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The included versions of ‘zlib’, ‘bzip2’, ‘xz’ and PCRE have been removed.
‘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 accordingly.
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 convenience.
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.
‘file.info(, 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 = TRUE)’.
(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 platforms.
‘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.
An experimental 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.
An experimental utility ‘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).
‘rbind.data.frame()’ 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 path.
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. (PR#16133)
New ‘get0()’ function, combining ‘exists()’ and ‘get()’ in one call, for efficiency.
‘match.call()’ 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 supports.
• ‘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 session.
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 Millar.
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 ordering.
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 ‘help.search()’, 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 concepts.
New ‘lengths()’ function for getting the lengths of all elements in a list.
New function ‘toTitleCase()’ in package ‘tools’, tailored to package titles.
The matrix methods of ‘cbind()’ and ‘rbind()’ allow matrices as inputs which have 2^31 or more elements. (For ‘cbind()’, wish of PR#16198.)
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 interactons 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’ (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_COMPILER_OPTIMIZE’.
‘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’ checks a ‘README.md’ file can be processed: this needs ‘pandoc’ installed.
‘R CMD check --as-cran’ checks the existence and accessibility of URLs in the ‘DESCRIPTION’, ‘CITATION’ and ‘NEWS.Rd’ files and in the help files.
‘R CMD check --as-cran’ reports non-ASCII characters in R source files when there is no package encoding declared in the ‘DESCRIPTION’ file.
‘R CMD check --as-cran’ reports (apparent) S3 methods exported but not registered.
It 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.)
These checks can also be selected by environment variables: see the ‘R Internals’ manual.
‘R CMD check --as-cran’ 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).
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.
Installation using external binary distributions of ‘zlib’, ‘bzip’, ‘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/Makevars.win’ (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’.
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 ‘environment’s and ‘refClass’es.
‘[<-’ 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 ‘...’ . (PR#15707)
‘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’ arguments.
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.