R 2.9.1 released
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.
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 < xlim. 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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