SIGNIFICANT USER-VISIBLE CHANGES:

• The behaviour of unlink(recursive = TRUE) for a symbolic link to a directory has changed: it now removes the link rather than the directory contents (just as rm -r does).On Windows it no longer follows reparse points (including junctions and symbolic links).

• Environment variable RD2DVI_INPUTENC has been renamed to RD2PDF_INPUTENC.
• .Deprecated() becomes a bit more flexible, getting an old argument.
• Even data-only packages without R code need a namespace and so may need to be installed under R 2.14.0 or later.
• assignInNamespace() has further restrictions on use apart from at top-level, as its help page has warned. Expect it to be disabled from programmatic use in the future.
• system() and system2() when capturing output report a non-zero status in the new "status" attribute.
• kronecker() now has an S4 generic in package methods on which packages can set methods. It will be invoked by X %x% Y if either X or Y is an S4 object.
• pdf() accepts forms like file = "lpr" in the same way as postscript().
• pdf() accepts file = NULL. This means that the device does NOT create a PDF file (but it can still be queried, e.g., for font metric info).
• format() (and hence print()) on "bibentry" objects now uses options("width") to set the output width.
• legend() gains a text.font argument. (Suggested by Tim Paine, PR#14719.)
• nchar() and nzchar() no longer accept factors (as integer vectors). (Wish of PR#6899.)
• summary() behaves slightly differently (or more precisely, its print() method does). For numeric inputs, the number of NAs is printed as an integer and not a real. For dates and datetimes, the number of NAs is included in the printed output (the latter being the wish of PR#14720).The "data.frame" method is more consistent with the default method: in particular it now applies zapsmall() to numeric/complex summaries.
• The number of items retained with options(warn = 0) can be set by options(nwarnings=).
• There is a new function assignInMyNamespace() which uses the namespace of the function it is called from.
• attach() allows the default name for an attached file to be overridden.
• bxp(), the work horse of boxplot(), now uses a more sensible default xlim in the case where at is specified differently from 1:n, see the discussion on R-devel, .
• New function paste0(), an efficient version of paste(*, sep=""), to be used in many places for more concise (and slightly more efficient) code.
• Function setClass() in package methods now returns, invisibly, a generator function for the new class, slightly preferred to calling new(), as explained on the setClass help page.
• The "dendrogram" method of str() now takes its default for last.str from option str.dendrogram.last.
• New simple fitted() method for "kmeans" objects.
• The traceback() function can now be called with an integer argument, to display a current stack trace. (Wish of PR#14770.)
• setGeneric() calls can be simplified when creating a new generic function by supplying the default method as the def argument. See ?setGeneric.
• serialize() has a new option xdr = FALSE which will use the native byte-order for binary serializations. In scenarios where only little-endian machines are involved (these days, close to universal) and (un)serialization takes an appreciable amount of time this may speed up noticeably transferring data between systems.
• The internal (un)serialization code is faster for long vectors, particularly with XDR on some platforms. (Based on a suggested patch by Michael Spiegel.)
• For consistency, circles with zero radius are omitted by points() and grid.circle(). Previously this was device-dependent, but they were usually invisible.
• NROW(x) and NCOL(x) now work whenever dim(x) looks appropriate, e.g., also for more generalized matrices.
• PCRE has been updated to version 8.30.
• The internal R_Srcref variable is now updated before the browser stops on entering a function. (Suggestion of PR#14818.)
• There are 'bare-bones' functions .colSums(), .rowSums(), .colMeans() and .rowMeans() for use in programming where ultimate speed is required.
• The formerly internal function .package_dependencies() from package tools for calculating (recursive) (reverse) dependencies on package databases has been renamed to package_dependencies() and is now exported.
• There is a new function optimHess() to compute the (approximate) Hessian for an optim() solution if hessian = TRUE was forgotten.
• .filled.contour() is a 'bare-bones' function to add a filled-contour rectangular plot to an already prepared plot region.
• The stepping in debugging and single-step browsing modes has changed slightly: now left braces at the start of the body are stepped over for if statements as well as for for and while statements. (Wish of PR#14814.)
• library() no longer warns about a conflict with a function from package:base if the function has the same code as the base one but with a different environment. (An example is Matrix::det().)
• When deparsing very large language objects, as.character() now inserts newlines after each line of approximately 500 bytes, rather than truncating to the first line.
• New function rWishart() generates Wishart-distributed random matrices.
• Packages may now specify actions to be taken when the package is loaded (setLoadActions()).
• options(max.print = Inf) and similar now give an error (instead of warnings later).
• The "difftime" replacement method of units tries harder to preserve other attributes of the argument. (Wish of PR#14839.)
• poly(raw = TRUE) no longer requires more unique points than the degree. (Requested by John Fox.)

• There is a new function mcmapply(), a parallel version of mapply(), and a wrapper mcMap(), a parallel version of Map().
• A default cluster can be registered by the new function setDefaultCluster(): this will be used by default in functions such as parLapply().
• clusterMap() has a new argument .scheduling to allow the use of load-balancing.
• There are new load-balancing functions parLapplyLB() and parSapplyLB().
• makePSOCKCluster() has a new option useXDR = FALSE which can be used to avoid byte-shuffling for serialization when all the nodes are known to be little-endian (or all big-endian).

• Non-ASCII vignettes without a declared encoding are no longer accepted.
• C/C++ code in packages is now compiled with -NDEBUG to mitigate against the C/C++ function assert being called in production use. Developers can turn this off during package development with PKG_CPPFLAGS = -UNDEBUG.
• R CMD INSTALL has a new option --dsym which on Mac OS X (Darwin) dumps the symbols alongside the .so file: this is helpful when debugging with valgrind (and especially when installing packages into R.framework). [This can also be enabled by setting the undocumented environment variable PKG_MAKE_DSYM, since R 2.12.0.]
• R CMD INSTALL will test loading under all installed sub-architectures even for packages without compiled code, unless the flag --no-multiarch is used. (Pure R packages can do things which are architecture-dependent: in the case which prompted this, looking for an icon in a Windows R executable.)
• There is a new option install.packages(type = "both") which tries source packages if binary packages are not available, on those platforms where the latter is the default.
• The meaning of install.packages(dependencies = TRUE) has changed: it now means to install the essential dependencies of the named packages plus the Suggests, but only the essential dependencies of dependencies. To get the previous behaviour, specify dependencies as a character vector.
• R CMD INSTALL --merge-multiarch is now supported on OS X and other Unix-alikes using multiple sub-architectures.
• R CMD INSTALL --libs-only now by default does a test load on Unix-alikes as well as on Windows: suppress with --no-test-load.

• R CMD check now gives a warning rather than a note if it finds inefficiently compressed datasets. With bzip2 and xz compression having been available since R 2.10.0, it only exceptionally makes sense to not use them.The environment variable _R_CHECK_COMPACT_DATA2_ is no longer consulted: the check is always done if _R_CHECK_COMPACT_DATA_ has a true value (its default).
• Where multiple sub-architectures are to be tested, R CMD check now runs the examples and tests for all the sub-architectures even if one fails.
• R CMD check can optionally report timings on various parts of the check: this is controlled by environment variable _R_CHECK_TIMINGS_ documented in 'Writing R Extensions'. Timings (in the style of R CMD BATCH) are given at the foot of the output files from running each test and the R code in each vignette.
• There are new options for more rigorous testing by R CMD check selected by environment variables - see the 'Writing R Extensions' manual.
• R CMD check now warns (rather than notes) on undeclared use of other packages in examples and tests: increasingly people are using the metadata in the DESCRIPTION file to compute information about packages, for example reverse dependencies.
• The defaults for some of the options in R CMD check (described in the 'R Internals' manual) have changed: checks for unsafe and .Internal() calls and for partial matching of arguments in R function calls are now done by default.
• R CMD check has more comprehensive facilities for checking compiled code and so gives fewer reports on entry points linked into .so/.dll files from libraries (including C++ and Fortran runtimes).Checking compiled code is now done on FreeBSD (as well as the existing supported platforms of Linux, Mac OS X, Solaris and Windows).
• R CMD build has more options for --compact-vignettes: see R CMD build --help.
• R CMD build has a new option --md5 to add an MD5 file (as done by CRAN): this is used by R CMD INSTALL to check the integrity of the distribution.If this option is not specified, any existing (and probably stale) MD5 file is removed.

• R CMD Rd2dvi is now defunct: use R CMD Rd2pdf.
• Options such --max-nsize, --max-vsize and the function mem.limits() are now defunct. (Options --min-nsize and--min-vsize remain available.)
• Use of library.dynam() without specifying all the first three arguments is now disallowed.Use of an argument chname in library.dynam() including the extension .so or .dll (which was never allowed according to the help page) is defunct. This also applies to library.dynam.unload() and to useDynLib directives in NAMESPACE files.
• The internal functions .readRDS() and .saveRDS() are now defunct.
• The off-line help() types "postscript" and "ps" are defunct.
• Sys.putenv(), replaced and deprecated in R 2.5.0, is finally removed.
• Some functions/objects which have been defunct for five or more years have been removed completely. These include .Alias(), La.chol(), La.chol2inv(), La.eigen(), Machine(), Platform(), Version, codes(), delay(), format.char(), getenv(), httpclient(), loadURL(), machine(), parse.dcf(), printNoClass(), provide(), read.table.url(), restart(), scan.url(), symbol.C(), symbol.For() and unix().
• The ENCODING argument to .C() is deprecated. It was intended to smooth the transition to multi-byte character strings, but can be replaced by the use of iconv() in the rare cases where it is still needed.

• Building with a positive value of --with-valgrind-instrumentation now also instruments logical, complex and raw vectors.
• There is experimental support for _link-time optimization_ with gcc 4.5.0 or later on platforms which support it.

• Passing R objects other than atomic vectors, functions, lists and environments to .C() is now deprecated and will give a warning. Most cases (especially NULL) are actually coding errors. NULL will be disallowed in future..C() now passes a pairlist as a SEXP to the compiled code. This is as was documented, but pairlists were in reality handled differently as a legacy from the early days of R.
• call_R and call_S are deprecated. They still exist in the headers and as entry points, but are no longer documented and should not be used for new code.

• str(x, width) now obeys its width argument also for function headers and other objects x where deparse() is applied.
• The convention for x %/% 0L for integer-mode x has been changed from 0L to NA_integer_. (PR#14754)
• The exportMethods directive in a NAMESPACE file now exports S4 generics as necessary, as the extensions manual said it does. The manual has also been updated to be a little more informative on this point.It is now required that there is an S4 generic (imported or created in the package) when methods are to be exported.
• Reference methods cannot safely use non-exported entries in the namespace. We now do not do so, and warn in the documentation.
• The namespace import code was warning when identical S4 generic functions were imported more than once, but should not (reported by Brian Ripley, then Martin Morgan).
• merge() is no longer allowed (in some ways) to create a data frame with duplicate column names (which confused PR#14786).
• Fixes for rendering raster images on X11 and Windows devices when the x-axis or y-axis scale is reversed.
• getAnywhere() found S3 methods as seen from the utils namespace and not from the environment from which it was called.
• selectMethod(f, sig) would not return inherited group methods when caching was off (as it is by default).
• dev.copy2pdf(out.type = "cairo") gave an error. (PR#14827)
• Virtual classes (e.g., class unions) had a NULL prototype even if that was not a legal subclass. See ?setClassUnion.
• The C prototypes for zdotc and zdotu in R_ext/BLAS.h have been changed to the more modern style rather than that used by f2c. (Patch by Berwin Turlach.)
• isGeneric() produced an error for primitives that can not have methods.
• .C() or .Fortran() had a lack-of-protection error if the registration information resulted in an argument being coerced to another type.
• boxplot(x=x, at=at) with non finite elements in x and non integer at could not generate a warning but failed.
• heatmap(x, symm=TRUE, RowSideColors=*) no longer draws the colors in reversed order.
• predict() was incorrect in the multivariate case, for p >= 2.
• print(x, max=m) is now consistent when x is a "Date"; also the "reached ... max.print .." messages are now consistently using single brackets.
• Closed the
• tag in pages generated by Rd2HTML(). (PR#14841.)
• Axis tick marks could go out of range when a log scale was used. (PR#14833.)
• Signature objects in methods were not allocated as S4 objects (caused a problem with trace() reported by Martin Morgan).

SIGNIFICANT USER-VISIBLE CHANGES:

• The behaviour of unlink(recursive = TRUE) for a symbolic link to a directory has changed: it now removes the link rather than the directory contents (just as rm -r does).On Windows it no longer follows reparse points (including junctions and symbolic links).

• Environment variable more...