Changes in R

Abstract

The ‘Changes in R’ article from the 2011-1 issue.

CHANGES IN R VERSION 2.13.0

SIGNIFICANT USER-VISIBLE CHANGES

• replicate() (by default) and vapply() (always) now return a higher-dimensional array instead of a matrix in the case where the inner function value is an array of dimension \(\ge 2\).

• Printing and formatting of floating point numbers is now using the correct number of digits, where it previously rarely differed by a few digits. (See “scientific” entry below.) This affects many *.Rout.save checks in packages.

NEW FEATURES

• normalizePath() has been moved to the base package (from utils): This is so it can be used by library() and friends.

  It now does tilde expansion.

  It gains new arguments winslash (to select the separator on Windows) and mustWork to control the action if a canonical path cannot be found.

• The previously barely documented limit of 256 bytes on a symbol name has been raised to 10,000 bytes (a sanity check). Long symbol names can sometimes occur when deparsing expressions (for example, in model.frame).

• reformulate() gains a intercept argument.

• cmdscale(add = FALSE) now uses the more common definition that there is a representation in n-1 or less dimensions, and only dimensions corresponding to positive eigenvalues are used. (Avoids confusion such as PR#14397.)

• Names used by c(), unlist(), cbind() and rbind() are marked with an encoding when this can be ascertained.

• R colours are now defined to refer to the sRGB color space.

  The PDF, PostScript, and Quartz graphics devices record this fact. X11 (and Cairo) and Windows just assume that your screen conforms.

• system.file() gains a mustWork argument (suggestion of Bill Dunlap).

• new.env(hash = TRUE) is now the default.

• list2env(envir = NULL) defaults to hashing (with a suitably sized environment) for lists of more than 100 elements.

• text() gains a formula method.

• IQR() now has a type argument which is passed to quantile().

• as.vector(), as.double(), etc., duplicate less when they leave the mode unchanged but remove attributes.

  as.vector(mode = "any") no longer duplicates when it does not remove attributes. This helps memory usage in matrix() and array().

  matrix() duplicates less if data is an atomic vector with attributes such as names (but no class).

  dim(x) <- NULL duplicates less if x has neither dimensions nor names (since this operation removes names and dimnames).

• setRepositories() gains an addURLs argument.

• chisq.test() now also returns a stdres component, for standardized residuals (which have unit variance, unlike the Pearson residuals).

• write.table() and friends gain a fileEncoding argument, to simplify writing files for use on other OSes (e.g. a spreadsheet intended for Windows or Mac OS X Excel).

• Assignment expressions of the form foo::bar(x) <- y and foo:::bar(x) <- y now work; the replacement functions used are foo::‘bar<-‘ and foo:::‘bar<-‘.

• Sys.getenv() gains a names argument so Sys.getenv(x, names = FALSE) can replace the common idiom of as.vector(Sys.getenv()). The default has been changed to not name a length-one result.

• Lazy loading of environments now preserves attributes and locked status. (The locked status of bindings and active bindings are still not preserved; this may be addressed in the future).

• options("install.lock") may be set to FALSE so that install.packages() defaults to –no-lock installs, or (on Windows) to TRUE so that binary installs implement locking.

• sort(partial = p) for large p now tries Shellsort if quicksort is not appropriate and so works for non-numeric atomic vectors.

• sapply() gets a new option simplify = "array" which returns a “higher rank” array instead of just a matrix when FUN() returns a dim() length of two or more.

  replicate() has this option set by default, and vapply() now behaves that way internally.

• aperm() becomes S3 generic and gets a table method which preserves the class.

• merge() and as.hclust() methods for objects of class "dendrogram" are now provided.

• as.POSIXlt.factor() now passes ... to the character method (suggestion of Joshua Ulrich).

• The character method of as.POSIXlt() now tries to find a format that works for all non-NA inputs, not just the first one.

• str() now has a method for class "Date" analogous to that for class "POSIXt".

• New function file.link() to create hard links on those file systems (POSIX, NTFS but not FAT) that support them.

• New Summary() group method for class "ordered" implements min(), max() and range() for ordered factors.

• mostattributes<-() now consults the "dim" attribute and not the dim() function, making it more useful for objects (such as data frames) from classes with methods for dim(). It also uses attr<-() in preference to the generics name<-(), dim<-() and dimnames<-(). (Related to PR#14469.)

• There is a new option "browserNLdisabled" to disable the use of an empty (e.g. via the ‘Return’ key) as a synonym for c in browser() or n under debug(). (Wish of PR#14472.)

• example() gains optional new arguments character.only and give.lines enabling programmatic exploration.

• serialize() and unserialize() are no longer described as ‘experimental’. The interface is now regarded as stable, although the serialization format may well change in future releases. (serialize() has a new argument version which would allow the current format to be written if that happens.)

  New functions saveRDS() and readRDS() are public versions of the ‘internal’ functions .saveRDS() and .readRDS() made available for general use. The dot-name versions remain available as several package authors have made use of them, despite the documentation.

  saveRDS() supports compress = "xz".

• Many functions when called with a not-open connection will now ensure that the connection is left not-open in the event of error. These include read.dcf(), dput(), dump(), load(), parse(), readBin(), readChar(), readLines(), save(), writeBin(), writeChar(), writeLines(), .readRDS(), .saveRDS() and tools::parse_Rd(), as well as functions calling these.

• Public functions find.package() and path.package() replace the internal dot-name versions.

• The default method for terms() now looks for a "terms" attribute if it does not find a "terms" component, and so works for model frames.

• httpd() handlers receive an additional argument containing the full request headers as a raw vector (this can be used to parse cookies, multi-part forms etc.). The recommended full signature for handlers is therefore function(url, query, body, headers, ...).

• file.edit() gains a fileEncoding argument to specify the encoding of the file(s).

• The format of the HTML package listings has changed. If there is more than one library tree, a table of links to libraries is provided at the top and bottom of the page. Where a library contains more than 100 packages, an alphabetic index is given at the top of the section for that library. (As a consequence, package names are now sorted case-insensitively whatever the locale.)

• isSeekable() now returns FALSE on connections which have non-default encoding. Although documented to record if ‘in principle’ the connection supports seeking, it seems safer to report FALSE when it may not work.

• R CMD REMOVE and remove.packages() now remove file R.css when removing all remaining packages in a library tree. (Related to the wish of PR#14475: note that this file is no longer installed.)

• unzip() now has a unzip argument like zip.file.extract(). This allows an external unzip program to be used, which can be useful to access features supported by Info-ZIP’s unzip version 6 which is now becoming more widely available.

• There is a simple zip() function, as wrapper for an external zip command.

• bzfile() connections can now read from concatenated bzip2 files (including files written with bzfile(open = "a")) and files created by some other compressors (such as the example of PR#14479).

• The primitive function c() is now of type BUILTIN.

• plot(<dendrogram>, .., nodePar=*) now obeys an optional xpd specification (allowing clipping to be turned off completely).

• nls(algorithm="port") now shares more code with nlminb(), and is more consistent with the other nls() algorithms in its return value.

• xz has been updated to 5.0.1 (very minor bugfix release).

• image() has gained a logical useRaster argument allowing it to use a bitmap raster for plotting a regular grid instead of polygons. This can be more efficient, but may not be supported by all devices. The default is FALSE.

• list.files()/dir() gains a new argument include.dirs() to include directories in the listing when recursive = TRUE.

• New function list.dirs() lists all directories, (even empty ones).

• file.copy() now (by default) copies read/write/execute permissions on files, moderated by the current setting of Sys.umask().

• Sys.umask() now accepts mode = NA and returns the current umask value (visibly) without changing it.

• There is a ! method for classes "octmode" and "hexmode": this allows xor(a, b) to work if both a and b are from one of those classes.

• as.raster() no longer fails for vectors or matrices containing NAs.

• New hook "before.new.plot" allows functions to be run just before advancing the frame in plot.new, which is potentially useful for custom figure layout implementations.

• Package tools has a new function compactPDF() to try to reduce the size of PDF files via qpdf or gs.

• tar() has a new argument extra_flags.

• dotchart() accepts more general objects x such as 1D tables which can be coerced by as.numeric() to a numeric vector, with a warning since that might not be appropriate.

• The previously internal function create.post() is now exported from utils, and the documentation for bug.report() and help.request() now refer to that for create.post().

  It has a new method = "mailto" on Unix-alikes similar to that on Windows: it invokes a default mailer via open (Mac OS X) or xdg-open or the default browser (elsewhere).

  The default for ccaddress is now getOption("ccaddress") which is by default unset: using the username as a mailing address nowadays rarely works as expected.

• The default for options("mailer") is now "mailto" on all platforms.

• unlink() now does tilde-expansion (like most other file functions).

• file.rename() now allows vector arguments (of the same length).

• The "glm" method for logLik() now returns an "nobs" attribute (which stats4::BIC() assumed it did).

  The "nls" method for logLik() gave incorrect results for zero weights.

• There is a new generic function nobs() in package stats, to extract from model objects a suitable value for use in BIC calculations. An S4 generic derived from it is defined in package stats4.

• Code for S4 reference-class methods is now examined for possible errors in non-local assignments.

• findClasses, getGeneric, findMethods and hasMethods are revised to deal consistently with the package= argument and be consistent with soft namespace policy for finding objects.

• tools::Rdiff() now has the option to return not only the status but a character vector of observed differences (which are still by default sent to stdout).

• The startup environment variables , , and are now treated more consistently. In all cases an empty value is considered to be set and will stop the default being used, and for the last two tilde expansion is performed on the file name. (Note that setting an empty value is probably impossible on Windows.)

• Using R –no-environ CMD, R –no-site-file CMD or R –no-init-file CMD sets environment variables so these settings are passed on to child R processes, notably those run by INSTALL, check and build. R –vanilla CMD sets these three options (but not –no-restore).

• smooth.spline() is somewhat faster. With cv=NA it allows some leverage computations to be skipped,

• The internal (C) function scientific(), at the heart of R’s format.info(x), format(x), print(x), etc, for numeric x, has been re-written in order to provide slightly more correct results, fixing PR#14491, notably in border cases including when digits >= 16, thanks to substantial contributions (code and experiments) from Petr Savicky. This affects a noticable amount of numeric output from R.

• A new function grepRaw() has been introduced for finding subsets of raw vectors. It supports both literal searches and regular expressions.

• Package compiler is now provided as a standard package. See ?compiler::compile for information on how to use the compiler. This package implements a byte code compiler for R: by default the compiler is not used in this release. See the ‘R Installation and Administration Manual’ for how to compile the base and recommended packages.

• Providing an exportPattern directive in a NAMESPACE file now causes classes to be exported according to the same pattern, for example the default from package.skeleton() to specify all names starting with a letter. An explicit directive to exportClassPattern will still over-ride.

• There is an additional marked encoding "bytes" for character strings. This is intended to be used for non-ASCII strings which should be treated as a set of bytes, and never re-encoded as if they were in the encoding of the currrent locale: useBytes = TRUE is autmatically selected in functions such as writeBin(), writeLines(), grep() and strsplit().

  Only a few character operations are supported (such as substr()).

  Printing, format() and cat() will represent non-ASCII bytes in such strings by a \\xab escape.

• The new function removeSource() removes the internally stored source from a function.

• "srcref" attributes now include two additional line number values, recording the line numbers in the order they were parsed.

• New functions have been added for source reference access: getSrcFilename(), getSrcDirectory(), getSrcLocation() and getSrcref().

• Sys.chmod() has an extra argument use_umask which defaults to true and restricts the file mode by the current setting of umask. This means that all the R functions which manipulate file/directory permissions by default respect umask, notably R CMD INSTALL.

• tempfile() has an extra argument fileext to create a temporary filename with a specified extension. (Suggestion and initial implementation by Dirk Eddelbuettel.)

  There are improvements in the way Sweave() and Stangle() handle non-ASCII vignette sources, especially in a UTF-8 locale: see ‘Writing R Extensions’ which now has a subsection on this topic.

• factanal() now returns the rotation matrix if a rotation such as "promax" is used, and hence factor correlations are displayed. (Wish of PR#12754.)

• The gctorture2() function provides a more refined interface to the GC torture process. Environment variables , , and can also be used to control the GC torture process.

• file.copy(from, to) no longer regards it as an error to supply a zero-length from: it now simply does nothing.

• rstandard.glm gains a type argument which can be used to request standardized Pearson residuals.

• A start on a Turkish translation, thanks to Murat Alkan.

• .libPaths() calls normalizePath(winslash = "/") on the paths: this helps (usually) present them in a user-friendly form and should detect duplicate paths accessed via different symbolic links.

SWEAVE CHANGES

• Sweave() has options to produce PNG and JPEG figures, and to use a custom function to open a graphics device (see ?RweaveLatex).
  (Based in part on the contribution of PR#14418.)

• The default for Sweave() is to produce only PDF figures (rather than both EPS and PDF).

• Environment variable can be used to supply defaults for existing or new options to be applied after the Sweave driver setup has been run.

• The Sweave manual is now included as a vignette in the utils package.

• Sweave() handles keep.source=TRUE much better: it could duplicate some lines and omit comments. (Reported by John Maindonald and others.)

C-LEVEL FACILITIES

• Because they use a C99 interface which a C++ compiler is not required to support, Rvprintf and REvprintf are only defined by R_ext/Print.h in C++ code if the macro R_USE_C99_IN_CXX is defined when it is included.

• pythag duplicated the C99 function hypot. It is no longer provided, but is used as a substitute for hypot in the very unlikely event that the latter is not available.

• R_inspect(obj) and R_inspect3(obj, deep, pvec) are (hidden) C-level entry points to the internal inspect function and can be used for C-level debugging (e.g., in conjunction with the p command in gdb).

• Compiling R with –enable-strict-barrier now also enables additional checking for use of unprotected objects. In combination with gctorture() or gctorture2() and a C-level debugger this can be useful for tracking down memory protection issues.

UTILITIES

• R CMD Rdiff is now implemented in R on Unix-alikes (as it has been on Windows since R 2.12.0).

• R CMD build no longer does any cleaning in the supplied package directory: all the cleaning is done in the copy.

  It has a new option –install-args to pass arguments to R CMD INSTALL for –build (but not when installing to rebuild vignettes).

  There is new option, –resave-data, to call tools::resaveRdaFiles() on the data directory, to compress tabular files (.tab, .csv etc) and to convert .R files to .rda files. The default, –resave-data=gzip, is to do so in a way compatible even with years-old versions of R, but better compression is given by –resave-data=best, requiring R >= 2.10.0.

  It now adds a datalist file for data directories of more than 1Mb.

  Patterns in .Rbuildignore are now also matched against all directory names (including those of empty directories).

  There is a new option, –compact-vignettes, to try reducing the size of PDF files in the inst/doc directory. Currently this tries qpdf: other options may be used in future.

  When re-building vignettes and a inst/doc/Makefile file is found, make clean is run if the makefile has a clean: target.

  After re-building vignettes the default clean-up operation will remove any directories (and not just files) created during the process: e.g. one package created a .R_cache directory.

  Empty directories are now removed unless the option –keep-empty-dirs is given (and a few packages do deliberately include empty directories).

  If there is a field BuildVignettes in the package DESCRIPTION file with a false value, re-building the vignettes is skipped.

• R CMD check now also checks for filenames that are case-insensitive matches to Windows’ reserved file names with extensions, such as nul.Rd, as these have caused problems on some Windows systems.

  It checks for inefficiently saved data/*.rda and data/*.RData files, and reports on those large than 100Kb. A more complete check (including of the type of compression, but potentially much slower) can be switched on by setting environment variable to TRUE.

  The types of files in the data directory are now checked, as packages are still misusing it for non-R data files.

  It now extracts and runs the R code for each vignette in a separate directory and R process: this is done in the package’s declared encoding. Rather than call tools::checkVignettes(), it calls tool::buildVignettes() to see if the vignettes can be re-built as they would be by R CMD build. Option –use-valgrind now applies only to these runs, and not when running code to rebuild the vignettes. This version does a much better job of suppressing output from successful vignette tests.

  The 00check.log file is a more complete record of what is output to stdout: in particular contains more details of the tests.

  It now check all syntactically valid Rd usage entries, and warns about assignments (unless these give the usage of replacement functions).

  .tar.xz compressed tarballs are now allowed, if tar supports them (and setting environment variable to internal ensures so on all platforms).

• R CMD check now warns if it finds inst/doc/makefile, and R CMD build renames such a file to inst/doc/Makefile.

INSTALLATION

• Installing R no longer tries to find perl, and R CMD no longer tries to substitute a full path for awk nor perl – this was a legacy from the days when they were used by R itself. Because a couple of packages do use awk, it is set as the make (rather than environment) variable .

• make check will now fail if there are differences from the reference output when testing package examples and if environment variable is set to a true value.

• The C99 double complex type is now required.

  The C99 complex trigonometric functions (such as csin) are not currently required (FreeBSD lacks most of them): substitutes are used if they are missing.

• The C99 system call va_copy is now required.

• If environment variable is set during configuration (for example in config.site) it is used unchanged in file etc/ldpaths rather than being appended to.

• configure looks for support for OpenMP and if found compiles R with appropriate flags and also makes them available for use in packages: see ‘Writing R Extensions’.

  This is currently experimental, and is only used in R with a single thread for colSums() and colMeans(). Expect it to be more widely used in later versions of R.

  This can be disabled by the –disable-openmp flag.

PACKAGE INSTALLATION

• R CMD INSTALL –clean now removes copies of a src directory which are created when multiple sub-architectures are in use. (Following a comment from Berwin Turlach.)

• File R.css is now installed on a per-package basis (in the package’s html directory) rather than in each library tree, and this is used for all the HTML pages in the package. This helps when installing packages with static HTML pages for use on a webserver. It will also allow future versions of R to use different stylesheets for the packages they install.

• A top-level file .Rinstignore in the package sources can list (in the same way as .Rbuildignore) files under inst that should not be installed. (Why should there be any such files? Because all the files needed to re-build vignettes need to be under inst/doc, but they may not need to be installed.)

• R CMD INSTALL has a new option –compact-docs to compact any PDFs under the inst/doc directory. Currently this uses qpdf, which must be installed (see ‘Writing R Extensions’).

• There is a new option –lock which can be used to cancel the effect of –no-lock or –pkglock earlier on the command line.

• Option –pkglock can now be used with more than one package, and is now the default if only one package is specified.

• Argument lock of install.packages() can now be use for Mac binary installs as well as for Windows ones. The value "pkglock" is now accepted, as well as TRUE and FALSE (the default).

• There is a new option –no-clean-on-error for R CMD INSTALL to retain a partially installed package for forensic analysis.

• Packages with names ending in . are not portable since Windows does not work correctly with such directory names. This is now warned about in R CMD check, and will not be allowed in R 2.14.x.

• The vignette indices are more comprehensive (in the style of browseVignetttes()).

DEPRECATED & DEFUNCT

• require(save = TRUE) is defunct, and use of the save argument is deprecated.

• R CMD check –no-latex is defunct: use –no-manual instead.

• R CMD Sd2Rd is defunct.

• The gamma argument to hsv(), rainbow(), and rgb2hsv() is deprecated and no longer has any effect.

• The previous options for R CMD build –binary (–auto-zip, –use-zip-data and –no-docs) are deprecated (or defunct): use the new option –install-args instead.

• When a character value is used for the EXPR argument in switch(), only a single unnamed alternative value is now allowed.

• The wrapper utils::link.html.help() is no longer available.

• Zip-ing data sets in packages (and hence R CMD INSTALL options –use-zip-data and –auto-zip, as well as the ZipData: yes field in a DESCRIPTION file) is defunct.

  Installed packages with zip-ed data sets can still be used, but a warning that they should be re-installed will be given.

• The ‘experimental’ alternative specification of a name space via .Export() etc is now defunct.

• The option –unsafe to R CMD INSTALL is deprecated: use the identical option –no-lock instead.

• The entry point pythag in Rmath.h is deprecated in favour of the C99 function hypot. A wrapper for hypot is provided for R 2.13.x only.

• Direct access to the "source" attribute of functions is deprecated; use deparse(fn, control="useSource") to access it, and removeSource(fn) to remove it.

• R CMD build –binary is now formally deprecated: R CMD INSTALL –build has long been the preferred alternative.

• Single-character package names are deprecated (and R is already disallowed to avoid confusion in Depends: fields).

BUG FIXES

• drop.terms and the [ method for class "terms" no longer add back an intercept. (Reported by Niels Hansen.)

• aggregate preserves the class of a column (e.g. a date) under some circumstances where it discarded the class previously.

• p.adjust() now always returns a vector result, as documented. In previous versions it copied attributes (such as dimensions) from the p argument: now it only copies names.

• On PDF and PostScript devices, a line width of zero was recorded verbatim and this caused problems for some viewers (a very thin line combined with a non-solid line dash pattern could also cause a problem). On these devices, the line width is now limited at 0.01 and for very thin lines with complex dash patterns the device may force the line dash pattern to be solid. (Reported by Jari Oksanen.)

• The str() method for class "POSIXt" now gives sensible output for 0-length input.

• The one- and two-argument complex maths functions failed to warn if NAs were generated (as their numeric analogues do).

• Added .requireCachedGenerics to the dont.mind list for library() to avoid warnings about duplicates.

• $<-.data.frame messed with the class attribute, breaking any S4 subclass. The S4 data.frame class now has its own $<- method, and turns dispatch on for this primitive.

• Map() did not look up a character argument f in the correct frame, thanks to lazy evaluation. (PR#14495)

• file.copy() did not tilde-expand from and to when to was a directory. (PR#14507)

• It was possible (but very rare) for the loading test in R CMD INSTALL to crash a child R process and so leave around a lock directory and a partially installed package. That test is now done in a separate process.

• plot(<formula>, data=<matrix>,..) now works in more cases; similarly for points(), lines() and text().

• edit.default() contained a manual dispatch for matrices (the "matrix" class didn’t really exist when it was written). This caused an infinite recursion in the no-GUI case and has now been removed.

• data.frame(check.rows = TRUE) sometimes worked when it should have detected an error. (PR#14530)

• scan(sep= , strip.white=TRUE) sometimes stripped trailing spaces from within quoted strings. (The real bug in PR#14522.)

• The rank-correlation methods for cor() and cov() with use = "complete.obs" computed the ranks before removing missing values, whereas the documentation implied incomplete cases were removed first. (PR#14488)

  They also failed for 1-row matrices.

• The perpendicular adjustment used in placing text and expressions in the margins of plots was not scaled by par("mex"). (Part of PR#14532.)

• Quartz Cocoa device now catches any Cocoa exceptions that occur during the creation of the device window to prevent crashes. It also imposes a limit of \(144 \text{ft}^2\) on the area used by a window to catch user errors (unit misinterpretation) early.

• The browser (invoked by debug(), browser() or otherwise) would display attributes such as "wholeSrcref" that were intended for internal use only.

• R’s internal filename completion now properly handles filenames with spaces in them even when the readline library is used. This resolves PR#14452 provided the internal filename completion is used (e.g., by setting rc.settings(files = TRUE)).

• Inside uniroot(f, ...), -Inf function values are now replaced by a maximally negative value.

• rowsum() could silently over/underflow on integer inputs (reported by Bill Dunlap).

• as.matrix() did not handle "dist" objects with zero rows.

CHANGES IN R VERSION 2.12.2 patched

NEW FEATURES

• max() and min() work harder to ensure that NA has precedence over NaN, so e.g. min(NaN, NA) is NA. (This was not previously documented except for within a single numeric vector, where compiler optimizations often defeated the code.)

BUG FIXES

• A change to the C function R_tryEval had broken error messages in S4 method selection; the error message is now printed.

• PDF output with a non-RGB color model used RGB for the line stroke color. (PR#14511)

• stats4::BIC() assumed without checking that an object of class "logLik" has an "nobs" attribute: glm() fits did not and so BIC() failed for them.

• In some circumstances a one-sided mantelhaen.test() reported the p-value for the wrong tail. (PR#14514)

• Passing the invalid value lty = NULL to axis() sent an invalid value to the graphics device, and might cause the device to segfault.

• Sweave() with concordance=TRUE could lead to invalid PDF files; Sweave.sty has been updated to avoid this.

• Non-ASCII characters in the titles of help pages were not rendered properly in some locales, and could cause errors or warnings.

• checkRd() gave a spurious error if the \\href macro was used.

CHANGES IN R VERSION 2.12.2

SIGNIFICANT USER-VISIBLE CHANGES

• Complex arithmetic (notably z^n for complex z and integer n) gave incorrect results since R 2.10.0 on platforms without C99 complex support. This and some lesser issues in trignometric functions have been corrected.

  Such platforms were rare (we know of Cygwin and FreeBSD). However, because of new compiler optimizations in the way complex arguments are handled, the same code was selected on x86_64 Linux with gcc 4.5.x at the default -O2 optimization (but not at -O).

• There is a workaround for crashes seen with several packages on systems using zlib 1.2.5: see the INSTALLATION section.

NEW FEATURES

• PCRE has been updated to 8.12 (two bug-fix releases since 8.10).

• rep(), seq(), seq.int() and seq_len() report more often when the first element is taken of an argument of incorrect length.

• The Cocoa back-end for the quartz() graphics device on Mac OS X provides a way to disable event loop processing temporarily (useful, e.g., for forked instances of R).

• kernel()’s default for m was not appropriate if coef was a set of coefficients. (Reported by Pierre Chausse.)

• bug.report() has been updated for the current R bug tracker, which does not accept emailed submissions.

• R CMD check now checks for the correct use of $(LAPACK_LIBS) (as well as $(BLAS_LIBS)), since several CRAN recent submissions have ignored ‘Writing R Extensions’.

INSTALLATION

• The zlib sources in the distribution are now built with all symbols remapped: this is intended to avoid problems seen with packages such as XML and rggobi which link to zlib.so.1 on systems using zlib 1.2.5.

• The default for and with gfortran on x86_64 Linux has been changed back to -g -O2: however, setting -g -O may still be needed for gfortran 4.3.x.

PACKAGE INSTALLATION

• A LazyDataCompression field in the DESCRIPTION file will be used to set the value for the –data-compress option of R CMD INSTALL.

• Files R/sysdata.rda of more than 1Mb are now stored in the lazyload database using xz compression: this for example halves the installed size of package Imap.

• R CMD INSTALL now ensures that directories installed from inst have search permission for everyone.

  It no longer installs files inst/doc/Rplots.ps and inst/doc/Rplots.pdf. These are almost certainly left-overs from Sweave runs, and are often large.

DEPRECATED & DEFUNCT

• The ‘experimental’ alternative specification of a name space via .Export() etc is now deprecated.

• zip.file.extract() is now deprecated.

• Zip-ing data sets in packages (and hence R CMD INSTALL –use-zip-data and the ZipData: yes field in a DESCRIPTION file) is deprecated: using efficiently compressed .rda images and lazy-loading of data has superseded it.

BUG FIXES

• identical() could in rare cases generate a warning about non-pairlist attributes on CHARSXPs. As these are used for internal purposes, the attribute check should be skipped. (Reported by Niels Richard Hansen).

• If the filename extension (usually .Rnw) was not included in a call to Sweave(), source references would not work properly and the keep.source option failed. (PR#14459)

• format.data.frame() now keeps zero character column names.

• pretty(x) no longer raises an error when x contains solely non-finite values. (PR#14468)

• The plot.TukeyHSD() function now uses a line width of 0.5 for its reference lines rather than lwd = 0 (which caused problems for some PDF and PostScript viewers).

• The big.mark argument to prettyNum(), format(), etc. was inserted reversed if it was more than one character long.

• R CMD check failed to check the filenames under man for Windows’ reserved names.

• The "Date" and "POSIXt" methods for seq() could overshoot when to was supplied and by was specified in months or years.

• The internal method of untar() now restores hard links as file copies rather than symbolic links (which did not work for cross-directory links).

• unzip() did not handle zip files which contained filepaths with two or more leading directories which were not in the zipfile and did not already exist. (It is unclear if such zipfiles are valid and the third-party C code used did not support them, but PR#14462 created one.)

• combn(n, m) now behaves more regularly for the border case \(m = 0\). (PR#14473)

• The rendering of numbers in plotmath expressions (e.g. expression(10^2)) used the current settings for conversion to strings rather than setting the defaults, and so could be affected by what has been done before. (PR#14477)

• The methods of napredict() and naresid() for na.action = na.exclude fits did not work correctly in the very rare event that every case had been omitted in the fit. (Reported by Simon Wood.)

• weighted.residuals(drop0=TRUE) returned a vector when the residuals were a matrix (e.g. those of class "mlm"). (Reported by Bill Dunlap.)

• Package HTML index files <pkg>/html/00Index.html were generated with a stylesheet reference that was not correct for static browsing in libraries.

• ccf(na.action = na.pass) was not implemented.

• The parser accepted some incorrect numeric constants, e.g. 20x2. (Reported by Olaf Mersmann.)

• format(*, zero.print) did not always replace the full zero parts.

• Fixes for subsetting or subassignment of "raster" objects when not both i and j are specified.

• R CMD INSTALL was not always respecting the ZipData: yes field of a DESCRIPTION file (although this is frequently incorrectly specified for packages with no data or which specify lazy-loading of data).

  R CMD INSTALL –use-zip-data was incorrectly implemented as –use-zipdata since R 2.9.0.

• source(file, echo=TRUE) could fail if the file contained #line directives. It now recovers more gracefully, but may still display the wrong line if the directive gives incorrect information.

• atan(1i) returned NaN+Infi (rather than 0+Infi) on platforms without C99 complex support.

• library() failed to cache S4 metadata (unlike loadNamespace()) causing failures in S4-using packages without a namespace (e.g. those using reference classes).

• The function qlogis(lp, log.p=TRUE) no longer prematurely overflows to Inf when exp(lp) is close to 1.

• Updating S4 methods for a group generic function requires resetting the methods tables for the members of the group (patch contributed by Martin Morgan).

• In some circumstances (including for package XML), R CMD INSTALL installed version-control directories from source packages.

• Added PROTECT calls to some constructed expressions used in C level eval calls.

• utils:::create.post() (used by bug.report() and help.request()) failed to quote arguments to the mailer, and so often failed.

• bug.report() was naive about how to extract maintainer email addresses from package descriptions, so would often try mailing to incorrect addresses.

• debugger() could fail to read the environment of a call to a function with a ... argument. (Reported by Charlie Roosen.)

• prettyNum(c(1i, NA), drop0=TRUE) or str(NA_complex_) now work correctly.