NEWS for R version 2.13.

0 (2011-04-13)
R News

NEWS

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 >= 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.

NEWS
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.

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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-ZIPs unzip version 6 which is now becoming more widely available.
There is a simple zip() function, as wrapper for an external zip command.

NEWS
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.

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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 R_ENVIRON_USER, R_ENVIRON, R_PROFILE_USER
and R_PROFILE 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 Rs 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.

NEWS
"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 R_GCTORTURE, R_GCTORTURE_WAIT, and
R_GCTORTURE_INHIBIT_RELEASE 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 SWEAVE_OPTIONS 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.

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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 --resavedata=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
_R_CHECK_COMPACT_DATA2_ 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 packages 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

NEWS
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 TAR 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 AWK.
make check will now fail if there are differences from the reference output when
testing package examples and if environment variable R_STRICT_PACKAGE_CHECK 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 R_LD_LIBRARY_PATH 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 packages 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).

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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:

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NEWS
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 didnt
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 ft2 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.

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Rs 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).

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NEWS
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 FFLAGS and FCFLAGS 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)

NEWS

13
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).

14

NEWS
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.

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 S4 reference class utility methods copy(), field(), getRefClass() and getClass() have been added to package methods.
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 FCLIBS 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.

NEWS

15
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.

16

NEWS
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 packages CITATION file now defaults to ASCII rather than Latin1: 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)

NEWS

17
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 texinfos 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.)

18

NEWS
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 R_DVIPSCMD, R_LATEXCMD, R_MAKEINDEXCMD, R_PDFLATEXCMD
are no longer used nor set in an R session. (With the move to tools::texi2dvi(),
the conventional environment variables LATEX, MAKEINDEX and PDFLATEX will be used.
options("dvipscmd") defaults to the value of DVIPS, 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 userdefined 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 !=).

NEWS

19
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 singlebyte 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.)

20

NEWS
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). --with-system-bzlib
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 TAR 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 --no-manual.
R CMD Sd2Rd is formally deprecated and will be removed in R 2.13.0.

NEWS

21

PACKAGE INSTALLATION:
install.packages() has a new argument libs_only to optionally pass --libsonly 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 --no-lock 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.
NB: 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 PERL5LIB and PERLLIB.
R CMD check has a new argument --extra-arch 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 R_LIBS 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 --multiarch to check the package under all of the installed
sub-architectures and --no-multiarch 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 --nomultiarch).
It will skip the check for non-ascii characters in code or data if the environment
variables _R_CHECK_ASCII_CODE_ or _R_CHECK_ASCII_DATA_ are respectively set to
FALSE. (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 R_LIBS will
always be used.

22

NEWS
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 subarchitecture.
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.

NEWS

23
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)

24

NEWS
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 Pangos 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.

NEWS

25
R CMD check now runs the package-specific tests with LANGUAGE=en 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 TEXINPUTS
was set (reported by Martin Morgan).
The command-line parser could mistake --file=size... 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.

26

NEWS
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)

CHANGES IN R VERSION 2.11.1

NEW FEATURES:
R CMD INSTALL checks if dependent packages are available early on in the installation
of source packages, thereby giving clearer error messages.
R CMD INSTALL --build now names the file in the format used for Mac OS X binary
files on that platform.
BIC() in package stats4 now also works with multiple fitted models, analogously to
AIC().

DEPRECATED & DEFUNCT:

Use of file extension .C for C++ code in packages is now deprecated: it has caused
problems for some makes on case-insensitive file systems (although it currently works
with the recommended toolkits).

INSTALLATION:
Command gnutar is preferred to tar when configure sets TAR. This is needed on Mac
OS 10.6, where the default tar, bsdtar 2.6.2, has been reported to produce archives
with illegal extensions to tar (according to the POSIX standard).

BUG FIXES:
The C function mkCharLenCE now no longer reads past len bytes (unlikely to be a
problem except in user code). (PR#14246)
On systems without any default LD_LIBRARY_PATH (not even /usr/local/lib),
[DY]LIB_LIBRARY_PATH is now set without a trailing colon. (PR#13637)
More efficient implementation of utf8ToInt() on long multi-byte strings with many
multi-byte characters. (PR#14262)
aggregate.ts() gave platform-dependent results due to rounding error for ndeltat
!= 1.
package.skeleton() sometimes failed to fix filenames for .R or .Rd files to start
with an alphanumeric. (PR#14253)
It also failed when only an S4 class without any methods was defined. (PR#14280)
splinefun(method = "monoH.FC") was not quite monotone in rare cases.
(PR#14215)
Rhttpd no longer crashes due to SIGPIPE when the client closes the connection prematurely. (PR#14266)
format.POSIXlt() could cause a stack overflow and crash when used on very long
vectors. (PR#14267)

NEWS

27
Rd2latex() incorrectly escaped special characters in \usage sections.
mcnemar.test() could alter the levels (dropping unused levels) if passed x and y as
factors (reported by Greg Snow).
Rd2pdf sometimes needed a further pdflatex pass to get hyperlinked pages correct.
interaction() produced malformed results when levels were duplicated, causing
segfaults in split().
cut(d, breaks = <n>) now also works for "Date" or "POSIXt" argument d.
(PR#14288)
memDecompress() could decompress incompletely rare xz-compressed input due to
incorrect documentation of xz utils. (Report and patch from Olaf Mersmann.)
The S4 initialize() methods for "matrix", "array", and "ts" have been fixed to
call validObject(). (PR#14284)
R CMD INSTALL now behaves the same way with or without --no-multiarch on
platforms with only one installed architecture. (It used to clean the src directory
without --no-multiarch.)
[<-.data.frame was not quite careful enough in assigning (and potentially deleting)
columns right-to-left. (PR#14263)
rbeta(n, a, b) no longer occasionally returns NaN for a >> 1 > b. (PR#14291)
pnorm(x, log.p = TRUE) could return NaN not -Inf for x near (minus for
lower.tail=TRUE) the largest representable number.
Compressed data files *.(txt|tab|csv).(gz|bz2|xz) were not recognized for the
list of data topics and hence for packages using LazyData. (PR#14273)
textConnection() did an unnecessary translation on strings in a foreign encoding
(e.g. UTF-8 strings on Windows) and so was slower than it could have been on very
long input strings. (PR#14286)
tools::Rd2txt() did not render poorly written Rd files consistently with other renderers.
It computed widths of strings that would be print()ed with escapes incorrectly, for
example in the computation of column width for \tabular.
na.action() did not extract the na.action component as documented.
do.call()ing NextMethod in erronous ways no longer segfaults. (PR#13487)

CHANGES IN R VERSION 2.11.0

SIGNIFICANT USER-VISIBLE CHANGES:
Packages must have been installed under R >= 2.10.0, as the current help system is
the only one now supported.
A port to 64-bit Windows is now available as well as binary package repositiories: see
the R Administration and Installation Manual.
Argument matching for primitive functions is now done in the same way as for interpreted functions except for the deliberate exceptions
call switch .C .Fortran .Call .External

all of which use positional matching for their first argument, and also some internaluse-only primitives.

28

NEWS
The default device for command-line R at the console on Mac OS X is now quartz()
and not X11().

NEW FEATURES:
The open modes for connections are now interpreted more consistently. open = "r"
is now equivalent to open = "rt" for all connections. The default open = "" now
means "rt" for all connections except the compressed-file connections gzfile(),
bzfile() and xzfile() for which it means "rb".
R CMD INSTALL now uses the internal untar() function in package utils: this ensures
that all platforms can install bzip2- and xz-compressed tarballs. In case this causes
problems (as it has on some Windows file systems when run from Cygwin tools) it can
be overridden by the environment variable R_INSTALL_TAR: setting this to a modern
external tar program will speed up unpacking of large (tens of Mb or more) tarballs.
help(try.all.packages = TRUE) is much faster (although the time taken by the
OS to find all the packages the first time it is used can dominate the time).
R CMD check has a new option --timings to record per-example timings in file
<pkg>.Rcheck/<pkg>-Ex.timings.
The TRE library has been updated to version 0.8.0 (minor bugfixes).
grep[l], [g]sub and [g]regexpr now work in bytes in an 8-bit locales if there is no
marked UTF-8 input string: this will be somewhat faster, and for [g]sub() give the
result in the native encoding rather than in UTF-8 (which returns to the behaviour
prior to R 2.10.0).
A new argument skipCalls has been added to browser() so that it can report the
original context when called by other debugging functions.
More validity checking of UTF-8 and MBCS strings is done by agrep() and the
regular-expression matching functions.
The undocumented restriction on gregexpr() to length(text) > 0 has been removed.
Package tcltk now sends strings to Tcl in UTF-8: this means that strings with a
marked UTF-8 encoding are supported in non-UTF-8 locales.
The graphics engine now supports rendering of raster (bitmap) images, though not
all graphics devices can provide (full) support. Packages providing graphics devices
(e.g., Cairo, RSvgDevice, cairoDevice) will need to be reinstalled.
There is also support in the graphics engine for capturing raster images from graphics
devices (again not supported on all graphics devices).
R CMD check now also checks if the package and namespace can be unloaded:
this provides a check of the .Last.lib() and .onUnload() hook functions (unless
--install=fake).
prop.table(x) now accepts a one-dimensional table for x.
A new function vapply() has been added, based on a suggestion from Bill Dunlap. It
requires that a template for the function value be specified, and uses it to determine
the output type and to check for consistency in the function values.
The main HTML help page now links to a reformatted copy of this NEWS file. (Suggested by Henrik Bengtsson.) Package index files link to the package DESCRIPTION
and NEWS files and a list of demos when using dynamic help.
The [ method for class "AsIs" allows the next method to change the underlying class.
(Wish of Jens Oehlschl
agel.)

NEWS

29
write.csv[2] no longer allow argument append to be changed: as ever, direct calls
to write.table() give more flexibility as well as more room for error.
The index page for HTML help for a package now collapses multiple signatures for
S4 methods into a single entry.
The use of .required by require() and detach() has been replaced by .Depends
which is set from the Depends field of a package (even in packages with name spaces).
By default detach() prevents such dependencies from being detached: this can be
overridden by the argument force.
bquote() has been extended to work on function definitions. (Wish of PR#14031).
detach() when applied to an object other than a package returns the environment
that has been detached, to parallel attach().
readline() in non-interactive use returns "" and does not attempt to read from the
terminal.
New function file_ext() in package tools.
xtfrm() is now primitive and internally generic, as this allows S4 methods to be set
on it without name-space scoping issues.
There are now "AsIs" and "difftime" methods, and the default method uses
unclass(x) if is.numeric(x) is true (which will be faster but relies on is.numeric()
having been set correctly for the class).
is.numeric(x) is now false for a "difftime" object (multiplication and division
make no sense for such objects).
The default method of weighted.mean(x, w) coerces w to be numeric (aka double);
previously only integer weights were coerced. Zero weights are handled specially so
an infinite value with zero weight does not force an NaN result.
There is now a "difftime" method.
bug.report() now has arguments package and lib.loc to generate bug reports
about packages. When this is used, it looks for a BugReports field in the package
DESCRIPTION file, which will be assumed to be a URL at which to submit the report,
and otherwise generates an email to the package maintainer. (Suggested by Barry
Rowlingson.)
quantile() now has a method for the date-time class "POSIXt", and types 1 and 3
(which never interpolate) work for Dates and ordered factors.
length(<POSIXlt>) now returns the length of the corresponding abstract timedatevector rather than always 9 (the length of the underlying list structure). (Wish of
PR#14073 and PR#10507.)
The readline completion backend no longer sorts possible completions alphabetically
(e.g., function argument names) if R was built with readline >= 6.
select.list() gains a graphics argument to allow Windows/Mac users to choose
the text interface. This changes the behaviour of new.packages(ask=TRUE) to be
like update.packages(ask=TRUE) on those platforms in using a text menu: use
ask="graphics" for a graphical menu.
New function chooseBioCmirror() to set the "BioC_mirror" option.
The R grammar now prevents using the argument name in signatures of S4 methods
for $ and $<-, since they will always be called with a character string value for name.
The implicit S4 generic functions have been changed to reflect this: packages which
included name in the signature of their methods need to be updated and re-installed.

30

NEWS
The handling of the method argument of glm() has been refined following suggestions
by Ioannis Kosmidis and Heather Turner.
str() gains a new argument list.len with default 99, limiting the number of list()
items (per level), thanks to suggestions from David Winsenius.
Having formal arguments of an S4 method in a different order from the generic is now
an error (the warning having been ignored by some package maintainers for a long
time).
New functions enc2native() and enc2utf8() convert character vectors with possibly
marked encodings to the current locale and UTF-8 respectively.
Unrecognized escapes and embedded nuls in character strings are now an error, not
just a warning. Thus option "warnEscapes" is no longer needed. rawToChar() now
removes trailing nuls silently, but other embedded nuls become errors.
Informational messages about masked objects displayed when a package is attached
are now more compact, using strwrap() instead of one object per line.
print.rle() gains argument prefix.
download.file() gains a "curl" method, mainly for use on platforms which have
curl but not wget, but also for some hard-to-access URLs.
In Rd, \eqn and \deqn will render in HTML (and convert to text) upper- and
lower-case Greek letters (entered as \alpha . . . ), ..., ..., \ge and \le.
utf8ToInt() and intToUtf8() now map NA inputs to NA outputs.
file() has a new argument raw which may help if it is used with something other
than a regular file, e.g. a character device.
New function strtoi(), a wrapper for the C function strtol.
as.octmode() and as.hexmode() now allow inputs of length other than one.
The format() and print() methods for "octmode" now preserve names and dimensions (as those for "hexmode" did).
The format() methods for classes "octmode" and "hexmode" gain a width argument.
seq.int() returns an integer result in some further cases where seq() does, e.g.
seq.int(1L, 9L, by = 2L).
Added \subsection{}{} macro to Rd syntax, for subsections within sections.
n-dimensional arrays with dimension names can now be indexed by an n-column
character matrix. The indices are matched against the dimension names. NA indices
are propagated to the result. Unmatched values and "" are not allowed and result in
an error.
interaction(drop=TRUE) uses less memory (related to PR#14121).
summary() methods have been added to the "srcref" and "srcfile" classes, and
various encoding issues have been cleaned up.
If option "checkPackageLicense" is set to TRUE (not currently the default), users
will be asked to agree to non-known-to-be-FOSS package licences at first use.
Checking setAs(a, b) methods only gives a message instead of a warning, when one
of a or b is unknown.
New function norm() to compute a matrix norm. norm() and also backsolve() and
sample() have implicit S4 generics.
Files Renviron.site and Rprofile.site can have architecture-specific versions
on systems with sub-architectures.

NEWS

31
R CMD check now (by default) also checks Rd files for auto-generated content in need
of editing, and missing argument descriptions.
aggregate() gains a formula method thanks to a contribution by Arni Magnusson.
The data frame method now allows summary functions to return arbitrarily many
values.
path.expand() now propagates NA values rather than converting them to "NA".
file.show() now disallows NA values for file names, headers, and pager.
The fuzz used by seq() and seq.int() has been reduced from 1e-7 to 1e-10, which
should be ample for the double-precision calculations used in R. It ensures that the
fuzz never comes into play with sequences of integers (wish of PR#14169).
The default value of RSiteSearch(restrict=) has been changed to include vignettes
but to exclude R-help. The R-help archives available have been split, with a new
option of "Rhelp10" for those from 2010.
New function rasterImage() in the graphics package for drawing raster images.
stats:::extractAIC.coxph() now omits aliased terms when computing the degrees
of freedom (suggestion of Terry Therneau).
cor() and cov() now test for misuse with non-numeric arguments, such as the nonbug report PR#14207.
pchisq(ncp =, log.p = TRUE) is more accurate for probabilities near one. E.g.
pchisq(80, 4, ncp=1, log.p=TRUE). (Maybe what was meant in PR#14216.)
maintainer() has been added, to give convenient access to the name of the maintainer
of a package (contributed by David Scott).
sample() and sample.int() allow zero items to be sampled from a zero-length input.
sample.int() gains a default value size=n to be more similar to sample().
switch() returned NULL on error (not previously documented on the help page): it
now does so invisibly, analogously to if-without-else.
It is now primitive: this means that argument EXPR is always matched to the first
argument and there is no danger of partial matching to later named arguments.
Primitive functions UseMethod(), attr(), attr<-(), on.exit(), retracemem() and
substitute() now use standard argument matching (rather than positional matching). This means that all multi-argument primitives which are not internal now use
standard argument matching except where positional matching is desirable (as for
switch(), call(), .C() ...).
All the one-argument primitives now check that any name supplied for their first
argument is a partial match to the argument name as documented on the help page:
this also applies to replacement functions of two arguments.
base::which() uses a new .Internal function when arr.ind is FALSE resulting in
a 10x speedup. Thanks to Patrick Aboyoun for implementation suggestions.
Help conversion to text now uses the first part of \enc{}{} markup if it is representable in the current output encoding. On the other hand, conversion to LaTeX
with the default outputEncoding = "ASCII" uses the second part.
A new class "listOfMethods" has been introduced to represent the methods in a
methods table, to replace the deprecated class "MethodsList".
any() and all() return early if possible. This may speed up operations on long
vectors.

32

NEWS
strptime() now accepts "%z" (for the offset from UTC in the RFC822 format of
+/-hhmm).
The PCRE library has been updated to version 8.02, a bug-fix release which also
updates tables to Unicode 5.02.
Functions which may use a graphical select.list() (including menu() and
install.packages()) now check on a Unix-alike that Tk can be started (and not
just capabilities("tcltk") && capabilities("X11")).
The parser no longer marks strings containing octal or hex escapes as being in UTF-8
when entered in a UTF-8 locale.
On platforms with cairo but not Pango (notably Mac OS X) the initial default X11()
type is set to "Xlib": this avoids several problems with font selection when done by
cairo rather than Pango (at least on Mac OS X).
New function arrayInd() such that which(x, arr.ind = TRUE) for an array x is
now equivalent to arrayInd(which(x), dim(x), dimnames(x)).

DEPRECATED & DEFUNCT:

Bundles of packages are defunct.
stats::clearNames() is defunct: use unname().
Basic regular expressions are defunct, and strsplit(), grep(), grepl(), sub(),
gsub(), regexpr() and gregexpr() no longer have an extended argument.
methods::trySilent() is defunct.
index.search() (which was deprecated in 2.10.0) is no longer exported and has a
different argument list.
Use of multiple arguments to return() is now defunct.
The use of UseMethod() with more than two arguments is now defunct.
In the methods package, the "MethodsList" metadata objects which had been superseded by hash tables (environments) since R 2.8.0 are being phased out. Objects
of this class are no longer assigned or used as metadata by the package.
getMethods() is now deprecated, with its internal use replaced by findMethods()
and other changes. Creating objects from the "MethodsList" class is also deprecated.
Parsing strings containing both octal/hex and Unicode escapes now gives a warning
and will become an error in R 2.12.0.

INSTALLATION:
UTF-8 is now used for the reference manual and package manuals. This requires
LaTeX 2005/12/01 or later.
configure looks for a POSIX compliant tr, Solariss /usr/ucb/tr having been found
to cause Rdiff to malfunction.
configure is now generated with autoconf 2.65, which works better on recent systems and on Mac OS X.

PACKAGE INSTALLATION:
Characters in R source which are not translatable to the current locale are now handled
more tolerantly: these will be converted to hex codes with a warning. Such characters
are only really portable if they appear in comments.

NEWS

33
R CMD INSTALL now tests that the installed package can be loaded (and backs out the
installation if it cannot): this can be suppressed by --no-test-load. This avoids
installing/updating a package that cannot be used: common causes of failures to load
are missing/incompatible external software and missing/broken dependent packages.
Package installation on Windows for a package with a src directory now checks if
a DLL is created unless there is a src/Makefile.win file: this helps catch broken
installations where the toolchain has not reported problems in building the DLL.
(Note: this can be any DLL, not just one named <pkg-name>.dll.)

BUG FIXES:
Using with(), eval() etc with a list with some unnamed elements now works.
(PR#14035)
The "quick" dispatch of S4 methods for primitive functions was not happening,
forcing a search each time. (Dispatch for closures was not affected.) A side effect is
that default values for arguments in a method that do not have defaults in the generic
will now be ignored.
Trying to dispatch S4 methods for primitives during the search for inherited methods
slows that search down and potentially could cause an infinite recursion. An internal
switch was added to turn off all such methods from findInheritedMethods().
R framework installation (on Mac OS X) would not work properly if a rogue
Resources directory was present at the top level. Such a non-symlink will now be renamed to Resources.old (and anything previously named Resources.old removed)
as part of the framework installation process.
The checks for conforming S4 method arguments could fail when the signature of the
generic function omitted some of the formal arguments (in addition to ...). Arguments omitted from the method definition but conforming (per the documentation)
should now be ignored (treated as "ANY") in dispatching.
The computations for S4 method evaluation when ... was in the signature could
fail, treating ... as an ordinary symbol. This has been fixed, for the known cases.
Various ar() fitting methods have more protection for singular fits.
callNextMethod now works again with the drop= argument in [
parse() and parse_Rd() miscounted columns when multibyte UTF-8 characters were
present.
Formatting of help pages has had minor improvements: extra blank lines have been
removed from the text format, and empty package labels removed from HTML.
cor(A, B) where A is n 1 and B a 1-dimensional array segfaulted or gave an internal
error. (The case cor(B, A) was PR#7116.)
cut.POSIXt() applied to a start value after the DST transition on a DST-change
day could give the wrong time for argument breaks in units of days or longer.
(PR#14208)
do_par() UNPROTECTed too early (PR#14214)
Subassignment x[[....]] <- y didnt check for a zero-length right hand side, and
inserted a rubbish value. (PR#14217)
fisher.test() no longer gives a P-value very slightly > 1, in some borderline cases.
Internal function matchArgs() no longer modifies the general purpose bits of the
SEXPs that make up the formals list of R functions. This fixes an invalid error message

34

NEWS
that would occur when a garbage collection triggered a second call to matchArgs for
the same function via a finalizer.
gsub() in 2.10.x could fail from stack overflow for extremely long strings due to
temporary data being allocated on the stack. Also, gsub() with fixed=TRUE is in
some circumstances considerably faster.
Several primitives, including attributes(), attr<-() interactive(), nargs() and
proc.time(), did not check that they were called with the correct number of arguments.
A potential race condition in list.files() when other processes are operating on
the directory has been fixed; the code now dynamically allocates memory for file
listings in a single pass instead of making an initial count pass.
mean(x, trim=, na.rm = FALSE) failed to return NA if x contained missing values.
(Reported by Bill Dunlap.)
Extreme tail behavior of, pbeta() {and hence pf()}, e.g., pbeta(x, 3, 2200,
lower.tail=FALSE, log.p=TRUE) now returns finite values instead of jumping to
-Inf too early. (PR#14230).
parse(text=x) misbehaved for objects x that were not coerced internally to character, notably symbols. (Reported to R-devel by Bill Dunlap.)
The internal C function coerceSymbol now handles coercion to character, and warns
if coercion fails (rather than silently returning NULL). This allows a name to be given
where a character vector is required in functions which coerce internally.
The interpretation by strptime() of "%c" was non-standard (not that it is ever
advisable to use locale- and system-specific input formats).
capabilities("X11") now works the same way on Mac OS X as on other platforms (and
as documented: it was always true for R built with --with-aqua, as the CRAN
builds are).
The X11() device with cairo but not Pango (notably Mac OS X) now checks validity
of text strings in UTF-8 locales (since Pango does but cairo it seems does not).
read.fwf() misread multi-line records when n was specified. (PR#14241)
all.equal(tolerance = e) passes the numeric tolerance also to the comparison of
the attributes.
pgamma(0, 0), a boundary case, now returns 0, its limit from the left, rather than
the limit from the right.
Issuing POST requests to the internal web server could stall the request under certain
circumstances.
gzcon( <textConnection> ), an error, no longer damages the connection (in a way
to have it segfault). (PR#14237)
All the results from hist() now use the nominal breaks not those adjusted by the
numeric fuzz: in recent versions the nominal breaks were reported but the density
referred to the intervals used in the calculation which mattered very slightly for one
of the extreme bins. (Based on a report by Martin Becker.)
If xy[z].coords (used internally by many graphics functions) are given a list as x,
they now check that the list has suitable names and give a more informative error
message. (PR#13936)

NEWS

35

CHANGES IN R VERSION 2.10.1 patched

NEW FEATURES:
The handling of line textures in the postscript() and pdf() devices was set up for
round end caps (the only type which existed at the time): it has now been adjusted
for butt endcaps.
lchoose(a, k) is now defined as log(abs(choose(a,k))), analogously to
lfactorial().
Although \eqn{} in Rd files is defined as a verbatim macro, many packages expected
... and ... to be interpreted there (as was the case in R < 2.10.0), so this is now
done (using an ellipsis in HTML rendering).
Escaping of braces in quoted strings in R-code sections of Rd files is allowed again.
This had been changed for the new Rd format in R 2.10.0 but was only documented
on the developer site and was handled inconsistently by the converters: text and
example conversion removed the escapes but HTML conversion did not.
The PCRE library has been updated to version 8.01, a bug-fix release.
tools::readNEWS() now accepts a digit as the first character of a news section.

BUG FIXES:
Using read.table(header=TRUE) on a header with an embedded new line would copy
part of the header into the data. (PR#14103)
qpois(p = 1, lambda = 0) now gives 0 as for all other p. (PR#14135)
Functions related to string comparison (e.g. unique(), match()) could cause crashes
when used with strings not in the native encoding, e.g. UTF-8 strings on Windows.
(PR#14114 and PR#14125)
x[ , drop=TRUE] dropped an NA level even if it was in use.
The dynamic HTML help system reported the wrong MIME type for the style sheet.
tools::codoc() (used by R CMD check) was missing cases where the function had
no arguments but was documented to have some.
Help links containing special characters (e.g. "?") were not generated correctly when
rendered in HTML. (PR#14155)
lchoose(a, k) no longer wrongly gives NaN for negative a.
ks.test() could give a p-value that was off by one observation due to rounding error.
(PR#14145)
readBin()/readChar() when reading millions of character strings in a single call
used excessive amounts of memory (which also slowed them down).
R CMD SHLIB could fail if used with paths that were not alphanumeric, e.g. contained
+. (PR#14168)
sprintf() was not re-entrant, which potentially caused problems if an
as.character() method called it.
The quartz() device did not restore the clipping region when filling the background
for a new page. This could be observed in multi-page bitmap output as stale outer
regions of the plot.
p.adjust(method, n) now works correctly for the rare case n > length(p), also
when method differs from "bonferroni" or "none", thanks to a patch from Gordon
Smyth.

36

NEWS
tools::showNonASCII() failed to detect non-ASCII characters if iconv() (incorrectly) converted them to different ASCII characters. (Seen on Windows only.)
tcrossprod() wrongly failed in some cases when one of the arguments was a vector
and the other a matrix.
[cr]bind(..., deparse.level=2) was not always giving names when documented
to do so. (Discovered whilst investigating PR#14189.)
match(incomparables=<non-NULL>) could in rare cases infinite-loop.
poisson.test() needed to pass argument conf.level to binom.test().
(PR#14195)
The "nls" method for df.residual() gave incorrect results for models fitted with
na.action = na.exclude. (PR#14194)
A change to options(scipen=) was only implemented when printing next occurred,
even though it should have affected intervening calls to axis(), contour() and
filledcontour().
prettyNum(drop0trailing=TRUE) did not handle signs of imaginary parts of complex
numbers correctly (and this was used by str(): PR#14201).
system.time() had the sys.child component wrong (copied user.child instead)
on systems with HAVE_GETRUSAGE. (PR#14210)
Changing both line texture and line cap (end) resulted in the latter to be omitted
form the PDF code. In addition, line cap (end) and join are now set explicitly in
PDF output to ensure correct defaults.
The suppression of auto-rotation in bitmap() and dev2bitmap() with the
"pdfwrite" device was not working correctly.
plot(ecdf(), log="x") no longer gives an incorrect warning.
read.fwf() works again when argument file is a connection.
Startup files will now be found if their paths exceed 255 bytes. (PR#14228)
contrasts<- (in the stats package) no longer has an undeclared dependence on methods (introduced in 2.10.0).

CHANGES IN R VERSION 2.10.1

NEW FEATURES:
The PCRE library has been updated to version 8.00.
R CMD INSTALL has new options --no-R, --no-libs, --no-data, --no-help,
--no-demo, --no-exec, and --no-inst to suppress installation of the specified
part of the package. These are intended for special purposes (e.g. building a database
of help pages without fully installing all packages).
The documented line-length limit of 4095 bytes when reading from the console now
also applies also to parse(file="") (which previously had a limit of around 1024
bytes).
A Bioconductor mirror can be set for use by setRepositories() via the
option "BioC_mirror", e.g.
the European mirror can be selected by
options(BioC_mirror="http://bioconductor.statistik.tu-dortmund.de").
Double-clicking in a tk_select.list() list box now selects the item and closes the
list box (as happens on the Windows select.list() widget).

NEWS

37

INSTALLATION:
configure will be able to find a usable libtiff in some rare circumstances where it
did not previously (where libtiff needed to be linked explicitly against -ljpeg).
Making refman.pdf works around a problem with the indexing with hyperref 6.79d
and later.

DEPRECATED & DEFUNCT:

The extended argument is deprecated in strsplit(), grep(), grepl(), sub(),
gsub(), regexpr() and gregexpr() (not just the value extended = FALSE) and
will be removed in R 2.11.0.

BUG FIXES:
trigamma(x) and other psigamma(x, n) calls are now accurate for very large abs(x).
(PR#14020)
[g]sub(perl=FALSE, fixed=FALSE) could use excessive stack space when used with
a very long vector containing some non-ASCII strings.
The default method of weighted.mean(na.rm = TRUE) did not omit weights for NA
observations in 2.10.0. (PR#14032)
[g]regexpr(pattern, fixed = TRUE) returned match positions in bytes (not characters) in an MBCS locale if pattern was a single byte.
[g]sub(fixed = TRUE) with a single-byte pattern could conceivably have matched
part of a multibyte character in a non-UTF-8 MBCS.
findLineNum() and setBreakpoint() would sometimes fail if the specified file was
not in the current directory.
Package tcltks demo(tkdensity) was broken in 2.9.0 when demo() was changed to
set par(ask = TRUE).
gsub() with backrefs could fail on extremely long strings (hundreds of thousands of
characters) due to integer overflow in a length calculation.
abline(untf=TRUE) now uses a better x-grid in log-scale, e.g., for plot(c(1,300),
c(1,300), log="xy"); abline(4,1, untf=TRUE).
detach()/unloadNamespace() arrange to flush the packages lazyload cache of R
objects once the package/namespace is no longer needed.
There have been small fixes to the rendering of help, e.g. \command is now rendered
verbatim (so e.g. -- is not interpreted, PR#14045).
Also, there are many small changes to help files where the new converters were not
rendering them in the same way as before.
available.packages() would fail when run on a repository with no packages meeting
the filtering conditions. (PR#14042)
rep(x, times, each = 2) gave invalid results when the times argument was a vector longer than x. Reported by Bill Dunlap.
An error when unloadNamespace() attempted to run the .onUnload() function gave
an error in the reporting function and so was not reported properly.
Text help rendering did not handle very long input lines properly.
promptMethods() generated signature documentation improperly.

38

NEWS
pgamma(x, a, lower.tail=FALSE) and qgamma(...) are now considerably more
accurate in some regions for very small a. qgamma() now correctly returns 0 instead
of NaN in similar extreme cases, and qgamma() no longer warns in the case of small
a, see (PR#12324).
unname() now also removes names from a zero length vector.
Printing results from ls.str() no longer evaluates unevaluated calls.
complete.cases() failed on a 0-column data frame argument.
(Underlies
PR#14066.)
It could return nonsensical results if no input determined the number of cases (seen
in the no-segfault tests).
An error in nls() with a long formula could cause a segfault. (PR#14059)
qchisq(p, df, ncp, lower.tail = FALSE) with ncp >= 80 was inaccurate for
small p (as the help page said): it is now less inaccurate. (In part, PR#13999.)
For ncp less than but close to 80, pchisq() and qchisq() are more accurate for
probablilities very close to 1 (a series expansion was truncated slightly too early).
pchisq(x, df, ncp) can no longer return values just larger than one for large values
of ncp.
intToUtf8() could fail when asked to produce 10Mb or more strings, something it
was never intended to do: unfortunately Windows crashed R (other OSes reported a
lack of resources). (PR#14068)
chisq.test() could fail when given argument x or y which deparsed to more than
one line. (Reported by Laurent Gauthier.)
S4 methods are uncached whenever the name space containing them is unloaded (by
unloadNamespace() as well as by detach(unload = TRUE)).
The internal record-keeping by dyn.load/dyn.unload was incomplete, which could
crash R if a DLL that registered .External routines had earlier been unloaded.
bessel[JY](x, nu) with nu a negative integer (a singular case) is now correct, analogously to besselI(), see PR#13556.
tools::file_path_as_absolute() doubled the file separator when applied to a file
such as "/vmunix" or (on Windows) "d:/afile" in a directory for which getwd()
would return a path with a trailing separator (largely cosmetic, as reasonable file
systems handle such a path correctly). (Perhaps what was meant by PR#14078.)
unsplit(drop = TRUE) applied to a data frame failed to pass drop to the computation of row names. (PR#14084)
The "difftime" method of mean() ignored its na.rm argument.
tcltk::tk_select.list() is now more likely to remove the widget immediately after
selection is complete.
Adding/subtracting a "difftime" object to/from a "POSIXt" or "Date" object works
again (it was broken by the addition of Ops.difftime).
Conversion to latex of an Rd file with no aliases failed.
wilcox.test(conf.int=TRUE) has achieved.level corrected and, for exact=FALSE,
now returns a estimate component which does not depend on the alternative used.
help.search() failed when the package argument was specified. (PR#14113)
switch(EXPR = "A") now returns NULL, as does switch(1) (which used to signal an
error).

NEWS

39

CHANGES IN R VERSION 2.10.0

SIGNIFICANT USER-VISIBLE CHANGES:
Package help is now converted from Rd by the R-based converters that were first
introduced in 2.9.0. This means

Packages that were installed by R-devel after 2009-08-09 should not be used with
earlier versions of R, and most aspects of package help (including the runnable
examples) will be missing if they are so used.
Text, HTML and latex help and examples for packages installed under the new
system are converted on-demand from stored parsed Rd files. (Conversions stored
in packages installed under R < 2.10.0 are used if no parsed Rd files are found.
It is recommended that such packages be re-installed.)
HTML help is now generated dynamically using an HTTP server running in the R
process and listening on the loopback interface.

Those worried about security implications of such a server can disable it by setting
the environment variable R_DISABLE_HTTPD to a non-empty value. This disables
help.start() and HTML help (so text help is shown instead).
The Java/Javascript search engine has been replaced by an HTML interface to
help.search(). help.start() no longer has an argument searchEngine as it
is no longer needed.
The HTML help can now locate cross-references of the form \link[pkg]{foo}
and \link[pkg:foo]{bar} where foo is an alias in the package, rather than the
documented (basename of a) filename (since the documentation has been much
ignored).
NEW FEATURES:
polygon(), pdf() and postscript() now have an argument fillOddEven (default
FALSE), which controls the mode used for polygon fills of self-intersecting shapes.
New debugonce() function; further, getOption("deparse.max.lines") is now observed when debugging, from a code suggestion by John Brzustowski. (PR#13647/8)
plot() methods for "stepfun" and hence "ecdf" no longer plot points by default
for n >= 1000.
[g]sub(perl=TRUE) now also supports "\E" in order to end "\U" and "\L" case
changes, thanks to a patch from Bill Dunlap.
factor(), levels()<-, etc, now ensure that the resulting factor levels are unique (as
was always the implied intention). Factors with duplicated levels are still constructible
by low-level means, but are now declared illegal.
New print() (S3) method for class "function", also used for auto-printing. Further,
.Primitive functions now print and auto-print identically. The new method is based
on code suggestions by Romain Francois.
The print() and toLatex() methods for class "sessionInfo" now show the locale
in a nicer format and have arguments to suppress locale information.
In addition to previously only round(), there are other Math group (S3) methods for
"difftime", such as floor(), signif(), abs(), etc.
For completeness, old.packages() and available.packages() allow arguments
type to be specified (you could always specify arguments available or contriburl).

40

NEWS
available.packages() by default only returns information on the latest versions of
packages whose version requirements are satisfied by the currently running R.
tools::write_PACKAGES() has a new argument latestOnly, which defaults to TRUE
when only the latest versions in the repository will be listed in the index.
getOption() has a new argument default that is returned if the specified option is
not set. This simplifies querying a value and checking whether it is NULL or not.
parse() now warns if the requested encoding is not supported.
The "table" method of as.data.frame() gains a stringsAsFactors argument to
allow the classifying factors to be returned as character vectors rather than the default
factor type.
If model.frame.default() encounters a character variable where xlev indicates a
factor, it now converts the variable to a factor (with a warning).
curve() now returns a list containing the points that were drawn.
spineplot() now accepts axes = FALSE, for consistency with other functions called
by plot.factor().
The Kendall and Spearman methods of cor.test() can optionally use continuity
correction when not computing exact p-values. (The Kendall case is the wish of
PR#13691.)
R now keeps track of line numbers during execution for code sourced with
options(keep.source = TRUE). The source reference is displayed by debugging functions such as traceback(), browser(), recover(), and dump.frames(), and is stored
as an attribute on each element returned by sys.calls().
More functions now have an implicit (S4) generic definition.
quantile.default() now disallows factors (wish of PR#13631) and its help documents what numeric-like properties its input need to have to work correctly.
weighted.mean() is now generic and has "Date", "POSIXct" and "POSIXlt" methods.
Naming subscripts (e.g. x[i=1, j=2]) in data.frame methods for [ and [[ now gives
a warning. (Names are ignored in the default method, but could have odd semantics
for other methods, and do for the data.frame ones.)
as.data.frame() has an "aovproj" method. (Wish of PR#13505)
as.character(x) for numeric x no longer produces strings such as "0.30", i.e., with
trailing zeros. This change also renders levels construction in factor() more consistent.
codocClasses(), which checks consistency of the documentation of S4 class slots,
now does so in considerably more cases. The documentation of inherited slots (from
superclasses) is now optional. This affects R CMD check <pkg> when the package
defines S4 classes.
codoc() now also checks S4 methods for code/documentation mismatches.
for(), while(), and repeat() loops now always return NULL as their (invisible)
value. This change was needed to address a reference counting bug without creating
performance penalties for some common use cases.
The print() method for ls.str() results now obeys an optional digits argument.
The method argument of glm() now allows user-contributed methods.
More general reorder.default() replaces functionality of reorder.factor() and
reorder.character().

NEWS

41
The function aspell() has been added to provide an interface to the Aspell spellchecker.
Filters RdTextFilter() and SweaveTeXFilter() have been added to the tools package to provide support for aspell() or other spell checkers.
xtabs() with the new argument sparse = TRUE now returns a sparse Matrix, using
package Matrix.
contr.sum() etc gain an argument sparse which allows sparse matrices to be returned.
contrasts() also gains a sparse argument which it passes to the actual contrast
function if that has a formal argument sparse.
contrasts(f, .) <- val now also works when val is a sparse Matrix. It is planned
that model.matrix() will work with such factors f in the future.
readNEWS() will recognize a UTF-8 byte-order mark (BOM) in the NEWS file. However, it is safer to use only ASCII code there because not all editors recognize BOMs.
New utility function inheritedSlotNames() for S4 class programming.
tabulate() now allows NAs to pass through (and be ignored).
If debug() is called on an S3 generic function then all methods are debugged as well.
Outlier symbols drawn by boxplot() now obey the outlwd argument. Reported by
Jurgen Kluge.
svd(x) and eigen(x) now behave analogously to qr(x) in accepting logical matrices
x.
File NEWS is now in UTF-8, and has a BOM (often invisible) on the first line, and
Emacs local variables set for UTF-8 at the end. RShowDoc("NEWS") should display
this correctly, given suitable fonts.
terms.formula(simplify = TRUE) now does not deparse the LHS and so preserves
non-standard responses such as a: b (requested by Sundar Dorai-Raj).
New function news() for building and querying R or package news information.
z^n for integer n and complex z is more accurate now if |n| <= 65536.
factor(NULL) now returns the same as factor(character(0)) instead of an error,
and table(NULL) consequently does analogously.
as.data.frame.vector() (and its copies) is slightly faster by avoiding a copy if there
are no names (following a suggestion of Tim Hesterberg).
writeLines(), writeBin() and writeChar() have a new argument useBytes. If
false, character strings with marked encodings are translated to the current locale (as
before) but if true they are written byte-by-byte.
iconv() has a new argument mark which can be used (by experts) to suppress the
declaration of encodings.
DESCRIPTION files LinkingTo specs are now recognized as installation dependencies,
and included in package management computations.
Standardized DESCRIPTION file License specs are now available for package management computations.
"\uxxxx" and "\Uxxxxxxxx" escapes can now be parsed to a UTF-8 encoded string
even in non-UTF-8 locales (this has been implemented on Windows since R 2.7.0). The
semantics have been changed slightly: a string containing such escapes is always stored
in UTF-8 (and hence is suitable for portably including Unicode text in packages).

42

NEWS
New as.raw() method for "tclObj" objects (wish of PR#13758).
Rd.sty now makes a better job of setting email addresses, including using a
monospaced font.
textConnection() gains an encoding argument to determine how input strings with
marked encodings will be handled.
R CMD Rd2pdf is available as a shortcut for R CMD Rd2dvi --pdf.
R CMD check now checks links where a package is specified (\link[pkg]{file} or
\link[pkg:file]{topic}), if the package is available. It notes if the package is not
available, as in many cases this is an error in the link.
identical() gains three logical arguments, which allow for even more differentiation,
notably -0 and 0.
legend() now can specify the border color of filled boxes, thanks to a patch from
Frederic Schutz.
Indexing with a vector index to [[ ]] has now been extended to all recursive types.
Pairlists may now be assigned as elements of lists. (Lists could always be created
with pairlist elements, but [[<- didnt support assigning them.)
The parser now supports C-preprocessor-like #line directives, so error messages and
source references may refer to the original file rather than an intermediate one.
New functions findLineNum() and setBreakpoint() work with the source references
to find the location of source lines and set breakpoints (using trace()) at those lines.
Namespace importing is more careful about warning on masked generics, thanks to a
patch by Yohan Chalabi.
detach() now has an argument character.only with the same meaning as for
library() or require().
available.packages() gains a filters argument for specifying the filtering operations performed on the packages found in the repositories. A new built-in
"license/FOSS" filter only retains packages for which installation can proceed solely
based on packages which can be verified as Free or Open Source Software (FOSS)
employing the available license specifications.
In registering an S3 class by a call to setOldClass(), the data part (e.g., the object
type) required for the class can be included as one of the superclasses in the Classes
argument.
The argument f to showMethods() can be an expression evaluating to a generic function, allowing methods to be shown for non-exported generics and other nonstandard
cases.
sprintf() now supports %o for octal conversions.
New function Sys.readlink() for information about symbolic links, including if a
file is a symbolic link.
Package tools has new functions checkRdaFiles() and resaveRdaFiles() to report
on the format of .rda/.RData data files, and to re-save them in a different compressed format, including choosing the most compact format available.
A new INSTALL option, --resave-data, makes use of this.
File ~/.R/config is used in preference to ~/.Rconfig, and these are now documented in R Installation and Administration.
Logic operations with complex numbers now work, as they were always documented
to, and as in S.

NEWS

43
arrows() and segments() allow one of x1 or y1 to be omitted to simplify the specification of vertical or horizontal lines (suggestion of Tim Hesterberg).
approxfun() is faster by avoiding repeated NA checks (diagnosis and patch by Karline
Soetaert & Thomas Petzoldt).
There are the beginnings of a Nynorsk translation by Karl Ove Hufthammer.
stripchart() allows par bg to be passed in for the background colour for pch = 21
(wish of PR#13984).
New generic function .DollarNames() to enable class authors to customize completion after the $ extractor.
load(), save(), dput() and dump() now open a not-yet-open connection in the
appropriate mode (as other functions using connections directly already did).

REGULAR EXPRESSIONS:
A different regular expression engine is used for basic and extended regexps and is
also for approximate matching. This is based on the TRE library of Ville Laurikari,
a modified copy of which is included in the R sources.
This is often faster, especially in a MBCS locale.
Some known differences are that it is less tolerant of invalid inputs in MBCS locales,
and in its interpretation of undefined (extended) regexps such as "^*". Also, the
interpretation of ranges such as [W-z] in caseless matching is no longer to map the
range to lower case.
This engine may in future be used in literal mode for fixed = TRUE, and there is a
compile-time option in src/main/grep.c to do so.
The use of repeated boundary regexps in gsub() and gregexpr() as warned about
in the help page does not work in this engine (it did in the previous one since 2005).
Extended (and basic) regexps now support same set of options as for fixed = TRUE
and perl = TRUE, including useBytes and support for UTF-8-encoded strings in
non-UTF-8 locales.
agrep() now has full support for MBCS locales with a modest speed penalty. This
enables help.search() to use approximate matching character-wise rather than bytewise.
[g]sub use a single-pass algorithm instead of matching twice and so is usually faster.
The perl = TRUE versions now work correctly in a non-UTF-8 MBCS locale, by
translating the inputs to UTF-8.
useBytes = TRUE now inhibits the translation of inputs with marked encodings.
strsplit() gains a useBytes argument.
The algorithm used by strsplit() has been reordered to batch by elements of split:
this can be much faster for fixed = FALSE (as multiple compilation of regexps is
avoided).
The help pages, including ?regexp, have been updated and should be consulted for
details of the new implementations.

HELP & Rd FILE CHANGES:

A new dynamic HTML help system is used by default, and may be controlled using
tools::startDynamicHelp(). With this enabled, HTML help pages will be generated on request, resolving links by searching through the current .libPaths(). The
user may set options("help.ports") to control which IP port is used by the server.

44

NEWS
help.start() no longer sets options(htmlhelp = TRUE) (it used to on Unix but not
on Windows). Nor does it on Unix reset the "browser" option if given an argument
of that name.
Arguments update and remote are now available on all platforms: the default is
update = FALSE since the http server will update the package index at first use.
help() has a new argument help_type (with default set by the option of that name)
to supersede arguments offline, htmlhelp and chmhelp (although for now they still
work if help_type is unset). There is a new type, "PDF" to allow offline PDF (rather
than PostScript).
A function offline_help_helper() will be used if this exists in the workspace or
further down the search path, otherwise the function of that name in the utils name
space is used.
Plain text help is now used as the fallback for HTML help (as it always was for
Compiled HTML help on Windows).
It is possible to ask for static HTML pages to be prebuilt via the configure option
--enable-prebuilt-html. This may be useful for those who wish to make HTML
help available outside R, e.g. on a local web site.
An experimental tag \Sexpr has been added to Rd files, to evaluate expressions at
build, install, or render time. Currently install time and render time evaluation are
supported.
Tags \if, \ifelse and \out have been added to allow format-specific (or more general, using \Sexpr) conditional text in man pages.
The parse_Rd() parser has been made more tolerant of coding errors in Rd files:
now all syntax errors are reported as warnings, and an attempt is made to continue
parsing.
parse_Rd() now has an argument fragment (default FALSE) to accept small fragments
of Rd files (so that \Sexpr can output Rd code which is then parsed).
parse_Rd() now always converts its input to UTF-8. The Rd2* rendering functions
have a new argument, outputEncoding, which controls how their output is encoded.
parse_Rd() no longer includes the newline as part of a "%"-style comment.
There have been various bug fixes and code reorganization in the Rd renderers
Rd2HTML, Rd2latex, Rd2txt, and Rd2ex.
All example files are now created with either ASCII or UTF-8 encoding, and the
encoding is only marked in the file if there is any non-UTF-8 code (previously it was
marked if the help file had non-ASCII contents, possibly in other sections).
print.Rd() now adds necessary escape characters so that printing and re-parsing an
Rd object should produce an equivalent object.
parse_Rd() was incorrectly handling multiple backslashes in R code strings, converting 4n+3 backslashes to 2n+1 instead of 2n+2.
parse_Rd() now recognizes the \var tag within a quoted string in R-like text.
parse_Rd() now treats the argument of \command as LaTeX-like, rather than verbatim.

COMPRESSION:
New function untar() to list or unpack tar archives, possibly compressed. This uses
either an external tar command or an internal implementation.

NEWS

45
New function tar() to create (possibly compressed) tar archives.
New functions memCompress() and memDecompress() for in-memory compression and
decompression.
bzfile() has a compress argument to select the amount of effort put into compression
when writing.
New function xzfile() for use with xz-compressed files. (This can also read files
compressed by some versions of lzma.)
gzfile() looks at the file header and so can now also read bzip2-ed files and xzcompressed files.
There are the new options of save(compress = "bzip2") and "xz" to use bzip2
or xz compression (which will be slower, but can give substantially smaller files).
Argument compression_level gives finer control over the space/time tradeoffs.
load() can read such saves (but only as from this version of R).
R CMD INSTALL/check and tools::writePACKAGES accept a wider range of compressed tar archives. Precisely how wide depends on the capabilities of the host
systems tar command: they almost always include .tar.bz2 archives, and with
modern versions of tar other forms of compression such as lzma and xz, and arbitrary extensions.
R CMD INSTALL has a new option --data-compress to control the compression used
when lazy-loading data. New possibilities are --data-compress=bzip2 which will
give ca 15% better compression at the expense of slower installation times, and
--data-compress=xz, often giving even better compression on large datasets at the
expense of much longer installation times. (The latter is used for the recommended
packages: it is particularly effective for survival.)
file() for open = "", "r" or "rt" will automagically detect compressed files (from
gzip, bzip2 or xz). This means that compressed files can be specified by file name
(rather than via a gzfile() connection) to read.table(), readlines(), scan()
and so on.
data()
can
handle
compressed
text
files
with
extensions
.{txt,tab,csv}.{gz,bz2,xz} .

DEPRECATED & DEFUNCT:

png(type="cairo1") is defunct: the value is no longer recognized.
tools::Rd_parse() is defunct (as this version of R uses only Rd version 2).
Use of file ~/.Rconf (which was deprecated in favour of ~/.Rconfig in 2004) has
finally been removed.
Bundles of packages are deprecated. See Writing R Extensions for the steps needed
to unbundle a bundle.
help() arguments offline, htmlhelp and chmhelp are deprecated in favour of
help_type.
clearNames() (in package stats) is deprecated for unname().
Basic regular expressions (extended = FALSE) are deprecated in strsplit, grep and
friends. There is a precise POSIX standard for them, but it is not what recent RE
engines implement, and it seems that in almost all cases package authors intended
fixed = TRUE when using extended = FALSE.
methods::trySilent() is deprecated in favour of try(silent=TRUE) or more efficiently and flexibly something like tryCatch(error = function(e) e).

46

NEWS
index.search() is deprecated: there are no longer directories of types other than
help.

INSTALLATION:
cairo >= 1.2 is now required (1.2.0 was released in July 2006) for cairo-based graphics
devices (which remain optional).
A suitable iconv() is now required: support for configure option --without-iconv
has been withdrawn (it was deprecated in R 2.5.0).
Perl is no longer essential. R can be built without it, but scripts R CMD build,
check, Rprof and Sd2d currently require it.
A system glob function is now essential (a working Sys.glob() has been assumed
since R 2.9.0 at least).
C99 support for MBCS is now required, and configure option --disable-mbcs has
been withdrawn.
Having a version of tar capable of automagically detecting compressed archives is
useful for utils::untar(), and so gtar (a common name for GNU tar) is preferred
to tar: set environment variable TAR to specify a particular tar command.

INTERNATIONALIZATION:
There is some makefile support for adding/updating translations in packages: see
po/README and Writing R Extensions.
There is support for the use of dngettext for C-level translations in packages: see
Writing R Extensions.

BUG FIXES:
Assigning an extra 0-length column to a data frame by DF[, "foo"] <- value now
works in most cases (by filling with NAs) or fails. (It used to give a corrupt data
frame.)
validObject() avoids an error during evaluation in the case of various incorrect slot
definitions.
n:m now returns a result of type "integer" in a few more boundary cases.
The zap.ind argument to printCoefmat() did not usually work as other code attempted to ensure that non-zero values had a non-zero representation.
printCoefmat() formatted groups of columns together, not just the cs.ind group
but also the zap.ind group and a residual group. It now formats all columns except
the cs.ind group separately (and zaps the zap.ind group column-by-column). The
main effect will be see in the output from print.anova(), as this grouped SS-like
columns in the zap.ind group.
R_ReplDLLinit() initializes the top-level jump so that some embedded applications
on Windows no longer crash on error.
identical() failed to take the encoding of character strings into account, so identical
byte patterns are not necessarily identical strings, and similarly Latin-1 and UTF-8
versions of the same string differ in byte pattern.
methods(f) used to warn unnecessarily for an S4 generic f which had been created
based on an existing S3 generic.
The check for consistent ordering of superclasses was not ignoring all conditional
relations (the symptom was usually spurious warnings for classes extending "array").

NEWS

47
Trying to assign into a raw vector with an index vector containing NAs could cause a
segfault. Reported by Herve Pag`es.
Rscript could segfault if (by user error) its filename argument was missing. Reported
by Martin Morgan.
getAnywhere() (and functions that use it, including argument completion in the
console) did not handle special built-in functions. Reported by Romain Francois.
order() was missing a PROTECT() call and so could segfault when called on character
data under certain (rare) circumstances involving marked non-native encodings.
prettyNum(z, drop0trailing=TRUE) did not work correctly when z was a complex
vector. Consequently, str(z, ...) also did not. (PR#13985)
make distclean removed too many files in etc/ if builddir = srcdir.
R CMD replaced TEXINPUTS rather than appending to it (as documented and intended).
help.start() no longer fails on unix when "browser" is a function.
pbeta(x, ..., log.p = TRUE) is sometimes more accurate, e.g., for very small x.
Unserializing a pre-2.8 workspace containing pure ASCII character objects with a
Latin-1 or UTF-8 encoding would corrupt the CHARSXP cache.