Changes in R

The ‘Changes in R’ article from the 2010-2 issue.

CHANGES IN R VERSION 2.12.1

NEW FEATURES

• The DVI/PDF reference manual now includes the help pages for all the standard packages: splines, stats4 and tcltk were previously omitted (intentionally).

• http://www.rforge.net has been added to the default set of repositories known to setRepositories().

• xz-utils has been updated to version 5.0.0.

• reshape() now makes use of sep when forming names during reshaping to wide format. (PR#14435)

• legend() allows the length of lines to be set by the end user via the new argument seg.len.

• New reference class utility methods copy(), field(), getRefClass() and getClass() have been added.

• When a character value is used for the EXPR argument in switch(), a warning is given if more than one unnamed alternative value is given. This will become an error in R 2.13.0.

• StructTS(type = "BSM") now allows series with just two seasons. (Reported by Birgit Erni.)

INSTALLATION

• The PDF reference manual is now built as PDF version 1.5 with object compression, which on platforms for which this is not the default (notably MiKTeX) halves its size.

• Variable can be set during configuration, for any additional library flags needed when linking a shared object with the Fortran 9x compiler. (Needed with Solaris Studio 12.2.)

BUG FIXES

• seq.int() no longer sometimes evaluates arguments twice. (PR#14388)

• The data.frame method of format() failed if a column name was longer than 256 bytes (the maximum length allowed for an R name).

• predict(<lm object>, type ="terms", ...) failed if both terms and interval were specified. (Reported by Bill Dunlap.)

  Also, if se.fit = TRUE the standard errors were reported for all terms, not just those selected by a non-null terms.

• The TRE regular expressions engine could terminate R rather than give an error when given certain invalid regular expressions. (PR#14398)

• cmdscale(eig = TRUE) was documented to return \(n-1\) eigenvalues but in fact only returned k. It now returns all \(n\) eigenvalues.

  cmdscale(add = TRUE) failed to centre the return configuration and sometimes lost the labels on the points. Its return value was described wrongly (it is always a list and contains component ac).

• promptClass() in package methods now works for reference classes and gives a suitably specialized skeleton of documentation.

  Also, callSuper() now works via the methods() invocation as well as for initially specified methods.

• download.file() could leave the destination file open if the URL was not able to be opened. (PR#14414)

• Assignment of an environment to functions or as an attribute to other objects now works for S4 subclasses of "environment".

• Use of [[<- for S4 subclasses of "environment" generated an infinite recursion from the method. The method has been replaced by internal code.

• In a reference class S4 method, callSuper() now works in initialize() methods when there is no explicit superclass method.

• ! dropped attributes such as names and dimensions from a length-zero argument. (PR#14424)

• When list2env() created an environment it was missing a PROTECT call and so was vulnerable to garbage collection.

• Sweave() with keep.source=TRUE dropped comments at the start and end of code chunks. It could also fail when \\SweaveInput was combined with named chunks.

• The Fortran code used by nls(algorithm = "port") could infinite-loop when compiled with high optimization on a modern version of gcc, and SAFE_FFLAGS is now used to make this less likely. (PR#14427, seen with 32-bit Windows using gcc 4.5.0 used from R 2.12.0.)

• sapply() with default simplify = TRUE and mapply() with default SIMPLIFY = TRUE wrongly simplified language-like results, as, e.g., in mapply(1:2, c(3,7), FUN = function(i,j) call(’:’,i,j)).

• Backreferences to undefined patterns in [g]sub(pcre = TRUE) could cause a segfault. (PR#14431)

• The format() (and hence the print()) method for class "Date" rounded fractional dates towards zero: it now always rounds them down.

• Reference S4 class creation could generate ambiguous inheritance patterns under very special circumstances.

• [[<- turned S4 subclasses of "environment" into plain environments.

• Long titles for help pages were truncated in package indices and a few other places.

• Additional utilities now work correctly with S4 subclasses of "environment" (rm, locking tools and active bindings).

• spec.ar() now also work for the "ols" method. (Reported by Hans-Ruedi Kuensch.)

• The initialization of objects from S4 subclasses of "environment" now allocates a new environment object.

• R CMD check has more protection against (probably erroneous) example or test output which is invalid in the current locale.

• qr.X() with column names and pivoting now also pivots the column names. (PR#14438)

• unit.pmax() and unit.pmin() in package grid gave incorrect results when all inputs were of length 1. (PR#14443)

• The parser for NAMESPACE files ignored misspelled directives, rather than signalling an error. For 2.12.x a warning will be issued, but this will be correctly reported as an error in later releases. (Reported by Charles Berry.)

• Fix for subsetting of "raster" objects when only one of i or j is specified.

• grid.raster() in package grid did not accept "nativeRaster" objects (like rasterImage() does).

• Rendering raster images in PDF output was resetting the clipping region.

• Rendering of raster images on Cairo X11 device was wrong, particularly when a small image was being scaled up using interpolation.

  With Cairo < 1.6, will be better than before, though still a little clunky. With Cairo >= 1.6, should be sweet as.

• Several bugs fixed in read.DIF(): single column inputs caused errors, cells marked as "character" could be converted to other types, and (in Windows) copying from the clipboard failed.

CHANGES IN R VERSION 2.12.0

NEW FEATURES

• Reading a package’s CITATION file now defaults to ASCII rather than Latin-1: a package with a non-ASCII CITATION file should declare an encoding in its DESCRIPTION file and use that encoding for the CITATION file.

• difftime() now defaults to the "tzone" attribute of "POSIXlt" objects rather than to the current timezone as set by the default for the tz argument. (Wish of PR#14182.)

• pretty() is now generic, with new methods for "Date" and "POSIXt" classes (based on code contributed by Felix Andrews).

• unique() and match() are now faster on character vectors where all elements are in the global CHARSXP cache and have unmarked encoding (ASCII). Thanks to Matthew Dowle for suggesting improvements to the way the hash code is generated in unique.c.

• The enquote() utility, in use internally, is exported now.

• .C() and .Fortran() now map non-zero return values (other than NA_LOGICAL) for logical vectors to TRUE: it has been an implicit assumption that they are treated as true.

• The print() methods for "glm" and "lm" objects now insert linebreaks in long calls in the same way that the print() methods for "summary.[g]lm" objects have long done. This does change the layout of the examples for a number of packages, e.g. MASS. (PR#14250)

• constrOptim() can now be used with method "SANN". (PR#14245)

  It gains an argument hessian to be passed to optim(), which allows all the ... arguments to be intended for f() and grad(). (PR#14071)

• curve() now allows expr to be an object of mode "expression" as well as "call" and "function".

• The "POSIX[cl]t" methods for Axis() have been replaced by a single method for "POSIXt".

  There are no longer separate plot() methods for "POSIX[cl]t" and "Date": the default method has been able to handle those classes for a long time. This inter alia allows a single date-time object to be supplied, the wish of PR#14016.

  The methods had a different default ("") for xlab.

• Classes "POSIXct", "POSIXlt" and "difftime" have generators .POSIXct(), .POSIXlt() and .difftime(). Package authors are advised to make use of them (they are available from R 2.11.0) to proof against planned future changes to the classes.

  The ordering of the classes has been changed, so "POSIXt" is now the second class. See the document ‘Updating packages for changes in R 2.12.x’ on http://developer.r-project.org for the consequences for a handful of CRAN packages.

• The "POSIXct" method of as.Date() allows a timezone to be specified (but still defaults to UTC).

• New list2env() utility function as an inverse of as.list(<environment>) and for fast multi-assign() to existing environment. as.environment() is now generic and uses list2env() as list method.

• There are several small changes to output which ‘zap’ small numbers, e.g. in printing quantiles of residuals in summaries from "lm" and "glm" fits, and in test statistics in print.anova().

• Special names such as "dim", "names", etc, are now allowed as slot names of S4 classes, with "class" the only remaining exception.

• File .Renviron can have architecture-specific versions such as .Renviron.i386 on systems with sub-architectures.

• installed.packages() has a new argument subarch to filter on sub-architecture.

• The summary() method for packageStatus() now has a separate print() method.

• The default summary() method returns an object inheriting from class "summaryDefault" which has a separate print() method that calls zapsmall() for numeric/complex values.

• The startup message now includes the platform and if used, sub-architecture: this is useful where different (sub-)architectures run on the same OS.

• The getGraphicsEvent() mechanism now allows multiple windows to return graphics events, through the new functions setGraphicsEventHandlers(), setGraphicsEventEnv(), and getGraphicsEventEnv(). (Currently implemented in the windows() and X11() devices.)

• tools::texi2dvi() gains an index argument, mainly for use by R CMD Rd2pdf.

  It avoids the use of texindy by texinfo‘s texi2dvi >= 1.157, since that does not emulate ’makeindex’ well enough to avoid problems with special characters (such as (, {, !) in indices.

• The ability of readLines() and scan() to re-encode inputs to marked UTF-8 strings on Windows since R 2.7.0 is extended to non-UTF-8 locales on other OSes.

• scan() gains a fileEncoding argument to match read.table().

• points() and lines() gain "table" methods to match plot(). (Wish of PR#10472.)

• Sys.chmod() allows argument mode to be a vector, recycled along paths.

• There are |, & and xor() methods for classes "octmode" and "hexmode", which work bitwise.

• Environment variables , , , are no longer used nor set in an R session. (With the move to tools::texi2dvi(), the conventional environment variables , and will be used. options("dvipscmd") defaults to the value of , then to "dvips".)

• New function isatty() to see if terminal connections are redirected.

• summaryRprof() returns the sampling interval in component sample.interval and only returns in by.self data for functions with non-zero self times.

• print(x) and str(x) now indicate if an empty list x is named.

• install.packages() and remove.packages() with lib unspecified and multiple libraries in .libPaths() inform the user of the library location used with a message rather than a warning.

• There is limited support for multiple compressed streams on a file: all of [bgx]zfile() allow streams to be appended to an existing file, but bzfile() reads only the first stream.

• Function person() in package utils now uses a given/family scheme in preference to first/middle/last, is vectorized to handle an arbitrary number of persons, and gains a role argument to specify person roles using a controlled vocabulary (the MARC relator terms).

• Package utils adds a new "bibentry" class for representing and manipulating bibliographic information in enhanced BibTeX style, unifying and enhancing the previously existing mechanisms.

• A bibstyle() function has been added to the tools package with default JSS style for rendering "bibentry" objects, and a mechanism for registering other rendering styles.

• Several aspects of the display of text help are now customizable using the new Rd2txt_options() function. options("help_text_width") is no longer used.

• Added \\href tag to the Rd format, to allow hyperlinks to URLs without displaying the full URL.

• Added \\newcommand and \\renewcommand tags to the Rd format, to allow user-defined macros.

• New toRd() generic in the tools package to convert objects to fragments of Rd code, and added "fragment" argument to Rd2txt(), Rd2HTML(), and Rd2latex() to support it.

• Directory R_HOME/share/texmf now follows the TDS conventions, so can be set as a texmf tree (‘root directory’ in MiKTeX parlance).

• S3 generic functions now use correct S4 inheritance when dispatching on an S4 object. See ?Methods, section on “Methods for S3 Generic Functions” for recommendations and details.

• format.pval() gains a ... argument to pass arguments such as nsmall to format(). (Wish of PR#9574)

• legend() supports title.adj. (Wish of PR#13415)

• Added support for subsetting "raster" objects, plus assigning to a subset, conversion to a matrix (of colour strings), and comparisons (== and !=).

• Added a new parseLatex() function (and related functions deparseLatex() and latexToUtf8()) to support conversion of bibliographic entries for display in R.

• Text rendering of \\itemize in help uses a Unicode bullet in UTF-8 and most single-byte Windows locales.

• Added support for polygons with holes to the graphics engine. This is implemented for the pdf(), postscript(), x11(type="cairo"), windows(), and quartz() devices (and associated raster formats), but not for x11(type="Xlib") or xfig() or pictex(). The user-level interface is the polypath() function in graphics and grid.path() in grid.

• File NEWS is now generated at installation with a slightly different format: it will be in UTF-8 on platforms using UTF-8, and otherwise in ASCII. There is also a PDF version, NEWS.pdf, installed at the top-level of the R distribution.

• kmeans(x, 1) now works. Further, kmeans now returns between and total sum of squares.

• arrayInd() and which() gain an argument useNames. For arrayInd, the default is now false, for speed reasons.

• As is done for closures, the default print method for the formula class now displays the associated environment if it is not the global environment.

• A new facility has been added for inserting code into a package without re-installing it, to facilitate testing changes which can be selectively added and backed out. See ?insertSource.

• New function readRenviron to (re-)read files in the format of ~/.Renviron and Renviron.site.

• require() will now return FALSE (and not fail) if loading the package or one of its dependencies fails.

• aperm() now allows argument perm to be a character vector when the array has named dimnames (as the results of table() calls do). Similarly, array() allows MARGIN to be a character vector. (Based on suggestions of Michael Lachmann.)

• Package utils now exports and documents functions aspell_package_Rd_files() and aspell_package_vignettes() for spell checking package Rd files and vignettes using Aspell, Ispell or Hunspell.

• Package news can now be given in Rd format, and news() prefers these inst/NEWS.Rd files to old-style plain text NEWS or inst/NEWS files.

• New simple function packageVersion().

• The PCRE library has been updated to version 8.10.

• The standard Unix-alike terminal interface declares its name to readline as ‘R’, so that can be used for conditional sections in ~/.inputrc files.

• ‘Writing R Extensions’ now stresses that the standard sections in .Rd files (other than \\alias, \\keyword and \\note) are intended to be unique, and the conversion tools now drop duplicates with a warning.

  The .Rd conversion tools also warn about an unrecognized type in a \\docType section.

• ecdf() objects now have a quantile() method.

• format() methods for date-time objects now attempt to make use of a "tzone" attribute with "%Z" and "%z" formats, but it is not always possible. (Wish of PR#14358.)

• tools::texi2dvi(file, clean = TRUE) now works in more cases (e.g. where emulation is used and when file is not in the current directory).

• New function droplevels() to remove unused factor levels.

• system(command, intern = TRUE) now gives an error on a Unix-alike (as well as on Windows) if command cannot be run. It reports a non-success exit status from running command as a warning.

  On a Unix-alike an attempt is made to return the actual exit status of the command in system(intern = FALSE): previously this had been system-dependent but on POSIX-compliant systems the value return was 256 times the status.

• system() has a new argument ignore.stdout which can be used to (portably) ignore standard output.

• system(intern = TRUE) and pipe() connections are guaranteed to be available on all builds of R.

• Sys.which() has been altered to return "" if the command is not found (even on Solaris).

• A facility for defining reference-based S4 classes (in the OOP style of Java, C++, etc.) has been added experimentally to package methods; see ?ReferenceClasses.

• The predict method for "loess" fits gains an na.action argument which defaults to na.pass rather than the previous default of na.omit.

  Predictions from "loess" fits are now named from the row names of newdata.

• Parsing errors detected during Sweave() processing will now be reported referencing their original location in the source file.

• New adjustcolor() utility, e.g., for simple translucent color schemes.

• qr() now has a trivial lm method with a simple (fast) validity check.

• An experimental new programming model has been added to package methods for reference (OOP-style) classes and methods. See ?ReferenceClasses.

• bzip2 has been updated to version 1.0.6 (bug-fix release). now requires at least version 1.0.6.

• R now provides jss.cls and jss.bst (the class and bib style file for the Journal of Statistical Software) as well as RJournal.bib and Rnews.bib, and R CMD ensures that the .bst and .bib files are found by BibTeX.

• Functions using the environment variable no longer quote the value when making system calls. This allows values such as tar –force-local, but does require additional quotes in, e.g., TAR = "’/path with spaces/mytar’".

DEPRECATED & DEFUNCT

• Supplying the parser with a character string containing both octal/hex and Unicode escapes is now an error.

• File extension .C for C++ code files in packages is now defunct.

• R CMD check no longer supports configuration files containing Perl configuration variables: use the environment variables documented in ‘R Internals’ instead.

• The save argument of require() now defaults to FALSE and save = TRUE is now deprecated. (This facility is very rarely actually used, and was superseded by the Depends field of the DESCRIPTION file long ago.)

• R CMD check –no-latex is deprecated in favour of .

• R CMD Sd2Rd is formally deprecated and will be removed in R 2.13.0.

PACKAGE INSTALLATION

• install.packages() has a new argument libs_only to optionally pass to R CMD INSTALL and works analogously for Windows binary installs (to add support for 64- or 32-bit Windows).

• When sub-architectures are in use, the installed architectures are recorded in the Archs field of the DESCRIPTION file. There is a new default filter, "subarch", in available.packages() to make use of this.

  Code is compiled in a copy of the src directory when a package is installed for more than one sub-architecture: this avoid problems with cleaning the sources between building sub-architectures.

• R CMD INSTALL –libs-only no longer overrides the setting of locking, so a previous version of the package will be restored unless is specified.

UTILITIES

• R CMD Rprof|build|check are now based on R rather than Perl scripts. The only remaining Perl scripts are the deprecated R CMD Sd2Rd and install-info.pl (used only if install-info is not found) as well as some maintainer-mode-only scripts.

  because these have been completely rewritten, users should not expect undocumented details of previous implementations to have been duplicated.

  R CMD no longer manipulates the environment variables and .

• R CMD check has a new argument to confine tests to those needed to check an additional sub-architecture.

  Its check for “Subdirectory ‘inst’ contains no files” is more thorough: it looks for files, and warns if there are only empty directories.

  Environment variables such as and those used for customization can be set for the duration of checking via a file ~/.R/check.Renviron (in the format used by .Renviron, and with sub-architecture specific versions such as ~/.R/check.Renviron.i386 taking precedence).

  There are new options to check the package under all of the installed sub-architectures and to confine checking to the sub-architecture under which check is invoked. If neither option is supplied, a test is done of installed sub-architectures and all those which can be run on the current OS are used.

  Unless multiple sub-architectures are selected, the install done by check for testing purposes is only of the current sub-architecture (via R CMD INSTALL –no-multiarch).

  It will skip the check for non-ascii characters in code or data if the environment variables or are respectively set to . (Suggestion of Vince Carey.)

• R CMD build no longer creates an INDEX file (R CMD INSTALL does so), and –force removes (rather than overwrites) an existing INDEX file.

  It supports a file ~/.R/build.Renviron analogously to check.

  It now runs build-time \\Sexpr expressions in help files.

• R CMD Rd2dvi makes use of tools::texi2dvi() to process the package manual. It is now implemented entirely in R (rather than partially as a shell script).

• R CMD Rprof now uses utils::summaryRprof() rather than Perl. It has new arguments to select one of the tables and to limit the number of entries printed.

• R CMD Sweave now runs R with –vanilla so the environment setting of will always be used.

C-LEVEL FACILITIES

• lang5() and lang6() (in addition to pre-existing lang[1-4]()) convenience functions for easier construction of eval() calls. If you have your own definition, do wrap it inside #ifndef lang5 .... #endif to keep it working with old and new R.

• Header R.h now includes only the C headers it itself needs, hence no longer includes errno.h. (This helps avoid problems when it is included from C++ source files.)

• Headers Rinternals.h and R_ext/Print.h include the C++ versions of stdio.h and stdarg.h respectively if included from a C++ source file.

INSTALLATION

• A C99 compiler is now required, and more C99 language features will be used in the R sources.

• Tcl/Tk >= 8.4 is now required (increased from 8.3).

• System functions access, chdir and getcwd are now essential to configure R. (In practice they have been required for some time.)

• make check compares the output of the examples from several of the base packages to reference output rather than the previous output (if any). Expect some differences due to differences in floating-point computations between platforms.

• File NEWS is no longer in the sources, but generated as part of the installation. The primary source for changes is now doc/NEWS.Rd.

• The popen system call is now required to build R. This ensures the availability of system(intern = TRUE), pipe() connections and printing from postscript().

• The pkg-config file libR.pc now also works when R is installed using a sub-architecture.

• R has always required a BLAS that conforms to IE60559 arithmetic, but after discovery of more real-world problems caused by a BLAS that did not, this is tested more thoroughly in this version.

BUG FIXES

• Calls to selectMethod() by default no longer cache inherited methods. This could previously corrupt methods used by as().

• The densities of non-central chi-squared are now more accurate in some cases in the extreme tails, e.g. dchisq(2000, 2, 1000), as a series expansion was truncated too early. (PR#14105)

• pt() is more accurate in the left tail for ncp large, e.g. pt(-1000, 3, 200). (PR#14069)

• The default C function (R_binary) for binary ops now sets the S4 bit in the result if either argument is an S4 object. (PR#13209)

• source(echo=TRUE) failed to echo comments that followed the last statement in a file.

• S4 classes that contained one of "matrix", "array" or "ts" and also another class now accept superclass objects in new(). Also fixes failure to call validObject() for these classes.

• Conditional inheritance defined by argument test in methods::setIs() will no longer be used in S4 method selection (caching these methods could give incorrect results). See ?setIs.

• The signature of an implicit generic is now used by setGeneric() when that does not use a definition nor explicitly set a signature.

• A bug in callNextMethod() for some examples with "..." in the arguments has been fixed. See file src/library/methods/tests/nextWithDots.R in the sources.

• match(x, table) (and hence %in%) now treat "POSIXlt" consistently with, e.g., "POSIXct".

• Built-in code dealing with environments (get(), assign(), parent.env(), is.environment() and others) now behave consistently to recognize S4 subclasses; is.name() also recognizes subclasses.

• The abs.tol control parameter to nlminb() now defaults to 0.0 to avoid false declarations of convergence in objective functions that may go negative.

• The standard Unix-alike termination dialog to ask whether to save the workspace takes a EOF response as n to avoid problems with a damaged terminal connection. (PR#14332)

• Added warn.unused argument to hist.default() to allow suppression of spurious warnings about graphical parameters used with plot=FALSE. (PR#14341)

• predict.lm(), summary.lm(), and indeed lm() itself had issues with residual DF in zero-weighted cases (the latter two only in connection with empty models). (Thanks to Bill Dunlap for spotting the predict() case.)

• aperm() treated resize = NA as resize = TRUE.

• constrOptim() now has an improved convergence criterion, notably for cases where the minimum was (very close to) zero; further, other tweaks inspired from code proposals by Ravi Varadhan.

• Rendering of S3 and S4 methods in man pages has been corrected and made consistent across output formats.

• Simple markup is now allowed in \\title sections in .Rd files.

• The behaviour of as.logical() on factors (to use the levels) was lost in R 2.6.0 and has been restored.

• prompt() did not backquote some default arguments in the \\usage section. (Reported by Claudia Beleites.)

• writeBin() disallows attempts to write 2GB or more in a single call. (PR#14362)

• new() and getClass() will now work if Class is a subclass of "classRepresentation" and should also be faster in typical calls.

• The summary() method for data frames makes a better job of names containing characters invalid in the current locale.

• [[ sub-assignment for factors could create an invalid factor (reported by Bill Dunlap).

• Negate(f) would not evaluate argument f until first use of returned function (reported by Olaf Mersmann).

• quietly=FALSE is now also an optional argument of library(), and consequently, quietly is now propagated also for loading dependent packages, e.g., in require(*, quietly=TRUE).

• If the loop variable in a for loop was deleted, it would be recreated as a global variable. (Reported by Radford Neal; the fix includes his optimizations as well.)

• Task callbacks could report the wrong expression when the task involved parsing new code. (PR#14368)

• getNamespaceVersion() failed; this was an accidental change in 2.11.0. (PR#14374)

• identical() returned FALSE for external pointer objects even when the pointer addresses were the same.

• L$a@x[] <- val did not duplicate in a case it should have.

• tempfile() now always gives a random file name (even if the directory is specified) when called directly after startup and before the R RNG had been used. (PR#14381)

• quantile(type=6) behaved inconsistently. (PR#14383)

• backSpline(.) behaved incorrectly when the knot sequence was decreasing. (PR#14386)

• The reference BLAS included in R was assuming that 0*x and x*0 were always zero (whereas they could be NA or NaN in IEC 60559 arithmetic). This was seen in results from tcrossprod, and for example that log(0) %*% 0 gave 0.

• The calculation of whether text was completely outside the device region (in which case, you draw nothing) was wrong for screen devices (which have [0, 0] at top-left). The symptom was (long) text disappearing when resizing a screen window (to make it smaller). (PR#14391)

• model.frame(drop.unused.levels = TRUE) did not take into account NA values of factors when deciding to drop levels. (PR#14393)

• library.dynam.unload required an absolute path for libpath. (PR#14385)

  Both library() and loadNamespace() now record absolute paths for use by searchpaths() and getNamespaceInfo(ns, "path").

• The self-starting model NLSstClosestX failed if some deviation was exactly zero. (PR#14384)

• X11(type = "cairo") (and other devices such as png using cairographics) and which use Pango font selection now work around a bug in Pango when very small fonts (those with sizes between 0 and 1 in Pango’s internal units) are requested. (PR#14369)

• Added workaround for the font problem with X11(type = "cairo") and similar on Mac OS X whereby italic and bold styles were interchanged. (PR#13463 amongst many other reports.)

• source(chdir = TRUE) failed to reset the working directory if it could not be determined – that is now an error.

• Fix for crash of example(rasterImage) on x11(type="Xlib").

• Force Quartz to bring the on-screen display up-to-date immediately before the snapshot is taken by grid.cap() in the Cocoa implementation. (PR#14260)

• model.frame had an unstated 500 byte limit on variable names. (Example reported by Terry Therneau.)

• The 256-byte limit on names is now documented.

• Subassignment by [, [[ or $ on an expression object with value NULL coerced the object to a list.

CHANGES IN R VERSION 2.11.1 patched

NEW FEATURES

• install.packages() has a new optional argument INSTALL_opts which can be used to pass options to R CMD INSTALL for source-package installs.

• R CMD check now runs the package-specific tests with to facilitate comparison to .Rout.save files.

• sessionInfo() gives more detailed platform information, including 32/64-bit and the sub-architecture if one is used.

DEPRECATED & DEFUNCT

• The use of Perl configuration variables for R CMD check (as previously documented in ‘Writing R Extensions’) is deprecated and will be removed in R 2.12.0. Use the environment variables documented in ‘R Internals’ instead.

BUG FIXES

• R CMD Rd2dvi failed if run from a path containing space(s). This also affected R CMD check, which calls Rd2dvi.

• stripchart() could fail with an empty factor level. (PR#14317)

• Text help rendering of \\tabular{} has been improved: under some circumstances leading blank columns were not rendered.

• strsplit(x, fixed=TRUE) marked UTF-8 strings with the local encoding when no splits were found.

• weighted.mean(NA, na.rm=TRUE) and similar now returns NaN again, as it did prior to R 2.10.0.

• R CMD had a typo in its detection of whether the environment variable was set (reported by Martin Morgan).

• The command-line parser could mistake for one of the options for setting limits for Ncells or Vcells.

• The internal strptime() could corrupt its copy of the timezone which would then lead to spurious warnings. (PR#14338)

• dir.create(recursive = TRUE) could fail if one of the components existed but was a directory on a read-only file system. (Seen on Solaris, where the error code returned is not even listed as possible on the man page.)

• The postscript() and pdf() devices will now allow lwd values less than 1 (they used to force such values to be 1).

• Fixed font face for CID fonts in pdf() graphics output. (PR#14326)

• GERaster() now checks for width or height of zero and does nothing in those cases; previously the behaviour was undefined, probably device-specific, and possibly dangerous.

• wilcox.test(x, y, conf.int = TRUE) failed with an unhelpful message if x and y were constant vectors, and similarly in the one-sample case. (PR#14329)

• Improperly calling Recall() from outside a function could cause a segfault. (Reported by Robert McGehee.)

• \\Sexpr[result=rd] in an Rd file added a spurious newline, which was displayed as extra whitespace when rendered.

• require(save = TRUE) recorded the names of packages it failed to load.

• packageStatus() could return a data frame with duplicate row names which could then not be printed.

• txtProgressBar(style = 2) did not work correctly.

  txtProgressBar(style = 3) did not display until a non-minimum value was set.

• contour() did not display dashed line types properly when contour lines were labelled. (Reported by David B. Thompson.)

• tools::undoc() again detects undocumented data objects. Of course, this also affects R CMD check.

• ksmooth(x,NULL) no longer segfaults.

• approxfun(), approx(), splinefun() and spline() could be confused by x values that were different but so close as to print identically. (PR#14377)

Note

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