% -*- coding: utf-8 -*- \newcommand{\PR}{\Sexpr[results=rd]{tools:::Rd_expr_PR(#1)}} \newcommand{\Rlogo}{\if{html}{\figure{../../html/logo.jpg}}\if{latex}{\figure{logo.jpg}{options: width=0.5in}}} \newcommand{\CRANpkg}{\href{http://CRAN.R-project.org/package=#1}{\pkg{#1}}} \name{NEWS} \title{R News} \encoding{UTF-8} \section{\Rlogo CHANGES IN R-devel}{ \subsection{NEW FEATURES}{ \itemize{ \item \code{anyNA()} gains a \code{recursive} argument. } } %% \subsection{BUG FIXES}{ %% \itemize{ %% } %% } } \section{\Rlogo CHANGES IN R 3.1.0 patched}{ \subsection{NEW FEATURES}{ \itemize{ \item \command{configure} option \option{--with-internal-tzcode} can now be used with variable \code{rsharedir}. \item \code{tools::buildVignette()} and \code{tools::buildVignettes()} with \code{clean = FALSE} no longer remove any created files. \code{buildvignette()} gains a \code{keep} argument for more cleaning customization. \item The Bioconductor \sQuote{version} used by \code{setRepositories()} can now be set by environment variable \env{R_BIOC_VERSION} at runtime, not just when \R is installed. (It has been stated that Bioconductor will switch from version 2.14 to version 3.0 during the lifetime of the \R 3.1 series.) } } \subsection{INSTALLATION and INCLUDED SOFTWARE}{ \itemize{ \item The included version of PCRE has been updated to 8.35. } } \subsection{BUG FIXES}{ \itemize{ \item When \code{attach()} notices conflicts, it does so compatibly with \code{library()}, using \code{message()}. \item \command{R CMD Sweave} no longer cleans any files, compatibly with versions of \R prior to 3.1.0. \item \code{dbinom(x,n)}, \code{pbinom()}, \code{dpois()}, etc, are slightly less restrictive in checking if \code{n} is integer-valued. (Wish of \PR{15734}.) \item \code{pchisq(x, df, ncp, log.p = TRUE)} is more accurate and no longer underflows for small \code{x} and \code{ncp < 80}, e.g, for \code{pchisq(1e-5, df = 100, ncp = 1, log = TRUE)}. (Based on \PR{15635} and a suggestion by Roby Joehanes.) \item The \code{s} (\dQuote{step into}) command in the debugger would cause \R to step into expressions evaluated there, not just into functions being debugged. (\PR{15770}) \item The third-party code used by \code{strptime()} rejected time-zone offsets of more than \code{+1200}. (\PR{15768}) \item (Windows only.) \code{png(type = "cairo", antialias = "gray")} was not accepted. ((\PR{15760})) \item Use of \code{save(..., envir=)} with named objects could fail. (\PR{15758}) } } } \section{\Rlogo CHANGES IN R 3.1.0}{ \subsection{NEW FEATURES}{ \itemize{ \item \code{type.convert()} (and hence by default \code{read.table()}) returns a character vector or factor when representing a numeric input as a double would lose accuracy. Similarly for complex inputs. If a file contains numeric data with unrepresentable numbers of decimal places that are intended to be read as numeric, specify \code{colClasses} in \code{read.table()} to be \code{"numeric"}. \item \code{tools::Rdiff(useDiff = FALSE)} is closer to the POSIX definition of \command{diff -b} (as distinct from the description in the \command{man} pages of most systems). \item New function \code{anyNA()}, a version of \code{any(is.na(.))} which is fast for atomic vectors, based on a proposal by Tim Hesterberg. (Wish of \PR{15239}.) \item \code{arrayInd(*, useNames = TRUE)} and, analogously, \code{which(*, arr.ind = TRUE)} now make use of \code{names(.dimnames)} when available. \item \code{is.unsorted()} now also works for \code{raw} vectors. \item The \code{"table"} method for \code{as.data.frame()} (also useful as \code{as.data.frame.table()}) now passes \code{sep} and \code{base} arguments to \code{provideDimnames()}. \item \code{uniroot()} gets new optional arguments, notably \code{extendInt}, allowing to auto-extend the search interval when needed. The return value has an extra component, \code{init.it}. % advertize at all? % \item New \code{.lm.fit()} for benchmark lovers but not Joe % Average. %% TODO: change in ../src/library/compiler/noweb/compiler.nw + ..../R/cmp.R \item \code{switch(f, ...)} now warns when \code{f} is a factor, as this typically happens accidentally where the useR meant to pass a character string, but \code{f} is treated as integer (as always documented). \item The parser has been modified to use less memory. \item The way the unary operators (\code{+ - !}) handle attributes is 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. \item \code{colorRamp()} and \code{colorRampPalette()} now allow non-opaque colours and a ramp in opacity via the new argument \code{alpha = TRUE}. (Suggested by Alberto Krone-Martins, but optionally as there are existing uses which expect only RGB values.) % https://stat.ethz.ch/pipermail/r-devel/2013-July/067046.html \item \code{grid.show.layout()} and \code{grid.show.viewport()} get an optional \code{vp.ex} argument. \item There is a new function \code{find_gs_cmd()} in the \pkg{tools} package to locate a GhostScript executable. (This is an enhanced version of a previously internal function there.) \item \code{object.size()} gains a \code{format()} method. \item There is a new family, \code{"ArialMT"}, for the \code{pdf()} and \code{postscript()} devices. This will only be rendered correctly on viewers which have access to Monotype TrueType fonts (which are sometimes requested by journals). \item The text and PDF news files, including \file{NEWS} and \file{NEWS.2}, have been moved to the \file{doc} directory. \item \code{combn(x, simplify = TRUE)} now gives a factor result for factor input \code{x} (previously user error). (Related to \PR{15442}.) \item Added \code{utils::fileSnapshot()} and \code{utils::changedFiles()} functions to allow snapshots and comparison of directories of files. \item \code{make.names(names, unique=TRUE)} now tries to preserve existing names. (Suggestion of \PR{15452}.) \item New functions \code{cospi(x)}, \code{sinpi(x)}, and \code{tanpi(x)}, for more accurate computation of \code{cos(pi*x)}, etc, both in \R{} and the C API. Using these gains accuracy in some cases, e.g., inside \code{lgamma()} or \code{besselI()}. (Suggested by Morten Welinder in \PR{15529}.) \item \code{print.table(x, zero.print = ".")} now also has an effect when \code{x} is not integer-valued. \item There is more support to explore the system's idea of time-zone names. \code{Sys.timezone()} tries to give the current system setting by name (and succeeds at least on Linux, OS X, Solaris and Windows), and \code{OlsonNames()} lists the names in the system's Olson database. \code{Sys.timezone(location = FALSE)} gives the previous behaviour. \item Platforms with a 64-bit \code{time_t} type are allowed to handle conversions between the \code{"POSIXct"} and \code{"POSIXlt"} classes for date-times outside the 32-bit range (before 1902 or after 2037): the existing workarounds are used on other platforms. (Note that time-zone information for post-2037 is speculative at best, and the OS services are tested for known errors and so not used on OS X.) Currently \code{time_t} is usually \code{long} and hence 64-bit on Unix-alike 64-bit platforms: however it several cases the time-zone database is 32-bit. On \R for Windows it is 64-bit (for both architectures as from this version). \item The \code{"save.defaults"} option can include a value for \code{compression_level}. (Wish of \PR{15579}.) \item \code{colSums()} and friends now have support for arrays and data-frame columns with \eqn{2^{31}}{2^31} or more elements. \item \code{as.factor()} is faster when \code{f} is an unclassed integer vector (for example, when called from \code{tapply()}). \item \code{fft()} now works with longer inputs, from the 12 million previously supported up to 2 billion. (\PR{15593}) \item Complex \code{svd()} now uses LAPACK subroutine \code{ZGESDD}, the complex analogue of the routine used for the real case. \item Sweave now outputs \file{.tex} files in UTF-8 if the input encoding is declared to be UTF-8, regardless of the local encoding. The UTF-8 encoding may now be declared using a LaTeX comment containing the string \code{\%\\SweaveUTF8} on a line by itself. \item \code{file.copy()} gains a \code{copy.date} argument. \item Printing of date-times will make use of the time-zone abbreviation in use at the time, if known. For example, for Paris pre-1940 this could be \samp{LMT}, \samp{PMT}, \samp{WET} or \samp{WEST}. To enable this, the \code{"POSIXlt"} class has an optional component \code{"zone"} recording the abbreviation for each element. For platforms which support it, there is also a component \code{"gmtoff"} recording the offset from GMT where known. \item (On Windows, by default on OS X and optionally elsewhere.) The system C function \code{strftime} has been replaced by a more comprehensive version with closer conformance to the POSIX 2008 standard. \item \code{dnorm(x, log = FALSE)} is more accurate (but somewhat slower) for |x| > 5; as suggested in \PR{15620}. \item Some versions of the \code{tiff()} device have further compression options. \item \code{read.table()}, \code{readLines()} and \code{scan()} have a new argument to influence the treatment of embedded nuls. \item Avoid duplicating the right hand side values in complex assignments when possible. This reduces copying of replacement values in expressions such as \code{Z$a <- a0} and \code{ans[[i]] <- tmp}: some package code has relied on there being copies. Also, a number of other changes to reduce copying of objects; all contributed by or based on suggestions by Michael Lawrence. \item The \code{fast} argument of \code{KalmanLike()}, \code{KalmanRun()} and \code{KalmanForecast()} has been replaced by \code{update}, which instead of updating \code{mod} in place, optionally returns the updated model in an attribute \code{"mod"} of the return value. \item \code{arima()} and \code{makeARIMA()} get a new optional argument \code{SSinit}, allowing the choice of a different \bold{s}tate \bold{s}pace initialization which has been observed to be more reliable close to non-stationarity: see \PR{14682}. \item \code{warning()} has a new argument \code{noBreaks.}, to simplify post-processing of output with \code{options(warn = 1)}. \item \code{pushBack()} gains an argument \code{encoding}, to support reading of UTF-8 characters using \code{scan()}, \code{read.table()} and related functions in a non-UTF-8 locale. \item \code{all.equal.list()} gets a new argument \code{use.names} which by default labels differing components by names (if they match) rather than by integer index. Saved \R output in packages may need to be updated. \item The methods for \code{all.equal()} and \code{attr.all.equal()} now have argument \code{check.attributes} after \code{\dots} so it cannot be partially nor positionally matched (as it has been, unintentionally). A side effect is that some previously undetected errors of passing empty arguments (no object between commas) to \code{all.equal()} are detected and reported. There are explicit checks that \code{check.attributes} is logical, \code{tolerance} is numeric and \code{scale} is \code{NULL} or numeric. This catches some unintended positional matching. The message for \code{all.equal.numeric()} reports a \code{"scaled difference"} only for \code{scale != 1}. \item \code{all.equal()} now has a \code{"POSIXt"} method replacing the \code{"POSIXct"} method. \item The \code{"Date"} and \code{"POSIXt"} methods of \code{seq()} allows \code{by = "quarter"} for completeness (\code{by = "3 months"} always worked). \item \code{file.path()} removes any trailing separator on Windows, where they are invalid (although sometimes accepted). This is intended to enhance the portability of code written by those using POSIX file systems (where a trailing \code{/} can be used to confine path matching to directories). \item New function \code{agrepl()} which like \code{grepl()} returns a logical vector. \item \code{fifo()} is now supported on Windows. (\PR{15600}) \item \code{sort.list(method = "radix")} now allows negative integers (wish of \PR{15644}). \item Some functionality of \code{print.ts()} is now available in \code{.preformat.ts()} for more modularity.% and format.ts() might follow \item \code{mcparallel()} gains an option \code{detach = TRUE} which allows execution of code independently of the current session. It is based on a new \code{estranged = TRUE} argument to \code{mcfork()} which forks child processes such that they become independent of the parent process. \item The \code{pdf()} device omits circles and text at extremely small sizes, since some viewers were failing on such files. \item The rightmost break for the \code{"months"}, \code{"quarters"} and \code{"years"} cases of \code{hist.POSIXlt()} has been increased by a day. (Inter alia, fixes \PR{15717}.) \item The handling of \code{DF[i,] <- a} where \code{i} is of length 0 is improved. (Inter alia, fixes \PR{15718}.) \item \code{hclust()} gains a new method \code{"ward.D2"} which implements Ward's method correctly. The previous \code{"ward"} method is \code{"ward.D"} now, with the old name still working. Thanks to research and proposals by Pierre Legendre. \item The \code{sunspot.month} dataset has been amended and updated from the official source, whereas the \code{sunspots} and \code{sunspot.year} datasets will remain immutable. The documentation and source links have been updated correspondingly. \item The \code{summary()} method for \code{"lm"} fits warns if the fit is essentially perfect, as most of the summary may be computed inaccurately (and with platform-dependent values). Programmers who use \code{summary()} in order to extract just a component which will be reliable (e.g. \code{$cov.unscaled}) should wrap their calls in \code{suppressWarnings()}. } } \subsection{INSTALLATION and INCLUDED SOFTWARE}{ \itemize{ \item The included version of LAPACK has been updated to 3.5.0. \item There is some support for parallel testing of an installation, by setting \env{TEST_MC_CORES} to an integer greater than one to indicate the maximum number of cores to be used in parallel. (It is worth specifying at least 8 cores if available.) Most of these require a \command{make} program (such as GNU \command{make} and \command{dmake}) which supports the \command{${MAKE} -j nproc} syntax. Except on Windows: the tests of standard package examples in \command{make check} are done in parallel. This also applies to running \code{tools::testInstalledPackages()}. The more time-consuming regression tests are done in parallel. The package checks in \command{make check-devel} and \command{make check-recommended} are done in parallel. \item More of \command{make check} will work if recommended packages are not installed: but recommended packages remain needed for thorough checking of an \R build. \item The version of \samp{tzcode} included in \file{src/extra/tzone} has been updated. (Formerly used only on Windows.) \item The included (64-bit) time-zone conversion code and Olson time-zone database can be used instead of the system version: use \command{configure} option \option{--with-internal-tzcode}. This is the default on Windows and OS X. (Note that this does not currently work if a non-default \code{rsharedir} \command{configure} variable is used.) (It might be necessary to set environment variable \env{TZ} on OSes where this is not already set, although the system timezone is deduced correctly on at least Linux, OS X and Windows.) This option also switches to the version of \code{strftime} included in directory \file{src/extra/tzone}. \item \command{configure} now tests for a C++11-compliant compiler by testing some basic features. This by default tries flags for the compiler specified by \samp{CXX}, but an alternative compiler, options and standard can be specified by variables \samp{CXX1X}, \samp{CXX1XFLAGS} and \samp{CXX1XSTD} (e.g. \samp{-std=gnu++11}). \item \R{} can now optionally be compiled to use reference counting instead of the \code{NAMED} mechanism by defining \code{SWITCH_TO_REFCNT} in \file{Rinternals.h}. This may become the default in the future. \item There is a new option \option{--use-system-tre} to use a suitable system \pkg{tre} library: at present this means a version from their \command{git} repository, after corrections. (Wish of \PR{15660}.) } } \subsection{PACKAGE INSTALLATION}{ \itemize{ \item The \code{CRANextra} repository is no longer a default repository on Windows: all the binary versions of packages from CRAN are now on CRAN, although \code{CRANextra} contains packages from Omegahat and elsewhere used by CRAN packages. \item Only vignettes sources in directory \file{vignettes} are considered to be vignettes and hence indexed as such. \item In the \file{DESCRIPTION} file, \preformatted{ License: X11} is no longer recognized as valid. Use \samp{MIT} or \samp{BSD_2_clause} instead, both of which need \samp{+ file LICENSE}. \item For consistency, entries in \file{.Rinstignore} are now matched case-insensitively on all platforms. \item Help for S4 methods with very long signatures now tries harder to split the description in the \samp{Usage} field to no more than 80 characters per line (some packages had over 120 characters). \item \command{R CMD INSTALL --build} (not Windows) now defaults to the internal \code{tar()} unless \env{R_INSTALL_TAR} is set. \item There is support for compiling C++11 code in packages on suitable platforms: see \sQuote{Writing R Extensions}. \item Fake installs now install the contents of directory \file{inst}: some packages use this to install e.g. C++ headers for use by other packages that are independent of the package itself. Option \option{--no-inst} can be used to get the previous behaviour. } } \subsection{DEBUGGING}{ \itemize{ \item The behaviour of the code browser has been made more consistent, in part following the suggestions in \PR{14985}. \item Calls to \code{browser()} are now consistent with calls to the browser triggered by \code{debug()}, in that \kbd{Enter} will default to \code{n} rather than \code{c}. \item A new browser command \code{s} has been added, to \dQuote{step into} function calls. \item A new browser command \code{f} has been added, to \dQuote{finish} the current loop or function. \item Within the browser, the command \code{help} will display a short list of available commands. } } \subsection{UTILITIES}{ \itemize{ \item Only vignettes sources in directory \file{vignettes} are considered to be vignettes by \command{R CMD check}. That has been the preferred location since \R 2.14.0 and is now obligatory. \item For consistency, \command{R CMD build} now matches entries in \file{.Rbuildignore} and \file{vignettes/.install_extras} case-insensitively on all platforms (not just on Windows). \item \code{checkFF()} (called by \command{R CMD check} by default) can optionally check foreign function calls for consistency with the registered type and argument count. This is the default for \command{R CMD check --as-cran} or can be enabled by setting environment variable \env{_R_CHECK_FF_CALLS_} to \samp{registration} (but is in any case suppressed by \option{--install=no}). Because this checks calls in which \code{.NAME} is an \R object and not just a literal character string, some other problems are detected for such calls. Functions \code{suppressForeignCheck()} and \code{dontCheck()} have been added to allow package authors to suppress false positive reports. \item \command{R CMD check --as-cran} warns about a false value of the \file{DESCRIPTION} field \samp{BuildVignettes} for Open Source packages, and ignores it. (An Open Source package needs to have complete sources for its vignettes which should be usable on a suitably well-equipped system). \item \command{R CMD check --no-rebuild-vignettes} is defunct:\cr \command{R CMD check --no-build-vignettes} has been preferred since \R 3.0.0. \item \command{R CMD build --no-vignettes} is defunct:\cr \command{R CMD build --no-build-vignettes} has been preferred since \R 3.0.0. \item \command{R CMD Sweave} and \command{R CMD Stangle} now process both Sweave and non-Sweave vignettes. The \code{tools::buildVignette()} function has been added to do the same tasks from within \R. \item The flags returned by \command{R CMD config --ldflags} and (where installed) \command{pkg-config --libs libR} are now those needed to link a front-end against the (shared or static) \R library. \item \file{Sweave.sty} has a new option \samp{[inconsolata]}. \item \command{R CMD check} customizations such as \env{_R_CHECK_DEPENDS_ONLY_} make available packages only in \samp{LinkingTo} only for installation, and not for loading/runtime tests. \item \command{tools::checkFF()} reports on \code{.C} and \code{.Fortran} calls with \code{DUP = FALSE} if argument \code{check_DUP} is true. This is selected by \command{R CMD check} by default. \item \command{R CMD check --use-gct} can be tuned to garbage-collect less frequently using \code{gctorture2()} \emph{via} the setting of environment variable \env{_R_CHECK_GCT_N_}. \item Where supported, \code{tools::texi2dvi()} limits the number of passes tried to 20. } } \subsection{C-LEVEL FACILITIES}{ \itemize{ \item (Windows only) A function \code{R_WaitEvent()} has been added (with declaration in header\file{R.h}) to block execution until the next event is received by \R. \item Remapping in the \file{Rmath.h} header can be suppressed by defining \samp{R_NO_REMAP_RMATH}. \item The remapping of \code{rround()} in header \file{Rmath.h} has been removed: use \code{fround()} instead. \item \code{ftrunc()} in header \file{Rmath.h} is now a wrapper for the C99 function \code{trunc()}, which might as well be used in C code: \code{ftrunc()} is still needed for portable C++ code. \item The never-documented remapping of \code{prec()} to \code{fprec()} in header \file{Rmath.h} has been removed. \item The included LAPACK subset now contains \code{ZGESDD} and \code{ZGELSD}. \item The function \code{LENGTH()} now checks that it is only applied to vector arguments. However, in packages \code{length()} should be used. (In \R{} itself \code{LENGTH()} is a macro without the function overhead of \code{length()}.) \item Calls to \code{SET_VECTOR_ELT()} and \code{SET_STRING_ELT()} are now checked for indices which are in-range: several packages were writing one element beyond the allocated length. \item \code{allocVector3} has been added which allows custom allocators to be used for individual vector allocations. } } \subsection{DEPRECATED AND DEFUNCT}{ \itemize{ \item \code{chol(pivot = TRUE, LINPACK = TRUE)} is defunct. Arguments \code{EISPACK} for \code{eigen()} and \code{LINPACK} for \code{chol()}, \code{chol2inv()}, \code{solve()} and \code{svd()} are ignored: LAPACK is always used. \item \code{.find.package()} and \code{.path.package()} are defunct: only the versions without the initial dot introduced in \R 2.13.0 have ever been in the API. \item Partial matching when using the \code{$} operator \emph{on data frames} now throws a warning and may become defunct in the future. If partial matching is intended, replace \code{foo$bar} by \code{foo[["bar", exact = FALSE]]}. \item The long-deprecated use of \code{\\synopsis} in the \samp{Usage} section of \file{.Rd} files has been removed: such sections are now ignored (with a warning). \item \code{package.skeleton()}'s deprecated argument \code{namespace} has been removed. \item Many methods are no longer exported by package \pkg{stats}. They are all registered on their generic, which should be called rather than calling a method directly. \item Functions \code{readNEWS()} and \code{checkNEWS()} in package \pkg{tools} are defunct. \item \code{download.file(method = "lynx")} is deprecated. \item \code{.C(DUP = FALSE)} and \code{.Fortran(DUP = FALSE)} are now deprecated, and may be disabled in future versions of \R. As their help has long said, \code{.Call()} is much preferred. \command{R CMD check} notes such usages (by default). \item The workaround of setting \env{R_OSX_VALGRIND} has been removed: it is not needed in current valgrind. } } \subsection{BUG FIXES}{ \itemize{ \item Calling \code{lm.wfit()} with no non-zero weights gave an array-overrun in the Fortran code and a not very sensible answer. It is now special-cased with a simpler answer (no \code{qr} component). \item Error messages involving non-syntactic names (e.g. as produced by \code{`\\r`} when that object does not exist) now encode the control characters. (Reported by Hadley Wickham.) \item \code{getGraphicsEvent()} caused 100\% usage of one CPU in Windows. (PR#15500) \item \code{nls()} with no \code{start} argument may now work inside another function (scoping issue). \item \code{pbeta()} and similar work better for very large (billions) \code{ncp}. \item Where time zones have changed abbreviations over the years, the software tries to more consistently use the abbreviation appropriate to the time or if that is unknown, the current abbreviation. On some platforms where the C function \code{localtime} changed the \code{tzname} variables the reported abbreviation could have been that of the last time converted. \item \code{all.equal(list(1), identity)} now works. \item Bug fix for pushing viewports in \pkg{grid} (reported by JJ Allaire and Kevin Ushey). NOTE for anyone poking around within the graphics engine display list (despite the warnings not to) that this changes what is recorded by \pkg{grid} on the graphics engine display list. \item Extra checks have been added for unit resolution and conversion in \pkg{grid}, to catch instances of division-by-zero. This may introduce error messages in existing code and/or produce a different result in existing code (but only where a non-finite location or dimension may now become zero). \item Some bugs in TRE have been corrected by updating from the \command{git} repository. This allows \R to be installed on some platforms for which this was a blocker (\PR{15087} suggests Linux on ARM and HP-UX). \item \code{?} applied to a call to an S4 generic failed in several cases. (\PR{15680}) \item The implicit S4 generics for primitives with \code{\dots} in their argument list were incorrect. (\PR{15690}) \item Bug fixes to \code{methods::callGeneric()}. (\PR{15691}) \item The bug fix to \code{aggregrate()} in \PR{15004} introduced a new bug in the case of no grouping variables. (\PR{15699}) \item In rare cases printing deeply nested lists overran a buffer by one byte and on a few platforms segfaulted. (\PR{15679}) \item The dendrogram method of \code{as.dendrogram()} was hidden accidentally, (\PR{15703}), and \code{order.dendrogram(d)} gave too much for a leaf \code{d}. (\PR{15702}) \item \R would try to kill processes on exit that have pids ever used by a child process spawned by \code{mcparallel} even though the current process with that pid was not actually its child. \item \code{cophenetic()} applied to a \code{"dendrogram"} object sometimes incorrectly returned a \code{"Labels"} attribute with dimensions. (\PR{15706}) \item \code{printCoefmat()} called from quite a few \code{print()} methods now obeys small \code{getOption("width")} settings, line wrapping the \samp{"signif. codes"} legend appropriately. (\PR{15708}) \item \code{model.matrix()} assumed that the stored dimnames for a matrix was \code{NULL} or length 2, but length 1 occurred. \item The clipping region for a device was sometimes used in base graphics before it was set. } } } \section{\Rlogo CHANGES IN R 3.0.3}{ \subsection{NEW FEATURES}{ \itemize{ \item On Windows there is support for making \file{.texi} manuals using \command{texinfo} 5.0 or later: the setting is in file \file{src/gnuwin32/MkRules.dist}. A packaging of the Perl script and modules for \command{texinfo} 5.2 has been made available at \url{http://www.stats.ox.ac.uk/pub/Rtools/}. \item \code{write.table()} now handles matrices of \eqn{2^{31}}{2^31} or more elements, for those with large amounts of patience and disc space. \item There is a new function, \code{La_version()}, to report the version of LAPACK in use. \item The HTML version of \sQuote{An Introduction to R} now has links to PNG versions of the figures. \item There is some support to produce manuals in ebook formats. (See \file{doc/manual/Makefile}. Suggested by Mauro Cavalcanti.) \item On a Unix-alike \code{Sys.timezone()} returns \code{NA} if the environment variable \env{TZ} is unset, to distinguish it from an empty string which on some OSes means the \samp{UTC} time zone. \item The backtick may now be escaped in strings, to allow names containing them to be constructed, e.g. \code{`\\``}. (\PR{15621}) \item \code{read.table()}, \code{readLines()} and \code{scan()} now warn when an embedded nul is found in the input. (Related to \PR{15625} which was puzzled by the behaviour in this unsupported case.) \item (Windows only.) \code{file.symlink()} works around the undocumented restriction of the Windows system call to backslashes. (Wish of \PR{15631}.) \item \code{KalmanForecast(fast = FALSE)} is now the default, and the help contains an example of how \code{fast = TRUE} can be used in this version. (The usage will change in 3.1.0.) \item \code{strptime()} now checks the locale only when locale-specific formats are used and caches the locale in use: this can halve the time taken on OSes with slow system functions (e.g. OS X). \item \code{strptime()} and the \code{format()} methods for classes \code{"POSIXct"}, \code{"POSIXlt"} and \code{"Date"} recognize strings with marked encodings: this allows, for example, UTF-8 French month names to be read on (French) Windows. \item \code{iconv(to = "utf8")} is now accepted on all platforms (some implementations did already, but GNU \pkg{libiconv} did not: however converted strings were not marked as being in UTF-8). The official name, \code{"UTF-8"} is still preferred. \item \code{available.packages()} is better protected against corrupt metadata files. (A recurring problem with Debian package \pkg{shogun-r}: \PR{14713}.) \item Finalizers are marked to be run at garbage collection, but run only at a somewhat safer later time (when interrupts are checked). This circumvents some problems with finalizers running arbitrary code during garbage collection (the known instances being running \code{options()} and (C-level) \code{path.expand()} re-entrantly). } } \subsection{INSTALLATION and INCLUDED SOFTWARE}{ \itemize{ \item The included version of PCRE has been updated to 8.34. This fixes bugs and makes the behaviour closer to Perl 5.18. In particular, the concept of \sQuote{space} includes \samp{VT} and hence agrees with POSIX's. } } \subsection{PACKAGE INSTALLATION}{ \itemize{ \item The new field \samp{SysDataCompression} in the \file{DESCRIPTION} file allows user control over the compression used for \file{sysdata.rda} objects in the lazy-load database. \item \code{install.packages(dependencies = value)} for \code{value = NA} (the default) or \code{value = TRUE} omits packages only in \code{LinkingTo} for binary package installs. } } \subsection{C-LEVEL FACILITIES}{ \itemize{ \item The long undocumented remapping of \code{rround()} to \code{Rf_fround()} in header \file{Rmath.h} is now formally deprecated: use \code{fround()} directly. \item Remapping of \code{prec()} and \code{trunc()} in the \file{Rmath.h} header has been disabled in C++ code (it has caused breakage with \code{libc++} headers). } } \subsection{BUG FIXES}{ \itemize{ \item \code{getParseData()} truncated the imaginary part of complex number constants. (Reported by Yihui Xie.) \item \code{dbeta(x, a, b)} with \code{a} or \code{b} within a factor of 2 of the largest representable number could infinite-loop. (Reported by Ioannis Kosmidis.) \item \code{provideDimnames()} failed for arrays with a 0 dimension. (\PR{15465}) \item \code{rbind()} and \code{cbind()} did not handle list objects correctly. (\PR{15468}) \item \code{replayPlot()} now checks if it is replaying a plot from the same session. \item \code{rasterImage()} and \code{grid.raster()} now give error on an empty (zero-length) raster. (Reported by Ben North.) \item \code{plot.lm()} would sometimes scramble the labels in plot type 5. (\PR{15458} and \PR{14837}) \item \code{min()} did not handle \code{NA_character_} values properly. (Reported by Magnus Thor Torfason.) \item (Windows only.) \code{readRegistry()} would duplicate default values for keys. (\PR{15455}) \item \code{str(..., strict.width = "cut")} did not handle it properly when more than one line needed to be cut. (Reported by Gerrit Eichner.) \item Removing subclass back-references when S4 classes were removed or their namespace unloaded had several bugs (e.g., \PR{15481}). \item \code{aggregate()} could fail when there were too many levels present in the \code{by} argument. (\PR{15004}) \item \code{namespaceImportFrom()} needed to detect primitive functions when checking for duplicated imports (reported by Karl Forner). \item \code{getGraphicsEvent()} did not exit when a user closed the graphics window. (\PR{15208}) \item Errors in vignettes were not always captured and displayed properly. (\PR{15495}) \item \code{contour()} could fail when dealing with extremely small z values. (\PR{15454}) \item Several functions did not handle zero-length vectors properly, including \code{browseEnv()}, \code{format()}, \code{gl()}, \code{relist()} and \code{summary.data.frame()}. (E.g., \PR{15499}) \item \code{Sweave()} did not restore the \R{} output to the console if it was interrupted by a user in the middle of evaluating a code chunk. (Reported by Michael Sumner.) \item Fake installs of packages with vignettes work again. \item Illegal characters in the input caused \code{parse()} (and thus \code{source()}) to segfault. (\PR{15518}) \item The nonsensical use of \code{nmax = 1} in \code{duplicated()} or \code{unique()} is now silently ignored. \item \code{qcauchy(p, *)} is now fully accurate even when p is very close to 1. (\PR{15521}) \item The \code{validmu()} and \code{valideta()} functions in the standard \code{glm()} families now also report non-finite values, rather than failing. \item Saved vignette results (in a \file{.Rout.save} file) were not being compared to the new ones during \command{R CMD check}. \item Double-clicking outside of the list box (e.g. on the scrollbar) of a Tk listbox widget generated by \code{tk_select.list()} no longer causes the window to close. (\PR{15407}) \item Improved handling of edge cases in \code{parallel::splitindices()}. (\PR{15552}) \item HTML display of results from \code{help.search()} and \code{??} sometimes contained badly constructed links. \item \code{c()} and related functions such as \code{unlist()} converted raw vectors to invalid logical vectors. (\PR{15535}) \item (Windows only) When a call to \code{system2()} specified one of \code{stdin}, \code{stdout} or \code{stderr} to be a file, but the command was not found (e.g. it contained its arguments, or the program was not on the \env{PATH}), it left the file open and unusable until \R terminated. (Reported by Mathew McLean.) \item The \code{bmp()} device was not recording \code{res = NA} correctly: it is now recorded as 72 ppi. \item Several potential problems with compiler-specific behaviour have been identified using the \sQuote{Undefined Behaviour Sanitizer} in conjunction with the \command{clang} compiler. \item \code{hcl()} now honours \code{NA} inputs (previously they were mapped to black). \item Some translations in base packages were being looked up in the main catalog rather than that for the package. \item As a result of the 3.0.2 change about \sQuote{the last second before the epoch}, most conversions which should have given \code{NA} returned that time. (The platforms affected include Linux and OS X, but not Windows nor Solaris.) \item \code{rowsum()} has more support for matrices and dataframes with \eqn{2^{31}}{2^31} or more elements. (\PR{15587}) \item \code{predict(, interval = "confidence", scale = )} now works. (\PR{15564}) \item The bug fix in 3.0.2 for \PR{15411} was too aggressive, and sometimes removed spaces that should not have been removed. (\PR{15583}) \item Running \R code in a \pkg{tcltk} callback failed to set the busy flag, which will be needed to tell OS X not to \sQuote{App Nap}. \item The code for date-times before 1902 assumed that the offset from GMT in 1902 was a whole number of minutes: that was not true of Paris (as recorded on some platforms). \item Using \code{Sys.setlocale} to set \code{LC_NUMERIC} to \code{"C"} (to restore the sane behavior) no longer gives a warning. \item \code{deparse()} now deparses complex vectors in a way that re-parses to the original values. (\PR{15534}, patch based on code submitted by Alex Bertram.) \item In some extreme cases (more than \eqn{10^{15}}{10^15}) integer inputs to \code{dpqrxxx()} functions might have been rounded up by one (with a warning about being non-integer). (\PR{15624}) \item Plotting symbol \code{pch = 14} had the triangle upside down on some devices (typically screen devices). The triangle is supposed to be point up. (Reported by Bill Venables.) \item \code{getSrcref()} did not work on method definitions if \code{rematchDefinition()} had been used. \item \code{KalmanForecast(fast = FALSE)} reported a (harmless) stack imbalance. \item The count of observations used by \code{KalmanRun()} did not take missing values into account. \item In locales where the abbreviated name of one month is a partial match for the full name of a later one, the \code{\%B} format in \code{strptime()} could fail. An example was French on OS X, where \samp{juin} is abbreviated to \samp{jui} and partially matches \code{juillet}. Similarly for weekday names. \item \code{pbeta(x, a, b, log.p = TRUE)} sometimes underflowed to zero for very small and very differently sized \code{a}, \code{b}. (\PR{15641}) \item \code{approx()} and \code{approxfun()} now handle infinite values with the \code{"constant"} method. (\PR{15655}) \item \code{stripchart()} again respects reversed limits in \code{xlim} and \code{ylim}. (\PR{15664}) } } } \section{\Rlogo CHANGES IN R 3.0.2}{ \subsection{NEW FEATURES}{ \itemize{ \item The \file{NEWS} files have been re-organized. This file contains news for \R >= 3.0.0: news for the 0.x.y, 1.x.y and 2.x.y releases is in files \file{NEWS.0}, \file{NEWS.1} and \file{NEWS.2}. The latter files are now installed when \R is installed. An HTML version of news from 2.10.0 to 2.15.3 is available as \file{doc/html/NEWS.2.html}. \item \code{sum()} for integer arguments now uses an integer accumulator of at least 64 bits and so will be more accurate in the very rare case that a cumulative sum exceeds \eqn{2^{53}}{2^53} (necessarily summing more than 4 million elements). \item The \code{example()} and \code{tools::Rd2ex()} functions now have parameters to allow them to ignore \code{\\dontrun} markup in examples. (Suggested by Peter Solymos.) \item \code{str(x)} is considerably faster for very large lists, or factors with 100,000 levels, the latter as in \PR{15337}. \item \code{col2rgb()} now converts factors to character strings not integer codes (suggested by Bryan Hanson). \item \code{tail(warnings())} now works, via the new \code{`[`} method. \item There is now support for the LaTeX style file \file{zi4.sty} which has in some distributions replaced \file{inconsolata.sty}. \item \code{unlist(x)} now typically returns all non-list \code{x}s unchanged, not just the \dQuote{vector} ones. Consequently, \code{format(lst)} now also works when the list \code{lst} has non-vector elements. \item The \code{tools::getVignetteInfo()} function has been added to give information about installed vignettes. \item New \code{assertCondition()}, etc. utilities in \pkg{tools}, useful for testing. \item Profiling now records non-inlined calls from byte-compiled code to \code{BUILTIN} functions. \item Various functions in \pkg{stats} and elsewhere that use non-standard evaluation are now more careful to follow the namespace scoping rules. E.g. \code{stats::lm()} can now find \code{stats::model.frame()} even if \pkg{stats} is not on the search path or if some package defines a function of that name. \item If an invalid/corrupt \code{.Random.seed} object is encountered in the workspace it is ignored with a warning rather than giving an error. (This allows \R itself to rely on a working RNG, e.g. to choose a random port.) \item \code{seq()} and \code{seq.int()} give more explicit error messages if called with invalid (e.g. \code{NaN}) inputs. \item When \code{parse()} finds a syntax error, it now makes partial parse information available up to the location of the error. (Request of Reijo Sund.) \item Methods invoked by \code{NextMethod()} had a different dynamic parent to the generic. This was causing trouble where S3 methods invoked via lazy evaluation could lose track of their generic. (\PR{15267}) \item Code for the negative binomial distribution now treats the case \code{size == 0} as a one-point distribution at zero. \item \code{abbreviate()} handles without warning non-ASCII input strings which require no abbreviation. \item \code{read.dcf()} no longer has a limit of 8191 bytes per line. (Wish of \PR{15250}.) \item \code{formatC(x)} no longer copies the class of \code{x} to the result, to avoid misuse creating invalid objects as in \PR{15303}. A warning is given if a class is discarded. \item Dataset \code{npk} has been copied from \CRANpkg{MASS} to allow more tests to be run without recommended packages being installed. \item The initialization of the regression coefficients for non-degenerate differenced models in \code{arima()} has been changed and in some examples avoids a local maximum. (\PR{15396}) \item \code{termplot()} now has an argument \code{transform.x} to control the display of individual terms in the plot. (\PR{15329}) \item \code{format()} now supports \code{digits = 0}, to display \code{nsmall} decimal places. \item There is a new read-only \code{par()} parameter called \code{"page"}, which returns a logical value indicating whether the next \code{plot.new()} call will start a new page. \item Processing Sweave and Rd documents to PDF now renders backticks and single quotes better in several instances, including in \samp{\\code} and \samp{\\samp} expressions. \item \code{utils::modifyList()} gets a new argument \code{keep.null} allowing \code{NULL} components in the replacement to be retained, instead of causing corresponding components to be deleted. \item \code{tools::pkgVignettes()} gains argument \code{check}; if set to \code{TRUE}, it will warn when it appears a vignette requests a non-existent vignette engine. } } \subsection{UTILITIES}{ \itemize{ \item \command{R CMD check --as-cran} checks the line widths in usage and examples sections of the package Rd files. \item \command{R CMD check --as-cran} now implies \option{--timings}. \item \command{R CMD check} looks for command \command{gfile} if a suitable \command{file} is not found. (Although \command{file} is not from GNU, OpenCSW on Solaris installs it as \command{gfile}.) \item \command{R CMD build} (with the internal \code{tar}) checks the permissions of \file{configure} and \file{cleanup} files and adds execute permission to the recorded permissions for these files if needed, with a warning. This is useful on OSes and file systems which do not support execute permissions (notably, on Windows). \item \command{R CMD build} now weaves and tangles all vignettes, so suggested packages are not required during package installation if the source tarball was prepared with current \command{R CMD build}. \item \code{checkFF()} (used by \command{R CMD check}) does a better job of detecting calls from other packages, including not reporting those where a function has been copied from another namespace (e.g. as a default method). It now reports calls where \code{.NAME} is a symbol registered in another package. \item On Unix-alike systems, \command{R CMD INSTALL} now installs packages group writably whenever the library (\code{lib.loc}) is group writable. Hence, \code{update.packages()} works for other group members (suggested originally and from a patch by Dirk Eddelbuettel). \item \command{R CMD javareconf} now supports the use of symbolic links for \env{JAVA_HOME} on platforms which have \command{realpath}. So it is now possible to use \preformatted{R CMD javareconf JAVA_HOME=/usr/lib/jvm/java-1.7.0} on a Linux system and record that value rather than the frequently-changing full path such as \file{/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.25.x86_64}. \item (Windows only.) \command{Rscript -e} requires a non-empty argument for consistency with Unix versions of \R. (Also \command{Rterm -e} and \command{R -e}.) \item \command{R CMD check} does more thorough checking of declared packages and namespaces. It reports \itemize{ \item packages declared in more than one of the \samp{Depends}, \samp{Imports}, \samp{Suggests} and \samp{Enhances} fields of the \file{DESCRIPTION} file. \item namespaces declared in \samp{Imports} but not imported from, neither in the \file{NAMESPACE} file nor using the \code{::} nor \code{:::} operators. \item packages which are used in \code{library()} or \code{requires()} calls in the \R code but were already put on the search path \emph{via} \samp{Depends}. \item packages declared in \samp{Depends} not imported \emph{via} the \file{NAMESPACE} file (except the standard packages). Objects used from \samp{Depends} packages should be imported to avoid conflicts and to allow correct operation when the namespace is loaded but not attached. \item objects imported \emph{via} \code{:::} calls where \code{::} would do. \item objects imported by \code{::} which are not exported. \item objects imported by \code{:::} calls which do not exist. } See \sQuote{Writing R Extensions} for good practice. \item \command{R CMD check} optionally checks for non-standard top-level files and directories (which are often mistakes): this is enabled for \option{--as-cran}. \item LaTeX style file \code{upquote.sty} is no longer included (the version was several years old): it is no longer used in \R. A much later version is commonly included in LaTeX distributions but does not play well with the \code{ae} fonts which are the default for Sweave vignettes. \item \command{R CMD build} makes more use of the \file{build} sub-directory of package sources, for example to record information about the vignettes. \item \command{R CMD check} analyses \code{:::} calls. } } \subsection{INSTALLATION and INCLUDED SOFTWARE}{ \itemize{ \item The macros used for the texinfo manuals have been changed to work better with the incompatible changes made in \command{texinfo 5.x}. \item The minimum version for a system \code{xz} library is now 5.0.3 (was 4.999). This is in part to avoid 5.0.2, which can compress in ways other versions cannot decompress. \item The included version of PCRE has been updated to 8.33. \item The included version of \code{zlib} has been updated to 1.2.8, a bug-fix release. \item The included version of xz utils's \code{liblzma} has been updated to 5.0.5. \item Since \command{javareconf} (see above) is used when \R is installed, a stable link for \env{JAVA_HOME} can be supplied then. \item Configuring with \option{--disable-byte-compilation} will override the \file{DESCRIPTION} files of recommended packages, which typically require byte-compilation. \item More of the installation and checking process will work even when \env{TMPDIR} is set to a path containing spaces, but this is not recommended and external software (such as \command{texi2dvi}) may fail. } } \subsection{PACKAGE INSTALLATION}{ \itemize{ \item Installation is aborted immediately if a \code{LinkingTo} package is not installed. \item \command{R CMD INSTALL} has a new option \code{--no-byte-compile} which will override a \samp{ByteCompile} field in the package's \file{DESCRIPTION} file. \item License \samp{BSD} is deprecated: use \samp{BSD_3_clause} or \samp{BSD_2_clause} instead. License \samp{X11} is deprecated: use \samp{MIT} or \samp{BSD_2_clause} instead. \item Version requirements for \code{LinkingTo} packages are now recognized: they are checked at installation. (Fields with version requirements were previously silently ignored.) \item The limit of 500 \code{S3method} entries in a \code{NAMESPACE} file has been removed. \item The default \sQuote{version} of Bioconductor for its packages has been changed to the upcoming \samp{2.13}, but this can be set by the environment variable \env{R_BIOC_VERSION} when \R is installed. } } \subsection{C-LEVEL FACILITIES}{ \itemize{ \item \file{Rdefines.h} has been tweaked so it can be included in C++ code after \file{R_ext/Boolean.h} (which is included by \file{R.h}). Note that \file{Rdefines.h} is not kept up-to-date, and \file{Rinternals.h} is preferred for new code. \item \code{eval} and \code{applyClosure} are now protected against package code supplying an invalid \code{rho}. } } \subsection{DEPRECATED AND DEFUNCT}{ \itemize{ \item The unused \code{namespace} argument to \code{package.skeleton()} is now formally deprecated and will be removed in \R 3.1.0. \item \code{plclust()} is deprecated: use the \code{plot()} method for class \code{"hclust"} instead. \item Functions \code{readNEWS()} and \code{checkNEWS()} in package \pkg{tools} are deprecated (and they have not worked with current \file{NEWS} files for a long time). } } \subsection{DOCUMENTATION}{ \itemize{ \item \sQuote{An Introduction to R} has a new chapter on using \R as a scripting language including interacting with the OS. } } \subsection{BUG FIXES}{ \itemize{ \item \code{help.request()} could not determine the current version of \R on CRAN. (\PR{15241}) \item On Windows, \code{file.info()} failed on root directories unless the path was terminated with an explicit \code{"."}. (\PR{15302}) \item The \code{regmatches<-()} replacement function mishandled results coming from \code{regexpr()}. (\PR{15311}) \item The help for \code{setClass()} and \code{representation()} still suggested the deprecated argument \code{representation=}. (\PR{15312}) \item \command{R CMD config} failed in an installed build of \R 3.0.1 (only) when a sub-architecture was used. (Reported by Berwin Turlach.) \item On Windows, the installer modified the \file{etc/Rconsole} and \file{etc/Rprofile.site} files even when default options were chosen, so the MD5 sums did not refer to the installed versions. (Reported by Tal Galili.) \item \code{plot(hclust(), cex =)} respects \code{cex} again (and possibly others similarly). (Reported by Peter Langfelder.) \item If multiple packages were checked by \command{R CMD check}, and one was written for a different OS, it would set \command{--no-install} for all following packages as well as itself. \item \code{qr.coef()} and related functions did not properly coerce real vectors to complex when necessary. (\PR{15332}) \item \code{ftable(a)} now fixes up empty \code{dimnames} such that the result is printable. \item \code{package.skeleton()} was not starting its search for function objects in the correct place if \code{environment} was supplied. (Reported by Karl Forner.) \item Parsing code was changing the length field of vectors and confusing the memory manager. (\PR{15345}) \item The Fortran routine \code{ZHER2K} in the reference BLAS had a comment-out bug in two places. This caused trouble with \code{eigen()} for Hermitian matrices. (\PR{15345} and report from Robin Hankin) \item \code{vignette()} and \code{browseVignettes()} did not display non-Sweave vignettes properly. \item Two warning/error messages have been corrected: the (optional) warning produced by a partial name match with a pairlist, the error message from a zero-length argument to the \code{:} operator. (Found by Radford Neal; \PR{15358}, \PR{15356}) \item \code{svd()} returned \code{NULL} rather than omitting components as documented. (Found by Radford Neal; \PR{15360}) \item \code{mclapply()} and \code{mcparallel()} with \code{silent = TRUE} could break a process that uses \code{stdout} output unguarded against broken pipes (e.g., \code{zip} will fail silently). To work around such issues, they now replace \code{stdout} with a descriptor pointed to \file{/dev/null} instead. For this purpose, internal \code{closeStdout} and \code{closeStderr} functions have gained the \code{to.null} flag. \item \code{log()}, \code{signif()} and \code{round()} now raise an error if a single named argument is not named \code{x}. (\PR{15361}) \item \code{deparse()} now deparses raw vectors in a form that is syntactically correct. (\PR{15369}) \item The \code{jpeg} driver in Sweave created a JPEG file, but gave it a \file{.png} extension. (\PR{15370}) \item Deparsing of infix operators with named arguments is improved. (\PR{15350}) \item \code{mget()}, \code{seq.int()} and \code{numericDeriv()} did not duplicate arguments properly. (\PR{15352}, \PR{15353}, \PR{15354}) \item \code{kmeans(algorithm = "Hartigan-Wong")} now always stops iterating in the QTran stage. (\PR{15364}). \item \code{read.dcf()} re-allocated incorrectly and so could segfault when called on a file with lines of more than 100 bytes. \item On systems where \code{mktime()} does not set \code{errno}, the last second before the epoch could not be converted from \code{POSIXlt} to \code{POSIXct}. (Reported by Bill Dunlap.) \item \code{add1.glm()} miscalculated F-statistics when df > 1. (Bill Dunlap, \PR{15386}). \item \code{stem()} now discards infinite inputs rather than hanging. (\PR{15376}) \item The parser now enforces C99 syntax for floating point hexadecimal constants (e.g. \code{0x1.1p0}), rather than returning unintended values for malformed constants. (\PR{15234}) \item \code{model.matrix()} now works with very long LHS names (more than 500 bytes). (\PR{15377}) \item \code{integrate()} reverts to the pre-2.12.0 behaviour: from 2.12.0 to 3.0.1 it sometimes failed to achieve the requested tolerance and reported error estimates that were exceeded. (\PR{15219}) \item \code{strptime()} now handles \samp{\%W} fields with value 0. (\PR{15915}) \item \R is now better protected against people trying to interact with the console in startup code. (\PR{15325}) \item Subsetting 1D arrays often lost dimnames (\PR{15301}). \item Unary \code{+} on a logical vector did not coerce to integer, although unary \code{-} did. \item \code{na.omit()} and \code{na.exclude()} added a row to a zero-row data frame. (\PR{15399}) \item All the (where necessary cut-down) vignettes are installed if \R was configured with \option{--without-recommended-packages}. \item \code{source()} did not display filenames when reporting syntax errors. \item Syntax error reports misplaced the caret pointing out the bad token. \item (Windows only) Starting \R with \command{R} (instead of \command{Rterm} or \command{Rgui}) would lose any zero-length strings from the command line arguments. (\PR{15406}) \item Errors in the encoding specified on the command line via \command{--encoding=foo} were not handled properly. (\PR{15405}) \item If \code{x} is a symbol, \code{is.vector(x, "name")} now returns \code{TRUE}, since \code{"name"} and \code{"symbol"} should be synonyms. (Reported by Hervé Pagès.) \item \command{R CMD rtags} works on platforms (such as OS X) with a XSI-conformant shell command \command{echo}. (\PR{15231}) \item \code{is.unsorted(NA)} returns false as documented (rather than \code{NA}). \item \command{R CMD LINK} did not know about sub-architectures. \item \code{system()} and \code{system2()} are better protected against users who misguidedly have spaces in the temporary directory path. \item \code{file.show()} and \code{edit()} are now more likely to work on file paths containing spaces. (Where external utilities are used, not the norm on Windows nor in \command{R.app} which should previously have worked.) \item Packages using the \pkg{methods} package are more likely to work when they import it but it is not attached. (Several parts of its C code were looking for its \R functions on the search path rather than in its namespace.) \item \code{lgamma(-x)} is no longer \code{NaN} for very small x. \item (Windows) \code{system2()} now respects specifying \code{stdout} and \code{stderr} as files if called from \command{Rgui}. (\PR{15393}) \item Closing an \code{x11()} device whilst \code{locator()} or \code{identify()} is in progress no longer hangs \R. (\PR{15253}) \item \code{list.dirs(full.names = FALSE)} was not implemented. (\PR{15170}) \item \code{format()} sometimes added unnecessary spaces. (\PR{15411}) \item \code{all.equal(check.names = FALSE)} would ignore the request to ignore the names and would check them as attributes. \item The symbol set by \code{tools::Rd2txt_options(itemBullet=)} was not respected in some locales. (\PR{15435}) \item \code{mcMap()} was not exported by package \pkg{parallel}. (\PR{15439}) \item \code{plot()} for \code{TukeyHSD} objects did not balance \code{dev.hold()} and \code{dev.flush()} calls on multi-page plots. (\PR{15449}) } } } \section{\Rlogo CHANGES IN R 3.0.1}{ \subsection{NEW FEATURES}{ \itemize{ \item \code{chooseCRANmirror()} and \code{chooseBioCmirror()} gain an \code{ind} argument (like \code{setRepositories()}). \item \code{mcparallel} has a new argument \code{mc.interactive} which can modify the interactive flag in the child process. The new default is \code{FALSE} which makes child processes non-interactive by default (this prevents lock-ups due to children waiting for interactive input). \item \code{scan()} now warns when end-of-file occurs within a quoted string. \item \code{count.fields()} is now consistent with \code{scan()} in its handling of newlines in quoted strings. Instead of triggering an error, this results in the current line receiving \code{NA} as the field count, with the next line getting the total count of the two lines. \item The default method of \code{image()} will plot axes of the class of \code{xlim} and \code{ylim} (and hence of \code{x} and \code{y} if there is a suitable \code{range()} method). Based on a suggestion of Michael Sumner. \item \code{load()} now has a \code{verbose} argument for debugging support, to print the names of objects just before loading them. \item When loading a serialized object encounters a reference to a namespace which cannot be loaded, this is replaced by a reference to the global environment, with a warning. \item \code{pairs()} gains a \code{line.main} option for title placement. \item The remaining instances in which serialization to a raw vector was limited to 2GB have been unlimited on a 64-bit platform, and in most cases serialization to a vector of more than 1GB will be substantially faster. } } \subsection{UTILITIES}{ \itemize{ \item \command{R CMD config} now make use of personal \file{Makevars} files under \file{~/.R} and a site file \file{Makevars.site}, in the same way as \command{R CMD SHLIB} and \command{R CMD INSTALL}. This makes the utility more useful in package \command{configure} scripts. On Windows finding the personal files may require the environment variable \env{HOME} set. The old behaviour can be obtained with the new options \option{--no-user-files} and \option{--no-site-files}. } } \subsection{PACKAGE INSTALLATION}{ \itemize{ \item Alternatives to the site and user customization files \file{Makevars.site} and \file{~/.R/Makevars} can be specified \emph{via} the environment variables \env{R_MAKEVARS_SITE} and \env{R_MAKEVARS_USER} respectively. These can be used to suppress the use of the default files by setting an empty value (where possible) or a non-existent path. } } \subsection{BUG FIXES}{ \itemize{ \item \code{sys.source()} did not report error locations when \code{keep.source = TRUE}. \item \code{as.POSIXct.numeric} was coercing \code{origin} using the \code{tz} argument and not \code{"GMT"} as documented (\PR{14973}). \item The active binding to assign fields in reference classes has been cleaned up to reduce dependence on the class' package environment, also fixing bug in initializing read-only fields (inspired by a report from Hadley Wickham). \item \code{str(d)} no longer gives an error when \code{names(d)} contain illegal multibyte strings (\PR{15247}). \item Profiling of built-in functions with \code{line.profiling= TRUE} did not record the line from which they were called. \item \code{citation(pkg)} dropped the header and footer specified in the \file{CITATION} file (\PR{15257}). \item Quotes were handled differently when reading the first line and reading the rest, so \code{read.table()} misread some files that contained quote characters (\PR{15245}). \item \code{cat()} with \code{sep} a character vector of length greater than one and more than one argument was using separators inconsistently (\PR{15261}). \item On Windows in \R 3.0.0, \code{savePlot()} failed because of an incorrect check on the argument count. \item \code{unzip(list = TRUE)} returned \code{Names} as a factor and not a character vector (as documented) for the internal method. (Noticed by Sean O'Riordain.) \item \code{contourLines()} now checks more comprehensively for conformance of its \code{x}, \code{y} and \code{z} arguments (it was used incorrectly in package \CRANpkg{R2G2}). \item Saved graphics display lists are \R version-specific. Attempting to load workspaces containing them (or some other version-specific objects) aborted the load in \R 3.0.0 and earlier; now it does a partial load and generates a warning instead. \item In \R 3.0.0, \code{identify()} and \code{locator()} did not record information correctly, so replaying a graph (e.g. by copying it to another device) would fail. (\PR{15271}) \item Calling \code{file.copy()} or \code{dirname()} with the invalid input \code{""} (which was being used in packages, despite not being a file path) could have caused a segfault. \code{dirname("")} is now \code{""} rather than \code{"."} (unless it segfaulted). \item \code{supsmu()} could read/write outside its input vectors for very short inputs (seen in package \CRANpkg{rms} for \code{n = 4}). \item \code{as.dendrogram()}'s \code{hclust} method uses less memory and hence gets considerably faster for large (n ~ 1000) clusterings, thanks to Daniel Müllner. (\PR{15174}) \item The return value when all workers failed from \code{parallel::mclapply(mc.preschedule = TRUE)} was a list of strings and not of error objects. (Spotted by Karl Forner and Bernd Bischl.) \item In \R 3.0.0, when \code{help()} found multiple pages with the same alias, the HTML display of all the selections was not produced. (\PR{15282}) \item \code{splinefun(method="monoH.FC")} now produces a function with first argument named \code{x} and allows \code{deriv=3}, as documented. (\PR{15273}) \item \code{summaryRprof()} would only read the first \code{chunksize} lines of an \code{Rprof} file produced with \code{line.profiling=TRUE}. By default, this is the first 100 seconds. (\PR{15288}) \item \code{lsfit()} produced an incorrect error message when argument \code{x} had more columns than rows or \code{x} had a different number of rows than \code{y}. (Spotted by Renaud Gaujoux.) \item Binary operations on equal length vectors copied the class name from the second operand when the first had no class name, but did not set the object bit. (\PR{15299}) \item The \code{trace()} method for reference generator objects failed after those objects became function definitions. \item \code{write.table()} did not check that factors were constructed correctly, and so caused a segment fault when writing bad ones. (\PR{15300}) \item The internal HTTP server no longer chokes on POST requests without body. It will also pass-through other request types for custom handlers (with the method stored in Request-Method header) instead of failing. } } } \section{\Rlogo CHANGES IN R 3.0.0}{ \subsection{SIGNIFICANT USER-VISIBLE CHANGES}{ \itemize{ \item Packages need to be (re-)installed under this version (3.0.0) of \R. \item There is a subtle change in behaviour for numeric index values \eqn{2^{31}}{2^31} and larger. These never used to be legitimate and so were treated as \code{NA}, sometimes with a warning. They are now legal for long vectors so there is no longer a warning, and \code{x[2^31] <- y} will now extend the vector on a 64-bit platform and give an error on a 32-bit one. \item It is now possible for 64-bit builds to allocate amounts of memory limited only by the OS. It may be wise to use OS facilities (e.g. \command{ulimit} in a \command{bash} shell, \command{limit} in \command{csh}), to set limits on overall memory consumption of an \R process, particularly in a multi-user environment. A number of packages need a limit of at least 4GB of virtual memory to load. 64-bit Windows builds of \R are by default limited in memory usage to the amount of RAM installed: this limit can be changed by command-line option \option{--max-mem-size} or setting environment variable \env{R_MAX_MEM_SIZE}. \item Negative numbers for colours are consistently an error: previously they were sometimes taken as transparent, sometimes mapped into the current palette and sometimes an error. } } \subsection{NEW FEATURES}{ \itemize{ \item \code{identical()} has a new argument, \code{ignore.environment}, used when comparing functions (with default \code{FALSE} as before). \item There is a new option, \code{options(CBoundsCheck=)}, which controls how \code{.C()} and \code{.Fortran()} pass arguments to compiled code. If true (which can be enabled by setting the environment variable \env{R_C_BOUNDS_CHECK} to \samp{yes}), raw, integer, double and complex arguments are always copied, and checked for writing off either end of the array on return from the compiled code (when a second copy is made). This also checks individual elements of character vectors passed to \code{.C()}. This is not intended for routine use, but can be very helpful in finding segfaults in package code. \item In \code{layout()}, the limits on the grid size have been raised (again). \item New simple \code{provideDimnames()} utility function. \item Where methods for \code{length()} return a double value which is representable as an integer (as often happens for package \CRANpkg{Matrix}), this is converted to an integer. \item Matrix indexing of dataframes by two-column numeric indices is now supported for replacement as well as extraction. \item \code{setNames()} now has a default for its \code{object} argument, useful for a character result. \item \code{StructTS()} has a revised additive constant in the \code{loglik} component of the result: the previous definition is returned as the \code{loglik0} component. However, the help page has always warned of a lack of comparability of log-likelihoods for non-stationary models. (Suggested by Jouni Helske.) \item The logic in \code{aggregate.formula()} 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. \item \code{install.packages()} has a new argument \code{quiet} to reduce the amount of output shown. \item Setting an element of the graphics argument \code{lwd} to a negative or infinite value is now an error. Lines corresponding to elements with values \code{NA} or \code{NaN} are silently omitted. Previously the behaviour was device-dependent. \item Setting graphical parameters \code{cex}, \code{col}, \code{lty}, \code{lwd} and \code{pch} in \code{par()} now requires a length-one argument. Previously some silently took the first element of a longer vector, but not always when documented to do so. \item \code{Sys.which()} when used with inputs which would be unsafe in a shell (e.g. absolute paths containing spaces) now uses appropriate quoting. \item \code{as.tclObj()} has been extended to handle raw vectors. Previously, it only worked in the other direction. (Contributed by Charlie Friedemann, \PR{14939}.) \item New functions \code{cite()} and \code{citeNatbib()} have been added, to allow generation of in-text citations from \code{"bibentry"} objects. A \code{cite()} function may be added to \code{bibstyle()} environments. \item A \code{sort()} method has been added for \code{"bibentry"} objects. \item The \code{bibstyle()} function now defaults to setting the default bibliography style. The \code{getBibstyle()} function has been added to report the name of the current default style. \item \code{scatter.smooth()} now has an argument \code{lpars} to pass arguments to \code{lines()}. \item \code{pairs()} has a new \code{log} argument, to allow some or all variables to be plotted on logarithmic scale. (In part, wish of \PR{14919}.) \item \code{split()} gains a \code{sep} argument. \item \code{termplot()} does a better job when given a model with interactions (and no longer attempts to plot interaction terms). \item The parser now incorporates code from Romain Francois' \CRANpkg{parser} package, to support more detailed computation on the code, such as syntax highlighting, comment-based documentation, etc. Functions \code{getParseData()} and \code{getParseText()} access the data. \item There is a new function \code{rep_len()} analogous to \code{rep.int()} for when speed is required (and names are not). \item The undocumented use \code{rep(NULL, length.out = n)} for \code{n > 0} (which returns \code{NULL}) now gives a warning. \item \code{demo()} gains an \code{encoding} argument for those packages with non-ASCII demos: it defaults to the package encoding where there is one. \item \code{strwrap()} converts inputs with a marked encoding to the current locale: previously it made some attempt to pass through as bytes inputs invalid in the current locale. \item Specifying both \code{rate} and \code{scale} to \code{[dpqr]gamma} is a warning (if they are essentially the same value) or an error. \item \code{merge()} works in more cases where the data frames include matrices. (Wish of \PR{14974}.) \item \code{optimize()} and \code{uniroot()} no longer use a shared parameter object across calls. (\code{nlm()}, \code{nlminb()} and \code{optim()} with numerical derivatives still do, as documented.) \item The \code{all.equal()} method for date-times is now documented: times are regarded as equal (by default) if they differ by up to 1 msec. \item \code{duplicated()} and \code{unique()} gain a \code{nmax} argument which can be used to make them much more efficient when it is known that there are only a small number of unique entries. This is done automatically for factors. \item Functions \code{rbinom()}, \code{rgeom()}, \code{rhyper()}, \code{rpois()}, \code{rnbinom(),} \code{rsignrank()} and \code{rwilcox()} now return integer (not double) vectors. This halves the storage requirements for large simulations. \item \code{sort()}, \code{sort.int()} and \code{sort.list()} now use radix sorting for factors of less than 100,000 levels when \code{method} is not supplied. So does \code{order()} if called with a single factor, unless \code{na.last = NA}. \item \code{diag()} as used to generate a diagonal matrix has been re-written in C for speed and less memory usage. It now forces the result to be numeric in the case \code{diag(x)} since it is said to have \sQuote{zero off-diagonal entries}. \item \code{backsolve()} (and \code{forwardsolve()}) are now internal functions, for speed and support for large matrices. \item More matrix algebra functions (e.g. \code{chol()} and \code{solve()}) accept logical matrices (and coerce to numeric). \item \code{sample.int()} has some support for \eqn{n \ge 2^{31}}{n >= 2^31}: see its help for the limitations. A different algorithm is used for \code{(n, size, replace = FALSE, prob = NULL)} for \code{n > 1e7} and \code{size <= n/2}. This is much faster and uses less memory, but does give different results. \item \code{approxfun()} and \code{splinefun()} now return a wrapper to an internal function in the \pkg{stats} namespace rather than a \code{.C()} or \code{.Call()} call. This is more likely to work if the function is saved and used in a different session. \item The functions \code{.C()}, \code{.Call()}, \code{.External()} and \code{.Fortran()} now give an error (rather than a warning) if called with a named first argument. \item \code{Sweave()} by default now reports the locations in the source file(s) of each chunk. \item \code{clearPushBack()} is now a documented interface to a long-existing internal call. \item \code{aspell()} gains filters for \R code, Debian Control Format and message catalog files, and support for \R level dictionaries. In addition, package \pkg{utils} now provides functions \code{aspell_package_R_files()} and \code{aspell_package_C_files()} for spell checking \R and C level message strings in packages. \item \code{bibentry()} gains some support for \dQuote{incomplete} entries with a \samp{crossref} field. \item \code{gray()} and \code{gray.colors()} finally allow \code{alpha} to be specified. \item \code{monthplot()} gains parameters to control the look of the reference lines. (Suggestion of Ian McLeod.) \item Added support for new \code{\%~\%} relation (\dQuote{is distributed as}) in plotmath. \item \code{domain = NA} is accepted by \code{gettext()} and \code{ngettext()}, analogously to \code{stop()} etc. \item \code{termplot()} gains a new argument \code{plot = FALSE} which returns information to allow the plots to be modified for use as part of other plots, but does not plot them. (Contributed by Terry Therneau, \PR{15076}.) \item \code{quartz.save()}, formerly an undocumented part of \command{R.app}, is now available to copy a device to a \code{quartz()} device. \code{dev.copy2pdf()} optionally does this for PDF output: \code{quartz.save()} defaults to PNG. \item The default method of \code{pairs()} now allows \code{text.panel = NULL} and the use of \code{.panel = NULL} is now documented. \item \code{setRefClass()} and \code{getRefClass()} now return class generator functions, similar to \code{setClass()}, but still with the reference fields and methods as before (suggestion of Romain Francois). \item New functions \code{bitwNot()}, \code{bitwAnd()}, \code{bitwOr()} and \code{bitwXor()}, using the internal interfaces previously used for classes \code{"octmode"} and \code{"hexmode"}. Also \code{bitwShiftL()} and \code{bitwShiftR()} for shifting bits in elements of integer vectors. \item New option \code{"deparse.cutoff"} to control the deparsing of language objects such as calls and formulae when printing. (Suggested by a comment of Sarah Goslee.) \item \code{colors()} gains an argument \code{distinct}. \item New \code{demo(colors)} and \code{demo(hclColors)}, with utility functions. \item \code{list.files()} (aka \code{dir()}) gains a new optional argument \code{no..} which allows to exclude \code{"."} and \code{".."} from listings. \item Multiple time series are also of class \code{"matrix"}; consequently, \code{head()}, e.g., is more useful. \item \code{encodeString()} preserves UTF-8 marked encodings. Thus if factor levels are marked as UTF-8 an attempt is made to print them in UTF-8 in \command{RGui} on Windows. \item \code{readLines()} and \code{scan()} (and hence \code{read.table()}) in a UTF-8 locale now discard a UTF-8 byte-order-mark (BOM). Such BOMs are allowed but not recommended by the Unicode Standard: however Microsoft applications can produce them and so they are sometimes found on websites. The encoding name \code{"UTF-8-BOM"} for a connection will ensure that a UTF-8 BOM is discarded. \item \code{mapply(FUN, a1, ..)} now also works when \code{a1} (or a further such argument) needs a \code{length()} method (which the documented arguments never do). (Requested by Hervé Pagès; with a patch.) \item \code{.onDetach()} is supported as an alternative to \code{.Last.lib}. Unlike \code{.Last.lib}, this does not need to be exported from the package's namespace. \item The \code{srcfile} argument to \code{parse()} may now be a character string, to be used in error messages. \item The \code{format()} method for \code{ftable} objects gains a \code{method} argument, propagated to \code{write.ftable()} and \code{print()}, allowing more compact output, notably for LaTeX formatting, thanks to Marius Hofert. \item The \code{utils::process.events()} function has been added to trigger immediate event handling. \item \code{Sys.which()} now returns \code{NA} (not \code{""}) for \code{NA} inputs (related to \PR{15147}). \item The \code{print()} method for class \code{"htest"} gives fewer trailing spaces (wish of \PR{15124}). Also print output from \code{HoltWinters()}, \code{nls()} and others. \item \code{loadNamespace()} allows a version specification to be given, and this is used to check version specifications given in the \samp{Imports} field when a namespace is loaded. \item \code{setClass()} has a new argument, \code{slots}, clearer and less ambiguous than \code{representation}. It is recommended for future code, but should be back-compatible. At the same time, the allowed slot specification is slightly more general. See the documentation for details. \item \code{mget()} now has a default for \code{envir} (the frame from which it is called), for consistency with \code{get()} and \code{assign()}. \item \code{close()} now returns an integer status where available, invisibly. (Wish of \PR{15088}.) \item The internal method of \code{tar()} can now store paths too long for the \samp{ustar} format, using the (widely supported) GNU extension. It can also store long link names, but these are much less widely supported. There is support for larger files, up to the \samp{ustar} limit of 8GB. \item Local reference classes have been added to package \pkg{methods}. These are a technique for avoiding unneeded copying of large components of objects while retaining standard \R functional behavior. See \code{?LocalReferenceClasses}. \item \code{untar()} has a new argument \code{restore_times} which if false (not the default) discards the times in the tarball. This is useful if they are incorrect (some tarballs submitted to \acronym{CRAN} have times in a local time zone or many years in the past even though the standard required them to be in UTC). \item \code{replayplot()} cannot (and will not attempt to) replay plots recorded under \R < 3.0.0. It may crash the \R session if an attempt is made to replay plots created in a different build of \R >= 3.0.0. \item Palette changes get recorded on the display list, so replaying plots (including when resizing screen devices and using \code{dev.copy()}) will work better when the palette is changed during a plot. \item \code{chol(pivot = TRUE)} now defaults to LAPACK, not LINPACK. \item The \code{parse()} function has a new parameter \code{keep.source}, which defaults to \code{options("keep.source")}. \item Profiling via \code{Rprof()} now optionally records information at the statement level, not just the function level. \item The \code{Rprof()} function now quotes function names in in its output file on Windows, to be consistent with the quoting in Unix. \item Profiling via \code{Rprof()} now optionally records information about time spent in GC. \item The HTML help page for a package now displays non-vignette documentation files in a more accessible format. \item To support \code{options(stringsAsFactors = FALSE)}, \code{model.frame()}, \code{model.matrix()} and \code{replications()} now automatically convert character vectors to factors without a warning. \item The \code{print} method for objects of class \code{"table"} now detects tables with 0-extents and prints the results as, e.g., \samp{< table of extent 0 x 1 x 2 >}. (Wish of \PR{15198}.) \item Deparsing involving calls to anonymous functions has been made closer to reversible by the addition of extra parentheses. \item The function \code{utils::packageName()} has been added as a lightweight version of \code{methods::getPackageName()}. \item \code{find.package(lib.loc = NULL)} now treats loaded namespaces preferentially in the same way as attached packages have been for a long time. \item In Windows, the Change Directory dialog now defaults to the current working directory, rather than to the last directory chosen in that dialog. \item \code{available.packages()} gains a \code{"license/restricts_use"} filter which retains only packages for which installation can proceed solely based on packages which are guaranteed not to restrict use. \item New \code{check_packages_in_dir()} function in package \pkg{tools} for conveniently checking source packages along with their reverse dependencies. \item R's completion mechanism has been improved to handle help requests (starting with a question mark). In particular, help prefixes are now supported, as well as quoted help topics. To support this, completion inside quotes are now handled by R by default on all platforms. \item The memory manager now allows the strategy used to balance garbage collection and memory growth to be controlled by setting the environment variable \env{R_GC_MEM_GROW}. See \code{?Memory} for more details. \item (\sQuote{For experts only}, as the introductory manual says.) The use of environment variables \env{R_NSIZE} and \env{R_VSIZE} to control the initial (= minimum) garbage collection trigger for number of cons cels and size of heap has been restored: they can be overridden by the command-line options \code{--min-nsize} and \code{--min-vsize}; see \code{?Memory}. \item On Windows, the device name for bitmap devices as reported by \code{.Device} and \code{.Devices} no longer includes the file name. This is for consistency with other platforms and was requested by the \CRANpkg{lattice} maintainer. \code{win.metafile()} still uses the file name: the exact form is used by package \CRANpkg{tkrplot}. \item \code{set.seed(NULL)} re-initializes \code{.Random.seed} as done at the beginning of the session if not already set. (Suggestion of Bill Dunlap.) \item The \code{breaks} argument in \code{hist.default()} can now be a function that returns the breakpoints to be used (previously it could only return the suggested number of breakpoints). \item File \file{share/licenses/licenses.db} has some clarifications, especially as to which variants of \sQuote{BSD} and \sQuote{MIT} is intended and how to apply them to packages. The problematic licence \sQuote{Artistic-1.0} has been removed. } } \subsection{LONG VECTORS}{ This section applies only to 64-bit platforms. \itemize{ \item There is support for vectors longer than \eqn{2^{31}-1}{2^31 - 1} elements. This applies to raw, logical, integer, double, complex and character vectors, as well as lists. (Elements of character vectors remain limited to \eqn{2^{31}-1}{2^31 - 1} bytes.) \item Most operations which can sensibly be done with long vectors work: others may return the error \sQuote{long vectors not supported yet}. Most of these are because they explicitly work with integer indices (e.g. \code{anyDuplicated()} and \code{match()}) or because other limits (e.g. of character strings or matrix dimensions) would be exceeded or the operations would be extremely slow. \item \code{length()} returns a double for long vectors, and lengths can be set to \eqn{2^{31}}{2^31} or more by the replacement function with a double value. \item Most aspects of indexing are available. Generally double-valued indices can be used to access elements beyond \eqn{2^{31}-1}{2^31 - 1}. \item There is some support for matrices and arrays with each dimension less than \eqn{2^{31}}{2^31} but total number of elements more than that. Only some aspects of matrix algebra work for such matrices, often taking a very long time. In other cases the underlying Fortran code has an unstated restriction (as was found for complex \code{svd()}). \item \code{dist()} can produce dissimilarity objects for more than 65536 rows (but for example \code{hclust()} cannot process such objects). \item \code{serialize()} to a raw vector is unlimited in size (except by resources). \item The C-level function \code{R_alloc} can now allocate \eqn{2^{35}}{2^35} or more bytes. \item \code{agrep()} and \code{grep()} will return double vectors of indices for long vector inputs. \item Many calls to \code{.C()} have been replaced by \code{.Call()} to allow long vectors to be supported (now or in the future). Regrettably several packages had copied the non-API \code{.C()} calls and so failed. \item \code{.C()} and \code{.Fortran()} do not accept long vector inputs. This is a precaution as it is very unlikely that existing code will have been written to handle long vectors (and the \R wrappers often assume that \code{length(x)} is an integer). \item Most of the methods for \code{sort()} work for long vectors. \code{rank()}, \code{sort.list()} and \code{order()} support long vectors (slowly except for radix sorting). \item \code{sample()} can do uniform sampling from a long vector. } } \subsection{PERFORMANCE IMPROVEMENTS}{ \itemize{ \item More use has been made of \R objects representing registered entry points, which is more efficient as the address is provided by the loader once only when the package is loaded. This has been done for packages \code{base}, \code{methods}, \code{splines} and \code{tcltk}: it was already in place for the other standard packages. Since these entry points are always accessed by the \R entry points they do not need to be in the load table which can be substantially smaller and hence searched faster. This does mean that \code{.C} / \code{.Fortran} / \code{.Call} calls copied from earlier versions of \R may no longer work -- but they were never part of the API. \item Many \code{.Call()} calls in package \pkg{base} have been migrated to \code{.Internal()} calls. \item \code{solve()} makes fewer copies, especially when \code{b} is a vector rather than a matrix. \item \code{eigen()} makes fewer copies if the input has dimnames. \item Most of the linear algebra functions make fewer copies when the input(s) are not double (e.g. integer or logical). \item A foreign function call (\code{.C()} etc) in a package without a \code{PACKAGE} argument will only look in the first DLL specified in the \file{NAMESPACE} file of the package rather than searching all loaded DLLs. A few packages needed \code{PACKAGE} arguments added. \item The \code{@<-} operator is now implemented as a primitive, which should reduce some copying of objects when used. Note that the operator object must now be in package \pkg{base}: do not try to import it explicitly from package \pkg{methods}. } } \subsection{PACKAGE INSTALLATION}{ \itemize{ \item The transitional support for installing packages without namespaces (required since \R 2.14.0) has been removed. \command{R CMD build} will still add a namespace, but a \code{.First.lib()} function will need to be converted. \command{R CMD INSTALL} no longer adds a namespace (so installation will fail), and a \code{.First.lib()} function in a package will be ignored (with an installation warning for now). As an exception, packages without a \file{R} directory and no \file{NAMESPACE} file can still be installed. \item Packages can specify in their \file{DESCRIPTION file} a line like \preformatted{ Biarch: yes } to be installed on Windows with \option{--force-biarch}. \item Package vignettes can now be processed by other engines besides \code{Sweave}; see \sQuote{Writing R Extensions} and the \code{tools::vignetteEngine} help topic for details. \item The \file{*.R} tangled source code for vignettes is now included in tarballs when \command{R CMD build} is used to produce them. In \R 3.0.0, \file{*.R} files not in the sources will be produced at install time, but eventually this will be dropped. \item The package type \code{"mac.binary"} now looks in a path in the repository without any Mac subtype (which used to be \samp{universal} or \samp{leopard}): it looks in \file{bin/macosx/contrib/3.0} rather than \file{bin/macosx/leopard/contrib/2.15}). This is the type used for the \acronym{CRAN} binary distribution for OS X as from \R 3.0.0. \item File \file{etc/Makeconf} makes more use of the macros \code{$(CC)}, \code{$(CXX)}, \code{$(F77)} and \code{$(FC)}, so the compiler in use can be changed by setting just these (and if necessary the corresponding flags and \code{FLIBS}) in file \file{~/.R/Makevars}. This is convenient for those working with binary distributions of \R, e.g. on OS X. } } \subsection{UTILITIES}{ \itemize{ \item \command{R CMD check} now gives a warning rather than a note if it finds calls to \code{abort}, \code{assert} or \code{exit} in compiled code, and has been able to find the \file{.o} file in which the calls occur. Such calls can terminate the \R process which loads the package. \item The location of the build and check environment files can now be specified by the environment variables \env{R_BUILD_ENVIRON} and \env{R_CHECK_ENVIRON}, respectively. \item \command{R CMD Sweave} gains a \option{--compact} option to control possibly reducing the size of the PDF file it creates when \option{--pdf} is given. \item \command{R CMD build} now omits Eclipse's \file{.metadata} directories, and \command{R CMD check} warns if it finds them. \item \command{R CMD check} now does some checks on functions defined within reference classes, including of \code{.Call()} etc calls. \item \command{R CMD check --as-cran} notes assignments to the global environment, calls to \code{data()} which load into the global environment, and calls to \code{attach()}. \item \command{R CMD build} by default uses the internal method of \code{tar()} to prepare the tarball. This is more likely to produce a tarball compatible with \command{R CMD INSTALL} and \command{R CMD check}: an external \command{tar} program, including options, can be specified \emph{via} the environment variable \env{R_BUILD_TAR}. \item \code{tools::massageExamples()} is better protected against packages which re-define base functions such as \code{cat()} and \code{get()} and so can cause \command{R CMD check} to fail when checking examples. \item \command{R CMD javareconf} has been enhanced to be more similar to the code used by \command{configure}. There is now a test that a JNI program can be compiled (like \command{configure} did) and only working settings are used. It makes use of custom settings from configuration recorded in \file{etc/javaconf}. \item The \option{--no-vignettes} argument of \command{R CMD build} has been renamed to the more accurate \option{--no-build-vignettes}: its action has always been to (re)build vignettes and never omitted them. \command{R CMD check} accepts \option{--no-build-vignettes} as a preferred synonym for \option{--no-rebuild-vignettes}. } } \subsection{DEPRECATED AND DEFUNCT}{ \itemize{ \item The \code{ENCODING} argument to \code{.C()} is defunct. Use \code{iconv()} instead. \item The \code{.Internal(eval.with.vis)} non-API function has been removed. \item Support for the converters for use with \code{.C()} has been removed, including the oft misused non-API header \file{R_ext/RConverters.h}. \item The previously deprecated uses of \code{array()} with a 0-length \code{dim} argument and \code{tapply()} with a 0-length \code{INDEX} list are now errors. \item \samp{Translation} packages are defunct. \item Calling \code{rep()} or \code{rep.int()} on a pairlist or other non-vector object is now an error. \item Several non-API entry points have been transferred to packages (e.g. \code{R_zeroin2}) or replaced by different non-API entry points (e.g. \code{R_tabulate}). \item The \sQuote{internal} graphics device invoked by \code{.Call("R_GD_nullDevice", package = "grDevices")} has been removed: use \code{pdf(file = NULL)} instead. \item The \code{.Fortran()} entry point \code{"dqrls"} which has not been used by \R since version 2.15.1 is no longer available. \item Functions \code{traceOn()} and \code{traceOff()} in package \pkg{methods} are now defunct. \item Function \code{CRAN.packages()} is finally defunct. \item Use of \code{col2rgb(0)} is defunct: use \code{par("bg")} or \code{NA} instead. \item The long-defunct functions \code{Rd_parse()}, \code{anovalist.lm()}, \code{categpry()}, \code{clearNames()}, \code{gammaCody()}, \code{glm.fit.null()}, \code{lm.fit.null()}, \code{lm.wfit.null()}, \code{manglePackageNames()}, \code{mauchley.test()}, \code{package.contents()}, \code{print.coefmat()}, \code{reshapeLong()}, \code{reshapeWide()}, \code{tkclose()}, \code{tkcmd()}, \code{tkfile.dir()}, \code{tkfile.tail()}, \code{tkopen()}, \code{tkputs()}, \code{tkread()}, \code{trySilent()} and \code{zip.file.extract()} have been removed entirely (but are still documented in the help system). \item The unused \code{dataPath} argument to \code{attachNamespace()} has been removed. \item \code{grid.prompt()} has been removed: use \code{devAskNewPage()} instead. \item The long-deprecated \code{intensities} component is no longer returned by \code{hist()}. \item \code{mean()} for data frames and \code{sd()} for data frames and matrices are defunct. \item \code{chol(pivot = FALSE, LINPACK = TRUE)}, \code{ch2inv(LINPACK = TRUE)}, \code{eigen(EISPACK = TRUE)}, \code{solve(LINPACK = TRUE)} and \code{svd(LINPACK = TRUE)} are defunct: LAPACK will be used, with a warning. \item The \code{keep.source} argument to \code{library()} and \code{require()} is defunct. This option needs to be set at install time. \item Documentation for \code{real()}, \code{as.real()} and \code{is.real()} has been moved to \sQuote{defunct} and the functions removed. \item The \code{maxRasters} argument of \code{pdf()} (unused since \R 2.14.0) has been removed. \item The unused \code{fontsmooth} argument has been removed from the \code{quartz()} device. \item All the (non-API) EISPACK entry points in \R have been removed. \item \code{chol(pivot = TRUE, LINPACK = TRUE)} is deprecated. \item The long-deprecated use of \code{\\synopsis} in the \samp{Usage} section of \file{.Rd} files will be removed in \R 3.1.0. \item \code{.find.package()} and \code{.path.package()} are deprecated: only the public versions without the dot have ever been in the API. \item In a package's \file{DESCRIPTION} file, \preformatted{ License: X11} is deprecated, since it includes \sQuote{Copyright (C) 1996 X Consortium} which cannot be appropriate for a current \R package. Use \sQuote{MIT} or \sQuote{BSD_2_clause} instead. } } \subsection{CODE MIGRATION}{ \itemize{ \item The C code underlying base graphics has been migrated to the \pkg{graphics} package (and hence no longer uses \code{.Internal()} calls). \item Most of the \code{.Internal()} calls used in the \pkg{stats} package have been migrated to C code in that package. This means that a number of \code{.Internal()} calls which have been used by packages no longer exist, including \code{.Internal(cor)} \code{.Internal(cov)}, \code{.Internal(optimhess)} and \code{.Internal(update.formula)}. \item Some \code{.External()} calls to the \code{base} package (really to the \R executable or shared library) have been moved to more appropriate packages. Packages should not have been using such calls, but some did (mainly those used by \code{integrate()}). } } \subsection{PACKAGE parallel}{ \itemize{ \item There is a new function \code{mcaffinity()} which allows getting or setting the CPU affinity mask for the current \R process on systems that supports this (currently only Linux has been tested successfully). It has no effect on systems which do not support process affinity. Users are not expected to use this function directly (with the exception of fixing libraries that break affinity settings like OpenBLAS) -- the function is rather intended to support affinity control in high-level parallel functions. In the future, \R may supplement lack of affinity control in the OS by its own bookkeeping via \code{mcaffinity()} related to processes and threads it spawns. \item \code{mcparallel()} has a new argument \code{mc.affinity} which attempts to set the affinity of the child process according to the specification contained therein. \item The port used by socket clusters is chosen randomly: this should help to avoid clashes observed when two users of a multi-user machine try to create a cluster at the same time. To reproduce the previous behaviour set environment variable \env{R_PARALLEL_PORT} to \code{10187}. } } \subsection{C-LEVEL FACILITIES}{ \itemize{ \item There has been some minor re-organization of the non-API header files. In particular, \file{Rinternals.h} no longer includes the non-API header \file{R_exts/PrtUtil.h}, and that no longer includes \file{R_exts/Print.h}. \item Passing \code{NULL} to \code{.C()} is now an error. \item \code{.C()} and \code{.Fortran()} now warn if \code{"single"} arguments are used with \code{DUP = FALSE}, as changes to such arguments are not returned to the caller. \item C entry points \code{R_qsort} and \code{R_qsort_I} now have \code{start} and \code{end} as \code{size_t} to allow them to work with longer vectors on 64-bit platforms. Code using them should be recompiled. \item A few recently added C entry points were missing the remapping to \code{Rf_}, notably \code{[dpq]nbinom_mu}. \item Some of the interface pointers formerly available only to \command{R.app} are now available to front-ends on all Unix-alikes: one has been added for the interface to \code{View()}. \item \code{PACKAGE = ""} is now an error in \code{.C()} etc calls: it was always contrary to the documentation. \item Entry point \code{rcont2} has been migrated to package \pkg{stats} and so is no longer available. \item \code{R_SVN_REVISION} in \file{Rversion.h} is now an integer (rather than a string) and hence usable as e.g. \code{#if R_SVN_REVISION < 70000}. \item The entry points \code{rgb2hsv} and \code{hsv2rgb} have been migrated to package \pkg{grDevices} and so are no longer available. \item \code{R_GE_version} has been increased to \code{10} and \code{name2col} removed (use \code{R_GE_str2col} instead). \R internal colour codes are now defined using the typedef \code{rcolor}. \item The \code{REPROTECT} macro now checks that the protect index is valid. \item Several non-API entry points no longer used by \R have been removed, including the Fortran entry points \code{chol}, \code{chol2inv}, \code{cg}, \code{ch} and \code{rg}, and the C entry points \code{Brent_fmin}, \code{fft_factor} and \code{fft_work}. \item If a \code{.External} call is registered with a number of arguments (other than \code{-1}), the number of arguments passed is checked for each call (as for other foreign function calls). \item It is now possible to write custom connection implementations outside core R using \file{R_ext/Connections.h}. Please note that the implementation of connections is still considered internal and may change in the future (see the above file for details). } } \subsection{INTERNATIONALIZATION}{ \itemize{ \item The management of translations has been converted to \R code: see \code{?tools::update_pkg_po}. \item The translations for the \R interpreter and \command{RGui.exe} are now part of the \pkg{base} package (rather than having sources in directory \file{po} and being installed to \file{share/locale}). Thus the \pkg{base} package supports three translation domains, \code{R-base}, \code{R} and \code{RGui}. \item The compiled translations which ship with \R are all installed to the new package \pkg{translations} for easier updating. The first package of that name found on \code{.libPaths()} at the start of the \R session will be used. (It is possible messages will be used before \code{.libPaths()} is set up in which case the default translations will be used: set environment variable \env{R_TRANSLATIONS} to point to the location of the intended \pkg{translations} package to use this right from the start.) \item The translations form a separate group in the Windows installer, so can be omitted if desired. \item The markup for many messages has been changed to make them easier to translate, incorporating suggestions from Łukasz Daniel. } } \subsection{INSTALLATION}{ \itemize{ \item There is again support for building without using the C \sQuote{long double} type. This is required by C99, but system implementations can be slow or flawed. Use \command{configure} option \option{--disable-long-double}. \item \command{make pdf} and \command{make install-pdf} now make and install the full reference index (including all base and recommended packages). \item The 'reference manual' on the Windows GUI menu and included in the installer is now the full reference index, including all base and recommended packages. \item \R help pages and manuals have no ISBNs because ISBN rules no longer allow constantly changing content to be assigned an ISBN. \item The Windows installer no longer installs a Start Menu link to the static help pages; as most pages are generated dynamically, this led to a lot of broken links. \item Any custom settings for Java configuration are recorded in file \file{etc/javaconf} for subsequent use by \command{R CMD javareconf}. \item There is now support for \command{makeinfo} version 5.0 (which requires a slightly different \file{.texi} syntax). \item The minimum versions for \option{--use-system-zlib} and \code{--use-system-pcre} are now tested as 1.2.5 and 8.10 respectively. \item On Windows, the stack size is reduced to 16MB on 32-bit systems: misguided users were launching many threads without controlling the stack size. \item \command{configure} no longer looks for file \file{~/.Rconfig}: \file{~/.R/config} has long been preferred. } } \subsection{BUG FIXES}{ \itemize{ \item When \command{R CMD build} is run in an encoding other than the one specified in the package's \file{DESCRIPTION} file it tries harder to expand the \code{authors@R} field in the specified encoding. (\PR{14958}) \item If \command{R CMD INSTALL} is required to expand the \code{authors@R} field of the \file{DESCRIPTION} file, it tries harder to do so in the encoding specified for the package (rather than using ASCII escapes). \item Fix in package \pkg{grid} for pushing a viewport into a layout cell, where the layout is within a viewport that has zero physical 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.) \item \code{solve(A, b)} for a vector \code{b} gave the answer names from \code{colnames(A)} for \code{LINPACK = TRUE} but not in the default case. \item \code{La.svd()} accepts logical matrices (as documented, and as \code{svd()} did). \item \code{legend()} now accepts negative \code{pch} values, in the same way \code{points()} long has. \item Parse errors when installing files now correctly display the name of the file containing the bad code. \item In Windows, tcltk windows were not always properly constructed. (\PR{15150}) \item The internal functions implementing \code{parse()}, \code{tools::parseLatex()} and \code{tools::parse_Rd()} were not reentrant, leading to errors in rare circumstances such as a garbage collection triggering a recursive call. \item Field assignments in reference class objects via \code{$<-} were not being checked because the magic incantation to turn methods on for that primitive operator had been inadvertently omitted. %$ \item \code{setHook(hookname, value, action="replace")} set the hook to be the value, rather than a list containing the value as documented. (\PR{15167}) \item If a package used a \file{NEWS.Rd} file, the main HTML package index page did not link to it. (Reported by Dirk Eddelbuettel.) \item The primitive implementation of \code{@<-} was not checking the class of the replacement. It now does a check, quicker but less general than \code{slot<-}. See the help. \item \code{split(x, f)} now recycles classed objects \code{x} in the same way as vectors. (Reported by Martin Morgan.) \item \code{pbeta(.28, 1/2, 2200, lower.tail=FALSE, log.p=TRUE)} is no longer \code{-Inf}; ditto for corresponding \code{pt()} and \code{pf()} calls, such as \code{pt(45, df=5000, lower.tail=FALSE, log.p=TRUE)}. (\PR{15162}) \item The Windows graphics device would crash \R{} if a user attempted to load the graphics history from a variable that was not a saved history. (\PR{15230}) \item The workspace size for the \code{predict()} method for \code{loess()} could exceed the maximum integer size. (Reported by Hiroyuki Kawakatsu.) \item \code{ftable(x, row.vars, col.vars)} now also works when the \code{*.vars} arguments are (integer or character vectors) of length zero. \item Calling \code{cat()} on a malformed UTF-8 string could cause the Windows GUI to lock up. (\PR{15227}) \item \code{removeClass(cc)} gave "node stack overflow" for some class definitions containing \code{"array"} or \code{"matrix"}. } } } \section{CHANGES in previous versions}{ \itemize{ \item Older news can be found in text format in files \ifelse{html}{\href{../NEWS.0}{NEWS.0}, \href{../NEWS.1}{NEWS.1} and \href{../NEWS.2}{NEWS.2}}{\file{NEWS.0}, \file{NEWS.1} and \file{NEWS.2}} in the \file{doc} directory. News in HTML format for \R versions from 2.10.0 to 2.15.3 is in \ifelse{html}{\url{NEWS.2.html}}{\file{doc/html/NEWS.2.html}}. } }