R 2.9.1 released

June 26, 2009
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As announced by Peter Dalgaard this morning, the latest update to R, R 2.9.1, has been released on schedule. If you roll your own builds of R, the sources are available now on CRAN. As of this writing none of the binary releases (for Windows and MacOS) have been updated yet: it will probably be a few days before those builds are completed by the R Core Team and propagated to the CRAN mirrors. This is a maintenance release and fixes a number of mostly minor issues. The complete list of changes appears after the jump. CHANGES IN R VERSION…

As announced by Peter Dalgaard this morning, the latest update to R, R 2.9.1, has been released on schedule. If you roll your own builds of R, the sources are available now on CRAN. As of this writing none of the binary releases (for Windows and MacOS) have been updated yet: it will probably be a few days before those builds are completed by the R Core Team and propagated to the CRAN mirrors.

This is a maintenance release and fixes a number of mostly minor issues. The complete list of changes appears after the jump.

    CHANGES IN R VERSION 2.9.1

NEW FEATURES

 o New function anyDuplicated(x) returns 0 (= FALSE) or the index
  of the first duplicated entry of x.

 o matplot(), matlines() and matpoints() now also obey a 'lend'
  argument, determining line end styles. (Wish of PR#13619).

 o bw.SJ(), bw.bcv() and bw.ucv() now gain an optional 'tol'
  argument allowing more accurate estimates.

 o new.packages() no longer regards packages with the same name
  as a member of an installed bundle as 'new' (this is now
  consistent with the dependency checks in install.packages()).

  It no longer reports on partially installed bundles (since
  members can be updated individually if a bundle is unbundled).

 o old.packages() and hence updates.packages() will look for
  updates to members of package bundles before updates to the
  whole bundle: this allow bundles to be split and installations
  updated.

 o nlminb() gives better non-convergence messages in some cases.

 o S3 method dispatch will support S4 class inheritance for S3
  methods, for primitives and via UseMethod(), if the argument
  S3methods=TRUE is given to setClass(). S4 method dispatch
  will use S3 per-object inheritance if S3Class() is set on the
  object. See ?Methods and the paper referenced there.

 o R CMD INSTALL is more tolerant of (malformed) packages with a
  'man' directory but no validly named .Rd files.

 o R CMD check now reports where options are used that cause some
  of the checks to be skipped.

 o RSiteSearch has been updated to be consistent with the new
  layout of the search site itself, which now includes separate
  options for vignettes, views, and r-sig-mixed-models, as well
  as changed names for r-help. (Contributed by Jonathan Baron.)

 o That R CMD check makes use of a
  <pkg>/tests/Examples/<pkg>-Ex.Rout.save file as a reference
  result is now documented in 'Writing R Extensions'.

DEPRECATED & DEFUNCT

 o print.atomic() (defunct since 1.9.0) has been removed since it
  caused confusion for an S4 class union "atomic".

 o png(type="cairo1") is deprecated -- it was only needed for
  platforms with 1.0 <= cairo < 1.2.

BUG FIXES

 o The ... argument was not handled properly when ... was found
  in the enclosure of the current function, rather than in the
  function header itself. (This caused integrate() to fail in
  certain cases.)

 o col2rgb("#00000080", TRUE) would return the background colour.
  (Reported by Hadley Wickham.)

 o interaction() now ensures that the levels of the result are unique.

 o packageDescription() and hence sessionInfo() now report the correct
  package version also for a non-attached loaded namespace of
  a version different from the default lib.loc.

 o smoothScatter() now also works when e.g. xlim[2] < xlim[1].

 o Invalid use of sprintf() such as sprintf("%S%") now give an error
  instead of a segmentation fault, as do very unusual cases such as
  sprintf("%s", tryCatch(stop(), error=identity)). (It was
  always documented that misuse could crash R in
  platform-dependent ways.)

 o parse_Rd() would mishandle braces when they occurred at
  the start of a line within an R string in an Rd file (reported
  by Alex Couture-Beil) or when they occurred in an R comment
  (reported by Mark Bravington).

 o readNEWS() missed version numbers with more than one digit.

 o building R --without-x no longer fails (PR#13665)

 o printCoefmat(cbind(0,1)) now works too (PR#13677)

 o bw.SJ(c(1:99, 1e6)) now works too.

 o Rd2txt() could not handle empty descriptions of items in an Rd
  file (reported by Mark Bravington), and did not wrap long lists
  of arguments if they were given in a single item.

 o stars() would do a partial plot when called with plot = FALSE;
  it now consistently returns the locations of the stars.

 o Rd2latex() could not handle empty sections.

 o old.packages() and hence update.packages() would fail on a
  repository which contained only one package but with multiple
  versions of that package.

 o as.character.Rd() added extra braces when displaying two-argument
  macros. (Report and fix by Manuel Eugster.)

 o unsplit() was misbehaving in the case of single-column data
  frames. (Reported by Will Gray.)

 o as(I(1), "vector") and similar coercions from objects of
  "unregistered" S3 classes now work.

 o srcref records produced by parse() and parse_Rd() did not record
  the encoding of the source file. (Reported by Romain Francois.)

 o The X11 version of View() was misbehaving in MBCS locales, and
  PgUp/PgDn now behave better, thanks to a patch from Ei-ji Nakama.

 o R CMD check looked at the environment variable PDFLATEX, but
  as from R 2.8.1 R CMD Rd2dvi used R_PDFLATEXCMD in
  preference, and that was set by R CMD (and not PDFLATEX). Now
  R CMD check looks at R_PDFLATEXCMD.

 o sprintf() now signals an error when the result of single format
  specification would be longer than the limit (8192 bytes); it would
  return "somewhat random" results or segfault previously. (PR#13667)
  Further, arguments of type "language" or "symbol" are no longer
  allowed, as these, e.g., sprintf("%s", quote(list())), typically
  lead to unexpected results or hard to understand error messages.

 o The new (in 2.9.0) 'stringsAsFactors' argument to expand.grid()
  was not working: it now does work but has default TRUE for
  backwards compatibility.

 o tcrossprod(<1d-array>, <matrix>) now does work when the arguments
  are of compatible dimensions.

 o qbinom() now is accurate also in (large size, small prob)
  cases. (PR#13711)

 o The calculation of the Spearman p-value in cor.test() is
  slightly more accurate in some cases. (PR#13574)

 o The digamma(), trigamma() and psigamma() functions could be
  inaccurate for values of x around 1e-15 due to cancellation.
  (PR#13714).

 o median.default() was altered in 2.8.1 to use sum() rather
  than mean(), although it was still documented to use mean().
  This caused problems for POSIXt objects, for which mean() but
  not sum() makes sense, so the change has been reverted.

 o Assigning an extra 0-length column to a data frame by
  DF$foo <- value gave a corrupt data frame rather than failing.
  (PR#13724) This also happened for DF[["foo"]] <- value.

 o R CMD INSTALL no longer gives a spurious warning about old R
  versions ignoring multiple dependencies, if the conditions are
  known to be satisfied.

 o The test for setting dim() allowed a value with two or more
  NAs to be set on a 0-length object. (PR#13729) Also, it
  allowed an even number of negative values.

 o xtfrm(), rank(), sort() and order() did not always make use of
  custom comparison methods specific to the class of elements
  being sorted.

 o Increase NAMED value on 'seq' value in for() loop so loop code
  cannot modify 'seq' value.

 o Prevent rectangles of size < 0.5 pixel from disappearing in
  Quartz when using rastered backend. (PR#13744)

 o Printing _NA_complex_ had a low-level thinko; patch thanks to
  Bill Dunlap.

 o CP1257 encoding for postscript/PDF has been corrected. (PR#13736)

 o aov() with an error term was evaluating the ... arguments in
  2.9.0 whilst checking their names, so could fail by evaluating
  them in the wrong place. (PR#13733)

 o The print() method for arima() failed if all coefs were fixed.

 o R CMD INSTALL --no-latex was not implemented in 2.9.0 (only).

 o Added a needed PROTECT call in RunFinalizers to handle cases where
  the routine is called recursively from a GC in a finalizer.

 o Constructing error messages about unused arguments in calls to
  closures no longer evaluates the arguments.

 o qr(x, LAPACK=TRUE) did not coerce integer x to numeric.

 o qr.coef() misbehaved in the LAPACK case with a matrix RHS, so
  that solve(qr(x, LAPACK=TRUE)) gave wrong results. (Found by
  Avraham Adler, PR#13762 by Ravi Varadhan.)


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