[R] R 3.2.0 is released

[Peter Dalgaard]

The build system rolled up R-3.2.0.tar.gz (codename "Full of Ingredients") this morning.

The list below details the changes in this release.

You can get the source code from

http://cran.r-project.org/src/base/R-3/R-3.2.0.tar.gz

or wait for it to be mirrored at a CRAN site nearer to you.

Binaries for various platforms will appear in due course.


For the R Core Team,

Peter Dalgaard


These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:

MD5 (AUTHORS) = eb97a5cd38acb1cfc6408988bffef765
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = a699fa0eeef280b78134f0abe0b1c1b0
MD5 (INSTALL) = 3964b9119adeaab9ceb633773fc94aac
MD5 (NEWS) = 99876f56fc07a7eb20825b85add9b66e
MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8
MD5 (NEWS.1) = eb78c4d053ec9c32b815cf0c2ebea801
MD5 (NEWS.2) = 8e2f4d1d5228663ae598a09bf1e2bc6b
MD5 (R-latest.tar.gz) = 66fa17ad457d7e618191aa0f52fc402e
MD5 (README) = aece1dfbd18c1760128c3787f5456af6
MD5 (RESOURCES) = a59076c1ac7e9bab0f0a38b3f57a3914
MD5 (THANKS) = ba00f6cc68a823e1741cfa6011f40ccb
MD5 (R-3/R-3.2.0.tar.gz) = 66fa17ad457d7e618191aa0f52fc402e


This is the relevant part of the NEWS file

CHANGES IN 3.2.0:

 NEW FEATURES:

   * anyNA() gains a recursive argument.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

     (In part, wish of PR#15819.)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

   * New function isLoadedNamespace() for readability and speed.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

 INSTALLATION and INCLUDED SOFTWARE:

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

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

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

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

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

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

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

 UTILITIES:

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

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

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

   * The HTML generated by tools::Rd2HTML() and tools::toHTML()
     methods is now 'XHTML 1.0 Strict'.

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

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

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

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

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

   * R CMD check --as-cran now:

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

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

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

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

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

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

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

 C-LEVEL FACILITIES:

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

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

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

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

   * isPairList() now returns TRUE for DOTSXP.

 WINDOWS BUILD CHANGES:

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

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

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

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

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

 PACKAGE INSTALLATION:

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

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

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

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

 DEPRECATED AND DEFUNCT:

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

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

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

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

 BUG FIXES:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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