NetBSD-Bugs archive

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index][Old Index]

PR/16047 CVS commit: pkgsrc/math/R

The following reply was made to PR kern/16047; it has been noted by GNATS.

From: "Ryo ONODERA" <>
Subject: PR/16047 CVS commit: pkgsrc/math/R
Date: Wed, 13 May 2015 12:48:06 +0000

 Module Name:	pkgsrc
 Committed By:	ryoon
 Date:		Wed May 13 12:48:06 UTC 2015
 Modified Files:
 	pkgsrc/math/R: Makefile PLIST distinfo
 	pkgsrc/math/R/patches: patch-ac patch-ad
 Log Message:
 Update to 3.2.0
 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).
 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.
 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
     * Omegahat is no longer listed as providing Windows binary
       packages, e.g. by setRepositories().  It has no binary packages
       available for R 3.1.x and those for earlier versions were 32-bit
     * 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.
 To generate a diff of this commit:
 cvs rdiff -u -r1.154 -r1.155 pkgsrc/math/R/Makefile
 cvs rdiff -u -r1.20 -r1.21 pkgsrc/math/R/PLIST
 cvs rdiff -u -r1.63 -r1.64 pkgsrc/math/R/distinfo
 cvs rdiff -u -r1.33 -r1.34 pkgsrc/math/R/patches/patch-ac
 cvs rdiff -u -r1.17 -r1.18 pkgsrc/math/R/patches/patch-ad
 Please note that diffs are not public domain; they are subject to the
 copyright notices on the relevant files.

Home | Main Index | Thread Index | Old Index