Package Release Info


Update Info: openSUSE-2016-886
Available in Package Hub : 12 GA-SP5





Change Logs

* Fri Apr 15 2016
- CHANGES IN R 3.2.5:
    ? format.POSIXlt() behaved incorrectly in R 3.2.4.  E.g. the output
    of format(as.POSIXlt(paste0(1940:2000,"-01-01"), tz = "CET"),
    usetz = TRUE) ended in two "CEST" time formats.
    ? A typo in the Makefile for src/extra/xz prevented builds of
    liblzma.a. (Notice that this will become unbundled in 3.3.0.)
* Thu Mar 17 2016
- upstrem releases minorst bug fix release
  NEWS: The 3.2.4 release had two annoyances which we would rather
  not have in an "ultra-stable" release, designed to hang around
  for the duration of the 3.3 series. One was a relatively minor
  Makefile issue affecting system using R's bundled lzma library.
  The other, rather more serious, affected printing and formatting
  of POSIXlt objects, which would unpredictably get the Daylight
  Savings Time wrong.
* Fri Mar 11 2016
- Some version numbers of recommended packages corrected
* Fri Mar 11 2016
- Release numbers for sub-packages improved
* Fri Mar 11 2016
- added MakefileTypo.patch to enable building for 12.2
  was a one charcter show stopper
* Thu Mar 10 2016
- upstream release 3.2.4, only minor improvements
  CHANGES IN R 3.2.4:
    ? install.packages() and related functions now give a more
    informative warning when an attempt is made to install a base
    ? summary(x) now prints with less rounding when x contains infinite
    values. (Request of PR#16620.)
    ? provideDimnames() gets an optional unique argument.
    ? shQuote() gains type = "cmd2" for quoting in cmd.exe in Windows.
    (Response to PR#16636.)
    ? The data.frame method of rbind() gains an optional argument
    stringsAsFactors (instead of only depending on
    ? smooth(x, *) now also works for long vectors.
    ? tools::texi2dvi() has a workaround for problems with the texi2dvi
    script supplied by texinfo 6.1.
    It extracts more error messages from the LaTeX logs when in
    emulation mode.
    ? R CMD check will leave a log file build_vignettes.log from the
    re-building of vignettes in the .Rcheck directory if there is a
    problem, and always if environment variable
    _R_CHECK_ALWAYS_LOG_VIGNETTE_OUTPUT_ is set to a true value.
    ? Use of SUPPORT_OPENMP from header Rconfig.h is deprecated in
    favour of the standard OpenMP define _OPENMP.
    (This has been the recommendation in the manual for a while now.)
    ? The make macro AWK which is long unused by R itself but recorded
    in file etc/Makeconf is deprecated and will be removed in R
    ? The C header file S.h is no longer documented: its use should be
    replaced by R.h.
* Mon Mar 07 2016
- The big split up. What was a monolithic R-base*rpm now is
  divided over 30 something packages, with the following layout.
  R-base-3.2.3: dummy packages, contains all of R
  Use R-base, if you donĀ“t have a good understandig what it means
  to install only parts of it!
  R-base-devel-3.2.3: dummy, contains R-core-devel
  R-core-3.2.3: R core, no packages at all
  R-core-devel-3.2.3: devel files
  R-core-libs-3.2.3: contains Rlib
  R-core-doc-3.2.3: all the documentation of R-core
  R-core-packages-3.2.3: dummy package to load all core packages, that are
  Each of these packages may be installed alone.
  R-recommended-packages-3.2.3: dummy package to load all recommeded
    packages, that are
    R-Matrix-1.2.3, R-Matrix-devel-1.2.3,
  Each of these packages may be installed alone.
* Fri Dec 11 2015
- Upstream release R-3.2.3
  CHANGES IN R 3.2.3:
  * Some recently-added Windows time zone names have been added to
    the conversion table used to convert these to Olson names.
    (Including those relating to changes for Russia in Oct 2014, as
    in PR#16503.)
  * (Windows) Compatibility information has been added to the
    manifests for Rgui.exe, Rterm.exe and Rscript.exe.  This should
    allow win.version() and to report the actual Windows
    version up to Windows 10.
  * Windows "wininet" FTP first tries EPSV / PASV mode rather than
    only using active mode (reported by Dan Tenenbaum).
  * which.min(x) and which.max(x) may be much faster for logical and
    integer x and now also work for long vectors.
  * The 'emulation' part of tools::texi2dvi() has been somewhat
    enhanced, including supporting quiet = TRUE.  It can be selected
    by texi2dvi = "emulation".
    (Windows) MiKTeX removed its texi2dvi.exe command in Sept 2015:
    tools::texi2dvi() tries texify.exe if it is not found.
  * (Windows only) Shortcuts for printing and saving have been added
    to menus in Rgui.exe.  (Request of PR#16572.)
  * loess(..., iterTrace=TRUE) now provides diagnostics for
    robustness iterations, and the print() method for
    summary(<loess>) shows slightly more.
  * The included version of PCRE has been updated to 8.38, a bug-fix
  * View() now displays nested data frames in a more friendly way.
    (Request with patch in PR#15915.)
  * The included configuration code for libintl has been updated to
    that from gettext version - this should only affect how
    an external library is detected (and the only known instance is
    under OpenBSD).  (Wish of PR#16464.)
  * configure has a new argument --disable-java to disable the checks
    for Java.
  * The configure default for MAIN_LDFLAGS has been changed for the
    FreeBSD, NetBSD and Hurd OSes to one more likely to work with
    compilers other than gcc (FreeBSD 10 defaults to clang).
  * configure now supports the OpenMP flags -fopenmp=libomp (clang)
    and -qopenmp (Intel C).
  * Various macros can be set to override the default behaviour of
    configure when detecting OpenMP: see file
  * Source installation on Windows has been modified to allow for
    MiKTeX installations without texi2dvi.exe.  See file
  * regexpr(pat, x, perl = TRUE) with Python-style named capture did
    not work correctly when x contained NA strings.  (PR#16484)
  * The description of dataset ToothGrowth has been
    improved/corrected.  (PR#15953)
  * model.tables(type = "means") and hence TukeyHSD() now support
    "aov" fits without an intercept term.  (PR#16437)
  * close() now reports the status of a pipe() connection opened with
    an explicit open argument.  (PR#16481)
  * Coercing a list without names to a data frame is faster if the
    elements are very long. (PR#16467)
  * (Unix-only) Under some rare circumstances piping the output from
    Rscript or R -f could result in attempting to close the input
    file twice, possibly crashing the process.  (PR#16500)
  * (Windows) was out of step with win.version() and did
    not report Windows 8.
  * topenv(baseenv()) returns baseenv() again as in R 3.1.0 and
    earlier.  This also fixes compilerJIT(3) when used in .Rprofile.
  * detach()ing the methods package keeps .isMethodsDispatchOn()
    true, as long as the methods namespace is not unloaded.
  * Removed some spurious warnings from configure about the
    preprocessor not finding header files.  (PR#15989)
  * rchisq(*, df=0, ncp=0) now returns 0 instead of NaN, and
    dchisq(*, df=0, ncp=*) also no longer returns NaN in limit cases
    (where the limit is unique).  (PR#16521)
  * pchisq(*, df=0, ncp > 0, log.p=TRUE) no longer underflows (for
    ncp > ~60).
  * nchar(x, "w") returned -1 for characters it did not know about
    (e.g. zero-width spaces): it now assumes 1.  It now knows about
    most zero-width characters and a few more double-width
  * Help for which.min() is now more precise about behavior with
    logical arguments.  (PR#16532)
  * The print width of character strings marked as "latin1" or
    "bytes" was in some cases computed incorrectly.
  * abbreviate() did not give names to the return value if minlength
    was zero, unlike when it was positive.
  * (Windows only) dir.create() did not always warn when it failed to
    create a directory.  (PR#16537)
  * When operating in a non-UTF-8 multibyte locale (e.g. an East
    Asian locale on Windows), grep() and related functions did not
    handle UTF-8 strings properly.  (PR#16264)
  * read.dcf() sometimes misread lines longer than 8191 characters.
    (Reported by Herv'e Pag`es with a patch.)
  * within(df, ..) no longer drops columns whose name start with a
  * The built-in HTTP server converted entire Content-Type to
    lowercase including parameters which can cause issues for
    multi-part form boundaries (PR#16541).
  * Modifying slots of S4 objects could fail when the methods package
    was not attached. (PR#16545)
  * splineDesign(*, outer.ok=TRUE) (splines) is better now
    (PR#16549), and interpSpline() now allows sparse=TRUE for speedup
    with non-small sizes.
  * If the expression in the traceback was too long, traceback() did
    not report the source line number.  (Patch by Kirill M"uller.)
  * The browser did not truncate the display of the function when
    exiting with options("deparse.max.lines") set.  (PR#16581)
  * When bs(*, Boundary.knots=) had boundary knots inside the data
    range, extrapolation was somewhat off.  (Patch by Trevor Hastie.)
  * var() and hence sd() warn about factor arguments which are
    deprecated now. (PR#16564)
  * loess(*, weights = *) stored wrong weights and hence gave
    slightly wrong predictions for newdata.  (PR#16587)
  * aperm(a, *) now preserves names(dim(a)).
  * poly(x, ..) now works when either raw=TRUE or coef is specified.
  * data(package=*) is more careful in determining the path.
  * prettyNum(*, decimal.mark, big.mark): fixed bug introduced when
    fixing PR#16411.
* Thu Dec 10 2015
- Reverse the whole split. Back to the big package.
  Had user reports of broken installations.
  R-base, R-base-devel and R-base-libs are provided for now.
  The big split will come for 3.3.0
* Wed Dec 09 2015
- R-base was changed from a giant monolith to thirty-some packages.
  There were requests to use the libs without the interpreter.
  Furthermore it is now possible to use a frugal installation of R.
  The following binaries are built now:
  R-base-3.2.2-5.1.x86_64.rpm : A Meta-package. Use this, and it looks
    just like it looked the last 10 years.
  Requires base and recommended packages.
  R-base-devel-3.2.2-5.1.x86_64.rpm: Just for backward compatibility.
  R-core-devel-3.2.2-5.1.x86_64.rpm : The R-core packages install
    a bare-bones R. No packages inculded.
  R-tools-3.2.2-5.1.x86_64.rpm : All the base packages.
  R-recommended-3.2.2-5.1.x86_64.rpm : A meta-package including all
    recommended packages.
  R-spatial-7.3.10-5.1.x86_64.rpm : All recommended packaged.
    Note: They now have their own version
  numbers, so it should be much easier to
  use newer Versions of the recommended
  And the source RPM for all the above.
* Wed Aug 19 2015
- Disable building man files for openSUSE:42.
* Mon Aug 17 2015
- Upstream release 3.2.2
- Most important
  CHANGES IN R 3.2.2:
  * It is now easier to use secure downloads from https:// URLs on
    builds which support them: no longer do non-default options need
    to be selected to do so.  In particular, packages can be
    installed from repositories which offer https:// URLs, and those
    listed by setRepositories() now do so (for some of their
    Support for https:// URLs is available on Windows, and on other
    platforms if support for libcurl was compiled in and if that
    supports the https protocol (system installations can be expected
    to do).  So https:// support can be expected except on rather old
    OSes (an example being OS X 'Snow Leopard', where a non-system
    version of libcurl can be used).
    (Windows only) The default method for accessing URLs _via_
    download.file() and url() has been changed to be "wininet" using
    Windows API calls.  This changes the way proxies need to be set
    and security settings made: there have been some reports of sites
    being inaccessible under the new default method (but the previous
    methods remain available).
  * cmdscale() gets new option list. for increased flexibility when a
    list should be returned.
  * configure now supports texinfo version 6.0, which (unlike the
    change from 4.x to 5.0) is a minor update.  (Wish of PR#16456.)
  * (Non-Windows only) download.file() with default method = "auto"
    now chooses "libcurl" if that is available and a https:// or
    ftps:// URL is used.
  * (Windows only) setInternet2(TRUE) is now the default.  The
    command-line option --internet2 and environment variable
    R_WIN_INTERNET2 are now ignored.
    Thus by default the "internal" method for download.file() and
    url() uses the "wininet" method: to revert to the previous
    default use setInternet2(FALSE).
    This means that https:// can be read by default by
    download.file() (they have been readable by file() and url()
    since R 3.2.0).
    There are implications for how proxies need to be set (see
    ?download.file): also, cacheOK = FALSE is not supported.
  * chooseCRANmirror() and chooseBioCmirror() now offer HTTPS mirrors
    in preference to HTTP mirrors.  This changes the interpretation
    of their ind arguments: see their help pages.
  * capture.output() gets optional arguments type and split to pass
    to sink(), and hence can be used to capture messages.
  * Header Rconfig.h now defines HAVE_ALLOCA_H if the platform has
    the alloca.h header (it is needed to define alloca on Solaris and
    AIX, at least: see 'Writing R Extensions' for how to use it).
  * The libtool script generated by configure has been modified to
    support FreeBSD >= 10 (PR#16410).
  * The HTML help page links to demo code failed due to a change in R
    3.2.0.  (PR#16432)
  * If the na.action argument was used in model.frame(), the original
    data could be modified. (PR#16436)
  * getGraphicsEvent() could cause a crash if a graphics window was
    closed while it was in use. (PR#16438)
  * matrix(x, nr, nc, byrow = TRUE) failed if x was an object of type
  * strptime() could overflow the allocated storage on the C stack
    when the timezone had a non-standard format much longer than the
    standard formats. (Part of PR#16328.)
  * options(OutDec = s) now signals a warning (which will become an
    error in the future) when s is not a string with exactly one
    character, as that has been a documented requirement.
  * prettyNum() gains a new option input.d.mark which together with
    other changes, e.g., the default for decimal.mark, fixes some
    format()ting variants with non-default getOption("OutDec") such
    as in PR#16411.
  * download.packages() failed for type equal to either "both" or
    "binary".  (Reported by Dan Tenenbaum.)
  * The dendrogram method of labels() is much more efficient for
    large dendrograms, now using rapply().  (Comment #15 of PR#15215)
  * The "port" algorithm of nls() could give spurious errors.
    (Reported by Radford Neal.)
  * Reference classes that inherited from reference classes in
    another package could invalidate methods of the inherited class.
    Fixing this requires adding the ability for methods to be
    "external", with the object supplied explicitly as the first
    argument, named .self. See "Inter-Package Superclasses" in the
  * readBin() could fail on the SPARC architecture due to alignment
    issues.  (Reported by Radford Neal.)
  * qt(*, df=Inf, ncp=.) now uses the natural qnorm() limit instead
    of returning NaN. (PR#16475)
  * Auto-printing of S3 and S4 values now searches for print() in the
    base namespace and show() in the methods namespace instead of
    searching the global environment.
  * polym() gains a coefs = NULL argument and returns class "poly"
    just like poly() which gets a new simple=FALSE option.  They now
    lead to correct predict()ions, e.g., on subsets of the original
  * rhyper(nn, <large>) now works correctly. (PR#16489)
  * ttkimage() did not (and could not) work so was removed. Ditto for
    tkimage.cget() and tkimage.configure(). Added two Ttk widgets and
    missing subcommands for Tk's image command: ttkscale(),
    ttkspinbox(), tkimage.delete(), tkimage.height(),
    tkimage.inuse(), tkimage.type(), tkimage.types(),
    tkimage.width(). (PR#15372, PR#16450)
  * getClass("foo") now also returns a class definition when it is
    found in the cache more than once.
* Thu Jun 18 2015
- Upstream release 3.2.1
- Improvement of build: include libcurl and texlive-dvips/
- Most important
  CHANGES IN R 3.2.1:
  * utf8ToInt() now checks that its input is valid UTF-8 and returns
    NA if it is not.
  * install.packages() now allows type = "both" with repos = NULL if
    it can infer the type of file.
  * nchar(x, *) and nzchar(x) gain a new argument keepNA which
    governs how the result for NAs in x is determined.  For the R
    3.2.x series, the default remains FALSE which is fully back
    compatible.  From R 3.3.0, the default will change to keepNA = NA
    and you are advised to consider this for code portability.
  * news() more flexibly extracts dates from package NEWS.Rd files.
  * lengths(x) now also works (trivially) for atomic x and hence can
    be used more generally as an efficient replacement of sapply(x,
    length) and similar.
  * The included version of PCRE has been updated to 8.37, a bug-fix
  * diag() no longer duplicates a matrix when extracting its
  * as.character.srcref() gains an argument to allow characters
    corresponding to a range of source references to be extracted.
  * acf() and ccf() now guarantee values strictly in [-1,1] (instead
    of sometimes very slightly outside). PR#15832.
  * as.integer("111111111111") now gives NA (with a warning) as it
    does for the corresponding numeric or negative number coercions.
    Further, as.integer(M + 0.1) now gives M (instead of NA) when M
    is the maximal representable integer.
  * On some platforms nchar(x, "c") and nchar(x, "w") would return
    values (possibly NA) for inputs which were declared to be UTF-8
    but were not, or for invalid strings without a marked encoding in
    a multi-byte locale, rather than give an error.  Additional
    checks have been added to mitigate this.
  * apply(a, M, function(u) c(X = ., Y = .)) again has dimnames
    containing "X" and "Y" (as in R < 3.2.0).
  * (Windows only) In some cases, the --clean option to R CMD INSTALL
    could fail.  (PR#16178)
  * (Windows only) choose.files() would occasionally include
    characters from the result of an earlier call in the result of a
    later one.  (PR#16270)
  * A change in RSiteSearch() in R 3.2.0 caused it to submit invalid
    URLs.  (PR#16329)
  * Rscript and command line R silently ignored incomplete statements
    at the end of a script; now they are reported as parse errors.
  * Parse data for very long strings was not stored.  (PR#16354)
  * plotNode(), the workhorse of the plot method for "dendrogram"s is
    no longer recursive, thanks to Suharto Anggono, and hence also
    works for deeply nested dendrograms.  (PR#15215)
  * The parser could overflow internally when given numbers in
    scientific format with extremely large exponents.  (PR#16358)
  * If the CRAN mirror was not set, install.packages(type = "both")
    and related functions could repeatedly query the user for it.
    (Part of PR#16362)
  * The low-level functions .rowSums() etc. did not check the length
    of their argument, so could segfault. (PR#16367)
  * The quietly argument of library() is now correctly propagated
    from .getRequiredPackages2().
  * Under some circumstances using the internal PCRE when building R
    fron source would cause external libs such as -llzma to be
    omitted from the main link.
  * The .Primitive default methods of the logic operators, i.e., !, &
    and |, now give correct error messages when appropriate, e.g.,
    for `&`(TRUE) or `!`().  (PR#16385)
  * cummax(x) now correctly propagates NAs also when x is of type
    integer and begins with an NA.
  * summaryRprof() could fail when the profile contained only two
    records.  (PR#16395)
  * HTML vignettes opened using vignette() did not support links into
    the rest of the HTML help system.  (Links worked properly when
    the vignette was opened using browseVignettes() or from within
    the help system.)
  * arima(*, xreg = .) (for d >= 1) computes estimated variances
    based on a the number of effective observations as in R version
    3.0.1 and earlier.  (PR#16278)
  * slotNames(.) is now correct for "signature" objects (mostly used
    internally in methods).
  * On some systems, the first string comparison after a locale
    change would result in NA.
* Thu Apr 16 2015
- Upstream release 3.2.0
- Most important
  CHANGES IN 3.2.0:
  * anyNA() gains a recursive argument.
  * When x is missing and names is not false (including the default
    value), Sys.getenv(x, names) returns an object of class "Dlist"
    and hence prints tidily.
  * (Windows.)  shell() no longer consults the environment variable
    SHELL: too many systems have been encountered where it was set
    incorrectly (usually to a path where software was compiled, not
    where it was installed).  R_SHELL, the preferred way to select a
    non-default shell, can be used instead.
  * Some unusual arguments to embedFonts() can now be specified as
    character vectors, and the defaults have been changed
  * Functions in the Summary group duplicate less.  (PR#15798)
  * (Unix-alikes.) system(cmd, input = ) now uses
    'shell-execution-environment' redirection, which will be more
    natural if cmd is not a single command (but requires a
    POSIX-compliant shell). (Wish of PR#15508)
  * read.fwf() and read.DIF() gain a fileEncoding argument, for
  * Graphics devices can add attributes to their description in
    .Device and .Devices.  Several of those included with R use a
    "filepath" attribute.
  * pmatch() uses hashing in more cases and so is faster at the
    expense of using more memory. (PR#15697)
  * pairs() gains new arguments to select sets of variables to be
    plotted against each other.
  *, extra_cols = FALSE) allows a minimal set of columns
    to be computed on Unix-alikes: on some systems without
    properly-configured caching this can be significantly faster with
    large file lists.
  * New function dir.exists() in package base to test efficiently
    whether one or more paths exist and are directories.
  * dput() and friends gain new controls hexNumeric and digits17
    which output double and complex quantities as, respectively,
    binary fractions (exactly, see sprintf("%a")) and as decimals
    with up to 17 significant digits.
  * save(), saveRDS() and serialize() now support ascii = NA which
    writes ASCII files using sprintf("%a") for double/complex
    quantities.  This is read-compatible with ascii = TRUE but avoids
    binary->decimal->binary conversions with potential loss of
    precision.  Unfortunately the Windows C runtime's lack of C99
    compliance means that the format cannot be read correctly there
    in R before 3.1.2.
  * The default for formatC(decimal.mark =) has been changed to be
    getOption("OutDec"); this makes it more consistent with format()
    and suitable for use in print methods, e.g. those for classes
    "density", "ecdf", "stepfun" and "summary.lm".
    getOption("OutDec") is now consulted by the print method for
    class "kmeans", by cut(), dendrogram(), plot.ts() and quantile()
    when constructing labels and for the report from legend(trace =
    (In part, wish of PR#15819.)
  * printNum() and hence format() and formatC() give a warning if
    big.mark and decimal.mark are set to the same value (period and
    comma are not uncommonly used for each, and this is a check that
    conventions have not got mixed).
  * merge() can create a result which uses long vectors on 64-bit
  * dget() gains a new argument keep.source which defaults to FALSE
    for speed (dput() and dget() are most often used for data objects
    where this can make dget() many times faster).
  * Packages may now use a file of common macro definitions in their
    help files, and may import definitions from other packages.
  * A number of macros have been added in the new share/Rd directory
    for use in package overview help pages, and promptPackage() now
    makes use of them.
  * tools::parse_Rd() gains a new permissive argument which converts
    unrecognized macros into text.  This is used by
    utils:::format.bibentry to allow LaTeX markup to be ignored.
  * options(OutDec =) can now specify a multi-byte character, e.g.,
    options(OutDec = "\u00b7") in a UTF-8 locale.
  * is.recursive(x) is no longer true when x is an external pointer,
    a weak reference or byte code; the first enables all.equal(x, x)
    when x <- getClass(.).
  * ls() (aka objects()) and as.list.environment() gain a new
    argument sorted.
  * The "source" attribute (which has not been added to functions by
    R since before R version 2.14.0) is no longer treated as special.
  * Function returnValue() has been added to give on.exit() code
    access to a function's return value for debugging purposes.
  * crossprod(x, y) allows more matrix coercions when x or y are
    vectors, now equalling t(x) %*% y in these cases (also reported
    by Radford Neal).  Similarly, tcrossprod(x,y) and %*% work in
    more cases with vector arguments.
  * Utility function dynGet() useful for detecting cycles, aka
    infinite recursions.
  * The byte-code compiler and interpreter include new instructions
    that allow many scalar subsetting and assignment and scalar
    arithmetic operations to be handled more efficiently. This can
    result in significant performance improvements in scalar
    numerical code.
  * apply(m, 2, identity) is now the same as the matrix m when it has
    _named_ row names.
  * A new function debuggingState() has been added, allowing to
    temporarily turn off debugging.
  * example() gets a new optional argument run.donttest and
    tools::Rd2ex() a corresponding commentDonttest, with a default
    such that example(..) in help examples will run \donttest code
    only if used interactively (a change in behaviour).
  * gains an optional argument make.row.names, for
    potential speedup.
  * New function extSoftVersion() to report on the versions of
    third-party software in use in this session.  Currently reports
    versions of zlib, bzlib, the liblzma from xz, PCRE, ICU, TRE and
    the iconv implementation.
    A similar function grSoftVersion() in package grDevices reports
    on third-party graphics software.
    Function tcltk::tclVersion() reports the Tcl/Tk version.
  * Calling callGeneric() without arguments now works with primitive
    generics to some extent.
  * vapply(x, FUN, FUN.VALUE) is more efficient notably for large
    length(FUN.VALUE); as extension of PR#16061.
  * as.table() now allows tables with one or more dimensions of
    length 0 (such as as.table(integer())).
  * names(x) <- NULL now clears the names of call and ... objects.
  * library() will report a warning when an insufficient dependency
    version is masking a sufficient one later on the library search
  * A new plot() method for class "raster" has been added.
  * New check_packages_in_dir_changes() function in package tools for
    conveniently analyzing how changing sources impacts the check
    results of their reverse dependencies.
  * Speed-up from Peter Haverty for ls() and
    methods:::.requirePackage() speeding up package loading.
  * New get0() function, combining exists() and get() in one call,
    for efficiency.
  * gains an envir argument for specifying the
    environment from which to retrieve the ... in the call, if any;
    this environment was wrong (or at least undesirable) when the
    definition argument was a function.
  * topenv() has been made .Internal() for speedup, based on Peter
    Haverty's proposal in PR#16140.
  * getOption() no longer calls options() in the main case.
  * Optional use of libcurl (version 7.28.0 from Oct 2012 or later)
    for Internet access:
  * capabilities("libcurl") reports if this is available.
  * libcurlVersion() reports the version in use, and other
    details of the "libcurl" build including which URL schemes it
  * curlGetHeaders() retrieves the headers for http://, https://,
    ftp:// and ftps:// URLs: analysis of these headers can
    provide insights into the `existence' of a URL (it might for
    example be permanently redirected) and is so used in R CMD
    check --as-cran.
  * download.file() has a new optional method "libcurl" which
    will handle more URL schemes, follow redirections, and allows
    simultaneous downloads of multiple URLs.
  * url() has a new method "libcurl" which handles more URL
    schemes and follows redirections.  The default method is
    controlled by a new option url.method, which applies also to
    the opening of URLs _via_ file() (which happens implicitly in
    functions such as read.table.)
  * When file() or url() is invoked with a https:// or ftps://
    URL which the current method cannot handle, it switches to a
    suitable method if one is available.
  * (Windows.) The DLLs internet.dll and internet2.dll have been
    merged.  In this version it is safe to switch (repeatedly)
    between the internal and Windows internet functions within an R
    The Windows internet functions are still selected by flag
  - -internet2 or setInternet2().  This can be overridden for an
    url() connection _via_ its new method argument.
    download.file() has new method "wininet", selected as the default
    by --internet2 or setInternet2().
  * parent.env<- can no longer modify the parent of a locked
    namespace or namespace imports environment.  Contributed by Karl
  * New function isLoadedNamespace() for readability and speed.
  * names(env) now returns all the object names of an environment
    env, equivalently to ls(env, all.names = TRUE, sorted = FALSE)
    and also to the names of the corresponding list,
    names(as.list(env, all.names = TRUE)).  Note that although
    names() returns a character vector, the names have no particular
  * The memory manager now grows the heap more aggressively. This
    reduces the number of garbage collections, in particular while
    data or code are loaded, at the expense of slightly increasing
    the memory footprint.
  * New function trimws() for removing leading/trailing whitespace.
  * cbind() and rbind() now consider S4 inheritance during S3
    dispatch and also obey deparse.level.
  * cbind() and rbind() will delegate recursively to methods::cbind2
    (methods::rbind2) when at least one argument is an S4 object and
    S3 dispatch fails (due to ambiguity).
  * (Windows.)  download.file(quiet = FALSE) now uses text rather
    than Windows progress bars in non-interactive use.
  * New function hsearch_db() in package utils for building and
    retrieving the help search database used by, along
    with functions for inspecting the concepts and keywords in the
    help search database.
  * New function .getNamespaceInfo(), a no-check version of
    getNamespaceInfo() mostly for internal speedups.
  * The help search system now takes \keyword entries in Rd files
    which are not standard keywords (as given in KEYWORDS in the R
    documentation directory) as concepts.  For standard keyword
    entries the corresponding descriptions are additionally taken as
  * New lengths() function for getting the lengths of all elements in
    a list.
  * New function toTitleCase() in package tools, tailored to package
  * The matrix methods of cbind() and rbind() allow matrices as
    inputs which have 2^31 or more elements.  (For cbind(), wish of
  * The default method of image() has an explicit check for a numeric
    or logical matrix (which was always required).
  * URLencode() will not by default encode further URLs which appear
    to be already encoded.
  * BIC(mod) and BIC(mod, mod2) now give non-NA numbers for arima()
    fitted models, as nobs(mod) now gives the number of "used"
    observations for such models.  This fixes PR#16198, quite
    differently than proposed there.
  * The print() methods for "htest", "pairwise.htest" and
    "power.htest" objects now have a digits argument defaulting to (a
    function of) getOption("digits"), and influencing all printed
    numbers coherently.  Unavoidably, this changes the display of
    such test results in some cases.
  * Code completion for namespaces now recognizes all loaded
    namespaces, rather than only the ones that are also attached.
  * The code completion mechanism can now be replaced by a
    user-specified completer function, for (temporary) situations
    where the usual code completion is inappropriate.
  * unzip() will now warn if it is able to detect truncation when
    unpacking a file of 4GB or more (related to PR#16243).
  * methods() reports S4 in addition to S3 methods; output is
    simplified when the class argument is used.  .S3methods() and
    methods::.S4methods() report S3 and S4 methods separately.
  * Higher order functions such as the apply functions and Reduce()
    now force arguments to the functions they apply in order to
    eliminate undesirable interactions between lazy evaluation and
    variable capture in closures.  This resolves PR#16093.
  * The \donttest sections of R's help files can be tested by
    make check TEST_DONTTEST=TRUE .
  * It is possible to request the use of system valgrind headers
    _via_ configure option --with-system-valgrind-headers: note the
    possible future incompatibility of such headers discussed in the
    'R Installation and Administration' manual. (Wish of PR#16068.)
  * The included version of liblzma has been updated to xz-utils
    5.0.7 (minor bug fixes from 5.0.5).
  * configure options --with-system-zlib, --with-system-bzlib and
  - -with-system-pcre are now the default.  For the time being there
    is fallback to the versions included in the R sources if no
    system versions are found or (unlikely) if they are too old.
    Linux users should check that the -devel or -dev versions of
    packages zlib, bzip2/libbz2 and pcre as well as
    xz-devel/liblzma-dev (or similar names) are installed.
  * configure by default looks for the texi2any script from texinfo
    5.1 or later, rather than the makeinfo program.  (makeinfo is a
    link to the Perl script texi2any in texinfo 5.x.)
  * R CMD INSTALL gains an option --built-timestamp=STAMP allowing
    100% reproducible package building, thanks to Dirk Eddelbuettel.
  * There is support for testing the \dontrun and \donttest parts of
    examples in packages.
    tools::testInstalledPackage() accepts new arguments
    commentDontrun = FALSE and commentDonttest = FALSE.
    R CMD check gains options --run-dontrun and --run-donttest.
  * The HTML generated by tools::Rd2HTML() and tools::toHTML()
    methods is now 'XHTML 1.0 Strict'.
  * The compiler package's utility function setCompilerOptions() now
    returns the old values invisibly. The initial optimization level
    can also be set with the environment variable
  * R CMD build adds a NeedsCompilation field if one is not already
    present in the DESCRIPTION file.
  * R CMD check gains option --test-dir to specify an alternative set
    of tests to run.
  * R CMD check will now by default continue with testing after many
    types of errors, and will output a summary count of errors at the
    end if any have occurred.
  * R CMD check now checks that the Title and Description fields are
    correctly terminated.
  * R CMD check --as-cran now:
  * checks a file can be processed: this needs pandoc
  * checks the existence and accessibility of URLs in the
    DESCRIPTION, CITATION, NEWS.Rd and files and in the
    help files (provided the build has libcurl support).
  * reports non-ASCII characters in R source files when there is
    no package encoding declared in the DESCRIPTION file.
  * reports (apparent) S3 methods exported but not registered.
  * reports overwriting registered S3 methods from
    base/recommended packages.  (Such methods are replaced in the
    affected package for the rest of the session, even if the
    replacing namespace is unloaded.)
  * reports if the Title field does not appear to be in title
    case (see 'Writing R Extensions': there may be false
    positives, but note that technical words should be
    single-quoted and will then be accepted).
    Most of these checks can also be selected by environment
    variables: see the 'R Internals' manual.
  * New C API utility logspace_sum(logx[], n).
  * Entry points rbinom_mu, rnbinom_mu and rmultinom are remapped (by
    default) to Rf_rbinom_mu etc.  This requires packages using them
    to be re-installed.
  * .C(DUP = FALSE) and .Fortran(DUP = FALSE) are now ignored, so
    arguments are duplicated if DUP = TRUE would do so.  As their
    help has long said, .Call() is much preferred.
  * New entry point R_allocLD, like R_alloc but guaranteed to have
    sufficient alignment for long double pointers.
  * isPairList() now returns TRUE for DOTSXP.
  A number of changes to the Windows build system are in development.
  The following are currently in place.
  * Installation using external binary distributions of zlib, bzip2,
    liblzma, pcre, libpng, jpeglib and libtiff is now required, and
    the build instructions have been revised.
  * A new make target rsync-extsoft has been added to obtain copies
    of the external libraries from CRAN.
  * Building the manuals now requires texi2any from texinfo 5.1 or
    later.  CRAN binary builds include the manuals, but by default
    builds from source will not, and they will be accessed from CRAN.
    See the comments in src/gnuwin32/MkRules.dist for how to specify
    the location of texi2any.
  * (Windows) Changes have been made to support an experimental
    Windows toolchain based on GCC 4.9.2.  The default toolchain
    continues to be based on GCC 4.6.3, as the new toolchain is not
    yet stable enough.  A change to a new toolchain is expected
    during the R 3.2.x lifetime.
  * (Windows) The use of macro ZLIB_LIBS in file src/
    (which has not been documented for a long time) now requires an
    external libz.a to be available (it is part of the 'goodies' used
    to compile Windows binary packages).  It would be simpler to use
  - lz instead.
  * The default for option pkgType on platforms using binary packages
    is now "both", so source packages will be tried if binary
    versions are not available or not up to date.
    There are options for what install.packages(type = "both")
    (possibly called _via_ update.packages()) will do if compilation
    of a source package is desirable: see ?options (under utils).
    If you intend not to accept updates as source packages, you
    should use update.packages(type = "binary").
  * download.file(method = "lynx") is defunct.
  * Building R using the included versions of zlib, bzip2, xz and
    PCRE is deprecated: these are frozen (bar essential bug-fixes)
    and will be removed for R 3.3.0.
  * The configure option --with-valgrind-instrumentation=3 has been
    withdrawn, as it did not work with recent valgrind headers: it is
    now treated as level 2.
  * The MethodsList class in package methods had been deprecated in R
    2.11.0 and is defunct now.  Functions using it are defunct if
    they had been deprecated in R 2.11.0, and are deprecated now,
  * Fixed two obscure bugs in pairlist subassignment, reported by
    Radford Neal as part of pqR issue 16.
  * Fixes for bugs in handling empty arguments and argument matching
    by name in log().
  * all.equal() gains methods for environments and refClasses.
  * [<- and [[<- gain S4 data.frame methods to avoid corruption of S4
    class information by the S3 methods.
  * callNextMethod() should now work within a .local call when ... is
    absent from formals(.local).
  * dput(pairlist(x)) generates a call to the pairlist constructor
    instead of the list constructor.
  * Fix missing() when arguments are propagated through ... .
  * eigen(m) now defaults to symmetric = TRUE even when the dimnames
    are asymmetric if the matrix is otherwise symmetric.  (PR#16151)
  * Fix issues with forwarding ... through callGeneric() and
    callNextMethod().  (PR#16141)
  * callGeneric() now works after a callNextMethod().
  * Subclass information is kept consistent when replacing an
    ordinary S4 class with an "old class" _via_ the S4Class argument
    to setOldClass(). Thus, for example, a data.frame is valid for a
    list argument in the signature, and a factor is valid for vector
  * In qbeta() the inversion of pbeta() is much more sophisticated.
    This works better in corner cases some of which failed completely
    previously (PR#15755), or were using too many iterations.
  * Auto-printing no longer duplicates objects when printing is
    dispatched to a method.
  * kmeans(x, k) would fail when nrow(x) >= 42949673.  (Comment 6 of
  * 'Abbreviated' locale-specific day and month names could have been
    truncated in those rare locales where there are the same as the
    full names.
  * An irrelevant warning message from updating subclass information
    was silenced (the namespace would not be writable in this case).
* Mon Mar 09 2015
- Upstream release 3.1.3
- Most important
  CHANGES IN R 3.1.3:
  * The internal method of download.file() can now handle files
    larger than 2GB on 32-bit builds which support such files (tested
    on 32-bit R running on 64-bit Windows).
  * kruskal.test() warns on more types of suspicious input.
  * The as.dendrogram() method for "hclust" objects gains a check
    argument protecting against memory explosion for invalid inputs.
  * capabilities() has a new item long.double which indicates if the
    build uses a long double type which is longer than double.
  * nlm() no longer modifies the callback argument in place (a new
    vector is allocated for each invocation, which mimics the
    implicit duplication that occurred in R < 3.1.0); note that this
    is a change from the previously documented behavior. (PR#15958)
  * icuSetCollate() now accepts locale = "ASCII" which uses the basic
    C function strcmp and so collates strings byte-by-byte in
    numerical order.
  * sessionInfo() tries to report the OS version in use (not just
    that compiled under, and including details of Linux
  * model.frame() (used by lm() and many other modelling functions)
    now warns when it drops contrasts from factors.  (Wish of
  * install.packages() and friends now accept the value type =
    "binary" as a synonym for the native binary type on the platform
    (if it has one).
  * Single source or binary files can be supplied for
    install.packages(type = "both") and the appropriate type and
    repos = NULL will be inferred.
  * New function pcre_config() to report on some of the configuration
    options of the version of PCRE in use.  In particular, this
    reports if regular expressions using \p{xx} are supported.
  * (Windows.) download.file(cacheOK = FALSE) is now supported when
    internet2.dll is used.
  * browseURL() has been updated to work with Firefox 36.0 which has
    dropped support for the -remote interface.
  * The included version of PCRE has been updated to 8.36.
  * configure accepts MAKEINFO=texi2any as another way to ensure
    texinfo 5.x is used when both 5.x and 4.x are installed.
  * R CMD check now checks the packages used in \donttest sections of
    the examples are specified in the DESCRIPTION file.  (These are
    needed to run the examples interactively.)
  * R CMD check checks for the undeclared use of GNU extensions in
    Makefiles, and for Makefiles with a missing final linefeed.
    R CMD build will correct line endings in all Makefiles, not just
    those in the src directory.
  * R CMD check notes uses of library() and require() in package
    code: see the section 'Suggested packages' of 'Writing R
    Extensions' for good practice.
  * The configure option --with-valgrind-instrumentation=3 is
    deprecated and will be removed in R 3.2.0.
  * (Windows.) Rscript.exe was missing a manifest specifying the
    modern style for common controls (e.g., the download progress
  * If a package had extra documentation files but no vignette, the
    HTML help system produced an empty index page.
  * The parser now gives an error if a null character is included in
    a string using Unicode escapes. (PR#16046)
  * qr.Q() failed on complex arguments due to pre-3.0(!) typo.
  * abs() failed with named arguments when the argument was complex.
  * "noquote" objects may now be used as columns in dataframes.
  * Some values with extremely long names were printed incorrectly.
  * Extremely large exponents on zero expressed in scientific
    notation (e.g. 0.0e50000) could give NaN.  (PR#15976)
  * download.file() reported downloaded sizes as 0KB if less than
    1MB, only for R 3.1.2 and only on big-endian platforms.
  * prompt() did not escape percent signs in the automatically
    generated usage section of help files.
  * drop.terms() dropped some of the attributes of the object it was
    working with.  (PR#16029)
  * (Windows.) The command completion in Rgui.exe messed up the
    console.  (PR#15791)
  * (Windows.) The choose.files() command returned a blank string
    when the user asked for a single file but cancelled the request.
  * Math2 S4 group generics failed to correctly dispatch "structure"-
    and "nonStructure"-derived classes.
  * loadNamespace() imposed undocumented restrictions on the
    versionCheck parameter.  (Reported by Geoff Lee.)
  * Rare over-runs detected by AddressSanitizer in substr() and its
    replacement version have been avoided.
    _Inter alia_ that fix gives the documented behaviour for
    substr(x, 1, 2) <- "" (subsequently reported as PR#16214).
  * Loading packages incorrectly defining an S4 generic followed by a
    function of the same name caused an erroneous cyclic namespace
    dependency error.
  * Declared vignette encodings are now always passed to the vignette
  * Port Tomas Kalibera's fix from R-devel that restores the
    loadMethod() fast path, effectively doubling the speed of S4
  * power.t.test() and power.prop.test() now make use of the
    extendInt option of uniroot() and hence work in more extreme
    cases.  (PR#15792)
  * If a package was updated and attached when its namespace was
    already loaded, it could end up with parts from one version and
    parts from the other.  (PR#16120)
  * tools:::.Rdconv() didn't accept --encoding= due to a typo.
  * Unix-alike builds without a suitable makeinfo were documented to
    link the missing HTML manuals to CRAN, but did not.
  * save(*, ascii=TRUE) and load() now correctly deal with NaN's.
  * split.Date() retains fractional representations while avoiding
    incomplete class propagation.
  * R_ext/Lapack.h had not been updated for changes made by LAPACK to
    the argument lists of its (largely internal) functions dlaed2 and
    dlaed3.  (PR#16157)
  * RShowDoc("NEWS", "txt") had not been updated for the layout
    changes of R 3.1.0.
  * The xtfrm() method for class "Surv" has been corrected and its
    description expanded.
  * mode(x) <- y would incorrectly evaluate x before changing its
    mode. (PR#16215)
  * besselJ(1, 2^64) and besselY(..) now signal a warning, returning
    NaN instead of typically segfaulting. (Issue 3 of PR#15554)
  * HTML conversion of \href markup in .Rd files did not remove the
    backslash from \% and so gave an invalid URL.  In a related
    change, the \ escape is now required in such URLs.
* Fri Dec 12 2014
- Remove tex(inconsolata.sty) BuildRequires for SLE_12 builds (like
  older SLE releases).
* Fri Oct 31 2014
- Upstream release 3.1.2
- Most important
  CHANGES IN R 3.1.2:
  * embedFonts() now defaults to format = "ps2write" for .ps and .eps
    files.  This is available in Ghostscript 9.x (since 2010) whereas
    the previous default, format = "pswrite", was removed in
    Ghostscript 9.10.
  * For consistency with [dpqr]norm(), [dp]lnorm(sdlog = 0) model a
    point mass at exp(mulog) rather than return NaN (for an error).
  * capabilities() now reports if ICU is compiled in for use for
    collation (it is only actually used if a suitable locale is set
    for collation, and never for a C locale).
  * (OS X only.) Package tcltk checks when loaded if it is linked
    against the CRAN X11-based Tcl/Tk and if so that the Tcl/Tk
    component and the X11 libraries are installed.  This allows more
    informative error messages to be given advising the installation
    of the missing component or of XQuartz.
    The X11() device and X11-based versions of the data editor and
    viewer (invoked by edit() and View() for data frames and matrices
    from command-line R) check that the X11 libraries are installed
    and if not advises installing XQuartz.
  * icuSetCollate() allows locale = "default", and locale = "none" to
    use OS services rather than ICU for collation.
    Environment variable R_ICU_LOCALE can be used to set the default
    ICU locale, in case the one derived from the OS locale is
    inappropriate (this is currently necessary on Windows).
  * New function icuGetCollate() to report on the ICU collation
    locale in use (if any).
  * utils::URLencode() was updated to use unreserved and reserved
    characters from RFC 3986, <URL:>, instead of RFC 1738.
  * unique(warnings()) and c(warnings()) are now supported.
  * The Bioconductor 'version' used by setRepositories() now defaults
    to 3.0. (It can be set at runtime _via_ environment variable
  * The configure script reports on the more important
    capabilities/options which will not be compiled in.
    More types of external BLAS are recognized by name in that
  * When building R as a shared library, the -L${R_HOME}/lib${R_ARCH}
    flag is placed earlier in the link commands used during
    installation and when packages are installed: this helps ensure
    that the current build has priority if an R shared library has
    already been installed by e.g. install-libR in a library
    mentioned in LDFLAGS (and not in 'your system's library
    directory' as documented). (Wish of PR#15790.)
  * LaTeX package upquote is no longer required for R's use of
  * (Windows only) If both 32 and 64 bit versions of R are installed,
    the bin/R.exe and bin/Rscript.exe executables now run 64 bit R.
    (To run 32 bit R, overwrite these files with copies of
  * Running R CMD check with _R_CHECK_DEPENDS_ONLY_ true now makes
    the VignetteBuilder packages available even if they are listed in
    Suggests, since they are needed to recognise and process
    non-Sweave vignettes.
  * R CMD check now reports empty importFrom declarations in a
    NAMESPACE file, as these are common errors (writing
    importFrom(Pkg) where import(Pkg) was intended).
  * R CMD check now by default checks code usage directly on the
    package namespace without loading and attaching the package and
    its suggests and enhances.  For good practice with packages in
    the Suggests field, see SS1.1.3.1 of 'Writing R Extensions'.  For
    use of lazy-data objects in the package's own code, see ?data.
  * dmultinom() did not handle non-finite probabilities correctly.
  * prettyNum(x, zero.print=*) now also works when x contains NAs.
  * A longstanding bug exhibited by nlminb() on Windows was traced to
    a compiler bug in gcc 4.6.3; a workaround has been put in place.
    (PR#15244 and PR#15914).
  * Rendering of \command in HTML versions of help pages has been
    improved: this is particularly evident on the help page for
  * as.hexmode(x) and as.octmode(x) now behave correctly for some
    numeric x, e.g., c(NA, 1) or c(1, pi).
  * drop1() failed if the scope argument had no variables to drop.
  * edit() (and hence fix()) failed if an object had a non-character
    attribute named "source" (an attribute that had been used in R
    prior to version 2.14.0).
  * callGeneric() could fail if the generic had ... as a formal
    argument. (PR#15937).
  * Forking in package parallel called C entry point exit in the
    child.  This was unsafe (_exit should have been called), and
    could flush stdin of the main R process (seen most often on
    As good practice, stdout is now flushed before forking a child.
  * R objects such as list(`a\b` = 1) now print correctly.
  * getAnywhere("C_pbinom") now returns correctly a single object
    (rather than unlisting it).
  * The confint() method for nls() fits failed it these has specified
    parameter limits despite using an algorithm other than "port".
  * Subclassing an S4 class failed if the class required arguments to
    the generator, through its initialize() method.
  * removeSource() did not properly handle expressions containing
    arguments that were supplied as missing, e.g.  x[i,]. (PR#15957)
  * as.environment(list()) now works, and as.list() of such an
    environment is now the same as list().
  * Several tcltk functions failed when run in unusual environments.
  * options(list()) now works (trivially). (PR#15979)
  * merge(<dendrogram>, ..) now works correctly for two `independent'
    dendrograms (PR#15648), and still compatibly via adjust = "auto"
    e.g. for two branches of an existing dendrogram.
  * The plot method for "hclust" objects gets an optional argument
    check; When that is true (the default) it checks more carefully
    for valid input.
  * (Windows only) If a user chose to install 64 bit R but not 32 bit
    R, the bin/R and bin/Rscript executables failed to run.
  * Various possible buffer overruns have been prevented, and missed
    memory protection added. (PR#15990)
  * Rscript no longer passes --args to R when there are no extra
    ("user") arguments.
  * objects like getClass("refClass")@prototype now print() and str()
    without error.
  * identical() now also looks at the S4 bit.
  * hist(x, breaks) is more robust in adding a small fuzz to few
    breaks when some are very large. (PR#15988)
  * sub() and gsub() did not handle regular expressions like "\s{2,}"
    properly if the text contained NA or non-ascii elements in a
    UTF-8 locale.  Part of this was due to a bug in the TRE library.
  * RShowDoc("NEWS") now displays the PDF version.
  * Matrices and arrays with last dimension zero did not print at all
    or incompletely.  (PR#16012)
  * plot.histogram() and hence hist() now respect the xaxs, yaxs and
    lab graphics parameters.  (PR#16021)
  * bw.SJ(x) and other bw.*() no longer segfault when x contains
    non-finite values. (PR#16024)
  * R CMD Rd2pdf unintentionally ignored its --os option.
  * The internal method of download.file() was not reporting file
    sizes and progress correctly on files larger than 2GB (inherited
    from libxml2).  This is corrected for 64-bit builds (32-bit
    platforms may not support such files, but where possible will be
    supported in future versions of R).
  * Work around a bug in OS X Yosemite where key environment
    variables may be duplicated causing issues in subprocesses. The
    duplicates are now removed on R startup (via Rprofile).
  * Adjust X11 auto-launch detection in DISPLAY on OS X to recognize
    latest XQuartz.
* Thu Jul 10 2014
- Added Provides: R-parallel
- Upstream release 3.1.1
- Most impotant
  CHANGES IN R 3.1.1:
  CHANGES IN R 3.1.1:
  * When attach() reports conflicts, it does so compatibly with
    library() by using message().
  * R CMD Sweave no longer cleans any files by default, compatibly
    with versions of R prior to 3.1.0.  There are new options
  - -clean, --clean=default and --clean=keepOuts.
  * tools::buildVignette() and tools::buildVignettes() with clean =
    FALSE no longer remove any created files.  buildvignette() gains
    a keep argument for more cleaning customization.
  * The Bioconductor 'version' used by setRepositories() can now be
    set by environment variable R_BIOC_VERSION at runtime, not just
    when R is installed.  (It has been stated that Bioconductor will
    switch from 'version' 2.14 to 'version' 3.0 during the lifetime
    of the R 3.1 series.)
  * Error messages from bugs in embedded Sexpr code in Sweave
    documents now report the source location.
  * type.convert(), read.table() and similar read.*() functions get a
    new numerals argument, specifying how numeric input is converted
    when its conversion to double precision loses accuracy.  The
    default value, "allow.loss" allows accuracy loss, as in R
    versions before 3.1.0.
  * For some compilers, integer addition could overflow without a
    warning.  R's internal code for both integer addition and
    subtraction is more robust now.  (PR#15774)
  * The function determining the default number of knots for
    smooth.spline() is now exported, as .nknots.smspl().
  * dbeta(, a,b), pbeta(), qbeta() and rbeta() are now defined also
    for a = 0, b = 0, or infinite a and b (where they typically
    returned NaN before).
  * Many package authors report that the RStudio graphics device does
    not work correctly with their package's use of  The
    new option = TRUE) replaces the RStudio
    override by the default device as selected by R itself, still
    respecting environment variables R_INTERACTIVE_DEVICE and
  * readRDS() now returns visibly.
  * Modifying internal logical scalar constants now results in an
    error instead of a warning.
  * install.packages(repos = NULL) now accepts http:// or ftp:// URLs
    of package archives as well as file paths, and will download as
    required.  In most cases repos = NULL can be deduced from the
    extension of the URL.
  * The warning when using partial matching with the $ operator on
    data frames is now only given when
    options("warnPartialMatchDollar") is TRUE.
  * Package help requests like package?foo now try the package foo
    whether loaded or not.
  * General help requests now default to trying all loaded packages,
    not just those on the search path.
  * Added a new function promptImport(), to generate a help page for
    a function that was imported from another package (and presumably
    re-exported, or help would not be needed).
  * configure option --with-internal-tzcode can now be used with
    variable rsharedir.
  * The included version of PCRE has been updated to 8.35.
  * There is a new target make uninstall-libR to remove an installed
    shared/static libR.
    make install-libR now works if a sub-architecture is used,
    although the user will need to specify libdir differently for
    different sub-architectures.
  * There is more extensive advice on which LaTeX packages are
    required to install R or to make package manuals (as done by R
    CMD check) in the 'Writing R Extensions' manual.
  * Compilers/linkers were handling the visibility controls in
    src/extra/xz inconsistently (and apparently in some cases
    incorrectly), so it has been simplified.  (PR#15327)
  * (Windows) There is updated support for the use of ICU for
    collation: see the 'R Installation and Administration Manual'.
  * dbinom(x, n), pbinom(), dpois(), etc, are slightly less
    restrictive in checking if n is integer-valued.  (Wish of
  * pchisq(x, df, ncp, log.p = TRUE) is more accurate and no longer
    underflows for small x and ncp < 80, e.g, for pchisq(1e-5, df =
    100, ncp = 1, log = TRUE).  (Based on PR#15635 and a suggestion
    by Roby Joehanes.)
  * The s ("step into") command in the debugger would cause R to step
    into expressions evaluated there, not just into functions being
    debugged.  (PR#15770)
  * The C code used by strptime() rejected time-zone offsets of more
    than +1200 (+1245, +1300 and +1400 can occur).  (PR#15768)
  * (Windows only.)  png(type = "cairo", antialias = "gray") was not
    accepted.  (PR#15760)
  * Use of save(..., envir=) with named objects could fail.
  * Sweave() mis-parsed Sexpr expressions that contained backslashes.
  * The return value from options(foo = NULL) was not the previous
    value of the option.  (PR#15781)
  * enc2utf8() and enc2native() did not always mark the encoding of
    the return values when it was known.
  * dnbinom(x, size = <large>, mu, log = TRUE) no longer underflows
    to -Inf for large mu, thanks to a suggestion from Alessandro
    Mammana (MPI MolGen, Berlin).
  * pbeta(x, a, b, log = TRUE) no longer behaves discontinuously (in
    a small x-region) because of denormalized numbers.  Also,
    pbeta(1-1e-12, 1e30, 1.001, log=TRUE) now terminates "in real
  * The "CRAN" filter (see available.packages()) no longer removes
    duplicates other than of packages on CRAN, and does not fail if
    there is no CRAN repository in getOption("repos").
  * The device listing from dev2bitmap() and bitmap() was truncated
    to 1000 characters: modern versions of GhostScript on most
    platforms have many more devices.
  * (Windows.)  Commands such as Sys.which() and pipe() which needed
    to find the full path to a command could segfault if the 'long'
    path name was much longer than the 'short' path name (which
    Sys.which() returns), as the behaviour of the Windows API call
    had changed.
  * R CMD build will fail with an error if one of the packages
    specified in the VignetteBuilder field is not installed.
    (Without loading those packages it cannot be ascertained which
    files are intended to be vignettes. This means that the
    VignetteBuilder packages have to be installed for package
    checking too.)  (Wish of PR#15775.)
  * Misguided attempts to use chull() with non-finite points now give
    an error (related to PR#15777).
  * For a formula with exactly 32 variables the 32nd variable was
    aliased to the intercept in some C-level computations of terms,
    so that for example attempting to remove it would remove the
    intercept instead (and leave a corrupt internal structure).
  * anyDuplicated() silently returned wrong values when the first
    duplicate was at an index which was too large to be stored in an
    integer vector (although a lot of RAM and patience would have
    been needed to encounter this).
  * tools::Rd2ex(commentDontrun = FALSE) failed if the block had only
    one line.
  * Hexadecimal constants such as 0x110p-5L which were incorrectly
    qualified by L were parsed incorrectly since R 3.0.0, with a
    slightly garbled warning. (PR#15753)
  * system() returned success on some platforms even if the system
    was unable to launch a process. (PR#15796)
  * (Windows Rgui console.)  Unbuffered output was sometimes not
    output immediately if the prompt was not on the last line of the
  * The built-in help server did not declare the encoding for the
    DESCRIPTION or other text files to be the package encoding, so
    non-ASCII characters could be displayed incorrectly.
  * R is now trying harder to not cleanup child processes that were
    not spawned by mcparallel() on platforms that provide information
    about the source process of the SIGCHLD signal. This allows 3rd
    party libraries to manage the exit status of children that they
    spawn without R interfering.
  * mcmapply() was only parallelizing if the number of jobs was
    bigger than the number of cores. It now parallelizes if the
    number of jobs is more than one.
  * Auto-printing would re-evaluate its argument when trying to
    dispatch to a print method.  This is now avoided when possible.
  * Unserializing (including load() and readRDS()) could silently
    return incorrect numeric values from ASCII saves if there was a
    read error.
  * getParseData() could return incorrect values for the parents of
    some elements. (Reported by Andrew Redd.)
  * Attempting to use data frames of 2^31 or more rows with merge()
    or to create a merged data frame of that size now gives a clearer
    error message.
  * parse() did not check its file argument was a connection if it
    was not a character string, so e.g. parse(FALSE) attempted to
    read from stdin.
    Nor did dump() and dput().
  * The "help.try.all.packages" option was ignored when the shortcut
    syntax for help was used, e.g. ?foo.
  * A potential segfault in string allocation has been fixed.  (Found
    by Radford Neal.)
  * Potential memory protection errors in sort() and D() have been
    fixed. (Found by Radford Neal.)
  * Fixed a lack of error checking in graphics event functions.
    (Found by Radford Neal; a different patch used here than the one
    in pqR.)
  * numericDeriv() sometimes miscalculated the gradient.  (PR#15849,
    reported originally by Radford Neal)
* Fri Jun 20 2014
- added parallel provides
* Fri May 09 2014
- Removed / commented out symlink to %{_bindir}/r
  new package 'littler' should be used instead for packages
  that need /usr/bin/r