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  <changelog author="detlef.steuer@gmx.de" date="1394107200">- Upstream release 3.0.3
- Most important
  CHANGES IN R 3.0.3:
  NEW FEATURES:
  * On Windows there is support for making .texi manuals using
    texinfo 5.0 or later: the setting is in file
    src/gnuwin32/MkRules.dist.
    A packaging of the Perl script and modules for texinfo 5.2 has
    been made available at &lt;URL:
    http://www.stats.ox.ac.uk/pub/Rtools/&gt;.
  * write.table() now handles matrices of 2^31 or more elements, for
    those with large amounts of patience and disc space.
  * There is a new function, La_version(), to report the version of
    LAPACK in use.
  * The HTML version of 'An Introduction to R' now has links to PNG
    versions of the figures.
  * There is some support to produce manuals in ebook formats. (See
    doc/manual/Makefile.  Suggested by Mauro Cavalcanti.)
  * On a Unix-alike Sys.timezone() returns NA if the environment
    variable TZ is unset, to distinguish it from an empty string
    which on some OSes means the UTC time zone.
  * The backtick may now be escaped in strings, to allow names
    containing them to be constructed, e.g. `\``.  (PR#15621)
  * read.table(), readLines() and 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.)
  * (Windows only.)  file.symlink() works around the undocumented
    restriction of the Windows system call to backslashes.  (Wish of
    PR#15631.)
  * KalmanForecast(fast = FALSE) is now the default, and the help
    contains an example of how fast = TRUE can be used in this
    version.  (The usage will change in 3.1.0.)
  * 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).
  * strptime() and the format() methods for classes "POSIXct",
    "POSIXlt" and "Date" recognize strings with marked encodings:
    this allows, for example, UTF-8 French month names to be read on
    (French) Windows.
  * iconv(to = "utf8") is now accepted on all platforms (some
    implementations did already, but GNU libiconv did not: however
    converted strings were not marked as being in UTF-8).  The
    official name, "UTF-8" is still preferred.
  * available.packages() is better protected against corrupt metadata
    files.  (A recurring problem with Debian package shogun-r:
    PR#14713.)
  * 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 options() and (C-level) path.expand()
    re-entrantly).</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1397131200">- Upstream release 3.1.0
- Most impotant
  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| &gt; 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 &lt;- a0 and ans[[i]] &lt;- 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,] &lt;- 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.)</changelog>
  <changelog author="darin@darins.net" date="1398772800">- Created symlink to %{_bindir}/r
  Many CRAN packages ship with scripts which call %{_bindir}/r,
  which creates a dependency on it, this fixes that.</changelog>
  <changelog author="darin@darins.net" date="1398945600">-  Add make dependency for Rcmd</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1399636800">- Removed / commented out symlink to %{_bindir}/r
  new package 'littler' should be used instead for packages
  that need /usr/bin/r</changelog>
  <changelog author="darin@darins.net" date="1403265600">- added parallel provides</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1404993600">- Added Provides: R-parallel
- Upstream release 3.1.1
- Most impotant
  CHANGES IN R 3.1.1:
  CHANGES IN R 3.1.1:
  NEW FEATURES:
  * When attach() reports conflicts, it does so compatibly with
    library() by using message().
  * R CMD Sweave no longer cleans any files by default, compatibly
    with versions of R prior to 3.1.0.  There are new options
  - -clean, --clean=default and --clean=keepOuts.
  * tools::buildVignette() and tools::buildVignettes() with clean =
    FALSE no longer remove any created files.  buildvignette() gains
    a keep argument for more cleaning customization.
  * The Bioconductor 'version' used by setRepositories() can now be
    set by environment variable 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.)
  * Error messages from bugs in embedded Sexpr code in Sweave
    documents now report the source location.
  * type.convert(), read.table() and similar read.*() functions get a
    new numerals argument, specifying how numeric input is converted
    when its conversion to double precision loses accuracy.  The
    default value, "allow.loss" allows accuracy loss, as in R
    versions before 3.1.0.
  * For some compilers, integer addition could overflow without a
    warning.  R's internal code for both integer addition and
    subtraction is more robust now.  (PR#15774)
  * The function determining the default number of knots for
    smooth.spline() is now exported, as .nknots.smspl().
  * dbeta(, a,b), pbeta(), qbeta() and rbeta() are now defined also
    for a = 0, b = 0, or infinite a and b (where they typically
    returned NaN before).
  * Many package authors report that the RStudio graphics device does
    not work correctly with their package's use of dev.new().  The
    new option dev.new(noRStudioGD = TRUE) replaces the RStudio
    override by the default device as selected by R itself, still
    respecting environment variables R_INTERACTIVE_DEVICE and
    R_DEFAULT_DEVICE.
  * readRDS() now returns visibly.
  * Modifying internal logical scalar constants now results in an
    error instead of a warning.
  * install.packages(repos = NULL) now accepts http:// or ftp:// URLs
    of package archives as well as file paths, and will download as
    required.  In most cases repos = NULL can be deduced from the
    extension of the URL.
  * The warning when using partial matching with the $ operator on
    data frames is now only given when
    options("warnPartialMatchDollar") is TRUE.
  * Package help requests like package?foo now try the package foo
    whether loaded or not.
  * General help requests now default to trying all loaded packages,
    not just those on the search path.
  * Added a new function promptImport(), to generate a help page for
    a function that was imported from another package (and presumably
    re-exported, or help would not be needed).
  INSTALLATION and INCLUDED SOFTWARE:
  * configure option --with-internal-tzcode can now be used with
    variable rsharedir.
  * The included version of PCRE has been updated to 8.35.
  * There is a new target make uninstall-libR to remove an installed
    shared/static libR.
    make install-libR now works if a sub-architecture is used,
    although the user will need to specify libdir differently for
    different sub-architectures.
  * There is more extensive advice on which LaTeX packages are
    required to install R or to make package manuals (as done by R
    CMD check) in the 'Writing R Extensions' manual.
  * Compilers/linkers were handling the visibility controls in
    src/extra/xz inconsistently (and apparently in some cases
    incorrectly), so it has been simplified.  (PR#15327)
  * (Windows) There is updated support for the use of ICU for
    collation: see the 'R Installation and Administration Manual'.
  BUG FIXES:
  * dbinom(x, n), pbinom(), dpois(), etc, are slightly less
    restrictive in checking if n is integer-valued.  (Wish of
    PR#15734.)
  * pchisq(x, df, ncp, log.p = TRUE) is more accurate and no longer
    underflows for small x and ncp &lt; 80, e.g, for pchisq(1e-5, df =
    100, ncp = 1, log = TRUE).  (Based on PR#15635 and a suggestion
    by Roby Joehanes.)
  * The s ("step into") command in the debugger would cause R to step
    into expressions evaluated there, not just into functions being
    debugged.  (PR#15770)
  * The C code used by strptime() rejected time-zone offsets of more
    than +1200 (+1245, +1300 and +1400 can occur).  (PR#15768)
  * (Windows only.)  png(type = "cairo", antialias = "gray") was not
    accepted.  (PR#15760)
  * Use of save(..., envir=) with named objects could fail.
    (PR#15758)
  * Sweave() mis-parsed Sexpr expressions that contained backslashes.
    (PR#15779)
  * The return value from options(foo = NULL) was not the previous
    value of the option.  (PR#15781)
  * enc2utf8() and enc2native() did not always mark the encoding of
    the return values when it was known.
  * dnbinom(x, size = &lt;large&gt;, mu, log = TRUE) no longer underflows
    to -Inf for large mu, thanks to a suggestion from Alessandro
    Mammana (MPI MolGen, Berlin).
  * pbeta(x, a, b, log = TRUE) no longer behaves discontinuously (in
    a small x-region) because of denormalized numbers.  Also,
    pbeta(1-1e-12, 1e30, 1.001, log=TRUE) now terminates "in real
    time".
  * The "CRAN" filter (see available.packages()) no longer removes
    duplicates other than of packages on CRAN, and does not fail if
    there is no CRAN repository in getOption("repos").
  * The device listing from dev2bitmap() and bitmap() was truncated
    to 1000 characters: modern versions of GhostScript on most
    platforms have many more devices.
  * (Windows.)  Commands such as Sys.which() and pipe() which needed
    to find the full path to a command could segfault if the 'long'
    path name was much longer than the 'short' path name (which
    Sys.which() returns), as the behaviour of the Windows API call
    had changed.
  * R CMD build will fail with an error if one of the packages
    specified in the VignetteBuilder field is not installed.
    (Without loading those packages it cannot be ascertained which
    files are intended to be vignettes. This means that the
    VignetteBuilder packages have to be installed for package
    checking too.)  (Wish of PR#15775.)
  * Misguided attempts to use chull() with non-finite points now give
    an error (related to PR#15777).
  * For a formula with exactly 32 variables the 32nd variable was
    aliased to the intercept in some C-level computations of terms,
    so that for example attempting to remove it would remove the
    intercept instead (and leave a corrupt internal structure).
    (PR#15735)
  * anyDuplicated() silently returned wrong values when the first
    duplicate was at an index which was too large to be stored in an
    integer vector (although a lot of RAM and patience would have
    been needed to encounter this).
  * tools::Rd2ex(commentDontrun = FALSE) failed if the block had only
    one line.
  * Hexadecimal constants such as 0x110p-5L which were incorrectly
    qualified by L were parsed incorrectly since R 3.0.0, with a
    slightly garbled warning. (PR#15753)
  * system() returned success on some platforms even if the system
    was unable to launch a process. (PR#15796)
  * (Windows Rgui console.)  Unbuffered output was sometimes not
    output immediately if the prompt was not on the last line of the
    console.
  * The built-in help server did not declare the encoding for the
    DESCRIPTION or other text files to be the package encoding, so
    non-ASCII characters could be displayed incorrectly.
  * R is now trying harder to not cleanup child processes that were
    not spawned by mcparallel() on platforms that provide information
    about the source process of the SIGCHLD signal. This allows 3rd
    party libraries to manage the exit status of children that they
    spawn without R interfering.
  * mcmapply() was only parallelizing if the number of jobs was
    bigger than the number of cores. It now parallelizes if the
    number of jobs is more than one.
  * Auto-printing would re-evaluate its argument when trying to
    dispatch to a print method.  This is now avoided when possible.
  * Unserializing (including load() and readRDS()) could silently
    return incorrect numeric values from ASCII saves if there was a
    read error.
  * getParseData() could return incorrect values for the parents of
    some elements. (Reported by Andrew Redd.)
  * Attempting to use data frames of 2^31 or more rows with merge()
    or to create a merged data frame of that size now gives a clearer
    error message.
  * parse() did not check its file argument was a connection if it
    was not a character string, so e.g. parse(FALSE) attempted to
    read from stdin.
    Nor did dump() and dput().
  * The "help.try.all.packages" option was ignored when the shortcut
    syntax for help was used, e.g. ?foo.
  * A potential segfault in string allocation has been fixed.  (Found
    by Radford Neal.)
  * Potential memory protection errors in sort() and D() have been
    fixed. (Found by Radford Neal.)
  * Fixed a lack of error checking in graphics event functions.
    (Found by Radford Neal; a different patch used here than the one
    in pqR.)
  * numericDeriv() sometimes miscalculated the gradient.  (PR#15849,
    reported originally by Radford Neal)</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1414756800">- Upstream release 3.1.2
- Most important
  CHANGES IN R 3.1.2:
  NEW FEATURES:
  * embedFonts() now defaults to format = "ps2write" for .ps and .eps
    files.  This is available in Ghostscript 9.x (since 2010) whereas
    the previous default, format = "pswrite", was removed in
    Ghostscript 9.10.
  * For consistency with [dpqr]norm(), [dp]lnorm(sdlog = 0) model a
    point mass at exp(mulog) rather than return NaN (for an error).
  * capabilities() now reports if ICU is compiled in for use for
    collation (it is only actually used if a suitable locale is set
    for collation, and never for a C locale).
  * (OS X only.) Package tcltk checks when loaded if it is linked
    against the CRAN X11-based Tcl/Tk and if so that the Tcl/Tk
    component and the X11 libraries are installed.  This allows more
    informative error messages to be given advising the installation
    of the missing component or of XQuartz.
    The X11() device and X11-based versions of the data editor and
    viewer (invoked by edit() and View() for data frames and matrices
    from command-line R) check that the X11 libraries are installed
    and if not advises installing XQuartz.
  * icuSetCollate() allows locale = "default", and locale = "none" to
    use OS services rather than ICU for collation.
    Environment variable R_ICU_LOCALE can be used to set the default
    ICU locale, in case the one derived from the OS locale is
    inappropriate (this is currently necessary on Windows).
  * New function icuGetCollate() to report on the ICU collation
    locale in use (if any).
  * utils::URLencode() was updated to use unreserved and reserved
    characters from RFC 3986, &lt;URL:
    http://tools.ietf.org/html/rfc3986&gt;, instead of RFC 1738.
  * unique(warnings()) and c(warnings()) are now supported.
  * The Bioconductor 'version' used by setRepositories() now defaults
    to 3.0. (It can be set at runtime _via_ environment variable
    R_BIOC_VERSION.)
  INSTALLATION and INCLUDED SOFTWARE:
  * The configure script reports on the more important
    capabilities/options which will not be compiled in.
    More types of external BLAS are recognized by name in that
    report.
  * When building R as a shared library, the -L${R_HOME}/lib${R_ARCH}
    flag is placed earlier in the link commands used during
    installation and when packages are installed: this helps ensure
    that the current build has priority if an R shared library has
    already been installed by e.g. install-libR in a library
    mentioned in LDFLAGS (and not in 'your system's library
    directory' as documented). (Wish of PR#15790.)
  * LaTeX package upquote is no longer required for R's use of
    inconsolata.
  * (Windows only) If both 32 and 64 bit versions of R are installed,
    the bin/R.exe and bin/Rscript.exe executables now run 64 bit R.
    (To run 32 bit R, overwrite these files with copies of
    bin/i386/Rfe.exe.)
  UTILITIES:
  * Running R CMD check with _R_CHECK_DEPENDS_ONLY_ true now makes
    the VignetteBuilder packages available even if they are listed in
    Suggests, since they are needed to recognise and process
    non-Sweave vignettes.
  * R CMD check now reports empty importFrom declarations in a
    NAMESPACE file, as these are common errors (writing
    importFrom(Pkg) where import(Pkg) was intended).
  * R CMD check now by default checks code usage directly on the
    package namespace without loading and attaching the package and
    its suggests and enhances.  For good practice with packages in
    the Suggests field, see SS1.1.3.1 of 'Writing R Extensions'.  For
    use of lazy-data objects in the package's own code, see ?data.
  BUG FIXES:
  * dmultinom() did not handle non-finite probabilities correctly.
  * prettyNum(x, zero.print=*) now also works when x contains NAs.
  * A longstanding bug exhibited by nlminb() on Windows was traced to
    a compiler bug in gcc 4.6.3; a workaround has been put in place.
    (PR#15244 and PR#15914).
  * Rendering of \command in HTML versions of help pages has been
    improved: this is particularly evident on the help page for
    INSTALL.
  * as.hexmode(x) and as.octmode(x) now behave correctly for some
    numeric x, e.g., c(NA, 1) or c(1, pi).
  * drop1() failed if the scope argument had no variables to drop.
    (PR#15935)
  * edit() (and hence fix()) failed if an object had a non-character
    attribute named "source" (an attribute that had been used in R
    prior to version 2.14.0).
  * callGeneric() could fail if the generic had ... as a formal
    argument. (PR#15937).
  * Forking in package parallel called C entry point exit in the
    child.  This was unsafe (_exit should have been called), and
    could flush stdin of the main R process (seen most often on
    Solaris).
    As good practice, stdout is now flushed before forking a child.
  * R objects such as list(`a\b` = 1) now print correctly.
  * getAnywhere("C_pbinom") now returns correctly a single object
    (rather than unlisting it).
  * The confint() method for nls() fits failed it these has specified
    parameter limits despite using an algorithm other than "port".
    (PR#15960)
  * Subclassing an S4 class failed if the class required arguments to
    the generator, through its initialize() method.
  * removeSource() did not properly handle expressions containing
    arguments that were supplied as missing, e.g.  x[i,]. (PR#15957)
  * as.environment(list()) now works, and as.list() of such an
    environment is now the same as list().
  * Several tcltk functions failed when run in unusual environments.
    (PR#15970)
  * options(list()) now works (trivially). (PR#15979)
  * merge(&lt;dendrogram&gt;, ..) now works correctly for two `independent'
    dendrograms (PR#15648), and still compatibly via adjust = "auto"
    e.g. for two branches of an existing dendrogram.
  * The plot method for "hclust" objects gets an optional argument
    check; When that is true (the default) it checks more carefully
    for valid input.
  * (Windows only) If a user chose to install 64 bit R but not 32 bit
    R, the bin/R and bin/Rscript executables failed to run.
    (PR#15981)
  * Various possible buffer overruns have been prevented, and missed
    memory protection added. (PR#15990)
  * Rscript no longer passes --args to R when there are no extra
    ("user") arguments.
  * objects like getClass("refClass")@prototype now print() and str()
    without error.
  * identical() now also looks at the S4 bit.
  * hist(x, breaks) is more robust in adding a small fuzz to few
    breaks when some are very large. (PR#15988)
  * sub() and gsub() did not handle regular expressions like "\s{2,}"
    properly if the text contained NA or non-ascii elements in a
    UTF-8 locale.  Part of this was due to a bug in the TRE library.
    (PR#16009)
  * RShowDoc("NEWS") now displays the PDF version.
  * Matrices and arrays with last dimension zero did not print at all
    or incompletely.  (PR#16012)
  * plot.histogram() and hence hist() now respect the xaxs, yaxs and
    lab graphics parameters.  (PR#16021)
  * bw.SJ(x) and other bw.*() no longer segfault when x contains
    non-finite values. (PR#16024)
  * R CMD Rd2pdf unintentionally ignored its --os option.
  * The internal method of download.file() was not reporting file
    sizes and progress correctly on files larger than 2GB (inherited
    from libxml2).  This is corrected for 64-bit builds (32-bit
    platforms may not support such files, but where possible will be
    supported in future versions of R).
  * Work around a bug in OS X Yosemite where key environment
    variables may be duplicated causing issues in subprocesses. The
    duplicates are now removed on R startup (via Rprofile).
    (PR#16042)
  * Adjust X11 auto-launch detection in DISPLAY on OS X to recognize
    latest XQuartz.</changelog>
  <changelog author="sbahling@suse.com" date="1418385600">- Remove tex(inconsolata.sty) BuildRequires for SLE_12 builds (like
  older SLE releases).</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1425902400">- Upstream release 3.1.3
- Most important
  CHANGES IN R 3.1.3:
  NEW FEATURES:
  * The internal method of download.file() can now handle files
    larger than 2GB on 32-bit builds which support such files (tested
    on 32-bit R running on 64-bit Windows).
  * kruskal.test() warns on more types of suspicious input.
  * The as.dendrogram() method for "hclust" objects gains a check
    argument protecting against memory explosion for invalid inputs.
  * capabilities() has a new item long.double which indicates if the
    build uses a long double type which is longer than double.
  * nlm() no longer modifies the callback argument in place (a new
    vector is allocated for each invocation, which mimics the
    implicit duplication that occurred in R &lt; 3.1.0); note that this
    is a change from the previously documented behavior. (PR#15958)
  * icuSetCollate() now accepts locale = "ASCII" which uses the basic
    C function strcmp and so collates strings byte-by-byte in
    numerical order.
  * sessionInfo() tries to report the OS version in use (not just
    that compiled under, and including details of Linux
    distributions).
  * model.frame() (used by lm() and many other modelling functions)
    now warns when it drops contrasts from factors.  (Wish of
    PR#16119)
  * install.packages() and friends now accept the value type =
    "binary" as a synonym for the native binary type on the platform
    (if it has one).
  * Single source or binary files can be supplied for
    install.packages(type = "both") and the appropriate type and
    repos = NULL will be inferred.
  * New function pcre_config() to report on some of the configuration
    options of the version of PCRE in use.  In particular, this
    reports if regular expressions using \p{xx} are supported.
  * (Windows.) download.file(cacheOK = FALSE) is now supported when
    internet2.dll is used.
  * browseURL() has been updated to work with Firefox 36.0 which has
    dropped support for the -remote interface.
  INSTALLATION and INCLUDED SOFTWARE:
  * The included version of PCRE has been updated to 8.36.
  * configure accepts MAKEINFO=texi2any as another way to ensure
    texinfo 5.x is used when both 5.x and 4.x are installed.
  UTILITIES:
  * R CMD check now checks the packages used in \donttest sections of
    the examples are specified in the DESCRIPTION file.  (These are
    needed to run the examples interactively.)
  * R CMD check checks for the undeclared use of GNU extensions in
    Makefiles, and for Makefiles with a missing final linefeed.
    R CMD build will correct line endings in all Makefiles, not just
    those in the src directory.
  * R CMD check notes uses of library() and require() in package
    code: see the section 'Suggested packages' of 'Writing R
    Extensions' for good practice.
  DEPRECATED AND DEFUNCT:
  * The configure option --with-valgrind-instrumentation=3 is
    deprecated and will be removed in R 3.2.0.
  BUG FIXES:
  * (Windows.) Rscript.exe was missing a manifest specifying the
    modern style for common controls (e.g., the download progress
    bar).
  * If a package had extra documentation files but no vignette, the
    HTML help system produced an empty index page.
  * The parser now gives an error if a null character is included in
    a string using Unicode escapes. (PR#16046)
  * qr.Q() failed on complex arguments due to pre-3.0(!) typo.
    (PR#16054)
  * abs() failed with named arguments when the argument was complex.
    (PR#16047)
  * "noquote" objects may now be used as columns in dataframes.
    (PR#15997)
  * Some values with extremely long names were printed incorrectly.
    (PR#15999)
  * Extremely large exponents on zero expressed in scientific
    notation (e.g. 0.0e50000) could give NaN.  (PR#15976)
  * download.file() reported downloaded sizes as 0KB if less than
    1MB, only for R 3.1.2 and only on big-endian platforms.
  * prompt() did not escape percent signs in the automatically
    generated usage section of help files.
  * drop.terms() dropped some of the attributes of the object it was
    working with.  (PR#16029)
  * (Windows.) The command completion in Rgui.exe messed up the
    console.  (PR#15791)
  * (Windows.) The choose.files() command returned a blank string
    when the user asked for a single file but cancelled the request.
    (PR#16074)
  * Math2 S4 group generics failed to correctly dispatch "structure"-
    and "nonStructure"-derived classes.
  * loadNamespace() imposed undocumented restrictions on the
    versionCheck parameter.  (Reported by Geoff Lee.)
  * Rare over-runs detected by AddressSanitizer in substr() and its
    replacement version have been avoided.
    _Inter alia_ that fix gives the documented behaviour for
    substr(x, 1, 2) &lt;- "" (subsequently reported as PR#16214).
  * Loading packages incorrectly defining an S4 generic followed by a
    function of the same name caused an erroneous cyclic namespace
    dependency error.
  * Declared vignette encodings are now always passed to the vignette
    engine.
  * Port Tomas Kalibera's fix from R-devel that restores the
    loadMethod() fast path, effectively doubling the speed of S4
    dispatch.
  * power.t.test() and power.prop.test() now make use of the
    extendInt option of uniroot() and hence work in more extreme
    cases.  (PR#15792)
  * If a package was updated and attached when its namespace was
    already loaded, it could end up with parts from one version and
    parts from the other.  (PR#16120)
  * tools:::.Rdconv() didn't accept --encoding= due to a typo.
    (PR#16121)
  * Unix-alike builds without a suitable makeinfo were documented to
    link the missing HTML manuals to CRAN, but did not.
  * save(*, ascii=TRUE) and load() now correctly deal with NaN's.
    (PR#16137)
  * split.Date() retains fractional representations while avoiding
    incomplete class propagation.
  * R_ext/Lapack.h had not been updated for changes made by LAPACK to
    the argument lists of its (largely internal) functions dlaed2 and
    dlaed3.  (PR#16157)
  * RShowDoc("NEWS", "txt") had not been updated for the layout
    changes of R 3.1.0.
  * The xtfrm() method for class "Surv" has been corrected and its
    description expanded.
  * mode(x) &lt;- y would incorrectly evaluate x before changing its
    mode. (PR#16215)
  * besselJ(1, 2^64) and besselY(..) now signal a warning, returning
    NaN instead of typically segfaulting. (Issue 3 of PR#15554)
  * HTML conversion of \href markup in .Rd files did not remove the
    backslash from \% and so gave an invalid URL.  In a related
    change, the \ escape is now required in such URLs.</changelog>
</package>
<package pkgid="2dbea7b4bd244c76879e0aa1ef4548f5e005ecfe55d83ab8c30b8a38bcf0428a" name="R-gnu13-ohpc" arch="src">
  <version epoch="0" ver="4.2.1" rel="310.ohpc.1.2"/>
  <changelog author="detlef.steuer@gmx.de" date="1394107200">- Upstream release 3.0.3
- Most important
  CHANGES IN R 3.0.3:
  NEW FEATURES:
  * On Windows there is support for making .texi manuals using
    texinfo 5.0 or later: the setting is in file
    src/gnuwin32/MkRules.dist.
    A packaging of the Perl script and modules for texinfo 5.2 has
    been made available at &lt;URL:
    http://www.stats.ox.ac.uk/pub/Rtools/&gt;.
  * write.table() now handles matrices of 2^31 or more elements, for
    those with large amounts of patience and disc space.
  * There is a new function, La_version(), to report the version of
    LAPACK in use.
  * The HTML version of 'An Introduction to R' now has links to PNG
    versions of the figures.
  * There is some support to produce manuals in ebook formats. (See
    doc/manual/Makefile.  Suggested by Mauro Cavalcanti.)
  * On a Unix-alike Sys.timezone() returns NA if the environment
    variable TZ is unset, to distinguish it from an empty string
    which on some OSes means the UTC time zone.
  * The backtick may now be escaped in strings, to allow names
    containing them to be constructed, e.g. `\``.  (PR#15621)
  * read.table(), readLines() and 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.)
  * (Windows only.)  file.symlink() works around the undocumented
    restriction of the Windows system call to backslashes.  (Wish of
    PR#15631.)
  * KalmanForecast(fast = FALSE) is now the default, and the help
    contains an example of how fast = TRUE can be used in this
    version.  (The usage will change in 3.1.0.)
  * 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).
  * strptime() and the format() methods for classes "POSIXct",
    "POSIXlt" and "Date" recognize strings with marked encodings:
    this allows, for example, UTF-8 French month names to be read on
    (French) Windows.
  * iconv(to = "utf8") is now accepted on all platforms (some
    implementations did already, but GNU libiconv did not: however
    converted strings were not marked as being in UTF-8).  The
    official name, "UTF-8" is still preferred.
  * available.packages() is better protected against corrupt metadata
    files.  (A recurring problem with Debian package shogun-r:
    PR#14713.)
  * 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 options() and (C-level) path.expand()
    re-entrantly).</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1397131200">- Upstream release 3.1.0
- Most impotant
  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| &gt; 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 &lt;- a0 and ans[[i]] &lt;- 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,] &lt;- 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.)</changelog>
  <changelog author="darin@darins.net" date="1398772800">- Created symlink to %{_bindir}/r
  Many CRAN packages ship with scripts which call %{_bindir}/r,
  which creates a dependency on it, this fixes that.</changelog>
  <changelog author="darin@darins.net" date="1398945600">-  Add make dependency for Rcmd</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1399636800">- Removed / commented out symlink to %{_bindir}/r
  new package 'littler' should be used instead for packages
  that need /usr/bin/r</changelog>
  <changelog author="darin@darins.net" date="1403265600">- added parallel provides</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1404993600">- Added Provides: R-parallel
- Upstream release 3.1.1
- Most impotant
  CHANGES IN R 3.1.1:
  CHANGES IN R 3.1.1:
  NEW FEATURES:
  * When attach() reports conflicts, it does so compatibly with
    library() by using message().
  * R CMD Sweave no longer cleans any files by default, compatibly
    with versions of R prior to 3.1.0.  There are new options
  - -clean, --clean=default and --clean=keepOuts.
  * tools::buildVignette() and tools::buildVignettes() with clean =
    FALSE no longer remove any created files.  buildvignette() gains
    a keep argument for more cleaning customization.
  * The Bioconductor 'version' used by setRepositories() can now be
    set by environment variable 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.)
  * Error messages from bugs in embedded Sexpr code in Sweave
    documents now report the source location.
  * type.convert(), read.table() and similar read.*() functions get a
    new numerals argument, specifying how numeric input is converted
    when its conversion to double precision loses accuracy.  The
    default value, "allow.loss" allows accuracy loss, as in R
    versions before 3.1.0.
  * For some compilers, integer addition could overflow without a
    warning.  R's internal code for both integer addition and
    subtraction is more robust now.  (PR#15774)
  * The function determining the default number of knots for
    smooth.spline() is now exported, as .nknots.smspl().
  * dbeta(, a,b), pbeta(), qbeta() and rbeta() are now defined also
    for a = 0, b = 0, or infinite a and b (where they typically
    returned NaN before).
  * Many package authors report that the RStudio graphics device does
    not work correctly with their package's use of dev.new().  The
    new option dev.new(noRStudioGD = TRUE) replaces the RStudio
    override by the default device as selected by R itself, still
    respecting environment variables R_INTERACTIVE_DEVICE and
    R_DEFAULT_DEVICE.
  * readRDS() now returns visibly.
  * Modifying internal logical scalar constants now results in an
    error instead of a warning.
  * install.packages(repos = NULL) now accepts http:// or ftp:// URLs
    of package archives as well as file paths, and will download as
    required.  In most cases repos = NULL can be deduced from the
    extension of the URL.
  * The warning when using partial matching with the $ operator on
    data frames is now only given when
    options("warnPartialMatchDollar") is TRUE.
  * Package help requests like package?foo now try the package foo
    whether loaded or not.
  * General help requests now default to trying all loaded packages,
    not just those on the search path.
  * Added a new function promptImport(), to generate a help page for
    a function that was imported from another package (and presumably
    re-exported, or help would not be needed).
  INSTALLATION and INCLUDED SOFTWARE:
  * configure option --with-internal-tzcode can now be used with
    variable rsharedir.
  * The included version of PCRE has been updated to 8.35.
  * There is a new target make uninstall-libR to remove an installed
    shared/static libR.
    make install-libR now works if a sub-architecture is used,
    although the user will need to specify libdir differently for
    different sub-architectures.
  * There is more extensive advice on which LaTeX packages are
    required to install R or to make package manuals (as done by R
    CMD check) in the 'Writing R Extensions' manual.
  * Compilers/linkers were handling the visibility controls in
    src/extra/xz inconsistently (and apparently in some cases
    incorrectly), so it has been simplified.  (PR#15327)
  * (Windows) There is updated support for the use of ICU for
    collation: see the 'R Installation and Administration Manual'.
  BUG FIXES:
  * dbinom(x, n), pbinom(), dpois(), etc, are slightly less
    restrictive in checking if n is integer-valued.  (Wish of
    PR#15734.)
  * pchisq(x, df, ncp, log.p = TRUE) is more accurate and no longer
    underflows for small x and ncp &lt; 80, e.g, for pchisq(1e-5, df =
    100, ncp = 1, log = TRUE).  (Based on PR#15635 and a suggestion
    by Roby Joehanes.)
  * The s ("step into") command in the debugger would cause R to step
    into expressions evaluated there, not just into functions being
    debugged.  (PR#15770)
  * The C code used by strptime() rejected time-zone offsets of more
    than +1200 (+1245, +1300 and +1400 can occur).  (PR#15768)
  * (Windows only.)  png(type = "cairo", antialias = "gray") was not
    accepted.  (PR#15760)
  * Use of save(..., envir=) with named objects could fail.
    (PR#15758)
  * Sweave() mis-parsed Sexpr expressions that contained backslashes.
    (PR#15779)
  * The return value from options(foo = NULL) was not the previous
    value of the option.  (PR#15781)
  * enc2utf8() and enc2native() did not always mark the encoding of
    the return values when it was known.
  * dnbinom(x, size = &lt;large&gt;, mu, log = TRUE) no longer underflows
    to -Inf for large mu, thanks to a suggestion from Alessandro
    Mammana (MPI MolGen, Berlin).
  * pbeta(x, a, b, log = TRUE) no longer behaves discontinuously (in
    a small x-region) because of denormalized numbers.  Also,
    pbeta(1-1e-12, 1e30, 1.001, log=TRUE) now terminates "in real
    time".
  * The "CRAN" filter (see available.packages()) no longer removes
    duplicates other than of packages on CRAN, and does not fail if
    there is no CRAN repository in getOption("repos").
  * The device listing from dev2bitmap() and bitmap() was truncated
    to 1000 characters: modern versions of GhostScript on most
    platforms have many more devices.
  * (Windows.)  Commands such as Sys.which() and pipe() which needed
    to find the full path to a command could segfault if the 'long'
    path name was much longer than the 'short' path name (which
    Sys.which() returns), as the behaviour of the Windows API call
    had changed.
  * R CMD build will fail with an error if one of the packages
    specified in the VignetteBuilder field is not installed.
    (Without loading those packages it cannot be ascertained which
    files are intended to be vignettes. This means that the
    VignetteBuilder packages have to be installed for package
    checking too.)  (Wish of PR#15775.)
  * Misguided attempts to use chull() with non-finite points now give
    an error (related to PR#15777).
  * For a formula with exactly 32 variables the 32nd variable was
    aliased to the intercept in some C-level computations of terms,
    so that for example attempting to remove it would remove the
    intercept instead (and leave a corrupt internal structure).
    (PR#15735)
  * anyDuplicated() silently returned wrong values when the first
    duplicate was at an index which was too large to be stored in an
    integer vector (although a lot of RAM and patience would have
    been needed to encounter this).
  * tools::Rd2ex(commentDontrun = FALSE) failed if the block had only
    one line.
  * Hexadecimal constants such as 0x110p-5L which were incorrectly
    qualified by L were parsed incorrectly since R 3.0.0, with a
    slightly garbled warning. (PR#15753)
  * system() returned success on some platforms even if the system
    was unable to launch a process. (PR#15796)
  * (Windows Rgui console.)  Unbuffered output was sometimes not
    output immediately if the prompt was not on the last line of the
    console.
  * The built-in help server did not declare the encoding for the
    DESCRIPTION or other text files to be the package encoding, so
    non-ASCII characters could be displayed incorrectly.
  * R is now trying harder to not cleanup child processes that were
    not spawned by mcparallel() on platforms that provide information
    about the source process of the SIGCHLD signal. This allows 3rd
    party libraries to manage the exit status of children that they
    spawn without R interfering.
  * mcmapply() was only parallelizing if the number of jobs was
    bigger than the number of cores. It now parallelizes if the
    number of jobs is more than one.
  * Auto-printing would re-evaluate its argument when trying to
    dispatch to a print method.  This is now avoided when possible.
  * Unserializing (including load() and readRDS()) could silently
    return incorrect numeric values from ASCII saves if there was a
    read error.
  * getParseData() could return incorrect values for the parents of
    some elements. (Reported by Andrew Redd.)
  * Attempting to use data frames of 2^31 or more rows with merge()
    or to create a merged data frame of that size now gives a clearer
    error message.
  * parse() did not check its file argument was a connection if it
    was not a character string, so e.g. parse(FALSE) attempted to
    read from stdin.
    Nor did dump() and dput().
  * The "help.try.all.packages" option was ignored when the shortcut
    syntax for help was used, e.g. ?foo.
  * A potential segfault in string allocation has been fixed.  (Found
    by Radford Neal.)
  * Potential memory protection errors in sort() and D() have been
    fixed. (Found by Radford Neal.)
  * Fixed a lack of error checking in graphics event functions.
    (Found by Radford Neal; a different patch used here than the one
    in pqR.)
  * numericDeriv() sometimes miscalculated the gradient.  (PR#15849,
    reported originally by Radford Neal)</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1414756800">- Upstream release 3.1.2
- Most important
  CHANGES IN R 3.1.2:
  NEW FEATURES:
  * embedFonts() now defaults to format = "ps2write" for .ps and .eps
    files.  This is available in Ghostscript 9.x (since 2010) whereas
    the previous default, format = "pswrite", was removed in
    Ghostscript 9.10.
  * For consistency with [dpqr]norm(), [dp]lnorm(sdlog = 0) model a
    point mass at exp(mulog) rather than return NaN (for an error).
  * capabilities() now reports if ICU is compiled in for use for
    collation (it is only actually used if a suitable locale is set
    for collation, and never for a C locale).
  * (OS X only.) Package tcltk checks when loaded if it is linked
    against the CRAN X11-based Tcl/Tk and if so that the Tcl/Tk
    component and the X11 libraries are installed.  This allows more
    informative error messages to be given advising the installation
    of the missing component or of XQuartz.
    The X11() device and X11-based versions of the data editor and
    viewer (invoked by edit() and View() for data frames and matrices
    from command-line R) check that the X11 libraries are installed
    and if not advises installing XQuartz.
  * icuSetCollate() allows locale = "default", and locale = "none" to
    use OS services rather than ICU for collation.
    Environment variable R_ICU_LOCALE can be used to set the default
    ICU locale, in case the one derived from the OS locale is
    inappropriate (this is currently necessary on Windows).
  * New function icuGetCollate() to report on the ICU collation
    locale in use (if any).
  * utils::URLencode() was updated to use unreserved and reserved
    characters from RFC 3986, &lt;URL:
    http://tools.ietf.org/html/rfc3986&gt;, instead of RFC 1738.
  * unique(warnings()) and c(warnings()) are now supported.
  * The Bioconductor 'version' used by setRepositories() now defaults
    to 3.0. (It can be set at runtime _via_ environment variable
    R_BIOC_VERSION.)
  INSTALLATION and INCLUDED SOFTWARE:
  * The configure script reports on the more important
    capabilities/options which will not be compiled in.
    More types of external BLAS are recognized by name in that
    report.
  * When building R as a shared library, the -L${R_HOME}/lib${R_ARCH}
    flag is placed earlier in the link commands used during
    installation and when packages are installed: this helps ensure
    that the current build has priority if an R shared library has
    already been installed by e.g. install-libR in a library
    mentioned in LDFLAGS (and not in 'your system's library
    directory' as documented). (Wish of PR#15790.)
  * LaTeX package upquote is no longer required for R's use of
    inconsolata.
  * (Windows only) If both 32 and 64 bit versions of R are installed,
    the bin/R.exe and bin/Rscript.exe executables now run 64 bit R.
    (To run 32 bit R, overwrite these files with copies of
    bin/i386/Rfe.exe.)
  UTILITIES:
  * Running R CMD check with _R_CHECK_DEPENDS_ONLY_ true now makes
    the VignetteBuilder packages available even if they are listed in
    Suggests, since they are needed to recognise and process
    non-Sweave vignettes.
  * R CMD check now reports empty importFrom declarations in a
    NAMESPACE file, as these are common errors (writing
    importFrom(Pkg) where import(Pkg) was intended).
  * R CMD check now by default checks code usage directly on the
    package namespace without loading and attaching the package and
    its suggests and enhances.  For good practice with packages in
    the Suggests field, see SS1.1.3.1 of 'Writing R Extensions'.  For
    use of lazy-data objects in the package's own code, see ?data.
  BUG FIXES:
  * dmultinom() did not handle non-finite probabilities correctly.
  * prettyNum(x, zero.print=*) now also works when x contains NAs.
  * A longstanding bug exhibited by nlminb() on Windows was traced to
    a compiler bug in gcc 4.6.3; a workaround has been put in place.
    (PR#15244 and PR#15914).
  * Rendering of \command in HTML versions of help pages has been
    improved: this is particularly evident on the help page for
    INSTALL.
  * as.hexmode(x) and as.octmode(x) now behave correctly for some
    numeric x, e.g., c(NA, 1) or c(1, pi).
  * drop1() failed if the scope argument had no variables to drop.
    (PR#15935)
  * edit() (and hence fix()) failed if an object had a non-character
    attribute named "source" (an attribute that had been used in R
    prior to version 2.14.0).
  * callGeneric() could fail if the generic had ... as a formal
    argument. (PR#15937).
  * Forking in package parallel called C entry point exit in the
    child.  This was unsafe (_exit should have been called), and
    could flush stdin of the main R process (seen most often on
    Solaris).
    As good practice, stdout is now flushed before forking a child.
  * R objects such as list(`a\b` = 1) now print correctly.
  * getAnywhere("C_pbinom") now returns correctly a single object
    (rather than unlisting it).
  * The confint() method for nls() fits failed it these has specified
    parameter limits despite using an algorithm other than "port".
    (PR#15960)
  * Subclassing an S4 class failed if the class required arguments to
    the generator, through its initialize() method.
  * removeSource() did not properly handle expressions containing
    arguments that were supplied as missing, e.g.  x[i,]. (PR#15957)
  * as.environment(list()) now works, and as.list() of such an
    environment is now the same as list().
  * Several tcltk functions failed when run in unusual environments.
    (PR#15970)
  * options(list()) now works (trivially). (PR#15979)
  * merge(&lt;dendrogram&gt;, ..) now works correctly for two `independent'
    dendrograms (PR#15648), and still compatibly via adjust = "auto"
    e.g. for two branches of an existing dendrogram.
  * The plot method for "hclust" objects gets an optional argument
    check; When that is true (the default) it checks more carefully
    for valid input.
  * (Windows only) If a user chose to install 64 bit R but not 32 bit
    R, the bin/R and bin/Rscript executables failed to run.
    (PR#15981)
  * Various possible buffer overruns have been prevented, and missed
    memory protection added. (PR#15990)
  * Rscript no longer passes --args to R when there are no extra
    ("user") arguments.
  * objects like getClass("refClass")@prototype now print() and str()
    without error.
  * identical() now also looks at the S4 bit.
  * hist(x, breaks) is more robust in adding a small fuzz to few
    breaks when some are very large. (PR#15988)
  * sub() and gsub() did not handle regular expressions like "\s{2,}"
    properly if the text contained NA or non-ascii elements in a
    UTF-8 locale.  Part of this was due to a bug in the TRE library.
    (PR#16009)
  * RShowDoc("NEWS") now displays the PDF version.
  * Matrices and arrays with last dimension zero did not print at all
    or incompletely.  (PR#16012)
  * plot.histogram() and hence hist() now respect the xaxs, yaxs and
    lab graphics parameters.  (PR#16021)
  * bw.SJ(x) and other bw.*() no longer segfault when x contains
    non-finite values. (PR#16024)
  * R CMD Rd2pdf unintentionally ignored its --os option.
  * The internal method of download.file() was not reporting file
    sizes and progress correctly on files larger than 2GB (inherited
    from libxml2).  This is corrected for 64-bit builds (32-bit
    platforms may not support such files, but where possible will be
    supported in future versions of R).
  * Work around a bug in OS X Yosemite where key environment
    variables may be duplicated causing issues in subprocesses. The
    duplicates are now removed on R startup (via Rprofile).
    (PR#16042)
  * Adjust X11 auto-launch detection in DISPLAY on OS X to recognize
    latest XQuartz.</changelog>
  <changelog author="sbahling@suse.com" date="1418385600">- Remove tex(inconsolata.sty) BuildRequires for SLE_12 builds (like
  older SLE releases).</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1425902400">- Upstream release 3.1.3
- Most important
  CHANGES IN R 3.1.3:
  NEW FEATURES:
  * The internal method of download.file() can now handle files
    larger than 2GB on 32-bit builds which support such files (tested
    on 32-bit R running on 64-bit Windows).
  * kruskal.test() warns on more types of suspicious input.
  * The as.dendrogram() method for "hclust" objects gains a check
    argument protecting against memory explosion for invalid inputs.
  * capabilities() has a new item long.double which indicates if the
    build uses a long double type which is longer than double.
  * nlm() no longer modifies the callback argument in place (a new
    vector is allocated for each invocation, which mimics the
    implicit duplication that occurred in R &lt; 3.1.0); note that this
    is a change from the previously documented behavior. (PR#15958)
  * icuSetCollate() now accepts locale = "ASCII" which uses the basic
    C function strcmp and so collates strings byte-by-byte in
    numerical order.
  * sessionInfo() tries to report the OS version in use (not just
    that compiled under, and including details of Linux
    distributions).
  * model.frame() (used by lm() and many other modelling functions)
    now warns when it drops contrasts from factors.  (Wish of
    PR#16119)
  * install.packages() and friends now accept the value type =
    "binary" as a synonym for the native binary type on the platform
    (if it has one).
  * Single source or binary files can be supplied for
    install.packages(type = "both") and the appropriate type and
    repos = NULL will be inferred.
  * New function pcre_config() to report on some of the configuration
    options of the version of PCRE in use.  In particular, this
    reports if regular expressions using \p{xx} are supported.
  * (Windows.) download.file(cacheOK = FALSE) is now supported when
    internet2.dll is used.
  * browseURL() has been updated to work with Firefox 36.0 which has
    dropped support for the -remote interface.
  INSTALLATION and INCLUDED SOFTWARE:
  * The included version of PCRE has been updated to 8.36.
  * configure accepts MAKEINFO=texi2any as another way to ensure
    texinfo 5.x is used when both 5.x and 4.x are installed.
  UTILITIES:
  * R CMD check now checks the packages used in \donttest sections of
    the examples are specified in the DESCRIPTION file.  (These are
    needed to run the examples interactively.)
  * R CMD check checks for the undeclared use of GNU extensions in
    Makefiles, and for Makefiles with a missing final linefeed.
    R CMD build will correct line endings in all Makefiles, not just
    those in the src directory.
  * R CMD check notes uses of library() and require() in package
    code: see the section 'Suggested packages' of 'Writing R
    Extensions' for good practice.
  DEPRECATED AND DEFUNCT:
  * The configure option --with-valgrind-instrumentation=3 is
    deprecated and will be removed in R 3.2.0.
  BUG FIXES:
  * (Windows.) Rscript.exe was missing a manifest specifying the
    modern style for common controls (e.g., the download progress
    bar).
  * If a package had extra documentation files but no vignette, the
    HTML help system produced an empty index page.
  * The parser now gives an error if a null character is included in
    a string using Unicode escapes. (PR#16046)
  * qr.Q() failed on complex arguments due to pre-3.0(!) typo.
    (PR#16054)
  * abs() failed with named arguments when the argument was complex.
    (PR#16047)
  * "noquote" objects may now be used as columns in dataframes.
    (PR#15997)
  * Some values with extremely long names were printed incorrectly.
    (PR#15999)
  * Extremely large exponents on zero expressed in scientific
    notation (e.g. 0.0e50000) could give NaN.  (PR#15976)
  * download.file() reported downloaded sizes as 0KB if less than
    1MB, only for R 3.1.2 and only on big-endian platforms.
  * prompt() did not escape percent signs in the automatically
    generated usage section of help files.
  * drop.terms() dropped some of the attributes of the object it was
    working with.  (PR#16029)
  * (Windows.) The command completion in Rgui.exe messed up the
    console.  (PR#15791)
  * (Windows.) The choose.files() command returned a blank string
    when the user asked for a single file but cancelled the request.
    (PR#16074)
  * Math2 S4 group generics failed to correctly dispatch "structure"-
    and "nonStructure"-derived classes.
  * loadNamespace() imposed undocumented restrictions on the
    versionCheck parameter.  (Reported by Geoff Lee.)
  * Rare over-runs detected by AddressSanitizer in substr() and its
    replacement version have been avoided.
    _Inter alia_ that fix gives the documented behaviour for
    substr(x, 1, 2) &lt;- "" (subsequently reported as PR#16214).
  * Loading packages incorrectly defining an S4 generic followed by a
    function of the same name caused an erroneous cyclic namespace
    dependency error.
  * Declared vignette encodings are now always passed to the vignette
    engine.
  * Port Tomas Kalibera's fix from R-devel that restores the
    loadMethod() fast path, effectively doubling the speed of S4
    dispatch.
  * power.t.test() and power.prop.test() now make use of the
    extendInt option of uniroot() and hence work in more extreme
    cases.  (PR#15792)
  * If a package was updated and attached when its namespace was
    already loaded, it could end up with parts from one version and
    parts from the other.  (PR#16120)
  * tools:::.Rdconv() didn't accept --encoding= due to a typo.
    (PR#16121)
  * Unix-alike builds without a suitable makeinfo were documented to
    link the missing HTML manuals to CRAN, but did not.
  * save(*, ascii=TRUE) and load() now correctly deal with NaN's.
    (PR#16137)
  * split.Date() retains fractional representations while avoiding
    incomplete class propagation.
  * R_ext/Lapack.h had not been updated for changes made by LAPACK to
    the argument lists of its (largely internal) functions dlaed2 and
    dlaed3.  (PR#16157)
  * RShowDoc("NEWS", "txt") had not been updated for the layout
    changes of R 3.1.0.
  * The xtfrm() method for class "Surv" has been corrected and its
    description expanded.
  * mode(x) &lt;- y would incorrectly evaluate x before changing its
    mode. (PR#16215)
  * besselJ(1, 2^64) and besselY(..) now signal a warning, returning
    NaN instead of typically segfaulting. (Issue 3 of PR#15554)
  * HTML conversion of \href markup in .Rd files did not remove the
    backslash from \% and so gave an invalid URL.  In a related
    change, the \ escape is now required in such URLs.</changelog>
</package>
<package pkgid="3042c04f472224d59185d828899a888b6fc38e0c24e62edc331b5286e2511226" name="R-gnu13-ohpc" arch="x86_64">
  <version epoch="0" ver="4.2.1" rel="310.ohpc.1.2"/>
  <changelog author="detlef.steuer@gmx.de" date="1394107200">- Upstream release 3.0.3
- Most important
  CHANGES IN R 3.0.3:
  NEW FEATURES:
  * On Windows there is support for making .texi manuals using
    texinfo 5.0 or later: the setting is in file
    src/gnuwin32/MkRules.dist.
    A packaging of the Perl script and modules for texinfo 5.2 has
    been made available at &lt;URL:
    http://www.stats.ox.ac.uk/pub/Rtools/&gt;.
  * write.table() now handles matrices of 2^31 or more elements, for
    those with large amounts of patience and disc space.
  * There is a new function, La_version(), to report the version of
    LAPACK in use.
  * The HTML version of 'An Introduction to R' now has links to PNG
    versions of the figures.
  * There is some support to produce manuals in ebook formats. (See
    doc/manual/Makefile.  Suggested by Mauro Cavalcanti.)
  * On a Unix-alike Sys.timezone() returns NA if the environment
    variable TZ is unset, to distinguish it from an empty string
    which on some OSes means the UTC time zone.
  * The backtick may now be escaped in strings, to allow names
    containing them to be constructed, e.g. `\``.  (PR#15621)
  * read.table(), readLines() and 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.)
  * (Windows only.)  file.symlink() works around the undocumented
    restriction of the Windows system call to backslashes.  (Wish of
    PR#15631.)
  * KalmanForecast(fast = FALSE) is now the default, and the help
    contains an example of how fast = TRUE can be used in this
    version.  (The usage will change in 3.1.0.)
  * 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).
  * strptime() and the format() methods for classes "POSIXct",
    "POSIXlt" and "Date" recognize strings with marked encodings:
    this allows, for example, UTF-8 French month names to be read on
    (French) Windows.
  * iconv(to = "utf8") is now accepted on all platforms (some
    implementations did already, but GNU libiconv did not: however
    converted strings were not marked as being in UTF-8).  The
    official name, "UTF-8" is still preferred.
  * available.packages() is better protected against corrupt metadata
    files.  (A recurring problem with Debian package shogun-r:
    PR#14713.)
  * 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 options() and (C-level) path.expand()
    re-entrantly).</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1397131200">- Upstream release 3.1.0
- Most impotant
  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| &gt; 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 &lt;- a0 and ans[[i]] &lt;- 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,] &lt;- 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.)</changelog>
  <changelog author="darin@darins.net" date="1398772800">- Created symlink to %{_bindir}/r
  Many CRAN packages ship with scripts which call %{_bindir}/r,
  which creates a dependency on it, this fixes that.</changelog>
  <changelog author="darin@darins.net" date="1398945600">-  Add make dependency for Rcmd</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1399636800">- Removed / commented out symlink to %{_bindir}/r
  new package 'littler' should be used instead for packages
  that need /usr/bin/r</changelog>
  <changelog author="darin@darins.net" date="1403265600">- added parallel provides</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1404993600">- Added Provides: R-parallel
- Upstream release 3.1.1
- Most impotant
  CHANGES IN R 3.1.1:
  CHANGES IN R 3.1.1:
  NEW FEATURES:
  * When attach() reports conflicts, it does so compatibly with
    library() by using message().
  * R CMD Sweave no longer cleans any files by default, compatibly
    with versions of R prior to 3.1.0.  There are new options
  - -clean, --clean=default and --clean=keepOuts.
  * tools::buildVignette() and tools::buildVignettes() with clean =
    FALSE no longer remove any created files.  buildvignette() gains
    a keep argument for more cleaning customization.
  * The Bioconductor 'version' used by setRepositories() can now be
    set by environment variable 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.)
  * Error messages from bugs in embedded Sexpr code in Sweave
    documents now report the source location.
  * type.convert(), read.table() and similar read.*() functions get a
    new numerals argument, specifying how numeric input is converted
    when its conversion to double precision loses accuracy.  The
    default value, "allow.loss" allows accuracy loss, as in R
    versions before 3.1.0.
  * For some compilers, integer addition could overflow without a
    warning.  R's internal code for both integer addition and
    subtraction is more robust now.  (PR#15774)
  * The function determining the default number of knots for
    smooth.spline() is now exported, as .nknots.smspl().
  * dbeta(, a,b), pbeta(), qbeta() and rbeta() are now defined also
    for a = 0, b = 0, or infinite a and b (where they typically
    returned NaN before).
  * Many package authors report that the RStudio graphics device does
    not work correctly with their package's use of dev.new().  The
    new option dev.new(noRStudioGD = TRUE) replaces the RStudio
    override by the default device as selected by R itself, still
    respecting environment variables R_INTERACTIVE_DEVICE and
    R_DEFAULT_DEVICE.
  * readRDS() now returns visibly.
  * Modifying internal logical scalar constants now results in an
    error instead of a warning.
  * install.packages(repos = NULL) now accepts http:// or ftp:// URLs
    of package archives as well as file paths, and will download as
    required.  In most cases repos = NULL can be deduced from the
    extension of the URL.
  * The warning when using partial matching with the $ operator on
    data frames is now only given when
    options("warnPartialMatchDollar") is TRUE.
  * Package help requests like package?foo now try the package foo
    whether loaded or not.
  * General help requests now default to trying all loaded packages,
    not just those on the search path.
  * Added a new function promptImport(), to generate a help page for
    a function that was imported from another package (and presumably
    re-exported, or help would not be needed).
  INSTALLATION and INCLUDED SOFTWARE:
  * configure option --with-internal-tzcode can now be used with
    variable rsharedir.
  * The included version of PCRE has been updated to 8.35.
  * There is a new target make uninstall-libR to remove an installed
    shared/static libR.
    make install-libR now works if a sub-architecture is used,
    although the user will need to specify libdir differently for
    different sub-architectures.
  * There is more extensive advice on which LaTeX packages are
    required to install R or to make package manuals (as done by R
    CMD check) in the 'Writing R Extensions' manual.
  * Compilers/linkers were handling the visibility controls in
    src/extra/xz inconsistently (and apparently in some cases
    incorrectly), so it has been simplified.  (PR#15327)
  * (Windows) There is updated support for the use of ICU for
    collation: see the 'R Installation and Administration Manual'.
  BUG FIXES:
  * dbinom(x, n), pbinom(), dpois(), etc, are slightly less
    restrictive in checking if n is integer-valued.  (Wish of
    PR#15734.)
  * pchisq(x, df, ncp, log.p = TRUE) is more accurate and no longer
    underflows for small x and ncp &lt; 80, e.g, for pchisq(1e-5, df =
    100, ncp = 1, log = TRUE).  (Based on PR#15635 and a suggestion
    by Roby Joehanes.)
  * The s ("step into") command in the debugger would cause R to step
    into expressions evaluated there, not just into functions being
    debugged.  (PR#15770)
  * The C code used by strptime() rejected time-zone offsets of more
    than +1200 (+1245, +1300 and +1400 can occur).  (PR#15768)
  * (Windows only.)  png(type = "cairo", antialias = "gray") was not
    accepted.  (PR#15760)
  * Use of save(..., envir=) with named objects could fail.
    (PR#15758)
  * Sweave() mis-parsed Sexpr expressions that contained backslashes.
    (PR#15779)
  * The return value from options(foo = NULL) was not the previous
    value of the option.  (PR#15781)
  * enc2utf8() and enc2native() did not always mark the encoding of
    the return values when it was known.
  * dnbinom(x, size = &lt;large&gt;, mu, log = TRUE) no longer underflows
    to -Inf for large mu, thanks to a suggestion from Alessandro
    Mammana (MPI MolGen, Berlin).
  * pbeta(x, a, b, log = TRUE) no longer behaves discontinuously (in
    a small x-region) because of denormalized numbers.  Also,
    pbeta(1-1e-12, 1e30, 1.001, log=TRUE) now terminates "in real
    time".
  * The "CRAN" filter (see available.packages()) no longer removes
    duplicates other than of packages on CRAN, and does not fail if
    there is no CRAN repository in getOption("repos").
  * The device listing from dev2bitmap() and bitmap() was truncated
    to 1000 characters: modern versions of GhostScript on most
    platforms have many more devices.
  * (Windows.)  Commands such as Sys.which() and pipe() which needed
    to find the full path to a command could segfault if the 'long'
    path name was much longer than the 'short' path name (which
    Sys.which() returns), as the behaviour of the Windows API call
    had changed.
  * R CMD build will fail with an error if one of the packages
    specified in the VignetteBuilder field is not installed.
    (Without loading those packages it cannot be ascertained which
    files are intended to be vignettes. This means that the
    VignetteBuilder packages have to be installed for package
    checking too.)  (Wish of PR#15775.)
  * Misguided attempts to use chull() with non-finite points now give
    an error (related to PR#15777).
  * For a formula with exactly 32 variables the 32nd variable was
    aliased to the intercept in some C-level computations of terms,
    so that for example attempting to remove it would remove the
    intercept instead (and leave a corrupt internal structure).
    (PR#15735)
  * anyDuplicated() silently returned wrong values when the first
    duplicate was at an index which was too large to be stored in an
    integer vector (although a lot of RAM and patience would have
    been needed to encounter this).
  * tools::Rd2ex(commentDontrun = FALSE) failed if the block had only
    one line.
  * Hexadecimal constants such as 0x110p-5L which were incorrectly
    qualified by L were parsed incorrectly since R 3.0.0, with a
    slightly garbled warning. (PR#15753)
  * system() returned success on some platforms even if the system
    was unable to launch a process. (PR#15796)
  * (Windows Rgui console.)  Unbuffered output was sometimes not
    output immediately if the prompt was not on the last line of the
    console.
  * The built-in help server did not declare the encoding for the
    DESCRIPTION or other text files to be the package encoding, so
    non-ASCII characters could be displayed incorrectly.
  * R is now trying harder to not cleanup child processes that were
    not spawned by mcparallel() on platforms that provide information
    about the source process of the SIGCHLD signal. This allows 3rd
    party libraries to manage the exit status of children that they
    spawn without R interfering.
  * mcmapply() was only parallelizing if the number of jobs was
    bigger than the number of cores. It now parallelizes if the
    number of jobs is more than one.
  * Auto-printing would re-evaluate its argument when trying to
    dispatch to a print method.  This is now avoided when possible.
  * Unserializing (including load() and readRDS()) could silently
    return incorrect numeric values from ASCII saves if there was a
    read error.
  * getParseData() could return incorrect values for the parents of
    some elements. (Reported by Andrew Redd.)
  * Attempting to use data frames of 2^31 or more rows with merge()
    or to create a merged data frame of that size now gives a clearer
    error message.
  * parse() did not check its file argument was a connection if it
    was not a character string, so e.g. parse(FALSE) attempted to
    read from stdin.
    Nor did dump() and dput().
  * The "help.try.all.packages" option was ignored when the shortcut
    syntax for help was used, e.g. ?foo.
  * A potential segfault in string allocation has been fixed.  (Found
    by Radford Neal.)
  * Potential memory protection errors in sort() and D() have been
    fixed. (Found by Radford Neal.)
  * Fixed a lack of error checking in graphics event functions.
    (Found by Radford Neal; a different patch used here than the one
    in pqR.)
  * numericDeriv() sometimes miscalculated the gradient.  (PR#15849,
    reported originally by Radford Neal)</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1414756800">- Upstream release 3.1.2
- Most important
  CHANGES IN R 3.1.2:
  NEW FEATURES:
  * embedFonts() now defaults to format = "ps2write" for .ps and .eps
    files.  This is available in Ghostscript 9.x (since 2010) whereas
    the previous default, format = "pswrite", was removed in
    Ghostscript 9.10.
  * For consistency with [dpqr]norm(), [dp]lnorm(sdlog = 0) model a
    point mass at exp(mulog) rather than return NaN (for an error).
  * capabilities() now reports if ICU is compiled in for use for
    collation (it is only actually used if a suitable locale is set
    for collation, and never for a C locale).
  * (OS X only.) Package tcltk checks when loaded if it is linked
    against the CRAN X11-based Tcl/Tk and if so that the Tcl/Tk
    component and the X11 libraries are installed.  This allows more
    informative error messages to be given advising the installation
    of the missing component or of XQuartz.
    The X11() device and X11-based versions of the data editor and
    viewer (invoked by edit() and View() for data frames and matrices
    from command-line R) check that the X11 libraries are installed
    and if not advises installing XQuartz.
  * icuSetCollate() allows locale = "default", and locale = "none" to
    use OS services rather than ICU for collation.
    Environment variable R_ICU_LOCALE can be used to set the default
    ICU locale, in case the one derived from the OS locale is
    inappropriate (this is currently necessary on Windows).
  * New function icuGetCollate() to report on the ICU collation
    locale in use (if any).
  * utils::URLencode() was updated to use unreserved and reserved
    characters from RFC 3986, &lt;URL:
    http://tools.ietf.org/html/rfc3986&gt;, instead of RFC 1738.
  * unique(warnings()) and c(warnings()) are now supported.
  * The Bioconductor 'version' used by setRepositories() now defaults
    to 3.0. (It can be set at runtime _via_ environment variable
    R_BIOC_VERSION.)
  INSTALLATION and INCLUDED SOFTWARE:
  * The configure script reports on the more important
    capabilities/options which will not be compiled in.
    More types of external BLAS are recognized by name in that
    report.
  * When building R as a shared library, the -L${R_HOME}/lib${R_ARCH}
    flag is placed earlier in the link commands used during
    installation and when packages are installed: this helps ensure
    that the current build has priority if an R shared library has
    already been installed by e.g. install-libR in a library
    mentioned in LDFLAGS (and not in 'your system's library
    directory' as documented). (Wish of PR#15790.)
  * LaTeX package upquote is no longer required for R's use of
    inconsolata.
  * (Windows only) If both 32 and 64 bit versions of R are installed,
    the bin/R.exe and bin/Rscript.exe executables now run 64 bit R.
    (To run 32 bit R, overwrite these files with copies of
    bin/i386/Rfe.exe.)
  UTILITIES:
  * Running R CMD check with _R_CHECK_DEPENDS_ONLY_ true now makes
    the VignetteBuilder packages available even if they are listed in
    Suggests, since they are needed to recognise and process
    non-Sweave vignettes.
  * R CMD check now reports empty importFrom declarations in a
    NAMESPACE file, as these are common errors (writing
    importFrom(Pkg) where import(Pkg) was intended).
  * R CMD check now by default checks code usage directly on the
    package namespace without loading and attaching the package and
    its suggests and enhances.  For good practice with packages in
    the Suggests field, see SS1.1.3.1 of 'Writing R Extensions'.  For
    use of lazy-data objects in the package's own code, see ?data.
  BUG FIXES:
  * dmultinom() did not handle non-finite probabilities correctly.
  * prettyNum(x, zero.print=*) now also works when x contains NAs.
  * A longstanding bug exhibited by nlminb() on Windows was traced to
    a compiler bug in gcc 4.6.3; a workaround has been put in place.
    (PR#15244 and PR#15914).
  * Rendering of \command in HTML versions of help pages has been
    improved: this is particularly evident on the help page for
    INSTALL.
  * as.hexmode(x) and as.octmode(x) now behave correctly for some
    numeric x, e.g., c(NA, 1) or c(1, pi).
  * drop1() failed if the scope argument had no variables to drop.
    (PR#15935)
  * edit() (and hence fix()) failed if an object had a non-character
    attribute named "source" (an attribute that had been used in R
    prior to version 2.14.0).
  * callGeneric() could fail if the generic had ... as a formal
    argument. (PR#15937).
  * Forking in package parallel called C entry point exit in the
    child.  This was unsafe (_exit should have been called), and
    could flush stdin of the main R process (seen most often on
    Solaris).
    As good practice, stdout is now flushed before forking a child.
  * R objects such as list(`a\b` = 1) now print correctly.
  * getAnywhere("C_pbinom") now returns correctly a single object
    (rather than unlisting it).
  * The confint() method for nls() fits failed it these has specified
    parameter limits despite using an algorithm other than "port".
    (PR#15960)
  * Subclassing an S4 class failed if the class required arguments to
    the generator, through its initialize() method.
  * removeSource() did not properly handle expressions containing
    arguments that were supplied as missing, e.g.  x[i,]. (PR#15957)
  * as.environment(list()) now works, and as.list() of such an
    environment is now the same as list().
  * Several tcltk functions failed when run in unusual environments.
    (PR#15970)
  * options(list()) now works (trivially). (PR#15979)
  * merge(&lt;dendrogram&gt;, ..) now works correctly for two `independent'
    dendrograms (PR#15648), and still compatibly via adjust = "auto"
    e.g. for two branches of an existing dendrogram.
  * The plot method for "hclust" objects gets an optional argument
    check; When that is true (the default) it checks more carefully
    for valid input.
  * (Windows only) If a user chose to install 64 bit R but not 32 bit
    R, the bin/R and bin/Rscript executables failed to run.
    (PR#15981)
  * Various possible buffer overruns have been prevented, and missed
    memory protection added. (PR#15990)
  * Rscript no longer passes --args to R when there are no extra
    ("user") arguments.
  * objects like getClass("refClass")@prototype now print() and str()
    without error.
  * identical() now also looks at the S4 bit.
  * hist(x, breaks) is more robust in adding a small fuzz to few
    breaks when some are very large. (PR#15988)
  * sub() and gsub() did not handle regular expressions like "\s{2,}"
    properly if the text contained NA or non-ascii elements in a
    UTF-8 locale.  Part of this was due to a bug in the TRE library.
    (PR#16009)
  * RShowDoc("NEWS") now displays the PDF version.
  * Matrices and arrays with last dimension zero did not print at all
    or incompletely.  (PR#16012)
  * plot.histogram() and hence hist() now respect the xaxs, yaxs and
    lab graphics parameters.  (PR#16021)
  * bw.SJ(x) and other bw.*() no longer segfault when x contains
    non-finite values. (PR#16024)
  * R CMD Rd2pdf unintentionally ignored its --os option.
  * The internal method of download.file() was not reporting file
    sizes and progress correctly on files larger than 2GB (inherited
    from libxml2).  This is corrected for 64-bit builds (32-bit
    platforms may not support such files, but where possible will be
    supported in future versions of R).
  * Work around a bug in OS X Yosemite where key environment
    variables may be duplicated causing issues in subprocesses. The
    duplicates are now removed on R startup (via Rprofile).
    (PR#16042)
  * Adjust X11 auto-launch detection in DISPLAY on OS X to recognize
    latest XQuartz.</changelog>
  <changelog author="sbahling@suse.com" date="1418385600">- Remove tex(inconsolata.sty) BuildRequires for SLE_12 builds (like
  older SLE releases).</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1425902400">- Upstream release 3.1.3
- Most important
  CHANGES IN R 3.1.3:
  NEW FEATURES:
  * The internal method of download.file() can now handle files
    larger than 2GB on 32-bit builds which support such files (tested
    on 32-bit R running on 64-bit Windows).
  * kruskal.test() warns on more types of suspicious input.
  * The as.dendrogram() method for "hclust" objects gains a check
    argument protecting against memory explosion for invalid inputs.
  * capabilities() has a new item long.double which indicates if the
    build uses a long double type which is longer than double.
  * nlm() no longer modifies the callback argument in place (a new
    vector is allocated for each invocation, which mimics the
    implicit duplication that occurred in R &lt; 3.1.0); note that this
    is a change from the previously documented behavior. (PR#15958)
  * icuSetCollate() now accepts locale = "ASCII" which uses the basic
    C function strcmp and so collates strings byte-by-byte in
    numerical order.
  * sessionInfo() tries to report the OS version in use (not just
    that compiled under, and including details of Linux
    distributions).
  * model.frame() (used by lm() and many other modelling functions)
    now warns when it drops contrasts from factors.  (Wish of
    PR#16119)
  * install.packages() and friends now accept the value type =
    "binary" as a synonym for the native binary type on the platform
    (if it has one).
  * Single source or binary files can be supplied for
    install.packages(type = "both") and the appropriate type and
    repos = NULL will be inferred.
  * New function pcre_config() to report on some of the configuration
    options of the version of PCRE in use.  In particular, this
    reports if regular expressions using \p{xx} are supported.
  * (Windows.) download.file(cacheOK = FALSE) is now supported when
    internet2.dll is used.
  * browseURL() has been updated to work with Firefox 36.0 which has
    dropped support for the -remote interface.
  INSTALLATION and INCLUDED SOFTWARE:
  * The included version of PCRE has been updated to 8.36.
  * configure accepts MAKEINFO=texi2any as another way to ensure
    texinfo 5.x is used when both 5.x and 4.x are installed.
  UTILITIES:
  * R CMD check now checks the packages used in \donttest sections of
    the examples are specified in the DESCRIPTION file.  (These are
    needed to run the examples interactively.)
  * R CMD check checks for the undeclared use of GNU extensions in
    Makefiles, and for Makefiles with a missing final linefeed.
    R CMD build will correct line endings in all Makefiles, not just
    those in the src directory.
  * R CMD check notes uses of library() and require() in package
    code: see the section 'Suggested packages' of 'Writing R
    Extensions' for good practice.
  DEPRECATED AND DEFUNCT:
  * The configure option --with-valgrind-instrumentation=3 is
    deprecated and will be removed in R 3.2.0.
  BUG FIXES:
  * (Windows.) Rscript.exe was missing a manifest specifying the
    modern style for common controls (e.g., the download progress
    bar).
  * If a package had extra documentation files but no vignette, the
    HTML help system produced an empty index page.
  * The parser now gives an error if a null character is included in
    a string using Unicode escapes. (PR#16046)
  * qr.Q() failed on complex arguments due to pre-3.0(!) typo.
    (PR#16054)
  * abs() failed with named arguments when the argument was complex.
    (PR#16047)
  * "noquote" objects may now be used as columns in dataframes.
    (PR#15997)
  * Some values with extremely long names were printed incorrectly.
    (PR#15999)
  * Extremely large exponents on zero expressed in scientific
    notation (e.g. 0.0e50000) could give NaN.  (PR#15976)
  * download.file() reported downloaded sizes as 0KB if less than
    1MB, only for R 3.1.2 and only on big-endian platforms.
  * prompt() did not escape percent signs in the automatically
    generated usage section of help files.
  * drop.terms() dropped some of the attributes of the object it was
    working with.  (PR#16029)
  * (Windows.) The command completion in Rgui.exe messed up the
    console.  (PR#15791)
  * (Windows.) The choose.files() command returned a blank string
    when the user asked for a single file but cancelled the request.
    (PR#16074)
  * Math2 S4 group generics failed to correctly dispatch "structure"-
    and "nonStructure"-derived classes.
  * loadNamespace() imposed undocumented restrictions on the
    versionCheck parameter.  (Reported by Geoff Lee.)
  * Rare over-runs detected by AddressSanitizer in substr() and its
    replacement version have been avoided.
    _Inter alia_ that fix gives the documented behaviour for
    substr(x, 1, 2) &lt;- "" (subsequently reported as PR#16214).
  * Loading packages incorrectly defining an S4 generic followed by a
    function of the same name caused an erroneous cyclic namespace
    dependency error.
  * Declared vignette encodings are now always passed to the vignette
    engine.
  * Port Tomas Kalibera's fix from R-devel that restores the
    loadMethod() fast path, effectively doubling the speed of S4
    dispatch.
  * power.t.test() and power.prop.test() now make use of the
    extendInt option of uniroot() and hence work in more extreme
    cases.  (PR#15792)
  * If a package was updated and attached when its namespace was
    already loaded, it could end up with parts from one version and
    parts from the other.  (PR#16120)
  * tools:::.Rdconv() didn't accept --encoding= due to a typo.
    (PR#16121)
  * Unix-alike builds without a suitable makeinfo were documented to
    link the missing HTML manuals to CRAN, but did not.
  * save(*, ascii=TRUE) and load() now correctly deal with NaN's.
    (PR#16137)
  * split.Date() retains fractional representations while avoiding
    incomplete class propagation.
  * R_ext/Lapack.h had not been updated for changes made by LAPACK to
    the argument lists of its (largely internal) functions dlaed2 and
    dlaed3.  (PR#16157)
  * RShowDoc("NEWS", "txt") had not been updated for the layout
    changes of R 3.1.0.
  * The xtfrm() method for class "Surv" has been corrected and its
    description expanded.
  * mode(x) &lt;- y would incorrectly evaluate x before changing its
    mode. (PR#16215)
  * besselJ(1, 2^64) and besselY(..) now signal a warning, returning
    NaN instead of typically segfaulting. (Issue 3 of PR#15554)
  * HTML conversion of \href markup in .Rd files did not remove the
    backslash from \% and so gave an invalid URL.  In a related
    change, the \ escape is now required in such URLs.</changelog>
</package>
<package pkgid="84dc0e04fd4eda3eebf059286fa1615e3811f9552211d98434c682b1d7f298a2" name="R-gnu14-ohpc" arch="aarch64">
  <version epoch="0" ver="4.5.0" rel="330.ohpc.1.1"/>
  <changelog author="detlef.steuer@gmx.de" date="1394107200">- Upstream release 3.0.3
- Most important
  CHANGES IN R 3.0.3:
  NEW FEATURES:
  * On Windows there is support for making .texi manuals using
    texinfo 5.0 or later: the setting is in file
    src/gnuwin32/MkRules.dist.
    A packaging of the Perl script and modules for texinfo 5.2 has
    been made available at &lt;URL:
    http://www.stats.ox.ac.uk/pub/Rtools/&gt;.
  * write.table() now handles matrices of 2^31 or more elements, for
    those with large amounts of patience and disc space.
  * There is a new function, La_version(), to report the version of
    LAPACK in use.
  * The HTML version of 'An Introduction to R' now has links to PNG
    versions of the figures.
  * There is some support to produce manuals in ebook formats. (See
    doc/manual/Makefile.  Suggested by Mauro Cavalcanti.)
  * On a Unix-alike Sys.timezone() returns NA if the environment
    variable TZ is unset, to distinguish it from an empty string
    which on some OSes means the UTC time zone.
  * The backtick may now be escaped in strings, to allow names
    containing them to be constructed, e.g. `\``.  (PR#15621)
  * read.table(), readLines() and 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.)
  * (Windows only.)  file.symlink() works around the undocumented
    restriction of the Windows system call to backslashes.  (Wish of
    PR#15631.)
  * KalmanForecast(fast = FALSE) is now the default, and the help
    contains an example of how fast = TRUE can be used in this
    version.  (The usage will change in 3.1.0.)
  * 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).
  * strptime() and the format() methods for classes "POSIXct",
    "POSIXlt" and "Date" recognize strings with marked encodings:
    this allows, for example, UTF-8 French month names to be read on
    (French) Windows.
  * iconv(to = "utf8") is now accepted on all platforms (some
    implementations did already, but GNU libiconv did not: however
    converted strings were not marked as being in UTF-8).  The
    official name, "UTF-8" is still preferred.
  * available.packages() is better protected against corrupt metadata
    files.  (A recurring problem with Debian package shogun-r:
    PR#14713.)
  * 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 options() and (C-level) path.expand()
    re-entrantly).</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1397131200">- Upstream release 3.1.0
- Most impotant
  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| &gt; 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 &lt;- a0 and ans[[i]] &lt;- 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,] &lt;- 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.)</changelog>
  <changelog author="darin@darins.net" date="1398772800">- Created symlink to %{_bindir}/r
  Many CRAN packages ship with scripts which call %{_bindir}/r,
  which creates a dependency on it, this fixes that.</changelog>
  <changelog author="darin@darins.net" date="1398945600">-  Add make dependency for Rcmd</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1399636800">- Removed / commented out symlink to %{_bindir}/r
  new package 'littler' should be used instead for packages
  that need /usr/bin/r</changelog>
  <changelog author="darin@darins.net" date="1403265600">- added parallel provides</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1404993600">- Added Provides: R-parallel
- Upstream release 3.1.1
- Most impotant
  CHANGES IN R 3.1.1:
  CHANGES IN R 3.1.1:
  NEW FEATURES:
  * When attach() reports conflicts, it does so compatibly with
    library() by using message().
  * R CMD Sweave no longer cleans any files by default, compatibly
    with versions of R prior to 3.1.0.  There are new options
  - -clean, --clean=default and --clean=keepOuts.
  * tools::buildVignette() and tools::buildVignettes() with clean =
    FALSE no longer remove any created files.  buildvignette() gains
    a keep argument for more cleaning customization.
  * The Bioconductor 'version' used by setRepositories() can now be
    set by environment variable 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.)
  * Error messages from bugs in embedded Sexpr code in Sweave
    documents now report the source location.
  * type.convert(), read.table() and similar read.*() functions get a
    new numerals argument, specifying how numeric input is converted
    when its conversion to double precision loses accuracy.  The
    default value, "allow.loss" allows accuracy loss, as in R
    versions before 3.1.0.
  * For some compilers, integer addition could overflow without a
    warning.  R's internal code for both integer addition and
    subtraction is more robust now.  (PR#15774)
  * The function determining the default number of knots for
    smooth.spline() is now exported, as .nknots.smspl().
  * dbeta(, a,b), pbeta(), qbeta() and rbeta() are now defined also
    for a = 0, b = 0, or infinite a and b (where they typically
    returned NaN before).
  * Many package authors report that the RStudio graphics device does
    not work correctly with their package's use of dev.new().  The
    new option dev.new(noRStudioGD = TRUE) replaces the RStudio
    override by the default device as selected by R itself, still
    respecting environment variables R_INTERACTIVE_DEVICE and
    R_DEFAULT_DEVICE.
  * readRDS() now returns visibly.
  * Modifying internal logical scalar constants now results in an
    error instead of a warning.
  * install.packages(repos = NULL) now accepts http:// or ftp:// URLs
    of package archives as well as file paths, and will download as
    required.  In most cases repos = NULL can be deduced from the
    extension of the URL.
  * The warning when using partial matching with the $ operator on
    data frames is now only given when
    options("warnPartialMatchDollar") is TRUE.
  * Package help requests like package?foo now try the package foo
    whether loaded or not.
  * General help requests now default to trying all loaded packages,
    not just those on the search path.
  * Added a new function promptImport(), to generate a help page for
    a function that was imported from another package (and presumably
    re-exported, or help would not be needed).
  INSTALLATION and INCLUDED SOFTWARE:
  * configure option --with-internal-tzcode can now be used with
    variable rsharedir.
  * The included version of PCRE has been updated to 8.35.
  * There is a new target make uninstall-libR to remove an installed
    shared/static libR.
    make install-libR now works if a sub-architecture is used,
    although the user will need to specify libdir differently for
    different sub-architectures.
  * There is more extensive advice on which LaTeX packages are
    required to install R or to make package manuals (as done by R
    CMD check) in the 'Writing R Extensions' manual.
  * Compilers/linkers were handling the visibility controls in
    src/extra/xz inconsistently (and apparently in some cases
    incorrectly), so it has been simplified.  (PR#15327)
  * (Windows) There is updated support for the use of ICU for
    collation: see the 'R Installation and Administration Manual'.
  BUG FIXES:
  * dbinom(x, n), pbinom(), dpois(), etc, are slightly less
    restrictive in checking if n is integer-valued.  (Wish of
    PR#15734.)
  * pchisq(x, df, ncp, log.p = TRUE) is more accurate and no longer
    underflows for small x and ncp &lt; 80, e.g, for pchisq(1e-5, df =
    100, ncp = 1, log = TRUE).  (Based on PR#15635 and a suggestion
    by Roby Joehanes.)
  * The s ("step into") command in the debugger would cause R to step
    into expressions evaluated there, not just into functions being
    debugged.  (PR#15770)
  * The C code used by strptime() rejected time-zone offsets of more
    than +1200 (+1245, +1300 and +1400 can occur).  (PR#15768)
  * (Windows only.)  png(type = "cairo", antialias = "gray") was not
    accepted.  (PR#15760)
  * Use of save(..., envir=) with named objects could fail.
    (PR#15758)
  * Sweave() mis-parsed Sexpr expressions that contained backslashes.
    (PR#15779)
  * The return value from options(foo = NULL) was not the previous
    value of the option.  (PR#15781)
  * enc2utf8() and enc2native() did not always mark the encoding of
    the return values when it was known.
  * dnbinom(x, size = &lt;large&gt;, mu, log = TRUE) no longer underflows
    to -Inf for large mu, thanks to a suggestion from Alessandro
    Mammana (MPI MolGen, Berlin).
  * pbeta(x, a, b, log = TRUE) no longer behaves discontinuously (in
    a small x-region) because of denormalized numbers.  Also,
    pbeta(1-1e-12, 1e30, 1.001, log=TRUE) now terminates "in real
    time".
  * The "CRAN" filter (see available.packages()) no longer removes
    duplicates other than of packages on CRAN, and does not fail if
    there is no CRAN repository in getOption("repos").
  * The device listing from dev2bitmap() and bitmap() was truncated
    to 1000 characters: modern versions of GhostScript on most
    platforms have many more devices.
  * (Windows.)  Commands such as Sys.which() and pipe() which needed
    to find the full path to a command could segfault if the 'long'
    path name was much longer than the 'short' path name (which
    Sys.which() returns), as the behaviour of the Windows API call
    had changed.
  * R CMD build will fail with an error if one of the packages
    specified in the VignetteBuilder field is not installed.
    (Without loading those packages it cannot be ascertained which
    files are intended to be vignettes. This means that the
    VignetteBuilder packages have to be installed for package
    checking too.)  (Wish of PR#15775.)
  * Misguided attempts to use chull() with non-finite points now give
    an error (related to PR#15777).
  * For a formula with exactly 32 variables the 32nd variable was
    aliased to the intercept in some C-level computations of terms,
    so that for example attempting to remove it would remove the
    intercept instead (and leave a corrupt internal structure).
    (PR#15735)
  * anyDuplicated() silently returned wrong values when the first
    duplicate was at an index which was too large to be stored in an
    integer vector (although a lot of RAM and patience would have
    been needed to encounter this).
  * tools::Rd2ex(commentDontrun = FALSE) failed if the block had only
    one line.
  * Hexadecimal constants such as 0x110p-5L which were incorrectly
    qualified by L were parsed incorrectly since R 3.0.0, with a
    slightly garbled warning. (PR#15753)
  * system() returned success on some platforms even if the system
    was unable to launch a process. (PR#15796)
  * (Windows Rgui console.)  Unbuffered output was sometimes not
    output immediately if the prompt was not on the last line of the
    console.
  * The built-in help server did not declare the encoding for the
    DESCRIPTION or other text files to be the package encoding, so
    non-ASCII characters could be displayed incorrectly.
  * R is now trying harder to not cleanup child processes that were
    not spawned by mcparallel() on platforms that provide information
    about the source process of the SIGCHLD signal. This allows 3rd
    party libraries to manage the exit status of children that they
    spawn without R interfering.
  * mcmapply() was only parallelizing if the number of jobs was
    bigger than the number of cores. It now parallelizes if the
    number of jobs is more than one.
  * Auto-printing would re-evaluate its argument when trying to
    dispatch to a print method.  This is now avoided when possible.
  * Unserializing (including load() and readRDS()) could silently
    return incorrect numeric values from ASCII saves if there was a
    read error.
  * getParseData() could return incorrect values for the parents of
    some elements. (Reported by Andrew Redd.)
  * Attempting to use data frames of 2^31 or more rows with merge()
    or to create a merged data frame of that size now gives a clearer
    error message.
  * parse() did not check its file argument was a connection if it
    was not a character string, so e.g. parse(FALSE) attempted to
    read from stdin.
    Nor did dump() and dput().
  * The "help.try.all.packages" option was ignored when the shortcut
    syntax for help was used, e.g. ?foo.
  * A potential segfault in string allocation has been fixed.  (Found
    by Radford Neal.)
  * Potential memory protection errors in sort() and D() have been
    fixed. (Found by Radford Neal.)
  * Fixed a lack of error checking in graphics event functions.
    (Found by Radford Neal; a different patch used here than the one
    in pqR.)
  * numericDeriv() sometimes miscalculated the gradient.  (PR#15849,
    reported originally by Radford Neal)</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1414756800">- Upstream release 3.1.2
- Most important
  CHANGES IN R 3.1.2:
  NEW FEATURES:
  * embedFonts() now defaults to format = "ps2write" for .ps and .eps
    files.  This is available in Ghostscript 9.x (since 2010) whereas
    the previous default, format = "pswrite", was removed in
    Ghostscript 9.10.
  * For consistency with [dpqr]norm(), [dp]lnorm(sdlog = 0) model a
    point mass at exp(mulog) rather than return NaN (for an error).
  * capabilities() now reports if ICU is compiled in for use for
    collation (it is only actually used if a suitable locale is set
    for collation, and never for a C locale).
  * (OS X only.) Package tcltk checks when loaded if it is linked
    against the CRAN X11-based Tcl/Tk and if so that the Tcl/Tk
    component and the X11 libraries are installed.  This allows more
    informative error messages to be given advising the installation
    of the missing component or of XQuartz.
    The X11() device and X11-based versions of the data editor and
    viewer (invoked by edit() and View() for data frames and matrices
    from command-line R) check that the X11 libraries are installed
    and if not advises installing XQuartz.
  * icuSetCollate() allows locale = "default", and locale = "none" to
    use OS services rather than ICU for collation.
    Environment variable R_ICU_LOCALE can be used to set the default
    ICU locale, in case the one derived from the OS locale is
    inappropriate (this is currently necessary on Windows).
  * New function icuGetCollate() to report on the ICU collation
    locale in use (if any).
  * utils::URLencode() was updated to use unreserved and reserved
    characters from RFC 3986, &lt;URL:
    http://tools.ietf.org/html/rfc3986&gt;, instead of RFC 1738.
  * unique(warnings()) and c(warnings()) are now supported.
  * The Bioconductor 'version' used by setRepositories() now defaults
    to 3.0. (It can be set at runtime _via_ environment variable
    R_BIOC_VERSION.)
  INSTALLATION and INCLUDED SOFTWARE:
  * The configure script reports on the more important
    capabilities/options which will not be compiled in.
    More types of external BLAS are recognized by name in that
    report.
  * When building R as a shared library, the -L${R_HOME}/lib${R_ARCH}
    flag is placed earlier in the link commands used during
    installation and when packages are installed: this helps ensure
    that the current build has priority if an R shared library has
    already been installed by e.g. install-libR in a library
    mentioned in LDFLAGS (and not in 'your system's library
    directory' as documented). (Wish of PR#15790.)
  * LaTeX package upquote is no longer required for R's use of
    inconsolata.
  * (Windows only) If both 32 and 64 bit versions of R are installed,
    the bin/R.exe and bin/Rscript.exe executables now run 64 bit R.
    (To run 32 bit R, overwrite these files with copies of
    bin/i386/Rfe.exe.)
  UTILITIES:
  * Running R CMD check with _R_CHECK_DEPENDS_ONLY_ true now makes
    the VignetteBuilder packages available even if they are listed in
    Suggests, since they are needed to recognise and process
    non-Sweave vignettes.
  * R CMD check now reports empty importFrom declarations in a
    NAMESPACE file, as these are common errors (writing
    importFrom(Pkg) where import(Pkg) was intended).
  * R CMD check now by default checks code usage directly on the
    package namespace without loading and attaching the package and
    its suggests and enhances.  For good practice with packages in
    the Suggests field, see SS1.1.3.1 of 'Writing R Extensions'.  For
    use of lazy-data objects in the package's own code, see ?data.
  BUG FIXES:
  * dmultinom() did not handle non-finite probabilities correctly.
  * prettyNum(x, zero.print=*) now also works when x contains NAs.
  * A longstanding bug exhibited by nlminb() on Windows was traced to
    a compiler bug in gcc 4.6.3; a workaround has been put in place.
    (PR#15244 and PR#15914).
  * Rendering of \command in HTML versions of help pages has been
    improved: this is particularly evident on the help page for
    INSTALL.
  * as.hexmode(x) and as.octmode(x) now behave correctly for some
    numeric x, e.g., c(NA, 1) or c(1, pi).
  * drop1() failed if the scope argument had no variables to drop.
    (PR#15935)
  * edit() (and hence fix()) failed if an object had a non-character
    attribute named "source" (an attribute that had been used in R
    prior to version 2.14.0).
  * callGeneric() could fail if the generic had ... as a formal
    argument. (PR#15937).
  * Forking in package parallel called C entry point exit in the
    child.  This was unsafe (_exit should have been called), and
    could flush stdin of the main R process (seen most often on
    Solaris).
    As good practice, stdout is now flushed before forking a child.
  * R objects such as list(`a\b` = 1) now print correctly.
  * getAnywhere("C_pbinom") now returns correctly a single object
    (rather than unlisting it).
  * The confint() method for nls() fits failed it these has specified
    parameter limits despite using an algorithm other than "port".
    (PR#15960)
  * Subclassing an S4 class failed if the class required arguments to
    the generator, through its initialize() method.
  * removeSource() did not properly handle expressions containing
    arguments that were supplied as missing, e.g.  x[i,]. (PR#15957)
  * as.environment(list()) now works, and as.list() of such an
    environment is now the same as list().
  * Several tcltk functions failed when run in unusual environments.
    (PR#15970)
  * options(list()) now works (trivially). (PR#15979)
  * merge(&lt;dendrogram&gt;, ..) now works correctly for two `independent'
    dendrograms (PR#15648), and still compatibly via adjust = "auto"
    e.g. for two branches of an existing dendrogram.
  * The plot method for "hclust" objects gets an optional argument
    check; When that is true (the default) it checks more carefully
    for valid input.
  * (Windows only) If a user chose to install 64 bit R but not 32 bit
    R, the bin/R and bin/Rscript executables failed to run.
    (PR#15981)
  * Various possible buffer overruns have been prevented, and missed
    memory protection added. (PR#15990)
  * Rscript no longer passes --args to R when there are no extra
    ("user") arguments.
  * objects like getClass("refClass")@prototype now print() and str()
    without error.
  * identical() now also looks at the S4 bit.
  * hist(x, breaks) is more robust in adding a small fuzz to few
    breaks when some are very large. (PR#15988)
  * sub() and gsub() did not handle regular expressions like "\s{2,}"
    properly if the text contained NA or non-ascii elements in a
    UTF-8 locale.  Part of this was due to a bug in the TRE library.
    (PR#16009)
  * RShowDoc("NEWS") now displays the PDF version.
  * Matrices and arrays with last dimension zero did not print at all
    or incompletely.  (PR#16012)
  * plot.histogram() and hence hist() now respect the xaxs, yaxs and
    lab graphics parameters.  (PR#16021)
  * bw.SJ(x) and other bw.*() no longer segfault when x contains
    non-finite values. (PR#16024)
  * R CMD Rd2pdf unintentionally ignored its --os option.
  * The internal method of download.file() was not reporting file
    sizes and progress correctly on files larger than 2GB (inherited
    from libxml2).  This is corrected for 64-bit builds (32-bit
    platforms may not support such files, but where possible will be
    supported in future versions of R).
  * Work around a bug in OS X Yosemite where key environment
    variables may be duplicated causing issues in subprocesses. The
    duplicates are now removed on R startup (via Rprofile).
    (PR#16042)
  * Adjust X11 auto-launch detection in DISPLAY on OS X to recognize
    latest XQuartz.</changelog>
  <changelog author="sbahling@suse.com" date="1418385600">- Remove tex(inconsolata.sty) BuildRequires for SLE_12 builds (like
  older SLE releases).</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1425902400">- Upstream release 3.1.3
- Most important
  CHANGES IN R 3.1.3:
  NEW FEATURES:
  * The internal method of download.file() can now handle files
    larger than 2GB on 32-bit builds which support such files (tested
    on 32-bit R running on 64-bit Windows).
  * kruskal.test() warns on more types of suspicious input.
  * The as.dendrogram() method for "hclust" objects gains a check
    argument protecting against memory explosion for invalid inputs.
  * capabilities() has a new item long.double which indicates if the
    build uses a long double type which is longer than double.
  * nlm() no longer modifies the callback argument in place (a new
    vector is allocated for each invocation, which mimics the
    implicit duplication that occurred in R &lt; 3.1.0); note that this
    is a change from the previously documented behavior. (PR#15958)
  * icuSetCollate() now accepts locale = "ASCII" which uses the basic
    C function strcmp and so collates strings byte-by-byte in
    numerical order.
  * sessionInfo() tries to report the OS version in use (not just
    that compiled under, and including details of Linux
    distributions).
  * model.frame() (used by lm() and many other modelling functions)
    now warns when it drops contrasts from factors.  (Wish of
    PR#16119)
  * install.packages() and friends now accept the value type =
    "binary" as a synonym for the native binary type on the platform
    (if it has one).
  * Single source or binary files can be supplied for
    install.packages(type = "both") and the appropriate type and
    repos = NULL will be inferred.
  * New function pcre_config() to report on some of the configuration
    options of the version of PCRE in use.  In particular, this
    reports if regular expressions using \p{xx} are supported.
  * (Windows.) download.file(cacheOK = FALSE) is now supported when
    internet2.dll is used.
  * browseURL() has been updated to work with Firefox 36.0 which has
    dropped support for the -remote interface.
  INSTALLATION and INCLUDED SOFTWARE:
  * The included version of PCRE has been updated to 8.36.
  * configure accepts MAKEINFO=texi2any as another way to ensure
    texinfo 5.x is used when both 5.x and 4.x are installed.
  UTILITIES:
  * R CMD check now checks the packages used in \donttest sections of
    the examples are specified in the DESCRIPTION file.  (These are
    needed to run the examples interactively.)
  * R CMD check checks for the undeclared use of GNU extensions in
    Makefiles, and for Makefiles with a missing final linefeed.
    R CMD build will correct line endings in all Makefiles, not just
    those in the src directory.
  * R CMD check notes uses of library() and require() in package
    code: see the section 'Suggested packages' of 'Writing R
    Extensions' for good practice.
  DEPRECATED AND DEFUNCT:
  * The configure option --with-valgrind-instrumentation=3 is
    deprecated and will be removed in R 3.2.0.
  BUG FIXES:
  * (Windows.) Rscript.exe was missing a manifest specifying the
    modern style for common controls (e.g., the download progress
    bar).
  * If a package had extra documentation files but no vignette, the
    HTML help system produced an empty index page.
  * The parser now gives an error if a null character is included in
    a string using Unicode escapes. (PR#16046)
  * qr.Q() failed on complex arguments due to pre-3.0(!) typo.
    (PR#16054)
  * abs() failed with named arguments when the argument was complex.
    (PR#16047)
  * "noquote" objects may now be used as columns in dataframes.
    (PR#15997)
  * Some values with extremely long names were printed incorrectly.
    (PR#15999)
  * Extremely large exponents on zero expressed in scientific
    notation (e.g. 0.0e50000) could give NaN.  (PR#15976)
  * download.file() reported downloaded sizes as 0KB if less than
    1MB, only for R 3.1.2 and only on big-endian platforms.
  * prompt() did not escape percent signs in the automatically
    generated usage section of help files.
  * drop.terms() dropped some of the attributes of the object it was
    working with.  (PR#16029)
  * (Windows.) The command completion in Rgui.exe messed up the
    console.  (PR#15791)
  * (Windows.) The choose.files() command returned a blank string
    when the user asked for a single file but cancelled the request.
    (PR#16074)
  * Math2 S4 group generics failed to correctly dispatch "structure"-
    and "nonStructure"-derived classes.
  * loadNamespace() imposed undocumented restrictions on the
    versionCheck parameter.  (Reported by Geoff Lee.)
  * Rare over-runs detected by AddressSanitizer in substr() and its
    replacement version have been avoided.
    _Inter alia_ that fix gives the documented behaviour for
    substr(x, 1, 2) &lt;- "" (subsequently reported as PR#16214).
  * Loading packages incorrectly defining an S4 generic followed by a
    function of the same name caused an erroneous cyclic namespace
    dependency error.
  * Declared vignette encodings are now always passed to the vignette
    engine.
  * Port Tomas Kalibera's fix from R-devel that restores the
    loadMethod() fast path, effectively doubling the speed of S4
    dispatch.
  * power.t.test() and power.prop.test() now make use of the
    extendInt option of uniroot() and hence work in more extreme
    cases.  (PR#15792)
  * If a package was updated and attached when its namespace was
    already loaded, it could end up with parts from one version and
    parts from the other.  (PR#16120)
  * tools:::.Rdconv() didn't accept --encoding= due to a typo.
    (PR#16121)
  * Unix-alike builds without a suitable makeinfo were documented to
    link the missing HTML manuals to CRAN, but did not.
  * save(*, ascii=TRUE) and load() now correctly deal with NaN's.
    (PR#16137)
  * split.Date() retains fractional representations while avoiding
    incomplete class propagation.
  * R_ext/Lapack.h had not been updated for changes made by LAPACK to
    the argument lists of its (largely internal) functions dlaed2 and
    dlaed3.  (PR#16157)
  * RShowDoc("NEWS", "txt") had not been updated for the layout
    changes of R 3.1.0.
  * The xtfrm() method for class "Surv" has been corrected and its
    description expanded.
  * mode(x) &lt;- y would incorrectly evaluate x before changing its
    mode. (PR#16215)
  * besselJ(1, 2^64) and besselY(..) now signal a warning, returning
    NaN instead of typically segfaulting. (Issue 3 of PR#15554)
  * HTML conversion of \href markup in .Rd files did not remove the
    backslash from \% and so gave an invalid URL.  In a related
    change, the \ escape is now required in such URLs.</changelog>
</package>
<package pkgid="20aa1d54af7a735aac04b9451d864318a914d22429c7df460706b6c40c543b25" name="R-gnu14-ohpc" arch="src">
  <version epoch="0" ver="4.5.0" rel="330.ohpc.1.1"/>
  <changelog author="detlef.steuer@gmx.de" date="1394107200">- Upstream release 3.0.3
- Most important
  CHANGES IN R 3.0.3:
  NEW FEATURES:
  * On Windows there is support for making .texi manuals using
    texinfo 5.0 or later: the setting is in file
    src/gnuwin32/MkRules.dist.
    A packaging of the Perl script and modules for texinfo 5.2 has
    been made available at &lt;URL:
    http://www.stats.ox.ac.uk/pub/Rtools/&gt;.
  * write.table() now handles matrices of 2^31 or more elements, for
    those with large amounts of patience and disc space.
  * There is a new function, La_version(), to report the version of
    LAPACK in use.
  * The HTML version of 'An Introduction to R' now has links to PNG
    versions of the figures.
  * There is some support to produce manuals in ebook formats. (See
    doc/manual/Makefile.  Suggested by Mauro Cavalcanti.)
  * On a Unix-alike Sys.timezone() returns NA if the environment
    variable TZ is unset, to distinguish it from an empty string
    which on some OSes means the UTC time zone.
  * The backtick may now be escaped in strings, to allow names
    containing them to be constructed, e.g. `\``.  (PR#15621)
  * read.table(), readLines() and 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.)
  * (Windows only.)  file.symlink() works around the undocumented
    restriction of the Windows system call to backslashes.  (Wish of
    PR#15631.)
  * KalmanForecast(fast = FALSE) is now the default, and the help
    contains an example of how fast = TRUE can be used in this
    version.  (The usage will change in 3.1.0.)
  * 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).
  * strptime() and the format() methods for classes "POSIXct",
    "POSIXlt" and "Date" recognize strings with marked encodings:
    this allows, for example, UTF-8 French month names to be read on
    (French) Windows.
  * iconv(to = "utf8") is now accepted on all platforms (some
    implementations did already, but GNU libiconv did not: however
    converted strings were not marked as being in UTF-8).  The
    official name, "UTF-8" is still preferred.
  * available.packages() is better protected against corrupt metadata
    files.  (A recurring problem with Debian package shogun-r:
    PR#14713.)
  * 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 options() and (C-level) path.expand()
    re-entrantly).</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1397131200">- Upstream release 3.1.0
- Most impotant
  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| &gt; 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 &lt;- a0 and ans[[i]] &lt;- 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,] &lt;- 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.)</changelog>
  <changelog author="darin@darins.net" date="1398772800">- Created symlink to %{_bindir}/r
  Many CRAN packages ship with scripts which call %{_bindir}/r,
  which creates a dependency on it, this fixes that.</changelog>
  <changelog author="darin@darins.net" date="1398945600">-  Add make dependency for Rcmd</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1399636800">- Removed / commented out symlink to %{_bindir}/r
  new package 'littler' should be used instead for packages
  that need /usr/bin/r</changelog>
  <changelog author="darin@darins.net" date="1403265600">- added parallel provides</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1404993600">- Added Provides: R-parallel
- Upstream release 3.1.1
- Most impotant
  CHANGES IN R 3.1.1:
  CHANGES IN R 3.1.1:
  NEW FEATURES:
  * When attach() reports conflicts, it does so compatibly with
    library() by using message().
  * R CMD Sweave no longer cleans any files by default, compatibly
    with versions of R prior to 3.1.0.  There are new options
  - -clean, --clean=default and --clean=keepOuts.
  * tools::buildVignette() and tools::buildVignettes() with clean =
    FALSE no longer remove any created files.  buildvignette() gains
    a keep argument for more cleaning customization.
  * The Bioconductor 'version' used by setRepositories() can now be
    set by environment variable 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.)
  * Error messages from bugs in embedded Sexpr code in Sweave
    documents now report the source location.
  * type.convert(), read.table() and similar read.*() functions get a
    new numerals argument, specifying how numeric input is converted
    when its conversion to double precision loses accuracy.  The
    default value, "allow.loss" allows accuracy loss, as in R
    versions before 3.1.0.
  * For some compilers, integer addition could overflow without a
    warning.  R's internal code for both integer addition and
    subtraction is more robust now.  (PR#15774)
  * The function determining the default number of knots for
    smooth.spline() is now exported, as .nknots.smspl().
  * dbeta(, a,b), pbeta(), qbeta() and rbeta() are now defined also
    for a = 0, b = 0, or infinite a and b (where they typically
    returned NaN before).
  * Many package authors report that the RStudio graphics device does
    not work correctly with their package's use of dev.new().  The
    new option dev.new(noRStudioGD = TRUE) replaces the RStudio
    override by the default device as selected by R itself, still
    respecting environment variables R_INTERACTIVE_DEVICE and
    R_DEFAULT_DEVICE.
  * readRDS() now returns visibly.
  * Modifying internal logical scalar constants now results in an
    error instead of a warning.
  * install.packages(repos = NULL) now accepts http:// or ftp:// URLs
    of package archives as well as file paths, and will download as
    required.  In most cases repos = NULL can be deduced from the
    extension of the URL.
  * The warning when using partial matching with the $ operator on
    data frames is now only given when
    options("warnPartialMatchDollar") is TRUE.
  * Package help requests like package?foo now try the package foo
    whether loaded or not.
  * General help requests now default to trying all loaded packages,
    not just those on the search path.
  * Added a new function promptImport(), to generate a help page for
    a function that was imported from another package (and presumably
    re-exported, or help would not be needed).
  INSTALLATION and INCLUDED SOFTWARE:
  * configure option --with-internal-tzcode can now be used with
    variable rsharedir.
  * The included version of PCRE has been updated to 8.35.
  * There is a new target make uninstall-libR to remove an installed
    shared/static libR.
    make install-libR now works if a sub-architecture is used,
    although the user will need to specify libdir differently for
    different sub-architectures.
  * There is more extensive advice on which LaTeX packages are
    required to install R or to make package manuals (as done by R
    CMD check) in the 'Writing R Extensions' manual.
  * Compilers/linkers were handling the visibility controls in
    src/extra/xz inconsistently (and apparently in some cases
    incorrectly), so it has been simplified.  (PR#15327)
  * (Windows) There is updated support for the use of ICU for
    collation: see the 'R Installation and Administration Manual'.
  BUG FIXES:
  * dbinom(x, n), pbinom(), dpois(), etc, are slightly less
    restrictive in checking if n is integer-valued.  (Wish of
    PR#15734.)
  * pchisq(x, df, ncp, log.p = TRUE) is more accurate and no longer
    underflows for small x and ncp &lt; 80, e.g, for pchisq(1e-5, df =
    100, ncp = 1, log = TRUE).  (Based on PR#15635 and a suggestion
    by Roby Joehanes.)
  * The s ("step into") command in the debugger would cause R to step
    into expressions evaluated there, not just into functions being
    debugged.  (PR#15770)
  * The C code used by strptime() rejected time-zone offsets of more
    than +1200 (+1245, +1300 and +1400 can occur).  (PR#15768)
  * (Windows only.)  png(type = "cairo", antialias = "gray") was not
    accepted.  (PR#15760)
  * Use of save(..., envir=) with named objects could fail.
    (PR#15758)
  * Sweave() mis-parsed Sexpr expressions that contained backslashes.
    (PR#15779)
  * The return value from options(foo = NULL) was not the previous
    value of the option.  (PR#15781)
  * enc2utf8() and enc2native() did not always mark the encoding of
    the return values when it was known.
  * dnbinom(x, size = &lt;large&gt;, mu, log = TRUE) no longer underflows
    to -Inf for large mu, thanks to a suggestion from Alessandro
    Mammana (MPI MolGen, Berlin).
  * pbeta(x, a, b, log = TRUE) no longer behaves discontinuously (in
    a small x-region) because of denormalized numbers.  Also,
    pbeta(1-1e-12, 1e30, 1.001, log=TRUE) now terminates "in real
    time".
  * The "CRAN" filter (see available.packages()) no longer removes
    duplicates other than of packages on CRAN, and does not fail if
    there is no CRAN repository in getOption("repos").
  * The device listing from dev2bitmap() and bitmap() was truncated
    to 1000 characters: modern versions of GhostScript on most
    platforms have many more devices.
  * (Windows.)  Commands such as Sys.which() and pipe() which needed
    to find the full path to a command could segfault if the 'long'
    path name was much longer than the 'short' path name (which
    Sys.which() returns), as the behaviour of the Windows API call
    had changed.
  * R CMD build will fail with an error if one of the packages
    specified in the VignetteBuilder field is not installed.
    (Without loading those packages it cannot be ascertained which
    files are intended to be vignettes. This means that the
    VignetteBuilder packages have to be installed for package
    checking too.)  (Wish of PR#15775.)
  * Misguided attempts to use chull() with non-finite points now give
    an error (related to PR#15777).
  * For a formula with exactly 32 variables the 32nd variable was
    aliased to the intercept in some C-level computations of terms,
    so that for example attempting to remove it would remove the
    intercept instead (and leave a corrupt internal structure).
    (PR#15735)
  * anyDuplicated() silently returned wrong values when the first
    duplicate was at an index which was too large to be stored in an
    integer vector (although a lot of RAM and patience would have
    been needed to encounter this).
  * tools::Rd2ex(commentDontrun = FALSE) failed if the block had only
    one line.
  * Hexadecimal constants such as 0x110p-5L which were incorrectly
    qualified by L were parsed incorrectly since R 3.0.0, with a
    slightly garbled warning. (PR#15753)
  * system() returned success on some platforms even if the system
    was unable to launch a process. (PR#15796)
  * (Windows Rgui console.)  Unbuffered output was sometimes not
    output immediately if the prompt was not on the last line of the
    console.
  * The built-in help server did not declare the encoding for the
    DESCRIPTION or other text files to be the package encoding, so
    non-ASCII characters could be displayed incorrectly.
  * R is now trying harder to not cleanup child processes that were
    not spawned by mcparallel() on platforms that provide information
    about the source process of the SIGCHLD signal. This allows 3rd
    party libraries to manage the exit status of children that they
    spawn without R interfering.
  * mcmapply() was only parallelizing if the number of jobs was
    bigger than the number of cores. It now parallelizes if the
    number of jobs is more than one.
  * Auto-printing would re-evaluate its argument when trying to
    dispatch to a print method.  This is now avoided when possible.
  * Unserializing (including load() and readRDS()) could silently
    return incorrect numeric values from ASCII saves if there was a
    read error.
  * getParseData() could return incorrect values for the parents of
    some elements. (Reported by Andrew Redd.)
  * Attempting to use data frames of 2^31 or more rows with merge()
    or to create a merged data frame of that size now gives a clearer
    error message.
  * parse() did not check its file argument was a connection if it
    was not a character string, so e.g. parse(FALSE) attempted to
    read from stdin.
    Nor did dump() and dput().
  * The "help.try.all.packages" option was ignored when the shortcut
    syntax for help was used, e.g. ?foo.
  * A potential segfault in string allocation has been fixed.  (Found
    by Radford Neal.)
  * Potential memory protection errors in sort() and D() have been
    fixed. (Found by Radford Neal.)
  * Fixed a lack of error checking in graphics event functions.
    (Found by Radford Neal; a different patch used here than the one
    in pqR.)
  * numericDeriv() sometimes miscalculated the gradient.  (PR#15849,
    reported originally by Radford Neal)</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1414756800">- Upstream release 3.1.2
- Most important
  CHANGES IN R 3.1.2:
  NEW FEATURES:
  * embedFonts() now defaults to format = "ps2write" for .ps and .eps
    files.  This is available in Ghostscript 9.x (since 2010) whereas
    the previous default, format = "pswrite", was removed in
    Ghostscript 9.10.
  * For consistency with [dpqr]norm(), [dp]lnorm(sdlog = 0) model a
    point mass at exp(mulog) rather than return NaN (for an error).
  * capabilities() now reports if ICU is compiled in for use for
    collation (it is only actually used if a suitable locale is set
    for collation, and never for a C locale).
  * (OS X only.) Package tcltk checks when loaded if it is linked
    against the CRAN X11-based Tcl/Tk and if so that the Tcl/Tk
    component and the X11 libraries are installed.  This allows more
    informative error messages to be given advising the installation
    of the missing component or of XQuartz.
    The X11() device and X11-based versions of the data editor and
    viewer (invoked by edit() and View() for data frames and matrices
    from command-line R) check that the X11 libraries are installed
    and if not advises installing XQuartz.
  * icuSetCollate() allows locale = "default", and locale = "none" to
    use OS services rather than ICU for collation.
    Environment variable R_ICU_LOCALE can be used to set the default
    ICU locale, in case the one derived from the OS locale is
    inappropriate (this is currently necessary on Windows).
  * New function icuGetCollate() to report on the ICU collation
    locale in use (if any).
  * utils::URLencode() was updated to use unreserved and reserved
    characters from RFC 3986, &lt;URL:
    http://tools.ietf.org/html/rfc3986&gt;, instead of RFC 1738.
  * unique(warnings()) and c(warnings()) are now supported.
  * The Bioconductor 'version' used by setRepositories() now defaults
    to 3.0. (It can be set at runtime _via_ environment variable
    R_BIOC_VERSION.)
  INSTALLATION and INCLUDED SOFTWARE:
  * The configure script reports on the more important
    capabilities/options which will not be compiled in.
    More types of external BLAS are recognized by name in that
    report.
  * When building R as a shared library, the -L${R_HOME}/lib${R_ARCH}
    flag is placed earlier in the link commands used during
    installation and when packages are installed: this helps ensure
    that the current build has priority if an R shared library has
    already been installed by e.g. install-libR in a library
    mentioned in LDFLAGS (and not in 'your system's library
    directory' as documented). (Wish of PR#15790.)
  * LaTeX package upquote is no longer required for R's use of
    inconsolata.
  * (Windows only) If both 32 and 64 bit versions of R are installed,
    the bin/R.exe and bin/Rscript.exe executables now run 64 bit R.
    (To run 32 bit R, overwrite these files with copies of
    bin/i386/Rfe.exe.)
  UTILITIES:
  * Running R CMD check with _R_CHECK_DEPENDS_ONLY_ true now makes
    the VignetteBuilder packages available even if they are listed in
    Suggests, since they are needed to recognise and process
    non-Sweave vignettes.
  * R CMD check now reports empty importFrom declarations in a
    NAMESPACE file, as these are common errors (writing
    importFrom(Pkg) where import(Pkg) was intended).
  * R CMD check now by default checks code usage directly on the
    package namespace without loading and attaching the package and
    its suggests and enhances.  For good practice with packages in
    the Suggests field, see SS1.1.3.1 of 'Writing R Extensions'.  For
    use of lazy-data objects in the package's own code, see ?data.
  BUG FIXES:
  * dmultinom() did not handle non-finite probabilities correctly.
  * prettyNum(x, zero.print=*) now also works when x contains NAs.
  * A longstanding bug exhibited by nlminb() on Windows was traced to
    a compiler bug in gcc 4.6.3; a workaround has been put in place.
    (PR#15244 and PR#15914).
  * Rendering of \command in HTML versions of help pages has been
    improved: this is particularly evident on the help page for
    INSTALL.
  * as.hexmode(x) and as.octmode(x) now behave correctly for some
    numeric x, e.g., c(NA, 1) or c(1, pi).
  * drop1() failed if the scope argument had no variables to drop.
    (PR#15935)
  * edit() (and hence fix()) failed if an object had a non-character
    attribute named "source" (an attribute that had been used in R
    prior to version 2.14.0).
  * callGeneric() could fail if the generic had ... as a formal
    argument. (PR#15937).
  * Forking in package parallel called C entry point exit in the
    child.  This was unsafe (_exit should have been called), and
    could flush stdin of the main R process (seen most often on
    Solaris).
    As good practice, stdout is now flushed before forking a child.
  * R objects such as list(`a\b` = 1) now print correctly.
  * getAnywhere("C_pbinom") now returns correctly a single object
    (rather than unlisting it).
  * The confint() method for nls() fits failed it these has specified
    parameter limits despite using an algorithm other than "port".
    (PR#15960)
  * Subclassing an S4 class failed if the class required arguments to
    the generator, through its initialize() method.
  * removeSource() did not properly handle expressions containing
    arguments that were supplied as missing, e.g.  x[i,]. (PR#15957)
  * as.environment(list()) now works, and as.list() of such an
    environment is now the same as list().
  * Several tcltk functions failed when run in unusual environments.
    (PR#15970)
  * options(list()) now works (trivially). (PR#15979)
  * merge(&lt;dendrogram&gt;, ..) now works correctly for two `independent'
    dendrograms (PR#15648), and still compatibly via adjust = "auto"
    e.g. for two branches of an existing dendrogram.
  * The plot method for "hclust" objects gets an optional argument
    check; When that is true (the default) it checks more carefully
    for valid input.
  * (Windows only) If a user chose to install 64 bit R but not 32 bit
    R, the bin/R and bin/Rscript executables failed to run.
    (PR#15981)
  * Various possible buffer overruns have been prevented, and missed
    memory protection added. (PR#15990)
  * Rscript no longer passes --args to R when there are no extra
    ("user") arguments.
  * objects like getClass("refClass")@prototype now print() and str()
    without error.
  * identical() now also looks at the S4 bit.
  * hist(x, breaks) is more robust in adding a small fuzz to few
    breaks when some are very large. (PR#15988)
  * sub() and gsub() did not handle regular expressions like "\s{2,}"
    properly if the text contained NA or non-ascii elements in a
    UTF-8 locale.  Part of this was due to a bug in the TRE library.
    (PR#16009)
  * RShowDoc("NEWS") now displays the PDF version.
  * Matrices and arrays with last dimension zero did not print at all
    or incompletely.  (PR#16012)
  * plot.histogram() and hence hist() now respect the xaxs, yaxs and
    lab graphics parameters.  (PR#16021)
  * bw.SJ(x) and other bw.*() no longer segfault when x contains
    non-finite values. (PR#16024)
  * R CMD Rd2pdf unintentionally ignored its --os option.
  * The internal method of download.file() was not reporting file
    sizes and progress correctly on files larger than 2GB (inherited
    from libxml2).  This is corrected for 64-bit builds (32-bit
    platforms may not support such files, but where possible will be
    supported in future versions of R).
  * Work around a bug in OS X Yosemite where key environment
    variables may be duplicated causing issues in subprocesses. The
    duplicates are now removed on R startup (via Rprofile).
    (PR#16042)
  * Adjust X11 auto-launch detection in DISPLAY on OS X to recognize
    latest XQuartz.</changelog>
  <changelog author="sbahling@suse.com" date="1418385600">- Remove tex(inconsolata.sty) BuildRequires for SLE_12 builds (like
  older SLE releases).</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1425902400">- Upstream release 3.1.3
- Most important
  CHANGES IN R 3.1.3:
  NEW FEATURES:
  * The internal method of download.file() can now handle files
    larger than 2GB on 32-bit builds which support such files (tested
    on 32-bit R running on 64-bit Windows).
  * kruskal.test() warns on more types of suspicious input.
  * The as.dendrogram() method for "hclust" objects gains a check
    argument protecting against memory explosion for invalid inputs.
  * capabilities() has a new item long.double which indicates if the
    build uses a long double type which is longer than double.
  * nlm() no longer modifies the callback argument in place (a new
    vector is allocated for each invocation, which mimics the
    implicit duplication that occurred in R &lt; 3.1.0); note that this
    is a change from the previously documented behavior. (PR#15958)
  * icuSetCollate() now accepts locale = "ASCII" which uses the basic
    C function strcmp and so collates strings byte-by-byte in
    numerical order.
  * sessionInfo() tries to report the OS version in use (not just
    that compiled under, and including details of Linux
    distributions).
  * model.frame() (used by lm() and many other modelling functions)
    now warns when it drops contrasts from factors.  (Wish of
    PR#16119)
  * install.packages() and friends now accept the value type =
    "binary" as a synonym for the native binary type on the platform
    (if it has one).
  * Single source or binary files can be supplied for
    install.packages(type = "both") and the appropriate type and
    repos = NULL will be inferred.
  * New function pcre_config() to report on some of the configuration
    options of the version of PCRE in use.  In particular, this
    reports if regular expressions using \p{xx} are supported.
  * (Windows.) download.file(cacheOK = FALSE) is now supported when
    internet2.dll is used.
  * browseURL() has been updated to work with Firefox 36.0 which has
    dropped support for the -remote interface.
  INSTALLATION and INCLUDED SOFTWARE:
  * The included version of PCRE has been updated to 8.36.
  * configure accepts MAKEINFO=texi2any as another way to ensure
    texinfo 5.x is used when both 5.x and 4.x are installed.
  UTILITIES:
  * R CMD check now checks the packages used in \donttest sections of
    the examples are specified in the DESCRIPTION file.  (These are
    needed to run the examples interactively.)
  * R CMD check checks for the undeclared use of GNU extensions in
    Makefiles, and for Makefiles with a missing final linefeed.
    R CMD build will correct line endings in all Makefiles, not just
    those in the src directory.
  * R CMD check notes uses of library() and require() in package
    code: see the section 'Suggested packages' of 'Writing R
    Extensions' for good practice.
  DEPRECATED AND DEFUNCT:
  * The configure option --with-valgrind-instrumentation=3 is
    deprecated and will be removed in R 3.2.0.
  BUG FIXES:
  * (Windows.) Rscript.exe was missing a manifest specifying the
    modern style for common controls (e.g., the download progress
    bar).
  * If a package had extra documentation files but no vignette, the
    HTML help system produced an empty index page.
  * The parser now gives an error if a null character is included in
    a string using Unicode escapes. (PR#16046)
  * qr.Q() failed on complex arguments due to pre-3.0(!) typo.
    (PR#16054)
  * abs() failed with named arguments when the argument was complex.
    (PR#16047)
  * "noquote" objects may now be used as columns in dataframes.
    (PR#15997)
  * Some values with extremely long names were printed incorrectly.
    (PR#15999)
  * Extremely large exponents on zero expressed in scientific
    notation (e.g. 0.0e50000) could give NaN.  (PR#15976)
  * download.file() reported downloaded sizes as 0KB if less than
    1MB, only for R 3.1.2 and only on big-endian platforms.
  * prompt() did not escape percent signs in the automatically
    generated usage section of help files.
  * drop.terms() dropped some of the attributes of the object it was
    working with.  (PR#16029)
  * (Windows.) The command completion in Rgui.exe messed up the
    console.  (PR#15791)
  * (Windows.) The choose.files() command returned a blank string
    when the user asked for a single file but cancelled the request.
    (PR#16074)
  * Math2 S4 group generics failed to correctly dispatch "structure"-
    and "nonStructure"-derived classes.
  * loadNamespace() imposed undocumented restrictions on the
    versionCheck parameter.  (Reported by Geoff Lee.)
  * Rare over-runs detected by AddressSanitizer in substr() and its
    replacement version have been avoided.
    _Inter alia_ that fix gives the documented behaviour for
    substr(x, 1, 2) &lt;- "" (subsequently reported as PR#16214).
  * Loading packages incorrectly defining an S4 generic followed by a
    function of the same name caused an erroneous cyclic namespace
    dependency error.
  * Declared vignette encodings are now always passed to the vignette
    engine.
  * Port Tomas Kalibera's fix from R-devel that restores the
    loadMethod() fast path, effectively doubling the speed of S4
    dispatch.
  * power.t.test() and power.prop.test() now make use of the
    extendInt option of uniroot() and hence work in more extreme
    cases.  (PR#15792)
  * If a package was updated and attached when its namespace was
    already loaded, it could end up with parts from one version and
    parts from the other.  (PR#16120)
  * tools:::.Rdconv() didn't accept --encoding= due to a typo.
    (PR#16121)
  * Unix-alike builds without a suitable makeinfo were documented to
    link the missing HTML manuals to CRAN, but did not.
  * save(*, ascii=TRUE) and load() now correctly deal with NaN's.
    (PR#16137)
  * split.Date() retains fractional representations while avoiding
    incomplete class propagation.
  * R_ext/Lapack.h had not been updated for changes made by LAPACK to
    the argument lists of its (largely internal) functions dlaed2 and
    dlaed3.  (PR#16157)
  * RShowDoc("NEWS", "txt") had not been updated for the layout
    changes of R 3.1.0.
  * The xtfrm() method for class "Surv" has been corrected and its
    description expanded.
  * mode(x) &lt;- y would incorrectly evaluate x before changing its
    mode. (PR#16215)
  * besselJ(1, 2^64) and besselY(..) now signal a warning, returning
    NaN instead of typically segfaulting. (Issue 3 of PR#15554)
  * HTML conversion of \href markup in .Rd files did not remove the
    backslash from \% and so gave an invalid URL.  In a related
    change, the \ escape is now required in such URLs.</changelog>
</package>
<package pkgid="63290e362fd82c6ce8a3683835b913c0cb6ab2a95e37df261fce1c521a37eef8" name="R-gnu14-ohpc" arch="x86_64">
  <version epoch="0" ver="4.5.0" rel="330.ohpc.1.1"/>
  <changelog author="detlef.steuer@gmx.de" date="1394107200">- Upstream release 3.0.3
- Most important
  CHANGES IN R 3.0.3:
  NEW FEATURES:
  * On Windows there is support for making .texi manuals using
    texinfo 5.0 or later: the setting is in file
    src/gnuwin32/MkRules.dist.
    A packaging of the Perl script and modules for texinfo 5.2 has
    been made available at &lt;URL:
    http://www.stats.ox.ac.uk/pub/Rtools/&gt;.
  * write.table() now handles matrices of 2^31 or more elements, for
    those with large amounts of patience and disc space.
  * There is a new function, La_version(), to report the version of
    LAPACK in use.
  * The HTML version of 'An Introduction to R' now has links to PNG
    versions of the figures.
  * There is some support to produce manuals in ebook formats. (See
    doc/manual/Makefile.  Suggested by Mauro Cavalcanti.)
  * On a Unix-alike Sys.timezone() returns NA if the environment
    variable TZ is unset, to distinguish it from an empty string
    which on some OSes means the UTC time zone.
  * The backtick may now be escaped in strings, to allow names
    containing them to be constructed, e.g. `\``.  (PR#15621)
  * read.table(), readLines() and 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.)
  * (Windows only.)  file.symlink() works around the undocumented
    restriction of the Windows system call to backslashes.  (Wish of
    PR#15631.)
  * KalmanForecast(fast = FALSE) is now the default, and the help
    contains an example of how fast = TRUE can be used in this
    version.  (The usage will change in 3.1.0.)
  * 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).
  * strptime() and the format() methods for classes "POSIXct",
    "POSIXlt" and "Date" recognize strings with marked encodings:
    this allows, for example, UTF-8 French month names to be read on
    (French) Windows.
  * iconv(to = "utf8") is now accepted on all platforms (some
    implementations did already, but GNU libiconv did not: however
    converted strings were not marked as being in UTF-8).  The
    official name, "UTF-8" is still preferred.
  * available.packages() is better protected against corrupt metadata
    files.  (A recurring problem with Debian package shogun-r:
    PR#14713.)
  * 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 options() and (C-level) path.expand()
    re-entrantly).</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1397131200">- Upstream release 3.1.0
- Most impotant
  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| &gt; 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 &lt;- a0 and ans[[i]] &lt;- 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,] &lt;- 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.)</changelog>
  <changelog author="darin@darins.net" date="1398772800">- Created symlink to %{_bindir}/r
  Many CRAN packages ship with scripts which call %{_bindir}/r,
  which creates a dependency on it, this fixes that.</changelog>
  <changelog author="darin@darins.net" date="1398945600">-  Add make dependency for Rcmd</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1399636800">- Removed / commented out symlink to %{_bindir}/r
  new package 'littler' should be used instead for packages
  that need /usr/bin/r</changelog>
  <changelog author="darin@darins.net" date="1403265600">- added parallel provides</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1404993600">- Added Provides: R-parallel
- Upstream release 3.1.1
- Most impotant
  CHANGES IN R 3.1.1:
  CHANGES IN R 3.1.1:
  NEW FEATURES:
  * When attach() reports conflicts, it does so compatibly with
    library() by using message().
  * R CMD Sweave no longer cleans any files by default, compatibly
    with versions of R prior to 3.1.0.  There are new options
  - -clean, --clean=default and --clean=keepOuts.
  * tools::buildVignette() and tools::buildVignettes() with clean =
    FALSE no longer remove any created files.  buildvignette() gains
    a keep argument for more cleaning customization.
  * The Bioconductor 'version' used by setRepositories() can now be
    set by environment variable 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.)
  * Error messages from bugs in embedded Sexpr code in Sweave
    documents now report the source location.
  * type.convert(), read.table() and similar read.*() functions get a
    new numerals argument, specifying how numeric input is converted
    when its conversion to double precision loses accuracy.  The
    default value, "allow.loss" allows accuracy loss, as in R
    versions before 3.1.0.
  * For some compilers, integer addition could overflow without a
    warning.  R's internal code for both integer addition and
    subtraction is more robust now.  (PR#15774)
  * The function determining the default number of knots for
    smooth.spline() is now exported, as .nknots.smspl().
  * dbeta(, a,b), pbeta(), qbeta() and rbeta() are now defined also
    for a = 0, b = 0, or infinite a and b (where they typically
    returned NaN before).
  * Many package authors report that the RStudio graphics device does
    not work correctly with their package's use of dev.new().  The
    new option dev.new(noRStudioGD = TRUE) replaces the RStudio
    override by the default device as selected by R itself, still
    respecting environment variables R_INTERACTIVE_DEVICE and
    R_DEFAULT_DEVICE.
  * readRDS() now returns visibly.
  * Modifying internal logical scalar constants now results in an
    error instead of a warning.
  * install.packages(repos = NULL) now accepts http:// or ftp:// URLs
    of package archives as well as file paths, and will download as
    required.  In most cases repos = NULL can be deduced from the
    extension of the URL.
  * The warning when using partial matching with the $ operator on
    data frames is now only given when
    options("warnPartialMatchDollar") is TRUE.
  * Package help requests like package?foo now try the package foo
    whether loaded or not.
  * General help requests now default to trying all loaded packages,
    not just those on the search path.
  * Added a new function promptImport(), to generate a help page for
    a function that was imported from another package (and presumably
    re-exported, or help would not be needed).
  INSTALLATION and INCLUDED SOFTWARE:
  * configure option --with-internal-tzcode can now be used with
    variable rsharedir.
  * The included version of PCRE has been updated to 8.35.
  * There is a new target make uninstall-libR to remove an installed
    shared/static libR.
    make install-libR now works if a sub-architecture is used,
    although the user will need to specify libdir differently for
    different sub-architectures.
  * There is more extensive advice on which LaTeX packages are
    required to install R or to make package manuals (as done by R
    CMD check) in the 'Writing R Extensions' manual.
  * Compilers/linkers were handling the visibility controls in
    src/extra/xz inconsistently (and apparently in some cases
    incorrectly), so it has been simplified.  (PR#15327)
  * (Windows) There is updated support for the use of ICU for
    collation: see the 'R Installation and Administration Manual'.
  BUG FIXES:
  * dbinom(x, n), pbinom(), dpois(), etc, are slightly less
    restrictive in checking if n is integer-valued.  (Wish of
    PR#15734.)
  * pchisq(x, df, ncp, log.p = TRUE) is more accurate and no longer
    underflows for small x and ncp &lt; 80, e.g, for pchisq(1e-5, df =
    100, ncp = 1, log = TRUE).  (Based on PR#15635 and a suggestion
    by Roby Joehanes.)
  * The s ("step into") command in the debugger would cause R to step
    into expressions evaluated there, not just into functions being
    debugged.  (PR#15770)
  * The C code used by strptime() rejected time-zone offsets of more
    than +1200 (+1245, +1300 and +1400 can occur).  (PR#15768)
  * (Windows only.)  png(type = "cairo", antialias = "gray") was not
    accepted.  (PR#15760)
  * Use of save(..., envir=) with named objects could fail.
    (PR#15758)
  * Sweave() mis-parsed Sexpr expressions that contained backslashes.
    (PR#15779)
  * The return value from options(foo = NULL) was not the previous
    value of the option.  (PR#15781)
  * enc2utf8() and enc2native() did not always mark the encoding of
    the return values when it was known.
  * dnbinom(x, size = &lt;large&gt;, mu, log = TRUE) no longer underflows
    to -Inf for large mu, thanks to a suggestion from Alessandro
    Mammana (MPI MolGen, Berlin).
  * pbeta(x, a, b, log = TRUE) no longer behaves discontinuously (in
    a small x-region) because of denormalized numbers.  Also,
    pbeta(1-1e-12, 1e30, 1.001, log=TRUE) now terminates "in real
    time".
  * The "CRAN" filter (see available.packages()) no longer removes
    duplicates other than of packages on CRAN, and does not fail if
    there is no CRAN repository in getOption("repos").
  * The device listing from dev2bitmap() and bitmap() was truncated
    to 1000 characters: modern versions of GhostScript on most
    platforms have many more devices.
  * (Windows.)  Commands such as Sys.which() and pipe() which needed
    to find the full path to a command could segfault if the 'long'
    path name was much longer than the 'short' path name (which
    Sys.which() returns), as the behaviour of the Windows API call
    had changed.
  * R CMD build will fail with an error if one of the packages
    specified in the VignetteBuilder field is not installed.
    (Without loading those packages it cannot be ascertained which
    files are intended to be vignettes. This means that the
    VignetteBuilder packages have to be installed for package
    checking too.)  (Wish of PR#15775.)
  * Misguided attempts to use chull() with non-finite points now give
    an error (related to PR#15777).
  * For a formula with exactly 32 variables the 32nd variable was
    aliased to the intercept in some C-level computations of terms,
    so that for example attempting to remove it would remove the
    intercept instead (and leave a corrupt internal structure).
    (PR#15735)
  * anyDuplicated() silently returned wrong values when the first
    duplicate was at an index which was too large to be stored in an
    integer vector (although a lot of RAM and patience would have
    been needed to encounter this).
  * tools::Rd2ex(commentDontrun = FALSE) failed if the block had only
    one line.
  * Hexadecimal constants such as 0x110p-5L which were incorrectly
    qualified by L were parsed incorrectly since R 3.0.0, with a
    slightly garbled warning. (PR#15753)
  * system() returned success on some platforms even if the system
    was unable to launch a process. (PR#15796)
  * (Windows Rgui console.)  Unbuffered output was sometimes not
    output immediately if the prompt was not on the last line of the
    console.
  * The built-in help server did not declare the encoding for the
    DESCRIPTION or other text files to be the package encoding, so
    non-ASCII characters could be displayed incorrectly.
  * R is now trying harder to not cleanup child processes that were
    not spawned by mcparallel() on platforms that provide information
    about the source process of the SIGCHLD signal. This allows 3rd
    party libraries to manage the exit status of children that they
    spawn without R interfering.
  * mcmapply() was only parallelizing if the number of jobs was
    bigger than the number of cores. It now parallelizes if the
    number of jobs is more than one.
  * Auto-printing would re-evaluate its argument when trying to
    dispatch to a print method.  This is now avoided when possible.
  * Unserializing (including load() and readRDS()) could silently
    return incorrect numeric values from ASCII saves if there was a
    read error.
  * getParseData() could return incorrect values for the parents of
    some elements. (Reported by Andrew Redd.)
  * Attempting to use data frames of 2^31 or more rows with merge()
    or to create a merged data frame of that size now gives a clearer
    error message.
  * parse() did not check its file argument was a connection if it
    was not a character string, so e.g. parse(FALSE) attempted to
    read from stdin.
    Nor did dump() and dput().
  * The "help.try.all.packages" option was ignored when the shortcut
    syntax for help was used, e.g. ?foo.
  * A potential segfault in string allocation has been fixed.  (Found
    by Radford Neal.)
  * Potential memory protection errors in sort() and D() have been
    fixed. (Found by Radford Neal.)
  * Fixed a lack of error checking in graphics event functions.
    (Found by Radford Neal; a different patch used here than the one
    in pqR.)
  * numericDeriv() sometimes miscalculated the gradient.  (PR#15849,
    reported originally by Radford Neal)</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1414756800">- Upstream release 3.1.2
- Most important
  CHANGES IN R 3.1.2:
  NEW FEATURES:
  * embedFonts() now defaults to format = "ps2write" for .ps and .eps
    files.  This is available in Ghostscript 9.x (since 2010) whereas
    the previous default, format = "pswrite", was removed in
    Ghostscript 9.10.
  * For consistency with [dpqr]norm(), [dp]lnorm(sdlog = 0) model a
    point mass at exp(mulog) rather than return NaN (for an error).
  * capabilities() now reports if ICU is compiled in for use for
    collation (it is only actually used if a suitable locale is set
    for collation, and never for a C locale).
  * (OS X only.) Package tcltk checks when loaded if it is linked
    against the CRAN X11-based Tcl/Tk and if so that the Tcl/Tk
    component and the X11 libraries are installed.  This allows more
    informative error messages to be given advising the installation
    of the missing component or of XQuartz.
    The X11() device and X11-based versions of the data editor and
    viewer (invoked by edit() and View() for data frames and matrices
    from command-line R) check that the X11 libraries are installed
    and if not advises installing XQuartz.
  * icuSetCollate() allows locale = "default", and locale = "none" to
    use OS services rather than ICU for collation.
    Environment variable R_ICU_LOCALE can be used to set the default
    ICU locale, in case the one derived from the OS locale is
    inappropriate (this is currently necessary on Windows).
  * New function icuGetCollate() to report on the ICU collation
    locale in use (if any).
  * utils::URLencode() was updated to use unreserved and reserved
    characters from RFC 3986, &lt;URL:
    http://tools.ietf.org/html/rfc3986&gt;, instead of RFC 1738.
  * unique(warnings()) and c(warnings()) are now supported.
  * The Bioconductor 'version' used by setRepositories() now defaults
    to 3.0. (It can be set at runtime _via_ environment variable
    R_BIOC_VERSION.)
  INSTALLATION and INCLUDED SOFTWARE:
  * The configure script reports on the more important
    capabilities/options which will not be compiled in.
    More types of external BLAS are recognized by name in that
    report.
  * When building R as a shared library, the -L${R_HOME}/lib${R_ARCH}
    flag is placed earlier in the link commands used during
    installation and when packages are installed: this helps ensure
    that the current build has priority if an R shared library has
    already been installed by e.g. install-libR in a library
    mentioned in LDFLAGS (and not in 'your system's library
    directory' as documented). (Wish of PR#15790.)
  * LaTeX package upquote is no longer required for R's use of
    inconsolata.
  * (Windows only) If both 32 and 64 bit versions of R are installed,
    the bin/R.exe and bin/Rscript.exe executables now run 64 bit R.
    (To run 32 bit R, overwrite these files with copies of
    bin/i386/Rfe.exe.)
  UTILITIES:
  * Running R CMD check with _R_CHECK_DEPENDS_ONLY_ true now makes
    the VignetteBuilder packages available even if they are listed in
    Suggests, since they are needed to recognise and process
    non-Sweave vignettes.
  * R CMD check now reports empty importFrom declarations in a
    NAMESPACE file, as these are common errors (writing
    importFrom(Pkg) where import(Pkg) was intended).
  * R CMD check now by default checks code usage directly on the
    package namespace without loading and attaching the package and
    its suggests and enhances.  For good practice with packages in
    the Suggests field, see SS1.1.3.1 of 'Writing R Extensions'.  For
    use of lazy-data objects in the package's own code, see ?data.
  BUG FIXES:
  * dmultinom() did not handle non-finite probabilities correctly.
  * prettyNum(x, zero.print=*) now also works when x contains NAs.
  * A longstanding bug exhibited by nlminb() on Windows was traced to
    a compiler bug in gcc 4.6.3; a workaround has been put in place.
    (PR#15244 and PR#15914).
  * Rendering of \command in HTML versions of help pages has been
    improved: this is particularly evident on the help page for
    INSTALL.
  * as.hexmode(x) and as.octmode(x) now behave correctly for some
    numeric x, e.g., c(NA, 1) or c(1, pi).
  * drop1() failed if the scope argument had no variables to drop.
    (PR#15935)
  * edit() (and hence fix()) failed if an object had a non-character
    attribute named "source" (an attribute that had been used in R
    prior to version 2.14.0).
  * callGeneric() could fail if the generic had ... as a formal
    argument. (PR#15937).
  * Forking in package parallel called C entry point exit in the
    child.  This was unsafe (_exit should have been called), and
    could flush stdin of the main R process (seen most often on
    Solaris).
    As good practice, stdout is now flushed before forking a child.
  * R objects such as list(`a\b` = 1) now print correctly.
  * getAnywhere("C_pbinom") now returns correctly a single object
    (rather than unlisting it).
  * The confint() method for nls() fits failed it these has specified
    parameter limits despite using an algorithm other than "port".
    (PR#15960)
  * Subclassing an S4 class failed if the class required arguments to
    the generator, through its initialize() method.
  * removeSource() did not properly handle expressions containing
    arguments that were supplied as missing, e.g.  x[i,]. (PR#15957)
  * as.environment(list()) now works, and as.list() of such an
    environment is now the same as list().
  * Several tcltk functions failed when run in unusual environments.
    (PR#15970)
  * options(list()) now works (trivially). (PR#15979)
  * merge(&lt;dendrogram&gt;, ..) now works correctly for two `independent'
    dendrograms (PR#15648), and still compatibly via adjust = "auto"
    e.g. for two branches of an existing dendrogram.
  * The plot method for "hclust" objects gets an optional argument
    check; When that is true (the default) it checks more carefully
    for valid input.
  * (Windows only) If a user chose to install 64 bit R but not 32 bit
    R, the bin/R and bin/Rscript executables failed to run.
    (PR#15981)
  * Various possible buffer overruns have been prevented, and missed
    memory protection added. (PR#15990)
  * Rscript no longer passes --args to R when there are no extra
    ("user") arguments.
  * objects like getClass("refClass")@prototype now print() and str()
    without error.
  * identical() now also looks at the S4 bit.
  * hist(x, breaks) is more robust in adding a small fuzz to few
    breaks when some are very large. (PR#15988)
  * sub() and gsub() did not handle regular expressions like "\s{2,}"
    properly if the text contained NA or non-ascii elements in a
    UTF-8 locale.  Part of this was due to a bug in the TRE library.
    (PR#16009)
  * RShowDoc("NEWS") now displays the PDF version.
  * Matrices and arrays with last dimension zero did not print at all
    or incompletely.  (PR#16012)
  * plot.histogram() and hence hist() now respect the xaxs, yaxs and
    lab graphics parameters.  (PR#16021)
  * bw.SJ(x) and other bw.*() no longer segfault when x contains
    non-finite values. (PR#16024)
  * R CMD Rd2pdf unintentionally ignored its --os option.
  * The internal method of download.file() was not reporting file
    sizes and progress correctly on files larger than 2GB (inherited
    from libxml2).  This is corrected for 64-bit builds (32-bit
    platforms may not support such files, but where possible will be
    supported in future versions of R).
  * Work around a bug in OS X Yosemite where key environment
    variables may be duplicated causing issues in subprocesses. The
    duplicates are now removed on R startup (via Rprofile).
    (PR#16042)
  * Adjust X11 auto-launch detection in DISPLAY on OS X to recognize
    latest XQuartz.</changelog>
  <changelog author="sbahling@suse.com" date="1418385600">- Remove tex(inconsolata.sty) BuildRequires for SLE_12 builds (like
  older SLE releases).</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1425902400">- Upstream release 3.1.3
- Most important
  CHANGES IN R 3.1.3:
  NEW FEATURES:
  * The internal method of download.file() can now handle files
    larger than 2GB on 32-bit builds which support such files (tested
    on 32-bit R running on 64-bit Windows).
  * kruskal.test() warns on more types of suspicious input.
  * The as.dendrogram() method for "hclust" objects gains a check
    argument protecting against memory explosion for invalid inputs.
  * capabilities() has a new item long.double which indicates if the
    build uses a long double type which is longer than double.
  * nlm() no longer modifies the callback argument in place (a new
    vector is allocated for each invocation, which mimics the
    implicit duplication that occurred in R &lt; 3.1.0); note that this
    is a change from the previously documented behavior. (PR#15958)
  * icuSetCollate() now accepts locale = "ASCII" which uses the basic
    C function strcmp and so collates strings byte-by-byte in
    numerical order.
  * sessionInfo() tries to report the OS version in use (not just
    that compiled under, and including details of Linux
    distributions).
  * model.frame() (used by lm() and many other modelling functions)
    now warns when it drops contrasts from factors.  (Wish of
    PR#16119)
  * install.packages() and friends now accept the value type =
    "binary" as a synonym for the native binary type on the platform
    (if it has one).
  * Single source or binary files can be supplied for
    install.packages(type = "both") and the appropriate type and
    repos = NULL will be inferred.
  * New function pcre_config() to report on some of the configuration
    options of the version of PCRE in use.  In particular, this
    reports if regular expressions using \p{xx} are supported.
  * (Windows.) download.file(cacheOK = FALSE) is now supported when
    internet2.dll is used.
  * browseURL() has been updated to work with Firefox 36.0 which has
    dropped support for the -remote interface.
  INSTALLATION and INCLUDED SOFTWARE:
  * The included version of PCRE has been updated to 8.36.
  * configure accepts MAKEINFO=texi2any as another way to ensure
    texinfo 5.x is used when both 5.x and 4.x are installed.
  UTILITIES:
  * R CMD check now checks the packages used in \donttest sections of
    the examples are specified in the DESCRIPTION file.  (These are
    needed to run the examples interactively.)
  * R CMD check checks for the undeclared use of GNU extensions in
    Makefiles, and for Makefiles with a missing final linefeed.
    R CMD build will correct line endings in all Makefiles, not just
    those in the src directory.
  * R CMD check notes uses of library() and require() in package
    code: see the section 'Suggested packages' of 'Writing R
    Extensions' for good practice.
  DEPRECATED AND DEFUNCT:
  * The configure option --with-valgrind-instrumentation=3 is
    deprecated and will be removed in R 3.2.0.
  BUG FIXES:
  * (Windows.) Rscript.exe was missing a manifest specifying the
    modern style for common controls (e.g., the download progress
    bar).
  * If a package had extra documentation files but no vignette, the
    HTML help system produced an empty index page.
  * The parser now gives an error if a null character is included in
    a string using Unicode escapes. (PR#16046)
  * qr.Q() failed on complex arguments due to pre-3.0(!) typo.
    (PR#16054)
  * abs() failed with named arguments when the argument was complex.
    (PR#16047)
  * "noquote" objects may now be used as columns in dataframes.
    (PR#15997)
  * Some values with extremely long names were printed incorrectly.
    (PR#15999)
  * Extremely large exponents on zero expressed in scientific
    notation (e.g. 0.0e50000) could give NaN.  (PR#15976)
  * download.file() reported downloaded sizes as 0KB if less than
    1MB, only for R 3.1.2 and only on big-endian platforms.
  * prompt() did not escape percent signs in the automatically
    generated usage section of help files.
  * drop.terms() dropped some of the attributes of the object it was
    working with.  (PR#16029)
  * (Windows.) The command completion in Rgui.exe messed up the
    console.  (PR#15791)
  * (Windows.) The choose.files() command returned a blank string
    when the user asked for a single file but cancelled the request.
    (PR#16074)
  * Math2 S4 group generics failed to correctly dispatch "structure"-
    and "nonStructure"-derived classes.
  * loadNamespace() imposed undocumented restrictions on the
    versionCheck parameter.  (Reported by Geoff Lee.)
  * Rare over-runs detected by AddressSanitizer in substr() and its
    replacement version have been avoided.
    _Inter alia_ that fix gives the documented behaviour for
    substr(x, 1, 2) &lt;- "" (subsequently reported as PR#16214).
  * Loading packages incorrectly defining an S4 generic followed by a
    function of the same name caused an erroneous cyclic namespace
    dependency error.
  * Declared vignette encodings are now always passed to the vignette
    engine.
  * Port Tomas Kalibera's fix from R-devel that restores the
    loadMethod() fast path, effectively doubling the speed of S4
    dispatch.
  * power.t.test() and power.prop.test() now make use of the
    extendInt option of uniroot() and hence work in more extreme
    cases.  (PR#15792)
  * If a package was updated and attached when its namespace was
    already loaded, it could end up with parts from one version and
    parts from the other.  (PR#16120)
  * tools:::.Rdconv() didn't accept --encoding= due to a typo.
    (PR#16121)
  * Unix-alike builds without a suitable makeinfo were documented to
    link the missing HTML manuals to CRAN, but did not.
  * save(*, ascii=TRUE) and load() now correctly deal with NaN's.
    (PR#16137)
  * split.Date() retains fractional representations while avoiding
    incomplete class propagation.
  * R_ext/Lapack.h had not been updated for changes made by LAPACK to
    the argument lists of its (largely internal) functions dlaed2 and
    dlaed3.  (PR#16157)
  * RShowDoc("NEWS", "txt") had not been updated for the layout
    changes of R 3.1.0.
  * The xtfrm() method for class "Surv" has been corrected and its
    description expanded.
  * mode(x) &lt;- y would incorrectly evaluate x before changing its
    mode. (PR#16215)
  * besselJ(1, 2^64) and besselY(..) now signal a warning, returning
    NaN instead of typically segfaulting. (Issue 3 of PR#15554)
  * HTML conversion of \href markup in .Rd files did not remove the
    backslash from \% and so gave an invalid URL.  In a related
    change, the \ escape is now required in such URLs.</changelog>
</package>
<package pkgid="2dc6e9ff69e056c649ca669a6f12dc0fdc7c4971a7b21635076cd13182254503" name="R-gnu15-ohpc" arch="aarch64">
  <version epoch="0" ver="4.6.0" rel="350.ohpc.2.6"/>
  <changelog author="detlef.steuer@gmx.de" date="1394107200">- Upstream release 3.0.3
- Most important
  CHANGES IN R 3.0.3:
  NEW FEATURES:
  * On Windows there is support for making .texi manuals using
    texinfo 5.0 or later: the setting is in file
    src/gnuwin32/MkRules.dist.
    A packaging of the Perl script and modules for texinfo 5.2 has
    been made available at &lt;URL:
    http://www.stats.ox.ac.uk/pub/Rtools/&gt;.
  * write.table() now handles matrices of 2^31 or more elements, for
    those with large amounts of patience and disc space.
  * There is a new function, La_version(), to report the version of
    LAPACK in use.
  * The HTML version of 'An Introduction to R' now has links to PNG
    versions of the figures.
  * There is some support to produce manuals in ebook formats. (See
    doc/manual/Makefile.  Suggested by Mauro Cavalcanti.)
  * On a Unix-alike Sys.timezone() returns NA if the environment
    variable TZ is unset, to distinguish it from an empty string
    which on some OSes means the UTC time zone.
  * The backtick may now be escaped in strings, to allow names
    containing them to be constructed, e.g. `\``.  (PR#15621)
  * read.table(), readLines() and 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.)
  * (Windows only.)  file.symlink() works around the undocumented
    restriction of the Windows system call to backslashes.  (Wish of
    PR#15631.)
  * KalmanForecast(fast = FALSE) is now the default, and the help
    contains an example of how fast = TRUE can be used in this
    version.  (The usage will change in 3.1.0.)
  * 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).
  * strptime() and the format() methods for classes "POSIXct",
    "POSIXlt" and "Date" recognize strings with marked encodings:
    this allows, for example, UTF-8 French month names to be read on
    (French) Windows.
  * iconv(to = "utf8") is now accepted on all platforms (some
    implementations did already, but GNU libiconv did not: however
    converted strings were not marked as being in UTF-8).  The
    official name, "UTF-8" is still preferred.
  * available.packages() is better protected against corrupt metadata
    files.  (A recurring problem with Debian package shogun-r:
    PR#14713.)
  * 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 options() and (C-level) path.expand()
    re-entrantly).</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1397131200">- Upstream release 3.1.0
- Most impotant
  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| &gt; 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 &lt;- a0 and ans[[i]] &lt;- 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,] &lt;- 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.)</changelog>
  <changelog author="darin@darins.net" date="1398772800">- Created symlink to %{_bindir}/r
  Many CRAN packages ship with scripts which call %{_bindir}/r,
  which creates a dependency on it, this fixes that.</changelog>
  <changelog author="darin@darins.net" date="1398945600">-  Add make dependency for Rcmd</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1399636800">- Removed / commented out symlink to %{_bindir}/r
  new package 'littler' should be used instead for packages
  that need /usr/bin/r</changelog>
  <changelog author="darin@darins.net" date="1403265600">- added parallel provides</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1404993600">- Added Provides: R-parallel
- Upstream release 3.1.1
- Most impotant
  CHANGES IN R 3.1.1:
  CHANGES IN R 3.1.1:
  NEW FEATURES:
  * When attach() reports conflicts, it does so compatibly with
    library() by using message().
  * R CMD Sweave no longer cleans any files by default, compatibly
    with versions of R prior to 3.1.0.  There are new options
  - -clean, --clean=default and --clean=keepOuts.
  * tools::buildVignette() and tools::buildVignettes() with clean =
    FALSE no longer remove any created files.  buildvignette() gains
    a keep argument for more cleaning customization.
  * The Bioconductor 'version' used by setRepositories() can now be
    set by environment variable 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.)
  * Error messages from bugs in embedded Sexpr code in Sweave
    documents now report the source location.
  * type.convert(), read.table() and similar read.*() functions get a
    new numerals argument, specifying how numeric input is converted
    when its conversion to double precision loses accuracy.  The
    default value, "allow.loss" allows accuracy loss, as in R
    versions before 3.1.0.
  * For some compilers, integer addition could overflow without a
    warning.  R's internal code for both integer addition and
    subtraction is more robust now.  (PR#15774)
  * The function determining the default number of knots for
    smooth.spline() is now exported, as .nknots.smspl().
  * dbeta(, a,b), pbeta(), qbeta() and rbeta() are now defined also
    for a = 0, b = 0, or infinite a and b (where they typically
    returned NaN before).
  * Many package authors report that the RStudio graphics device does
    not work correctly with their package's use of dev.new().  The
    new option dev.new(noRStudioGD = TRUE) replaces the RStudio
    override by the default device as selected by R itself, still
    respecting environment variables R_INTERACTIVE_DEVICE and
    R_DEFAULT_DEVICE.
  * readRDS() now returns visibly.
  * Modifying internal logical scalar constants now results in an
    error instead of a warning.
  * install.packages(repos = NULL) now accepts http:// or ftp:// URLs
    of package archives as well as file paths, and will download as
    required.  In most cases repos = NULL can be deduced from the
    extension of the URL.
  * The warning when using partial matching with the $ operator on
    data frames is now only given when
    options("warnPartialMatchDollar") is TRUE.
  * Package help requests like package?foo now try the package foo
    whether loaded or not.
  * General help requests now default to trying all loaded packages,
    not just those on the search path.
  * Added a new function promptImport(), to generate a help page for
    a function that was imported from another package (and presumably
    re-exported, or help would not be needed).
  INSTALLATION and INCLUDED SOFTWARE:
  * configure option --with-internal-tzcode can now be used with
    variable rsharedir.
  * The included version of PCRE has been updated to 8.35.
  * There is a new target make uninstall-libR to remove an installed
    shared/static libR.
    make install-libR now works if a sub-architecture is used,
    although the user will need to specify libdir differently for
    different sub-architectures.
  * There is more extensive advice on which LaTeX packages are
    required to install R or to make package manuals (as done by R
    CMD check) in the 'Writing R Extensions' manual.
  * Compilers/linkers were handling the visibility controls in
    src/extra/xz inconsistently (and apparently in some cases
    incorrectly), so it has been simplified.  (PR#15327)
  * (Windows) There is updated support for the use of ICU for
    collation: see the 'R Installation and Administration Manual'.
  BUG FIXES:
  * dbinom(x, n), pbinom(), dpois(), etc, are slightly less
    restrictive in checking if n is integer-valued.  (Wish of
    PR#15734.)
  * pchisq(x, df, ncp, log.p = TRUE) is more accurate and no longer
    underflows for small x and ncp &lt; 80, e.g, for pchisq(1e-5, df =
    100, ncp = 1, log = TRUE).  (Based on PR#15635 and a suggestion
    by Roby Joehanes.)
  * The s ("step into") command in the debugger would cause R to step
    into expressions evaluated there, not just into functions being
    debugged.  (PR#15770)
  * The C code used by strptime() rejected time-zone offsets of more
    than +1200 (+1245, +1300 and +1400 can occur).  (PR#15768)
  * (Windows only.)  png(type = "cairo", antialias = "gray") was not
    accepted.  (PR#15760)
  * Use of save(..., envir=) with named objects could fail.
    (PR#15758)
  * Sweave() mis-parsed Sexpr expressions that contained backslashes.
    (PR#15779)
  * The return value from options(foo = NULL) was not the previous
    value of the option.  (PR#15781)
  * enc2utf8() and enc2native() did not always mark the encoding of
    the return values when it was known.
  * dnbinom(x, size = &lt;large&gt;, mu, log = TRUE) no longer underflows
    to -Inf for large mu, thanks to a suggestion from Alessandro
    Mammana (MPI MolGen, Berlin).
  * pbeta(x, a, b, log = TRUE) no longer behaves discontinuously (in
    a small x-region) because of denormalized numbers.  Also,
    pbeta(1-1e-12, 1e30, 1.001, log=TRUE) now terminates "in real
    time".
  * The "CRAN" filter (see available.packages()) no longer removes
    duplicates other than of packages on CRAN, and does not fail if
    there is no CRAN repository in getOption("repos").
  * The device listing from dev2bitmap() and bitmap() was truncated
    to 1000 characters: modern versions of GhostScript on most
    platforms have many more devices.
  * (Windows.)  Commands such as Sys.which() and pipe() which needed
    to find the full path to a command could segfault if the 'long'
    path name was much longer than the 'short' path name (which
    Sys.which() returns), as the behaviour of the Windows API call
    had changed.
  * R CMD build will fail with an error if one of the packages
    specified in the VignetteBuilder field is not installed.
    (Without loading those packages it cannot be ascertained which
    files are intended to be vignettes. This means that the
    VignetteBuilder packages have to be installed for package
    checking too.)  (Wish of PR#15775.)
  * Misguided attempts to use chull() with non-finite points now give
    an error (related to PR#15777).
  * For a formula with exactly 32 variables the 32nd variable was
    aliased to the intercept in some C-level computations of terms,
    so that for example attempting to remove it would remove the
    intercept instead (and leave a corrupt internal structure).
    (PR#15735)
  * anyDuplicated() silently returned wrong values when the first
    duplicate was at an index which was too large to be stored in an
    integer vector (although a lot of RAM and patience would have
    been needed to encounter this).
  * tools::Rd2ex(commentDontrun = FALSE) failed if the block had only
    one line.
  * Hexadecimal constants such as 0x110p-5L which were incorrectly
    qualified by L were parsed incorrectly since R 3.0.0, with a
    slightly garbled warning. (PR#15753)
  * system() returned success on some platforms even if the system
    was unable to launch a process. (PR#15796)
  * (Windows Rgui console.)  Unbuffered output was sometimes not
    output immediately if the prompt was not on the last line of the
    console.
  * The built-in help server did not declare the encoding for the
    DESCRIPTION or other text files to be the package encoding, so
    non-ASCII characters could be displayed incorrectly.
  * R is now trying harder to not cleanup child processes that were
    not spawned by mcparallel() on platforms that provide information
    about the source process of the SIGCHLD signal. This allows 3rd
    party libraries to manage the exit status of children that they
    spawn without R interfering.
  * mcmapply() was only parallelizing if the number of jobs was
    bigger than the number of cores. It now parallelizes if the
    number of jobs is more than one.
  * Auto-printing would re-evaluate its argument when trying to
    dispatch to a print method.  This is now avoided when possible.
  * Unserializing (including load() and readRDS()) could silently
    return incorrect numeric values from ASCII saves if there was a
    read error.
  * getParseData() could return incorrect values for the parents of
    some elements. (Reported by Andrew Redd.)
  * Attempting to use data frames of 2^31 or more rows with merge()
    or to create a merged data frame of that size now gives a clearer
    error message.
  * parse() did not check its file argument was a connection if it
    was not a character string, so e.g. parse(FALSE) attempted to
    read from stdin.
    Nor did dump() and dput().
  * The "help.try.all.packages" option was ignored when the shortcut
    syntax for help was used, e.g. ?foo.
  * A potential segfault in string allocation has been fixed.  (Found
    by Radford Neal.)
  * Potential memory protection errors in sort() and D() have been
    fixed. (Found by Radford Neal.)
  * Fixed a lack of error checking in graphics event functions.
    (Found by Radford Neal; a different patch used here than the one
    in pqR.)
  * numericDeriv() sometimes miscalculated the gradient.  (PR#15849,
    reported originally by Radford Neal)</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1414756800">- Upstream release 3.1.2
- Most important
  CHANGES IN R 3.1.2:
  NEW FEATURES:
  * embedFonts() now defaults to format = "ps2write" for .ps and .eps
    files.  This is available in Ghostscript 9.x (since 2010) whereas
    the previous default, format = "pswrite", was removed in
    Ghostscript 9.10.
  * For consistency with [dpqr]norm(), [dp]lnorm(sdlog = 0) model a
    point mass at exp(mulog) rather than return NaN (for an error).
  * capabilities() now reports if ICU is compiled in for use for
    collation (it is only actually used if a suitable locale is set
    for collation, and never for a C locale).
  * (OS X only.) Package tcltk checks when loaded if it is linked
    against the CRAN X11-based Tcl/Tk and if so that the Tcl/Tk
    component and the X11 libraries are installed.  This allows more
    informative error messages to be given advising the installation
    of the missing component or of XQuartz.
    The X11() device and X11-based versions of the data editor and
    viewer (invoked by edit() and View() for data frames and matrices
    from command-line R) check that the X11 libraries are installed
    and if not advises installing XQuartz.
  * icuSetCollate() allows locale = "default", and locale = "none" to
    use OS services rather than ICU for collation.
    Environment variable R_ICU_LOCALE can be used to set the default
    ICU locale, in case the one derived from the OS locale is
    inappropriate (this is currently necessary on Windows).
  * New function icuGetCollate() to report on the ICU collation
    locale in use (if any).
  * utils::URLencode() was updated to use unreserved and reserved
    characters from RFC 3986, &lt;URL:
    http://tools.ietf.org/html/rfc3986&gt;, instead of RFC 1738.
  * unique(warnings()) and c(warnings()) are now supported.
  * The Bioconductor 'version' used by setRepositories() now defaults
    to 3.0. (It can be set at runtime _via_ environment variable
    R_BIOC_VERSION.)
  INSTALLATION and INCLUDED SOFTWARE:
  * The configure script reports on the more important
    capabilities/options which will not be compiled in.
    More types of external BLAS are recognized by name in that
    report.
  * When building R as a shared library, the -L${R_HOME}/lib${R_ARCH}
    flag is placed earlier in the link commands used during
    installation and when packages are installed: this helps ensure
    that the current build has priority if an R shared library has
    already been installed by e.g. install-libR in a library
    mentioned in LDFLAGS (and not in 'your system's library
    directory' as documented). (Wish of PR#15790.)
  * LaTeX package upquote is no longer required for R's use of
    inconsolata.
  * (Windows only) If both 32 and 64 bit versions of R are installed,
    the bin/R.exe and bin/Rscript.exe executables now run 64 bit R.
    (To run 32 bit R, overwrite these files with copies of
    bin/i386/Rfe.exe.)
  UTILITIES:
  * Running R CMD check with _R_CHECK_DEPENDS_ONLY_ true now makes
    the VignetteBuilder packages available even if they are listed in
    Suggests, since they are needed to recognise and process
    non-Sweave vignettes.
  * R CMD check now reports empty importFrom declarations in a
    NAMESPACE file, as these are common errors (writing
    importFrom(Pkg) where import(Pkg) was intended).
  * R CMD check now by default checks code usage directly on the
    package namespace without loading and attaching the package and
    its suggests and enhances.  For good practice with packages in
    the Suggests field, see SS1.1.3.1 of 'Writing R Extensions'.  For
    use of lazy-data objects in the package's own code, see ?data.
  BUG FIXES:
  * dmultinom() did not handle non-finite probabilities correctly.
  * prettyNum(x, zero.print=*) now also works when x contains NAs.
  * A longstanding bug exhibited by nlminb() on Windows was traced to
    a compiler bug in gcc 4.6.3; a workaround has been put in place.
    (PR#15244 and PR#15914).
  * Rendering of \command in HTML versions of help pages has been
    improved: this is particularly evident on the help page for
    INSTALL.
  * as.hexmode(x) and as.octmode(x) now behave correctly for some
    numeric x, e.g., c(NA, 1) or c(1, pi).
  * drop1() failed if the scope argument had no variables to drop.
    (PR#15935)
  * edit() (and hence fix()) failed if an object had a non-character
    attribute named "source" (an attribute that had been used in R
    prior to version 2.14.0).
  * callGeneric() could fail if the generic had ... as a formal
    argument. (PR#15937).
  * Forking in package parallel called C entry point exit in the
    child.  This was unsafe (_exit should have been called), and
    could flush stdin of the main R process (seen most often on
    Solaris).
    As good practice, stdout is now flushed before forking a child.
  * R objects such as list(`a\b` = 1) now print correctly.
  * getAnywhere("C_pbinom") now returns correctly a single object
    (rather than unlisting it).
  * The confint() method for nls() fits failed it these has specified
    parameter limits despite using an algorithm other than "port".
    (PR#15960)
  * Subclassing an S4 class failed if the class required arguments to
    the generator, through its initialize() method.
  * removeSource() did not properly handle expressions containing
    arguments that were supplied as missing, e.g.  x[i,]. (PR#15957)
  * as.environment(list()) now works, and as.list() of such an
    environment is now the same as list().
  * Several tcltk functions failed when run in unusual environments.
    (PR#15970)
  * options(list()) now works (trivially). (PR#15979)
  * merge(&lt;dendrogram&gt;, ..) now works correctly for two `independent'
    dendrograms (PR#15648), and still compatibly via adjust = "auto"
    e.g. for two branches of an existing dendrogram.
  * The plot method for "hclust" objects gets an optional argument
    check; When that is true (the default) it checks more carefully
    for valid input.
  * (Windows only) If a user chose to install 64 bit R but not 32 bit
    R, the bin/R and bin/Rscript executables failed to run.
    (PR#15981)
  * Various possible buffer overruns have been prevented, and missed
    memory protection added. (PR#15990)
  * Rscript no longer passes --args to R when there are no extra
    ("user") arguments.
  * objects like getClass("refClass")@prototype now print() and str()
    without error.
  * identical() now also looks at the S4 bit.
  * hist(x, breaks) is more robust in adding a small fuzz to few
    breaks when some are very large. (PR#15988)
  * sub() and gsub() did not handle regular expressions like "\s{2,}"
    properly if the text contained NA or non-ascii elements in a
    UTF-8 locale.  Part of this was due to a bug in the TRE library.
    (PR#16009)
  * RShowDoc("NEWS") now displays the PDF version.
  * Matrices and arrays with last dimension zero did not print at all
    or incompletely.  (PR#16012)
  * plot.histogram() and hence hist() now respect the xaxs, yaxs and
    lab graphics parameters.  (PR#16021)
  * bw.SJ(x) and other bw.*() no longer segfault when x contains
    non-finite values. (PR#16024)
  * R CMD Rd2pdf unintentionally ignored its --os option.
  * The internal method of download.file() was not reporting file
    sizes and progress correctly on files larger than 2GB (inherited
    from libxml2).  This is corrected for 64-bit builds (32-bit
    platforms may not support such files, but where possible will be
    supported in future versions of R).
  * Work around a bug in OS X Yosemite where key environment
    variables may be duplicated causing issues in subprocesses. The
    duplicates are now removed on R startup (via Rprofile).
    (PR#16042)
  * Adjust X11 auto-launch detection in DISPLAY on OS X to recognize
    latest XQuartz.</changelog>
  <changelog author="sbahling@suse.com" date="1418385600">- Remove tex(inconsolata.sty) BuildRequires for SLE_12 builds (like
  older SLE releases).</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1425902400">- Upstream release 3.1.3
- Most important
  CHANGES IN R 3.1.3:
  NEW FEATURES:
  * The internal method of download.file() can now handle files
    larger than 2GB on 32-bit builds which support such files (tested
    on 32-bit R running on 64-bit Windows).
  * kruskal.test() warns on more types of suspicious input.
  * The as.dendrogram() method for "hclust" objects gains a check
    argument protecting against memory explosion for invalid inputs.
  * capabilities() has a new item long.double which indicates if the
    build uses a long double type which is longer than double.
  * nlm() no longer modifies the callback argument in place (a new
    vector is allocated for each invocation, which mimics the
    implicit duplication that occurred in R &lt; 3.1.0); note that this
    is a change from the previously documented behavior. (PR#15958)
  * icuSetCollate() now accepts locale = "ASCII" which uses the basic
    C function strcmp and so collates strings byte-by-byte in
    numerical order.
  * sessionInfo() tries to report the OS version in use (not just
    that compiled under, and including details of Linux
    distributions).
  * model.frame() (used by lm() and many other modelling functions)
    now warns when it drops contrasts from factors.  (Wish of
    PR#16119)
  * install.packages() and friends now accept the value type =
    "binary" as a synonym for the native binary type on the platform
    (if it has one).
  * Single source or binary files can be supplied for
    install.packages(type = "both") and the appropriate type and
    repos = NULL will be inferred.
  * New function pcre_config() to report on some of the configuration
    options of the version of PCRE in use.  In particular, this
    reports if regular expressions using \p{xx} are supported.
  * (Windows.) download.file(cacheOK = FALSE) is now supported when
    internet2.dll is used.
  * browseURL() has been updated to work with Firefox 36.0 which has
    dropped support for the -remote interface.
  INSTALLATION and INCLUDED SOFTWARE:
  * The included version of PCRE has been updated to 8.36.
  * configure accepts MAKEINFO=texi2any as another way to ensure
    texinfo 5.x is used when both 5.x and 4.x are installed.
  UTILITIES:
  * R CMD check now checks the packages used in \donttest sections of
    the examples are specified in the DESCRIPTION file.  (These are
    needed to run the examples interactively.)
  * R CMD check checks for the undeclared use of GNU extensions in
    Makefiles, and for Makefiles with a missing final linefeed.
    R CMD build will correct line endings in all Makefiles, not just
    those in the src directory.
  * R CMD check notes uses of library() and require() in package
    code: see the section 'Suggested packages' of 'Writing R
    Extensions' for good practice.
  DEPRECATED AND DEFUNCT:
  * The configure option --with-valgrind-instrumentation=3 is
    deprecated and will be removed in R 3.2.0.
  BUG FIXES:
  * (Windows.) Rscript.exe was missing a manifest specifying the
    modern style for common controls (e.g., the download progress
    bar).
  * If a package had extra documentation files but no vignette, the
    HTML help system produced an empty index page.
  * The parser now gives an error if a null character is included in
    a string using Unicode escapes. (PR#16046)
  * qr.Q() failed on complex arguments due to pre-3.0(!) typo.
    (PR#16054)
  * abs() failed with named arguments when the argument was complex.
    (PR#16047)
  * "noquote" objects may now be used as columns in dataframes.
    (PR#15997)
  * Some values with extremely long names were printed incorrectly.
    (PR#15999)
  * Extremely large exponents on zero expressed in scientific
    notation (e.g. 0.0e50000) could give NaN.  (PR#15976)
  * download.file() reported downloaded sizes as 0KB if less than
    1MB, only for R 3.1.2 and only on big-endian platforms.
  * prompt() did not escape percent signs in the automatically
    generated usage section of help files.
  * drop.terms() dropped some of the attributes of the object it was
    working with.  (PR#16029)
  * (Windows.) The command completion in Rgui.exe messed up the
    console.  (PR#15791)
  * (Windows.) The choose.files() command returned a blank string
    when the user asked for a single file but cancelled the request.
    (PR#16074)
  * Math2 S4 group generics failed to correctly dispatch "structure"-
    and "nonStructure"-derived classes.
  * loadNamespace() imposed undocumented restrictions on the
    versionCheck parameter.  (Reported by Geoff Lee.)
  * Rare over-runs detected by AddressSanitizer in substr() and its
    replacement version have been avoided.
    _Inter alia_ that fix gives the documented behaviour for
    substr(x, 1, 2) &lt;- "" (subsequently reported as PR#16214).
  * Loading packages incorrectly defining an S4 generic followed by a
    function of the same name caused an erroneous cyclic namespace
    dependency error.
  * Declared vignette encodings are now always passed to the vignette
    engine.
  * Port Tomas Kalibera's fix from R-devel that restores the
    loadMethod() fast path, effectively doubling the speed of S4
    dispatch.
  * power.t.test() and power.prop.test() now make use of the
    extendInt option of uniroot() and hence work in more extreme
    cases.  (PR#15792)
  * If a package was updated and attached when its namespace was
    already loaded, it could end up with parts from one version and
    parts from the other.  (PR#16120)
  * tools:::.Rdconv() didn't accept --encoding= due to a typo.
    (PR#16121)
  * Unix-alike builds without a suitable makeinfo were documented to
    link the missing HTML manuals to CRAN, but did not.
  * save(*, ascii=TRUE) and load() now correctly deal with NaN's.
    (PR#16137)
  * split.Date() retains fractional representations while avoiding
    incomplete class propagation.
  * R_ext/Lapack.h had not been updated for changes made by LAPACK to
    the argument lists of its (largely internal) functions dlaed2 and
    dlaed3.  (PR#16157)
  * RShowDoc("NEWS", "txt") had not been updated for the layout
    changes of R 3.1.0.
  * The xtfrm() method for class "Surv" has been corrected and its
    description expanded.
  * mode(x) &lt;- y would incorrectly evaluate x before changing its
    mode. (PR#16215)
  * besselJ(1, 2^64) and besselY(..) now signal a warning, returning
    NaN instead of typically segfaulting. (Issue 3 of PR#15554)
  * HTML conversion of \href markup in .Rd files did not remove the
    backslash from \% and so gave an invalid URL.  In a related
    change, the \ escape is now required in such URLs.</changelog>
</package>
<package pkgid="042c64dee675fa1dc928cdfe8587f4892d1f76ff4b4a724d2604979bc4c37c48" name="R-gnu15-ohpc" arch="src">
  <version epoch="0" ver="4.6.0" rel="350.ohpc.2.6"/>
  <changelog author="detlef.steuer@gmx.de" date="1394107200">- Upstream release 3.0.3
- Most important
  CHANGES IN R 3.0.3:
  NEW FEATURES:
  * On Windows there is support for making .texi manuals using
    texinfo 5.0 or later: the setting is in file
    src/gnuwin32/MkRules.dist.
    A packaging of the Perl script and modules for texinfo 5.2 has
    been made available at &lt;URL:
    http://www.stats.ox.ac.uk/pub/Rtools/&gt;.
  * write.table() now handles matrices of 2^31 or more elements, for
    those with large amounts of patience and disc space.
  * There is a new function, La_version(), to report the version of
    LAPACK in use.
  * The HTML version of 'An Introduction to R' now has links to PNG
    versions of the figures.
  * There is some support to produce manuals in ebook formats. (See
    doc/manual/Makefile.  Suggested by Mauro Cavalcanti.)
  * On a Unix-alike Sys.timezone() returns NA if the environment
    variable TZ is unset, to distinguish it from an empty string
    which on some OSes means the UTC time zone.
  * The backtick may now be escaped in strings, to allow names
    containing them to be constructed, e.g. `\``.  (PR#15621)
  * read.table(), readLines() and 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.)
  * (Windows only.)  file.symlink() works around the undocumented
    restriction of the Windows system call to backslashes.  (Wish of
    PR#15631.)
  * KalmanForecast(fast = FALSE) is now the default, and the help
    contains an example of how fast = TRUE can be used in this
    version.  (The usage will change in 3.1.0.)
  * 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).
  * strptime() and the format() methods for classes "POSIXct",
    "POSIXlt" and "Date" recognize strings with marked encodings:
    this allows, for example, UTF-8 French month names to be read on
    (French) Windows.
  * iconv(to = "utf8") is now accepted on all platforms (some
    implementations did already, but GNU libiconv did not: however
    converted strings were not marked as being in UTF-8).  The
    official name, "UTF-8" is still preferred.
  * available.packages() is better protected against corrupt metadata
    files.  (A recurring problem with Debian package shogun-r:
    PR#14713.)
  * 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 options() and (C-level) path.expand()
    re-entrantly).</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1397131200">- Upstream release 3.1.0
- Most impotant
  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| &gt; 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 &lt;- a0 and ans[[i]] &lt;- 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,] &lt;- 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.)</changelog>
  <changelog author="darin@darins.net" date="1398772800">- Created symlink to %{_bindir}/r
  Many CRAN packages ship with scripts which call %{_bindir}/r,
  which creates a dependency on it, this fixes that.</changelog>
  <changelog author="darin@darins.net" date="1398945600">-  Add make dependency for Rcmd</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1399636800">- Removed / commented out symlink to %{_bindir}/r
  new package 'littler' should be used instead for packages
  that need /usr/bin/r</changelog>
  <changelog author="darin@darins.net" date="1403265600">- added parallel provides</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1404993600">- Added Provides: R-parallel
- Upstream release 3.1.1
- Most impotant
  CHANGES IN R 3.1.1:
  CHANGES IN R 3.1.1:
  NEW FEATURES:
  * When attach() reports conflicts, it does so compatibly with
    library() by using message().
  * R CMD Sweave no longer cleans any files by default, compatibly
    with versions of R prior to 3.1.0.  There are new options
  - -clean, --clean=default and --clean=keepOuts.
  * tools::buildVignette() and tools::buildVignettes() with clean =
    FALSE no longer remove any created files.  buildvignette() gains
    a keep argument for more cleaning customization.
  * The Bioconductor 'version' used by setRepositories() can now be
    set by environment variable 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.)
  * Error messages from bugs in embedded Sexpr code in Sweave
    documents now report the source location.
  * type.convert(), read.table() and similar read.*() functions get a
    new numerals argument, specifying how numeric input is converted
    when its conversion to double precision loses accuracy.  The
    default value, "allow.loss" allows accuracy loss, as in R
    versions before 3.1.0.
  * For some compilers, integer addition could overflow without a
    warning.  R's internal code for both integer addition and
    subtraction is more robust now.  (PR#15774)
  * The function determining the default number of knots for
    smooth.spline() is now exported, as .nknots.smspl().
  * dbeta(, a,b), pbeta(), qbeta() and rbeta() are now defined also
    for a = 0, b = 0, or infinite a and b (where they typically
    returned NaN before).
  * Many package authors report that the RStudio graphics device does
    not work correctly with their package's use of dev.new().  The
    new option dev.new(noRStudioGD = TRUE) replaces the RStudio
    override by the default device as selected by R itself, still
    respecting environment variables R_INTERACTIVE_DEVICE and
    R_DEFAULT_DEVICE.
  * readRDS() now returns visibly.
  * Modifying internal logical scalar constants now results in an
    error instead of a warning.
  * install.packages(repos = NULL) now accepts http:// or ftp:// URLs
    of package archives as well as file paths, and will download as
    required.  In most cases repos = NULL can be deduced from the
    extension of the URL.
  * The warning when using partial matching with the $ operator on
    data frames is now only given when
    options("warnPartialMatchDollar") is TRUE.
  * Package help requests like package?foo now try the package foo
    whether loaded or not.
  * General help requests now default to trying all loaded packages,
    not just those on the search path.
  * Added a new function promptImport(), to generate a help page for
    a function that was imported from another package (and presumably
    re-exported, or help would not be needed).
  INSTALLATION and INCLUDED SOFTWARE:
  * configure option --with-internal-tzcode can now be used with
    variable rsharedir.
  * The included version of PCRE has been updated to 8.35.
  * There is a new target make uninstall-libR to remove an installed
    shared/static libR.
    make install-libR now works if a sub-architecture is used,
    although the user will need to specify libdir differently for
    different sub-architectures.
  * There is more extensive advice on which LaTeX packages are
    required to install R or to make package manuals (as done by R
    CMD check) in the 'Writing R Extensions' manual.
  * Compilers/linkers were handling the visibility controls in
    src/extra/xz inconsistently (and apparently in some cases
    incorrectly), so it has been simplified.  (PR#15327)
  * (Windows) There is updated support for the use of ICU for
    collation: see the 'R Installation and Administration Manual'.
  BUG FIXES:
  * dbinom(x, n), pbinom(), dpois(), etc, are slightly less
    restrictive in checking if n is integer-valued.  (Wish of
    PR#15734.)
  * pchisq(x, df, ncp, log.p = TRUE) is more accurate and no longer
    underflows for small x and ncp &lt; 80, e.g, for pchisq(1e-5, df =
    100, ncp = 1, log = TRUE).  (Based on PR#15635 and a suggestion
    by Roby Joehanes.)
  * The s ("step into") command in the debugger would cause R to step
    into expressions evaluated there, not just into functions being
    debugged.  (PR#15770)
  * The C code used by strptime() rejected time-zone offsets of more
    than +1200 (+1245, +1300 and +1400 can occur).  (PR#15768)
  * (Windows only.)  png(type = "cairo", antialias = "gray") was not
    accepted.  (PR#15760)
  * Use of save(..., envir=) with named objects could fail.
    (PR#15758)
  * Sweave() mis-parsed Sexpr expressions that contained backslashes.
    (PR#15779)
  * The return value from options(foo = NULL) was not the previous
    value of the option.  (PR#15781)
  * enc2utf8() and enc2native() did not always mark the encoding of
    the return values when it was known.
  * dnbinom(x, size = &lt;large&gt;, mu, log = TRUE) no longer underflows
    to -Inf for large mu, thanks to a suggestion from Alessandro
    Mammana (MPI MolGen, Berlin).
  * pbeta(x, a, b, log = TRUE) no longer behaves discontinuously (in
    a small x-region) because of denormalized numbers.  Also,
    pbeta(1-1e-12, 1e30, 1.001, log=TRUE) now terminates "in real
    time".
  * The "CRAN" filter (see available.packages()) no longer removes
    duplicates other than of packages on CRAN, and does not fail if
    there is no CRAN repository in getOption("repos").
  * The device listing from dev2bitmap() and bitmap() was truncated
    to 1000 characters: modern versions of GhostScript on most
    platforms have many more devices.
  * (Windows.)  Commands such as Sys.which() and pipe() which needed
    to find the full path to a command could segfault if the 'long'
    path name was much longer than the 'short' path name (which
    Sys.which() returns), as the behaviour of the Windows API call
    had changed.
  * R CMD build will fail with an error if one of the packages
    specified in the VignetteBuilder field is not installed.
    (Without loading those packages it cannot be ascertained which
    files are intended to be vignettes. This means that the
    VignetteBuilder packages have to be installed for package
    checking too.)  (Wish of PR#15775.)
  * Misguided attempts to use chull() with non-finite points now give
    an error (related to PR#15777).
  * For a formula with exactly 32 variables the 32nd variable was
    aliased to the intercept in some C-level computations of terms,
    so that for example attempting to remove it would remove the
    intercept instead (and leave a corrupt internal structure).
    (PR#15735)
  * anyDuplicated() silently returned wrong values when the first
    duplicate was at an index which was too large to be stored in an
    integer vector (although a lot of RAM and patience would have
    been needed to encounter this).
  * tools::Rd2ex(commentDontrun = FALSE) failed if the block had only
    one line.
  * Hexadecimal constants such as 0x110p-5L which were incorrectly
    qualified by L were parsed incorrectly since R 3.0.0, with a
    slightly garbled warning. (PR#15753)
  * system() returned success on some platforms even if the system
    was unable to launch a process. (PR#15796)
  * (Windows Rgui console.)  Unbuffered output was sometimes not
    output immediately if the prompt was not on the last line of the
    console.
  * The built-in help server did not declare the encoding for the
    DESCRIPTION or other text files to be the package encoding, so
    non-ASCII characters could be displayed incorrectly.
  * R is now trying harder to not cleanup child processes that were
    not spawned by mcparallel() on platforms that provide information
    about the source process of the SIGCHLD signal. This allows 3rd
    party libraries to manage the exit status of children that they
    spawn without R interfering.
  * mcmapply() was only parallelizing if the number of jobs was
    bigger than the number of cores. It now parallelizes if the
    number of jobs is more than one.
  * Auto-printing would re-evaluate its argument when trying to
    dispatch to a print method.  This is now avoided when possible.
  * Unserializing (including load() and readRDS()) could silently
    return incorrect numeric values from ASCII saves if there was a
    read error.
  * getParseData() could return incorrect values for the parents of
    some elements. (Reported by Andrew Redd.)
  * Attempting to use data frames of 2^31 or more rows with merge()
    or to create a merged data frame of that size now gives a clearer
    error message.
  * parse() did not check its file argument was a connection if it
    was not a character string, so e.g. parse(FALSE) attempted to
    read from stdin.
    Nor did dump() and dput().
  * The "help.try.all.packages" option was ignored when the shortcut
    syntax for help was used, e.g. ?foo.
  * A potential segfault in string allocation has been fixed.  (Found
    by Radford Neal.)
  * Potential memory protection errors in sort() and D() have been
    fixed. (Found by Radford Neal.)
  * Fixed a lack of error checking in graphics event functions.
    (Found by Radford Neal; a different patch used here than the one
    in pqR.)
  * numericDeriv() sometimes miscalculated the gradient.  (PR#15849,
    reported originally by Radford Neal)</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1414756800">- Upstream release 3.1.2
- Most important
  CHANGES IN R 3.1.2:
  NEW FEATURES:
  * embedFonts() now defaults to format = "ps2write" for .ps and .eps
    files.  This is available in Ghostscript 9.x (since 2010) whereas
    the previous default, format = "pswrite", was removed in
    Ghostscript 9.10.
  * For consistency with [dpqr]norm(), [dp]lnorm(sdlog = 0) model a
    point mass at exp(mulog) rather than return NaN (for an error).
  * capabilities() now reports if ICU is compiled in for use for
    collation (it is only actually used if a suitable locale is set
    for collation, and never for a C locale).
  * (OS X only.) Package tcltk checks when loaded if it is linked
    against the CRAN X11-based Tcl/Tk and if so that the Tcl/Tk
    component and the X11 libraries are installed.  This allows more
    informative error messages to be given advising the installation
    of the missing component or of XQuartz.
    The X11() device and X11-based versions of the data editor and
    viewer (invoked by edit() and View() for data frames and matrices
    from command-line R) check that the X11 libraries are installed
    and if not advises installing XQuartz.
  * icuSetCollate() allows locale = "default", and locale = "none" to
    use OS services rather than ICU for collation.
    Environment variable R_ICU_LOCALE can be used to set the default
    ICU locale, in case the one derived from the OS locale is
    inappropriate (this is currently necessary on Windows).
  * New function icuGetCollate() to report on the ICU collation
    locale in use (if any).
  * utils::URLencode() was updated to use unreserved and reserved
    characters from RFC 3986, &lt;URL:
    http://tools.ietf.org/html/rfc3986&gt;, instead of RFC 1738.
  * unique(warnings()) and c(warnings()) are now supported.
  * The Bioconductor 'version' used by setRepositories() now defaults
    to 3.0. (It can be set at runtime _via_ environment variable
    R_BIOC_VERSION.)
  INSTALLATION and INCLUDED SOFTWARE:
  * The configure script reports on the more important
    capabilities/options which will not be compiled in.
    More types of external BLAS are recognized by name in that
    report.
  * When building R as a shared library, the -L${R_HOME}/lib${R_ARCH}
    flag is placed earlier in the link commands used during
    installation and when packages are installed: this helps ensure
    that the current build has priority if an R shared library has
    already been installed by e.g. install-libR in a library
    mentioned in LDFLAGS (and not in 'your system's library
    directory' as documented). (Wish of PR#15790.)
  * LaTeX package upquote is no longer required for R's use of
    inconsolata.
  * (Windows only) If both 32 and 64 bit versions of R are installed,
    the bin/R.exe and bin/Rscript.exe executables now run 64 bit R.
    (To run 32 bit R, overwrite these files with copies of
    bin/i386/Rfe.exe.)
  UTILITIES:
  * Running R CMD check with _R_CHECK_DEPENDS_ONLY_ true now makes
    the VignetteBuilder packages available even if they are listed in
    Suggests, since they are needed to recognise and process
    non-Sweave vignettes.
  * R CMD check now reports empty importFrom declarations in a
    NAMESPACE file, as these are common errors (writing
    importFrom(Pkg) where import(Pkg) was intended).
  * R CMD check now by default checks code usage directly on the
    package namespace without loading and attaching the package and
    its suggests and enhances.  For good practice with packages in
    the Suggests field, see SS1.1.3.1 of 'Writing R Extensions'.  For
    use of lazy-data objects in the package's own code, see ?data.
  BUG FIXES:
  * dmultinom() did not handle non-finite probabilities correctly.
  * prettyNum(x, zero.print=*) now also works when x contains NAs.
  * A longstanding bug exhibited by nlminb() on Windows was traced to
    a compiler bug in gcc 4.6.3; a workaround has been put in place.
    (PR#15244 and PR#15914).
  * Rendering of \command in HTML versions of help pages has been
    improved: this is particularly evident on the help page for
    INSTALL.
  * as.hexmode(x) and as.octmode(x) now behave correctly for some
    numeric x, e.g., c(NA, 1) or c(1, pi).
  * drop1() failed if the scope argument had no variables to drop.
    (PR#15935)
  * edit() (and hence fix()) failed if an object had a non-character
    attribute named "source" (an attribute that had been used in R
    prior to version 2.14.0).
  * callGeneric() could fail if the generic had ... as a formal
    argument. (PR#15937).
  * Forking in package parallel called C entry point exit in the
    child.  This was unsafe (_exit should have been called), and
    could flush stdin of the main R process (seen most often on
    Solaris).
    As good practice, stdout is now flushed before forking a child.
  * R objects such as list(`a\b` = 1) now print correctly.
  * getAnywhere("C_pbinom") now returns correctly a single object
    (rather than unlisting it).
  * The confint() method for nls() fits failed it these has specified
    parameter limits despite using an algorithm other than "port".
    (PR#15960)
  * Subclassing an S4 class failed if the class required arguments to
    the generator, through its initialize() method.
  * removeSource() did not properly handle expressions containing
    arguments that were supplied as missing, e.g.  x[i,]. (PR#15957)
  * as.environment(list()) now works, and as.list() of such an
    environment is now the same as list().
  * Several tcltk functions failed when run in unusual environments.
    (PR#15970)
  * options(list()) now works (trivially). (PR#15979)
  * merge(&lt;dendrogram&gt;, ..) now works correctly for two `independent'
    dendrograms (PR#15648), and still compatibly via adjust = "auto"
    e.g. for two branches of an existing dendrogram.
  * The plot method for "hclust" objects gets an optional argument
    check; When that is true (the default) it checks more carefully
    for valid input.
  * (Windows only) If a user chose to install 64 bit R but not 32 bit
    R, the bin/R and bin/Rscript executables failed to run.
    (PR#15981)
  * Various possible buffer overruns have been prevented, and missed
    memory protection added. (PR#15990)
  * Rscript no longer passes --args to R when there are no extra
    ("user") arguments.
  * objects like getClass("refClass")@prototype now print() and str()
    without error.
  * identical() now also looks at the S4 bit.
  * hist(x, breaks) is more robust in adding a small fuzz to few
    breaks when some are very large. (PR#15988)
  * sub() and gsub() did not handle regular expressions like "\s{2,}"
    properly if the text contained NA or non-ascii elements in a
    UTF-8 locale.  Part of this was due to a bug in the TRE library.
    (PR#16009)
  * RShowDoc("NEWS") now displays the PDF version.
  * Matrices and arrays with last dimension zero did not print at all
    or incompletely.  (PR#16012)
  * plot.histogram() and hence hist() now respect the xaxs, yaxs and
    lab graphics parameters.  (PR#16021)
  * bw.SJ(x) and other bw.*() no longer segfault when x contains
    non-finite values. (PR#16024)
  * R CMD Rd2pdf unintentionally ignored its --os option.
  * The internal method of download.file() was not reporting file
    sizes and progress correctly on files larger than 2GB (inherited
    from libxml2).  This is corrected for 64-bit builds (32-bit
    platforms may not support such files, but where possible will be
    supported in future versions of R).
  * Work around a bug in OS X Yosemite where key environment
    variables may be duplicated causing issues in subprocesses. The
    duplicates are now removed on R startup (via Rprofile).
    (PR#16042)
  * Adjust X11 auto-launch detection in DISPLAY on OS X to recognize
    latest XQuartz.</changelog>
  <changelog author="sbahling@suse.com" date="1418385600">- Remove tex(inconsolata.sty) BuildRequires for SLE_12 builds (like
  older SLE releases).</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1425902400">- Upstream release 3.1.3
- Most important
  CHANGES IN R 3.1.3:
  NEW FEATURES:
  * The internal method of download.file() can now handle files
    larger than 2GB on 32-bit builds which support such files (tested
    on 32-bit R running on 64-bit Windows).
  * kruskal.test() warns on more types of suspicious input.
  * The as.dendrogram() method for "hclust" objects gains a check
    argument protecting against memory explosion for invalid inputs.
  * capabilities() has a new item long.double which indicates if the
    build uses a long double type which is longer than double.
  * nlm() no longer modifies the callback argument in place (a new
    vector is allocated for each invocation, which mimics the
    implicit duplication that occurred in R &lt; 3.1.0); note that this
    is a change from the previously documented behavior. (PR#15958)
  * icuSetCollate() now accepts locale = "ASCII" which uses the basic
    C function strcmp and so collates strings byte-by-byte in
    numerical order.
  * sessionInfo() tries to report the OS version in use (not just
    that compiled under, and including details of Linux
    distributions).
  * model.frame() (used by lm() and many other modelling functions)
    now warns when it drops contrasts from factors.  (Wish of
    PR#16119)
  * install.packages() and friends now accept the value type =
    "binary" as a synonym for the native binary type on the platform
    (if it has one).
  * Single source or binary files can be supplied for
    install.packages(type = "both") and the appropriate type and
    repos = NULL will be inferred.
  * New function pcre_config() to report on some of the configuration
    options of the version of PCRE in use.  In particular, this
    reports if regular expressions using \p{xx} are supported.
  * (Windows.) download.file(cacheOK = FALSE) is now supported when
    internet2.dll is used.
  * browseURL() has been updated to work with Firefox 36.0 which has
    dropped support for the -remote interface.
  INSTALLATION and INCLUDED SOFTWARE:
  * The included version of PCRE has been updated to 8.36.
  * configure accepts MAKEINFO=texi2any as another way to ensure
    texinfo 5.x is used when both 5.x and 4.x are installed.
  UTILITIES:
  * R CMD check now checks the packages used in \donttest sections of
    the examples are specified in the DESCRIPTION file.  (These are
    needed to run the examples interactively.)
  * R CMD check checks for the undeclared use of GNU extensions in
    Makefiles, and for Makefiles with a missing final linefeed.
    R CMD build will correct line endings in all Makefiles, not just
    those in the src directory.
  * R CMD check notes uses of library() and require() in package
    code: see the section 'Suggested packages' of 'Writing R
    Extensions' for good practice.
  DEPRECATED AND DEFUNCT:
  * The configure option --with-valgrind-instrumentation=3 is
    deprecated and will be removed in R 3.2.0.
  BUG FIXES:
  * (Windows.) Rscript.exe was missing a manifest specifying the
    modern style for common controls (e.g., the download progress
    bar).
  * If a package had extra documentation files but no vignette, the
    HTML help system produced an empty index page.
  * The parser now gives an error if a null character is included in
    a string using Unicode escapes. (PR#16046)
  * qr.Q() failed on complex arguments due to pre-3.0(!) typo.
    (PR#16054)
  * abs() failed with named arguments when the argument was complex.
    (PR#16047)
  * "noquote" objects may now be used as columns in dataframes.
    (PR#15997)
  * Some values with extremely long names were printed incorrectly.
    (PR#15999)
  * Extremely large exponents on zero expressed in scientific
    notation (e.g. 0.0e50000) could give NaN.  (PR#15976)
  * download.file() reported downloaded sizes as 0KB if less than
    1MB, only for R 3.1.2 and only on big-endian platforms.
  * prompt() did not escape percent signs in the automatically
    generated usage section of help files.
  * drop.terms() dropped some of the attributes of the object it was
    working with.  (PR#16029)
  * (Windows.) The command completion in Rgui.exe messed up the
    console.  (PR#15791)
  * (Windows.) The choose.files() command returned a blank string
    when the user asked for a single file but cancelled the request.
    (PR#16074)
  * Math2 S4 group generics failed to correctly dispatch "structure"-
    and "nonStructure"-derived classes.
  * loadNamespace() imposed undocumented restrictions on the
    versionCheck parameter.  (Reported by Geoff Lee.)
  * Rare over-runs detected by AddressSanitizer in substr() and its
    replacement version have been avoided.
    _Inter alia_ that fix gives the documented behaviour for
    substr(x, 1, 2) &lt;- "" (subsequently reported as PR#16214).
  * Loading packages incorrectly defining an S4 generic followed by a
    function of the same name caused an erroneous cyclic namespace
    dependency error.
  * Declared vignette encodings are now always passed to the vignette
    engine.
  * Port Tomas Kalibera's fix from R-devel that restores the
    loadMethod() fast path, effectively doubling the speed of S4
    dispatch.
  * power.t.test() and power.prop.test() now make use of the
    extendInt option of uniroot() and hence work in more extreme
    cases.  (PR#15792)
  * If a package was updated and attached when its namespace was
    already loaded, it could end up with parts from one version and
    parts from the other.  (PR#16120)
  * tools:::.Rdconv() didn't accept --encoding= due to a typo.
    (PR#16121)
  * Unix-alike builds without a suitable makeinfo were documented to
    link the missing HTML manuals to CRAN, but did not.
  * save(*, ascii=TRUE) and load() now correctly deal with NaN's.
    (PR#16137)
  * split.Date() retains fractional representations while avoiding
    incomplete class propagation.
  * R_ext/Lapack.h had not been updated for changes made by LAPACK to
    the argument lists of its (largely internal) functions dlaed2 and
    dlaed3.  (PR#16157)
  * RShowDoc("NEWS", "txt") had not been updated for the layout
    changes of R 3.1.0.
  * The xtfrm() method for class "Surv" has been corrected and its
    description expanded.
  * mode(x) &lt;- y would incorrectly evaluate x before changing its
    mode. (PR#16215)
  * besselJ(1, 2^64) and besselY(..) now signal a warning, returning
    NaN instead of typically segfaulting. (Issue 3 of PR#15554)
  * HTML conversion of \href markup in .Rd files did not remove the
    backslash from \% and so gave an invalid URL.  In a related
    change, the \ escape is now required in such URLs.</changelog>
</package>
<package pkgid="265b932521747b2e2ab6004c02f055951307a7831ce305a003357483c9c37e70" name="R-gnu15-ohpc" arch="x86_64">
  <version epoch="0" ver="4.6.0" rel="350.ohpc.2.6"/>
  <changelog author="detlef.steuer@gmx.de" date="1394107200">- Upstream release 3.0.3
- Most important
  CHANGES IN R 3.0.3:
  NEW FEATURES:
  * On Windows there is support for making .texi manuals using
    texinfo 5.0 or later: the setting is in file
    src/gnuwin32/MkRules.dist.
    A packaging of the Perl script and modules for texinfo 5.2 has
    been made available at &lt;URL:
    http://www.stats.ox.ac.uk/pub/Rtools/&gt;.
  * write.table() now handles matrices of 2^31 or more elements, for
    those with large amounts of patience and disc space.
  * There is a new function, La_version(), to report the version of
    LAPACK in use.
  * The HTML version of 'An Introduction to R' now has links to PNG
    versions of the figures.
  * There is some support to produce manuals in ebook formats. (See
    doc/manual/Makefile.  Suggested by Mauro Cavalcanti.)
  * On a Unix-alike Sys.timezone() returns NA if the environment
    variable TZ is unset, to distinguish it from an empty string
    which on some OSes means the UTC time zone.
  * The backtick may now be escaped in strings, to allow names
    containing them to be constructed, e.g. `\``.  (PR#15621)
  * read.table(), readLines() and 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.)
  * (Windows only.)  file.symlink() works around the undocumented
    restriction of the Windows system call to backslashes.  (Wish of
    PR#15631.)
  * KalmanForecast(fast = FALSE) is now the default, and the help
    contains an example of how fast = TRUE can be used in this
    version.  (The usage will change in 3.1.0.)
  * 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).
  * strptime() and the format() methods for classes "POSIXct",
    "POSIXlt" and "Date" recognize strings with marked encodings:
    this allows, for example, UTF-8 French month names to be read on
    (French) Windows.
  * iconv(to = "utf8") is now accepted on all platforms (some
    implementations did already, but GNU libiconv did not: however
    converted strings were not marked as being in UTF-8).  The
    official name, "UTF-8" is still preferred.
  * available.packages() is better protected against corrupt metadata
    files.  (A recurring problem with Debian package shogun-r:
    PR#14713.)
  * 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 options() and (C-level) path.expand()
    re-entrantly).</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1397131200">- Upstream release 3.1.0
- Most impotant
  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| &gt; 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 &lt;- a0 and ans[[i]] &lt;- 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,] &lt;- 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.)</changelog>
  <changelog author="darin@darins.net" date="1398772800">- Created symlink to %{_bindir}/r
  Many CRAN packages ship with scripts which call %{_bindir}/r,
  which creates a dependency on it, this fixes that.</changelog>
  <changelog author="darin@darins.net" date="1398945600">-  Add make dependency for Rcmd</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1399636800">- Removed / commented out symlink to %{_bindir}/r
  new package 'littler' should be used instead for packages
  that need /usr/bin/r</changelog>
  <changelog author="darin@darins.net" date="1403265600">- added parallel provides</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1404993600">- Added Provides: R-parallel
- Upstream release 3.1.1
- Most impotant
  CHANGES IN R 3.1.1:
  CHANGES IN R 3.1.1:
  NEW FEATURES:
  * When attach() reports conflicts, it does so compatibly with
    library() by using message().
  * R CMD Sweave no longer cleans any files by default, compatibly
    with versions of R prior to 3.1.0.  There are new options
  - -clean, --clean=default and --clean=keepOuts.
  * tools::buildVignette() and tools::buildVignettes() with clean =
    FALSE no longer remove any created files.  buildvignette() gains
    a keep argument for more cleaning customization.
  * The Bioconductor 'version' used by setRepositories() can now be
    set by environment variable 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.)
  * Error messages from bugs in embedded Sexpr code in Sweave
    documents now report the source location.
  * type.convert(), read.table() and similar read.*() functions get a
    new numerals argument, specifying how numeric input is converted
    when its conversion to double precision loses accuracy.  The
    default value, "allow.loss" allows accuracy loss, as in R
    versions before 3.1.0.
  * For some compilers, integer addition could overflow without a
    warning.  R's internal code for both integer addition and
    subtraction is more robust now.  (PR#15774)
  * The function determining the default number of knots for
    smooth.spline() is now exported, as .nknots.smspl().
  * dbeta(, a,b), pbeta(), qbeta() and rbeta() are now defined also
    for a = 0, b = 0, or infinite a and b (where they typically
    returned NaN before).
  * Many package authors report that the RStudio graphics device does
    not work correctly with their package's use of dev.new().  The
    new option dev.new(noRStudioGD = TRUE) replaces the RStudio
    override by the default device as selected by R itself, still
    respecting environment variables R_INTERACTIVE_DEVICE and
    R_DEFAULT_DEVICE.
  * readRDS() now returns visibly.
  * Modifying internal logical scalar constants now results in an
    error instead of a warning.
  * install.packages(repos = NULL) now accepts http:// or ftp:// URLs
    of package archives as well as file paths, and will download as
    required.  In most cases repos = NULL can be deduced from the
    extension of the URL.
  * The warning when using partial matching with the $ operator on
    data frames is now only given when
    options("warnPartialMatchDollar") is TRUE.
  * Package help requests like package?foo now try the package foo
    whether loaded or not.
  * General help requests now default to trying all loaded packages,
    not just those on the search path.
  * Added a new function promptImport(), to generate a help page for
    a function that was imported from another package (and presumably
    re-exported, or help would not be needed).
  INSTALLATION and INCLUDED SOFTWARE:
  * configure option --with-internal-tzcode can now be used with
    variable rsharedir.
  * The included version of PCRE has been updated to 8.35.
  * There is a new target make uninstall-libR to remove an installed
    shared/static libR.
    make install-libR now works if a sub-architecture is used,
    although the user will need to specify libdir differently for
    different sub-architectures.
  * There is more extensive advice on which LaTeX packages are
    required to install R or to make package manuals (as done by R
    CMD check) in the 'Writing R Extensions' manual.
  * Compilers/linkers were handling the visibility controls in
    src/extra/xz inconsistently (and apparently in some cases
    incorrectly), so it has been simplified.  (PR#15327)
  * (Windows) There is updated support for the use of ICU for
    collation: see the 'R Installation and Administration Manual'.
  BUG FIXES:
  * dbinom(x, n), pbinom(), dpois(), etc, are slightly less
    restrictive in checking if n is integer-valued.  (Wish of
    PR#15734.)
  * pchisq(x, df, ncp, log.p = TRUE) is more accurate and no longer
    underflows for small x and ncp &lt; 80, e.g, for pchisq(1e-5, df =
    100, ncp = 1, log = TRUE).  (Based on PR#15635 and a suggestion
    by Roby Joehanes.)
  * The s ("step into") command in the debugger would cause R to step
    into expressions evaluated there, not just into functions being
    debugged.  (PR#15770)
  * The C code used by strptime() rejected time-zone offsets of more
    than +1200 (+1245, +1300 and +1400 can occur).  (PR#15768)
  * (Windows only.)  png(type = "cairo", antialias = "gray") was not
    accepted.  (PR#15760)
  * Use of save(..., envir=) with named objects could fail.
    (PR#15758)
  * Sweave() mis-parsed Sexpr expressions that contained backslashes.
    (PR#15779)
  * The return value from options(foo = NULL) was not the previous
    value of the option.  (PR#15781)
  * enc2utf8() and enc2native() did not always mark the encoding of
    the return values when it was known.
  * dnbinom(x, size = &lt;large&gt;, mu, log = TRUE) no longer underflows
    to -Inf for large mu, thanks to a suggestion from Alessandro
    Mammana (MPI MolGen, Berlin).
  * pbeta(x, a, b, log = TRUE) no longer behaves discontinuously (in
    a small x-region) because of denormalized numbers.  Also,
    pbeta(1-1e-12, 1e30, 1.001, log=TRUE) now terminates "in real
    time".
  * The "CRAN" filter (see available.packages()) no longer removes
    duplicates other than of packages on CRAN, and does not fail if
    there is no CRAN repository in getOption("repos").
  * The device listing from dev2bitmap() and bitmap() was truncated
    to 1000 characters: modern versions of GhostScript on most
    platforms have many more devices.
  * (Windows.)  Commands such as Sys.which() and pipe() which needed
    to find the full path to a command could segfault if the 'long'
    path name was much longer than the 'short' path name (which
    Sys.which() returns), as the behaviour of the Windows API call
    had changed.
  * R CMD build will fail with an error if one of the packages
    specified in the VignetteBuilder field is not installed.
    (Without loading those packages it cannot be ascertained which
    files are intended to be vignettes. This means that the
    VignetteBuilder packages have to be installed for package
    checking too.)  (Wish of PR#15775.)
  * Misguided attempts to use chull() with non-finite points now give
    an error (related to PR#15777).
  * For a formula with exactly 32 variables the 32nd variable was
    aliased to the intercept in some C-level computations of terms,
    so that for example attempting to remove it would remove the
    intercept instead (and leave a corrupt internal structure).
    (PR#15735)
  * anyDuplicated() silently returned wrong values when the first
    duplicate was at an index which was too large to be stored in an
    integer vector (although a lot of RAM and patience would have
    been needed to encounter this).
  * tools::Rd2ex(commentDontrun = FALSE) failed if the block had only
    one line.
  * Hexadecimal constants such as 0x110p-5L which were incorrectly
    qualified by L were parsed incorrectly since R 3.0.0, with a
    slightly garbled warning. (PR#15753)
  * system() returned success on some platforms even if the system
    was unable to launch a process. (PR#15796)
  * (Windows Rgui console.)  Unbuffered output was sometimes not
    output immediately if the prompt was not on the last line of the
    console.
  * The built-in help server did not declare the encoding for the
    DESCRIPTION or other text files to be the package encoding, so
    non-ASCII characters could be displayed incorrectly.
  * R is now trying harder to not cleanup child processes that were
    not spawned by mcparallel() on platforms that provide information
    about the source process of the SIGCHLD signal. This allows 3rd
    party libraries to manage the exit status of children that they
    spawn without R interfering.
  * mcmapply() was only parallelizing if the number of jobs was
    bigger than the number of cores. It now parallelizes if the
    number of jobs is more than one.
  * Auto-printing would re-evaluate its argument when trying to
    dispatch to a print method.  This is now avoided when possible.
  * Unserializing (including load() and readRDS()) could silently
    return incorrect numeric values from ASCII saves if there was a
    read error.
  * getParseData() could return incorrect values for the parents of
    some elements. (Reported by Andrew Redd.)
  * Attempting to use data frames of 2^31 or more rows with merge()
    or to create a merged data frame of that size now gives a clearer
    error message.
  * parse() did not check its file argument was a connection if it
    was not a character string, so e.g. parse(FALSE) attempted to
    read from stdin.
    Nor did dump() and dput().
  * The "help.try.all.packages" option was ignored when the shortcut
    syntax for help was used, e.g. ?foo.
  * A potential segfault in string allocation has been fixed.  (Found
    by Radford Neal.)
  * Potential memory protection errors in sort() and D() have been
    fixed. (Found by Radford Neal.)
  * Fixed a lack of error checking in graphics event functions.
    (Found by Radford Neal; a different patch used here than the one
    in pqR.)
  * numericDeriv() sometimes miscalculated the gradient.  (PR#15849,
    reported originally by Radford Neal)</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1414756800">- Upstream release 3.1.2
- Most important
  CHANGES IN R 3.1.2:
  NEW FEATURES:
  * embedFonts() now defaults to format = "ps2write" for .ps and .eps
    files.  This is available in Ghostscript 9.x (since 2010) whereas
    the previous default, format = "pswrite", was removed in
    Ghostscript 9.10.
  * For consistency with [dpqr]norm(), [dp]lnorm(sdlog = 0) model a
    point mass at exp(mulog) rather than return NaN (for an error).
  * capabilities() now reports if ICU is compiled in for use for
    collation (it is only actually used if a suitable locale is set
    for collation, and never for a C locale).
  * (OS X only.) Package tcltk checks when loaded if it is linked
    against the CRAN X11-based Tcl/Tk and if so that the Tcl/Tk
    component and the X11 libraries are installed.  This allows more
    informative error messages to be given advising the installation
    of the missing component or of XQuartz.
    The X11() device and X11-based versions of the data editor and
    viewer (invoked by edit() and View() for data frames and matrices
    from command-line R) check that the X11 libraries are installed
    and if not advises installing XQuartz.
  * icuSetCollate() allows locale = "default", and locale = "none" to
    use OS services rather than ICU for collation.
    Environment variable R_ICU_LOCALE can be used to set the default
    ICU locale, in case the one derived from the OS locale is
    inappropriate (this is currently necessary on Windows).
  * New function icuGetCollate() to report on the ICU collation
    locale in use (if any).
  * utils::URLencode() was updated to use unreserved and reserved
    characters from RFC 3986, &lt;URL:
    http://tools.ietf.org/html/rfc3986&gt;, instead of RFC 1738.
  * unique(warnings()) and c(warnings()) are now supported.
  * The Bioconductor 'version' used by setRepositories() now defaults
    to 3.0. (It can be set at runtime _via_ environment variable
    R_BIOC_VERSION.)
  INSTALLATION and INCLUDED SOFTWARE:
  * The configure script reports on the more important
    capabilities/options which will not be compiled in.
    More types of external BLAS are recognized by name in that
    report.
  * When building R as a shared library, the -L${R_HOME}/lib${R_ARCH}
    flag is placed earlier in the link commands used during
    installation and when packages are installed: this helps ensure
    that the current build has priority if an R shared library has
    already been installed by e.g. install-libR in a library
    mentioned in LDFLAGS (and not in 'your system's library
    directory' as documented). (Wish of PR#15790.)
  * LaTeX package upquote is no longer required for R's use of
    inconsolata.
  * (Windows only) If both 32 and 64 bit versions of R are installed,
    the bin/R.exe and bin/Rscript.exe executables now run 64 bit R.
    (To run 32 bit R, overwrite these files with copies of
    bin/i386/Rfe.exe.)
  UTILITIES:
  * Running R CMD check with _R_CHECK_DEPENDS_ONLY_ true now makes
    the VignetteBuilder packages available even if they are listed in
    Suggests, since they are needed to recognise and process
    non-Sweave vignettes.
  * R CMD check now reports empty importFrom declarations in a
    NAMESPACE file, as these are common errors (writing
    importFrom(Pkg) where import(Pkg) was intended).
  * R CMD check now by default checks code usage directly on the
    package namespace without loading and attaching the package and
    its suggests and enhances.  For good practice with packages in
    the Suggests field, see SS1.1.3.1 of 'Writing R Extensions'.  For
    use of lazy-data objects in the package's own code, see ?data.
  BUG FIXES:
  * dmultinom() did not handle non-finite probabilities correctly.
  * prettyNum(x, zero.print=*) now also works when x contains NAs.
  * A longstanding bug exhibited by nlminb() on Windows was traced to
    a compiler bug in gcc 4.6.3; a workaround has been put in place.
    (PR#15244 and PR#15914).
  * Rendering of \command in HTML versions of help pages has been
    improved: this is particularly evident on the help page for
    INSTALL.
  * as.hexmode(x) and as.octmode(x) now behave correctly for some
    numeric x, e.g., c(NA, 1) or c(1, pi).
  * drop1() failed if the scope argument had no variables to drop.
    (PR#15935)
  * edit() (and hence fix()) failed if an object had a non-character
    attribute named "source" (an attribute that had been used in R
    prior to version 2.14.0).
  * callGeneric() could fail if the generic had ... as a formal
    argument. (PR#15937).
  * Forking in package parallel called C entry point exit in the
    child.  This was unsafe (_exit should have been called), and
    could flush stdin of the main R process (seen most often on
    Solaris).
    As good practice, stdout is now flushed before forking a child.
  * R objects such as list(`a\b` = 1) now print correctly.
  * getAnywhere("C_pbinom") now returns correctly a single object
    (rather than unlisting it).
  * The confint() method for nls() fits failed it these has specified
    parameter limits despite using an algorithm other than "port".
    (PR#15960)
  * Subclassing an S4 class failed if the class required arguments to
    the generator, through its initialize() method.
  * removeSource() did not properly handle expressions containing
    arguments that were supplied as missing, e.g.  x[i,]. (PR#15957)
  * as.environment(list()) now works, and as.list() of such an
    environment is now the same as list().
  * Several tcltk functions failed when run in unusual environments.
    (PR#15970)
  * options(list()) now works (trivially). (PR#15979)
  * merge(&lt;dendrogram&gt;, ..) now works correctly for two `independent'
    dendrograms (PR#15648), and still compatibly via adjust = "auto"
    e.g. for two branches of an existing dendrogram.
  * The plot method for "hclust" objects gets an optional argument
    check; When that is true (the default) it checks more carefully
    for valid input.
  * (Windows only) If a user chose to install 64 bit R but not 32 bit
    R, the bin/R and bin/Rscript executables failed to run.
    (PR#15981)
  * Various possible buffer overruns have been prevented, and missed
    memory protection added. (PR#15990)
  * Rscript no longer passes --args to R when there are no extra
    ("user") arguments.
  * objects like getClass("refClass")@prototype now print() and str()
    without error.
  * identical() now also looks at the S4 bit.
  * hist(x, breaks) is more robust in adding a small fuzz to few
    breaks when some are very large. (PR#15988)
  * sub() and gsub() did not handle regular expressions like "\s{2,}"
    properly if the text contained NA or non-ascii elements in a
    UTF-8 locale.  Part of this was due to a bug in the TRE library.
    (PR#16009)
  * RShowDoc("NEWS") now displays the PDF version.
  * Matrices and arrays with last dimension zero did not print at all
    or incompletely.  (PR#16012)
  * plot.histogram() and hence hist() now respect the xaxs, yaxs and
    lab graphics parameters.  (PR#16021)
  * bw.SJ(x) and other bw.*() no longer segfault when x contains
    non-finite values. (PR#16024)
  * R CMD Rd2pdf unintentionally ignored its --os option.
  * The internal method of download.file() was not reporting file
    sizes and progress correctly on files larger than 2GB (inherited
    from libxml2).  This is corrected for 64-bit builds (32-bit
    platforms may not support such files, but where possible will be
    supported in future versions of R).
  * Work around a bug in OS X Yosemite where key environment
    variables may be duplicated causing issues in subprocesses. The
    duplicates are now removed on R startup (via Rprofile).
    (PR#16042)
  * Adjust X11 auto-launch detection in DISPLAY on OS X to recognize
    latest XQuartz.</changelog>
  <changelog author="sbahling@suse.com" date="1418385600">- Remove tex(inconsolata.sty) BuildRequires for SLE_12 builds (like
  older SLE releases).</changelog>
  <changelog author="detlef.steuer@gmx.de" date="1425902400">- Upstream release 3.1.3
- Most important
  CHANGES IN R 3.1.3:
  NEW FEATURES:
  * The internal method of download.file() can now handle files
    larger than 2GB on 32-bit builds which support such files (tested
    on 32-bit R running on 64-bit Windows).
  * kruskal.test() warns on more types of suspicious input.
  * The as.dendrogram() method for "hclust" objects gains a check
    argument protecting against memory explosion for invalid inputs.
  * capabilities() has a new item long.double which indicates if the
    build uses a long double type which is longer than double.
  * nlm() no longer modifies the callback argument in place (a new
    vector is allocated for each invocation, which mimics the
    implicit duplication that occurred in R &lt; 3.1.0); note that this
    is a change from the previously documented behavior. (PR#15958)
  * icuSetCollate() now accepts locale = "ASCII" which uses the basic
    C function strcmp and so collates strings byte-by-byte in
    numerical order.
  * sessionInfo() tries to report the OS version in use (not just
    that compiled under, and including details of Linux
    distributions).
  * model.frame() (used by lm() and many other modelling functions)
    now warns when it drops contrasts from factors.  (Wish of
    PR#16119)
  * install.packages() and friends now accept the value type =
    "binary" as a synonym for the native binary type on the platform
    (if it has one).
  * Single source or binary files can be supplied for
    install.packages(type = "both") and the appropriate type and
    repos = NULL will be inferred.
  * New function pcre_config() to report on some of the configuration
    options of the version of PCRE in use.  In particular, this
    reports if regular expressions using \p{xx} are supported.
  * (Windows.) download.file(cacheOK = FALSE) is now supported when
    internet2.dll is used.
  * browseURL() has been updated to work with Firefox 36.0 which has
    dropped support for the -remote interface.
  INSTALLATION and INCLUDED SOFTWARE:
  * The included version of PCRE has been updated to 8.36.
  * configure accepts MAKEINFO=texi2any as another way to ensure
    texinfo 5.x is used when both 5.x and 4.x are installed.
  UTILITIES:
  * R CMD check now checks the packages used in \donttest sections of
    the examples are specified in the DESCRIPTION file.  (These are
    needed to run the examples interactively.)
  * R CMD check checks for the undeclared use of GNU extensions in
    Makefiles, and for Makefiles with a missing final linefeed.
    R CMD build will correct line endings in all Makefiles, not just
    those in the src directory.
  * R CMD check notes uses of library() and require() in package
    code: see the section 'Suggested packages' of 'Writing R
    Extensions' for good practice.
  DEPRECATED AND DEFUNCT:
  * The configure option --with-valgrind-instrumentation=3 is
    deprecated and will be removed in R 3.2.0.
  BUG FIXES:
  * (Windows.) Rscript.exe was missing a manifest specifying the
    modern style for common controls (e.g., the download progress
    bar).
  * If a package had extra documentation files but no vignette, the
    HTML help system produced an empty index page.
  * The parser now gives an error if a null character is included in
    a string using Unicode escapes. (PR#16046)
  * qr.Q() failed on complex arguments due to pre-3.0(!) typo.
    (PR#16054)
  * abs() failed with named arguments when the argument was complex.
    (PR#16047)
  * "noquote" objects may now be used as columns in dataframes.
    (PR#15997)
  * Some values with extremely long names were printed incorrectly.
    (PR#15999)
  * Extremely large exponents on zero expressed in scientific
    notation (e.g. 0.0e50000) could give NaN.  (PR#15976)
  * download.file() reported downloaded sizes as 0KB if less than
    1MB, only for R 3.1.2 and only on big-endian platforms.
  * prompt() did not escape percent signs in the automatically
    generated usage section of help files.
  * drop.terms() dropped some of the attributes of the object it was
    working with.  (PR#16029)
  * (Windows.) The command completion in Rgui.exe messed up the
    console.  (PR#15791)
  * (Windows.) The choose.files() command returned a blank string
    when the user asked for a single file but cancelled the request.
    (PR#16074)
  * Math2 S4 group generics failed to correctly dispatch "structure"-
    and "nonStructure"-derived classes.
  * loadNamespace() imposed undocumented restrictions on the
    versionCheck parameter.  (Reported by Geoff Lee.)
  * Rare over-runs detected by AddressSanitizer in substr() and its
    replacement version have been avoided.
    _Inter alia_ that fix gives the documented behaviour for
    substr(x, 1, 2) &lt;- "" (subsequently reported as PR#16214).
  * Loading packages incorrectly defining an S4 generic followed by a
    function of the same name caused an erroneous cyclic namespace
    dependency error.
  * Declared vignette encodings are now always passed to the vignette
    engine.
  * Port Tomas Kalibera's fix from R-devel that restores the
    loadMethod() fast path, effectively doubling the speed of S4
    dispatch.
  * power.t.test() and power.prop.test() now make use of the
    extendInt option of uniroot() and hence work in more extreme
    cases.  (PR#15792)
  * If a package was updated and attached when its namespace was
    already loaded, it could end up with parts from one version and
    parts from the other.  (PR#16120)
  * tools:::.Rdconv() didn't accept --encoding= due to a typo.
    (PR#16121)
  * Unix-alike builds without a suitable makeinfo were documented to
    link the missing HTML manuals to CRAN, but did not.
  * save(*, ascii=TRUE) and load() now correctly deal with NaN's.
    (PR#16137)
  * split.Date() retains fractional representations while avoiding
    incomplete class propagation.
  * R_ext/Lapack.h had not been updated for changes made by LAPACK to
    the argument lists of its (largely internal) functions dlaed2 and
    dlaed3.  (PR#16157)
  * RShowDoc("NEWS", "txt") had not been updated for the layout
    changes of R 3.1.0.
  * The xtfrm() method for class "Surv" has been corrected and its
    description expanded.
  * mode(x) &lt;- y would incorrectly evaluate x before changing its
    mode. (PR#16215)
  * besselJ(1, 2^64) and besselY(..) now signal a warning, returning
    NaN instead of typically segfaulting. (Issue 3 of PR#15554)
  * HTML conversion of \href markup in .Rd files did not remove the
    backslash from \% and so gave an invalid URL.  In a related
    change, the \ escape is now required in such URLs.</changelog>
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