[R] R 2.7.0 is released

From: Peter Dalgaard <P.Dalgaard_at_biostat.ku.dk>
Date: Tue, 22 Apr 2008 10:16:54 +0200


I've rolled up R-2.7.0.tar.gz a short while ago. This is a development release which contains a number of new features.

Also, a number of mostly minor bugs have been fixed. See the full list of changes below.

You can get it (later today) from

http://cran.r-project.org/src/base/R-2/R-2.7.0.tar.gz

or wait for it to be mirrored at a CRAN site nearer to you. In case of impatience, try http://www.biostat.ku.dk/~pd/R-release

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:

9eaee3eceec1d5f72cea5640ca90768c R-latest.tar.gz 9eaee3eceec1d5f72cea5640ca90768c R-2.7.0.tar.gz 3f4331cd3d66c36b9e350b0576fa8f42 FAQ
020479f381d5f9038dcb18708997f5da RESOURCES eb723b61539feef013de476e68b5c50a COPYING a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB 070cca21d9f8a6af15f992edb47a24d5 AUTHORS 1ad28cbc84485ccdf4ce5721b34ed645 THANKS f7a51a08be0aab537123b0fc66cd0e79 NEWS
ff4bd9073ef440b1eb43b1428ce96872 ONEWS
4f004de59e24a52d0f500063b4603bcb OONEWS 433182754c05c2cf7a04ad0da474a1d0 README 70447ae7f2c35233d3065b004aa4f331 INSTALL

This is the relevant part of the NEWS file:

                CHANGES IN R VERSION 2.7.0


SIGNIFICANT USER-VISIBLE CHANGES     o The default graphics device in non-interactive use is now

        pdf() rather than postscript().  [PDF viewers are now
        more widely available than PostScript viewers.]

        The default width and height for pdf() and bitmap() have been
        changed to 7 (inches) to match the screen devices.

    o   Most users of the X11() device will see a new device that has
        different fonts, anti-aliasing of lines and fonts and
        supports semi-transparent colours.

    o   Considerable efforts have been made to make the default output
        from graphics devices as similar as possible (and in
        particular close to that from postscript/pdf).  Many devices
        were misinterpreting 'pointsize' in some way, for example as
        being in device units (pixels) rather than in points.

    o   Packages which include graphics devices need to be re-installed
        for this version of R, with recently updated versions.


NEW FEATURES     o The apse code used by agrep() has been updated to version

        0.16, with various bug fixes.

        agrep() now supports multibyte character sets.

    o any() and all() avoid coercing zero-length arguments (which

        used a surprising amount of memory) since they cannot affect
        the answer.

        Coercion of other than integer arguments now gives a warning
        as this is often a mistake (e.g. writing all(pr) > 0 instead
        of all(pr > 0) ).

    o   as.Date(), as.POSIXct() and as.POSIXlt() now convert numeric
        arguments (days or seconds since some epoch) provided the
        'origin' argument is specified.

    o   New function as.octmode() to create objects such as file
        permissions.

    o   as.POSIXlt() is now generic, and it and as.POSIXct() gain a
        '...' argument.  The character/factor methods now accept a
        'format' argument (analogous to that for as.Date).

    o   New function browseVignettes() lists available vignettes in an
        HTML browser with links to PDF, Rnw, and R files.

    o   There are new capabilities "aqua" (for the AQUA GUI and quartz()
        device on Mac OS X) and "cairo" (for cairo-based graphics
        devices).

    o   New function checkNEWS() in package 'tools' that detects common
        errors in NEWS file formatting.

    o   deparse() gains a new argument 'nlines' to limit the number of
        lines of output, and this is used internally to make several
        functions more efficient.

    o   deriv() now knows the derivatives of digamma(x), trigamma(x)
        and psigamma(x, deriv) (wrt to x).

    o   dir.create() has a new argument 'mode', used on Unix-alikes

(only) to set the permissions on the created directory.
o Where an array is dropped to a length-one vector by drop() or [, drop = TRUE], the result now has names if exactly one of the dimensions was named. (This is compatible with S.) Previously there were no names. o The 'incomparables' argument to duplicated(), unique() and match() is now implemented, and passed to match() from merge(). o dyn.load() gains a 'DLLpath' argument to specify the path for dependent DLLs: currently only used on Windows. o The spreadsheet edit() methods (and used by fix()) for data frames and matrices now warn when classes are discarded. When editing a data frame, columns of unknown type (that is not numeric, logical, character or factor) are now converted to character (instead of numeric). o file.create() has a new argument 'showWarnings' (default TRUE) to show an informative warning when creation fails, and dir.create() warns under more error conditions.

    o New higher-order functions Find(), Negate() and Position().

    o [dpqr]gamma(*, shape = 0) now work as limits of 'shape -> 0',

        corresponding to the point distribution with all mass at 0.

    o An informative warning (in addition to the error message) will

        be given when the basic, extended or perl mode of grep(),
        strsplit() and friends fails to compile the pattern.

    o   More study is done of perl=TRUE patterns in grep() and friends
        when length(x) > 10: this should improve performance on long
        vectors.

    o   grep(), strsplit() and friends with fixed=TRUE or perl=TRUE
        work in UTF-8 and preserve the UTF-8 encoding for UTF-8 inputs
        where supported.

    o help.search() now builds the database about 3x times faster.

    o iconv() now accepts "UTF8" on all platforms (many did, but not

        e.g. libiconv as used on Windows).

    o identity() convenience function to be used for programming.

    o In addition to warning when 'pkgs' is not found,

        install.packages() now reports if it finds a valid package
        with only a case mismatch in the name.

    o intToUtf8() now marks the Encoding of its output.

    o The function is() now works with S3 inheritance; that is, with

        objects having multiple strings in the class attribute.

    o Extensions to condition number computation for matrices, notably

        complex ones are provided, both in kappa() and the new rcond().

    o list.file() gains a 'ignore.case' argument, to allow

        case-insensitive matching on some Windows/MacOS file systems.

    o ls.str() and lsf.str() have slightly changed arguments and

        defaults such that ls.str() {no arguments} works when debugging.

    o Under Unix, utils::make.packages.html() can now be used directly

        to set up linked HTML help pages, optionally without creating
        the package listing and search database (which can be much
        faster).

    o   new.packages() now knows about the front-end package gnomeGUI

(which does not install into a library).
o optim(*, control = list(...)) now warns when '...' contains unexpected names, instead of silently ignoring them. o The options "browser" and "editor" may now be set to functions, just as "pager" already could. o packageDescription() makes use of installed metadata where available (for speed, e.g. in make.packages.html()). o pairwise.t.test() and pairwise.wilcox.test() now more explicitly allow paired tests. In the former case it is now flagged as an error if both 'paired' and 'pool.SD' are set TRUE (formerly, 'paired' was silently ignored), and one-sided tests are generated according to 'alternative' also if 'pool.SD' is TRUE. o paste() and file.path() are now completely internal, for speed.
(This speeds up make.packages.html(packages=FALSE)
severalfold, for example.) o paste() now sets the encoding on the result under some circumstances (see ?paste). o predict.loess() now works when loess() was fitted with transformed explanatory variables, e.g, loess(y ~ log(x) + log(z)). o print(<data.frame>)'s new argument 'row.names' allows to suppress printing rownames. o print() and str() now also "work" for 'logLik' vectors longer than one. o Progress-bar functions txtProgressBar(), tkProgressBar() in package tcltk and winProgressBar() (Windows only). o readChar() gains an argument 'useBytes' to allow it to read a fixed number of bytes in an MBCS locale.

    o readNEWS() has been moved to the tools package.

    o round() and signif() now do internal argument matching if

        supplied with two arguments and at least one is named.

    o New function showNonASCII() in package tools to aid detection

        of non-ASCII characters in .R and .Rd files.

    o The [dpq]signrank() functions now typically use considerably

        less memory than previously, thanks to a patch from Ivo
        Ugrina.

    o   spec.ar() now uses frequency(x) when calculating the
        frequencies of the estimated spectrum, so that for monthly
        series the frequencies are now per year (as for spec.pgram)
        rather than per month as before.

    o spline() gets an 'xout' argument, analogously to approx().

    o sprintf() now does all the conversions needed in a first pass if

        length(fmt) == 1, and so can be many times faster if called
        with long vector arguments.

    o   [g]sub(useBytes = FALSE) now sets the encoding on changed
        elements of the result when working on an element of known
        encoding.  (This was previously done only for perl = TRUE.)

    o   New function Sys.chmod(), a wrapper for 'chmod' on platforms
        which support it.  (On Windows it handles only the read-only
        bit.)

    o   New function Sys.umask(), a wrapper for 'umask' on platforms
        which support it.

    o   New bindings ttk*() in package tcltk for the 'themed widgets'
        of Tk 8.5.  The tcltk demos make use of these widgets where
        available.

    o   write.table(d, row.names=FALSE) is faster when 'd' has millions of
        rows; in particular for a data frame with automatic row names.

(Suggestion from Martin Morgan.)

    o The parser limit on string size has been removed.

    o If a NEWS file is present in the root of a source package, it

        is installed (analogously to LICENSE, LICENCE and COPYING).

    o Rd conversion to 'example' now quotes aliases which contain

        spaces.

    o The handling of DST on dates outside the range 1902-2037 has

        been improved.  Dates after 2037 are assumed to have the same
        DST rules as currently predicted for the 2030's (rather than
        the 1970s), and dates prior to 1902 are assumed to have no DST
        and the same offset as in 1902 (if known, otherwise as in the
        1970s).

    o   On platforms where we can detect that mktime sets errno

(e.g. Solaris and the code used on Windows but not Linux nor
Mac OS X), 1969-12-31 23:59:59 GMT is converted from POSIXlt to POSIXct as -1 and not NA. o The definition of 'whitespace' used by the parser is slightly wider: it includes Unicode space characters on Windows and in UTF-8 locales on machines which use Unicode wide characters. o The src/extra/intl sources have been updated to those from gettext 0.17. o New flag --interactive on Unix-alikes forces the session to be interactive (as --ess does on Windows). o x[<zero-length>] <- NULL is always a no-op: previously type-checking was done on the replacement value and so this failed, whereas we now assume NULL can be promoted to any zero-length vector-like object. Other cases of a zero-length index are done more efficiently. o There is a new option in Rd markup of \donttest{} to mark example code that should be run by example() but not tested
(e.g. because it might fail in some locales).
o The error handler in the parser now reports line numbers for more syntax errors (MBCS and Unicode encoding errors, line length and context stack overflows, and mis-specified argument lists to functions). o The "MethodsList" objects originally used for method selection are being phased out. New utilities provide simpler alternatives (see ?findMethods), and direct use of the mangled names for the objects is now deprecated. o Creating new S4 class and method definitions in an environment that could not be identified (as package, namespace or global) previously generated an error. It now results in creating and using an artificial package name from the current date/time, with a warning. See ?getPackageName. o Unix-alikes now give a warning on startup if locale settings fail. (The Windows port has long done so.) o Parsing and scanning of numerical constants is now done by R's own C code. This ensures cross-platform consistency, and mitigates the effects of setting LC_NUMERIC (within base R it only applies to output -- packages may differ). The format accepted is more general than before and includes binary exponents in hexadecimal constants: see ?NumericConstants for details. o Dependence specifications for R or packages in the Depends field in a DESCRIPTION file can now make use of operators < > == and != (in addition to <= and >=): such packages will not be installable nor loadable in R < 2.7.0. There can be multiple mentions of R or a package in the Depends field in a DESCRIPTION file: only the first mention will be used in R < 2.7.0.

GRAPHICS CHANGES     o The default graphics devices in interactive and

        non-interactive sessions are now configurable via environment
        variables R_INTERACTIVE_DEVICE and R_DEFAULT_DEVICE
        respectively.

    o   New function dev.new() to launch a new copy of the default
        graphics device (and taking care if it is "pdf" or
        "postscript" not to trample on the file of an already running
        copy).

    o   dev.copy2eps() uses dev.displaylist() to detect screen
        devices, rather than list them in the function.

    o New function dev.copy2pdf(), the analogue of dev.copy2eps().

    o dev.interactive() no longer treats a graphics device as

        interactive if it has a display list (but devices can still
        register themselves on the list of interactive devices).

    o   The X11() and windows() graphics devices have a new argument
        'title' to set the window title.

    o   X11() now has the defaults for all of its arguments set by the
        new function X11.options(), inter alia replacing options
        "gamma", "colortype" and "X11fonts".

    o ps.options() now warns on unused option 'append'.

        xfig() no longer takes default arguments from ps.options().

(This was not documented prior to 2.6.1 patched.)
pdf() now takes defaults from the new function pdf.options() rather that from ps.options() (and the latter was not documented prior to 2.6.1 patched). The defaults for all arguments other than 'file' in postscript() and pdf() can now be set by ps.options() or pdf.options() o New functions setEPS() and setPS() as wrappers to ps.options() to set appropriate defaults for figures for inclusion in other documents and for spooling to a printer respectively. o The meaning of numeric 'pch' has been extended where MBCSes are supported. Now negative integer values indicate Unicode points, integer values in 32-127 represent ASCII characters, and 128-255 are valid only in single-byte locales.
(Previously what happened with negative pch values was
undocumented: they were replaced by the current setting of par("pch").) o Graphics devices can say if they can rotate text well
(e.g. postscript() and pdf() can) and if so the device's
native text becomes the default for contour labels rather than using Hershey fonts. o The setting of the line spacing (par("cra")[2]) on the X11() and windows() devices is now comparable with postscript() etc, and roughly 20% smaller than before (it used to depend on the locale for X11). (So is the pictex() device, now 20% larger.) This affects the margin size in plots, and should result in better-looking plots. o There is a per-device setting for whether new frames need confirmation. This is controlled by either par("ask") or grid.prompt() and affects all subsequent plots on the device using base or grid graphics. o There is a new version of the X11() device based on cairo graphics which is selected by type "cairo" or "nbcairo", and is available on machines with cairo installed and preferably pango (which most machines with gtk+ >= 2.8 will have). This version supports translucent colours and normally does a better job of font selection so it has been possible to display (e.g.) English, Polish, Russian and Japanese text on a single X11() window. It is the default where available. There is a companion function, savePlot(), to save the current plot to a PNG file. On Unix-alikes, devices jpeg() and png() also accept type = "cairo", and with that option do not need a running X server. The meaning of capabilities("jpeg") and capabilities("png") has changed to reflect this. On MacOS X, there is a further type = "quartz". The default type is selected by the new option "bitmapType", and is "quartz" or "cairo" where available. Where cairo 1.2 or later is supported, there is a svg() device to write SVG files, and cairo_pdf() and cairo_ps() devices to write (possibly bitmap) PDF and postscript files via cairo. Some features require cairo >= 1.2, and some which are nominally supported under 1.2 seem to need 1.4 to work well.

    o There are new bmp() and tiff() devices.

    o New function devSize() to report the size of the current

        graphics device surface (in inches or device units).  This
        gives the same information as par("din"), but independent of
        the graphics subsystem.

    o   New base graphics function clip() to set the clipping region (in
        user coordinates).

    o   New functions grconvertX() and grconvertY() to convert between
        coordinate systems in base graphics.

    o identify() recycles its 'labels' argument if necessary.

    o stripchart() is now a generic function, with default and

        formula methods defined.  Additional graphics parameters may
        be included in the call.  Formula handling is now
        similar to boxplot().

    o   strwidth() and strheight() gain 'font' and 'vfont' arguments and
        accept in-line pars such as 'family' in the same way as text()
        does.  (Longstanding wish of PR#776)

    o   example(ask=TRUE) now applies to grid graphics (e.g. from
        lattice) as well as to base graphics.

    o   Option "device.ask.default" replaces "par.ask.default" now it
        applies also to grid.prompt().

    o   plot.formula() only prompts between plots for interactive
        devices (it used to prompt for all devices).

    o   When plot.default() is called with y=NULL it now calls Axis()
        with the 'y' it constructs rather than use the default axis.


DEPRECATED & DEFUNCT     o In package installation, SaveImage: yes is defunct and

        lazyloading is attempted instead.

    o $ on an atomic vector or S4 object is now defunct.

    o Partial matching in [[ is now only performed if explicitly

        requested (by exact=FALSE or exact=NA).

    o Command-line completion has been moved from package 'rcompgen'

        to package 'utils': the former no longer exists as a separate
        package in the R distribution.

    o   The S4 pseudo-classes "single" and double have been removed.

(The S4 class for a REALSXP is "numeric": for back-compatibility
as(x, "double") coerces to "numeric".)

    o gpar(gamma=) in the grid package is now defunct.

    o Several S4 class definition utilities, get*(), have been said

        to be deprecated since R 1.8.0; these are now formally deprecated.
        Ditto for removeMethodsObject().

    o   Use of the graphics headers Rgraphics.h and Rdevices.h is
        deprecated, and these will be unavailable in R 2.8.0.

(They are hardly used except in graphics devices, for which
there is an updated API in this version of R.) o options("par.ask.default") is deprecated in favour of "device.ask.default". o The 'device-independent' family "symbol" is deprecated as it was highly locale- and device-dependent (it only did something useful in single-byte locales on most devices) and font=5
(base) or fontface=5 (grid) did the job it was intended to do
more reliably.

    o gammaCody() is now formally deprecated.

    o Two low-level functions using MethodsList metadata objects

(mlistMetaName() and getAllMethods()) are deprecated.

    o Setting par(gamma=) is now deprecated, and the windows()

        device (the only known example) no longer allows it.

    o The C macro 'allocString' will be removed in 2.8.0 -- use

        'mkChar', or 'allocVector' directly if really necessary.

INSTALLATION     o Tcl/Tk >= 8.3 (released in 2000) is now required to build

        package tcltk.

    o configure first tries TCL_INCLUDE_SPEC and TK_INCLUDE_SPEC

        when looking for Tcl/Tk headers.  (The existing scheme did
        not work for the ActiveTcl package on Mac OS X.)

    o   The Windows build only supports Windows 2000 or later (XP,
        Vista, Server 2003 and Server 2008).

    o   New option --enable-R-static-lib installs libR.a which can
        be linked to a front-end via 'R CMD config --ldflags'.
        The tests/Embedding examples now work with a static R
        library.

    o   Netscape (which was discontinued in Feb 2008) is no longer
        considered when selecting a browser.

    o   xdg-open (the freedesktop.org interface to
        kfmclient/gnome-open/...) is considered as a possible browser,
        after real browsers such as firefox, mozilla and opera.

    o   The search for tclConfig.sh and tkConfig.sh now only looks in
        directories with names containing $(LIBnn) in the hope of
        finding the version for the appropriate architecture

(e.g. x86_64 or i386).

    o libtool has been updated to version 2.2.

    o Use of --with-system-zlib, --with-system-bzlib or

        --with-system-pcre now requires version >= 1.2.3, 1.0.5, 7.6
        respectively, for security.


UTILITIES     o Rdconv now removes empty sections including alias and keyword

        entries, with a note.

    o Keyword entries are no longer mandatory in Rd files.

    o R CMD INSTALL now also installs tangled versions of all vignettes.

    o R CMD check now warns if spaces or non-ASCII characters are

        used in file paths, since these are not in general portable.

    o R CMD check (via massage-examples.pl) now checks all examples

        with a 7 inch square device region on A4 paper, for
        locale-independence and to be similar to viewing examples on
        an on-screen device.

        If a package declares an encoding in the DESCRIPTION file,
        the examples are assumed to be in that encoding when running
        the tests. (This avoids errors in running latin1 examples in a
        UTF-8 locale.)

    o   R CMD check uses pdflatex (if available) to check the typeset
        version of the manual, producing PDF rather than DVI.  (This
        is a better check since the package reference manuals on CRAN
        are in PDF.)

    o   R CMD Rd2dvi gains a --encoding argument to be passed to
        R CMD Rdconv, to set the default encoding for conversions.
        If this is not supplied and the files are package sources and
        the DESCRIPTION file contains an Encoding field, that is used
        for the default encoding.

    o   available.packages() (and hence install.packages() etc) now
        supports subdirectories in a repository, and
        tools::write_PACKAGES() can now produce PACKAGES files
        including subdirectories.

    o   The default for 'stylepath' in Sweave's (default) RweaveLatex
        driver can be set by the environment variable
        SWEAVE_STYLEPATH_DEFAULT: see ?RweaveLatex.


C-LEVEL FACILITIES     o Both the Unix and Windows interfaces for embedding now make

        use of 'const char *' declarations where appropriate.

    o Rprintf() and REprintf() now use 'const char *' for their format

        argument -- this should reduce warnings when called from C++.

    o There is a new description of the interface for graphics

        devices in the 'R Internals' manual, and several new entry
        points.  The API has been updated to version R_GE_version = 5,
        and graphics devices will need to be updated accordingly.

    o   Graphics devices can now select to be sent text in UTF-8, even
        if the current locale is not UTF-8 (and so enable text entered
        in UTF-8 to be plotted).  This is used by postscript(), pdf()
        and the windows() family of devices, as well as the new
        cairo-based devices.

    o   More Lapack routines are available (and declared in R_Ext/Lapack.h),
        notably for (reciprocal) condition number estimation of complex
        matrices.

    o Experimental utility R_has_slot supplementing R_do_slot.

    o There is a new public interface to the encoding info stored on

        CHARSXPs, getCharCE and mkCharCE using the enumeration type
        cetype_t.

    o   A new header 'R_ext/Visibility.h' contains some definitions for
        controlling the visibility of entry points, and how to control
        visibility is now documented in 'Writing R Extensions'.


BUG FIXES     o pt(x, df) is now even more accurate in some cases (e.g. 12 instead

        of 8 significant digits), when x^2 << df, thanks to a remark from
        Ian Smith, related to PR#9945.

    o   co[rv](use = "complete.obs") now always gives an error if there
        are no complete cases: they used to give NA if
        method = "pearson" but an error for the other two methods.

(Note that this is pretty arbitrary, but zero-length vectors
always give an error so it is at least consistent.) cor(use="pair") used to give diagonal 1 even if the variable was completely missing for the rank methods but NA for the Pearson method: it now gives NA in all cases. cor(use="pair") for the rank methods gave a matrix result with dimensions > 0 even if one of the inputs had 0 columns. o Supplying edit.row.names = TRUE when editing a matrix without row names is now an error and not a segfault. (PR#10500) o The error handler in the parser reported unexpected & as && and | as ||.

    o ps.options(reset = TRUE) had not reset for a long time.

    o paste() and file.path() no longer allow NA_character_ for

        their 'sep' and 'collapse' arguments.

    o by() failed for 1-column matrices and dataframes. (PR#10506)

        However, to preserve the old behaviour, the default method
        when operating on a vector still passes subsets of the vector
        to FUN, and this is now documented.

    o   Better behaviour of str.default() for non-default
        'strict.width' (it was calling str() rather than str.default()
        internally); also, more useful handling of options("str").

    o   wilcox.test(exact=FALSE, conf.int=TRUE) could fail in some
        extreme two-sample problems.  (Reported by Wolfgang Huber.)

    o   par(pch=) would accept a multi-byte string but only use the
        first byte.  This would lead to incorrect results in an MBCS
        locale if a non-ASCII character was supplied.

    o   There are some checks for valid C-style formats in, e.g.
        png(filename=).  (PR#10571)

    o   vector() was misinterpreting some double 'length' values, e.g,
        NaN and NA_real_ were interpreted as zero.  Also, invalid
        types of 'length' were interpreted as -1 and hence reported as
        negative.  (length<- shared the code and hence the same
        misinterpretations.)

    o   A basic class "S4" was added to correspond to the "S4" object
        type, so that objects with this type will print, etc.  The
        class is VIRTUAL, since all actual S4 objects must have a real
        class.

    o   Classes with no slots that contain only VIRTUAL classes are now
        VIRTUAL, as was intended but confused by having an empty S4
        object as prototype. ## backed out temporarily ##

    o   format.AsIs() discarded dimnames, causing dataframes with matrix
        variables to be printed without using the column names, unlike
        what happens in S-PLUS (Tim Hesterberg, PR#10730).

    o   xspline() and grid::grid.xspline() work in device coordinates
        and now correct for anisotropy in the device coordinate
        system.

    o   grid.locator() now indicates to the graphics device that it is
        is in 'graphics input' mode (as locator() and identify()
        always have).  This means that devices can now indicate the
        'graphics input' mode by e.g. a change of cursor.

    o   Locales without encoding specification and non-UTF-8 locales
        now work properly on Mac OS X.  Note that locales without
        encoding specification always use UTF-8 encoding in Mac OS X

(except for specials "POSIX" and "C") - this is different from
other operating systems.

    o iconv() now correctly handles to="" and from="" on Mac OS X.

    o In diag()'s argument list, drop the explicit default (' = n')

        for 'ncol' which is ugly when making diag() generic.

    o S4 classes with the same name from different packages were not

        recognized because of a bug in caching the new definition.

    o jpeg() and png() no longer maintain a display list, as they

        are not interactive devices.

    o Using attr(x, "names") <- value (instead of the correct

        names<-) with 'value' a pairlist (instead of the correct
        character vector) worked incorrectly.  (PR#10807)

    o   Using [<- to add a column to a data frame dropped other
        attributes whereas [[<- and $<- did not: now all preserve
        attributes.  (PR#10873)

    o   File access functions such as file.exists(), file.info(),
        dirname() and unlink() now treat an NA filename as a
        non-existent file and not the file "NA".

    o   r<foo>(), the random number generators, are now more consistent
        in warning when NA's (specifically NaN's) are generated.

    o   rnorm(n, mu = Inf) now returns rep(Inf, n) instead of NaN;
        similar changes are applied to rlnorm(), rexp(), etc.

    o   [l]choose() now warns when rounding non-integer 'k' instead of
        doing so silently.  (May help confused users such as PR#10766.)

    o   gamma() was warning incorrectly for most negative values as being
        too near a negative integer.  This also affected other
        functions making use of its C-level implementation.

    o dumpMethod() and dumpMethods() now work again.

    o package.skeleton() now also works for code_files with only

        metadata (e.g. S4 setClass) definitions; it handles S4 classes and
        methods, producing documentation and NAMESPACE exports if requested.

    o   Some methods package utilities (implicitGeneric(), makeGeneric())
        will be more robust in dealing with primitive functions (not a
        useful idea to call them with primitives, though)

    o   Making a MethodsList from a function with no methods table will
        return an empty list, rather than cause an error (questionably
        a bug, but caused some obscure failures).

    o   setAs() now catches 2 arguments in the method definition, if
        they do not match the arguments of coerce().

    o   S4 methods with missing arguments in the definition are handled
        correctly  when non-signature arguments exist, and check for
        conflicting local names in the method definition.

    o   qgamma() and qchisq() could be inaccurate for small p,
        e.g. qgamma(1.2e-10, shape = 19) was 2.52 rather than 2.73.

    o   dbeta(.., ncp) is now more accurate for large ncp, and typically no
        longer underflows for give.log = TRUE.

    o coerce() is now a proper S4 object and so prints correctly.

    o @ now checks it is being applied to an S4 object, and if not

        gives a warning (which will become an error in 2.8.0).

    o dump() and friends now warn that all S4 objects (even those

        based on vectors) are not source()able, with a stronger wording.

    o read.dcf(all = TRUE) was leaking connections.

    o scan() with a non-default separator could skip nul bytes,

        including those entered as \0 with allowEscapes=TRUE.  This
        was different from the default separator.

    o   determinant(matrix(,0,0)) now returns a correct "det" result;
        also value 1 or 0 depending on 'logarithm', rather than numeric(0).

    o   Name space 'grDevices' was not unloading its DLL when the
        name space was unloaded.

    o   getNativeSymbolInfo() was unaware of non-registered Fortran
        names, because one of the C support routines ignored them.

    o   load() again reads correctly character strings with embedded nuls.

(This was broken in 2.6.x, but worked in earlier versions.)
CHANGES IN R VERSION 2.6.2 patched

BUG FIXES     o src/extra/pcre has been updated to PCRE 7.6 (bugfix release).

    o unlink(..., recursive=TRUE) no longer crashes on some platforms

        if a directory cannot be opened.

    o Loading in 2.6.2 a saved workspace could give an unimportant

        warning in a non-UTF-8 multibyte locale (in particular a CJK
        locale on Windows) which is now suppressed.

    o   print() methods are more consistent in returning the original
        argument invisibly.

    o   Using the X11 data editor (e.g. via edit(), fix() or View())
        could crash if the 'End' key was used and all the columns
        would have fitted into the window.

    o   Creating a new page on an X11() device (by plot.new() or
        grid.newpage()) did not flush out the XClearWindow call, so
        the X11 window might not be refreshed immediately.

    o   libtool has been updated to version 1.5.26, which avoids
        many spurious configure warnings on Darwin/Mac OS X.

    o   l10n_info() now recognizes how Darwin/Mac OS X reports
        Latin-1 locales (as charset ISO8859-1 rather than ISO-8859-1).

    o   Checking examples which used grid (e.g. via lattice) without
        attaching grid no longer give errors from grid_plot_hook().

    o   kappa(m, exact=TRUE) no longer wrongly uses 'exact=FALSE' when m
        is an 'lm' or 'qr' object because the kappa.tri(x, exact=TRUE)
        now works correctly.

    o   help(topic, offline=TRUE) misbehaved when there were multiple
        matches to 'topic'.  (PR#10859)

    o   The 'multilib' changes on Linux broke the use of
        sub-architectures without a main architecture.

    o   source(echo=TRUE) would skip lines consisting entirely of the
        letter t. (PR#10923)

    o bzip2 has been updated to 1.0.5 (security fix).

-- 
   O__  ---- Peter Dalgaard             Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark      Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard_at_biostat.ku.dk)              FAX: (+45) 35327907

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