[R] R 2.7.1 is released

From: Peter Dalgaard <P.Dalgaard_at_biostat.ku.dk>
Date: Mon, 23 Jun 2008 10:01:43 +0200

I've rolled up R-2.7.1.tar.gz a short while ago.

This is a maintenance release and fixes a number of mostly minor bugs and platform issues.
Notably, the numeric interpretation of "-", "+", and "." has reverted to pre-2.7.0 behaviour

See the full list of changes below.

You can get it (in a short while) from


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:

70447ae7f2c35233d3065b004aa4f331 INSTALL 433182754c05c2cf7a04ad0da474a1d0 README 4f004de59e24a52d0f500063b4603bcb OONEWS ff4bd9073ef440b1eb43b1428ce96872 ONEWS
1cff51aab2e4f3ce66200a700ede143b NEWS
1ad28cbc84485ccdf4ce5721b34ed645 THANKS 070cca21d9f8a6af15f992edb47a24d5 AUTHORS a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB eb723b61539feef013de476e68b5c50a COPYING 020479f381d5f9038dcb18708997f5da RESOURCES a04d059fa76b105566aad359d38864a0 FAQ
b1ca7e499b7a0ea8ec4eb95a2231e97b R-2.7.1.tar.gz b1ca7e499b7a0ea8ec4eb95a2231e97b R-latest.tar.gz

Here is the relevant bit of the NEWS file:

                CHANGES IN R VERSION 2.7.1

NEW FEATURES     o tools::texi2dvi() has a new argument 'texinputs' to allow the

        TeX and bibtex input paths to be specified (even on MiKTeX).

    o dev.copy2pdf() gains an 'out.type' argument to allow it to be

        used with cairo_pdf() or quartz(type = "pdf").

    o poly() has additional checks against user error (as in PR#11243).

    o The Mac OS quartz() device draws contiguous lines much faster.

    o A field containing just a sign is no longer regarded as numeric

(it was on all platforms in 2.7.0, but not on most in earlier
        versions of R). Similarly, '.' is now always non-numeric.

    o CITATION files are now read in Latin-1: quite a few were

        failing if used in a multibyte locale such as UTF-8.

    o The DESCRIPTION file of a package can specify an 'OS_type' field

        as either 'unix' or 'windows' to confine installation to that
        OS type.

    o   HoltWinters() now uses optimize() rather than optim for
        one-parameter problems which should be more reliable (PR#11469).

    o axis() now respects the setting of par("xpd") when clipping.

    o The 'factor' method of format() now preserves names, dims and

        dimnames in the same way as for character and numeric inputs.

o read.DIF(*, transpose=TRUE) now allows to correctly read DIF files produced by some versions of Excel.

DEPRECATED & DEFUNCT     o The use of unserialize() on character strings is deprecated:

        that was a format used in R < 2.4.0.

    o The use of embedded nuls in character strings is deprecated:

        They will no longer be allowed in R 2.8.0.

UTILITIES     o R CMD check checks for possible check directories in the

        sources -- in mid-2008 there were about 20 examples on CRAN.

    o R CMD build tries harder to clean up the inst/doc directory

        from the remnants of earlier builds.

        It also removes any directories with extension .Rcheck, and
        files .DS_Store and ._* (created by tar on Mac OS X under some
        circumstances: it now sets environment variables to ask for
        such files not to be created by that tar.)

BUG FIXES     o Encoding<- on NA_character_ converted it to "NA".

    o Adobe Symbol was missing from the encodings in


    o diag(matrix(x, 0, 0)) now returns a 0-length vector of the

        correct mode, instead of always numeric.

    o The parser sometimes accepted invalid quoted strings in a UTF-8


    o plot.default(x, y) now dispatches to Axis() methods whether

        y is NULL or not.

    o On Mac OS X, the Cocoa Quartz window could close without warning

        under certain circumstances (specific autorelease pool flush).

    o Plotting symbols with separate border and fill colours (e.g.,

        plot(pch = 21)) now works with transparent 'col', but opaque
        or semi-transparent 'bg'.  Previously, if 'col' was
        transparent then 'bg' was ignored and nothing was drawn.

    o   file.path() did not work correctly in 2.7.0 if the components
        had different encodings.

    o   merge() failed if there were no common columns and one of the
        inputs had zero rows.

    o expand.grid() failed if an input had length 0.

    o match() does again truncate strings at embedded nuls (as newly

        documented in 2.7.0).

    o Because of a typo, 'pointsize' in png(type="cairo") (and jpeg,

        bmp, tiff) devices was being interpreted in pixels not bigpoints.

    o is() was wrong for some S3 class objects with class of length

        greater than one.

    o undoc() / codoc() were not checking all S4 methods in some cases.

    o Use of textConnection(NULL, mode="w") could segfault.

    o Use of strwidth/height(units="user") (the default) is again an

        error before a user coordinate system has been set on the
        device, rather than giving nonsensical values (the effect of

    o   Rare string width calculations in package grid were not
        interpreting the string encoding correctly.

    o hasMethods(f, env) {without specified 'package'} now works better.

    o A missing PROTECT could cause segfaults on string

        comparisons. (PR#11421)

    o str(structure(1, classID = "Pooh")) now works fine.

    o A missing PROTECT could cause segfaults in if() if coercion of

        the condition was required or a warning was to be given.

    o plot(<table>) now uses a sensible default main title.

    o validObject() called with complete=TRUE did not use inherited

        validity methods for slot classes.

    o Several bugs fixed in as(): the initial method lookup was not

        using the table with inherited methods (so inheritance had to
        be recomputed each time); coerce() should not be called
        directly--it can insert invalid inherited methods; the
        constructed as() methods were not retaining the function's

    o   influence.measures(<glm-object>) now computes the same
        Cook's distance approximations as cooks.distance().

    o   plot(<glm>, which=5) uses more correct Cook's distance contours;

(fix to fix to PR#9316).
o pdf() and postscript() were not working correctly in 2.7.0 with UTF-8 encoded data in a non-UTF-8 MBCS (e.g. EUC-JP on Unix, CJK locales on Windows). o conformMethod(), called by setMethod(), now checks better about argument names in wrong order. Whereas it only warns currently, it is planned to become an error in the future. o The predict() method for prcomp() had an incorrect check for the number of columns of 'newdata' if the columns were not named. o The axis() function now distinguishes between setting "at" to NULL or a zero-length vector, treating the latter as a request for no ticks. This corrects the handling of the "x" parameter to rug().

    o glob2rx("*[*") now produces a correct regular expression.

    o The canvas is no longer painted on copy or save in Cocoa Quartz.

    o identify() in Quartz can now be terminated by either using popup

        menu equivalent (Ctrl-click or second mouse button) or by pressing
        the <Esc> key. The latter was documented but did not work.

    o   tools:::.check_package_depends() {called from 'R CMD check'} now
        also works correctly when directory-name != package-name.

    o Source references were sometimes off by a line.

    o The quartz() parameter 'antialias' is no longer ignored.

    o The Quartz device is now trying hard to remove anti-aliasing

        effects for rasterized backends in plots that use adjacent,
        borderless rectangles such as image().

    o   The srcfilecopy() function now adds a timestamp to the object it

    o parse() would lose a token when run on stdin().

    o socketConnection() was using internally the class "socket"

        and not "sockconn", which caused a conflict with make.socket().

o Quartz is now trying harder to find the proper font for a given family which resolves font issues on Mac OS X 10.4. Full font names and PostScript names can be used interchangeably. (Note, however that italic/oblique font faces of Helvetica are not included in the Mac OS X 10.4 system). o qf() no longer gives NaN when one of df1 and df2 is large and the other is infinite (including if both are infinite); it is more accurate e.g. for qf(1e-18, 2,4).

    o qbeta(-1e10, 50, 40, log.p=TRUE) no longer hangs.

    o Cocoa Quartz backend autodetection of display DPI was not

        correct for screens rotated by 90 or 270 degrees.

    o selectMethod("coerce", .) now uses a correct default for

        'useInherited', and hence no longer may mess up the method cache.

    o show() now also works on "unregistered" S3 class objects.

    o formatC(*, format="fg", flag="#") is no longer dropping trailing


    o read.table(file = stdin()) with invalid input could leave the

        connection in an invalid state and hence cause a later
        segfault.  (PR#11627)

    o read.DIF() did not obey the default 'stringsAsFactors = TRUE'.

    o The 'noquote' method for c() now works correctly with three or

        more arguments.

    o symbol() in plotmath expressions works again with non-ASCII

        input on devices that use UTF-8 for the symbol font.

   O__  ---- Peter Dalgaard             Ă˜ster 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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