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R-core-libs-3.5.0-bp153.1.380 RPM for x86_64

From OpenSuSE Leap 15.3 for x86_64

Name: R-core-libs Distribution: SUSE Linux Enterprise 15 SP3
Version: 3.5.0 Vendor: openSUSE
Release: bp153.1.380 Build date: Tue May 18 10:06:29 2021
Group: System/Libraries Build host: goat07
Size: 5707913 Source RPM: R-base-3.5.0-bp153.1.380.src.rpm
Summary: R language libraries
This package contains the files from R/lib to make their usage
possible without installing a complete R. (I.e. VTK uses this)




GPL-2.0-only OR GPL-3.0-only


* 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      no longer valid (e.g. because some other process has cleaned up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
      of SAFE_FFLAGS.
    * 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.
* Tue May 03 2016
  - tre.patch was removed.
* Tue May 03 2016
  - and libbz2-devel needed, too.
* Tue May 03 2016
  - added BuildRequires: bzip2
    for i586.
* Tue May 03 2016
  - upstream release 3.3.0
    CHANGES IN R 3.3.0:
    * nchar(x, *)'s argument keepNA governing how the result for NAs in
      x is determined, gets a new default keepNA = NA which returns NA
      where x is NA, except for type = "width" which still returns 2,
      the formatting / printing width of NA.
    * All builds have support for https: URLs in the default methods
      for download.file(), url() and code making use of them.
      Unfortunately that cannot guarantee that any particular https:
      URL can be accessed.  For example, server and client have to
      successfully negotiate a cryptographic protocol (TLS/SSL, ...)
      and the server's identity has to be verifiable _via_ the
      available certificates.  Different access methods may allow
      different protocols or use private certificate bundles: we
      encountered a https: CRAN mirror which could be accessed by one
      browser but not by another nor by download.file() on the same
      Linux machine.
    * The print method for methods() gains a byclass argument.
    * New functions validEnc() and validUTF8() to give access to the
      validity checks for inputs used by grep() and friends.
    * Experimental new functionality for S3 method checking, notably
      Also, the names of the R 'language elements' are exported as
      character vector tools::langElts.
    * str(x) now displays "Time-Series" also for matrix (multivariate)
      time-series, i.e. when is.ts(x) is true.
    * (Windows only) The GUI menu item to install local packages now
      accepts *.tar.gz files as well as *.zip files (but defaults to
      the latter).
    * New programmeR's utility function chkDots().
    * D() now signals an error when given invalid input, rather than
      silently returning NA.  (Request of John Nash.)
    * formula objects are slightly more "first class": e.g., formula()
      or new("formula", y ~ x) are now valid.  Similarly, for "table",
      "ordered" and "summary.table".  Packages defining S4 classes with
      the above S3/S4 classes as slots should be reinstalled.
    * New function strrep() for repeating the elements of a character
    * rapply() preserves attributes on the list when how = "replace".
    * New S3 generic function sigma() with methods for extracting the
      estimated standard deviation aka "residual standard deviation"
      from a fitted model.
    * news() now displays R and package news files within the HTML help
      system if it is available.  If no news file is found, a visible
      NULL is returned to the console.
    * as.raster(x) now also accepts raw arrays x assuming values in
    * Subscripting of matrix/array objects of type "expression" is now
    * type.convert("i") now returns a factor instead of a complex value
      with zero real part and missing imaginary part.
    * Graphics devices cairo_pdf() and cairo_ps() now allow non-default
      values of the cairographics 'fallback resolution' to be set.
      This now defaults to 300 on all platforms: that is the default
      documented by cairographics, but apparently was not used by all
      system installations.
    * file() gains an explicit method argument rather than implicitly
      using getOption("url.method", "default").
    * Thanks to a patch from Tomas Kalibera, x[x != 0] is now typically
      faster than x[which(x != 0)] (in the case where x has no NAs, the
      two are equivalent).
    * read.table() now always uses the names for a named colClasses
      argument (previously names were only used when colClasses was too
      short). (In part, wish of PR#16478.)
    * (Windows only) download.file() with default method = "auto" and a
      ftps:// URL chooses "libcurl" if that is available.
    * The out-of-the box Bioconductor mirror has been changed to one
      using https://: use chooseBioCmirror() to choose a http:// mirror
      if required.
    * The data frame and formula methods for aggregate() gain a drop
    * available.packages() gains a repos argument.
    * The undocumented switching of methods for url() on https: and
      ftps: URLs is confined to method = "default" (and documented).
    * smoothScatter() gains a ret.selection argument.
    * qr() no longer has a ... argument to pass additional arguments to
    * [ has a method for class "table".
    * It is now possible (again) to replayPlot() a display list
      snapshot that was created by recordPlot() in a different R
      It is still not a good idea to use snapshots as a persistent
      storage format for R plots, but it is now not completely silly to
      use a snapshot as a format for transferring an R plot between two
      R sessions.
      The underlying changes mean that packages providing graphics
      devices (e.g., Cairo, RSvgDevice, cairoDevice, tikzDevice) will
      need to be reinstalled.
      Code for restoring snapshots was contributed by Jeroen Ooms and
      JJ Allaire.
      Some testing code is available at <URL:>.
    * tools::undoc(dir = D) and codoc(dir = D) now also work when D is
      a directory whose normalizePath()ed version does not end in the
      package name, e.g. from a symlink.
    * abbreviate() has more support for multi-byte character sets - it
      no longer removes bytes within characters and knows about Latin
      vowels with accents.  It is still only really suitable for (most)
      European languages, and still warns on non-ASCII input.
      abbreviate(use.classes = FALSE) is now implemented, and that is
      more suitable for non-European languages.
    * match(x, table) is faster (sometimes by an order of magnitude)
      when x is of length one and incomparables is unchanged, thanks to
      Peter Haverty (PR#16491).
    * More consistent, partly not back-compatible behavior of NA and
      NaN coercion to complex numbers, operations less often resulting
      in complex NA (NA_complex_).
    * lengths() considers methods for length and [[ on x, so it should
      work automatically on any objects for which appropriate methods
      on those generics are defined.
    * The logic for selecting the default screen device on OS X has
      been simplified: it is now quartz() if that is available even if
      environment variable DISPLAY has been set by the user.
      The choice can easily be overridden _via_ environment variable
    * On Unix-like platforms which support the getline C library
      function, system(*,intern = TRUE) no longer truncates (output)
      lines longer than 8192 characters, thanks to Karl Millar.
    * rank() gains a ties.method = "last" option, for convenience (and
    * regmatches(invert = NA) can now be used to extract both
      non-matched and matched substrings.
    * data.frame() gains argument fix.empty.names;
      gets new cut.names, col.names and fix.empty.names.
    * plot(x ~ x, *) now warns that it is the same as plot(x ~ 1, *).
    * recordPlot() has new arguments load and attach to allow package
      names to be stored as part of a recorded plot.  replayPlot() has
      new argument reloadPkgs to load/attach any package names that
      were stored as part of a recorded plot.
    * S4 dispatch works within calls to .Internal(). This means
      explicit S4 generics are no longer needed for unlist() and
    * Only font family names starting with "Hershey" (and not "Her" as
      before) are given special treatment by the graphics engine.
    * S4 values are automatically coerced to vector (via as.vector)
      when subassigned into atomic vectors.
    * findInterval() gets a option.
    * The version of LAPACK included in the sources has been updated to
      3.6.0, including those 'deprecated' routines which were
      previously included.  _Ca_ 40 double-complex routines have been
      added at the request of a package maintainer.
      As before, the details of what is included are in
      src/modules/lapack/README and this now gives information on
      earlier additions.
    * tapply() has been made considerably more efficient without
      changing functionality, thanks to proposals from Peter Haverty
      and Suharto Anggono.  (PR#16640)
    * match.arg(arg) (the one-argument case) is faster; so is  (PR#16640)
    * The format method for object_size objects now also accepts
      "binary" units such as "KiB" and e.g., "Tb".  (Partly from
    * Profiling now records calls of the form foo::bar and some similar
      cases directly rather than as calls to <Anonymous>.  Contributed
      by Winston Chang.
    * New string utilities startsWith(x, prefix) and endsWith(x,
      suffix).  Also provide speedups for some grepl("^...",*) uses
      (related to proposals in PR#16490).
    * Reference class finalizers run at exit, as well as on garbage
    * Avoid parallel dependency on stats for port choice and random
      number seeds.  (PR#16668)
    * The radix sort algorithm and implementation from data.table
      (forder) replaces the previous radix (counting) sort and adds a
      new method for order().  Contributed by Matt Dowle and Arun
      Srinivasan, the new algorithm supports logical, integer (even
      with large values), real, and character vectors.  It outperforms
      all other methods, but there are some caveats (see ?sort).
    * The order() function gains a method argument for choosing between
      "shell" and "radix".
    * New function grouping() returns a permutation that stably
      rearranges data so that identical values are adjacent.  The
      return value includes extra partitioning information on the
      groups.  The implementation came included with the new radix
    * rhyper(nn, m, n, k) no longer returns NA when one of the three
      parameters exceeds the maximal integer.
    * switch() now warns when no alternatives are provided.
    * parallel::detectCores() now has default logical = TRUE on all
      platforms - as this was the default on Windows, this change only
      affects Sparc Solaris.
      Option logical = FALSE is now supported on Linux and recent
      versions of OS X (for the latter, thanks to a suggestion of Kyaw
    * hist() for "Date" or "POSIXt" objects would sometimes give
      misleading labels on the breaks, as they were set to the day
      before the start of the period being displayed.  The display
      format has been changed, and the shift of the start day has been
      made conditional on right = TRUE (the default).  (PR#16679)
    * R now uses a new version of the logo (donated to the R Foundation
      by RStudio).  It is defined in .svg format, so will resize
      without unnecessary degradation when displayed on HTML
      pages-there is also a vector PDF version.  Thanks to Dirk
      Eddelbuettel for producing the corresponding X11 icon.
    * New function .traceback() returns the stack trace which
      traceback() prints.
    * lengths() dispatches internally.
    * dotchart() gains a pt.cex argument to control the size of points
      separately from the size of plot labels.  Thanks to Michael
      Friendly and Milan Bouchet-Valat for ideas and patches.
    * as.roman(ch) now correctly deals with more diverse character
      vectors ch; also arithmetic with the resulting roman numbers
      works in more cases.  (PR#16779)
    * prcomp() gains a new option rank. allowing to directly aim for
      less than min(n,p) PC's.  The summary() and its print() method
      have been amended, notably for this case.
    * gzcon() gains a new option text, which marks the connection as
      text-oriented (so e.g. pushBack() works).  It is still always
      opened in binary mode.
    * The import() namespace directive now accepts an argument except
      which names symbols to exclude from the imports. The except
      expression should evaluate to a character vector (after
      substituting symbols for strings). See Writing R Extensions.
    * New convenience function Rcmd() in package tools for invoking R
      CMD tools from within R.
    * New functions makevars_user() and makevars_site() in package
      tools to determine the location of the user and site specific
      Makevars files for customizing package compilation.
* 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 don´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.



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