Package Release Info


Update Info: Base Release
Available in Package Hub : 15 SP2





Change Logs

Version: 3.5.0-bp150.2.5
* Mon Apr 23 2018
- CHANGES IN R 3.5.0:
  * All packages are by default byte-compiled on installation.  This
    makes the installed packages larger (usually marginally so) and
    may affect the format of messages and tracebacks (which often
    exclude .Call and similar).
  * factor() now uses order() to sort its levels, rather than
    sort.list().  This allows factor() to support custom vector-like
    objects if methods for the appropriate generics are defined.  It
    has the side effect of making factor() succeed on empty or
    length-one non-atomic vector(-like) types (e.g., "list"), where
    it failed before.
  * diag() gets an optional names argument: this may require updates
    to packages defining S4 methods for it.
  * chooseCRANmirror() and chooseBioCmirror() no longer have a
    useHTTPS argument, not needed now all R builds support https://
  * New summary() method for warnings() with a (somewhat
    experimental) print() method.
  * (methods package.) .self is now automatically registered as a
    global variable when registering a reference class method.
  * tempdir(check = TRUE) recreates the tempdir() directory if it is
    no longer valid (e.g. because some other process has cleaned up
    the /tmp directory).
  * New askYesNo() function and "askYesNo" option to ask the user
    binary response questions in a customizable but consistent way.
    (Suggestion of PR#17242.)
  * New low level utilities ...elt(n) and ...length() for working
    with ... parts inside a function.
  * isTRUE() is more tolerant and now true in
    x <- rlnorm(99)
    isTRUE(median(x) == quantile(x)["50%"])
    New function isFALSE() defined analogously to isTRUE().
  * The default symbol table size has been increased from 4119 to
    49157; this may improve the performance of symbol resolution when
    many packages are loaded.  (Suggested by Jim Hester.)
  * line() gets a new option iter = 1.
  * Reading from connections in text mode is buffered, significantly
    improving the performance of readLines(), as well as scan() and
    read.table(), at least when specifying colClasses.
  * order() is smarter about picking a default sort method when its
    arguments are objects.
  * available.packages() has two new arguments which control if the
    values from the per-session repository cache are used (default
    true, as before) and if so how old cached values can be to be
    used (default one hour).
    These arguments can be passed from install.packages(),
    update.packages() and functions calling that: to enable this
    available.packages(), packageStatus() and download.file() gain a
    ... argument.
  * packageStatus()'s upgrade() method no longer ignores its ...
    argument but passes it to install.packages().
  * installed.packages() gains a ... argument to allow arguments
    (including noCache) to be passed from new.packages(),
    old.packages(), update.packages() and packageStatus().
  * factor(x, levels, labels) now allows duplicated labels (not
    duplicated levels!).  Hence you can map different values of x to
    the same level directly.
  * Attempting to use names<-() on an S4 derivative of a basic type
    no longer emits a warning.
  * The list method of within() gains an option keepAttrs = FALSE for
    some speed-up.
  * system() and system2() now allow the specification of a maximum
    elapsed time ('timeout').
  * debug() supports debugging of methods on any object of S4 class
    "genericFunction", including group generics.
  * Attempting to increase the length of a variable containing NULL
    using length()<- still has no effect on the target variable, but
    now triggers a warning.
  * type.convert() becomes a generic function, with additional
    methods that operate recursively over list and data.frame
    objects. Courtesy of Arni Magnusson (PR#17269).
  * lower.tri(x) and upper.tri(x) only needing dim(x) now work via
    new functions .row() and .col(), so no longer call as.matrix() by
    default in order to work efficiently for all kind of matrix-like
  * print() methods for "xgettext" and "xngettext" now use
    encodeString() which keeps, e.g. "\n", visible.  (Wish of
  * package.skeleton() gains an optional encoding argument.
  * approx(), spline(), splinefun() and approxfun() also work for
    long vectors.
  * deparse() and dump() are more useful for S4 objects, dput() now
    using the same internal C code instead of its previous imperfect
    workaround R code.  S4 objects now typically deparse perfectly,
    i.e., can be recreated identically from deparsed code.
    dput(), deparse() and dump() now print the names() information
    only once, using the more readable (tag = value) syntax, notably
    for list()s, i.e., including data frames.
    These functions gain a new control option "niceNames" (see
    .deparseOpts()), which when set (as by default) also uses the
    (tag = value) syntax for atomic vectors.  On the other hand,
    without deparse options "showAttributes" and "niceNames", names
    are no longer shown also for lists.  as.character(list( c (one =
    1))) now includes the name, as as.character(list(list(one = 1)))
    has always done.
    m:n now also deparses nicely when m > n.
    The "quoteExpressions" option, also part of "all", no longer
    quote()s formulas as that may not re-parse identically.
  * If the option setWidthOnResize is set and TRUE, R run in a
    terminal using a recent readline library will set the width
    option when the terminal is resized.  Suggested by Ralf Goertz.
  * If multiple on.exit() expressions are set using add = TRUE then
    all expressions will now be run even if one signals an error.
  * mclapply() gets an option affinity.list which allows more
    efficient execution with heterogeneous processors, thanks to
    Helena Kotthaus.
  * The character methods for as.Date() and as.POSIXlt() are more
    flexible _via_ new arguments tryFormats and optional: see their
    help pages.
  * on.exit() gains an optional argument after with default TRUE.
    Using after = FALSE with add = TRUE adds an exit expression
    before any existing ones. This way the expressions are run in a
    first-in last-out fashion. (From Lionel Henry.)
  * On Windows, file.rename() internally retries the operation in
    case of error to attempt to recover from possible anti-virus
  * Command line completion on :: now also includes lazy-loaded data.
  * If the TZ environment variable is set when date-time functions
    are first used, it is recorded as the session default and so will
    be used rather than the default deduced from the OS if TZ is
    subsequently unset.
  * There is now a [ method for class "DLLInfoList".
  * glm() and get the same singular.ok = TRUE argument that
    lm() has had forever.  As a consequence, in glm(*, method =
    <your_own>), user specified methods need to accept a singular.ok
    argument as well.
  * aspell() gains a filter for Markdown (.md and .Rmd) files.
  * intToUtf8(multiple = FALSE) gains an argument to allow surrogate
    pairs to be interpreted.
  * The maximum number of DLLs that can be loaded into R e.g. _via_
    dyn.load() has been increased up to 614 when the OS limit on the
    number of open files allows.
  * Sys.timezone() on a Unix-alike caches the value at first use in a
    session: _inter alia_ this means that setting TZ later in the
    session affects only the _current_ time zone and not the _system_
    Sys.timezone() is now used to find the system timezone to pass to
    the code used when R is configured with --with-internal-tzcode.
  * When tar() is used with an external command which is detected to
    be GNU tar or libarchive tar (aka bsdtar), a different
    command-line is generated to circumvent line-length limits in the
  * system(*, intern = FALSE), system2() (when not capturing output),
    file.edit() and now issue a warning when the external
    command cannot be executed.
  * The "default" ("lm" etc) methods of vcov() have gained new
    optional argument complete = TRUE which makes the vcov() methods
    more consistent with the coef() methods in the case of singular
    designs.  The former (back-compatible) behavior is given by
    vcov(*, complete = FALSE).
  * coef() methods (for lm etc) also gain a complete = TRUE optional
    argument for consistency with vcov().
    For "aov", both coef() and vcov() methods remain back-compatibly
    consistent, using the _other_ default, complete = FALSE.
  * attach(*, pos = 1) is now an error instead of a warning.
  * New function getDefaultCluster() in package parallel to get the
    default cluster set via setDefaultCluster().
  * str(x) for atomic objects x now treats both cases of is.vector(x)
    similarly, and hence much less often prints "atomic".  This is a
    slight non-back-compatible change producing typically both more
    informative and shorter output.
  * write.dcf() gets optional argument useBytes.
  * New, partly experimental packageDate() which tries to get a valid
    "Date" object from a package DESCRIPTION file, thanks to
    suggestions in PR#17324.
  * tools::resaveRdaFiles() gains a version argument, for use when
    packages should remain compatible with earlier versions of R.
  * ar.yw(x) and hence by default ar(x) now work when x has NAs,
    mostly thanks to a patch by Pavel Krivitsky in PR#17366.  The
    ar.yw.default()'s AIC computations have become more efficient by
    using determinant().
  * New warnErrList() utility (from package nlme, improved).
  * By default the (arbitrary) signs of the loadings from princomp()
    are chosen so the first element is non-negative.
  * If --default-packages is not used, then Rscript now checks the
    environment variable R_SCRIPT_DEFAULT_PACKAGES. If this is set,
    then it takes precedence over R_DEFAULT_PACKAGES. If default
    packages are not specified on the command line or by one of these
    environment variables, then Rscript now uses the same default
    packages as R. For now, the previous behavior of not including
    methods can be restored by setting the environment variable
    R_SCRIPT_LEGACY to yes.
  * When a package is found more than once, the warning from
    find.package(*, verbose=TRUE) lists all library locations.
  * POSIXt objects can now also be rounded or truncated to month or
  * stopifnot() can be used alternatively via new argument exprs
    which is nicer and useful when testing several expressions in one
  * The environment variable R_MAX_VSIZE can now be used to specify
    the maximal vector heap size. On macOS, unless specified by this
    environment variable, the maximal vector heap size is set to the
    maximum of 16GB and the available physical memory. This is to
    avoid having the R process killed when macOS over-commits memory.
  * sum(x) and sum(x1,x2,..,x<N>) with many or long logical or
    integer vectors no longer overflows (and returns NA with a
    warning), but returns double numbers in such cases.
  * Single components of "POSIXlt" objects can now be extracted and
    replaced via [ indexing with 2 indices.
  * S3 method lookup now searches the namespace registry after the
    top level environment of the calling environment.
  * Arithmetic sequences created by 1:n, seq_along, and the like now
    use compact internal representations via the ALTREP framework.
    Coercing integer and numeric vectors to character also now uses
    the ALTREP framework to defer the actual conversion until first
  * Finalizers are now run with interrupts suspended.
  * merge() gains new option no.dups and by default suffixes the
    second of two duplicated column names, thanks to a proposal by
    Scott Ritchie (and Gabe Becker).
  * scale.default(x, center, scale) now also allows center or scale
    to be "numeric-alike", i.e., such that as.numeric(.) coerces them
    correctly.  This also eliminates a wrong error message in such
  * par*apply and par*applyLB gain an optional argument chunk.size
    which allows to specify the granularity of scheduling.
  * Some methods, notably the matrix one, are now
    more careful in not accepting duplicated or NA row names, and by
    default produce unique non-NA row names.  This is based on new
    function .rowNamesDF(x, make.names = *) <- rNms where the logical
    argument make.names allows to specify _how_ invalid row names
    rNms are handled.  .rowNamesDF() is a "workaround" compatible
  * R has new serialization format (version 3) which supports custom
    serialization of ALTREP framework objects.  These objects can
    still be serialized in format 2, but less efficiently.
    Serialization format 3 also records the current native encoding
    of unflagged strings and converts them when de-serialized in R
    running under different native encoding.  Format 3 comes with new
    serialization magic numbers (RDA3, RDB3, RDX3).  Format 3 can be
    selected by version = 3 in save(), serialize() and saveRDS(), but
    format 2 remains the default for all serialization and saving of
    the workspace.  Serialized data in format 3 cannot be read by
    versions of R prior to version 3.5.0.
  * The "Date" and "date-time" classes "POSIXlt" and "POSIXct" now
    have a working `length<-` method, as wished in PR#17387.
  * optim(*, control = list(warn.1d.NelderMead = FALSE)) allows to
    turn off the warning when applying the default "Nelder-Mead"
    method to 1-dimensional problems.
  * matplot(.., panel.first = .) etc now work, as log becomes
    explicit argument and ... is passed to plot() unevaluated, as
    suggested by Sebastian Meyer in PR#17386.
  * Interrupts can be suspended while evaluating an expression using
    suspendInterrupts.  Subexpression can be evaluated with
    interrupts enabled using allowInterrupts.  These functions can be
    used to make sure cleanup handlers cannot be interrupted.
  * R 3.5.0 includes a framework that allows packages to provide
    alternate representations of basic R objects (ALTREP).  The
    framework is still experimental and may undergo changes in future
    R releases as more experience is gained. For now, documentation
    is provided in <URL:>.
  * install.packages() for source packages now has the possibility to
    set a 'timeout' (elapsed-time limit).  For serial installs this
    uses the timeout argument of system2(): for parallel installs it
    requires the timeout utility command from GNU coreutils.
  * It is now possible to set 'timeouts' (elapsed-time limits) for
    most parts of R CMD check _via_ environment variables documented
    in the 'R Internals' manual.
  * The 'BioC extra' repository which was dropped from Bioconductor
    3.6 and later has been removed from setRepositories().  This
    changes the mapping for 6-8 used by setRepositories(ind=).
  * R CMD check now also applies the settings of environment
    the re-building of vignettes.
  * R CMD check with environment variable _R_CHECK_DEPENDS_ONLY_ set
    to a true value makes test-suite-management packages available
    and (for the time being) works around a common omission of
    rmarkdown from the VignetteBuilder field.
  * Support for a system Java on macOS has been removed - install a
    fairly recent Oracle Java (see 'R Installation and
    Administration' SSC.3.2).
  * configure works harder to set additional flags in SAFE_FFLAGS
    only where necessary, and to use flags which have little or no
    effect on performance.
    In rare circumstances it may be necessary to override the setting
  * C99 functions expm1, hypot, log1p and nearbyint are now required.
  * configure sets a -std flag for the C++ compiler for all supported
    C++ standards (e.g., -std=gnu++11 for the C++11 compiler).
    Previously this was not done in a few cases where the default
    standard passed the tests made (e.g. clang 6.0.0 for C++11).
  * 'Writing R Extensions' documents macros MAYBE_REFERENCED,
    MAYBE_SHARED and MARK_NOT_MUTABLE that should be used by package
    C code instead NAMED or SET_NAMED.
  * The object header layout has been changed to support merging the
    ALTREP branch. This requires re-installing packages that use
    compiled code.
  * 'Writing R Extensions' now documents the R_tryCatch,
    R_tryCatchError, and R_UnwindProtect functions.
  * NAMEDMAX has been raised to 3 to allow protection of intermediate
    results from (usually ill-advised) assignments in arguments to
    BUILTIN functions. Package C code using SET_NAMED may need to be
  * Sys.timezone(location = FALSE) is defunct, and is ignored (with a
  * methods:::bind_activation() is defunct now; it typically has been
    unneeded for years.
    The undocumented 'hidden' objects .__H__.cbind and .__H__.rbind
    in package base are deprecated (in favour of cbind and rbind).
  * The declaration of pythag() in Rmath.h has been removed - the
    entry point has not been provided since R 2.14.0.
  * printCoefmat() now also works without column names.
  * The S4 methods on Ops() for the "structure" class no longer cause
    infinite recursion when the structure is not an S4 object.
  * nlm(f, ..) for the case where f() has a "hessian" attribute now
    computes LL' = H + uI correctly.  (PR#17249).
  * An S4 method that "rematches" to its generic and overrides the
    default value of a generic formal argument to NULL no longer
    drops the argument from its formals.
  * Rscript can now accept more than one argument given on the #!
    line of a script. Previously, one could only pass a single
    argument on the #! line in Linux.
  * Connections are now written correctly with encoding "UTF-16LE".
  * Evaluation of ..0 now signals an error.  When ..1 is used and ...
    is empty, the error message is more appropriate.
  * (Windows mainly.)  Unicode code points which require surrogate
    pairs in UTF-16 are now handled.  All systems should properly
    handle surrogate pairs, even those systems that do not need to
    make use of them.  (PR#16098)
  * stopifnot(e, e2, ...) now evaluates the expressions sequentially
    and in case of an error or warning shows the relevant expression
    instead of the full stopifnot(..)  call.
  * path.expand() on Windows now accepts paths specified as
    UTF-8-encoded character strings even if not representable in the
    current locale.  (PR#17120)
  * line(x, y) now correctly computes the medians of the left and
    right group's x-values and in all cases reproduces straight
  * Extending S4 classes with slots corresponding to special
    attributes like dim and dimnames now works.
  * Fix for legend() when fill has multiple values the first of which
    is NA (all colours used to default to par(fg)).  (PR#17288)
  * installed.packages() did not remove the cached value for a
    library tree that had been emptied (but would not use the old
    value, just waste time checking it).
  * The documentation for installed.packages(noCache = TRUE)
    incorrectly claimed it would refresh the cache.
  * aggregate(<data.frame>) no longer uses spurious names in some
    cases.  (PR#17283)
  * object.size() now also works for long vectors.
  * packageDescription() tries harder to solve re-encoding issues,
    notably seen in some Windows locales.  This fixes the citation()
    issue in PR#17291.
  * poly(<matrix>, 3) now works, thanks to prompting by Marc
  * readLines() no longer segfaults on very large files with embedded
    '\0' (aka 'nul') characters.  (PR#17311)
  * ns() (package splines) now also works for a single observation.
    interpSpline() gives a more friendly error message when the
    number of points is less than four.
  * dist(x, method = "canberra") now uses the correct definition; the
    result may only differ when x contains values of differing signs,
    e.g. not for 0-1 data.
  * methods:::cbind() and methods:::rbind() avoid deep recursion,
    thanks to Suharto Anggono via PR#17300.
  * Arithmetic with zero-column data frames now works more
    consistently; issue raised by Bill Dunlap.
    Arithmetic with data frames gives a data frame for ^ (which
    previously gave a numeric matrix).
  * pretty(x, n) for large n or large diff(range(x)) now works better
    (though it was never meant for large n); internally it uses the
    same rounding fuzz (1e-10) as seq.default() - as it did up to
    2010-02-03 when both were 1e-7.
  * Internal C-level R_check_class_and_super() and hence
    R_check_class_etc() now also consider non-direct super classes
    and hence return a match in more cases.  This e.g., fixes
    behaviour of derived classes in package Matrix.
  * Reverted unintended change in behavior of return calls in on.exit
    expressions introduced by stack unwinding changes in R 3.3.0.
  * Attributes on symbols are now detected and prevented; attempt to
    add an attribute to a symbol results in an error.
  * fisher.test(*, workspace = <n>) now may also increase the
    internal stack size which allows larger problem to be solved,
    fixing PR#1662.
  * The methods package no longer directly copies slots (attributes)
    into a prototype that is of an "abnormal" (reference) type, like
    a symbol.
  * The methods package no longer attempts to call length<-() on NULL
    (during the bootstrap process).
  * The methods package correctly shows methods when there are
    multiple methods with the same signature for the same generic
    (still not fully supported, but at least the user can see them).
  * sys.on.exit() is now always evaluated in the right frame. (From
    Lionel Henry.)
  * seq.POSIXt(*, by = "<n> DSTdays") now should work correctly in
    all cases and is faster.  (PR#17342)
  * .C() when returning a logical vector now always maps values other
    than FALSE and NA to TRUE (as documented).
  * Subassignment with zero length vectors now coerces as documented
    Further, x <- numeric(); x[1] <- character() now signals an error
    'replacement has length zero' (or a translation of that) instead
    of doing nothing.
  * (Package parallel.)  mclapply(), pvec() and mcparallel() (when
    mccollect() is used to collect results) no longer leave zombie
    processes behind.
  * R CMD INSTALL <pkg> now produces the intended error message when,
    e.g., the LazyData field is invalid.
  * as.matrix(dd) now works when the data frame dd contains a column
    which is a data frame or matrix, including a 0-column matrix/d.f.
  * mclapply(X, mc.cores) now follows its documentation and calls
    lapply() in case mc.cores = 1 also in the case mc.preschedule is
    false.  (PR#17373)
  * aggregate(<data.frame>, drop=FALSE) no longer calls the function
    on <empty> parts but sets corresponding results to NA.  (Thanks
    to Suharto Anggono's patches in PR#17280).
  * The duplicated() method for data frames is now based on the list
    method (instead of string coercion).  Consequently unique() is
    better distinguishing data frame rows, fixing PR#17369 and
    PR#17381.  The methods for matrices and arrays are changed
  * Calling names() on an S4 object derived from "environment"
    behaves (by default) like calling names() on an ordinary
  * read.table() with a non-default separator now supports quotes
    following a non-whitespace character, matching the behavior of
  * parLapplyLB and parSapplyLB have been fixed to do load balancing
    (dynamic scheduling).  This also means that results of
    computations depending on random number generators will now
    really be non-reproducible, as documented.
  * Indexing a list using dollar and empty string (l$"") returns
  * Using \usage{ data(<name>, package="<pkg>") } no longer produces
    R CMD check warnings.
  * match.arg() more carefully chooses the environment for
    constructing default choices, fixing PR#17401 as proposed by
    Duncan Murdoch.
  * Deparsing of consecutive ! calls is now consistent with deparsing
    unary - and + calls and creates code that can be reparsed
    exactly; thanks to a patch by Lionel Henry in PR#17397.  (As a
    side effect, this uses fewer parentheses in some other deparsing
    involving ! calls.)
* Wed Mar 28 2018
- added gcc-c++ build dependency
* Tue Mar 20 2018
- Setting correctly R_UNZIPCMD
  Corrects this bug:
* Thu Mar 15 2018
- upstrem updated to 3.4.4
  CHANGES IN R 3.4.4:
  * Sys.timezone() tries more heuristics on Unix-alikes and so is
    more likely to succeed (especially on Linux).  For the slowest
    method, a warning is given recommending that TZ is set to avoid
    the search.
  * The version of LAPACK included in the sources has been updated to
    3.8.0 (for the routines used by R, a very minor bug-fix change).
  * parallel::detectCores(logical = FALSE) is ignored on Linux
    systems, since the information is not available with virtualized
  * configure will use pkg-config to find the flags to link to jpeg
    if available (as it should be for the recently-released jpeg-9c
    and libjpeg-turbo).  (This amends the code added in R 3.3.0 as
    the module name in jpeg-9c is not what that tested for.)
  * Sys.timezone(location = FALSE) (which was a stop-gap measure for
    Windows long ago) is deprecated.  It no longer returns the value
    of environment variable TZ (usually a location).
  * Legacy support of make macros such as CXX1X is formally
    deprecated: use the CXX11 forms instead.
  * power.prop.test() now warns when it cannot solve the problem,
    typically because of impossible constraints. (PR#17345)
  * removeSource() no longer erroneously removes NULL in certain
    cases, thanks to D'enes T'oth.
  * nls(`NO [mol/l]` ~ f(t)) and nls(y ~ a) now work.  (Partly from
  * R CMD build checks for GNU cp rather than assuming Linux has it.
    (PR#17370 says 'Alpine Linux' does not.)
  * Non-UTF-8 multibyte character handling fixed more permanently
  * sum(<large ints>, <stuff>) is more consistent.  (PR#17372)
  * rf() and rbeta() now also work correctly when ncp is not scalar,
    notably when (partly) NA.  (PR#17375)
  * R CMD INSTALL now correctly sets C++ compiler flags when all
    source files are in sub-directories of src.
* Mon Mar 12 2018
- Do not buildrequire xorg-x11-devel but individual x libs.
* Thu Nov 30 2017
- upstream updated to 3.4.3
  CHANGES IN R 3.4.3:
  * A workaround has been added for the changes in location of
    time-zone files in macOS 10.13 'High Sierra' and again in
    10.13.1, so the default time zone is deduced correctly from the
    system setting when R is configured with --with-internal-tzcode
    (the default on macOS).
  * R CMD javareconf has been updated to recognize the use of a Java
    9 SDK on macOS.
  * raw(0) & raw(0) and raw(0) | raw(0) again return raw(0) (rather
    than logical(0)).
  * intToUtf8() converts integers corresponding to surrogate code
    points to NA rather than invalid UTF-8, as well as values larger
    than the current Unicode maximum of 0x10FFFF.  (This aligns with
    the current RFC3629.)
  * Fix calling of methods on S4 generics that dispatch on ... when
    the call contains ....
  * Following Unicode 'Corrigendum 9', the UTF-8 representations of
    U+FFFE and U+FFFF are now regarded as valid by utf8ToInt().
  * range(c(TRUE, NA), finite = TRUE) and similar no longer return
    NA. (Reported by Lukas Stadler.)
  * The self starting function attr(SSlogis, "initial") now also
    works when the y values have exact minimum zero and is slightly
    changed in general, behaving symmetrically in the y range.
  * The printing of named raw vectors is now formatted nicely as for
    other such atomic vectors, thanks to Lukas Stadler.
* Fri Sep 29 2017
- upstream update to 3.4.2
  CHANGES IN R 3.4.2:
  * Setting the LC_ALL category in Sys.setlocale() invalidates any
    cached locale-specific day/month names and the AM/PM indicator
    for strptime() (as setting LC_TIME has since R 3.1.0).
  * The version of LAPACK included in the sources has been updated to
    3.7.1, a bug-fix release.
  * The default for tools::write_PACKAGES(rds_compress=) has been
    changed to "xz" to match the compression used by CRAN.
  * c() and unlist() are now more efficient in constructing the
    names(.) of their return value, thanks to a proposal by Suharto
    Anggono.  (PR#17284)
  * R CMD check checks for and R CMD build corrects CRLF line endings
    in shell scripts configure and cleanup (even on Windows).
  * The order of selection of OpenMP flags has been changed: Oracle
    Developer Studio 12.5 accepts -fopenmp and -xopenmp but only the
    latter enables OpenMP so it is now tried first.
  * within(List, rm(x1, x2)) works correctly again, including when
    List[["x2"]] is NULL.
  * regexec(pattern, text, *) now applies as.character(.) to its
    first two arguments, as documented.
  * write.table() and related functions, writeLines(), and perhaps
    other functions writing text to connections did not signal errors
    when the writes failed, e.g. due to a disk being full.  Errors
    will now be signalled if detected during the write, warnings if
    detected when the connection is closed.  (PR#17243)
  * rt() assumed the ncp parameter was a scalar.  (PR#17306)
  * menu(choices) with more than 10 choices which easily fit into one
    getOption("width")-line no longer erroneously repeats choices.
  * length()<- on a pairlist succeeds.  (<URL:>)
  * Language objects such as quote(("\n")) or R functions are
    correctly printed again, where R 3.4.1 accidentally duplicated
    the backslashes.
  * Construction of names() for very large objects in c() and
    unlist() now works, thanks to Suharto Anggono's patch proposals
    in PR#17292.
  * Resource leaks (and similar) reported by Steve Grubb fixed.
    (PR#17314, PR#17316, PR#17317, PR#17318, PR#17319, PR#17320)
  * model.matrix(~1, mf) now gets the row names from mf also when
    they differ from 1:nrow(mf), fixing PR#14992 thanks to the
    suggestion by Sebastian Meyer.
  * sigma(fm) now takes the correct denominator degrees of freedom
    for a fitted model with NA coefficients.  (PR#17313)
  * hist(x, "FD") no longer "dies" with a somewhat cryptic error
    message when x has extreme outliers or IQR() zero: nclass.FD(x)
    tries harder to find a robust bin width h in the latter case, and
    hist.default(*, breaks) now checks and corrects a too large
    breaks number.  (PR#17274)
  * callNextMethod() works for ... methods.
  * qr.coef(qd, y) now has correct names also when qd is a complex QR
    or stems from qr(*, LAPACK=TRUE).
  * Setting options(device = *) to an invalid function no longer
    segfaults when plotting is initiated.  (PR#15883)
  * encodeString(<very large string>) no longer segfaults.
  * It is again possible to use configure --enable-maintainer-mode
    without having installed notangle (it was required in R
  * S4 method dispatch on ... calls the method by name instead of
    .Method (for consistency with default dispatch), and only
    attempts to pass non-missing arguments from the generic.
  * readRDS(textConnection(.)) works again.  (PR#17325)
  * (1:n)[-n] no longer segfaults for n <- 2.2e9 (on a platform with
    enough RAM).
  * x <- 1:2; tapply(x, list(x, x), function(x) "")[1,2] now
    correctly returns NA.  (PR#17333)
  * Running of finalizers after explicit GC request moved from the R
    interface do_gc to the C interface R_gc.  This helps with
    reclaiming inaccessible connections.
  * and ??topic matching topics in vignettes with
    multiple file name extensions (e.g., *.md.rsp but not *.Rmd)
    failed with an error when using options(help_type = "html").
  * The X11 device no longer uses the Xlib backing store (PR#16497).
  * array(character(), 1) now gives (a 1D array with) NA as has been
    documented for a long time as in the other cases of zero-length
    array initialization and also compatibly with matrix(character(),
  * ).  As mentioned there, this also fixes PR#17333.
  * splineDesign(.., derivs = 4) no longer segfaults.
  * fisher.test(*, hybrid=TRUE) now (again) will use the hybrid
    method when Cochran's conditions are met, fixing PR#16654.
* Thu Jul 27 2017
-  Corrected "bug" "
  R now installs zip and unzip, what in turn eases the installation
  of packages directly from github via devtools.
* Fri Jun 30 2017
- upstream update to 3.4.1
  CHANGES IN R 3.4.1:
  * The deprecated support for PCRE versions older than 8.20 has been
  * getParseData() gave incorrect column information when code
    contained multi-byte characters.  (PR#17254)
  * Asking for help using expressions like ?stats::cor() did not
    work.  (PR#17250)
  * readRDS(url(....)) now works.
  * R CMD Sweave again returns status = 0 on successful completion.
  * Vignettes listed in .Rbuildignore were not being ignored
    properly.  (PR#17246)
  * file.mtime() no longer returns NA on Windows when the file or
    directory is being used by another process.  This affected
    installed.packages(), which is now protected against this.
  * R CMD INSTALL Windows .zip file obeys --lock and --pkglock flags.
  * (Windows only) The choose.files() function could return incorrect
    results when called with multi = FALSE.  (PR#17270)
  * aggregate(<data.frame>, drop = FALSE) now also works in case of
    near-equal numbers in by.  (PR#16918)
  * fourfoldplot() could encounter integer overflow when calculating
    the odds ratio. (PR#17286)
  * parse() no longer gives spurious warnings when extracting srcrefs
    from a file not encoded in the current locale.
    This was seen from R CMD check with inst/doc/*.R files, and check
    has some additional protection for such files.
  * print.noquote(x) now always returns its argument x (invisibly).
  * Non-UTF-8 multibyte character sets were not handled properly in
    source references.  (PR#16732)
* Fri Apr 21 2017
- upstream update to 3.4.0
  CHANGES IN R 3.4.0:
  * (Unix-alike) The default methods for download.file() and url()
    now choose "libcurl" except for file:// URLs.  There will be
    small changes in the format and wording of messages, including in
    rare cases if an issue is a warning or an error.  For example,
    when HTTP re-direction occurs, some messages refer to the final
    URL rather than the specified one.
    Those who use proxies should check that their settings are
    compatible (see ?download.file: the most commonly used forms work
    for both "internal" and "libcurl").
  * table() has been amended to be more internally consistent and
    become back compatible to R <= 2.7.2 again.  Consequently,
    table(1:2, exclude = NULL) no longer contains a zero count for
    <NA>, but useNA = "always" continues to do so.
  * summary.default() no longer rounds, but its print method does
    resulting in less extraneous rounding, notably of numbers in the
    ten thousands.
  * factor(x, exclude = L) behaves more rationally when x or L are
    character vectors.  Further, exclude = <factor> now behaves as
    documented for long.
  * Arithmetic, logic (&, |) and comparison (aka 'relational', e.g.,
    <, ==) operations with arrays now behave consistently, notably
    for arrays of length zero.
    Arithmetic between length-1 arrays and longer non-arrays had
    silently dropped the array attributes and recycled.  This now
    gives a warning and will signal an error in the future, as it has
    always for logic and comparison operations in these cases (e.g.,
    compare matrix(1,1) + 2:3 and matrix(1,1) < 2:3).
  * The JIT ('Just In Time') byte-code compiler is now enabled by
    default at its level 3. This means functions will be compiled on
    first or second use and top-level loops will be compiled and then
    run.  (Thanks to Tomas Kalibera for extensive work to make this
    For now, the compiler will not compile code containing explicit
    calls to browser(): this is to support single stepping from the
    browser() call.
    JIT compilation can be disabled for the rest of the session using
    compiler::enableJIT(0) or by setting environment variable
    R_ENABLE_JIT to 0.
  * xtabs() works more consistently with NAs, also in its result no
    longer setting them to 0.  Further, a new logical option addNA
    allows to count NAs where appropriate.  Additionally, for the
    case sparse = TRUE, the result's dimnames are identical to the
    default case's.
  * Matrix products now consistently bypass BLAS when the inputs have
    NaN/Inf values. Performance of the check of inputs has been
    improved. Performance when BLAS is used is improved for
    matrix/vector and vector/matrix multiplication (DGEMV is now used
    instead of DGEMM).
    One can now choose from alternative matrix product
    implementations _via_ options(matprod = ).  The "internal"
    implementation is not optimized for speed but consistent in
    precision with other summations in R (using long double
    accumulators where available).  "blas" calls BLAS directly for
    best speed, but usually with undefined behavior for inputs with
  * factor() now uses order() to sort its levels, not sort.list().
    This makes factor() support custom vector-like objects if methods
    for the appropriate generics are defined. This change has the
    side effect of making factor() succeed on empty or length-one
    non-atomic vector(-like) types (e.g., list), where it failed
  * User errors such as integrate(f, 0:1, 2) are now caught.
  * Add signature argument to debug(), debugonce(), undebug() and
    isdebugged() for more conveniently debugging S3 and S4 methods.
    (Based on a patch by Gabe Becker.)
  * Add utils::debugcall() and utils::undebugcall() for debugging the
    function that would be called by evaluating the given expression.
    When the call is to an S4 generic or standard S3 generic,
    debugcall() debugs the method that would be dispatched. A number
    of internal utilities were added to support this, most notably
    utils::isS3stdGeneric().  (Based on a patch by Gabe Becker.)
  * Add utils::strcapture(). Given a character vector and a regular
    expression containing capture expressions, strcapture() will
    extract the captured tokens into a tabular data structure,
    typically a data.frame.
  * str() and strOptions() get a new option drop.deparse.attr with
    improved but _changed_ default behaviour for expressions.  For
    expression objects x, str(x) now may remove extraneous white
    space and truncate long lines.
  * str(<looooooooong_string>) is no longer very slow; inspired by
    Mikko Korpela's proposal in PR#16527.
  * str(x)'s default method is more "accurate" and hence somewhat
    more generous in displaying character vectors; this will
    occasionally change R outputs (and need changes to some
  * .Rout(.save) files).
    For a classed integer vector such as x <- xtabs(~ c(1,9,9,9)),
    str(x) now shows both the class and "int", instead of only the
  * isSymmetric(m) is much faster for large asymmetric matrices m
    _via_ pre-tests and a new option tol1 (with which strict back
    compatibility is possible but not the default).
  * The result of eigen() now is of class "eigen" in the default case
    when eigenvectors are computed.
  * Zero-length date and date-time objects (of classes "POSIX[cl]?t")
    now print() "recognizably".
  * xy.coords() and xyz.coords() get a new setLab option.
  * The method argument of sort.list(), order() and gains
    an "auto" option (the default) which should behave the same as
    before when method was not supplied.
  * stopifnot(E, ..) now reports differences when E is a call to
    all.equal() and that is not true.
  * boxplot(<formula>, *) gain optional arguments drop, sep, and
    lex.order to pass to split.default() which itself gains an
    argument lex.order to pass to interaction() for more flexibility.
  * The plot() method for ppr() has enhanced default labels (xmin and
  * gains an explicit useHash option (with a back
    compatible default).
  * identical() gains an ignore.srcref option which drops "srcref"
    and similar attributes when true (as by default).
  * diag(x, nrow = n) now preserves typeof(x), also for logical,
    integer and raw x (and as previously for complex and numeric).
  * smooth.spline() now allows direct specification of lambda, gets a
    hatvalues() method and keeps tol in the result, and optionally
    parts of the internal matrix computations.
  * addNA() is faster now, e.g. when applied twice.  (Part of
  * New option rstandard(<lm>, type = "predicted") provides the
    "PRESS"-related leave-one-out cross-validation errors for linear
  * After seven years of deprecation, duplicated factor levels now
    produce a warning when printed and an error in levels<- instead
    of a warning.
  * Invalid factors, e.g., with duplicated levels (invalid but
    constructable) now give a warning when printed, _via_ new
    function .valid.factor().
  * sessionInfo() has been updated for Apple's change in OS naming as
    from '10.12' ('macOS Sierra' _vs_ 'OS X El Capitan').
    Its toLatex() method now includes the running component.
  * options(interrupt=) can be used to specify a default action for
    user interrupts.  For now, if this option is not set and the
    error option is set, then an unhandled user interrupt invokes the
    error option.  (This may be dropped in the future as interrupt
    conditions are not error conditions.)
  * In most cases user interrupt handlers will be called with a
    "resume" restart available.  Handlers can invoke this restart to
    resume computation. At the browser prompt the r command will
    invoke a "resume" restart if one is available. Some read
    operations cannot be resumed properly when interrupted and do not
    provide a "resume" restart.
  * Radix sort is now chosen by method = "auto" for for
    double vectors (and hence used for sort() for unclassed double
    vectors), excluding 'long' vectors. = "radix") no longer rounds double vectors.
  * The default and data.frame methods for stack() preserve the names
    of empty elements in the levels of the ind column of the return
    value.  Set the new drop argument to TRUE for the previous
  * Speedup in simplify2array() and hence sapply() and mapply() (for
    the case of names and common length > 1), thanks to Suharto
    Anggono's PR#17118.
  * table(x, exclude = NULL) now sets useNA = "ifany" (instead of
    "always").  Together with the bug fixes for this case, this
    recovers more consistent behaviour compatible to older versions
    of R.  As a consequence, summary() for a logical vector no longer
    reports (zero) counts for NA when there are no NAs.
  * dump.frames() gets a new option include.GlobalEnv which allows to
    also dump the global environment, thanks to Andreas Kersting's
    proposal in PR#17116.
  * system.time() now uses message() instead of cat() when terminated
    early, such that suppressMessages() has an effect; suggested by
    Ben Bolker.
  * citation() supports inst/CITATION files from package source
    trees, with lib.loc pointing to the directory containing the
  * try() gains a new argument outFile with a default that can be
    modified _via_ options(try.outFile = .), useful notably for
  * The unexported low-level functions in package parallel for
    passing serialized R objects to and from forked children now
    support long vectors on 64-bit platforms.  This removes some
    limits on higher-level functions such as mclapply() (but
    returning gigabyte results from forked processes _via_
    serialization should be avoided if at all possible).
  * Connections now print() without error even if invalid, e.g. after
    having been destroyed.
  * apropos() and find(simple.words = FALSE) no longer match object
    names starting with . which are known to be internal objects
    (such as .__S3MethodsTable__.).
  * Convenience function hasName() has been added; it is intended to
    replace the common idiom !is.null(x$name) without the usually
    unintended partial name matching.
  * strcapture() no longer fixes column names nor coerces strings to
    factors (suggested by Bill Dunlap).
  * strcapture() returns NA for non-matching values in x (suggested
    by Bill Dunlap).
  * source() gets new optional arguments, notably exprs; this is made
    use of in the new utility function withAutoprint().
  * sys.source() gets a new toplevel.env argument.  This argument is
    useful for frameworks running package tests; contributed by Tomas
  * Sys.setFileTime() and file.copy( = TRUE) will set
    timestamps with fractions of seconds on platforms/filesystems
    which support this.
  * (Windows only.) now returns file timestamps including
    fractions of seconds; it has done so on other platforms since R
    2.14.0.  (NB: some filesystems do not record modification and
    access timestamps to sub-second resolution.)
  * The license check enabled by options(checkPackageLicense = TRUE)
    is now done when the package's namespace is first loaded.
  * ppr() and supsmu() get an optional trace argument, and ppr(..,
    sm.method = ..spline) is no longer limited to sample size n <=
  * The POSIXct method for print() gets optional tz and usetz
    arguments, thanks to a report from Jennifer S. Lyon.
  * New function check_packages_in_dir_details() in package tools for
    analyzing package-check log files to obtain check details.
  * Package tools now exports function CRAN_package_db() for
    obtaining information about current packages in the CRAN package
    repository, and several functions for obtaining the check status
    of these packages.
  * The (default) Stangle driver Rtangle allows annotate to be a
    function and gets a new drop.evalFALSE option.
  * The default method for quantile(x, prob) should now be monotone
    in prob, even in border cases, see PR#16672.
  * now tries to extract an email address from a
    BugReports field, and if there is none, from a Contacts field.
  * The format() and print() methods for object.size() results get
    new options standard and digits; notably, standard = "IEC" and
    standard = "SI" allow more standard (but less common)
    abbreviations than the default ones, e.g. for kilobytes.  (From
    contributions by Henrik Bengtsson.)
  * If a reference class has a validity method, validObject will be
    called automatically from the default initialization method for
    reference classes.
  * tapply() gets new option default = NA allowing to change the
    previously hardcoded value.
  * read.dcf() now consistently interprets any 'whitespace' to be
    stripped to include newlines.
  * The maximum number of DLLs that can be loaded into R e.g. _via_
    dyn.load() can now be increased by setting the environment
    variable R_MAX_NUM_DLLS before starting R.
  * Assigning to an element of a vector beyond the current length now
    over-allocates by a small fraction. The new vector is marked
    internally as growable, and the true length of the new vector is
    stored in the truelength field. This makes building up a vector
    result by assigning to the next element beyond the current length
    more efficient, though pre-allocating is still preferred.  The
    implementation is subject to change and not intended to be used
    in packages at this time.
  * Loading the parallel package namespace no longer sets or changes
    the .Random.seed, even if R_PARALLEL_PORT is unset.
    NB: This can break reproducibility of output, and did for a CRAN
  * Methods "wget" and "curl" for download.file() now give an R error
    rather than a non-zero return value when the external command has
    a non-zero status.
  * Encoding name "utf8" is mapped to "UTF-8".  Many implementations
    of iconv accept "utf8", but not GNU libiconv (including the late
    2016 version 1.15).
  * sessionInfo() shows the full paths to the library or executable
    files providing the BLAS/LAPACK implementations currently in use
    (not available on Windows).
  * The binning algorithm used by bandwidth selectors bw.ucv(),
    bw.bcv() and bw.SJ() switches to a version linear in the input
    size n for n > nb/2.  (The calculations are the same, but for
    larger n/nb it is worth doing the binning in advance.)
  * There is a new option PCRE_study which controls when grep(perl =
    TRUE) and friends 'study' the compiled pattern.  Previously this
    was done for 11 or more input strings: it now defaults to 10 or
    more (but most examples need many more for the difference from
    studying to be noticeable).
  * grep(perl = TRUE) and friends can now make use of PCRE's
    Just-In-Time mechanism, for PCRE >= 8.20 on platforms where JIT
    is supported.  It is used by default whenever the pattern is
    studied (see the previous item).  (Based on a patch from Mikko
    This is controlled by a new option PCRE_use_JIT.
    Note that in general this makes little difference to the speed,
    and may take a little longer: its benefits are most evident on
    strings of thousands of characters.  As a side effect it reduces
    the chances of C stack overflow in the PCRE library on very long
    strings (millions of characters, but see next item).
    Warning: segfaults were seen using PCRE with JIT enabled on
    64-bit Sparc builds.
  * There is a new option PCRE_limit_recursion for grep(perl = TRUE)
    and friends to set a recursion limit taking into account R's
    estimate of the remaining C stack space (or 10000 if that is not
    available).  This reduces the chance of C stack overflow, but
    because it is conservative may report a non-match (with a
    warning) in examples that matched before.  By default it is
    enabled if any input string has 1000 or more bytes.  (PR#16757)
  * getGraphicsEvent() now works on X11(type = "cairo") devices.
    Thanks to Frederick Eaton (for reviving an earlier patch).
  * There is a new argument onIdle for getGraphicsEvent(), which
    allows an R function to be run whenever there are no pending
    graphics events.  This is currently only supported on X11
    devices.  Thanks to Frederick Eaton.
  * The deriv() and similar functions now can compute derivatives of
    log1p(), sinpi() and similar one-argument functions, thanks to a
    contribution by Jerry Lewis.
  * median() gains a formal ... argument, so methods with extra
    arguments can be provided.
  * strwrap() reduces indent if it is more than half width rather
    than giving an error.  (Suggested by Bill Dunlap.)
  * When the condition code in if(.) or while(.) is not of length
    one, an error instead of a warning may be triggered by setting an
    environment variable, see the help page.
  * Formatting and printing of bibliography entries (bibentry) is
    more flexible and better documented.  Apart from setting
    options(citation.bibtex.max = 99) you can also use
    print(<citation>, bibtex=TRUE) (or format(..)) to get the BibTeX
    entries in the case of more than one entry.  This also affects
    citation().  Contributions to enable style = "html+bibtex" are
  * Entry points R_MakeExternalPtrFn and R_ExternalPtrFn are now
    declared in header Rinternals.h to facilitate creating and
    retrieving an R external pointer from a C function pointer
    without ISO C warnings about the conversion of function pointers.
  * There was an exception for the native Solaris C++ compiler to the
    dropping (in R 3.3.0) of legacy C++ headers from headers such as
    R.h and Rmath.h - this has now been removed.  That compiler has
    strict C++98 compliance hence does not include extensions in its
    (non-legacy) C++ headers: some packages will need to request
    C++11 or replace non-C++98 calls such as lgamma: see SS1.6.4 of
    'Writing R Extensions'.
    Because it is needed by about 70 CRAN packages, headers R.h and
    Rmath.h still declare
    use namespace std;
    when included on Solaris.
  * When included from C++, the R headers now use forms such as
    std::FILE directly rather than including the line
    using std::FILE;
    C++ code including these headers might be relying on the latter.
  * Headers R_ext/BLAS.h and R_ext/Lapack.h have many improved
    declarations including const for double-precision complex
    routines. _Inter alia_ this avoids warnings when passing 'string
    literal' arguments from C++11 code.
  * Headers for Unix-only facilities R_ext/GetX11Image.h,
    R_ext/QuartzDevice.h and R_ext/eventloop.h are no longer
    installed on Windows.
  * No-longer-installed headers GraphicsBase.h, RGraphics.h,
    Rmodules/RX11.h and Rmodules/Rlapack.h which had a LGPL license
    no longer do so.
  * HAVE_UINTPTR_T is now defined where appropriate by Rconfig.h so
    that it can be included before Rinterface.h when CSTACK_DEFNS is
    defined and a C compiler (not C++) is in use.  Rinterface.h now
    includes C header stdint.h or C++11 header cstdint where needed.
  * Package tools has a new function
    package_native_routine_registration_skeleton() to assist adding
    native-symbol registration to a package.  See its help and SS5.4.1
    of 'Writing R Extensions' for how to use it.  (At the time it was
    added it successfully automated adding registration to over 90%
    of CRAN packages which lacked it.  Many of the failures were
    newly-detected bugs in the packages, e.g. 50 packages called
    entry points with varying numbers of arguments and 65 packages
    called entry points not in the package.)
  * readline headers (and not just the library) are required unless
    configuring with --with-readline=no.
  * configure now adds a compiler switch for C++11 code, even if the
    compiler supports C++11 by default.  (This ensures that g++ 6.x
    uses C++11 mode and not its default mode of C++14 with 'GNU
    The tests for C++11 compliance are now much more comprehensive.
    For gcc < 4.8, the tests from R 3.3.0 are used in order to
    maintain the same behaviour on Linux distributions with long-term
  * An alternative compiler for C++11 is now specified with CXX11,
    not CXX1X. Likewise C++11 flags are specified with CXX11FLAGS and
    the standard (e.g., -std=gnu++11 is specified with CXX11STD.
  * configure now tests for a C++14-compliant compiler by testing
    some basic features.  This by default tries flags for the
    compiler specified by CXX11, but an alternative compiler, options
    and standard can be specified by variables CXX14, CXX14FLAGS and
    CXX14STD (e.g., -std=gnu++14).
  * There is a new macro CXXSTD to help specify the standard for C++
    code, e.g. -std=c++98.  This makes it easier to work with
    compilers which default to a later standard: for example, with
    CXX=g++6 CXXSTD=-std=c++98 configure will select commands for g++
    6.x which conform to C++11 and C++14 where specified but
    otherwise use C++98.
  * Support for the defunct IRIX and OSF/1 OSes and Alpha CPU has
    been removed.
  * configure checks that the compiler specified by $CXX $CXXFLAGS is
    able to compile C++ code.
  * configure checks for the required header sys/select.h (or
    sys/time.h on legacy systems) and system call select and aborts
    if they are not found.
  * If available, the POSIX 2008 system call utimensat will be used
    by Sys.setFileTime() and file.copy( = TRUE).  This may
    result in slightly more accurate file times.  (It is available on
    Linux and FreeBSD but not macOS.)
  * The minimum version requirement for libcurl has been reduced to
    7.22.0, although at least 7.28.0 is preferred and earlier
    versions are little tested.  (This is to support Debian 7
    'Wheezy' LTS and Ubuntu 'Precise' 12.04 LTS, although the latter
    is close to end-of-life.)
  * configure tests for a C++17-compliant compiler.  The tests are
    experimental and subject to change in the future.
  * (Windows only) Tcl/Tk version 8.6.4 is now included in the binary
    builds.  The tcltk*.chm help file is no longer included; please
    consult the online help at <URL:> instead.
  * The version of LAPACK included in the sources has been updated to
    3.7.0: no new routines have been added to R.
  * There is support for compiling C++14 or C++17 code in packages on
    suitable platforms: see 'Writing R Extensions' for how to request
  * The order of flags when LinkingTo other packages has been changed
    so their include directories come earlier, before those specified
    in CPPFLAGS.  This will only have an effect if non-system include
    directories are included with -I flags in CPPFLAGS (and so not
    the default -I/usr/local/include which is treated as a system
    include directory on most platforms).
  * Packages which register native routines for .C or .Fortran need
    to be re-installed for this version (unless installed with
    R-devel SVN revision r72375 or later).
  * Make variables with names containing CXX1X are deprecated in
    favour of those using CXX11, but for the time being are still
    made available _via_ file etc/Makeconf.  Packages using them
    should be converted to the new forms and made dependent on R (>=
* Tue Apr 18 2017
- And again that ldconfig call. Newline was obviously wrong.
  Hopefully correct now.
* Tue Apr 04 2017
- Jan Engelhardt <> asked for reverting the change
  to the ldconfig call. So be it.
* Tue Mar 21 2017
- improvements for
  a) calling /sbin/ldconfig, which no longer gives a warning
  b) unregistering info-pages in %preun instead of %postun
* Tue Mar 07 2017
- a change in OBS now requires a BuildRequire: shadow for
  some openSUSE releases.
* Mon Mar 06 2017
- upstream release 3.3.3
- Most important changes
  CHANGES IN R 3.3.3:
  * Changes when redirection of a http:// URL to a https:// URL is
  * The internal methods of download.file() and url() now report
    that they cannot follow this (rather than failing silently).
  * (Unix-alike) download.file(method = "auto") (the default)
    re-tries with method = "libcurl".
  * (Unix-alike) url(method = "default") with an explicit open
    argument re-tries with method = "libcurl".  This covers many
    of the usages, e.g. readLines() with a URL argument.
  * The configure check for the zlib version is now robust to
    versions longer than 5 characters, including 1.2.11.
  * Environmental variable _R_CHECK_TESTS_NLINES_ controls how R CMD
    check reports failing tests (see SS8 of the 'R Internals' manual).
  * (C-level Native routine registration.)  The undocumented styles
    field of the components of R_CMethodDef and R_FortranMethodDef is
  * vapply(x, *) now works with long vectors x.  (PR#17174)
  * isS3method("") and similar are correct now.
  * grepRaw(<long>, <short>, fixed = TRUE) now works, thanks to a
    patch by Mikko Korpela.  (PR#17132)
  * Package installation into a library where the package exists
    _via_ symbolic link now should work wherever Sys.readlink()
    works, resolving PR#16725.
  * "Cincinnati" was missing an "n" in the precip dataset.
  * Fix buffer overflow vulnerability in pdf() when loading an
    encoding file.  Reported by Talos (TALOS-2016-0227).
  * getDLLRegisteredRoutines() now produces its warning correctly
    when multiple DLLs match, thanks to Matt Dowle's PR#17184.
  * Sys.timezone() now returns non-NA also on platforms such as
    Ubuntu 14.04.5 LTS, thanks to Mikko Korpela's PR#17186.
  * format(x) for an illegal "POSIXlt" object x no longer segfaults.
  * methods(f) now also works for f "(" or "{".
  * (Windows only) dir.create() did not check the length of the path
    to create, and so could overflow a buffer and crash R.
  * On some systems, very small hexadecimal numbers in hex notation
    would underflow to zero.  (PR#17199)
  * pmin() and pmax() now work again for ordered factors and 0-length
    S3 classed objects, thanks to Suharto Anggono's PR#17195 and
  * did not do any validity checking on a package's
    BugReports field.  It now ignores an empty field, removes leading
    whitespace and only attempts to open http:// and https:// URLs,
    falling back to emailing the maintainer.
  * Bandwidth selectors bw.ucv() and bw.SJ() gave incorrect answers
    or incorrectly reported an error (because of integer overflow)
    for inputs longer than 46341.  Similarly for bw.bcv() at length
    Another possible integer overflow is checked and may result in an
    error report (rather than an incorrect result) for much longer
    inputs (millions for a smooth distribution).
  * findMethod() failed if the active signature had expanded beyond
    what a particular package used. (Example with packages XR and
    XRJulia on CRAN.)
  * qbeta() underflowed too early in some very asymmetric cases.
  * R CMD Rd2pdf had problems with packages with non-ASCII titles in
    .Rd files (usually the titles were omitted).
* Mon Oct 31 2016
- upstream release 3.3.2
- Most important changes
  CHANGES IN R 3.3.2:
  * extSoftVersion() now reports the version (if any) of the readline
    library in use.
  * The version of LAPACK included in the sources has been updated to
    3.6.1, a bug-fix release including a speedup for the
    non-symmetric case of eigen().
  * Use options(deparse.max.lines=) to limit the number of lines
    recorded in .Traceback and other deparsing activities.
  * format(<AsIs>) looks more regular, also for non-character atomic
  * abbreviate() gains an option named = TRUE.
  * The online documentation for package methods is extensively
    rewritten.  The goals are to simplify documentation for basic
    use, to note old features not recommended and to correct
    out-of-date information.
  * Calls to setMethod() no longer print a message when creating a
    generic function in those cases where that is natural: S3
    generics and primitives.
  * Versions of the readline library >= 6.3 had been changed so that
    terminal window resizes were not signalled to readline: code has
    been added using a explicit signal handler to work around that
    (when R is compiled against readline >= 6.3).  (PR#16604)
  * configure works better with Oracle Developer Studio 12.5.
  * R CMD check reports more dubious flags in files
    src/Makevars[.in], including -w and -g.
  * R CMD check has been set up to filter important warnings from
    recent versions of gfortran with -Wall -pedantic: this now
    reports non-portable GNU extensions such as out-of-order
  * R CMD config works better with paths containing spaces, even
    those of home directories (as reported by Ken Beath).
  * Use of the C/C++ macro NO_C_HEADERS is deprecated (no C headers
    are included by R headers from C++ as from R 3.3.0, so it should
    no longer be needed).
  * The check for non-portable flags in R CMD check could be stymied
    by src/Makevars files which contained targets.
  * (Windows only) When using certain desktop themes in Windows 7 or
    higher, Alt-Tab could cause Rterm to stop accepting input.
    (PR#14406; patch submitted by Jan Gleixner.)
  * pretty(d, ..) behaves better for date-time d (PR#16923).
  * When an S4 class name matches multiple classes in the S4 cache,
    perform a dynamic search in order to obey namespace imports.
    This should eliminate annoying messages about multiple hits in
    the class cache.  Also, pass along the package from the
    ClassExtends object when looking up superclasses in the cache.
  * sample(NA_real_) now works.
  * Packages using non-ASCII encodings in their code did not install
    data properly on systems using different encodings.
  * merge(df1, df2) now also works for data frames with column names
    "na.last", "decreasing", or "method".  (PR#17119)
  * contour() caused a segfault if the labels argument had length
    zero.  (Reported by Bill Dunlap.)
  * unique(warnings()) works more correctly, thanks to a new
    duplicated.warnings() method.
  * findInterval(x, vec = numeric(), all.inside = TRUE) now returns
    0s as documented.  (Reported by Bill Dunlap.)
  * (Windows only) R CMD SHLIB failed when a symbol in the resulting
    library had the same name as a keyword in the .def file.
  * pmax() and pmin() now work with (more ?)  classed objects, such
    as "Matrix" from the Matrix package, as documented for a long
  * axis(side, x = D) and hence Axis() and plot() now work correctly
    for "Date" and time objects D, even when "time goes backward",
    e.g., with decreasing xlim.  (Reported by William May.)
  * str(I(matrix(..))) now looks as always intended.
  * plot.ts(), the plot() method for time series, now respects cex,
    lwd and lty.  (Reported by Greg Werbin.)
  * parallel::mccollect() now returns a named list (as documented)
    when called with wait = FALSE.  (Reported by Michel Lang.)
  * If a package added a class to a class union in another package,
    loading the first package gave erroneous warnings about
    "undefined subclass".
  * c()'s argument use.names is documented now, as belonging to the
    (C internal) default method.  In "parallel", argument recursive
    is also moved from the generic to the default method, such that
    the formal argument list of base generic c() is just (...).
  * rbeta(4, NA) and similarly rgamma() and rnbinom() now return
    NaN's with a warning, as other r<dist>(), and as documented.
  * Using options(checkPackageLicense = TRUE) no longer requires
    acceptance of the licence for non-default standard packages such
    as compiler.  (Reported by Mikko Korpela.)
  * split(<very_long>, *) now works even when the split off parts are
    long. (PR#17139)
  * min() and max() now also work correctly when the argument list
    starts with character(0).  (PR#17160)
  * Subsetting very large matrices (prod(dim(.)) >= 2^31) now works
    thanks to Michael Schubmehl's PR#17158.
  * bartlett.test() used residual sums of squares instead of
    variances, when the argument was a list of lm objects.  (Reported
    by Jens Ledet Jensen).
  * plot(<lm>, which = *) now correctly labels the contour lines for
    the standardized residuals for which = 6.  It also takes the
    correct p in case of singularities (also for which = 5).
  * xtabs(~ exclude) no longer fails from wrong scope, thanks to
    Suharto Anggono's PR#17147.
  * Reference class calls to methods() did not re-analyse previously
    defined methods, meaning that calls to methods defined later
    would fail. (Reported by Charles Tilford).
  * findInterval(x, vec, = TRUE) misbehaved in some cases.
    (Reported by Dmitriy Chernykh.)
* Fri Jul 01 2016
- Fix typo in Group tag.
* Tue Jun 21 2016
- upstream release 3.3.1
- Most important changes
  CHANGES IN R 3.3.1:
  * R CMD INSTALL and hence install.packages() gave an internal error
    installing a package called description from a tarball on a
    case-insensitive file system.
  * match(x, t) (and hence x %in% t) failed when x was of length one,
    and either character and x and t only differed in their Encoding
    or when x and t where complex with NAs or NaNs.  (PR#16885.)
  * unloadNamespace(ns) also works again when ns is a 'namespace', as
    from getNamespace().
  * rgamma(1,Inf) or rgamma(1, 0,0) no longer give NaN but the
    correct limit.
  * length(baseenv()) is correct now.
  * pretty(d, ..) for date-time d rarely failed when "halfmonth" time
    steps were tried (PR#16923) and on 'inaccurate' platforms such as
    32-bit windows or a configuration with --disable-long-double; see
    comment #15 of PR#16761.
  * In text.default(x, y, labels), the rarely(?) used default for
    labels is now correct also for the case of a 2-column matrix x
    and missing y.
  * as.factor(c(a = 1L)) preserves names() again as in R < 3.1.0.
  * strtrim(""[0], 0[0]) now works.
  * Use of Ctrl-C to terminate a reverse incremental search started
    by Ctrl-R in the readline-based Unix terminal interface is now
    supported for readline >= 6.3 (Ctrl-G always worked).  (PR#16603)
  * diff(<difftime>) now keeps the "units" attribute, as subtraction
    already did, PR#16940.
* Wed May 18 2016
- further cleanup of spec file.
  Removed unneeded explicit Requires for
  Removed removal of backup file that was meanwhile removed upstream.
* Wed May 11 2016
- clean up of spec file after comments from  Jan Engelhardt in
  Some unneeded explicit BuildRequires removed.
Version: 3.2.5-5.1
* Fri Apr 15 2016
- CHANGES IN R 3.2.5:
    ? format.POSIXlt() behaved incorrectly in R 3.2.4.  E.g. the output
    of format(as.POSIXlt(paste0(1940:2000,"-01-01"), tz = "CET"),
    usetz = TRUE) ended in two "CEST" time formats.
    ? A typo in the Makefile for src/extra/xz prevented builds of
    liblzma.a. (Notice that this will become unbundled in 3.3.0.)
* Thu Mar 17 2016
- upstrem releases minorst bug fix release
  NEWS: The 3.2.4 release had two annoyances which we would rather
  not have in an "ultra-stable" release, designed to hang around
  for the duration of the 3.3 series. One was a relatively minor
  Makefile issue affecting system using R's bundled lzma library.
  The other, rather more serious, affected printing and formatting
  of POSIXlt objects, which would unpredictably get the Daylight
  Savings Time wrong.
* Fri Mar 11 2016
- Some version numbers of recommended packages corrected
* Fri Mar 11 2016
- Release numbers for sub-packages improved
* Fri Mar 11 2016
- added MakefileTypo.patch to enable building for 12.2
  was a one charcter show stopper
* Thu Mar 10 2016
- upstream release 3.2.4, only minor improvements
  CHANGES IN R 3.2.4:
    ? install.packages() and related functions now give a more
    informative warning when an attempt is made to install a base
    ? summary(x) now prints with less rounding when x contains infinite
    values. (Request of PR#16620.)
    ? provideDimnames() gets an optional unique argument.
    ? shQuote() gains type = "cmd2" for quoting in cmd.exe in Windows.
    (Response to PR#16636.)
    ? The data.frame method of rbind() gains an optional argument
    stringsAsFactors (instead of only depending on
    ? smooth(x, *) now also works for long vectors.
    ? tools::texi2dvi() has a workaround for problems with the texi2dvi
    script supplied by texinfo 6.1.
    It extracts more error messages from the LaTeX logs when in
    emulation mode.
    ? R CMD check will leave a log file build_vignettes.log from the
    re-building of vignettes in the .Rcheck directory if there is a
    problem, and always if environment variable
    _R_CHECK_ALWAYS_LOG_VIGNETTE_OUTPUT_ is set to a true value.
    ? Use of SUPPORT_OPENMP from header Rconfig.h is deprecated in
    favour of the standard OpenMP define _OPENMP.
    (This has been the recommendation in the manual for a while now.)
    ? The make macro AWK which is long unused by R itself but recorded
    in file etc/Makeconf is deprecated and will be removed in R
    ? The C header file S.h is no longer documented: its use should be
    replaced by R.h.
* Mon Mar 07 2016
- The big split up. What was a monolithic R-base*rpm now is
  divided over 30 something packages, with the following layout.
  R-base-3.2.3: dummy packages, contains all of R
  Use R-base, if you donĀ“t have a good understandig what it means
  to install only parts of it!
  R-base-devel-3.2.3: dummy, contains R-core-devel
  R-core-3.2.3: R core, no packages at all
  R-core-devel-3.2.3: devel files
  R-core-libs-3.2.3: contains Rlib
  R-core-doc-3.2.3: all the documentation of R-core
  R-core-packages-3.2.3: dummy package to load all core packages, that are
  Each of these packages may be installed alone.
  R-recommended-packages-3.2.3: dummy package to load all recommeded
    packages, that are
    R-Matrix-1.2.3, R-Matrix-devel-1.2.3,
  Each of these packages may be installed alone.
* Fri Dec 11 2015
- Upstream release R-3.2.3
  CHANGES IN R 3.2.3:
  * Some recently-added Windows time zone names have been added to
    the conversion table used to convert these to Olson names.
    (Including those relating to changes for Russia in Oct 2014, as
    in PR#16503.)
  * (Windows) Compatibility information has been added to the
    manifests for Rgui.exe, Rterm.exe and Rscript.exe.  This should
    allow win.version() and to report the actual Windows
    version up to Windows 10.
  * Windows "wininet" FTP first tries EPSV / PASV mode rather than
    only using active mode (reported by Dan Tenenbaum).
  * which.min(x) and which.max(x) may be much faster for logical and
    integer x and now also work for long vectors.
  * The 'emulation' part of tools::texi2dvi() has been somewhat
    enhanced, including supporting quiet = TRUE.  It can be selected
    by texi2dvi = "emulation".
    (Windows) MiKTeX removed its texi2dvi.exe command in Sept 2015:
    tools::texi2dvi() tries texify.exe if it is not found.
  * (Windows only) Shortcuts for printing and saving have been added
    to menus in Rgui.exe.  (Request of PR#16572.)
  * loess(..., iterTrace=TRUE) now provides diagnostics for
    robustness iterations, and the print() method for
    summary(<loess>) shows slightly more.
  * The included version of PCRE has been updated to 8.38, a bug-fix
  * View() now displays nested data frames in a more friendly way.
    (Request with patch in PR#15915.)
  * The included configuration code for libintl has been updated to
    that from gettext version - this should only affect how
    an external library is detected (and the only known instance is
    under OpenBSD).  (Wish of PR#16464.)
  * configure has a new argument --disable-java to disable the checks
    for Java.
  * The configure default for MAIN_LDFLAGS has been changed for the
    FreeBSD, NetBSD and Hurd OSes to one more likely to work with
    compilers other than gcc (FreeBSD 10 defaults to clang).
  * configure now supports the OpenMP flags -fopenmp=libomp (clang)
    and -qopenmp (Intel C).
  * Various macros can be set to override the default behaviour of
    configure when detecting OpenMP: see file
  * Source installation on Windows has been modified to allow for
    MiKTeX installations without texi2dvi.exe.  See file
  * regexpr(pat, x, perl = TRUE) with Python-style named capture did
    not work correctly when x contained NA strings.  (PR#16484)
  * The description of dataset ToothGrowth has been
    improved/corrected.  (PR#15953)
  * model.tables(type = "means") and hence TukeyHSD() now support
    "aov" fits without an intercept term.  (PR#16437)
  * close() now reports the status of a pipe() connection opened with
    an explicit open argument.  (PR#16481)
  * Coercing a list without names to a data frame is faster if the
    elements are very long. (PR#16467)
  * (Unix-only) Under some rare circumstances piping the output from
    Rscript or R -f could result in attempting to close the input
    file twice, possibly crashing the process.  (PR#16500)
  * (Windows) was out of step with win.version() and did
    not report Windows 8.
  * topenv(baseenv()) returns baseenv() again as in R 3.1.0 and
    earlier.  This also fixes compilerJIT(3) when used in .Rprofile.
  * detach()ing the methods package keeps .isMethodsDispatchOn()
    true, as long as the methods namespace is not unloaded.
  * Removed some spurious warnings from configure about the
    preprocessor not finding header files.  (PR#15989)
  * rchisq(*, df=0, ncp=0) now returns 0 instead of NaN, and
    dchisq(*, df=0, ncp=*) also no longer returns NaN in limit cases
    (where the limit is unique).  (PR#16521)
  * pchisq(*, df=0, ncp > 0, log.p=TRUE) no longer underflows (for
    ncp > ~60).
  * nchar(x, "w") returned -1 for characters it did not know about
    (e.g. zero-width spaces): it now assumes 1.  It now knows about
    most zero-width characters and a few more double-width
  * Help for which.min() is now more precise about behavior with
    logical arguments.  (PR#16532)
  * The print width of character strings marked as "latin1" or
    "bytes" was in some cases computed incorrectly.
  * abbreviate() did not give names to the return value if minlength
    was zero, unlike when it was positive.
  * (Windows only) dir.create() did not always warn when it failed to
    create a directory.  (PR#16537)
  * When operating in a non-UTF-8 multibyte locale (e.g. an East
    Asian locale on Windows), grep() and related functions did not
    handle UTF-8 strings properly.  (PR#16264)
  * read.dcf() sometimes misread lines longer than 8191 characters.
    (Reported by Herv'e Pag`es with a patch.)
  * within(df, ..) no longer drops columns whose name start with a
  * The built-in HTTP server converted entire Content-Type to
    lowercase including parameters which can cause issues for
    multi-part form boundaries (PR#16541).
  * Modifying slots of S4 objects could fail when the methods package
    was not attached. (PR#16545)
  * splineDesign(*, outer.ok=TRUE) (splines) is better now
    (PR#16549), and interpSpline() now allows sparse=TRUE for speedup
    with non-small sizes.
  * If the expression in the traceback was too long, traceback() did
    not report the source line number.  (Patch by Kirill M"uller.)
  * The browser did not truncate the display of the function when
    exiting with options("deparse.max.lines") set.  (PR#16581)
  * When bs(*, Boundary.knots=) had boundary knots inside the data
    range, extrapolation was somewhat off.  (Patch by Trevor Hastie.)
  * var() and hence sd() warn about factor arguments which are
    deprecated now. (PR#16564)
  * loess(*, weights = *) stored wrong weights and hence gave
    slightly wrong predictions for newdata.  (PR#16587)
  * aperm(a, *) now preserves names(dim(a)).
  * poly(x, ..) now works when either raw=TRUE or coef is specified.
  * data(package=*) is more careful in determining the path.
  * prettyNum(*, decimal.mark, big.mark): fixed bug introduced when
    fixing PR#16411.
* Thu Dec 10 2015
- Reverse the whole split. Back to the big package.
  Had user reports of broken installations.
  R-base, R-base-devel and R-base-libs are provided for now.
  The big split will come for 3.3.0
* Wed Dec 09 2015
- R-base was changed from a giant monolith to thirty-some packages.
  There were requests to use the libs without the interpreter.
  Furthermore it is now possible to use a frugal installation of R.
  The following binaries are built now:
  R-base-3.2.2-5.1.x86_64.rpm : A Meta-package. Use this, and it looks
    just like it looked the last 10 years.
  Requires base and recommended packages.
  R-base-devel-3.2.2-5.1.x86_64.rpm: Just for backward compatibility.
  R-core-devel-3.2.2-5.1.x86_64.rpm : The R-core packages install
    a bare-bones R. No packages inculded.
  R-tools-3.2.2-5.1.x86_64.rpm : All the base packages.
  R-recommended-3.2.2-5.1.x86_64.rpm : A meta-package including all
    recommended packages.
  R-spatial-7.3.10-5.1.x86_64.rpm : All recommended packaged.
    Note: They now have their own version
  numbers, so it should be much easier to
  use newer Versions of the recommended
  And the source RPM for all the above.
* Wed Aug 19 2015
- Disable building man files for openSUSE:42.
* Mon Aug 17 2015
- Upstream release 3.2.2
- Most important
  CHANGES IN R 3.2.2:
  * It is now easier to use secure downloads from https:// URLs on
    builds which support them: no longer do non-default options need
    to be selected to do so.  In particular, packages can be
    installed from repositories which offer https:// URLs, and those
    listed by setRepositories() now do so (for some of their
    Support for https:// URLs is available on Windows, and on other
    platforms if support for libcurl was compiled in and if that
    supports the https protocol (system installations can be expected
    to do).  So https:// support can be expected except on rather old
    OSes (an example being OS X 'Snow Leopard', where a non-system
    version of libcurl can be used).
    (Windows only) The default method for accessing URLs _via_
    download.file() and url() has been changed to be "wininet" using
    Windows API calls.  This changes the way proxies need to be set
    and security settings made: there have been some reports of sites
    being inaccessible under the new default method (but the previous
    methods remain available).
  * cmdscale() gets new option list. for increased flexibility when a
    list should be returned.
  * configure now supports texinfo version 6.0, which (unlike the
    change from 4.x to 5.0) is a minor update.  (Wish of PR#16456.)
  * (Non-Windows only) download.file() with default method = "auto"
    now chooses "libcurl" if that is available and a https:// or
    ftps:// URL is used.
  * (Windows only) setInternet2(TRUE) is now the default.  The
    command-line option --internet2 and environment variable
    R_WIN_INTERNET2 are now ignored.
    Thus by default the "internal" method for download.file() and
    url() uses the "wininet" method: to revert to the previous
    default use setInternet2(FALSE).
    This means that https:// can be read by default by
    download.file() (they have been readable by file() and url()
    since R 3.2.0).
    There are implications for how proxies need to be set (see
    ?download.file): also, cacheOK = FALSE is not supported.
  * chooseCRANmirror() and chooseBioCmirror() now offer HTTPS mirrors
    in preference to HTTP mirrors.  This changes the interpretation
    of their ind arguments: see their help pages.
  * capture.output() gets optional arguments type and split to pass
    to sink(), and hence can be used to capture messages.
  * Header Rconfig.h now defines HAVE_ALLOCA_H if the platform has
    the alloca.h header (it is needed to define alloca on Solaris and
    AIX, at least: see 'Writing R Extensions' for how to use it).
  * The libtool script generated by configure has been modified to
    support FreeBSD >= 10 (PR#16410).
  * The HTML help page links to demo code failed due to a change in R
    3.2.0.  (PR#16432)
  * If the na.action argument was used in model.frame(), the original
    data could be modified. (PR#16436)
  * getGraphicsEvent() could cause a crash if a graphics window was
    closed while it was in use. (PR#16438)
  * matrix(x, nr, nc, byrow = TRUE) failed if x was an object of type
  * strptime() could overflow the allocated storage on the C stack
    when the timezone had a non-standard format much longer than the
    standard formats. (Part of PR#16328.)
  * options(OutDec = s) now signals a warning (which will become an
    error in the future) when s is not a string with exactly one
    character, as that has been a documented requirement.
  * prettyNum() gains a new option input.d.mark which together with
    other changes, e.g., the default for decimal.mark, fixes some
    format()ting variants with non-default getOption("OutDec") such
    as in PR#16411.
  * download.packages() failed for type equal to either "both" or
    "binary".  (Reported by Dan Tenenbaum.)
  * The dendrogram method of labels() is much more efficient for
    large dendrograms, now using rapply().  (Comment #15 of PR#15215)
  * The "port" algorithm of nls() could give spurious errors.
    (Reported by Radford Neal.)
  * Reference classes that inherited from reference classes in
    another package could invalidate methods of the inherited class.
    Fixing this requires adding the ability for methods to be
    "external", with the object supplied explicitly as the first
    argument, named .self. See "Inter-Package Superclasses" in the
  * readBin() could fail on the SPARC architecture due to alignment
    issues.  (Reported by Radford Neal.)
  * qt(*, df=Inf, ncp=.) now uses the natural qnorm() limit instead
    of returning NaN. (PR#16475)
  * Auto-printing of S3 and S4 values now searches for print() in the
    base namespace and show() in the methods namespace instead of
    searching the global environment.
  * polym() gains a coefs = NULL argument and returns class "poly"
    just like poly() which gets a new simple=FALSE option.  They now
    lead to correct predict()ions, e.g., on subsets of the original
  * rhyper(nn, <large>) now works correctly. (PR#16489)
  * ttkimage() did not (and could not) work so was removed. Ditto for
    tkimage.cget() and tkimage.configure(). Added two Ttk widgets and
    missing subcommands for Tk's image command: ttkscale(),
    ttkspinbox(), tkimage.delete(), tkimage.height(),
    tkimage.inuse(), tkimage.type(), tkimage.types(),
    tkimage.width(). (PR#15372, PR#16450)
  * getClass("foo") now also returns a class definition when it is
    found in the cache more than once.
* Thu Jun 18 2015
- Upstream release 3.2.1
- Improvement of build: include libcurl and texlive-dvips/
- Most important
  CHANGES IN R 3.2.1:
  * utf8ToInt() now checks that its input is valid UTF-8 and returns
    NA if it is not.
  * install.packages() now allows type = "both" with repos = NULL if
    it can infer the type of file.
  * nchar(x, *) and nzchar(x) gain a new argument keepNA which
    governs how the result for NAs in x is determined.  For the R
    3.2.x series, the default remains FALSE which is fully back
    compatible.  From R 3.3.0, the default will change to keepNA = NA
    and you are advised to consider this for code portability.
  * news() more flexibly extracts dates from package NEWS.Rd files.
  * lengths(x) now also works (trivially) for atomic x and hence can
    be used more generally as an efficient replacement of sapply(x,
    length) and similar.
  * The included version of PCRE has been updated to 8.37, a bug-fix
  * diag() no longer duplicates a matrix when extracting its
  * as.character.srcref() gains an argument to allow characters
    corresponding to a range of source references to be extracted.
  * acf() and ccf() now guarantee values strictly in [-1,1] (instead
    of sometimes very slightly outside). PR#15832.
  * as.integer("111111111111") now gives NA (with a warning) as it
    does for the corresponding numeric or negative number coercions.
    Further, as.integer(M + 0.1) now gives M (instead of NA) when M
    is the maximal representable integer.
  * On some platforms nchar(x, "c") and nchar(x, "w") would return
    values (possibly NA) for inputs which were declared to be UTF-8
    but were not, or for invalid strings without a marked encoding in
    a multi-byte locale, rather than give an error.  Additional
    checks have been added to mitigate this.
  * apply(a, M, function(u) c(X = ., Y = .)) again has dimnames
    containing "X" and "Y" (as in R < 3.2.0).
  * (Windows only) In some cases, the --clean option to R CMD INSTALL
    could fail.  (PR#16178)
  * (Windows only) choose.files() would occasionally include
    characters from the result of an earlier call in the result of a
    later one.  (PR#16270)
  * A change in RSiteSearch() in R 3.2.0 caused it to submit invalid
    URLs.  (PR#16329)
  * Rscript and command line R silently ignored incomplete statements
    at the end of a script; now they are reported as parse errors.
  * Parse data for very long strings was not stored.  (PR#16354)
  * plotNode(), the workhorse of the plot method for "dendrogram"s is
    no longer recursive, thanks to Suharto Anggono, and hence also
    works for deeply nested dendrograms.  (PR#15215)
  * The parser could overflow internally when given numbers in
    scientific format with extremely large exponents.  (PR#16358)
  * If the CRAN mirror was not set, install.packages(type = "both")
    and related functions could repeatedly query the user for it.
    (Part of PR#16362)
  * The low-level functions .rowSums() etc. did not check the length
    of their argument, so could segfault. (PR#16367)
  * The quietly argument of library() is now correctly propagated
    from .getRequiredPackages2().
  * Under some circumstances using the internal PCRE when building R
    fron source would cause external libs such as -llzma to be
    omitted from the main link.
  * The .Primitive default methods of the logic operators, i.e., !, &
    and |, now give correct error messages when appropriate, e.g.,
    for `&`(TRUE) or `!`().  (PR#16385)
  * cummax(x) now correctly propagates NAs also when x is of type
    integer and begins with an NA.
  * summaryRprof() could fail when the profile contained only two
    records.  (PR#16395)
  * HTML vignettes opened using vignette() did not support links into
    the rest of the HTML help system.  (Links worked properly when
    the vignette was opened using browseVignettes() or from within
    the help system.)
  * arima(*, xreg = .) (for d >= 1) computes estimated variances
    based on a the number of effective observations as in R version
    3.0.1 and earlier.  (PR#16278)
  * slotNames(.) is now correct for "signature" objects (mostly used
    internally in methods).
  * On some systems, the first string comparison after a locale
    change would result in NA.
* Thu Apr 16 2015
- Upstream release 3.2.0
- Most important
  CHANGES IN 3.2.0:
  * anyNA() gains a recursive argument.
  * When x is missing and names is not false (including the default
    value), Sys.getenv(x, names) returns an object of class "Dlist"
    and hence prints tidily.
  * (Windows.)  shell() no longer consults the environment variable
    SHELL: too many systems have been encountered where it was set
    incorrectly (usually to a path where software was compiled, not
    where it was installed).  R_SHELL, the preferred way to select a
    non-default shell, can be used instead.
  * Some unusual arguments to embedFonts() can now be specified as
    character vectors, and the defaults have been changed
  * Functions in the Summary group duplicate less.  (PR#15798)
  * (Unix-alikes.) system(cmd, input = ) now uses
    'shell-execution-environment' redirection, which will be more
    natural if cmd is not a single command (but requires a
    POSIX-compliant shell). (Wish of PR#15508)
  * read.fwf() and read.DIF() gain a fileEncoding argument, for
  * Graphics devices can add attributes to their description in
    .Device and .Devices.  Several of those included with R use a
    "filepath" attribute.
  * pmatch() uses hashing in more cases and so is faster at the
    expense of using more memory. (PR#15697)
  * pairs() gains new arguments to select sets of variables to be
    plotted against each other.
  *, extra_cols = FALSE) allows a minimal set of columns
    to be computed on Unix-alikes: on some systems without
    properly-configured caching this can be significantly faster with
    large file lists.
  * New function dir.exists() in package base to test efficiently
    whether one or more paths exist and are directories.
  * dput() and friends gain new controls hexNumeric and digits17
    which output double and complex quantities as, respectively,
    binary fractions (exactly, see sprintf("%a")) and as decimals
    with up to 17 significant digits.
  * save(), saveRDS() and serialize() now support ascii = NA which
    writes ASCII files using sprintf("%a") for double/complex
    quantities.  This is read-compatible with ascii = TRUE but avoids
    binary->decimal->binary conversions with potential loss of
    precision.  Unfortunately the Windows C runtime's lack of C99
    compliance means that the format cannot be read correctly there
    in R before 3.1.2.
  * The default for formatC(decimal.mark =) has been changed to be
    getOption("OutDec"); this makes it more consistent with format()
    and suitable for use in print methods, e.g. those for classes
    "density", "ecdf", "stepfun" and "summary.lm".
    getOption("OutDec") is now consulted by the print method for
    class "kmeans", by cut(), dendrogram(), plot.ts() and quantile()
    when constructing labels and for the report from legend(trace =
    (In part, wish of PR#15819.)
  * printNum() and hence format() and formatC() give a warning if
    big.mark and decimal.mark are set to the same value (period and
    comma are not uncommonly used for each, and this is a check that
    conventions have not got mixed).
  * merge() can create a result which uses long vectors on 64-bit
  * dget() gains a new argument keep.source which defaults to FALSE
    for speed (dput() and dget() are most often used for data objects
    where this can make dget() many times faster).
  * Packages may now use a file of common macro definitions in their
    help files, and may import definitions from other packages.
  * A number of macros have been added in the new share/Rd directory
    for use in package overview help pages, and promptPackage() now
    makes use of them.
  * tools::parse_Rd() gains a new permissive argument which converts
    unrecognized macros into text.  This is used by
    utils:::format.bibentry to allow LaTeX markup to be ignored.
  * options(OutDec =) can now specify a multi-byte character, e.g.,
    options(OutDec = "\u00b7") in a UTF-8 locale.
  * is.recursive(x) is no longer true when x is an external pointer,
    a weak reference or byte code; the first enables all.equal(x, x)
    when x <- getClass(.).
  * ls() (aka objects()) and as.list.environment() gain a new
    argument sorted.
  * The "source" attribute (which has not been added to functions by
    R since before R version 2.14.0) is no longer treated as special.
  * Function returnValue() has been added to give on.exit() code
    access to a function's return value for debugging purposes.
  * crossprod(x, y) allows more matrix coercions when x or y are
    vectors, now equalling t(x) %*% y in these cases (also reported
    by Radford Neal).  Similarly, tcrossprod(x,y) and %*% work in
    more cases with vector arguments.
  * Utility function dynGet() useful for detecting cycles, aka
    infinite recursions.
  * The byte-code compiler and interpreter include new instructions
    that allow many scalar subsetting and assignment and scalar
    arithmetic operations to be handled more efficiently. This can
    result in significant performance improvements in scalar
    numerical code.
  * apply(m, 2, identity) is now the same as the matrix m when it has
    _named_ row names.
  * A new function debuggingState() has been added, allowing to
    temporarily turn off debugging.
  * example() gets a new optional argument run.donttest and
    tools::Rd2ex() a corresponding commentDonttest, with a default
    such that example(..) in help examples will run \donttest code
    only if used interactively (a change in behaviour).
  * gains an optional argument make.row.names, for
    potential speedup.
  * New function extSoftVersion() to report on the versions of
    third-party software in use in this session.  Currently reports
    versions of zlib, bzlib, the liblzma from xz, PCRE, ICU, TRE and
    the iconv implementation.
    A similar function grSoftVersion() in package grDevices reports
    on third-party graphics software.
    Function tcltk::tclVersion() reports the Tcl/Tk version.
  * Calling callGeneric() without arguments now works with primitive
    generics to some extent.
  * vapply(x, FUN, FUN.VALUE) is more efficient notably for large
    length(FUN.VALUE); as extension of PR#16061.
  * as.table() now allows tables with one or more dimensions of
    length 0 (such as as.table(integer())).
  * names(x) <- NULL now clears the names of call and ... objects.
  * library() will report a warning when an insufficient dependency
    version is masking a sufficient one later on the library search
  * A new plot() method for class "raster" has been added.
  * New check_packages_in_dir_changes() function in package tools for
    conveniently analyzing how changing sources impacts the check
    results of their reverse dependencies.
  * Speed-up from Peter Haverty for ls() and
    methods:::.requirePackage() speeding up package loading.
  * New get0() function, combining exists() and get() in one call,
    for efficiency.
  * gains an envir argument for specifying the
    environment from which to retrieve the ... in the call, if any;
    this environment was wrong (or at least undesirable) when the
    definition argument was a function.
  * topenv() has been made .Internal() for speedup, based on Peter
    Haverty's proposal in PR#16140.
  * getOption() no longer calls options() in the main case.
  * Optional use of libcurl (version 7.28.0 from Oct 2012 or later)
    for Internet access:
  * capabilities("libcurl") reports if this is available.
  * libcurlVersion() reports the version in use, and other
    details of the "libcurl" build including which URL schemes it
  * curlGetHeaders() retrieves the headers for http://, https://,
    ftp:// and ftps:// URLs: analysis of these headers can
    provide insights into the `existence' of a URL (it might for
    example be permanently redirected) and is so used in R CMD
    check --as-cran.
  * download.file() has a new optional method "libcurl" which
    will handle more URL schemes, follow redirections, and allows
    simultaneous downloads of multiple URLs.
  * url() has a new method "libcurl" which handles more URL
    schemes and follows redirections.  The default method is
    controlled by a new option url.method, which applies also to
    the opening of URLs _via_ file() (which happens implicitly in
    functions such as read.table.)
  * When file() or url() is invoked with a https:// or ftps://
    URL which the current method cannot handle, it switches to a
    suitable method if one is available.
  * (Windows.) The DLLs internet.dll and internet2.dll have been
    merged.  In this version it is safe to switch (repeatedly)
    between the internal and Windows internet functions within an R
    The Windows internet functions are still selected by flag
  - -internet2 or setInternet2().  This can be overridden for an
    url() connection _via_ its new method argument.
    download.file() has new method "wininet", selected as the default
    by --internet2 or setInternet2().
  * parent.env<- can no longer modify the parent of a locked
    namespace or namespace imports environment.  Contributed by Karl
  * New function isLoadedNamespace() for readability and speed.
  * names(env) now returns all the object names of an environment
    env, equivalently to ls(env, all.names = TRUE, sorted = FALSE)
    and also to the names of the corresponding list,
    names(as.list(env, all.names = TRUE)).  Note that although
    names() returns a character vector, the names have no particular
  * The memory manager now grows the heap more aggressively. This
    reduces the number of garbage collections, in particular while
    data or code are loaded, at the expense of slightly increasing
    the memory footprint.
  * New function trimws() for removing leading/trailing whitespace.
  * cbind() and rbind() now consider S4 inheritance during S3
    dispatch and also obey deparse.level.
  * cbind() and rbind() will delegate recursively to methods::cbind2
    (methods::rbind2) when at least one argument is an S4 object and
    S3 dispatch fails (due to ambiguity).
  * (Windows.)  download.file(quiet = FALSE) now uses text rather
    than Windows progress bars in non-interactive use.
  * New function hsearch_db() in package utils for building and
    retrieving the help search database used by, along
    with functions for inspecting the concepts and keywords in the
    help search database.
  * New function .getNamespaceInfo(), a no-check version of
    getNamespaceInfo() mostly for internal speedups.
  * The help search system now takes \keyword entries in Rd files
    which are not standard keywords (as given in KEYWORDS in the R
    documentation directory) as concepts.  For standard keyword
    entries the corresponding descriptions are additionally taken as
  * New lengths() function for getting the lengths of all elements in
    a list.
  * New function toTitleCase() in package tools, tailored to package
  * The matrix methods of cbind() and rbind() allow matrices as
    inputs which have 2^31 or more elements.  (For cbind(), wish of
  * The default method of image() has an explicit check for a numeric
    or logical matrix (which was always required).
  * URLencode() will not by default encode further URLs which appear
    to be already encoded.
  * BIC(mod) and BIC(mod, mod2) now give non-NA numbers for arima()
    fitted models, as nobs(mod) now gives the number of "used"
    observations for such models.  This fixes PR#16198, quite
    differently than proposed there.
  * The print() methods for "htest", "pairwise.htest" and
    "power.htest" objects now have a digits argument defaulting to (a
    function of) getOption("digits"), and influencing all printed
    numbers coherently.  Unavoidably, this changes the display of
    such test results in some cases.
  * Code completion for namespaces now recognizes all loaded
    namespaces, rather than only the ones that are also attached.
  * The code completion mechanism can now be replaced by a
    user-specified completer function, for (temporary) situations
    where the usual code completion is inappropriate.
  * unzip() will now warn if it is able to detect truncation when
    unpacking a file of 4GB or more (related to PR#16243).
  * methods() reports S4 in addition to S3 methods; output is
    simplified when the class argument is used.  .S3methods() and
    methods::.S4methods() report S3 and S4 methods separately.
  * Higher order functions such as the apply functions and Reduce()
    now force arguments to the functions they apply in order to
    eliminate undesirable interactions between lazy evaluation and
    variable capture in closures.  This resolves PR#16093.
  * The \donttest sections of R's help files can be tested by
    make check TEST_DONTTEST=TRUE .
  * It is possible to request the use of system valgrind headers
    _via_ configure option --with-system-valgrind-headers: note the
    possible future incompatibility of such headers discussed in the
    'R Installation and Administration' manual. (Wish of PR#16068.)
  * The included version of liblzma has been updated to xz-utils
    5.0.7 (minor bug fixes from 5.0.5).
  * configure options --with-system-zlib, --with-system-bzlib and
  - -with-system-pcre are now the default.  For the time being there
    is fallback to the versions included in the R sources if no
    system versions are found or (unlikely) if they are too old.
    Linux users should check that the -devel or -dev versions of
    packages zlib, bzip2/libbz2 and pcre as well as
    xz-devel/liblzma-dev (or similar names) are installed.
  * configure by default looks for the texi2any script from texinfo
    5.1 or later, rather than the makeinfo program.  (makeinfo is a
    link to the Perl script texi2any in texinfo 5.x.)
  * R CMD INSTALL gains an option --built-timestamp=STAMP allowing
    100% reproducible package building, thanks to Dirk Eddelbuettel.
  * There is support for testing the \dontrun and \donttest parts of
    examples in packages.
    tools::testInstalledPackage() accepts new arguments
    commentDontrun = FALSE and commentDonttest = FALSE.
    R CMD check gains options --run-dontrun and --run-donttest.
  * The HTML generated by tools::Rd2HTML() and tools::toHTML()
    methods is now 'XHTML 1.0 Strict'.
  * The compiler package's utility function setCompilerOptions() now
    returns the old values invisibly. The initial optimization level
    can also be set with the environment variable
  * R CMD build adds a NeedsCompilation field if one is not already
    present in the DESCRIPTION file.
  * R CMD check gains option --test-dir to specify an alternative set
    of tests to run.
  * R CMD check will now by default continue with testing after many
    types of errors, and will output a summary count of errors at the
    end if any have occurred.
  * R CMD check now checks that the Title and Description fields are
    correctly terminated.
  * R CMD check --as-cran now:
  * checks a file can be processed: this needs pandoc
  * checks the existence and accessibility of URLs in the
    DESCRIPTION, CITATION, NEWS.Rd and files and in the
    help files (provided the build has libcurl support).
  * reports non-ASCII characters in R source files when there is
    no package encoding declared in the DESCRIPTION file.
  * reports (apparent) S3 methods exported but not registered.
  * reports overwriting registered S3 methods from
    base/recommended packages.  (Such methods are replaced in the
    affected package for the rest of the session, even if the
    replacing namespace is unloaded.)
  * reports if the Title field does not appear to be in title
    case (see 'Writing R Extensions': there may be false
    positives, but note that technical words should be
    single-quoted and will then be accepted).
    Most of these checks can also be selected by environment
    variables: see the 'R Internals' manual.
  * New C API utility logspace_sum(logx[], n).
  * Entry points rbinom_mu, rnbinom_mu and rmultinom are remapped (by
    default) to Rf_rbinom_mu etc.  This requires packages using them
    to be re-installed.
  * .C(DUP = FALSE) and .Fortran(DUP = FALSE) are now ignored, so
    arguments are duplicated if DUP = TRUE would do so.  As their
    help has long said, .Call() is much preferred.
  * New entry point R_allocLD, like R_alloc but guaranteed to have
    sufficient alignment for long double pointers.
  * isPairList() now returns TRUE for DOTSXP.
  A number of changes to the Windows build system are in development.
  The following are currently in place.
  * Installation using external binary distributions of zlib, bzip2,
    liblzma, pcre, libpng, jpeglib and libtiff is now required, and
    the build instructions have been revised.
  * A new make target rsync-extsoft has been added to obtain copies
    of the external libraries from CRAN.
  * Building the manuals now requires texi2any from texinfo 5.1 or
    later.  CRAN binary builds include the manuals, but by default
    builds from source will not, and they will be accessed from CRAN.
    See the comments in src/gnuwin32/MkRules.dist for how to specify
    the location of texi2any.
  * (Windows) Changes have been made to support an experimental
    Windows toolchain based on GCC 4.9.2.  The default toolchain
    continues to be based on GCC 4.6.3, as the new toolchain is not
    yet stable enough.  A change to a new toolchain is expected
    during the R 3.2.x lifetime.
  * (Windows) The use of macro ZLIB_LIBS in file src/
    (which has not been documented for a long time) now requires an
    external libz.a to be available (it is part of the 'goodies' used
    to compile Windows binary packages).  It would be simpler to use
  - lz instead.
  * The default for option pkgType on platforms using binary packages
    is now "both", so source packages will be tried if binary
    versions are not available or not up to date.
    There are options for what install.packages(type = "both")
    (possibly called _via_ update.packages()) will do if compilation
    of a source package is desirable: see ?options (under utils).
    If you intend not to accept updates as source packages, you
    should use update.packages(type = "binary").
  * download.file(method = "lynx") is defunct.
  * Building R using the included versions of zlib, bzip2, xz and
    PCRE is deprecated: these are frozen (bar essential bug-fixes)
    and will be removed for R 3.3.0.
  * The configure option --with-valgrind-instrumentation=3 has been
    withdrawn, as it did not work with recent valgrind headers: it is
    now treated as level 2.
  * The MethodsList class in package methods had been deprecated in R
    2.11.0 and is defunct now.  Functions using it are defunct if
    they had been deprecated in R 2.11.0, and are deprecated now,
  * Fixed two obscure bugs in pairlist subassignment, reported by
    Radford Neal as part of pqR issue 16.
  * Fixes for bugs in handling empty arguments and argument matching
    by name in log().
  * all.equal() gains methods for environments and refClasses.
  * [<- and [[<- gain S4 data.frame methods to avoid corruption of S4
    class information by the S3 methods.
  * callNextMethod() should now work within a .local call when ... is
    absent from formals(.local).
  * dput(pairlist(x)) generates a call to the pairlist constructor
    instead of the list constructor.
  * Fix missing() when arguments are propagated through ... .
  * eigen(m) now defaults to symmetric = TRUE even when the dimnames
    are asymmetric if the matrix is otherwise symmetric.  (PR#16151)
  * Fix issues with forwarding ... through callGeneric() and
    callNextMethod().  (PR#16141)
  * callGeneric() now works after a callNextMethod().
  * Subclass information is kept consistent when replacing an
    ordinary S4 class with an "old class" _via_ the S4Class argument
    to setOldClass(). Thus, for example, a data.frame is valid for a
    list argument in the signature, and a factor is valid for vector
  * In qbeta() the inversion of pbeta() is much more sophisticated.
    This works better in corner cases some of which failed completely
    previously (PR#15755), or were using too many iterations.
  * Auto-printing no longer duplicates objects when printing is
    dispatched to a method.
  * kmeans(x, k) would fail when nrow(x) >= 42949673.  (Comment 6 of
  * 'Abbreviated' locale-specific day and month names could have been
    truncated in those rare locales where there are the same as the
    full names.
  * An irrelevant warning message from updating subclass information
    was silenced (the namespace would not be writable in this case).
* Mon Mar 09 2015
- Upstream release 3.1.3
- Most important
  CHANGES IN R 3.1.3:
  * 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 < 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
  * model.frame() (used by lm() and many other modelling functions)
    now warns when it drops contrasts from factors.  (Wish of
  * 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.
  * 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.
  * 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.
  * The configure option --with-valgrind-instrumentation=3 is
    deprecated and will be removed in R 3.2.0.
  * (Windows.) Rscript.exe was missing a manifest specifying the
    modern style for common controls (e.g., the download progress
  * 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.
  * abs() failed with named arguments when the argument was complex.
  * "noquote" objects may now be used as columns in dataframes.
  * Some values with extremely long names were printed incorrectly.
  * 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.
  * 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) <- "" (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
  * Port Tomas Kalibera's fix from R-devel that restores the
    loadMethod() fast path, effectively doubling the speed of S4
  * 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.
  * 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.
  * 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) <- 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.
* Fri Dec 12 2014
- Remove tex(inconsolata.sty) BuildRequires for SLE_12 builds (like
  older SLE releases).
* Fri Oct 31 2014
- Upstream release 3.1.2
- Most important
  CHANGES IN R 3.1.2:
  * 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, <URL:>, 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
  * 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
  * 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
  * (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
  * 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.
  * 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
  * 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.
  * 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
    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".
  * 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.
  * options(list()) now works (trivially). (PR#15979)
  * merge(<dendrogram>, ..) 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.
  * 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.
  * 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).
  * Adjust X11 auto-launch detection in DISPLAY on OS X to recognize
    latest XQuartz.
* Thu Jul 10 2014
- Added Provides: R-parallel
- Upstream release 3.1.1
- Most impotant
  CHANGES IN R 3.1.1:
  CHANGES IN R 3.1.1:
  * 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  The
    new option = TRUE) replaces the RStudio
    override by the default device as selected by R itself, still
    respecting environment variables R_INTERACTIVE_DEVICE and
  * 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).
  * 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'.
  * dbinom(x, n), pbinom(), dpois(), etc, are slightly less
    restrictive in checking if n is integer-valued.  (Wish of
  * pchisq(x, df, ncp, log.p = TRUE) is more accurate and no longer
    underflows for small x and ncp < 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.
  * Sweave() mis-parsed Sexpr expressions that contained backslashes.
  * 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 = <large>, 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
  * 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).
  * 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
  * 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)
* Fri Jun 20 2014
- added parallel provides
* Fri May 09 2014
- Removed / commented out symlink to %{_bindir}/r
  new package 'littler' should be used instead for packages
  that need /usr/bin/r