods slows that search down and potentially
      could cause an infinite recursion.  An internal switch was added
      to turn off all such methods from findInheritedMethods().

    • R framework installation (on Mac OS X) would not work properly if
      a rogue Resources directory was present at the top level.  Such a
      non-symlink will now be renamed to Resources.old (and anything
      previously named Resources.old removed) as part of the framework
      installation process.

    • The checks for conforming S4 method arguments could fail when the
      signature of the generic function omitted some of the formal
      arguments (in addition to ...).  Arguments omitted from the
      method definition but conforming (per the documentation) should
      now be ignored (treated as "ANY") in dispatching.

    • The computations for S4 method evaluation when ...  was in the
      signature could fail, treating ... as an ordinary symbol.  This
      has been fixed, for the known cases.

    • Various ar() fitting methods have more protection for singular
      fits.

    • callNextMethod now works again with the drop= argument in [

    • parse() and parse_Rd() miscounted columns when multibyte UTF-8
      characters were present.

    • Formatting of help pages has had minor improvements: extra blank
      lines have been removed from the text format, and empty package
      labels removed from HTML.

    • cor(A, B) where A is n x 1 and B a 1-dimensional array segfaulted
      or gave an internal error.  (The case cor(B, A) was PR#7116.)

    • cut.POSIXt() applied to a start value after the DST transition on
      a DST-change day could give the wrong time for argument breaks in
      units of days or longer.  (PR#14208)

    • do_par() UNPROTECTed too early (PR#14214)

    • Subassignment x[[....]] <- y didn't check for a zero-length right
      hand side, and inserted a rubbish value.  (PR#14217)

    • fisher.test() no longer gives a P-value *very* slightly > 1, in
      some borderline cases.

    • Internal function matchArgs() no longer modifies the general
      purpose bits of the SEXPs that make up the formals list of R
      functions.  This fixes an invalid error message that would occur
      when a garbage collection triggered a second call to matchArgs
      for the same function _via_ a finalizer.

    • gsub() in 2.10.x could fail from stack overflow for extremely
      long strings due to temporary data being allocated on the stack.
      Also, gsub() with fixed=TRUE is in some circumstances
      considerably faster.

    • Several primitives, including attributes(), attr<-()
      interactive(), nargs() and proc.time(), did not check that they
      were called with the correct number of arguments.

    • A potential race condition in list.files() when other processes
      are operating on the directory has been fixed; the code now
      dynamically allocates memory for file listings in a single pass
      instead of making an initial count pass.

    • mean(x, trim=, na.rm = FALSE) failed to return NA if x contained
      missing values.  (Reported by Bill Dunlap.)

    • Extreme tail behavior of, pbeta() {and hence pf()}, e.g.,
      pbeta(x, 3, 2200, lower.tail=FALSE, log.p=TRUE) now returns
      finite values instead of jumping to -Inf too early.  (PR#14230).

    • parse(text=x) misbehaved for objects x that were not coerced
      internally to character, notably symbols.  (Reported to R-devel
      by Bill Dunlap.)

    • The internal C function coerceSymbol now handles coercion to
      character, and warns if coercion fails (rather than silently
      returning NULL).  This allows a name to be given where a
      character vector is required in functions which coerce
      internally.

    • The interpretation by strptime() of "%c" was non-standard (not
      that it is ever advisable to use locale- and system-specific
      input formats).

    • capabilities("X11") now works the same way on Mac OS X as on
      other platforms (and as documented: it was always true for R
      built with --with-aqua, as the CRAN builds are).

    • The X11() device with cairo but not Pango (notably Mac OS X) now
      checks validity of text strings in UTF-8 locales (since Pango
      does but cairo it seems does not).

    • read.fwf() misread multi-line records when n was specified.
      (PR#14241)

    • all.equal(tolerance = e) passes the numeric tolerance also to the
      comparison of the attributes.

    • pgamma(0, 0), a boundary case, now returns 0, its limit from the
      left, rather than the limit from the right.

    • Issuing POST requests to the internal web server could stall the
      request under certain circumstances.

    • gzcon( <textConnection> ), an error, no longer damages the
      connection (in a way to have it segfault).  (PR#14237)

    • All the results from hist() now use the nominal breaks not those
      adjusted by the numeric ‘fuzz’: in recent versions the nominal
      breaks were reported but the 'density' referred to the intervals
      used in the calculation - which mattered very slightly for one of
      the extreme bins.  (Based on a report by Martin Becker.)

    • If xy[z].coords (used internally by many graphics functions) are
      given a list as x, they now check that the list has suitable
      names and give a more informative error message.  (PR#13936)

CHANGES IN R VERSION 2.10.1 patched:

  NEW FEATURES:

    • The handling of line textures in the postscript() and pdf()
      devices was set up for round end caps (the only type which
      existed at the time): it has now been adjusted for butt endcaps.

    • lchoose(a, k) is now defined as log(abs(choose(a,k))),
      analogously to lfactorial().

    • Although \eqn{} in Rd files is defined as a ‘verbatim’ macro,
      many packages expected ... and \ldots to be interpreted there (as
      was the case in R < 2.10.0), so this is now done (using an
      ellipsis in HTML rendering).

    • Escaping of braces in quoted strings in R-code sections of Rd
      files is allowed again.  This had been changed for the new Rd
      format in R 2.10.0 but was only documented on the developer site
      and was handled inconsistently by the converters: text and
      example conversion removed the escapes but HTML conversion did
      not.

    • The PCRE library has been updated to version 8.01, a bug-fix
      release.

    • tools::readNEWS() now accepts a digit as the first character of a
      news section.

  BUG FIXES:

    • Using read.table(header=TRUE) on a header with an embedded new
      line would copy part of the header into the data.  (PR#14103)

    • qpois(p = 1, lambda = 0) now gives 0 as for all other p.
      (PR#14135)

    • Functions related to string comparison (e.g. unique(), match())
      could cause crashes when used with strings not in the native
      encoding, e.g. UTF-8 strings on Windows.  (PR#14114 and PR#14125)

    • x[ , drop=TRUE] dropped an NA level even if it was in use.

    • The dynamic HTML help system reported the wrong MIME type for the
      style sheet.

    • tools::codoc() (used by R CMD check) was missing cases where the
      function had no arguments but was documented to have some.

    • Help links containing special characters (e.g. "?") were not
      generated correctly when rendered in HTML.  (PR#14155)

    • lchoose(a, k) no longer wrongly gives NaN for negative a.

    • ks.test() could give a p-value that was off by one observation
      due to rounding error.  (PR#14145)

    • readBin()/readChar() when reading millions of character strings
      in a single call used excessive amounts of memory (which also
      slowed them down).

    • R CMD SHLIB could fail if used with paths that were not
      alphanumeric, e.g. contained +.  (PR#14168)

    • sprintf() was not re-entrant, which potentially caused problems
      if an as.character() method called it.

    • The quartz() device did not restore the clipping region when
      filling the background for a new page.  This could be observed in
      multi-page bitmap output as stale outer regions of the plot.

    • p.adjust(method, n) now works correctly for the rare case n >
      length(p), also when method differs from "bonferroni" or "none",
      thanks to a patch from Gordon Smyth.

    • tools::showNonASCII() failed to detect non-ASCII characters if
      iconv() (incorrectly) converted them to different ASCII
      characters.  (Seen on Windows only.)

    • tcrossprod() wrongly failed in some cases when one of the
      arguments was a vector and the other a matrix.

    • [cr]bind(..., deparse.level=2) was not always giving names when
      documented to do so.  (Discovered whilst investigating PR#14189.)

    • match(incomparables=<non-NULL>) could in rare cases
      infinite-loop.

    • poisson.test() needed to pass argument conf.level to
      binom.test().  (PR#14195)

    • The "nls" method for df.residual() gave incorrect results for
      models fitted with na.action = na.exclude.  (PR#14194)

    • A change to options(scipen=) was only implemented when printing
      next occurred, even though it should have affected intervening
      calls to axis(), contour() and filledcontour().

    • prettyNum(drop0trailing=TRUE) did not handle signs of imaginary
      parts of complex numbers correctly (and this was used by str():
      PR#14201).

    • system.time() had the sys.child component wrong (copied
      user.child instead) on systems with HAVE_GETRUSAGE.  (PR#14210)

    • Changing both line texture and line cap (end) resulted in the
      latter to be omitted form the PDF code.  In addition, line cap
      (end) and join are now set explicitly in PDF output to ensure
      correct defaults.

    • The suppression of auto-rotation in bitmap() and dev2bitmap()
      with the "pdfwrite" device was not working correctly.

    • plot(ecdf(), log="x") no longer gives an incorrect warning.

    • read.fwf() works again when argument file is a connection.

    • Startup files will now be found if their paths exceed 255 bytes.
      (PR#14228)

    • contrasts<- (in the stats package) no longer has an undeclared
      dependence on methods (introduced in 2.10.0).

CHANGES IN R VERSION 2.10.1:

  NEW FEATURES:

    • The PCRE library has been updated to version 8.00.

    • R CMD INSTALL has new options --no-R, --no-libs, --no-data,
      --no-help, --no-demo, --no-exec, and --no-inst to suppress
      installation of the specified part of the package.  These are
      intended for special purposes (e.g. building a database of help
      pages without fully installing all packages).

    • The documented line-length limit of 4095 bytes when reading from
      the console now also applies also to parse(file="") (which
      previously had a limit of around 1024 bytes).

    • A Bioconductor mirror can be set for use by setRepositories()
      _via_ the option "BioC_mirror", e.g. the European mirror can be
      selected by
      options(BioC_mirror="http://bioconductor.statistik.tu-dortmund.de").

    • Double-clicking in a tk_select.list() list box now selects the
      item and closes the list box (as happens on the Windows
      select.list() widget).

  INSTALLATION:

    • configure will be able to find a usable libtiff in some rare
      circumstances where it did not previously (where libtiff needed
      to be linked explicitly against -ljpeg).

    • Making refman.pdf works around a problem with the indexing with
      hyperref 6.79d and later.

  DEPRECATED & DEFUNCT:

    • The extended argument is deprecated in strsplit(), grep(),
      grepl(), sub(), gsub(), regexpr() and gregexpr() (not just the
      value extended = FALSE) and will be removed in R 2.11.0.

  BUG FIXES:

    • trigamma(x) and other psigamma(x, n) calls are now accurate for
      very large abs(x).  (PR#14020)

    • [g]sub(perl=FALSE, fixed=FALSE) could use excessive stack space
      when used with a very long vector containing some non-ASCII
      strings.

    • The default method of weighted.mean(na.rm = TRUE) did not omit
      weights for NA observations in 2.10.0.  (PR#14032)

    • [g]regexpr(pattern, fixed = TRUE) returned match positions in
      bytes (not characters) in an MBCS locale if pattern was a single
      byte.

      [g]sub(fixed = TRUE) with a single-byte pattern could conceivably
      have matched part of a multibyte character in a non-UTF-8 MBCS.

    • findLineNum() and setBreakpoint() would sometimes fail if the
      specified file was not in the current directory.

    • Package tcltk's demo(tkdensity) was broken in 2.9.0 when demo()
      was changed to set par(ask = TRUE).

    • gsub() with backrefs could fail on extremely long strings
      (hundreds of thousands of characters) due to integer overflow in
      a length calculation.

    • abline(untf=TRUE) now uses a better x-grid in log-scale, e.g.,
      for plot(c(1,300), c(1,300), log="xy"); abline(4,1, untf=TRUE).

    • detach()/unloadNamespace() arrange to flush the package's
      lazyload cache of R objects once the package/namespace is no
      longer needed.

    • There have been small fixes to the rendering of help, e.g.
      \command is now rendered verbatim (so e.g. -- is not interpreted,
      PR#14045).

      Also, there are many small changes to help files where the new
      converters were not rendering them in the same way as before.

    • available.packages() would fail when run on a repository with no
      packages meeting the filtering conditions.  (PR#14042)

    • rep(x, times, each = 2) gave invalid results when the times
      argument was a vector longer than x.  Reported by Bill Dunlap.

    • An error when unloadNamespace() attempted to run the .onUnload()
      function gave an error in the reporting function and so was not
      reported properly.

    • Text help rendering did not handle very long input lines
      properly.

    • promptMethods() generated signature documentation improperly.

    • pgamma(x, a, lower.tail=FALSE) and qgamma(...) are now
      considerably more accurate in some regions for very small a.
      qgamma() now correctly returns 0 instead of NaN in similar
      extreme cases, and qgamma() no longer warns in the case of small
      a, see (PR#12324).

    • unname() now also removes names from a zero length vector.

    • Printing results from ls.str() no longer evaluates unevaluated
      calls.

    • complete.cases() failed on a 0-column data frame argument.
      (Underlies PR#14066.)

      It could return nonsensical results if no input determined the
      number of cases (seen in the no-segfault tests).

    • An error in nls() with a long formula could cause a segfault.
      (PR#14059)

    • qchisq(p, df, ncp, lower.tail = FALSE) with ncp >= 80 was
      inaccurate for small p (as the help page said): it is now less
      inaccurate.  (In part, PR#13999.)

      For ncp less than but close to 80, pchisq() and qchisq() are more
      accurate for probablilities very close to 1 (a series expansion
      was truncated slightly too early).

      pchisq(x, df, ncp) can no longer return values just larger than
      one for large values of ncp.

    • intToUtf8() could fail when asked to produce 10Mb or more
      strings, something it was never intended to do: unfortunately
      Windows crashed R (other OSes reported a lack of resources).
      (PR#14068)

    • chisq.test() could fail when given argument x or y which deparsed
      to more than one line.  (Reported by Laurent Gauthier.)

    • S4 methods are uncached whenever the name space containing them
      is unloaded (by unloadNamespace() as well as by detach(unload =
      TRUE)).

    • The internal record-keeping by dyn.load/dyn.unload was
      incomplete, which could crash R if a DLL that registered
      .External routines had earlier been unloaded.

    • bessel[JY](x, nu) with nu a negative integer (a singular case) is
      now correct, analogously to besselI(), see PR#13556.

    • tools::file_path_as_absolute() doubled the file separator when
      applied to a file such as "/vmunix" or (on Windows) "d:/afile" in
      a directory for which getwd() would return a path with a trailing
      separator (largely cosmetic, as reasonable file systems handle
      such a path correctly).  (Perhaps what was meant by PR#14078.)

    • unsplit(drop = TRUE) applied to a data frame failed to pass drop
      to the computation of row names.  (PR#14084)

    • The "difftime" method of mean() ignored its na.rm argument.

    • tcltk::tk_select.list() is now more likely to remove the widget
      immediately after selection is complete.

    • Adding/subtracting a "difftime" object to/from a "POSIXt" or
      "Date" object works again (it was broken by the addition of
      Ops.difftime).

    • Conversion to latex of an Rd file with no aliases failed.

    • wilcox.test(conf.int=TRUE) has achieved.level corrected and, for
      exact=FALSE, now returns a estimate component which does not
      depend on the alternative used.

    • help.search() failed when the package argument was specified.
      (PR#14113)

    • switch(EXPR = "A") now returns NULL, as does switch(1) (which
      used to signal an error).

CHANGES IN R VERSION 2.10.0:

  SIGNIFICANT USER-VISIBLE CHANGES:

    • Package help is now converted from Rd by the R-based converters
      that were first introduced in 2.9.0.  This means

        • Packages that were installed by R-devel after 2009-08-09
          should not be used with earlier versions of R, and most
          aspects of package help (including the runnable examples)
          will be missing if they are so used.

        • Text, HTML and latex help and examples for packages installed
          under the new system are converted on-demand from stored
          parsed Rd files.  (Conversions stored in packages installed
          under R < 2.10.0 are used if no parsed Rd files are found.
          It is recommended that such packages be re-installed.)

    • HTML help is now generated dynamically using an HTTP server
      running in the R process and listening on the loopback interface.

        • Those worried about security implications of such a server
          can disable it by setting the environment variable
          R_DISABLE_HTTPD to a non-empty value.  This disables
          help.start() and HTML help (so text help is shown instead).

        • The Java/Javascript search engine has been replaced by an
          HTML interface to help.search().  help.start() no longer has
          an argument searchEngine as it is no longer needed.

        • The HTML help can now locate cross-references of the form
          \link[pkg]{foo} and \link[pkg:foo]{bar} where foo is an alias
          in the package, rather than the documented (basename of a)
          filename (since the documentation has been much ignored).

  NEW FEATURES:

    • polygon(), pdf() and postscript() now have an argument
      fillOddEven (default FALSE), which controls the mode used for
      polygon fills of self-intersecting shapes.

    • New debugonce() function; further, getOption("deparse.max.lines")
      is now observed when debugging, from a code suggestion by John
      Brzustowski.  (PR#13647/8)

    • plot() methods for "stepfun" and hence "ecdf" no longer plot
      points by default for n >= 1000.

    • [g]sub(perl=TRUE) now also supports "\E" in order to *end* "\U"
      and "\L" case changes, thanks to a patch from Bill Dunlap.

    • factor(), levels()<-, etc, now ensure that the resulting factor
      levels are unique (as was always the implied intention).  Factors
      with duplicated levels are still constructible by low-level
      means, but are now declared illegal.

    • New print() (S3) method for class "function", also used for
      auto-printing.  Further, .Primitive functions now print and
      auto-print identically.  The new method is based on code
      suggestions by Romain François.

    • The print() and toLatex() methods for class "sessionInfo" now
      show the locale in a nicer format and have arguments to suppress
      locale information.

    • In addition to previously only round(), there are other Math
      group (S3) methods for "difftime", such as floor(), signif(),
      abs(), etc.

    • For completeness, old.packages() and available.packages() allow
      arguments type to be specified (you could always specify
      arguments available or contriburl).

    • available.packages() by default only returns information on the
      latest versions of packages whose version requirements are
      satisfied by the currently running R.

    • tools::write_PACKAGES() has a new argument latestOnly, which
      defaults to TRUE when only the latest versions in the repository
      will be listed in the index.

    • getOption() has a new argument default that is returned if the
      specified option is not set.  This simplifies querying a value
      and checking whether it is NULL or not.

    • parse() now warns if the requested encoding is not supported.

    • The "table" method of as.data.frame() gains a stringsAsFactors
      argument to allow the classifying factors to be returned as
      character vectors rather than the default factor type.

    • If model.frame.default() encounters a character variable where
      xlev indicates a factor, it now converts the variable to a factor
      (with a warning).

    • curve() now returns a list containing the points that w§ere
      drawn.

    • spineplot() now accepts axes = FALSE, for consistency with other
      functions called by plot.factor().

    • The Kendall and Spearman methods of cor.test() can optionally use
      continuity correction when not computing exact p-values.  (The
      Kendall case is the wish of PR#13691.)

    • R now keeps track of line numbers during execution for code
      sourced with options(keep.source = TRUE).  The source reference
      is displayed by debugging functions such as traceback(),
      browser(), recover(), and dump.frames(), and is stored as an
      attribute on each element returned by sys.calls().

    • More functions now have an implicit (S4) generic definition.

    • quantile.default() now disallows factors (wish of PR#13631) and
      its help documents what numeric-like properties its input need to
      have to work correctly.

    • weighted.mean() is now generic and has "Date", "POSIXct" and
      "POSIXlt" methods.

    • Naming subscripts (e.g. x[i=1, j=2]) in data.frame methods for [
      and [[ now gives a warning.  (Names are ignored in the default
      method, but could have odd semantics for other methods, and do
      for the data.frame ones.)

    • as.data.frame() has an "aovproj" method.  (Wish of PR#13505)

    • as.character(x) for numeric x no longer produces strings such as
      "0.30", i.e., with trailing zeros.  This change also renders
      levels construction in factor() more consistent.

    • codocClasses(), which checks consistency of the documentation of
      S4 class slots, now does so in considerably more cases.  The
      documentation of inherited slots (from superclasses) is now
      optional.  This affects R CMD check <pkg> when the package
      defines S4 classes.

    • codoc() now also checks S4 methods for code/documentation
      mismatches.

    • for(), while(), and repeat() loops now always return NULL as
      their (invisible) value.  This change was needed to address a
      reference counting bug without creating performance penalties for
      some common use cases.

    • The print() method for ls.str() results now obeys an optional
      digits argument.

    • The method argument of glm() now allows user-contributed methods.

    • More general reorder.default() replaces functionality of
      reorder.factor() and reorder.character().

    • The function aspell() has been added to provide an interface to
      the Aspell spell-checker.

    • Filters RdTextFilter() and SweaveTeXFilter() have been added to
      the tools package to provide support for aspell() or other spell
      checkers.

    • xtabs() with the new argument sparse = TRUE now returns a sparse
      Matrix, using package Matrix.

    • contr.sum() etc gain an argument sparse which allows sparse
      matrices to be returned.

      contrasts() also gains a sparse argument which it passes to the
      actual contrast function if that has a formal argument sparse.

      contrasts(f, .) <- val now also works when val is a sparse
      Matrix.  It is planned that model.matrix() will work with such
      factors f in the future.

    • readNEWS() will recognize a UTF-8 byte-order mark (BOM) in the
      NEWS file.  However, it is safer to use only ASCII code there
      because not all editors recognize BOMs.

    • New utility function inheritedSlotNames() for S4 class
      programming.

    • tabulate() now allows NAs to pass through (and be ignored).

    • If debug() is called on an S3 generic function then all methods
      are debugged as well.

    • Outlier symbols drawn by boxplot() now obey the outlwd argument.
      Reported by Jurgen Kluge.

    • svd(x) and eigen(x) now behave analogously to qr(x) in accepting
      logical matrices x.

    • File NEWS is now in UTF-8, and has a BOM (often invisible) on the
      first line, and Emacs local variables set for UTF-8 at the end.
      RShowDoc("NEWS") should display this correctly, given suitable
      fonts.

    • terms.formula(simplify = TRUE) now does not deparse the LHS and
      so preserves non-standard responses such as `a: b` (requested by
      Sundar Dorai-Raj).

    • New function news() for building and querying R or package news
      information.

    • z^n for integer n and complex z is more accurate now if |n| <=
      65536.

    • factor(NULL) now returns the same as factor(character(0)) instead
      of an error, and table(NULL) consequently does analogously.

    • as.data.frame.vector() (and its copies) is slightly faster by
      avoiding a copy if there are no names (following a suggestion of
      Tim Hesterberg).

    • writeLines(), writeBin() and writeChar() have a new argument
      useBytes.  If false, character strings with marked encodings are
      translated to the current locale (as before) but if true they are
      written byte-by-byte.

    • iconv() has a new argument mark which can be used (by experts) to
      suppress the declaration of encodings.

    • DESCRIPTION file's LinkingTo specs are now recognized as
      installation dependencies, and included in package management
      computations.

    • Standardized DESCRIPTION file License specs are now available for
      package management computations.

    • "\uxxxx" and "\Uxxxxxxxx" escapes can now be parsed to a UTF-8
      encoded string even in non-UTF-8 locales (this has been
      implemented on Windows since R 2.7.0).  The semantics have been
      changed slightly: a string containing such escapes is always
      stored in UTF-8 (and hence is suitable for portably including
      Unicode text in packages).

    • New as.raw() method for "tclObj" objects (wish of PR#13758).

    • Rd.sty now makes a better job of setting email addresses,
      including using a monospaced font.

    • textConnection() gains an encoding argument to determine how
      input strings with marked encodings will be handled.

    • R CMD Rd2pdf is available as a shortcut for R CMD Rd2dvi --pdf.

    • R CMD check now checks links where a package is specified
      (\link[pkg]{file} or \link[pkg:file]{topic}), if the package is
      available.  It notes if the package is not available, as in many
      cases this is an error in the link.

    • identical() gains three logical arguments, which allow for even
      more differentiation, notably -0 and 0.

    • legend() now can specify the border color of filled boxes, thanks
      to a patch from Frederic Schutz.

    • Indexing with a vector index to [[ ]] has now been extended to
      all recursive types.

    • Pairlists may now be assigned as elements of lists.  (Lists could
      always be created with pairlist elements, but [[<- didn't support
      assigning them.)

    • The parser now supports C-preprocessor-like #line directives, so
      error messages and source references may refer to the original
      file rather than an intermediate one.

    • New functions findLineNum() and setBreakpoint() work with the
      source references to find the location of source lines and set
      breakpoints (using trace()) at those lines.

    • Namespace importing is more careful about warning on masked
      generics, thanks to a patch by Yohan Chalabi.

    • detach() now has an argument character.only with the same meaning
      as for library() or require().

    • available.packages() gains a filters argument for specifying the
      filtering operations performed on the packages found in the
      repositories.  A new built-in "license/FOSS" filter only retains
      packages for which installation can proceed solely based on
      packages which can be verified as Free or Open Source Software
      (FOSS) employing the available license specifications.

    • In registering an S3 class by a call to setOldClass(), the data
      part (e.g., the object type) required for the class can be
      included as one of the superclasses in the Classes argument.

    • The argument f to showMethods() can be an expression evaluating
      to a generic function, allowing methods to be shown for
      non-exported generics and other nonstandard cases.

    • sprintf() now supports %o for octal conversions.

    • New function Sys.readlink() for information about symbolic links,
      including if a file is a symbolic link.

    • Package tools has new functions checkRdaFiles() and
      resaveRdaFiles() to report on the format of .rda/.RData data
      files, and to re-save them in a different compressed format,
      including choosing the most compact format available.

      A new INSTALL option, --resave-data, makes use of this.

    • File ~/.R/config is used in preference to ~/.Rconfig, and these
      are now documented in ‘R Installation and Administration’.

    • Logic operations with complex numbers now work, as they were
      always documented to, and as in S.

    • arrows() and segments() allow one of x1 or y1 to be omitted to
      simplify the specification of vertical or horizontal lines
      (suggestion of Tim Hesterberg).

    • approxfun() is faster by avoiding repeated NA checks (diagnosis
      and patch by Karline Soetaert & Thomas Petzoldt).

    • There are the beginnings of a Nynorsk translation by Karl Ove
      Hufthammer.

    • stripchart() allows par bg to be passed in for the background
      colour for pch = 21 (wish of PR#13984).

    • New generic function .DollarNames() to enable class authors to
      customize completion after the $ extractor.

    • load(), save(), dput() and dump() now open a not-yet-open
      connection in the appropriate mode (as other functions using
      connections directly already did).

  REGULAR EXPRESSIONS:

    • A different regular expression engine is used for basic and
      extended regexps and is also for approximate matching.  This is
      based on the TRE library of Ville Laurikari, a modified copy of
      which is included in the R sources.

      This is often faster, especially in a MBCS locale.

      Some known differences are that it is less tolerant of invalid
      inputs in MBCS locales, and in its interpretation of undefined
      (extended) regexps such as "^*".  Also, the interpretation of
      ranges such as [W-z] in caseless matching is no longer to map the
      range to lower case.

      This engine may in future be used in ‘literal’ mode for fixed =
      TRUE, and there is a compile-time option in src/main/grep.c to do
      so.

    • The use of repeated boundary regexps in gsub() and gregexpr() as
      warned about in the help page does not work in this engine (it
      did in the previous one since 2005).

    • Extended (and basic) regexps now support same set of options as
      for fixed = TRUE and perl = TRUE, including useBytes and support
      for UTF-8-encoded strings in non-UTF-8 locales.

    • agrep() now has full support for MBCS locales with a modest speed
      penalty.  This enables help.search() to use approximate matching
      character-wise rather than byte-wise.

    • [g]sub use a single-pass algorithm instead of matching twice and
      so is usually faster.

    • The perl = TRUE versions now work correctly in a non-UTF-8 MBCS
      locale, by translating the inputs to UTF-8.

    • useBytes = TRUE now inhibits the translation of inputs with
      marked encodings.

    • strsplit() gains a useBytes argument.

    • The algorithm used by strsplit() has been reordered to batch by
      elements of split: this can be much faster for fixed = FALSE (as
      multiple compilation of regexps is avoided).

    • The help pages, including ?regexp, have been updated and should
      be consulted for details of the new implementations.

  HELP & Rd FILE CHANGES:

    • A new dynamic HTML help system is used by default, and may be
      controlled using tools::startDynamicHelp().  With this enabled,
      HTML help pages will be generated on request, resolving links by
      searching through the current .libPaths().  The user may set
      options("help.ports") to control which IP port is used by the
      server.

    • help.start() no longer sets options(htmlhelp = TRUE) (it used to
      on Unix but not on Windows).  Nor does it on Unix reset the
      "browser" option if given an argument of that name.

      Arguments update and remote are now available on all platforms:
      the default is update = FALSE since the http server will update
      the package index at first use.

    • help() has a new argument help_type (with default set by the
      option of that name) to supersede arguments offline, htmlhelp and
      chmhelp (although for now they still work if help_type is unset).
      There is a new type, "PDF" to allow offline PDF (rather than
      PostScript).

      A function offline_help_helper() will be used if this exists in
      the workspace or further down the search path, otherwise the
      function of that name in the utils name space is used.

    • Plain text help is now used as the fallback for HTML help (as it
      always was for Compiled HTML help on Windows).

    • It is possible to ask for static HTML pages to be prebuilt _via_
      the configure option --enable-prebuilt-html.  This may be useful
      for those who wish to make HTML help available outside R, e.g. on
      a local web site.

    • An experimental tag \Sexpr has been added to Rd files, to
      evaluate expressions at build, install, or render time.
      Currently install time and render time evaluation are supported.

    • Tags \if, \ifelse and \out have been added to allow
      format-specific (or more general, using \Sexpr) conditional text
      in man pages.

    • The parse_Rd() parser has been made more tolerant of coding
      errors in Rd files: now all syntax errors are reported as
      warnings, and an attempt is made to continue parsing.

    • parse_Rd() now has an argument fragment (default FALSE) to accept
      small fragments of Rd files (so that \Sexpr can output Rd code
      which is then parsed).

    • parse_Rd() now always converts its input to UTF-8.  The Rd2*
      rendering functions have a new argument, outputEncoding, which
      controls how their output is encoded.

    • parse_Rd() no longer includes the newline as part of a "%"-style
      comment.

    • There have been various bug fixes and code reorganization in the
      Rd renderers Rd2HTML, Rd2latex, Rd2txt, and Rd2ex.

      All example files are now created with either ASCII or UTF-8
      encoding, and the encoding is only marked in the file if there is
      any non-UTF-8 code (previously it was marked if the help file had
      non-ASCII contents, possibly in other sections).

    • print.Rd() now adds necessary escape characters so that printing
      and re-parsing an Rd object should produce an equivalent object.

    • parse_Rd() was incorrectly handling multiple backslashes in R
      code strings, converting 4n+3 backslashes to 2n+1 instead of
      2n+2.

    • parse_Rd() now recognizes the \var tag within a quoted string in
      R-like text.

    • parse_Rd() now treats the argument of \command as LaTeX-like,
      rather than verbatim.

  COMPRESSION:

    • New function untar() to list or unpack tar archives, possibly
      compressed.  This uses either an external tar command or an
      internal implementation.

    • New function tar() to create (possibly compressed) tar archives.

    • New functions memCompress() and memDecompress() for in-memory
      compression and decompression.

    • bzfile() has a compress argument to select the amount of effort
      put into compression when writing.

    • New function xzfile() for use with xz-compressed files.  (This
      can also read files compressed by some versions of lzma.)

    • gzfile() looks at the file header and so can now also read
      bzip2-ed files and xz-compressed files.

    • There are the new options of save(compress = "bzip2") and "xz" to
      use bzip2 or xz compression (which will be slower, but can give
      substantially smaller files).  Argument compression_level gives
      finer control over the space/time tradeoffs.

      load() can read such saves (but only as from this version of R).

    • R CMD INSTALL/check and tools::writePACKAGES accept a wider range
      of compressed tar archives.  Precisely how wide depends on the
      capabilities of the host system's tar command: they almost always
      include .tar.bz2 archives, and with modern versions of tar other
      forms of compression such as lzma and xz, and arbitrary
      extensions.

    • R CMD INSTALL has a new option --data-compress to control the
      compression used when lazy-loading data.  New possibilities are
      --data-compress=bzip2 which will give ca 15% better compression
      at the expense of slower installation times, and
      --data-compress=xz, often giving even better compression on large
      datasets at the expense of much longer installation times.  (The
      latter is used for the recommended packages: it is particularly
      effective for survival.)

    • file() for open = "", "r" or "rt" will automagically detect
      compressed files (from gzip, bzip2 or xz).  This means that
      compressed files can be specified by file name (rather than _via_
      a gzfile() connection) to read.table(), readlines(), scan() and
      so on.

    • data() can handle compressed text files with extensions
      .{txt,tab,csv}.{gz,bz2,xz} .

  DEPRECATED & DEFUNCT:

    • png(type="cairo1") is defunct: the value is no longer recognized.

    • tools::Rd_parse() is defunct (as this version of R uses only Rd
      version 2).

    • Use of file ~/.Rconf (which was deprecated in favour of
      ~/.Rconfig in 2004) has finally been removed.

    • Bundles of packages are deprecated.  See ‘Writing R Extensions’
      for the steps needed to unbundle a bundle.

    • help() arguments offline, htmlhelp and chmhelp are deprecated in
      favour of help_type.

    • clearNames() (in package stats) is deprecated for unname().

    • Basic regular expressions (extended = FALSE) are deprecated in
      strsplit, grep and friends.  There is a precise POSIX standard
      for them, but it is not what recent RE engines implement, and it
      seems that in almost all cases package authors intended fixed =
      TRUE when using extended = FALSE.

    • methods::trySilent() is deprecated in favour of try(silent=TRUE)
      or - more efficiently and flexibly - something like
      tryCatch(error = function(e) e).

    • index.search() is deprecated: there are no longer directories of
      types other than help.

  INSTALLATION:

    • cairo >= 1.2 is now required (1.2.0 was released in July 2006)
      for cairo-based graphics devices (which remain optional).

    • A suitable iconv() is now required: support for configure option
      --without-iconv has been withdrawn (it was deprecated in R
      2.5.0).

    • Perl is no longer ‘essential’.  R can be built without it, but
      scripts R CMD build, check, Rprof and Sd2d currently require it.

    • A system glob function is now essential (a working Sys.glob() has
      been assumed since R 2.9.0 at least).

    • C99 support for MBCS is now required, and configure option
      --disable-mbcs has been withdrawn.

    • Having a version of tar capable of automagically detecting
      compressed archives is useful for utils::untar(), and so gtar (a
      common name for GNU tar) is preferred to tar: set environment
      variable TAR to specify a particular tar command.

  INTERNATIONALIZATION:

    • There is some makefile support for adding/updating translations
      in packages: see po/README and ‘Writing R Extensions’.

      There is support for the use of dngettext for C-level
      translations in packages: see ‘Writing R Extensions’.

  BUG FIXES:

    • Assigning an extra 0-length column to a data frame by DF[, "foo"]
      <- value now works in most cases (by filling with NAs) or fails.
      (It used to give a corrupt data frame.)

    • validObject() avoids an error during evaluation in the case of
      various incorrect slot definitions.

    • n:m now returns a result of type "integer" in a few more boundary
      cases.

    • The zap.ind argument to printCoefmat() did not usually work as
      other code attempted to ensure that non-zero values had a
      non-zero representation.

    • printCoefmat() formatted groups of columns together, not just the
      cs.ind group but also the zap.ind group and a residual group.  It
      now formats all columns except the cs.ind group separately (and
      zaps the zap.ind group column-by-column).  The main effect will
      be see in the output from print.anova(), as this grouped SS-like
      columns in the zap.ind group.

    • R_ReplDLLinit() initializes the top-level jump so that some
      embedded applications on Windows no longer crash on error.

    • identical() failed to take the encoding of character strings into
      account, so identical byte patterns are not necessarily identical
      strings, and similarly Latin-1 and UTF-8 versions of the same
      string differ in byte pattern.

    • methods(f) used to warn unnecessarily for an S4 generic f which
      had been created based on an existing S3 generic.

    • The check for consistent ordering of superclasses was not
      ignoring all conditional relations (the symptom was usually
      spurious warnings for classes extending "array").

    • Trying to assign into a raw vector with an index vector
      containing NAs could cause a segfault.  Reported by Hervé Pagès.

    • Rscript could segfault if (by user error) its filename argument
      was missing.  Reported by Martin Morgan.

    • getAnywhere() (and functions that use it, including argument
      completion in the console) did not handle special built-in
      functions.  Reported by Romain Francois.

    • order() was missing a PROTECT() call and so could segfault when
      called on character data under certain (rare) circumstances
      involving marked non-native encodings.

    • prettyNum(z, drop0trailing=TRUE) did not work correctly when z
      was a complex vector.  Consequently, str(z, ...) also did not.
      (PR#13985)

    • make distclean removed too many files in etc/ if builddir =
      srcdir.

    • R CMD replaced TEXINPUTS rather than appending to it (as
      documented and intended).

    • help.start() no longer fails on unix when "browser" is a
      function.

    • pbeta(x, ..., log.p = TRUE) is sometimes more accurate, e.g., for
      very small x.

    • Unserializing a pre-2.8 workspace containing pure ASCII character
      objects with a Latin-1 or UTF-8 encoding would corrupt the
      CHARSXP cache.

