R News
CHANGES IN R VERSION 2.14.2:
NEW FEATURES:
o The internal untar() (as used by default by R CMD INSTALL) now
knows about some pax headers which bsdtar (e.g., the default tar
for Mac OS >= 10.6) can incorrectly include in tar files, and
will skip them with a warning.
o PCRE has been upgraded to version 8.21: as well as bug fixes and
greater Perl compatibility, this adds a JIT pattern compiler,
about which PCRE's news says 'large performance benefits can be
had in many situations'. This is supported on most but not all R
platforms.
o Function compactPDF() in package tools now takes the default for
argument gs_quality from environment variable GS_QUALITY: there
is a new value "none", the ultimate default, which prevents
GhostScript being used in preference to qpdf just because
environment variable R_GSCMD is set. If R_GSCMD is unset or set
to "", the function will try to find a suitable GhostScript
executable.
o The included version of zlib has been updated to 1.2.6.
o For consistency with the logLik() method, nobs() for "nls" files
now excludes observations with zero weight. (Reported by Berwin
Turlach.)
UTILITIES:
o R CMD check now reports by default on licenses not according to
the description in 'Writing R Extensions'.
o R CMD check has a new option --as-cran to turn on most of the
customizations that CRAN uses for its incoming checks.
PACKAGE INSTALLATION:
o R CMD INSTALL will now no longer install certain file types from
inst/doc: these are almost certainly mistakes and for some
packages are wasting a lot of space. These are Makefile, files
generated by running LaTeX, and unless the package uses a
vignettes directory, PostScript and image bitmap files.
Note that only PDF vignettes have ever been supported: some of
these files come from DVI/PS output from the Sweave defaults
prior to R 2.13.0.
BUG FIXES:
o R configured with --disable-openmp would mistakenly set
HAVE_OPENMP (internal) and SUPPORT_OPENMP (in Rconfig.h) even
though no OpenMP flags were populated.
o The getS3method() implementation had an old computation to find
an S4 default method.
o readLines() could overflow a buffer if the last line of the file
was not terminated. (PR#14766)
o R CMD check could miss undocumented S4 objects in packages which
used S4 classes but did not Depends: methods in their DESCRIPTION
file.
o The HTML Help Search page had malformed links. (PR#14769)
o A couple of instances of lack of protection of SEXPs have been
squashed. (PR#14772, PR#14773)
o image(x, useRaster=TRUE) misbehaved on single-column x.
(PR#14774)
o Negative values for options("max.print") or the max argument to
print.default() caused crashes. Now the former are ignored and
the latter trigger an error. (PR#14779)
o The text of a function body containing more than 4096 bytes was
not properly saved by the parser when entered at the console.
o Forgetting the #endif tag in an Rd file could cause the parser to
go into a loop. (Reported by Hans-Jorg Bibiko.)
o str(*, ....., strict.width="cut") now also obeys list.len = n.
(Reported by S?ren Vogel.)
o Printing of arrays did not have enough protection (C level),
e.g., in the context of capture.output(). (Reported by Herv?
Pag?s and Martin Morgan.)
o pdf(file = NULL) would produce a spurious file named NA.
(PR#14808)
o list2env() did not check the type of its envir argument.
(PR#14807)
o svg() could segfault if called with a non-existent file path.
(PR#14790)
o make install can install to a path containing + characters.
(PR#14798)
o The edit() function did not respect the options("keep.source")
setting. (Reported by Cleridy Lennert.)
o predict.lm(*, type="terms", terms=*, se.fit=TRUE) did not work.
(PR#14817)
o There is a partial workaround for errors in the TRE
regular-expressions engine with named classes and repeat counts
of at least 2 in a MBCS locale (PR#14408): these are avoided when
TRE is in 8-bit mode (e.g. for useBytes = TRUE and when all the
data are ASCII).
o The C function R_ReplDLLdo1() did not call top-level handlers.
o The Quartz device was unable to detect window sessions on Mac OS
X 10.7 (Lion) and higher and thus it was not used as the default
device on the console. Since Lion any application can use window
sessions, so Quartz will now be the default device if the user's
window session is active and R is not run via ssh which is at
least close to the behavior in prior OS X versions.
o mclapply() would fail in code assembling the translated error
message if some (but not all) cores encountered an error.
o format.POSIXlt(x) raised an arithmetic exception when x was an
invalid object of class "POSIXlt" and parts were empty.
o installed.packages() has some more protection against package
installs going on in parallel.
o .Primitive() could be mis-used to call .Internal() entry points.
CHANGES IN R VERSION 2.14.1:
NEW FEATURES:
o parallel::detectCores() is now able to find the number of
physical cores (rather than CPUs) on Sparc Solaris.
It can also do so on most versions of Windows; however the
default remains detectCores(logical = TRUE) on that platform.
o Reference classes now keep a record of which fields are locked.
$lock() with no arguments returns the names of the locked fields.
o HoltWinters() reports a warning rather than an error for some
optimization failures (where the answer might be a reasonable
one).
o tools::dependsOnPkg() now accepts the shorthand dependencies =
"all".
o parallel::clusterExport() now allows specification of an
environment from which to export.
o The quartz() device now does tilde expansion on its file
argument.
o tempfile() on a Unix-alike now takes the process ID into account.
This is needed with multicore (and as part of parallel) because
the parent and all the children share a session temporary
directory, and they can share the C random number stream used to
produce the unique part. Further, two children can call
tempfile() simultaneously.
o Option print in Sweave's RweaveLatex() driver now emulates
auto-printing rather than printing (which can differ for an S4
object by calling show() rather than print()).
o filled.contour() now accepts infinite values: previously it might
have generated invalid graphics files (e.g. containing NaN
values).
INSTALLATION:
o On 64-bit Linux systems, configure now only sets LIBnn to lib64
if /usr/lib64 exists. This may obviate setting LIBnn explicitly
on Debian-derived systems.
It is still necessary to set LIBnn = lib (or lib32) for 32-bit
builds of R on a 64-bit OS on those Linux distributions capable
for supporting that concept.
o configure looks for inconsolata.sty, and if not found adjusts the
default R_RD4PDF to not use it (with a warning, since it is
needed for high-quality rendering of manuals).
PACKAGE INSTALLATION:
o R CMD INSTALL will now do a test load for all sub-architectures
for which code was compiled (rather than just the primary
sub-architecture).
UTILITIES:
o When checking examples under more than one sub-architecture, R
CMD check now uses a separate directory examples_arch for each
sub-architecture, and leaves the output in file
pkgname-Ex_arch.Rout. Some packages expect their examples to be
run in a clean directory ....
BUG FIXES:
o stack() now gives an error if no vector column is selected,
rather than returning a 1-column data frame (contrary to its
documentation).
o summary.mlm() did not handle objects where the formula had been
specified by an expression. (Reported by Helios de Rosario
Martinez).
o tools::deparseLatex(dropBraces=TRUE) could drop text as well as
braces.
o colormodel = "grey" (new in R 2.14.0)) did not always work in
postscript() and pdf().
o file.append() could return TRUE for failures. (PR#14727)
o gzcon() connections are no longer subject to garbage collection:
it was possible for this to happen when unintended (e.g. when
calling load()).
o nobs() does not count zero-weight observations for glm() fits,
for consistency with lm(). This affects the BIC() values
reported for such glm() fits. (Spotted by Bill Dunlap.)
o options(warn = 0) failed to end a (C-level) context with more
than 50 accumulated warnings. (Spotted by Jeffrey Horner.)
o The internal plot.default() code did not do sanity checks on a
cex argument, so invalid input could cause problems. (Reported
by Ben Bolker.)
o anyDuplicated(<array>, MARGIN=0) no longer fails. (Reported by
Herv? Pag?s.)
o read.dcf() removes trailing blanks: unfortunately on some
platforms this included \xa0 (non-breaking space) which is the
trailing byte of a UTF-8 character. It now only considers ASCII
space and tab to be 'blank'.
o There was a sign error in part of the calculations for the
variance returned by KalmanSmooth(). (PR#14738)
o pbinom(10, 1e6, 0.01, log.p = TRUE) was NaN thanks to the buggy
fix to PR#14320 in R 2.11.0. (PR#14739)
o RweaveLatex() now emulates auto-printing rather than printing, by
calling methods::show() when auto-printing would.
o duplicated() ignored fromLast for a one-column data frame.
(PR#14742)
o source() and related functions did not put the correct timestamp
on the source references; srcfilecopy() has gained a new argument
timestamp to support this fix. (PR#14750)
o LaTeX conversion of Rd files did not correctly handle
preformatted backslashes. (PR#14751)
o HTML conversion of Rd files did not handle markup within tabular
cells properly. (PR#14708)
o source() on an empty file with keep.source = TRUE tried to read
from stdin(), in R 2.14.0 only. (PR#14753)
o The code to check Rd files in packages would abort if duplicate
description sections were present.
CHANGES IN R VERSION 2.14.0:
SIGNIFICANT USER-VISIBLE CHANGES:
o All packages must have a namespace, and one is created on
installation if not supplied in the sources. This means that any
package without a namespace must be re-installed under this
version of R (but previously-installed data-only packages without
R code can still be used).
o The yLineBias of the X11() and windows() families of devices has
been changed from 0.1 to 0.2: this changes slightly the vertical
positioning of text in the margins (including axis annotations).
This is mainly for consistency with other devices such as
quartz() and pdf(). (Wish of PR#14538.)
There is a new graphics parameter "ylbias" which allows the
y-line bias of the graphics device to be tweaked, including to
reproduce output from earlier versions of R.
o Labeling of the p-values in various anova tables has been
rationalized to be either "Pr(>F)" or "Pr(>Chi)" (i.e. the
"Pr(F)", "Pr(Chi)" and "P(>|Chi|)" variants have been
eliminated). Code which extracts the p value _via_ indexing by
name may need adjustment.
o :: can now be used for datasets made available for lazy-loading
in packages with namespaces (which makes it consistent with its
use for data-only packages without namespaces in earlier versions
of R).
o There is a new package parallel.
It incorporates (slightly revised) copies of packages multicore
and snow (excluding MPI, PVM and NWS clusters). Code written to
use the higher-level API functions in those packages should work
unchanged (apart from changing any references to their namespaces
to a reference to parallel, and links explicitly to multicore or
snow on help pages).
It also contains support for multiple RNG streams following
L'Ecuyer _et al_ (2002), with support for both mclapply and snow
clusters. This replaces functions like clusterSetupRNG() from
snow (which are not in parallel).
The version released for R 2.14.0 contains base functionality:
higher-level convenience functions are planned (and some are
already available in the 'R-devel' version of R).
o Building PDF manuals (for R itself or packages, e.g. _via_ R CMD
check) by default requires the LaTeX package inconsolata: see the
section on 'Making the manuals' in the 'R Installation and
Administration Manual'.
o axTicks(*, log=TRUE) has changed in some cases to satisfy the
documented behavior and be consistent.
NEW FEATURES:
o txtProgressBar() can write to an open connection instead of the
console.
o Non-portable package names ending in . are no longer allowed.
Nor are single-character package names (R was already
disallowed).
o regexpr() and gregexpr() with perl = TRUE allows Python-style
named captures. (Wish and contribution of PR#14518.)
o The placement of 'plotmath' text in the margins of plots done by
base graphics now makes the same vertical adjustment as ordinary
text, so using ordinary and plotmath text on the same margin line
will seem better aligned (but not exactly aligned, since ordinary
text has descenders below the baseline and plotmath places them
on the baseline). (Related to PR#14537.)
o sunflowerplot() now has a formula interface. (Wish of PR#14541.)
o iconv() has a new argument toRaw to handle encodings such as
UTF-16 with embedded nuls (as was possible before the CHARSXP
cache was introduced).
It will also accept as input the type of list generated with
toRaw = TRUE.
o Garbage-collecting an unused input text connection no longer
gives a warning (since it 'connects' to nothing outside R).
o read.table() and scan() have gained a text argument, to allow
reading data from a (possibly literal) character string.
o optim(*, method = .) now allows method = "Brent" as an interface
to optimize(), for use in cases such as mle() where optim() is
used internally.
o mosaicplot() gains a border argument. (Wish of PR#14550.)
o smooth.spline() gains a tol argument which controls how different
x values need to be to be treated as distinct. The default has
been changed to be more reliable for inputs whose range is small
compared to their maximum absolute value. (Wish of PR#14452.)
o gl() runs faster by avoiding calling factor().
o The print() method for object.size() accepts B as well as b as an
abbreviation for 'bytes'.
o unlink() gains a force argument to work like rm -f and if
possible override restrictive permissions.
o pbirthday() and qbirthday() now use exact calculations for
coincident = 2.
o unzip() and unz() connections have been updated with support for
more recent Zip64 features (including large file sizes and bzip2
compression, but not UTF-8 file names).
unzip() has a new option to restore file times from those
recorded (in an unknown timezone) in the zip file.
o update.packages() now accepts a character vector of package names
for the oldPkgs argument. (Suggestion of Tal Galili.)
o The special reference class fields .self and .refClassDef are now
read-only to prevent corrupting the object.
o decompose() now returns the original series as part of its value,
so it can be used (rather than reconstructed) when plotting.
(Suggestion of Rob Hyndman.)
o Rao's efficient score test has been implemented for glm objects.
Specifically, the add1, drop1, and anova methods now allow test =
"Rao".
o If a saved workspace (e.g. .RData) contains objects that cannot
be loaded, R will now start with an warning message and an empty
workspace, rather than failing to start.
o strptime() now accepts times such as 24:00 for midnight at the
end of the day, for although these are disallowed by POSIX
1003.1-2008, ISO 8601:2004 allows them.
o Assignment of names() to S4 objects now checks for a
corresponding "names" slot, and generates a warning or an error
if that slot is not defined. See the section on slots in
?Classes.
o The default methods for is.finite(), is.infinite() and is.nan()
now signal an error if their argument is not an atomic vector.
o The formula method for plot() no longer places package stats on
the search path (it loads the namespace instead).
o There now is a genuine "function" method for plot() rather than
the generic dispatching internally to graphics::plot.function().
It is now exported, so can be called directly as plot.function().
o The one-sided ks.test() allows exact = TRUE to be specified in
the presence of ties (but the approximate calculation remains the
default: the 'exact' computation makes assumptions known to be
invalid in the presence of ties).
o The behaviour of curve(add = FALSE) has changed: it now no longer
takes the default x limits from the previous plot (if any):
rather they default to c(0, 1) just as the "function" method for
plot(). To get the previous behaviour use curve(add = NA), which
also takes the default for log-scaling of the x-axis from the
previous plot.
o Both curve() and the plot() method for functions have a new
argument xname to facilitate plots such as sin(t) _vs_ t.
o The local argument to source() can specify an environment as well
as TRUE (parent.env()) and FALSE (.GlobalEnv). It gives better
error messages for other values, such as NA.
o vcov() gains methods for classes "summary.lm" and "summary.glm".
o The plot() method for class "profile.nls" gains ylab and lty
arguments, and passes ... on to plot.default.
o Character-string arguments such as the mode argument of vector(),
as.vector() and is.vector() and the description argument of
file() are required to be of length exactly one, rather than any
further elements being silently discarded. This helps catch
incorrect usage in programming.
o The length argument of vector() and its wrappers such as
numeric() is required to be of length exactly one (other values
are now an error rather than giving a warning as previously).
o vector(len) and length(x) <- len no longer accept TRUE/FALSE for
len (not that they were ever documented to, but there was
special-casing in the C code).
o There is a new function Sys.setFileTime() to set the time of a
file (including a directory). See its help for exactly which
times it sets on various OSes.
o The file times reported by file.info() are reported to sub-second
resolution on systems which support it. (Currently the POSIX
2008 and FreeBSD/Darwin/NetBSD methods are detected.)
o New function getCall(m) as an abstraction for m$call, enabling
update()'s default method to apply more universally. (NB: this
can be masked by existing functions in packages.)
o Sys.info() gains a euser component to report the 'effective' user
on OSes which have that concept.
o The result returned by try() now contains the original error
condition object as the "condition" attribute.
o All packages with R code are lazy-loaded irrespective of the
LazyLoad field in the DESCRIPTION file. A warning is given if
the LazyLoad field is overridden.
o Rd markup has a new \figure tag so that figures can be included
in help pages when converted to HTML or LaTeX. There are
examples on the help pages for par() and points().
o The built-in httpd server now allows access to files in the
session temporary directory tempdir(), addressed as the /session
directory on the httpd server.
o Development versions of R are no longer referred to by the number
under which they might be released, e.g. in the startup banner, R
--version and sessionUtils(). The correct way to refer to a
development version of R is 'R-devel', preferably with the date
and SVN version number.
E.g. R-devel (2011-07-04 r56266)
o There is a new function texi2pdf() in package tools, currently a
convenience wrapper for texi2dvi(pdf = TRUE).
o There are two new options for typesetting PDF manuals from Rd
files. These are beramono and inconsolata, and used the named
font for monospaced output. They are intended to be used in
combination with times, and times,inconsolata,hyper is now the
default for the reference manual and package manuals. If you do
not have that font installed, you can set R_RD4PF to one of the
other options: see the 'R Installation and Administration
Manual'.
o Automatic printing for reference classes is now done by the
$show() method. A method is defined for class envRefClass and
may be overridden for user classes (see the ?ReferenceClasses
example). S4 show() methods should no longer be needed for
reference classes.
o tools::Rdiff (by default) and R CMD Rdiff now ignore differences
in pointer values when comparing printed environments, compiled
byte code, etc.
o The "source" attribute on functions created with keep.source=TRUE
has been replaced with a "srcref" attribute. The "srcref"
attribute references an in-memory copy of the source file using
the "srcfilecopy" class or the new "srcfilealias" class.
*NB:* This means that functions sourced with keep.source = TRUE
and saved (e.g., by save() or readRDS()) in earlier versions of R
will no longer show the original sources (including comments).
o New items User Manuals and Technical Papers have been added to
the HTML help main page. These link to vignettes in the base and
recommended packages and to a collection of papers about R
issues, respectively.
o Documentation and messages have been standardized to use
"namespace" rather than "name space".
o setGeneric() now looks in the default packages for a non-generic
version of a function if called from a package with a namespace.
(It always did for packages without a namespace.)
o Setting the environment variable _R_WARN_ON_LOCKED_BINDINGS_ will
give a warning if an attempt is made to change a locked binding.
o \SweaveInput is now supported when generating concordances in
Sweave().
o findLineNum() and setBreakpoint() now allow the environment to be
specified indirectly; the latter gains a clear argument to allow
it to call untrace().
o The body of a closure can be one of further types of R objects,
including environments and external pointers.
o The Rd2HTML() function in package tools now has a stylesheet
argument, allowing pages to be displayed in alternate formats.
o New function requireNamespace() analogous to require(), returning
a logical value after attempting to load a namespace.
o There is a new type of RNG, "L'Ecuyer-CMRG", implementing
L'Ecuyer (1999)'s 'combined multiple-recursive generator'
MRG32k3a. See the comments on ?RNG.
o help.search() and ?? can now display vignettes and demos as well
as help pages. The new option "help.search.types" controls the
types of documentation and the order of their display.
This also applies to HTML searches, which now give results in all
of help pages, vignettes and demos.
o socketConnection() now has a timeout argument. It is now
documented that large values (package snow used a year) do not
work on some OSes.
o The initialization of the random-number generator now uses the
process ID as well as the current time, just in case two R
processes are launched very rapidly on a machine with
low-resolution wall clock (some have a resolution of a second;
modern systems have microsecond-level resolution).
o New function pskill() in the tools package to send a terminate
signal to one or more processes, plus constants such as SIGTERM
to provide a portable way to refer to signals (since the numeric
values are OS-dependent).
o New function psnice() in the tools package to return or change
the 'niceness' of a process. (Refers to the 'priority class' on
Windows.)
o list.dirs() gains a recursive argument.
o An Authors@R field in a package DESCRIPTION file can now be used
to generate Author and Maintainer fields if needed, and to
auto-generate package citations.
o New utility getElement() for accessing either a list component or
a slot in an S4 object.
o stars() gains a col.lines argument, thanks to Dustin Sallings.
(Wish of PR#14657.)
o New function regmatches() for extracting or replacing matched or
non-matched substrings from match data obtained by regexpr(),
gregexpr() and regexec().
o help(package = "pkg_name", help_type = "HTML") now gives HTML
help on the package rather than text help. (This gives direct
access to the HTML version of the package manual shown _via_
help.start()'s 'Packages' menu.)
o agrep() gains a fixed argument to optionally allow approximate
regular expression matching, and a costs argument to specify
possibly different integer match costs for insertions, deletions
and substitutions.
o read.dcf() and write.dcf() gain a keep.white argument to indicate
fields where whitespace should be kept as is.
o available.packages() now works around servers that fail to return
an error code when PACKAGES.gz does not exist. (Patch submitted
by Seth Schommer.)
o readBin() can now read more than 2^31 - 1 bytes in a single call
(the previously documented limitation).
o New function regexec() for finding the positions of matches as
well as all substrings corresponding to parenthesized
subexpressions of the given regular expression.
o New function adist() in package utils for computing 'edit'
(generalized Levenshtein) distances between strings.
o Class "raster" gains an is.na method to avoid confusion from the
misuse of the matrix method (such as PR#14618).
o The identical() function gains an ignore.bytecode argument to
control comparison of compiled functions.
o pmin and pmax now warn if an argument is partially recycled (wish
of PR#14638).
o The default for image(useRaster=) is now taken from option
"preferRaster": for the small print see ?image.
o str() now displays reference class objects and their fields,
rather than treating them as classical S4 classes.
o New function aregexec() in package utils for finding the
positions of approximate string matches as well as all substrings
corresponding to parenthesized subexpressions of the given
regular expression.
o download.file() has an extra argument to pass additional
command-line options to the non-default methods using
command-line utilities.
cacheOK = FALSE is now supported for method = "curl".
o interaction.plot(*, type = .) now also allows type "o" or "c".
o axTicks(*, log=TRUE) did sometimes give more values than the
ticks in the corresponding graphics::axis(). By default, it now
makes use of the new (graphics-package independent) axisTicks()
which can make use of a new utility .axisPars(). Further, it now
returns a decreasing sequence (as for log=FALSE) when usr is
decreasing.
o Using fix() or edit() on a R object (except perhaps a matrix or
data frame) writes its temporary file with extension .R so
editors which select their mode based on the extension will
select a suitable mode.
GRAPHICS DEVICES:
o The pdf() device makes use of Flate compression: this is
controlled by the new logical argument compress, and is enabled
by default.
o Devices svg(), cairo_pdf() and cairo_ps() gain a family argument.
On a Unix-alike X11() gains a family argument. This is one of
the x11.options() and so can be passed as an argument to the
bmp(), jpeg(), png() and tiff() devices.
Analogous changes have been made on Windows, so all built-in R
graphics devices now have a family argument except pictex()
(which has no means to change fonts).
o The bmp(), jpeg(), png() and tiff() devices now make use of the
antialias argument for type = "quartz".
o There are several new built-in font mappings for X11(type =
"Xlib"): see the help on X11Fonts().
o There is a new type X11(type = "dbcairo") which updates the
screen less frequently: see its help page.
o The X11() device now makes use of cursors to distinguish its
states. The normal cursor is an arrow (rather than a crosshair);
the crosshair is used when the locator is in use, and a watch
cursor is shown when plotting computations are being done.
(These are the standard names for X11 cursors: how they are
actually displayed depends on the window manager.)
o New functions dev.hold() and dev.flush() for use with graphics
devices with buffering. These are used for most of the
high-level graphics functions such as boxplot(), so that the plot
is only displayed when the page is complete.
Currently implemented for windows(buffered = TRUE), quartz() and
the cairographics-based X11() types with buffering (which are the
default on-screen devices).
o New function dev.capture() for capture of bitmap snapshots of
image-based devices (a superset of the functionality provided by
grid.cap() in grid).
o The default colormodel for pdf() and postscript() is now called
"srgb" to more accurately describe it. (Instead of "rgb", and in
the case of postscript() it no longer switches to and from the
gray colorspace, by default.)
The colormodel for postscript() which does use both gray and sRGB
colorspaces is now called "srgb+gray".
Plots which are known to use only black/white/transparent can
advantageously use colormodel = "gray" (just as before, but there
is now slightly more advantage in doing so).
o postscript() with values colormodel = "rgb" and colormodel =
"rgb-nogray" give the behaviour prior to R 2.13.0 of uncalibrated
RGB, which under some circumstances can be rendered much faster
by a viewer.
pdf(colormodel = "rgb") gives the behaviour prior to R 2.13.0 of
uncalibrated RGB, which under some circumstances can be rendered
faster by a viewer, and the files will be smaller (by about 9KB
if compression is not used).
o The postscript() device only includes the definition of the sRGB
colorspace in the output file for the colormodels which use it.
o The postscript() and pdf() devices now output greyscale raster
images (and not RGB) when colormodel = "gray".
o postscript(colormodel = "gray") now accepts non-grey colours and
uses their luminance (as pdf() long has).
o colormodel = "grey" is allowed as an alternative name for
postscript() and pdf().
o pdf() in the default sRGB colorspace outputs many fewer changes
of colorspace, which may speed up rendering in some viewing
applications.
o There is a new function dev.capabilities() to query the
capabilities of the current device. The initial set of
capabilities are support for semi-transparent colours, rendering
and capturing raster images, the locator and for interactive
events.
o For pdf(), maxRasters is increased as needed so the argument is
no longer used.
SWEAVE & VIGNETTES:
o Options keep.source = TRUE, figs.only = FALSE are now the
default.
o The way the type of user-defined options is determined has
changed. Previously they were all regarded as logical: now the
type is determined by the value given at first use.
o The allowed values of logical options are now precisely those
allowed for character inputs to as.logical(): this means that t
and f are no longer allowed (although T and F still are).
o The preferred location for vignette sources is now the directory
vignettes and not inst/doc: R CMD build will now re-build
vignettes in directory vignettes and copy the .Rnw (etc) files
and the corresponding PDFs to inst/doc. Further files to be
copied to inst/doc can be specified _via_ the file
vignettes/.install_extras.
o R CMD Sweave now supports a --driver option to select the Sweave
driver: the default is equivalent to --driver=RweaveLatex.
o R CMD Sweave and R CMD Stangle support options --encoding and
--options.
o The Rtangle() driver allows output = "stdout" or output =
"stderr" to select the output or message connection. This is
convenient for scripting using something like
R CMD Stangle --options='output="stdout"' foo.Rnw > foo2.R
o There is a new option pdf.compress controlling whether PDF
figures are generated using Flate compression (they are by
default).
o R CMD Sweave now has a --pdf option to produce a PDF version of
the processed Sweave document.
o It is no longer allowed to have two vignettes with the same
vignette basename (e.g. vig.Rnw and vig.Snw). (Previously one
vignette hid the other in the vignette() function.)
C-LEVEL FACILITIES:
o Function R_tmpnam2 has been added to the API to allow a temporary
filename to include a specified extension.
PACKAGE INSTALLATION:
o Package DESCRIPTION file field KeepSource forces the package to
be installed with keep.source = TRUE (or FALSE). (Suggestion of
Greg Snow. Note that as all packages are lazy-loaded, this is
now only relevant at installation.)
There are corresponding options --with-keep.source and
--without-keep.source for R CMD INSTALL.
o R CMD INSTALL has a new option --byte-compile to byte-compile the
packages during installation (since all packages are now
lazy-loaded). This can be controlled on a per-package basis by
the optional field ByteCompile in the DESCRIPTION file.
o A package R code but without a NAMESPACE file will have a default
one created at R CMD build or R CMD INSTALL time, so all packages
will be installed with namespaces. A consequence of this is that
.First.lib() functions need to be copied to .onLoad() (usually)
or .onAttach(). For the time being, if there is an
auto-generated NAMESPACE file and no .onLoad() nor .onAttach()
function is found but .First.lib() is, it will be run as the
attach hook (unless the package is one of a list of known
exceptions, when it will be run as the load hook).
o A warning is given if test-loading a package changes a locked
binding in a package other than itself. It is likely that this
will be disallowed in future releases. (There are _pro tem_ some
exceptions to the warning.)
o A dependency on SVN revision is allowed for R, e.g. R (>=
r56550). This should be used in conjunction with a version
number, e.g. R (>= 2.14.0), R (>= r56550) to distinguish between
R-patched and R-devel versions with the same SVN revision.
o installed.packages() now hashes the names of its cache files to
avoid very rare problems with excessively long path names.
(PR#14669)
o A top-level COPYING file in a package is no longer installed
(file names LICENSE or LICENCE having long been preferred).
UTILITIES:
o R CMD check now gives an error if the R code in a vignette fails
to run, unless this is caused by a missing package.
o R CMD check now unpacks tarballs in the same way as R CMD
INSTALL, including making use of the environment variable
R_INSTALL_TAR to override the default behaviour.
o R CMD check performs additional code analysis of package startup
functions, and notifies about incorrect argument lists and
(incorrect) calls to functions which modify the search path or
inappropriately generate messages.
o R CMD check now also checks compiled code for symbols
corresponding to functions which might terminate R or write to
stdout/stderr instead of the console.
o R CMD check now uses a pdf() device when checking examples
(rather than postscript()).
o R CMD check now checks line-endings of makefiles and
C/C++/Fortran sources in subdirectories of src as well as in src
itself.
o R CMD check now reports as a NOTE what look like methods
documented with their full names even if there is a namespace and
they are exported. In almost all cases they are intended to be
used only as methods and should use the \method markup. In the
other rare cases the recommended form is to use a function such
as coefHclust which would not get confused with a method,
document that and register it in the NAMESPACE file by
s3method(coef, hclust, coefHclust).
o The default for the environment variable _R_CHECK_COMPACT_DATA2_
is now true: thus if using the newer forms of compression
introduced in R 2.10.0 would be beneficial is now checked (by
default).
o Reference output for a vignette can be supplied when checking a
package by R CMD check: see 'Writing R Extensions'.
o R CMD Rd2dvi allows the use of LaTeX package inputenx rather than
inputenc: the value of the environment variable RD2DVI_INPUTENC
is used. (LaTeX package inputenx is an optional install which
provides greater coverage of the UTF-8 encoding.)
o Rscript on a Unix-alike now accepts file names containing spaces
(provided these are escaped or quoted in the shell).
o R CMD build on a Unix-alike (only) now tries to preserve dates on
files it copies from its input directory. (This was the
undocumented behaviour prior to R 2.13.0.)
DEPRECATED AND DEFUNCT:
o require() no longer has a save argument.
o The gamma argument to hsv(), rainbow(), and rgb2hsv() has been
removed.
o The --no-docs option for R CMD build --binary is defunct: use
--install-args instead.
o The option --unsafe to R CMD INSTALL is defunct: use the
identical option --no-lock instead.
o The entry point pythag formerly in Rmath.h is defunct: use
instead the C99 function hypot.
o R CMD build --binary is formally defunct: R CMD INSTALL --build
has long been the preferred alternative.
o zip.file.extract() is now defunct: use unzip() or unz() instead.
o R CMD Rd2dvi without the --pdf option is now deprecated: only PDF
output will be supported in future releases (since this allows
the use of fonts only supported for PDF), and only R CMD Rd2pdf
will be available.
o Options such as --max-nsize and the function mem.limits() are now
deprecated: these limits are nowadays almost never used, and are
reported by gc() when they are in use.
o Forms like binomial(link = "link") for GLM families deprecated
since R 2.4.0 are now defunct.
o The declarativeOnly argument to loadNamespace() (not relevant
since R 2.13.0) has been removed.
o Use of library.dynam() without specifying all the first three
arguments is deprecated. (It is often called from a namespace,
and the defaults are only appropriate to a package.)
Use of chname in library.dynam() with the extension .so or .dll
(which is clearly not allowed according to the help page) is
deprecated. This also applies to library.dynam.unload() and
useDynLib directives in NAMESPACE files.
o It is deprecated to use mean(x) and sd(x) directly on data frames
(or also matrices, for sd) x, instead of simply using sapply.
In the same spirit, median(x) now gives an error for a data frame
x (it often gave nonsensical results).
o The keep.source argument to library() and require() is
deprecated: it was only used for packages installed without
lazy-loading, and now all packages are lazy-loaded.
o Using a false value for the DESCRIPTION field LazyLoad is
deprecated.
INSTALLATION:
o The base and recommended packages are now byte-compiled
(equivalent to make bytecode in R 2.13.x).
o Configure option --with-system-zlib now only makes use of the
basic interface of zlib and not the C function gzseek which has
shown erroneous behaviour in zlib 1.2.4 and 1.2.5.
o The zlib in the R sources is now version 1.2.5. (This is safe
even on 32-bit Linux systems because only the basic interface is
now used.)
o The .afm files in package grDevices are now installed as
compressed files (as long done on Windows), saving ca 2MB on the
installed size.
o The non-screen cairo-based devices are no longer in the X11
module and so can be installed without X11. (We have never seen
a Unix-alike system with cairographics installed but not X11, but
a user might select --without-x.)
o Configure will try to use -fobjc-exceptions for the Objective-C
compiler (if present) to ensure that even compilers that do not
enable exceptions by default (such as vanilla gcc) can be used.
(Objective-C is currently only used on Mac OS X.)
o The system call times is required.
o The C99 functions acosh, asinh, atanh, snprintf and vsnprintf are
now required.
o There is no longer support for making DVI manuals _via_ make dvi,
make install-dvi and similar. Only PDF manuals are supported (to
allow the use of fonts which are only available for PDF.)
o The configure arguments used during configuration of R are
included as a comment in Makeconf for informative purposes on
Unix-alikes in a form suitable for shell execution. Note that
those are merely command-line arguments, they do not include
environment variables (one more reason to use configure variables
instead) or site configuration settings.
o Framework installation now supports DESTDIR (Mac OS X only).
o Java detection (R CMD javareconf) works around bogus
java.library.path property in recent Oracle Java binaries.
BUG FIXES:
o The locale category LC_MONETARY was only being set on startup on
Windows: that is now done on Unix-alikes where supported.
o Reference class utilities will detect an attempt to modify
methods or fields in a locked class definition (e.g., in a
namespace) and generate an error.
o The formula methods for lines(), points() and text() now work
even if package stats is not on the search path.
o In principle, S4 classes from different packages could have the
same name. This has not previously worked. Changes have now
been installed that should allow such classes and permit methods
to use them. New functions className() and multipleClasses() are
related tools for programming.
o Work around an issue in Linux (a system select call resetting tv)
which prevented internet operations from timing out properly.
o Several stack trampling and overflow issues have been fixed in
TRE, triggered by agrep and friends with long patterns.
(PR#14627)
o ("design infelicity") Field assignments in reference classes are
now consistent with slots in S4 classes: the assigned value must
come from the declared class (if any) for the field or from a
subclass.
o The methods objects constructed for "coerce" and "coerce<-" were
lacking some essential information in the generic, defined and
target slots; as() did not handle duplicate class definitions
correctly.
o The parser no longer accepts the digit 8 in an octal character
code in a string, nor does it accept unterminated strings in a
file. (Reported by Bill Dunlap.)
o The print() method for class "summary.aov" did not pass on
argument digits when summary() was called on a single object, and
hence used more digits than documented.
o The X11() device's cairo back-end produced incorrect capture
snapshot images on big-endian machines.
o loglin() gave a spurious error when argument margin consisted of
a single element of length one. (PR#14690)
o loess() is better protected against misuse, e.g. zero-length
span. (PR#14691)
o HoltWinters() checks that the optimization succeeded. (PR#14694)
o The (undocumented) inclusion of superclass objects in default
initializing of reference classes overwrote explicit field
arguments. The bug is fixed, the feature documented and a test
added.
o round(x, -Inf) now does something sensible (return zero rather
than NA).
o signif(x, -Inf) now behaves as documented (signif(x, 1)) rather
than giving zero.
o The "table" method for Axis() hardcoded side = 1, hence calls to
plot(<vector>, <table>) labelled the wrong axis. (PR#14699)
o Creating a connection might fail under gctorture(TRUE).
o stack() and unstack() converted character columns to factors.
unstack() sometimes produced incorrect results (a list or a
vector) if the factor on which to un-split had only one level.
o On some systems help(".C", help_type = "pdf") and similar
generated file names that TeX was unable to handle.
o Non-blocking listening socket connections continued to report
isIncomplete() as true even when the peer had closed down and all
available input had been read.
o The revised HTML search system now generates better hyperlinks to
help topics found: previously it gave problems with help pages
with names containing e.g. spaces and slashes.
o A late change in R 2.13.2 broke \Sexpr expressions in Rd files.
o The creation of ticks on log axes (including by axTicks())
sometimes incorrectly omitted a tick at one end of the range by
rounding error in a platform-dependent way. This could be seen
in the examples for axTicks(), where with axis limits c(0.2, 88)
the tick for 0.2 was sometimes omitted.
o qgamma() for small shape underflows to 0 rather than sometimes
giving NaN. (PR#8528, PR#14710)
o mapply() now gives an explicit error message (rather than an
obscure one) if inputs of zero and positive length are mixed.
o Setting a Hershey font family followed by string height query
would crash R.
o R CMD javareconf -e would fail for some shells due to a shift
error. Also the resulting paths will no longer contain
$(JAVA_HOME) as that can result in an unintended substitution
based on Makeconf instead of the shell setting.
CHANGES IN R VERSION 2.13.2:
NEW FEATURES:
o mem.limits() now reports values larger than the maximum integer
(previously documented to be reported as NA), and allows larger
values to be set, including Inf to remove the limit.
o The print() methods for classes "Date", "POSIXct" and "POSIXlt"
respect the option "max.print" and so are much faster for very
long datetime vectors. (Suggestion of Yohan Chalabi.)
o untar2() now works around errors generated with tar files that
use more than the standard 6 digits for the checksum. (PR#14654)
o install.packages() with Ncpus > 1 guards against simultaneous
installation of indirect dependencies as well as direct ones.
o Sweave now knows about a few more Windows' encodings (including
cp1250 and cp1257) and some inputenx encodings such as koi8-r.
o postscript(colormodel = "rgb-nogray") no longer sets the sRGB
colorspace for each colour and so some viewers may render its
files much faster than the default colormodel ="rgb".
o The default for pdf(maxRasters=) has been increased from 64 to
1000.
o readBin() now warns if signed = FALSE is used inappropriately
(rather than being silently ignored).
It enforces the documented limit of 2^31-1 bytes in a single
call.
o PCRE has been updated to version 8.13, a bug-fix release with
updated Unicode tables (version 6.0.0). An additional patch
(r611 from PCRE 8.20-to-be) has been added to fix a collation
symbol recognition issue.
INSTALLATION:
o It is possible to build in src/extra/xdr on more platforms.
(Needed since glibc 2.14 hides its RPC implementation.)
o configure will find the Sun TI-RPC implementation of xdr (in
libtirpc) provided its header files are in the search path: see
the 'R Installation and Administration Manual'.
PACKAGE INSTALLATION:
o Using a broad exportPattern directive in a NAMESPACE file is no
longer allowed to export internal objects such as .onLoad and
.__S3MethodsTable__. .
These are also excluded from imports, along with .First.lib.
BUG FIXES:
o fisher.test() had a buglet: If arguments were factors with unused
levels, levels were dropped and you would get an error saying
that there should be at least two levels, inconsistently with
pre-tabulated data. (Reported by Michael Fay).
o package.skeleton() will no longer dump S4 objects supplied
directly rather than in a code file. These cannot be restored
correctly from the dumped version.
o Build-time expressions in help files did not have access to
functions in the package being built (with R CMD build).
o Because quote() did not mark its result as being in use,
modification of the result could in some circumstances modify the
original call.
o Plotting pch = '.' now guarantees at least a one-pixel dot if cex
> 0.
o The very-rarely-used command-line option --max-vsize was
incorrectly interpreted as a number of Vcells and not in bytes as
documented. (Spotted by Christophe Rhodes.)
o The HTML generated by Rd2HTML() comes closer to being standards
compliant.
o filter(x, recursive = TRUE) gave incorrect results on a series
containing NAs. (Spotted by Bill Dunlap.)
o Profiling stats::mle() fits with a fixed parameter was not
supported. (PR#14646)
o retracemem() was still using positional matching. (PR#14650)
o The quantile method for "ecdf" objects now works and is
documented.
o xtabs(~ .., ..., sparse=TRUE) now also works together with an
exclude = .. specification.
o decompose() computed an incorrect seasonal component for time
series with odd frequencies.
o The pdf() device only includes the definition of the sRGB
colorspace in the output file for the "rgb" colormodel (and not
for "gray" nor "cmyk"): this saves ca 9KB in the output file.
o .hasSlot() wrongly gave FALSE in some cases.
o Sweave() with keep.source=TRUE could generate spurious NA lines
when a chunk reference appeared last in a code chunk.
o \Sexpr[results=rd] in an .Rd file now first tries
parse_Rd(fragment=FALSE) to allow Rd section-level macros to be
inserted.
o The print() method for class "summary.aov" did not pass on
arguments such as signif.stars when summary() was called on a
single object. (PR#14684)
o In rare cases ks.test() could return a p-value very slightly less
than 0 by rounding error. (PR#14671)
o If trunc() was called on a "POSIXlt" vector and the result was
subsetted, all but the first element was converted to NA.
(PR#14679)
o cbind() and rbind() could cause memory corruption when used on a
combination of raw and logical/integer vectors.
CHANGES IN R VERSION 2.13.1:
NEW FEATURES:
o iconv() no longer translates NA strings as "NA".
o persp(box = TRUE) now warns if the surface extends outside the
box (since occlusion for the box and axes is computed assuming
the box is a bounding box). (PR#202)
o RShowDoc() can now display the licences shipped with R, e.g.
RShowDoc("GPL-3").
o New wrapper function showNonASCIIfile() in package tools.
o nobs() now has a "mle" method in package stats4.
o trace() now deals correctly with S4 reference classes and
corresponding reference methods (e.g., $trace()) have been added.
o xz has been updated to 5.0.3 (very minor bugfix release).
o tools::compactPDF() gets more compression (usually a little,
sometimes a lot) by using the compressed object streams of PDF
1.5.
o cairo_ps(onefile = TRUE) generates encapsulated EPS on platforms
with cairo >= 1.6.
o Binary reads (e.g. by readChar() and readBin()) are now supported
on clipboard connections. (Wish of PR#14593.)
o as.POSIXlt.factor() now passes ... to the character method
(suggestion of Joshua Ulrich). [Intended for R 2.13.0 but
accidentally removed before release.]
o vector() and its wrappers such as integer() and double() now warn
if called with a length argument of more than one element. This
helps track down user errors such as calling double(x) instead of
as.double(x).
INSTALLATION:
o Building the vignette PDFs in packages grid and utils is now part
of running make from an SVN checkout on a Unix-alike: a separate
make vignettes step is no longer required.
These vignettes are now made with keep.source = TRUE and hence
will be laid out differently.
o make install-strip failed under some configuration options.
o Packages can customize non-standard installation of compiled code
via a src/install.libs.R script. This allows packages that have
architecture-specific binaries (beyond the package's shared
objects/DLLs) to be installed in a multi-architecture setting.
SWEAVE & VIGNETTES:
o Sweave() and Stangle() gain an encoding argument to specify the
encoding of the vignette sources if the latter do not contain a
\usepackage[]{inputenc} statement specifying a single input
encoding.
o There is a new Sweave option figs.only = TRUE to run each figure
chunk only for each selected graphics device, and not first using
the default graphics device. This will become the default in R
2.14.0.
o Sweave custom graphics devices can have a custom function
foo.off() to shut them down.
o Warnings are issued when non-portable filenames are found for
graphics files (and chunks if split = TRUE). Portable names are
regarded as alphanumeric plus hyphen, underscore, plus and hash
(periods cause problems with recognizing file extensions).
o The Rtangle() driver has a new option show.line.nos which is by
default false; if true it annotates code chunks with a comment
giving the line number of the first line in the sources (the
behaviour of R >= 2.12.0).
o Package installation tangles the vignette sources: this step now
converts the vignette sources from the vignette/package encoding
to the current encoding, and records the encoding (if not ASCII)
in a comment line at the top of the installed .R file.
LICENCE:
o No parts of R are now licensed solely under GPL-2. The licences
for packages rpart and survival have been changed, which means
that the licence terms for R as distributed are GPL-2 | GPL-3.
DEPRECATED AND DEFUNCT:
o The internal functions .readRDS() and .saveRDS() are now
deprecated in favour of the public functions readRDS() and
saveRDS() introduced in R 2.13.0.
o Switching off lazy-loading of code _via_ the LazyLoad field of
the DESCRIPTION file is now deprecated. In future all packages
will be lazy-loaded.
o The off-line help() types "postscript" and "ps" are deprecated.
UTILITIES:
o R CMD check on a multi-architecture installation now skips the
user's .Renviron file for the architecture-specific tests (which
do read the architecture-specific Renviron.site files). This is
consistent with single-architecture checks, which use
--no-environ.
o R CMD build now looks for DESCRIPTION fields BuildResaveData and
BuildKeepEmpty for per-package overrides. See 'Writing R
Extensions'.
BUG FIXES:
o plot.lm(which = 5) was intended to order factor levels in
increasing order of mean standardized residual. It ordered the
factor labels correctly, but could plot the wrong group of
residuals against the label. (PR#14545)
o mosaicplot() could clip the factor labels, and could overlap them
with the cells if a non-default value of cex.axis was used.
(Related to PR#14550.)
o dataframe[[row,col]] now dispatches on [[ methods for the
selected column. (Spotted by Bill Dunlap).
o sort.int() would strip the class of an object, but leave its
object bit set. (Reported by Bill Dunlap.)
o pbirthday() and qbirthday() did not implement the algorithm
exactly as given in their reference and so were unnecessarily
inaccurate.
pbirthday() now solves the approximate formula analytically
rather than using uniroot() on a discontinuous function.
The description of the problem was inaccurate: the probability is
a tail probability ('2 _or more_ people share a birthday')
o Complex arithmetic sometimes warned incorrectly about producing
NAs when there were NaNs in the input.
o seek(origin = "current") incorrectly reported it was not
implemented for a gzfile() connection.
o c(), unlist(), cbind() and rbind() could silently overflow the
maximum vector length and cause a segfault. (PR#14571)
o The fonts argument to X11(type = "Xlib") was being ignored.
o Reading (e.g. with readBin()) from a raw connection was not
advancing the pointer, so successive reads would read the same
value. (Spotted by Bill Dunlap.)
o Parsed text containing embedded newlines was printed incorrectly
by as.character.srcref(). (Reported by Hadley Wickham.)
o decompose() used with a series of a non-integer number of periods
returned a seasonal component shorter than the original series.
(Reported by Rob Hyndman.)
o fields = list() failed for setRefClass(). (Reported by Michael
Lawrence.)
o Reference classes could not redefine an inherited field which had
class "ANY". (Reported by Janko Thyson.)
o Methods that override previously loaded versions will now be
installed and called. (Reported by Iago Mosqueira.)
o addmargins() called numeric(apos) rather than
numeric(length(apos)).
o The HTML help search sometimes produced bad links. (PR#14608)
o Command completion will no longer be broken if tail.default() is
redefined by the user. (Problem reported by Henrik Bengtsson.)
o LaTeX rendering of markup in titles of help pages has been
improved; in particular, \eqn{} may be used there.
o isClass() used its own namespace as the default of the where
argument inadvertently.
o Rd conversion to latex mishandled multi-line titles (including
cases where there was a blank line in the \title section). (It
seems this happened only in 2.13.0 patched.)
o postscript() with an sRGB colormodel now uses sRGB for raster
images (in R 2.13.[01] it used uncalibrated RGB).
There is no longer an undocumented 21845-pixel limit on raster
images.
CHANGES IN R VERSION 2.13.0:
SIGNIFICANT USER-VISIBLE CHANGES:
o 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.
o 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:
o 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.
o 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).
o reformulate() gains a intercept argument.
o 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.)
o Names used by c(), unlist(), cbind() and rbind() are marked with
an encoding when this can be ascertained.
o 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.
o system.file() gains a mustWork argument (suggestion of Bill
Dunlap).
o new.env(hash = TRUE) is now the default.
o list2env(envir = NULL) defaults to hashing (with a suitably sized
environment) for lists of more than 100 elements.
o text() gains a formula method.
o IQR() now has a type argument which is passed to quantile().
o 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).
o setRepositories() gains an addURLs argument.
o chisq.test() now also returns a stdres component, for
standardized residuals (which have unit variance, unlike the
Pearson residuals).
o 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).
o 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<-`.
o 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.
o 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).
o 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.
o sort(partial = p) for large p now tries Shellsort if quicksort is
not appropriate and so works for non-numeric atomic vectors.
o 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.
o aperm() becomes S3 generic and gets a table method which
preserves the class.
o merge() and as.hclust() methods for objects of class "dendrogram"
are now provided.
o The character method of as.POSIXlt() now tries to find a format
that works for all non-NA inputs, not just the first one.
o str() now has a method for class "Date" analogous to that for
class "POSIXt".
o New function file.link() to create hard links on those file
systems (POSIX, NTFS but not FAT) that support them.
o New Summary() group method for class "ordered" implements min(),
max() and range() for ordered factors.
o 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.)
o 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.)
o example() gains optional new arguments character.only and
give.lines enabling programmatic exploration.
o 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.
readRDS() no longer wraps non-file connections in a call to
gzcon(), for efficiency (see its documentation).
saveRDS() supports compress = "xz".
o 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.
o Public functions find.package() and path.package() replace the
internal dot-name versions.
o 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.
o 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,
...).
o file.edit() gains a fileEncoding argument to specify the encoding
of the file(s).
o 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.)
o 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.
o 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.)
o unzip() now has a unzip argument like zip.file.extract(). This
allows an external unzip program to be used, which can be useful
to access features supported by Info-ZIP's unzip version 6 which
is now becoming more widely available.
o There is a simple zip() function, as wrapper for an external zip
command.
o 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).
o The primitive function c() is now of type BUILTIN.
o plot(<dendrogram>, .., nodePar=*) now obeys an optional xpd
specification (allowing clipping to be turned off completely).
o nls(algorithm="port") now shares more code with nlminb(), and is
more consistent with the other nls() algorithms in its return
value.
o xz has been updated to 5.0.1 (very minor bugfix release).
o 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.
o list.files()/dir() gains a new argument include.dirs() to include
directories in the listing when recursive = TRUE.
o New function list.dirs() lists all directories, (even empty
ones).
o file.copy() now (by default) copies read/write/execute
permissions on files, moderated by the current setting of
Sys.umask().
o Sys.umask() now accepts mode = NA and returns the current umask
value (visibly) without changing it.
o 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.
o as.raster() no longer fails for vectors or matrices containing
NAs.
o 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.
o Package tools has a new function compactPDF() to try to reduce
the size of PDF files _via_ qpdf or gs.
o tar() has a new argument extra_flags.
o 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.
o 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.
o The default for options("mailer") is now "mailto" on all
platforms.
o unlink() now does tilde-expansion (like most other file
functions).
o file.rename() now allows vector arguments (of the same length).
o 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.
o 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.
o Code for S4 reference-class methods is now examined for possible
errors in non-local assignments.
o findClasses, getGeneric, findMethods and hasMethods are revised
to deal consistently with the package= argument and be consistent
with soft namespace policy for finding objects.
o 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).
o 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.)
o 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).
o smooth.spline() is somewhat faster. With cv=NA it allows some
leverage computations to be skipped,
o The internal (C) function scientific(), at the heart of R's
format.info(x), format(x), print(x), etc, for numeric x, has been
re-written in order to provide slightly more correct results,
fixing PR#14491, notably in border cases including when digits >=
16, thanks to substantial contributions (code and experiments)
from Petr Savicky. This affects a noticeable amount of numeric
output from R.
o A new function grepRaw() has been introduced for finding subsets
of raw vectors. It supports both literal searches and regular
expressions.
o 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.
o 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.
o 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 current locale: useBytes = TRUE
is automatically 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.
o The new function removeSource() removes the internally stored
source from a function.
o "srcref" attributes now include two additional line number
values, recording the line numbers in the order they were parsed.
o New functions have been added for source reference access:
getSrcFilename(), getSrcDirectory(), getSrcLocation() and
getSrcref().
o 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.
o 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.
o factanal() now returns the rotation matrix if a rotation such as
"promax" is used, and hence factor correlations are displayed.
(Wish of PR#12754.)
o 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.
o file.copy(from, to) no longer regards it as an error to supply a
zero-length from: it now simply does nothing.
o rstandard.glm() gains a type argument which can be used to
request standardized Pearson residuals.
o A start on a Turkish translation, thanks to Murat Alkan.
o .libPaths() calls normalizePath(winslash = "/") on the paths:
this helps (usually) to present them in a user-friendly form and
should detect duplicate paths accessed via different symbolic
links.
o download.file() can be now used with external methods even if
there are spaces in the URL or the target filename.
SWEAVE CHANGES:
o 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.)
o The default for Sweave() is to produce only PDF figures (rather
than both EPS and PDF).
o 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.
o The Sweave manual is now included as a vignette in the utils
package.
o Sweave() handles keep.source=TRUE much better: it could duplicate
some lines and omit comments. (Reported by John Maindonald and
others.)
C-LEVEL FACILITIES:
o 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.
o 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.
o 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).
o 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:
o R CMD Rdiff is now implemented in R on Unix-alikes (as it has
been on Windows since R 2.12.0).
o R CMD build no longer does any cleaning in the supplied package
directory: all the cleaning is done in the copy.
It has a new option --install-args to pass arguments to R CMD
INSTALL for --build (but not when installing to rebuild
vignettes).
There is new option, --resave-data, to call
tools::resaveRdaFiles() on the data directory, to compress
tabular files (.tab, .csv etc) and to convert .R files to .rda
files. The default, --resave-data=gzip, is to do so in a way
compatible even with years-old versions of R, but better
compression is given by --resave-data=best, requiring R >=
2.10.0.
It now adds a datalist file for data directories of more than
1Mb.
Patterns in .Rbuildignore are now also matched against all
directory names (including those of empty directories).
There is a new option, --compact-vignettes, to try reducing the
size of PDF files in the inst/doc directory. Currently this
tries qpdf: other options may be used in future.
When re-building vignettes and a inst/doc/Makefile file is found,
make clean is run if the makefile has a clean: target.
After re-building vignettes the default clean-up operation will
remove any directories (and not just files) created during the
process: e.g. one package created a .R_cache directory.
Empty directories are now removed unless the option
--keep-empty-dirs is given (and a few packages do deliberately
include empty directories).
If there is a field BuildVignettes in the package DESCRIPTION
file with a false value, re-building the vignettes is skipped.
o 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 package's
declared encoding. Rather than call tools::checkVignettes(), it
calls tools::buildVignettes() to see if the vignettes can be
re-built as they would be by R CMD build. Option --use-valgrind
now applies only to these runs, and not when running code to
rebuild the vignettes. This version does a much better job of
suppressing output from successful vignette tests.
The 00check.log file is a more complete record of what is output
to stdout: in particular contains more details of the tests.
It now checks 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).
o R CMD check now warns if it finds inst/doc/makefile, and R CMD
build renames such a file to inst/doc/Makefile.
INSTALLATION:
o 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.
o 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.
o 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.
o The C99 system call va_copy is now required.
o 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.
o 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:
o 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.)
o File R.css is now installed on a per-package basis (in the
package's html directory) rather than in each library tree, and
this is used for all the HTML pages in the package. This helps
when installing packages with static HTML pages for use on a
webserver. It will also allow future versions of R to use
different stylesheets for the packages they install.
o 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.)
o 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').
o There is a new option --lock which can be used to cancel the
effect of --no-lock or --pkglock earlier on the command line.
o Option --pkglock can now be used with more than one package, and
is now the default if only one package is specified.
o 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).
o There is a new option --no-clean-on-error for R CMD INSTALL to
retain a partially installed package for forensic analysis.
o 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.
o The vignette indices are more comprehensive (in the style of
browseVignetttes()).
DEPRECATED & DEFUNCT:
o require(save = TRUE) is defunct, and use of the save argument is
deprecated.
o R CMD check --no-latex is defunct: use --no-manual instead.
o R CMD Sd2Rd is defunct.
o The gamma argument to hsv(), rainbow(), and rgb2hsv() is
deprecated and no longer has any effect.
o 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.
o When a character value is used for the EXPR argument in switch(),
only a single unnamed alternative value is now allowed.
o The wrapper utils::link.html.help() is no longer available.
o 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.
o The 'experimental' alternative specification of a namespace via
.Export() etc is now defunct.
o The option --unsafe to R CMD INSTALL is deprecated: use the
identical option --no-lock instead.
o 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.
o Direct access to the "source" attribute of functions is
deprecated; use deparse(fn, control="useSource") to access it,
and removeSource(fn) to remove it.
o R CMD build --binary is now formally deprecated: R CMD INSTALL
--build has long been the preferred alternative.
o Single-character package names are deprecated (and R is already
disallowed to avoid confusion in Depends: fields).
BUG FIXES:
o drop.terms and the [ method for class "terms" no longer add back
an intercept. (Reported by Niels Hansen.)
o aggregate preserves the class of a column (e.g. a date) under
some circumstances where it discarded the class previously.
o 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.
o 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.)
o The str() method for class "POSIXt" now gives sensible output for
0-length input.
o The one- and two-argument complex maths functions failed to warn
if NAs were generated (as their numeric analogues do).
o Added .requireCachedGenerics to the dont.mind list for library()
to avoid warnings about duplicates.
o $<-.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.
o Map() did not look up a character argument f in the correct
frame, thanks to lazy evaluation. (PR#14495)
o file.copy() did not tilde-expand from and to when to was a
directory. (PR#14507)
o 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.
o plot(<formula>, data=<matrix>,..) now works in more cases;
similarly for points(), lines() and text().
o edit.default() contained a manual dispatch for matrices (the
"matrix" class didn't really exist when it was written). This
caused an infinite recursion in the no-GUI case and has now been
removed.
o data.frame(check.rows = TRUE) sometimes worked when it should
have detected an error. (PR#14530)
o scan(sep= , strip.white=TRUE) sometimes stripped trailing spaces
from within quoted strings. (The real bug in PR#14522.)
o 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.
o The perpendicular adjustment used in placing text and expressions
in the margins of plots was not scaled by par("mex"). (Part of
PR#14532.)
o 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 ft^2 on the area used by a window to
catch user errors (unit misinterpretation) early.
o The browser (invoked by debug(), browser() or otherwise) would
display attributes such as "wholeSrcref" that were intended for
internal use only.
o R's internal filename completion now properly handles filenames
with spaces in them even when the readline library is used. This
resolves PR#14452 provided the internal filename completion is
used (e.g., by setting rc.settings(files = TRUE)).
o Inside uniroot(f, ...), -Inf function values are now replaced by
a maximally *negative* value.
o rowsum() could silently over/underflow on integer inputs
(reported by Bill Dunlap).
o as.matrix() did not handle "dist" objects with zero rows.
CHANGES IN R VERSION 2.12.2 patched:
NEW FEATURES:
o 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:
o A change to the C function R_tryEval had broken error messages in
S4 method selection; the error message is now printed.
o PDF output with a non-RGB color model used RGB for the line
stroke color. (PR#14511)
o 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.
o In some circumstances a one-sided mantelhaen.test() reported the
p-value for the wrong tail. (PR#14514)
o Passing the invalid value lty = NULL to axis() sent an invalid
value to the graphics device, and might cause the device to
segfault.
o Sweave() with concordance=TRUE could lead to invalid PDF files;
Sweave.sty has been updated to avoid this.
o Non-ASCII characters in the titles of help pages were not
rendered properly in some locales, and could cause errors or
warnings.
o checkRd() gave a spurious error if the \href macro was used.
CHANGES IN R VERSION 2.12.2:
SIGNIFICANT USER-VISIBLE CHANGES:
o 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 trigonometric 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).
o There is a workaround for crashes seen with several packages on
systems using zlib 1.2.5: see the INSTALLATION section.
NEW FEATURES:
o PCRE has been updated to 8.12 (two bug-fix releases since 8.10).
o rep(), seq(), seq.int() and seq_len() report more often when the
first element is taken of an argument of incorrect length.
o 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).
o kernel()'s default for m was not appropriate if coef was a set of
coefficients. (Reported by Pierre Chausse.)
o bug.report() has been updated for the current R bug tracker,
which does not accept emailed submissions.
o 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:
o 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.
o 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:
o A LazyDataCompression field in the DESCRIPTION file will be used
to set the value for the --data-compress option of R CMD INSTALL.
o 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.
o 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:
o The 'experimental' alternative specification of a namespace via
.Export() etc is now deprecated.
o zip.file.extract() is now deprecated.
o 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:
o 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).
o 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)
o format.data.frame() now keeps zero character column names.
o pretty(x) no longer raises an error when x contains solely
non-finite values. (PR#14468)
o 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).
o The big.mark argument to prettyNum(), format(), etc. was inserted
reversed if it was more than one character long.
o R CMD check failed to check the filenames under man for Windows'
reserved names.
o The "Date" and "POSIXt" methods for seq() could overshoot when to
was supplied and by was specified in months or years.
o The internal method of untar() now restores hard links as file
copies rather than symbolic links (which did not work for
cross-directory links).
o 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.)
o combn(n, m) now behaves more regularly for the border case m = 0.
(PR#14473)
o 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)
o 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.)
o weighted.residuals(drop0=TRUE) returned a vector when the
residuals were a matrix (e.g. those of class "mlm"). (Reported
by Bill Dunlap.)
o Package HTML index files <pkg>/html/00Index.html were generated
with a stylesheet reference that was not correct for static
browsing in libraries.
o ccf(na.action = na.pass) was not implemented.
o The parser accepted some incorrect numeric constants, e.g. 20x2.
(Reported by Olaf Mersmann.)
o format(*, zero.print) did not always replace the full zero parts.
o Fixes for subsetting or subassignment of "raster" objects when
not both i and j are specified.
o 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.
o 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.
o atan(1i) returned NaN+Infi (rather than 0+Infi) on platforms
without C99 complex support.
o library() failed to cache S4 metadata (unlike loadNamespace())
causing failures in S4-using packages without a namespace (e.g.
those using reference classes).
o The function qlogis(lp, log.p=TRUE) no longer prematurely
overflows to Inf when exp(lp) is close to 1.
o Updating S4 methods for a group generic function requires
resetting the methods tables for the members of the group (patch
contributed by Martin Morgan).
o In some circumstances (including for package XML), R CMD INSTALL
installed version-control directories from source packages.
o Added PROTECT calls to some constructed expressions used in C
level eval calls.
o utils:::create.post() (used by bug.report() and help.request())
failed to quote arguments to the mailer, and so often failed.
o bug.report() was naive about how to extract maintainer email
addresses from package descriptions, so would often try mailing
to incorrect addresses.
o debugger() could fail to read the environment of a call to a
function with a ... argument. (Reported by Charlie Roosen.)
o prettyNum(c(1i, NA), drop0=TRUE) or str(NA_complex_) now work
correctly.
CHANGES IN R VERSION 2.12.1:
NEW FEATURES:
o The DVI/PDF reference manual now includes the help pages for all
the standard packages: splines, stats4 and tcltk were previously
omitted (intentionally).
o <URL: http://www.rforge.net> has been added to the default set of
repositories known to setRepositories().
o xz-utils has been updated to version 5.0.0.
o reshape() now makes use of sep when forming names during
reshaping to wide format. (PR#14435)
o legend() allows the length of lines to be set by the end user
_via_ the new argument seg.len.
o New S4 reference class utility methods copy(), field(),
getRefClass() and getClass() have been added to package methods.
o 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.
o StructTS(type = "BSM") now allows series with just two seasons.
(Reported by Birgit Erni.)
INSTALLATION:
o 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.
o 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:
o seq.int() no longer sometimes evaluates arguments twice.
(PR#14388)
o The data.frame method of format() failed if a column name was
longer than 256 bytes (the maximum length allowed for an R name).
o 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.
o The TRE regular expressions engine could terminate R rather than
give an error when given certain invalid regular expressions.
(PR#14398)
o 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).
o 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.
o download.file() could leave the destination file open if the URL
was not able to be opened. (PR#14414)
o Assignment of an environment to functions or as an attribute to
other objects now works for S4 subclasses of "environment".
o Use of [[<- for S4 subclasses of "environment" generated an
infinite recursion from the method. The method has been replaced
by internal code.
o In a reference class S4 method, callSuper() now works in
initialize() methods when there is no explicit superclass method.
o ! dropped attributes such as names and dimensions from a
length-zero argument. (PR#14424)
o When list2env() created an environment it was missing a PROTECT
call and so was vulnerable to garbage collection.
o 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.
o 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.)
o 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)).
o Backreferences to undefined patterns in [g]sub(pcre = TRUE) could
cause a segfault. (PR#14431)
o The format() (and hence the print()) method for class "Date"
rounded fractional dates towards zero: it now always rounds them
down.
o Reference S4 class creation could generate ambiguous inheritance
patterns under very special circumstances.
o [[<- turned S4 subclasses of "environment" into plain
environments.
o Long titles for help pages were truncated in package indices and
a few other places.
o Additional utilities now work correctly with S4 subclasses of
"environment" (rm, locking tools and active bindings).
o spec.ar() now also work for the "ols" method. (Reported by
Hans-Ruedi Kuensch.)
o The initialization of objects from S4 subclasses of "environment"
now allocates a new environment object.
o R CMD check has more protection against (probably erroneous)
example or test output which is invalid in the current locale.
o qr.X() with column names and pivoting now also pivots the column
names. (PR#14438)
o unit.pmax() and unit.pmin() in package grid gave incorrect
results when all inputs were of length 1. (PR#14443)
o 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.)
o Fix for subsetting of "raster" objects when only one of i or j is
specified.
o grid.raster() in package grid did not accept "nativeRaster"
objects (like rasterImage() does).
o Rendering raster images in PDF output was resetting the clipping
region.
o 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.
o 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:
o Reading a package's CITATION file now defaults to ASCII rather
than Latin-1: a package with a non-ASCII CITATION file should
declare an encoding in its DESCRIPTION file and use that encoding
for the CITATION file.
o 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.)
o pretty() is now generic, with new methods for "Date" and "POSIXt"
classes (based on code contributed by Felix Andrews).
o 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.
o The enquote() utility, in use internally, is exported now.
o .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.
o 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)
o 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)
o curve() now allows expr to be an object of mode "expression" as
well as "call" and "function".
o 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.
o 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 <URL: http://developer.r-project.org> for
the consequences for a handful of CRAN packages.
o The "POSIXct" method of as.Date() allows a timezone to be
specified (but still defaults to UTC).
o 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.
o 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().
o Special names such as "dim", "names", etc, are now allowed as
slot names of S4 classes, with "class" the only remaining
exception.
o File .Renviron can have architecture-specific versions such as
.Renviron.i386 on systems with sub-architectures.
o installed.packages() has a new argument subarch to filter on
sub-architecture.
o The summary() method for packageStatus() now has a separate
print() method.
o The default summary() method returns an object inheriting from
class "summaryDefault" which has a separate print() method that
calls zapsmall() for numeric/complex values.
o The startup message now includes the platform and if used,
sub-architecture: this is useful where different
(sub-)architectures run on the same OS.
o 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.)
o tools::texi2dvi() gains an index argument, mainly for use by R
CMD Rd2pdf.
It avoids the use of texindy by texinfo's texi2dvi >= 1.157,
since that does not emulate 'makeindex' well enough to avoid
problems with special characters (such as (, {, !) in indices.
o 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.
o scan() gains a fileEncoding argument to match read.table().
o points() and lines() gain "table" methods to match plot(). (Wish
of PR#10472.)
o Sys.chmod() allows argument mode to be a vector, recycled along
paths.
o There are |, & and xor() methods for classes "octmode" and
"hexmode", which work bitwise.
o 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".)
o New function isatty() to see if terminal connections are
redirected.
o summaryRprof() returns the sampling interval in component
sample.interval and only returns in by.self data for functions
with non-zero self times.
o print(x) and str(x) now indicate if an empty list x is named.
o 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.
o 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.
o 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).
o Package utils adds a new "bibentry" class for representing and
manipulating bibliographic information in enhanced BibTeX style,
unifying and enhancing the previously existing mechanisms.
o 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.
o 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.
o Added \href tag to the Rd format, to allow hyperlinks to URLs
without displaying the full URL.
o Added \newcommand and \renewcommand tags to the Rd format, to
allow user-defined macros.
o 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.
o Directory R_HOME/share/texmf now follows the TDS conventions, so
can be set as a texmf tree ('root directory' in MiKTeX parlance).
o 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.
o format.pval() gains a ... argument to pass arguments such as
nsmall to format(). (Wish of PR#9574)
o legend() supports title.adj. (Wish of PR#13415)
o Added support for subsetting "raster" objects, plus assigning to
a subset, conversion to a matrix (of colour strings), and
comparisons (== and !=).
o Added a new parseLatex() function (and related functions
deparseLatex() and latexToUtf8()) to support conversion of
bibliographic entries for display in R.
o Text rendering of \itemize in help uses a Unicode bullet in UTF-8
and most single-byte Windows locales.
o 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.
o 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.
o kmeans(x, 1) now works. Further, kmeans now returns between and
total sum of squares.
o arrayInd() and which() gain an argument useNames. For arrayInd,
the default is now false, for speed reasons.
o 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.
o 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.
o New function readRenviron to (re-)read files in the format of
~/.Renviron and Renviron.site.
o require() will now return FALSE (and not fail) if loading the
package or one of its dependencies fails.
o 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.)
o 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.
o 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.
o New simple function packageVersion().
o The PCRE library has been updated to version 8.10.
o The standard Unix-alike terminal interface declares its name to
readline as 'R', so that can be used for conditional sections in
~/.inputrc files.
o '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.
o ecdf() objects now have a quantile() method.
o 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.)
o 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).
o New function droplevels() to remove unused factor levels.
o 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.
o system() has a new argument ignore.stdout which can be used to
(portably) ignore standard output.
o system(intern = TRUE) and pipe() connections are guaranteed to be
available on all builds of R.
o Sys.which() has been altered to return "" if the command is not
found (even on Solaris).
o 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.
o 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.
o Parsing errors detected during Sweave() processing will now be
reported referencing their original location in the source file.
o New adjustcolor() utility, e.g., for simple translucent color
schemes.
o qr() now has a trivial lm method with a simple (fast) validity
check.
o An experimental new programming model has been added to package
methods for reference (OOP-style) classes and methods. See
?ReferenceClasses.
o bzip2 has been updated to version 1.0.6 (bug-fix release).
--with-system-bzlib now requires at least version 1.0.6.
o 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.
o 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:
o Supplying the parser with a character string containing both
octal/hex and Unicode escapes is now an error.
o File extension .C for C++ code files in packages is now defunct.
o R CMD check no longer supports configuration files containing
Perl configuration variables: use the environment variables
documented in 'R Internals' instead.
o 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.)
o R CMD check --no-latex is deprecated in favour of --no-manual.
o R CMD Sd2Rd is formally deprecated and will be removed in R
2.13.0.
PACKAGE INSTALLATION:
o install.packages() has a new argument libs_only to optionally
pass --libs-only to R CMD INSTALL and works analogously for
Windows binary installs (to add support for 64- or 32-bit
Windows).
o 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.
o 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:
o 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.
o 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 --no-multiarch).
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.)
o 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.
o 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).
o 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.
o R CMD Sweave now runs R with --vanilla so the environment setting
of R_LIBS will always be used.
C-LEVEL FACILITIES:
o 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.
o 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.)
o 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:
o A C99 compiler is now required, and more C99 language features
will be used in the R sources.
o Tcl/Tk >= 8.4 is now required (increased from 8.3).
o System functions access, chdir and getcwd are now essential to
configure R. (In practice they have been required for some
time.)
o 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.
o 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.
o The popen system call is now required to build R. This ensures
the availability of system(intern = TRUE), pipe() connections and
printing from postscript().
o The pkg-config file libR.pc now also works when R is installed
using a sub-architecture.
o 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:
o Calls to selectMethod() by default no longer cache inherited
methods. This could previously corrupt methods used by as().
o 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)
o pt() is more accurate in the left tail for ncp large, e.g.
pt(-1000, 3, 200). (PR#14069)
o 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)
o source(echo=TRUE) failed to echo comments that followed the last
statement in a file.
o 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.
o 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.
o The signature of an implicit generic is now used by setGeneric()
when that does not use a definition nor explicitly set a
signature.
o 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.
o match(x, table) (and hence %in%) now treat "POSIXlt" consistently
with, e.g., "POSIXct".
o 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.
o 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.
o 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)
o Added warn.unused argument to hist.default() to allow suppression
of spurious warnings about graphical parameters used with
plot=FALSE. (PR#14341)
o 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.)
o aperm() treated resize = NA as resize = TRUE.
o 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.
o Rendering of S3 and S4 methods in man pages has been corrected
and made consistent across output formats.
o Simple markup is now allowed in \title sections in .Rd files.
o The behaviour of as.logical() on factors (to use the levels) was
lost in R 2.6.0 and has been restored.
o prompt() did not backquote some default arguments in the \usage
section. (Reported by Claudia Beleites.)
o writeBin() disallows attempts to write 2GB or more in a single
call. (PR#14362)
o new() and getClass() will now work if Class is a subclass of
"classRepresentation" and should also be faster in typical calls.
o The summary() method for data frames makes a better job of names
containing characters invalid in the current locale.
o [[ sub-assignment for factors could create an invalid factor
(reported by Bill Dunlap).
o Negate(f) would not evaluate argument f until first use of
returned function (reported by Olaf Mersmann).
o 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).
o 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.)
o Task callbacks could report the wrong expression when the task
involved parsing new code. (PR#14368)
o getNamespaceVersion() failed; this was an accidental change in
2.11.0. (PR#14374)
o identical() returned FALSE for external pointer objects even when
the pointer addresses were the same.
o L$a@x[] <- val did not duplicate in a case it should have.
o 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)
o quantile(type=6) behaved inconsistently. (PR#14383)
o backSpline(.) behaved incorrectly when the knot sequence was
decreasing. (PR#14386)
o 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.
o 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)
o model.frame(drop.unused.levels = TRUE) did not take into account
NA values of factors when deciding to drop levels. (PR#14393)
o 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").
o The self-starting model NLSstClosestX failed if some deviation
was exactly zero. (PR#14384)
o X11(type = "cairo") (and other devices such as png using
cairographics) and which use Pango font selection now work around
a bug in Pango when very small fonts (those with sizes between 0
and 1 in Pango's internal units) are requested. (PR#14369)
o 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.)
o source(chdir = TRUE) failed to reset the working directory if it
could not be determined - that is now an error.
o Fix for crash of example(rasterImage) on x11(type="Xlib").
o 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)
o model.frame had an unstated 500 byte limit on variable names.
(Example reported by Terry Therneau.)
o The 256-byte limit on names is now documented.
o 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:
o install.packages() has a new optional argument INSTALL_opts which
can be used to pass options to R CMD INSTALL for source-package
installs.
o R CMD check now runs the package-specific tests with LANGUAGE=en
to facilitate comparison to .Rout.save files.
o sessionInfo() gives more detailed platform information, including
32/64-bit and the sub-architecture if one is used.
DEPRECATED & DEFUNCT:
o 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:
o R CMD Rd2dvi failed if run from a path containing space(s). This
also affected R CMD check, which calls Rd2dvi.
o stripchart() could fail with an empty factor level. (PR#14317)
o Text help rendering of \tabular{} has been improved: under some
circumstances leading blank columns were not rendered.
o strsplit(x, fixed=TRUE) marked UTF-8 strings with the local
encoding when no splits were found.
o weighted.mean(NA, na.rm=TRUE) and similar now returns NaN again,
as it did prior to R 2.10.0.
o R CMD had a typo in its detection of whether the environment
variable TEXINPUTS was set (reported by Martin Morgan).
o The command-line parser could mistake --file=size... for one of
the options for setting limits for Ncells or Vcells.
o The internal strptime() could corrupt its copy of the timezone
which would then lead to spurious warnings. (PR#14338)
o 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.)
o The postscript() and pdf() devices will now allow lwd values less
than 1 (they used to force such values to be 1).
o Fixed font face for CID fonts in pdf() graphics output.
(PR#14326)
o 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.
o 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)
o Improperly calling Recall() from outside a function could cause a
segfault. (Reported by Robert McGehee.)
o \Sexpr[result=rd] in an Rd file added a spurious newline, which
was displayed as extra whitespace when rendered.
o require(save = TRUE) recorded the names of packages it failed to
load.
o packageStatus() could return a data frame with duplicate row
names which could then not be printed.
o txtProgressBar(style = 2) did not work correctly.
txtProgressBar(style = 3) did not display until a non-minimum
value was set.
o contour() did not display dashed line types properly when contour
lines were labelled. (Reported by David B. Thompson.)
o tools::undoc() again detects undocumented data objects. Of
course, this also affects R CMD check.
o ksmooth(x,NULL) no longer segfaults.
o 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:
o R CMD INSTALL checks if dependent packages are available early on
in the installation of source packages, thereby giving clearer
error messages.
o R CMD INSTALL --build now names the file in the format used for
Mac OS X binary files on that platform.
o BIC() in package stats4 now also works with multiple fitted
models, analogously to AIC().
DEPRECATED & DEFUNCT:
o 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:
o 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:
o The C function mkCharLenCE now no longer reads past len bytes
(unlikely to be a problem except in user code). (PR#14246)
o 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)
o More efficient implementation of utf8ToInt() on long multi-byte
strings with many multi-byte characters. (PR#14262)
o aggregate.ts() gave platform-dependent results due to rounding
error for ndeltat != 1.
o 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)
o splinefun(method = "monoH.FC") was not quite monotone in rare
cases. (PR#14215)
o Rhttpd no longer crashes due to SIGPIPE when the client closes
the connection prematurely. (PR#14266)
o format.POSIXlt() could cause a stack overflow and crash when used
on very long vectors. (PR#14267)
o Rd2latex() incorrectly escaped special characters in \usage
sections.
o mcnemar.test() could alter the levels (dropping unused levels) if
passed x and y as factors (reported by Greg Snow).
o Rd2pdf sometimes needed a further pdflatex pass to get
hyperlinked pages correct.
o interaction() produced malformed results when levels were
duplicated, causing segfaults in split().
o cut(d, breaks = <n>) now also works for "Date" or "POSIXt"
argument d. (PR#14288)
o memDecompress() could decompress incompletely rare xz-compressed
input due to incorrect documentation of xz utils. (Report and
patch from Olaf Mersmann.)
o The S4 initialize() methods for "matrix", "array", and "ts" have
been fixed to call validObject(). (PR#14284)
o 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.)
o [<-.data.frame was not quite careful enough in assigning (and
potentially deleting) columns right-to-left. (PR#14263)
o rbeta(n, a, b) no longer occasionally returns NaN for a >> 1 > b.
(PR#14291)
o pnorm(x, log.p = TRUE) could return NaN not -Inf for x near
(minus for lower.tail=TRUE) the largest representable number.
o 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)
o 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)
o 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.
o na.action() did not extract the na.action component as
documented.
o do.call()ing NextMethod in erroneous ways no longer segfaults.
(PR#13487)
CHANGES IN R VERSION 2.11.0:
SIGNIFICANT USER-VISIBLE CHANGES:
o Packages must have been installed under R >= 2.10.0, as the
current help system is the only one now supported.
o A port to 64-bit Windows is now available as well as binary
package repositories: see the 'R Administration and Installation
Manual'.
o 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 internal-use-only primitives.
o The default device for command-line R at the console on Mac OS X
is now quartz() and not X11().
NEW FEATURES:
o 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".
o 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.
o 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).
o R CMD check has a new option --timings to record per-example
timings in file <pkg>.Rcheck/<pkg>-Ex.timings.
o The TRE library has been updated to version 0.8.0 (minor
bugfixes).
o 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).
o A new argument skipCalls has been added to browser() so that it
can report the original context when called by other debugging
functions.
o More validity checking of UTF-8 and MBCS strings is done by
agrep() and the regular-expression matching functions.
o The undocumented restriction on gregexpr() to length(text) > 0
has been removed.
o 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.
o 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).
o 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).
o prop.table(x) now accepts a one-dimensional table for x.
o 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.
o 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.
o The [ method for class "AsIs" allows the next method to change
the underlying class. (Wish of Jens Oehlschl?gel.)
o 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.
o The index page for HTML help for a package now collapses multiple
signatures for S4 methods into a single entry.
o 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 namespaces). By default detach() prevents
such dependencies from being detached: this can be overridden by
the argument force.
o bquote() has been extended to work on function definitions.
(Wish of PR#14031).
o detach() when applied to an object other than a package returns
the environment that has been detached, to parallel attach().
o readline() in non-interactive use returns "" and does not attempt
to read from the 'terminal'.
o New function file_ext() in package tools.
o 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).
o is.numeric(x) is now false for a "difftime" object
(multiplication and division make no sense for such objects).
o 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.
o 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.)
o 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.
o length(<POSIXlt>) now returns the length of the corresponding
abstract timedate-vector rather than always 9 (the length of the
underlying list structure). (Wish of PR#14073 and PR#10507.)
o The readline completion backend no longer sorts possible
completions alphabetically (e.g., function argument names) if R
was built with readline >= 6.
o 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.
o New function chooseBioCmirror() to set the "BioC_mirror" option.
o 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.
o The handling of the method argument of glm() has been refined
following suggestions by Ioannis Kosmidis and Heather Turner.
o str() gains a new argument list.len with default 99, limiting the
number of list() items (per level), thanks to suggestions from
David Winsenius.
o 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).
o New functions enc2native() and enc2utf8() convert character
vectors with possibly marked encodings to the current locale and
UTF-8 respectively.
o 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.
o Informational messages about masked objects displayed when a
package is attached are now more compact, using strwrap() instead
of one object per line.
o print.rle() gains argument prefix.
o 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.
o In Rd, \eqn and \deqn will render in HTML (and convert to text)
upper- and lower-case Greek letters (entered as \alpha ...),
\ldots, ..., \ge and \le.
o utf8ToInt() and intToUtf8() now map NA inputs to NA outputs.
o 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.
o New function strtoi(), a wrapper for the C function strtol.
o 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.
o seq.int() returns an integer result in some further cases where
seq() does, e.g. seq.int(1L, 9L, by = 2L).
o Added \subsection{}{} macro to Rd syntax, for subsections within
sections.
o 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.
o interaction(drop=TRUE) uses less memory (related to PR#14121).
o summary() methods have been added to the "srcref" and "srcfile"
classes, and various encoding issues have been cleaned up.
o 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.
o Checking setAs(a, b) methods only gives a message instead of a
warning, when one of a or b is unknown.
o New function norm() to compute a matrix norm. norm() and also
backsolve() and sample() have implicit S4 generics.
o Files Renviron.site and Rprofile.site can have
architecture-specific versions on systems with sub-architectures.
o R CMD check now (by default) also checks Rd files for
auto-generated content in need of editing, and missing argument
descriptions.
o 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.
o path.expand() now propagates NA values rather than converting
them to "NA".
o file.show() now disallows NA values for file names, headers, and
pager.
o 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).
o 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.
o New function rasterImage() in the graphics package for drawing
raster images.
o stats:::extractAIC.coxph() now omits aliased terms when computing
the degrees of freedom (suggestion of Terry Therneau).
o cor() and cov() now test for misuse with non-numeric arguments,
such as the non-bug report PR#14207.
o 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.)
o maintainer() has been added, to give convenient access to the
name of the maintainer of a package (contributed by David Scott).
o 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().
o 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.
o 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() ...).
o 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.
o base::which() uses a new .Internal function when arr.ind is FALSE
resulting in a 10x speedup. Thanks to Patrick Aboyoun for
implementation suggestions.
o 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.
o A new class "listOfMethods" has been introduced to represent the
methods in a methods table, to replace the deprecated class
"MethodsList".
o any() and all() return early if possible. This may speed up
operations on long vectors.
o strptime() now accepts "%z" (for the offset from UTC in the
RFC822 format of +/-hhmm).
o The PCRE library has been updated to version 8.02, a bug-fix
release which also updates tables to Unicode 5.02.
o 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")).
o The parser no longer marks strings containing octal or hex
escapes as being in UTF-8 when entered in a UTF-8 locale.
o 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).
o 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:
o Bundles of packages are defunct.
o stats::clearNames() is defunct: use unname().
o Basic regular expressions are defunct, and strsplit(), grep(),
grepl(), sub(), gsub(), regexpr() and gregexpr() no longer have
an extended argument.
o methods::trySilent() is defunct.
o index.search() (which was deprecated in 2.10.0) is no longer
exported and has a different argument list.
o Use of multiple arguments to return() is now defunct.
o The use of UseMethod() with more than two arguments is now
defunct.
o 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.
o Parsing strings containing both octal/hex and Unicode escapes now
gives a warning and will become an error in R 2.12.0.
INSTALLATION:
o UTF-8 is now used for the reference manual and package manuals.
This requires LaTeX '2005/12/01' or later.
o configure looks for a POSIX compliant tr, Solaris's /usr/ucb/tr
having been found to cause Rdiff to malfunction.
o configure is now generated with autoconf 2.65, which works better
on recent systems and on Mac OS X.
PACKAGE INSTALLATION:
o 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.
o 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.
o 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:
o Using with(), eval() etc with a list with some unnamed elements
now works. (PR#14035)
o 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.
o 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().
o 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.
o 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.
o 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.
o Various ar() fitting methods have more protection for singular
fits.
o callNextMethod now works again with the drop= argument in [
o parse() and parse_Rd() miscounted columns when multibyte UTF-8
characters were present.
o 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.
o cor(A, B) where A is n x 1 and B a 1-dimensional array segfaulted
or gave an internal error. (The case cor(B, A) was PR#7116.)
o 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)
o do_par() UNPROTECTed too early (PR#14214)
o Subassignment x[[....]] <- y didn't check for a zero-length right
hand side, and inserted a rubbish value. (PR#14217)
o fisher.test() no longer gives a P-value *very* slightly > 1, in
some borderline cases.
o 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 that would occur
when a garbage collection triggered a second call to matchArgs
for the same function _via_ a finalizer.
o 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.
o Several primitives, including attributes(), attr<-()
interactive(), nargs() and proc.time(), did not check that they
were called with the correct number of arguments.
o 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.
o mean(x, trim=, na.rm = FALSE) failed to return NA if x contained
missing values. (Reported by Bill Dunlap.)
o 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).
o parse(text=x) misbehaved for objects x that were not coerced
internally to character, notably symbols. (Reported to R-devel
by Bill Dunlap.)
o 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.
o The interpretation by strptime() of "%c" was non-standard (not
that it is ever advisable to use locale- and system-specific
input formats).
o 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).
o 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).
o read.fwf() misread multi-line records when n was specified.
(PR#14241)
o all.equal(tolerance = e) passes the numeric tolerance also to the
comparison of the attributes.
o pgamma(0, 0), a boundary case, now returns 0, its limit from the
left, rather than the limit from the right.
o Issuing POST requests to the internal web server could stall the
request under certain circumstances.
o gzcon( <textConnection> ), an error, no longer damages the
connection (in a way to have it segfault). (PR#14237)
o 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.)
o 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)
CHANGES IN R VERSION 2.10.1 patched:
NEW FEATURES:
o 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.
o lchoose(a, k) is now defined as log(abs(choose(a,k))),
analogously to lfactorial().
o Although \eqn{} in Rd files is defined as a 'verbatim' macro,
many packages expected ... and \ldots to be interpreted there (as
was the case in R < 2.10.0), so this is now done (using an
ellipsis in HTML rendering).
o 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.
o The PCRE library has been updated to version 8.01, a bug-fix
release.
o tools::readNEWS() now accepts a digit as the first character of a
news section.
BUG FIXES:
o Using read.table(header=TRUE) on a header with an embedded new
line would copy part of the header into the data. (PR#14103)
o qpois(p = 1, lambda = 0) now gives 0 as for all other p.
(PR#14135)
o 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)
o x[ , drop=TRUE] dropped an NA level even if it was in use.
o The dynamic HTML help system reported the wrong MIME type for the
style sheet.
o tools::codoc() (used by R CMD check) was missing cases where the
function had no arguments but was documented to have some.
o Help links containing special characters (e.g. "?") were not
generated correctly when rendered in HTML. (PR#14155)
o lchoose(a, k) no longer wrongly gives NaN for negative a.
o ks.test() could give a p-value that was off by one observation
due to rounding error. (PR#14145)
o readBin()/readChar() when reading millions of character strings
in a single call used excessive amounts of memory (which also
slowed them down).
o R CMD SHLIB could fail if used with paths that were not
alphanumeric, e.g. contained +. (PR#14168)
o sprintf() was not re-entrant, which potentially caused problems
if an as.character() method called it.
o 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.
o 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.
o tools::showNonASCII() failed to detect non-ASCII characters if
iconv() (incorrectly) converted them to different ASCII
characters. (Seen on Windows only.)
o tcrossprod() wrongly failed in some cases when one of the
arguments was a vector and the other a matrix.
o [cr]bind(..., deparse.level=2) was not always giving names when
documented to do so. (Discovered whilst investigating PR#14189.)
o match(incomparables=<non-NULL>) could in rare cases
infinite-loop.
o poisson.test() needed to pass argument conf.level to
binom.test(). (PR#14195)
o The "nls" method for df.residual() gave incorrect results for
models fitted with na.action = na.exclude. (PR#14194)
o 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().
o prettyNum(drop0trailing=TRUE) did not handle signs of imaginary
parts of complex numbers correctly (and this was used by str():
PR#14201).
o system.time() had the sys.child component wrong (copied
user.child instead) on systems with HAVE_GETRUSAGE. (PR#14210)
o 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.
o The suppression of auto-rotation in bitmap() and dev2bitmap()
with the "pdfwrite" device was not working correctly.
o plot(ecdf(), log="x") no longer gives an incorrect warning.
o read.fwf() works again when argument file is a connection.
o Startup files will now be found if their paths exceed 255 bytes.
(PR#14228)
o 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:
o The PCRE library has been updated to version 8.00.
o 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).
o 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).
o 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").
o 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).
INSTALLATION:
o 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).
o Making refman.pdf works around a problem with the indexing with
hyperref 6.79d and later.
DEPRECATED & DEFUNCT:
o 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:
o trigamma(x) and other psigamma(x, n) calls are now accurate for
very large abs(x). (PR#14020)
o [g]sub(perl=FALSE, fixed=FALSE) could use excessive stack space
when used with a very long vector containing some non-ASCII
strings.
o The default method of weighted.mean(na.rm = TRUE) did not omit
weights for NA observations in 2.10.0. (PR#14032)
o [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.
o findLineNum() and setBreakpoint() would sometimes fail if the
specified file was not in the current directory.
o Package tcltk's demo(tkdensity) was broken in 2.9.0 when demo()
was changed to set par(ask = TRUE).
o gsub() with backrefs could fail on extremely long strings
(hundreds of thousands of characters) due to integer overflow in
a length calculation.
o 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).
o detach()/unloadNamespace() arrange to flush the package's
lazyload cache of R objects once the package/namespace is no
longer needed.
o 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.
o available.packages() would fail when run on a repository with no
packages meeting the filtering conditions. (PR#14042)
o rep(x, times, each = 2) gave invalid results when the times
argument was a vector longer than x. Reported by Bill Dunlap.
o An error when unloadNamespace() attempted to run the .onUnload()
function gave an error in the reporting function and so was not
reported properly.
o Text help rendering did not handle very long input lines
properly.
o promptMethods() generated signature documentation improperly.
o 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).
o unname() now also removes names from a zero length vector.
o Printing results from ls.str() no longer evaluates unevaluated
calls.
o 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).
o An error in nls() with a long formula could cause a segfault.
(PR#14059)
o 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 probabilities 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.
o 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)
o chisq.test() could fail when given argument x or y which deparsed
to more than one line. (Reported by Laurent Gauthier.)
o S4 methods are uncached whenever the namespace containing them is
unloaded (by unloadNamespace() as well as by detach(unload =
TRUE)).
o 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.
o bessel[JY](x, nu) with nu a negative integer (a singular case) is
now correct, analogously to besselI(), see PR#13556.
o 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.)
o unsplit(drop = TRUE) applied to a data frame failed to pass drop
to the computation of row names. (PR#14084)
o The "difftime" method of mean() ignored its na.rm argument.
o tcltk::tk_select.list() is now more likely to remove the widget
immediately after selection is complete.
o Adding/subtracting a "difftime" object to/from a "POSIXt" or
"Date" object works again (it was broken by the addition of
Ops.difftime).
o Conversion to latex of an Rd file with no aliases failed.
o 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.
o help.search() failed when the package argument was specified.
(PR#14113)
o switch(EXPR = "A") now returns NULL, as does switch(1) (which
used to signal an error).
CHANGES IN R VERSION 2.10.0:
SIGNIFICANT USER-VISIBLE CHANGES:
o Package help is now converted from Rd by the R-based converters
that were first introduced in 2.9.0. This means
o 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.
o 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.)
o HTML help is now generated dynamically using an HTTP server
running in the R process and listening on the loopback interface.
o 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).
o 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.
o 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:
o polygon(), pdf() and postscript() now have an argument
fillOddEven (default FALSE), which controls the mode used for
polygon fills of self-intersecting shapes.
o New debugonce() function; further, getOption("deparse.max.lines")
is now observed when debugging, from a code suggestion by John
Brzustowski. (PR#13647/8)
o plot() methods for "stepfun" and hence "ecdf" no longer plot
points by default for n >= 1000.
o [g]sub(perl=TRUE) now also supports "\E" in order to *end* "\U"
and "\L" case changes, thanks to a patch from Bill Dunlap.
o 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.
o 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 Fran?ois.
o The print() and toLatex() methods for class "sessionInfo" now
show the locale in a nicer format and have arguments to suppress
locale information.
o In addition to previously only round(), there are other Math
group (S3) methods for "difftime", such as floor(), signif(),
abs(), etc.
o For completeness, old.packages() and available.packages() allow
arguments type to be specified (you could always specify
arguments available or contriburl).
o available.packages() by default only returns information on the
latest versions of packages whose version requirements are
satisfied by the currently running R.
o 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.
o 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.
o parse() now warns if the requested encoding is not supported.
o 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.
o If model.frame.default() encounters a character variable where
xlev indicates a factor, it now converts the variable to a factor
(with a warning).
o curve() now returns a list containing the points that w?ere
drawn.
o spineplot() now accepts axes = FALSE, for consistency with other
functions called by plot.factor().
o 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.)
o 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().
o More functions now have an implicit (S4) generic definition.
o 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.
o weighted.mean() is now generic and has "Date", "POSIXct" and
"POSIXlt" methods.
o 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.)
o as.data.frame() has an "aovproj" method. (Wish of PR#13505)
o 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.
o 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.
o codoc() now also checks S4 methods for code/documentation
mismatches.
o 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.
o The print() method for ls.str() results now obeys an optional
digits argument.
o The method argument of glm() now allows user-contributed methods.
o More general reorder.default() replaces functionality of
reorder.factor() and reorder.character().
o The function aspell() has been added to provide an interface to
the Aspell spell-checker.
o Filters RdTextFilter() and SweaveTeXFilter() have been added to
the tools package to provide support for aspell() or other spell
checkers.
o xtabs() with the new argument sparse = TRUE now returns a sparse
Matrix, using package Matrix.
o 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.
o 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.
o New utility function inheritedSlotNames() for S4 class
programming.
o tabulate() now allows NAs to pass through (and be ignored).
o If debug() is called on an S3 generic function then all methods
are debugged as well.
o Outlier symbols drawn by boxplot() now obey the outlwd argument.
Reported by Jurgen Kluge.
o svd(x) and eigen(x) now behave analogously to qr(x) in accepting
logical matrices x.
o 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.
o 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).
o New function news() for building and querying R or package news
information.
o z^n for integer n and complex z is more accurate now if |n| <=
65536.
o factor(NULL) now returns the same as factor(character(0)) instead
of an error, and table(NULL) consequently does analogously.
o 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).
o 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.
o iconv() has a new argument mark which can be used (by experts) to
suppress the declaration of encodings.
o DESCRIPTION file's LinkingTo specs are now recognized as
installation dependencies, and included in package management
computations.
o Standardized DESCRIPTION file License specs are now available for
package management computations.
o "\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).
o New as.raw() method for "tclObj" objects (wish of PR#13758).
o Rd.sty now makes a better job of setting email addresses,
including using a monospaced font.
o textConnection() gains an encoding argument to determine how
input strings with marked encodings will be handled.
o R CMD Rd2pdf is available as a shortcut for R CMD Rd2dvi --pdf.
o 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.
o identical() gains three logical arguments, which allow for even
more differentiation, notably -0 and 0.
o legend() now can specify the border color of filled boxes, thanks
to a patch from Frederic Schutz.
o Indexing with a vector index to [[ ]] has now been extended to
all recursive types.
o Pairlists may now be assigned as elements of lists. (Lists could
always be created with pairlist elements, but [[<- didn't support
assigning them.)
o 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.
o 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.
o Namespace importing is more careful about warning on masked
generics, thanks to a patch by Yohan Chalabi.
o detach() now has an argument character.only with the same meaning
as for library() or require().
o 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.
o 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.
o 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.
o sprintf() now supports %o for octal conversions.
o New function Sys.readlink() for information about symbolic links,
including if a file is a symbolic link.
o 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.
o File ~/.R/config is used in preference to ~/.Rconfig, and these
are now documented in 'R Installation and Administration'.
o Logic operations with complex numbers now work, as they were
always documented to, and as in S.
o 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).
o approxfun() is faster by avoiding repeated NA checks (diagnosis
and patch by Karline Soetaert & Thomas Petzoldt).
o There are the beginnings of a Nynorsk translation by Karl Ove
Hufthammer.
o stripchart() allows par bg to be passed in for the background
colour for pch = 21 (wish of PR#13984).
o New generic function .DollarNames() to enable class authors to
customize completion after the $ extractor.
o 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:
o 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.
o 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).
o 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.
o 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 byte-wise.
o [g]sub use a single-pass algorithm instead of matching twice and
so is usually faster.
o The perl = TRUE versions now work correctly in a non-UTF-8 MBCS
locale, by translating the inputs to UTF-8.
o useBytes = TRUE now inhibits the translation of inputs with
marked encodings.
o strsplit() gains a useBytes argument.
o 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).
o The help pages, including ?regexp, have been updated and should
be consulted for details of the new implementations.
HELP & Rd FILE CHANGES:
o 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.
o 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.
o 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 namespace is used.
o Plain text help is now used as the fallback for HTML help (as it
always was for Compiled HTML help on Windows).
o 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.
o 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.
o Tags \if, \ifelse and \out have been added to allow
format-specific (or more general, using \Sexpr) conditional text
in man pages.
o 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.
o 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).
o 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.
o parse_Rd() no longer includes the newline as part of a "%"-style
comment.
o 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).
o print.Rd() now adds necessary escape characters so that printing
and re-parsing an Rd object should produce an equivalent object.
o parse_Rd() was incorrectly handling multiple backslashes in R
code strings, converting 4n+3 backslashes to 2n+1 instead of
2n+2.
o parse_Rd() now recognizes the \var tag within a quoted string in
R-like text.
o parse_Rd() now treats the argument of \command as LaTeX-like,
rather than verbatim.
COMPRESSION:
o New function untar() to list or unpack tar archives, possibly
compressed. This uses either an external tar command or an
internal implementation.
o New function tar() to create (possibly compressed) tar archives.
o New functions memCompress() and memDecompress() for in-memory
compression and decompression.
o bzfile() has a compress argument to select the amount of effort
put into compression when writing.
o New function xzfile() for use with xz-compressed files. (This
can also read files compressed by some versions of lzma.)
o gzfile() looks at the file header and so can now also read
bzip2-ed files and xz-compressed files.
o 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).
o 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 system's 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.
o 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.)
o 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.
o data() can handle compressed text files with extensions
.{txt,tab,csv}.{gz,bz2,xz} .
DEPRECATED & DEFUNCT:
o png(type="cairo1") is defunct: the value is no longer recognized.
o tools::Rd_parse() is defunct (as this version of R uses only Rd
version 2).
o Use of file ~/.Rconf (which was deprecated in favour of
~/.Rconfig in 2004) has finally been removed.
o Bundles of packages are deprecated. See 'Writing R Extensions'
for the steps needed to unbundle a bundle.
o help() arguments offline, htmlhelp and chmhelp are deprecated in
favour of help_type.
o clearNames() (in package stats) is deprecated for unname().
o 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.
o methods::trySilent() is deprecated in favour of try(silent=TRUE)
or - more efficiently and flexibly - something like
tryCatch(error = function(e) e).
o index.search() is deprecated: there are no longer directories of
types other than help.
INSTALLATION:
o cairo >= 1.2 is now required (1.2.0 was released in July 2006)
for cairo-based graphics devices (which remain optional).
o A suitable iconv() is now required: support for configure option
--without-iconv has been withdrawn (it was deprecated in R
2.5.0).
o Perl is no longer 'essential'. R can be built without it, but
scripts R CMD build, check, Rprof and Sd2d currently require it.
o A system glob function is now essential (a working Sys.glob() has
been assumed since R 2.9.0 at least).
o C99 support for MBCS is now required, and configure option
--disable-mbcs has been withdrawn.
o 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:
o 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:
o 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.)
o validObject() avoids an error during evaluation in the case of
various incorrect slot definitions.
o n:m now returns a result of type "integer" in a few more boundary
cases.
o 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.
o 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.
o R_ReplDLLinit() initializes the top-level jump so that some
embedded applications on Windows no longer crash on error.
o 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.
o methods(f) used to warn unnecessarily for an S4 generic f which
had been created based on an existing S3 generic.
o The check for consistent ordering of superclasses was not
ignoring all conditional relations (the symptom was usually
spurious warnings for classes extending "array").
o Trying to assign into a raw vector with an index vector
containing NAs could cause a segfault. Reported by Herv? Pag?s.
o Rscript could segfault if (by user error) its filename argument
was missing. Reported by Martin Morgan.
o getAnywhere() (and functions that use it, including argument
completion in the console) did not handle special built-in
functions. Reported by Romain Francois.
o order() was missing a PROTECT() call and so could segfault when
called on character data under certain (rare) circumstances
involving marked non-native encodings.
o prettyNum(z, drop0trailing=TRUE) did not work correctly when z
was a complex vector. Consequently, str(z, ...) also did not.
(PR#13985)
o make distclean removed too many files in etc/ if builddir =
srcdir.
o R CMD replaced TEXINPUTS rather than appending to it (as
documented and intended).
o help.start() no longer fails on unix when "browser" is a
function.
o pbeta(x, ..., log.p = TRUE) is sometimes more accurate, e.g., for
very small x.
o Unserializing a pre-2.8 workspace containing pure ASCII character
objects with a Latin-1 or UTF-8 encoding would corrupt the
CHARSXP cache.
