New Features

• install.packages(NULL) now lists packages only once even if they occur in more than one repository (as the latest compatible version of those available will always be downloaded).
• approxfun() and approx() now accept a 'rule' of length two, for easy specification of different interpolation rules on left and right.
• They no longer segfault for invalid zero-length specification of 'yleft, 'yright', or 'f'.
• seq_along(x) is now equivalent to seq_len(length(x)) even where length() has an S3/S4 method; previously it (intentionally) always used the default method for length().
• PCRE has been updated to version 7.9 (for bug fixes).
• agrep() uses 64-bit ints where available on 32-bit platforms and so may do a better job with complex matches. (E.g. PR#13789, which failed only on 32-bit systems.)

Deprecated & Defunct

• R CMD Rd2txt is deprecated, and will be removed in 2.10.0. (It is just a wrapper for R CMD Rdconv -t txt.)
• tools::Rd_parse() is deprecated and will be removed in 2.10.0 (which will use only Rd version 2).

Bug Fixes

• parse_Rd() still did not handle source reference encodings properly.
• The C utility function PrintValue no longer attempts to print attributes for CHARSXPs as those attributes are used internally for the CHARSXP cache. This fixes a segfault when calling it on a CHARSXP from C code.
• PDF graphics output was producing two instances of anything drawn with the symbol font face. (Report from Baptiste Auguie.)
• length(x) <- newval and grep() could cause memory corruption. (PR#13837)
• If model.matrix() was given too large a model, it could crash R. (PR#13838, fix found by Olaf Mersmann.)
• gzcon() (used by load()) would re-open an open connection, leaking a file descriptor each time. (PR#13841)
• The checks for inconsistent inheritance reported by setClass() now detect inconsistent superclasses and give better warning messages.
• print.anova() failed to recognize the column labelled P(>Chi) from a Poisson/binomial GLM anova as a p-value column in order to format it appropriately (and as a consequence it gave no significance stars).
• A missing PROTECT caused rare segfaults during calls to load(). (PR#13880, fix found by Bill Dunlap.)
• gsub() in a non-UTF-8 locale with a marked UTF-8 input could in rare circumstances overrun a buffer and so segfault.
• R CMD Rdconv --version was not working correctly.
• Missing PROTECTs in nlm() caused "random" errors. (PR#13381 by Adam D.I. Kramer, analysis and suggested fix by Bill Dunlap.)
• Some extreme cases of pbeta(log.p = TRUE) are more accurate (finite values < -700 rather than -Inf). (PR#13786)
• pbeta() now reports on more cases where the asymptotic expansions lose accuracy (the underlying TOMS708 C code was ignoring some of these, including the PR#13786 example).
• new.env(hash = TRUE, size = NA)now works the way it has been documented to for a long time.
• tcltk::tk_choose.files(multi = TRUE) produces better-formatted output with filenames containing spaces. (PR#13875)
• R CMD check --use-valgrind did not run valgrind on the package tests.
• The tclvalue() and the print() and as.xxx methods for class "tclObj" crashed R with an invalid object -- seen with an object saved from an earlier session.
• R CMD BATCH garbled options -d (useful for valgrind, although --debugger=valgrind always worked)
• INSTALL with LazyData and Encoding declared in DESCRIPTION might have left options("encoding") set for the rest of the package installation.