[R] R 3.1.0 is released

Peter Dalgaard pd.mes at cbs.dk
Thu Apr 10 12:07:38 CEST 2014


(Resend with correct Subject field.)

The build system rolled up R-3.1.0.tar.gz (codename "Spring Dance") this morning.

The list below details the changes in this release.

You can get the source code from

http://cran.r-project.org/src/base/R-3/R-3.1.0.tar.gz

or wait for it to be mirrored at a CRAN site nearer to you.

Binaries for various platforms will appear in due course.

(There seems to be a minor mishap with the NEWS file not getting copied to CRAN. I'll attend to that shortly.)


For the R Core Team

Peter Dalgaard


These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:

MD5 (AUTHORS) = cbf6da8f886ccd8d0dda0cc7ffd1b8ec
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = 2978039f3d69bde1d31c5a3699dbe88a
MD5 (INSTALL) = 3964b9119adeaab9ceb633773fc94aac
MD5 (NEWS.html) = d88192d6e47eec39df1fe6ba3d673ae0
MD5 (R-latest.tar.gz) = a1ee52446bee81820409661e6d114ab1
MD5 (README) = e259ae5dd943b8547f0b7719664e815b
MD5 (RESOURCES) = c7cb32499ebbf85deb064aab282f93a4
MD5 (THANKS) = d4b45e302b7cad0fc4bb50d2cfe69649
MD5 (R-3/R-3.1.0.tar.gz) = a1ee52446bee81820409661e6d114ab1



This is the relevant part of the NEWS file


CHANGES IN R 3.1.0:

 NEW FEATURES:

   * type.convert() (and hence by default 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
     colClasses in read.table() to be "numeric".

   * tools::Rdiff(useDiff = FALSE) is closer to the POSIX definition
     of diff -b (as distinct from the description in the man pages of
     most systems).

   * New function anyNA(), a version of any(is.na(.)) which is fast
     for atomic vectors, based on a proposal by Tim Hesterberg. (Wish
     of PR#15239.)

   * arrayInd(*, useNames = TRUE) and, analogously, which(*, arr.ind =
     TRUE) now make use of names(.dimnames) when available.

   * is.unsorted() now also works for raw vectors.

   * The "table" method for as.data.frame() (also useful as
     as.data.frame.table()) now passes sep and base arguments to
     provideDimnames().

   * uniroot() gets new optional arguments, notably extendInt,
     allowing to auto-extend the search interval when needed.  The
     return value has an extra component, init.it.

   * switch(f, ...) now warns when f is a factor, as this typically
     happens accidentally where the useR meant to pass a character
     string, but f is treated as integer (as always documented).

   * The parser has been modified to use less memory.

   * The way the unary operators (+ - !) 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.

   * colorRamp() and colorRampPalette() now allow non-opaque colours
     and a ramp in opacity via the new argument alpha = TRUE.
     (Suggested by Alberto Krone-Martins, but optionally as there are
     existing uses which expect only RGB values.)

   * grid.show.layout() and grid.show.viewport() get an optional vp.ex
     argument.

   * There is a new function find_gs_cmd() in the tools package to
     locate a GhostScript executable.  (This is an enhanced version of
     a previously internal function there.)

   * object.size() gains a format() method.

   * There is a new family, "ArialMT", for the pdf() and postscript()
     devices.  This will only be rendered correctly on viewers which
     have access to Monotype TrueType fonts (which are sometimes
     requested by journals).

   * The text and PDF news files, including NEWS and NEWS.2, have been
     moved to the doc directory.

   * combn(x, simplify = TRUE) now gives a factor result for factor
     input x (previously user error).  (Related to PR#15442.)

   * Added utils::fileSnapshot() and utils::changedFiles() functions
     to allow snapshots and comparison of directories of files.

   * make.names(names, unique=TRUE) now tries to preserve existing
     names. (Suggestion of PR#15452.)

   * New functions cospi(x), sinpi(x), and tanpi(x), for more accurate
     computation of cos(pi*x), etc, both in R and the C API.  Using
     these gains accuracy in some cases, e.g., inside lgamma() or
     besselI().  (Suggested by Morten Welinder in PR#15529.)

   * print.table(x, zero.print = ".") now also has an effect when x is
     not integer-valued.

   * There is more support to explore the system's idea of time-zone
     names.  Sys.timezone() tries to give the current system setting
     by name (and succeeds at least on Linux, OS X, Solaris and
     Windows), and OlsonNames() lists the names in the system's Olson
     database. Sys.timezone(location = FALSE) gives the previous
     behaviour.

   * Platforms with a 64-bit time_t type are allowed to handle
     conversions between the "POSIXct" and "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 time_t is usually 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).

   * The "save.defaults" option can include a value for
     compression_level.  (Wish of PR#15579.)

   * colSums() and friends now have support for arrays and data-frame
     columns with 2^31 or more elements.

   * as.factor() is faster when f is an unclassed integer vector (for
     example, when called from tapply()).

   * fft() now works with longer inputs, from the 12 million
     previously supported up to 2 billion.  (PR#15593)

   * Complex svd() now uses LAPACK subroutine ZGESDD, the complex
     analogue of the routine used for the real case.

   * Sweave now outputs .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 %\SweaveUTF8 on a line by itself.

   * file.copy() gains a copy.date argument.

   * 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 LMT, PMT, WET or WEST.  To enable
     this, the "POSIXlt" class has an optional component "zone"
     recording the abbreviation for each element.

     For platforms which support it, there is also a component
     "gmtoff" recording the offset from GMT where known.

   * (On Windows, by default on OS X and optionally elsewhere.)  The
     system C function strftime has been replaced by a more
     comprehensive version with closer conformance to the POSIX 2008
     standard.

   * dnorm(x, log = FALSE) is more accurate (but somewhat slower) for
     |x| > 5; as suggested in PR#15620.

   * Some versions of the tiff() device have further compression
     options.

   * read.table(), readLines() and scan() have a new argument to
     influence the treatment of embedded nuls.

   * Avoid duplicating the right hand side values in complex
     assignments when possible.  This reduces copying of replacement
     values in expressions such as Z$a <- a0 and 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.

   * The fast argument of KalmanLike(), KalmanRun() and
     KalmanForecast() has been replaced by update, which instead of
     updating mod in place, optionally returns the updated model in an
     attribute "mod" of the return value.

   * arima() and makeARIMA() get a new optional argument SSinit,
     allowing the choice of a different *s*tate *s*pace initialization
     which has been observed to be more reliable close to
     non-stationarity: see PR#14682.

   * warning() has a new argument noBreaks., to simplify
     post-processing of output with options(warn = 1).

   * pushBack() gains an argument encoding, to support reading of
     UTF-8 characters using scan(), read.table() and related functions
     in a non-UTF-8 locale.

   * all.equal.list() gets a new argument 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.

   * The methods for all.equal() and attr.all.equal() now have
     argument check.attributes after ... 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 all.equal()
     are detected and reported.

     There are explicit checks that check.attributes is logical,
     tolerance is numeric and scale is NULL or numeric.  This catches
     some unintended positional matching.

     The message for all.equal.numeric() reports a "scaled difference"
     only for scale != 1.

   * all.equal() now has a "POSIXt" method replacing the "POSIXct"
     method.

   * The "Date" and "POSIXt" methods of seq() allows by = "quarter"
     for completeness (by = "3 months" always worked).

   * 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 / can be used to confine path matching
     to directories).

   * New function agrepl() which like grepl() returns a logical
     vector.

   * fifo() is now supported on Windows. (PR#15600)

   * sort.list(method = "radix") now allows negative integers (wish of
     PR#15644).

   * Some functionality of print.ts() is now available in
     .preformat.ts() for more modularity.

   * mcparallel() gains an option detach = TRUE which allows execution
     of code independently of the current session.  It is based on a
     new estranged = TRUE argument to mcfork() which forks child
     processes such that they become independent of the parent
     process.

   * The pdf() device omits circles and text at extremely small sizes,
     since some viewers were failing on such files.

   * The rightmost break for the "months", "quarters" and "years"
     cases of hist.POSIXlt() has been increased by a day.  (Inter
     alia, fixes PR#15717.)

   * The handling of DF[i,] <- a where i is of length 0 is improved.
     (Inter alia, fixes PR#15718.)

   * hclust() gains a new method "ward.D2" which implements Ward's
     method correctly.  The previous "ward" method is "ward.D" now,
     with the old name still working.  Thanks to research and
     proposals by Pierre Legendre.

   * The sunspot.month dataset has been amended and updated from the
     official source, whereas the sunspots and sunspot.year datasets
     will remain immutable. The documentation and source links have
     been updated correspondingly.

   * The summary() method for "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 summary() in order to extract just a
     component which will be reliable (e.g. $cov.unscaled) should wrap
     their calls in suppressWarnings().

 INSTALLATION and INCLUDED SOFTWARE:

   * The included version of LAPACK has been updated to 3.5.0.

   * There is some support for parallel testing of an installation, by
     setting 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 make program (such as GNU make and dmake) which supports the
     $MAKE -j nproc syntax.

     Except on Windows: the tests of standard package examples in make
     check are done in parallel.  This also applies to running
     tools::testInstalledPackages().

     The more time-consuming regression tests are done in parallel.

     The package checks in make check-devel and make check-recommended
     are done in parallel.

   * More of make check will work if recommended packages are not
     installed: but recommended packages remain needed for thorough
     checking of an R build.

   * The version of tzcode included in src/extra/tzone has been
     updated.  (Formerly used only on Windows.)

   * The included (64-bit) time-zone conversion code and Olson
     time-zone database can be used instead of the system version: use
     configure option --with-internal-tzcode.  This is the default on
     Windows and OS X.  (Note that this does not currently work if a
     non-default rsharedir configure variable is used.)

     (It might be necessary to set environment variable 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 strftime included in
     directory src/extra/tzone.

   * configure now tests for a C++11-compliant compiler by testing
     some basic features.  This by default tries flags for the
     compiler specified by CXX, but an alternative compiler, options
     and standard can be specified by variables CXX1X, CXX1XFLAGS and
     CXX1XSTD (e.g. -std=gnu++11).

   * R can now optionally be compiled to use reference counting
     instead of the NAMED mechanism by defining SWITCH_TO_REFCNT in
     Rinternals.h. This may become the default in the future.

   * There is a new option --use-system-tre to use a suitable system
     tre library: at present this means a version from their git
     repository, after corrections.  (Wish of PR#15660.)

 PACKAGE INSTALLATION:

   * The CRANextra repository is no longer a default repository on
     Windows: all the binary versions of packages from CRAN are now on
     CRAN, although CRANextra contains packages from Omegahat and
     elsewhere used by CRAN packages.

   * Only vignettes sources in directory vignettes are considered to
     be vignettes and hence indexed as such.

   * In the DESCRIPTION file,

         License: X11

     is no longer recognized as valid.  Use MIT or BSD_2_clause
     instead, both of which need + file LICENSE.

   * For consistency, entries in .Rinstignore are now matched
     case-insensitively on all platforms.

   * Help for S4 methods with very long signatures now tries harder to
     split the description in the Usage field to no more than 80
     characters per line (some packages had over 120 characters).

   * R CMD INSTALL --build (not Windows) now defaults to the internal
     tar() unless R_INSTALL_TAR is set.

   * There is support for compiling C++11 code in packages on suitable
     platforms: see 'Writing R Extensions'.

   * Fake installs now install the contents of directory inst: some
     packages use this to install e.g. C++ headers for use by other
     packages that are independent of the package itself.  Option
     --no-inst can be used to get the previous behaviour.

 DEBUGGING:

   * The behaviour of the code browser has been made more consistent,
     in part following the suggestions in PR#14985.

   * Calls to browser() are now consistent with calls to the browser
     triggered by debug(), in that Enter will default to n rather than
     c.

   * A new browser command s has been added, to "step into" function
     calls.

   * A new browser command f has been added, to "finish" the current
     loop or function.

   * Within the browser, the command help will display a short list of
     available commands.

 UTILITIES:

   * Only vignettes sources in directory vignettes are considered to
     be vignettes by R CMD check.  That has been the preferred
     location since R 2.14.0 and is now obligatory.

   * For consistency, R CMD build now matches entries in .Rbuildignore
     and vignettes/.install_extras case-insensitively on all platforms
     (not just on Windows).

   * checkFF() (called by 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 R CMD check
     --as-cran or can be enabled by setting environment variable
     _R_CHECK_FF_CALLS_ to registration (but is in any case suppressed
     by --install=no).  Because this checks calls in which .NAME is an
     R object and not just a literal character string, some other
     problems are detected for such calls.

     Functions suppressForeignCheck() and dontCheck() have been added
     to allow package authors to suppress false positive reports.

   * R CMD check --as-cran warns about a false value of the
     DESCRIPTION field 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).

   * R CMD check --no-rebuild-vignettes is defunct:
     R CMD check --no-build-vignettes has been preferred since R
     3.0.0.

   * R CMD build --no-vignettes is defunct:
     R CMD build --no-build-vignettes has been preferred since R
     3.0.0.

   * R CMD Sweave and R CMD Stangle now process both Sweave and
     non-Sweave vignettes.  The tools::buildVignette() function has
     been added to do the same tasks from within R.

   * The flags returned by R CMD config --ldflags and (where
     installed) pkg-config --libs libR are now those needed to link a
     front-end against the (shared or static) R library.

   * Sweave.sty has a new option [inconsolata].

   * R CMD check customizations such as _R_CHECK_DEPENDS_ONLY_ make
     available packages only in LinkingTo only for installation, and
     not for loading/runtime tests.

   * tools::checkFF() reports on .C and .Fortran calls with DUP =
     FALSE if argument check_DUP is true.  This is selected by R CMD
     check by default.

   * R CMD check --use-gct can be tuned to garbage-collect less
     frequently using gctorture2() _via_ the setting of environment
     variable _R_CHECK_GCT_N_.

   * Where supported, tools::texi2dvi() limits the number of passes
     tried to 20.

 C-LEVEL FACILITIES:

   * (Windows only) A function R_WaitEvent() has been added (with
     declaration in headerR.h) to block execution until the next event
     is received by R.

   * Remapping in the Rmath.h header can be suppressed by defining
     R_NO_REMAP_RMATH.

   * The remapping of rround() in header Rmath.h has been removed: use
     fround() instead.

   * ftrunc() in header Rmath.h is now a wrapper for the C99 function
     trunc(), which might as well be used in C code: ftrunc() is still
     needed for portable C++ code.

   * The never-documented remapping of prec() to fprec() in header
     Rmath.h has been removed.

   * The included LAPACK subset now contains ZGESDD and ZGELSD.

   * The function LENGTH() now checks that it is only applied to
     vector arguments.  However, in packages length() should be used.
     (In R itself LENGTH() is a macro without the function overhead of
     length().)

   * Calls to SET_VECTOR_ELT() and SET_STRING_ELT() are now checked
     for indices which are in-range: several packages were writing one
     element beyond the allocated length.

   * allocVector3 has been added which allows custom allocators to be
     used for individual vector allocations.

 DEPRECATED AND DEFUNCT:

   * chol(pivot = TRUE, LINPACK = TRUE) is defunct.

     Arguments EISPACK for eigen() and LINPACK for chol(), chol2inv(),
     solve() and svd() are ignored: LAPACK is always used.

   * .find.package() and .path.package() are defunct: only the
     versions without the initial dot introduced in R 2.13.0 have ever
     been in the API.

   * Partial matching when using the $ operator _on data frames_ now
     throws a warning and may become defunct in the future. If partial
     matching is intended, replace foo$bar by foo[["bar", exact =
     FALSE]].

   * The long-deprecated use of \synopsis in the Usage section of .Rd
     files has been removed: such sections are now ignored (with a
     warning).

   * package.skeleton()'s deprecated argument namespace has been
     removed.

   * Many methods are no longer exported by package stats.  They are
     all registered on their generic, which should be called rather
     than calling a method directly.

   * Functions readNEWS() and checkNEWS() in package tools are
     defunct.

   * download.file(method = "lynx") is deprecated.

   * .C(DUP = FALSE) and .Fortran(DUP = FALSE) are now deprecated, and
     may be disabled in future versions of R.  As their help has long
     said, .Call() is much preferred.

     R CMD check notes such usages (by default).

   * The workaround of setting R_OSX_VALGRIND has been removed: it is
     not needed in current valgrind.

 BUG FIXES:

   * Calling 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 qr component).

   * Error messages involving non-syntactic names (e.g. as produced by
     `\r` when that object does not exist) now encode the control
     characters.  (Reported by Hadley Wickham.)

   * getGraphicsEvent() caused 100% usage of one CPU in Windows.
     (PR#15500)

   * nls() with no start argument may now work inside another function
     (scoping issue).

   * pbeta() and similar work better for very large (billions) ncp.

   * 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 localtime
     changed the tzname variables the reported abbreviation could have
     been that of the last time converted.

   * all.equal(list(1), identity) now works.

   * Bug fix for pushing viewports in 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 grid on the graphics engine display list.

   * Extra checks have been added for unit resolution and conversion
     in 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).

   * Some bugs in TRE have been corrected by updating from the 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).

   * ? applied to a call to an S4 generic failed in several cases.
     (PR#15680)
     which this was a blocker (PR#15087 suggests Linux on ARM and
     HP-UX).

   * ? applied to a call to an S4 generic failed in several cases.
     (PR#15680)

   * The implicit S4 generics for primitives with ... in their
     argument list were incorrect. (PR#15690)

   * Bug fixes to methods::callGeneric(). (PR#15691)

   * The bug fix to aggregrate() in PR#15004 introduced a new bug in
     the case of no grouping variables. (PR#15699)

   * In rare cases printing deeply nested lists overran a buffer by
     one byte and on a few platforms segfaulted. (PR#15679)

   * The dendrogram method of as.dendrogram() was hidden accidentally,
     (PR#15703), and order.dendrogram(d) gave too much for a leaf d.
     (PR#15702)

   * R would try to kill processes on exit that have pids ever used by
     a child process spawned by mcparallel even though the current
     process with that pid was not actually its child.

   * cophenetic() applied to a "dendrogram" object sometimes
     incorrectly returned a "Labels" attribute with dimensions.
     (PR#15706)

   * printCoefmat() called from quite a few print() methods now obeys
     small getOption("width") settings, line wrapping the "signif.
     codes" legend appropriately.  (PR#15708)

   * model.matrix() assumed that the stored dimnames for a matrix was
     NULL or length 2, but length 1 occurred.

   * The clipping region for a device was sometimes used in base
     graphics before it was set.



--
Peter Dalgaard, Professor
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com



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