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<!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> 4.0.0 and later can be found in file ‘<span class="file">NEWS.Rd</span>’ in the<span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> sources and files ‘<span class="file">NEWS</span>’ and ‘<span class="file">doc/html/NEWS.html</span>’in an <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> build.</p><h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.6.3</h3><h4>NEW FEATURES</h4><ul><li><p> The included LAPACK has been updated to version 3.9.0 (forthe included routines, just bug fixes).</p></li></ul><h4>BUG FIXES</h4><ul><li><p> Fixed a C level integer overflow in <code>rhyper()</code>; reportedby Benjamin Tyner in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17694">PR#17694</a>.</p></li><li><p> Uses of <code>url(gzcon(.))</code> needing to extend buffer sizehave failed (with HTTP/2 servers), reported by Gábor Csárdi.</p></li><li> <p><code>predict(loess(..), se=TRUE)</code> now errors out (instead ofseg.faulting etc) for large sample sizes, thanks to a report andpatch by Benjamin Tyner in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17121">PR#17121</a>.</p></li><li> <p><code>tools:assertCondition(., "error")</code> and hence<code>assertError()</code> no longer return errors twice (invisibly).</p></li><li> <p><code>update(form, new)</code> in the case of a long <code>new</code>formula sometimes wrongly eliminated the intercept from <code>form</code>,or (more rarely) added a garbage term (or seg.faulted !); the fixhappened by simplifying the C-level logic of <code>terms.formula()</code>.Reported by Mathias Ambühl in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16326">PR#16326</a>.</p></li><li><p> The error message from <code>stopifnot(.., <error producing call>)</code>again contains the full <code>"stopifnot(.......)"</code> call: Itsattempted suppression did not work consistently.</p></li><li><p> On Windows, <code>download.file(., , "wininet", headers=character())</code>would fail; reported with patch proposal by Kevin Ushey in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17710">PR#17710</a>.</p></li></ul><h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.6.2</h3><h4>NEW FEATURES</h4><ul><li> <p><code>runmed(x, *)</code> gains a new option <code>na.action</code>determining <em>how</em> to handle <code>NaN</code> or <code>NA</code> in <code>x</code>.</p></li><li> <p><code>dotchart()</code> gains new options <code>ann</code>, <code>xaxt</code>,<code>frame.plot</code> and <code>log</code>.</p></li></ul><h4>INSTALLATION on a UNIX-ALIKE</h4><ul><li><p> Detection of the C stack direction has been moved fromrun-time to <code>configure</code>: this is safer with LTO builds andallows the detection to be overridden – see file‘<span class="file">config.site</span>’.</p></li><li><p> Source-code changes enable installation on platforms using<code>gcc -fno-common</code> (the expected default for<code>gcc 10.x</code>).</p></li></ul><h4>C-LEVEL FACILITIES</h4><ul><li> <p><code>installTrChar</code> (which is nowadays is wrapped by<code>installChar</code>) is defined in ‘<span class="file">Rinternals.h</span>’. (Neitherare part of the API.)</p></li></ul><h4>PACKAGE INSTALLATION</h4><ul><li><p> Header ‘<span class="file">Rconfig.h</span>’ contains the value of<code>FC_LEN_T</code> deduced at installation which is used by theprototypes in headers ‘<span class="file">R_ext/BLAS.h</span>’ and‘<span class="file">R_ext/Lapack.h</span>’ but to avoid extensive breakage this isonly exposed when <code>USE_FC_LEN_T</code> is defined.</p><p>If a package's C/C++ calls to BLAS/LAPACK allow for the‘hidden’ arguments used by most Fortran compilers to passthe lengths of Fortran character arguments, define<code>USE_FC_LEN_T</code> and include ‘<span class="file">Rconfig.h</span>’ (possibly<em>via</em> ‘<span class="file">R.h</span>’) before including ‘<span class="file">R_ext/BLAS.h</span>’ or‘<span class="file">R_ext/Lapack.h</span>’.</p></li><li><p> A package with Fortran source code and perhaps C (but notC++) sources can request for its shared object/DLL to be linked bythe Fortran compiler by including a line <code>USE_FC_TO_LINK=</code> in‘<span class="file">src/Makevars[.win]</span>’ and using <code>$(SHLIB_OPENMP_FFLAGS)</code>as part of <code>PKG_LIBS</code>.</p><p>The known reason for doing so is a package which uses Fortran(only) OpenMP on a platform where the Fortran OpenMP runtime isincompatible with the C one (e.g. <code>gfortran</code> 9.xwith <code>clang</code>).</p></li></ul><h4>UTILITIES</h4><ul><li> <p><code>R CMD check</code> has a new option to mitigate checksleaving files/directories in ‘<span class="file">/tmp</span>’. See the ‘RInternals’ manual – this is part of <code>--as-cran</code>.</p></li></ul><h4>Windows</h4><ul><li><p> The default standard for C++ in package installation isC++11 (as it has been on other platforms where available since <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>3.6.0: the default toolchain on Windows was defaulting to C++98).</p></li></ul><h4>DEPRECATED AND DEFUNCT</h4><ul><li><p> Support for specifying C++98 in package installation isdeprecated.</p></li><li><p> Support in <code>R CMD config</code> for <span class="samp">F77</span>,<span class="samp">FCPIFCPLAGS</span>, <span class="samp">CPP</span>, <span class="samp">CXXCPP</span> and <span class="samp">CXX98</span> andsimilar is deprecated. (<span class="samp">CPP</span> is found from the system<code>make</code> and may well not be set.)</p><p>Use <span class="samp">$CC -E</span> and <span class="samp">$CXX -E</span> instead of <span class="samp">CPP</span> and<span class="samp">CXXCPP</span>.</p></li></ul><h4>BUG FIXES</h4><ul><li> <p><code>runmed(x, *)</code> when <code>x</code> contains missing valuesnow works consistently for both <code>algorithm="Stuetzle"</code> and<code>"Turlach"</code>, and no longer segfaults for <code>"Turlach"</code>, asreported by Hilmar Berger.</p></li><li> <p><code>apply(diag(3), 2:3, mean)</code> now gives a helpful error message.</p></li><li> <p><code>dgamma(x, shape, log=TRUE)</code> now longer overflowsto <code>Inf</code> for shape < 1 and very small <code>x</code>, fixing<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17577">PR#17577</a>, reported by Jonathan Rougier.</p></li><li><p> Buffer overflow in building error messages fixed. Reportedby Benjamin Tremblay.</p></li><li> <p><code>options(str = .)</code> is correctly initialized atpackage <span class="pkg">utils</span> load time, now. A consequence is that<code>str()</code> in scripts now is more consistent to interactive use,e.g., when displaying function(**) argument lists.</p></li><li> <p><code>as.numeric(<call>)</code> now gives correct error message.</p></li><li><p> Printing <code>ls.str()</code> no longer wrongly shows<code>"<missing>"</code> in rare cases.</p></li><li><p> Auto-printing S4 objects no longer duplicates the object,for faster speed and reduced memory consumption. Reported by AaronLun.</p></li><li> <p><code>pchisq(<LRG>, <LRG>, ncp=100)</code> no longer takespractically forever in some cases. Hence ditto for corresponding<code>qchisq()</code> calls.</p></li><li> <p><code>x %% L</code> for finite <code>x</code> no longer returns<code>NaN</code> when <code>L</code> is infinite, nor suffers from cancellationfor large finite <code>L</code>, thanks to Long Qu's <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17611">PR#17611</a>.</p><p>Analogously, <code>x %/% L</code> and <code>L %/% x</code> suffer less fromcancellation and return values corresponding to limits for large<code>L</code>.</p></li><li> <p><code>grepl(NA, *)</code> now returns <code>logical</code> as documented.</p></li><li> <p><code>options(warn=1e11)</code> is an error now, instead of laterleading to C stack overflow because of infinite recursion.</p></li><li> <p><code>R_tryCatch</code> no longer transfers control for allconditions. Reported and patch provided by Lionel Henry in<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17617">PR#17617</a>.</p></li><li> <p><code>format(object.size(.), digits=NULL)</code> now works, fixing<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17628">PR#17628</a> reported by Jonathan Carroll.</p></li><li> <p><code>get_all_vars(f, d)</code> now also works for cases, e.g. where<code>d</code> contains a matrix. Reported by Simon Wood in 2009 and patchprovided by Ben Bolker in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=13624">PR#13624</a>.</p><p>Additionally, it now also works when some variables are data frames,fixing <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14905">PR#14905</a>, reported by Patrick Breheny.</p></li><li> <p><code>barplot()</code> could get spacings wrong if there were exactly twobars <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15522">PR#15522</a>. Patch by Michael Chirico.</p></li><li> <p><code>power.t.test()</code> works in more cases when returning valuesof n smaller than 2.</p></li><li> <p><code>dotchart(*, pch=., groups=.)</code> now works better. Reportedby Robert and confirmed by Nic Rochette in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16953">PR#16953</a>.</p></li><li> <p><code>canCoerce(obj, cl)</code> no longer assumes<code>length(class(obj)) == 1</code>.</p></li><li> <p><code>plot.formula(*, subset = *)</code> now also works in a boundarycase reported by Robert Schlicht (TU Dresden).</p></li><li> <p><code>readBin()</code> and <code>writeBin()</code> of a<code>rawConnection()</code> now also work in large cases, thanks to areport and proposal by Taeke Harkema in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17665">PR#17665</a>.</p></li></ul><h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.6.1</h3><h4>INSTALLATION on a UNIX-ALIKE</h4><ul><li><p> The default detection of the shell variable <code>libNN</code> isoverridden for derivatives of Debian Linux, some of which havestarted to have a ‘<span class="file">/usr/lib64</span>’ directory.(E.g. Ubuntu 19.04.) As before, it can be specified in‘<span class="file">config.site</span>’.</p></li></ul><h4>UTILITIES</h4><ul><li> <p><code>R CMD config</code> knows the values of <code>AR</code> and<code>RANLIB</code>, often set for LTO builds.</p></li></ul><h4>DEPRECATED AND DEFUNCT</h4><ul><li><p> The use of a character vector with <code>.Fortran()</code> isformally deprecated and gives a non-portability warning. (It haslong been strongly discouraged in ‘Writing R Extensions’.)</p></li></ul><h4>BUG FIXES</h4><ul><li><p> On Windows, GUI package installation via <code>menuInstallPkgs()</code>works again, thanks to Len Weil's and Duncan Murdoch's <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17556">PR#17556</a>.</p></li><li> <p><code>R CMD check</code> on <code>data()</code> fixing <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17558">PR#17558</a>thanks to Duncan Murdoch.</p></li><li> <p><code>quasi(*, variance = list(..))</code> now works moreefficiently, and should work in all cases fixing <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17560">PR#17560</a>.Further, <code>quasi(var = mu(1-mu))</code> and <code>quasi(var = "mu ^ 3")</code>now work, and <code>quasi(variance = "log(mu)")</code> now gives a correcterror message.</p></li><li><p> Creation of lazy loading database during package installation isagain robust to Rprofile changing the current working directory(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17559">PR#17559</a>).</p></li><li> <p><code>boxplot(y ~ f, horizontal=TRUE)</code> now produces correct x-and y-labels.</p></li><li> <p><code>rbind.data.frame()</code> allows to keep <code><NA></code> levelsfrom factor columns (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17562">PR#17562</a>) via new option <code>factor.exclude</code>.</p><p>Additionally, it works in one more case with matrix-columns whichhad been reported on 2017-01-16 by Krzysztof Banas.</p></li><li><p> Correct messaging in C++ pragma checks in <span class="pkg">tools</span> code for<code>R CMD check</code>, fixing <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17566">PR#17566</a> thanks to Xavier Robin.</p></li><li><p>print()ing and auto-printing no longer differs for<code>function</code>s with a user defined <code>print.function</code>, thanks toBill Dunlap's report.</p></li><li><p> On Windows, <code>writeClipboard(.., format = <n>)</code> nowdoes correctly pass <code>format</code> to the underlying C code, thanks toa bug report (with patch) by Jenny Bryan.</p></li><li> <p><code>as.data.frame()</code> treats 1D arrays the same as vectors,<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17570">PR#17570</a>.</p></li><li><p> Improvements in <code>smoothEnds(x, *)</code> working with<code>NA</code>s (towards <code>runmed()</code> working in that case, in the nextversion of R).</p></li><li> <p><code>vcov(glm(<quasi>), dispersion = *)</code> works correctlyagain, fixing <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17571">PR#17571</a> thanks to Pavel Krivitsky.</p></li><li> <p><code>R CMD INSTALL</code> of binary packages on Windows nowworks also with per-directory locking.</p></li><li> <p><code>R CMD INSTALL</code> and <code>install.packages()</code> on Windowsare now more robust against a locked file in an earlier installationof the package to be installed. The default value of option<code>install.lock</code> on Windows has been changed to <code>TRUE</code>.</p></li><li><p> On Unix alikes (when <code>readline</code> is active), onlyexpand tilde (<code>~</code>) file names starting with a tilde, instead ofalmost all tildes.</p></li><li><p> In R documentation (‘<span class="file">*.Rd</span>’) files, <span class="samp">\item [..]</span> is nolonger treated specially when rendered in LaTeX and hence pdf, butrather shows the brackets in all cases.</p></li></ul><h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.6.0</h3><h4>SIGNIFICANT USER-VISIBLE CHANGES</h4><ul><li><p> Serialization format version 3 becomes the default forserialization and saving of the workspace (<code>save()</code>,<code>serialize()</code>, <code>saveRDS()</code>, <code>compiler::cmpfile()</code>).Serialized data in format 3 cannot be read by versions of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> priorto version 3.5.0. Serialization format version 2 is stillsupported and can be selected by <code>version = 2</code> in thesave/serialization functions. The default can be changed back forthe whole <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> session by setting environment variables<span class="env">R_DEFAULT_SAVE_VERSION</span> and <span class="env">R_DEFAULT_SERIALIZE_VERSION</span>to <code>2</code>. For maximal back-compatibility, files‘<span class="file">vignette.rds</span>’ and ‘<span class="file">partial.rdb</span>’ generated by <code>RCMD build</code> are in serialization format version 2, and resave bydefault produces files in serialization format version 2 (unlessthe original is already in format version 3).</p></li><li><p> The default method for generating from a discrete uniformdistribution (used in <code>sample()</code>, for instance) has beenchanged. This addresses the fact, pointed out by Ottoboni andStark, that the previous method made <code>sample()</code> noticeablynon-uniform on large populations. See <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17494">PR#17494</a> for adiscussion. The previous method can be requested using<code>RNGkind()</code> or <code>RNGversion()</code> if necessary forreproduction of old results. Thanks to Duncan Murdoch forcontributing the patch and Gabe Becker for further assistance.</p><p>The output of <code>RNGkind()</code> has been changed to also return the‘kind’ used by <code>sample()</code>.</p></li></ul><h4>NEW FEATURES</h4><ul><li> <p><code>Sys.setFileTime()</code> has been vectorized so arguments<code>path</code> and <code>time</code> of length greater than one are nowsupported.</p></li><li> <p><code>axis()</code> gets new option <code>gap.axis = NA</code> forspecifying a multiplication factor for the minimal “gap”(distance) between axis labels drawn. Its default is <code>1</code>for labels <em>parallel</em> to the axis, and <code>0.25</code> forperpendicular ones.</p><p>Perpendicular labels no longer overlap, fixing bug <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17384">PR#17384</a>.</p></li><li><p> The default method of <code>plot()</code> gains new arguments<code>xgap.axis = NA</code> and <code>ygap.axis = NA</code> to be passed tothe x– and y– <code>axis(.., gap.axis=*)</code> calls.</p></li><li> <p><code>removeSource()</code> now works not only for functions butalso for some language objects.</p></li><li> <p><code>as.call()</code>, <code>rep.int()</code>, <code>rep_len()</code> and<code>nchar()</code> dispatch internally.</p></li><li> <p><code>is(object, class2)</code> looks for <code>class2</code> in thecalling namespace after looking in the namespace of<code>class(object)</code>.</p></li><li> <p><code>extendrange(.., f)</code> with a length-2 <code>f</code> nowextends separately to the left and the right.</p></li><li> <p><code>lengths()</code> dispatches internally to S4 methods.</p></li><li> <p><code>download.file()</code> on Windows now uses <code>URLdecode()</code>to determine the file extension, and uses binary transfer(<code>mode = "wb"</code>) also for file extension ‘<span class="file">.rds</span>’.</p><p>The help page for <code>download.file()</code> now contains the sameinformation on all platforms.</p></li><li><p> Setting <span class="samp">C</span> locale for collation <em>via</em> environmentvariables <span class="env">LC_ALL</span> and <span class="env">LC_COLLATE</span> and <em>via</em> a callto <code>Sys.setlocale()</code> now takes precedence over environmentvariable <span class="env">R_ICU_LOCALE</span>.</p></li><li><p> There is a new function, <code>nullfile()</code>, to give the filename of the null system device (e.g., ‘<span class="file">/dev/null</span>’) on thecurrent platform.</p></li><li><p> There are two new options, <code>keep.parse.data</code> and<code>keep.parse.data.pkgs</code>, which control whether parse data areincluded into sources when <code>keep.source</code> or<code>keep.source.pkgs</code> is <code>TRUE</code>. By default,<code>keep.parse.data.pkgs</code> is now <code>FALSE</code>, which changesprevious behavior and significantly reduces space and time overheadwhen sources are kept when installing packages.</p></li><li><p> In <code>rapply(x, ..)</code>, <code>x</code> can also be“list-like” and of length <i>>= 2^{31}</i>.</p></li><li> <p><code>trimws()</code> gets new optional <code>whitespace</code>argument, allowing more extensive definitions of “space”,such as including Unicode spaces (as wished in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17431">PR#17431</a>).</p></li><li> <p><code>weighted.mean()</code> no longer coerces the weights to adouble/numeric vector, since <code>sum()</code> now handles integeroverflow. This makes <code>weighted.mean()</code> more polymorphic andendomorphic, but be aware that the results are no longerguaranteed to be a vector of type <span class="samp">double</span>.</p></li><li><p> When loading namespaces, S3 method registrations whichoverwrite previous registrations are now noted by default (using<code>packageStartupMessage()</code>).</p></li><li> <p><code>compiler::cmpfile()</code> gains a <code>version</code> argument, foruse when the output file should be saved in serialization format 2.</p></li><li><p> The axis labeling in the default method of <code>pairs()</code>may now be toggled by new options <code>horOdd</code> and <code>verOdd</code>.</p></li><li><p> (Not Windows nor macOS.) Package <span class="pkg">tcltk</span> now supports anenvironment variable <span class="env">R_DONT_USE_TK</span> which if set disables Tkinitialization. This is intended for use to circumvent errors inloading the package, e.g. with recent Linux running underan address sanitizer.</p></li><li><p> The <code>numeric</code> method of <code>all.equal()</code> getsoptional arguments <code>countEQ</code> and <code>formatFUN</code>. If<code>countEQ</code> is true, the mean error is more sensible when manyentries are <b>eq</b>ual.</p></li><li> <p><code>outer(x,y, FUN = "*")</code> is more efficient using<code>tcrossprod(u,v)</code> instead of <code>u %*% t(v)</code>.</p></li><li> <p><code>vcov(<mlm>)</code> is more efficient via new optionalarguments in <code>summary.mlm()</code>.</p></li><li><p> The default method of <code>summary()</code> gets an option tochoose the <em>kind</em> of <code>quantile()</code>s to use; wish of<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17438">PR#17438</a>.</p></li><li><p> Fitting multiple linear models <em>via</em> <code>lm()</code> doeswork with <em>matrix</em> offsets, as suggested in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17407">PR#17407</a>.</p></li><li><p> The new functions <code>mem.maxVSize()</code> and<code>mem.maxMSize()</code> allow the maximal size of the vector heapand the maximal number of nodes allowed in the current <code>R</code>process to be queried and set.</p></li><li> <p><code>news()</code> gains support for ‘<span class="file">NEWS.md</span>’ files.</p></li><li><p> An effort has been started to have our reference manuals,i.e., all help pages. show platform-independent information (ratherthan Windows or Unix-alike specifics visible only on that platform).Consequently, the Windows version of <code>X11()</code> / <code>x11()</code>got identical formal arguments to the Unix one.</p></li><li> <p><code>sessionInfo()$running</code> has been factored out in a newvariable <code>osVersion</code>.</p></li><li> <p><code>slice.index()</code> now also works for multi-dimensionalmargins.</p></li><li> <p><code>untar()</code> used with an external <code>tar</code> commandassumes this supports decompression including <code>xz</code> andautomagically detecting the compression type. This has been trueof all mainstream implementations since 2009 (for GNU<code>tar</code>, since version 1.22): older implementations arestill supported <em>via</em> the new argument<code>support_old_tars</code> whose default is controlled by environmentvariable <span class="env">R_SUPPORT_OLD_TARS</span>. (It looks like NetBSD andOpenBSD have ‘older’ <code>tar</code> commands for thispurpose.)</p></li><li><p> The new function <code>asplit()</code> allow splitting an array ormatrix by its margins.</p></li><li><p> New functions <code>errorCondition()</code> and<code>warningCondition()</code> provide a convenient way to createstructured error and warning objects.</p><p><code>.Deprecated()</code> now signals a warning of class<code>"deprecatedWarning"</code>, and <code>.Defunct()</code> now signals anerror of class <code>"defunctError"</code>.</p></li><li><p> Many ‘package not found’ errors are now signaled aserrors of class <code>"packageNotFoundError"</code>.</p></li><li><p> As an experimental feature, when <code>loadNamespace()</code> failsbecause the requested package is not available the error isinitially signaled with a <code>retry_loadNamespace</code> restartavailable. This allows a calling handler to try to install thepackage and continue.</p></li><li> <p><code>S3method()</code> directives in ‘<span class="file">NAMESPACE</span>’ can nowalso be used to perform <em>delayed</em> S3 method registration.</p></li><li><p> Experimentally, setting environment variable<span class="env">_R_CHECK_LENGTH_1_LOGIC2_</span> will lead to warnings (or errorsif the variable is set to a ‘true’ value) when <code>&&</code> or<code>||</code> encounter and use arguments of length more than one.</p></li><li><p> Added <code>"lines"</code> and <code>"chars"</code> coordinate systemsto <code>grconvertX()</code> and <code>grconvertY()</code>.</p></li><li> <p><code>getOption()</code> is more efficient notably for the rarecase when called with two arguments, from several contributors in<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17394">PR#17394</a>.</p></li><li><p> In <code>.col(dim)</code> and <code>.row(dim)</code>, <code>dim</code> now mayalso be an integer-valued <code>"double"</code>.</p></li><li> <p><code>sQuote()</code> and <code>dQuote()</code> get an explicit <code>q</code>argument with obvious default instead of using<code>getOption("fancyQuotes")</code> implicitly and unconditionally.</p></li><li> <p><code>unzip()</code> can list archives with comments and withspaces in file names even using an external <code>unzip</code> command.</p></li><li><p> Command line completion has a new setting<code>rc.settings(dots = FALSE)</code> to remove <code>...</code> from thelist of possible function arguments.</p></li><li> <p><code>library()</code> no longer checks packages with compiledcode match <span class="samp">R.version$platform</span>. <code>loadNamespace()</code>never has, and increasingly the ‘canonical name’ does notreflect the important characteristics of compiled code.</p></li><li><p> The primitive functions <code>drop()</code> and <code>unclass()</code>now avoid duplicating their data for atomic vectors that are largeenough, by returning <code>ALTREP</code> wrapper objects with adjustedattributes. <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>-level assignments to change attributes will alsouse wrapper objects to avoid duplicating data for larger atomicvectors. <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> functions like <code>structure()</code> and <code>unname()</code>will therefore not duplicate data in these settings. Genericvectors as produced by <code>list()</code> are not yet covered by thisoptimization but may be in due course.</p></li><li><p> In <code>formals()</code>, <code>envir</code> becomes an optionalargument instead of being hardwired.</p></li><li><p> Instead of signalling an error for an invalid S4 object<code>x</code>, <code>str(x)</code> now gives a warning and subsequently stillshows most parts of <code>x</code>, e.g., when slots are missing.</p></li><li> <p><code>gamma(x)</code> and <code>lgamma(x)</code> no longer warn whencorrectly returning <code>Inf</code> or underflowing to zero. Thishelps maximum likelihood and similar computations.</p></li><li> <p><code>convertColor()</code> is now vectorized, so a lot faster forconverting many colours at once. The new argument<code>vectorized</code> to <code>colorConverter()</code> ensures thatnon-vectorized colour converters still work. (Thanks to BrodieGaslam.)</p></li><li> <p><code>download.file()</code> and <code>url()</code> get new argument<code>headers</code> for custom HTTP headers, e.g., allowing to performbasic http authentication, thanks to a patch contributed by GáborCsárdi.</p></li><li><p> File-based connection functions <code>file()</code>,<code>gzfile()</code>, <code>bzfile()</code> and <code>xzfile()</code> now signal anerror when used on a directory.</p></li><li><p> For <code>approx()</code>, <code>splinefun()</code> <em>etc</em>, a newsetting <code>ties = c("ordered", <fun>)</code> allows skipping thesorting and still treat ties.</p></li><li> <p><code>format(x)</code> gives a more user friendly error message inthe case where no method is defined. A minimal method is providedin <code>format.default(x)</code> when <code>isS4(x)</code> is true.</p></li><li> <p><code>which(x)</code> now also works when <code>x</code> is a longvector, thanks to Suharto Anggono's <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17201">PR#17201</a>. <strong>NB</strong>: thismay return a double result, breaking the previous guarantee of aninteger result.</p></li><li> <p><code>seq.default()</code> is more careful to return an<code>integer</code> (as opposed to <code>double</code>) result when itsarguments are large and/or classed objects; see comment #9 ofSuharto Anggono's <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17497">PR#17497</a>.</p></li><li><p> The <code>plot()</code> method for <code>lm</code> and <code>glm</code> fits,<code>plot.lm()</code>, gains a new option <code>iter.smooth</code> with adefault of <code>0</code> for binomial fits, no longer down-weightingwhen smoothing the residuals.</p></li><li> <p><code>zip()</code> passes its list of files <em>via</em> standardinput to the external command when too long for the command line(on some platforms).</p></li><li> <p><code>data()</code> gains an <code>overwrite</code> argument.</p></li><li> <p><code>t.test()</code> now also returns the standard error (inlist component <code>stderr</code>).</p></li><li> <p><code>model.matrix(*, contrasts.arg = CC)</code> now warns aboutinvalid <code>contrasts.arg</code>s.</p></li><li><p> Performance of <code>substr()</code> and <code>substring()</code> has beenimproved.</p></li><li> <p><code>stopifnot()</code> has been simplified thanks to SuhartoAnggono's proposals to become considerably faster for cheapexpressions.</p></li><li><p> The default ‘user agent’ has been changed whenaccessing <span class="samp">http://</span> and <span class="samp">https://</span> sites using<span class="samp">libcurl</span>. (A site was found which caused <span class="samp">libcurl</span> toinfinite-loop with the previous default.)</p></li><li> <p><code>sessionInfo()</code> now also contains <code>RNGkind()</code> andprints it when it differs from the default; based on a proposal andpatch by Gabe Becker in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17535">PR#17535</a>.Also, <code>RNGversion(getRversion())</code> works directly.</p></li><li> <p><code>library()</code> and <code>require()</code> now allow more controlover handling search path conflicts when packages areattached. The policy is controlled by the new<code>conflicts.policy</code> option.</p></li><li> <p><code>barplot()</code> gets a formula method, thanks to a patchproposal by Arni Magnusson in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17521">PR#17521</a>.</p></li><li> <p><code>pmax()</code> and <code>pmin(x)</code> now also work for longvectors, thanks to Suharto Anggono's <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17533">PR#17533</a>.</p></li><li> <p><code>bxp()</code> now warns when omitting duplicated arguments.</p></li><li><p> New <code>hcl.colors()</code> function to provide wide range ofHCL-based colour palettes with much better perceptual propertiesthan the existing RGB/HSV-based palettes like <code>rainbow()</code>.</p><p>Also a new <code>hcl.pals()</code> function to list available palettenames for <code>hcl.colors()</code>.</p><p>Contributed by Achim Zeileis.</p></li><li><p> The default colours for <code>image()</code> and<code>filled.contour()</code> are now based on <code>hcl.colors()</code>.</p></li><li><p> The palette-generating functions <code>rainbow()</code>,<code>gray.colors()</code>, etc. get a new <code>rev</code> argumentto facilitate reversing the order of colors.</p></li><li><p> New <code>str2lang()</code> and <code>str2expression()</code> as streamlinedversions of <code>parse(text=., keep.source=FALSE)</code> allow to abstracttypical call constructions, e.g., in <code>formula</code> manipulations.(Somewhat experimental)</p></li><li><p> Add <code>update_PACKAGES()</code> for incrementally updating apackage repository index, instead of rebuilding the index fromscratch. Thanks to Gabe Becker in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17544">PR#17544</a> for the patch, basedon part of his <span class="pkg">switchr</span> package.</p></li></ul><h4>INSTALLATION on a UNIX-ALIKE</h4><ul><li><p> The options selected for the C++ compiler default to theC++11 standard if supported, otherwise to the C++98 standard.</p></li><li><p> Visibility macros such as <span class="samp">C_VISIBILITY</span> can now beuser-set (including to empty), e.g. in ‘<span class="file">config.site</span>’.</p></li><li><p> Macro <span class="samp">FCLIBS</span>, which has sometimes been needed onSolaris, has been renamed to <span class="samp">FCLIBS_XTRA</span>.</p></li><li><p> Macro <span class="samp">F77</span> is always set to the value of <span class="samp">FC</span>, sothe latter should be set to user-select the Fortran compiler forboth fixed-form and free-form Fortran. In particular,<code>gfortran</code> is now the first choice for <span class="samp">F77</span>, not<code>f95</code>.</p><p>Macros <span class="samp">FFLAGS</span> and <span class="samp">FCFLAGS</span> remain distinct to allowfor a compiler which needs a flag to select free- or fixed-formFortran (most use the source-file extension to choose: ‘<span class="file">.f</span>’is fixed-form and ‘<span class="file">.f90</span>’ and ‘<span class="file">.f95</span>’ are free-form).</p><p>If only one of them is set, its value is used for both.</p></li><li><p> The special-casing of <span class="samp">CFLAGS</span>, <span class="samp">CXXFLAGS</span> and<span class="samp">FFLAGS</span> for Intel compilers on Linux has been removed: we donot have recent experience but the generic defaults now chosen arethe same as those previously special-cased for <span class="samp">x86_64</span>.</p><p>If necessary, override the defaults on the <code>configure</code>command line or in file ‘<span class="file">config.site</span>’.</p></li><li><p> Long-untested <code>configure</code> support for HP-UX and veryold versions of Linux has been removed.</p></li><li> <p><code>configure --with-blas</code> (without specifying a value)includes OpenBLAS in its search (before ATLAS and a genericBLAS). This follows recent versions of the <span class="samp">ax_blas</span>autoconf macro.</p></li><li><p> The <code>configure</code> macro <span class="samp">MAKEINFO</span> has beenupdated to <span class="samp">TEXI2ANY</span>.</p></li><li><p> Support for <code>make install-strip</code> has been enhanced.</p></li></ul><h4>PACKAGE INSTALLATION</h4><ul><li><p> Source package installation is by default ‘staged’:the package is installed into a temporary location under the finallibrary directory and moved into place once the installation iscomplete. The benefit is that partially-installed packages arehidden from other <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> sessions.</p><p>The overall default is set by environment variable<span class="env">R_INSTALL_STAGED</span>. <code>R CMD INSTALL</code> has new options<span class="option">--staged-install</span> and <span class="option">--no-staged-install</span>, andpackages can use the <span class="samp">StagedInstall</span> field in their‘<span class="file">DESCRIPTION</span>’ file to opt out. (That opt-out is a temporarymeasure which may be withdrawn in future.)</p><p>Staged installation requires either <span class="option">--pkglock</span> or<span class="option">--lock</span>, one of which is used by default.</p></li><li><p> The interpretation of source code with extension ‘<span class="file">.f</span>’is changing. Previously this denoted FORTRAN 77 code, but currentcompilers no longer have a FORTRAN 77 mode and interpret it as‘fixed-form’ Fortran 90 (or later where supported) code.Extensions ‘<span class="file">.f90</span>’ and ‘<span class="file">.f95</span>’ continue to indicate‘free-form’ Fortran code.</p><p>Legal FORTRAN 77 code is also legal fixed-form Fortran 9x; howeverthis change legitimizes the use of later features, in particularto replace features marked ‘obsolescent’ in Fortran 90 and‘deleted’ in Fortran 2018 which <code>gfortran</code> 8.x andlater warn about.</p></li><li><p> Packages containing files in the ‘<span class="file">src</span>’ directory withextensions ‘<span class="file">.f90</span>’ or ‘<span class="file">.f95</span>’ are now linked using the Cor C++ compiler rather than the Fortran 9x compiler. This isconsistent with fixed-form Fortran code and allows mixing of C++and free-form Fortran on most platforms.</p><p>Consequentially, a package which includes free-form Fortran 9xcode which uses OpenMP should include <span class="samp">SHLIB_OPENMP_CFLAGS</span>(or the <span class="samp">CXXFLAGS</span> version if they also include C++ code) in<span class="samp">PKG_LIBS</span> rather than <span class="samp">SHLIB_OPENMP_FCFLAGS</span> —fortunately on almost all current platforms they are the sameflag.</p></li><li><p> Macro <span class="samp">PKG_FFLAGS</span> will be used for the compilation ofboth fixed-form and free-form Fortran code unless<span class="samp">PKG_FCFLAGS</span> is also set (in ‘<span class="file">src/Makevars</span>’ or‘<span class="file">src/Makevars.win</span>’).</p></li><li><p> The make macro <span class="samp">F_VISIBILITY</span> is now preferred forboth fixed-form and free-form Fortran, for use in‘<span class="file">src/Makevars</span>’ and similar.</p></li><li> <p><code>R CMD INSTALL</code> gains a new option <span class="option">--strip</span>which (where supported) strips installed shared object(s): thiscan also be achieved by setting the environment variable<span class="env">_R_SHLIB_STRIP_</span> to a true value.</p><p>The new option <span class="option">--strip-lib</span> attempts stripping ofstatic and shared libraries installed under ‘<span class="file">lib</span>’.</p><p>These are most useful on platforms using GNU <code>binutils</code> (suchas Linux) and compiling with <span class="option">-g</span> flags.</p></li><li><p> There is more support for installing UTF-8-encoded packagesin a strict Latin-1 locale (and probably for other Latin locales):non-ASCII comments in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> code (and ‘<span class="file">NAMESPACE</span>’ files) areworked around better.</p></li></ul><h4>UTILITIES</h4><ul><li> <p><code>R CMD check</code> now optionally checks makefiles forcorrect and portable use of the <span class="samp">SHLIB_OPENMP_*FLAGS</span> macros.</p></li><li> <p><code>R CMD check</code> now evaluates <code>\Sexpr{}</code>expressions (including those in macros) before checking thecontents of ‘<span class="file">Rd</span>’ files and so detects issues both inevaluating the expressions and in the expanded contents.</p></li><li> <p><code>R CMD check</code> now lists missing packages separatedby commas and with regular quotes such as to be useful as argumentin calling <code>install.packages(c(..))</code>; from a suggestion byMarcel Ramos.</p></li><li> <p><code>tools::Rd2latex()</code> now uses UTF-8 as its defaultoutput encoding.</p></li><li> <p><code>R CMD check</code> now checks line endings of files withextension ‘<span class="file">.hpp</span>’ and those under ‘<span class="file">inst/include</span>’. Thecheck now includes that a non-empty file is terminated with anewline.</p><p><code>R CMD build</code> will correct line endings in such files.</p></li><li> <p><code>R CMD check</code> now tries re-building all vignettesrather than stopping at the first error: whilst doing so it adds‘bookmarks’ to the log. By default (see the ‘RInternals’ manual) it re-builds each vignette in a separateprocess.</p><p>It now checks for duplicated vignette titles (also known as‘index entries’): they are used as hyperlinks on<acronym><span class="acronym">CRAN</span></acronym> package pages and so do need to be unique.</p></li><li> <p><code>R CMD check</code> has more comprehensive checks on the‘<span class="file">data</span>’ directory and the functioning of <code>data()</code> in apackage.</p></li><li> <p><code>R CMD check</code> now checks<code>autoconf</code>-generated ‘<span class="file">configure</span>’ files have theircorresponding source files, including optionally attempting toregenerate them on platforms with <code>autoreconf</code>.</p></li><li> <p><code>R CMD build</code> has a new option<span class="option">--compression</span> to select the compression used for the tarball.</p></li><li> <p><code>R CMD build</code> now removes ‘<span class="file">src/*.mod</span>’ files onall platforms.</p></li></ul><h4>C-LEVEL FACILITIES</h4><ul><li><p> New pointer protection C functions <code>R_PreserveInMSet</code> and<code>R_ReleaseFromMSet</code> have been introduced to replace<code>UNPROTECT_PTR</code>, which is not safe to mix with <code>UNPROTECT</code>(and with <code>PROTECT_WITH_INDEX</code>). Intended for use in parsersonly.</p></li><li> <p><code>NAMEDMAX</code> has been raised to 7 to allow furtherprotection of intermediate results from (usually ill-advised)assignments in arguments to <code>BUILTIN</code> functions. Properlywritten package code should not be affected.</p></li><li> <p><code>R_unif_index</code> is now considered to be part of the C API.</p></li><li> <p><code>R_GetCurrentEnv()</code> allows C code to retrieve the currentenvironment.</p></li></ul><h4>DEPRECATED AND DEFUNCT</h4><ul><li><p> Argument <code>compressed</code> of <code>untar()</code> isdeprecated — it is only used for external <code>tar</code> commandswhich increasingly for extraction auto-detect compression andignore their <span class="option">zjJ</span> flags.</p></li><li> <p><code>var(f)</code> and hence <code>sd(f)</code> now give an error for<code>factor</code> arguments; they gave a deprecation warning since <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>3.2.3, <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16564">PR#16564</a>.</p></li><li><p> Package <span class="pkg">tools</span>' <code>vignetteDepends()</code> has beendeprecated (it called a function deprecated since Feb 2016), beingpartly replaced by newly exported <code>vignetteInfo()</code>.</p></li><li><p> The <code>f77_f2c</code> script has been removed: itno longer sufficed to compile the ‘<span class="file">.f</span>’ files in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>.</p></li><li><p> The deprecated legacy support of <code>make</code> macros suchas <span class="samp">CXX1X</span> has been removed: use the <span class="samp">CXX11</span> formsinstead.</p></li><li><p> Make macro <span class="samp">F77_VISIBILITY</span> is deprecated in favour of<span class="samp">F_VISIBILITY</span>.</p></li><li><p> Make macros <span class="samp">F77</span>, <span class="samp">FCPIFCPLAGS</span> and<span class="samp">SHLIB_OPENMP_FCFLAGS</span> are deprecated in favour of <span class="samp">FC</span>,<span class="samp">FPICFLAGS</span> and <span class="samp">SHLIB_OPENMP_FFLAGS</span> respectively.</p></li><li> <p><code>$.data.frame</code> had become an expensive version ofthe default method, so has been removed. (Thanks to Radford Nealfor picking this up and to Duncan Murdoch for providing a patch.)</p></li></ul><h4>BUG FIXES</h4><ul><li> <p><code>replayPlot(r)</code> now also works in the same <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> sessionwhen <code>r</code> has been “reproduced” from serialization,typically after saving to and reading from an RDS file.</p></li><li> <p><code>substr()</code> and <code>substring()</code> now signal an errorwhen the input is invalid UTF-8.</p></li><li> <p><code>file.copy()</code> now works also when its argument <code>to</code>is of length greater than one.</p></li><li> <p><code>mantelhaen.test()</code> no longer suffers from integeroverflow in largish cases, thanks to Ben Bolker's <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17383">PR#17383</a>.</p></li><li><p> Calling <code>setGeneric("foo")</code> in a package no longerfails when the enclosing environment of the implicit generic<code>foo()</code> is <code>.GlobalEnv</code>.</p></li><li> <p><code>untar(file("<some>.tar.gz"), *)</code> now gives a bettererror message, suggesting to use <code>gzfile()</code> instead.</p></li><li><p> Method dispatch uses more relevant environments when lookingup class definitions.</p></li><li><p> The documentation for <code>identify()</code> incorrectly claimedthat the indices of identified points were returned in the orderthat the points were selected. <code>identify()</code> now has a newargument <code>order</code> to allow the return value to include theorder in which points were identified; the documentation has beenupdated. Reported by Richard Rowe and Samuel Granjeaud.</p></li><li> <p><code>order(...., decreasing=c(TRUE, FALSE))</code> could fail insome cases. Reported from StackOverflow via Karl Nordström.</p></li><li><p> User macros in Rd files now accept empty and multi-linearguments.</p></li><li><p> Changes in <code>print.*()</code>, thanks to Lionel Henry'spatches in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17398">PR#17398</a>:</p><ul><li><p> Printing lists, pairlists or attributes containing callswith S3 class no longer evaluate those.</p></li><li><p> Printing S4 objects within lists and pairlists dispatcheswith <code>show()</code> rather than <code>print()</code>, as withauto-printing.</p></li><li><p> The indexing tags (names or <code>[[<n>]]</code>) of recursivedata structures are now printed correctly in complex cases.</p></li><li><p> Arguments supplied to <code>print()</code> are now properlyforwarded to methods when printing lists, pairlists orattributes containing S3 objects.</p></li><li><p> The print parameters are now preserved when printing S3objects or deparsing symbols and calls. Previously, printinglists containing S3 objects or expressions would reset theseparameters.</p></li><li><p> Printing lists, pairlists or attributes containingfunctions now uses <code>srcref</code> attributes if present.</p></li></ul></li><li><p> Calling <code>install.packages()</code> with a length zero<code>pkgs</code> argument now is a no-op (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17422">PR#17422</a>).</p></li><li> <p><code>unlist(x)</code> now returns a correct <code>factor</code> when<code>x</code> is a nested list with factor leaves, fixing <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=12572">PR#12572</a>and <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17419">PR#17419</a>.</p></li><li><p> The documentation <code>help(family)</code> gives more detailsabout the <code>aic</code> component, thanks to Ben Bolker's prompting.</p></li><li><p> The documentation for <code>attributes</code> and<code>`attributes<-`</code> now gives <code>x</code> as name of the first andmain argument which the implementation has been requiring, fixing<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17434">PR#17434</a>. For consistency, the first argument name is alsochanged from <code>obj</code> to <code>x</code> for <code>`mostattributes<-`</code>.</p></li><li> <p><code>strwidth()</code> now uses <code>par("font")</code> as defaultfont face (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17352">PR#17352</a>).</p></li><li> <p><code>plot(<table>, log="x")</code> no longer warns about <code>log</code>.</p></li><li><p> The <code>print()</code> method for <code>"htest"</code> objects nowformats the test statistic and parameter directly and hence nolonger rounds to units <em>before</em> the decimal point. Consequently,printing of <code>t.test()</code> results with a small number of digitsnow shows non-large <code>df</code>'s to the full precision (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17444">PR#17444</a>).</p></li><li> <p><code>kruskal.test()</code> and <code>fligner.test()</code> no longererroneously insist on numeric <code>g</code> group arguments (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16719">PR#16719</a>).</p></li><li><p> Printing a news db via the browser now does a much betterjob (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17433">PR#17433</a>).</p></li><li> <p><code>print.aov()</code> missed column names in the multivariate casedue to misspelling (reported by Chris Andrews).</p></li><li> <p><code>axis()</code> now creates valid <code>at</code> locations also forsmall subnormal number ranges in log scale plots.</p></li><li> <p><code>format.POSIXlt()</code> now also recycles the <code>zone</code>and <code>gmtoff</code> list components to full length when needed,and its internal C code detects <code>have_zone</code> in more cases.In some cases, this changes its output to become compatible with<code>format.POSIXct()</code>.</p></li><li><p> On Windows, <code>detectCores()</code> in package <span class="pkg">parallel</span>now detects processors in all processor groups, not just the group<span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> is running in (impacts particularly systems with more than 64logical processors). Reported by Arunkumar Srinivasan.</p></li><li><p> On Windows, <code>socketSelect()</code> would hang with more than64 sockets, and hence <code>parallel::clusterApplyLB()</code> would hangwith more than 64 workers. Reported by Arunkumar Srinivasan.</p></li><li> <p><code>as(1L, "double")</code> now does coerce (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17457">PR#17457</a>).</p></li><li> <p><code>lm.influence()</code>, <code>influence.measures()</code>,<code>rstudent()</code> etc now work (more) correctly for multivariatemodels (<code>"mlm"</code>), thanks to (anonymous) stackoverflow remarks.</p></li><li> <p><code>sample.int(2.9, *, replace=TRUE)</code> again behaves asdocumented and as in R < 3.0.0, namely identically to<code>sample.int(2, ..)</code>.</p></li><li><p> Fixes to <code>convertColor()</code> for chromatic adaptation;thanks to Brodie Gaslam <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17473">PR#17473</a>.</p></li><li><p> Using <code>\Sexpr[stage=install]{..}</code> to create an‘<span class="file">Rd</span>’ section no longer gives a warning in <code>R CMDcheck</code>; problem originally posted by Gábor Csárdi, then reportedas <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17479">PR#17479</a> with a partial patch by Duncan Murdoch.</p></li><li><p> Parse data now include a special node for equal assignment.</p></li><li> <p><code>split.default()</code> no longer relies on <code>[[<-()</code>, soit behaves as expected when splitting an object by a factor withthe empty string as one of its levels. Thanks to Brad Friedman forthe report.</p></li><li><p> Line numbers in messages about ‘<span class="file">.Rd</span>’ files are now morereliable, thanks to a patch from Duncan Murdoch.</p></li><li><p> In the <code>numeric</code> method for <code>all.equal()</code>, anumeric <code>scale</code> argument is now checked to be positive andallowed to be of length > 1. (The latter worked originally andwith a warning in recent years).</p></li><li><p> Deferred string conversions now record the <code>OutDec</code>option setting when not equal to the default. Reported by MichaelSannella.</p></li><li><p> When <code>y</code> is numeric and <code>f</code> a <code>factor</code>,<code>plot(y ~ f)</code> nicely uses "y" and "f" as y- and x-labels.The more direct <code>boxplot(y ~ f)</code> now does too. The newargument <code>ann = FALSE</code> may be used to suppress these.</p></li><li><p> Subassignment to no/empty rows of a data frame is moreconsistent and typically a no-op in all cases instead of sometimesan error; part of Emil Bode's <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17483">PR#17483</a>.</p></li><li><p> Calls like <code>formatC(*, zero.print = "< 0.001")</code> nolonger give an error and are further improved via new optionalargument <code>replace.zero</code>. Reported by David Hugh-Jones.</p></li><li> <p><code>methods::formalArgs("<fn>")</code> now finds the samefunction as <code>formals("<fn>")</code>, fixing Emil Bode's <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17499">PR#17499</a>.</p></li><li><p> The <span class="pkg">methods</span> package better handles duplicated classnames across packages.</p></li><li><p> The default method of <code>seq()</code> now avoids integeroverflow, thanks to the report and "cumsum" patch of SuhartoAnggono's <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17497">PR#17497</a>.</p></li><li> <p><code>sub()</code> no longer loses encodings for non-ASCIIreplacements (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17509">PR#17509</a>).</p></li><li><p> Fix for rotated raster image on X11 device. (Partialfix for <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17148">PR#17148</a>; thanks to Mikko Korpela).</p></li><li> <p><code>formula(model.frame(frml, ..))</code> now returns <code>frml</code>in all cases, thanks to Bill Dunlap. The previous behavior isavailable as <code>DF2formula(<model.frame>)</code>.</p></li><li> <p><code>ar.ols()</code> also returns scalar <code>var.pred</code> inunivariate case (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17517">PR#17517</a>).</p></li><li> <p><code>normalizePath()</code> now treats <code>NA</code> path as non-existentand normalizes it to <code>NA</code>. <code>file.access()</code> treats <code>NA</code>file name as non-existent. <code>file.edit()</code> and connectionfunctions such as <code>file()</code> now treat <code>NA</code> file names aserrors.</p></li><li><p> The internal <code>regularize.values()</code> auxiliary of<code>approx()</code>, <code>splinefun()</code> etc now warns again when thereare ties and the caller did not specify <code>ties</code>. Further, it nolonger duplicates <code>x</code> and <code>y</code> unnecessarily when <code>x</code>is already sorted (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17515">PR#17515</a>).</p></li><li> <p><code>strtoi("", base)</code> now gives <code>NA</code> on all platforms,following its documentation. Reported by Michael Chirico.</p></li><li><p> In the definition of an S4 class, prototype elements arechecked against the slots of the class, with giving a prototypefor an undefined slot now being an error. (Reported by BillDunlap.)</p></li><li><p> From <code>setClassUnion()</code>, if environment variable<span class="env">_R_METHODS_SHOW_CHECKSUBCLASSES</span> is setto true, the internal <code>.checkSubclasses()</code> utility printsdebugging info to see where it is used.</p></li><li> <p><code>max.col(m)</code> with an <code>m</code> of zero columns nowreturns integer <code>NA</code> (instead of <code>1</code>).</p></li><li> <p><code>axTicks()</code> no longer returns small “almost zero”numbers (in exponential format) instead of zero, fixing IlarioGelmetti's <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17534">PR#17534</a>.</p></li><li> <p><code>isSymmetric(matrix(0, dimnames=list("A","b")))</code> is<code>FALSE</code> again, as always documented.</p></li><li><p> The <code>cairo_pdf</code> graphics device (and other Cairo-baseddevices) now clip correctly to the right and bottom border.</p><p>There was an off-by-one-pixel bug, reported by Lee Kelvin.</p></li><li> <p><code>as.roman(3) <= 2:4</code> and all other comparisons now work,as do group <code>"Summary"</code> function calls such as<code>max(as.roman(sample(20)))</code> and <code>as.roman(NA)</code>.(Partly reported by Bill Dunlap in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17542">PR#17542</a>.)</p></li><li> <p><code>reformulate("x", response = "sin(y)")</code> no longer producesextra back quotes, <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17359">PR#17359</a>, and gains new optional argument<code>env</code>.</p></li><li><p> When reading console input from ‘<span class="file">stdin</span>’ with re-encoding(<code>R --encoding=enc < input</code>) the code on a Unix-alike nowensures that each converted input line is terminated with anewline even if re-encoding fails.</p></li><li> <p><code>as.matrix.data.frame()</code> now produces better strings fromlogicals, thanks to <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17548">PR#17548</a> from Gabe Becker.</p></li><li><p> The S4 generic signature of <code>rowSums()</code>,<code>rowMeans()</code>, <code>colSums()</code> and <code>colMeans()</code> isrestricted to <code>"x"</code>.</p></li><li> <p><code>match(x, tab)</code> now works for long <em>character</em>vectors <code>x</code>, thanks to <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17552">PR#17552</a> by Andreas Kersting.</p></li><li><p> Class unions are unloaded when their namespace isunloaded (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17531">PR#17531</a>, adapted from a patch by Brodie Gaslam).</p></li><li> <p><code>selectMethod()</code> is robust to ANY-truncation of methodsignatures (thanks to Herve Pages for the report).</p></li></ul><h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.5.3</h3><h4>INSTALLATION on a UNIX-ALIKE</h4><ul><li><p> Detection of flags for C++98/11/14/17 has been improved: inparticular if CXX??STD is set, it is tried first with noadditional flags.</p></li></ul><h4>PACKAGE INSTALLATION</h4><ul><li><p> New macro <span class="samp">F_VISIBILITY</span> as an alternative to<span class="samp">F77_VISIBILITY</span>. This will become the preferred form in<span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.6.0.</p></li></ul><h4>BUG FIXES</h4><ul><li> <p><code>writeLines(readLines(fnam), fnam)</code> now works as expected,thanks to Peter Meissner's <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17528">PR#17528</a>.</p></li><li> <p><code>setClassUnion()</code> no longer warns, but uses <code>message()</code>for now, when encountering “non local” subclasses of class members.</p></li><li> <p><code>stopifnot(exprs = T)</code> no longer fails.</p></li></ul><h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.5.2</h3><h4>PACKAGE INSTALLATION</h4><ul><li><p> New macro <span class="samp">CXX_VISIBILITY</span> analogous to<span class="samp">C_VISIBILITY</span> (which several packages have been misusing forC++ code) for the default C++ compiler (but not necessarily one usedfor non-default C++ dialects like C++14).</p></li></ul><h4>TESTING</h4><ul><li><p> The random number generator tests in‘<span class="file">tests/p-r-random-tests.R</span>’ no longer fail occasionally asthey now randomly sample from “certified” random seeds.</p></li></ul><h4>BUG FIXES</h4><ul><li><p> The <code>"glm"</code> method of <code>drop1()</code> miscalculated thescore test (<code>test="Rao"</code>) when the model contained an offset.</p></li><li><p> Linear multiple empty models such as <code>lm(y ~ 0)</code>now have a correctly dimensioned empty coefficient matrix;reported by Brett Presnell.</p></li><li> <p><code>vcov(<empty mlm>)</code> and hence <code>confint()</code> nowwork (via a consistency change in <code>summary.lm()</code>).</p></li><li> <p><code>confint(<multiple lm()>)</code> now works correctly;reported on R-devel by Steven Pav.</p></li><li> <p><code>quade.test()</code> now also works correctly when itsarguments are not yet sorted along <code>groups</code>, fixing <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15842">PR#15842</a>.</p></li><li><p> Installation on a Unix-alike tries harder to link to the<span class="samp">pthread</span> library where required (rather than relying onOpenMP to provide it: configuring with <span class="option">--disable-openmp</span>was failing on some Linux systems).</p></li><li><p> The <code>data.frame</code> method for <code>print(x)</code> is fast nowalso for large data frames <code>x</code> and got an optional argument<code>max</code>, thanks to suggestions by Juan Telleria.</p></li><li> <p><code>hist()</code> no longer integer overflows in very rarecases, fixing <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17450">PR#17450</a>.</p></li><li> <p><code>untar()</code> ignored a character <code>compressed</code>argument: however many external <code>tar</code> programs ignorethe flags which should have been set and automagically choose thecompression type, and if appropriate <code>gzip</code> or<code>bzip2</code> compression would have been chosen from the magicheader of the tarball.</p></li><li> <p><code>zapsmall(x)</code> now works for more “number-like” objects.</p></li><li><p> The tools-internal function called from <code>R CMDINSTALL</code> now gets a <code>warnOption = 1</code> argument and only sets<code>options(warn = warnOption)</code> when that increases the warninglevel (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17453">PR#17453</a>).</p></li><li><p> Analogously, the tools-internal function called from <code>R CMDcheck</code> gets a <code>warnOption = 1</code> argument and uses the largerof that and <code>getOption("warn")</code>, also allowing to be run withincreased warning level.</p></li><li><p> Parse data now have deterministic parent nodes (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16041">PR#16041</a>).</p></li><li><p> Calling <code>match()</code> with length one <code>x</code> and POSIXlt<code>table</code> gave a segfault (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17459">PR#17459</a>).</p></li><li><p> Fork clusters could hang due to a race condition in clusterinitialization (<code>makeCluster()</code>).</p></li><li> <p><code>nextn(n)</code> now also works for larger <code>n</code> and nolonger loops infinitely for e.g, <code>n <- 214e7</code>.</p></li><li> <p><code>cooks.distance()</code> and <code>rstandard()</code> now workcorrectly for multiple linear models (<code>"mlm"</code>).</p></li><li> <p><code>polym()</code> and corresponding <code>lm()</code> prediction nowalso work for a boundary "vector" case fixing <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17474">PR#17474</a>,reported by Alexandre Courtiol.</p></li><li><p> With a very large number of variables <code>terms()</code> couldsegfault (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17480">PR#17480</a>).</p></li><li> <p><code>cut(rep(0, 7))</code> now works, thanks to Joey Reid andBenjamin Tyner (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16802">PR#16802</a>).</p></li><li> <p><code>download.file(*, method = "curl", cacheOK = FALSE)</code>should work now on Windows, thanks to Kevin Ushey's patch in<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17323">PR#17323</a>.</p></li><li> <p><code>duplicated(<dataframe with 'f'>)</code> now works, too,thanks to Andreas Kersting's <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17485">PR#17485</a>; ditto for<code>anyDuplicated()</code>.</p></li><li> <p><code>legend(*, cex = 1:2)</code> now works less badly.</p></li><li><p> The <code>print()</code> method for <code>POSIXct</code> and<code>POSIXlt</code> now correctly obeys <code>getOption("max.print")</code>,fixing a long-standing typo, and it also gets a correspondingoptional <code>max</code> argument.</p></li><li><p> Unserialization of raw vectors serialized in ASCIIrepresentation now works correctly.</p></li><li> <p><code><data frame>[TRUE, <new>] <- list(c1, c2)</code> now workscorrectly, thanks to Suharto Anggono's <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15362">PR#15362</a> and Emil Bode'spatch in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17504">PR#17504</a>.</p></li><li> <p><code>seq.int(*, by=by, length=n)</code> no longer wrongly“drops fractional parts” when <code>by</code> is integer, thanksto Suharto Anggono's report <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17506">PR#17506</a>.</p></li><li><p> Buffering is disabled for <code>file()</code> connections tonon-regular files (like sockets), as well as <code>fifo()</code> and<code>pipe()</code> connections. Fixes <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17470">PR#17470</a>, reported by ChrisCulnane.</p></li></ul><h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.5.1</h3><h4>BUG FIXES</h4><ul><li> <p><code>file("stdin")</code> is no longer considered seekable.</p></li><li> <p><code>dput()</code> and <code>dump()</code> are no longer truncatingwhen <code>options(deparse.max.lines = *)</code> is set.</p></li><li><p> Calls with an S3 class are no longer evaluated when printed,fixing part of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17398">PR#17398</a>, thanks to a patch from Lionel Henry.</p></li><li><p> Allow <code>file</code> argument of <code>Rscript</code> to include spaceeven when it is first on the command line.</p></li><li> <p><code>callNextMethod()</code> uses the generic from theenvironment of the calling method. Reported by Hervé Pagès withwell documented examples.</p></li><li><p> Compressed file connections are marked as blocking.</p></li><li> <p><code>optim(*, lower = c(-Inf, -Inf))</code> no longer warns (andswitches the method), thanks to a suggestion by John Nash.</p></li><li> <p><code>predict(fm, newdata)</code> is now correct also for modelswhere the formula has terms such as <code>splines::ns(..)</code> or<code>stats::poly(..)</code>, fixing <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17414">PR#17414</a>, based on a patch fromDuncan Murdoch.</p></li><li> <p><code>simulate.lm(glm(*, gaussian(link = <non-default>)))</code>has been corrected, fixing <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17415">PR#17415</a> thanks to Alex Courtiol.</p></li><li> <p><code>unlist(x)</code> no longer fails in some cases of nestedempty lists. Reported by Steven Nydick.</p></li><li> <p><code>qr.coef(qr(<all 0, w/ colnames>))</code> now works.Reported by Kun Ren.</p></li><li><p> The radix sort is robust to vectors with >1 billion elements(but long vectors are still unsupported). Thanks to Matt Dowle forthe fix.</p></li><li><p> Terminal connections (e.g., stdin) are no longerbuffered. Fixes <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17432">PR#17432</a>.</p></li><li> <p><code>deparse(x)</code>, <code>dput(x)</code> and <code>dump()</code> nowrespect <code>c()</code>'s argument names <code>recursive</code> and<code>use.names</code>, e.g., for <code>x <- setNames(0, "recursive")</code>,thanks to Suharto Anggono's <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17427">PR#17427</a>.</p></li><li><p> Unbuffered connections now work with encoding conversion.Reported by Stephen Berman.</p></li><li> <p>‘<span class="file">.Renviron</span>’ on Windows with <code>Rgui</code> is again bydefault searched for in user documents directory when invoked<em>via</em> the launcher icon. Reported by Jeroen Ooms.</p></li><li> <p><code>printCoefmat()</code> now also works with explicit<code>right=TRUE</code>.</p></li><li> <p><code>print.noquote()</code> now also works with explicit<code>quote=FALSE</code>.</p></li><li><p> The default method for <code>pairs(.., horInd=*, verInd=*)</code>now gets the correct order, thanks to reports by Chris Andrews andGerrit Eichner. Additionally, when <code>horInd</code> or <code>verInd</code>contain only a subset of variables, all the axes are labeledcorrectly now.</p></li><li> <p><code>agrep("..|..", .., fixed=FALSE)</code> now matches when itshould, thanks to a reminder by Andreas Kolter.</p></li><li> <p><code>str(ch)</code> now works for more invalid multibyte strings.</p></li></ul><h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.5.0</h3><h4>SIGNIFICANT USER-VISIBLE CHANGES</h4><ul><li><p> All packages are by default byte-compiled on installation.This makes the installed packages larger (usually marginally so)and may affect the format of messages and tracebacks (which oftenexclude <code>.Call</code> and similar).</p></li></ul><h4>NEW FEATURES</h4><ul><li> <p><code>factor()</code> now uses <code>order()</code> to sort its levels,rather than <code>sort.list()</code>. This allows <code>factor()</code> tosupport custom vector-like objects if methods for the appropriategenerics are defined. It has the side effect of making<code>factor()</code> succeed on empty or length-one non-atomicvector(-like) types (e.g., <code>"list"</code>), where it failed before.</p></li><li> <p><code>diag()</code> gets an optional <code>names</code> argument: thismay require updates to packages defining S4 methods for it.</p></li><li> <p><code>chooseCRANmirror()</code> and <code>chooseBioCmirror()</code> nolonger have a <code>useHTTPS</code> argument, not needed now all <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>builds support <span class="samp">https://</span> downloads.</p></li><li><p> New <code>summary()</code> method for <code>warnings()</code> with a(somewhat experimental) <code>print()</code> method.</p></li><li><p> (<span class="pkg">methods</span> package.) <code>.self</code> is now automaticallyregistered as a global variable when registering a reference classmethod.</p></li><li> <p><code>tempdir(check = TRUE)</code> recreates the <code>tempdir()</code>directory if it is no longer valid (e.g. because someother process has cleaned up the ‘<span class="file">/tmp</span>’ directory).</p></li><li><p> New <code>askYesNo()</code> function and <code>"askYesNo"</code> optionto ask the user binary response questions in a customizable butconsistent way. (Suggestion of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17242">PR#17242</a>.)</p></li><li><p> New low level utilities <code>...elt(n)</code> and <code>...length()</code>for working with <code>...</code> parts inside a function.</p></li><li> <p><code>isTRUE()</code> is more tolerant and now truein </p><pre> x <- rlnorm(99)isTRUE(median(x) == quantile(x)["50%"])</pre><p>New function <code>isFALSE()</code> defined analogously to <code>isTRUE()</code>.</p></li><li><p> The default symbol table size has been increased from 4119to 49157; this may improve the performance of symbol resolutionwhen many packages are loaded. (Suggested by Jim Hester.)</p></li><li> <p><code>line()</code> gets a new option <code>iter = 1</code>.</p></li><li><p> Reading from connections in text mode is buffered,significantly improving the performance of <code>readLines()</code>, aswell as <code>scan()</code> and <code>read.table()</code>, at least whenspecifying <code>colClasses</code>.</p></li><li> <p><code>order()</code> is smarter about picking a default sort<code>method</code> when its arguments are objects.</p></li><li> <p><code>available.packages()</code> has two new arguments whichcontrol if the values from the per-session repository cache areused (default true, as before) and if so how old cached values canbe used (default one hour).</p><p>These arguments can be passed from <code>install.packages()</code>,<code>update.packages()</code> and functions calling that: to enablethis <code>available.packages()</code>, <code>packageStatus()</code> and<code>download.file()</code> gain a <code>...</code> argument.</p></li><li> <p><code>packageStatus()</code>'s <code>upgrade()</code> method no longerignores its <code>...</code> argument but passes it to<code>install.packages()</code>.</p></li><li> <p><code>installed.packages()</code> gains a <code>...</code> argument toallow arguments (including <code>noCache</code>) to be passed from<code>new.packages()</code>, <code>old.packages()</code>,<code>update.packages()</code> and <code>packageStatus()</code>.</p></li><li> <p><code>factor(x, levels, labels)</code> now allows duplicated<code>labels</code> (not duplicated <code>levels</code>!). Hence you can mapdifferent values of <code>x</code> to the same level directly.</p></li><li><p> Attempting to use <code>names<-()</code> on an S4 derivative of abasic type no longer emits a warning.</p></li><li><p> The <code>list</code> method of <code>within()</code> gains an option<code>keepAttrs = FALSE</code> for some speed-up.</p></li><li> <p><code>system()</code> and <code>system2()</code> now allow thespecification of a maximum elapsed time (‘timeout’).</p></li><li> <p><code>debug()</code> supports debugging of methods on any objectof S4 class <code>"genericFunction"</code>, including group generics.</p></li><li><p> Attempting to increase the length of a variable containing<code>NULL</code> using <code>length()<-</code> still has no effect on thetarget variable, but now triggers a warning.</p></li><li> <p><code>type.convert()</code> becomes a generic function, withadditional methods that operate recursively over list and<code>data.frame</code> objects. Courtesy of Arni Magnusson(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17269">PR#17269</a>).</p></li><li> <p><code>lower.tri(x)</code> and <code>upper.tri(x)</code> only needing<code>dim(x)</code> now work via new functions <code>.row()</code> and<code>.col()</code>, so no longer call <code>as.matrix()</code> by default inorder to work efficiently for all kind of matrix-like objects.</p></li><li> <p><code>print()</code> methods for <code>"xgettext"</code> and<code>"xngettext"</code> now use <code>encodeString()</code> which keeps,e.g. <code>"\n"</code>, visible. (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17298">PR#17298</a>.)</p></li><li> <p><code>package.skeleton()</code> gains an optional <code>encoding</code>argument.</p></li><li> <p><code>approx()</code>, <code>spline()</code>, <code>splinefun()</code> and<code>approxfun()</code> also work for long vectors.</p></li><li> <p><code>deparse()</code> and <code>dump()</code> are more useful for S4objects, <code>dput()</code> now using the same internal C code insteadof its previous imperfect workaround R code. S4 objects nowtypically deparse perfectly, i.e., can be recreated identicallyfrom deparsed code.</p><p><code>dput()</code>, <code>deparse()</code> and <code>dump()</code> now print the<code>names()</code> information only once, using the more readable<code>(tag = value)</code> syntax, notably for <code>list()</code>s, i.e.,including data frames.</p><p>These functions gain a new control option <code>"niceNames"</code> (see<code>.deparseOpts()</code>), which when set (as by default) also usesthe <code>(tag = value)</code> syntax for atomic vectors. On the otherhand, without deparse options <code>"showAttributes"</code> and<code>"niceNames"</code>, names are no longer shown also for lists.<code>as.character(list( c (one = 1)))</code> now includes the name, as<code>as.character(list(list(one = 1)))</code> has always done.</p><p><code>m:n</code> now also deparses nicely when <i>m > n</i>.</p><p>The <code>"quoteExpressions"</code> option, also part of <code>"all"</code>,no longer <code>quote()</code>s formulas as that may not re-parseidentically. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17378">PR#17378</a>)</p></li><li><p> If the option <code>setWidthOnResize</code> is set and <code>TRUE</code>,<span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> run in a terminal using a recent <code>readline</code> library willset the <code>width</code> option when the terminal isresized. Suggested by Ralf Goertz.</p></li><li><p> If multiple <code>on.exit()</code> expressions are set using<code>add = TRUE</code> then all expressions will now be run even if onesignals an error.</p></li><li> <p><code>mclapply()</code> gets an option <code>affinity.list</code> whichallows more efficient execution with heterogeneous processors,thanks to Helena Kotthaus.</p></li><li><p> The <code>character</code> methods for <code>as.Date()</code> and<code>as.POSIXlt()</code> are more flexible <em>via</em> new arguments<code>tryFormats</code> and <code>optional</code>: see their help pages.</p></li><li> <p><code>on.exit()</code> gains an optional argument <code>after</code>with default <code>TRUE</code>. Using <code>after = FALSE</code> with<code>add = TRUE</code> adds an exit expression before anyexisting ones. This way the expressions are run in a first-inlast-out fashion. (From Lionel Henry.)</p></li><li><p> On Windows, <code>file.rename()</code> internally retries theoperation in case of error to attempt to recover from possibleanti-virus interference.</p></li><li><p> Command line completion on <span class="samp">::</span> now also includeslazy-loaded data.</p></li><li><p> If the <span class="env">TZ</span> environment variable is set when date-timefunctions are first used, it is recorded as the session defaultand so will be used rather than the default deduced from the OSif <span class="env">TZ</span> is subsequently unset.</p></li><li><p> There is now a <code>[</code> method for class <code>"DLLInfoList"</code>.</p></li><li> <p><code>glm()</code> and <code>glm.fit</code> get the same<code>singular.ok = TRUE</code> argument that <code>lm()</code> has hadforever. As a consequence, in <code>glm(*, method = <your_own>)</code>,user specified methods need to accept a <code>singular.ok</code>argument as well.</p></li><li> <p><code>aspell()</code> gains a filter for Markdown (‘<span class="file">.md</span>’ and‘<span class="file">.Rmd</span>’) files.</p></li><li> <p><code>intToUtf8(multiple = FALSE)</code> gains an argument toallow surrogate pairs to be interpreted.</p></li><li><p> The maximum number of DLLs that can be loaded into Re.g. <em>via</em> <code>dyn.load()</code> has been increased up to 614when the OS limit on the number of open files allows.</p></li><li> <p><code>Sys.timezone()</code> on a Unix-alike caches the value atfirst use in a session: <em>inter alia</em> this means that setting<span class="env">TZ</span> later in the session affects only the <em>current</em> timezone and not the <em>system</em> one.</p><p><code>Sys.timezone()</code> is now used to find the system timezone topass to the code used when <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> is configured with<span class="option">--with-internal-tzcode</span>.</p></li><li><p> When <code>tar()</code> is used with an external command which isdetected to be GNU <code>tar</code> or libarchive <code>tar</code> (aka<code>bsdtar</code>), a different command-line is generated tocircumvent line-length limits in the shell.</p></li><li> <p><code>system(*, intern = FALSE)</code>, <code>system2()</code> (when notcapturing output), <code>file.edit()</code> and <code>file.show()</code> nowissue a warning when the external command cannot be executed.</p></li><li><p> The “default” (<code>"lm"</code> etc) methods of<code>vcov()</code> have gained new optional argument <code>complete =TRUE</code> which makes the <code>vcov()</code> methods more consistent withthe <code>coef()</code> methods in the case of singular designs. Theformer (back-compatible) behavior is given by <code>vcov(*,complete = FALSE)</code>.</p></li><li> <p><code>coef()</code> methods (for <code>lm</code> etc) also gain a<code>complete = TRUE</code> optional argument for consistency with<code>vcov()</code>. <br />For <code>"aov"</code>, both <code>coef()</code> and <code>vcov()</code> methodsremain back-compatibly consistent, using the <em>other</em> default,<code>complete = FALSE</code>.</p></li><li> <p><code>attach(*, pos = 1)</code> is now an error instead of awarning.</p></li><li><p> New function <code>getDefaultCluster()</code> in package<span class="pkg">parallel</span> to get the default cluster set via<code>setDefaultCluster()</code>.</p></li><li> <p><code>str(x)</code> for atomic objects <code>x</code> now treats bothcases of <code>is.vector(x)</code> similarly, and hence much less oftenprints <code>"atomic"</code>. This is a slight non-back-compatiblechange producing typically both more informative and shorteroutput.</p></li><li> <p><code>gc()</code> gets new argument <code>full</code>.</p></li><li> <p><code>write.dcf()</code> gets optional argument <code>useBytes</code>.</p></li><li><p> New, partly experimental <code>packageDate()</code> which tries toget a valid <code>"Date"</code> object from a package ‘<span class="file">DESCRIPTION</span>’file, thanks to suggestions in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17324">PR#17324</a>.</p></li><li> <p><code>tools::resaveRdaFiles()</code> gains a <code>version</code>argument, for use when packages should remain compatible withearlier versions of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>.</p></li><li> <p><code>ar.yw(x)</code> and hence by default <code>ar(x)</code> now workwhen <code>x</code> has <code>NA</code>s, mostly thanks to a patch by PavelKrivitsky in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17366">PR#17366</a>. The <code>ar.yw.default()</code>'s AICcomputations have become more efficient by using<code>determinant()</code>.</p></li><li><p> New <code>warnErrList()</code> utility (from package <span class="pkg">nlme</span>,improved).</p></li><li><p> By default the (arbitrary) signs of the loadings from<code>princomp()</code> are chosen so the first element is non-negative.</p></li><li><p> If <span class="option">--default-packages</span> is not used, then<code>Rscript</code> now checks the environment variable<span class="env">R_SCRIPT_DEFAULT_PACKAGES</span>. If this is set, then it takesprecedence over <span class="env">R_DEFAULT_PACKAGES</span>. If default packages arenot specified on the command line or by one of these environmentvariables, then <code>Rscript</code> now uses the same defaultpackages as <code>R</code>. For now, the previous behavior of notincluding <span class="pkg">methods</span> can be restored by setting the environmentvariable <span class="env">R_SCRIPT_LEGACY</span> to <span class="samp">yes</span>.</p></li><li><p> When a package is found more than once, the warning from<code>find.package(*, verbose=TRUE)</code> lists all library locations.</p></li><li><p> POSIXt objects can now also be rounded or truncated to monthor year.</p></li><li> <p><code>stopifnot()</code> can be used alternatively via new argument<code>exprs</code> which is nicer and useful when testing severalexpressions in one call.</p></li><li><p> The environment variable <span class="env">R_MAX_VSIZE</span> can now be usedto specify the maximal vector heap size. On macOS, unless specifiedby this environment variable, the maximal vector heap size is set tothe maximum of 16GB and the available physical memory. This is toavoid having the <code>R</code> process killed when macOS over-commitsmemory.</p></li><li> <p><code>sum(x)</code> and <code>sum(x1, x2, .., x<N>)</code> with many orlong logical or integer vectors no longer overflows (and returns<code>NA</code> with a warning), but returns <code>double</code> numbers insuch cases.</p></li><li><p> Single components of <code>"POSIXlt"</code> objects can now beextracted and replaced via <code>[</code> indexing with 2 indices.</p></li><li><p> S3 method lookup now searches the namespace registry afterthe top level environment of the calling environment.</p></li><li><p> Arithmetic sequences created by <code>1:n</code>,<code>seq_along</code>, and the like now use compact internalrepresentations via the <code>ALTREP</code> framework. Coercing integerand numeric vectors to character also now uses the <code>ALTREP</code>framework to defer the actual conversion until first use.</p></li><li><p> Finalizers are now run with interrupts suspended.</p></li><li> <p><code>merge()</code> gains new option <code>no.dups</code> and bydefault suffixes the second of two duplicated column names,thanks to a proposal by Scott Ritchie (and Gabe Becker).</p></li><li> <p><code>scale.default(x, center, scale)</code> now also allows<code>center</code> or <code>scale</code> to be “numeric-alike”, i.e.,such that <code>as.numeric(.)</code> coerces them correctly. This alsoeliminates a wrong error message in such cases.</p></li><li> <p><code>par*apply</code> and <code>par*applyLB</code> gain an optionalargument <code>chunk.size</code> which allows to specify the granularity ofscheduling.</p></li><li><p> Some <code>as.data.frame()</code> methods, notably the<code>matrix</code> one, are now more careful in not acceptingduplicated or <code>NA</code> row names, and by default produce uniquenon-NA row names. This is based on new function<code>.rowNamesDF(x, make.names = *) <- rNms</code> where the logicalargument <code>make.names</code> allows to specify <em>how</em> invalidrow names <code>rNms</code> are handled. <code>.rowNamesDF()</code> is a“workaround” compatible default.</p></li><li><p> R has new serialization format (version 3) which supportscustom serialization of <code>ALTREP</code> framework objects. Theseobjects can still be serialized in format 2, but less efficiently.Serialization format 3 also records the current native encoding ofunflagged strings and converts them when de-serialized in Rrunning under different native encoding. Format 3 comes with newserialization magic numbers (RDA3, RDB3, RDX3). Format 3 can beselected by <code>version = 3</code> in <code>save()</code>,<code>serialize()</code> and <code>saveRDS()</code>, but format 2 remains thedefault for all serialization and saving of the workspace.Serialized data in format 3 cannot be read by versions of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> priorto version 3.5.0.</p></li><li><p> The <code>"Date"</code> and “date-time” classes<code>"POSIXlt"</code> and <code>"POSIXct"</code> now have a working<code>length<-()</code> method, as wished in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17387">PR#17387</a>.</p></li><li> <p><code>optim(*, control = list(warn.1d.NelderMead = FALSE))</code>allows to turn off the warning when applying the default<code>"Nelder-Mead"</code> method to 1-dimensional problems.</p></li><li> <p><code>matplot(.., panel.first = .)</code> etc now work, as<code>log</code> becomes explicit argument and <code>...</code> is passed to<code>plot()</code> unevaluated, as suggested by Sebastian Meyer in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17386">PR#17386</a>.</p></li><li><p> Interrupts can be suspended while evaluating an expressionusing <code>suspendInterrupts</code>. Subexpression can be evaluatedwith interrupts enabled using <code>allowInterrupts</code>. Thesefunctions can be used to make sure cleanup handlers cannot beinterrupted.</p></li><li> <p><span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.5.0 includes a framework that allows packages toprovide alternate representations of basic <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> objects(<code>ALTREP</code>). The framework is still experimental and mayundergo changes in future <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> releases as more experience isgained. For now, documentation is provided in<a href="https://svn.r-project.org/R/branches/ALTREP/ALTREP.html">https://svn.r-project.org/R/branches/ALTREP/ALTREP.html</a>.</p></li></ul><h4>UTILITIES</h4><ul><li> <p><code>install.packages()</code> for source packages now has thepossibility to set a ‘timeout’ (elapsed-time limit). Forserial installs this uses the <code>timeout</code> argument of<code>system2()</code>: for parallel installs it requires the<code>timeout</code> utility command from GNU <span class="pkg">coreutils</span>.</p></li><li><p> It is now possible to set ‘timeouts’ (elapsed-timelimits) for most parts of <code>R CMD check</code> <em>via</em>environment variables documented in the ‘R Internals’manual.</p></li><li><p> The ‘BioC extra’ repository which was dropped fromBioconductor 3.6 and later has been removed from<code>setRepositories()</code>. This changes the mapping for 6–8 usedby <code>setRepositories(ind=)</code>.</p></li><li> <p><code>R CMD check</code> now also applies the settings ofenvironment variables <span class="env">_R_CHECK_SUGGESTS_ONLY_</span> and<span class="env">_R_CHECK_DEPENDS_ONLY_</span> to the re-building of vignettes.</p></li><li> <p><code>R CMD check</code> with environment variable<span class="env">_R_CHECK_DEPENDS_ONLY_</span> set to a true value makestest-suite-management packages available and (for the time being)works around a common omission of <a href="https://CRAN.R-project.org/package=rmarkdown"><span class="pkg">rmarkdown</span></a> from the<span class="samp">VignetteBuilder</span> field.</p></li></ul><h4>INSTALLATION on a UNIX-ALIKE</h4><ul><li><p> Support for a system Java on macOS has beenremoved — install a fairly recent Oracle Java (see ‘RInstallation and Administration’ §C.3.2).</p></li><li> <p><code>configure</code> works harder to set additional flags in<span class="samp">SAFE_FFLAGS</span> only where necessary, and to use flags whichhave little or no effect on performance.</p><p>In rare circumstances it may be necessary to override thesetting of <span class="samp">SAFE_FFLAGS</span>.</p></li><li><p> C99 functions <code>expm1</code>, <code>hypot</code>, <code>log1p</code> and<code>nearbyint</code> are now required.</p></li><li> <p><code>configure</code> sets a <span class="option">-std</span> flag for the C++compiler for all supported C++ standards (e.g., <span class="option">-std=gnu++11</span>for the C++11 compiler). Previously this was not done in a fewcases where the default standard passed the tests made(e.g. <code>clang 6.0.0</code> for C++11).</p></li></ul><h4>C-LEVEL FACILITIES</h4><ul><li> <p>‘Writing R Extensions’ documents macros<code>MAYBE_REFERENCED</code>, <code>MAYBE_SHARED</code> and<code>MARK_NOT_MUTABLE</code> that should be used by package <code>C</code>code instead <code>NAMED</code> or <code>SET_NAMED</code>.</p></li><li><p> The object header layout has been changed to support mergingthe <code>ALTREP</code> branch. This requires re-installing packagesthat use compiled code.</p></li><li> <p>‘Writing R Extensions’ now documents the<code>R_tryCatch</code>, <code>R_tryCatchError</code>, and<code>R_UnwindProtect</code> functions.</p></li><li> <p><code>NAMEDMAX</code> has been raised to 3 to allow protection ofintermediate results from (usually ill-advised) assignments inarguments to <code>BUILTIN</code> functions. Package <code>C</code> code using<code>SET_NAMED</code> may need to be revised.</p></li></ul><h4>DEPRECATED AND DEFUNCT</h4><ul><li> <p><code>Sys.timezone(location = FALSE)</code> is defunct, and isignored (with a warning).</p></li><li> <p><code>methods:::bind_activation()</code> is defunct now; ittypically has been unneeded for years.</p><p>The undocumented ‘hidden’ objects <code>.__H__.cbind</code> and<code>.__H__.rbind</code> in package <span class="pkg">base</span> are deprecated (infavour of <code>cbind</code> and <code>rbind</code>).</p></li><li><p> The declaration of <code>pythag()</code> in ‘<span class="file">Rmath.h</span>’ hasbeen removed — the entry point has not been provided since <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>2.14.0.</p></li></ul><h4>BUG FIXES</h4><ul><li> <p><code>printCoefmat()</code> now also works without column names.</p></li><li><p> The S4 methods on <code>Ops()</code> for the <code>"structure"</code> class nolonger cause infinite recursion when the structure is not an S4 object.</p></li><li> <p><code>nlm(f, ..)</code> for the case where <code>f()</code> has a<code>"hessian"</code> attribute now computes<i>LL' = H + µI</i> correctly. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17249">PR#17249</a>).</p></li><li><p> An S4 method that “rematches” to its generic andoverrides the default value of a generic formal argument to<code>NULL</code> no longer drops the argument from its formals.</p></li><li> <p><code>Rscript</code> can now accept more than one argument given onthe <span class="samp">#!</span> line of a script. Previously, one could only pass asingle argument on the <span class="samp">#!</span> line in Linux.</p></li><li><p> Connections are now written correctly with encoding<code>"UTF-16LE"</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16737">PR#16737</a>).</p></li><li><p> Evaluation of <code>..0</code> now signals an error. When<code>..1</code> is used and <code>...</code> is empty, the error message ismore appropriate.</p></li><li><p> (Windows mainly.) Unicode code points which requiresurrogate pairs in UTF-16 are now handled. All systems shouldproperly handle surrogate pairs, even those systems that do notneed to make use of them. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16098">PR#16098</a>)</p></li><li> <p><code>stopifnot(e, e2, ...)</code> now evaluates theexpressions sequentially and in case of an error or warning showsthe relevant expression instead of the full <code>stopifnot(..)</code>call.</p></li><li> <p><code>path.expand()</code> on Windows now accepts paths specified asUTF-8-encoded character strings even if not representable in thecurrent locale. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17120">PR#17120</a>)</p></li><li> <p><code>line(x, y)</code> now correctly computes the medians of theleft and right group's x-values and in all cases reproducesstraight lines.</p></li><li><p> Extending S4 classes with slots corresponding to specialattributes like <code>dim</code> and <code>dimnames</code> now works.</p></li><li><p> Fix for <code>legend()</code> when <code>fill</code> has multiple valuesthe first of which is <code>NA</code> (all colours used to default to<code>par(fg)</code>). (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17288">PR#17288</a>)</p></li><li> <p><code>installed.packages()</code> did not remove the cached valuefor a library tree that had been emptied (but would not use theold value, just waste time checking it).</p></li><li><p> The documentation for <code>installed.packages(noCache = TRUE)</code>incorrectly claimed it would refresh the cache.</p></li><li> <p><code>aggregate(<data.frame>)</code> no longer uses spurious namesin some cases. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17283">PR#17283</a>)</p></li><li> <p><code>object.size()</code> now also works for long vectors.</p></li><li> <p><code>packageDescription()</code> tries harder to solvere-encoding issues, notably seen in some Windows locales. Thisfixes the <code>citation()</code> issue in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17291">PR#17291</a>.</p></li><li> <p><code>poly(<matrix>, 3)</code> now works, thanks to prompting byMarc Schwartz.</p></li><li> <p><code>readLines()</code> no longer segfaults on very large fileswith embedded <code>'\0'</code> (aka ‘nul’) characters.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17311">PR#17311</a>)</p></li><li> <p><code>ns()</code> (package <span class="pkg">splines</span>) now also works for asingle observation. <code>interpSpline()</code> gives a more friendlyerror message when the number of points is less than four.</p></li><li> <p><code>dist(x, method = "canberra")</code> now uses the correctdefinition; the result may only differ when <code>x</code> containsvalues of differing signs, e.g. not for 0-1 data.</p></li><li> <p><code>methods:::cbind()</code> and <code>methods:::rbind()</code> avoiddeep recursion, thanks to Suharto Anggono via <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17300">PR#17300</a>.</p></li><li><p> Arithmetic with zero-column data frames now works moreconsistently; issue raised by Bill Dunlap.</p><p>Arithmetic with data frames gives a data frame for <code>^</code> (whichpreviously gave a numeric matrix).</p></li><li> <p><code>pretty(x, n)</code> for large <code>n</code> or large<code>diff(range(x))</code> now works better (thoughit was never meant for large <code>n</code>); internally it uses thesame rounding fuzz (1e-10) as <code>seq.default()</code> — as it did upto 2010-02-03 when both were 1e-7.</p></li><li><p> Internal C-level <code>R_check_class_and_super()</code> and hence<code>R_check_class_etc()</code> now also consider non-direct superclasses and hence return a match in more cases. This e.g., fixesbehaviour of derived classes in package <a href="https://CRAN.R-project.org/package=Matrix"><span class="pkg">Matrix</span></a>.</p></li><li><p> Reverted unintended change in behavior of <code>return</code>calls in <code>on.exit</code> expressions introduced by stack unwindingchanges in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.3.0.</p></li><li><p> Attributes on symbols are now detected and prevented; attemptto add an attribute to a symbol results in an error.</p></li><li> <p><code>fisher.test(*, workspace = <n>)</code> now may also increasethe internal stack size which allows larger problem to be solved,fixing <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=1662">PR#1662</a>.</p></li><li><p> The <span class="pkg">methods</span> package no longer directly copies slots(attributes) into a prototype that is of an “abnormal”(reference) type, like a symbol.</p></li><li><p> The <span class="pkg">methods</span> package no longer attempts to call<code>length<-()</code> on <code>NULL</code> (during the bootstrap process).</p></li><li><p> The <span class="pkg">methods</span> package correctly shows methods when thereare multiple methods with the same signature for the same generic(still not fully supported, but at least the user can see them).</p></li><li> <p><code>sys.on.exit()</code> is now always evaluated in the rightframe. (From Lionel Henry.)</p></li><li> <p><code>seq.POSIXt(*, by = "<n> DSTdays")</code> now should workcorrectly in all cases and is faster. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17342">PR#17342</a>)</p></li><li> <p><code>.C()</code> when returning a logical vector now always mapsvalues other than FALSE and NA to TRUE (as documented).</p></li><li><p> Subassignment with zero length vectors now coerces asdocumented (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17344">PR#17344</a>).<br />Further, <code>x <- numeric(); x[1] <- character()</code> now signalsan error ‘<code style="white-space: pre;">replacement has length zero</code>’ (or atranslation of that) instead of doing nothing.</p></li><li><p> (Package <span class="pkg">parallel</span>.) <code>mclapply()</code>, <code>pvec()</code>and <code>mcparallel()</code> (when <code>mccollect()</code> is used tocollect results) no longer leave zombie processes behind.</p></li><li> <p><code>R CMD INSTALL <pkg></code> now produces the intended errormessage when, e.g., the <code>LazyData</code> field is invalid.</p></li><li> <p><code>as.matrix(dd)</code> now works when the data frame <code>dd</code>contains a column which is a data frame or matrix, including a0-column matrix/d.f. .</p></li><li> <p><code>mclapply(X, mc.cores)</code> now follows its documentationand calls <code>lapply()</code> in case <code>mc.cores = 1</code> also in thecase <code>mc.preschedule</code> is false. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17373">PR#17373</a>)</p></li><li> <p><code>aggregate(<data.frame>, drop=FALSE)</code> no longer callsthe function on <empty> parts but sets corresponding results to<code>NA</code>. (Thanks to Suharto Anggono's patches in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17280">PR#17280</a>).</p></li><li><p> The <code>duplicated()</code> method for data frames is now basedon the <code>list</code> method (instead of string coercion). Consequently<code>unique()</code> is better distinguishing data frame rows, fixing<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17369">PR#17369</a> and <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17381">PR#17381</a>. The methods for matrices and arraysare changed accordingly.</p></li><li><p> Calling <code>names()</code> on an S4 object derived from<code>"environment"</code> behaves (by default) like calling<code>names()</code> on an ordinary environment.</p></li><li> <p><code>read.table()</code> with a non-default separator nowsupports quotes following a non-whitespace character, matching thebehavior of <code>scan()</code>.</p></li><li> <p><code>parLapplyLB</code> and <code>parSapplyLB</code> have been fixed to doload balancing (dynamic scheduling). This also means that results ofcomputations depending on random number generators will now really benon-reproducible, as documented.</p></li><li><p> Indexing a list using dollar and empty string (<code>l$""</code>)returns NULL.</p></li><li><p> Using <code> \usage{ data(<name>, package="<pkg>") } </code>no longer produces <code>R CMD check</code> warnings.</p></li><li> <p><code>match.arg()</code> more carefully chooses the environmentfor constructing default <code>choices</code>, fixing <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17401">PR#17401</a> asproposed by Duncan Murdoch.</p></li><li><p> Deparsing of consecutive <code>!</code> calls is now consistentwith deparsing unary <code>-</code> and <code>+</code> calls and creates codethat can be reparsed exactly; thanks to a patch by Lionel Henry in<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17397">PR#17397</a>. (As a side effect, this uses fewer parentheses insome other deparsing involving <code>!</code> calls.)</p></li></ul><h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.4.4</h3><h4>NEW FEATURES</h4><ul><li> <p><code>Sys.timezone()</code> tries more heuristics on Unix-alikes and sois more likely to succeed (especially on Linux). For the slowestmethod, a warning is given recommending that <span class="env">TZ</span> is set toavoid the search.</p></li><li><p> The version of LAPACK included in the sources has beenupdated to 3.8.0 (for the routines used by <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>, a very minor bug-fixchange).</p></li><li> <p><code>parallel::detectCores(logical = FALSE)</code> is ignored onLinux systems, since the information is not available withvirtualized OSes.</p></li></ul><h4>INSTALLATION on a UNIX-ALIKE</h4><ul><li> <p><code>configure</code> will use <code>pkg-config</code> to find theflags to link to <code>jpeg</code> if available (as it should be for therecently-released <code>jpeg-9c</code> and <code>libjpeg-turbo</code>). (Thisamends the code added in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.3.0 as the module name in<code>jpeg-9c</code> is not what that tested for.)</p></li></ul><h4>DEPRECATED AND DEFUNCT</h4><ul><li> <p><code>Sys.timezone(location = FALSE)</code> (which was a stop-gapmeasure for Windows long ago) is deprecated. It no longer returnsthe value of environment variable <span class="env">TZ</span> (usually a location).</p></li><li><p> Legacy support of <code>make</code> macros such as <span class="samp">CXX1X</span>is formally deprecated: use the <span class="samp">CXX11</span> forms instead.</p></li></ul><h4>BUG FIXES</h4><ul><li> <p><code>power.prop.test()</code> now warns when it cannot solve theproblem, typically because of impossible constraints. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17345">PR#17345</a>)</p></li><li> <p><code>removeSource()</code> no longer erroneously removes<code>NULL</code> in certain cases, thanks to Dénes Tóth.</p></li><li> <p><code>nls(`NO [mol/l]` ~ f(t))</code> and <code>nls(y ~ a)</code> nowwork. (Partly from <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17367">PR#17367</a>)</p></li><li> <p><code>R CMD build</code> checks for GNU <code>cp</code> ratherthan assuming Linux has it. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17370">PR#17370</a> says ‘AlpineLinux’ does not.)</p></li><li><p> Non-UTF-8 multibyte character handling fixed morepermanently (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16732">PR#16732</a>).</p></li><li> <p><code>sum(<large ints>, <stuff>)</code> is more consistent.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17372">PR#17372</a>)</p></li><li> <p><code>rf()</code> and <code>rbeta()</code> now also work correctly when<code>ncp</code> is not scalar, notably when (partly) <code>NA</code>.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17375">PR#17375</a>)</p></li><li> <p><code>is.na(NULL)</code> no longer warns. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16107">PR#16107</a>)</p></li><li> <p><code>R CMD INSTALL</code> now correctly sets C++ compiler flagswhen all source files are in sub-directories of ‘<span class="file">src</span>’.</p></li></ul><h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.4.3</h3><h4>INSTALLATION on a UNIX-ALIKE</h4><ul><li><p> A workaround has been added for the changes in location oftime-zone files in macOS 10.13 ‘High Sierra’ andagain in 10.13.1, so the default time zone is deducedcorrectly from the system setting when <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> is configured with<span class="option">--with-internal-tzcode</span> (the default on macOS).</p></li><li> <p><code>R CMD javareconf</code> has been updated to recognize theuse of a Java 9 SDK on macOS.</p></li></ul><h4>BUG FIXES</h4><ul><li> <p><code>raw(0) & raw(0)</code> and <code>raw(0) | raw(0)</code>again return <code>raw(0)</code> (rather than <code>logical(0)</code>).</p></li><li> <p><code>intToUtf8()</code> converts integers corresponding tosurrogate code points to <code>NA</code> rather than invalid UTF-8, aswell as values larger than the current Unicode maximum of<code>0x10FFFF</code>. (This aligns with the current RFC3629.)</p></li><li><p> Fix calling of methods on S4 generics that dispatch on<code>...</code> when the call contains <code>...</code>.</p></li><li><p> Following Unicode ‘Corrigendum 9’, the UTF-8representations of U+FFFE and U+FFFF are now regarded as valid by<code>utf8ToInt()</code>.</p></li><li> <p><code>range(c(TRUE, NA), finite = TRUE)</code> and similar no longerreturn <code>NA</code>. (Reported by Lukas Stadler.)</p></li><li><p> The self starting function <code>attr(SSlogis, "initial")</code>now also works when the y values have exact minimum zero and isslightly changed in general, behaving symmetrically in the y range.</p></li><li><p> The printing of named raw vectors is now formatted nicely asfor other such atomic vectors, thanks to Lukas Stadler.</p></li></ul><h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.4.2</h3><h4>NEW FEATURES</h4><ul><li><p> Setting the <code>LC_ALL</code> category in <code>Sys.setlocale()</code>invalidates any cached locale-specific day/month names and theAM/PM indicator for <code>strptime()</code> (as setting <code>LC_TIME</code>has since <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.1.0).</p></li><li><p> The version of LAPACK included in the sources has beenupdated to 3.7.1, a bug-fix release.</p></li><li><p> The default for <code>tools::write_PACKAGES(rds_compress=)</code>has been changed to <code>"xz"</code> to match the compression used by<acronym><span class="acronym">CRAN</span></acronym>.</p></li><li> <p><code>c()</code> and <code>unlist()</code> are now more efficient inconstructing the <code>names(.)</code> of their return value, thanks toa proposal by Suharto Anggono. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17284">PR#17284</a>)</p></li></ul><h4>UTILITIES</h4><ul><li> <p><code>R CMD check</code> checks for and <code>R CMD build</code>corrects CRLF line endings in shell scripts <code>configure</code>and <code>cleanup</code> (even on Windows).</p></li></ul><h4>INSTALLATION on a UNIX-ALIKE</h4><ul><li><p> The order of selection of OpenMP flags has been changed:Oracle Developer Studio 12.5 accepts <span class="option">-fopenmp</span> and<span class="option">-xopenmp</span> but only the latter enables OpenMP so it is nowtried first.</p></li></ul><h4>BUG FIXES</h4><ul><li> <p><code>within(List, rm(x1, x2))</code> works correctly again,including when <code>List[["x2"]]</code> is <code>NULL</code>.</p></li><li> <p><code>regexec(pattern, text, *)</code> now applies<code>as.character(.)</code> to its first two arguments, as documented.</p></li><li> <p><code>write.table()</code> and related functions,<code>writeLines()</code>, and perhaps other functions writing text toconnections did not signal errors when the writes failed,e.g. due to a disk being full. Errors will now besignalled if detected during the write, warnings if detected whenthe connection is closed. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17243">PR#17243</a>)</p></li><li> <p><code>rt()</code> assumed the <code>ncp</code> parameter was a scalar. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17306">PR#17306</a>)</p></li><li> <p><code>menu(choices)</code> with more than 10 choices which easilyfit into one <code>getOption("width")</code>-line no longer erroneouslyrepeats choices. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17312">PR#17312</a>)</p></li><li> <p><code>length()<-</code> on a pairlist succeeds.(<a href="https://stat.ethz.ch/pipermail/r-devel/2017-July/074680.html">https://stat.ethz.ch/pipermail/r-devel/2017-July/074680.html</a>)</p></li><li><p> Language objects such as <code>quote(("\n"))</code> or <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>functions are correctly printed again, where <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.4.1 accidentallyduplicated the backslashes.</p></li><li><p> Construction of <code>names()</code> for very large objects in<code>c()</code> and <code>unlist()</code> now works, thanks to SuhartoAnggono's patch proposals in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17292">PR#17292</a>.</p></li><li><p> Resource leaks (and similar) reported by Steve Grubb fixed.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17314">PR#17314</a>, <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17316">PR#17316</a>, <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17317">PR#17317</a>, <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17318">PR#17318</a>, <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17319">PR#17319</a>, <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17320">PR#17320</a>)</p></li><li> <p><code>model.matrix(~1, mf)</code> now gets the row names from<code>mf</code> also when they differ from <code>1:nrow(mf)</code>, fixing<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14992">PR#14992</a> thanks to the suggestion by Sebastian Meyer.</p></li><li> <p><code>sigma(fm)</code> now takes the correct denominator degreesof freedom for a fitted model with <code>NA</code> coefficients. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17313">PR#17313</a>)</p></li><li> <p><code>hist(x, "FD")</code> no longer “dies” with a somewhatcryptic error message when <code>x</code> has extreme outliers or<code>IQR()</code> zero: <code>nclass.FD(x)</code> tries harder to find arobust bin width <i>h</i> in the latter case, and<code>hist.default(*, breaks)</code> now checks and corrects a too large<code>breaks</code> number. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17274">PR#17274</a>)</p></li><li> <p><code>callNextMethod()</code> works for <code>...</code> methods.</p></li><li> <p><code>qr.coef(qd, y)</code> now has correct names also when<code>qd</code> is a complex QR or stems from <code>qr(*, LAPACK=TRUE)</code>.</p></li><li><p> Setting <code>options(device = *)</code> to an invalid function nolonger segfaults when plotting is initiated. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15883">PR#15883</a>)</p></li><li> <p><code>encodeString(<very large string>)</code> no longersegfaults. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15885">PR#15885</a>)</p></li><li><p> It is again possible to use <code>configure--enable-maintainer-mode</code> without having installed<code>notangle</code> (it was required in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.4.[01]).</p></li><li><p> S4 method dispatch on <code>...</code> calls the method by nameinstead of <code>.Method</code> (for consistency with default dispatch),and only attempts to pass non-missing arguments from the generic.</p></li><li> <p><code>readRDS(textConnection(.))</code> works again. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17325">PR#17325</a>)</p></li><li> <p><code>(1:n)[-n]</code> no longer segfaults for <code>n <- 2.2e9</code>(on a platform with enough RAM).</p></li><li> <p><code>x <- 1:2; tapply(x, list(x, x), function(x) "")[1,2]</code>now correctly returns <code>NA</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17333">PR#17333</a>)</p></li><li><p> Running of finalizers after explicit GC request moved fromthe <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> interface <code>do_gc</code> to the <code>C</code> interface<code>R_gc</code>. This helps with reclaiming inaccessible connections.</p></li><li> <p><code>help.search(topic)</code> and <code>??topic</code> matching topicsin vignettes with multiple file name extensions (e.g.,‘<span class="file">*.md.rsp</span>’ but not ‘<span class="file">*.Rmd</span>’) failed with an errorwhen using <code>options(help_type = "html")</code>.</p></li><li><p> The X11 device no longer uses the Xlib backing store (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16497">PR#16497</a>).</p></li><li> <p><code>array(character(), 1)</code> now gives (a 1D array with)<code>NA</code> as has been documented for a long time as in the othercases of zero-length array initialization and also compatibly with<code>matrix(character(), *)</code>. As mentioned there, this alsofixes <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17333">PR#17333</a>.</p></li><li> <p><code>splineDesign(.., derivs = 4)</code> no longer segfaults.</p></li><li> <p><code>fisher.test(*, hybrid=TRUE)</code> now (again) will use thehybrid method when Cochran's conditions are met, fixing <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16654">PR#16654</a>.</p></li></ul><h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.4.1</h3><h4>INSTALLATION on a UNIX-ALIKE</h4><ul><li><p> The deprecated support for PCRE versions older than 8.20has been removed.</p></li></ul><h4>BUG FIXES</h4><ul><li> <p><code>getParseData()</code> gave incorrect column information whencode contained multi-byte characters. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17254">PR#17254</a>)</p></li><li><p> Asking for help using expressions like <code>?stats::cor()</code>did not work. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17250">PR#17250</a>)</p></li><li> <p><code>readRDS(url(....))</code> now works.</p></li><li> <p><code>R CMD Sweave</code> again returns <span class="samp">status = 0</span> onsuccessful completion.</p></li><li><p> Vignettes listed in ‘<span class="file">.Rbuildignore</span>’ were not beingignored properly. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17246">PR#17246</a>)</p></li><li> <p><code>file.mtime()</code> no longer returns NA on Windows when thefile or directory is being used by another process. This affected<code>installed.packages()</code>, which is now protected against this.</p></li><li> <p><code>R CMD INSTALL</code> Windows .zip file obeys <code>--lock</code>and <code>--pkglock</code> flags.</p></li><li><p> (Windows only) The <code>choose.files()</code> function couldreturn incorrect results when called with <code>multi = FALSE</code>.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17270">PR#17270</a>)</p></li><li> <p><code>aggregate(<data.frame>, drop = FALSE)</code> now also works incase of near-equal numbers in <code>by</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16918">PR#16918</a>)</p></li><li> <p><code>fourfoldplot()</code> could encounter integer overflow whencalculating the odds ratio. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17286">PR#17286</a>)</p></li><li> <p><code>parse()</code> no longer gives spurious warnings whenextracting srcrefs from a file not encoded in the current locale.</p><p>This was seen from <code>R CMD check</code> with ‘<span class="file">inst/doc/*.R</span>’files, and <code>check</code> has some additional protection for such files.</p></li><li> <p><code>print.noquote(x)</code> now always returns its argument<code>x</code> (invisibly).</p></li><li><p> Non-UTF-8 multibyte character sets were not handled properlyin source references. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16732">PR#16732</a>)</p></li></ul><h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.4.0</h3><h4>SIGNIFICANT USER-VISIBLE CHANGES</h4><ul><li><p> (Unix-alike)The default methods for <code>download.file()</code> and <code>url()</code>now choose <code>"libcurl"</code> except for <span class="samp">file://</span>URLs. There will be small changes in the format and wording ofmessages, including in rare cases if an issue is a warning or anerror. For example, when HTTP re-direction occurs, some messagesrefer to the final URL rather than the specified one.</p><p>Those who use proxies should check that their settings arecompatible (see <code>?download.file</code>: the most commonly usedforms work for both <code>"internal"</code> and <code>"libcurl"</code>).</p></li><li> <p><code>table()</code> has been amended to be more internallyconsistent and become back compatible to <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> <i><=</i> 2.7.2again. Consequently, <code>table(1:2, exclude = NULL)</code> no longercontains a zero count for <code><NA></code>, but <code>useNA = "always"</code>continues to do so.</p></li><li> <p><code>summary.default()</code> no longer rounds, but its printmethod does resulting in less extraneous rounding, notably ofnumbers in the ten thousands.</p></li><li> <p><code>factor(x, exclude = L)</code> behaves more rationally when<code>x</code> or <code>L</code> are character vectors. Further,<code>exclude = <factor></code> now behaves as documented for long.</p></li><li><p> Arithmetic, logic (<code>&</code>, <code>|</code>) and comparison (aka‘relational’, e.g., <code><</code>, <code>==</code>) operations witharrays now behave consistently, notably for arrays of length zero.</p><p>Arithmetic between length-1 arrays and longer non-arrays hadsilently dropped the array attributes and recycled. This nowgives a warning and will signal an error in the future, as it hasalways for logic and comparison operations in these cases (e.g.,compare <code>matrix(1,1) + 2:3</code> and <code>matrix(1,1) < 2:3</code>).</p></li><li><p> The JIT (‘Just In Time’) byte-code compiler is nowenabled by default at its level 3. This means functions will becompiled on first or second use and top-level loops will becompiled and then run. (Thanks to Tomas Kalibera for extensivework to make this possible.)</p><p>For now, the compiler will not compile code containing explicitcalls to <code>browser()</code>: this is to support single stepping fromthe <code>browser()</code> call.</p><p>JIT compilation can be disabled for the rest of the session using<code>compiler::enableJIT(0)</code> or by setting environment variable<span class="env">R_ENABLE_JIT</span> to <code>0</code>.</p></li><li> <p><code>xtabs()</code> works more consistently with <code>NA</code>s, alsoin its result no longer setting them to <code>0</code>. Further, a newlogical option <code>addNA</code> allows to count <code>NA</code>s whereappropriate. Additionally, for the case <code>sparse = TRUE</code>, theresult's <code>dimnames</code> are identical to the default case's.</p></li><li><p> Matrix products now consistently bypass BLAS when the inputshave <code>NaN</code>/<code>Inf</code> values. Performance of the check ofinputs has been improved. Performance when BLAS is used isimproved for matrix/vector and vector/matrix multiplication (DGEMVis now used instead of DGEMM).</p><p>One can now choose from alternative matrix product implementations<em>via</em> <code>options(matprod = )</code>. The <code>"internal"</code>implementation is not optimized for speed but consistent inprecision with other summations in R (using <code>long double</code>accumulators where available). <code>"blas"</code> calls BLAS directlyfor best speed, but usually with undefined behavior for inputswith <code>NaN</code>/<code>Inf</code>.</p></li></ul><h4>NEW FEATURES</h4><ul><li><p> User errors such as <code>integrate(f, 0:1, 2)</code> are now caught.</p></li><li><p> Add <code>signature</code> argument to <code>debug()</code>,<code>debugonce()</code>, <code>undebug()</code> and <code>isdebugged()</code> formore conveniently debugging S3 and S4 methods. (Based on a patch byGabe Becker.)</p></li><li><p> Add <code>utils::debugcall()</code> and<code>utils::undebugcall()</code> for debugging the function that wouldbe called by evaluating the given expression. When the call is toan S4 generic or standard S3 generic, <code>debugcall()</code> debugs themethod that would be dispatched. A number of internal utilitieswere added to support this, most notably<code>utils::isS3stdGeneric()</code>. (Based on a patch by Gabe Becker.)</p></li><li><p> Add <code>utils::strcapture()</code>. Given a character vector anda regular expression containing capture expressions,<code>strcapture()</code> will extract the captured tokens into atabular data structure, typically a <code>data.frame</code>.</p></li><li> <p><code>str()</code> and <code>strOptions()</code> get a new option<code>drop.deparse.attr</code> with improved but <em>changed</em> defaultbehaviour for expressions. For <code>expression</code> objects<code>x</code>, <code>str(x)</code> now may remove extraneous white space andtruncate long lines.</p></li><li> <p><code>str(<looooooooong_string>)</code> is no longer very slow;inspired by Mikko Korpela's proposal in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16527">PR#16527</a>.</p></li><li> <p><code>str(x)</code>'s default method is more “accurate” andhence somewhat more generous in displaying character vectors; thiswill occasionally change <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> outputs (and need changes to some‘<span class="file">*.Rout(.save)</span>’ files).<br />For a classed integer vector such as <code>x <- xtabs(~ c(1,9,9,9))</code>,<code>str(x)</code> now shows both the class and <code>"int"</code>, insteadof only the latter.</p></li><li> <p><code>isSymmetric(m)</code> is much faster for large asymmetricmatrices <code>m</code> <em>via</em> pre-tests and a new option <code>tol1</code>(with which strict back compatibility is possible but not thedefault).</p></li><li><p> The result of <code>eigen()</code> now is of class <code>"eigen"</code>in the default case when eigenvectors are computed.</p></li><li><p> Zero-length date and date-time objects (of classes<code>"POSIX[cl]?t"</code>) now <code>print()</code> “recognizably”.</p></li><li> <p><code>xy.coords()</code> and <code>xyz.coords()</code> get a new<code>setLab</code> option.</p></li><li><p> The <code>method</code> argument of <code>sort.list()</code>,<code>order()</code> and <code>sort.int()</code> gains an <code>"auto"</code> option(the default) which should behave the same as before when<code>method</code> was not supplied.</p></li><li> <p><code>stopifnot(E, ..)</code> now reports differences when<code>E</code> is a call to <code>all.equal()</code> and that is not true.</p></li><li> <p><code>boxplot(<formula>, *)</code> gain optional arguments<code>drop</code>, <code>sep</code>, and <code>lex.order</code> to pass to<code>split.default()</code> which itself gains an argument<code>lex.order</code> to pass to <code>interaction()</code> for moreflexibility.</p></li><li><p> The <code>plot()</code> method for <code>ppr()</code> has enhanceddefault labels (<code>xmin</code> and <code>main</code>).</p></li><li> <p><code>sample.int()</code> gains an explicit <code>useHash</code> option(with a back compatible default).</p></li><li> <p><code>identical()</code> gains an <code>ignore.srcref</code> optionwhich drops <code>"srcref"</code> and similar attributes when true (asby default).</p></li><li> <p><code>diag(x, nrow = n)</code> now preserves <code>typeof(x)</code>, alsofor logical, integer and raw <code>x</code> (and as previously forcomplex and numeric).</p></li><li> <p><code>smooth.spline()</code> now allows direct specification of<code>lambda</code>, gets a <code>hatvalues()</code> method and keeps<code>tol</code> in the result, and optionally parts of the internalmatrix computations.</p></li><li> <p><code>addNA()</code> is faster now, e.g. when applied twice.(Part of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16895">PR#16895</a>.)</p></li><li><p> New option <code>rstandard(<lm>, type = "predicted")</code>provides the “PRESS”–related leave-one-outcross-validation errors for linear models.</p></li><li><p> After seven years of deprecation, duplicated factor levelsnow produce a warning when printed and an error in <code>levels<-</code>instead of a warning.</p></li><li><p> Invalid factors, e.g., with duplicated levels (invalid butconstructable) now give a warning when printed, <em>via</em> newfunction <code>.valid.factor()</code>.</p></li><li> <p><code>sessionInfo()</code> has been updated for Apple's change inOS naming as from ‘10.12’ (‘macOS Sierra’ <em>vs</em>‘OS X El Capitan’).</p><p>Its <code>toLatex()</code> method now includes the <code>running</code>component.</p></li><li> <p><code>options(interrupt=)</code> can be used to specify a defaultaction for user interrupts. For now, if this option is not setand the <code>error</code> option is set, then an unhandled userinterrupt invokes the <code>error</code> option. (This may be dropped inthe future as <code>interrupt</code> conditions are not <code>error</code>conditions.)</p></li><li><p> In most cases user interrupt handlers will be called with a<code>"resume"</code> restart available. Handlers can invoke thisrestart to resume computation. At the browser prompt the <code>r</code>command will invoke a <code>"resume"</code> restart if one isavailable. Some read operations cannot be resumed properly wheninterrupted and do not provide a <code>"resume"</code> restart.</p></li><li><p> Radix sort is now chosen by <code>method = "auto"</code> for<code>sort.int()</code> for double vectors (and hence used for<code>sort()</code> for unclassed double vectors), excluding‘long’ vectors.</p><p><code>sort.int(method = "radix")</code> no longer rounds double vectors.</p></li><li><p> The <code>default</code> and <code>data.frame</code> methods for<code>stack()</code> preserve the names of empty elements in the levelsof the <code>ind</code> column of the return value. Set the new<code>drop</code> argument to <code>TRUE</code> for the previous behavior.</p></li><li><p> Speedup in <code>simplify2array()</code> and hence <code>sapply()</code> and<code>mapply()</code> (for the case of names and common length > 1),thanks to Suharto Anggono's <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17118">PR#17118</a>.</p></li><li> <p><code>table(x, exclude = NULL)</code> now sets<code>useNA = "ifany"</code> (instead of <code>"always"</code>).Together with the bug fixes for this case, this recovers moreconsistent behaviour compatible to older versions of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>. Asa consequence, <code>summary()</code> for a logical vector no longerreports (zero) counts for <code>NA</code> when there are no <code>NA</code>s.</p></li><li> <p><code>dump.frames()</code> gets a new option<code>include.GlobalEnv</code> which allows to also dump the globalenvironment, thanks to Andreas Kersting's proposal in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17116">PR#17116</a>.</p></li><li> <p><code>system.time()</code> now uses <code>message()</code> instead of<code>cat()</code> when terminated early, such that<code>suppressMessages()</code> has an effect; suggested by Ben Bolker.</p></li><li> <p><code>citation()</code> supports ‘<span class="file">inst/CITATION</span>’ files frompackage source trees, with <code>lib.loc</code> pointing to thedirectory containing the package.</p></li><li> <p><code>try()</code> gains a new argument <code>outFile</code> with adefault that can be modified <em>via</em><code>options(try.outFile = .)</code>, useful notably for <code>Sweave</code>.</p></li><li><p> The unexported low-level functions in package <span class="pkg">parallel</span>for passing serialized <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> objects to and from forked children nowsupport long vectors on 64-bit platforms. This removes somelimits on higher-level functions such as <code>mclapply()</code> (butreturning gigabyte results from forked processes <em>via</em>serialization should be avoided if at all possible).</p></li><li><p> Connections now <code>print()</code> without error even ifinvalid, e.g. after having been destroyed.</p></li><li> <p><code>apropos()</code> and <code>find(simple.words = FALSE)</code> nolonger match object names starting with <span class="samp">.</span> which are knownto be internal objects (such as <code>.__S3MethodsTable__.</code>).</p></li><li><p> Convenience function <code>hasName()</code> has been added; itis intended to replace the common idiom <code>!is.null(x$name)</code>without the usually unintended partial name matching.</p></li><li> <p><code>strcapture()</code> no longer fixes column names nor coercesstrings to factors (suggested by Bill Dunlap).</p></li><li> <p><code>strcapture()</code> returns <code>NA</code> for non-matchingvalues in <code>x</code> (suggested by Bill Dunlap).</p></li><li> <p><code>source()</code> gets new optional arguments, notably<code>exprs</code>; this is made use of in the new utility function<code>withAutoprint()</code>.</p></li><li> <p><code>sys.source()</code> gets a new <code>toplevel.env</code> argument.This argument is useful for frameworks running package tests;contributed by Tomas Kalibera.</p></li><li> <p><code>Sys.setFileTime()</code> and<code>file.copy(copy.date = TRUE)</code> will set timestamps withfractions of seconds on platforms/filesystems which support this.</p></li><li><p> (Windows only.) <code>file.info()</code> now returns filetimestamps including fractions of seconds; it has done so on otherplatforms since <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.14.0. (NB: some filesystems do notrecord modification and access timestamps to sub-secondresolution.)</p></li><li><p> The license check enabled by<code>options(checkPackageLicense = TRUE)</code> is now done when thepackage's namespace is first loaded.</p></li><li> <p><code>ppr()</code> and <code>supsmu()</code> get an optional<code>trace</code> argument, and <code>ppr(.., sm.method = ..spline)</code> isno longer limited to sample size <i>n <= 2500</i>.</p></li><li><p> The <code>POSIXct</code> method for <code>print()</code> gets optional<code>tz</code> and <code>usetz</code> arguments, thanks to a report fromJennifer S. Lyon.</p></li><li><p> New function <code>check_packages_in_dir_details()</code> inpackage <span class="pkg">tools</span> for analyzing package-check log files toobtain check details.</p></li><li><p> Package <span class="pkg">tools</span> now exports function<code>CRAN_package_db()</code> for obtaining information about currentpackages in the <acronym><span class="acronym">CRAN</span></acronym> package repository, and severalfunctions for obtaining the check status of these packages.</p></li><li><p> The (default) Stangle driver <code>Rtangle</code> allows<code>annotate</code> to be a function and gets a new<code>drop.evalFALSE</code> option.</p></li><li><p> The default method for <code>quantile(x, prob)</code> should nowbe monotone in <code>prob</code>, even in border cases, see <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16672">PR#16672</a>.</p></li><li> <p><code>bug.report()</code> now tries to extract an email addressfrom a <span class="samp">BugReports</span> field, and if there is none, from a<span class="samp">Contacts</span> field.</p></li><li><p> The <code>format()</code> and <code>print()</code> methods for<code>object.size()</code> results get new options <code>standard</code> and<code>digits</code>; notably, <code>standard = "IEC"</code> and<code>standard = "SI"</code> allow more standard (but less common)abbreviations than the default ones, e.g. for kilobytes.(From contributions by Henrik Bengtsson.)</p></li><li><p> If a reference class has a validity method,<code>validObject</code> will be called automatically from thedefault initialization method for reference classes.</p></li><li> <p><code>tapply()</code> gets new option <code>default = NA</code>allowing to change the previously hardcoded value.</p></li><li> <p><code>read.dcf()</code> now consistently interprets any‘whitespace’ to be stripped to include newlines.</p></li><li><p> The maximum number of DLLs that can be loaded into Re.g. <em>via</em> <code>dyn.load()</code> can now be increased bysetting the environment variable <code>R_MAX_NUM_DLLS</code> beforestarting R.</p></li><li><p> Assigning to an element of a vector beyond the currentlength now over-allocates by a small fraction. The new vector ismarked internally as growable, and the true length of the newvector is stored in the <code>truelength</code> field. This makesbuilding up a vector result by assigning to the next elementbeyond the current length more efficient, though pre-allocating isstill preferred. The implementation is subject to change and notintended to be used in packages at this time.</p></li><li><p> Loading the <span class="pkg">parallel</span> package namespace no longer setsor changes the <code>.Random.seed</code>, even if <span class="env">R_PARALLEL_PORT</span>is unset.</p><p>NB: This can break reproducibility of output, and did for a<acronym><span class="acronym">CRAN</span></acronym> package.</p></li><li><p> Methods <code>"wget"</code> and <code>"curl"</code> for<code>download.file()</code> now give an <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> error rather than a non-zeroreturn value when the external command has a non-zero status.</p></li><li><p> Encoding name <code>"utf8"</code> is mapped to <code>"UTF-8"</code>.Many implementations of <code>iconv</code> accept <code>"utf8"</code>, but notGNU <span class="pkg">libiconv</span> (including the late 2016 version 1.15).</p></li><li> <p><code>sessionInfo()</code> shows the full paths to the library orexecutable files providing the BLAS/LAPACK implementationscurrently in use (not available on Windows).</p></li><li><p> The binning algorithm used by bandwidth selectors<code>bw.ucv()</code>, <code>bw.bcv()</code> and <code>bw.SJ()</code> switches to aversion linear in the input size <code>n</code> for <code>n > nb/2</code>.(The calculations are the same, but for larger <code>n/nb</code> it isworth doing the binning in advance.)</p></li><li><p> There is a new option <code>PCRE_study</code> which controls when<code>grep(perl = TRUE)</code> and friends ‘study’ the compiledpattern. Previously this was done for 11 or more input strings:it now defaults to 10 or more (but most examples need many morefor the difference from studying to be noticeable).</p></li><li> <p><code>grep(perl = TRUE)</code> and friends can now make use ofPCRE's Just-In-Time mechanism, for PCRE <i>>=</i> 8.20 onplatforms where JIT is supported. It is used by default wheneverthe <code>pattern</code> is studied (see the previous item). (Based ona patch from Mikko Korpela.)</p><p>This is controlled by a new option <code>PCRE_use_JIT</code>.</p><p>Note that in general this makes little difference to the speed,and may take a little longer: its benefits are most evident onstrings of thousands of characters. As a side effect it reducesthe chances of C stack overflow in the PCRE library on very longstrings (millions of characters, but see next item).</p><p>Warning: segfaults were seen using PCRE with JIT enabled on 64-bitSparc builds.</p></li><li><p> There is a new option <code>PCRE_limit_recursion</code> for<code>grep(perl = TRUE)</code> and friends to set a recursion limittaking into account <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>'s estimate of the remaining C stack space(or 10000 if that is not available). This reduces the chance of Cstack overflow, but because it is conservative may report anon-match (with a warning) in examples that matched before. Bydefault it is enabled if any input string has 1000 or more bytes.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16757">PR#16757</a>)</p></li><li> <p><code>getGraphicsEvent()</code> now works on<code>X11(type = "cairo")</code> devices. Thanks to Frederick Eaton (forreviving an earlier patch).</p></li><li><p> There is a new argument <code>onIdle</code> for<code>getGraphicsEvent()</code>, which allows an R function to be runwhenever there are no pending graphics events. This is currentlyonly supported on X11 devices. Thanks to Frederick Eaton.</p></li><li><p> The <code>deriv()</code> and similar functions now can computederivatives of <code>log1p()</code>, <code>sinpi()</code> and similarone-argument functions, thanks to a contribution by Jerry Lewis.</p></li><li> <p><code>median()</code> gains a formal <code>...</code> argument, somethods with extra arguments can be provided.</p></li><li> <p><code>strwrap()</code> reduces <code>indent</code> if it is more thanhalf <code>width</code> rather than giving an error. (Suggested by BillDunlap.)</p></li><li><p> When the condition <code>code</code> in <code>if(.)</code> or<code>while(.)</code> is not of length one, an error instead of awarning may be triggered by setting an environment variable, seethe help page.</p></li><li><p> Formatting and printing of bibliography entries(<code>bibentry</code>) is more flexible and better documented. Apartfrom setting <code>options(citation.bibtex.max = 99)</code> you can alsouse <code>print(<citation>, bibtex=TRUE)</code> (or <code>format(..)</code>)to get the BibTeX entries in the case of more than one entry.This also affects <code>citation()</code>.Contributions to enable <code>style = "html+bibtex"</code> are welcome.</p></li></ul><h4>C-LEVEL FACILITIES</h4><ul><li><p> Entry points <code>R_MakeExternalPtrFn</code> and<code>R_ExternalPtrFn</code> are now declared in header‘<span class="file">Rinternals.h</span>’ to facilitate creating and retrieving an <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>external pointer from a C function pointer without ISO C warningsabout the conversion of function pointers.</p></li><li><p> There was an exception for the native Solaris C++ compilerto the dropping (in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.3.0) of legacy C++ headers from headerssuch as ‘<span class="file">R.h</span>’ and ‘<span class="file">Rmath.h</span>’ — this has now beenremoved. That compiler has strict C++98 compliance hence does notinclude extensions in its (non-legacy) C++ headers: somepackages will need to request C++11 or replace non-C++98 callssuch as <code>lgamma</code>: see §1.6.4 of ‘Writing R Extensions’.</p><p>Because it is needed by about 70 CRAN packages, headers ‘<span class="file">R.h</span>’and ‘<span class="file">Rmath.h</span>’ still declare </p><pre>use namespace std;</pre><p>when included on Solaris.</p></li><li><p> When included from C++, the <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> headers now use forms such as<code>std::FILE</code> directly rather than including the line </p><pre>using std::FILE;</pre><p>C++ code including these headers might be relying on the latter.</p></li><li><p> Headers ‘<span class="file">R_ext/BLAS.h</span>’ and ‘<span class="file">R_ext/Lapack.h</span>’ havemany improved declarations including <code>const</code> fordouble-precision complex routines. <em>Inter alia</em> this avoidswarnings when passing ‘string literal’ arguments from C++11code.</p></li><li><p> Headers for Unix-only facilities ‘<span class="file">R_ext/GetX11Image.h</span>’,‘<span class="file">R_ext/QuartzDevice.h</span>’ and ‘<span class="file">R_ext/eventloop.h</span>’ are nolonger installed on Windows.</p></li><li><p> No-longer-installed headers ‘<span class="file">GraphicsBase.h</span>’,‘<span class="file">RGraphics.h</span>’, ‘<span class="file">Rmodules/RX11.h</span>’ and‘<span class="file">Rmodules/Rlapack.h</span>’ which had a LGPL license no longer do so.</p></li><li> <p><code>HAVE_UINTPTR_T</code> is now defined where appropriate by<code>Rconfig.h</code> so that it can be included before<code>Rinterface.h</code> when <code>CSTACK_DEFNS</code> is defined and a Ccompiler (not C++) is in use. <code>Rinterface.h</code> now includes Cheader ‘<span class="file">stdint.h</span>’ or C++11 header ‘<span class="file">cstdint</span>’ whereneeded.</p></li><li><p> Package <span class="pkg">tools</span> has a new function<code>package_native_routine_registration_skeleton()</code> to assistadding native-symbol registration to a package. See its help and§5.4.1 of ‘Writing R Extensions’ for how to use it. (Atthe time it was added it successfully automated addingregistration to over 90% of <acronym><span class="acronym">CRAN</span></acronym> packages which lackedit. Many of the failures were newly-detected bugs in thepackages, e.g. 50 packages called entry points with varyingnumbers of arguments and 65 packages called entry points not inthe package.)</p></li></ul><h4>INSTALLATION on a UNIX-ALIKE</h4><ul><li> <p><code>readline</code> headers (and not just the library) arerequired unless configuring with <span class="option">--with-readline=no</span>.</p></li><li> <p><code>configure</code> now adds a compiler switch for C++11code, even if the compiler supports C++11 by default. (Thisensures that <code>g++</code> 6.x uses C++11 mode and not its defaultmode of C++14 with ‘GNU extensions’.)</p><p>The tests for C++11 compliance are now much more comprehensive.For gcc < 4.8, the tests from R 3.3.0 are used in order to maintainthe same behaviour on Linux distributions with long-term support.</p></li><li><p> An alternative compiler for C++11 is now specified with<span class="samp">CXX11</span>, not <span class="samp">CXX1X</span>. Likewise C++11 flags are specifiedwith <span class="samp">CXX11FLAGS</span> and the standard (e.g., <span class="samp">-std=gnu++11</span>)is specified with <span class="samp">CXX11STD</span>.</p></li><li> <p><code>configure</code> now tests for a C++14-compliant compilerby testing some basic features. This by default tries flags forthe compiler specified by <span class="samp">CXX11</span>, but an alternative compiler,options and standard can be specified by variables <span class="samp">CXX14</span>,<span class="samp">CXX14FLAGS</span> and <span class="samp">CXX14STD</span> (e.g., <span class="option">-std=gnu++14</span>).</p></li><li><p> There is a new macro <code>CXXSTD</code> to help specify thestandard for C++ code, e.g. <span class="option">-std=c++98</span>. Thismakes it easier to work with compilers which default to a laterstandard: for example, with <code>CXX=g++6 CXXSTD=-std=c++98</code><code>configure</code> will select commands for <code>g++</code> 6.xwhich conform to C++11 and C++14 where specified but otherwise useC++98.</p></li><li><p> Support for the defunct IRIX and OSF/1 OSes and Alpha CPUhas been removed.</p></li><li> <p><code>configure</code> checks that the compiler specified by<span class="samp">$CXX $CXXFLAGS</span> is able to compile C++ code.</p></li><li> <p><code>configure</code> checks for the required header‘<span class="file">sys/select.h</span>’ (or ‘<span class="file">sys/time.h</span>’ on legacy systems) andsystem call <code>select</code> and aborts if they are not found.</p></li><li><p> If available, the POSIX 2008 system call <code>utimensat</code>will be used by <code>Sys.setFileTime()</code> and<code>file.copy(copy.date = TRUE)</code>. This may result in slightlymore accurate file times. (It is available on Linux and FreeBSDbut not macOS.)</p></li><li><p> The minimum version requirement for <code>libcurl</code> has beenreduced to 7.22.0, although at least 7.28.0 is preferred andearlier versions are little tested. (This is to support Debian 7‘Wheezy’ LTS and Ubuntu ‘Precise’ 12.04 LTS,although the latter is close to end-of-life.)</p></li><li> <p><code>configure</code> tests for a C++17-compliant compiler.The tests are experimental and subject to change in the future.</p></li></ul><h4>INCLUDED SOFTWARE</h4><ul><li><p> (Windows only) Tcl/Tk version 8.6.4 is now included in thebinary builds. The ‘<span class="file">tcltk*.chm</span>’ help file is no longerincluded; please consult the online help at<a href="http://www.tcl.tk/man/">http://www.tcl.tk/man/</a> instead.</p></li><li><p> The version of LAPACK included in the sources has beenupdated to 3.7.0: no new routines have been added to <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>.</p></li></ul><h4>PACKAGE INSTALLATION</h4><ul><li><p> There is support for compiling C++14 or C++17 code inpackages on suitable platforms: see ‘Writing R Extensions’for how to request this.</p></li><li><p> The order of flags when <span class="samp">LinkingTo</span> other packages hasbeen changed so their include directories come earlier, beforethose specified in <code>CPPFLAGS</code>. This will only have an effectif non-system include directories are included with <span class="option">-I</span>flags in <code>CPPFLAGS</code> (and so not the default<code>-I/usr/local/include</code> which is treated as a system includedirectory on most platforms).</p></li><li><p> Packages which register native routines for <code>.C</code> or<code>.Fortran</code> need to be re-installed for this version (unlessinstalled with R-devel SVN revision r72375 or later).</p></li><li><p> Make variables with names containing <code>CXX1X</code> aredeprecated in favour of those using <code>CXX11</code>, but for the timebeing are still made available <em>via</em> file‘<span class="file">etc/Makeconf</span>’. Packages using them should be converted tothe new forms and made dependent on <span class="samp">R (>= 3.4.0)</span>.</p></li></ul><h4>UTILITIES</h4><ul><li><p> Running <code>R CMD check --as-cran</code> with<span class="env">_R_CHECK_CRAN_INCOMING_REMOTE_</span> false now skips tests thatrequire remote access. The remaining (local) tests typicallyrun quickly compared to the remote tests.</p></li><li> <p><code>R CMD build</code> will now give priority to vignettesproduced from files in the ‘<span class="file">vignettes</span>’ directory over thosein the ‘<span class="file">inst/doc</span>’ directory, with a warning that the latterare being ignored.</p></li><li> <p><code>R CMD config</code> gains a <span class="option">--all</span> option forprinting names and values of all basic configure variables.</p><p>It now knows about all the variables used for the C++98, C++11 andC++14 standards.</p></li><li> <p><code>R CMD check</code> now checks that output files in‘<span class="file">inst/doc</span>’ are newer than the source files in ‘<span class="file">vignettes</span>’.</p></li><li><p> For consistency with other package subdirectories, filesnamed ‘<span class="file">*.r</span>’ in the ‘<span class="file">tests</span>’ directory are now recognizedas tests by <code>R CMD check</code>. (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17143">PR#17143</a>.)</p></li><li> <p><code>R CMD build</code> and <code>R CMD check</code> now use the<em>union</em> of <span class="env">R_LIBS</span> and <code>.libPaths()</code>. They may notbe equivalent, e.g., when the latter is determined by<span class="env">R_PROFILE</span>.</p></li><li> <p><code>R CMD build</code> now preserves dates when it copies filesin preparing the tarball. (Previously on Windows it changed thedates on all files; on Unix, it changed some dates when installingvignettes.)</p></li><li><p> The new option <code>R CMD check --no-stop-on-test-error</code>allows running the remaining tests (under ‘<span class="file">tests/</span>’) even ifone gave an error.</p></li><li><p> Check customization <em>via</em> environment variables todetect side effects of <code>.Call()</code> and <code>.External()</code> callswhich alter their arguments is described in §8 of the ‘RInternals’ manual.</p></li><li> <p><code>R CMD check</code> now checks any <span class="samp">BugReports</span> fieldto be non-empty and a suitable single URL.</p></li><li> <p><code>R CMD check --as-cran</code> now NOTEs if the packagedoes not register its native routines or does not declare itsintentions on (native) symbol search. (This will become a WARNINGin due course.)</p></li></ul><h4>DEPRECATED AND DEFUNCT</h4><ul><li><p> (Windows only) Function <code>setInternet2()</code> is defunct.</p></li><li><p> Installation support for <code>readline</code> emulations based on<code>editline</code> (aka <code>libedit</code>) is deprecated.</p></li><li><p> Use of the C/C++ macro <span class="samp">NO_C_HEADERS</span> is defunct andsilently ignored.</p></li><li> <p><code>unix.time()</code>, a traditional synonym for<code>system.time()</code>, has been deprecated.</p></li><li> <p><code>structure(NULL, ..)</code> is now deprecated as you cannotset attributes on <code>NULL</code>.</p></li><li><p> Header ‘<span class="file">Rconfig.h</span>’ no longer defines<span class="samp">SUPPORT_OPENMP</span>; instead use <span class="samp">_OPENMP</span> (as documentedfor a long time).</p></li><li><p> (C-level Native routine registration.) The deprecated<code>styles</code> member of the <code>R_CMethodDef</code> and<code>R_FortranMethodDef</code> structures has been removed.Packages using these will need to be re-installed for <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.4.0.</p></li><li><p> The deprecated support for PCRE versions older than 8.20will be removed in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.4.1. (Versions 8.20–8.31 will still beaccepted but remain deprecated.)</p></li></ul><h4>BUG FIXES</h4><ul><li><p> Getting or setting <code>body()</code> or <code>formals()</code> onnon-functions for now signals a warning and may become an errorfor setting.</p></li><li> <p><code>match(x, t)</code>, <code>duplicated(x)</code> and<code>unique(x)</code> work as documented for complex numbers with <code>NA</code>sor <code>NaN</code>s, where all those containing <code>NA</code> do match,whereas in the case of <code>NaN</code>'s both real and imaginary partsmust match, compatibly with how <code>print()</code> and <code>format()</code>work for complex numbers.</p></li><li> <p><code>deparse(<complex>, options = "digits17")</code> prints morenicely now, mostly thanks to a suggestion by Richie Cotton.</p></li><li><p> Rotated symbols in plotmath expressions are now positionedcorrectly on <code>x11(type = "Xlib")</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16948">PR#16948</a>)</p></li><li> <p><code>as<-()</code> avoids an infinite loop when a virtual classis interposed between a subclass and an actual superclass.</p></li><li><p> Fix level propagation in <code>unlist()</code> when the listcontains zero-length lists or factors.</p></li><li><p> Fix S3 dispatch on S4 objects when the <span class="pkg">methods</span> package isnot attached.</p></li><li><p> Internal S4 dispatch sets <code>.Generic</code> in the methodframe for consistency with <code>standardGeneric()</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16929">PR#16929</a>)</p></li><li><p> Fix <code>order(x, decreasing = TRUE)</code> when <code>x</code> is aninteger vector containing <code>MAX_INT</code>. Ported from a fix MattDowle made to <a href="https://CRAN.R-project.org/package=data.table"><span class="pkg">data.table</span></a>.</p></li><li><p> Fix caching by <code>callNextMethod()</code>, resolves <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16973">PR#16973</a>and <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16974">PR#16974</a>.</p></li><li> <p><code>grouping()</code> puts NAs last, to be consistent with thedefault behavior of <code>order()</code>.</p></li><li><p> Point mass limit cases: <code>qpois(-2, 0)</code> now gives<code>NaN</code> with a warning and <code>qgeom(1, 1)</code> is <code>0</code>.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16972">PR#16972</a>)</p></li><li> <p><code>table()</code> no longer drops an <code>"NaN"</code> factor level,and better obeys <code>exclude = <chr></code>, thanks to Suharto Anggono'spatch for <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16936">PR#16936</a>. Also, in the case of <code>exclude = NULL</code>and <code>NA</code>s, these are tabulated correctly (again).</p><p>Further, <code>table(1:2, exclude = 1, useNA = "ifany")</code> no longererroneously reports <code><NA></code> counts.</p><p>Additionally, all cases of empty <code>exclude</code> are equivalent,and <code>useNA</code> is not overwritten when specified (as it was by<code>exclude = NULL</code>).</p></li><li> <p><code>wilcox.test(x, conf.int=TRUE)</code> no longer errors out incases where the confidence interval is not available, such as for<code>x = 0:2</code>.</p></li><li> <p><code>droplevels(f)</code> now keeps <NA> levels when present.</p></li><li><p> In integer arithmetic, <code>NULL</code> is now treated as<code>integer(0)</code> whereas it was previously treated as <code>double(0)</code>.</p></li><li><p> The radix sort considers <code>NA_real_</code> and <code>NaN</code> tobe equivalent in rank (like the other sort algorithms).</p></li><li><p> When <code>index.return=TRUE</code> is passed to <code>sort.int()</code>,the radix sort treats <code>NA</code>s like <code>sort.list()</code> does(like the other sort algorithms).</p></li><li><p> When in <code>tabulate(bin, nbin)</code> <code>length(bin)</code> islarger than the maximal integer, the result is now of type<code>double</code> and hence no longer silently overflows to wrongvalues. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17140">PR#17140</a>)</p></li><li> <p><code>as.character.factor()</code> respects S4 inheritance whenchecking the type of its argument. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17141">PR#17141</a>)</p></li><li><p> The <code>factor</code> method for <code>print()</code> no longer setsthe class of the factor to <code>NULL</code>, which would violate abasic constraint of an S4 object.</p></li><li> <p><code>formatC(x, flag = f)</code> allows two new flags, andsignals an error for invalid flags also in the case of characterformatting.</p></li><li><p> Reading from <code>file("stdin")</code> now also closes theconnection and hence no longer leaks memory when reading from afull pipe, thanks to Gábor Csárdi, see thread starting at<a href="https://stat.ethz.ch/pipermail/r-devel/2016-November/073360.html">https://stat.ethz.ch/pipermail/r-devel/2016-November/073360.html</a>.</p></li><li><p> Failure to create file in <code>tempdir()</code> for compressed<code>pdf()</code> graphics device no longer errors (then latersegfaults). There is now a warning instead of error andcompression is turned off for the device. Thanks to AlecWysoker (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17191">PR#17191</a>).</p></li><li><p> Asking for <code>methods()</code> on <code>"|"</code> returns only S3methods. See<a href="https://stat.ethz.ch/pipermail/r-devel/2016-December/073476.html">https://stat.ethz.ch/pipermail/r-devel/2016-December/073476.html</a>.</p></li><li> <p><code>dev.capture()</code> using Quartz Cocoa device (macOS) returnedinvalid components if the back-end chose to use ARGB instead of RGBAimage format. (Reported by Noam Ross.)</p></li><li> <p><code>seq("2", "5")</code> now works too, equivalently to<code>"2":"5"</code> and <code>seq.int()</code>.</p></li><li> <p><code>seq.int(to = 1, by = 1)</code> is now correct, other cases areinteger (instead of <code>double</code>) when <code>seq()</code> is integertoo, and the "non-finite" error messages are consistent between<code>seq.default()</code> and <code>seq.int()</code>, no longer mentioning<code>NaN</code> etc.</p></li><li> <p><code>rep(x, times)</code> and <code>rep.int(x, times)</code> now workwhen <code>times</code> is larger than the largest value representablein an integer vector. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16932">PR#16932</a>)</p></li><li> <p><code>download.file(method = "libcurl")</code> does not check forURL existence before attempting downloads; this is more robust toservers that do not support HEAD or range-based retrieval, but maycreate empty or incomplete files for aborted download requests.</p></li><li><p> Bandwidth selectors <code>bw.ucv()</code>, <code>bw.bcv()</code> and<code>bw.SJ()</code> now avoid integer overflow for large sample sizes.</p></li><li> <p><code>str()</code> no longer shows <code>"list output truncated"</code>,in cases that list was not shown at all. Thanks to Neal Fultz(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17219">PR#17219</a>)</p></li><li><p> Fix for <code>cairo_pdf()</code> (and <code>svg()</code> and<code>cairo_ps()</code>) when replaying a saved display list that containsa mix of <span class="pkg">grid</span> and <span class="pkg">graphics</span> output.(Report by Yihui Xie.)</p></li><li><p> The <code>str()</code> and <code>as.hclust()</code> methods for<code>"dendrogram"</code> now also work for deeply nested dendrogramsthanks to non-recursive implementations by Bradley Broom.</p></li><li> <p><code>sample()</code> now uses two uniforms for added precisionwhen the uniform generator is <code>Knuth-TAOCP</code>,<code>Knuth-TAOCP-2002</code>, or a user-defined generator and thepopulation size is <i>2^25</i> or greater.</p></li><li><p> If a vignette in the ‘<span class="file">vignettes</span>’ directory is listed in‘<span class="file">.Rbuildignore</span>’, <code>R CMD build</code> would not include itin the tarball, but would include it in the vignette database,leading to a check warning. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17246">PR#17246</a>)</p></li><li> <p><code>tools::latexToUtf8()</code> infinite looped on certaininputs. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17138">PR#17138</a>)</p></li><li> <p><code>terms.formula()</code> ignored argument names when determiningwhether two terms were identical. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17235">PR#17235</a>)</p></li><li> <p><code>callNextMethod()</code> was broken when called from a methodthat augments the formal arguments of a primitive generic.</p></li><li><p> Coercion of an S4 object to a vector during sub-assignmentinto a vector failed to dispatch through the <code>as.vector()</code>generic (often leading to a segfault).</p></li><li><p> Fix problems in command completion: Crash (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17222">PR#17222</a>)and junk display in Windows, handling special characters infilenames on all systems.</p></li></ul><h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.3.3</h3><h4>NEW FEATURES</h4><ul><li><p> Changes when redirection of a <span class="samp">http://</span> URL to a<span class="samp">https://</span> URL is encountered:</p><ul><li><p> The internal methods of <code>download.file()</code> and<code>url()</code> now report that they cannot follow this (ratherthan failing silently).</p></li><li><p> (Unix-alike) <code>download.file(method = "auto")</code> (thedefault) re-tries with <code>method = "libcurl"</code>.</p></li><li><p> (Unix-alike) <code>url(method = "default")</code> with anexplicit <code>open</code> argument re-tries with<code>method = "libcurl"</code>. This covers many of the usages,e.g. <code>readLines()</code> with a URL argument.</p></li></ul></li></ul><h4>INSTALLATION on a UNIX-ALIKE</h4><ul><li><p> The <code>configure</code> check for the <code>zlib</code> version isnow robust to versions longer than 5 characters, including<code>1.2.11</code>.</p></li></ul><h4>UTILITIES</h4><ul><li><p> Environmental variable <span class="env">_R_CHECK_TESTS_NLINES_</span> controlshow <code>R CMD check</code> reports failing tests (see §8 of the‘R Internals’ manual).</p></li></ul><h4>DEPRECATED AND DEFUNCT</h4><ul><li><p> (C-level Native routine registration.) The undocumented<code>styles</code> field of the components of <code>R_CMethodDef</code> and<code>R_FortranMethodDef</code> is deprecated.</p></li></ul><h4>BUG FIXES</h4><ul><li> <p><code>vapply(x, *)</code> now works with long vectors <code>x</code>.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17174">PR#17174</a>)</p></li><li> <p><code>isS3method("is.na.data.frame")</code> and similar arecorrect now. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17171">PR#17171</a>)</p></li><li> <p><code>grepRaw(<long>, <short>, fixed = TRUE)</code> now works,thanks to a patch by Mikko Korpela. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17132">PR#17132</a>)</p></li><li><p> Package installation into a library where the package exists<em>via</em> symbolic link now should work wherever<code>Sys.readlink()</code> works, resolving <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16725">PR#16725</a>.</p></li><li> <p><code>"Cincinnati"</code> was missing an <code>"n"</code> in the<code>precip</code> dataset.</p></li><li><p> Fix buffer overflow vulnerability in <code>pdf()</code> whenloading an encoding file. Reported by Talos (TALOS-2016-0227).</p></li><li> <p><code>getDLLRegisteredRoutines()</code> now produces its warningcorrectly when multiple DLLs match, thanks to Matt Dowle's <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17184">PR#17184</a>.</p></li><li> <p><code>Sys.timezone()</code> now returns non-NA also on platformssuch as <span class="samp">Ubuntu 14.04.5 LTS</span>, thanks to Mikko Korpela's<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17186">PR#17186</a>.</p></li><li> <p><code>format(x)</code> for an illegal <code>"POSIXlt"</code> object<code>x</code> no longer segfaults.</p></li><li> <p><code>methods(f)</code> now also works for <code>f</code> <code>"("</code>or <code>"{"</code>.</p></li><li><p> (Windows only) <code>dir.create()</code> did not check the lengthof the path to create, and so could overflow a buffer and crash<span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17206">PR#17206</a>)</p></li><li><p> On some systems, very small hexadecimal numbers in hex notationwould underflow to zero. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17199">PR#17199</a>)</p></li><li> <p><code>pmin()</code> and <code>pmax()</code> now work again for<code>ordered</code> factors and 0-length S3 classed objects, thanks toSuharto Anggono's <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17195">PR#17195</a> and <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17200">PR#17200</a>.</p></li><li> <p><code>bug.report()</code> did not do any validity checking on apackage's <span class="samp">BugReports</span> field. It now ignores an empty field,removes leading whitespace and only attempts to open<span class="samp">http://</span> and <span class="samp">https://</span> URLs, falling back to emailingthe maintainer.</p></li><li><p> Bandwidth selectors <code>bw.ucv()</code> and<code>bw.SJ()</code> gave incorrect answers or incorrectly reported anerror (because of integer overflow) for inputs longer than46341. Similarly for <code>bw.bcv()</code> at length 5793.</p><p>Another possible integer overflow is checked and may result in anerror report (rather than an incorrect result) for much longerinputs (millions for a smooth distribution).</p></li><li> <p><code>findMethod()</code> failed if the active signature hadexpanded beyond what a particular package used. (Example withpackages <a href="https://CRAN.R-project.org/package=XR"><span class="pkg">XR</span></a> and <a href="https://CRAN.R-project.org/package=XRJulia"><span class="pkg">XRJulia</span></a> on <acronym><span class="acronym">CRAN</span></acronym>.)</p></li><li> <p><code>qbeta()</code> underflowed too early in some very asymmetriccases. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17178">PR#17178</a>)</p></li><li> <p><code>R CMD Rd2pdf</code> had problems with packages withnon-ASCII titles in ‘<span class="file">.Rd</span>’ files (usually the titles wereomitted).</p></li></ul><h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.3.2</h3><h4>NEW FEATURES</h4><ul><li> <p><code>extSoftVersion()</code> now reports the version (if any) ofthe <code>readline</code> library in use.</p></li><li><p> The version of LAPACK included in the sources has beenupdated to 3.6.1, a bug-fix release including a speedup for thenon-symmetric case of <code>eigen()</code>.</p></li><li><p> Use <code>options(deparse.max.lines=)</code> to limit the numberof lines recorded in <code>.Traceback</code> and other deparsingactivities.</p></li><li> <p><code>format(<AsIs>)</code> looks more regular, also fornon-character atomic matrices.</p></li><li> <p><code>abbreviate()</code> gains an option <code>named = TRUE</code>.</p></li><li><p> The online documentation for package <span class="pkg">methods</span> isextensively rewritten. The goals are to simplifydocumentation for basic use, to note old features notrecommended and to correct out-of-date information.</p></li><li><p> Calls to <code>setMethod()</code> no longer print a message whencreating a generic function in those cases where that isnatural: S3 generics and primitives.</p></li></ul><h4>INSTALLATION and INCLUDED SOFTWARE</h4><ul><li><p> Versions of the <code>readline</code> library >= 6.3 had beenchanged so that terminal window resizes were not signalled to<code>readline</code>: code has been added using a explicit signalhandler to work around that (when <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> is compiled against readline>= 6.3). (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16604">PR#16604</a>)</p></li><li> <p><code>configure</code> works better with Oracle DeveloperStudio 12.5.</p></li></ul><h4>UTILITIES</h4><ul><li> <p><code>R CMD check</code> reports more dubious flags in files‘<span class="file">src/Makevars[.in]</span>’, including <span class="option">-w</span> and <span class="option">-g</span>.</p></li><li> <p><code>R CMD check</code> has been set up to filter importantwarnings from recent versions of <code>gfortran</code> with<span class="option">-Wall -pedantic</span>: this now reports non-portable GNUextensions such as out-of-order declarations.</p></li><li> <p><code>R CMD config</code> works better with paths containingspaces, even those of home directories (as reported by Ken Beath).</p></li></ul><h4>DEPRECATED AND DEFUNCT</h4><ul><li><p> Use of the C/C++ macro <span class="samp">NO_C_HEADERS</span> is deprecated(no C headers are included by <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> headers from C++ as from <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>3.3.0, so it should no longer be needed).</p></li></ul><h4>BUG FIXES</h4><ul><li><p> The check for non-portable flags in <code>R CMD check</code>could be stymied by ‘<span class="file">src/Makevars</span>’ files which containedtargets.</p></li><li><p> (Windows only) When using certain desktop themes in Windows7 or higher, <kbd>Alt-Tab</kbd> could cause <code>Rterm</code> to stopaccepting input. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14406">PR#14406</a>; patch submitted by Jan Gleixner.)</p></li><li> <p><code>pretty(d, ..)</code> behaves better for date-time <code>d</code>(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16923">PR#16923</a>).</p></li><li><p> When an S4 class name matches multiple classes in the S4cache, perform a dynamic search in order to obey namespaceimports. This should eliminate annoying messages about multiplehits in the class cache. Also, pass along the package from the<code>ClassExtends</code> object when looking up superclasses in thecache.</p></li><li> <p><code>sample(NA_real_)</code> now works.</p></li><li><p> Packages using non-ASCII encodings in their code did notinstall data properly on systems using different encodings.</p></li><li> <p><code>merge(df1, df2)</code> now also works for data frames withcolumn names <code>"na.last"</code>, <code>"decreasing"</code>, or<code>"method"</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17119">PR#17119</a>)</p></li><li> <p><code>contour()</code> caused a segfault if the <code>labels</code>argument had length zero. (Reported by Bill Dunlap.)</p></li><li> <p><code>unique(warnings())</code> works more correctly, thanks to anew <code>duplicated.warnings()</code> method.</p></li><li> <p><code>findInterval(x, vec = numeric(), all.inside = TRUE)</code>now returns <code>0</code>s as documented. (Reported by Bill Dunlap.)</p></li><li><p> (Windows only) <code>R CMD SHLIB</code> failed when a symbolin the resulting library had the same name as a keyword inthe ‘<span class="file">.def</span>’ file. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17130">PR#17130</a>)</p></li><li> <p><code>pmax()</code> and <code>pmin()</code> now work with (more ?)classed objects, such as <code>"Matrix"</code> from the <a href="https://CRAN.R-project.org/package=Matrix"><span class="pkg">Matrix</span></a>package, as documented for a long time.</p></li><li> <p><code>axis(side, x = D)</code> and hence <code>Axis()</code> and<code>plot()</code> now work correctly for <code>"Date"</code> and timeobjects <code>D</code>, even when “time goes backward”, e.g.,with decreasing <code>xlim</code>. (Reported by William May.)</p></li><li> <p><code>str(I(matrix(..)))</code> now looks as always intended.</p></li><li> <p><code>plot.ts()</code>, the <code>plot()</code> method for time series,now respects <code>cex</code>, <code>lwd</code> and <code>lty</code>. (Reported byGreg Werbin.)</p></li><li> <p><code>parallel::mccollect()</code> now returns a named list (asdocumented) when called with <code>wait = FALSE</code>. (Reported byMichel Lang.)</p></li><li><p> If a package added a class to a class union in anotherpackage, loading the first package gave erroneous warningsabout “undefined subclass”.</p></li><li> <p><code>c()</code>'s argument <code>use.names</code> is documented now, asbelonging to the (C internal) default method. In“parallel”, argument <code>recursive</code> is also moved fromthe generic to the default method, such that the formal argument listof <span class="pkg">base</span> generic <code>c()</code> is just <code>(...)</code>.</p></li><li> <p><code>rbeta(4, NA)</code> and similarly <code>rgamma()</code> and<code>rnbinom()</code> now return <code>NaN</code>'s with a warning, as otherr<dist>(), and as documented. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17155">PR#17155</a>)</p></li><li><p> Using <code>options(checkPackageLicense = TRUE)</code> no longerrequires acceptance of the licence for non-default standardpackages such as <span class="pkg">compiler</span>. (Reported by Mikko Korpela.)</p></li><li> <p><code>split(<very_long>, *)</code> now works even when the splitoff parts are long. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17139">PR#17139</a>)</p></li><li> <p><code>min()</code> and <code>max()</code> now also work correctly whenthe argument list starts with <code>character(0)</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17160">PR#17160</a>)</p></li><li><p> Subsetting very large matrices (<code>prod(dim(.)) >= 2^31</code>)now works thanks to Michael Schubmehl's <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17158">PR#17158</a>.</p></li><li> <p><code>bartlett.test()</code> used residual sums of squaresinstead of variances, when the argument was a list of <code>lm</code> objects.(Reported by Jens Ledet Jensen).</p></li><li> <p><code>plot(<lm>, which = *)</code> now correctly labels thecontour lines for the standardized residuals for <code>which = 6</code>.It also takes the correct <i>p</i> in case of singularities (alsofor <code>which = 5</code>). (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17161">PR#17161</a>)</p></li><li> <p><code>xtabs(~ exclude)</code> no longer fails from wrong scope,thanks to Suharto Anggono's <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=17147">PR#17147</a>.</p></li><li><p> Reference class calls to <code>methods()</code> did notre-analyse previously defined methods, meaning that calls tomethods defined later would fail. (Reported by Charles Tilford).</p></li><li> <p><code>findInterval(x, vec, left.open = TRUE)</code> misbehaved in somecases. (Reported by Dmitriy Chernykh.)</p></li></ul><h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.3.1</h3><h4>BUG FIXES</h4><ul><li> <p><code>R CMD INSTALL</code> and hence <code>install.packages()</code>gave an internal error installing a package called<span class="pkg">description</span> from a tarball on a case-insensitive file system.</p></li><li> <p><code>match(x, t)</code> (and hence <code>x %in% t</code>) failedwhen <code>x</code> was of length one, and either <code>character</code> and <code>x</code>and <code>t</code> only differed in their <code>Encoding</code> or when<code>x</code> and <code>t</code> where <code>complex</code> with <code>NA</code>s or <code>NaN</code>s.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16885">PR#16885</a>.)</p></li><li> <p><code>unloadNamespace(ns)</code> also works again when <code>ns</code> is a‘namespace’, as from <code>getNamespace()</code>.</p></li><li> <p><code>rgamma(1, Inf)</code> or <code>rgamma(1, 0, 0)</code> no longer give<code>NaN</code> but the correct limit.</p></li><li> <p><code>length(baseenv())</code> is correct now.</p></li><li> <p><code>pretty(d, ..)</code> for date-time <code>d</code> rarely failedwhen <code>"halfmonth"</code> time steps were tried (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16923">PR#16923</a>) andon ‘inaccurate’ platforms such as 32-bit Windows ora configuration with <code>--disable-long-double</code>; see comment#15 of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16761">PR#16761</a>.</p></li><li><p> In <code>text.default(x, y, labels)</code>, the rarely(?) useddefault for <code>labels</code> is now correct also for the case of a2-column matrix <code>x</code> and missing <code>y</code>.</p></li><li> <p><code>as.factor(c(a = 1L))</code> preserves <code>names()</code> againas in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> < 3.1.0.</p></li><li> <p><code>strtrim(""[0], 0[0])</code> now works.</p></li><li><p> Use of <code>Ctrl-C</code> to terminate a reverse incrementalsearch started by <code>Ctrl-R</code> in the <code>readline</code>-based Unixterminal interface is now supported when <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> was compiled against<code>readline</code> >= 6.0 (<code>Ctrl-G</code> always worked).(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16603">PR#16603</a>)</p></li><li> <p><code>diff(<difftime>)</code> now keeps the <code>"units"</code>attribute, as subtraction already did, <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16940">PR#16940</a>.</p></li></ul><h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.3.0</h3><h4>SIGNIFICANT USER-VISIBLE CHANGES</h4><ul><li> <p><code>nchar(x, *)</code>'s argument <code>keepNA</code> governing howthe result for <code>NA</code>s in <code>x</code> is determined, gets a newdefault <code>keepNA = NA</code> which returns <code>NA</code> where<code>x</code> is <code>NA</code>, except for <code>type = "width"</code> which stillreturns <code>2</code>, the formatting / printing width of <code>NA</code>.</p></li><li><p> All builds have support for <span class="samp">https:</span> URLs in thedefault methods for <code>download.file()</code>, <code>url()</code> and codemaking use of them.</p><p>Unfortunately that cannot guarantee that any particular<span class="samp">https:</span> URL can be accessed. For example, server and clienthave to successfully negotiate a cryptographic protocol (TLS/SSL,...) and the server's identity has to be verifiable <em>via</em>the available certificates. Different access methods may allowdifferent protocols or use private certificate bundles: weencountered a <span class="samp">https:</span> CRAN mirror which could be accessed byone browser but not by another nor by <code>download.file()</code> onthe same Linux machine.</p></li></ul><h4>NEW FEATURES</h4><ul><li><p> The <code>print</code> method for <code>methods()</code> gains a<code>byclass</code> argument.</p></li><li><p> New functions <code>validEnc()</code> and <code>validUTF8()</code> togive access to the validity checks for inputs used by<code>grep()</code> and friends.</p></li><li><p> Experimental new functionality for S3 method checking, notably<code>isS3method()</code>.</p><p>Also, the names of the <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> ‘language elements’ are exportedas character vector <code>tools::langElts</code>.</p></li><li> <p><code>str(x)</code> now displays <code>"Time-Series"</code> also formatrix (multivariate) time-series, i.e. when <code>is.ts(x)</code> is true.</p></li><li><p> (Windows only) The GUI menu item to install local packagesnow accepts ‘<span class="file">*.tar.gz</span>’ files as well as ‘<span class="file">*.zip</span>’ files(but defaults to the latter).</p></li><li><p> New programmeR's utility function <code>chkDots()</code>.</p></li><li> <p><code>D()</code> now signals an error when given invalid input,rather than silently returning <code>NA</code>. (Request of John Nash.)</p></li><li> <p><code>formula</code> objects are slightly more “first class”:e.g., <code>formula()</code> or <code>new("formula", y ~ x)</code> are nowvalid. Similarly, for <code>"table"</code>, <code>"ordered"</code> and<code>"summary.table"</code>. Packages defining S4 classes with the aboveS3/S4 classes as slots should be reinstalled.</p></li><li><p> New function <code>strrep()</code> for repeating the elements of acharacter vector.</p></li><li> <p><code>rapply()</code> preserves attributes on the list when<code>how = "replace"</code>.</p></li><li><p> New S3 generic function <code>sigma()</code> with methods forextracting the estimated standard deviation aka “residualstandard deviation” from a fitted model.</p></li><li> <p><code>news()</code> now displays <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> and package news files withinthe HTML help system if it is available. If no news file is found,a visible <code>NULL</code> is returned to the console.</p></li><li> <p><code>as.raster(x)</code> now also accepts <code>raw</code> arrays<code>x</code> assuming values in <code>0:255</code>.</p></li><li><p> Subscripting of matrix/array objects of type<code>"expression"</code> is now supported.</p></li><li> <p><code>type.convert("i")</code> now returns a factor instead of acomplex value with zero real part and missing imaginary part.</p></li><li><p> Graphics devices <code>cairo_pdf()</code> and <code>cairo_ps()</code>now allow non-default values of the cairographics ‘fallbackresolution’ to be set.</p><p>This now defaults to 300 on all platforms: that is the defaultdocumented by cairographics, but apparently was not used by allsystem installations.</p></li><li> <p><code>file()</code> gains an explicit <code>method</code> argumentrather than implicitly using<code>getOption("url.method", "default")</code>.</p></li><li><p> Thanks to a patch from Tomas Kalibera, <code>x[x != 0]</code> isnow typically faster than <code>x[which(x != 0)]</code> (in the casewhere <code>x</code> has no NAs, the two are equivalent).</p></li><li> <p><code>read.table()</code> now always uses the names for a named<code>colClasses</code> argument (previously names were only used when<code>colClasses</code> was too short). (In part, wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16478">PR#16478</a>.)</p></li><li><p> (Windows only) <code>download.file()</code> with default<code>method = "auto"</code> and a <span class="samp">ftps://</span> URL chooses<code>"libcurl"</code> if that is available.</p></li><li><p> The out-of-the box Bioconductor mirror has been changed toone using <span class="samp">https://</span>: use <code>chooseBioCmirror()</code> to choosea <span class="samp">http://</span> mirror if required.</p></li><li><p> The data frame and formula methods for <code>aggregate()</code>gain a <code>drop</code> argument.</p></li><li> <p><code>available.packages()</code> gains a <code>repos</code> argument.</p></li><li><p> The undocumented switching of methods for <code>url()</code> on<span class="samp">https:</span> and <span class="samp">ftps:</span> URLs is confined to<code>method = "default"</code> (and documented).</p></li><li> <p><code>smoothScatter()</code> gains a <code>ret.selection</code> argument.</p></li><li> <p><code>qr()</code> no longer has a <code>...</code> argument to passadditional arguments to methods.</p></li><li> <p><code>[</code> has a method for class <code>"table"</code>.</p></li><li><p> It is now possible (again) to <code>replayPlot()</code> adisplay list snapshot that was created by <code>recordPlot()</code>in a different <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> session.</p><p>It is still not a good idea to use snapshots as a persistentstorage format for <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> plots, but it is now not completely silly touse a snapshot as a format for transferring an R plot between twoR sessions.</p><p>The underlying changes mean that packages providing graphicsdevices (e.g., <a href="https://CRAN.R-project.org/package=Cairo"><span class="pkg">Cairo</span></a>, <a href="https://CRAN.R-project.org/package=RSvgDevice"><span class="pkg">RSvgDevice</span></a>,<a href="https://CRAN.R-project.org/package=cairoDevice"><span class="pkg">cairoDevice</span></a>, <a href="https://CRAN.R-project.org/package=tikzDevice"><span class="pkg">tikzDevice</span></a>) will need to bereinstalled.</p><p>Code for restoring snapshots was contributed by Jeroen Oomsand JJ Allaire.</p><p>Some testing code is available at<a href="https://github.com/pmur002/R-display-list">https://github.com/pmur002/R-display-list</a>.</p></li><li> <p><code>tools::undoc(dir = D)</code> and <code>codoc(dir = D)</code> nowalso work when <code>D</code> is a directory whose <code>normalizePath()</code>edversion does not end in the package name, e.g. from a symlink.</p></li><li> <p><code>abbreviate()</code> has more support for multi-bytecharacter sets – it no longer removes bytes within characters andknows about Latin vowels with accents. It is still onlyreally suitable for (most) European languages, and still warns onnon-ASCII input.</p><p><code>abbreviate(use.classes = FALSE)</code> is now implemented, andthat is more suitable for non-European languages.</p></li><li> <p><code>match(x, table)</code> is faster (sometimes by an order ofmagnitude) when <code>x</code> is of length one and <code>incomparables</code>is unchanged, thanks to Peter Haverty (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16491">PR#16491</a>).</p></li><li><p> More consistent, partly not back-compatible behavior of<code>NA</code> and <code>NaN</code> coercion to complex numbers, operationsless often resulting in complex <code>NA</code> (<code>NA_complex_</code>).</p></li><li> <p><code>lengths()</code> considers methods for <code>length</code> and<code>[[</code> on <code>x</code>, so it should work automatically on anyobjects for which appropriate methods on those generics aredefined.</p></li><li><p> The logic for selecting the default screen device on OS Xhas been simplified: it is now <code>quartz()</code> if that isavailable even if environment variable <span class="env">DISPLAY</span> has been setby the user.</p><p>The choice can easily be overridden <em>via</em> environmentvariable <span class="env">R_INTERACTIVE_DEVICE</span>.</p></li><li><p> On Unix-like platforms which support the <code>getline</code> Clibrary function, <code>system(*, intern = TRUE)</code> no longertruncates (output) lines longer than 8192 characters, thanks toKarl Millar. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16544">PR#16544</a>)</p></li><li> <p><code>rank()</code> gains a <code>ties.method = "last"</code> option,for convenience (and symmetry).</p></li><li> <p><code>regmatches(invert = NA)</code> can now be used to extractboth non-matched and matched substrings.</p></li><li> <p><code>data.frame()</code> gains argument <code>fix.empty.names</code>;<code>as.data.frame.list()</code> gets new <code>cut.names</code>,<code>col.names</code> and <code>fix.empty.names</code>.</p></li><li> <p><code>plot(x ~ x, *)</code> now warns that it is the same as<code>plot(x ~ 1, *)</code>.</p></li><li> <p><code>recordPlot()</code> has new arguments <code>load</code> and<code>attach</code> to allow package names to be stored as part of arecorded plot. <code>replayPlot()</code> has new argument<code>reloadPkgs</code> to load/attach any package names that werestored as part of a recorded plot.</p></li><li><p> S4 dispatch works within calls to <code>.Internal()</code>. Thismeans explicit S4 generics are no longer needed for<code>unlist()</code> and <code>as.vector()</code>.</p></li><li><p> Only font family names starting with <span class="samp">"Hershey"</span> (andnot <span class="samp">"Her"</span> as before) are given special treatment by thegraphics engine.</p></li><li><p> S4 values are automatically coerced to vector (<em>via</em><code>as.vector</code>) when subassigned into atomic vectors.</p></li><li> <p><code>findInterval()</code> gets a <code>left.open</code> option.</p></li><li><p> The version of LAPACK included in the sources has beenupdated to 3.6.0, including those ‘deprecated’ routineswhich were previously included. <em>Ca</em> 40 double-complexroutines have been added at the request of a package maintainer.</p><p>As before, the details of what is included are in‘<span class="file">src/modules/lapack/README</span>’ and this now gives information onearlier additions.</p></li><li> <p><code>tapply()</code> has been made considerably more efficientwithout changing functionality, thanks to proposals from PeterHaverty and Suharto Anggono. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16640">PR#16640</a>)</p></li><li> <p><code>match.arg(arg)</code> (the one-argument case) is faster; sois <code>sort.int()</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16640">PR#16640</a>)</p></li><li><p> The <code>format</code> method for <code>object_size</code> objects nowalso accepts “binary” units such as <code>"KiB"</code> and e.g.,<code>"Tb"</code>. (Partly from <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16649">PR#16649</a>.)</p></li><li><p> Profiling now records calls of the form <code>foo::bar</code> andsome similar cases directly rather than as calls to<code><Anonymous></code>. Contributed by Winston Chang.</p></li><li><p> New string utilities <code>startsWith(x, prefix)</code> and<code>endsWith(x, suffix)</code>. Also provide speedups for some<code>grepl("^...", *)</code> uses (related to proposals in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16490">PR#16490</a>).</p></li><li><p> Reference class finalizers run at exit, as well as ongarbage collection.</p></li><li><p> Avoid <span class="pkg">parallel</span> dependency on <span class="pkg">stats</span> for portchoice and random number seeds. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16668">PR#16668</a>)</p></li><li><p> The radix sort algorithm and implementation from<a href="https://CRAN.R-project.org/package=data.table"><span class="pkg">data.table</span></a> (<code>forder</code>) replaces the previous radix(counting) sort and adds a new method for <code>order()</code>.Contributed by Matt Dowle and Arun Srinivasan, the new algorithmsupports logical, integer (even with large values), real, andcharacter vectors. It outperforms all other methods, but thereare some caveats (see <code>?sort</code>).</p></li><li><p> The <code>order()</code> function gains a <code>method</code> argumentfor choosing between <code>"shell"</code> and <code>"radix"</code>.</p></li><li><p> New function <code>grouping()</code> returns a permutation thatstably rearranges data so that identical values are adjacent. Thereturn value includes extra partitioning information on thegroups. The implementation came included with the new radix sort.</p></li><li> <p><code>rhyper(nn, m, n, k)</code> no longer returns <code>NA</code> whenone of the three parameters exceeds the maximal integer.</p></li><li> <p><code>switch()</code> now warns when no alternatives are provided.</p></li><li> <p><code>parallel::detectCores()</code> now has default <code>logical= TRUE</code> on all platforms – as this was the default on Windows,this change only affects Sparc Solaris.</p><p>Option <code>logical = FALSE</code> is now supported on Linux and recentversions of OS X (for the latter, thanks to a suggestion of KyawSint).</p></li><li> <p><code>hist()</code> for <code>"Date"</code> or <code>"POSIXt"</code> objectswould sometimes give misleading labels on the breaks, as theywere set to the day before the start of the period beingdisplayed. The display format has been changed, and the shift of thestart day has been made conditional on <code>right = TRUE</code> (thedefault). (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16679">PR#16679</a>)</p></li><li> <p><span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> now uses a new version of the logo (donated to the RFoundation by RStudio). It is defined in ‘<span class="file">.svg</span>’ format, sowill resize without unnecessary degradation when displayed onHTML pages—there is also a vector PDF version. Thanks toDirk Eddelbuettel for producing the corresponding X11 icon.</p></li><li><p> New function <code>.traceback()</code> returns the stack tracewhich <code>traceback()</code> prints.</p></li><li> <p><code>lengths()</code> dispatches internally.</p></li><li> <p><code>dotchart()</code> gains a <code>pt.cex</code> argument to controlthe size of points separately from the size of plot labels.Thanks to Michael Friendly and Milan Bouchet-Valat for ideasand patches.</p></li><li> <p><code>as.roman(ch)</code> now correctly deals with more diversecharacter vectors <code>ch</code>; also arithmetic with the resultingroman numbers works in more cases. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16779">PR#16779</a>)</p></li><li> <p><code>prcomp()</code> gains a new option <code>rank.</code> allowing todirectly aim for less than <code>min(n,p)</code> PC's. The<code>summary()</code> and its <code>print()</code> method have been amended,notably for this case.</p></li><li> <p><code>gzcon()</code> gains a new option <code>text</code>, which marksthe connection as text-oriented (so e.g. <code>pushBack()</code>works). It is still always opened in binary mode.</p></li><li><p> The <code>import()</code> namespace directive now accepts anargument <code>except</code> which names symbols to exclude from theimports. The <code>except</code> expression should evaluate to acharacter vector (after substituting symbols for strings). SeeWriting R Extensions.</p></li><li><p> New convenience function <code>Rcmd()</code> in package<span class="pkg">tools</span> for invoking <code>R CMD</code> tools from within <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>.</p></li><li><p> New functions <code>makevars_user()</code> and<code>makevars_site()</code> in package <span class="pkg">tools</span> to determine thelocation of the user and site specific ‘<span class="file">Makevars</span>’ files forcustomizing package compilation.</p></li></ul><h4>UTILITIES</h4><ul><li> <p><code>R CMD check</code> has a new option<span class="option">--ignore-vignettes</span> for use with non-Sweave vignetteswhose <span class="samp">VignetteBuilder</span> package is not available.</p></li><li> <p><code>R CMD check</code> now by default checks code usage(<em>via</em> <a href="https://CRAN.R-project.org/package=codetools"><span class="pkg">codetools</span></a>) with only the base packageattached. Functions from default packages other than <span class="pkg">base</span>which are used in the package code but not imported are reportedas undefined globals, with a suggested addition to the<code>NAMESPACE</code> file.</p></li><li> <p><code>R CMD check --as-cran</code> now also checks DOIs inpackage ‘<span class="file">CITATION</span>’ and Rd files.</p></li><li> <p><code>R CMD Rdconv</code> and <code>R CMD Rd2pdf</code> each havea new option <span class="option">--RdMacros=pkglist</span> which allows Rd macrosto be specified before processing.</p></li></ul><h4>DEPRECATED AND DEFUNCT</h4><ul><li><p> The previously included versions of <code>zlib</code>,<code>bzip2</code>, <code>xz</code> and PCRE have been removed, so suitableexternal (usually system) versions are required (see the‘R Installation and Administration’ manual).</p></li><li><p> The unexported and undocumented Windows-only devices<code>cairo_bmp()</code>, <code>cairo_png()</code> and <code>cairo_tiff()</code>have been removed. (These devices should be used ase.g. <code>bmp(type = "cairo")</code>.)</p></li><li><p> (Windows only) Function <code>setInternet2()</code> has no effectand will be removed in due course. The choice between methods<code>"internal"</code> and <code>"wininet"</code> is now made by the<code>method</code> arguments of <code>url()</code> and <code>download.file()</code>and their defaults can be set <em>via</em> options. Theout-of-the-box default remains <code>"wininet"</code> (as it has beensince <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.2.2).</p></li><li> <p><code>[<-</code> with an S4 value into a list currently embeds theS4 object into its own list such that the end result is roughlyequivalent to using <code>[[<-</code>. That behavior is deprecated. Inthe future, the S4 value will be coerced to a list with<code>as.list()</code>.</p></li><li><p> Package <span class="pkg">tools</span>' functions<code>package.dependencies()</code>, <code>pkgDepends()</code>, etc aredeprecated now, mostly in favor of <code>package_dependencies()</code>which is both more flexible and efficient.</p></li></ul><h4>INSTALLATION and INCLUDED SOFTWARE</h4><ul><li><p> Support for very old versions of <code>valgrind</code>(e.g., 3.3.0) has been removed.</p></li><li><p> The included <code>libtool</code> script (generated by<code>configure</code>) has been updated to version 2.4.6 (from 2.2.6a).</p></li><li> <p><code>libcurl</code> version 7.28.0 or later with support for the<code>https</code> protocol is required for installation (except onWindows).</p></li><li><p> BSD networking is now required (except on Windows) and so<code>capabilities("http/ftp")</code> is always true.</p></li><li> <p><code>configure</code> uses <code>pkg-config</code> for PNG, TIFFand JPEG where this is available. This should work better withmultiple installs and with those using static libraries.</p></li><li><p> The minimum supported version of OS X is 10.6 (‘SnowLeopard’): even that has been unsupported by Apple since 2012.</p></li><li><p> The <code>configure</code> default on OS X is<span class="option">--disable-R-framework</span>: enable this if you intend toinstall under ‘<span class="file">/Library/Frameworks</span>’ and use with <code>R.app</code>.</p></li><li><p> The minimum preferred version of PCRE has since <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.0.0been 8.32 (released in Nov 2012). Versions 8.10 to 8.31 are nowdeprecated (with warnings from <code>configure</code>), but willstill be accepted until <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.4.0.</p></li><li> <p><code>configure</code> looks for C functions <code>__cospi</code>,<code>__sinpi</code> and <code>__tanpi</code> and uses these if <code>cospi</code><em>etc</em> are not found. (OS X is the main instance.)</p></li><li><p> (Windows) R is now built using <code>gcc</code>4.9.3. This build will require recompilation of at least those packagesthat include C++ code, and possibly others. A build of R-devel usingthe older toolchain will be temporarily available for comparisonpurposes.</p><p>During the transition, the environment variable<span class="env">R_COMPILED_BY</span> has been defined to indicate which toolchainwas used to compile R (and hence, which should be used to compilecode in packages). The <code>COMPILED_BY</code> variable described belowwill be a permanent replacement for this.</p></li><li><p> (Windows) A <code>make</code> and <code>R CMD config</code> variablenamed <code>COMPILED_BY</code> has been added. This indicateswhich toolchain was used to compile R (and hence, which should beused to compile code in packages).</p></li></ul><h4>PACKAGE INSTALLATION</h4><ul><li><p> The <code>make</code> macro <code>AWK</code> which used to be madeavailable to files such as ‘<span class="file">src/Makefile</span>’ is no longer set.</p></li></ul><h4>C-LEVEL FACILITIES</h4><ul><li><p> The API call <code>logspace_sum</code> introduced in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.2.0 isnow remapped as an entry point to <code>Rf_logspace_sum</code>, and itsfirst argument has gained a <code>const</code> qualifier. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16470">PR#16470</a>)</p><p>Code using it will need to be reinstalled.</p><p>Similarly, entry point <code>log1pexp</code> also defined in‘<span class="file">Rmath.h</span>’ is remapped there to <code>Rf_log1pexp</code></p></li><li> <p><code>R_GE_version</code> has been increased to <code>11</code>.</p></li><li><p> New API call <code>R_orderVector1</code>, a fasterone-argument version of <code>R_orderVector</code>.</p></li><li><p> When <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> headers such as ‘<span class="file">R.h</span>’ and ‘<span class="file">Rmath.h</span>’ arecalled from C++ code in packages they include the C++ versions ofsystem headers such as ‘<span class="file"><cmath></span>’ rather than the legacyheaders such as ‘<span class="file"><math.h></span>’. (Headers ‘<span class="file">Rinternals.h</span>’ and‘<span class="file">Rinterface.h</span>’ already did, and inclusion of system headerscan still be circumvented by defining <code>NO_C_HEADERS</code>,including as from this version for those two headers.)</p><p>The manual has long said that <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> headers should <b>not</b> beincluded within an <code>extern "C"</code> block, and almost all thepackages affected by this change were doing so.</p></li><li><p> Including header ‘<span class="file">S.h</span>’ from C++ code would fail on someplatforms, and so gives a compilation error on all.</p></li><li><p> The deprecated header ‘<span class="file">Rdefines.h</span>’ is now compatiblewith defining <code>R_NO_REMAP</code>.</p></li><li><p> The connections interface now includes a function<code>R_GetConnection()</code> which allows packages implementingconnections to convert R <code>connection</code> objects to<code>Rconnection</code> handles. Code which previouslyused the low-level R-internal <code>getConnection()</code> entry pointshould switch.</p></li></ul><h4>BUG FIXES</h4><ul><li><p> C-level <code>asChar(x)</code> is fixed for when <code>x</code> is not avector, and it returns <code>"TRUE"</code>/<code>"FALSE"</code> instead of<code>"T"</code>/<code>"F"</code> for logical vectors.</p></li><li><p> The first arguments of <code>.colSums()</code> etc (with aninitial dot) are now named <code>x</code> rather than <code>X</code> (matching<code>colSums()</code>): thus error messages are corrected.</p></li><li><p> A <code>coef()</code> method for class <code>"maov"</code> has beenadded to allow <code>vcov()</code> to work with multivariateresults. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16380">PR#16380</a>)</p></li><li> <p><code>method = "libcurl"</code> connections signal errors ratherthan retrieving HTTP error pages (where the ISP reports theerror).</p></li><li> <p><code>xpdrows.data.frame()</code> was not checking for uniquerow names; in particular, this affected assignment to non-existingrows <em>via</em> numerical indexing. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16570">PR#16570</a>)</p></li><li> <p><code>tail.matrix()</code> did not work for zero rows matrices,and could produce row “labels” such as <code>"[1e+05,]"</code>.</p></li><li><p> Data frames with a column named <code>"stringsAsFactors"</code>now format and print correctly. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16580">PR#16580</a>)</p></li><li> <p><code>cor()</code> is now guaranteed to return a value withabsolute value less than or equal to 1. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16638">PR#16638</a>)</p></li><li><p> Array subsetting now keeps <code>names(dim(.))</code>.</p></li><li><p> Blocking socket connection selection recovers moregracefully on signal interrupts.</p></li><li><p> The <code>data.frame</code> method of <code>rbind()</code> construction<code>row.names</code> works better in borderline integer cases, butmay change the names assigned. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16666">PR#16666</a>)</p></li><li><p> (X11 only) <code>getGraphicsEvent()</code> miscoded buttons andmissed mouse motion events. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16700">PR#16700</a>)</p></li><li> <p><code>methods(round)</code> now also lists <code>round.POSIXt</code>.</p></li><li> <p><code>tar()</code> now works with the default <code>files = NULL</code>.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16716">PR#16716</a>)</p></li><li><p> Jumps to outer contexts, for example in error recovery, nowmake intermediate jumps to contexts where <code>on.exit()</code> actionsare established instead of trying to run all <code>on.exit()</code>actions before jumping to the final target. This unwinds the stackgradually, releases resources held on the stack, and significantlyreduces the chance of a segfault when running out of C stackspace. Error handlers established using<code>withCallingHandlers()</code> and <code>options("error")</code>specifications are ignored when handling a C stack overflow erroras attempting one of these would trigger a cascade of C stackoverflow errors. (These changes resolve <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16753">PR#16753</a>.)</p></li><li><p> The spacing could be wrong when printing a complex array.(Report and patch by Lukas Stadler.)</p></li><li> <p><code>pretty(d, n, min.n, *)</code> for date-time objects <code>d</code>works again in border cases with large <code>min.n</code>, returns a<code>labels</code> attribute also for small-range dates and in such casesits returned length is closer to the desired <code>n</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16761">PR#16761</a>)Additionally, it finally does cover the range of <code>d</code>, as italways claimed.</p></li><li> <p><code>tsp(x) <- NULL</code> did not handle correctly objectsinheriting from both <code>"ts"</code> and <code>"mts"</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16769">PR#16769</a>)</p></li><li> <p><code>install.packages()</code> could give false errors when<code>options("pkgType")</code> was <code>"binary"</code>. (Reported byJose Claudio Faria.)</p></li><li><p> A bug fix in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.0.2 fixed problems with <code>locator()</code>in X11, but introduced problems in Windows. Now both should befixed. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15700">PR#15700</a>)</p></li><li> <p><code>download.file()</code> with <code>method = "wininet"</code>incorrectly warned of download file length difference whenreported length was unknown. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16805">PR#16805</a>)</p></li><li> <p><code>diag(NULL, 1)</code> crashed because of missed typechecking. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16853">PR#16853</a>)</p></li></ul><h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.2.5</h3><h4>BUG FIXES</h4><ul><li> <p><code>format.POSIXlt()</code> behaved incorrectly in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.2.4.E.g. the output of<code>format(as.POSIXlt(paste0(1940:2000, "-01-01"), tz = "CET"),usetz = TRUE)</code> ended in two <code>"CEST"</code> time formats.</p></li></ul><h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.2.4</h3><h4>NEW FEATURES</h4><ul><li> <p><code>install.packages()</code> and related functions now give amore informative warning when an attempt is made to install a basepackage.</p></li><li> <p><code>summary(x)</code> now prints with less rounding when<code>x</code> contains infinite values. (Request of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16620">PR#16620</a>.)</p></li><li> <p><code>provideDimnames()</code> gets an optional <code>unique</code> argument.</p></li><li> <p><code>shQuote()</code> gains <code>type = "cmd2"</code> for quotingin <code>cmd.exe</code> in Windows. (Response to <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16636">PR#16636</a>.)</p></li><li><p> The <code>data.frame</code> method of <code>rbind()</code> gains anoptional argument <code>stringsAsFactors</code> (instead of onlydepending on <code>getOption("stringsAsFactors")</code>).</p></li><li> <p><code>smooth(x, *)</code> now also works for long vectors.</p></li><li> <p><code>tools::texi2dvi()</code> has a workaround for problems withthe <code>texi2dvi</code> script supplied by <span class="pkg">texinfo 6.1</span>.</p><p>It extracts more error messages from the LaTeX logs when inemulation mode.</p></li></ul><h4>UTILITIES</h4><ul><li> <p><code>R CMD check</code> will leave a log file‘<span class="file">build_vignettes.log</span>’ from the re-building of vignettes inthe ‘<span class="file">.Rcheck</span>’ directory if there is a problem, and always ifenvironment variable <span class="env">_R_CHECK_ALWAYS_LOG_VIGNETTE_OUTPUT_</span> isset to a true value.</p></li></ul><h4>DEPRECATED AND DEFUNCT</h4><ul><li><p> Use of <span class="samp">SUPPORT_OPENMP</span> from header ‘<span class="file">Rconfig.h</span>’ isdeprecated in favour of the standard OpenMP define <span class="samp">_OPENMP</span>.</p><p>(This has been the recommendation in the manual for a while now.)</p></li><li><p> The <code>make</code> macro <code>AWK</code> which is long unused by<span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> itself but recorded in file ‘<span class="file">etc/Makeconf</span>’ is deprecatedand will be removed in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.3.0.</p></li><li><p> The C header file ‘<span class="file">S.h</span>’ is no longer documented: itsuse should be replaced by ‘<span class="file">R.h</span>’.</p></li></ul><h4>BUG FIXES</h4><ul><li> <p><code>kmeans(x, centers = <1-row>)</code> now works. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16623">PR#16623</a>)</p></li><li> <p><code>Vectorize()</code> now checks for clashes in argument names.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16577">PR#16577</a>)</p></li><li> <p><code>file.copy(overwrite = FALSE)</code> would signal a successfulcopy when none had taken place. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16576">PR#16576</a>)</p></li><li> <p><code>ngettext()</code> now uses the same default domain as<code>gettext()</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14605">PR#14605</a>)</p></li><li> <p><code>array(.., dimnames = *)</code> now warns aboutnon-<code>list</code> dimnames and, from <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.3.0, will signal the sameerror for invalid dimnames as <code>matrix()</code> has always done.</p></li><li> <p><code>addmargins()</code> now adds dimnames for the extendedmargins in all cases, as always documented.</p></li><li> <p><code>heatmap()</code> evaluated its <code>add.expr</code> argumentin the wrong environment. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16583">PR#16583</a>)</p></li><li> <p><code>require()</code> etc now give the correct entry of<code>lib.loc</code> in the warning about an old version of a packagemasking a newer required one.</p></li><li><p> The internal deparser did not add parentheses whennecessary, e.g. before <code>[]</code> or <code>[[]]</code>. (Reported byLukas Stadler; additional fixes included as well).</p></li><li> <p><code>as.data.frame.vector(*, row.names=*)</code> no longerproduces ‘corrupted’ data frames from row names of incorrectlength, but rather warns about them. This will become an error.</p></li><li> <p><code>url</code> connections with <code>method = "libcurl"</code> aredestroyed properly. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16681">PR#16681</a>)</p></li><li> <p><code>withCallingHandler()</code> now (again) handles warningseven during S4 generic's argument evaluation. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16111">PR#16111</a>)</p></li><li> <p><code>deparse(..., control = "quoteExpressions")</code>incorrectly quoted empty expressions. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16686">PR#16686</a>)</p></li><li> <p><code>format()</code>ting datetime objects (<code>"POSIX[cl]?t"</code>)could segfault or recycle wrongly. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16685">PR#16685</a>)</p></li><li> <p><code>plot.ts(<matrix>, las = 1)</code> now does use <code>las</code>.</p></li><li> <p><code>saveRDS(*, compress = "gzip")</code> now works asdocumented. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16653">PR#16653</a>)</p></li><li><p> (Windows only) The <code>Rgui</code> front end did notalways initialize the console properly, and could cause<span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> to crash. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16698">PR#16698</a>)</p></li><li> <p><code>dummy.coef.lm()</code> now works in more cases, thanks to aproposal by Werner Stahel (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16665">PR#16665</a>). In addition, it now worksfor multivariate linear models (<code>"mlm"</code>, <code>manova</code>)thanks to a proposal by Daniel Wollschlaeger.</p></li><li><p> The <code>as.hclust()</code> method for <code>"dendrogram"</code>sfailed often when there were ties in the heights.</p></li><li> <p><code>reorder()</code> and <code>midcache.dendrogram()</code> now arenon-recursive and hence applicable to somewhat deeply nesteddendrograms, thanks to a proposal by Suharto Anggono in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16424">PR#16424</a>.</p></li><li> <p><code>cor.test()</code> now calculates very small p valuesmore accurately (affecting the result only in extreme notstatistically relevant cases). (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16704">PR#16704</a>)</p></li><li> <p><code>smooth(*, do.ends=TRUE)</code> did not always work correctlyin <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> versions between 3.0.0 and 3.2.3.</p></li><li> <p><code>pretty(D)</code> for date-time objects <code>D</code> now alsoworks well if <code>range(D)</code> is (much) smaller than a second. Inthe case of only one unique value in <code>D</code>, the pretty rangenow is more symmetric around that value than previously.<br />Similarly, <code>pretty(dt)</code> no longer returns a length 5 vectorwith duplicated entries for <code>Date</code> objects <code>dt</code> whichspan only a few days.</p></li><li><p> The figures in help pages such as <code>?points</code> wereaccidentally damaged, and did not appear in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.2.3.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16708">PR#16708</a>)</p></li><li> <p><code>available.packages()</code> sometimes deleted the wrongfile when cleaning up temporary files. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16712">PR#16712</a>)</p></li><li><p> The <code>X11()</code> device sometimes froze on Red HatEnterprise Linux 6. It now waits for <code>MapNotify</code> eventsinstead of <code>Expose</code> events, thanks to SiteshwarVashisht. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16497">PR#16497</a>)</p></li><li> <p><code>[dpqr]nbinom(*, size=Inf, mu=.)</code> now works as limitcase, for ‘dpq’ as the Poisson. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16727">PR#16727</a>)<br /><code>pnbinom()</code> no longer loops infinitely in border cases.</p></li><li> <p><code>approxfun(*, method="constant")</code> and hence <code>ecdf()</code>which calls the former now correctly “predict” <code>NaN</code>values as <code>NaN</code>.</p></li><li> <p><code>summary.data.frame()</code> now displays <code>NA</code>s in<code>Date</code> columns in all cases. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16709">PR#16709</a>)</p></li></ul><h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.2.3</h3><h4>NEW FEATURES</h4><ul><li><p> Some recently-added Windows time zone names have been addedto the conversion table used to convert these to Olson names.(Including those relating to changes for Russia in Oct 2014, as in<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16503">PR#16503</a>.)</p></li><li><p> (Windows) Compatibility information has been added to themanifests for ‘<span class="file">Rgui.exe</span>’, ‘<span class="file">Rterm.exe</span>’ and‘<span class="file">Rscript.exe</span>’. This should allow <code>win.version()</code> and<code>Sys.info()</code> to report the actual Windows version up toWindows 10.</p></li><li><p> Windows <code>"wininet"</code> FTP first tries EPSV / PASV moderather than only using active mode (reported by Dan Tenenbaum).</p></li><li> <p><code>which.min(x)</code> and <code>which.max(x)</code> may be muchfaster for logical and integer <code>x</code> and now also work for longvectors.</p></li><li><p> The ‘emulation’ part of <code>tools::texi2dvi()</code> hasbeen somewhat enhanced, including supporting <code>quiet = TRUE</code>.It can be selected by <code>texi2dvi = "emulation"</code>.</p><p>(Windows) MiKTeX removed its <code>texi2dvi.exe</code> command in Sept2015: <code>tools::texi2dvi()</code> tries <code>texify.exe</code> if it isnot found.</p></li><li><p> (Windows only) Shortcuts for printing and saving havebeen added to menus in <code>Rgui.exe</code>. (Request of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16572">PR#16572</a>.)</p></li><li> <p><code>loess(..., iterTrace=TRUE)</code> now provides diagnosticsfor robustness iterations, and the <code>print()</code> method for<code>summary(<loess>)</code> shows slightly more.</p></li><li><p> The included version of PCRE has been updated to 8.38, abug-fix release.</p></li><li> <p><code>View()</code> now displays nested data frames in a morefriendly way. (Request with patch in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15915">PR#15915</a>.)</p></li></ul><h4>INSTALLATION and INCLUDED SOFTWARE</h4><ul><li><p> The included configuration code for <code>libintl</code> has beenupdated to that from <code>gettext</code> version 0.19.5.1 — thisshould only affect how an external library is detected (and theonly known instance is under OpenBSD). (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16464">PR#16464</a>.)</p></li><li> <p><code>configure</code> has a new argument<span class="option">--disable-java</span> to disable the checks for Java.</p></li><li><p> The <code>configure</code> default for <code>MAIN_LDFLAGS</code> hasbeen changed for the FreeBSD, NetBSD and Hurd OSes to one morelikely to work with compilers other than <code>gcc</code> (FreeBSD 10defaults to <code>clang</code>).</p></li><li> <p><code>configure</code> now supports the OpenMP flags<span class="option">-fopenmp=libomp</span> (clang) and <span class="option">-qopenmp</span> (Intel C).</p></li><li><p> Various macros can be set to override the defaultbehaviour of <code>configure</code> when detecting OpenMP: see file‘<span class="file">config.site</span>’.</p></li><li><p> Source installation on Windows has been modified to allowfor MiKTeX installations without <code>texi2dvi.exe</code>. See file‘<span class="file">MkRules.dist</span>’.</p></li></ul><h4>BUG FIXES</h4><ul><li> <p><code>regexpr(pat, x, perl = TRUE)</code> with Python-style namedcapture did not work correctly when <code>x</code> contained <code>NA</code>strings. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16484">PR#16484</a>)</p></li><li><p> The description of dataset <code>ToothGrowth</code> has beenimproved/corrected. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15953">PR#15953</a>)</p></li><li> <p><code>model.tables(type = "means")</code> and hence<code>TukeyHSD()</code> now support <code>"aov"</code> fits without anintercept term. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16437">PR#16437</a>)</p></li><li> <p><code>close()</code> now reports the status of a <code>pipe()</code>connection opened with an explicit <code>open</code> argument.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16481">PR#16481</a>)</p></li><li><p> Coercing a list without names to a data frame is faster ifthe elements are very long. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16467">PR#16467</a>)</p></li><li><p> (Unix-only) Under some rare circumstances piping the outputfrom <code>Rscript</code> or <code>R -f</code> could result inattempting to close the input file twice, possibly crashing theprocess. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16500">PR#16500</a>)</p></li><li><p> (Windows) <code>Sys.info()</code> was out of step with<code>win.version()</code> and did not report Windows 8.</p></li><li> <p><code>topenv(baseenv())</code> returns <code>baseenv()</code> again asin <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.1.0 and earlier. This also fixes <code>compilerJIT(3)</code>when used in ‘<span class="file">.Rprofile</span>’.</p></li><li> <p><code>detach()</code>ing the <span class="pkg">methods</span> package keeps<code>.isMethodsDispatchOn()</code> true, as long as the methodsnamespace is not unloaded.</p></li><li><p> Removed some spurious warnings from <code>configure</code> about thepreprocessor not finding header files. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15989">PR#15989</a>)</p></li><li> <p><code>rchisq(*, df=0, ncp=0)</code> now returns <code>0</code> insteadof <code>NaN</code>, and <code>dchisq(*, df=0, ncp=*)</code> also no longerreturns <code>NaN</code> in limit cases (where the limit is unique).(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16521">PR#16521</a>)</p></li><li> <p><code>pchisq(*, df=0, ncp > 0, log.p=TRUE)</code> no longerunderflows (for ncp > ~60).</p></li><li> <p><code>nchar(x, "w")</code> returned -1 for characters it did notknow about (e.g. zero-width spaces): it now assumes 1.It now knows about most zero-width characters and a few moredouble-width characters.</p></li><li><p> Help for <code>which.min()</code> is now more precise aboutbehavior with logical arguments. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16532">PR#16532</a>)</p></li><li><p> The print width of character strings marked as<code>"latin1"</code> or <code>"bytes"</code> was in some cases computedincorrectly.</p></li><li> <p><code>abbreviate()</code> did not give names to the return valueif <code>minlength</code> was zero, unlike when it was positive.</p></li><li><p> (Windows only) <code>dir.create()</code> did not always warnwhen it failed to create a directory. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16537">PR#16537</a>)</p></li><li><p> When operating in a non-UTF-8 multibyte locale(e.g. an East Asian locale on Windows), <code>grep()</code> andrelated functions did not handle UTF-8 strings properly.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16264">PR#16264</a>)</p></li><li> <p><code>read.dcf()</code> sometimes misread lines longer than 8191characters. (Reported by Hervé Pagès with a patch.)</p></li><li> <p><code>within(df, ..)</code> no longer drops columns whose namestart with a <code>"."</code>.</p></li><li><p> The built-in <code>HTTP</code> server converted entire<code>Content-Type</code> to lowercase including parameters whichcan cause issues for multi-part form boundaries (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16541">PR#16541</a>).</p></li><li><p> Modifying slots of S4 objects could fail when the<span class="pkg">methods</span> package was not attached. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16545">PR#16545</a>)</p></li><li> <p><code>splineDesign(*, outer.ok=TRUE)</code> (<span class="pkg">splines</span>) is better now(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16549">PR#16549</a>), and <code>interpSpline()</code> now allows <code>sparse=TRUE</code>for speedup with non-small sizes.</p></li><li><p> If the expression in the traceback was too long,<code>traceback()</code> did not report the source line number. (Patchby Kirill Müller.)</p></li><li><p> The browser did not truncate the display of the function whenexiting with <code>options("deparse.max.lines")</code> set.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16581">PR#16581</a>)</p></li><li><p> When <code>bs(*, Boundary.knots=)</code> had boundary knots insidethe data range, extrapolation was somewhat off. (Patch by TrevorHastie.)</p></li><li> <p><code>var()</code> and hence <code>sd()</code> warn about<code>factor</code> arguments which are deprecated now. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16564">PR#16564</a>)</p></li><li> <p><code>loess(*, weights = *)</code> stored wrong weights and hencegave slightly wrong predictions for <code>newdata</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16587">PR#16587</a>)</p></li><li> <p><code>aperm(a, *)</code> now preserves <code>names(dim(a))</code>.</p></li><li> <p><code>poly(x, ..)</code> now works when either <code>raw=TRUE</code> or<code>coef</code> is specified. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16597">PR#16597</a>)</p></li><li> <p><code>data(package=*)</code> is more careful in determining the path.</p></li><li> <p><code>prettyNum(*, decimal.mark, big.mark)</code>: fixed bugintroduced when fixing <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16411">PR#16411</a>.</p></li></ul><h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.2.2</h3><h4>SIGNIFICANT USER-VISIBLE CHANGES</h4><ul><li><p> It is now easier to use secure downloads from<span class="samp">https://</span> URLs on builds which support them: no longer donon-default options need to be selected to do so. In particular,packages can be installed from repositories which offer<span class="samp">https://</span> URLs, and those listed by <code>setRepositories()</code>now do so (for some of their mirrors).</p><p>Support for <span class="samp">https://</span> URLs is available on Windows, and onother platforms if support for <code>libcurl</code> was compiled in andif that supports the <code>https</code> protocol (system installationscan be expected to do). So <span class="samp">https://</span> support can beexpected except on rather old OSes (an example being OS X‘Snow Leopard’, where a non-system version of<code>libcurl</code> can be used).</p><p>(Windows only) The default method for accessing URLs <em>via</em><code>download.file()</code> and <code>url()</code> has been changed to be<code>"wininet"</code> using Windows API calls. This changes the wayproxies need to be set and security settings made: there have beensome reports of <span class="samp">ftp:</span> sites being inaccessible under the new defaultmethod (but the previous methods remain available).</p></li></ul><h4>NEW FEATURES</h4><ul><li> <p><code>cmdscale()</code> gets new option <code>list.</code> for increasedflexibility when a list should be returned.</p></li><li> <p><code>configure</code> now supports <code>texinfo</code> version 6.0,which (unlike the change from 4.x to 5.0) is a minor update.(Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16456">PR#16456</a>.)</p></li><li><p> (Non-Windows only) <code>download.file()</code> with default<code>method = "auto"</code> now chooses <code>"libcurl"</code> if that isavailable and a <span class="samp">https://</span> or <span class="samp">ftps://</span> URL is used.</p></li><li><p> (Windows only) <code>setInternet2(TRUE)</code> is now the default.The command-line option <code>--internet2</code> and environmentvariable <span class="env">R_WIN_INTERNET2</span> are now ignored.</p><p>Thus by default the <code>"internal"</code> method for<code>download.file()</code> and <code>url()</code> uses the <code>"wininet"</code>method: to revert to the previous default use<code>setInternet2(FALSE)</code>.</p><p>This means that <span class="samp">https://</span> URLs can be read by default by<code>download.file()</code> (they have been readable by <code>file()</code>and <code>url()</code> since <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.2.0).</p><p>There are implications for how proxies need to be set (see<code>?download.file</code>).</p></li><li> <p><code>chooseCRANmirror()</code> and <code>chooseBioCmirror()</code> nowoffer HTTPS mirrors in preference to HTTP mirrors. This changesthe interpretation of their <code>ind</code> arguments: see their helppages.</p></li><li> <p><code>capture.output()</code> gets optional arguments <code>type</code>and <code>split</code> to pass to <code>sink()</code>, and hence can be used tocapture messages.</p></li></ul><h4>C-LEVEL FACILITIES</h4><ul><li><p> Header ‘<span class="file">Rconfig.h</span>’ now defines <code>HAVE_ALLOCA_H</code> ifthe platform has the ‘<span class="file">alloca.h</span>’ header (it is needed todefine <code>alloca</code> on Solaris and AIX, at least: see‘Writing R Extensions’ for how to use it).</p></li></ul><h4>INSTALLATION and INCLUDED SOFTWARE</h4><ul><li><p> The <code>libtool</code> script generated by<code>configure</code> has been modified to support FreeBSD >= 10(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16410">PR#16410</a>).</p></li></ul><h4>BUG FIXES</h4><ul><li><p> The HTML help page links to demo code failed due to a changein <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.2.0. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16432">PR#16432</a>)</p></li><li><p> If the <code>na.action</code> argument was used in<code>model.frame()</code>, the original data could bemodified. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16436">PR#16436</a>)</p></li><li> <p><code>getGraphicsEvent()</code> could cause a crash if a graphicswindow was closed while it was in use. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16438">PR#16438</a>)</p></li><li> <p><code>matrix(x, nr, nc, byrow = TRUE)</code> failed if <code>x</code>was an object of type <code>"expression"</code>.</p></li><li> <p><code>strptime()</code> could overflow the allocated storage onthe C stack when the timezone had a non-standard format muchlonger than the standard formats. (Part of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16328">PR#16328</a>.)</p></li><li> <p><code>options(OutDec = s)</code> now signals a warning (which willbecome an error in the future) when <code>s</code> is not a string withexactly one character, as that has been a documented requirement.</p></li><li> <p><code>prettyNum()</code> gains a new option <code>input.d.mark</code>which together with other changes, e.g., the default for<code>decimal.mark</code>, fixes some <code>format()</code>ting variants withnon-default <code>getOption("OutDec")</code> such as in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16411">PR#16411</a>.</p></li><li> <p><code>download.packages()</code> failed for <code>type</code> equal toeither <code>"both"</code> or <code>"binary"</code>. (Reported by DanTenenbaum.)</p></li><li><p> The <code>dendrogram</code> method of <code>labels()</code> is much moreefficient for large dendrograms, now using <code>rapply()</code>.(Comment #15 of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15215">PR#15215</a>)</p></li><li><p> The <code>"port"</code> algorithm of <code>nls()</code> could givespurious errors. (Reported by Radford Neal.)</p></li><li><p> Reference classes that inherited from reference classes inanother package could invalidate methods of the inheritedclass. Fixing this requires adding the ability for methods to be“external”, with the object supplied explicitly as the firstargument, named <code>.self</code>. See "Inter-Package Superclasses"in the documentation.</p></li><li> <p><code>readBin()</code> could fail on the SPARC architecturedue to alignment issues. (Reported by Radford Neal.)</p></li><li> <p><code>qt(*, df=Inf, ncp=.)</code> now uses the natural<code>qnorm()</code> limit instead of returning <code>NaN</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16475">PR#16475</a>)</p></li><li><p> Auto-printing of S3 and S4 values now searches for<code>print()</code> in the base namespace and <code>show()</code> in the<span class="pkg">methods</span> namespace instead of searching the globalenvironment.</p></li><li> <p><code>polym()</code> gains a <code>coefs = NULL</code> argument andreturns class <code>"poly"</code> just like <code>poly()</code> which gets anew <code>simple=FALSE</code> option. They now lead to correct<code>predict()</code>ions, e.g., on subsets of the original data.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16239">PR#16239</a>)</p></li><li> <p><code>rhyper(nn, <large>)</code> now works correctly. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16489">PR#16489</a>)</p></li><li> <p><code>ttkimage()</code> did not (and could not) work so wasremoved. Ditto for <code>tkimage.cget()</code> and<code>tkimage.configure()</code>. Added two Ttk widgets and missingsubcommands for Tk's <code>image</code> command:<code>ttkscale()</code>,<code>ttkspinbox()</code>,<code>tkimage.delete()</code>,<code>tkimage.height()</code>,<code>tkimage.inuse()</code>,<code>tkimage.type()</code>,<code>tkimage.types()</code>,<code>tkimage.width()</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15372">PR#15372</a>, <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16450">PR#16450</a>)</p></li><li> <p><code>getClass("foo")</code> now also returns a class definition when it isfound in the cache more than once.</p></li></ul><h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.2.1</h3><h4>NEW FEATURES</h4><ul><li> <p><code>utf8ToInt()</code> now checks that its input is valid UTF-8and returns <code>NA</code> if it is not.</p></li><li> <p><code>install.packages()</code> now allows <code>type = "both"</code>with <code>repos = NULL</code> if it can infer the type of file.</p></li><li> <p><code>nchar(x, *)</code> and <code>nzchar(x)</code> gain a new argument<code>keepNA</code> which governs how the result for <code>NA</code>s in<code>x</code> is determined. For <code>nzchar()</code> in general and<code>nchar()</code> in the <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.2.x series, the defaultremains <code>FALSE</code> which is fully back compatible.From <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.3.0, <code>nchar()</code>'s default will change to<code>keepNA = NA</code> and you are advised to consider this for codeportability.</p></li><li> <p><code>news()</code> more flexibly extracts dates from package‘<span class="file">NEWS.Rd</span>’ files.</p></li><li> <p><code>lengths(x)</code> now also works (trivially) for atomic<code>x</code> and hence can be used more generally as an efficientreplacement of <code>sapply(x, length)</code> and similar.</p></li><li><p> The included version of PCRE has been updated to 8.37, abug-fix release.</p></li><li> <p><code>diag()</code> no longer duplicates a matrix when extractingits diagonal.</p></li><li> <p><code>as.character.srcref()</code> gains an argument to allowcharacters corresponding to a range of source references to beextracted.</p></li></ul><h4>BUG FIXES</h4><ul><li> <p><code>acf()</code> and <code>ccf()</code> now guarantee values strictlyin <i>[-1,1]</i> (instead of sometimes very slightly outside). <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15832">PR#15832</a>.</p></li><li> <p><code>as.integer("111111111111")</code> now gives NA (with a warning) asit does for the corresponding numeric or negative numbercoercions. Further, <code>as.integer(M + 0.1)</code> now gives <code>M</code>(instead of NA) when M is the maximal representable integer.</p></li><li><p> On some platforms <code>nchar(x, "c")</code> and <code>nchar(x, "w")</code>would return values (possibly <code>NA</code>) for inputs which weredeclared to be UTF-8 but were not, or for invalid strings without amarked encoding in a multi-byte locale, rather than give anerror. Additional checks have been added to mitigate this.</p></li><li> <p><code>apply(a, M, function(u) c(X = ., Y = .))</code> againhas dimnames containing "X" and "Y" (as in R < 3.2.0).</p></li><li><p> (Windows only) In some cases, the <code>--clean</code> optionto <code>R CMD INSTALL</code> could fail. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16178">PR#16178</a>)</p></li><li><p> (Windows only) <code>choose.files()</code> would occasionallyinclude characters from the result of an earlier call inthe result of a later one. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16270">PR#16270</a>)</p></li><li><p> A change in <code>RSiteSearch()</code> in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.2.0 caused it tosubmit invalid URLs. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16329">PR#16329</a>)</p></li><li> <p><code>Rscript</code> and command line <code>R</code> silentlyignored incomplete statements at the end of a script; now theyare reported as parse errors. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16350">PR#16350</a>)</p></li><li><p> Parse data for very long strings was not stored. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16354">PR#16354</a>)</p></li><li> <p><code>plotNode()</code>, the workhorse of the <code>plot</code> methodfor <code>"dendrogram"</code>s is no longer recursive, thanks to SuhartoAnggono, and hence also works for deeply nested dendrograms. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15215">PR#15215</a>)</p></li><li><p> The parser could overflow internally when given numbersin scientific format with extremely large exponents. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16358">PR#16358</a>)</p></li><li><p> If the CRAN mirror was not set, <code>install.packages(type = "both")</code>and related functions could repeatedly query the user for it.(Part of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16362">PR#16362</a>)</p></li><li><p> The low-level functions <code>.rowSums()</code> etc. did notcheck the length of their argument, so could segfault. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16367">PR#16367</a>)</p></li><li><p> The <code>quietly</code> argument of <code>library()</code> is nowcorrectly propagated from <code>.getRequiredPackages2()</code>.</p></li><li><p> Under some circumstances using the internal PCRE whenbuilding <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> from source would cause external libs such as<code>-llzma</code> to be omitted from the main link.</p></li><li><p> The .Primitive default methods of the logic operators, i.e.,<code>!</code>, <code>&</code> and <code>|</code>, now give correct error messageswhen appropriate, e.g., for <code>`&`(TRUE)</code> or <code>`!`()</code>.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16385">PR#16385</a>)</p></li><li> <p><code>cummax(x)</code> now correctly propagates <code>NA</code>s alsowhen <code>x</code> is of type <code>integer</code> and begins with an <code>NA</code>.</p></li><li> <p><code>summaryRprof()</code> could fail when the profile containedonly two records. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16395">PR#16395</a>)</p></li><li><p> HTML vignettes opened using <code>vignette()</code> did not supportlinks into the rest of the HTML help system. (Links worked properlywhen the vignette was opened using <code>browseVignettes()</code> or fromwithin the help system.)</p></li><li> <p><code>arima(*, xreg = .)</code> (for <i>d >= 1</i>)computes estimated variances based on a the number of effectiveobservations as in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> version 3.0.1 and earlier. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16278">PR#16278</a>)</p></li><li> <p><code>slotNames(.)</code> is now correct for <code>"signature"</code>objects (mostly used internally in <span class="pkg">methods</span>).</p></li><li><p> On some systems, the first string comparison aftera locale change would result in <code>NA</code>.</p></li></ul><h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.2.0</h3><h4>NEW FEATURES</h4><ul><li> <p><code>anyNA()</code> gains a <code>recursive</code> argument.</p></li><li><p> When <code>x</code> is missing and <code>names</code> is not false(including the default value), <code>Sys.getenv(x, names)</code> returnsan object of class <code>"Dlist"</code> and hence prints tidily.</p></li><li><p> (Windows.) <code>shell()</code> no longer consults theenvironment variable <span class="env">SHELL</span>: too many systems have beenencountered where it was set incorrectly (usually to a path wheresoftware was compiled, not where it was installed).<span class="env">R_SHELL</span>, the preferred way to select a non-default shell,can be used instead.</p></li><li><p> Some unusual arguments to <code>embedFonts()</code> can now bespecified as character vectors, and the defaults have been changedaccordingly.</p></li><li><p> Functions in the <code>Summary</code> group duplicate less.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15798">PR#15798</a>)</p></li><li><p> (Unix-alikes.) <code>system(cmd, input = )</code> now uses‘shell-execution-environment’ redirection, which will bemore natural if <code>cmd</code> is not a single command (but requires aPOSIX-compliant shell). (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15508">PR#15508</a>)</p></li><li> <p><code>read.fwf()</code> and <code>read.DIF()</code> gain a<code>fileEncoding</code> argument, for convenience.</p></li><li><p> Graphics devices can add attributes to their description in<code>.Device</code> and <code>.Devices</code>. Several of those included with<span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> use a <code>"filepath"</code> attribute.</p></li><li> <p><code>pmatch()</code> uses hashing in more cases and so is fasterat the expense of using more memory. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15697">PR#15697</a>)</p></li><li> <p><code>pairs()</code> gains new arguments to select sets ofvariables to be plotted against each other.</p></li><li> <p><code>file.info(, extra_cols = FALSE)</code> allows a minimal setof columns to be computed on Unix-alikes: on some systems withoutproperly-configured caching this can be significantly faster withlarge file lists.</p></li><li><p> New function <code>dir.exists()</code> in package <span class="pkg">base</span> totest efficiently whether one or more paths exist and aredirectories.</p></li><li> <p><code>dput()</code> and friends gain new controls<span class="samp">hexNumeric</span> and <span class="samp">digits17</span> which output double andcomplex quantities as, respectively, binary fractions (exactly,see <code>sprintf("%a")</code>) and as decimals with up to 17significant digits.</p></li><li> <p><code>save()</code>, <code>saveRDS()</code> and <code>serialize()</code> nowsupport <code>ascii = NA</code> which writes ASCII files using<code>sprintf("%a")</code> for double/complex quantities. This isread-compatible with <code>ascii = TRUE</code> but avoidsbinary->decimal->binary conversions with potential loss ofprecision. Unfortunately the Windows C runtime's lack of C99compliance means that the format cannot be read correctly there in<span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> before 3.1.2.</p></li><li><p> The default for <code>formatC(decimal.mark =)</code> has beenchanged to be <code>getOption("OutDec")</code>; this makes it moreconsistent with <code>format()</code> and suitable for use in printmethods, e.g. those for classes <code>"density"</code>, <code>"ecdf"</code>,<code>"stepfun"</code> and <code>"summary.lm"</code>.</p><p><code>getOption("OutDec")</code> is now consulted by the print methodfor class <code>"kmeans"</code>, by <code>cut()</code>, <code>dendrogram()</code>,<code>plot.ts()</code> and <code>quantile()</code> when constructing labelsand for the report from <code>legend(trace = TRUE)</code>.</p><p>(In part, wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15819">PR#15819</a>.)</p></li><li> <p><code>printNum()</code> and hence <code>format()</code> and<code>formatC()</code> give a warning if <code>big.mark</code> and<code>decimal.mark</code> are set to the same value (period and commaare not uncommonly used for each, and this is a check thatconventions have not got mixed).</p></li><li> <p><code>merge()</code> can create a result which uses long vectorson 64-bit platforms.</p></li><li> <p><code>dget()</code> gains a new argument <code>keep.source</code> whichdefaults to <code>FALSE</code> for speed (<code>dput()</code> and<code>dget()</code> are most often used for data objects where this canmake <code>dget()</code> many times faster).</p></li><li><p> Packages may now use a file of common macro definitions intheir help files, and may import definitions from other packages.</p></li><li><p> A number of macros have been added in the new‘<span class="file">share/Rd</span>’ directory for use in package overview help pages,and <code>promptPackage()</code> now makes use of them.</p></li><li> <p><code>tools::parse_Rd()</code> gains a new <code>permissive</code>argument which converts unrecognized macros into text. This isused by <code>utils:::format.bibentry</code> to allow LaTeX markup to beignored.</p></li><li> <p><code>options(OutDec =)</code> can now specify a multi-bytecharacter, e.g., <code>options(OutDec = "\u00b7")</code> in a UTF-8locale.</p></li><li> <p><code>is.recursive(x)</code> is no longer true when <code>x</code> is anexternal pointer, a weak reference or byte code; the first enables<code>all.equal(x, x)</code> when <code>x <- getClass(.)</code>.</p></li><li> <p><code>ls()</code> (aka <code>objects()</code>) and<code>as.list.environment()</code> gain a new argument <code>sorted</code>.</p></li><li><p> The <code>"source"</code> attribute (which has not been added tofunctions by <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> since before <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> version 2.14.0) is no longertreated as special.</p></li><li><p> Function <code>returnValue()</code> has been added to give<code>on.exit()</code> code access to a function's return value fordebugging purposes.</p></li><li> <p><code>crossprod(x, y)</code> allows more matrix coercions when<code>x</code> or <code>y</code> are vectors, now equalling<code>t(x) %*% y</code> in these cases (also reported by Radford Neal).Similarly, <code>tcrossprod(x,y)</code> and <code>%*%</code> work in morecases with vector arguments.</p></li><li><p> Utility function <code>dynGet()</code> useful for detectingcycles, aka infinite recursions.</p></li><li><p> The byte-code compiler and interpreter include newinstructions that allow many scalar subsetting and assignment andscalar arithmetic operations to be handled more efficiently. Thiscan result in significant performance improvements in scalarnumerical code.</p></li><li> <p><code>apply(m, 2, identity)</code> is now the same as the matrix<code>m</code> when it has <em>named</em> row names.</p></li><li><p> A new function <code>debuggingState()</code> has been added,allowing to temporarily turn off debugging.</p></li><li> <p><code>example()</code> gets a new optional argument<code>run.donttest</code> and <code>tools::Rd2ex()</code> a corresponding<code>commentDonttest</code>, with a default such that<code>example(..)</code> in help examples will run <code>\donttest</code>code only if used interactively (a change in behaviour).</p></li><li> <p><code>rbind.data.frame()</code> gains an optional argument<code>make.row.names</code>, for potential speedup.</p></li><li><p> New function <code>extSoftVersion()</code> to report on theversions of third-party software in use in this session.Currently reports versions of <code>zlib</code>, <code>bzlib</code>, the<code>liblzma</code> from <code>xz</code>, PCRE, ICU, TRE and the <code>iconv</code>implementation.</p><p>A similar function <code>grSoftVersion()</code> in package <span class="pkg">grDevices</span>reports on third-party graphics software.</p><p>Function <code>tcltk::tclVersion()</code> reports the Tcl/Tk version.</p></li><li><p> Calling <code>callGeneric()</code> without arguments now workswith primitive generics to some extent.</p></li><li> <p><code>vapply(x, FUN, FUN.VALUE)</code> is more efficient notablyfor large <code>length(FUN.VALUE)</code>; as extension of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16061">PR#16061</a>.</p></li><li> <p><code>as.table()</code> now allows tables with one or moredimensions of length 0 (such as <code>as.table(integer())</code>).</p></li><li> <p><code>names(x) <- NULL</code> now clears the names of calland <code>...</code> objects.</p></li><li> <p><code>library()</code> will report a warning when an insufficientdependency version is masking a sufficient one later on thelibrary search path.</p></li><li><p> A new <code>plot()</code> method for class <code>"raster"</code> hasbeen added.</p></li><li><p> New <code>check_packages_in_dir_changes()</code> function inpackage <span class="pkg">tools</span> for conveniently analyzing how changingsources impacts the check results of their reverse dependencies.</p></li><li><p> Speed-up from Peter Haverty for <code>ls()</code> and<code>methods:::.requirePackage()</code> speeding up package loading.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16133">PR#16133</a>)</p></li><li><p> New <code>get0()</code> function, combining <code>exists()</code> and<code>get()</code> in one call, for efficiency.</p></li><li> <p><code>match.call()</code> gains an <code>envir</code> argument forspecifying the environment from which to retrievethe <code>...</code> in the call, if any; this environment was wrong(or at least undesirable) when the <code>definition</code> argument wasa function.</p></li><li> <p><code>topenv()</code> has been made <code>.Internal()</code> forspeedup, based on Peter Haverty's proposal in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16140">PR#16140</a>.</p></li><li> <p><code>getOption()</code> no longer calls <code>options()</code> in the maincase.</p></li><li><p> Optional use of <code>libcurl</code> (version 7.28.0 from Oct 2012or later) for Internet access:</p><ul><li> <p><code>capabilities("libcurl")</code> reports if this isavailable.</p></li><li> <p><code>libcurlVersion()</code> reports the version in use, andother details of the <code>"libcurl"</code> build including which URLschemes it supports.</p></li><li> <p><code>curlGetHeaders()</code> retrieves the headers for<span class="samp">http://</span>, <span class="samp">https://</span>, <span class="samp">ftp://</span> and<span class="samp">ftps://</span> URLs: analysis of these headers can provideinsights into the ‘existence’ of a URL (it might for example bepermanently redirected) and is so used in <code>R CMDcheck --as-cran</code>.</p></li><li> <p><code>download.file()</code> has a new optional method<code>"libcurl"</code> which will handle more URL schemes, followredirections, and allows simultaneous downloads of multipleURLs.</p></li><li> <p><code>url()</code> has a new method <code>"libcurl"</code> whichhandles more URL schemes and follows redirections. The defaultmethod is controlled by a new option <code>url.method</code>, whichapplies also to the opening of URLs <em>via</em> <code>file()</code>(which happens implicitly in functions such as<code>read.table</code>.)</p></li><li><p> When <code>file()</code> or <code>url()</code> is invoked with a<code>https://</code> or <code>ftps://</code> URL which the current methodcannot handle, it switches to a suitable method if one isavailable.</p></li></ul></li><li><p> (Windows.) The DLLs ‘<span class="file">internet.dll</span>’ and‘<span class="file">internet2.dll</span>’ have been merged. In this version it is safeto switch (repeatedly) between the internal and Windows internetfunctions within an <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> session.</p><p>The Windows internet functions are still selected by flag<span class="option">--internet2</span> or <code>setInternet2()</code>. This can beoverridden for an <code>url()</code> connection <em>via</em> its new<code>method</code> argument.</p><p><code>download.file()</code> has new method <code>"wininet"</code>, selectedas the default by <span class="option">--internet2</span> or <code>setInternet2()</code>.</p></li><li> <p><code>parent.env<-</code> can no longer modify the parent of alocked namespace or namespace imports environment. Contributed byKarl Millar.</p></li><li><p> New function <code>isNamespaceLoaded()</code> for readability and speed.</p></li><li> <p><code>names(env)</code> now returns all the object names of an<code>environment</code> <code>env</code>, equivalently to<code>ls(env, all.names = TRUE, sorted = FALSE)</code> and also tothe names of the corresponding list,<code>names(as.list(env, all.names = TRUE))</code>.Note that although <code>names()</code> returns a character vector, thenames have no particular ordering.</p></li><li><p> The memory manager now grows the heap more aggressively. Thisreduces the number of garbage collections, in particular whiledata or code are loaded, at the expense of slightly increasing thememory footprint.</p></li><li><p> New function <code>trimws()</code> for removing leading/trailingwhitespace.</p></li><li> <p><code>cbind()</code> and <code>rbind()</code> now consider S4 inheritanceduring S3 dispatch and also obey <code>deparse.level</code>.</p></li><li> <p><code>cbind()</code> and <code>rbind()</code> will delegate recursivelyto <code>methods::cbind2</code> (<code>methods::rbind2</code>) when at leastone argument is an S4 object and S3 dispatch fails (due toambiguity).</p></li><li><p> (Windows.) <code>download.file(quiet = FALSE)</code> now usestext rather than Windows progress bars in non-interactive use.</p></li><li><p> New function <code>hsearch_db()</code> in package <span class="pkg">utils</span> forbuilding and retrieving the help search database used by<code>help.search()</code>, along with functions for inspecting theconcepts and keywords in the help search database.</p></li><li><p> New function <code>.getNamespaceInfo()</code>, a no-check versionof <code>getNamespaceInfo()</code> mostly for internal speedups.</p></li><li><p> The help search system now takes <span class="samp">\keyword</span> entries inRd files which are not standard keywords (as given in‘<span class="file">KEYWORDS</span>’ in the <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> documentation directory) as concepts.For standard keyword entries the corresponding descriptions areadditionally taken as concepts.</p></li><li><p> New <code>lengths()</code> function for getting the lengths of allelements in a list.</p></li><li><p> New function <code>toTitleCase()</code> in package <span class="pkg">tools</span>,tailored to package titles.</p></li><li><p> The matrix methods of <code>cbind()</code> and <code>rbind()</code>allow matrices as inputs which have <i>2^31</i> or moreelements. (For <code>cbind()</code>, wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16198">PR#16198</a>.)</p></li><li><p> The default method of <code>image()</code> has an explicit checkfor a numeric or logical matrix (which was always required).</p></li><li> <p><code>URLencode()</code> will not by default encode further URLswhich appear to be already encoded.</p></li><li> <p><code>BIC(mod)</code> and <code>BIC(mod, mod2)</code> now give non-NAnumbers for <code>arima()</code> fitted models, as <code>nobs(mod)</code> nowgives the number of “used” observations for such models.This fixes <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16198">PR#16198</a>, quite differently than proposed there.</p></li><li><p> The <code>print()</code> methods for <code>"htest"</code>,<code>"pairwise.htest"</code> and <code>"power.htest"</code> objects now havea <code>digits</code> argument defaulting to (a function of)<code>getOption("digits")</code>, and influencing all printed numberscoherently. Unavoidably, this changes the display of such testresults in some cases.</p></li><li><p> Code completion for namespaces now recognizes all loadednamespaces, rather than only the ones that are also attached.</p></li><li><p> The code completion mechanism can now be replaced by auser-specified completer function, for (temporary) situationswhere the usual code completion is inappropriate.</p></li><li> <p><code>unzip()</code> will now warn if it is able to detect truncationwhen unpacking a file of 4GB or more (related to <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16243">PR#16243</a>).</p></li><li> <p><code>methods()</code> reports S4 in addition to S3 methods;output is simplified when the <code>class</code> argument isused. <code>.S3methods()</code> and <code>methods::.S4methods()</code> reportS3 and S4 methods separately.</p></li><li><p> Higher order functions such as the <code>apply</code> functionsand <code>Reduce()</code> now force arguments to the functions they applyin order to eliminate undesirable interactions between lazyevaluation and variable capture in closures. This resolves<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16093">PR#16093</a>.</p></li></ul><h4>INSTALLATION and INCLUDED SOFTWARE</h4><ul><li><p> The <code>\donttest</code> sections of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>'s help files can betested by<br /><code>make check TEST_DONTTEST=TRUE</code> .</p></li><li><p> It is possible to request the use of system<code>valgrind</code> headers <em>via</em> <code>configure</code> option<span class="option">--with-system-valgrind-headers</span>: note the possible futureincompatibility of such headers discussed in the 'R Installationand Administration' manual. (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16068">PR#16068</a>.)</p></li><li><p> The included version of <code>liblzma</code> has been updated to<code>xz-utils</code> 5.0.7 (minor bug fixes from 5.0.5).</p></li><li> <p><code>configure</code> options <span class="option">--with-system-zlib</span>,<span class="option">--with-system-bzlib</span> and <span class="option">--with-system-pcre</span> arenow the default. For the time being there is fallback to theversions included in the <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> sources if no system versions arefound or (unlikely) if they are too old.</p><p>Linux users should check that the <code>-devel</code> or <code>-dev</code>versions of packages <span class="pkg">zlib</span>, <span class="pkg">bzip2</span>/<span class="pkg">libbz2</span> and<span class="pkg">pcre</span> as well as <span class="pkg">xz-devel</span>/<span class="pkg">liblzma-dev</span> (orsimilar names) are installed.</p></li><li> <p><code>configure</code> by default looks for the<code>texi2any</code> script from <span class="pkg">texinfo</span> 5.1 or later, ratherthan the <code>makeinfo</code> program. (<code>makeinfo</code> is alink to the Perl script <code>texi2any</code> in <span class="pkg">texinfo</span> 5.x.)</p></li><li> <p><code>R CMD INSTALL</code> gains an option<span class="option">--built-timestamp=STAMP</span> allowing 100% reproduciblepackage building, thanks to Dirk Eddelbuettel.</p></li></ul><h4>UTILITIES</h4><ul><li><p> There is support for testing the <code>\dontrun</code> and<code>\donttest</code> parts of examples in packages.</p><p><code>tools::testInstalledPackage()</code> accepts new arguments<code>commentDontrun = FALSE</code> and <code>commentDonttest = FALSE</code>.</p><p><code>R CMD check</code> gains options <span class="option">--run-dontrun</span> and<span class="option">--run-donttest</span>.</p></li><li><p> The <acronym><span class="acronym">HTML</span></acronym> generated by <code>tools::Rd2HTML()</code> and<code>tools::toHTML()</code> methods is now‘<acronym><span class="acronym">XHTML</span></acronym> 1.0 Strict’.</p></li><li><p> The <span class="pkg">compiler</span> package's utility function<code>setCompilerOptions()</code> now returns the old valuesinvisibly. The initial optimization level can also be set with theenvironment variable <span class="env">R_COMPILER_OPTIMIZE</span>.</p></li><li> <p><code>R CMD build</code> adds a <span class="samp">NeedsCompilation</span> fieldif one is not already present in the ‘<span class="file">DESCRIPTION</span>’ file.</p></li><li> <p><code>R CMD check</code> gains option <span class="option">--test-dir</span> tospecify an alternative set of tests to run.</p></li><li> <p><code>R CMD check</code> will now by default continue withtesting after many types of errors, and will output a summarycount of errors at the end if any have occurred.</p></li><li> <p><code>R CMD check</code> now checks that the <span class="samp">Title</span> and<span class="samp">Description</span> fields are correctly terminated.</p></li><li> <p><code>R CMD check --as-cran</code> now:</p><ul><li><p> checks a ‘<span class="file">README.md</span>’ file can be processed: thisneeds <code>pandoc</code> installed.</p></li><li><p> checks the existence and accessibility of URLs in the‘<span class="file">DESCRIPTION</span>’, ‘<span class="file">CITATION</span>’, ‘<span class="file">NEWS.Rd</span>’ and‘<span class="file">README.md</span>’ files and in the help files (provided the buildhas <code>libcurl</code> support).</p></li><li><p> reports non-ASCII characters in R source files when thereis no package encoding declared in the ‘<span class="file">DESCRIPTION</span>’ file.</p></li><li><p> reports (apparent) S3 methods exported but not registered.</p></li><li><p> reports overwriting registered S3 methods frombase/recommended packages. (Such methods are replaced in theaffected package for the rest of the session, even if thereplacing namespace is unloaded.)</p></li><li><p> reports if the <code>Title</code> field does not appear to be intitle case (see ‘Writing R Extensions’: there may befalse positives, but note that technical words should besingle-quoted and will then be accepted).</p></li></ul><p>Most of these checks can also be selected by environmentvariables: see the ‘R Internals’ manual.</p></li></ul><h4>C-LEVEL FACILITIES</h4><ul><li><p> New C API utility <code>logspace_sum(logx[], n)</code>.</p></li><li><p> Entry points <code>rbinom_mu</code>, <code>rnbinom_mu</code> and<code>rmultinom</code> are remapped (by default) to <code>Rf_rbinom_mu</code>etc. This requires packages using them to be re-installed.</p></li><li> <p><code>.C(DUP = FALSE)</code> and <code>.Fortran(DUP = FALSE)</code> arenow ignored, so arguments are duplicated if <code>DUP = TRUE</code>would do so. As their help has long said, <code>.Call()</code> is muchpreferred.</p></li><li><p> New entry point <code>R_allocLD</code>, like <code>R_alloc</code> butguaranteed to have sufficient alignment for <code>long double</code>pointers.</p></li><li> <p><code>isPairList()</code> now returns <code>TRUE</code> for DOTSXP.</p></li></ul><h4>WINDOWS BUILD CHANGES</h4><p>A number of changes to the Windows build system are in development.The following are currently in place.</p><ul><li><p> Installation using external binary distributionsof <span class="pkg">zlib</span>, <span class="pkg">bzip2</span>, <span class="pkg">liblzma</span>, <span class="pkg">pcre</span>,<span class="pkg">libpng</span>, <span class="pkg">jpeglib</span> and <span class="pkg">libtiff</span> is now required,and the build instructions have been revised.</p></li><li><p> A new <code>make</code> target <code>rsync-extsoft</code> has beenadded to obtain copies of the external libraries from<acronym><span class="acronym">CRAN</span></acronym>.</p></li><li><p> Building the manuals now requires <code>texi2any</code> from<span class="pkg">texinfo</span> 5.1 or later. <acronym><span class="acronym">CRAN</span></acronym> binary builds includethe manuals, but by default builds from source will not, and theywill be accessed from <acronym><span class="acronym">CRAN</span></acronym>. See the comments in‘<span class="file">src/gnuwin32/MkRules.dist</span>’ for how to specify the locationof <code>texi2any</code>.</p></li><li><p> (Windows) Changes have been made to support an experimentalWindows toolchain based on GCC 4.9.2. The default toolchaincontinues to be based on GCC 4.6.3, as the new toolchain is notyet stable enough. A change to a new toolchain is expected duringthe R 3.2.x lifetime.</p></li></ul><h4>PACKAGE INSTALLATION</h4><ul><li><p> (Windows) The use of macro <code>ZLIB_LIBS</code> in file‘<span class="file">src/Makevars.win</span>’ (which has not been documented for a longtime) now requires an external ‘<span class="file">libz.a</span>’ to be available (it ispart of the ‘goodies’ used to compile Windows binarypackages). It would be simpler to use <code>-lz</code> instead.</p></li><li><p> The default for option <code>pkgType</code> on platforms usingbinary packages is now <code>"both"</code>, so source packages will betried if binary versions are not available or not up to date.</p><p>There are options for what <code>install.packages(type = "both")</code>(possibly called <em>via</em> <code>update.packages()</code>) will do ifcompilation of a source package is desirable: see <code>?options</code>(under <span class="pkg">utils</span>).</p><p>If you intend not to accept updates as source packages, you shoulduse <code>update.packages(type = "binary")</code>.</p></li></ul><h4>DEPRECATED AND DEFUNCT</h4><ul><li> <p><code>download.file(method = "lynx")</code> is defunct.</p></li><li><p> Building <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> using the included versions of <code>zlib</code>,<code>bzip2</code>, <code>xz</code> and PCRE is deprecated: these are frozen(bar essential bug-fixes) and will be removed for <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.3.0.</p></li><li><p> The <code>configure</code> option<span class="option">--with-valgrind-instrumentation=3</span> has been withdrawn, asit did not work with recent <code>valgrind</code> headers: it is nowtreated as level <code>2</code>.</p></li><li><p> The <code>MethodsList</code> class in package <span class="pkg">methods</span> hadbeen deprecated in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.11.0 and is defunct now. Functions usingit are defunct if they had been deprecated in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.11.0, and aredeprecated now, otherwise.</p></li></ul><h4>BUG FIXES</h4><ul><li><p> Fixed two obscure bugs in pairlist subassignment, reported byRadford Neal as part of pqR issue 16.</p></li><li><p> Fixes for bugs in handling empty arguments and argumentmatching by name in <code>log()</code>.</p></li><li> <p><code>all.equal()</code> gains methods for <code>environment</code>s and<code>refClass</code>es.</p></li><li> <p><code>[<-</code> and <code>[[<-</code> gain S4 <code>data.frame</code> methodsto avoid corruption of S4 class information by the S3 methods.</p></li><li> <p><code>callNextMethod()</code> should now work within a <code>.local</code>call when <code>...</code> is absent from <code>formals(.local)</code>.</p></li><li> <p><code>dput(pairlist(x))</code> generates a call to the<code>pairlist</code> constructor instead of the <code>list</code>constructor.</p></li><li><p> Fix <code>missing()</code> when arguments are propagated through<code>...</code> . (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15707">PR#15707</a>)</p></li><li> <p><code>eigen(m)</code> now defaults to <code>symmetric = TRUE</code> evenwhen the dimnames are asymmetric if the matrix is otherwisesymmetric. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16151">PR#16151</a>)</p></li><li><p> Fix issues with forwarding <code>...</code> through<code>callGeneric()</code> and <code>callNextMethod()</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16141">PR#16141</a>)</p></li><li> <p><code>callGeneric()</code> now works after a <code>callNextMethod()</code>.</p></li><li><p> Subclass information is kept consistent when replacing anordinary S4 class with an “old class” <em>via</em> the<code>S4Class</code> argument to <code>setOldClass()</code>. Thus, forexample, a <code>data.frame</code> is valid for a <code>list</code> argumentin the signature, and a <code>factor</code> is valid for <code>vector</code>arguments.</p></li><li><p> In <code>qbeta()</code> the inversion of <code>pbeta()</code> is muchmore sophisticated. This works better in corner cases some ofwhich failed completely previously (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15755">PR#15755</a>), or were usingtoo many iterations.</p></li><li><p> Auto-printing no longer duplicates objects when printing isdispatched to a method.</p></li><li> <p><code>kmeans(x, k)</code> would fail when <code>nrow(x) >= 42949673</code>.(Comment 6 of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15364">PR#15364</a>)</p></li><li> <p>‘Abbreviated’ locale-specific day and month namescould have been truncated in those rare locales where there arethe same as the full names.</p></li><li><p> An irrelevant warning message from updating subclassinformation was silenced (the namespace would not be writablein this case).</p></li></ul><h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.1.3</h3><h4>NEW FEATURES</h4><ul><li><p> The internal method of <code>download.file()</code> can now handlefiles larger than 2GB on 32-bit builds which support such files(tested on 32-bit <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> running on 64-bit Windows).</p></li><li> <p><code>kruskal.test()</code> warns on more types of suspicious input.</p></li><li><p> The <code>as.dendrogram()</code> method for <code>"hclust"</code>objects gains a <code>check</code> argument protecting against memoryexplosion for invalid inputs.</p></li><li> <p><code>capabilities()</code> has a new item <code>long.double</code>which indicates if the build uses a <code>long double</code> type whichis longer than <code>double</code>.</p></li><li> <p><code>nlm()</code> no longer modifies the callback argument inplace (a new vector is allocated for each invocation, which mimicsthe implicit duplication that occurred in R < 3.1.0); note thatthis is a change from the previously documentedbehavior. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15958">PR#15958</a>)</p></li><li> <p><code>icuSetCollate()</code> now accepts <code>locale = "ASCII"</code>which uses the basic C function <code>strcmp</code> and so collatesstrings byte-by-byte in numerical order.</p></li><li> <p><code>sessionInfo()</code> tries to report the OS version in use(not just that compiled under, and including details of Linuxdistributions).</p></li><li> <p><code>model.frame()</code> (used by <code>lm()</code> and many othermodelling functions) now warns when it drops contrastsfrom factors. (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16119">PR#16119</a>)</p></li><li> <p><code>install.packages()</code> and friends now accept the value<code>type = "binary"</code> as a synonym for the native binary type onthe platform (if it has one).</p></li><li><p> Single source or binary files can be supplied for<code>install.packages(type = "both")</code> and the appropriate typeand <code>repos = NULL</code> will be inferred.</p></li><li><p> New function <code>pcre_config()</code> to report on some of theconfiguration options of the version of PCRE in use. Inparticular, this reports if regular expressions using<span class="samp">\p{xx}</span> are supported.</p></li><li><p> (Windows.) <code>download.file(cacheOK = FALSE)</code> is nowsupported when ‘<span class="file">internet2.dll</span>’ is used.</p></li><li> <p><code>browseURL()</code> has been updated to work with Firefox36.0 which has dropped support for the <span class="option">-remote</span> interface.</p></li></ul><h4>INSTALLATION and INCLUDED SOFTWARE</h4><ul><li><p> The included version of PCRE has been updated to 8.36.</p></li><li> <p><code>configure</code> accepts <span class="samp">MAKEINFO=texi2any</span> asanother way to ensure <span class="pkg">texinfo</span> 5.x is used when both 5.x and4.x are installed.</p></li></ul><h4>UTILITIES</h4><ul><li> <p><code>R CMD check</code> now checks the packages used in<code>\donttest</code> sections of the examples are specified in the‘<span class="file">DESCRIPTION</span>’ file.(These are needed to run the examples interactively.)</p></li><li> <p><code>R CMD check</code> checks for the undeclared use of GNUextensions in Makefiles, and for Makefiles with a missing finallinefeed.</p><p><code>R CMD build</code> will correct line endings in all Makefiles,not just those in the ‘<span class="file">src</span>’ directory.</p></li><li> <p><code>R CMD check</code> notes uses of <code>library()</code> and<code>require()</code> in package code: see the section‘Suggested packages’ of ‘Writing R Extensions’ forgood practice.</p></li></ul><h4>DEPRECATED AND DEFUNCT</h4><ul><li><p> The <code>configure</code> option<span class="option">--with-valgrind-instrumentation=3</span> is deprecated and willbe removed in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.2.0.</p></li></ul><h4>BUG FIXES</h4><ul><li><p> (Windows.) <code>Rscript.exe</code> was missing amanifest specifying the modern style for common controls (e.g.,the download progress bar).</p></li><li><p> If a package had extra documentation files but no vignette,the HTML help system produced an empty index page.</p></li><li><p> The parser now gives an error if a null character is includedin a string using Unicode escapes. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16046">PR#16046</a>)</p></li><li> <p><code>qr.Q()</code> failed on complex arguments due topre-3.0(!) typo. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16054">PR#16054</a>)</p></li><li> <p><code>abs()</code> failed with named arguments when the argumentwas complex. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16047">PR#16047</a>)</p></li><li> <p><code>"noquote"</code> objects may now be used as columns indata frames. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15997">PR#15997</a>)</p></li><li><p> Some values with extremely long names were printedincorrectly. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15999">PR#15999</a>)</p></li><li><p> Extremely large exponents on zero expressed in scientificnotation (e.g. <code>0.0e50000</code>) could give <code>NaN</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15976">PR#15976</a>)</p></li><li> <p><code>download.file()</code> reported downloaded sizes as 0KB ifless than 1MB, only for <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.1.2 and only on big-endian platforms.</p></li><li> <p><code>prompt()</code> did not escape percent signs in theautomatically generated usage section of help files.</p></li><li> <p><code>drop.terms()</code> dropped some of the attributes of theobject it was working with. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16029">PR#16029</a>)</p></li><li><p> (Windows.) The command completion in <code>Rgui.exe</code>messed up the console. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15791">PR#15791</a>)</p></li><li><p> (Windows.) The <code>choose.files()</code> command returned ablank string when the user asked for a single file but cancelledthe request. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16074">PR#16074</a>)</p></li><li> <p><code>Math2</code> S4 group generics failed to correctly dispatch<code>"structure"</code>- and <code>"nonStructure"</code>-derived classes.</p></li><li> <p><code>loadNamespace()</code> imposed undocumented restrictionson the <code>versionCheck</code> parameter. (Reported by Geoff Lee.)</p></li><li><p> Rare over-runs detected by AddressSanitizer in<code>substr()</code> and its replacement version have been avoided.</p><p><em>Inter alia</em> that fix gives the documented behaviour for<code>substr(x, 1, 2) <- ""</code> (subsequently reported as<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16214">PR#16214</a>).</p></li><li><p> Loading packages incorrectly defining an S4 generic followedby a function of the same name caused an erroneous cyclicnamespace dependency error.</p></li><li><p> Declared vignette encodings are now always passed to thevignette engine.</p></li><li><p> Port Tomas Kalibera's fix from R-devel that restores the<code>loadMethod()</code> fast path, effectively doubling the speed ofS4 dispatch.</p></li><li> <p><code>power.t.test()</code> and <code>power.prop.test()</code> now makeuse of the <code>extendInt</code> option of <code>uniroot()</code> and hencework in more extreme cases. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15792">PR#15792</a>)</p></li><li><p> If a package was updated and attached when its namespace wasalready loaded, it could end up with parts from one version andparts from the other. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16120">PR#16120</a>)</p></li><li> <p><code>tools:::.Rdconv()</code> didn't accept <code>--encoding=</code> dueto a typo. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16121">PR#16121</a>)</p></li><li><p> Unix-alike builds without a suitable <code>makeinfo</code> weredocumented to link the missing HTML manuals to CRAN, but did not.</p></li><li> <p><code>save(*, ascii=TRUE)</code> and <code>load()</code> now correctlydeal with <code>NaN</code>'s. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16137">PR#16137</a>)</p></li><li> <p><code>split.Date()</code> retains fractional representations whileavoiding incomplete class propagation.</p></li><li> <p>‘<span class="file">R_ext/Lapack.h</span>’ had not been updated for changes madeby LAPACK to the argument lists of its (largely internal)functions <code>dlaed2</code> and <code>dlaed3</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16157">PR#16157</a>)</p></li><li> <p><code>RShowDoc("NEWS", "txt")</code> had not been updated for thelayout changes of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.1.0.</p></li><li><p> The <code>xtfrm()</code> method for class <code>"Surv"</code> has beencorrected and its description expanded.</p></li><li> <p><code>mode(x) <- y</code> would incorrectly evaluate <code>x</code> beforechanging its mode. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16215">PR#16215</a>)</p></li><li> <p><code>besselJ(1, 2^64)</code> and <code>besselY(..)</code> now signal awarning, returning <code>NaN</code> instead of typicallysegfaulting. (Issue 3 of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15554">PR#15554</a>)</p></li><li><p> HTML conversion of <span class="samp">\href</span> markup in ‘<span class="file">.Rd</span>’ filesdid not remove the backslash from <span class="samp">\%</span> and so gave aninvalid URL. In a related change, the <span class="samp">\</span> escape is nowrequired in such URLs.</p></li></ul><h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.1.2</h3><h4>NEW FEATURES</h4><ul><li> <p><code>embedFonts()</code> now defaults to<code>format = "ps2write"</code> for ‘<span class="file">.ps</span>’ and ‘<span class="file">.eps</span>’ files.This is available in Ghostscript 9.x (since 2010) whereas theprevious default, <code>format = "pswrite"</code>, was removed inGhostscript 9.10.</p></li><li><p> For consistency with <code>[dpqr]norm()</code>,<code>[dp]lnorm(sdlog = 0)</code> model a point mass at<code>exp(mulog)</code> rather than return <code>NaN</code> (for an error).</p></li><li> <p><code>capabilities()</code> now reports if ICU is compiled in foruse for collation (it is only actually used if a suitable localeis set for collation, and never for a <code>C</code> locale).</p></li><li><p> (OS X only.) Package <span class="pkg">tcltk</span> checks when loaded if it islinked against the CRAN X11-based Tcl/Tk and if so that the Tcl/Tkcomponent and the X11 libraries are installed. This allows moreinformative error messages to be given advising the installationof the missing component or of XQuartz.</p><p>The <code>X11()</code> device and X11-based versions of the data editorand viewer (invoked by <code>edit()</code> and <code>View()</code> for dataframes and matrices from command-line <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>) check that the X11libraries are installed and if not advises installing XQuartz.</p></li><li> <p><code>icuSetCollate()</code> allows <code>locale = "default"</code>, and<code>locale = "none"</code> to use OS services rather than ICU forcollation.</p><p>Environment variable <span class="env">R_ICU_LOCALE</span> can be used to set thedefault ICU locale, in case the one derived from the OS locale isinappropriate (this is currently necessary on Windows).</p></li><li><p> New function <code>icuGetCollate()</code> to report on the ICUcollation locale in use (if any).</p></li><li> <p><code>utils::URLencode()</code> was updated to use unreserved andreserved characters from RFC 3986(<a href="http://tools.ietf.org/html/rfc3986">http://tools.ietf.org/html/rfc3986</a>) instead of RFC 1738.</p></li><li> <p><code>unique(warnings())</code> and <code>c(warnings())</code> are nowsupported.</p></li><li><p> The Bioconductor ‘version’ used by<code>setRepositories()</code> now defaults to <code>3.0</code>. (It can beset at runtime <em>via</em> environment variable<span class="env">R_BIOC_VERSION</span>.)</p></li><li><p> Omegahat is no longer listed as providing Windows binarypackages, e.g. by <code>setRepositories()</code>. It has no binarypackages available for <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.1.x and those for earlier versionswere 32-bit only.</p></li></ul><h4>INSTALLATION and INCLUDED SOFTWARE</h4><ul><li><p> The <code>configure</code> script reports on the more importantcapabilities/options which will not be compiled in.</p><p>More types of external BLAS are recognized by name in that report.</p></li><li><p> When building <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> as a shared library, the<span class="option">-L${R_HOME}/lib${R_ARCH}</span> flag is placed earlier in thelink commands used during installation and when packages areinstalled: this helps ensure that the current build has priorityif an <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> shared library has already been installed bye.g. <code>install-libR</code> in a library mentioned in<span class="env">LDFLAGS</span> (and not in ‘your system's library directory’as documented). (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15790">PR#15790</a>.)</p></li><li><p> LaTeX package <span class="pkg">upquote</span> is no longer required for <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>'suse of <span class="pkg">inconsolata</span>.</p></li><li><p> (Windows only) If both 32- and 64-bit versions of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> areinstalled, the ‘<span class="file">bin/R.exe</span>’ and ‘<span class="file">bin/Rscript.exe</span>’ executablesnow run 64-bit <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>. (To run 32-bit <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>, overwrite these fileswith copies of ‘<span class="file">bin/i386/Rfe.exe</span>’.)</p></li></ul><h4>UTILITIES</h4><ul><li><p> Running <code>R CMD check</code> with<span class="env">_R_CHECK_DEPENDS_ONLY_</span> true now makes the<span class="samp">VignetteBuilder</span> packages available even if they arelisted in <span class="samp">Suggests</span>, since they are needed to recognise andprocess non-Sweave vignettes.</p></li><li> <p><code>R CMD check</code> now reports empty <code>importFrom</code>declarations in a ‘<span class="file">NAMESPACE</span>’ file, as these are commonerrors (writing <code>importFrom(<var>Pkg</var>)</code> where<code>import(<var>Pkg</var>)</code> was intended).</p></li><li> <p><code>R CMD check</code> now by default checks code usagedirectly on the package namespace without loading and attachingthe package and its suggests and enhances. For good practice withpackages in the <span class="samp">Suggests</span> field, see §1.1.3.1 of‘Writing R Extensions’. For use of lazy-data objects inthe package's own code, see <code>?data</code>.</p></li></ul><h4>BUG FIXES</h4><ul><li> <p><code>dmultinom()</code> did not handle non-finite probabilitiescorrectly.</p></li><li> <p><code>prettyNum(x, zero.print=*)</code> now also works when<code>x</code> contains <code>NA</code>s.</p></li><li><p> A longstanding bug exhibited by <code>nlminb()</code> on Windowswas traced to a compiler bug in gcc 4.6.3; a workaround has beenput in place. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15244">PR#15244</a> and <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15914">PR#15914</a>).</p></li><li><p> Rendering of <code>\command</code> in HTML versions of help pageshas been improved: this is particularly evident on the help pagefor <code>INSTALL</code>.</p></li><li> <p><code>as.hexmode(x)</code> and <code>as.octmode(x)</code> now behavecorrectly for some numeric <code>x</code>, e.g., <code>c(NA, 1)</code> or<code>c(1, pi)</code>.</p></li><li> <p><code>drop1()</code> failed if the <code>scope</code> argument hadno variables to drop. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15935">PR#15935</a>)</p></li><li> <p><code>edit()</code> (and hence <code>fix()</code>) failed ifan object had a non-character attribute named <code>"source"</code>(an attribute that had been used in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> prior to version 2.14.0).</p></li><li> <p><code>callGeneric()</code> could fail if the generic had<code>...</code> as a formal argument. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15937">PR#15937</a>).</p></li><li><p> Forking in package <span class="pkg">parallel</span> called C entry point<code>exit</code> in the child. This was unsafe (<code>_exit</code> shouldhave been called), and could flush <code>stdin</code> of the main <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>process (seen most often on Solaris).</p><p>As good practice, <code>stdout</code> is now flushed before forking a child.</p></li><li> <p><span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> objects such as <code>list(`a\b` = 1)</code> now print correctly.</p></li><li> <p><code>getAnywhere("C_pbinom")</code> now returns correctly asingle object (rather than unlisting it).</p></li><li><p> The <code>confint()</code> method for <code>nls()</code> fits failed itthese has specified parameter limits despite using an algorithmother than <code>"port"</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15960">PR#15960</a>)</p></li><li><p> Subclassing an S4 class failed if the class requiredarguments to the generator, through its <code>initialize()</code> method.</p></li><li> <p><code>removeSource()</code> did not properly handle expressionscontaining arguments that were supplied as missing, e.g.<code>x[i,]</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15957">PR#15957</a>)</p></li><li> <p><code>as.environment(list())</code> now works, and<code>as.list()</code> of such an environment is now the same as<code>list()</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15926">PR#15926</a>)</p></li><li><p> Several <span class="pkg">tcltk</span> functions failed when run in unusualenvironments. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15970">PR#15970</a>)</p></li><li> <p><code>options(list())</code> now works (trivially). (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15979">PR#15979</a>)</p></li><li> <p><code>merge(<dendrogram>, ..)</code> now works correctly for two‘independent’ dendrograms (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15648">PR#15648</a>), and still compatibly<em>via</em> <code>adjust = "auto"</code> e.g. for two branches of anexisting dendrogram.</p></li><li><p> The <code>plot</code> method for <code>"hclust"</code> objects gets anoptional argument <code>check</code>; when that is true (the default) itchecks more carefully for valid input.</p></li><li><p> (Windows only) If a user chose to install 64 bit <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> but not32 bit <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>, the ‘<span class="file">bin/R</span>’ and ‘<span class="file">bin/Rscript</span>’ executablesfailed to run. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15981">PR#15981</a>)</p></li><li><p> Various possible buffer overruns have been prevented,and missed memory protection added. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15990">PR#15990</a>)</p></li><li> <p><code>Rscript</code> no longer passes <code>--args</code> to<code>R</code> when there are no extra (“user”) arguments.</p></li><li><p> objects like <code>getClass("refClass")@prototype</code> now<code>print()</code> and <code>str()</code> without error.</p></li><li> <p><code>identical()</code> now also looks at the S4 bit.</p></li><li> <p><code>hist(x, breaks)</code> is more robust in adding a small fuzzto few breaks when some are very large. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15988">PR#15988</a>)</p></li><li> <p><code>sub()</code> and <code>gsub()</code> did not handle regularexpressions like <code>"\s{2,}"</code> properly if the textcontained <code>NA</code> or non-ASCII elements in a UTF-8locale. Part of this was due to a bug in the TRE library.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16009">PR#16009</a>)</p></li><li> <p><code>RShowDoc("NEWS")</code> now displays the PDF version.</p></li><li><p> Matrices and arrays with last dimension zero did not printat all or incompletely. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16012">PR#16012</a>)</p></li><li> <p><code>plot.histogram()</code> and hence <code>hist()</code> now respectthe <code>xaxs</code>, <code>yaxs</code> and <code>lab</code> graphics parameters.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16021">PR#16021</a>)</p></li><li> <p><code>bw.SJ(x)</code> and other bw.*() no longer segfault when<code>x</code> contains non-finite values. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16024">PR#16024</a>)</p></li><li> <p><code>R CMD Rd2pdf</code> unintentionally ignored its<span class="option">--os</span> option.</p></li><li><p> The internal method of <code>download.file()</code> was notreporting file sizes and progress correctly on files larger than2GB (inherited from <code>libxml2</code>). This is corrected for 64-bitbuilds (32-bit platforms may not support such files, but wherepossible will be supported in future versions of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>).</p></li><li><p> Work around a bug in OS X Yosemite where key environmentvariables may be duplicated causing issues in subprocesses. Theduplicates are now removed on <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> startup (<em>via</em>Rprofile). (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=16042">PR#16042</a>)</p></li><li><p> Adjust X11 auto-launch detection in DISPLAY on OS X torecognize latest XQuartz.</p></li></ul><h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.1.1</h3><h4>NEW FEATURES</h4><ul><li><p> When <code>attach()</code> reports conflicts, it does socompatibly with <code>library()</code> by using <code>message()</code>.</p></li><li> <p><code>R CMD Sweave</code> no longer cleans any files bydefault, compatibly with versions of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> prior to 3.1.0. There arenew options <span class="option">--clean</span>, <span class="option">--clean=default</span> and<span class="option">--clean=keepOuts</span>.</p></li><li> <p><code>tools::buildVignette()</code> and <code>tools::buildVignettes()</code>with <code>clean = FALSE</code> no longer remove any created files.<code>buildvignette()</code> gains a <code>keep</code> argument for morecleaning customization.</p></li><li><p> The Bioconductor ‘version’ used by<code>setRepositories()</code> can now be set by environment variable<span class="env">R_BIOC_VERSION</span> at runtime, not just when <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> is installed.(It has been stated that Bioconductor will switch from‘version’ 2.14 to ‘version’ 3.0 during the lifetimeof the <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.1 series.)</p></li><li><p> Error messages from bugs in embedded <span class="samp">Sexpr</span> codein Sweave documents now report the source location.</p></li><li> <p><code>type.convert()</code>, <code>read.table()</code> and similar<code>read.*()</code> functions get a new <code>numerals</code> argument,specifying how numeric input is converted when its conversion todouble precision loses accuracy. The default value,<code>"allow.loss"</code> allows accuracy loss, as in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> versions before3.1.0.</p></li><li><p> For some compilers, integer addition could overflow withouta warning. <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>'s internal code for both integer addition andsubtraction is more robust now. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15774">PR#15774</a>)</p></li><li><p> The function determining the default number of knots for<code>smooth.spline()</code> is now exported, as <code>.nknots.smspl()</code>.</p></li><li> <p><code>dbeta(, a,b)</code>, <code>pbeta()</code>, <code>qbeta()</code> and<code>rbeta()</code> are now defined also for <i>a = 0</i>, <i>b = 0</i>,or infinite <i>a</i> and <i>b</i> (where they typically returned<code>NaN</code> before).</p></li><li><p> Many package authors report that the RStudio graphics devicedoes not work correctly with their package's use of<code>dev.new()</code>. The new option <code>dev.new(noRStudioGD =TRUE)</code> replaces the RStudio override by the default device asselected by <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> itself, still respecting environment variables<span class="env">R_INTERACTIVE_DEVICE</span> and <span class="env">R_DEFAULT_DEVICE</span>.</p></li><li> <p><code>readRDS()</code> now returns visibly.</p></li><li><p> Modifying internal logical scalar constants now results inan error instead of a warning.</p></li><li> <p><code>install.packages(repos = NULL)</code> now accepts<span class="samp">http://</span> or <span class="samp">ftp://</span> URLs of package archives as wellas file paths, and will download as required. In most cases<code>repos = NULL</code> can be deduced from the extension of the URL.</p></li><li><p> The warning when using partial matching with the <code>$</code>operator on data frames is now only given when<code>options("warnPartialMatchDollar")</code> is <code>TRUE</code>.</p></li><li><p> Package help requests like <code>package?foo</code> nowtry the package <code>foo</code> whether loaded or not.</p></li><li><p> General help requests now default to trying all loadedpackages, not just those on the search path.</p></li><li><p> Added a new function <code>promptImport()</code>, to generate ahelp page for a function that was imported from another package(and presumably re-exported, or help would not be needed).</p></li></ul><h4>INSTALLATION and INCLUDED SOFTWARE</h4><ul><li> <p><code>configure</code> option <span class="option">--with-internal-tzcode</span>can now be used with variable <code>rsharedir</code>.</p></li><li><p> The included version of PCRE has been updated to 8.35.</p></li><li><p> There is a new target <code>make uninstall-libR</code> toremove an installed shared/static ‘<span class="file">libR</span>’.</p><p><code>make install-libR</code> now works if a sub-architecture isused, although the user will need to specify <code>libdir</code>differently for different sub-architectures.</p></li><li><p> There is more extensive advice on which LaTeX packages arerequired to install <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> or to make package manuals (as done by<code>R CMD check</code>) in the ‘Writing R Extensions’manual.</p></li><li><p> Compilers/linkers were handling the visibility control in‘<span class="file">src/extra/xz</span>’ inconsistently (and apparently in some casesincorrectly), so it has been simplified. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15327">PR#15327</a>)</p></li><li><p> (Windows) There is updated support for the use of ICU forcollation: see the ‘R Installation and Administration Manual’.</p></li></ul><h4>BUG FIXES</h4><ul><li> <p><code>dbinom(x, n)</code>, <code>pbinom()</code>, <code>dpois()</code>, etc,are slightly less restrictive in checking if <code>n</code> isinteger-valued. (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15734">PR#15734</a>.)</p></li><li> <p><code>pchisq(x, df, ncp, log.p = TRUE)</code> is more accurate andno longer underflows for small <code>x</code> and <code>ncp < 80</code>, e.g,for <code>pchisq(1e-5, df = 100, ncp = 1, log = TRUE)</code>.(Based on <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15635">PR#15635</a> and a suggestion by Roby Joehanes.)</p></li><li><p> The <code>s</code> (“step into”) command in the debuggerwould cause <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> to step into expressions evaluated there,not just into functions being debugged. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15770">PR#15770</a>)</p></li><li><p> The C code used by <code>strptime()</code> rejected time-zoneoffsets of more than <code>+1200</code> (<code>+1245</code>, <code>+1300</code> and<code>+1400</code> can occur). (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15768">PR#15768</a>)</p></li><li><p> (Windows only.)<code>png(type = "cairo", antialias = "gray")</code>was not accepted. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15760">PR#15760</a>)</p></li><li><p> Use of <code>save(..., envir=)</code> with named objects couldfail. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15758">PR#15758</a>)</p></li><li> <p><code>Sweave()</code> mis-parsed <span class="samp">Sexpr</span> expressions thatcontained backslashes. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15779">PR#15779</a>)</p></li><li><p> The return value from <code>options(foo = NULL)</code> was notthe previous value of the option. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15781">PR#15781</a>)</p></li><li> <p><code>enc2utf8()</code> and <code>enc2native()</code> did not alwaysmark the encoding of the return values when it was known.</p></li><li> <p><code>dnbinom(x, size = <large>, mu, log = TRUE)</code> no longerunderflows to -Inf for large <code>mu</code>, thanks to a suggestionfrom Alessandro Mammana (MPI MolGen, Berlin).</p></li><li> <p><code>pbeta(x, a, b, log = TRUE)</code> no longer behavesdiscontinuously (in a small x-region) because of denormalizednumbers. Also, <code>pbeta(1-1e-12, 1e30, 1.001, log=TRUE)</code> nowterminates “in real time”.</p></li><li><p> The <code>"CRAN"</code> filter (see <code>available.packages()</code>)no longer removes duplicates other than of packages on CRAN, anddoes not fail if there is no CRAN repository in<code>getOption("repos")</code>.</p></li><li><p> The device listing from <code>dev2bitmap()</code> and<code>bitmap()</code> was truncated to 1000 characters: modern versionsof GhostScript on most platforms have many more devices.</p></li><li><p> (Windows.) Commands such as <code>Sys.which()</code> and<code>pipe()</code> which needed to find the full path to a commandcould segfault if the ‘long’ path name was much longer thanthe ‘short’ path name (which <code>Sys.which()</code> returns),as the behaviour of the Windows API call had changed.</p></li><li> <p><code>R CMD build</code> will fail with an error if one of thepackages specified in the <span class="samp">VignetteBuilder</span> field is notinstalled. (Without loading those packages it cannot beascertained which files are intended to be vignettes. This meansthat the <span class="samp">VignetteBuilder</span> packages have to be installed forpackage checking too.)(Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15775">PR#15775</a>.)</p></li><li><p> Misguided attempts to use <code>chull()</code> with non-finitepoints now give an error (related to <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15777">PR#15777</a>).</p></li><li><p> For a formula with exactly 32 variables the 32nd variablewas aliased to the intercept in some C-level computations ofterms, so that for example attempting to remove it would removethe intercept instead (and leave a corrupt internal structure).(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15735">PR#15735</a>)</p></li><li> <p><code>anyDuplicated()</code> silently returned wrong values whenthe first duplicate was at an index which was too large to bestored in an integer vector (although a lot of RAM and patiencewould have been needed to encounter this).</p></li><li> <p><code>tools::Rd2ex(commentDontrun = FALSE)</code> failed if theblock had only one line.</p></li><li><p> Hexadecimal constants such as <code>0x110p-5L</code> which wereincorrectly qualified by <code>L</code> were parsed incorrectly since <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>3.0.0, with a slightly garbled warning. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15753">PR#15753</a>)</p></li><li> <p><code>system()</code> returned success on some platforms even ifthe system was unable to launch a process. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15796">PR#15796</a>)</p></li><li><p> (Windows <code>Rgui</code> console.) Unbuffered output wassometimes not output immediately if the prompt was not on the lastline of the console.</p></li><li><p> The built-in help server did not declare the encoding forthe ‘<span class="file">DESCRIPTION</span>’ or other text files to be the packageencoding, so non-ASCII characters could be displayed incorrectly.</p></li><li> <p><span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> is now trying harder to not cleanup child processesthat were not spawned by <code>mcparallel()</code> on platforms thatprovide information about the source process of the <code>SIGCHLD</code>signal. This allows 3rd party libraries to manage the exit statusof children that they spawn without <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> interfering.</p></li><li> <p><code>mcmapply()</code> was only parallelizing if the number ofjobs was bigger than the number of cores. It now parallelizes ifthe number of jobs is more than one.</p></li><li><p> Auto-printing would re-evaluate its argument when trying todispatch to a print method. This is now avoided when possible.</p></li><li><p> Unserializing (including <code>load()</code> and <code>readRDS()</code>)could silently return incorrect numeric values from ASCII saves ifthere was a read error.</p></li><li> <p><code>getParseData()</code> could return incorrect values forthe parents of some elements. (Reported by Andrew Redd.)</p></li><li><p> Attempting to use data frames of 2^31 or more rows with<code>merge()</code> or to create a merged data frame of that size nowgives a clearer error message.</p></li><li> <p><code>parse()</code> did not check its <code>file</code> argument was aconnection if it was not a character string, soe.g. <code>parse(FALSE)</code> attempted to read from <code>stdin</code>.</p><p>Nor did <code>dump()</code> and <code>dput()</code>.</p></li><li><p> The <code>"help.try.all.packages"</code> option was ignored whenthe shortcut syntax for help was used, e.g. <code>?foo</code>.</p></li><li><p> A potential segfault in string allocation has been fixed.(Found by Radford Neal.)</p></li><li><p> Potential memory protection errors in <code>sort()</code> and<code>D()</code> have been fixed. (Found by Radford Neal.)</p></li><li><p> Fixed a lack of error checking in graphics event functions.(Found by Radford Neal; a different patch used here than theone in pqR.)</p></li><li> <p><code>numericDeriv()</code> sometimes miscalculated the gradient.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15849">PR#15849</a>, reported originally by Radford Neal)</p></li></ul><h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.1.0</h3><h4>NEW FEATURES</h4><ul><li> <p><code>type.convert()</code> (and hence by default<code>read.table()</code>) returns a character vector or factor whenrepresenting a numeric input as a double would lose accuracy.Similarly for complex inputs.</p><p>If a file contains numeric data with unrepresentable numbers ofdecimal places that are intended to be read as numeric, specify<code>colClasses</code> in <code>read.table()</code> to be <code>"numeric"</code>.</p></li><li> <p><code>tools::Rdiff(useDiff = FALSE)</code> is closer to the POSIXdefinition of <code>diff -b</code> (as distinct from the descriptionin the <code>man</code> pages of most systems).</p></li><li><p> New function <code>anyNA()</code>, a version of<code>any(is.na(.))</code> which is fast for atomic vectors, based on aproposal by Tim Hesterberg. (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15239">PR#15239</a>.)</p></li><li> <p><code>arrayInd(*, useNames = TRUE)</code> and, analogously,<code>which(*, arr.ind = TRUE)</code> now make use of<code>names(.dimnames)</code> when available.</p></li><li> <p><code>is.unsorted()</code> now also works for <code>raw</code> vectors.</p></li><li><p> The <code>"table"</code> method for <code>as.data.frame()</code> (alsouseful as <code>as.data.frame.table()</code>) now passes <code>sep</code> and<code>base</code> arguments to <code>provideDimnames()</code>.</p></li><li> <p><code>uniroot()</code> gets new optional arguments, notably<code>extendInt</code>, allowing to auto-extend the search interval whenneeded. The return value has an extra component, <code>init.it</code>.</p></li><li> <p><code>switch(f, ...)</code> now warns when <code>f</code> is a factor,as this typically happens accidentally where the useR meant topass a character string, but <code>f</code> is treated as integer (asalways documented).</p></li><li><p> The parser has been modified to use less memory.</p></li><li><p> The way the unary operators (<code>+ - !</code>) handle attributesis now more consistent. If there is no coercion, all attributes(including class) are copied from the input to the result:otherwise only names, dims and dimnames are.</p></li><li> <p><code>colorRamp()</code> and <code>colorRampPalette()</code> now allownon-opaque colours and a ramp in opacity <em>via</em> the new argument<code>alpha = TRUE</code>. (Suggested by Alberto Krone-Martins, butoptionally as there are existing uses which expect only RGB values.)</p></li><li> <p><code>grid.show.layout()</code> and <code>grid.show.viewport()</code>get an optional <code>vp.ex</code> argument.</p></li><li><p> There is a new function <code>find_gs_cmd()</code> in the<span class="pkg">tools</span> package to locate a GhostScript executable. (This isan enhanced version of a previously internal function there.)</p></li><li> <p><code>object.size()</code> gains a <code>format()</code> method.</p></li><li><p> There is a new family, <code>"ArialMT"</code>, for the<code>pdf()</code> and <code>postscript()</code> devices. This will only berendered correctly on viewers which have access to MonotypeTrueType fonts (which are sometimes requested by journals).</p></li><li><p> The text and PDF news files, including ‘<span class="file">NEWS</span>’ and‘<span class="file">NEWS.2</span>’, have been moved to the ‘<span class="file">doc</span>’ directory.</p></li><li> <p><code>combn(x, simplify = TRUE)</code> now gives a factor resultfor factor input <code>x</code> (previously user error).(Related to <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15442">PR#15442</a>.)</p></li><li><p> Added <code>utils::fileSnapshot()</code> and<code>utils::changedFiles()</code> functions to allow snapshots andcomparison of directories of files.</p></li><li> <p><code>make.names(names, unique=TRUE)</code> now tries to preserveexisting names. (Suggestion of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15452">PR#15452</a>.)</p></li><li><p> New functions <code>cospi(x)</code>, <code>sinpi(x)</code>, and<code>tanpi(x)</code>, for more accurate computation of<code>cos(pi*x)</code>, etc, both in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> and the C API. Using thesegains accuracy in some cases, e.g., inside <code>lgamma()</code> or<code>besselI()</code>. (Suggested by Morten Welinder in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15529">PR#15529</a>.)</p></li><li> <p><code>print.table(x, zero.print = ".")</code> now also has aneffect when <code>x</code> is not integer-valued.</p></li><li><p> There is more support to explore the system's idea oftime-zone names. <code>Sys.timezone()</code> tries to give the currentsystem setting by name (and succeeds at least on Linux, OS X,Solaris and Windows), and <code>OlsonNames()</code> lists the names inthe system's Olson database. <code>Sys.timezone(location = FALSE)</code>gives the previous behaviour.</p></li><li><p> Platforms with a 64-bit <code>time_t</code> type are allowed tohandle conversions between the <code>"POSIXct"</code> and<code>"POSIXlt"</code> classes for date-times outside the 32-bit range(before 1902 or after 2037): the existing workarounds are used onother platforms. (Note that time-zone information for post-2037is speculative at best, and the OS services are tested for knownerrors and so not used on OS X.)</p><p>Currently <code>time_t</code> is usually <code>long</code> and hence 64-bit onUnix-alike 64-bit platforms: however in several cases thetime-zone database is 32-bit. For <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> for Windows it is 64-bit(for both architectures as from this version).</p></li><li><p> The <code>"save.defaults"</code> option can include a value for<code>compression_level</code>. (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15579">PR#15579</a>.)</p></li><li> <p><code>colSums()</code> and friends now have support for arrays anddata-frame columns with <i>2^31</i> or more elements.</p></li><li> <p><code>as.factor()</code> is faster when <code>f</code> is an unclassedinteger vector (for example, when called from <code>tapply()</code>).</p></li><li> <p><code>fft()</code> now works with longer inputs, from the 12million previously supported up to 2 billion. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15593">PR#15593</a>)</p></li><li><p> Complex <code>svd()</code> now uses LAPACK subroutine<code>ZGESDD</code>, the complex analogue of the routine used for thereal case.</p></li><li><p> Sweave now outputs ‘<span class="file">.tex</span>’ files in UTF-8 if theinput encoding is declared to be UTF-8, regardless of thelocal encoding. The UTF-8 encoding may now be declared usinga LaTeX comment containing the string <code>%\SweaveUTF8</code>on a line by itself.</p></li><li> <p><code>file.copy()</code> gains a <code>copy.date</code> argument.</p></li><li><p> Printing of date-times will make use of the time-zoneabbreviation in use at the time, if known. For example, for Parispre-1940 this could be <span class="samp">LMT</span>, <span class="samp">PMT</span>, <span class="samp">WET</span> or<span class="samp">WEST</span>. To enable this, the <code>"POSIXlt"</code> class has anoptional component <code>"zone"</code> recording the abbreviation foreach element.</p><p>For platforms which support it, there is also a component<code>"gmtoff"</code> recording the offset from GMT where known.</p></li><li><p> (On Windows, by default on OS X and optionally elsewhere.)The system C function <code>strftime</code> has been replaced by a morecomprehensive version with closer conformance to the POSIX 2008standard.</p></li><li> <p><code>dnorm(x, log = FALSE)</code> is more accurate (but somewhatslower) for |x| > 5; as suggested in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15620">PR#15620</a>.</p></li><li><p> Some versions of the <code>tiff()</code> device have furthercompression options.</p></li><li> <p><code>read.table()</code>, <code>readLines()</code> and <code>scan()</code>have a new argument to influence the treatment of embedded nuls.</p></li><li><p> Avoid duplicating the right hand side values in complexassignments when possible. This reduces copying of replacementvalues in expressions such as <code>Z$a <- a0</code> and<code>ans[[i]] <- tmp</code>: some package code has relied on therebeing copies.</p><p>Also, a number of other changes to reduce copying of objects; allcontributed by or based on suggestions by Michael Lawrence.</p></li><li><p> The <code>fast</code> argument of <code>KalmanLike()</code>,<code>KalmanRun()</code> and <code>KalmanForecast()</code> has been replacedby <code>update</code>, which instead of updating <code>mod</code> in place,optionally returns the updated model in an attribute <code>"mod"</code>of the return value.</p></li><li> <p><code>arima()</code> and <code>makeARIMA()</code> get a new optionalargument <code>SSinit</code>, allowing the choice of a different<b>s</b>tate <b>s</b>pace initialization which has been observedto be more reliable close to non-stationarity: see <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14682">PR#14682</a>.</p></li><li> <p><code>warning()</code> has a new argument <code>noBreaks.</code>, tosimplify post-processing of output with <code>options(warn = 1)</code>.</p></li><li> <p><code>pushBack()</code> gains an argument <code>encoding</code>, tosupport reading of UTF-8 characters using <code>scan()</code>,<code>read.table()</code> and related functions in a non-UTF-8 locale.</p></li><li> <p><code>all.equal.list()</code> gets a new argument <code>use.names</code>which by default labels differing components by names (if theymatch) rather than by integer index. Saved <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> output in packages mayneed to be updated.</p></li><li><p> The methods for <code>all.equal()</code> and<code>attr.all.equal()</code> now have argument <code>check.attributes</code>after <code>...</code> so it cannot be partially nor positionallymatched (as it has been, unintentionally).</p><p>A side effect is that some previously undetected errors of passingempty arguments (no object between commas) to <code>all.equal()</code>are detected and reported.</p><p>There are explicit checks that <code>check.attributes</code> is logical,<code>tolerance</code> is numeric and <code>scale</code> is <code>NULL</code> ornumeric. This catches some unintended positional matching.</p><p>The message for <code>all.equal.numeric()</code> reports a<code>"scaled difference"</code> only for <code>scale != 1</code>.</p></li><li> <p><code>all.equal()</code> now has a <code>"POSIXt"</code> methodreplacing the <code>"POSIXct"</code> method.</p></li><li><p> The <code>"Date"</code> and <code>"POSIXt"</code> methods of<code>seq()</code> allows <code>by = "quarter"</code> for completeness(<code>by = "3 months"</code> always worked).</p></li><li> <p><code>file.path()</code> removes any trailing separator onWindows, where they are invalid (although sometimes accepted).This is intended to enhance the portability of code written bythose using POSIX file systems (where a trailing <code>/</code> can beused to confine path matching to directories).</p></li><li><p> New function <code>agrepl()</code> which like <code>grepl()</code>returns a logical vector.</p></li><li> <p><code>fifo()</code> is now supported on Windows. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15600">PR#15600</a>)</p></li><li> <p><code>sort.list(method = "radix")</code> now allows negativeintegers (wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15644">PR#15644</a>).</p></li><li><p> Some functionality of <code>print.ts()</code> is now available in<code>.preformat.ts()</code> for more modularity.</p></li><li> <p><code>mcparallel()</code> gains an option <code>detach = TRUE</code>which allows execution of code independently of the currentsession. It is based on a new <code>estranged = TRUE</code> argument to<code>mcfork()</code> which forks child processes such that they becomeindependent of the parent process.</p></li><li><p> The <code>pdf()</code> device omits circles and text at extremelysmall sizes, since some viewers were failing on such files.</p></li><li><p> The rightmost break for the <code>"months"</code>,<code>"quarters"</code> and <code>"years"</code> cases of<code>hist.POSIXlt()</code> has been increased by a day. (Inter alia,fixes <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15717">PR#15717</a>.)</p></li><li><p> The handling of <code>DF[i,] <- a</code> where <code>i</code> is oflength 0 is improved. (Inter alia, fixes <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15718">PR#15718</a>.)</p></li><li> <p><code>hclust()</code> gains a new method <code>"ward.D2"</code> whichimplements Ward's method correctly. The previous <code>"ward"</code>method is <code>"ward.D"</code> now, with the old name still working.Thanks to research and proposals by Pierre Legendre.</p></li><li><p> The <code>sunspot.month</code> dataset has been amended andupdated from the official source, whereas the <code>sunspots</code> and<code>sunspot.year</code> datasets will remain immutable. Thedocumentation and source links have been updated correspondingly.</p></li><li><p> The <code>summary()</code> method for <code>"lm"</code> fits warns ifthe fit is essentially perfect, as most of the summary may becomputed inaccurately (and with platform-dependent values).</p><p>Programmers who use <code>summary()</code> in order to extract justa component which will be reliable (e.g., <code>$cov.unscaled</code>)should wrap their calls in <code>suppressWarnings()</code>.</p></li></ul><h4>INSTALLATION and INCLUDED SOFTWARE</h4><ul><li><p> The included version of LAPACK has been updated to 3.5.0.</p></li><li><p> There is some support for parallel testing of aninstallation, by setting <span class="env">TEST_MC_CORES</span> to an integergreater than one to indicate the maximum number of cores to beused in parallel. (It is worth specifying at least 8 cores ifavailable.) Most of these require a <code>make</code> program (suchas GNU <code>make</code> and <code>dmake</code>) which supports the<code>$MAKE -j nproc</code> syntax.</p><p>Except on Windows: the tests of standard package examples in<code>make check</code> are done in parallel. This also applies torunning <code>tools::testInstalledPackages()</code>.</p><p>The more time-consuming regression tests are done in parallel.</p><p>The package checks in <code>make check-devel</code> and <code>makecheck-recommended</code> are done in parallel.</p></li><li><p> More of <code>make check</code> will work if recommended packagesare not installed: but recommended packages remain needed forthorough checking of an <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> build.</p></li><li><p> The version of <span class="samp">tzcode</span> included in‘<span class="file">src/extra/tzone</span>’ has been updated. (Formerly used only onWindows.)</p></li><li><p> The included (64-bit) time-zone conversion code and Olsontime-zone database can be used instead of the system version: use<code>configure</code> option <span class="option">--with-internal-tzcode</span>. Thisis the default on Windows and OS X. (Note that this does notcurrently work if a non-default <code>rsharedir</code><code>configure</code> variable is used.)</p><p>(It might be necessary to set environment variable <span class="env">TZ</span> onOSes where this is not already set, although the system timezone isdeduced correctly on at least Linux, OS X and Windows.)</p><p>This option also switches to the version of <code>strftime</code>included in directory ‘<span class="file">src/extra/tzone</span>’.</p></li><li> <p><code>configure</code> now tests for a C++11-compliant compilerby testing some basic features. This by default tries flags forthe compiler specified by <span class="samp">CXX</span>, but an alternative compiler,options and standard can be specified by variables <span class="samp">CXX1X</span>,<span class="samp">CXX1XFLAGS</span> and <span class="samp">CXX1XSTD</span> (e.g., <span class="samp">-std=gnu++11</span>).</p></li><li> <p><span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> can now optionally be compiled to use referencecounting instead of the <code>NAMED</code> mechanism by defining<code>SWITCH_TO_REFCNT</code> in ‘<span class="file">Rinternals.h</span>’. This may becomethe default in the future.</p></li><li><p> There is a new option <span class="option">--use-system-tre</span> to use asuitable system <span class="pkg">tre</span> library: at present this means a versionfrom their <code>git</code> repository, after corrections.(Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15660">PR#15660</a>.)</p></li></ul><h4>PACKAGE INSTALLATION</h4><ul><li><p> The <code>CRANextra</code> repository is no longer a defaultrepository on Windows: all the binary versions of packages fromCRAN are now on CRAN, although <code>CRANextra</code> contains packagesfrom Omegahat and elsewhere used by CRAN packages.</p></li><li><p> Only vignettes sources in directory ‘<span class="file">vignettes</span>’ areconsidered to be vignettes and hence indexed as such.</p></li><li><p> In the ‘<span class="file">DESCRIPTION</span>’ file, </p><pre> License: X11</pre><p>is no longer recognized as valid. Use <span class="samp">MIT</span> or<span class="samp">BSD_2_clause</span> instead, both of which need <span class="samp">+ file LICENSE</span>.</p></li><li><p> For consistency, entries in ‘<span class="file">.Rinstignore</span>’ are now matchedcase-insensitively on all platforms.</p></li><li><p> Help for S4 methods with very long signatures now triesharder to split the description in the <span class="samp">Usage</span> field to nomore than 80 characters per line (some packages had over 120characters).</p></li><li> <p><code>R CMD INSTALL --build</code> (not Windows) now defaults tothe internal <code>tar()</code> unless <span class="env">R_INSTALL_TAR</span> is set.</p></li><li><p> There is support for compiling C++11 code in packages onsuitable platforms: see ‘Writing R Extensions’.</p></li><li><p> Fake installs now install the contents of directory‘<span class="file">inst</span>’: some packages use this to install e.g. C++ headersfor use by other packages that are independent of the packageitself. Option <span class="option">--no-inst</span> can be used to get the previousbehaviour.</p></li></ul><h4>DEBUGGING</h4><ul><li><p> The behaviour of the code browser has been made moreconsistent, in part following the suggestions in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14985">PR#14985</a>.</p></li><li><p> Calls to <code>browser()</code> are now consistent with callsto the browser triggered by <code>debug()</code>, in that <kbd>Enter</kbd>will default to <code>n</code> rather than <code>c</code>.</p></li><li><p> A new browser command <code>s</code> has been added, to“step into” function calls.</p></li><li><p> A new browser command <code>f</code> has been added, to“finish” the current loop or function.</p></li><li><p> Within the browser, the command <code>help</code> willdisplay a short list of available commands.</p></li></ul><h4>UTILITIES</h4><ul><li><p> Only vignettes sources in directory ‘<span class="file">vignettes</span>’ areconsidered to be vignettes by <code>R CMD check</code>. That hasbeen the preferred location since <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.14.0 and is now obligatory.</p></li><li><p> For consistency, <code>R CMD build</code> now matches entriesin ‘<span class="file">.Rbuildignore</span>’ and ‘<span class="file">vignettes/.install_extras</span>’case-insensitively on all platforms (not just on Windows).</p></li><li> <p><code>checkFF()</code> (called by <code>R CMD check</code> bydefault) can optionally check foreign function calls forconsistency with the registered type and argument count. This isthe default for <code>R CMD check --as-cran</code> or can be enabledby setting environment variable <span class="env">_R_CHECK_FF_CALLS_</span> to<span class="samp">registration</span> (but is in any case suppressed by<span class="option">--install=no</span>). Because this checks calls in which<code>.NAME</code> is an <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> object and not just a literal characterstring, some other problems are detected for such calls.</p><p>Functions <code>suppressForeignCheck()</code> and <code>dontCheck()</code>have been added to allow package authors to suppress falsepositive reports.</p></li><li> <p><code>R CMD check --as-cran</code> warns about a false value ofthe ‘<span class="file">DESCRIPTION</span>’ field <span class="samp">BuildVignettes</span> for Open Sourcepackages, and ignores it. (An Open Source package needs to havecomplete sources for its vignettes which should be usable on asuitably well-equipped system).</p></li><li> <p><code>R CMD check --no-rebuild-vignettes</code> is defunct:<br /><code>R CMD check --no-build-vignettes</code> has been preferred since<span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.0.0.</p></li><li> <p><code>R CMD build --no-vignettes</code> is defunct:<br /><code>R CMD build --no-build-vignettes</code> has been preferred since<span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.0.0.</p></li><li> <p><code>R CMD Sweave</code> and <code>R CMD Stangle</code> nowprocess both Sweave and non-Sweave vignettes. The<code>tools::buildVignette()</code> function has been added to do thesame tasks from within <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>.</p></li><li><p> The flags returned by <code>R CMD config --ldflags</code> and(where installed) <code>pkg-config --libs libR</code> are now thoseneeded to link a front-end against the (shared or static) <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>library.</p></li><li> <p>‘<span class="file">Sweave.sty</span>’ has a new option <span class="samp">[inconsolata]</span>.</p></li><li> <p><code>R CMD check</code> customizations such as<span class="env">_R_CHECK_DEPENDS_ONLY_</span> make available packages only in<span class="samp">LinkingTo</span> only for installation, and not forloading/runtime tests.</p></li><li> <p><code>tools::checkFF()</code> reports on <code>.C</code> and<code>.Fortran</code> calls with <code>DUP = FALSE</code> if argument<code>check_DUP</code> is true. This is selected by<code>R CMD check</code> by default.</p></li><li> <p><code>R CMD check --use-gct</code> can be tuned togarbage-collect less frequently using <code>gctorture2()</code><em>via</em> the setting of environment variable<span class="env">_R_CHECK_GCT_N_</span>.</p></li><li><p> Where supported, <code>tools::texi2dvi()</code> limits the numberof passes tried to 20.</p></li></ul><h4>C-LEVEL FACILITIES</h4><ul><li><p> (Windows only) A function <code>R_WaitEvent()</code> has beenadded (with declaration in header‘<span class="file">R.h</span>’) to block executionuntil the next event is received by <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>.</p></li><li><p> Remapping in the ‘<span class="file">Rmath.h</span>’ header can be suppressed bydefining <span class="samp">R_NO_REMAP_RMATH</span>.</p></li><li><p> The remapping of <code>rround()</code> in header ‘<span class="file">Rmath.h</span>’has been removed: use <code>fround()</code> instead.</p></li><li> <p><code>ftrunc()</code> in header ‘<span class="file">Rmath.h</span>’ is now a wrapperfor the C99 function <code>trunc()</code>, which might as well be usedin C code: <code>ftrunc()</code> is still needed for portable C++ code.</p></li><li><p> The never-documented remapping of <code>prec()</code> to<code>fprec()</code> in header ‘<span class="file">Rmath.h</span>’ has been removed.</p></li><li><p> The included LAPACK subset now contains <code>ZGESDD</code> and<code>ZGELSD</code>.</p></li><li><p> The function <code>LENGTH()</code> now checks that it is onlyapplied to vector arguments. However, in packages <code>length()</code>should be used. (In <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> itself <code>LENGTH()</code> is a macro withoutthe function overhead of <code>length()</code>.)</p></li><li><p> Calls to <code>SET_VECTOR_ELT()</code> and <code>SET_STRING_ELT()</code>are now checked for indices which are in-range: several packageswere writing one element beyond the allocated length.</p></li><li> <p><code>allocVector3</code> has been added which allows customallocators to be used for individual vector allocations.</p></li></ul><h4>DEPRECATED AND DEFUNCT</h4><ul><li> <p><code>chol(pivot = TRUE, LINPACK = TRUE)</code> is defunct.</p><p>Arguments <code>EISPACK</code> for <code>eigen()</code> and <code>LINPACK</code> for<code>chol()</code>, <code>chol2inv()</code>, <code>solve()</code> and <code>svd()</code>are ignored: LAPACK is always used.</p></li><li> <p><code>.find.package()</code> and <code>.path.package()</code> aredefunct: only the versions without the initial dot introduced in<span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.13.0 have ever been in the API.</p></li><li><p> Partial matching when using the <code>$</code> operator <em>ondata frames</em> now throws a warning and may become defunct in thefuture. If partial matching is intended, replace <code>foo$bar</code>by <code>foo[["bar", exact = FALSE]]</code>.</p></li><li><p> The long-deprecated use of <code>\synopsis</code> in the<span class="samp">Usage</span> section of ‘<span class="file">.Rd</span>’ files has been removed: suchsections are now ignored (with a warning).</p></li><li> <p><code>package.skeleton()</code>'s deprecated argument<code>namespace</code> has been removed.</p></li><li><p> Many methods are no longer exported by package <span class="pkg">stats</span>.They are all registered on their generic, which should be calledrather than calling a method directly.</p></li><li><p> Functions <code>readNEWS()</code> and <code>checkNEWS()</code> inpackage <span class="pkg">tools</span> are defunct.</p></li><li> <p><code>download.file(method = "lynx")</code> is deprecated.</p></li><li> <p><code>.C(DUP = FALSE)</code> and <code>.Fortran(DUP = FALSE)</code> arenow deprecated, and may be disabled in future versions of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>. Astheir help has long said, <code>.Call()</code> is much preferred.</p><p><code>R CMD check</code> notes such usages (by default).</p></li><li><p> The workaround of setting <span class="env">R_OSX_VALGRIND</span> has beenremoved: it is not needed in current valgrind.</p></li></ul><h4>BUG FIXES</h4><ul><li><p> Calling <code>lm.wfit()</code> with no non-zero weights gave anarray-overrun in the Fortran code and a not very sensible answer.It is now special-cased with a simpler answer (no <code>qr</code>component).</p></li><li><p> Error messages involving non-syntactic names (e.g., as producedby <code>`\r`</code> when that object does not exist) now encodethe control characters. (Reported by Hadley Wickham.)</p></li><li> <p><code>getGraphicsEvent()</code> caused 100% usage of one CPU inWindows. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15500">PR#15500</a>)</p></li><li> <p><code>nls()</code> with no <code>start</code> argument may now workinside another function (scoping issue).</p></li><li> <p><code>pbeta()</code> and similar work better for very large(billions) <code>ncp</code>.</p></li><li><p> Where time zones have changed abbreviations over the years,the software tries to more consistently use the abbreviationappropriate to the time or if that is unknown, the currentabbreviation. On some platforms where the C function<code>localtime</code> changed the <code>tzname</code> variables the reportedabbreviation could have been that of the last time converted.</p></li><li> <p><code>all.equal(list(1), identity)</code> now works.</p></li><li><p> Bug fix for pushing viewports in <span class="pkg">grid</span> (reported byJJ Allaire and Kevin Ushey).</p><p>NOTE for anyone poking around within the graphics engine displaylist (despite the warnings not to) that this changes whatis recorded by <span class="pkg">grid</span> on the graphics engine display list.</p></li><li><p> Extra checks have been added for unit resolution andconversion in <span class="pkg">grid</span>, to catch instances of division-by-zero.This may introduce error messages in existing code and/or producea different result in existing code (but only where a non-finitelocation or dimension may now become zero).</p></li><li><p> Some bugs in TRE have been corrected by updating from the<code>git</code> repository. This allows <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> to be installed on someplatforms for which this was a blocker (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15087">PR#15087</a> suggests Linuxon ARM and HP-UX).</p></li><li> <p><code>?</code> applied to a call to an S4 generic failed inseveral cases. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15680">PR#15680</a>)</p></li><li><p> The implicit S4 generics for primitives with <code>...</code> intheir argument list were incorrect. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15690">PR#15690</a>)</p></li><li><p> Bug fixes to <code>methods::callGeneric()</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15691">PR#15691</a>)</p></li><li><p> The bug fix to <code>aggregrate()</code> in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15004">PR#15004</a> introduceda new bug in the case of no grouping variables. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15699">PR#15699</a>)</p></li><li><p> In rare cases printing deeply nested lists overran a bufferby one byte and on a few platforms segfaulted. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15679">PR#15679</a>)</p></li><li><p> The dendrogram method of <code>as.dendrogram()</code> was hiddenaccidentally, (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15703">PR#15703</a>), and <code>order.dendrogram(d)</code> gavetoo much for a leaf <code>d</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15702">PR#15702</a>)</p></li><li> <p><span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> would try to kill processes on exit that have pids everused by a child process spawned by <code>mcparallel</code> even thoughthe current process with that pid was not actually its child.</p></li><li> <p><code>cophenetic()</code> applied to a <code>"dendrogram"</code> objectsometimes incorrectly returned a <code>"Labels"</code> attribute withdimensions. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15706">PR#15706</a>)</p></li><li> <p><code>printCoefmat()</code> called from quite a few <code>print()</code>methods now obeys small <code>getOption("width")</code> settings,line wrapping the <span class="samp">"signif. codes"</span> legend appropriately.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15708">PR#15708</a>)</p></li><li> <p><code>model.matrix()</code> assumed that the stored dimnames for amatrix was <code>NULL</code> or length 2, but length 1 occurred.</p></li><li><p> The clipping region for a device was sometimes used in basegraphics before it was set.</p></li></ul><h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.0.3</h3><h4>NEW FEATURES</h4><ul><li><p> On Windows there is support for making ‘<span class="file">.texi</span>’ manualsusing <code>texinfo</code> 5.0 or later: the setting is in file‘<span class="file">src/gnuwin32/MkRules.dist</span>’.</p><p>A packaging of the Perl script and modules for <code>texinfo</code>5.2 has been made available at<a href="http://www.stats.ox.ac.uk/pub/Rtools/">http://www.stats.ox.ac.uk/pub/Rtools/</a>.</p></li><li> <p><code>write.table()</code> now handles matrices of<i>2^31</i> or more elements, for those with large amountsof patience and disc space.</p></li><li><p> There is a new function, <code>La_version()</code>, to report theversion of LAPACK in use.</p></li><li><p> The HTML version of ‘An Introduction to R’ now haslinks to PNG versions of the figures.</p></li><li><p> There is some support to produce manuals in ebookformats. (See ‘<span class="file">doc/manual/Makefile</span>’. Suggested by MauroCavalcanti.)</p></li><li><p> On a Unix-alike <code>Sys.timezone()</code> returns <code>NA</code> ifthe environment variable <span class="env">TZ</span> is unset, to distinguish it froman empty string which on some OSes means the <span class="samp">UTC</span> time zone.</p></li><li><p> The backtick may now be escaped in strings, to allow namescontaining them to be constructed, e.g. <code>`\``</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15621">PR#15621</a>)</p></li><li> <p><code>read.table()</code>, <code>readLines()</code> and <code>scan()</code>now warn when an embedded nul is found in the input. (Related to<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15625">PR#15625</a> which was puzzled by the behaviour in this unsupportedcase.)</p></li><li><p> (Windows only.) <code>file.symlink()</code> works around theundocumented restriction of the Windows system call tobackslashes. (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15631">PR#15631</a>.)</p></li><li> <p><code>KalmanForecast(fast = FALSE)</code> is now the default, andthe help contains an example of how <code>fast = TRUE</code> can be usedin this version. (The usage will change in 3.1.0.)</p></li><li> <p><code>strptime()</code> now checks the locale only whenlocale-specific formats are used and caches the locale in use:this can halve the time taken on OSes with slow systemfunctions (e.g., OS X).</p></li><li> <p><code>strptime()</code> and the <code>format()</code> methods forclasses <code>"POSIXct"</code>, <code>"POSIXlt"</code> and <code>"Date"</code>recognize strings with marked encodings: this allows, for example,UTF-8 French month names to be read on (French) Windows.</p></li><li> <p><code>iconv(to = "utf8")</code> is now accepted on all platforms(some implementations did already, but GNU <span class="pkg">libiconv</span> did not:however converted strings were not marked as being in UTF-8). Theofficial name, <code>"UTF-8"</code> is still preferred.</p></li><li> <p><code>available.packages()</code> is better protected againstcorrupt metadata files. (A recurring problem with Debian package<span class="pkg">shogun-r</span>: <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14713">PR#14713</a>.)</p></li><li><p> Finalizers are marked to be run at garbage collection, butrun only at a somewhat safer later time (when interrupts arechecked). This circumvents some problems with finalizers runningarbitrary code during garbage collection (the known instances beingrunning <code>options()</code> and (C-level) <code>path.expand()</code>re-entrantly).</p></li></ul><h4>INSTALLATION and INCLUDED SOFTWARE</h4><ul><li><p> The included version of PCRE has been updated to 8.34. Thisfixes bugs and makes the behaviour closer to Perl 5.18. Inparticular, the concept of ‘space’ includes <span class="samp">VT</span> andhence agrees with POSIX's.</p></li></ul><h4>PACKAGE INSTALLATION</h4><ul><li><p> The new field <span class="samp">SysDataCompression</span> in the‘<span class="file">DESCRIPTION</span>’ file allows user control over the compressionused for ‘<span class="file">sysdata.rda</span>’ objects in the lazy-load database.</p></li><li> <p><code>install.packages(dependencies = value)</code> for <code>value =NA</code> (the default) or <code>value = TRUE</code> omits packages only in<code>LinkingTo</code> for binary package installs.</p></li></ul><h4>C-LEVEL FACILITIES</h4><ul><li><p> The long undocumented remapping of <code>rround()</code> to<code>Rf_fround()</code> in header ‘<span class="file">Rmath.h</span>’ is now formallydeprecated: use <code>fround()</code> directly.</p></li><li><p> Remapping of <code>prec()</code> and <code>trunc()</code> in the‘<span class="file">Rmath.h</span>’ header has been disabled in C++ code (it has causedbreakage with <code>libc++</code> headers).</p></li></ul><h4>BUG FIXES</h4><ul><li> <p><code>getParseData()</code> truncated the imaginary part ofcomplex number constants. (Reported by Yihui Xie.)</p></li><li> <p><code>dbeta(x, a, b)</code> with <code>a</code> or <code>b</code> within afactor of 2 of the largest representable number couldinfinite-loop. (Reported by Ioannis Kosmidis.)</p></li><li> <p><code>provideDimnames()</code> failed for arrays with a 0dimension. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15465">PR#15465</a>)</p></li><li> <p><code>rbind()</code> and <code>cbind()</code> did not handlelist objects correctly. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15468">PR#15468</a>)</p></li><li> <p><code>replayPlot()</code> now checks if it is replaying a plotfrom the same session.</p></li><li> <p><code>rasterImage()</code> and <code>grid.raster()</code> now giveerror on an empty (zero-length) raster. (Reported by Ben North.)</p></li><li> <p><code>plot.lm()</code> would sometimes scramble the labelsin plot type 5. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15458">PR#15458</a> and <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14837">PR#14837</a>)</p></li><li> <p><code>min()</code> did not handle <code>NA_character_</code> valuesproperly. (Reported by Magnus Thor Torfason.)</p></li><li><p> (Windows only.) <code>readRegistry()</code> would duplicatedefault values for keys. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15455">PR#15455</a>)</p></li><li> <p><code>str(..., strict.width = "cut")</code> did not handleit properly when more than one line needed to be cut. (Reportedby Gerrit Eichner.)</p></li><li><p> Removing subclass back-references when S4 classes wereremoved or their namespace unloaded had several bugs (e.g., <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15481">PR#15481</a>).</p></li><li> <p><code>aggregate()</code> could fail when there were too manylevels present in the <code>by</code> argument. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15004">PR#15004</a>)</p></li><li> <p><code>namespaceImportFrom()</code> needed to detect primitivefunctions when checking for duplicated imports (reported byKarl Forner).</p></li><li> <p><code>getGraphicsEvent()</code> did not exit when a user closedthe graphics window. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15208">PR#15208</a>)</p></li><li><p> Errors in vignettes were not always captured and displayedproperly. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15495">PR#15495</a>)</p></li><li> <p><code>contour()</code> could fail when dealing with extremelysmall z values. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15454">PR#15454</a>)</p></li><li><p> Several functions did not handle zero-length vectors properly,including <code>browseEnv()</code>, <code>format()</code>, <code>gl()</code>,<code>relist()</code> and <code>summary.data.frame()</code>. (E.g., <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15499">PR#15499</a>)</p></li><li> <p><code>Sweave()</code> did not restore the <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> output to theconsole if it was interrupted by a user in the middle of evaluatinga code chunk. (Reported by Michael Sumner.)</p></li><li><p> Fake installs of packages with vignettes work again.</p></li><li><p> Illegal characters in the input caused <code>parse()</code>(and thus <code>source()</code>) to segfault. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15518">PR#15518</a>)</p></li><li><p> The nonsensical use of <code>nmax = 1</code> in<code>duplicated()</code> or <code>unique()</code> is now silently ignored.</p></li><li> <p><code>qcauchy(p, *)</code> is now fully accurate even when p isvery close to 1. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15521">PR#15521</a>)</p></li><li><p> The <code>validmu()</code> and <code>valideta()</code> functions in thestandard <code>glm()</code> families now also report non-finite values,rather than failing.</p></li><li><p> Saved vignette results (in a ‘<span class="file">.Rout.save</span>’ file) werenot being compared to the new ones during <code>R CMD check</code>.</p></li><li><p> Double-clicking outside of the list box (e.g., on the scrollbar)of a Tk listbox widget generated by <code>tk_select.list()</code> nolonger causes the window to close. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15407">PR#15407</a>)</p></li><li><p> Improved handling of edge cases in<code>parallel::splitindices()</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15552">PR#15552</a>)</p></li><li><p> HTML display of results from <code>help.search()</code> and<code>??</code> sometimes contained badly constructed links.</p></li><li> <p><code>c()</code> and related functions such as <code>unlist()</code>converted raw vectors to invalid logical vectors. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15535">PR#15535</a>)</p></li><li><p> (Windows only) When a call to <code>system2()</code> specifiedone of <code>stdin</code>, <code>stdout</code> or <code>stderr</code> to be a file,but the command was not found (e.g., it contained its arguments,or the program was not on the <span class="env">PATH</span>), it left the file openand unusable until <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> terminated. (Reported by Mathew McLean.)</p></li><li><p> The <code>bmp()</code> device was not recording <code>res = NA</code>correctly: it is now recorded as 72 ppi.</p></li><li><p> Several potential problems with compiler-specific behaviourhave been identified using the ‘Undefined BehaviourSanitizer’ in conjunction with the <code>clang</code> compiler.</p></li><li> <p><code>hcl()</code> now honours <code>NA</code> inputs (previously theywere mapped to black).</p></li><li><p> Some translations in base packages were being looked up inthe main catalog rather than that for the package.</p></li><li><p> As a result of the 3.0.2 change about ‘the lastsecond before the epoch’, most conversions which should have given<code>NA</code> returned that time. (The platforms affected includeLinux and OS X, but not Windows nor Solaris.)</p></li><li> <p><code>rowsum()</code> has more support for matrices and data frameswith <i>2^31</i> or more elements. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15587">PR#15587</a>)</p></li><li> <p><code>predict(<lm object>, interval = "confidence", scale =<something>)</code> now works. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15564">PR#15564</a>)</p></li><li><p> The bug fix in 3.0.2 for <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15411">PR#15411</a> was too aggressive,and sometimes removed spaces that should not have been removed.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15583">PR#15583</a>)</p></li><li><p> Running <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> code in a <span class="pkg">tcltk</span> callback failed to set thebusy flag, which will be needed to tell OS X not to ‘App Nap’.</p></li><li><p> The code for date-times before 1902 assumed that the offsetfrom GMT in 1902 was a whole number of minutes: that was not trueof Paris (as recorded on some platforms).</p></li><li><p> Using <code>Sys.setlocale</code> to set <code>LC_NUMERIC</code> to<code>"C"</code> (to restore the sane behavior) no longer gives awarning.</p></li><li> <p><code>deparse()</code> now deparses complex vectors in a way thatre-parses to the original values. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15534">PR#15534</a>, patch based on codesubmitted by Alex Bertram.)</p></li><li><p> In some extreme cases (more than <i>10^15</i>)integer inputs to <code>dpqrxxx()</code> functions might have beenrounded up by one (with a warning about being non-integer).(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15624">PR#15624</a>)</p></li><li><p> Plotting symbol <code>pch = 14</code> had the triangle upside downon some devices (typically screen devices). The triangle issupposed to be point up. (Reported by Bill Venables.)</p></li><li> <p><code>getSrcref()</code> did not work on method definitions if<code>rematchDefinition()</code> had been used.</p></li><li> <p><code>KalmanForecast(fast = FALSE)</code> reported a (harmless)stack imbalance.</p></li><li><p> The count of observations used by <code>KalmanRun()</code> did nottake missing values into account.</p></li><li><p> In locales where the abbreviated name of one month is apartial match for the full name of a later one, the <code>%B</code>format in <code>strptime()</code> could fail. An example was French onOS X, where <span class="samp">juin</span> is abbreviated to <span class="samp">jui</span> and partiallymatches <code>juillet</code>. Similarly for weekday names.</p></li><li> <p><code>pbeta(x, a, b, log.p = TRUE)</code> sometimes underflowed tozero for very small and very differently sized <code>a</code>, <code>b</code>.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15641">PR#15641</a>)</p></li><li> <p><code>approx()</code> and <code>approxfun()</code> now handle infinitevalues with the <code>"constant"</code> method. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15655">PR#15655</a>)</p></li><li> <p><code>stripchart()</code> again respects reversed limits in<code>xlim</code> and <code>ylim</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15664">PR#15664</a>)</p></li></ul><h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.0.2</h3><h4>NEW FEATURES</h4><ul><li><p> The ‘<span class="file">NEWS</span>’ files have been re-organized.</p><p>This file contains news for <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> >= 3.0.0: news for the 0.x.y, 1.x.yand 2.x.y releases is in files ‘<span class="file">NEWS.0</span>’, ‘<span class="file">NEWS.1</span>’ and‘<span class="file">NEWS.2</span>’. The latter files are now installed when <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> isinstalled. An HTML version of news from 2.10.0 to 2.15.3 isavailable as ‘<span class="file">doc/html/NEWS.2.html</span>’.</p></li><li> <p><code>sum()</code> for integer arguments now uses an integeraccumulator of at least 64 bits and so will be more accurate inthe very rare case that a cumulative sum exceeds<i>2^53</i> (necessarily summing more than 4 millionelements).</p></li><li><p> The <code>example()</code> and <code>tools::Rd2ex()</code> functions nowhave parameters to allow them to ignore <code>\dontrun</code> markup inexamples. (Suggested by Peter Solymos.)</p></li><li> <p><code>str(x)</code> is considerably faster for very large lists,or factors with 100,000 levels, the latter as in <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15337">PR#15337</a>.</p></li><li> <p><code>col2rgb()</code> now converts factors to character stringsnot integer codes (suggested by Bryan Hanson).</p></li><li> <p><code>tail(warnings())</code> now works, <em>via</em> the new<code>`[`</code> method.</p></li><li><p> There is now support for the LaTeX style file ‘<span class="file">zi4.sty</span>’which has in some distributions replaced ‘<span class="file">inconsolata.sty</span>’.</p></li><li> <p><code>unlist(x)</code> now typically returns all non-list<code>x</code>s unchanged, not just the “vector” ones.Consequently, <code>format(lst)</code> now also works when the list<code>lst</code> has non-vector elements.</p></li><li><p> The <code>tools::getVignetteInfo()</code> function has been addedto give information about installed vignettes.</p></li><li><p> New <code>assertCondition()</code>, etc. utilities in <span class="pkg">tools</span>, usefulfor testing.</p></li><li><p> Profiling now records non-inlined calls from byte-compiledcode to <code>BUILTIN</code> functions.</p></li><li><p> Various functions in <span class="pkg">stats</span> and elsewhere that usenon-standard evaluation are now more careful to follow thenamespace scoping rules. E.g., <code>stats::lm()</code> can now find<code>stats::model.frame()</code> even if <span class="pkg">stats</span> is not on thesearch path or if some package defines a function of that name.</p></li><li><p> If an invalid/corrupt <code>.Random.seed</code> object isencountered in the workspace it is ignored with a warning ratherthan giving an error. (This allows <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> itself to rely on a workingRNG, e.g. to choose a random port.)</p></li><li> <p><code>seq()</code> and <code>seq.int()</code> give more explicit errormessages if called with invalid (e.g., <code>NaN</code>) inputs.</p></li><li><p> When <code>parse()</code> finds a syntax error, it now makespartial parse information available up to the location of theerror. (Request of Reijo Sund.)</p></li><li><p> Methods invoked by <code>NextMethod()</code> had a differentdynamic parent to the generic. This was causing trouble where S3methods invoked <em>via</em> lazy evaluation could lose track oftheir generic. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15267">PR#15267</a>)</p></li><li><p> Code for the negative binomial distribution now treats the case<code>size == 0</code> as a one-point distribution at zero.</p></li><li> <p><code>abbreviate()</code> handles without warning non-ASCII inputstrings which require no abbreviation.</p></li><li> <p><code>read.dcf()</code> no longer has a limit of 8191 bytes perline. (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15250">PR#15250</a>.)</p></li><li> <p><code>formatC(x)</code> no longer copies the class of <code>x</code> tothe result, to avoid misuse creating invalid objects as in<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15303">PR#15303</a>. A warning is given if a class is discarded.</p></li><li><p> Dataset <code>npk</code> has been copied from <a href="https://CRAN.R-project.org/package=MASS"><span class="pkg">MASS</span></a> toallow more tests to be run without recommended packages beinginstalled.</p></li><li><p> The initialization of the regression coefficients fornon-degenerate differenced models in <code>arima()</code> has beenchanged and in some examples avoids a local maximum. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15396">PR#15396</a>)</p></li><li> <p><code>termplot()</code> now has an argument <code>transform.x</code>to control the display of individual terms in the plot.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15329">PR#15329</a>)</p></li><li> <p><code>format()</code> now supports <code>digits = 0</code>, todisplay <code>nsmall</code> decimal places.</p></li><li><p> There is a new read-only <code>par()</code> parameter called<code>"page"</code>, which returns a logical value indicating whetherthe next <code>plot.new()</code> call will start a new page.</p></li><li><p> Processing Sweave and Rd documents to PDF now rendersbackticks and single quotes better in several instances, includingin <span class="samp">\code</span> and <span class="samp">\samp</span> expressions.</p></li><li> <p><code>utils::modifyList()</code> gets a new argument <code>keep.null</code>allowing <code>NULL</code> components in the replacement to be retained,instead of causing corresponding components to be deleted.</p></li><li> <p><code>tools::pkgVignettes()</code> gains argument <code>check</code>;if set to <code>TRUE</code>, it will warn when it appears a vignette requestsa non-existent vignette engine.</p></li></ul><h4>UTILITIES</h4><ul><li> <p><code>R CMD check --as-cran</code> checks the line widths inusage and examples sections of the package Rd files.</p></li><li> <p><code>R CMD check --as-cran</code> now implies <span class="option">--timings</span>.</p></li><li> <p><code>R CMD check</code> looks for command <code>gfile</code> if asuitable <code>file</code> is not found. (Although <code>file</code> isnot from GNU, OpenCSW on Solaris installs it as <code>gfile</code>.)</p></li><li> <p><code>R CMD build</code> (with the internal <code>tar</code>) checksthe permissions of ‘<span class="file">configure</span>’ and ‘<span class="file">cleanup</span>’ files andadds execute permission to the recorded permissions for thesefiles if needed, with a warning. This is useful on OSes and filesystems which do not support execute permissions (notably, onWindows).</p></li><li> <p><code>R CMD build</code> now weaves and tangles all vignettes,so suggested packages are not required during package installationif the source tarball was prepared with current<code>R CMD build</code>.</p></li><li> <p><code>checkFF()</code> (used by <code>R CMD check</code>) does abetter job of detecting calls from other packages, including notreporting those where a function has been copied from anothernamespace (e.g., as a default method). It now reports calls where<code>.NAME</code> is a symbol registered in another package.</p></li><li><p> On Unix-alike systems, <code>R CMD INSTALL</code> now installs packagesgroup writably whenever the library (<code>lib.loc</code>) is groupwritable. Hence, <code>update.packages()</code> works for other groupmembers (suggested originally and from a patch by Dirk Eddelbuettel).</p></li><li> <p><code>R CMD javareconf</code> now supports the use of symboliclinks for <span class="env">JAVA_HOME</span> on platforms which have<code>realpath</code>. So it is now possible touse </p><pre>R CMD javareconf JAVA_HOME=/usr/lib/jvm/java-1.7.0</pre><p>on a Linux system and record that value rather than thefrequently-changing full path such as‘<span class="file">/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.25.x86_64</span>’.</p></li><li><p> (Windows only.) <code>Rscript -e</code> requires a non-emptyargument for consistency with Unix versions of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>. (Also<code>Rterm -e</code> and <code>R -e</code>.)</p></li><li> <p><code>R CMD check</code> does more thorough checking ofdeclared packages and namespaces. It reports</p><ul><li><p> packages declared in more than one of the<span class="samp">Depends</span>, <span class="samp">Imports</span>, <span class="samp">Suggests</span> and<span class="samp">Enhances</span> fields of the ‘<span class="file">DESCRIPTION</span>’ file.</p></li><li><p> namespaces declared in <span class="samp">Imports</span> but notimported from, neither in the ‘<span class="file">NAMESPACE</span>’ file nor usingthe <code>::</code> nor <code>:::</code> operators.</p></li><li><p> packages which are used in <code>library()</code> or<code>requires()</code> calls in the <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> code but were already put onthe search path <em>via</em> <span class="samp">Depends</span>.</p></li><li><p> packages declared in <span class="samp">Depends</span> not imported<em>via</em> the ‘<span class="file">NAMESPACE</span>’ file (except the standardpackages). Objects used from <span class="samp">Depends</span> packages should beimported to avoid conflicts and to allow correct operation whenthe namespace is loaded but not attached.</p></li><li><p> objects imported <em>via</em> <code>:::</code> calls where<code>::</code> would do.</p></li><li><p> objects imported by <code>::</code> which are not exported.</p></li><li><p> objects imported by <code>:::</code> calls which do not exist.</p></li></ul><p>See ‘Writing R Extensions’ for good practice.</p></li><li> <p><code>R CMD check</code> optionally checks for non-standardtop-level files and directories (which are often mistakes): thisis enabled for <span class="option">--as-cran</span>.</p></li><li><p> LaTeX style file <code>upquote.sty</code> is no longer included(the version was several years old): it is no longer used in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>.A much later version is commonly included in LaTeX distributionsbut does not play well with the <code>ae</code> fonts which are thedefault for Sweave vignettes.</p></li><li> <p><code>R CMD build</code> makes more use of the ‘<span class="file">build</span>’sub-directory of package sources, for example to recordinformation about the vignettes.</p></li><li> <p><code>R CMD check</code> analyses <code>:::</code> calls.</p></li></ul><h4>INSTALLATION and INCLUDED SOFTWARE</h4><ul><li><p> The macros used for the texinfo manuals have been changed towork better with the incompatible changes made in <code>texinfo5.x</code>.</p></li><li><p> The minimum version for a system <code>xz</code> library is now5.0.3 (was 4.999). This is in part to avoid 5.0.2, which cancompress in ways other versions cannot decompress.</p></li><li><p> The included version of PCRE has been updated to 8.33.</p></li><li><p> The included version of <code>zlib</code> has been updated to1.2.8, a bug-fix release.</p></li><li><p> The included version of xz utils's <code>liblzma</code> has beenupdated to 5.0.5.</p></li><li><p> Since <code>javareconf</code> (see above) is used when <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> isinstalled, a stable link for <span class="env">JAVA_HOME</span> can be supplied then.</p></li><li><p> Configuring with <span class="option">--disable-byte-compilation</span> willoverride the ‘<span class="file">DESCRIPTION</span>’ files of recommended packages,which typically require byte-compilation.</p></li><li><p> More of the installation and checking process will work evenwhen <span class="env">TMPDIR</span> is set to a path containing spaces, but this isnot recommended and external software (such as<code>texi2dvi</code>) may fail.</p></li></ul><h4>PACKAGE INSTALLATION</h4><ul><li><p> Installation is aborted immediately if a <code>LinkingTo</code>package is not installed.</p></li><li> <p><code>R CMD INSTALL</code> has a new option<code>--no-byte-compile</code> which will override a <span class="samp">ByteCompile</span>field in the package's ‘<span class="file">DESCRIPTION</span>’ file.</p></li><li><p> License <span class="samp">BSD</span> is deprecated: use <span class="samp">BSD_3_clause</span>or <span class="samp">BSD_2_clause</span> instead.</p><p>License <span class="samp">X11</span> is deprecated: use <span class="samp">MIT</span> or<span class="samp">BSD_2_clause</span> instead.</p></li><li><p> Version requirements for <code>LinkingTo</code> packages are nowrecognized: they are checked at installation. (Fields withversion requirements were previously silently ignored.)</p></li><li><p> The limit of 500 <code>S3method</code> entries in a<code>NAMESPACE</code> file has been removed.</p></li><li><p> The default ‘version’ of Bioconductor for itspackages has been changed to the upcoming <span class="samp">2.13</span>, but thiscan be set by the environment variable <span class="env">R_BIOC_VERSION</span> when<span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> is installed.</p></li></ul><h4>C-LEVEL FACILITIES</h4><ul><li> <p>‘<span class="file">Rdefines.h</span>’ has been tweaked so it can be included inC++ code after ‘<span class="file">R_ext/Boolean.h</span>’ (which is included by‘<span class="file">R.h</span>’).</p><p>Note that ‘<span class="file">Rdefines.h</span>’ is not kept up-to-date, and‘<span class="file">Rinternals.h</span>’ is preferred for new code.</p></li><li> <p><code>eval</code> and <code>applyClosure</code> are now protectedagainst package code supplying an invalid <code>rho</code>.</p></li></ul><h4>DEPRECATED AND DEFUNCT</h4><ul><li><p> The unused <code>namespace</code> argument to<code>package.skeleton()</code> is now formally deprecated and will beremoved in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.1.0.</p></li><li> <p><code>plclust()</code> is deprecated: use the <code>plot()</code> methodfor class <code>"hclust"</code> instead.</p></li><li><p> Functions <code>readNEWS()</code> and <code>checkNEWS()</code> inpackage <span class="pkg">tools</span> are deprecated (and they have not worked withcurrent ‘<span class="file">NEWS</span>’ files for a long time).</p></li></ul><h4>DOCUMENTATION</h4><ul><li> <p>‘An Introduction to R’ has a new chapter on using <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>as a scripting language including interacting with the OS.</p></li></ul><h4>BUG FIXES</h4><ul><li> <p><code>help.request()</code> could not determine the current versionof <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> on CRAN. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15241">PR#15241</a>)</p></li><li><p> On Windows, <code>file.info()</code> failed on root directories unlessthe path was terminated with an explicit <code>"."</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15302">PR#15302</a>)</p></li><li><p> The <code>regmatches<-()</code> replacement function mishandledresults coming from <code>regexpr()</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15311">PR#15311</a>)</p></li><li><p> The help for <code>setClass()</code> and<code>representation()</code> still suggested the deprecated argument<code>representation=</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15312">PR#15312</a>)</p></li><li> <p><code>R CMD config</code> failed in an installed build of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>3.0.1 (only) when a sub-architecture was used. (Reported byBerwin Turlach.)</p></li><li><p> On Windows, the installer modified the ‘<span class="file">etc/Rconsole</span>’and ‘<span class="file">etc/Rprofile.site</span>’ files even when default options werechosen, so the MD5 sums did not refer to the installed versions.(Reported by Tal Galili.)</p></li><li> <p><code>plot(hclust(), cex =)</code> respects <code>cex</code> again(and possibly others similarly). (Reported by Peter Langfelder.)</p></li><li><p> If multiple packages were checked by <code>R CMD check</code>,and one was written for a different OS, it would set<code>--no-install</code> for all following packages as well asitself.</p></li><li> <p><code>qr.coef()</code> and related functions did not properly coercereal vectors to complex when necessary. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15332">PR#15332</a>)</p></li><li> <p><code>ftable(a)</code> now fixes up empty <code>dimnames</code> suchthat the result is printable.</p></li><li> <p><code>package.skeleton()</code> was not starting its search forfunction objects in the correct place if <code>environment</code> wassupplied. (Reported by Karl Forner.)</p></li><li><p> Parsing code was changing the length field of vectors andconfusing the memory manager. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15345">PR#15345</a>)</p></li><li><p> The Fortran routine <code>ZHER2K</code> in the reference BLAShad a comment-out bug in two places.This caused trouble with <code>eigen()</code> for Hermitian matrices.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15345">PR#15345</a> and report from Robin Hankin)</p></li><li> <p><code>vignette()</code> and <code>browseVignettes()</code> did notdisplay non-Sweave vignettes properly.</p></li><li><p> Two warning/error messages have been corrected:the (optional) warning produced by a partial name matchwith a pairlist, the error message from a zero-length argument tothe <code>:</code> operator. (Found by Radford Neal; <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15358">PR#15358</a>,<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15356">PR#15356</a>)</p></li><li> <p><code>svd()</code> returned <code>NULL</code> rather than omittingcomponents as documented. (Found by Radford Neal; <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15360">PR#15360</a>)</p></li><li> <p><code>mclapply()</code> and <code>mcparallel()</code> with<code>silent = TRUE</code> could break a process that uses<code>stdout</code> outputunguarded against broken pipes (e.g., <code>zip</code> will failsilently). To work around such issues, they now replace<code>stdout</code> with a descriptor pointed to ‘<span class="file">/dev/null</span>’instead. For this purpose, internal <code>closeStdout</code> and<code>closeStderr</code> functions have gained the <code>to.null</code> flag.</p></li><li> <p><code>log()</code>, <code>signif()</code> and <code>round()</code> now raise anerror if a single named argument is not named <code>x</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15361">PR#15361</a>)</p></li><li> <p><code>deparse()</code> now deparses raw vectors in a form thatis syntactically correct. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15369">PR#15369</a>)</p></li><li><p> The <code>jpeg</code> driver in Sweave created a JPEG file, but gaveit a ‘<span class="file">.png</span>’ extension. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15370">PR#15370</a>)</p></li><li><p> Deparsing of infix operators with named arguments isimproved. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15350">PR#15350</a>)</p></li><li> <p><code>mget()</code>, <code>seq.int()</code> and <code>numericDeriv()</code>did not duplicate arguments properly. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15352">PR#15352</a>, <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15353">PR#15353</a>,<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15354">PR#15354</a>)</p></li><li> <p><code>kmeans(algorithm = "Hartigan-Wong")</code> now always stopsiterating in the QTran stage. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15364">PR#15364</a>).</p></li><li> <p><code>read.dcf()</code> re-allocated incorrectly and so couldsegfault when called on a file with lines of more than 100 bytes.</p></li><li><p> On systems where <code>mktime()</code> does not set <code>errno</code>,the last second before the epoch could not be converted from<code>POSIXlt</code> to <code>POSIXct</code>. (Reported by Bill Dunlap.)</p></li><li> <p><code>add1.glm()</code> miscalculated F-statistics when df > 1. (BillDunlap, <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15386">PR#15386</a>).</p></li><li> <p><code>stem()</code> now discards infinite inputs rather thanhanging. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15376">PR#15376</a>)</p></li><li><p> The parser now enforces C99 syntax for floating pointhexadecimal constants (e.g., <code>0x1.1p0</code>), rather than returningunintended values for malformed constants. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15234">PR#15234</a>)</p></li><li> <p><code>model.matrix()</code> now works with very long LHSnames (more than 500 bytes). (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15377">PR#15377</a>)</p></li><li> <p><code>integrate()</code> reverts to the pre-2.12.0 behaviour: from2.12.0 to 3.0.1 it sometimes failed to achieve the requestedtolerance and reported error estimates that were exceeded.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15219">PR#15219</a>)</p></li><li> <p><code>strptime()</code> now handles <span class="samp">%W</span> fields with value0. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15915">PR#15915</a>)</p></li><li> <p><span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> is now better protected against people trying to interactwith the console in startup code. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15325">PR#15325</a>)</p></li><li><p> Subsetting 1D arrays often lost dimnames (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15301">PR#15301</a>).</p></li><li><p> Unary <code>+</code> on a logical vector did not coerce tointeger, although unary <code>-</code> did.</p></li><li> <p><code>na.omit()</code> and <code>na.exclude()</code> added a rowto a zero-row data frame. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15399">PR#15399</a>)</p></li><li><p> All the (where necessary cut-down) vignettes are installedif <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> was configured with <span class="option">--without-recommended-packages</span>.</p></li><li> <p><code>source()</code> did not display filenames when reportingsyntax errors.</p></li><li><p> Syntax error reports misplaced the caret pointing out the badtoken.</p></li><li><p> (Windows only) Starting <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> with <code>R</code> (instead of<code>Rterm</code> or <code>Rgui</code>) would lose anyzero-length strings from the command line arguments. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15406">PR#15406</a>)</p></li><li><p> Errors in the encoding specified on the command line<em>via</em> <code>--encoding=foo</code> were not handled properly.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15405">PR#15405</a>)</p></li><li><p> If <code>x</code> is a symbol, <code>is.vector(x, "name")</code> nowreturns <code>TRUE</code>, since <code>"name"</code> and <code>"symbol"</code>should be synonyms. (Reported by Hervé Pagès.)</p></li><li> <p><code>R CMD rtags</code> works on platforms (such as OS X)with a XSI-conformant shell command <code>echo</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15231">PR#15231</a>)</p></li><li> <p><code>is.unsorted(NA)</code> returns false as documented (rather than<code>NA</code>).</p></li><li> <p><code>R CMD LINK</code> did not know about sub-architectures.</p></li><li> <p><code>system()</code> and <code>system2()</code> are better protectedagainst users who misguidedly have spaces in the temporarydirectory path.</p></li><li> <p><code>file.show()</code> and <code>edit()</code> are now more likely towork on file paths containing spaces. (Where external utilitiesare used, not the norm on Windows nor in <code>R.app</code> whichshould previously have worked.)</p></li><li><p> Packages using the <span class="pkg">methods</span> package are more likely towork when they import it but it is not attached. (Several partsof its C code were looking for its <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> functions on the search pathrather than in its namespace.)</p></li><li> <p><code>lgamma(-x)</code> is no longer <code>NaN</code> for very small x.</p></li><li><p> (Windows) <code>system2()</code> now respects specifying<code>stdout</code> and <code>stderr</code> as files if called from<code>Rgui</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15393">PR#15393</a>)</p></li><li><p> Closing an <code>x11()</code> device whilst <code>locator()</code> or<code>identify()</code> is in progress no longer hangs <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15253">PR#15253</a>)</p></li><li> <p><code>list.dirs(full.names = FALSE)</code> was not implemented.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15170">PR#15170</a>)</p></li><li> <p><code>format()</code> sometimes added unnecessary spaces.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15411">PR#15411</a>)</p></li><li> <p><code>all.equal(check.names = FALSE)</code> would ignore the requestto ignore the names and would check them as attributes.</p></li><li><p> The symbol set by <code>tools::Rd2txt_options(itemBullet=)</code>was not respected in some locales. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15435">PR#15435</a>)</p></li><li> <p><code>mcMap()</code> was not exported by package<span class="pkg">parallel</span>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15439">PR#15439</a>)</p></li><li> <p><code>plot()</code> for <code>TukeyHSD</code> objects did not balance<code>dev.hold()</code> and <code>dev.flush()</code> calls on multi-page plots.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15449">PR#15449</a>)</p></li></ul><h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.0.1</h3><h4>NEW FEATURES</h4><ul><li> <p><code>chooseCRANmirror()</code> and <code>chooseBioCmirror()</code> gainan <code>ind</code> argument (like <code>setRepositories()</code>).</p></li><li> <p><code>mcparallel</code> has a new argument <code>mc.interactive</code>which can modify the interactive flag in the child process. Thenew default is <code>FALSE</code> which makes child processesnon-interactive by default (this prevents lock-ups due to childrenwaiting for interactive input).</p></li><li> <p><code>scan()</code> now warns when end-of-file occurs withina quoted string.</p></li><li> <p><code>count.fields()</code> is now consistent with <code>scan()</code>in its handling of newlines in quoted strings. Instead oftriggering an error, this results in the current line receiving<code>NA</code> as the field count, with the next line getting the totalcount of the two lines.</p></li><li><p> The default method of <code>image()</code> will plot axes of theclass of <code>xlim</code> and <code>ylim</code> (and hence of <code>x</code> and<code>y</code> if there is a suitable <code>range()</code> method). Based ona suggestion of Michael Sumner.</p></li><li> <p><code>load()</code> now has a <code>verbose</code> argument fordebugging support, to print the names of objects just beforeloading them.</p></li><li><p> When loading a serialized object encounters a reference to anamespace which cannot be loaded, this is replaced by a referenceto the global environment, with a warning.</p></li><li> <p><code>pairs()</code> gains a <code>line.main</code> option for title placement.</p></li><li><p> The remaining instances in which serialization to a rawvector was limited to 2GB have been unlimited on a 64-bitplatform, and in most cases serialization to a vector of more than1GB will be substantially faster.</p></li></ul><h4>UTILITIES</h4><ul><li> <p><code>R CMD config</code> now make use of personal‘<span class="file">Makevars</span>’ files under ‘<span class="file">~/.R</span>’ and a site file‘<span class="file">Makevars.site</span>’, in the same way as <code>R CMD SHLIB</code> and<code>R CMD INSTALL</code>. This makes the utility more useful inpackage <code>configure</code> scripts.</p><p>On Windows finding the personal files may require the environmentvariable <span class="env">HOME</span> set.</p><p>The old behaviour can be obtained with the new options<span class="option">--no-user-files</span> and <span class="option">--no-site-files</span>.</p></li></ul><h4>PACKAGE INSTALLATION</h4><ul><li><p> Alternatives to the site and user customization files‘<span class="file">Makevars.site</span>’ and ‘<span class="file">~/.R/Makevars</span>’ can be specified<em>via</em> the environment variables <span class="env">R_MAKEVARS_SITE</span> and<span class="env">R_MAKEVARS_USER</span> respectively. These can be used to suppressthe use of the default files by setting an empty value (wherepossible) or a non-existent path.</p></li></ul><h4>BUG FIXES</h4><ul><li> <p><code>sys.source()</code> did not report error locations when<code>keep.source = TRUE</code>.</p></li><li> <p><code>as.POSIXct.numeric</code> was coercing <code>origin</code> usingthe <code>tz</code> argument and not <code>"GMT"</code> as documented(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14973">PR#14973</a>).</p></li><li><p> The active binding to assign fields in reference classeshas been cleaned up to reduce dependence on the class' packageenvironment, also fixing bug in initializing read-only fields(inspired by a report from Hadley Wickham).</p></li><li> <p><code>str(d)</code> no longer gives an error when <code>names(d)</code>contain illegal multibyte strings (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15247">PR#15247</a>).</p></li><li><p> Profiling of built-in functions with <code>line.profiling=TRUE</code> did not record the line from which they were called.</p></li><li> <p><code>citation(pkg)</code> dropped the header and footer specifiedin the ‘<span class="file">CITATION</span>’ file (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15257">PR#15257</a>).</p></li><li><p> Quotes were handled differently when reading the first lineand reading the rest, so <code>read.table()</code> misread some filesthat contained quote characters (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15245">PR#15245</a>).</p></li><li> <p><code>cat()</code> with <code>sep</code> a character vector of lengthgreater than one and more than one argument was using separatorsinconsistently (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15261">PR#15261</a>).</p></li><li><p> On Windows in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.0.0, <code>savePlot()</code> failed because ofan incorrect check on the argument count.</p></li><li> <p><code>unzip(list = TRUE)</code> returned <code>Names</code> as a factorand not a character vector (as documented) for the internal method.(Noticed by Sean O'Riordain.)</p></li><li> <p><code>contourLines()</code> now checks more comprehensively forconformance of its <code>x</code>, <code>y</code> and <code>z</code> arguments (itwas used incorrectly in package <a href="https://CRAN.R-project.org/package=R2G2"><span class="pkg">R2G2</span></a>).</p></li><li><p> Saved graphics display lists are <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> version-specific.Attempting to load workspaces containing them (or some otherversion-specific objects) aborted the load in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.0.0 andearlier; now it does a partial load and generates a warninginstead.</p></li><li><p> In <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.0.0, <code>identify()</code> and <code>locator()</code> didnot record information correctly, so replaying a graph (e.g., bycopying it to another device) would fail. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15271">PR#15271</a>)</p></li><li><p> Calling <code>file.copy()</code> or <code>dirname()</code> with theinvalid input <code>""</code> (which was being used in packages, despitenot being a file path) could have caused a segfault.</p><p><code>dirname("")</code> is now <code>""</code> rather than <code>"."</code> (unlessit segfaulted).</p></li><li> <p><code>supsmu()</code> could read/write outside its input vectorsfor very short inputs (seen in package <a href="https://CRAN.R-project.org/package=rms"><span class="pkg">rms</span></a> for <code>n = 4</code>).</p></li><li> <p><code>as.dendrogram()</code>'s <code>hclust</code> method uses lessmemory and hence gets considerably faster for large (n ~ 1000)clusterings, thanks to Daniel Müllner. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15174">PR#15174</a>)</p></li><li><p> The return value when all workers failed from<code>parallel::mclapply(mc.preschedule = TRUE)</code> was a list ofstrings and not of error objects. (Spotted by Karl Forner andBernd Bischl.)</p></li><li><p> In <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.0.0, when <code>help()</code> found multiple pages withthe same alias, the HTML display of all the selections was notproduced. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15282">PR#15282</a>)</p></li><li> <p><code>splinefun(method="monoH.FC")</code> now produces afunction with first argument named <code>x</code> and allows<code>deriv=3</code>, as documented. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15273">PR#15273</a>)</p></li><li> <p><code>summaryRprof()</code> would only read the first<code>chunksize</code> lines of an <code>Rprof</code> file produced with<code>line.profiling=TRUE</code>. By default, this is the first 100seconds. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15288">PR#15288</a>)</p></li><li> <p><code>lsfit()</code> produced an incorrect error message whenargument <code>x</code> had more columns than rows or <code>x</code> had adifferent number of rows than <code>y</code>. (Spotted by Renaud Gaujoux.)</p></li><li><p> Binary operations on equal length vectors copied theclass name from the second operand when the first had noclass name, but did not set the object bit. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15299">PR#15299</a>)</p></li><li><p> The <code>trace()</code> method for reference generator objectsfailed after those objects became function definitions.</p></li><li> <p><code>write.table()</code> did not check that factors wereconstructed correctly, and so caused a segment fault whenwriting bad ones. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15300">PR#15300</a>)</p></li><li><p> The internal HTTP server no longer chokes on POST requestswithout body. It will also pass-through other request types forcustom handlers (with the method stored in Request-Method header)instead of failing.</p></li></ul><h3><img src="../help/figures/../../html/Rlogo.svg" class="toplogo" alt="[R logo]" /> CHANGES IN R 3.0.0</h3><h4>SIGNIFICANT USER-VISIBLE CHANGES</h4><ul><li><p> Packages need to be (re-)installed under this version(3.0.0) of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>.</p></li><li><p> There is a subtle change in behaviour for numeric indexvalues <i>2^31</i> and larger. These never used to belegitimate and so were treated as <code>NA</code>, sometimes with awarning. They are now legal for long vectors so there is nolonger a warning, and <code>x[2^31] <- y</code> will now extend thevector on a 64-bit platform and give an error on a 32-bit one.</p></li><li><p> It is now possible for 64-bit builds to allocate amounts ofmemory limited only by the OS. It may be wise to use OSfacilities (e.g., <code>ulimit</code> in a <code>bash</code> shell,<code>limit</code> in <code>csh</code>), to set limits on overall memoryconsumption of an <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> process, particularly in a multi-userenvironment. A number of packages need a limit of at least 4GB ofvirtual memory to load.</p><p>64-bit Windows builds of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> are by default limited in memory usageto the amount of RAM installed: this limit can be changed bycommand-line option <span class="option">--max-mem-size</span> or setting environmentvariable <span class="env">R_MAX_MEM_SIZE</span>.</p></li><li><p> Negative numbers for colours are consistently an error:previously they were sometimes taken as transparent, sometimesmapped into the current palette and sometimes an error.</p></li></ul><h4>NEW FEATURES</h4><ul><li> <p><code>identical()</code> has a new argument,<code>ignore.environment</code>, used when comparing functions (withdefault <code>FALSE</code> as before).</p></li><li><p> There is a new option, <code>options(CBoundsCheck=)</code>, whichcontrols how <code>.C()</code> and <code>.Fortran()</code> pass arguments tocompiled code. If true (which can be enabled by setting theenvironment variable <span class="env">R_C_BOUNDS_CHECK</span> to <span class="samp">yes</span>), raw,integer, double and complex arguments are always copied, andchecked for writing off either end of the array on return from thecompiled code (when a second copy is made). This also checksindividual elements of character vectors passed to <code>.C()</code>.</p><p>This is not intended for routine use, but can be very helpful infinding segfaults in package code.</p></li><li><p> In <code>layout()</code>, the limits on the grid size have beenraised (again).</p></li><li><p> New simple <code>provideDimnames()</code> utility function.</p></li><li><p> Where methods for <code>length()</code> return a double valuewhich is representable as an integer (as often happens for package<a href="https://CRAN.R-project.org/package=Matrix"><span class="pkg">Matrix</span></a>), this is converted to an integer.</p></li><li><p> Matrix indexing of data frames by two-column numeric indicesis now supported for replacement as well as extraction.</p></li><li> <p><code>setNames()</code> now has a default for its <code>object</code>argument, useful for a character result.</p></li><li> <p><code>StructTS()</code> has a revised additive constant in the<code>loglik</code> component of the result: the previous definition isreturned as the <code>loglik0</code> component. However, the help page hasalways warned of a lack of comparability of log-likelihoods fornon-stationary models. (Suggested by Jouni Helske.)</p></li><li><p> The logic in <code>aggregate.formula()</code> has been revised.It is now possible to use a formula stored in a variable;previously, it had to be given explicitly in the function call.</p></li><li> <p><code>install.packages()</code> has a new argument <code>quiet</code> toreduce the amount of output shown.</p></li><li><p> Setting an element of the graphics argument <code>lwd</code> to anegative or infinite value is now an error. Lines correspondingto elements with values <code>NA</code> or <code>NaN</code> are silentlyomitted.</p><p>Previously the behaviour was device-dependent.</p></li><li><p> Setting graphical parameters <code>cex</code>, <code>col</code>,<code>lty</code>, <code>lwd</code> and <code>pch</code> in <code>par()</code> now requires alength-one argument. Previously some silently took the firstelement of a longer vector, but not always when documented to do so.</p></li><li> <p><code>Sys.which()</code> when used with inputs which would beunsafe in a shell (e.g., absolute paths containing spaces) now usesappropriate quoting.</p></li><li> <p><code>as.tclObj()</code> has been extended to handle raw vectors.Previously, it only worked in the other direction.(Contributed by Charlie Friedemann, <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14939">PR#14939</a>.)</p></li><li><p> New functions <code>cite()</code> and <code>citeNatbib()</code> havebeen added, to allow generation of in-text citations from<code>"bibentry"</code> objects. A <code>cite()</code> function may be addedto <code>bibstyle()</code> environments.</p></li><li><p> A <code>sort()</code> method has been added for <code>"bibentry"</code>objects.</p></li><li><p> The <code>bibstyle()</code> function now defaults to setting thedefault bibliography style. The <code>getBibstyle()</code> functionhas been added to report the name of the current default style.</p></li><li> <p><code>scatter.smooth()</code> now has an argument <code>lpars</code> topass arguments to <code>lines()</code>.</p></li><li> <p><code>pairs()</code> has a new <code>log</code> argument, to allow someor all variables to be plotted on logarithmic scale.(In part, wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14919">PR#14919</a>.)</p></li><li> <p><code>split()</code> gains a <code>sep</code> argument.</p></li><li> <p><code>termplot()</code> does a better job when given a model withinteractions (and no longer attempts to plot interaction terms).</p></li><li><p> The parser now incorporates code from Romain Francois'<a href="https://CRAN.R-project.org/package=parser"><span class="pkg">parser</span></a> package, to support more detailed computation onthe code, such as syntax highlighting, comment-baseddocumentation, etc. Functions <code>getParseData()</code> and<code>getParseText()</code> access the data.</p></li><li><p> There is a new function <code>rep_len()</code> analogous to<code>rep.int()</code> for when speed is required (and names are not).</p></li><li><p> The undocumented use <code>rep(NULL, length.out = n)</code> for<code>n > 0</code> (which returns <code>NULL</code>) now gives a warning.</p></li><li> <p><code>demo()</code> gains an <code>encoding</code> argument for thosepackages with non-ASCII demos: it defaults to the package encodingwhere there is one.</p></li><li> <p><code>strwrap()</code> converts inputs with a marked encoding tothe current locale: previously it made some attempt to passthrough as bytes inputs invalid in the current locale.</p></li><li><p> Specifying both <code>rate</code> and <code>scale</code> to<code>[dpqr]gamma</code> is a warning (if they are essentially the samevalue) or an error.</p></li><li> <p><code>merge()</code> works in more cases where the data framesinclude matrices. (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14974">PR#14974</a>.)</p></li><li> <p><code>optimize()</code> and <code>uniroot()</code> no longer use ashared parameter object across calls. (<code>nlm()</code>,<code>nlminb()</code> and <code>optim()</code> with numerical derivativesstill do, as documented.)</p></li><li><p> The <code>all.equal()</code> method for date-times is nowdocumented: times are regarded as equal (by default) if theydiffer by up to 1 msec.</p></li><li> <p><code>duplicated()</code> and <code>unique()</code> gain a <code>nmax</code>argument which can be used to make them much more efficient whenit is known that there are only a small number of unique entries.This is done automatically for factors.</p></li><li><p> Functions <code>rbinom()</code>, <code>rgeom()</code>, <code>rhyper()</code>,<code>rpois()</code>, <code>rnbinom(),</code> <code>rsignrank()</code> and<code>rwilcox()</code> now return integer (not double) vectors. Thishalves the storage requirements for large simulations.</p></li><li> <p><code>sort()</code>, <code>sort.int()</code> and <code>sort.list()</code> nowuse radix sorting for factors of less than 100,000 levels when<code>method</code> is not supplied. So does <code>order()</code> if calledwith a single factor, unless <code>na.last = NA</code>.</p></li><li> <p><code>diag()</code> as used to generate a diagonal matrix has beenre-written in C for speed and less memory usage. It now forcesthe result to be numeric in the case <code>diag(x)</code> since it issaid to have ‘zero off-diagonal entries’.</p></li><li> <p><code>backsolve()</code> (and <code>forwardsolve()</code>) are nowinternal functions, for speed and support for large matrices.</p></li><li><p> More matrix algebra functions (e.g., <code>chol()</code> and<code>solve()</code>) accept logical matrices (and coerce to numeric).</p></li><li> <p><code>sample.int()</code> has some support for <i>n >= 2^31</i>: see its help for the limitations.</p><p>A different algorithm is used for <code>(n, size, replace = FALSE,prob = NULL)</code> for <code>n > 1e7</code> and <code>size <= n/2</code>. Thisis much faster and uses less memory, but does give different results.</p></li><li> <p><code>approxfun()</code> and <code>splinefun()</code> now return awrapper to an internal function in the <span class="pkg">stats</span> namespacerather than a <code>.C()</code> or <code>.Call()</code> call. This is morelikely to work if the function is saved and used in a differentsession.</p></li><li><p> The functions <code>.C()</code>, <code>.Call()</code>,<code>.External()</code> and <code>.Fortran()</code> now give an error (ratherthan a warning) if called with a named first argument.</p></li><li> <p><code>Sweave()</code> by default now reports the locations inthe source file(s) of each chunk.</p></li><li> <p><code>clearPushBack()</code> is now a documented interface to along-existing internal call.</p></li><li> <p><code>aspell()</code> gains filters for <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> code, Debian ControlFormat and message catalog files, and support for <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> leveldictionaries. In addition, package <span class="pkg">utils</span> now providesfunctions <code>aspell_package_R_files()</code> and<code>aspell_package_C_files()</code> for spell checking <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> and C levelmessage strings in packages.</p></li><li> <p><code>bibentry()</code> gains some support for “incomplete”entries with a <span class="samp">crossref</span> field.</p></li><li> <p><code>gray()</code> and <code>gray.colors()</code> finally allow<code>alpha</code> to be specified.</p></li><li> <p><code>monthplot()</code> gains parameters to control the look ofthe reference lines. (Suggestion of Ian McLeod.)</p></li><li><p> Added support for new <code>%~%</code> relation(“is distributed as”) in plotmath.</p></li><li> <p><code>domain = NA</code> is accepted by <code>gettext()</code> and<code>ngettext()</code>, analogously to <code>stop()</code> etc.</p></li><li> <p><code>termplot()</code> gains a new argument <code>plot = FALSE</code>which returns information to allow the plots to be modified foruse as part of other plots, but does not plot them.(Contributed by Terry Therneau, <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15076">PR#15076</a>.)</p></li><li> <p><code>quartz.save()</code>, formerly an undocumented part of<code>R.app</code>, is now available to copy a device to a<code>quartz()</code> device. <code>dev.copy2pdf()</code> optionally doesthis for PDF output: <code>quartz.save()</code> defaults to PNG.</p></li><li><p> The default method of <code>pairs()</code> now allows<code>text.panel = NULL</code> and the use of <code><foo>.panel = NULL</code>is now documented.</p></li><li> <p><code>setRefClass()</code> and <code>getRefClass()</code> now returnclass generator functions, similar to <code>setClass()</code>, butstill with the reference fields and methods as before(suggestion of Romain Francois).</p></li><li><p> New functions <code>bitwNot()</code>, <code>bitwAnd()</code>,<code>bitwOr()</code> and <code>bitwXor()</code>, using the internalinterfaces previously used for classes <code>"octmode"</code> and<code>"hexmode"</code>.</p><p>Also <code>bitwShiftL()</code> and <code>bitwShiftR()</code> for shifting bitsin elements of integer vectors.</p></li><li><p> New option <code>"deparse.cutoff"</code> to control the deparsingof language objects such as calls and formulae when printing.(Suggested by a comment of Sarah Goslee.)</p></li><li> <p><code>colors()</code> gains an argument <code>distinct</code>.</p></li><li><p> New <code>demo(colors)</code> and <code>demo(hclColors)</code>, withutility functions.</p></li><li> <p><code>list.files()</code> (aka <code>dir()</code>) gains a new optionalargument <code>no..</code> which allows to exclude <code>"."</code> and<code>".."</code> from listings.</p></li><li><p> Multiple time series are also of class <code>"matrix"</code>;consequently, <code>head()</code>, e.g., is more useful.</p></li><li> <p><code>encodeString()</code> preserves UTF-8 marked encodings.Thus if factor levels are marked as UTF-8 an attempt is made toprint them in UTF-8 in <code>RGui</code> on Windows.</p></li><li> <p><code>readLines()</code> and <code>scan()</code> (and hence<code>read.table()</code>) in a UTF-8 locale now discard a UTF-8byte-order-mark (BOM). Such BOMs are allowed but not recommendedby the Unicode Standard: however Microsoft applications canproduce them and so they are sometimes found on websites.</p><p>The encoding name <code>"UTF-8-BOM"</code> for a connection willensure that a UTF-8 BOM is discarded.</p></li><li> <p><code>mapply(FUN, a1, ..)</code> now also works when <code>a1</code> (ora further such argument) needs a <code>length()</code> method (which thedocumented arguments never do). (Requested by Hervé Pagès; with apatch.)</p></li><li> <p><code>.onDetach()</code> is supported as an alternative to<code>.Last.lib</code>. Unlike <code>.Last.lib</code>, this does not need tobe exported from the package's namespace.</p></li><li><p> The <code>srcfile</code> argument to <code>parse()</code> may now be acharacter string, to be used in error messages.</p></li><li><p> The <code>format()</code> method for <code>ftable</code> objects gainsa <code>method</code> argument, propagated to <code>write.ftable()</code> and<code>print()</code>, allowing more compact output, notably for LaTeXformatting, thanks to Marius Hofert.</p></li><li><p> The <code>utils::process.events()</code> function has been addedto trigger immediate event handling.</p></li><li> <p><code>Sys.which()</code> now returns <code>NA</code> (not <code>""</code>) for<code>NA</code> inputs (related to <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15147">PR#15147</a>).</p></li><li><p> The <code>print()</code> method for class <code>"htest"</code> givesfewer trailing spaces (wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15124">PR#15124</a>).</p><p>Also print output from <code>HoltWinters()</code>, <code>nls()</code> and others.</p></li><li> <p><code>loadNamespace()</code> allows a version specification to begiven, and this is used to check version specifications given inthe <span class="samp">Imports</span> field when a namespace is loaded.</p></li><li> <p><code>setClass()</code> has a new argument, <code>slots</code>, clearerand less ambiguous than <code>representation</code>. It is recommendedfor future code, but should be back-compatible. At the same time,the allowed slot specification is slightly more general. See thedocumentation for details.</p></li><li> <p><code>mget()</code> now has a default for <code>envir</code> (the framefrom which it is called), for consistency with <code>get()</code> and<code>assign()</code>.</p></li><li> <p><code>close()</code> now returns an integer status where available,invisibly. (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15088">PR#15088</a>.)</p></li><li><p> The internal method of <code>tar()</code> can now store paths toolong for the <span class="samp">ustar</span> format, using the (widely supported) GNUextension. It can also store long link names, but these are muchless widely supported. There is support for larger files, up tothe <span class="samp">ustar</span> limit of 8GB.</p></li><li><p> Local reference classes have been added to package<span class="pkg">methods</span>. These are a technique for avoiding unneededcopying of large components of objects while retaining standard <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>functional behavior. See <code>?LocalReferenceClasses</code>.</p></li><li> <p><code>untar()</code> has a new argument <code>restore_times</code> whichif false (not the default) discards the times in the tarball.This is useful if they are incorrect (some tarballs submitted to<acronym><span class="acronym">CRAN</span></acronym> have times in a local time zone or many years in thepast even though the standard required them to be in UTC).</p></li><li> <p><code>replayplot()</code> cannot (and will not attempt to) replayplots recorded under <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> < 3.0.0. It may crash the <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> session ifan attempt is made to replay plots created in a different build of<span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> >= 3.0.0.</p></li><li><p> Palette changes get recorded on the display list, soreplaying plots (including when resizing screen devices and using<code>dev.copy()</code>) will work better when the palette is changedduring a plot.</p></li><li> <p><code>chol(pivot = TRUE)</code> now defaults to LAPACK, not LINPACK.</p></li><li><p> The <code>parse()</code> function has a new parameter<code>keep.source</code>, which defaults to <code>options("keep.source")</code>.</p></li><li><p> Profiling <em>via</em> <code>Rprof()</code> now optionally recordsinformation at the statement level, not just the function level.</p></li><li><p> The <code>Rprof()</code> function now quotes function names inin its output file on Windows, to be consistent with the quotingin Unix.</p></li><li><p> Profiling <em>via</em> <code>Rprof()</code> now optionally recordsinformation about time spent in GC.</p></li><li><p> The HTML help page for a package now displays non-vignettedocumentation files in a more accessible format.</p></li><li><p> To support <code>options(stringsAsFactors = FALSE)</code>,<code>model.frame()</code>, <code>model.matrix()</code> and<code>replications()</code> now automatically convert charactervectors to factors without a warning.</p></li><li><p> The <code>print</code> method for objects of class <code>"table"</code>now detects tables with 0-extents and prints the results as, e.g.,<span class="samp">< table of extent 0 x 1 x 2 ></span>. (Wish of <a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15198">PR#15198</a>.)</p></li><li><p> Deparsing involving calls to anonymous functions has beenmade closer to reversible by the addition of extra parentheses.</p></li><li><p> The function <code>utils::packageName()</code> has been added asa lightweight version of <code>methods::getPackageName()</code>.</p></li><li> <p><code>find.package(lib.loc = NULL)</code> now treats loadednamespaces preferentially in the same way as attached packageshave been for a long time.</p></li><li><p> In Windows, the Change Directory dialog now defaults tothe current working directory, rather than to the last directorychosen in that dialog.</p></li><li> <p><code>available.packages()</code> gains a<code>"license/restricts_use"</code> filter which retains only packagesfor which installation can proceed solely based on packages whichare guaranteed not to restrict use.</p></li><li><p> New <code>check_packages_in_dir()</code> function in package<span class="pkg">tools</span> for conveniently checking source packages along withtheir reverse dependencies.</p></li><li><p> R's completion mechanism has been improved to handle helprequests (starting with a question mark). In particular, helpprefixes are now supported, as well as quoted help topics. Tosupport this, completion inside quotes are now handled by R bydefault on all platforms.</p></li><li><p> The memory manager now allows the strategy used to balancegarbage collection and memory growth to be controlled by settingthe environment variable <span class="env">R_GC_MEM_GROW</span>. See <code>?Memory</code>for more details.</p></li><li><p> (‘For experts only’, as the introductory manualsays.) The use of environment variables <span class="env">R_NSIZE</span> and<span class="env">R_VSIZE</span> to control the initial (= minimum) garbagecollection trigger for number of cons cels and size of heap hasbeen restored: they can be overridden by the command-line options<code>--min-nsize</code> and <code>--min-vsize</code>; see <code>?Memory</code>.</p></li><li><p> On Windows, the device name for bitmap devices as reportedby <code>.Device</code> and <code>.Devices</code> no longer includes the filename. This is for consistency with other platforms and wasrequested by the <a href="https://CRAN.R-project.org/package=lattice"><span class="pkg">lattice</span></a> maintainer.</p><p><code>win.metafile()</code> still uses the file name: the exact form isused by package <a href="https://CRAN.R-project.org/package=tkrplot"><span class="pkg">tkrplot</span></a>.</p></li><li> <p><code>set.seed(NULL)</code> re-initializes <code>.Random.seed</code> asdone at the beginning of the session if not already set.(Suggestion of Bill Dunlap.)</p></li><li><p> The <code>breaks</code> argument in <code>hist.default()</code> can now bea function that returns the breakpoints to be used (previously itcould only return the suggested number of breakpoints).</p></li><li><p> File ‘<span class="file">share/licenses/licenses.db</span>’ has someclarifications, especially as to which variants of ‘BSD’and ‘MIT’ is intended and how to apply them to packages.The problematic licence ‘Artistic-1.0’ has been removed.</p></li></ul><h4>LONG VECTORS</h4><p>This section applies only to 64-bit platforms.</p><ul><li><p> There is support for vectors longer than <i>2^31- 1</i> elements. This applies to raw, logical, integer, double,complex and character vectors, as well as lists. (Elements ofcharacter vectors remain limited to <i>2^31 - 1</i>bytes.)</p></li><li><p> Most operations which can sensibly be done with long vectorswork: others may return the error ‘long vectors notsupported yet’. Most of these are because they explicitly workwith integer indices (e.g., <code>anyDuplicated()</code> and<code>match()</code>) or because other limits (e.g., of character stringsor matrix dimensions) would be exceeded or the operations would beextremely slow.</p></li><li> <p><code>length()</code> returns a double for long vectors, andlengths can be set to <i>2^31</i> or more by thereplacement function with a double value.</p></li><li><p> Most aspects of indexing are available. Generallydouble-valued indices can be used to access elements beyond<i>2^31 - 1</i>.</p></li><li><p> There is some support for matrices and arrays with eachdimension less than <i>2^31</i> but total number ofelements more than that. Only some aspects of matrix algebra workfor such matrices, often taking a very long time. In other casesthe underlying Fortran code has an unstated restriction (as wasfound for complex <code>svd()</code>).</p></li><li> <p><code>dist()</code> can produce dissimilarity objects for morethan 65536 rows (but for example <code>hclust()</code> cannot processsuch objects).</p></li><li> <p><code>serialize()</code> to a raw vector is unlimited in size(except by resources).</p></li><li><p> The C-level function <code>R_alloc</code> can now allocate<i>2^35</i> or more bytes.</p></li><li> <p><code>agrep()</code> and <code>grep()</code> will return double vectorsof indices for long vector inputs.</p></li><li><p> Many calls to <code>.C()</code> have been replaced by<code>.Call()</code> to allow long vectors to be supported (now or inthe future). Regrettably several packages had copied the non-API<code>.C()</code> calls and so failed.</p></li><li> <p><code>.C()</code> and <code>.Fortran()</code> do not accept long vectorinputs. This is a precaution as it is very unlikely that existingcode will have been written to handle long vectors (and the <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>wrappers often assume that <code>length(x)</code> is an integer).</p></li><li><p> Most of the methods for <code>sort()</code> work for long vectors.</p><p><code>rank()</code>, <code>sort.list()</code> and <code>order()</code> supportlong vectors (slowly except for radix sorting).</p></li><li> <p><code>sample()</code> can do uniform sampling from a long vector.</p></li></ul><h4>PERFORMANCE IMPROVEMENTS</h4><ul><li><p> More use has been made of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> objects representing registeredentry points, which is more efficient as the address is providedby the loader once only when the package is loaded.</p><p>This has been done for packages <code>base</code>, <code>methods</code>,<code>splines</code> and <code>tcltk</code>: it was already in place for theother standard packages.</p><p>Since these entry points are always accessed by the <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> entrypoints they do not need to be in the load table which can besubstantially smaller and hence searched faster. This does meanthat <code>.C</code> / <code>.Fortran</code> / <code>.Call</code> calls copied fromearlier versions of <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> may no longer work – but they were neverpart of the API.</p></li><li><p> Many <code>.Call()</code> calls in package <span class="pkg">base</span> have beenmigrated to <code>.Internal()</code> calls.</p></li><li> <p><code>solve()</code> makes fewer copies, especially when <code>b</code>is a vector rather than a matrix.</p></li><li> <p><code>eigen()</code> makes fewer copies if the input has dimnames.</p></li><li><p> Most of the linear algebra functions make fewer copies whenthe input(s) are not double (e.g., integer or logical).</p></li><li><p> A foreign function call (<code>.C()</code> etc) in a packagewithout a <code>PACKAGE</code> argument will only look in the first DLLspecified in the ‘<span class="file">NAMESPACE</span>’ file of the package rather thansearching all loaded DLLs. A few packages needed <code>PACKAGE</code>arguments added.</p></li><li><p> The <code>@<-</code> operator is now implemented as a primitive,which should reduce some copying of objects when used. Note thatthe operator object must now be in package <span class="pkg">base</span>: do not tryto import it explicitly from package <span class="pkg">methods</span>.</p></li></ul><h4>PACKAGE INSTALLATION</h4><ul><li><p> The transitional support for installing packages withoutnamespaces (required since <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.14.0) has been removed.<code>R CMD build</code> will still add a namespace, but a<code>.First.lib()</code> function will need to be converted.</p><p><code>R CMD INSTALL</code> no longer adds a namespace (soinstallation will fail), and a <code>.First.lib()</code> function in apackage will be ignored (with an installation warning for now).</p><p>As an exception, packages without a ‘<span class="file">R</span>’ directory and no‘<span class="file">NAMESPACE</span>’ file can still be installed.</p></li><li><p> Packages can specify in their ‘<span class="file">DESCRIPTION file</span>’ a linelike </p><pre> Biarch: yes</pre><p>to be installed on Windows with <span class="option">--force-biarch</span>.</p></li><li><p> Package vignettes can now be processed by other enginesbesides <code>Sweave</code>; see ‘Writing R Extensions’ and the<code>tools::vignetteEngine</code> help topic for details.</p></li><li><p> The ‘<span class="file">*.R</span>’ tangled source code for vignettes is nowincluded in tarballs when <code>R CMD build</code> is used to producethem. In <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 3.0.0, ‘<span class="file">*.R</span>’ files not in the sources will beproduced at install time, but eventually this will be dropped.</p></li><li><p> The package type <code>"mac.binary"</code> now looks in a path inthe repository without any Mac subtype (which used to be<span class="samp">universal</span> or <span class="samp">leopard</span>): it looks in‘<span class="file">bin/macosx/contrib/3.0</span>’ rather than‘<span class="file">bin/macosx/leopard/contrib/2.15</span>’). This is the type usedfor the <acronym><span class="acronym">CRAN</span></acronym> binary distribution for OS X as from <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>3.0.0.</p></li><li><p> File ‘<span class="file">etc/Makeconf</span>’ makes more use of the macros<code>$(CC)</code>, <code>$(CXX)</code>, <code>$(F77)</code> and <code>$(FC)</code>, sothe compiler in use can be changed by setting just these (and ifnecessary the corresponding flags and <code>FLIBS</code>) in file‘<span class="file">~/.R/Makevars</span>’.</p><p>This is convenient for those working with binary distributions of<span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>, e.g. on OS X.</p></li></ul><h4>UTILITIES</h4><ul><li> <p><code>R CMD check</code> now gives a warning rather than anote if it finds calls to <code>abort</code>, <code>assert</code> or<code>exit</code> in compiled code, and has been able to find the‘<span class="file">.o</span>’ file in which the calls occur.</p><p>Such calls can terminate the <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> process which loads the package.</p></li><li><p> The location of the build and check environment files cannow be specified by the environment variables<span class="env">R_BUILD_ENVIRON</span> and <span class="env">R_CHECK_ENVIRON</span>, respectively.</p></li><li> <p><code>R CMD Sweave</code> gains a <span class="option">--compact</span> optionto control possibly reducing the size of the PDF file it createswhen <span class="option">--pdf</span> is given.</p></li><li> <p><code>R CMD build</code> now omits Eclipse's ‘<span class="file">.metadata</span>’directories, and <code>R CMD check</code> warns if it finds them.</p></li><li> <p><code>R CMD check</code> now does some checks on functionsdefined within reference classes, including of <code>.Call()</code> etccalls.</p></li><li> <p><code>R CMD check --as-cran</code> notes assignments to theglobal environment, calls to <code>data()</code> which load into theglobal environment, and calls to <code>attach()</code>.</p></li><li> <p><code>R CMD build</code> by default uses the internal method of<code>tar()</code> to prepare the tarball. This is more likely toproduce a tarball compatible with <code>R CMD INSTALL</code> and<code>R CMD check</code>: an external <code>tar</code> program,including options, can be specified <em>via</em> the environmentvariable <span class="env">R_BUILD_TAR</span>.</p></li><li> <p><code>tools::massageExamples()</code> is better protected againstpackages which re-define base functions such as <code>cat()</code> and<code>get()</code> and so can cause <code>R CMD check</code> to fail whenchecking examples.</p></li><li> <p><code>R CMD javareconf</code> has been enhanced to be moresimilar to the code used by <code>configure</code>.</p><p>There is now a test that a JNI program can be compiled (like<code>configure</code> did) and only working settings are used.</p><p>It makes use of custom settings from configuration recorded in‘<span class="file">etc/javaconf</span>’.</p></li><li><p> The <span class="option">--no-vignettes</span> argument of <code>R CMDbuild</code> has been renamed to the more accurate<span class="option">--no-build-vignettes</span>: its action has always been to(re)build vignettes and never omitted them.</p><p><code>R CMD check</code> accepts <span class="option">--no-build-vignettes</span> as apreferred synonym for <span class="option">--no-rebuild-vignettes</span>.</p></li></ul><h4>DEPRECATED AND DEFUNCT</h4><ul><li><p> The <code>ENCODING</code> argument to <code>.C()</code> is defunct.Use <code>iconv()</code> instead.</p></li><li><p> The <code>.Internal(eval.with.vis)</code> non-API function hasbeen removed.</p></li><li><p> Support for the converters for use with <code>.C()</code> has beenremoved, including the oft misused non-API header‘<span class="file">R_ext/RConverters.h</span>’.</p></li><li><p> The previously deprecated uses of <code>array()</code> with a0-length <code>dim</code> argument and <code>tapply()</code> with a 0-length<code>INDEX</code> list are now errors.</p></li><li> <p><span class="samp">Translation</span> packages are defunct.</p></li><li><p> Calling <code>rep()</code> or <code>rep.int()</code> on a pairlist orother non-vector object is now an error.</p></li><li><p> Several non-API entry points have been transferred topackages (e.g., <code>R_zeroin2</code>) or replaced by different non-APIentry points (e.g., <code>R_tabulate</code>).</p></li><li><p> The ‘internal’ graphics device invoked by<code>.Call("R_GD_nullDevice", package = "grDevices")</code> hasbeen removed: use <code>pdf(file = NULL)</code> instead.</p></li><li><p> The <code>.Fortran()</code> entry point <code>"dqrls"</code> which hasnot been used by <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> since version 2.15.1 is no longer available.</p></li><li><p> Functions <code>traceOn()</code> and <code>traceOff()</code> in package<span class="pkg">methods</span> are now defunct.</p></li><li><p> Function <code>CRAN.packages()</code> is finally defunct.</p></li><li><p> Use of <code>col2rgb(0)</code> is defunct: use <code>par("bg")</code> or<code>NA</code> instead.</p></li><li><p> The long-defunct functions <code>Rd_parse()</code>,<code>anovalist.lm()</code>, <code>categpry()</code>, <code>clearNames()</code>,<code>gammaCody()</code>, <code>glm.fit.null()</code>, <code>lm.fit.null()</code>,<code>lm.wfit.null()</code>, <code>manglePackageNames()</code>,<code>mauchley.test()</code>, <code>package.contents()</code>,<code>print.coefmat()</code>, <code>reshapeLong()</code>,<code>reshapeWide()</code>, <code>tkclose()</code>, <code>tkcmd()</code>,<code>tkfile.dir()</code>, <code>tkfile.tail()</code>, <code>tkopen()</code>,<code>tkputs()</code>, <code>tkread()</code>, <code>trySilent()</code> and<code>zip.file.extract()</code> have been removed entirely (but arestill documented in the help system).</p></li><li><p> The unused <code>dataPath</code> argument to<code>attachNamespace()</code> has been removed.</p></li><li> <p><code>grid.prompt()</code> has been removed: use<code>devAskNewPage()</code> instead.</p></li><li><p> The long-deprecated <code>intensities</code> component is nolonger returned by <code>hist()</code>.</p></li><li> <p><code>mean()</code> for data frames and <code>sd()</code> for dataframes and matrices are defunct.</p></li><li> <p><code>chol(pivot = FALSE, LINPACK = TRUE)</code>,<code>ch2inv(LINPACK = TRUE)</code>, <code>eigen(EISPACK = TRUE)</code>,<code>solve(LINPACK = TRUE)</code> and <code>svd(LINPACK = TRUE)</code> aredefunct: LAPACK will be used, with a warning.</p></li><li><p> The <code>keep.source</code> argument to <code>library()</code> and<code>require()</code> is defunct. This option needs to be setat install time.</p></li><li><p> Documentation for <code>real()</code>, <code>as.real()</code> and<code>is.real()</code> has been moved to ‘defunct’ and thefunctions removed.</p></li><li><p> The <code>maxRasters</code> argument of <code>pdf()</code> (unused since<span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> 2.14.0) has been removed.</p></li><li><p> The unused <code>fontsmooth</code> argument has been removed fromthe <code>quartz()</code> device.</p></li><li><p> All the (non-API) EISPACK entry points in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> have been removed.</p></li><li> <p><code>chol(pivot = TRUE, LINPACK = TRUE)</code> is deprecated.</p></li><li><p> The long-deprecated use of <code>\synopsis</code> in the<span class="samp">Usage</span> section of ‘<span class="file">.Rd</span>’ files will be removed in <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>3.1.0.</p></li><li> <p><code>.find.package()</code> and <code>.path.package()</code> aredeprecated: only the public versions without the dot have everbeen in the API.</p></li><li><p> In a package's ‘<span class="file">DESCRIPTION</span>’ file, </p><pre> License: X11</pre><p>is deprecated, since it includes‘Copyright (C) 1996 X Consortium’ which cannot beappropriate for a current <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> package. Use ‘MIT’ or‘BSD_2_clause’ instead.</p></li></ul><h4>CODE MIGRATION</h4><ul><li><p> The C code underlying base graphics has been migrated to the<span class="pkg">graphics</span> package (and hence no longer uses<code>.Internal()</code> calls).</p></li><li><p> Most of the <code>.Internal()</code> calls used in the <span class="pkg">stats</span>package have been migrated to C code in that package.</p><p>This means that a number of <code>.Internal()</code> calls which havebeen used by packages no longer exist, including<code>.Internal(cor)</code> <code>.Internal(cov)</code>,<code>.Internal(optimhess)</code> and <code>.Internal(update.formula)</code>.</p></li><li><p> Some <code>.External()</code> calls to the <code>base</code> package(really to the <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> executable or shared library) have been moved tomore appropriate packages. Packages should not have been usingsuch calls, but some did (mainly those used by <code>integrate()</code>).</p></li></ul><h4>PACKAGE parallel</h4><ul><li><p> There is a new function <code>mcaffinity()</code> which allowsgetting or setting the CPU affinity mask for the current <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> process onsystems that supports this (currently only Linux has been testedsuccessfully). It has no effect on systems which do not supportprocess affinity. Users are not expected to use this functiondirectly (with the exception of fixing libraries that breakaffinity settings like OpenBLAS) – the function is ratherintended to support affinity control in high-level parallelfunctions. In the future, <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> may supplement lack of affinitycontrol in the OS by its own bookkeeping <em>via</em> <code>mcaffinity()</code>related to processes and threads it spawns.</p></li><li> <p><code>mcparallel()</code> has a new argument <code>mc.affinity</code>which attempts to set the affinity of the child process accordingto the specification contained therein.</p></li><li><p> The port used by socket clusters is chosen randomly: thisshould help to avoid clashes observed when two users of amulti-user machine try to create a cluster at the same time. Toreproduce the previous behaviour set environment variable<span class="env">R_PARALLEL_PORT</span> to <code>10187</code>.</p></li></ul><h4>C-LEVEL FACILITIES</h4><ul><li><p> There has been some minor re-organization of the non-APIheader files. In particular, ‘<span class="file">Rinternals.h</span>’ no longerincludes the non-API header ‘<span class="file">R_exts/PrtUtil.h</span>’, and that nolonger includes ‘<span class="file">R_exts/Print.h</span>’.</p></li><li><p> Passing <code>NULL</code> to <code>.C()</code> is now an error.</p></li><li> <p><code>.C()</code> and <code>.Fortran()</code> now warn if<code>"single"</code> arguments are used with <code>DUP = FALSE</code>, aschanges to such arguments are not returned to the caller.</p></li><li><p> C entry points <code>R_qsort</code> and <code>R_qsort_I</code> now have<code>start</code> and <code>end</code> as <code>size_t</code> to allow them to workwith longer vectors on 64-bit platforms. Code using them shouldbe recompiled.</p></li><li><p> A few recently added C entry points were missing theremapping to <code>Rf_</code>, notably <code>[dpq]nbinom_mu</code>.</p></li><li><p> Some of the interface pointers formerly available only to<code>R.app</code> are now available to front-ends on allUnix-alikes: one has been added for the interface to<code>View()</code>.</p></li><li> <p><code>PACKAGE = ""</code> is now an error in <code>.C()</code> etc calls:it was always contrary to the documentation.</p></li><li><p> Entry point <code>rcont2</code> has been migrated to package<span class="pkg">stats</span> and so is no longer available.</p></li><li> <p><code>R_SVN_REVISION</code> in ‘<span class="file">Rversion.h</span>’ is now an integer(rather than a string) and hence usable as e.g.<code>#if R_SVN_REVISION < 70000</code>.</p></li><li><p> The entry points <code>rgb2hsv</code> and <code>hsv2rgb</code> have beenmigrated to package <span class="pkg">grDevices</span> and so are no longer available.</p></li><li> <p><code>R_GE_version</code> has been increased to <code>10</code> and<code>name2col</code> removed (use <code>R_GE_str2col</code> instead). <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>internal colour codes are now defined using the typedef<code>rcolor</code>.</p></li><li><p> The <code>REPROTECT</code> macro now checks that the protect indexis valid.</p></li><li><p> Several non-API entry points no longer used by <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> have beenremoved, including the Fortran entry points <code>chol</code>,<code>chol2inv</code>, <code>cg</code>, <code>ch</code> and <code>rg</code>, and the Centry points <code>Brent_fmin</code>, <code>fft_factor</code> and <code>fft_work</code>.</p></li><li><p> If a <code>.External</code> call is registered with a number ofarguments (other than <code>-1</code>), the number of arguments passedis checked for each call (as for other foreign function calls).</p></li><li><p> It is now possible to write custom connectionimplementations outside core R using ‘<span class="file">R_ext/Connections.h</span>’.Please note that the implementation of connections is stillconsidered internal and may change in the future (see the abovefile for details).</p></li></ul><h4>INTERNATIONALIZATION</h4><ul><li><p> The management of translations has been converted to <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span>code: see <code>?tools::update_pkg_po</code>.</p></li><li><p> The translations for the <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> interpreter and<code>RGui.exe</code> are now part of the <span class="pkg">base</span> package (rather thanhaving sources in directory ‘<span class="file">po</span>’ and being installed to‘<span class="file">share/locale</span>’). Thus the <span class="pkg">base</span> package supports threetranslation domains, <code>R-base</code>, <code>R</code> and <code>RGui</code>.</p></li><li><p> The compiled translations which ship with <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> are allinstalled to the new package <span class="pkg">translations</span> for easierupdating. The first package of that name found on<code>.libPaths()</code> at the start of the <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> session will be used.(It is possible messages will be used before <code>.libPaths()</code> isset up in which case the default translations will be used: setenvironment variable <span class="env">R_TRANSLATIONS</span> to point to the locationof the intended <span class="pkg">translations</span> package to use this right fromthe start.)</p></li><li><p> The translations form a separate group in the Windowsinstaller, so can be omitted if desired.</p></li><li><p> The markup for many messages has been changed to make themeasier to translate, incorporating suggestions from Łukasz Daniel.</p></li></ul><h4>INSTALLATION</h4><ul><li><p> There is again support for building without using the C‘long double’ type. This is required by C99, but systemimplementations can be slow or flawed. Use <code>configure</code>option <span class="option">--disable-long-double</span>.</p></li><li> <p><code>make pdf</code> and <code>make install-pdf</code> now makeand install the full reference index (including all base andrecommended packages).</p></li><li><p> The 'reference manual' on the Windows GUI menu and includedin the installer is now the full reference index, including allbase and recommended packages.</p></li><li> <p><span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> help pages and manuals have no ISBNs because ISBNrules no longer allow constantly changing content to be assignedan ISBN.</p></li><li><p> The Windows installer no longer installs a Start Menulink to the static help pages; as most pages are generateddynamically, this led to a lot of broken links.</p></li><li><p> Any custom settings for Java configuration are recorded infile ‘<span class="file">etc/javaconf</span>’ for subsequent use by <code>R CMDjavareconf</code>.</p></li><li><p> There is now support for <code>makeinfo</code> version 5.0(which requires a slightly different ‘<span class="file">.texi</span>’ syntax).</p></li><li><p> The minimum versions for <span class="option">--use-system-zlib</span> and<code>--use-system-pcre</code> are now tested as 1.2.5 and 8.10respectively.</p></li><li><p> On Windows, the stack size is reduced to 16MB on 32-bitsystems: misguided users were launching many threads withoutcontrolling the stack size.</p></li><li> <p><code>configure</code> no longer looks for file‘<span class="file">~/.Rconfig</span>’: ‘<span class="file">~/.R/config</span>’ has long been preferred.</p></li></ul><h4>BUG FIXES</h4><ul><li><p> When <code>R CMD build</code> is run in an encoding other thanthe one specified in the package's ‘<span class="file">DESCRIPTION</span>’ file ittries harder to expand the <code>authors@R</code> field in the specifiedencoding. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=14958">PR#14958</a>)</p></li><li><p> If <code>R CMD INSTALL</code> is required to expand the<code>authors@R</code> field of the ‘<span class="file">DESCRIPTION</span>’ file, it triesharder to do so in the encoding specified for the package (ratherthan using ASCII escapes).</p></li><li><p> Fix in package <span class="pkg">grid</span> for pushing a viewport into alayout cell, where the layout is within a viewport that has zerophysical width OR where the layout has zero total relative width(likewise for height). The layout column widths (or row heights)in this case were being calculated with non-finite values.(Reported by Winston Chang.)</p></li><li> <p><code>solve(A, b)</code> for a vector <code>b</code> gave the answernames from <code>colnames(A)</code> for <code>LINPACK = TRUE</code> but not inthe default case.</p></li><li> <p><code>La.svd()</code> accepts logical matrices (as documented, andas <code>svd()</code> did).</p></li><li> <p><code>legend()</code> now accepts negative <code>pch</code> values, inthe same way <code>points()</code> long has.</p></li><li><p> Parse errors when installing files now correctly displaythe name of the file containing the bad code.</p></li><li><p> In Windows, tcltk windows were not always properly constructed.(<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15150">PR#15150</a>)</p></li><li><p> The internal functions implementing <code>parse()</code>,<code>tools::parseLatex()</code> and <code>tools::parse_Rd()</code> were notreentrant, leading to errors in rare circumstances such as agarbage collection triggering a recursive call.</p></li><li><p> Field assignments in reference class objects <em>via</em><code>$<-</code> were not being checkedbecause the magic incantation to turn methods on for thatprimitive operator had been inadvertently omitted.</p></li><li> <p><code>setHook(hookname, value, action="replace")</code> set thehook to be the value, rather than a list containing the value asdocumented. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15167">PR#15167</a>)</p></li><li><p> If a package used a ‘<span class="file">NEWS.Rd</span>’ file, the main HTMLpackage index page did not link to it. (Reported by DirkEddelbuettel.)</p></li><li><p> The primitive implementation of <code>@<-</code> was notchecking the class of the replacement. It now does a check,quicker but less general than <code>slot<-</code>. See the help.</p></li><li> <p><code>split(x, f)</code> now recycles classed objects <code>x</code> inthe same way as vectors. (Reported by Martin Morgan.)</p></li><li> <p><code>pbeta(.28, 1/2, 2200, lower.tail=FALSE, log.p=TRUE)</code>is no longer <code>-Inf</code>; ditto for corresponding <code>pt()</code> and<code>pf()</code> calls, such as <code>pt(45, df=5000, lower.tail=FALSE,log.p=TRUE)</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15162">PR#15162</a>)</p></li><li><p> The Windows graphics device would crash <span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> if a userattempted to load the graphics history from a variable that wasnot a saved history. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15230">PR#15230</a>)</p></li><li><p> The workspace size for the <code>predict()</code>method for <code>loess()</code> could exceed the maximum integer size.(Reported by Hiroyuki Kawakatsu.)</p></li><li> <p><code>ftable(x, row.vars, col.vars)</code> now also works when the<code>*.vars</code> arguments are (integer or character vectors) oflength zero.</p></li><li><p> Calling <code>cat()</code> on a malformed UTF-8 string could causethe Windows GUI to lock up. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15227">PR#15227</a>)</p></li><li> <p><code>removeClass(cc)</code> gave "node stack overflow" for someclass definitions containing <code>"array"</code> or <code>"matrix"</code>.</p></li></ul><h3>CHANGES in previous versions</h3><ul><li><p> Older news can be found in text format in files<a href="../NEWS.0">NEWS.0</a>, <a href="../NEWS.1">NEWS.1</a>and <a href="../NEWS.2">NEWS.2</a>in the ‘<span class="file">doc</span>’ directory. News in HTML format for<span style="font-family: Courier New, Courier; color: #666666;"><b>R</b></span> versions from 2.10.0 to 2.15.3 is in<a href="NEWS.2.html">NEWS.2.html</a>.</p></li></ul></body></html>