doc/html/NEWS.2.html - R - Git at Google


            
            <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"><html xmlns="http://www.w3.org/1999/xhtml"><head><title>R: R News</title>

            
            <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />

            
            <link rel="stylesheet" type="text/css" href="R.css" />

            
            </head><body>


            <table width="100%" summary="page for NEWS"><tr><td>NEWS</td><td style="text-align: right;">R Documentation</td></tr></table>


            <h2> R News</h2>


            <h3>LATER NEWS</h3>


            <p>News for <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.0.0 and later can be found in file &lsquo;<span class="file">NEWS.Rd</span>&rsquo; in the

            
            <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> sources and files &lsquo;<span class="file">NEWS</span>&rsquo; and &lsquo;<span class="file">doc/html/NEWS.html</span>&rsquo;

            
            in an <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> build.

            
            </p>


            <h3><img class="toplogo" src="../help/figures/../../html/Rlogo.svg" alt="[R logo]" /> CHANGES IN R VERSION 2.15.3</h3>


            <h4>NEW FEATURES</h4>


            <ul>

            
            <li> <p><code>lgamma(x)</code> for very small <code>x</code> (in the

            
            denormalized range) is no longer <code>Inf</code> with a warning.

            
            </p>

            
            </li>

            
            <li> <p><code>image()</code> now sorts an unsorted <code>breaks</code> vector,

            
            with a warning.

            
            </p>

            
            </li>

            
            <li><p> The internal methods for <code>tar()</code> and <code>untar()</code> do

            
            a slightly more general job for &lsquo;ustar&rsquo;-style handling of

            
            paths of more than 100 bytes.

            
            </p>

            
            </li>

            
            <li><p> Packages <span class="pkg">compiler</span> and <span class="pkg">parallel</span> have been added

            
            to the reference index (&lsquo;<span class="file">refman.pdf</span>&rsquo;).

            
            </p>

            
            </li>

            
            <li> <p><code>untar(tar = "internal")</code> has some support for

            
            <code>pax</code> headers as produced by e.g. <code>gnutar --posix</code>

            
            (which seems prevalent on OpenSUSE 12.2) or

            
            <code>bsdtar --format pax</code>, including long path and link names.

            
            </p>

            
            </li>

            
            <li> <p><code>sQuote()</code> and <code>dQuote()</code> now handle 0-length

            
            inputs.  (Suggestion of Ben Bolker.)

            
            </p>

            
            </li>

            
            <li> <p><code>summaryRprof()</code> returns zero-row data frames rather

            
            than throw an error if no events are recorded, for consistency.

            
            </p>

            
            </li>

            
            <li><p> The included version of PCRE has been updated to 8.32.

            
            </p>

            
            </li>

            
            <li><p> The <span class="pkg">tcltk</span> namespace can now be re-loaded after

            
            unloading.

            
            </p>

            
            <p>The Tcl/Tk event loop is inhibited in a forked child from package

            
            <span class="pkg">parallel</span> (as in e.g. <code>mclapply()</code>).

            
            </p>

            
            </li>

            
            <li> <p><code>parallel::makeCluster()</code> recognizes the value

            
            <span class="samp">random</span> for the environment variable <span class="env">R_PARALLEL_PORT</span>:

            
            this chooses a random value for the port and reduces the chance of

            
            conflicts when multiple users start a cluster at the same time.

            
            </p>

            
            </li></ul>


            <h4>UTILITIES</h4>


            <ul>

            
            <li><p> The default for <span class="env">TAR</span> on Windows for <code>R CMD

            
            	build</code> has been changed to be <span class="samp">internal</span> if no

            
            <code>tar</code> command is on the path.

            
            </p>

            
            <p>This enables most packages to be built &lsquo;out of the box&rsquo;

            
            without <code>Rtools</code>: the main exceptions are those which need

            
            to be installed to re-build vignettes and need <code>Rtools</code>

            
            for installation (usually because they contain compiled code).

            
            </p>

            
            </li></ul>


            <h4>C-LEVEL FACILITIES</h4>


            <ul>

            
            <li><p> On a 64-bit Windows platform with enough RAM, <code>R_alloc</code>

            
            can now allocate up to just under 32GB like other 64-bit

            
            platforms.

            
            </p>

            
            </li></ul>


            <h4>DEPRECATED AND DEFUNCT</h4>


            <ul>

            
            <li><p> Use of <code>col2rgb(0)</code> is deprecated (see the help page

            
            for its limitations).

            
            </p>

            
            </li>

            
            <li><p> The deprecated <code>intensities</code> component returned by

            
            <code>hist()</code> is no longer recognized by the <code>plot()</code> method

            
            and will be removed in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.0.0.

            
            </p>

            
            </li>

            
            <li> <p><code>real()</code>, <code>as.real()</code> and <code>is.real()</code> are now

            
            formally deprecated and give a warning.

            
            </p>

            
            </li>

            
            <li><p> This is formal notice that the non-API EISPACK entry points

            
            in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> will be removed shortly.

            
            </p>

            
            </li></ul>


            <h4>INSTALLATION</h4>


            <ul>

            
            <li><p> The <code>configure</code> tests for Objective C and Objective

            
            C++ now work on Mac OS 10.8 with Xcode 4.5.2 (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15107">PR#15107</a>).

            
            </p>

            
            </li>

            
            <li><p> The cairo-based versions of <code>X11()</code> now work with

            
            current versions of cairographics (e.g., 1.12.10).  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15168">PR#15168</a>)

            
            </p>

            
            <p>A workaround for earlier versions of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> is to use

            
            <code>X11.options(type = "nbcairo")</code>.

            
            </p>

            
            </li>

            
            <li><p> Configuration and <code>R CMD javareconf</code> now come up

            
            with a smaller set of library paths for Java on Oracle-format JDK

            
            (including OpenJDK).  This helps avoid conflicts between libraries

            
            (such as <code>libjpeg</code>) supplied in the JDK and system

            
            libraries.  This can always be overridden if needed: see the

            
            &lsquo;R Installation and Administration&rsquo; manual.

            
            </p>

            
            </li></ul>


            <h4>BUG FIXES</h4>


            <ul>

            
            <li> <p><code>beta(a, b)</code> could overflow to infinity in its

            
            calculations when one of <code>a</code> and <code>b</code> was less than one.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15075">PR#15075</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>lbeta(a, b)</code> no longer gives <code>NaN</code> if <code>a</code> or

            
            <code>b</code> is very small (in the denormalized range).

            
            </p>

            
            </li>

            
            <li> <p><code>bquote()</code> is now able to substitute default arguments in

            
            single-argument functions.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15077">PR#15077</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>browseEnv(html = FALSE)</code> would segfault if called from

            
            <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> (not <code>R.app</code>) on a CRAN-style Mac OS X build of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>.

            
            </p>

            
            </li>

            
            <li> <p><span class="samp">[[&lt;-</span> for lists (generic vectors) needed to increment

            
            <code>NAMED</code> count when RHS is used more than once. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15098">PR#15098</a>)

            
            </p>

            
            </li>

            
            <li><p> On Windows, warnings about opening a file or pipe with a

            
            non-ASCII description were sometimes output in UTF-8 rather than

            
            in the current locale's character set.

            
            </p>

            
            </li>

            
            <li><p> The <code>call()</code> function did not duplicate its arguments.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15115">PR#15115</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>TukeyHSD()</code> could give <code>NA</code> results with some

            
            <span class="samp">na.action</span> methods such as <code>na.exclude()</code>.

            
            (Hinted at on R-help by John Fox.)

            
            </p>

            
            </li>

            
            <li><p> The deprecated <code>svd(X, LINPACK = TRUE)</code> could alter

            
            <code>X</code> in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.15.[12].  (Reported by Bill Dunlap.)

            
            </p>

            
            </li>

            
            <li><p> Under Windows, <code>file.link()</code> and <code>file.symlink()</code>

            
            used the link name twice, so would always fail. (Reported

            
            by Rui Barradas/Oliver Soong).

            
            </p>

            
            </li>

            
            <li> <p><code>summaryRprof(memory = "both")</code> mixed up the units of

            
            Vcells and Ncells: it now works in bytes.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15138">PR#15138</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>tools::Rd2HTML()</code> would sometimes delete text. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15134">PR#15134</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>plot()</code> failed for <code>"table"</code> objects containing

            
            just one entry.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15118">PR#15118</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>embedFonts()</code> needed to quote some filepaths.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15149">PR#15149</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>parallel::mccollect()</code> handled <code>NULL</code> returns

            
            incorrectly (removing the element rather than setting it to

            
            <code>NULL</code>).

            
            </p>

            
            </li>

            
            <li><p> The full reference index (&lsquo;<span class="file">fullrefman.pdf</span>&rsquo;) was missing

            
            packages <span class="pkg">compiler</span> and <span class="pkg">parallel</span>.

            
            </p>

            
            </li>

            
            <li><p> The report for

            
            <code>optim(method = "L-BFGS-B", control = list(trace = 1))</code>

            
            reported the last completed and not the current iteration, unlike

            
            other methods and trace levels.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15103">PR#15103</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>qt(1e-12, 1.2)</code> no longer gives <code>NaN</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>dt(1e160, 1.2, log=TRUE)</code> no longer gives <code>-Inf</code>.

            
            </p>

            
            </li>

            
            <li><p> On Windows the <code>untar()</code> function now quotes the

            
            directory name when using an external <code>tar</code> utility, so

            
            <code>R CMD check</code> will handle pathnames containing spaces.

            
            </p>

            
            </li>

            
            <li><p> The version for Windows 8 and Windows Server 2012 is now

            
            displayed by <code>win.version()</code>.  (Reported by Gabor

            
            Grothendieck.)

            
            </p>

            
            </li>

            
            <li><p> The custom Windows installer target <code>myR</code> in the

            
            installer &lsquo;<span class="file">Makefile</span>&rsquo; did not work in 2.15.2.  (Reported

            
            by Erich Neuwirth.)

            
            </p>

            
            </li>

            
            <li> <p><code>aperm(matrix(1:6, 2, dimnames=list(A={}, B={})), "A")</code>

            
            no longer segfaults.

            
            </p>

            
            </li>

            
            <li><p> Expressions involving user defined operators were not

            
            always deparsed faithfully. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15179">PR#15179</a>)

            
            </p>

            
            </li>

            
            <li><p> The <code>enc2utf8()</code> function converted <code>NA_character_</code>

            
            to <code>"NA"</code> in non-UTF-8 locales. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15201">PR#15201</a>)

            
            </p>

            
            </li>

            
            <li><p> The <code>exclude</code> argument to <code>xtabs()</code> was ignored

            
            for <code>"factor"</code> arguments.

            
            </p>

            
            </li>

            
            <li><p> On Windows, work around an event-timing problem when

            
            the RGui console was closed from the &lsquo;X&rsquo; control and the closure

            
            cancelled. (This would on some 64-bit systems crash <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>, typically

            
            those with a slow GPU relative to the CPU.)

            
            </p>

            
            </li>

            
            <li><p> On unix <code>Rscript</code> will pass the <code>r_arch</code> setting

            
            it was compiled with on to the R process so that the architecture

            
            of <code>Rscript</code> and that of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> will match unless overridden.

            
            </p>

            
            </li>

            
            <li><p> On Windows, <code>basename()</code>, <code>dirname()</code> and

            
            <code>file.choose()</code> have more support for long non-ASCII file

            
            names with 260 or more bytes when expressed in UTF-8.

            
            </p>

            
            </li></ul>


            <h3><img class="toplogo" src="../help/figures/../../html/Rlogo.svg" alt="[R logo]" /> CHANGES IN R VERSION 2.15.2</h3>


            <h4>NEW FEATURES</h4>


            <ul>

            
            <li><p> The <code>X11()</code> window gains an icon: the

            
            latter may be especially useful on Ubuntu's &lsquo;Unity&rsquo;

            
            interface.

            
            </p>

            
            <p>The <code>WM_CLASS</code> should be set in circumstances where the

            
            Window Manager failed to make use of X11 resource settings.

            
            </p>

            
            <p>(Contributed by Philip Johnson.)

            
            </p>

            
            </li>

            
            <li><p> The <code>"Date"</code> and <code>"POSIXt"</code> methods for

            
            <code>cut()</code> will accept an unsorted <code>breaks</code> argument (as

            
            the default method does, although this was undocumented).

            
            (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14961">PR#14961</a>.)

            
            </p>

            
            </li>

            
            <li><p> Reference class methods (in the <span class="pkg">methods</span> package) that

            
            use other methods in an indirect way (e.g., by <code>sapply()</code>)

            
            must tell the code analysis to include that method.  They can now

            
            do so by invoking <code>$usingMethods()</code>.

            
            </p>

            
            </li>

            
            <li><p> More Polish translations are available: for the

            
            <code>RGui</code> menus and for several recommended packages.

            
            </p>

            
            </li>

            
            <li><p> Multistratum MANOVA works. In fact, it seems to have done so

            
            for years in spite of the help page claiming it did not.

            
            </p>

            
            </li>

            
            <li> <p><code>qqline()</code> has new optional arguments

            
            <code>distribution</code>, <code>probs</code> and <code>qtype</code>, following the

            
            example of <a href="https://CRAN.R-project.org/package=lattice"><span class="pkg">lattice</span></a>'s <code>panel.qqmathline()</code>.

            
            </p>

            
            </li>

            
            <li><p> The handling of single quotes in the <code>en@quot</code>

            
            pseudo-language has been slightly improved.  Double quotes are no

            
            longer converted.

            
            </p>

            
            </li>

            
            <li><p> New functions <code>checkPoFiles()</code> and <code>checkPoFile()</code>

            
            have been added to the <span class="pkg">tools</span> package to check for

            
            consistency of format strings in translation files.

            
            </p>

            
            </li>

            
            <li> <p><code>model.matrix(~1, ...)</code> now also contains the same

            
            rownames that less trivial formulae produce.  (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14992">PR#14992</a>,

            
            changes the output of several packages.)

            
            </p>

            
            </li>

            
            <li><p> Misuse of <code>rep()</code> on undocumented types of objects

            
            (e.g., calls) is now reported as an error.

            
            </p>

            
            </li>

            
            <li><p> The included LAPACK has been updated to 3.4.1, with some

            
            patches from the current SVN sources.  (<em>Inter alia</em>, this

            
            resolves <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14692">PR#14692</a>.)

            
            </p>

            
            </li>

            
            <li> <p><code>file.copy(recursive = TRUE)</code> has some additional

            
            checks on user error leading to attempted infinite recursion (and on

            
            some platforms to crashing <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>).

            
            </p>

            
            </li>

            
            <li><p> PCRE has been updated to version 8.31, a bug-fix release.

            
            </p>

            
            </li>

            
            <li><p> The included version of <code>liblzma</code> has been updated to

            
            version 5.0.4, a minor bug-fix release.

            
            </p>

            
            </li>

            
            <li><p> New function <code>.bincode()</code>, a &lsquo;bare-bones&rsquo;

            
            version of <code>cut.default(labels = FALSE)</code> for use in packages

            
            with <code>image()</code> methods.

            
            </p>

            
            </li>

            
            <li><p> The HTML manuals now use directional single quotes.

            
            </p>

            
            </li>

            
            <li> <p><code>maintainer()</code> now converts embedded new lines to

            
            spaces.  It no longer gives a non-obvious error for non-installed

            
            packages.

            
            </p>

            
            </li>

            
            <li><p> The <code>X11()</code> device has some protection against

            
            being used with forked processes <em>via</em> package <span class="pkg">parallel</span>.

            
            </p>

            
            </li>

            
            <li><p> Setting the environment variable <span class="env">R_OSX_VALGRIND</span> (to

            
            any value) allows <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> to be run under <code>valgrind</code> on Mac OS

            
            10.6 and 10.7 (<code>valgrind</code> currently has very limited

            
            support for 10.8), provided <code>system()</code> is not used (directly

            
            or indirectly).  This should not be needed for <code>valgrind</code>

            
            &gt;= 3.8.1.

            
            </p>

            
            </li>

            
            <li><p> The <code>model.frame()</code> method for <code>"lm"</code> uses

            
            <code>xlevels</code>: this is safer if <code>data</code> was supplied or

            
            <code>model = FALSE</code> was used and the levels of factors used in

            
            the fit had been re-ordered since fitting.

            
            </p>

            
            <p>Similarly, <code>model.frame(fm, data=&lt;data&gt;)</code> copies across

            
            the variables used for safe prediction from the fit.

            
            </p>

            
            </li>

            
            <li><p> Functions such as <code>parLapply()</code> in package

            
            <span class="pkg">parallel</span> can make use of a default cluster if one is set.

            
            (Reported by Martin Morgan.)

            
            </p>

            
            </li>

            
            <li> <p><code>chol(pivot = TRUE, LINPACK = FALSE)</code> is now available

            
            using LAPACK 3.2 subroutine <code>DPSTRF</code>.

            
            </p>

            
            </li>

            
            <li><p> The functions <code>.C()</code>, <code>.Call()</code>,

            
            <code>.External()</code> and <code>.Fortran()</code> now check that they are

            
            called with an unnamed first argument: the formal arguments were

            
            changed from <code>name=</code> to <code>.NAME=</code> in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.13.0, but some

            
            packages were still using the old name.  This is currently a

            
            warning, but will be an error in future.

            
            </p>

            
            </li>

            
            <li> <p><code>step()</code> no longer tries to improve a model with

            
            AIC of <code>-Inf</code> (a perfect fit).

            
            </p>

            
            </li>

            
            <li> <p><code>spline()</code> and <code>splinefun()</code> gain a new method

            
            <code>"hyman"</code>, an implementation of Hyman's method of

            
            constructing monotonic interpolation splines.  (Based on

            
            contributions of Simon Wood and Rob Hyndman.)

            
            </p>

            
            </li>

            
            <li><p> On Windows, the C stack size has been increased to 64MB (it

            
            has been 10MB since the days of 32MB RAM systems).

            
            </p>

            
            </li></ul>


            <h4>PERFORMANCE IMPROVEMENTS</h4>


            <ul>

            
            <li> <p><code>array()</code> is now implemented in C code (for speed) when

            
            <code>data</code> is atomic or an unclassed list (so it is known that

            
            <code>as.vector(data)</code> will have no class to be used by <code>rep()</code>).

            
            </p>

            
            </li>

            
            <li> <p><code>rep()</code> is faster and uses less memory,

            
            substantially so in some common cases (e.g., if <code>times</code> is of

            
            length one or <code>length.out</code> is given, and <code>each = 1</code>).

            
            </p>

            
            </li>

            
            <li> <p><code>findInterval()</code>, <code>tabulate()</code>, <code>cut()</code>,

            
            <code>hist()</code> and <code>image.default()</code> all use <code>.Call()</code>

            
            and are more efficient.

            
            </p>

            
            </li>

            
            <li> <p><code>duplicated()</code>, <code>unique()</code> and similar now

            
            support vectors of lengths above <i>2^29</i> on 64-bit

            
            platforms.

            
            </p>

            
            </li>

            
            <li><p> Omitting <code>PACKAGE</code> in <code>.C()</code> etc calls was

            
            supposed to make use of the DLL from the namespace within which

            
            the enclosing function was defined.  It was less successful in

            
            doing so than it might be, and gave no indication it had failed.

            
            </p>

            
            <p>A new search strategy is very successful and gives a warning

            
            when it fails.  In most cases this is because the entry point is

            
            not actually provided by that package (and so <code>PACKAGE</code>

            
            should be used to indicate which package is intended) but in some

            
            the namespace does not have a DLL specified by a

            
            <code>useDynLib()</code> directive so <code>PACKAGE</code> is required.

            
            </p>

            
            </li></ul>


            <h4>UTILITIES</h4>


            <ul>

            
            <li> <p><code>R CMD check</code> now checks if a package can be loaded

            
            by <code>library(pkgname, lib.loc = "somewhere")</code> without being on

            
            the library search path (unless it is already installed in

            
            <code>.Library</code>, when it always will be).

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD check --as-cran</code> notes &lsquo;hidden&rsquo; files

            
            and directories (with names starting with a dot) that are not

            
            needed for the operation of <code>R CMD INSTALL</code> or <code>R CMD

            
            	build</code>: such files should be excluded from the published tarball.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD check</code> (if checking subdirectories) checks

            
            that the <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> code in any demos is ASCII and can be parsed, and

            
            warns if not.

            
            </p>

            
            </li>

            
            <li><p> When <code>R CMD Rd2pdf</code> is used with &lsquo;<span class="file">inputenx.sty</span>&rsquo;,

            
            it allows further characters (mainly for Eastern European

            
            languages) by including &lsquo;<span class="file">ix-utf8enc.dfu</span>&rsquo; (if available).

            
            (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14989">PR#14989</a>.)

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD build</code> now omits several types of hidden

            
            files/directories, including &lsquo;<span class="file">inst/doc/.Rinstignore</span>&rsquo;,

            
            &lsquo;<span class="file">vignettes/.Rinstignore</span>&rsquo;, (&lsquo;<span class="file">.Rinstignore</span>&rsquo; should be at

            
            top level), &lsquo;<span class="file">.deps</span>&rsquo; under &lsquo;<span class="file">src</span>&rsquo;, &lsquo;<span class="file">.Renviron</span>&rsquo;,

            
            &lsquo;<span class="file">.Rprofile</span>&rsquo;, &lsquo;<span class="file">.Rproj.user</span>&rsquo;, &lsquo;<span class="file">.backups</span>&rsquo;,

            
            &lsquo;<span class="file">.cvsignore</span>&rsquo;, &lsquo;<span class="file">.cproject</span>&rsquo;, &lsquo;<span class="file">.directory</span>&rsquo;,

            
            &lsquo;<span class="file">.dropbox</span>&rsquo;, &lsquo;<span class="file">.exrc</span>&rsquo;, &lsquo;<span class="file">.gdb.history</span>&rsquo;,

            
            &lsquo;<span class="file">.gitattributes</span>&rsquo;, &lsquo;<span class="file">.gitignore</span>&rsquo;, &lsquo;<span class="file">.gitmodules</span>&rsquo;,

            
            &lsquo;<span class="file">.hgignore</span>&rsquo;, &lsquo;<span class="file">.hgtags</span>&rsquo;, &lsquo;<span class="file">.htaccess</span>&rsquo;,

            
            &lsquo;<span class="file">.latex2html-init</span>&rsquo;, &lsquo;<span class="file">.project</span>&rsquo;, &lsquo;<span class="file">.seed</span>&rsquo;,

            
            &lsquo;<span class="file">.settings</span>&rsquo;, &lsquo;<span class="file">.tm_properties</span>&rsquo; and various leftovers.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD check</code> now checks for <code>.C()</code>,

            
            <code>.Call()</code>, <code>.External()</code> and <code>.Fortran()</code> calls in

            
            other packages, and gives a warning on those found from <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> itself

            
            (which are not part of the API and change without notice: many

            
            will be changed for <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.0.0).

            
            </p>

            
            </li></ul>


            <h4>C-LEVEL FACILITIES</h4>


            <ul>

            
            <li><p> The limit for <code>R_alloc</code> on 64-bit platforms has been

            
            raised to just under 32GB (from just under 16GB).

            
            </p>

            
            </li>

            
            <li><p> The misuse of <code>.C("name", ..., PACKAGE = foo)</code> where

            
            <code>foo</code> is an arbitrary <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> object is now an error.

            
            </p>

            
            <p>The misuse <code>.C("name",..., PACKAGE = "")</code> is now warned about

            
            in <code>R CMD check</code>, and will be an error in future.

            
            </p>

            
            </li></ul>


            <h4>DEPRECATED AND DEFUNCT</h4>


            <ul>

            
            <li><p> Use of <code>array()</code> with a 0-length <code>dim</code> argument is

            
            deprecated with a warning (and was contrary to the documentation).

            
            </p>

            
            </li>

            
            <li><p> Use of <code>tapply()</code> with a 0-length <code>INDEX</code> list is

            
            deprecated with a warning.

            
            </p>

            
            </li>

            
            <li> <p><span class="samp">Translation</span> packages are deprecated.

            
            </p>

            
            </li>

            
            <li><p> Calling <code>rep()</code> or <code>rep.int()</code> on a pairlist is

            
            deprecated and will give a warning.  In any case, <code>rep()</code>

            
            converted a pairlist to a list so you may as well do that

            
            explicitly.

            
            </p>

            
            </li>

            
            <li><p> Entry point <code>rcont2</code> is no longer part of the API, and

            
            will move to package <span class="pkg">stats</span> in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.0.0.

            
            </p>

            
            </li>

            
            <li><p> The &lsquo;internal&rsquo; graphics device invoked by

            
            <code>.Call("R_GD_nullDevice", package = "grDevices")</code> is about to

            
            be removed: use <code>pdf(file = NULL)</code> instead.

            
            </p>

            
            </li>

            
            <li> <p><code>eigen(EISPACK = TRUE)</code>,

            
            <code>chol(pivot = FALSE, LINPACK = TRUE)</code>,

            
            <code>chol2inv(LINPACK = TRUE)</code>, <code>solve(LINPACK = TRUE)</code> and

            
            <code>svd(LINPACK = TRUE)</code> are deprecated and give a warning.

            
            </p>

            
            <p>They were provided for compatibility with <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 1.7.0 (Mar 2003)!

            
            </p>

            
            </li>

            
            <li><p> The &lsquo;internal function&rsquo; <code>kappa.tri()</code> has been

            
            renamed to <code>.kappa_tri()</code> so it is not inadvertently called

            
            as a method for class <code>"tri"</code>.

            
            </p>

            
            </li>

            
            <li><p> Functions <code>sessionData()</code> and <code>browseAll()</code> in

            
            package <span class="pkg">methods</span> are on a help page describing them as

            
            &lsquo;deprecated&rsquo; and are now formally deprecated.

            
            </p>

            
            </li></ul>


            <h4>PACKAGE INSTALLATION</h4>


            <ul>

            
            <li><p> For a Windows or Mac OS X binary package install,

            
            <code>install.packages()</code> will check if a source package is

            
            available on the same repositories, and report if it is a later

            
            version or there is a source package but no binary package

            
            available.

            
            </p>

            
            <p>This check can be suppressed: see the help page.

            
            </p>

            
            </li>

            
            <li> <p><code>install.packages(type = "both")</code> has been enhanced.

            
            In interactive use it will ask whether to choose the source

            
            version of a package if the binary version is older and contains

            
            compiled code, and also asks if source packages with no binary

            
            version should be installed).

            
            </p>

            
            </li></ul>


            <h4>INSTALLATION</h4>


            <ul>

            
            <li><p> There is a new <code>configure</code> option

            
            <span class="option">--with-libtiff</span> (mainly in case the system installation

            
            needs to be avoided).

            
            </p>

            
            </li>

            
            <li><p> LAPACK 3.4.1 does use some Fortran 90 features, so

            
            <code>g77</code> no longer suffices.

            
            </p>

            
            </li>

            
            <li><p> If an external LAPACK is used, it must be version 3.2 or later.

            
            </p>

            
            </li></ul>


            <h4>BUG FIXES</h4>


            <ul>

            
            <li><p> On Windows, starting <code>Rterm</code> via <code>R.exe</code>

            
            caused Ctrl-C to misbehave.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14948">PR#14948</a>)

            
            </p>

            
            </li>

            
            <li><p> The <code>tools::latexToUtf8()</code> function missed conversions that

            
            were contained within braces.

            
            </p>

            
            </li>

            
            <li><p> Long timezone specifications (such as a file name preceded

            
            by <code>:</code>) could crash <code>as.POSIXlt</code>.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14945">PR#14945</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD build --resave-data</code> could fail if there was no

            
            &lsquo;<span class="file">data</span>&rsquo; directory but there was an &lsquo;<span class="file">R/sysdata.rda</span>&rsquo; file.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14947">PR#14947</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>is.na()</code> misbehaved on a 0-column data frame.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14959">PR#14959</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>anova.lmlist()</code> failed if <code>test</code> was

            
            supplied.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14960">PR#14960</a>)

            
            </p>

            
            <p>It was unable to compute Cp tests for object of class <code>"lm"</code>

            
            (it assumed class <code>"glm"</code>).

            
            </p>

            
            </li>

            
            <li><p> The <code>formula</code> method for <code>sunflowerplot()</code> now

            
            allows <code>xlab</code> and <code>ylab</code> to be set.  (Reported by Gerrit

            
            Eichner.)

            
            </p>

            
            </li>

            
            <li><p> The <code>"POSIXt"</code> and <code>"Date"</code> methods for <code>hist()</code>

            
            could fail on Windows where adjustments to the right-hand boundary

            
            crossed a DST transition time.

            
            </p>

            
            </li>

            
            <li><p> On Windows, the code in <code>as.POSIXct()</code> to handle

            
            incorrectly specified <code>isdst</code> fields might have resulted in

            
            <code>NA</code> being returned.

            
            </p>

            
            </li>

            
            <li> <p><code>aov()</code> and <code>manova()</code> gave spurious warning about

            
            singular error model in the multiresponse case.

            
            </p>

            
            </li>

            
            <li><p> In <code>ns()</code> and <code>bs()</code>, specifying <code>knots = NULL</code>

            
            is now equivalent to omitting it, also when <code>df</code> is

            
            specified.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14970">PR#14970</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>sprintf()</code> did not accept numbered arguments ending

            
            in zero.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14975">PR#14975</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>rWishart()</code> could overflow the C stack and maybe crash

            
            the <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> process for dimensions of several hundreds or more.

            
            (Reported by Michael Braun on R-sig-mac.)

            
            </p>

            
            </li>

            
            <li><p> Base package vignettes (e.g., <code>vignette("Sweave")</code>) were

            
            not fully installed in builds of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> from the tarball.

            
            </p>

            
            </li>

            
            <li> <p><code>lchoose()</code> and <code>choose()</code> could overflow the C

            
            stack and crash <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>.

            
            </p>

            
            </li>

            
            <li><p> When given a 0-byte file and asked to keep source

            
            references, <code>parse()</code> read input from <code>stdin()</code>

            
            instead.

            
            </p>

            
            </li>

            
            <li> <p><code>pdf(compress = TRUE)</code> did not delete temporary files

            
            it created until the end of the <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> session.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14991">PR#14991</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>logLik()</code> did not detect the error of applying it

            
            to a multiple-response linear model.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15000">PR#15000</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>file.copy(recursive = TRUE)</code> did not always report

            
            <code>FALSE</code> for a failure two or more directories deep.

            
            </p>

            
            </li>

            
            <li> <p><code>qgeom()</code> could return <code>-1</code> for extremely small

            
            <code>q</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14967">PR#14967</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>smooth.spline()</code> used <code>DUP = FALSE</code> which allowed

            
            its compiled C code to change the function: this was masked by the

            
            default byte-compilation. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14965">PR#14965</a>)

            
            </p>

            
            </li>

            
            <li><p> In Windows, the GUI preferences for foreground color were

            
            not always respected.  (Reported by Benjamin Wells.)

            
            </p>

            
            </li>

            
            <li><p> On OS X, the Quartz versions of the bitmap devices did not

            
            respect <code>antialias = "none"</code>.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15006">PR#15006</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>unique()</code> and similar would infinite-loop if called on

            
            a vector of length &gt; <i>2^29</i> (but reported that the

            
            vector was too long for <i>2^30</i> or more).

            
            </p>

            
            </li>

            
            <li> <p><code>parallel::stopCluster()</code> now works with MPI

            
            clusters without <a href="https://CRAN.R-project.org/package=snow"><span class="pkg">snow</span></a> being on the search path.

            
            </p>

            
            </li>

            
            <li> <p><code>terms.formula()</code> could exhaust the stack, and the

            
            stack check did not always catch this before the segfault.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15013">PR#15013</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>sort.list(method = "radix")</code> could give incorrect

            
            results on certain compilers (seen with <code>clang</code> on Mac OS

            
            10.7 and <code>Xcode 4.4.1</code>).

            
            </p>

            
            </li>

            
            <li> <p><code>backsolve(T, b)</code> gave incorrect results when

            
            <code>nrows(b) &gt; ncols(T)</code> and <code>b</code> had more than one column.

            
            </p>

            
            <p>It could segfault or give nonsense if <code>k</code> was specified as

            
            more than <code>ncols(T)</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>smooth.spline()</code> did not check that a specified

            
            numeric <code>spar</code> was of length 1, and gave corrupt results if

            
            it was of length 0.

            
            </p>

            
            </li>

            
            <li><p> Protection added to <code>do_system</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15025">PR#15025</a>)

            
            </p>

            
            </li>

            
            <li><p> Printing of vectors with names &gt; 1000 characters now works

            
            correctly rather than truncating. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15028">PR#15028</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>qr()</code> for a complex matrix did not pivot the column names.

            
            </p>

            
            </li>

            
            <li> <p><code>--with-blas='-framework vecLib'</code> now also works on OS X 10.8.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD check</code> no longer fails with an error if

            
            a &lsquo;<span class="file">DESCRIPTION</span>&rsquo; file incorrectly contains a blank line.

            
            (Reported by Bill Dunlap.)

            
            </p>

            
            </li>

            
            <li> <p><code>install.packages(type = "both")</code> could call

            
            <code>chooseCRANmirror()</code> twice.

            
            </p>

            
            </li>

            
            <li> <p><code>lm.wfit()</code> could segfault in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.15.1 if all the

            
            weights were zero. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15044">PR#15044</a>)

            
            </p>

            
            </li>

            
            <li><p> A malformed package name could cause <code>R CMD INSTALL</code>

            
            to write outside the target library.

            
            </p>

            
            </li>

            
            <li><p> Some of the quality control functions

            
            (e.g., <code>tools::checkFF()</code>) were wrongly identifying the source

            
            of S4 methods in a package and so not checking them.

            
            </p>

            
            </li>

            
            <li><p> The default type of display by <code>browseEnv()</code> when using

            
            <code>R.app</code> on Mac OS X has been incorrect for a long time.

            
            </p>

            
            </li>

            
            <li><p> The implementation of <code>importMethodsFrom</code> in a

            
            <code>NAMESPACE</code> file could be confused and fail to find generics

            
            when importing from multiple packages (reported and fixed by

            
            Michael Lawrence).

            
            </p>

            
            </li>

            
            <li><p> The detection of the C stack direction is better protected

            
            against compiler optimization. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15011">PR#15011</a>)

            
            </p>

            
            </li>

            
            <li><p> Long custom line types would sometimes segfault on the

            
            cairographics-based devices. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15055">PR#15055</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>tools::checkPoFile()</code> unprotected too early in its C

            
            code and so segfaulted from time to time.

            
            </p>

            
            </li>

            
            <li><p> The Fortran code underlying <code>nlminb()</code> could

            
            infinite-loop if any of the input functions returned <code>NA</code> or

            
            <code>NaN</code>.  This is now an error for the gradient or Hessian, and

            
            a warning for the function (with the value replaced by

            
            <code>Inf</code>).  (In part, <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15052">PR#15052</a>.)

            
            </p>

            
            </li>

            
            <li><p> The code for creating <code>coerce()</code> methods could

            
            generate false notes about ambiguous selection; the notes have

            
            been suppressed for this function.

            
            </p>

            
            </li>

            
            <li> <p><code>arima.sim()</code> could give too long an output in some

            
            corner cases (in part, <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15068">PR#15068</a>).

            
            </p>

            
            </li>

            
            <li> <p><code>anova.glm()</code> with <code>test = "Rao"</code> didn't work when

            
            models included an offset. (Reported by Søren Feodor Nielsen.)

            
            </p>

            
            </li>

            
            <li> <p><code>as.data.frame.matrix()</code> could return invalid data

            
            frame with no <code>row.names</code> attribute for 0-row matrix. (Reported

            
            by Hervé Pagès.)

            
            </p>

            
            </li>

            
            <li><p> Compilation with the <code>vecLib</code> or <code>Accelerate</code>

            
            frameworks on OS X without using that also for LAPACK is more

            
            likely to be successful.

            
            </p>

            
            </li></ul>


            <h3><img class="toplogo" src="../help/figures/../../html/Rlogo.svg" alt="[R logo]" /> CHANGES IN R VERSION 2.15.1</h3>


            <h4>NEW FEATURES</h4>


            <ul>

            
            <li> <p><code>source()</code> now uses <code>withVisible()</code> rather than

            
            <code>.Internal(eval.with.vis)</code>.  This sometimes alters tracebacks

            
            slightly.

            
            </p>

            
            </li>

            
            <li> <p><code>install.packages("pkg_version.tgz")</code> on Mac OS X now

            
            has sanity checks that this is actually a binary package (as

            
            people have tried it with incorrectly named source packages).

            
            </p>

            
            </li>

            
            <li> <p><code>splineDesign()</code> and <code>spline.des()</code> in package

            
            <span class="pkg">splines</span> have a new option <code>sparse</code> which can be used

            
            for efficient construction of a sparse B-spline design matrix

            
            (<em>via</em> <a href="https://CRAN.R-project.org/package=Matrix"><span class="pkg">Matrix</span></a>).

            
            </p>

            
            </li>

            
            <li> <p><code>norm()</code> now allows <code>type = "2"</code> (the

            
            &lsquo;spectral&rsquo; or 2-norm) as well, mainly for didactical

            
            completeness.

            
            </p>

            
            </li>

            
            <li> <p><code>pmin()</code> and <code>pmax())</code> now also work when one of

            
            the inputs is of length zero and others are not, returning a

            
            zero-length vector, analogously to, say, <code>+</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>colorRamp()</code> (and hence <code>colorRampPalette()</code>) now

            
            also works for the boundary case of just one color when the ramp is

            
            flat.

            
            </p>

            
            </li>

            
            <li> <p><code>.C()</code> gains some protection against the misuse of

            
            character vector arguments.  (An all too common error is to pass

            
            <code>character(N)</code>, which initializes the elements to <code>""</code>,

            
            and then attempt to edit the strings in-place, sometimes forgetting

            
            to terminate them.)

            
            </p>

            
            </li>

            
            <li><p> Calls to the new function <code>globalVariables()</code> in

            
            package <span class="pkg">utils</span> declare that functions and other objects in a

            
            package should be treated as globally defined, so that <code>CMD

            
                  check</code> will not note them.

            
            </p>

            
            </li>

            
            <li> <p><code>print(packageDescription(*))</code> trims the <code>Collate</code>

            
            field by default.

            
            </p>

            
            </li>

            
            <li><p> The included copy of <code>zlib</code> has been updated to version

            
            1.2.7.

            
            </p>

            
            </li>

            
            <li><p> A new option <code>"show.error.locations"</code> has been added.

            
            When set to <code>TRUE</code>, error messages will contain the

            
            location of the most recent call containing source reference

            
            information. (Other values are supported as well; see

            
            <code>?options</code>.)

            
            </p>

            
            </li>

            
            <li><p> The NA warning messages from e.g. <code>pchisq()</code> now report

            
            the call to the closure and not that of the <code>.Internal</code>.

            
            </p>

            
            </li>

            
            <li><p> Added Polish translations by Łukasz Daniel.

            
            </p>

            
            </li></ul>


            <h4>PERFORMANCE IMPROVEMENTS</h4>


            <ul>

            
            <li><p> In package <span class="pkg">parallel</span>, <code>makeForkCluster()</code> and the

            
            multicore-based functions use native byte-order for serialization

            
            (deferred from 2.15.0).

            
            </p>

            
            </li>

            
            <li> <p><code>lm.fit()</code>, <code>lm.wfit()</code>, <code>glm.fit()</code> and

            
            <code>lsfit()</code> do less copying of objects, mainly by using

            
            <code>.Call()</code> rather than <code>.Fortran()</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>.C()</code> and <code>.Fortran()</code> do less copying: arguments

            
            which are raw, logical, integer, real or complex vectors and are

            
            unnamed are not copied before the call, and (named or not) are not

            
            copied after the call.  Lists are no longer copied (they are

            
            supposed to be used read-only in the C code).

            
            </p>

            
            </li>

            
            <li> <p><code>tabulate()</code> makes use of <code>.C(DUP = FALSE)</code> and

            
            hence does not copy <code>bin</code>.  (Suggested by Tim Hesterberg.)

            
            It also avoids making a copy of a factor argument <code>bin</code>.

            
            </p>

            
            </li>

            
            <li><p> Other functions (often or always) doing less copying include

            
            <code>cut()</code>, <code>dist()</code>, the complex case of <code>eigen()</code>,

            
            <code>hclust()</code>, <code>image()</code>, <code>kmeans()</code>, <code>loess()</code>,

            
            <code>stl()</code> and <code>svd(LINPACK = TRUE)</code>.

            
            </p>

            
            </li>

            
            <li><p> There is less copying when using primitive replacement

            
            functions such as <code>names()</code>, <code>attr()</code> and

            
            <code>attributes()</code>.

            
            </p>

            
            </li></ul>


            <h4>DEPRECATED AND DEFUNCT</h4>


            <ul>

            
            <li><p> The converters for use with <code>.C()</code> (see

            
            <code>?getCConverterDescriptions</code>) are deprecated: use the

            
            <code>.Call()</code> interface instead.  There are no known examples

            
            (they were never fully documented).

            
            </p>

            
            </li></ul>


            <h4>UTILITIES</h4>


            <ul>

            
            <li><p> For <code>R CMD check</code>, a few people have reported

            
            problems with junctions on Windows (although they were tested on

            
            Windows 7, XP and Server 2008 machines and it is unknown under

            
            what circumstances the problems occur).  Setting the environment

            
            variable <span class="env">R_WIN_NO_JUNCTIONS</span> to a non-empty value (e.g., in

            
            &lsquo;<span class="file">~/.R/check.Renviron</span>&rsquo;) will force copies to be used instead.

            
            </p>

            
            </li></ul>


            <h4>INSTALLATION</h4>


            <ul>

            
            <li> <p><code>R CMD INSTALL</code> with <span class="env">_R_CHECK_INSTALL_DEPENDS_</span>

            
            set to a true value (as done by <code>R CMD check --as-cran</code>)

            
            now restricts the packages available when lazy-loading as well

            
            as when test-loading (since packages such as <a href="https://CRAN.R-project.org/package=ETLUtils"><span class="pkg">ETLUtils</span></a>

            
            and <a href="https://CRAN.R-project.org/package=agsemisc"><span class="pkg">agsemisc</span></a> had top-level calls to <code>library()</code>

            
            for undeclared packages).

            
            </p>

            
            <p>This check is now also available on Windows.

            
            </p>

            
            </li></ul>


            <h4>C-LEVEL FACILITIES</h4>


            <ul>

            
            <li><p> C entry points <code>mkChar</code> and <code>mkCharCE</code> now check

            
            that the length of the string they are passed does not exceed

            
            <i>2^31-1</i> bytes: they used to overflow with

            
            unpredictable consequences.

            
            </p>

            
            </li>

            
            <li><p> C entry points <code>R_GetCurrentSrcref</code> and

            
            <code>R_GetSrcFilename</code> have been added to the API to allow

            
            debuggers access to the source references on the stack.

            
            </p>

            
            </li></ul>


            <h4>WINDOWS-SPECIFIC CHANGES</h4>


            <ul>

            
            <li><p> Windows-specific changes will now be announced in this file

            
            (&lsquo;<span class="file">NEWS</span>&rsquo;).  Changes up and including <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.15.0 remain in the

            
            &lsquo;<span class="file">CHANGES</span>&rsquo; file.

            
            </p>

            
            </li>

            
            <li><p> There are two new environment variables which

            
            control the defaults for command-line options.

            
            </p>

            
            <p>If <span class="env">R_WIN_INTERNET2</span> is set to a non-empty value, it is as if

            
            <span class="option">--internet2</span> was used.

            
            </p>

            
            <p>If <span class="env">R_MAX_MEM_SIZE</span> is set, it gives the default memory limit

            
            if <span class="option">--max-mem-size</span> is not specified: invalid values being

            
            ignored.

            
            </p>

            
            </li></ul>


            <h4>BUG FIXES</h4>


            <ul>

            
            <li> <p><code>lsfit()</code> lost the names from the residuals.

            
            </p>

            
            </li>

            
            <li><p> More cases in which <code>merge()</code> could create a data frame

            
            with duplicate column names now give warnings.  Cases where

            
            names specified in <code>by</code> match multiple columns are errors.

            
            </p>

            
            </li>

            
            <li><p> Nonsense uses such as <code>seq(1:50, by = 5)</code> (from package

            
            <a href="https://CRAN.R-project.org/package=plotrix"><span class="pkg">plotrix</span></a>) and <code>seq.int(1:50, by = 5)</code> are now errors.

            
            </p>

            
            </li>

            
            <li><p> The residuals in the 5-number summary printed by

            
            <code>summary()</code> on an <code>"lm"</code> object are now explicitly

            
            labelled as weighted residuals when non-constant weights are

            
            present.  (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14840">PR#14840</a>.)

            
            </p>

            
            </li>

            
            <li> <p><code>tracemem()</code> reported that all objects were copied

            
            by <code>.C()</code> or <code>.Fortran()</code> whereas only some object types

            
            were ever copied.

            
            </p>

            
            <p>It also reported and marked as copies <em>some</em> transformations

            
            such as <code>rexp(n, x)</code>: it no longer does so.

            
            </p>

            
            </li>

            
            <li><p> The <code>plot()</code> method for class <code>"stepfun"</code> only

            
            used the optional <code>xval</code> argument to compute <code>xlim</code> and

            
            not the points at which to plot (as documented).  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14864">PR#14864</a>)

            
            </p>

            
            </li>

            
            <li><p> Names containing characters which need to be escaped were

            
            not deparsed properly.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14846">PR#14846</a>)

            
            </p>

            
            </li>

            
            <li><p> Trying to update (recommended) packages in

            
            &lsquo;<span class="file">R_HOME/library</span>&rsquo; without write access is now dealt with more

            
            gracefully.  Further, such package updates may be skipped (with a

            
            warning), when a newer installed version is already going to be

            
            used from <code>.libPaths()</code>.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14866">PR#14866</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>hclust()</code> is now fast again (as up to end of 2003),

            
            with a different fix for the &quot;median&quot;/&quot;centroid&quot; problem.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=4195">PR#4195</a>).

            
            </p>

            
            </li>

            
            <li> <p><code>get_all_vars()</code> failed when the data came entirely

            
            from vectors in the global environment. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14847">PR#14847</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD check</code> with <span class="env">_R_CHECK_NO_RECOMMENDED_</span>

            
            set to a true value (as done by the <code>--as-cran</code> option)

            
            could issue false errors if there was an indirect dependency

            
            on a recommended package.

            
            </p>

            
            </li>

            
            <li> <p><code>formatC()</code> uses the C entry point <code>str_signif</code>

            
            which could write beyond the length allocated for the output string.

            
            </p>

            
            </li>

            
            <li><p> Missing default argument added to implicit S4 generic for

            
            <code>backsolve()</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14883">PR#14883</a>)

            
            </p>

            
            </li>

            
            <li><p> Some bugs have been fixed in handling load actions that

            
            could fail to export assigned items or generate spurious warnings

            
            in <code>CMD check</code> on loading.

            
            </p>

            
            </li>

            
            <li><p> For <code>tiff(type = "windows")</code>, the numbering of per-page

            
            files except the last was off by one.

            
            </p>

            
            </li>

            
            <li><p> On Windows, loading package <span class="pkg">stats</span> (which is done for

            
            a default session) would switch line endings on &lsquo;<span class="file">stdout</span>&rsquo;

            
            and &lsquo;<span class="file">stderr</span>&rsquo; from CRLF to LF.  This affected

            
            <code>Rterm</code> and <code>R CMD BATCH</code>.

            
            </p>

            
            </li>

            
            <li><p> On Windows, the compatibility function <code>x11()</code> had

            
            not kept up with changes to <code>windows()</code>, and issued

            
            warnings about bad parameters. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14880">PR#14880</a>)

            
            </p>

            
            </li>

            
            <li><p> On Windows, the <code>Sys.glob()</code> function did not handle

            
            UNC paths as it was designed to try to do. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14884">PR#14884</a>)

            
            </p>

            
            </li>

            
            <li><p> In package <span class="pkg">parallel</span>, <code>clusterApply()</code> and similar

            
            failed to handle a (pretty pointless) length-1 argument. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14898">PR#14898</a>)

            
            </p>

            
            </li>

            
            <li><p> Quartz Cocoa display reacted asynchronously to

            
            <code>dev.flush()</code> which means that the redraw could be performed

            
            after the plot has been already modified by subsequent code. The

            
            redraw is now done synchronously in <code>dev.flush()</code> to allow

            
            animations without sleep cycles.

            
            </p>

            
            </li>

            
            <li><p> Source locations reported in <code>traceback()</code> were

            
            incorrect when byte-compiled code was on the stack.

            
            </p>

            
            </li>

            
            <li> <p><code>plogis(x, lower = FALSE, log.p = TRUE)</code> no longer

            
            underflows early for large x (e.g., 800).

            
            </p>

            
            </li>

            
            <li> <p><code>?Arithmetic</code>'s &ldquo;<code>1 ^ y</code> and <code>y ^ 0</code>

            
            are <code>1</code>, <em>always</em>&rdquo; now also applies for <code>integer</code>

            
            vectors <code>y</code>.

            
            </p>

            
            </li>

            
            <li><p> X11-based pixmap devices like <code>png(type = "Xlib")</code> were

            
            trying to set the cursor style, which triggered some warnings and

            
            hangs.

            
            </p>

            
            </li>

            
            <li><p> Code executed by the built-in HTTP server no longer allows

            
            other HTTP clients to re-enter <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> until the current worker

            
            evaluation finishes, to prevent cascades.

            
            </p>

            
            </li>

            
            <li><p> The <code>plot()</code> and <code>Axis()</code> methods for class

            
            <code>"table"</code> now respect graphical parameters such as

            
            <code>cex.axis</code>.  (Reported by Martin Becker.)

            
            </p>

            
            </li>

            
            <li><p> Under some circumstances <code>package.skeleton()</code> would

            
            give out progress reports that could not be translated and so were

            
            displayed by question marks.  Now they are always in English.

            
            (This was seen for CJK locales on Windows, but may have occurred

            
            elsewhere.)

            
            </p>

            
            </li>

            
            <li><p> The evaluator now keeps track of source references outside

            
            of functions, e.g. when <code>source()</code> executes a script.

            
            </p>

            
            </li>

            
            <li><p> The replacement method for <code>window()</code> now works

            
            correctly for multiple time series of class <code>"mts"</code>.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14925">PR#14925</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>is.unsorted()</code> gave incorrect results on non-atomic

            
            objects such as data frames.  (Reported by Matthew Dowle.)

            
            </p>

            
            </li>

            
            <li><p> The value returned by <code>tools::psnice()</code> for invalid

            
            <code>pid</code> values was not always <code>NA</code> as documented.

            
            </p>

            
            </li>

            
            <li><p> Closing an <code>X11()</code> window while <code>locator()</code> was

            
            active could abort the <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> process.

            
            </p>

            
            </li>

            
            <li> <p><code>getMethod(f, sig)</code> produced an incorrect error message

            
            in some cases when <code>f</code> was not a string).

            
            </p>

            
            </li>

            
            <li><p> Using a string as a &ldquo;call&rdquo; in an error condition

            
            with <code>options(showErrorCalls=TRUE)</code> could cause a segfault.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14931">PR#14931</a>)

            
            </p>

            
            </li>

            
            <li><p> The string <code>"infinity"</code> allowed by C99 was not accepted

            
            as a numerical string value by e.g. <code>scan()</code> and

            
            <code>as.numeric()</code>.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14933">PR#14933</a>)

            
            </p>

            
            </li>

            
            <li><p> In <code>legend()</code>, setting some entries of <code>lwd</code> to

            
            <code>NA</code> was inconsistent (depending on the graphics device) in

            
            whether it would suppress those lines; now it consistently does

            
            so.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14926">PR#14926</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>by()</code> failed for a zero-row data frame.  (Reported by

            
            Weiqiang Qian.)

            
            </p>

            
            </li>

            
            <li><p> The Yates' correction in <code>chisq.test()</code> could be bigger

            
            than the terms it corrected, previously leading to an infinite

            
            test statistic in some corner cases which are now reported as

            
            <code>NaN</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>xgettext()</code> and related functions sometimes returned

            
            items that were not strings for translation. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14935">PR#14935</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>plot(&lt;lm&gt;, which=5)</code> now correctly labels the factor

            
            level combinations for the special case where all

            
            <i>h[i,i]</i> are the same. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14837">PR#14837</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>Sys.glob()</code> caused a segfault if the first element of

            
            <code>path</code> was <code>NA_character</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14990">PR#14990</a>)

            
            </p>

            
            </li></ul>


            <h3><img class="toplogo" src="../help/figures/../../html/Rlogo.svg" alt="[R logo]" /> CHANGES IN R VERSION 2.15.0</h3>


            <h4>SIGNIFICANT USER-VISIBLE CHANGES</h4>


            <ul>

            
            <li><p> The behaviour of <code>unlink(recursive = TRUE)</code> for a

            
            symbolic link to a directory has changed: it now removes the link

            
            rather than the directory contents (just as <code>rm -r</code> does).

            
            </p>

            
            <p>On Windows it no longer follows reparse points (including

            
            junctions and symbolic links).

            
            </p>

            
            </li></ul>


            <h4>NEW FEATURES</h4>


            <ul>

            
            <li><p> Environment variable <span class="env">RD2DVI_INPUTENC</span> has been renamed

            
            to <span class="env">RD2PDF_INPUTENC</span>.

            
            </p>

            
            </li>

            
            <li> <p><code>.Deprecated()</code> becomes a bit more flexible, getting an

            
            <code>old</code> argument.

            
            </p>

            
            </li>

            
            <li><p> Even data-only packages without <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> code need a namespace and

            
            so may need to be installed under <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.14.0 or later.

            
            </p>

            
            </li>

            
            <li> <p><code>assignInNamespace()</code> has further restrictions on use

            
            apart from at top-level, as its help page has warned.

            
            Expect it to be disabled from programmatic use in the future.

            
            </p>

            
            </li>

            
            <li> <p><code>system()</code> and <code>system2()</code> when capturing output

            
            report a non-zero status in the new <code>"status"</code> attribute.

            
            </p>

            
            </li>

            
            <li> <p><code>kronecker()</code> now has an S4 generic in package

            
            <span class="pkg">methods</span> on which packages can set methods.  It will be

            
            invoked by <code>X %x% Y</code> if either <code>X</code> or <code>Y</code> is an S4

            
            object.

            
            </p>

            
            </li>

            
            <li> <p><code>pdf()</code> accepts forms like <code>file = "|lpr"</code> in the

            
            same way as <code>postscript()</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>pdf()</code> accepts <code>file = NULL</code>.

            
            This means that the device does NOT create a PDF file

            
            (but it can still be queried, e.g., for font metric info).

            
            </p>

            
            </li>

            
            <li> <p><code>format()</code> (and hence <code>print()</code>) on

            
            <code>"bibentry"</code> objects now uses <code>options("width")</code> to

            
            set the output width.

            
            </p>

            
            </li>

            
            <li> <p><code>legend()</code> gains a <code>text.font</code> argument. (Suggested

            
            by Tim Paine, <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14719">PR#14719</a>.)

            
            </p>

            
            </li>

            
            <li> <p><code>nchar()</code> and <code>nzchar()</code> no longer accept factors

            
            (as integer vectors).  (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=6899">PR#6899</a>.)

            
            </p>

            
            </li>

            
            <li> <p><code>summary()</code> behaves slightly differently (or more

            
            precisely, its <code>print()</code> method does).  For numeric inputs, the

            
            number of NAs is printed as an integer and not a real.  For dates

            
            and datetimes, the number of NAs is included in the printed output

            
            (the latter being the wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14720">PR#14720</a>).

            
            </p>

            
            <p>The <code>"data.frame"</code> method is more consistent with the default

            
            method: in particular it now applies <code>zapsmall()</code> to

            
            numeric/complex summaries.

            
            </p>

            
            </li>

            
            <li><p> The number of items retained with <code>options(warn = 0)</code>

            
            can be set by <code>options(nwarnings=)</code>.

            
            </p>

            
            </li>

            
            <li><p> There is a new function <code>assignInMyNamespace()</code> which

            
            uses the namespace of the function it is called from.

            
            </p>

            
            </li>

            
            <li> <p><code>attach()</code> allows the default name for an attached file

            
            to be overridden.

            
            </p>

            
            </li>

            
            <li> <p><code>bxp()</code>, the work horse of <code>boxplot()</code>, now uses a

            
            more sensible default <code>xlim</code> in the case where <code>at</code> is

            
            specified differently from <code>1:n</code>, see the discussion on R-devel,

            
            <a href="https://stat.ethz.ch/pipermail/r-devel/2011-November/062586.html">https://stat.ethz.ch/pipermail/r-devel/2011-November/062586.html</a>.

            
            </p>

            
            </li>

            
            <li><p> New function <code>paste0()</code>, an efficient version of

            
            <code>paste(*, sep="")</code>, to be used in many places for more

            
            concise (and slightly more efficient) code.

            
            </p>

            
            </li>

            
            <li><p> Function <code>setClass()</code> in package <span class="pkg">methods</span> now

            
            returns, invisibly, a generator function for the new class,

            
            slightly preferred to calling <code>new()</code>, as explained on the

            
            <code>setClass</code> help page.

            
            </p>

            
            </li>

            
            <li><p> The <code>"dendrogram"</code> method of <code>str()</code> now takes

            
            its default for <code>last.str</code> from option <code>str.dendrogram.last</code>.

            
            </p>

            
            </li>

            
            <li><p> New simple <code>fitted()</code> method for <code>"kmeans"</code> objects.

            
            </p>

            
            </li>

            
            <li><p> The <code>traceback()</code> function can now be called with

            
            an integer argument, to display a current stack trace. (Wish of

            
            <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14770">PR#14770</a>.)

            
            </p>

            
            </li>

            
            <li> <p><code>setGeneric()</code> calls can be simplified when creating

            
            a new generic function by supplying the default method as the

            
            <code>def</code> argument.  See <code>?setGeneric</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>serialize()</code> has a new option <code>xdr = FALSE</code> which

            
            will use the native byte-order for binary serializations.  In

            
            scenarios where only little-endian machines are involved (these

            
            days, close to universal) and (un)serialization takes an

            
            appreciable amount of time this may speed up noticeably

            
            transferring data between systems.

            
            </p>

            
            </li>

            
            <li><p> The internal (un)serialization code is faster for long

            
            vectors, particularly with XDR on some platforms.  (Based on a

            
            suggested patch by Michael Spiegel.)


            </p>

            
            </li>

            
            <li><p> For consistency, circles with zero radius are omitted by

            
            <code>points()</code> and <code>grid.circle()</code>.  Previously this was

            
            device-dependent, but they were usually invisible.

            
            </p>

            
            </li>

            
            <li> <p><code>NROW(x)</code> and <code>NCOL(x)</code> now work whenever

            
            <code>dim(x)</code> looks appropriate, e.g., also for more generalized

            
            matrices.

            
            </p>

            
            </li>

            
            <li><p> PCRE has been updated to version 8.30.

            
            </p>

            
            </li>

            
            <li><p> The internal <code>R_Srcref</code> variable is now updated

            
            before the browser stops on entering a function.  (Suggestion of

            
            <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14818">PR#14818</a>.)

            
            </p>

            
            </li>

            
            <li><p> There are &lsquo;bare-bones&rsquo; functions <code>.colSums()</code>,

            
            <code>.rowSums()</code>, <code>.colMeans()</code> and <code>.rowMeans()</code> for

            
            use in programming where ultimate speed is required.

            
            </p>

            
            </li>

            
            <li><p> The formerly internal function

            
            <code>.package_dependencies()</code> from package <span class="pkg">tools</span> for

            
            calculating (recursive) (reverse) dependencies on package databases

            
            has been renamed to <code>package_dependencies()</code> and is now

            
            exported.

            
            </p>

            
            </li>

            
            <li><p> There is a new function <code>optimHess()</code> to compute the

            
            (approximate) Hessian for an <code>optim()</code> solution if

            
            <code>hessian = TRUE</code> was forgotten.

            
            </p>

            
            </li>

            
            <li> <p><code>.filled.contour()</code> is a &lsquo;bare-bones&rsquo; function to

            
            add a filled-contour rectangular plot to an already prepared plot

            
            region.

            
            </p>

            
            </li>

            
            <li><p> The stepping in debugging and single-step browsing modes has

            
            changed slightly: now left braces at the start of the body are

            
            stepped over for <code>if</code> statements as well as for <code>for</code> and

            
            <code>while</code> statements.  (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14814">PR#14814</a>.)

            
            </p>

            
            </li>

            
            <li> <p><code>library()</code> no longer warns about a conflict with a

            
            function from <code>package:base</code> if the function has the same

            
            code as the base one but with a different environment.  (An

            
            example is <code>Matrix::det()</code>.)

            
            </p>

            
            </li>

            
            <li><p> When deparsing very large language objects,

            
            <code>as.character()</code> now inserts newlines after each line of

            
            approximately 500 bytes, rather than truncating to the first

            
            line.

            
            </p>

            
            </li>

            
            <li><p> New function <code>rWishart()</code> generates Wishart-distributed

            
            random matrices.

            
            </p>

            
            </li>

            
            <li><p> Packages may now specify actions to be taken when the

            
            package is loaded (<code>setLoadActions()</code>).

            
            </p>

            
            </li>

            
            <li> <p><code>options(max.print = Inf)</code> and similar now give an

            
            error (instead of warnings later).

            
            </p>

            
            </li>

            
            <li><p> The <code>"difftime"</code> replacement method of <code>units</code>

            
            tries harder to preserve other attributes of the argument.  (Wish

            
            of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14839">PR#14839</a>.)

            
            </p>

            
            </li>

            
            <li> <p><code>poly(raw = TRUE)</code> no longer requires more unique

            
            points than the degree.  (Requested by John Fox.)

            
            </p>

            
            </li></ul>


            <h4>PACKAGE parallel</h4>


            <ul>

            
            <li><p> There is a new function <code>mcmapply()</code>, a parallel version

            
            of <code>mapply()</code>, and a wrapper <code>mcMap()</code>, a parallel

            
            version of <code>Map()</code>.

            
            </p>

            
            </li>

            
            <li><p> A default cluster can be registered by the new function

            
            <code>setDefaultCluster()</code>: this will be used by default in

            
            functions such as <code>parLapply()</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>clusterMap()</code> has a new argument <code>.scheduling</code> to

            
            allow the use of load-balancing.

            
            </p>

            
            </li>

            
            <li><p> There are new load-balancing functions <code>parLapplyLB()</code>

            
            and <code>parSapplyLB()</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>makePSOCKCluster()</code> has a new option <code>useXDR =

            
            	FALSE</code> which can be used to avoid byte-shuffling for

            
            serialization when all the nodes are known to be little-endian (or

            
            all big-endian).

            
            </p>

            
            </li></ul>


            <h4>PACKAGE INSTALLATION</h4>


            <ul>

            
            <li><p> Non-ASCII vignettes without a declared encoding are no

            
            longer accepted.

            
            </p>

            
            </li>

            
            <li><p> C/C++ code in packages is now compiled with <code>-NDEBUG</code>

            
            to mitigate against the C/C++ function <code>assert</code> being called

            
            in production use.  Developers can turn this off during package

            
            development with <code>PKG_CPPFLAGS = -UNDEBUG</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD INSTALL</code> has a new option <span class="option">--dsym</span>

            
            which on Mac OS X (Darwin) dumps the symbols alongside the

            
            &lsquo;<span class="file">.so</span>&rsquo; file: this is helpful when debugging with

            
            <code>valgrind</code> (and especially when installing packages into

            
            &lsquo;<span class="file">R.framework</span>&rsquo;).  [This can also be enabled by setting the

            
            undocumented environment variable <span class="env">PKG_MAKE_DSYM</span>, since <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>

            
            2.12.0.]

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD INSTALL</code> will test loading under all installed

            
            sub-architectures even for packages without compiled code, unless

            
            the flag <span class="option">--no-multiarch</span> is used.  (Pure <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> packages can

            
            do things which are architecture-dependent: in the case which

            
            prompted this, looking for an icon in a Windows <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> executable.)

            
            </p>

            
            </li>

            
            <li><p> There is a new option <code>install.packages(type = "both")</code>

            
            which tries source packages if binary packages are not available,

            
            on those platforms where the latter is the default.

            
            </p>

            
            </li>

            
            <li><p> The meaning of <code>install.packages(dependencies = TRUE)</code>

            
            has changed: it now means to install the essential dependencies of

            
            the named packages plus the <span class="samp">Suggests</span>, but only the

            
            essential dependencies of dependencies.  To get the previous

            
            behaviour, specify <code>dependencies</code> as a character vector.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD INSTALL --merge-multiarch</code> is now supported

            
            on OS X and other Unix-alikes using multiple sub-architectures.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD INSTALL --libs-only</code> now by default does a

            
            test load on Unix-alikes as well as on Windows: suppress with

            
            <span class="option">--no-test-load</span>.

            
            </p>

            
            </li></ul>


            <h4>UTILITIES</h4>


            <ul>

            
            <li> <p><code>R CMD check</code> now gives a warning rather than a

            
            note if it finds inefficiently compressed datasets.  With

            
            <code>bzip2</code> and <code>xz</code> compression having been

            
            available since <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.10.0, it only exceptionally makes sense to

            
            not use them.

            
            </p>

            
            <p>The environment variable <span class="env">_R_CHECK_COMPACT_DATA2_</span> is

            
            no longer consulted: the check is always done if

            
            <span class="env">_R_CHECK_COMPACT_DATA_</span> has a true value (its default).

            
            </p>

            
            </li>

            
            <li><p> Where multiple sub-architectures are to be tested,

            
            <code>R CMD check</code> now runs the examples and tests for all the

            
            sub-architectures even if one fails.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD check</code> can optionally report timings on

            
            various parts of the check: this is controlled by environment

            
            variable <span class="env">_R_CHECK_TIMINGS_</span> documented in &lsquo;Writing R

            
            Extensions&rsquo;.  Timings (in the style of <code>R CMD BATCH</code>) are

            
            given at the foot of the output files from running each test and

            
            the <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> code in each vignette.

            
            </p>

            
            </li>

            
            <li><p> There are new options for more rigorous testing by

            
            <code>R CMD check</code> selected by environment variables &ndash; see

            
            the &lsquo;Writing R Extensions&rsquo; manual.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD check</code> now warns (rather than notes) on

            
            undeclared use of other packages in examples and tests:

            
            increasingly people are using the metadata in the

            
            &lsquo;<span class="file">DESCRIPTION</span>&rsquo; file to compute information about packages,

            
            for example reverse dependencies.

            
            </p>

            
            </li>

            
            <li><p> The defaults for some of the options in <code>R CMD

            
            	 check</code> (described in the &lsquo;R Internals&rsquo; manual) have

            
            changed: checks for unsafe and <code>.Internal()</code> calls and

            
            for partial matching of arguments in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> function calls are now

            
            done by default.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD check</code> has more comprehensive facilities for

            
            checking compiled code and so gives fewer reports on entry points

            
            linked into &lsquo;<span class="file">.so</span>&rsquo;/&lsquo;<span class="file">.dll</span>&rsquo; files from libraries

            
            (including C++ and Fortran runtimes).

            
            </p>

            
            <p>Checking compiled code is now done on FreeBSD (as well as the

            
            existing supported platforms of Linux, Mac OS X, Solaris and

            
            Windows).

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD build</code> has more options for

            
            <span class="option">--compact-vignettes</span>: see <code>R CMD build --help</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD build</code> has a new option <span class="option">--md5</span> to

            
            add an &lsquo;<span class="file">MD5</span>&rsquo; file (as done by CRAN): this is used by <code>R

            
            	 CMD INSTALL</code> to check the integrity of the distribution.

            
            </p>

            
            <p>If this option is not specified, any existing (and probably

            
            stale) &lsquo;<span class="file">MD5</span>&rsquo; file is removed.

            
            </p>

            
            </li></ul>


            <h4>DEPRECATED AND DEFUNCT</h4>


            <ul>

            
            <li> <p><code>R CMD Rd2dvi</code> is now defunct: use <code>R CMD Rd2pdf</code>.

            
            </p>

            
            </li>

            
            <li><p> Options such <span class="option">--max-nsize</span>, <span class="option">--max-vsize</span> and

            
            the function <code>mem.limits()</code> are now defunct.  (Options

            
            <span class="option">--min-nsize</span> and <span class="option">--min-vsize</span> remain available.)

            
            </p>

            
            </li>

            
            <li><p> Use of <code>library.dynam()</code> without specifying all the

            
            first three arguments is now disallowed.

            
            </p>

            
            <p>Use of an argument <code>chname</code> in <code>library.dynam()</code>

            
            including the extension &lsquo;<span class="file">.so</span>&rsquo; or &lsquo;<span class="file">.dll</span>&rsquo; (which was never

            
            allowed according to the help page) is defunct.  This also applies

            
            to <code>library.dynam.unload()</code> and to <code>useDynLib</code>

            
            directives in &lsquo;<span class="file">NAMESPACE</span>&rsquo; files.

            
            </p>

            
            </li>

            
            <li><p> The internal functions <code>.readRDS()</code> and

            
            <code>.saveRDS()</code> are now defunct.

            
            </p>

            
            </li>

            
            <li><p> The off-line <code>help()</code> types <span class="samp">"postscript"</span> and

            
            <span class="samp">"ps"</span> are defunct.

            
            </p>

            
            </li>

            
            <li> <p><code>Sys.putenv()</code>, replaced and deprecated in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.5.0, is

            
            finally removed.

            
            </p>

            
            </li>

            
            <li><p> Some functions/objects which have been defunct for five or

            
            more years have been removed completely.  These include

            
            <code>.Alias()</code>, <code>La.chol()</code>, <code>La.chol2inv()</code>,

            
            <code>La.eigen()</code>, <code>Machine()</code>, <code>Platform()</code>,

            
            <code>Version</code>, <code>codes()</code>, <code>delay()</code>,

            
            <code>format.char()</code>, <code>getenv()</code>, <code>httpclient()</code>,

            
            <code>loadURL()</code>, <code>machine()</code>, <code>parse.dcf()</code>,

            
            <code>printNoClass()</code>, <code>provide()</code>, <code>read.table.url()</code>,

            
            <code>restart()</code>, <code>scan.url()</code>, <code>symbol.C()</code>,

            
            <code>symbol.For()</code> and <code>unix()</code>.

            
            </p>

            
            </li>

            
            <li><p> The <code>ENCODING</code> argument to <code>.C()</code> is deprecated.

            
            It was intended to smooth the transition to multi-byte character

            
            strings, but can be replaced by the use of <code>iconv()</code> in the

            
            rare cases where it is still needed.

            
            </p>

            
            </li></ul>


            <h4>INSTALLATION</h4>


            <ul>

            
            <li><p> Building with a positive value of

            
            <span class="option">--with-valgrind-instrumentation</span> now also instruments logical,

            
            complex and raw vectors.

            
            </p>

            
            </li></ul>


            <h4>C-LEVEL FACILITIES</h4>


            <ul>

            
            <li><p> Passing <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> objects other than atomic vectors, functions,

            
            lists and environments to <code>.C()</code> is now deprecated and will

            
            give a warning.  Most cases (especially <code>NULL</code>) are actually

            
            coding errors.  <code>NULL</code> will be disallowed in future.

            
            </p>

            
            <p><code>.C()</code> now passes a pairlist as a <code>SEXP</code> to the compiled

            
            code.  This is as was documented, but pairlists were in reality

            
            handled differently as a legacy from the early days of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>.

            
            </p>

            
            </li>

            
            <li> <p><code>call_R</code> and <code>call_S</code> are deprecated.  They still

            
            exist in the headers and as entry points, but are no longer

            
            documented and should not be used for new code.

            
            </p>

            
            </li></ul>


            <h4>BUG FIXES</h4>


            <ul>

            
            <li> <p><code>str(x, width)</code> now obeys its <code>width</code>

            
            argument also for function headers and other objects <code>x</code>

            
            where <code>deparse()</code> is applied.

            
            </p>

            
            </li>

            
            <li><p> The convention for <code>x %/% 0L</code> for integer-mode <code>x</code>

            
            has been changed from <code>0L</code> to <code>NA_integer_</code>.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14754">PR#14754</a>)

            
            </p>

            
            </li>

            
            <li><p> The <code>exportMethods</code> directive in a &lsquo;<span class="file">NAMESPACE</span>&rsquo;

            
            file now exports S4 generics as necessary, as the extensions

            
            manual said it does.  The manual has also been updated to be a

            
            little more informative on this point.

            
            </p>

            
            <p>It is now required that there is an S4 generic (imported or

            
            created in the package) when methods are to be exported.

            
            </p>

            
            </li>

            
            <li><p> Reference methods cannot safely use non-exported entries

            
            in the namespace.  We now do not do so, and warn in the documentation.

            
            </p>

            
            </li>

            
            <li><p> The namespace import code was warning when identical

            
            S4 generic functions were imported more than once, but should

            
            not (reported by Brian Ripley, then Martin Morgan).

            
            </p>

            
            </li>

            
            <li> <p><code>merge()</code> is no longer allowed (in some ways) to create

            
            a data frame with duplicate column names (which confused

            
            <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14786">PR#14786</a>).

            
            </p>

            
            </li>

            
            <li><p> Fixes for rendering raster images on X11 and Windows devices

            
            when the x-axis or y-axis scale is reversed.

            
            </p>

            
            </li>

            
            <li> <p><code>getAnywhere()</code> found S3 methods as seen from the

            
            <span class="pkg">utils</span> namespace and not from the environment from which it

            
            was called.

            
            </p>

            
            </li>

            
            <li> <p><code>selectMethod(f, sig)</code> would not return inherited group

            
            methods when caching was off (as it is by default).

            
            </p>

            
            </li>

            
            <li> <p><code>dev.copy2pdf(out.type = "cairo")</code> gave an error.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14827">PR#14827</a>)

            
            </p>

            
            </li>

            
            <li><p> Virtual classes (e.g., class unions) had a <code>NULL</code>

            
            prototype even if that was not a legal subclass.  See

            
            <code>?setClassUnion</code>.

            
            </p>

            
            </li>

            
            <li><p> The C prototypes for <code>zdotc</code> and <code>zdotu</code> in

            
            &lsquo;<span class="file">R_ext/BLAS.h</span>&rsquo; have been changed to the more modern style

            
            rather than that used by <code>f2c</code>.  (Patch by Berwin Turlach.)

            
            </p>

            
            </li>

            
            <li> <p><code>isGeneric()</code> produced an error for primitives that

            
            can not have methods.

            
            </p>

            
            </li>

            
            <li> <p><code>.C()</code> or <code>.Fortran()</code> had a lack-of-protection

            
            error if the registration information resulted in an argument

            
            being coerced to another type.

            
            </p>

            
            </li>

            
            <li> <p><code>boxplot(x=x, at=at)</code> with non finite elements in <code>x</code>

            
            and non integer <code>at</code> could not generate a warning but failed.

            
            </p>

            
            </li>

            
            <li> <p><code>heatmap(x, symm=TRUE, RowSideColors=*)</code> no longer

            
            draws the colors in reversed order.

            
            </p>

            
            </li>

            
            <li> <p><code>predict(&lt;ar&gt;)</code> was incorrect in the multivariate case,

            
            for p &gt;= 2.

            
            </p>

            
            </li>

            
            <li> <p><code>print(x, max=m)</code> is now consistent when <code>x</code> is a

            
            <code>"Date"</code>; also the &ldquo;reached ... max.print ..&rdquo; messages

            
            are now consistently using single brackets.

            
            </p>

            
            </li>

            
            <li><p> Closed the <span class="samp">&lt;li&gt;</span> tag in pages generated by <code>

            
                  Rd2HTML()</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14841">PR#14841</a>)

            
            </p>

            
            </li>

            
            <li><p> Axis tick marks could go out of range when a log scale was

            
            used.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14833">PR#14833</a>)

            
            </p>

            
            </li>

            
            <li><p> Signature objects in methods were not allocated as S4

            
            objects (caused a problem with <code>trace()</code> reported by Martin Morgan).

            
            </p>

            
            </li></ul>


            <h3><img class="toplogo" src="../help/figures/../../html/Rlogo.svg" alt="[R logo]" /> CHANGES IN R VERSION 2.14.2</h3>


            <h4>NEW FEATURES</h4>


            <ul>

            
            <li><p> The internal <code>untar()</code> (as used by default by

            
            <code>R CMD INSTALL</code>) now knows about some <code>pax</code>

            
            headers which <code>bsdtar</code> (e.g., the default <code>tar</code> for

            
            Mac OS &gt;= 10.6) can incorrectly include in <code>tar</code> files,

            
            and will skip them with a warning.

            
            </p>

            
            </li>

            
            <li><p> PCRE has been upgraded to version 8.21: as well as bug fixes

            
            and greater Perl compatibility, this adds a JIT pattern compiler,

            
            about which PCRE's news says

            
            &lsquo;large performance benefits can be had in many situations&rsquo;.

            
            This is supported on most but not all <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> platforms.

            
            </p>

            
            </li>

            
            <li><p> Function <code>compactPDF()</code> in package <span class="pkg">tools</span> now

            
            takes the default for argument <code>gs_quality</code> from environment

            
            variable <span class="env">GS_QUALITY</span>: there is a new value <code>"none"</code>, the

            
            ultimate default, which prevents GhostScript being used in

            
            preference to <code>qpdf</code> just because environment variable

            
            <span class="env">R_GSCMD</span> is set.  If <span class="env">R_GSCMD</span> is unset or set to

            
            <code>""</code>, the function will try to find a suitable GhostScript

            
            executable.

            
            </p>

            
            </li>

            
            <li><p> The included version of zlib has been updated to 1.2.6.

            
            </p>

            
            </li>

            
            <li><p> For consistency with the <code>logLik()</code> method,

            
            <code>nobs()</code> for <code>"nls"</code> files now excludes observations

            
            with zero weight.  (Reported by Berwin Turlach.)

            
            </p>

            
            </li></ul>


            <h4>UTILITIES</h4>


            <ul>

            
            <li> <p><code>R CMD check</code> now reports by default on licenses not

            
            according to the description in &lsquo;Writing R Extensions&rsquo;.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD check</code> has a new option <span class="option">--as-cran</span> to

            
            turn on most of the customizations that CRAN uses for its incoming

            
            checks.

            
            </p>

            
            </li></ul>


            <h4>PACKAGE INSTALLATION</h4>


            <ul>

            
            <li> <p><code>R CMD INSTALL</code> will now no longer install certain

            
            file types from &lsquo;<span class="file">inst/doc</span>&rsquo;: these are almost certainly

            
            mistakes and for some packages are wasting a lot of space.  These

            
            are &lsquo;<span class="file">Makefile</span>&rsquo;, files generated by running LaTeX, and unless

            
            the package uses a &lsquo;<span class="file">vignettes</span>&rsquo; directory, PostScript and

            
            image bitmap files.

            
            </p>

            
            <p>Note that only PDF vignettes have ever been supported: some of

            
            these files come from DVI/PS output from the Sweave defaults prior

            
            to <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.13.0.

            
            </p>

            
            </li></ul>


            <h4>BUG FIXES</h4>


            <ul>

            
            <li><p> R configured with <span class="option">--disable-openmp</span> would mistakenly

            
            set <code>HAVE_OPENMP</code> (internal) and <code>SUPPORT_OPENMP</code> (in

            
            &lsquo;<span class="file">Rconfig.h</span>&rsquo;) even though no OpenMP flags were populated.

            
            </p>

            
            </li>

            
            <li><p> The <code>getS3method()</code> implementation had an old

            
            computation to find an S4 default method.

            
            </p>

            
            </li>

            
            <li> <p><code>readLines()</code> could overflow a buffer if the last line

            
            of the file was not terminated.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14766">PR#14766</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD check</code> could miss undocumented S4 objects in

            
            packages which used S4 classes but did not <span class="samp">Depends: methods</span>

            
            in their &lsquo;<span class="file">DESCRIPTION</span>&rsquo; file.

            
            </p>

            
            </li>

            
            <li><p> The HTML Help Search page had malformed links.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14769">PR#14769</a>)

            
            </p>

            
            </li>

            
            <li><p> A couple of instances of lack of protection of <code>SEXP</code>s

            
            have been squashed. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14772">PR#14772</a>, <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14773">PR#14773</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>image(x, useRaster=TRUE)</code> misbehaved on single-column

            
            <code>x</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14774">PR#14774</a>)

            
            </p>

            
            </li>

            
            <li><p> Negative values for <code>options("max.print")</code> or the <code>max</code>

            
            argument to <code>print.default()</code> caused crashes.  Now the former

            
            are ignored and the latter trigger an error.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14779">PR#14779</a>)

            
            </p>

            
            </li>

            
            <li><p> The text of a function body containing more than 4096

            
            bytes was not properly saved by the parser when entered

            
            at the console.

            
            </p>

            
            </li>

            
            <li><p> Forgetting the <code>#endif</code> tag in an Rd file could cause

            
            the parser to go into a loop.  (Reported by Hans-Jorg Bibiko.)

            
            </p>

            
            </li>

            
            <li> <p><code>str(*, ....., strict.width="cut")</code> now also obeys

            
            <code>list.len = n</code>.  (Reported by Sören Vogel.)

            
            </p>

            
            </li>

            
            <li><p> Printing of arrays did not have enough protection (C level),

            
            e.g., in the context of <code>capture.output()</code>.  (Reported by

            
            Hervé Pagès and Martin Morgan.)

            
            </p>

            
            </li>

            
            <li> <p><code>pdf(file = NULL)</code> would produce a spurious file named

            
            &lsquo;<span class="file">NA</span>&rsquo;.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14808">PR#14808</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>list2env()</code> did not check the type of its <code>envir</code>

            
            argument. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14807">PR#14807</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>svg()</code> could segfault if called with a non-existent

            
            file path.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14790">PR#14790</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>make install</code> can install to a path containing

            
            <span class="samp">+</span> characters. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14798">PR#14798</a>)

            
            </p>

            
            </li>

            
            <li><p> The <code>edit()</code> function did not respect the

            
            <code>options("keep.source")</code> setting. (Reported by Cleridy

            
            Lennert.)

            
            </p>

            
            </li>

            
            <li> <p><code>predict.lm(*, type="terms", terms=*, se.fit=TRUE)</code> did

            
            not work.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14817">PR#14817</a>)

            
            </p>

            
            </li>

            
            <li><p> There is a partial workaround for errors in the TRE

            
            regular-expressions engine with named classes and repeat counts of

            
            at least 2 in a MBCS locale (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14408">PR#14408</a>): these are avoided when

            
            TRE is in 8-bit mode (e.g., for <code>useBytes = TRUE</code> and when all

            
            the data are ASCII).

            
            </p>

            
            </li>

            
            <li><p> The C function <code>R_ReplDLLdo1()</code> did not call top-level

            
            handlers.

            
            </p>

            
            </li>

            
            <li><p> The Quartz device was unable to detect window sessions on

            
            Mac OS X 10.7 (Lion) and higher and thus it was not used as the

            
            default device on the console.  Since Lion any application can use

            
            window sessions, so Quartz will now be the default device if the

            
            user's window session is active and <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> is not run via

            
            <code>ssh</code> which is at least close to the behavior in prior OS

            
            X versions.

            
            </p>

            
            </li>

            
            <li> <p><code>mclapply()</code> would fail in code assembling the translated

            
            error message if some (but not all) cores encountered an error.

            
            </p>

            
            </li>

            
            <li> <p><code>format.POSIXlt(x)</code> raised an arithmetic exception when

            
            <code>x</code> was an invalid object of class <code>"POSIXlt"</code> and parts

            
            were empty.

            
            </p>

            
            </li>

            
            <li> <p><code>installed.packages()</code> has some more protection against

            
            package installs going on in parallel.

            
            </p>

            
            </li>

            
            <li> <p><code>.Primitive()</code> could be mis-used to call

            
            <code>.Internal()</code> entry points.

            
            </p>

            
            </li></ul>


            <h3><img class="toplogo" src="../help/figures/../../html/Rlogo.svg" alt="[R logo]" /> CHANGES IN R VERSION 2.14.1</h3>


            <h4>NEW FEATURES</h4>


            <ul>

            
            <li> <p><code>parallel::detectCores()</code> is now able to find the

            
            number of physical cores (rather than CPUs) on Sparc Solaris.

            
            </p>

            
            <p>It can also do so on most versions of Windows; however the default

            
            remains <code>detectCores(logical = TRUE)</code> on that platform.

            
            </p>

            
            </li>

            
            <li><p> Reference classes now keep a record of which fields are

            
            locked.  <code>$lock()</code> with no arguments returns the names

            
            of the locked fields.

            
            </p>

            
            </li>

            
            <li> <p><code>HoltWinters()</code> reports a warning rather than an error

            
            for some optimization failures (where the answer might be a

            
            reasonable one).

            
            </p>

            
            </li>

            
            <li> <p><code>tools::dependsOnPkg()</code> now accepts the shorthand

            
            <code>dependencies = "all"</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>parallel::clusterExport()</code> now allows specification of

            
            an environment from which to export.

            
            </p>

            
            </li>

            
            <li><p> The <code>quartz()</code> device now does tilde expansion on its

            
            <code>file</code> argument.

            
            </p>

            
            </li>

            
            <li> <p><code>tempfile()</code> on a Unix-alike now takes the process ID

            
            into account.  This is needed with <a href="https://CRAN.R-project.org/package=multicore"><span class="pkg">multicore</span></a> (and as part of

            
            <span class="pkg">parallel</span>) because the parent and all the children share a

            
            session temporary directory, and they can share the C random

            
            number stream used to produce the unique part.  Further, two

            
            children can call <code>tempfile()</code> simultaneously.

            
            </p>

            
            </li>

            
            <li><p> Option <code>print</code> in Sweave's <code>RweaveLatex()</code> driver

            
            now emulates auto-printing rather than printing (which can differ

            
            for an S4 object by calling <code>show()</code> rather than

            
            <code>print()</code>).

            
            </p>

            
            </li>

            
            <li> <p><code>filled.contour()</code> now accepts infinite values:

            
            previously it might have generated invalid graphics files

            
            (e.g., containing NaN values).

            
            </p>

            
            </li></ul>


            <h4>INSTALLATION</h4>


            <ul>

            
            <li><p> On 64-bit Linux systems, <code>configure</code> now only sets

            
            <span class="samp">LIBnn</span> to <code>lib64</code> if &lsquo;<span class="file">/usr/lib64</span>&rsquo; exists.  This

            
            may obviate setting <span class="samp">LIBnn</span> explicitly on Debian-derived

            
            systems.

            
            </p>

            
            <p>It is still necessary to set <span class="samp">LIBnn = lib</span> (or

            
            <span class="samp">lib32</span>) for 32-bit builds of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> on a 64-bit OS on those Linux

            
            distributions capable for supporting that concept.

            
            </p>

            
            </li>

            
            <li> <p><code>configure</code> looks for &lsquo;<span class="file">inconsolata.sty</span>&rsquo;, and if

            
            not found adjusts the default <span class="env">R_RD4PDF</span> to not use it (with a

            
            warning, since it is needed for high-quality rendering of manuals).

            
            </p>

            
            </li></ul>


            <h4>PACKAGE INSTALLATION</h4>


            <ul>

            
            <li> <p><code>R CMD INSTALL</code> will now do a test load for all

            
            sub-architectures for which code was compiled (rather than just

            
            the primary sub-architecture).

            
            </p>

            
            </li></ul>


            <h4>UTILITIES</h4>


            <ul>

            
            <li><p> When checking examples under more than one sub-architecture,

            
            <code>R CMD check</code> now uses a separate directory

            
            &lsquo;<span class="file">examples_arch</span>&rsquo; for each sub-architecture, and leaves the

            
            output in file &lsquo;<span class="file">pkgname-Ex_arch.Rout</span>&rsquo;.  Some packages

            
            expect their examples to be run in a clean directory ....

            
            </p>

            
            </li></ul>


            <h4>BUG FIXES</h4>


            <ul>

            
            <li> <p><code>stack()</code> now gives an error if no vector column is

            
            selected, rather than returning a 1-column data frame (contrary to

            
            its documentation).

            
            </p>

            
            </li>

            
            <li> <p><code>summary.mlm()</code> did not handle objects where the

            
            formula had been specified by an expression.  (Reported by

            
            Helios de Rosario Martinez).

            
            </p>

            
            </li>

            
            <li> <p><code>tools::deparseLatex(dropBraces=TRUE)</code> could drop

            
            text as well as braces.

            
            </p>

            
            </li>

            
            <li> <p><code>colormodel = "grey"</code> (new in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.14.0))

            
            did not always work in <code>postscript()</code> and <code>pdf()</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>file.append()</code> could return <code>TRUE</code> for failures.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14727">PR#14727</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>gzcon()</code> connections are no longer subject to garbage

            
            collection: it was possible for this to happen when unintended

            
            (e.g., when calling <code>load()</code>).

            
            </p>

            
            </li>

            
            <li> <p><code>nobs()</code> does not count zero-weight observations for

            
            <code>glm()</code> fits, for consistency with <code>lm()</code>.  This affects

            
            the <code>BIC()</code> values reported for such <code>glm()</code> fits.

            
            (Spotted by Bill Dunlap.)

            
            </p>

            
            </li>

            
            <li> <p><code>options(warn = 0)</code> failed to end a (C-level) context

            
            with more than 50 accumulated warnings.  (Spotted by Jeffrey

            
            Horner.)

            
            </p>

            
            </li>

            
            <li><p> The internal <code>plot.default()</code> code did not do sanity

            
            checks on a <code>cex</code> argument, so invalid input could cause

            
            problems.  (Reported by Ben Bolker.)

            
            </p>

            
            </li>

            
            <li> <p><code>anyDuplicated(&lt;array&gt;, MARGIN=0)</code> no longer fails.

            
            (Reported by Hervé Pagès.)

            
            </p>

            
            </li>

            
            <li> <p><code>read.dcf()</code> removes trailing blanks: unfortunately

            
            on some platforms this included <code>\xa0</code> (non-breaking space)

            
            which is the trailing byte of a UTF-8 character.  It now only

            
            considers ASCII space and tab to be &lsquo;blank&rsquo;.

            
            </p>

            
            </li>

            
            <li><p> There was a sign error in part of the calculations for the

            
            variance returned by <code>KalmanSmooth()</code>.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14738">PR#14738</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>pbinom(10, 1e6, 0.01, log.p = TRUE)</code> was <code>NaN</code>

            
            thanks to the buggy fix to <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14320">PR#14320</a> in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.11.0.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14739">PR#14739</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>RweaveLatex()</code> now emulates auto-printing rather than

            
            printing, by calling <code>methods::show()</code> when auto-printing

            
            would.

            
            </p>

            
            </li>

            
            <li> <p><code>duplicated()</code> ignored <code>fromLast</code> for a

            
            one-column data frame.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14742">PR#14742</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>source()</code> and related functions did not put the correct

            
            timestamp on the source references; <code>srcfilecopy()</code> has gained

            
            a new argument <code>timestamp</code> to support this fix. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14750">PR#14750</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>srcfilecopy()</code> has gained a new argument <code>isFile</code>

            
            and now records the working directory, to allow debuggers to find

            
            the original source file.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14826">PR#14826</a>)

            
            </p>

            
            </li>

            
            <li><p> LaTeX conversion of Rd files did not correctly handle

            
            preformatted backslashes.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14751">PR#14751</a>)

            
            </p>

            
            </li>

            
            <li><p> HTML conversion of Rd files did not handle markup within

            
            tabular cells properly.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14708">PR#14708</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>source()</code> on an empty file with <code>keep.source =

            
            	TRUE</code> tried to read from <code>stdin()</code>, in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.14.0 only.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14753">PR#14753</a>)

            
            </p>

            
            </li>

            
            <li><p> The code to check Rd files in packages would abort if

            
            duplicate description sections were present.

            
            </p>

            
            </li></ul>


            <h3><img class="toplogo" src="../help/figures/../../html/Rlogo.svg" alt="[R logo]" /> CHANGES IN R VERSION 2.14.0</h3>


            <h4>SIGNIFICANT USER-VISIBLE CHANGES</h4>


            <ul>

            
            <li><p> All packages must have a namespace, and one is created on

            
            installation if not supplied in the sources.  This means that any

            
            package without a namespace must be re-installed under this

            
            version of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> (but previously-installed data-only packages without

            
            <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> code can still be used).

            
            </p>

            
            </li>

            
            <li><p> The <code>yLineBias</code> of the <code>X11()</code> and

            
            <code>windows()</code> families of devices has been changed from 0.1 to

            
            0.2: this changes slightly the vertical positioning of text in the

            
            margins (including axis annotations).  This is mainly for

            
            consistency with other devices such as <code>quartz()</code> and

            
            <code>pdf()</code>.  (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14538">PR#14538</a>.)

            
            </p>

            
            <p>There is a new graphics parameter <code>"ylbias"</code> which

            
            allows the y-line bias of the graphics device to be tweaked,

            
            including to reproduce output from earlier versions of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>.

            
            </p>

            
            </li>

            
            <li><p> Labeling of the p-values in various anova tables has been

            
            rationalized to be either <code>"Pr(&gt;F)"</code> or <code>"Pr(&gt;Chi)"</code>

            
            (i.e., the <code>"Pr(F)"</code>, <code>"Pr(Chi)"</code> and <code>"P(&gt;|Chi|)"</code>

            
            variants have been eliminated).  Code which extracts the p value

            
            <em>via</em> indexing by name may need adjustment.

            
            </p>

            
            </li>

            
            <li> <p><code>::</code> can now be used for datasets made available for

            
            lazy-loading in packages with namespaces (which makes it consistent

            
            with its use for data-only packages without namespaces in earlier

            
            versions of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>).

            
            </p>

            
            </li>

            
            <li><p> There is a new package <span class="pkg">parallel</span>.

            
            </p>

            
            <p>It incorporates (slightly revised) copies of packages

            
            <a href="https://CRAN.R-project.org/package=multicore"><span class="pkg">multicore</span></a> and <a href="https://CRAN.R-project.org/package=snow"><span class="pkg">snow</span></a> (excluding MPI, PVM and NWS

            
            clusters).  Code written to use the higher-level API functions in

            
            those packages should work unchanged (apart from changing any

            
            references to their namespaces to a reference to <span class="pkg">parallel</span>,

            
            and links explicitly to <a href="https://CRAN.R-project.org/package=multicore"><span class="pkg">multicore</span></a> or <a href="https://CRAN.R-project.org/package=snow"><span class="pkg">snow</span></a> on help

            
            pages).

            
            </p>

            
            <p>It also contains support for multiple RNG streams following

            
            L'Ecuyer <em>et al</em> (2002), with support for both

            
            <code>mclapply</code> and <a href="https://CRAN.R-project.org/package=snow"><span class="pkg">snow</span></a> clusters.  This replaces functions

            
            like <code>clusterSetupRNG()</code> from <a href="https://CRAN.R-project.org/package=snow"><span class="pkg">snow</span></a> (which are not in

            
            <span class="pkg">parallel</span>).

            
            </p>

            
            <p>The version released for <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.14.0 contains base functionality:

            
            higher-level convenience functions are planned (and some are

            
            already available in the &lsquo;R-devel&rsquo; version of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>).

            
            </p>

            
            </li>

            
            <li><p> Building PDF manuals (for <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> itself or packages,

            
            e.g. <em>via</em> <code>R CMD check</code>) by default requires the

            
            LaTeX package <span class="samp">inconsolata</span>: see the section on

            
            &lsquo;Making the manuals&rsquo; in the &lsquo;R Installation and

            
            Administration Manual&rsquo;.

            
            </p>

            
            </li>

            
            <li> <p><code>axTicks(*, log=TRUE)</code> has changed in some cases to

            
            satisfy the documented behavior and be consistent.

            
            </p>

            
            </li></ul>


            <h4>NEW FEATURES</h4>


            <ul>

            
            <li> <p><code>txtProgressBar()</code> can write to an open connection

            
            instead of the console.

            
            </p>

            
            </li>

            
            <li><p> Non-portable package names ending in &lsquo;<span class="file">.</span>&rsquo; are no longer

            
            allowed.  Nor are single-character package names (<span class="pkg">R</span> was

            
            already disallowed).

            
            </p>

            
            </li>

            
            <li> <p><code>regexpr()</code> and <code>gregexpr()</code> with <code>perl =

            
            	TRUE</code> allows Python-style named captures.  (Wish and

            
            contribution of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14518">PR#14518</a>.)

            
            </p>

            
            </li>

            
            <li><p> The placement of &lsquo;plotmath&rsquo; text in the margins of

            
            plots done by base graphics now makes the same vertical adjustment

            
            as ordinary text, so using ordinary and plotmath text on the same

            
            margin line will seem better aligned (but not exactly aligned,

            
            since ordinary text has descenders below the baseline and plotmath

            
            places them on the baseline).  (Related to <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14537">PR#14537</a>.)

            
            </p>

            
            </li>

            
            <li> <p><code>sunflowerplot()</code> now has a formula interface.

            
            (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14541">PR#14541</a>.)

            
            </p>

            
            </li>

            
            <li> <p><code>iconv()</code> has a new argument <code>toRaw</code> to handle

            
            encodings such as <code>UTF-16</code> with embedded nuls (as was

            
            possible before the <code>CHARSXP</code> cache was introduced).

            
            </p>

            
            <p>It will also accept as input the type of list generated with

            
            <code>toRaw = TRUE</code>.

            
            </p>

            
            </li>

            
            <li><p> Garbage-collecting an unused input text connection no longer

            
            gives a warning (since it &lsquo;connects&rsquo; to nothing outside

            
            <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>).

            
            </p>

            
            </li>

            
            <li> <p><code>read.table()</code> and <code>scan()</code> have gained a

            
            <code>text</code> argument, to allow reading data from a (possibly

            
            literal) character string.

            
            </p>

            
            </li>

            
            <li> <p><code>optim(*, method = .)</code> now allows <code>method = "Brent"</code>

            
            as an interface to <code>optimize()</code>, for use in cases such as

            
            <code>mle()</code> where <code>optim()</code> is used internally.

            
            </p>

            
            </li>

            
            <li> <p><code>mosaicplot()</code> gains a <code>border</code> argument.

            
            (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14550">PR#14550</a>.)

            
            </p>

            
            </li>

            
            <li> <p><code>smooth.spline()</code> gains a <code>tol</code> argument which

            
            controls how different <code>x</code> values need to be to be treated as

            
            distinct.  The default has been changed to be more reliable for

            
            inputs whose range is small compared to their maximum absolute

            
            value.  (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14452">PR#14452</a>.)

            
            </p>

            
            </li>

            
            <li> <p><code>gl()</code> runs faster by avoiding calling <code>factor()</code>.

            
            </p>

            
            </li>

            
            <li><p> The <code>print()</code> method for <code>object.size()</code> accepts

            
            <span class="samp">B</span> as well as <span class="samp">b</span> as an abbreviation for &lsquo;bytes&rsquo;.

            
            </p>

            
            </li>

            
            <li> <p><code>unlink()</code> gains a <code>force</code> argument to work like

            
            <code>rm -f</code> and if possible override restrictive permissions.

            
            </p>

            
            </li>

            
            <li> <p><code>pbirthday()</code> and <code>qbirthday()</code> now use exact

            
            calculations for <code>coincident = 2</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>unzip()</code> and <code>unz()</code> connections have been

            
            updated with support for more recent Zip64 features (including

            
            large file sizes and <code>bzip2</code> compression, but not UTF-8

            
            file names).

            
            </p>

            
            <p><code>unzip()</code> has a new option to restore file times from those

            
            recorded (in an unknown timezone) in the zip file.

            
            </p>

            
            </li>

            
            <li> <p><code>update.packages()</code> now accepts a character vector of

            
            package names for the <code>oldPkgs</code> argument.  (Suggestion of

            
            Tal Galili.)

            
            </p>

            
            </li>

            
            <li><p> The special reference class fields <code>.self</code> and

            
            <code>.refClassDef</code> are now read-only to prevent corrupting

            
            the object.

            
            </p>

            
            </li>

            
            <li> <p><code>decompose()</code> now returns the original series as part

            
            of its value, so it can be used (rather than reconstructed) when

            
            plotting.  (Suggestion of Rob Hyndman.)

            
            </p>

            
            </li>

            
            <li><p> Rao's efficient score test has been implemented for

            
            <code>glm</code> objects.  Specifically, the <code>add1</code>, <code>drop1</code>,

            
            and <code>anova</code> methods now allow <code>test = "Rao"</code>.

            
            </p>

            
            </li>

            
            <li><p> If a saved workspace (e.g., &lsquo;<span class="file">.RData</span>&rsquo;) contains objects

            
            that cannot be loaded, <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> will now start with an warning message

            
            and an empty workspace, rather than failing to start.

            
            </p>

            
            </li>

            
            <li> <p><code>strptime()</code> now accepts times such as <span class="samp">24:00</span> for

            
            midnight at the end of the day, for although these are disallowed by

            
            POSIX 1003.1-2008, ISO 8601:2004 allows them.

            
            </p>

            
            </li>

            
            <li><p> Assignment of <code>names()</code> to S4 objects now checks for

            
            a corresponding <code>"names"</code> slot, and generates a warning or

            
            an error if that slot is not defined.  See the section on slots

            
            in <code>?Classes</code>.

            
            </p>

            
            </li>

            
            <li><p> The default methods for <code>is.finite()</code>, <code>is.infinite()</code>

            
            and <code>is.nan()</code> now signal an error if their argument is not

            
            an atomic vector.

            
            </p>

            
            </li>

            
            <li><p> The formula method for <code>plot()</code> no longer places

            
            package <span class="pkg">stats</span> on the search path (it loads the namespace

            
            instead).

            
            </p>

            
            </li>

            
            <li><p> There now is a genuine <code>"function"</code> method for

            
            <code>plot()</code> rather than the generic dispatching internally to

            
            <code>graphics::plot.function()</code>.  It is now exported, so can be

            
            called directly as <code>plot.function()</code>.

            
            </p>

            
            </li>

            
            <li><p> The one-sided <code>ks.test()</code> allows <code>exact = TRUE</code> to

            
            be specified in the presence of ties (but the approximate

            
            calculation remains the default: the &lsquo;exact&rsquo; computation

            
            makes assumptions known to be invalid in the presence of ties).

            
            </p>

            
            </li>

            
            <li><p> The behaviour of <code>curve(add = FALSE)</code> has changed: it

            
            now no longer takes the default x limits from the previous plot

            
            (if any): rather they default to <code>c(0, 1)</code> just as the

            
            <code>"function"</code> method for <code>plot()</code>.  To get the previous

            
            behaviour use <code>curve(add = NA)</code>, which also takes the default for

            
            log-scaling of the x-axis from the previous plot.

            
            </p>

            
            </li>

            
            <li><p> Both <code>curve()</code> and the <code>plot()</code> method for

            
            functions have a new argument <code>xname</code> to facilitate plots

            
            such as <code>sin(t)</code> <em>vs</em> <code>t</code>.

            
            </p>

            
            </li>

            
            <li><p> The <code>local</code> argument to <code>source()</code> can specify an

            
            environment as well as <code>TRUE</code> (<code>parent.env()</code>) and

            
            <code>FALSE</code> (<code>.GlobalEnv</code>).  It gives better error messages

            
            for other values, such as <code>NA</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>vcov()</code> gains methods for classes <code>"summary.lm"</code> and

            
            <code>"summary.glm"</code>.

            
            </p>

            
            </li>

            
            <li><p> The <code>plot()</code> method for class <code>"profile.nls"</code>

            
            gains <code>ylab</code> and <code>lty</code> arguments, and passes

            
            <code>...</code> on to <code>plot.default</code>.

            
            </p>

            
            </li>

            
            <li><p> Character-string arguments such as the <code>mode</code> argument

            
            of <code>vector()</code>, <code>as.vector()</code> and <code>is.vector()</code> and

            
            the <code>description</code> argument of <code>file()</code> are required to

            
            be of length exactly one, rather than any further elements being

            
            silently discarded.  This helps catch incorrect usage in

            
            programming.

            
            </p>

            
            </li>

            
            <li><p> The <code>length</code> argument of <code>vector()</code> and its

            
            wrappers such as <code>numeric()</code> is required to be of length

            
            exactly one (other values are now an error rather than giving a

            
            warning as previously).

            
            </p>

            
            </li>

            
            <li> <p><code>vector(len)</code> and <code>length(x) &lt;- len</code> no longer

            
            accept <code>TRUE</code>/<code>FALSE</code> for <code>len</code> (not that they

            
            were ever documented to, but there was special-casing in the C

            
            code).

            
            </p>

            
            </li>

            
            <li><p> There is a new function <code>Sys.setFileTime()</code> to set the

            
            time of a file (including a directory).  See its help for exactly

            
            which times it sets on various OSes.

            
            </p>

            
            </li>

            
            <li><p> The file times reported by <code>file.info()</code> are reported

            
            to sub-second resolution on systems which support it.  (Currently

            
            the POSIX 2008 and FreeBSD/Darwin/NetBSD methods are detected.)

            
            </p>

            
            </li>

            
            <li><p> New function <code>getCall(m)</code> as an abstraction for

            
            <code>m$call</code>, enabling <code>update()</code>'s default method to apply

            
            more universally.  (NB: this can be masked by existing functions

            
            in packages.)

            
            </p>

            
            </li>

            
            <li> <p><code>Sys.info()</code> gains a <code>euser</code> component to report

            
            the &lsquo;effective&rsquo; user on OSes which have that concept.

            
            </p>

            
            </li>

            
            <li><p> The result returned by <code>try()</code> now contains the

            
            original error condition object as the <code>"condition"</code>

            
            attribute.

            
            </p>

            
            </li>

            
            <li><p> All packages with <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> code are lazy-loaded irrespective of

            
            the <span class="samp">LazyLoad</span> field in the &lsquo;<span class="file">DESCRIPTION</span>&rsquo; file.  A

            
            warning is given if the <span class="samp">LazyLoad</span> field is overridden.

            
            </p>

            
            </li>

            
            <li> <p><code>Rd</code> markup has a new <span class="samp">\figure</span> tag so that

            
            figures can be included in help pages when converted to HTML or

            
            LaTeX.  There are examples on the help pages for <code>par()</code> and

            
            <code>points()</code>.

            
            </p>

            
            </li>

            
            <li><p> The built-in httpd server now allows access to files

            
            in the session temporary directory <code>tempdir()</code>,

            
            addressed as the &lsquo;<span class="file">/session</span>&rsquo; directory on the httpd

            
            server.

            
            </p>

            
            </li>

            
            <li><p> Development versions of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> are no longer referred to by the

            
            number under which they might be released, e.g., in the startup

            
            banner, <code>R --version</code> and <code>sessionUtils()</code>.  The

            
            correct way to refer to a development version of R is

            
            &lsquo;R-devel&rsquo;, preferably with the date and SVN version number.<br />

            
            E.g., <span class="samp">R-devel (2011-07-04 r56266)</span>

            
            </p>

            
            </li>

            
            <li><p> There is a new function <code>texi2pdf()</code> in package

            
            <span class="pkg">tools</span>, currently a convenience wrapper for

            
            <code>texi2dvi(pdf = TRUE)</code>.

            
            </p>

            
            </li>

            
            <li><p> There are two new options for typesetting PDF manuals from

            
            Rd files.  These are <span class="samp">beramono</span> and <span class="samp">inconsolata</span>, and

            
            used the named font for monospaced output. They are intended to

            
            be used in combination with <span class="samp">times</span>, and

            
            <span class="samp">times,inconsolata,hyper</span> is now the default for the

            
            reference manual and package manuals.  If you do not have that

            
            font installed, you can set <span class="env">R_RD4PF</span> to one of the other

            
            options: see the &lsquo;R Installation and Administration Manual&rsquo;.

            
            </p>

            
            </li>

            
            <li><p> Automatic printing for reference classes is now done by

            
            the <code>$show()</code> method.  A method is defined for class

            
            <span class="samp">envRefClass</span> and may be overridden for user classes (see

            
            the <code>?ReferenceClasses</code> example).  S4 <code>show()</code> methods

            
            should no longer be needed for reference classes.

            
            </p>

            
            </li>

            
            <li> <p><code>tools::Rdiff</code> (by default) and <code>R CMD Rdiff</code>

            
            now ignore differences in pointer values when comparing printed

            
            environments, compiled byte code, etc.

            
            </p>

            
            </li>

            
            <li><p> The <code>"source"</code> attribute on functions created with

            
            <code>keep.source=TRUE</code> has been replaced with a <code>"srcref"</code>

            
            attribute.  The <code>"srcref"</code> attribute references an in-memory

            
            copy of the source file using the <code>"srcfilecopy"</code> class or

            
            the new <code>"srcfilealias"</code> class.

            
            </p>

            
            <p><strong>NB:</strong> This means that functions sourced with

            
            <code>keep.source = TRUE</code> and saved (e.g., by <code>save()</code> or

            
            <code>readRDS()</code>) in earlier versions of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> will no longer show

            
            the original sources (including comments).

            
            </p>

            
            </li>

            
            <li><p> New items <span class="samp">User Manuals</span> and

            
            <a href="http://developer.r-project.org/TechDocs">Technical Papers</a>

            
            have been added to the HTML help main page.  These link to

            
            vignettes in the base and recommended packages and to a

            
            collection of papers about R issues, respectively.

            
            </p>

            
            </li>

            
            <li><p> Documentation and messages have been standardized to

            
            use &ldquo;namespace&rdquo; rather than &ldquo;name space&rdquo;.

            
            </p>

            
            </li>

            
            <li> <p><code>setGeneric()</code> now looks in the default packages for

            
            a non-generic version of a function if called from a package with a

            
            namespace.  (It always did for packages without a namespace.)

            
            </p>

            
            </li>

            
            <li><p> Setting the environment variable

            
            <span class="env">_R_WARN_ON_LOCKED_BINDINGS_</span> will give a warning if an

            
            attempt is made to change a locked binding.

            
            </p>

            
            </li>

            
            <li> <p><code>\SweaveInput</code> is now supported when generating

            
            concordances in <code>Sweave()</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>findLineNum()</code> and <code>setBreakpoint()</code> now allow

            
            the environment to be specified indirectly; the latter gains

            
            a <code>clear</code> argument to allow it to call <code>untrace()</code>.

            
            </p>

            
            </li>

            
            <li><p> The body of a closure can be one of further types of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>

            
            objects, including environments and external pointers.

            
            </p>

            
            </li>

            
            <li><p> The <code>Rd2HTML()</code> function in package <span class="pkg">tools</span> now has

            
            a <code>stylesheet</code> argument, allowing pages to be displayed in

            
            alternate formats.

            
            </p>

            
            </li>

            
            <li><p> New function <code>requireNamespace()</code> analogous to

            
            <code>require()</code>, returning a logical value after attempting to

            
            load a namespace.

            
            </p>

            
            </li>

            
            <li><p> There is a new type of RNG, <code>"L'Ecuyer-CMRG"</code>,

            
            implementing L'Ecuyer (1999)'s &lsquo;combined multiple-recursive

            
            generator&rsquo; <span class="samp">MRG32k3a</span>.  See the comments on <code>?RNG</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>help.search()</code> and <code>??</code> can now display

            
            vignettes and demos as well as help pages.  The new option

            
            <code>"help.search.types"</code> controls the types of documentation

            
            and the order of their display.

            
            </p>

            
            <p>This also applies to HTML searches, which now give results in all

            
            of help pages, vignettes and demos.

            
            </p>

            
            </li>

            
            <li> <p><code>socketConnection()</code> now has a <code>timeout</code> argument.

            
            It is now documented that large values (package <a href="https://CRAN.R-project.org/package=snow"><span class="pkg">snow</span></a> used a

            
            year) do not work on some OSes.

            
            </p>

            
            </li>

            
            <li><p> The initialization of the random-number generator now uses

            
            the process ID as well as the current time, just in case two <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>

            
            processes are launched very rapidly on a machine with

            
            low-resolution wall clock (some have a resolution of a second;

            
            modern systems have microsecond-level resolution).

            
            </p>

            
            </li>

            
            <li><p> New function <code>pskill()</code> in the <span class="pkg">tools</span> package to

            
            send a terminate signal to one or more processes, plus constants

            
            such as <code>SIGTERM</code> to provide a portable way to refer to

            
            signals (since the numeric values are OS-dependent).

            
            </p>

            
            </li>

            
            <li><p> New function <code>psnice()</code> in the <span class="pkg">tools</span> package to

            
            return or change the &lsquo;niceness&rsquo; of a process.  (Refers to

            
            the &lsquo;priority class&rsquo; on Windows.)

            
            </p>

            
            </li>

            
            <li> <p><code>list.dirs()</code> gains a <code>recursive</code> argument.

            
            </p>

            
            </li>

            
            <li><p> An <span class="samp">Authors@R</span> field in a package &lsquo;<span class="file">DESCRIPTION</span>&rsquo;

            
            file can now be used to generate <span class="samp">Author</span> and

            
            <span class="samp">Maintainer</span> fields if needed, and to auto-generate package

            
            citations.

            
            </p>

            
            </li>

            
            <li><p> New utility <code>getElement()</code> for accessing either a list

            
            component or a slot in an S4 object.

            
            </p>

            
            </li>

            
            <li> <p><code>stars()</code> gains a <code>col.lines</code> argument, thanks to

            
            Dustin Sallings. (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14657">PR#14657</a>.)

            
            </p>

            
            </li>

            
            <li><p> New function <code>regmatches()</code> for extracting or replacing

            
            matched or non-matched substrings from match data obtained by

            
            <code>regexpr()</code>, <code>gregexpr()</code> and <code>regexec()</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>help(package = "pkg_name", help_type = "HTML")</code> now

            
            gives HTML help on the package rather than text help.  (This gives

            
            direct access to the HTML version of the package manual shown

            
            <em>via</em> <code>help.start()</code>'s &lsquo;Packages&rsquo; menu.)

            
            </p>

            
            </li>

            
            <li> <p><code>agrep()</code> gains a <code>fixed</code> argument to optionally

            
            allow approximate regular expression matching, and a <code>costs</code>

            
            argument to specify possibly different integer match costs for

            
            insertions, deletions and substitutions.

            
            </p>

            
            </li>

            
            <li> <p><code>read.dcf()</code> and <code>write.dcf()</code> gain a

            
            <code>keep.white</code> argument to indicate fields where whitespace

            
            should be kept as is.

            
            </p>

            
            </li>

            
            <li> <p><code>available.packages()</code> now works around servers that

            
            fail to return an error code when &lsquo;<span class="file">PACKAGES.gz</span>&rsquo; does not

            
            exist.  (Patch submitted by Seth Schommer.)

            
            </p>

            
            </li>

            
            <li> <p><code>readBin()</code> can now read more than

            
            <i>2^31 - 1</i> bytes in a single call (the previously

            
            documented limitation).

            
            </p>

            
            </li>

            
            <li><p> New function <code>regexec()</code> for finding the positions of

            
            matches as well as all substrings corresponding to parenthesized

            
            subexpressions of the given regular expression.

            
            </p>

            
            </li>

            
            <li><p> New function <code>adist()</code> in package <span class="pkg">utils</span> for

            
            computing &lsquo;edit&rsquo; (generalized Levenshtein) distances between

            
            strings.

            
            </p>

            
            </li>

            
            <li><p> Class <code>"raster"</code> gains an <code>is.na</code> method to avoid

            
            confusion from the misuse of the matrix method (such as <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14618">PR#14618</a>).

            
            </p>

            
            </li>

            
            <li><p> The <code>identical()</code> function gains an

            
            <code>ignore.bytecode</code> argument to control comparison of

            
            compiled functions.

            
            </p>

            
            </li>

            
            <li> <p><code>pmin</code> and <code>pmax</code> now warn if an argument is

            
            partially recycled (wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14638">PR#14638</a>).

            
            </p>

            
            </li>

            
            <li><p> The default for <code>image(useRaster=)</code> is now taken from

            
            option <code>"preferRaster"</code>: for the small print see <code>?image</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>str()</code> now displays reference class objects and their

            
            fields, rather than treating them as classical S4 classes.

            
            </p>

            
            </li>

            
            <li><p> New function <code>aregexec()</code> in package <span class="pkg">utils</span> for

            
            finding the positions of approximate string matches as well as all

            
            substrings corresponding to parenthesized subexpressions of the

            
            given regular expression.

            
            </p>

            
            </li>

            
            <li> <p><code>download.file()</code> has an <code>extra</code> argument to pass

            
            additional command-line options to the non-default methods using

            
            command-line utilities.

            
            </p>

            
            <p><code>cacheOK = FALSE</code> is now supported for <code>method = "curl"</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>interaction.plot(*, type = .)</code> now also allows type

            
            <code>"o"</code> or <code>"c"</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>axTicks(*, log=TRUE)</code> did sometimes give more values

            
            than the ticks in the corresponding <code>graphics::axis()</code>.  By

            
            default, it now makes use of the new (<span class="pkg">graphics</span>-package

            
            independent) <code>axisTicks()</code> which can make use of a new

            
            utility <code>.axisPars()</code>.  Further, it now returns a decreasing

            
            sequence (as for <code>log=FALSE</code>) when <code>usr</code> is decreasing.

            
            </p>

            
            </li>

            
            <li><p> Using <code>fix()</code> or <code>edit()</code> on a <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> object (except

            
            perhaps a matrix or data frame) writes its temporary file with

            
            extension &lsquo;<span class="file">.R</span>&rsquo; so editors which select their mode based on

            
            the extension will select a suitable mode.

            
            </p>

            
            </li></ul>


            <h4>GRAPHICS DEVICES</h4>


            <ul>

            
            <li><p> The <code>pdf()</code> device makes use of Flate compression: this

            
            is controlled by the new logical argument <code>compress</code>, and is

            
            enabled by default.

            
            </p>

            
            </li>

            
            <li><p> Devices <code>svg()</code>, <code>cairo_pdf()</code> and

            
            <code>cairo_ps()</code> gain a <code>family</code> argument.

            
            </p>

            
            <p>On a Unix-alike <code>X11()</code> gains a <code>family</code> argument.  This

            
            is one of the <code>x11.options()</code> and so can be passed as an

            
            argument to the <code>bmp()</code>, <code>jpeg()</code>, <code>png()</code> and

            
            <code>tiff()</code> devices.

            
            </p>

            
            <p>Analogous changes have been made on Windows, so all built-in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>

            
            graphics devices now have a <code>family</code> argument except

            
            <code>pictex()</code> (which has no means to change fonts).

            
            </p>

            
            </li>

            
            <li><p> The <code>bmp()</code>, <code>jpeg()</code>, <code>png()</code> and <code>tiff()</code>

            
            devices now make use of the <code>antialias</code> argument for

            
            <code>type = "quartz"</code>.

            
            </p>

            
            </li>

            
            <li><p> There are several new built-in font mappings for

            
            <code>X11(type = "Xlib")</code>: see the help on <code>X11Fonts()</code>.

            
            </p>

            
            </li>

            
            <li><p> There is a new type <code>X11(type = "dbcairo")</code> which

            
            updates the screen less frequently: see its help page.

            
            </p>

            
            </li>

            
            <li><p> The <code>X11()</code> device now makes use of cursors to

            
            distinguish its states.  The normal cursor is an arrow (rather

            
            than a crosshair); the crosshair is used when the locator is in

            
            use, and a watch cursor is shown when plotting computations are

            
            being done.  (These are the standard names for X11 cursors: how

            
            they are actually displayed depends on the window manager.)

            
            </p>

            
            </li>

            
            <li><p> New functions <code>dev.hold()</code> and <code>dev.flush()</code> for

            
            use with graphics devices with buffering.  These are used for most

            
            of the high-level graphics functions such as <code>boxplot()</code>, so

            
            that the plot is only displayed when the page is complete.

            
            </p>

            
            <p>Currently implemented for <code>windows(buffered = TRUE)</code>,

            
            <code>quartz()</code> and the cairographics-based <code>X11()</code> types

            
            with buffering (which are the default on-screen devices).

            
            </p>

            
            </li>

            
            <li><p> New function <code>dev.capture()</code> for capture of bitmap

            
            snapshots of image-based devices (a superset of the functionality

            
            provided by <code>grid.cap()</code> in <code>grid</code>).

            
            </p>

            
            </li>

            
            <li><p> The default <code>colormodel</code> for <code>pdf()</code> and

            
            <code>postscript()</code> is now called <code>"srgb"</code> to more accurately

            
            describe it.  (Instead of <code>"rgb"</code>, and in the case of

            
            <code>postscript()</code> it no longer switches to and from the gray

            
            colorspace, by default.)

            
            </p>

            
            <p>The <code>colormodel</code> for <code>postscript()</code> which does use both

            
            gray and sRGB colorspaces is now called <code>"srgb+gray"</code>.

            
            </p>

            
            <p>Plots which are known to use only black/white/transparent can

            
            advantageously use <code>colormodel = "gray"</code> (just as before, but

            
            there is now slightly more advantage in doing so).

            
            </p>

            
            </li>

            
            <li> <p><code>postscript()</code> with values <code>colormodel = "rgb"</code> and

            
            <code>colormodel = "rgb-nogray"</code> give the behaviour prior to <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>

            
            2.13.0 of uncalibrated RGB, which under some circumstances can be

            
            rendered much faster by a viewer.

            
            </p>

            
            <p><code>pdf(colormodel = "rgb")</code> gives the behaviour prior to <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>

            
            2.13.0 of uncalibrated RGB, which under some circumstances can be

            
            rendered faster by a viewer, and the files will be smaller (by

            
            about 9KB if compression is not used).

            
            </p>

            
            </li>

            
            <li><p> The <code>postscript()</code> device only includes the definition

            
            of the sRGB colorspace in the output file for the colormodels

            
            which use it.

            
            </p>

            
            </li>

            
            <li><p> The <code>postscript()</code> and <code>pdf()</code> devices now output

            
            greyscale raster images (and not RGB) when <code>colormodel = "gray"</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>postscript(colormodel = "gray")</code> now accepts non-grey

            
            colours and uses their luminance (as <code>pdf()</code> long has).

            
            </p>

            
            </li>

            
            <li> <p><code>colormodel = "grey"</code> is allowed as an alternative name

            
            for <code>postscript()</code> and <code>pdf()</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>pdf()</code> in the default sRGB colorspace outputs many

            
            fewer changes of colorspace, which may speed up rendering in some

            
            viewing applications.

            
            </p>

            
            </li>

            
            <li><p> There is a new function <code>dev.capabilities()</code> to query

            
            the capabilities of the current device.  The initial set of

            
            capabilities are support for semi-transparent colours, rendering

            
            and capturing raster images, the locator and for interactive

            
            events.

            
            </p>

            
            </li>

            
            <li><p> For <code>pdf()</code>, <code>maxRasters</code> is increased as needed

            
            so the argument is no longer used.

            
            </p>

            
            </li></ul>


            <h4>SWEAVE &amp; VIGNETTES</h4>


            <ul>

            
            <li><p> Options <code>keep.source = TRUE, figs.only = FALSE</code>

            
            are now the default.

            
            </p>

            
            </li>

            
            <li><p> The way the type of user-defined options is determined has

            
            changed.  Previously they were all regarded as logical: now the

            
            type is determined by the value given at first use.

            
            </p>

            
            </li>

            
            <li><p> The allowed values of logical options are now precisely

            
            those allowed for character inputs to <code>as.logical()</code>: this

            
            means that <span class="samp">t</span> and <span class="samp">f</span> are no longer allowed (although

            
            <code>T</code> and <code>F</code> still are).

            
            </p>

            
            </li>

            
            <li><p> The preferred location for vignette sources is now the

            
            directory &lsquo;<span class="file">vignettes</span>&rsquo; and not &lsquo;<span class="file">inst/doc</span>&rsquo;: <code>R CMD

            
                  build</code> will now re-build vignettes in directory &lsquo;<span class="file">vignettes</span>&rsquo;

            
            and copy the &lsquo;<span class="file">.Rnw</span>&rsquo; (etc) files and the corresponding PDFs to

            
            &lsquo;<span class="file">inst/doc</span>&rsquo;.  Further files to be copied to &lsquo;<span class="file">inst/doc</span>&rsquo;

            
            can be specified <em>via</em> the file

            
            &lsquo;<span class="file">vignettes/.install_extras</span>&rsquo;.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD Sweave</code> now supports a <span class="option">--driver</span>

            
            option to select the Sweave driver: the default is equivalent to

            
            <span class="option">--driver=RweaveLatex</span>.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD Sweave</code> and <code>R CMD Stangle</code> support

            
            options <span class="option">--encoding</span> and <span class="option">--options</span>.

            
            </p>

            
            </li>

            
            <li><p> The <code>Rtangle()</code> driver allows <code>output = "stdout"</code>

            
            or <code>output = "stderr"</code> to select the output or message

            
            connection.  This is convenient for scripting using something like

            
            </p>

            
            <pre>    R CMD Stangle --options='output="stdout"' foo.Rnw &gt; foo2.R</pre>

            
            </li>

            
            <li><p> There is a new option <code>pdf.compress</code> controlling

            
            whether PDF figures are generated using Flate compression (they

            
            are by default).

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD Sweave</code> now has a <span class="option">--pdf</span> option to

            
            produce a PDF version of the processed Sweave document.

            
            </p>

            
            </li>

            
            <li><p> It is no longer allowed to have two vignettes with the

            
            same vignette basename (e.g., &lsquo;<span class="file">vig.Rnw</span>&rsquo; and &lsquo;<span class="file">vig.Snw</span>&rsquo;).

            
            (Previously one vignette hid the other in the <code>vignette()</code>

            
            function.)

            
            </p>

            
            </li></ul>


            <h4>C-LEVEL FACILITIES</h4>


            <ul>

            
            <li><p> Function <code>R_tmpnam2</code> has been added to the API to allow

            
            a temporary filename to include a specified extension.

            
            </p>

            
            </li></ul>


            <h4>PACKAGE INSTALLATION</h4>


            <ul>

            
            <li><p> Package &lsquo;<span class="file">DESCRIPTION</span>&rsquo; file field <span class="samp">KeepSource</span>

            
            forces the package to be installed with <code>keep.source =

            
            	TRUE</code> (or <code>FALSE</code>).  (Suggestion of Greg Snow.  Note that

            
            as all packages are lazy-loaded, this is now only relevant at

            
            installation.)

            
            </p>

            
            <p>There are corresponding options <span class="option">--with-keep.source</span> and

            
            <span class="option">--without-keep.source</span> for <code>R CMD INSTALL</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD INSTALL</code> has a new option

            
            <span class="option">--byte-compile</span> to byte-compile the packages during

            
            installation (since all packages are now lazy-loaded).  This can

            
            be controlled on a per-package basis by the optional field

            
            <span class="samp">ByteCompile</span> in the &lsquo;<span class="file">DESCRIPTION</span>&rsquo; file.

            
            </p>

            
            </li>

            
            <li><p> A package <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> code but without a &lsquo;<span class="file">NAMESPACE</span>&rsquo; file will

            
            have a default one created at <code>R CMD build</code> or <code>R

            
                  CMD INSTALL</code> time, so all packages will be installed with

            
            namespaces.  A consequence of this is that <code>.First.lib()</code>

            
            functions need to be copied to <code>.onLoad()</code> (usually) or

            
            <code>.onAttach()</code>.  For the time being, if there is an

            
            auto-generated &lsquo;<span class="file">NAMESPACE</span>&rsquo; file and no <code>.onLoad()</code> nor

            
            <code>.onAttach()</code> function is found but <code>.First.lib()</code> is,

            
            it will be run as the attach hook (unless the package is one of a

            
            list of known exceptions, when it will be run as the load hook).

            
            </p>

            
            </li>

            
            <li><p> A warning is given if test-loading a package changes a

            
            locked binding in a package other than itself.  It is likely that

            
            this will be disallowed in future releases.  (There are <em>pro

            
            tem</em> some exceptions to the warning.)

            
            </p>

            
            </li>

            
            <li><p> A dependency on SVN revision is allowed for <code>R</code>,

            
            e.g. <code>R (&gt;= r56550)</code>.  This should be used in conjunction with a

            
            version number, e.g. <code>R (&gt;= 2.14.0), R (&gt;= r56550)</code> to

            
            distinguish between R-patched and R-devel versions with the same

            
            SVN revision.

            
            </p>

            
            </li>

            
            <li> <p><code>installed.packages()</code> now hashes the names of its

            
            cache files to avoid very rare problems with excessively long path

            
            names.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14669">PR#14669</a>)

            
            </p>

            
            </li>

            
            <li><p> A top-level &lsquo;<span class="file">COPYING</span>&rsquo; file in a package is no longer

            
            installed (file names &lsquo;<span class="file">LICENSE</span>&rsquo; or &lsquo;<span class="file">LICENCE</span>&rsquo; having long

            
            been preferred).

            
            </p>

            
            </li></ul>


            <h4>UTILITIES</h4>


            <ul>

            
            <li> <p><code>R CMD check</code> now gives an error if the <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> code in a

            
            vignette fails to run, unless this is caused by a missing package.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD check</code> now unpacks tarballs in the same way

            
            as <code>R CMD INSTALL</code>, including making use of the

            
            environment variable <span class="env">R_INSTALL_TAR</span> to override the default

            
            behaviour.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD check</code> performs additional code analysis of

            
            package startup functions, and notifies about incorrect argument

            
            lists and (incorrect) calls to functions which modify the search

            
            path or inappropriately generate messages.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD check</code> now also checks compiled code for

            
            symbols corresponding to functions which might terminate <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> or

            
            write to &lsquo;<span class="file">stdout</span>&rsquo;/&lsquo;<span class="file">stderr</span>&rsquo; instead of the console.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD check</code> now uses a <code>pdf()</code> device when

            
            checking examples (rather than <code>postscript()</code>).

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD check</code> now checks line-endings of makefiles

            
            and C/C++/Fortran sources in subdirectories of &lsquo;<span class="file">src</span>&rsquo; as well

            
            as in &lsquo;<span class="file">src</span>&rsquo; itself.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD check</code> now reports as a NOTE what look like

            
            methods documented with their full names even if there is a

            
            namespace and they are exported.  In almost all cases they are

            
            intended to be used only as methods and should use the

            
            <span class="samp">\method</span> markup.  In the other rare cases the recommended

            
            form is to use a function such as <code>coefHclust</code> which would

            
            not get confused with a method, document that and register it in

            
            the &lsquo;<span class="file">NAMESPACE</span>&rsquo; file by <code>s3method(coef, hclust,

            
                  coefHclust)</code>.

            
            </p>

            
            </li>

            
            <li><p> The default for the environment variable

            
            <span class="env">_R_CHECK_COMPACT_DATA2_</span> is now true: thus if using the newer

            
            forms of compression introduced in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.10.0 would be beneficial

            
            is now checked (by default).

            
            </p>

            
            </li>

            
            <li><p> Reference output for a vignette can be supplied when

            
            checking a package by <code>R CMD check</code>: see &lsquo;Writing R

            
            Extensions&rsquo;.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD Rd2dvi</code> allows the use of LaTeX package

            
            <span class="samp">inputenx</span> rather than <span class="samp">inputenc</span>: the value of the

            
            environment variable <span class="env">RD2DVI_INPUTENC</span> is used.  (LaTeX package

            
            <span class="samp">inputenx</span> is an optional install which provides greater

            
            coverage of the UTF-8 encoding.)

            
            </p>

            
            </li>

            
            <li> <p><code>Rscript</code> on a Unix-alike now accepts file names

            
            containing spaces (provided these are escaped or quoted in the

            
            shell).

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD build</code> on a Unix-alike (only) now tries to

            
            preserve dates on files it copies from its input directory.  (This

            
            was the undocumented behaviour prior to <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.13.0.)

            
            </p>

            
            </li></ul>


            <h4>DEPRECATED AND DEFUNCT</h4>


            <ul>

            
            <li> <p><code>require()</code> no longer has a <code>save</code> argument.

            
            </p>

            
            </li>

            
            <li><p> The <code>gamma</code> argument to <code>hsv()</code>,

            
            <code>rainbow()</code>, and <code>rgb2hsv()</code> has been removed.

            
            </p>

            
            </li>

            
            <li><p> The <span class="option">--no-docs</span> option for

            
            <code>R CMD build --binary</code> is defunct: use

            
            <span class="option">--install-args</span> instead.

            
            </p>

            
            </li>

            
            <li><p> The option <span class="option">--unsafe</span> to <code>R CMD INSTALL</code> is

            
            defunct: use the identical option <span class="option">--no-lock</span> instead.

            
            </p>

            
            </li>

            
            <li><p> The entry point <code>pythag</code> formerly in &lsquo;<span class="file">Rmath.h</span>&rsquo; is

            
            defunct: use instead the C99 function <code>hypot</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD build --binary</code> is formally defunct:

            
            <code>R CMD INSTALL --build</code> has long been the preferred

            
            alternative.

            
            </p>

            
            </li>

            
            <li> <p><code>zip.file.extract()</code> is now defunct: use

            
            <code>unzip()</code> or <code>unz()</code> instead.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD Rd2dvi</code> without the <span class="option">--pdf</span> option is

            
            now deprecated: only PDF output will be supported in future

            
            releases (since this allows the use of fonts only supported for

            
            PDF), and only <code>R CMD Rd2pdf</code> will be available.

            
            </p>

            
            </li>

            
            <li><p> Options such as <span class="option">--max-nsize</span> and the function

            
            <code>mem.limits()</code> are now deprecated: these limits are nowadays

            
            almost never used, and are reported by <code>gc()</code> when they are

            
            in use.

            
            </p>

            
            </li>

            
            <li><p> Forms like <code>binomial(link = "link")</code> for GLM families

            
            deprecated since <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.4.0 are now defunct.

            
            </p>

            
            </li>

            
            <li><p> The <code>declarativeOnly</code> argument to

            
            <code>loadNamespace()</code> (not relevant since <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.13.0) has been

            
            removed.

            
            </p>

            
            </li>

            
            <li><p> Use of <code>library.dynam()</code> without specifying all the

            
            first three arguments is deprecated.  (It is often called from a

            
            namespace, and the defaults are only appropriate to a package.)

            
            </p>

            
            <p>Use of <code>chname</code> in <code>library.dynam()</code> with the extension

            
            &lsquo;<span class="file">.so</span>&rsquo; or <code>.dll</code> (which is clearly not allowed according

            
            to the help page) is deprecated.  This also applies to

            
            <code>library.dynam.unload()</code> and <code>useDynLib</code> directives in

            
            &lsquo;<span class="file">NAMESPACE</span>&rsquo; files.

            
            </p>

            
            </li>

            
            <li><p> It is deprecated to use <code>mean(x)</code> and <code>sd(x)</code>

            
            directly on data frames (or also matrices, for <code>sd</code>)

            
            <code>x</code>, instead of simply using <code>sapply</code>.

            
            </p>

            
            <p>In the same spirit, <code>median(x)</code> now gives an error for a data

            
            frame <code>x</code> (it often gave nonsensical results).

            
            </p>

            
            </li>

            
            <li><p> The <code>keep.source</code> argument to <code>library()</code> and

            
            <code>require()</code> is deprecated: it was only used for packages

            
            installed without lazy-loading, and now all packages are

            
            lazy-loaded.

            
            </p>

            
            </li>

            
            <li><p> Using a false value for the &lsquo;<span class="file">DESCRIPTION</span>&rsquo; field

            
            <span class="samp">LazyLoad</span> is deprecated.

            
            </p>

            
            </li></ul>


            <h4>INSTALLATION</h4>


            <ul>

            
            <li><p> The base and recommended packages are now byte-compiled

            
            (equivalent to <code>make bytecode</code> in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.13.x).

            
            </p>

            
            </li>

            
            <li><p> Configure option <span class="option">--with-system-zlib</span> now only makes

            
            use of the basic interface of <code>zlib</code> and not the

            
            C function <span class="samp">gzseek</span> which has shown erroneous behaviour in

            
            <code>zlib</code> 1.2.4 and 1.2.5.

            
            </p>

            
            </li>

            
            <li><p> The <code>zlib</code> in the R sources is now version 1.2.5.

            
            (This is safe even on 32-bit Linux systems because only the basic

            
            interface is now used.)

            
            </p>

            
            </li>

            
            <li><p> The &lsquo;<span class="file">.afm</span>&rsquo; files in package <span class="pkg">grDevices</span> are now

            
            installed as compressed files (as long done on Windows), saving ca

            
            2MB on the installed size.

            
            </p>

            
            </li>

            
            <li><p> The non-screen cairo-based devices are no longer in the X11

            
            module and so can be installed without X11.  (We have never seen a

            
            Unix-alike system with cairographics installed but not X11, but a

            
            user might select <span class="option">--without-x</span>.)

            
            </p>

            
            </li>

            
            <li><p> Configure will try to use <span class="option">-fobjc-exceptions</span> for the

            
            Objective-C compiler (if present) to ensure that even compilers

            
            that do not enable exceptions by default (such as vanilla gcc) can

            
            be used.  (Objective-C is currently only used on Mac OS X.)

            
            </p>

            
            </li>

            
            <li><p> The system call <code>times</code> is required.

            
            </p>

            
            </li>

            
            <li><p> The C99 functions <code>acosh</code>, <code>asinh</code>, <code>atanh</code>,

            
            <code>snprintf</code> and <code>vsnprintf</code> are now required.

            
            </p>

            
            </li>

            
            <li><p> There is no longer support for making DVI manuals <em>via</em>

            
            <code>make dvi</code>, <code>make install-dvi</code> and similar.  Only

            
            PDF manuals are supported (to allow the use of fonts which are

            
            only available for PDF.)

            
            </p>

            
            </li>

            
            <li><p> The &lsquo;<span class="file">configure</span>&rsquo; arguments used during configuration of

            
            <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> are included as a comment in &lsquo;<span class="file">Makeconf</span>&rsquo; for informative

            
            purposes on Unix-alikes in a form suitable for shell execution.

            
            Note that those are merely command-line arguments, they do not

            
            include environment variables (one more reason to use configure

            
            variables instead) or site configuration settings.

            
            </p>

            
            </li>

            
            <li><p> Framework installation now supports <code>DESTDIR</code>

            
            (Mac OS X only).

            
            </p>

            
            </li>

            
            <li><p> Java detection (<code>R CMD javareconf</code>) works around bogus

            
            <code>java.library.path</code> property in recent Oracle Java binaries.

            
            </p>

            
            </li></ul>


            <h4>BUG FIXES</h4>


            <ul>

            
            <li><p> The locale category <span class="samp">LC_MONETARY</span> was only being set on

            
            startup on Windows: that is now done on Unix-alikes where

            
            supported.

            
            </p>

            
            </li>

            
            <li><p> Reference class utilities will detect an attempt to modify

            
            methods or fields in a locked class definition (e.g., in a

            
            namespace) and generate an error.

            
            </p>

            
            </li>

            
            <li><p> The formula methods for <code>lines()</code>, <code>points()</code> and

            
            <code>text()</code> now work even if package <span class="pkg">stats</span> is not on the

            
            search path.

            
            </p>

            
            </li>

            
            <li><p> In principle, S4 classes from different packages could

            
            have the same name.  This has not previously worked.  Changes

            
            have now been installed that should allow such classes and

            
            permit methods to use them.  New functions <code>className()</code>

            
            and <code>multipleClasses()</code> are related tools for programming.

            
            </p>

            
            </li>

            
            <li><p> Work around an issue in Linux (a system <code>select</code> call

            
            resetting <code>tv</code>) which prevented internet operations from

            
            timing out properly.

            
            </p>

            
            </li>

            
            <li><p> Several stack trampling and overflow issues have been fixed

            
            in TRE, triggered by <code>agrep</code> and friends with long patterns.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14627">PR#14627</a>)

            
            </p>

            
            </li>

            
            <li><p> (&ldquo;design infelicity&rdquo;) Field assignments in reference

            
            classes are now consistent with slots in S4 classes:  the

            
            assigned value must come from the declared class (if any) for the field

            
            or from a subclass.

            
            </p>

            
            </li>

            
            <li><p> The methods objects constructed for <code>"coerce"</code> and

            
            <code>"coerce&lt;-"</code> were lacking some essential information in the

            
            <code>generic</code>, <code>defined</code> and <code>target</code> slots;

            
            <code>as()</code> did not handle duplicate class definitions correctly.

            
            </p>

            
            </li>

            
            <li><p> The parser no longer accepts the digit <code>8</code> in an octal

            
            character code in a string, nor does it accept unterminated

            
            strings in a file.  (Reported by Bill Dunlap.)

            
            </p>

            
            </li>

            
            <li><p> The <code>print()</code> method for class <code>"summary.aov"</code> did

            
            not pass on argument <code>digits</code> when <code>summary()</code> was

            
            called on a single object, and hence used more digits than

            
            documented.

            
            </p>

            
            </li>

            
            <li><p> The <code>X11()</code> device's cairo back-end produced incorrect

            
            capture snapshot images on big-endian machines.

            
            </p>

            
            </li>

            
            <li> <p><code>loglin()</code> gave a spurious error when argument

            
            <code>margin</code> consisted of a single element of length one.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14690">PR#14690</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>loess()</code> is better protected against misuse,

            
            e.g. zero-length <code>span</code>.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14691">PR#14691</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>HoltWinters()</code> checks that the optimization

            
            succeeded. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14694">PR#14694</a>)

            
            </p>

            
            </li>

            
            <li><p> The (undocumented) inclusion of superclass objects in

            
            default initializing of reference classes overwrote explicit

            
            field arguments. The bug is fixed, the feature documented and a

            
            test added.

            
            </p>

            
            </li>

            
            <li> <p><code>round(x, -Inf)</code> now does something sensible (return

            
            zero rather than <code>NA</code>).

            
            </p>

            
            </li>

            
            <li> <p><code>signif(x, -Inf)</code> now behaves as documented

            
            (<code>signif(x, 1)</code>) rather than giving zero.

            
            </p>

            
            </li>

            
            <li><p> The <code>"table"</code> method for <code>Axis()</code> hardcoded

            
            <code>side = 1</code>, hence calls to <code>plot(&lt;vector&gt;, &lt;table&gt;)</code>

            
            labelled the wrong axis. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14699">PR#14699</a>)

            
            </p>

            
            </li>

            
            <li><p> Creating a connection might fail under <code>gctorture(TRUE)</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>stack()</code> and <code>unstack()</code> converted character

            
            columns to factors.

            
            </p>

            
            <p><code>unstack()</code> sometimes produced incorrect results (a list or a

            
            vector) if the factor on which to un-split had only one level.

            
            </p>

            
            </li>

            
            <li><p> On some systems <code>help(".C", help_type = "pdf")</code> and

            
            similar generated file names that TeX was unable to handle.

            
            </p>

            
            </li>

            
            <li><p> Non-blocking listening socket connections continued to

            
            report <code>isIncomplete()</code> as true even when the peer had closed

            
            down and all available input had been read.

            
            </p>

            
            </li>

            
            <li><p> The revised HTML search system now generates better

            
            hyperlinks to help topics found: previously it gave problems with

            
            help pages with names containing e.g. spaces and slashes.

            
            </p>

            
            </li>

            
            <li><p> A late change in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.13.2 broke <span class="samp">\Sexpr</span> expressions

            
            in Rd files.

            
            </p>

            
            </li>

            
            <li><p> The creation of ticks on log axes (including by

            
            <code>axTicks()</code>) sometimes incorrectly omitted a tick at one end

            
            of the range by rounding error in a platform-dependent way.  This

            
            could be seen in the examples for <code>axTicks()</code>, where with

            
            axis limits <code>c(0.2, 88)</code> the tick for <code>0.2</code> was

            
            sometimes omitted.

            
            </p>

            
            </li>

            
            <li> <p><code>qgamma()</code> for small <code>shape</code> underflows to

            
            <code>0</code> rather than sometimes giving <code>NaN</code>.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=8528">PR#8528</a>, <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14710">PR#14710</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>mapply()</code> now gives an explicit error message (rather

            
            than an obscure one) if inputs of zero and positive length are

            
            mixed.

            
            </p>

            
            </li>

            
            <li><p> Setting a Hershey font family followed by string height

            
            query would crash R.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD javareconf -e</code> would fail for some shells due to

            
            a shift error. Also the resulting paths will no longer contain

            
            <code>$(JAVA_HOME)</code> as that can result in an unintended

            
            substitution based on &lsquo;<span class="file">Makeconf</span>&rsquo; instead of the shell

            
            setting.

            
            </p>

            
            </li></ul>


            <h3><img class="toplogo" src="../help/figures/../../html/Rlogo.svg" alt="[R logo]" /> CHANGES IN R VERSION 2.13.2</h3>


            <h4>NEW FEATURES</h4>


            <ul>

            
            <li> <p><code>mem.limits()</code> now reports values larger than the

            
            maximum integer (previously documented to be reported as

            
            <code>NA</code>), and allows larger values to be set, including

            
            <code>Inf</code> to remove the limit.

            
            </p>

            
            </li>

            
            <li><p> The <code>print()</code> methods for classes <code>"Date"</code>,

            
            <code>"POSIXct"</code> and <code>"POSIXlt"</code> respect the option

            
            <code>"max.print"</code> and so are much faster for very long datetime

            
            vectors.  (Suggestion of Yohan Chalabi.)

            
            </p>

            
            </li>

            
            <li> <p><code>untar2()</code> now works around errors generated with

            
            <code>tar</code> files that use more than the standard 6 digits for the

            
            checksum. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14654">PR#14654</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>install.packages()</code> with <code>Ncpus &gt; 1</code> guards

            
            against simultaneous installation of indirect dependencies as well

            
            as direct ones.

            
            </p>

            
            </li>

            
            <li><p> Sweave now knows about a few more Windows' encodings

            
            (including <code>cp1250</code> and <code>cp1257</code>) and some

            
            <code>inputenx</code> encodings such as <code>koi8-r</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>postscript(colormodel = "rgb-nogray")</code> no longer sets

            
            the sRGB colorspace for each colour and so some viewers may render

            
            its files much faster than the default <code>colormodel ="rgb"</code>.

            
            </p>

            
            </li>

            
            <li><p> The default for <code>pdf(maxRasters=)</code> has been increased

            
            from 64 to 1000.

            
            </p>

            
            </li>

            
            <li> <p><code>readBin()</code> now warns if <code>signed = FALSE</code> is used

            
            inappropriately (rather than being silently ignored).

            
            </p>

            
            <p>It enforces the documented limit of <i>2^31-1</i> bytes

            
            in a single call.

            
            </p>

            
            </li>

            
            <li><p> PCRE has been updated to version 8.13, a bug-fix release

            
            with updated Unicode tables (version 6.0.0).  An additional patch

            
            (r611 from PCRE 8.20-to-be) has been added to fix a collation

            
            symbol recognition issue.

            
            </p>

            
            </li></ul>


            <h4>INSTALLATION</h4>


            <ul>

            
            <li><p> It is possible to build in &lsquo;<span class="file">src/extra/xdr</span>&rsquo; on more

            
            platforms.  (Needed since glibc 2.14 hides its RPC implementation.)

            
            </p>

            
            </li>

            
            <li> <p><code>configure</code> will find the Sun TI-RPC implementation

            
            of xdr (in &lsquo;<span class="file">libtirpc</span>&rsquo;) provided its header files are in the

            
            search path: see the &lsquo;R Installation and Administration

            
            Manual&rsquo;.

            
            </p>

            
            </li></ul>


            <h4>PACKAGE INSTALLATION</h4>


            <ul>

            
            <li><p> Using a broad <code>exportPattern</code> directive in a

            
            &lsquo;<span class="file">NAMESPACE</span>&rsquo; file is no longer allowed to export internal

            
            objects such as <code>.onLoad</code> and <code>.__S3MethodsTable__.</code> .

            
            </p>

            
            <p>These are also excluded from imports, along with <code>.First.lib</code>.

            
            </p>

            
            </li></ul>


            <h4>BUG FIXES</h4>


            <ul>

            
            <li> <p><code>fisher.test()</code> had a buglet: If arguments were factors

            
            with unused levels, levels were dropped and you would get an error

            
            saying that there should be at least two levels, inconsistently

            
            with pre-tabulated data.  (Reported by Michael Fay).

            
            </p>

            
            </li>

            
            <li> <p><code>package.skeleton()</code> will no longer dump S4 objects

            
            supplied directly rather than in a code file.  These cannot be

            
            restored correctly from the dumped version.

            
            </p>

            
            </li>

            
            <li><p> Build-time expressions in help files did not have access

            
            to functions in the package being built (with <code>R CMD build</code>).

            
            </p>

            
            </li>

            
            <li><p> Because <code>quote()</code> did not mark its result as being in

            
            use, modification of the result could in some circumstances

            
            modify the original call.

            
            </p>

            
            </li>

            
            <li><p> Plotting <code>pch = '.'</code> now guarantees at least a one-pixel

            
            dot if <code>cex &gt; 0</code>.

            
            </p>

            
            </li>

            
            <li><p> The very-rarely-used command-line option

            
            <span class="option">--max-vsize</span> was incorrectly interpreted as a number of

            
            Vcells and not in bytes as documented.  (Spotted by Christophe

            
            Rhodes.)

            
            </p>

            
            </li>

            
            <li><p> The HTML generated by <code>Rd2HTML()</code> comes closer to

            
            being standards compliant.

            
            </p>

            
            </li>

            
            <li> <p><code>filter(x, recursive = TRUE)</code> gave incorrect results on a

            
            series containing <code>NA</code>s.  (Spotted by Bill Dunlap.)

            
            </p>

            
            </li>

            
            <li><p> Profiling <code>stats::mle()</code> fits with a <code>fixed</code>

            
            parameter was not supported.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14646">PR#14646</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>retracemem()</code> was still using positional matching.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14650">PR#14650</a>)

            
            </p>

            
            </li>

            
            <li><p> The <code>quantile</code> method for <code>"ecdf"</code> objects now

            
            works and is documented.

            
            </p>

            
            </li>

            
            <li> <p><code>xtabs(~ .., ..., sparse=TRUE)</code> now also works together

            
            with an <code>exclude = ..</code> specification.

            
            </p>

            
            </li>

            
            <li> <p><code>decompose()</code> computed an incorrect seasonal component for

            
            time series with odd frequencies.

            
            </p>

            
            </li>

            
            <li><p> The <code>pdf()</code> device only includes the definition of the

            
            sRGB colorspace in the output file for the <code>"rgb"</code> colormodel

            
            (and not for <code>"gray"</code> nor <code>"cmyk"</code>): this saves ca

            
            9KB in the output file.

            
            </p>

            
            </li>

            
            <li> <p><code>.hasSlot()</code> wrongly gave <code>FALSE</code> in some cases.

            
            </p>

            
            </li>

            
            <li> <p><code>Sweave()</code> with <code>keep.source=TRUE</code> could generate

            
            spurious <code>NA</code> lines when a chunk reference appeared last in

            
            a code chunk.

            
            </p>

            
            </li>

            
            <li> <p><span class="samp">\Sexpr[results=rd]</span> in an &lsquo;<span class="file">.Rd</span>&rsquo; file now first tries

            
            <code>parse_Rd(fragment=FALSE)</code> to allow Rd section-level macros

            
            to be inserted.

            
            </p>

            
            </li>

            
            <li><p> The <code>print()</code> method for class <code>"summary.aov"</code> did

            
            not pass on arguments such as <code>signif.stars</code> when

            
            <code>summary()</code> was called on a single object.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14684">PR#14684</a>)

            
            </p>

            
            </li>

            
            <li><p> In rare cases <code>ks.test()</code> could return a p-value

            
            very slightly less than 0 by rounding error.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14671">PR#14671</a>)

            
            </p>

            
            </li>

            
            <li><p> If <code>trunc()</code> was called on a <code>"POSIXlt"</code> vector

            
            and the result was subsetted, all but the first element was

            
            converted to <code>NA</code>.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14679">PR#14679</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>cbind()</code> and <code>rbind()</code> could cause memory

            
            corruption when used on a combination of raw and logical/integer

            
            vectors.

            
            </p>

            
            </li></ul>


            <h3><img class="toplogo" src="../help/figures/../../html/Rlogo.svg" alt="[R logo]" /> CHANGES IN R VERSION 2.13.1</h3>


            <h4>NEW FEATURES</h4>


            <ul>

            
            <li> <p><code>iconv()</code> no longer translates <code>NA</code> strings as

            
            <code>"NA"</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>persp(box = TRUE)</code> now warns if the surface extends

            
            outside the box (since occlusion for the box and axes is computed

            
            assuming the box is a bounding box). (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=202">PR#202</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>RShowDoc()</code> can now display the licences shipped with

            
            <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>, e.g. <code>RShowDoc("GPL-3")</code>.

            
            </p>

            
            </li>

            
            <li><p> New wrapper function <code>showNonASCIIfile()</code> in package

            
            <span class="pkg">tools</span>.

            
            </p>

            
            </li>

            
            <li> <p><code>nobs()</code> now has a <code>"mle"</code> method in package

            
            <span class="pkg">stats4</span>.

            
            </p>

            
            </li>

            
            <li> <p><code>trace()</code> now deals correctly with S4 reference classes

            
            and corresponding reference methods (e.g., <code>$trace()</code>)

            
            have been added.

            
            </p>

            
            </li>

            
            <li> <p><code>xz</code> has been updated to 5.0.3 (very minor bugfix

            
            release).

            
            </p>

            
            </li>

            
            <li> <p><code>tools::compactPDF()</code> gets more compression (usually a

            
            little, sometimes a lot) by using the compressed object streams of

            
            PDF 1.5.

            
            </p>

            
            </li>

            
            <li> <p><code>cairo_ps(onefile = TRUE)</code> generates encapsulated EPS

            
            on platforms with cairo &gt;= 1.6.

            
            </p>

            
            </li>

            
            <li><p> Binary reads (e.g., by <code>readChar()</code> and <code>readBin()</code>)

            
            are now supported on clipboard connections.  (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14593">PR#14593</a>.)

            
            </p>

            
            </li>

            
            <li> <p><code>as.POSIXlt.factor()</code> now passes <code>...</code> to the

            
            character method (suggestion of Joshua Ulrich).  [Intended for <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>

            
            2.13.0 but accidentally removed before release.]

            
            </p>

            
            </li>

            
            <li> <p><code>vector()</code> and its wrappers such as <code>integer()</code>

            
            and <code>double()</code> now warn if called with a <code>length</code>

            
            argument of more than one element.  This helps track down user

            
            errors such as calling <code>double(x)</code> instead of

            
            <code>as.double(x)</code>.

            
            </p>

            
            </li></ul>


            <h4>INSTALLATION</h4>


            <ul>

            
            <li><p> Building the vignette PDFs in packages <span class="pkg">grid</span> and

            
            <span class="pkg">utils</span> is now part of running <code>make</code> from an SVN

            
            checkout on a Unix-alike: a separate <code>make vignettes</code> step

            
            is no longer required.

            
            </p>

            
            <p>These vignettes are now made with <code>keep.source = TRUE</code> and

            
            hence will be laid out differently.

            
            </p>

            
            </li>

            
            <li> <p><code>make install-strip</code> failed under some configuration

            
            options.

            
            </p>

            
            </li>

            
            <li><p> Packages can customize non-standard installation of compiled

            
            code via a <code>src/install.libs.R</code> script. This allows packages that

            
            have architecture-specific binaries (beyond the package's shared

            
            objects/DLLs) to be installed in a multi-architecture setting.

            
            </p>

            
            </li></ul>


            <h4>SWEAVE &amp; VIGNETTES</h4>


            <ul>

            
            <li> <p><code>Sweave()</code> and <code>Stangle()</code> gain an <code>encoding</code>

            
            argument to specify the encoding of the vignette sources if the

            
            latter do not contain a <span class="samp">\usepackage[]{inputenc}</span> statement

            
            specifying a single input encoding.

            
            </p>

            
            </li>

            
            <li><p> There is a new Sweave option <code>figs.only = TRUE</code> to run

            
            each figure chunk only for each selected graphics device, and not

            
            first using the default graphics device.   This will become the

            
            default in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.14.0.

            
            </p>

            
            </li>

            
            <li><p> Sweave custom graphics devices can have a custom function

            
            <code>foo.off()</code> to shut them down.

            
            </p>

            
            </li>

            
            <li><p> Warnings are issued when non-portable filenames are found

            
            for graphics files (and chunks if <code>split = TRUE</code>).  Portable

            
            names are regarded as alphanumeric plus hyphen, underscore, plus

            
            and hash (periods cause problems with recognizing file

            
            extensions).

            
            </p>

            
            </li>

            
            <li><p> The <code>Rtangle()</code> driver has a new option

            
            <code>show.line.nos</code> which is by default false; if true it

            
            annotates code chunks with a comment giving the line number of the

            
            first line in the sources (the behaviour of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> &gt;= 2.12.0).

            
            </p>

            
            </li>

            
            <li><p> Package installation tangles the vignette sources: this step

            
            now converts the vignette sources from the vignette/package

            
            encoding to the current encoding, and records the encoding (if not

            
            ASCII) in a comment line at the top of the installed &lsquo;<span class="file">.R</span>&rsquo;

            
            file.

            
            </p>

            
            </li></ul>


            <h4>LICENCE</h4>


            <ul>

            
            <li><p> No parts of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> are now licensed solely under GPL-2.  The

            
            licences for packages <a href="https://CRAN.R-project.org/package=rpart"><span class="pkg">rpart</span></a> and <a href="https://CRAN.R-project.org/package=survival"><span class="pkg">survival</span></a> have been

            
            changed, which means that the licence terms for <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> as distributed

            
            are GPL-2 | GPL-3.

            
            </p>

            
            </li></ul>


            <h4>DEPRECATED AND DEFUNCT</h4>


            <ul>

            
            <li><p> The internal functions <code>.readRDS()</code> and

            
            <code>.saveRDS()</code> are now deprecated in favour of the public

            
            functions <code>readRDS()</code> and <code>saveRDS()</code> introduced in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>

            
            2.13.0.

            
            </p>

            
            </li>

            
            <li><p> Switching off lazy-loading of code <em>via</em> the

            
            <span class="samp">LazyLoad</span> field of the &lsquo;<span class="file">DESCRIPTION</span>&rsquo; file is now

            
            deprecated.  In future all packages will be lazy-loaded.

            
            </p>

            
            </li>

            
            <li><p> The off-line <code>help()</code> types <span class="samp">"postscript"</span> and

            
            <span class="samp">"ps"</span> are deprecated.

            
            </p>

            
            </li></ul>


            <h4>UTILITIES</h4>


            <ul>

            
            <li> <p><code>R CMD check</code> on a multi-architecture installation now

            
            skips the user's &lsquo;<span class="file">.Renviron</span>&rsquo; file for the

            
            architecture-specific tests (which do read the

            
            architecture-specific &lsquo;<span class="file">Renviron.site</span>&rsquo; files).  This is

            
            consistent with single-architecture checks, which use

            
            <span class="option">--no-environ</span>.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD build</code> now looks for &lsquo;<span class="file">DESCRIPTION</span>&rsquo;

            
            fields <span class="samp">BuildResaveData</span> and <span class="samp">BuildKeepEmpty</span> for

            
            per-package overrides.  See &lsquo;Writing R Extensions&rsquo;.

            
            </p>

            
            </li></ul>


            <h4>BUG FIXES</h4>


            <ul>

            
            <li> <p><code>plot.lm(which = 5)</code> was intended to order factor

            
            levels in increasing order of mean standardized residual.   It

            
            ordered the factor labels correctly, but could plot the wrong

            
            group of residuals against the label.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14545">PR#14545</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>mosaicplot()</code> could clip the factor labels, and could

            
            overlap them with the cells if a non-default value of

            
            <code>cex.axis</code> was used.  (Related to <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14550">PR#14550</a>.)

            
            </p>

            
            </li>

            
            <li> <p><code>dataframe[[row,col]]</code> now dispatches on <code>[[</code>

            
            methods for the selected column.  (Spotted by Bill Dunlap).

            
            </p>

            
            </li>

            
            <li> <p><code>sort.int()</code> would strip the class of an object, but

            
            leave its object bit set.  (Reported by Bill Dunlap.)

            
            </p>

            
            </li>

            
            <li> <p><code>pbirthday()</code> and <code>qbirthday()</code> did not implement

            
            the algorithm exactly as given in their reference and so were

            
            unnecessarily inaccurate.

            
            </p>

            
            <p><code>pbirthday()</code> now solves the approximate formula analytically

            
            rather than using <code>uniroot()</code> on a discontinuous function.

            
            </p>

            
            <p>The description of the problem was inaccurate: the probability is

            
            a tail probability (&lsquo;2 <em>or more</em> people share a birthday&rsquo;)

            
            </p>

            
            </li>

            
            <li><p> Complex arithmetic sometimes warned incorrectly about

            
            producing NAs when there were NaNs in the input.

            
            </p>

            
            </li>

            
            <li> <p><code>seek(origin = "current")</code> incorrectly reported it was

            
            not implemented for a <code>gzfile()</code> connection.

            
            </p>

            
            </li>

            
            <li> <p><code>c()</code>, <code>unlist()</code>, <code>cbind()</code> and

            
            <code>rbind()</code> could silently overflow the maximum vector length

            
            and cause a segfault.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14571">PR#14571</a>)

            
            </p>

            
            </li>

            
            <li><p> The <code>fonts</code> argument to <code>X11(type = "Xlib")</code> was

            
            being ignored.

            
            </p>

            
            </li>

            
            <li><p> Reading (e.g., with <code>readBin()</code>) from a raw connection

            
            was not advancing the pointer, so successive reads would read the

            
            same value.  (Spotted by Bill Dunlap.)

            
            </p>

            
            </li>

            
            <li><p> Parsed text containing embedded newlines was printed

            
            incorrectly by <code>as.character.srcref()</code>.  (Reported by Hadley

            
            Wickham.)

            
            </p>

            
            </li>

            
            <li> <p><code>decompose()</code> used with a series of a non-integer

            
            number of periods returned a seasonal component shorter than the

            
            original series.  (Reported by Rob Hyndman.)

            
            </p>

            
            </li>

            
            <li> <p><code>fields = list()</code> failed for <code>setRefClass()</code>.

            
            (Reported by Michael Lawrence.)

            
            </p>

            
            </li>

            
            <li><p> Reference classes could not redefine an inherited field

            
            which had class <code>"ANY"</code>. (Reported by Janko Thyson.)

            
            </p>

            
            </li>

            
            <li><p> Methods that override previously loaded versions will now

            
            be installed and called.  (Reported by Iago Mosqueira.)

            
            </p>

            
            </li>

            
            <li> <p><code>addmargins()</code> called <code>numeric(apos)</code> rather than

            
            <code>numeric(length(apos))</code>.

            
            </p>

            
            </li>

            
            <li><p> The HTML help search sometimes produced bad links.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14608">PR#14608</a>)

            
            </p>

            
            </li>

            
            <li><p> Command completion will no longer be broken if

            
            <code>tail.default()</code> is redefined by the user. (Problem reported

            
            by Henrik Bengtsson.)

            
            </p>

            
            </li>

            
            <li><p> LaTeX rendering of markup in titles of help pages has been

            
            improved; in particular, <code>\eqn{}</code> may be used there.

            
            </p>

            
            </li>

            
            <li> <p><code>isClass()</code> used its own namespace as the default of

            
            the <code>where</code> argument inadvertently.

            
            </p>

            
            </li>

            
            <li><p> Rd conversion to latex mishandled multi-line titles

            
            (including cases where there was a blank line in the <span class="samp">\title</span>

            
            section).  (It seems this happened only in 2.13.0 patched.)

            
            </p>

            
            </li>

            
            <li> <p><code>postscript()</code> with an sRGB colormodel now uses sRGB

            
            for raster images (in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.13.[01] it used uncalibrated RGB).

            
            </p>

            
            <p>There is no longer an undocumented 21845-pixel limit on raster images.

            
            </p>

            
            </li></ul>


            <h3><img class="toplogo" src="../help/figures/../../html/Rlogo.svg" alt="[R logo]" /> CHANGES IN R VERSION 2.13.0</h3>


            <h4>SIGNIFICANT USER-VISIBLE CHANGES</h4>


            <ul>

            
            <li> <p><code>replicate()</code> (by default) and <code>vapply()</code> (always)

            
            now return a higher-dimensional array instead of a matrix in the case

            
            where the inner function value is an array of dimension &gt;= 2.

            
            </p>

            
            </li>

            
            <li><p> Printing and formatting of floating point numbers is now

            
            using the correct number of digits, where it previously rarely

            
            differed by a few digits. (See &ldquo;scientific&rdquo; entry below.)

            
            This affects <em>many</em> &lsquo;<span class="file">*.Rout.save</span>&rsquo; checks in packages.

            
            </p>

            
            </li></ul>


            <h4>NEW FEATURES</h4>


            <ul>

            
            <li> <p><code>normalizePath()</code> has been moved to the <span class="pkg">base</span>

            
            package (from <span class="pkg">utils</span>): this is so it can be used by

            
            <code>library()</code> and friends.

            
            </p>

            
            <p>It now does tilde expansion.

            
            </p>

            
            <p>It gains new arguments <code>winslash</code> (to select the separator on

            
            Windows) and <code>mustWork</code> to control the action if a canonical

            
            path cannot be found.

            
            </p>

            
            </li>

            
            <li><p> The previously barely documented limit of 256 bytes on a

            
            symbol name has been raised to 10,000 bytes (a sanity check).

            
            Long symbol names can sometimes occur when deparsing expressions

            
            (for example, in <code>model.frame</code>).

            
            </p>

            
            </li>

            
            <li> <p><code>reformulate()</code> gains a <code>intercept</code> argument.

            
            </p>

            
            </li>

            
            <li> <p><code>cmdscale(add = FALSE)</code> now uses the more common

            
            definition that there is a representation in <code>n-1</code> or less

            
            dimensions, and only dimensions corresponding to positive

            
            eigenvalues are used.  (Avoids confusion such as <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14397">PR#14397</a>.)

            
            </p>

            
            </li>

            
            <li><p> Names used by <code>c()</code>, <code>unlist()</code>, <code>cbind()</code>

            
            and <code>rbind()</code> are marked with an encoding when this can be

            
            ascertained.

            
            </p>

            
            </li>

            
            <li><p> R colours are now defined to refer to the sRGB color space.

            
            </p>

            
            <p>The PDF, PostScript, and Quartz graphics devices record this fact.

            
            X11 (and cairo) and Windows just assume that your screen conforms.

            
            </p>

            
            </li>

            
            <li> <p><code>system.file()</code> gains a <code>mustWork</code> argument

            
            (suggestion of Bill Dunlap).

            
            </p>

            
            </li>

            
            <li> <p><code>new.env(hash = TRUE)</code> is now the default.

            
            </p>

            
            </li>

            
            <li> <p><code>list2env(envir = NULL)</code> defaults to hashing (with a

            
            suitably sized environment) for lists of more than 100 elements.

            
            </p>

            
            </li>

            
            <li> <p><code>text()</code> gains a formula method.

            
            </p>

            
            </li>

            
            <li> <p><code>IQR()</code> now has a <code>type</code> argument which is passed

            
            to <code>quantile()</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>as.vector()</code>, <code>as.double()</code> etc duplicate less

            
            when they leave the mode unchanged but remove attributes.

            
            </p>

            
            <p><code>as.vector(mode = "any")</code> no longer duplicates when it does

            
            not remove attributes.  This helps memory usage in <code>matrix()</code>

            
            and <code>array()</code>.

            
            </p>

            
            <p><code>matrix()</code> duplicates less if <code>data</code> is an atomic vector

            
            with attributes such as names (but no class).

            
            </p>

            
            <p><code>dim(x) &lt;- NULL</code> duplicates less if <code>x</code> has neither

            
            dimensions nor names (since this operation removes names and

            
            dimnames).

            
            </p>

            
            </li>

            
            <li> <p><code>setRepositories()</code> gains an <code>addURLs</code> argument.

            
            </p>

            
            </li>

            
            <li> <p><code>chisq.test()</code> now also returns a <code>stdres</code>

            
            component, for standardized residuals (which have unit variance,

            
            unlike the Pearson residuals).

            
            </p>

            
            </li>

            
            <li> <p><code>write.table()</code> and friends gain a <code>fileEncoding</code>

            
            argument, to simplify writing files for use on other OSes (e.g., a

            
            spreadsheet intended for Windows or Mac OS X Excel).

            
            </p>

            
            </li>

            
            <li><p> Assignment expressions of the form <code>foo::bar(x) &lt;- y</code>

            
            and <code>foo:::bar(x) &lt;- y</code> now work; the replacement functions

            
            used are <code>foo::`bar&lt;-`</code> and <code>foo:::`bar&lt;-`</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>Sys.getenv()</code> gains a <code>names</code> argument so

            
            <code>Sys.getenv(x, names = FALSE)</code> can replace the common idiom

            
            of <code>as.vector(Sys.getenv())</code>.  The default has been changed

            
            to not name a length-one result.

            
            </p>

            
            </li>

            
            <li><p> Lazy loading of environments now preserves attributes and

            
            locked status. (The locked status of bindings and active bindings

            
            are still not preserved; this may be addressed in the future).

            
            </p>

            
            </li>

            
            <li> <p><code>options("install.lock")</code> may be set to <code>FALSE</code>

            
            so that <code>install.packages()</code> defaults to <span class="option">--no-lock</span>

            
            installs, or (on Windows) to <code>TRUE</code> so that binary installs

            
            implement locking.

            
            </p>

            
            </li>

            
            <li> <p><code>sort(partial = p)</code> for large <code>p</code> now tries

            
            Shellsort if quicksort is not appropriate and so works for

            
            non-numeric atomic vectors.

            
            </p>

            
            </li>

            
            <li> <p><code>sapply()</code> gets a new option <code>simplify = "array"</code>

            
            which returns a &ldquo;higher rank&rdquo; array instead of just a matrix

            
            when <code>FUN()</code> returns a <code>dim()</code> length of two or more.

            
            </p>

            
            <p><code>replicate()</code> has this option set by default, and

            
            <code>vapply()</code> now behaves that way internally.

            
            </p>

            
            </li>

            
            <li> <p><code>aperm()</code> becomes S3 generic and gets a <code>table</code>

            
            method which preserves the class.

            
            </p>

            
            </li>

            
            <li> <p><code>merge()</code> and <code>as.hclust()</code> methods for objects of

            
            class <code>"dendrogram"</code> are now provided.

            
            </p>

            
            </li>

            
            <li><p> The character method of <code>as.POSIXlt()</code> now tries to

            
            find a format that works for all non-<code>NA</code> inputs, not just

            
            the first one.

            
            </p>

            
            </li>

            
            <li> <p><code>str()</code> now has a method for class <code>"Date"</code>

            
            analogous to that for class <code>"POSIXt"</code>.

            
            </p>

            
            </li>

            
            <li><p> New function <code>file.link()</code> to create hard links on

            
            those file systems (POSIX, NTFS but not FAT) that support them.

            
            </p>

            
            </li>

            
            <li><p> New <code>Summary()</code> group method for class <code>"ordered"</code>

            
            implements <code>min()</code>, <code>max()</code> and <code>range()</code> for

            
            ordered factors.

            
            </p>

            
            </li>

            
            <li> <p><code>mostattributes&lt;-()</code> now consults the <code>"dim"</code>

            
            attribute and not the <code>dim()</code> function, making it more useful

            
            for objects (such as data frames) from classes with methods for

            
            <code>dim()</code>.  It also uses <code>attr&lt;-()</code> in preference to the

            
            generics <code>name&lt;-()</code>, <code>dim&lt;-()</code> and <code>dimnames&lt;-()</code>.

            
            (Related to <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14469">PR#14469</a>.)

            
            </p>

            
            </li>

            
            <li><p> There is a new option <code>"browserNLdisabled"</code> to disable

            
            the use of an empty (e.g., via the &lsquo;Return&rsquo; key) as a synonym

            
            for <code>c</code> in <code>browser()</code> or <code>n</code> under <code>debug()</code>.

            
            (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14472">PR#14472</a>.)

            
            </p>

            
            </li>

            
            <li> <p><code>example()</code> gains optional new arguments

            
            <code>character.only</code> and <code>give.lines</code> enabling programmatic

            
            exploration.

            
            </p>

            
            </li>

            
            <li> <p><code>serialize()</code> and <code>unserialize()</code> are no longer

            
            described as &lsquo;experimental&rsquo;.  The interface is now regarded

            
            as stable, although the serialization format may well change in

            
            future releases.  (<code>serialize()</code> has a new argument

            
            <code>version</code> which would allow the current format to be written

            
            if that happens.)

            
            </p>

            
            <p>New functions <code>saveRDS()</code> and <code>readRDS()</code> are public

            
            versions of the &lsquo;internal&rsquo; functions <code>.saveRDS()</code> and

            
            <code>.readRDS()</code> made available for general use.  The dot-name

            
            versions remain available as several package authors have made use

            
            of them, despite the documentation.  <code>readRDS()</code> no longer

            
            wraps non-file connections in a call to <code>gzcon()</code>, for

            
            efficiency (see its documentation).

            
            </p>

            
            <p><code>saveRDS()</code> supports <code>compress = "xz"</code>.

            
            </p>

            
            </li>

            
            <li><p> Many functions when called with a not-open connection will

            
            now ensure that the connection is left not-open in the event of

            
            error.  These include <code>read.dcf()</code>, <code>dput()</code>,

            
            <code>dump()</code>, <code>load()</code>, <code>parse()</code>, <code>readBin()</code>,

            
            <code>readChar()</code>, <code>readLines()</code>, <code>save()</code>,

            
            <code>writeBin()</code>, <code>writeChar()</code>, <code>writeLines()</code>,

            
            <code>.readRDS()</code>, <code>.saveRDS()</code> and <code>tools::parse_Rd()</code>,

            
            as well as functions calling these.

            
            </p>

            
            </li>

            
            <li><p> Public functions <code>find.package()</code> and <code>path.package()</code>

            
            replace the internal dot-name versions.

            
            </p>

            
            </li>

            
            <li><p> The default method for <code>terms()</code> now looks for a

            
            <code>"terms"</code> attribute if it does not find a <code>"terms"</code>

            
            component, and so works for model frames.

            
            </p>

            
            </li>

            
            <li> <p><code>httpd()</code> handlers receive an additional argument

            
            containing the full request headers as a raw vector (this can be

            
            used to parse cookies, multi-part forms etc.). The recommended

            
            full signature for handlers is therefore <code>function(url,

            
            	query, body, headers, ...)</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>file.edit()</code> gains a <code>fileEncoding</code> argument to

            
            specify the encoding of the file(s).

            
            </p>

            
            </li>

            
            <li><p> The format of the HTML package listings has changed.  If

            
            there is more than one library tree , a table of links to

            
            libraries is provided at the top and bottom of the page.  Where a

            
            library contains more than 100 packages, an alphabetic index is

            
            given at the top of the section for that library.  (As a

            
            consequence, package names are now sorted case-insensitively

            
            whatever the locale.)

            
            </p>

            
            </li>

            
            <li> <p><code>isSeekable()</code> now returns <code>FALSE</code> on connections

            
            which have non-default <code>encoding</code>.  Although documented to

            
            record if &lsquo;in principle&rsquo; the connection supports seeking,

            
            it seems safer to report <code>FALSE</code> when it may not work.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD REMOVE</code> and <code>remove.packages()</code> now

            
            remove file <code>R.css</code> when removing all remaining packages in a

            
            library tree.  (Related to the wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14475">PR#14475</a>: note that this

            
            file is no longer installed.)

            
            </p>

            
            </li>

            
            <li> <p><code>unzip()</code> now has a <code>unzip</code> argument like

            
            <code>zip.file.extract()</code>.  This allows an external

            
            <code>unzip</code> program to be used, which can be useful to access

            
            features supported by Info-ZIP's <code>unzip</code> version 6 which

            
            is now becoming more widely available.

            
            </p>

            
            </li>

            
            <li><p> There is a simple <code>zip()</code> function, as wrapper for an

            
            external <code>zip</code> command.

            
            </p>

            
            </li>

            
            <li> <p><code>bzfile()</code> connections can now read from concatenated

            
            <code>bzip2</code> files (including files written with

            
            <code>bzfile(open = "a")</code>) and files created by some other

            
            compressors (such as the example of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14479">PR#14479</a>).

            
            </p>

            
            </li>

            
            <li><p> The primitive function <code>c()</code> is now of type BUILTIN.

            
            </p>

            
            </li>

            
            <li> <p><code>plot(&lt;dendrogram&gt;, .., nodePar=*)</code> now obeys an optional

            
            <code>xpd</code> specification (allowing clipping to be turned off

            
            completely).

            
            </p>

            
            </li>

            
            <li> <p><code>nls(algorithm="port")</code> now shares more code with

            
            <code>nlminb()</code>, and is more consistent with the other

            
            <code>nls()</code> algorithms in its return value.

            
            </p>

            
            </li>

            
            <li> <p><code>xz</code> has been updated to 5.0.1 (very minor bugfix

            
            release).

            
            </p>

            
            </li>

            
            <li> <p><code>image()</code> has gained a logical <code>useRaster</code>

            
            argument allowing it to use a bitmap raster for plotting a

            
            regular grid instead of polygons. This can be more efficient, but

            
            may not be supported by all devices. The default is <code>FALSE</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>list.files()</code>/<code>dir()</code> gains a new argument

            
            <code>include.dirs()</code> to include directories in the listing when

            
            <code>recursive = TRUE</code>.

            
            </p>

            
            </li>

            
            <li><p> New function <code>list.dirs()</code> lists all directories,

            
            (even empty ones).

            
            </p>

            
            </li>

            
            <li> <p><code>file.copy()</code> now (by default) copies

            
            read/write/execute permissions on files, moderated by the current

            
            setting of <code>Sys.umask()</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>Sys.umask()</code> now accepts <code>mode = NA</code> and returns

            
            the current <code>umask</code> value (visibly) without changing it.

            
            </p>

            
            </li>

            
            <li><p> There is a <code>!</code> method for classes <code>"octmode"</code> and

            
            <code>"hexmode"</code>: this allows <code>xor(a, b)</code> to work if both

            
            <code>a</code> and <code>b</code> are from one of those classes.

            
            </p>

            
            </li>

            
            <li> <p><code>as.raster()</code> no longer fails for vectors or matrices

            
            containing <code>NA</code>s.

            
            </p>

            
            </li>

            
            <li><p> New hook <code>"before.new.plot"</code> allows functions to be run

            
            just before advancing the frame in <code>plot.new</code>, which is

            
            potentially useful for custom figure layout implementations.

            
            </p>

            
            </li>

            
            <li><p> Package <span class="pkg">tools</span> has a new function <code>compactPDF()</code>

            
            to try to reduce the size of PDF files <em>via</em> <code>qpdf</code>

            
            or <code>gs</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>tar()</code> has a new argument <code>extra_flags</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>dotchart()</code> accepts more general objects <code>x</code> such

            
            as 1D tables which can be coerced by <code>as.numeric()</code> to a

            
            numeric vector, with a warning since that might not be

            
            appropriate.

            
            </p>

            
            </li>

            
            <li><p> The previously internal function <code>create.post()</code> is now

            
            exported from <span class="pkg">utils</span>, and the documentation for

            
            <code>bug.report()</code> and <code>help.request()</code> now refer to that

            
            for <code>create.post()</code>.

            
            </p>

            
            <p>It has a new <code>method = "mailto"</code> on Unix-alikes similar to

            
            that on Windows: it invokes a default mailer via <code>open</code>

            
            (Mac OS X) or <code>xdg-open</code> or the default browser (elsewhere).

            
            </p>

            
            <p>The default for <code>ccaddress</code> is now

            
            <code>getOption("ccaddress")</code> which is by default unset: using the

            
            username as a mailing address nowadays rarely works as expected.

            
            </p>

            
            </li>

            
            <li><p> The default for <code>options("mailer")</code> is now

            
            <code>"mailto"</code> on all platforms.

            
            </p>

            
            </li>

            
            <li> <p><code>unlink()</code> now does tilde-expansion (like most other

            
            file functions).

            
            </p>

            
            </li>

            
            <li> <p><code>file.rename()</code> now allows vector arguments (of the

            
            same length).

            
            </p>

            
            </li>

            
            <li><p> The <code>"glm"</code> method for <code>logLik()</code> now returns an

            
            <code>"nobs"</code> attribute (which <code>stats4::BIC()</code> assumed it

            
            did).

            
            </p>

            
            <p>The <code>"nls"</code> method for <code>logLik()</code> gave incorrect results

            
            for zero weights.

            
            </p>

            
            </li>

            
            <li><p> There is a new generic function <code>nobs()</code> in package

            
            <span class="pkg">stats</span>, to extract from model objects a suitable value for

            
            use in BIC calculations.  An S4 generic derived from it is defined

            
            in package <span class="pkg">stats4</span>.

            
            </p>

            
            </li>

            
            <li><p> Code for S4 reference-class methods is now examined for

            
            possible errors in non-local assignments.

            
            </p>

            
            </li>

            
            <li> <p><code>findClasses</code>, <code>getGeneric</code>, <code>findMethods</code>

            
            and <code>hasMethods</code> are revised to deal consistently with

            
            the <code>package=</code> argument and be consistent with soft namespace

            
            policy for finding objects.

            
            </p>

            
            </li>

            
            <li> <p><code>tools::Rdiff()</code> now has the option to return not only

            
            the status but a character vector of observed differences (which

            
            are still by default sent to &lsquo;<span class="file">stdout</span>&rsquo;).

            
            </p>

            
            </li>

            
            <li><p> The startup environment variables <span class="env">R_ENVIRON_USER</span>,

            
            <span class="env">R_ENVIRON</span>, <span class="env">R_PROFILE_USER</span> and <span class="env">R_PROFILE</span> are now

            
            treated more consistently.  In all cases an empty value is

            
            considered to be set and will stop the default being used, and for

            
            the last two tilde expansion is performed on the file name.  (Note

            
            that setting an empty value is probably impossible on Windows.)

            
            </p>

            
            </li>

            
            <li><p> Using <code>R --no-environ CMD</code>, <code>R

            
            	--no-site-file CMD</code> or <code>R --no-init-file CMD</code> sets

            
            environment variables so these settings are passed on to child <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>

            
            processes, notably those run by <code>INSTALL</code>, <code>check</code> and

            
            <code>build</code>. <code>R --vanilla CMD</code> sets these three options

            
            (but not <span class="option">--no-restore</span>).

            
            </p>

            
            </li>

            
            <li> <p><code>smooth.spline()</code> is somewhat faster.  With

            
            <code>cv=NA</code> it allows some leverage computations to be skipped,

            
            </p>

            
            </li>

            
            <li><p> The internal (C) function <span class="samp">scientific()</span>, at the heart

            
            of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>'s <code>format.info(x)</code>, <code>format(x)</code>, <code>print(x)</code>,

            
            etc, for numeric <code>x</code>, has been re-written in order to provide

            
            slightly more correct results, fixing <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14491">PR#14491</a>, notably in

            
            border cases including when <code>digits &gt;= 16</code>, thanks to

            
            substantial contributions (code and experiments) from Petr

            
            Savicky.  This affects a noticeable amount of numeric output from

            
            <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>.

            
            </p>

            
            </li>

            
            <li><p> A new function <code>grepRaw()</code> has been introduced for

            
            finding subsets of raw vectors. It supports both literal searches

            
            and regular expressions.

            
            </p>

            
            </li>

            
            <li><p> Package <span class="pkg">compiler</span> is now provided as a standard

            
            package.  See <code>?compiler::compile</code> for information on how to

            
            use the compiler.  This package implements a byte code compiler

            
            for <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>: by default the compiler is not used in this release.  See

            
            the &lsquo;R Installation and Administration Manual&rsquo; for how to

            
            compile the base and recommended packages.

            
            </p>

            
            </li>

            
            <li><p> Providing an <code>exportPattern</code> directive in a NAMESPACE

            
            file now causes classes to be exported according to the same

            
            pattern, for example the default from <code>package.skeleton()</code>

            
            to specify all names starting with a letter.  An explicit

            
            directive to <code>exportClassPattern</code> will still over-ride.

            
            </p>

            
            </li>

            
            <li><p> There is an additional marked encoding <code>"bytes"</code> for

            
            character strings.  This is intended to be used for non-ASCII

            
            strings which should be treated as a set of bytes, and never

            
            re-encoded as if they were in the encoding of the current locale:

            
            <code>useBytes = TRUE</code> is automatically selected in functions such

            
            as <code>writeBin()</code>, <code>writeLines()</code>, <code>grep()</code> and

            
            <code>strsplit()</code>.

            
            </p>

            
            <p>Only a few character operations are supported (such as <code>substr()</code>).

            
            </p>

            
            <p>Printing, <code>format()</code> and <code>cat()</code> will represent non-ASCII

            
            bytes in such strings by a <span class="samp">\xab</span> escape.

            
            </p>

            
            </li>

            
            <li><p> The new function <code>removeSource()</code> removes the internally

            
            stored source from a function.

            
            </p>

            
            </li>

            
            <li> <p><code>"srcref"</code> attributes now include two additional

            
            line number values, recording the line numbers in the order they

            
            were parsed.

            
            </p>

            
            </li>

            
            <li><p> New functions have been added for source reference access:

            
            <code>getSrcFilename()</code>, <code>getSrcDirectory()</code>,

            
            <code>getSrcLocation()</code> and <code>getSrcref()</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>Sys.chmod()</code> has an extra argument <code>use_umask</code>

            
            which defaults to true and restricts the file mode by the current

            
            setting of <code>umask</code>.  This means that all the <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> functions

            
            which manipulate file/directory permissions by default respect

            
            <code>umask</code>, notably <code>R CMD INSTALL</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>tempfile()</code> has an extra argument <code>fileext</code> to

            
            create a temporary filename with a specified extension.

            
            (Suggestion and initial implementation by Dirk Eddelbuettel.)

            
            </p>

            
            <p>There are improvements in the way <code>Sweave()</code> and

            
            <code>Stangle()</code> handle non-ASCII vignette sources, especially in

            
            a UTF-8 locale: see &lsquo;Writing R Extensions&rsquo; which now has a

            
            subsection on this topic.

            
            </p>

            
            </li>

            
            <li> <p><code>factanal()</code> now returns the rotation matrix if a

            
            rotation such as <code>"promax"</code> is used, and hence factor

            
            correlations are displayed.  (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=12754">PR#12754</a>.)

            
            </p>

            
            </li>

            
            <li><p> The <code>gctorture2()</code> function provides a more refined

            
            interface to the GC torture process.  Environment variables

            
            <span class="env">R_GCTORTURE</span>, <span class="env">R_GCTORTURE_WAIT</span>, and

            
            <span class="env">R_GCTORTURE_INHIBIT_RELEASE</span> can also be used to control the

            
            GC torture process.

            
            </p>

            
            </li>

            
            <li> <p><code>file.copy(from, to)</code> no longer regards it as an error

            
            to supply a zero-length <code>from</code>: it now simply does nothing.

            
            </p>

            
            </li>

            
            <li> <p><code>rstandard.glm()</code> gains a <code>type</code> argument which can

            
            be used to request standardized Pearson residuals.

            
            </p>

            
            </li>

            
            <li><p> A start on a Turkish translation, thanks to Murat Alkan.

            
            </p>

            
            </li>

            
            <li> <p><code>.libPaths()</code> calls <code>normalizePath(winslash = "/")</code>

            
            on the paths: this helps (usually) to present them in a

            
            user-friendly form and should detect duplicate paths accessed via

            
            different symbolic links.

            
            </p>

            
            </li>

            
            <li> <p><code>download.file()</code> can be now used with external methods

            
            even if there are spaces in the URL or the target filename.

            
            </p>

            
            </li>

            
            <li><p> The first formal argument of <code>.C()</code>, <code>.Fortran()</code>,

            
            <code>.Call()</code> and <code>.External()</code> is now referred to a

            
            <code>.NAME</code> rather than <code>name</code>: however actual calls should

            
            have an unnamed first argument.

            
            </p>

            
            </li></ul>


            <h4>SWEAVE CHANGES</h4>


            <ul>

            
            <li> <p><code>Sweave()</code> has options to produce PNG and JPEG figures,

            
            and to use a custom function to open a graphics device (see

            
            <code>?RweaveLatex</code>).<br />

            
            (Based in part on the contribution of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14418">PR#14418</a>.)

            
            </p>

            
            </li>

            
            <li><p> The default for <code>Sweave()</code> is to produce only PDF

            
            figures (rather than both EPS and PDF).

            
            </p>

            
            </li>

            
            <li><p> Environment variable <span class="env">SWEAVE_OPTIONS</span> can be used to

            
            supply defaults for existing or new options to be applied after

            
            the Sweave driver setup has been run.

            
            </p>

            
            </li>

            
            <li><p> The Sweave manual is now included as a vignette in the

            
            <span class="pkg">utils</span> package.

            
            </p>

            
            </li>

            
            <li> <p><code>Sweave()</code> handles <code>keep.source=TRUE</code> much better:

            
            it could duplicate some lines and omit comments. (Reported by John

            
            Maindonald and others.)

            
            </p>

            
            </li></ul>


            <h4>C-LEVEL FACILITIES</h4>


            <ul>

            
            <li><p> Because they use a C99 interface which a C++ compiler is not

            
            required to support, <code>Rvprintf</code> and <code>REvprintf</code> are only

            
            defined by &lsquo;<span class="file">R_ext/Print.h</span>&rsquo; in C++ code if the macro

            
            <code>R_USE_C99_IN_CXX</code> is defined when it is included.

            
            </p>

            
            </li>

            
            <li> <p><code>pythag</code> duplicated the C99 function <code>hypot</code>.  It

            
            is no longer provided, but is used as a substitute for <code>hypot</code>

            
            in the very unlikely event that the latter is not available.

            
            </p>

            
            </li>

            
            <li> <p><code>R_inspect(obj)</code> and <code>R_inspect3(obj, deep, pvec)</code>

            
            are (hidden) C-level entry points to the internal <code>inspect</code>

            
            function and can be used for C-level debugging (e.g., in conjunction

            
            with the <code>p</code> command in <code>gdb</code>).

            
            </p>

            
            </li>

            
            <li><p> Compiling R with <span class="option">--enable-strict-barrier</span> now also

            
            enables additional checking for use of unprotected objects. In

            
            combination with <code>gctorture()</code> or <code>gctorture2()</code> and a

            
            C-level debugger this can be useful for tracking down memory

            
            protection issues.

            
            </p>

            
            </li></ul>


            <h4>UTILITIES</h4>


            <ul>

            
            <li> <p><code>R CMD Rdiff</code> is now implemented in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> on

            
            Unix-alikes (as it has been on Windows since <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.12.0).

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD build</code> no longer does any cleaning in the

            
            supplied package directory: all the cleaning is done in the copy.

            
            </p>

            
            <p>It has a new option <span class="option">--install-args</span> to pass arguments to

            
            <code>R CMD INSTALL</code> for <span class="option">--build</span> (but not when

            
            installing to rebuild vignettes).

            
            </p>

            
            <p>There is new option, <span class="option">--resave-data</span>, to call

            
            <code>tools::resaveRdaFiles()</code> on the &lsquo;<span class="file">data</span>&rsquo; directory, to

            
            compress tabular files (&lsquo;<span class="file">.tab</span>&rsquo;, &lsquo;<span class="file">.csv</span>&rsquo; etc) and to

            
            convert &lsquo;<span class="file">.R</span>&rsquo; files to &lsquo;<span class="file">.rda</span>&rsquo; files.  The default,

            
            <span class="option">--resave-data=gzip</span>, is to do so in a way compatible even

            
            with years-old versions of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>, but better compression is given by

            
            <span class="option">--resave-data=best</span>, requiring <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> &gt;= 2.10.0.

            
            </p>

            
            <p>It now adds a &lsquo;<span class="file">datalist</span>&rsquo; file for &lsquo;<span class="file">data</span>&rsquo; directories of

            
            more than 1Mb.

            
            </p>

            
            <p>Patterns in &lsquo;<span class="file">.Rbuildignore</span>&rsquo; are now also matched against all

            
            directory names (including those of empty directories).

            
            </p>

            
            <p>There is a new option, <span class="option">--compact-vignettes</span>, to try

            
            reducing the size of PDF files in the &lsquo;<span class="file">inst/doc</span>&rsquo; directory.

            
            Currently this tries <code>qpdf</code>: other options may be used in

            
            future.

            
            </p>

            
            <p>When re-building vignettes and a &lsquo;<span class="file">inst/doc/Makefile</span>&rsquo; file is

            
            found, <code>make clean</code> is run if the makefile has a

            
            <code>clean:</code> target.

            
            </p>

            
            <p>After re-building vignettes the default clean-up operation will

            
            remove any directories (and not just files) created during the

            
            process: e.g., one package created a &lsquo;<span class="file">.R_cache</span>&rsquo; directory.

            
            </p>

            
            <p>Empty directories are now removed unless the option

            
            <span class="option">--keep-empty-dirs</span> is given (and a few packages do

            
            deliberately include empty directories).

            
            </p>

            
            <p>If there is a field <code>BuildVignettes</code> in the package

            
            &lsquo;<span class="file">DESCRIPTION</span>&rsquo; file with a false value, re-building the

            
            vignettes is skipped.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD check</code> now also checks for filenames that are

            
            case-insensitive matches to Windows' reserved file names with

            
            extensions, such as &lsquo;<span class="file">nul.Rd</span>&rsquo;, as these have caused problems

            
            on some Windows systems.

            
            </p>

            
            <p>It checks for inefficiently saved &lsquo;<span class="file">data/*.rda</span>&rsquo; and

            
            &lsquo;<span class="file">data/*.RData</span>&rsquo; files, and reports on those large than 100Kb.

            
            A more complete check (including of the type of compression, but

            
            potentially much slower) can be switched on by setting environment

            
            variable <span class="env">_R_CHECK_COMPACT_DATA2_</span> to <span class="samp">TRUE</span>.

            
            </p>

            
            <p>The types of files in the &lsquo;<span class="file">data</span>&rsquo; directory are now checked,

            
            as packages are <em>still</em> misusing it for non-<span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> data files.

            
            </p>

            
            <p>It now extracts and runs the <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> code for each vignette in a

            
            separate directory and <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> process: this is done in the package's

            
            declared encoding.  Rather than call

            
            <code>tools::checkVignettes()</code>, it calls

            
            <code>tools::buildVignettes()</code> to see if the vignettes can be

            
            re-built as they would be by <code>R CMD build</code>.  Option

            
            <span class="option">--use-valgrind</span> now applies only to these runs, and not

            
            when running code to rebuild the vignettes.  This version does a

            
            much better job of suppressing output from successful vignette

            
            tests.

            
            </p>

            
            <p>The &lsquo;<span class="file">00check.log</span>&rsquo; file is a more complete record of what is

            
            output to &lsquo;<span class="file">stdout</span>&rsquo;: in particular contains more details of

            
            the tests.

            
            </p>

            
            <p>It now checks all syntactically valid Rd usage entries, and warns

            
            about assignments (unless these give the usage of replacement

            
            functions).

            
            </p>

            
            <p>&lsquo;<span class="file">.tar.xz</span>&rsquo; compressed tarballs are now allowed, if

            
            <code>tar</code> supports them (and setting environment variable

            
            <span class="env">TAR</span> to <span class="samp">internal</span> ensures so on all platforms).

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD check</code> now warns if it finds

            
            &lsquo;<span class="file">inst/doc/makefile</span>&rsquo;, and <code>R CMD build</code> renames such a

            
            file to &lsquo;<span class="file">inst/doc/Makefile</span>&rsquo;.

            
            </p>

            
            </li></ul>


            <h4>INSTALLATION</h4>


            <ul>

            
            <li><p> Installing <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> no longer tries to find <code>perl</code>, and

            
            <code>R CMD</code> no longer tries to substitute a full path for

            
            <code>awk</code> nor <code>perl</code> &ndash; this was a legacy from the

            
            days when they were used by <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> itself.  Because a couple of

            
            packages do use <code>awk</code>, it is set as the <code>make</code>

            
            (rather than environment) variable <span class="env">AWK</span>.

            
            </p>

            
            </li>

            
            <li> <p><code>make check</code> will now fail if there are differences

            
            from the reference output when testing package examples and if

            
            environment variable <span class="env">R_STRICT_PACKAGE_CHECK</span> is set to a true

            
            value.

            
            </p>

            
            </li>

            
            <li><p> The C99 double complex type is now required.

            
            </p>

            
            <p>The C99 complex trigonometric functions (such as <span class="samp">csin</span>) are

            
            not currently required (FreeBSD lacks most of them): substitutes

            
            are used if they are missing.

            
            </p>

            
            </li>

            
            <li><p> The C99 system call <span class="samp">va_copy</span> is now required.

            
            </p>

            
            </li>

            
            <li><p> If environment variable <span class="env">R_LD_LIBRARY_PATH</span> is set

            
            during configuration (for example in &lsquo;<span class="file">config.site</span>&rsquo;) it is

            
            used unchanged in file &lsquo;<span class="file">etc/ldpaths</span>&rsquo; rather than being

            
            appended to.

            
            </p>

            
            </li>

            
            <li> <p><code>configure</code> looks for support for OpenMP and if

            
            found compiles <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> with appropriate flags and also makes them

            
            available for use in packages: see &lsquo;Writing R Extensions&rsquo;.

            
            </p>

            
            <p>This is currently experimental, and is only used in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> with a

            
            single thread for <code>colSums()</code> and <code>colMeans()</code>.  Expect

            
            it to be more widely used in later versions of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>.

            
            </p>

            
            <p>This can be disabled by the <span class="option">--disable-openmp</span> flag.

            
            </p>

            
            </li></ul>


            <h4>PACKAGE INSTALLATION</h4>


            <ul>

            
            <li> <p><code>R CMD INSTALL --clean</code> now removes copies of a

            
            &lsquo;<span class="file">src</span>&rsquo; directory which are created when multiple

            
            sub-architectures are in use.  (Following a comment from

            
            Berwin Turlach.)

            
            </p>

            
            </li>

            
            <li><p> File &lsquo;<span class="file">R.css</span>&rsquo; is now installed on a per-package basis

            
            (in the package's &lsquo;<span class="file">html</span>&rsquo; directory) rather than in each

            
            library tree, and this is used for all the HTML pages in the

            
            package.  This helps when installing packages with static HTML

            
            pages for use on a webserver.  It will also allow future versions

            
            of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> to use different stylesheets for the packages they install.

            
            </p>

            
            </li>

            
            <li><p> A top-level file &lsquo;<span class="file">.Rinstignore</span>&rsquo; in the package sources

            
            can list (in the same way as &lsquo;<span class="file">.Rbuildignore</span>&rsquo;) files under

            
            <code>inst</code> that should not be installed.  (Why should there be any

            
            such files?  Because all the files needed to re-build vignettes

            
            need to be under <code>inst/doc</code>, but they may not need to be

            
            installed.)

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD INSTALL</code> has a new option

            
            <span class="option">--compact-docs</span> to compact any PDFs under the

            
            &lsquo;<span class="file">inst/doc</span>&rsquo; directory.  Currently this uses <code>qpdf</code>,

            
            which must be installed (see &lsquo;Writing R Extensions&rsquo;).

            
            </p>

            
            </li>

            
            <li><p> There is a new option <span class="option">--lock</span> which can be used to

            
            cancel the effect of <span class="option">--no-lock</span> or <span class="option">--pkglock</span> earlier

            
            on the command line.

            
            </p>

            
            </li>

            
            <li><p> Option <span class="option">--pkglock</span> can now be used with more than one

            
            package, and is now the default if only one package is specified.

            
            </p>

            
            </li>

            
            <li><p> Argument <code>lock</code> of <code>install.packages()</code> can now be

            
            use for Mac binary installs as well as for Windows ones.  The

            
            value <code>"pkglock"</code> is now accepted, as well as <code>TRUE</code> and

            
            <code>FALSE</code> (the default).

            
            </p>

            
            </li>

            
            <li><p> There is a new option <span class="option">--no-clean-on-error</span> for

            
            <code>R CMD INSTALL</code> to retain a partially installed package for

            
            forensic analysis.

            
            </p>

            
            </li>

            
            <li><p> Packages with names ending in &lsquo;<span class="file">.</span>&rsquo; are not portable

            
            since Windows does not work correctly with such directory names.

            
            This is now warned about in <code>R CMD check</code>, and will not be

            
            allowed in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.14.x.

            
            </p>

            
            </li>

            
            <li><p> The vignette indices are more comprehensive (in the style of

            
            <code>browseVignetttes()</code>).

            
            </p>

            
            </li></ul>


            <h4>DEPRECATED &amp; DEFUNCT</h4>


            <ul>

            
            <li> <p><code>require(save = TRUE)</code> is defunct, and use of the

            
            <code>save</code> argument is deprecated.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD check --no-latex</code> is defunct: use

            
            <span class="option">--no-manual</span> instead.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD Sd2Rd</code> is defunct.

            
            </p>

            
            </li>

            
            <li><p> The <code>gamma</code> argument to <code>hsv()</code>,

            
            <code>rainbow()</code>, and <code>rgb2hsv()</code> is deprecated

            
            and no longer has any effect.

            
            </p>

            
            </li>

            
            <li><p> The previous options for <code>R CMD build --binary</code>

            
            (<span class="option">--auto-zip</span>, <span class="option">--use-zip-data</span> and

            
            <span class="option">--no-docs</span>) are deprecated (or defunct):

            
            use the new option <span class="option">--install-args</span> instead.

            
            </p>

            
            </li>

            
            <li><p> When a character value is used for the <code>EXPR</code>

            
            argument in <code>switch()</code>, only a single unnamed alternative

            
            value is now allowed.

            
            </p>

            
            </li>

            
            <li><p> The wrapper <code>utils::link.html.help()</code> is no longer

            
            available.

            
            </p>

            
            </li>

            
            <li><p> Zip-ing data sets in packages (and hence <code>R CMD

            
            	INSTALL</code> options <span class="option">--use-zip-data</span> and <span class="option">--auto-zip</span>, as

            
            well as the <span class="samp">ZipData: yes</span> field in a <code>DESCRIPTION</code> file)

            
            is defunct.

            
            </p>

            
            <p>Installed packages with zip-ed data sets can still be used, but a

            
            warning that they should be re-installed will be given.

            
            </p>

            
            </li>

            
            <li><p> The &lsquo;experimental&rsquo; alternative specification of a

            
            namespace via <code>.Export()</code> etc is now defunct.

            
            </p>

            
            </li>

            
            <li><p> The option <span class="option">--unsafe</span> to <code>R CMD INSTALL</code> is

            
            deprecated: use the identical option <span class="option">--no-lock</span> instead.

            
            </p>

            
            </li>

            
            <li><p> The entry point <code>pythag</code> in &lsquo;<span class="file">Rmath.h</span>&rsquo; is deprecated

            
            in favour of the C99 function <code>hypot</code>.  A wrapper for

            
            <code>hypot</code> is provided for <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.13.x only.

            
            </p>

            
            </li>

            
            <li><p> Direct access to the <code>"source"</code> attribute of functions

            
            is deprecated; use <code>deparse(fn, control="useSource")</code> to access

            
            it, and <code>removeSource(fn)</code> to remove it.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD build --binary</code> is now formally deprecated:

            
            <code>R CMD INSTALL --build</code> has long been the preferred

            
            alternative.

            
            </p>

            
            </li>

            
            <li><p> Single-character package names are deprecated (and <span class="pkg">R</span>

            
            is already disallowed to avoid confusion in <span class="samp">Depends:</span>

            
            fields).

            
            </p>

            
            </li></ul>


            <h4>BUG FIXES</h4>


            <ul>

            
            <li> <p><code>drop.terms</code> and the <code>[</code> method for class

            
            <code>"terms"</code> no longer add back an intercept.  (Reported by

            
            Niels Hansen.)

            
            </p>

            
            </li>

            
            <li> <p><code>aggregate</code> preserves the class of a column (e.g., a

            
            date) under some circumstances where it discarded the class

            
            previously.

            
            </p>

            
            </li>

            
            <li> <p><code>p.adjust()</code> now always returns a vector result, as

            
            documented.  In previous versions it copied attributes (such as

            
            dimensions) from the <code>p</code> argument: now it only copies names.

            
            </p>

            
            </li>

            
            <li><p> On PDF and PostScript devices, a line width of zero was

            
            recorded verbatim and this caused problems for some viewers

            
            (a very thin line combined with a non-solid line dash pattern

            
            could also cause a problem).  On these devices, the line width is

            
            now limited at 0.01 and for very thin lines with complex dash

            
            patterns the device may force the line dash pattern to be solid.

            
            (Reported by Jari Oksanen.)

            
            </p>

            
            </li>

            
            <li><p> The <code>str()</code> method for class <code>"POSIXt"</code> now gives

            
            sensible output for 0-length input.

            
            </p>

            
            </li>

            
            <li><p> The one- and two-argument complex maths functions failed to

            
            warn if NAs were generated (as their numeric analogues do).

            
            </p>

            
            </li>

            
            <li><p> Added <code>.requireCachedGenerics</code> to the <code>dont.mind</code>

            
            list for <code>library()</code> to avoid warnings about duplicates.

            
            </p>

            
            </li>

            
            <li> <p><code>$&lt;-.data.frame</code> messed with the class attribute,

            
            breaking any S4 subclass.  The S4 <code>data.frame</code> class now has its own

            
            <code>$&lt;-</code> method, and turns dispatch on for this primitive.

            
            </p>

            
            </li>

            
            <li> <p><code>Map()</code> did not look up a character argument <code>f</code>

            
            in the correct frame, thanks to lazy evaluation.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14495">PR#14495</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>file.copy()</code> did not tilde-expand <code>from</code> and <code>to</code>

            
            when <code>to</code> was a directory.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14507">PR#14507</a>)

            
            </p>

            
            </li>

            
            <li><p> It was possible (but very rare) for the loading test in

            
            <code>R CMD INSTALL</code> to crash a child <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> process and so leave

            
            around a lock directory and a partially installed package.  That

            
            test is now done in a separate process.

            
            </p>

            
            </li>

            
            <li> <p><code>plot(&lt;formula&gt;, data=&lt;matrix&gt;,..)</code> now works in more

            
            cases; similarly for <code>points()</code>, <code>lines()</code> and

            
            <code>text()</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>edit.default()</code> contained a manual dispatch for matrices

            
            (the <code>"matrix"</code> class didn't really exist when it was written).

            
            This caused an infinite recursion in the no-GUI case and has now

            
            been removed.

            
            </p>

            
            </li>

            
            <li> <p><code>data.frame(check.rows = TRUE)</code> sometimes worked when

            
            it should have detected an error.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14530">PR#14530</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>scan(sep= , strip.white=TRUE)</code> sometimes stripped

            
            trailing spaces from within quoted strings.  (The real bug in

            
            <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14522">PR#14522</a>.)

            
            </p>

            
            </li>

            
            <li><p> The rank-correlation methods for <code>cor()</code> and

            
            <code>cov()</code> with <code>use = "complete.obs"</code> computed the ranks

            
            before removing missing values, whereas the documentation implied

            
            incomplete cases were removed first.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14488">PR#14488</a>)

            
            </p>

            
            <p>They also failed for 1-row matrices.

            
            </p>

            
            </li>

            
            <li><p> The perpendicular adjustment used in placing text and

            
            expressions in the margins of plots was not scaled by

            
            <code>par("mex")</code>. (Part of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14532">PR#14532</a>.)

            
            </p>

            
            </li>

            
            <li><p> Quartz Cocoa device now catches any Cocoa exceptions that

            
            occur during the creation of the device window to prevent crashes.

            
            It also imposes a limit of 144 ft^2 on the area used by a window

            
            to catch user errors (unit misinterpretation) early.

            
            </p>

            
            </li>

            
            <li><p> The browser (invoked by <code>debug()</code>, <code>browser()</code>

            
            or otherwise) would display attributes such as <code>"wholeSrcref"</code>

            
            that were intended for internal use only.

            
            </p>

            
            </li>

            
            <li><p> R's internal filename completion now properly handles

            
            filenames with spaces in them even when the readline library is

            
            used.  This resolves <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14452">PR#14452</a> provided the internal filename

            
            completion is used (e.g., by setting <code>rc.settings(files =

            
            	TRUE)</code>).

            
            </p>

            
            </li>

            
            <li><p> Inside <code>uniroot(f, ...)</code>, <code>-Inf</code> function values

            
            are now replaced by a maximally <b>negative</b> value.

            
            </p>

            
            </li>

            
            <li> <p><code>rowsum()</code> could silently over/underflow on integer

            
            inputs (reported by Bill Dunlap).

            
            </p>

            
            </li>

            
            <li> <p><code>as.matrix()</code> did not handle <code>"dist"</code> objects with

            
            zero rows.

            
            </p>

            
            </li></ul>


            <h3><img class="toplogo" src="../help/figures/../../html/Rlogo.svg" alt="[R logo]" /> CHANGES IN R VERSION 2.12.2 patched</h3>


            <h4>NEW FEATURES</h4>


            <ul>

            
            <li> <p><code>max()</code> and <code>min()</code> work harder to ensure that

            
            <code>NA</code> has precedence over <code>NaN</code>,

            
            so e.g. <code>min(NaN, NA)</code> is <code>NA</code>.

            
            (This was not previously documented except

            
            for within a single numeric vector, where compiler optimizations

            
            often defeated the code.)

            
            </p>

            
            </li></ul>


            <h4>BUG FIXES</h4>


            <ul>

            
            <li><p> A change to the C function <span class="samp">R_tryEval</span> had broken error

            
            messages in S4 method selection; the error message is now printed.

            
            </p>

            
            </li>

            
            <li><p> PDF output with a non-RGB color model used RGB for the line

            
            stroke color.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14511">PR#14511</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>stats4::BIC()</code> assumed without checking that an object

            
            of class <code>"logLik"</code> has an <code>"nobs"</code> attribute:

            
            <code>glm()</code> fits did not and so <code>BIC()</code> failed for them.

            
            </p>

            
            </li>

            
            <li><p> In some circumstances a one-sided <code>mantelhaen.test()</code>

            
            reported the p-value for the wrong tail.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14514">PR#14514</a>)

            
            </p>

            
            </li>

            
            <li><p> Passing the invalid value <code>lty = NULL</code> to <code>axis()</code>

            
            sent an invalid value to the graphics device, and might cause the

            
            device to segfault.

            
            </p>

            
            </li>

            
            <li> <p><code>Sweave()</code> with <code>concordance=TRUE</code> could lead to

            
            invalid PDF files; &lsquo;<span class="file">Sweave.sty</span>&rsquo; has been updated to avoid

            
            this.

            
            </p>

            
            </li>

            
            <li><p> Non-ASCII characters in the titles of help pages were

            
            not rendered properly in some locales, and could cause errors

            
            or warnings.

            
            </p>

            
            </li>

            
            <li> <p><code>checkRd()</code> gave a spurious error if the <code>\href</code>

            
            macro was used.

            
            </p>

            
            </li></ul>


            <h3><img class="toplogo" src="../help/figures/../../html/Rlogo.svg" alt="[R logo]" /> CHANGES IN R VERSION 2.12.2</h3>


            <h4>SIGNIFICANT USER-VISIBLE CHANGES</h4>


            <ul>

            
            <li><p> Complex arithmetic (notably <code>z^n</code> for complex <code>z</code>

            
            and integer <code>n</code>) gave incorrect results since <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.10.0 on

            
            platforms without C99 complex support.  This and some

            
            lesser issues in trigonometric functions have been corrected.

            
            </p>

            
            <p>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 <code>gcc 4.5.x</code> at the default <code>-O2</code> optimization

            
            (but not at <code>-O</code>).

            
            </p>

            
            </li>

            
            <li><p> There is a workaround for crashes seen with several packages

            
            on systems using <span class="samp">zlib 1.2.5</span>: see the INSTALLATION section.

            
            </p>

            
            </li></ul>


            <h4>NEW FEATURES</h4>


            <ul>

            
            <li><p> PCRE has been updated to 8.12 (two bug-fix releases since 8.10).

            
            </p>

            
            </li>

            
            <li> <p><code>rep()</code>, <code>seq()</code>, <code>seq.int()</code> and

            
            <code>seq_len()</code> report more often when the first element is taken

            
            of an argument of incorrect length.

            
            </p>

            
            </li>

            
            <li><p> The Cocoa back-end for the <code>quartz()</code> graphics device

            
            on Mac OS X provides a way to disable event loop processing

            
            temporarily (useful, e.g., for forked instances of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>).

            
            </p>

            
            </li>

            
            <li> <p><code>kernel()</code>'s default for <code>m</code> was not appropriate

            
            if <code>coef</code> was a set of coefficients.  (Reported by Pierre

            
            Chausse.)

            
            </p>

            
            </li>

            
            <li> <p><code>bug.report()</code> has been updated for the current <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> bug

            
            tracker, which does not accept emailed submissions.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD check</code> now checks for the correct use of

            
            <span class="samp">$(LAPACK_LIBS)</span> (as well as <span class="samp">$(BLAS_LIBS)</span>), since

            
            several CRAN recent submissions have ignored &lsquo;Writing R

            
            Extensions&rsquo;.

            
            </p>

            
            </li></ul>


            <h4>INSTALLATION</h4>


            <ul>

            
            <li><p> The <span class="samp">zlib</span> sources in the distribution are now built

            
            with all symbols remapped: this is intended to avoid problems seen

            
            with packages such as <a href="https://CRAN.R-project.org/package=XML"><span class="pkg">XML</span></a> and <a href="https://CRAN.R-project.org/package=rggobi"><span class="pkg">rggobi</span></a> which link to

            
            &lsquo;<span class="file">zlib.so.1</span>&rsquo; on systems using <span class="samp">zlib 1.2.5</span>.

            
            </p>

            
            </li>

            
            <li><p> The default for <span class="env">FFLAGS</span> and <span class="env">FCFLAGS</span> with

            
            <code>gfortran</code> on x86_64 Linux has been changed back to <span class="samp">-g

            
            	-O2</span>:  however, setting <span class="samp">-g -O</span> may still be needed for

            
            <code>gfortran 4.3.x</code>.

            
            </p>

            
            </li></ul>


            <h4>PACKAGE INSTALLATION</h4>


            <ul>

            
            <li><p> A <span class="samp">LazyDataCompression</span> field in the &lsquo;<span class="file">DESCRIPTION</span>&rsquo;

            
            file will be used to set the value for the

            
            <span class="option">--data-compress</span> option of <code>R CMD INSTALL</code>.

            
            </p>

            
            </li>

            
            <li><p> Files &lsquo;<span class="file">R/sysdata.rda</span>&rsquo; of more than 1Mb are now stored

            
            in the lazyload database using <code>xz</code> compression: this for

            
            example halves the installed size of package <a href="https://CRAN.R-project.org/package=Imap"><span class="pkg">Imap</span></a>.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD INSTALL</code> now ensures that directories

            
            installed from &lsquo;<span class="file">inst</span>&rsquo; have search permission for everyone.

            
            </p>

            
            <p>It no longer installs files &lsquo;<span class="file">inst/doc/Rplots.ps</span>&rsquo; and

            
            &lsquo;<span class="file">inst/doc/Rplots.pdf</span>&rsquo;.  These are almost certainly left-overs

            
            from <code>Sweave</code> runs, and are often large.

            
            </p>

            
            </li></ul>


            <h4>DEPRECATED &amp; DEFUNCT</h4>


            <ul>

            
            <li><p> The &lsquo;experimental&rsquo; alternative specification of a

            
            namespace via <code>.Export()</code> etc is now deprecated.

            
            </p>

            
            </li>

            
            <li> <p><code>zip.file.extract()</code> is now deprecated.

            
            </p>

            
            </li>

            
            <li><p> Zip-ing data sets in packages (and hence <code>R CMD

            
            	INSTALL --use-zip-data</code> and the <span class="samp">ZipData: yes</span> field in a

            
            <code>DESCRIPTION</code> file) is deprecated: using efficiently

            
            compressed &lsquo;<span class="file">.rda</span>&rsquo; images and lazy-loading of data has

            
            superseded it.

            
            </p>

            
            </li></ul>


            <h4>BUG FIXES</h4>


            <ul>

            
            <li> <p><code>identical()</code> 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).

            
            </p>

            
            </li>

            
            <li><p> If the filename extension (usually &lsquo;<span class="file">.Rnw</span>&rsquo;) was not

            
            included in a call to <code>Sweave()</code>, source references would not

            
            work properly and the <code>keep.source</code> option failed.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14459">PR#14459</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>format.data.frame()</code> now keeps zero character column names.

            
            </p>

            
            </li>

            
            <li> <p><code>pretty(x)</code> no longer raises an error when <code>x</code>

            
            contains solely non-finite values. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14468">PR#14468</a>)

            
            </p>

            
            </li>

            
            <li><p> The <code>plot.TukeyHSD()</code> function now uses a line width of

            
            0.5 for its reference lines rather than <span class="samp">lwd = 0</span> (which

            
            caused problems for some PDF and PostScript viewers).

            
            </p>

            
            </li>

            
            <li><p> The <code>big.mark</code> argument to <code>prettyNum()</code>,

            
            <code>format()</code>, etc. was inserted reversed if it was more than

            
            one character long.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD check</code> failed to check the filenames under

            
            &lsquo;<span class="file">man</span>&rsquo; for Windows' reserved names.

            
            </p>

            
            </li>

            
            <li><p> The <code>"Date"</code> and <code>"POSIXt"</code> methods for

            
            <code>seq()</code> could overshoot when <code>to</code> was supplied and

            
            <code>by</code> was specified in months or years.

            
            </p>

            
            </li>

            
            <li><p> The internal method of <code>untar()</code> now restores hard

            
            links as file copies rather than symbolic links (which did not

            
            work for cross-directory links).

            
            </p>

            
            </li>

            
            <li> <p><code>unzip()</code> 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 <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14462">PR#14462</a> created one.)

            
            </p>

            
            </li>

            
            <li> <p><code>combn(n, m)</code> now behaves more regularly for the border

            
            case <i>m = 0</i>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14473">PR#14473</a>)

            
            </p>

            
            </li>

            
            <li><p> The rendering of numbers in plotmath expressions (e.g.,

            
            <code>expression(10^2)</code>) used the current settings for conversion

            
            to strings rather than setting the defaults, and so could be

            
            affected by what has been done before.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14477">PR#14477</a>)

            
            </p>

            
            </li>

            
            <li><p> The methods of <code>napredict()</code> and <code>naresid()</code> for

            
            <code>na.action = na.exclude</code> fits did not work correctly in the

            
            very rare event that every case had been omitted in the fit.

            
            (Reported by Simon Wood.)

            
            </p>

            
            </li>

            
            <li> <p><code>weighted.residuals(drop0=TRUE)</code> returned a vector when

            
            the residuals were a matrix (e.g., those of class <code>"mlm"</code>).

            
            (Reported by Bill Dunlap.)

            
            </p>

            
            </li>

            
            <li><p> Package HTML index files &lsquo;<span class="file">&lt;pkg&gt;/html/00Index.html</span>&rsquo; were

            
            generated with a stylesheet reference that was not correct for

            
            static browsing in libraries.

            
            </p>

            
            </li>

            
            <li> <p><code>ccf(na.action = na.pass)</code> was not implemented.

            
            </p>

            
            </li>

            
            <li><p> The parser accepted some incorrect numeric constants,

            
            e.g. <code>20x2</code>.  (Reported by Olaf Mersmann.)

            
            </p>

            
            </li>

            
            <li> <p><code>format(*, zero.print)</code> did not always replace the full

            
            zero parts.

            
            </p>

            
            </li>

            
            <li><p> Fixes for subsetting or subassignment of <code>"raster"</code>

            
            objects when not both <code>i</code> and <code>j</code> are specified.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD INSTALL</code> was not always respecting the

            
            <span class="samp">ZipData: yes</span> field of a &lsquo;<span class="file">DESCRIPTION</span>&rsquo; file (although

            
            this is frequently incorrectly specified for packages with no data

            
            or which specify lazy-loading of data).

            
            </p>

            
            <p><code>R CMD INSTALL --use-zip-data</code> was incorrectly implemented

            
            as <span class="option">--use-zipdata</span> since <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.9.0.

            
            </p>

            
            </li>

            
            <li> <p><code>source(file, echo=TRUE)</code> could fail if the file

            
            contained <span class="samp">#line</span> directives.  It now recovers more gracefully, but

            
            may still display the wrong line if the directive gives incorrect

            
            information.

            
            </p>

            
            </li>

            
            <li> <p><code>atan(1i)</code> returned <code>NaN+Infi</code> (rather than

            
            <code>0+Infi</code>) on platforms without C99 complex support.

            
            </p>

            
            </li>

            
            <li> <p><code>library()</code> failed to cache S4 metadata (unlike

            
            <code>loadNamespace()</code>) causing failures in S4-using packages

            
            without a namespace (e.g., those using reference classes).

            
            </p>

            
            </li>

            
            <li><p> The function <code>qlogis(lp, log.p=TRUE)</code> no longer

            
            prematurely overflows to <code>Inf</code> when exp(lp) is close to 1.

            
            </p>

            
            </li>

            
            <li><p> Updating S4 methods for a group generic function requires

            
            resetting the methods tables for the members of the group (patch

            
            contributed by Martin Morgan).

            
            </p>

            
            </li>

            
            <li><p> In some circumstances (including for package <a href="https://CRAN.R-project.org/package=XML"><span class="pkg">XML</span></a>),

            
            <code>R CMD INSTALL</code> installed version-control directories from

            
            source packages.

            
            </p>

            
            </li>

            
            <li><p> Added <code>PROTECT</code> calls to some constructed expressions

            
            used in C level <code>eval</code> calls.

            
            </p>

            
            </li>

            
            <li> <p><code>utils:::create.post()</code> (used by <code>bug.report()</code>

            
            and <code>help.request()</code>) failed to quote arguments to the

            
            mailer, and so often failed.

            
            </p>

            
            </li>

            
            <li> <p><code>bug.report()</code> was naive about how to extract

            
            maintainer email addresses from package descriptions, so would

            
            often try mailing to incorrect addresses.

            
            </p>

            
            </li>

            
            <li> <p><code>debugger()</code> could fail to read the environment of a

            
            call to a function with a <code>...</code> argument.  (Reported by

            
            Charlie Roosen.)

            
            </p>

            
            </li>

            
            <li> <p><code>prettyNum(c(1i, NA), drop0=TRUE)</code> or

            
            <code>str(NA_complex_)</code> now work correctly.

            
            </p>

            
            </li></ul>


            <h3><img class="toplogo" src="../help/figures/../../html/Rlogo.svg" alt="[R logo]" /> CHANGES IN R VERSION 2.12.1</h3>


            <h4>NEW FEATURES</h4>


            <ul>

            
            <li><p> The DVI/PDF reference manual now includes the help pages for

            
            all the standard packages: <span class="pkg">splines</span>, <span class="pkg">stats4</span> and

            
            <span class="pkg">tcltk</span> were previously omitted (intentionally).

            
            </p>

            
            </li>

            
            <li> <p><a href="http://www.rforge.net">http://www.rforge.net</a> has been added to the default

            
            set of repositories known to <code>setRepositories()</code>.

            
            </p>

            
            </li>

            
            <li><p> xz-utils has been updated to version 5.0.0.

            
            </p>

            
            </li>

            
            <li> <p><code>reshape()</code> now makes use of <code>sep</code> when forming

            
            names during reshaping to wide format.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14435">PR#14435</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>legend()</code> allows the length of lines to be set by the

            
            end user <em>via</em> the new argument <code>seg.len</code>.

            
            </p>

            
            </li>

            
            <li><p> New S4 reference class utility methods <code>copy()</code>,

            
            <code>field()</code>, <code>getRefClass()</code> and <code>getClass()</code> have

            
            been added to package <span class="pkg">methods</span>.

            
            </p>

            
            </li>

            
            <li><p> When a character value is used for the <code>EXPR</code>

            
            argument in <code>switch()</code>, a warning is given if more than

            
            one unnamed alternative value is given.  This will become an

            
            error in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.13.0.

            
            </p>

            
            </li>

            
            <li> <p><code>StructTS(type = "BSM")</code> now allows series with just

            
            two seasons.  (Reported by Birgit Erni.)

            
            </p>

            
            </li></ul>


            <h4>INSTALLATION</h4>


            <ul>

            
            <li><p> 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.

            
            </p>

            
            </li>

            
            <li><p> Variable <span class="env">FCLIBS</span> 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.)

            
            </p>

            
            </li></ul>


            <h4>BUG FIXES</h4>


            <ul>

            
            <li> <p><code>seq.int()</code> no longer sometimes evaluates arguments

            
            twice.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14388">PR#14388</a>)

            
            </p>

            
            </li>

            
            <li><p> The <code>data.frame</code> method of <code>format()</code> failed if a

            
            column name was longer than 256 bytes (the maximum length allowed

            
            for an <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> name).

            
            </p>

            
            </li>

            
            <li> <p><code>predict(&lt;lm object&gt;, type ="terms", ...)</code> failed if

            
            both <code>terms</code> and <code>interval</code> were specified.  (Reported

            
            by Bill Dunlap.)

            
            </p>

            
            <p>Also, if <code>se.fit = TRUE</code> the standard errors were reported

            
            for all terms, not just those selected by a non-null <code>terms</code>.

            
            </p>

            
            </li>

            
            <li><p> The TRE regular expressions engine could terminate <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> rather

            
            than give an error when given certain invalid regular expressions.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14398">PR#14398</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>cmdscale(eig = TRUE)</code> was documented to return <i>n-1</i>

            
            eigenvalues but in fact only returned <code>k</code>.  It now returns

            
            all <i>n</i> eigenvalues.

            
            </p>

            
            <p><code>cmdscale(add = TRUE)</code> 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 <code>ac</code>).

            
            </p>

            
            </li>

            
            <li> <p><code>promptClass()</code> in package <span class="pkg">methods</span> now works for

            
            reference classes and gives a suitably specialized skeleton of

            
            documentation.

            
            </p>

            
            <p>Also, <code>callSuper()</code> now works via the <code>methods()</code>

            
            invocation as well as for initially specified methods.

            
            </p>

            
            </li>

            
            <li> <p><code>download.file()</code> could leave the destination file open

            
            if the URL was not able to be opened.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14414">PR#14414</a>)

            
            </p>

            
            </li>

            
            <li><p> Assignment of an environment to functions or as an attribute

            
            to other objects now works for S4 subclasses of <code>"environment"</code>.

            
            </p>

            
            </li>

            
            <li><p> Use of <span class="samp">[[&lt;-</span> for S4 subclasses of

            
            <code>"environment"</code> generated an infinite recursion from the

            
            method.  The method has been replaced by internal code.

            
            </p>

            
            </li>

            
            <li><p> In a reference class S4 method, <code>callSuper()</code> now works in

            
            <code>initialize()</code> methods when there is no explicit superclass

            
            method.

            
            </p>

            
            </li>

            
            <li> <p><span class="samp">!</span> dropped attributes such as names and dimensions from a

            
            length-zero argument.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14424">PR#14424</a>)

            
            </p>

            
            </li>

            
            <li><p> When <code>list2env()</code> created an environment it was missing

            
            a <code>PROTECT</code> call and so was vulnerable to garbage collection.

            
            </p>

            
            </li>

            
            <li> <p><code>Sweave()</code> with <code>keep.source=TRUE</code> dropped

            
            comments at the start and end of code chunks.  It could also

            
            fail when <span class="samp">\SweaveInput</span> was combined with named chunks.

            
            </p>

            
            </li>

            
            <li><p> The Fortran code used by <code>nls(algorithm = "port")</code>

            
            could infinite-loop when compiled with high optimization on a

            
            modern version of <code>gcc</code>, and <code>SAFE_FFLAGS</code> is now used

            
            to make this less likely.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14427">PR#14427</a>, seen with 32-bit Windows

            
            using <code>gcc 4.5.0</code> used from <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.12.0.)

            
            </p>

            
            </li>

            
            <li> <p><code>sapply()</code> with default <code>simplify = TRUE</code> and

            
            <code>mapply()</code> with default <code>SIMPLIFY = TRUE</code> wrongly

            
            simplified language-like results, as, e.g., in

            
            <code>mapply(1:2, c(3,7), FUN = function(i,j) call(':',i,j))</code>.

            
            </p>

            
            </li>

            
            <li><p> Backreferences to undefined patterns in

            
            <code>[g]sub(pcre = TRUE)</code> could cause a segfault.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14431">PR#14431</a>)

            
            </p>

            
            </li>

            
            <li><p> The <code>format()</code> (and hence the <code>print()</code>) method

            
            for class <code>"Date"</code> rounded fractional dates towards zero: it

            
            now always rounds them down.

            
            </p>

            
            </li>

            
            <li><p> Reference S4 class creation could generate ambiguous

            
            inheritance patterns under very special circumstances.

            
            </p>

            
            </li>

            
            <li> <p><span class="samp">[[&lt;-</span> turned S4 subclasses of <code>"environment"</code> into

            
            plain environments.

            
            </p>

            
            </li>

            
            <li><p> Long titles for help pages were truncated in package indices

            
            and a few other places.

            
            </p>

            
            </li>

            
            <li><p> Additional utilities now work correctly with S4 subclasses of

            
            <code>"environment"</code> (<code>rm</code>, locking tools and active

            
            bindings).

            
            </p>

            
            </li>

            
            <li> <p><code>spec.ar()</code> now also work for the <code>"ols"</code> method.

            
            (Reported by Hans-Ruedi Kuensch.)

            
            </p>

            
            </li>

            
            <li><p> The initialization of objects from S4 subclasses of

            
            <code>"environment"</code> now allocates a new environment object.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD check</code> has more protection against (probably

            
            erroneous) example or test output which is invalid in the current

            
            locale.

            
            </p>

            
            </li>

            
            <li> <p><code>qr.X()</code> with column names and pivoting now also pivots

            
            the column names.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14438">PR#14438</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>unit.pmax()</code> and <code>unit.pmin()</code> in package

            
            <span class="pkg">grid</span> gave incorrect results when all inputs were of length 1.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14443">PR#14443</a>)

            
            </p>

            
            </li>

            
            <li><p> The parser for &lsquo;<span class="file">NAMESPACE</span>&rsquo; 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.)

            
            </p>

            
            </li>

            
            <li><p> Fix for subsetting of <code>"raster"</code> objects when only one

            
            of <code>i</code> or <code>j</code> is specified.

            
            </p>

            
            </li>

            
            <li> <p><code>grid.raster()</code> in package <span class="pkg">grid</span> did not accept

            
            <code>"nativeRaster"</code> objects (like <code>rasterImage()</code> does).

            
            </p>

            
            </li>

            
            <li><p> Rendering raster images in PDF output was resetting the

            
            clipping region.

            
            </p>

            
            </li>

            
            <li><p> Rendering of raster images on cairo X11 device was wrong,

            
            particularly when a small image was being scaled up using

            
            interpolation.

            
            </p>

            
            <p>With cairo &lt; 1.6, will be better than before, though still a

            
            little clunky.  With cairo &gt;= 1.6, should be sweet as.

            
            </p>

            
            </li>

            
            <li><p> Several bugs fixed in <code>read.DIF()</code>:  single column

            
            inputs caused errors, cells marked as <code>"character"</code> could

            
            be converted to other types, and (in Windows) copying from the

            
            clipboard failed.

            
            </p>

            
            </li></ul>


            <h3><img class="toplogo" src="../help/figures/../../html/Rlogo.svg" alt="[R logo]" /> CHANGES IN R VERSION 2.12.0</h3>


            <h4>NEW FEATURES</h4>


            <ul>

            
            <li><p> Reading a package's &lsquo;<span class="file">CITATION</span>&rsquo; file now defaults to

            
            ASCII rather than Latin-1: a package with a non-ASCII

            
            &lsquo;<span class="file">CITATION</span>&rsquo; file should declare an encoding in its

            
            &lsquo;<span class="file">DESCRIPTION</span>&rsquo; file and use that encoding for the

            
            &lsquo;<span class="file">CITATION</span>&rsquo; file.

            
            </p>

            
            </li>

            
            <li> <p><code>difftime()</code> now defaults to the <code>"tzone"</code>

            
            attribute of <code>"POSIXlt"</code> objects rather than to the current

            
            timezone as set by the default for the <code>tz</code> argument.  (Wish

            
            of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14182">PR#14182</a>.)

            
            </p>

            
            </li>

            
            <li> <p><code>pretty()</code> is now generic, with new methods for

            
            <code>"Date"</code> and <code>"POSIXt"</code> classes (based on code

            
            contributed by Felix Andrews).

            
            </p>

            
            </li>

            
            <li> <p><code>unique()</code> and <code>match()</code> are now faster on

            
            character vectors where all elements are in the global <code>CHARSXP</code>

            
            cache and have unmarked encoding (ASCII).  Thanks to Matthew

            
            Dowle for suggesting improvements to the way the hash code is

            
            generated in &lsquo;<span class="file">unique.c</span>&rsquo;.

            
            </p>

            
            </li>

            
            <li><p> The <code>enquote()</code> utility, in use internally, is exported now.

            
            </p>

            
            </li>

            
            <li> <p><code>.C()</code> and <code>.Fortran()</code> now map non-zero return

            
            values (other than <code>NA_LOGICAL</code>) for logical vectors to

            
            <code>TRUE</code>: it has been an implicit assumption that they are

            
            treated as true.

            
            </p>

            
            </li>

            
            <li><p> The <code>print()</code> methods for <code>"glm"</code> and <code>"lm"</code>

            
            objects now insert linebreaks in long calls in the same way that

            
            the <code>print()</code> methods for <code>"summary.[g]lm"</code> objects

            
            have long done.  This does change the layout of the examples for

            
            a number of packages, e.g. <a href="https://CRAN.R-project.org/package=MASS"><span class="pkg">MASS</span></a>.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14250">PR#14250</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>constrOptim()</code> can now be used with method

            
            <code>"SANN"</code>.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14245">PR#14245</a>)

            
            </p>

            
            <p>It gains an argument <code>hessian</code> to be passed to

            
            <code>optim()</code>, which allows all the <code>...</code> arguments to be

            
            intended for <code>f()</code> and <code>grad()</code>.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14071">PR#14071</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>curve()</code> now allows <code>expr</code> to be an object of

            
            mode <code>"expression"</code> as well as <code>"call"</code> and

            
            <code>"function"</code>.

            
            </p>

            
            </li>

            
            <li><p> The <code>"POSIX[cl]t"</code> methods for <code>Axis()</code> have been

            
            replaced by a single method for <code>"POSIXt"</code>.

            
            </p>

            
            <p>There are no longer separate <code>plot()</code> methods for

            
            <code>"POSIX[cl]t"</code> and <code>"Date"</code>: the default method has

            
            been able to handle those classes for a long time.  This

            
            <em>inter alia</em> allows a single date-time object to be

            
            supplied, the wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14016">PR#14016</a>.

            
            </p>

            
            <p>The methods had a different default (<code>""</code>) for <code>xlab</code>.

            
            </p>

            
            </li>

            
            <li><p> Classes <code>"POSIXct"</code>, <code>"POSIXlt"</code> and

            
            <code>"difftime"</code> have generators <code>.POSIXct()</code>,

            
            <code>.POSIXlt()</code> and <code>.difftime()</code>.  Package authors are

            
            advised to make use of them (they are available from <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.11.0) to

            
            proof against planned future changes to the classes.

            
            </p>

            
            <p>The ordering of the classes has been changed, so <code>"POSIXt"</code>

            
            is now the second class.  See the document &lsquo;Updating

            
            packages for changes in R 2.12.x&rsquo; on

            
            <a href="http://developer.r-project.org">http://developer.r-project.org</a> for the consequences for a

            
            handful of CRAN packages.

            
            </p>

            
            </li>

            
            <li><p> The <code>"POSIXct"</code> method of <code>as.Date()</code> allows a

            
            timezone to be specified (but still defaults to UTC).

            
            </p>

            
            </li>

            
            <li><p> New <code>list2env()</code> utility function as an inverse of

            
            <code>as.list(&lt;environment&gt;)</code> and for fast multi-<code>assign()</code>

            
            to existing environment.  <code>as.environment()</code> is now generic

            
            and uses <code>list2env()</code> as list method.

            
            </p>

            
            </li>

            
            <li><p> There are several small changes to output which &lsquo;zap&rsquo;

            
            small numbers, e.g. in printing quantiles of residuals in

            
            summaries from <code>"lm"</code> and <code>"glm"</code> fits, and in test

            
            statistics in <code>print.anova()</code>.

            
            </p>

            
            </li>

            
            <li><p> Special names such as <code>"dim"</code>, <code>"names"</code>, etc, are

            
            now allowed as slot names of S4 classes, with <code>"class"</code> the

            
            only remaining exception.

            
            </p>

            
            </li>

            
            <li><p> File &lsquo;<span class="file">.Renviron</span>&rsquo; can have architecture-specific versions

            
            such as &lsquo;<span class="file">.Renviron.i386</span>&rsquo; on systems with sub-architectures.

            
            </p>

            
            </li>

            
            <li> <p><code>installed.packages()</code> has a new argument

            
            <code>subarch</code> to filter on sub-architecture.

            
            </p>

            
            </li>

            
            <li><p> The <code>summary()</code> method for <code>packageStatus()</code> now

            
            has a separate <code>print()</code> method.

            
            </p>

            
            </li>

            
            <li><p> The default <code>summary()</code> method returns an object

            
            inheriting from class <code>"summaryDefault"</code> which has a

            
            separate <code>print()</code> method that calls <code>zapsmall()</code> for

            
            numeric/complex values.

            
            </p>

            
            </li>

            
            <li><p> The startup message now includes the platform and if used,

            
            sub-architecture: this is useful where different

            
            (sub-)architectures run on the same OS.

            
            </p>

            
            </li>

            
            <li><p> The <code>getGraphicsEvent()</code> mechanism now allows multiple windows

            
            to return graphics events, through the new functions

            
            <code>setGraphicsEventHandlers()</code>, <code>setGraphicsEventEnv()</code>, and

            
            <code>getGraphicsEventEnv()</code>.  (Currently implemented in the

            
            <code>windows()</code> and <code>X11()</code> devices.)

            
            </p>

            
            </li>

            
            <li> <p><code>tools::texi2dvi()</code> gains an <code>index</code> argument,

            
            mainly for use by <code>R CMD Rd2pdf</code>.

            
            </p>

            
            <p>It avoids the use of <code>texindy</code> by <code>texinfo</code>'s

            
            <code>texi2dvi &gt;= 1.157</code>, since that does not emulate

            
            'makeindex' well enough to avoid problems with special characters

            
            (such as <span class="samp">(</span>, <span class="samp">{</span>, <span class="samp">!</span>) in indices.

            
            </p>

            
            </li>

            
            <li><p> The ability of <code>readLines()</code> and <code>scan()</code> to

            
            re-encode inputs to marked UTF-8 strings on Windows since <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.7.0

            
            is extended to non-UTF-8 locales on other OSes.

            
            </p>

            
            </li>

            
            <li> <p><code>scan()</code> gains a <code>fileEncoding</code> argument to

            
            match <code>read.table()</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>points()</code> and <code>lines()</code> gain <code>"table"</code>

            
            methods to match <code>plot()</code>.  (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=10472">PR#10472</a>.)

            
            </p>

            
            </li>

            
            <li> <p><code>Sys.chmod()</code> allows argument <code>mode</code> to be a

            
            vector, recycled along <code>paths</code>.

            
            </p>

            
            </li>

            
            <li><p> There are <code>|</code>, <code>&amp;</code> and <code>xor()</code> methods for

            
            classes <code>"octmode"</code> and <code>"hexmode"</code>, which work

            
            bitwise.

            
            </p>

            
            </li>

            
            <li><p> Environment variables <span class="env">R_DVIPSCMD</span>, <span class="env">R_LATEXCMD</span>,

            
            <span class="env">R_MAKEINDEXCMD</span>, <span class="env">R_PDFLATEXCMD</span> are no longer used

            
            nor set in an <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> session.  (With the move to

            
            <code>tools::texi2dvi()</code>, the conventional environment variables

            
            <span class="env">LATEX</span>, <span class="env">MAKEINDEX</span> and <span class="env">PDFLATEX</span> will be used.

            
            <code>options("dvipscmd")</code> defaults to the value of <span class="env">DVIPS</span>,

            
            then to <code>"dvips"</code>.)

            
            </p>

            
            </li>

            
            <li><p> New function <code>isatty()</code> to see if terminal connections are

            
            redirected.

            
            </p>

            
            </li>

            
            <li> <p><code>summaryRprof()</code> returns the sampling interval in

            
            component <code>sample.interval</code> and only returns in

            
            <code>by.self</code> data for functions with non-zero self times.

            
            </p>

            
            </li>

            
            <li> <p><code>print(x)</code> and <code>str(x)</code> now indicate if an empty

            
            list <code>x</code> is named.

            
            </p>

            
            </li>

            
            <li> <p><code>install.packages()</code> and <code>remove.packages()</code> with

            
            <code>lib</code> unspecified and multiple libraries in

            
            <code>.libPaths()</code> inform the user of the library location used

            
            with a message rather than a warning.

            
            </p>

            
            </li>

            
            <li><p> There is limited support for multiple compressed streams on a

            
            file: all of <code>[bgx]zfile()</code> allow streams to be appended to an

            
            existing file, but <code>bzfile()</code> reads only the first stream.

            
            </p>

            
            </li>

            
            <li><p> Function <code>person()</code> in package <span class="pkg">utils</span> now uses

            
            a given/family scheme in preference to first/middle/last, is

            
            vectorized to handle an arbitrary number of persons, and gains a

            
            <code>role</code> argument to specify person roles using a controlled

            
            vocabulary (the MARC relator terms).

            
            </p>

            
            </li>

            
            <li><p> Package <span class="pkg">utils</span> adds a new <code>"bibentry"</code> class

            
            for representing and manipulating bibliographic information in

            
            enhanced BibTeX style, unifying and enhancing the previously

            
            existing mechanisms.

            
            </p>

            
            </li>

            
            <li><p> A <code>bibstyle()</code> function has been added to the

            
            <span class="pkg">tools</span> package with default JSS style for rendering

            
            <code>"bibentry"</code> objects, and a mechanism for registering other

            
            rendering styles.

            
            </p>

            
            </li>

            
            <li><p> Several aspects of the display of text help are now

            
            customizable using the new <code>Rd2txt_options()</code> function.

            
            options(<code>"help_text_width"</code>) is no longer used.

            
            </p>

            
            </li>

            
            <li><p> Added <span class="samp">\href</span> tag to the Rd format, to allow

            
            hyperlinks to URLs without displaying the full URL.

            
            </p>

            
            </li>

            
            <li><p> Added <span class="samp">\newcommand</span> and <span class="samp">\renewcommand</span> tags

            
            to the Rd format, to allow user-defined macros.

            
            </p>

            
            </li>

            
            <li><p> New <code>toRd()</code> generic in the <span class="pkg">tools</span> package to

            
            convert objects to fragments of Rd code, and added

            
            <code>"fragment"</code> argument to <code>Rd2txt()</code>, <code>Rd2HTML()</code>,

            
            and <code>Rd2latex()</code> to support it.

            
            </p>

            
            </li>

            
            <li><p> Directory &lsquo;<span class="file">R_HOME/share/texmf</span>&rsquo; now follows the TDS

            
            conventions, so can be set as a <code>texmf</code> tree (&lsquo;root

            
            directory&rsquo; in MiKTeX parlance).

            
            </p>

            
            </li>

            
            <li><p> S3 generic functions now use correct S4 inheritance when

            
            dispatching on an S4 object.  See <code>?Methods</code>, section on

            
            &ldquo;Methods for S3 Generic Functions&rdquo; for recommendations

            
            and details.

            
            </p>

            
            </li>

            
            <li> <p><code>format.pval()</code> gains a <code>...</code> argument to pass

            
            arguments such as <code>nsmall</code> to <code>format()</code>.  (Wish of

            
            <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=9574">PR#9574</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>legend()</code> supports <code>title.adj</code>.  (Wish of

            
            <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=13415">PR#13415</a>)

            
            </p>

            
            </li>

            
            <li><p> Added support for subsetting <code>"raster"</code> objects, plus

            
            assigning to a subset, conversion to a matrix (of colour

            
            strings), and comparisons (<span class="samp">==</span> and <span class="samp">!=</span>).

            
            </p>

            
            </li>

            
            <li><p> Added a new <code>parseLatex()</code> function (and related

            
            functions <code>deparseLatex()</code> and <code>latexToUtf8()</code>) to

            
            support conversion of bibliographic entries for display in R.

            
            </p>

            
            </li>

            
            <li><p> Text rendering of <span class="samp">\itemize</span> in help uses a Unicode

            
            bullet in UTF-8 and most single-byte Windows locales.

            
            </p>

            
            </li>

            
            <li><p> Added support for polygons with holes to the graphics

            
            engine.  This is implemented for the <code>pdf()</code>,

            
            <code>postscript()</code>, <code>x11(type="cairo")</code>, <code>windows()</code>,

            
            and <code>quartz()</code> devices (and associated raster formats),

            
            but not for <code>x11(type="Xlib")</code> or <code>xfig()</code> or

            
            <code>pictex()</code>.  The user-level interface is the

            
            <code>polypath()</code> function in <span class="pkg">graphics</span> and

            
            <code>grid.path()</code> in <span class="pkg">grid</span>.

            
            </p>

            
            </li>

            
            <li><p> File &lsquo;<span class="file">NEWS</span>&rsquo; 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,

            
            &lsquo;<span class="file">NEWS.pdf</span>&rsquo;, installed at the top-level of the R distribution.

            
            </p>

            
            </li>

            
            <li> <p><code>kmeans(x, 1)</code> now works.  Further, <code>kmeans</code> now

            
            returns between and total sum of squares.

            
            </p>

            
            </li>

            
            <li> <p><code>arrayInd()</code> and <code>which()</code> gain an argument

            
            <code>useNames</code>.  For <code>arrayInd</code>, the default is now false,

            
            for speed reasons.

            
            </p>

            
            </li>

            
            <li><p> As is done for closures, the default <code>print</code> method for

            
            the formula class now displays the associated environment if it is

            
            not the global environment.

            
            </p>

            
            </li>

            
            <li><p> 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

            
            <code>?insertSource</code>.

            
            </p>

            
            </li>

            
            <li><p> New function <code>readRenviron</code> to (re-)read files in the

            
            format of &lsquo;<span class="file">~/.Renviron</span>&rsquo; and &lsquo;<span class="file">Renviron.site</span>&rsquo;.

            
            </p>

            
            </li>

            
            <li> <p><code>require()</code> will now return <code>FALSE</code> (and not fail)

            
            if loading the package or one of its dependencies fails.

            
            </p>

            
            </li>

            
            <li> <p><code>aperm()</code> now allows argument <code>perm</code> to be a

            
            character vector when the array has named dimnames (as the results

            
            of <code>table()</code> calls do).  Similarly, <code>array()</code> allows

            
            <code>MARGIN</code> to be a character vector.  (Based on suggestions of

            
            Michael Lachmann.)

            
            </p>

            
            </li>

            
            <li><p> Package <span class="pkg">utils</span> now exports and documents functions

            
            <code>aspell_package_Rd_files()</code> and

            
            <code>aspell_package_vignettes()</code> for spell checking package Rd

            
            files and vignettes using Aspell, Ispell or Hunspell.

            
            </p>

            
            </li>

            
            <li><p> Package news can now be given in Rd format, and

            
            <code>news()</code> prefers these &lsquo;<span class="file">inst/NEWS.Rd</span>&rsquo; files to old-style

            
            plain text &lsquo;<span class="file">NEWS</span>&rsquo; or &lsquo;<span class="file">inst/NEWS</span>&rsquo; files.

            
            </p>

            
            </li>

            
            <li><p> New simple function <code>packageVersion()</code>.

            
            </p>

            
            </li>

            
            <li><p> The PCRE library has been updated to version 8.10.

            
            </p>

            
            </li>

            
            <li><p> The standard Unix-alike terminal interface declares its name

            
            to readline as 'R', so that can be used for conditional sections

            
            in &lsquo;<span class="file">~/.inputrc</span>&rsquo; files.

            
            </p>

            
            </li>

            
            <li> <p>&lsquo;Writing R Extensions&rsquo; now stresses that the standard

            
            sections in &lsquo;<span class="file">.Rd</span>&rsquo; files (other than <span class="samp">\alias</span>,

            
            <span class="samp">\keyword</span> and <span class="samp">\note</span>) are intended to be unique, and

            
            the conversion tools now drop duplicates with a warning.

            
            </p>

            
            <p>The &lsquo;<span class="file">.Rd</span>&rsquo; conversion tools also warn about an unrecognized type

            
            in a <span class="samp">\docType</span> section.

            
            </p>

            
            </li>

            
            <li> <p><code>ecdf()</code> objects now have a <code>quantile()</code> method.

            
            </p>

            
            </li>

            
            <li> <p><code>format()</code> methods for date-time objects now attempt to make

            
            use of a <code>"tzone"</code> attribute with <code>"%Z"</code> and

            
            <code>"%z"</code> formats, but it is not always possible.  (Wish of

            
            <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14358">PR#14358</a>.)

            
            </p>

            
            </li>

            
            <li> <p><code>tools::texi2dvi(file, clean = TRUE)</code> now works in more

            
            cases (e.g., where emulation is used and when &lsquo;<span class="file">file</span>&rsquo; is not in

            
            the current directory).

            
            </p>

            
            </li>

            
            <li><p> New function <code>droplevels()</code> to remove unused factor levels.

            
            </p>

            
            </li>

            
            <li> <p><code>system(command, intern = TRUE)</code> now gives an error on

            
            a Unix-alike (as well as on Windows) if <code>command</code> cannot be

            
            run.  It reports a non-success exit status from running

            
            <code>command</code> as a warning.

            
            </p>

            
            <p>On a Unix-alike an attempt is made to return the actual exit

            
            status of the command in <code>system(intern = FALSE)</code>: previously

            
            this had been system-dependent but on POSIX-compliant systems the

            
            value return was 256 times the status.

            
            </p>

            
            </li>

            
            <li> <p><code>system()</code> has a new argument <code>ignore.stdout</code>

            
            which can be used to (portably) ignore standard output.

            
            </p>

            
            </li>

            
            <li> <p><code>system(intern = TRUE)</code> and <code>pipe()</code> connections

            
            are guaranteed to be available on all builds of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>.

            
            </p>

            
            </li>

            
            <li> <p><code>Sys.which()</code> has been altered to return <code>""</code> if

            
            the command is not found (even on Solaris).

            
            </p>

            
            </li>

            
            <li><p> A facility for defining reference-based S4 classes (in the

            
            OOP style of Java, C++, etc.) has been added experimentally to

            
            package <span class="pkg">methods</span>; see <code>?ReferenceClasses</code>.

            
            </p>

            
            </li>

            
            <li><p> The <code>predict</code> method for <code>"loess"</code> fits gains an

            
            <code>na.action</code> argument which defaults to <code>na.pass</code> rather

            
            than the previous default of <code>na.omit</code>.

            
            </p>

            
            <p>Predictions from <code>"loess"</code> fits are now named from the row

            
            names of <code>newdata</code>.

            
            </p>

            
            </li>

            
            <li><p> Parsing errors detected during <code>Sweave()</code> processing

            
            will now be reported referencing their original location in the

            
            source file.

            
            </p>

            
            </li>

            
            <li><p> New <code>adjustcolor()</code> utility, e.g., for simple

            
            translucent color schemes.

            
            </p>

            
            </li>

            
            <li> <p><code>qr()</code> now has a trivial <code>lm</code> method with a

            
            simple (fast) validity check.

            
            </p>

            
            </li>

            
            <li><p> An experimental new programming model has been added to

            
            package <span class="pkg">methods</span> for reference (OOP-style) classes and

            
            methods.  See <code>?ReferenceClasses</code>.

            
            </p>

            
            </li>

            
            <li><p> bzip2 has been updated to version 1.0.6 (bug-fix release).

            
            <span class="option">--with-system-bzlib</span> now requires at least version 1.0.6.

            
            </p>

            
            </li>

            
            <li><p> R now provides &lsquo;<span class="file">jss.cls</span>&rsquo; and &lsquo;<span class="file">jss.bst</span>&rsquo; (the class

            
            and bib style file for the Journal of Statistical Software) as

            
            well as &lsquo;<span class="file">RJournal.bib</span>&rsquo; and &lsquo;<span class="file">Rnews.bib</span>&rsquo;, and

            
            <code>R CMD</code> ensures that the &lsquo;<span class="file">.bst</span>&rsquo; and &lsquo;<span class="file">.bib</span>&rsquo; files

            
            are found by BibTeX.

            
            </p>

            
            </li>

            
            <li><p> Functions using the <span class="env">TAR</span> environment variable no longer

            
            quote the value when making <code>system</code> calls.  This allows

            
            values such as <span class="samp">tar --force-local</span>, but does require

            
            additional quotes in, e.g., <code>TAR = "'/path with spaces/mytar'"</code>.

            
            </p>

            
            </li></ul>


            <h4>DEPRECATED &amp; DEFUNCT</h4>


            <ul>

            
            <li><p> Supplying the parser with a character string containing both

            
            octal/hex and Unicode escapes is now an error.

            
            </p>

            
            </li>

            
            <li><p> File extension &lsquo;<span class="file">.C</span>&rsquo; for C++ code files in packages is

            
            now defunct.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD check</code> no longer supports configuration

            
            files containing Perl configuration variables: use the environment

            
            variables documented in &lsquo;R Internals&rsquo; instead.

            
            </p>

            
            </li>

            
            <li><p> The <code>save</code> argument of <code>require()</code> now defaults to

            
            <code>FALSE</code> and <code>save = TRUE</code> is now deprecated.  (This

            
            facility is very rarely actually used, and was superseded by the

            
            <span class="samp">Depends</span> field of the &lsquo;<span class="file">DESCRIPTION</span>&rsquo; file long ago.)

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD check --no-latex</code> is deprecated in favour of

            
            <span class="option">--no-manual</span>.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD Sd2Rd</code> is formally deprecated and will be

            
            removed in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.13.0.

            
            </p>

            
            </li></ul>


            <h4>PACKAGE INSTALLATION</h4>


            <ul>

            
            <li> <p><code>install.packages()</code> has a new argument

            
            <code>libs_only</code> to optionally pass <span class="option">--libs-only</span> to

            
            <code>R CMD INSTALL</code> and works analogously for Windows binary

            
            installs (to add support for 64- or 32-bit Windows).

            
            </p>

            
            </li>

            
            <li><p> When sub-architectures are in use, the installed

            
            architectures are recorded in the <code>Archs</code> field of the

            
            &lsquo;<span class="file">DESCRIPTION</span>&rsquo; file.  There is a new default filter,

            
            <code>"subarch"</code>, in <code>available.packages()</code> to make use of

            
            this.

            
            </p>

            
            <p>Code is compiled in a copy of the &lsquo;<span class="file">src</span>&rsquo; directory when a

            
            package is installed for more than one sub-architecture: this

            
            avoid problems with cleaning the sources between building

            
            sub-architectures.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD INSTALL --libs-only</code> no longer overrides the

            
            setting of locking, so a previous version of the package will be

            
            restored unless <span class="option">--no-lock</span> is specified.

            
            </p>

            
            </li></ul>


            <h4>UTILITIES</h4>


            <ul>

            
            <li> <p><code>R CMD Rprof|build|check</code> are now based on <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> rather

            
            than Perl scripts.  The only remaining Perl scripts are the

            
            deprecated <code>R CMD Sd2Rd</code> and <code>install-info.pl</code> (used

            
            only if <code>install-info</code> is not found) as well as some

            
            maintainer-mode-only scripts.

            
            </p>

            
            <p><strong>NB:</strong> because these have been completely rewritten, users

            
            should not expect undocumented details of previous

            
            implementations to have been duplicated.

            
            </p>

            
            <p><code>R CMD</code> no longer manipulates the environment variables

            
            <span class="env">PERL5LIB</span> and <span class="env">PERLLIB</span>.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD check</code> has a new argument <span class="option">--extra-arch</span>

            
            to confine tests to those needed to check an additional

            
            sub-architecture.

            
            </p>

            
            <p>Its check for &ldquo;Subdirectory 'inst' contains no files&rdquo; is

            
            more thorough: it looks for files, and warns if there are only

            
            empty directories.

            
            </p>

            
            <p>Environment variables such as <span class="env">R_LIBS</span> and those used for

            
            customization can be set for the duration of checking <em>via</em> a file

            
            &lsquo;<span class="file">~/.R/check.Renviron</span>&rsquo; (in the format used by

            
            &lsquo;<span class="file">.Renviron</span>&rsquo;, and with sub-architecture specific versions

            
            such as &lsquo;<span class="file">~/.R/check.Renviron.i386</span>&rsquo; taking precedence).

            
            </p>

            
            <p>There are new options <span class="option">--multiarch</span> to check the package

            
            under all of the installed sub-architectures and

            
            <span class="option">--no-multiarch</span> to confine checking to the

            
            sub-architecture under which <code>check</code> 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.

            
            </p>

            
            <p>Unless multiple sub-architectures are selected, the install done

            
            by <code>check</code> for testing purposes is only of the current

            
            sub-architecture (<em>via</em> <code>R CMD INSTALL --no-multiarch</code>).

            
            </p>

            
            <p>It will skip the check for non-ascii characters in code or data

            
            if the environment variables <span class="env">_R_CHECK_ASCII_CODE_</span> or

            
            <span class="env">_R_CHECK_ASCII_DATA_</span> are respectively set to <span class="env">FALSE</span>.

            
            (Suggestion of Vince Carey.)

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD build</code> no longer creates an &lsquo;<span class="file">INDEX</span>&rsquo; file

            
            (<code>R CMD INSTALL</code> does so), and <span class="option">--force</span> removes

            
            (rather than overwrites) an existing &lsquo;<span class="file">INDEX</span>&rsquo; file.

            
            </p>

            
            <p>It supports a file &lsquo;<span class="file">~/.R/build.Renviron</span>&rsquo; analogously to

            
            <code>check</code>.

            
            </p>

            
            <p>It now runs build-time <span class="samp">\Sexpr</span> expressions in help files.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD Rd2dvi</code> makes use of <code>tools::texi2dvi()</code>

            
            to process the package manual.  It is now implemented entirely in

            
            <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> (rather than partially as a shell script).

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD Rprof</code> now uses <code>utils::summaryRprof()</code>

            
            rather than Perl.  It has new arguments to select one of the

            
            tables and to limit the number of entries printed.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD Sweave</code> now runs <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> with <span class="option">--vanilla</span> so

            
            the environment setting of <span class="env">R_LIBS</span> will always be used.

            
            </p>

            
            </li></ul>


            <h4>C-LEVEL FACILITIES</h4>


            <ul>

            
            <li> <p><code>lang5()</code> and <code>lang6()</code> (in addition to

            
            pre-existing <code>lang[1-4]()</code>) convenience functions for easier

            
            construction of <code>eval()</code> calls.  If you have your own

            
            definition, do wrap it inside <code>#ifndef lang5 .... #endif</code>

            
            to keep it working with old and new <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>.

            
            </p>

            
            </li>

            
            <li><p> Header &lsquo;<span class="file">R.h</span>&rsquo; now includes only the C headers it itself needs,

            
            hence no longer includes <code>errno.h</code>.  (This helps avoid problems

            
            when it is included from C++ source files.)

            
            </p>

            
            </li>

            
            <li><p> Headers &lsquo;<span class="file">Rinternals.h</span>&rsquo; and &lsquo;<span class="file">R_ext/Print.h</span>&rsquo; include

            
            the C++ versions of &lsquo;<span class="file">stdio.h</span>&rsquo; and &lsquo;<span class="file">stdarg.h</span>&rsquo;

            
            respectively if included from a C++ source file.

            
            </p>

            
            </li></ul>


            <h4>INSTALLATION</h4>


            <ul>

            
            <li><p> A C99 compiler is now required, and more C99 language features

            
            will be used in the <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> sources.

            
            </p>

            
            </li>

            
            <li><p> Tcl/Tk &gt;= 8.4 is now required (increased from 8.3).

            
            </p>

            
            </li>

            
            <li><p> System functions <code>access</code>, <code>chdir</code> and

            
            <code>getcwd</code> are now essential to configure <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>.  (In practice

            
            they have been required for some time.)

            
            </p>

            
            </li>

            
            <li> <p><code>make check</code> 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.

            
            </p>

            
            </li>

            
            <li><p> File &lsquo;<span class="file">NEWS</span>&rsquo; is no longer in the sources, but generated as

            
            part of the installation.  The primary source for changes is now

            
            &lsquo;<span class="file">doc/NEWS.Rd</span>&rsquo;.

            
            </p>

            
            </li>

            
            <li><p> The <code>popen</code> system call is now required to build <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>.

            
            This ensures the availability of <code>system(intern = TRUE)</code>,

            
            <code>pipe()</code> connections and printing from <code>postscript()</code>.

            
            </p>

            
            </li>

            
            <li><p> The <code>pkg-config</code> file &lsquo;<span class="file">libR.pc</span>&rsquo; now also works

            
            when <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> is installed using a sub-architecture.

            
            </p>

            
            </li>

            
            <li> <p><span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 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.

            
            </p>

            
            </li></ul>


            <h4>BUG FIXES</h4>


            <ul>

            
            <li><p> Calls to <code>selectMethod()</code> by default no longer cache

            
            inherited methods.  This could previously corrupt methods used by

            
            <code>as()</code>.

            
            </p>

            
            </li>

            
            <li><p> The densities of non-central chi-squared are now more accurate

            
            in some cases in the extreme tails,

            
            e.g. <code>dchisq(2000, 2, 1000)</code>,

            
            as a series expansion was truncated too early.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14105">PR#14105</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>pt()</code> is more accurate in the left tail for <code>ncp</code>

            
            large, e.g. <code>pt(-1000, 3, 200)</code>.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14069">PR#14069</a>)

            
            </p>

            
            </li>

            
            <li><p> The default C function (<code>R_binary</code>) for binary ops now

            
            sets the S4 bit in the result if either argument is an S4 object.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=13209">PR#13209</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>source(echo=TRUE)</code> failed to echo comments that

            
            followed the last statement in a file.

            
            </p>

            
            </li>

            
            <li><p> S4 classes that contained one of <code>"matrix"</code>,

            
            <code>"array"</code> or <code>"ts"</code> and also another class now accept

            
            superclass objects in <code>new()</code>.  Also fixes failure to call

            
            <code>validObject()</code> for these classes.

            
            </p>

            
            </li>

            
            <li><p> Conditional inheritance defined by argument <code>test</code> in

            
            <code>methods::setIs()</code> will no longer be used in S4 method

            
            selection (caching these methods could give incorrect results).

            
            See <code>?setIs</code>.

            
            </p>

            
            </li>

            
            <li><p> The signature of an implicit generic is now used by

            
            <code>setGeneric()</code> when that does not use a definition nor

            
            explicitly set a signature.

            
            </p>

            
            </li>

            
            <li><p> A bug in <code>callNextMethod()</code> for some examples with

            
            <code>"..."</code> in the arguments has been fixed.  See file

            
            &lsquo;<span class="file">src/library/methods/tests/nextWithDots.R</span>&rsquo; in the sources.

            
            </p>

            
            </li>

            
            <li> <p><code>match(x, table)</code> (and hence <code>%in%</code>) now treat

            
            <code>"POSIXlt"</code> consistently with, e.g., <code>"POSIXct"</code>.

            
            </p>

            
            </li>

            
            <li><p> Built-in code dealing with environments (<code>get()</code>,

            
            <code>assign()</code>, <code>parent.env()</code>, <code>is.environment()</code> and

            
            others) now behave consistently to recognize S4 subclasses;

            
            <code>is.name()</code> also recognizes subclasses.

            
            </p>

            
            </li>

            
            <li><p> The <code>abs.tol</code> control parameter to <code>nlminb()</code>

            
            now defaults to <code>0.0</code> to avoid false declarations of

            
            convergence in objective functions that may go negative.

            
            </p>

            
            </li>

            
            <li><p> The standard Unix-alike termination dialog to ask whether to

            
            save the workspace takes a EOF response as <code>n</code> to avoid

            
            problems with a damaged terminal connection.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14332">PR#14332</a>)

            
            </p>

            
            </li>

            
            <li><p> Added <code>warn.unused</code> argument to <code>hist.default()</code>

            
            to allow suppression of spurious warnings about graphical

            
            parameters used with <code>plot=FALSE</code>.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14341">PR#14341</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>predict.lm()</code>, <code>summary.lm()</code>, and indeed

            
            <code>lm()</code> 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

            
            <code>predict()</code> case.)

            
            </p>

            
            </li>

            
            <li> <p><code>aperm()</code> treated <code>resize = NA</code> as <code>resize =

            
                  TRUE</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>constrOptim()</code> 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.

            
            </p>

            
            </li>

            
            <li><p> Rendering of S3 and S4 methods in man pages has been

            
            corrected and made consistent across output formats.

            
            </p>

            
            </li>

            
            <li><p> Simple markup is now allowed in <span class="samp">\title</span> sections

            
            in &lsquo;<span class="file">.Rd</span>&rsquo; files.

            
            </p>

            
            </li>

            
            <li><p> The behaviour of <code>as.logical()</code> on factors (to use the

            
            levels) was lost in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.6.0 and has been restored.

            
            </p>

            
            </li>

            
            <li> <p><code>prompt()</code> did not backquote some default arguments in

            
            the <span class="samp">\usage</span> section.  (Reported by Claudia Beleites.)

            
            </p>

            
            </li>

            
            <li> <p><code>writeBin()</code> disallows attempts to write 2GB or

            
            more in a single call. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14362">PR#14362</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>new()</code> and <code>getClass()</code> will now work if Class

            
            is a subclass of <code>"classRepresentation"</code> and should also be

            
            faster in typical calls.

            
            </p>

            
            </li>

            
            <li><p> The <code>summary()</code> method for data frames makes a better

            
            job of names containing characters invalid in the current locale.

            
            </p>

            
            </li>

            
            <li> <p><code>[[</code> sub-assignment for factors could create an invalid

            
            factor (reported by Bill Dunlap).

            
            </p>

            
            </li>

            
            <li> <p><code>Negate(f)</code> would not evaluate argument <code>f</code>

            
            until first use of returned function (reported by Olaf Mersmann).

            
            </p>

            
            </li>

            
            <li> <p><code>quietly=FALSE</code> is now also an optional argument of

            
            <code>library()</code>, and consequently, <code>quietly</code> is now

            
            propagated also for loading dependent packages, e.g., in

            
            <code>require(*, quietly=TRUE)</code>.

            
            </p>

            
            </li>

            
            <li><p> If the loop variable in a <code>for</code> loop was deleted, it

            
            would be recreated as a global variable.  (Reported by Radford

            
            Neal; the fix includes his optimizations as well.)

            
            </p>

            
            </li>

            
            <li><p> Task callbacks could report the wrong expression when

            
            the task involved parsing new code. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14368">PR#14368</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>getNamespaceVersion()</code> failed; this was an

            
            accidental change in 2.11.0. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14374">PR#14374</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>identical()</code> returned <code>FALSE</code> for external

            
            pointer objects even when the pointer addresses were the same.

            
            </p>

            
            </li>

            
            <li> <p><code>L$a@x[] &lt;- val</code> did not duplicate in a case it should have.

            
            </p>

            
            </li>

            
            <li> <p><code>tempfile()</code> now always gives a random file name (even

            
            if the directory is specified) when called directly after

            
            startup and before the <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> RNG had been used.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14381">PR#14381</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>quantile(type=6)</code> behaved inconsistently.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14383">PR#14383</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>backSpline(.)</code> behaved incorrectly when the knot

            
            sequence was decreasing.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14386">PR#14386</a>)

            
            </p>

            
            </li>

            
            <li><p> The reference BLAS included in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> was assuming that

            
            <code>0*x</code> and <code>x*0</code> were always zero (whereas they could be

            
            <code>NA</code> or <code>NaN</code> in IEC 60559 arithmetic).  This was seen

            
            in results from <code>tcrossprod</code>, and for example that

            
            <code>log(0) %*% 0</code> gave <code>0</code>.

            
            </p>

            
            </li>

            
            <li><p> 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).  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14391">PR#14391</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>model.frame(drop.unused.levels = TRUE)</code> did not

            
            take into account <code>NA</code> values of factors when deciding to

            
            drop levels. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14393">PR#14393</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>library.dynam.unload</code> required an absolute path for

            
            <code>libpath</code>.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14385">PR#14385</a>)

            
            </p>

            
            <p>Both <code>library()</code> and <code>loadNamespace()</code> now record

            
            absolute paths for use by <code>searchpaths()</code> and

            
            <code>getNamespaceInfo(ns, "path")</code>.

            
            </p>

            
            </li>

            
            <li><p> The self-starting model <code>NLSstClosestX</code> failed if some

            
            deviation was exactly zero.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14384">PR#14384</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>X11(type = "cairo")</code> (and other devices such as

            
            <code>png</code> 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.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14369">PR#14369</a>)

            
            </p>

            
            </li>

            
            <li><p> Added workaround for the font problem with <code>X11(type =

            
                  "cairo")</code> and similar on Mac OS X whereby italic and bold styles

            
            were interchanged.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=13463">PR#13463</a> amongst many other reports.)

            
            </p>

            
            </li>

            
            <li> <p><code>source(chdir = TRUE)</code> failed to reset the working

            
            directory if it could not be determined &ndash; that is now an error.

            
            </p>

            
            </li>

            
            <li><p> Fix for crash of <code>example(rasterImage)</code> on

            
            <code>x11(type="Xlib")</code>.

            
            </p>

            
            </li>

            
            <li><p> Force Quartz to bring the on-screen display up-to-date

            
            immediately before the snapshot is taken by <code>grid.cap()</code>

            
            in the Cocoa implementation. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14260">PR#14260</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>model.frame</code> had an unstated 500 byte limit on

            
            variable names.  (Example reported by Terry Therneau.)

            
            </p>

            
            </li>

            
            <li><p> The 256-byte limit on names is now documented.

            
            </p>

            
            </li>

            
            <li><p> Subassignment by <code>[</code>, <code>[[</code> or <code>$</code> on an

            
            expression object with value <code>NULL</code> coerced the object to a

            
            list.

            
            </p>

            
            </li></ul>


            <h3><img class="toplogo" src="../help/figures/../../html/Rlogo.svg" alt="[R logo]" /> CHANGES IN R VERSION 2.11.1 patched</h3>


            <h4>NEW FEATURES</h4>


            <ul>

            
            <li> <p><code>install.packages()</code> has a new optional argument

            
            <code>INSTALL_opts</code> which can be used to pass options to

            
            <code>R CMD INSTALL</code> for source-package installs.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD check</code> now runs the package-specific tests

            
            with <span class="env">LANGUAGE=en</span> to facilitate comparison to

            
            &lsquo;<span class="file">.Rout.save</span>&rsquo; files.

            
            </p>

            
            </li>

            
            <li> <p><code>sessionInfo()</code> gives more detailed platform

            
            information, including 32/64-bit and the sub-architecture if one

            
            is used.

            
            </p>

            
            </li></ul>


            <h4>DEPRECATED &amp; DEFUNCT</h4>


            <ul>

            
            <li><p> The use of Perl configuration variables for <code>R CMD

            
            	check</code> (as previously documented in &lsquo;Writing R

            
            Extensions&rsquo;) is deprecated and will be removed in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.12.0.  Use

            
            the environment variables documented in &lsquo;R Internals&rsquo;

            
            instead.

            
            </p>

            
            </li></ul>


            <h4>BUG FIXES</h4>


            <ul>

            
            <li> <p><code>R CMD Rd2dvi</code> failed if run from a path containing

            
            space(s).  This also affected <code>R CMD check</code>, which calls

            
            <code>Rd2dvi</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>stripchart()</code> could fail with an empty factor

            
            level.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14317">PR#14317</a>)

            
            </p>

            
            </li>

            
            <li><p> Text help rendering of <span class="samp">\tabular{}</span> has been

            
            improved: under some circumstances leading blank columns were

            
            not rendered.

            
            </p>

            
            </li>

            
            <li> <p><code>strsplit(x, fixed=TRUE)</code> marked UTF-8 strings with the

            
            local encoding when no splits were found.

            
            </p>

            
            </li>

            
            <li> <p><code>weighted.mean(NA, na.rm=TRUE)</code> and similar now returns

            
            <code>NaN</code> again, as it did prior to <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.10.0.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD</code> had a typo in its detection of whether the

            
            environment variable <span class="env">TEXINPUTS</span> was set (reported by Martin

            
            Morgan).

            
            </p>

            
            </li>

            
            <li><p> The command-line parser could mistake

            
            <span class="option">--file=size...</span> for one of the options for setting limits

            
            for Ncells or Vcells.

            
            </p>

            
            </li>

            
            <li><p> The internal <code>strptime()</code> could corrupt its copy of the

            
            timezone which would then lead to spurious warnings. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14338">PR#14338</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>dir.create(recursive = TRUE)</code> 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.)

            
            </p>

            
            </li>

            
            <li><p> The <code>postscript()</code> and <code>pdf()</code> devices will now

            
            allow <code>lwd</code> values less than 1 (they used to force such

            
            values to be 1).

            
            </p>

            
            </li>

            
            <li><p> Fixed font face for CID fonts in <code>pdf()</code> graphics output.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14326">PR#14326</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>GERaster()</code> 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.

            
            </p>

            
            </li>

            
            <li> <p><code>wilcox.test(x, y, conf.int = TRUE)</code> failed with an unhelpful

            
            message if <code>x</code> and <code>y</code> were constant vectors, and

            
            similarly in the one-sample case.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14329">PR#14329</a>)

            
            </p>

            
            </li>

            
            <li><p> Improperly calling <code>Recall()</code> from outside a function

            
            could cause a segfault.  (Reported by Robert McGehee.)

            
            </p>

            
            </li>

            
            <li> <p><span class="samp">\Sexpr[result=rd]</span> in an Rd file added a

            
            spurious newline, which was displayed as extra whitespace when

            
            rendered.

            
            </p>

            
            </li>

            
            <li> <p><code>require(save = TRUE)</code> recorded the names of packages

            
            it failed to load.

            
            </p>

            
            </li>

            
            <li> <p><code>packageStatus()</code> could return a data frame with

            
            duplicate row names which could then not be printed.

            
            </p>

            
            </li>

            
            <li> <p><code>txtProgressBar(style = 2)</code> did not work correctly.

            
            </p>

            
            <p><code>txtProgressBar(style = 3)</code> did not display until a

            
            non-minimum value was set.

            
            </p>

            
            </li>

            
            <li> <p><code>contour()</code> did not display dashed line types

            
            properly when contour lines were labelled. (Reported by

            
            David B. Thompson.)

            
            </p>

            
            </li>

            
            <li> <p><code>tools::undoc()</code> again detects undocumented data

            
            objects.  Of course, this also affects <code>R CMD check</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>ksmooth(x,NULL)</code> no longer segfaults.

            
            </p>

            
            </li>

            
            <li> <p><code>approxfun()</code>, <code>approx()</code>, <code>splinefun()</code>

            
            and <code>spline()</code> could be confused by <code>x</code> values that

            
            were different but so close as to print identically.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14377">PR#14377</a>)

            
            </p>

            
            </li></ul>


            <h3><img class="toplogo" src="../help/figures/../../html/Rlogo.svg" alt="[R logo]" /> CHANGES IN R VERSION 2.11.1</h3>


            <h4>NEW FEATURES</h4>


            <ul>

            
            <li> <p><code>R CMD INSTALL</code> checks if dependent packages are

            
            available early on in the installation of source packages,

            
            thereby giving clearer error messages.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD INSTALL --build</code> now names the file in the

            
            format used for Mac OS X binary files on that platform.

            
            </p>

            
            </li>

            
            <li> <p><code>BIC()</code> in package <span class="pkg">stats4</span> now also works with

            
            multiple fitted models, analogously to <code>AIC()</code>.

            
            </p>

            
            </li></ul>


            <h4>DEPRECATED &amp; DEFUNCT</h4>


            <ul>

            
            <li><p> Use of file extension &lsquo;<span class="file">.C</span>&rsquo; for C++ code in packages is now

            
            deprecated: it has caused problems for some <code>make</code>s on

            
            case-insensitive file systems (although it currently works

            
            with the recommended toolkits).

            
            </p>

            
            </li></ul>


            <h4>INSTALLATION</h4>


            <ul>

            
            <li><p> Command <code>gnutar</code> is preferred to <code>tar</code>

            
            when configure sets <span class="env">TAR</span>.  This is needed on Mac OS 10.6,

            
            where the default <code>tar</code>, <code>bsdtar 2.6.2</code>, has been

            
            reported to produce archives with illegal extensions to tar

            
            (according to the POSIX standard).

            
            </p>

            
            </li></ul>


            <h4>BUG FIXES</h4>


            <ul>

            
            <li><p> The C function <code>mkCharLenCE</code> now no longer reads past

            
            <code>len</code> bytes (unlikely to be a problem except in user

            
            code).  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14246">PR#14246</a>)

            
            </p>

            
            </li>

            
            <li><p> On systems without any default <span class="env">LD_LIBRARY_PATH</span> (not

            
            even &lsquo;<span class="file">/usr/local/lib</span>&rsquo;), <span class="env">[DY]LIB_LIBRARY_PATH</span> is now

            
            set without a trailing colon.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=13637">PR#13637</a>)

            
            </p>

            
            </li>

            
            <li><p> More efficient implementation of <code>utf8ToInt()</code> on long

            
            multi-byte strings with many multi-byte characters.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14262">PR#14262</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>aggregate.ts()</code> gave platform-dependent results due to

            
            rounding error for <code>ndeltat != 1</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>package.skeleton()</code> sometimes failed to fix filenames

            
            for &lsquo;<span class="file">.R</span>&rsquo; or &lsquo;<span class="file">.Rd</span>&rsquo; files to start with an alphanumeric.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14253">PR#14253</a>)

            
            </p>

            
            <p>It also failed when only an S4 class without any methods was

            
            defined.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14280">PR#14280</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>splinefun(method = "monoH.FC")</code> was not

            
            quite monotone in rare cases.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14215">PR#14215</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>Rhttpd</code> no longer crashes due to <code>SIGPIPE</code> when

            
            the client closes the connection prematurely.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14266">PR#14266</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>format.POSIXlt()</code> could cause a stack overflow and

            
            crash when used on very long vectors.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14267">PR#14267</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>Rd2latex()</code> incorrectly escaped special characters in

            
            <span class="samp">\usage</span> sections.

            
            </p>

            
            </li>

            
            <li> <p><code>mcnemar.test()</code> could alter the levels (dropping

            
            unused levels) if passed <code>x</code> and <code>y</code> as factors

            
            (reported by Greg Snow).

            
            </p>

            
            </li>

            
            <li> <p><code>Rd2pdf</code> sometimes needed a further

            
            <code>pdflatex</code> pass to get hyperlinked pages correct.

            
            </p>

            
            </li>

            
            <li> <p><code>interaction()</code> produced malformed results when levels were

            
            duplicated, causing segfaults in <code>split()</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>cut(d, breaks = &lt;n&gt;)</code> now also works for <code>"Date"</code>

            
            or <code>"POSIXt"</code> argument <code>d</code>.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14288">PR#14288</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>memDecompress()</code> could decompress incompletely rare

            
            <code>xz</code>-compressed input due to incorrect documentation of

            
            <code>xz utils</code>.  (Report and patch from Olaf Mersmann.)

            
            </p>

            
            </li>

            
            <li><p> The S4 <code>initialize()</code> methods for <code>"matrix"</code>,

            
            <code>"array"</code>, and <code>"ts"</code> have been fixed to call

            
            <code>validObject()</code>.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14284">PR#14284</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD INSTALL</code> now behaves the same way with or

            
            without <span class="option">--no-multiarch</span> on platforms with only one

            
            installed architecture.  (It used to clean the &lsquo;<span class="file">src</span>&rsquo;

            
            directory without <span class="option">--no-multiarch</span>.)

            
            </p>

            
            </li>

            
            <li> <p><code>[&lt;-.data.frame</code> was not quite careful enough in

            
            assigning (and potentially deleting) columns

            
            right-to-left.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14263">PR#14263</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>rbeta(n, a, b)</code> no longer occasionally returns

            
            <code>NaN</code> for <code>a &gt;&gt; 1 &gt; b</code>.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14291">PR#14291</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>pnorm(x, log.p = TRUE)</code> could return <code>NaN</code> not

            
            <code>-Inf</code> for <code>x</code> near (minus for <code>lower.tail=TRUE</code>)

            
            the largest representable number.

            
            </p>

            
            </li>

            
            <li><p> Compressed data files &lsquo;<span class="file">*.(txt|tab|csv).(gz|bz2|xz)</span>&rsquo;

            
            were not recognized for the list of data topics and hence for

            
            packages using <code>LazyData</code>.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14273">PR#14273</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>textConnection()</code> 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.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14286">PR#14286</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>tools::Rd2txt()</code> did not render poorly written Rd

            
            files consistently with other renderers.

            
            </p>

            
            <p>It computed widths of strings that would be <code>print()</code>ed with

            
            escapes incorrectly, for example in the computation of column

            
            width for <span class="samp">\tabular</span>.

            
            </p>

            
            </li>

            
            <li> <p><code>na.action()</code> did not extract the <code>na.action</code>

            
            component as documented.

            
            </p>

            
            </li>

            
            <li> <p><code>do.call()</code>ing <code>NextMethod</code> in erroneous ways no

            
            longer segfaults. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=13487">PR#13487</a>)

            
            </p>

            
            </li></ul>


            <h3><img class="toplogo" src="../help/figures/../../html/Rlogo.svg" alt="[R logo]" /> CHANGES IN R VERSION 2.11.0</h3>


            <h4>SIGNIFICANT USER-VISIBLE CHANGES</h4>


            <ul>

            
            <li><p> Packages must have been installed under <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> &gt;= 2.10.0, as the

            
            current help system is the only one now supported.

            
            </p>

            
            </li>

            
            <li><p> A port to 64-bit Windows is now available as well as binary

            
            package repositories: see the &lsquo;R Administration and

            
            Installation Manual&rsquo;.

            
            </p>

            
            </li>

            
            <li><p> Argument matching for primitive functions is now done in the

            
            same way as for interpreted functions except for the deliberate

            
            exceptions

            
            </p>

            
            <pre>

            
            	 call switch .C .Fortran .Call .External

            
                   </pre>

            
            <p>all of which use positional matching for their first argument,

            
            and also some internal-use-only primitives.

            
            </p>

            
            </li>

            
            <li><p> The default device for command-line <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> at the console on Mac OS X

            
            is now <code>quartz()</code> and not <code>X11()</code>.

            
            </p>

            
            </li></ul>


            <h4>NEW FEATURES</h4>


            <ul>

            
            <li><p> The <code>open</code> modes for connections are now interpreted

            
            more consistently.  <code>open = "r"</code> is now equivalent to

            
            <code>open = "rt"</code> for all connections.  The default <code>open =

            
                   ""</code> now means <code>"rt"</code> for all connections except the

            
            compressed-file connections <code>gzfile()</code>, <code>bzfile()</code> and

            
            <code>xzfile()</code> for which it means <code>"rb"</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD INSTALL</code> now uses the internal <code>untar()</code>

            
            function in package <span class="pkg">utils</span>: this ensures that all platforms

            
            can install <code>bzip2</code>- and <code>xz</code>-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 <span class="env">R_INSTALL_TAR</span>:

            
            setting this to a modern external tar program will speed up

            
            unpacking of large (tens of Mb or more) tarballs.

            
            </p>

            
            </li>

            
            <li> <p><code>help(try.all.packages = TRUE)</code> 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).

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD check</code> has a new option <span class="option">--timings</span>

            
            to record per-example timings in file

            
            &lsquo;<span class="file">&lt;pkg&gt;.Rcheck/&lt;pkg&gt;-Ex.timings</span>&rsquo;.

            
            </p>

            
            </li>

            
            <li><p> The TRE library has been updated to version 0.8.0 (minor bugfixes).

            
            </p>

            
            </li>

            
            <li> <p><code>grep[l]</code>, <code>[g]sub</code> and <code>[g]regexpr</code> 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 <code>[g]sub()</code>

            
            give the result in the native encoding rather than in UTF-8

            
            (which returns to the behaviour prior to <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.10.0).

            
            </p>

            
            </li>

            
            <li><p> A new argument <code>skipCalls</code> has been added to

            
            <code>browser()</code> so that it can report the original context when

            
            called by other debugging functions.

            
            </p>

            
            </li>

            
            <li><p> More validity checking of UTF-8 and MBCS strings is done by

            
            <code>agrep()</code> and the regular-expression matching functions.

            
            </p>

            
            </li>

            
            <li><p> The undocumented restriction on <code>gregexpr()</code> to

            
            <code>length(text) &gt; 0</code> has been removed.

            
            </p>

            
            </li>

            
            <li><p> Package <span class="pkg">tcltk</span> 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.

            
            </p>

            
            </li>

            
            <li><p> 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., <code>Cairo</code>,

            
            <code>RSvgDevice</code>, <code>cairoDevice</code>) will need to be reinstalled.

            
            </p>

            
            <p>There is also support in the graphics engine for capturing

            
            raster images from graphics devices (again not supported

            
            on all graphics devices).

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD check</code> now also checks if the package and

            
            namespace can be unloaded: this provides a check of the

            
            <code>.Last.lib()</code> and <code>.onUnload()</code> hook functions (unless

            
            <span class="option">--install=fake</span>).

            
            </p>

            
            </li>

            
            <li> <p><code>prop.table(x)</code> now accepts a one-dimensional table for

            
            <code>x</code>.

            
            </p>

            
            </li>

            
            <li><p> A new function <code>vapply()</code> 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.

            
            </p>

            
            </li>

            
            <li><p> The main HTML help page now links to a reformatted copy of

            
            this &lsquo;<span class="file">NEWS</span>&rsquo; file.  (Suggested by Henrik Bengtsson.)  Package

            
            index files link to the package &lsquo;<span class="file">DESCRIPTION</span>&rsquo; and

            
            &lsquo;<span class="file">NEWS</span>&rsquo; files and a list of demos when using dynamic help.

            
            </p>

            
            </li>

            
            <li><p> The <code>[</code> method for class <code>"AsIs"</code> allows the next

            
            method to change the underlying class.  (Wish of Jens

            
            Oehlschlägel.)

            
            </p>

            
            </li>

            
            <li> <p><code>write.csv[2]</code> no longer allow argument <code>append</code>

            
            to be changed: as ever, direct calls to <code>write.table()</code> give

            
            more flexibility as well as more room for error.

            
            </p>

            
            </li>

            
            <li><p> The index page for HTML help for a package now collapses

            
            multiple signatures for S4 methods into a single entry.

            
            </p>

            
            </li>

            
            <li><p> The use of <code>.required</code> by <code>require()</code> and

            
            <code>detach()</code> has been replaced by <code>.Depends</code> which is set

            
            from the <code>Depends</code> field of a package (even in packages with

            
            namespaces).  By default <code>detach()</code> prevents such

            
            dependencies from being detached: this can be overridden by the

            
            argument <code>force</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>bquote()</code> has been extended to work on function

            
            definitions.  (Wish of

            
            <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14031">PR#14031</a>).

            
            </p>

            
            </li>

            
            <li> <p><code>detach()</code> when applied to an object other than a

            
            package returns the environment that has been detached, to

            
            parallel <code>attach()</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>readline()</code> in non-interactive use returns <code>""</code>

            
            and does not attempt to read from the &lsquo;terminal&rsquo;.

            
            </p>

            
            </li>

            
            <li><p> New function <code>file_ext()</code> in package <span class="pkg">tools</span>.

            
            </p>

            
            </li>

            
            <li> <p><code>xtfrm()</code> is now primitive and internally generic, as

            
            this allows S4 methods to be set on it without name-space scoping

            
            issues.

            
            </p>

            
            <p>There are now <code>"AsIs"</code> and <code>"difftime"</code> methods, and

            
            the default method uses <code>unclass(x)</code> if <code>is.numeric(x)</code>

            
            is true (which will be faster but relies on <code>is.numeric()</code>

            
            having been set correctly for the class).

            
            </p>

            
            </li>

            
            <li> <p><code>is.numeric(x)</code> is now false for a <code>"difftime"</code>

            
            object (multiplication and division make no sense for such

            
            objects).

            
            </p>

            
            </li>

            
            <li><p> The default method of <code>weighted.mean(x, w)</code> coerces

            
            <code>w</code> 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 <code>NaN</code>

            
            result.

            
            </p>

            
            <p>There is now a <code>"difftime"</code> method.

            
            </p>

            
            </li>

            
            <li> <p><code>bug.report()</code> now has arguments <code>package</code> and

            
            <code>lib.loc</code> to generate bug reports about packages.  When

            
            this is used, it looks for a <code>BugReports</code> field in the

            
            package &lsquo;<span class="file">DESCRIPTION</span>&rsquo; 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.)

            
            </p>

            
            </li>

            
            <li> <p><code>quantile()</code> now has a method for the date-time class

            
            <code>"POSIXt"</code>, and types 1 and 3 (which never interpolate) work

            
            for Dates and ordered factors.

            
            </p>

            
            </li>

            
            <li> <p><code>length(&lt;POSIXlt&gt;)</code> now returns the length of the

            
            corresponding abstract timedate-vector rather than always 9 (the

            
            length of the underlying list structure).  (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14073">PR#14073</a>

            
            and <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=10507">PR#10507</a>.)

            
            </p>

            
            </li>

            
            <li><p> The <code>readline</code> completion backend no longer sorts

            
            possible completions alphabetically (e.g., function argument

            
            names) if <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> was built with <code>readline &gt;= 6</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>select.list()</code> gains a <code>graphics</code> argument to

            
            allow Windows/Mac users to choose the text interface.  This

            
            changes the behaviour of <code>new.packages(ask=TRUE)</code> to be like

            
            <code>update.packages(ask=TRUE)</code> on those platforms in using a

            
            text menu: use ask=<code>"graphics"</code> for a graphical menu.

            
            </p>

            
            </li>

            
            <li><p> New function <code>chooseBioCmirror()</code> to set the

            
            <code>"BioC_mirror"</code> option.

            
            </p>

            
            </li>

            
            <li><p> The <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> grammar now prevents using the argument <code>name</code>

            
            in signatures of S4 methods for <code>$</code> and <code>$&lt;-</code>, since

            
            they will always be called with a character string value for

            
            <code>name</code>.  The implicit S4 generic functions have been

            
            changed to reflect this: packages which included <code>name</code> in

            
            the signature of their methods need to be updated and

            
            re-installed.

            
            </p>

            
            </li>

            
            <li><p> The handling of the <code>method</code> argument of <code>glm()</code>

            
            has been refined following suggestions by Ioannis Kosmidis and

            
            Heather Turner.

            
            </p>

            
            </li>

            
            <li> <p><code>str()</code> gains a new argument <code>list.len</code> with

            
            default 99, limiting the number of <code>list()</code> items (per

            
            level), thanks to suggestions from David Winsenius.

            
            </p>

            
            </li>

            
            <li><p> 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).

            
            </p>

            
            </li>

            
            <li><p> New functions <code>enc2native()</code> and <code>enc2utf8()</code>

            
            convert character vectors with possibly marked encodings to the

            
            current locale and UTF-8 respectively.

            
            </p>

            
            </li>

            
            <li><p> Unrecognized escapes and embedded nuls in character strings are

            
            now an error, not just a warning.  Thus option <code>"warnEscapes"</code>

            
            is no longer needed.  <code>rawToChar()</code> now removes trailing nuls

            
            silently, but other embedded nuls become errors.

            
            </p>

            
            </li>

            
            <li><p> Informational messages about masked objects displayed when a

            
            package is attached are now more compact, using <code>strwrap()</code>

            
            instead of one object per line.

            
            </p>

            
            </li>

            
            <li> <p><code>print.rle()</code> gains argument <code>prefix</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>download.file()</code> gains a <code>"curl"</code> method, mainly

            
            for use on platforms which have <code>curl</code> but not

            
            <code>wget</code>, but also for some hard-to-access URLs.

            
            </p>

            
            </li>

            
            <li><p> In <code>Rd</code>, <span class="samp">\eqn</span> and <span class="samp">\deqn</span> will render in

            
            HTML (and convert to text) upper- and lower-case Greek letters

            
            (entered as <span class="samp">\alpha</span> ...), <span class="samp">\ldots</span>, <span class="samp">\dots</span>,

            
            <span class="samp">\ge</span> and <span class="samp">\le</span>.

            
            </p>

            
            </li>

            
            <li> <p><code>utf8ToInt()</code> and <code>intToUtf8()</code> now map <code>NA</code> inputs

            
            to <code>NA</code> outputs.

            
            </p>

            
            </li>

            
            <li> <p><code>file()</code> has a new argument <code>raw</code> which may help

            
            if it is used with something other than a regular file, e.g. a

            
            character device.

            
            </p>

            
            </li>

            
            <li><p> New function <code>strtoi()</code>, a wrapper for the C function

            
            <code>strtol</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>as.octmode()</code> and <code>as.hexmode()</code> now allow inputs

            
            of length other than one.

            
            </p>

            
            <p>The <code>format()</code> and <code>print()</code> methods for

            
            <code>"octmode"</code> now preserve names and dimensions (as those for

            
            <code>"hexmode"</code> did).

            
            </p>

            
            <p>The <code>format()</code> methods for classes <code>"octmode"</code> and

            
            <code>"hexmode"</code> gain a <code>width</code> argument.

            
            </p>

            
            </li>

            
            <li> <p><code>seq.int()</code> returns an integer result in some further cases

            
            where <code>seq()</code> does, e.g. <code>seq.int(1L, 9L, by = 2L)</code>.

            
            </p>

            
            </li>

            
            <li><p> Added <span class="samp">\subsection{}{}</span> macro to Rd syntax, for

            
            subsections within sections.

            
            </p>

            
            </li>

            
            <li><p> n-dimensional arrays with dimension names can now be indexed

            
            by an n-column character matrix.  The indices are matched against

            
            the dimension names.  <code>NA</code> indices are propagated to the

            
            result.  Unmatched values and <code>""</code> are not allowed and

            
            result in an error.

            
            </p>

            
            </li>

            
            <li> <p><code>interaction(drop=TRUE)</code> uses less memory (related to

            
            <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14121">PR#14121</a>).

            
            </p>

            
            </li>

            
            <li> <p><code>summary()</code> methods have been added to the

            
            <code>"srcref"</code> and <code>"srcfile"</code> classes, and various

            
            encoding issues have been cleaned up.

            
            </p>

            
            </li>

            
            <li><p> If option <code>"checkPackageLicense"</code> is set to <code>TRUE</code> (not

            
            currently the default), users will be asked to agree to

            
            non-known-to-be-FOSS package licences at first use.

            
            </p>

            
            </li>

            
            <li><p> Checking <code>setAs(a, b)</code> methods only gives a message

            
            instead of a warning, when one of <code>a</code> or <code>b</code> is

            
            unknown.

            
            </p>

            
            </li>

            
            <li><p> New function <code>norm()</code> to compute a matrix norm.

            
            <code>norm()</code> and also <code>backsolve()</code> and <code>sample()</code>

            
            have implicit S4 generics.

            
            </p>

            
            </li>

            
            <li><p> Files &lsquo;<span class="file">Renviron.site</span>&rsquo; and &lsquo;<span class="file">Rprofile.site</span>&rsquo; can have

            
            architecture-specific versions on systems with sub-architectures.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD check</code> now (by default) also checks Rd files

            
            for auto-generated content in need of editing, and missing

            
            argument descriptions.

            
            </p>

            
            </li>

            
            <li> <p><code>aggregate()</code> gains a formula method thanks to a

            
            contribution by Arni Magnusson.  The data frame method now allows

            
            summary functions to return arbitrarily many values.

            
            </p>

            
            </li>

            
            <li> <p><code>path.expand()</code> now propagates <code>NA</code> values rather

            
            than converting them to <code>"NA"</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>file.show()</code> now disallows <code>NA</code> values for file names,

            
            headers, and pager.

            
            </p>

            
            </li>

            
            <li><p> The &lsquo;fuzz&rsquo; used by <code>seq()</code> and <code>seq.int()</code> has

            
            been reduced from <code>1e-7</code> to <code>1e-10</code>, which should be

            
            ample for the double-precision calculations used in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>.  It

            
            ensures that the fuzz never comes into play with sequences of

            
            integers (wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14169">PR#14169</a>).

            
            </p>

            
            </li>

            
            <li><p> The default value of <code>RSiteSearch(restrict=)</code> has been

            
            changed to include vignettes but to exclude R-help.  The R-help

            
            archives available have been split, with a new option of

            
            <code>"Rhelp10"</code> for those from 2010.

            
            </p>

            
            </li>

            
            <li><p> New function <code>rasterImage()</code> in the <code>graphics</code>

            
            package for drawing raster images.

            
            </p>

            
            </li>

            
            <li> <p><code>stats:::extractAIC.coxph()</code> now omits aliased terms

            
            when computing the degrees of freedom (suggestion of Terry

            
            Therneau).

            
            </p>

            
            </li>

            
            <li> <p><code>cor()</code> and <code>cov()</code> now test for misuse with

            
            non-numeric arguments, such as the non-bug report <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14207">PR#14207</a>.

            
            </p>

            
            </li>

            
            <li> <p><code>pchisq(ncp =, log.p = TRUE)</code> is more accurate for

            
            probabilities near one.  E.g., <code>pchisq(80, 4, ncp=1,

            
                   log.p=TRUE)</code>.  (Maybe what was meant in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14216">PR#14216</a>.)

            
            </p>

            
            </li>

            
            <li> <p><code>maintainer()</code> has been added, to give convenient

            
            access to the name of the maintainer of a package (contributed by

            
            David Scott).

            
            </p>

            
            </li>

            
            <li> <p><code>sample()</code> and <code>sample.int()</code> allow zero items to

            
            be sampled from a zero-length input.  <code>sample.int()</code> gains a

            
            default value <code>size=n</code> to be more similar to

            
            <code>sample()</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>switch()</code> returned <code>NULL</code> on error (not

            
            previously documented on the help page): it now does so

            
            invisibly, analogously to if-without-else.

            
            </p>

            
            <p>It is now primitive: this means that argument <code>EXPR</code> is

            
            always matched to the first argument and there is no danger of

            
            partial matching to later named arguments.

            
            </p>

            
            </li>

            
            <li><p> Primitive functions <code>UseMethod()</code>, <code>attr()</code>,

            
            <code>attr&lt;-()</code>, <code>on.exit()</code>, <code>retracemem()</code> and

            
            <code>substitute()</code> 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

            
            <code>switch()</code>, <code>call()</code>, <code>.C()</code> ...).

            
            </p>

            
            </li>

            
            <li><p> 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.

            
            </p>

            
            </li>

            
            <li> <p><code>base::which()</code> uses a new <code>.Internal</code> function

            
            when <code>arr.ind</code> is <code>FALSE</code> resulting in a 10x speedup.

            
            Thanks to Patrick Aboyoun for implementation suggestions.

            
            </p>

            
            </li>

            
            <li><p> Help conversion to text now uses the first part of

            
            <span class="samp">\enc{}{}</span> markup if it is representable in the current

            
            output encoding.  On the other hand, conversion to LaTeX with the

            
            default <code>outputEncoding = "ASCII"</code> uses the second part.

            
            </p>

            
            </li>

            
            <li><p> A new class <code>"listOfMethods"</code> has been introduced to

            
            represent the methods in a methods table, to replace the

            
            deprecated class <code>"MethodsList"</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>any()</code> and <code>all()</code> return early if possible.

            
            This may speed up operations on long vectors.

            
            </p>

            
            </li>

            
            <li> <p><code>strptime()</code> now accepts <code>"%z"</code> (for the offset

            
            from UTC in the RFC822 format of <code>+/-hhmm</code>).

            
            </p>

            
            </li>

            
            <li><p> The PCRE library has been updated to version 8.02, a bug-fix

            
            release which also updates tables to Unicode 5.02.

            
            </p>

            
            </li>

            
            <li><p> Functions which may use a graphical <code>select.list()</code>

            
            (including <code>menu()</code> and <code>install.packages()</code>) now check

            
            on a Unix-alike that Tk can be started (and not just

            
            <code>capabilities("tcltk") &amp;&amp; capabilities("X11")</code>).

            
            </p>

            
            </li>

            
            <li><p> The parser no longer marks strings containing octal or hex

            
            escapes as being in UTF-8 when entered in a UTF-8 locale.

            
            </p>

            
            </li>

            
            <li><p> On platforms with cairo but not Pango (notably Mac OS X) the

            
            initial default <code>X11()</code> type is set to <code>"Xlib"</code>: this avoids

            
            several problems with font selection when done by cairo rather

            
            than Pango (at least on Mac OS X).

            
            </p>

            
            </li>

            
            <li><p> New function <code>arrayInd()</code> such that <code>which(x,

            
                   arr.ind = TRUE)</code> for an array 'x' is now equivalent to

            
            <code>arrayInd(which(x), dim(x), dimnames(x))</code>.

            
            </p>

            
            </li></ul>


            <h4>DEPRECATED &amp; DEFUNCT</h4>


            <ul>

            
            <li><p> Bundles of packages are defunct.

            
            </p>

            
            </li>

            
            <li> <p><code>stats::clearNames()</code> is defunct: use <code>unname()</code>.

            
            </p>

            
            </li>

            
            <li><p> Basic regular expressions are defunct, and

            
            <code>strsplit()</code>, <code>grep()</code>, <code>grepl()</code>, <code>sub()</code>,

            
            <code>gsub()</code>, <code>regexpr()</code> and <code>gregexpr()</code> no longer

            
            have an <code>extended</code> argument.

            
            </p>

            
            </li>

            
            <li> <p><code>methods::trySilent()</code> is defunct.

            
            </p>

            
            </li>

            
            <li> <p><code>index.search()</code> (which was deprecated in 2.10.0) is no

            
            longer exported and has a different argument list.

            
            </p>

            
            </li>

            
            <li><p> Use of multiple arguments to <code>return()</code> is now defunct.

            
            </p>

            
            </li>

            
            <li><p> The use of <code>UseMethod()</code> with more than two arguments

            
            is now defunct.

            
            </p>

            
            </li>

            
            <li><p> In the <span class="pkg">methods</span> package, the <code>"MethodsList"</code>

            
            metadata objects which had been superseded by hash tables

            
            (environments) since <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.8.0 are being phased out.  Objects of

            
            this class are no longer assigned or used as metadata by the

            
            package.

            
            </p>

            
            <p><code>getMethods()</code> is now deprecated, with its internal use replaced

            
            by <code>findMethods()</code> and other changes.  Creating objects from the

            
            <code>"MethodsList"</code> class is also deprecated.

            
            </p>

            
            </li>

            
            <li><p> Parsing strings containing both octal/hex and Unicode escapes

            
            now gives a warning and will become an error in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.12.0.

            
            </p>

            
            </li></ul>


            <h4>INSTALLATION</h4>


            <ul>

            
            <li><p> UTF-8 is now used for the reference manual and package

            
            manuals.  This requires LaTeX &lsquo;2005/12/01&rsquo; or later.

            
            </p>

            
            </li>

            
            <li> <p><code>configure</code> looks for a POSIX compliant

            
            <code>tr</code>, Solaris's <code>/usr/ucb/tr</code> having been found

            
            to cause <code>Rdiff</code> to malfunction.

            
            </p>

            
            </li>

            
            <li> <p><code>configure</code> is now generated with <code>autoconf

            
                   2.65</code>, which works better on recent systems and on Mac OS X.

            
            </p>

            
            </li></ul>


            <h4>PACKAGE INSTALLATION</h4>


            <ul>

            
            <li><p> Characters in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 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.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD INSTALL</code> now tests that the installed package

            
            can be loaded (and backs out the installation if it cannot): this

            
            can be suppressed by <span class="option">--no-test-load</span>.  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.

            
            </p>

            
            </li>

            
            <li><p> Package installation on Windows for a package with a

            
            &lsquo;<span class="file">src</span>&rsquo; directory now checks if a DLL is created unless there

            
            is a &lsquo;<span class="file">src/Makefile.win</span>&rsquo; 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

            
            &lsquo;<span class="file">&lt;pkg-name&gt;.dll</span>&rsquo;.)

            
            </p>

            
            </li></ul>


            <h4>BUG FIXES</h4>


            <ul>

            
            <li><p> Using <code>with()</code>, <code>eval()</code> etc with a list with some

            
            unnamed elements now works.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14035">PR#14035</a>)

            
            </p>

            
            </li>

            
            <li><p> The <code>"quick"</code> 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.

            
            </p>

            
            </li>

            
            <li><p> 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

            
            <code>findInheritedMethods()</code>.

            
            </p>

            
            </li>

            
            <li> <p><span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> framework installation (on Mac OS X) would not work

            
            properly if a rogue <code>Resources</code> directory was present at the

            
            top level.  Such a non-symlink will now be renamed to

            
            <code>Resources.old</code> (and anything previously named

            
            <code>Resources.old</code> removed) as part of the framework

            
            installation process.

            
            </p>

            
            </li>

            
            <li><p> 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 <code>...</code>).  Arguments omitted

            
            from the method definition but conforming (per the documentation)

            
            should now be ignored (treated as <code>"ANY"</code>) in dispatching.

            
            </p>

            
            </li>

            
            <li><p> The computations for S4 method evaluation when <code>...</code>

            
            was in the signature could fail, treating <code>...</code> as an

            
            ordinary symbol.  This has been fixed, for the known cases.

            
            </p>

            
            </li>

            
            <li><p> Various <code>ar()</code> fitting methods have more protection for

            
            singular fits.

            
            </p>

            
            </li>

            
            <li> <p><code>callNextMethod</code> now works again with the <code>drop=</code>

            
            argument in <span class="samp">[</span>

            
            </p>

            
            </li>

            
            <li> <p><code>parse()</code> and <code>parse_Rd()</code> miscounted columns when

            
            multibyte UTF-8 characters were present.

            
            </p>

            
            </li>

            
            <li><p> 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.

            
            </p>

            
            </li>

            
            <li> <p><code>cor(A, B)</code> where <code>A</code> is <i>n x 1</i>

            
            and <code>B</code> a 1-dimensional array segfaulted or gave an internal

            
            error.  (The case <code>cor(B, A)</code> was

            
            <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=7116">PR#7116</a>.)

            
            </p>

            
            </li>

            
            <li> <p><code>cut.POSIXt()</code> applied to a start value after the DST

            
            transition on a DST-change day could give the wrong time for

            
            argument <code>breaks</code> in units of days or longer.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14208">PR#14208</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>do_par()</code> <code>UNPROTECT</code>ed too early  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14214">PR#14214</a>)

            
            </p>

            
            </li>

            
            <li><p> Subassignment <code>x[[....]] &lt;- y</code> didn't check for a

            
            zero-length right hand side, and inserted a rubbish

            
            value.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14217">PR#14217</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>fisher.test()</code> no longer gives a P-value <strong>very</strong>

            
            slightly &gt; 1, in some borderline cases.

            
            </p>

            
            </li>

            
            <li><p> Internal function <code>matchArgs()</code> no longer modifies the

            
            general purpose bits of the <code>SEXP</code>s that make up the formals

            
            list of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> functions.  This fixes an invalid error message that

            
            would occur when a garbage collection triggered a second call to

            
            <code>matchArgs</code> for the same function <em>via</em> a finalizer.

            
            </p>

            
            </li>

            
            <li> <p><code>gsub()</code> in 2.10.x could fail from stack overflow for

            
            extremely long strings due to temporary data being allocated on

            
            the stack.  Also, <code>gsub()</code> with <code>fixed=TRUE</code> is in some

            
            circumstances considerably faster.

            
            </p>

            
            </li>

            
            <li><p> Several primitives, including <code>attributes()</code>,

            
            <code>attr&lt;-()</code> <code>interactive()</code>, <code>nargs()</code> and

            
            <code>proc.time()</code>, did not check that they were called with the

            
            correct number of arguments.

            
            </p>

            
            </li>

            
            <li><p> A potential race condition in <code>list.files()</code> 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.

            
            </p>

            
            </li>

            
            <li> <p><code>mean(x, trim=, na.rm = FALSE)</code> failed to return <code>NA</code> if

            
            <code>x</code> contained missing values.  (Reported by Bill Dunlap.)

            
            </p>

            
            </li>

            
            <li><p> Extreme tail behavior of, <code>pbeta()</code> {and hence

            
            <code>pf()</code>}, e.g., <code>pbeta(x, 3, 2200, lower.tail=FALSE,

            
                   log.p=TRUE)</code> now returns finite values instead of jumping to

            
            <code>-Inf</code> too early.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14230">PR#14230</a>).

            
            </p>

            
            </li>

            
            <li> <p><code>parse(text=x)</code> misbehaved for objects <code>x</code> that

            
            were not coerced internally to character, notably symbols.

            
            (Reported to R-devel by Bill Dunlap.)

            
            </p>

            
            </li>

            
            <li><p> The internal C function <code>coerceSymbol</code> now handles

            
            coercion to character, and warns if coercion fails (rather than

            
            silently returning <code>NULL</code>).  This allows a name to be given

            
            where a character vector is required in functions which coerce

            
            internally.

            
            </p>

            
            </li>

            
            <li><p> The interpretation by <code>strptime()</code> of <code>"%c"</code> was

            
            non-standard (not that it is ever advisable to use locale- and

            
            system-specific input formats).

            
            </p>

            
            </li>

            
            <li><p> capabilities(<code>"X11"</code>) now works the same way on Mac OS X as on

            
            other platforms (and as documented: it was always true for R

            
            built with <span class="option">--with-aqua</span>, as the CRAN builds are).

            
            </p>

            
            </li>

            
            <li><p> The <code>X11()</code> 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).

            
            </p>

            
            </li>

            
            <li> <p><code>read.fwf()</code> misread multi-line records when n was specified.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14241">PR#14241</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>all.equal(tolerance = e)</code> passes the numeric

            
            tolerance also to the comparison of the attributes.

            
            </p>

            
            </li>

            
            <li> <p><code>pgamma(0, 0)</code>, a boundary case, now returns 0, its

            
            limit from the left, rather than the limit from the right.

            
            </p>

            
            </li>

            
            <li><p> Issuing <code>POST</code> requests to the internal web server could stall

            
            the request under certain circumstances.

            
            </p>

            
            </li>

            
            <li> <p><code>gzcon( &lt;textConnection&gt; )</code>, an error, no longer

            
            damages the connection (in a way to have it

            
            segfault).  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14237">PR#14237</a>)

            
            </p>

            
            </li>

            
            <li><p> All the results from <code>hist()</code> now use the nominal

            
            <code>breaks</code> not those adjusted by the numeric &lsquo;fuzz&rsquo;:

            
            in recent versions the nominal <code>breaks</code> were reported but

            
            the 'density' referred to the intervals used in the calculation

            
            &ndash; which mattered very slightly for one of the extreme bins.

            
            (Based on a report by Martin Becker.)

            
            </p>

            
            </li>

            
            <li><p> If <code>xy[z].coords</code> (used internally by many graphics

            
            functions) are given a list as <code>x</code>, they now check that

            
            the list has suitable names and give a more informative error

            
            message.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=13936">PR#13936</a>)

            
            </p>

            
            </li></ul>


            <h3><img class="toplogo" src="../help/figures/../../html/Rlogo.svg" alt="[R logo]" /> CHANGES IN R VERSION 2.10.1 patched</h3>


            <h4>NEW FEATURES</h4>


            <ul>

            
            <li><p> The handling of line textures in the <code>postscript()</code> and

            
            <code>pdf()</code> devices was set up for round end caps (the only type

            
            which existed at the time): it has now been adjusted for butt

            
            endcaps.

            
            </p>

            
            </li>

            
            <li> <p><code>lchoose(a, k)</code> is now defined as

            
            <code>log(abs(choose(a,k)))</code>, analogously to <code>lfactorial()</code>.

            
            </p>

            
            </li>

            
            <li><p> Although <code>\eqn{}</code> in Rd files is defined as a

            
            &lsquo;verbatim&rsquo; macro, many packages expected <code>\dots</code> and

            
            <code>\ldots</code> to be interpreted there (as was the case in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> &lt;

            
            2.10.0), so this is now done (using an ellipsis in HTML

            
            rendering).

            
            </p>

            
            </li>

            
            <li><p> Escaping of braces in quoted strings in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>-code sections of

            
            Rd files is allowed again.  This had been changed for the new Rd

            
            format in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 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.

            
            </p>

            
            </li>

            
            <li><p> The PCRE library has been updated to version 8.01, a bug-fix

            
            release.

            
            </p>

            
            </li>

            
            <li> <p><code>tools::readNEWS()</code> now accepts a digit as the first

            
            character of a news section.

            
            </p>

            
            </li></ul>


            <h4>BUG FIXES</h4>


            <ul>

            
            <li><p> Using <code>read.table(header=TRUE)</code> on a header with an

            
            embedded new line would copy part of the header into the data.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14103">PR#14103</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>qpois(p = 1, lambda = 0)</code> now gives 0 as for all other

            
            <code>p</code>.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14135">PR#14135</a>)

            
            </p>

            
            </li>

            
            <li><p> Functions related to string comparison

            
            (e.g., <code>unique()</code>, <code>match()</code>) could cause crashes when

            
            used with strings not in the native encoding, e.g., UTF-8 strings

            
            on Windows.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14114">PR#14114</a> and <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14125">PR#14125</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>x[ , drop=TRUE]</code> dropped an <code>NA</code> level even if it

            
            was in use.

            
            </p>

            
            </li>

            
            <li><p> The dynamic HTML help system reported the wrong MIME type

            
            for the style sheet.

            
            </p>

            
            </li>

            
            <li> <p><code>tools::codoc()</code> (used by <code>R CMD check</code>) was

            
            missing cases where the function had no arguments but was

            
            documented to have some.

            
            </p>

            
            </li>

            
            <li><p> Help links containing special characters (e.g., <code>"?"</code>)

            
            were not generated correctly when rendered in

            
            HTML.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14155">PR#14155</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>lchoose(a, k)</code> no longer wrongly gives <code>NaN</code> for

            
            negative <code>a</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>ks.test()</code> could give a p-value that was off by one

            
            observation due to rounding error.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14145">PR#14145</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>readBin()</code>/<code>readChar()</code> when reading millions of

            
            character strings in a single call used excessive amounts of

            
            memory (which also slowed them down).

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD SHLIB</code> could fail if used with paths that

            
            were not alphanumeric, e.g. contained <code>+</code>.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14168">PR#14168</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>sprintf()</code> was not re-entrant, which potentially

            
            caused problems if an <code>as.character()</code> method called it.

            
            </p>

            
            </li>

            
            <li><p> The <code>quartz()</code> 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>

            
            </li>

            
            <li> <p><code>p.adjust(method, n)</code> now works correctly for the

            
            rare case <code>n &gt; length(p)</code>, also when method differs from

            
            <code>"bonferroni"</code> or <code>"none"</code>, thanks to a patch from

            
            Gordon Smyth.

            
            </p>

            
            </li>

            
            <li> <p><code>tools::showNonASCII()</code> failed to detect non-ASCII characters

            
            if <code>iconv()</code> (incorrectly) converted them to different ASCII

            
            characters.  (Seen on Windows only.)

            
            </p>

            
            </li>

            
            <li> <p><code>tcrossprod()</code> wrongly failed in some cases when one of the

            
            arguments was a vector and the other a matrix.

            
            </p>

            
            </li>

            
            <li> <p><code>[cr]bind(..., deparse.level=2)</code> was not always giving

            
            names when documented to do so.  (Discovered whilst investigating

            
            <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14189">PR#14189</a>.)

            
            </p>

            
            </li>

            
            <li> <p><code>match(incomparables=&lt;non-NULL&gt;)</code> could in rare cases

            
            infinite-loop.

            
            </p>

            
            </li>

            
            <li> <p><code>poisson.test()</code> needed to pass argument

            
            <code>conf.level</code> to <code>binom.test()</code>.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14195">PR#14195</a>)

            
            </p>

            
            </li>

            
            <li><p> The <code>"nls"</code> method for <code>df.residual()</code> gave

            
            incorrect results for models fitted with <code>na.action =

            
                   na.exclude</code>.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14194">PR#14194</a>)

            
            </p>

            
            </li>

            
            <li><p> A change to <code>options(scipen=)</code> was only implemented

            
            when printing next occurred, even though it should have affected

            
            intervening calls to <code>axis()</code>, <code>contour()</code> and

            
            <code>filledcontour()</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>prettyNum(drop0trailing=TRUE)</code> did not handle signs of

            
            imaginary parts of complex numbers correctly (and this was used

            
            by <code>str()</code>: <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14201">PR#14201</a>).

            
            </p>

            
            </li>

            
            <li> <p><code>system.time()</code> had the <code>sys.child</code> component

            
            wrong (copied <code>user.child</code> instead) on systems with

            
            <code>HAVE_GETRUSAGE</code>.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14210">PR#14210</a>)

            
            </p>

            
            </li>

            
            <li><p> 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.

            
            </p>

            
            </li>

            
            <li><p> The suppression of auto-rotation in <code>bitmap()</code> and

            
            <code>dev2bitmap()</code> with the <code>"pdfwrite"</code> device was not

            
            working correctly.

            
            </p>

            
            </li>

            
            <li> <p><code>plot(ecdf(), log="x")</code> no longer gives an incorrect

            
            warning.

            
            </p>

            
            </li>

            
            <li> <p><code>read.fwf()</code> works again when argument <code>file</code> is

            
            a connection.

            
            </p>

            
            </li>

            
            <li><p> Startup files will now be found if their paths exceed 255

            
            bytes.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14228">PR#14228</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>contrasts&lt;-</code> (in the <span class="pkg">stats</span> package) no longer has an

            
            undeclared dependence on <span class="pkg">methods</span> (introduced in 2.10.0).

            
            </p>

            
            </li></ul>


            <h3><img class="toplogo" src="../help/figures/../../html/Rlogo.svg" alt="[R logo]" /> CHANGES IN R VERSION 2.10.1</h3>


            <h4>NEW FEATURES</h4>


            <ul>

            
            <li><p> The PCRE library has been updated to version 8.00.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD INSTALL</code> has new options <span class="option">--no-R</span>,

            
            <span class="option">--no-libs</span>, <span class="option">--no-data</span>, <span class="option">--no-help</span>,

            
            <span class="option">--no-demo</span>, <span class="option">--no-exec</span>, and <span class="option">--no-inst</span> 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).

            
            </p>

            
            </li>

            
            <li><p> The documented line-length limit of 4095 bytes when reading

            
            from the console now also applies also to <code>parse(file="")</code>

            
            (which previously had a limit of around 1024 bytes).

            
            </p>

            
            </li>

            
            <li><p> A Bioconductor mirror can be set for use by

            
            <code>setRepositories()</code> <em>via</em> the option <code>"BioC_mirror"</code>,

            
            e.g. the European mirror can be selected by

            
            <code>options(BioC_mirror="http://bioconductor.statistik.tu-dortmund.de")</code>.

            
            </p>

            
            </li>

            
            <li><p> Double-clicking in a <code>tk_select.list()</code> list box now

            
            selects the item and closes the list box (as happens on the

            
            Windows <code>select.list()</code> widget).

            
            </p>

            
            </li></ul>


            <h4>INSTALLATION</h4>


            <ul>

            
            <li> <p><code>configure</code> will be able to find a usable

            
            <code>libtiff</code> in some rare circumstances where it did not

            
            previously (where <code>libtiff</code> needed to be linked explicitly against

            
            <code>-ljpeg</code>).

            
            </p>

            
            </li>

            
            <li><p> Making <code>refman.pdf</code> works around a problem with the indexing

            
            with <code>hyperref 6.79d</code> and later.

            
            </p>

            
            </li></ul>


            <h4>DEPRECATED &amp; DEFUNCT</h4>


            <ul>

            
            <li><p> The <code>extended</code> argument is deprecated in

            
            <code>strsplit()</code>, <code>grep()</code>, <code>grepl()</code>, <code>sub()</code>,

            
            <code>gsub()</code>, <code>regexpr()</code> and <code>gregexpr()</code> (not just

            
            the value <code>extended = FALSE</code>) and will be removed in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>

            
            2.11.0.

            
            </p>

            
            </li></ul>


            <h4>BUG FIXES</h4>


            <ul>

            
            <li> <p><code>trigamma(x)</code> and other <code>psigamma(x, n)</code> calls

            
            are now accurate for very large <code>abs(x)</code>.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14020">PR#14020</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>[g]sub(perl=FALSE, fixed=FALSE)</code> could use excessive

            
            stack space when used with a very long vector containing some

            
            non-ASCII strings.

            
            </p>

            
            </li>

            
            <li><p> The default method of <code>weighted.mean(na.rm = TRUE)</code>

            
            did not omit weights for <code>NA</code> observations in 2.10.0.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14032">PR#14032</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>[g]regexpr(pattern, fixed = TRUE)</code> returned match

            
            positions in bytes (not characters) in an MBCS locale if

            
            <code>pattern</code> was a single byte.

            
            </p>

            
            <p><code>[g]sub(fixed = TRUE)</code> with a single-byte pattern could

            
            conceivably have matched part of a multibyte character in a

            
            non-UTF-8 MBCS.

            
            </p>

            
            </li>

            
            <li> <p><code>findLineNum()</code> and <code>setBreakpoint()</code> would

            
            sometimes fail if the specified file was not in the current

            
            directory.

            
            </p>

            
            </li>

            
            <li><p> Package <span class="pkg">tcltk</span>'s <code>demo(tkdensity)</code> was broken in

            
            2.9.0 when <code>demo()</code> was changed to set <code>par(ask = TRUE)</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>gsub()</code> with backrefs could fail on extremely long strings

            
            (hundreds of thousands of characters) due to integer overflow

            
            in a length calculation.

            
            </p>

            
            </li>

            
            <li> <p><code>abline(untf=TRUE)</code> now uses a better x-grid in

            
            log-scale, e.g., for <code>plot(c(1,300), c(1,300), log="xy");

            
            	abline(4,1, untf=TRUE)</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>detach()</code>/<code>unloadNamespace()</code> arrange to flush

            
            the package's lazyload cache of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> objects once the

            
            package/namespace is no longer needed.

            
            </p>

            
            </li>

            
            <li><p> There have been small fixes to the rendering of help,

            
            e.g. <code>\command</code> is now rendered verbatim

            
            (so e.g. <code>--</code> is not interpreted, <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14045">PR#14045</a>).

            
            </p>

            
            <p>Also, there are many small changes to help files where the new

            
            converters were not rendering them in the same way as before.

            
            </p>

            
            </li>

            
            <li> <p><code>available.packages()</code> would fail when run on a

            
            repository with no packages meeting the filtering conditions.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14042">PR#14042</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>rep(x, times, each = 2)</code> gave invalid results when the

            
            <code>times</code> argument was a vector longer than <code>x</code>.

            
            Reported by Bill Dunlap.

            
            </p>

            
            </li>

            
            <li><p> An error when <code>unloadNamespace()</code> attempted to run the

            
            <code>.onUnload()</code> function gave an error in the reporting

            
            function and so was not reported properly.

            
            </p>

            
            </li>

            
            <li><p> Text help rendering did not handle very long input lines

            
            properly.

            
            </p>

            
            </li>

            
            <li> <p><code>promptMethods()</code> generated signature documentation

            
            improperly.

            
            </p>

            
            </li>

            
            <li> <p><code>pgamma(x, a, lower.tail=FALSE)</code> and

            
            <code>qgamma(...)</code> are now considerably more accurate in some

            
            regions for very small <code>a</code>.  <code>qgamma()</code> now correctly

            
            returns <code>0</code> instead of <code>NaN</code> in similar extreme cases,

            
            and <code>qgamma()</code> no longer warns in the case of small

            
            <code>a</code>, see (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=12324">PR#12324</a>).

            
            </p>

            
            </li>

            
            <li> <p><code>unname()</code> now also removes names from a zero length vector.

            
            </p>

            
            </li>

            
            <li><p> Printing results from <code>ls.str()</code> no longer evaluates

            
            unevaluated calls.

            
            </p>

            
            </li>

            
            <li> <p><code>complete.cases()</code> failed on a 0-column data frame

            
            argument.  (Underlies <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14066">PR#14066</a>.)

            
            </p>

            
            <p>It could return nonsensical results if no input determined the

            
            number of cases (seen in the no-segfault tests).

            
            </p>

            
            </li>

            
            <li><p> An error in <code>nls()</code> with a long formula could cause a

            
            segfault.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14059">PR#14059</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>qchisq(p, df, ncp, lower.tail = FALSE)</code> with

            
            <code>ncp &gt;= 80</code> was inaccurate for small <code>p</code> (as the help page

            
            said): it is now less inaccurate.  (In part,

            
            <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=13999">PR#13999</a>.)

            
            </p>

            
            <p>For <code>ncp</code> less than but close to 80, <code>pchisq()</code> and

            
            <code>qchisq()</code> are more accurate for probabilities very close

            
            to 1 (a series expansion was truncated slightly too early).

            
            </p>

            
            <p><code>pchisq(x, df, ncp)</code> can no longer return values just larger

            
            than one for large values of <code>ncp</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>intToUtf8()</code> could fail when asked to produce 10Mb or more

            
            strings, something it was never intended to do: unfortunately

            
            Windows crashed <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> (other OSes reported a lack of resources).

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14068">PR#14068</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>chisq.test()</code> could fail when given argument

            
            <code>x</code> or <code>y</code> which deparsed to more than one line.

            
            (Reported by Laurent Gauthier.)

            
            </p>

            
            </li>

            
            <li><p> S4 methods are uncached whenever the namespace containing

            
            them is unloaded (by <code>unloadNamespace()</code> as well as by

            
            <code>detach(unload = TRUE))</code>.

            
            </p>

            
            </li>

            
            <li><p> The internal record-keeping by

            
            <code>dyn.load</code>/<code>dyn.unload</code> was incomplete, which could

            
            crash <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> if a DLL that registered <code>.External</code> routines had

            
            earlier been unloaded.

            
            </p>

            
            </li>

            
            <li> <p><code>bessel[JY](x, nu)</code> with <code>nu</code> a negative integer (a

            
            singular case) is now correct, analogously to <code>besselI()</code>,

            
            see <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=13556">PR#13556</a>.

            
            </p>

            
            </li>

            
            <li> <p><code>tools::file_path_as_absolute()</code> doubled the file

            
            separator when applied to a file such as &lsquo;<span class="file">&quot;/vmunix&quot;</span>&rsquo; or (on

            
            Windows) &lsquo;<span class="file">&quot;d:/afile&quot;</span>&rsquo; in a directory for which

            
            <code>getwd()</code> would return a path with a trailing separator

            
            (largely cosmetic, as reasonable file systems handle such a path

            
            correctly).  (Perhaps what was meant by <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14078">PR#14078</a>.)

            
            </p>

            
            </li>

            
            <li> <p><code>unsplit(drop = TRUE)</code> applied to a data frame failed

            
            to pass <code>drop</code> to the computation of row names.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14084">PR#14084</a>)

            
            </p>

            
            </li>

            
            <li><p> The <code>"difftime"</code> method of <code>mean()</code> ignored its

            
            <code>na.rm</code> argument.

            
            </p>

            
            </li>

            
            <li> <p><code>tcltk::tk_select.list()</code> is now more likely to remove the

            
            widget immediately after selection is complete.

            
            </p>

            
            </li>

            
            <li><p> Adding/subtracting a <code>"difftime"</code> object to/from a

            
            <code>"POSIXt"</code> or <code>"Date"</code> object works again (it was

            
            broken by the addition of <code>Ops.difftime</code>).

            
            </p>

            
            </li>

            
            <li><p> Conversion to latex of an Rd file with no aliases failed.

            
            </p>

            
            </li>

            
            <li> <p><code>wilcox.test(conf.int=TRUE)</code> has achieved.level

            
            corrected and, for <code>exact=FALSE</code>, now returns a

            
            <code>estimate</code> component which does not depend on the

            
            alternative used.

            
            </p>

            
            </li>

            
            <li> <p><code>help.search()</code> failed when the package argument was

            
            specified.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14113">PR#14113</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>switch(EXPR = "A")</code> now returns <code>NULL</code>, as does

            
            <code>switch(1)</code> (which used to signal an error).

            
            </p>

            
            </li></ul>


            <h3><img class="toplogo" src="../help/figures/../../html/Rlogo.svg" alt="[R logo]" /> CHANGES IN R VERSION 2.10.0</h3>


            <h4>SIGNIFICANT USER-VISIBLE CHANGES</h4>


            <ul>

            
            <li><p> Package help is now converted from <code>Rd</code> by the <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>-based

            
            converters that were first introduced in 2.9.0.  This means

            
            </p>


            <ul>

            
            <li><p> Packages that were installed by R-devel after 2009-08-09

            
            should not be used with earlier versions of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>, and most

            
            aspects of package help (including the runnable examples)

            
            will be missing if they are so used.

            
            </p>

            
            </li>

            
            <li><p> 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 <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> &lt; 2.10.0 are used if no parsed Rd files

            
            are found.  It is recommended that such packages be

            
            re-installed.)

            
            </p>

            
            </li></ul>


            </li>

            
            <li><p> HTML help is now generated dynamically using an HTTP server

            
            running in the <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> process and listening on the loopback

            
            interface.

            
            </p>


            <ul>

            
            <li><p> Those worried about security implications of such

            
            a server can disable it by setting the environment variable

            
            <span class="env">R_DISABLE_HTTPD</span> to a non-empty value.  This disables

            
            <code>help.start()</code> and HTML help (so text help is shown

            
            instead).

            
            </p>

            
            </li>

            
            <li><p> The Java/Javascript search engine has been replaced by an

            
            HTML interface to <code>help.search()</code>.  <code>help.start()</code> no

            
            longer has an argument <code>searchEngine</code> as it is no longer

            
            needed.

            
            </p>

            
            </li>

            
            <li><p> The HTML help can now locate cross-references of the form

            
            <code>\link[pkg]{foo}</code> and <code>\link[pkg:foo]{bar}</code>

            
            where <code>foo</code> is an alias in the package, rather than the

            
            documented (basename of a) filename (since the documentation

            
            has been much ignored).

            
            </p>

            
            </li></ul>


            </li></ul>


            <h4>NEW FEATURES</h4>


            <ul>

            
            <li> <p><code>polygon()</code>, <code>pdf()</code> and <code>postscript()</code> now

            
            have an argument <code>fillOddEven</code> (default <code>FALSE</code>),

            
            which controls the mode used for polygon fills of

            
            self-intersecting shapes.

            
            </p>

            
            </li>

            
            <li><p> New <code>debugonce()</code> function; further,

            
            <code>getOption("deparse.max.lines")</code> is now observed when

            
            debugging, from a code suggestion by John Brzustowski.

            
            (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=13647">PR#13647</a>/8)

            
            </p>

            
            </li>

            
            <li> <p><code>plot()</code> methods for <code>"stepfun"</code> and hence

            
            <code>"ecdf"</code> no longer plot points by default for <code>n &gt;= 1000</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>[g]sub(perl=TRUE)</code> now also supports <code>"\E"</code>

            
            in order to <strong>end</strong> <code>"\U"</code> and <code>"\L"</code> case changes,

            
            thanks to a patch from Bill Dunlap.

            
            </p>

            
            </li>

            
            <li> <p><code>factor()</code>, <code>levels()&lt;-</code>, 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.

            
            </p>

            
            </li>

            
            <li><p> New <code>print()</code> (S3) method for class <code>"function"</code>,

            
            also used for auto-printing.  Further, <code>.Primitive</code>

            
            functions now print and auto-print identically.  The new method

            
            is based on code suggestions by Romain François.

            
            </p>

            
            </li>

            
            <li><p> The <code>print()</code> and <code>toLatex()</code> methods for class

            
            <code>"sessionInfo"</code> now show the locale in a nicer format and

            
            have arguments to suppress locale information.

            
            </p>

            
            </li>

            
            <li><p> In addition to previously only <code>round()</code>, there are

            
            other <code>Math</code> group (S3) methods for <code>"difftime"</code>,

            
            such as <code>floor()</code>, <code>signif()</code>, <code>abs()</code>, etc.

            
            </p>

            
            </li>

            
            <li><p> For completeness, <code>old.packages()</code> and

            
            <code>available.packages()</code> allow arguments <code>type</code> to be

            
            specified (you could always specify arguments <code>available</code>

            
            or <code>contriburl</code>).

            
            </p>

            
            </li>

            
            <li> <p><code>available.packages()</code> by default only returns

            
            information on the latest versions of packages whose version

            
            requirements are satisfied by the currently running <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>.

            
            </p>

            
            </li>

            
            <li> <p><code>tools::write_PACKAGES()</code> has a new argument

            
            <code>latestOnly</code>, which defaults to <code>TRUE</code> when only the

            
            latest versions in the repository will be listed in the index.

            
            </p>

            
            </li>

            
            <li> <p><code>getOption()</code> has a new argument <code>default</code> that

            
            is returned if the specified option is not set.  This simplifies

            
            querying a value and checking whether it is <code>NULL</code> or not.

            
            </p>

            
            </li>

            
            <li> <p><code>parse()</code> now warns if the requested encoding is not supported.

            
            </p>

            
            </li>

            
            <li><p> The <code>"table"</code> method of <code>as.data.frame()</code> gains a

            
            <code>stringsAsFactors</code> argument to allow the classifying

            
            factors to be returned as character vectors rather than the

            
            default factor type.

            
            </p>

            
            </li>

            
            <li><p> If <code>model.frame.default()</code> encounters a character

            
            variable where <code>xlev</code> indicates a factor, it now converts

            
            the variable to a factor (with a warning).

            
            </p>

            
            </li>

            
            <li> <p><code>curve()</code> now returns a list containing the points that

            
            w§ere drawn.

            
            </p>

            
            </li>

            
            <li> <p><code>spineplot()</code> now accepts <code>axes = FALSE</code>, for

            
            consistency with other functions called by <code>plot.factor()</code>.

            
            </p>

            
            </li>

            
            <li><p> The Kendall and Spearman methods of <code>cor.test()</code> can

            
            optionally use continuity correction when not computing exact

            
            p-values.  (The Kendall case is the wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=13691">PR#13691</a>.)

            
            </p>

            
            </li>

            
            <li> <p><span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> now keeps track of line numbers during execution for code

            
            sourced with <code>options(keep.source = TRUE)</code>.  The source

            
            reference is displayed by debugging functions such as

            
            <code>traceback()</code>, <code>browser()</code>, <code>recover()</code>, and

            
            <code>dump.frames()</code>, and is stored as an attribute on each

            
            element returned by <code>sys.calls()</code>.

            
            </p>

            
            </li>

            
            <li><p> More functions now have an implicit (S4) generic definition.

            
            </p>

            
            </li>

            
            <li> <p><code>quantile.default()</code> now disallows factors (wish of

            
            <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=13631">PR#13631</a>) and its help

            
            documents what numeric-like properties its input need to have to

            
            work correctly.

            
            </p>

            
            </li>

            
            <li> <p><code>weighted.mean()</code> is now generic and has <code>"Date"</code>,

            
            <code>"POSIXct"</code> and <code>"POSIXlt"</code> methods.

            
            </p>

            
            </li>

            
            <li><p> Naming subscripts (e.g., <code>x[i=1, j=2]</code>) in

            
            <code>data.frame</code> methods for <code>[</code> and <code>[[</code> 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.)

            
            </p>

            
            </li>

            
            <li> <p><code>as.data.frame()</code> has an <code>"aovproj"</code> method.

            
            (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=13505">PR#13505</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>as.character(x)</code> for numeric <code>x</code> no longer

            
            produces strings such as <code>"0.30"</code>, i.e., with trailing

            
            zeros.  This change also renders levels construction in

            
            <code>factor()</code> more consistent.

            
            </p>

            
            </li>

            
            <li> <p><code>codocClasses()</code>, 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 <code>R CMD check &lt;pkg&gt;</code> when

            
            the package defines S4 classes.

            
            </p>

            
            </li>

            
            <li> <p><code>codoc()</code> now also checks S4 methods for code/documentation

            
            mismatches.

            
            </p>

            
            </li>

            
            <li> <p><code>for()</code>, <code>while()</code>, and <code>repeat()</code> 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.

            
            </p>

            
            </li>

            
            <li><p> The <code>print()</code> method for <code>ls.str()</code> results now

            
            obeys an optional <code>digits</code> argument.

            
            </p>

            
            </li>

            
            <li><p> The <code>method</code> argument of <code>glm()</code> now allows

            
            user-contributed methods.

            
            </p>

            
            </li>

            
            <li><p> More general <code>reorder.default()</code> replaces functionality of

            
            <code>reorder.factor()</code> and <code>reorder.character()</code>.

            
            </p>

            
            </li>

            
            <li><p> The function <code>aspell()</code> has been added to provide an

            
            interface to the <code>Aspell</code> spell-checker.

            
            </p>

            
            </li>

            
            <li><p> Filters <code>RdTextFilter()</code> and <code>SweaveTeXFilter()</code>

            
            have been added to the tools package to provide support for

            
            <code>aspell()</code> or other spell checkers.

            
            </p>

            
            </li>

            
            <li> <p><code>xtabs()</code> with the new argument <code>sparse = TRUE</code>

            
            now returns a sparse Matrix, using package <a href="https://CRAN.R-project.org/package=Matrix"><span class="pkg">Matrix</span></a>.

            
            </p>

            
            </li>

            
            <li> <p><code>contr.sum()</code> etc gain an argument <code>sparse</code>

            
            which allows sparse matrices to be returned.

            
            </p>

            
            <p><code>contrasts()</code> also gains a <code>sparse</code> argument which it

            
            passes to the actual contrast function if that has a formal

            
            argument <code>sparse</code>.

            
            </p>

            
            <p><code>contrasts(f, .) &lt;- val</code> now also works when <code>val</code>

            
            is a sparse Matrix.  It is planned that <code>model.matrix()</code>

            
            will work with such factors <code>f</code> in the future.

            
            </p>

            
            </li>

            
            <li> <p><code>readNEWS()</code> will recognize a UTF-8 byte-order mark

            
            (BOM) in the &lsquo;<span class="file">NEWS</span>&rsquo; file.  However, it is safer to use only

            
            ASCII code there because not all editors recognize BOMs.

            
            </p>

            
            </li>

            
            <li><p> New utility function <code>inheritedSlotNames()</code> for S4

            
            class programming.

            
            </p>

            
            </li>

            
            <li> <p><code>tabulate()</code> now allows NAs to pass through (and be ignored).

            
            </p>

            
            </li>

            
            <li><p> If <code>debug()</code> is called on an S3 generic function then

            
            all methods are debugged as well.

            
            </p>

            
            </li>

            
            <li><p> Outlier symbols drawn by <code>boxplot()</code> now obey the

            
            <code>outlwd</code> argument.  Reported by Jurgen Kluge.

            
            </p>

            
            </li>

            
            <li> <p><code>svd(x)</code> and <code>eigen(x)</code> now behave analogously to

            
            <code>qr(x)</code> in accepting logical matrices <code>x</code>.

            
            </p>

            
            </li>

            
            <li><p> File &lsquo;<span class="file">NEWS</span>&rsquo; is now in UTF-8, and has a BOM (often

            
            invisible) on the first line, and <code>Emacs</code> local variables

            
            set for UTF-8 at the end.  <code>RShowDoc("NEWS")</code> should display

            
            this correctly, given suitable fonts.

            
            </p>

            
            </li>

            
            <li> <p><code>terms.formula(simplify = TRUE)</code> now does not deparse

            
            the LHS and so preserves non-standard responses such as <code>`a:

            
                   b`</code> (requested by Sundar Dorai-Raj).

            
            </p>

            
            </li>

            
            <li><p> New function <code>news()</code> for building and querying <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> or

            
            package news information.

            
            </p>

            
            </li>

            
            <li> <p><code>z^n</code> for integer <code>n</code> and complex <code>z</code> is more

            
            accurate now if <code>|n| &lt;= 65536</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>factor(NULL)</code> now returns the same as

            
            <code>factor(character(0))</code> instead of an error, and

            
            <code>table(NULL)</code> consequently does analogously.

            
            </p>

            
            </li>

            
            <li> <p><code>as.data.frame.vector()</code> (and its copies) is slightly faster

            
            by avoiding a copy if there are no names (following a

            
            suggestion of Tim Hesterberg).

            
            </p>

            
            </li>

            
            <li> <p><code>writeLines()</code>, <code>writeBin()</code> and

            
            <code>writeChar()</code> have a new argument <code>useBytes</code>.  If

            
            false, character strings with marked encodings are translated to

            
            the current locale (as before) but if true they are written

            
            byte-by-byte.

            
            </p>

            
            </li>

            
            <li> <p><code>iconv()</code> has a new argument <code>mark</code> which can be

            
            used (by experts) to suppress the declaration of encodings.

            
            </p>

            
            </li>

            
            <li> <p>&lsquo;<span class="file">DESCRIPTION</span>&rsquo; file's <code>LinkingTo</code> specs are now

            
            recognized as installation dependencies, and included in package

            
            management computations.

            
            </p>

            
            </li>

            
            <li><p> Standardized &lsquo;<span class="file">DESCRIPTION</span>&rsquo; file <code>License</code> specs

            
            are now available for package management computations.

            
            </p>

            
            </li>

            
            <li> <p><code>"\uxxxx"</code> and <code>"\Uxxxxxxxx"</code> escapes can now be

            
            parsed to a UTF-8 encoded string even in non-UTF-8 locales (this

            
            has been implemented on Windows since <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 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).

            
            </p>

            
            </li>

            
            <li><p> New <code>as.raw()</code> method for <code>"tclObj"</code> objects (wish

            
            of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=13758">PR#13758</a>).

            
            </p>

            
            </li>

            
            <li> <p><code>Rd.sty</code> now makes a better job of setting email addresses,

            
            including using a monospaced font.

            
            </p>

            
            </li>

            
            <li> <p><code>textConnection()</code> gains an <code>encoding</code> argument

            
            to determine how input strings with marked encodings will be

            
            handled.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD Rd2pdf</code> is available as a shortcut for

            
            <code>R CMD Rd2dvi --pdf</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD check</code> now checks links where a package is

            
            specified (<code>\link[pkg]{file}</code> or

            
            <code>\link[pkg:file]{topic}</code>), if the package is available.

            
            It notes if the package is not available, as in many cases this

            
            is an error in the link.

            
            </p>

            
            </li>

            
            <li> <p><code>identical()</code> gains three logical arguments, which

            
            allow for even more differentiation, notably <code>-0</code> and

            
            <code>0</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>legend()</code> now can specify the <code>border</code> color of

            
            filled boxes, thanks to a patch from Frederic Schutz.

            
            </p>

            
            </li>

            
            <li><p> Indexing with a vector index to <code>[[ ]]</code> has now been

            
            extended to all recursive types.

            
            </p>

            
            </li>

            
            <li><p> Pairlists may now be assigned as elements of lists.  (Lists

            
            could always be created with pairlist elements, but <code>[[&lt;-</code>

            
            didn't support assigning them.)

            
            </p>

            
            </li>

            
            <li><p> The parser now supports C-preprocessor-like <code>#line</code>

            
            directives, so error messages and source references may refer to

            
            the original file rather than an intermediate one.

            
            </p>

            
            </li>

            
            <li><p> New functions <code>findLineNum()</code> and

            
            <code>setBreakpoint()</code> work with the source references to find

            
            the location of source lines and set breakpoints (using

            
            <code>trace()</code>) at those lines.

            
            </p>

            
            </li>

            
            <li><p> Namespace importing is more careful about warning on masked

            
            generics, thanks to a patch by Yohan Chalabi.

            
            </p>

            
            </li>

            
            <li> <p><code>detach()</code> now has an argument <code>character.only</code>

            
            with the same meaning as for <code>library()</code> or

            
            <code>require()</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>available.packages()</code> gains a <code>filters</code>

            
            argument for specifying the filtering operations performed on the

            
            packages found in the repositories.  A new built-in

            
            <code>"license/FOSS"</code> 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.

            
            </p>

            
            </li>

            
            <li><p> In registering an S3 class by a call to

            
            <code>setOldClass()</code>, the data part (e.g., the object type)

            
            required for the class can be included as one of the superclasses

            
            in the Classes argument.

            
            </p>

            
            </li>

            
            <li><p> The argument <code>f</code> to <code>showMethods()</code> can be an

            
            expression evaluating to a generic function, allowing methods to

            
            be shown for non-exported generics and other nonstandard cases.

            
            </p>

            
            </li>

            
            <li> <p><code>sprintf()</code> now supports <code>%o</code> for octal

            
            conversions.

            
            </p>

            
            </li>

            
            <li><p> New function <code>Sys.readlink()</code> for information about symbolic

            
            links, including if a file is a symbolic link.

            
            </p>

            
            </li>

            
            <li><p> Package <span class="pkg">tools</span> has new functions

            
            <code>checkRdaFiles()</code> and <code>resaveRdaFiles()</code> to report on

            
            the format of &lsquo;<span class="file">.rda</span>&rsquo;/&lsquo;<span class="file">.RData</span>&rsquo; data files, and to

            
            re-save them in a different compressed format, including choosing

            
            the most compact format available.

            
            </p>

            
            <p>A new <code>INSTALL</code> option, <span class="option">--resave-data</span>, makes use

            
            of this.

            
            </p>

            
            </li>

            
            <li><p> File &lsquo;<span class="file">~/.R/config</span>&rsquo; is used in preference to

            
            &lsquo;<span class="file">~/.Rconfig</span>&rsquo;, and these are now documented in &lsquo;R

            
            Installation and Administration&rsquo;.

            
            </p>

            
            </li>

            
            <li><p> Logic operations with complex numbers now work, as they were always

            
            documented to, and as in S.

            
            </p>

            
            </li>

            
            <li> <p><code>arrows()</code> and <code>segments()</code> allow one of <code>x1</code>

            
            or <code>y1</code> to be omitted to simplify the specification of

            
            vertical or horizontal lines (suggestion of Tim Hesterberg).

            
            </p>

            
            </li>

            
            <li> <p><code>approxfun()</code> is faster by avoiding repeated <code>NA</code>

            
            checks (diagnosis and patch by Karline Soetaert &amp; Thomas

            
            Petzoldt).

            
            </p>

            
            </li>

            
            <li><p> There are the beginnings of a Nynorsk translation by Karl Ove

            
            Hufthammer.

            
            </p>

            
            </li>

            
            <li> <p><code>stripchart()</code> allows <code>par</code> <code>bg</code> to be

            
            passed in for the background colour for <code>pch = 21</code> (wish of

            
            <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=13984">PR#13984</a>).

            
            </p>

            
            </li>

            
            <li><p> New generic function <code>.DollarNames()</code> to enable class authors

            
            to customize completion after the <code>$</code> extractor.

            
            </p>

            
            </li>

            
            <li> <p><code>load()</code>, <code>save()</code>, <code>dput()</code> and

            
            <code>dump()</code> now open a not-yet-open connection in the

            
            appropriate mode (as other functions using connections directly

            
            already did).

            
            </p>

            
            </li></ul>


            <h4>REGULAR EXPRESSIONS</h4>


            <ul>

            
            <li><p> 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 <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> sources.

            
            </p>

            
            <p>This is often faster, especially in a MBCS locale.

            
            </p>

            
            <p>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 <code>"^*"</code>.  Also, the interpretation of

            
            ranges such as <code>[W-z]</code> in caseless matching is no longer to map

            
            the range to lower case.

            
            </p>

            
            <p>This engine may in future be used in &lsquo;literal&rsquo; mode for

            
            <code>fixed = TRUE</code>, and there is a compile-time option in

            
            <code>src/main/grep.c</code> to do so.

            
            </p>

            
            </li>

            
            <li><p> The use of repeated boundary regexps in <code>gsub()</code> and

            
            <code>gregexpr()</code> as warned about in the help page does not work

            
            in this engine (it did in the previous one since 2005).

            
            </p>

            
            </li>

            
            <li><p> Extended (and basic) regexps now support same set of options

            
            as for <code>fixed = TRUE</code> and <code>perl = TRUE</code>, including

            
            <code>useBytes</code> and support for UTF-8-encoded strings in

            
            non-UTF-8 locales.

            
            </p>

            
            </li>

            
            <li> <p><code>agrep()</code> now has full support for MBCS locales with a modest

            
            speed penalty.  This enables <code>help.search()</code> to use approximate

            
            matching character-wise rather than byte-wise.

            
            </p>

            
            </li>

            
            <li> <p><code>[g]sub</code> use a single-pass algorithm instead of

            
            matching twice and so is usually faster.

            
            </p>

            
            </li>

            
            <li><p> The <code>perl = TRUE</code> versions now work correctly in a

            
            non-UTF-8 MBCS locale, by translating the inputs to UTF-8.

            
            </p>

            
            </li>

            
            <li> <p><code>useBytes = TRUE</code> now inhibits the translation of inputs with

            
            marked encodings.

            
            </p>

            
            </li>

            
            <li> <p><code>strsplit()</code> gains a <code>useBytes</code> argument.

            
            </p>

            
            </li>

            
            <li><p> The algorithm used by <code>strsplit()</code> has been reordered

            
            to batch by elements of <code>split</code>: this can be much faster for

            
            <code>fixed = FALSE</code> (as multiple compilation of regexps is avoided).

            
            </p>

            
            </li>

            
            <li><p> The help pages, including <code>?regexp</code>, have been updated

            
            and should be consulted for details of the new implementations.

            
            </p>

            
            </li></ul>


            <h4>HELP &amp; Rd FILE CHANGES</h4>


            <ul>

            
            <li><p> A new dynamic HTML help system is used by default, and may be

            
            controlled using <code>tools::startDynamicHelp()</code>.  With this enabled,

            
            HTML help pages will be generated on request, resolving links

            
            by searching through the current <code>.libPaths()</code>.  The user

            
            may set options(<code>"help.ports"</code>) to control which IP port is used

            
            by the server.

            
            </p>

            
            </li>

            
            <li> <p><code>help.start()</code> no longer sets <code>options(htmlhelp =

            
                   TRUE)</code> (it used to on Unix but not on Windows).  Nor does it on

            
            Unix reset the <code>"browser"</code> option if given an argument of

            
            that name.

            
            </p>

            
            <p>Arguments <code>update</code> and <code>remote</code> are now available

            
            on all platforms: the default is <code>update = FALSE</code> since the

            
            http server will update the package index at first use.

            
            </p>

            
            </li>

            
            <li> <p><code>help()</code> has a new argument <code>help_type</code> (with

            
            default set by the option of that name) to supersede arguments

            
            <code>offline</code>, <code>htmlhelp</code> and <code>chmhelp</code>

            
            (although for now they still work if <code>help_type</code> is

            
            unset).  There is a new type, <code>"PDF"</code> to allow offline PDF

            
            (rather than PostScript).

            
            </p>

            
            <p>A function <code>offline_help_helper()</code> will be used if this exists

            
            in the workspace or further down the search path, otherwise

            
            the function of that name in the <span class="pkg">utils</span> namespace is used.

            
            </p>

            
            </li>

            
            <li><p> Plain text help is now used as the fallback for HTML help (as

            
            it always was for Compiled HTML help on Windows).

            
            </p>

            
            </li>

            
            <li><p> It is possible to ask for static HTML pages to be prebuilt

            
            <em>via</em> the configure option <span class="option">--enable-prebuilt-html</span>.  This

            
            may be useful for those who wish to make HTML help available

            
            outside R, e.g. on a local web site.

            
            </p>

            
            </li>

            
            <li><p> An experimental tag <code>\Sexpr</code> has been added to Rd

            
            files, to evaluate expressions at build, install, or render time.

            
            Currently install time and render time evaluation are supported.

            
            </p>

            
            </li>

            
            <li><p> Tags <code>\if</code>, <code>\ifelse</code> and <code>\out</code> have been

            
            added to allow format-specific (or more general, using

            
            <code>\Sexpr</code>) conditional text in man pages.

            
            </p>

            
            </li>

            
            <li><p> The <code>parse_Rd()</code> 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.

            
            </p>

            
            </li>

            
            <li> <p><code>parse_Rd()</code> now has an argument <code>fragment</code>

            
            (default <code>FALSE</code>) to accept small fragments of Rd files (so

            
            that <code>\Sexpr</code> can output Rd code which is then parsed).

            
            </p>

            
            </li>

            
            <li> <p><code>parse_Rd()</code> now always converts its input to UTF-8.

            
            The <code>Rd2*</code> rendering functions have a new argument,

            
            <code>outputEncoding</code>, which controls how their output is

            
            encoded.

            
            </p>

            
            </li>

            
            <li> <p><code>parse_Rd()</code> no longer includes the newline as part of

            
            a <code>"%"</code>-style comment.

            
            </p>

            
            </li>

            
            <li><p> There have been various bug fixes and code reorganization in

            
            the Rd renderers <code>Rd2HTML</code>, <code>Rd2latex</code>, <code>Rd2txt</code>,

            
            and <code>Rd2ex</code>.

            
            </p>

            
            <p>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).

            
            </p>

            
            </li>

            
            <li> <p><code>print.Rd()</code> now adds necessary escape characters so that

            
            printing and re-parsing an Rd object should produce an

            
            equivalent object.

            
            </p>

            
            </li>

            
            <li> <p><code>parse_Rd()</code> was incorrectly handling multiple backslashes in

            
            <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> code strings, converting 4n+3 backslashes to 2n+1 instead

            
            of 2n+2.

            
            </p>

            
            </li>

            
            <li> <p><code>parse_Rd()</code> now recognizes the <code>\var</code> tag within

            
            a quoted string in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>-like text.

            
            </p>

            
            </li>

            
            <li> <p><code>parse_Rd()</code> now treats the argument of

            
            <code>\command</code> as LaTeX-like, rather than verbatim.

            
            </p>

            
            </li></ul>


            <h4>COMPRESSION</h4>


            <ul>

            
            <li><p> New function <code>untar()</code> to list or unpack tar archives,

            
            possibly compressed.  This uses either an external <code>tar</code>

            
            command or an internal implementation.

            
            </p>

            
            </li>

            
            <li><p> New function <code>tar()</code> to create (possibly compressed)

            
            tar archives.

            
            </p>

            
            </li>

            
            <li><p> New functions <code>memCompress()</code> and

            
            <code>memDecompress()</code> for in-memory compression and

            
            decompression.

            
            </p>

            
            </li>

            
            <li> <p><code>bzfile()</code> has a <code>compress</code> argument to select

            
            the amount of effort put into compression when writing.

            
            </p>

            
            </li>

            
            <li><p> New function <code>xzfile()</code> for use with

            
            <code>xz</code>-compressed files.  (This can also read files

            
            compressed by some versions of <code>lzma</code>.)

            
            </p>

            
            </li>

            
            <li> <p><code>gzfile()</code> looks at the file header and so can now also

            
            read <code>bzip2</code>-ed files and <code>xz</code>-compressed files.

            
            </p>

            
            </li>

            
            <li><p> There are the new options of <code>save(compress = "bzip2")</code>

            
            and <code>"xz"</code> to use <code>bzip2</code> or <code>xz</code>

            
            compression (which will be slower, but can give substantially

            
            smaller files).  Argument <code>compression_level</code> gives finer

            
            control over the space/time tradeoffs.

            
            </p>

            
            <p><code>load()</code> can read such saves (but only as from this version of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>).

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD INSTALL</code>/<code>check</code> and

            
            <code>tools::writePACKAGES</code> accept a wider range of compressed

            
            tar archives.  Precisely how wide depends on the capabilities of

            
            the host system's <code>tar</code> command: they almost always

            
            include <code>.tar.bz2</code> archives, and with modern versions of

            
            <code>tar</code> other forms of compression such as <code>lzma</code>

            
            and <code>xz</code>, and arbitrary extensions.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD INSTALL</code> has a new option

            
            <span class="option">--data-compress</span> to control the compression used when

            
            lazy-loading data.  New possibilities are

            
            <span class="option">--data-compress=bzip2</span> which will give ca 15% better

            
            compression at the expense of slower installation times, and

            
            <span class="option">--data-compress=xz</span>, 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 <a href="https://CRAN.R-project.org/package=survival"><span class="pkg">survival</span></a>.)

            
            </p>

            
            </li>

            
            <li> <p><code>file()</code> for open = <code>""</code>, <code>"r"</code> or

            
            <code>"rt"</code> will automagically detect compressed files (from

            
            <code>gzip</code>, <code>bzip2</code> or <code>xz</code>).  This means

            
            that compressed files can be specified by file name (rather than

            
            <em>via</em> a <code>gzfile()</code> connection) to <code>read.table()</code>,

            
            <code>readlines()</code>, <code>scan()</code> and so on.

            
            </p>

            
            </li>

            
            <li> <p><code>data()</code> can handle compressed text files with extensions

            
            &lsquo;<span class="file">.{txt,tab,csv}.{gz,bz2,xz}</span>&rsquo; .

            
            </p>

            
            </li></ul>


            <h4>DEPRECATED &amp; DEFUNCT</h4>


            <ul>

            
            <li> <p><code>png(type="cairo1")</code> is defunct: the value is no longer

            
            recognized.

            
            </p>

            
            </li>

            
            <li> <p><code>tools::Rd_parse()</code> is defunct (as this version of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>

            
            uses only Rd version 2).

            
            </p>

            
            </li>

            
            <li><p> Use of file &lsquo;<span class="file">~/.Rconf</span>&rsquo; (which was deprecated in favour

            
            of &lsquo;<span class="file">~/.Rconfig</span>&rsquo; in 2004) has finally been removed.

            
            </p>

            
            </li>

            
            <li><p> Bundles of packages are deprecated.  See &lsquo;Writing R

            
            Extensions&rsquo; for the steps needed to unbundle a bundle.

            
            </p>

            
            </li>

            
            <li> <p><code>help()</code> arguments <code>offline</code>, <code>htmlhelp</code> and

            
            <code>chmhelp</code> are deprecated in favour of <code>help_type</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>clearNames()</code> (in package <span class="pkg">stats</span>) is deprecated

            
            for <code>unname()</code>.

            
            </p>

            
            </li>

            
            <li><p> Basic regular expressions (<code>extended = FALSE</code>) are

            
            deprecated in <code>strsplit</code>, <code>grep</code> 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 <code>fixed = TRUE</code> when using <code>extended =

            
                   FALSE</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>methods::trySilent()</code> is deprecated in favour of

            
            <code>try(silent=TRUE)</code> or &ndash; more efficiently and flexibly &ndash;

            
            something like <code>tryCatch(error = function(e) e)</code>.

            
            </p>

            
            </li>

            
            <li> <p><code>index.search()</code> is deprecated: there are no longer

            
            directories of types other than <code>help</code>.

            
            </p>

            
            </li></ul>


            <h4>INSTALLATION</h4>


            <ul>

            
            <li><p> cairo &gt;= 1.2 is now required (1.2.0 was released in July 2006)

            
            for cairo-based graphics devices (which remain optional).

            
            </p>

            
            </li>

            
            <li><p> A suitable <code>iconv()</code> is now required: support for

            
            configure option <span class="option">--without-iconv</span> has been withdrawn (it

            
            was deprecated in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.5.0).

            
            </p>

            
            </li>

            
            <li><p> Perl is no longer &lsquo;essential&rsquo;.  <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> can be built

            
            without it, but scripts <code>R CMD build</code>, <code>check</code>,

            
            <code>Rprof</code> and <code>Sd2d</code> currently require it.

            
            </p>

            
            </li>

            
            <li><p> A system <code>glob</code> function is now essential (a working

            
            <code>Sys.glob()</code> has been assumed since <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.9.0 at least).

            
            </p>

            
            </li>

            
            <li><p> C99 support for MBCS is now required, and configure option

            
            <span class="option">--disable-mbcs</span> has been withdrawn.

            
            </p>

            
            </li>

            
            <li><p> Having a version of <code>tar</code> capable of automagically

            
            detecting compressed archives is useful for

            
            <code>utils::untar()</code>, and so <code>gtar</code> (a common name for

            
            GNU <code>tar</code>) is preferred to <code>tar</code>: set environment

            
            variable <span class="env">TAR</span> to specify a particular <code>tar</code> command.

            
            </p>

            
            </li></ul>


            <h4>INTERNATIONALIZATION</h4>


            <ul>

            
            <li><p> There is some makefile support for adding/updating translations

            
            in packages: see <code>po/README</code> and &lsquo;Writing R Extensions&rsquo;.

            
            </p>

            
            <p>There is support for the use of <code>dngettext</code> for C-level

            
            translations in packages: see &lsquo;Writing R Extensions&rsquo;.

            
            </p>

            
            </li></ul>


            <h4>BUG FIXES</h4>


            <ul>

            
            <li><p> Assigning an extra 0-length column to a data frame by

            
            <code>DF[, "foo"] &lt;- value</code> now works in most cases (by filling

            
            with <code>NA</code>s) or fails.  (It used to give a corrupt data

            
            frame.)

            
            </p>

            
            </li>

            
            <li> <p><code>validObject()</code> avoids an error during evaluation in the case

            
            of various incorrect slot definitions.

            
            </p>

            
            </li>

            
            <li> <p><code>n:m</code> now returns a result of type <code>"integer"</code> in

            
            a few more boundary cases.

            
            </p>

            
            </li>

            
            <li><p> The <code>zap.ind</code> argument to <code>printCoefmat()</code> did

            
            not usually work as other code attempted to ensure that non-zero

            
            values had a non-zero representation.

            
            </p>

            
            </li>

            
            <li> <p><code>printCoefmat()</code> formatted groups of columns together,

            
            not just the <code>cs.ind</code> group but also the <code>zap.ind</code>

            
            group and a residual group.  It now formats all columns except

            
            the <code>cs.ind</code> group separately (and zaps the <code>zap.ind</code>

            
            group column-by-column).  The main effect will be see in the

            
            output from <code>print.anova()</code>, as this grouped SS-like columns

            
            in the <code>zap.ind</code> group.

            
            </p>

            
            </li>

            
            <li> <p><code>R_ReplDLLinit()</code> initializes the top-level jump so

            
            that some embedded applications on Windows no longer crash on

            
            error.

            
            </p>

            
            </li>

            
            <li> <p><code>identical()</code> 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.

            
            </p>

            
            </li>

            
            <li> <p><code>methods(f)</code> used to warn unnecessarily for an S4

            
            generic <code>f</code> which had been created based on an existing S3

            
            generic.

            
            </p>

            
            </li>

            
            <li><p> The check for consistent ordering of superclasses was not

            
            ignoring all conditional relations (the symptom was usually

            
            spurious warnings for classes extending <code>"array"</code>).

            
            </p>

            
            </li>

            
            <li><p> Trying to assign into a raw vector with an index vector

            
            containing <code>NA</code>s could cause a segfault.  Reported by Hervé

            
            Pagès.

            
            </p>

            
            </li>

            
            <li> <p><code>Rscript</code> could segfault if (by user error) its

            
            filename argument was missing.  Reported by Martin Morgan.

            
            </p>

            
            </li>

            
            <li> <p><code>getAnywhere()</code> (and functions that use it, including argument

            
            completion in the console) did not handle special built-in

            
            functions.  Reported by Romain Francois.

            
            </p>

            
            </li>

            
            <li> <p><code>order()</code> was missing a <code>PROTECT()</code> call and so

            
            could segfault when called on character data under certain (rare)

            
            circumstances involving marked non-native encodings.

            
            </p>

            
            </li>

            
            <li> <p><code>prettyNum(z, drop0trailing=TRUE)</code> did not work

            
            correctly when <code>z</code> was a complex vector.  Consequently,

            
            <code>str(z, ...)</code> also did not.  (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=13985">PR#13985</a>)

            
            </p>

            
            </li>

            
            <li> <p><code>make distclean</code> removed too many files in

            
            <code>etc/</code> if builddir = srcdir.

            
            </p>

            
            </li>

            
            <li> <p><code>R CMD</code> replaced <code>TEXINPUTS</code> rather than

            
            appending to it (as documented and intended).

            
            </p>

            
            </li>

            
            <li> <p><code>help.start()</code> no longer fails on unix when

            
            <code>"browser"</code> is a function.

            
            </p>

            
            </li>

            
            <li> <p><code>pbeta(x, ..., log.p = TRUE)</code> is sometimes more accurate,

            
            e.g., for very small <code>x</code>.

            
            </p>

            
            </li>

            
            <li><p> Unserializing a pre-2.8 workspace containing pure ASCII

            
            character objects with a Latin-1 or UTF-8 encoding would corrupt

            
            the <code>CHARSXP</code> cache.

            
            </p>

            
            </li></ul>


            <h3>OLDER NEWS</h3>


            <p>News for <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.9.2 patched and earlier can be found in files

            
            such as &lsquo;<span class="file">NEWS.2</span>&rsquo; in the &lsquo;<span class="file">doc</span>&rsquo; directory.

            
            </p>


            </body></html>